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Protein & Cell 2017年第1期8卷 77-77页

作者： Shawn Burgess Linzhao Cheng Feng Gu Junjiu Huang Zhiwei Huang Shuo Lin Jinsong Li Wei Li Wei Qin Yujie Sun Zhou Songyang wensheng Wei Qiang Wu Haoyi Wang Xiaoqun Wang Jing-Wei Xiong Jianzhong Xi Hui Yang Bin Zhou Bo Zhang National Human Genome Research Institute NIH Bethesda MD USA Division of Hematology in Department of Medicine Johns Hopkins University School of Medicine Baltimore MD 21205 USA Stem Cell Program in the Institute for Cell Engineering Johns Hopkins University School of Medicine Baltimore MD 21205 USA center for Vision Research Eye Hospital Wenzhou Medical University Wenzhou 325035 China Stem Cell and Functional genomics Laboratory School of Life Sciences Sun Yat-sen University Guangzhou 510275 China HIT center of Life Sciences Harbin Institute of Technology Harbin 150080 China Department of Molecular Cell and Developmental Biology University of California Los Angeles Los Angeles CA 90095 USA Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200031 China State Key Laboratory of Stem cell and Reproductive Biology Institute of Zoology Chinese Academy of Sciences Beijing 100101 China College of Chemical Biology and Biotechnology Peking University Shenzhen Graduate School Shenzhen 518055 China PKU BIOPIC Beijing 100871 China BIOPIC ICG CLS and School of Life Sciences Peking University Beijing 100871 China center for Comparative Biomedicine Institute of Systems Biomedicine Shanghai Jiao Tong University Shanghai 200240 China Institute of Biophysics Chinese Academy of Sciences Beijing 100101 China Institute of Molecular Medicine Peking University Beijing 100871 China College of Engineering Peking University Beijing 106871 China Laboratory of Disease Models in Non-Human Primates Institute of Neuroscience Shanghai Chinese Academy of Sciences Shanghai 200031 China College of Life Sciences Peking University Beijing 100871 China

In the original publication of this article the Figure 1E legend has been incorrectly published.

关键词： Erratum Questions NgAgo

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Discovery of Simple Sequence Repeat Markers through Transcriptome Analysis of Baccaurea motleyana

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Journal of Food Science and Engineering 2020年第2期10卷 33-46页

作者： Khairun Hisam Nasir Muhammad Fairuz Mohd Yusof Mohd Shahril Firdaus Abdul Razak Siti NorsaidahIbrahim Mira Farzana Mohamad Moktar Khadijah Awang Mohd Shukri Mat Ali Centre for Molecular Marker Discovery and Validation(CMDV) Agri-Omic dan BioinformaticsBiotechnology and Nanotechnology Research CentreMalaysian Agricultural Research and Development Institute(MARDI)Serdang 43400SelangorMalaysia Industrial Crop Research Centre Malaysian Agricultural Research and Development Institute(MARDI)Serdang 43400SelangorMalaysia Horticulture Research Centre Malaysian Agricultural Research and Development Institute(MARDI)Serdang 43400SelangorMalaysia

Baccaurea motleyana(rambai)is underutilized fruits that are native to Malaysia,Indonesia and *** this study,a total of 54,779 unigenes identified from rambai transcriptome were used for simple sequence repeat(SSR)analysis by MIcroSAtellite(MISA).A total of 20,420 SSRs were found to be distributed within 37.27%of the total number of *** repeats represented the main type,accounting for 64.04%,followed by trinucleotide repeats(20.28%)and dinucleotide repeats(19.94%).Gene annotation to seven databases has a success ratio of 68.53%(National center for Biotechnology Information(NCBI)protein sequences),53.68%(NCBI nucleotide sequences),27.43%(Kyoto Encyclopedia of Genes and Genome Ortholog),56.0%(SwissProt),52.44%(Protein family),53.99%(Gene Ontology)and 26.44%(Kluster of Orthologous Group).Further rambai SSRs were randomly selected and validated to ***(rambai),***(tampoi),***(jentik-jentik),***(pupor)and ***(setambun).

关键词： Baccaurea SSR transcriptome gene annotation and SSR validation

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Gut Microbiome Alterations in COVID-19

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genomics, Proteomics & bioinformatics 2021年第5期19卷 679-688页

作者： Tao Zuo Xiaojian Wu Weiping Wen Ping Lan Guangdong Institute of Gastroenterology The Sixth Affiliated Hospital of Sun Yat-sen UniversitySun Yat-sen UniversityGuangzhou 510655China center for Fecal Microbiota Transplantation Research The Sixth Affiliated Hospital of Sun Yat-sen UniversitySun Yat-sen UniversityGuangzhou 510655China Department of Colorectal Surgery The Sixth Affiliated Hospital of Sun Yat-sen UniversitySun Yat-sen UniversityGuangzhou 510655China Department of Otorhinolaryngology Head and Neck SurgeryThe First Affiliated Hospital of Sun Yat-sen UniversitySun Yat-sen UniversityGuangzhou 510080China Guangzhou Key Laboratory of Otorhinolaryngology Guangzhou 510080China Department of Otorhinolaryngology Head and Neck SurgeryThe Sixth Affiliated Hospital of Sun Yat-sen UniversitySun Yat-sen UniversityGuangzhou 510655China

Since the outset of the coronavirus disease 2019(COVID-19)pandemic,the gut microbiome in COVID-19 has garnered substantial interest,given its significant roles in human health and *** evidence is unveiling that the gut microbiome is broadly altered in COVID-19,including the bacterial microbiome,mycobiome,and ***,the gut microbial ecological network is significantly weakened and becomes sparse in patients with COVID-19,together with a decrease in gut microbiome *** the existence of severe acute respiratory syndrome coronavirus type 2(SARS-CoV-2),the gut microbiome of patients with COVID-19 is also characterized by enrichment of opportunistic bacteria,fungi,and eukaryotic viruses,which are also associated with disease severity and ***,a multitude of symbiotic bacteria and bacteriophages are decreased in abundance in patients with *** gut microbiome features persist in a significant subset of patients with COVID-19 even after disease resolution,coinciding with‘long COVID’(also known as postacute sequelae of COVID-19).The broadly-altered gut microbiome is largely a consequence of SARS-CoV-2 infection and its downstream detrimental effects on the systemic host immunity and the gut *** impaired host immunity and distorted gut microbial ecology,particularly loss of low-abundance beneficial bacteria and blooms of opportunistic fungi including Candida,may hinder the reassembly of the gut microbiome post *** investigation is necessary to fully understand the role of the gut microbiome in host immunity against SARS-CoV-2 infection,as well as the long-term effect of COVID-19 on the gut microbiome in relation to the host health after the pandemic.

关键词： COVID-19 Gut Microbiome Immunity Infection

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LINC01614 expression in gastric cancer and its prognostic value based on bioinformatics analyses

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Journal of Hainan Medical University 2020年第10期26卷 42-46页

作者： Hui-Jie Wu Jing-Yuan Zhou Song-Da Chen Ling-Yu Zhu Jia-Hao Liang Ai-QunLiu Department of Endoscopy center Guangxi Medical University Cancer HospitalNanningGuangxi530021 Department of Hepatobiliary Surgery Guangxi Medical University Cancer HospitalNanningGuangxi530021

Objective:To identify the potential role and prognostic value of LINC01614 in gastric cancer. Methods: qRT-PCR was applied to analyze the LINC01614 expression in gastric cancer tissue and paired adjacent normal tissue, and gastric cell line. And the RNA-Seq data downloaded from the TCGA and GEO database was employed to analyze and validate the LINC01614 expression in gastric cancer tissue and adjacent normal tissue. And the analyses of relationship between LINC01614 expression level and clinical features was done to clarify the role of LINC01614 in gastric cancer. The survival analysis was used to identify the prognostic value of LINC01614. And the pathways that LINC01614 may enroll was ***: The qRT-PCR showed that LINC01614 was increased in gastric cancer tissue and gastric cancer cell line (P < 0.005). And the expression of LINC01614 was significantly different in cancer tissue and adjacent normal tissue according to datasets analyses (P < 0.001). And it was found that LINC01614 expression was significantly correlated with histologic grade and residual tumor (P = 0.0177 and 0.0218, respectively). Survival analysis indicated that low expression of LINC01614 patients have longer overall survival than high expression one (HR = 1.520, 95% CI: 1.094 ~ 2.110). After all, enriched pathways showed that LINC01614 may act in carcinogenesis through various ***: LINC01614 is high expressed in gastric cancer and high expression of LINC01614 is related to poor prognosis. LINC01614 may be a potential prognostic biomarker for gastric cancer.

关键词： Stomach adenocarcinoma LINC01614 RNA Long Noncoding bioinformatics

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Cloning,identification and bioinformatics analysis of a putative aquaporin from Trichinella spiralis(TsAQP)

Cloning,identification and bioinformatics analysis of a puta...

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中国畜牧兽医学会兽医寄生虫学分会第十三次学术研讨会

作者： Cui Jian-Min Zhang Nian-Zhang Li Wen-Hui Yan Hong-Bin Fu Bao-Quan State Key Laboratory of Veterinary Etiological Biology Key Laboratory of Veterinary Public Health of the Ministry of AgricultureKey Laboratory of Veterinary Parasitology of Gansu ProvinceLanzhou Veterinary Research InstituteChinese Academy of Agricultural Sciences Jiangsu Co-innovation center for Prevention and Control of Important Animal Infectious Disease

Vaccination as one of prevention strategies against the Trichinella spiralis infection in hosts is an ongoing ***,no ideal vaccine candidates have been identified until ***,identification of more effective antigens in essential life stages of the parasite as vaccine candidates is of *** the present study,we identified a novel aquaporin gene in ***(TsAQP),and the potential antigenicity of TsAQP was evaluated by prediction of *** results revealed that a total of11 post-translational modification(PTM) sites falling into 4 categories,including N-glycosylation sites,casein kinase Ⅱ phosphorylation sites,protein kinase C phosphorylation sites and N-myristoylation sites,were predicted in the *** belongs to membrane intrinsic protein with high hydrophobicity and the main hydrophobic domains were distributed at amino acid positions 21-43,54-71,83-91,107-121,163-174,187-200 and 242-261,up to 38.5%of the *** TsAQP protein mainly consisted of helixes(39.58%) and loops(50%).The advanced structure of TsAQP using homology modeling method showed that the protein was formed from 6 membrane-spanning domains connecting by 5 *** on these analyses,6 potential B-cell epitopes and 4 potential T-cell epitopes were further *** results suggested that TsAQP could be a promising candidate for vaccine antigen against ***.

关键词： T.spiralis Aquaporin Cloning bioinformatics analysis

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Combining the high-throughput maize phenotyping and quantitative trait loci analysis to reveal the dynamic genetic architecture of maize plant growth

Combining the high-throughput maize phenotyping and quantita...

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2016年全国植物生物学大会

作者： Xuehai Zhang Chenglong Huang Di Wu Feng Qiao Ke Wang Yingjie Xiao Guoxing Chen Lizhong Xiong Wanneng Yang Jianbing Yan National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural University National center of Plant Gene Research (Wuhan) Huazhong Agricultural University College of Engineering Huazhong Agricultural University MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River Huazhong Agricultural University

With the increasing demands in crop breeding for novel traits,plant research community faces to quantitatively analyze the structure and function of large numbers of plants. A clear goal of highthroughput phenotyping is to bridge the gap between genomics and phenomics. In this study,we obtained 106 traits from a maize recombinant inbred line population across 16 development stages using the automatic phenotyping *** results showed that the exponential model had better predication ability for biomass accumulation,even in the early growth stage. QTL mapping with high density genetic linkage map was used to uncover the genetic basis of these complex agronomic traits,and have identified 2265 QTLs for all investigated traits. We also conduct the traits-loci network analysis and 3 house-keeping loci were detected in the hub points for 2 traits. These results reveal the dynamic genetic architecture of maize plant growth thus enhance maize ideotype breeding in the near future.

关键词： maize high-throughput phenotyping dynamic genetic architecture QTL mapping

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Cloning and bioinformatics analysis of Thioredoxin peroxidasegene TsTPx1-3 from Trichinella spiralis

Cloning and bioinformatics analysis of Thioredoxin peroxidas...

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中国畜牧兽医学会兽医寄生虫学分会第十三次学术研讨会

作者： Nian-Zhang ZHANG Jin-Yi LIU Wen-Hui LI Hong-Bin YAN Zi-Gang QU Jian-Min CUI Yang YANG Bao-Quan FU State Key Laboratory of Veterinary Etiological Biology Key Laboratory of Veterinary Public Health of the Ministry of AgricultureKey Laboratory of Veterinary Parasitology of Gansu ProvinceLanzhou Veterinary Research InstituteChinese Academy of Agricultural Sciences Jiangsu Co-innovation center for Prevention and Control of Important Animal Infectious Disease

The intracellular parasitic nematode,Trichinella spiralis,is known as the pathogen of a severe foodborne zoonosis,*** the parasite rapid growth and generative propagation phases,the environment of their cells exist a ...

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Creating a large scale of male sterile mutants via the CRISPRI/CAS9 technology and dissecting molecular mechanism of genic male sterility in maize

Creating a large scale of male sterile mutants via the CRISP...

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第十九届中国作物学会学术年会

作者：万向元 Zhongzhi International Institute of Agricultural Biosciences Biology and Agriculture Research Center University of Science and Technology Beijing Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding Beijing Solidwill Sci-Tech Co.Ltd.

【Background】As one of the most important crops, maize not only has been a source of the food, feed, and industrial feedstock for biofuel and bioproducts but also became as a model plant system for addressing fundamental questions in genetics. Male sterility is a very useful trait for hybrid vigor utilization and hybrid seed production. The identification and characterization of genic male-sterility(GMS) genes in maize and other plants have deepened our understanding of the molecular mechanisms controlling anther and pollen development, and enabled the development and efficient use of many biotechnology-based male-sterility(BMS) systems for crop hybrid breeding. 【Results】Here, I will report the main progress on three aspects in our lab:(1) Creating a large scale of maize male-sterility mutants via the CRISPRI/CAS9 technology based on three sets of transcriptomics(RNA-Seq) data from maize anthers during eight anther developmental stages, by which we can predict many potential GMS genes;(2) Identifying and characterizing several GMS genes such as ZmMs7, ZmMs20, ZmMs25, ZmMs30, and ZmMs33, as well as many GMS-related microRNAs(miRNAs), competing endogenous RNAs(ceRNAs) and ceRNA-miRNA-target gene pairs in maize, and then constructing a putative regulatory network for maize anther and pollen development by comparative genomics analysis of the GMS genes in maize, Arabidopsis and rice;and(3) Introducing the features of two BMS systems(e.g. A Multiple Control Sterile System and A Universal Dominant Male-sterility System developed in our lab) for propagating male sterile lines and producing hybrid seeds in maize and other plants. Finally, I would like to provide my perspectives on the studies of GMS genes and the development of novel BMS systems in maize and other plants. 【Conclusion】 The continuous exploration of GMS genes and BMS systems will enhance our understanding of the molecular regulatory networks controlling male fertility and greatly facilitate hybrid vigor utiliz

关键词： maize Genic Male Sterility(GMS) male sterile mutants CRISPRI/CAS9 molecular mechanism biotechnology-based male-sterility system hybrid vigor utilization

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Multilocus Sequence Typing of the Guangdong Isolates of <i>Riemerella anatipestifer</i>from Ducks in China

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Open Journal of Animal Sciences 2015年第3期5卷 332-342页

作者： B. F. Zhu Mike Chao X. F. Yang D. Zhou Henry Fok College of Life Science Shaoguan University Shaoguan China Joint Laboratory of Animal Infectious Diseases Diagnostic Center Harbin Veterinary Research Institute CAAS-Shaoguan University Shaoguan China Department of Biology Science of College of Nature Science California State University San Bernardino USA College of Life Science and Foof Engineering Nanchang University Nanchang China

It is a very important significance to explore the bacterial typing methods rapidly, accurately and understand the genetic relation between isolates for controlling effectively the disease and preventing the dissemination and diffusion of the pathogen. The changes in the genetic material nucleotide sequences result in variation and evolution of bacteria, the development of molecular biology and genomics make typing of bacteria from phenotype to molecular typing. Riemerella anatipestifer is the causative agent of polyserositis of ducks and geese. We studied 54 isolates of Riemerella anatipestifer from Guangdong in China by multicolor sequence typing (MLST). The result showed that 54 isolates of Riemerella anatipestifer were divided into 14 STs, and among E3, b12xiao and Cb1 three isolates have with independent of type STs. It was found that there was high homology of RA and low genetic variability in the same area. The synonymous mutation and non synonymous mutation rate: dN/dS in seven housekeeping genes was lower than 0.25. Cluster analysis showed that the 54 isolates were clustered into 5 groups. eBRUST analysis showed that all isolates were clustered into one Group. It also proved that the genetic relationship was very closed in duck plague pathogen in this area;the source may be the same ancestors.

关键词： MLST Remerella anatipestifer Phylogenetic Relationship Mutation Rate

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Mechanism of the Rpn13-induced activation of Uch37

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Protein & Cell 2014年第8期5卷 616-630页

作者： Lianying Jiao Songying Ouyang Neil Shaw Gaojie Song Yingang Feng Fengfeng Niu Weicheng Qiu Hongtao Zhu Li-Wei Hung Xiaobing Zuo V. Eleonora Shtykova Ping Zhu Yu-Hui Dong Ruxiang Xu Zhi-Jie Liu National Laboratory of Biomacromolecules Institute of Biophysics Chinese Academy of Sciences Beijing 100101 China iHuman Institute ShanghaiTech University Shanghai 201210 China Shandong Provincial Key Laboratory ofEnergy-Genetics Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of Sciences Qingdao 266101 China Physics Division 'Los Alamos National Laboratory Los Alamos NM 87545 USA X-ray Science Division Argonne National Laboratory 9700 South Cass Avenue Argonne IL 60439 USA Institute of Crystallography~ Russian Academy of Sciences 59 Leninsky Pr. 117333 Moscow Russian Federation center for Multi-disciplinary Research Institute of High Energy Physics Chinese Academy of Sciences Beijing 100049China Department of Nerosurgery The Military General Hospital of Beijing PLA Beijing 100700 China

Uch37 is a de-ubiquitinating enzyme that is activated by Rpn13 and involved in the proteasomal degradation of proteins. The full-length Uch37 was shown to exhibit low iso-peptidase activity and is thought to be auto-inhibited. Structural comparisons revealed that within a homo- dimer of Uch37, each of the catalytic domains was blocking the other＇s ubiquitin （Ub）-binding site. This blockage likely prevented Ub from entering the active site of Uch37 and might form the basis of auto-inhibition. To understand the mode of auto-inhibition clearly and shed light on the activation mechanism of Uch37 by Rpn13, we investigated the Uch37-Rpn13 complex using a combi- nation of mutagenesis, biochemical, NMR, and small- angle X-ray scattering （SAXS） techniques. Our results also proved that Uch37 oligomerized in solution and had very low activity against the fluorogenic substrate ubi- quitin-7-amino-4-methylcoumarin （Ub-AMC） of de-ubiq- uitinating enzymes. Uch37AHb＇Hc＇KEKE, a truncation removal of the C-terminal extension region （residues 256- 329） converted oligomeric Uch37 into a monomeric form that exhibited iso-peptidase activity comparable to that of a truncation-containing the Uch37 catalytic domain only. We also demonstrated that Rpn13C （Rpn13 residues 270- 407） could disrupt the oligomerization of Uch37 by sequestering Uch37 and forming a Uch37-Rpn13 com- plex. Uch37 was activated in such a complex, exhibiting 12-fold-higher activity than Uch37 alone. Time-resolved SAXS （TR-SAXS） and FRET experiments supported the proposed mode of auto-inhibition and the activation mechanism of Uch37 by Rpn13. Rpn13 activated Uch37 by forming a 1：1 stoichiometric complex in which the active site of Uch37 was accessible to Ub.

关键词： Uch37-Rpn13 complex de-ubiquitination,SAXS analysis oligomerization iso-peptidase

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