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第五届全国生物信息学与系统生物学学术大会暨国际生物信息...

作者： Xiu-Jun GONG HuaYU Yuan-Fang LI School of Computer Science and Technology Tianjin UniversityWeijin Rd No.92Nankan Clayton School of IT Faculty of Information TechnologyMonash University

The identification and analysis of tissue specificity of genes and gene expressions have a direct and profound impacton the further understanding of a wide array of problems of much *** its significance,our understanding of gene tissue specificity is still quite fragmented and *** developeda large-scale and extensible knowledge acquisition and representation system -the Specifictome -to acquire,organizeand disseminate tissue specificity knowledge for humanand other model organisms such as mouse,rat,and so onusing novel statistical machine learning and Semantic Web technologies. BackgroundrAn important part of understanding the human genome and biology is the study of tissue-specific gene expressionsand regulations,which is a complex *** is a result of a large number of interacting factors and can beexhibited in a number of ways, including developmental stages,gene expression levels,a gene’s structural characteristics (promoters,etc.) and gene regulatory and interaction *** inherent complexity makes tissue specificityresearch a very challenging *** severaltissue specific databases such as TiGER,TiProD,tissueInfo,tissueDistributionDBsandTiSGeDprovide web services to extract the TS and HK genes and their genomic features by predefinedthresholdvalues. However,there is no widely acceptedcriterion to judge which gene is expressedin a specific tissue only by the expression patterns. Methods:In this research,we 1) uncover the co-expression patterns of TS genes using constrained Bayesian mixture models,2) discover and evaluate the sequence significant patterns of TS genes using Bayesian factor analysis,3) build stable and reliable TS gene regulatory networks,and 4) develop a comprehensive knowledge atlas for the expression and regulations of TS genes using semantic web technologies. Results:We have integrated three types of expression data sets:microarray,EST and SAGE for identifying TS and housekeeping genes and used pu

关键词： tissue specificity Bayes learning semantic web motif discovery regulatory network

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PsyMuKB: An Integrative De Novo Variant Knowledge Base for Developmental Disorders

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Genomics, Proteomics & Bioinformatics 2019年第4期17卷 453-464页

作者： Guan Ning Lin Sijia Guo Xian Tan Weidi Wang Wei Qian Weichen Song Jingru Wang Shunying Yu Zhen Wang Donghong Cui Han Wang Shanghai Mental Health Center Shanghai Jiao Tong University School of MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai 200030China Shanghai Key Laboratory of Psychotic Disorders Shanghai 200030China Brain Science and Technology Research Center Shanghai Jiao Tong UniversityShanghai 200030China College of Information Science and Technology Northeast Normal UniversityChangchun 130117China Institution of Computational Biology Northeast Normal UniversityChangchun 130117China

De novo variants(DNVs)are one of the most significant contributors to severe earlyonset genetic disorders such as autism spectrum disorder,intellectual disability,and other developmental and neuropsychiatric(DNP)***,a plethora of DNVs have been identified using next-generation sequencing,and many efforts have been made to understand their impact at the gene ***,there has been little exploration of the effects at the isoform *** brain contains a high level of alternative splicing and regulation,and exhibits a more divergent splicing program than other ***,it is crucial to explore variants at the transcriptional regulation level to better interpret the mechanisms underlying DNP *** facilitate a better usage and improve the isoform-level interpretation of variants,we developed NeuroPsychiatric Mutation Knowledge Base(PsyMuKB).It contains a comprehensive,carefully curated list of DNVs with transcriptional and translational annotations to enable identification of isoformspecific *** allows a flexible search of genes or variants and provides both table-based descriptions and associated visualizations,such as expression,transcript genomic structures,protein interactions,and the mutation sites mapped on the protein *** also provides an easy-to-use web interface,allowing users to rapidly visualize the locations and characteristics of mutations and the expression patterns of the impacted genes and *** thus constitutes a valuable resource for identifying tissue-specific DNVs for further functional studies of related *** is freely accessible at http://***.

关键词： De novo mutation Developmental and neuropsychiatric disorders Database Isoforms tissue specificity

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Commentary: PROTACs make undruggable targets druggable: Challenge and opportunity

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Acta Pharmaceutica Sinica B 2021年第10期11卷 3335-3336页

作者： Bin Lu Jianpin Ye The Second Affiliated Hospital Hengyang Medical SchoolUniversity of South ChinaHengyang 421001China Protein Quality Control and Diseases Laboratory School of Laboratory Medicine and Life SciencesWenzhou Medical UniversityWenzhou 325035China Zhengzhou Central Hospital Affiliated to Zhengzhou University Zhengzhou 450000China

Proteostasis(protein homeostasis) ensures precise adjustment of cellular demand to proteins in the stress conditions, which is essential in the maintenance of health environment inside cells and is indispensable for t... 详细信息

关键词： Proteostasis Protein degradation Drug discovery Autophagy E3 ligase Ubiquitination Drug resistance Off-target effect tissue specificity

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Characterisation and Expression Analysis of Sox9 in the Multiocellated Racerunner, Eremias multiocellata

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Asian Herpetological Research 2014年第2期5卷 104-112页

作者： Ying XIN Huihui WANG Xiaolong TANG Songsong LU Weixin LI Yang ZHANG Shiwei LIANG Qiang CHEN Institute of Biochemistry and Molecular Biology School of Life Science Lanzhou University

Sox9 is an important member of Sox family which is involved in a variety of developmental processes including sex determination and gonadal differentiation. The cDNA of Sox9 from multiocellated racerunner E. multiocellata was cloned using reverse transcription-polymerase chain reaction （RT-PCR） and rapid amplification of cDNA ends （RACE）. The sequence contains a 1497 bp open reading frame, which encodes a 498 amino acid protein with a predicted molecular weight of 55.45 kDa. EmSox9 displays high similarity to those of reptiles, and shows an overall amino acid identity of 〉82%. We also investigated the tissue-specific expression of EmSox9 mRNA by realtime quantitative PCR. Sox9 mRNA is present in brain, heart, liver, kidney, gonads and muscle tissues of adult E. multiocellata, with the highest expression in brain and testis. The results indicate that Sox9 may play important roles in some tissues during E. multiocellata neural and gonadal development.

关键词： Sox9 HMG-box RACE Eremias multiocellata tissue specificity

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Decellularized Disc Hydrogels for hBMSCs tissue-specific differentiation and tissue regeneration

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Bioactive Materials 2021年第10期6卷 3541-3556页

作者： Yizhong Peng Xiangcheng Qing Hui Lin Donghua Huang Jinye Li Shuo Tian Sheng Liu Xiao Lv Kaige Ma Rui Li Zilong Rao Ying Bai Songfeng Chen Ming Lei Daping Quan Zengwu Shao Department of Orthopaedics Union HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430022China Musculoskeletal Tumor Center Department of OrthopedicsThe Second Affiliated Hospital of Zhejiang University School of MedicineHangzhouChina School of Chemistry Sun Yat-sen UniversityGuangzhou510127China School of Materials Science and Engineering Sun Yat-sen UniversityGuangzhou510127China Department of Orthopaedic Surgery The First Affiliated Hospital of Zhengzhou UniversityZhengzhou City450052China

tissue specificity,a key factor in the decellularized tissue matrix(DTM),has shown bioactive functionalities in tuning cell fate-e.g.,the differentiation of mesenchymal stem ***,cell fate is also determined by the living microenvironment,including material composition and spatial ***,two neighboring tissues within intervertebral discs,the nucleus pulposus(NP)and annulus fibrosus(AF),were carefully processed into DTM hydrogels(abbreviated DNP-G and DAF-G,respectively)to determine the tissue-specific effects on stem cell fate,such as specific components and different culturing methods,as well as in vivo *** differences in their protein compositions were identified by proteomic ***,the fate of human bone marrow mesenchymal stem cells(hBMSCs)also responds to both culturing methods and ***,hBMSCs cultured with DNP-G(3D)differentiated into NP-like cells,while hBMSCs cultured with DAF-G(2D)underwent AF-like differentiation,indicating a close correlation with the native microenvironments of NP and AF cells,***,we found that the integrin-mediated RhoA/LATS/YAP1 signaling pathway was activated in DAF-G(2D)-induced AF-specific ***,the activation of YAP1 determined the tendency of NP-or AF-specific differentiation and played opposite regulatory ***,DNP-G and DAF-G specifically promoted tissue regeneration in NP degeneration and AF defect rat models,*** conclusion,DNP-G and DAF-G can specifically determine the fate of stem cells through the integrin-mediated RhoA/LATS/YAP1 signaling pathway,and this tissue specificity is both compositional and spatial,supporting the utilization of tissue-specific DTM in advanced treatments of intervertebral disc degeneration.

关键词： tissue specificity Decellularized tissue matrix Intervertebral disc Differentiation YAP1

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Endophytic fungal diversity of endemic carnivorous plant Nepenthes khasiana in Meghalaya,India

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Studies in Fungi 2021年第1期6卷 138-150页

作者： Naseem F Kayang H Microbial Ecology laboratory Department of BotanyNorth Eastern Hill UniversityShillongMeghalaya-793022India

The present investigation deals with the isolation of endophytic fungi from leaf,stem,root and pitcher cup tissue segments of the endemic carnivorous plant Nepenthes khaisana collected from its natural habitat for a period of one year at monthly *** of 576 tissue segments inoculated,a total of 39 fungal endophytes along with mycelia sterilia were isolated from the host *** assess the diversity of fungal endophytes,the colonization frequency(%CF)was first recorded using past software and MS *** fungal isolates were mainly composed of the phylum Ascomycota,followed by Zygomycota and *** highest percentage colonization frequency on an average of three replicates were recorded in pitcher cup tissues followed by root,stem and least was recorded in leaf of the host *** the isolates,Globisporangium irregulare(83.33%)showed high%CF in leaf,Juxtiphoma eupyrena(83.33%)reported to have maximum%CF in the stem,Talaromyces ruber(66.66%)was recorded high%CF in root and mycelia sterilia(white)were showed the highest%CF in the segments of *** diversity index analyses of Shannon-Weiner,Simpson’s index,species richness and species evenness of diversity showed that leaf of *** has the highest diversity than the other parts of the ***,with the help of the present finding,we conclude that the distribution of fungal endophytes and their%colonization frequencies vary within different tissues of the host plant and thus,this confirms tissue specificity nature of endophytic fungi.

关键词： Colonization frequency Diversity indices Natural habitat Pitcher plant tissue specificity

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General trends of protein expression and localization reveal the rule of bio-complexity realization

General trends of protein expression and localization reveal...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息...

作者：杨冬 Dingchen Li Fan Zhong Dong Li Ying Jiang Fuchu He State Key Laboratory of Proteomics Beijing Proteome Research CenterBeijing Institute of Radiation Medicine Institutes of Biomedical Sciences and Department of Chemistry Fudan University

Background:During evolution,proteins containing newly emerged domains and the increasing proportion of multi-domain proteins in the full Genome-Encoded Proteome(GEP) have substantially contributed to increasing biological ***,it is not known how these two potential structural factors are preferentially utilized at given physiological states,until our most recent study found that multidomain proteins or only older domain- containing proteins are significantly overrepresented in certain-state proteomes(CSPs,i.e., all the proteins expressed at certain physiological states) compared with GEP,which indicates biological complexity under certain conditions is more significantly realized by diverse domain organization than by the emergence of new types of *** further explore the regular utilization pattern in the view of protein spatial distribution at levels ranging from organelles to organs,we investigated the relationships between protein domain characters and protein subcelluar localization width(SLW) or tissue specificity(TS). Methods:To calculate SLW,we collected high confident subcellular location information in Swiss-Prot,GOA,human protein atlas(HPA),MitoP2,Human Liver Organelle Proteome(HLOP) and related references and *** identification is based on RPS-BLAST against Pfam and SMART(Etissue or cell types) in which the gene is expressed. Results:The integrated atlas contains subcellular localization information with high confidence of more than 13000 human proteins,including the subcellular locations for different splice isoforms as complete as *** on this atlas,we found that SLW positively correlates with DN value,while it negatively correlates with DA value,that is, multi-domain proteins or only older domain-containing proteins tend to be localized at more subcellular *** addition,SLW negatively correlate with TS,*** with more subcellular location

关键词： Biological complexity protein domain proteome subcellular localization tissue specificity

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