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Transcriptome pathway

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https://www.readbyqxmd.com/read/28651038/elevated-adipsin-levels-are-associated-with-pulmonary-arterial-hypertension-in-systemic-sclerosis
#1
Benjamin D Korman, Roberta Goncalves Marangoni, Monique Hinchcliff, Sanjiv J Shah, Mary Carns, Aileen Hoffmann, Rosalind Ramsey-Goldman, John Varga
INTRODUCTION: Adipose tissues secrete adipokines, peptides with potent effects modulating fibrosis, inflammation, and vascular homeostasis. Dysregulated adipose tissue biology and adipokine balance have been recently implicated in systemic sclerosis (SSc). We sought to determine if altered circulating adipokine levels correlate with SSc disease subsets or clinical manifestations. MATERIALS AND METHODS: Multiplex assays were used to measure circulating adipokine levels in 198 patients with SSc and 33 healthy controls...
June 26, 2017: Arthritis & Rheumatology
https://www.readbyqxmd.com/read/28651000/assessing-the-impact-of-benzo-a-pyrene-on-marine-mussels-application-of-a-novel-targeted-low-density-microarray-complementing-classical-biomarker-responses
#2
Mohamed Banni, Susanna Sforzini, Volker M Arlt, Audrey Barranger, Lorna J Dallas, Caterina Oliveri, Yann Aminot, Beniamina Pacchioni, Caterina Millino, Gerolamo Lanfranchi, James W Readman, Michael N Moore, Aldo Viarengo, Awadhesh N Jha
Despite the increasing use of mussels in environmental monitoring and ecotoxicological studies, their genomes and gene functions have not been thoroughly explored. Several cDNA microarrays were recently proposed for Mytilus spp., but putatively identified partial transcripts have rendered the generation of robust transcriptional responses difficult in terms of pathway identification. We developed a new low density oligonucleotide microarray with 465 probes covering the same number of genes. Target genes were selected to cover most of the well-known biological processes in the stress response documented over the last decade in bivalve species at the cellular and tissue levels...
2017: PloS One
https://www.readbyqxmd.com/read/28650988/transcriptomic-analysis-to-uncover-genes-affecting-cold-resistance-in-the-chinese-honey-bee-apis-cerana-cerana
#3
Kai Xu, Qingsheng Niu, Huiting Zhao, Yali Du, Yusuo Jiang
The biological activity and geographical distribution of honey bees is strongly temperature-dependent, due to their ectothermic physiology. In China, the endemic Apis cerana cerana exhibits stronger cold hardiness than Western honey bees, making the former species important pollinators of winter-flowering plants. Although studies have examined behavioral and physiological mechanisms underlying cold resistance in bees, data are scarce regarding the exact molecular mechanisms. Here, we investigated gene expression in A...
2017: PloS One
https://www.readbyqxmd.com/read/28650075/isl1-controls-patterning-and-mineralization-of-enamel-in-the-continuously-renewing-mouse-incisor
#4
Adrien Naveau, Bin Zhang, Bo Meng, McGarrett T Sutherland, Michaela Prochazkova, Timothy Wen, Pauline Marangoni, Kyle B Jones, Timothy C Cox, Bernhard Ganss, Andrew H Jheon, Ophir D Klein
Rodents are characterized by continuously renewing incisors whose growth is fueled by epithelial and mesenchymal stem cells housed in the proximal compartments of the tooth. The epithelial stem cells reside in structures known as the labial (toward the lip) and lingual (toward the tongue) cervical loops (laCL and liCL, respectively). An important feature of the rodent incisor is that enamel, the outer, highly mineralized layer, is asymmetrically distributed, as it is normally generated by the laCL but not the liCL...
June 26, 2017: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
https://www.readbyqxmd.com/read/28649439/mechanisms-of-action-of-sacubitril-valsartan-on-cardiac-remodeling-a-systems-biology-approach
#5
Oriol Iborra-Egea, Carolina Gálvez-Montón, Santiago Roura, Isaac Perea-Gil, Cristina Prat-Vidal, Carolina Soler-Botija, Antoni Bayes-Genis
Sacubitril/Valsartan, proved superiority over other conventional heart failure management treatments, but its mechanisms of action remains obscure. In this study, we sought to explore the mechanistic details for Sacubitril/Valsartan in heart failure and post-myocardial infarction remodeling, using an in silico, systems biology approach. Myocardial transcriptome obtained in response to myocardial infarction in swine was analyzed to address post-infarction ventricular remodeling. Swine transcriptome hits were mapped to their human equivalents using Reciprocal Best (blast) Hits, Gene Name Correspondence, and InParanoid database...
2017: NPJ Systems Biology and Applications
https://www.readbyqxmd.com/read/28649425/opposing-activities-of-oncogenic-mir17hg-and-tumor-suppressive-mir100hg-clusters-and-their-gene-targets-regulate-replicative-senescence-in-human-adult-stem-cells
#6
Mary F Lopez, Ping Niu, Lu Wang, Maryann Vogelsang, Meenakshi Gaur, Bryan Krastins, Yueqiang Zhao, Aibek Smagul, Aliya Nussupbekova, Aikan A Akanov, I King Jordan, Victoria V Lunyak
Growing evidence suggests that many diseases of aging, including diseases associated with robust changes and adipose deports, may be caused by resident adult stem cell exhaustion due to the process called cellular senescence. Understanding how microRNA pathways can regulate cellular senescence is crucial for the development of novel diagnostic and therapeutic strategies to combat these pathologies. Herein, using integrated transcriptomic and semi-quantitative proteomic analysis, we provide a system level view of the regulation of human adipose-derived stem cell senescence by a subset of mature microRNAs (termed senescence-associated-microRNAs) produced by biogenesis of oncogenic MIR17HG and tumor-suppressive MIR100HG clusters...
2017: NPJ Aging and Mechanisms of Disease
https://www.readbyqxmd.com/read/28649314/hierarchical-cortical-transcriptome-disorganization-in-autism
#7
Michael V Lombardo, Eric Courchesne, Nathan E Lewis, Tiziano Pramparo
BACKGROUND: Autism spectrum disorders (ASD) are etiologically heterogeneous and complex. Functional genomics work has begun to identify a diverse array of dysregulated transcriptomic programs (e.g., synaptic, immune, cell cycle, DNA damage, WNT signaling, cortical patterning and differentiation) potentially involved in ASD brain abnormalities during childhood and adulthood. However, it remains unclear whether such diverse dysregulated pathways are independent of each other or instead reflect coordinated hierarchical systems-level pathology...
2017: Molecular Autism
https://www.readbyqxmd.com/read/28649278/dynamics-of-gene-expression-during-development-and-expansion-of-vegetative-stem-internodes-of-bioenergy-sorghum
#8
Tesfamichael H Kebrom, Brian McKinley, John E Mullet
BACKGROUND: Bioenergy sorghum accumulates 75% of shoot biomass in stem internodes. Grass stem internodes are formed during vegetative growth and elongate in response to developmental and environmental signals. To identify genes and molecular mechanisms that modulate the extent of internode growth, we conducted microscopic and transcriptomic analyses of four successive sub-apical vegetative internodes representing different stages of internode development of the bioenergy sorghum genotype R...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28648885/chlorpyrifos-exposure-in-common-carp-cyprinus-carpio-l-leads-to-oxidative-stress-and-immune-responses
#9
Ziwei Zhang, Qi Liu, Jingzeng Cai, Jie Yang, Qiang Shen, Shiwen Xu
Chlorpyrifos (CPF) is an environmental pollutant with increasing importance due to its high toxicity to fish and aquatic animals. To understand how CPF impacts immune response and oxidative stress in common carp (Cyprinus carpio L.), we investigated the transcriptomic profiles of the head kidneys from common carp exposed to CPF for 15days. A total of 52, 297, 928 and 52, 273, 784 high quality clean reads were obtained from CPF exposure groups, 44,677,578 and 44,106,696 high quality clean reads were obtained from corresponding control groups...
June 22, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28648882/transcriptome-analysis-of-the-hepatopancreas-in-exopalaemon-carinicauda-infected-with-an-ahpnd-causing-strain-of-vibrio-parahaemolyticus
#10
Qianqian Ge, Jian Li, Jiajia Wang, Jitao Li, Hongxing Ge, Qianqian Zhai
Acute hepatopancreatic necrosis disease (AHPND) caused by Vibrio parahaemolyticus carrying toxin-producing plasmid, has led to severe mortalities in multiple shrimp species throughout Asia. In order to understand the immunological response of shrimp to infection by AHPND-causing strain of V. parahaemolyticus (VPAHPND), the transcriptomic profiles of the hepatopancreas from severe AHPND-infected (BS_G), AHPND-survived (KB_G) and non-infected (PBS_G) Exopalaemon carinicauda groups were obtained using HiSeq™ 2500 (Illumina)...
June 22, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28648749/transcriptome-profiling-of-3d-co-cultured-cardiomyocytes-and-endothelial-cells-under-oxidative-stress-using-a-photocrosslinkable-hydrogel-system
#11
Xiaoshan Yue, Aylin Acun, Pinar Zorlutuna
Myocardial infarction (MI) is one of the most common among cardiovascular diseases. Endothelial cells (ECs) are considered to have protective effects on cardiomyocytes (CMs) under stress conditions such as MI; however, the paracrine CM-EC crosstalk and the resulting endogenous cellular responses that could contribute to this protective effect are not thoroughly investigated. Here we created biomimetic synthetic tissues containing CMs and human induced pluripotent stem cell (hiPSC)-derived ECs (iECs), which showed improved cell survival compared to single cultures under conditions mimicking the aftermath of MI, and performed high-throughput RNA-sequencing to identify target pathways that could govern CM-iEC crosstalk and the resulting improvement in cell viability...
June 22, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/28647779/transcriptome-profiling-and-digital-gene-expression-analysis-of-the-skin-of-dybowski-s-frog-rana-dybowskii-exposed-to-aeromonas-hydrophila
#12
Yi-Gang Xu, Long-Hui Chai, Wen Shi, Dan-Dan Wang, Jing-Yu Zhang, Xiang-Hong Xiao
Recently, populations of Rana dybowskii, an important amphibian species in Northeast China, have decreased, mainly owing to the disease caused by Aeromonas hydrophila. However, effective control methods have not yet been developed. In order to explore the immune responses of R. dybowskii upon exposure to A. hydrophila infection, Illumina high-throughput transcriptome sequencing and digital gene expression (DGE) technology were employed to investigate transcriptomic changes in the skin of R. dybowskii exposed to A...
June 24, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28647608/a-route-based-pathway-analysis-framework-integrating-mutation-information-and-gene-expression-data
#13
Yue Zhao, Tham H Hoang, Pujan Joshi, Seung-Hyun Hong, Charles Giardina, Dong-Guk Shin
We propose a new way of analyzing biological pathways in which the analysis combines both transcriptome data and mutation information and uses the outcome to identify "routes" of aberrant pathways potentially responsible for the etiology of disease. Each pathway route is encoded as a Bayesian Network which is initialized with a sequence of conditional probabilities which are designed to encode directionality of regulatory relationships encoded in the pathways, i.e. activation and inhibition relationships. First, we demonstrate the effectiveness of our model through simulation in which the model was able to easily separate Test samples from Control samples using fictitiously perturbed pathway routes...
June 21, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28647346/sting-is-involved-in-antiviral-immune-response-against-vzv-infection-via-the-induction-of-type-i-and-iii-ifn-pathways
#14
Ji-Ae Kim, Seul-Ki Park, Seong-Wook Seo, Chan-Hee Lee, Ok Sarah Shin
Varicella Zoster Virus (VZV) is a human-restricted α-herpesvirus that exhibits tropism for the skin. The VZV host receptors and downstream signaling pathways responsible for the antiviral innate immune response in the skin are not completely understood. Here, we show that stimulator of interferon genes (STING) mediates an important host defense against VZV infection in dermal cells including human dermal fibroblasts (HDFs) and HaCaT keratinocytes. Inhibition of STING using small interfering RNA (siRNA) or short hairpin RNA (shRNA)-mediated gene disruption resulted in enhanced viral replication but diminished IRF3 phosphorylation and induction of IFNs and pro-inflammatory cytokines...
June 21, 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/28647319/in-vitro-stimulation-of-vitellogenin-expression-by-insulin-in-the-mud-crab-scylla-paramamosain-mediated-through-pi3k-akt-tor-pathway
#15
Xiaoshuai Huang, Biyun Feng, Huiyang Huang, Haihui Ye
Vitellogenin (vtg) synthesis, known as vitellogenesis, is one of most important processes in the ovarian development of oviparous animals. Recently, multiple insulin-like peptides (ILPs) have been reported in crustacean species due to the application of transcriptome sequencing. In this context, the present study reports that the addition of an exogenous ILP, bovine insulin, stimulates vtg (termed Sp-vtg) expression in hepatopancreatic explants from the mud crab, Scylla paramamosain, by in vitro experiments...
June 21, 2017: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/28646867/a-high-quality-annotated-transcriptome-of-swine-peripheral-blood
#16
Haibo Liu, Timothy P L Smith, Dan J Nonneman, Jack C M Dekkers, Christopher K Tuggle
BACKGROUND: High throughput gene expression profiling assays of peripheral blood are widely used in biomedicine, as well as in animal genetics and physiology research. Accurate, comprehensive, and precise interpretation of such high throughput assays relies on well-characterized reference genomes and/or transcriptomes. However, neither the reference genome nor the peripheral blood transcriptome of the pig have been sufficiently assembled and annotated to support such profiling assays in this emerging biomedical model organism...
June 24, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28646367/ifn%C3%AE-producing-cd4-t-lymphocytes-the-double-edged-swords-in-tuberculosis
#17
Pawan Kumar
IFNγ-producing CD4(+) T cells (IFNγ(+)CD4(+) T cells) are the key orchestrators of protective immunity against Mycobacterium tuberculosis (Mtb). Primarily, these cells act by enabling Mtb-infected macrophages to enforce phagosome-lysosome fusion, produce reactive nitrogen intermediates (RNIs), and activate autophagy pathways. However, TB is a heterogeneous disease and a host of clinical and experimental findings has also implicated IFNγ(+)CD4(+) T cells in TB pathogenesis. High frequency of IFNγ(+)CD4(+) T cells is the most invariable feature of the active disease...
December 2017: Clinical and Translational Medicine
https://www.readbyqxmd.com/read/28646221/aberrant-activation-of-the-human-sex-determining-gene-in-early-embryonic-development-results-in-postnatal-growth-retardation-and-lethality-in-mice
#18
Tatsuo Kido, Zhaoyu Sun, Yun-Fai Chris Lau
Sexual dimorphisms are prevalent in development, physiology and diseases in humans. Currently, the contributions of the genes on the male-specific region of the Y chromosome (MSY) in these processes are uncertain. Using a transgene activation system, the human sex-determining gene hSRY is activated in the single-cell embryos of the mouse. Pups with hSRY activated (hSRY(ON)) are born of similar sizes as those of non-activated controls. However, they retard significantly in postnatal growth and development and all die of multi-organ failure before two weeks of age...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28646076/transcriptomic-and-proteomic-profiling-provides-insight-into-mesangial-cell-function-in-iga-nephropathy
#19
Peidi Liu, Emelie Lassén, Viji Nair, Celine C Berthier, Miyuki Suguro, Carina Sihlbom, Matthias Kretzler, Christer Betsholtz, Börje Haraldsson, Wenjun Ju, Kerstin Ebefors, Jenny Nyström
IgA nephropathy (IgAN), the most common GN worldwide, is characterized by circulating galactose-deficient IgA (gd-IgA) that forms immune complexes. The immune complexes are deposited in the glomerular mesangium, leading to inflammation and loss of renal function, but the complete pathophysiology of the disease is not understood. Using an integrated global transcriptomic and proteomic profiling approach, we investigated the role of the mesangium in the onset and progression of IgAN. Global gene expression was investigated by microarray analysis of the glomerular compartment of renal biopsy specimens from patients with IgAN (n=19) and controls (n=22)...
June 23, 2017: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/28645581/improvement-of-isopropanol-tolerance-of-escherichia-coli-using-adaptive-laboratory-evolution-and-omics-technologies
#20
Takaaki Horinouchi, Aki Sakai, Hazuki Kotani, Kumi Tanabe, Chikara Furusawa
Isopropanol (IPA) is the secondary alcohol that can be dehydrated to yield propylene. To produce IPA using microorganisms, a significant issue is that the toxicity of IPA causes retardation or inhibition of cell growth, decreasing the yield. One possible strategy to overcome this problem is to improve IPA tolerance of production organisms. For the understanding of tolerance to IPA, we performed parallel adaptive laboratory evolution (ALE) of Escherichia coli under IPA stress. To identify the genotypic change during ALE, we performed genome re-sequencing analyses of obtained tolerant strains...
June 20, 2017: Journal of Biotechnology
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