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Functional genomics

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https://www.readbyqxmd.com/read/28214997/the-human-rit2-core-promoter-short-tandem-repeat-predominant-allele-is-species-specific-in-length-a-selective-advantage-for-human-evolution
#1
Babak Emamalizadeh, Abofazl Movafagh, Hossein Darvish, Somayeh Kazeminasab, Monavvar Andarva, Pegah Namdar-Aligoodarzi, Mina Ohadi
Evolutionary analyses of the critical core promoter interval support a selective advantage for expanding the length of certain short tandem repeats (STRs) in humans. We recently reported genome-wide data on human core promoter STRs that are "exceptionally long" (≥6-repeats). Near the top of the list, the neuron-specific gene, RIT2, contains one of the longest GA-STRs at 11-repeats. In the present study, we analyzed the evolutionary implications of this STR across species. We also studied this STR in a sample of 2,143 Iranian human subjects that encompassed a number of neuropsychiatric disorders and controls...
February 18, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28214915/evaluation-of-the-gard-assay-in-a-blind-cosmetics-europe-study
#2
Henrik Johansson, Robin Gradin, Andy Forreryd, Maria Agemark, Kathrin Zeller, Angelica Johansson, Olivia Larne, Erwin van Vliet, Carl Borrebaeck, Malin Lindstedt
Chemical hypersensitivity is an immunological response towards foreign substances, commonly referred to as sensitizers, which gives rise primarily to the clinical symptoms known as allergic contact dermatitis. For the purpose of mitigating risks associated with consumer products, chemicals are screened for sensitizing effects. Historically, such predictive screenings have been performed using animal models. However, due to industrial and regulatory demand, animal models for the purpose of sensitization assessment are being replaced by animal-free testing methods, a global trend that is spreading across industries and market segments...
February 17, 2017: ALTEX
https://www.readbyqxmd.com/read/28214593/jak-stat-pathway-directed-therapy-of-t-cell-leukemia-lymphoma-inspired-by-functional-and-structural-genomics
#3
REVIEW
Thomas A Waldmann
Abnormal activation of the γc cytokine JAK/STAT signaling pathway assessed by STAT3 or STAT5b phosphorylation was present in a proportion of many T-cell malignancies. Activating mutations of STAT3/STAT5b and JAK1/3 were present in some but not in all cases with constitutive signaling pathway activation. Using shRNA analysis pSTAT malignant T-cell lines were addicted to JAKs/STATs whether they were mutated or not. Activating JAK/STAT mutations were not sufficient to support leukemic cell proliferation but only augmented upstream pathway signals...
February 15, 2017: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/28214592/role-of-a-p53-polymorphism-in-the-development-of-nonfunctional-pituitary-adenomas
#4
Garima Yagnik, Arman Jahangiri, Rebecca Chen, Jeffrey R Wagner, Manish K Aghi
Non-functional pituitary adenomas (NFPAs) are among the commonest intracranial neoplasms. While histologically benign, NFPAs sometimes become large enough to limit therapeutic options and reduce quality of life. Investigations of the molecular etiology of NFPAs have failed to identify prevalent genetic changes and, while a role for p53 has been suggested, TP53 gene alterations have yet to be described in NFPAs. We found that the polymorphism rs1042522:C > G in codon 72 of exon 4 of the TP53 gene, whose C variant produces a proline and is more common in most ethnicities, has a G variant producing an arginine in 79...
February 15, 2017: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/28214526/recent-advances-in-human-genetics-and-epigenetics-of-adiposity-pathway-to-precision-medicine
#5
Tove Fall, Michael Mendelson, Elizabeth K Speliotes
Obesity is a heritable trait that contributes to substantial global morbidity and mortality. Here, we summarize findings from the last decade of genetic and epigenetic research focused on unravelling the underpinnings of adiposity. More than 140 genetic regions are now known to influence adiposity traits. The genetics of general adiposity, as measured by body mass index, and that of abdominal obesity, as measured by waist to hip ratio, have distinct biological backgrounds. Expression of genes associated with general adiposity are enriched in the nervous system...
February 15, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28214512/dynamics-and-context-dependent-roles-of-dna-methylation
#6
REVIEW
Christina Ambrosi, Massimiliano Manzo, Tuncay Baubec
DNA methylation is one of the most extensively studied epigenetic marks. It is involved in transcriptional gene silencing, it plays important roles during mammalian development and its perturbation is often associated with human diseases. In mammalian genomes, DNA methylation is a prevalent modification that decorates the majority of cytosines. It is found at the promoters and enhancers of inactive genes, at repetitive elements and within transcribed gene bodies. Its presence at promoters is dynamically linked to gene activity, suggesting that it could directly influence gene expression patterns and cellular identity...
February 15, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28214218/implication-of-downregulation-and-prospective-pathway-signaling-of-microrna-375-in-lung-squamous-cell-carcinoma
#7
Wen-Jie Chen, Ting-Qing Gan, Hui Qin, Su-Ning Huang, Li-Hua Yang, Ye-Ying Fang, Zu-Yun Li, Lin-Jiang Pan, Gang Chen
BACKGROUND: Lung cancer is one of the most typical cancers in the world. Altered expression profiles of microRNA-375(miR-375) are linked to many diseases including lung cancer. However, the relationship between miR-375 and lung squamous cell carcinoma (LUSC) is controversial. METHODS: We first evaluated the 23 LUSCs and the paired normal lung tissues by qRT-PCR. Then we analyzed the LUSC samples with miR-375 expression based on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO)...
January 22, 2017: Pathology, Research and Practice
https://www.readbyqxmd.com/read/28213959/combining-induced-pluripotent-stem-cells-and-genome-editing-technologies-for-clinical-applications
#8
Chia-Yu Chang, Hsiao-Chien Ting, Hong-Lin Su, Jing-Ren Jeng
In this review, we introduce current developments in induced pluripotent stem cells (iPSCs), site-specific nuclease (SSN)-mediated genome editing tools, and the combined application of these two novel technologies in biomedical research and therapeutic trials. The sustainable pluripotent property of iPSCs in vitro not only provides unlimited cell sources for basic research but also benefits precision medicines for human diseases. In addition, rapidly evolving SSN tools efficiently tailor genetic manipulations for exploring gene functions and can be utilized to correct genetic defects of congenital diseases in the near future...
February 17, 2017: Cell Transplantation
https://www.readbyqxmd.com/read/28213905/a-ten-gene-containing-genomic-island-determines-flagellin-glycosylation-implication-for-its-regulatory-role-in-motility-and-virulence-of-xanthomonas-oryzae-pv-oryzae
#9
Chao Yu, Huamin Chen, Fang Tian, Fenghuan Yang, Xiaochen Yuan, Ching-Hong Yang, Chenyang He
Flagellin glycosylation plays crucial roles in flagellar assembly, motility and virulence in several pathogenic bacteria. However, little is known about the genetic determinants and biological functions of flagellin glycosylation in Xanthomonas oryzae pv. oryzae (Xoo), the causal pathogen of bacterial blight of rice. Here, the structure, regulation and functions of a ten-gene cluster gigX (glycosylation island genes of Xoo), which was embedded in a flagellar regulon were characterized. gigX1 through gigX10, encoded putative enzymes or proteins involved in glycan biosynthesis and transfer, including a nucleotide sugar transaminase, an acyl-carrier protein (ACP), a 3-oxoacyl-ACP synthase, a 3-oxoacyl-ACP reductase, a dehydrogenase, an acetyltransferase, a ring hydroxylating dioxygenase, a hypothetical protein, a methyltransferanse, and a glycosyltransferase, respectively...
February 18, 2017: Molecular Plant Pathology
https://www.readbyqxmd.com/read/28213901/high-throughput-assays-to-assess-the-functional-impact-of-genetic-variants-a-road-towards-genomic-driven-medicine
#10
J Ipe, M Swart, K S Burgess, T C Skaar
No abstract text is available yet for this article.
February 18, 2017: Clinical and Translational Science
https://www.readbyqxmd.com/read/28213741/assembly-of-photoactive-orange-carotenoid-protein-from-its-domains-unravels-a-carotenoid-shuttle-mechanism
#11
Marcus Moldenhauer, Nikolai N Sluchanko, David Buhrke, Dmitry V Zlenko, Neslihan N Tavraz, Franz-Josef Schmitt, Peter Hildebrandt, Eugene G Maksimov, Thomas Friedrich
The photoswitchable orange carotenoid protein (OCP) is indispensable for cyanobacterial photoprotection by quenching phycobilisome fluorescence upon photoconversion from the orange OCP(O) to the red OCP(R) form. Cyanobacterial genomes frequently harbor, besides genes for orange carotenoid proteins (OCPs), several genes encoding homologs of OCP's N- or C-terminal domains (NTD, CTD). Unlike the well-studied NTD homologs, called Red Carotenoid Proteins (RCPs), the role of CTD homologs remains elusive. We show how OCP can be reassembled from its functional domains...
February 17, 2017: Photosynthesis Research
https://www.readbyqxmd.com/read/28213571/mir-146a-b-a-family-with-shared-seeds-and-different-roots
#12
Mark Paterson, Alison J Kriegel
MicroRNAs are small, non-coding, RNAs known for their powerful modulation of molecular processes, making them a major focus for studying pathological mechanisms. The human miR-146 family of microRNAs consists of two member genes - MIR146A and MIR146B These two miRNAs are located on different chromosomes and exhibit differential regulation in many cases. However, they are nearly identical in sequence and share a seed sequence, thus they are predicted to target the same set of genes. A large proportion of the miR-146 literature focuses on its role in regulating the innate immune response in the context of various pathologies by modulating two widely studied target genes in the toll-like receptor signaling cascade...
February 17, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28213570/blunted-transcriptional-response-to-skeletal-muscle-ischemia-in-rats-with-chronic-kidney-disease-potential-role-for-impaired-ischemia-induced-angiogenesis
#13
Rafael U Heiss, Fabian Fahlbusch, Johannes Jacobi, Christoph Daniel, Arif B Ekici, Nada Cordasic, Kerstin Amann, Andrea Hartner, Karl F Hilgers
Chronic kidney disease (CKD) is associated with increased cardiovascular morbidity and mortality. Previous studies indicated an impairment of ischemia-induced angiogenesis in skeletal muscle of rats with CKD. We performed a systematic comparison of early gene expression in response to ischemia in rats with or without CKD to identify potential molecular mechanisms underlying impaired angiogenesis in CKD. CKD was induced in male rats by 5/6 nephrectomy (SNX); control rats were sham operated (sham). Eight weeks later, ischemia of the right limb was induced by ligation and resection of the femoral artery...
February 17, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28213543/functional-characterization-of-a-28-kb-catabolic-island-from-pseudomonas-sp-m1-involved-in-biotransformation-of-%C3%AE-myrcene-and-related-plant-derived-volatiles
#14
Pedro Soares-Castro, Pedro Montenegro-Silva, Hermann J Heipieper, Pedro M Santos
Pseudomonas sp. M1 is able to mineralize highly hydrophobic and recalcitrant compounds such as benzene, phenol and their methylated/halogenated derivatives, as well as the backbone of several monoterpenes. The ability to use such spectrum of compounds as sole carbon source is, most probably, associated with a genetic background evolved under different environmental constraints. The outstanding performance of M1 strain regarding β-myrcene catabolism was elucidated in this work, with focus on the biocatalytical potential of β-myrcene-associated core-code, comprised in a 28-kb genomic island (GI), predicted to be organized in 8 transcriptional units...
February 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28213540/characterization-of-the-physical-and-functional-interplay-between-mazf1-bif-and-its-noncognate-antitoxins-from-bifidobacterium-longum
#15
Yanxia Wei, Yang Li, Fan Yang, Qiong Wu, Dianbin Liu, Xiangyang Li, Hui Hua, Xiaomei Liu, Yugang Wang, Kuiyang Zheng, Renxian Tang
Bifidobacterium longum strain JDM301, a widely used commercial strain in China, encodes at least two MazEF-like modules and one RelBE-like toxin-antitoxin (TA) systems in its chromosome, designated as MazE1F1(Bif), MazE2F2(Bif) and RelBE(Bif), respectively. Bacterial TA systems play an important role in several stress responses, but the relationship between these TA systems is largely unknown. In this study, the interaction between MazF1(Bif) and MazE2(Bif) or RelB(Bif) was assessed in B. longum strain JDM301...
February 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28213515/hendra-virus-fusion-protein-transmembrane-domain-contributes-to-pre-fusion-protein-stability
#16
Stacy Webb, Tamas Nagy, Hunter Moseley, Michael Fried, Rebecca Ellis Dutch
Enveloped viruses utilize fusion (F) proteins studding the surface of the virus to facilitate membrane fusion with a target cell membrane. Fusion of the viral envelope with a cellular membrane is required for release of viral genomic material so the virus can ultimately reproduce and spread. To drive fusion, the F protein undergoes an irreversible conformational change, transitioning from a meta-stable pre-fusion conformation to a more thermodynamically stable post-fusion structure. Understanding the elements which control stability of the pre-fusion state and triggering to the post-fusion conformation is important for understanding F protein function...
February 17, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28213503/inhibition-of-inflammatory-gene-transcription-by-il-10-is-associated-with-rapid-suppression-of-lipopolysaccharide-induced-enhancer-activation
#17
Evan A Conaway, Dalila C de Oliveira, Christine M McInnis, Scott B Snapper, Bruce H Horwitz
IL-10 limits the magnitude of inflammatory gene expression following microbial stimuli and is essential to prevent inflammatory disease; however, the molecular basis for IL-10-mediated inhibition remains elusive. Using a genome-wide approach, we demonstrate that inhibition of transcription is the primary mechanism for IL-10-mediated suppression in LPS-stimulated macrophages and that inhibited genes can be divided into two clusters. Genes in the first cluster are inhibited only if IL-10 is included early in the course of LPS stimulation and is strongly enriched for IFN-inducible genes...
February 17, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28213501/immature-lymphocytes-inhibit-rag1-and-rag2-transcription-and-v-d-j-recombination-in-response-to-dna-double-strand-breaks
#18
Megan R Fisher, Adrian Rivera-Reyes, Noah B Bloch, David G Schatz, Craig H Bassing
Mammalian cells have evolved a common DNA damage response (DDR) that sustains cellular function, maintains genomic integrity, and suppresses malignant transformation. In pre-B cells, DNA double-strand breaks (DSBs) induced at Igκ loci by the Rag1/Rag2 (RAG) endonuclease engage this DDR to modulate transcription of genes that regulate lymphocyte-specific processes. We previously reported that RAG DSBs induced at one Igκ allele signal through the ataxia telangiectasia mutated (ATM) kinase to feedback-inhibit RAG expression and RAG cleavage of the other Igκ allele...
February 17, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28213476/editing-of-mitochondrial-transcripts-nad3-and-cox2-by-dek10-is-essential-for-mitochondrial-function-and-maize-plant-development
#19
Weiwei Qi, Zhongrui Tian, Lei Lu, Xiuzu Chen, Xinze Chen, Wei Zhang, Rentao Song
Respiration, the core of mitochondrial metabolism, depends on the function of five respiratory complexes. Many respiratory chain related proteins are encoded by the mitochondrial genome and their RNAs undergo post-transcriptional modifications by nuclear genome expressed factors, including pentatricopeptide repeat (PPR) proteins. Maize defective kernel 10 (dek10) is a classic mutant with small kernels and delayed development. Through positional cloning we found that Dek10 encodes an E-subgroup PPR protein localized in mitochondria...
February 17, 2017: Genetics
https://www.readbyqxmd.com/read/28213447/the-drosophila-postsynaptic-deg-enac-channel-ppk29-contributes-to-excitatory-neurotransmission
#20
Alexis Hill, Xingguo Zheng, Xiling Li, Ross McKinney, Dion Dickman, Yehuda Ben-Shahar
The protein family of Degenerin/Epithelial Sodium Channels (DEG/ENaC) is comprised of diverse animal-specific, non-voltage-gated ion channels that play important roles in regulating cationic gradients across epithelial barriers. Some family members are also enriched in neural tissues in both vertebrates and invertebrates. However, the specific neurophysiological functions of most DEG/ENaC-encoding genes remain poorly understood. The fruit fly Drosophila melanogaster is an excellent model for deciphering the functions of DEG/ENaC genes because its genome encodes an exceptionally large number of DEG/ENaC subunits termed pickpocket (ppk) 1-31 Here we demonstrate that ppk29 contributes specifically to the postsynaptic modulation of excitatory synaptic transmission at the larval neuromuscular junction (NMJ)...
February 17, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
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