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Computational Challenges in Deciphering Genomic Structures of Bacteria

Journal of Computer Science & Technology 2010年第1期25卷 53-70页

作者：徐鹰 Computational Systems Biology Laboratory Department of Biochemistry and Molecular Biology and Institute of Bioinformatics The University of Georgia BESC BioEnergy Science Center College of Computer Science and Technology Jilin University

This article addresses how the functionalities of the cellular machinery of a bacterium might have constrained the genomic arrangement of its genes during evolution and how we can study such problems using computational approaches, taking full advantage of the rapidly increasing pool of the sequenced bacterial genomes, potentially leading to a much improved understanding of why a bacterial genome is organized in the way it is. This article discusses a number of challenging computational problems in elucidating the genomic structures at multiple levels and the information that is encoded through these genomic structures, gearing towards the ultimate understanding of the governing rules of bacterial genome organization.

关键词： bioinformatics microbial genomics genome structure comparative genome analysis biological pathways

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Integrated transcriptomic and proteomic study on the different molecular mechanisms of PC12 cell growth on chitosan and collagen/chitosan films

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Regenerative Biomaterials 2020年第6期7卷 553-565页

作者： Xiaoying Lu Yan Huang Yayun Qu Yiwen Zhang Zequn Zhang State Key Laboratory of Bioelectronics School of Biological Science and Medical EngineeringSoutheast UniversityNanjing 210096China SQ Medical Device Co. LtdNanjing 210008China

The purpose of this article is to integrate the transcriptomic analysis and the proteomic profiles and to reveal and compare the different molecular mechanisms of PC12 cell growth on the surface of chitosan films and collagen/chitosan ***,the chitosan films and the collagen/chitosan films were ***,the cell viability assay was performed;the cell viability of the PC12 cells cultured on the collagen/chitosan films for 24 h was significantly higher than that on the chitosan ***,with cDNA microarray,the numbers of differentially expressed genes of PC12 cells on the surface of chitosan and collagen/chitosan films were 13349 and 5165,***,the biological pathway analysis indicated that the differentially expressed genes were involved in 40 pathways directly related to cell adhesion and *** integrated transcriptomic and our previous proteomic analysis revealed that three biological pathways-extracellular matrix-receptor interaction,focal adhesion and regulation of actin cytoskeleton-were regulated in the processes of protein adsorption,cell adhesion and *** adsorbed proteins on the material surfaces further influenced the expression of important downstream genes by regulating the expression of related receptor genes in these three *** comparison,chitosan films had a strong inhibitory effect on PC12 cell adhesion and growth,resulting in the significantly lower cell viability on its surface;on the contrary,collagen/chitosan films were more conducive to promoting PC12 cell adhesion and growth,resulting in higher cell viability.

关键词： chitosan film and collagen/chitosan film protein adsorption and cell growth cDNA microarray and proteomics biological pathways

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Global Genomic Arrangement of Bacterial Genes Is Closely Tied with the Total Transcriptional Efficiency

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Genomics, Proteomics & Bioinformatics 2013年第1期11卷 66-71页

作者： Qin Ma Ying Xu Computational Systems Biology Laboratory Department of Biochemistry and Molecular Biology and Institute of BioinformaticsUniversity of Georgia BioEnergy Science Center College of Computer Science and Technology Jilin University

The availability of a large number of sequenced bacterial genomes allows researchers not only to derive functional and regulation information about specific organisms but also to study the fundamental properties of the organization of a genome. Here we address an important and chal- lenging question regarding the global arrangement of operons in a bacterial genome： why operons in a bacterial genome are arranged in the way they are. We have previously studied this question and found that operons of more frequently activated pathways tend to be more clustered together in a genome. Specifically, we have developed a simple sequential distance-based pseudo energy func- tion and found that the arrangement of operons in a bacterial genome tend to minimize the clus- teredness function （C value） in comparison with artificially-generated alternatives, for a variety of bacterial genomes. Here we extend our previous work, and report a number of new observations：（a） operons of the same pathways tend to group into a few clusters rather than one; and （b） the global arrangement of these operon clusters tend to minimize a new ＂energy＂ function （C＋ value） that reflects the efficiency of the transcriptional activation of the encoded pathways. These obser- vations provide insights into further study of the genomic organization of genes in bacteria.

关键词： Global genoic arrangement Bacterial genome Chromosomal supercoils biological pathways Gene expression

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Preterm Birth,From the biological Knowledges to the Prevention:An Overview

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Maternal-Fetal Medicine 2020年第3期2卷 162-171页

作者： Tosto Valentina Giardina Irene Tsibizova Valentina Di Renzo Gian Carlo Department of Obstetrics and Gynecology and Center for Perinatal and Reproductive Medicine University of PerugiaSanta Maria della Misericordia University HospitalPerugia 06132Italy Department of Obstetrics and Gynecology Almazov National Medical Research CenterSt.Petersburg 191014Russia

The time of birth is a critical determinant of perinatal and long-term outcomes,and even trans-generational *** birth is still the leading cause of infant mortality and ***,rates of preterm birth remain high *** parturition is a complex syndrome,which can be induced by several factors such as infection,cervical pathology,uterine overdistension,progesterone deficiency,vascular alterations(utero-placental ischemia,decidual hemorrhage),maternal and fetal stress,allograft reaction,allergic phenomena,and probably other several unknown *** mechanisms responsible for early labor activation have been partially identified and involve receptors,chemokines,and inflammatory *** is very useful to understand the cellular and biochemical pathways responsible for preterm labor activation to identify,treat,and prevent negative outcome in a timely *** and clinicians play a key role in improving biochemical knowledge on preterm delivery,identifying risk factors,and applying multilevel preventive strategies.

关键词： Premature birth biological pathways Inflammation Prevention strategies

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Construction of gene/protein interaction networks and enrichment pathway analysis for paroxysmal nocturnal hemoglobinuria and aplastic anemia

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Medical Theory and Hypothesis 2023年第2期6卷 19-26页

作者： Gong-Xi Liu Zheng-Di Sun Chao Zhou Jun-Yu Wei Jing Zhuang Department of Oncology Weifang Traditional Chinese HospitalWeifang 261000China

Background:To develop a protein-protein interaction network of Paroxysmal nocturnal hemoglobinuria(PNH)and Aplastic anemia(AA)based on genetic genes and to predict pathways underlying the molecular complexes in the ***:In this research,the PNH and AA-related genes were screened through Online Mendelian Inheritance in Man(OMIM).The plugins and Cytoscape were used to search literature and build a protein-protein interaction ***:The protein-protein interaction network contains two molecular complexes that are five higher than the correlation integral *** target genes of this study were obtained:CD59,STAT3,TERC,TNF,AKT1,C5AR1,EPO,IL6,IL10 and so *** also found that many factors regulate biological behaviors:neutrophils,macrophages,vascular endothelial growth factor,immunoglobulin,interleukin,cytokine receptor,interleukin-6 receptor,tumor necrosis factor,and so *** research provides a bioinformatics foundation for further explaining the mechanism of common development of ***:This indicates that the PNH and AA is a complex process regulated by many cellular pathways and multiple genes.

关键词： protein interaction networks paroxysmal nocturnal hemoglobinuria Online Mendelian Inheritance in Man database aplastic anemia biological pathways

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