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Developmental transcriptome

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https://www.readbyqxmd.com/read/28100297/transcriptional-analysis-of-mating-and-pre-infection-stages-of-the-anther-smut-microbotryum-lychnidis-dioicae
#1
Su San Toh, Zehua Chen, David J Schultz, Christina A Cuomo, Michael H Perlin
Microbotryum lychnidis-dioicae is an obligate biotrophic parasite of the wildflower species, Silene latifolia. This dikaryotic fungus, commonly known as an anther smut, requires that haploid, yeast-like sporidia of opposite mating types fuse and differentiate into dikaryotic hyphae that penetrate host tissue as part of the fungal lifecycle. Mating occurs under conditions of cool temperatures and limited nutrients. Further development requires host cues or chemical mimics, including a variety of lipids, e.g...
January 17, 2017: Microbiology
https://www.readbyqxmd.com/read/28095645/what-we-can-learn-from-a-tadpole-about-ciliopathies-and-airway-diseases-using-systems-biology-in-xenopus-to-study-cilia-and-mucociliary-epithelia
#2
REVIEW
Peter Walentek, Ian K Quigley
Over the past years, the Xenopus embryo has emerged as an incredibly useful model organism for studying the formation and function of cilia and ciliated epithelia in vivo. This has led to a variety of findings elucidating the molecular mechanisms of ciliated cell specification, basal body biogenesis, cilia assembly and ciliary motility. These findings also revealed the deep functional conservation of signaling, transcriptional, post-transcriptional and protein networks employed in the formation and function of vertebrate ciliated cells...
January 17, 2017: Genesis: the Journal of Genetics and Development
https://www.readbyqxmd.com/read/28094170/common-developmental-genome-deprogramming-in-schizophrenia-role-of-integrative-nuclear-fgfr1-signaling-infs
#3
S T Narla, Y-W Lee, C A Benson, P Sarder, K J Brennand, E K Stachowiak, M K Stachowiak
The watershed-hypothesis of schizophrenia asserts that over 200 different mutations dysregulate distinct pathways that converge on an unspecified common mechanism(s) that controls disease ontogeny. Consistent with this hypothesis, our RNA-sequencing of neuron committed cells (NCCs) differentiated from established iPSCs of 4 schizophrenia patients and 4 control subjects uncovered a dysregulated transcriptome of 1349 mRNAs common to all patients. Data reveals a global dysregulation of developmental genome, deconstruction of coordinated mRNA networks, and the formation of aberrant, new coordinated mRNA networks indicating a concerted action of the responsible factor(s)...
January 13, 2017: Schizophrenia Research
https://www.readbyqxmd.com/read/28094016/a-single-cell-roadmap-of-lineage-bifurcation-in-human-esc-models-of-embryonic-brain-development
#4
Zizhen Yao, John K Mich, Sherman Ku, Vilas Menon, Anne-Rachel Krostag, Refugio A Martinez, Leon Furchtgott, Heather Mulholland, Susan Bort, Margaret A Fuqua, Ben W Gregor, Rebecca D Hodge, Anu Jayabalu, Ryan C May, Samuel Melton, Angelique M Nelson, N Kiet Ngo, Nadiya V Shapovalova, Soraya I Shehata, Michael W Smith, Leah J Tait, Carol L Thompson, Elliot R Thomsen, Chaoyang Ye, Ian A Glass, Ajamete Kaykas, Shuyuan Yao, John W Phillips, Joshua S Grimley, Boaz P Levi, Yanling Wang, Sharad Ramanathan
During human brain development, multiple signaling pathways generate diverse cell types with varied regional identities. Here, we integrate single-cell RNA sequencing and clonal analyses to reveal lineage trees and molecular signals underlying early forebrain and mid/hindbrain cell differentiation from human embryonic stem cells (hESCs). Clustering single-cell transcriptomic data identified 41 distinct populations of progenitor, neuronal, and non-neural cells across our differentiation time course. Comparisons with primary mouse and human gene expression data demonstrated rostral and caudal progenitor and neuronal identities from early brain development...
January 5, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/28090703/differentiation-of-islet-progenitors-regulated-by-nicotinamide-into-transcriptome-verified-%C3%AE-cells-that-ameliorate-diabetes
#5
Fang-Xu Jiang, Kevin Li, Michael Archer, Munish Mehta, Emma Jamieson, Adrian Charles, Jan E Dickinson, Masahito Matsumoto, Grant Morahan
Developmental stage-specific differentiation of stem or progenitor cells into safe and functional cells is of fundamental importance in regenerative medicine, including β-cell replacement. However, the differentiation of islet progenitor cells (IPCs) into insulin-secreting β cells remains elusive. Here, we report that the multi-functional molecule nicotinamide (NIC) is a specific differentiation regulator of mouse IPCs. The differentiated cells regulated by NIC exhibited many characteristics of adult β cells, including ameliorating preclinical diabetes and a highly comparable transcriptome profile...
January 16, 2017: Stem Cells
https://www.readbyqxmd.com/read/28089430/high-variability-of-expression-profiles-of-homeologous-genes-for-wnt-hh-notch-and-hippo-signaling-pathways-in-xenopus-laevis
#6
Tatsuo Michiue, Takayoshi Yamamoto, Yuuri Yasuoka, Toshiyasu Goto, Takafumi Ikeda, Kei Nagura, Takuya Nakayama, Masanori Taira, Tsutomu Kinoshita
Cell signaling pathways, such as Wnt, Hedgehog (Hh), Notch, and Hippo, are essential for embryogenesis, organogenesis, and tissue homeostasis. In this study, we analyzed 415 genes involved in these pathways in the allotetraploid frog, Xenopus laevis. Most genes are retained in two subgenomes called L and S (193 homeologous gene pairs and 29 singletons). This conservation rate of homeologs is much higher than that of all genes in the X. laevis genome (86.9% vs 60.2%). Among singletons, 24 genes are retained in the L subgenome, a rate similar to the average for all genes (82...
January 12, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28087653/identification-of-regulatory-networks-and-hub-genes-controlling-soybean-seed-set-and-size-using-rna-sequencing-analysis
#7
Juan Du, Shoudong Wang, Cunman He, Bin Zhou, Yong-Ling Ruan, Huixia Shou
To understand the gene expression networks controlling soybean seed set and size, transcriptome analyses were performed in three early seed developmental stages, using two genotypes with contrasting seed size. The two-dimensional data set provides a comprehensive and systems-level view on dynamic gene expression networks underpinning soybean seed set and subsequent development. Using pairwise comparisons and weighted gene coexpression network analyses, we identified modules of coexpressed genes and hub genes for each module...
January 13, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28087624/tissue-specific-regulation-of-alternative-polyadenylation-represses-expression-of-neuronal-ankyrin-isoform-in-c-elegans-epidermal-development
#8
Fei Chen, Andrew D Chisholm, Yishi Jin
Differential mRNA polyadenylation plays an important role in shaping the neuronal transcriptome. In C. elegans, several ankyrin isoforms are produced from the unc-44 locus through alternative polyadenylation. Here, we identify a key role for an intronic polyadenylation site (PAS) in temporal- and tissue-specific regulation of UNC-44/ankyrin isoforms. Removing an intronic PAS results in ectopic expression of the neuronal ankyrin isoform in non-neural tissues. This mis-expression underlies epidermal developmental defects in mutants of the conserved tumor suppressor death-associated protein kinase, dapk-1 We previously reported that the use of this intronic PAS depends on the nuclear polyadenylation factor SYDN-1, which inhibits the RNA polymerase II CTD phosphatase SSUP-72...
January 13, 2017: Development
https://www.readbyqxmd.com/read/28081440/a-knockout-screen-of-apiap2-genes-reveals-networks-of-interacting-transcriptional-regulators-controlling-the-plasmodium-life-cycle
#9
Katarzyna Modrzynska, Claudia Pfander, Lia Chappell, Lu Yu, Catherine Suarez, Kirsten Dundas, Ana Rita Gomes, David Goulding, Julian C Rayner, Jyoti Choudhary, Oliver Billker
A family of apicomplexa-specific proteins containing AP2 DNA-binding domains (ApiAP2s) was identified in malaria parasites. This family includes sequence-specific transcription factors that are key regulators of development. However, functions for the majority of ApiAP2 genes remain unknown. Here, a systematic knockout screen in Plasmodium berghei identified ten ApiAP2 genes that were essential for mosquito transmission: four were critical for the formation of infectious ookinetes, and three were required for sporogony...
January 11, 2017: Cell Host & Microbe
https://www.readbyqxmd.com/read/28081283/transcriptome-analysis-of-peach-prunus-persica-l-batsch-during-the-late-stage-of-fruit-ripening
#10
H F Pan, Y Sheng, Z H Gao, H L Chen, Y J Qi, X K Yi, G H Qin, J Y Zhang
Fruit ripening is a complex developmental process, the details of which remain largely unknown in fleshy fruits. In this paper, the fruit flesh of two peach varieties, "Zhongyou9" (a nectarine; Prunus persica L. Batsch) and its mutant "Hongyu", was analyzed by RNA-seq technology during two stages of ripening at 20-day intervals. One hundred and eighty significant upregulated and two hundred and thirty-five downregulated genes were identified in the experiment. Many of these genes were related to plant hormones, chlorophyll breakdown, accumulation of aroma and flavor volatiles, and stress...
December 23, 2016: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28073951/nod-factors-potentiate-auxin-signaling-for-transcriptional-regulation-and-lateral-root-formation-in-medicago-truncatula
#11
Violaine Herrbach, Ximena Chirinos, David Rengel, Kokoévi Agbevenou, Rémy Vincent, Stéphanie Pateyron, Stéphanie Huguet, Sandrine Balzergue, Asher Pasha, Nicholas Provart, Clare Gough, Sandra Bensmihen
Nodulation (Nod) factors (NFs) are symbiotic molecules produced by rhizobia that are essential for establishment of the rhizobium-legume endosymbiosis. Purified NFs can stimulate lateral root formation (LRF) in Medicago truncatula, but little is known about the molecular mechanisms involved. Using a combination of reporter constructs, pharmacological and genetic approaches, we show that NFs act on early steps of LRF in M. truncatula, independently of the ethylene signaling pathway and of the cytokinin receptor MtCRE1, but in interaction with auxin...
January 10, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28072866/the-regulatory-roles-of-microrna-in-effects-of-2-2-4-4-tetrabromodiphenyl-ether-bde47-on-the-transcriptome-of-zebrafish-larvae
#12
Jing Zhao, Ting Xu, Daqiang Yin, Bo Zhang, Jianfeng Bai
The developmental neurotoxicity caused by environmental pollutants has received great concern; however, there were still barely known about the underlying toxic mechanisms, especially the influence of varieties of regulatory factors such as microRNA (miRNA). A representative flame retardant, 2,2',4,4'-tetrabromodiphenyl ether (BDE47), was found to disrupt zebrafish development in visual perception and bone formation in previous study, thus here we investigated its effects on miRNA expression profiling of 6 days post fertilization (dpf) zebrafish larvae by deep sequencing...
2017: PloS One
https://www.readbyqxmd.com/read/28071834/molecular-profiling-of-human-ips-derived-hypothalamic-neurons-provides-developmental-insights-to-genetic-loci-for-body-weight-regulation
#13
Li Yao, Yuanhang Liu, Zhifang Qiu, Satish Kumar, Joanne E Curran, John Blangero, Yidong Chen, Donna M Lehman
BACKGROUND/OBJECTIVES: Recent data suggests that common genetic risk for metabolic disorders such as obesity may be human-specific and exert effects through the central nervous system. To overcome the limitation of human tissue access for study, we have generated induced human pluripotent stem cell (hiPSC)-derived neuronal cultures which recapture many features of hypothalamic neurons within the arcuate nucleus. Here we have comprehensively characterized this model across development, benchmarked these neurons to in vivo events, and demonstrate a link between obesity risk variants and hypothalamic development...
January 10, 2017: Journal of Neuroendocrinology
https://www.readbyqxmd.com/read/28070461/transcriptome-analysis-of-the-oriental-melon-cucumis-melo-l-var-makuwa-during-fruit-development
#14
Ah-Young Shin, Yong-Min Kim, Namjin Koo, Su Min Lee, Seokhyeon Nahm, Suk-Yoon Kwon
BACKGROUND: The oriental melon (Cucumis melo L. var. makuwa) is one of the most important cultivated cucurbits grown widely in Korea, Japan, and northern China. It is cultivated because its fruit has a sweet aromatic flavor and is rich in soluble sugars, organic acids, minerals, and vitamins. In order to elucidate the genetic and molecular basis of the developmental changes that determine size, color, and sugar contents of the fruit, we performed de novo transcriptome sequencing to analyze the genes expressed during fruit development...
2017: PeerJ
https://www.readbyqxmd.com/read/28069074/a-next-generation-microarray-further-reveals-stage-enriched-gene-expression-pattern-in-the-blood-fluke-schistosoma-japonicum
#15
Pengfei Cai, Shuai Liu, Xianyu Piao, Nan Hou, Hong You, Donald P McManus, Qijun Chen
BACKGROUND: Schistosomiasis is caused by infection with blood flukes of the genus Schistosoma, and ranks, in terms of disability-adjusted life years (DALYs), as the third most important neglected tropical disease. Schistosomes have several discrete life stages involving dramatic morphological changes during their development, which require subtle gene expression modulations to complete the complex life-cycle. RESULTS: In the current study, we employed a second generation schistosome DNA chip printed with the most comprehensive probe array for studying the Schistosoma japonicum transcriptome, to explore stage-associated gene expression in different developmental phases of S...
January 10, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28068920/comparative-transcriptomics-provide-insight-into-the-morphogenesis-and-evolution-of-fistular-leaves-in-allium
#16
Siyuan Zhu, Shouwei Tang, Zhijian Tan, Yongting Yu, Qiuzhong Dai, Touming Liu
BACKGROUND: Fistular leaves frequently appear in Allium species, and previous developmental studies have proposed that the process of fistular leaf formation involves programmed cell death. However, molecular evidence for the role of programmed cell death in the formation of fistular leaf cavities has yet to be reported. RESULTS: In this study, we characterized the leaf transcriptomes of nine Allium species, including six fistular- and three solid-leaved species...
January 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28064470/genome-wide-association-study-discovered-genetic-variation-and-candidate-genes-of-fibre-quality-traits-in-gossypium-hirsutum-l
#17
Zhengwen Sun, Xingfen Wang, Zhengwen Liu, Qishen Gu, Yan Zhang, Zhikun Li, Huifeng Ke, Jun Yang, Jinhua Wu, Liqiang Wu, Guiyin Zhang, Caiying Zhang, Zhiying Ma
Genetic improvement of fibre quality is one of the main breeding goals for the upland cotton, Gossypium hirsutum, but there are difficulties with precise selection of traits. Therefore, it is important to improve the understanding of the genetic basis of phenotypic variation. In this study, we conducted phenotyping and genetic variation analyses of 719 diverse accessions of upland cotton based on multiple environment tests and a recently developed Cotton 63K Illumina Infinium SNP array and performed a genome-wide association study (GWAS) of fibre quality traits...
January 8, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28062755/evolutionary-conservation-and-divergence-of-gene-coexpression-networks-in-gossypium-cotton-seeds
#18
Guanjing Hu, Ran Hovav, Corrinne E Grover, Adi Faigenboim-Doron, Noa Kadmon, Justin T Page, Joshua A Udall, Jonathan F Wendel
The cotton genus (Gossypium) provides a superior system for the study of diversification, genome evolution, polyploidization, and human-mediated selection. To gain insight into phenotypic diversification in cotton seeds, we conducted coexpression network analysis of developing seeds from diploid and allopolyploid cotton species and explored network properties. Key network modules and functional associations were identified related to seed oil content and seed weight. We compared species-specific networks to reveal topological changes, including rewired edges and differentially coexpressed genes, associated with speciation, polyploidy, and cotton domestication...
January 6, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28060419/a-molecular-roadmap-of-definitive-erythropoiesis-from-human-induced-pluripotent-stem-cells
#19
Muhammad A Razaq, Stephen Taylor, David J Roberts, Lee Carpenter
Human induced pluripotent stem cells (hiPSCs) are being considered for use in understanding haematopoietic disorders and as a potential source of in vitro manufactured red cells. Here, we show that hiPSCs are able to recapitulate various stages of developmental erythropoiesis. We show that primitive erythroblasts arise first, express CD31(+) with CD235a(+) , embryonic globins and red cell markers, but fail to express the hallmark red cell transcripts of adult erythropoiesis. When hiPSC-derived CD45(+) CD235a(-) haematopoietic progenitors are isolated on day 12 and further differentiated on OP9 stroma, they selectively express CD36(+) and CD235a(+) , adult erythroid transcripts for transcription factors (e...
January 6, 2017: British Journal of Haematology
https://www.readbyqxmd.com/read/28057603/the-protein-expression-landscape-of-mitosis-and-meiosis-in-diploid-budding-yeast
#20
Emmanuelle Becker, Emmanuelle Com, Régis Lavigne, Marie-Hélène Guilleux, Bertrand Evrard, Charles Pineau, Michael Primig
: Saccharomyces cerevisiae is an established model organism for the molecular analysis of fundamental biological processes. The genomes of numerous strains have been sequenced, and the transcriptome and proteome of major phases during the haploid and diploid yeast life cycle have been determined. However, much less is known about dynamic changes of the proteome when cells switch from mitotic growth to meiotic development. We report a quantitative protein profiling analysis of yeast cell division and differentiation based on mass spectrometry...
January 2, 2017: Journal of Proteomics
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