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https://www.readbyqxmd.com/read/29352511/draft-genome-and-reference-transcriptomic-resources-for-the-urticating-pine-defoliator-thaumetopoea-pityocampa-lepidoptera-notodontidae
#1
B Gschloessl, F Dorkeld, H Berges, G Beydon, O Bouchez, M Branco, A Bretaudeau, C Burban, E Dubois, P Gauthier, E Lhuillier, J Nichols, S Nidelet, S Rocha, L Sauné, R Streiff, M Gautier, C Kerdelhué
The pine processionary moth Thaumetopoea pityocampa (Lepidoptera: Notodontidae) is the main pine defoliator in the Mediterranean region. Its urticating larvae cause severe human and animal health concerns in the invaded areas. This species shows a high phenotypic variability for various traits, such as phenology, fecundity, and tolerance to extreme temperatures. This study presents the construction and analysis of extensive genomic and transcriptomic resources, which are an obligate prerequisite to understand their underlying genetic architecture...
January 20, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29352292/rna-seq-of-kaposi-s-sarcoma-reveals-alterations-in-glucose-and-lipid-metabolism
#2
For Yue Tso, Andrew V Kossenkov, Salum J Lidenge, Owen Ngalamika, John R Ngowi, Julius Mwaiselage, Jayamanna Wickramasinghe, Eun Hee Kwon, John T West, Paul M Lieberman, Charles Wood
Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiologic agent of Kaposi's sarcoma (KS). It is endemic in a number of sub-Saharan African countries with infection rate of >50%. The high prevalence of HIV-1 coupled with late presentation of advanced cancer staging make KS the leading cancer in the region with poor prognosis and high mortality. Disease markers and cellular functions associated with KS tumorigenesis remain ill-defined. Several studies have attempted to investigate changes of the gene profile with in vitro infection of monoculture models, which are not likely to reflect the cellular complexity of the in vivo lesion environment...
January 19, 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29352281/differential-dna-methylation-and-transcription-profiles-in-date-palm-roots-exposed-to-salinity
#3
Ibtisam Al-Harrasi, Rashid Al-Yahyai, Mahmoud W Yaish
As a salt-adaptive plant, the date palm (Phoenix dactylifera L.) requires a suitable mechanism to adapt to the stress of saline soils. There is growing evidence that DNA methylation plays an important role in regulating gene expression in response to abiotic stresses, including salinity. Thus, the present study sought to examine the differential methylation status that occurs in the date palm genome when plants are exposed to salinity, and to identify salinity responsive genes that are regulated by DNA methylation...
2018: PloS One
https://www.readbyqxmd.com/read/29352262/microbial-regulation-of-the-l-cell-transcriptome
#4
Tulika Arora, Rozita Akrami, Ramona Pais, Linda Bergqvist, Bengt R Johansson, Thue W Schwartz, Frank Reimann, Fiona M Gribble, Fredrik Bäckhed
L cells are an important class of enteroendocrine cells secreting hormones such as glucagon like peptide-1 and peptide YY that have several metabolic and physiological effects. The gut is home to trillions of bacteria affecting host physiology, but there has been limited understanding about how the microbiota affects gene expression in L cells. Thus, we rederived the reporter mouse strain, GLU-Venus expressing yellow fluorescent protein under the control of the proglucagon gene, as germ-free (GF). Lpos cells from ileum and colon of GF and conventionally raised (CONV-R) GLU-Venus mice were isolated and subjected to transcriptomic profiling...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29352257/robust-phenotype-prediction-from-gene-expression-data-using-differential-shrinkage-of-co-regulated-genes
#5
Kourosh Zarringhalam, David Degras, Christoph Brockel, Daniel Ziemek
Discovery of robust diagnostic or prognostic biomarkers is a key to optimizing therapeutic benefit for select patient cohorts - an idea commonly referred to as precision medicine. Most discovery studies to derive such markers from high-dimensional transcriptomics datasets are weakly powered with sample sizes in the tens of patients. Therefore, highly regularized statistical approaches are essential to making generalizable predictions. At the same time, prior knowledge-driven approaches have been successfully applied to the manual interpretation of high-dimensional transcriptomics datasets...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29352247/high-content-analysis-identifies-unique-morphological-features-of-reprogrammed-cardiomyocytes
#6
Matthew D Sutcliffe, Philip M Tan, Antonio Fernandez-Perez, Young-Jae Nam, Nikhil V Munshi, Jeffrey J Saucerman
Direct reprogramming of fibroblasts into cardiomyocytes is a promising approach for cardiac regeneration but still faces challenges in efficiently generating mature cardiomyocytes. Systematic optimization of reprogramming protocols requires scalable, objective methods to assess cellular phenotype beyond what is captured by transcriptional signatures alone. To address this question, we automatically segmented reprogrammed cardiomyocytes from immunofluorescence images and analyzed cell morphology. We also introduce a method to quantify sarcomere structure using Haralick texture features, called SarcOmere Texture Analysis (SOTA)...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29352240/transcriptome-analysis-in-spleen-reveals-differential-regulation-of-response-to-newcastle-disease-virus-in-two-chicken-lines
#7
Jibin Zhang, Michael G Kaiser, Melissa S Deist, Rodrigo A Gallardo, David A Bunn, Terra R Kelly, Jack C M Dekkers, Huaijun Zhou, Susan J Lamont
Enhancing genetic resistance of chickens to Newcastle Disease Virus (NDV) provides a promising way to improve poultry health, and to alleviate poverty and food insecurity in developing countries. In this study, two inbred chicken lines with different responses to NDV, Fayoumi and Leghorn, were challenged with LaSota NDV strain at 21 days of age. Through transcriptome analysis, gene expression in spleen at 2 and 6 days post-inoculation was compared between NDV-infected and control groups, as well as between chicken lines...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29352201/cross-species-transcriptional-analysis-reveals-conserved-and-host-specific-neoplastic-processes-in-mammalian-glioma
#8
Nina P Connolly, Amol C Shetty, Jesse A Stokum, Ina Hoeschele, Marni B Siegel, C Ryan Miller, Anthony J Kim, Cheng-Ying Ho, Eduardo Davila, J Marc Simard, Scott E Devine, John H Rossmeisl, Eric C Holland, Jeffrey A Winkles, Graeme F Woodworth
Glioma is a unique neoplastic disease that develops exclusively in the central nervous system (CNS) and rarely metastasizes to other tissues. This feature strongly implicates the tumor-host CNS microenvironment in gliomagenesis and tumor progression. We investigated the differences and similarities in glioma biology as conveyed by transcriptomic patterns across four mammalian hosts: rats, mice, dogs, and humans. Given the inherent intra-tumoral molecular heterogeneity of human glioma, we focused this study on tumors with upregulation of the platelet-derived growth factor signaling axis, a common and early alteration in human gliomagenesis...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29352183/environmental-enrichment-increases-transcriptional-and-epigenetic-differentiation-between-mouse-dorsal-and-ventral-dentate-gyrus
#9
Tie-Yuan Zhang, Christopher L Keown, Xianglan Wen, Junhao Li, Dulcie A Vousden, Christoph Anacker, Urvashi Bhattacharyya, Richard Ryan, Josie Diorio, Nicholas O'Toole, Jason P Lerch, Eran A Mukamel, Michael J Meaney
Early life experience influences stress reactivity and mental health through effects on cognitive-emotional functions that are, in part, linked to gene expression in the dorsal and ventral hippocampus. The hippocampal dentate gyrus (DG) is a major site for experience-dependent plasticity associated with sustained transcriptional alterations, potentially mediated by epigenetic modifications. Here, we report comprehensive DNA methylome, hydroxymethylome and transcriptome data sets from mouse dorsal and ventral DG...
January 19, 2018: Nature Communications
https://www.readbyqxmd.com/read/29352122/comparative-transcriptomic-and-proteomic-analysis-of-arthrobacter-sp-cgmcc-3584-responding-to-dissolved-oxygen-for-camp-production
#10
Huanqing Niu, Junzhi Wang, Wei Zhuang, Dong Liu, Yong Chen, Chenjie Zhu, Hanjie Ying
Arthrobacter sp. CGMCC 3584 is able to produce high yields of extracellular cyclic adenosine monophosphate (cAMP), which plays a vital role in the field of treatment of disease and animal food, during aerobic fermentation. However, the molecular basis of cAMP production in Arthrobacter species is rarely explored. Here, for the first time, we report the comparative transcriptomic and proteomic study of Arthrobacter cells to elucidate the higher productivity of cAMP under high oxygen supply. We finally obtained 14...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29352121/efficient-differentiation-of-human-pluripotent-stem-cells-into-skeletal-muscle-cells-by-combining-rna-based-myod1-expression-and-pou5f1-silencing
#11
Tomohiko Akiyama, Saeko Sato, Nana Chikazawa-Nohtomi, Atsumi Soma, Hiromi Kimura, Shunichi Wakabayashi, Shigeru B H Ko, Minoru S H Ko
Direct generation of skeletal muscle cells from human pluripotent stem cells (hPSCs) would be beneficial for drug testing, drug discovery, and disease modelling in vitro. Here we show a rapid and robust method to induce myogenic differentiation of hPSCs by introducing mRNA encoding MYOD1 together with siRNA-mediated knockdown of POU5F1 (also known as OCT4 or OCT3/4). This integration-free approach generates functional skeletal myotubes with sarcomere-like structure and a fusion capacity in several days. The POU5F1 silencing facilitates MYOD1 recruitment to the target promoters, which results in the significant activation of myogenic genes in hPSCs...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29352091/precursors-of-human-cd4-cytotoxic-t-lymphocytes-identified-by-single-cell-transcriptome-analysis
#12
Veena S Patil, Ariel Madrigal, Benjamin J Schmiedel, James Clarke, Patrick O'Rourke, Aruna D de Silva, Eva Harris, Bjoern Peters, Gregory Seumois, Daniela Weiskopf, Alessandro Sette, Pandurangan Vijayanand
CD4+ cytotoxic T lymphocytes (CD4-CTLs) have been reported to play a protective role in several viral infections. However, little is known in humans about the biology of CD4-CTL generation, their functional properties, and heterogeneity, especially in relation to other well-described CD4+ memory T cell subsets. We performed single-cell RNA sequencing in more than 9000 cells to unravel CD4-CTL heterogeneity, transcriptional profile, and clonality in humans. Single-cell differential gene expression analysis revealed a spectrum of known transcripts, including several linked to cytotoxic and costimulatory function that are expressed at higher levels in the TEMRA (effector memory T cells expressing CD45RA) subset, which is highly enriched for CD4-CTLs, compared with CD4+ T cells in the central memory (TCM) and effector memory (TEM) subsets...
January 19, 2018: Science Immunology
https://www.readbyqxmd.com/read/29351989/iterative-random-forests-to-discover-predictive-and-stable-high-order-interactions
#13
Sumanta Basu, Karl Kumbier, James B Brown, Bin Yu
Genomics has revolutionized biology, enabling the interrogation of whole transcriptomes, genome-wide binding sites for proteins, and many other molecular processes. However, individual genomic assays measure elements that interact in vivo as components of larger molecular machines. Understanding how these high-order interactions drive gene expression presents a substantial statistical challenge. Building on random forests (RFs) and random intersection trees (RITs) and through extensive, biologically inspired simulations, we developed the iterative random forest algorithm (iRF)...
January 19, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29351810/identify-down-syndrome-transcriptome-associations-using-integrative-analysis-of-microarray-database-and-correlation-interaction-network
#14
Min Chen, Jiayan Wang, Yingjun Luo, Kailing Huang, Xiaoshun Shi, Yanhui Liu, Jin Li, Zhengfei Lai, Shuya Xue, Haimei Gao, Allen Chen, Dunjin Chen
BACKGROUND: Long non-coding RNAs (lncRNAs) have previously been emerged as key players in a series of biological processes. Dysregulation of lncRNA is correlated to human diseases including neurological disorders. Here, we developed a multi-step bioinformatics analysis to study the functions of a particular Down syndrome-associated gene DSCR9 including the lncRNAs. The method is named correlation-interaction-network (COIN), based on which a pipeline is implemented. Co-expression gene network analysis and biological network analysis results are presented...
January 19, 2018: Human Genomics
https://www.readbyqxmd.com/read/29351734/eogd-the-euplotes-octocarinatus-genome-database
#15
Ruan-Lin Wang, Wei Miao, Wei Wang, Jie Xiong, Ai-Hua Liang
BACKGROUND: Euplotes, a ciliated protozoan, is a useful unicellular model organism. Studies on Euplotes have provided excellent insights into various basic biological principles. We have recently sequenced the macronuclear genome of the common freshwater species Euplotes octocarinatus to provide novel insights into Euplotes genetics and molecular biology. RESULTS: In this study, we present the E. octocarinatus Genome Database (EOGD), a functional annotation and analysis platform for the global study of the Euplotes genome...
January 19, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29351633/evolutionary-genetics-of-cytoplasmic-incompatibility-genes-cifa-and-cifb-in-prophage-wo-of-wolbachia
#16
Amelia R I Lindsey, Danny W Rice, Sarah R Bordenstein, Andrew W Brooks, Seth R Bordenstein, Irene L G Newton
The bacterial endosymbiont Wolbachia manipulates arthropod reproduction to facilitate its maternal spread through host populations. The most common manipulation is cytoplasmic incompatibility (CI): Wolbachia-infected males produce modified sperm that cause embryonic mortality, unless rescued by embryos harboring the same Wolbachia. The genes underlying CI, cifA and cifB, were recently identified in the eukaryotic association module of Wolbachia's prophage WO. Here, we use transcriptomic and genomic approaches to address three important evolutionary facets of the cif genes...
January 17, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29351586/computational-deconvolution-of-transcriptomics-data-from-mixed-cell-populations
#17
Francisco Avila Cobos, Jo Vandesompele, Pieter Mestdagh, Katleen De Preter
Contact: Katleen.DePreter@UGent.be. Supplementary information: Supplementary data are available at Bioinformatics online.
January 16, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29351567/whole-thorax-irradiation-of-non-human-primates-induces-persistent-nuclear-damage-and-gene-expression-changes-in-peripheral-blood-cells
#18
Shanaz A Ghandhi, Helen C Turner, Igor Shuryak, Gregory O Dugan, J Daniel Bourland, John D Olson, Janet A Tooze, Shad R Morton, Ines Batinic-Haberle, J Mark Cline, Sally A Amundson
We investigated the cytogenetic and gene expression responses of peripheral blood cells of non-human primates (NHP, Macaca mulatta) that were whole-thorax irradiated with a single dose of 10 Gy. In this model, partial irradiation of NHPs in the thoracic region (Whole Thorax Lung Irradiation, WTLI) allows the study of late radiation-induced lung injury, while avoiding acute radiation syndromes related to hematopoietic and gastrointestinal injury. A transient drop in circulating lymphocytes and platelets was seen by 9 days, followed by elevations in respiratory rate, circulating neutrophils, lymphocytes, and monocytes at 60-100 days, corresponding to computed tomography (CT) and histologic evidence of pneumonitis, and elective euthanasia of four animals...
2018: PloS One
https://www.readbyqxmd.com/read/29351515/understanding-key-mechanisms-of-exercise-induced-cardiac-protection-to-mitigate-disease-current-knowledge-and-emerging-concepts
#19
Bianca C Bernardo, Jenny Y Y Ooi, Kate L Weeks, Natalie L Patterson, Julie R McMullen
The benefits of exercise on the heart are well recognized, and clinical studies have demonstrated that exercise is an intervention that can improve cardiac function in heart failure patients. This has led to significant research into understanding the key mechanisms responsible for exercise-induced cardiac protection. Here, we summarize molecular mechanisms that regulate exercise-induced cardiac myocyte growth and proliferation. We discuss in detail the effects of exercise on other cardiac cells, organelles, and systems that have received less or little attention and require further investigation...
January 1, 2018: Physiological Reviews
https://www.readbyqxmd.com/read/29351317/hafts-are-novel-lncrna-transcripts-from-aflatoxin-exposure
#20
B Alex Merrick, Justin S Chang, Dhiral P Phadke, Meredith A Bostrom, Ruchir R Shah, Xinguo Wang, Oksana Gordon, Garron M Wright
The transcriptome can reveal insights into precancer biology. We recently conducted RNA-Seq analysis on liver RNA from male rats exposed to the carcinogen, aflatoxin B1 (AFB1), for 90 days prior to liver tumor onset. Among >1,000 differentially expressed transcripts, several novel, unannotated Cufflinks-assembled transcripts, or HAfTs (Hepatic Aflatoxin Transcripts) were found. We hypothesized PCR-cloning and RACE (rapid amplification of cDNA ends) could further HAfT identification. Sanger data was obtained for 6 transcripts by PCR and 16 transcripts by 5'- and 3'-RACE...
2018: PloS One
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