35 results on '"Yeong-Shin Lin"'
Search Results
2. The evolution and structure of snake venom phosphodiesterase (svPDE) highlight its importance in venom actions
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Cheng-Tsung Pan, Chien-Chu Lin, I-Jin Lin, Kun-Yi Chien, Yeong-Shin Lin, Hsiao-Han Chang, and Wen-Guey Wu
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General Immunology and Microbiology ,General Neuroscience ,General Medicine ,General Biochemistry, Genetics and Molecular Biology - Abstract
For decades, studies of snake venoms focused on the venom-ome-specific toxins (VSTs). VSTs are dominant soluble proteins believed to contribute to the main venomous effects and emerged into gene clusters for fast adaptation and diversification of snake venoms. However, the conserved minor venom components, such as snake venom phosphodiesterase (svPDE), remain largely unexplored. Here, we focus on svPDE by genomic and transcriptomic analysis across snake clades and demonstrate that soluble svPDE is co-opted from the ancestral membrane-attached ENPP3 (ectonucleotide pyrophosphatase/phosphodiesterase 3) gene by replacing the original 5’ exon with the exon encoding a signal peptide. Notably, the exons, promoters and transcription/translation starts have been replaced multiple times during snake evolution, suggesting the evolutionary necessity of svPDE. The structural and biochemical analyses also show that svPDE shares the similar functions with ENPP family, suggesting its perturbation to the purinergic signaling and insulin transduction in venomous effects.Significance StatementWe provided a case of the evolutionary co-option strategy in which the secretory svPDE, one of the minor venom components, is generated from the ancestral membrane-anchored ENPP3 gene by using an alternative 5’ exon. The first exon of the svPDE transcript encodes a signal peptide instead of the transmembrane domain of the ENPP3. Multiple replacement events of genomic elements during snake evolution maintain the expression of the svPDE transcripts, suggesting the crucial function of svPDE. Also, the structures and biochemical analyses indicate that svPDE reuse the original functions of ENPP3 in the bitten tissues and may interfere with normal cell signaling. Together, our study reveals the evolution of svPDE and suggests the importance of minor venom components.
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- 2022
3. A genome-wide association study (GWAS) of the personality constructs in CPAI-2 in Taiwanese Hakka populations
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Pei-Ying Kao, Ming-Hui Chen, Wei-An Chang, Mei-Lin Pan, Wei-Der Shu, Yuh-Jyh Jong, Hsien-Da Huang, Cheng-Yan Wang, Hong-Yan Chu, Cheng-Tsung Pan, Yih-Lan Liu, and Yeong-Shin Lin
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Multidisciplinary - Abstract
Here in this study we adopted genome-wide association studies (GWAS) to investigate the genetic components of the personality constructs in the Chinese Personality Assessment Inventory 2 (CPAI-2) in Taiwanese Hakka populations, who are likely the descendants of a recent admixture between a group of Chinese immigrants with high emigration intention and a group of the Taiwanese aboriginal population generally without it. A total of 279 qualified participants were examined and genotyped by an Illumina array with 547,644 SNPs to perform the GWAS. Although our sample size is small and that unavoidably limits our statistical power (Type 2 error but not Type 1 error), we still found three genomic regions showing strong association with Enterprise, Diversity, and Logical vs. Affective Orientation, respectively. Multiple genes around the identified regions were reported to be nervous system related, which suggests that genetic variants underlying the certain personalities should indeed exist in the nearby areas. It is likely that the recent immigration and admixture history of the Taiwanese Hakka people created strong linkage disequilibrium between the emigration intention-related genetic variants and their neighboring genetic markers, so that we could identify them despite with only limited statistical power.
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- 2023
4. MicroRNA retrocopies generated via L1-mediated retrotransposition in placental mammals help to reveal how their parental genes were transcribed
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Yeong-Shin Lin and Cheng Tsung Pan
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Parents ,Retroelements ,Gene duplication ,lcsh:Medicine ,Retrotransposon ,Biology ,Genome ,Article ,Non-coding RNAs ,Exon ,Placenta ,microRNA ,Homologous chromosome ,medicine ,Animals ,lcsh:Science ,Gene ,Genetics ,Multidisciplinary ,Eutheria ,Comparative genomics ,lcsh:R ,Exons ,Embryonic stem cell ,MicroRNAs ,medicine.anatomical_structure ,lcsh:Q - Abstract
In mammalian genomes, most retrocopies emerged via the L1 retrotransposition machinery. The hallmarks of an L1-mediated retrocopy, i.e., the intronlessness, the presence of a 3′ poly-A tail, and the TSDs at both ends, were frequently used to identify retrotransposition events. However, most previous studies only focused on protein-coding genes as their possible parental sources and thus only a few retrocopies derived from non-coding genes were reported. Remarkably, none of them was from microRNAs. Here in this study, we found several retrocopies generated from the mir-302–367 cluster gene (MIR302CHG), and identified a novel alternatively spliced exon encoding mir-302a. The other recognized microRNA retrotransposition events are primate-specific with mir-373 and mir-498 as their parental genes. The 3′ poly-A tracts of these two retrocopy groups were directly attached to the end of the microRNA precursor homologous regions, which suggests that their parental transcripts might alternatively terminate at the end of mir-373 and mir-498. All the three parental microRNAs are highly expressed in specific tissues with elevated retrotransposon activity, such as the embryonic stem cells and the placenta. This might be the reason that our first microRNA retrocopy findings were derived from these three microRNA genes.
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- 2020
5. Global Investigation of Immune Repertoire Suggests Kawasaki Disease Has Infectious Cause
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Sung-Chou Li, Ho-Chang Kuo, Cheng Tsung Pan, Fu Chen Huang, Yeong-Shin Lin, Lien Hung Huang, and Ying Hsien Huang
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Male ,Immunoglobulin Variable Region ,Immunoglobulins ,chemical and pharmacologic phenomena ,Mucocutaneous Lymph Node Syndrome ,030204 cardiovascular system & hematology ,Autoimmune Diseases ,Blood cell ,03 medical and health sciences ,0302 clinical medicine ,Risk Factors ,Humans ,Medicine ,030212 general & internal medicine ,Respiratory Tract Infections ,B cell ,B-Lymphocytes ,biology ,business.industry ,RNA ,General Medicine ,medicine.disease ,Complementarity Determining Regions ,Immunoglobulin Class Switching ,V(D)J Recombination ,medicine.anatomical_structure ,Infectious disease (medical specialty) ,Case-Control Studies ,Immunology ,biology.protein ,Immunoglobulin Joining Region ,Immunoglobulin heavy chain ,Female ,Kawasaki disease ,Antibody ,Cardiology and Cardiovascular Medicine ,business ,J-segment ,Antibody Diversity - Abstract
Background Kawasaki disease (KD) severely threatens young children's health worldwide. The pathogenic mechanism of KD has not yet been solved, so there is still debate over whether KD is an infectious disease or an autoimmune disease.Methods and Results:To solve this problem, an immune repertoire analysis of KD was conducted. We collected blood cell RNA samples and prepared them into amplicons with iRepertoire kits. The amplicons were sequenced and analyzed with the iRepertoire pipeline. We first identified KD-specific VJ and VDJ forms that had the potential to serve as biomarkers of KD. In addition, the KD-specific VDJ forms were contributed mostly by immunoglobulin G. The D50 value analysis showed that B-cell diversity in KD is decreased, suggesting unique immunoglobulins are produced in KD. Moreover, V, D and J segment usage in IgA, IgG and IgM was consistent with previous KD studies. Further comparison showed no difference in CDR3 peptide length between KD and fever controls (subjects with fever but not diagnosed as KD), indicting KD had B-cell selection phenomenon that has a non-autoimmune pattern. The comparison of amino acid usage of the CDR3 region demonstrated a preference for hydrophilic amino acids in KD. Conclusions The results of D50 value, VDJ usage and CDR3 peptide length analyses suggested the characteristics of infectious disease for KD.
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- 2019
6. Multiomics analyses identified epigenetic modulation of the S100A gene family in Kawasaki disease and their significant involvement in neutrophil transendothelial migration
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Sung-Chou Li, Lien Hung Huang, Ying Hsien Huang, Cheng Tsung Pan, Yeong-Shin Lin, and Ho-Chang Kuo
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Epigenomics ,0301 basic medicine ,lcsh:QH426-470 ,lcsh:Medicine ,Mucocutaneous Lymph Node Syndrome ,Biology ,Cell Line ,Epigenesis, Genetic ,03 medical and health sciences ,Gene expression ,Genetics ,Humans ,Gene family ,Epigenetics ,Promoter Regions, Genetic ,Molecular Biology ,Gene ,Genetics (clinical) ,DNA methylation ,Kawasaki disease ,Research ,Gene Expression Profiling ,CpG marker ,S100 Proteins ,lcsh:R ,Transendothelial and Transepithelial Migration ,Promoter ,Sequence Analysis, DNA ,Methylation ,Molecular biology ,Correlation ,lcsh:Genetics ,030104 developmental biology ,Gene Expression Regulation ,CpG site ,S100A gene family ,CpG Islands ,Female ,Leukocyte transendothelial migration ,Genome-Wide Association Study ,Developmental Biology - Abstract
Background Kawasaki disease (KD) is a prevalent pediatric disease worldwide and can cause coronary artery aneurysm as a severe complication. Typically, DNA methylation is thought to repress the expression of nearby genes. However, the cases in which DNA methylation promotes gene expression have been reported. In addition, globally, to what extent DNA methylation affects gene expression and how it contributes to the pathogenesis of KD are not yet well understood. Methods To address these important biological questions, we enrolled subjects, collected DNA and RNA samples from the subjects’ total white blood cells, and performed DNA methylation (M450K) and gene expression (HTA 2.0) microarray assays. Results By analyzing the variation ratios of CpG beta values (methylation percentage) and gene expression intensities, we first concluded that the CpG markers close (− 1500 bp to + 500 bp) to the transcription start sites had higher variation ratios, reflecting significant regulation capacities. Next, we observed that, globally speaking, gene expression was modestly negatively correlated (correlation rho ≈ − 0.2) with the DNA methylation status of both upstream and downstream CpG markers in the promoter region. Third, we found that specific CpG markers were hypo-methylated in disease samples compared with healthy samples and hyper-methylated in convalescent samples compared with disease samples, promoting and repressing S100A genes’ expressions, respectively. Finally, using an in vitro cell model, we demonstrated that S100A family proteins enhanced leukocyte transendothelial migration in KD. Conclusions This is the first study to integrate genome-wide DNA methylation with gene expression assays in KD and showed that the S100A family plays important roles in the pathogenesis of KD. Electronic supplementary material The online version of this article (10.1186/s13148-018-0557-1) contains supplementary material, which is available to authorized users.
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- 2018
7. DNA barcode identification of fish products in Taiwan: Government-commissioned authentication cases
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Qiu Ren, Yeong-Shin Lin, Han-Yang Lin, Chia Hao Chang, and Kwang-Tsao Shao
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Government ,business.industry ,010401 analytical chemistry ,Internet privacy ,04 agricultural and veterinary sciences ,Fish products ,040401 food science ,01 natural sciences ,DNA barcoding ,Authentication (law) ,0104 chemical sciences ,Biotechnology ,0404 agricultural biotechnology ,Order (business) ,Mitochondrial cytochrome ,%22">Fish ,Medicine ,Identification (biology) ,business ,Food Science - Abstract
Mislabeling of fish products not only impacts consumer finances, but can also be deleterious to public health. Fish products may be mislabeled for reasons including ambiguity of common fish names, challenging morphological identification, or willful intention to deceive. We reveal a high rate of mislabeling (70%) in 34 samples from 17 cases entrusted to us by three different Customs offices and one Coastal Patrol Office in Taiwan using DNA barcoding based on a partial segment of the mitochondrial cytochrome c oxidase subunit I gene (COI). In order to reduce the mislabeling of imported fish products, the authorities should take some actions into consideration, such as institutionalizating molecular authentication of fish products, standardizing the usage of common fish names, and legislating for penalties.
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- 2016
8. Additional file 1: of Multiomics analyses identified epigenetic modulation of the S100A gene family in Kawasaki disease and their significant involvement in neutrophil transendothelial migration
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Lien-Hung Huang, Ho-Chang Kuo, Cheng-Tsung Pan, Yeong-Shin Lin, Ying-Hsien Huang, and Sung-Chou Li
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hemic and lymphatic diseases - Abstract
Demographic data. A total of 24 healthy control subjects (HC), 21 fever control subjects (FC), and 18 KD patients participated in this study. Each HC and FC subject contributed one tube of blood sample, whereas each KD patients contributed two tubes of blood samples, one at the acute phase before IVIG treatment (KD1) and one 3Â weeks after IVIG treatment (KD3). (DOC 100 kb)
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- 2018
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9. Triple-layer dissection of the lung adenocarcinoma transcriptome – regulation at the gene, transcript, and exon levels
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Feng-Chi Chen, Chang-Huain Hsieh, Min-Kung Hsu, Jen Liang Su, Ching-Chia Cheng, Yeong-Shin Lin, and I-Ching Wu
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Lung Neoplasms ,Time Factors ,Regulome ,Adenocarcinoma of Lung ,Biology ,Adenocarcinoma ,Transfection ,differential expression ,Transcriptome ,Exon ,alternative splicing ,transcriptome analysis ,Proto-Oncogene Proteins ,Databases, Genetic ,medicine ,Biomarkers, Tumor ,Humans ,Genetic Predisposition to Disease ,RNA, Messenger ,Gene ,Genetic Association Studies ,Cell Proliferation ,Proto-Oncogene Proteins c-ets ,Gene Expression Profiling ,Alternative splicing ,Exons ,Aldehyde Dehydrogenase ,medicine.disease ,lung adenocarcinoma ,transcript-specific regulation ,Gene expression profiling ,HEK293 Cells ,Phenotype ,Oncology ,RNA splicing ,Cancer research ,RNA Interference ,Adenovirus E1A Proteins ,Research Paper ,Signal Transduction - Abstract
Lung adenocarcinoma is one of the most deadly human diseases. However, the molecular mechanisms underlying this disease, particularly RNA splicing, have remained underexplored. Here, we report a triple-level (gene-, transcript-, and exon-level) analysis of lung adenocarcinoma transcriptomes from 77 paired tumor and normal tissues, as well as an analysis pipeline to overcome genetic variability for accurate differentiation between tumor and normal tissues. We report three major results. First, more than 5,000 differentially expressed transcripts/exonic regions occur repeatedly in lung adenocarcinoma patients. These transcripts/exonic regions are enriched in nicotine metabolism and ribosomal functions in addition to the pathways enriched for differentially expressed genes (cell cycle, extracellular matrix receptor interaction, and axon guidance). Second, classification models based on rationally selected transcripts or exonic regions can reach accuracies of 0.93 to 1.00 in differentiating tumor from normal tissues. Of the 28 selected exonic regions, 26 regions correspond to alternative exons located in such regulators as tumor suppressor (GDF10), signal receptor (LYVE1), vascular-specific regulator (RASIP1), ubiquitination mediator (RNF5), and transcriptional repressor (TRIM27). Third, classification systems based on 13 to 14 differentially expressed genes yield accuracies near 100%. Genes selected by both detection methods include C16orf59, DAP3, ETV4, GABARAPL1, PPAR, RADIL, RSPO1, SERTM1, SRPK1, ST6GALNAC6, and TNXB. Our findings imply a multilayered lung adenocarcinoma regulome in which transcript-/exon-level regulation may be dissociated from gene-level regulation. Our described method may be used to identify potentially important genes/transcripts/exonic regions for the tumorigenesis of lung adenocarcinoma and to construct accurate tumor vs. normal classification systems for this disease.
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- 2015
10. Divergent Alanyl-tRNA Synthetase Genes of Vanderwaltozyma polyspora Descended from a Common Ancestor through Whole-Genome Duplication Followed by Asymmetric Evolution
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Yi Hsueh Lee, Chih Yao Chang, Yeong-Shin Lin, Chia Pei Chang, and Chien Chia Wang
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Gene isoform ,Genetics ,Nonsynonymous substitution ,Nuclear gene ,Base Sequence ,biology ,Alanine-tRNA Ligase ,Genes, Fungal ,Molecular Sequence Data ,Articles ,Cell Biology ,biology.organism_classification ,Evolution, Molecular ,Saccharomycetales ,Phylogenetics ,Gene Duplication ,Gene Expression Regulation, Fungal ,Gene duplication ,Amino Acid Sequence ,Molecular Biology ,Gene ,Phylogeny ,Synteny - Abstract
Cytoplasmic and mitochondrial forms of a eukaryotic aminoacyl-tRNA synthetase (aaRS) are generally encoded by two distinct nuclear genes, one of eukaryotic origin and the other of mitochondrial origin. However, in most known yeasts, only the mitochondrial-origin alanyl-tRNA synthetase (AlaRS) gene is retained and plays a dual-functional role. Here, we present a novel scenario of AlaRS evolution in the yeast Vanderwaltozyma polyspora. V. polyspora possesses two significantly diverged AlaRS gene homologues, one encoding the cytoplasmic form and the other its mitochondrial counterpart. Clever selection of transcription and translation initiation sites enables the two isoforms to be localized and thus functional in their respective cellular compartments. However, the two isoforms can also be stably expressed and function in the reciprocal compartments by insertion or removal of a mitochondrial targeting signal. Synteny and phylogeny analyses revealed that the AlaRS homologues of V. polyspora arose from a dual-functional common ancestor through whole-genome duplication (WGD). Moreover, the mitochondrial form had higher synonymous (1.6-fold) and nonsynonymous (2.8-fold) substitution rates than did its cytoplasmic counterpart, presumably due to a lesser constraint imposed on components of the mitochondrial translational apparatus. Our study suggests that asymmetric evolution confers the divergence between the AlaRS paralogues of V. polyspora.
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- 2015
11. Phylogenetic relationships of Acheilognathidae (Cypriniformes: Cyprinoidea) as revealed from evidence of both nuclear and mitochondrial gene sequence variation: Evidence for necessary taxonomic revision in the family and the identification of cryptic species
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Sungmin Kim, Martin Reichard, Tetsuya Sado, Shunping He, Takahiro Morosawa, Hyeyoung Koo, Chia Hao Chang, Kazuhiko Uehara, Fan Li, Wei-Jen Chen, Jae-Seong Lee, Carl Smith, Won Kim, Masaki Miya, Richard L. Mayden, Yeong-Shin Lin, Sébastien Lavoué, and Kwang-Tsao Shao
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Likelihood Functions ,Species complex ,Phylogenetic tree ,Cyprinidae ,Tanakia ,Genetic Variation ,Zoology ,Bayes Theorem ,Sequence Analysis, DNA ,Biology ,Subspecies ,biology.organism_classification ,Biological Evolution ,Monophyly ,Genes, Mitochondrial ,European bitterling ,Phylogenetics ,Genetics ,Animals ,Clade ,Molecular Biology ,Phylogeny ,Ecology, Evolution, Behavior and Systematics - Abstract
Bitterlings are relatively small cypriniform species and extremely interesting evolutionarily due to their unusual reproductive behaviors and their coevolutionary relationships with freshwater mussels. As a group, they have attracted a great deal of attention in biological studies. Understanding the origin and evolution of their mating system demands a well-corroborated hypothesis of their evolutionary relationships. In this study, we provide the most comprehensive phylogenetic reconstruction of species relationships of the group based on partitioned maximum likelihood and Bayesian methods using DNA sequence variation of nuclear and mitochondrial genes on 41 species, several subspecies and three undescribed species. Our findings support the monophyly of the Acheilognathidae. Two of the three currently recognized genera are not monophyletic and the family can be subdivided into six clades. These clades are further regarded as genera based on both their phylogenetic relationships and a reappraisal of morphological characters. We present a revised classification for the Acheilognathidae with five genera/lineages: Rhodeus, Acheilognathus (new constitution), Tanakia (new constitution), Paratanakia gen. nov., and Pseudorhodeus gen. nov. and an unnamed clade containing five species currently referred to as "Acheilognathus". Gene trees of several bitterling species indicate that the taxa are not monophyletic. This result highlights a potentially dramatic underestimation of species diversity in this family. Using our new phylogenetic framework, we discuss the evolution of the Acheilognathidae relative to classification, taxonomy and biogeography. (C) 2014 Elsevier Inc. All rights reserved.
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- 2014
12. Evolutionary gain of highly divergent tRNA specificities by two isoforms of human histidyl-tRNA synthetase
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Chia Pei Chang, Chien Chia Wang, Yi Hsueh Lee, Yeong-Shin Lin, Yu Ju Cheng, and Yi Yi Kuo
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0301 basic medicine ,Gene isoform ,Context (language use) ,Saccharomyces cerevisiae ,Biology ,Histidine-tRNA Ligase ,Substrate Specificity ,Evolution, Molecular ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,chemistry.chemical_compound ,RNA, Transfer ,Protein biosynthesis ,Escherichia coli ,Humans ,Aminoacylation ,Amino Acid Sequence ,Molecular Biology ,Gene ,Phylogeny ,Pharmacology ,Genetics ,Aminoacyl tRNA synthetase ,Cell Biology ,Mitochondria ,Isoenzymes ,030104 developmental biology ,chemistry ,Cytoplasm ,Transfer RNA ,Molecular Medicine ,Subfunctionalization ,Mutant Proteins ,Bacillus subtilis - Abstract
The discriminator base N73 is a key identity element of tRNAHis. In eukaryotes, N73 is an "A" in cytoplasmic tRNAHis and a "C" in mitochondrial tRNAHis. We present evidence herein that yeast histidyl-tRNA synthetase (HisRS) recognizes both A73 and C73, but somewhat prefers A73 even within the context of mitochondrial tRNAHis. In contrast, humans possess two distinct yet closely related HisRS homologues, with one encoding the cytoplasmic form (with an extra N-terminal WHEP domain) and the other encoding its mitochondrial counterpart (with an extra N-terminal mitochondrial targeting signal). Despite these two isoforms sharing high sequence similarities (81% identity), they strongly preferred different discriminator bases (A73 or C73). Moreover, only the mitochondrial form recognized the anticodon as a strong identity element. Most intriguingly, swapping the discriminator base between the cytoplasmic and mitochondrial tRNAHis isoacceptors conveniently switched their enzyme preferences. Similarly, swapping seven residues in the active site between the two isoforms readily switched their N73 preferences. This study suggests that the human HisRS genes, while descending from a common ancestor with dual function for both types of tRNAHis, have acquired highly specialized tRNA recognition properties through evolution.
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- 2016
13. Evolutionary information hidden in a single protein structure
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Yeong-Shin Lin, Jenn-Kang Hwang, Chien Hua Shih, Chih Min Chang, and Wei-Cheng Lo
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Genetics ,Sequence Homology, Amino Acid ,Protein Conformation ,Computational biology ,Biology ,Biochemistry ,Homologous Sequences ,Enzymes ,Protein Structure, Tertiary ,Conserved sequence ,Evolution, Molecular ,Protein Subunits ,Protein structure ,Structural Biology ,Catalytic Domain ,Evolutionary information ,Amino acid residue ,Databases, Protein ,Contact number ,Sequence Alignment ,Molecular Biology ,Conserved Sequence - Abstract
The knowledge of conserved sequences in proteins is valuable in identifying functionally or structurally important residues. Generating the conservation profile of a sequence requires aligning families of homologous sequences and having knowledge of their evolutionary relationships. Here, we report that the conservation profile at the residue level can be quantitatively derived from a single protein structure with only backbone information. We found that the reciprocal packing density profiles of protein structures closely resemble their sequence conservation profiles. For a set of 554 nonhomologous enzymes, 74% (408/554) of the proteins have a correlation coefficient > 0.5 between these two profiles. Our results indicate that the three-dimensional structure, instead of being a mere scaffold for positioning amino acid residues, exerts such strong evolutionary constraints on the residues of the protein that its profile of sequence conservation essentially reflects that of its structural characteristics. Proteins 2012;. © 2012 Wiley Periodicals, Inc.
- Published
- 2012
14. Proportion of Solvent-Exposed Amino Acids in a Protein and Rate of Protein Evolution
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Yeong-Shin Lin, Wei Lun Hsu, Wen-Hsiung Li, and Jenn-Kang Hwang
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chemistry.chemical_classification ,Principal Component Analysis ,Saccharomyces cerevisiae Proteins ,Proteins ,Saccharomyces cerevisiae ,Biology ,Yeast ,Protein evolution ,Amino acid ,Evolution, Molecular ,Solvent ,Protein structure ,Biochemistry ,chemistry ,Codon usage bias ,Gene expression ,Solvents ,Genetics ,Regression Analysis ,Amino Acids ,Selection, Genetic ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Selection (genetic algorithm) - Abstract
Translational selection, including gene expression, protein abundance, and codon usage bias, has been suggested as the single dominant determinant of protein evolutionary rate in yeast. Here, we show that protein structure is also an important determinant. Buried residues, which are responsible for maintaining protein structure or are located on a stable interaction surface between 2 subunits, are usually under stronger evolutionary constraints than solvent-exposed residues. Our partial correlation analysis shows that, when whole proteins are included, the variance of evolutionary rate explained by the proportion of solvent-exposed residues (P(exposed)) can reach two-thirds of that explained by translational selection, indicating that P(exposed) is the most important determinant of protein evolutionary rate next only to translational selection. Our result suggests that proteins with many residues under selective constraint (e.g., maintaining structure or intermolecular interaction) tend to evolve slowly, supporting the "fitness (functional) density" hypothesis.
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- 2007
15. Differentiation of visual spectra and nuptial colorations of two Paratanakia himantegus subspecies (Cyprinoidea: Acheilognathidae) in response to the distinct photic conditions of their habitats
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Hong Young Yan, Kazuhiko Anraku, Yeong-Shin Lin, Wen Chung Fu, Chia Hao Chang, and Yi Ta Shao
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Spectral sensitivity ,Stimulus modality ,Paratanakia himantegus ,Habitat ,Ecology ,Zoology ,Animal Science and Zoology ,Sensory system ,Photic zone ,Subspecies ,Biology ,Spectral line ,Research Article - Abstract
Background Vision, an important sensory modality of many animals, exhibits plasticity in that it adapts to environmental conditions to maintain its sensory efficiency. Nuptial coloration is used to attract mates and hence should be tightly coupled to vision. In Taiwan, two closely related bitterlings (Paratanakia himantegus himantegus and Paratanakia himantegus chii) with different male nuptial colorations reside in different habitats. We compared the visual spectral sensitivities of these subspecies with the ambient light spectra of their habitats to determine whether their visual abilities correspond with photic parameters and correlate with nuptial colorations. Results The electroretinogram (ERG) results revealed that the relative spectral sensitivity of P. h. himantegus was higher at 670 nm, but lower at 370 nm, than the sensitivity of P. h. chii. Both bitterlings could perceive and reflect UV light, but the UV reflection patterns differed between genders. Furthermore, the relative irradiance intensity of the light spectra in the habitat of P. h. himantegus was higher at long wavelengths (480–700 nm), but lower at short wavelengths (350–450 nm), than the light spectra in the habitats of P. h. chii. Conclusions Two phylogenetically closely related bitterlings, P. h. himantegus and P. h. chii, dwell in different waters and exhibit different nuptial colorations and spectral sensitivities, which may be the results of speciation by sensory drive. Sensory ability and signal diversity accommodating photic environment may promote diversity of bitterling fishes. UV light was demonstrated to be a possible component of bitterling visual communication. The UV cue may assist bitterlings in gender identification.
- Published
- 2015
16. The fragment transformation method to detect the protein structural motifs
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Chih Hao Lu, Yeong-Shin Lin, Shi Yu Chang, Yu Ching Chen, Chin-Sheng Yu, and Jenn-Kang Hwang
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Genetics ,Sequence analysis ,Amino Acid Motifs ,Molecular Sequence Data ,Structural alignment ,Computational Biology ,Computational biology ,Biology ,Biochemistry ,Peptide Fragments ,Protein Structure, Secondary ,Structural genomics ,Structural bioinformatics ,Protein structure ,Structural Biology ,Multiple EM for Motif Elicitation ,Amino Acid Sequence ,Databases, Protein ,Structural motif ,Sequence motif ,Molecular Biology - Abstract
To identify functional structural motifs from protein structures of unknown function becomes increasingly important in recent years due to the progress of the structural genomics initiatives. Although certain structural patterns such as the Asp-His-Ser catalytic triad are easy to detect because of their conserved residues and stringently constrained geometry, it is usually more challenging to detect a general structural motifs like, for example, the betabetaalpha-metal binding motif, which has a much more variable conformation and sequence. At present, the identification of these motifs usually relies on manual procedures based on different structure and sequence analysis tools. In this study, we develop a structural alignment algorithm combining both structural and sequence information to identify the local structure motifs. We applied our method to the following examples: the betabetaalpha-metal binding motif and the treble clef motif. The betabetaalpha-metal binding motif plays an important role in nonspecific DNA interactions and cleavage in host defense and apoptosis. The treble clef motif is a zinc-binding motif adaptable to diverse functions such as the binding of nucleic acid and hydrolysis of phosphodiester bonds. Our results are encouraging, indicating that we can effectively identify these structural motifs in an automatic fashion. Our method may provide a useful means for automatic functional annotation through detecting structural motifs associated with particular functions.
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- 2006
17. The complete mitochondrial genome of the crocodile shark, Pseudocarcharias kamoharai (Chondrichthyes, Lamnidae)
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Kwang-Tsao Shao, Yeong-Shin Lin, Chia Hao Chang, and Hsuan-Ching Ho
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Mitochondrial DNA ,Base Composition ,biology ,Pseudocarcharias ,Anatomy ,Crocodile ,biology.organism_classification ,Chondrichthyes ,Genome ,DNA, Mitochondrial ,Genes, Mitochondrial ,RNA, Transfer ,Evolutionary biology ,biology.animal ,Transfer RNA ,Genome, Mitochondrial ,Genetics ,Lamnidae ,Sharks ,Animals ,human activities ,Molecular Biology ,Gene - Abstract
The complete mitochondrial genome of the crocodile shark consists of 16,688 bp and includes 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, 1 replication origin region, and 1 control region. The mitochondrial gene arrangement of the crocodile shark is the same as that of most vertebrates. Base composition of the genome is A (32.0%), T (31.0%), C (23.7%) and G (13.3%).
- Published
- 2014
18. Reassessment of morphological characteristics in freshwater eels (genus Anguilla, Anguillidae) shows congruence with molecular phylogeny estimates
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Chyng-Shyan Tzeng, Jenn Kang Hwang, and Yeong-Shin Lin
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Synapomorphy ,biology ,Phylogenetic tree ,Zoology ,Morphology (biology) ,biology.organism_classification ,Taxon ,Anguillidae ,Phylogenetics ,Molecular phylogenetics ,Genetics ,Animal Science and Zoology ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Distance matrices in phylogeny - Abstract
The morphology-based phylogeny of freshwater eels, proposed by V. Ege in 1939, has been accepted as the basis of eel classification since that time. However, this has been called into question by recent molecular studies. Most of the morphological characteristics recognized by Ege are morphometric. Since methods for the application of morphometric data to phylogeny construction have not been fully established, it is unclear whether the observed discrepancies between morphological and molecular data arise from intrinsic differences or from flawed analyses. Here, we have used two methods to assemble evolutionary trees from distance matrices constructed according to Ege's data, the neighbor-joining (NJ) method and the minimum network (MinNet) method; the latter is based on an evolutionary algorithm. After reanalysing Ege's morphological data, we found that both methods gave results consistent with those based on molecular data, although not with Ege's original classification. Therefore, we speculate that some morphological features Ege used to subdivide the eel groups may not be synapomorphic as he proposed, but symplesiomorphic or convergent . The method developed here may prove useful for constructing phylogeny for taxon groups where only continuous morphometric characteristics are recognized, such as the freshwater eels.
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- 2005
19. The complete mitochondrial genome of the salmon shark, Lamna ditropis (Chondrichthyes, Lamnidae)
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Aaron B. Carlisle, Yeong-Shin Lin, Kwang-Tsao Shao, Nian-Hong Jang-Liaw, Hua Hsun Hsu, Chia Hao Chang, and Yun Chih Liao
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0301 basic medicine ,Mitochondrial DNA ,Molecular Sequence Data ,Genome ,DNA, Mitochondrial ,03 medical and health sciences ,Gene Order ,Genetics ,Lamnidae ,Animals ,Molecular Biology ,Gene ,Base Composition ,biology ,Base Sequence ,Sequence Analysis, DNA ,biology.organism_classification ,Lamna ,Chondrichthyes ,030104 developmental biology ,Genes, Mitochondrial ,Salmon shark ,Transfer RNA ,Genome, Mitochondrial ,Sharks ,human activities - Abstract
The complete mitochondrial genome of the salmon shark consists of 16,699 bp and includes 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, 1 replication origin region and 1 control region. The mitochondrial gene arrangement of the salmon shark is the same as that of most vertebrates. Base composition of the genome is A (29.6%), T (28.6%), C (27.1%), and G (14.8%).
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- 2014
20. The complete mitochondrial genome of the sand tiger shark, Carcharias taurus (Chondrichthyes, Odontaspididae)
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Rima W. Jabado, Yeong-Shin Lin, Kwang-Tsao Shao, and Chia Hao Chang
- Subjects
Mitochondrial DNA ,Base Composition ,biology ,Zoology ,Sequence Analysis, DNA ,Ribosomal RNA ,biology.organism_classification ,Genome ,Chondrichthyes ,Carcharias ,Mitochondria ,Fishery ,Sand tiger shark ,Genome Size ,Transfer RNA ,Gene Order ,Genome, Mitochondrial ,Genetics ,Sharks ,Animals ,human activities ,Molecular Biology ,Gene - Abstract
The complete mitochondrial genome of the sand tiger shark consists of 16,773 bp and including 13 protein-coding genes, 2 ribosomal RNA, 22 transfer RNA genes, 1 replication origin region and 1 control region. The mitochondrial gene arrangement of the sand tiger shark is the same as the one observed in most vertebrates. Base composition of the genome is A (31.8%), T (28.7%), C (26.3%) and G (13.2%).
- Published
- 2014
21. The complete mitochondrial genome of the shortfin mako, Isurus oxyrinchus (Chondrichthyes, Lamnidae)
- Author
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Kwang-Tsao Shao, Pin Xuan Su, Chia Hao Chang, Hsuan-Ching Ho, An Yi Tsai, and Yeong-Shin Lin
- Subjects
Isurus ,Mitochondrial DNA ,Base Composition ,biology ,Anatomy ,Sequence Analysis, DNA ,Ribosomal RNA ,biology.organism_classification ,Genome ,DNA, Mitochondrial ,Open Reading Frames ,RNA, Transfer ,Seahorse ,Evolutionary biology ,RNA, Ribosomal ,Transfer RNA ,Genome, Mitochondrial ,Genetics ,Lamnidae ,Sharks ,Animals ,Molecular Biology ,Gene - Abstract
The complete mitochondrial genome of the shortfin mako (Isurus oxyrinchus) was determined by using a PCR-based method. The total length of mitochondrial DNA is 16,701 bp and includes 13 protein-coding genes, 2 ribosomal RNA, 22 transfer RNA genes, 1 replication origin region, and 1 control region. The mitochondrial gene arrangement of the tiger tail seahorse is also matching the one observed in the most vertebrate creatures. Base composition of the genome is A (28.8%), T (28.0%), C (28.0%), and G (15.2%) with an A + T rich hallmark as that of other vertebrate mitochondrial genomes.
- Published
- 2013
22. Complete mitochondrial genome of the megamouth shark Megachasma pelagios (Chondrichthyes, Megachasmidae)
- Author
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Nian-Hong Jang-Liaw, Kwang-Tsao Shao, Chia Hao Chang, Yeong-Shin Lin, and Wei-Chuan Chiang
- Subjects
Genetics ,Mitochondrial DNA ,biology ,Molecular Sequence Data ,Vertebrate ,chemical and pharmacologic phenomena ,Genes, rRNA ,Megamouth shark ,Sequence Analysis, DNA ,Ribosomal RNA ,biology.organism_classification ,Chondrichthyes ,Genome ,DNA, Mitochondrial ,Genes, Mitochondrial ,RNA, Transfer ,biology.animal ,Transfer RNA ,Genome, Mitochondrial ,Sharks ,Animals ,human activities ,Molecular Biology ,Gene - Abstract
Here we describe the complete mitochondrial genome sequence of the megamouth shark, Megachasma pelagios, which is an extremely rare species of deepwater shark. The circle genome (16,694 bp) consists of 13 protein coding, 22 tRNA, 2 rRNA genes and 1 control region. It has the typical vertebrate mitochondrial gene arrangement.
- Published
- 2013
23. The complete mitochondrial genome of the big-eye thresher shark, Alopias superciliosus (Chondrichthyes, Alopiidae)
- Author
-
Chia Hao Chang, Yun Chih Liao, Kwang-Tsao Shao, Hsuan-Ching Ho, and Yeong-Shin Lin
- Subjects
Genetics ,Mitochondrial DNA ,Base Composition ,biology ,Molecular Sequence Data ,Proteins ,Replication Origin ,Ribosomal RNA ,biology.organism_classification ,Genome ,law.invention ,RNA, Transfer ,law ,RNA, Ribosomal ,Alopias superciliosus ,Transfer RNA ,Genome, Mitochondrial ,Sharks ,Animals ,Thresher shark ,Molecular Biology ,Gene ,Polymerase chain reaction - Abstract
The complete mitochondrial genome of the big-eye thresher shark was sequenced using a polymerase chain reaction (PCR)-based method. The total length of mitochondrial DNA is 16,719 bp and includes 13 protein-coding genes, 2 ribosomal RNA, 22 transfer RNA genes, 1 replication origin region and 1 control region. The mitochondrial gene arrangement of the big-eye thresher shark is the same as the one observed in the most vertebrates. Base composition of the genome is A (31.8%), T (28.9%), C (25.8%) and G (13.5%).
- Published
- 2013
24. The complete mitochondrial genome of the three-spot seahorse, Hippocampus trimaculatus (Teleostei, Syngnathidae)
- Author
-
Kwang-Tsao Shao, Yeong-Shin Lin, Chia Hao Chang, and Yun Chih Liao
- Subjects
Genetics ,Mitochondrial DNA ,Base Composition ,biology ,RNA ,Proteins ,biology.organism_classification ,Genome ,DNA, Mitochondrial ,Smegmamorpha ,chemistry.chemical_compound ,chemistry ,RNA, Transfer ,Seahorse ,RNA, Ribosomal ,Transfer RNA ,Genome, Mitochondrial ,Hippocampus trimaculatus ,Animals ,Molecular Biology ,Gene ,DNA - Abstract
The complete mitochondrial genome of the three-spot seahorse was sequenced using a polymerase chain reaction-based method. The total length of mitochondrial DNA is 16,535 bp and includes 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. The mitochondrial gene order of the three-spot seahorse also conforms to the distinctive vertebrate mitochondrial gene order. The base composition of the genome is A (32.7%), T (29.3%), C (23.4%), and G (14.6%) with an A + T-rich hallmark as that of other vertebrate mitochondrial genomes.
- Published
- 2013
25. The complete mitochondrial genome of the tiger tail seahorse, Hippocampus comes (Teleostei, Syngnathidae)
- Author
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Nian-Hong Jang-Liaw, Han-Yang Lin, Chia Hao Chang, Hsuan-Ching Ho, Kwang-Tsao Shao, and Yeong-Shin Lin
- Subjects
Genetics ,Mitochondrial DNA ,biology ,RNA ,Proteins ,Ribosomal RNA ,biology.organism_classification ,Genome ,DNA, Mitochondrial ,Smegmamorpha ,RNA, Transfer ,Seahorse ,RNA, Ribosomal ,Transfer RNA ,Hippocampus comes ,Genome, Mitochondrial ,Animals ,Molecular Biology ,Gene - Abstract
The complete mitochondrial genome of the tiger tail seahorse was sequenced using a polymerase chain reaction-based method. The total length of mitochondrial DNA is 16,525 bp and includes 13 protein-coding genes, 2 ribosomal RNA, 22 transfer RNA genes, and a control region. The mitochondrial gene arrangement of the tiger tail seahorse is also matching the one observed in the most vertebrate creatures. Base composition of the genome is A (32.8%), T (29.8%), C (23.0%), and G (14.4%) with an A+T-rich hallmark as that of other vertebrate mitochondrial genomes.
- Published
- 2013
26. Complete mitochondrial genome of the longfin mako shark,Isurus paucus(Chondrichthyes, Lamnidae)
- Author
-
Nian-Hong Jang-Liaw, Yeong-Shin Lin, Kwang-Tsao Shao, Wei Chuan Chiang, and Chia Hao Chang
- Subjects
0301 basic medicine ,Mitochondrial DNA ,Isurus ,Base Sequence ,biology ,Zoology ,Pelagic zone ,Longfin mako ,biology.organism_classification ,DNA, Mitochondrial ,Tropical waters ,Chondrichthyes ,Genome ,Fishery ,03 medical and health sciences ,030104 developmental biology ,RNA, Transfer ,Genome, Mitochondrial ,Sharks ,Genetics ,Lamnidae ,Animals ,Base Pairing ,Molecular Biology - Abstract
Here we describe the complete mitochondrial genome sequence of the longfin mako, Isurus paucus, which is a pelagic shark found in temperate and tropical waters. The circle genome (16,704 bp) consists of 13 protein coding, 22 tRNA, 2 rRNA genes and 1 control region. It has the typical vertebrate mitochondrial gene arrangement.
- Published
- 2014
27. Using a strategy based on the concept of convergent evolution to identify residue substitutions responsible for thermal adaptation
- Author
-
Yeong-Shin Lin
- Subjects
Hot Temperature ,Molecular Sequence Data ,Adaptation, Biological ,Biology ,Biochemistry ,Protein Structure, Secondary ,Conserved sequence ,Evolution, Molecular ,Protein structure ,Structural Biology ,Phylogenetics ,Convergent evolution ,Amino Acid Sequence ,Molecular Biology ,Conserved Sequence ,Phylogeny ,Thermostability ,Phylogenetic tree ,Bacteria ,Ecology ,Protein Stability ,Thermophile ,biology.organism_classification ,Archaea ,Amino Acid Substitution ,Evolutionary biology ,Thermodynamics - Abstract
Factors that are related to thermostability of proteins have been extensively studied in recent years, especially by comparing thermophiles and mesophiles. However, most of them are global characters. It is still not clear how to identify specific residues or fragments which may be more relevant to protein thermostability. Moreover, some of the differences among the thermophiles and mesophiles may be due to phylogenetic differences instead of thermal adaptation. To resolve these problems, I adopted a strategy to identify residue substitutions evolved convergently in thermophiles or mesophiles. These residues may therefore be responsible for thermal adaptation. Four classes of genomes were utilized in this study, including thermophilic archaea, mesophilic archaea, thermophilic bacteria, and mesophilic bacteria. For most clusters of orthologous groups (COGs) with sequences from all of these four classes of genomes, I can identify specific residues or fragments that may potentially be responsible for thermal adaptation. Functional or structural constraints (represented as sequence conservation) were suggested to have higher impact on thermal adaptation than secondary structure or solvent accessibility does. I further compared thermophilic archaea and mesophilic bacteria, and found that the most diverged fragments may not necessarily correspond to the thermostability-determining ones. The usual approach to compare thermophiles and mesophiles without considering phylogenetic relationships may roughly identify sequence features contributing to thermostability; however, to specifically identify residue substitutions responsible for thermal adaptation, one should take sequence evolution into consideration.
- Published
- 2008
28. Codon-usage bias versus gene conversion in the evolution of yeast duplicate genes
- Author
-
Yeong-Shin Lin, Wen-Hsiung Li, Jake K. Byrnes, and Jenn-Kang Hwang
- Subjects
Genetics ,Mutation ,Multidisciplinary ,Concerted evolution ,biology ,Saccharomyces cerevisiae ,Genes, Fungal ,Saccharomyces bayanus ,Biological Sciences ,biology.organism_classification ,medicine.disease_cause ,Codon usage bias ,Gene Duplication ,Yeasts ,Gene duplication ,medicine ,Gene conversion ,Codon ,DNA, Fungal ,Gene ,Phylogeny - Abstract
Many Saccharomyces cerevisiae duplicate genes that were derived from an ancient whole-genome duplication (WGD) unexpectedly show a small synonymous divergence ( K S ), a higher sequence similarity to each other than to orthologues in Saccharomyces bayanus , or slow evolution compared with the orthologue in Kluyveromyces waltii , a non-WGD species. This decelerated evolution was attributed to gene conversion between duplicates. Using ≈300 WGD gene pairs in four species and their orthologues in non-WGD species, we show that codon-usage bias and protein-sequence conservation are two important causes for decelerated evolution of duplicate genes, whereas gene conversion is effective only in the presence of strong codon-usage bias or protein-sequence conservation. Furthermore, we find that change in mutation pattern or in tDNA copy number changed codon-usage bias and increased the K S distance between K. waltii and S. cerevisiae . Intriguingly, some proteins showed fast evolution before the radiation of WGD species but little or no sequence divergence between orthologues and paralogues thereafter, indicating that functional conservation after the radiation may also be responsible for decelerated evolution in duplicates.
- Published
- 2006
29. Protein complexity, gene duplicability and gene dispensability in the yeast genome
- Author
-
Wen-Hsiung Li, Yeong-Shin Lin, and Jenn-Kang Hwang
- Subjects
Genetics ,Models, Genetic ,Protein subunit ,Structural gene ,Computational Biology ,General Medicine ,Biology ,SYT1 ,Article ,Protein Structure, Tertiary ,Fungal Proteins ,SCN3A ,Gene Duplication ,Yeasts ,Gene cluster ,HSPA2 ,Genome, Fungal ,HSPA9 ,TAF15 - Abstract
Using functional genomic and protein structural data we studied the effects of protein complexity (here defined as the number of subunit types in a protein) on gene dispensability and gene duplicability. We found that in terms of gene duplicability the major distinction in protein complexity is between hetero-complexes, each of which includes at least two different types of subunits (polypeptides), and homo-complexes, which include monomers and complexes that consist of only subunits of one polypeptide type. However, gene dispensability decreases only gradually as the number of subunit types in a protein complex increases. These observations suggest that the dosage balance hypothesis can explain well gene duplicability of complex proteins, but cannot completely explain the difference in dispensabilities between hetero-complex subunits. It is likely that knocking out a gene coding for a hetero-complex subunit would disrupt the function of the whole complex, so that the deletion effect on fitness would increase with protein complexity. We also found that multi-domain polypeptide genes are less dispensable but more duplicable than single-domain polypeptide genes. Duplicate genes derived from the whole genome duplication event in yeast are more dispensable (except for ribosomal protein genes) than other duplicate genes. Further, we found that subunits of the same protein complex tend to have similar expression levels and similar effects of gene deletion on fitness. Finally, we estimated that in yeast the contribution of duplicate genes to genetic robustness against null mutation is approximately 9%, smaller than previously estimated. In yeast, protein complexity may serve as a better indicator of gene dispensability than do duplicate genes.
- Published
- 2006
30. The complete mitochondrial genome of theRhodeus shitaiensis(Teleostei, Cypriniformes, Acheilognathidae)
- Author
-
Yeong-Shin Lin, Chia Hao Chang, Kwang-Tsao Shao, and Fan Li
- Subjects
Genetics ,Base Composition ,Mitochondrial DNA ,biology ,Ribosomal RNA ,biology.organism_classification ,Genome ,Cypriniformes ,Open Reading Frames ,Open reading frame ,Genes, Mitochondrial ,Rhodeus shitaiensis ,Genome, Mitochondrial ,Transfer RNA ,Animals ,Molecular Biology ,Gene - Abstract
The complete mitochondrial genome of the Rhodeus shitaiensis was determined by using a PCR-based method. The total length of mitochondrial DNA of this bitterling is 16,774 bp and includes 13 protein-coding genes, 2 ribosomal RNA, 22 transfer RNA genes, 1 replication origin region and 1 control region. The mitochondrial gene arrangement of the R. shitaiensis is also matching the one observed in the most vertebrate creatures. Base composition of the genome is A (28.7%), T (26.5%), C (27.4%) and G (17.4%) with an A + T rich hallmark as that of other vertebrate mitochondrial genomes.
- Published
- 2013
31. The complete mitochondrial genome of the great white shark, Carcharodon carcharias (Chondrichthyes, Lamnidae)
- Author
-
Yi Chiao Fang, Chia Hao Chang, Hsuan-Ching Ho, Yeong-Shin Lin, and Kwang-Tsao Shao
- Subjects
Base Composition ,Mitochondrial DNA ,food.ingredient ,biology ,Sequence Analysis, DNA ,Anatomy ,Ribosomal RNA ,biology.organism_classification ,Genome ,Carcharodon ,Great white shark ,Genes, Mitochondrial ,food ,Evolutionary biology ,biology.animal ,Gene Order ,Genome, Mitochondrial ,Transfer RNA ,Sharks ,Genetics ,Lamnidae ,Animals ,human activities ,Molecular Biology ,Gene - Abstract
The complete mitochondrial genome of the great white shark having 16,744 bp and including 13 protein-coding genes, 2 ribosomal RNA, 22 transfer RNA genes, 1 replication origin region and 1 control region. The mitochondrial gene arrangement of the great white shark is the same as the one observed in the most vertebrates. Base composition of the genome is A (30.6%), T (28.7%), C (26.9%) and G (13.9%).
- Published
- 2013
32. Prediction of the bonding states of cysteines using the support vector machines based on multiple feature vectors and cysteine state sequences
- Author
-
Jenn-Kang Hwang, Yu Ching Chen, Chih-Jen Lin, and Yeong-Shin Lin
- Subjects
chemistry.chemical_classification ,business.industry ,Feature vector ,information science ,Computational Biology ,Proteins ,Pattern recognition ,State (functional analysis) ,Matthews correlation coefficient ,Biochemistry ,Amino acid ,Data set ,Support vector machine ,Local sequence ,chemistry ,Structural Biology ,Sequence Analysis, Protein ,Cystine ,Artificial intelligence ,Cysteine ,Amino Acids ,business ,Molecular Biology ,Mathematics - Abstract
The support vector machine (SVM) method is used to predict the bonding states of cysteines. Besides using local descriptors such as the local sequences, we include global information, such as amino acid compositions and the patterns of the states of cysteines (bonded or nonbonded), or cysteine state sequences, of the proteins. We found that SVM based on local sequences or global amino acid compositions yielded similar prediction accuracies for the data set comprising 4136 cysteine-containing segments extracted from 969 nonhomologous proteins. However, the SVM method based on multiple feature vectors (combining local sequences and global amino acid compositions) significantly improves the prediction accuracy, from 80% to 86%. If coupled with cysteine state sequences, SVM based on multiple feature vectors yields 90% in overall prediction accuracy and a 0.77 Matthews correlation coefficient, around 10% and 22% higher than the corresponding values obtained by SVM based on local sequence information.
- Published
- 2004
33. A phylogeny of freshwater eels inferred from mitochondrial genes
- Author
-
Chyng-Shyan Tzeng, Yeong-Shin Lin, and Yu Ping Poh
- Subjects
Anguilla rostrata ,Phylogenetic tree ,biology ,Cytochrome b ,Ecology ,Molecular Sequence Data ,Zoology ,Sequence Analysis, DNA ,Subspecies ,biology.organism_classification ,Anguilla ,Cytochrome b Group ,DNA, Mitochondrial ,Dorsal fin ,Evolution, Molecular ,Anguillidae ,Phylogenetics ,RNA, Ribosomal ,Genetics ,Animals ,Japanese eel ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Phylogeny - Abstract
The genus Anguilla Shaw of Family Anguillidae consists entirely of freshwater eels, including 15 species and 2 subspecies. Conventionally, variegated markings and the length of the dorsal fin are the major morphological features used for reconstruction of phylogenetic relationships. The evolutionary history of these species remains unclear, especially for the Atlantic eels, whose habitats are far from the Metropolis in the Indo-Pacific region. This study reexamined the phylogenetic relationships of 12 Anguilla species by sequencing of the cytochrome b and 12S rRNA genes. In our analysis, species bearing similar coloration patterns or dorsal fin morphology are not necessarily clustered in the same clade, indicating that these morphological features might be unstable or might have occurred independently in different lineages during evolution. Combining our molecular data and geographical evidence, we speculate that (1) Anguilla first radiated about 20 million years ago, (2) the ancestors of Atlantic eels did not migrate by drifting through the Tethys Seaway at the leptocephali stage but instead trekked across the Central American Isthmus to the Sargasso Sea for spawning at the adult stage, and (3) multiple radiation events had occurred at the Metropolis during Anguilla evolution.
- Published
- 2001
34. A simple method using PyrosequencingTM to identify de novo SNPs in pooled DNA samples
- Author
-
Wei Ting Chang, Cheng Tsung Pan, Yeong-Shin Lin, Tzi-Yuan Wang, Fu Guo Robert Liu, and Wen-Hsiung Li
- Subjects
Genetics ,Single-nucleotide polymorphism ,Sequence Analysis, DNA ,Biology ,Polymorphism, Single Nucleotide ,Diphosphates ,chemistry.chemical_compound ,chemistry ,Gene Frequency ,Polymorphism (computer science) ,Pyrosequencing ,SNP ,Methods Online ,Computer Simulation ,Pooled dna ,Allele ,Allele frequency ,DNA ,Algorithms - Abstract
A practical way to reduce the cost of surveying single-nucleotide polymorphism (SNP) in a large number of individuals is to measure the allele frequencies in pooled DNA samples. Pyrosequencing(TM) has been frequently used for this application because signals generated by this approach are proportional to the amount of DNA templates. The Pyrosequencing(TM) pyrogram is determined by the dispensing order of dNTPs, which is usually designed based on the known SNPs to avoid asynchronistic extensions of heterozygous sequences. Therefore, utilizing the pyrogram signals to identify de novo SNPs in DNA pools has never been undertook. Here, in this study we developed an algorithm to address this issue. With the sequence and pyrogram of the wild-type allele known in advance, we could use the pyrogram obtained from the pooled DNA sample to predict the sequence of the unknown mutant allele (de novo SNP) and estimate its allele frequency. Both computational simulation and experimental Pyrosequencing(TM) test results suggested that our method performs well. The web interface of our method is available at http://life.nctu.edu.tw/∼yslin/PSM/.
- Published
- 2010
35. Authenticating the use of dried seahorses in the traditional Chinese medicine market in Taiwan using molecular forensics
- Author
-
Nian-Hong Jang-Liaw, Yeong-Shin Lin, Chia Hao Chang, Yi Chiao Fang, and Kwang-Tsao Shao
- Subjects
Pharmacology ,biology ,Traditional medicine ,Hippocampus spinosissimus ,Zoology ,Hippocampus kuda ,Hippocampus kelloggi ,Molecular forensics ,biology.organism_classification ,IUCN Red List ,Seahorse ,Hippocampus histrix ,nervous system ,Hippocampus comes ,Hippocampus capensis ,Hippocampus trimaculatus ,Food Science - Abstract
Seahorse, which has a unique appearance and exhibits male pregnancy, is a useful component of traditional Chinese medicine (TCM). With the growing demand for TCM, vast amounts of seahorses are harvested from the wild every year and traded internationally. This study investigated 58 dried seahorse samples collected from 23 Chinese herbal medicine stores across Taiwan using molecular forensics. Results showed that eight seahorse species were present in the Taiwan TCM market. Among them, Knysna seahorse (Hippocampus capensis) has an endangered status according to the International Union for Conservation of Nature (IUCN) Red List, while the West African seahorse (Hippocampus algiricus), tiger tail seahorse (Hippocampus comes), thorny seahorse (Hippocampus histrix), great seahorse (Hippocampus kelloggi), yellow seahorse (Hippocampus kuda), hedgehog seahorse (Hippocampus spinosissimus), and three-spot seahorse (Hippocampus trimaculatus) have vulnerable status.
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