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Molecular level biodegradation of phenol and its derivatives through dmp operon of Pseudomonas putida:A bio-molecular modeling and docking analysis

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Journal of Environmental Sciences 2015年第10期27卷 144-151页

作者： Sujay ray Arundhati Banerjee Department of Biochemistry and Biophysics University of Kalyani Department of Biotechnology Bengal College of Engineering and TechnologyShahid Sukumar SaraniBidhannagarDurgapur-713212West BengalIndia Department of Biotechnology National Institute of Technology

Participation of Pseudomonas putida-derived methyl phenol（dmp） operon and Dmp R protein in the biodegradation of phenol or other harmful, organic, toxic pollutants was investigated at a molecular level. Documentation documents that P. putida has Dmp R protein which positively regulates dmp operon in the presence of inducers; like phenols. From the operon,phenol hydroxylase encoded by dmp n gene, participates in degrading phenols after dmp operon is expressed. For the purpose, the 3-D models of the four domains from Dmp R protein and of the DnA sequences from the two Upstream Activation Sequences（UAS）present at the promoter region of the operon were demonstrated using discrete molecular modeling techniques. The best modeled structures satisfying their stereo-chemical properties were selected in each of the cases. To stabilize the individual structures, energy optimization was performed. In the presence of inducers, probable interactions among domains and then the two independent DnA structures with the fourth domain were perused by manifold molecular docking simulations. The complex structures were made to be stable by minimizing their overall energy. Responsible amino acid residues, nucleotide bases and binding patterns for the biodegradation, were examined. In the presence of the inducers, the biodegradation process is initiated by the interaction of phe50 from the first protein domain with the inducers. Only after the interaction of the last domain with the DnA sequences individually, the operon is expressed. This novel residue level study is paramount for initiating transcription in the operon; thereby leading to expression of phenol hydroxylase followed by phenol biodegradation.

关键词： Biodegradation dmp operon Docking simulations Modeling Phenol P.putida

Evolutionary conservation and DnA binding properties of the Ssh7 proteins from Sulfolobus shibatae

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Science China(Life Sciences) 2002年第6期45卷 583-592页

作者：陈绪林郭荣黄力 ray Hong Pomona College CA91711

The thermoacidophilic archaeon Sulfolobus shibatae synthesizes a large amount of the 7-ku DMA binding proteins known as Ssh7. Our hybridization experiments showed that two Ssh7-encoding genes existed in the genome of S. shibatae. These two genes, designated ssh7a and ssh7b, have been cloned, sequenced and expressed in Escherichia coli. The two Ssh7 proteins differ only at three amino acid positions. In addition, the c/s-regulatory sequences of the ssh7a and ssh7b genes are highly conserved. These results suggest the presence of a selective pressure to maintain not only the sequence but also the expression of the two genes. We have also found that there are two genes encoding the 7-ku protein in Sulfolobus solfataricus. Based on this and other studies, we suggest that the gene encoding the 7-ku protein underwent duplication before the separation of Sulfolobus species. Binding of native Ssh7 and recombinant (r)Ssh7 to short duplex DnA fragments was analyzed by electrophoretic mobility shift assays. Both native and recombinant forms of the protein behaved in a similar fashion in the assays, suggesting that the interaction of Ssh7 with DnA is not affected either by specific lysine methylation found in the native Ssh7 proteins or by the difference between the two Ssh7 isomers in amino acid sequence. Our data show that Ssh7 binds duplex DnA fragments with a binding size of - 6.6 base pairs and an apparent dissociation constant of (0.7-1.0)×10-7 mol/L under the assay conditions employed in the present study. In addition, Ssh7 binds more tightly to negatively supercoiled DnA than to linear or relaxed DnA.

关键词： hyperthermophilic archaea, DnA binding proteins, ssh7a/ssh7b genes, protein-DnA interaction.

Interplay between genome organization and epigenomic alterations of pericentromeric DnA in cancer

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Journal of genetics and Genomics 2021年第3期48卷 184-197页

作者： Subhadip Kundu M.D.ray Ashok Sharma Laboratory of Chromatin and Cancer Epigenetics Department of BiochemistryAll India Institute of Medical SciencesAnsari NagarNew Delhi 110029India Department of Surgical Oncology IRCHAll India Institute of Medical SciencesAnsari NagarNew Delhi 110029India

In eukaryotic genome biology,the genomic organization inside the three-dimensional(3D)nucleus is highly complex,and whether this organization governs gene expression is poorly *** lamina(nL)is a filamentous meshwork of proteins present at the lining of inner nuclear membrane that serves as an anchoring platform for genome *** chromatin domains termed as lamina-associated domains(LADs),play a major role in silencing genes at the nuclear *** interaction of the nL and genome is dynamic and ***,many genes change their positions during developmental processes or under disease conditions such as cancer,to activate certain sorts of genes and/or silence *** heterochromatin(PCH)is mostly in the silenced region within the genome,which localizes at the nuclear *** show that several genes located at the PCH are aberrantly expressed in *** interesting question is that despite being localized in the pericentromeric region,how these genes still manage to overcome pericentromeric *** epigenetic mechanisms control the expression of the pericentromeric region,recent studies about genome organization and genome-nuclear lamina interaction have shed light on a new aspect of pericentromeric gene regulation through a complex and coordinated interplay between epigenomic remodeling and genomic organization in Cancer.

关键词： LADs Pericentromere Heterochromatin gene regulation Epigenetics Cancer Genome organization

Auxin regulation involved in gynoecium morphogenesis of papaya flowers

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Horticulture Research 2019年第1期6卷 237-247页

作者： Ping Zhou Mahpara Fatima Xinyi Ma Juan Liu ray Ming College of Life Sciences FAFU and UIUC Joint Center for Genomics and BiotechnologyFujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhou 350002 FujianChina Fruit Research Institute Fujian Academy of Agricultural SciencesFuzhou 350013 FujianChina College of Agriculture Fujian Agriculture and Forestry UniversityFuzhou 350002 FujianChina Department of Plant Biology University of Illinois at Urbana-ChampaignUrbanaIL 61801USA

The morphogenesis of gynoecium is crucial for propagation and productivity of fruit *** trioecious papaya(Carica papaya),highly differentiated morphology of gynoecium in flowers of different sex types is controlled by gene networks and influenced by environmental factors,but the regulatory mechanism in gynoecium morphogenesis is *** and dioecious papaya varieties were used for analysis of differentially expressed genes followed by experiments using auxin and an auxin transporter *** first compared differential gene expression in functional and rudimentary gynoecium at early stage of their development and detected significant difference in phytohormone modulating and transduction processes,particularly *** auxin signal transduction in rudimentary gynoecium was *** determine the role auxin plays in the papaya gynoecium,auxin transport inhibitor(n-1-naphthylphthalamic acid,nPA)and synthetic auxin analogs with different concentrations gradient were sprayed to the trunk apex of male and female plants of dioecious *** of auxin transport by 10 mg/L nPA treatment resulted in female fertility restoration in male flowers,while female flowers did not show *** treatment with higher concentration(30 and 50 mg/L)caused deformed flowers in both male and female *** hypothesize that the occurrence of rudimentary gynoecium patterning might associate with auxin homeostasis *** auxin concentration and auxin homeostasis might be crucial for functional gynoecium morphogenesis in papaya *** results will lead to further investigation on the auxin homeostasis and gynoecium morphogenesis in papaya.

关键词： papaya morphogenesis flowers

DnA methylome and transcriptome landscapes revealed differential characteristics of dioecious flowers in papaya

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Horticulture Research 2020年第1期7卷 1584-1598页

作者： Ping Zhou Xiaodan Zhang Mahpara Fatima Xinyi Ma Hongkun Fang Hansong Yan ray Ming College of Life Sciences FAFU and UIUC Joint Center for Genomics and BiotechnologyFujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry University350002 FuzhouFujianChina Fruit Research Institute Fujian Academy of Agricultural Sciences350013 FuzhouFujianChina Department of Plant Biology University of Illinois at Urbana-ChampaignUrbanaIL 61801USA College of Agriculture Fujian Agriculture and Forestry University350002 FuzhouFujianChina

Separate sexes in dioecious plants display different morphology and physiological *** differences between the two sexes lie in their highly differentiated floral characteristics and in sex-related phenotype,which is genetically determined and epigenetically *** dioecious papaya(Carica papaya L.),global comparisons of epigenetic DnA methylation and gene expressions were still *** conducted bisulfite sequencing of early-stage flowers grown in three seasons(spring,summer and winter)and compared their methylome and transcriptome profiles to investigate the differential characteristics of male and female in *** variances between female and male papaya were conserved among three different ***,combined genome-scale transcriptomic evidence revealed that most methylation variances did not have influence on the expression profiles of neighboring genes,and the differentially expressed genes were most overrepresented in phytohormone signal transduction *** analyses showed diverse stress-responsive methylation alteration in male and female *** flower methylation was more responsive to stress whereas female flower methylation varied less under *** flowering of male papaya in spring might be associated with the variation in the transcription of CpSVP and CpAP1 coinciding with their gene-specific *** findings provide insights into the sex-specific DnA methylation and gene expression landscapes of dioecious papaya and a foundation to investigate the correlation between differentiated floral characteristics and their candidate genes.

关键词： papaya flowers landscape

Physiological Basis of Stagnant Flooding Tolerance in Rice

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Rice science 2017年第2期24卷 73-84页

作者： Sandhya R.KUAnAR Anuprita ray Santosh K.SETHI Krishnendu CHATTOPADHYAY Ramani K.SARKAR Crop Physiology&Biochemistry Division National Rice Research InstituteCuttack 753006India

Stagnant flooding(SF) is an important constraint which prolonges partial submergence damages of rice plants and reduces grain yield. Due to the heterogeneity in flood-prone ecosystem, many different types of traditional rice varieties are being grown by the farmers. The local landraces adapted to extreme in water availability could be the sources of new gene(s) which would be utilized to improve the adaptability of rice to SF with high yield. The main goal of this study is to identify new genetic resources tolerant to SF based on morpho-physiological traits. A total of 16 rice varieties were selected after initial screening from more than 400 rice varieties which were collected from eastern states of India. The increase rate of plant height was higher under SF compared to control, whereas no such trend was observed in the increment rate of aboveground total dry weight and culm dry weight. Area of aerenchyma gas spaces per tiller increased whereas root oxidase activity decreased under SF. The reduction of root oxidase activity, leaf area, and leaf dry weight was higher in susceptible varieties under SF compared to control. Stability index for different grain yield and yield attributes revealed that the impact of SF differed among different varieties. Correlation coefficient studies among different parameters taking stability index showed significant association with the grain yield. Based on the findings, it was concluded that maintenance of equivalent panicle weight and panicle number, plant height and harvest index at the maturity stage, leaf area, leaf and culm dry weights, root oxidase activity and tiller numbers at the flowering stage under SF compared to control help the plant to counteract the adverse effects of SF.

关键词： morpho-physiological trait rice stagnant flooding yield

The splicing factor Prp31 is essential for photoreceptor development in Drosophila

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Protein & Cell 2010年第3期1卷 267-274页

作者： Payal ray Xiaoyan Luo Elizabeth J.Rao Amina Basha Elvin A.Woodruff III Jane Y.Wu Department of neurology Northwestern University Feinberg Medical SchoolChicagoIL 60611USA Magnify Inc. 2316 Riverside DrNashvilleTN 37216USA Present address:Trumbull College Yale UniversityNew HavenCT 06511USA

Retinitis pigmentosa is a leading cause of blindness and a progressive retinal disorder,affecting millions of people *** disease is characterized by photoreceptor degeneration,eventually leading to complete *** dominant(adRP)has been associated with mutations in at least four ubiquitously expressed genes encoding pre-mRnA splicing factors—Prp3,Prp8,Prp31 and *** function of adRPassociated splicing factor genes and molecular mechanisms by which mutations in these genes cause cell-type specific photoreceptor degeneration in humans remain to be *** investigate the in vivo function of these adRP-associated splicing factor genes,we examined Drosophila in which expression of fly Prp31 homolog was *** analyses show that CG6876 is the likely candidate of Drosophila melanogaster Prp31 homolog(DmPrp31).Predicted peptide sequence for CG6876 shows 57%similarity to the Homo sapiens Prp31 protein(HsPrp31).Reduction of the endogenous Prp31 by RnAi-mediated knockdown speci-fically in the eye leads to reduction of eye size or complete absence of eyes with remarkable features of photoreceptor degeneration and recapitulates the bimodal expressivity of human Prp31 mutations in adRP *** transgenic DmPrp31RnAi flies provide a useful tool for identifying genetic modifiers or interacting genes for *** of the human Prp31 in these animals leads to a partial rescue of the eye *** results indicate that the Drosophila CG6876 is the fly ortholog of mammalian Prp31 gene.

关键词： Drosophila photoreceptor degeneration retinitis pigmentosa Prp31

PGD: Pineapple Genomics Database

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Horticulture Research 2018年第1期5卷 276-284页

作者： Huimin Xu Qingyi Yu Yan Shi Xiuting Hua Haibao Tang Long Yang ray Ming Jisen Zhang Center for Genomics and Biotechnology Haixia Institute of Science and TechnologyFujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry University350002FuzhouChina College of Resource and Environment Fujian Agriculture and Forestry University350002FuzhouChina Department of Plant Pathology and Microbiology Texas A&M AgriLife ResearchTexas A&M University SystemDallasTX75252USA Agricultural Big-Data Research Center and College of Plant Protection Shandong Agricultural University271018TaianChina Department of Plant Biology University of Illinois at Urbana-ChampaignUrbanaIL61801USA

Pineapple occupies an important phylogenetic position as its reference genome is a model for studying the evolution the Bromeliaceae family and the crassulacean acid metabolism(CAM)***,we developed a pineapple genomics database(PGD,http://***/pineapple/html/***)as a central online platform for storing and integrating genomic,transcriptomic,function annotation and genetic marker data for pineapple(Ananas comosus(L.)Merr.).The PGD currently hosts significant search tools and available datasets for researchers to study comparative genomics,gene expression,gene co-expression molecular marker,and gene annotation of ***(L).PGD also performed a series of additional pages for a genomic browser that visualizes genomic data interactively,bulk data download,a detailed user manual,and data integration *** was developed with the capacity to integrate future data resources,and will be used as a long-term and open access database to facilitate the study of the biology,distribution,and the evolution of pineapple and the relative plant *** email-based helpdesk is also available to offer support with the website and requests of specific datasets from the research community.

关键词： database browser email

Investigation of experimental observables in search of the chiral magnetic effect in heavy-ion collisions in the STAR experiment

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Chinese Physics C 2022年第1期46卷 129-145页

作者： Subikash Choudhury Xin Dong Jim Drachenberg James Dunlop ShinIchi Esumi Yicheng Feng Evan Finch Yu Hu Jiangyong Jia Jerome Lauret Wei Li Jinfeng Liao Yufu Lin Mike Lisa Takafumi niida Robert Lanny ray Masha Sergeeva Diyu Shen Shuzhe Shi Paul Sorensen Aihong Tang Prithwish Tribedy gene Van Buren Sergei Voloshin Fuqiang Wang Gang Wang Haojie Xu Zhiwan Xu nanxi Yao Jie Zhao Fudan University Shanghai200433 Lawrence Berkeley national Laboratory BerkeleyCalifornia 94720 Abilene Christian University AbileneTexas 79699 Brookhaven national Laboratory UptonNew York 11973 University of Tsukuba TsukubaIbaraki 305-8571 Purdue University West LafayetteIndiana 47907 Southern Connecticut State University New HavenConnecticut 06515 State University of new York Stony BrookNew York 11794 Rice University HoustonTexas 77251 Physics Department and Center for Exploration of Energy and Matter Indiana University2401 N Milo B.Sampson LaneBloomingtonIN 47408 College of Physics and Technology Guangxi Normal UniversityGuilin541004 Central China normal University WuhanHubei 430079 Ohio State University ColumbusOhio 43210 University of Texas AustinTexas 78712 University of California Los AngelesCalifornia 90095 Department of Physics McGill University3600 University StreetMontrealQCH3A 2T8 Wayne State University DetroitMichigan 48201 Huzhou University HuzhouZhejiang 313000

The chiral magnetic effect(CME)is a novel transport phenomenon,arising from the interplay between quantum anomalies and strong magnetic fields in chiral *** high-energy nuclear collisions,the CME may survive the expansion of the quark-gluon plasma fireball and be detected in *** the past two decades,experimental searches for the CME have attracted extensive interest at the Relativistic Heavy Ion Collider(RHIC)and the Large Hadron Collider(LHC).The main goal of this study is to investigate three pertinent experimental approaches:the$\gamma$correlator,the R correlator,and the signed balance *** exploit simple Monte Carlo simulations and a realistic event generator(EBE-AVFD)to verify the equivalence of the core components among these methods and to ascertain their sensitivities to the CME signal and the background contributions for the isobar collisions at the RHIC.

关键词： chiral magnetic effect anisotropic flow heavy-ion collisions quark-gluon plasma