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Predicting tbx22 Zebrafish Protein Structure Using Multi-Level Prediction Tools and Demonstration of Conserved Structural Domains in Relation to Orthologous tbx22 Proteins in Humans

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Journal of Biosciences and Medicines 2016年第3期4卷 79-92页

作者： Vijay P. Boominathan Tracie Ferreira Department of Bioengineering University of Massachusetts Dartmouth North Dartmouth MA USA

Biological functions of proteins play a key role in the development of any organism. The gene tbx 22 is a member of a phylogenetically conserved family of genes, which share a common DNA binding domain: T box. This study examines the similarity in the developmental pattern influenced by the transcription factor TBX22 and tbx22 in H. sapiens and D. rerio respectively. Secondary and tertiary structures of the proteins are predicted using standard structure prediction software’s like Phyre 2, Predict Protein, SWISSMODEL, PSIPRED and the homology of the proteins were compared to each other. Protein homology prediction shows more than 65% between the 2 organisms. Superimposing the predicted protein structures reveals conserved domains between the human and zebrafish proteins. Additional supporting data from Genomatix MATBASE, MATINSPECTOR show higher matrix family scores for BRAC (Brachury gene mesoderm developmental factor) in Human and Zebrafish. transcription factor and promoter element analysis with Transcriptome Viewer, Gene 2 Promoter and Genomeinspector reveal a high degree of homology between the 2 organisms. Bioinformatic-Proteomics and protein structural analysis approaches shown here explain in detail the relationship between the Human and Zebrafish tbx22 Gene-Protein-Transcrip- tion factor. These studies also support zebrafish as a predictive model for numerous developmental pattering events in higher vertebrates.

关键词： T-box tbx22 transcription factors Genomatix Protein Prediction Superimposed Models

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Essential vitamins for an effective T cell response

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World Journal of Immunology 2016年第1期6卷 39-59页

作者： Ritobrata Goswami Mark H Kaplan Institute of Life Sciences Ahmedabad University Department of Pediatrics Wells Center for Pediatric ResearchIndiana University

Effective adaptive immune responses rely upon appropriate activation of T cells by antigenic peptidemajor histocompatibility complex on the surface of antigen presenting cells(APCs).Activation relies on additional signals including co-stimulatory molecules on the surface of the APCs that promote T cell expansion.The immune response is further sculpted by the cytokine environment.However,T cells also respond to other environmental signals including hormones,neurotransmitters,and vitamins.In this review,we summarize the mechanisms through which vitamins A and D impact immune responses,particularly in the context of T cell responses.

关键词： Vitamin D Retinoic acid T helper cells Cytokines transcription factors Allergy Autoimmune diseases

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Over-Expression of a transcription Factor OsDREB2A （p） Gene in Rice Enhances Drought or Salt Tolerance

Over-Expression of a Transcription Factor OsDREB2A （p） Gen...

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中国植物生理学会第十次会员代表大会暨全国学术年会

作者： Ray Wu Department of Molecular Biology ＆ Genetics Cornell University Ithaca NY 14853 USA

＜正＞The plant DREBs/CBFs transcription factors play a critical roles in plant development and abiotic stress responses. In this study, a putative rice OsDREB2A gene was expressed under the stress inducible promoter

关键词： transcription factors OsDREB2A drought stress salt stress transgenic rice

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Decoding the Signaling Network for Abscisic Acid and Gibberellins:an Approach That Integrates Bioinformatics and Experimental Biology

Decoding the Signaling Network for Abscisic Acid and Gibbere...

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第二届植物分子育种国际会议

作者： C.Ross P.Ruas Department of Biological Sciences University of NevadaLas VegasNevada89154USA

Seeds comprise 0% of the human diet, while cereals such as rice and wheat comprise 52.5% of the world diet (***/es/ess/chartroom/default.asp). To meet the needs in food of the rapidly growing world population, crop breeders have put a tremendous amount of effort to improving the yield and quality of crops. However, drastic yield losses of cereal crops still result from preharvest sprouting and abiotic stresses (unfavorable environmental conditions).

关键词： Rice Biotechnology Bioinformatics Comparative Genomics Abscisic acid Gibberellins Signaling Perharvest-sprouting Germination Dormancy Stresses WRKY transcription factors

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Genome-Wide Identification and Comprehensive Analysis of the NAC transcription Factor Family in Sesamum indicum

Genome-Wide Identification and Comprehensive Analysis of the...

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2017年中国作物学会学术年会

作者：张玉娟 Huihui Gong Donghua Li Yanyan Wang Rong Zhou Jingyin Yu Jun You 张秀荣 Key Laboratory of Biology and Genetic Improvement of Oil Crops Ministry of Agriculture Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences Cotton Research Center Cotton Research CenterShandong Academy of Agricultural SciencesHuanghuaihai Key Laboratory of Cotton Genetic Improvement and Cultivation Physiology of the Ministry of Agriculture

The NAM,ATAF1/2 and CUC2(NAC) family,a large family of plant-specific transcription factors(TFs),involved in many aspects of physiological processes and a variety of abiotic stresses.To date,little information is known about the NAC family in Sesamum indicum.During this study,87 NAC genes were identified from the sesame genome and phylogenetically clustered into nine groups with the NAC genes from Arabidopsis.The physical positions,duplication patterns,phylogeny,conserved motifs and gene structure of these 87 SiNAC genes were investigated.Expression profiles of SiNAC genes in different tissues including root,stem,leaf,flower,seed and capsule and in response to waterlogging and drought stresses were analyzed using the RNA-seq data.In addition,the expression of 30 SiNAC genes distributed in different subgroups was analyzed by qRT-PCR under cold,osmotic,and salt stresses.The results showed that expression diversity of SiNAC genes among different tissues and various abiotic stress treatments,indicating their contribution to plant developmental processes and multiple stresses resistance in sesame.Taken together,this study identifies some tissue-specific and abiotic stress-responsive candidate SiNAC genes for further functional assays in sesame,and provides valuable information for understanding of abiotic stress responses and signal transduction mediated by SiNACs in sesame.

关键词： Sesame transcription factors NAC Abiotic stress Phylogenetic relationship Gene expression

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Identification and characterization of bZIP transcription factor family in sesame

Identification and characterization of bZIP transcription fa...

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中国作物学会油料作物专业委员会第八次会员代表大会暨学术...

作者： WANG Yan-yan ZHANG Yu-juan ZHOU Rong Komivi Dossa YU Jing-yin LI Dong-hua LIU Ai-li Marie Ali Mmadi ZHANG Xiu-rong YOU Jun Key Laboratory of Biology and Genetic Improvement of Oil Crops Ministry of AgricultureOil Crops Research InstituteChinese Academy of Agricultural Sciences Cotton Research Center Cotton Research CenterShandong Academy of Agricultural SciencesHuanghuaihai Key Laboratory of Cotton Genetic Improvement and Cultivation Physiology of the Ministry of Agriculture

Basic leucine zipper(bZIP) gene family is one of the largest transcription factor families in plants.Members of this family play important roles in multiple biological processes such as light signaling,seed maturation,flower development as well as abiotic and biotic stress responses.Nonetheless,genome-wide comprehensive analysis of bZIP family is lacking in sesame.In present study,63 bZIP genes distributed on 14 linkage groups were identified in sesame,and denominated as SibZIP01-SibZIP63.Besides,all members of SibZIP family were divided into 9 groups based on phylogenetic relationship of Arabidopsis bZIPs,which was further supported by analysis of conserved motifs and gene structures.Promoter analysis showed that all SibZIP genes harbor cis-elements related to stress responsiveness in their promoter regions.Expression analyses of SibZIP genes based on transcriptome data showed that these genes have different expression patterns in different tissues.Additionally,we showed that a majority of SibZIPs(85.71%) exhibited significant transcriptional changes in responses to abiotic stresses,including drought,waterlogging,osmotic,salt,and cold,suggesting that SibZIPs may play a cardinal role in regulation of stress responses of sesame.Together,these results provide new insights into stress-responsive SibZIP genes and pave the way for future studies of SibZIPs mediated abiotic stress response in sesame.

关键词： sesame transcription factors bZIP abiotic stress gene expression

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Temporal and spatial origins models of neural subtypes in nuclei septum

Temporal and spatial origins models of neural subtypes in nu...

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中国神经科学学会第九届全国学术会议暨第五次会员代表大会

作者： Bin WEI,Zeng-Jing HUANG,Zhen-Gang YANG~* Laboratory of Neural Stem Cell and Development,Institute of Brain Science,Fudan University,Shanghai 200032 China

＜正＞Septum has very important roles in connections between forebrain and middle brain.Since its neurons project into hippocampus,it make great role in the regulation of learning and memory.In the past decades,septum has been separately defined into lateral septum（LS） and medial septum（MS） by the anatomical differences.In our recent work,we identified two markers,sp8 and sox6,to distinguish LS with MS.In addition,LS can subdivide into dorsal（LSD）,medial（LSI） and ventral（LSV） parts.By using markers we proved that MS neurons are also found similarly in the Diagonal Bind of Broca（DBB）.Most of the neurons in LSI express GABA-ergic marker calbindin （CB）,which express Sp8,some of them express Nkx2.1.Neurons in LSV express GABA-ergic marker calretinin（CR）, which colabelling with Sp8,Pax6,and Emx1.Neurons in MS/DBB may have diverse origins,GABA-ergic marker PV express sox6,Chat express Nkx2.1 but not Sox6,nNOS express both Nkx2.1 and Sox6.By BrdU fate mapping,we found MS neurons born at fist,from Embyronic（E） 10.5 to 12.5.While LS neurons born later from E12.5 to E14.5.By using electroporation（ET） reporter plasmid,combined with Cre-Loxp technology,we specifically followed the septal routes of the progenitors of Emxl-lineage,directly verified the embryonic dorsal part origins of septum.Similarly,we can explore the multiple origins model:medial,ventral,and the ventral-caudal part origins.In sum,we are unraveling the diversity of septum’s neurons,which is the result of the different temporal and spatial origins.

关键词： septum neural development differentiation transcription factors

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Identification of endophytic fungi responsive miRNA involved in the regulation of sesquiterpenoid biosynthesis in Atractylodes lancea

Identification of endophytic fungi responsive miRNA involved...

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中国植物学会第十六次全国会员代表大会暨85周年学术年会

作者： Jie Yuan Fei Chen Hurong Yang Piaoxue Chen Wei Zhang Mengjun Tang Xia Li Chuanchao Dai Jiangsu Key Laboratory for Microbes and Functional Genomics Jiangsu Engineering and Technology Research Center for Industrialization of Microbial ResourcesCollege of Life SciencesNanjing Normal University Jiangsu High-Quality Rice Research and Development Center Nanjing Branch of China National Center for Rice ImprovementInstitute of Food CropsJiangsu Academy of Agricultural Sciences

Endophytes have been considered long-term safe and effective methods for inducing plant secondary metabolite biosynthesis.However,the underlying microRNAs associated with endophyte induced terpenoid biosynthesis are unknown.To elucidate the molecular mechanism at the miRNA level,we identified endophytic fungiresponsive miRNAs in A.lancea shoots and analyzed the function of their targets using a high-throughput platform.A total of 153 known miRNAs and 83 novel miRNAs were differentially expressed in A.lancea after endophytes Gilmaniella sp.AL12 inoculation.Subsequently,51,570 potential targets were predicted.Gene ontology(GO) enrichment analyses showed prominent enrichment in signal transduction for the targets of down-regulated miRNA.Furthermore,novelir5,novelir44,and novelir37 were predicted to be involved in regulating sesquiterpenoid biosynthesis in A.lancea.,Moreover,we proposed that novelir44 may be a hub miRNA functioning in regulating sesquiterpenoids biosynthesis by targeting 1-deoxyD-xylulose 5-phosphate synthase(DXS) and many transcription factors such as WRKY,APETALA2/Ethylene-Response factors(AP2/ERF),basic Helix-Loop-Helix(bHLH),heat stress,and Nuclear transcription factor Y subunit A(NF-YA).This study provides the first insight into endophytes-induced plant terpenoid biosynthesis at the miRNA expression level and will provide knowledge about beneficial plant-endophyte interactions.

关键词： Endophytes Atractylodes lancea Sesquiterpenoids MicroRNA transcription factors

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R2R3-MYB Protein GhMYB36 from Cotton Confers Drought Tolerance in Arabidopsis

R2R3-MYB Protein GhMYB36 from Cotton Confers Drought Toleran...

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江苏省遗传学会2017年学术研讨会——“技术创新与遗传...

作者：刘廷利 Jialiang Kan Xiaoshuang Liu Fan Liu Xitie Ling Tianzi Chen Yuwen Yang Jinyan Wang 张保龙 Provincial Key Laboratory of Agrobiology Jiangsu Academy of Agricultural Sciences

MYB transcription factors（TFs） are a large group of functionally diverse proteins and present in all eukaryotes. In plants, R2R3-MYB proteins are predominant among MYB TFs but their function in cotton remains largely unclear. In our study, we isolated GhMYB36, a gene encoding a R2R3-type MYB protein in Gossypium hirsutum, that is highly induced by PEG treatments. In addition, GhMYB36-silenced cotton plants were more sensitive to drought and exhibited greater malondialdehyde（MDA） content and lower total antioxidant activity than the control plants. GhMYB36 transgenic Arabidopsis plants showed better drought tolerance. The agro-infiltration-based transient expression of fused GhMYB36-GFP in tobacco cells indicated that GhMYB36 was located in the cell nucleus. Collectively, our results suggest that GhMYB36 functions as a R2R3-type MYB protein and is essential to the improvement of drought tolerance in plants.

关键词： transcription factors drought tolerance transgenic plants transient expression R2R3-type MYB proteins

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Networks of biochemical mechanisms, transcriptional regulation, and ionic transport underpin salinity tolerance in cotton

Networks of biochemical mechanisms, transcriptional regulati...

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中国生物工程学会第十一届学术年会暨2017年全国生物技...

作者： Muhammad Ali Abid Chengzhen Liang Waqas Malik Zhigang Meng Zhu Tao Zhaoghong Meng Javaria Ashraf Sandui Guo Rui Zhang Biotechnology Research Institute Chinese Academy of Agricultural Sciences Genomics Lab Department of Plant Breeding and Genetics Faculty of Agricultural Sciences and Technology Bahauddin Zakariya University

Salt stress is a severe threat to agricultural productivity in many parts of the world. Cotton(Gossypium hirsutum) is an economically important fiber crop globally, and is regarded as a model crop for salinity tolerance research. Although cotton is a relatively salt-tolerant plant, its growth and development, as well as fiber yield and quality, are greatly reduced by severe salt conditions. Salinity tolerance studies in cotton have focused on finding the key molecular genetic processes activated in response to salt stress, for breeding salt-tolerant cotton genotypes. In response to salt stress, cotton exhibits a variety of changes at the molecular, biochemical,and physiological levels. Photosynthetic pathways and metabolism play pivotal roles in redox balance and ion homeostasis. Several stress signaling pathways e.g. abscisic acid, salt overly sensitive(SOS),mitogen-activated protein kinase(MAPK), reactive oxygen species(ROS),and membrane bound Na+/H+antiporters, all participate in salinity tolerance. The activation and regulation of specific genes drive this physiological and biochemical plasticity. In cotton, the roles of several transcription factors(e.g. WRKY, ZFP, NAC, DREB, bZIP and ERF) in salt stress tolerance have been well documented. We also highlight the potential areas for future investigation to elucidate the key pathways for effective breeding of salt-tolerant cotton genotypes.

关键词： Cotton Salt stress Antioxidants Na+/H+ antiporters transcription factors

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