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Perspectives on studying molecular adaptations of amphibians in the genomic era

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Zoological Research 2020年第4期41卷 351-364页

作者： yan-bo sun Yi Zhang Kai Wang Laboratory of Ecology and Evolutionary Biology Yunnan UniversityKunmingYunnan 650091China State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China Sam Noble Oklahoma Museum of Natural History and Department of Biology University of OklahomaNormanOklahoma 73072USA

Understanding the genetic mechanisms underlying particular adaptations/phenotypes of organisms is one of the core issues of evolutionary *** use of genomic data has greatly advanced our understandings on this issue,as well as other aspects of evolutionary biology,including molecular adaptation,speciation,and even conservation of endangered *** the well-recognized advantages,usages of genomic data are still limited to non-mammal vertebrate groups,partly due to the difficulties in assembling large or highly heterozygous *** this is particularly the case for amphibians,nonetheless,several comparative and population genomic analyses have shed lights into the speciation and adaptation processes of amphibians in a complex landscape,giving a promising hope for a wider application of genomics in the previously believed challenging groups of *** the same time,these pioneer studies also allow us to realize numerous challenges in studying the molecular adaptations and/or phenotypic evolutionary mechanisms of *** this review,we first summarize the recent progresses in the study of adaptive evolution of amphibians based on genomic data,and then we give perspectives regarding how to effectively identify key pathways underlying the evolution of complex traits in the genomic era,as well as directions for future research.

关键词： Molecular adaptation Gene subnetwork Phenotypic evolution Transposable element Amphibians

AutoSeqMan:batch assembly of contigs for Sanger sequences

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Zoological Research 2018年第2期39卷 123-126页

作者： Jie-Qiong Jin yan-bo sun State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences

With the wide application of DNA sequencing technology, DNA sequences are still increasingly generated through the Sanger sequencing platform. SeqMan （in the LaserGene package） is an excellent program with an easy-to-use graphical user interface （GUI） employed to assemble Sanger sequences into contigs. However, with increasing data size, larger sample sets and more sequenced loci make contig assemble complicated due to the considerable number of manual operations required to run SeqMan. Here, we present the ＇autoSeqMan＇ software program, which can automatedly assemble contigs using SeqMan scripting language. There are two main modules available, namely, ＇Classification＇ and ＇Assembly＇. Classification first undertakes preprocessing work, whereas Assembly generates a SeqMan script to consecutively assemble contigs for the classified files. Through comparison with manual operation, we showed that autoSeqMan saved substantial time in the preprocessing and assembly of Sanger sequences. We hope this tool will be useful for those with large sample sets to analyze, but with little programming experience. It is freely available at https：//***/ sun-yanbo/autoSeqMan.

关键词： Batch processing Sanger sequences Contig assembly SeqMan

Capture Probe: a java tool for designing probes for capture Hi-C applications

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Zoological Research 2020年第1期41卷 94-96页

作者： Yun-Fei Ma Adeniyi CAdeola yan-bo sun Hai-Bing Xie Ya-Ping Zhang State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic AnimalsKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China Kunming College of Life Science University of Chinese Academy of SciencesKunmingYunnan 650204China University of Chinese Academy of Sciences Beijing 100049China State Key Laboratory for Conservation and Utilization of Bio-resource and Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan ProvinceYunnan UniversityKunmingYunnan 650091China

DEAR EDITOR,Many functional elements associated with traits and diseases are located in non-coding regions and act on distant target genes via chromatin looping and folding,making it difficult for scientists to reveal the genetic regulatory *** Hi-C is a newly developed chromosome conformation capture technology based on hybridization capture between probes and target genomic *** can identify interactions among target loci and all other loci in a genome with low cost and high ***,we developed CaptureProbe,a user-friendly,graphical Java tool for the design of capture probes across a range of target sites or *** parameters helped to achieve and optimize the designed *** testing of CaptureProbe showed high efficiency in the design success ratio of target loci and probe ***,this program will help scientists conduct genome spatial interaction research.

关键词： Capture EDIT Probe

Integrative analyses of RNA editing,alternative splicing,and expression of young genes in human brain transcriptome by deep RNA sequencing

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Journal of Molecular Cell Biology 2015年第4期7卷 314-325页

作者： Dong-Dong Wu Ling-Qun Ye yan Li yan-bo sun Yi Shao Chunyan Chen Zhu Zhu Li Zhong Lu Wang David MIrwin Yong EZhang Ya-Ping Zhang State Key Laboratory of Genetic Resources and Evolution Yunnan Laboratory of Molecular Biology of Domestic AnimalsKunming Institute of ZoologyChinese Academy of SciencesKunming 650223China Kunming College of Life Science University of Chinese Academy of SciencesKunming 650204China University of Chinese Academy of Sciences BeijingChina Key Laboratory of Zoological Systematics and Evolution Institute of ZoologyChinese Academy of SciencesBeijingChina Laboratory for Conservation and Utilization of Bio-resource Yunnan UniversityKunming 650091China Department of Laboratory Medicine and Pathobiology University of TorontoTorontoCanada Banting and Best Diabetes Centre University of TorontoTorontoCanada

Next-generation RNA sequencing has been successfully used for identification of transcript assembly,evaluation of gene expression levels,and detection of post-transcriptional *** these large-scale studies,additional comprehensive RNA-seq data from different subregions of the human brain are required to fully evaluate the evolutionary patterns experienced by the human brain ***,we provide a total of 6.5 billion RNA-seq reads fromdifferent subregions of the human brain.A significant correlation was observed between the levels of alternative splicing and RNA editing,which might be explained by a competition between the molecularmachineries responsible for the splicing and editing of *** protein-coding genesdemonstrate biased expression to the neocortical and non-neocortical regions during evolution on the lineage leading to *** found that a significantly greater number of young human protein-coding genes are expressed in the putamen,a tissue that was also observed to have the highest level of RNA-editing *** putamen,which previously received little attention,plays an important role in cognitive ability,and our data suggest a potential contribution of the putamen to human evolution.

关键词： RNA editing human brain transcriptome young gene human brain evolution

Expression ofα2-Na/K-ATPase in C57BL/6J Mice Inner Ear and Its Relationship with Age-related Hearing Loss

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Current Medical Science 2021年第1期41卷 153-157页

作者： Yun LIU Han-qi CHU yan-bo sun Dan BING Liang-qiang ZHOU Jin CHEN Qing-guo CHEN Zhi-hui DU Department of Otolaryngology-Head and Neck Surgery Tongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China Department of Otolaryngology-Head and Neck Surgery the Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China

K^(+)cycling in the cochlea is critical to maintain *** sodium-potassium pumps are proved to participate in K^(+)cycling,such as Na/***α2-Na/K-ATPase is an important isoform of Na/*** expression ofα2-Na/K-ATPase in the cochlea is not *** this study,we used C57BL/6 mice as a model of presbycusis and implemented immunohistochemistry staining and quantitative real time-PCR,and theα2-Na/K-ATPase expression pattern was confirmed in the inner *** was foundα2-Na/K-ATPase was expressed widely in cochlea and its mRNA and protein expression was gradually reduced with aging(4-,14-,26-and 48-weeks old mice).We suspected that,the down-regulation ofα2-Na/K-ATPase expression might be associated with the remodeling of K^(+)cycling,degeneration of morphological structure and decrease of hearing function in aging C57 *** conclusion,we speculated that the reduction ofα2-Na/K-ATPase might play an important role in the pathogenesis of age-related hearing loss.

关键词： α2-Na/K-ATPase C57BL/6J mouse inner ear age-related hearing loss K^(+)cycling

Expression Patterns and Implications of LaminBl in Rat Cochleae

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Current Medical Science 2019年第2期39卷 305-309页

作者： Zhi-hui DU Jin CHEN Qing-guo CHEN Liang-qiang ZHOU Dan BING Yun LIU yan-bo sun Peng-jun LI Fan QI Hong-mei ZHU Han-qi CHU Department of Otolaryngology-Head and Neck Surgery Tongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan 430030China

LaminB1,a major component of the nuclear lamina,is a potent regulator of cellular proliferation and senescence and also known to be essential for neuronal migration and brain ***,the expression patterns of LaminB1 in the rat cochleae are still not fully *** *** blotting,and quantitative real-time PCR,we identified the distribution and expression of LaminB1 in the rat *** staining indicated that LaminBl was mainly localized in the auditory hair cells(HCs),spiral ganglion cells(SGC),stria vascularis(STV,including spiral ligament),Reissner's membrane(RM),and limbus laminae spiralis(LLS).Western blotting analysis illustrated that the distribution of LaminBl in rat cochleae was characterized by tissue *** LaminB1 protein was expressed more in SGC and basilar membrane(BM)than in ***,the mRNA expression of LaminB1 displayed difference in cochlear *** observations preliminarily revealed the expression patterns of LaminB1,providing a theoretical basis for further study on the role of LaminB1 in auditory function.

关键词： LaminB1 cochleae rat hair cell spiral ganglion cell stria vascularis

Nocturnal to Diurnal Transition in the Common Ancestor of Haplorrhines:Evidence from Genomic-Scan for Positively Selected Genes

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Journal of Genetics and Genomics 2015年第1期42卷 33-37页

作者： Xue Cao yan-bo sun David M.Irwin Guo-Dong Wang Ya-Ping Zhang State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology University of Chinese Academy of Sciences Kunming College of Life Science University of Chinese Academy of Sciences Department of Laboratory Medicine and Pathobiology University of TorontoI King's College CircleTorontoOntario M5S 1A8Canada Laboratory for Conservation and Utilization of Bio-resources Yunnan University

Transition from a nocturnal to a diurnal lifestyle represents a major shift in primate evolution, plays a central role in the adaptation of these species to new habitats, and is involved in modifications to their physiological and social behaviors （Heesy and Ross, 2001; Shultz et al., 2011）. However, two core problems concerning the circadian rhythm transition re- mains unresolved. First, there is controversy concerning the activity pattern of the ancestral primate （Heesy and Ross, 2001; Tan et al., 2005）. Second, the transition process for circadian rhythm in primate evolutionary history is unre- solved. Although most research suggests that primates trans- formed from a nocturnal to a diurnal circadian rhythm in the lineage leading to the common ancestor of the anthropoids or the haplorrhines （anthropoids and tarsier）（Ross, 2000; Heesy and Ross, 2001）, evidence has been insufficient to determine whether this occurred in the lineage leading to the common ancestor of the haplorrhines or the anthroooids.

关键词： Nocturnal to Diurnal Transition in the Common Ancestor of Haplorrhines

Traffic safety helmet wear detection based on improved YOLOv5 network

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Optoelectronics Letters 2025年第1期21卷 35-42页

作者： GUI Dongdong sun bo College of Software Southeast University Quanzhou Equipment Research Centre Haixi Institute Chinese Academy of Sciences

Aiming at the problem that the current traffic safety helmet detection model can't balance the accuracy of detection with the size of the model and the poor generalization of the model, a method based on improving you only look once version 5(YOLOv5) is proposed. By incorporating the lightweight Ghost Net module into the YOLOv5 backbone network, we effectively reduce the model size. The addition of the receptive fields block(RFB) module enhances feature extraction and improves the feature acquisition capability of the lightweight model. Subsequently, the high-performance lightweight convolution, GSConv, is integrated into the neck structure for further model size compression. Moreover, the baseline model's loss function is substituted with efficient insertion over union(EIoU), accelerating network convergence and enhancing detection precision. Experimental results corroborate the effectiveness of this improved algorithm in real-world traffic scenarios.

关键词： Traffic control

A Novel Model for Describing Rail Weld Irregularities and Predicting Wheel-Rail Forces Using a Machine Learning Approach

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Computer Modeling in Engineering & Sciences 2025年第1期142卷 555-577页

作者： Linlin sun Zihui Wang Shukun Cui Ziquan yan Weiping Hu Qingchun Meng State Key Laboratory of High-Speed Railway Track System China Academy of Railway Sciences Corporation LimitedBeijing100081China Railway Engineering Research Institute China Academy of Railway Sciences Corporation LimitedBeijing100081China School of Aeronautic Science and Engineering Beihang UniversityBeijing100191China

Rail weld irregularities are one of the primary excitation sources for vehicle-track interaction dynamics in modern high-speed *** can cause significant wheel-rail dynamic interactions,leading to wheel-rail noise,component damage,and *** researchers have employed the vehicle-track interaction dynamic model to study the dynamic interactions between wheel and rail induced by rail weld geometry ***,the cosine wave model used to simulate rail weld irregularities mainly focuses on the maximum value and neglects the geometric *** this study,novel theoretical models were developed for three categories of rail weld irregularities,based on measurements of the high-speed railway from Beijing to *** vertical dynamic forces in the time and frequency domains were compared under different running *** forces generated by the rail weld irregularities that were measured and modeled,respectively,were compared to validate the accuracy of the proposed ***,based on the numerical study,the impact force due to rail weld irrregularity is modeled using an Artificial Neural Network(ANN),and the optimum combination of parameters for this model is *** results showed that the proposed model provided a more accurate wheel/rail dynamic evaluation caused by rail weld irregularities than that established in the *** ANN model used in this paper can effectively predict the impact force due to rail weld irrregularity while reducing the computation time.

关键词： Rail weld irregularity high-speed railway vehicle-track coupled dynamics wheel/rail dynamic vertical force artificial neural networks