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RNA metabolism

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https://www.readbyqxmd.com/read/29341863/distinct-gene-signatures-predict-insulin-resistance-in-young-mice-with-high-fat-diet-induced-obesity
#1
Katherine Chen, Alice Jih, Olivia Osborn, Sarah T Kavaler, Wenxian Fu, Roman Sasik, Rintaro Saito, Jane J Kim
Highly inbred C57BL/6 mice show wide variation in their degree of insulin resistance in response to diet-induced obesity even though they are almost genetically identical. Here we employed transcriptional profiling by RNA sequencing (RNA-Seq) of visceral adipose tissue (VAT) and liver in young mice to determine how gene expression patterns correlate with the later development of high-fat diet (HFD)-induced insulin resistance in adulthood. To accomplish this goal, we partially removed and banked tissues from pubertal mice...
January 8, 2018: Physiological Genomics
https://www.readbyqxmd.com/read/29340699/long-term-expression-of-glomerular-genes-in-diabetic-nephropathy
#2
Dominik Chittka, Bernhard Banas, Laura Lennartz, Franz Josef Putz, Kathrin Eidenschink, Sebastian Beck, Thomas Stempfl, Christoph Moehle, Simone Reichelt-Wurm, Miriam C Banas
Background: Although diabetic nephropathy (DN) is the most common cause for end-stage renal disease in western societies, its pathogenesis still remains largely unclear. A different gene pattern of diabetic and healthy kidney cells is one of the probable explanations. Numerous signalling pathways have emerged as important pathophysiological mechanisms for diabetes-induced renal injury. Methods: Glomerular cells, as podocytes or mesangial cells, are predominantly involved in the development of diabetic renal lesions...
January 11, 2018: Nephrology, Dialysis, Transplantation
https://www.readbyqxmd.com/read/29339782/loss-of-disease-tolerance-during-citrobacter-rodentium-infection-is-associated-with-impaired-epithelial-differentiation-and-hyperactivation-of-t-cell-responses
#3
Eugene Kang, Guangyan Zhou, Mitra Yousefi, Romain Cayrol, Jianguo Xia, Samantha Gruenheid
Citrobacter rodentium is an intestinal mouse pathogen widely used as a model to study the mucosal response to infection. Inbred mouse strains suffer one of two fates following infection: self-limiting colitis or fatal diarrheal disease. We previously reported that Rspo2 is a major genetic determinant of the outcome of C. rodentium infection; Rspo2 induction during infection of susceptible mice leads to loss of intestinal function and mortality. Rspo2 induction does not impact bacterial colonization, but rather, impedes the ability of the host to tolerate C...
January 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29338886/overweight-and-obesity-status-in-pregnant-women-are-related-to-intestinal-microbiota-and-serum-metabolic-and-inflammatory-profiles
#4
Noora Houttu, Kati Mokkala, Kirsi Laitinen
BACKGROUND: Overweight and obesity may predispose women to clinical complications during their pregnancy. We hypothesize that a higher degree of overweight status is related to a range of aberrations in biomarkers already in early pregnancy. Our objective was to investigate whether intestinal microbiota, serum metabolic and inflammatory profiles differ in relation to the degree of overweight status in pregnant women. METHODS: This study investigated 52 overweight and 47 obese pregnant women in early pregnancy...
December 27, 2017: Clinical Nutrition: Official Journal of the European Society of Parenteral and Enteral Nutrition
https://www.readbyqxmd.com/read/29338076/hypoxia-inducible-transcription-factors-hif1a-and-hif2a-increase-in-aging-mucosal-tissues
#5
J L Ebersole, M J Novak, L Orraca, J Martinez-Gonzalez, S Kirakodu, K C Chen, A Stromberg, O A Gonzalez
Hypoxia (ie. oxygen deprivation) activates the hypoxia-signaling pathway, primarily via hypoxia inducible transcription factors (HIF) for numerous target genes, which mediate angiogenesis, metabolism, coagulation, among other processes to try to replenish tissues with blood and oxygen. Hypoxia signaling dysregulation also commonly occurs during chronic inflammation. We sampled gingival tissues from rhesus monkeys (M. mulatta; 3-25 years old) and total RNA was isolated for microarray analysis. HIF1A, HIF1B, and HIF2A were significantly different in healthy aged tissues, and both HIF1A and HIF3A were positively correlated with aging...
January 16, 2018: Immunology
https://www.readbyqxmd.com/read/29337107/trna-derived-small-non-coding-rnas-in-human-disease
#6
Lei Zhu, Xuesha Liu, Wencheng Pu, Yong Peng
Besides attending protein synthesis, transfer RNA (tRNA) is an important regulatory non-coding RNA (ncRNA) that participates in various cellular processes, including cellular metabolism and cell death. Fragments generated from pre- or mature tRNAs by specific endonucleases cleavage (tRNA-derived small non-coding RNA [tsncRNAs]), rather than random degradation products, are newly defined functional small non-coding RNAs (sncRNAs). They can be regulated in bacteria, yeast, plants and animals to respond to stress conditions, resulting in regulation of gene expressions at both transcriptional and post-transcriptional level...
January 11, 2018: Cancer Letters
https://www.readbyqxmd.com/read/29336831/ultraviolet-radiation-significantly-enhances-the-molecular-response-to-dispersant-and-sweet-crude-oil-exposure-in-nematostella-vectensis
#7
Ann M Tarrant, Samantha L Payton, Adam M Reitzel, Danielle T Porter, Matthew J Jenny
Estuarine organisms are subjected to combinations of anthropogenic and natural stressors, which together can reduce an organisms' ability to respond to either stress or can potentiate or synergize the cellular impacts for individual stressors. Nematostella vectensis (starlet sea anemone) is a useful model for investigating novel and evolutionarily conserved cellular and molecular responses to environmental stress. Using RNA-seq, we assessed global changes in gene expression in Nematostella in response to dispersant and/or sweet crude oil exposure alone or combined with ultraviolet radiation (UV)...
January 4, 2018: Marine Environmental Research
https://www.readbyqxmd.com/read/29336564/benzophenone-4-promotes-the-growth-of-a-pseudomonas-sp-and-biogenic-oxidation-of-mn-ii
#8
Yangyang Chang, Yaohui Bai, Yang Huo, Jiuhui Qu
Interactions between microbes and micropollutants (MPs) play a crucial role in water purification or treatment. Current studies have generally focused on the direct degradation or co-metabolism of MPs. Considering the increasing interest in and importance of the roles of MPs in microbial metabolism, we adopted a Mn(II)-oxidizing Pseudomonas sp. QJX-1 using tyrosine (Tyr) as the sole carbon and nitrogen source to investigate the effects of seven MPs on its growth and function. Six MPs exhibited an inhibition effect on bacterial growth and Mn(II) oxidation...
January 16, 2018: Environmental Science & Technology
https://www.readbyqxmd.com/read/29336483/glucose-metabolism-during-in-vitro-maturation-of-mouse-oocytes-an-study-using-rna-interference
#9
Hong-Li Xie, Shuai Zhu, Jie Zhang, Jing Wen, Hong-Jie Yuan, Liu-Zhu Pan, Ming-Jiu Luo, Jing-He Tan
In previous studies on glucose metabolism during in vitro maturation, intact cumulus-oocyte complexes (COCs) were treated with enzyme inhibitors/activators. Because inhibitors/activators may have non-specificity and/or toxicity, and culture of COCs cannot differentiate whether glucose metabolism of cumulus cells (CCs) or that of the oocyte supports oocyte maturation, results from the previous studies must be verified by silencing genes in either CCs or cumulus-denuded oocytes (DOs). In this study, RNAi was adopted to specify the effects of glucose metabolism in CCs or DOs on oocyte maturation...
January 16, 2018: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29335913/analyzing-the-interactions-of-mrnas-mirnas-lncrnas-and-circrnas-to-predict-competing-endogenous-rna-networks-in-glioblastoma
#10
Yang Yuan, Li Jiaoming, Wang Xiang, Liu Yanhui, Jiang Shu, Gou Maling, Mao Qing
Cross-talk between competitive endogenous RNAs (ceRNAs) may play a critical role in revealing potential mechanisms of tumor development and physiology. Glioblastoma is the most common type of malignant primary brain tumor, and the mechanisms of tumor genesis and development in glioblastoma are unclear. Here, to investigate the role of non-coding RNAs and the ceRNA network in glioblastoma, we performed paired-end RNA sequencing and microarray analyses to obtain the expression profiles of mRNAs, lncRNAs, circRNAs and miRNAs...
January 15, 2018: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/29335535/a-multi-omics-study-of-the-grapevine-downy-mildew-plasmopara-viticola-pathosystem-unveils-a-complex-protein-coding-and-noncoding-based-arms-race-during-infection
#11
Matteo Brilli, Elisa Asquini, Mirko Moser, Pier Luigi Bianchedi, Michele Perazzolli, Azeddine Si-Ammour
Fungicides are applied intensively to prevent downy mildew infections of grapevines (Vitis vinifera) with high impact on the environment. In order to develop alternative strategies we sequenced the genome of the oomycete pathogen Plasmopara viticola causing this disease. We show that it derives from a Phytophthora-like ancestor that switched to obligate biotrophy by losing genes involved in nitrogen metabolism and γ-Aminobutyric acid catabolism. By combining multiple omics approaches we characterized the pathosystem and identified a RxLR effector that trigger an immune response in the wild species V...
January 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29335528/exd2-governs-germ-stem-cell-homeostasis-and-lifespan-by-promoting-mitoribosome-integrity-and-translation
#12
Joana Silva, Suvi Aivio, Philip A Knobel, Laura J Bailey, Andreu Casali, Maria Vinaixa, Isabel Garcia-Cao, Étienne Coyaud, Alexis A Jourdain, Pablo Pérez-Ferreros, Ana M Rojas, Albert Antolin-Fontes, Sara Samino-Gené, Brian Raught, Acaimo González-Reyes, Lluís Ribas de Pouplana, Aidan J Doherty, Oscar Yanes, Travis H Stracker
Mitochondria are subcellular organelles that are critical for meeting the bioenergetic and biosynthetic needs of the cell. Mitochondrial function relies on genes and RNA species encoded both in the nucleus and mitochondria, and on their coordinated translation, import and respiratory complex assembly. Here, we characterize EXD2 (exonuclease 3'-5' domain-containing 2), a nuclear-encoded gene, and show that it is targeted to the mitochondria and prevents the aberrant association of messenger RNAs with the mitochondrial ribosome...
January 15, 2018: Nature Cell Biology
https://www.readbyqxmd.com/read/29334613/reduced-mir-144-3p-expression-in-serum-and-bone-mediates-osteoporosis-pathogenesis-by-targeting-rank
#13
Chunqing Wang, Hanliang He, Yu Jiang, Liang Wang, Youjia Xu
Osteoblasts and osteoclasts are responsible for the formation and resorption of bone, respectively. An imbalance between these two processes results in a disease called osteoporosis, in which a decreased level of bone strength increases the risk of a bone fracture. MicroRNAs (miRNAs) are small non-coding RNA molecules of 18-25 nucleotides that have been previously shown to control bone metabolism by regulating osteoblast and osteoclast differentiation. In the present study, we detected the expression pattern of 10 miRNAs in patient serum samples, and identified six miRNAs altered expression in patients with osteoporosis relative to non-osteoporosis...
January 15, 2018: Biochemistry and Cell Biology, Biochimie et Biologie Cellulaire
https://www.readbyqxmd.com/read/29331924/gene-expression-patterns-regulating-the-seed-metabolism-in-relation-to-deterioration-ageing-of-primed-mung-bean-vigna-radiata-l-seeds
#14
Satyendra Nath Sharma, Ankita Maheshwari, Chitra Sharma, Nidhi Shukla
We are proposing mechanisms to account for the loss of viability (seed deterioration/ageing) and enhancement in seed quality (post-storage priming treatment). In order to understand the regulatory mechanism of these traits, we conducted controlled deterioration (CD) test for up to 8 d using primed mung bean seeds and examined how CD effects the expression of many genes, regulating the seed metabolism in relation to CD and priming. Germination declined progressively with increased duration of CD, and the priming treatment completely/partially reversed the inhibition depending on the duration of CD...
January 5, 2018: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29331464/somatic-cell-count-based-selection-reduces-susceptibility-to-energy-shortage-during-early-lactation-in-a-sheep-model
#15
J Bouvier-Muller, C Allain, F Enjalbert, Y Farizon, D Portes, G Foucras, R Rupp
During the transition from late gestation to early lactation ruminants experience a negative energy balance (NEB), which is considered to increase susceptibility to mammary infections. Our previous study in 2 divergent lines of sheep selected for high and low somatic cell score (SCS) suggested an association between the response to NEB and genetic susceptibility to mastitis. Forty-eight early-lactation primiparous dairy ewes from the 2 SCS genetic lines were allocated to 2 homogeneous subgroups-an NEB group, which was energy restricted and received 60% of the energy requirements for 15 d, and a control-fed group-to obtain 4 balanced groups of 12 ewes: high-SCS positive energy balance, low-SCS positive energy balance, high-SCS NEB, and low-SCS NEB...
January 10, 2018: Journal of Dairy Science
https://www.readbyqxmd.com/read/29330790/transcriptional-profiling-using-rna-seq-to-study-hypoxia-mediated-gene-regulation
#16
Surendra K Shukla, Ryan J King, Pankaj K Singh
Exposing cells to a hypoxic environment leads to significant physiological and molecular alterations. Most of the hypoxic responses are regulated by the transcription factors known as hypoxia-inducible factors (HIFs). HIF1, a heterodimer of hypoxia-stabilized subunit HIF-1alpha and a constitutively expressed subunit HIF-1beta, serves as a key transcription factor that regulates gene expressions which are involved in cell growth, metabolism, and proliferation. The global expression patterns can be analyzed by utilizing RNA-Seq to understand the cellular alterations in hypoxia...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29330785/genetic-knockdown-and-pharmacologic-inhibition-of-hypoxia-inducible-factor-hif-hydroxylases
#17
Christina Pickel, Cormac T Taylor, Carsten C Scholz
Reduced oxygen supply that does not satisfy tissue and cellular demand (hypoxia) regularly occurs both in health and disease. Hence, the capacity for cellular oxygen sensing is of vital importance for each cell to be able to alter its energy metabolism and promote adaptation to hypoxia. The hypoxia-inducible factor (HIF) prolyl hydroxylases 1-3 (PHD1-3) and the asparagine hydroxylase factor-inhibiting HIF (FIH) are the primary cellular oxygen sensors, which confer cellular oxygen-dependent sensitivity upon HIF as well as other hypoxia-sensitive pathways, such as nuclear factor κB (NF-κB)...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29330721/transcriptomic-analysis-and-discovery-of-genes-in-the-response-of-arachis-hypogaea-to-drought-stress
#18
Xiaobo Zhao, Chunjuan Li, Shubo Wan, Tingting Zhang, Caixia Yan, Shihua Shan
The peanut (Arachis hypogaea) is an important crop species that is threatened by drought stress. The genome sequences of peanut, which was officially released in 2016, may help explain the molecular mechanisms that underlie drought tolerance in this species. We report here a gene expression profiling of A. hypogaea to gain a global view of its drought resistance. Using whole-transcriptome sequencing, we analysed differential gene expression in response to drought stress in the drought-resistant peanut cultivar J11...
January 12, 2018: Molecular Biology Reports
https://www.readbyqxmd.com/read/29330289/brca1-through-its-e3-ligase-activity-regulates-the-transcription-factor-oct1-and-carbohydrate-metabolism
#19
Karina Vázquez-Arreguín, Jessica Maddox, Jinsuk Kang, Dongju Park, Reuben R Cano, Rachel E Factor, Thomas Ludwig, Dean Tantin
The tumor suppressor BRCA1 regulates the DNA damage response (DDR) and other processes that remain incompletely defined. Among these, BRCA1 heterodimerizes with BARD1 to ubiquitylate targets via its N-terminal E3 ligase activity. Here it is demonstrated that BRCA1 promotes oxidative metabolism by degrading Oct1 (POU2F1), a transcription factor with pro-glycolytic and tumorigenic effects. BRCA1 E3 ubiquitin ligase mutation skews cells towards a glycolytic metabolic profile while elevating Oct1 protein. CRISPR-mediated Oct1 deletion reverts the glycolytic phenotype...
January 12, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29329517/genome-wide-analyses-of-direct-target-genes-of-four-rice-nac-domain-transcription-factors-involved-in-drought-tolerance
#20
Pil Joong Chung, Harin Jung, Yang Do Choi, Ju-Kon Kim
BACKGROUND: Plant stress responses and mechanisms determining tolerance are controlled by diverse sets of genes. Transcription factors (TFs) have been implicated in conferring drought tolerance under drought stress conditions, and the identification of their target genes can elucidate molecular regulatory networks that orchestrate tolerance mechanisms. RESULTS: We generated transgenic rice plants overexpressing the 4 rice TFs, OsNAC5, 6, 9, and 10, under the control of the root-specific RCc3 promoter...
January 12, 2018: BMC Genomics
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