International Journal of Molecular Sciences

10 pages, 1384 KiB

Open AccessArticle

ATR-FTIR Spectroscopy for the Assessment of Biochemical Changes in Skin Due to Cutaneous Squamous Cell Carcinoma

by Cássio A. Lima¹, Viviane P. Goulart¹, Luciana Côrrea², Thiago M. Pereira^1,3 and Denise M. Zezell^1,*

¹ Center for Lasers and Applications, Instituto de Pesquisas Energéticas e Nucleares, IPEN-CNEN/SP, São Paulo SP 05508-000, Brazil

² School of Dentistry, Universidade de São Paulo, São Paulo SP 05508-000, Brazil

³ Instituto de Ciência e Tecnologia (ICT), Universidade Federal de São Paulo, São José dos Campos SP 12.231-280, Brazil

Int. J. Mol. Sci. 2015, 16(4), 6621-6630; https://doi.org/10.3390/ijms16046621 - 24 Mar 2015

Cited by 51 | Viewed by 7969

Abstract

Nonmelanoma skin cancers represent 95% of cutaneous neoplasms. Among them, squamous cell carcinoma (SCC) is the more aggressive form and shows a pattern of possible metastatic profile. In this work, we used Fourier transform infrared spectroscopy (FTIR) spectroscopy to assess the biochemical changes [...] Read more.

Nonmelanoma skin cancers represent 95% of cutaneous neoplasms. Among them, squamous cell carcinoma (SCC) is the more aggressive form and shows a pattern of possible metastatic profile. In this work, we used Fourier transform infrared spectroscopy (FTIR) spectroscopy to assess the biochemical changes in normal skin caused by squamous cell carcinoma induced by multi-stage chemical carcinogenesis in mice. Changes in the absorption intensities and shifts were observed in the vibrational modes associated to proteins, indicating changes in secondary conformation in the neoplastic tissue. Hierarchical cluster analysis was performed to evaluate the potential of the technique to differentiate the spectra of neoplastic and normal skin tissue, so that the accuracy obtained for this classification was 86.4%. In this sense, attenuated total reflection (ATR)-FTIR spectroscopy provides a useful tool to complement histopathological analysis in the clinical routine for the diagnosis of cutaneous squamous cell carcinoma. Full article

(This article belongs to the Special Issue Laser Application in Life Sciences)

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14 pages, 4000 KiB

Open AccessArticle

A Soluble Pyrophosphatase Is Essential to Oogenesis and Is Required for Polyphosphate Metabolism in the Red Flour Beetle (Tribolium castaneum)

by Klébea Carvalho¹, Lupis Ribeiro¹, Jorge Moraes^1,2, José Roberto Da Silva^1,2, Evenilton P. Costa³, Jackson Souza-Menezes¹, Carlos Logullo^2,3, Rodrigo Nunes Da Fonseca^1,2,† and Eldo Campos^1,2,*,†

¹ Laboratory of Integrated Biochemistry—Hatisaburo Masuda, Universidade Federal do Rio de Janeiro, Núcleo em Ecologia e Desenvolvimento Sócio Ambiental de Macaé, Avenida São José do Barreto, 764, São José do Barreto, Macaé, RJ CEP 27965-045, Brazil

² Nacional Institute of Science and Technology—Molecular Entomology, Rio de Janeiro, RJ CEP 21941-590, Brazil

³ Laboratory of Chemistry and Function of Proteins and Peptides and Unity of Animal Experimentation, Biotecnology and Bioscience Center, Universidade Estadual do Norte Fluminense, Avenida Alberto Lamego, 2000, Horto, Campos dos Goytacazes, RJ CEP 28015-620, Brazil

^† These authors contributed equally to this work.

Int. J. Mol. Sci. 2015, 16(4), 6631-6644; https://doi.org/10.3390/ijms16046631 - 24 Mar 2015

Cited by 2 | Viewed by 6718

Abstract

Polyphosphates have been found in all cell types examined to date and play diverse roles depending on the cell type. In eukaryotic organisms, polyphosphates have been mainly investigated in mammalian cells with few studies on insects. Some studies have demonstrated that a pyrophosphatase [...] Read more.

Polyphosphates have been found in all cell types examined to date and play diverse roles depending on the cell type. In eukaryotic organisms, polyphosphates have been mainly investigated in mammalian cells with few studies on insects. Some studies have demonstrated that a pyrophosphatase regulates polyphosphate metabolism, and most of them were performed on trypanosomatids. Here, we investigated the effects of sPPase gene knocked down in oogenesis and polyphosphate metabolism in the red flour beetle (Tribolium castaneum). A single sPPase gene was identified in insect genome and is maternally provided at the mRNA level and not restricted to any embryonic or extraembryonic region during embryogenesis. After injection of Tc-sPPase dsRNA, female survival was reduced to 15% of the control (dsNeo RNA), and egg laying was completely impaired. The morphological analysis by nuclear DAPI staining of the ovarioles in Tc-sPPase dsRNA-injected females showed that the ovariole number is diminished, degenerated oocytes can be observed, and germarium is reduced. The polyphosphate level was increased in cytoplasmic and nuclear fractions in Tc-sPPase RNAi; Concomitantly, the exopolyphosphatase activity decreased in both fractions. Altogether, these data suggest a role for sPPase in the regulation on polyphosphate metabolism in insects and provide evidence that Tc-sPPase is essential to oogenesis. Full article

(This article belongs to the Special Issue Advances in Reproductive Biology)

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23 pages, 2914 KiB

Open AccessArticle

Antitumor Effects of Vitamin D Analogs on Hamster and Mouse Melanoma Cell Lines in Relation to Melanin Pigmentation

by Tomasz Wasiewicz¹, Paulina Szyszka^1,2, Miroslawa Cichorek³, Zorica Janjetovic⁴, Robert C. Tuckey⁵, Andrzej T. Slominski⁴ and Michal A. Zmijewski^1,*

¹ Department of Histology, Medical University of Gdańsk, Dębinki 1a, 80-211 Gdańsk, Poland

² Department of Endocrinology and Internal Medicine, Medical University of Gdańsk, Dębinki 1a, 80-211 Gdańsk, Poland

³ Department of Embryology, Medical University of Gdańsk, Dębinki 1a, 80-211 Gdańsk, Poland

⁴ Department of Dermatology, University of Alabama Birmingham, VA Medical Center, Birmingham, AL 35294, USA

⁵ School of Chemistry and Biochemistry, the University of Western Australia, Crawley, Perth, WA 6009, Australia

Int. J. Mol. Sci. 2015, 16(4), 6645-6667; https://doi.org/10.3390/ijms16046645 - 24 Mar 2015

Cited by 45 | Viewed by 8309

Abstract

Deregulated melanogenesis is involved in melanomagenesis and melanoma progression and resistance to therapy. Vitamin D analogs have anti-melanoma activity. While the hypercalcaemic effect of the active form of Vitamin D (1,25(OH)₂D₃) limits its therapeutic use, novel Vitamin D analogs [...] Read more.

Deregulated melanogenesis is involved in melanomagenesis and melanoma progression and resistance to therapy. Vitamin D analogs have anti-melanoma activity. While the hypercalcaemic effect of the active form of Vitamin D (1,25(OH)₂D₃) limits its therapeutic use, novel Vitamin D analogs with a modified side chain demonstrate low calcaemic activity. We therefore examined the effect of secosteroidal analogs, both classic (1,25(OH)₂D₃ and 25(OH)D₃), and novel relatively non-calcemic ones (20(OH)D₃, calcipotriol, 21(OH)pD, pD and 20(OH)pL), on proliferation, colony formation in monolayer and soft-agar, and mRNA and protein expression by melanoma cells. Murine B16-F10 and hamster Bomirski Ab cell lines were shown to be effective models to study how melanogenesis affects anti-melanoma treatment. Novel Vitamin D analogs with a short side-chain and lumisterol-like 20(OH)pL efficiently inhibited rodent melanoma growth. Moderate pigmentation sensitized rodent melanoma cells towards Vitamin D analogs, and altered expression of key genes involved in Vitamin D signaling, which was opposite to the effect on heavily pigmented cells. Interestingly, melanogenesis inhibited ligand-induced Vitamin D receptor translocation and ligand-induced expression of VDR and CYP24A1 genes. These findings indicate that melanogenesis can affect the anti-melanoma activity of Vitamin D analogs in a complex manner. Full article

(This article belongs to the Section Biochemistry)

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9 pages, 948 KiB

Open AccessArticle

Four Novel p.N385K, p.V36A, c.1033–1034insT and c.1417–1418delCT Mutations in the Sphingomyelin Phosphodiesterase 1 (SMPD1) Gene in Patients with Types A and B Niemann-Pick Disease (NPD)

by Masoumeh Dehghan Manshadi¹, Behnam Kamalidehghan², Fatemeh Keshavarzi³, Omid Aryani⁴, Sepideh Dadgar⁴, Ahoora Arastehkani¹, Mahdi Tondar⁵, Fatemeh Ahmadipour², Goh Yong Meng⁶ and Massoud Houshmand^4,7,*

¹ Department of Biology, Science and Research Branch, Islamic Azad University, Kurdistan 6614996164, Iran

² Department of Pharmacy, Faculty of Medicine, University of Malaya (UM), Kuala Lumpur 50603, Malaysia

³ Department of Biology, Sanandaj Branch, Islamic Azad University, Kurdistan 6616935391, Iran

⁴ Medical Genetics Department, Special Medical Center, Tehran 1599666615, Iran

⁵ Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC 20057, USA

⁶ Department of Animal Science, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang 43400, Malaysia

⁷ Medical Genetics Department, National Institute for Genetic Engineering and Biotechnology (NIGEB), Tehran 1497716316, Iran

Int. J. Mol. Sci. 2015, 16(4), 6668-6676; https://doi.org/10.3390/ijms16046668 - 24 Mar 2015

Cited by 11 | Viewed by 5696

Abstract

Background: Types A and B Niemann-Pick disease (NPD) are autosomal-recessive lysosomal storage disorders caused by the deficient activity of acid sphingomyelinase due to mutations in the sphingomyelin phosphodiesterase 1 (SMPD1) gene. Methods: In order to determine the prevalence and distribution of [...] Read more.

Background: Types A and B Niemann-Pick disease (NPD) are autosomal-recessive lysosomal storage disorders caused by the deficient activity of acid sphingomyelinase due to mutations in the sphingomyelin phosphodiesterase 1 (SMPD1) gene. Methods: In order to determine the prevalence and distribution of SMPD1 gene mutations, the genomic DNA of 15 unrelated Iranian patients with types A and B NPD was examined using PCR, DNA sequencing and bioinformatics analysis. Results: Of 8 patients with the p.G508R mutation, 5 patients were homozygous, while the other 3 were heterozygous. One patient was heterozygous for both the p.N385K and p.G508R mutations. Another patient was heterozygous for both the p.A487V and p.G508R mutations. Two patients (one homozygous and one heterozygous) showed the p.V36A mutation. One patient was homozygous for the c.1033–1034insT mutation. One patient was homozygous for the c.573delT mutation, and 1 patient was homozygous for the c.1417–1418delCT mutation. Additionally, bioinformatics analysis indicated that two new p.V36A and p.N385K mutations decreased the acid sphingomyelinase (ASM) protein stability, which might be evidence to suggest the pathogenicity of these mutations. Conclusion: with detection of these new mutations, the genotypic spectrum of types A and B NPD is extended, facilitating the definition of disease-related mutations. However, more research is essential to confirm the pathogenic effect of these mutations. Full article

(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)

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17 pages, 2945 KiB

Open AccessArticle

Long Noncoding RNA MALAT-1 Enhances Stem Cell-Like Phenotypes in Pancreatic Cancer Cells

by Feng Jiao^1,2,†, Hai Hu^1,2,†, Ting Han^1,2,†, Cuncun Yuan³, Lei Wang^1,2, Ziliang Jin², Zhen Guo² and Liwei Wang^1,2,*

^† Current Address: GEOMAR Helmholtz Centre for Ocean Research Kiel, Marine Natural Products Chemistry, Am Kiel-Kanal 44, Kiel 24106, Germany.

¹ Department of Medical Oncology and Pancreatic Cancer Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, China

² Shanghai Key Laboratory of Pancreatic Diseases, Shanghai 201620, China

³ Department of Pathology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, China

^† These authors contributed equally to this work.

Int. J. Mol. Sci. 2015, 16(4), 6677-6693; https://doi.org/10.3390/ijms16046677 - 24 Mar 2015

Cited by 149 | Viewed by 9725

Abstract

Cancer stem cells (CSCs) play a vital role in tumor initiation, progression, metastasis, chemoresistance, and recurrence. The mechanisms that maintain the stemness of these cells remain largely unknown. Our previous study indicated that MALAT-1 may serve as an oncogenic long noncoding RNA in [...] Read more.

Cancer stem cells (CSCs) play a vital role in tumor initiation, progression, metastasis, chemoresistance, and recurrence. The mechanisms that maintain the stemness of these cells remain largely unknown. Our previous study indicated that MALAT-1 may serve as an oncogenic long noncoding RNA in pancreatic cancer by promoting epithelial-mesenchymal transition (EMT) and regulating CSCs markers expression. More significantly, there is emerging evidence that the EMT process may give rise to CSCs, or at least cells with stem cell-like properties. Therefore, we hypothesized that MALAT-1 might enhance stem cell-like phenotypes in pancreatic cancer cells. In this study, our data showed that MALAT-1 could increase the proportion of pancreatic CSCs, maintain self-renewing capacity, decrease the chemosensitivity to anticancer drugs, and accelerate tumor angiogenesis in vitro. In addition, subcutaneous nude mouse xenografts revealed that MALAT-1 could promote tumorigenicity of pancreatic cancer cells in vivo. The underlying mechanisms may involve in increased expression of self-renewal related factors Sox2. Collectively, we for the first time found the potential effects of MALAT-1 on the stem cell-like phenotypes in pancreatic cancer cells, suggesting a novel role of MALAT-1 in tumor stemness, which remains to be fully elucidated. Full article

(This article belongs to the Special Issue Pre-mRNA Splicing 2015)

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24 pages, 7245 KiB

Open AccessReview

Limitations and Extensions of the Lock-and-Key Principle: Differences between Gas State, Solution and Solid State Structures

by Hans-Jörg Schneider

Universität des Saarlandes, FR Organische Chemie, D 66041 Saarbrücken, Germany

Int. J. Mol. Sci. 2015, 16(4), 6694-6717; https://doi.org/10.3390/ijms16046694 - 25 Mar 2015

Cited by 35 | Viewed by 9311

Abstract

The lock-and-key concept is discussed with respect to necessary extensions. Formation of supramolecular complexes depends not only, and often not even primarily on an optimal geometric fit between host and guest. Induced fit and allosteric interactions have long been known as important modifications. [...] Read more.

The lock-and-key concept is discussed with respect to necessary extensions. Formation of supramolecular complexes depends not only, and often not even primarily on an optimal geometric fit between host and guest. Induced fit and allosteric interactions have long been known as important modifications. Different binding mechanisms, the medium used and pH effects can exert a major influence on the affinity. Stereoelectronic effects due to lone pair orientation can lead to variation of binding constants by orders of magnitude. Hydrophobic interactions due to high-energy water inside cavities modify the mechanical lock-and-key picture. That optimal affinities are observed if the cavity is only partially filled by the ligand can be in conflict with the lock-and-key principle. In crystals other forces than those between host and guest often dominate, leading to differences between solid state and solution structures. This is exemplified in particular with calixarene complexes, which by X-ray analysis more often than other hosts show guest molecules outside their cavity. In view of this the particular problems with the identification of weak interactions in crystals is discussed. Full article

(This article belongs to the Special Issue Supramolecular Interactions)

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Graphical abstract

39 pages, 1213 KiB

Open AccessReview

Understanding FRET as a Research Tool for Cellular Studies

by Dilip Shrestha^1,2, Attila Jenei¹, Péter Nagy¹

, György Vereb^1,2

and János Szöllősi^1,2,*

¹ Department of Biophysics and Cell Biology, University of Debrecen, Egyetem tér 1, Nagyerdei Krt. 98, Debrecen 4032, Hungary

² MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen 4032, Hungary

Int. J. Mol. Sci. 2015, 16(4), 6718-6756; https://doi.org/10.3390/ijms16046718 - 25 Mar 2015

Cited by 166 | Viewed by 20482

Abstract

Communication of molecular species through dynamic association and/or dissociation at various cellular sites governs biological functions. Understanding these physiological processes require delineation of molecular events occurring at the level of individual complexes in a living cell. Among the few non-invasive approaches with nanometer [...] Read more.

Communication of molecular species through dynamic association and/or dissociation at various cellular sites governs biological functions. Understanding these physiological processes require delineation of molecular events occurring at the level of individual complexes in a living cell. Among the few non-invasive approaches with nanometer resolution are methods based on Förster Resonance Energy Transfer (FRET). FRET is effective at a distance of 1–10 nm which is equivalent to the size of macromolecules, thus providing an unprecedented level of detail on molecular interactions. The emergence of fluorescent proteins and SNAP- and CLIP- tag proteins provided FRET with the capability to monitor changes in a molecular complex in real-time making it possible to establish the functional significance of the studied molecules in a native environment. Now, FRET is widely used in biological sciences, including the field of proteomics, signal transduction, diagnostics and drug development to address questions almost unimaginable with biochemical methods and conventional microscopies. However, the underlying physics of FRET often scares biologists. Therefore, in this review, our goal is to introduce FRET to non-physicists in a lucid manner. We will also discuss our contributions to various FRET methodologies based on microscopy and flow cytometry, while describing its application for determining the molecular heterogeneity of the plasma membrane in various cell types. Full article

(This article belongs to the Special Issue Förster Resonance Energy Transfer (FRET) 2015)

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26 pages, 2021 KiB

Open AccessArticle

In Silico Analysis of the Genes Encoding Proteins that Are Involved in the Biosynthesis of the RMS/MAX/D Pathway Revealed New Roles of Strigolactones in Plants

by Marek Marzec^1,*

and Aleksandra Muszynska²

¹ Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice 40-032, Poland

² Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben 06466, Germany

Int. J. Mol. Sci. 2015, 16(4), 6757-6782; https://doi.org/10.3390/ijms16046757 - 25 Mar 2015

Cited by 61 | Viewed by 10543

Abstract

Strigolactones were described as a new group of phytohormones in 2008 and since then notable large number of their functions has been uncovered, including the regulation of plant growth and development, interactions with other organisms and a plant’s response to different abiotic stresses. [...] Read more.

Strigolactones were described as a new group of phytohormones in 2008 and since then notable large number of their functions has been uncovered, including the regulation of plant growth and development, interactions with other organisms and a plant’s response to different abiotic stresses. In the last year, investigations of the strigolactone biosynthesis pathway in two model species, Arabidopsis thaliana and Oryza sativa, resulted in great progress in understanding the functions of four enzymes that are involved in this process. We performed in silico analyses, including the identification of the cis-regulatory elements in the promoters of genes encoding proteins of the strigolactone biosynthesis pathway and the identification of the miRNAs that are able to regulate their posttranscriptional level. We also searched the databases that contain the microarray data for the genes that were analyzed from both species in order to check their expression level under different growth conditions. The results that were obtained indicate that there are universal regulations of expression of all of the genes that are involved in the strigolactone biosynthesis in Arabidopsis and rice, but on the other hand each stage of strigolactone production may be additionally regulated independently. This work indicates the presence of crosstalk between strigolactones and almost all of the other phytohormones and suggests the role of strigolactones in the response to abiotic stresses, such as wounding, cold or flooding, as well as in the response to biotic stresses. Full article

(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)

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18 pages, 1570 KiB

Open AccessArticle

Towards Understanding the Decomposition/Isomerism Channels of Stratospheric Bromine Species: Ab Initio and Quantum Topology Study

by Saadullah G. Aziz¹, Abdulrahman O. Alyoubi¹, Shaaban A. Elroby^1,2

, Osman I. Osman¹

and Rifaat H. Hilal^1,3,*

¹ Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah B.O. 208203, Saudi Arabia

² Chemistry Department, Faculty of Science, Beni Suef University, Beni Suef 6251, Egypt

³ Chemistry Department, Faculty of Science, Cairo University, Cairo 12613, Egypt

Int. J. Mol. Sci. 2015, 16(4), 6783-6800; https://doi.org/10.3390/ijms16046783 - 25 Mar 2015

Cited by 7 | Viewed by 6239

Abstract

The present study aims at a fundamental understanding of bonding characteristics of the C–Br and O–Br bonds. The target molecular systems are the isomeric CH₃OBr/BrCH₂OH system and their decomposition products. Calculations of geometries and frequencies at different density functional [...] Read more.

The present study aims at a fundamental understanding of bonding characteristics of the C–Br and O–Br bonds. The target molecular systems are the isomeric CH₃OBr/BrCH₂OH system and their decomposition products. Calculations of geometries and frequencies at different density functional theory (DFT) and Hartree–Fock/Møller–Plesset (HF/MP2) levels have been performed. Results have been assessed and evaluated against those obtained at the coupled cluster single-double (Triplet) (CCSD(T)) level of theory. The characteristics of the C–Br and O–Br bonds have been identified via analysis of the electrostatic potential, natural bond orbital (NBO), and quantum theory of atoms in molecules (QTAIM). Analysis of the electrostatic potential (ESP) maps enabled the quantitative characterization of the Br σ-holes. Its magnitude seems very sensitive to the environment and the charge accumulated in the adjacent centers. Some quantum topological parameters, namely Ñ²ρ, ellipticity at bond critical points and the Laplacian bond order, were computed and discussed. The potential energy function for internal rotation has been computed and Fourier transformed to characterize the conformational preferences and origin of the barriers. NBO energetic components for rotation about the C–Br and O–Br bonds as a function of torsion angle have been computed and displayed. Full article

(This article belongs to the Special Issue Chemical Bond and Bonding 2015)

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17 pages, 854 KiB

Open AccessArticle

Preservation of Renal Blood Flow by the Antioxidant EUK-134 in LPS-Treated Pigs

by Sheldon Magder^1,*, Dimitrios G. Parthenis² and Imad Al Ghouleh^3,*

¹ Critical Care Division, Royal Victoria Hospital, 687 Pine Ave W, Montreal, QC H3A 1A1, Canada

² Vascular Surgery of Nikaia, Peiraeous 18454, Greece

³ Vascular Medicine Institute and Department of Pharmacology and Chemical Biology, University of Pittsburgh, Room E1228-2B, 200 Lothrop St, Pittsburgh, PA 15261, USA

Int. J. Mol. Sci. 2015, 16(4), 6801-6817; https://doi.org/10.3390/ijms16046801 - 25 Mar 2015

Cited by 4 | Viewed by 6331

Abstract

Sepsis is associated with an increase in reactive oxygen species (ROS), however, the precise role of ROS in the septic process remains unknown. We hypothesized that treatment with EUK-134 (manganese-3-methoxy N,N'-bis(salicyclidene)ethylene-diamine chloride), a compound with superoxide dismutase and catalase activity, [...] Read more.

Sepsis is associated with an increase in reactive oxygen species (ROS), however, the precise role of ROS in the septic process remains unknown. We hypothesized that treatment with EUK-134 (manganese-3-methoxy N,N'-bis(salicyclidene)ethylene-diamine chloride), a compound with superoxide dismutase and catalase activity, attenuates the vascular manifestations of sepsis in vivo. Pigs were instrumented to measure cardiac output and blood flow in renal, superior mesenteric and femoral arteries, and portal vein. Animals were treated with saline (control), lipopolysaccharide (LPS; 10 µg·kg⁻¹·h⁻¹), EUK-134, or EUK-134 plus LPS. Results show that an LPS-induced increase in pulmonary artery pressure (PAP) as well as a trend towards lower blood pressure (BP) were both attenuated by EUK-134. Renal blood flow decreased with LPS whereas superior mesenteric, portal and femoral flows did not change. Importantly, EUK-134 decreased the LPS-induced fall in renal blood flow and this was associated with a corresponding decrease in LPS-induced protein nitrotyrosinylation in the kidney. PO₂, pH, base excess and systemic vascular resistance fell with LPS and were unaltered by EUK-134. EUK-134 also had no effect on LPS-associated increase in CO. Interestingly, EUK-134 alone resulted in higher CO, BP, PAP, mean circulatory filling pressure, and portal flow than controls. Taken together, these data support a protective role for EUK-134 in the renal circulation in sepsis. Full article

(This article belongs to the Special Issue Oxidative Stress in Cardiovascular Disease 2015)

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13 pages, 5150 KiB

Open AccessArticle

Nano SiO₂ and MgO Improve the Properties of Porous β-TCP Scaffolds via Advanced Manufacturing Technology

by Chengde Gao^1,2,†, Pingpin Wei^3,†, Pei Feng², Tao Xiao^4,5, Cijun Shuai^2,4,* and Shuping Peng^1,3,*

¹ Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, China

² State Key Laboratory of High Performance Complex Manufacturing, Central South University, Changsha 410083, China

³ Cancer Research Institute, Central South University, Changsha 410078, China

⁴ Orthopedic Biomedical Materials Institute, Central South University, Changsha 410083, China

⁵ Department of Orthopedics, the Second Xiangya Hospital, Central South University, Changsha 410011, China

^† These authors contributed equally to this work.

Int. J. Mol. Sci. 2015, 16(4), 6818-6830; https://doi.org/10.3390/ijms16046818 - 25 Mar 2015

Cited by 39 | Viewed by 6743

Abstract

Nano SiO₂ and MgO particles were incorporated into β-tricalcium phosphate (β-TCP) scaffolds to improve the mechanical and biological properties. The porous cylindrical β-TCP scaffolds doped with 0.5 wt % SiO₂, 1.0 wt % MgO, 0.5 wt % SiO₂ + [...] Read more.

Nano SiO₂ and MgO particles were incorporated into β-tricalcium phosphate (β-TCP) scaffolds to improve the mechanical and biological properties. The porous cylindrical β-TCP scaffolds doped with 0.5 wt % SiO₂, 1.0 wt % MgO, 0.5 wt % SiO₂ + 1.0 wt % MgO were fabricated via selective laser sintering respectively and undoped β-TCP scaffold was also prepared as control. The phase composition and mechanical strength of the scaffolds were evaluated. X-ray diffraction analysis indicated that the phase transformation from β-TCP to α-TCP was inhibited after the addition of MgO. The compressive strength of scaffold was improved from 3.12 ± 0.36 MPa (β-TCP) to 5.74 ± 0.62 MPa (β-TCP/SiO₂), 9.02 ± 0.55 MPa (β-TCP/MgO) and 10.43 ± 0.28 MPa (β-TCP/SiO₂/MgO), respectively. The weight loss and apatite-forming ability of the scaffolds were evaluated by soaking them in simulated body fluid. The results demonstrated that both SiO₂ and MgO dopings slowed down the degradation rate and improved the bioactivity of β-TCP scaffolds. In vitro cell culture studies indicated that SiO₂ and MgO dopings facilitated cell attachment and proliferation. Combined addition of SiO₂ and MgO were found optimal in enhancing both the mechanical and biological properties of β-TCP scaffold. Full article

(This article belongs to the Section Materials Science)

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11 pages, 738 KiB

Open AccessArticle

Sex-Specific Diurnal Immobility Induced by Forced Swim Test in Wild Type and Clock Gene Deficient Mice

by Ningyue Li, Yanhua Xu, Xiaojuan Chen, Qing Duan and Mei Zhao^*

Key Lab of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing 100101, China

Int. J. Mol. Sci. 2015, 16(4), 6831-6841; https://doi.org/10.3390/ijms16046831 - 25 Mar 2015

Cited by 9 | Viewed by 5984

Abstract

Objective: The link between alterations in circadian rhythms and depression are well established, but the underlying mechanisms are far less elucidated. We investigated the circadian characteristics of immobility behavior in wild type (WT) mice and mice with mutations in core Clock genes. Methods: [...] Read more.

Objective: The link between alterations in circadian rhythms and depression are well established, but the underlying mechanisms are far less elucidated. We investigated the circadian characteristics of immobility behavior in wild type (WT) mice and mice with mutations in core Clock genes. Methods: All mice were tested with forced swim test (FST) at 4 h intervals. Results: These experiments revealed significant diurnal rhythms associated with immobility behavior in both male and female WT mice with sex-different circadian properties. In addition, male mice showed significantly less immobility during the night phase in comparison to female mice. Female Per1^Brdm1 mice also showed significant rhythmicity. However, the timing of rhythmicity was very different from that observed in female wild type mice. Male Per1^Brdm1 mice showed a pattern of rhythmicity similar to that of wild type mice. Furthermore, female Per1^Brdm1 mice showed higher duration of immobility in comparison to male Per1^Brdm1 mice in both daytime and early night phases. Neither Per2^Brdm1 nor Clock^Δ19 mice showed significant rhythmicity, but both female Per2^Brdm1 and Clock^Δ19 mice had lower levels of immobility, compared to males. Conclusions: This study highlights the differences in the circadian characteristics of immobility induced by FST in WT, Clock^Δ19, Per1, and Per2 deficient mice. Full article

(This article belongs to the Section Biochemistry)

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13 pages, 1513 KiB

Open AccessArticle

Hepatitis A Virus Genotype Distribution during a Decade of Universal Vaccination of Preadolescents

by Lucía D’Andrea^1,†, Francisco J. Pérez-Rodríguez^1,†, Montserrat De Castellarnau¹, Sandra Manzanares², Josep Lite³, Susana Guix¹

, Albert Bosch¹

and Rosa M. Pintó^1,*

¹ Enteric Virus Laboratory, Department of Microbiology and Institute of Nutrition and Food Safety, University of Barcelona, Diagonal 643, 08028 Barcelona, Spain

² Public Health Agency of Barcelona, Plaça Lesseps 1, 08023 Barcelona, Spain

³ Microbiology Unit, CatLab, 08232 Viladecavalls, Spain

^† These authors contributed equally to this work.

Int. J. Mol. Sci. 2015, 16(4), 6842-6854; https://doi.org/10.3390/ijms16046842 - 25 Mar 2015

Cited by 18 | Viewed by 6504

Abstract

A universal vaccination program among preadolescents was implemented in Catalonia, Spain, during the period of 1999–2013 and its effectiveness has been clearly demonstrated by an overall significant attack rate reduction. However, reductions were not constant over time, and increases were again observed in [...] Read more.

A universal vaccination program among preadolescents was implemented in Catalonia, Spain, during the period of 1999–2013 and its effectiveness has been clearly demonstrated by an overall significant attack rate reduction. However, reductions were not constant over time, and increases were again observed in 2002–2009 due to the occurrence of huge outbreaks. In the following years, in the absence of large outbreaks, the attack rate decreased again to very low levels. However, an increase of symptomatic cases in the <5 age group has recently been observed. This is an unexpected observation since children younger than 6 are mostly asymptomatic. Such a long vaccination campaign offers the opportunity to analyze not only the effectiveness of vaccination, but also the influence of the circulating genotypes on the incidence of hepatitis A among the different age groups. This study has revealed the emergence of genotype IC during a foodborne outbreak, the short-lived circulation of vaccine-escape variants isolated during an outbreak among the men-having-sex-with-men group, and the association of genotype IIIA with the increase of symptomatic cases among the very young. From a public health perspective, two conclusions may be drawn: vaccination is better at an early age, and the vaccination schedule must be complete and include all recommended vaccine doses. Full article

(This article belongs to the Special Issue Viral Hepatitis Research)

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13 pages, 1027 KiB

Open AccessArticle

Resistance Training Regulates Cardiac Function through Modulation of miRNA-214

by Stéphano Freitas Soares Melo¹, Valério Garrone Barauna², Miguel Araújo Carneiro Júnior³, Luiz Henrique Marchesi Bozi¹, Lucas Rios Drummond³, Antônio José Natali³ and Edilamar Menezes De Oliveira^1,*

¹ Laboratory of Biochemistry and Molecular Biology of the Exercise, School of Physical Education and Sport, University of Sao Paulo, Sao Paulo 05508-030, Brazil

² Laboratory of Molecular Physiology, Health Sciences Center, Federal University of Espírito Santo, Vitória 29043-900, Brazil

³ Department of Physical Education, Federal University of Viçosa, Viçosa, Minas Gerais 36570-900, Brazil

Int. J. Mol. Sci. 2015, 16(4), 6855-6867; https://doi.org/10.3390/ijms16046855 - 26 Mar 2015

Cited by 44 | Viewed by 7422

Abstract

Aims: To determine the effects of resistance training (RT) on the expression of microRNA (miRNA)-214 and its target in sarcoplasmic reticulum Ca²⁺-ATPase (SERCA2a), and on the morphological and mechanical properties of isolated left ventricular myocytes. Main methods: Male Wistar rats were [...] Read more.

Aims: To determine the effects of resistance training (RT) on the expression of microRNA (miRNA)-214 and its target in sarcoplasmic reticulum Ca²⁺-ATPase (SERCA2a), and on the morphological and mechanical properties of isolated left ventricular myocytes. Main methods: Male Wistar rats were divided into two groups (n = 7/group): Control (CO) or trained (TR). The exercise-training protocol consisted of: 4 × 12 bouts, 5×/week during 8 weeks, with 80% of one repetition maximum. Key findings: RT increased the left ventricular myocyte width by 15% and volume by 12%, compared with control animals (p < 0.05). The time to half relaxation and time to peak were 8.4% and 4.4% lower, respectively, in cells from TR group as compared to CO group (p < 0.05). RT decreased miRNA-214 level by 18.5% while its target SERCA2a expression were 18.5% higher (p < 0.05). Significance: Our findings showed that RT increases single left ventricular myocyte dimensions and also leads to faster cell contraction and relaxation. These mechanical adaptations may be related to the augmented expression of SERCA2a which, in turn, may be associated with the epigenetic modification of decreased miRNA-214 expression. Full article

(This article belongs to the Collection Regulation by Non-coding RNAs)

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22 pages, 5337 KiB

Open AccessArticle

Exploring the Balance between Folding and Functional Dynamics in Proteins and RNA

by Jovaun Jackson, Kien Nguyen and Paul Charles Whitford^*

Department of Physics, Northeastern University, 360 Huntington Ave, Boston, MA 02115, USA

Int. J. Mol. Sci. 2015, 16(4), 6868-6889; https://doi.org/10.3390/ijms16046868 - 26 Mar 2015

Cited by 18 | Viewed by 6990

Abstract

As our understanding of biological dynamics continues to be refined, it is becoming clear that biomolecules can undergo transitions between ordered and disordered states as they execute functional processes. From a computational perspective, studying disorder events poses a challenge, as they typically occur [...] Read more.

As our understanding of biological dynamics continues to be refined, it is becoming clear that biomolecules can undergo transitions between ordered and disordered states as they execute functional processes. From a computational perspective, studying disorder events poses a challenge, as they typically occur on long timescales, and the associated molecules are often large (i.e., hundreds of residues). These size and time requirements make it advantageous to use computationally inexpensive models to characterize large-scale dynamics, where more highly detailed models can provide information about individual sub-steps associated with function. To reduce computational demand, one often uses a coarse-grained representation of the molecule or a simplified description of the energetics. In order to use simpler models to identify transient disorder in RNA and proteins, it is imperative that these models can accurately capture structural fluctuations about folded configurations, as well as the overall stability of each molecule. Here, we explore a class of simplified model for which all non-hydrogen atoms are explicitly represented. We find that this model can provide a consistent description of protein folding and native-basin dynamics for several representative biomolecules. We additionally show that the native-basin fluctuations of tRNA and the ribosome are robust to variations in the model. Finally, the extended variable loop in tRNA^Ile is predicted to be very dynamic, which may facilitate biologically-relevant rearrangements. Together, this study provides a foundation that will aid in the application of simplified models to study disorder during function in ribonucleoprotein (RNP) assemblies. Full article

(This article belongs to the Special Issue Functions of Transfer RNAs)

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12 pages, 1393 KiB

Open AccessArticle

Tumour Cell Membrane Poration and Ablation by Pulsed Low-Intensity Electric Field with Carbon Nanotubes

by Lijun Wang^†, Dun Liu^†, Ru Zhou, Zhigang Wang^* and Alfred Cuschieri

¹ Institute for Medical Science and Technology (IMSaT), College of Medicine, Dentistry and Nursing, University of Dundee, Dundee DD2 1FD, UK

^† These authors contributed equally to this work.

Int. J. Mol. Sci. 2015, 16(4), 6890-6901; https://doi.org/10.3390/ijms16046890 - 26 Mar 2015

Cited by 18 | Viewed by 6809

Abstract

Electroporation is a physical method to increase permeabilization of cell membrane by electrical pulses. Carbon nanotubes (CNTs) can potentially act like “lighting rods” or exhibit direct physical force on cell membrane under alternating electromagnetic fields thus reducing the required field strength. A cell [...] Read more.

Electroporation is a physical method to increase permeabilization of cell membrane by electrical pulses. Carbon nanotubes (CNTs) can potentially act like “lighting rods” or exhibit direct physical force on cell membrane under alternating electromagnetic fields thus reducing the required field strength. A cell poration/ablation system was built for exploring these effects of CNTs in which two-electrode sets were constructed and two perpendicular electric fields could be generated sequentially. By applying this system to breast cancer cells in the presence of multi-walled CNTs (MWCNTs), the effective pulse amplitude was reduced to 50 V/cm (main field)/15 V/cm (alignment field) at the optimized pulse frequency (5 Hz) of 500 pulses. Under these conditions instant cell membrane permeabilization was increased to 38.62%, 2.77-fold higher than that without CNTs. Moreover, we also observed irreversible electroporation occurred under these conditions, such that only 39.23% of the cells were viable 24 h post treatment, in contrast to 87.01% cell viability without presence of CNTs. These results indicate that CNT-enhanced electroporation has the potential for tumour cell ablation by significantly lower electric fields than that in conventional electroporation therapy thus avoiding potential risks associated with the use of high intensity electric pulses. Full article

(This article belongs to the Special Issue Bioactive Nanoparticles)

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9 pages, 1565 KiB

Open AccessCommunication

Anti-Inflammatory Effect of Streptochlorin via TRIF-Dependent Signaling Pathways in Cellular and Mouse Models

by Do-Wan Shim^1,†, Hee Jae Shin^2,†, Ji-Won Han¹, Woo-Young Shin¹, Xiao Sun¹, Eun-Jeong Shim¹, Tack-Joong Kim³

, Tae-Bong Kang¹ and Kwang-Ho Lee^1,*

¹ Department of Biotechnology, College of Biomedical and Health Science, Konkuk University, Chungju 380-150, Korea

² Marine Natural Products Chemistry Laboratory, Korea Institute of Ocean Science & Technology, 787 Haeanro, Ansan 426-744, Korea

³ Division of Biological Science and Technology, Yonsei University, Wonju 222-710, Korea

^† These authors contributed equally to this work.

Int. J. Mol. Sci. 2015, 16(4), 6902-6910; https://doi.org/10.3390/ijms16046902 - 26 Mar 2015

Cited by 10 | Viewed by 6581

Abstract

Streptochlorin, a small compound derived from marine actinomycete, has been shown to have anti-angiogenic, anti-tumor, and anti-allergic activities. However, the anti-inflammatory effects and underlying mechanisms have not yet been reported. In the present study, we investigated the effect of streptochlorin on lipopolysaccharide (LPS)-induced [...] Read more.

Streptochlorin, a small compound derived from marine actinomycete, has been shown to have anti-angiogenic, anti-tumor, and anti-allergic activities. However, the anti-inflammatory effects and underlying mechanisms have not yet been reported. In the present study, we investigated the effect of streptochlorin on lipopolysaccharide (LPS)-induced inflammatory responses in vitro and in vivo. Streptochlorin attenuated the production of proinflammatory mediators such as nitric oxide, cyclooxygenase-2, pro-interleukin (IL)-1β, and IL-6 in LPS-stimulated RAW264.7 cells through inhibition of the Toll/interleukin-1 receptor (TIR)-domain-containing adapter-inducing interferon-β (TRIF)-dependent signaling pathway. Furthermore, streptochlorin suppressed the infiltration of immune cells such as neutrophils into the lung and proinflammatory cytokine production such as IL-6 and TNF-α in broncho-alveolar lavage fluid (BALF) in the LPS-induced acute lung injury (ALI) mouse model. Streptochlorin has potent anti-inflammatory effects through regulating TRIF-dependent signaling pathways, suggesting that streptochlorin may provide a valuable therapeutic strategy in treating various inflammatory diseases. Full article

(This article belongs to the Special Issue Bioactivity of Marine Natural Products)

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21 pages, 1478 KiB

Open AccessArticle

Functionalization of Magnetite Nanoparticles as Oil Spill Collector

by Ayman M. Atta^1,2,*, Hamad A. Al-Lohedan¹

and Sami A. Al-Hussain^1,3

¹ Surfactants Research Chair, Chemistry Department, College of Science, King Saud University, Riyadh 11541, Saudi Arabia

² Egyptian Petroleum Research Institute, 1 Ahmad Elzomor St., Nasr City, Cairo 11727, Egypt

³ Chemistry Department, Faculty of Science, Al-Imam Muhammad Bin Saud Islamic University, Riyadh 11632, Saudi Arabia

Int. J. Mol. Sci. 2015, 16(4), 6911-6931; https://doi.org/10.3390/ijms16046911 - 26 Mar 2015

Cited by 72 | Viewed by 10757

Abstract

In the present study, a new magnetic powder based on magnetite can be used as a petroleum crude oil collector. Amidoximes based on rosin as a natural product can be prepared from a reaction between hydroxylamine and rosin/acrylonitrile adducts. The produced rosin amidoximes [...] Read more.

In the present study, a new magnetic powder based on magnetite can be used as a petroleum crude oil collector. Amidoximes based on rosin as a natural product can be prepared from a reaction between hydroxylamine and rosin/acrylonitrile adducts. The produced rosin amidoximes were used as capping agents for magnetite nanoparticles to prepare hydrophobic coated magnetic powders. A new class of monodisperse hydrophobic magnetite nanoparticles was prepared by a simple and inexpensive co-precipitation method. Iron ions and iodine were prepared by the reaction between ferric chloride and potassium iodide. The structure and morphology of magnetite capped with rosin amidoxime were characterized by Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), transmission electron microscopy (TEM), zeta potential, thermogravimetric analysis (TGA) and dynamic light scattering (DLS). The magnetic properties were determined from vibrating sample magnetometer (VSM) analyses. These prepared magnetite nanoparticles were tested as bioactive nanosystems and their antimicrobial effects were investigated. The prepared nanomaterials were examined as a crude oil collector using magnetic fields. The results show promising data for the separation of the petroleum crude oil from aqueous solution in environmental pollution cleanup. Full article

(This article belongs to the Special Issue Magnetic Nanoparticles 2015)

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13 pages, 1800 KiB

Open AccessArticle

Multi-Layer Electrospun Membrane Mimicking Tendon Sheath for Prevention of Tendon Adhesions

by Shichao Jiang^1,†, Hede Yan^2,†, Dapeng Fan^1,†, Jialin Song¹ and Cunyi Fan^1,*

¹ Department of Orthopaedics, Shanghai Jiaotong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai 200233, China

² Department of Orthopaedics, the Second Affiliated Hospital of Wenzhou Medical University, 109 West Xueyuan Road, Wenzhou 325027, China

^† These authors contributed equally to this work.

Int. J. Mol. Sci. 2015, 16(4), 6932-6944; https://doi.org/10.3390/ijms16046932 - 26 Mar 2015

Cited by 44 | Viewed by 7486

Abstract

Defect of the tendon sheath after tendon injury is a main reason for tendon adhesions, but it is a daunting challenge for the biomimetic substitute of the tendon sheath after injury due to its multi-layer membrane-like structure and complex biologic functions. In this [...] Read more.

Defect of the tendon sheath after tendon injury is a main reason for tendon adhesions, but it is a daunting challenge for the biomimetic substitute of the tendon sheath after injury due to its multi-layer membrane-like structure and complex biologic functions. In this study, a multi-layer membrane with celecoxib-loaded poly(l-lactic acid)-polyethylene glycol (PELA) electrospun fibrous membrane as the outer layer, hyaluronic acid (HA) gel as middle layer, and PELA electrospun fibrous membrane as the inner layer was designed. The anti-adhesion efficacy of this multi-layer membrane was compared with a single-layer use in rabbit flexor digitorum profundus tendon model. The surface morphology showed that both PELA fibers and celecoxib-loaded PELA fibers in multi-layer membrane were uniform in size, randomly arrayed, very porous, and smooth without beads. Multi-layer membrane group had fewer peritendinous adhesions and better gliding than the PELA membrane group and control group in gross and histological observation. The similar mechanical characteristic and collagen expression of tendon repair site in the three groups indicated that the multi-layer membrane did not impair tendon healing. Taken together, our results demonstrated that such a biomimetic multi-layer sheath could be used as a potential strategy in clinics for promoting tendon gliding and preventing adhesion without poor tendon healing. Full article

(This article belongs to the Special Issue Biomaterials for Tissue Engineering)

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15 pages, 6814 KiB

Open AccessArticle

Effects of Aflatoxin B₁ on T-Cell Subsets and mRNA Expression of Cytokines in the Intestine of Broilers

by Min Jiang^1,†, Xi Peng^1,2,†, Jing Fang^1,2,*, Hengmin Cui^1,2, Zhengqiang Yu¹ and Zhengli Chen²

¹ Key Laboratory of Animal Diseases and Environmental Hazards of Sichuan Province, Ya’an 625014, Sichuan, China

² College of Veterinary Medicine, Sichuan Agricultural University, Ya’an 625014, Sichuan, China

^† These authors contributed equally to this work.

Int. J. Mol. Sci. 2015, 16(4), 6945-6959; https://doi.org/10.3390/ijms16046945 - 27 Mar 2015

Cited by 47 | Viewed by 6385

Abstract

This study was conducted to investigate the effects of aflatoxin B₁ (AFB₁) on T-cell subsets and mRNA expression of cytokines in the small intestine of broilers. One hundred and fifty-six one-day-old healthy Cobb broilers were randomly divided into control group [...] Read more.

This study was conducted to investigate the effects of aflatoxin B₁ (AFB₁) on T-cell subsets and mRNA expression of cytokines in the small intestine of broilers. One hundred and fifty-six one-day-old healthy Cobb broilers were randomly divided into control group (0 mg/kg AFB₁) and AFB₁ group (0.6 mg/kg AFB₁) with three replicates per group and 26 birds per replicate for 21 days, respectively. At 7, 14, and 21 days of age, the duodenum, jejunum and ileum were sampled for analyzing T cell subsets (CD3⁺, CD3⁺CD4⁺ and CD3⁺CD8⁺) by flow cytometry as well as IL-2, IL-4, IL-6, IL-10, IL-17, IFN-γ and TNF-α mRNA expression by qRT-PCR. The percentages of T-cells in the intra-epithelial lymphocytes (IELs) and lamina propria lymphocytes (LPLs) of duodenum, jejunum and ileum in the AFB₁ group showed a decreased tendency in comparison to the control group. The mRNA expression of cytokines in the three intestinal segments in the AFB₁ group presented a general decline compared with the control groups. Our data demonstrated that 0.6 mg/kg AFB₁ in the broilers diet could reduce the percentages of T-cell subsets and the expression level of cytokine mRNA in the small intestine, implying that the immune function of the intestinal mucosa might be affected. The reduction of cytokines mRNA expression may be closely associated with the decreased proportions of T cells subsets induced by AFB₁. Full article

(This article belongs to the Section Molecular Toxicology)

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18 pages, 7396 KiB

Open AccessArticle

Application of Single Molecule Fluorescence Microscopy to Characterize the Penetration of a Large Amphiphilic Molecule in the Stratum Corneum of Human Skin

by Pierre Volz¹, Alexander Boreham¹, Alexander Wolf¹, Tai-Yang Kim¹, Jens Balke¹, Janna Frombach², Sabrina Hadam²

, Zahra Afraz², Fiorenza Rancan²

, Ulrike Blume-Peytavi²

, Annika Vogt^2,*

and Ulrike Alexiev^1,*

¹ Department of Physics, Institute of Experimental Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany

² Clinical Research Center for Hair and Skin Science, Department of Dermatology, Charité-Universitaetsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany

Int. J. Mol. Sci. 2015, 16(4), 6960-6977; https://doi.org/10.3390/ijms16046960 - 27 Mar 2015

Cited by 22 | Viewed by 10660

Abstract

We report here on the application of laser-based single molecule total internal reflection fluorescence microscopy (TIRFM) to study the penetration of molecules through the skin. Penetration of topically applied drug molecules is often observed to be limited by the size of the respective [...] Read more.

We report here on the application of laser-based single molecule total internal reflection fluorescence microscopy (TIRFM) to study the penetration of molecules through the skin. Penetration of topically applied drug molecules is often observed to be limited by the size of the respective drug. However, the molecular mechanisms which govern the penetration of molecules through the outermost layer of the skin are still largely unknown. As a model compound we have chosen a larger amphiphilic molecule (fluorescent dye ATTO-Oxa12) with a molecular weight >700 Da that was applied to excised human skin. ATTO-Oxa12 penetrated through the stratum corneum (SC) into the viable epidermis as revealed by TIRFM of cryosections. Single particle tracking of ATTO-Oxa12 within SC sheets obtained by tape stripping allowed us to gain information on the localization as well as the lateral diffusion dynamics of these molecules. ATTO-Oxa12 appeared to be highly confined in the SC lipid region between (intercellular space) or close to the envelope of the corneocytes. Three main distinct confinement sizes of 52 ± 6, 118 ± 4, and 205 ± 5 nm were determined. We conclude that for this amphiphilic model compound several pathways through the skin exist. Full article

(This article belongs to the Special Issue Laser Application in Life Sciences)

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37 pages, 1192 KiB

Open AccessReview

A Review of Polyphenolics in Oak Woods

by Bo Zhang^1,2, Jian Cai^1,3, Chang-Qing Duan¹, Malcolm J. Reeves^1,4 and Fei He^1,*

¹ Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China

² College of Food Science and Engineering, Gansu Agricultural University, Lanzhou 730070, China

³ College of Agronomy and Biotechnology, China Agricultural University, Beijing 100094, China

⁴ Institute of Food, Nutrition and Human Health, Massey University, Palmerston North 4442, New Zealand

Int. J. Mol. Sci. 2015, 16(4), 6978-7014; https://doi.org/10.3390/ijms16046978 - 27 Mar 2015

Cited by 144 | Viewed by 12850

Abstract

Polyphenolics, which are ubiquitous in plants, currently are among the most studied phytochemicals because of their perceptible chemical properties and antioxidant activity. Oak barrels and their alternatives, which are widely used in winemaking nowadays, contribute polyphenolics to wines and are thought to play [...] Read more.

Polyphenolics, which are ubiquitous in plants, currently are among the most studied phytochemicals because of their perceptible chemical properties and antioxidant activity. Oak barrels and their alternatives, which are widely used in winemaking nowadays, contribute polyphenolics to wines and are thought to play crucial roles in the development of wines during aging. This study summarizes the detailed information of polyphenolics in oak woods and their products by examining their structures and discussing their chemical reactions during wine aging. This paper evaluates the most recent developments in polyphenolic chemistry by summarizing their extraction, separation, and their identification by the use of chromatographic and spectral techniques. In addition, this paper also introduces polyphenol bioactive ingredients in other plant foods. Full article

(This article belongs to the Special Issue Bioactive Phenolics and Polyphenols)

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12 pages, 3195 KiB

Open AccessCommunication

Identification of an AMPK Phosphorylation Site in Drosophila TSC2 (gigas) that Regulate Cell Growth

by Myungjin Kim^* and Jun Hee Lee

Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA

Int. J. Mol. Sci. 2015, 16(4), 7015-7026; https://doi.org/10.3390/ijms16047015 - 27 Mar 2015

Cited by 22 | Viewed by 10822

Abstract

AMP-activated protein kinase (AMPK) is an important metabolic regulator that mediates cellular adaptation to diverse stresses. One of the AMPK substrates, tuberous sclerosis complex 2 (TSC2), was suggested to mediate AMPK-induced silencing of mTOR complex 1 (mTORC1) signaling that is critical for cell [...] Read more.

AMP-activated protein kinase (AMPK) is an important metabolic regulator that mediates cellular adaptation to diverse stresses. One of the AMPK substrates, tuberous sclerosis complex 2 (TSC2), was suggested to mediate AMPK-induced silencing of mTOR complex 1 (mTORC1) signaling that is critical for cell growth. However, it is not known whether the AMPK-dependent TSC2 phosphorylation, originally observed in mammalian cells, is conserved in invertebrates. Here we show that energy depletion inhibits mTORC1 signaling through the AMPK-TSC2 axis in Drosophila S2 cells. We have discovered an AMPK phosphorylation site in TSC2-like genes from many different invertebrate species including Drosophila. The site (Ser1338 in Drosophila TSC2) is specifically and efficiently phosphorylated by AMPK in vitro. To evaluate the functional role of this phosphorylation site in vivo, we generated transgenic flies that can express identical amount of either wild-type or phosphorylation-resistant mutant Drosophila TSC2 in a tissue-specific manner. In response to transgenic Sestrin induction, which causes ectopic AMPK activation and subsequent mTORC1 inhibition, wild-type Drosophila TSC2 synergistically reduced tissue growth in the dorsal epithelium of Drosophila wings. However, phosphorylation-resistant mutant Drosophila TSC2 was unable to show such a growth-inhibiting effect, suggesting that this phosphorylation is important for AMPK-dependent regulation of cell growth. Full article

(This article belongs to the Special Issue Molecular Machinery of Cell Growth Regulation)

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18 pages, 816 KiB

Open AccessArticle

Antiangiogenesis, Loss of Cell Adhesion and Apoptosis Are Involved in the Antitumoral Activity of Proteases from V. cundinamarcensis (C. candamarcensis) in Murine Melanoma B16F1

by Dalton Dittz^1,†

, Cinthia Figueiredo^1,†, Fernanda O. Lemos^1,†, Celso T. R. Viana², Silvia P. Andrade², Elaine M. Souza-Fagundes², Ricardo T. Fujiwara³, Carlos E. Salas^4,* and Miriam T. P. Lopes¹

¹ Departamento de Farmacologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av Antônio Carlos 6627, 31270-901 Belo Horizonte, Brazil

² Departamento de Fisiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av Antônio Carlos 6627, 31270-901 Belo Horizonte, Brazil

³ Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av Antônio Carlos 6627, 31270-901 Belo Horizonte, Brazil

⁴ Departamento de Bioquímica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av Antônio Carlos 6627, 31270-901 Belo Horizonte, Brazil

^† These authors contributed equally to this work.

Int. J. Mol. Sci. 2015, 16(4), 7027-7044; https://doi.org/10.3390/ijms16047027 - 27 Mar 2015

Cited by 13 | Viewed by 5760

Abstract

The proteolytic enzymes from V. cundinamarcensis latex, (P1G10), display healing activity in animal models following various types of lesions. P1G10 or the purified isoforms act as mitogens on fibroblast and epithelial cells by stimulating angiogenesis and wound healing in gastric and cutaneous ulcers [...] Read more.

The proteolytic enzymes from V. cundinamarcensis latex, (P1G10), display healing activity in animal models following various types of lesions. P1G10 or the purified isoforms act as mitogens on fibroblast and epithelial cells by stimulating angiogenesis and wound healing in gastric and cutaneous ulcers models. Based on evidence that plant proteinases act as antitumorals, we verified this effect on a murine melanoma model. The antitumoral effect analyzed mice survival and tumor development after subcutaneous administration of P1G10 into C57BL/6J mice bearing B16F1 low metastatic melanoma. Possible factors involved in the antitumoral action were assessed, i.e., cytotoxicity, cell adhesion and apoptosis in vitro, haemoglobin (Hb), vascular endothelial growth factor (VEGF), tumor growth factor-β (TGF-β), tumor necrosis factor-α (TNF-α) content and N-acetyl-glucosaminidase (NAG) activity. We observed that P1G10 inhibited angiogenesis measured by the decline of Hb and VEGF within the tumor, and TGF-β displayed a non-significant increase and TNF-α showed a minor non-significant reduction. On the other hand, there was an increase in NAG activity. In treated B16F1 cells, apoptosis was induced along with decreased cell binding to extracellular matrix components (ECM) and anchorage, without impairing viability. Full article

(This article belongs to the Section Biochemistry)

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12 pages, 727 KiB

Open AccessArticle

Rapid Characterization of Fatty Acids in Oleaginous Microalgae by Near-Infrared Spectroscopy

by Bin Liu^1,2

, Jin Liu^2,3, Tianpeng Chen², Bo Yang^1,2, Yue Jiang⁴, Dong Wei¹

and Feng Chen^2,5,*

¹ School of Light Industry and Food Sciences, South China University of Technology, Guangzhou 510640, China

² Institute for Food and Bioresource Engineering, College of Engineering, Peking University, Beijing 100871, China

³ Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA

⁴ The School of Food Science and Technology, Jiangnan University, Wuxi 214122, China

⁵ Singapore-Peking University Research Centre for a Sustainable Low-Carbon Future, CREATE Tower 138602, Singapore

Int. J. Mol. Sci. 2015, 16(4), 7045-7056; https://doi.org/10.3390/ijms16047045 - 27 Mar 2015

Cited by 19 | Viewed by 6962

Abstract

The key properties of microalgal biodiesel are largely determined by the composition of its fatty acid methyl esters (FAMEs). The gas chromatography (GC) based techniques for fatty acid analysis involve energy-intensive and time-consuming procedures and thus are less suitable for high-throughput screening applications. [...] Read more.

The key properties of microalgal biodiesel are largely determined by the composition of its fatty acid methyl esters (FAMEs). The gas chromatography (GC) based techniques for fatty acid analysis involve energy-intensive and time-consuming procedures and thus are less suitable for high-throughput screening applications. In the present study, a novel quantification method for microalgal fatty acids was established based on the near-infrared spectroscopy (NIRS) technique. The lyophilized cells of oleaginous Chlorella containing different contents of lipids were scanned by NIRS and their fatty acid profiles were determined by GC-MS. NIRS models were developed based on the chemometric correlation of the near-infrared spectra with fatty acid profiles in algal biomass. The optimized NIRS models showed excellent performances for predicting the contents of total fatty acids, C16:0, C18:0, C18:1 and C18:3, with the coefficient of determination (R²) being 0.998, 0.997, 0.989, 0.991 and 0.997, respectively. Taken together, the NIRS method established here bypasses the procedures of cell disruption, oil extraction and transesterification, is rapid, reliable, and of great potential for high-throughput applications, and will facilitate the screening of microalgal mutants and optimization of their growth conditions for biodiesel production. Full article

(This article belongs to the Special Issue Microalgal Biotechnology)

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20 pages, 1175 KiB

Open AccessArticle

Elevated Levels of Endocannabinoids in Chronic Hepatitis C May Modulate Cellular Immune Response and Hepatic Stellate Cell Activation

by Eleonora Patsenker^1,*, Philip Sachse¹, Andrea Chicca², María Salomé Gachet², Vreni Schneider¹, Johan Mattsson³, Christian Lanz³, Mathias Worni⁴, Andrea De Gottardi⁴, Mariam Semmo⁵, Jochen Hampe⁶, Clemens Schafmayer⁷, Rudolf Brenneisen³, Jürg Gertsch², Felix Stickel^1,† and Nasser Semmo^1,4,†

¹ Department of Clinical Research, University of Bern, Bern 3010, Switzerland

² Institute of Biochemistry and Molecular Medicine, University of Bern, Bern 3012, Switzerland

³ Department of Clinical Research, Laboratory of Phytopharmacology, Bioanalytics and Pharmacokinetics, University of Bern, Bern 3010, Switzerland

⁴ Department of Visceral Surgery and Medicine, Inselspital, University of Bern, Bern 3010, Switzerland

⁵ Department of Nephrology, Inselspital, University of Bern, Bern 3010, Switzerland

⁶ Department of Medicine II, Division of Gastroenterology, University of Dresden, Dresden 01307, Germany

⁷ Department of Visceral Surgery, University of Schleswig-Holstein, Campus Kiel, Kiel 24105, Germany

^† These authors contributed equally to this work.

Int. J. Mol. Sci. 2015, 16(4), 7057-7076; https://doi.org/10.3390/ijms16047057 - 27 Mar 2015

Cited by 34 | Viewed by 7819

Abstract

The endocannabinoid (EC) system is implicated in many chronic liver diseases, including hepatitis C viral (HCV) infection. Cannabis consumption is associated with fibrosis progression in patients with chronic hepatitis C (CHC), however, the role of ECs in the development of CHC has never [...] Read more.

The endocannabinoid (EC) system is implicated in many chronic liver diseases, including hepatitis C viral (HCV) infection. Cannabis consumption is associated with fibrosis progression in patients with chronic hepatitis C (CHC), however, the role of ECs in the development of CHC has never been explored. To study this question, anandamide (AEA) and 2-arachidonoyl glycerol (2-AG) were quantified in samples of HCV patients and healthy controls by gas and liquid chromatography mass spectrometry. Fatty acid amide hydrolase (FAAH) and monoaclyglycerol lipase (MAGL) activity was assessed by [³H]AEA and [³H]2-AG hydrolysis, respectively. Gene expression and cytokine release were assayed by TaqMan PCR and ELISpot, respectively. AEA and 2-AG levels were increased in plasma of HCV patients, but not in liver tissues. Hepatic FAAH and MAGL activity was not changed. In peripheral blood mononuclear cells (PBMC), ECs inhibited IFN-γ, TNF-α, and IL-2 secretion. Inhibition of IL-2 by endogenous AEA was stronger in PBMC from HCV patients. In hepatocytes, 2-AG induced the expression of IL-6, -17A, -32 and COX-2, and enhanced activation of hepatic stellate cells (HSC) co-cultivated with PBMC from subjects with CHC. In conclusion, ECs are increased in plasma of patients with CHC and might reveal immunosuppressive and profibrogenic effects. Full article

(This article belongs to the Special Issue Viral Hepatitis Research)

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21 pages, 2529 KiB

Open AccessArticle

Blunt Snout Bream (Megalobrama amblycephala) MyD88 and TRAF6: Characterisation, Comparative Homology Modelling and Expression

by Ngoc Tuan Tran, Han Liu, Ivan Jakovlić and Wei-Min Wang^*

College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China

Int. J. Mol. Sci. 2015, 16(4), 7077-7097; https://doi.org/10.3390/ijms16047077 - 30 Mar 2015

Cited by 24 | Viewed by 6083

Abstract

MyD88 and TRAF6 play an essential role in the innate immune response in most animals. This study reports the full-length MaMyD88 and MaTRAF6 genes identified from the blunt snout bream (Megalobrama amblycephala) transcriptome profile. MaMyD88 is 2501 base pairs (bp) [...] Read more.

MyD88 and TRAF6 play an essential role in the innate immune response in most animals. This study reports the full-length MaMyD88 and MaTRAF6 genes identified from the blunt snout bream (Megalobrama amblycephala) transcriptome profile. MaMyD88 is 2501 base pairs (bp) long, encoding a putative protein of 284 amino acids (aa), including the N-terminal DEATH domain of 78 aa and the C-terminal TIR domain of 138 aa. MaTRAF6 is 2252 bp long, encoding a putative protein of 542 aa, including the N-terminal low-complexity region, RING domain (40 aa), a coiled-coil region (64 aa) and C-terminal MATH domain (147 aa). Coding regions of MaMyD88 and MaTRAF6 genomic sequences consisted of five and six exons, respectively. Physicochemical and functional characteristics of the proteins were analysed. Alpha helices were dominant in the secondary structure of the proteins. Homology models of the MaMyD88 and MaTRAF6 domains were constructed applying the comparative modelling method. RT-qPCR was used to analyse the expression of MaMyD88 and MaTRAF6 mRNA transcripts in response to Aeromonas hydrophila challenge. Both genes were highly upregulated in the liver, spleen and kidney during the first 24 h after the challenge. While MyD88 and TRAF6 have been reported in various aquatic species, this is the first report and characterisation of these genes in blunt snout bream. This research also provides evidence of the important roles of these two genes in the blunt snout bream innate immune system. Full article

(This article belongs to the Section Biochemistry)

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14 pages, 1041 KiB

Open AccessArticle

Identification and Functional Analysis of MicroRNAs and Their Targets in Platanus acerifolia under Lead (Pb) Stress

by Yuanlong Wang¹, Zhenli Zhao¹, Minjie Deng¹, Rongning Liu^1,2, Suyan Niu¹ and Guoqiang Fan^1,*

¹ Institute of Paulownia, Henan Agricultural University, 95 Wenhua Road, Jinshui District, Zhengzhou 450002, China

² Department of Landscape Architecture, Henan Vocational College of Agriculture, Zhengzhou 451450, China

Int. J. Mol. Sci. 2015, 16(4), 7098-7111; https://doi.org/10.3390/ijms16047098 - 30 Mar 2015

Cited by 24 | Viewed by 6332

Abstract

MicroRNAs (miRNAs) play important regulatory roles in development and stress responses in plants. Lead (Pb) is a non-essential element that is highly toxic to living organisms. Platanus acerifolia is grown as a street tree in cities throughout temperate regions for its importance in [...] Read more.

MicroRNAs (miRNAs) play important regulatory roles in development and stress responses in plants. Lead (Pb) is a non-essential element that is highly toxic to living organisms. Platanus acerifolia is grown as a street tree in cities throughout temperate regions for its importance in improving the urban ecological environment. MiRNAs that respond to abiotic stresses have been identified in plants; however, until now, the influence of Pb stress on P. acerifolia miRNAs has not been reported. To identify miRNAs and predict their target genes under Pb stress, two small RNA and two degradome libraries were constructed from Pb-treated and Pb-free leaves of P. acerifolia seedlings. After sequencing, 55 known miRNAs and 129 novel miRNAs were obtained, and 104 target genes for the miRNAs were identified by degradome sequencing. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed to predict the functions of the targets. The expressions of eight differentially expressed miRNAs were validated by quantitative real-time polymerase chain reaction (qRT-PCR). This is the first report about P. acerifolia miRNAs and their target genes under Pb stress. This study has provided data for further research into molecular mechanisms involved in resistance of P. acerifolia to Pb stress. Full article

(This article belongs to the Special Issue Effects of Herbicides and Heavy Metals to the Structure and Function of Plant Cells)

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21 pages, 3243 KiB

Open AccessArticle

MicroRNA-16 Modulates HuR Regulation of Cyclin E1 in Breast Cancer Cells

by Xun Guo, Melanie C. Connick, Jennifer Vanderhoof, Mohammad-Ali Ishak and Rebecca S. Hartley^*

Department of Cell Biology and Physiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA

Int. J. Mol. Sci. 2015, 16(4), 7112-7132; https://doi.org/10.3390/ijms16047112 - 30 Mar 2015

Cited by 40 | Viewed by 7483

Abstract

RNA binding protein (RBPs) and microRNAs (miRNAs or miRs) are post-transcriptional regulators of gene expression that are implicated in development of cancers. Although their individual roles have been studied, the crosstalk between RBPs and miRNAs is under intense investigation. Here, we show that [...] Read more.

RNA binding protein (RBPs) and microRNAs (miRNAs or miRs) are post-transcriptional regulators of gene expression that are implicated in development of cancers. Although their individual roles have been studied, the crosstalk between RBPs and miRNAs is under intense investigation. Here, we show that in breast cancer cells, cyclin E1 upregulation by the RBP HuR is through specific binding to regions in the cyclin E1 mRNA 3' untranslated region (3'UTR) containing U-rich elements. Similarly, miR-16 represses cyclin E1, dependent on its cognate binding sites in the cyclin E1 3'UTR. Evidence in the literature indicates that HuR can regulate miRNA expression and recruit or dissociate RNA-induced silencing complexes (RISC). Despite this, miR-16 and HuR do not affect the other’s expression level or binding to the cyclin E1 3'UTR. While HuR overexpression partially blocks miR-16 repression of a reporter mRNA containing the cyclin E1 3'UTR, it does not block miR-16 repression of endogenous cyclin E1 mRNA. In contrast, miR-16 blocks HuR-mediated upregulation of cyclin E1. Overall our results suggest that miR-16 can override HuR upregulation of cyclin E1 without affecting HuR expression or association with the cyclin E1 mRNA. Full article

(This article belongs to the Special Issue Post-Transcriptional Gene Regulation by Ribonucleoprotein Complexes)

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10 pages, 1109 KiB

Open AccessReview

Unfolding the Unfolded Protein Response: Unique Insights into Brain Ischemia

by Thomas H. Sanderson¹, Molly Gallaway² and Rita Kumar^3,*

¹ Cardiovascular Research Institute and Department of Emergency Medicine, Wayne State University School of Medicine, Detroit, MI 48201, USA

² Department of Emergency Medicine, Wayne State University School of Medicine, Detroit, MI 48201, USA

³ Cardiovascular Research Institute and Departments of Emergency Medicine and Physiology, Wayne State University School of Medicine, Detroit, MI 48201, USA

Int. J. Mol. Sci. 2015, 16(4), 7133-7142; https://doi.org/10.3390/ijms16047133 - 30 Mar 2015

Cited by 42 | Viewed by 6938

Abstract

The endoplasmic reticulum (ER) is responsible for processing of proteins that are destined to be secreted, enclosed in a vesicle, or incorporated in the plasma membrane. Nascent peptides that enter the ER undergo a series of highly regulated processing steps to reach maturation [...] Read more.

The endoplasmic reticulum (ER) is responsible for processing of proteins that are destined to be secreted, enclosed in a vesicle, or incorporated in the plasma membrane. Nascent peptides that enter the ER undergo a series of highly regulated processing steps to reach maturation as they transit the ER. Alterations in the intracellular environment that induce ER stress are thought to interrupt these processing steps, and result in unfolding of proteins in the ER. Accumulation of unfolded proteins concurrently activates three transmembrane stress sensors, IRE1, ATF6 and PERK, and is referred to as the Unfolded Protein Response (UPR). Our understanding of the mechanisms of UPR induction has been assembled primarily from experiments inducing ER stress with chemical and genetic manipulations. However, physiological stress often induces activation of ER stress sensors in a distinct manner from the canonical UPR. The unique activation profiles in vivo have prompted us to examine the mechanism of UPR activation in neurons following cerebral ischemia. Full article

(This article belongs to the Special Issue Neurological Injuries’ Monitoring, Tracking and Treatment)

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16 pages, 1141 KiB

Open AccessArticle

Organocatalytic Upgrading of Furfural and 5-Hydroxymethyl Furfural to C₁₀ and C₁₂ Furoins with Quantitative Yield and Atom-Efficiency

by Hongjun Zang^† and Eugene Y. X. Chen^*

¹ Department of Chemistry, Colorado State University, Fort Collins, CO 80523-1872, USA

^† Current address: Department of Environment and Chemical Engineering, Tianjin Polytechnic University, Tianjin 300387, China

Int. J. Mol. Sci. 2015, 16(4), 7143-7158; https://doi.org/10.3390/ijms16047143 - 30 Mar 2015

Cited by 42 | Viewed by 9428

Abstract

There is increasing interest in the upgrading of C₅ furfural (FF) and C₆ 5-hydroxymethyl furfural (HMF) into C₁₀ and C₁₂ furoins as higher energy-density intermediates for renewable chemicals, materials, and biofuels. This work utilizes the organocatalytic approach, using the [...] Read more.

There is increasing interest in the upgrading of C₅ furfural (FF) and C₆ 5-hydroxymethyl furfural (HMF) into C₁₀ and C₁₂ furoins as higher energy-density intermediates for renewable chemicals, materials, and biofuels. This work utilizes the organocatalytic approach, using the in situ generated N,S-heterocyclic carbene catalyst derived from thiazolium ionic liquids (ILs), to achieve highly efficient self-coupling reactions of FF and HMF. Specifically, variations of the thiazolium IL structure have led to the most active and efficient catalyst system of the current series, which is derived from a new thiazolium IL carrying the electron-donating acetate group at the 5-ring position. For FF coupling by this IL (0.1 mol %, 60 °C, 1 h), when combined with Et₃N, furoin was obtained in >99% yield. A 97% yield of the C₁₂ furoin was also achieved from the HMF coupling by this catalyst system (10 mol % loading, 120 °C, 3 h). On the other hand, the thiazolium IL bearing the electron-withdrawing group at the 5-ring position is the least active and efficient catalyst. The mechanistic aspects of the coupling reaction by the thiazolium catalyst system have also been examined and a mechanism has been proposed. Full article

(This article belongs to the Special Issue Green Chemistry and the Biorefinery)

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14 pages, 3029 KiB

Open AccessArticle

A Double-Edged Sword: The Role of VEGF in Wound Repair and Chemoattraction of Opportunist Pathogens

by Eric Birkenhauer and Suresh Neethirajan^*

BioNano Laboratory, School of Engineering, University of Guelph, Guelph, ON N1G 2W1, Canada

Int. J. Mol. Sci. 2015, 16(4), 7159-7172; https://doi.org/10.3390/ijms16047159 - 30 Mar 2015

Cited by 20 | Viewed by 6646

Abstract

Wound healing is a complex process essential to repairing damaged tissues and preventing infection. Skin is the first line of defense, a chief physical barrier to microbe entry. Wound healing is a physical rebuilding process, but at the same time it is an [...] Read more.

Wound healing is a complex process essential to repairing damaged tissues and preventing infection. Skin is the first line of defense, a chief physical barrier to microbe entry. Wound healing is a physical rebuilding process, but at the same time it is an inflammatory event. In turn, molecules for wound repair are secreted by fibroblasts and others present at the wound site. Vascular endothelial growth factor (VEGF) is a critical cytokine that exhibits chemoattractant properties, recruiting other immune cells to the site. Although generally beneficial, VEGF may also act as a chemoattractant for invading microorganisms, such as Pseudomonas aeruginosa. P. aeruginosa is problematic during wound infection due to its propensity to form biofilms and exhibit heightened antimicrobial resistance. Here, we explored the influence of VEGF gradients (in a microfluidic device wound model) on the motility and chemotactic properties of P. aeruginosa. At lower concentrations, VEGF had little effect on motility, but as the maximal concentration within the gradient increased, P. aeruginosa cells exhibited directed movement along the gradient. Our data provide evidence that while beneficial, VEGF, in excess, may aid colonization by P. aeruginosa. This highlights the necessity for the efficient resolution of inflammation. Understanding the dynamics of wound colonization may lead to new/enhanced therapeutics to hasten recovery. Full article

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22 pages, 3742 KiB

Open AccessReview

Interaction of tRNA with Eukaryotic Ribosome

by Dmitri Graifer^1,2 and Galina Karpova^1,2,*

¹ Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, pr. Lavrentieva, 8, 630090 Novosibirsk, Russia

² Department of Natural Sciences, Novosibirsk State University, ul. Pirogova, 2, 630090 Novosibirsk, Russia

Int. J. Mol. Sci. 2015, 16(4), 7173-7194; https://doi.org/10.3390/ijms16047173 - 30 Mar 2015

Cited by 15 | Viewed by 9407

Abstract

This paper is a review of currently available data concerning interactions of tRNAs with the eukaryotic ribosome at various stages of translation. These data include the results obtained by means of cryo-electron microscopy and X-ray crystallography applied to various model ribosomal complexes, site-directed [...] Read more.

This paper is a review of currently available data concerning interactions of tRNAs with the eukaryotic ribosome at various stages of translation. These data include the results obtained by means of cryo-electron microscopy and X-ray crystallography applied to various model ribosomal complexes, site-directed cross-linking with the use of tRNA derivatives bearing chemically or photochemically reactive groups in the CCA-terminal fragment and chemical probing of 28S rRNA in the region of the peptidyl transferase center. Similarities and differences in the interactions of tRNAs with prokaryotic and eukaryotic ribosomes are discussed with concomitant consideration of the extent of resemblance between molecular mechanisms of translation in eukaryotes and bacteria. Full article

(This article belongs to the Special Issue Functions of Transfer RNAs)

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15 pages, 795 KiB

Open AccessArticle

In Vitro Investigation of Self-Assembled Nanoparticles Based on Hyaluronic Acid-Deoxycholic Acid Conjugates for Controlled Release Doxorubicin: Effect of Degree of Substitution of Deoxycholic Acid

by Wen-Hao Wei, Xue-Meng Dong and Chen-Guang Liu^*

College of Marine Life Science, Ocean University of China, Yusan Road No. 5, Qingdao 266003, China

Int. J. Mol. Sci. 2015, 16(4), 7195-7209; https://doi.org/10.3390/ijms16047195 - 31 Mar 2015

Cited by 29 | Viewed by 7777

Abstract

Self-assembled nanoparticles based on a hyaluronic acid-deoxycholic acid (HD) chemical conjugate with different degree of substitution (DS) of deoxycholic acid (DOCA) were prepared. The degree of substitution (DS) was determined by titration method. The nanoparticles were loaded with doxorubicin (DOX) as the model [...] Read more.

Self-assembled nanoparticles based on a hyaluronic acid-deoxycholic acid (HD) chemical conjugate with different degree of substitution (DS) of deoxycholic acid (DOCA) were prepared. The degree of substitution (DS) was determined by titration method. The nanoparticles were loaded with doxorubicin (DOX) as the model drug. The human cervical cancer (HeLa) cell line was utilized for in vitro studies and cell cytotoxicity of DOX incorporated in the HD nanoparticles was accessed by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. In addition, cellular uptake of fluorescently labeled nanoparticles was also investigated. An increase in the degree of deoxycholic acid substitution reduced the size of the nanoparticles and also enhanced their drug encapsulation efficiency (EE), which increased with the increase of DS. A higher degree of deoxycholic acid substitution also lead to a lower release rate and an initial burst release of doxorubicin from the nanoparticles. In summary, the degree of substitution allows the modulation of the particle size, drug encapsulation efficiency, drug release rate, and cell uptake efficiency of the nanoparticles. The herein developed hyaluronic acid-deoxycholic acid conjugates are a good candidate for drug delivery and could potentiate therapeutic formulations for doxorubicin–mediated cancer therapy. Full article

(This article belongs to the Special Issue Bioactive Nanoparticles 2014)

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20 pages, 2796 KiB

Open AccessArticle

Study of Linkage between Glutathione Pathway and the Antibiotic Resistance of Escherichia coli from Patients’ Swabs

by Marketa Kominkova^1,2, Petr Michalek^1,2, Kristyna Cihalova^1,2, Roman Guran^1,2

, Natalia Cernei^1,2, Lukas Nejdl^1,2, Kristyna Smerkova^1,2, Simona Dostalova^1,2, Dagmar Chudobova^1,2, Zbynek Heger^1,2, Radek Vesely³, Jaromir Gumulec^2,4, Jindrich Kynicky⁵, Kledi Xhaxhiu², Ondrej Zitka^1,2, Vojtech Adam^1,2 and Rene Kizek^1,2,*

¹ Department of Chemistry and Biochemistry, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic

² Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic

³ Clinic of Traumatology at the Medical Faculty, Masaryk University of Brno, Ponavka 6, CZ-662 50 Brno, Czech Republic

⁴ Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Komenskeho Namesti 2, CZ-662 43 Brno, Czech Republic

⁵ Karel Englis College, Sujanovo Nam. 356/1, CZ-602 00 Brno, Czech Republic

Int. J. Mol. Sci. 2015, 16(4), 7210-7229; https://doi.org/10.3390/ijms16047210 - 31 Mar 2015

Cited by 10 | Viewed by 6833

Abstract

In this work, we focused on the differences between bacterial cultures of E. coli obtained from swabs of infectious wounds of patients compared to laboratory E. coli. In addition, blocking of the protein responsible for the synthesis of glutathione (γ-glutamylcysteine synthase—GCL) using 10 [...] Read more.

In this work, we focused on the differences between bacterial cultures of E. coli obtained from swabs of infectious wounds of patients compared to laboratory E. coli. In addition, blocking of the protein responsible for the synthesis of glutathione (γ-glutamylcysteine synthase—GCL) using 10 mM buthionine sulfoximine was investigated. Each E. coli showed significant differences in resistance to antibiotics. According to the determined resistance, E. coli were divided into experimental groups based on a statistical evaluation of their properties as more resistant and more sensitive. These groups were also used for finding the differences in a dependence of the glutathione pathway on resistance to antibiotics. More sensitive E. coli showed the same kinetics of glutathione synthesis while blocking GCL (K_m 0.1 µM), as compared to non-blocking. In addition, the most frequent mutations in genes of glutathione synthetase, glutathione peroxidase and glutathione reductase were observed in this group compared to laboratory E.coli. The group of “more resistant” E. coli exhibited differences in K_m between 0.3 and 0.8 µM. The number of mutations compared to the laboratory E. coli was substantially lower compared to the other group. Full article

(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)

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31 pages, 789 KiB

Open AccessReview

Male Reproductive Cancers and Infertility: A Mutual Relationship

by Eva Tvrda^1,2

, Ashok Agarwal^1,* and Nawaf Alkuhaimi^1,3

¹ Center for Reproductive Medicine, Cleveland Clinic, Mail Code X-11, 10681 Carnegie Avenue, Cleveland, OH 44195, USA

² Department of Animal Physiology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture, Tr. A. Hlinku 2, 94976 Nitra, Slovakia

³ College of Medicine, Alfaisal University, P.O. Box 50927, 11533 Riyadh, Saudi Arabia

Int. J. Mol. Sci. 2015, 16(4), 7230-7260; https://doi.org/10.3390/ijms16047230 - 31 Mar 2015

Cited by 46 | Viewed by 11062

Abstract

Reproductive dysfunction and malignancies related to the male gender represent a serious health concern, whose incidence has significantly risen over the past years. Prior to treatment, testicular or prostate cancer patients often display poor semen characteristics similar to subfertile or infertile patients. This [...] Read more.

Reproductive dysfunction and malignancies related to the male gender represent a serious health concern, whose incidence has significantly risen over the past years. Prior to treatment, testicular or prostate cancer patients often display poor semen characteristics similar to subfertile or infertile patients. This fact is underscored by cases where the malignancy is often diagnosed in males who undergo a general fertility screening. This review aims to examine the associations between male infertility and reproductive cancers focusing on common etiologies and biological mechanisms underlining these pathologies. Furthermore, we discuss compelling epidemiological data hypothesizing that male reproductive failure may act as a precursor of future andrological malignancies, including testicular or prostate cancer, thus providing a stimulus for a more specific research in male reproductive health and emphasizing the importance of this relation for physicians taking care of male patients with a reproductive disease. Full article

(This article belongs to the Special Issue Advances in Reproductive Biology)

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12 pages, 1210 KiB

Open AccessArticle

Glycolic Acid-Catalyzed Deamidation of Asparagine Residues in Degrading PLGA Matrices: A Computational Study

by Noriyoshi Manabe, Ryota Kirikoshi and Ohgi Takahashi^*

Faculty of Pharmaceutical Sciences, Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan

Int. J. Mol. Sci. 2015, 16(4), 7261-7272; https://doi.org/10.3390/ijms16047261 - 31 Mar 2015

Cited by 12 | Viewed by 6755

Abstract

Poly(lactic-co-glycolic acid) (PLGA) is a strong candidate for being a drug carrier in drug delivery systems because of its biocompatibility and biodegradability. However, in degrading PLGA matrices, the encapsulated peptide and protein drugs can undergo various degradation reactions, including deamidation at [...] Read more.

Poly(lactic-co-glycolic acid) (PLGA) is a strong candidate for being a drug carrier in drug delivery systems because of its biocompatibility and biodegradability. However, in degrading PLGA matrices, the encapsulated peptide and protein drugs can undergo various degradation reactions, including deamidation at asparagine (Asn) residues to give a succinimide species, which may affect their potency and/or safety. Here, we show computationally that glycolic acid (GA) in its undissociated form, which can exist in high concentration in degrading PLGA matrices, can catalyze the succinimide formation from Asn residues by acting as a proton-transfer mediator. A two-step mechanism was studied by quantum-chemical calculations using Ace-Asn-Nme (Ace = acetyl, Nme = NHCH₃) as a model compound. The first step is cyclization (intramolecular addition) to form a tetrahedral intermediate, and the second step is elimination of ammonia from the intermediate. Both steps involve an extensive bond reorganization mediated by a GA molecule, and the first step was predicted to be rate-determining. The present findings are expected to be useful in the design of more effective and safe PLGA devices. Full article

(This article belongs to the Special Issue Chemical Bond and Bonding 2015)

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16 pages, 2647 KiB

Open AccessArticle

Residue Asn277 Affects the Stability and Substrate Specificity of the SMG1 Lipase from Malassezia globosa

by Dongming Lan^1,†, Qian Wang^1,†, Jinxin Xu², Pengfei Zhou¹, Bo Yang^1,* and Yonghua Wang^3,*

¹ School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China

² State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China

³ College of Light Industry and Food Sciences, South China University of Technology, Guangzhou 510640, China

^† These authors contributed equally to this work.

Int. J. Mol. Sci. 2015, 16(4), 7273-7288; https://doi.org/10.3390/ijms16047273 - 31 Mar 2015

Cited by 15 | Viewed by 5979

Abstract

Thermostability and substrate specificity are important characteristics of enzymes for industrial application, which can be improved by protein engineering. SMG1 lipase from Malassezia globosa is a mono- and diacylglycerol lipase (MDL) that shows activity toward mono- and diacylglycerols, but no activity toward triacylglycerols. [...] Read more.

Thermostability and substrate specificity are important characteristics of enzymes for industrial application, which can be improved by protein engineering. SMG1 lipase from Malassezia globosa is a mono- and diacylglycerol lipase (MDL) that shows activity toward mono- and diacylglycerols, but no activity toward triacylglycerols. SMG1 lipase is considered a potential biocatalyst applied in oil/fat modification and its crystal structure revealed that an interesting residue-Asn277 may contribute to stabilize loop 273–278 and the 3₁₀4 helix which are important to enzyme characterization. In this study, to explore its role in affecting the stability and catalytic activity, mutagenesis of N277 with Asp (D), Val (V), Leu (L) and Phe (F) was conducted. Circular dichroism (CD) spectral analysis and half-life measurement showed that the N277D mutant has better thermostability. The melting temperature and half-life of the N277D mutant were 56.6 °C and 187 min, respectively, while that was 54.6 °C and 121 min for SMG1 wild type (WT). Biochemical characterization of SMG1 mutants were carried out to test whether catalytic properties were affected by mutagenesis. N277D had similar enzymatic properties as SMG1 WT, but N277F showed a different substrate selectivity profile as compared to other SMG1 mutants. Analysis of the SMG1 3D model suggested that N277D formed a salt bridge via its negative charged carboxyl group with a positively charged guanidino group of R227, which might contribute to confer N277D higher temperature stability. These findings not only provide some clues to understand the molecular basis of the lipase structure/function relationship but also lay the framework for engineering suitable MDL lipases for industrial applications. Full article

(This article belongs to the Section Biochemistry)

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15 pages, 875 KiB

Open AccessArticle

Efficiency of ITS Sequences for DNA Barcoding in Passiflora (Passifloraceae)

by Giovanna Câmara Giudicelli, Geraldo Mäder and Loreta Brandão de Freitas^*

Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, P.O. Box 15053, 91501-970 Porto Alegre, Brazil

Int. J. Mol. Sci. 2015, 16(4), 7289-7303; https://doi.org/10.3390/ijms16047289 - 1 Apr 2015

Cited by 25 | Viewed by 7503

Abstract

DNA barcoding is a technique for discriminating and identifying species using short, variable, and standardized DNA regions. Here, we tested for the first time the performance of plastid and nuclear regions as DNA barcodes in Passiflora. This genus is a largely variable, [...] Read more.

DNA barcoding is a technique for discriminating and identifying species using short, variable, and standardized DNA regions. Here, we tested for the first time the performance of plastid and nuclear regions as DNA barcodes in Passiflora. This genus is a largely variable, with more than 900 species of high ecological, commercial, and ornamental importance. We analyzed 1034 accessions of 222 species representing the four subgenera of Passiflora and evaluated the effectiveness of five plastid regions and three nuclear datasets currently employed as DNA barcodes in plants using barcoding gap, applied similarity-, and tree-based methods. The plastid regions were able to identify less than 45% of species, whereas the nuclear datasets were efficient for more than 50% using “best match” and “best close match” methods of TaxonDNA software. All subgenera presented higher interspecific pairwise distances and did not fully overlap with the intraspecific distance, and similarity-based methods showed better results than tree-based methods. The nuclear ribosomal internal transcribed spacer 1 (ITS1) region presented a higher discrimination power than the other datasets and also showed other desirable characteristics as a DNA barcode for this genus. Therefore, we suggest that this region should be used as a starting point to identify Passiflora species. Full article

(This article belongs to the Special Issue Plant Molecular Biology)

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16 pages, 1861 KiB

Open AccessArticle

Role of Long-Range Protein Dynamics in Different Thymidylate Synthase Catalyzed Reactions

by Thelma Abeysinghe and Amnon Kohen^*

Department of Chemistry, University of Iowa, Iowa City, IA 52242-1727, USA

Int. J. Mol. Sci. 2015, 16(4), 7304-7319; https://doi.org/10.3390/ijms16047304 - 1 Apr 2015

Cited by 4 | Viewed by 6564

Abstract

Recent studies of Escherichia coli thymidylate synthase (ecTSase) showed that a highly conserved residue, Y209, that is located 8 Å away from the reaction site, plays a key role in the protein’s dynamics. Those crystallographic studies indicated that Y209W mutant is [...] Read more.

Recent studies of Escherichia coli thymidylate synthase (ecTSase) showed that a highly conserved residue, Y209, that is located 8 Å away from the reaction site, plays a key role in the protein’s dynamics. Those crystallographic studies indicated that Y209W mutant is a structurally identical but dynamically altered relative to the wild type (WT) enzyme, and that its turnover catalytic rate governed by a slow hydride-transfer has been affected. The most challenging test of an examination of a fast chemical conversion that precedes the rate-limiting step has been achieved here. The physical nature of both fast and slow C-H bond activations have been compared between the WT and mutant by means of observed and intrinsic kinetic isotope effects (KIEs) and their temperature dependence. The findings indicate that the proton abstraction step has not been altered as much as the hydride transfer step. Additionally, the comparison indicated that other kinetic steps in the TSase catalyzed reaction were substantially affected, including the order of the substrate binding. Enigmatically, although Y209 is H-bonded to 3'-OH of 2'-deoxyuridine-5'-monophosphate (dUMP), its altered dynamics is more pronounced on the binding of the remote cofactor, (6R)-N⁵,N¹⁰-methylene-5,6,7,8-tetrahydrofolate (CH₂H₄folate), revealing the importance of long-range dynamics of the enzymatic complex and its catalytic function. Full article

(This article belongs to the Special Issue Proteins and Protein-Ligand Interactions)

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14 pages, 2543 KiB

Open AccessArticle

Enhancement of Phenol Biodegradation by Pseudochrobactrum sp. through Ultraviolet-Induced Mutation

by Zhen Mao^*, Chenyang Yu and Lingling Xin

School of Environment Science and Spatial Informatics, China University of Mining and Technology, Xuzhou 221008, China

Int. J. Mol. Sci. 2015, 16(4), 7320-7333; https://doi.org/10.3390/ijms16047320 - 1 Apr 2015

Cited by 23 | Viewed by 5757

Abstract

The phenol-degrading efficiency of Pseudochrobactrum sp. was enhanced by ultraviolet (UV) irradiation. First, a bacterial strain, Pseudochrobactrum sp. XF1, was isolated from the activated sludge in a coking plant. It was subjected to mutation by UV radiation for 120 s and a mutant [...] Read more.

The phenol-degrading efficiency of Pseudochrobactrum sp. was enhanced by ultraviolet (UV) irradiation. First, a bacterial strain, Pseudochrobactrum sp. XF1, was isolated from the activated sludge in a coking plant. It was subjected to mutation by UV radiation for 120 s and a mutant strain with higher phenol-degrading efficiency, Pseudochrobactrum sp. XF1-UV, was selected. The mutant strain XF1-UV was capable of degrading 1800 mg/L phenol completely within 48 h and had higher tolerance to hydrogen ion concentration and temperature variation than the wild type. Haldane’s kinetic model was used to fit the exponential growth data and the following kinetic parameters were obtained: μ_max = 0.092 h⁻¹, Ks = 22.517 mg/L, and Ki = 1126.725 mg/L for XF1, whereas μ_max = 0.110 h⁻¹, Ks = 23.934 mg/L, and Ki = 1579.134 mg/L for XF1-UV. Both XF1 and XF1-UV degraded phenol through the ortho-pathway; but the phenol hydroxylase activity of XF1-UV1 was higher than that of XF1, therefore, the mutant strain biodegraded phenol faster. Taken together, our results suggest that Pseudochrobactrum sp. XF1-UV could be a promising candidate for bioremediation of phenol-containing wastewaters. Full article

(This article belongs to the Section Green Chemistry)

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18 pages, 1443 KiB

Open AccessArticle

Development of an Efficient Electroporation Method for Iturin A-Producing Bacillus subtilis ZK

by Zhi Zhang^1,2, Zhong-Tao Ding^1,2, Dan Shu¹, Di Luo¹ and Hong Tan^1,*

¹ Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, the Chinese Academy of Sciences, No. 9 Section 4, Renmin Nan Road, Chengdu 610041, China

² University of the Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China

Int. J. Mol. Sci. 2015, 16(4), 7334-7351; https://doi.org/10.3390/ijms16047334 - 1 Apr 2015

Cited by 21 | Viewed by 9360

Abstract

In order to efficiently introduce DNA into B. subtilis ZK, which produces iturin A at a high level, we optimized seven electroporation conditions and explored an efficient electroporation method. Using the optimal conditions, the electroporation efficiency was improved to 1.03 × 10⁷ [...] Read more.

In order to efficiently introduce DNA into B. subtilis ZK, which produces iturin A at a high level, we optimized seven electroporation conditions and explored an efficient electroporation method. Using the optimal conditions, the electroporation efficiency was improved to 1.03 × 10⁷ transformants/μg of DNA, an approximately 10,000-fold increase in electroporation efficiency. This efficiency is the highest electroporation efficiency for B. subtilis and enables the construction of a directed evolution library or the knockout of a gene in B. subtilis ZK for molecular genetics studies. In the optimization process, the combined effects of three types of wall-weakening agents were evaluated using a response surface methodology (RSM) design, which led to a two orders of magnitude increase in electroporation efficiency. To the best of our limited knowledge, this study provides the first demonstration of using an RSM design for optimization of the electroporation conditions for B. subtilis. To validate the electroporation efficiency, a case study was performed and a gene (rapC) was inactivated in B. subtilis ZK using a suicide plasmid pMUTIN4. Moreover, we found that the rapC mutants exhibited a marked decrease in iturin A production, suggesting that the rapC gene was closely related to the iturin A production. Full article

(This article belongs to the Section Biochemistry)

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23 pages, 2436 KiB

Open AccessArticle

Characterization and Structure Prediction of Partial Length Protein Sequences of pcoA, pcoR and chrB Genes from Heavy Metal Resistant Bacteria from the Klip River, South Africa

by Patience Chihomvu^*, Peter Stegmann and Michael Pillay

Department of Biotechnology, Vaal University of Technology, Private Bag X021, Vanderbijlpark 1900, South Africa

Int. J. Mol. Sci. 2015, 16(4), 7352-7374; https://doi.org/10.3390/ijms16047352 - 1 Apr 2015

Cited by 36 | Viewed by 7682

Abstract

The Klip River has suffered from severe anthropogenic effects from industrial activities such as mining. Long-term exposure to heavy metal pollution has led to the development of heavy metal resistant strains of Pseudomonas sp. KR23, Lysinibacillus sp. KR25, and E. coli KR29. The [...] Read more.

The Klip River has suffered from severe anthropogenic effects from industrial activities such as mining. Long-term exposure to heavy metal pollution has led to the development of heavy metal resistant strains of Pseudomonas sp. KR23, Lysinibacillus sp. KR25, and E. coli KR29. The objectives of this study were to characterize the genetics of copper and chromate resistance of the isolates. Copper and chromate resistance determinants were cloned and sequenced. Open reading frames (ORFs) related to the genes CopA and CopR were identified in E. coli KR29, PcoA in Lysinibacillus sp. KR25 and none related to chromate resistance were detected. The 3D-models predicted by I-TASSER disclose that the PcoA proteins consist of β-sheets, which form a part of the cupredoxin domain of the CopA copper resistance family of genes. The model for PcoR_29 revealed the presence of a helix turn helix; this forms part of a DNA binding protein, which is part of a heavy metal transcriptional regulator. The bacterial strains were cured using ethidium bromide. The genes encoding for heavy metal resistance and antibiotic resistance were found to be located on the chromosome for both Pseudomonas sp. (KR23) and E. coli (KR29). For Lysinibacillus (KR25) the heavy metal resistance determinants are suspected to be located on a mobile genetic element, which was not detected using gel electrophoresis. Full article

(This article belongs to the Section Biochemistry)

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2 pages, 607 KiB

Open AccessCorrection

Correction: Mezei, Z.A., et al; Factor XIII B Subunit Polymorphisms and the Risk of Coronary Artery Disease. Int. J. Mol. Sci. 2015, 16, 1143–1159

by IJMS Editorial Office

MDPI AG, Klybeckstrasse 64, CH-4057 Basel, Switzerland

Int. J. Mol. Sci. 2015, 16(4), 7375-7376; https://doi.org/10.3390/ijms16047375 - 1 Apr 2015

Cited by 1 | Viewed by 4026

Abstract

In the recently published paper [1], Section 2.6 was inadvertently deleted during copyediting. This error was not detected by the handling editor or the authors during proofreading. [...] Full article

17 pages, 3748 KiB

Open AccessArticle

Role of Glucokinase in the Subcellular Localization of Glucokinase Regulatory Protein

by Ling Jin¹, Tingting Guo¹, Zhixin Li², Zhen Lei³, Hui Li¹, Yiqing Mao¹, Xi Wang¹, Na Zhou¹, Yizhuang Zhang¹, Ruobi Hu¹, Xuehui Zhang¹, Gang Niu^4,*, David M. Irwin^1,5,* and Huanran Tan^1,*

¹ Department of Pharmacology, Peking University, Health Science Center, Beijing 100191, China

² Department of Integrated Traditional Chinese and Western Medicine, Peking University, Health Science Center, Beijing 100191, China

³ Department of Pharmacology, Ningxia Medical University, Yinchuan 750004, China

⁴ Beijing N&N Genetech Company, Beijing 100082, China

⁵ Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada

Int. J. Mol. Sci. 2015, 16(4), 7377-7393; https://doi.org/10.3390/ijms16047377 - 2 Apr 2015

Cited by 10 | Viewed by 7249

Abstract

Glucokinase (GCK) is the rate-limiting enzyme of liver glucose metabolism. Through protein-protein interactions, glucokinase regulatory protein (GCKR) post-transcriptionally regulates GCK function in the liver, and causes its nuclear localization. However the role of GCK in regulating GCKR localization is unknown. In the present [...] Read more.

Glucokinase (GCK) is the rate-limiting enzyme of liver glucose metabolism. Through protein-protein interactions, glucokinase regulatory protein (GCKR) post-transcriptionally regulates GCK function in the liver, and causes its nuclear localization. However the role of GCK in regulating GCKR localization is unknown. In the present study, using in vitro and in vivo models, we examined the levels of GCK and GCKR, and their subcellular localization. We found that total cellular levels of GCKR did not vary in the in vivo models, but its subcellular localization did. In animals with normal levels of GCK, GCKR is mainly localized to the nuclei of hepatocytes. In seven-day old rats and liver-specific Gck gene knockout mice (animals that lack or have reduced levels of GCK protein), GCKR was found primarily in the cytoplasm. The interaction of GCK with GCKR was further examined using in vitro models where we varied the levels of GCK and GCKR. Varying the level of GCK protein had no effect on total cellular GCKR protein levels. Taken together, our results indicate that GCK is important for the localization of GCKR to the nucleus and raises the possibility that GCKR may have functions in addition to those regulating GCK activity in the cytoplasm. Full article

(This article belongs to the Section Biochemistry)

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19 pages, 1256 KiB

Open AccessReview

Identification of Inhibitors of Biological Interactions Involving Intrinsically Disordered Proteins

by Daniela Marasco^* and Pasqualina Liana Scognamiglio^†

¹ Department of Pharmacy, Centro Interuniversitario di Ricerca sui Peptidi Bioattivi (CIRPEB), University of Naples "Federico II", DFM-Scarl, 80134 Naples, Italy

^† Permanent address: Center for Advanced Biomaterials for Health Care@CRIB, Istituto Italiano di Tecnologia, 80125 Naples, Italy.

Int. J. Mol. Sci. 2015, 16(4), 7394-7412; https://doi.org/10.3390/ijms16047394 - 2 Apr 2015

Cited by 42 | Viewed by 6753

Abstract

Protein–protein interactions involving disordered partners have unique features and represent prominent targets in drug discovery processes. Intrinsically Disordered Proteins (IDPs) are involved in cellular regulation, signaling and control: they bind to multiple partners and these high-specificity/low-affinity interactions play crucial roles in many human [...] Read more.

Protein–protein interactions involving disordered partners have unique features and represent prominent targets in drug discovery processes. Intrinsically Disordered Proteins (IDPs) are involved in cellular regulation, signaling and control: they bind to multiple partners and these high-specificity/low-affinity interactions play crucial roles in many human diseases. Disordered regions, terminal tails and flexible linkers are particularly abundant in DNA-binding proteins and play crucial roles in the affinity and specificity of DNA recognizing processes. Protein complexes involving IDPs are short-lived and typically involve short amino acid stretches bearing few “hot spots”, thus the identification of molecules able to modulate them can produce important lead compounds: in this scenario peptides and/or peptidomimetics, deriving from structure-based, combinatorial or protein dissection approaches, can play a key role as hit compounds. Here, we propose a panoramic review of the structural features of IDPs and how they regulate molecular recognition mechanisms focusing attention on recently reported drug-design strategies in the field of IDPs. Full article

(This article belongs to the Special Issue In-Silico Prediction and Characterization of Intrinsic Disorder in Proteins)

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15 pages, 2352 KiB

Open AccessArticle

The Relevance of miRNA-21 in HSV-Induced Inflammation in a Mouse Model

by Bunsoon Choi¹, Hyoun-Ah Kim², Chang-Hee Suh²

, Hae Ok Byun¹, Ju-Yang Jung² and Seonghyang Sohn^1,3,*

¹ Department of Microbiology, Ajou University School of Medicine, Suwon 443-380, Korea

² Department of Rheumatology, Ajou University School of Medicine, Suwon 443-380, Korea

³ Department of Biomedical Sciences, Graduate School of Ajou University, Suwon 443-380, Korea

Int. J. Mol. Sci. 2015, 16(4), 7413-7427; https://doi.org/10.3390/ijms16047413 - 2 Apr 2015

Cited by 30 | Viewed by 7377

Abstract

The purpose of this study was to clarify the correlation between microRNA-21 (miR-21) expression and inflammation in a herpes simplex virus (HSV)-induced Behçet’s Disease (BD) mouse model. miR-21 was compared between BD patients and healthy controls in peripheral blood mononuclear cells (PBMC). For [...] Read more.

The purpose of this study was to clarify the correlation between microRNA-21 (miR-21) expression and inflammation in a herpes simplex virus (HSV)-induced Behçet’s Disease (BD) mouse model. miR-21 was compared between BD patients and healthy controls in peripheral blood mononuclear cells (PBMC). For miR-21 inhibition, miR-21 antagomir was applied to BD mice. The change of symptoms was monitored. The levels of cytokines and related molecules were determined by ELISA and real time qPCR. Treatment with colchicine or pentoxifylline down-regulated the level of miR-21 with improved symptoms in mice. miR-21 inhibition was accompanied by down-regulated serum levels of IL-17 and IL-6. The expression levels of PDCD4, RhoB, PD-1, IL-12p35, and toll-like receptor-4 were also regulated by miR-21 inhibition. miR-21 was correlated with HSV-induced BD-like inflammation in mice and BD patients. The expression of miR-21 was regulated by antagomir in mice. Full article

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17 pages, 2867 KiB

Open AccessArticle

Thermoresponsive Interplay of Water Insoluble Poly(2-alkyl-2-oxazoline)s Composition and Supramolecular Host–Guest Interactions

by Victor R. de la Rosa¹, Werner M. Nau² and Richard Hoogenboom^1,*

¹ Supramolecular Chemistry Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4, 9000 Ghent, Belgium

² Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, D 28759 Bremen, Germany

Int. J. Mol. Sci. 2015, 16(4), 7428-7444; https://doi.org/10.3390/ijms16047428 - 2 Apr 2015

Cited by 13 | Viewed by 6359

Abstract

A series of water insoluble poly[(2-ethyl-2-oxazoline)-ran-(2-nonyl-2-oxazoline)] amphiphilic copolymers was synthesized and their solubility properties in the presence of different supramolecular host molecules were investigated. The resulting polymer-cavitand assemblies exhibited a thermoresponsive behavior that could be modulated by variation of the copolymer [...] Read more.

A series of water insoluble poly[(2-ethyl-2-oxazoline)-ran-(2-nonyl-2-oxazoline)] amphiphilic copolymers was synthesized and their solubility properties in the presence of different supramolecular host molecules were investigated. The resulting polymer-cavitand assemblies exhibited a thermoresponsive behavior that could be modulated by variation of the copolymer composition and length. Interestingly, the large number of hydrophobic nonyl units across the polymer chain induced the formation of kinetically-trapped nanoparticles in solution. These nanoparticles further agglomerate into larger aggregates at a temperature that is dependent on the polymer composition and the cavitand type and concentration. The present research expands the understanding on the supramolecular interactions between water insoluble copolymers and supramolecular host molecules. Full article

(This article belongs to the Special Issue Supramolecular Polymers and Their Assemblies)

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17 pages, 4089 KiB

Open AccessArticle

Analysis of Bacterial and Archaeal Communities along a High-Molecular-Weight Polyacrylamide Transportation Pipeline System in an Oil Field

by Cai-Yun Li¹, Jing-Yan Li², Serge Maurice Mbadinga¹

, Jin-Feng Liu¹, Ji-Dong Gu³ and Bo-Zhong Mu^1,*

¹ State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology,130 Meilong Road, Shanghai 200237, China

² Daqing Oilfield Limited Company, Daqing 163453, China

³ School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China

Int. J. Mol. Sci. 2015, 16(4), 7445-7461; https://doi.org/10.3390/ijms16047445 - 2 Apr 2015

Cited by 18 | Viewed by 8410

Abstract

Viscosity loss of high-molecular-weight partially hydrolyzed polyacrylamide (HPAM) solution was observed in a water injection pipeline before being injected into subterranean oil wells. In order to investigate the possible involvement of microorganisms in HPAM viscosity loss, both bacterial and archaeal community compositions of [...] Read more.

Viscosity loss of high-molecular-weight partially hydrolyzed polyacrylamide (HPAM) solution was observed in a water injection pipeline before being injected into subterranean oil wells. In order to investigate the possible involvement of microorganisms in HPAM viscosity loss, both bacterial and archaeal community compositions of four samples collected from different points of the transportation pipeline were analyzed using PCR-amplification of the 16S rRNA gene and clone library construction method together with the analysis of physicochemical properties of HPAM solution and environmental factors. Further, the relationship between environmental factors and HPAM properties with microorganisms were delineated by canonical correspondence analysis (CCA). Diverse bacterial and archaeal groups were detected in the four samples. The microbial community of initial solution S1 gathered from the make-up tank is similar to solution S2 gathered from the first filter, and that of solution S3 obtained between the first and the second filter is similar to that of solution S4 obtained between the second filter and the injection well. Members of the genus Acinetobacter sp. were detected with high abundance in S3 and S4 in which HPAM viscosity was considerably reduced, suggesting that they likely played a considerable role in HPAM viscosity loss. This study presents information on microbial community diversity in the HPAM transportation pipeline and the possible involvement of microorganisms in HPAM viscosity loss and biodegradation. The results will help to understand the microbial community contribution made to viscosity change and are beneficial for providing information for microbial control in oil fields. Full article

(This article belongs to the Special Issue Microbial Metabolism of Toxic Organic Pollutants and Transformation of Metals/Metalloids and Ecotoxicity Assessment)

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16 pages, 3050 KiB

Open AccessArticle

The Neuronal-Specific SGK1.1 (SGK1_v2) Kinase as a Transcriptional Modulator of BAG4, Brox, and PPP1CB Genes Expression

by Rebeca González-Fernández¹, Julio Ávila¹

, María F. Arteaga^2,3, Cecilia M. Canessa^2,4 and Pablo Martín-Vasallo^1,*

¹ Laboratorio de Biología del Desarrollo, UD de Bioquímica y Biología Molecular and Centro de Investigaciones Biomédicas de Canarias (CIBICAN), Universidad de La Laguna, Av Astrofísico Sánchez s/n, La Laguna, Tenerife 38201, Spain

² Department of Cellular and Molecular Physiology, Yale University, 333 Cedar Street, New Haven, CT 06510, USA

³ Department of Medicine A, Hematology, Hemostaseology, Oncology and Pneumology, University of Muenster, Muenster 48149, Germany

⁴ Department of Basic Medical Sciences, Tsinghua University School of Medicine, Beijing 100084, China

Int. J. Mol. Sci. 2015, 16(4), 7462-7477; https://doi.org/10.3390/ijms16047462 - 2 Apr 2015

Cited by 4 | Viewed by 5847

Abstract

The Serum- and Glucocorticoid-induced Kinase 1, SGK1, exhibits a broad range of cellular functions that include regulation of the number of ion channels in plasma membrane and modulation of signaling pathways of cell survival. This diversity of functions is made possible by various [...] Read more.

The Serum- and Glucocorticoid-induced Kinase 1, SGK1, exhibits a broad range of cellular functions that include regulation of the number of ion channels in plasma membrane and modulation of signaling pathways of cell survival. This diversity of functions is made possible by various regulatory processes acting upon the SGK1 gene, giving rise to various isoforms: SGK1_v1–5, each with distinct properties and distinct aminotermini that serve to target proteins to different subcellular compartments. Among cellular effects of SGK1 expression is to indirectly modulate gene transcription by phosphorylating transcriptional factors of the FOXO family. Here we examined if SGK1.1 (SGK1_v2; NM_001143676), which associates primarily to the plasma membrane, is also able to regulate gene expression. Using a differential gene expression approach we identified six genes upregulated by SGK1.1 in HeLa cells. Further analysis of transcript and protein levels validated two genes: BCL2-associated athanogene 4 (BAG-4) and Brox. The results indicate that SGK1.1 regulates gene transcription upon a different set of genes some of which participate in cell survival pathways (BAG-4) and others in intracellular vesicular traffic (Brox). Full article

(This article belongs to the Section Biochemistry)

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15 pages, 2057 KiB

Open AccessArticle

SLM Produced Porous Titanium Implant Improvements for Enhanced Vascularization and Osteoblast Seeding

by Julia Matena¹, Svea Petersen², Matthias Gieseke³, Andreas Kampmann⁴, Michael Teske², Martin Beyerbach⁵, Hugo Murua Escobar^1,6, Heinz Haferkamp⁷, Nils-Claudius Gellrich⁴ and Ingo Nolte^1,*

¹ Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, D-30559 Hannover, Germany

² Institute for Biomedical Engineering, Rostock University Medical Center, D-18119 Rostock, Germany

³ Materials and Processes Department, Laser Zentrum Hannover e.V., D-30419 Hannover, Germany

⁴ Clinic for Cranio-Maxillo-Facial Surgery, Hannover Medical School, D-30625 Hannover, Germany

⁵ Institute for Biometry, Epidemiology and Information Processing, University of Veterinary Medicine Hannover, Foundation, D-30559 Hannover, Germany

⁶ Division of Medicine Clinic III, Hematology, Oncology and Palliative Medicine, University of Rostock, D-18057 Rostock, Germany

⁷ Institut fuer Werkstoffkunde, Leibniz Universitaet Hannover, D-30823 Hannover, Germany

Int. J. Mol. Sci. 2015, 16(4), 7478-7492; https://doi.org/10.3390/ijms16047478 - 2 Apr 2015

Cited by 84 | Viewed by 8641

Abstract

To improve well-known titanium implants, pores can be used for increasing bone formation and close bone-implant interface. Selective Laser Melting (SLM) enables the production of any geometry and was used for implant production with 250-µm pore size. The used pore size supports vessel [...] Read more.

To improve well-known titanium implants, pores can be used for increasing bone formation and close bone-implant interface. Selective Laser Melting (SLM) enables the production of any geometry and was used for implant production with 250-µm pore size. The used pore size supports vessel ingrowth, as bone formation is strongly dependent on fast vascularization. Additionally, proangiogenic factors promote implant vascularization. To functionalize the titanium with proangiogenic factors, polycaprolactone (PCL) coating can be used. The following proangiogenic factors were examined: vascular endothelial growth factor (VEGF), high mobility group box 1 (HMGB1) and chemokine (C-X-C motif) ligand 12 (CXCL12). As different surfaces lead to different cell reactions, titanium and PCL coating were compared. The growing into the porous titanium structure of primary osteoblasts was examined by cross sections. Primary osteoblasts seeded on the different surfaces were compared using Live Cell Imaging (LCI). Cross sections showed cells had proliferated, but not migrated after seven days. Although the cell count was lower on titanium PCL implants in LCI, the cell count and cell spreading area development showed promising results for titanium PCL implants. HMGB1 showed the highest migration capacity for stimulating the endothelial cell line. Future perspective would be the incorporation of HMGB1 into PCL polymer for the realization of a slow factor release. Full article

(This article belongs to the Special Issue Artificial Organs)

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27 pages, 751 KiB

Open AccessReview

Impacts of Gut Bacteria on Human Health and Diseases

by Yu-Jie Zhang¹, Sha Li², Ren-You Gan³

, Tong Zhou¹, Dong-Ping Xu¹ and Hua-Bin Li^1,*

¹ Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China

² School of Chinese Medicine, The University of Hong Kong, Sassoon Road, Hong Kong, China

³ School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China

Int. J. Mol. Sci. 2015, 16(4), 7493-7519; https://doi.org/10.3390/ijms16047493 - 2 Apr 2015

Cited by 727 | Viewed by 76996

Abstract

Gut bacteria are an important component of the microbiota ecosystem in the human gut, which is colonized by 10¹⁴ microbes, ten times more than the human cells. Gut bacteria play an important role in human health, such as supplying essential nutrients, synthesizing [...] Read more.

Gut bacteria are an important component of the microbiota ecosystem in the human gut, which is colonized by 10¹⁴ microbes, ten times more than the human cells. Gut bacteria play an important role in human health, such as supplying essential nutrients, synthesizing vitamin K, aiding in the digestion of cellulose, and promoting angiogenesis and enteric nerve function. However, they can also be potentially harmful due to the change of their composition when the gut ecosystem undergoes abnormal changes in the light of the use of antibiotics, illness, stress, aging, bad dietary habits, and lifestyle. Dysbiosis of the gut bacteria communities can cause many chronic diseases, such as inflammatory bowel disease, obesity, cancer, and autism. This review summarizes and discusses the roles and potential mechanisms of gut bacteria in human health and diseases. Full article

(This article belongs to the Section Biochemistry)

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15 pages, 885 KiB

Open AccessArticle

A New Series of Kinked Liquid Crystals: 2-(6-Alkoxynaphthalen-2-yl)-6-methoxyquinolines

by Win-Long Chia^* and Chih-Wei Liu

Department of Chemistry, Fu Jen Catholic University, New Taipei City 24205, Taiwan

Int. J. Mol. Sci. 2015, 16(4), 7520-7534; https://doi.org/10.3390/ijms16047520 - 2 Apr 2015

Cited by 4 | Viewed by 5247

Abstract

A new series of 2-(6-alkoxynaphthalen-2-yl)-6-methoxyquinolines (nO-NpQOMe, n = 3–8) liquid crystal compounds, a linear molecular structure with two kinks, were synthesized using a short two-step reaction with overall yields between 43% and 58%. Spectral analyses were in accord with the expected [...] Read more.

A new series of 2-(6-alkoxynaphthalen-2-yl)-6-methoxyquinolines (nO-NpQOMe, n = 3–8) liquid crystal compounds, a linear molecular structure with two kinks, were synthesized using a short two-step reaction with overall yields between 43% and 58%. Spectral analyses were in accord with the expected structures. Thermotropic behavior of these liquid crystal compounds were investigated using polarized optical microscopy and differential scanning calorimetry. All compounds exhibited purely enantiotropic nematic phase at the medium–high temperature range of 162.4–234.2 °C. However, short ranges of nematic phase, 20.5–16.6 °C at heating and 46.7–37.0 °C at cooling, were observed in these linear liquid-crystalline compounds with two kinks. Full article

(This article belongs to the Special Issue Advances in Anisotropic and Smart Materials)

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16 pages, 3769 KiB

Open AccessArticle

Enzymatic Synthesis of Magnetic Nanoparticles

by Arati G. Kolhatkar¹, Chamath Dannongoda², Katerina Kourentzi³, Andrew C. Jamison¹, Ivan Nekrashevich⁴, Archana Kar³, Eliedonna Cacao³, Ulrich Strych⁵, Irene Rusakova⁶, Karen S. Martirosyan², Dmitri Litvinov⁴

, T. Randall Lee^1,*

and Richard C. Willson^3,5,7,*

¹ Department of Chemistry and Texas Center for Superconductivity, University of Houston, Houston, TX 77204, USA

² Department of Physics and Astronomy, University of Texas at Brownsville, Brownsville, TX 78520, USA

³ Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, USA

⁴ Department of Electrical and Computer Engineering, University of Houston, Houston, TX 77204, USA

⁵ Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA

⁶ Department of Physics and Texas Center for Superconductivity, University of Houston, Houston, TX 77204, USA

⁷ Centro de Biotecnología FEMSA, Departamento de Biotecnología e Ingeniería de Alimentos, Tecnológico de Monterrey, Campus Monterrey, Monterrey, NL 64849, Mexico

Int. J. Mol. Sci. 2015, 16(4), 7535-7550; https://doi.org/10.3390/ijms16047535 - 3 Apr 2015

Cited by 11 | Viewed by 8695

Abstract

We report the first in vitro enzymatic synthesis of paramagnetic and antiferromagnetic nanoparticles toward magnetic ELISA reporting. With our procedure, alkaline phosphatase catalyzes the dephosphorylation of l-ascorbic-2-phosphate, which then serves as a reducing agent for salts of iron, gadolinium, and holmium, forming magnetic [...] Read more.

We report the first in vitro enzymatic synthesis of paramagnetic and antiferromagnetic nanoparticles toward magnetic ELISA reporting. With our procedure, alkaline phosphatase catalyzes the dephosphorylation of l-ascorbic-2-phosphate, which then serves as a reducing agent for salts of iron, gadolinium, and holmium, forming magnetic precipitates of Fe_45±14Gd_5±2O_50±15 and Fe_42±4Ho_6±4O_52±5. The nanoparticles were found to be paramagnetic at 300 K and antiferromagnetic under 25 K. Although weakly magnetic at 300 K, the room-temperature magnetization of the nanoparticles found here is considerably greater than that of analogous chemically-synthesized Ln_xFe_yO_z (Ln = Gd, Ho) samples reported previously. At 5 K, the nanoparticles showed a significantly higher saturation magnetization of 45 and 30 emu/g for Fe_45±14Gd_5±2O_50±15 and Fe_42±4Ho_6±4O_52±5, respectively. Our approach of enzymatically synthesizing magnetic labels reduces the cost and avoids diffusional mass-transfer limitations associated with pre-synthesized magnetic reporter particles, while retaining the advantages of magnetic sensing. Full article

(This article belongs to the Special Issue Magnetic Nanoparticles 2015)

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14 pages, 573 KiB

Open AccessArticle

In Vitro Cytotoxic Evaluation of MgO Nanoparticles and Their Effect on the Expression of ROS Genes

by Rangarajulu Senthil Kumaran^1,*, Yong-Keun Choi¹

, Vijay Singh², Hak-Jin Song¹, Kyung-Guen Song³, Kwang Jin Kim⁴ and Hyung Joo Kim¹

¹ Department of Biological Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-Gu, Seoul 143701, Korea

² Department of Chemical Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-Gu, Seoul 143701, Korea

³ Water Environment Center, Korea Institute of Science and Technology, P.O. Box 131, Cheongryang-Gu, Seoul 130650, Korea

⁴ Urban Agriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju 560500, Korea

Int. J. Mol. Sci. 2015, 16(4), 7551-7564; https://doi.org/10.3390/ijms16047551 - 3 Apr 2015

Cited by 43 | Viewed by 6808

Abstract

Water-dispersible MgO nanoparticles were tested to investigate their cytotoxic effects on oxidative stress gene expression. In this in vitro study, genes related to reactive oxygen species (ROS), glutathione S-transferase (GST) and catalase, were quantified using real-time polymerase chain reactions (molecular level) and [...] Read more.

Water-dispersible MgO nanoparticles were tested to investigate their cytotoxic effects on oxidative stress gene expression. In this in vitro study, genes related to reactive oxygen species (ROS), glutathione S-transferase (GST) and catalase, were quantified using real-time polymerase chain reactions (molecular level) and molecular beacon technologies (cellular level). The monodispersed MgO nanoparticles, 20 nm in size, were used to treat human cancer cell lines (liver cancer epithelial cells) at different concentrations (25, 75 and 150 µg/mL) and incubation times (24, 48 and 72 h). Both the genetic and cellular cytotoxic screening methods produced consistent results, showing that GST and catalase ROS gene expression was maximized at 150 µg/mL nanoparticle treatment with 48 h incubation. However, the genotoxic effect of MgO nanoparticles was not significant compared with control experiments, which indicates its significant potential applications in nanomedicine as a diagnostic and therapeutic tool. Full article

(This article belongs to the Special Issue Bioactive Nanoparticles)

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12 pages, 927 KiB

Open AccessArticle

Insulin Induces Phosphorylation of Serine Residues of Translationally Controlled Tumor Protein in 293T Cells

by Jeehye Maeng^†, Miyoung Kim^†, Hyukjin Lee and Kyunglim Lee^*

¹ Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul 120-750, Korea

^† These authors contributed equally to this work.

Int. J. Mol. Sci. 2015, 16(4), 7565-7576; https://doi.org/10.3390/ijms16047565 - 3 Apr 2015

Cited by 3 | Viewed by 5169

Abstract

Insulin induces the activation of Na,K-ATPase while translationally controlled tumor protein (TCTP) inhibits this enzyme and the associated pump activity. Because binding of insulin with its membrane receptor is known to mediate the phosphorylation of multiple intracellular proteins, phosphorylation of TCTP by insulin [...] Read more.

Insulin induces the activation of Na,K-ATPase while translationally controlled tumor protein (TCTP) inhibits this enzyme and the associated pump activity. Because binding of insulin with its membrane receptor is known to mediate the phosphorylation of multiple intracellular proteins, phosphorylation of TCTP by insulin might be related to the sodium pump regulation. We therefore examined whether insulin induces TCTP phosphorylation in embryonic kidney 293T cells. Using immunoprecipitation and Western blotting, we found that insulin phosphorylates serine (Ser) residues of TCTP. Following fractionation of the insulin-treated cells into cytosol and membrane fractions, phosphorylated TCTP at its Ser residue (p-Ser-TCTP) was detected exclusively in the cytosolic part and not in the membrane fraction. Phosphorylation of TCTP reached maximum in about 10 min after insulin treatment in 293T cells. In studies of cell-type specificity of insulin-mediated phosphorylation of TCTP, insulin did not phosphorylate TCTP in HeLa cells. Computational prediction and immunoprecipitation using several constructs having Ser to Ala mutation at potential p-Ser sites of TCTP revealed that insulin phosphorylated the serine-9 and -15 residues of TCTP. Elucidations of how insulin-mediated TCTP phosphorylation promotes Na,K-ATPase activation, may offer potential therapeutic approaches to diseases associated with vascular activity and sodium pump dysregulation. Full article

(This article belongs to the Section Biochemistry)

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10 pages, 1578 KiB

Open AccessArticle

Poly-γ-Glutamic Acid Induces Apoptosis via Reduction of COX-2 Expression in TPA-Induced HT-29 Human Colorectal Cancer Cells

by Eun Ju Shin^1,2, Mi Jeong Sung^1,2, Jae Ho Park^1,2, Hye Jeong Yang², Myung Sunny Kim², Haeng Jeon Hur² and Jin-Taek Hwang^1,2,*

¹ Department of Food Biotechnology, University of Science & Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 305-333, Korea

² Korea Food Research Institute, 1201 Anyangpangyoro, Bundang-gu, Seongnam-si, Gyeonggi-do 463-746, Korea

Int. J. Mol. Sci. 2015, 16(4), 7577-7586; https://doi.org/10.3390/ijms16047577 - 3 Apr 2015

Cited by 15 | Viewed by 6309

Abstract

Poly-γ-glutamic acid (PGA) is one of the bioactive compounds found in cheonggukjang, a fast-fermented soybean paste widely utilized in Korean cooking. PGA is reported to have a number of beneficial health effects, and interestingly, it has been identified as a possible anti-cancer [...] Read more.

Poly-γ-glutamic acid (PGA) is one of the bioactive compounds found in cheonggukjang, a fast-fermented soybean paste widely utilized in Korean cooking. PGA is reported to have a number of beneficial health effects, and interestingly, it has been identified as a possible anti-cancer compound through its ability to promote apoptosis in cancer cells, although the precise molecular mechanisms remain unclear. Our findings demonstrate that PGA inhibits the pro-proliferative functions of the phorbol ester 12-O-tetradecanoylphorbol-13-acetate (TPA), a known chemical carcinogen in HT-29 human colorectal cancer cells. This inhibition was accompanied by hallmark apoptotic phenotypes, including DNA fragmentation and the cleavage of poly (ADP-ribose) polymerase (PARP) and caspase 3. In addition, PGA treatment reduced the expression of genes known to be overexpressed in colorectal cancer cells, including cyclooxygenase 2 (COX-2) and inducible nitric oxide synthase (iNOS). Lastly, PGA promoted activation of 5' adenosine monophosphate-activated protein (AMPK) in HT-29 cells. Taken together, our results suggest that PGA treatment enhances apoptosis in colorectal cancer cells, in part by modulating the activity of the COX-2 and AMPK signaling pathways. These anti-cancer functions of PGA make it a promising compound for future study. Full article

(This article belongs to the Special Issue Bioactive Phytochemicals in Functional Foods for Cancer Prevention)

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8 pages, 691 KiB

Open AccessArticle

A New and Practical Synthetic Method for the Synthesis of 6-O-Methyl-scutellarein: One Metabolite of Scutellarin in Vivo

by Hang Lin^1,2,3, Wei Zhang^1,2,3, Ze-Xi Dong^1,2,3, Ting Gu^1,2,3, Nian-Guang Li^1,2,3,*, Zhi-Hao Shi⁴, Jun Kai^1,2,3, Cheng Qu^1,2,3, Guan-Xiong Shang^1,2,3, Yu-Ping Tang^1,2,3,*, Fang Fang^1,2,3, He-Min Li^1,2,3, Jian-Ping Yang^1,2,3 and Jin-Ao Duan^1,2,3

¹ National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu, China

² Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu, China

³ Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu, China

⁴ Department of Organic Chemistry, China Pharmaceutical University, Nanjing 211198, Jiangsu, China

Int. J. Mol. Sci. 2015, 16(4), 7587-7594; https://doi.org/10.3390/ijms16047587 - 3 Apr 2015

Cited by 16 | Viewed by 5649

Abstract

Scutellarin (1) has been used for the treatment of angina pectoris, cerebral infarction and coronary heart disease with a large market share in China. Pharmacokinetic studies on scutellarin showed that scutellarin (1) is readily converted into its metabolites in [...] Read more.

Scutellarin (1) has been used for the treatment of angina pectoris, cerebral infarction and coronary heart disease with a large market share in China. Pharmacokinetic studies on scutellarin showed that scutellarin (1) is readily converted into its metabolites in vivo. In this paper, a new and practical synthetic method for the synthesis of 6-O-methyl-scutellarein (3) (one metabolite of scutellarin in vivo) is reported. The benzyl bromide was firstly used to selectively replace the acetyl group at C-7 in 7, and was then used to protect the hydroxy groups at C-4' in 10, 6-O-methyl-scutellarein (3) is obtained in high yield through these methods. Full article

(This article belongs to the Section Biochemistry)

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13 pages, 1679 KiB

Open AccessArticle

Isolation and Heterologous Expression of a Polygalacturonase Produced by Fusarium oxysporum f. sp. cubense Race 1 and 4

by Zhangyong Dong^1,2 and Zhenzhong Wang^2,*

¹ Department of Plant Protection, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China

² Laboratory of Physiological Plant Pathology, South China Agricultural University, Guangzhou 510642, China

Int. J. Mol. Sci. 2015, 16(4), 7595-7607; https://doi.org/10.3390/ijms16047595 - 3 Apr 2015

Cited by 11 | Viewed by 6983

Abstract

Fusarium wilt (Panama disease) caused by Fusarium oxysporum f. sp. cubense (FOC) represents a significant threat to banana (Musa spp.) production. Musa AAB is susceptible to Race 1 (FOC1) and Race 4 (FOC4), while Cavendish Musa AAA is found to be resistant [...] Read more.

Fusarium wilt (Panama disease) caused by Fusarium oxysporum f. sp. cubense (FOC) represents a significant threat to banana (Musa spp.) production. Musa AAB is susceptible to Race 1 (FOC1) and Race 4 (FOC4), while Cavendish Musa AAA is found to be resistant to FOC1 but still susceptible to Race 4. A polygalacturonase (PGC3) was purified from the supernatant of Fusarium oxysporum f. sp. cubense race 4 (FOC4), which is the pathogen of Fusarium wilt. PGC3 had an apparent molecular weight of 45 kDa according to SDS-PAGE. The enzyme hydrolyzed polygalacturonic acid in an exo-manner, as demonstrated by analysis of degradation products. The K_m and V_max values of PGC3 from FOC4 were determined to be 0.70 mg·mL⁻¹ and 101.01 Units·mg·protein⁻¹·min⁻¹, respectively. Two pgc3 genes encoding PGC3 from FOC4 and FOC1, both genes of 1368 bp in length encode 456 amino-acid residues with a predicted signal peptide sequence of 21 amino acids. There are 16 nucleotide sites difference between FOC4-pgc3 and FOC1-pgc3, only leading to four amino acid residues difference. In order to obtain adequate amounts of protein required for functional studies, two genes were cloned into the expression vector pPICZaA and then expressed in Pichia pastoris strains of SMD1168. The recombinant PGC3, r-FOC1-PGC3 and r-FOC4-PGC3, were expressed and purified as active proteins. The optimal PGC3 activity was observed at 50 °C and pH 4.5. Both recombinant PGC3 retained >40% activity at pH 3–7 and >50% activity in 10–50 °C. Both recombinant PGC3 proteins could induce a response but with different levels of tissue maceration and necrosis in banana plants. In sum, our results indicate that PGC3 is an exo-PG and can be produced with full function in P. pastoris. Full article

(This article belongs to the Special Issue Plant Microbe Interaction)

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19 pages, 2466 KiB

Open AccessArticle

The WRKY Transcription Factor Genes in Eggplant (Solanum melongena L.) and Turkey Berry (Solanum torvum Sw.)

by Xu Yang^1,†, Cao Deng^2,†, Yu Zhang¹, Yufu Cheng^1,*, Qiuyue Huo¹ and Linbao Xue¹

¹ College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China

² DNA Stories Bioinformatics Services Co., Ltd., Chengdu 610000, China

^† These authors contributed equally to this work.

Int. J. Mol. Sci. 2015, 16(4), 7608-7626; https://doi.org/10.3390/ijms16047608 - 7 Apr 2015

Cited by 29 | Viewed by 7342

Abstract

WRKY transcription factors, which play critical roles in stress responses, have not been characterized in eggplant or its wild relative, turkey berry. The recent availability of RNA-sequencing data provides the opportunity to examine WRKY genes from a global perspective. We identified 50 and [...] Read more.

WRKY transcription factors, which play critical roles in stress responses, have not been characterized in eggplant or its wild relative, turkey berry. The recent availability of RNA-sequencing data provides the opportunity to examine WRKY genes from a global perspective. We identified 50 and 62 WRKY genes in eggplant (SmelWRKYs) and turkey berry (StorWRKYs), respectively, all of which could be classified into three groups (I–III) based on the WRKY protein structure. The SmelWRKYs and StorWRKYs contain ~76% and ~95% of the number of WRKYs found in other sequenced asterid species, respectively. Positive selection analysis revealed that different selection constraints could have affected the evolution of these groups. Positively-selected sites were found in Groups IIc and III. Branch-specific selection pressure analysis indicated that most WRKY domains from SmelWRKYs and StorWRKYs are conserved and have evolved at low rates since their divergence. Comparison to homologous WRKY genes in Arabidopsis revealed several potential pathogen resistance-related SmelWRKYs and StorWRKYs, providing possible candidate genetic resources for improving stress tolerance in eggplant and probably other Solanaceae plants. To our knowledge, this is the first report of a genome-wide analyses of the SmelWRKYs and StorWRKYs. Full article

(This article belongs to the Section Biochemistry)

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17 pages, 1495 KiB

Open AccessArticle

Phenotypic and Molecular Convergence of 2q23.1 Deletion Syndrome with Other Neurodevelopmental Syndromes Associated with Autism Spectrum Disorder

by Sureni V. Mullegama¹, Joseph T. Alaimo¹, Li Chen^1,2 and Sarah H. Elsea^1,*

¹ Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA

² Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China

Int. J. Mol. Sci. 2015, 16(4), 7627-7643; https://doi.org/10.3390/ijms16047627 - 7 Apr 2015

Cited by 34 | Viewed by 10867

Abstract

Roughly 20% of autism spectrum disorders (ASD) are syndromic with a well-established genetic cause. Studying the genes involved can provide insight into the molecular and cellular mechanisms of ASD. 2q23.1 deletion syndrome (causative gene, MBD5) is a recently identified genetic neurodevelopmental disorder [...] Read more.

Roughly 20% of autism spectrum disorders (ASD) are syndromic with a well-established genetic cause. Studying the genes involved can provide insight into the molecular and cellular mechanisms of ASD. 2q23.1 deletion syndrome (causative gene, MBD5) is a recently identified genetic neurodevelopmental disorder associated with ASD. Mutations in MBD5 have been found in ASD cohorts. In this study, we provide a phenotypic update on the prevalent features of 2q23.1 deletion syndrome, which include severe intellectual disability, seizures, significant speech impairment, sleep disturbance, and autistic-like behavioral problems. Next, we examined the phenotypic, molecular, and network/pathway relationships between nine neurodevelopmental disorders associated with ASD: 2q23.1 deletion Rett, Angelman, Pitt-Hopkins, 2q23.1 duplication, 5q14.3 deletion, Kleefstra, Kabuki make-up, and Smith-Magenis syndromes. We show phenotypic overlaps consisting of intellectual disability, speech delay, seizures, sleep disturbance, hypotonia, and autistic-like behaviors. Molecularly, MBD5 possibly regulates the expression of UBE3A, TCF4, MEF2C, EHMT1 and RAI1. Network analysis reveals that there could be indirect protein interactions, further implicating function for these genes in common pathways. Further, we show that when MBD5 and RAI1 are haploinsufficient, they perturb several common pathways that are linked to neuronal and behavioral development. These findings support further investigations into the molecular and pathway relationships among genes linked to neurodevelopmental disorders and ASD, which will hopefully lead to common points of regulation that may be targeted toward therapeutic intervention. Full article

(This article belongs to the Special Issue The Identification of the Genetic Components of Autism Spectrum Disorders)

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11 pages, 680 KiB

Open AccessArticle

Serum Selenium and Ceruloplasmin in Nigerians with Peripartum Cardiomyopathy

by Kamilu M. Karaye^1,2,*, Isah A. Yahaya³, Krister Lindmark^2,4 and Michael Y. Henein^2,4

¹ Department of Medicine, Bayero University and Aminu Kano Teaching Hospital, PO Box 4445, Kano, Nigeria

² Department of Public Health and Clinical Medicine, Umea University, SE-901 87 Umea, Sweden

³ Department of Chemical Pathology, Bayero University and Aminu Kano Teaching Hospital, Kano, Nigeria

⁴ Department of Cardiology, Umea Heart Centre, SE-901 85 Umea, Sweden

Int. J. Mol. Sci. 2015, 16(4), 7644-7654; https://doi.org/10.3390/ijms16047644 - 7 Apr 2015

Cited by 49 | Viewed by 6331

Abstract

The study aimed to determine if selenium deficiency, serum ceruloplasmin and traditional birth practices are risk factors for peripartum cardiomyopathy (PPCM), in Kano, Nigeria. This is a case-control study carried out in three hospitals, and PPCM patients were followed up for six months. [...] Read more.

The study aimed to determine if selenium deficiency, serum ceruloplasmin and traditional birth practices are risk factors for peripartum cardiomyopathy (PPCM), in Kano, Nigeria. This is a case-control study carried out in three hospitals, and PPCM patients were followed up for six months. Critically low serum selenium concentration was defined as <70 µg/L. A total of 39 PPCM patients and 50 controls were consecutively recruited after satisfying the inclusion criteria. Mean serum selenium in patients (61.7 ± 14.9 µg/L) was significantly lower than in controls (118.4 ± 45.6 µg/L) (p < 0.001). The prevalence of serum selenium <70 µg/L was significantly higher among patients (76.9%) than controls (22.0%) (p < 0.001). The mean ceruloplasmin and prevalence of socio-economic indices, multiparity, pregnancy-induced hypertension, obesity and twin pregnancy were not different between the groups (p > 0.05). Logistic regression showed that rural residency significantly increased the odds for serum selenium <70 µg/L by 2.773-fold (p = 0.037). Baseline serum levels of selenium and ceruloplasmin were not associated with six-month mortality. This study has shown that selenium deficiency is a risk factor for PPCM in Kano, Nigeria, and is related to rural residency. However, serum ceruloplasmin, customary birth practices and some other characteristics were not associated with PPCM in the study area. Full article

(This article belongs to the Special Issue Pathogenesis of Cardiac Arrhythmias and Heart Failure)

17 pages, 3645 KiB

Open AccessArticle

In Utero Exposure to Low-Dose Alcohol Induces Reprogramming of Mammary Development and Tumor Risk in MMTV-erbB-2 Transgenic Mice

by Zhikun Ma, Amanda J. Blackwelder, Harry Lee, Ming Zhao and Xiaohe Yang^*

Julius L. Chambers Biomedical/Biotechnology Research Institute and Department of Biology, North Carolina Central University, Kannapolis, NC 28081, USA

Int. J. Mol. Sci. 2015, 16(4), 7655-7671; https://doi.org/10.3390/ijms16047655 - 7 Apr 2015

Cited by 5 | Viewed by 5975

Abstract

There is increasing evidence that prenatal exposure to environmental factors may modify breast cancer risk later in life. This study aimed to investigate the effects of in utero exposure to low-dose alcohol on mammary development and tumor risk. Pregnant MMTV-erbB-2 mice were exposed [...] Read more.

There is increasing evidence that prenatal exposure to environmental factors may modify breast cancer risk later in life. This study aimed to investigate the effects of in utero exposure to low-dose alcohol on mammary development and tumor risk. Pregnant MMTV-erbB-2 mice were exposed to alcohol (6 g/kg/day) between day 13 and day 19 of gestation, and the female offspring were examined for tumor risk. Whole mount analysis indicated that in utero exposure to low-dose alcohol induced significant increases in ductal extension at 10 weeks of age. Molecular analysis showed that in utero alcohol exposure induced upregulation of ERα signaling and activation of Akt and Erk1/2 in pubertal mammary glands. However, enhanced signaling in the EGFR/erbB-2 pathway appeared to be more prominent in 10-week-old glands than did signaling in the other pathways. Interestingly, tumor development in mice with in utero exposure to low-dose alcohol was slightly delayed compared to control mice, but tumor multiplicity was increased. The results indicate that in utero exposure to low-dose alcohol induces the reprogramming of mammary development by mechanisms that include altered signaling in the estrogen receptor (ER) and erbB-2 pathways. The intriguing tumor development pattern might be related to alcohol dose and exposure conditions, and warrants further investigation. Full article

(This article belongs to the Special Issue Advances in Molecular Oncology 2014)

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10 pages, 1120 KiB

Open AccessArticle

Design of an Osteoinductive Extracellular Fibronectin Matrix Protein for Bone Tissue Engineering

by Sujin Lee^1,†, Dong-Sung Lee^2,†, Ilsan Choi¹, Le B. Hang Pham¹ and Jun-Hyeog Jang^1,*

¹ Department of Biochemistry, College of Medicine, Inha University, Incheon 400-712, Korea

² Department of Biomedical Chemistry, Konkuk University, Chung-Ju 380-701, Korea

^† These authors contributed equally to this work.

Int. J. Mol. Sci. 2015, 16(4), 7672-7681; https://doi.org/10.3390/ijms16047672 - 7 Apr 2015

Cited by 16 | Viewed by 6445

Abstract

Integrin-mediated cell-matrix interactions play an important role in osteogenesis. Here, we constructed a novel osteoinductive fibronectin matrix protein (oFN) for bone tissue engineering, designed to combine the integrin-binding modules from fibronectin (iFN) and a strong osteoinductive growth factor, bone morphogenetic protein-2. Compared with [...] Read more.

Integrin-mediated cell-matrix interactions play an important role in osteogenesis. Here, we constructed a novel osteoinductive fibronectin matrix protein (oFN) for bone tissue engineering, designed to combine the integrin-binding modules from fibronectin (iFN) and a strong osteoinductive growth factor, bone morphogenetic protein-2. Compared with iFN, the purified oFN matrix protein caused a significant increase in cell adhesion and osteogenic differentiation of pre-osteoblast MC3T3-E1 cells (p < 0.05). Full article

(This article belongs to the Special Issue Protein Engineering)

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25 pages, 776 KiB

Open AccessArticle

Interactive Effects of Dietary Lipid and Phenotypic Feed Efficiency on the Expression of Nuclear and Mitochondrial Genes Involved in the Mitochondrial Electron Transport Chain in Rainbow Trout

by Jonathan C. Eya^1,*, Vitalis O. Ukwuaba¹, Rodrigue Yossa¹ and Ann L. Gannam²

¹ Department of Biology/Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112, USA

² USFWS, Abernathy Fish Technology Center, Longview, WA 98632, USA

Int. J. Mol. Sci. 2015, 16(4), 7682-7706; https://doi.org/10.3390/ijms16047682 - 7 Apr 2015

Cited by 7 | Viewed by 6302

Abstract

A 2 × 3 factorial study was conducted to evaluate the effects of dietary lipid level on the expression of mitochondrial and nuclear genes involved in electron transport chain in all-female rainbow trout Oncorhynchus mykiss. Three practical diets with a fixed crude [...] Read more.

A 2 × 3 factorial study was conducted to evaluate the effects of dietary lipid level on the expression of mitochondrial and nuclear genes involved in electron transport chain in all-female rainbow trout Oncorhynchus mykiss. Three practical diets with a fixed crude protein content of 40%, formulated to contain 10% (40/10), 20% (40/20) and 30% (40/30) dietary lipid, were fed to apparent satiety to triplicate groups of either low-feed efficient (F120; 217.66 ± 2.24 g initial average mass) or high-feed efficient (F136; 205.47 ± 1.27 g) full-sib families of fish, twice per day, for 90 days. At the end of the experiment, the results showed that there is an interactive effect of the dietary lipid levels and the phenotypic feed efficiency (growth rate and feed efficiency) on the expression of the mitochondrial genes nd1 (NADH dehydrogenase subunit 1), cytb (Cytochrome b), cox1 (Cytochrome c oxidase subunits 1), cox2 (Cytochrome c oxidase subunits 2) and atp6 (ATP synthase subunit 6) and nuclear genes ucp2α (uncoupling proteins 2 alpha), ucp2β (uncoupling proteins 2 beta), pparα (peroxisome proliferator-activated receptor alpha), pparβ (peroxisome proliferatoractivated receptor beta) and ppargc1α (proliferator-activated receptor gamma coactivator 1 alpha) in fish liver, intestine and muscle, except on ppargc1α in the muscle which was affected by the diet and the family separately. Also, the results revealed that the expression of mitochondrial genes is associated with that of nuclear genes involved in electron transport chain in fish liver, intestine and muscle. Furthermore, this work showed that the expression of mitochondrial genes parallels with the expression of genes encoding uncoupling proteins (UCP) in the liver and the intestine of rainbow trout. This study for the first time presents the molecular basis of the effects of dietary lipid level on mitochondrial and nuclear genes involved in mitochondrial electron transport chain in fish. Full article

(This article belongs to the Special Issue Gene-Nutrient Interactions)

16 pages, 3416 KiB

Open AccessArticle

Combined Enzymatic and Mechanical Cell Disruption and Lipid Extraction of Green Alga Neochloris oleoabundans

by Dongqin Wang¹, Yanqun Li^1,2,*, Xueqiong Hu¹, Weimin Su² and Min Zhong¹

¹ College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China

² Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Zhanjiang 524088, China

Int. J. Mol. Sci. 2015, 16(4), 7707-7722; https://doi.org/10.3390/ijms16047707 - 7 Apr 2015

Cited by 82 | Viewed by 9856

Abstract

Microalgal biodiesel is one of the most promising renewable fuels. The wet technique for lipids extraction has advantages over the dry method, such as energy-saving and shorter procedure. The cell disruption is a key factor in wet oil extraction to facilitate the intracellular [...] Read more.

Microalgal biodiesel is one of the most promising renewable fuels. The wet technique for lipids extraction has advantages over the dry method, such as energy-saving and shorter procedure. The cell disruption is a key factor in wet oil extraction to facilitate the intracellular oil release. Ultrasonication, high-pressure homogenization, enzymatic hydrolysis and the combination of enzymatic hydrolysis with high-pressure homogenization and ultrasonication were employed in this study to disrupt the cells of the microalga Neochloris oleoabundans. The cell disruption degree was investigated. The cell morphology before and after disruption was assessed with scanning and transmission electron microscopy. The energy requirements and the operation cost for wet cell disruption were also estimated. The highest disruption degree, up to 95.41%, assessed by accounting method was achieved by the combination of enzymatic hydrolysis and high-pressure homogenization. A lipid recovery of 92.6% was also obtained by the combined process. The combined process was found to be more efficient and economical compared with the individual process. Full article

(This article belongs to the Special Issue Microalgal Biotechnology)

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15 pages, 429 KiB

Open AccessArticle

Genome-Wide Expression in Visceral Adipose Tissue from Obese Prepubertal Children

by Concepción M. Aguilera^1,†

, Carolina Gomez-Llorente^1,†

, Inés Tofe², Mercedes Gil-Campos², Ramón Cañete^2,*

and Ángel Gil^1,*

¹ Department of Biochemistry and Molecular Biology II, Institute of Nutrition and Food Technology, Centre for Biomedical Research, University of Granada, Armilla, 18100 Granada, Spain

² Unit of Pediatric Endocrinology, Reina Sofia University Hospital, Avda Menéndez Pidal s/n. 14004 Córdoba, Spain

^† These authors contributed equally to this work

Int. J. Mol. Sci. 2015, 16(4), 7723-7737; https://doi.org/10.3390/ijms16047723 - 8 Apr 2015

Cited by 62 | Viewed by 7687

Abstract

Characterization of the genes expressed in adipose tissue (AT) is key to understanding the pathogenesis of obesity and to developing treatments for this condition. Our objective was to compare the gene expression in visceral AT (VAT) between obese and normal-weight prepubertal children. A [...] Read more.

Characterization of the genes expressed in adipose tissue (AT) is key to understanding the pathogenesis of obesity and to developing treatments for this condition. Our objective was to compare the gene expression in visceral AT (VAT) between obese and normal-weight prepubertal children. A total of fifteen obese and sixteen normal-weight children undergoing abdominal elective surgery were selected. RNA was extracted from VAT biopsies. Microarray experiments were independently performed for each sample (six obese and five normal-weight samples). Validation by quantitative PCR (qPCR) was performed on an additional 10 obese and 10 normal-weight VAT samples. Of 1276 differentially expressed genes (p < 0.05), 245 were more than two-fold higher in obese children than in normal-weight children. As validated by qPCR, expression was upregulated in genes involved in lipid and amino acid metabolism (CES1, NPRR3 and BHMT2), oxidative stress and extracellular matrix regulation (TNMD and NQO1), adipogenesis (CRYAB and AFF1) and inflammation (ANXA1); by contrast, only CALCRL gene expression was confirmed to be downregulated. In conclusion, this study in prepubertal children demonstrates the up- and down-regulation of genes that encode molecules that were previously proposed to influence the pathogenesis of adulthood obesity, as well as previously unreported dysregulated genes that may be candidate genes in the aetiology of obesity. Full article

(This article belongs to the Special Issue Gene-Nutrient Interactions)

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10 pages, 2879 KiB

Open AccessArticle

Investigation of Förster Resonance Energy Transfer (FRET) and Competition of Fluorescent Dyes on DNA Microparticles

by Jieun Kim, Jae Sung Lee and Jong Bum Lee^*

Department of Chemical Engineering, University of Seoul, Seoul 130-743, Korea

Int. J. Mol. Sci. 2015, 16(4), 7738-7747; https://doi.org/10.3390/ijms16047738 - 8 Apr 2015

Cited by 2 | Viewed by 5970

Abstract

Fluorescent labeling is widely used to investigate the structural stability and changes to DNA nano- and microstructures. Despite this, the conventional method for observing DNA structures has several limitations in terms of cost-efficiency. This paper introduces a DNA spherical particle stained with DNA [...] Read more.

Fluorescent labeling is widely used to investigate the structural stability and changes to DNA nano- and microstructures. Despite this, the conventional method for observing DNA structures has several limitations in terms of cost-efficiency. This paper introduces a DNA spherical particle stained with DNA intercalating dyes (SYBR Green and SYTOX Orange) as tracers and reports the interaction between multiple dyes. The interference between the dyes was analyzed in terms of Förster resonance energy transfer (FRET) and competition. The changes in the fluorescence intensity by FRET were uniform, regardless of the sequence. The competition effect could occur when several dyes were added simultaneously. These properties are expected to help in the design of multicolor tracers in bioimaging and environmental applications. Full article

(This article belongs to the Special Issue Förster Resonance Energy Transfer (FRET) 2015)

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5 pages, 608 KiB

Open AccessEditorial

Lipidomics: An Evolving Discipline in Molecular Sciences

by Giuseppe Astarita^1,2,* and Mario Ollero^3,4,*

¹ Waters Corporation, Milford, MA 01757, USA

² Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC 20515, USA

³ Université Paris Est—Créteil Val-de-Marne, Créteil 94010, France

⁴ INSERM, U955, Créteil 94010, France

Int. J. Mol. Sci. 2015, 16(4), 7748-7752; https://doi.org/10.3390/ijms16047748 - 8 Apr 2015

Cited by 6 | Viewed by 4973

Abstract

Recent advances in technologies for lipid analysis have contributed to the consolidation of lipidomics as a distinct discipline in molecular sciences [1–6]. [...] Full article

(This article belongs to the Special Issue Bioactive Lipids and Lipidomics)

23 pages, 3839 KiB

Open AccessReview

Biological Mechanisms Underlying the Ultraviolet Radiation-Induced Formation of Skin Wrinkling and Sagging I: Reduced Skin Elasticity, Highly Associated with Enhanced Dermal Elastase Activity, Triggers Wrinkling and Sagging

by Genji Imokawa^1,* and Koichi Ishida²

¹ Research Institute for Biological Functions, Chubu University, 1200 Matsumoto, Kasugai, Aichi 487-8501, Japan

² Skin Care Products Research, Kao Corporation, Tokyo 131-8501, Japan

Int. J. Mol. Sci. 2015, 16(4), 7753-7775; https://doi.org/10.3390/ijms16047753 - 8 Apr 2015

Cited by 149 | Viewed by 17932

Abstract

The repetitive exposure of skin to ultraviolet B (UVB) preferentially elicits wrinkling while ultraviolet A (UVA) predominantly elicits sagging. In chronically UVB or UVA-exposed rat skin there is a similar tortuous deformation of elastic fibers together with decreased skin elasticity, whose magnitudes are [...] Read more.

The repetitive exposure of skin to ultraviolet B (UVB) preferentially elicits wrinkling while ultraviolet A (UVA) predominantly elicits sagging. In chronically UVB or UVA-exposed rat skin there is a similar tortuous deformation of elastic fibers together with decreased skin elasticity, whose magnitudes are greater in UVB-exposed skin than in UVA-exposed skin. Comparison of skin elasticity with the activity of matrix metalloproteinases (MMPs) in the dermis of ovariectomized rats after UVB or UVA irradiation demonstrates that skin elasticity is more significantly decreased in ovariectomized rats than in sham-operated rats, which is accompanied by a reciprocal increase in elastase activity but not in the activities of collagenases I or IV. Clinical studies using animal skin and human facial skin demonstrated that topical treatment with a specific inhibitor or an inhibitory extract of skin fibroblast-derived elastase distinctly attenuates UVB and sunlight-induced formation of wrinkling. Our results strongly indicated that the upregulated activity of skin fibroblast-derived elastase plays a pivotal role in wrinkling and/or sagging of the skin via the impairment of elastic fiber configuration and the subsequent loss of skin elasticity. Full article

(This article belongs to the Collection Radiation Toxicity in Cells)

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20 pages, 4008 KiB

Open AccessReview

Biological Mechanisms Underlying the Ultraviolet Radiation-Induced Formation of Skin Wrinkling and Sagging II: Over-Expression of Neprilysin Plays an Essential Role

by Genji Imokawa^1,*, Hiroaki Nakajima² and Koichi Ishida³

¹ Research Institute for Biological Functions, Chubu University, 1200 Matsumoto, Kasugai, Aichi 487-8501, Japan

² School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura, Hachioji, Tokyo 192-0982, Japan

³ Skin Care Products Research, Kao Corporation, Tokyo 131-8501, Japan

Int. J. Mol. Sci. 2015, 16(4), 7776-7795; https://doi.org/10.3390/ijms16047776 - 8 Apr 2015

Cited by 56 | Viewed by 12542

Abstract

Our previous studies strongly indicated that the up-regulated activity of skin fibroblast-derived elastase plays a pivotal role in wrinkling and/or sagging of the skin via the impairment of elastic fiber configuration and the subsequent loss of skin elasticity. Fortunately, we succeeded in identifying [...] Read more.

Our previous studies strongly indicated that the up-regulated activity of skin fibroblast-derived elastase plays a pivotal role in wrinkling and/or sagging of the skin via the impairment of elastic fiber configuration and the subsequent loss of skin elasticity. Fortunately, we succeeded in identifying human skin fibroblast-derived elastase as a previously known enzyme, neprilysin or neutral endopeptidase (NEP). We have also characterized epithelial-mesenchymal paracrine cytokine interactions between UVB-exposed-keratinocytes and dermal fibroblasts and found that interleukin-1α and granulocyte macrophage colony stimulatory factor (GM-CSF) are intrinsic cytokines secreted by UVB-exposed keratinocytes that stimulate the expression of neprilysin by fibroblasts. On the other hand, direct UVA exposure of human fibroblasts significantly stimulates the secretion of IL-6 and also elicits a significant increase in the gene expression of matrix metallo-protease(MMP)-1 as well as neprilysin (to a lesser extent), which is followed by distinct increases in their protein and enzymatic activity levels. Direct UVA exposure of human keratinocytes also stimulates the secretion of IL-6, IL-8 and GM-CSF but not of IL-1 and endothelin-1. These findings suggest that GM-CSF secreted by UVA-exposed keratinocytes as well as IL-6 secreted by UVA-exposed dermal fibroblasts play important and additional roles in UVA-induced sagging and wrinkling by up-regulation of neprilysin and MMP-1, respectively, in dermal fibroblasts. Full article

(This article belongs to the Collection Radiation Toxicity in Cells)

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6 pages, 806 KiB

Open AccessReview

Inflammatory Biomarkers as Differential Predictors of Antidepressant Response

by Kenji Hashimoto

Division of Clinical Neuroscience, Chiba University Center for Forensic Mental Health, 1-8-1 Inohana, Chiba 260-7680, Japan

Int. J. Mol. Sci. 2015, 16(4), 7796-7801; https://doi.org/10.3390/ijms16047796 - 8 Apr 2015

Cited by 110 | Viewed by 10140

Abstract

Although antidepressants are generally effective in the treatment of major depressive disorder (MDD), it can still take weeks before patients feel the full antidepressant effects. Despite the efficacy of standard treatments, approximately two-thirds of patients with MDD fail to respond to pharmacotherapy. Therefore, [...] Read more.

Although antidepressants are generally effective in the treatment of major depressive disorder (MDD), it can still take weeks before patients feel the full antidepressant effects. Despite the efficacy of standard treatments, approximately two-thirds of patients with MDD fail to respond to pharmacotherapy. Therefore, the identification of blood biomarkers that can predict the treatment response to antidepressants would be highly useful in order to improve this situation. This article discusses inflammatory molecules as predictive biomarkers for antidepressant responses to several classes of antidepressants, including the N-methyl-d-aspartate (NMDA) receptor antagonist ketamine. Full article

(This article belongs to the Special Issue The Pathophysiology of Neuropsychiatric Disorders and New Therapeutic Targets)

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37 pages, 2338 KiB

Open AccessReview

Mushroom Lectins: Specificity, Structure and Bioactivity Relevant to Human Disease

by Mohamed Ali Abol Hassan^1,†, Razina Rouf^1,†, Evelin Tiralongo², Tom W. May³ and Joe Tiralongo^1,*

¹ Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, QLD 4222, Australia

² School of Pharmacy and Griffith Health Institute, Griffith University, Gold Coast Campus, Gold Coast, QLD 4222, Australia

³ Royal Botanic Gardens Melbourne, South Yarra, VIC 3141, Australia

^† These authors contributed equally to this work.

Int. J. Mol. Sci. 2015, 16(4), 7802-7838; https://doi.org/10.3390/ijms16047802 - 8 Apr 2015

Cited by 124 | Viewed by 13129

Abstract

Lectins are non-immunoglobulin proteins that bind diverse sugar structures with a high degree of selectivity. Lectins play crucial role in various biological processes such as cellular signaling, scavenging of glycoproteins from the circulatory system, cell–cell interactions in the immune system, differentiation and protein [...] Read more.

Lectins are non-immunoglobulin proteins that bind diverse sugar structures with a high degree of selectivity. Lectins play crucial role in various biological processes such as cellular signaling, scavenging of glycoproteins from the circulatory system, cell–cell interactions in the immune system, differentiation and protein targeting to cellular compartments, as well as in host defence mechanisms, inflammation, and cancer. Among all the sources of lectins, plants have been most extensively studied. However, more recently fungal lectins have attracted considerable attention due to their antitumor, antiproliferative and immunomodulatory activities. Given that only 10% of mushroom species are known and have been taxonomically classified, mushrooms represent an enormous unexplored source of potentially useful and novel lectins. In this review we provide an up-to-date summary on the biochemical, molecular and structural properties of mushroom lectins, as well as their versatile applications specifically focusing on mushroom lectin bioactivity. Full article

(This article belongs to the Special Issue Glycosylation and Glycoproteins)

12 pages, 1936 KiB

Open AccessArticle

Genetic Variability and Population Structure of Salvia lachnostachys: Implications for Breeding and Conservation Programs

by Marianna Erbano¹, Guilherme Schnell e Schühli² and Élide Pereira dos Santos^3,*

¹ Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Paraná, 80210-170 Curitiba, Paraná, Brazil

² Embrapa Florestas, 83411-000 Colombo, Paraná, Brazil

³ Departamento de Botânica, Setor de Ciências Biológicas, Universidade Federal do Paraná, 81530-900 Curitiba, Paraná, Brazil

Int. J. Mol. Sci. 2015, 16(4), 7839-7850; https://doi.org/10.3390/ijms16047839 - 8 Apr 2015

Cited by 40 | Viewed by 6621

Abstract

The genetic diversity and population structure of Salvia lachnostachys Benth were assessed. Inter Simple Sequence Repeat (ISSR) molecular markers were used to investigate the restricted distribution of S. lachnostachys in Parana State, Brazil. Leaves of 73 individuals representing three populations were collected. DNA [...] Read more.

The genetic diversity and population structure of Salvia lachnostachys Benth were assessed. Inter Simple Sequence Repeat (ISSR) molecular markers were used to investigate the restricted distribution of S. lachnostachys in Parana State, Brazil. Leaves of 73 individuals representing three populations were collected. DNA was extracted and submitted to PCR-ISSR amplification with nine tested primers. Genetic diversity parameters were evaluated. Our analysis indicated 95.6% polymorphic loci (stress value 0.02) with a 0.79 average Simpson’s index. The Nei-Li distance dendrogram and principal component analysis largely recovered the geographical origin of each sample. Four major clusters were recognized representing each collected population. Nei’s gene diversity and Shannon’s information index were 0.25 and 0.40 respectively. As is typical for outcrossing herbs, the majority of genetic variation occurred at the population level (81.76%). A high gene flow (Nm = 2.48) was observed with a correspondingly low fixation index. These values were generally similar to previous studies on congeneric species. The results of principal coordinate analysis (PCA) and of arithmetic average (UPGMA) were consistent and all three populations appear distinct as in STRUCTURE analysis. In addition, this analysis indicated a majority intrapopulation genetic variation. Despite the human pressure on natural populations our study found high levels of genetic diversity for S. lachnostachys. This was the first molecular assessment for this endemic species with medicinal proprieties and the results can guide for subsequent bioprospection, breeding programs or conservation actions. Full article

(This article belongs to the Special Issue Plant Molecular Biology)

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10 pages, 1092 KiB

Open AccessArticle

The Photodynamic Antibacterial Effects of Silicon Phthalocyanine (Pc) 4

by Matthew L. Dimaano¹, Chantal Rozario¹, Michelle M. Nerandzic², Curtis J. Donskey², Minh Lam¹ and Elma D. Baron^1,3,*

¹ Department of Dermatology, Case Western Reserve University, Cleveland, OH 44106, USA

² Research Service, Geriatric Research Education and Clinical Center, Cleveland Veterans Affairs Medical Center, Cleveland, OH 44106, USA

³ Department of Dermatology, Cleveland Veterans Affairs Medical Center, Cleveland, OH 44106, USA

Int. J. Mol. Sci. 2015, 16(4), 7851-7860; https://doi.org/10.3390/ijms16047851 - 8 Apr 2015

Cited by 21 | Viewed by 5926

Abstract

The emergence of antibiotic-resistant strains in facultative anaerobic Gram-positive coccal bacteria, such as methicillin-resistant Staphylococcus aureus (MRSA), is a global health issue. Typically, MRSA strains are found associated with institutions like hospitals but recent data suggest that they are becoming more prevalent in [...] Read more.

The emergence of antibiotic-resistant strains in facultative anaerobic Gram-positive coccal bacteria, such as methicillin-resistant Staphylococcus aureus (MRSA), is a global health issue. Typically, MRSA strains are found associated with institutions like hospitals but recent data suggest that they are becoming more prevalent in community-acquired infections. It is thought that the incidence and prevalence of bacterial infections will continue to increase as (a) more frequent use of broad-spectrum antibiotics and immunosuppressive medications; (b) increased number of invasive medical procedures; and (c) higher incidence of neutropenia and HIV infections. Therefore, more optimal treatments, such as photodynamic therapy (PDT), are warranted. PDT requires the interaction of light, a photosensitizing agent, and molecular oxygen to induce cytotoxic effects. In this study, we investigated the efficacy and characterized the mechanism of cytotoxicity induced by photodynamic therapy sensitized by silicon phthalocyanine (Pc) 4 on (a) methicillin-sensitive Staphylococcus aureus (MSSA) (ATCC 25923); (b) community acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) (ATCC 43300); and (c) hospital acquired methicillin-resistant Staphylococcus aureus (HA-MRSA) (PFGE type 300). Our data include confocal image analysis, which confirmed that Pc 4 is taken up by all S. aureus strains, and viable cell recovery assay, which showed that concentrations as low as 1.0 μM Pc 4 incubated for 3 h at 37 °C followed by light at 2.0 J/cm² can reduce cell survival by 2–5 logs. These results are encouraging, but before PDT can be utilized as an alternative treatment for eradicating resistant strains, we must first characterize the mechanism of cell death that Pc 4-based PDT employs in eliminating these pathogens. Full article

(This article belongs to the Special Issue Advances in Photodynamic Therapy)

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15 pages, 1343 KiB

Open AccessArticle

Antiproliferative, Antibacterial and Antifungal Activity of the Lichen Xanthoria parietina and Its Secondary Metabolite Parietin

by Adriana Basile¹, Daniela Rigano²

, Stefano Loppi³, Annalisa Di Santi⁴, Angela Nebbioso⁴, Sergio Sorbo⁵, Barbara Conte¹, Luca Paoli³, Francesca De Ruberto¹, Anna Maria Molinari⁴, Lucia Altucci^4,6,* and Paola Bontempo^4,*

¹ Department of Biological Sciences—Plant Biology Section, University of Naples "Federico II", Naples 80126, Italy

² Department of Pharmacy, University of Naples "Federico II", Naples 80131, Italy

³ Department of Life Sciences, University of Siena, Siena 53100, Italy

⁴ Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Naples 80138, Italy

⁵ Interdepartmental Service Centre for Electron Microscopy C.I.S.M.E., University of Naples "Federico II", via Foria 223, Naples 80139, Italy

⁶ Institute of Genetics and Biophysics (IGB), Adriano Buzzati Traverso, Naples 80131, Italy

Int. J. Mol. Sci. 2015, 16(4), 7861-7875; https://doi.org/10.3390/ijms16047861 - 9 Apr 2015

Cited by 90 | Viewed by 11774

Abstract

Lichens are valuable natural resources used for centuries throughout the world as medicine, food, fodder, perfume, spices and dyes, as well as for other miscellaneous purposes. This study investigates the antiproliferative, antibacterial and antifungal activity of the acetone extract of the lichen Xanthoria [...] Read more.

Lichens are valuable natural resources used for centuries throughout the world as medicine, food, fodder, perfume, spices and dyes, as well as for other miscellaneous purposes. This study investigates the antiproliferative, antibacterial and antifungal activity of the acetone extract of the lichen Xanthoria parietina (Linnaeus) Theodor Fries and its major secondary metabolite, parietin. The extract and parietin were tested for antimicrobial activity against nine American Type Culture Collection standard and clinically isolated bacterial strains, and three fungal strains. Both showed strong antibacterial activity against all bacterial strains and matched clinical isolates, particularly against Staphylococcus aureus from standard and clinical sources. Among the fungi tested, Rhizoctonia solani was the most sensitive. The antiproliferative effects of the extract and parietin were also investigated in human breast cancer cells. The extract inhibited proliferation and induced apoptosis, both effects being accompanied by modulation of expression of cell cycle regulating genes such as p16, p27, cyclin D1 and cyclin A. It also mediated apoptosis by activating extrinsic and intrinsic cell death pathways, modulating Tumor Necrosis Factor-related apoptosis-inducing ligand (TRAIL) and B-cell lymphoma 2 (Bcl-2), and inducing Bcl-2-associated agonist of cell death (BAD) phosphorylation. Our results indicate that Xanthoria parietina is a major potential source of antimicrobial and anticancer substances. Full article

(This article belongs to the Special Issue Bioactive Phytochemicals in Functional Foods for Cancer Prevention)

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14 pages, 1900 KiB

Open AccessArticle

The Changes of Angiogenesis and Immune Cell Infiltration in the Intra- and Peri-Tumoral Melanoma Microenvironment

by Vladimir Zidlik¹, Svetlana Brychtova^2,*, Magdalena Uvirova¹, Dusan Ziak¹ and Jana Dvorackova^1,3

¹ CGB Laboratory, a.s., Laboratory of Molecular Genetics and Pathology, AGEL Research and Training Institute—Ostrava-Vitkovice Branch, Korenskeho 10, Ostrava 71000, Czech Republic

² Institute of Clinical and Molecular Pathology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hnevotinska 3, Olomouc 77515, Czech Republic

³ Department of Pathology, Faculty of Medicine, University of Ostrava, Syllabova 19, Ostrava 70300, Czech Republic

Int. J. Mol. Sci. 2015, 16(4), 7876-7889; https://doi.org/10.3390/ijms16047876 - 9 Apr 2015

Cited by 21 | Viewed by 5983

Abstract

Malignant melanoma (MM) urgently needs identification of new markers with better predictive value than currently-used clinical and histological parameters. Cancer cells stimulate the formation of a specialized tumor microenvironment, which reciprocally affects uncontrolled proliferation and migration. However, this microenvironment is heterogeneous with different [...] Read more.

Malignant melanoma (MM) urgently needs identification of new markers with better predictive value than currently-used clinical and histological parameters. Cancer cells stimulate the formation of a specialized tumor microenvironment, which reciprocally affects uncontrolled proliferation and migration. However, this microenvironment is heterogeneous with different sub-compartments defined by their access to oxygen and nutrients. This study evaluated microvascular density (MVD), CD3⁺ lymphocytes (TILs) and FOXP3⁺ T-regulatory lymphocytes (Tregs) on formalin-fixed paraffin-embedded tissue sections using light microscopy. We analyzed 82 malignant melanomas, divided according to the AJCC TNM classification into four groups—pT1 (35), pT2 (17), pT3 (18) and pT4 (12)—and 25 benign pigmented nevi. All parameters were measured in both the central areas of tumors (C) and at their periphery (P). A marked increase in all parameters was found in melanomas compared to nevi (p = 0.0001). There was a positive correlation between MVD, TILs, FOXP3⁺ Tregs and the vertical growth phase. The results show that MVD, TILs and FOXP3⁺ Tregs substantially influence cutaneous melanoma microenvironment. We found significant topographic differences of the parameters between central areas of tumors and their boundaries. Full article

(This article belongs to the Section Biochemistry)

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10 pages, 670 KiB

Open AccessArticle

APOE Polymorphisms Contribute to Reduced Atorvastatin Response in Chilean Amerindian Subjects

by Jenny Lagos, Tomás Zambrano, Alexy Rosales and Luis A. Salazar^*

Center of Molecular Biology and Pharmacogenetics, Department of Basic Sciences, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera (BIOREN-UFRO), Av. Francisco Salazar 01145, 4811230 Temuco, Chile

Int. J. Mol. Sci. 2015, 16(4), 7890-7899; https://doi.org/10.3390/ijms16047890 - 9 Apr 2015

Cited by 24 | Viewed by 6169

Abstract

Genetic factors can determine the high variability observed in response to lipid-lowering therapy with statins. Nonetheless, the frequency of single nucleotide polymorphisms (SNPs) and their impact can vary due to ethnicity. Because the Chilean population carries a strong Amerindian background, the objective of [...] Read more.

Genetic factors can determine the high variability observed in response to lipid-lowering therapy with statins. Nonetheless, the frequency of single nucleotide polymorphisms (SNPs) and their impact can vary due to ethnicity. Because the Chilean population carries a strong Amerindian background, the objective of this study was to evaluate the influence of apolipoprotein E (APOE) variants (rs429358, rs7412) and the 1959C>T SNP (rs5925) in the low-density lipoprotein receptor (LDLR) in response to atorvastatin treatment in hypercholesterolemic individuals. A hundred and thirty nine subjects undergoing statin therapy were included. Identification of Amerindian mtDNA haplogroups was determined by polymerase chain reaction (PCR) and PCR followed by restriction fragment length polymorphism (RFLP), respectively. SNPs were determined by PCR-RFLP. Out of the 139 individuals studied, 84.4% had an Amerindian background, according to mtDNA analysis. In relation to APOE variants, carriers of the E3/4 genotype presented lower cholesterol reduction compared to genotype E3/3 (LDL-C: −18% vs. −29%, p ˂ 0.001). On the other hand, the LDLR rs5925 SNP was not related to atorvastatin response (p = 0.5760). Our results suggest that APOE SNPs are potential predictors to atorvastatin therapy in Amerindian Chilean subjects. Full article

(This article belongs to the Special Issue Human Single Nucleotide Polymorphisms and Disease Diagnostics)

17 pages, 1960 KiB

Open AccessArticle

Posttraumatic Inflammation as a Key to Neuroregeneration after Traumatic Spinal Cord Injury

by Arash Moghaddam^1,*,†, Christopher Child^1,*,†, Thomas Bruckner², Hans Jürgen Gerner¹, Volker Daniel³ and Bahram Biglari⁴

¹ Heidelberg Trauma Research Group, Trauma and Reconstructive Surgery, Center for Orthopedics, Trauma Surgery and Spinal Cord Injury, Heidelberg University Hospital, Schlierbacher Landstraße 200a, D-69118 Heidelberg, Germany

² Institute for Medical Biometry and Informatics, Heidelberg University Hospital, Im Neuenheimer Feld 305, D-69120 Heidelberg, Germany

³ Department of Transplantation Immunology, Institute of Immunology, University of Heidelberg, Im Neuenheimer Feld 305, D-69120 Heidelberg, Germany

⁴ Berufsgenossenschaftliche Unfallklinik Ludwigshafen, Department of Paraplegiology, Ludwig-Guttmann-Straße-13, D-67071 Ludwigshafen, Germany

^† These authors contributed equally to this work.

Int. J. Mol. Sci. 2015, 16(4), 7900-7916; https://doi.org/10.3390/ijms16047900 - 9 Apr 2015

Cited by 55 | Viewed by 7985

Abstract

Pro- and anti-inflammatory cytokines might have a large impact on the secondary phase and on the neurological outcome of patients with acute spinal cord injury (SCI). We measured the serum levels of different cytokines (Interferon-γ, Tumor Necrosis Factor-α, Interleukin-1β, IL-6, IL-8, IL-10, and [...] Read more.

Pro- and anti-inflammatory cytokines might have a large impact on the secondary phase and on the neurological outcome of patients with acute spinal cord injury (SCI). We measured the serum levels of different cytokines (Interferon-γ, Tumor Necrosis Factor-α, Interleukin-1β, IL-6, IL-8, IL-10, and Vascular Endothelial Growth Factor) over a 12-week period in 40 acute traumatic SCI patients: at admission on average one hour after initial trauma; at four, nine, 12, and 24 h; Three, and seven days after admission; and two, four, eight, and twelve weeks after admission. This was done using a Luminex Performance Human High Sensitivity Cytokine Panel. SCI was classified using the American Spinal Injury Association (ASIA) Impairment Scale (AIS) at time of admission and after 12 weeks. TNFα, IL-1β, IL-6, IL-8, and IL-10 concentrations were significantly higher in patients without neurological remission and in patients with an initial AIS A (p < 0.05). This study shows significant differences in cytokine concentrations shown in traumatic SCI patients with different neurological impairments and within a 12-week period. IL-8 and IL-10 are potential peripheral markers for neurological remission and rehabilitation after traumatic SCI. Furthermore our cytokine expression pattern of the acute, subacute, and intermediate phase of SCI establishes a possible basis for future studies to develop standardized monitoring, prognostic, and tracking techniques. Full article

(This article belongs to the Special Issue Neurological Injuries’ Monitoring, Tracking and Treatment)

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15 pages, 1200 KiB

Open AccessReview

Pathogenesis of Renal Disease in Systemic Lupus Erythematosus—The Role of Autoantibodies and Lymphocytes Subset Abnormalities

by Desmond Y. H. Yap and Kar N. Lai^*

Nephrology Division, Department of Medicine, The University of Hong Kong, Hong Kong, China

Int. J. Mol. Sci. 2015, 16(4), 7917-7931; https://doi.org/10.3390/ijms16047917 - 9 Apr 2015

Cited by 64 | Viewed by 10693

Abstract

Lupus nephritis (LN) is a common and severe organ manifestation of systemic lupus erythematosus (SLE), and is associated with significant patient morbidity and mortality. Autoantibodies and aberrations in lymphocyte subsets have putative roles in the pathogenesis of SLE and LN, and might reflect [...] Read more.

Lupus nephritis (LN) is a common and severe organ manifestation of systemic lupus erythematosus (SLE), and is associated with significant patient morbidity and mortality. Autoantibodies and aberrations in lymphocyte subsets have putative roles in the pathogenesis of SLE and LN, and might reflect disease activity and are amenable to immunosuppressive treatments. Anti-DNA is one of the well-studied autoantibodies, which correlates with disease activity and has direct nephritogenic effects on resident renal cells and various glomerular components. Other important autoantibodies in the pathogenesis of LN include anti-C1q, anti-α-actinin and anti-nucleosome antibodies. Changes in naive and memory B cells and plasma cells have been observed in SLE and LN patients. These B cell subsets exert diverse effects during pathogenesis of LN such as production of autoantibodies, secretion of proinflammatory and anti-inflammatory cytokines and presentation of auto-antigens to effector cells. Aberration of T lymphocytes, especially the T-helper subsets, is also highly pertinent in the development of LN. In this context, important T helper subsets include Th1, Th2, Th9, Th17, T_Reg and follicular T-helper cells. The growing knowledge on these autoantibodies and lymphocyte subset abnormalities will enhance our understanding of SLE and LN, and hence help devise better strategies for disease monitoring and treatment. Full article

(This article belongs to the Special Issue Molecular and Cellular Mechanisms in the Pathogenesis of Systemic Lupus Erythematosus)

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12 pages, 827 KiB

Open AccessArticle

Promotion of Ni²⁺ Removal by Masking Toxicity to Sulfate-Reducing Bacteria: Addition of Citrate

by Junwei Qian^1,†, Xiaoyu Zhu^1,†, Yong Tao^1,*, Yan Zhou², Xiaohong He¹ and Daping Li^1,*

¹ Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences & Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China

² College of Life Science, Sichuan University, Chengdu 610064, China

^† These authors contributed equally to this work.

Int. J. Mol. Sci. 2015, 16(4), 7932-7943; https://doi.org/10.3390/ijms16047932 - 9 Apr 2015

Cited by 14 | Viewed by 6437

Abstract

The sulfate-reducing bioprocess is a promising technology for the treatment of heavy metal-containing wastewater. This work was conducted to investigate the possibility of promoting heavy metal removal by the addition of citrate to mask Ni²⁺ toxicity to sulfate-reducing bacteria (SRB) in batch [...] Read more.

The sulfate-reducing bioprocess is a promising technology for the treatment of heavy metal-containing wastewater. This work was conducted to investigate the possibility of promoting heavy metal removal by the addition of citrate to mask Ni²⁺ toxicity to sulfate-reducing bacteria (SRB) in batch reactors. SRB growth was completely inhibited in Ni²⁺-containing medium (1 mM) when lactate served as the sole carbon resource, leading to no sulfate reduction and Ni²⁺ removal. However, after the addition of citrate, SRB grew well, and sulfate was quickly reduced to sulfide. Simultaneously, the Ni-citrate complex was biodegraded to Ni²⁺ and acetate. The NiS precipitate was then formed, and Ni²⁺ was completely removed from the solution. It was suggested that the addition of citrate greatly alleviates Ni²⁺ toxicity to SRB and improves the removal of Ni²⁺, which was confirmed by quantitative real-time PCR targeting dissimilatory sulfite reductase (dsrAB) genes. Analysis of the carbon metabolism indicated that lactate instead of acetate served as the electron donor for sulfate reduction. This study offers a potential approach to increase the removal of heavy metals from wastewater in the single stage SRB-based bioprocess. Full article

(This article belongs to the Special Issue Microbial Metabolism of Toxic Organic Pollutants and Transformation of Metals/Metalloids and Ecotoxicity Assessment)

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16 pages, 1962 KiB

Open AccessArticle

Psoralea glandulosa as a Potential Source of Anticancer Agents for Melanoma Treatment

by Alejandro Madrid^1,*, Venera Cardile², César González³, Ivan Montenegro⁴, Joan Villena⁵, Silvia Caggia², Adriana Graziano² and Alessandra Russo^6,*

¹ Departamento de Química, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Avda. Leopoldo Carvallo 270, Playa Ancha, 2340000 Valparaíso, Chile

² Department of Biomedical Sciences, University of Catania, V. le A. Doria 6, 95125 Catania, Italy

³ Departamento de Química, Universidad Técnica Federico Santa María, Av. España N° 1680, 2340000 Valparaíso, Chile

⁴ Escuela de Obstetricia y Puericultura, Facultad de medicina, Universidad de Valparaíso, Blanco N° 1911, 2340000 Valparaíso, Chile

⁵ Centro de Investigaciones Biomédicas (CIB), Escuela de Medicina, Universidad de Valparaíso, Av. Hontaneda N° 2664, 2340000 Valparaíso, Chile

⁶ Department of Drug Sciences, Biochemistry Section, University of Catania, V. le A. Doria 6, 95125 Catania, Italy

Int. J. Mol. Sci. 2015, 16(4), 7944-7959; https://doi.org/10.3390/ijms16047944 - 9 Apr 2015

Cited by 23 | Viewed by 7178

Abstract

With the aim of identifying novel agents with antigrowth and pro-apoptotic activity on melanoma cancer, the present study was undertaken to investigate the biological activity of the resinous exudate of aerial parts from Psoralea glandulosa, and its active components (bakuchiol (1 [...] Read more.

With the aim of identifying novel agents with antigrowth and pro-apoptotic activity on melanoma cancer, the present study was undertaken to investigate the biological activity of the resinous exudate of aerial parts from Psoralea glandulosa, and its active components (bakuchiol (1), 3-hydroxy-bakuchiol (2) and 12-hydroxy-iso-bakuchiol (3)) against melanoma cells (A2058). In addition, the effect in cancer cells of bakuchiol acetate (4), a semi-synthetic derivative of bakuchiol, was examined. The results obtained show that the resinous exudate inhibited the growth of cancer cells with IC₅₀ value of 10.5 μg/mL after 48 h of treatment, while, for pure compounds, the most active was the semi-synthetic compound 4. Our data also demonstrate that resin is able to induce apoptotic cell death, which could be related to an overall action of the meroterpenes present. In addition, our data seem to indicate that the apoptosis correlated to the tested products appears, at least in part, to be associated with an increase of reactive oxygen species (ROS) production. In summary, our study provides the first evidence that P. glandulosa may be considered a source of useful molecules in the development of analogues with more potent efficacy against melanoma cells. Full article

(This article belongs to the Special Issue Advances in Molecular Oncology 2014)

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16 pages, 1992 KiB

Open AccessArticle

Synthesis of Spongy-Like Mesoporous Hydroxyapatite from Raw Waste Eggshells for Enhanced Dissolution of Ibuprofen Loaded via Supercritical CO₂

by Abdul-Rauf Ibrahim^†

, Xiangyun Li^†, Yulan Zhou, Yan Huang, Wenwen Chen, Hongtao Wang and Jun Li^*

¹ Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, National Engineering Laboratory for Green Chemical Productions of Alcohols, Ethers and Esters, Xiamen University, Xiamen 361005, China

^† These authors contributed equally to this work.

Int. J. Mol. Sci. 2015, 16(4), 7960-7975; https://doi.org/10.3390/ijms16047960 - 9 Apr 2015

Cited by 52 | Viewed by 8097

Abstract

The use of cheaper and recyclable biomaterials (like eggshells) to synthesize high purity hydroxyapatite (HAp) with better properties (small particle size, large surface area and pore volume) for applications (in environmental remediation, bone augmentation and replacement, and drug delivery systems) is vital since [...] Read more.

The use of cheaper and recyclable biomaterials (like eggshells) to synthesize high purity hydroxyapatite (HAp) with better properties (small particle size, large surface area and pore volume) for applications (in environmental remediation, bone augmentation and replacement, and drug delivery systems) is vital since high-purity synthetic calcium sources are expensive. In this work, pure and mesoporous HAp nanopowder with large pore volume (1.4 cm³/g) and surface area (284.1 m²/g) was produced from raw eggshells at room temperature using a simple two-step procedure. The control of precursor droplets could stabilize the pH value of the reaction solution, because of the size of the needle (of the syringe pump used for precursor additions) leading to production of HAp with high surface area and pore size. The as-produced HAp revealed high ibuprofen (as a model drug) loading (1.38 g/g HAp), enhanced dissolution and controllable release of the drug via solute-saturated supercritical carbon dioxide. Full article

(This article belongs to the Special Issue Biomaterials for Tissue Engineering)

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19 pages, 1343 KiB

Open AccessArticle

RNA Sequencing Identifies Upregulated Kyphoscoliosis Peptidase and Phosphatidic Acid Signaling Pathways in Muscle Hypertrophy Generated by Transgenic Expression of Myostatin Propeptide

by Yuanxin Miao^1,2, Jinzeng Yang³, Zhong Xu^1,2, Lu Jing^1,2, Shuhong Zhao^1,2 and Xinyun Li^1,2,*

¹ Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China

² The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China

³ Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, USA

Int. J. Mol. Sci. 2015, 16(4), 7976-7994; https://doi.org/10.3390/ijms16047976 - 9 Apr 2015

Cited by 20 | Viewed by 9207

Abstract

Myostatin (MSTN), a member of the transforming growth factor-β superfamily, plays a crucial negative role in muscle growth. MSTN mutations or inhibitions can dramatically increase muscle mass in most mammal species. Previously, we generated a transgenic mouse model of muscle hypertrophy via the [...] Read more.

Myostatin (MSTN), a member of the transforming growth factor-β superfamily, plays a crucial negative role in muscle growth. MSTN mutations or inhibitions can dramatically increase muscle mass in most mammal species. Previously, we generated a transgenic mouse model of muscle hypertrophy via the transgenic expression of the MSTN N-terminal propeptide cDNA under the control of the skeletal muscle-specific MLC1 promoter. Here, we compare the mRNA profiles between transgenic mice and wild-type littermate controls with a high-throughput RNA sequencing method. The results show that 132 genes were significantly differentially expressed between transgenic mice and wild-type control mice; 97 of these genes were up-regulated, and 35 genes were down-regulated in the skeletal muscle. Several genes that had not been reported to be involved in muscle hypertrophy were identified, including up-regulated myosin binding protein H (mybph), and zinc metallopeptidase STE24 (Zmpste24). In addition, kyphoscoliosis peptidase (Ky), which plays a vital role in muscle growth, was also up-regulated in the transgenic mice. Interestingly, a pathway analysis based on grouping the differentially expressed genes uncovered that cardiomyopathy-related pathways and phosphatidic acid (PA) pathways (Dgki, Dgkz, Plcd4) were up-regulated. Increased PA signaling may increase mTOR signaling, resulting in skeletal muscle growth. The findings of the RNA sequencing analysis help to understand the molecular mechanisms of muscle hypertrophy caused by MSTN inhibition. Full article

(This article belongs to the Section Biochemistry)

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13 pages, 1643 KiB

Open AccessArticle

Antimicrobial Action of Water-Soluble β-Chitosan against Clinical Multi-Drug Resistant Bacteria

by Seong-Cheol Park^†

, Joung-Pyo Nam^†, Jun-Ho Kim, Young-Min Kim, Jae-Woon Nah^* and Mi-Kyeong Jang^*

¹ Department of Polymer Science and Engineering, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 540-950, Korea

^† These authors contributed equally to this work.

Int. J. Mol. Sci. 2015, 16(4), 7995-8007; https://doi.org/10.3390/ijms16047995 - 10 Apr 2015

Cited by 48 | Viewed by 7076

Abstract

Recently, the number of patients infected by drug-resistant pathogenic microbes has increased remarkably worldwide, and a number of studies have reported new antibiotics from natural sources. Among them, chitosan, with a high molecular weight and α-conformation, exhibits potent antimicrobial activity, but useful applications [...] Read more.

Recently, the number of patients infected by drug-resistant pathogenic microbes has increased remarkably worldwide, and a number of studies have reported new antibiotics from natural sources. Among them, chitosan, with a high molecular weight and α-conformation, exhibits potent antimicrobial activity, but useful applications as an antibiotic are limited by its cytotoxicity and insolubility at physiological pH. In the present study, the antibacterial activity of low molecular weight water-soluble (LMWS) α-chitosan (α1k, α5k, and α10k with molecular masses of 1, 5, and 10 kDa, respectively) and β-chitosan (β1k, β5k, and β10k) was compared using a range of pathogenic bacteria containing drug-resistant bacteria isolated from patients at different pH. Interestingly, β5k and β10k exhibited potent antibacterial activity, even at pH 7.4, whereas only α10k was effective at pH 7.4. The active target of β-chitosan is the bacterial membrane, where the leakage of calcein is induced in artificial PE/PG vesicles, bacterial mimetic membrane. Moreover, scanning electron microscopy showed that they caused significant morphological changes on the bacterial surfaces. An in vivo study utilizing a bacteria-infected mouse model found that LMWS β-chitosan could be used as a candidate in anti-infective or wound healing therapeutic applications. Full article

(This article belongs to the Special Issue Antimicrobial Polymers 2016)

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19 pages, 4002 KiB

Open AccessArticle

Nitrogen Removal from Micro-Polluted Reservoir Water by Indigenous Aerobic Denitrifiers

by Ting-Lin Huang^*, Shi-Lei Zhou, Hai-Han Zhang, Na Zhou, Lin Guo, Shi-Yu Di and Zi-Zhen Zhou

School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China

Int. J. Mol. Sci. 2015, 16(4), 8008-8026; https://doi.org/10.3390/ijms16048008 - 10 Apr 2015

Cited by 25 | Viewed by 6447

Abstract

Treatment of micro-polluted source water is receiving increasing attention because of environmental awareness on a global level. We isolated and identified aerobic denitrifying bacteria Zoogloea sp. N299, Acinetobacter sp. G107, and Acinetobacter sp. 81Y and used these to remediate samples of their native [...] Read more.

Treatment of micro-polluted source water is receiving increasing attention because of environmental awareness on a global level. We isolated and identified aerobic denitrifying bacteria Zoogloea sp. N299, Acinetobacter sp. G107, and Acinetobacter sp. 81Y and used these to remediate samples of their native source water. We first domesticated the isolated strains in the source water, and the 48-h nitrate removal rates of strains N299, G107, and 81Y reached 33.69%, 28.28%, and 22.86%, respectively, with no nitrite accumulation. We then conducted a source-water remediation experiment and cultured the domesticated strains (each at a dry cell weight concentration of 0.4 ppm) together in a sample of source water at 20–26 °C and a dissolved oxygen concentration of 3–7 mg/L for 60 days. The nitrate concentration of the system decreased from 1.57 ± 0.02 to 0.42 ± 0.01 mg/L and that of a control system decreased from 1.63 ± 0.02 to 1.30 ± 0.01 mg/L, each with no nitrite accumulation. Total nitrogen of the bacterial system changed from 2.31 ± 0.12 to 1.09 ± 0.01 mg/L, while that of the control system changed from 2.51 ± 0.13 to 1.72 ± 0.06 mg/L. The densities of aerobic denitrification bacteria in the experimental and control systems ranged from 2.8 × 10⁴ to 2 × 10⁷ cfu/mL and from 7.75 × 10³ to 5.5 × 10⁵ cfu/mL, respectively. The permanganate index in the experimental and control systems decreased from 5.94 ± 0.12 to 3.10 ± 0.08 mg/L and from 6.02 ± 0.13 to 3.61 ± 0.11 mg/L, respectively, over the course of the experiment. Next, we supplemented samples of the experimental and control systems with additional bacteria or additional source water and cultivated the systems for another 35 days. The additional bacteria did little to improve the water quality. The additional source water provided supplemental carbon and brought the nitrate removal rate in the experimental system to 16.97%, while that in the control system reached only 3.01%, with no nitrite accumulation in either system. Our results show that aerobic denitrifying bacteria remain highly active after domestication and demonstrate the applicability of such organisms in the bioremediation of oligotrophic ecosystems. Full article

(This article belongs to the Section Molecular Toxicology)

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13 pages, 1154 KiB

Open AccessArticle

Development of Carbon Nanotube Modified Cement Paste with Microencapsulated Phase-Change Material for Structural–Functional Integrated Application

by Hongzhi Cui^1,*, Shuqing Yang² and Shazim Ali Memon^3,*

¹ Guangdong Provincial Key Laboratory of Durability for Marine Civil Engineering, College of Civil Engineering, Shenzhen University, Shenzhen 518060, China

² Department of Civil and Environmental Engineering, School of Engineering, The Hong Kong University of Science and Technology, Hong Kong 999077, China

³ Department of Civil Engineering, COMSATS Institute of Information Technology, Abbottabad Campus, Abbottabad 22010, Pakistan

Int. J. Mol. Sci. 2015, 16(4), 8027-8039; https://doi.org/10.3390/ijms16048027 - 10 Apr 2015

Cited by 72 | Viewed by 7635

Abstract

Microencapsulated phase-change materials (MPCM) can be used to develop a structural–functional integrated cement paste having high heat storage efficiency and suitable mechanical strength. However, the incorporation of MPCM has been found to degrade the mechanical properties of cement based composites. Therefore, in this [...] Read more.

Microencapsulated phase-change materials (MPCM) can be used to develop a structural–functional integrated cement paste having high heat storage efficiency and suitable mechanical strength. However, the incorporation of MPCM has been found to degrade the mechanical properties of cement based composites. Therefore, in this research, the effect of carbon nanotubes (CNTs) on the properties of MPCM cement paste was evaluated. Test results showed that the incorporation of CNTs in MPCM cement paste accelerated the cement hydration reaction. SEM micrograph showed that CNTs were tightly attached to the cement hydration products. At the age of 28 days, the percentage increase in flexural and compressive strength with different dosage of CNTs was found to be up to 41% and 5% respectively. The optimum dosage of CNTs incorporated in MPCM cement paste was found to be 0.5 wt %. From the thermal performance test, it was found that the cement paste panels incorporated with different percentages of MPCM reduced the temperature measured at the center of the room by up to 4.6 °C. Inverse relationship was found between maximum temperature measured at the center of the room and the dosage of MPCM. Full article

(This article belongs to the Special Issue Advances in Anisotropic and Smart Materials)

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19 pages, 1592 KiB

Open AccessArticle

Heavy Metal Complexation of Thiol-Containing Peptides from Soy Glycinin Hydrolysates

by Xiuzhen Ding, Yufei Hua, Yeming Chen, Caimeng Zhang and Xiangzhen Kong^*

State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China

Int. J. Mol. Sci. 2015, 16(4), 8040-8058; https://doi.org/10.3390/ijms16048040 - 10 Apr 2015

Cited by 29 | Viewed by 6616

Abstract

Many thiol-containing molecules show heavy metal complexation ability and are used as antidotes. In this study, the potential function associated with thiol-containing peptides (TCPs) from soy protein hydrolysates as natural detoxicants for heavy metals is reported. TCPs enriched by Thiopropyl-Sepharose 6B covalent chromatography [...] Read more.

Many thiol-containing molecules show heavy metal complexation ability and are used as antidotes. In this study, the potential function associated with thiol-containing peptides (TCPs) from soy protein hydrolysates as natural detoxicants for heavy metals is reported. TCPs enriched by Thiopropyl-Sepharose 6B covalent chromatography had different molecular weight distributions as well as different numbers of proton dissociable groups, depending on the proteases and degree of hydrolysis. The major contribution of sulfhydryl groups was confirmed by the largest pH decrease between 8.0 and 8.5 of the pH titration curves. The complexation of TCPs with heavy metalswas evaluated by stability constants (β_n) of TCP-metal complexes whose stoichiometry was found to be 1:1 (ML) and 1:2 (ML₂). TCPs from degree of hydrolysis of 25% hydrolysates gave high affinities towards Hg²⁺, Cd²⁺, and Pb²⁺ (giving similar or even bigger lgβ values than that of glutathione). A significantly positive correlation was found between the logarithm of stability constants for ML₂ (lgβ₂) and the sulfhydryl group content. Molecular weight distribution of TCPs affected the complexation with Pb²⁺ notably more than Hg²⁺ and Cd²⁺. These results suggest that soy TCPs have the potential to be used in the formulation of functional foods to counteract heavy metal accumulation in humans. Full article

(This article belongs to the Special Issue Bioactive Carbohydrates and Peptides)

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11 pages, 1837 KiB

Open AccessCommunication

Expression of the Aryl Hydrocarbon Receptor in Growth Plate Cartilage and the Impact of Its Local Modulation on Longitudinal Bone Growth

by Therése Cedervall^1,*, Pia Monica Lind² and Lars Sävendahl¹

¹ Department of Women's and Children's Health, Pediatric Endocrinology Unit, Astrid Lindgren Children's Hospital, Q2:08, Karolinska University Hospital Solna, S-171 76 Stockholm, Sweden

² Department of Medical Sciences, Occupational and Environmental Medicine, Uppsala University Hospital, 751 85 Uppsala, Sweden

Int. J. Mol. Sci. 2015, 16(4), 8059-8069; https://doi.org/10.3390/ijms16048059 - 10 Apr 2015

Cited by 9 | Viewed by 5062

Abstract

Although dioxin has been reported to impair bone growth in both humans and animals, the underlying mechanisms have not been clarified. We conducted this study to rule out if dioxin may directly target the growth plate, via local modulation of the aryl hydrocarbon [...] Read more.

Although dioxin has been reported to impair bone growth in both humans and animals, the underlying mechanisms have not been clarified. We conducted this study to rule out if dioxin may directly target the growth plate, via local modulation of the aryl hydrocarbon receptor (AhR). Initial studies in rare tissue samples of the human growth plate confirmed that the AhR protein is widely expressed in growth plate cartilage. To explore the local role of the AhR, mechanistic studies were performed in a well-established model of cultured fetal rat metatarsal bones. The longitudinal growth of these bones was monitored while being exposed to AhR modulators. The AhR agonist, 2,3,7,8-tetrachlorodibenzo-p-dioxin, did not affect bone growth at any concentrations tested (1 pM–10 nM). In contrast, the AhR antagonist, alpha-naphthoflavone, suppressed bone growth and increased chondrocyte apoptosis, although only at a high, potentially cytotoxic concentration (50 µM). We conclude that although the AhR is widely expressed in the growth plate, bone growth is not modulated when locally activated, and therefore, dioxin-induced growth failure is likely mediated through systemic rather than local actions. Full article

(This article belongs to the Section Molecular Toxicology)

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32 pages, 2463 KiB

Open AccessReview

Iron Oxide Nanoparticles for Magnetically-Guided and Magnetically-Responsive Drug Delivery

by Joan Estelrich^1,*, Elvira Escribano², Josep Queralt³ and Maria Antònia Busquets¹

¹ Departament de Fisicoquímica; Facultat de Farmàcia; Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain

² Departament de Farmàcia i Tecnologia Farmacèutica, Facultat de Farmàcia, Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain

³ Departament de Fisiologia, Facultat de Farmàcia; Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain

Int. J. Mol. Sci. 2015, 16(4), 8070-8101; https://doi.org/10.3390/ijms16048070 - 10 Apr 2015

Cited by 415 | Viewed by 21502

Abstract

In this review, we discuss the recent advances in and problems with the use of magnetically-guided and magnetically-responsive nanoparticles in drug delivery and magnetofection. In magnetically-guided nanoparticles, a constant external magnetic field is used to transport magnetic nanoparticles loaded with drugs to a [...] Read more.

In this review, we discuss the recent advances in and problems with the use of magnetically-guided and magnetically-responsive nanoparticles in drug delivery and magnetofection. In magnetically-guided nanoparticles, a constant external magnetic field is used to transport magnetic nanoparticles loaded with drugs to a specific site within the body or to increase the transfection capacity. Magnetofection is the delivery of nucleic acids under the influence of a magnetic field acting on nucleic acid vectors that are associated with magnetic nanoparticles. In magnetically-responsive nanoparticles, magnetic nanoparticles are encapsulated or embedded in a larger colloidal structure that carries a drug. In this last case, an alternating magnetic field can modify the structure of the colloid, thereby providing spatial and temporal control over drug release. Full article

(This article belongs to the Special Issue Magnetic Nanoparticles 2015)

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8 pages, 952 KiB

Open AccessArticle

Anti-Inflammatory Effect of Emodin via Attenuation of NLRP3 Inflammasome Activation

by Ji-Won Han¹, Do-Wan Shim¹, Woo-Young Shin¹, Kang-Hyuk Heo¹, Su-Bin Kwak¹, Eun-Jeong Sim¹, Jae-Hyun Jeong², Tae-Bong Kang¹ and Kwang-Ho Lee^1,*

¹ Department of Biotechnology, College of Biomedical & Health Science, Research Institute of Inflammatory Diseases, Konkuk University, Chungju 380-701, Korea

² Department of Food Science & Technology, Korea National University of Transportation, Chungju 368-701, Korea

Int. J. Mol. Sci. 2015, 16(4), 8102-8109; https://doi.org/10.3390/ijms16048102 - 10 Apr 2015

Cited by 78 | Viewed by 9127

Abstract

Emodin, an active constituent of oriental herbs, is widely used to treat allergy, inflammation, and other symptoms. This study provides the scientific basis for the anti-inflammasome effects of emodin on both in vitro and in vivo experimental models. Bone marrow-derived macrophages were used [...] Read more.

Emodin, an active constituent of oriental herbs, is widely used to treat allergy, inflammation, and other symptoms. This study provides the scientific basis for the anti-inflammasome effects of emodin on both in vitro and in vivo experimental models. Bone marrow-derived macrophages were used to study the effects of emodin on inflammasome activation by using inflammasome inducers such as ATP, nigericin, and silica crystals. The lipopolysaccharide (LPS)-induced endotoxin shock model was employed to study the effect of emodin on in vivo efficacy. Emodin treatment attenuated interleukin (IL)-1β secretion via the inhibition of NOD-like receptor family, pyrin domain containing 3 (NLRP3) inflammasome activation induced by ATP, nigericin, and silica crystals. Further, emodin ameliorated the severity of NLRP3 inflammasome-mediated symptoms in LPS-induced endotoxin mouse models. This study is the first to reveal mechanism-based evidence, especially with respect to regulation of inflammasome activation, substantiating traditional claims of emodin in the treatment of inflammation-related disorders. Full article

(This article belongs to the Special Issue Bioactive Phytochemicals and Functional Food Ingredients in Fruits and Vegetables)

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18 pages, 2427 KiB

Open AccessArticle

Sequence Features of Drosha and Dicer Cleavage Sites Affect the Complexity of IsomiRs

by Julia Starega-Roslan^†, Tomasz M. Witkos^†,‡, Paulina Galka-Marciniak and Wlodzimierz J. Krzyzosiak^*

¹ Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Str., 61-704 Poznan, Poland

^† These authors contributed equally to this work.

^‡ Present address: Faculty of Life Sciences, University of Manchester, M13 9PT Manchester, UK.

Int. J. Mol. Sci. 2015, 16(4), 8110-8127; https://doi.org/10.3390/ijms16048110 - 10 Apr 2015

Cited by 42 | Viewed by 9636

Abstract

The deep-sequencing of small RNAs has revealed that different numbers and proportions of miRNA variants called isomiRs are formed from single miRNA genes and that this effect is attributable mainly to imprecise cleavage by Drosha and Dicer. Factors that influence the degree of [...] Read more.

The deep-sequencing of small RNAs has revealed that different numbers and proportions of miRNA variants called isomiRs are formed from single miRNA genes and that this effect is attributable mainly to imprecise cleavage by Drosha and Dicer. Factors that influence the degree of cleavage precision of Drosha and Dicer are under investigation, and their identification may improve our understanding of the mechanisms by which cells modulate the regulatory potential of miRNAs. In this study, we focused on the sequences and structural determinants of Drosha and Dicer cleavage sites, which may explain the generation of homogeneous miRNAs (in which a single isomiR strongly predominates) as well as the generation of heterogeneous miRNAs. Using deep-sequencing data for small RNAs, we demonstrate that the generation of homogeneous miRNAs requires more sequence constraints at the cleavage sites than the formation of heterogeneous miRNAs. Additionally, our results indicate that specific Drosha cleavage sites have more sequence determinants in miRNA precursors than specific cleavage sites for Dicer and that secondary structural motifs in the miRNA precursors influence the precision of Dicer cleavage. Together, we present the sequence and structural features of Drosha and Dicer cleavage sites that influence the heterogeneity of the released miRNAs. Full article

(This article belongs to the Special Issue RNA Interference)

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14 pages, 1205 KiB

Open AccessArticle

Chemical Conversion Pathways and Kinetic Modeling for the OH-Initiated Reaction of Triclosan in Gas-Phase

by Xue Zhang¹, Chenxi Zhang^1,2, Xiaomin Sun^1,*, Lingyan Kang¹ and Yan Zhao^1,3

¹ Environment Research Institute, Shandong University, Jinan 250100, China

² Department of Resource and Environment, Binzhou University, Binzhou 256600, China

³ School of Life Sciences, Qufu Normal University, Qufu 273165, China

Int. J. Mol. Sci. 2015, 16(4), 8128-8141; https://doi.org/10.3390/ijms16048128 - 10 Apr 2015

Cited by 4 | Viewed by 7389

Abstract

As a widely used antimicrobial additive in daily consumption, attention has been paid to the degradation and conversion of triclosan for a long time. The quantum chemistry calculation and the canonical variational transition state theory are employed to investigate the mechanism and kinetic [...] Read more.

As a widely used antimicrobial additive in daily consumption, attention has been paid to the degradation and conversion of triclosan for a long time. The quantum chemistry calculation and the canonical variational transition state theory are employed to investigate the mechanism and kinetic property. Besides addition and abstraction, oxidation pathways and further conversion pathways are also considered. The OH radicals could degrade triclosan to phenols, aldehydes, and other easily degradable substances. The conversion mechanisms of triclosan to the polychlorinated dibenzopdioxin and furan (PCDD/Fs) and polychlorinated biphenyls (PCBs) are clearly illustrated and the toxicity would be strengthened in such pathways. Single radical and diradical pathways are compared to study the conversion mechanism of dichlorodibenzo dioxin (DCDD). Furthermore, thermochemistry is discussed in detail. Kinetic property is calculated and the consequent ratio of k_add/k_total and k_abs/k_total at 298.15 K are 0.955 and 0.045, respectively. Thus, the OH radical addition reactions are predominant, the substitute position of OH radical on triclosan is very important to generate PCDD and furan, and biradical is also a vital intermediate to produce dioxin. Full article

(This article belongs to the Special Issue Solution Chemical Kinetics)

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9 pages, 1934 KiB

Open AccessCommunication

Characterization of the Recognition Specificity of BH2, a Monoclonal Antibody Prepared against the HLA-B27 Heavy Chain

by Hui-Chun Yu^1,2,†, Kuang-Yung Huang^1,2,3,†, Ming-Chi Lu^2,3, Hsien-Lu Huang⁴, Wei-Ting Liu¹, Wen-Chien Lee⁵, Su-Qin Liu², Hsien-Bin Huang^1,* and Ning-Sheng Lai^2,3,*

¹ Department of Life Science and Institute of Molecular Biology, National Chung Cheng University, Chia-Yi 621, Taiwan

² Section of Allergy, Immunology and Rheumatology, Department of Medicine, Buddhist DaLin Tzu-Chi Hospital, Chia-Yi 622, Taiwan

³ School of Medicine, Tzu-Chi University, Hualien 970, Taiwan

⁴ Department of Nutrition and Health Science, Fooyin University, Kaohsiung 831, Taiwan

⁵ Department of Chemical Engineering, National Chung Cheng University, Chia-Yi 621, Taiwan

^† These authors contributed equally to this work.

Int. J. Mol. Sci. 2015, 16(4), 8142-8150; https://doi.org/10.3390/ijms16048142 - 13 Apr 2015

Cited by 4 | Viewed by 5525

Abstract

BH2, a monoclonal antibody prepared against the denatured human leukocytic antigen-B27 heavy chain (HLA-B27 HC), can immunoprecipitate the misfolded HLA-B27 HC complexed with Bip in the endoplasmic reticulum and recognize the homodimerized HLA-B27 HC that is often observed on the cell membrane of [...] Read more.

BH2, a monoclonal antibody prepared against the denatured human leukocytic antigen-B27 heavy chain (HLA-B27 HC), can immunoprecipitate the misfolded HLA-B27 HC complexed with Bip in the endoplasmic reticulum and recognize the homodimerized HLA-B27 HC that is often observed on the cell membrane of patients suffered from ankylosing spondylitis (AS). However, the recognition specificity of BH2 toward the other molecules of HLA-B type and toward the different types of HLA molecules remained uncharacterized. In this study, we carried out the HLA-typing by using the Luminex Technology to characterize the recognition specificity of BH2 and analyzed the binding domain of HLA-B27 HC by BH2. Our results indicated that BH2 preferably binds to molecules of HLA-B and -C rather than HLA-A and the binding site is located within the α2 domain of HLA-B27 HC. Full article

(This article belongs to the Section Biochemistry)

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17 pages, 197 KiB

Open AccessArticle

From ELF to Compressibility in Solids

by Julia Contreras-García^1,2,3,*, Miriam Marqués^1,4,5, José Manuel Menéndez^1,4 and José Manuel Recio^1,4

¹ MALTA-Consolider Team, Universidad de Oviedo, E-33006 Oviedo, Spain

² Université Pierre et Marie Curie, Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, F-75005 Paris, France

³ Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7616, Laboratoire de Chimie Théorique, F-75005 Paris, France

⁴ Departamento de Química Física y Analítica, Universidad de Oviedo, E-33006 Oviedo, Spain

⁵ Departamento de Física Teórica, Universidad de Valladolid, E-47011 Valladolid, Spain

Int. J. Mol. Sci. 2015, 16(4), 8151-8167; https://doi.org/10.3390/ijms16048151 - 13 Apr 2015

Cited by 11 | Viewed by 6325

Abstract

Understanding the electronic nature of materials’ compressibility has alwaysbeen a major issue behind tabulation and rationalization of bulk moduli. This is especiallybecause this understanding is one of the main approaches to the design and proposal of newmaterials with a desired (e.g., ultralow) compressibility. [...] Read more.

Understanding the electronic nature of materials’ compressibility has alwaysbeen a major issue behind tabulation and rationalization of bulk moduli. This is especiallybecause this understanding is one of the main approaches to the design and proposal of newmaterials with a desired (e.g., ultralow) compressibility. It is well recognized that the softestpart of the solid will be the one responsible for its compression at the first place. In chemicalterms, this means that the valence will suffer the main consequences of pressurization.It is desirable to understand this response to pressure in terms of the valence properties(charge, volume, etc.). One of the possible approaches is to consider models of electronicseparability, such as the bond charge model (BCM), which provides insight into the cohesionof covalent crystals in analogy with the classical ionic model. However, this model relies onempirical parametrization of bond and lone pair properties. In this contribution, we havecoupled electron localization function (ELF) ab initio data with the bond charge modeldeveloped by Parr in order to analyze solid state compressibility from first principles andmoreover, to derive general trends and shed light upon superhard behavior. Full article

(This article belongs to the Special Issue Chemical Bond and Bonding 2015)

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18 pages, 2843 KiB

Open AccessArticle

Quercetin Improves Postischemic Recovery of Heart Function in Doxorubicin-Treated Rats and Prevents Doxorubicin-Induced Matrix Metalloproteinase-2 Activation and Apoptosis Induction

by Monika Barteková¹, Petra Šimončíková¹, Mária Fogarassyová¹, Monika Ivanová¹, Ľudmila Okruhlicová¹, Narcisa Tribulová¹, Ima Dovinová² and Miroslav Barančík^1,*

¹ Institute for Heart Research, Slovak Academy of Sciences, Bratislava 84005, Slovakia

² Institute of Normal and Pathological Physiology, Slovak Academy of Sciences, Bratislava 84005, Slovakia

Int. J. Mol. Sci. 2015, 16(4), 8168-8185; https://doi.org/10.3390/ijms16048168 - 13 Apr 2015

Cited by 69 | Viewed by 6945

Abstract

Quercetin (QCT) is flavonoid that possesses various biological functions including anti-oxidative and radical-scavenging activities. Moreover, QCT exerts some preventive actions in treatment of cardiovascular diseases. The aim of present study was to explore effects of prolonged administration of QCT on changes induced by [...] Read more.

Quercetin (QCT) is flavonoid that possesses various biological functions including anti-oxidative and radical-scavenging activities. Moreover, QCT exerts some preventive actions in treatment of cardiovascular diseases. The aim of present study was to explore effects of prolonged administration of QCT on changes induced by repeated application of doxorubicin (DOX) in rat hearts. We focused on the ultrastructure of myocardium, matrix metalloproteinases (MMPs), biometric parameters, and apoptosis induction. Our aim was also to examine effects of QCT on ischemic tolerance in hearts exposed to chronic effects of DOX, and to determine possible mechanisms underlying effects of QCT. Our results showed that QCT prevented several negative chronic effects of DOX: (I) reversed DOX-induced blood pressure increase; (II) mediated improvement of deleterious effects of DOX on ultrastructure of left ventricle; (III) prevented DOX-induced effects on tissue MMP-2 activation; and (iv) reversed effects of DOX on apoptosis induction and superoxide dismutase inhibition. Moreover, we showed that rat hearts exposed to effects of QCT were more resistant to ischemia/reperfusion injury. Effects of QCT on modulation of ischemic tolerance were linked to Akt kinase activation and connexin-43 up-regulation. Taken together, these results demonstrate that prolonged treatment with QCT prevented negative chronic effects of DOX on blood pressure, cellular damage, MMP-2 activation, and apoptosis induction. Moreover, QCT influenced myocardial responses to acute ischemic stress. These facts bring new insights into mechanisms of QCT action on rat hearts exposed to the chronic effects of DOX. Full article

(This article belongs to the Section Biochemistry)

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15 pages, 1070 KiB

Open AccessArticle

Surface Modification of ZnO Nanorods with Hamilton Receptors

by Lukas Zeininger¹, Martin Klaumünzer², Wolfgang Peukert² and Andreas Hirsch^1,*

¹ Institute of Organic Chemistry, Friedrich-Alexander Universität Erlangen-Nürnberg, Henkestrasse 42, 91054 Erlangen, Germany

² Institute of Particle Technology, Friedrich-Alexander Universität Erlangen-Nürnberg, Cauerstrasse 4, 91058 Erlangen, Germany

Int. J. Mol. Sci. 2015, 16(4), 8186-8200; https://doi.org/10.3390/ijms16048186 - 13 Apr 2015

Cited by 7 | Viewed by 7195

Abstract

A new prototype of a Hamilton receptor suitable for the functionalization of inorganic nanoparticles was synthesized and characterized. The hydrogen bonding receptor was coupled to a catechol moiety, which served as anchor group for the functionalization of metal oxides, in particular zinc oxide. [...] Read more.

A new prototype of a Hamilton receptor suitable for the functionalization of inorganic nanoparticles was synthesized and characterized. The hydrogen bonding receptor was coupled to a catechol moiety, which served as anchor group for the functionalization of metal oxides, in particular zinc oxide. Synthesized zinc oxide nanorods [ZnO] were used for surface functionalization. The wet-chemical functionalization procedure towards monolayer-grafted particles [ZnO-HR] is described and a detailed characterization study is presented. In addition, the detection of specific cyanurate molecules is demonstrated. The hybrid structures [ZnO-HR-CA] were stable towards agglomeration and exhibited enhanced dispersability in apolar solvents. This observation, in combination with several spectroscopic experiments gave evidence of the highly directional supramolecular recognition at the surface of nanoparticles. Full article

(This article belongs to the Special Issue Supramolecular Interactions)

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12 pages, 757 KiB

Open AccessArticle

Mutation Breeding of Extracellular Polysaccharide-Producing Microalga Crypthecodinium cohnii by a Novel Mutagenesis with Atmospheric and Room Temperature Plasma

by Bin Liu^1,2

, Zheng Sun^2,3,†

, Xiaonian Ma^2,†, Bo Yang^1,2, Yue Jiang⁴, Dong Wei¹

and Feng Chen^2,5,*

¹ School of Light Industry and Food Sciences, South China University of Technology, Guangzhou 510641, China

² Institute for Food and Bioresource Engineering, College of Engineering, Peking University, Beijing 100871, China

³ College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China

⁴ School of Food Science, Jiangnan University, Wuxi 214122, China

⁵ Singapore-Peking University Research Centre for a Sustainable Low-Carbon Future, CREATE Tower 138602, Singapore

^† These authors contributed equally to this work.

Int. J. Mol. Sci. 2015, 16(4), 8201-8212; https://doi.org/10.3390/ijms16048201 - 13 Apr 2015

Cited by 50 | Viewed by 8177

Abstract

Extracellular polysaccharides (EPS) produced by marine microalgae have the potential to be used as antioxidants, antiviral agents, immunomodulators, and anti-inflammatory agents. Although the marine microalga Crypthecodinium cohnii releases EPS during the process of docosahexaenoic acid (DHA) production, the yield of EPS remains relatively [...] Read more.

Extracellular polysaccharides (EPS) produced by marine microalgae have the potential to be used as antioxidants, antiviral agents, immunomodulators, and anti-inflammatory agents. Although the marine microalga Crypthecodinium cohnii releases EPS during the process of docosahexaenoic acid (DHA) production, the yield of EPS remains relatively low. To improve the EPS production, a novel mutagenesis of C. cohnii was conducted by atmospheric and room temperature plasma (ARTP). Of the 12 mutants obtained, 10 mutants exhibited significantly enhanced EPS yield on biomass as compared with the wild type strain. Among them, mutant M7 was the best as it could produce an EPS volumetric yield of 1.02 g/L, EPS yield on biomass of 0.39 g/g and EPS yield on glucose of 94 mg/g, which were 33.85%, 85.35% and 57.17% higher than that of the wild type strain, respectively. Results of the present study indicated that mutagenesis of the marine microalga C. cohnii by ARTP was highly effective leading to the high-yield production of EPS. Full article

(This article belongs to the Special Issue Microalgal Biotechnology)

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14 pages, 1339 KiB

Open AccessArticle

High Insulin Levels in KK-Ay Diabetic Mice Cause Increased Cortical Bone Mass and Impaired Trabecular Micro-Structure

by Cen Fu¹, Xiaolin Zhang², Fei Ye^2,* and Jianhong Yang^1,*

¹ College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China

² Beijing Key Laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, Institute of MateriaMedica, Chinese Academy of Medical Sciences, Beijing 100050, China

Int. J. Mol. Sci. 2015, 16(4), 8213-8226; https://doi.org/10.3390/ijms16048213 - 13 Apr 2015

Cited by 25 | Viewed by 7333

Abstract

Type 2 diabetes mellitus (T2DM) is a chronic disease characterized by hyperglycemia, hyperinsulinemia and complications, including obesity and osteoporosis. Rodents have been widely used to model human T2DM and investigate its effect on the skeleton. We aimed to investigate skeletal alterations in Yellow [...] Read more.

Type 2 diabetes mellitus (T2DM) is a chronic disease characterized by hyperglycemia, hyperinsulinemia and complications, including obesity and osteoporosis. Rodents have been widely used to model human T2DM and investigate its effect on the skeleton. We aimed to investigate skeletal alterations in Yellow Kuo Kondo (KK-Ay) diabetic mice displaying high insulin and glucose levels. Bone mineral density (BMD), micro-architecture and bone metabolism-related genes were analyzed. The total femoral areal BMD (aBMD), cortical volumetric BMD (vBMD) and thickness were significantly increased in KK-Ay mice, while the trabecular vBMD and mineralized bone volume/tissue volume (BV/TV), trabecular thickness and number were decreased compared to C57BL mice. The expression of both osteoblast-related genes, such as osteocalcin (OC), bone sialoprotein, Type I Collagen, osteonectin, RUNX2 and OSX, and osteoclast-related genes, such as TRAP and TCIRG, were up-regulated in KK-Ay mice. Correlation analyses showed that serum insulin levels were positively associated with aBMD, cortical vBMD and thickness and negatively associated with trabecular vBMD and micro-architecture. In addition, serum insulin levels were positively related to osteoblast-related and osteoclast-related gene expression. Our data suggest that high insulin levels in KK-Ay diabetic mice may increase cortical bone mass and impair trabecular micro-structure by up-regulating osteoblast-and osteoclast-related gene expression. Full article

(This article belongs to the Section Biochemistry)

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27 pages, 865 KiB

Open AccessReview

MicroRNAs Regulate Bone Development and Regeneration

by Sijie Fang, Yuan Deng, Ping Gu and Xianqun Fan^*

Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200011, China

Int. J. Mol. Sci. 2015, 16(4), 8227-8253; https://doi.org/10.3390/ijms16048227 - 13 Apr 2015

Cited by 98 | Viewed by 9099

Abstract

MicroRNAs (miRNAs) are endogenous small noncoding ~22-nt RNAs, which have been reported to play a crucial role in maintaining bone development and metabolism. Osteogenesis originates from mesenchymal stem cells (MSCs) differentiating into mature osteoblasts and each period of bone formation is inseparable from [...] Read more.

MicroRNAs (miRNAs) are endogenous small noncoding ~22-nt RNAs, which have been reported to play a crucial role in maintaining bone development and metabolism. Osteogenesis originates from mesenchymal stem cells (MSCs) differentiating into mature osteoblasts and each period of bone formation is inseparable from the delicate regulation of various miRNAs. Of note, apprehending the sophisticated circuit between miRNAs and osteogenic homeostasis is of great value for artificial skeletal regeneration for severe bone defects. In this review, we highlight how different miRNAs interact with diverse osteo-related genes and endeavor to sketch the contours of potential manipulations of miRNA-modulated bone repair. Full article

(This article belongs to the Special Issue Artificial Organs)

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12 pages, 1857 KiB

Open AccessArticle

Revisiting the Formation and Tunable Dissociation of a [2]Pseudorotaxane Formed by Slippage Approach

by Ken Cham-Fai Leung^1,2,*

, Kwun-Ngai Lau³ and Wing-Yan Wong³

¹ Department of Chemistry and Institute of Creativity, The Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong, China

² Institute of Molecular Functional Materials, University Grants Committee, Hong Kong, China

³ Department of Chemistry, The Chinese University of Hong Kong, Shatin, NT, Hong Kong, China

Int. J. Mol. Sci. 2015, 16(4), 8254-8265; https://doi.org/10.3390/ijms16048254 - 13 Apr 2015

Cited by 3 | Viewed by 6491

Abstract

A new [2]pseudorotaxane DB24C8É1-H·PF₆ with dibenzo[24]crown-8 (DB24C8) crown ether-dibenzylammonium (1-H·PF₆) binding which was formed by slippage approach at different solvents and temperature, had been isolated and characterized by NMR spectroscopy and mass spectrometry. [...] Read more.

A new [2]pseudorotaxane DB24C8É1-H·PF₆ with dibenzo[24]crown-8 (DB24C8) crown ether-dibenzylammonium (1-H·PF₆) binding which was formed by slippage approach at different solvents and temperature, had been isolated and characterized by NMR spectroscopy and mass spectrometry. The [2]pseudorotaxane DB24C8É1-H·PF₆ was stable at room temperature. The dissociation rate of [2]pseudorotaxane DB24C8É1-H·PF₆ could be tuned by using different stimuli such as triethylamine (TEA)/diisopropylethylamine (DIPEA) and dimethyl sulfoxide (DMSO). In particular, the dissociation of [2]pseudorotaxane DB24C8É1-H·PF₆ by an excess of TEA/DIPEA base mixture possessed a long and sustained, complete dissociation over 60 days. Other stimuli by DMSO possessed a relatively fast dissociation over 24 h. Full article

(This article belongs to the Special Issue Supramolecular Interactions)

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28 pages, 3012 KiB

Open AccessReview

Biohydrogen Production: Strategies to Improve Process Efficiency through Microbial Routes

by Kuppam Chandrasekhar^†, Yong-Jik Lee^† and Dong-Woo Lee^*

¹ School of Applied Biosciences, Kyungpook National University, Daegu 702-701, Korea

^† These authors contributed equally to this work.

Int. J. Mol. Sci. 2015, 16(4), 8266-8293; https://doi.org/10.3390/ijms16048266 - 14 Apr 2015

Cited by 338 | Viewed by 29719

Abstract

The current fossil fuel-based generation of energy has led to large-scale industrial development. However, the reliance on fossil fuels leads to the significant depletion of natural resources of buried combustible geologic deposits and to negative effects on the global climate with emissions of [...] Read more.

The current fossil fuel-based generation of energy has led to large-scale industrial development. However, the reliance on fossil fuels leads to the significant depletion of natural resources of buried combustible geologic deposits and to negative effects on the global climate with emissions of greenhouse gases. Accordingly, enormous efforts are directed to transition from fossil fuels to nonpolluting and renewable energy sources. One potential alternative is biohydrogen (H₂), a clean energy carrier with high-energy yields; upon the combustion of H₂, H₂O is the only major by-product. In recent decades, the attractive and renewable characteristics of H₂ led us to develop a variety of biological routes for the production of H₂. Based on the mode of H₂ generation, the biological routes for H₂ production are categorized into four groups: photobiological fermentation, anaerobic fermentation, enzymatic and microbial electrolysis, and a combination of these processes. Thus, this review primarily focuses on the evaluation of the biological routes for the production of H₂. In particular, we assess the efficiency and feasibility of these bioprocesses with respect to the factors that affect operations, and we delineate the limitations. Additionally, alternative options such as bioaugmentation, multiple process integration, and microbial electrolysis to improve process efficiency are discussed to address industrial-level applications. Full article

(This article belongs to the Special Issue Photosynthesis and Biological Hydrogen Production)

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16 pages, 1195 KiB

Open AccessArticle

Area-Specific Cell Stimulation via Surface-Mediated Gene Transfer Using Apatite-Based Composite Layers

by Yushin Yazaki^1,2, Ayako Oyane^2,*, Yu Sogo³, Atsuo Ito³, Atsushi Yamazaki¹ and Hideo Tsurushima^2,4

¹ Department of Resources and Environmental Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan

² Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology, Central 4, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan

³ Health Research Institute, National Institute of Advanced Industrial Science and Technology, Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan

⁴ Department of Neurosurgery, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8575, Japan

Int. J. Mol. Sci. 2015, 16(4), 8294-8309; https://doi.org/10.3390/ijms16048294 - 14 Apr 2015

Cited by 3 | Viewed by 8377

Abstract

Surface-mediated gene transfer systems using biocompatible calcium phosphate (CaP)-based composite layers have attracted attention as a tool for controlling cell behaviors. In the present study we aimed to demonstrate the potential of CaP-based composite layers to mediate area-specific dual gene transfer and to [...] Read more.

Surface-mediated gene transfer systems using biocompatible calcium phosphate (CaP)-based composite layers have attracted attention as a tool for controlling cell behaviors. In the present study we aimed to demonstrate the potential of CaP-based composite layers to mediate area-specific dual gene transfer and to stimulate cells on an area-by-area basis in the same well. For this purpose we prepared two pairs of DNA–fibronectin–apatite composite (DF-Ap) layers using a pair of reporter genes and pair of differentiation factor genes. The results of the area-specific dual gene transfer successfully demonstrated that the cells cultured on a pair of DF-Ap layers that were adjacently placed in the same well showed specific gene expression patterns depending on the gene that was immobilized in theunderlying layer. Moreover, preliminary real-time PCR results indicated that multipotential C3H10T1/2 cells may have a potential to change into different types of cells depending on the differentiation factor gene that was immobilized in the underlying layer, even in the same well. Because DF-Ap layers have a potential to mediate area-specific cell stimulation on their surfaces, they could be useful in tissue engineering applications. Full article

(This article belongs to the Special Issue Biomaterials for Tissue Engineering)

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14 pages, 1410 KiB

Open AccessArticle

Selection of Reference Genes for MicroRNA Quantitative Expression Analysis in Chinese Perch, Siniperca chuatsi

by Xin Zhu^1,2, Yu-Long Li¹, Dun-Xue Chen¹, Ping Wu¹, Tan Yi^1,2, Tao Chen², Jian-She Zhang^1,3,* and Wu-Ying Chu^1,3,*

¹ Department of Bioengineering and Environmental Science, Changsha University, Changsha 410003, China

² College of Veterinary Medicine, Hunan Agriculture University, Changsha 410128, China

³ Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Changde 415000, China

Int. J. Mol. Sci. 2015, 16(4), 8310-8323; https://doi.org/10.3390/ijms16048310 - 14 Apr 2015

Cited by 24 | Viewed by 5529

Abstract

Real-time quantitative reverse transcription PCR (RT-qPCR) is one of the most effective and sensitive techniques in gene expression assay, for which selection of reference genes is a prerequisite. In teleost species, such as Chinese perch, the expression profiling of miRNAs as reference genes [...] Read more.

Real-time quantitative reverse transcription PCR (RT-qPCR) is one of the most effective and sensitive techniques in gene expression assay, for which selection of reference genes is a prerequisite. In teleost species, such as Chinese perch, the expression profiling of miRNAs as reference genes for RT-qPCR has not been intensively studied. In the present study, the expression profiles of six miRNAs (miR-101a, miR-146a, miR-22a, miR-23a, miR-26a and let-7a) and one small nuclear RNA (U6) were assayed with RT-qPCR in different adult tissues, developmental stages and growth conditions of Chinese perch, Siniperca chuatsi. The analyses revealed that embryonic developmental stage is an important variability factor in the expression stability of miRNAs. All six miRNAs exhibited better expression consistency than U6 in most of the conditions examined, and therefore, they may be more suitable as a reference gene for miRNA quantification. When different tissues and developmental stages were considered, miR-22a demonstrated the most consistent expression pattern, and the best combination of reference genes was miR-22a and miR-23a. Our study offers useful data for selecting miRNAs as reference genes for RT-qPCR analysis of miRNAs in teleost fishes under different conditions. Full article

(This article belongs to the Section Biochemistry)

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13 pages, 7672 KiB

Open AccessArticle

Molecular Characterization of Sec2 Loci in Wheat—Secale africanum Derivatives Demonstrates Genomic Divergence of Secale Species

by Guangrong Li, Hongjun Zhang, Li Zhou, Dan Gao, Mengping Lei, Jie Zhang and Zujun Yang^*

School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China

Int. J. Mol. Sci. 2015, 16(4), 8324-8336; https://doi.org/10.3390/ijms16048324 - 14 Apr 2015

Cited by 4 | Viewed by 5336

Abstract

The unique 75 K γ-secalins encoded by Sec2 loci in Secale species is composed of almost half rye storage proteins. The chromosomal location of Sec2 loci in wild Secale species, Secale africanum, was carried out by the wheat—S. africanum derivatives, [...] Read more.

The unique 75 K γ-secalins encoded by Sec2 loci in Secale species is composed of almost half rye storage proteins. The chromosomal location of Sec2 loci in wild Secale species, Secale africanum, was carried out by the wheat—S. africanum derivatives, which were identified by genomic in situ hybridization and multi-color fluorescence in situ hybridization. The Sec2 gene-specific PCR analysis indicated that the S. cereale Sec2 was located on chromosome 2R, while the S. africanum Sec2 was localized on chromosome 6R^afr of S. africanum. A total of 38 Sec2 gene sequences were isolated from S. africanum, S. cereale and S. sylvestre by PCR-based cloning. Phylogenetic analysis showed that S. africanum Sec2 diverged from S. cereale Sec2 approximately 2–3 million years ago. The illegitimate recombination of chromosome 2R–6R involving the Sec2 loci region may accelerate sequence variation during evolutionary process from wild to cultivated Secale species. Full article

(This article belongs to the Special Issue Plant Molecular Biology)

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14 pages, 3573 KiB

Open AccessArticle

Using a Novel MicroRNA Delivery System to Inhibit Osteoclastogenesis

by Yanlan Yao^1,2,†, Tingting Jia^1,2,†, Yang Pan³, Hongna Gou^1,2, Yulong Li^1,2, Yu Sun¹, Rui Zhang¹, Kuo Zhang^1,2, Guigao Lin¹, Jiehong Xie¹, Jinming Li^1,2,* and Lunan Wang^1,2,*

¹ National Center for Clinical Laboratories, Beijing Hospital, No. 1 Dahua Road, Dongdan, Beijing 100730, China

² Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 9 Santiao, Dongdan, Beijing 100730, China

³ Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control (CDC), Beijing 100013, China

^† These authors contributed equally to this work.

Int. J. Mol. Sci. 2015, 16(4), 8337-8350; https://doi.org/10.3390/ijms16048337 - 14 Apr 2015

Cited by 35 | Viewed by 6270

Abstract

Previously, we developed a novel microRNA (miRNA) delivery system based on bacteriophage MS2 virus-like particles (MS2 VLPs). In this current study, we used this system to transport miR-146a into human peripheral blood mononuclear cells (PBMCs), and demonstrated the inhibition of osteoclastogenesis in precursors. [...] Read more.

Previously, we developed a novel microRNA (miRNA) delivery system based on bacteriophage MS2 virus-like particles (MS2 VLPs). In this current study, we used this system to transport miR-146a into human peripheral blood mononuclear cells (PBMCs), and demonstrated the inhibition of osteoclastogenesis in precursors. Two cytokines, receptor activator of NF-κB ligand (RANKL), and macrophage-colony stimulating factor (M-CSF) were used to induce osteoclastogenesis. MS2 VLPs were transfected into PBMCs. qRT-PCR was applied to measure expression levels of miR-146a and osteoclast (OC)-specific genes. Western blot (WB) was conducted to evaluate miR-146a downstream target proteins: epidermal growth factor receptor (EGFR) and tumor necrosis factor (TNF) receptor-associated factor 6 (TRAF6). The formation and activity of OCs were assessed by cytochemical staining and bone resorption assay, respectively. In PBMCs treated with MS2-miR146a VLPs, qRT-PCR assays showed increased expression of miR-146a (p < 0.01) and decreased expression of all four OC-specific genes (p < 0.05). WB results indicated decreased expression of EGFR (p < 0.01) and TRAF6 (p < 0.05). The number of OCs decreased markedly and bone resorption assay demonstrated inhibited activity. This miR-146a delivery system could be applied to induce overexpression of miR-146a and to inhibit the differentiation and function of OCs. Full article

(This article belongs to the Section Biochemistry)

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13 pages, 720 KiB

Open AccessArticle

Determination of Oxidized Phosphatidylcholines by Hydrophilic Interaction Liquid Chromatography Coupled to Fourier Transform Mass Spectrometry

by Pia Sala^1,2,†, Sandra Pötz^1,2,†, Martina Brunner¹, Martin Trötzmüller¹, Alexander Fauland^1,2, Alexander Triebl¹, Jürgen Hartler^3,4, Ernst Lankmayr² and Harald C. Köfeler^1,4,*

¹ Core Facility for Mass Spectrometry, Medical University of Graz, Stiftingtalstrasse 24, Graz 8010, Austria

² Institute of Analytical Chemistry and Food Chemistry, Graz University of Technology, Stremayrgasse 9/II, Graz 8010, Austria

³ Bioinformatics Group, Institute for Knowledge Discovery, Graz University of Technology, Petersgasse 14, Graz 8010, Austria

⁴ Omics Center Graz, Stiftingtalstrasse 24, Graz 8010, Austria

^† These authors contributed equally to this work.

Int. J. Mol. Sci. 2015, 16(4), 8351-8363; https://doi.org/10.3390/ijms16048351 - 14 Apr 2015

Cited by 20 | Viewed by 6520

Abstract

A novel liquid chromatography-mass spectrometry (LC-MS) approach for analysis of oxidized phosphatidylcholines by an Orbitrap Fourier Transform mass spectrometer in positive electrospray ionization (ESI) coupled to hydrophilic interaction liquid chromatography (HILIC) was developed. This method depends on three selectivity criteria for separation and [...] Read more.

A novel liquid chromatography-mass spectrometry (LC-MS) approach for analysis of oxidized phosphatidylcholines by an Orbitrap Fourier Transform mass spectrometer in positive electrospray ionization (ESI) coupled to hydrophilic interaction liquid chromatography (HILIC) was developed. This method depends on three selectivity criteria for separation and identification: retention time, exact mass at a resolution of 100,000 and collision induced dissociation (CID) fragment spectra in a linear ion trap. The process of chromatography development showed the best separation properties with a silica-based Kinetex column. This type of chromatography was able to separate all major lipid classes expected in mammalian samples, yielding increased sensitivity of oxidized phosphatidylcholines over reversed phase chromatography. Identification of molecular species was achieved by exact mass on intact molecular ions and CID tandem mass spectra containing characteristic fragments. Due to a lack of commercially available standards, method development was performed with copper induced oxidation products of palmitoyl-arachidonoyl-phosphatidylcholine, which resulted in a plethora of lipid species oxidized at the arachidonoyl moiety. Validation of the method was done with copper oxidized human low-density lipoprotein (LDL) prepared by ultracentrifugation. In these LDL samples we could identify 46 oxidized molecular phosphatidylcholine species out of 99 possible candidates. Full article

(This article belongs to the Special Issue Fourier Transform Mass Spectrometry in Molecular Sciences)

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18 pages, 3715 KiB

Open AccessArticle

Identification and Immune Functional Characterization of Pigeon TLR7

by Dan Xiong^1,2,†, Li Song^1,2,†, Zhiming Pan^1,2,*, Xiang Chen^1,2, Shizhong Geng^1,2 and Xinan Jiao^1,2,*

¹ Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China

² Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China

^† These authors contributed equally to this work.

Int. J. Mol. Sci. 2015, 16(4), 8364-8381; https://doi.org/10.3390/ijms16048364 - 14 Apr 2015

Cited by 10 | Viewed by 6367

Abstract

Toll-like receptor 7 (TLR7) is activated by single-stranded RNA and synthetic imidazoquinoline components, and induces interferon production. In this study, we cloned the TLR7 gene from King pigeon (Columba livia). The TLR7 open reading frame is 3144 bp and encodes a [...] Read more.

Toll-like receptor 7 (TLR7) is activated by single-stranded RNA and synthetic imidazoquinoline components, and induces interferon production. In this study, we cloned the TLR7 gene from King pigeon (Columba livia). The TLR7 open reading frame is 3144 bp and encodes a 1047-amino acid protein, consisting of a canonical TLR composition with 15 leucine-rich repeats (LRRs). Amino acid-inserting modifications were found at position 15 of LRR2, LRR11, LRR13, and LRR14 and position 10 of LRR10. The tissue distribution of pigeon TLR7 suggests that immune-associated tissues, especially the spleen and liver, have high TLR7 expression. HEK293T cells transfected with pigeon TLR7 plasmid responded to the agonist R848, indicating a functional TLR7 homolog. Following R848 stimulation of pigeon peripheral blood mononuclear cells, the levels of IFN-γ, IL-6, IL-8, CCL5, and IL-10 mRNA, assessed using quantitative real-time PCR, were significantly up-regulated. After Newcastle disease virus vaccine strain LaSota inoculation and agonist R848 injection, the level of TLR7 mRNA in the spleen of pigeons increased significantly in the R848-injected group, but decreased in the LaSota-inoculated group at three day post-infection (d.p.i.). The mRNA levels of inflammatory cytokines and chemokines were significantly upregulated in both LaSota-inoculated and R848-injected groups. Triggering pigeon TLR7 leads to robust up-regulation of inflammatory cytokines and chemokines, suggesting an important role in the innate immune response. Full article

(This article belongs to the Section Biochemistry)

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15 pages, 1307 KiB

Open AccessArticle

Production and Evaluation of Virus-Like Particles Displaying Immunogenic Epitopes of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV)

by Ambika Mosale Venkatesh Murthy¹, Yanyan Ni², Xiangjin Meng² and Chenming Zhang^1,*

¹ Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, USA

² Center for Molecular Medicine and Infectious Disease, Department of Biomedical Sciences & Pathobiology, College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24060, USA

Int. J. Mol. Sci. 2015, 16(4), 8382-8396; https://doi.org/10.3390/ijms16048382 - 14 Apr 2015

Cited by 17 | Viewed by 7644

Abstract

Porcine reproductive and respiratory syndrome (PRRS) is the most significant infectious disease currently affecting the swine industry worldwide. Several inactivated and modified live vaccines (MLV) have been developed to curb PRRSV infections. However, the efficacy and safety of these vaccines are unsatisfactory, and [...] Read more.

Porcine reproductive and respiratory syndrome (PRRS) is the most significant infectious disease currently affecting the swine industry worldwide. Several inactivated and modified live vaccines (MLV) have been developed to curb PRRSV infections. However, the efficacy and safety of these vaccines are unsatisfactory, and hence, there is a strong demand for the development of new PRRS universal vaccines. Virus-like particle (VLP)-based vaccines are gaining increasing acceptance compared to subunit vaccines, as they present the antigens in a more veritable conformation and are readily recognized by the immune system. Hepatitis B virus core antigen (HBcAg) has been successfully used as a carrier for more than 100 viral sequences. In this study, hybrid HBcAg VLPs were generated by fusion of the conserved protective epitopes of PRRSV and expressed in E. coli. An optimized purification protocol was developed to obtain hybrid HBcAg VLP protein from the inclusion bodies. This hybrid HBcAg VLP protein self-assembled to 23-nm VLPs that were shown to block virus infection of susceptible cells when tested on MARC 145 cells. Together with the safety of non-infectious and non-replicable VLPs and the low cost of production through E. coli fermentation, this hybrid VLP could be a promising vaccine candidate for PRRS. Full article

(This article belongs to the Special Issue Protein Engineering)

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18 pages, 911 KiB

Open AccessArticle

Transcriptional Responses of Glutathione Transferase Genes in Ruditapes philippinarum Exposed to Microcystin-LR

by Bruno Reis¹, Mariana Carneiro¹, João Machado¹, Joana Azevedo¹, Vitor Vasconcelos^1,2

and José Carlos Martins^1,*

¹ CIIMAR/CIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal

² Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4069-007 Porto, Portugal

Int. J. Mol. Sci. 2015, 16(4), 8397-8414; https://doi.org/10.3390/ijms16048397 - 15 Apr 2015

Cited by 10 | Viewed by 5086

Abstract

Glutathione Transferases (GSTs) are phase II detoxification enzymes known to be involved in the molecular response against microcystins (MCs) induced toxicity. However, the individual role of the several GST isoforms in the MC detoxification process is still unknown. In this study, the time-dependent [...] Read more.

Glutathione Transferases (GSTs) are phase II detoxification enzymes known to be involved in the molecular response against microcystins (MCs) induced toxicity. However, the individual role of the several GST isoforms in the MC detoxification process is still unknown. In this study, the time-dependent changes on gene expression of several GST isoforms (pi, mu, sigma 1, sigma 2) in parallel with enzymatic activity of total GST were investigated in gills and hepatopancreas of the bivalve Ruditapes philippinarum exposed to pure MC-LR (10 and 100 µg/L). No significant changes in GST enzyme activities were found on both organs. In contrast, MC-LR affected the transcriptional activities of these detoxification enzymes both in gills and hepatopancreas. GST transcriptional changes in gills promoted by MC-LR were characterized by an early (12 h) induction of mu and sigma 1 transcripts. On the other hand, the GST transcriptional changes in hepatopancreas were characterized by a later induction (48 h) of mu transcript, but also by an early inhibition (6 h) of the four transcripts. The different transcription patterns obtained for the tested GST isoforms in this study highlight the potential divergent physiological roles played by these isoenzymes during the detoxification of MC-LR. Full article

(This article belongs to the Section Molecular Toxicology)

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15 pages, 4011 KiB

Open AccessArticle

Autophagy Induction by Silibinin Positively Contributes to Its Anti-Metastatic Capacity via AMPK/mTOR Pathway in Renal Cell Carcinoma

by Feng Li^1,†, Zhenkun Ma^1,†, Zhenfeng Guan¹, Yule Chen¹, Kaijie Wu¹, Peng Guo¹, Xinyang Wang², Dalin He^1,2,* and Jin Zeng^1,*

¹ Department of Urology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China

² Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China, Xi'an 710061, China

^† These authors contributed equally to this work.

Int. J. Mol. Sci. 2015, 16(4), 8415-8429; https://doi.org/10.3390/ijms16048415 - 15 Apr 2015

Cited by 55 | Viewed by 8381

Abstract

Silibinin, a dietary cancer chemopreventive flavonoid from the seeds of milk thistle, has been reported to exhibit anti-metastatic effects on renal cell carcinoma (RCC), but the mechanism underlying this phenomenon is not fully understood. The present study aimed at examining the potential role [...] Read more.

Silibinin, a dietary cancer chemopreventive flavonoid from the seeds of milk thistle, has been reported to exhibit anti-metastatic effects on renal cell carcinoma (RCC), but the mechanism underlying this phenomenon is not fully understood. The present study aimed at examining the potential role of autophagy in regulating silibinin-induced anti-metastatic effects on RCC cells. Using RCC ACHN and 786-O cells as a model system in vitro, we found that silibinin treatment increased the expression of LC3-II, resulted in the formation of autophagolysosome vacuoles, and caused a punctate fluorescence pattern with the monomeric red fluorescence protein-enhanced green fluorescence protein-LC3 (mRFP-EGFP-LC3) protein, which all are markers for cellular autophagy. Autophagy flux was induced by silibinin in RCC cells, as determined by LC3 turnover assay. Mechanically, the adenosine 5'-monophosphate activated protein kinase (AMPK)/mammalian target of rapamycin (mTOR) pathway was identified as involved in regulation of silibinin-induced autophagy. Furthermore, autophagy induction was demonstrated to positively contribute to silibinin-induced anti-metastatic effects on RCC cells in vitro. Activation of autophagy enhanced silibinin-induced inhibition of migration and invasion of RCC cells, while inhibition of autophagy attenuated it. These findings thus provide new information about the potential link between autophagy and metastasis inhibition induced by silibinin, and the induction of autophagy may shed some light into future treatment strategies for metastatic RCC. Full article

(This article belongs to the Special Issue Bioactive Phytochemicals in Functional Foods for Cancer Prevention)

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24 pages, 2460 KiB

Open AccessArticle

Alternative Bio-Based Solvents for Extraction of Fat and Oils: Solubility Prediction, Global Yield, Extraction Kinetics, Chemical Composition and Cost of Manufacturing

by Anne-Gaëlle Sicaire¹, Maryline Vian^1,*, Frédéric Fine², Florent Joffre³, Patrick Carré⁴, Sylvain Tostain⁵ and Farid Chemat¹

¹ GREEN (Groupe de Recherche en Eco-Extraction de Produits Naturels), Université d'Avignon et des Pays de Vaucluse, INRA, UMR 408, 84000 Avignon, France

² CETIOM (Centre Technique Interprofessionnel des Oléagineux et du Chanvre industriel), 11 rue Monge, 33600 Pessac, France

³ ITERG (Institut des Corps Gras), 11 rue Monge, 33600 Pessac, France

⁴ CREOL (Centre de Recherche et d'Expérimentation sur les oléagineux), 11 rue Monge, 33600 Pessac, France

⁵ SAIPOL (Société Agro Industrielle de Patrimoine Oléagineux), Boulevard Maritime, 76530 Grand-Couronne, France

Int. J. Mol. Sci. 2015, 16(4), 8430-8453; https://doi.org/10.3390/ijms16048430 - 15 Apr 2015

Cited by 152 | Viewed by 15649

Abstract

The present study was designed to evaluate the performance of alternative bio-based solvents, more especially 2-methyltetrahydrofuran, obtained from crop’s byproducts for the substitution of petroleum solvents such as hexane in the extraction of fat and oils for food (edible oil) and non-food (bio [...] Read more.

The present study was designed to evaluate the performance of alternative bio-based solvents, more especially 2-methyltetrahydrofuran, obtained from crop’s byproducts for the substitution of petroleum solvents such as hexane in the extraction of fat and oils for food (edible oil) and non-food (bio fuel) applications. First a solvent selection as well as an evaluation of the performance was made with Hansen Solubility Parameters and the COnductor-like Screening MOdel for Realistic Solvation (COSMO-RS) simulations. Experiments were performed on rapeseed oil extraction at laboratory and pilot plant scale for the determination of lipid yields, extraction kinetics, diffusion modeling, and complete lipid composition in term of fatty acids and micronutrients (sterols, tocopherols and tocotrienols). Finally, economic and energetic evaluations of the process were conducted to estimate the cost of manufacturing using 2-methyltetrahydrofuran (MeTHF) as alternative solvent compared to hexane as petroleum solvent. Full article

(This article belongs to the Special Issue Green Chemistry and the Biorefinery)

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36 pages, 3078 KiB

Open AccessReview

Changes of Water Hydrogen Bond Network with Different Externalities

by Lin Zhao^1,2,*, Kai Ma^1,† and Zi Yang^2,†

¹ School of Environmental Science and Engineering, Tianjin University, No. 92 Weijin Road, Tianjin 300072, China

² School of Chemical Engineering and Technology, Tianjin University, No. 92 Weijin Road, Tianjin 300072, China

^† These authors contributed equally to this work.

Int. J. Mol. Sci. 2015, 16(4), 8454-8489; https://doi.org/10.3390/ijms16048454 - 15 Apr 2015

Cited by 79 | Viewed by 13111

Abstract

It is crucial to uncover the mystery of water cluster and structural motif to have an insight into the abundant anomalies bound to water. In this context, the analysis of influence factors is an alternative way to shed light on the nature of [...] Read more.

It is crucial to uncover the mystery of water cluster and structural motif to have an insight into the abundant anomalies bound to water. In this context, the analysis of influence factors is an alternative way to shed light on the nature of water clusters. Water structure has been tentatively explained within different frameworks of structural models. Based on comprehensive analysis and summary of the studies on the response of water to four externalities (i.e., temperature, pressure, solutes and external fields), the changing trends of water structure and a deduced intrinsic structural motif are put forward in this work. The variations in physicochemical and biological effects of water induced by each externality are also discussed to emphasize the role of water in our daily life. On this basis, the underlying problems that need to be further studied are formulated by pointing out the limitations attached to current study techniques and to outline prominent studies that have come up recently. Full article

(This article belongs to the Special Issue Solution Chemical Kinetics)

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15 pages, 2348 KiB

Open AccessArticle

¹H NMR-Based Metabolic Profiling Reveals the Effects of Fluoxetine on Lipid and Amino Acid Metabolism in Astrocytes

by Shunjie Bai^1,2,3,4,†, Chanjuan Zhou^2,3,†, Pengfei Cheng^2,3,†, Yuying Fu^2,3,†, Liang Fang^2,3, Wen Huang⁵, Jia Yu^1,2,3,4, Weihua Shao^2,3, Xinfa Wang^2,3, Meiling Liu^2,3, Jingjing Zhou^2,3 and Peng Xie^1,2,3,6,*

¹ Department of Neurology, Yongchuan Hospital, Chongqing Medical University, Chongqing 402460, China

² Chongqing Key Laboratory of Neurobiology, Chongqing 400016, China

³ Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing 400016, China

⁴ Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China

⁵ Department of Neurology, Xinqiao Hospital, Third Military Medical University, Chongqing 400016, China

⁶ Department of Neurology, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China

^† These authors contributed equally to this work.

Int. J. Mol. Sci. 2015, 16(4), 8490-8504; https://doi.org/10.3390/ijms16048490 - 15 Apr 2015

Cited by 16 | Viewed by 8048

Abstract

Fluoxetine, a selective serotonin reuptake inhibitor (SSRI), is a prescribed and effective antidepressant and generally used for the treatment of depression. Previous studies have revealed that the antidepressant mechanism of fluoxetine was related to astrocytes. However, the therapeutic mechanism underlying its mode of [...] Read more.

Fluoxetine, a selective serotonin reuptake inhibitor (SSRI), is a prescribed and effective antidepressant and generally used for the treatment of depression. Previous studies have revealed that the antidepressant mechanism of fluoxetine was related to astrocytes. However, the therapeutic mechanism underlying its mode of action in astrocytes remains largely unclear. In this study, primary astrocytes were exposed to 10 µM fluoxetine; 24 h post-treatment, a high-resolution proton nuclear magnetic resonance (¹H NMR)-based metabolomic approach coupled with multivariate statistical analysis was used to characterize the metabolic variations of intracellular metabolites. The orthogonal partial least-squares discriminant analysis (OPLS-DA) score plots of the spectra demonstrated that the fluoxetine-treated astrocytes were significantly distinguished from the untreated controls. In total, 17 differential metabolites were identified to discriminate the two groups. These key metabolites were mainly involved in lipids, lipid metabolism-related molecules and amino acids. This is the ﬁrst study to indicate that fluoxetine may exert antidepressant action by regulating the astrocyte’s lipid and amino acid metabolism. These findings should aid our understanding of the biological mechanisms underlying fluoxetine therapy. Full article

(This article belongs to the Section Biochemistry)

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12 pages, 2327 KiB

Open AccessArticle

Decisive Interactions between the Heterocyclic Moiety and the Cluster Observed in Polyoxometalate-Surfactant Hybrid Crystals

by Saki Otobe¹, Natsumi Fujioka¹, Takuro Hirano¹, Eri Ishikawa², Haruo Naruke³, Katsuhiko Fujio¹ and Takeru Ito^1,*

¹ Department of Chemistry, School of Science, Tokai University, 4-1-1 Kitakaname, Hiratsuka 259-1292, Japan

² Department of Applied Chemistry, College of Engineering, Chubu University, 1200 Matsumoto, Kasugai, Aichi 487-8501, Japan

³ Chemical Resources Laboratory, Tokyo Institute of Technology, 4259-R1-23, Nagatsuta, Midori-ku, Yokohama 226-8503, Japan

Int. J. Mol. Sci. 2015, 16(4), 8505-8516; https://doi.org/10.3390/ijms16048505 - 16 Apr 2015

Cited by 6 | Viewed by 5695

Abstract

Inorganic-organic hybrid crystals were successfully obtained as single crystals by using polyoxotungstate anion and cationic dodecylpyridazinium (C₁₂pda) and dodecylpyridinium (C₁₂py) surfactants. The decatungstate (W₁₀) anion was used as the inorganic component, and the crystal structures were compared. [...] Read more.

Inorganic-organic hybrid crystals were successfully obtained as single crystals by using polyoxotungstate anion and cationic dodecylpyridazinium (C₁₂pda) and dodecylpyridinium (C₁₂py) surfactants. The decatungstate (W₁₀) anion was used as the inorganic component, and the crystal structures were compared. In the crystal comprising C₁₂pda (C₁₂pda-W₁₀), the heterocyclic moiety directly interacted with W₁₀, which contributed to a build-up of the crystal structure. On the other hand, the crystal consisting of C₁₂py (C₁₂py-W₁₀) had similar crystal packing and molecular arrangement to those in the W₁₀ crystal hybridized with other pyridinium surfactants. These results indicate the significance of the heterocyclic moiety of the surfactant to construct hybrid crystals with polyoxometalate anions. Full article

(This article belongs to the Special Issue Chemical Bond and Bonding 2015)

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19 pages, 4160 KiB

Open AccessArticle

Genome-Wide Identification and Evolution of HECT Genes in Soybean

by Xianwen Meng^1,2, Chen Wang^1,2, Siddiq Ur Rahman^1,2, Yaxu Wang^1,2, Ailan Wang^1,2 and Shiheng Tao^1,2,*

¹ College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling 712100, China

² Bioinformatics Center, Northwest A&F University, Yangling 712100, China

Int. J. Mol. Sci. 2015, 16(4), 8517-8535; https://doi.org/10.3390/ijms16048517 - 16 Apr 2015

Cited by 17 | Viewed by 7682

Abstract

Proteins containing domains homologous to the E6-associated protein (E6-AP) carboxyl terminus (HECT) are an important class of E3 ubiquitin ligases involved in the ubiquitin proteasome pathway. HECT-type E3s play crucial roles in plant growth and development. However, current understanding of plant HECT genes [...] Read more.

Proteins containing domains homologous to the E6-associated protein (E6-AP) carboxyl terminus (HECT) are an important class of E3 ubiquitin ligases involved in the ubiquitin proteasome pathway. HECT-type E3s play crucial roles in plant growth and development. However, current understanding of plant HECT genes and their evolution is very limited. In this study, we performed a genome-wide analysis of the HECT domain-containing genes in soybean. Using high-quality genome sequences, we identified 19 soybean HECT genes. The predicted HECT genes were distributed unevenly across 15 of 20 chromosomes. Nineteen of these genes were inferred to be segmentally duplicated gene pairs, suggesting that in soybean, segmental duplications have made a significant contribution to the expansion of the HECT gene family. Phylogenetic analysis showed that these HECT genes can be divided into seven groups, among which gene structure and domain architecture was relatively well-conserved. The Ka/Ks ratios show that after the duplication events, duplicated HECT genes underwent purifying selection. Moreover, expression analysis reveals that 15 of the HECT genes in soybean are differentially expressed in 14 tissues, and are often highly expressed in the flowers and roots. In summary, this work provides useful information on which further functional studies of soybean HECT genes can be based. Full article

(This article belongs to the Special Issue Plant Molecular Biology)

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19 pages, 2486 KiB

Open AccessArticle

Characterization of Peptides Found in Unprocessed and Extruded Amaranth (Amaranthus hypochondriacus) Pepsin/Pancreatin Hydrolysates

by Alvaro Montoya-Rodríguez^1,2, Jorge Milán-Carrillo¹, Cuauhtémoc Reyes-Moreno¹ and Elvira González De Mejía^2,*

¹ North West Regional Program in Biotechnology, University of Sinaloa, FCQB-UAS, AP 1354, CP 80000 Culiacán, Sinaloa, Mexico

² Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, 228 ERML, MC-051, 1201 West Gregory Drive, Urbana, IL 61801, USA

Int. J. Mol. Sci. 2015, 16(4), 8536-8554; https://doi.org/10.3390/ijms16048536 - 16 Apr 2015

Cited by 15 | Viewed by 7720

Abstract

The objectives of this study were to characterize peptides found in unprocessed amaranth hydrolysates (UAH) and extruded amaranth hydrolysates (EAH) and to determine the effect of the hydrolysis time on the profile of peptides produced. Amaranth grain was extruded in a single screw [...] Read more.

The objectives of this study were to characterize peptides found in unprocessed amaranth hydrolysates (UAH) and extruded amaranth hydrolysates (EAH) and to determine the effect of the hydrolysis time on the profile of peptides produced. Amaranth grain was extruded in a single screw extruder at 125 °C of extrusion temperature and 130 rpm of screw speed. Unprocessed and extruded amaranth flour were hydrolyzed with pepsin/pancreatin enzymes following a kinetic at 10, 25, 60, 90, 120 and 180 min for each enzyme. After 180 min of pepsin hydrolysis, aliquots were taken at each time during pancreatin hydrolysis to characterize the hydrolysates by MALDI-TOF/MS-MS. Molecular masses (MM) (527, 567, 802, 984, 1295, 1545, 2034 and 2064 Da) of peptides appeared consistently during hydrolysis, showing high intensity at 10 min (2064 Da), 120 min (802 Da) and 180 min (567 Da) in UAH. EAH showed high intensity at 10 min (2034 Da) and 120 min (984, 1295 and 1545 Da). Extrusion produced more peptides with MM lower than 1000 Da immediately after 10 min of hydrolysis. Hydrolysis time impacted on the peptide profile, as longer the time lower the MM in both amaranth hydrolysates. Sequences obtained were analyzed for their biological activity at BIOPEP, showing important inhibitory activities related to chronic diseases. These peptides could be used as a food ingredient/supplement in a healthy diet to prevent the risk to develop chronic diseases. Full article

(This article belongs to the Special Issue Bioactive Proteins and Peptides Derived from Food)

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14 pages, 8861 KiB

Open AccessArticle

Micro RNA-124a Regulates Lipolysis via Adipose Triglyceride Lipase and Comparative Gene Identification 58

by Suman K. Das¹, Elke Stadelmeyer¹, Silvia Schauer¹, Anna Schwarz¹, Heimo Strohmaier², Thiery Claudel³, Rudolf Zechner⁴, Gerald Hoefler^1,* and Paul W. Vesely^1,4,*

¹ Institute of Pathology, Medical University of Graz, Auenbruggerplatz 25, 8036 Graz, Austria

² Center for Medical Research, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria

³ Hans Popper Laboratory of Molecular Hepatology, Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria

⁴ Institute of Molecular Biosciences, Karl Franzens University of Graz, Heinrichstraße 31, 8010 Graz, Austria

Int. J. Mol. Sci. 2015, 16(4), 8555-8568; https://doi.org/10.3390/ijms16048555 - 16 Apr 2015

Cited by 27 | Viewed by 8330

Abstract

Lipolysis is the biochemical pathway responsible for the catabolism of cellular triacylglycerol (TG). Lipolytic TG breakdown is a central metabolic process leading to the generation of free fatty acids (FA) and glycerol, thereby regulating lipid, as well as energy homeostasis. The precise tuning [...] Read more.

Lipolysis is the biochemical pathway responsible for the catabolism of cellular triacylglycerol (TG). Lipolytic TG breakdown is a central metabolic process leading to the generation of free fatty acids (FA) and glycerol, thereby regulating lipid, as well as energy homeostasis. The precise tuning of lipolysis is imperative to prevent lipotoxicity, obesity, diabetes and other related metabolic disorders. Here, we present our finding that miR-124a attenuates RNA and protein expression of the major TG hydrolase, adipose triglyceride lipase (ATGL/PNPLA2) and its co-activator comparative gene identification 58 (CGI-58/ABHD5). Ectopic expression of miR-124a in adipocytes leads to reduced lipolysis and increased cellular TG accumulation. This phenotype, however, can be rescued by overexpression of truncated Atgl lacking its 3'UTR, which harbors the identified miR-124a target site. In addition, we observe a strong negative correlation between miR-124a and Atgl expression in various murine tissues. Moreover, miR-124a regulates the expression of Atgl and Cgi-58 in murine white adipose tissue during fasting as well as the expression of Atgl in murine liver, during fasting and re-feeding. Together, these results point to an instrumental role of miR-124a in the regulation of TG catabolism. Therefore, we suggest that miR-124a may be involved in the regulation of several cellular and organismal metabolic parameters, including lipid storage and plasma FA concentration. Full article

(This article belongs to the Collection Regulation by Non-coding RNAs)

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22 pages, 846 KiB

Open AccessReview

Potential Biological Applications of Bio-Based Anacardic Acids and Their Derivatives

by Fatma B. Hamad¹ and Egid B. Mubofu^2,*

¹ Chemistry Department, Dar es Salaam University College of Education, P.O. Box 2329, Dar es Salaam, Tanzania

² Chemistry Department, University of Dar es Salaam, P.O. Box 35061, Dar es Salaam, Tanzania

Int. J. Mol. Sci. 2015, 16(4), 8569-8590; https://doi.org/10.3390/ijms16048569 - 16 Apr 2015

Cited by 118 | Viewed by 14726

Abstract

Cashew nut shells (CNS), which are agro wastes from cashew nut processing factories, have proven to be among the most versatile bio-based renewable materials in the search for functional materials and chemicals from renewable resources. CNS are produced in the cashew nut processing [...] Read more.

Cashew nut shells (CNS), which are agro wastes from cashew nut processing factories, have proven to be among the most versatile bio-based renewable materials in the search for functional materials and chemicals from renewable resources. CNS are produced in the cashew nut processing process as waste, but they contain cashew nut shell liquid (CNSL) up to about 30–35 wt. % of the nut shell weight depending on the method of extraction. CNSL is a mixture of anacardic acid, cardanol, cardol, and methyl cardol, and the structures of these phenols offer opportunities for the development of diverse products. For anacardic acid, the combination of phenolic, carboxylic, and a 15-carbon alkyl side chain functional group makes it attractive in biological applications or as a synthon for the synthesis of a multitude of bioactive compounds. Anacardic acid, which is about 65% of a CNSL mixture, can be extracted from the agro waste. This shows that CNS waste can be used to extract useful chemicals and thus provide alternative green sources of chemicals, apart from relying only on the otherwise declining petroleum based sources. This paper reviews the potential of anacardic acids and their semi-synthetic derivatives for antibacterial, antitumor, and antioxidant activities. The review focuses on natural anacardic acids from CNS and other plants and their semi-synthetic derivatives as possible lead compounds in medicine. In addition, the use of anacardic acid as a starting material for the synthesis of various biologically active compounds and complexes is reported. Full article

(This article belongs to the Special Issue Green Chemistry and the Biorefinery)

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16 pages, 3912 KiB

Open AccessArticle

VEGFR-1 Overexpression Identifies a Small Subgroup of Aggressive Prostate Cancers in Patients Treated by Prostatectomy

by Maria Christina Tsourlakis^1,†, Puya Khosrawi^1,†, Philipp Weigand¹, Martina Kluth¹, Claudia Hube-Magg¹, Sarah Minner¹, Christina Koop¹, Markus Graefen², Hans Heinzer², Corinna Wittmer¹, Guido Sauter¹, Till Krech¹, Waldemar Wilczak¹, Hartwig Huland², Ronald Simon^1,*, Thorsten Schlomm^2,3 and Stefan Steurer¹

¹ Institute of Pathology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, D-210246 Hamburg, Germany

² Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, D-210246 Hamburg, Germany

³ Department of Urology, Section for translational Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, D-210246 Hamburg, Germany

^† These authors contributed equally to this work.

Int. J. Mol. Sci. 2015, 16(4), 8591-8606; https://doi.org/10.3390/ijms16048591 - 16 Apr 2015

Cited by 6 | Viewed by 7044

Abstract

The VEGFR-1 is suggested to promote tumor progression. In the current study we analyzed prevalence and prognostic impact of the VEGFR-1 by immunohistochemistry on a tissue microarray containing more than 3000 prostate cancer specimens. Results were compared to tumor phenotype, ETS-related gene (ERG) [...] Read more.

The VEGFR-1 is suggested to promote tumor progression. In the current study we analyzed prevalence and prognostic impact of the VEGFR-1 by immunohistochemistry on a tissue microarray containing more than 3000 prostate cancer specimens. Results were compared to tumor phenotype, ETS-related gene (ERG) status, and biochemical recurrence. Membranous VEGFR-1 expression was detectable in 32.6% of 2669 interpretable cancers and considered strong in 1.7%, moderate in 6.7% and weak in 24.2% of cases. Strong VEGFR-1 expression was associated with TMPRSS2:ERG fusion status as determined by fluorescence in situ hybridization (FISH) and immunohistochemistry (p < 0.0001 each). Elevated VEGFR-1 expression was linked to high Gleason grade and advanced pT stage in TMPRSS2:ERG negative cancers (p = 0.0008 and p = 0.001), while these associations were absent in TMPRSS2:ERG positive cancers. VEGFR-1 expression was also linked to phosphatase and tensin homolog (PTEN) deletions. A comparison with prostate specific antigen (PSA) recurrence revealed that the 1.7% of prostate cancers with the highest VEGFR-1 levels had a strikingly unfavorable prognosis. This could be seen in all cancers, in the subsets of TMPRSS2:ERG positive or negative, PTEN deleted or undeleted carcinomas (p < 0.0001 each). High level VEGFR-1 expression is infrequent in prostate cancer, but identifies a subgroup of aggressive cancers, which may be candidates for anti-VEGFR-1 targeted therapy. Full article

(This article belongs to the Special Issue Advances in Molecular Oncology)

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14 pages, 1458 KiB

Open AccessArticle

Quantitative Analysis of PMLA Nanoconjugate Components after Backbone Cleavage

by Hui Ding^*, Rameshwar Patil, Jose Portilla-Arias, Keith L. Black, Julia Y. Ljubimova and Eggehard Holler

Department of Neurosurgery, Cedars-Sinai Medical Center, 110 N. 127 S. San Vincente, Advanced Health Science Pavilion A8220, Los Angeles, CA 90048, USA

Int. J. Mol. Sci. 2015, 16(4), 8607-8620; https://doi.org/10.3390/ijms16048607 - 16 Apr 2015

Cited by 5 | Viewed by 5972

Abstract

Multifunctional polymer nanoconjugates containing multiple components show great promise in cancer therapy, but in most cases complete analysis of each component is difficult. Polymalic acid (PMLA) based nanoconjugates have demonstrated successful brain and breast cancer treatment. They consist of multiple components including targeting [...] Read more.

Multifunctional polymer nanoconjugates containing multiple components show great promise in cancer therapy, but in most cases complete analysis of each component is difficult. Polymalic acid (PMLA) based nanoconjugates have demonstrated successful brain and breast cancer treatment. They consist of multiple components including targeting antibodies, Morpholino antisense oligonucleotides (AONs), and endosome escape moieties. The component analysis of PMLA nanoconjugates is extremely difficult using conventional spectrometry and HPLC method. Taking advantage of the nature of polyester of PMLA, which can be cleaved by ammonium hydroxide, we describe a method to analyze the content of antibody and AON within nanoconjugates simultaneously using SEC-HPLC by selectively cleaving the PMLA backbone. The selected cleavage conditions only degrade PMLA without affecting the integrity and biological activity of the antibody. Although the amount of antibody could also be determined using the bicinchoninic acid (BCA) method, our selective cleavage method gives more reliable results and is more powerful. Our approach provides a new direction for the component analysis of polymer nanoconjugates and nanoparticles. Full article

(This article belongs to the Section Materials Science)

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14 pages, 1387 KiB

Open AccessArticle

Effect of the Characters of Chitosans Used and Regeneration Conditions on the Yield and Physicochemical Characteristics of Regenerated Products

by Chu Hsi Hsu^1,2, Szu Kai Chen¹, Wei Yu Chen¹, Min Lang Tsai^1,* and Rong Huei Chen^1,*

¹ Department of Food Science, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung 20224, Taiwan

² Department of Food and Beverage Management, Yuanpei University of Medical Technology, 306, Yuanpei Street, Hsinchu 30015, Taiwan

Int. J. Mol. Sci. 2015, 16(4), 8621-8634; https://doi.org/10.3390/ijms16048621 - 17 Apr 2015

Cited by 20 | Viewed by 5299

Abstract

The objective of this study was to explore the effect of the character of chitosans used, and the regeneration conditions employed on, the yield and physicochemical characteristics of regenerated products. Different concentrations of acetic acid were used to dissolve chitosans of 61.7% and [...] Read more.

The objective of this study was to explore the effect of the character of chitosans used, and the regeneration conditions employed on, the yield and physicochemical characteristics of regenerated products. Different concentrations of acetic acid were used to dissolve chitosans of 61.7% and 94.9% degree of deacetylation (DD), and weight-average molecular weight (Mw) of 176 and 97 kDa, respectively; they were then precipitated with an 8 N NaOH solution, followed by washing and neutral and freeze drying to get the regenerated products. Yields of regenerated products and their physicochemical properties, such as ash content, bulk density, Mw, polydispersity index (PDI), DD, and crystallinity were measured. A higher concentration of acetic acid used resulted in a higher yield. The purity of the regenerated product increased significantly, whereas the bulk density and crystallinity decreased significantly after regeneration. The regeneration process showed its merits of narrowing down the PDI of regenerated products. The DD and structure of chitosan was changed insignificantly after the regeneration process. Full article

(This article belongs to the Special Issue Chitins 2015)

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20 pages, 3747 KiB

Open AccessArticle

Interleukin-1 Receptor Antagonist Reduces Neonatal Lipopolysaccharide-Induced Long-Lasting Neurobehavioral Deficits and Dopaminergic Neuronal Injury in Adult Rats

by Yi Pang¹, Lu-Tai Tien², Hobart Zhu¹, Juying Shen¹, Camilla F. Wright¹, Tembra K. Jones¹, Samir A. Mamoon¹, Abhay J. Bhatt¹, Zhengwei Cai¹ and Lir-Wan Fan^1,*

¹ Department of Pediatrics, Division of Newborn Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA

² School of Medicine, Fu Jen Catholic University, Xinzhuang Dist, New Taipei City 24205, Taiwan

Int. J. Mol. Sci. 2015, 16(4), 8635-8654; https://doi.org/10.3390/ijms16048635 - 17 Apr 2015

Cited by 24 | Viewed by 9411

Abstract

Our previous study showed that a single lipopolysaccharide (LPS) treatment to neonatal rats could induce a long-lasting neuroinflammatory response and dopaminergic system injury late in life. This is evidenced by a sustained activation of microglia and elevated interleukin-1β (IL-1β) levels, as well as [...] Read more.

Our previous study showed that a single lipopolysaccharide (LPS) treatment to neonatal rats could induce a long-lasting neuroinflammatory response and dopaminergic system injury late in life. This is evidenced by a sustained activation of microglia and elevated interleukin-1β (IL-1β) levels, as well as reduced tyrosine hydroxylase (TH) expression in the substantia nigra (SN) of P70 rat brain. The object of the current study was to test whether co-administration of IL-1 receptor antagonist (IL-1ra) protects against LPS-induced neurological dysfunction later in life. LPS (1 mg/kg) with or without IL-1ra (0.1 mg/kg), or sterile saline was injected intracerebrally into postnatal day 5 (P5) Sprague-Dawley male rat pups. Motor behavioral tests were carried out from P7 to P70 with subsequent examination of brain injury. Our results showed that neonatal administration of IL-1ra significantly attenuated LPS-induced motor behavioral deficits, loss of TH immunoreactive neurons, as well as microglia activation in the SN of P70 rats. These data suggest that IL-1β may play a pivotal role in mediating a chronic neuroinflammation status by a single LPS exposure in early postnatal life, and blockading IL-1β might be a novel approach to protect the dopaminergic system against perinatal infection/inflammation exposure. Full article

(This article belongs to the Special Issue Molecular Research in Neurotoxicology)

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21 pages, 3373 KiB

Open AccessReview

Pathological Bases for a Robust Application of Cancer Molecular Classification

by Salvador J. Diaz-Cano

King's Health Partners, Cancer Studies, King's College Hospital-Viapath, Denmark Hill, London SE5-9RS, UK

Int. J. Mol. Sci. 2015, 16(4), 8655-8675; https://doi.org/10.3390/ijms16048655 - 17 Apr 2015

Cited by 9 | Viewed by 8227

Abstract

Any robust classification system depends on its purpose and must refer to accepted standards, its strength relying on predictive values and a careful consideration of known factors that can affect its reliability. In this context, a molecular classification of human cancer must refer [...] Read more.

Any robust classification system depends on its purpose and must refer to accepted standards, its strength relying on predictive values and a careful consideration of known factors that can affect its reliability. In this context, a molecular classification of human cancer must refer to the current gold standard (histological classification) and try to improve it with key prognosticators for metastatic potential, staging and grading. Although organ-specific examples have been published based on proteomics, transcriptomics and genomics evaluations, the most popular approach uses gene expression analysis as a direct correlate of cellular differentiation, which represents the key feature of the histological classification. RNA is a labile molecule that varies significantly according with the preservation protocol, its transcription reflect the adaptation of the tumor cells to the microenvironment, it can be passed through mechanisms of intercellular transference of genetic information (exosomes), and it is exposed to epigenetic modifications. More robust classifications should be based on stable molecules, at the genetic level represented by DNA to improve reliability, and its analysis must deal with the concept of intratumoral heterogeneity, which is at the origin of tumor progression and is the byproduct of the selection process during the clonal expansion and progression of neoplasms. The simultaneous analysis of multiple DNA targets and next generation sequencing offer the best practical approach for an analytical genomic classification of tumors. Full article

(This article belongs to the Special Issue Molecular Classification of Human Cancer: Diagnosis and Treatment)

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23 pages, 1061 KiB

Open AccessReview

Non-Coding RNAs in Saliva: Emerging Biomarkers for Molecular Diagnostics

by Blanca Majem¹, Marina Rigau¹, Jaume Reventós^1,2 and David T. Wong^3,*

¹ Research Unit in Biomedicine and Translational Oncology, Lab 209, Collserola Building, Vall Hebron Research Institute (VHIR) and University Hospital, Pg. Vall Hebron 119-129, 08035 Barcelona, Spain

² IDIBELL-Bellvitge Biomedical Research Institute & Universitat Internacional de Catalunya, 08908 Barcelona, Spain

³ Center for Oral/Head & Neck Oncology Research, University of California, Los Angeles, CA 90095, USA

Int. J. Mol. Sci. 2015, 16(4), 8676-8698; https://doi.org/10.3390/ijms16048676 - 17 Apr 2015

Cited by 59 | Viewed by 8987

Abstract

Saliva is a complex body fluid that comprises secretions from the major and minor salivary glands, which are extensively supplied by blood. Therefore, molecules such as proteins, DNA, RNA, etc., present in plasma could be also present in saliva. Many studies have [...] Read more.

Saliva is a complex body fluid that comprises secretions from the major and minor salivary glands, which are extensively supplied by blood. Therefore, molecules such as proteins, DNA, RNA, etc., present in plasma could be also present in saliva. Many studies have reported that saliva body fluid can be useful for discriminating several oral diseases, but also systemic diseases including cancer. Most of these studies revealed messenger RNA (mRNA) and proteomic biomarker signatures rather than specific non-coding RNA (ncRNA) profiles. NcRNAs are emerging as new regulators of diverse biological functions, playing an important role in oncogenesis and tumor progression. Indeed, the small size of these molecules makes them very stable in different body fluids and not as susceptible as mRNAs to degradation by ribonucleases (RNases). Therefore, the development of a non-invasive salivary test, based on ncRNAs profiles, could have a significant applicability to clinical practice, not only by reducing the cost of the health system, but also by benefitting the patient. Here, we summarize the current status and clinical implications of the ncRNAs present in human saliva as a source of biological information. Full article

(This article belongs to the Special Issue Emerging Classes of Biomarkers for Molecular Diagnostics)

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20 pages, 1033 KiB

Open AccessReview

Modulation of the Genome and Epigenome of Individuals Susceptible to Autism by Environmental Risk Factors

by Costas Koufaris and Carolina Sismani^*

Department of Cytogenetics and Genomics, the Cyprus Institute of Neurology and Genetics, P.O. Box 3462, Nicosia 1683, Cyprus

Int. J. Mol. Sci. 2015, 16(4), 8699-8718; https://doi.org/10.3390/ijms16048699 - 20 Apr 2015

Cited by 21 | Viewed by 8117

Abstract

Diverse environmental factors have been implicated with the development of autism spectrum disorders (ASD). Genetic factors also underlie the differential vulnerability to environmental risk factors of susceptible individuals. Currently the way in which environmental risk factors interact with genetic factors to increase the [...] Read more.

Diverse environmental factors have been implicated with the development of autism spectrum disorders (ASD). Genetic factors also underlie the differential vulnerability to environmental risk factors of susceptible individuals. Currently the way in which environmental risk factors interact with genetic factors to increase the incidence of ASD is not well understood. A greater understanding of the metabolic, cellular, and biochemical events involved in gene x environment interactions in ASD would have important implications for the prevention and possible treatment of the disorder. In this review we discuss various established and more alternative processes through which environmental factors implicated in ASD can modulate the genome and epigenome of genetically-susceptible individuals. Full article

(This article belongs to the Special Issue The Identification of the Genetic Components of Autism Spectrum Disorders)

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25 pages, 1188 KiB

Open AccessArticle

Synthesis, Biological Evaluation and 2D-QSAR Study of Halophenyl Bis-Hydrazones as Antimicrobial and Antitubercular Agents

by Hatem A. Abdel-Aziz^1,2,*

, Wagdy M. Eldehna^3,†

, Mohamed Fares^3,†, Sara T. A. Al-Rashood¹, Khalid A. Al-Rashood¹, Marwa M. Abdel-Aziz⁴ and Dalia H. Soliman^3,5

¹ Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia

² Department of Applied Organic Chemistry, National Research Centre, Dokki, Cairo 12622, Egypt

³ Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo 11829, Egypt

⁴ The Regional Center for Mycology and Biotechnology, Al-Azhar University, Cairo 11759, Egypt

⁵ Pharmaceutical Chemistry Department, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo 11754, Egypt

^† These authors contributed equally to this work.

Int. J. Mol. Sci. 2015, 16(4), 8719-8743; https://doi.org/10.3390/ijms16048719 - 20 Apr 2015

Cited by 31 | Viewed by 6883

Abstract

In continuation of our endeavor towards the development of potent and effective antimicrobial agents, three series of halophenyl bis-hydrazones (14a–n, 16a–d, 17a and 17b) were synthesized and evaluated for their potential antibacterial, antifungal and antimycobacterial [...] Read more.

In continuation of our endeavor towards the development of potent and effective antimicrobial agents, three series of halophenyl bis-hydrazones (14a–n, 16a–d, 17a and 17b) were synthesized and evaluated for their potential antibacterial, antifungal and antimycobacterial activities. These efforts led to the identification of five molecules 14c, 14g, 16b, 17a and 17b (MIC range from 0.12 to 7.81 μg/mL) with broad antimicrobial activity against Mycobacterium tuberculosis; Aspergillus fumigates; Gram positive bacteria, Staphylococcus aureus, Streptococcus pneumonia, and Bacillis subtilis; and Gram negative bacteria, Salmonella typhimurium, Klebsiella pneumonia, and Escherichia coli. Three of the most active compounds, 16b, 17a and 17b, were also devoid of apparent cytotoxicity to lung cancer cell line A549. Amphotericin B and ciprofloxacin were used as references for antifungal and antibacterial screening, while isoniazid and pyrazinamide were used as references for antimycobacterial activity. Furthermore, three Quantitative Structure Activity Relationship (QSAR) models were built to explore the structural requirements controlling the different activities of the prepared bis-hydrazones. Full article

(This article belongs to the Section Biochemistry)

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17 pages, 1366 KiB

Open AccessArticle

Addition of Interleukin-21 for Expansion of T-Cells for Adoptive Immunotherapy of Murine Melanoma

by Christine Kathryn Zoon^1,*, Wen Wan², Laura Graham³ and Harry D. Bear³

¹ Department of Surgery, Virginia Commonwealth University Health System, Richmond, VA 23298, USA

² Department of Biostatistics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA

³ Division of Surgical Oncology, Virginia Commonwealth University Massey Cancer Center, Richmond, VA 23298, USA

Int. J. Mol. Sci. 2015, 16(4), 8744-8760; https://doi.org/10.3390/ijms16048744 - 20 Apr 2015

Cited by 7 | Viewed by 6349

Abstract

We previously demonstrated that interleukin (IL)-7/15 was superior to IL-2 for expansion of T cells in vitro for adoptive immunotherapy. We sought to ascertain whether IL-21 would further improve yield and therapeutic efficacy of T cells in culture. Naïve T cell receptor (TcR) [...] Read more.

We previously demonstrated that interleukin (IL)-7/15 was superior to IL-2 for expansion of T cells in vitro for adoptive immunotherapy. We sought to ascertain whether IL-21 would further improve yield and therapeutic efficacy of T cells in culture. Naïve T cell receptor (TcR) transgenic splenocytes or antigen-sensitized lymph node cells were harvested from PMEL-1 mice and exposed to bryostatin-1 and ionomycin (B/I) for 18 h. Cells were then cultured in IL-2, IL-21, IL-7/15 or IL-7/15/21 for six days. Harvested cells were analyzed by flow cytometry and used to treat C57Bl/6 mice injected intravenously with B16 melanoma. Lungs were harvested and metastases counted 14 days after treatment. Culturing lymphocytes in IL-7/15/21 increased expansion compared to IL-2 or IL-7/15. IL-21 and IL-7/15/21 increased CD8+ cells compared to IL-2 or IL-7/15. IL-21 preferentially expanded a CD8+CD44−CD62L+ T “naïve” population, whereas IL-7/15/21 increased CD8+CD44+CD62Lhigh central-memory T cells. T cells grown in IL-7/15/21 were more effective at reducing metastases than IL-2. The addition of IL-21 to IL-7/15 induced greater expansion of lymphocytes in culture and increased the yield of CD8+ T central-memory cells vs. IL-7/15 alone. This may have significant impact on future clinical trials of adoptive immunotherapy, particularly for generating adequate numbers of lymphocytes for treatment. Full article

(This article belongs to the Special Issue Mechanism of Action and Applications of Cytokines in Immunotherapy)

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11 pages, 927 KiB

Open AccessArticle

Chemicals from Agave sisalana Biomass: Isolation and Identification

by Jener David Gonçalves Santos¹, Ivo Jose Curcino Vieira², Raimundo Braz-Filho^2,3 and Alexsandro Branco^1,*

¹ Laboratório de Fitoquímica, Departamento de Saúde, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia 44031-460, Brazil

² LCQUI-CCT, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro 28013-600, Brazil

³ LCQUI-CCT, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes-RJ/DEQUIM-ICE, Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro 23894-374, Brazil

Int. J. Mol. Sci. 2015, 16(4), 8761-8771; https://doi.org/10.3390/ijms16048761 - 20 Apr 2015

Cited by 32 | Viewed by 10212

Abstract

Agave sisalana (sisal) is known worldwide as a source of hard fibers, and Brazil is the largest producer of sisal. Nonetheless, the process of removing the fibers of the sisal leaf generates 95% waste. In this study, we applied chemical sequential steps (hydrothermal [...] Read more.

Agave sisalana (sisal) is known worldwide as a source of hard fibers, and Brazil is the largest producer of sisal. Nonetheless, the process of removing the fibers of the sisal leaf generates 95% waste. In this study, we applied chemical sequential steps (hydrothermal extraction, precipitation, liquid-liquid extraction, crystallization, SiO₂ and Sephadex LH 20 column chromatography) to obtain pectin, mannitol, succinic acid, kaempferol and a mixture of saponins as raw chemicals from sisal biomass. The structural identification of these compounds was performed though spectrometric methods, such as Infrared (IR), Ultraviolet (UV), Mass spectrometry (MS) and Nuclear magnetic resonance (NMR). All the sisal chemicals found in this work are used by both the chemical and pharmaceutical industries as excipients or active principles in products. Full article

(This article belongs to the Special Issue Green Chemistry and the Biorefinery)

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17 pages, 797 KiB

Open AccessArticle

Melanogenesis-Inducing Effect of Cirsimaritin through Increases in Microphthalmia-Associated Transcription Factor and Tyrosinase Expression

by Hyo Jung Kim^1,†, Il Soon Kim^2,†, Yin Dong¹, Ik-Soo Lee², Jin Sook Kim², Jong-Sang Kim³

, Je-Tae Woo^1,4 and Byung-Yoon Cha^1,*

¹ Research Institute for Biological Functions, Chubu University, 1200 Matsumoto, Kasugai, Aichi 487-8501, Japan

² KM Convergence Research Division, Korea Institute of Oriental Medicine, Daejeon 305-811, Korea

³ School of Food Science and Biotechnology, Kyungpook National University, Daegu 702-701, Korea

⁴ Department of Research and Development, Erina Co., Inc., 1-9-2 Hagashi-Shinbashi, Minato-ku, Tokyo 105-0021, Japan

^† These authors contributed equally to this work.

Int. J. Mol. Sci. 2015, 16(4), 8772-8788; https://doi.org/10.3390/ijms16048772 - 20 Apr 2015

Cited by 37 | Viewed by 8432

Abstract

The melanin-inducing properties of cirsimaritin were investigated in murine B16F10 cells. Cirsimaritin is an active flavone with methoxy groups, which is isolated from the branches of Lithocarpus dealbatus. Tyrosinase activity and melanin content in murine B16F10 melanoma cells were increased by cirsimaritin [...] Read more.

The melanin-inducing properties of cirsimaritin were investigated in murine B16F10 cells. Cirsimaritin is an active flavone with methoxy groups, which is isolated from the branches of Lithocarpus dealbatus. Tyrosinase activity and melanin content in murine B16F10 melanoma cells were increased by cirsimaritin in a dose-dependent manner. Western blot analysis revealed that tyrosinase, tyrosinase-related protein (TRP) 1, TRP2 protein levels were enhanced after treatment with cirsimaritin for 48 h. Cirsimaritin also upregulated the expression of microphthalmia-associated transcription factor (MITF) after 24 h of treatment. Furthermore, cirsimaritin induced phosphorylation of cyclic adenosine monophosphate (cAMP) response element-binding protein (CREB) in a dose-dependent manner after treatment for 15 min. The cirsimaritin-mediated increase of tyrosinase activity was significantly attenuated by H89, a cAMP-dependent protein kinase A inhibitor. These findings indicate that cirsimaritin stimulates melanogenesis in B16F10 cells by activation of CREB as well as upregulation of MITF and tyrosinase expression, which was activated by cAMP signaling. Finally, the melanogenic effect of cirsimaritin was confirmed in human epidermal melanocytes. These results support the putative application of cirsimaritin in ultraviolet photoprotection and hair coloration treatments. Full article

(This article belongs to the Section Biochemistry)

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22 pages, 1823 KiB

Open AccessArticle

Potential Natural Products for Alzheimer’s Disease: Targeted Search Using the Internal Ribosome Entry Site of Tau and Amyloid-β Precursor Protein

by Yun-Chieh Tasi^1,†, Ting-Yu Chin^2,5,†, Ying-Ju Chen², Chun-Chih Huang³, Shou-Lun Lee^4,* and Tzong-Yuan Wu^2,5,*

¹ Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 11490, Taiwan

² Department of Bioscience Technology, Chung Yuan Christian University, Taoyuan 32032, Taiwan

³ New Bellus Enterprise Co., Ltd., Tainan 72042, Taiwan

⁴ Department of Biological Science and Technology, China Medical University, Taichung 40402, Taiwan

⁵ Program and Center of Nanoscience Technology, Chung Yuan Christian University, Taoyuan 32032, Taiwan

^† These authors contributed equally to this work.

Int. J. Mol. Sci. 2015, 16(4), 8789-8810; https://doi.org/10.3390/ijms16048789 - 20 Apr 2015

Cited by 12 | Viewed by 8768

Abstract

Overexpression of the amyloid precursor protein (APP) and the hyperphosphorylation of the tau protein are vital in the understanding of the cause of Alzheimer’s disease (AD). As a consequence, regulation of the expression of both APP and tau proteins is one important approach [...] Read more.

Overexpression of the amyloid precursor protein (APP) and the hyperphosphorylation of the tau protein are vital in the understanding of the cause of Alzheimer’s disease (AD). As a consequence, regulation of the expression of both APP and tau proteins is one important approach in combating AD. The APP and tau proteins can be targeted at the levels of transcription, translation and protein structural integrity. This paper reports the utilization of a bi-cistronic vector containing either APP or tau internal ribosome entry site (IRES) elements flanked by β-galactosidase gene (cap-dependent) and secreted alkaline phosphatase (SEAP) (cap-independent) to discern the mechanism of action of memantine, an N-methyl-d-aspartate (NMDA) receptor antagonist. Results indicate that memantine could reduce the activity of both the APP and tau IRES at a concentration of ~10 μM (monitored by SEAP activity) without interfering with the cap-dependent translation as monitored by the β-galactosidase assay. Western blot analysis of the tau protein in neuroblastoma (N2A) and rat hippocampal cells confirmed the halting of the expression of the tau proteins. We also employed this approach to identify a preparation named NB34, extracts of Boussingaultia baselloides (madeira-vine) fermented with Lactobacillus spp., which can function similarly to memantine in both IRES of APP and Tau. The water maze test demonstrated that NB34 could improve the spatial memory of a high fat diet induced neurodegeneration in apolipoprotein E-knockout (ApoE^−/−) mice. These results revealed that the bi-cistronic vector provided a simple, and effective platform in screening and establishing the mechanistic action of potential compounds for the treatment and management of AD. Full article

(This article belongs to the Special Issue Neurological Injuries’ Monitoring, Tracking and Treatment)

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15 pages, 881 KiB

Open AccessArticle

Selected Tea and Tea Pomace Extracts Inhibit Intestinal α-Glucosidase Activity in Vitro and Postprandial Hyperglycemia in Vivo

by Jungbae Oh^1,†, Sung-Hoon Jo^1,†, Justin S. Kim^1,†, Kyoung-Soo Ha¹, Jung-Yun Lee², Hwang-Yong Choi², Seok-Yeong Yu¹, Young-In Kwon^2,* and Young-Cheul Kim^1,*

¹ Department of Nutrition, University of Massachusetts, Amherst, MA 01003, USA

² Department of Food and Nutrition, Hannam University, Daejeon 305-811, Korea

^† These authors contributed equally to this work.

Int. J. Mol. Sci. 2015, 16(4), 8811-8825; https://doi.org/10.3390/ijms16048811 - 21 Apr 2015

Cited by 39 | Viewed by 10422

Abstract

Type 2 diabetes mellitus (T2DM) is a metabolic disorder characterized by postprandial hyperglycemia, which is an early defect of T2DM and thus a primary target for anti-diabetic drugs. A therapeutic approach is to inhibit intestinal α-glucosidase, the key enzyme for dietary carbohydrate digestion, [...] Read more.

Type 2 diabetes mellitus (T2DM) is a metabolic disorder characterized by postprandial hyperglycemia, which is an early defect of T2DM and thus a primary target for anti-diabetic drugs. A therapeutic approach is to inhibit intestinal α-glucosidase, the key enzyme for dietary carbohydrate digestion, resulting in delayed rate of glucose absorption. Although tea extracts have been reported to have anti-diabetic effects, the potential bioactivity of tea pomace, the main bio waste of tea beverage processing, is largely unknown. We evaluated the anti-diabetic effects of three selected tea water extracts (TWE) and tea pomace extracts (TPE) by determining the relative potency of extracts on rat intestinal α-glucosidase activity in vitro as well as hypoglycemic effects in vivo. Green, oolong, and black tea bags were extracted in hot water and the remaining tea pomace were dried and further extracted in 70% ethanol. The extracts were determined for intestinal rat α-glucosidases activity, radical scavenging activity, and total phenolic content. The postprandial glucose-lowering effects of TWE and TPE of green and black tea were assessed in male Sprague-Dawley (SD) rats and compared to acarbose, a known pharmacological α-glucosidase inhibitor. The IC₅₀ values of all three tea extracts against mammalian α-glucosidase were lower or similar in TPE groups than those of TWE groups. TWE and TPE of green tea exhibited the highest inhibitory effects against α-glucosidase activity with the IC₅₀ of 2.04 ± 0.31 and 1.95 ± 0.37 mg/mL respectively. Among the specific enzymes tested, the IC₅₀ values for TWE (0.16 ± 0.01 mg/mL) and TPE (0.13 ± 0.01 mg/mL) of green tea against sucrase activity were the lowest compared to those on maltase and glucoamylase activities. In the animal study, the blood glucose level at 30 min after oral intake (0.5 g/kg body wt) of TPE and TWE of both green and black tea was significantly reduced compared to the control in sucrose-loaded SD rats. The TPE of all three teas had significantly higher phenolic content than those of the TWE groups, which correlated strongly with the DPPH radical scavenging activity. This is the first report of tea pomace extract significantly inhibits intestinal α-glucosidase, resulting in delayed glucose absorption and thereby suppressed postprandial hyperglycemia. Our data suggest that tea pomace-derived bioactives may have great potential for further development as nutraceutical products and the reuse of otherwise biowaste as valuable bioresources for the industry. Full article

(This article belongs to the Special Issue Bioactive Phytochemicals and Functional Food Ingredients in Fruits and Vegetables)

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18 pages, 913 KiB

Open AccessArticle

Processed vs. Non-Processed Biowastes for Agriculture: Effects of Post-Harvest Tomato Plants and Biochar on Radish Growth, Chlorophyll Content and Protein Production

by Chiara Mozzetti Monterumici¹, Daniele Rosso², Enzo Montoneri³, Marco Ginepro⁴, Andrea Baglieri⁵, Etelvino Henrique Novotny⁶

, Witold Kwapinski⁷ and Michèle Negre^1,*

¹ Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università di Torino, Largo P. Braccini 2, I-10095 Grugliasco, Italy

² ACEA Pinerolese Industriale SpA, Via Vigone 42, I-10064 Pinerolo, Italy

³ Biowaste Processing, Via XXIV Maggio 25, I-37126 Verona, Italy

⁴ Dipartimento di Chimica, Università di Torino, Via Giuria 7, I-10125 Torino, Italy

⁵ Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Via S. Sofia 98, I-95123 Catania, Italy

⁶ Embrapa Solos, Rua Jardim Botânico, 1024, CEP-22460-000 Rio de Janeiro, RJ, Brazil

⁷ Chemical and Environmental Science Department, University of Limerick, Castletroy, Limerick, Ireland

Int. J. Mol. Sci. 2015, 16(4), 8826-8843; https://doi.org/10.3390/ijms16048826 - 21 Apr 2015

Cited by 32 | Viewed by 7063

Abstract

The aim of this work was to address the issue of processed vs. non-processed biowastes for agriculture, by comparing materials widely differing for the amount of process energy consumption. Thus, residual post harvest tomato plants (TP), the TP hydrolysates obtained at pH 13 [...] Read more.

The aim of this work was to address the issue of processed vs. non-processed biowastes for agriculture, by comparing materials widely differing for the amount of process energy consumption. Thus, residual post harvest tomato plants (TP), the TP hydrolysates obtained at pH 13 and 60 °C, and two known biochar products obtained by 650 °C pyrolysis were prepared. All products were characterized and used in a cultivation of radish plants. The chemical composition and molecular nature of the materials was investigated by solid state ¹³C NMR spectrometry, elemental analysis and potentiometric titration. The plants were analysed for growth and content of chlorophyll, carotenoids and soluble proteins. The results show that the TP and the alkaline hydrolysates contain lignin, hemicellulose, protein, peptide and/or amino acids moieties, and several mineral elements. The biochar samples contain also similar mineral elements, but the organic fraction is characterized mainly by fused aromatic rings. All materials had a positive effect on radish growth, mainly on the diameter of roots. The best performances in terms of plant growth were given by miscanthus originated biochar and TP. The most significant effect was the enhancement of soluble protein content in the plants treated with the lowest energy consumption non processed TP. The significance of these findings for agriculture and the environment is discussed. Full article

(This article belongs to the Special Issue Green Chemistry and the Biorefinery)

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17 pages, 2028 KiB

Open AccessArticle

Effects of Paeonol on Anti-Neuroinflammatory Responses in Microglial Cells

by Chingju Lin¹, Hsiao-Yun Lin², Jia-Hong Chen³, Wen-Pei Tseng⁴, Pei-Ying Ko⁵, Yu-Shu Liu⁶, Wei-Lan Yeh⁷ and Dah-Yuu Lu^2,8,*

¹ Department of Physiology, School of Medicine, China Medical University, Taichung 40402, Taiwan

² Graduate Institute of Neural and Cognitive Sciences, China Medical University, Taichung 40402, Taiwan

³ Department of General Surgery, Taichung Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung 42743, Taiwan

⁴ Graduate Institute of Sports and Health, National Changhua University of Education, Changhua 500, Taiwan

⁵ Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung 40402, Taiwan

⁶ Graduate Institute of Basic Medical Science, China Medical University, Taichung 40402, Taiwan

⁷ Department of Cell and Tissue Engineering, Changhua Christian Hospital, Changhua 500, Taiwan

⁸ Department of Photonics and Communication Engineering, Asia University, Taichung 40402, Taiwan

Int. J. Mol. Sci. 2015, 16(4), 8844-8860; https://doi.org/10.3390/ijms16048844 - 21 Apr 2015

Cited by 52 | Viewed by 7855

Abstract

Increasing studies suggest that inflammatory processes in the central nervous system mediated by microglial activation plays an important role in numerous neurodegenerative diseases. Development of planning for microglial suppression is considered a key strategy in the search for neuroprotection. Paeonol is a major [...] Read more.

Increasing studies suggest that inflammatory processes in the central nervous system mediated by microglial activation plays an important role in numerous neurodegenerative diseases. Development of planning for microglial suppression is considered a key strategy in the search for neuroprotection. Paeonol is a major phenolic component of Moutan Cortex, widely used as a nutrient supplement in Chinese medicine. In this study, we investigated the effects of paeonol on microglial cells stimulated by inflammagens. Paeonol significantly inhibited the release of nitric oxide (NO) and the expressions of inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2). Treatment with paeonol also reduced reactive oxygen species (ROS) production and inhibited an ATP-induced increased cell migratory activity. Furthermore, the inhibitory effects of neuroinflammation by paeonol were found to be regulated by phosphorylated adenosine monophosphate-activated protein kinase-α (AMPK-α) and glycogen synthase kinase 3 α/β (GSK 3α/β). Treatment with AMPK or GSK3 inhibitors reverse the inhibitory effect of neuroinflammation by paeonol in microglial cells. Furthermore, paeonol treatment also showed significant improvement in the rotarod performance and microglial activation in the mouse model as well. The present study is the first to report a novel inhibitory role of paeonol on neuroinflammation, and presents a new candidate agent for the development of therapies for inflammation-related neurodegenerative diseases. Full article

(This article belongs to the Section Biochemistry)

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23 pages, 718 KiB

Open AccessReview

A Review of the Effect of Diet on Cardiovascular Calcification

by Rachel Nicoll^1,*, John McLaren Howard² and Michael Y. Henein¹

¹ Department of Public Health and Clinical Medicine and Heart Centre, Umea University, Umea SE-901 87, Sweden

² Acumen Lab, Tiverton, Devon EX16 6BL, UK

Int. J. Mol. Sci. 2015, 16(4), 8861-8883; https://doi.org/10.3390/ijms16048861 - 21 Apr 2015

Cited by 46 | Viewed by 12773

Abstract

Cardiovascular (CV) calcification is known as sub-clinical atherosclerosis and is recognised as a predictor of CV events and mortality. As yet there is no treatment for CV calcification and conventional CV risk factors are not consistently correlated, leaving clinicians uncertain as to optimum [...] Read more.

Cardiovascular (CV) calcification is known as sub-clinical atherosclerosis and is recognised as a predictor of CV events and mortality. As yet there is no treatment for CV calcification and conventional CV risk factors are not consistently correlated, leaving clinicians uncertain as to optimum management for these patients. For this reason, a review of studies investigating diet and serum levels of macro- and micronutrients was carried out. Although there were few human studies of macronutrients, nevertheless transfats and simple sugars should be avoided, while long chain ω-3 fats from oily fish may be protective. Among the micronutrients, an intake of 800 μg/day calcium was beneficial in those without renal disease or hyperparathyroidism, while inorganic phosphorus from food preservatives and colas may induce calcification. A high intake of magnesium (≥380 mg/day) and phylloquinone (500 μg/day) proved protective, as did a serum 25(OH)D concentration of ≥75 nmol/L. Although oxidative damage appears to be a cause of CV calcification, the antioxidant vitamins proved to be largely ineffective, while supplementation of α-tocopherol may induce calcification. Nevertheless other antioxidant compounds (epigallocatechin gallate from green tea and resveratrol from red wine) were protective. Finally, a homocysteine concentration >12 µmol/L was predictive of CV calcification, although a plasma folate concentration of >39.4 nmol/L could both lower homocysteine and protect against calcification. In terms of a dietary programme, these recommendations indicate avoiding sugar and the transfats and preservatives found in processed foods and drinks and adopting a diet high in oily fish and vegetables. The micronutrients magnesium and vitamin K may be worthy of further investigation as a treatment option for CV calcification. Full article

(This article belongs to the Special Issue Oxidative Stress in Cardiovascular Disease 2015)

12 pages, 671 KiB

Open AccessReview

Undetected Toxicity Risk in Pharmacogenetic Testing for Dihydropyrimidine Dehydrogenase

by Felicia Stefania Falvella¹, Marta Caporale², Stefania Cheli¹, Antonia Martinetti², Rosa Berenato², Claudia Maggi², Monica Niger², Francesca Ricchini², Ilaria Bossi², Maria Di Bartolomeo², Elisa Sottotetti², Francesca Futura Bernardi³, Filippo De Braud², Emilio Clementi^4,5 and Filippo Pietrantonio^2,*

¹ Unit of Clinical Pharmacology, Department of Biomedical and Clinical Sciences, University Hospital "Luigi Sacco", Università di Milano, Milan 20157, Italy

² Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian, Milan 20133, Italy

³ Department of Experimental Medicine, Section of Pharmacology "L. Donatelli", Faculty of Medicine and Surgery, Second University of Naples, Naples 80138, Italy

⁴ Scientific Institute, IRCCS E. Medea, Bosisio Parini, Lecco 23842, Italy

⁵ Unit of Clinical Pharmacology, Department of Biomedical and Clinical Sciences, Consiglio Nazionale delle Ricerche Institute of Neuroscience, University Hospital "Luigi Sacco", Università di Milano, Milan 20157, Italy

Int. J. Mol. Sci. 2015, 16(4), 8884-8895; https://doi.org/10.3390/ijms16048884 - 21 Apr 2015

Cited by 14 | Viewed by 6622

Abstract

Fluoropyrimidines, the mainstay agents for the treatment of colorectal cancer, alone or as a part of combination therapies, cause severe adverse reactions in about 10%–30% of patients. Dihydropyrimidine dehydrogenase (DPD), a key enzyme in the catabolism of 5-fluorouracil, has been intensively investigated in [...] Read more.

Fluoropyrimidines, the mainstay agents for the treatment of colorectal cancer, alone or as a part of combination therapies, cause severe adverse reactions in about 10%–30% of patients. Dihydropyrimidine dehydrogenase (DPD), a key enzyme in the catabolism of 5-fluorouracil, has been intensively investigated in relation to fluoropyrimidine toxicity, and several DPD gene (DPYD) polymorphisms are associated with decreased enzyme activity and increased risk of fluoropyrimidine-related toxicity. In patients carrying non-functional DPYD variants (c.1905+1G>A, c.1679T>G, c.2846A>T), fluoropyrimidines should be avoided or reduced according to the patients’ homozygous or heterozygous status, respectively. For other common DPYD variants (c.496A>G, c.1129-5923C>G, c.1896T>C), conflicting data are reported and their use in clinical practice still needs to be validated. The high frequency of DPYD polymorphism and the lack of large prospective trials may explain differences in studies’ results. The epigenetic regulation of DPD expression has been recently investigated to explain the variable activity of the enzyme. DPYD promoter methylation and its regulation by microRNAs may affect the toxicity risk of fluoropyrimidines. The studies we reviewed indicate that pharmacogenetic testing is promising to direct personalised dosing of fluoropyrimidines, although further investigations are needed to establish the role of DPD in severe toxicity in patients treated for colorectal cancer. Full article

(This article belongs to the Special Issue Emerging Classes of Biomarkers for Molecular Diagnostics)

38 pages, 1042 KiB

Open AccessArticle

Chemical Bonding: The Orthogonal Valence-Bond View

by Alexander F. Sax

Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria

Int. J. Mol. Sci. 2015, 16(4), 8896-8933; https://doi.org/10.3390/ijms16048896 - 21 Apr 2015

Cited by 5 | Viewed by 7136

Abstract

Chemical bonding is the stabilization of a molecular system by charge- and spin-reorganization processes in chemical reactions. These processes are said to be local, because the number of atoms involved is very small. With multi-configurational self-consistent field (MCSCF) wave functions, these processes can [...] Read more.

Chemical bonding is the stabilization of a molecular system by charge- and spin-reorganization processes in chemical reactions. These processes are said to be local, because the number of atoms involved is very small. With multi-configurational self-consistent field (MCSCF) wave functions, these processes can be calculated, but the local information is hidden by the delocalized molecular orbitals (MO) used to construct the wave functions. The transformation of such wave functions into valence bond (VB) wave functions, which are based on localized orbitals, reveals the hidden information; this transformation is called a VB reading of MCSCF wave functions. The two-electron VB wave functions describing the Lewis electron pair that connects two atoms are frequently called covalent or neutral, suggesting that these wave functions describe an electronic situation where two electrons are never located at the same atom; such electronic situations and the wave functions describing them are called ionic. When the distance between two atoms decreases, however, every covalent VB wave function composed of non-orthogonal atomic orbitals changes its character from neutral to ionic. However, this change in the character of conventional VB wave functions is hidden by its mathematical form. Orthogonal VB wave functions composed of orthonormalized orbitals never change their character. When localized fragment orbitals are used instead of atomic orbitals, one can decide which local information is revealed and which remains hidden. In this paper, we analyze four chemical reactions by transforming the MCSCF wave functions into orthogonal VB wave functions; we show how the reactions are influenced by changing the atoms involved or by changing their local symmetry. Using orthogonal instead of non-orthogonal orbitals is not just a technical issue; it also changes the interpretation, revealing the properties of wave functions that remain otherwise undetected. Full article

(This article belongs to the Special Issue Chemical Bond and Bonding 2015)

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15 pages, 2035 KiB

Open AccessArticle

Reconciling Experiment and Theory in the Use of Aryl-Extended Calix[4]pyrrole Receptors for the Experimental Quantification of Chloride–π Interactions in Solution

by Antonio Bauzá¹

, David Quiñonero¹, Antonio Frontera^1,*

and Pablo Ballester^2,3,*

¹ Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain

² Catalan Institution for Research and Advanced Studies (ICREA), 08018 Barcelona, Spain

³ Institute of Chemical Research of Catalonia (ICIQ), 43007 Tarragona, Spain

Int. J. Mol. Sci. 2015, 16(4), 8934-8948; https://doi.org/10.3390/ijms16048934 - 22 Apr 2015

Cited by 12 | Viewed by 6705

Abstract

In this manuscript we consider from a theoretical point of view the recently reported experimental quantification of anion–π interactions (the attractive force between electron deficient aromatic rings and anions) in solution using aryl extended calix[4]pyrrole receptors as model systems. Experimentally, two series of [...] Read more.

In this manuscript we consider from a theoretical point of view the recently reported experimental quantification of anion–π interactions (the attractive force between electron deficient aromatic rings and anions) in solution using aryl extended calix[4]pyrrole receptors as model systems. Experimentally, two series of calix[4]pyrrole receptors functionalized, respectively, with two and four aryl rings at the meso positions, were used to assess the strength of chloride–π interactions in acetonitrile solution. As a result of these studies the contribution of each individual chloride–π interaction was quantified to be very small (<1 kcal/mol). This result is in contrast with the values derived from most theoretical calculations. Herein we report a theoretical study using high-level density functional theory (DFT) calculations that provides a plausible explanation for the observed disagreement between theory and experiment. The study reveals the existence of molecular interactions between solvent molecules and the aromatic walls of the receptors that strongly modulate the chloride–π interaction. In addition, the obtained theoretical results also suggest that the chloride-calix[4]pyrrole complex used as reference to dissect experimentally the contribution of the chloride–π interactions to the total binding energy for both the two and four-wall aryl-extended calix[4]pyrrole model systems is probably not ideal. Full article

(This article belongs to the Special Issue Supramolecular Interactions)

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19 pages, 716 KiB

Open AccessArticle

Novel Systems Modeling Methodology in Comparative Microbial Metabolomics: Identifying Key Enzymes and Metabolites Implicated in Autism Spectrum Disorders

by Colin Heberling^1,2,* and Prasad Dhurjati²

¹ Department of Biotechnology, Johns Hopkins University, Rockville, MD 20850, USA

² Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA

Int. J. Mol. Sci. 2015, 16(4), 8949-8967; https://doi.org/10.3390/ijms16048949 - 22 Apr 2015

Cited by 10 | Viewed by 7220

Abstract

Autism spectrum disorders are a group of mental illnesses highly correlated with gastrointestinal dysfunction. Recent studies have shown that there may be one or more microbial “fingerprints” in terms of the composition characterizing individuals with autism, which could be used for diagnostic purposes. [...] Read more.

Autism spectrum disorders are a group of mental illnesses highly correlated with gastrointestinal dysfunction. Recent studies have shown that there may be one or more microbial “fingerprints” in terms of the composition characterizing individuals with autism, which could be used for diagnostic purposes. This paper proposes a computational approach whereby metagenomes characteristic of “healthy” and autistic individuals are artificially constructed via genomic information, analyzed for the enzymes coded within, and then these enzymes are compared in detail. This is a text mining application. A custom-designed online application was built and used for the comparative metabolomics study and made publically available. Several of the enzyme-catalyzing reactions involved with the amino acid glutamate were curiously missing from the “autism” microbiome and were coded within almost every organism included in the “control” microbiome. Interestingly, there exists a leading hypothesis regarding autism and glutamate involving a neurological excitation/inhibition imbalance; but the association with this study is unclear. The results included data on the transsulfuration and transmethylation pathways, involved with oxidative stress, also of importance to autism. The results from this study are in alignment with leading hypotheses in the field, which is impressive, considering the purely in silico nature of this study. The present study provides new insight into the complex metabolic interactions underlying autism, and this novel methodology has potential to be useful for developing new hypotheses. However, limitations include sparse genome data availability and conflicting literature experimental data. We believe our software tool and methodology has potential for having great utility as data become more available, comprehensive and reliable. Full article

(This article belongs to the Special Issue The Identification of the Genetic Components of Autism Spectrum Disorders)

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20 pages, 1575 KiB

Open AccessArticle

A Two-Step Nanofiltration Process for the Production of Phenolic-Rich Fractions from Artichoke Aqueous Extracts

by Alfredo Cassano^1,*

, Carmela Conidi¹, René Ruby Figueroa¹ and Roberto Castro Muñoz²

¹ Institute on Membrane Technology, ITM-CNR, c/o University of Calabria, via Pietro Bucci, 17/C, 87036 Rende (CS), Italy

² Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnologia, Av. Acueducto, 5/n, Col. Barrio La Laguna Ticomán, C.P. 07340, Mexico

Int. J. Mol. Sci. 2015, 16(4), 8968-8987; https://doi.org/10.3390/ijms16048968 - 22 Apr 2015

Cited by 39 | Viewed by 7842

Abstract

Commercial nanofiltration (NF) membranes in spiral-wound configuration (NP030 from Microdyn Nadir and Desal DK from GE Water & Process Technologies) were used in a sequential design in order to produce a separated fraction of phenolic and sugar compounds from an aqueous artichoke extract. [...] Read more.

Commercial nanofiltration (NF) membranes in spiral-wound configuration (NP030 from Microdyn Nadir and Desal DK from GE Water & Process Technologies) were used in a sequential design in order to produce a separated fraction of phenolic and sugar compounds from an aqueous artichoke extract. For both membranes, the effect of transmembrane pressure (TMP) on the permeation flux was evaluated. In optimized conditions of TMP, the NP030 membrane exhibited high rejections of apigenin, cynarin and chlorogenic acid (higher than 85%); on the other hand, very low rejections of fructose, glucose and sucrose (lower than 4%) were measured. Starting from an extract with a total antioxidant activity (TAA) of 5.28 mM trolox a retentate fraction with a TAA of 47.75 mM trolox was obtained. The NF permeate from the NP030 membrane was processed with the Desal DK membrane in optimized conditions of TMP producing a permeate stream free of phenolic and sugar compounds. Accordingly, as most part of phenolic compounds was removed in the first NF step, the concentration of sugar compounds in the NF retentate had much higher results than that of phenolic compounds. Full article

(This article belongs to the Special Issue Bioactive Phenolics and Polyphenols)

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9 pages, 3475 KiB

Open AccessCommunication

Xeroderma Pigmentosum: Low Prevalence of Germline XPA Mutations in a Brazilian XP Population

by Karina Miranda Santiago^1,2, Amanda França de Nóbrega², Rafael Malagoli Rocha³, Silvia Regina Rogatto^4,5 and Maria Isabel Achatz^2,4,*

¹ International Research Center, A.C. Camargo Cancer Center, São Paulo, SP 01508-010, Brazil

² Department of Oncogenetics, A.C. Camargo Cancer Center, São Paulo, SP 01509-900, Brazil

³ Molecular Morphology Group, Investigative Pathology Department, A.C. Camargo Cancer Center, São Paulo, SP 01509-900, Brazil

⁴ International Research Center, A.C. Camargo Cancer Center, National Institute of Science and Technology in Oncogenomics (INCITO), São Paulo, SP 01508-010, Brazil

⁵ Department of Urology, Faculty of Medicine, University of São Paulo State, Botucatu, SP 18618-970, Brazil

Int. J. Mol. Sci. 2015, 16(4), 8988-8996; https://doi.org/10.3390/ijms16048988 - 22 Apr 2015

Cited by 9 | Viewed by 9952

Abstract

Xeroderma pigmentosum (XP) is a rare autosomal recessive disorder characterized by DNA repair defects that cause photophobia, sunlight-induced cancers, and neurodegeneration. Prevalence of germline mutations in the nucleotide excision repair gene XPA vary significantly in different populations. No Brazilian patients have been reported [...] Read more.

Xeroderma pigmentosum (XP) is a rare autosomal recessive disorder characterized by DNA repair defects that cause photophobia, sunlight-induced cancers, and neurodegeneration. Prevalence of germline mutations in the nucleotide excision repair gene XPA vary significantly in different populations. No Brazilian patients have been reported to carry a germline mutation in this gene. In this study, the germline mutational status of XPA was determined in Brazilian patients exhibiting major clinical features of XP syndrome. The study was conducted on 27 unrelated patients from select Brazilian families. A biallelic inactivating transition mutation c.619C>T (p.Arg207Ter) was identified in only one patient with a history of neurological impairment and mild skin abnormalities. These findings suggest that XP syndrome is rarely associated with inherited disease-causing XPA mutations in the Brazilian population. Additionally, this report demonstrates the effectiveness of genotype-phenotype correlation as a valuable tool to guide direct genetic screening. Full article

(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)

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20 pages, 763 KiB

Open AccessReview

Economically Viable Components from Jerusalem Artichoke (Helianthus tuberosus L.) in a Biorefinery Concept

by Eva Johansson^1,*

, Thomas Prade², Irini Angelidaki³, Sven-Erik Svensson⁴, William R. Newson¹, Ingólfur Bragi Gunnarsson³ and Helena Persson Hovmalm¹

¹ Department of Plant Breeding, the Swedish University of Agricultural Sciences, Box 101, SE-230 53 Alnarp, Sweden

² Environmental and Energy Systems Studies, Lund University, Box 118, SE-221 00 Lund, Sweden

³ Department of Environmental Engineering, Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark

⁴ Department of Biosystems and Technology, the Swedish University of Agricultural Sciences, Box 103, SE-230 53 Alnarp, Sweden

Int. J. Mol. Sci. 2015, 16(4), 8997-9016; https://doi.org/10.3390/ijms16048997 - 22 Apr 2015

Cited by 56 | Viewed by 9323

Abstract

Biorefinery applications are receiving growing interest due to climatic and waste disposal issues and lack of petroleum resources. Jerusalem artichoke (Helianthus tuberosus L.) is suitable for biorefinery applications due to high biomass production and limited cultivation requirements. This paper focuses on the [...] Read more.

Biorefinery applications are receiving growing interest due to climatic and waste disposal issues and lack of petroleum resources. Jerusalem artichoke (Helianthus tuberosus L.) is suitable for biorefinery applications due to high biomass production and limited cultivation requirements. This paper focuses on the potential of Jerusalem artichoke as a biorefinery crop and the most viable products in such a case. The carbohydrates in the tubers were found to have potential for production of platform chemicals, e.g., succinic acid. However, economic analysis showed that production of platform chemicals as a single product was too expensive to be competitive with petrochemically produced sugars. Therefore, production of several products from the same crop is a must. Additional products are protein based ones from tubers and leaves and biogas from residues, although both are of low value and amount. High bioactive activity was found in the young leaves of the crop, and the sesquiterpene lactones are of specific interest, as other compounds from this group have shown inhibitory effects on several human diseases. Thus, future focus should be on understanding the usefulness of small molecules, to develop methods for their extraction and purification and to further develop sustainable and viable methods for the production of platform chemicals. Full article

(This article belongs to the Special Issue Green Chemistry and the Biorefinery)

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Int. J. Mol. Sci., Volume 16, Issue 4 (April 2015) – 143 articles , Pages 6621-9036

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