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Int. J. Mol. Sci., Volume 15, Issue 6 (June 2014), Pages 9173-11203

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Open AccessCommunication Expression of Human Endogenous Retrovirus env Genes in the Blood of Breast Cancer Patients
Int. J. Mol. Sci. 2014, 15(6), 9173-9183; doi:10.3390/ijms15069173
Received: 28 February 2014 / Revised: 13 May 2014 / Accepted: 13 May 2014 / Published: 26 May 2014
Cited by 7 | PDF Full-text (480 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Human endogenous retroviruses (HERV) env proteins have been recently reported to be significantly up-regulated in certain cancers. Specifically, mRNA and protein levels of HERV-K (HML-2) are up-regulated in the blood plasma or serum of breast cancer patients. Here, we collected blood samples [...] Read more.
Human endogenous retroviruses (HERV) env proteins have been recently reported to be significantly up-regulated in certain cancers. Specifically, mRNA and protein levels of HERV-K (HML-2) are up-regulated in the blood plasma or serum of breast cancer patients. Here, we collected blood samples of 49 breast cancer patients and analyzed mRNA expressions of various HERVs env genes including HERV-R, HERV-H, HERV-K, and HERV-P by real-time PCR. The expression of env genes were significantly increased in the blood of primary breast cancer patients but were decreased in patients undergoing chemotherapy to a similar level with benign patients. When we compared the group currently undergoing chemotherapy and those patients undergoing chemotherapy simultaneously with radiotherapy, HERVs env genes were reduced more in the chemotherapy only group, suggesting that chemotherapy is more effective in reducing HERV env gene expression than is radiotherapy. Among chemotherapy groups, HERV env gene expression was the lowest in the taxotere- or taxol-treated group, suggesting that taxotere and taxol can reduce HERVs env expression. These data suggest the potential to use HERVs env genes as a diagnosis marker for primary breast cancer, and further studies are needed to identify the mechanism and physiological significance of the reduction of HERV env gene expression during chemotherapy. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle A Simple Three-Step Method for Design and Affinity Testing of New Antisense Peptides: An Example of Erythropoietin
Int. J. Mol. Sci. 2014, 15(6), 9209-9223; doi:10.3390/ijms15069209
Received: 30 March 2014 / Revised: 9 May 2014 / Accepted: 12 May 2014 / Published: 26 May 2014
Cited by 4 | PDF Full-text (545 KB) | HTML Full-text | XML Full-text
Abstract
Antisense peptide technology is a valuable tool for deriving new biologically active molecules and performing peptide–receptor modulation. It is based on the fact that peptides specified by the complementary (antisense) nucleotide sequences often bind to each other with a higher specificity and [...] Read more.
Antisense peptide technology is a valuable tool for deriving new biologically active molecules and performing peptide–receptor modulation. It is based on the fact that peptides specified by the complementary (antisense) nucleotide sequences often bind to each other with a higher specificity and efficacy. We tested the validity of this concept on the example of human erythropoietin, a well-characterized and pharmacologically relevant hematopoietic growth factor. The purpose of the work was to present and test simple and efficient three-step procedure for the design of an antisense peptide targeting receptor-binding site of human erythropoietin. Firstly, we selected the carboxyl-terminal receptor binding region of the molecule (epitope) as a template for the antisense peptide modeling; Secondly, we designed an antisense peptide using mRNA transcription of the epitope sequence in the 3'→5' direction and computational screening of potential paratope structures with BLAST; Thirdly, we evaluated sense–antisense (epitope–paratope) peptide binding and affinity by means of fluorescence spectroscopy and microscale thermophoresis. Both methods showed similar Kd values of 850 and 816 µM, respectively. The advantages of the methods were: fast screening with a small quantity of the sample needed, and measurements done within the range of physicochemical parameters resembling physiological conditions. Antisense peptides targeting specific erythropoietin region(s) could be used for the development of new immunochemical methods. Selected antisense peptides with optimal affinity are potential lead compounds for the development of novel diagnostic substances, biopharmaceuticals and vaccines. Full article
(This article belongs to the collection Proteins and Protein-Ligand Interactions)
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Open AccessArticle The Application of an Emerging Technique for Protein–Protein Interaction Interface Mapping: The Combination of Photo-Initiated Cross-Linking Protein Nanoprobes with Mass Spectrometry
Int. J. Mol. Sci. 2014, 15(6), 9224-9241; doi:10.3390/ijms15069224
Received: 17 January 2014 / Revised: 6 May 2014 / Accepted: 9 May 2014 / Published: 26 May 2014
Cited by 5 | PDF Full-text (1150 KB) | HTML Full-text | XML Full-text
Abstract
Protein–protein interaction was investigated using a protein nanoprobe capable of photo-initiated cross-linking in combination with high-resolution and tandem mass spectrometry. This emerging experimental approach introduces photo-analogs of amino acids within a protein sequence during its recombinant expression, preserves native protein structure and [...] Read more.
Protein–protein interaction was investigated using a protein nanoprobe capable of photo-initiated cross-linking in combination with high-resolution and tandem mass spectrometry. This emerging experimental approach introduces photo-analogs of amino acids within a protein sequence during its recombinant expression, preserves native protein structure and is suitable for mapping the contact between two proteins. The contact surface regions involved in the well-characterized interaction between two molecules of human 14-3-3ζ regulatory protein were used as a model. The employed photo-initiated cross-linking techniques extend the number of residues shown to be within interaction distance in the contact surface of the 14-3-3ζ dimer (Gln8–Met78). The results of this study are in agreement with our previously published data from molecular dynamic calculations based on high-resolution chemical cross-linking data and Hydrogen/Deuterium exchange mass spectrometry. The observed contact is also in accord with the 14-3-3ζ X-ray crystal structure (PDB 3dhr). The results of the present work are relevant to the structural biology of transient interaction in the 14-3-3ζ protein, and demonstrate the ability of the chosen methodology (the combination of photo-initiated cross-linking protein nanoprobes and mass spectrometry analysis) to map the protein-protein interface or regions with a flexible structure. Full article
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Open AccessArticle Genetic Isolation among the Northwestern, Southwestern and Central-Eastern Indian Ocean Populations of the Pronghorn Spiny Lobster Panulirus penicillatus
Int. J. Mol. Sci. 2014, 15(6), 9242-9254; doi:10.3390/ijms15069242
Received: 10 April 2014 / Revised: 14 May 2014 / Accepted: 16 May 2014 / Published: 26 May 2014
Cited by 4 | PDF Full-text (457 KB) | HTML Full-text | XML Full-text
Abstract
The pronghorn spiny lobster Panulirus penicillatus is a highly valuable species which is widely distributed in Indo-West Pacific and Eastern Pacific regions. Mitochondrial DNA control region sequences (566–571 bp) were determined to investigate the population genetic structure of this species in the [...] Read more.
The pronghorn spiny lobster Panulirus penicillatus is a highly valuable species which is widely distributed in Indo-West Pacific and Eastern Pacific regions. Mitochondrial DNA control region sequences (566–571 bp) were determined to investigate the population genetic structure of this species in the Indian Ocean. In total, 236 adult individuals of Panulirus penicillatus were collected from five locations in the Indian Ocean region. Almost all individuals had a unique haplotype. Intrapopulation haplotype (h) and nucleotide (π) diversities were high for each locality, ranging from h = 0.9986–1.0000 and π = 0.031593–0.043441. We observed distinct genetic isolation of population located at the northwestern and southwestern edge of the species range. Gene flow was found within localities in the central and eastern region of the Indian Ocean, probably resulting from an extended planktonic larval stage and prevailing ocean currents. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
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Open AccessArticle Searching for “Environmentally-Benign” Antifouling Biocides
Int. J. Mol. Sci. 2014, 15(6), 9255-9284; doi:10.3390/ijms15069255
Received: 31 March 2014 / Revised: 1 May 2014 / Accepted: 9 May 2014 / Published: 26 May 2014
Cited by 4 | PDF Full-text (622 KB) | HTML Full-text | XML Full-text
Abstract
As the result of the ecological impacts from the use of tributyltins (TBT) in shipping, environmental legislation for the registration of chemicals for use in the environment has grown to a monumental challenge requiring product dossiers to include information on the environmental [...] Read more.
As the result of the ecological impacts from the use of tributyltins (TBT) in shipping, environmental legislation for the registration of chemicals for use in the environment has grown to a monumental challenge requiring product dossiers to include information on the environmental fate and behavior of any chemicals. Specifically, persistence, bioaccumulation and toxicity, collectively known as PBT, are properties of concern in the assessment of chemicals. However, existing measurements of PBT properties are a cumbersome and expensive process, and thus not applied in the early stages of the product discovery and development. Inexpensive methods for preliminary PBT screening would minimize risks arising with the subsequent registration of products. In this article, we evaluated the PBT properties of compounds reported to possess anti-fouling properties using QSAR (quantitative structure-activity relationship) prediction programs such as BIOWIN™ (a biodegradation probability program), KOWWIN™ (log octanol-water partition coefficient calculation program) and ECOSAR™ (Ecological Structure Activity Relationship Programme). The analyses identified some small (Mr < 400) synthetic and natural products as potential candidates for environmentally benign biocides. We aim to demonstrate that while these methods of estimation have limitations, when applied with discretion, they are powerful tools useful in the early stages of research for compound selection for further development as anti-foulants. Full article
(This article belongs to the Special Issue New Non (Limited)-Toxic Antifouling Solutions)
Open AccessArticle Proteome Analysis of Subsarcolemmal Cardiomyocyte Mitochondria: A Comparison of Different Analytical Platforms
Int. J. Mol. Sci. 2014, 15(6), 9285-9301; doi:10.3390/ijms15069285
Received: 3 April 2014 / Revised: 9 May 2014 / Accepted: 16 May 2014 / Published: 26 May 2014
PDF Full-text (1377 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Mitochondria are complex organelles that play critical roles in diverse aspects of cellular function. Heart disease and a number of other pathologies are associated with perturbations in the molecular machinery of the mitochondria. Therefore, comprehensive, unbiased examination of the mitochondrial proteome represents [...] Read more.
Mitochondria are complex organelles that play critical roles in diverse aspects of cellular function. Heart disease and a number of other pathologies are associated with perturbations in the molecular machinery of the mitochondria. Therefore, comprehensive, unbiased examination of the mitochondrial proteome represents a powerful approach toward system-level insights into disease mechanisms. A crucial aspect in proteomics studies is design of bioanalytical strategies that maximize coverage of the complex repertoire of mitochondrial proteins. In this study, we evaluated the performance of gel-based and gel-free multidimensional platforms for profiling of the proteome in subsarcolemmal mitochondria harvested from rat heart. We compared three different multidimensional proteome fractionation platforms: polymeric reversed-phase liquid chromatography at high pH (PLRP), sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and isoelectric focusing (IEF) separations combined with liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS), and bioinformatics for protein identification. Across all three platforms, a total of 1043 proteins were identified. Among the three bioanalytical strategies, SDS-PAGE followed by LC-MS/MS provided the best coverage of the mitochondrial proteome. With this platform, 890 proteins with diverse physicochemical characteristics were identified; the mitochondrial protein panel encompassed proteins with various functional roles including bioenergetics, protein import, and mitochondrial fusion. Taken together, results of this study provide a large-scale view of the proteome in subsarcolemmal mitochondria from the rat heart, and aid in the selection of optimal bioanalytical platforms for differential protein expression profiling of mitochondria in health and disease. Full article
(This article belongs to the collection Advances in Proteomic Research)
Open AccessArticle Rare Variants in Genes Encoding MuRF1 and MuRF2 Are Modifiers of Hypertrophic Cardiomyopathy
Int. J. Mol. Sci. 2014, 15(6), 9302-9313; doi:10.3390/ijms15069302
Received: 7 March 2014 / Revised: 23 April 2014 / Accepted: 30 April 2014 / Published: 26 May 2014
Cited by 9 | PDF Full-text (218 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Modifier genes contribute to the diverse clinical manifestations of hypertrophic cardiomyopathy (HCM), but are still largely unknown. Muscle ring finger (MuRF) proteins are a class of muscle-specific ubiquitin E3-ligases that appear to modulate cardiac mass and function by regulating the ubiquitin-proteasome system. [...] Read more.
Modifier genes contribute to the diverse clinical manifestations of hypertrophic cardiomyopathy (HCM), but are still largely unknown. Muscle ring finger (MuRF) proteins are a class of muscle-specific ubiquitin E3-ligases that appear to modulate cardiac mass and function by regulating the ubiquitin-proteasome system. In this study we screened all the three members of the MuRF family, MuRF1, MuRF2 and MuRF3, in 594 unrelated HCM patients and 307 healthy controls by targeted resequencing. Identified rare variants were confirmed by capillary Sanger sequencing. The prevalence of rare variants in both MuRF1 and MuRF2 in HCM patients was higher than that in control subjects (MuRF1 13/594 (2.2%) vs. 1/307 (0.3%), p = 0.04; MuRF2 22/594 (3.7%) vs. 2/307 (0.7%); p = 0.007). Patients with rare variants in MuRF1 or MuRF2 were younger (p = 0.04) and had greater maximum left ventricular wall thickness (p = 0.006) than those without such variants. Mutations in genes encoding sarcomere proteins were present in 19 (55.9%) of the 34 HCM patients with rare variants in MuRF1 and MuRF2. These data strongly supported that rare variants in MuRF1 and MuRF2 are associated with higher penetrance and more severe clinical manifestations of HCM. The findings suggest that dysregulation of the ubiquitin-proteasome system contributes to the pathogenesis of HCM. Full article
(This article belongs to the Section Molecular Diagnostics)
Open AccessArticle Maize ZmRACK1 Is Involved in the Plant Response to Fungal Phytopathogens
Int. J. Mol. Sci. 2014, 15(6), 9343-9359; doi:10.3390/ijms15069343
Received: 29 March 2014 / Revised: 25 April 2014 / Accepted: 13 May 2014 / Published: 26 May 2014
Cited by 6 | PDF Full-text (2028 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The receptor for activated C kinase 1 (RACK1) belongs to a protein subfamily containing a tryptophan-aspartic acid-domain (WD) repeat structure. Compelling evidence indicates that RACK1 can interact with many signal molecules and affect different signal transduction pathways. In this study, we cloned [...] Read more.
The receptor for activated C kinase 1 (RACK1) belongs to a protein subfamily containing a tryptophan-aspartic acid-domain (WD) repeat structure. Compelling evidence indicates that RACK1 can interact with many signal molecules and affect different signal transduction pathways. In this study, we cloned a maize RACK1 gene (ZmRACK1) by RT-PCR. The amino acid sequence of ZmRACK1 had seven WD repeats in which there were typical GH (glycine-histidine) and WD dipeptides. Comparison with OsRACK1 from rice revealed 89% identity at the amino acid level. Expression pattern analysis by RT-PCR showed that ZmRACK1 was expressed in all analyzed tissues of maize and that its transcription in leaves was induced by abscisic acid and jasmonate at a high concentration. Overexpression of ZmRACK1 in maize led to a reduction in symptoms caused by Exserohilum turcicum (Pass.) on maize leaves. The expression levels of the pathogenesis-related protein genes, PR-1 and PR-5, increased 2.5–3 times in transgenic maize, and reactive oxygen species production was more active than in the wild-type. Yeast two-hybrid assays showed that ZmRACK1 could interact with RAC1, RAR1 and SGT1. This study and previous work leads us to believe that ZmRACK1 may form a complex with regulators of plant disease resistance to coordinate maize reactions to pathogens. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Therapeutic Effect of Bone Marrow Mesenchymal Stem Cells on Laser-Induced Retinal Injury in Mice
Int. J. Mol. Sci. 2014, 15(6), 9372-9385; doi:10.3390/ijms15069372
Received: 1 April 2014 / Revised: 29 April 2014 / Accepted: 12 May 2014 / Published: 27 May 2014
Cited by 3 | PDF Full-text (2814 KB) | HTML Full-text | XML Full-text
Abstract
Stem cell therapy has shown encouraging results for neurodegenerative diseases. The retina provides a convenient locus to investigate stem cell functions and distribution in the nervous system. In the current study, we investigated the therapeutic potential of bone marrow mesenchymal stem cells [...] Read more.
Stem cell therapy has shown encouraging results for neurodegenerative diseases. The retina provides a convenient locus to investigate stem cell functions and distribution in the nervous system. In the current study, we investigated the therapeutic potential of bone marrow mesenchymal stem cells (MSCs) by systemic transplantation in a laser-induced retinal injury model. MSCs from C57BL/6 mice labeled with green fluorescent protein (GFP) were injected via the tail vein into mice after laser photocoagulation. We found that the average diameters of laser spots and retinal cell apoptosis were decreased in the MSC-treated group. Interestingly, GFP-MSCs did not migrate to the injured retina. Further examination revealed that the mRNA expression levels of glial fibrillary acidic protein and matrix metalloproteinase-2 were lower in the injured eyes after MSC transplantation. Our results suggest that intravenously injected MSCs have the ability to inhibit retinal cell apoptosis, reduce the inflammatory response and limit the spreading of damage in the laser-injured retina of mice. Systemic MSC therapy might play a role in neuroprotection, mainly by regulation of the intraocular microenvironment. Full article
(This article belongs to the Special Issue Neurological Injuries’ Monitoring, Tracking and Treatment)
Open AccessArticle The Transcriptomes of the Crucian Carp Complex (Carassius auratus) Provide Insights into the Distinction between Unisexual Triploids and Sexual Diploids
Int. J. Mol. Sci. 2014, 15(6), 9386-9406; doi:10.3390/ijms15069386
Received: 29 January 2014 / Revised: 15 May 2014 / Accepted: 16 May 2014 / Published: 27 May 2014
Cited by 2 | PDF Full-text (683 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Both sexual reproduction and unisexual reproduction are adaptive strategies for species survival and evolution. Unisexual animals have originated largely by hybridization, which tends to elevate their heterozygosity. However, the extent of genetic diversity resulting from hybridization and the genomic differences that determine [...] Read more.
Both sexual reproduction and unisexual reproduction are adaptive strategies for species survival and evolution. Unisexual animals have originated largely by hybridization, which tends to elevate their heterozygosity. However, the extent of genetic diversity resulting from hybridization and the genomic differences that determine the type of reproduction are poorly understood. In Carassius auratus, sexual diploids and unisexual triploids coexist. These two forms are similar morphologically but differ markedly in their modes of reproduction. Investigation of their genomic differences will be useful to study genome diversity and the development of reproductive mode. We generated transcriptomes for the unisexual and sexual populations. Genes were identified using homology searches and an ab initio method. Estimation of the synonymous substitution rate in the orthologous pairs indicated that the hybridization of gibel carp occurred 2.2 million years ago. Microsatellite genotyping in each individual from the gibel carp population indicated that most gibel carp genes were not tri-allelic. Molecular function and pathway comparisons suggested few gene expansions between them, except for the progesterone-mediated oocyte maturation pathway, which is enriched in gibel carp. Differential expression analysis identified highly expressed genes in gibel carp. The transcriptomes provide information on genetic diversity and genomic differences, which should assist future studies in functional genomics. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Quantitative Proteomics to Characterize Specific Histone H2A Proteolysis in Chronic Lymphocytic Leukemia and the Myeloid THP-1 Cell Line
Int. J. Mol. Sci. 2014, 15(6), 9407-9421; doi:10.3390/ijms15069407
Received: 6 February 2014 / Revised: 30 April 2014 / Accepted: 21 May 2014 / Published: 27 May 2014
Cited by 1 | PDF Full-text (1090 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Proteome studies on hematological malignancies contribute to the understanding of the disease mechanism and to the identification of new biomarker candidates. With the isobaric tag for relative and absolute quantitation (iTRAQ) method we analyzed the protein expression between B-cells of healthy people [...] Read more.
Proteome studies on hematological malignancies contribute to the understanding of the disease mechanism and to the identification of new biomarker candidates. With the isobaric tag for relative and absolute quantitation (iTRAQ) method we analyzed the protein expression between B-cells of healthy people and chronic lymphocytic leukemia (CLL) B-cells. CLL is the most common lymphoid cancer of the blood and is characterized by a variable clinical course. By comparing samples of patients with an aggressive vs. indolent disease, we identified a limited list of differentially regulated proteins. The enhanced sensitivity attributed to the iTRAQ labels led to the discovery of a previously reported but still not clarified proteolytic product of histone H2A (cH2A) which we further investigated in light of the suggested functional properties of this modification. In the exploratory proteome study the Histone H2A peptide was up-regulated in CLL samples but a more specific and sensitive screening of a larger patient cohort indicated that cH2A is of myeloid origin. Our subsequent quantitative analysis led to a more profound characterization of the clipping in acute monocytic leukemia THP-1 cells subjected to induced differentiation. Full article
(This article belongs to the Special Issue Mass Spectrometry Application in Biology) Print Edition available
Open AccessArticle Synthesis, Characterization and Photocatalytic Activity of New Photocatalyst ZnBiSbO4 under Visible Light Irradiation
Int. J. Mol. Sci. 2014, 15(6), 9459-9480; doi:10.3390/ijms15069459
Received: 9 March 2014 / Revised: 9 May 2014 / Accepted: 16 May 2014 / Published: 28 May 2014
Cited by 4 | PDF Full-text (943 KB) | HTML Full-text | XML Full-text
Abstract
In this paper, ZnBiSbO4 was synthesized by a solid-state reaction method for the first time. The structural and photocatalytic properties of ZnBiSbO4 had been characterized by X-ray diffraction, scanning electron microscopy, X-ray photoelectron spectroscopy, Fourier-transform infrared spectroscopy, transmission electron microscope [...] Read more.
In this paper, ZnBiSbO4 was synthesized by a solid-state reaction method for the first time. The structural and photocatalytic properties of ZnBiSbO4 had been characterized by X-ray diffraction, scanning electron microscopy, X-ray photoelectron spectroscopy, Fourier-transform infrared spectroscopy, transmission electron microscope and UV-visible spectrometer. ZnBiSbO4 crystallized with a pyrochlore-type structure and a tetragonal crystal system. The band gap of ZnBiSbO4 was estimated to be 2.49 eV. The photocatalytic degradation of indigo carmine was realized under visible light irradiation with ZnBiSbO4 as a catalyst compared with nitrogen-doped TiO2 (N-TiO2) and CdBiYO4. The results showed that ZnBiSbO4 owned higher photocatalytic activity compared with N-TiO2 or CdBiYO4 for the photocatalytic degradation of indigo carmine under visible light irradiation. The reduction of the total organic carbon, the formation of inorganic products, SO42− and NO3, and the evolution of CO2 revealed the continuous mineralization of indigo carmine during the photocatalytic process. One possible photocatalytic degradation pathway of indigo carmine was obtained. The phytotoxicity of the photocatalytic-treated indigo carmine (IC) wastewater was detected by examining its effect on seed germination and growth. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle A Novel VHH Antibody Targeting the B Cell-Activating Factor for B-Cell Lymphoma
Int. J. Mol. Sci. 2014, 15(6), 9481-9496; doi:10.3390/ijms15069481
Received: 21 April 2014 / Revised: 13 May 2014 / Accepted: 14 May 2014 / Published: 28 May 2014
Cited by 1 | PDF Full-text (647 KB) | HTML Full-text | XML Full-text
Abstract
Objective: To construct an immune alpaca phage display library, in order to obtain a single domain anti-BAFF (B cell-activating factor) antibody. Methods: Using phage display technology, we constructed an immune alpaca phage display library, selected anti-BAFF single domain antibodies (sdAbs), cloned three [...] Read more.
Objective: To construct an immune alpaca phage display library, in order to obtain a single domain anti-BAFF (B cell-activating factor) antibody. Methods: Using phage display technology, we constructed an immune alpaca phage display library, selected anti-BAFF single domain antibodies (sdAbs), cloned three anti-BAFF single-domain antibody genes into expression vector pSJF2, and expressed them efficiently in Escherichia coli. The affinity of different anti-BAFF sdAbs were measured by Bio layer interferometry. The in vitro biological function of three sdAbs was investigated by cell counting kit-8 (CCK-8) assay and a competitive enzyme-linked immunosorbent assay (ELISA). Results: We obtained three anti-BAFF single domain antibodies (anti-BAFF64, anti-BAFF52 and anti-BAFFG3), which were produced in high yield in Escherichia coli and inhibited tumor cell proliferation in vitro. Conclusion: The selected anti-BAFF antibodies could be candidates for B-cell lymphoma therapies. Full article
(This article belongs to the Section Molecular Diagnostics)
Open AccessArticle Evaluation of Zosteric Acid for Mitigating Biofilm Formation of Pseudomonas putida Isolated from a Membrane Bioreactor System
Int. J. Mol. Sci. 2014, 15(6), 9497-9518; doi:10.3390/ijms15069497
Received: 3 December 2013 / Revised: 17 April 2014 / Accepted: 17 April 2014 / Published: 28 May 2014
Cited by 3 | PDF Full-text (790 KB) | HTML Full-text | XML Full-text
Abstract
This study provides data to define an efficient biocide-free strategy based on zosteric acid to counteract biofilm formation on the membranes of submerged bioreactor system plants. 16S rRNA gene phylogenetic analysis showed that gammaproteobacteria was the prevalent taxa on fouled membranes of [...] Read more.
This study provides data to define an efficient biocide-free strategy based on zosteric acid to counteract biofilm formation on the membranes of submerged bioreactor system plants. 16S rRNA gene phylogenetic analysis showed that gammaproteobacteria was the prevalent taxa on fouled membranes of an Italian wastewater plant. Pseudomonas was the prevalent genus among the cultivable membrane-fouler bacteria and Pseudomonas putida was selected as the target microorganism to test the efficacy of the antifoulant. Zosteric acid was not a source of carbon and energy for P. putida cells and, at 200 mg/L, it caused a reduction of bacterial coverage by 80%. Biofilm experiments confirmed the compound caused a significant decrease in biomass (−97%) and thickness (−50%), and it induced a migration activity of the peritrichous flagellated P. putida over the polycarbonate surface not amenable to a biofilm phenotype. The low octanol-water partitioning coefficient and the high water solubility suggested a low bioaccumulation potential and the water compartment as its main environmental recipient and capacitor. Preliminary ecotoxicological tests did not highlight direct toxicity effects toward Daphnia magna. For green algae Pseudokirchneriella subcapitata an effect was observed at concentrations above 100 mg/L with a significant growth of protozoa that may be connected to a concurrent algal growth inhibition. Full article
(This article belongs to the Section Green Chemistry)
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Open AccessArticle Identification of Differentially Expressed miRNAs between White and Black Hair Follicles by RNA-Sequencing in the Goat (Capra hircus)
Int. J. Mol. Sci. 2014, 15(6), 9531-9545; doi:10.3390/ijms15069531
Received: 12 April 2014 / Revised: 12 May 2014 / Accepted: 14 May 2014 / Published: 28 May 2014
Cited by 7 | PDF Full-text (1336 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
MicroRNAs (miRNAs) play a key role in many biological processes by regulating gene expression at the post-transcriptional level. A number of miRNAs have been identified from livestock species. However, compared with other animals, such as pigs and cows, the number of miRNAs [...] Read more.
MicroRNAs (miRNAs) play a key role in many biological processes by regulating gene expression at the post-transcriptional level. A number of miRNAs have been identified from livestock species. However, compared with other animals, such as pigs and cows, the number of miRNAs identified in goats is quite low, particularly in hair follicles. In this study, to investigate the functional roles of miRNAs in goat hair follicles of goats with different coat colors, we sequenced miRNAs from two hair follicles samples (white and black) using Solexa sequencing. A total of 35,604,016 reads were obtained, which included 30,878,637 clean reads (86.73%). MiRDeep2 software identified 214 miRNAs. Among them, 205 were conserved among species and nine were novel miRNAs. Furthermore, DESeq software identified six differentially expressed miRNAs. Quantitative PCR confirmed differential expression of two miRNAs, miR-10b and miR-211. KEGG pathways were analyzed using the DAVID website for the predicted target genes of the differentially expressed miRNAs. Several signaling pathways including Notch and MAPK pathways may affect the process of coat color formation. Our study showed that the identified miRNAs might play an essential role in black and white follicle formation in goats. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Nipple Discharge of CA15-3, CA125, CEA and TSGF as a New Biomarker Panel for Breast Cancer
Int. J. Mol. Sci. 2014, 15(6), 9546-9565; doi:10.3390/ijms15069546
Received: 29 December 2013 / Revised: 14 May 2014 / Accepted: 16 May 2014 / Published: 28 May 2014
Cited by 7 | PDF Full-text (673 KB) | HTML Full-text | XML Full-text
Abstract
Breast cancer is the second leading cause of cancer death in women. Serum biomarkers such as cancer antigen 15-3 (CA15-3), cancer antigen 125 (CA125), and carcinoembryonic antigen (CEA) can be used as diagnostic and prognostic factors and can also provide valuable information [...] Read more.
Breast cancer is the second leading cause of cancer death in women. Serum biomarkers such as cancer antigen 15-3 (CA15-3), cancer antigen 125 (CA125), and carcinoembryonic antigen (CEA) can be used as diagnostic and prognostic factors and can also provide valuable information during follow-up. However, serum protein biomarkers show limited diagnostic sensitivity and specificity in stand-alone assays because their levels reflect tumor burden. To validate whether biomarkers in nipple discharge may serve as novel biomarkers for breast cancer, we composed a panel of potential cancer biomarkers, including CA15-3, CA125, CEA, and malignant tumor-specific growth factor (TSGF), and evaluated their expression in both serum and nipple discharge in order to explore the expression and significance of estrogen receptor (ER), progestrone receptor (PR), epidermal growth factor receptor type 2 (HER2/neu), CA15-3, CA125, CEA, and TSGF expression for their combined predictive value for breast cancer and in judging the prognosis of breast cancer. Univariate analysis revealed that combined detection of CA15-3, CA125, CEA, and TSGF in nipple discharge served as novel biomarkers for the diagnosis and prognosis of breast cancer, but in the multivariate analyses the adverse effects of the four biomarkers combination in nipple discharge positivity on overall survival were lost. Multivariate analysis revealed that the positivity of the combined detection of the four biomarkers in both nipple discharge and serum was significantly higher than that of other detection methods. Thus, the combined detection of these four biomarkers both in serum and nipple discharge was retained as an independent prognostic variable in breast cancer patients. Our results indicate that CA15-3, CA125, CEA, and TSGF in nipple discharge can serve as novel biomarkers in the diagnosis and prognosis of breast cancer. Full article
(This article belongs to the Special Issue Molecular Bases of Cancer Research)
Open AccessArticle New Coumarins and Anti-Inflammatory Constituents from the Fruits of Cnidium monnieri
Int. J. Mol. Sci. 2014, 15(6), 9566-9578; doi:10.3390/ijms15069566
Received: 3 March 2014 / Revised: 7 May 2014 / Accepted: 13 May 2014 / Published: 28 May 2014
Cited by 2 | PDF Full-text (278 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The fruit of Cnidium monnieri is commercially used as healthcare products for the improvement of impotence and skin diseases. Three new coumarins, 3'-O-methylmurraol (1), rel-(1'S,2'S)-1'-O-methylphlojodicarpin (2), and (1'S [...] Read more.
The fruit of Cnidium monnieri is commercially used as healthcare products for the improvement of impotence and skin diseases. Three new coumarins, 3'-O-methylmurraol (1), rel-(1'S,2'S)-1'-O-methylphlojodicarpin (2), and (1'S,2'S)-1'-O-methylvaginol (3), have been isolated from the fruits of C. monnieri, together with 14 known compounds (417). The structures of these new compounds were determined through spectroscopic and MS analyses. Compounds 1, 412, and 1417 exhibited inhibition (IC50 ≤ 7.31 µg/mL) of superoxide anion generation by human neutrophils in response to formyl-l-methionyl-l-leucyl-l-phenylalanine/cytochalasin B (fMLP/CB). Compounds 7, 911, 15, and 17 inhibited fMLP/CB-induced elastase release with IC50 values ≤7.83 µg/mL. This investigation reveals that bioactive isolates (especially 6, 7, 14, and 17) could be further developed as potential candidates for the treatment or prevention of various inflammatory diseases. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
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Open AccessArticle Differential Proteomic Analysis of the Pancreas of Diabetic db/db Mice Reveals the Proteins Involved in the Development of Complications of Diabetes Mellitus
Int. J. Mol. Sci. 2014, 15(6), 9579-9593; doi:10.3390/ijms15069579
Received: 4 April 2014 / Revised: 14 May 2014 / Accepted: 19 May 2014 / Published: 30 May 2014
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Abstract
Type 2 diabetes mellitus is characterized by hyperglycemia and insulin-resistance. Diabetes results from pancreatic inability to secrete the insulin needed to overcome this resistance. We analyzed the protein profile from the pancreas of ten-week old diabetic db/db and wild type [...] Read more.
Type 2 diabetes mellitus is characterized by hyperglycemia and insulin-resistance. Diabetes results from pancreatic inability to secrete the insulin needed to overcome this resistance. We analyzed the protein profile from the pancreas of ten-week old diabetic db/db and wild type mice through proteomics. Pancreatic proteins were separated in two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and significant changes in db/db mice respect to wild type mice were observed in 27 proteins. Twenty five proteins were identified by matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) and their interactions were analyzed using search tool for the retrieval of interacting genes/proteins (STRING) and database for annotation, visualization and integrated discovery (DAVID). Some of these proteins were Pancreatic α-amylase, Cytochrome b5, Lithostathine-1, Lithostathine-2, Chymotrypsinogen B, Peroxiredoxin-4, Aspartyl aminopeptidase, Endoplasmin, and others, which are involved in the metabolism of carbohydrates and proteins, as well as in oxidative stress, and inflammation. Remarkably, these are mostly endoplasmic reticulum proteins related to peptidase activity, i.e., they are involved in proteolysis, glucose catabolism and in the tumor necrosis factor-mediated signaling pathway. These results suggest mechanisms for insulin resistance, and the chronic inflammatory state observed in diabetes. Full article
(This article belongs to the collection Advances in Proteomic Research)
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Open AccessArticle Flowering as the Most Highly Sensitive Period of Grapevine (Vitis vinifera L. cv Mourvèdre) to the Botryosphaeria Dieback Agents Neofusicoccum parvum and Diplodia seriata Infection
Int. J. Mol. Sci. 2014, 15(6), 9644-9669; doi:10.3390/ijms15069644
Received: 8 April 2014 / Revised: 4 May 2014 / Accepted: 13 May 2014 / Published: 30 May 2014
Cited by 6 | PDF Full-text (880 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Botryosphaeria dieback is a fungal grapevine trunk disease that currently represents a threat for viticulture worldwide because of the important economical losses due to reduced yield of affected plants and their premature death. Neofusicoccum parvum and Diplodia seriata are among the causal [...] Read more.
Botryosphaeria dieback is a fungal grapevine trunk disease that currently represents a threat for viticulture worldwide because of the important economical losses due to reduced yield of affected plants and their premature death. Neofusicoccum parvum and Diplodia seriata are among the causal agents. Vine green stems were artificially infected with N. parvum or D. seriata at the onset of three different phenological stages (G stage (separated clusters), flowering and veraison). Highest mean lesion lengths were recorded at flowering. Major proteome changes associated to artificial infections during the three different phenological stages were also reported using two dimensional gel electrophoresis (2D)-based analysis. Twenty (G stage), 15 (flowering) and 13 (veraison) differentially expressed protein spots were subjected to nanoLC-MS/MS and a total of 247, 54 and 25 proteins were respectively identified. At flowering, a weaker response to the infection was likely activated as compared to the other stages, and some defense-related proteins were even down regulated (e.g., superoxide dismutase, major latex-like protein, and pathogenesis related protein 10). Globally, the flowering period seemed to represent the period of highest sensitivity of grapevine to Botryosphaeria dieback agent infection, possibly being related to the high metabolic activity in the inflorescences. Full article
(This article belongs to the collection Advances in Proteomic Research)
Open AccessArticle Clinical Impact of Tumor-Infiltrating Inflammatory Cells in Primary Small Cell Esophageal Carcinoma
Int. J. Mol. Sci. 2014, 15(6), 9718-9734; doi:10.3390/ijms15069718
Received: 1 May 2014 / Revised: 16 May 2014 / Accepted: 22 May 2014 / Published: 30 May 2014
Cited by 2 | PDF Full-text (1616 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Primary small cell esophageal carcinoma is a rare and aggressive type of gastrointestinal cancer with poor prognosis. In the present study, the impact of tumour infiltrating inflammatory cells on clinico-pathological characteristics and the patients’ prognosis were analysed. A total of 36 small [...] Read more.
Primary small cell esophageal carcinoma is a rare and aggressive type of gastrointestinal cancer with poor prognosis. In the present study, the impact of tumour infiltrating inflammatory cells on clinico-pathological characteristics and the patients’ prognosis were analysed. A total of 36 small cell esophageal carcinomas, 19 adjacent normal tissues and 16 esophageal squamous cell carcinoma samples were collected. Qualified pathologists examined eosinophils, neutrophils, lymphocytes and macrophages on histochemical slides. The infiltration of eosinophils and macrophages in small cell esophageal carcinoma was significantly increased as compared with tumor adjacent normal tissues, and was significantly less in esophageal squamous cell carcinoma. Macrophage count was significantly associated with (p = 0.015) lymph node—stage in small cell esophageal carcinoma. When we grouped patients into two groups by counts of infiltrated inflammatory cells, Kaplan-Meier analysis revealed that high macrophage infiltration group (p = 0.004) and high eosinophil infiltration group (p = 0.027) had significantly enhanced survival. In addition, multivariate analysis unveiled that eosinophil count (p = 0.002) and chemotherapy (Yes vs. No, p = 0.001) were independent prognostic indicators. Taken together, infiltration of macrophages and eosinophils into the solid tumor appear to be important in the progression of small cell esophageal carcinoma and patients’ prognosis. Full article
(This article belongs to the Special Issue Advances in Molecular Oncology 2014)
Open AccessArticle Genotypic Characterization of Escherichia coli O157:H7 Isolates from Different Sources in the North-West Province, South Africa, Using Enterobacterial Repetitive Intergenic Consensus PCR Analysis
Int. J. Mol. Sci. 2014, 15(6), 9735-9747; doi:10.3390/ijms15069735
Received: 12 March 2014 / Revised: 4 May 2014 / Accepted: 6 May 2014 / Published: 30 May 2014
Cited by 3 | PDF Full-text (528 KB) | HTML Full-text | XML Full-text
Abstract
In many developing countries, proper hygiene is not strictly implemented when animals are slaughtered and meat products become contaminated. Contaminated meat may contain Escherichia coli (E. coli) O157:H7 that could cause diseases in humans if these food products are consumed [...] Read more.
In many developing countries, proper hygiene is not strictly implemented when animals are slaughtered and meat products become contaminated. Contaminated meat may contain Escherichia coli (E. coli) O157:H7 that could cause diseases in humans if these food products are consumed undercooked. In the present study, a total of 94 confirmed E. coli O157:H7 isolates were subjected to the enterobacterial repetitive intergenic consensus (ERIC) polymerase chain reaction (PCR) typing to generate genetic fingerprints. The ERIC fragments were resolved by electrophoresis on 2% (w/v) agarose gels. The presence, absence and intensity of band data were obtained, exported to Microsoft Excel (Microsoft Office 2003) and used to generate a data matrix. The unweighted pair group method with arithmetic mean (UPGMA) and complete linkage algorithms were used to analyze the percentage of similarity and matrix data. Relationships between the various profiles and/or lanes were expressed as dendrograms. Data from groups of related lanes were compiled and reported on cluster tables. ERIC fragments ranged from one to 15 per isolate, and their sizes varied from 0.25 to 0.771 kb. A large proportion of the isolates produced an ERIC banding pattern with three duplets ranging in sizes from 0.408 to 0.628 kb. Eight major clusters (I–VIII) were identified. Overall, the remarkable similarities (72% to 91%) between the ERIC profiles for the isolate from animal species and their corresponding food products indicated some form of contamination, which may not exclude those at the level of the abattoirs. These results reveal that ERIC PCR analysis can be reliable in comparing the genetic profiles of E. coli O157:H7 from different sources in the North-West Province of South Africa. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Gamma Knife Treatment of Brainstem Metastases
Int. J. Mol. Sci. 2014, 15(6), 9748-9761; doi:10.3390/ijms15069748
Received: 30 March 2014 / Revised: 1 May 2014 / Accepted: 5 May 2014 / Published: 30 May 2014
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Abstract
The management of brainstem metastases is challenging. Surgical treatment is usually not an option, and chemotherapy is of limited utility. Stereotactic radiosurgery has emerged as a promising palliative treatment modality in these cases. The goal of this study is to assess our [...] Read more.
The management of brainstem metastases is challenging. Surgical treatment is usually not an option, and chemotherapy is of limited utility. Stereotactic radiosurgery has emerged as a promising palliative treatment modality in these cases. The goal of this study is to assess our single institution experience treating brainstem metastases with Gamma Knife radiosurgery (GKRS). This retrospective chart review studied 41 patients with brainstem metastases treated with GKRS. The most common primary tumors were lung, breast, renal cell carcinoma, and melanoma. Median age at initial treatment was 59 years. Nineteen (46%) of the patients received whole brain radiation therapy (WBRT) prior to or concurrent with GKRS treatment. Thirty (73%) of the patients had a single brainstem metastasis. The average GKRS dose was 17 Gy. Post-GKRS overall survival at six months was 42%, at 12 months was 22%, and at 24 months was 13%. Local tumor control was achieved in 91% of patients, and there was one patient who had a fatal brain hemorrhage after treatment. Karnofsky performance score (KPS) >80 and the absence of prior WBRT were predictors for improved survival on multivariate analysis (HR 0.60 (p = 0.02), and HR 0.28 (p = 0.02), respectively). GKRS was an effective treatment for brainstem metastases, with excellent local tumor control. Full article
(This article belongs to the Special Issue Brain Metastasis 2014)
Open AccessArticle Corilagin Attenuates Aerosol Bleomycin-Induced Experimental Lung Injury
Int. J. Mol. Sci. 2014, 15(6), 9762-9779; doi:10.3390/ijms15069762
Received: 18 February 2013 / Revised: 16 March 2014 / Accepted: 22 May 2014 / Published: 30 May 2014
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Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressing lethal disease with few clinically effective therapies. Corilagin is a tannin derivative which shows anti-inflammatory and antifibrotics properties and is potentiated in treating IPF. Here, we investigated the effect of corilagin on lung injury following [...] Read more.
Idiopathic pulmonary fibrosis (IPF) is a progressing lethal disease with few clinically effective therapies. Corilagin is a tannin derivative which shows anti-inflammatory and antifibrotics properties and is potentiated in treating IPF. Here, we investigated the effect of corilagin on lung injury following bleomycin exposure in an animal model of pulmonary fibrosis. Corilagin abrogated bleomycin-induced lung fibrosis as assessed by H&E; Masson’s trichrome staining and lung hydroxyproline content in lung tissue. Corilagin reduced the number of apoptotic lung cells and prevented lung epithelial cells from membrane breakdown, effluence of lamellar bodies and thickening of the respiratory membrane. Bleomycin exposure induced expression of MDA, IKKα, phosphorylated IKKα (p-IKKα), NF-κB P65, TNF-α and IL-1β, and reduced I-κB expression in mice lung tissue or in BALF. These changes were reversed by high-dose corilagin (100 mg/kg i.p) more dramatically than by low dose (10 mg/kg i.p). Last, corilagin inhibits TGF-β1 production and α-SMA expression in lung tissue samples. Taken together, these findings confirmed that corilagin attenuates bleomycin-induced epithelial injury and fibrosis via inactivation of oxidative stress, proinflammatory cytokine release and NF-κB and TGF-β1 signaling. Corilagin may serve as a promising therapeutic agent for pulmonary fibrosis. Full article
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Open AccessArticle Multiplex Hydrolysis Probe Real-Time PCR for Simultaneous Detection of Hepatitis A Virus and Hepatitis E Virus
Int. J. Mol. Sci. 2014, 15(6), 9780-9788; doi:10.3390/ijms15069780
Received: 11 February 2014 / Revised: 31 March 2014 / Accepted: 21 April 2014 / Published: 30 May 2014
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Abstract
Detection of hepatitis viral infections has traditionally relied on the circulating antibody test using the enzyme-linked immunosorbent assay. However, multiplex real-time PCR has been increasingly used for a variety of viral nucleic acid detections and has proven to be superior to traditional [...] Read more.
Detection of hepatitis viral infections has traditionally relied on the circulating antibody test using the enzyme-linked immunosorbent assay. However, multiplex real-time PCR has been increasingly used for a variety of viral nucleic acid detections and has proven to be superior to traditional methods. Hepatitis A virus (HAV) and hepatitis E virus (HEV) are the major causes of acute hepatitis worldwide; both HAV and HEV infection are a main public health problem. In the present study, a one-step multiplex reverse transcriptase quantitative polymerase chain reaction assay using hydrolysis probes was developed for simultaneously detecting HAV and HEV. This novel detection system proved specific to the target viruses, to be highly sensitive and to be applicable to clinical sera samples, making it useful for rapid, accurate and feasible identification of HAV and HEV. Full article
(This article belongs to the Section Molecular Diagnostics)
Open AccessArticle Preparation and Enzymatic Degradation of Porous Crosslinked Polylactides of Biomass Origin
Int. J. Mol. Sci. 2014, 15(6), 9793-9808; doi:10.3390/ijms15069793
Received: 15 April 2014 / Revised: 13 May 2014 / Accepted: 20 May 2014 / Published: 2 June 2014
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Abstract
To understand the enzymatic degradation behavior of crosslinked polylactide (PLA), the preparation and enzymatic degradation of both thermoplastic (linear) and crosslinked PLAs that have pore structures with different dimensions were carried out. The porous structures of the linear PLA samples were of [...] Read more.
To understand the enzymatic degradation behavior of crosslinked polylactide (PLA), the preparation and enzymatic degradation of both thermoplastic (linear) and crosslinked PLAs that have pore structures with different dimensions were carried out. The porous structures of the linear PLA samples were of micro and nanoporous nature, and prepared by batch foaming with supercritical CO2 and compared with the porous structures of crosslinked PLA (Lait-X) created by the salt leaching method. The surface and cross-sectional morphologies of the porous structures were investigated by using scanning electron microscopy. The morphological analysis of porous Lait-X showed a rapid loss of physical features within 120 h of exposure to proteinase-K enzymatic degradation at 37 °C. Due to the higher affinity for water, enhanced enzymatic activity as compared to the linear PLA porous structures in the micro and nanoporous range was observed. Full article
(This article belongs to the Special Issue Biodegradability of Materials)
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Open AccessArticle Genetic Variants in Human Leukocyte Antigen-DP Influence Both Hepatitis C Virus Persistence and Hepatitis C Virus F Protein Generation in the Chinese Han Population
Int. J. Mol. Sci. 2014, 15(6), 9826-9843; doi:10.3390/ijms15069826
Received: 3 March 2014 / Revised: 19 May 2014 / Accepted: 21 May 2014 / Published: 3 June 2014
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Abstract
Chronic hepatitis C is a serious liver disease that often results in cirrhosis or hepatocellular carcinoma. The aim of this study was to assess the association of human leukocyte antigen-DP (HLA-DP) variants with risk of chronic hepatitis C virus [...] Read more.
Chronic hepatitis C is a serious liver disease that often results in cirrhosis or hepatocellular carcinoma. The aim of this study was to assess the association of human leukocyte antigen-DP (HLA-DP) variants with risk of chronic hepatitis C virus (HCV) or anti-F antibody generation. We selected two single nucleotide polymorphisms (SNPs) in a region including HLA-DPA1 (rs3077) and HLA-DPB1 (rs9277534) and genotyped SNPs in 702 cases and 342 healthy controls from the Chinese population using TaqMan SNP genotyping assay. Moreover, the exon 2 of the HLA-DPA1 and HLA-DPB1 genes were amplified and determined by sequencing-based typing (SBT). The results showed that rs3077 significantly increased the risk of chronic HCV infection in additive models and dominant models (odds ratio (OR) = 1.32 and 1.53). The rs3077 also contributed to decrease the risk of anti-F antibody generation in additive models and dominant models (OR = 0.46 and 0.56). Subsequent analyses revealed the risk haplotypes (DPA1*0103-DPB1*0501 and DPA1*0103-DPB1*0201) and protective haplotypes (DPA1*0202-DPB1*0501 and DPA1*0202-DPB1*0202) to chronic HCV infection. Moreover, we also found that the haplotype of DPA1*0103-DPB1*0201 and DPA1*0202-DPB1*0202 were associated with the anti-F antibody generation. Our findings show that genetic variants in HLA-DP gene are associated with chronic HCV infection and anti-F antibody generation. Full article
(This article belongs to the Special Issue Molecular Bases of Cancer Research)
Open AccessArticle Qualitative Analysis of the Helical Electronic Energy of Inherently Chiral Calix[4]arenes: An Approach to Effectively Assign Their Absolute Configuration
Int. J. Mol. Sci. 2014, 15(6), 9844-9858; doi:10.3390/ijms15069844
Received: 27 March 2014 / Revised: 4 May 2014 / Accepted: 12 May 2014 / Published: 3 June 2014
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Abstract
For all microhelices on aromatic rings of inherently chiral calix[4]arene, an expression was derived from one approximation and one hypothesis on the basis of the electron-on-a-helix model of Tinoco and Woody as follows: 1/E = μ (HK Δ [...] Read more.
For all microhelices on aromatic rings of inherently chiral calix[4]arene, an expression was derived from one approximation and one hypothesis on the basis of the electron-on-a-helix model of Tinoco and Woody as follows: 1/E = μ (HK Δα2) , where μ = 1 for the right-handed microhelix and μ = −1 for the left-handed microhelix; and H and K are constant and greater than zero. The expression correlates microhelical electronic energy (E) with the atom polarizability difference (Δα) on both microhelix ends, which intuitively and clearly shows the impact of helical substituent polarizability on helical electronic energy. The case analysis almost entirely proves that the qualitative analysis of the helical electronic energy of inherently chiral calix[4]arenes with the expression is scientific and can be used to effectively assign their absolute configuration Full article
Open AccessArticle Ginsenoside Rd Attenuates Mitochondrial Permeability Transition and Cytochrome c Release in Isolated Spinal Cord Mitochondria: Involvement of Kinase-Mediated Pathways
Int. J. Mol. Sci. 2014, 15(6), 9859-9877; doi:10.3390/ijms15069859
Received: 25 April 2014 / Revised: 8 May 2014 / Accepted: 21 May 2014 / Published: 3 June 2014
Cited by 4 | PDF Full-text (1555 KB) | HTML Full-text | XML Full-text
Abstract
Ginsenoside Rd (Rd), one of the main active ingredients in Panax ginseng, has multifunctional activity via different mechanisms and neuroprotective effects that are exerted probably via its antioxidant or free radical scavenger action. However, the effects of Rd on spinal cord mitochondrial [...] Read more.
Ginsenoside Rd (Rd), one of the main active ingredients in Panax ginseng, has multifunctional activity via different mechanisms and neuroprotective effects that are exerted probably via its antioxidant or free radical scavenger action. However, the effects of Rd on spinal cord mitochondrial dysfunction and underlying mechanisms are still obscure. In this study, we sought to investigate the in vitro effects of Rd on mitochondrial integrity and redox balance in isolated spinal cord mitochondria. We verified that Ca2+ dissipated the membrane potential, provoked mitochondrial swelling and decreased NAD(P)H matrix content, which were all attenuated by Rd pretreatment in a dose-dependent manner. In contrast, Rd was not able to inhibit Ca2+ induced mitochondrial hydrogen peroxide generation. The results of Western blot showed that Rd significantly increased the expression of p-Akt and p-ERK, but had no effects on phosphorylation of PKC and p38. In addition, Rd treatment significantly attenuated Ca2+ induced cytochrome c release, which was partly reversed by antagonists of Akt and ERK, but not p-38 inhibitor. The effects of bisindolylmaleimide, a PKC inhibitor, on Rd-induced inhibition of cytochrome c release seem to be at the level of its own detrimental activity on mitochondrial function. Furthermore, we also found that pretreatment with Rd in vivo (10 and 50 mg/kg) protected spinal cord mitochondria against Ca2+ induced mitochondrial membrane potential dissipation and cytochrome c release. It is concluded that Rd regulate mitochondrial permeability transition pore formation and cytochrome c release through protein kinases dependent mechanism involving activation of intramitochondrial Akt and ERK pathways. Full article
(This article belongs to the Special Issue Neuroprotective Strategies 2014)
Open AccessArticle High Cytoplasmic Expression of Krüppel-like Factor 4 Is an Independent Prognostic Factor of Better Survival in Hepatocellular Carcinoma
Int. J. Mol. Sci. 2014, 15(6), 9894-9906; doi:10.3390/ijms15069894
Received: 6 March 2014 / Revised: 26 May 2014 / Accepted: 26 May 2014 / Published: 3 June 2014
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Abstract
Hepatocellular carcinoma (HCC) is the second leading cause of cancer-related mortality in the world. Hepatocarcinogenesis is complex, with an extraordinary molecular heterogeneity. Krüppel-like factor 4 (KLF4) plays an important role in cell proliferation and differentiation, and it can function as a tumor [...] Read more.
Hepatocellular carcinoma (HCC) is the second leading cause of cancer-related mortality in the world. Hepatocarcinogenesis is complex, with an extraordinary molecular heterogeneity. Krüppel-like factor 4 (KLF4) plays an important role in cell proliferation and differentiation, and it can function as a tumor suppressor or an oncoprotein, depending on tissue type. The role of KLF4 in HCC remains controversial. The aim of this study was to explore the clinical significance of KLF4 expression in HCC. The study included 205 patients with surgical resection. We performed immunostaining for KLF4 and Ki-67 to investigate the correlations of the clinicopathological parameters of HCC and to examine the proliferative index. KLF4 staining was observed in the cytoplasm of non-tumorous hepatocytes and tumor cells. We subdivided the immunohistological staining results for KLF4 into low expression (Staining 0 and 1+) and high expression (Staining 2+ and 3+) subgroups. The expression of KLF4 was significantly correlated with tumor differentiation (p = 0.001). The Ki-67 proliferative index was significantly lower in well-differentiated HCCs (0.781% ± 1.02% vs. 2.16% ± 3.14%, p = 0.012), but not significantly different between low-KLF4 expression and high-KLF4 expression (1.87% ± 2.93% vs. 2.51% ± 3.28%, p = 0.32). Kaplan–Meier analysis showed that a high expression of KLF4 was significantly correlated with a longer disease-specific survival (p = 0.019). Univariate and multivariate analyses showed that high KLF4 expression was an independent predictor of a better disease-specific survival (p = 0.017; hazard ratio = 0.398; 95% confidence interval: 0.19–0.85). High cytoplasmic expression of KLF4 was associated with better disease-specific survival and was an independently favorable prognostic factor in hepatocellular carcinoma. These promising results suggest that KLF4 may play an anti-oncogenic role in hepatocarcinogenesis. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle The Influence of Ecological and Conventional Plant Production Systems on Soil Microbial Quality under Hops (Humulus lupulus)
Int. J. Mol. Sci. 2014, 15(6), 9907-9923; doi:10.3390/ijms15069907
Received: 3 April 2014 / Revised: 7 May 2014 / Accepted: 9 May 2014 / Published: 3 June 2014
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Abstract
The knowledge about microorganisms—activity and diversity under hop production is still limited. We assumed that, different systems of hop production (within the same soil and climatic conditions) significantly influence on the composition of soil microbial populations and its functional activity (metabolic potential). [...] Read more.
The knowledge about microorganisms—activity and diversity under hop production is still limited. We assumed that, different systems of hop production (within the same soil and climatic conditions) significantly influence on the composition of soil microbial populations and its functional activity (metabolic potential). Therefore, we compared a set of soil microbial properties in the field experiment of two hop production systems (a) ecological based on the use of probiotic preparations and organic fertilization (b) conventional—with the use of chemical pesticides and mineral fertilizers. Soil analyses included following microbial properties: The total number microorganisms, a bunch of soil enzyme activities, the catabolic potential was also assessed following Biolog EcoPlates®. Moreover, the abundance of ammonia-oxidizing archaea (AOA) was characterized by terminal restriction fragment length polymorphism analysis (T-RFLP) of PCR ammonia monooxygenase α-subunit (amoA) gene products. Conventional and ecological systems of hop production were able to affect soil microbial state in different seasonal manner. Favorable effect on soil microbial activity met under ecological, was more probably due to livestock-based manure and fermented plant extracts application. No negative influence on conventional hopyard soil was revealed. Both type of production fulfilled fertilizing demands. Under ecological production it was due to livestock-based manure fertilizers and fermented plant extracts application. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessCommunication 2,2',2''-Terpyridine-Catalyzed Synthesis of Cyclic Carbonates from Epoxides and Carbon Dioxide under Solvent-Free Conditions
Int. J. Mol. Sci. 2014, 15(6), 9945-9951; doi:10.3390/ijms15069945
Received: 10 March 2014 / Revised: 15 April 2014 / Accepted: 16 May 2014 / Published: 4 June 2014
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Abstract An efficient coupling reaction of epoxides with CO2 affording cyclic carbonates with the use of 2,2',2''-terpyridine as catalyst under solvent-free conditions has been developed. Full article
(This article belongs to the Section Green Chemistry)
Open AccessArticle Morphology, Composition, and Bioactivity of Strontium-Doped Brushite Coatings Deposited on Titanium Implants via Electrochemical Deposition
Int. J. Mol. Sci. 2014, 15(6), 9952-9962; doi:10.3390/ijms15069952
Received: 25 April 2014 / Revised: 13 May 2014 / Accepted: 22 May 2014 / Published: 4 June 2014
Cited by 7 | PDF Full-text (1459 KB) | HTML Full-text | XML Full-text
Abstract
Surface modification techniques have been applied to generate titanium implant surfaces that promote osseointegration for use in dental applications. In this study, strontium-doped brushite coatings were deposited on titanium by electrochemical deposition. The phase composition of the coating was investigated by energy [...] Read more.
Surface modification techniques have been applied to generate titanium implant surfaces that promote osseointegration for use in dental applications. In this study, strontium-doped brushite coatings were deposited on titanium by electrochemical deposition. The phase composition of the coating was investigated by energy dispersive X-ray spectroscopy and X-ray diffraction. The surface morphologies of the coatings were studied through scanning electron microscopy, and the cytocompatibility and bioactivity of the strontium-doped brushite coatings were evaluated using cultured osteoblasts. Osteoblast proliferation was enhanced by the addition of strontium, suggesting a possible mechanism by which strontium incorporation in brushite coatings increased bone formation surrounding the implants. Cell growth was also strongly influenced by the composition of the deposited coatings, with a 10% Sr-doped brushite coating inducing the greatest amount of bone formation among the tested materials. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle Characterization of Two Homogalacturonan Pectins with Immunomodulatory Activity from Green Tea
Int. J. Mol. Sci. 2014, 15(6), 9963-9978; doi:10.3390/ijms15069963
Received: 5 April 2014 / Revised: 25 April 2014 / Accepted: 20 May 2014 / Published: 4 June 2014
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Abstract
Two natural homogalacturonan (HG) pectins (MW ca. 20 kDa) were isolated from green tea based on their immunomodulatory activity. The crude tea polysaccharides (TPS1 and TPS2) were obtained from green tea leaves by hot water extraction and followed by 40% [...] Read more.
Two natural homogalacturonan (HG) pectins (MW ca. 20 kDa) were isolated from green tea based on their immunomodulatory activity. The crude tea polysaccharides (TPS1 and TPS2) were obtained from green tea leaves by hot water extraction and followed by 40% and 70% ethanol precipitation, respectively. Two homogenous water soluble polysaccharides (TPS1-2a and TPS1-2b) were obtained from TPS1 after purification with gel permeation, which gave a higher phagocytic effect than TPS2. A combination of composition, methylation and configuration analyses, as well as NMR (nuclear magnetic resonance) spectroscopy revealed that TPS1-2a and TPS1-2b were homogalacturonan (HG) pectins consisting of a backbone of 1,4-linked α-d-galacturonic acid (GalA) residues with 28.4% and 26.1% of carboxyl groups as methyl ester, respectively. The immunological assay results demonstrated that TPS1-2, which consisted mainly of HG pectins, showed phagocytosis-enhancing activity in HL-60 cells. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
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Open AccessArticle Selective Isolation of Trypsin Inhibitor and Lectin from Soybean Whey by Chitosan/Tripolyphosphate/Genipin Co-Crosslinked Beads
Int. J. Mol. Sci. 2014, 15(6), 9979-9990; doi:10.3390/ijms15069979
Received: 1 March 2014 / Revised: 20 May 2014 / Accepted: 22 May 2014 / Published: 4 June 2014
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Abstract
Selective isolation of Kunitz trypsin inhibitor (KTI) and lectin from soybean whey solutions by different types of chitosan beads was investigated. The chitosan beads were co-crosslinked with tripolyphosphate/genipin in solutions at pH 5, 7 or 9 (CB5, CB7, CB9). The maximum adsorption [...] Read more.
Selective isolation of Kunitz trypsin inhibitor (KTI) and lectin from soybean whey solutions by different types of chitosan beads was investigated. The chitosan beads were co-crosslinked with tripolyphosphate/genipin in solutions at pH 5, 7 or 9 (CB5, CB7, CB9). The maximum adsorption ratios of chitosan beads to KTI and lectin were observed at pH 4.4 and 5.4, respectively; highly selective separation was also demonstrated at these pHs. The adsorption ratios increased with temperature, rising between 5 and 25 °C. CB9 produced the best adsorption ratio, followed by CB7 then CB5. The critical interaction governing absorption of chitosan beads to KTI and lectin could be hydrogen bonding. At pH 9, KTI and lectin desorbed efficiently from CB7 with desorption ratios of 80.9% and 81.4%, respectively. The desorption was most likely caused predominantly by electrostatic repulsion. KTI and lectin can effectively be selectively isolated from soybean whey using this novel separation technique. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Concentration of Antifouling Biocides and Metals in Sediment Core Samples in the Northern Part of Hiroshima Bay
Int. J. Mol. Sci. 2014, 15(6), 9991-10004; doi:10.3390/ijms15069991
Received: 3 March 2014 / Revised: 15 April 2014 / Accepted: 23 April 2014 / Published: 4 June 2014
Cited by 3 | PDF Full-text (1104 KB) | HTML Full-text | XML Full-text
Abstract
Accumulation of Ot alternative antifoulants in sediment is the focus of this research. Much research had been done on surface sediment, but in this report, the accumulation in the sediment core was studied. The Ot alternative antifoulants, Diuron, Sea-Nine211, and Irgarol 1051, [...] Read more.
Accumulation of Ot alternative antifoulants in sediment is the focus of this research. Much research had been done on surface sediment, but in this report, the accumulation in the sediment core was studied. The Ot alternative antifoulants, Diuron, Sea-Nine211, and Irgarol 1051, and the latter’s degradation product, M1, were investigated in five samples from the northern part of Hiroshima Bay. Ot compounds (tributyltin (TBT) and triphenyltin (TPT)) were also investigated for comparison. In addition, metal (Pb, Cu, Zn, Fe and Mn) levels and chronology were measured to better understand what happens after accumulation on the sea floor. It was discovered that Ot alternative antifoulant accumulation characteristics in sediment were like Ot compounds, with the concentration in the sediment core being much higher than surface sediment. The concentration in sediment seems to have been affected by the regulation of Ot compounds in 1990, due to the concentration of Ot alternative antifoulants and Ot compounds at the survey point in front of the dock, showing an increase from almost the same layer after the regulation. Full article
(This article belongs to the Special Issue New Non (Limited)-Toxic Antifouling Solutions)
Open AccessArticle Elucidation of the Specific Formation of Homo- and Heterodimeric Forms of ThbZIP1 and Its Role in Stress
Int. J. Mol. Sci. 2014, 15(6), 10005-10017; doi:10.3390/ijms150610005
Received: 8 April 2014 / Revised: 25 April 2014 / Accepted: 21 May 2014 / Published: 4 June 2014
Cited by 2 | PDF Full-text (1438 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Protein–protein interactions are important for the molecular understanding of the biological processes of proteins. The dimerization of bZIPs (basic leucine zipper proteins) is involved in modifying binding site specificities, altering dimer stability, and permitting a new set of specific protein-to-protein interactions to [...] Read more.
Protein–protein interactions are important for the molecular understanding of the biological processes of proteins. The dimerization of bZIPs (basic leucine zipper proteins) is involved in modifying binding site specificities, altering dimer stability, and permitting a new set of specific protein-to-protein interactions to occur at the promoter. In the present study, we studied the whether ThbZIP1 form homo- and heterodimers using the yeast two-hybrid method. Five bZIP genes were cloned from Tamarix hispida to investigate their interaction with ThbZIP1. Our results showed that ThbZIP1 can form homodimers with itself, and three out of five bZIPs could interact with the ThbZIP1 protein to form heterodimers. Real-time RT-PCR results suggested that these ThbZIPs can all respond to abiotic stresses and abscisic acid (ABA), and shared very similar expression patterns in response to NaCl, ABA or PEG6000. Subcellular localization studies showed that all ThbZIPs are targeted to the nucleus. Our results showed that ThbZIP1 are dimeric proteins, which can form homo- or heterodimers. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle A New Criterion to Evaluate Water Vapor Interference in Protein Secondary Structural Analysis by FTIR Spectroscopy
Int. J. Mol. Sci. 2014, 15(6), 10018-10033; doi:10.3390/ijms150610018
Received: 16 February 2014 / Revised: 26 May 2014 / Accepted: 27 May 2014 / Published: 4 June 2014
PDF Full-text (313 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Second derivative and Fourier self-deconvolution (FSD) are two commonly used techniques to resolve the overlapped component peaks from the often featureless amide I band in Fourier transform infrared (FTIR) curve-fitting approach for protein secondary structural analysis. Yet, the reliability of these two [...] Read more.
Second derivative and Fourier self-deconvolution (FSD) are two commonly used techniques to resolve the overlapped component peaks from the often featureless amide I band in Fourier transform infrared (FTIR) curve-fitting approach for protein secondary structural analysis. Yet, the reliability of these two techniques is greatly affected by the omnipresent water vapor in the atmosphere. Several criteria are currently in use as quality controls to ensure the protein absorption spectrum is negligibly affected by water vapor interference. In this study, through a second derivative study of liquid water, we first argue that the previously established criteria cannot guarantee a reliable evaluation of water vapor interference due to a phenomenon that we refer to as sample’s absorbance-dependent water vapor interference. Then, through a comparative study of protein and liquid water, we show that a protein absorption spectrum can still be significantly affected by water vapor interference even though it satisfies the established criteria. At last, we propose to use the comparison between the second derivative spectra of protein and liquid water as a new criterion to better evaluate water vapor interference for more reliable second derivative and FSD treatments on the protein amide I band. Full article
(This article belongs to the collection Proteins and Protein-Ligand Interactions)
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Open AccessArticle Genetic Variation of the Endangered Gentiana lutea L. var. aurantiaca (Gentianaceae) in Populations from the Northwest Iberian Peninsula
Int. J. Mol. Sci. 2014, 15(6), 10052-10066; doi:10.3390/ijms150610052
Received: 10 April 2014 / Revised: 21 May 2014 / Accepted: 26 May 2014 / Published: 5 June 2014
Cited by 6 | PDF Full-text (502 KB) | HTML Full-text | XML Full-text
Abstract
Gentiana lutea L. (G. lutea L.) is an endangered plant, patchily distributed along the mountains of Central and Southern Europe. In this study, inter-simple sequence repeat (ISSR) markers were used to investigate the genetic variation in this species within and among [...] Read more.
Gentiana lutea L. (G. lutea L.) is an endangered plant, patchily distributed along the mountains of Central and Southern Europe. In this study, inter-simple sequence repeat (ISSR) markers were used to investigate the genetic variation in this species within and among populations of G. lutea L. var. aurantiaca of the Cantabrian Mountains (Northwest Iberian Peninsula). Samples of G. lutea L. collected at different locations of the Pyrenees and samples of G. lutea L. subsp. vardjanii of the Dolomites Alps were also analyzed for comparison. Using nine ISSR primers, 106 bands were generated, and 89.6% of those were polymorphic. The populations from the Northwest Iberian Peninsula were clustered in three different groups, with a significant correlation between genetic and geographic distances. Gentiana lutea L. var. aurantiaca showed 19.8% private loci and demonstrated a remarkable level of genetic variation, both among populations and within populations; those populations with the highest level of isolation show the lowest genetic variation within populations. The low number of individuals, as well as the observed genetic structure of the analyzed populations makes it necessary to protect them to ensure their survival before they are too small to persist naturally. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
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Open AccessArticle Direct Analysis of hCGβcf Glycosylation in Normal and Aberrant Pregnancy by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry
Int. J. Mol. Sci. 2014, 15(6), 10067-10082; doi:10.3390/ijms150610067
Received: 25 April 2014 / Revised: 20 May 2014 / Accepted: 21 May 2014 / Published: 5 June 2014
Cited by 2 | PDF Full-text (552 KB) | HTML Full-text | XML Full-text
Abstract
The analysis of human chorionic gonadotropin (hCG) in clinical chemistry laboratories by specific immunoassay is well established. However, changes in glycosylation are not as easily assayed and yet alterations in hCG glycosylation is associated with abnormal pregnancy. hCGβ-core fragment (hCGβcf) was isolated [...] Read more.
The analysis of human chorionic gonadotropin (hCG) in clinical chemistry laboratories by specific immunoassay is well established. However, changes in glycosylation are not as easily assayed and yet alterations in hCG glycosylation is associated with abnormal pregnancy. hCGβ-core fragment (hCGβcf) was isolated from the urine of women, pregnant with normal, molar and hyperemesis gravidarum pregnancies. Each sample was subjected to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS) analysis following dithiothreitol (DTT) reduction and fingerprint spectra of peptide hCGβ 6–40 were analyzed. Samples were variably glycosylated, where most structures were small, core and largely mono-antennary. Larger single bi-antennary and mixtures of larger mono-antennary and bi-antennary moieties were also observed in some samples. Larger glycoforms were more abundant in the abnormal pregnancies and tri-antennary carbohydrate moieties were only observed in the samples from molar and hyperemesis gravidarum pregnancies. Given that such spectral profiling differences may be characteristic, development of small sample preparation for mass spectral analysis of hCG may lead to a simpler and faster approach to glycostructural analysis and potentially a novel clinical diagnostic test. Full article
(This article belongs to the Special Issue Mass Spectrometry Application in Biology) Print Edition available
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Open AccessArticle A Comprehensive Insight into Tetracycline Resistant Bacteria and Antibiotic Resistance Genes in Activated Sludge Using Next-Generation Sequencing
Int. J. Mol. Sci. 2014, 15(6), 10083-10100; doi:10.3390/ijms150610083
Received: 30 March 2014 / Revised: 9 May 2014 / Accepted: 22 May 2014 / Published: 5 June 2014
Cited by 7 | PDF Full-text (894 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
In order to comprehensively investigate tetracycline resistance in activated sludge of sewage treatment plants, 454 pyrosequencing and Illumina high-throughput sequencing were used to detect potential tetracycline resistant bacteria (TRB) and antibiotic resistance genes (ARGs) in sludge cultured with different concentrations of tetracycline. [...] Read more.
In order to comprehensively investigate tetracycline resistance in activated sludge of sewage treatment plants, 454 pyrosequencing and Illumina high-throughput sequencing were used to detect potential tetracycline resistant bacteria (TRB) and antibiotic resistance genes (ARGs) in sludge cultured with different concentrations of tetracycline. Pyrosequencing of 16S rRNA gene revealed that tetracycline treatment greatly affected the bacterial community structure of the sludge. Nine genera consisting of Sulfuritalea, Armatimonas, Prosthecobacter, Hyphomicrobium, Azonexus, Longilinea, Paracoccus, Novosphingobium and Rhodobacter were identified as potential TRB in the sludge. Results of qPCR, molecular cloning and metagenomic analysis consistently indicated that tetracycline treatment could increase both the abundance and diversity of the tet genes, but decreased the occurrence and diversity of non-tetracycline ARG, especially sulfonamide resistance gene sul2. Cluster analysis showed that tetracycline treatment at subinhibitory concentrations (5 mg/L) was found to pose greater effects on the bacterial community composition, which may be responsible for the variations of the ARGs abundance. This study indicated that joint use of 454 pyrosequencing and Illumina high-throughput sequencing can be effectively used to explore ARB and ARGs in the environment, and future studies should include an in-depth investigation of the relationship between microbial community, ARGs and antibiotics in sewage treatment plant (STP) sludge. Full article
(This article belongs to the Special Issue Metagenomics: a Powerful Lens Viewing the Microbial World)
Open AccessArticle Systemic Injection of Low-Dose Lipopolysaccharide Fails to Break down the Blood–Brain Barrier or Activate the TLR4-MyD88 Pathway in Neonatal Rat Brain
Int. J. Mol. Sci. 2014, 15(6), 10101-10115; doi:10.3390/ijms150610101
Received: 24 January 2014 / Revised: 29 April 2014 / Accepted: 26 May 2014 / Published: 5 June 2014
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Abstract
We aimed to investigate whether peripheral low-dose lipopolysaccharide (LPS) induces the breakdown of the blood–brain barrier (BBB) and/or the activation of toll-like receptor 4 (TLR4) in the neonatal rat brain. Neonatal rats received intraperitoneal injections of low-dose LPS (0.3 mg/kg∙bw), and the [...] Read more.
We aimed to investigate whether peripheral low-dose lipopolysaccharide (LPS) induces the breakdown of the blood–brain barrier (BBB) and/or the activation of toll-like receptor 4 (TLR4) in the neonatal rat brain. Neonatal rats received intraperitoneal injections of low-dose LPS (0.3 mg/kg∙bw), and the BBB compromise was detected by Evans Blue extravasation and electron microscopy. Meanwhile, TLR4, adaptin myeloid differentiation factor 88 (MyD88), nuclear transcription factor kappa-B (NF-κB) p50 and tumor necrosis factor alpha (TNFα) in the neonatal rat brain were determined by quantitative real-time polymerase chain reaction (PCR) and Western Blot. Immunohistochemistry was used to determine the distribution and activation of microglia in the brain after LPS administration. It was demonstrated that Evans Blue extravasation was not observed in the brain parenchyma, and that tight junctions of cerebral endothelial cells remained intact after systemic injections of LPS in neonatal rats. Although intracerebroventricular injections of LPS activated microglia and up-regulated the expression of TLR4, MyD88, NF-κB p50 and TNFα in the neonatal rat brain, systemic LPS did not induce these responses. These findings indicate that while the neonatal rat brain responds to the direct intra-cerebral administration of LPS through robust TLR4 activation, systemic low-dose LPS does not induce the innate immune reaction or compromise the BBB in neonatal rats. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Pregnane-Type Steroids from the Formosan Soft Coral Scleronephthya flexilis
Int. J. Mol. Sci. 2014, 15(6), 10136-10149; doi:10.3390/ijms150610136
Received: 12 April 2014 / Revised: 19 May 2014 / Accepted: 23 May 2014 / Published: 6 June 2014
Cited by 5 | PDF Full-text (2615 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Three pregnane-type steroids, including a new metabolite, 3β-methoxy-5,20-pregnadiene (1) along with two known analogues, 3β-acetoxy-5,20-pregnadiene (2) and 5α-pregna-1,20-dien-3-one (3) were isolated from the soft coral Scleronephthya flexilis. Standard spectroscopic techniques were used to determine the [...] Read more.
Three pregnane-type steroids, including a new metabolite, 3β-methoxy-5,20-pregnadiene (1) along with two known analogues, 3β-acetoxy-5,20-pregnadiene (2) and 5α-pregna-1,20-dien-3-one (3) were isolated from the soft coral Scleronephthya flexilis. Standard spectroscopic techniques were used to determine the structure of new steroid 1. The absolute stereochemistry of steroid 2 was confirmed by X-ray diffraction analysis. Steroid 3 exhibited potent activity against MOLT-4 tumor cells. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Total Protein Extraction for Metaproteomics Analysis of Methane Producing Biofilm: The Effects of Detergents
Int. J. Mol. Sci. 2014, 15(6), 10169-10184; doi:10.3390/ijms150610169
Received: 9 April 2014 / Revised: 23 May 2014 / Accepted: 23 May 2014 / Published: 6 June 2014
Cited by 4 | PDF Full-text (995 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Protein recovery is crucial for shotgun metaproteomics to study the in situ functionality of microbial populations from complex biofilms but still poorly addressed by far. To fill this knowledge gap, we systematically evaluated the sample preparation with extraction buffers comprising four detergents [...] Read more.
Protein recovery is crucial for shotgun metaproteomics to study the in situ functionality of microbial populations from complex biofilms but still poorly addressed by far. To fill this knowledge gap, we systematically evaluated the sample preparation with extraction buffers comprising four detergents for the metaproteomics analysis of a terephthalate-degrading methanogenic biofilm using an on-line two-dimensional liquid chromatography tandem mass spectrometry (2D-LC-MS/MS) system. Totally, 1018 non-repeated proteins were identified with the four treatments. On the whole, each treatment could recover the biofilm proteins with specific distributions of molecular weight, hydrophobicity, and isoelectric point. The extraction buffers containing zwitterionic and anionic detergents were found to harvest the proteins with better efficiency and quality, allowing identification up to 76.2% of total identified proteins with the LC-MS/MS analysis. According to the annotation with a relevant metagenomic database, we further observed different taxonomic profiles of bacterial and archaeal members and discriminable patterns of the functional expression among the extraction buffers used. Overall, the finding of the present study provides first insight to the effect of the detergents on the characteristics of extractable proteins from biofilm and the developed protocol combined with nano 2D-LC/MS/MS analysis can improve the metaproteomics studies on microbial functionality of biofilms in the wastewater treatment systems. Full article
(This article belongs to the collection Advances in Proteomic Research)
Open AccessArticle The Cross Talk between cGMP Signal Pathway and PKC in Pulmonary Endothelial Cell Angiogenesis
Int. J. Mol. Sci. 2014, 15(6), 10185-10198; doi:10.3390/ijms150610185
Received: 15 April 2014 / Revised: 4 May 2014 / Accepted: 14 May 2014 / Published: 6 June 2014
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Abstract
Angiogenic proliferation of vascular endothelial cells is believed to play an important role in pulmonary vascular remodeling in pulmonary arterial hypertension. In the present study, we found that c-GMP (cyclic guanosine monophosphate) inhibited the proliferation and tube formation of pulmonary vascular endothelial [...] Read more.
Angiogenic proliferation of vascular endothelial cells is believed to play an important role in pulmonary vascular remodeling in pulmonary arterial hypertension. In the present study, we found that c-GMP (cyclic guanosine monophosphate) inhibited the proliferation and tube formation of pulmonary vascular endothelial cells induced by TGF-β1, and that this process was reversed by PKG (protein kinase G) inhibitor and PKC (protein kinase C) inhibitor. In addition, small interfering RNA (siRNA) targeting ERK also reduced cellular proliferation. Furthermore, western blotting showed that cGMP down-regulated the phosphorylation level of ERK1/2, which was reversed not only by PKG inhibitor but also by PKC inhibitor. Silencing different PKC isoforms showed that PKCΔ, PKCγ and PKCα were involved in ERK phosphorylation, suggesting that PKC kinases have a permissive action. Three subtypes, PKCΔ, PKCγ and PKCα are likely to be involved the phosphorylation suppression of ERK included cGMP. Taken together, these data suggest that ERK phosphorylation mediates the proliferation of pulmonary vascular endothelial cells, and PKC kinases have a permissive action in this process. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Direct Interaction between Selenoprotein P and Tubulin
Int. J. Mol. Sci. 2014, 15(6), 10199-10214; doi:10.3390/ijms150610199
Received: 19 March 2014 / Revised: 12 May 2014 / Accepted: 23 May 2014 / Published: 6 June 2014
Cited by 2 | PDF Full-text (3430 KB) | HTML Full-text | XML Full-text
Abstract
Selenium (Se), an essential trace element for human health, mainly exerts its biological function via selenoproteins. Among the 25 selenoproteins identified in human, selenoprotein P (SelP) is the only one that contains multiple selenocysteines (Sec) in the sequence, and has been suggested [...] Read more.
Selenium (Se), an essential trace element for human health, mainly exerts its biological function via selenoproteins. Among the 25 selenoproteins identified in human, selenoprotein P (SelP) is the only one that contains multiple selenocysteines (Sec) in the sequence, and has been suggested to function as a Se transporter. Upon feeding a selenium-deficient diet, mice lacking SelP develop severe neurological dysfunction and exhibit widespread brainstem neurodegeneration, indicating an important role of SelP in normal brain function. To further elucidate the function of SelP in the brain, SelP was screened by the yeast two-hybrid system from a human fetal brain cDNA library for interactive proteins. Our results demonstrated that SelP interacts with tubulin, alpha 1a (TUBA1A). The interaction between SelP and tubulin was verified by fluorescence resonance energy transfer (FRET) and co-immunoprecipitation (co-IP) assays. We further found that SelP interacts with the C-terminus of tubulin by its His-rich domain, as demonstrated by FRET and Isothermal Titration Calorimetry (ITC) assays. The implications of the interaction between SelP and tubulin in the brain and in Alzheimer’s disease are discussed. Full article
(This article belongs to the collection Proteins and Protein-Ligand Interactions)
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Open AccessArticle Screening and Functional Analysis of the Peroxiredoxin Specifically Expressed in Bursaphelenchus xylophilus—The Causative Agent of Pine Wilt Disease
Int. J. Mol. Sci. 2014, 15(6), 10215-10232; doi:10.3390/ijms150610215
Received: 21 April 2014 / Revised: 25 May 2014 / Accepted: 26 May 2014 / Published: 10 June 2014
Cited by 2 | PDF Full-text (1593 KB) | HTML Full-text | XML Full-text
Abstract
The pine wood nematode, Bursaphelenchus xylophilus, is the causal agent of pine wilt disease. Accurately differentiating B. xylophilus from other nematodes species, especially its related species B. mucronatus, is important for pine wood nematode detection. Thus, we attempted to identify [...] Read more.
The pine wood nematode, Bursaphelenchus xylophilus, is the causal agent of pine wilt disease. Accurately differentiating B. xylophilus from other nematodes species, especially its related species B. mucronatus, is important for pine wood nematode detection. Thus, we attempted to identify a specific protein in the pine wood nematode using proteomics technology. Here, we compared the proteomes of B. xylophilus and B. mucronatus using Two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization -time-of-flight/time-of-flight (MALDI-TOF/TOF-MS) technologies. In total, 15 highly expressed proteins were identified in B. xylophilus compared with B. mucronatus. Subsequently, the specificity of the proteins identified was confirmed by PCR using the genomic DNA of other nematode species. Finally, a gene encoding a specific protein (Bx-Prx) was obtained. This gene was cloned and expressed in E. coli. The in situ hybridisation pattern of Bx-Prx showed that it was expressed strongly in the tail of B. xylophilus. RNAi was used to assess the function of Bx-Prx, the results indicated that the gene was associated with the reproduction and pathogenicity of B. xylophilus. This discovery provides fundamental information for identifying B. xylophilus via a molecular approach. Moreover, the purified recombinant protein has potential as a candidate diagnostic antigen of pine wilt disease, which may lead to a new immunological detection method for the pine wood nematode. Full article
(This article belongs to the collection Advances in Proteomic Research)
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Open AccessArticle SUMOylation of FOXM1B Alters Its Transcriptional Activity on Regulation of MiR-200 Family and JNK1 in MCF7 Human Breast Cancer Cells
Int. J. Mol. Sci. 2014, 15(6), 10233-10251; doi:10.3390/ijms150610233
Received: 28 April 2014 / Revised: 28 May 2014 / Accepted: 3 June 2014 / Published: 10 June 2014
Cited by 10 | PDF Full-text (1037 KB) | HTML Full-text | XML Full-text
Abstract
Transcription factor Forkhead Box Protein M1 (FOXM1) is a well-known master regulator in controlling cell-cycle pathways essential for DNA replication and mitosis, as well as cell proliferation. Among the three major isoforms of FOXM1, FOXM1B is highly associated with tumor growth and [...] Read more.
Transcription factor Forkhead Box Protein M1 (FOXM1) is a well-known master regulator in controlling cell-cycle pathways essential for DNA replication and mitosis, as well as cell proliferation. Among the three major isoforms of FOXM1, FOXM1B is highly associated with tumor growth and metastasis. The activities of FOXM1B are modulated by post-translational modifications (PTMs), such as phosphorylation, but whether it is modified by small ubiquitin-related modifier (SUMO) remains unknown. The aim of the current study was to determine whether FOXM1B is post-translationally modified by SUMO proteins and also to identify SUMOylation of FOXM1B on its target gene transcription activity. Here we report that FOXM1B is clearly defined as a SUMO target protein at the cellular levels. Moreover, a SUMOylation protease, SENP2, significantly decreased SUMOylation of FOXM1B. Notably, FOXM1B is selectively SUMOylated at lysine residue 463. While SUMOylation of FOXM1B is required for full repression of its target genes MiR-200b/c and p21, SUMOylation of FOXM1B is essential for full activation of JNK1 gene. Overall, we provide evidence that FOXM1B is post-translationally modified by SUMO and SUMOylation of FOXM1B plays a functional role in regulation of its target gene activities. Full article
(This article belongs to the Special Issue Signalling Molecules and Signal Transduction in Cells 2014)
Open AccessArticle The Calcium Phosphate Matrix of FGF-2-Apatite Composite Layers Contributes to Their Biological Effects
Int. J. Mol. Sci. 2014, 15(6), 10252-10270; doi:10.3390/ijms150610252
Received: 25 April 2014 / Accepted: 28 May 2014 / Published: 10 June 2014
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Abstract
The purpose of the present study was to fabricate fibroblast growth factor (FGF)-2-apatite composite layers on titanium (Ti) pins in one step at 25 °C using a supersaturated calcium phosphate (CaP) solution, and to evaluate the physicochemical characteristics and biological effects of [...] Read more.
The purpose of the present study was to fabricate fibroblast growth factor (FGF)-2-apatite composite layers on titanium (Ti) pins in one step at 25 °C using a supersaturated calcium phosphate (CaP) solution, and to evaluate the physicochemical characteristics and biological effects of the coated Ti pins compared with coated Ti pins fabricated at 37 °C. Ti pins were immersed in a supersaturated CaP solution containing 0.5, 1.0, or 2.0 µg/mL FGF-2 at 25 °C for 24 h (25F0.5, 25F1.0, and 25F2.0) or containing 4.0 µg/mL FGF-2 at 37 °C for 48 h (37F4.0). Except for the 25F0.5, the chemical compositions and the mitogenic activity levels of FGF-2 of the composite layers formed by these two methods were similar, except for the Ca/P molar ratio, which was markedly smaller at 25 °C (1.55–1.56 ± 0.01–0.02, p = 0.0008–0.0045) than at 37 °C (1.67 ± 0.11). Thus, either the apatite was less mature or the amount of amorphous calcium phosphate was higher in the composite layer formed at 25 °C. In vivo, the pin tract infection rate by visual inspection for 37F4.0 (45%) was lower than that for 25F1.0 (80%, p = 0.0213), and the rate of osteomyelitis for 37F4.0 (35%) was lower than that for 25F0.5 (75%, p = 0.0341). The extraction torque for 37F4.0 (0.276 ± 0.117 Nm) was higher than that for 25F0.5 (0.192 ± 0.117 Nm, p = 0.0142) and that for 25F1.0 (0.176 ± 0.133 Nm, p = 0.0079). The invasion rate of S. aureus for 37F4.0 (35%) was lower than that for 25F0.5 (75%, p = 0.0110). On the whole, the FGF-2-apatite composite layer formed at 25 °C tended to be less effective at improving fixation strength in the bone-pin interface and resisting pin tract infections. These results suggest that the chemistry of the calcium phosphate matrix that embeds FGF-2, in addition to FGF-2 content and activity, has a significant impact on composite infection resistance and fixation strength. Full article
(This article belongs to the Special Issue Biologic Coatings for Orthopaedic Implant)
Open AccessArticle Eicosapentaenoic Acid Protects against Palmitic Acid-Induced Endothelial Dysfunction via Activation of the AMPK/eNOS Pathway
Int. J. Mol. Sci. 2014, 15(6), 10334-10349; doi:10.3390/ijms150610334
Received: 16 February 2014 / Revised: 12 May 2014 / Accepted: 22 May 2014 / Published: 10 June 2014
Cited by 16 | PDF Full-text (1876 KB) | HTML Full-text | XML Full-text
Abstract
Recent studies have shown that free fatty acids are associated with chronic inflammation, which may be involved in vascular injury. The intake of eicosapentaenoic acid (EPA) can decrease cardiovascular disease risks, but the protective mechanisms of EPA on endothelial cells remain unclear. [...] Read more.
Recent studies have shown that free fatty acids are associated with chronic inflammation, which may be involved in vascular injury. The intake of eicosapentaenoic acid (EPA) can decrease cardiovascular disease risks, but the protective mechanisms of EPA on endothelial cells remain unclear. In this study, primary human umbilical vein endothelial cells (HUVECs) treated with palmitic acid (PA) were used to explore the protective effects of EPA. The results revealed that EPA attenuated PA-induced cell death and activation of apoptosis-related proteins, such as caspase-3, p53 and Bax. Additionally, EPA reduced the PA-induced increase in the generation of reactive oxygen species, the activation of NADPH oxidase, and the upregulation of inducible nitric oxide synthase (iNOS). EPA also restored the PA-mediated reduction of endothelial nitric oxide synthase (eNOS) and AMP-activated protein kinase (AMPK) phosphorylation. Using AMPK siRNA and the specific inhibitor compound C, we found that EPA restored the PA-mediated inhibitions of eNOS and AKT activities via activation of AMPK. Furthermore, the NF-κB signals that are mediated by p38 mitogen-activated protein kinase (MAPK) were involved in protective effects of EPA. In summary, these results provide new insight into the possible molecular mechanisms by which EPA protects against atherogenesis via the AMPK/eNOS-related pathway. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Functional Characterization of NIPBL Physiological Splice Variants and Eight Splicing Mutations in Patients with Cornelia de Lange Syndrome
Int. J. Mol. Sci. 2014, 15(6), 10350-10364; doi:10.3390/ijms150610350
Received: 9 April 2014 / Revised: 12 May 2014 / Accepted: 20 May 2014 / Published: 10 June 2014
Cited by 3 | PDF Full-text (919 KB) | HTML Full-text | XML Full-text
Abstract
Cornelia de Lange syndrome (CdLS) is a congenital developmental disorder characterized by distinctive craniofacial features, growth retardation, cognitive impairment, limb defects, hirsutism, and multisystem involvement. Mutations in five genes encoding structural components (SMC1A, SMC3, RAD21) or functionally associated [...] Read more.
Cornelia de Lange syndrome (CdLS) is a congenital developmental disorder characterized by distinctive craniofacial features, growth retardation, cognitive impairment, limb defects, hirsutism, and multisystem involvement. Mutations in five genes encoding structural components (SMC1A, SMC3, RAD21) or functionally associated factors (NIPBL, HDAC8) of the cohesin complex have been found in patients with CdLS. In about 60% of the patients, mutations in NIPBL could be identified. Interestingly, 17% of them are predicted to change normal splicing, however, detailed molecular investigations are often missing. Here, we report the first systematic study of the physiological splicing of the NIPBL gene, that would reveal the identification of four new splicing isoforms ΔE10, ΔE12, ΔE33,34, and B’. Furthermore, we have investigated nine mutations affecting splice-sites in the NIPBL gene identified in twelve CdLS patients. All mutations have been examined on the DNA and RNA level, as well as by in silico analyses. Although patients with mutations affecting NIPBL splicing show a broad clinical variability, the more severe phenotypes seem to be associated with aberrant transcripts resulting in a shift of the reading frame. Full article
(This article belongs to the Special Issue Pre-mRNA Splicing)
Open AccessArticle Up-Regulation of Rhoa/Rho Kinase Pathway by Translationally Controlled Tumor Protein in Vascular Smooth Muscle Cells
Int. J. Mol. Sci. 2014, 15(6), 10365-10376; doi:10.3390/ijms150610365
Received: 25 April 2014 / Revised: 30 May 2014 / Accepted: 3 June 2014 / Published: 10 June 2014
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Abstract
Translationally controlled tumor protein (TCTP), a repressor for Na,K-ATPase has been implicated in the development of systemic hypertension, as proved by TCTP-over-expressing transgenic (TCTP-TG) mice. Aorta of TCTP-TG exhibited hypercontractile response compared to that of non-transgenic mice (NTG) suggesting dys-regulation of signaling [...] Read more.
Translationally controlled tumor protein (TCTP), a repressor for Na,K-ATPase has been implicated in the development of systemic hypertension, as proved by TCTP-over-expressing transgenic (TCTP-TG) mice. Aorta of TCTP-TG exhibited hypercontractile response compared to that of non-transgenic mice (NTG) suggesting dys-regulation of signaling pathways involved in the vascular contractility by TCTP. Because dys-regulation of RhoA/Rho kinase pathway is implicated in increased vascular contractility, we examined whether TCTP induces alterations in RhoA pathway in vascular smooth muscle cells (VSMCs). We found that TCTP over-expression by adenovirus infection up-regulated RhoA pathway including the expression of RhoA, and its downstream signalings, phosphorylation of myosin phosphatase target protein (MYPT-1), and myosin light chain (MLC). Conversely, lentiviral silencing of TCTP reduced the RhoA expression and Rho kinase signalings. Using immunohistochemical and Western blotting studies on aortas from TCTP-TG confirmed the elevated expression of RhoA and increase in p-MLC (phosphorylated MLC). In contrast, down-regulation of RhoA and p-MLC were found in aortas from heterozygous mice with deleted allele of TCTP (TCTP+/−). We conclude that up-regulation of TCTP induces RhoA-mediated pathway, and that TCTP-induced RhoA plays a role in the regulation in vasculature. Modulation of TCTP may offer a therapeutic target for hypertension and in vascular contractility dysfunction. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle The Metallothionein Gene, TaMT3, from Tamarix androssowii Confers Cd2+ Tolerance in Tobacco
Int. J. Mol. Sci. 2014, 15(6), 10398-10409; doi:10.3390/ijms150610398
Received: 4 April 2014 / Revised: 16 May 2014 / Accepted: 16 May 2014 / Published: 10 June 2014
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Abstract
Cadmium (Cd) is a nonessential microelement and low concentration Cd2+ has strong toxicity to plant growth. Plant metallothioneins, a class of low molecular, cystein(Cys)-rich and heavy-metal binding proteins, play an important role in both metal chaperoning and scavenging of reactive oxygen [...] Read more.
Cadmium (Cd) is a nonessential microelement and low concentration Cd2+ has strong toxicity to plant growth. Plant metallothioneins, a class of low molecular, cystein(Cys)-rich and heavy-metal binding proteins, play an important role in both metal chaperoning and scavenging of reactive oxygen species (ROS) with their large number of cysteine residues and therefore, protect plants from oxidative damage. In this study, a metallothionein gene, TaMT3, isolated from Tamarix androssowii was transformed into tobacco (Nicotiana tobacum) through Agrobacterium-mediated leaf disc method, and correctly expressed under the control of 35S promoter. Under Cd2+ stress, the transgenic tobacco showed significant increases of superoxide dismutase (SOD) activity and chlorophyll concentration, but decreases of peroxidase (POD) activity and malondialdehyde (MDA) accumulation when compared to the non-transgenic tobacco. Vigorous growth of transgenic tobacco was observed at the early development stages, resulting in plant height and fresh weight were significantly larger than those of the non-transgenic tobacco under Cd2+ stress. These results demonstrated that the expression of the exogenous TaMT3 gene increased the ability of ROS cleaning-up, indicating a stronger tolerance to Cd2+ stress. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Prediction of Protein S-Nitrosylation Sites Based on Adapted Normal Distribution Bi-Profile Bayes and Chou’s Pseudo Amino Acid Composition
Int. J. Mol. Sci. 2014, 15(6), 10410-10423; doi:10.3390/ijms150610410
Received: 14 February 2014 / Revised: 12 May 2014 / Accepted: 20 May 2014 / Published: 10 June 2014
Cited by 20 | PDF Full-text (745 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Protein S-nitrosylation is a reversible post-translational modification by covalent modification on the thiol group of cysteine residues by nitric oxide. Growing evidence shows that protein S-nitrosylation plays an important role in normal cellular function as well as in various pathophysiologic [...] Read more.
Protein S-nitrosylation is a reversible post-translational modification by covalent modification on the thiol group of cysteine residues by nitric oxide. Growing evidence shows that protein S-nitrosylation plays an important role in normal cellular function as well as in various pathophysiologic conditions. Because of the inherent chemical instability of the S-NO bond and the low abundance of endogenous S-nitrosylated proteins, the unambiguous identification of S-nitrosylation sites by commonly used proteomic approaches remains challenging. Therefore, computational prediction of S-nitrosylation sites has been considered as a powerful auxiliary tool. In this work, we mainly adopted an adapted normal distribution bi-profile Bayes (ANBPB) feature extraction model to characterize the distinction of position-specific amino acids in 784 S-nitrosylated and 1568 non-S-nitrosylated peptide sequences. We developed a support vector machine prediction model, iSNO-ANBPB, by incorporating ANBPB with the Chou’s pseudo amino acid composition. In jackknife cross-validation experiments, iSNO-ANBPB yielded an accuracy of 65.39% and a Matthew’s correlation coefficient (MCC) of 0.3014. When tested on an independent dataset, iSNO-ANBPB achieved an accuracy of 63.41% and a MCC of 0.2984, which are much higher than the values achieved by the existing predictors SNOSite, iSNO-PseAAC, the Li et al. algorithm, and iSNO-AAPair. On another training dataset, iSNO-ANBPB also outperformed GPS-SNO and iSNO-PseAAC in the 10-fold crossvalidation test. Full article
Open AccessArticle Triterpenoid Saponins from Stauntonia chinensis Ameliorate Insulin Resistance via the AMP-Activated Protein Kinase and IR/IRS-1/PI3K/Akt Pathways in Insulin-Resistant HepG2 Cells
Int. J. Mol. Sci. 2014, 15(6), 10446-10458; doi:10.3390/ijms150610446
Received: 11 April 2014 / Revised: 20 May 2014 / Accepted: 26 May 2014 / Published: 10 June 2014
Cited by 9 | PDF Full-text (1562 KB) | HTML Full-text | XML Full-text
Abstract
Inflammation and oxidative stress play crucial roles in the etiology of type 2 diabetes mellitus. In this study, we examined the anti-diabetic effects of triterpenoid saponins extracted from Stauntonia chinensis on stimulating glucose uptake by insulin-resistant human HepG2 cells. The results showed [...] Read more.
Inflammation and oxidative stress play crucial roles in the etiology of type 2 diabetes mellitus. In this study, we examined the anti-diabetic effects of triterpenoid saponins extracted from Stauntonia chinensis on stimulating glucose uptake by insulin-resistant human HepG2 cells. The results showed that saponin 6 significantly increased glucose uptake and glucose catabolism. Saponin 6 also enhanced the phosphorylation of AMP-activated protein kinase (AMPK) and activated the insulin receptor (IR)/insulin receptor substrate-1 (IRS-1)/phosphoinositide 3-kinase (PI3K)/Akt pathway. Therefore, our results suggest that saponins from S. chinensis improve glucose uptake and catabolism in hepatic cells by stimulating the AMPK and the IR/IRS-1/PI3K/Akt signaling pathways. The results also imply that saponins from S. chinensis can enhance glucose uptake and insulin sensitivity, representing a promising treatment for type 2 diabetes mellitus. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Computational Study on Substrate Specificity of a Novel Cysteine Protease 1 Precursor from Zea mays
Int. J. Mol. Sci. 2014, 15(6), 10459-10478; doi:10.3390/ijms150610459
Received: 31 March 2014 / Revised: 27 May 2014 / Accepted: 28 May 2014 / Published: 11 June 2014
Cited by 2 | PDF Full-text (2809 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Cysteine protease 1 precursor from Zea mays (zmCP1) is classified as a member of the C1A family of peptidases (papain-like cysteine protease) in MEROPS (the Peptidase Database). The 3D structure and substrate specificity of the zmCP1 is still unknown. This study is [...] Read more.
Cysteine protease 1 precursor from Zea mays (zmCP1) is classified as a member of the C1A family of peptidases (papain-like cysteine protease) in MEROPS (the Peptidase Database). The 3D structure and substrate specificity of the zmCP1 is still unknown. This study is the first one to build the 3D structure of zmCP1 by computer-assisted homology modeling. In order to determine the substrate specificity of zmCP1, docking study is used for rapid and convenient analysis of large populations of ligand–enzyme complexes. Docking results show that zmCP1 has preference for P1 position and P2 position for Arg and a large hydrophobic residue (such as Phe). Gly147, Gly191, Cys189, and Asp190 are predicted to function as active residues at the S1 subsite, and the S2 subsite contains Leu283, Leu193, Ala259, Met194, and Ala286. SIFt results indicate that Gly144, Arg268, Trp308, and Ser311 play important roles in substrate binding. Then Molecular Mechanics-Poisson-Boltzmann Surface Area (MM-PBSA) method was used to explain the substrate specificity for P1 position of zmCp1. This study provides insights into the molecular basis of zmCP1 activity and substrate specificity. Full article
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Open AccessArticle Estrogen Rapidly Enhances Incisional Pain of Ovariectomized Rats Primarily through the G Protein-Coupled Estrogen Receptor
Int. J. Mol. Sci. 2014, 15(6), 10479-10491; doi:10.3390/ijms150610479
Received: 20 April 2014 / Revised: 10 May 2014 / Accepted: 13 May 2014 / Published: 11 June 2014
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Abstract
It has become increasingly apparent that the pain threshold of females and males varies in an estrogen dependent manner. To investigate the modulation of pain by estrogen and the molecular mechanisms involved in this process. A total of 48 rats were ovariectomized [...] Read more.
It has become increasingly apparent that the pain threshold of females and males varies in an estrogen dependent manner. To investigate the modulation of pain by estrogen and the molecular mechanisms involved in this process. A total of 48 rats were ovariectomized (OVX). At 14 and 20 days after OVX, rats were divided into eight groups: groups 1–4 were administered drugs intravenously (IV); groups 5–8 were administered through intrathecal (IT) catheter. Hind paw incision was made in all animals to determine incisional pain. Paw withdraw threshold (PWT) was tested prior to and 24 h after incision. The test drugs were applied 24 h after the incision. Rats were either IV or IT administered with: 17-β-estradiol (E2), G protein-coupled estrogen receptor (GPER)-selective agonist (G1), GPER-selective antagonist (G15) and E2 (G15 + E2), or solvent. Before and 30 min after IV drug administration and 20 min during the IT catheter administration, PWT was tested and recorded. 24 h after incisional surgery, the PWT of all rats significantly decreased. Both in the IV group and IT group: administration of E2 and G1 significantly decreased PWT. Neither administration of G15 + E2 nor solvent significantly changed PWT. Estrogen causes rapid reduction in the mechanical pain threshold of OVX rats via GPER. Full article
(This article belongs to the collection G Protein-Coupled Receptor Signaling and Regulation)
Open AccessArticle On Interlayer Stability and High-Cycle Simulator Performance of Diamond-Like Carbon Layers for Articulating Joint Replacements
Int. J. Mol. Sci. 2014, 15(6), 10527-10540; doi:10.3390/ijms150610527
Received: 28 April 2014 / Revised: 29 April 2014 / Accepted: 20 May 2014 / Published: 11 June 2014
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Abstract
Diamond like carbon (DLC) coatings have been proven to be an excellent choice for wear reduction in many technical applications. However, for successful adaption to the orthopaedic field, layer performance, stability and adhesion in physiologically relevant setups are crucial and not consistently [...] Read more.
Diamond like carbon (DLC) coatings have been proven to be an excellent choice for wear reduction in many technical applications. However, for successful adaption to the orthopaedic field, layer performance, stability and adhesion in physiologically relevant setups are crucial and not consistently investigated. In vitro wear testing as well as adequate corrosion tests of interfaces and interlayers are of great importance to verify the long term stability of DLC coated load bearing implants in the human body. DLC coatings were deposited on articulating lumbar spinal disks made of CoCr28Mo6 biomedical implant alloy using a plasma-activated chemical vapor deposition (PACVD) process. As an adhesion promoting interlayer, tantalum films were deposited by magnetron sputtering. Wear tests of coated and uncoated implants were performed in physiological solution up to a maximum of 101 million articulation cycles with an amplitude of ±2° and −3/+6° in successive intervals at a preload of 1200 N. The implants were characterized by gravimetry, inductively coupled plasma optical emission spectrometry (ICP-OES) and cross section scanning electron microscopy (SEM) analysis. It is shown that DLC coated surfaces with uncontaminated tantalum interlayers perform very well and no corrosive or mechanical failure could be observed. This also holds true in tests featuring overload and third-body wear by cortical bone chips present in the bearing pairs. Regarding the interlayer tolerance towards interlayer contamination (oxygen), limits for initiation of potential failure modes were established. It was found that mechanical failure is the most critical aspect and this mode is hypothetically linked to the α-β tantalum phase switch induced by increasing oxygen levels as observed by X-ray diffraction (XRD). It is concluded that DLC coatings are a feasible candidate for near zero wear articulations on implants, potentially even surpassing the performance of ceramic vs. ceramic. Full article
(This article belongs to the Special Issue Biologic Coatings for Orthopaedic Implant)
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Open AccessArticle Mitigating the Effects of Xuebijing Injection on Hematopoietic Cell Injury Induced by Total Body Irradiation with γ rays by Decreasing Reactive Oxygen Species Levels
Int. J. Mol. Sci. 2014, 15(6), 10541-10553; doi:10.3390/ijms150610541
Received: 22 April 2014 / Revised: 26 May 2014 / Accepted: 28 May 2014 / Published: 12 June 2014
Cited by 6 | PDF Full-text (3863 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Hematopoietic injury is the most common side effect of radiotherapy. However, the methods available for the mitigating of radiation injury remain limited. Xuebijing injection (XBJ) is a traditional Chinese medicine used to treat sepsis in the clinic. In this study, we investigated [...] Read more.
Hematopoietic injury is the most common side effect of radiotherapy. However, the methods available for the mitigating of radiation injury remain limited. Xuebijing injection (XBJ) is a traditional Chinese medicine used to treat sepsis in the clinic. In this study, we investigated the effects of XBJ on the survival rate in mice with hematopoietic injury induced by γ ray ionizing radiation (IR). Mice were intraperitoneally injected with XBJ daily for seven days after total body irradiation (TBI). Our results showed that XBJ (0.4 mL/kg) significantly increased 30-day survival rates in mice exposed to 7.5 Gy TBI. This effect may be attributable to improved preservation of white blood cells (WBCs) and hematopoietic cells, given that bone marrow (BM) cells from XBJ-treated mice produced more granulocyte-macrophage colony forming units (CFU-GM) than that in the 2 Gy/TBI group. XBJ also decreased the levels of reactive oxygen species (ROS) by increasing glutathione (GSH) and superoxide dismutase (SOD) levels in serum and attenuated the increased BM cell apoptosis caused by 2 Gy/TBI. In conclusion, these findings suggest that XBJ enhances the survival rate of irradiated mice and attenuates the effects of radiation on hematopoietic injury by decreasing ROS production in BM cells, indicating that XBJ may be a promising therapeutic candidate for reducing hematopoietic radiation injury. Full article
(This article belongs to the Section Molecular Toxicology)
Open AccessArticle Biochemical Properties of a New Cold-Active Mono- and Diacylglycerol Lipase from Marine Member Janibacter sp. Strain HTCC2649
Int. J. Mol. Sci. 2014, 15(6), 10554-10566; doi:10.3390/ijms150610554
Received: 29 April 2014 / Revised: 15 May 2014 / Accepted: 22 May 2014 / Published: 12 June 2014
Cited by 5 | PDF Full-text (2326 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Mono- and di-acylglycerol lipase has been applied to industrial usage in oil modification for its special substrate selectivity. Until now, the reported mono- and di-acylglycerol lipases from microorganism are limited, and there is no report on the mono- and di-acylglycerol lipase from [...] Read more.
Mono- and di-acylglycerol lipase has been applied to industrial usage in oil modification for its special substrate selectivity. Until now, the reported mono- and di-acylglycerol lipases from microorganism are limited, and there is no report on the mono- and di-acylglycerol lipase from bacteria. A predicted lipase (named MAJ1) from marine Janibacter sp. strain HTCC2649 was purified and biochemical characterized. MAJ1 was clustered in the family I.7 of esterase/lipase. The optimum activity of the purified MAJ1 occurred at pH 7.0 and 30 °C. The enzyme retained 50% of the optimum activity at 5 °C, indicating that MAJ1 is a cold-active lipase. The enzyme activity was stable in the presence of various metal ions, and inhibited in EDTA. MAJ1 was resistant to detergents. MAJ1 preferentially hydrolyzed mono- and di-acylglycerols, but did not show activity to triacylglycerols of camellia oil substrates. Further, MAJ1 is low homologous to that of the reported fungal diacylglycerol lipases, including Malassezia globosa lipase 1 (SMG1), Penicillium camembertii lipase U-150 (PCL), and Aspergillus oryzae lipase (AOL). Thus, we identified a novel cold-active bacterial lipase with a sn-1/3 preference towards mono- and di-acylglycerides for the first time. Moreover, it has the potential, in oil modification, for special substrate selectivity. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle The Role of Circulating MicroRNA-126 (miR-126): A Novel Biomarker for Screening Prediabetes and Newly Diagnosed Type 2 Diabetes Mellitus
Int. J. Mol. Sci. 2014, 15(6), 10567-10577; doi:10.3390/ijms150610567
Received: 2 January 2014 / Revised: 19 April 2014 / Accepted: 23 May 2014 / Published: 12 June 2014
Cited by 21 | PDF Full-text (778 KB) | HTML Full-text | XML Full-text
Abstract
Recent studies suggested an association of endothelial microRNA-126 (miR-126) with type 2 diabetes mellitus (T2DM). In the current study, we examined whether circulating miR-126 is associated with T2DM and pre-diabetic syndrome. The study included 82 subjects with impaired glucose tolerance (IGT), 75 [...] Read more.
Recent studies suggested an association of endothelial microRNA-126 (miR-126) with type 2 diabetes mellitus (T2DM). In the current study, we examined whether circulating miR-126 is associated with T2DM and pre-diabetic syndrome. The study included 82 subjects with impaired glucose tolerance (IGT), 75 subjects with impaired fasting glucose (IFG), 160 patients with newly diagnosed T2DM, and 138 healthy individuals. Quantitative polymerase chain reaction (qPCR) was used to examine serum miR-126. Serum miR-126 was significantly lower in IGT/IFG subjects and T2DM patients than in healthy controls (p < 0.05). After six months of treatment (diet control and exercise in IGT/IFG subjects, insulin plus diet control and exercise in T2DM patients), serum miR-126 increased significantly (p < 0.05). An analysis based on serum miR-126 in the sample revealed a significantly higher odds ratio (OR) for the subjects with the lowest 1/3 of serum miR-126 for T2DM (OR: 3.500, 95% confidence interval: 1.901–6.445, p < 0.05) than subjects within the highest 1/3 of serum miR-126. Such an association was still apparent after adjusting for other major risk factors. The area under the curve (AUC) for the receiver-operating characteristic (ROC) analysis was 0.792 (95% confidence interval: 0.707–0.877, p < 0.001). These results encourage the use of serum miR-126 as a biomarker for pre-diabetes and diabetes mellitus, as well as therapeutic response. Full article
(This article belongs to the Section Molecular Diagnostics)
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Open AccessArticle Genistein Inhibits Osteoclastic Differentiation of RAW 264.7 Cells via Regulation of ROS Production and Scavenging
Int. J. Mol. Sci. 2014, 15(6), 10605-10621; doi:10.3390/ijms150610605
Received: 11 February 2014 / Revised: 22 May 2014 / Accepted: 30 May 2014 / Published: 12 June 2014
Cited by 13 | PDF Full-text (1935 KB) | HTML Full-text | XML Full-text
Abstract
Genistein, a phytoestrogen, has been demonstrated to have a bone-sparing and antiresorptive effect. Genistein can inhibit the osteoclast formation of receptor activator of nuclear factor-κB ligand (RANKL)-induced RAW 264.7 cells by preventing the translocation of nuclear factor-κB (NF-κB), a redox-sensitive factor, to [...] Read more.
Genistein, a phytoestrogen, has been demonstrated to have a bone-sparing and antiresorptive effect. Genistein can inhibit the osteoclast formation of receptor activator of nuclear factor-κB ligand (RANKL)-induced RAW 264.7 cells by preventing the translocation of nuclear factor-κB (NF-κB), a redox-sensitive factor, to the nucleus. Therefore, the suppressive effect of genistein on the reactive oxygen species (ROS) level during osteoclast differentiation and the mechanism associated with the control of ROS levels by genistein were investigated. The cellular antioxidant capacity and inhibitory effect of genistein were confirmed. The translation and activation of nicotinamide adenine dinucleotide phosphate (NADPH) oxidase 1 (Nox1), as well as the disruption of the mitochondrial electron transport chain system were obviously suppressed by genistein in a dose-dependent manner. The induction of phase II antioxidant enzymes, such as superoxide dismutase 1 (SOD1) and heme oxygenase-1 (HO-1), was enhanced by genistein. In addition, the translational induction of nuclear factor erythroid 2-related factor 2 (Nrf2) was notably increased by genistein. These results provide that the inhibitory effects of genistein on RANKL-stimulated osteoclast differentiation is likely to be attributed to the control of ROS generation through suppressing the translation and activation of Nox1 and the disruption of the mitochondrial electron transport chain system, as well as ROS scavenging through the Nrf2-mediated induction of phase II antioxidant enzymes, such as SOD1 and HO-1. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle On the Influence of Crosslinker on Template Complexation in Molecularly Imprinted Polymers: A Computational Study of Prepolymerization Mixture Events with Correlations to Template-Polymer Recognition Behavior and NMR Spectroscopic Studies
Int. J. Mol. Sci. 2014, 15(6), 10622-10634; doi:10.3390/ijms150610622
Received: 20 March 2014 / Revised: 7 May 2014 / Accepted: 20 May 2014 / Published: 12 June 2014
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Abstract
Aspects of the molecular-level basis for the function of ethylene glycol dimethacrylate and trimethylolproprane trimethacrylate crosslinked methacrylic acid copolymers molecularly imprinted with (S)-propranolol have been studied using a series of all-component and all-atom molecular dynamics studies of the corresponding prepolymerization [...] Read more.
Aspects of the molecular-level basis for the function of ethylene glycol dimethacrylate and trimethylolproprane trimethacrylate crosslinked methacrylic acid copolymers molecularly imprinted with (S)-propranolol have been studied using a series of all-component and all-atom molecular dynamics studies of the corresponding prepolymerization systems. The crosslinking agents were observed to contribute to template complexation, and the results were contrasted with previously reported template-recognition behavior of the corresponding polymers. Differences in the extent to which the two crosslinkers interacted with the functional monomer were identified, and correlations were made to polymer-ligand recognition behavior and the results of nuclear magnetic resonance spectroscopic studies studies. This study demonstrates the importance of considering the functional monomer–crosslinker interaction when designing molecularly imprinted polymers, and highlights the often neglected general contribution of crosslinker to determining the nature of molecularly imprinted polymer-template selectivity. Full article
(This article belongs to the Section Molecular Recognition)
Open AccessArticle Brain Metastases from Lung Cancer Show Increased Expression of DVL1, DVL3 and Beta-Catenin and Down-Regulation of E-Cadherin
Int. J. Mol. Sci. 2014, 15(6), 10635-10651; doi:10.3390/ijms150610635
Received: 23 January 2014 / Revised: 14 May 2014 / Accepted: 27 May 2014 / Published: 13 June 2014
Cited by 7 | PDF Full-text (1020 KB) | HTML Full-text | XML Full-text
Abstract
The susceptibility of brain to secondary formation from lung cancer primaries is a well-known phenomenon. In contrast, the molecular basis for invasion and metastasis to the brain is largely unknown. In the present study, 31 brain metastases that originated from primary lung [...] Read more.
The susceptibility of brain to secondary formation from lung cancer primaries is a well-known phenomenon. In contrast, the molecular basis for invasion and metastasis to the brain is largely unknown. In the present study, 31 brain metastases that originated from primary lung carcinomas were analyzed regarding over expression of Dishevelled-1 (DVL1), Dishevelled-3 (DVL3), E-cadherin (CDH1) and beta-catenin (CTNNB1). Protein expressions and localizations were analyzed by immunohistochemistry. Genetic alterations of E-cadherin were tested by polymerase chain reaction (PCR)/loss of heterozygosity (LOH). Heteroduplex was used to investigate mutations in beta-catenin. DVL1 and DVL3 showed over expression in brain metastasis in 87.1% and 90.3% of samples respectively. Nuclear staining was observed in 54.8% of cases for DVL1 and 53.3% for DVL3. The main effector of the Wnt signaling, beta-catenin, was up-regulated in 56%, and transferred to the nucleus in 36% of metastases. When DVL1 and DVL3 were up-regulated the number of cases with nuclear beta-catenin significantly increased (p = 0.0001). Down-regulation of E-cadherin was observed in 80% of samples. Genetic analysis showed 36% of samples with LOH of the CDH1. In comparison to other lung cancer pathologies, the diagnoses adenocarcinoma and small cell lung cancer (SCLC) were significantly associated to CDH1 LOH (p = 0.001). Microsatellite instability was detected in one metastasis from adenocarcinoma. Exon 3 of beta-catenin was not targeted. Altered expression of Dishevelled-1, Dishevelled-3, E-cadherin and beta-catenin were present in brain metastases which indicates that Wnt signaling is important and may contribute to better understanding of genetic profile conditioning lung cancer metastasis to the brain. Full article
(This article belongs to the Special Issue Brain Metastasis 2014)
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Open AccessArticle Weighted Risk Score-Based Multifactor Dimensionality Reduction to Detect Gene-Gene Interactions in Nasopharyngeal Carcinoma
Int. J. Mol. Sci. 2014, 15(6), 10724-10737; doi:10.3390/ijms150610724
Received: 4 March 2014 / Revised: 21 April 2014 / Accepted: 3 June 2014 / Published: 13 June 2014
Cited by 2 | PDF Full-text (729 KB) | HTML Full-text | XML Full-text
Abstract
Determining the complex relationships between diseases, polymorphisms in human genes and environmental factors is challenging. Multifactor dimensionality reduction (MDR) has been proven to be capable of effectively detecting the statistical patterns of epistasis, although classification accuracy is required for this approach. The [...] Read more.
Determining the complex relationships between diseases, polymorphisms in human genes and environmental factors is challenging. Multifactor dimensionality reduction (MDR) has been proven to be capable of effectively detecting the statistical patterns of epistasis, although classification accuracy is required for this approach. The imbalanced dataset can cause seriously negative effects on classification accuracy. Moreover, MDR methods cannot quantitatively assess the disease risk of genotype combinations. Hence, we introduce a novel weighted risk score-based multifactor dimensionality reduction (WRSMDR) method that uses the Bayesian posterior probability of polymorphism combinations as a new quantitative measure of disease risk. First, we compared the WRSMDR to the MDR method in simulated datasets. Our results showed that the WRSMDR method had reasonable power to identify high-order gene-gene interactions, and it was more effective than MDR at detecting four-locus models. Moreover, WRSMDR reveals more information regarding the effect of genotype combination on the disease risk, and the result was easier to determine and apply than with MDR. Finally, we applied WRSMDR to a nasopharyngeal carcinoma (NPC) case-control study and identified a statistically significant high-order interaction among three polymorphisms: rs2860580, rs11865086 and rs2305806. Full article
(This article belongs to the collection Human Single Nucleotide Polymorphisms and Disease Diagnostics)
Open AccessArticle Damage of Neuroblastoma Cell SH-SY5Y Mediated by MPP+ Inhibits Proliferation of T-Cell Leukemia Jurkat by Co-Culture System
Int. J. Mol. Sci. 2014, 15(6), 10738-10750; doi:10.3390/ijms150610738
Received: 3 January 2014 / Revised: 19 May 2014 / Accepted: 3 June 2014 / Published: 13 June 2014
Cited by 3 | PDF Full-text (814 KB) | HTML Full-text | XML Full-text
Abstract
The adaptive immune system has implications in pathology of Parkinson’s disease (PD). Research data demonstrated that the peripheral CD4+ T-cell population decreased in pathogenesis of PD. The effect of damaged dopaminergic neurons on peripheral T cells of PD is still unknown. [...] Read more.
The adaptive immune system has implications in pathology of Parkinson’s disease (PD). Research data demonstrated that the peripheral CD4+ T-cell population decreased in pathogenesis of PD. The effect of damaged dopaminergic neurons on peripheral T cells of PD is still unknown. In this study, we constructed a neuronal and glial cells co-culture model by using human neuroblastoma cells SH-SY5Y and gliomas cells U87. After the co-culture cells were treated with neurotoxin 1-methyl-4-phenylpyridinium (MPP+) for 24 h, the conditioned media was harvested and used to cultivate T-cell leukemia Jurkat cells for another 24 h. We then analyzed the cell proliferation, cell cycle and necrosis effect of Jurkat cells. The results showed that co-culture medium of SH-SY5Y and U87 cells with MPP+ treatment inhibited the proliferation of Jurkat cells compared to control medium without MPP+, even though the same concentration of MPP+ had very little toxicity to the Jurkat cell. Furthermore, co-culture medium with low concentration of MPP+ (100 µM) arrested Jurkat cells cycle in G2/M phase through increasing cell cycle division 2 (CDC2) and CyclinB1 expression level, whereas co-culture medium with high concentration of MPP+ (500 µM) induced Jurkat cell necrosis through cellular swelling and membrane breakage. Our data implies that damaged dopamine neurons with glial cells can lead to the reduced number or inhibited proliferation activity of peripheral T cells. Full article
(This article belongs to the Special Issue Neuroprotective Strategies 2014)
Open AccessArticle Cytotoxic Effects of Dillapiole on Embryonic Development of Mouse Blastocysts in Vitro and in Vivo
Int. J. Mol. Sci. 2014, 15(6), 10751-10765; doi:10.3390/ijms150610751
Received: 21 March 2014 / Revised: 25 May 2014 / Accepted: 6 June 2014 / Published: 13 June 2014
Cited by 2 | PDF Full-text (1100 KB) | HTML Full-text | XML Full-text
Abstract
We examined the cytotoxic effects of dillapiole, a phenylpropanoid with antileishmanial, anti-inflammatory, antifungal, and acaricidal activities, on the blastocyst stage of mouse embryos, subsequent embryonic attachment and outgrowth in vitro, and in vivo implantation via embryo transfer. Blastocysts treated with 2.5–10 [...] Read more.
We examined the cytotoxic effects of dillapiole, a phenylpropanoid with antileishmanial, anti-inflammatory, antifungal, and acaricidal activities, on the blastocyst stage of mouse embryos, subsequent embryonic attachment and outgrowth in vitro, and in vivo implantation via embryo transfer. Blastocysts treated with 2.5–10 μM dillapiole exhibited a significant increase in apoptosis and corresponding decrease in total cell number. Notably, the implantation success rates of blastocysts pretreated with dillapiole were lower than those of their control counterparts. Moreover, in vitro treatment with 2.5–10 μM dillapiole was associated with increased resorption of post-implantation embryos and decreased fetal weight. Our results collectively indicate that dillapiole induces apoptosis and retards early post-implantation development, both in vitro and in vivo. However, the extent to which this organic compound exerts teratogenic effects on early human development is not known at present. Further studies are required to establish effective protection strategies against the cytotoxic effects of dillapiole. Full article
(This article belongs to the Section Molecular Toxicology)
Open AccessArticle Role of Candida albicans-Secreted Aspartyl Proteinases (Saps) in Severe Early Childhood Caries
Int. J. Mol. Sci. 2014, 15(6), 10766-10779; doi:10.3390/ijms150610766
Received: 12 April 2014 / Revised: 13 May 2014 / Accepted: 16 May 2014 / Published: 13 June 2014
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Abstract
Candida albicans is strongly associated with severe early childhood caries (S-ECC). However, the roles of secreted aspartyl proteinases (Saps), an important virulence factor of C. albicans, in the progress of S-ECC are not clear. In our study, the Saps activities were [...] Read more.
Candida albicans is strongly associated with severe early childhood caries (S-ECC). However, the roles of secreted aspartyl proteinases (Saps), an important virulence factor of C. albicans, in the progress of S-ECC are not clear. In our study, the Saps activities were evaluated by the yeast nitrogen base–bovine serum albumi (YNB–BSA) agar plate method and by the MTT method with bovine serum albumin (BSA) as the substrate. Genotypes of C. albicans and gene expression of Sap1–5 were evaluated. The relationships of Saps activities and genotypes with S-ECC were analyzed. The results showed that enzyme activities of Saps in the S-ECC group were significantly higher than those in the caries free (CF) group (p < 0.05). Genotypes A, B and C were detected in the S-ECC group, and genotypes A and C were detected in the CF group. In the genotype A group, Saps activity in the S-ECC group was significantly different from that in the CF group (p < 0.05). The gene expression level of Sap1 in the S-ECC group was significantly higher than that in the CF group (p = 0.001), while Sap4 expression was significantly lower than that in the CF group (p = 0.029). It can be concluded that Sap1–5 are the predominant proteinase genes expressed in C. albicans from dental biofilm and Sap1 may play an important role in the development of S-ECC. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle An Efficient Agrobacterium-Mediated Transformation System for Poplar
Int. J. Mol. Sci. 2014, 15(6), 10780-10793; doi:10.3390/ijms150610780
Received: 1 March 2014 / Revised: 3 June 2014 / Accepted: 4 June 2014 / Published: 13 June 2014
Cited by 3 | PDF Full-text (859 KB) | HTML Full-text | XML Full-text
Abstract
Poplar is a model system for the regeneration and genetic transformation of woody plants. To shorten the time required for studies of transgenic poplar, efforts have been made to optimize transformation methods that use Agrobacterium tumefaciens. In this study, an Agrobacterium [...] Read more.
Poplar is a model system for the regeneration and genetic transformation of woody plants. To shorten the time required for studies of transgenic poplar, efforts have been made to optimize transformation methods that use Agrobacterium tumefaciens. In this study, an Agrobacterium infective suspension was treated at 4 °C for at least 10 h before infecting explants. By transforming the Populus hybrid clone “Nanlin895” (Populus deltoides × P. euramericana) with Agrobacterium harboring the PBI121:CarNAC6 binary vector, we showed that the transformation efficiency was improved significantly by multiple independent factors, including an Agrobacterium infective suspension with an OD600 of 0.7, an Agrobacterium infection for 120 min, an Agrobacterium infective suspension at a pH of 5.0, an acetosyringone concentration of 200 µM, a cocultivation at 28 °C, a cocultivation for 72 h and a sucrose concentration of 30 g/L in the cocultivation medium. We also showed that preculture of wounded leaf explants for two days increased the regeneration rate. The integration of the desired gene into transgenic poplars was detected using selective medium containing kanamycin, followed by southern blot analysis. The expression of the transgene in the transgenic lines was confirmed by northern blot analysis. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
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Open AccessArticle High-Salt Intake Suppressed MicroRNA-133a Expression in Dahl SS Rat Myocardium
Int. J. Mol. Sci. 2014, 15(6), 10794-10805; doi:10.3390/ijms150610794
Received: 3 May 2014 / Revised: 6 June 2014 / Accepted: 9 June 2014 / Published: 16 June 2014
Cited by 2 | PDF Full-text (1953 KB) | HTML Full-text | XML Full-text
Abstract
Salt-sensitive individuals show earlier and more serious cardiac damage than nonsalt-sensitive ones. Some studies have suggested that microRNA-133a could reduce cardiac hypertrophy and myocardial fibrosis. The current study aims to investigate the different functions of high-salt intake on salt-sensitive (SS) rats and [...] Read more.
Salt-sensitive individuals show earlier and more serious cardiac damage than nonsalt-sensitive ones. Some studies have suggested that microRNA-133a could reduce cardiac hypertrophy and myocardial fibrosis. The current study aims to investigate the different functions of high-salt intake on salt-sensitive (SS) rats and Sprague-Dawley (SD) rats and the involvement of microRNA-133a in these roles. After high-salt intervention, the left ventricular mass (LVW) and left ventricular mass index (LVMI) of the salt-sensitive high salt (SHS) group were obviously higher than those of the salt-sensitive low salt (SLS) group. However, the difference between the Sprague-Dawley high salt (DHS) group and the Sprague-Dawley low salt (DLS) group was not significant. Compared with SLS group, collagen I and connective tissue growth factor (CTGF) in the heart of SHS group were significantly higher, whereas no statistical difference was observed between the DHS group and the DLS group. Compared with low-salt diet, microRNA-133a in the heart of both strains were significantly decreased, but that in the SHS group decreased more significantly. These results suggest that high salt intervention could down-regulate the expression of myocardial microRNA-133a, which may be one of the mechanisms involved in myocardial fibrosis in salt-sensitive hypertension. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
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Open AccessArticle Metabolic Profiling of Somatic Tissues from Monochamus alternatus (Coleoptera: Cerambycidae) Reveals Effects of Irradiation on Metabolism
Int. J. Mol. Sci. 2014, 15(6), 10806-10820; doi:10.3390/ijms150610806
Received: 12 May 2014 / Revised: 9 June 2014 / Accepted: 10 June 2014 / Published: 16 June 2014
Cited by 2 | PDF Full-text (4656 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
A high-level of sexual sterility is of importance for the sterile insect technique (SIT). However, the use of high-dose-intensity gamma radiation to induce sterility has negative impacts not only on reproductive cells but also on somatic cells. In this study, we investigated [...] Read more.
A high-level of sexual sterility is of importance for the sterile insect technique (SIT). However, the use of high-dose-intensity gamma radiation to induce sterility has negative impacts not only on reproductive cells but also on somatic cells. In this study, we investigated the metabolite differences in somatic tissues between non-irradiated, 20-Gy-irradiated, and 40-Gy-irradiated male Monochamus alternatus, an important vector of the pathogenic nematode, Bursaphelenchus xylophilus, which kills Asian pines. The results showed that metabolite levels changed moderately in the 20-Gy samples but were markedly altered in the 40-Gy samples compared with the non-irradiated samples. Twenty-six and 53 metabolites were disturbed by 20-Gy and 40-Gy radiation, respectively. Thirty-six metabolites were found to be markedly altered in the 40-Gy samples but were not changed significantly in the 20-Gy samples. The comprehensive metabolomic disorders induced by 40-Gy radiation dysregulated six metabolic pathways involved in the life process. The findings presented in this manuscript will contribute to our knowledge of the characteristic metabolic changes associated with gamma-radiation-induced damage to somatic cells and will allow for better exploration of the SIT for the control of this target pest. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Continuous Flow Atmospheric Pressure Laser Desorption/Ionization Using a 6–7-µm-Band Mid-Infrared Tunable Laser for Biomolecular Mass Spectrometry
Int. J. Mol. Sci. 2014, 15(6), 10821-10834; doi:10.3390/ijms150610821
Received: 20 March 2014 / Revised: 28 May 2014 / Accepted: 4 June 2014 / Published: 16 June 2014
Cited by 1 | PDF Full-text (1605 KB) | HTML Full-text | XML Full-text
Abstract
A continuous flow atmospheric pressure laser desorption/ionization technique using a porous stainless steel probe and a 6–7-µm-band mid-infrared tunable laser was developed. This ion source is capable of direct ionization from a continuous flow with a high temporal stability. The 6–7-µm wavelength [...] Read more.
A continuous flow atmospheric pressure laser desorption/ionization technique using a porous stainless steel probe and a 6–7-µm-band mid-infrared tunable laser was developed. This ion source is capable of direct ionization from a continuous flow with a high temporal stability. The 6–7-µm wavelength region corresponds to the characteristic absorption bands of various molecular vibration modes, including O–H, C=O, CH3 and C–N bonds. Consequently, many organic compounds and solvents, including water, have characteristic absorption peaks in this region. This ion source requires no additional matrix, and utilizes water or acetonitrile as the solvent matrix at several absorption peak wavelengths (6.05 and 7.27 µm, respectively). The distribution of multiply-charged peptide ions is extremely sensitive to the temperature of the heated capillary, which is the inlet of the mass spectrometer. This ionization technique has potential for the interface of liquid chromatography/mass spectrometry (LC/MS). Full article
(This article belongs to the Special Issue Mass Spectrometry Application in Biology) Print Edition available
Open AccessArticle Comparisons of Non-Gaussian Statistical Models in DNA Methylation Analysis
Int. J. Mol. Sci. 2014, 15(6), 10835-10854; doi:10.3390/ijms150610835
Received: 24 March 2014 / Revised: 12 May 2014 / Accepted: 10 June 2014 / Published: 16 June 2014
Cited by 1 | PDF Full-text (596 KB) | HTML Full-text | XML Full-text
Abstract
As a key regulatory mechanism of gene expression, DNA methylation patterns are widely altered in many complex genetic diseases, including cancer. DNA methylation is naturally quantified by bounded support data; therefore, it is non-Gaussian distributed. In order to capture such properties, we [...] Read more.
As a key regulatory mechanism of gene expression, DNA methylation patterns are widely altered in many complex genetic diseases, including cancer. DNA methylation is naturally quantified by bounded support data; therefore, it is non-Gaussian distributed. In order to capture such properties, we introduce some non-Gaussian statistical models to perform dimension reduction on DNA methylation data. Afterwards, non-Gaussian statistical model-based unsupervised clustering strategies are applied to cluster the data. Comparisons and analysis of different dimension reduction strategies and unsupervised clustering methods are presented. Experimental results show that the non-Gaussian statistical model-based methods are superior to the conventional Gaussian distribution-based method. They are meaningful tools for DNA methylation analysis. Moreover, among several non-Gaussian methods, the one that captures the bounded nature of DNA methylation data reveals the best clustering performance. Full article
(This article belongs to the Special Issue Identification and Roles of the Structure of DNA)
Open AccessArticle Bacterial Cellulose Membranes Used as Artificial Substitutes for Dural Defection in Rabbits
Int. J. Mol. Sci. 2014, 15(6), 10855-10867; doi:10.3390/ijms150610855
Received: 3 April 2014 / Revised: 22 May 2014 / Accepted: 3 June 2014 / Published: 16 June 2014
Cited by 2 | PDF Full-text (1942 KB) | HTML Full-text | XML Full-text
Abstract
To improve the efficacy and safety of dural repair in neurosurgical procedures, a new dural material derived from bacterial cellulose (BC) was evaluated in a rabbit model with dural defects. We prepared artificial dura mater using bacterial cellulose which was incubated and [...] Read more.
To improve the efficacy and safety of dural repair in neurosurgical procedures, a new dural material derived from bacterial cellulose (BC) was evaluated in a rabbit model with dural defects. We prepared artificial dura mater using bacterial cellulose which was incubated and fermented from Acetobacter xylinum. The dural defects of the rabbit model were repaired with BC membranes. All surgeries were performed under sodium pentobarbital anesthesia, and all efforts were made to minimize suffering. All animals were humanely euthanized by intravenous injection of phenobarbitone, at each time point, after the operation. Then, the histocompatibility and inflammatory effects of BC were examined by histological examination, real-time fluorescent quantitative polymerase chain reaction (PCR) and Western Blot. BC membranes evenly covered the surface of brain without adhesion. There were seldom inflammatory cells surrounding the membrane during the early postoperative period. The expression of inflammatory cytokines IL-1β, IL-6 and TNF-α as well as iNOS and COX-2 were lower in the BC group compared to the control group at 7, 14 and 21 days after implantation. BC can repair dural defects in rabbit and has a decreased inflammatory response compared to traditional materials. However, the long-term effects need to be validated in larger animals. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Proteomic Analysis of Embryogenesis and the Acquisition of Seed Dormancy in Norway Maple (Acer platanoides L.)
Int. J. Mol. Sci. 2014, 15(6), 10868-10891; doi:10.3390/ijms150610868
Received: 24 April 2014 / Revised: 16 May 2014 / Accepted: 30 May 2014 / Published: 17 June 2014
Cited by 3 | PDF Full-text (1509 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The proteome of zygotic embryos of Acer platanoides L. was analyzed via high-resolution 2D-SDS-PAGE and MS/MS in order to: (1) identify significant physiological processes associated with embryo development; and (2) identify changes in the proteome of the embryo associated with the acquisition [...] Read more.
The proteome of zygotic embryos of Acer platanoides L. was analyzed via high-resolution 2D-SDS-PAGE and MS/MS in order to: (1) identify significant physiological processes associated with embryo development; and (2) identify changes in the proteome of the embryo associated with the acquisition of seed dormancy. Seventeen spots were identified as associated with morphogenesis at 10 to 13 weeks after flowering (WAF). Thirty-three spots were associated with maturation of the embryo at 14 to 22 WAF. The greatest changes in protein abundance occurred at 22 WAF, when seeds become fully mature. Overall, the stage of morphogenesis was characterized by changes in the abundance of proteins (tubulins and actin) associated with the growth and development of the embryo. Enzymes related to energy supply were especially elevated, most likely due to the energy demand associated with rapid growth and cell division. The stage of maturation is crucial to the establishment of seed dormancy and is associated with a higher abundance of proteins involved in genetic information processing, energy and carbon metabolism and cellular and antioxidant processes. Results indicated that a glycine-rich RNA-binding protein and proteasome proteins may be directly involved in dormancy acquisition control, and future studies are warranted to verify this association. Full article
(This article belongs to the collection Advances in Proteomic Research)
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Open AccessArticle Activation of mGluR5 Attenuates NMDA-Induced Neurotoxicity through Disruption of the NMDAR-PSD-95 Complex and Preservation of Mitochondrial Function in Differentiated PC12 Cells
Int. J. Mol. Sci. 2014, 15(6), 10892-10907; doi:10.3390/ijms150610892
Received: 17 April 2014 / Revised: 16 May 2014 / Accepted: 30 May 2014 / Published: 17 June 2014
Cited by 4 | PDF Full-text (824 KB) | HTML Full-text | XML Full-text
Abstract
Glutamate-mediated toxicity is implicated in various neuropathologic conditions, and activation of ionotropic and metabotropic glutamate receptors is considered to be the most important mechanism. It has been reported that pharmacological saturation of metabotropic glutamate receptors (mGluRs) can facilitate N-methyl-d-aspartate receptor (NMDAR) [...] Read more.
Glutamate-mediated toxicity is implicated in various neuropathologic conditions, and activation of ionotropic and metabotropic glutamate receptors is considered to be the most important mechanism. It has been reported that pharmacological saturation of metabotropic glutamate receptors (mGluRs) can facilitate N-methyl-d-aspartate receptor (NMDAR) related signaling cascades, but the mechanism leading to mGluR-NMDAR interactions in excitotoxic neuronal injury has remained unidentified. In the present study, we investigated the role of mGluR5 in the regulation of N-methyl-d-aspartate (NMDA)-induced excitotoxicity in differentiated PC12 cells. We found that activation of mGluR5 with the specific agonist R,S-2-chloro-5-hydroxyphenylglycine (CHPG) increased cell viability and inhibited lactate dehydrogenase (LDH) release in a dose-dependent manner. CHPG also inhibited an increase in the Bax/Bcl-2 ratio, attenuated cleavage of caspase-9 and caspase-3, and reduced apoptotic cell death after NMDA treatment. The NMDA-induced mitochondrial dysfunction, as indicated by mitochondrial reactive oxygen species (ROS) generation, collapse of mitochondrial membrane potential (MMP), and cytochrome c release, was also partly prevented by CHPG treatment. Furthermore, CHPG blocked the NMDA-induced interaction of NMDAR with postsynaptic density protein-95 (PSD-95), but had no effects on intracellular calcium concentrations. All these results indicated that activation of mGluR5 protects differentiated PC12 cells from NMDA-induced neuronal excitotoxicity by disrupting NMDAR-PSD-95 interaction, which might be an ideal target for investigating therapeutic strategies in various neurological diseases where excitotoxicity may contribute to their pathology. Full article
(This article belongs to the collection G Protein-Coupled Receptor Signaling and Regulation)
Open AccessArticle Synthesis and Antioxidant Activity Evaluation of New Compounds from Hydrazinecarbothioamide and 1,2,4-Triazole Class Containing Diarylsulfone and 2,4-Difluorophenyl Moieties
Int. J. Mol. Sci. 2014, 15(6), 10908-10925; doi:10.3390/ijms150610908
Received: 15 April 2014 / Revised: 7 June 2014 / Accepted: 10 June 2014 / Published: 17 June 2014
Cited by 13 | PDF Full-text (503 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
In the present investigation, new hydrazinecarbothioamides 46 were synthesized by reaction of 4-(4-X-phenylsulfonyl)benzoic acids hydrazides (X= H, Cl, Br) 13 with 2,4-difluorophenyl isothiocyanate and further these were treated with sodium hydroxide to obtain 1,2,4-triazole-3-thione derivatives 79 [...] Read more.
In the present investigation, new hydrazinecarbothioamides 46 were synthesized by reaction of 4-(4-X-phenylsulfonyl)benzoic acids hydrazides (X= H, Cl, Br) 13 with 2,4-difluorophenyl isothiocyanate and further these were treated with sodium hydroxide to obtain 1,2,4-triazole-3-thione derivatives 79. The reaction of 79 with α-halogenated ketones, in basic media, afforded new S-alkylated derivatives 1015. The structures of the synthesized compounds have been established on the basis of 1H-NMR, 13C-NMR, IR, mass spectral studies and elemental analysis. The antioxidant activity of all compounds has been screened. Hydrazinecarbothioamides 46 showed excellent antioxidant activity and 1,2,4-triazole-3-thiones 79 showed good antioxidant activity using the DPPH method. Full article
Open AccessArticle The Constituents of Michelia compressa var. formosana and Their Bioactivities
Int. J. Mol. Sci. 2014, 15(6), 10926-10935; doi:10.3390/ijms150610926
Received: 2 April 2014 / Revised: 8 May 2014 / Accepted: 19 May 2014 / Published: 17 June 2014
Cited by 2 | PDF Full-text (214 KB) | HTML Full-text | XML Full-text | Correction
Abstract
Phytochemical investigation of the heartwood of Michelia compressa afforded forty-four compounds, which were identified by comparison of experimental and literature analytical and spectroscopic data. Some compounds were evaluated for their anti-inflammatory and anticancer bioactivities. The result showed that soemerine (1) [...] Read more.
Phytochemical investigation of the heartwood of Michelia compressa afforded forty-four compounds, which were identified by comparison of experimental and literature analytical and spectroscopic data. Some compounds were evaluated for their anti-inflammatory and anticancer bioactivities. The result showed that soemerine (1) and cyathisterol (2) exhibited significant nitric oxide (NO) inhibition, with IC50 values of 8.5 ± 0.3 and 9.6 ± 0.5 µg/mL, respectively. In addition, liriodenine (3) and oliveroline (4) exhibited cytotoxicity to human nasopharyngeal carcinoma (NPC-TW01), non-small cell lung carcinoma (NCI-H226), T cell leukemia (Jurkat), renal carcinoma (A498), lung carcinoma (A549) and fibrosarcoma (HT1080) cell lines with IC50 values in the range of 15.7–3.68 μM. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle HSPC117 Is Regulated by Epigenetic Modification and Is Involved in the Migration of JEG-3 Cells
Int. J. Mol. Sci. 2014, 15(6), 10936-10949; doi:10.3390/ijms150610936
Received: 23 October 2013 / Revised: 29 May 2014 / Accepted: 30 May 2014 / Published: 17 June 2014
PDF Full-text (526 KB) | HTML Full-text | XML Full-text
Abstract
The human hematopoietic stem/progenitor cell 117 (HSPC117) protein is an essential component of protein complexes and has been identified to be involved in many important functions. However, how this gene expression is regulated and whether the HSPC117 gene affects cell migration is [...] Read more.
The human hematopoietic stem/progenitor cell 117 (HSPC117) protein is an essential component of protein complexes and has been identified to be involved in many important functions. However, how this gene expression is regulated and whether the HSPC117 gene affects cell migration is still unknown. The aim of this study was to identify whether HSPC117 mRNA expression is regulated by epigenetic modification and whether HSPC117 expression level affects the expression of matrix metalloproteinase 2 (MMP 2), matrix metalloproteinase 14 (MMP 14), and tissue inhibitor of metalloproteinases 2 (TIMP 2), and further affects human placenta choriocarcinoma cell (JEG-3) migration speed. In our epigenetic modification experiment, JEG-3 cells were cultured in medium with the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine (5-aza-dC), the histone deacetylase (HDAC) inhibitor trichostatin A (TSA), or both inhibitors. Then, the HSPC117 mRNA and protein expressions were assessed using real-time quantitative PCR (qPCR) and Western blot assay. The results showed that, compared to the control, HSPC117 mRNA expression was increased by TSA or 5-aza-dC. The highest HSPC117 expression level was found after treatment with both 5-aza-dC and TSA. Further, in order to investigate the effect of HSPC117 on MMP 2, MMP 14, and TIMP 2 mRNA expressions, pEGFP-C1-HSPC117 plasmids were transfected into JEG-3 cells to improve the expression of HSPC117 in the JEG-3 cells. Then, the mRNA expression levels of MMP 2, MMP 14, TIMP 2, and the speed of cell migration were assessed using the scratch wound assay. The results showed that over-expression of HSPC117 mRNA reduced MMP 2 and MMP 14 mRNA expression, while TIMP 2 mRNA expression was up-regulated. The scratch wound assay showed that the migration speed of JEG-3 cells was slower than the non-transfected group and the C1-transfected group. All of these results indicate that HSPC117 mRNA expression is regulated by epigenetic modification; over-expression of HSPC117 decreases MMP 2 and MMP 14 transcription, reduces cell migration speed, and increases TIMP 2 transcription. Full article
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Open AccessArticle Poly(3-hydroxybutyrate)/ZnO Bionanocomposites with Improved Mechanical, Barrier and Antibacterial Properties
Int. J. Mol. Sci. 2014, 15(6), 10950-10973; doi:10.3390/ijms150610950
Received: 12 May 2014 / Revised: 2 June 2014 / Accepted: 5 June 2014 / Published: 17 June 2014
Cited by 25 | PDF Full-text (1780 KB) | HTML Full-text | XML Full-text
Abstract
Poly(3-hydroxybutyrate) (PHB)-based bionanocomposites incorporating different contents of ZnO nanoparticles were prepared via solution casting technique. The nanoparticles were dispersed within the biopolymer without the need for surfactants or coupling agents. The morphology, thermal, mechanical, barrier, migration and antibacterial properties of the nanocomposites [...] Read more.
Poly(3-hydroxybutyrate) (PHB)-based bionanocomposites incorporating different contents of ZnO nanoparticles were prepared via solution casting technique. The nanoparticles were dispersed within the biopolymer without the need for surfactants or coupling agents. The morphology, thermal, mechanical, barrier, migration and antibacterial properties of the nanocomposites were investigated. The nanoparticles acted as nucleating agents, increasing the crystallization temperature and the degree of crystallinity of the matrix, and as mass transport barriers, hindering the diffusion of volatiles generated during the decomposition process, leading to higher thermal stability. The Young’s modulus, tensile and impact strength of the biopolymer were enhanced by up to 43%, 32% and 26%, respectively, due to the strong matrix-nanofiller interfacial adhesion attained via hydrogen bonding interactions, as revealed by the FT-IR spectra. Moreover, the nanocomposites exhibited reduced water uptake and superior gas and vapour barrier properties compared to neat PHB. They also showed antibacterial activity against both Gram-positive and Gram-negative bacteria, which was progressively improved upon increasing ZnO concentration. The migration levels of PHB/ZnO composites in both non-polar and polar simulants decreased with increasing nanoparticle content, and were well below the current legislative limits for food packaging materials. These biodegradable nanocomposites show great potential as an alternative to synthetic plastic packaging materials especially for use in food and beverage containers and disposable applications. Full article
(This article belongs to the Special Issue Biodegradable Materials)
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Open AccessArticle Physical Exercise Promotes Recovery of Neurological Function after Ischemic Stroke in Rats
Int. J. Mol. Sci. 2014, 15(6), 10974-10988; doi:10.3390/ijms150610974
Received: 23 February 2014 / Revised: 12 June 2014 / Accepted: 13 June 2014 / Published: 18 June 2014
Cited by 4 | PDF Full-text (1521 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Although physical exercise is an effective strategy for treatment of ischemic stroke, the underlying protective mechanisms are still not well understood. It has been recently demonstrated that neural progenitor cells play a vital role in the recovery of neurological function (NF) through [...] Read more.
Although physical exercise is an effective strategy for treatment of ischemic stroke, the underlying protective mechanisms are still not well understood. It has been recently demonstrated that neural progenitor cells play a vital role in the recovery of neurological function (NF) through differentiation into mature neurons. In the current study, we observed that physical exercise significantly reduced the infarct size and improved damaged neural functional recovery after an ischemic stroke. Furthermore, we found that the treatment not only exhibited a significant increase in the number of neural progenitor cells and neurons but also decreased the apoptotic cells in the peri-infarct region, compared to a control in the absence of exercise. Importantly, the insulin-like growth factor-1 (IGF-1)/Akt signaling pathway was dramatically activated in the peri-infarct region of rats after physical exercise training. Therefore, our findings suggest that physical exercise directly influences the NF recovery process by increasing neural progenitor cell count via activation of the IGF-1/Akt signaling pathway. Full article
(This article belongs to the Special Issue Neuroprotective Strategies 2014)
Open AccessArticle Correlation between BPI Gene Upstream CpG Island Methylation and mRNA Expression in Piglets
Int. J. Mol. Sci. 2014, 15(6), 10989-10998; doi:10.3390/ijms150610989
Received: 12 May 2014 / Revised: 28 May 2014 / Accepted: 9 June 2014 / Published: 18 June 2014
Cited by 1 | PDF Full-text (710 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Diarrhea and edematous disease are two major causes of mortality in postweaning piglets, and these conditions lead to huge economic losses in the swine industry. E. coli F18 is the primary causative agent of these two diseases. Bactericidal/permeability-increasing protein (BPI) plays an [...] Read more.
Diarrhea and edematous disease are two major causes of mortality in postweaning piglets, and these conditions lead to huge economic losses in the swine industry. E. coli F18 is the primary causative agent of these two diseases. Bactericidal/permeability-increasing protein (BPI) plays an important role in the natural defense of the host. The aim of this study was to determine the correlation between BPI gene upstream CpG island methylation and mRNA expression. In this study, bisulfite sequencing PCR (BSP) was used to detect the methylation status of the BPI gene upstream CpG island and fluorescence quantitative PCR was used to detect BPI expression in the duodenum of piglets from birth to weaning age. BPI upstream CpG islands were shown to have many putative transcription factor binding sites, 10 CpG sites and every CpG site was methylated. The CpG island methylation level was lowest in 30-day piglets and was significantly lower than levels in 8-day piglets (p < 0.05). BPI mRNA expression was significantly higher in 30-day piglets than at any other age (p < 0.05). Pearson’s correlation analysis showed that the methylation status of the CpG island was negatively correlated with BPI mRNA expression. Statistical significances were found in CpG_1, CpG_3, CpG_4, CpG_7 and CpG_10 (p < 0.05). The data indicate that BPI expression is improved by demethylation of the BPI gene upstream CpG island. Furthermore, CpG_1, CpG_3, CpG_4, CpG_7 and CpG_10 may be critical sites in the regulation of BPI gene expression. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle The Effects of CoCl2 on HIF-1α Protein under Experimental Conditions of Autoprogressive Hypoxia Using Mouse Models
Int. J. Mol. Sci. 2014, 15(6), 10999-11012; doi:10.3390/ijms150610999
Received: 28 February 2014 / Revised: 10 June 2014 / Accepted: 11 June 2014 / Published: 18 June 2014
Cited by 3 | PDF Full-text (949 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
It is well known that cobalt chloride (CoCl2) can enhance the stability of hypoxia-inducible factor (HIF)-1α. The aim of this study is to detect the effect of CoCl2 on the hypoxia tolerance of mice which were repeatedly exposed to [...] Read more.
It is well known that cobalt chloride (CoCl2) can enhance the stability of hypoxia-inducible factor (HIF)-1α. The aim of this study is to detect the effect of CoCl2 on the hypoxia tolerance of mice which were repeatedly exposed to autoprogressive hypoxia. Balb/c mice were randomly divided into groups of chemical pretreatment and normal saline (NS), respectively injected with CoCl2 and NS 3 h before exposure to hypoxia for 0 run (H0), 1 run (H1), and 4 runs (H4). Western Blot, electrophoretic mobility shift assay (EMSA), extracellular recordings population spikes in area cornus ammonis I (CA 1) of mouse hippocampal slices and real-time were used in this study. Our results demonstrated that the tolerance of mice to hypoxia, the changes of HIF-1α protein level and HIF-1 DNA binding activity in mice hippocampus, the mRNA level of erythropoietin (EPO) and vascular endothelial growth factor (VEGF), and the disappearance time of population spikes of hippocampal slices were substantially different between the control group and the CoCl2 group. Over-induction of HIF-1α by pretreatment with CoCl2 before hypoxia did not increase the hypoxia tolerance. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Celecoxib Suppresses the Phosphorylation of STAT3 Protein and Can Enhance the Radiosensitivity of Medulloblastoma-Derived Cancer Stem-Like Cells
Int. J. Mol. Sci. 2014, 15(6), 11013-11029; doi:10.3390/ijms150611013
Received: 17 March 2014 / Revised: 27 May 2014 / Accepted: 12 June 2014 / Published: 18 June 2014
Cited by 7 | PDF Full-text (4407 KB) | HTML Full-text | XML Full-text
Abstract
Medulloblastoma (MB) is a malignant primary brain tumor with poor prognosis. MB-derived CD133/Nestin double-positive cells (MB-DPs) exhibit cancer stem-like cell (CSC)-like properties that may contribute to chemoradioresistance, tumorigenesis and recurrence. In various tumors, signal transducer and activator of transcription 3 (STAT3) upregulation [...] Read more.
Medulloblastoma (MB) is a malignant primary brain tumor with poor prognosis. MB-derived CD133/Nestin double-positive cells (MB-DPs) exhibit cancer stem-like cell (CSC)-like properties that may contribute to chemoradioresistance, tumorigenesis and recurrence. In various tumors, signal transducer and activator of transcription 3 (STAT3) upregulation including MB which can regulate the expression of Nestin. Celecoxib, a selective COX-2 inhibitor, has been shown to potentially reduce STAT3 phosphorylation. The aim of the present study was to investigate the role of celecoxib in enhancing the effects of ionizing radiotherapy (IR) on MB-DP. MB-DPs and MB-derived CD133/Nestin double-negative cells (MB-DNs) were isolated from medulloblastoma cell line Daoy. Then, both of them were treated with celecoxib in different concentrations, and cell viability was assessed. The assays of cell survival, sphere formation, radiosensitivity, colony formation, apoptotic activity and mouse xenografting experiments in MB-DPs and MB-DNs treated with celecoxib alone, radiation alone, or celecoxib combined with radiation were further evaluated. We isolated MB-DPs from MB cell line Daoy, which exhibited typical CSC-like characteristics. Microarray analysis and Western blotting both indicated the upregulation of Janus kinase (JAK)-STAT cascade and STAT3 phosphorylation. Incubation with celecoxib dose-dependently suppressed the CSC-like properties and enhanced the IR effect on the induction of apoptosis, as detected by TUNEL assay and staining for Caspase 3 and Annexin V. Finally, celecoxib also enhanced the IR effect to suppress tumorigenesis and synergistically improve the recipient survival in orthotopic MB-derived CD133/Nestin double-positive cells (MB-DP cells) bearing mice. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Cellulose Nanocrystals/ZnO as a Bifunctional Reinforcing Nanocomposite for Poly(vinyl alcohol)/Chitosan Blend Films: Fabrication, Characterization and Properties
Int. J. Mol. Sci. 2014, 15(6), 11040-11053; doi:10.3390/ijms150611040
Received: 4 April 2014 / Revised: 14 May 2014 / Accepted: 26 May 2014 / Published: 18 June 2014
Cited by 6 | PDF Full-text (689 KB) | HTML Full-text | XML Full-text
Abstract
In this study, cellulose nanocrystals/zinc oxide (CNCs/ZnO) nanocomposites were dispersed as bifunctional nano-sized fillers into poly(vinyl alcohol) (PVA) and chitosan (Cs) blend by a solvent casting method to prepare PVA/Cs/CNCs/ZnO bio-nanocomposites films. The morphology, thermal, mechanical and UV-vis absorption properties, as well [...] Read more.
In this study, cellulose nanocrystals/zinc oxide (CNCs/ZnO) nanocomposites were dispersed as bifunctional nano-sized fillers into poly(vinyl alcohol) (PVA) and chitosan (Cs) blend by a solvent casting method to prepare PVA/Cs/CNCs/ZnO bio-nanocomposites films. The morphology, thermal, mechanical and UV-vis absorption properties, as well antimicrobial effects of the bio-nanocomposite films were investigated. It demonstrated that CNCs/ZnO were compatible with PVA/Cs and dispersed homogeneously in the polymer blend matrix. CNCs/ZnO improved tensile strength and modulus of PVA/Cs significantly. Tensile strength and modulus of bio-nanocomposite films increased from 55.0 to 153.2 MPa and from 395 to 932 MPa, respectively with increasing nano-sized filler amount from 0 to 5.0 wt %. The thermal stability of PVA/Cs was also enhanced at 1.0 wt % CNCs/ZnO loading. UV light can be efficiently absorbed by incorporating ZnO nanoparticles into a PVA/Cs matrix, signifying that these bio-nanocomposite films show good UV-shielding effects. Moreover, the biocomposites films showed antibacterial activity toward the bacterial species Salmonella choleraesuis and Staphylococcus aureus. The improved physical properties obtained by incorporating CNCs/ZnO can be useful in variety uses. Full article
(This article belongs to the Special Issue Biodegradable Materials)
Open AccessArticle A Single Nucleotide Polymorphism in the Stromal Cell-Derived Factor 1 Gene Is Associated with Coronary Heart Disease in Chinese Patients
Int. J. Mol. Sci. 2014, 15(6), 11054-11063; doi:10.3390/ijms150611054
Received: 26 May 2014 / Revised: 6 June 2014 / Accepted: 13 June 2014 / Published: 19 June 2014
Cited by 5 | PDF Full-text (726 KB) | HTML Full-text | XML Full-text
Abstract
Coronary heart disease (CHD) is highly prevalent globally and a major cause of mortality. Genetic predisposition is a non-modifiable risk factor associated with CHD. Eighty-four Chinese patients with CHD and 253 healthy Chinese controls without CHD were recruited. Major clinical data were [...] Read more.
Coronary heart disease (CHD) is highly prevalent globally and a major cause of mortality. Genetic predisposition is a non-modifiable risk factor associated with CHD. Eighty-four Chinese patients with CHD and 253 healthy Chinese controls without CHD were recruited. Major clinical data were collected, and a single nucleotide polymorphism (SNP) in the stromal cell-derived factor 1 (SDF-1) gene at position 801 (G to A, rs1801157) in the 3'-untranslated region was identified. The correlation between rs1801157 genotypes and CHD was evaluated by a multivariate logistic regression analysis. The allele frequency in the CHD and control groups was in Hardy-Weinberg equilibrium (HWE) (p > 0.05). The frequency of the GG genotype in the CHD group (59.5%) was significantly higher than that in the control group (49.8%) (p = 0.036). A number of variables, including male sex, age, presence of hypertension, and the levels of low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), triglycerides (TG), uric acid, and total bilirubin, were associated with CHD in a primary univariate analysis. In a multivariable logistic regression analysis, the GG genotype (GG:AA, odds ratio (OR) = 2.31, 95% confidence interval (CI) = 1.21–5.23), male sex, advanced age (≥60 years), presence of hypertension, LDL-C level ≥ 3.33 mg/dL, HDL-C level < 1.03 mg/dL, and TG level ≥ 1.7 mg/dL were independent risk factors for CHD. Full article
(This article belongs to the Section Molecular Diagnostics)
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Open AccessArticle Does Prop-2-ynylideneamine, HC≡CCH=NH, Exist in Space? A Theoretical and Computational Investigation
Int. J. Mol. Sci. 2014, 15(6), 11064-11081; doi:10.3390/ijms150611064
Received: 25 March 2014 / Revised: 6 May 2014 / Accepted: 12 May 2014 / Published: 19 June 2014
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Abstract
MP2, DFT and CCSD methods with 6-311++G** and aug-cc-pvdz basis sets have been used to probe the structural changes and relative energies of E-prop-2-ynylideneamine (I), Z-prop-2-ynylideneamine (II), prop-1,2-diene-1-imine (III) and vinyl cyanide (IV). The energy near-equivalence and provenance of preference of isomers [...] Read more.
MP2, DFT and CCSD methods with 6-311++G** and aug-cc-pvdz basis sets have been used to probe the structural changes and relative energies of E-prop-2-ynylideneamine (I), Z-prop-2-ynylideneamine (II), prop-1,2-diene-1-imine (III) and vinyl cyanide (IV). The energy near-equivalence and provenance of preference of isomers and tautomers were investigated by NBO calculations using HF and B3LYP methods with 6-311++G** and aug-cc-pvdz basis sets. All substrates have Cs symmetry. The optimized geometries were found to be mainly theoretical method dependent. All elected levels of theory have computed I/II total energy of isomerization (ΔE) of 1.707 to 3.707 kJ/mol in favour of II at 298.15 K. MP2 and CCSD methods have indicated clearly the preference of II over III; while the B3LYP functional predicted nearly similar total energies. All tested levels of theory yielded a global II/IV tautomerization total energy (ΔE) of 137.3–148.4 kJ/mol in support of IV at 298.15 K. The negative values of ΔS indicated that IV is favoured at low temperature. At high temperature, a reverse tautomerization becomes spontaneous and II is preferred. The existence of II in space was debated through the interpretation and analysis of the thermodynamic and kinetic studies of this tautomerization reaction and the presence of similar compounds in the Interstellar Medium (ISM). Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
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Open AccessArticle The Structure and Dynamics of BmR1 Protein from Brugia malayi: In Silico Approaches
Int. J. Mol. Sci. 2014, 15(6), 11082-11099; doi:10.3390/ijms150611082
Received: 28 January 2014 / Revised: 25 March 2014 / Accepted: 4 June 2014 / Published: 19 June 2014
Cited by 1 | PDF Full-text (1772 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Brugia malayi is a filarial nematode, which causes lymphatic filariasis in humans. In 1995, the disease has been identified by the World Health Organization (WHO) as one of the second leading causes of permanent and long-term disability and thus it is targeted [...] Read more.
Brugia malayi is a filarial nematode, which causes lymphatic filariasis in humans. In 1995, the disease has been identified by the World Health Organization (WHO) as one of the second leading causes of permanent and long-term disability and thus it is targeted for elimination by year 2020. Therefore, accurate filariasis diagnosis is important for management and elimination programs. A recombinant antigen (BmR1) from the Bm17DIII gene product was used for antibody-based filariasis diagnosis in “Brugia Rapid”. However, the structure and dynamics of BmR1 protein is yet to be elucidated. Here we study the three dimensional structure and dynamics of BmR1 protein using comparative modeling, threading and ab initio protein structure prediction. The best predicted structure obtained via an ab initio method (Rosetta) was further refined and minimized. A total of 5 ns molecular dynamics simulation were performed to investigate the packing of the protein. Here we also identified three epitopes as potential antibody binding sites from the molecular dynamics average structure. The structure and epitopes obtained from this study can be used to design a binder specific against BmR1, thus aiding future development of antigen-based filariasis diagnostics to complement the current diagnostics. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
Open AccessArticle New Dihydro-β-agarofuran Sesquiterpenes from Parnassia wightiana Wall: Isolation, Identification and Cytotoxicity against Cancer Cells
Int. J. Mol. Sci. 2014, 15(6), 11111-11125; doi:10.3390/ijms150611111
Received: 10 April 2014 / Revised: 1 June 2014 / Accepted: 4 June 2014 / Published: 20 June 2014
Cited by 2 | PDF Full-text (499 KB) | HTML Full-text | XML Full-text
Abstract
Five new (48) and three known (13) dihydro-β-agarofuran sesquiterpene polyesters were isolated from the whole plants of Parnassia wightiana. The structures of all compounds were elucidated through spectroscopic analysis including 2D-NMR and HR-MS. [...] Read more.
Five new (48) and three known (13) dihydro-β-agarofuran sesquiterpene polyesters were isolated from the whole plants of Parnassia wightiana. The structures of all compounds were elucidated through spectroscopic analysis including 2D-NMR and HR-MS. The absolute configuration of these compounds was established by X-ray diffraction analysis, comparison of NOESY spectra and biogenetic means. The cytotoxities of compounds 28 were evaluated in vitro against HL-60, SMMC-7721, A549, MCF-7 and SW480 cell lines. Compounds 57 exhibited the highest activities with IC50 values of 11.8–30.1 μM in most cases. The SAR revealed that the introduction of hydroxyl group was able to significantly improve the activities of the compounds for most of the cell lines. Full article
(This article belongs to the Section Green Chemistry)
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Open AccessArticle TRAF6 Inhibition Rescues Dexamethasone-Induced Muscle Atrophy
Int. J. Mol. Sci. 2014, 15(6), 11126-11141; doi:10.3390/ijms150611126
Received: 2 May 2014 / Revised: 2 June 2014 / Accepted: 5 June 2014 / Published: 20 June 2014
Cited by 4 | PDF Full-text (2878 KB) | HTML Full-text | XML Full-text
Abstract
Tumor necrosis factor receptor-associated factor 6 (TRAF6), a unique E3 ubiquitin ligase and adaptor protein, is involved in activation of various signaling cascades. Recent studies identify TRAF6 as one of the novel regulators of skeletal muscle atrophy. The role of TRAF6 in [...] Read more.
Tumor necrosis factor receptor-associated factor 6 (TRAF6), a unique E3 ubiquitin ligase and adaptor protein, is involved in activation of various signaling cascades. Recent studies identify TRAF6 as one of the novel regulators of skeletal muscle atrophy. The role of TRAF6 in glucocorticoid-induced muscle atrophy, however, remains to be elucidated. In this study, we show that TRAF6 and its downstream signaling molecules, muscle atrophy F-box (MAFBx) and muscle ring finger 1 (MuRF1), were all upregulated in dexamethasone-induced atrophy of mouse C2C12 myotubes or mouse tibialis anterior (TA) muscle. To further investigate the role of TRAF6 in dexamethasone-induced muscle atrophy, TRAF6-siRNA was used to transfect cultured C2C12 myotubes or was injected into the TA muscle of mice respectively, and we note that TRAF6 knockdown attenuated dexamethasone-induced muscle atrophy in vitro and in vivo, and concomitantly decreased the expression of MuRF1 and MAFBx. Our findings suggest that a decreased expression of TRAF6 could rescue dexamethasone-induced skeletal muscle atrophy through, at least in part, regulation of the expression of MAFBx and MuRF1. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Genetic Variations of TAP1 Gene Exon 3 Affects Gene Expression and Escherichia coli F18 Resistance in Piglets
Int. J. Mol. Sci. 2014, 15(6), 11161-11171; doi:10.3390/ijms150611161
Received: 12 April 2014 / Revised: 22 May 2014 / Accepted: 27 May 2014 / Published: 20 June 2014
Cited by 3 | PDF Full-text (945 KB) | HTML Full-text | XML Full-text
Abstract
Firstly, our research group identified Sutai pigs’ phenotypes that exhibited extreme resistance and susceptibility to the Escherichia coli F18 respectively, and then eight ETEC (Enterotoxigenic Escherichia coli) F18-resistant piglets and eight ETEC F18-sensitive piglets were selected. Then, the TAP1 [...] Read more.
Firstly, our research group identified Sutai pigs’ phenotypes that exhibited extreme resistance and susceptibility to the Escherichia coli F18 respectively, and then eight ETEC (Enterotoxigenic Escherichia coli) F18-resistant piglets and eight ETEC F18-sensitive piglets were selected. Then, the TAP1 (Transporter associated with antigen processing) mRNA relative expression levels were analyzed in 11 tissues of the resistant and susceptible phenotypes. Simultaneously, we detected the genetic variations in exon 3 of the TAP1 gene and evaluated the TAP1 mRNA expression levels among the different genotype pigs to study the effects of the genetic variation on gene expression, and the E. coli F18 resistance. The results revealed higher expression levels in the resistant genotypes than that in the susceptible genotypes in 11 tissues, with significant differences in the spleen, lymph node, lung, thymus, duodenum and jejunum. Furthermore, a G729A mutation was identified in the TAP1 gene exon 3, and this mutation deviates from Hardy-Weinberg equilibrium (p < 0.01). The TAP1 mRNA levels in GG genotype were significantly higher than that in the other two genotypes, with significant differences in the liver, lung, kidney, thymus, lymph node, duodenum and jejunum tissues. We speculated that high expression of the TAP1 gene might confer resistance against the E. coli F18, the G729A mutation had a significant effect on the mRNA expression, and individuals with the GG genotype possessed a stronger ability to resist the E. coli F18 infection. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Generation and Analysis of Expressed Sequence Tags (ESTs) from Halophyte Atriplex canescens to Explore Salt-Responsive Related Genes
Int. J. Mol. Sci. 2014, 15(6), 11172-11189; doi:10.3390/ijms150611172
Received: 20 May 2014 / Revised: 11 June 2014 / Accepted: 12 June 2014 / Published: 23 June 2014
Cited by 4 | PDF Full-text (711 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Little information is available on gene expression profiling of halophyte A. canescens. To elucidate the molecular mechanism for stress tolerance in A. canescens, a full-length complementary DNA library was generated from A. canescens exposed to 400 mM NaCl, and provided [...] Read more.
Little information is available on gene expression profiling of halophyte A. canescens. To elucidate the molecular mechanism for stress tolerance in A. canescens, a full-length complementary DNA library was generated from A. canescens exposed to 400 mM NaCl, and provided 343 high-quality ESTs. In an evaluation of 343 valid EST sequences in the cDNA library, 197 unigenes were assembled, among which 190 unigenes (83.1% ESTs) were identified according to their significant similarities with proteins of known functions. All the 343 EST sequences have been deposited in the dbEST GenBank under accession numbers JZ535802 to JZ536144. According to Arabidopsis MIPS functional category and GO classifications, we identified 193 unigenes of the 311 annotations EST, representing 72 non-redundant unigenes sharing similarities with genes related to the defense response. The sets of ESTs obtained provide a rich genetic resource and 17 up-regulated genes related to salt stress resistance were identified by qRT-PCR. Six of these genes may contribute crucially to earlier and later stage salt stress resistance. Additionally, among the 343 unigenes sequences, 22 simple sequence repeats (SSRs) were also identified contributing to the study of A. canescens resources. Full article
(This article belongs to the Special Issue Metagenomics: a Powerful Lens Viewing the Microbial World)
Open AccessArticle A-769662 Protects Osteoblasts from Hydrogen Dioxide-Induced Apoptosis through Activating of AMP-Activated Protein Kinase (AMPK)
Int. J. Mol. Sci. 2014, 15(6), 11190-11203; doi:10.3390/ijms150611190
Received: 17 March 2014 / Revised: 14 April 2014 / Accepted: 4 May 2014 / Published: 23 June 2014
Cited by 5 | PDF Full-text (1844 KB) | HTML Full-text | XML Full-text
Abstract
Here we report that 5'-monophosphate (AMP)-activated protein kinase (AMPK) agonist A-769662 inhibited hydrogen peroxide (H2O2)-induced viability loss and apoptosis of human and mouse osteoblast cells. H2O2-induced moderate AMPK activation in osteoblast cells, which was [...] Read more.
Here we report that 5'-monophosphate (AMP)-activated protein kinase (AMPK) agonist A-769662 inhibited hydrogen peroxide (H2O2)-induced viability loss and apoptosis of human and mouse osteoblast cells. H2O2-induced moderate AMPK activation in osteoblast cells, which was enhanced by A-769662. Inactivation of AMPK by its inhibitor compound C, or by target shRNA-mediated silencing and kinase dead (KD) mutation exacerbated H2O2-induced cytotoxicity in osteoblast cells. A-769662-mediated protective effect against H2O2 was also blocked by AMPK inhibition or depletion. A-769662 inhibited reactive oxygen species (ROS) accumulation by H2O2 in osteoblast cells. Meanwhile, H2O2-induced ATP depletion was inhibited by A-769662, but was aggravated by compound C. Further, H2O2 induced AMPK-dependent and pro-survival autophagy in cultured osteoblast cells, which was enhanced by A-769662. Our results suggested that activation of AMPK by H2O2 is anti-apoptosis and pro-survival in osteoblast cells, probably due to its anti-oxidant, pro-autophagy and ATP preservation abilities, and A-769662-mediated cell-protective effect in osteoblast cells requires AMPK activation. Our study suggests that A-769662 might be further investigated as a novel anti-osteonecrosis agent. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)

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Open AccessReview Molecular Mechanisms of Liver Fibrosis in HIV/HCV Coinfection
Int. J. Mol. Sci. 2014, 15(6), 9184-9208; doi:10.3390/ijms15069184
Received: 30 March 2014 / Revised: 15 May 2014 / Accepted: 15 May 2014 / Published: 26 May 2014
Cited by 12 | PDF Full-text (1048 KB) | HTML Full-text | XML Full-text
Abstract
Chronic hepatitis C virus (HCV) infection is an important cause of morbidity and mortality in people coinfected with human immunodeficiency virus (HIV). Several studies have shown that HIV infection promotes accelerated HCV hepatic fibrosis progression, even with HIV replication under full antiretroviral [...] Read more.
Chronic hepatitis C virus (HCV) infection is an important cause of morbidity and mortality in people coinfected with human immunodeficiency virus (HIV). Several studies have shown that HIV infection promotes accelerated HCV hepatic fibrosis progression, even with HIV replication under full antiretroviral control. The pathogenesis of accelerated hepatic fibrosis among HIV/HCV coinfected individuals is complex and multifactorial. The most relevant mechanisms involved include direct viral effects, immune/cytokine dysregulation, altered levels of matrix metalloproteinases and fibrosis biomarkers, increased oxidative stress and hepatocyte apoptosis, HIV-associated gut depletion of CD4 cells, and microbial translocation. In addition, metabolic alterations, heavy alcohol use, as well drug use, may have a potential role in liver disease progression. Understanding the pathophysiology and regulation of liver fibrosis in HIV/HCV co-infection may lead to the development of therapeutic strategies for the management of all patients with ongoing liver disease. In this review, we therefore discuss the evidence and potential molecular mechanisms involved in the accelerated liver fibrosis seen in patients coinfected with HIV and HCV. Full article
(This article belongs to the collection Molecular Mechanisms of Human Liver Diseases)
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Open AccessReview Adipose-Derived Stem Cells: A Review of Signaling Networks Governing Cell Fate and Regenerative Potential in the Context of Craniofacial and Long Bone Skeletal Repair
Int. J. Mol. Sci. 2014, 15(6), 9314-9330; doi:10.3390/ijms15069314
Received: 13 February 2014 / Revised: 16 May 2014 / Accepted: 20 May 2014 / Published: 26 May 2014
Cited by 10 | PDF Full-text (236 KB) | HTML Full-text | XML Full-text
Abstract
Improvements in medical care, nutrition and social care are resulting in a commendable change in world population demographics with an ever increasing skew towards an aging population. As the proportion of the world’s population that is considered elderly increases, so does the [...] Read more.
Improvements in medical care, nutrition and social care are resulting in a commendable change in world population demographics with an ever increasing skew towards an aging population. As the proportion of the world’s population that is considered elderly increases, so does the incidence of osteodegenerative disease and the resultant burden on healthcare. The increasing demand coupled with the limitations of contemporary approaches, have provided the impetus to develop novel tissue regeneration therapies. The use of stem cells, with their potential for self-renewal and differentiation, is one potential solution. Adipose-derived stem cells (ASCs), which are relatively easy to harvest and readily available have emerged as an ideal candidate. In this review, we explore the potential for ASCs to provide tangible therapies for craniofacial and long bone skeletal defects, outline key signaling pathways that direct these cells and describe how the developmental signaling program may provide clues on how to guide these cells in vivo. This review also provides an overview of the importance of establishing an osteogenic microniche using appropriately customized scaffolds and delineates some of the key challenges that still need to be overcome for adult stem cell skeletal regenerative therapy to become a clinical reality. Full article
(This article belongs to the Special Issue Signal Transduction of Tissue Repair)
Open AccessReview A View of Pre-mRNA Splicing from RNase R Resistant RNAs
Int. J. Mol. Sci. 2014, 15(6), 9331-9342; doi:10.3390/ijms15069331
Received: 8 April 2014 / Revised: 8 May 2014 / Accepted: 16 May 2014 / Published: 26 May 2014
Cited by 11 | PDF Full-text (918 KB) | HTML Full-text | XML Full-text
Abstract
During pre-mRNA splicing, exons in the primary transcript are precisely connected to generate an mRNA. Intron lariat RNAs are formed as by-products of this process. In addition, some exonic circular RNAs (circRNAs) may also result from exon skipping as by-products. Lariat RNAs [...] Read more.
During pre-mRNA splicing, exons in the primary transcript are precisely connected to generate an mRNA. Intron lariat RNAs are formed as by-products of this process. In addition, some exonic circular RNAs (circRNAs) may also result from exon skipping as by-products. Lariat RNAs and circRNAs are both RNase R resistant RNAs. RNase R is a strong 3' to 5' exoribonuclease, which efficiently degrades linear RNAs, such as mRNAs and rRNAs; therefore, the circular parts of lariat RNAs and the circRNAs can be segregated from eukaryotic total RNAs by their RNase R resistance. Thus, RNase R resistant RNAs could provide unexplored splicing information not available from mRNAs. Analyses of these RNAs identified repeating splicing phenomena, such as re-splicing of mature mRNAs and nested splicing. Moreover, circRNA might function as microRNA sponges. There is an enormous variety of endogenous circRNAs, which are generally synthesized in cells and tissues. Full article
(This article belongs to the Special Issue Pre-mRNA Splicing)
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Open AccessReview MicroRNA Function in the Profibrogenic Interplay upon Chronic Liver Disease
Int. J. Mol. Sci. 2014, 15(6), 9360-9371; doi:10.3390/ijms15069360
Received: 16 March 2014 / Revised: 6 May 2014 / Accepted: 12 May 2014 / Published: 27 May 2014
Cited by 4 | PDF Full-text (476 KB) | HTML Full-text | XML Full-text
Abstract
In chronic liver disease leading to fibrosis, hepatic stellate cells (HSC) differentiate into myofibroblasts. Myofibroblastic HSC have taken center stage during liver fibrogenesis, due to their remarkable synthesis of extracellular matrix proteins, their secretion of profibrogenic mediators and their contribution to hypertension, [...] Read more.
In chronic liver disease leading to fibrosis, hepatic stellate cells (HSC) differentiate into myofibroblasts. Myofibroblastic HSC have taken center stage during liver fibrogenesis, due to their remarkable synthesis of extracellular matrix proteins, their secretion of profibrogenic mediators and their contribution to hypertension, due to elevated contractility. MicroRNAs (miRNAs) are small, noncoding RNA molecules of 19–24 nucleotides in length. By either RNA interference or inhibition of translational initiation and elongation, each miRNA is able to inhibit the gene expression of a wide panel of targeted transcripts. Recently, it was shown that altered miRNA patterns after chronic liver disease highly affect the progression of fibrosis by their potential to target the expression of extracellular matrix proteins and the synthesis of mediators of profibrogenic pathways. Here, we underline the role of miRNAs in the interplay of the profibrogenic cell communication pathways upon myofibroblastic differentiation of hepatic stellate cells in the chronically injured liver. Full article
(This article belongs to the collection Molecular Mechanisms of Human Liver Diseases)
Open AccessReview Novel Aspects of the Liver Microenvironment in Hepatocellular Carcinoma Pathogenesis and Development
Int. J. Mol. Sci. 2014, 15(6), 9422-9458; doi:10.3390/ijms15069422
Received: 7 March 2014 / Revised: 13 May 2014 / Accepted: 14 May 2014 / Published: 27 May 2014
Cited by 12 | PDF Full-text (555 KB) | HTML Full-text | XML Full-text
Abstract
Hepatocellular carcinoma (HCC) is a prevalent primary liver cancer that is derived from hepatocytes and is characterised by high mortality rate and poor prognosis. While HCC is driven by cumulative changes in the hepatocyte genome, it is increasingly recognised that the liver [...] Read more.
Hepatocellular carcinoma (HCC) is a prevalent primary liver cancer that is derived from hepatocytes and is characterised by high mortality rate and poor prognosis. While HCC is driven by cumulative changes in the hepatocyte genome, it is increasingly recognised that the liver microenvironment plays a pivotal role in HCC propensity, progression and treatment response. The microenvironmental stimuli that have been recognised as being involved in HCC pathogenesis are diverse and include intrahepatic cell subpopulations, such as immune and stellate cells, pathogens, such as hepatitis viruses, and non-cellular factors, such as abnormal extracellular matrix (ECM) and tissue hypoxia. Recently, a number of novel environmental influences have been shown to have an equally dramatic, but previously unrecognized, role in HCC progression. Novel aspects, including diet, gastrointestinal tract (GIT) microflora and circulating microvesicles, are now being recognized as increasingly important in HCC pathogenesis. This review will outline aspects of the HCC microenvironment, including the potential role of GIT microflora and microvesicles, in providing new insights into tumourigenesis and identifying potential novel targets in the treatment of HCC. Full article
(This article belongs to the collection Molecular Mechanisms of Human Liver Diseases)
Open AccessReview Molecular Biology of Brain Metastasis
Int. J. Mol. Sci. 2014, 15(6), 9519-9530; doi:10.3390/ijms15069519
Received: 28 March 2014 / Revised: 17 April 2014 / Accepted: 9 May 2014 / Published: 28 May 2014
Cited by 4 | PDF Full-text (333 KB) | HTML Full-text | XML Full-text
Abstract
Metastasis to the central nervous system (CNS) remains a major cause of morbidity and mortality in patients with systemic cancer. As the length of survival in patients with systemic cancer improves, thanks to multimodality therapies, focusing on metastases to the CNS becomes [...] Read more.
Metastasis to the central nervous system (CNS) remains a major cause of morbidity and mortality in patients with systemic cancer. As the length of survival in patients with systemic cancer improves, thanks to multimodality therapies, focusing on metastases to the CNS becomes of paramount importance. Unique interactions between the brain’s micro-environment, blood-brain barrier, and tumor cells are hypothesized to promote distinct molecular features in CNS metastases that may require tailored therapeutic approaches. This review will focus on the pathophysiology, epigenetics, and immunobiology of brain metastases in order to understand the metastatic cascade. Cancer cells escape the primary tumor, intravasate into blood vessels, survive the hematogenous dissemination to the CNS, arrest in brain capillaries, extravasate, proliferate, and develop angiogenic abilities to establish metastases. Molecular biology, genetics, and epigenetics are rapidly expanding, enabling us to advance our knowledge of the underlying mechanisms involved. Research approaches using cell lines that preferentially metastasize in vivo to the brain and in vitro tissue-based studies unfold new molecular leads into the disease. It is important to identify and understand the molecular pathways of the metastatic cascade in order to target the investigation and development of more effective therapies and research directions. Full article
(This article belongs to the Special Issue Brain Metastasis 2014)
Open AccessReview NOD-Like Receptors in Intestinal Homeostasis and Epithelial Tissue Repair
Int. J. Mol. Sci. 2014, 15(6), 9594-9627; doi:10.3390/ijms15069594
Received: 20 March 2014 / Revised: 16 May 2014 / Accepted: 20 May 2014 / Published: 30 May 2014
Cited by 9 | PDF Full-text (499 KB) | HTML Full-text | XML Full-text
Abstract
The intestinal epithelium constitutes a dynamic physical barrier segregating the luminal content from the underlying mucosal tissue. Following injury, the epithelial integrity is restored by rapid migration of intestinal epithelial cells (IECs) across the denuded area in a process known as wound [...] Read more.
The intestinal epithelium constitutes a dynamic physical barrier segregating the luminal content from the underlying mucosal tissue. Following injury, the epithelial integrity is restored by rapid migration of intestinal epithelial cells (IECs) across the denuded area in a process known as wound healing. Hence, through a sequence of events involving restitution, proliferation and differentiation of IECs the gap is resealed and homeostasis reestablished. Relapsing damage followed by healing of the inflamed mucosa is a hallmark of several intestinal disorders including inflammatory bowel diseases (IBD). While several regulatory peptides, growth factors and cytokines stimulate restitution of the epithelial layer after injury, recent evidence in the field underscores the contribution of innate immunity in controlling this process. In particular, nucleotide-binding and oligomerization domain-like receptors (NLRs) play critical roles in sensing the commensal microbiota, maintaining homeostasis, and regulating intestinal inflammation. Here, we review the process of intestinal epithelial tissue repair and we specifically focus on the impact of NLR-mediated signaling mechanisms involved in governing epithelial wound healing during disease. Full article
(This article belongs to the Special Issue Signal Transduction of Tissue Repair)
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Open AccessReview Computational and Experimental Approaches to Reveal the Effects of Single Nucleotide Polymorphisms with Respect to Disease Diagnostics
Int. J. Mol. Sci. 2014, 15(6), 9670-9717; doi:10.3390/ijms15069670
Received: 8 April 2014 / Revised: 15 May 2014 / Accepted: 16 May 2014 / Published: 30 May 2014
Cited by 12 | PDF Full-text (1288 KB) | HTML Full-text | XML Full-text
Abstract
DNA mutations are the cause of many human diseases and they are the reason for natural differences among individuals by affecting the structure, function, interactions, and other properties of DNA and expressed proteins. The ability to predict whether a given mutation is [...] Read more.
DNA mutations are the cause of many human diseases and they are the reason for natural differences among individuals by affecting the structure, function, interactions, and other properties of DNA and expressed proteins. The ability to predict whether a given mutation is disease-causing or harmless is of great importance for the early detection of patients with a high risk of developing a particular disease and would pave the way for personalized medicine and diagnostics. Here we review existing methods and techniques to study and predict the effects of DNA mutations from three different perspectives: in silico, in vitro and in vivo. It is emphasized that the problem is complicated and successful detection of a pathogenic mutation frequently requires a combination of several methods and a knowledge of the biological phenomena associated with the corresponding macromolecules. Full article
(This article belongs to the collection Human Single Nucleotide Polymorphisms and Disease Diagnostics)
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Open AccessReview Inhibitors of Acetylcholinesterase and Butyrylcholinesterase Meet Immunity
Int. J. Mol. Sci. 2014, 15(6), 9809-9825; doi:10.3390/ijms15069809
Received: 5 February 2014 / Revised: 6 March 2014 / Accepted: 11 March 2014 / Published: 2 June 2014
Cited by 11 | PDF Full-text (434 KB) | HTML Full-text | XML Full-text
Abstract
Acetylcholinesterase (AChE) inhibitors are widely used for the symptomatic treatment of Alzheimer’s disease and other dementias. More recent use is for myasthenia gravis. Many of these inhibitors interact with the second known cholinesterase, butyrylcholinesterase (BChE). Further, evidence shows that acetylcholine plays a [...] Read more.
Acetylcholinesterase (AChE) inhibitors are widely used for the symptomatic treatment of Alzheimer’s disease and other dementias. More recent use is for myasthenia gravis. Many of these inhibitors interact with the second known cholinesterase, butyrylcholinesterase (BChE). Further, evidence shows that acetylcholine plays a role in suppression of cytokine release through a “cholinergic anti-inflammatory pathway” which raises questions about the role of these inhibitors in the immune system. This review covers research and discussion of the role of the inhibitors in modulating the immune response using as examples the commonly available drugs, donepezil, galantamine, huperzine, neostigmine and pyridostigmine. Major attention is given to the cholinergic anti-inflammatory pathway, a well-described link between the central nervous system and terminal effector cells in the immune system. Full article
(This article belongs to the Section Molecular Toxicology)
Open AccessReview SPECT and PET Serve as Molecular Imaging Techniques and in Vivo Biomarkers for Brain Metastases
Int. J. Mol. Sci. 2014, 15(6), 9878-9893; doi:10.3390/ijms15069878
Received: 30 March 2014 / Revised: 13 May 2014 / Accepted: 14 May 2014 / Published: 3 June 2014
Cited by 4 | PDF Full-text (432 KB) | HTML Full-text | XML Full-text
Abstract
Nuclear medicine techniques (single photon emission computerized tomography, SPECT, and positron emission tomography, PET) represent molecular imaging tools, able to provide in vivo biomarkers of different diseases. To investigate brain tumours and metastases many different radiopharmaceuticals imaged by SPECT and PET can [...] Read more.
Nuclear medicine techniques (single photon emission computerized tomography, SPECT, and positron emission tomography, PET) represent molecular imaging tools, able to provide in vivo biomarkers of different diseases. To investigate brain tumours and metastases many different radiopharmaceuticals imaged by SPECT and PET can be used. In this review the main and most promising radiopharmaceuticals available to detect brain metastases are reported. Furthermore the diagnostic contribution of the combination of SPECT and PET data with radiological findings (magnetic resonance imaging, MRI) is discussed. Full article
(This article belongs to the Special Issue Brain Metastasis 2014)
Open AccessReview Steatosis and Steatohepatitis: Complex Disorders
Int. J. Mol. Sci. 2014, 15(6), 9924-9944; doi:10.3390/ijms15069924
Received: 14 February 2014 / Revised: 1 May 2014 / Accepted: 20 May 2014 / Published: 3 June 2014
Cited by 5 | PDF Full-text (284 KB) | HTML Full-text | XML Full-text
Abstract
Non-alcoholic fatty liver disease (NAFLD) which includes steatosis and steatohepatitis, in particular non-alcoholic steatohepatitis (NASH), is a rising health problem world-wide and should be separated from alcoholic steatohepatitis (ASH). NAFLD is regarded as hepatic manifestation of the metabolic syndrome (MetSy), being tightly [...] Read more.
Non-alcoholic fatty liver disease (NAFLD) which includes steatosis and steatohepatitis, in particular non-alcoholic steatohepatitis (NASH), is a rising health problem world-wide and should be separated from alcoholic steatohepatitis (ASH). NAFLD is regarded as hepatic manifestation of the metabolic syndrome (MetSy), being tightly linked to obesity and type 2 diabetes mellitus (T2DM). Development of steatosis, liver fibrosis and cirrhosis often progresses towards hepatocellular carcinogenesis and frequently results in the indication for liver transplantation, underlining the clinical significance of this disease complex. Work on different murine models and several human patients studies led to the identification of different molecular key players as well as epigenetic factors like miRNAs and SNPs, which have a promoting or protecting function in AFLD/ASH or NAFLD/NASH. To which extent they might be translated into human biology and pathogenesis is still questionable and needs further investigation regarding diagnostic parameters, drug development and a better understanding of the genetic impact. In this review we give an overview about the currently available knowledge and recent findings regarding the development and progression of this disease. Full article
(This article belongs to the collection Molecular Mechanisms of Human Liver Diseases)
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Open AccessReview Cytotoxic Autophagy in Cancer Therapy
Int. J. Mol. Sci. 2014, 15(6), 10034-10051; doi:10.3390/ijms150610034
Received: 3 April 2014 / Revised: 17 April 2014 / Accepted: 19 May 2014 / Published: 5 June 2014
Cited by 22 | PDF Full-text (553 KB) | HTML Full-text | XML Full-text
Abstract
Autophagy is a process of cellular self-digestion, whereby the cell degrades subcellular materials in order to generate energy and metabolic precursors in order to prolong survival, classically under conditions of nutrient deprivation. Autophagy can also involve the degradation of damaged or aged [...] Read more.
Autophagy is a process of cellular self-digestion, whereby the cell degrades subcellular materials in order to generate energy and metabolic precursors in order to prolong survival, classically under conditions of nutrient deprivation. Autophagy can also involve the degradation of damaged or aged organelles, and misfolded or damaged proteins to eliminate these components that might otherwise be deleterious to cellular survival. Consequently, autophagy has generally been considered a prosurvival response. Many, if not most chemotherapeutic drugs and radiation also promote autophagy, which is generally considered a cytoprotective response, in that its inhibition frequently promotes apoptotic cells death. Furthermore, it has been shown that conventional chemotherapeutic drugs and radiation alone rarely induce a form of autophagy that leads to cell death. However, there are multiple examples in the literature where newer chemotherapeutic agents, drug combinations or drugs in combination with radiation promote autophagic cell death. This review will describe autophagic cell death induced in breast tumor cells, lung cancer cells as well as glioblastoma, demonstrating that it cannot be concluded that stress induced autophagy is, of necessity, cytoprotective in function. Full article
(This article belongs to the collection Programmed Cell Death and Apoptosis)
Open AccessReview The Role of AhR in Autoimmune Regulation and Its Potential as a Therapeutic Target against CD4 T Cell Mediated Inflammatory Disorder
Int. J. Mol. Sci. 2014, 15(6), 10116-10135; doi:10.3390/ijms150610116
Received: 17 February 2014 / Revised: 26 March 2014 / Accepted: 27 March 2014 / Published: 5 June 2014
Cited by 2 | PDF Full-text (484 KB) | HTML Full-text | XML Full-text
Abstract
AhR has recently emerged as a critical physiological regulator of immune responses affecting both innate and adaptive systems. Since the AhR signaling pathway represents an important link between environmental stimulators and immune-mediated inflammatory disorder, it has become the object of great interest [...] Read more.
AhR has recently emerged as a critical physiological regulator of immune responses affecting both innate and adaptive systems. Since the AhR signaling pathway represents an important link between environmental stimulators and immune-mediated inflammatory disorder, it has become the object of great interest among researchers recently. The current review discusses new insights into the mechanisms of action of a select group of inflammatory autoimmune diseases and the ligand-activated AhR signaling pathway. Representative ligands of AhR, both exogenous and endogenous, are also reviewed relative to their potential use as tools for understanding the role of AhR and as potential therapeutics for the treatment of various inflammatory autoimmune diseases, with a focus on CD4 helper T cells, which play important roles both in self-immune tolerance and in inflammatory autoimmune diseases. Evidence indicating the potential use of these ligands in regulating inflammation in various diseases is highlighted, and potential mechanisms of action causing immune system effects mediated by AhR signaling are also discussed. The current review will contribute to a better understanding of the role of AhR and its signaling pathway in CD4 helper T cell mediated inflammatory disorder. Considering the established importance of AhR in immune regulation and its potential as a therapeutic target, we also think that both further investigation into the molecular mechanisms of immune regulation that are mediated by the ligand-specific AhR signaling pathway, and integrated research and development of new therapeutic drug candidates targeting the AhR signaling pathway should be pursued urgently. Full article
(This article belongs to the Special Issue Mechanisms of Toxicity of Dioxins and Related Compounds)
Open AccessReview BMP-Functionalised Coatings to Promote Osteogenesis for Orthopaedic Implants
Int. J. Mol. Sci. 2014, 15(6), 10150-10168; doi:10.3390/ijms150610150
Received: 17 April 2014 / Revised: 13 May 2014 / Accepted: 22 May 2014 / Published: 6 June 2014
Cited by 6 | PDF Full-text (1228 KB) | HTML Full-text | XML Full-text
Abstract
The loss of bone integrity can significantly compromise the aesthetics and mobility of patients and can be treated using orthopaedic implants. Over the past decades; various orthopaedic implants; such as allografts; xenografts and synthetic materials; have been developed and widely used in [...] Read more.
The loss of bone integrity can significantly compromise the aesthetics and mobility of patients and can be treated using orthopaedic implants. Over the past decades; various orthopaedic implants; such as allografts; xenografts and synthetic materials; have been developed and widely used in clinical practice. However; most of these materials lack intrinsic osteoinductivity and thus cannot induce bone formation. Consequently; osteoinductive functionalisation of orthopaedic implants is needed to promote local osteogenesis and implant osteointegration. For this purpose; bone morphogenetic protein (BMP)-functionalised coatings have proven to be a simple and effective strategy. In this review; we summarise the current knowledge and recent advances regarding BMP-functionalised coatings for orthopaedic implants. Full article
(This article belongs to the Special Issue Biologic Coatings for Orthopaedic Implant)
Open AccessReview Mechanisms of Enzyme-Catalyzed Reduction of Two Carcinogenic Nitro-Aromatics, 3-Nitrobenzanthrone and Aristolochic Acid I: Experimental and Theoretical Approaches
Int. J. Mol. Sci. 2014, 15(6), 10271-10295; doi:10.3390/ijms150610271
Received: 24 March 2014 / Revised: 30 May 2014 / Accepted: 30 May 2014 / Published: 10 June 2014
Cited by 10 | PDF Full-text (2569 KB) | HTML Full-text | XML Full-text
Abstract
This review summarizes the results found in studies investigating the enzymatic activation of two genotoxic nitro-aromatics, an environmental pollutant and carcinogen 3-nitrobenzanthrone (3-NBA) and a natural plant nephrotoxin and carcinogen aristolochic acid I (AAI), to reactive species forming covalent DNA adducts. Experimental [...] Read more.
This review summarizes the results found in studies investigating the enzymatic activation of two genotoxic nitro-aromatics, an environmental pollutant and carcinogen 3-nitrobenzanthrone (3-NBA) and a natural plant nephrotoxin and carcinogen aristolochic acid I (AAI), to reactive species forming covalent DNA adducts. Experimental and theoretical approaches determined the reasons why human NAD(P)H:quinone oxidoreductase (NQO1) and cytochromes P450 (CYP) 1A1 and 1A2 have the potential to reductively activate both nitro-aromatics. The results also contributed to the elucidation of the molecular mechanisms of these reactions. The contribution of conjugation enzymes such as N,O-acetyltransferases (NATs) and sulfotransferases (SULTs) to the activation of 3-NBA and AAI was also examined. The results indicated differences in the abilities of 3-NBA and AAI metabolites to be further activated by these conjugation enzymes. The formation of DNA adducts generated by both carcinogens during their reductive activation by the NOQ1 and CYP1A1/2 enzymes was investigated with pure enzymes, enzymes present in subcellular cytosolic and microsomal fractions, selective inhibitors, and animal models (including knock-out and humanized animals). For the theoretical approaches, flexible in silico docking methods as well as ab initio calculations were employed. The results summarized in this review demonstrate that a combination of experimental and theoretical approaches is a useful tool to study the enzyme-mediated reaction mechanisms of 3-NBA and AAI reduction. Full article
Open AccessReview Erythropoietin Action in Stress Response, Tissue Maintenance and Metabolism
Int. J. Mol. Sci. 2014, 15(6), 10296-10333; doi:10.3390/ijms150610296
Received: 20 February 2014 / Revised: 23 May 2014 / Accepted: 28 May 2014 / Published: 10 June 2014
Cited by 20 | PDF Full-text (2646 KB) | HTML Full-text | XML Full-text
Abstract
Erythropoietin (EPO) regulation of red blood cell production and its induction at reduced oxygen tension provides for the important erythropoietic response to ischemic stress. The cloning and production of recombinant human EPO has led to its clinical use in patients with anemia [...] Read more.
Erythropoietin (EPO) regulation of red blood cell production and its induction at reduced oxygen tension provides for the important erythropoietic response to ischemic stress. The cloning and production of recombinant human EPO has led to its clinical use in patients with anemia for two and half decades and has facilitated studies of EPO action. Reports of animal and cell models of ischemic stress in vitro and injury suggest potential EPO benefit beyond red blood cell production including vascular endothelial response to increase nitric oxide production, which facilitates oxygen delivery to brain, heart and other non-hematopoietic tissues. This review discusses these and other reports of EPO action beyond red blood cell production, including EPO response affecting metabolism and obesity in animal models. Observations of EPO activity in cell and animal model systems, including mice with tissue specific deletion of EPO receptor (EpoR), suggest the potential for EPO response in metabolism and disease. Full article
(This article belongs to the Special Issue Signal Transduction of Tissue Repair)
Open AccessReview Viral Metagenomics on Animals as a Tool for the Detection of Zoonoses Prior to Human Infection?
Int. J. Mol. Sci. 2014, 15(6), 10377-10397; doi:10.3390/ijms150610377
Received: 12 March 2014 / Revised: 24 May 2014 / Accepted: 28 May 2014 / Published: 10 June 2014
Cited by 8 | PDF Full-text (1481 KB) | HTML Full-text | XML Full-text
Abstract
Many human viral infections have a zoonotic, i.e., wild or domestic animal, origin. Several zoonotic viruses are transmitted to humans directly via contact with an animal or indirectly via exposure to the urine or feces of infected animals or the bite [...] Read more.
Many human viral infections have a zoonotic, i.e., wild or domestic animal, origin. Several zoonotic viruses are transmitted to humans directly via contact with an animal or indirectly via exposure to the urine or feces of infected animals or the bite of a bloodsucking arthropod. If a virus is able to adapt and replicate in its new human host, human-to-human transmissions may occur, possibly resulting in an epidemic, such as the A/H1N1 flu pandemic in 2009. Thus, predicting emerging zoonotic infections is an important challenge for public health officials in the coming decades. The recent development of viral metagenomics, i.e., the characterization of the complete viral diversity isolated from an organism or an environment using high-throughput sequencing technologies, is promising for the surveillance of such diseases and can be accomplished by analyzing the viromes of selected animals and arthropods that are closely in contact with humans. In this review, we summarize our current knowledge of viral diversity within such animals (in particular blood-feeding arthropods, wildlife and domestic animals) using metagenomics and present its possible future application for the surveillance of zoonotic and arboviral diseases. Full article
(This article belongs to the Special Issue Metagenomics: a Powerful Lens Viewing the Microbial World)
Open AccessReview Alternative Splicing in Plant Immunity
Int. J. Mol. Sci. 2014, 15(6), 10424-10445; doi:10.3390/ijms150610424
Received: 14 April 2014 / Revised: 12 May 2014 / Accepted: 14 May 2014 / Published: 10 June 2014
Cited by 11 | PDF Full-text (727 KB) | HTML Full-text | XML Full-text
Abstract
Alternative splicing (AS) occurs widely in plants and can provide the main source of transcriptome and proteome diversity in an organism. AS functions in a range of physiological processes, including plant disease resistance, but its biological roles and functional mechanisms remain poorly [...] Read more.
Alternative splicing (AS) occurs widely in plants and can provide the main source of transcriptome and proteome diversity in an organism. AS functions in a range of physiological processes, including plant disease resistance, but its biological roles and functional mechanisms remain poorly understood. Many plant disease resistance (R) genes undergo AS, and several R genes require alternatively spliced transcripts to produce R proteins that can specifically recognize pathogen invasion. In the finely-tuned process of R protein activation, the truncated isoforms generated by AS may participate in plant disease resistance either by suppressing the negative regulation of initiation of immunity, or by directly engaging in effector-triggered signaling. Although emerging research has shown the functional significance of AS in plant biotic stress responses, many aspects of this topic remain to be understood. Several interesting issues surrounding the AS of R genes, especially regarding its functional roles and regulation, will require innovative techniques and additional research to unravel. Full article
(This article belongs to the Special Issue Pre-mRNA Splicing)
Open AccessReview Mass Spectrometry Methodology in Lipid Analysis
Int. J. Mol. Sci. 2014, 15(6), 10492-10507; doi:10.3390/ijms150610492
Received: 22 April 2014 / Revised: 22 May 2014 / Accepted: 28 May 2014 / Published: 11 June 2014
Cited by 8 | PDF Full-text (1591 KB) | HTML Full-text | XML Full-text
Abstract
Lipidomics is an emerging field, where the structures, functions and dynamic changes of lipids in cells, tissues or body fluids are investigated. Due to the vital roles of lipids in human physiological and pathological processes, lipidomics is attracting more and more attentions. [...] Read more.
Lipidomics is an emerging field, where the structures, functions and dynamic changes of lipids in cells, tissues or body fluids are investigated. Due to the vital roles of lipids in human physiological and pathological processes, lipidomics is attracting more and more attentions. However, because of the diversity and complexity of lipids, lipid analysis is still full of challenges. The recent development of methods for lipid extraction and analysis and the combination with bioinformatics technology greatly push forward the study of lipidomics. Among them, mass spectrometry (MS) is the most important technology for lipid analysis. In this review, the methodology based on MS for lipid analysis was introduced. It is believed that along with the rapid development of MS and its further applications to lipid analysis, more functional lipids will be identified as biomarkers and therapeutic targets and for the study of the mechanisms of disease. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
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Open AccessReview MicroRNAs in Brain Metastases: Potential Role as Diagnostics and Therapeutics
Int. J. Mol. Sci. 2014, 15(6), 10508-10526; doi:10.3390/ijms150610508
Received: 16 April 2014 / Revised: 22 May 2014 / Accepted: 6 June 2014 / Published: 11 June 2014
Cited by 4 | PDF Full-text (1439 KB) | HTML Full-text | XML Full-text
Abstract
Brain metastases remain a daunting adversary that negatively impact patient survival. Metastatic brain tumors affect up to 45% of all cancer patients with systemic cancer and account for ~20% of all cancer-related deaths. A complex network of non-coding RNA molecules, microRNAs (miRNAs), [...] Read more.
Brain metastases remain a daunting adversary that negatively impact patient survival. Metastatic brain tumors affect up to 45% of all cancer patients with systemic cancer and account for ~20% of all cancer-related deaths. A complex network of non-coding RNA molecules, microRNAs (miRNAs), regulate tumor metastasis. The brain micro-environment modulates metastatic tumor growth; however, defining the precise genetic events that promote metastasis in the brain niche represents an important, unresolved problem. Understanding these events will reveal disease-based targets and offer effective strategies to treat brain metastases. Effective therapeutic strategies based upon the biology of brain metastases represent an urgent, unmet need with immediate potential for clinical impact. Studies have demonstrated the ability of miRNAs to distinguish normal from cancerous cells, primary from secondary brain tumors, and correctly categorize metastatic brain tumor tissue of origin based solely on miRNA profiles. Interestingly, manipulation of miRNAs has proven effective in cancer treatment. With the promise of reduced toxicity, increased efficacy and individually directed personalized anti-cancer therapy, using miRNA in the treatment of metastatic brain tumors may prove very useful and improve patient outcome. In this review, we focus on the potential of miRNAs as diagnostic and therapeutic targets for the treatment of metastatic brain lesions. Full article
(This article belongs to the Special Issue Brain Metastasis 2014)
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Open AccessReview Molecular Mechanism and Treatment of Viral Hepatitis-Related Liver Fibrosis
Int. J. Mol. Sci. 2014, 15(6), 10578-10604; doi:10.3390/ijms150610578
Received: 4 May 2014 / Revised: 9 June 2014 / Accepted: 9 June 2014 / Published: 12 June 2014
Cited by 10 | PDF Full-text (753 KB) | HTML Full-text | XML Full-text
Abstract
Hepatic fibrosis is a wound-healing response to various chronic stimuli, including viral hepatitis B or C infection. Activated myofibroblasts, predominantly derived from the hepatic stellate cells (HSCs), regulate the balance between matrix metalloproteinases and their tissue inhibitors to maintain extracellular matrix homeostasis. [...] Read more.
Hepatic fibrosis is a wound-healing response to various chronic stimuli, including viral hepatitis B or C infection. Activated myofibroblasts, predominantly derived from the hepatic stellate cells (HSCs), regulate the balance between matrix metalloproteinases and their tissue inhibitors to maintain extracellular matrix homeostasis. Transforming growth factor-β and platelet-derived growth factor are classic profibrogenic signals that activate HSC proliferation. In addition, proinflammatory cytokines and chemokines coordinate macrophages, T cells, NK/NKT cells, and liver sinusoidal endothelial cells in complex fibrogenic and regression processes. In addition, fibrogenesis involves angiogenesis, metabolic reprogramming, autophagy, microRNA, and epigenetic regulations. Hepatic inflammation is the driving force behind liver fibrosis; however, host single nucleotide polymorphisms and viral factors, including the genotype, viral load, viral mutation, and viral proteins, have been associated with fibrosis progression. Eliminating the underlying etiology is the most crucial antifibrotic therapy. Growing evidence has indicated that persistent viral suppression with antiviral therapy can result in fibrosis regression, reduced liver disease progression, decreased hepatocellular carcinoma, and improved chances of survival. Preclinical studies and clinical trials are currently examining several investigational agents that target key fibrogenic pathways; the results are promising and shed light on this debilitating illness. Full article
(This article belongs to the collection Molecular Mechanisms of Human Liver Diseases)
Open AccessReview Sperm-Egg Fusion: A Molecular Enigma of Mammalian Reproduction
Int. J. Mol. Sci. 2014, 15(6), 10652-10668; doi:10.3390/ijms150610652
Received: 9 April 2014 / Revised: 13 May 2014 / Accepted: 30 May 2014 / Published: 13 June 2014
Cited by 16 | PDF Full-text (697 KB) | HTML Full-text | XML Full-text
Abstract
The mechanism of gamete fusion remains largely unknown on a molecular level despite its indisputable significance. Only a few of the molecules required for membrane interaction are known, among them IZUMO1, which is present on sperm, tetraspanin CD9, which is present on [...] Read more.
The mechanism of gamete fusion remains largely unknown on a molecular level despite its indisputable significance. Only a few of the molecules required for membrane interaction are known, among them IZUMO1, which is present on sperm, tetraspanin CD9, which is present on the egg, and the newly found oolema protein named Juno. A concept of a large multiprotein complex on both membranes forming fusion machinery has recently emerged. The Juno and IZUMO1, up to present, is the only known extracellular receptor pair in the process of fertilization, thus, facilitating the essential binding of gametes. However, neither IZUMO1 nor Juno appears to be the fusogenic protein. At the same time, the tetraspanin is expected to play a role in organizing the egg membrane order and to interact laterally with other factors. This review summarizes, to present, the known molecules involved in the process of sperm-egg fusion. The complexity and expected redundancy of the involved factors makes the process an intricate and still poorly understood mechanism, which is difficult to comprehend in its full distinction. Full article
(This article belongs to the Special Issue Cellular and Molecular Mechanisms of Sperm-Egg Interaction)
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Open AccessReview Carriers in Cell-Based Therapies for Neurological Disorders
Int. J. Mol. Sci. 2014, 15(6), 10669-10723; doi:10.3390/ijms150610669
Received: 14 March 2014 / Revised: 19 May 2014 / Accepted: 30 May 2014 / Published: 13 June 2014
Cited by 4 | PDF Full-text (886 KB) | HTML Full-text | XML Full-text
Abstract
There is a pressing need for long-term neuroprotective and neuroregenerative therapies to promote full function recovery of injuries in the human nervous system resulting from trauma, stroke or degenerative diseases. Although cell-based therapies are promising in supporting repair and regeneration, direct introduction [...] Read more.
There is a pressing need for long-term neuroprotective and neuroregenerative therapies to promote full function recovery of injuries in the human nervous system resulting from trauma, stroke or degenerative diseases. Although cell-based therapies are promising in supporting repair and regeneration, direct introduction to the injury site is plagued by problems such as low transplanted cell survival rate, limited graft integration, immunorejection, and tumor formation. Neural tissue engineering offers an integrative and multifaceted approach to tackle these complex neurological disorders. Synergistic therapeutic effects can be obtained from combining customized biomaterial scaffolds with cell-based therapies. Current scaffold-facilitated cell transplantation strategies aim to achieve structural and functional rescue via offering a three-dimensional permissive and instructive environment for sustainable neuroactive factor production for prolonged periods and/or cell replacement at the target site. In this review, we intend to highlight important considerations in biomaterial selection and to review major biodegradable or non-biodegradable scaffolds used for cell transplantation to the central and peripheral nervous system in preclinical and clinical trials. Expanded knowledge in biomaterial properties and their prolonged interaction with transplanted and host cells have greatly expanded the possibilities for designing suitable carrier systems and the potential of cell therapies in the nervous system. Full article
(This article belongs to the Special Issue Neuroprotective Strategies 2014)
Open AccessReview Contribution of Chitinase A’s C-Terminal Vacuolar Sorting Determinant to the Study of Soluble Protein Compartmentation
Int. J. Mol. Sci. 2014, 15(6), 11030-11039; doi:10.3390/ijms150611030
Received: 28 March 2014 / Revised: 6 June 2014 / Accepted: 9 June 2014 / Published: 18 June 2014
Cited by 2 | PDF Full-text (890 KB) | HTML Full-text | XML Full-text
Abstract
Plant chitinases have been studied for their importance in the defense of crop plants from pathogen attacks and for their peculiar vacuolar sorting determinants. A peculiarity of the sequence of many family 19 chitinases is the presence of a C-terminal extension [...] Read more.
Plant chitinases have been studied for their importance in the defense of crop plants from pathogen attacks and for their peculiar vacuolar sorting determinants. A peculiarity of the sequence of many family 19 chitinases is the presence of a C-terminal extension that seems to be important for their correct recognition by the vacuole sorting machinery. The 7 amino acids long C-terminal vacuolar sorting determinant (CtVSD) of tobacco chitinase A is necessary and sufficient for the transport to the vacuole. This VSD shares no homology with other CtVSDs such as the phaseolin’s tetrapeptide AFVY (AlaPheValTyr) and it is also sorted by different mechanisms. While a receptor for this signal has not yet been convincingly identified, the research using the chitinase CtVSD has been very informative, leading to the observation of phenomena otherwise difficult to observe such as the presence of separate vacuoles in differentiating cells and the existence of a Golgi-independent route to the vacuole. Thanks to these new insights in the endoplasmic reticulum (ER)-to-vacuole transport, GFPChi (Green Fluorescent Protein carrying the chitinase A CtVSD) and other markers based on chitinase signals will continue to help the investigation of vacuolar biogenesis in plants. Full article
(This article belongs to the Special Issue Plant Cell Compartmentation and Volume Control)
Open AccessReview Coactivator Recruitment of AhR/ARNT1
Int. J. Mol. Sci. 2014, 15(6), 11100-11110; doi:10.3390/ijms150611100
Received: 16 April 2014 / Revised: 27 May 2014 / Accepted: 7 June 2014 / Published: 19 June 2014
Cited by 3 | PDF Full-text (1081 KB) | HTML Full-text | XML Full-text
Abstract
A common feature of nuclear receptors (NRs) is the transformation of external cell signals into specific transcriptions of the signal molecule. Signal molecules function as ligands for NRs and, after their uptake, activated NRs form homo- or heterodimers at promoter recognition sequences [...] Read more.
A common feature of nuclear receptors (NRs) is the transformation of external cell signals into specific transcriptions of the signal molecule. Signal molecules function as ligands for NRs and, after their uptake, activated NRs form homo- or heterodimers at promoter recognition sequences of the specific genes in the nucleus. Another common feature of NRs is their dependence on coactivators, which bridge the basic transcriptional machinery and other cofactors to the target genes, in order to initiate transcription and to unwind histone-bound DNA for exposing additional promoter recognition sites via their histone acetyltransferase (HAT) function. In this review, we focus on our recent findings related to the recruitment of steroid receptor coactivator 1 (SRC1/NCoA1) by the estrogen receptor-α (ERα) and by the arylhydrocarbon receptor/arylhydrocarbon receptor nuclear translocator 1 (AhR/ARNT1) complex. We also describe the extension of our previously published findings regarding the binding between ARNT1.1 exon16 and SRC1e exon 21, via in silico analyses of androgen receptor (AR) NH2-carboxyl-terminal interactions, the results of which were verified by in vitro experiments. Based on these data, we suggest a newly derived tentative binding site of nuclear coactivator 2/glucocorticoid receptor interacting protein-1/transcriptional intermediary factor 2 (NCOA-2/ GRIP-1/TIF-2) for ARNT1.1 exon 16. Furthermore, results obtained by immunoprecipitation have revealed a second leucine-rich binding site for hARNT1.1 exon 16 in SRC1e exon 21 (LSSTDLL). Finally, we discuss the role of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) as an endocrine disruptor for estrogen related transcription. Full article
(This article belongs to the Special Issue Mechanisms of Toxicity of Dioxins and Related Compounds)
Open AccessReview Identification of Drivers from Cancer Genome Diversity in Hepatocellular Carcinoma
Int. J. Mol. Sci. 2014, 15(6), 11142-11160; doi:10.3390/ijms150611142
Received: 2 April 2014 / Revised: 12 June 2014 / Accepted: 16 June 2014 / Published: 20 June 2014
Cited by 5 | PDF Full-text (431 KB) | HTML Full-text | XML Full-text
Abstract
Hepatocellular carcinoma (HCC) is one of the most common cancers with a dismal outcome. The complicated molecular pathogenesis of HCC caused by tumor heterogeneity makes it difficult to identify druggable targets useful for treating HCC patients. One approach that has a potential [...] Read more.
Hepatocellular carcinoma (HCC) is one of the most common cancers with a dismal outcome. The complicated molecular pathogenesis of HCC caused by tumor heterogeneity makes it difficult to identify druggable targets useful for treating HCC patients. One approach that has a potential for the improvement of patient prognosis is the identification of cancer driver genes that play a critical role in the development of HCC. Recent technological advances of high-throughput methods, such as gene expression profiles, DNA copy number alterations and somatic mutations, have expanded our understanding of the comprehensive genetic profiles of HCC. Integrative analysis of these omics profiles enables us to classify the molecular subgroups of HCC patients. As each subgroup classified according to genetic profiles has different clinical features, such as recurrence rate and prognosis, the tumor subclassification tools are useful in clinical practice. Furthermore, a global genetic analysis, including genome-wide RNAi functional screening, makes it possible to identify cancer vulnerable genes. Identification of common cancer driver genes in HCC leads to the development of an effective molecular target therapy. Full article
(This article belongs to the collection Molecular Mechanisms of Human Liver Diseases)

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Open AccessTechnical Note A Cautionary Note on the Use of Split-YFP/BiFC in Plant Protein-Protein Interaction Studies
Int. J. Mol. Sci. 2014, 15(6), 9628-9643; doi:10.3390/ijms15069628
Received: 3 April 2014 / Revised: 17 April 2014 / Accepted: 20 May 2014 / Published: 30 May 2014
Cited by 11 | PDF Full-text (1208 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Since its introduction in plants 10 years ago, the bimolecular fluorescence complementation (BiFC) method, or split-YFP (yellow fluorescent protein), has gained popularity within the plant biology field as a method to study protein-protein interactions. BiFC is based on the restoration of fluorescence [...] Read more.
Since its introduction in plants 10 years ago, the bimolecular fluorescence complementation (BiFC) method, or split-YFP (yellow fluorescent protein), has gained popularity within the plant biology field as a method to study protein-protein interactions. BiFC is based on the restoration of fluorescence after the two non-fluorescent halves of a fluorescent protein are brought together by a protein-protein interaction event. The major drawback of BiFC is that the fluorescent protein halves are prone to self-assembly independent of a protein-protein interaction event. To circumvent this problem, several modifications of the technique have been suggested, but these modifications have not lead to improvements in plant BiFC protocols. Therefore, it remains crucial to include appropriate internal controls. Our literature survey of recent BiFC studies in plants shows that most studies use inappropriate controls, and a qualitative rather than quantitative read-out of fluorescence. Therefore, we provide a cautionary note and beginner’s guideline for the setup of BiFC experiments, discussing each step of the protocol, including vector choice, plant expression systems, negative controls, and signal detection. In addition, we present our experience with BiFC with respect to self-assembly, peptide linkers, and incubation temperature. With this note, we aim to provide a guideline that will improve the quality of plant BiFC experiments. Full article
(This article belongs to the collection Proteins and Protein-Ligand Interactions)
Open AccessCorrection Correction: Mutsuzaki, H., et al. Improved Bonding of Partially Osteomyelitic Bone to Titanium Pins Owing to Biomimetic Coating of Apatite. Int. J. Mol. Sci. 2013, 14, 24366–24379.
Int. J. Mol. Sci. 2014, 15(6), 9789-9792; doi:10.3390/ijms15069789
Received: 25 April 2014 / Accepted: 30 April 2014 / Published: 30 May 2014
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Abstract
In the original version of the manuscript [1] there was an inadvertent error. The words “25 °C for 48 h” should be replaced with “25 °C for 24 h”. The authors carried out the coating experiments at 25 °C for 1, 3, [...] Read more.
In the original version of the manuscript [1] there was an inadvertent error. The words “25 °C for 48 h” should be replaced with “25 °C for 24 h”. The authors carried out the coating experiments at 25 °C for 1, 3, 6, 12, 24 and 48 h. The apatite coatings formed at 25 °C for 24 and 48 h were found to be identical in physicochemical nature, which was revealed by SEM, EDX, XRD and chemical analysis. Thus, in the animal experiments, the authors used apatite-coated Ti pins fabricated at 25 °C for 24 h. Several corrections are thus required in the abstract, the main text, the figure legends, and the figures (Table 1). The authors would like to apologize for any inconvenience this may have caused to readers of the journal. [...] Full article
(This article belongs to the Special Issue Biologic Coatings for Orthopaedic Implant)

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