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Gene module

Joanna M Sadowska, Fei Wei, Jia Guo, Jordi Guillem-Marti, Maria-Pau Ginebra, Yin Xiao
Immune cells are sensitive to the microstructural and textural properties of materials. Tuning the structural features of synthetic bone grafts could be a valuable strategy to regulate the specific response of the immune system, which in turn modulates the activity of bone cells. The aim of this study was to analyse the effect of the structural characteristics of biomimetic calcium deficient hydroxyapatite (CDHA) on the innate immune response of macrophages and the subsequent impact on osteogenesis and osteoclastogenesis...
July 31, 2018: Biomaterials
Wen-Qi Dong, Hong-Jie Sun, Yu Zhang, Hong-Jun Lin, Jian-Rong Chen, Hua-Chang Hong
Low concentrations of arsenic (As) contamination in aquatic environment is a worldwide issue, which is of great concern. To evaluate the impact of low concentrations of As on zebrafish, we measured the growth, antioxidant enzymes including superoxide dismutase (SOD) and catalase (CAT), oxidative damage (malondialdehyde, MDA) and apoptosis-related genes (nrf2, p53 and c-jun) of adult zebrafish after exposing to different AsIII concentrations (0, 10, 50, 100 or 150 μg L-1 ) for 28 d. Results indicated that exposure to low AsIII concentrations decreased the zebrafish weight by 14%, increased the activities of SOD and CAT by 23-41% and 31-59%, decreased the contents of MDA by 29-54%, and modulated transcription of apoptosis related genes...
August 3, 2018: Chemosphere
Yumei Diao, Mohammed Ferdous-Ur Rahman, Yuri Vyatkin, Ani Azatyan, Georges St Laurent, Philipp Kapranov, Peter G Zaphiropoulos
Hedgehog (HH) signaling is involved in many physiological processes, and pathway deregulation can result in a wide range of malignancies. Glioma-associated oncogene 1 (GLI1) is a transcription factor and a terminal effector of the HH cascade. Despite its crucial role in tumorigenesis, our understanding of the GLI1 cellular targets is quite limited. In this study, we identified multiple new GLI1 target genes using a combination of different genomic surveys and then subjected them to in-depth validation in human cancer cell lines...
August 11, 2018: Molecular Oncology
Anne Riemann, Sarah Reime, Oliver Thews
Hypoxia can control the expression of miRNAs in tumors which play an important role for the control of the malignant behavior. The aim of the study was to analyze whether extracellular acidosis, a common feature of tumors, also has an impact on the miRNA expression in isolated cells as well as in solid tumors. MiRNA expression was analyzed in two rat tumor cell lines (AT1 prostate and Walker-256 mammary carcinomas) by NGS and qPCR. In vivo the same cell lines were implanted subcutaneously and the tumor pH was modulated by inspiratory hypoxia and inhibition of the respiratory chain...
August 11, 2018: International Journal of Cancer. Journal International du Cancer
Brad A Davidson, Shahzeb Hassan, Eric Joshua Garcia, Nahid Tayebi, Ellen Sidransky
Gaucher disease is an autosomal recessive lysosomal storage disorder resulting from mutations in the gene GBA1 that lead to a deficiency in the enzyme glucocerebrosidase. Accumulation of the enzyme's substrates, glucosylceramide and glucosylsphingosine, result in symptoms ranging from skeletal and visceral involvement to neurological manifestations. Nonetheless, there is significant variability in clinical presentations amongst patients, with limited correlation between genotype and phenotype. Contributing to this clinical variation are genetic modifiers that influence the phenotypic outcome of the disorder...
August 10, 2018: Human Mutation
Yihan Dong, Aurelio Teleman, Christoph Jedmowski, Markus Wirtz, Ruediger Hell
Low temperature is one of the most important environmental factors that affects global survival of humans and animals and equally importantly the distribution of plants and crop productivity. Survival of metazoan cells under cold stress requires regulation of the sensor-kinase Target Of Rapamycin (TOR). TOR controls growth of eukaryotic cells by adjusting anabolic and catabolic metabolism. Previous studies identified the Thyroid Adenoma Associated (THADA) gene as the major effect locus by positive selection in the evolution of modern human adapted to cold...
August 11, 2018: Plant Biology
Rachel Waller, Mark Murphy, Claire J Garwood, Luke Jennings, Paul R Heath, Annabelle Chambers, Fiona E Matthews, Carol Brayne, Paul G Ince, Stephen B Wharton, Julie E Simpson
Oxidative stress and oxidative DNA damage are early features of mild cognitive impairment and Alzheimer's disease (AD), occurring before the formation of classical AD neuropathology, and resulting from an imbalance between pro- and anti-oxidants. Astrocytes play a major neuroprotective role, producing high levels of anti-oxidants including metallothionein-I and -II (MT-I/II). In the present study we characterized the immunoreactive profile of MT-I/II in the temporal cortex of the Cognitive Function and Ageing Study (CFAS) aging population-representative neuropathology cohort, and examined H2 O2 -modulation of MT transcription by human astrocytes...
August 10, 2018: Glia
Kristina Keidel, Fabian Amman, Ilona Bibova, Jakub Drzmisek, Vladimir Benes, David Hot, Branislav Vecerek
Bordetella pertussis is the causative agent of human whooping cough (pertussis), a highly contagious respiratory disease which despite massive vaccination programs remains the major cause of infant morbidity and mortality. The requirement of the RNA chaperone Hfq for virulence of B. pertussis suggested that Hfq-dependent small regulatory RNAs are involved in the modulation of gene expression in this re-emerging pathogen. High through-put RNA sequencing revealed hundreds of putative non-coding RNAs including the RgtA sRNA...
August 10, 2018: RNA
Jiradej Makjaroen, Poorichaya Somparn, Kenneth Hodge, Witthaya Poomipak, Nattiya Hirankarn, Trairak Pisitkun
Interferon lambda (IFN-λ) is a relatively unexplored, yet promising anti-viral agent. IFN-λ has recently been tested in clinical trials of chronic hepatitis B virus infection (CHB), with the advantage that side effects may be limited compared with IFN-α, as IFN-λ receptors are found only in epithelial cells. To date, IFN-λ's downstream signaling pathway remains largely unelucidated, particularly via proteomics methods. Here, we report that IFN-λ3 inhibits HBV replication in HepG2.2.15 cells, reducing levels of both HBV transcripts and intracellular HBV DNA...
August 10, 2018: Molecular & Cellular Proteomics: MCP
Belal A Muhammad, Sheema Almozyan, Roya Babaei-Jadidi, Emenike K Onyido, Anas Saadeddin, Seyed Hossein Kashfi, Bradley Spencer-Dene, Mohammad Ilyas, Anbarasu Lourdusamy, Axel Behrens, Abdolrahman Shams Nateri
Wnt/β-catenin signaling plays a critical role during development of both normal and malignant colorectal cancer (CRC) tissues. Phosphorylation of β-catenin protein alters its trafficking and function. Such conventional allosteric regulation usually involves a highly specialized set of molecular interactions, which may specifically turn on a particular cell phenotype. This study identifies a novel transcription modulator with an FLYWCH/Zn-finger DNA-binding domain, called "FLYWCH1". Using a modified yeast-2-hybrid based Ras-Recruitment system, it is demonstrated that FLYWCH1 directly binds to unphosphorylated (nuclear) β-catenin efficiently suppressing the transcriptional activity of Wnt/β-catenin signaling that cannot be rescued by TCF4...
August 10, 2018: Molecular Cancer Research: MCR
Chanabasayya Vastrad, Basavaraj Vastrad
Therefore, the current study aimed to diagnose the genes associated in the pathogenesis of GBM. The differentially expressed genes (DEGs) were diagnosed using the limma software package. The ToppFun was used to perform pathway and Gene Ontology (GO) enrichment analysis of the DEGs. Protein-protein interaction (PPI) networks, extracted modules, miRNA-target genes regulatory network and miRNA-target genes regulatory network were used to obtain insight into the actions of DEGs. Survival analysis for DEGs carried out...
July 27, 2018: Pathology, Research and Practice
Yancun Yin, Maolei Xu, Ju Gao, Minjing Li
OBJECTIVE: Hepatocellular carcinoma (HCC) is one of the cancer types with poor prognosis. To effectively treat HCC, new molecular targets and therapeutic approaches must be identified. Alkaline ceramidase 3 (Acer3) hydrolyzed long-chain unsaturated ceramide to produce free fatty acids and sphingosine. However, whether and how Acer3 modulates progression of HCC remains largely unknown. METHODS: Acer3 mRNA levels in different types of human HCC samples or normal tissues were determined from Gene Expression across Normal and Tumor tissue (GENT) database...
July 27, 2018: Pathology, Research and Practice
Md Nazmul Haque, Il Soo Moon
BACKGROUND: The hippocampus is a vulnerable brain region that is implicated in learning and memory impairment by two pathophysiological features, that is, neurite regression and synaptic dysfunction, and stigmasterol (ST), a cholesterol-equivalent phytosterol, is known to facilitate neuromodulatory effects. PURPOSE: To investigate the neuromodulatory effects of ST on the development of central nervous system neurons and the molecular bases of these effects in primary hippocampal neurons...
July 15, 2018: Phytomedicine: International Journal of Phytotherapy and Phytopharmacology
Florian Gautier, Kateřina Eliášová, Jean-Charles Leplé, Zuzana Vondráková, Anne-Marie Lomenech, Claire Le Metté, Philippe Label, Guy Costa, Jean-François Trontin, Caroline Teyssier, Marie-Anne Lelu-Walter
BACKGROUND: To explore poorly understood differences between primary and subsequent somatic embryogenic lines of plants, we induced secondary (2ry ) and tertiary (3ry ) lines from cotyledonary somatic embryos (SEs) of two Douglas-fir genotypes: SD4 and TD17. The 2ry lines exhibited significantly higher embryogenic potential (SE yields) than the 1ry lines initiated from zygotic embryos (SD4, 2155 vs 477; TD17, 240 vs 29 g- 1 f.w.). Moreover, we observed similar differences in yield between 2ry and 3ry lines of SD4 (2400 vs 3921 g- 1 f...
August 10, 2018: BMC Plant Biology
Qiongfang Li, Bo Zhang, Naresh Kasoju, Jinmin Ma, Aidong Yang, Zhanfeng Cui, Hui Wang, Hua Ye
Variations in substrate chemistry and the micro-structure were shown to have a significant effect on the biology of human mesenchymal stromal cells (hMSCs). This occurs when differences in the surface properties indirectly modulate pathways within numerous signaling networks that control cell fate. To understand how the surface features affect hMSC gene expression, we performed RNA-sequencing analysis of bone marrow-derived hMSCs cultured on tissue culture-treated polystyrene (TCP) and poly(l-lactide) (PLLA) based substrates of differing topography (Fl: flat and Fs: fibrous) and chemistry (Pr: pristine and Am: aminated)...
August 9, 2018: International Journal of Molecular Sciences
Manuel Martínez-Bueno, Nina Oparina, Mikhail G Dozmorov, Miranda C Marion, Mary E Comeau, Gary Gilkeson, Diane Kamen, Michael Weisman, Jane Salmon, Joseph W McCune, John B Harley, Robert Kimberly, Judith A James, Joan Merrill, Courtney Montgomery, Carl D Langefeld, Marta E Alarcón-Riquelme
BANK1 is a susceptibility gene for several systemic autoimmune diseases in several populations. Using the genome-wide association study (GWAS) data from Europeans (EUR) and African Americans (AA), we performed an extensive fine mapping of ankyrin repeats 1 ( BANK1 ). To increase the SNP density, we used imputation followed by univariate and conditional analysis, combined with a haplotypic and expression quantitative trait locus (eQTL) analysis. The data from Europeans showed that the associated region was restricted to a minimal and dependent set of SNPs covering introns two and three, and exon two...
August 8, 2018: International Journal of Molecular Sciences
Julio Plaza-Díaz, Luis Fontana, Angel Gil
Maternal milk contains compounds that may affect newborn immunity. Among these are a group of oligosaccharides that are synthesized in the mammary gland from lactose; these oligosaccharides have been termed human milk oligosaccharides (HMOs). The amount of HMOs present in human milk is greater than the amount of protein. In fact, HMOs are the third-most abundant solid component in maternal milk after lactose and lipids, and are thus considered to be key components. The importance of HMOs may be explained by their inhibitory effects on the adhesion of microorganisms to the intestinal mucosa, the growth of pathogens through the production of bacteriocins and organic acids, and the expression of genes that are involved in inflammation...
August 8, 2018: Nutrients
Mariana A Ribeiro, Molly S Estill, Geysson J Fernandez, Leonardo N Moraes, Stephen A Krawetz, Wellerson R Scarano
Male fertility and spermatogenesis are directly linked to the Sertoli cell's ability to produce factors associated with germ cell development. Sertoli cells express receptors for FSH and testosterone, and are the major regulators of spermatogenesis. Recent studies report that regulatory RNA molecules, such as microRNAs (miRNAs), are able to modulate testicular function during spermatogenesis and that their altered expression may be involved in male infertility. miRNAs may play a role in the response to xenobiotics that have an adverse consequences to health...
August 7, 2018: Toxicology
Seungyeon Lee, Sungbin Park, Hyunkyung Lee, Dawoon Jeong, Juyeon Ham, Eun Ha Choi, Sun Jung Kim
Cold atmospheric plasma (CAP) has gained attention for use in cancer treatment owing to its ability to preferentially induce cancer cell death; however, the involved molecular mechanism remains to be elucidated. Herein, an epigenetic effect of CAP on cancer cells was examined by performing a genome-wide ChIP-seq for H3K4me3 in MCF-7 breast cancer cell line. Consequently, 899 genes showed significantly changed methylation level at H3K4 with constructing "Cellular Compromise, DNA Replication, Recombination, Repair, and Cell Cycle" as the top network...
August 7, 2018: Free Radical Biology & Medicine
Myles Brown
How diet and obesity impact diurnal changes in physiology remains unclear. In this issue of Cell, Guan et al. report that diet-induced obesity modulates the activity of circadian gene enhancers including those regulating lipid metabolism and show that the efficacy of lipid-lowering drugs depends on the time of administration.
August 9, 2018: Cell
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