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Developmental transcriptome

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https://www.readbyqxmd.com/read/29140570/rapid-screening-of-the-endodermal-differentiation-potential-of-human-pluripotent-stem-cells
#1
Richard Siller, Gareth J Sullivan
Human pluripotent stem cells (hPSCs) hold tremendous promise for regenerative medicine, disease modeling, toxicology screening, and developmental biology. These applications are hindered due to inherent differences in differentiation potential observed among different hPSC lines. This is particularly true for the differentiation of hPSCs toward the endodermal lineage. Several groups have developed methods to screen hPSCs for their endodermal differentiation potential (EP). Particularly notable studies include (i) the use of WNT3A expression as a predictive biomarker, (ii) an embryoid body-based screen, and (iii) a transcriptomics-based approach...
November 15, 2017: Current Protocols in Stem Cell Biology
https://www.readbyqxmd.com/read/29139534/beyond-the-sea-crepidula-atrasolea-as-a-spiralian-model-system
#2
Jonathan Q Henry, Maryna P Lesoway, Kimberly J Perry, C Cornelia Osborne, Marty Shankland, Deirdre C Lyons
This paper introduces the black-footed slipper snail, Crepidula atrasolea, as a new model for biological studies in the Spiralia. C. atrasolea is a calyptraeid gastropod, and congener of the Atlantic slipper snail, C. fornicata. Like C. fornicata, C. atrasolea shares a sedentary, filter-feeding, protandrous lifestyle, but is preferable as a developmental model because of its short generation time, year-round reproduction, and direct development. In our lab, individuals go from egg to reproductive females in under six months, as compared to an estimated 1-2 years for C...
2017: International Journal of Developmental Biology
https://www.readbyqxmd.com/read/29136644/developmentally-regulated-internal-transcription-initiation-during-meiosis-in-budding-yeast
#3
Sai Zhou, Rolf Sternglanz, Aaron M Neiman
Sporulation of budding yeast is a developmental process in which cells undergo meiosis to generate stress-resistant progeny. The dynamic nature of the budding yeast meiotic transcriptome has been well established by a number of genome-wide studies. Here we develop an analysis pipeline to systematically identify novel transcription start sites that reside internal to a gene. Application of this pipeline to data from a synchronized meiotic time course reveals over 40 genes that display specific internal initiations in mid-sporulation...
2017: PloS One
https://www.readbyqxmd.com/read/29136637/transcriptional-profiling-of-toll-like-receptor-2-deficient-primary-murine-brain-cells-during-toxoplasma-gondii-infection
#4
Kousuke Umeda, Sachi Tanaka, Fumiaki Ihara, Junya Yamagishi, Yutaka Suzuki, Yoshifumi Nishikawa
BACKGROUND: Toxoplasma gondii is capable of persisting in the brain, although it is efficiently eliminated by cellular immune responses in most other sites. While Toll-like receptor 2 (TLR2) reportedly plays important roles in protective immunity against the parasite, the relationship between neurological disorders induced by T. gondii infection and TLR2 function in the brain remains controversial with many unknowns. In this study, primary cultured astrocytes, microglia, neurons, and peritoneal macrophages obtained from wild-type and TLR2-deficient mice were exposed to T...
2017: PloS One
https://www.readbyqxmd.com/read/29131867/differential-transcriptome-analysis-reveals-genes-related-to-cold-tolerance-in-seabuckthorn-carpenter-moth-eogystia-hippophaecolus
#5
Mingming Cui, Ping Hu, Tao Wang, Jing Tao, Shixiang Zong
Seabuckthorn carpenter moth, Eogystia hippophaecolus (Lepidoptera: Cossidae), is an important pest of sea buckthorn (Hippophae rhamnoides), which is a shrub that has significant ecological and economic value in China. E. hippophaecolus is highly cold tolerant, but limited studies have been conducted to elucidate the molecular mechanisms underlying its cold resistance. Here we sequenced the E. hippophaecolus transcriptome using RNA-Seq technology and performed de novo assembly from the short paired-end reads...
2017: PloS One
https://www.readbyqxmd.com/read/29129811/transcriptome-scale-characterization-of-salt-responsive-bean-tcp-transcription
#6
Emre İlhan, İlker Büyük, Behcet İnal
TEOSINTE-BRANCHED1/CYCLOIDEA/PCF (TCP) proteins are important regulators of growth and developmental processes including branching, floral organ morphogenesis and leaf growth as well as stress response. This study identified 27 TCP genes of Phaseolus vulgaris (common bean), which were divided into three clusters based on phylogenetic relationship. In addition, this study showed that some of TCP genes such as Pvul-TCP-4 and Pvul-TCP-15 located on chromosomes 3 and 7, Pvul-TCP-7 and Pvul-TCP-20 located on chromosome 7 and 9, were segmentally duplicated...
November 9, 2017: Gene
https://www.readbyqxmd.com/read/29124815/diluted-seawater-affects-phytohormone-receptors-and-maintain-the-protonema-stage-in-physcomitrella-patens
#7
Zhenbing Zheng, Shan Gao, Li Huan, Guang-Ce Wang
Due to its highly efficient homologous recombination ability and unusual evolutionary position, the moss Physcomitrella patens has begun to attract more attention in genetic and evolutionary studies. Protonema, the filament stage of the gametophyte is of great significance in P. patens protoplast isolation. Moreover, protonema is widely used in genetic engineering. However, difficulties in the induction and state maintenance of protonema restrict its wider application. In this work, protonema was induced efficiently in a diluted seawater medium, and the filamentous state was maintained without further cell differentiation...
November 10, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29122003/docosahexaenoic-acid-mechanisms-of-action-on-the-bovine-oocyte-cumulus-complex
#8
Sebastien Elis, Mouhamad Oseikria, Anais Vitorino Carvalho, Priscila Silvana Bertevello, Emilie Corbin, Ana-Paula Teixeira-Gomes, Jérôme Lecardonnel, Catherine Archilla, Véronique Duranthon, Valérie Labas, Svetlana Uzbekova
BACKGROUND: Supplementation of bovine oocyte-cumulus complexes during in vitro maturation (IVM) with 1 μM of docosahexaenoic acid (DHA), C22:6 n-3 polyunsaturated fatty acid, was reported to improve in vitro embryo development. The objective of this paper was to decipher the mechanisms of DHA action. RESULTS: Transcriptomic analysis of 1 μM DHA-treated and control cumulus cells after 4 h IVM showed no significant difference in gene expression. MALDI-TOF mass spectrometry analysis of lipid profiles in DHA-treated and control oocytes and cumulus cells after IVM showed variations of only 3 out of 700 molecular species in oocytes and 7 out of 698 species in cumulus cells (p < 0...
November 9, 2017: Journal of Ovarian Research
https://www.readbyqxmd.com/read/29119346/structure-target-specificity-and-expression-of-pn_lnc_n13-a-long-non-coding-rna-differentially-expressed-in-apomictic-and-sexual-paspalum-notatum
#9
Ana Ochogavía, Giulio Galla, José Guillermo Seijo, Ana María González, Michele Bellucci, Fulvio Pupilli, Gianni Barcaccia, Emidio Albertini, Silvina Pessino
KEY MESSAGE: ncRNA PN_LNC_N13 shows contrasting expression in reproductive organs of sexual and apomictic Paspalum notatum genotypes. Apomictic plants set genetically maternal seeds whose embryos derive by parthenogenesis from unreduced egg cells, giving rise to clonal offspring. Several Paspalum notatum apomixis related genes were identified in prior work by comparative transcriptome analyses. Here, one of these candidates (namely N13) was characterized. N13 belongs to a Paspalum gene family including 30-60 members, of which at least eight are expressed at moderate levels in florets...
November 8, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/29118556/long-non-coding-rna-in-pancreatic-adenocarcinoma-and-pancreatic-neuroendocrine-tumors
#10
REVIEW
Dimitrios Moschovis, Maria Gazouli, Maria Tzouvala, Antonios Vezakis, George Karamanolis
Interest in non-coding regions of DNA has been increasing since the mapping of the human genome revealed that human DNA contains far fewer genes encoding proteins than previously expected. However, analysis of the derivatives of DNA transcription (transcriptomics) revealed that the majority of the genetic material is transcribed into non-coding RNA (ncRNA), indicating that these molecules probably provide the functional diversity and complexity of the physiology of the human body that cannot be attributed to the proteins...
2017: Annals of Gastroenterology: Quarterly Publication of the Hellenic Society of Gastroenterology
https://www.readbyqxmd.com/read/29116234/transcriptome-dynamics-revealed-by-a-gene-expression-atlas-of-the-early-arabidopsis-embryo
#11
Joakim Palovaara, Shunsuke Saiga, Jos R Wendrich, Nicole van 't Wout Hofland, J Paul van Schayck, Friederike Hater, Sumanth Mutte, Jouke Sjollema, Mark Boekschoten, Guido J Hooiveld, Dolf Weijers
During early plant embryogenesis, precursors for all major tissues and stem cells are formed. While several components of the regulatory framework are known, how cell fates are instructed by genome-wide transcriptional activity remains unanswered-in part because of difficulties in capturing transcriptome changes at cellular resolution. Here, we have adapted a two-component transgenic labelling system to purify cell-type-specific nuclear RNA and generate a transcriptome atlas of early Arabidopsis embryo development, with a focus on root stem cell niche formation...
November 2017: Nature Plants
https://www.readbyqxmd.com/read/29115918/xths-from-fragaria-vesca-genomic-structure-and-transcriptomic-analysis-in-ripening-fruit-and-other-tissues
#12
María Cecilia Opazo, Rodrigo Lizana, Yazmina Stappung, Thomas M Davis, Raúl Herrera, María Alejandra Moya-León
BACKGROUND: Fragaria vesca or 'woodland strawberry' has emerged as an attractive model for the study of ripening of non-climacteric fruit. It has several advantages, such as its small genome and its diploidy. The recent availability of the complete sequence of its genome opens the possibility for further analysis and its use as a reference species. Fruit softening is a physiological event and involves many biochemical changes that take place at the final stages of fruit development; among them, the remodeling of cell walls by the action of a set of enzymes...
November 7, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29115819/whole-life-stage-characterization-in-the-basic-biology-of-daphnia-magna-and-effects-of-tdcipp-on-growth-reproduction-survival-and-transcription-of-genes
#13
Han Li, Siliang Yuan, Guanyong Su, Meng Li, Qiangwei Wang, Guonian Zhu, Robert J Letcher, Yufei Li, Zhihua Han, Chunsheng Liu
Toxicity tests of chemicals have mainly focused on the partial life-cycle evaluation of model animals. Limited information is available for the evaluation of effects of chemicals from a whole-life-stage exposure perspective. The objective of this study was to perform a whole-life-stage characterization in the basic biology of Daphnia magna (D. magna) and evaluate the effects of a known organophosphate ester (OPE) contaminant, tris (1,3-dichloro-2-propyl) phosphate (TDCIPP), on growth, reproduction, survival and transcription of genes...
November 8, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/29114080/a-role-for-the-f-box-protein-hawaiian-skirt-in-plant-microrna-function
#14
Patricia L M Lang, Michael D Christie, Ezgi S Dogan, Rebecca Schwab, Jörg Hagmann, Anna-Lena Van de Weyer, Detlef Weigel, Emanuele Scacchi
As regulators of gene expression in multicellular organisms, microRNAs (miRNAs) are crucial for growth and development. While a plethora of factors involved in their biogenesis and action in Arabidopsis thaliana has been described, these processes and their fine-tuning are not fully understood. Here, we used plants expressing an artificial miRNA target mimic (MIM) to screen for negative regulators of miR156. We identified a new mutant allele of the F-box gene HAWAIIAN SKIRT (HWS; At3G61590), hws-5, as a suppressor of the MIM156-induced developmental and molecular phenotypes...
November 7, 2017: Plant Physiology
https://www.readbyqxmd.com/read/29111713/comprehensive-transcriptome-analysis-of-phytohormone-biosynthesis-and-signaling-genes-in-the-flowers-of-chinese-chinquapin-castanea-henryi
#15
Xiaoming Fan, Deyi Yuan, Xiaoming Tian, Zhoujun Zhu, Meilan Liu, Heping Cao
Chinese chinquapin (Castanea henryi) nut provides a rich source of starch and nutrients as food and feed, but its yield is restricted by a low ratio of female to male flowers. Little is known about the developmental programs underlying sex differentiation of the flowers. To investigate the involvement of phytohormones during sex differentiation, we described the morphology of male and female floral organs and the cytology of flower sex differentiation, analyzed endogenous levels of indole-3-acetic acid (IAA), gibberellins (GAs), cytokinins (CKs) and abscisic acid (ABA) in the flowers, investigated the effects of exogenous hormones on flower development, and evaluated the expression profiles of genes related to biosyntheses and signaling pathways of these four hormones using RNA-Seq combined with qPCR...
November 7, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/29110697/exutr-a-novel-pipeline-for-large-scale-prediction-of-3-utr-sequences-from-ngs-data
#16
Zixia Huang, Emma C Teeling
BACKGROUND: The three prime untranslated region (3'-UTR) is known to play a pivotal role in modulating gene expression by determining the fate of mRNA. Many crucial developmental events, such as mammalian spermatogenesis, tissue patterning, sex determination and neurogenesis, rely heavily on post-transcriptional regulation by the 3'-UTR. However, 3'-UTR biology seems to be a relatively untapped field, with only limited tools and 3'-UTR resources available. To elucidate the regulatory mechanisms of the 3'-UTR on gene expression, firstly the 3'-UTR sequences must be identified...
November 6, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29109714/characteristics-of-a-regulator-of-g-protein-signaling-rgs-rgsc-in-aspergillus-fumigatus
#17
Young Kim, In-Beom Heo, Jae-Hyuk Yu, Kwang-Soo Shin
The regulator of G-protein signaling (RGS) proteins have a conserved RGS domain that facilitates the intrinsic GTPase activity of an activated Gα subunit of heterotrimeric G protein, thereby attenuating signal transduction. Among six predicted RGS proteins in the opportunistic human pathogenic fungus Aspergillus fumigatus, only three (FlbA, GprK, and Rax1) have been studied. The unexplored RgsC composed of the Phox-associated (PXA), RGS, Phox homology (PX), and Nexin_C superfamily domains is highly conserved in many ascomycete fungi, suggesting a crucial role of RgsC in fungal biology...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29109696/low-dose-alkylphenol-exposure-promotes-mammary-epithelium-alterations-and-transgenerational-developmental-defects-but-does-not-enhance-tumorigenic-behavior-of-breast-cancer-cells
#18
Clémence Chamard-Jovenin, Charlène Thiebaut, Amand Chesnel, Emmanuel Bresso, Chloé Morel, Malika Smail-Tabbone, Marie-Dominique Devignes, Taha Boukhobza, Hélène Dumond
Fetal and neonatal exposure to long-chain alkylphenols has been suspected to promote breast developmental disorders and consequently to increase breast cancer risk. However, disease predisposition from developmental exposures remains unclear. In this work, human MCF-10A mammary epithelial cells were exposed in vitro to a low dose of a realistic (4-nonylphenol + 4-tert-octylphenol) mixture. Transcriptome and cell-phenotype analyses combined to functional and signaling network modeling indicated that long-chain alkylphenols triggered enhanced proliferation, migration ability, and apoptosis resistance and shed light on the underlying molecular mechanisms which involved the human estrogen receptor alpha 36 (ERα36) variant...
2017: Frontiers in Endocrinology
https://www.readbyqxmd.com/read/29107741/constructing-cell-lineages-from-single-cell-transcriptomes
#19
REVIEW
Jinmiao Chen, Laurent Rénia, Florent Ginhoux
Advances in single-cell RNA-sequencing have helped reveal the previously underappreciated level of cellular heterogeneity present during cellular differentiation. A static snapshot of single-cell transcriptomes provides a good representation of the various stages of differentiation as differentiation is rarely synchronized between cells. Data from numerous single-cell analyses has suggested that cellular differentiation and development can be conceptualized as continuous processes. Consequently, computational algorithms have been developed to infer lineage relationships between cell types and construct developmental trajectories along which cells are re-ordered such that similarity between successive cell pairs is maximized...
October 28, 2017: Molecular Aspects of Medicine
https://www.readbyqxmd.com/read/29107596/default-patterning-produces-pan-cortical-glutamatergic-and-cge-lge-like-gabaergic-neurons-from-human-pluripotent-stem-cells
#20
Crina M Floruta, Ruofei Du, Huining Kang, Jason L Stein, Jason P Weick
Default differentiation of human pluripotent stem cells has been promoted as a model of cortical development. In this study, a developmental transcriptome analysis of default-differentiated hPSNs revealed a gene expression program resembling in vivo CGE/LGE subpallial domains and GABAergic signaling. A combination of bioinformatic, functional, and immunocytochemical analysis further revealed that hPSNs consist of both cortical glutamatergic and CGE-like GABAergic neurons. This study provides a comprehensive characterization of the heterogeneous group of neurons produced by default differentiation and insight into future directed differentiation strategies...
November 14, 2017: Stem Cell Reports
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