32 results on '"Zuozhou Chen"'
Search Results
2. Variation of DNA Methylome of Zebrafish Cells under Cold Pressure.
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Bingshe Han, Wenhao Li, Zuozhou Chen, Qiongqiong Xu, Juntao Luo, Yingdi Shi, Xiaoxia Li, Xiaonan Yan, and Junfang Zhang
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Medicine ,Science - Abstract
DNA methylation is an essential epigenetic mechanism involved in multiple biological processes. However, the relationship between DNA methylation and cold acclimation remains poorly understood. In this study, Methylated DNA Immunoprecipitation Sequencing (MeDIP-seq) was performed to reveal a genome-wide methylation profile of zebrafish (Danio rerio) embryonic fibroblast cells (ZF4) and its variation under cold pressure. MeDIP-seq assay was conducted with ZF4 cells cultured at appropriate temperature of 28°C and at low temperature of 18°C for 5 (short-term) and 30 (long-term) days, respectively. Our data showed that DNA methylation level of whole genome increased after a short-term cold exposure and decreased after a long-term cold exposure. It is interesting that metabolism of folate pathway is significantly hypomethylated after short-term cold exposure, which is consistent with the increased DNA methylation level. 21% of methylation peaks were significantly altered after cold treatment. About 8% of altered DNA methylation peaks are located in promoter regions, while the majority of them are located in non-coding regions. Methylation of genes involved in multiple cold responsive biological processes were significantly affected, such as anti-oxidant system, apoptosis, development, chromatin modifying and immune system suggesting that those processes are responsive to cold stress through regulation of DNA methylation. Our data indicate the involvement of DNA methylation in cellular response to cold pressure, and put a new insight into the genome-wide epigenetic regulation under cold pressure.
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- 2016
- Full Text
- View/download PDF
3. EMS-SLAM: Edge-Assisted Multi-Agent System Simultaneous Localization and Mapping.
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Kai Hu, Lei Zhan, Longhao Zou, Zuozhou Chen, and Gabriel-Miro Muntean
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- 2023
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4. VaBUS: Edge-Cloud Real-Time Video Analytics via Background Understanding and Subtraction.
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Hanling Wang, Qing Li 0006, Heyang Sun, Zuozhou Chen, Yingqian Hao, Junkun Peng, Zhenhui Yuan, Junsheng Fu, and Yong Jiang 0001
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- 2023
- Full Text
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5. Metagenomics revealing molecular profiles of microbial community structure and metabolic capacity in Bamucuo lake, Tibet
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Cai Wei, Dan Sun, Wenliang Yuan, Lei Li, Chaoxu Dai, Zuozhou Chen, Xiaomin Zeng, Shihang Wang, Yuyang Zhang, Shouwen Jiang, Zhichao Wu, Dong Liu, Linhua Jiang, and Sihua Peng
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Biochemistry ,General Environmental Science - Abstract
Microorganisms play critical ecological roles in the global biogeochemical cycles. However, extensive information on the microbial communities in Qinghai-Tibet Plateau (QTP), which is the highest plateau in the world, is still lacking, particularly in high elevation locations above 4500 m. Here, we performed a survey of th e soil and water microbial communities in Bamucuo Lake, Tibet, by using shotgun metagenomic methods. In the soil and water samples, we reconstructed 75 almost complete metagenomic assembly genomes, and 74 of the metagenomic assembly genomes from the water sample represented novel species. Proteobacteria and Actinobacteria were found to be the dominant bacterial phyla, while Euryarchaeota was the dominant archaeal phylum. The largest virus, Pandoravirus salinus, was found in the soil microbial community. We concluded that the microorganisms in Bamucuo Lake are most likely to fix carbon mainly through the 3-hydroxypropionic bi-cycle pathway. This study, for the first time, characterized the microbial community composition and metabolic capacity in QTP high-elevation locations with 4555 m, confirming that QTP is a vast and valuable resource pool, in which many microorganisms can be used to develop new bioactive substances and new antibiotics to which pathogenic microorganisms have not yet developed resistance.
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- 2022
6. A hybrid Bayesian network learning method for constructing gene networks.
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Mingyi Wang, Zuozhou Chen, and Sylvie Cloutier
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- 2007
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7. Mining gene expression databases for local causal relationships using a simple constraint-based algorithm.
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Mingyi Wang, Huijuan Lu, Zuozhou Chen, and Ping Wu
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- 2006
- Full Text
- View/download PDF
8. Metagenomics Revealing Molecular Profiling of Microbial Community Structure and Metabolic Capacity In Bamucuo, Tibet
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Dan Sun, Cai Wei, Xiaoning Peng, Lei Li, Chaoxu Dai, Shouwen Jiang, Linhua Jiang, Sihua peng, Zhichao Wu, Xiaomin Zeng, Wenliang Yuan, Shihang Wang, Yifan Tang, and Zuozhou Chen
- Subjects
Microbial population biology ,Metagenomics ,Profiling (information science) ,Computational biology ,Biology - Abstract
Background: The Qinghai-Tibet Plateau (QTP) is the highest plateau in the world, and the microorganisms there play vital ecological roles in the global biogeochemical cycle; however, detailed information on the microbial communities in QTP is still lacking. Results: Here, we performed a landscape survey of the microorganisms in Bamucuo, Tibet, resulting in 160,212 (soil) and 135,994 (water) contigs by shotgun metagenomic methods, and generated 75 nearly complete metagenome-assembled genomes (MAGs). Proteobacteria, Actinobacteria and Firmicutes were found to be the three most dominant bacterial phyla, while Euryarchaeota was the most dominant archaeal phylum. Surprisingly, Pandoravirus salinus was found in the soil microbial community. The KEGG annotations showed that the genes related to metabolism accounted for 62.9% (soil) and 58.4% (water), respectively. Of the 75 MAGs, 63 were found to contain the genes related to all the six carbon fixation pathways, and the heavy metal resistance genes, the pressure response subsystem, and the secondary metabolite biosynthesis gene clusters (BGCs) were discovered to be abundant. Conclusions: We concluded that the microorganisms in Bamucuo fix carbon mainly through the 3-hydroxypropionic bi-cycle pathway; this study, for the first time, characterized the microbial community composition and metabolic capacity in QTP high-altitude areas (with an altitude of 4,555 meters), confirmed that QTP is a huge and valuable resource bank in which more new non-resistant antibiotics and many other bioactive substances could be developed, and provided the expanded information for further microbial community studies in QTP.
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- 2021
9. Ejector performance analysis under overall operating conditions considering adjustable nozzle structure
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Chaobin Dang, Xu Jin, Zuozhou Chen, and Eiji Hihara
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Test setup ,060102 archaeology ,Computer science ,020209 energy ,Mechanical Engineering ,Antenna aperture ,Nozzle ,Structure (category theory) ,Experimental data ,06 humanities and the arts ,02 engineering and technology ,Building and Construction ,Injector ,law.invention ,Method of characteristics ,law ,Control theory ,0202 electrical engineering, electronic engineering, information engineering ,0601 history and archaeology ,Point (geometry) - Abstract
The variable-geometry ejector (VGE) is feasible for unstable heat-source utilization; the ejector can be adjusted to its design point to obtain high efficiency. Moreover, as the adjustable nozzle in the VGE significantly affects the performance of the ejector, a theoretical model is necessary to evaluate VGE performance. In this study, a two-dimensional theoretical model was proposed based on an adjustable-nozzle theory. Method of characteristics was employed to accurately predict the driving-flow development in the mixing section. In addition, the suction-flow velocity distribution on the effective area was considered. The proposed model was validated by employing the data from literature and additional experimental data obtained from a VGE test setup using R134a. The validation result shows that the proposed model predicts the ejector performance accurately; moreover, the model is more adaptive while the nozzle configuration changes. The theoretical model, proposed herein, is practical for the design and application of the VGE.
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- 2017
10. Effects of the nozzle configuration on solar-powered variable geometry ejectors
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Xu Jin, Chaobin Dang, Eiji Hihara, Akihiko Shimizu, and Zuozhou Chen
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Materials science ,Renewable Energy, Sustainability and the Environment ,business.industry ,020209 energy ,Nozzle ,Flow (psychology) ,Refrigeration ,02 engineering and technology ,Injector ,Mechanics ,Mach wave ,Solar energy ,law.invention ,Physics::Fluid Dynamics ,symbols.namesake ,Mach number ,law ,0202 electrical engineering, electronic engineering, information engineering ,symbols ,General Materials Science ,Variable geometry ,business - Abstract
The variable geometry ejector (VGE) used in solar-powered ejector refrigeration systems enables performance regulation with unstable heat input, which is important in solar energy utilization; however, the ejector performance is significantly affected by the nozzle configuration. To study the effects of the nozzle configuration on the VGE and to optimize the VGE configuration, experimental investigations are conducted on a supersonic nozzle and a subsonic nozzle used in the VGE under a variety of operating conditions. The experimental results show a close relationship between the driving flow behavior and the ejector performance. The driving flow behavior is influenced by the occurrence of Mach waves, which is significantly influenced by the nozzle configuration. Numerical simulations are conducted that further explain the Mach wave behavior as well as the driving flow development inside the VGE. The results are significant for the optimization and application of the variable geometry ejector in solar-powered ejector refrigeration systems.
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- 2017
11. Investigations on driving flow expansion characteristics inside ejectors
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Chaobin Dang, Zuozhou Chen, and Eiji Hihara
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Fluid Flow and Transfer Processes ,Materials science ,020209 energy ,Mechanical Engineering ,Heat pump and refrigeration cycle ,Flow (psychology) ,Nozzle ,Boundary (topology) ,02 engineering and technology ,Mechanics ,Injector ,021001 nanoscience & nanotechnology ,Condensed Matter Physics ,Mach wave ,law.invention ,Physics::Fluid Dynamics ,Method of characteristics ,law ,Schlieren ,0202 electrical engineering, electronic engineering, information engineering ,0210 nano-technology - Abstract
This research investigates the Mach wave structure of the driving flow under off-design working conditions by both numerical and experimental methods. By adopting the method of characteristics as the simulation model, prediction of the driving flow regime inside an ejector is obtained. The simulation results are further validated by an experimental visualization method conducted using a Schlieren system. Through this investigation, the influence of Mach wave on the driving flow boundary development is discussed. The expansion wave from the nozzle exit increases the driving flow regime in the under-expanded condition, which has a negative impact on ejector performance. The results show that the Mach wave should be considered when the ejector is operated under off-design working conditions. The results also demonstrate that an appropriate nozzle structure design was able to restrain the effect of the expansion wave, which improves ejector performance. The results are significant for achieving a comprehensive understanding of the mechanism of an ejector, as well as for the applications, such as ejection refrigeration cycles.
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- 2017
12. The gene repressor complex NuRD interacts with the histone variant H3.3 at promoters of active genes
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Zuozhou Chen, Junfang Zhang, Keji Zhao, Qingsong Tang, Kairong Cui, and Daniel C. Kraushaar
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0301 basic medicine ,Multiprotein complex ,Repressor ,Epigenesis, Genetic ,Histones ,03 medical and health sciences ,Mice ,Genetics ,Nucleosome ,Histone code ,Animals ,Epigenetics ,Genetics (clinical) ,Regulation of gene expression ,Binding Sites ,biology ,Research ,3T3 Cells ,Cell biology ,Histone Code ,030104 developmental biology ,Histone ,Regulatory sequence ,biology.protein ,Mi-2 Nucleosome Remodeling and Deacetylase Complex ,Protein Binding - Abstract
The histone variant H3.3 is deposited across active genes, regulatory regions, and telomeres. It remains unclear how H3.3 interacts with chromatin modifying enzymes and thereby modulates gene activity. In this study, we performed a co-immunoprecipitation-mass spectrometry analysis of proteins associated with H3.3-containing nucleosomes and identified the nucleosome remodeling and deacetylase complex (NuRD) as a major H3.3-interactor. We show that the H3.3-NuRD interaction is dependent on the H3.3 lysine 4 residue and that NuRD binding occurs when lysine 4 is in its unmodified state. The majority of NuRD binding colocalizes with H3.3 and directly correlates with gene activity. H3.3 depletion led to reduced levels of NuRD at sites previously occupied by H3.3, as well as a global decrease in histone marks associated with gene activation. Our results demonstrate the importance of H3.3 in the maintenance of the cellular epigenetic landscape and reveal a highly prevalent interaction between the histone variant H3.3 and the multiprotein complex NuRD.
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- 2018
13. Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing.
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Cristian Coarfa, Fuli Yu, Christopher A. Miller 0003, Zuozhou Chen, R. Alan Harris, and Aleksandar Milosavljevic
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- 2010
- Full Text
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14. GO-Diff: Mining functional differentiation between EST-based transcriptomes.
- Author
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Zuozhou Chen, Weilin Wang, Xuefeng Bruce Ling, Jane Jijun Liu, and Liangbiao Chen
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- 2006
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15. Evolutionary suppression of erythropoiesis via the modulation of TGF-β signalling in an Antarctic icefish
- Author
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Xingxing Hu, Zuozhou Chen, Yanan Guo, Jiulin Chan, Shouwen Jiang, Qianghua Xu, Peng Hu, Zhichao Wu, Yun Liu, Dongsheng Zhang, Shihua Peng, Liangbiao Chen, and Chang Cai
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Antarctic Regions ,Notothenioidei ,Transforming Growth Factor beta ,Chionodraco hamatus ,Genetics ,Animals ,Erythropoiesis ,Selection, Genetic ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,biology ,Sequence Analysis, RNA ,Transforming growth factor beta ,Endoglin ,biology.organism_classification ,Biological Evolution ,Channichthyidae ,Perciformes ,TGF-beta Superfamily Proteins ,MicroRNAs ,Haematopoiesis ,biology.protein ,GATA transcription factor ,Transcriptome ,Signal Transduction - Abstract
The Antarctic icefish, a family (Channichthyidae) of teleosts within the perciform suborder Notothenioidei, are the only known vertebrates without oxygen-transporting haemoglobins and that are largely devoid of circulating erythrocytes. To elucidate the evo-devo mechanisms underpinning the suppressed erythropoiesis in the icefish, we conducted comparative studies on the transcriptomes and microRNAomes of the primary haematopoietic tissues between an icefish (Chionodraco hamatus) and two red-blooded notothenioids (Trematomus bernacchii and Gymnodraco acuticeps). We identified substantial remodelling of the haematopoietic programs in the icefish through which erythropoiesis is selectively suppressed. Experimental verification showed that erythropoietic suppression in the icefish may be attributable to the upregulation of TGF-β signalling, which coincides with reductions in multiple transcription factors essential for erythropoiesis and the upregulation of hundreds of microRNAs, the majority (> 80%) of which potentially target erythropoiesis regulating factors. Of the six microRNAs selected for verification, three miRNAs (miR-152, miR-1388 and miR-16b) demonstrated suppressive functions on GATA1 and ALAS2, which are two factors important for erythroid differentiation, resulting in reduced numbers of erythroids in microinjected zebra fish embryos. Codon substitution analyses of the genes of the TGF-β superfamily revealed signs of positive selection in TGF-β1 and endoglin in the lineages leading to Antarctic notothenioids. Both genes are previously known to function in erythropoietic suppression. These findings implied a general trend of erythropoietic suppression in the cold-adapted notothenioid lineages through evolutionary modulation of the multi-functional TGF-β signalling pathway. This trend is more pronounced in the haemoglobin-less icefish, which may pre-emptively hinder the otherwise defective erythroids from production.
- Published
- 2015
16. Investigation on a two-stage ejection refrigeration system
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Yijian He, Zuozhou Chen, Liming Tang, and Guangming Chen
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Materials science ,Control theory ,law ,Heat pump and refrigeration cycle ,Nuclear engineering ,Energy Engineering and Power Technology ,Refrigeration ,Context (language use) ,Stage (hydrology) ,Injector ,Industrial and Manufacturing Engineering ,law.invention ,Power (physics) - Abstract
Working under high condensing or low evaporating temperatures, a two-stage ejection refrigeration system is presented in order to effectively utilize low-grade heat in this context. The performance of the two-stage ejection refrigeration system is investigated under generating temperatures from 130 to 150 °C, condensing temperatures of 45–54 °C and evaporating temperatures from 6 to 30 °C. The experimental results show that the presented two-stage ejection refrigeration system can operate normally under a condensing temperature of 54 °C, which is higher than the normal condensing temperatures of a single-stage ejection refrigeration system. However, the extra power input to drive the 2nd ejector make such a system less efficient under condensing temperatures below 50 °C. Under those circumstances, through adjustment of operational strategies, an ejection refrigeration system should choose using single-stage ejector or two-stage ejector for different operational conditions, which greatly extends the application range of ejection refrigeration systems.
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- 2015
17. Variation of DNA Methylome of Zebrafish Cells under Cold Pressure
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Junfang Zhang, Qiongqiong Xu, Xiaonan Yan, Zuozhou Chen, Bingshe Han, Juntao Luo, Wenhao Li, Xiaoxia Li, and Yingdi Shi
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0301 basic medicine ,Embryo, Nonmammalian ,Acclimatization ,lcsh:Medicine ,Biochemistry ,Promoter Regions, Genetic ,lcsh:Science ,Zebrafish ,Epigenomics ,DNA methylation ,Multidisciplinary ,Fishes ,Animal Models ,Methylation ,Chromatin ,Nucleic acids ,Cold Temperature ,Osteichthyes ,Vertebrates ,Epigenetics ,DNA modification ,Chromatin modification ,Metabolic Networks and Pathways ,Research Article ,Chromosome biology ,Cell biology ,Biology ,Biosynthesis ,Research and Analysis Methods ,Promoter Regions ,03 medical and health sciences ,Model Organisms ,Folic Acid ,Epigenetics of physical exercise ,Genetics ,Cold acclimation ,Animals ,Gene Regulation ,Methylated DNA immunoprecipitation ,Biology and life sciences ,lcsh:R ,Organisms ,DNA ,Molecular biology ,Gene Ontology ,030104 developmental biology ,lcsh:Q ,Gene expression - Abstract
DNA methylation is an essential epigenetic mechanism involved in multiple biological processes. However, the relationship between DNA methylation and cold acclimation remains poorly understood. In this study, Methylated DNA Immunoprecipitation Sequencing (MeDIP-seq) was performed to reveal a genome-wide methylation profile of zebrafish (Danio rerio) embryonic fibroblast cells (ZF4) and its variation under cold pressure. MeDIP-seq assay was conducted with ZF4 cells cultured at appropriate temperature of 28°C and at low temperature of 18°C for 5 (short-term) and 30 (long-term) days, respectively. Our data showed that DNA methylation level of whole genome increased after a short-term cold exposure and decreased after a long-term cold exposure. It is interesting that metabolism of folate pathway is significantly hypomethylated after short-term cold exposure, which is consistent with the increased DNA methylation level. 21% of methylation peaks were significantly altered after cold treatment. About 8% of altered DNA methylation peaks are located in promoter regions, while the majority of them are located in non-coding regions. Methylation of genes involved in multiple cold responsive biological processes were significantly affected, such as anti-oxidant system, apoptosis, development, chromatin modifying and immune system suggesting that those processes are responsive to cold stress through regulation of DNA methylation. Our data indicate the involvement of DNA methylation in cellular response to cold pressure, and put a new insight into the genome-wide epigenetic regulation under cold pressure.
- Published
- 2016
18. Relationships among persistence of Bacillus thuringiensis and Cowpea trypsin inhibitor proteins, microbial properties and enzymatic activities in rhizosphere soil after repeated cultivation with transgenic cotton
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Zuozhou Chen, Lanzhou Chen, and Zhaoxiang Wu
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chemistry.chemical_classification ,Rhizosphere ,Ecology ,Transgene ,Trypsin inhibitor ,Soil Science ,Biology ,biology.organism_classification ,Agricultural and Biological Sciences (miscellaneous) ,Persistence (computer science) ,Enzyme ,Cry1Ac ,Agronomy ,chemistry ,Bacillus thuringiensis ,Insecticidal crystal proteins - Abstract
a b s t r a c t We evaluated the effect of transgenic cottons (Bacillus thuringiensis (Bt) and Bt with cowpea trypsin inhibitor (Bt-CpTI)) on soil ecosystems after three and four years of growth. The persistence and the rela- tionships among insecticidal crystal proteins 1Ac (Cry1Ac) and cowpea trypsin inhibitor (CpTI) proteins derived from transgenic cottons, microbial properties, and enzymatic activities in the rhizosphere soil were investigated in the repeated cultivation experiment. The Cry1Ac and CpTI proteins persisted in the rhizosphere soil of transgenic cotton, whereas no proteins were detected in the rhizosphere soil of non- transgenic cotton. The persistence of CpTI inhibited the degradation of Cry1Ac protein in the rhizosphere soil of Bt-CpTI cotton. Repeated measures analysis of variance indicated that the year of cultivation, the variety of cotton, the transgenic trait, and their interactions significantly influenced the microbial proper- ties and the enzymatic activities in rhizosphere soil. Overall, the repeated cultivation of transgenic cotton had significantly negative effects on the microbial properties and the enzymatic activities in rhizosphere soil compared to those in the rhizosphere soil of non-transgenic cotton.
- Published
- 2012
19. A gene family-based method for interspecies comparisons of sequencing-based transcriptomes and its use in environmental adaptation analysis
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Zuozhou Chen, Hua Ye, Liangbiao Chen, C.-H. Christina Cheng, and Longhai Zhou
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Expressed Sequence Tags ,Fish Proteins ,Genetics ,Protein family ,Gene Expression Profiling ,Adaptation, Biological ,Chromosome Mapping ,Environmental adaptation ,Computational biology ,Biology ,biology.organism_classification ,Notothenia angustata ,Perciformes ,Transcriptome ,Multigene Family ,Animals ,Gene family ,Perl ,Family based ,Molecular Biology ,computer ,Gene ,Ecosystem ,computer.programming_language - Abstract
We describe a new method for sequencing-based cross-species transcriptome comparisons and define a new metric for evaluating gene expression across species using protein-coding families as units of comparison. Using this measure transcriptomes from different species were evaluated by mapping them to gene families and integrating the mapping results with expression data. Statistical tests were applied to the transcriptome evaluation results to identify differentially expressed families. A Perl program named Pro-Diff was compiled to implement this method. To evaluate the method and provide an example of its use, two liver EST transcriptomes from two closely related fish that live in different temperature zones were compared. One EST library was from a recent sequencing project of Dissosticus mawsoni, a fish that lives in cold Antarctic sea waters, while the other was newly sequenced data (available at: http://www.fishgenome.org/ polarbank/) from Notothenia angustata, a species that lives in temperate near-shore water of southern New Zealand. Results from the comparison were consistent with results inferred from phenotype differences and also with our previously published Gene Ontology-based method. The Pro-Diff program and operation manual can be downloaded from: http://www.fishgenome.org/download/Prodiff.rar.
- Published
- 2010
20. Adaptive Evolution of Hepcidin Genes in Antarctic Notothenioid Fishes
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Yu Shen, Hua Ye, Peng Hu, Zuozhou Chen, C.-H. Christina Cheng, Lei Chen, Lixue Cao, Liangbiao Chen, and Qianghua Xu
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Fish Proteins ,inorganic chemicals ,congenital, hereditary, and neonatal diseases and abnormalities ,DNA, Complementary ,Molecular Sequence Data ,Adaptation, Biological ,Gene Expression ,Biology ,digestive system ,Eelpout ,Evolution, Molecular ,Hepcidins ,Phylogenetics ,Hepcidin ,hemic and lymphatic diseases ,Freezing ,Gene duplication ,Gene expression ,Genetics ,Animals ,Amino Acid Sequence ,Cysteine ,Molecular Biology ,Gene ,Peptide sequence ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,nutritional and metabolic diseases ,Blotting, Northern ,biology.organism_classification ,Perciformes ,biology.protein ,RNA ,Adaptation ,Antimicrobial Cationic Peptides - Abstract
Hepcidin is a small bioactive peptide with dual roles as an antimicrobial peptide and as the principal hormonal regulator of iron homeostasis in human and mouse. Hepcidin homologs of very similar structures are found in lower vertebrates, all comprise approximately 20-25 amino acids with 8 highly conserved cysteines forming 4 intramolecular disulfide bonds, giving hepcidin a hairpin structure. Hepcidins are particularly diverse in teleost fishes, which may be related to the diversity of aquatic environments with varying degree of pathogen challenge, oxygenation, and iron concentration, factors known to alter hepcidin expression in mammals. We characterized the diversity of hepcidin genes of the Antarctic notothenioid fishes that are endemic to the world's coldest and most oxygen-rich marine water. Notothenioid fishes have at least 4 hepcidin variants, in 2 distinctive structural types. Type I hepcidins comprise 3 distinct variants that are homologs of the widespread 8-cysteine hepcidins. Type II is a novel 4-cysteine variant and therefore only 2 possible disulfide bonds, highly expressed in hematopoietic tissues. Analyses of d(N)/d(S) substitution rate ratios and likelihood ratio test under site-specific models detected significant signal of positive Darwinian selection on the mature hepcidin-coding sequence, suggesting adaptive evolution of notothenioid hepcidins. Genomic polymerase chain reaction and Southern hybridization showed that the novel type II hepcidin occurs exclusively in lineages of the Antarctic notothenioid radiation but not in the basal non-Antarctic taxa, and lineage-specific positive selection was detected on the branch leading to the type II hepcidin clade under branch-site models, suggesting adaptive evolution of the reduced cysteine variant in response to the polar environment. We also isolated a structurally distinct 4-cysteine (4cys) hepcidin from an Antarctic eelpout that is unrelated to the notothenioids but inhabits the same freezing water. Neighbor-Joining (NJ) analyses of teleost hepcidins showed that the eelpout 4cys variant arose independently from the notothenioid version, which lends support to adaptive evolution of reduced cysteine hepcidin variants on cold selection. The NJ tree also showed taxonomic-specific expansions of hepcidin variants, indicating that duplication and diversification of hepcidin genes play important roles in evolutionary response to diverse ecological conditions.
- Published
- 2008
21. MINING GENE EXPRESSION DATABASES FOR LOCAL CAUSAL RELATIONSHIPS USING A SIMPLE CONSTRAINT-BASED ALGORITHM
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Zuozhou Chen, Huijuan Lu, Mingyi Wang, and Ping Wu
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Database ,Computer science ,Bayesian network ,Causal structure ,computer.software_genre ,Expression (mathematics) ,Data set ,Constraint (information theory) ,Artificial Intelligence ,Sample size determination ,Simple (abstract algebra) ,Computer Vision and Pattern Recognition ,Data mining ,Heuristics ,computer ,Software - Abstract
There is great potential in mining gene expression microarray databases to discover causal relationships in the gene-regulation pathway. Several methods using Bayesian networks have been reported. Most of them use a heuristics search based on the criteria for choosing a network, but these methods are often computationally intractable for microarray data with thousands of genes. In this work, a simple constrained-based, local causal discovery method is presented. This method is computationally feasible but does not attempt to discover complete causal structure. To show the effectiveness of this method, we have conducted simulations and applied this method to the data set from Hughes et al. from 300 expression profiles of yeast. Using this method, results of simulation data tests demonstrated that the accuracy ratios of causal relationships became higher when the sample size increased. From the yeast data set, a number of causal relations were found. A cursory analysis shows some of the relations have biological sense, others need further investigation.
- Published
- 2006
22. Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing
- Author
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Christopher A. Miller, Fuli Yu, Aleksandar Milosavljevic, R. Alan Harris, Cristian Coarfa, and Zuozhou Chen
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Epigenomics ,Bisulfite sequencing ,Computational biology ,Biology ,lcsh:Computer applications to medicine. Medical informatics ,Polymorphism, Single Nucleotide ,Biochemistry ,Genome ,DNA sequencing ,03 medical and health sciences ,0302 clinical medicine ,Structural Biology ,Databases, Genetic ,Indel ,lcsh:QH301-705.5 ,Molecular Biology ,Massively parallel ,030304 developmental biology ,Genetics ,0303 health sciences ,Massive parallel sequencing ,Base Sequence ,Applied Mathematics ,Genetic Variation ,DNA ,Sequence Analysis, DNA ,Computer Science Applications ,lcsh:Biology (General) ,030220 oncology & carcinogenesis ,lcsh:R858-859.7 ,DNA microarray ,Software - Abstract
Background Massively parallel sequencing readouts of epigenomic assays are enabling integrative genome-wide analyses of genomic and epigenomic variation. Pash 3.0 performs sequence comparison and read mapping and can be employed as a module within diverse configurable analysis pipelines, including ChIP-Seq and methylome mapping by whole-genome bisulfite sequencing. Results Pash 3.0 generally matches the accuracy and speed of niche programs for fast mapping of short reads, and exceeds their performance on longer reads generated by a new generation of massively parallel sequencing technologies. By exploiting longer read lengths, Pash 3.0 maps reads onto the large fraction of genomic DNA that contains repetitive elements and polymorphic sites, including indel polymorphisms. Conclusions We demonstrate the versatility of Pash 3.0 by analyzing the interaction between CpG methylation, CpG SNPs, and imprinting based on publicly available whole-genome shotgun bisulfite sequencing data. Pash 3.0 makes use of gapped k-mer alignment, a non-seed based comparison method, which is implemented using multi-positional hash tables. This allows Pash 3.0 to run on diverse hardware platforms, including individual computers with standard RAM capacity, multi-core hardware architectures and large clusters.
- Published
- 2010
23. Characterization of microRNAs in cephalochordates reveals a correlation between microRNA repertoire homology and morphological similarity in chordate evolution
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Zuozhou Chen, Hua Ye, Liangbiao Chen, Longhai Zhou, Zhonghua Dai, Yi-Quan Wang, Lixue Cao, and Sihua Peng
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Morphological similarity ,Molecular Sequence Data ,Sequence Homology ,ComputingMilieux_LEGALASPECTSOFCOMPUTING ,Chordate ,Homology (biology) ,Evolution, Molecular ,Species Specificity ,Chordata, Nonvertebrate ,microRNA ,ComputingMilieux_COMPUTERSANDEDUCATION ,Natural science ,Animals ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,DNA Primers ,Gene Library ,Genetics ,biology ,Base Sequence ,Reverse Transcriptase Polymerase Chain Reaction ,Repertoire ,Computational Biology ,Sequence Analysis, DNA ,biology.organism_classification ,Blotting, Northern ,ComputingMilieux_GENERAL ,MicroRNAs ,Evolutionary biology ,Christian ministry ,Developmental Biology - Abstract
Cephalochordates, urochordates, and vertebrates comprise the three extant groups of chordates. Although higher morphological and developmental similarity exists between cephalochordates and vertebrates, molecular phylogeny studies have instead suggested that the morphologically simplified urochordates are the closest relatives to vertebrates. MicroRNAs (miRNAs) are regarded as the major factors driving the increase of morphological complexity in early vertebrate evolution, and are extensively characterized in vertebrates and in a few species of urochordates. However, the comprehensive set of miRNAs in the basal chordates, namely the cephalochordates, remains undetermined. Through extensive sequencing of a small RNA library and genomic homology searches, we characterized 100 miRNAs from the cephalochordate amphioxus, Branchiostoma japonicum, and B. floridae. Analysis of the evolutionary history of the cephalochordate miRNAs showed that cephalochordates possess 54 miRNA families homologous to those of vertebrates, which is threefold higher than those shared between urochordates and vertebrates. The miRNA contents demonstrated a clear correlation between the extent of miRNA overlapping and morphological similarity among the three chordate groups, providing a strong evidence of miRNAs being the major genetic factors driving morphological complexity in early chordate evolution.
- Published
- 2009
24. Transcriptomic and genomic evolution under constant cold in Antarctic notothenioid fish
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Lei Chen, Zuozhou Chen, C.-H. Christina Cheng, Liangbiao Chen, Shouhong Sun, Hua Ye, Peng Hu, Zhonghua Dai, Lixue Cao, Junfang Zhang, Cheng Deng, Longhai Zhou, Yudong Jin, Yu Shen, and Qianghua Xu
- Subjects
Comparative genomics ,Genetics ,Genome evolution ,Tropical Climate ,Multidisciplinary ,Genome ,Hot Temperature ,Protein family ,Gene Expression Profiling ,Molecular Sequence Data ,Fishes ,Antarctic Regions ,Biology ,Biological Sciences ,Gene expression profiling ,Cold Temperature ,Evolution, Molecular ,Gene Duplication ,Gene duplication ,Gene family ,Animals ,Seawater ,Gene - Abstract
The antifreeze glycoprotein-fortified Antarctic notothenioid fishes comprise the predominant fish suborder in the isolated frigid Southern Ocean. Their ecological success undoubtedly entailed evolutionary acquisition of a full suite of cold-stable functions besides antifreeze protection. Prior studies of adaptive changes in these teleost fishes generally examined a single genotype or phenotype. We report here the genome-wide investigations of transcriptional and genomic changes associated with Antarctic notothenioid cold adaptation. We sequenced and characterized 33,560 ESTs from four tissues of the Antarctic notothenioid Dissostichus mawsoni and derived 3,114 nonredundant protein gene families and their expression profiles. Through comparative analyses of same-tissue transcriptome profiles of D. mawsoni and temperate/tropical teleost fishes, we identified 177 notothenioid protein families that were expressed many fold over the latter, indicating cold-related up-regulation. These up-regulated gene families operate in protein biosynthesis, protein folding and degradation, lipid metabolism, antioxidation, antiapoptosis, innate immunity, choriongenesis, and others, all of recognizable functional importance in mitigating stresses in freezing temperatures during notothenioid life histories. We further examined the genomic and evolutionary bases for this expressional up-regulation by comparative genomic hybridization of DNA from four pairs of Antarctic and basal non-Antarctic notothenioids to 10,700 D. mawsoni cDNA probes and discovered significant to astounding (3- to >300-fold, P < 0.05) Antarctic-specific duplications of 118 protein-coding genes, many of which correspond to the up-regulated gene families. Results of our integrative tripartite study strongly suggest that evolution under constant cold has resulted in dramatic genomic expansions of specific protein gene families, augmenting gene expression and gene functions contributing to physiological fitness of Antarctic notothenioids in freezing polar conditions.
- Published
- 2008
25. A hybrid Bayesian network learning method for constructing gene networks
- Author
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Sylvie Cloutier, Zuozhou Chen, and Mingyi Wang
- Subjects
Dependency (UML) ,Computer science ,Gene regulatory network ,Scale (descriptive set theory) ,Saccharomyces cerevisiae ,Machine learning ,computer.software_genre ,Biochemistry ,Bayes' theorem ,Structural Biology ,Artificial Intelligence ,Gene Expression Regulation, Fungal ,Computer Simulation ,Gene Regulatory Networks ,Oligonucleotide Array Sequence Analysis ,business.industry ,Gene Expression Profiling ,Organic Chemistry ,Cell Cycle ,Bayesian network ,Computational Biology ,Bayes Theorem ,Constraint (information theory) ,Gene expression profiling ,Computational Mathematics ,Metric (mathematics) ,Data mining ,Artificial intelligence ,business ,computer ,Algorithms - Abstract
A Bayesian network (BN) is a knowledge representation formalism that has proven to be a promising tool for analyzing gene expression data. Several problems still restrict its successful applications. Typical gene expression databases contain measurements for thousands of genes and no more than several hundred samples, but most existing BNs learning algorithms do not scale more than a few hundred variables. Current methods result in poor quality BNs when applied in such high-dimensional datasets. We propose a hybrid constraint-based scored-searching method that is effective for learning gene networks from DNA microarray data. In the first phase of this method, a novel algorithm is used to generate a skeleton BN based on dependency analysis. Then the resulting BN structure is searched by a scoring metric combined with the knowledge learned from the first phase. Computational tests have shown that the proposed method achieves more accurate results than state-of-the-art methods. This method can also be scaled beyond datasets with several hundreds of variables.
- Published
- 2007
26. Trehalose as a good candidate for enriching full-length cDNAs in cDNA library construction
- Author
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Liangbiao Chen, Longhai Zhou, Yu Shen, Cheng Deng, Zuozhou Chen, Yudong Jing, Lixue Cao, and Lei Chen
- Subjects
DNA, Complementary ,Sequence analysis ,cDNA library ,Reverse Transcriptase Polymerase Chain Reaction ,Fishes ,Trehalose ,Bioengineering ,Context (language use) ,CDNA Library Construction ,General Medicine ,Biology ,Applied Microbiology and Biotechnology ,Molecular biology ,Reverse transcriptase ,chemistry.chemical_compound ,Biochemistry ,chemistry ,Complementary DNA ,Animals ,Cloning, Molecular ,Biotechnology ,Thermostability ,Gene Library - Abstract
It has been reported that the disaccharide trehalose is capable of increasing the thermostability and thermoactivity of reverse transcriptase, and therefore improving the length of cDNA synthesis. However, no test has been done on how the disaccharide trehalose performs in the context of the entire cDNA synthesis processes, or whether it can seamlessly integrate into the commercially available cDNA synthesis kit. In this report, we optimized a protocol to incorporate trehalose in the Stratagene's cDNA library construction kit in order to demonstrate great improvement in cDNA's length (average length of 1.8 kb in the trehalose group versus 1.0 kb in the control). Sequence analysis of the cDNA clones showed that the addition of trehalose did not increase the error rate of the RT products but greatly increase the quantity of full-length in cDNA library.
- Published
- 2006
27. GO-Diff: Mining functional differentiation between EST-based transcriptomes
- Author
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Xuefeng B. Ling, Zuozhou Chen, Jane Jijun Liu, Liangbiao Chen, and Weilin Wang
- Subjects
Proteome ,Information Storage and Retrieval ,Computational biology ,Biology ,lcsh:Computer applications to medicine. Medical informatics ,Biochemistry ,Transcriptome ,Mice ,Structural Biology ,Gene expression ,Genetics ,Animals ,Databases, Protein ,lcsh:QH301-705.5 ,Molecular Biology ,Gene ,Natural Language Processing ,Oligonucleotide Array Sequence Analysis ,Expressed Sequence Tags ,Expressed sequence tag ,Gene ontology ,Microarray analysis techniques ,Gene Expression Profiling ,Applied Mathematics ,Chromosome Mapping ,Computer Science Applications ,lcsh:Biology (General) ,lcsh:R858-859.7 ,Functional profiling ,DNA microarray ,Software ,Transcription Factors - Abstract
Background Large-scale sequencing efforts produced millions of Expressed Sequence Tags (ESTs) collectively representing differentiated biochemical and functional states. Analysis of these EST libraries reveals differential gene expressions, and therefore EST data sets constitute valuable resources for comparative transcriptomics. To translate differentially expressed genes into a better understanding of the underlying biological phenomena, existing microarray analysis approaches usually involve the integration of gene expression with Gene Ontology (GO) databases to derive comparable functional profiles. However, methods are not available yet to process EST-derived transcription maps to enable GO-based global functional profiling for comparative transcriptomics in a high throughput manner. Results Here we present GO-Diff, a GO-based functional profiling approach towards high throughput EST-based gene expression analysis and comparative transcriptomics. Utilizing holistic gene expression information, the software converts EST frequencies into EST Coverage Ratios of GO Terms. The ratios are then tested for statistical significances to uncover differentially represented GO terms between the compared transcriptomes, and functional differences are thus inferred. We demonstrated the validity and the utility of this software by identifying differentially represented GO terms in three application cases: intra-species comparison; meta-analysis to test a specific hypothesis; inter-species comparison. GO-Diff findings were consistent with previous knowledge and provided new clues for further discoveries. A comprehensive test on the GO-Diff results using series of comparisons between EST libraries of human and mouse tissues showed acceptable levels of consistency: 61% for human-human; 69% for mouse-mouse; 47% for human-mouse. Conclusion GO-Diff is the first software integrating EST profiles with GO knowledge databases to mine functional differentiation between biological systems, e.g. tissues of the same species or the same tissue cross species. With rapid accumulation of EST resources in the public domain and expanding sequencing effort in individual laboratories, GO-Diff is useful as a screening tool before undertaking serious expression studies.
- Published
- 2006
28. Evaluation of Values of Ecosystem Service Function of the Plain Forestry in China.
- Author
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Zhipei, Li, Yuqing, Zhang, Qingke, Zhu, Shiyan, Tian, and Zuozhou, Chen
- Subjects
ECOSYSTEM services ,FORESTS & forestry ,MARKET value ,OPPORTUNITY costs ,RENMINBI ,SOIL conservation - Abstract
Abstract: In this paper, the market value method, shadow engineering method, opportunity cost method, substitute expense method and data of investigate are used to value the ecosystem service functions of the plain forestry in China. The valuation reveals that the total ecological value is estimated up to RMB 3097.49×10
8 Yuan per annum, of which, about RMB 306.77×108 Yuan is of the output of standing trees, about RMB 903.15×108 Yuan of erosion control, about RMB 496.39×108 Yuan of carbon fixation and oxygen production, about RMB 948.41×108 Yuan of air quality purifying, about RMB 393.78×108 Yuan of reducing wind and stabilizing sand, and about RMB 48.98×108 Yuan of recreation and ecotourism. the ecosystem service functions of the plain forestry in China provides the average value of RMB 12346.26 Yuan/(hm2 ·a). Compared to the direct benefits of forest ecosystem, indirect benefits are more important for the survival of human being. [Copyright &y& Elsevier]- Published
- 2011
- Full Text
- View/download PDF
29. Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing.
- Author
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Coarfa, Cristian, Fuli Yu, Miller, Christopher A., Zuozhou Chen, Harris, RAlan, and Milosavljevic, Aleksandar
- Subjects
NUCLEOTIDE sequence ,COMPUTER software ,GENOMICS - Abstract
Background: Massively parallel sequencing readouts of epigenomic assays are enabling integrative genome-wide analyses of genomic and epigenomic variation. Pash 3.0 performs sequence comparison and read mapping and can be employed as a module within diverse configurable analysis pipelines, including ChIP-Seq and methylome mapping by whole-genome bisulfite sequencing. Results: Pash 3.0 generally matches the accuracy and speed of niche programs for fast mapping of short reads, and exceeds their performance on longer reads generated by a new generation of massively parallel sequencing technologies. By exploiting longer read lengths, Pash 3.0 maps reads onto the large fraction of genomic DNA that contains repetitive elements and polymorphic sites, including indel polymorphisms. Conclusions: We demonstrate the versatility of Pash 3.0 by analyzing the interaction between CpG methylation, CpG SNPs, and imprinting based on publicly available whole-genome shotgun bisulfite sequencing data. Pash 3.0 makes use of gapped k-mer alignment, a non-seed based comparison method, which is implemented using multipositional hash tables. This allows Pash 3.0 to run on diverse hardware platforms, including individual computers with standard RAM capacity, multi-core hardware architectures and large clusters. [ABSTRACT FROM AUTHOR]
- Published
- 2010
- Full Text
- View/download PDF
30. Characterization of microRNAs in cephalochordates reveals a correlation between microRNA repertoire homology and morphological similarity in chordate evolution.
- Author
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Zhonghua Dai, Zuozhou Chen, Hua Ye, Longhai Zhou, Lixue Cao, Yiquan Wang, Sihua Peng, and Liangbiao Chen
- Subjects
- *
CHORDATA , *TUNICATA , *CEPHALOCHORDATA , *VERTEBRATES , *HOMOLOGY (Biology) , *RNA , *BIOLOGICAL evolution - Abstract
Cephalochordates, urochordates, and vertebrates comprise the three extant groups of chordates. Although higher morphological and developmental similarity exists between cephalochordates and vertebrates, molecular phylogeny studies have instead suggested that the morphologically simplified urochordates are the closest relatives to vertebrates. MicroRNAs (miRNAs) are regarded as the major factors driving the increase of morphological complexity in early vertebrate evolution, and are extensively characterized in vertebrates and in a few species of urochordates. However, the comprehensive set of miRNAs in the basal chordates, namely the cephalochordates, remains undetermined. Through extensive sequencing of a small RNA library and genomic homology searches, we characterized 100 miRNAs from the cephalochordate amphioxus, Branchiostoma japonicum, and B. floridae. Analysis of the evolutionary history of the cephalochordate miRNAs showed that cephalochordates possess 54 miRNA families homologous to those of vertebrates, which is threefold higher than those shared between urochordates and vertebrates. The miRNA contents demonstrated a clear correlation between the extent of miRNA overlapping and morphological similarity among the three chordate groups, providing a strong evidence of miRNAs being the major genetic factors driving morphological complexity in early chordate evolution. [ABSTRACT FROM AUTHOR]
- Published
- 2009
- Full Text
- View/download PDF
31. Transcriptomic and genomic evolution under constant cold in Antarctic notothenioid fish.
- Author
-
Zuozhou Chen, Cheng, C.-H. Christina, Junfang Zhang, Lixue Cao, Lei Chen, Longhai Zhou, Yudong Jin, Hua Ye, Cheng Deng, Zhonghua Dai, Qianghua Xu, Peng Hu, Shouhong Sun, Yu Shen, and Liangbiao Chen
- Subjects
- *
FISHES , *COLD adaptation , *DISSOSTICHUS mawsoni , *LIPID metabolism , *GENE expression - Abstract
The antifreeze glycoprotein-fortified Antarctic notothenioid fishes comprise the predominant fish suborder in the isolated frigid Southern Ocean. Their ecological success undoubtedly entailed evolutionary acquisition of a full suite of cold-stable functions besides antifreeze protection. Prior studies of adaptive changes in these teleost fishes generally examined a single genotype or phenotype. We report here the genome-wide investigations of transcriptional and genomic changes associated with Antarctic notothenioid cold adaptation. We sequenced and characterized 33,560 ESTs from four tissues of the Antarctic notothenioid Dissostichus mawsoni and derived 3,114 nonredundant protein gene families and their expression profiles. Through comparative analyses of same-tissue transcriptome profiles of D. mawsoni and temperate/tropical teleost fishes, we identified 177 notothenioid protein families that were expressed many fold over the latter, indicating cold-related up-regulation. These up-regulated gene families operate in protein biosynthesis, protein folding and degradation, lipid metabolism, antioxidation, antiapoptosis, innate immunity, choriongenesis, and others, all of recognizable functional importance in mitigating stresses in freezing temperatures during notothenioid life histories. We further examined the genomic and evolutionary bases for this expressional up-regulation by comparative genomic hybridization of DNA from four pairs of Antarctic and basal non-Antarctic notothenioids to 10,700 0. mawsoni cDNA probes and discovered significant to astounding (3- to >300-fold, P < 0.05) Antarctic-specific duplications of 118 protein-coding genes, many of which correspond to the up-regulated gene families. Results of our integrative tripartite study strongly suggest that evolution under constant cold has resulted in dramatic genomic expansions of specific protein gene families, augmenting gene expression and gene functions contributing to physiological fitness of Antarctic notothenioids in freezing polar conditions. [ABSTRACT FROM AUTHOR]
- Published
- 2008
- Full Text
- View/download PDF
32. Adaptive Evolution of Hepcidin Genes in Antarctic Notothenioid Fishes.
- Author
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Qianghua Xu, Cheng, Chi-Hing Christina, Peng Hu, Hua Ye, Zuozhou Chen, Lixue Cao, Lei Chen, Yu Shen, and Liangbiao Chen
- Published
- 2008
- Full Text
- View/download PDF
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