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https://www.readbyqxmd.com/read/28350989/mir-219-cooperates-with-mir-338-in-myelination-and-promotes-myelin-repair-in-the-cns
#1
Haibo Wang, Ana Lis Moyano, Zhangyan Ma, Yaqi Deng, Yifeng Lin, Chuntao Zhao, Liguo Zhang, Minqing Jiang, Xuelian He, Zhixing Ma, Fanghui Lu, Mei Xin, Wenhao Zhou, Sung Ok Yoon, Ernesto R Bongarzone, Q Richard Lu
A lack of sufficient oligodendrocyte myelination contributes to remyelination failure in demyelinating disorders. miRNAs have been implicated in oligodendrogenesis; however, their functions in myelin regeneration remained elusive. Through developmentally regulated targeted mutagenesis, we demonstrate that miR-219 alleles are critical for CNS myelination and remyelination after injury. Further deletion of miR-338 exacerbates the miR-219 mutant hypomyelination phenotype. Conversely, miR-219 overexpression promotes precocious oligodendrocyte maturation and regeneration processes in transgenic mice...
March 27, 2017: Developmental Cell
https://www.readbyqxmd.com/read/28350803/pharmacogenomic-identification-of-small-molecules-for-lineage-specific-manipulation-of-subventricular-zone-germinal-activity
#2
Kasum Azim, Diane Angonin, Guillaume Marcy, Francesca Pieropan, Andrea Rivera, Vanessa Donega, Claudio Cantù, Gareth Williams, Benedikt Berninger, Arthur M Butt, Olivier Raineteau
Strategies for promoting neural regeneration are hindered by the difficulty of manipulating desired neural fates in the brain without complex genetic methods. The subventricular zone (SVZ) is the largest germinal zone of the forebrain and is responsible for the lifelong generation of interneuron subtypes and oligodendrocytes. Here, we have performed a bioinformatics analysis of the transcriptome of dorsal and lateral SVZ in early postnatal mice, including neural stem cells (NSCs) and their immediate progenies, which generate distinct neural lineages...
March 2017: PLoS Biology
https://www.readbyqxmd.com/read/28346891/spatial-transcriptomics-paving-the-way-for-tissue-level-systems-biology
#3
REVIEW
Andreas E Moor, Shalev Itzkovitz
The tissues in our bodies are complex systems composed of diverse cell types that often interact in highly structured repeating anatomical units. External gradients of morphogens, directional blood flow, as well as the secretion and absorption of materials by cells generate distinct microenvironments at different tissue coordinates. Such spatial heterogeneity enables optimized function through division of labor among cells. Unraveling the design principles that govern this spatial division of labor requires techniques to quantify the entire transcriptomes of cells while accounting for their spatial coordinates...
March 24, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28346802/metabolome-profiling-of-partial-and-fully-reprogrammed-induced-pluripotent-stem-cells
#4
Soon-Jung Park, Sang A Lee, Nutan Prasain, Daekyeong Bae, Hyunsu Kang, Taewon Ha, Jong Soo Kim, Ki-Sung Hong, Charlie Mantel, Sung-Hwan Moon, Hal E Broxmeyer, Man Ryul Lee
Acquisition of proper metabolomic fate is required to convert somatic cells toward fully reprogrammed pluripotent stem cells. The majority of induced pluripotent stem cells (iPSCs) are partially reprogrammed and have a transcriptome different from that of the pluripotent stem cells. The metabolomic profile and mitochondrial metabolic functions required to achieve full reprogramming of somatic cells to iPSC status have not yet been elucidated. Clarification of the metabolites underlying reprogramming mechanisms should enable further optimization to enhance the efficiency of obtaining fully reprogrammed iPSCs...
March 27, 2017: Stem Cells and Development
https://www.readbyqxmd.com/read/28346544/epigenetic-silencing-of-v-d-j-recombination-is-a-major-determinant-for-selective-differentiation-of-mucosal-associated-invariant-t-cells-from-induced-pluripotent-stem-cells
#5
Yutaka Saito, Chie Sugimoto, Toutai Mituyama, Hiroshi Wakao
Mucosal-associated invariant T cells (MAITs) are innate-like T cells that play a pivotal role in the host defense against infectious diseases, and are also implicated in autoimmune diseases, metabolic diseases, and cancer. Recent studies have shown that induced pluripotent stem cells (iPSCs) derived from MAITs selectively redifferentiate into MAITs without altering their antigen specificity. Such a selective differentiation is a prerequisite for the use of MAITs in cell therapy and/or regenerative medicine...
2017: PloS One
https://www.readbyqxmd.com/read/28346528/correction-identification-of-a-putative-quantitative-trait-gene-for-resistance-to-obesity-in-mice-using-transcriptome-analysis-and-causal-inference-tests
#6
https://www.readbyqxmd.com/read/28346506/specific-expression-of-novel-long-non-coding-rnas-in-high-hyperdiploid-childhood-acute-lymphoblastic-leukemia
#7
Mathieu Lajoie, Simon Drouin, Maxime Caron, Pascal St-Onge, Manon Ouimet, Romain Gioia, Marie-Hélène Lafond, Ramon Vidal, Chantal Richer, Karim Oualkacha, Arnaud Droit, Daniel Sinnett
Pre-B cell childhood acute lymphoblastic leukemia (pre-B cALL) is a heterogeneous disease involving many subtypes typically stratified using a combination of cytogenetic and molecular-based assays. These methods, although widely used, rely on the presence of known chromosomal translocations, which is a limiting factor. There is therefore a need for robust, sensitive, and specific molecular biomarkers unaffected by such limitations that would allow better risk stratification and consequently better clinical outcome...
2017: PloS One
https://www.readbyqxmd.com/read/28346451/sc3-consensus-clustering-of-single-cell-rna-seq-data
#8
Vladimir Yu Kiselev, Kristina Kirschner, Michael T Schaub, Tallulah Andrews, Andrew Yiu, Tamir Chandra, Kedar N Natarajan, Wolf Reik, Mauricio Barahona, Anthony R Green, Martin Hemberg
Single-cell RNA-seq enables the quantitative characterization of cell types based on global transcriptome profiles. We present single-cell consensus clustering (SC3), a user-friendly tool for unsupervised clustering, which achieves high accuracy and robustness by combining multiple clustering solutions through a consensus approach (http://bioconductor.org/packages/SC3). We demonstrate that SC3 is capable of identifying subclones from the transcriptomes of neoplastic cells collected from patients.
March 27, 2017: Nature Methods
https://www.readbyqxmd.com/read/28346448/a-footprint-of-desiccation-tolerance-in-the-genome-of-xerophyta-viscosa
#9
Maria-Cecília D Costa, Mariana A S Artur, Julio Maia, Eef Jonkheer, Martijn F L Derks, Harm Nijveen, Brett Williams, Sagadevan G Mundree, José M Jiménez-Gómez, Thamara Hesselink, Elio G W M Schijlen, Wilco Ligterink, Melvin J Oliver, Jill M Farrant, Henk W M Hilhorst
Desiccation tolerance is common in seeds and various other organisms, but only a few angiosperm species possess vegetative desiccation tolerance. These 'resurrection species' may serve as ideal models for the ultimate design of crops with enhanced drought tolerance. To understand the molecular and genetic mechanisms enabling vegetative desiccation tolerance, we produced a high-quality whole-genome sequence for the resurrection plant Xerophyta viscosa and assessed transcriptome changes during its dehydration...
March 27, 2017: Nature Plants
https://www.readbyqxmd.com/read/28346370/de-novo-assembly-annotation-and-characterization-of-root-transcriptomes-of-three-caladium-cultivars-with-a-focus-on-necrotrophic-pathogen-resistance-defense-related-genes
#10
Zhe Cao, Zhanao Deng
Roots are vital to plant survival and crop yield, yet few efforts have been made to characterize the expressed genes in the roots of non-model plants (root transcriptomes). This study was conducted to sequence, assemble, annotate, and characterize the root transcriptomes of three caladium cultivars (Caladium × hortulanum) using RNA-Seq. The caladium cultivars used in this study have different levels of resistance to Pythiummyriotylum, the most damaging necrotrophic pathogen to caladium roots. Forty-six to 61 million clean reads were obtained for each caladium root transcriptome...
March 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28346141/insights-into-electrosensory-organ-development-physiology-and-evolutionfrom-a-lateral-line-enriched-transcriptome
#11
Melinda S Modrell, Mike Lyne, Adrian R Carr, Harold H Zakon, David Buckley, Alexander S Campbell, Marcus C Davis, Gos Micklem, Clare Vh Baker
The anamniote lateral line system, comprising mechanosensory neuromasts and electrosensory ampullary organs, is a useful model for investigating the developmental and evolutionary diversification of different organs and cell types. Zebrafish neuromast development is increasingly well understood, but neither zebrafish nor Xenopus is electroreceptive and our molecular understanding of ampullary organ development is rudimentary. We have used RNA-seq to generate a lateral line-enriched gene-set from late-larval paddlefish (Polyodon spathula)...
March 27, 2017: ELife
https://www.readbyqxmd.com/read/28346137/histone-gene-replacement-reveals-a-post-transcriptional-role-for-h3k36-in-maintaining-metazoan-transcriptome-fidelity
#12
Michael P Meers, Telmo Henriques, Christopher A Lavender, Daniel J McKay, Brian D Strahl, Robert J Duronio, Karen Adelman, A Gregory Matera
Histone H3 lysine 36 methylation (H3K36me) is thought to participate in a host of co-transcriptional regulatory events. To study the function of this residue independent from the enzymes that modify it, we used a 'histone replacement' system in Drosophila to generate a non-modifiable H3K36 lysine-to-arginine (H3K36R) mutant. We observed global dysregulation of mRNA levels in H3K36R animals that correlates with the incidence of H3K36me3. Similar to previous studies, we found that mutation of H3K36 also resulted in H4 hyperacetylation...
March 27, 2017: ELife
https://www.readbyqxmd.com/read/28345955/smoking-dependent-distal-to-proximal-repatterning-of-the-adult-human-small-airway-epithelium
#13
Jing Yang, Wu-Lin Zuo, Tomoya Fukui, IonWa Chao, Kazunori Gomi, Busub Lee, Michelle R Staudt, Robert J Kaner, Yael Strulovici-Barel, Jacqueline Salit, Ronald G Crystal, Renat Shaykhiev
RATIONALE: Small airways are the primary site of pathologic changes in chronic obstructive pulmonary disease (COPD), the major smoking-induced lung disorder. OBJECTIVES: Based on the concept of proximal-distal patterning that determines regional specialization of the airway epithelium during lung development, we hypothesized that a similar program operates in the adult human lung being altered by smoking leading to decreased regional identity of the small airway epithelium (SAE)...
March 27, 2017: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/28345896/transcriptomics-and-lipidomics-of-the-environmental-strain-rhodococcus-ruber-point-out-consumption-pathways-and-potential-metabolic-bottlenecks-for-polyethylene-degradation
#14
Kevin Gravouil, Romain Ferru-Clement, Steven Colas, Reynald Helye, Linette Kadri, Ludivine Bourdeau, Bouziane Moumen, Anne Mercier, Thierry Ferreira
Polyethylene (PE), one of the most prominent synthetic polymer used worldwide, is very poorly biodegradable in the natural environment. Consequently, PE represents by itself more than half of all plastic wastes. PE biodegradation is achieved through the combination of abiotic and biotic processes. Several microorganisms have been shown to grow on the surface of PE materials, among which are the species of the Rhodococcus genus, suggesting a potent ability of these microorganisms to use, at least partly, PE as a potent carbon source...
March 27, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28345615/transcriptome-analysis-of-molecular-mechanisms-responsible-for-light-stress-response-in-mythimna-separata-walker
#15
Yun Duan, ZhongJun Gong, RenHai Wu, Jin Miao, YueLi Jiang, Tong Li, XiaoBo Wu, YuQing Wu
Light is an important environmental signal for most insects. The Oriental Armyworm, Mythimna separata, is a serious pest of cereal crops worldwide, and is highly sensitive to light signals during its developmental and reproductive stages. However, molecular biological studies of its response to light stress are scarce, and related genomic information is not available. In this study, we sequenced and de novo assembled the transcriptomes of M. separata exposed to four different light conditions: dark, white light (WL), UV light (UVL) and yellow light (YL)...
March 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28345607/time-and-dose-dependent-actions-of-cardiotonic-steroids-on-transcriptome-and-intracellular-content-of-na-and-k-a-comparative-analysis
#16
Elizaveta A Klimanova, Artem M Tverskoi, Svetlana V Koltsova, Svetlana V Sidorenko, Olga D Lopina, Johanne Tremblay, Pavel Hamet, Leonid V Kapilevich, Sergei N Orlov
Recent studies demonstrated that in addition to Na(+),K(+)-ATPase inhibition cardiotonic steroids (CTSs) affect diverse intracellular signaling pathways. This study examines the relative impact of [Na(+)]i/[K(+)]i-mediated and -independent signaling in transcriptomic changes triggered by the endogenous CTSs ouabain and marinobufagenin (MBG) in human umbilical vein endothelial cells (HUVEC). We noted that prolongation of incubation increased the apparent affinity for ouabain estimated by the loss of [K(+)]i and gain of [Na(+)]i...
March 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28345372/screening-of-intestinal-crypt-organoids
#17
Svenja Ley, Olaf Galuba, Adrian Salathe, Nicolas Melin, Alexandra Aebi, Monika Pikiolek, Judith Knehr, Walter Carbone, Martin Beibel, Florian Nigsch, Guglielmo Roma, Giovanni d'Ario, Susan Kirkland, Laure C Bouchez, Caroline Gubser Keller, Tewis Bouwmeester, Christian N Parker, Heinz Ruffner
Oral and intestinal mucositis is a debilitating side effect of radiation treatment. A mouse model of radiation-induced mucositis leads to weight loss and tissue damage, reflecting the human ailment as it responds to keratinocyte growth factor (KGF), the standard-of-care treatment. Cultured intestinal crypt organoids allowed the development of an assay monitoring the effect of treatments of intestinal epithelium to radiation-induced damage. This in vitro assay resembles the mouse model as KGF and roof plate-specific spondin-1 (RSPO1) enhanced crypt organoid recovery following radiation...
January 1, 2017: SLAS Discov
https://www.readbyqxmd.com/read/28345264/blood-transcriptomes-and-de-novo-identification-of-candidate-loci-for-mating-success-in-lekking-great-snipe-gallinago-media
#18
Jacob Höglund, Biao Wang, Stein Are Saether, Mozes Pil Kyu Blom, Peder Fiske, Peter Halvarsson, Gavin J Horsburgh, Terry Burke, John Atle Kålås, Robert Ekblom
We assembled the great snipe blood transcriptome using data from fourteen lekking males, in order to de novo identify candidate genes related to sexual selection, and determined the expression profiles in relation to mating success. The three most highly transcribed genes were encoding different haemoglobin subunits. All tended to be overexpressed in males with high mating success. We also called Single Nucleotide Polymorphisms (SNPs) from the transcriptome data and found considerable genetic variation for many genes expressed during lekking...
March 27, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28345225/highly-potent-host-external-immunity-acts-as-a-strong-selective-force-enhancing-rapid-parasite-virulence-evolution
#19
Charlotte Rafaluk, Wentao Yang, Andreas Mitschke, Philip Rosenstiel, Hinrich Schulenburg, Gerrit Joop
Virulence is often under selection during host-parasite coevolution. In order to increase fitness, parasites are predicted to circumvent and overcome host immunity. A particular challenge for pathogens are external immune systems, chemical defence systems comprised of potent antimicrobial compounds released by prospective hosts into the environment. We carried out an evolution experiment, allowing for coevolution to occur, with the entomopathogenic fungus, Beauveria bassiana, and the red flour beetle, Tribolium castaneum, which has a well-documented external immune system with strong inhibitory effects against B...
March 26, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28345074/single-cell-rna-seq-and-computational-analysis-using-temporal-mixture-modelling-resolves-th1-tfh-fate-bifurcation-in-malaria
#20
Tapio Lönnberg, Valentine Svensson, Kylie R James, Daniel Fernandez-Ruiz, Ismail Sebina, Ruddy Montandon, Megan S F Soon, Lily G Fogg, Arya Sheela Nair, Urijah Liligeto, Michael J T Stubbington, Lam-Ha Ly, Frederik Otzen Bagger, Max Zwiessele, Neil D Lawrence, Fernando Souza-Fonseca-Guimaraes, Patrick T Bunn, Christian R Engwerda, William R Heath, Oliver Billker, Oliver Stegle, Ashraful Haque, Sarah A Teichmann
Differentiation of naïve CD4(+) T cells into functionally distinct T helper subsets is crucial for the orchestration of immune responses. Due to extensive heterogeneity and multiple overlapping transcriptional programs in differentiating T cell populations, this process has remained a challenge for systematic dissection in vivo. By using single-cell transcriptomics and computational analysis using a temporal mixtures of Gaussian processes model, termed GPfates, we reconstructed the developmental trajectories of Th1 and Tfh cells during blood-stage Plasmodium infection in mice...
March 3, 2017: Science Immunology
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