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Developmental transcriptome

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https://www.readbyqxmd.com/read/27907180/deep-staged-transcriptomic-resources-for-the-novel-coleopteran-models-atrachya-menetriesi-and-callosobruchus-maculatus
#1
Matthew A Benton, Nathan J Kenny, Kai H Conrads, Siegfried Roth, Jeremy A Lynch
Despite recent efforts to sample broadly across metazoan and insect diversity, current sequence resources in the Coleoptera do not adequately describe the diversity of the clade. Here we present deep, staged transcriptomic data for two coleopteran species, Atrachya menetriesi (Faldermann 1835) and Callosobruchus maculatus (Fabricius 1775). Our sampling covered key stages in ovary and early embryonic development in each species. We utilized this data to build combined assemblies for each species which were then analysed in detail...
2016: PloS One
https://www.readbyqxmd.com/read/27906199/microduplication-of-the-arid1a-gene-causes-intellectual-disability-with-recognizable-syndromic-features
#2
Marie Bidart, Michèle El Atifi, Sarra Miladi, John Rendu, Véronique Satre, Pierre F Ray, Caroline Bosson, Françoise Devillard, Daphné Lehalle, Valérie Malan, Jeanne Amiel, Maria Antonietta Mencarelli, Margherita Baldassarri, Alessandra Renieri, Jill Clayton-Smith, Gaëlle Vieville, Julien Thevenon, Florence Amblard, François Berger, Pierre-Simon Jouk, Charles Coutton
PURPOSE: To determine whether duplication of the ARID1A gene is responsible for a new recognizable syndrome. METHODS: We describe four patients with a 1p36.11 microduplication involving ARID1A as identified by array-comparative genomic hybridization . We performed comparative transcriptomic analysis of patient-derived fibroblasts using RNA sequencing and evaluated the impact of ARID1A duplication on the cell cycle using fluorescence-activated cell sorting. Functional relationships between differentially expressed genes were investigated with ingenuity pathway analysis (IPA)...
December 1, 2016: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/27898892/transcriptome-analyses-identify-five-transcription-factors-differentially-expressed-in-the-hypothalamus-of-post-versus-prepubertal-brahman-heifers
#3
M R S Fortes, L T Nguyen, M M D C A Weller, A Cánovas, A Islas-Trejo, L R Porto-Neto, A Reverter, S A Lehnert, G B Boe-Hansen, M G Thomas, J F Medrano, S S Moore
Puberty onset is a developmental process influenced by genetic determinants, environment, and nutrition. Mutations and regulatory gene networks constitute the molecular basis for the genetic determinants of puberty onset. The emerging knowledge of these genetic determinants presents opportunities for innovation in the breeding of early pubertal cattle. This paper presents new data on hypothalamic gene expression related to puberty in (Brahman) in age- and weight-matched heifers. Six postpubertal heifers were compared with 6 prepubertal heifers using whole-genome RNA sequencing methodology for quantification of global gene expression in the hypothalamus...
September 2016: Journal of Animal Science
https://www.readbyqxmd.com/read/27898811/de-novo-transcriptome-assembly-and-dynamic-spatial-gene-expression-analysis-in-red-clover
#4
Manohar Chakrabarti, Randy D Dinkins, Arthur G Hunt
Red clover ( L.) is a cool-season forage legume grown throughout the northeastern United States and is the most widely planted forage legume after alfalfa ( L.). Red clover provides high-value feed to the livestock because of high protein content and easy digestibility. To date, genomic resources for red clover are scarce. In the current study, a de novo transcriptome assembly of red clover was constructed representing different tissue types. The draft assembly consists of 37,565 contigs with N50 and average contig length of 1707 and 1262 bp, respectively...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27898762/an-expanded-maize-gene-expression-atlas-based-on-rna-sequencing-and-its-use-to-explore-root-development
#5
Scott C Stelpflug, Rajandeep S Sekhon, Brieanne Vaillancourt, Candice N Hirsch, C Robin Buell, Natalia de Leon, Shawn M Kaeppler
Comprehensive and systematic transcriptome profiling provides valuable insight into biological and developmental processes that occur throughout the life cycle of a plant. We have enhanced our previously published microarray-based gene atlas of maize ( L.) inbred B73 to now include 79 distinct replicated samples that have been interrogated using RNA sequencing (RNA-seq). The current version of the atlas includes 50 original array-based gene atlas samples, a time-course of 12 stalk and leaf samples postflowering, and an additional set of 17 samples from the maize seedling and adult root system...
March 2016: Plant Genome
https://www.readbyqxmd.com/read/27897982/maternal-fructose-intake-affects-transcriptome-changes-and-programmed-hypertension-in-offspring-in-later-life
#6
REVIEW
You-Lin Tain, Julie Y H Chan, Chien-Ning Hsu
Hypertension originates from early-life insults by so-called "developmental origins of health and disease" (DOHaD). Studies performed in the previous few decades indicate that fructose consumption is associated with an increase in hypertension rate. It is emerging field that tends to unfold the nutrient-gene interactions of maternal high-fructose (HF) intake on the offspring which links renal programming to programmed hypertension. Reprogramming interventions counteract disturbed nutrient-gene interactions induced by maternal HF intake and exert protective effects against developmentally programmed hypertension...
November 25, 2016: Nutrients
https://www.readbyqxmd.com/read/27889097/axonal-degeneration-is-regulated-by-a-transcriptional-program-that-coordinates-expression-of-pro-and-anti-degenerative-factors
#7
Maya Maor-Nof, Erez Romi, Hadas Sar Shalom, Valeria Ulisse, Calanit Raanan, Aviv Nof, Dena Leshkowitz, Roland Lang, Avraham Yaron
Developmental neuronal cell death and axonal elimination are controlled by transcriptional programs, of which their nature and the function of their components remain elusive. Here, we identified the dual specificity phosphatase Dusp16 as part of trophic deprivation-induced transcriptome in sensory neurons. Ablation of Dusp16 enhanced axonal degeneration in response to trophic withdrawal, suggesting that it has a protective function. Moreover, axonal skin innervation was severely reduced while neuronal elimination was increased in the Dusp16 knockout...
November 21, 2016: Neuron
https://www.readbyqxmd.com/read/27881993/transcriptome-analysis-and-identification-of-genes-associated-with-floral-transition-and-flower-development-in-sugar-apple-annona-squamosa-l
#8
Kaidong Liu, Shaoxian Feng, Yaoling Pan, Jundi Zhong, Yan Chen, Changchun Yuan, Haili Li
Sugar apple (Annona squamosa L.) is a semi-deciduous subtropical tree that progressively sheds its leaves in the spring. However, little information is available on the mechanism involved in flower developmental pattern. To gain a global perspective on the floral transition and flower development of sugar apple, cDNA libraries were prepared independently from inflorescent meristem and three flowering stages. Illumina sequencing generated 107,197,488 high quality reads that were assembled into 71,948 unigenes, with an average sequence length of 825...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27879624/transcriptome-analysis-identifies-key-candidate-genes-mediating-purple-ovary-coloration-in-asiatic-hybrid-lilies
#9
Leifeng Xu, Panpan Yang, Suxia Yuan, Yayan Feng, Hua Xu, Yuwei Cao, Jun Ming
Lily tepals have a short lifespan. Once the tepals senesce, the ornamental value of the flower is lost. Some cultivars have attractive purple ovaries and fruits which greatly enhance the ornamental value of Asiatic hybrid lilies. However, little is known about the molecular mechanisms of anthocyanin biosynthesis in Asiatic hybrid lily ovaries. To investigate the transcriptional network that governs purple ovary coloration in Asiatic hybrid lilies, we obtained transcriptome data from green ovaries (S1) and purple ovaries (S2) of Asiatic "Tiny Padhye"...
November 20, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27875998/transcriptome-profiling-and-comparison-of-maize-ear-heterosis-during-the-spikelet-and-floret-differentiation-stages
#10
Xiaojiao Hu, Hongwu Wang, Xizhou Diao, Zhifang Liu, Kun Li, Yujin Wu, Qianjin Liang, Hui Wang, Changling Huang
BACKGROUND: Hybridization is a prominent process in the evolution of crop plants that can give rise to gene expression variation, phenotypic novelty and heterosis. Maize is the most successful crop in utilizing heterosis. The development of hybrid maize ears exhibits strong heterotic vigor and greatly affects maize yield. However, a comprehensive perspective on transcriptional variation and its correlation with heterosis during maize ear development is not available. RESULTS: Using RNA sequencing technology, we investigated the transcriptome profiles of maize ears in the spikelet and floret differentiation stages of hybrid ZD808 and its parents CL11 and NG5...
November 22, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27872325/the-molecular-circuit-regulating-tooth-development-in-crocodilians
#11
S Tsai, A Abdelhamid, M K Khan, A Elkarargy, R B Widelitz, C M Chuong, P Wu
Alligators have robust regenerative potential for tooth renewal. In contrast, extant mammals can either renew their teeth once (diphyodont dentition, as found in humans) or not at all (monophyodont dentition, present in mice). Previously, the authors used multiple mitotic labeling to map putative stem cells in alligator dental laminae, which contain quiescent odontogenic progenitors. The authors demonstrated that alligator tooth cycle initiation is related to β-catenin/Wnt pathway activity in the dental lamina bulge...
December 2016: Journal of Dental Research
https://www.readbyqxmd.com/read/27867341/disorders-of-transcriptional-regulation-an-emerging-category-of-multiple-malformation-syndromes
#12
REVIEW
Kosuke Izumi
Some genetic disorders caused by mutations in genes encoding components of the transcriptional machinery as well as proteins involved in epigenetic modification of the genome share many overlapping features, such as facial dysmorphisms, growth problems and developmental delay/intellectual disability. As a basis for some shared phenotypic characteristics in these syndromes, a similar transcriptome disturbance, characterized by global transcriptional dysregulation, is believed to play a major role. In this review article, a general overview of gene transcription is provided, and the current knowledge of the mechanisms underlying some disorders of transcriptional regulation, such as Rubinstein- Taybi, Coffin-Siris, Cornelia de Lange, and CHOPS syndromes, are discussed...
October 2016: Molecular Syndromology
https://www.readbyqxmd.com/read/27864905/polyacrylamide-gel-as-a-culture-substrate-improves-in-vitro-oocyte-growth-from-porcine-early-antral-follicles
#13
Yasuhisa Munakata, Ryouka Kawahara-Miki, Koumei Shirasuna, Takehito Kuwayama, Hisataka Iwata
A major difference between in vivo and in vitro follicle culture is the stiffness of the substrate in which the follicles grow. In this study, we examined the effect of polyacrylamide gel (PAG), as a culture substrate, on the development of porcine oocytes derived from early antral follicles. Oocyte-granulosa cell complexes (OGCs) were collected from the early antral follicles of gilts, and incubated individually for 14 days in a 96-well culture plate with or without PAG. We then evaluated the number of granulosa cells present in OGCs as well as the abundance of ATP, lipid, and acetylated lysine in oocytes...
November 19, 2016: Molecular Reproduction and Development
https://www.readbyqxmd.com/read/27859288/exploring-key-cellular-processes-and-candidate-genes-regulating-the-primary-thickening-growth-of-moso-underground-shoots
#14
Qiang Wei, Chen Jiao, Lin Guo, Yulong Ding, Junjie Cao, Jianyuan Feng, Xiaobo Dong, Linyong Mao, Honghe Sun, Fen Yu, Guangyao Yang, Peijian Shi, Guodong Ren, Zhangjun Fei
The primary thickening growth of Moso (Phyllostachys edulis) underground shoots largely determines the culm circumference. However, its developmental mechanisms remain largely unknown. Using an integrated anatomy, mathematics and genomics approach, we systematically studied cellular and molecular mechanisms underlying the growth of Moso underground shoots. We discovered that the growth displayed a spiral pattern and pith played an important role in promoting the primary thickening process of Moso underground shoots and driving the evolution of culms with different sizes among different bamboo species...
November 12, 2016: New Phytologist
https://www.readbyqxmd.com/read/27853259/comparative-transcriptome-analysis-of-chinary-assamica-and-cambod-tea-camellia-sinensis-types-during-development-and-seasonal-variation-using-rna-seq-technology
#15
Ajay Kumar, Vandna Chawla, Eshita Sharma, Pallavi Mahajan, Ravi Shankar, Sudesh Kumar Yadav
Tea quality and yield is influenced by various factors including developmental tissue, seasonal variation and cultivar type. Here, the molecular basis of these factors was investigated in three tea cultivars namely, Him Sphurti (H), TV23 (T), and UPASI-9 (U) using RNA-seq. Seasonal variation in these cultivars was studied during active (A), mid-dormant (MD), dormant (D) and mid-active (MA) stages in two developmental tissues viz. young and old leaf. Development appears to affect gene expression more than the seasonal variation and cultivar types...
November 17, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27852726/thyroid-hormone-regulated-genes-in-cerebral-cortex-development
#16
Juan Bernal
The physiological and developmental effects of thyroid hormones are mainly due to the control of gene expression after interaction of T3 with the nuclear receptors. To understand the role of thyroid hormones on cerebral cortex development, knowledge of the genes regulated by T3 during specific stages of development is required. In our laboratory we previously identified genes regulated by T3 in primary cerebrocortical cells in culture. By comparing these data with transcriptomics of purified cell types from the developing cortex, the cellular targets of T3 can be identified...
November 16, 2016: Journal of Endocrinology
https://www.readbyqxmd.com/read/27852222/differential-gene-expression-in-varroa-jacobsoni-mites-following-a-host-shift-to-european-honey-bees-apis-mellifera
#17
Gladys K Andino, Michael Gribskov, Denis L Anderson, Jay D Evans, Greg J Hunt
BACKGROUND: Varroa mites are widely considered the biggest honey bee health problem worldwide. Until recently, Varroa jacobsoni has been found to live and reproduce only in Asian honey bee (Apis cerana) colonies, while V. destructor successfully reproduces in both A. cerana and A. mellifera colonies. However, we have identified an island population of V. jacobsoni that is highly destructive to A. mellifera, the primary species used for pollination and honey production. The ability of these populations of mites to cross the host species boundary potentially represents an enormous threat to apiculture, and is presumably due to genetic variation that exists among populations of V...
November 16, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27852218/rna-seq-based-transcriptomic-map-reveals-new-insights-into-mouse-salivary-gland-development-and-maturation
#18
Christian Gluck, Sangwon Min, Akinsola Oyelakin, Kirsten Smalley, Satrajit Sinha, Rose-Anne Romano
BACKGROUND: Mouse models have served a valuable role in deciphering various facets of Salivary Gland (SG) biology, from normal developmental programs to diseased states. To facilitate such studies, gene expression profiling maps have been generated for various stages of SG organogenesis. However these prior studies fall short of capturing the transcriptional complexity due to the limited scope of gene-centric microarray-based technology. Compared to microarray, RNA-sequencing (RNA-seq) offers unbiased detection of novel transcripts, broader dynamic range and high specificity and sensitivity for detection of genes, transcripts, and differential gene expression...
November 16, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27845378/sex-specific-effects-of-testosterone-on-the-sexually-dimorphic-transcriptome-and-epigenome-of-embryonic-neural-stem-progenitor-cells
#19
Matthew S Bramble, Lara Roach, Allen Lipson, Neerja Vashist, Ascia Eskin, Tuck Ngun, Jason E Gosschalk, Steven Klein, Hayk Barseghyan, Valerie A Arboleda, Eric Vilain
The mechanisms by which sex differences in the mammalian brain arise are poorly understood, but are influenced by a combination of underlying genetic differences and gonadal hormone exposure. Using a mouse embryonic neural stem cell (eNSC) model to understand early events contributing to sexually dimorphic brain development, we identified novel interactions between chromosomal sex and hormonal exposure that are instrumental to early brain sex differences. RNA-sequencing identified 103 transcripts that were differentially expressed between XX and XY eNSCs at baseline (FDR = 0...
November 15, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27843122/allele-specific-methylome-and-transcriptome-analysis-reveals-widespread-imprinting-in-the-human-placenta
#20
Hirotaka Hamada, Hiroaki Okae, Hidehiro Toh, Hatsune Chiba, Hitoshi Hiura, Kenjiro Shirane, Tetsuya Sato, Mikita Suyama, Nobuo Yaegashi, Hiroyuki Sasaki, Takahiro Arima
DNA methylation is globally reprogrammed after fertilization, and as a result, the parental genomes have similar DNA-methylation profiles after implantation except at the germline differentially methylated regions (gDMRs). We and others have previously shown that human blastocysts might contain thousands of transient maternally methylated gDMRs (transient mDMRs), whose maternal methylation is lost in embryonic tissues after implantation. In this study, we performed genome-wide allelic DNA methylation analyses of purified trophoblast cells from human placentas and, surprisingly, found that more than one-quarter of the transient-in-embryo mDMRs maintained their maternally biased DNA methylation...
November 3, 2016: American Journal of Human Genetics
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