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https://www.readbyqxmd.com/read/28439089/transcriptome-analysis-on-the-exoskeleton-formation-in-early-developmetal-stages-and-reconstruction-scenario-in-growth-moulting-in-litopenaeus-vannamei
#1
Yi Gao, Jiankai Wei, Jianbo Yuan, Xiaojun Zhang, Fuhua Li, Jianhai Xiang
Exoskeleton construction is an important issue in shrimp. To better understand the molecular mechanism of exoskeleton formation, development and reconstruction, the transcriptome of the entire developmental process in Litopenaeus vannamei, including nine early developmental stages and eight adult-moulting stages, was sequenced and analysed using Illumina RNA-seq technology. A total of 117,539 unigenes were obtained, with 41.2% unigenes predicting the full-length coding sequence. Gene Ontology, Clusters of Orthologous Group (COG), the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and functional annotation of all unigenes gave a better understanding of the exoskeleton developmental process in L...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28429739/a-large-scale-benchmark-of-gene-prioritization-methods
#2
Dimitri Guala, Erik L L Sonnhammer
In order to maximize the use of results from high-throughput experimental studies, e.g. GWAS, for identification and diagnostics of new disease-associated genes, it is important to have properly analyzed and benchmarked gene prioritization tools. While prospective benchmarks are underpowered to provide statistically significant results in their attempt to differentiate the performance of gene prioritization tools, a strategy for retrospective benchmarking has been missing, and new tools usually only provide internal validations...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28424525/genome-wide-detection-of-copy-number-variation-in-chinese-indigenous-sheep-using-an-ovine-high-density-600%C3%A2-k-snp-array
#3
Qing Ma, Xuexue Liu, Jianfei Pan, Lina Ma, Yuehui Ma, Xiaohong He, Qianjun Zhao, Yabin Pu, Yingkang Li, Lin Jiang
Copy number variants (CNVs) represent a form of genomic structural variation underlying phenotypic diversity. In this study, we used the Illumina Ovine SNP 600 K BeadChip array for genome-wide detection of CNVs in 48 Chinese Tan sheep. A total of 1,296 CNV regions (CNVRs), ranging from 1.2 kb to 2.3 Mb in length, were detected, representing approximately 4.7% of the entire ovine genome (Oar_v3.1). We combined our findings with five existing CNVR reports to generate a composite genome-wide dataset of 4,321 CNVRs, which revealed 556 (43%) novel CNVRs...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28421658/transcriptional-signatures-of-connectomic-subregions-of-the-human-striatum
#4
Linden Parkes, Ben Fulcher, Murat Yücel, Alex Fornito
Functionally distinct regions of the brain are thought to possess a characteristic connectional fingerprint - a profile of incoming and outgoing connections that defines the function of that area. This observation has motivated efforts to subdivide brain areas using their connectivity patterns. However, it remains unclear whether these connectomically-defined subregions can be distinguished at the molecular level. Here, we combine high-resolution diffusion-weighted magnetic resonance imaging with transcriptomic data to show that connectomically-defined subregions of the striatum carry distinct transcriptional signatures...
April 19, 2017: Genes, Brain, and Behavior
https://www.readbyqxmd.com/read/28420359/saikosaponins-induced-hepatotoxicity-in-mice-via-lipid-metabolism-dysregulation-and-oxidative-stress-a-proteomic-study
#5
Xiaoyu Li, Xiaojiaoyang Li, Junxian Lu, Youyi Huang, Lili Lv, Yongfu Luan, Runping Liu, Rong Sun
BACKGROUND: Radix Bupleuri (RB) has been popularly used for treating many liver diseases such as chronic hepatic inflammation and viral Hepatitis in China. Increasing clinical and experimental evidence indicates the potential hepatotoxicity of RB or prescriptions containing RB. Recently, Saikosaponins (SS) have been identified as major bioactive compounds isolated from RB, which may be also responsible for RB-induced liver injury. METHODS: Serum AST, ALT and LDH levels were determined to evaluate SS-induced liver injury in mice...
April 19, 2017: BMC Complementary and Alternative Medicine
https://www.readbyqxmd.com/read/28413437/gostag-gene-ontology-subtrees-to-tag-and-annotate-genes-within-a-set
#6
Brian D Bennett, Pierre R Bushel
BACKGROUND: Over-representation analysis (ORA) detects enrichment of genes within biological categories. Gene Ontology (GO) domains are commonly used for gene/gene-product annotation. When ORA is employed, often times there are hundreds of statistically significant GO terms per gene set. Comparing enriched categories between a large number of analyses and identifying the term within the GO hierarchy with the most connections is challenging. Furthermore, ascertaining biological themes representative of the samples can be highly subjective from the interpretation of the enriched categories...
2017: Source Code for Biology and Medicine
https://www.readbyqxmd.com/read/28412928/poplar-stem-transcriptome-is-massively-remodelled-in-response-to-single-or-repeated-mechanical-stimuli
#7
Lise Pomiès, Mélanie Decourteix, Jérôme Franchel, Bruno Moulia, Nathalie Leblanc-Fournier
BACKGROUND: Trees experience mechanical stimuli -like wind- that trigger thigmomorphogenetic syndrome, leading to modifications of plant growth and wood quality. This syndrome affects tree productivity but is also believed to improve tree acclimation to chronic wind. Wind is particularly challenging for trees, because of their stature and perenniality. Climate change forecasts are predicting that the occurrence of high wind will worsen, making it increasingly vital to understand the mechanisms regulating thigmomorphogenesis, especially in perennial plants...
April 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28412460/characterization-of-transcriptome-in-the-indian-meal-moth-plodia-interpunctella-lepidoptera-pyralidae-and-gene-expression-analysis-during-developmental-stages
#8
Pei-An Tang, Hai-Jing Wu, Hao Xue, Xing-Rong Ju, Wei Song, Qi-Lin Zhang, Ming-Long Yuan
The Indian meal moth Plodia interpunctella (Lepidoptera: Pyralidae) is a worldwide pest that causes serious damage to stored foods. Although many efforts have been conducted on this species due to its economic importance, the study of genetic basis of development, behavior and insecticide resistance has been greatly hampered due to lack of genomic information. In this study, we used high throughput sequencing platform to perform a de novo transcriptome assembly and tag-based digital gene expression profiling (DGE) analyses across four different developmental stages of P...
April 13, 2017: Gene
https://www.readbyqxmd.com/read/28408205/temporal-spatial-and-phenotypical-changes-of-pdgfr%C3%AE-expressing-fibroblasts-during-late-lung-development
#9
Mehari Endale, Shawn Ahlfeld, Erik Bao, Xiaoting Chen, Jenna Green, Zach Bess, Matthew T Weirauch, Yan Xu, Anne Karina Perl
Many studies have investigated the source and role of epithelial progenitors during lung development; such information is limited for fibroblast populations and their complex role in the developing lung. In this study, we characterized the spatial location, mRNA expression and Immunophenotyping of PDGFRα(+) fibroblasts during sacculation and alveolarization. Confocal microscopy identified spatial association of PDGFRα expressing fibroblasts with proximal epithelial cells of the branching bronchioles and the dilating acinar tubules at E16...
April 11, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28405199/comparative-analysis-of-expression-profiles-of-panicle-development-among-tolerant-and-sensitive-rice-in-response-to-drought-stress
#10
Haibin Wei, Chen Chen, Xiaosong Ma, Yu Zhang, Jing Han, Hanwei Mei, Shunwu Yu
Water deficit caused a serious threat to crops, especially panicle development at reproductive growth phase. We investigated grain yield components and gene expression profiles of panicle among tolerant and sensitive rice in response to drought stress. Panicle morphologies exhibited that secondary branches per panicle were more severely affected as compared to primary branches per panicle. Moreover, grain weight per panicle showed significant decrease for both tolerant and sensitive varieties except for MILT1444...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28403906/an-additional-k-means-clustering-step-improves-the-biological-features-of-wgcna-gene-co-expression-networks
#11
Juan A Botía, Jana Vandrovcova, Paola Forabosco, Sebastian Guelfi, Karishma D'Sa, John Hardy, Cathryn M Lewis, Mina Ryten, Michael E Weale
BACKGROUND: Weighted Gene Co-expression Network Analysis (WGCNA) is a widely used R software package for the generation of gene co-expression networks (GCN). WGCNA generates both a GCN and a derived partitioning of clusters of genes (modules). We propose k-means clustering as an additional processing step to conventional WGCNA, which we have implemented in the R package km2gcn (k-means to gene co-expression network, https://github.com/juanbot/km2gcn ). RESULTS: We assessed our method on networks created from UKBEC data (10 different human brain tissues), on networks created from GTEx data (42 human tissues, including 13 brain tissues), and on simulated networks derived from GTEx data...
April 12, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28388670/transcriptomic-and-physiological-analyses-of-medicago-sativa-l-roots-in-response-to-lead-stress
#12
Bo Xu, Yingzhe Wang, Shichao Zhang, Qiang Guo, Yan Jin, Jingjing Chen, Yunhang Gao, Hongxia Ma
Lead (Pb) is one of the nonessential and toxic metals that threaten the environment and human health. Medicago sativa L. is a legume with high salt tolerance and high biomass production. It is not only a globally important forage crop but is also an ideal plant for phytoremediation. However, the biological and molecular mechanisms that respond to heavy metals are still not well defined in M. sativa. In this study, de novo and strand-specific RNA-sequencing was performed to identify genes involved in the Pb stress response in M...
2017: PloS One
https://www.readbyqxmd.com/read/28379507/impact-of-male-fertility-status-on-the-transcriptome-of-the-bovine-epididymis
#13
Christine Légaré, Ayodélé Akintayo, Patrick Blondin, Ezequiel Calvo, Robert Sullivan
STUDY QUESTION: Can region-specific transcriptional profiling of the epididymis from fertile and sub-fertile bulls predict the etiology of fertility/sub-fertility in males? SUMMARY ANSWER: The highly regulated gene expression along the bovine epididymis is affected by the fertility status of bulls used for artificial insemination. WHAT IS KNOWN ALREADY: In mammals, sperm maturation and storage occur in the epididymis. Each epididymal segment has his own transcriptomic signature that modulates the intraluminal composition and consequently governs sequential modifications of the maturing male gamete...
April 3, 2017: Molecular Human Reproduction
https://www.readbyqxmd.com/read/28371781/assessment-of-semantic-similarity-between-proteins-using-information-content-and-topological-properties-of-the-gene-ontology-graph
#14
Pritha Dutta, Subhadip Basu, Mahantapas Kundu
The semantic similarity between two interacting proteins can be estimated by combining the similarity scores of the GO terms associated with the proteins. Greater number of similar GO annotations between two proteins indicates greater interaction affinity. Existing semantic similarity measures make use of the GO graph structure, the information content of GO terms, or a combination of both. In this paper, we present a hybrid approach which utilizes both the topological features of the GO graph and information contents of the GO terms...
March 31, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28367723/gene-expression-analysis-of-hypersensitivity-to-mosquito-bite-chronic-active-ebv-infection-and-nk-t-lymphoma-leukemia
#15
Kana Washio, Takashi Oka, Lamia Abdalkader, Michiko Muraoka, Akira Shimada, Megumi Oda, Hiaki Sato, Katsuyoshi Takata, Yoshitoyo Kagami, Norio Shimizu, Seiichi Kato, Hiroshi Kimura, Kazunori Nishizaki, Tadashi Yoshino, Hirokazu Tsukahara
The human herpes virus, Epstein-Barr virus (EBV), is a known oncogenic virus and plays important roles in life-threatening T/NK-cell lymphoproliferative disorders (T/NK-cell LPD) such as hypersensitivity to mosquito bite (HMB), chronic active EBV infection (CAEBV), and NK/T-cell lymphoma/leukemia. During the clinical courses of HMB and CAEBV, patients frequently develop malignant lymphomas and the diseases passively progress sequentially. In the present study, gene expression of CD16((-))CD56((+))-, EBV((+)) HMB, CAEBV, NK-lymphoma, and NK-leukemia cell lines, which were established from patients, was analyzed using oligonucleotide microarrays and compared to that of CD56(bright)CD16(dim/-) NK cells from healthy donors...
April 3, 2017: Leukemia & Lymphoma
https://www.readbyqxmd.com/read/28362488/serotonin-transporter-associated-protein-complexes-are-enriched-in-synaptic-vesicle-proteins-and-proteins-involved-in-energy-metabolism-and-ion-homeostasis
#16
Jana Haase, Joanna Grudzinska-Goebel, Heidi Kaastrup Müller, Agnieszka Münster-Wandowski, Elysian Chow, Kieran Wynne, Zohreh Farsi, Johannes-Friedrich Zander, Gudrun Ahnert-Hilger
The serotonin transporter (SERT) mediates Na(+)-dependent high-affinity serotonin uptake and plays a key role in regulating extracellular serotonin concentration in the brain and periphery. To gain novel insight into SERT regulation, we conducted a comprehensive proteomics screen to identify components of SERT-associated protein complexes in the brain by employing three independent approaches. In vivo SERT complexes were purified from rat brain using an immobilized high-affinity SERT ligand, amino-methyl citalopram...
April 21, 2017: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/28346370/de-novo-assembly-annotation-and-characterization-of-root-transcriptomes-of-three-caladium-cultivars-with-a-focus-on-necrotrophic-pathogen-resistance-defense-related-genes
#17
Zhe Cao, Zhanao Deng
Roots are vital to plant survival and crop yield, yet few efforts have been made to characterize the expressed genes in the roots of non-model plants (root transcriptomes). This study was conducted to sequence, assemble, annotate, and characterize the root transcriptomes of three caladium cultivars (Caladium × hortulanum) using RNA-Seq. The caladium cultivars used in this study have different levels of resistance to Pythiummyriotylum, the most damaging necrotrophic pathogen to caladium roots. Forty-six to 61 million clean reads were obtained for each caladium root transcriptome...
March 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28346054/genomic-regions-in-local-endangered-sheep-encode-potentially-favorable-genes
#18
Bianca Moioli, Roberto Steri, Gennaro Catillo
The economic evaluation of farm animal genetic resources plays a key role in developing conservation programs. However, to date, the link between diversity as assessed by neutral genetic markers and the functional diversity is not yet understood. Two genome-wide comparisons, using over 44,000 Single Nucleotide Polymorphisms, identified the markers with the highest difference in allele frequency between the Alpago endangered breed and two clusters, composed of four specialized dairy sheep, and four meat breeds respectively...
March 27, 2017: Animal Biotechnology
https://www.readbyqxmd.com/read/28338236/hsa-mir-3199-2-and-hsa-mir-1293-as-novel-prognostic-biomarkers-of-papillary-renal-cell-carcinoma-by-cox-ratio-risk-regression-model-screening
#19
Wen Luo, Lei Wang, Mao-Hua Luo, Yu-Zhu Huang, Hua Yang, Yu Zhou, Hong-Tao Jia, Xiu-Xin Wang
Papillary renal cell carcinoma(PRCC) is the second most common and aggressive renal cell carcinoma. Identification of novel microRNA biomarkers could be beneficial for the diagnosis and prognosis of PRCCpatients.We aimed to screen differentially expressed miRNAs that can act as prognostic factors and to predict the survival of PRCC patients. High-throughput data of miRNAs of 274 PRCC samples were downloaded from TCGA(The Cancer Genome Atlas) dataset and interested miRNAs were identified. Hierarchical clustering and principal component analysis (PCA) were performed on these miRNAs...
March 24, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28333638/a-comparative-study-for-identifying-the-chromosome-wide-spatial-clusters-from-high-throughput-chromatin-conformation-capture-data
#20
Xiangtao Li, Ka-Chun Wong
In the past years, the high-throughput sequencing technologies have enabled massive insights into genomic annotations. In contrast, the full-scale three-dimensional arrangements of genomic regions are relatively unknown. Thanks to the recent breakthroughs in High-throughput Chromosome Conformation Capture (Hi-C) techniques, non-negative matrix factorization (NMF) has been adopted to identify local spatial clusters of genomic regions from Hi-C data. However, such non-negative matrix factorization entails a high-dimensional non-convex objective function to be optimized with non-negative constraints...
March 20, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
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