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Gene function prediction

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https://www.readbyqxmd.com/read/29454093/silencing-circular-rna-hsa_circ_0000977-suppresses-pancreatic-ductal-adenocarcinoma-progression-by-stimulating-mir-874-3p-and-inhibiting-plk1-expression
#1
Wen-Jie Huang, Yun-Chao Wang, Song-Song Liu, Jia-Li Yang, Shi-Xiang Guo, Li-Jiang Wang, Huai-Zhi Wang, Ying-Fang Fan
Circular RNAs (CircRNAs) are a novel type of endogenous noncoding RNAs that regulate target gene expression by interacting with microRNA (miRNA). Emerging evidence shows that dysregulation of circRNAs plays important roles in biological and pathological processes, including cancer development and progression. The functional role of circRNA in PDAC (pancreatic ductal adenocarcinoma) remains to be investigated. In this study, high throughput microarray assay revealed that hsa_circ_0000977 was aberrantly up-regulated in pancreatic cancer tissues; this was also validated by qRT-PCR...
February 14, 2018: Cancer Letters
https://www.readbyqxmd.com/read/29453395/the-genes-of-the-sulphoquinovose-catabolism-in-escherichia-coli-are-also-associated-with-a-previously-unknown-pathway-of-lactose-degradation
#2
Anna Kaznadzey, Pavel Shelyakin, Evgeniya Belousova, Aleksandra Eremina, Uliana Shvyreva, Darya Bykova, Vera Emelianenko, Anastasiya Korosteleva, Maria Tutukina, Mikhail S Gelfand
Comparative genomics analysis of conserved gene cassettes demonstrated resemblance between a recently described cassette of genes involved in sulphoquinovose degradation in Escherichia coli K-12 MG1655 and a Bacilli cassette linked with lactose degradation. Six genes from both cassettes had similar functions related to carbohydrate metabolism, namely, hydrolase, aldolase, kinase, isomerase, transporter, and transcription factor. The Escherichia coli sulphoglycolysis cassette was thus predicted to be associated with lactose degradation...
February 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29453334/%C3%AE-catenin-independent-regulation-of-wnt-target-genes-by-ror2-and-atf2-atf4-in-colon-cancer-cells
#3
Oksana Voloshanenko, Uwe Schwartz, Dominique Kranz, Benedikt Rauscher, Michael Linnebacher, Iris Augustin, Michael Boutros
Wnt signaling is an evolutionarily conserved signaling route required for development and homeostasis. While canonical, β-catenin-dependent Wnt signaling is well studied and has been linked to many forms of cancer, much less is known about the role of non-canonical, β-catenin-independent Wnt signaling. Here, we aimed at identifying a β-catenin-independent Wnt target gene signature in order to understand the functional significance of non-canonical signaling in colon cancer cells. Gene expression profiling was performed after silencing of key components of Wnt signaling pathway and an iterative signature algorithm was applied to predict pathway-dependent gene signatures...
February 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29453308/sex-specific-mechanisms-of-resistance-vessel-endothelial-dysfunction-induced-by-cardiometabolic-risk-factors
#4
Ana P Davel, Qing Lu, M Elizabeth Moss, Sitara Rao, Imran J Anwar, Jennifer J DuPont, Iris Z Jaffe
BACKGROUND: The incidence of obesity is rising, particularly among women. Microvascular dysfunction is more common with female sex, obesity, and hyperlipidemia and predicts adverse cardiovascular outcomes, but the molecular mechanisms are unclear. Because obesity is associated with mineralocorticoid receptor (MR) activation, we tested the hypothesis that MR in endothelial cells contribute to sex differences in resistance vessel dysfunction in response to cardiometabolic risk factors. METHODS AND RESULTS: Male and female endothelial cell-specific MR knockout mice and MR-intact littermates were randomized to high-fat-diet-induced obesity or obesity with hyperlipidemia induced by adeno-associated virus-based vector targeting transfer of the mutant stable form (DY mutation) of the human PCSK9 (proprotein convertase subtilisin/kexin type 9) gene and compared with control diet...
February 16, 2018: Journal of the American Heart Association
https://www.readbyqxmd.com/read/29452748/knockout-of-human-muscle-genes-revealed-by-large-scale-whole-exome-studies
#5
Stefano Schiaffino
Large scale whole-exome sequence studies have revealed that a number of individuals from different populations have predicted loss-of-function of different genes due to nonsense, frameshift, or canonical splice-site mutations. Surprisingly, many of these mutations do not apparently show the deleterious phenotypic consequences expected from gene knockout. These homozygous null mutations, when confirmed, can provide insight into human gene function and suggest novel approaches to correct gene dysfunction, as the lack of the expected disease phenotype may reflect the existence of modifier genes that reveal potential therapeutic targets...
February 10, 2018: Molecular Genetics and Metabolism
https://www.readbyqxmd.com/read/29452422/asynchronous-and-pathological-windows-of-implantation-two-causes-of-recurrent-implantation-failure
#6
P Sebastian-Leon, N Garrido, J Remohí, A Pellicer, P Diaz-Gimeno
STUDY QUESTION: Is endometrial recurrent implantation failure (RIF) only a matter of an asynchronous (displaced) window of implantation (WOI), or could it also be a pathological (disrupted) WOI? SUMMARY ANSWER: Our predictive results demonstrate that both displaced and disrupted WOIs exist and can present independently or together in the same RIF patient. WHAT IS KNOWN ALREADY: Since 2002, many gene expression signatures associated with endometrial receptivity and RIF have been described...
February 14, 2018: Human Reproduction
https://www.readbyqxmd.com/read/29452392/pbrit-gene-prioritization-by-correlating-functional-and-phenotypic-annotations-through-integrative-data-fusion
#7
Ajay Anand Kumar, Lut Van Laer, Maaike Alaerts, Amin Ardeshirdavani, Yves Moreau, Kris Laukens, Bart Loeys, Geert Vandeweyer, Inanc Birol
Motivation: Computational gene prioritization can aid in disease gene identification. Here, we propose pBRIT (prioritization using Bayesian Ridge regression and Information Theoretic model), a novel adaptive and scalable prioritization tool, integrating Pubmed abstracts, Gene Ontology, Sequence similarities, Mammalian and Human Phenotype Ontology, Pathway, Interactions, Disease Ontology, Gene Association database and Human Genome Epidemiology database, into the prediction model.We explore and address effects of sparsity and inter-feature dependencies within annotation sources, and the impact of bias towards specific annotations...
February 14, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29452344/overexpression-of-blm-promotes-dna-damage-and-increased-sensitivity-to-platinum-salts-in-triple-negative-breast-and-serous-ovarian-cancers
#8
N J Birkbak, Y Li, S Pathania, A Greene-Colozzi, M Dreze, C Bowman-Colin, Z Sztupinszki, M Krzystanek, M Diossy, N Tung, P D Ryan, J E Garber, D P Silver, J D Iglehart, Z C Wang, D Szuts, Z Szallasi, A L Richardson
Background: Platinum based therapy is an effective treatment for a subset of triple negative breast cancer and ovarian cancer patients. In order to increase response rate and decrease unnecessary use, robust biomarkers that predict response to therapy are needed. Patients and methods: We performed an integrated genomic approach combining differential analysis of gene expression and DNA copy number in sensitive compared to resistant triple negative breast cancers in two independent neoadjuvant cisplatin treated cohorts...
February 14, 2018: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29452225/seminars-in-cell-and-developmental-biology-human-dendritic-cell-immunodeficiencies
#9
REVIEW
Venetia Bigley, Urszula Cytlak, Matthew Collin
The critical functions of dendritic cells (DCs) in immunity and tolerance have been demonstrated in many animal models but their non-redundant roles in humans are more difficult to probe. Human primary immunodeficiency (PID), resulting from single gene mutations, may result in DC deficiency or dysfunction. This relatively recent recognition illuminates the in vivo role of human DCs and the pathophysiology of the associated clinical syndromes. In this review, the development and function of DCs as established in murine models and human in vitro systems, is discussed...
February 13, 2018: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/29452169/expression-patterns-of-toll-like-receptor-tlr-2-tlr-4-and-myeloid-differentiation-primary-response-gene-88-myd88-in-renal-transplant-patients-developing-allograft-dysfunction-a-cohort-study
#10
Morteza Hosseinzadeh, Pedram Ahmadpoor, Mir Saeed Yekaninejad, Fatemeh Pourrezagholi, Farshad Foroughi, Mina Ghorbanpour, Mehri Barabadi, Sanaz K Shahbaz, Ghasem Solgi, Aliakbar Amirzargar
This cohort intends to determine the sequential dynamic changes in Toll-like receptor (TLR)-4, TLR-2, and myeloid differentiation primary response gene 88 (MYD88) mRNA expressions in PBMCs and biopsy samples from kidney allograft recipients in relation to graft function. This study enrolled 52 renal transplant patients, 27 with well functioning graft (WFG) and 25 graft dysfunction (GD). Peripheral blood samples pre- and post-transplantation (days 2, 90 and 180) were collected to analyze mRNA expression levels of TLR-2, TLR-4, and MYD88 genes in relation to allograft function during one-year follow up...
February 13, 2018: Transplant Immunology
https://www.readbyqxmd.com/read/29452030/comparative-phylogenetic-and-expression-analysis-of-small-gtpases-families-in-legume-and-non-legume-plants
#11
Ana Claudia Flores, Virginia Dalla Via, Virginia Savy, Ulises Mancini Villagra, María Eugenia Zanetti, Flavio Blanco
BACKGROUND: Small monomeric GTPases act as molecular switches in several processes that involve polar cell growth, participating mainly in vesicle trafficking and cytoskeleton rearrangements. This gene superfamily has largely expanded in plants through evolution as compared with other Kingdoms, leading to the suggestion that members of each subfamily might have acquired new functions associated to plant-specific processes. Legume plants engage in a nitrogen-fixing symbiotic interaction with rhizobia in a process that involves polar growth processes associated with the infection throughout the root hair...
February 16, 2018: Plant Signaling & Behavior
https://www.readbyqxmd.com/read/29451876/comparative-genomic-analysis-of-the-multispecies-probiotic-marketed-product-vsl-3
#12
François P Douillard, Diego Mora, Robyn T Eijlander, Michiel Wels, Willem M de Vos
Several probiotic-marketed formulations available for the consumers contain live lactic acid bacteria and/or bifidobacteria. The multispecies product commercialized as VSL#3 has been used for treating various gastro-intestinal disorders. However, like many other products, the bacterial strains present in VSL#3 have only been characterized to a limited extent and their efficacy as well as their predicted mode of action remain unclear, preventing further applications or comparative studies. In this work, the genomes of all eight bacterial strains present in VSL#3 were sequenced and characterized, to advance insights into the possible mode of action of this product and also to serve as a basis for future work and trials...
2018: PloS One
https://www.readbyqxmd.com/read/29451334/microrna-profiling-between-bacillus-thuringiensis-cry1ab-susceptible-and-resistant-european-corn-borer-ostrinia-nubilalis-h%C3%A3-bner
#13
T Yu, X Li, B-S Coates, Q Zhang, B-D Siegfried, X Zhou
Transgenic maize hybrids that express insecticidal Bacillus thuringiensis (Bt) crystalline (Cry) protein toxins effectively protect against the European corn borer, Ostrinia nubilalis, a devastating maize pest. Field monitoring and laboratory selections have detected varying levels of O. nubilalis resistance to Cry1Ab toxin. MicroRNAs (miRNAs) are short noncoding RNAs that are involved in post-transcriptional gene regulation. Their potential roles in the evolution of Bt resistance, however, remain largely unknown...
February 16, 2018: Insect Molecular Biology
https://www.readbyqxmd.com/read/29449542/long-non-coding-rnas-in-ischemic-stroke
#14
REVIEW
Mei-Hua Bao, Vivian Szeto, Burton B Yang, Shu-Zhen Zhu, Hong-Shuo Sun, Zhong-Ping Feng
Stroke is one of the leading causes of mortality and disability worldwide. Uncovering the cellular and molecular pathophysiological processes in stroke have been a top priority. Long non-coding (lnc) RNAs play critical roles in different kinds of diseases. In recent years, a bulk of aberrantly expressed lncRNAs have been screened out in ischemic stroke patients or ischemia insulted animals using new technologies such as RNA-seq, deep sequencing, and microarrays. Nine specific lncRNAs, antisense non-coding RNA in the INK4 locus (ANRIL), metastasis-associate lung adenocarcinoma transcript 1 (MALAT1), N1LR, maternally expressed gene 3 (MEG3), H19, CaMK2D-associated transcript 1 (C2dat1), Fos downstream transcript (FosDT), small nucleolar RNA host gene 14 (SNHG14), and taurine-upregulated gene 1 (TUG1), were found increased in cerebral ischemic animals and/or oxygen-glucose deprived (OGD) cells...
February 15, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29449408/enhancer-rna-profiling-predicts-transcription-factor-activity
#15
Joseph G Azofeifa, Mary A Allen, Josephina R Hendrix, Timothy Read, Jonathan D Rubin, Robin D Dowell
Transcription factors (TFs) exert their regulatory influence through the binding of enhancers, resulting in coordination of gene expression programs. Active enhancers are often characterized by the presence of short, unstable transcripts termed enhancer RNAs (eRNAs). While their function remains unclear, we demonstrate that eRNAs are a powerful readout of TF activity. We infer sites of eRNA origination across hundreds of publicly available nascent transcription data sets and show that eRNAs initiate from sites of TF binding...
February 15, 2018: Genome Research
https://www.readbyqxmd.com/read/29449061/c4a-mrna-expression-in-pbmcs-predicts-the-presence-and-severity-of-delusions-in-schizophrenia-and-bipolar-disorder-with-psychosis
#16
Jennifer K Melbourne, Cherise Rosen, Benjamin Feiner, Rajiv P Sharma
Altered immune function is an established finding in psychotic disorders such as schizophrenia and bipolar disorder with psychosis, though its role in their development and progression remains to be understood. Evidence suggests altered JAK-STAT1 pathway activity in peripheral blood cells from participants with schizophrenia compared to controls. Activation of this pathway leads to increased expression of complement component 4A (C4A), which has recently been implicated in schizophrenia. Here, we examine mRNA expression of C4A in peripheral blood cells from participants with schizophrenia, bipolar disorder and controls...
February 12, 2018: Schizophrenia Research
https://www.readbyqxmd.com/read/29448248/lncrna-gas5-overexpression-reverses-lps-induced-inflammatory-injury-and-apoptosis-through-up-regulating-klf2-expression-in-atdc5-chondrocytes
#17
Feng Li, Jianguang Sun, Shilei Huang, Gao Su, Guofu Pi
BACKGROUND/AIMS: Osteoarthritis (OA) is the most frequently occurring joint disease and characterized by degeneration of cartilage. As the unique cell type in cartilage, chondrocytes play a crucial role during OA. Our study explored the influence of long non-coding RNA (lncRNA) growth arrest-specific transcript 5 (GAS5) on lipopolysaccharides (LPS)-induced injury in ATDC5 cells. METHODS: Cell viability, apoptosis and expression of inflammatory cytokines were all assessed to evaluate LPS-induce inflammatory injury...
February 9, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29448188/genotype-phenotype-and-in-silico-pathogenicity-analysis-of-hexb-mutations-panel-based-sequencing-for-differential-diagnosis-of-gangliosidosis
#18
Nejat Mahdieh, Sahar Mikaeeli, Ali Reza Tavasoli, Zahra Rezaei, Majid Maleki, Bahareh Rabbani
OBJECTIVES: Gangliosidosis is an inherited metabolic disorder causing neurodegeneration and motor regression. Preventive diagnosis is the first choice for the affected families due to lack of straightforward therapy. Genetic studies could confirm the diagnosis and help families for carrier screening and prenatal diagnosis. An update of HEXB gene variants concerning genotype, phenotype and in silico analysis are presented. PATIENTS AND METHODS: Panel based next generation sequencing and direct sequencing of four cases were performed to confirm the clinical diagnosis and for reproductive planning...
February 8, 2018: Clinical Neurology and Neurosurgery
https://www.readbyqxmd.com/read/29448053/biomarkers-of-operational-tolerance-following-kidney-transplantation-the-immune-tolerance-network-studies-of-spontaneously-tolerant-kidney-transplant-recipients
#19
REVIEW
Kenneth A Newell, Andrew B Adams, Laurence A Turka
Studies of kidney transplant recipients who have developed spontaneous and sustained tolerance have revealed an association with B cells. Unexpectedly tolerant individuals are characterized by increased numbers and frequencies of B cells in the blood and increased expression of genes associated with B cells in the blood and urine. Comparisons of the B cell repertoires of tolerant individuals and those receiving immunosuppression reveal that not only are the B cells more numerous but developmental differences result in a repertoire comprised of more naïve and transitional B cells in the tolerant cohort...
February 12, 2018: Human Immunology
https://www.readbyqxmd.com/read/29447243/differences-in-the-intestinal-microbiota-between-uninfected-piglets-and-piglets-infected-with-porcine-epidemic-diarrhea-virus
#20
Mei-Zhou Huang, Sheng-Yi Wang, Hui Wang, Dong-An Cui, Ya-Jun Yang, Xi-Wang Liu, Xiao-Jun Kong, Jian-Yong Li
Porcine epidemic diarrhea, a disastrous gastrointestinal disease, causes great financial losses due to its high infectivity, morbidity and mortality in suckling piglets despite the development and application of various vaccines. In this study, high-throughput sequencing was used to explore differences in the intestinal microbiota between uninfected piglets and piglets infected with porcine epidemic diarrhea virus (PEDV). The results revealed that the small intestinal microbiota of suckling piglets infected with PEDV showed low diversity and was dominated by Proteobacteria (49...
2018: PloS One
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