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Gene expression regulation

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https://www.readbyqxmd.com/read/28227870/identifying-disease-network-perturbations-through-regression-on-gene-expression-and-pathway-topology-analysis
#1
Georgios N Dimitrakopoulos, Panos Balomenos, Aristidis G Vrahatis, Kyriakos Sgarbas, Anastasios Bezerianos, Georgios N Dimitrakopoulos, Panos Balomenos, Aristidis G Vrahatis, Kyriakos Sgarbas, Anastasios Bezerianos, Kyriakos Sgarbas, Panos Balomenos, Georgios N Dimitrakopoulos, Anastasios Bezerianos, Aristidis G Vrahatis
In Systems Biology, network-based approaches have been extensively used to effectively study complex diseases. An important challenge is the detection of network perturbations which disrupt regular biological functions as a result of a disease. In this regard, we introduce a network based pathway analysis method which isolates casual interactions with significant regulatory roles within diseased-perturbed pathways. Specifically, we use gene expression data with Random Forest regression models to assess the interactivity strengths of genes within disease-perturbed networks, using KEGG pathway maps as a source of prior-knowledge pertaining to pathway topology...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226226/microglia-function-in-the-central-nervous-system-during-health-and-neurodegeneration
#2
Marco Colonna, Oleg Butovsky
Microglia are resident cells of the brain that regulate brain development, maintenance of neuronal networks, and injury repair. Microglia serve as brain macrophages but are distinct from other tissue macrophages owing to their unique homeostatic phenotype and tight regulation by the central nervous system (CNS) microenvironment. They are responsible for the elimination of microbes, dead cells, redundant synapses, protein aggregates, and other particulate and soluble antigens that may endanger the CNS. Furthermore, as the primary source of proinflammatory cytokines, microglia are pivotal mediators of neuroinflammation and can induce or modulate a broad spectrum of cellular responses...
February 9, 2017: Annual Review of Immunology
https://www.readbyqxmd.com/read/28226195/global-transcriptional-response-of-human-liver-cells-to-ethanol-stress-of-different-strength-reveals-hormetic-behavior
#3
Wolfgang Schmidt-Heck, Eva C Wönne, Thomas Hiller, Uwe Menzel, Dirk Koczan, Georg Damm, Daniel Seehofer, Fanny Knöspel, Nora Freyer, Reinhard Guthke, Steven Dooley, Katrin Zeilinger
BACKGROUND: The liver is the major site for alcohol metabolism in the body and therefore, the primary target organ for ethanol-induced toxicity. In this study, we investigated the in vitro response of human liver cells to different ethanol concentrations in a perfused bioartificial liver device that mimics the complex architecture of the natural organ. METHODS: Primary human liver cells were cultured in the bioartificial liver device and treated for 24 hours with medium containing 150 mM (low), 300 mM (medium) or 600 mM (high) ethanol, while a control culture was kept untreated...
February 22, 2017: Alcoholism, Clinical and Experimental Research
https://www.readbyqxmd.com/read/28226194/melatonin-systemically-ameliorates-drought-stress-induced-damage-in-medicago-sativa-plants-by-modulating-nitro-oxidative-homeostasis-and-proline-metabolism
#4
Chrystalla Antoniou, Giannis Chatzimichail, Rafaella Xenofontos, Giannis Pavlou, Evangelia Panagiotou, Anastasis Christou, Vasileios Fotopoulos
Recent reports have uncovered the multifunctional role of melatonin in plant physiological responses under optimal and sub-optimal environmental conditions. In this study, we explored whether melatonin pretreatment could provoke priming effects in alfalfa (Medicago sativa L.) plants subsequently exposed to prolonged drought stress (7 days), by withholding watering. Results revealed that the rhizospheric application of melatonin (10 μM) remarkably enhanced the drought tolerance of alfalfa plants, as evidenced by the observed plant tolerant phenotype, as well as by the higher levels of chlorophyll fluorescence and stomatal conductance, compared with non-treated drought-stressed plants...
February 22, 2017: Journal of Pineal Research
https://www.readbyqxmd.com/read/28226188/effects-of-melatonin-on-seedling-growth-mineral-nutrition-and-nitrogen-metabolism-in-cucumber-under-nitrate-stress
#5
Ruimin Zhang, Yunkuo Sun, Zeyu Liu, Wen Jin, Yan Sun
In China, excessive use of nitrogen fertilizers in greenhouses leads to nitrate accumulations in soil and plants, which then limits productivity. Melatonin, an evolutionarily highly conserved molecule, has a wide range of functions in plants. We analyzed the effects of melatonin pretreatment on the growth, mineral nutrition, and nitrogen metabolism in cucumber (Cucumis sativus L. 'Jin You No. 1') when seedlings were exposed to nitrate stress. An application of 0.1 mM melatonin significantly improved the growth of plants and reduced their susceptibility to damage due to high nitrate levels (0...
February 22, 2017: Journal of Pineal Research
https://www.readbyqxmd.com/read/28225870/pdk2-promotes-chondrogenic-differentiation-of-mesenchymal-stem-cells-by-upregulation-of-sox6-and-activation-of-jnk-mapk-erk-pathway
#6
H Wang, X B Shan, Y J Qiao
This study was undertaken to clarify the role and mechanism of pyruvate dehydrogenase kinase isoform 2 (PDK2) in chondrogenic differentiation of mesenchymal stem cells (MSCs). MSCs were isolated from femurs and tibias of Sprague-Dawley rats, weighing 300-400 g (5 females and 5 males). Overexpression and knockdown of PDK2 were transfected into MSCs and then cell viability, adhesion and migration were assessed. Additionally, the roles of aberrant PDK2 in chondrogenesis markers SRY-related high mobility group-box 6 (Sox6), type ΙΙ procollagen gene (COL2A1), cartilage oligomeric matrix protein (COMP), aggrecan (AGC1), type ΙX procollagen gene (COL9A2) and collagen type 1 alpha 1 (COL1A1) were measured by quantitative reverse-transcription polymerase chain reaction (qRT-PCR)...
February 16, 2017: Brazilian Journal of Medical and Biological Research, Revista Brasileira de Pesquisas Médicas e Biológicas
https://www.readbyqxmd.com/read/28225779/combined-small-rna-and-degradome-sequencing-reveals-complex-microrna-regulation-of-catechin-biosynthesis-in-tea-camellia-sinensis
#7
Ping Sun, Chunzhen Cheng, Yuling Lin, Qiufang Zhu, Jinke Lin, Zhongxiong Lai
MicroRNAs are endogenous non-coding small RNAs playing crucial regulatory roles in plants. Tea, a globally popular non-alcoholic drink, is rich in health-enhancing catechins. In this study, 69 conserved and 47 novel miRNAs targeting 644 genes were identified by high-throughout sequencing. Predicted target genes of miRNAs were mainly involved in plant growth, signal transduction, morphogenesis and defense. To further identify targets of tea miRNAs, degradome sequencing and RNA ligase-mediated rapid amplification of 5'cDNA ends (RLM-RACE) were applied...
2017: PloS One
https://www.readbyqxmd.com/read/28225770/a-distal-intergenic-region-controls-pancreatic-endocrine-differentiation-by-acting-as-a-transcriptional-enhancer-and-as-a-polycomb-response-element
#8
Joris van Arensbergen, Sebastien Dussaud, Corinne Pardanaud-Glavieux, Javier García-Hurtado, Claire Sauty, Aline Guerci, Jorge Ferrer, Philippe Ravassard
Lineage-selective expression of developmental genes is dependent on the interplay between activating and repressive mechanisms. Gene activation is dependent on cell-specific transcription factors that recognize transcriptional enhancer sequences. Gene repression often depends on the recruitment of Polycomb group (PcG) proteins, although the sequences that underlie the recruitment of PcG proteins, also known as Polycomb response elements (PREs), remain poorly understood in vertebrates. While distal PREs have been identified in mammals, a role for positive-acting enhancers in PcG-mediated repression has not been described...
2017: PloS One
https://www.readbyqxmd.com/read/28225604/a-microfluidic-device-for-studying-controllable-hydrodynamic-flow-induced-cellular-responses
#9
Chunhong Zheng, Xiannian Zhang, Chunmei Li, Yuhong Pang, Yanyi Huang
Hydrodynamic flow is an essential stimulus in many cellular functions, regulating many mechanical sensitive pathways and closely associating with human health status and diseases. The flow pattern of blood in vessels is the key factor in causing atherosclerosis. Hemodynamics has great effect on endothelial cells' gene expression and biological functions. There are various tools that can be used for studying flow-induced cellular responses but most of them are either bulky or lack of precise controllability...
February 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28225180/microrna-216b-inhibits-cell-proliferation-and-migration-in-human-melanoma-by-targeting-foxm1-in-vitro-and-in-vivo
#10
Mengyao Sun, Xiaopeng Wang, Chen Tu, Shuang Wang, Jianqiang Qu, Shengxiang Xiao
MicroRNAs (miRNAs) play an increasingly important role in cancer growth by coordinately suppressing genes that controlcell migration, proliferationand invasion. The above results can be achieved through the regulation of gene expression by miRNAs bysuppressing translation or the directsequence-specific degradation of the targetedmRNA. In the present study, we indicate that the expression of miR-216b could be effectively repressed both in human melanoma tissues through a comparison with primary melanoma and in human melanoma cell lines through a comparison with a normal human keratinocyte line...
February 22, 2017: Cell Biology International
https://www.readbyqxmd.com/read/28225172/mir-144-affects-fatty-acid-composition-by-regulating-elovl6-expression-in-duck-hepatocytes
#11
Jun He, Yong Tian, Yan Zhao, Yali Liu, Zhengrong Tao, Guoqin Li, Dong Niu, Lizhi Lu, Yingru Lu
Lipid metabolism in duck is very important for both raisers and people's health. In our previous studies, we have detected that miR-144 is related to duck lipid metabolism and validated one of its target genes, elongation of very long chain fatty acids protein 6 (ELOVL6). In the present study, we isolated, cultured and identified duck hepatocytes, and transfected with miR-144 mimics/inhibitor to mediate the miR-144 level. The qRT-PCR results showed that the ELOVL6 expression in duck hepatocytes was down-/up-regulated, respectively...
February 22, 2017: Cell Biology International
https://www.readbyqxmd.com/read/28225069/testicular-dnmt3-expression-and-global-dna-methylation-are-down-regulated-by-gonadotropin-releasing-hormones-in-the-ricefield-eel-monopterus-albus
#12
Yize Zhang, Xin Sun, Lihong Zhang, Weimin Zhang
In vertebrates, DNA methyltransferase 3 (Dnmt3) homologues are responsible for de novo DNA methylation and play important roles in germ cell development. In the present study, four dnmt3 genes, dnmt3aa, dnmt3ab, dnmt3ba and dnmt3bb.1, were identified in ricefield eels. Real-time quantitative PCR analysis showed that all four dnmt3 mRNAs were detected broadly in tissues examined, with testicular expression at relatively high levels. In the testis, immunostaining for all four Dnmt3 forms was mainly localized to spermatocytes, which also contained highly methylated DNA...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28225068/relish2-mediates-bursicon-homodimer-induced-prophylactic-immunity-in-the-mosquito-aedes-aegypti
#13
Hongwei Zhang, Shengzhang Dong, Xi Chen, David Stanley, Brenda Beerntsen, Qili Feng, Qisheng Song
Bursicon is a neuropeptide hormone consisting of two cystine-knot proteins (burs α and burs β), responsible for cuticle tanning and other developmental processes in insects. Recent studies show that each bursicon subunit forms homodimers that induce prophylactic immunity in Drosophila melanogaster. Here, we investigated the hypothesis that bursicon homodimers act in prophylactic immunity in insects, and possibly arthropods, generally, using the mosquito, Aedes aegypti. We found that burs α and burs β are expressed in larvae, pupae and newly emerged adults...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28225036/three-tfl1-homologues-regulate-floral-initiation-in-the-biofuel-plant-jatropha-curcas
#14
Chaoqiong Li, Qiantang Fu, Longjian Niu, Li Luo, Jianghua Chen, Zeng-Fu Xu
Recent research revealed that TERMINAL FLOWER 1 (TFL1) homologues are involved in the critical developmental process of floral initiation in several plant species. In this study, the functions of three putative TFL1 homologues (JcTFL1a, JcTFL1b and JcTFL1c) in the biofuel plant Jatropha curcas were analysed using the transgenic approach. JcTFL1b and JcTFL1c, but not JcTFL1a, could complement the TFL1 function and rescue early flowering and determinate inflorescence phenotype in tfl1-14 Arabidopsis mutant, thus suggesting that JcTFL1b and JcTFL1c may be homologues of TFL1...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28225035/deep-sequencing-and-transcriptome-analyses-to-identify-genes-involved-in-secoiridoid-biosynthesis-in-the-tibetan-medicinal-plant-swertia-mussotii
#15
Yue Liu, Yi Wang, Fengxian Guo, Lin Zhan, Toni Mohr, Prisca Cheng, Naxin Huo, Ronghui Gu, Danning Pei, Jiaqing Sun, Li Tang, Chunlin Long, Luqi Huang, Yong Q Gu
Swertia mussotii Franch. is an important traditional Tibetan medicinal plant with pharmacological properties effective in the treatment of various ailments including hepatitis. Secoiridoids are the major bioactive compounds in S. mussotii. To better understand the secoiridoid biosynthesis pathway, we generated transcriptome sequences from the root, leaf, stem, and flower tissues, and performed de novo sequence assembly, yielding 98,613 unique transcripts with an N50 of 1,085 bp. Putative functions could be assigned to 35,029 transcripts (35...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28225027/variable-salinity-responses-of-12-alfalfa-genotypes-and-comparative-expression-analyses-of-salt-response-genes
#16
Devinder Sandhu, Monica V Cornacchione, Jorge F S Ferreira, Donald L Suarez
Twelve alfalfa genotypes that were selected for biomass under salinity, differences in Na and Cl concentrations in shoots and K/Na ratio were evaluated in this long-term salinity experiment. The selected plants were cloned to reduce genetic variability within each genotype. Salt tolerance (ST) index of the genotypes ranged from 0.39 to 1. The most salt-tolerant genotypes SISA14-1 (G03) and AZ-90ST (G10), the top performers for biomass, exhibited the least effect on shoot number and height. SISA14-1 (G03) accumulated low Na and Cl under salinity...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28225023/traditional-chinese-medicine-suppresses-left-ventricular-hypertrophy-by-targeting-extracellular-signal-regulated-kinases-signaling-pathway-in-spontaneously-hypertensive-rats
#17
Xingjiang Xiong, Xiaochen Yang, Lian Duan, Wei Liu, Yun Zhang, Yongmei Liu, Pengqian Wang, Shengjie Li, Xiaoke Li
Chinese herbal medicine Bu-Shen-Jiang-Ya decoction (BSJYD) is reported to be beneficial for hypertension. Over expression of extracellular signal regulated kinases (ERK) pathway plays an important role in left ventricular hypertrophy (LVH). This study aimed to observe effects of BSJYD on LVH in spontaneously hypertensive rats (SHRs) and explore its possible mechanism on regulation of ERK pathway. Sixty 12-week-old SHRs were randomly allocated into 5 groups: BSJYD high dose group, middle dose group, low dose group, captopril group, and control group...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28225006/altered-enhancer-transcription-underlies-huntington-s-disease-striatal-transcriptional-signature
#18
Stéphanie Le Gras, Céline Keime, Anne Anthony, Caroline Lotz, Lucie De Longprez, Emmanuel Brouillet, Jean-Christophe Cassel, Anne-Laurence Boutillier, Karine Merienne
Epigenetic and transcriptional alterations are both implicated in Huntington's disease (HD), a progressive neurodegenerative disease resulting in degeneration of striatal neurons in the brain. However, how impaired epigenetic regulation leads to transcriptional dysregulation in HD is unclear. Here, we investigated enhancer RNAs (eRNAs), a class of long non-coding RNAs transcribed from active enhancers. We found that eRNAs are expressed from many enhancers of mouse striatum and showed that a subset of those eRNAs are deregulated in HD vs control mouse striatum...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28224923/high-throughput-sequencing-reveals-modulation-of-micrornas-in-vigna-mungo-upon-mungbean-yellow-mosaic-india-virus-inoculation-highlighting-stress-regulation
#19
Anirban Kundu, Sujay Paul, Avishek Dey, Amita Pal
MicroRNAs (miRNAs) are 20-24 nucleotides long non-coding RNAs known to play important regulatory roles during biotic and abiotic stresses by controlling gene expression. Blackgram (Vigna mungo), an economically important grain legume is highly susceptible to pathogenic begomovirus Mungbean Yellow Mosaic India Virus (MYMIV) and resulting in high yield loss. In this study two different leaf-small-RNA libraries were prepared from the pooled RNA at three different time points of resistant V. mungo inbred line VM84 inoculated either with viruliferous or non-viruliferous whiteflies carrying MYMIV and performed high-throughput Illumina sequencing...
April 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28224922/multiple-garlic-allium-sativum-l-micrornas-regulate-the-immunity-against-the-basal-rot-fungus-fusarium-oxysporum-f-sp-cepae
#20
Subodh Kumar Chand, Satyabrata Nanda, Rukmini Mishra, Raj Kumar Joshi
The basal plate rot fungus, Fusarium oxysporum f. sp. cepae (FOC), is the most devastating pathogen posing a serious threat to garlic (Allium sativum L.) production worldwide. MicroRNAs (miRNAs) are key modulators of gene expression related to development and defense responses in eukaryotes. However, the miRNA species associated with garlic immunity against FOC are yet to be explored. In the present study, a small RNA library developed from FOC infected resistant garlic line was sequenced to identify immune responsive miRNAs...
April 2017: Plant Science: An International Journal of Experimental Plant Biology
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