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Developmental transcriptome

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https://www.readbyqxmd.com/read/28536883/identification-of-genes-related-to-skin-development-in-potato
#1
Vijaya K R Vulavala, Edna Fogelman, Lior Rozental, Adi Faigenboim, Zachariah Tanami, Oded Shoseyov, Idit Ginzberg
Newly identified genes that are preferentially expressed in potato skin include genes that are associated with the secondary cell wall and stress-related activities and contribute to the skin's protective function. Microarrays were used to compare the skin and tuber-flesh transcriptomes of potato, to identify genes that contribute to the unique characteristics of the skin as a protective tissue. Functional gene analysis indicated that genes involved in developmental processes such as cell division, cell differentiation, morphogenesis and secondary cell wall formation (lignification and suberization), and stress-related activities, are more highly expressed in the skin than in the tuber flesh...
May 23, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28536000/an-analysis-of-myod-dependent-transcription-using-crispr-cas9-gene-targeting-in-xenopus-tropicalis-embryos
#2
Caitlin McQueen, Mary Elizabeth Pownall
Myogenic regulatory factors (MRFs) are known to have essential roles in both the establishment and differentiation of the skeletal muscle cell lineage. MyoD is expressed early in the Xenopus mesoderm where it is present and active several hours before the activation of muscle differentiation genes. Previous studies in cultured cells and in Xenopus laevis have identified sets of genes that require MyoD prior to differentiation of skeletal muscle. Here we report results from experiments using CRISPR/Cas9 to target the MyoD gene in the diploid frog Xenopus tropicalis, that are analysed by RNA-seq at gastrula stages...
May 20, 2017: Mechanisms of Development
https://www.readbyqxmd.com/read/28534718/jasmonate-suppresses-seedling-soil-emergence-in-arabidopsis-thaliana
#3
Lulu Yao, Yuyu Zheng, Ziqiang Zhu
In addition to defense response, phytohormone jasmonate participates in various plant growth and developmental processes. Nonetheless, its role in the seedling stage is not well defined. We recently report that jasmonate suppresses hypocotyl elongation and promotes cotyledon unfolding in etiolated Arabidopsis seedlings. The molecular basis underlying this phenotype is that jasmonate treatment reduces the biochemical activity of CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) to stabilize several COP1-targetted transcription factors for eliciting a proportion of light responsive transcriptome...
May 23, 2017: Plant Signaling & Behavior
https://www.readbyqxmd.com/read/28534484/mir-132-212-is-required-for-maturation-of-binocular-matching-of-orientation-preference-and-depth-perception
#4
Raffaele Mazziotti, Laura Baroncelli, Nicholas Ceglia, Gabriele Chelini, Grazia Della Sala, Christophe Magnan, Debora Napoli, Elena Putignano, Davide Silingardi, Jonida Tola, Paola Tognini, J Simon C Arthur, Pierre Baldi, Tommaso Pizzorusso
MicroRNAs (miRNAs) are known to mediate post-transcriptional gene regulation, but their role in postnatal brain development is still poorly explored. We show that the expression of many miRNAs is dramatically regulated during functional maturation of the mouse visual cortex with miR-132/212 family being one of the top upregulated miRNAs. Age-downregulated transcripts are significantly enriched in miR-132/miR-212 putative targets and in genes upregulated in miR-132/212 null mice. At a functional level, miR-132/212 deletion affects development of receptive fields of cortical neurons determining a specific impairment of binocular matching of orientation preference, but leaving orientation and direction selectivity unaltered...
May 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28534463/gene-expression-analysis-of-bovine-embryonic-disc-trophoblast-and-parietal-hypoblast-at-the-start-of-gastrulation
#5
Peter L Pfeffer, Craig S Smith, Paul Maclean, Debra K Berg
In cattle early gastrulation-stage embryos (Stage 5), four tissues can be discerned: (i) the top layer of the embryonic disc consisting of embryonic ectoderm (EmE); (ii) the bottom layer of the disc consisting of mesoderm, endoderm and visceral hypoblast (MEH); (iii) the trophoblast (TB); and (iv) the parietal hypoblast. We performed microsurgery followed by RNA-seq to analyse the transcriptome of these four tissues as well as a developmentally earlier pre-gastrulation embryonic disc. The cattle EmE transcriptome was similar at Stages 4 and 5, characterised by the OCT4/SOX2/NANOG pluripotency network...
May 23, 2017: Zygote: the Biology of Gametes and Early Embryos
https://www.readbyqxmd.com/read/28534089/comparison-of-microbiomes-between-red-poultry-mite-populations-dermanyssus-gallinae-predominance-of-bartonella-like-bacteria
#6
Jan Hubert, Tomas Erban, Jan Kopecky, Bruno Sopko, Marta Nesvorna, Martina Lichovnikova, Sabine Schicht, Christina Strube, Olivier Sparagano
Blood feeding red poultry mites (RPM) serve as vectors of pathogenic bacteria and viruses among vertebrate hosts including wild birds, poultry hens, mammals, and humans. The microbiome of RPM has not yet been studied by high-throughput sequencing. RPM eggs, larvae, and engorged adult/nymph samples obtained in four poultry houses in Czechia were used for microbiome analyses by Illumina amplicon sequencing of the 16S ribosomal RNA (rRNA) gene V4 region. A laboratory RPM population was used as positive control for transcriptome analysis by pyrosequencing with identification of sequences originating from bacteria...
May 22, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28532419/a-survey-of-the-complex-transcriptome-from-the-highly-polyploid-sugarcane-genome-using-full-length-isoform-sequencing-and-de-novo-assembly-from-short-read-sequencing
#7
Nam V Hoang, Agnelo Furtado, Patrick J Mason, Annelie Marquardt, Lakshmi Kasirajan, Prathima P Thirugnanasambandam, Frederik C Botha, Robert J Henry
BACKGROUND: Despite the economic importance of sugarcane in sugar and bioenergy production, there is not yet a reference genome available. Most of the sugarcane transcriptomic studies have been based on Saccharum officinarum gene indices (SoGI), expressed sequence tags (ESTs) and de novo assembled transcript contigs from short-reads; hence knowledge of the sugarcane transcriptome is limited in relation to transcript length and number of transcript isoforms. RESULTS: The sugarcane transcriptome was sequenced using PacBio isoform sequencing (Iso-Seq) of a pooled RNA sample derived from leaf, internode and root tissues, of different developmental stages, from 22 varieties, to explore the potential for capturing full-length transcript isoforms...
May 22, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28531310/nascent-rna-sequencing-reveals-mechanisms-of-gene-regulation-in-the-human-malaria-parasite-plasmodium-falciparum
#8
Xueqing Maggie Lu, Gayani Batugedara, Michael Lee, Jacques Prudhomme, Evelien M Bunnik, Karine G Le Roch
Gene expression in Plasmodium falciparum is tightly regulated to ensure successful propagation of the parasite throughout its complex life cycle. The earliest transcriptomics studies in P. falciparum suggested a cascade of transcriptional activity over the course of the 48-hour intraerythrocytic developmental cycle (IDC); however, the just-in-time transcriptional model has recently been challenged by findings that show the importance of post-transcriptional regulation. To further explore the role of transcriptional regulation, we performed the first genome-wide nascent RNA profiling in P...
May 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28531178/zebrafish-exposure-to-environmentally-relevant-concentration-of-depleted-uranium-impairs-progeny-development-at-the-molecular-and-histological-levels
#9
Olivier Armant, Kewin Gombeau, Sophia Murat El Houdigui, Magali Floriani, Virginie Camilleri, Isabelle Cavalie, Christelle Adam-Guillermin
Uranium is an actinide naturally found in the environment. Anthropogenic activities lead to the release of increasing amounts of uranium and depleted uranium (DU) in the environment, posing potential risks to aquatic organisms due to radiological and chemical toxicity of this radionucleide. Although environmental contaminations with high levels of uranium have already been observed, chronic exposures of non-human species to levels close to the environmental quality standards remain scarcely characterized. The present study focused on the identification of the molecular pathways impacted by a chronic exposure of zebrafish to 20 μg/L of DU during 10 days...
2017: PloS One
https://www.readbyqxmd.com/read/28521943/developmental-regulation-and-evolution-of-scaling-novel-insights-through-the-study-of-onthophagus-beetles
#10
REVIEW
Sofia Casasa, Daniel B Schwab, Armin P Moczek
Scaling relationships play critical roles in defining biological shape, trait functionality, and species characteristics, yet the developmental basis of scaling and its evolution remain poorly resolved in most taxa. In the horned beetle genus Onthophagus, scaling relationships of most traits are largely comparable across many species, however, the morphology and scaling of horns, a recent evolutionary invention, has diversified dramatically, ranging from modestly to highly positively linear to more complex sigmoidal allometries...
February 2017: Current Opinion in Insect Science
https://www.readbyqxmd.com/read/28521939/developmental-and-evolutionary-mechanisms-shaping-butterfly-eyespots
#11
REVIEW
Patrícia Beldade, Carolina M Peralta
Butterfly eyespots are visually compelling models to study the reciprocal interactions between evolutionary and developmental processes that shape phenotypic variation. They are evolutionarily diversified, ecologically relevant, and developmentally tractable, and have made key contributions to linking genotype, development, phenotype and fitness. Advances in the availability of analytical tools (e.g. gene editing and visualization techniques) and resources (e.g. genomic and transcriptomic data) are boosting the detailed dissection of the mechanisms underlying eyespot development and evolution...
February 2017: Current Opinion in Insect Science
https://www.readbyqxmd.com/read/28520760/transcriptome-profiling-of-ontogeny-in-the-acridid-grasshopper-chorthippus-biguttulus
#12
Emma L Berdan, Jonas Finck, Paul R Johnston, Isabelle Waurick, Camila J Mazzoni, Frieder Mayer
Acridid grasshoppers (Orthoptera:Acrididae) are widely used model organisms for developmental, evolutionary, and neurobiological research. Although there has been recent influx of orthopteran transcriptomic resources, many use pooled ontogenetic stages obscuring information about changes in gene expression during development. Here we developed a de novo transcriptome spanning 7 stages in the life cycle of the acridid grasshopper Chorthippus biguttulus. Samples from different stages encompassing embryonic development through adults were used for transcriptomic profiling, revealing patterns of differential gene expression that highlight processes in the different life stages...
2017: PloS One
https://www.readbyqxmd.com/read/28514690/genomic-characterization-of-murine-monocytes-reveals-c-ebp%C3%AE-transcription-factor-dependence-of-ly6c-cells
#13
Alexander Mildner, Jörg Schönheit, Amir Giladi, Eyal David, David Lara-Astiaso, Erika Lorenzo-Vivas, Franziska Paul, Louise Chappell-Maor, Josef Priller, Achim Leutz, Ido Amit, Steffen Jung
Monocytes are circulating, short-lived mononuclear phagocytes, which in mice and man comprise two main subpopulations. Murine Ly6C(+) monocytes display developmental plasticity and are recruited to complement tissue-resident macrophages and dendritic cells on demand. Murine vascular Ly6C(-) monocytes patrol the endothelium, act as scavengers, and support vessel wall repair. Here we characterized population and single cell transcriptomes, as well as enhancer and promoter landscapes of the murine monocyte compartment...
May 16, 2017: Immunity
https://www.readbyqxmd.com/read/28514438/conversion-of-adult-endothelium-to-immunocompetent-haematopoietic-stem-cells
#14
Raphael Lis, Charles C Karrasch, Michael G Poulos, Balvir Kunar, David Redmond, Jose G Barcia Duran, Chaitanya R Badwe, William Schachterle, Michael Ginsberg, Jenny Xiang, Arash Rafii Tabrizi, Koji Shido, Zev Rosenwaks, Olivier Elemento, Nancy A Speck, Jason M Butler, Joseph M Scandura, Shahin Rafii
Developmental pathways that orchestrate the fleeting transition of endothelial cells into haematopoietic stem cells remain undefined. Here we demonstrate a tractable approach for fully reprogramming adult mouse endothelial cells to haematopoietic stem cells (rEC-HSCs) through transient expression of the transcription-factor-encoding genes Fosb, Gfi1, Runx1, and Spi1 (collectively denoted hereafter as FGRS) and vascular-niche-derived angiocrine factors. The induction phase (days 0-8) of conversion is initiated by expression of FGRS in mature endothelial cells, which results in endogenous Runx1 expression...
May 17, 2017: Nature
https://www.readbyqxmd.com/read/28512324/global-gene-expression-analysis-provides-insight-into-local-adaptation-to-geothermal-streams-in-tadpoles-of-the-andean-toad-rhinella-spinulosa
#15
Luis Pastenes, Camilo Valdivieso, Alex Di Genova, Dante Travisany, Andrew Hart, Martín Montecino, Ariel Orellana, Mauricio Gonzalez, Rodrigo A Gutiérrez, Miguel L Allende, Alejandro Maass, Marco A Méndez
The anuran Rhinella spinulosa is distributed along the Andes Range at altitudes that undergo wide daily and seasonal variation in temperature. One of the populations inhabits geothermal streams, a stable environment that influences life history traits such as the timing of metamorphosis. To investigate whether this population has undergone local adaptation to this unique habitat, we carried out transcriptome analyses in animals from two localities in two developmental stages (prometamorphic and metamorphic) and exposed them to two temperatures (20 and 25 °C)...
May 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28509351/a-transcriptome-based-assessment-of-the-astrocytic-dystrophin-associated-complex-in-the-developing-human-brain
#16
Matthew J Simon, Charles Murchison, Jeffrey J Iliff
Astrocytes play a critical role in regulating the interface between the cerebral vasculature and the central nervous system. Contributing to this is the astrocytic endfoot domain, a specialized structure that ensheathes the entirety of the vasculature and mediates signaling between endothelial cells, pericytes, and neurons. The astrocytic endfoot has been implicated as a critical element of the glymphatic pathway, and changes in protein expression profiles in this cellular domain are linked to Alzheimer's disease pathology...
May 16, 2017: Journal of Neuroscience Research
https://www.readbyqxmd.com/read/28509349/isolation-of-tissues-and-preservation-of-rna-from-intact-germinated-barley-grain
#17
Natalie S Betts, Oliver Berkowitz, Ruijie Liu, Helen M Collins, Birgitte Skadhauge, Christoph Dockter, Rachel A Burton, James Whelan, Geoffrey B Fincher
Isolated barley (Hordeum vulgare L.) aleurone layers have been widely used as a model system for studying gene expression and hormonal regulation in germinating cereal grains. A serious technological limitation of this approach has been the inability to confidently extrapolate conclusions obtained from isolated tissues back to the whole grain, where the co-location of several living and non-living tissues results in complex tissue-tissue interactions and regulatory pathways coordinated across the multiple tissues...
May 16, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28504560/small-rna-functions-are-required-for-growth-and-development-of-magnaporthe-oryzae
#18
Vidhyavathi Raman, Stacey A Simon, Feray Demirci, Mayumi Nakano, Blake C Meyers, Nicole M Donofrio
RNA interference (RNAi) is conserved in eukaryotic organisms, and it has been well studied in many animal and plant species and some fungal species, yet it is not well studied in fungal plant pathogens. In the rice blast fungus Magnaporthe oryzae, we examined small RNA (sRNA) and their biogenesis in the context of growth and pathogenicity. Through genetic and genomic analyses, we demonstrate that loss of a single gene encoding Dicer, RNA-dependent RNA polymerase, or Argonaute reduces sRNA levels. These three proteins are required for the biogenesis of sRNA-matching genome-wide regions (coding regions, repeats, and intergenic regions)...
May 15, 2017: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/28500720/casting-away-the-shadows-elucidating-the-role-of-light-mediated-posttranscriptional-control-in-plants
#19
REVIEW
Carlos E Hernando, Carolina Garcia, Julieta L Mateos
Light signals trigger precise changes in gene expression networks that activate distinctive developmental programs in plants. The transcriptome is shaped at different stages, both by the regulation of gene expression and also by posttranscriptional mechanisms that alter the sequence or abundance of the transcripts generated. Posttranscriptional mechanisms have attracted much interest in recent years with the advent of high-throughput technologies and bioinformatics tools. One such posttranscriptional process, alternative splicing, increases proteome diversity without increasing gene number by changing the function of individual proteins, while another, miRNA-mediated gene silencing, fine-tunes the amount of mRNA produced...
May 2017: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/28499347/the-dynamics-of-early-state-transcriptional-changes-and-aggregate-formation-in-a-huntington-s-disease-cell-model
#20
Martijn van Hagen, Diewertje G E Piebes, Wim C de Leeuw, Ilona M Vuist, Willeke M C van Roon-Mom, Perry D Moerland, Pernette J Verschure
BACKGROUND: Huntington's disease (HD) is a fatal neurodegenerative disorder caused by a CAG expansion in the Huntingtin (HTT) gene. Proteolytic cleavage of mutant huntingtin (Htt) protein with an expanded polyglutamine (polyQ) stretch results in production of Htt fragments that aggregate and induce impaired ubiquitin proteasome, mitochondrial functioning and transcriptional dysregulation. To understand the time-resolved relationship between aggregate formation and transcriptional changes at early disease stages, we performed temporal transcriptome profiling and quantification of aggregate formation in living cells in an inducible HD cell model...
May 12, 2017: BMC Genomics
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