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Search Results: 1 - 10 of 27852 matches for " JiDeng Ma "
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Developing a genome-wide selection model for genetic improvement of residual feed intake and carcass merit in a beef cattle breeding program
ZhiYao Zeng,GuoQing Tang,JiDeng Ma,Graham Plastow,Stephen Moore,SongJia Lai,XueWei Li,ZhiQuan Wang
Chinese Science Bulletin , 2012, DOI: 10.1007/s11434-012-5325-6
Abstract: Residual feed intake (RFI) and carcass merit (CM) are both complex traits emerging as critical targets for beef genetic improvement. RFI and CM traits are difficult and expensive to measure and genetic improvement for these traits through traditional selection methods is not very effective. Therefore, genome-wide selection using DNA markers may be a potential alternative for genetic improvement of these traits. In this study, the efficiency of a genome-wide selection model for genetic improvement of RFI and CM was assessed. The Illumina Bovine50K bead chip was used to genotype 922 beef cattle from the Kinsella Beef Research Ranch of the University of Alberta. A Bayes model and multiple marker regression using a stepwise method were used to conduct the association test. The number of significant SNP markers for carcass weight (CWT), carcass back fat (BF), carcass rib eye area (REA), carcass grade fat (GDF), lean meat yield (LMY), and residual feed intake (RFI) were 75, 54, 67, 57, 44 and 50, respectively. Bi-variate analysis of marker scores and phenotypes for all traits were made using DMU Software. The genetic parameter for each trait was estimated. The genetic correlations of marker score and phenotype for CWT, BF, REA, GDF, LMY and RFI were 0.75, 0.69, 0.87, 0.77, 0.78, and 0.85, respectively. The average prediction accuracies of phenotypic EBV for the six traits were increased by 0.05, 0.16, 0.24, 0.23, 0.17 and 0.19, respectively. The results of this study indicated that the two-trait marker-assisted evaluation model used was a suitable alternative of genetic evaluation for these traits in beef cattle.
MicroRNA Transcriptomes Relate Intermuscular Adipose Tissue to Metabolic Risk
Jideng Ma,Shuzhen Yu,Fengjiao Wang,Lin Bai,Jian Xiao,Yanzhi Jiang,Lei Chen,Jinyong Wang,Anan Jiang,Mingzhou Li,Xuewei Li
International Journal of Molecular Sciences , 2013, DOI: 10.3390/ijms14048611
Abstract: Intermuscular adipose tissue is located between the muscle fiber bundles in skeletal muscles, and has similar metabolic features to visceral adipose tissue, which has been found to be related to a number of obesity-related diseases. Although various miRNAs are known to play crucial roles in adipose deposition and adipogenesis, the microRNA transcriptome of intermuscular adipose tissue has not, until now, been studied. Here, we sequenced the miRNA transcriptomes of porcine intermuscular adipose tissue by small RNA-sequencing and compared it to a representative subcutaneous adipose tissue. We found that the inflammation- and diabetes-related miRNAs were significantly enriched in the intermuscular rather than in the subcutaneous adipose tissue. A functional enrichment analysis of the genes predicted to be targeted by the enriched miRNAs also indicated that intermuscular adipose tissue was associated mainly with immune and inflammation responses. Our results suggest that the intermuscular adipose tissue should be recognized as a potential metabolic risk factor of obesity.
Intrinsic Features in MicroRNA Transcriptomes Link Porcine Visceral Rather than Subcutaneous Adipose Tissues to Metabolic Risk
Jideng Ma, Zhi Jiang, Shen He, Yingkai Liu, Lei Chen, Keren Long, Long Jin, An'an Jiang, Li Zhu, Jinyong Wang, Mingzhou Li, Xuewei Li
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0080041
Abstract: MicroRNAs (miRNAs) are non-coding small RNA ~22 nucleotides in length that can regulate the expression of a wide range of coding genes at the post-transcriptional level. Visceral adipose tissues (VATs) and subcutaneous adipose tissues (SATs), the two main fat compartments in mammals, are anatomically, physiologically, metabolically, and clinically distinct. Various studies of adipose tissues have focused mainly on DNA methylation, and mRNA and protein expression, nonetheless little research sheds directly light on the miRNA transcriptome differences between these two distinct adipose tissue types. Here, we present a comprehensive investigation of miRNA transcriptomes across six variant porcine adipose tissues by small RNA-sequencing. We identified 219 known porcine miRNAs, 97 novel miRNA*s, and 124 miRNAs that are conserved to other mammals. A set of universally abundant miRNAs (i.e., miR-148a-3p, miR-143-3p, miR-27b-3p, miR-let-7a-1-5p, and miR-let-7f-5p) across the distinct adipose tissues was found. This set of miRNAs may play important housekeeping roles that are involved in adipogenesis. Clustering analysis indicated significant variations in miRNA expression between the VATs and SATs, and highlighted the role of the greater omentum in responding to potential metabolic risk because of the observed enrichment in this tissue of the immune- and inflammation-related miRNAs, such as the members of miR-17-92 cluster and miR-181 family. Differential expression of the miRNAs between the VATs and SATs, and miRNA target prediction analysis revealed that the VATs-specific enriched miRNAs were associated mainly with immune and inflammation responses. In summary, the differences of miRNA expression between the VATs and SATs revealed some of their intrinsic differences and indicated that the VATs might be closely associated with increased risk of metabolic disorders.
Transcriptional Profiling of Swine Lung Tissue after Experimental Infection with Actinobacillus pleuropneumoniae
Zhicai Zuo,Hengmin Cui,Mingzhou Li,Xi Peng,Ling Zhu,Ming Zhang,Jideng Ma,Zhiwen Xu,Meng Gan,Junliang Deng,Xuewei Li,Jing Fang
International Journal of Molecular Sciences , 2013, DOI: 10.3390/ijms140510626
Abstract: Porcine pleuropneumonia is a highly contagious respiratory disease that causes great economic losses worldwide. In this study, we aimed to explore the underlying relationship between infection and injury by investigation of the whole porcine genome expression profiles of swine lung tissues post-inoculated with experimentally Actinobacillus pleuropneumoniae. Expression profiling experiments of the control group and the treatment group were conducted using a commercially available Agilent Porcine Genechip including 43,603 probe sets. Microarray analysis was conducted on profiles of lung from challenged versus non-challenged swine. We found 11,929 transcripts, identified as differentially expressed at the p ≤0.01 level. There were 1188 genes annotated as swine genes in the GenBank Data Base. GO term analysis identified a total of 89 biological process categories, 82 cellular components and 182 molecular functions that were significantly affected, and at least 27 biological process categories that were related to the host immune response. Gene set enrichment analysis identified 13 pathways that were significantly associated with host response. Many proinflammatory-inflammatory cytokines were activated and involved in the regulation of the host defense response at the site of inflammation; while the cytokines involved in regulation of the host immune response were suppressed. All changes of genes and pathways of induced or repressed expression not only led to a decrease in antigenic peptides presented to T lymphocytes by APCs via the MHC and alleviated immune response injury induced by infection, but also stimulated stem cells to produce granulocytes (neutrophils, eosinophils, and basophils) and monocyte, and promote neutrophils and macrophages to phagocytose bacterial and foreign antigen at the site of inflammation. The defense function of swine infection with Actinobacillus pleuropneumoniae was improved, while its immune function was decreased.
Transcriptional Profiling of Hilar Nodes from Pigs after Experimental Infection with Actinobacillus Pleuropneumoniae
Shumin Yu,Zhicai Zuo,Hengmin Cui,Mingzhou Li,Xi Peng,Ling Zhu,Ming Zhang,Xuewei Li,Zhiwen Xu,Meng Gan,Junliang Deng,Jing Fang,Jideng Ma,Shengqun Su,Ya Wang,Liuhong Shen,Xiaoping Ma,Zhihua Ren,Bangyuan Wu,Yanchun Hu
International Journal of Molecular Sciences , 2013, DOI: 10.3390/ijms141223516
Abstract: The gram-negative bacterium Actinobacillus pleuropneumoniae ( APP) is an inhabitant of the porcine upper respiratory tract and the causative agent of porcine pleuropneumonia (PP). In recent years, knowledge about the proinflammatory cytokine and chemokine gene expression that occurs in lung and lymph node of the APP-infected swine has been advanced. However, systematic gene expression profiles on hilar nodes from pigs after infection with Actinobacillus pleuropneumoniae have not yet been reported. The transcriptional responses were studied in hilar nodes (HN) from swine experimentally infected with APP and the control groupusing Agilent Porcine Genechip, including 43,603 probe sets. 9,517 transcripts were identified as differentially expressed (DE) at the p ≤ 0.01 level by comparing the log2 (normalized signal) of the two groups named treatment group (TG) and controls (CG). Eight hundred and fifteen of these DE transcripts were annotated as pig genes in the GenBank database (DB). Two hundred and seventy-two biological process categories (BP), 75 cellular components and 171 molecular functions were substantially altered in the TG compared to CG. Many BP were involved in host immune responses ( i.e., signaling, signal transmission, signal transduction, response to stimulus, oxidation reduction, response to stress, immune system process, signaling pathway, immune response, cell surface receptor linked signaling pathway). Seven DE gene pathways (VEGF signaling pathway, Long-term potentiation, Ribosome, Asthma, Allograft rejection, Type I diabetes mellitus and Cardiac muscle contraction) and statistically significant associations with host responses were affected. Many cytokines (including NRAS, PI3K, MAPK14, CaM, HSP27, protein phosphatase 3, catalytic subunit and alpha isoform), mediating the proliferation and migration of endothelial cells and promoting survival and vascular permeability, were activated in TG, whilst many immunomodulatory cytokines were suppressed. The significant changes in the expression patterns of the genes, GO terms, and pathways, led to a decrease of antigenic peptides with antigen presenting cells presented to T lymphocytes via the major histocompatibility complex, and alleviated immune response induced APP of HN. The immune response ability of HN in the APP-infected pigs was weakened; however, cell proliferation and migration ability was enhanced.
Repertoire of Porcine MicroRNAs in Adult Ovary and Testis by Deep Sequencing
Mingzhou Li, Yingkai Liu, Tao Wang, Jiuqiang Guan, Zonggang Luo, Haosi Chen, Xin Wang, Lei Chen, Jideng Ma, Zhiping Mu, An-an Jiang, Li Zhu, Qiulei Lang, Xiaochuan Zhou, Jinyong Wang, Wenxian Zeng, Ning Li, Kui Li, Xiaolian Gao, Xuewei Li
International Journal of Biological Sciences , 2011,
Abstract: Background: MicroRNAs (miRNAs), a large family of short endogenous RNAs known to post-transcriptionally repress gene expression, participate in the regulation of almost every cellular process. Changes in miRNA expression are associated with many pathologies. Ovarian folliculogenesis and testicular spermatogenesis are complex and coordinated biological processes, in which tightly regulated expression and interaction of a multitude of genes could be regulated by these miRNAs. Identification and preliminary characterization of gonad-specific miRNAs would be a prerequisite for a thorough understanding of the role that miRNA-mediated posttranscriptional gene regulation plays in mammalian reproduction. Method: Here, we present the identification of a repertoire of porcine miRNAs in adult ovary and testis using deep sequencing technology. A bioinformatics pipeline was developed to distinguish authentic mature miRNA sequences from other classes of small RNAs represented in the sequencing data. Results: Using this approach, we detected 582 precursor hairpins (pre-miRNAs) encoding for 732 mature miRNAs, of which 673 are unique. Statistically, 224 unique miRNAs (out of 673, 33.28%) were identified which had significant differential expression (DE) between ovary and testis libraries (P < 0.001). Most of DE miRNAs located on the X chromosome (X-linked miRNAs) (24 out of 34, 70.59%) significantly up-regulated in ovary versus testis (P < 0.001). Predictably, X-linked miRNAs are expressed in a testis-preferential or testis-specific pattern. To explore the potential for co-expression among genomic location clusters of X-linked miRNAs, we surveyed the relationship between the distance separating miRNA loci and the coordinate expression patterns of 32 high confidence X-linked miRNAs in seven normal pig tissues using the real-time quantitative PCR (q-PCR) approach. Our results show that proximal pairs of miRNAs are generally co-expressed implying that miRNAs within 50 kb of genomic bases are typically derived from a common transcript. Conclusions: The present study characterizes the miRNA transcriptome of adult porcine gonads, with an emphasis on the co-expression patterns of X-linked miRNAs. Our report should facilitate studies of the organ-specific reproductive roles of miRNAs.
Mitochondrial DNA Evidence Indicates the Local Origin of Domestic Pigs in the Upstream Region of the Yangtze River
Long Jin, Mingwang Zhang, Jideng Ma, Jie Zhang, Chaowei Zhou, Yingkai Liu, Tao Wang, An-an Jiang, Lei Chen, Jinyong Wang, Zhongrong Jiang, Li Zhu, Surong Shuai, Ruiqiang Li, Mingzhou Li, Xuewei Li
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0051649
Abstract: Previous studies have indicated two main domestic pig dispersal routes in East Asia: one is from the Mekong region, through the upstream region of the Yangtze River (URYZ) to the middle and upstream regions of the Yellow River, the other is from the middle and downstream regions of the Yangtze River to the downstream region of the Yellow River, and then to northeast China. The URYZ was regarded as a passageway of the former dispersal route; however, this assumption remains to be further investigated. We therefore analyzed the hypervariable segements of mitochondrial DNA from 513 individual pigs mainly from Sichuan and the Tibet highlands and 1,394 publicly available sequences from domestic pigs and wild boars across Asia. From the phylogenetic tree, most of the samples fell into a mixed group that was difficult to distinguish by breed or geography. The total network analysis showed that the URYZ pigs possessed a dominant position in haplogroup A and domestic pigs shared the same core haplotype with the local wild boars, suggesting that pigs in group A were most likely derived from the URYZ pool. In addition, a region-wise network analysis determined that URYZ contains 42 haplotypes of which 22 are unique indicating the high diversity in this region. In conclusion, our findings confirmed that pigs from the URYZ were domesticated in situ.
The Equitable Total Chromatic Number of Some Join graphs  [PDF]
Gang MA, Ming MA
Open Journal of Applied Sciences (OJAppS) , 2012, DOI: 10.4236/ojapps.2012.24B023
Abstract: A proper total-coloring of graph G is said to be?equitable if the number of elements (vertices and edges) in any?two color classes differ by at most one, which the required?minimum number of colors is called the equitable total chromatic?number. In this paper, we prove some theorems on equitable?total coloring and derive the equitable total chromatic numbers?of Pm V?Sn, Pm V?Fn and Pm V Wn.
Improvements and Generalizations of Stochastic Knapsack and Multi-Armed Bandit Approximation Algorithms: Full Version
Will Ma
Computer Science , 2013,
Abstract: The multi-armed bandit (MAB) problem features the classical tradeoff between exploration and exploitation. The input specifies several stochastic arms which evolve with each pull, and the goal is to maximize the expected reward after a fixed budget of pulls. The celebrated work of Gittins et al. [GGW89] presumes a condition on the arms called the martingale assumption. Recently, A. Gupta et al. obtained an LP-based 1/48-approximation for the problem with the martingale assumption removed [GKMR11]. We improve the algorithm to a 4/27-approximation, with simpler analysis. Our algorithm also generalizes to the case of MAB superprocesses with (stochastic) multi-period actions. This generalization captures the framework introduced by Guha and Munagala in [GM07a, GM07b], and yields new results for their budgeted learning problems. Also, we obtain a (1/2-eps)-approximation for the variant of MAB where preemption (playing an arm, switching to another arm, then coming back to the first arm) is not allowed. This contains the stochastic knapsack problem of Dean, Goemans, and Vondrak [DGV08] with correlated rewards, where we are given a knapsack of fixed size, a set of jobs each with a joint distribution for its size and reward, and the objective is to maximize expected reward before the knapsack size is exhausted. Our (1/2-eps)-approximation improves the 1/16 and 1/8 approximations of [GKMR11] for correlated stochastic knapsack with cancellation and no cancellation, respectively, providing the first tight algorithm for these problems that matches the integrality gap of 2. We sample probabilities from an exponential-sized dynamic programming solution, whose existence is guaranteed by an LP projection argument. We hope this technique can also be applied to other dynamic programming problems which can be projected down onto a small LP.
Liouville Type Theorems for Lichnerowicz Equations and Ginzburg-Landau Equation: Survey  [PDF]
Li Ma
Advances in Pure Mathematics (APM) , 2011, DOI: 10.4236/apm.2011.13022
Abstract: In this survey paper, we firstly review some existence aspects of Lichnerowicz equation and Ginzburg-Landau equations. We then discuss the uniform bounds for both equations in Rn. In the last part of this report, we consider the Liouville type theorems for Lichnerowicz equation and Ginzburg-Landau equations in Rn via two approaches from the use of maximum principle and the monotonicity formula
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