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https://www.readbyqxmd.com/read/28438991/differentiation-of-v2a-interneurons-from-human-pluripotent-stem-cells
#1
Jessica C Butts, Dylan A McCreedy, Jorge Alexis Martinez-Vargas, Frederico N Mendoza-Camacho, Tracy A Hookway, Casey A Gifford, Praveen Taneja, Linda Noble-Haeusslein, Todd C McDevitt
The spinal cord consists of multiple neuronal cell types that are critical to motor control and arise from distinct progenitor domains in the developing neural tube. Excitatory V2a interneurons in particular are an integral component of central pattern generators that control respiration and locomotion; however, the lack of a robust source of human V2a interneurons limits the ability to molecularly profile these cells and examine their therapeutic potential to treat spinal cord injury (SCI). Here, we report the directed differentiation of CHX10(+) V2a interneurons from human pluripotent stem cells (hPSCs)...
April 24, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28438136/normalized-long-read-rna-sequencing-in-chicken-reveals-transcriptome-complexity-similar-to-human
#2
Richard I Kuo, Elizabeth Tseng, Lel Eory, Ian R Paton, Alan L Archibald, David W Burt
BACKGROUND: Despite the significance of chicken as a model organism, our understanding of the chicken transcriptome is limited compared to human. This issue is common to all non-human vertebrate annotations due to the difficulty in transcript identification from short read RNAseq data. While previous studies have used single molecule long read sequencing for transcript discovery, they did not perform RNA normalization and 5'-cap selection which may have resulted in lower transcriptome coverage and truncated transcript sequences...
April 24, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28437580/differential-gene-expression-in-narrow-and-broad-headed-european-glass-eels-anguilla-anguilla-points-to-a-transcriptomic-link-of-head-shape-dimorphism-with-growth-rate-and-chemotaxis
#3
J De Meyer, G E Maes, R P Dirks, D Adriaens
One of the major challenges in evolutionary biology is to understand the mechanisms underlying morphological dimorphism and plasticity, including the genomic basis of traits and links to ecology. At the yellow eel stage of the European eel (Anguilla anguilla), two morphotypes are found: broad- and narrow-heads. This dimorphism has been linked to dietary differences, with broad-heads feeding on harder, larger prey than narrow-heads. However, recent research showed that both morphotypes could be distinguished at the glass eel stage, the non-feeding predecessor of the yellow eel stage, implying that non-dietary factors play a role in the development of this head shape dimorphism...
April 24, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28431148/truncated-orf1-proteins-can-suppress-line-1-retrotransposition-in-trans
#4
Mark Sokolowski, May Chynces, Dawn deHaro, Claiborne M Christian, Victoria P Belancio
Long interspersed element 1 (L1) is an autonomous non-LTR retroelement that is active in mammalian genomes. Although retrotranspositionally incompetent and functional L1 loci are present in the same genomes, it remains unknown whether non-functional L1s have any trans effect on mobilization of active elements. Using bioinformatic analysis, we identified over a thousand of human L1 loci containing at least one stop codon in their ORF1 sequence. RNAseq analysis confirmed that many of these loci are expressed...
April 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28430882/inhibition-of-the-cardiac-myocyte-mineralocorticoid-receptor-ameliorates-doxorubicin-induced-cardiotoxicity
#5
Achim Lother, Stella Bergemann, Jessica Kowalski, Michael Huck, Ralf Gilsbach, Christoph Bode, Lutz Hein
Aim: HASH(0x47693e8) Anthracyclines such as doxorubicin are widely used in cancer therapy but their use is limited by cardiotoxicity. Up to date there is no established strategy for the prevention of anthracyclin-induced heart failure. In this study, we evaluated the role of the cardiac myocyte mineralocorticoid receptor (MR) during doxorubicin-induced cardiotoxicity. Methods and results: HASH(0x47e9010) A single high-dose or repetitive low-dose doxorubicin administration lead to markedly reduced left ventricular function in mice...
April 18, 2017: Cardiovascular Research
https://www.readbyqxmd.com/read/28429320/euglena-gracilis-genome-and-transcriptome-organelles-nuclear-genome-assembly-strategies-and-initial-features
#6
ThankGod Echezona Ebenezer, Mark Carrington, Michael Lebert, Steven Kelly, Mark C Field
Euglena gracilis is a major component of the aquatic ecosystem and together with closely related species, is ubiquitous worldwide. Euglenoids are an important group of protists, possessing a secondarily acquired plastid and are relatives to the Kinetoplastidae, which themselves have global impact as disease agents. To understand the biology of E. gracilis, as well as to provide further insight into the evolution and origins of the Kinetoplastidae, we embarked on sequencing the nuclear genome; the plastid and mitochondrial genomes are already in the public domain...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28426683/genome-wide-identification-and-characterization-of-mirnaome-from-tomato-solanum-lycopersicum-roots-and-root-knot-nematode-meloidogyne-incognita-during-susceptible-interaction
#7
Pritam Kaur, Neha Shukla, Gopal Joshi, Cheeni VijayaKumar, Arun Jagannath, Manu Agarwal, Shailendra Goel, Amar Kumar
Root-knot nematodes (RKNs, Meloidogyne spp.) are the most damaging plant parasites causing severe losses to crop production. The present study reports genome-wide identification and characterization of both tomato and RKN miRNAs simultaneously from RKN-infected susceptible tomato roots using high-throughput sequencing technique. RNAseq data from 11 small RNA libraries derived from 5 disease development stages identified 281 novel miRNAs of tomato in addition to 52 conserved and 4 variants of conserved miRNAs...
2017: PloS One
https://www.readbyqxmd.com/read/28423006/transcriptome-and-proteome-responses-in-rnalater-preserved-tissue-of-arabidopsis-thaliana
#8
Colin P S Kruse, Proma Basu, Darron R Luesse, Sarah E Wyatt
Tissue preservation is a minimal requirement for the success of plant RNA and protein expression studies. The standard of snap-freezing in liquid nitrogen is not always practical or possible. RNAlater, a concentrated solution of ammonium and cesium sulfates, has become a standard preservative in the absence of liquid nitrogen. Here, we demonstrate the effectiveness of RNAlater in preserving both RNA and proteins in Arabidopsis thaliana tissues for use in RNAseq and LC-MS/MS analysis of proteins. While successful in preserving plant material, a transcriptomic and proteomic response is evident...
2017: PloS One
https://www.readbyqxmd.com/read/28418402/transcriptome-sequencing-study-implicates-immune-related-genes-differentially-expressed-in-schizophrenia-new-data-and-a-meta-analysis
#9
A R Sanders, E I Drigalenko, J Duan, W Moy, J Freda, H H H Göring, P V Gejman
We undertook an RNA sequencing (RNAseq)-based transcriptomic profiling study on lymphoblastoid cell lines of a European ancestry sample of 529 schizophrenia cases and 660 controls, and found 1058 genes to be differentially expressed by affection status. These differentially expressed genes were enriched for involvement in immunity, especially the 697 genes with higher expression in cases. Comparing the current RNAseq transcriptomic profiling to our previous findings in an array-based study of 268 schizophrenia cases and 446 controls showed a highly significant positive correlation over all genes...
April 18, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28414090/rituximab-treatment-circumvents-the-prognostic-impact-of-tumor-infiltrating-t-cells-in-follicular-lymphoma-patients
#10
Luc Xerri, Sarah Huet, Jeffrey M Venstrom, Edith Szafer-Glusman, Bettina Fabiani, Danielle Canioni, Catherine Chassagne-Clément, Peggy Dartigues-Cuilléres, Fréderic Charlotte, Camille Laurent, Benedicte Gelas-Dore, Christopher R Bolen, Elizabeth Punnoose, Reda Bouabdallah, Pauline Brice, Franck Morschhauser, Guillaume Cartron, Daniel Olive, Gilles Salles
Previous immunohistochemical (IHC) studies showed controversial data about the prognostic value of tumor infiltrating lymphocytes (TIL) in follicular lymphoma (FL). In order to clarify this issue, a large series of FL samples from rituximab-treated patients enrolled in the randomized PRIMA trial were examined. IHC was quantified using automated image analysis in 417, 287, 418, 406, 379, and 369 patients for CD3, CD4, CD8, PD1, ICOS, and FOXP3; respectively. RNAseq analysis was used to quantify TIL-related mRNA transcripts from 148 patients...
April 13, 2017: Human Pathology
https://www.readbyqxmd.com/read/28409421/the-impact-of-microenvironment-on-the-synovial-sarcoma-transcriptome
#11
Huifeng Jin, Jared J Barrott, Matthew G Cable, Michael J Monument, Daniel M Lerman, Kyllie Smith-Fry, Dakota Nollner, Kevin B Jones
Synovial sarcoma (SS) is initiated by a t(X;18) chromosomal translocation and resultant SS18-SSX fusion oncogene. Only a few SS cell lines exist. None has been compared to its source tumor. In order to compare matched tumor and cell line pairs, we performed RNAseq on 3 tumor/cell line pairs from a genetically engineered mouse model of SS, as well as 2 pairs from human SS tumors. Transcriptomes of mouse tumors and derivative cell lines deviated significantly. Differentially expressed genes highlighted inflammatory infiltrates and metabolism...
April 13, 2017: Cancer Microenvironment: Official Journal of the International Cancer Microenvironment Society
https://www.readbyqxmd.com/read/28408365/immunomodulators-targeting-marco-expression-improve-resistance-to-post-influenza-bacterial-pneumonia
#12
Muzo Wu, John G Gibbons, Glen M Deloid, Alice S Bedugnis, Rajesh K Thimmulappa, Shyam Biswal, Lester Kobzik
Down-regulation of the alveolar macrophage (AM) macrophage receptor with collagenous structure (MARCO) leads to susceptibility to post-influenza bacterial pneumonia, a major cause of morbidity and mortality. We sought to determine whether immunomodulation of MARCO could improve host defense and resistance to secondary bacterial pneumonia. RNAseq analysis identified a striking increase of MARCO expression between days 9 and 11 after influenza infection and indicated important roles for Akt and Nrf2 in MARCO recovery...
April 13, 2017: American Journal of Physiology. Lung Cellular and Molecular Physiology
https://www.readbyqxmd.com/read/28405501/pdl1-expression-is-a-poor-prognosis-factor-in-soft-tissue-sarcomas
#13
François Bertucci, Pascal Finetti, Delphine Perrot, Agnès Leroux, Françoise Collin, Axel Le Cesne, Jean-Michel Coindre, Jean-Yves Blay, Daniel Birnbaum, Emilie Mamessier
Soft-tissue sarcomas (STS) are a group of rare, heterogeneous, and aggressive tumors, with high metastatic risk and relatively few efficient systemic therapies. In the quest for new treatments, the immune system represents an attractive therapeutic target. Recently, PD1/PDL1 inhibitors showed very promising results in patients with solid tumors. PDL1 expression has been rarely studied in STS, in small series only, by using immunohistochemistry (IHC), and with non-concordant prognostic implications. Here, we have analyzed PDL1 mRNA expression in 758 clinical STS samples retrospectively profiled using DNA microarrays and RNAseq, and searched for correlations with clinicopathological variables including metastasis-free survival (MFS) after surgery...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28405244/clusterization-in-head-and-neck-squamous-carcinomas-based-on-lncrna-expression-molecular-and-clinical-correlates
#14
Pelayo G de Lena, Abel Paz-Gallardo, Jesús M Paramio, Ramón García-Escudero
BACKGROUND: Long non-coding RNAs (lncRNAs) have emerged as key players in a remarkably variety of biological processes and pathologic conditions, including cancer. Next-generation sequencing technologies and bioinformatics procedures predict the existence of tens of thousands of lncRNAs, from which we know the functions of only a handful of them, and very little is known in cancer types such as head and neck squamous cell carcinomas (HNSCCs). RESULTS: Here, we use RNAseq expression data from The Cancer Genome Atlas (TCGA) and various statistic and software tools in order to get insight about the lncRNome in HNSCC...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28400082/immune-dysregulation-in-immunodeficiency-disorders-the-role-of-t-cell-receptor-sequencing
#15
REVIEW
Gabriel K Wong, James M Heather, Sara Barmettler, Mark Cobbold
Immune dysregulation is a prominent feature of primary immunodeficiency disorders, which commonly manifested as autoimmunity, cytopenias and inflammatory bowel disease. In partial T-cell immunodeficiency disorders, it has been proposed that the imbalance between effector and regulatory T-cells drives the breakdown of peripheral tolerance. While there is no robust test for immune dysregulation, the T-cell receptor repertoire is used as a surrogate marker, and has been shown to be perturbed in a number of immunodeficiency disorders featuring immune dysregulation including Omenn's Syndrome, Wiskott-Aldrich Syndrome, and common variable immunodeficiency...
April 8, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/28396347/serotype-specific-interactions-among-functional-domains-of-dengue-virus-2-non-structural-proteins-ns-5-and-ns3-are-crucial-for-viral-rna-replication
#16
Tadahisa Teramoto, Anuradha Balasubramanian, Kyung H Choi, Radhakrishnan Padmanabhan
Four serotypes of mosquito-borne Dengue virus (DENV), evolved from a common ancestor, are human pathogens of global significance, and there is no vaccine or antiviral drug available. The N-terminal domain of DENV NS5 has guanylyltransferase and methyltransferase (MTase) and the C-terminal region has the polymerase (POL) which are important for 5'-capping and RNA replication. The crystal structure of NS5 showed it as a dimer but the functional evidence for NS5 dimer is lacking. The results of our studies show that the substitution of DENV2 NS5 MTase or POL with that of DENV4 NS5 within DENV2 RNA resulted in severe attenuation of replication in the transfected BHK-21 cells...
April 10, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28393902/nitrate-application-or-p-deficiency-induce-a-decline-in-medicago-truncatula-n2-fixation-by-similar-changes-in-the-nodule-transcriptome
#17
Rebecca Liese, Joachim Schulze, Ricardo A Cabeza
Nitrogen fixation of Medicago truncatula is regulated by the nitrogen status of leaves through inducing a repeatedly occurring 24-h nodule activity rhythm that reduces per day nitrogen fixation. The hypotheses of the present study were that (1) long-term moderate whole-plant P deficiency in Medicago truncatula induces an according daily rhythm in nitrogenase activity comparable to that induced by nitrate application and (2), the changes in the nodule transcriptome that go along with a strong nitrogenase activity decline during the afternoon would be similar under P deficiency or after nitrate supply...
April 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28386015/lncatlas-database-for-subcellular-localisation-of-long-noncoding-rnas
#18
David Mas-Ponte, Joana Carlevaro-Fita, Emilio Palumbo, Toni Hermoso Pulido, Roderic Guigo, Rory Johnson
The subcellular localisation of long noncoding RNAs (lncRNAs) holds valuable clues to their molecular function. However, measuring localisation of newly-discovered lncRNAs involves time-consuming and costly experimental methods. We have created "LncATLAS", a comprehensive resource of lncRNA localisation in human cells based on RNA-sequencing datasets. Altogether, 6,768 GENCODE-annotated lncRNAs are represented across various compartments of 15 cell lines. We introduce "Relative concentration index" (RCI) as a useful measure of localisation derived from ensemble RNAseq measurements...
April 6, 2017: RNA
https://www.readbyqxmd.com/read/28383283/global-analysis-of-gene-expression-reveals-mrna-superinduction-is-required-for-the-inducible-immune-response-to-a-bacterial-pathogen
#19
Kevin C Barry, Nicholas T Ingolia, Russell E Vance
The inducible innate immune response to infection requires a concerted process of gene expression that is regulated at multiple levels. Most global analyses of the innate immune response have focused on transcription induced by defined immunostimulatory ligands, such as lipopolysaccharide. However, the response to pathogens involves additional complexity, as pathogens interfere with virtually every step of gene expression. How cells respond to pathogen-mediated disruption of gene expression to nevertheless initiate protective responses remains unclear...
April 6, 2017: ELife
https://www.readbyqxmd.com/read/28382148/nr1h3-expression-is-a-prognostic-factor-of-overall-survival-for-patients-with-muscle-invasive-bladder-cancer
#20
Junlong Wu, Fangning Wan, Haoyue Sheng, Guohai Shi, Yijun Shen, Guowen Lin, Bo Dai, Yiping Zhu, Dingwei Ye
BACKGROUND: Nuclear receptors (NRs) are a class of transcription factors that regulate many cellular functions through manipulation of gene expression and also play important roles in tumorigenesis, proliferation, progression and prognosis in various kinds of cancers according to recent studies. This work aimed to determine the predictive ability of NRs in muscle-invasive bladder cancer (MIBC). PATIENTS AND METHODS: A total of 308 MIBC patients with complete clinicopathological and RNASeq data from The Cancer Genome Atlas (TCGA) cohort were collected for filtration...
2017: Journal of Cancer
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