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Advances in Microbiology 2021年第10期11卷 529-540页

作者： Damilola Omotajo Hyuk Cho madhusudan choudhary Department of Biological Sciences Sam Houston State University Huntsville Texas USA Cumming School of Medicine University of Calgary Calgary Alberta Canada Department of Computer Science Sam Houston State University Huntsville Texas USA

The Shine-Dalgarno (SD) sequence, when present, is known to promote translation initiation in a bacterial cell. However, the thermodynamic stability of the messenger RNA (mRNA) through its secondary structures has an inhibitory effect on the efficiency of translation. This poses the question of whether bacterial mRNAs with SD have low secondary structure formation or not. About 3500 protein-coding genes in Rhodobacter sphaeroides were analyzed and a sliding window analysis of the last 100 nucleotides of the 5’ UTR and the first 100 nucleotides of ORFs was performed using RNAfold, a software for RNA secondary structure analysis. It was shown that mRNAs with SD are less stable than those without SD for genes located on the primary chromosome, but not for the plasmid encoded genes. Furthermore, mRNA stability is similar for genes within each chromosome except those encoded by the accessory chromosome (second chromosome). Results highlight the possible contribution of other factors like replicon-specific nucleotide composition (GC content), codon bias, and protein stability in determining the efficiency of translation initiation in both SD-dependent and SD-independent translation systems.

关键词： Shine-Dalgarno Sequence Secondary Structure Messenger RNA Translation Initiation

CtrA Is Nonessential for Cell Cycle Regulation in Rhodobacter sphaeroides

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Advances in Microbiology 2018年第7期8卷 558-577页

作者： Lin Lin Abha choudhary Anish Bavishi madhusudan choudhary Department of Biological Sciences Sam Houston State University Huntsville Texas USA

The bacterial cell cycle consists of a series of genetically coordinated biochemical and biophysical events. In Caulobacter crescentus, CtrA is an essential cell cycle regulator that modulates many cell cycle processes. In the present study, the role of the CtrA was investigated in Rhodobacter sphaeroides 2.4.1 by employing genetic, molecular, and bioinformatic approaches. Examination of the ctrA-null mutant revealed that the loss of CtrA did not affect growth characteristics and cell morphology in R. sphaeroides when grown under aerobic or photosynthetic growth conditions but slower growth was noticed in the anaerobic-dark-DMSO condition. Phylogenetic analyses demonstrated that CtrA has diversified its role in major lineages of α-Proteobacteria and has possibly been involved in adaptation to variable lifestyles. Analysis of the CtrA binding sites in the R. sphaeroides genome suggests that CtrA may regulate 127 genes involving different cellular processes. Protein homology searches revealed that only a small number of ctrA-regulated genes are homologous across C. crescentus, R. capsulatus, and R. sphaeroides. Comparison of the functions of putative ctrA-regulated genes in C. crescentus, R. capsulatus, and R. sphaeroides revealed that all three species possessed broad pathway control across a variety of cluster of orthologous gene functions (COGs). However, interestingly, it seems that the essentiality of CtrA in C. crescentus may depend more on the selective control that it exerts on a few critical cell cycle genes and pathways that are not controlled by CtrA in a similar fashion in R. capsulatus and R. sphaeroides.

关键词： CtrA Rhodobacter sphaeroides Cell Cycle Cell Cycle Regulation Symmetric Cell Division Motility

Bacterial Heavy Metal Resistance Genes and Bioremediation Potential

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Computational Molecular Bioscience 2019年第1期9卷 1-12页

作者： Hannah Johnson Hyuk Cho madhusudan choudhary Advanced Technology Cores Baylor College of Medicine Houston TX USA Department of Computer Science Sam Houston State University Huntsville TX USA Department of Biological Sciences Sam Houston State University Huntsville TX USA

There is a worldwide distribution of heavy metal pollution that can be managed with a bioremediation approach using microorganisms. Several bacterial species belonging to the Proteobacteria have been shown to tolerate heavy metal stress, including toxic salts of noblemetals. Rhodobacter sphaeroides, a model bacterium has previously been utilized for bioremediation studies. A bioinformatics approach was employed here to identify the distribution of genes associated with heavy metal tolerance among the sequenced bacterial genomes currently available on the NCBI database. The distribution of these genes among different groups of bacteria and the Cluster of Orthologous Groups (COGs) were further characterized. A total of 170,000 heavy metal related genes were identified across all bacterial species, with a majority of the genes found in Proteobacteria (46%) and Terrabacteria (39%). Analysis of COGs revealed that the majority of heavy metal related genes belong to metabolism (COG 3), including ionic transport, amino acid biosynthesis, and energy production.

关键词： Rhodobacter sphaeroides Heavy Metal Tolerance Genes Bioremediation

Cellular Localization of Gold and Mechanisms of Gold Resistance in Rhodobacter sphaeroides

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Advances in Microbiology 2017年第8期7卷 602-616页

作者： Hannah Johnson Ram C. Kafle madhusudan choudhary Department of Biological Sciences Sam Houston State University Huntsville TX USA Advanced Technology Cores Baylor College of Medicine Houston TX USA Department of Mathematics and Statistics Sam Houston State University Huntsville TX USA

Heavy metal pollution is a worldwide problem with many associated health risks, including bone loss, kidney damage, and several forms of cancer. There is a great need of bioremediation of these toxic metals from the environment, as well as implementing a monitoring system to control the spreading pollution. This study focuses on the bioremediation potential of Rhodobacter sphaeroides in the presence of the toxic gold chloride (AuCl3). Growth characteristics of the bacterial cells exposed to a range of toxic gold concentrations were analyzed through the growth kinetics and the colony forming units under aerobic, photosynthetic, and anaerobic growth conditions. The localization of the gold particles within two cellular fractions, cytoplasm and the plasma membrane, are analyzed using Inductively Coupled Plasma Optical Emission Spectroscopy (ICP-OES). Results of this study demonstrated the photosynthetic growth condition as best suited for the metal tolerance, compared to the aerobic and anaerobic growth conditions. Results also revealed the overall accumulation and localization of gold particles, while not different between the membrane and the cytoplasmic fractions increased at different concentrations of the gold contamination. The results of the localization under photosynthetic growth condition revealed the accumulation reached the highest very quickly, and an overall shift in localization of the gold particles from an equal distribution to an increase within the membrane fraction at the highest concentrations of gold contamination. The localization of the gold particles was validated by Transmission Electron Microscopy (TEM) where the results confirmed the increase in accumulation within the membrane, and photosynthetic membranes, of R. sphaeroides.

关键词： Rhodobacter sphaeroides Heavy Metal Bioremediation Inductively Coupled Plasma (ICP) Transmission Electron Microscopy (TEM)

The Effects of Different Carbon Sources on the Growth of Rhodobacter sphaeroides

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Advances in Microbiology 2019年第8期9卷 737-749页

作者： Noah Zavala Lorenzo Baeza Santos Gonzalez madhusudan choudhary Department of Biological Sciences Sam Houston State University Huntsville TX USA

Rhodobacter sphaeroides is a purple non-sulfur bacterium that belongs to the α-3 subdivision of Proteobacteria. R. sphaeroides is a model bacterial species because of its complex genome structure and expanded metabolic capabilities. The genome of R. sphaeroides consists of two circular chromosomes and five endogenous plasmids. It has the ability to grow under a wide variety of environmental conditions. It grows aerobically (~20% O2), semi-aerobically (~2% O2), and photosynthetically (under anaerobic condition plus light). It has been previously shown that many bacterial species utilize a number of alternate carbon sources for their optimal growth under a variety of growth conditions. We hypothesize that different or an additional carbon source in the minimal medium differentially affects the bacterial growth under dark-aerobic conditions. The bacterial growth kinetics and the number of cells in the bacterial culture were analyzed by measuring the optical density (OD at 600 nm) and the colony forming units (CFUs) at regular intervals of bacterial cultures. Results reveal that sodium succinate is the preferred sole carbon source for the optimal growth of R. sphaeroides. The results of growth kinetics and CFUs together concluded that from the tested carbon sources, sodium succinate is the best single carbon source in the minimal media for the optimal growth of R. sphaeroides. Interestingly, cell culture grown in SIS supplemented with sodium acetate exhibits a prolonged lag phase with the lowest ODs and CFUs that later switches to the growth-burst phase support previously discovered similar phenomenon of the growth-rate switch in the presence of acetate metabolism. Future work will utilize the aerobically grown R. sphaeroides’ cells as a biocatalyst to deplete the oxygen levels from natural gas streams and industrial gas pipelines.

关键词： Rhodobacter sphaeroides Aerobic Sistrom (SIS) Carbon Source Optical Density (OD) Colony Forming Units (CFUs)

Evolution of PE35 and PPE68 Gene Families in Mycobacterium: Roles of Horizontal Gene Transfer and Evolutionary Constraints

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Journal of Tuberculosis Research 2014年第4期2卷 181-198页

作者： Ashay Bavishi Lin Lin madhusudan choudhary Todd P. Primm Department of Biological Sciences Sam Houston State University Huntsville USA

Mycobacterium is a genus of bacteria with over a hundred non-pathogenic and pathogenic species, best recognized for certain members known to cause diseases such as tuberculosis and leprosy. Two novel protein families important in the pathogenesis of Mycobacterium species are the PE and PPE families. These two protein families affect the antigenic profiles, disturbing host immunity. To better understand the origin and evolution of these gene families and the differences in their composition between pathogenic and non-pathogenic strains, several bioinformatic analyses were conducted both among Mycobacterium and closely related species that contain PE35 and PPE68 gene homologs. The methods included protein homology searches (BLASTP), horizontal gene transfer analysis (IslandViewer), phylogenetic analysis, gene cluster analysis and structural and functional constraints. Results revealed that PE and PPE gene homologs were not only limited to Mycobacterium, but also existed in three other non-mycobacterial genera, Rhodococcus, Tsukamurella and Segniliparus, and were possibly initially acquired from non-mycobacterial microorganisms by multiple horizontal gene transfers. Results also demonstrated that PE and PPE genes were more diverse and more rapidly evolving in pathogenic Mycobacterium as compared with non-pathogenic Mycobacterium and other non-mycobacterial species. These findings possibly shed light on the diverse functions and origins of the PE/PPE proteins among these organisms.

关键词： PE35 PPE68 Horizontal Gene Transfer Mycobacterium

Multiple Chromosomes in Bacteria: Low Level of Evolutionary Constraint Drives the Rapid Genetic Divergence of Chromosome II

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Advances in Microbiology 2019年第7期9卷 656-677页

作者： Cheramie Trahan Ravi S. Pandey Utkarsh Singh Anushka choudhary Hyuk Cho Rajeev K. Azad madhusudan choudhary Department of Biological Sciences Sam Houston State University Huntsville TX USA Department of Biological Sciences University of North Texas Denton TX USA Department of Computer Science Sam Houston State University Huntsville TX USA Department of Mathematics University of North Texas Denton TX USA

Multiple chromosomes in bacteria are designated as a larger primary chromosome (CI) and smaller accessory chromosomes (CII and CIII). Although previous studies examined multiple chromosomes in several bacterial species, the evolutionary mechanisms for the origin of CIIs still remain unclear. In this study, the four following hypotheses were tested. 1) CIIs exhibit lower sequence conservation and sequence divergence compared to their corresponding CIs across species of Proteobacteria. 2) The differential sequence divergence of CI and CII depends on pathogenic and non-pathogenic lifestyles. 3) CIIs harbor a higher level of horizontal gene transfers (HGTs) than CIs. 4) Orthologs located on CIIs experience less purifying selection than their corresponding orthologs on CIs. Results reveal a higher level of sequence conservation of CIs than the sequence conservation of CIIs. There is no significant difference in HGT estimates between CIs and CIIs. A majority of orthologous genes of CIs and CIIs experience purifying selection;however, genes on CIIs were significantly less constrained than the corresponding ones on CIs. This finding is true for both pathogenic and non-pathogenic bacteria, but the selective constraints for non-pathogenic bacteria are relatively less constrained. It was concluded that the differential selective constraint is a potent driving force for the rapid evolution of CII. Therefore, gene expression analysis at the transcriptome and proteome levels may shed light on the gene regulation mechanisms that might affect the sequence divergence between CI and CII.

关键词： Multiple Chromosomes Proteobacteria Horizontal Gene Transfer Selective Constraint Pathogenic and Non-pathogenic Lifestyles

Analysis of Growth Characteristics and Differentially Expressed Homologous Genes in Rhodobacter sphaeroides under Normal and Simulated Microgravity Conditions

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Advances in Microbiology 2023年第11期13卷 539-558页

作者： Weerakkody Ranasinghe Eduardo Gutierrez Zelaya Alyson Sabrina Vazquez Ashleigh Ogg Rajesh Prabhu Balaraman Hyuk Cho madhusudan choudhary Department of Biological Sciences Sam Houston State University Huntsville Texas USA Department of Computer Science Sam Houston State University Huntsville Texas USA

The term “microgravity” is used to describe the “weightlessness” or “zero-g” circumstances that can only be found in space beyond earth’s atmosphere. Rhodobacter sphaeroides is a gram-negative purple phototroph, used as a model organism for this study due to its genomic complexity and metabolic versatility. Its genome has been completely sequenced, and profiles of the differential gene expression under aerobic, semi-aerobic, and photosynthetic conditions were examined. In this study, we hypothesized that R. sphaeroides will show altered growth characteristics, morphological properties, and gene expression patterns when grown under simulated microgravity. To test that, we measured the optical density and colony-forming units of cell cultures grown under both microgravity and normal gravity conditions. Differences in the cell morphology were observed using scanning electron microscopy (SEM) images by measuring the length and the surface area of the cells under both conditions. Furthermore, we also identified homologous genes of R. spheroides using the differential gene expression study of Acidovorax under microgravity in our laboratory. Growth kinetics results showed that R. sphaeroides cells grown under microgravity experience a shorter log phase and early stationary phase compared to the cells growing under normal gravity conditions. The length and surface area of the cells under microgravity were significantly higher confirming that bacterial cells experience altered morphological features when grown under microgravity conditions. Differentially expressed homologous gene analysis indicated that genes coding for several COG and GO functions, such as metabolism, signal-transduction, transcription, translation, chemotaxis, and cell motility are differentially expressed to adapt and survive microgravity.

关键词： Simulated Microgravity Differential Gene Expression Bacteria Gene Homology Space Exploration

Performance characterization of Bi_2O_3/Al nanoenergetics blasted micro-forming system

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Defence Technology（防务技术） 2019年第1期15卷 98-105页

作者： Vinay Kumar Patel Rishi Kant Anu choudhary madhusudan Painuly Shantanu Bhattacharya Department of Mechanical Engineering Govind Ballabh Pant Institute of Engineering & Technology Pauri-Garhwal Department of Mechanical Engineering Indian Institute of Technology Kanpur

This paper reports a novel micro-blast driven manufacturing process for micro-forming of Aluminum foils. The micro-blast is realized by using a nanoenergetic material system comprising of Bi_2O_3 microrods and aluminum particles. There is an enhanced need of forming of thin aluminum foil structures in small regions from point of view of drug packaging etc. The process developed caters to this need by using a single shot forming process using a micro-blast source. The micro-blast that is generated from an energetic composite system is made highly tunable by modulating the peak pressure generated through the blasting process and their impact in micro-forming of thin aluminum foils is observed through parametric studies. The engineering challenge involved in these experiments is to tune the blast pressure properties in order to address the forming of thin metal sheets with limiting boundary values as defined by the failure criteria. A variety of characterization techniques related to a thorough analysis of the synthesized material viz. X-ray diffraction(XRD), Scanning Electron Microscopy(SEM) etc, are used to tune the functional properties like gauge blast pressure etc, of material system. We have found a material system that can generate a maximum peak pressure of 73.8 MPa with pressurization rate of 2460 GPas^(-1) and that is able to accomplish micro-forming on thin metal foils(around 0.3 mm thickness). Experimental investigations demonstrate that tunabilty aspect of the energetic composites when exercised can enable variant processes such as embossing, coining, drilling etc. which may be of significant utility to drug packaging industries. A proper mathematical modeling of the forming process and critical process parameters therein have also been detailed.

关键词： Microforming Aluminum Foil Bi2O3 Nanoenergetic Tunability Process parameters

Urban heat mitigation by green and blue infrastructure:Drivers,effectiveness,and future needs

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The Innovation 2024年第2期5卷 145-166页

作者： Prashant Kumar Sisay E.Debele Soheila Khalili Christos H.Halios Jeetendra Sahani Nasrin Aghamohammadi Maria de Fatima Andrade Maria Athanassiadou Kamaldeep Bhui Nerea Calvillo Shi-Jie Cao Frederic Coulon Jill L.Edmondson David Fletcher Edmilson Dias de Freitas Hai Guo Matthew C.Hort madhusudan Katti Thomas Rodding Kjeldsen Steffen Lehmann Giuliano Maselli Locosselli Shelagh K.Malham Lidia Morawska Rajan Parajuli Christopher D.F.Rogers Runming Yao Fang Wang Jannis Wenk Laurence Jones Global Centre for Clean Air Research(GCARE) School of SustainabilityCivil and Environmental EngineeringFaculty of Engineering and Physical SciencesUniversity of SurreyGuildford GU27XHUK Institute for Sustainability University of SurreyGuildford GU27XHSurreyUK School of Built Environment University of ReadingWhiteknightsReading RG66BUUK School Design and the Built Environment Curtin University Sustainability Policy InstituteKent StBentley 6102Western Australia Harry Butler Institute Murdoch UniversityMurdoch 6150Western Australia Atmospheric Sciences Department Institute of AstronomyGeophysics and Atmospheric SciencesUniversity of Sao PauloSao Paulo 05508-090Brazil Met Office FitzRoy RoadExeter EX13PBUK Department of Psychiatry and Nuffield Department of Primary Care Health Sciences Wadham CollegeUniversity of OxfordOxfordUK Centre for Interdisciplinary Methodologies University of WarwickWarwickUK School of Architecture Southeast University2 SipailouNanjing 210096China Cranfield University School of WaterEnvironment and EnergyCranfield MK430ALUK Plants PhotosynthesisSoil ClusterSchool of BiosciencesUniversity of SheffieldSheffield S102TNUK UK Centre for Ecology&Hydrology Environment Centre WalesDeiniol RoadBangor LL572UWUK Air Quality Studies Department of Civil and Environmental EngineeringThe Hong Kong Polytechnic UniversityHong KongChina Department of Forestry and Environmental Resources Faculty Excellence Program for Leadership in Public ScienceNorth Carolina State UniversityChancellorRaleighNC 27695USA Departments of Architecture&Civil Engineering and Chemical EngineeringUniversity of BathBath BA27AYUK School of Architecture University of NevadaLas VegasNV 89154USA Department of Tropical Ecosystems Functioning Center of Nuclear Energy in AgricultureUniversity of São PauloPiracicaba 13416-000Sao PauloBrazil School of Ocean Sciences Bangor UniversityMenai BridgeAnglesey LL595 ABUK International Laboratory for Air Quality and Health Science and Engine

The combination of urbanization and global warming leads to urban overheating and compounds the frequency and intensity of extreme heat events due to climate ***,the risk of urban overheating can be mitigated by urban green-blue-grey infrastructure(GBGI),such as parks,wetlands,and engineered greening,which have the potential to effectively reduce summer air *** many reviews,the evidence bases on quantified GBGI cooling benefits remains partial and the practical recommendations for implementation are *** systematic literature review synthesizes the evidence base for heat mitigation and related co-benefits,identifies knowledge gaps,and proposes recommendations for their implementation to maximize their *** screening 27,486 papers,202 were reviewed,based on 51 GBGI types categorized under 10 main *** GBGI(green walls,parks,street trees)have been well researched for their urban cooling ***,several other GBGI have received negligible(zoological garden,golf course,estuary)or minimal(private garden,allotment)*** most efficient air cooling was observed in botanical gardens(5.0±3.5℃),wetlands(4.9±3.2℃),green walls(4.1±4.2℃),street trees(3.8±3.1℃),and vegetated balconies(3.8±2.7℃).Under changing climate conditions(2070–2100)with consideration of RCP8.5,there is a shift in climate subtypes,either within the same climate zone(e.g.,Dfa to Dfb and Cfb to Cfa)or across other climate zones(e.g.,Dfb[continental warm-summer humid]to BSk[dry,cold semi-arid]and Cwa[temperate]to Am[tropical]).These shifts may result in lower efficiency for the current GBGI in the *** the importance of multiple services,it is crucial to balance their functionality,cooling performance,and other related co-benefits when planning for the future *** global GBGI heat mitigation inventory can assist policymakers and urban planners in prioritizing effective interventions to reduce the risk of urban overheating,fi

关键词： estuary walls extreme