keyword
MENU ▼
Read by QxMD icon Read
search

RNA network

keyword
https://www.readbyqxmd.com/read/28732227/atm-supports-gammaherpesvirus-replication-by-attenuating-type-i-interferon-pathway
#1
Eric J Darrah, Kyle P Stoltz, Mitchell Ledwith, Vera L Tarakanova
Ataxia-Telangiectasia mutated (ATM) kinase participates in multiple networks, including DNA damage response, oxidative stress, and mitophagy. ATM also supports replication of diverse DNA and RNA viruses. Gammaherpesviruses are prevalent cancer-associated viruses that benefit from ATM expression during replication. This proviral role of ATM had been ascribed to its signaling within the DNA damage response network; other functions of ATM have not been considered. In this study increased type I interferon (IFN) responses were observed in ATM deficient gammaherpesvirus-infected macrophages...
July 18, 2017: Virology
https://www.readbyqxmd.com/read/28730478/high-content-imaging-and-rnai-screens-for-investigating-kinase-network-plasticity
#2
Simon R Stockwell, Sibylle Mittnacht
High-content imaging connects the information-rich method of microscopy with the systematic objective principles of software-driven analysis. Suited to automation and, therefore, considerable scale-up of study size, this approach can deliver multiparametric data over cell populations or at the level of the individual cell and has found considerable utility in reverse genetic and pharmacological screens. Here we present a method to screen small interfering RNA (siRNA) libraries allowing subsequent observation of the impact of each knockdown on two interlinked, high-content, G1-/S-phase cell cycle transition assays related to cyclin-dependent kinase (CDK) 2 activity...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28729028/micrornas-as-key-effectors-in-the-p53-network
#3
Frauke Goeman, Sabrina Strano, Giovanni Blandino
The guardian of the genome p53 is embedded in a fine-spun network of MicroRNAs. p53 is able to activate or repress directly the transcription of MicroRNAs that are participating in the tumor-suppressive mission of p53. On the other hand, the expression of p53 is under tight control of MicroRNAs that are either targeting directly p53 or factors that are modifying its protein level or activity. Although the most important function of p53 is suggested to be transcriptional regulation, there are several nontranscriptional functions described...
2017: International Review of Cell and Molecular Biology
https://www.readbyqxmd.com/read/28728565/identification-of-differential-co-expressed-gene-networks-in-early-rheumatoid-arthritis-achieving-sustained-drug-free-remission-after-treatment-with-a-tocilizumab-based-or-methotrexate-based-strategy
#4
Xavier M Teitsma, Johannes W G Jacobs, Michal Mokry, Michelle E A Borm, Attila Pethö-Schramm, Jacob M van Laar, Johannes W J Bijlsma, Floris P J Lafeber
BACKGROUND: Methotrexate is endorsed to be used as first-line treatment in rheumatoid arthritis (RA). However, a large proportion of patients need additional treatment with a biological disease-modifying anti-rheumatic drug (DMARD) to adequately suppress their disease activity. A better understanding of genotypes could help to distinguish between patients with different pathogenic mechanisms. The aim of this study was therefore to identify networks of genes within DMARD-naive early RA patients associated with achieving sustained drug-free remission (sDFR) after initiating tocilizumab plus methotrexate, tocilizumab, or methotrexate therapy...
July 20, 2017: Arthritis Research & Therapy
https://www.readbyqxmd.com/read/28727780/comparative-analysis-of-signature-genes-in-prrsv-infected-porcine-monocyte-derived-cells-to-different-stimuli
#5
Laura C Miller, Damarius S Fleming, Xiangdong Li, Darrell O Bayles, Frank Blecha, Yongming Sang
Monocyte-derived DCs (mDCs) are major target cells in porcine reproductive and respiratory syndrome virus (PRRSV) pathogenesis; however, the plasticity of mDCs in response to activation stimuli and PRRSV infection remains unstudied. In this study, we polarized mDCs, and applied genome-wide transcriptomic analysis and predicted protein-protein interaction networks to compare signature genes involved in mDCs activation and response to PRRSV infection. Porcine mDCs were polarized with mediators for 30 hours, then mock-infected, infected with PRRSV strain VR2332, or a highly pathogenic PRRSV strain (rJXwn06), for 5 h...
2017: PloS One
https://www.readbyqxmd.com/read/28727484/construction-and-analysis-of-circular-rna-molecular-regulatory-networks-in-liver-cancer
#6
Shuangchun Ren, Zhuoyuan Xin, Yinyan Xu, Jianting Xu, Guoqing Wang
Liver cancer is the sixth most prevalent cancer, and the third most frequent cause of cancer-related deaths. Circular RNAs (circRNAs), a kind of special endogenous ncRNAs, have been coming back to the forefront of cancer genomics research. In this study, we employed a systems biology approach to construct and analyze the circRNA molecular regulatory networks in the context of liver cancer. We detected a total of 127 differentially expressed circRNAs and 3,235 differentially expressed mRNAs. We selected the top-5 upregulated circRNAs to construct a circRNA-miRNA-mRNA network...
July 20, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28725177/characterization-of-lgr5-progenitor-cell-transcriptomes-after-neomycin-injury-in-the-neonatal-mouse-cochlea
#7
Shasha Zhang, Yuan Zhang, Pengfei Yu, Yao Hu, Han Zhou, Lingna Guo, Xiaochen Xu, Xiaocheng Zhu, Muhammad Waqas, Jieyu Qi, Xiaoli Zhang, Yan Liu, Fangyi Chen, Mingliang Tang, Xiaoyun Qian, Haibo Shi, Xia Gao, Renjie Chai
Lgr5+ supporting cells (SCs) are enriched hair cell (HC) progenitors in the cochlea. Both in vitro and in vivo studies have shown that HC injury can spontaneously activate Lgr5+ progenitors to regenerate HCs in the neonatal mouse cochlea. Promoting HC regeneration requires the understanding of the mechanism of HC regeneration, and this requires knowledge of the key genes involved in HC injury-induced self-repair responses that promote the proliferation and differentiation of Lgr5+ progenitors. Here, as expected, we found that neomycin-treated Lgr5+ progenitors (NLPs) had significantly greater HC regeneration ability, and greater but not significant proliferation ability compared to untreated Lgr5+ progenitors (ULPs) in response to neomycin exposure...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28723971/termination-factor-rho-from-the-control-of-pervasive-transcription-to-cell-fate-determination-in-bacillus-subtilis
#8
Vladimir Bidnenko, Pierre Nicolas, Aleksandra Grylak-Mielnicka, Olivier Delumeau, Sandrine Auger, Anne Aucouturier, Cyprien Guerin, Repoila Francis, Jacek Bardowski, Stéphane Aymerich, Elena Bidnenko
In eukaryotes, RNA species originating from pervasive transcription are regulators of various cellular processes, from the expression of individual genes to the control of cellular development and oncogenesis. In prokaryotes, the function of pervasive transcription and its output on cell physiology is still unknown. Most bacteria possess termination factor Rho, which represses pervasive, mostly antisense, transcription. Here, we investigate the biological significance of Rho-controlled transcription in the Gram-positive model bacterium Bacillus subtilis...
July 19, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28723948/integrative-functional-analyses-using-rainbow-trout-selected-for-tolerance-to-plant-diets-reveal-nutrigenomic-signatures-for-soy-utilization-without-the-concurrence-of-enteritis
#9
Jason Abernathy, Andreas Brezas, Kevin R Snekvik, Ronald W Hardy, Ken Overturf
Finding suitable alternative protein sources for diets of carnivorous fish species remains a major concern for sustainable aquaculture. Through genetic selection, we created a strain of rainbow trout that outperforms parental lines in utilizing an all-plant protein diet and does not develop enteritis in the distal intestine, as is typical with salmonids on long-term plant protein-based feeds. By incorporating this strain into functional analyses, we set out to determine which genes are critical to plant protein utilization in the absence of gut inflammation...
2017: PloS One
https://www.readbyqxmd.com/read/28723918/heterogeneity-of-p53-dependent-genomic-responses-following-ethanol-exposure-in-a-developmental-mouse-model-of-fetal-alcohol-spectrum-disorder
#10
Maria Camargo Moreno, Sandra M Mooney, Frank A Middleton
Prenatal ethanol exposure can produce structural and functional deficits in the brain and result in Fetal Alcohol Spectrum Disorder (FASD). In rodent models acute exposure to a high concentration of alcohol causes increased apoptosis in the developing brain. A single causal molecular switch that signals for this increase in apoptosis has yet to be identified. The protein p53 has been suggested to play a pivotal role in enabling cells to engage in pro-apoptotic processes, and thus figures prominently as a hub molecule in the intracellular cascade of responses elicited by alcohol exposure...
2017: PloS One
https://www.readbyqxmd.com/read/28721309/retinal-pigment-epithelial-cells-are-a-potential-reservoir-for-ebola-virus-in-the-human-eye
#11
Justine R Smith, Shawn Todd, Liam M Ashander, Theodosia Charitou, Yuefang Ma, Steven Yeh, Ian Crozier, Michael Z Michael, Binoy Appukuttan, Keryn A Williams, David J Lynn, Glenn A Marsh
PURPOSE: Success of Ebola virus (EBOV) as a human pathogen relates at the molecular level primarily to blockade the host cell type I interferon (IFN) antiviral response. Most individuals who survive Ebola virus disease (EVD) develop a chronic disease syndrome: approximately one-quarter of survivors suffer from uveitis, which has been associated with presence of EBOV within the eye. Clinical observations of post-Ebola uveitis indicate involvement of retinal pigment epithelial cells. METHODS: We inoculated ARPE-19 human retinal pigment epithelial cells with EBOV, and followed course of infection by immunocytochemistry and measurement of titer in culture supernatant...
July 2017: Translational Vision Science & Technology
https://www.readbyqxmd.com/read/28720711/gene-expression-networks-in-the-murine-pulmonary-myocardium-provide-insight-into-the-pathobiology-of-atrial-fibrillation
#12
Jordan K Boutilier, Rhonda L Taylor, Tracy Mann, Elyshia McNamara, Gary J Hoffman, Jacob Kenny, Rodney J Dilley, Peter Henry, Grant Morahan, Nigel G Laing, Kristen J Nowak
The pulmonary myocardium is a muscular coat surrounding the pulmonary and caval veins. Although its definitive physiological function is unknown, it may have a pathological role as the source of ectopic beats initiating atrial fibrillation. How the pulmonary myocardium gains pacemaker function is not clearly defined, although recent evidence indicates that changed transcriptional gene expression networks are at fault. The gene expression profile of this distinct cell type in situ was examined to investigate underlying molecular events that might contribute to atrial fibrillation...
July 18, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28720596/elongator-regulates-hypocotyl-growth-in-darkness-and-during-photomorphogenesis
#13
Magdalena Woloszynska, Olimpia Gagliardi, Filip Vandenbussche, Steven De Groeve, Luis Alonso Baez, Pia Neyt, Sabine Le Gall, Jorge Fung, Paloma Mas, Dominique Van Der Straeten, Mieke Van Lijsebettens
Elongator promotes RNA polymerase II-mediated transcript elongation through epigenetic activities such as histone acetylation. Elongator regulates growth, development, immune response, sensitivity to drought and abscisic acid. We demonstrate that elo mutants exhibit defective hypocotyl elongation but have a normal apical hook in darkness and are hyposensitive to light during photomorphogenesis. These elo phenotypes are supported by transcriptome changes, i.e. downregulation of circadian clock components, positive regulators of skoto- or photomorphogenesis, hormonal pathways and cell wall biogenesis-related factors...
July 18, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28719027/marker-of-coxsackievirus-b4-infection-in-saliva-of-patients-with-type-1-diabetes
#14
F Badia-Boungou, F Sane, E K Alidjinou, M Ternois, P A Opoko, J Haddad, C Stukens, C Lefevre, I Gueorguieva, M Hamze, M Ismail, J Weill, H G Monabéka, E Bouenizabila, D Moukassa, A A Abena, D Hober
BACKGROUND: Coxsackieviruses B (CV-B) are enteroviruses that have been reported to play a role in the pathogenesis of type 1 diabetes. Enteroviral RNA was detected in the gut mucosa of patients. The mucosal immunity is an interconnected network, therefore the response to enteroviruses possibly present in the gastrointestinal mucosa can be reflected by specific antibodies in the saliva. In the present study the anti-CV-B neutralizing activity of saliva samples from patients with type 1 diabetes was investigated...
July 18, 2017: Diabetes/metabolism Research and Reviews
https://www.readbyqxmd.com/read/28718405/rna-binding-proteins-in-cancer-old-players-and-new-actors
#15
REVIEW
Bruno Pereira, Marc Billaud, Raquel Almeida
RNA-binding proteins (RBPs) are key players in post-transcriptional events. The combination of versatility of their RNA-binding domains with structural flexibility enables RBPs to control the metabolism of a large array of transcripts. Perturbations in RBP-RNA networks activity have been causally associated with cancer development, but the rational framework describing these contributions remains fragmented. We review here the evidence that RBPs modulate multiple cancer traits, emphasize their functional diversity, and assess future trends in the study of RBPs in cancer...
July 2017: Trends in Cancer
https://www.readbyqxmd.com/read/28717649/circular-rna-profiling-and-bioinformatic-modeling-identify-its-regulatory-role-in-hepatic-steatosis
#16
Xing-Ya Guo, Chong-Xin He, Yu-Qin Wang, Chao Sun, Guang-Ming Li, Qing Su, Qin Pan, Jian-Gao Fan
Circular RNAs (circRNAs) exhibit a wide range of physiological and pathological activities. To uncover their role in hepatic steatosis, we investigated the expression profile of circRNAs in HepG2-based hepatic steatosis induced by high-fat stimulation. Differentially expressed circRNAs were subjected to validation using QPCR and functional analyses using principal component analysis, hierarchical clustering, target prediction, gene ontology (GO), and pathway annotation, respectively. Bioinformatic integration established the circRNA-miRNA-mRNA regulatory network so as to identify the mechanisms underlying circRNAs' metabolic effect...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28717200/genome-wide-rna-sequencing-analysis-identifies-a-distinct-fibrosis-gene-signature-in-the-conjunctiva-after-glaucoma-surgery
#17
Cynthia Yu-Wai-Man, Nicholas Owen, Jonathan Lees, Aristides D Tagalakis, Stephen L Hart, Andrew R Webster, Christine A Orengo, Peng T Khaw
Fibrosis-related events play a part in most blinding diseases worldwide. However, little is known about the mechanisms driving this complex multifactorial disease. Here we have carried out the first genome-wide RNA-Sequencing study in human conjunctival fibrosis. We isolated 10 primary fibrotic and 7 non-fibrotic conjunctival fibroblast cell lines from patients with and without previous glaucoma surgery, respectively. The patients were matched for ethnicity and age. We identified 246 genes that were differentially expressed by over two-fold and p < 0...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28716948/cooperative-repression-of-igf2r-translation-by-mir-195-and-rna-binding-protein-cugbp1
#18
Yuan Zhang, Yun Zhang, Lan Xiao, Ting-Xi Yu, Jun-Zhe Li, Jaladanki N Rao, Douglas J Turner, Myriam Gorospe, Jian-Ying Wang
Insulin-like growth factor type-2 (IGF2) receptor (IGF2R) recognizes mannose 6-phosphate-containing molecules and IGF2 and plays an important role in many pathophysiological processes including gut mucosal adaptation. However, the mechanisms that control cellular IGF2R abundance are poorly known. MicroRNAs (miRNAs) and RNA-binding proteins (RBP) critically regulate gene expression programs in mammalian cells by modulating the stability and translation of target mRNAs. Here we report that miRNA-195 (miR-195) and the RBP CUG-binding protein 1 (CUGBP1) jointly regulate IGF2R expression at the posttranscriptional level in intestinal epithelial cells...
July 17, 2017: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28716713/n-myc-regulates-growth-and-fiber-cell-differentiation-in-lens-development
#19
Gabriel R Cavalheiro, Gabriel E Matos-Rodrigues, Yilin Zhao, Anielle L Gomes, Deepti Anand, Danilo Predes, Silmara de Lima, Jose G Abreu, Deyou Zheng, Salil A Lachke, Ales Cvekl, Rodrigo A P Martins
Myc proto-oncogenes regulate diverse cellular processes during development, but their roles during morphogenesis of specific tissues are not fully understood. We found that c-myc regulates cell proliferation in mouse lens development and previous genome-wide studies suggested functional roles for N-myc in developing lens. Here, we examined the role of N-myc in mouse lens development. Genetic inactivation of N-myc in the surface ectoderm or lens vesicle impaired eye and lens growth, while "late" inactivation in lens fibers had no effect...
July 14, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28716407/overexpression-of-lsi1-in-cold-sensitive-rice-mediates-transcriptional-regulatory-networks-and-enhances-resistance-to-chilling-stress
#20
Changxun Fang, Pengli Zhang, Xin Jian, Weisi Chen, Hongmei Lin, Yingzhe Li, Wenxiong Lin
Frequent cold spells in late spring can damage early rice seedlings. However, overexpression of the silicon-uptake gene Lsi1 (Lsi1-OX) in cold-sensitive rice (Oryza sativa L., accession: Dular) notably enhances its chilling resistance. In this study, we found that continual chilling led to chlorophyll and RNA degradation in wild-type Dular leaves, whereas leaves from a Lsi1-OX line exhibited no obvious changes. A comparison of the global mRNA expression between the two rice lines showed that genes encoding photosynthesis-antenna proteins were downregulated and those encoding the proteasome were upregulated in the wild-type organism...
September 2017: Plant Science: An International Journal of Experimental Plant Biology
keyword
keyword
76951
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"