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Involvement of chromatin and histone acetylation in the regulation of HIV-LTR by thyroid hormone receptor

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Cell Research 2001年第1期11卷 8-16页

作者： SHAO CHUNG VICTOR HSIA, HUA WANG, YUN BO SHI (Unit on Molecular Morphogenesis, Laboratory of Molecular Embryology, national institute of child health and human development, national institute of health, Building 18T, Room 106, bethesda, md 2.892.5431, usa Unit on Molecular Morphogenesis Laboratory of Molecular Embryology National Institute of Child Health and Human Development National Institute of Health Building 18T Room 106 Bethesda MD 20892-5431 USA

The HIV-1 LTR controls the expression of HIV-1 viral genes and thus is critical for viral propagation and pathology. Numerous host factors have been shown to participate in the regulation of the LTR Promoter. Among them is the thyroid hormone (T3) receptor (TR). TR has been shown to bind to the critical region of the promoter that contain the NFkB and Sp1 binding sites. Interestingly, earlier transient transfection studies in tissue culture cells have yielded contradicting conclusions on the role of TR in LTR regulation, likely due to the use of different cell types and/or lack of proper chromatin organization. Here, using the frog oocyte as a model system that allows replication-coupled chromatin assembly, mimicking that in somatic cells, we demonstrate that unliganded heterodimers of TR and RXR (9-cis retinoic acid receptor) repress LTR while the addition of T3 relieves the repression and further activates the promoter. More importantly, we show that chromatin and unliganded TR/RXR synergize to repress the promoter in a histone deacetylase- dependent manner.

关键词： HIV thyroid hormone receptor histone acetylation transcriptional repression Xenopus oocyte.

Spatial and temporal regulation of collagenases-3, -4,and stromelysin -3 implicates distinct functions in apoptosis and tissue remodeling during frog metamorphosis

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Cell Research 1999年第2期9卷 91-105页

作者： DAMJANOVSKI SASHKO ATSUKO ISHIZUYAOKA YUN-BO SHI (Laboratory of Molecular Embryology, Building 18T, Rm. 106, national institute of child health and human development, national institutes of health, bethesda, md, 2.892. usa)(Department Of Histology and 1Laboratory of Molecular Embryology Building 18T Rm. 106 National Institute of Child Health and Human Development National Institutes of Health Bethesda MD 20892 USA 2Department of Histology and Neurobiology Dokkyo University School of Medicine Mibu Tochigi 321-02 Japan 1Laboratory of Molecular Embryology Building 18T Rm. 106 National Institute of Child Health and Human Development National Institutes of Health Bethesda MD 20892 USA

Matrix metalloproteinases (MMPs) are a family of extracellular proteases capable of degrading various proteinaceous components of the extracellular matrix (ECM).They have been implicated to play important roles in a number of developmental and pathological processes, such as tumor metastasis and inflammation. Relatively few studies have been carried out to investigate the function of MMPs during postembryonic organ-development. Using Xenopus laevis development as a model system, we demonstrate here that three MMPs, stromelysin-3 (ST3),collagenases-3 (Col3), and Col4, have distinct spatial and temporal expression profiles during metamorphosis as the tadpole transforms into a frog. In situ hybridizations reveal a tight, but distinct, association of individual MMPs with tissue remodeling in the tail and intestine during metamorphosis. In particular, ST3 expression is strongly correlated with apoptosis in both organs as demonstrated by analyses of serial sections with in situ hybridization for ST3 mRNA and TUNEL (terminal deoxyribonucleotidyl transferase-mediated dUTP-biotin nick end labeling) for apoptosis, respectively. On the other hand, Col3 and Col4 MMPs in Xenopus laevis development are present in regions where extensive connective tissue remodeling take place. These results indicate that ST3 is likely to play a role in ECM-remodeling that facilitateapoptotic tissue remodeling or resorption while Col3 and Col4 appear to participate in connective tissue degradation during development.

关键词： Apoptosis thyroid hormone matrix metalloproteinase extracellular matrix (ECM) amphibian

Chromatin remodeling regulated by steroid and nuclear receptors

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Cell Research 1997年第2期7卷 127-142页

作者： ALAN P WOLFFE(Laboratory of Molecular Embroyology Nat’l institute ofchild health and human development NIH Bldg, 18T,Rm. 106 bethesda, md 2.892.5431 usa. e-mail:awlme @helix. nih.gov) Laboratory of Molecular Embroyology Nat'l institute of child health and human development NIH Bldg 18T Rm. 106 Bethesda MD 20892-5431 USA. e-mail: awlme@helix.nih.govReceived 27October1997 Accepted 4November1997.

Coactivators and corepressors regulate transcriptionby controlling interactions between sequence-specific transcription factors, the basal transcriptional machinery andthe chromatin environment. This review consider the access of nuclear and steroid receptors to chromatin, theiruse of corepressors and coactivators to modify chromatinstructure and the implications for transcriptional *** assembly of specific nucleoprotein architectures andtargeted histone modification emerge as central controlling elements for gene expression.

关键词： Steroid receptor nuclear receptor coactitvator corepressor transcriptional activation nucleosome positioning histone modification transcriptional repression

Preoperative Serum Albumin Levels and Postoperative Acute Kidney Injury in Off-Pump Coronary Artery Bypass Surgery: A Single-Center Study in Bangladesh

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World Journal of Cardiovascular Surgery 2024年第8期14卷 131-144页

作者： Ahmad Pear Salahuddin md. Abir Tazim Chowdhury Munama Magdum Dewan Iftakher Reza Chowdhury Nittya Nanda Pal md. Nahedul Morshed md. Zafar-Al-Nimari Latifa Nasrin Farooque Ahmed Department of Cardiac Surgery National Heart Foundation Hospital and Research Institute (NHFH&RI) Dhaka Bangladesh Department of Cardiothoracic and Vascular Surgery Evercare Hospital Dhaka Dhaka Bangladesh national institute of Preventive and Social Medicine Dhaka Bangladesh Mother and child Welfare Center Cumilla Bangladesh

Background: Serum albumin, a vital plasma protein, helps maintain intravascular colloidal osmotic pressure, cardiac output, and renal function. Low preoperative serum albumin is linked to poor outcomes, including acute kidney injury (AKI), after off-pump coronary artery bypass (OPCAB) surgery. This study aimed to assess the relationship between preoperative serum albumin levels and early postoperative renal injury. Methods: This prospective comparative cross-sectional study was conducted from August 2019 to February 2021 at the national Heart Foundation Hospital & Research institute, Bangladesh. It included 160 adult patients with normal preoperative renal function undergoing OPCAB. Patients were divided into two groups: Group A (serum albumin ≥ 4.0 gm/dl) and Group B (serum albumin Results: Preoperative serum albumin was significantly different between groups (Group A: 4.21 ± 0.05 gm/dl, Group B: 3.69 ± 0.04 gm/dl, p = 0.028). Group B had a higher incidence of hypertension (71.25% vs. 51.25%, p st and 3rd postoperative days were higher in Group B (p th day. Postoperative AKI occurred in 18.75% of Group A and 36.25% of Group B. Multivariate regression indicated that low preoperative serum albumin is an independent risk factor for postoperative AKI (p = 0.012, OR = 1.815, CI: 0.675 - 1.162). Conclusion: Preoperative serum albumin level is a valuable predictor of postoperative renal function. Ensuring high normal serum albumin levels before surgery can help minimize the risk of postoperative AKI.

关键词： Serum Albumin Acute Kidney Injury (AKI) Off-Pump Coronary Artery Bypass Surgery Bangladesh

Biofunctionalization of fluorescent-magnetic-bifunctional nanospheres and their recognition and sorting of apoptotic cells

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Biofunctionalization of fluorescent-magnetic-bifunctional na...

Predicting disease genes for familial dilated cardiomyopathy based on the codon usage bias

第四届全国化学生物学学术会议暨国际化学与生物/医学交叉研讨会

作者： Guo-Ping Wang,Er-Qun Song,Hai-Yan Xie,Zhi-Ling Zhang,Zhi-Quan Tian," Chao Zuo," Dai-Wen Pang, Dao-Cheng Wu,and Yun-Bo Shi institute of Chemical Biology, College of Chemistry and Molecular Sciences, and State Key Laboratory of Virology, Wuhan University, Wuhan 430072, P. R. China. School of Life Science and Technology, Beijing institute of Technology, Beijing, P. R. China School of Life Science and Technology, Xi ’an Jiaotong University , P. R. China Laboratory of Gene Regulation and development, national institute child health and human development (NICHD), national institute of health (NIH), Building 18T Room 106, 18 LIBRARYDR MSC 5431, bethesda, md 2.892.5431, usa

Nanospheres ale becoming the materials of choice for rapidly increasing number of pharmaceutical applications and in biomedical *** the fluorescent and magnetic property into a single nanosphere would greatly increase its application potential in biomedical and biopharmaceutical *** describe here new methods for the biofunctionalization of bifunctional nanospheres(100-150 nm in diameter)with immunoglobulin G(IgG),avidin,and biotin to generate trifunctional nanospheres with a wide range of potential biomedical applications．

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Science Bulletin 2005年第18期 62-66页

作者： ZHOU Yanhong1,2, ZHOU Quanxiong1,2, LIU Huailan1,2 & WAN Honghui3 1. Center for bioinformatics, Huazhong University of Science and Technology, Wuhan 430074, China 2. Hubei bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China 3. Laboratory of bioinformatics, Maryland institute of Dynamic Ge-nomics, Silver Spring, md 20906, usa

Familial dilated cardiomyopathy (FDC) is a common monogenic disease mostly with autosomal dominant inheritance. Fifteen different loci for autosomal dominant FDC have been mapped; however, only eight FDC genes have been found, and it is still a big challenge to identify ad-ditional seven FDC genes in their chromosomal regions. We found that the codon usage frequencies in most of known FDC gene sequences are consistently biased, and significantly different from the average codon usage frequencies of human genes. This unique feature of codon usage was used to de-velop a novel approach to predicting FDC genes. Leave-one- out cross-validation results demonstrate that this approach can effectively detect FDC genes from numbers of genes in their chromosomal regions. Another advantage of this ap-proach is that it is solely based on DNA sequences and there-fore has the ability to identify potential FDC genes whose functions are completely unknown. Further, this approach has been used to analyze the seven FDC loci in which the FDC genes are still unknown. Both the detailed prediction results and the prediction program are available at http:// ***, which might provide help for relevant experimental researches to find new FDC genes.

关键词： familial dilated cardiomyopathy codon usage disease gene prediction.

iLBE for Computational Identification of Linear B-cell Epitopes by Integrating Sequence and Evolutionary Features

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Genomics, Proteomics & bioinformatics 2020年第5期18卷 593-600页

作者： md.Mehedi Hasan Mst.Shamima Khatun Hiroyuki Kurata Department of Bioscience and bioinformatics Kyushu Institute of TechnologyIizukaFukuoka 820-8502Japan Biomedical Informatics R&D Center Kyushu Institute of TechnologyIizukaFukuoka 820-8502Japan

Linear B-cell epitopes are critically important for immunological applications,such as vaccine design,immunodiagnostic test,and antibody production,as well as disease diagnosis and *** accurate identification of linear B-cell epitopes remains challenging despite several decades of *** this work,we have developed a novel predictor,Identification of Linear B-cell Epitope(i LBE),by integrating evolutionary and sequence-based *** successive feature vectors were optimized by a Wilcoxon-rank sum *** the random forest(RF)algorithm using the optimal consecutive feature vectors was applied to predict linear B-cell *** combined the RF scores by the logistic regression to enhance the prediction *** yielded an area under curve score of 0.809 on the training dataset and outperformed other prediction models on a comprehensive independent *** is a powerful computational tool to identify the linear B-cell epitopes and would help to develop penetrating diagnostic tests.A web application with curated datasets for iLBE is freely accessible at http://***/iLBE/.

关键词： Linear B-cell epitope BLAST Feature encoding Feature selection Random forest

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Pathogens causing diarrhoea among Bangladeshi children with malignancy: Results from two pilot studies

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World Journal of Clinical Cases 2020年第2期8卷 276-283页

作者： Sabina Karim Ferdousi Begum Afiqul Islam Monowar Ahmad Tarafdar Mamtaz Begum md Johirul Islam Bushra Malik md Shamim Ahsan Ameneh Khatami Harunor Rashid Department of Paediatric Haematology and Oncology National Institute of Cancer Research and HospitalMohakhaliDhaka 1212Bangladesh Department of Pediatric Hematology and Oncology Bangabandhu Sheikh Mujib Medical UniversityDhaka 1212Bangladesh Department of Community Medicine Z.H.Sikder Women’s Medical CollegeDhaka 1212Bangladesh Department of Cancer Epidemiology National Institute of Cancer Research and HospitalMohakhaliDhaka 1212Bangladesh national Centre for Immunisation Research and Surveillance The Children’s Hospital at WestmeadWestmeadNSW 2145Australia Medical Services Rangpur CantonmentRangpur 5400Bangladesh Department of Infectious Diseases and Microbiology The Children’s Hospital at WestmeadNSW 2145Australia Discipline of child and Adolescent health Faculty of Medicine and HealthUniversity of SydneyNSW 2145Australia

BACKGROUND Diarrhoea is a frequent symptom in children with cancer, and occurs due to a composite effect of underlying disease and immunosuppression consequent to therapy, malnutrition, and non-infective aetiologies such as mucositis. In a large proportion of cases, the aetiology of diarrhoea remains unknown but is often attributed to multiple pathogens including *** To identify and describe the pathogens causing diarrhoea in Bangladeshi children with *** Two cross-sectional pilot studies were conducted involving paediatric oncology patients with diarrhoea. Stool samples were collected from children who were hospitalised with or without being treated with chemotherapy during the study period, and had diarrhoea at any stage during their admission. In the first study,stool samples were tested by conventional microbiological methods and by polymerase chain reaction for parasites, and by immunoassays for Clostridium difficile. In the second study, conventional microbiology was conducted for bacteria and parasites including an enzyme-linked immunosorbent assay for Cryptosporidium antigen, and in a subset, immunoassays for Clostridium *** In the first study Giardia lamblia was detected in 68.5% of samples, Entamoeba histolytica in 13%, Cryptosporidium in 5.6%, non-toxigenic C. difficile in 22.4%, and other bacteria in 5.2%. In the second study, E. histolytica was detected in 10% of samples, Cryptosporidium in 4.3%, G. lamblia in 1.4%, C. difficile in 5.1%, and other bacteria in 5.7% of *** These pilot data suggest that parasites are important aetiologies of diarrhoea in Bangladeshi children with malignancy. While molecular diagnostic tools detect an array of stool pathogens with greater sensitivity, conventional diagnostic methods are also useful.

关键词： Bangladesh Cancer child Cryptosporidium Gastroenteritis Parasite

Mako:A Graph-based Pattern Growth Approach to Detect Complex Structural Variants

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Genomics, Proteomics & bioinformatics 2022年第1期20卷 205-218页

作者： Jiadong Lin Xiaofei Yang Walter Kosters Tun Xu Yanyan Jia Songbo Wang Qihui Zhu Mallory Ryan Li Guo Chengsheng Zhang The human Genome Structural Variation Consortium Charles Lee Scott E.Devine Evan E.Eichler Kai Ye School of Automation Science and Engineering Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China MOE Key Lab for Intelligent Networks&Networks Security Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China Genome institute the First Affiliated Hospital of Xi’an Jiaotong UniversityXi’an 710061China Leiden institute of Advanced Computer Science Faculty of ScienceLeiden UniversityLeiden 2311EZNetherland School of Computer Science and Technology Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China The Jackson Laboratory for Genomic Medicine FarmingtonCT 06032USA Precision Medicine Center the First Affiliated Hospital of Xi’an Jiaotong UniversityXi’an 710061China institute for Genome Sciences University of Maryland School of MedicineBaltimoreMD 21201USA Department of Genome Sciences University of Washington School of MedicineSeattleWA 98119USA Howard Hughes Medical institute University of WashingtonSeattleWA 98195USA The School of Life Science and Technology Xi’an Jiaotong UniversityXi’an 710049China 不详

Complex structural variants(CSVs) are genomic alterations that have more than two breakpoints and are considered as the simultaneous occurrence of simple structural ***,detecting the compounded mutational signals of CSVs is challenging through a commonly used model-match *** a result,there has been limited progress for CSV discovery compared with simple structural ***,we systematically analyzed the multi-breakpoint connection feature of CSVs,and proposed Mako,utilizing a bottom-up guided model-free strategy,to detect CSVs from paired-end short-read ***,we implemented a graph-based pattern growth approach,where the graph depicts potential breakpoint connections,and pattern growth enables CSV detection without pre-defined *** evaluations on both simulated and real datasets revealed that Mako outperformed other ***,validation rates of CSVs on real data based on experimental and computational validations as well as manual inspections are around 70%,where the medians of experimental and computational breakpoint shift are 13 bp and 26 bp,***,the Mako CSV subgraph effectively characterized the breakpoint connections of a CSV event and uncovered a total of 15 CSV types,including two novel types of adjacent segment swap and tandem dispersed *** analysis of these CSVs also revealed the impact of sequence homology on the formation of *** is publicly available at https://***/xjtu-omics/Mako.

关键词： Next-generation sequencing Complex structural variant Pattern growth Graph mining Formation mechanism

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