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Developmental transcriptome

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https://www.readbyqxmd.com/read/28339803/transcriptional-comparison-of-myogenesis-in-leghorn-and-low-score-normal-embryos
#1
J Griffin, N St-Pierre, M S Lilburn, M Wick
In a previous study, we reported on a quantitative transcriptomic method which confirmed the temporal transcription of developmental fast skeletal muscle myosin heavy chain (fsMyHC) embryonic isoforms in the embryonic Pectoralis major (PM) of the Single Comb White Leghorn (SCWL). The objective of the current study was to further investigate the transcriptional events underlying embryonic PM growth in the SCWL and a genotype exhibiting partial muscular dystrophy, the Low Score Normal (LSN). We hypothesized that within the SCWL and LSN embryos, there would be differences in the temporal transcription of the fsMyHC isoforms and other myogenic regulatory genes...
February 21, 2017: Poultry Science
https://www.readbyqxmd.com/read/28331573/evolution-of-the-spatula-alcatraz-gene-lineage-and-expression-analyses-in-the-basal-eudicot-bocconia-frutescens-l-papaveraceae
#2
Cecilia Zumajo-Cardona, Barbara Ann Ambrose, Natalia Pabón-Mora
BACKGROUND: SPATULA (SPT) and ALCATRAZ (ALC) are recent paralogs that belong to the large bHLH transcription factor family. Orthologs of these genes have been found in all core eudicots, whereas pre-duplication genes, named paleoSPATULA/ALCATRAZ, have been found in basal eudicots, monocots, basal angiosperms and gymnosperms. Nevertheless, functional studies have only been performed in Arabidopsis thaliana, where SPT and ALC are partially redundant in carpel and valve margin development and ALC has a unique role in the dehiscence zone...
2017: EvoDevo
https://www.readbyqxmd.com/read/28330224/transcriptome-wide-mining-suggests-conglomerate-of-genes-associated-with-tuberous-root-growth-and-development-in-aconitum-heterophyllum-wall
#3
Nikhil Malhotra, Hemant Sood, Rajinder Singh Chauhan
Tuberous roots of Aconitum heterophyllum constitute storage organ for secondary metabolites, however, molecular components contributing to their formation are not known. The transcriptomes of A. heterophyllum were analyzed to identify possible genes associated with tuberous root development by taking clues from genes implicated in other plant species. Out of 18 genes, eight genes encoding GDP-mannose pyrophosphorylase (GMPase), SHAGGY, Expansin, RING-box protein 1 (RBX1), SRF receptor kinase (SRF), β-amylase, ADP-glucose pyrophosphorylase (AGPase) and Auxin responsive factor 2 (ARF2) showed higher transcript abundance in roots (13-171 folds) compared to shoots...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28327625/early-metabolic-and-transcriptional-variations-in-fruit-of-natural-white-fruited-fragaria-vesca-genotypes
#4
Katja Härtl, Alisandra Denton, Katrin Franz-Oberdorf, Thomas Hoffmann, Melanie Spornraft, Björn Usadel, Wilfried Schwab
Strawberry fruits (Fragaria vesca) are valued for their sweet fruity flavor, juicy texture, and characteristic red color caused by anthocyanin pigments. To gain a deeper insight into the regulation of anthocyanin biosynthesis, we performed comparative metabolite profiling and transcriptome analyses of one red-fruited and two natural white-fruited strawberry varieties in two tissues and three ripening stages. Developing fruit of the three genotypes showed a distinctive pattern of polyphenol accumulation already in green receptacle and achenes...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28327131/transcriptome-analysis-of-pancreatic-cells-across-distant-species-highlights-novel-important-regulator-genes
#5
Estefania Tarifeño-Saldivia, Arnaud Lavergne, Alice Bernard, Keerthana Padamata, David Bergemann, Marianne L Voz, Isabelle Manfroid, Bernard Peers
BACKGROUND: Defining the transcriptome and the genetic pathways of pancreatic cells is of great interest for elucidating the molecular attributes of pancreas disorders such as diabetes and cancer. As the function of the different pancreatic cell types has been maintained during vertebrate evolution, the comparison of their transcriptomes across distant vertebrate species is a means to pinpoint genes under strong evolutionary constraints due to their crucial function, which have therefore preserved their selective expression in these pancreatic cell types...
March 21, 2017: BMC Biology
https://www.readbyqxmd.com/read/28322282/maternal-immune-activation-dysregulation-of-the-fetal-brain-transcriptome-and-relevance-to-the-pathophysiology-of-autism-spectrum-disorder
#6
M V Lombardo, H M Moon, J Su, T D Palmer, E Courchesne, T Pramparo
Maternal immune activation (MIA) via infection during pregnancy is known to increase risk for autism spectrum disorder (ASD). However, it is unclear how MIA disrupts fetal brain gene expression in ways that may explain this increased risk. Here we examine how MIA dysregulates rat fetal brain gene expression (at a time point analogous to the end of the first trimester of human gestation) in ways relevant to ASD-associated pathophysiology. MIA downregulates expression of ASD-associated genes, with the largest enrichments in genes known to harbor rare highly penetrant mutations...
March 21, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28320315/comparative-transcriptome-analyses-of-flower-development-in-four-species-of-achimenes-gesneriaceae
#7
Wade R Roberts, Eric H Roalson
BACKGROUND: Flowers have an amazingly diverse display of colors and shapes, and these characteristics often vary significantly among closely related species. The evolution of diverse floral form can be thought of as an adaptive response to pollination and reproduction, but it can also be seen through the lens of morphological and developmental constraints. To explore these interactions, we use RNA-seq across species and development to investigate gene expression and sequence evolution as they relate to the evolution of the diverse flowers in a group of Neotropical plants native to Mexico-magic flowers (Achimenes, Gesneriaceae)...
March 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28318367/combinatorial-control-of-messenger-rnas-by-pumilio-nanos-and-brain-tumor-proteins
#8
René M Arvola, Chase A Weidmann, Traci M Tanaka Hall, Aaron C Goldstrohm
Eukaryotes possess a vast array of RNA-binding proteins (RBPs) that affect mRNAs in diverse ways to control protein expression. Combinatorial regulation of mRNAs by RBPs is emerging as the rule. No example illustrates this as vividly as the partnership of three Drosophila RBPs, Pumilio, Nanos and Brain Tumor, which have overlapping functions in development, stem cell maintenance and differentiation, fertility and neurological processes. Here we synthesize thirty years of research with new insights into their molecular functions and mechanisms of action...
March 20, 2017: RNA Biology
https://www.readbyqxmd.com/read/28302071/sex-differences-in-the-molecular-signature-of-the-developing-mouse-hippocampus
#9
Joseph L Bundy, Cynthia Vied, Richard S Nowakowski
BACKGROUND: A variety of neurological disorders, including Alzheimer's disease, Parkinson's disease, major depressive disorder, dyslexia and autism, are differentially prevalent between females and males. To better understand the possible molecular basis for the sex-biased nature of neurological disorders, we used a developmental series of female and male mice at 1, 2, and 4 months of age to assess both mRNA and protein in the hippocampus with RNA-sequencing and mass-spectrometry, respectively...
March 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28302059/correspondence-of-d-melanogaster-and-c-elegans-developmental-stages-revealed-by-alternative-splicing-characteristics-of-conserved-exons
#10
Ruiqi Gao, Jingyi Jessica Li
BACKGROUND: We report a statistical study to find correspondence of D. melanogaster and C. elegans developmental stages based on alternative splicing (AS) characteristics of conserved cassette exons using modENCODE RNA-seq data. We identify "stage-associated exons" to capture the AS characteristics of each stage and use these exons to map pairwise stages within and between the two species by an overlap test. RESULTS: Within fly and worm, adjacent developmental stages are mapped to each other, i...
March 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28299719/the-non-coding-transcriptome-of-prostate-cancer-implications-for-clinical-practice
#11
REVIEW
Irene V Bijnsdorp, Martin E van Royen, Gerald W Verhaegh, Elena S Martens-Uzunova
Prostate cancer (PCa) is the most common type of cancer and the second leading cause of cancer-related death in men. Despite extensive research, the molecular mechanisms underlying PCa initiation and progression remain unclear, and there is increasing need of better biomarkers that can distinguish indolent from aggressive and life-threatening disease. With the advent of advanced genomic technologies in the last decade, it became apparent that the human genome encodes tens of thousands non-protein-coding RNAs (ncRNAs) with yet to be discovered function...
March 15, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28298915/transcriptomic-analysis-reveals-mechanisms-of-sterile-and-fertile-flower-differentiation-and-development-in-viburnum-macrocephalum-f-keteleeri
#12
Zhaogeng Lu, Jing Xu, Weixing Li, Li Zhang, Jiawen Cui, Qingsong He, Li Wang, Biao Jin
Sterile and fertile flowers are an important evolutionary developmental (evo-devo) phenotype in angiosperm flowers, playing important roles in pollinator attraction and sexual reproductive success. However, the gene regulatory mechanisms underlying fertile and sterile flower differentiation and development remain largely unknown. Viburnum macrocephalum f. keteleeri, which possesses fertile and sterile flowers in a single inflorescence, is a useful candidate species for investigating the regulatory networks in differentiation and development...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28297718/dnd1-maintains-germline-stem-cells-via-recruitment-of-the-ccr4-not-complex-to-target-mrnas
#13
Masashi Yamaji, Miki Jishage, Cindy Meyer, Hemant Suryawanshi, Evan Der, Misaki Yamaji, Aitor Garzia, Pavel Morozov, Sudhir Manickavel, Hannah L McFarland, Robert G Roeder, Markus Hafner, Thomas Tuschl
The vertebrate-conserved RNA-binding protein DND1 is required for the survival of primordial germ cells (PGCs), as well as the suppression of germ cell tumours in mice. Here we show that in mice DND1 binds a UU(A/U) trinucleotide motif predominantly in the 3' untranslated regions of mRNA, and destabilizes target mRNAs through direct recruitment of the CCR4-NOT deadenylase complex. Transcriptomic analysis reveals that the extent of suppression is dependent on the number of DND1-binding sites. This DND1-dependent mRNA destabilization is required for the survival of mouse PGCs and spermatogonial stem cells by suppressing apoptosis...
March 15, 2017: Nature
https://www.readbyqxmd.com/read/28295644/effect-of-vitrification-on-the-mrna-transcriptome-of-bovine-oocytes
#14
N Wang, C-Y Li, H-B Zhu, H-S Hao, H-Y Wang, C-L Yan, S-J Zhao, W-H Du, D Wang, Y Liu, Y-W Pang, X-M Zhao
Vitrification has been shown to decrease the developmental capacity of mammalian oocytes, and this is closely associated with the abnormal mRNA expressions of vitrified oocytes. However, the effect of vitrification on transcriptional machinery of oocytes examined by RNA sequencing (RNA-seq) has yet to be defined. In the present study, the mRNA transcriptomes of fresh and vitrified bovine oocytes were analysed by Smart-seq2 with the differently expressed genes determined by DEseq2 (an adjusted p-value of .05 and a minimum fold change of 2)...
March 12, 2017: Reproduction in Domestic Animals, Zuchthygiene
https://www.readbyqxmd.com/read/28295392/erecta-signaling-controls-arabidopsis-inflorescence-architecture-through-chromatin-mediated-activation-of-pre1-expression
#15
Hanyang Cai, Lihua Zhao, Lulu Wang, Man Zhang, Zhenxia Su, Yan Cheng, Heming Zhao, Yuan Qin
Flowering plants display a remarkable diversity in inflorescence architecture, and pedicel length is one of the key contributors to this diversity. In Arabidopsis thaliana, the receptor-like kinase ERECTA (ER) mediated signaling pathway plays important roles in regulating inflorescence architecture by promoting cell proliferation. However, the regulating mechanism remains elusive in the pedicel. Genetic interactions between ERECTA signaling and the chromatin remodeling complex SWR1 in the control of inflorescence architecture were studied...
March 13, 2017: New Phytologist
https://www.readbyqxmd.com/read/28295046/transcriptomic-immaturity-of-the-hippocampus-and-prefrontal-cortex-in-patients-with-alcoholism
#16
Tomoyuki Murano, Hisatsugu Koshimizu, Hideo Hagihara, Tsuyoshi Miyakawa
Alcoholism, which is defined as the recurring harmful use of alcohol despite its negative consequences, has a lifetime prevalence of 17.8%. Previous studies have shown that chronic alcohol consumption disrupts various brain functions and behaviours. However, the precise mechanisms that underlie alcoholism are currently unclear. Recently, we discovered "pseudo-immature" brain cell states of the dentate gyrus and prefrontal cortex (PFC) in mouse models of psychotic disorders and epileptic seizure. Similar pseudo-immaturity has been observed in patients with psychotic disorders, such as schizophrenia and bipolar disorder...
March 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28295044/novel-transcriptome-assembly-and-comparative-toxicity-pathway-analysis-in-mahi-mahi-coryphaena-hippurus-embryos-and-larvae-exposed-to-deepwater-horizon-oil
#17
Elvis Genbo Xu, Edward M Mager, Martin Grosell, E Starr Hazard, Gary Hardiman, Daniel Schlenk
The impacts of Deepwater Horizon (DWH) oil on morphology and function during embryonic development have been documented for a number of fish species, including the economically and ecologically important pelagic species, mahi-mahi (Coryphaena hippurus). However, further investigations on molecular events and pathways responsible for developmental toxicity have been largely restricted due to the limited molecular data available for this species. We sought to establish the de novo transcriptomic database from the embryos and larvae of mahi-mahi exposed to water accommodated fractions (HEWAFs) of two DWH oil types (weathered and source oil), in an effort to advance our understanding of the molecular aspects involved during specific toxicity responses...
March 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28291821/transcriptomic-profile-of-leg-muscle-during-early-growth-in-chicken
#18
Qian Xue, Genxi Zhang, Tingting Li, Jiaojiao Ling, Xiangqian Zhang, Jinyu Wang
The early growth pattern, especially the age of peak growth, of broilers affects the time to market and slaughter weight, which in turn affect the profitability of the poultry industry. However, the underlying mechanisms regulating chicken growth and development have rarely been studied. This study aimed to identify candidate genes involved in chicken growth and investigated the potential regulatory mechanisms of early growth in chicken. RNA sequencing was applied to compare the transcriptomes of chicken muscle tissues at three developmental stages during early growth...
2017: PloS One
https://www.readbyqxmd.com/read/28287567/experimental-design-for-laser-microdissection-rna-seq-lessons-from-an-analysis-of-maize-leaf-development
#19
Robyn M Johnston, Anne W Sylvester, Michael J Scanlon
Genes with important roles in development frequently have spatially and/or temporally restricted expression patterns. Often these gene transcripts are not detected or are not identified as differentially expressed (DE) in transcriptomic analyses of whole plant organs. Laser Microdissection RNA-Seq (LM RNA-Seq) is a powerful tool to identify genes that are DE in specific developmental domains. However, the choice of cellular domains to microdissect and compare, and the accuracy of the microdissections are crucial to the success of the experiments...
March 5, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28287176/de-novo-and-reference-transcriptome-assembly-of-transcripts-expressed-during-flowering-provide-insight-into-seed-setting-in-tetraploid-red-clover
#20
Mallikarjuna Rao Kovi, Helga Amdahl, Muath Alsheikh, Odd Arne Rognli
Red clover (Trifolium pratense L.) is one of the most important legume forage species in temperate livestock agriculture. Tetraploid red clover cultivars are generally producing less seed than diploid cultivars. Improving the seed setting potential of tetraploid cultivars is necessary to utilize the high forage quality and environmentally sustainable nitrogen fixation ability of red clover. In the current study, our aim was to identify candidate genes involved in seed setting. Two genotypes, 'Tripo' with weak seed setting and 'Lasang' with strong seed setting were selected for transcriptome analysis...
March 13, 2017: Scientific Reports
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