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Developmental transcriptome

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https://www.readbyqxmd.com/read/28647896/omics-based-hybrid-prediction-in-maize
#1
Matthias Westhues, Tobias A Schrag, Claas Heuer, Georg Thaller, H Friedrich Utz, Wolfgang Schipprack, Alexander Thiemann, Felix Seifert, Anita Ehret, Armin Schlereth, Mark Stitt, Zoran Nikoloski, Lothar Willmitzer, Chris C Schön, Stefan Scholten, Albrecht E Melchinger
Complementing genomic data with other "omics" predictors can increase the probability of success for predicting the best hybrid combinations using complex agronomic traits. Accurate prediction of traits with complex genetic architecture is crucial for selecting superior candidates in animal and plant breeding and for guiding decisions in personalized medicine. Whole-genome prediction has revolutionized these areas but has inherent limitations in incorporating intricate epistatic interactions. Downstream "omics" data are expected to integrate interactions within and between different biological strata and provide the opportunity to improve trait prediction...
June 24, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28644509/comparative-transcriptomic-analysis-of-two-important-life-stages-of-angiostrongylus-cantonensis-fifth-stage-larvae-and-female-adults
#2
Liang Yu, Binbin Cao, Ying Long, Meks Tukayo, Chonglv Feng, Wenzhen Fang, Damin Luo
The mechanisms involved in the fast growth of Angiostrongylus cantonensis from fifth-stage larvae (L5) to female adults and how L5 breaks through the blood-brain barrier in a permissive host remain unclear. In this work, we compared the transcriptomes of these two life stages to identify the main factors involved in the rapid growth and transition to adulthood. RNA samples from the two stages were sequenced and assembled de novo. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses of 1,346 differentially expressed genes between L5 and female adults was then undertaken...
April 2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28641110/sox11-expression-promotes-regeneration-of-some-retinal-ganglion-cell-types-but-kills-others
#3
Michael W Norsworthy, Fengfeng Bei, Riki Kawaguchi, Qing Wang, Nicholas M Tran, Yi Li, Benedikt Brommer, Yiming Zhang, Chen Wang, Joshua R Sanes, Giovanni Coppola, Zhigang He
At least 30 types of retinal ganglion cells (RGCs) send distinct messages through the optic nerve to the brain. Available strategies of promoting axon regeneration act on only some of these types. Here we tested the hypothesis that overexpressing developmentally important transcription factors in adult RGCs could reprogram them to a "youthful" growth-competent state and promote regeneration of other types. From a screen of transcription factors, we identified Sox11 as one that could induce substantial axon regeneration...
June 21, 2017: Neuron
https://www.readbyqxmd.com/read/28640939/global-transcriptome-and-co-expression-network-analyses-reveal-cultivar-specific-molecular-signatures-associated-with-seed-development-and-seed-size-weight-determination-in-chickpea
#4
Rohini Garg, Vikash K Singh, Mohan Singh Rajkumar, Vinay Kumar, Mukesh Jain
Seed development is an intricate process regulated via a complex transcriptional regulatory network. To understand the molecular mechanisms governing seed development and seed size/weight in chickpea, we performed a comprehensive analysis of transcriptome dynamics during seed development in two cultivars with contrasting seed size/weight (small seeded, Himchana 1 and large-seeded, JGK 3). Our analysis identified stage-specific expression for a significant proportion (>13%) of the genes. About one-fourth of total genes exhibited significant differential expression in JGK 3 as compared to Himchana 1...
June 22, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28640868/functional-metabolomics-as-a-tool-to-analyze-mediator-function-and-structure-in-plants
#5
Celine Davoine, Ilka N Abreu, Khalil Khajeh, Jeanette Blomberg, Brendan N Kidd, Kemal Kazan, Peer M Schenk, Lorenz Gerber, Ove Nilsson, Thomas Moritz, Stefan Björklund
Mediator is a multiprotein transcriptional co-regulator complex composed of four modules; Head, Middle, Tail, and Kinase. It conveys signals from promoter-bound transcriptional regulators to RNA polymerase II and thus plays an essential role in eukaryotic gene regulation. We describe subunit localization and activities of Mediator in Arabidopsis through metabolome and transcriptome analyses from a set of Mediator mutants. Functional metabolomic analysis based on the metabolite profiles of Mediator mutants using multivariate statistical analysis and heat-map visualization shows that different subunit mutants display distinct metabolite profiles, which cluster according to the reported localization of the corresponding subunits in yeast...
2017: PloS One
https://www.readbyqxmd.com/read/28637693/neuroblast-differentiation-during-development-and-in-neuroblastoma-requires-kif1b%C3%AE-mediated-transport-of-trka
#6
Stuart M Fell, Shuijie Li, Karin Wallis, Anna Kock, Olga Surova, Vilma Rraklli, Carolin S Höfig, Wenyu Li, Jens Mittag, Marie Arsenian Henriksson, Rajappa S Kenchappa, Johan Holmberg, Per Kogner, Susanne Schlisio
We recently identified pathogenic KIF1Bβ mutations in sympathetic nervous system malignancies that are defective in developmental apoptosis. Here we deleted KIF1Bβ in the mouse sympathetic nervous system and observed impaired sympathetic nervous function and misexpression of genes required for sympathoadrenal lineage differentiation. We discovered that KIF1Bβ is required for nerve growth factor (NGF)-dependent neuronal differentiation through anterograde transport of the NGF receptor TRKA. Moreover, pathogenic KIF1Bβ mutations identified in neuroblastoma impair TRKA transport...
May 15, 2017: Genes & Development
https://www.readbyqxmd.com/read/28630873/an-integrative-developmental-genomics-and-systems-biology-approach-to-identify-an-in-vivo-sox-trio-mediated-gene-regulatory-network-in-murine-embryos
#7
Wenqing Jean Lee, Sumantra Chatterjee, Sook Peng Yap, Siew Lan Lim, Xing Xing, Petra Kraus, Wenjie Sun, Xiaoming Hu, V Sivakamasundari, Hsiao Yun Chan, Prasanna R Kolatkar, Shyam Prabhakar, Thomas Lufkin
Embryogenesis is an intricate process involving multiple genes and pathways. Some of the key transcription factors controlling specific cell types are the Sox trio, namely, Sox5, Sox6, and Sox9, which play crucial roles in organogenesis working in a concerted manner. Much however still needs to be learned about their combinatorial roles during this process. A developmental genomics and systems biology approach offers to complement the reductionist methodology of current developmental biology and provide a more comprehensive and integrated view of the interrelationships of complex regulatory networks that occur during organogenesis...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28630437/phylogenetic-analysis-of-f-bzip-transcription-factors-indicates-conservation-of-the-zinc-deficiency-response-across-land-plants
#8
Pedro Humberto Castro, Grmay H Lilay, Antonio Muñoz-Mérida, Jan K Schjoerring, Herlânder Azevedo, Ana G L Assunção
Basic leucine zipper (bZIP) transcription factors control important developmental and physiological processes in plants. In Arabidopsis thaliana, the three gene F-bZIP subfamily has been associated with zinc deficiency and salt stress response. Benefiting from the present abundance of plant genomic data, we performed an evolutionary and structural characterization of plant F-bZIPs. We observed divergence during seed plant evolution, into two groups and inferred different selective pressures for each. Group 1 contains AtbZIP19 and AtbZIP23 and appears more conserved, whereas Group 2, containing AtbZIP24, is more prone to gene loss and expansion events...
June 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28628668/dose-dependent-effects-of-gamma-radiation-on-the-early-zebrafish-development-and-gene-expression
#9
Selma Hurem, Leonardo Martín Martín, Dag Anders Brede, Eystein Skjerve, Rasoul Nourizadeh-Lillabadi, Ole Christian Lind, Terje Christensen, Vidar Berg, Hans-Christian Teien, Brit Salbu, Deborah Helen Oughton, Peter Aleström, Jan Ludvig Lyche
Ionizing radiation from natural sources or anthropogenic activity has the potential to cause oxidative stress or genetic damage in living organisms, through the ionization and excitation of molecules and the subsequent production of free radicals and reactive oxygen species (ROS). The present work focuses on radiation-induced biological effects using the zebrafish (Danio rerio) vertebrate model. Changes in developmental traits and gene expression in zebrafish were assessed after continuous external gamma irradiation (0...
2017: PloS One
https://www.readbyqxmd.com/read/28627419/arx-polyalanine-expansion-mutations-lead-to-migration-impediment-in-the-rostral-cortex-coupled-with-a-developmental-deficit-of-calbindin-positive-cortical-gabaergic-interneurons
#10
K Lee, K Ireland, M Bleeze, C Shoubridge
The Aristaless-related homeobox gene (ARX) is indispensable for interneuron development. Patients with ARX polyalanine expansion mutations of the first two tracts (namely PA1 and PA2) suffer from intellectual disability of varying severity, with seizures a frequent comorbidity. The impact of PA1 and PA2 mutations on the brain development is unknown, hindering the search for therapeutic interventions. Here, we characterized the disturbances to cortical interneuron development in mice modeling the two most common ARX polyalanine expansion mutations in human...
June 13, 2017: Neuroscience
https://www.readbyqxmd.com/read/28626637/transcriptome-analysis-of-reproductive-tissue-differentiation-in-jatropha-curcas-linn
#11
Nisha Govender, Siju Senan, Zeti-Azura Mohamed-Hussein, Wickneswari Ratnam
Shoot and inflorescence are central physiological and developmental tissues of plants. Flowering is one of the most important agronomic traits for improvement of crop yield. To analyze the vegetative to reproductive tissue transition in Jatropha curcas, gene expression profiles were generated from shoot and inflorescence tissues. RNA isolated from both tissues was sequenced using the Ilumina HiSeq 2500 platform. Differential gene expression analysis identified key biological processes associated with vegetative to reproductive tissue transition...
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28625536/reconstructing-lineage-hierarchies-of-mouse-uterus-epithelial-development-using-single-cell-analysis
#12
Bingbing Wu, Chengrui An, Yu Li, Zi Yin, Lin Gong, Zhenli Li, Yixiao Liu, Boon Chin Heng, Dandan Zhang, Hongwei Ouyang, Xiaohui Zou
The endometrial layer comprises luminal and glandular epithelia that both develop from the same simple layer of fetal uterine epithelium. Mechanisms of uterine epithelial progenitor self-renewal and differentiation are unclear. This study aims to systematically analyze the molecular and cellular mechanisms of uterine epithelial development by single-cell analysis. An integrated set of single-cell transcriptomic data of uterine epithelial progenitors and their differentiated progenies is provided. Additionally the unique molecular signatures of these cells, characterized by sequential upregulation of specific epigenetic and metabolic activities, and activation of unique signaling pathways and transcription factors, were also investigated...
June 14, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/28622514/landscape-of-infiltrating-t-cells-in-liver-cancer-revealed-by-single-cell-sequencing
#13
Chunhong Zheng, Liangtao Zheng, Jae-Kwang Yoo, Huahu Guo, Yuanyuan Zhang, Xinyi Guo, Boxi Kang, Ruozhen Hu, Julie Y Huang, Qiming Zhang, Zhouzerui Liu, Minghui Dong, Xueda Hu, Wenjun Ouyang, Jirun Peng, Zemin Zhang
Systematic interrogation of tumor-infiltrating lymphocytes is key to the development of immunotherapies and the prediction of their clinical responses in cancers. Here, we perform deep single-cell RNA sequencing on 5,063 single T cells isolated from peripheral blood, tumor, and adjacent normal tissues from six hepatocellular carcinoma patients. The transcriptional profiles of these individual cells, coupled with assembled T cell receptor (TCR) sequences, enable us to identify 11 T cell subsets based on their molecular and functional properties and delineate their developmental trajectory...
June 15, 2017: Cell
https://www.readbyqxmd.com/read/28619522/integrated-analysis-of-paraquat-induced-micrornas-mrnas-changes-in-human-neural-progenitor-cells
#14
Mengling Yan, Tingting Dou, Wen Lv, Xinjin Wang, Lina Zhao, Xiuli Chang, Zhijun Zhou
Paraquat (PQ), one of the most widely used fast-acting and non-selective herbicides in the world is believed to act as a neurotoxicant, which increases the risk of developing Parkinson's disease (PD) by selectively impairing dopaminergic neurons. However, the mechanism of PQ on neural progenitor cells remains unclear. As regulator of mRNA expression, miRNA play a crucial role in neurotoxicity. Based on our previous study, we chose 10μM PQ, which induced ROS production and inhibited proliferation but not reduced the cell viability...
June 12, 2017: Toxicology in Vitro: An International Journal Published in Association with BIBRA
https://www.readbyqxmd.com/read/28618077/generation-of-a-microglial-developmental-index-in-mice-and-in-humans-reveals-a-sex-difference-in-maturation-and-immune-reactivity
#15
Richa Hanamsagar, Mark D Alter, Carina S Block, Haley Sullivan, Jessica L Bolton, Staci D Bilbo
Evidence suggests many neurological disorders emerge when normal neurodevelopmental trajectories are disrupted, i.e., when circuits or cells do not reach their fully mature state. Microglia play a critical role in normal neurodevelopment and are hypothesized to contribute to brain disease. We used whole transcriptome profiling with Next Generation sequencing of purified developing microglia to identify a microglial developmental gene expression program involving thousands of genes whose expression levels change monotonically (up or down) across development...
June 15, 2017: Glia
https://www.readbyqxmd.com/read/28618009/evidence-of-an-evolutionary-hourglass-pattern-in-herbivory-induced-transcriptomic-responses
#16
Matthew Durrant, Justin Boyer, Wenwu Zhou, Ian T Baldwin, Shuqing Xu
Herbivory-induced defenses are specific and activated in plants when elicitors, frequently found in the herbivores' oral secretions, are introduced into wounds during attack. While complex signaling cascades are known to be involved, it remains largely unclear how natural selection has shaped the evolution of these induced defenses. We analyzed herbivory-induced transcriptomic responses in wild tobacco, Nicotiana attenuata, using a phylotranscriptomic approach that measures the origin and sequence divergence of herbivory-induced genes...
June 15, 2017: New Phytologist
https://www.readbyqxmd.com/read/28615158/somatosensory-modulation-of-salivary-gene-expression-and-oral-feeding-in-preterm-infants-randomized-controlled-trial
#17
Steven Michael Barlow, Jill Lamanna Maron, Gil Alterovitz, Dongli Song, Bernard Joseph Wilson, Priya Jegatheesan, Balaji Govindaswami, Jaehoon Lee, Austin Oder Rosner
BACKGROUND: Despite numerous medical advances in the care of at-risk preterm neonates, oral feeding still represents one of the first and most advanced neurological challenges facing this delicate population. Objective, quantitative, and noninvasive assessment tools, as well as neurotherapeutic strategies, are greatly needed in order to improve feeding and developmental outcomes. Pulsed pneumatic orocutaneous stimulation has been shown to improve nonnutritive sucking (NNS) skills in preterm infants who exhibit delayed or disordered nipple feeding behaviors...
June 14, 2017: JMIR Research Protocols
https://www.readbyqxmd.com/read/28614664/molecular-mechanisms-of-developmental-toxicity-induced-by-graphene-oxide-at-predicted-environmental-concentrations
#18
Xingli Zhang, Qixing Zhou, Wei Zou, Xiangang Hu
Developmental toxicity is a critical issue in nanotoxicity. However, very little is known about the effects of graphene oxide (GO, a widely used carbon material) at predicted environmental concentrations on biological development or the specific molecular mechanisms. The present study established that the development of zebrafish embryos exposed to trace concentrations (1-100 μg/L) of GO was impaired because of DNA modification, protein carbonylation and excessive generation of reactive oxygen species (ROS), especially the superoxide radical...
June 14, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28609697/beyond-proteome-diversity-alternative-splicing-as-a-regulator-of-neuronal-transcript-dynamics
#19
REVIEW
Oriane Mauger, Peter Scheiffele
Brain development and function are governed by tightly controlled gene expression programs. Transcriptional repertoires in neurons are highly specific to developmental stage, neuronal cell type and can undergo rapid changes upon neuronal stimulation. Dedicated molecular mechanisms are required to achieve such fine-tuned regulation. In addition to transcriptional programs, post-transcriptional processes and notably alternative splicing substantially contribute to the elaboration of neuronal gene expression. While alternative splicing has been viewed primarily as a means for expanding proteome diversity, it emerges to also be a major regulator of transcript levels and dynamics...
June 10, 2017: Current Opinion in Neurobiology
https://www.readbyqxmd.com/read/28608572/identification-of-candidate-genes-involved-in-the-etiology-of-sporadic-tourette-syndrome-by-exome-sequencing
#20
Yosuke Eriguchi, Hitoshi Kuwabara, Aya Inai, Yuki Kawakubo, Fumichika Nishimura, Chihiro Kakiuchi, Mamoru Tochigi, Jun Ohashi, Naoto Aoki, Kayoko Kato, Hiroyuki Ishiura, Jun Mitsui, Shoji Tsuji, Koichiro Doi, Jun Yoshimura, Shinichi Morishita, Takafumi Shimada, Masaomi Furukawa, Tadashi Umekage, Tsukasa Sasaki, Kiyoto Kasai, Yukiko Kano
Tourette Syndrome (TS) is a neurodevelopmental disorder characterized by chronic motor and vocal tics. Although there is a large genetic contribution, the genetic architecture of TS remains unclear. Exome sequencing has successfully revealed the contribution of de novo mutations in sporadic cases with neuropsychiatric disorders such as autism and schizophrenia. Here, using exome sequencing, we investigated de novo mutations in individuals with sporadic TS to identify novel risk loci and elucidate the genetic background of TS...
June 13, 2017: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
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