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Int. J. Mol. Sci., Volume 20, Issue 5 (March-1 2019) – 253 articles

Cover Story (view full-size image): Pericytes are mesenchymal cells surrounding small blood vessels. The current study established novel methods for the isolation and culture of pericytes. The study also showed that pericytes have multilineage differentiation potential in vitro and contribute to bone fracture healing as a cellular source of osteogenic cells in vivo. View this paper.
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17 pages, 2157 KiB  
Article
Extracellular Spermine Activates DNA Methyltransferase 3A and 3B
by Taro Fukui, Kuniyasu Soda, Koichi Takao and Toshiki Rikiyama
Int. J. Mol. Sci. 2019, 20(5), 1254; https://doi.org/10.3390/ijms20051254 - 12 Mar 2019
Cited by 15 | Viewed by 5683
Abstract
We first demonstrated that long-term increased polyamine (spermine, spermidine, putrescine) intake elevated blood spermine levels in mice and humans, and lifelong consumption of polyamine-rich chow inhibited aging-associated increase in aberrant DNA methylation, inhibited aging-associated pathological changes, and extend lifespan of mouse. Because gene [...] Read more.
We first demonstrated that long-term increased polyamine (spermine, spermidine, putrescine) intake elevated blood spermine levels in mice and humans, and lifelong consumption of polyamine-rich chow inhibited aging-associated increase in aberrant DNA methylation, inhibited aging-associated pathological changes, and extend lifespan of mouse. Because gene methylation status is closely associated with aging-associated conditions and polyamine metabolism is closely associated with regulation of gene methylation, we investigated the effects of extracellular spermine supplementation on substrate concentrations and enzyme activities involved in gene methylation. Jurkat cells and human mammary epithelial cells were cultured with spermine and/or D,L-alpha-difluoromethylornithine (DFMO), an inhibitor of ornithine decarboxylase. Spermine supplementation inhibited enzymatic activities of adenosylmethionine decarboxylase in both cells. The ratio of decarboxylated S-adenosylmethionine to S-adenosyl-L-methionine increased by DFMO and decreased by spermine. In Jurkat cells cultured with DFMO, the protein levels of DNA methyltransferases (DNMTs) 1, 3A and 3B were not changed, however the activity of the three enzymes markedly decreased. The protein levels of these enzymes were not changed by addition of spermine, DNMT 3A and especially 3B were activated. We show that changes in polyamine metabolism dramatically affect substrate concentrations and activities of enzymes involved in gene methylation. Full article
(This article belongs to the Special Issue The Effect of Dietary Factors on Cancer)
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12 pages, 9009 KiB  
Article
Effects of Eleutherococcus Extract Mixture on Endochondral Bone Formation in Rats
by Donghun Lee, Sung Hyun Lee, Namhoon Cho, Young-Sik Kim, Jungbin Song and Hocheol Kim
Int. J. Mol. Sci. 2019, 20(5), 1253; https://doi.org/10.3390/ijms20051253 - 12 Mar 2019
Cited by 4 | Viewed by 4645
Abstract
Eleutherococcus extract mixture (EEM) is an herbal mixture of dried stem of Eleutherococcus sessiliflorus and germinated barley, which has been highly effective, in previous screening and among the traditional medicines to tonify innate qi and acquired qi, respectively. In this study, we [...] Read more.
Eleutherococcus extract mixture (EEM) is an herbal mixture of dried stem of Eleutherococcus sessiliflorus and germinated barley, which has been highly effective, in previous screening and among the traditional medicines to tonify innate qi and acquired qi, respectively. In this study, we investigate the effects of EEM on endochondral bone formation. Female adolescent rats were given EEM, growth hormone or vehicle for 10 days. Tetracycline was intraperitoneally injected to light the fluorescent band 72 h before sacrifice to determine endochondral bone formation. In order to evaluate endocrine or paracrine/autocrine mechanisms, expressions of insulin-like growth factor 1 (IGF1), insulin-like growth factor binding protein 3 (IGFBP3), or bone morphogenetic protein 2 (BMP2) were evaluated after EEM administration in liver or growth plate (GP). EEM oral administration significantly increased endochondral bone formation and proliferative and hypertrophic zonal heights of tibial GP. EEM also upregulated hepatic IGF1 and IGFBP3 mRNA expressions, and IGF1 and BMP2 expressions in GP. Taken together, EEM increases endochondral bone formation through stimulating proliferation and hypertrophy with upregulation of hepatic IGF1 and IGFBP3 expressions. Considering immunohistochemical studies, the effect of EEM may be due to increased local IGF1 and BMP2 expression in GP, which may be considered growth hormone (GH)-dependent endocrine and autocrine/paracrine pathways. Full article
(This article belongs to the Special Issue Traditional Medicine – Unraveling Its Molecular Mechanism, Volume 2)
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20 pages, 1507 KiB  
Review
Protein Interaction with Charged Macromolecules: From Model Polymers to Unfolded Proteins and Post-Translational Modifications
by Pavel Semenyuk and Vladimir Muronetz
Int. J. Mol. Sci. 2019, 20(5), 1252; https://doi.org/10.3390/ijms20051252 - 12 Mar 2019
Cited by 22 | Viewed by 7297
Abstract
Interaction of proteins with charged macromolecules is involved in many processes in cells. Firstly, there are many naturally occurred charged polymers such as DNA and RNA, polyphosphates, sulfated glycosaminoglycans, etc., as well as pronouncedly charged proteins such as histones or actin. Electrostatic interactions [...] Read more.
Interaction of proteins with charged macromolecules is involved in many processes in cells. Firstly, there are many naturally occurred charged polymers such as DNA and RNA, polyphosphates, sulfated glycosaminoglycans, etc., as well as pronouncedly charged proteins such as histones or actin. Electrostatic interactions are also important for “generic” proteins, which are not generally considered as polyanions or polycations. Finally, protein behavior can be altered due to post-translational modifications such as phosphorylation, sulfation, and glycation, which change a local charge of the protein region. Herein we review molecular modeling for the investigation of such interactions, from model polyanions and polycations to unfolded proteins. We will show that electrostatic interactions are ubiquitous, and molecular dynamics simulations provide an outstanding opportunity to look inside binding and reveal the contribution of electrostatic interactions. Since a molecular dynamics simulation is only a model, we will comprehensively consider its relationship with the experimental data. Full article
(This article belongs to the Special Issue Molecular Dynamics Simulations)
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25 pages, 2866 KiB  
Article
Comparable Genomic Copy Number Aberrations Differ across Astrocytoma Malignancy Grades
by Nives Pećina-Šlaus, Anja Kafka, Kristina Gotovac Jerčić, Monika Logara, Anja Bukovac, Robert Bakarić and Fran Borovečki
Int. J. Mol. Sci. 2019, 20(5), 1251; https://doi.org/10.3390/ijms20051251 - 12 Mar 2019
Cited by 14 | Viewed by 4769
Abstract
A collection of intracranial astrocytomas of different malignancy grades was analyzed for copy number aberrations (CNA) in order to identify regions that are driving cancer pathogenesis. Astrocytomas were analyzed by Array Comparative Genomic Hybridization (aCGH) and bioinformatics utilizing a Bioconductor package, Genomic Identification [...] Read more.
A collection of intracranial astrocytomas of different malignancy grades was analyzed for copy number aberrations (CNA) in order to identify regions that are driving cancer pathogenesis. Astrocytomas were analyzed by Array Comparative Genomic Hybridization (aCGH) and bioinformatics utilizing a Bioconductor package, Genomic Identification of Significant Targets in Cancer (GISTIC) 2.0.23 and DAVID software. Altogether, 1438 CNA were found of which losses prevailed. On our total sample, significant deletions affected 14 chromosomal regions, out of which deletions at 17p13.2, 9p21.3, 13q12.11, 22q12.3 remained significant even at 0.05 q-value. When divided into malignancy groups, the regions identified as significantly deleted in high grades were: 9p21.3; 17p13.2; 10q24.2; 14q21.3; 1p36.11 and 13q12.11, while amplified were: 3q28; 12q13.3 and 21q22.3. Low grades comprised significant deletions at 3p14.3; 11p15.4; 15q15.1; 16q22.1; 20q11.22 and 22q12.3 indicating their involvement in early stages of tumorigenesis. Significantly enriched pathways were: PI3K-Akt, Cytokine-cytokine receptor, the nucleotide-binding oligomerization domain (NOD)–like receptor, Jak-STAT, retinoic acid-inducible gene (RIG)-I-like receptor and Toll-like receptor pathways. HPV and herpex simplex infection and inflammation pathways were also represented. The present study brings new data to astrocytoma research amplifying the wide spectrum of changes that could help us identify the regions critical for tumorigenesis. Full article
(This article belongs to the Special Issue Advances in the Comprehension of the Molecular Basis of Cancer and New Therapeutic Strategies)
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14 pages, 2004 KiB  
Article
Bioavailability and In Vivo Antioxidant Activity of a Standardized Polyphenol Mixture Extracted from Brown Propolis
by Valeria Curti, Vincenzo Zaccaria, Arold Jorel Tsetegho Sokeng, Marco Dacrema, Irene Masiello, Anna Mascaro, Giuseppe D’Antona and Maria Daglia
Int. J. Mol. Sci. 2019, 20(5), 1250; https://doi.org/10.3390/ijms20051250 - 12 Mar 2019
Cited by 47 | Viewed by 6898
Abstract
Several lines of evidence demonstrate the antioxidant, anti-inflammatory and antimicrobial activities of propolis, mostly ascribed to its polyphenol content. However, little is known regarding the bioavailability of propolis in acute and prolonged settings of oral administration. In this study, we first determined the [...] Read more.
Several lines of evidence demonstrate the antioxidant, anti-inflammatory and antimicrobial activities of propolis, mostly ascribed to its polyphenol content. However, little is known regarding the bioavailability of propolis in acute and prolonged settings of oral administration. In this study, we first determined the content of the main polyphenols in a brown propolis extract obtained using a patented extraction method (Multi Dinamic Extraction—M.E.D.) by RP-HPLC-UV-PDA-MSn analysis, followed by the bioavailability of galangin and chrysin, the most abundant polyphenols in the mixture (7.8% and 7.5% respectively), following acute (single bolus of 500 mg/kg containing about 3.65 mg of the polyphenol mixture) and prolonged (100, 250 and 500 mg/kg body for 30 days) oral administration in 30 male 8 weeks old C57BL/6 wild-type mice. In the acute setting, blood was taken at 30 s and 5, 10, 15, 20, 25, 30, 45, 60 and 120 min following the oral bolus. In the prolonged setting, blood samples were obtained after 10, 20 or 30 days of administration. At the end of treatment, expression of antioxidant enzymes (superoxyde dismutase, SOD-1; catalase, CAT; glutathione peroxidase, GSS) was evaluated in liver tissue. Following both acute and prolonged administration, neither galangin nor chrysin were detectable in the plasma of mice, whereas the glucuronide metabolite of galangine was detectable 5 min after acute administration. At the end of the prolonged treatment SOD-1 was found to have increased significantly, unlike CAT and GSS. Overall, these data suggest that oral administration of whole brown propolis extract is followed by rapid absorption and metabolization of galangin followed by adaptations of the antioxidant first line defense system. Full article
(This article belongs to the Special Issue Bioactive Phytochemicals and Functional Food Ingredients in Fruits and Vegetables 2019)
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48 pages, 14448 KiB  
Article
Sirtuins in Alzheimer’s Disease: SIRT2-Related GenoPhenotypes and Implications for PharmacoEpiGenetics
by Ramón Cacabelos, Juan C. Carril, Natalia Cacabelos, Aleksey G. Kazantsev, Alex V. Vostrov, Lola Corzo, Pablo Cacabelos and Dmitry Goldgaber
Int. J. Mol. Sci. 2019, 20(5), 1249; https://doi.org/10.3390/ijms20051249 - 12 Mar 2019
Cited by 67 | Viewed by 6481
Abstract
Sirtuins (SIRT1-7) are NAD+-dependent protein deacetylases/ADP ribosyltransferases with important roles in chromatin silencing, cell cycle regulation, cellular differentiation, cellular stress response, metabolism and aging. Sirtuins are components of the epigenetic machinery, which is disturbed in Alzheimer’s disease (AD), contributing to AD [...] Read more.
Sirtuins (SIRT1-7) are NAD+-dependent protein deacetylases/ADP ribosyltransferases with important roles in chromatin silencing, cell cycle regulation, cellular differentiation, cellular stress response, metabolism and aging. Sirtuins are components of the epigenetic machinery, which is disturbed in Alzheimer’s disease (AD), contributing to AD pathogenesis. There is an association between the SIRT2-C/T genotype (rs10410544) (50.92%) and AD susceptibility in the APOEε4-negative population (SIRT2-C/C, 34.72%; SIRT2-T/T 14.36%). The integration of SIRT2 and APOE variants in bigenic clusters yields 18 haplotypes. The 5 most frequent bigenic genotypes in AD are 33CT (27.81%), 33CC (21.36%), 34CT (15.29%), 34CC (9.76%) and 33TT (7.18%). There is an accumulation of APOE-3/4 and APOE-4/4 carriers in SIRT2-T/T > SIRT2-C/T > SIRT2-C/C carriers, and also of SIRT2-T/T and SIRT2-C/T carriers in patients who harbor the APOE-4/4 genotype. SIRT2 variants influence biochemical, hematological, metabolic and cardiovascular phenotypes, and modestly affect the pharmacoepigenetic outcome in AD. SIRT2-C/T carriers are the best responders, SIRT2-T/T carriers show an intermediate pattern, and SIRT2-C/C carriers are the worst responders to a multifactorial treatment. In APOE-SIRT2 bigenic clusters, 33CC carriers respond better than 33TT and 34CT carriers, whereas 24CC and 44CC carriers behave as the worst responders. CYP2D6 extensive metabolizers (EM) are the best responders, poor metabolizers (PM) are the worst responders, and ultra-rapid metabolizers (UM) tend to be better responders that intermediate metabolizers (IM). In association with CYP2D6 genophenotypes, SIRT2-C/T-EMs are the best responders. Some Sirtuin modulators might be potential candidates for AD treatment. Full article
(This article belongs to the Special Issue Genomics of Brain Disorders)
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14 pages, 1624 KiB  
Review
The Impact of Tumor Heterogeneity on Diagnostics and Novel Therapeutic Strategies in Multiple Myeloma
by Leo Rasche, K. Martin Kortüm, Marc S. Raab and Niels Weinhold
Int. J. Mol. Sci. 2019, 20(5), 1248; https://doi.org/10.3390/ijms20051248 - 12 Mar 2019
Cited by 55 | Viewed by 7263
Abstract
Myeloma is characterized by extensive inter-patient genomic heterogeneity due to multiple different initiating events. A recent multi-region sequencing study demonstrated spatial differences, with progression events, such as TP53 mutations, frequently being restricted to focal lesions. In this review article, we describe the clinical [...] Read more.
Myeloma is characterized by extensive inter-patient genomic heterogeneity due to multiple different initiating events. A recent multi-region sequencing study demonstrated spatial differences, with progression events, such as TP53 mutations, frequently being restricted to focal lesions. In this review article, we describe the clinical impact of these two types of tumor heterogeneity. Target mutations are often dominant at one site but absent at other sites, which poses a significant challenge to personalized therapy in myeloma. The same holds true for high-risk subclones, which can be locally restricted, and as such not detectable at the iliac crest, which is the usual sampling site. Imaging can improve current risk classifiers and monitoring of residual disease, but does not allow for deciphering the molecular characteristics of tumor clones. In the era of novel immunotherapies, the clinical impact of heterogeneity certainly needs to be re-defined. Yet, preliminary observations indicate an ongoing impact of spatial heterogeneity on the efficacy of monoclonal antibodies. In conclusion, we recommend combining molecular tests with imaging to improve risk prediction and monitoring of residual disease. Overcoming intra-tumor heterogeneity is the prerequisite for curing myeloma. Novel immunotherapies are promising but research addressing their impact on the spatial clonal architecture is highly warranted. Full article
(This article belongs to the Special Issue Novel Therapeutic Strategies in Multiple Myeloma)
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13 pages, 1708 KiB  
Article
Efficient Editing of the Nuclear APT Reporter Gene in Chlamydomonas reinhardtii via Expression of a CRISPR-Cas9 Module
by Daniel Guzmán-Zapata, José M. Sandoval-Vargas, Karla S. Macedo-Osorio, Edgar Salgado-Manjarrez, José L. Castrejón-Flores, María del Carmen Oliver-Salvador, Noé V. Durán-Figueroa, Fabien Nogué and Jesús A. Badillo-Corona
Int. J. Mol. Sci. 2019, 20(5), 1247; https://doi.org/10.3390/ijms20051247 - 12 Mar 2019
Cited by 41 | Viewed by 7357
Abstract
The clustered regularly interspaced short palindromic repeat/CRISPR-associated protein 9 (CRISPR/Cas9) technology is a versatile and useful tool to perform genome editing in different organisms ranging from bacteria and yeast to plants and mammalian cells. For a couple of years, it was believed that [...] Read more.
The clustered regularly interspaced short palindromic repeat/CRISPR-associated protein 9 (CRISPR/Cas9) technology is a versatile and useful tool to perform genome editing in different organisms ranging from bacteria and yeast to plants and mammalian cells. For a couple of years, it was believed that the system was inefficient and toxic in the alga Chlamydomonas reinhardtii. However, recently the system has been successfully implemented in this model organism, albeit relying mostly on the electroporation of ribonucleoproteins (RNPs) into cell wall deficient strains. This requires a constant source of RNPs and limits the application of the technology to strains that are not necessarily the most relevant from a biotechnological point of view. Here, we show that transient expression of the Streptococcus pyogenes Cas9 gene and sgRNAs, targeted to the single-copy nuclear apt9 gene, encoding an adenine phosphoribosyl transferase (APT), results in efficient disruption at the expected locus. Introduction of indels to the apt9 locus results in cell insensitivity to the otherwise toxic compound 2-fluoroadenine (2-FA). We have used agitation with glass beads and particle bombardment to introduce the plasmids carrying the coding sequences for Cas9 and the sgRNAs in a cell-walled strain of C. reinhardtii (CC-125). Using sgRNAs targeting exons 1 and 3 of apt9, we obtained disruption efficiencies of 3 and 30% on preselected 2-FA resistant colonies, respectively. Our results show that transient expression of Cas9 and a sgRNA can be used for editing of the nuclear genome inexpensively and at high efficiency. Targeting of the APT gene could potentially be used as a pre-selection marker for multiplexed editing or disruption of genes of interest. Full article
(This article belongs to the Special Issue Genome Editing in Plants)
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16 pages, 2425 KiB  
Article
Characterization of Chickpea (Cicer arietinum L.) Flour Films: Effects of pH and Plasticizer Concentration
by Olga Díaz, Tania Ferreiro, José Luis Rodríguez-Otero and Ángel Cobos
Int. J. Mol. Sci. 2019, 20(5), 1246; https://doi.org/10.3390/ijms20051246 - 12 Mar 2019
Cited by 49 | Viewed by 5112
Abstract
The use of flours as a material for biopolymer-based film preparation has gained interest due to the fact that they are a natural mixture of compatible macromolecules and due to their low cost. Chickpea flour shows a promising composition for the development of [...] Read more.
The use of flours as a material for biopolymer-based film preparation has gained interest due to the fact that they are a natural mixture of compatible macromolecules and due to their low cost. Chickpea flour shows a promising composition for the development of edible films. The aim of this study was to characterize and evaluate the properties of chickpea flour films as affected by pH (7 or 10) and plasticizer concentration (1% or 3% w/v) of film-forming solutions. Water vapor permeability, solubility, color, opacity, mechanical properties, thermal stability, structural changes by Fourier transform infrared analysis, and microstructure of the films were determined. Glycerol content and pH influenced chickpea flour film properties, microstructure and structural organization; interactions were also observed. The 1% glycerol films showed lower water vapor permeability, thickness, radical scavenging capacity, elongation at break and puncture deformation, and higher dry matter content, swelling, opacity, elastic modulus, and tensile and puncture strengths than 3% glycerol films. Film-forming solutions at pH 10 produced films with higher thickness and swelling, and were greener than those from solutions at neutral pH. The changes were more intense in 1% glycerol films. Glycerol concentration and pH could be combined in order to obtain chickpea flour films with different properties according to different food packaging requirements. Full article
(This article belongs to the Special Issue Biopolymers as Food Packaging Materials)
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19 pages, 2880 KiB  
Article
Developmental Stage- and Genotype-Dependent Regulation of Specialized Metabolite Accumulation in Fruit Tissues of Different Citrus Varieties
by Roya Nadi, Behrouz Golein, Aurelio Gómez-Cadenas and Vicent Arbona
Int. J. Mol. Sci. 2019, 20(5), 1245; https://doi.org/10.3390/ijms20051245 - 12 Mar 2019
Cited by 13 | Viewed by 4326
Abstract
Flavor traits in citrus are the result of a blend of low molecular weight metabolites including sugars, acids, flavonoids and limonoids, these latter being mainly responsible for the characteristic bitter flavor in citrus. In this work, the genotype- and developmental stage-dependent accumulation of [...] Read more.
Flavor traits in citrus are the result of a blend of low molecular weight metabolites including sugars, acids, flavonoids and limonoids, these latter being mainly responsible for the characteristic bitter flavor in citrus. In this work, the genotype- and developmental stage-dependent accumulation of flavonoids and limonoids is addressed. To fulfill this goal, three models for citrus bitterness: bitter Duncan grapefruit, bittersweet Thomson orange and sweet Wase mandarin were selected from a total of eight different varieties. Compounds were annotated from LC/ESI-QqTOF-MS non-targeted metabolite profiles from albedo and pulp tissues. Results indicated that the specific blend of compounds providing the characteristic flavor trait is genotype-specific and hence under genetic control, but it is also regulated at the developmental level. Metabolite profiles in albedo mirrored those found in pulp, the edible part of the fruit, despite differences in the concentration and accumulation/depletion rates being found. This is particularly relevant for polymethoxylated flavones and glycosylated limonoids that showed a clear partitioning towards albedo and pulp tissues, respectively. Fruit ripening was characterized by a reduction in flavonoids and the accumulation of limonoid glycosides. However, bitter grapefruit showed higher levels of limonin A-ring lactone and naringin in contrast to sweeter orange and mandarin. Data indicated that the accumulation profile was compound class-specific and conserved among the studied varieties despite differing in the respective accumulation and/or depletion rate, leading to different specialized metabolite concentration at the full ripe stage, consistent with the flavor trait output. Full article
(This article belongs to the Special Issue Plant Metabolism in Crops: A Systems Biology Perspective)
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15 pages, 2659 KiB  
Article
Ginsenoside Rh2 Ameliorates Doxorubicin-Induced Senescence Bystander Effect in Breast Carcinoma Cell MDA-MB-231 and Normal Epithelial Cell MCF-10A
by Jin-Gang Hou, Byeong-Min Jeon, Yee-Jin Yun, Chang-Hao Cui and Sun-Chang Kim
Int. J. Mol. Sci. 2019, 20(5), 1244; https://doi.org/10.3390/ijms20051244 - 12 Mar 2019
Cited by 28 | Viewed by 6049
Abstract
The anthracycline antibiotic doxorubicin is commonly used antineoplastic drug in breast cancer treatment. Like most chemotherapy, doxorubicin does not selectively target tumorigenic cells with high proliferation rate and often causes serve side effects. In the present study, we demonstrated the cellular senescence and [...] Read more.
The anthracycline antibiotic doxorubicin is commonly used antineoplastic drug in breast cancer treatment. Like most chemotherapy, doxorubicin does not selectively target tumorigenic cells with high proliferation rate and often causes serve side effects. In the present study, we demonstrated the cellular senescence and senescence associated secretory phenotype (SASP) of both breast tumor cell MDA-MB-231 and normal epithelial cell MCF-10A induced by clinical dose of doxorubicin (100 nM). Senescence was confirmed by flattened morphology, increased level of beta galactose, accumulating contents of lysosome and mitochondrial, and elevated expression of p16 and p21 proteins. Similarly, SASP was identified by highly secreted proteins IL-6, IL-8, GRO, GM-CSF, MCP-1, and MMP1 by antibody array assay. Reciprocal experiments, determined by cell proliferation and apoptosis assays and cell migration and cell invasion, indicated that SASP of MDA-MB-231 cell induces growth arrest of MCF-10A, whereas SASP of MCF-10A significantly stimulates the proliferation of MDA-MB-231. Interestingly, SASP from both cells powerfully promotes the cell migration and cell invasion of MDA-MB-231 cells. Treatment with the natural product ginsenoside Rh2 does not prevent cellular senescence or exert senolytic. However, SASP from senescent cells treated with Rh2 greatly attenuated the above-mentioned bystander effect. Altogether, Rh2 is a potential candidate to ameliorate this unwanted chemotherapy-induced senescence bystander effect. Full article
(This article belongs to the Special Issue Health Promoting Effects of Phytochemicals)
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14 pages, 3312 KiB  
Article
Characterization of Stackebrandtia nassauensis GH 20 Beta-Hexosaminidase, a Versatile Biocatalyst for Chitobiose Degradation
by Meng Wang, Feng Zheng, Ting Wang, Yong-Mei Lyu, Matthew G. Alteen, Zhi-Peng Cai, Zhong-Li Cui, Li Liu and Josef Voglmeir
Int. J. Mol. Sci. 2019, 20(5), 1243; https://doi.org/10.3390/ijms20051243 - 12 Mar 2019
Cited by 16 | Viewed by 4724
Abstract
An unstudied β-N-acetylhexosaminidase (SnHex) from the soil bacterium Stackebrandtia nassauensis was successfully cloned and subsequently expressed as a soluble protein in Escherichia coli. Activity tests and the biochemical characterization of the purified protein revealed an optimum pH of 6.0 and [...] Read more.
An unstudied β-N-acetylhexosaminidase (SnHex) from the soil bacterium Stackebrandtia nassauensis was successfully cloned and subsequently expressed as a soluble protein in Escherichia coli. Activity tests and the biochemical characterization of the purified protein revealed an optimum pH of 6.0 and a robust thermal stability at 50 °C within 24 h. The addition of urea (1 M) or sodium dodecyl sulfate (1% w/v) reduced the activity of the enzyme by 44% and 58%, respectively, whereas the addition of divalent metal ions had no effect on the enzymatic activity. PUGNAc (O-(2-acetamido-2-deoxy-D-glucopyranosylidene)amino-N-phenylcarbamate) strongly inhibited the enzyme in sub-micromolar concentrations. The β-N-acetylhexosaminidase was able to hydrolyze β1,2-linked, β1,3-linked, β1,4-linked, and β1,6-linked GlcNAc residues from the non-reducing end of various tested glycan standards, including bisecting GlcNAc from one of the tested hybrid-type N-glycan substrates. A mutational study revealed that the amino acids D306 and E307 bear the catalytically relevant side acid/base side chains. When coupled with a chitinase, the β-N-acetylhexosaminidase was able to generate GlcNAc directly from colloidal chitin, which showed the potential of this enzyme for biotechnological applications. Full article
(This article belongs to the Special Issue Industrial Enzymes: Structure, Function and Applications)
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20 pages, 4504 KiB  
Article
Increased iNOS and Nitrosative Stress in Dopaminergic Neurons of MDMA-Exposed Rats
by Stefania Schiavone, Margherita Neri, Angela Bruna Maffione, Paolo Frisoni, Maria Grazia Morgese, Luigia Trabace and Emanuela Turillazzi
Int. J. Mol. Sci. 2019, 20(5), 1242; https://doi.org/10.3390/ijms20051242 - 12 Mar 2019
Cited by 19 | Viewed by 5171
Abstract
Several mechanisms underlying 3,4-Methylenedioxy-N-methylamphetamine (MDMA) neurotoxicity have been proposed, including neurochemical alterations and excitotoxicity mediated by reactive oxygen species (ROS), nitric oxide (NO), and reactive nitrogen species (RNS). However, ROS, NO, and RNS sources in the brain are not fully known. [...] Read more.
Several mechanisms underlying 3,4-Methylenedioxy-N-methylamphetamine (MDMA) neurotoxicity have been proposed, including neurochemical alterations and excitotoxicity mediated by reactive oxygen species (ROS), nitric oxide (NO), and reactive nitrogen species (RNS). However, ROS, NO, and RNS sources in the brain are not fully known. We aimed to investigate possible alterations in the expression of the ROS producer NOX enzymes (NOX2, NOX1, and NOX4), NO generators (iNOS, eNOS, and nNOS), markers of oxidative (8-hydroxy-2′-deoxyguanosine, 8OHdG), and nitrosative (3-nitrotyrosine, NT) stress, as well as the colocalization between cells positive for the dopamine transporter (DT1) and cells expressing the neuronal nuclei (NeuN) marker, in the frontal cortex of rats receiving saline or MDMA, sacrificed 6 h, 16 h, or 24 h after its administration. MDMA did not affect NOX2, NOX1, and NOX4 immunoreactivity, whereas iNOS expression was enhanced. The number of NT-positive cells was increased in MDMA-exposed animals, whereas no differences were detected in 8OHdG expression among experimental groups. MDMA and NT markers colocalized with DT1 positive cells. DT1 immunostaining was found in NeuN-positive stained cells. Virtually no colocalization was observed with microglia and astrocytes. Moreover, MDMA immunostaining was not found in NOX2-positive cells. Our results suggest that iNOS-derived nitrosative stress, but not NOX enzymes, may have a crucial role in the pathogenesis of MDMA-induced neurotoxicity, highlighting the specificity of different enzymatic systems in the development of neuropathological alterations induced by the abuse of this psychoactive compound. Full article
(This article belongs to the Special Issue Oxidative Stress and Brain Injury)
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0 pages, 2736 KiB  
Article
Proteome and Phosphoproteome Analysis in TNF Long Term-Exposed Primary Human Monocytes
by Bastian Welz, Rolf Bikker, Johannes Junemann, Martin Christmann, Konstantin Neumann, Mareike Weber, Leonie Hoffmeister, Katharina Preuß, Andreas Pich, René Huber and Korbinian Brand
Int. J. Mol. Sci. 2019, 20(5), 1241; https://doi.org/10.3390/ijms20051241 - 12 Mar 2019
Cited by 10 | Viewed by 5156
Abstract
To better understand the inflammation-associated mechanisms modulating and terminating tumor necrosis factor (TNF-)induced signal transduction and the development of TNF tolerance, we analyzed both the proteome and the phosphoproteome in TNF long term-incubated (i.e., 48 h) primary human monocytes using liquid chromatography-mass spectrometry. [...] Read more.
To better understand the inflammation-associated mechanisms modulating and terminating tumor necrosis factor (TNF-)induced signal transduction and the development of TNF tolerance, we analyzed both the proteome and the phosphoproteome in TNF long term-incubated (i.e., 48 h) primary human monocytes using liquid chromatography-mass spectrometry. Our analyses revealed the presence of a defined set of proteins characterized by reproducible changes in expression and phosphorylation patterns in long term TNF-treated samples. In total, 148 proteins and 569 phosphopeptides were significantly regulated (103 proteins increased, 45 proteins decreased; 377 peptides with increased and 192 peptides with decreased phosphorylation). A variety of these proteins are associated with the non-canonical nuclear factor κB (NF-κB) pathway (nuclear factor κB (NFKB) 2, v-rel reticuloendotheliosis viral oncogene homolog (REL) B, indolamin-2,3-dioxygenase (IDO), kynureninase (KYNU)) or involved in the negative regulation of the canonical NF-κB system. Within the phosphopeptides, binding motifs for specific kinases were identified. Glycogen synthase kinase (GSK) 3 proved to be a promising candidate, since it targets NF-κB inhibiting factors, such as CCAAT/enhancer binding protein (C/EBP) β. Our experiments demonstrate that both proteome and phosphoproteome analysis can be effectively applied to study protein/phosphorylation patterns of primary monocytes. These results provide new regulatory candidates and evidence for a complex network of specific but synergistically acting/cooperating mechanisms enabling the affected cells to resist sustained TNF exposure and resulting in the resolution of inflammation. Full article
(This article belongs to the Special Issue Tumor Necrosis Factor (TNF))
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14 pages, 1201 KiB  
Article
Muscle-Saturated Bioactive Lipids Are Increased with Aging and Influenced by High-Intensity Interval Training
by Ditte Søgaard, Marcin Baranowski, Steen Larsen, Michael Taulo Lund, Cathrine Munk Scheuer, Carina Vestergaard Abildskov, Sofie Greve Dideriksen, Flemming Dela and Jørn Wulff Helge
Int. J. Mol. Sci. 2019, 20(5), 1240; https://doi.org/10.3390/ijms20051240 - 12 Mar 2019
Cited by 23 | Viewed by 5114
Abstract
Ceramide and diacylglycerol are linked to insulin resistance in rodents, but in humans the data are inconsistent. Insulin resistance is frequently observed with aging, but the role of ceramide and diacylglycerol is not clarified. Training improves metabolic health and, therefore, we aimed to [...] Read more.
Ceramide and diacylglycerol are linked to insulin resistance in rodents, but in humans the data are inconsistent. Insulin resistance is frequently observed with aging, but the role of ceramide and diacylglycerol is not clarified. Training improves metabolic health and, therefore, we aimed to elucidate the influence of age and high-intensity interval training (HIIT) on ceramide and diacylglycerol content in muscle. Fourteen young (33 ± 1) and 22 older (63 ± 1) overweight to obese subjects performed 6 weeks HIIT three times a week. Maximal oxygen uptake and body composition were measured and muscle biopsies and fasting blood samples were obtained. Muscle ceramide and diacylglycerol were measured by gas-liquid chromatography and proteins in insulin signaling, lipid and glucose metabolism were measured by Western blotting. Content of ceramide and diacylglycerol total, saturated, C16:0 and C18:0 fatty acids and C18:1 ceramide were higher in older compared to young. HIIT reduced saturated and C18:0 ceramides, while the content of the proteins involved in glucose (GLUT4, glycogen synthase, hexokinase II, AKT) and lipid metabolism (adipose triglyceride lipase, fatty acid binding protein) were increased after HIIT. We demonstrate a higher content of saturated ceramide and diacylglycerol fatty acids in the muscle of older subjects compared to young. Moreover, the content of saturated ceramides was reduced and muscle glucose metabolism improved at protein level after HIIT. This study highlights an increased content of saturated ceramides in aging which could be speculated to influence insulin sensitivity. Full article
(This article belongs to the Special Issue Ceramide)
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22 pages, 976 KiB  
Review
The Role of Curcumin in the Modulation of Ageing
by Anna Bielak-Zmijewska, Wioleta Grabowska, Agata Ciolko, Agnieszka Bojko, Grażyna Mosieniak, Łukasz Bijoch and Ewa Sikora
Int. J. Mol. Sci. 2019, 20(5), 1239; https://doi.org/10.3390/ijms20051239 - 12 Mar 2019
Cited by 100 | Viewed by 15497
Abstract
It is believed that postponing ageing is more effective and less expensive than the treatment of particular age-related diseases. Compounds which could delay symptoms of ageing, especially natural products present in a daily diet, are intensively studied. One of them is curcumin. It [...] Read more.
It is believed that postponing ageing is more effective and less expensive than the treatment of particular age-related diseases. Compounds which could delay symptoms of ageing, especially natural products present in a daily diet, are intensively studied. One of them is curcumin. It causes the elongation of the lifespan of model organisms, alleviates ageing symptoms and postpones the progression of age-related diseases in which cellular senescence is directly involved. It has been demonstrated that the elimination of senescent cells significantly improves the quality of life of mice. There is a continuous search for compounds, named senolytic drugs, that selectively eliminate senescent cells from organisms. In this paper, we endeavor to review the current knowledge about the anti-ageing role of curcumin and discuss its senolytic potential. Full article
(This article belongs to the Special Issue Curcumin in Health and Disease)
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25 pages, 4934 KiB  
Article
The Impact of the C-Terminal Region on the Interaction of Topoisomerase II Alpha with Mitotic Chromatin
by Melissa Antoniou-Kourounioti, Michael L. Mimmack, Andrew C.G. Porter and Christine J. Farr
Int. J. Mol. Sci. 2019, 20(5), 1238; https://doi.org/10.3390/ijms20051238 - 12 Mar 2019
Cited by 23 | Viewed by 5133
Abstract
Type II topoisomerase enzymes are essential for resolving DNA topology problems arising through various aspects of DNA metabolism. In vertebrates two isoforms are present, one of which (TOP2A) accumulates on chromatin during mitosis. Moreover, TOP2A targets the mitotic centromere during prophase, persisting there [...] Read more.
Type II topoisomerase enzymes are essential for resolving DNA topology problems arising through various aspects of DNA metabolism. In vertebrates two isoforms are present, one of which (TOP2A) accumulates on chromatin during mitosis. Moreover, TOP2A targets the mitotic centromere during prophase, persisting there until anaphase onset. It is the catalytically-dispensable C-terminal domain of TOP2 that is crucial in determining this isoform-specific behaviour. In this study we show that, in addition to the recently identified chromatin tether domain, several other features of the alpha-C-Terminal Domain (CTD). influence the mitotic localisation of TOP2A. Lysine 1240 is a major SUMOylation target in cycling human cells and the efficiency of this modification appears to be influenced by T1244 and S1247 phosphorylation. Replacement of K1240 by arginine results in fewer cells displaying centromeric TOP2A accumulation during prometaphase-metaphase. The same phenotype is displayed by cells expressing TOP2A in which either of the mitotic phosphorylation sites S1213 or S1247 has been substituted by alanine. Conversely, constitutive modification of TOP2A by fusion to SUMO2 exerts the opposite effect. FRAP analysis of protein mobility indicates that post-translational modification of TOP2A can influence the enzyme’s residence time on mitotic chromatin, as well as its subcellular localisation. Full article
(This article belongs to the Collection Feature Papers in “Molecular Biology”)
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13 pages, 1435 KiB  
Article
CXCR2: A Novel Mediator of Mammary Tumor Bone Metastasis
by Bhawna Sharma, Kalyan C. Nannuru, Sugandha Saxena, Michelle L. Varney and Rakesh K. Singh
Int. J. Mol. Sci. 2019, 20(5), 1237; https://doi.org/10.3390/ijms20051237 - 12 Mar 2019
Cited by 13 | Viewed by 4085
Abstract
Most breast cancer patients die due to bone metastasis. Although metastasis accounts for 5% of the breast cancer cases, it is responsible for most of the deaths. Sometimes even before the detection of a primary tumor, most of the patients have bone and [...] Read more.
Most breast cancer patients die due to bone metastasis. Although metastasis accounts for 5% of the breast cancer cases, it is responsible for most of the deaths. Sometimes even before the detection of a primary tumor, most of the patients have bone and lymph node metastasis. Moreover, at the time of death, breast cancer patients have the bulk of the tumor burden in their bones. Therapy options are available for the treatment of primary tumors, but there are minimal options for treating breast cancer patients who have bone metastasis. C-X-C motif chemokine receptor type 2 (CXCR2) receptor-mediated signaling has been shown to play a critical role during bone-related inflammations and its ligands C-X-C motif chemokine ligand 6 (CXCL6) and 8 (CXCL8) aid in the resorption of bone during bone metastasis. In this study, we tested the hypothesis that CXCR2 contributes to mammary tumor-induced osteolysis and bone metastasis. In the present study, we examined the role of both tumor cell-derived and host-derived CXCR2 in influencing mammary tumor cell bone metastasis. For understanding the role of tumor cell-derived CXCR2, we utilized Cl66 CXCR2 knockdown (Cl66-shCXCR2) and Cl66-Control cells (Cl66-Control) and observed a significant decrease in tumor growth and tumor-induced osteolysis in Cl66-shCXCR2 cells in comparison with the Cl66-Control cells. Next, for understanding the role of host-derived CXCR2, we utilized mice with genomic knockdown of CXCR2 (Cxcr2−/−) and injected Cl66-Luciferase (Cl66-Luc) or 4T1-Luciferase (4T1-Luc) cells. We observed decreased bone destruction and metastasis in the bone of Cxcr2−/− mice. Our data suggest the importance of both tumor cell- and host-derived CXCR2 signaling in the bone metastasis of breast cancer cells. Full article
(This article belongs to the Special Issue Tumor Bone Microenvironment, Bone Turnover and Stem Cell)
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12 pages, 2198 KiB  
Article
Compromised Chondrocyte Differentiation Capacity in TERC Knockout Mouse Embryonic Stem Cells Derived by Somatic Cell Nuclear Transfer
by Wei-Fang Chang, Yun-Hsin Wu, Jie Xu and Li-Ying Sung
Int. J. Mol. Sci. 2019, 20(5), 1236; https://doi.org/10.3390/ijms20051236 - 12 Mar 2019
Cited by 6 | Viewed by 4212
Abstract
Mammalian telomere lengths are primarily regulated by telomerase, consisting of a reverse transcriptase protein (TERT) and an RNA subunit (TERC). We previously reported the generation of mouse Terc+/− and Terc−/− embryonic stem cells (ntESCs) by somatic cell nuclear transfer. [...] Read more.
Mammalian telomere lengths are primarily regulated by telomerase, consisting of a reverse transcriptase protein (TERT) and an RNA subunit (TERC). We previously reported the generation of mouse Terc+/− and Terc−/− embryonic stem cells (ntESCs) by somatic cell nuclear transfer. In the present work, we investigated the germ layer development competence of Terc−/−, Terc+/− and wild-type (Terc+/+) ntESCs. The telomere lengths are longest in wild-type but shortest in Terc−/− ntESCs, and correlate reversely with the population doubling time. Interestingly, while in vitro embryoid body (EB) differentiation assay reveals EB size difference among ntESCs of different genotypes, the more stringent in vivo teratoma assay demonstrates that Terc−/− ntESCs are severely defective in differentiating into the mesodermal lineage cartilage. Consistently, in a directed in vitro chondrocyte differentiation assay, the Terc−/− cells failed in forming Collagen II expressing cells. These findings underscore the significance in maintaining proper telomere lengths in stem cells and their derivatives for regenerative medicine. Full article
(This article belongs to the Special Issue Role of Telomeres and Telomerase in Cancer and Aging 2019)
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14 pages, 4126 KiB  
Article
Detection of Inflammation-Related Melanoma Small Extracellular Vesicle (sEV) mRNA Content Using Primary Melanocyte sEVs as a Reference
by Gina T. Bardi, Numan Al-Rayan, Jamaal L. Richie, Kavitha Yaddanapudi and Joshua L. Hood
Int. J. Mol. Sci. 2019, 20(5), 1235; https://doi.org/10.3390/ijms20051235 - 12 Mar 2019
Cited by 18 | Viewed by 4667
Abstract
Melanoma-derived small extracellular vesicles (sEVs) participate in tumor pathogenesis. Tumor pathogenesis is highly dependent on inflammatory processes. Given the potential for melanoma sEVs to carry tumor biomarkers, we explored the hypothesis that they may contain inflammation-related mRNA content. Biophysical characterization showed that human [...] Read more.
Melanoma-derived small extracellular vesicles (sEVs) participate in tumor pathogenesis. Tumor pathogenesis is highly dependent on inflammatory processes. Given the potential for melanoma sEVs to carry tumor biomarkers, we explored the hypothesis that they may contain inflammation-related mRNA content. Biophysical characterization showed that human primary melanocyte-derived sEVs trended toward being smaller and having less negative (more neutral) zeta potential than human melanoma sEVs (A-375, SKMEL-28, and C-32). Using primary melanocyte sEVs as the control population, RT-qPCR array results demonstrated similarities and differences in gene expression between melanoma sEV types. Upregulation of pro-angiogenic chemokine ligand CXCL1, CXCL2, and CXCL8 mRNAs in A-375 and SKMEL-28 melanoma sEVs was the most consistent finding. This paralleled increased production of CXCL1, CXCL2, and CXCL8 proteins by A-375 and SKMEL-28 sEV source cells. Overall, the use of primary melanocyte sEVs as a control sEV reference population facilitated the detection of inflammation-related melanoma sEV mRNA content. Full article
(This article belongs to the Special Issue Focus on Exosome-Based Cell-Cell Communication in Health and Disease)
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15 pages, 2359 KiB  
Article
Phylogeography of the Assassin Bug Sphedanolestes impressicollis in East Asia Inferred From Mitochondrial and Nuclear Gene Sequences
by Zhenyong Du, Tadashi Ishikawa, Hui Liu, Satoshi Kamitani, Osamu Tadauchi, Wanzhi Cai and Hu Li
Int. J. Mol. Sci. 2019, 20(5), 1234; https://doi.org/10.3390/ijms20051234 - 12 Mar 2019
Cited by 12 | Viewed by 3838
Abstract
The assassin bug, Sphedanolestes impressicollis (Hemiptera: Reduviidae), is widely distributed in East Asia. It is an ideal model for evaluating the effects of climatic fluctuation and geographical events on the distribution patterns of East Asian reduviids. Here, we used two mitochondrial genes and [...] Read more.
The assassin bug, Sphedanolestes impressicollis (Hemiptera: Reduviidae), is widely distributed in East Asia. It is an ideal model for evaluating the effects of climatic fluctuation and geographical events on the distribution patterns of East Asian reduviids. Here, we used two mitochondrial genes and one nuclear gene to investigate the phylogeographic pattern of the assassin bug based on comprehensive sampling in China, Japan, South Korea, Vietnam, and Laos. High levels of genetic differentiation were detected among the geographic populations classified into the northern and southern groups. A significant correlation was detected between genetic and geographical distances. The East China Sea land bridge served as a “dispersal corridor” during Pleistocene glaciation. The estimated divergence time indicated that the northern group may have separated from the eastern Chinese populations when the sea level rapidly rose during the “Ryukyu Coral Sea Stage” and the East China Sea land bridge was completely submerged. Demographic history and ecological niche modeling suggested that appropriate climatic conditions may have accounted for the rapid spread across the Korean Peninsula and Japan during the late Pleistocene. Our study underscores the pivotal roles of the Pleistocene sea level changes and climatic fluctuations in determining the distribution patterns of East Asian reduviids. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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19 pages, 6843 KiB  
Article
Combining Mechanochemistry and Spray Congealing for New Praziquantel Pediatric Formulations in Schistosomiasis Treatment
by Beatrice Albertini, Beatrice Perissutti, Serena Bertoni, Debora Zanolla, Erica Franceschinis, Dario Voinovich, Flavio Lombardo, Jennifer Keiser and Nadia Passerini
Int. J. Mol. Sci. 2019, 20(5), 1233; https://doi.org/10.3390/ijms20051233 - 12 Mar 2019
Cited by 11 | Viewed by 4690
Abstract
Praziquantel (PZQ) is the first line drug for the treatment of schistosome infections and is included in the WHO Model List of Essential Medicines for Children. In this study, the association of mechanochemical activation (MA) and the spray congealing (SC) technology was evaluated [...] Read more.
Praziquantel (PZQ) is the first line drug for the treatment of schistosome infections and is included in the WHO Model List of Essential Medicines for Children. In this study, the association of mechanochemical activation (MA) and the spray congealing (SC) technology was evaluated for developing a child-friendly PZQ dosage form, with better product handling and biopharmaceutical properties, compared to MA materials. A 1:1 by wt PZQ—Povidone coground—was prepared in a vibrational mill under cryogenic conditions, for favoring amorphization. PZQ was neat ground to obtain its polymorphic form (Form B), which has an improved solubility and bioactivity. Then, activated PZQ powders were loaded into microparticles (MPs) by the SC technology, using the self-emulsifying agent Gelucire® 50/13 as a carrier. Both, the activated powders and the corresponding loaded MPs were characterized for morphology, wettability, solubility, dissolution behavior, drug content, and drug solid state (Hot Stage Microscopy (HSM), Differential Scanning Calorimetry (DSC), X-Ray Powder Diffraction Studies (PXRD), and FT-IR). Samples were also in vitro tested for a comparison with PZQ against Schistosoma mansoni newly transformed schistosomula (NTS) and adults. MPs containing both MA systems showed a further increase of biopharmaceutical properties, compared to the milled powders, while maintaining PZQ bioactivity. MPs containing PZQ Form B represented the most promising product for designing a new PZQ formulation. Full article
(This article belongs to the Special Issue Paediatric Formulation: Design and Development)
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11 pages, 1389 KiB  
Article
Potential Functions of the Gastrointestinal Microbiome Inhabiting the Length of the Rat Digest Tract
by Dongyao Li, Haiqin Chen, Jianxin Zhao, Hao Zhang and Wei Chen
Int. J. Mol. Sci. 2019, 20(5), 1232; https://doi.org/10.3390/ijms20051232 - 12 Mar 2019
Cited by 4 | Viewed by 5747
Abstract
The rat is an important model animal used frequently in biological researches exploring the correlations between gut microbiome and a wide array of diseases. In this study, we used an extended ancestral-state reconstruction algorithm to predict the functional capabilities of the rat gastrointestinal [...] Read more.
The rat is an important model animal used frequently in biological researches exploring the correlations between gut microbiome and a wide array of diseases. In this study, we used an extended ancestral-state reconstruction algorithm to predict the functional capabilities of the rat gastrointestinal microbiome. Our results indicate an apparent tendency toward metabolic heterogeneity along the longitudinal and transverse axes of the rat gastrointestinal tract (GIT). This heterogeneity was suggested by the enriched small-molecule transport activity and amino acid metabolism in the upper GIT, the aerobic energy metabolism in the stomach and the mucolysis-related metabolism in the lower GIT mucus layer. In contrast to prior results, many functional overlaps were observed when the gastrointestinal microbiomes of different hosts were compared. These overlaps implied that although both the biogeographic location and host genotype were prominent driving forces in shaping the gastrointestinal microbiota, the microbiome functions were similar across hosts when observed under similar physicochemical conditions at identical anatomical sites. Our work effectively complements the rat microbial biogeography dataset we released in 2017 and, thus, contributes to a better understanding and prediction of disease-related alterations in microbial community function. Full article
(This article belongs to the Section Molecular Microbiology)
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17 pages, 5350 KiB  
Article
Pharmacokinetic and Metabolomic Studies with BIO 300, a Nanosuspension of Genistein, in a Nonhuman Primate Model
by Amrita K. Cheema, Khyati Y. Mehta, Paola T. Santiago, Oluseyi O. Fatanmi, Michael D. Kaytor and Vijay K. Singh
Int. J. Mol. Sci. 2019, 20(5), 1231; https://doi.org/10.3390/ijms20051231 - 12 Mar 2019
Cited by 26 | Viewed by 4411
Abstract
Genistein is a naturally occurring phytoestrogen isoflavone and is the active drug ingredient in BIO 300, a radiation countermeasure under advanced development for acute radiation syndrome (H-ARS) and for the delayed effects of acute radiation exposure (DEARE). Here we have assessed the pharmacokinetics [...] Read more.
Genistein is a naturally occurring phytoestrogen isoflavone and is the active drug ingredient in BIO 300, a radiation countermeasure under advanced development for acute radiation syndrome (H-ARS) and for the delayed effects of acute radiation exposure (DEARE). Here we have assessed the pharmacokinetics (PK) and safety of BIO 300 in the nonhuman primate (NHP). In addition, we analyzed serum samples from animals receiving a single dose of BIO 300 for global metabolomic changes using ultra-performance liquid chromatography (UPLC) quadrupole time-of-flight mass spectrometry (QTOF-MS). We present a comparison of how either intramuscularly (im) or orally (po) administered BIO 300 changed the metabolomic profile. We observed transient alterations in phenylalanine, tyrosine, glycerophosphocholine, and glycerophosphoserine which reverted back to near-normal levels 7 days after drug administration. We found a significant overlap in the metabolite profile changes induced by each route of administration; with the po route showing fewer metabolic alterations. Taken together, our results suggest that the administration of BIO 300 results in metabolic shifts that could provide an overall advantage to combat radiation injury. This initial assessment also highlights the utility of metabolomics and lipidomics to determine the underlying physiological mechanisms involved in the radioprotective efficacy of BIO 300. Full article
(This article belongs to the Section Molecular Biology)
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18 pages, 5089 KiB  
Article
Cytarabine-Resistant FLT3-ITD Leukemia Cells are Associated with TP53 Mutation and Multiple Pathway Alterations—Possible Therapeutic Efficacy of Cabozantinib
by Ya-Chen Ko, Chung-Yi Hu, Zheng-Hau Liu, Hwei-Fang Tien, Da-Liang Ou, Hsiung-Fei Chien and Liang-In Lin
Int. J. Mol. Sci. 2019, 20(5), 1230; https://doi.org/10.3390/ijms20051230 - 11 Mar 2019
Cited by 6 | Viewed by 4903
Abstract
Internal tandem duplication of FLT3 juxtamembrane domain (FLT3-ITD)-positive acute myeloid leukemia (AML) leads to poor clinical outcomes after chemotherapy. We aimed to establish a cytarabine-resistant line from FLT3-ITD-positive MV4-11 (MV4-11-P) cells and examine the development of resistance. The FLT3-ITD [...] Read more.
Internal tandem duplication of FLT3 juxtamembrane domain (FLT3-ITD)-positive acute myeloid leukemia (AML) leads to poor clinical outcomes after chemotherapy. We aimed to establish a cytarabine-resistant line from FLT3-ITD-positive MV4-11 (MV4-11-P) cells and examine the development of resistance. The FLT3-ITD mutation was retained in MV4-11-R; however, the protein was underglycosylated and less phosphorylated in these cells. Moreover, the phosphorylation of ERK1/2, Akt, MEK1/2 and p53 increased in MV4-11-R. The levels of Mcl-1 and p53 proteins were also elevated in MV4-11-R. A p53 D281G mutant emerged in MV4-11-R, in addition to the pre-existing R248W mutation. MV4-11-P and MV4-11-R showed similar sensitivity to cabozantinib, sorafenib, and MK2206, whereas MV4-11-R showed resistance to CI-1040 and idarubicin. MV4-11-R resistance may be associated with inhibition of Akt phosphorylation, but not ERK phosphorylation, after exposure to these drugs. The multi-kinase inhibitor cabozantinib inhibited FLT3-ITD signaling in MV4-11-R cells and MV4-11-R-derived tumors in mice. Cabozantinib effectively inhibited tumor growth and prolonged survival time in mice bearing MV4-11-R-derived tumors. Together, our findings suggest that Mcl-1 and Akt phosphorylation are potential therapeutic targets for p53 mutants and that cabozantinib is an effective treatment in cytarabine-resistant FLT3-ITD-positive AML. Full article
(This article belongs to the Special Issue Advances in Molecular Biology and Targeted Therapy of Leukemias)
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21 pages, 4003 KiB  
Article
Mitotic Catastrophe Induced in HeLa Tumor Cells by Photodynamic Therapy with Methyl-aminolevulinate
by Marta Mascaraque, Pablo Delgado-Wicke, Alejandra Damian, Silvia Rocío Lucena, Elisa Carrasco and Ángeles Juarranz
Int. J. Mol. Sci. 2019, 20(5), 1229; https://doi.org/10.3390/ijms20051229 - 11 Mar 2019
Cited by 13 | Viewed by 5803
Abstract
Photodynamic therapy (PDT) constitutes a cancer treatment modality based on the administration of a photosensitizer, which accumulates in tumor cells. The subsequent irradiation of the tumoral area triggers the formation of reactive oxygen species responsible for cancer cell death. One of the compounds [...] Read more.
Photodynamic therapy (PDT) constitutes a cancer treatment modality based on the administration of a photosensitizer, which accumulates in tumor cells. The subsequent irradiation of the tumoral area triggers the formation of reactive oxygen species responsible for cancer cell death. One of the compounds approved in clinical practice is methyl-aminolevulinate (MAL), a protoporphyrin IX (PpIX) precursor intermediate of heme synthesis. We have identified the mitotic catastrophe (MC) process after MAL-PDT in HeLa human carcinoma cells. The fluorescence microscopy revealed that PpIX was located mainly at plasma membrane and lysosomes of HeLa cells, although some fluorescence was also detected at endoplasmic reticulum and Golgi apparatus. Cell blockage at metaphase-anaphase transition was observed 24 h after PDT by phase contrast microscopy and flow cytometry. Mitotic apparatus components evaluation by immunofluorescence and Western blot indicated: multipolar spindles and disorganized chromosomes in the equatorial plate accompanied with dispersion of centromeres and alterations in aurora kinase proteins. The mitotic blockage induced by MAL-PDT resembled that induced by two compounds used in chemotherapy, taxol and nocodazole, both targeting microtubules. The alterations in tumoral cells provided evidence of MC induced by MAL-PDT, resolving mainly by apoptosis, directly or through the formation of multinucleate cells. Full article
(This article belongs to the Special Issue Cell Targets and Toxicity)
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11 pages, 2040 KiB  
Article
Discovery of Galangin as a Potential DPP-4 Inhibitor That Improves Insulin-Stimulated Skeletal Muscle Glucose Uptake: A Combinational Therapy for Diabetes
by Poonam Kalhotra, Veera C. S. R. Chittepu, Guillermo Osorio-Revilla and Tzayhri Gallardo-Velázquez
Int. J. Mol. Sci. 2019, 20(5), 1228; https://doi.org/10.3390/ijms20051228 - 11 Mar 2019
Cited by 32 | Viewed by 4951
Abstract
Dipeptidyl peptidase-4 (DPP-4) is a well-known therapeutic drug target proven to reduce blood glucose levels in diabetes mellitus, and clinically, DPP-4 inhibitors are used in combination with other anti-diabetic agents. However, side effects and skeletal muscle health are not considered in the treatment [...] Read more.
Dipeptidyl peptidase-4 (DPP-4) is a well-known therapeutic drug target proven to reduce blood glucose levels in diabetes mellitus, and clinically, DPP-4 inhibitors are used in combination with other anti-diabetic agents. However, side effects and skeletal muscle health are not considered in the treatment for diabetic patients. Recently, natural compounds have been proven to inhibit DPP-4 with fewer side effects. In this work, initially, molecular docking simulations revealed that a natural compound, Galangin, possess a binding energy of −24 KJ/mol and interaction residues SER 630 and TYR 547, that are responsible for potent DPP-4 inhibition. In vitro studies showed that galangin not only inhibits DPP-4 in a concentration-dependent manner but also regulates glucose levels, enabling the proliferation of rat L6 skeletal muscle cells. The combination of galangin with insulin benefits regulation of glucose levels significantly in comparison to galangin alone (p < 0.05). These findings suggest the beneficial effect of the use of galangin, both alone or in combination with insulin, to reduce glucose levels and improve skeletal muscle health in diabetes mellitus. Full article
(This article belongs to the Section Bioactives and Nutraceuticals)
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13 pages, 2335 KiB  
Article
Dietary Eriodictyol Alleviates Adiposity, Hepatic Steatosis, Insulin Resistance, and Inflammation in Diet-Induced Obese Mice
by Eun-Young Kwon and Myung-Sook Choi
Int. J. Mol. Sci. 2019, 20(5), 1227; https://doi.org/10.3390/ijms20051227 - 11 Mar 2019
Cited by 47 | Viewed by 5812
Abstract
The present study aimed to investigate the molecular mechanisms underlying the anti-obesity effect of flavonoid eriodictyol (ED) supplementation in mice fed with a high-fat diet (HFD). C57BL/6N mice were fed with normal diet (ND), HFD (40 kcal% fat), or HFD + 0.005% ( [...] Read more.
The present study aimed to investigate the molecular mechanisms underlying the anti-obesity effect of flavonoid eriodictyol (ED) supplementation in mice fed with a high-fat diet (HFD). C57BL/6N mice were fed with normal diet (ND), HFD (40 kcal% fat), or HFD + 0.005% (w/w) ED for 16 weeks. In HFD-induced obese mice, dietary ED supplementation significantly alleviated dyslipidemia and adiposity by downregulating the expression of lipogenesis-related genes in white adipose tissue (WAT), while enhancing fecal lipid excretion. ED additionally improved hepatic steatosis and decreased the production of pro-inflammatory cytokines by downregulating the expression of hepatic enzymes and the genes involved in lipogenesis and upregulating the expression of hepatic fatty acid oxidation-related enzymes and genes. In addition, ED improved insulin resistance (IR) by suppressing hepatic gluconeogenesis, enhancing glucose utilization, and modulating the production and release of two incretin hormones, namely gastric inhibitory polypeptide (GIP) and glucagon-like peptide-1 (GLP-1). Taken together, the current findings indicated that ED can protect against diet-induced obesity and related metabolic disturbances, including dyslipidemia, inflammation, fatty liver disease, and IR in diet-induced obese mice. Full article
(This article belongs to the Section Bioactives and Nutraceuticals)
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20 pages, 1253 KiB  
Review
Emerging Role of Eukaryote Ribosomes in Translational Control
by Nicole Dalla Venezia, Anne Vincent, Virginie Marcel, Frédéric Catez and Jean-Jacques Diaz
Int. J. Mol. Sci. 2019, 20(5), 1226; https://doi.org/10.3390/ijms20051226 - 11 Mar 2019
Cited by 48 | Viewed by 9727
Abstract
Translation is one of the final steps that regulate gene expression. The ribosome is the effector of translation through to its role in mRNA decoding and protein synthesis. Many mechanisms have been extensively described accounting for translational regulation. However it emerged only recently [...] Read more.
Translation is one of the final steps that regulate gene expression. The ribosome is the effector of translation through to its role in mRNA decoding and protein synthesis. Many mechanisms have been extensively described accounting for translational regulation. However it emerged only recently that ribosomes themselves could contribute to this regulation. Indeed, though it is well-known that the translational efficiency of the cell is linked to ribosome abundance, studies recently demonstrated that the composition of the ribosome could alter translation of specific mRNAs. Evidences suggest that according to the status, environment, development, or pathological conditions, cells produce different populations of ribosomes which differ in their ribosomal protein and/or RNA composition. Those observations gave rise to the concept of “specialized ribosomes”, which proposes that a unique ribosome composition determines the translational activity of this ribosome. The current review will present how technological advances have participated in the emergence of this concept, and to which extent the literature sustains this concept today. Full article
(This article belongs to the Special Issue Translational Control)
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21 pages, 8079 KiB  
Article
An Integrated Transcriptome and Proteome Analysis Reveals Putative Regulators of Adventitious Root Formation in Taxodium ‘Zhongshanshan’
by Zhiquan Wang, Jianfeng Hua, Yunlong Yin, Chunsun Gu, Chaoguang Yu, Qin Shi, Jinbo Guo, Lei Xuan and Fangyuan Yu
Int. J. Mol. Sci. 2019, 20(5), 1225; https://doi.org/10.3390/ijms20051225 - 11 Mar 2019
Cited by 42 | Viewed by 5108
Abstract
Adventitious root (AR) formation from cuttings is the primary manner for the commercial vegetative propagation of trees. Cuttings is also the main method for the vegetative reproduction of Taxodium ‘Zhongshanshan’, while knowledge of the molecular mechanisms regulating the processes is limited. Here, we [...] Read more.
Adventitious root (AR) formation from cuttings is the primary manner for the commercial vegetative propagation of trees. Cuttings is also the main method for the vegetative reproduction of Taxodium ‘Zhongshanshan’, while knowledge of the molecular mechanisms regulating the processes is limited. Here, we used mRNA sequencing and an isobaric tag for relative and absolute quantitation-based quantitative proteomic (iTRAQ) analysis to measure changes in gene and protein expression levels during AR formation in Taxodium ‘Zhongshanshan’. Three comparison groups were established to represent the three developmental stages in the AR formation process. At the transcript level, 4743 genes showed an expression difference in the comparison groups as detected by RNA sequencing. At the protein level, 4005 proteins differed in their relative abundance levels, as indicated by the quantitative proteomic analysis. A comparison of the transcriptome and proteome data revealed regulatory aspects of metabolism during AR formation and development. In summary, hormonal signal transduction is different at different developmental stages during AR formation. Other factors related to carbohydrate and energy metabolism and protein degradation and some transcription factor activity levels, were also correlated with AR formation. Studying the identified genes and proteins will provide further insights into the molecular mechanisms controlling AR formation. Full article
(This article belongs to the Special Issue Root Development in Plants)
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