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Search Results: 1 - 10 of 12084 matches for " Yanbin Yin "
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On the origin of microbial ORFans: quantifying the strength of the evidence for viral lateral transfer
Yanbin Yin, Daniel Fischer
BMC Evolutionary Biology , 2006, DOI: 10.1186/1471-2148-6-63
Abstract: We performed similarity searches by querying all current ORFans against the public virus protein database. Surprisingly, we found that only 2.8% of all microbial ORFans have detectable homologs in viruses, while the percentage of non-ORFans with detectable homologs in viruses is 7.9%, a significantly higher figure. This suggests that the current evidence for the origin of ORFans from lateral transfer from viruses is at best weak. However, an analysis of individual genomes revealed a number of organisms with much higher percentages, many of them belonging to the Firmicutes and Gamma-proteobacteria. We provide evidence suggesting that the current virus database may be biased towards those viruses attacking Firmicutes and Gamma-proteobacteria.We conclude that as more viral genomes are sequenced, more microbial ORFans will find homologs in viruses, but this trend may vary much for individual genomes. Thus, lateral transfer from viruses alone is unlikely to explain the origin of the majority of ORFans in the majority of prokaryotes and consequently, other, not necessarily exclusive, mechanisms are likely to better explain the origin of the increasing number of ORFans.ORFans are defined as ORFs (Open Reading Frames) having no sequence homologs in other genomes [1]. ORFans with homologs in the same genome are called paralogous ORFans, and those without any homolog whatsoever are called singleton ORFans. In addition, orthologous ORFans are defined as those ORFs with homologs only within very closely related microbial genomes [2]. Nearly all the fully sequenced genomes have a significant number of ORFans, although the percentages in different species vary much. Previous studies in our group [3], and subsequently repeated by others [4] have shown that as more genomes are being sequenced, the number of ORFans continues to grow. Despite their abundance, very few ORFans have been experimentally characterized [5-7], and thus, most ORFans in the database are annotated as hypotheti
Identification and investigation of ORFans in the viral world
Yanbin Yin, Daniel Fischer
BMC Genomics , 2008, DOI: 10.1186/1471-2164-9-24
Abstract: Almost one-third of all ORFs in 1,456 complete virus genomes correspond to ORFans, a figure significantly larger than that observed in prokaryotes. Like prokaryotic ORFans, viral ORFans are shorter and have a lower GC content than non-ORFans. Nevertheless, a statistically significant lower GC content is found only on a minority of viruses. By focusing on phages, we find that 38.4% of phage ORFs have no homologs in other phages, and 30.1% have no homologs neither in the viral nor in the prokaryotic world. Phages with different host ranges have different percentages of ORFans, reflecting different sampling status and suggesting various diversities. Similarity searches of the phage ORFeome (ORFans and non-ORFans) against prokaryotic genomes shows that almost half of the phage ORFs have prokaryotic homologs, suggesting the major role that horizontal transfer plays in bacterial evolution. Surprisingly, the percentage of phage ORFans with prokaryotic homologs is only 18.7%. This suggests that phage ORFans play a lesser role in horizontal transfer to prokaryotes, but may be among the major players contributing to the vast phage diversity.Although the current sampling of viral genomes is extremely low, ORFans and near-ORFans are likely to continue to grow in number as more genomes are sequenced. The abundance of phage ORFans may be partially due to the expected vast viral diversity, and may be instrumental in understanding viral evolution. The functions, origins and fates of the majority of viral ORFans remain a mystery. Further computational and experimental studies are likely to shed light on the mechanisms that have given rise to so many bacterial and viral ORFans.Genome-wide studies of microbial ORFans have been carried out for about ten years now [1,2]. One of the major surprises in these studies is the large percentage of ORFs (Open Reading Frames) having few or no homologs in the databases [3,4]. These are referred to as ORFans [1]. With hundreds of complete prokaryo
The cellulose synthase superfamily in fully sequenced plants and algae
Yanbin Yin, Jinling Huang, Ying Xu
BMC Plant Biology , 2009, DOI: 10.1186/1471-2229-9-99
Abstract: A single-copy gene is found in the six chlorophyte green algae, which is most closely related to the CslA and CslC families that are present in the seven land plants investigated in our analyses. Six proteins from poplar, grape and sorghum form a distinct family (CslJ), providing further support for the conclusions from two recent studies. CslB/E/G/H/J families have evolved significantly more rapidly than their widely distributed relatives, and tend to have intragenomic duplications, in particular in the grape genome.Our data suggest that the CslA and CslC families originated through an ancient gene duplication event in land plants. We speculate that the single-copy Csl gene in green algae may encode a mannan synthase. We confirm that the rest of the Csl families have a different evolutionary origin than CslA and CslC, and have proposed a model for the divergence order among them. Our study provides new insights about the evolution of this important gene family in plants.The first plant gene encoding a cellulose synthase catalytic subunit (CesA) was identified in 1996 in cotton based on its sequence similarity to a bacterial CesA [1]. In 2000, Richmond and Somerville identified 10 CesA genes and 31 cellulose synthases-like (Csl) genes in Arabidopsis, which were further classified into one CesA family and six Csl families (CslA/B/C/D/E/G) based on phylogenetic analyses [2]. Since then, the whole CesA and Csl gene repertoire has been cataloged in fully sequenced plants, including rice [3], poplar [4,5] and the moss Physcomitrella patens [6]. Additional CesA and Csl genes have also been found in diverse and not fully sequenced land plants such as maize [7], barley [8] and pine [9]; CesAs have been identified in streptophyte green algae such as Mesotaenium caldariorum [10,11] and in red alga Porphyra yezoensis [12,13] as well. Two additional Csl families (CslF and CslH) were found in these studies; together with the other six Csl families and one CesA family, they compr
Advances in G-protein coupled receptor research and related bioinformatics study
Yanbin Yin,Jingchu Luo,Ying Jiang
Chinese Science Bulletin , 2003, DOI: 10.1360/03tb9108
Abstract: G-protein coupled receptor (GPCR) is one of the most important protein families for drug target. GPCR agonists and antagonists occupy approximately one third of the world small molecule drug market. Much effort has been invested in GPCR study by both academic institutions and pharmaceutical industries. With seven-transmembrane domains, GPCR plays significant roles in intercellular signal transduction and is involved in a variety of biological pathways. With the availability of sequence data of human and other mammalian genomes, as well as their expressed sequence tag (EST) data, the bioinformatics and genomics approaches can be applied to identifying novel GPCR in the post genomic era. Deorphanizing GPCR or matching ligands with GPCR greatly facilitates target validation process and automatically provides a possible compound screening assay. Similarly, bioinformatics data mining approach could also be applied to the identification of GPCR peptide or protein ligands. Here we give a general review of recent advances in the study of GPCR structure, function, as well as GPCR and ligand identification with the emphasis on the bioinformatics database mining of GPCR and their peptide or protein ligands.
Genomic Arrangement of Regulons in Bacterial Genomes
Han Zhang, Yanbin Yin, Victor Olman, Ying Xu
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0029496
Abstract: Regulons, as groups of transcriptionally co-regulated operons, are the basic units of cellular response systems in bacterial cells. While the concept has been long and widely used in bacterial studies since it was first proposed in 1964, very little is known about how its component operons are arranged in a bacterial genome. We present a computational study to elucidate of the organizational principles of regulons in a bacterial genome, based on the experimentally validated regulons of E. coli and B. subtilis. Our results indicate that (1) genomic locations of transcriptional factors (TFs) are under stronger evolutionary constraints than those of the operons they regulate so changing a TF's genomic location will have larger impact to the bacterium than changing the genomic position of any of its target operons; (2) operons of regulons are generally not uniformly distributed in the genome but tend to form a few closely located clusters, which generally consist of genes working in the same metabolic pathways; and (3) the global arrangement of the component operons of all the regulons in a genome tends to minimize a simple scoring function, indicating that the global arrangement of regulons follows simple organizational principles.
Advances in G-protein coupled receptor research and related bioinformatics study
Yanbin Yin,Jingchu Luo,Ying Jiang,
YINYanbin
,LUOJingchu

科学通报(英文版) , 2003,
Abstract: G-protein coupled receptor (GPCR) is one of the most important protein families for drug target. GPCR agonists and antagonists occupy approximately one third of the world small molecule drug market. Much effort has been invested in GPCR study by both academic institutions and pharmaceutical industries. With seven-transmembrane do-mains, GPCR plays significant roles in intercellular signal transduction and is involved in a variety of biological path-ways. With the availability of sequence data of human and other mammalian genomes, as well as their expressed se-quence tag (EST) data, the bioinformatics and genomics approaches can be applied to identifying novel GPCR in the post genomic era. Deorphanizing GPCR or matching ligands with GPCR greatly facilitates target validation process and automatically provides a possible compound screening assay. Similarly, bioinformatics data mining approach could also be applied to the identification of GPCR peptide or protein ligands. Here we give a general review of recent advances in the study of GPCR structure, function, as well as GPCR and ligand identification with the emphasis on the bioinformatics database mining of GPCR and their peptide or protein ligands.
Low Expression of miR-196b Enhances the Expression of BCR-ABL1 and HOXA9 Oncogenes in Chronic Myeloid Leukemogenesis
Yue Liu, Wenling Zheng, Yanbin Song, Wenli Ma, Hong Yin
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0068442
Abstract: MicroRNAs (miRNAs) can function as tumor suppressors or oncogene promoters during tumor development. In this study, low levels of expression of miR-196b were detected in patients with chronic myeloid leukemia. Bisulfite genomic sequencing PCR and methylation-specific PCR were used to examine the methylation status of the CpG islands in the miR-196b promoter in K562 cells, patients with leukemia and healthy individuals. The CpG islands showed more methylation in patients with chronic myeloid leukemia compared with healthy individuals (P<0.05), which indicated that low expression of miR-196b may be associated with an increase in the methylation of CpG islands. The dual-luciferase reporter assay system demonstrated that BCR-ABL1 and HOXA9 are the target genes of miR-196b, which was consistent with predictions from bioinformatics software analyses. Further examination of cell function indicated that miR-196b acts to reduce BCR-ABL1 and HOXA9 protein levels, decrease cell proliferation rate and retard the cell cycle. A low level of expression of miR-196b can cause up-regulation of BCR-ABL1 and HOXA9 expression, which leads to the development of chronic myeloid leukemia. MiR-196b may represent an effective target for chronic myeloid leukemia therapy.
A MAC Scheme with QoS Guarantee for MANETs  [PDF]
Yanbin YANG, Yulin WEI
Int'l J. of Communications, Network and System Sciences (IJCNS) , 2009, DOI: 10.4236/ijcns.2009.28088
Abstract: IEEE 802.11 distributed coordination function (DCF) can alleviate the collision and hidden station problem, but it doesn’t differentiate traffic categories (TC). Therefore, it can’t provide sufficient QoS support for different traffic categories. Recently, a new contention-based enhanced distributed channel access (EDCA) scheme was proposed which provides a probabilistic QoS support. In this paper, an adaptive EDCA scheme with QoS guarantee for mobile ad hoc networks (MANETs) is proposed. In this scheme, the EDCA scheme and the token bucket algorithm (TBA) are combined to adjust the contention window (CW). Our scheme provides the traffic differentiation.
Deviations of Steady States of the Traveling Wave to a Competition Diffusion System with Random Perturbation  [PDF]
Xiaorong Hu, Yanbin Tang
Journal of Applied Mathematics and Physics (JAMP) , 2015, DOI: 10.4236/jamp.2015.35062
Abstract: This paper considers the asymptotic dynamics of steady states to the Lotka-Volterra competition diffusion systems with random perturbations by two-parameter white noise on the whole real line. By the fundamental solution of heat equation, we get the asymptotic fluctuating behaviors near the stable states respectively. That is, near the steady state (u,v)=(0,1), the mean value Eu(x,t) is shifted above the equilibrium u=0 and Ev(x,t) is shifted below the equilibrium v=1. However, near the steady state (u,v)=(1,0), the mean value Eu(x,t) is shifted below the equilibrium u =1 and Eu(x,t)=0.
Evolution of Plant Nucleotide-Sugar Interconversion Enzymes
Yanbin Yin, Jinling Huang, Xiaogang Gu, Maor Bar-Peled, Ying Xu
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0027995
Abstract: Nucleotide-diphospho-sugars (NDP-sugars) are the building blocks of diverse polysaccharides and glycoconjugates in all organisms. In plants, 11 families of NDP-sugar interconversion enzymes (NSEs) have been identified, each of which interconverts one NDP-sugar to another. While the functions of these enzyme families have been characterized in various plants, very little is known about their evolution and origin. Our phylogenetic analyses indicate that all the 11 plant NSE families are distantly related and most of them originated from different progenitor genes, which have already diverged in ancient prokaryotes. For instance, all NSE families are found in the lower land plant mosses and most of them are also found in aquatic algae, implicating that they have already evolved to be capable of synthesizing all the 11 different NDP-sugars. Particularly interesting is that the evolution of RHM (UDP-L-rhamnose synthase) manifests the fusion of genes of three enzymatic activities in early eukaryotes in a rather intriguing manner. The plant NRS/ER (nucleotide-rhamnose synthase/epimerase-reductase), on the other hand, evolved much later from the ancient plant RHMs through losing the N-terminal domain. Based on these findings, an evolutionary model is proposed to explain the origin and evolution of different NSE families. For instance, the UGlcAE (UDP-D-glucuronic acid 4-epimerase) family is suggested to have evolved from some chlamydial bacteria. Our data also show considerably higher sequence diversity among NSE-like genes in modern prokaryotes, consistent with the higher sugar diversity found in prokaryotes. All the NSE families are widely found in plants and algae containing carbohydrate-rich cell walls, while sporadically found in animals, fungi and other eukaryotes, which do not have or have cell walls with distinct compositions. Results of this study were shown to be highly useful for identifying unknown genes for further experimental characterization to determine their functions in the synthesis of diverse glycosylated molecules.
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