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goat transcriptome

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https://www.readbyqxmd.com/read/28800357/identification-of-differentially-expressed-genes-through-rna-sequencing-in-goats-capra-hircus-at-different-postnatal-stages
#1
Yaqiu Lin, Jiangjiang Zhu, Yong Wang, Qian Li, Sen Lin
Intramuscular fat (IMF) content and fatty acid composition of longissimus dorsi muscle (LM) change with growth, which partially determines the flavor and nutritional value of goat (Capra hircus) meat. However, unlike cattle, little information is available on the transcriptome-wide changes during different postnatal stages in small ruminants, especially goats. In this study, the sequencing reads of goat LM tissues collected from kid, youth, and adult period were mapped to the goat genome. Results showed that out of total 24 689 Unigenes, 20 435 Unigenes were annotated...
2017: PloS One
https://www.readbyqxmd.com/read/28766153/molecular-cloing-and-bioinformatics-analysis-of-lactate-dehydrogenase-from-taenia-multiceps
#2
Cheng Guo, Yu Wang, Xing Huang, Ning Wang, Ming Yan, Ran He, Xiaobin Gu, Yue Xie, Weimin Lai, Bo Jing, Xuerong Peng, Guangyou Yang
Coenurus cerebralis, the larval stage (metacestode or coenurus) of Taenia multiceps, parasitizes sheep, goats, and other ruminants and causes coenurosis. In this study, we isolated and characterized complementary DNAs that encode lactate dehydrogenase A (Tm-LDHA) and B (Tm-LDHB) from the transcriptome of T. multiceps and expressed recombinant Tm-LDHB (rTm-LDHB) in Escherichia coli. Bioinformatic analysis showed that both Tm-LDH genes (LDHA and LDHB) contain a 996-bp open reading frame and encode a protein of 331 amino acids...
August 1, 2017: Parasitology Research
https://www.readbyqxmd.com/read/28757165/an-efficient-platform-for-astrocyte-differentiation-from-human-induced-pluripotent-stem-cells
#3
Julia Tcw, Minghui Wang, Anna A Pimenova, Kathryn R Bowles, Brigham J Hartley, Emre Lacin, Saima I Machlovi, Rawan Abdelaal, Celeste M Karch, Hemali Phatnani, Paul A Slesinger, Bin Zhang, Alison M Goate, Kristen J Brennand
Growing evidence implicates the importance of glia, particularly astrocytes, in neurological and psychiatric diseases. Here, we describe a rapid and robust method for the differentiation of highly pure populations of replicative astrocytes from human induced pluripotent stem cells (hiPSCs), via a neural progenitor cell (NPC) intermediate. We evaluated this protocol across 42 NPC lines (derived from 30 individuals). Transcriptomic analysis demonstrated that hiPSC-astrocytes from four individuals are highly similar to primary human fetal astrocytes and characteristic of a non-reactive state...
August 8, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/28728371/expression-of-fox-related-genes-in-the-skin-follicles-of-inner-mongolia-cashmere-goat
#4
Wenjing Han, Xiaoyan Li, Lele Wang, Honghao Wang, Kun Yang, Zhixin Wang, Ruijun Wang, Rui Su, Zhihong Liu, Yanhong Zhao, Yanjun Zhang, Jinquan Li
Objective: The aim of this study was to investigate the expression of genes in cashmere goats at different periods of their fetal development. Methods: Bioinformatics analysis was used to evaluate data obtained by transcriptome sequencing of fetus skin samples collected from Inner Mongolia cashmere goats on days 45, 55, and 65 of fetal age. Results: We found that FoxN1, FoxE1, and FoxI3 genes of the Fox gene family were probably involved in the growth and development of the follicle and the formation of hair, which is consistent with previous findings...
June 27, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28694795/modulation-of-host-mirnas-transcriptome-in-lung-and-spleen-of-peste-des-petits-ruminants-virus-infected-sheep-and-goats
#5
Aruna Pandey, Amit R Sahu, Sajad A Wani, Shikha Saxena, Sonam Kanchan, Vaishali Sah, Kaushal K Rajak, Alok Khanduri, Aditya P Sahoo, Ashok K Tiwari, Bina Mishra, D Muthuchelvan, Bishnu P Mishra, Raj K Singh, Ravi K Gandham
Peste des petits ruminants (PPR) is one of the highly contagious viral disease, characterized by fever, sore mouth, conjunctivitis, gastroenteritis, and pneumonia, primarily affecting sheep and goats. Reports suggested variable host response in goats and sheep and this host response vis-a-vis the expression of microRNAs (miRNAs) has not been investigated. Here, miRNAs were sequenced and proteomics data were generated to identify the role of differentially expressed miRNA (DEmiRNA) in PPR virus (PPRV) infected lung and spleen tissues of sheep and goats...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28666525/untangling-genetic-risk-for-alzheimer-s-disease
#6
REVIEW
Anna A Pimenova, Towfique Raj, Alison M Goate
Alzheimer's disease (AD) is a genetically heterogeneous neurodegenerative disorder caused by fully penetrant single gene mutations in a minority of cases, while the majority of cases are sporadic or show modest familial clustering. These cases are of late onset and likely result from the interaction of many genes and the environment. More than 30 loci have been implicated in AD by a combination of linkage, genome-wide association, and whole genome/exome sequencing. We have learned from these studies that perturbations in endolysosomal, lipid metabolism, and immune response pathways substantially contribute to sporadic AD pathogenesis...
May 22, 2017: Biological Psychiatry
https://www.readbyqxmd.com/read/28651013/loss-of-prion-protein-induces-a-primed-state-of-type-i-interferon-responsive-genes
#7
Giulia Malachin, Malin R Reiten, Øyvind Salvesen, Håvard Aanes, Jorke H Kamstra, Kerstin Skovgaard, Peter M H Heegaard, Cecilie Ersdal, Arild Espenes, Michael A Tranulis, Maren K Bakkebø
The cellular prion protein (PrPC) has been extensively studied because of its pivotal role in prion diseases; however, its functions remain incompletely understood. A unique line of goats has been identified that carries a nonsense mutation that abolishes synthesis of PrPC. In these animals, the PrP-encoding mRNA is rapidly degraded. Goats without PrPC are valuable in re-addressing loss-of-function phenotypes observed in Prnp knockout mice. As PrPC has been ascribed various roles in immune cells, we analyzed transcriptomic responses to loss of PrPC in peripheral blood mononuclear cells (PBMCs) from normal goat kids (n = 8, PRNP+/+) and goat kids without PrPC (n = 8, PRNPTer/Ter) by mRNA sequencing...
2017: PloS One
https://www.readbyqxmd.com/read/28645321/genome-wide-analysis-of-dna-methylation-in-hypothalamus-and-ovary-of-capra-hircus
#8
Stefano Frattini, Emanuele Capra, Barbara Lazzari, Stephanie D McKay, Beatrice Coizet, Andrea Talenti, Debora Groppetti, Pietro Riccaboni, Alessandro Pecile, Stefania Chessa, Bianca Castiglioni, John L Williams, Giulio Pagnacco, Alessandra Stella, Paola Crepaldi
BACKGROUND: DNA methylation is a frequently studied epigenetic modification due to its role in regulating gene expression and hence in biological processes and in determining phenotypic plasticity in organisms. Rudimentary DNA methylation patterns for some livestock species are publically available: among these, goat methylome deserves to be further explored. RESULTS: Genome-wide DNA methylation maps of the hypothalamus and ovary from Saanen goats were generated using Methyl-CpG binding domain protein sequencing (MBD-seq)...
June 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28532450/lps-induced-systemic-inflammation-reveals-an-immunomodulatory-role-for-the-prion-protein-at-the-blood-brain-interface
#9
Ø Salvesen, M R Reiten, A Espenes, M K Bakkebø, M A Tranulis, C Ersdal
BACKGROUND: The cellular prion protein (PrP(C)) is an evolutionary conserved protein abundantly expressed not only in the central nervous system but also peripherally including the immune system. A line of Norwegian dairy goats naturally devoid of PrP(C) (PRNP (Ter/Ter)) provides a novel model for studying PrP(C) physiology. METHODS: In order to explore putative roles for PrP(C) in acute inflammatory responses, we performed a lipopolysaccharide (LPS, Escherichia coli O26:B6) challenge of 16 goats (8 PRNP (+/+) and 8 PRNP (Ter/Ter)) and included 10 saline-treated controls (5 of each PRNP genotype)...
May 22, 2017: Journal of Neuroinflammation
https://www.readbyqxmd.com/read/28301674/single-cell-transcriptome-profiling-revealed-differences-in-gene-expression-during-oocyte-maturation-in-haimen-white-goats
#10
X Y Yin, G H Cheng, H Y Guo, Q Wang, Y J Li, H Zhang
Juvenile in vitro embryo transfer is an important animal reproductive technology that can shorten the generation interval of livestock, explore the reproductive potential of dams with excellent genetic traits, accelerate genetic progress and production efficiency of the herd, and provide a wealth of genetic resources for livestock breeding. However, oocytes from kids do not develop as well as those from female goats during in vitro maturation. To identify differences during different stages of oocyte maturation, we used single cell transcriptome sequencing to compare gene expression in mature oocytes from kids and female goats...
March 15, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28017736/comparative-and-temporal-transcriptome-analysis-of-peste-des-petits-ruminants-virus-infected-goat-peripheral-blood-mononuclear-cells
#11
Siddappa Manjunath, Bishnu Prasad Mishra, Bina Mishra, Aditya Prasad Sahoo, Ashok K Tiwari, Kaushal Kishore Rajak, D Muthuchelvan, Shikha Saxena, Lakshman Santra, Amit Ranjan Sahu, Sajad Ahmad Wani, R P Singh, Y P Singh, Aruna Pandey, Sonam Kanchan, R K Singh, Gandham Ravi Kumar, Sarath Chandra Janga
Peste des petits ruminanats virus (PPRV), a morbillivirus causes an acute, highly contagious disease - peste des petits ruminants (PPR), affecting goats and sheep. Sungri/96 vaccine strain is widely used for mass vaccination programs in India against PPR and is considered the most potent vaccine providing long-term immunity. However, occurrence of outbreaks due to emerging PPR viruses may be a challenge. In this study, the temporal dynamics of immune response in goat peripheral blood mononuclear cells (PBMCs) infected with Sungri/96 vaccine virus was investigated by transcriptome analysis...
February 2, 2017: Virus Research
https://www.readbyqxmd.com/read/28003963/transcriptome-analysis-reveals-common-differential-and-global-gene-expression-profiles-in-bluetongue-virus-serotype-16-btv-16-infected-peripheral-blood-mononuclear-cells-pbmcs-in-sheep-and-goats
#12
Anjali Singh, Minakshi Prasad, Bina Mishra, Siddappa Manjunath, Amit Ranjan Sahu, G Bhuvana Priya, Sajad Ahmad Wani, Aditya Prasad Sahoo, Amit Kumar, Shweta Balodi, Anupama Deora, Shikha Saxena, Ravi Kumar Gandham
Bluetongue is an economically important infectious, arthropod borne viral disease of domestic and wild ruminants, caused by Bluetongue virus (BTV). Sheep are considered the most susceptible hosts, while cattle, buffalo and goats serve as reservoirs. The viral pathogenesis of BTV resulting in presence or absence of clinical disease among different hosts is not clearly understood. In the present study, transcriptome of sheep and goats peripheral blood mononuclear cells infected with BTV-16 was explored. The differentially expressed genes (DEGs) identified were found to be significantly enriched for immune system processes - NFκB signaling, MAPK signaling, Ras signaling, NOD signaling, RIG signaling, TNF signaling, TLR signaling, JAK-STAT signaling and VEGF signaling pathways...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/27903284/gp50-as-a-promising-early-diagnostic-antigen-for-taenia-multiceps-infection-in-goats-by-indirect-elisa
#13
Xing Huang, Jing Xu, Yu Wang, Cheng Guo, Lin Chen, Xiaobin Gu, Weimin Lai, Xuerong Peng, Guangyou Yang
BACKGROUND: Coenurosis is caused by coenurus, the metacestode of Taenia multiceps, which mainly parasitizes the brain and spinal cord of cattle, sheep and goats. To date, no widely-approved methods are available to identify early coenurus infection. METHODS: In this study, we identified a full-length cDNA that encodes GP50 (TmGP50) from the transcriptome of T. multiceps, and then cloned and expressed in E. coli. The native proteins in adult stage and coenurus were located via immunofluorescence assays, while the potential of recombinant TmGP50 protein (rTmGP50) for indirect ELISA-based serodiagnostics was assessed using native goat sera...
December 1, 2016: Parasites & Vectors
https://www.readbyqxmd.com/read/27884183/rna-sequencing-for-profiling-goat-milk-transcriptome-in-colostrum-and-mature-milk
#14
Alessandra Crisà, Fabrizio Ferrè, Giovanni Chillemi, Bianca Moioli
BACKGROUND: In this work we aimed at sequencing and assembling the goat milk transcriptome corresponding at colostrum and 120 days of lactation. To reconstruct transcripts we used both the genome as reference, and a de novo assembly approach. Additionally, we aimed at identifying the differentially expressed genes (DEGs) between the two lactation stages and at analyzing the expression of genes involved in oligosaccharides metabolism. RESULTS: A total of 44,635 different transcripts, organized in 33,757 tentative genes, were obtained using the goat genome as reference...
November 25, 2016: BMC Veterinary Research
https://www.readbyqxmd.com/read/27821074/a-quantitative-transcriptomic-analysis-of-the-physiological-significance-of-mtor-signaling-in-goat-fetal-fibroblasts
#15
Yuting Fu, Xu Zheng, Xiaoyang Jia, Uyanga Binderiya, Yanfeng Wang, Wenlei Bao, Lili Bao, Keyu Zhao, Yu Fu, Huifang Hao, Zhigang Wang
BACKGROUND: Mammalian target of rapamycin (mTOR) is an evolutionarily conserved serine/threonine kinase that is a central regulator of cell growth and metabolism. CCI-779 is a specific inhibitor of the mTORC1 signaling pathway. RESULTS: We performed comparative transcriptome profiling on Inner Mongolia Cashmere goat fetal fibroblasts (GFbs) that were treated with CCI-779 and untreated cells. A total of 365 differentially expressed genes (DEGs) appeared between untreated and CCI-779-treated GFbs, with an FDR ≤0...
November 7, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27818678/transcriptome-wide-analysis-reveals-the-role-of-ppar%C3%AE-controlling-the-lipid-metabolism-in-goat-mammary-epithelial-cells
#16
Hengbo Shi, Wangsheng Zhao, Changhui Zhang, Khuram Shahzad, Jun Luo, Juan J Loor
To explore the large-scale effect of peroxisome proliferator-activated receptor γ (PPARG) in goat mammary epithelial cells (GMEC), an oligonucleotide microarray platform was used for transcriptome profiling in cells overexpressing PPARG and incubated with or without rosiglitazone (ROSI, a PPARγ agonist). A total of 1143 differentially expressed genes (DEG) due to treatment were detected. The Dynamic Impact Approach (DIA) analysis uncovered the most impacted and induced pathways "fatty acid elongation in mitochondria," "glycosaminoglycan biosynthesis-keratan sulfate," and "pentose phosphate pathway...
2016: PPAR Research
https://www.readbyqxmd.com/read/27799057/integrative-network-analysis-of-nineteen-brain-regions-identifies-molecular-signatures-and-networks-underlying-selective-regional-vulnerability-to-alzheimer-s-disease
#17
Minghui Wang, Panos Roussos, Andrew McKenzie, Xianxiao Zhou, Yuji Kajiwara, Kristen J Brennand, Gabriele C De Luca, John F Crary, Patrizia Casaccia, Joseph D Buxbaum, Michelle Ehrlich, Sam Gandy, Alison Goate, Pavel Katsel, Eric Schadt, Vahram Haroutunian, Bin Zhang
BACKGROUND: Alzheimer's disease (AD) is the most common form of dementia, characterized by progressive cognitive impairment and neurodegeneration. However, despite extensive clinical and genomic studies, the molecular basis of AD development and progression remains elusive. METHODS: To elucidate molecular systems associated with AD, we developed a large scale gene expression dataset from 1053 postmortem brain samples across 19 cortical regions of 125 individuals with a severity spectrum of dementia and neuropathology of AD...
November 1, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27754706/transcriptome-wide-comparative-analysis-of-microrna-profiles-in-the-telogen-skins-of-liaoning-cashmere-goats-capra-hircus-and-fine-wool-sheep-ovis-aries-by-solexa-deep-sequencing
#18
COMPARATIVE STUDY
Jianping Li, HaiE Qu, Huaizhi Jiang, Zhihui Zhao, Qiaoling Zhang
Compare the microRNA (miRNA) trancriptomes of goat and sheep skin using Solexa sequencing to understand the development of skin and hair follicles (HFs). miRNA expression patterns vary in the two small RNA libraries from goat (G library) and sheep (S library) telogen skin samples. Analysis of the size distribution of 25.32 million clean reads revealed that most are 21-23 nucleotides. A total of 1910 known miRNAs and 2261 novel mature miRNAs were identified in this study. Among them, 107 novel miRNAs and 1246 known miRNAs were differentially expressed in the two libraries; 10 of the known miRNAs were identified using stem-loop quantitative real-time PCR...
November 2016: DNA and Cell Biology
https://www.readbyqxmd.com/read/27695037/comparative-transcriptome-analysis-reveals-that-a-ubiquitin-mediated-proteolysis-pathway-is-important-for-primary-and-secondary-hair-follicle-development-in-cashmere-goats
#19
COMPARATIVE STUDY
Xiao-Yang Ji, Jian-Xun Wang, Bin Liu, Zhu-Qing Zheng, Shao-Yin Fu, Getinet Mekuriaw Tarekegn, Xue Bai, Yong-Sheng Bai, Heng Li, Wen-Guang Zhang
BACKGROUND: The fleece of cashmere goats contains two distinct populations of fibers, a short and fine non-medullated insulating cashmere fiber and a long and coarse medullated guard hair. The former is produced by secondary follicles (SFs) and the later by primary follicles (PFs). Evidence suggests that the induction of PFs and SFs may require different signaling pathways. The regulation of BMP2/4 signaling by noggin and Edar signaling via Downless genes are essential for the induction of SFs and PFs, respectively...
2016: PloS One
https://www.readbyqxmd.com/read/27678198/web-based-bioinformatics-workflows-for-end-to-end-rna-seq-data-computation-and-analysis-in-agricultural-animal-species
#20
Weizhong Li, R Alexander Richter, Yunsup Jung, Qiyun Zhu, Robert W Li
BACKGROUND: Remarkable advances in Next Generation Sequencing (NGS) technologies, bioinformatics algorithms and computational technologies have significantly accelerated genomic research. However, complicated NGS data analysis still remains as a major bottleneck. RNA-seq, as one of the major area in the NGS field, also confronts great challenges in data analysis. RESULTS: To address the challenges in RNA-seq data analysis, we developed a web portal that offers three integrated workflows that can perform end-to-end compute and analysis, including sequence quality control, read-mapping, transcriptome assembly, reconstruction and quantification, and differential analysis...
September 27, 2016: BMC Genomics
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