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1
Dabdoub, Shareef Majed. "Applied Visual Analytics in Molecular, Cellular, and Microbiology." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1322602183.
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Mukherjee, Chiranjit. "High Resolution Characterization of the Human Oral Microbiome in Health and Disease." The Ohio State University, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=osu1574678346902957.
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Kondratowicz, Andrew Steven. "A bioinformatics approach to identifying novel genes involved in ebolavirus entry." Diss., University of Iowa, 2011. https://ir.uiowa.edu/etd/5003.
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Ebolavirus (EBOV) is a negative sense, single stranded RNA virus that causes Ebola hemorrhagic fever. This disease causes substantial morbidity and mortality in humans, with death occurring in 50-90% of cases. Despite years of intensive research, much of the molecular mechanism underlying the entry of EBOV remains unknown. We performed a bioinformatics screen to identify novel entry cofactors by correlating mRNA expression in a panel of human cancer cell lines with permissivity to the EBOV entry glycoprotein. This assay identified several known EBOV entry cofactors such as actin and the tyrosine kinase Axl. In addition, several genes involved in macropinocytosis and endosomal maturation were also correlated with EBOV permissivity.
Subsequent evaluation of plasma membrane proteins correlated by this screen showed T-cell immunoglobulin and mucin domain-1 (TIM-1) mRNA expression correlated extremely well with EBOV pseudovirion transduction. Depletion of TIM-1 from highly-permissive cells inhibits EBOV pseudovirion transduction. Conversely, expression of TIM-1 in poorly-permissive cells significantly and specifically enhances EBOV pseudovirion transduction and infection. TIM-1 binds to EBOV GP and this binding is important in the initial interaction between the virus and the host cell. ARD5, a TIM-1 mAb, significantly inhibits EBOV GP-mediated entry into several cell lines and primary human airway epithelia in a dose and time-dependent manner. Therefore, TIM-1 is the first receptor identified for EBOV.
Additionally, AMP-activated protein kinase (AMPK) mRNA correlated strongly with EBOV pseudovirion transduction. Compound C, a specific AMPK inhibitor, inhibited EBOV pseudovirion transduction and infection in a time and dose-dependent manner into several cell lines and primary human monocyte derived macrophages. Mouse embryonic fibroblasts (MEFs) lacking functional AMPK were significantly less permissive to EBOV GP-mediated infection that WT MEFs. Visualization of virus entry into these cells revealed that EBOV causes actin polymerization independently of AMPK, but AMPK-/- cells do not form lamellipodia in the presence of EBOV and, consequently, cannot internalize virus into cells by macropinocytosis.
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Smiley, Shawn Johnston. "Sequence Extension of the Tryptophan and Shikimate Operons in Clostridium Scatologenes ATCC 25775." TopSCHOLAR®, 2017. https://digitalcommons.wku.edu/theses/2058.
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3-Methylindole and 4-methylphenol are cytotoxic and malodorant compounds derived from tryptophan and tyrosine, respectively. Each is present in swine waste lagoons and contributes to malodorous emissions from agricultural facilities. Clostridium scatologenes ATCC 25775 produces both compounds and serves as a model organism to study their metabolism and function. Through the repeated assembly and annotation of the Clostridium scatologenes genome, we propose a novel pathway for tryptophan degradation and 3-methylindole production by this organism. The genome of Clostridium scatologenes was sequenced, and re-assembled into contigs. Key elements of the tryptophan and shikimate pathways were identified. Contigs containing these elements were extracted from assemblies and matched to the reference genome of Clostridium carboxidivorans. Sequence for both pathways was then extended and defined using these joined sequence fragments. This sequence could serve as a starting point for the isolation of genes related to 3-methylindole synthesis using biochemical and enzyme analysis
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Shankar, Vijay. "Extension of Multivariate Analyses to the Field of Microbial Ecology." Wright State University / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=wright1464358122.
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Marcinkiewicz, Ashley. "Bacterial and phage interactions influencing Vibrio parahaemolyticus ecology." Thesis, University of New Hampshire, 2016. http://pqdtopen.proquest.com/#viewpdf?dispub=10127507.
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<p> <i>Vibrio parahaemolyticus,</i> a human pathogenic bacterium, is a naturally occurring member of the microbiome of the Eastern oyster. As the nature of this symbiosis in unknown, the oyster presents the opportunity to investigate how microbial communities interact with a host as part of the ecology of an emergent pathogen of importance. To define how members of the oyster bacterial microbiome correlate with <i>V. parahaemolyticus,</i> I performed marker-based metagenetic sequencing analyses to identify and quantify the bacterial community in individual oysters after culturally-quantifying <i> V. parahaemolyticus</i> abundance. I concluded that despite shared environmental exposures, individual oysters from the same collection site varied both in microbiome community and <i>V. parahaemolyticus</i> abundance, and there may be an interaction with <i>V. parahaemolyticus</i> and <i> Bacillus</i> species. In addition, to elucidate the ecological origins of pathogenic New England ST36 populations, I performed whole genome sequencing and phylogenetic analyses. I concluded ST36 strains formed distinct subpopulations that correlated both with geographic region and unique phage content that can be used as a biomarker for more refined strain traceback. Furthermore, these subpopulations indicated there may have been multiple invasions of this non-native pathogen into the Atlantic coast.</p>
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Duong, An Duy. "Investigation of Pantoea stewartii Quorum-Sensing Controlled Regulators and Genes Important for Infection of Corn." Diss., Virginia Tech, 2018. http://hdl.handle.net/10919/93208.
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Bacteria interact with their eukaryotic hosts using a variety of mechanisms that range from being beneficial to detrimental. This dissertation focuses on Pantoea stewartii subspecies stewartii (P. stewartii), an endosymbiont in the corn flea beetle gut that causes Stewart's wilt disease in corn. Gaining insights into the interactions occurring between this bacterial pathogen and its plant host may lead to informed intervention strategies. This phytopathogen uses quorum sensing (QS) to coordinate cell density-dependent gene expression and successfully colonize corn leading to wilt disease. Prior to the research presented in this dissertation, the QS master regulator EsaR was shown to regulate two major virulence factors of P. stewartii, capsule production and surface motility. However, the function and integration of EsaR downstream targets in P. stewartii were still largely undefined. Moreover, only a draft genome of a reference strain of P. stewartii was publicly available for researchers, limiting bioinformatics and genome-scale genetic approaches with the organism. The work described in this dissertation has now addressed these important issues.
The function of two EsaR direct targets, LrhA and RcsA, was explored (Chapter Two) and the existence of integration in the regulation between them was discovered (Chapters Two and Four). RcsA and LrhA are transcription factors controlling capsule production and surface motility in P. stewartii, respectively. In Chapter Two, the RcsA and LrhA regulons were investigated using RNA-Seq. This led to the discovery of a potential regulatory interaction between them that was confirmed by qRT-PCR and transcriptional gene fusion assays. The involvement of LrhA in surface motility and virulence was also established in this project. A direct interaction between LrhA and promoter of rcsA was defined in Chapter Four. Additional direct regulatory targets of LrhA were also identified.
A project to generate a complete assembly of the P. stewartii genome (Chapter Three) enabled more thorough genome-wide analysis and revealed the existence of a previous unknown 66-kb region in the P. stewartii genome believed to contain genes important for motility and virulence. In addition, completion of the genome sequence permitted genes for two distinctive Type III secretion systems, used for interactions with corn or the corn flea beetle, to be placed on two mega-plasmids. Furthermore, the complete genome sequence facilitated a Tn-Seq approach (Chapter Five). Tn-Seq is a potent tool used to identify bacterial genes required for certain environmental test conditions. This project is a pioneering utilization of a Tn-Seq analysis in planta to investigate genes important for colonization and survival of P. stewartii within its corn host. It was discovered that OmpC and Lon are important to in planta growth and OmpA plays a role in plant virulence.
In conclusion, these studies have broadened our understanding about the role of the QS regulon and other genes important for the pathogenesis of this phytopathogen. This knowledge may now be applied toward the development of future disease intervention strategies against P. stewartii and other wilt-disease causing plant pathogens.<br>PHD
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Mostowy, Serge. "Comparative genomics of the Mycobacterium tuberculosis complex." Thesis, McGill University, 2005. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=111834.
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The study of microbial evolution has been recently accelerated by the advent of comparative genomics, an approach enabling investigation of organisms at the whole-genome level. Tools of comparative genomics, including the DNA microarray, have been applied in bacterial genomes towards studying heterogeneity in DNA content, and to monitor global gene expression. When focused upon the study of microbial pathogens, genome analysis has provided unprecedented insight into their evolution, virulence, and host adaptation. Contributing towards this, I herein explore the evolutionary change affecting genomes of the Mycobacterium tuberculosis complex (MTC), a group of closely related bacterial organisms responsible for causing tuberculosis (TB) across a diverse range of mammals. Despite the introduction nearly a century ago of BCG, a family of live attenuated vaccines intentioned on preventing human TB, the uncertainty surrounding its usefulness is punctuated by the reality that TB continues to be responsible for claiming over 2 million lives per year. As pursued throughout this thesis, a precise understanding of the differences in genomic content among the MTC, and its impact on gene expression and biological function, promises to expose underlying mechanisms of TB pathogenesis, and suggest rational approaches towards the design of improved diagnostics and vaccines to prevent disease.<br>With the availability of whole-genome sequence data and tools of comparative genomics, our publications have advanced the recognition that large sequence polymorphisms (LSPs) deleted from Mycobacterium tuberculosis, the causative agent of TB in humans, serve as accurate markers for molecular epidemiologic assessment and phylogenetic analysis. These LSPs have proven informative both for the types of genes that vary between strains, and for the molecular signatures that characterize different MTC members. Genomic analysis of atypical MTC has revealed their diversity and adaptability, illuminating previously unexpected directions of MTC evolution. As demonstrated from parallel analysis of BCG vaccines, a phylogenetic stratification of genotypes offers a predictive framework upon which to base future genetic and phenotypic studies of the MTC. Overall, the work presented in this thesis has provided unique insights and lessons having direct clinical relevance towards understanding TB pathogenesis and BCG vaccination.
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Ralston, Matthew T. "Assembling improved gene annotations in Clostridium acetobutylicum with RNA sequencing." Thesis, University of Delaware, 2015. http://pqdtopen.proquest.com/#viewpdf?dispub=1585177.
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<p> The <i>C. acetobutylicum</i> genome annotation has been markedly improved by integrating bioinformatic predictions with RNA sequencing(RNA-seq) data. Samples were acquired under butanol, butyrate, and unstressed treatments across various growth stages to sample the transcriptome from a range of physiologically relevant conditions. Analysis of an initial assembly revealed errors due to technical and biological background signals, challenges with few solutions. Hurdles for RNA-seq transcriptome mapping research include optimizing library complexity and sequencing depth, yet most studies in bacteria report low depth and ignore the effect of ribosomal RNA abundance and other sources on the effective sequencing depth. </p><p> In this work, workflows were established to address type I and II errors associated with these challenges. An integrative analysis method was developed to combine motif predictions, single-nucleotide resolution sequencing depth, and library complexity to resolve these errors during assembly curation. This contextualization minimized false positive error and determined gene boundaries, in some cases, to the exact basepair of prior studies. Curation of the pSOL1 megaplasmid reconciled transcriptome assembly statistics with findings from <i>E. coli</i>. </p><p> The resulting annotation can be readily explored and downloaded through a customized genome browser, enabling future genomic and transcriptomic research in this organism. This work demonstrates the first strand-specific transcriptome assembly in a <i>Clostridium</i> organism. This method can improve the precision of transcript boundary estimates in bacterial transcriptome mapping studies.</p>
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Caskey, John Russell. "Phenotypic alterations in Borrelia burgdorferi and implications for the persister cell hypothesis." Thesis, Tulane University, 2015. http://pqdtopen.proquest.com/#viewpdf?dispub=3680987.
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<p> Lyme disease is the most commonly reported vector-borne disease in the United States. The causative agent of Lyme disease, can alter gene expression to enable survival in a diverse set of conditions, including the tick midgut and the mammalian host. External environmental changes can trigger gene expression in <i>B. burgdorferi,</i> and the data demonstrate that <i> B. burgdorferi</i> can similarly alter gene expression as a stress-response when it is treated with the antibiotic doxycycine. After treatment with the minimum bactericidal concentration (MBC) of doxycycline, a subpopulation can alter its phenotype to survive antibiotic treatment, and to host adapt and successfully infect a mammalian host. Furthermore, our data demonstrate that if a population is treated with the MBC of doxycycline, a subpopulation may alter its phenotype to adopt a state of dormancy until the removal of the antibiotic, whereupon the subpopulation can regrow. We demonstrate that the chance of regrowth occurring increases as a population reaches stationary phase, and present a mathematical model for predicting the probability of a persister subpopulation within a larger population, and ascertain the quantity of a persister subpopulation. To determine which genes are expressed as stress-response genes, RNA Sequencing analysis, or RNASeq, was performed on treated, untreated, and treated and regrown <i>B. burgdorferi</i> samples. The results suggest several genes were significantly different in the treated group, compared to the untreated group, and in the untreated and regrown group compared to the untreated group, including a 50S ribosomal stress-response protein, coded from BB_0786. The appendices discuss the theory and methods that were used in RNA Sequencing (RNASeq) analysis, and provide an overview of the database that was created for the <i>B. burgdorferi</i> transcriptome. Additional studies may demonstrate further how persister subpopulations form, and which genes can trigger a persister state in <i>B. burgdorferi.</i></p>
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Keter, Nancy Rop. "Site-Directed Mutagenesis of Glutathione Transferase, GstB from Escherichia coli for Use in Bioremediation." Youngstown State University / OhioLINK, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=ysu1620836630780629.
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Eckstrom, Korin. "Evaluating The Resistome And Microbial Composition During Food Waste Feeding And Composting On A Vermont Poultry Farm." ScholarWorks @ UVM, 2018. https://scholarworks.uvm.edu/graddis/886.
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While commonly thought of as a waste product, food scraps and residuals represent an important opportunity for energy and nutrient recapture within the food system. As demands on production continue to increase, conservation of these valuable resources has become a priority area. In the wake of new legislation in Vermont, Act 148, the Universal Recycling Law, the fate of microbial species in food waste, scraps and residuals is increasingly important. The presence of antimicrobial resistance genes in all types of foods calls for an increased need to estimate risk of antibiotic resistance transfer and maintenance across all segments of food production and distribution systems, from farm to fork. Specifically, the fate of antibiotic resistance genes (ARGs) in these co-mingled food wastes has not been sufficiently characterized; as legislative programs increase in popularity, surveillance of these materials is pressing and should be documented to assess the risk and potential measures for mitigation and management as we approach commercial scales of implementation
Previous studies have relied on a combination of targeted techniques, such as 16S rRNA sequencing and qPCR on a specific subset of ARGs; however, these may not cover the full extent of resistance or microorganisms of concern in any given sample. As sequencing technologies improve and costs continue to drop, more comprehensive tools, such as shotgun metagenomic sequencing, can be applied to these problems for both surveillance and novel gene discovery. In this study, we leveraged the increased screening power of the Illumina HiSeq and shotgun metagenomic sequencing to identify and characterize ARGs, microbial communities, and associated virulence factors of food scraps, on-farm composts, and several consumer products. Isolates were also screened for antibiotic resistance to demonstrate the functionality of ARGs identified.
The resistome, microbiome, and virulence genes were characterized in all samples. Fifty unique ARGs were identified that spanned 8 major drug classes. Most frequently found were genes related to aminoglycoside, macrolide, and tetracycline resistance. Additionally, 54 distinct virulence factors and 495 bacterial species were identified. Virulence factors were present across the farm setting and mainly included gene transfer mechanisms, while bacteria clustered distinctly into site and farm, as well as separate on farm niches. The relationship between these categories was also assessed by both Pearson correlation and co-inertia analysis, with the most significant relationship being between ARGs and virulence factors (P = 0.05, RV = 0.67). While limited in this study, these patterns reinforce the finding that spread of antibiotic resistance genes may be dependent on the virulence factors present enabling transfer, rather than total microbial community composition.
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Warren, Andrew S. "Methods for Analysis of Prokaryotic Genome Architecture." Diss., Virginia Tech, 2017. http://hdl.handle.net/10919/86660.
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Research in comparative microbial genomics has largely been organized around the concept of reference genomes. Reference genomes provide a useful comparative touchstone for closely related organisms. However, they do not necessarily represent the biological diversity in a group of genomes. Currently there are more than 96,000 bacterial genomes sequenced and this number is rapidly increasing. Some closely related groups have large numbers of genomes sequenced creating interesting comparative challenges: E. coli more than 5,400 isolates, S. aureus almost 9,000. As this sampling through sequencing becomes both deeper and broader, reference genome based methods become less effective at characterizing groups of organisms.
Functional motifs can help explain the organizing principles behind cellular systems in bacteria which have yet to be well understood. Currently there are relatively few bioinformatic tools for analyzing potential patterns at the level of genome organization that do not depend directly on sequence similarity. We present a framework for conducting genomic data mining to look for patterns that currently require human expert designation. We establish new computational methods for identifying patterns in prokaryotic genome construction through a mapping of genomic features, using semantic similarity, independent of a particular corpus to better approximate functional similarity.
We also present an algorithm for creating whole genome multiple sequence comparisons and a model for representing the similarities and di erences among sequences as a graph of syntenic gene families. This e ort touches on several di erent research fronts: graph representation of genomes and their alignments, synteny block analysis, whole genome sequence alignment, pan-genome analysis, multiple sequence alignment, and genome rearrangement analysis. Though our approach was originally developed from a pan-genome perspective for prokaryotes, the methods involved have the potential to speed up more expensive computation such as phylogenetic tree construction and SNP analysis. Novel elements include the contextualization of synteny analysis both between and within multi-contig genomes and an analytical framework for detecting genome level evolutionary events such as insertions, inversions, translocations, and fusions.<br>Ph. D.<br>Research in comparative microbial genomics has largely been organized around the concept of reference genomes. Reference genomes provide a useful comparative touchstone for closely related organisms. However, they do not necessarily well represent the biological diversity in a group of genomes. As sampling through sequencing becomes both deeper and broader, reference genome based methods become less effective at characterizing groups of organisms. We present an algorithm for creating whole genome multiple sequence comparisons and a model for representing the similarities and differences among sequences as a graph of syntenic gene families called a pan-synteny graph.
As the evolutionary distance between organisms increase sequence similarity and homology detection tend to break down. However, similarities in the functional characteristics of certain genes and gene modules may persist or have converged over time. Detecting and defining patterns in these functional similarities, in relation to conserved gene order, is a largely unexplored problem. To create a model for representing the architectural similarity of functional modules, using ontologies and semantic similarity, we present a corpus independent semantic similarity method, and describe a computational framework for using semantic similarity and pan-synteny graphs.
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Lambert, Caroline L. "Identification and Description of Burkholderia pseudomallei Proteins that Bind HostComplement-Regulatory Proteins via in silico and in vitro Analyses." University of Toledo Health Science Campus / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=mco1533315186098586.
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Mandal, Rabindra Kumar. "Genetic Determinants of Salmonella and Campylobacter Required for In Vitro Fitness." Thesis, University of Arkansas, 2016. http://pqdtopen.proquest.com/#viewpdf?dispub=10249279.
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<p>Non-typhoidal Salmonella (NTS) and Campylobacter play a major role in foodborne illness caused by the consumption of food contaminated by pathogens worldwide. A comprehensive understanding of the genetic factors that increase the survival fitness of these foodborne pathogens will effectively help us formulate mitigation strategies without affecting the nutrition ecology. The objective of this study was to identify the genetic determinants of Salmonella and Campylobacter that are required for fitness under various in vitro conditions. For the purpose, we used a high throughput Transposon sequencing (Tn-seq) that utilizes next generation sequencing (NGS) to screen hundreds of thousands of mutants simultaneously. In Chapter 1, we reviewed the technical aspects of different Tn-seq methods along with their pros and cons and compressive summary of recently published studies using Tn-seq methods. In Chapter 2, we exposed complex Tn5 library of Salmonella Typhimurium 14028S (S. Typhimurium) to the mimicked host stressors in vitro conditions. Such as low acidic pH (pH 3) found in the stomach, osmotic (3% NaCl) and short chain fatty acid (SCFAs, 100 mM Propionate) found in intestine, and oxidation (1mM H2O2) and starvation (12-day survival in PBS) found in macrophage. There was an overlapping set of 339 conditionally essential genes (CEGs) required by S. Typhimurium to overcome these host stressors. In Chapter 3, we screened of S. Typhimurium Tn5 library for desiccation survival. Salmonella spp. is the most notable and frequent cause of contamination in low-water activity foods. We identified 61 genes and 6 intergenic regions required for fitness during desiccation stress. In Chapter 4, the essential genome of Campylobacter jejuni (C. jejuni) NCTC 11168 and C. jejuni 81-176 was investigated using Tn-seq. We identified 166 essential protein-coding genes and 20 essential transfer RNA (tRNA) in C. jejuni NCTC 11168 which were intolerant to Tn5 insertions during in vitro growth. The reconstructed library C. jejuni 81-176 had 384 protein coding genes with zero Tn5 insertions. The genetic determinants Salmonella and Campylobacter identified in this study have high potential to be explored as food safety intervention, therapeutic and vaccine target to curb the spread of the foodborne pathogens making world a safer place.
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Alnaji, Fadi. "Isolation and analysis of recombinants from mixed virus infections of poliovirus using next generation sequencing (NGS) and bioinformatics." Thesis, University of Warwick, 2016. http://wrap.warwick.ac.uk/98260/.
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RNA virus recombination is a key evolutionary mechanism and a driver of genetic diversity. In recent studies using an in vitro “CRE-REP” assay involving replication-compromised parental genomes, recombination was shown to be a biphasic process involving an initial imprecise crossover event which was followed by a resolution process that resulted in the formation of genome-length recombinants (Lowry K. et al 2014). We have extended this study to investigate recombination during dual infection by unmodified parental viruses in the absence of selection. Recombinants were generated by co-infecting HeLa cells with poliovirus type 1 Mahoney and type 3 Leon for 5-hours, followed by RNA extraction, cDNA synthesis, and PCR amplification. Amplified PCR products of both type 1/3 and type 3/1 recombinants were readily detected, cloned individually and sequenced by Sanger sequencing. Within 25 clones sequenced, 18 unique recombination junctions were detected. To get a comprehensive overview of the range of recombination junctions within the virus population the data produced from next generation sequencing of pooled amplified cDNA from dually infected cells was analysed. A bioinformatics pipeline was developed to specifically detect and quantify recombinants within this population. Three types of junctions were identified, precise (i.e. at the same position in both genomes) and imprecise, including both insertions (as seen in the Lowry 2014 study) and deletions. In an analysis of the P2 region of the poliovirus genome, we identified several hundred different precise and imprecise junctions. The data analysis suggests that recombination is a random event; no correlation between the nucleotide base composition or RNA structure near the junctions’ locations of both donor and recipient viral genomes and the recombination frequency was detected. These studies contribute to our understanding of the molecular mechanism of genetic recombination in RNA viruses and suggest ways in which it might be controlled during the development of novel vaccines with reduced recombination potential.
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Gonzalez, Galarza Faviel. "The development of a database and bioinformatics applications for the investigation of immune genes." Thesis, University of Liverpool, 2011. http://livrepository.liverpool.ac.uk/4973/.
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The extensive allelic variability observed in several genes related to the immune response and its significance in transplantation, disease association studies and diversity in human populations has led the scientific community to analyse these variants among individuals. This thesis is focussed on the development of a database and software applications for the investigation of several immune genes and the frequencies of their corresponding alleles in worldwide human populations. The approach presented in this thesis includes the design of a relational database, a web interface, the design of models for data exchange and the development of online searching mechanisms for the analysis of allele, haplotype and genotype frequencies. At present, the database contains data from more than 1000 populations covering more than four million unrelated individuals. The repertory of datasets available in the database encompasses different polymorphic regions such as Human Leukocyte Antigens (HLA), Killer-cell Immunoglobulin-like Receptors (KIR), Major histocompatibility complex Class I chain-related (MIC) genes and a number of cytokine gene polymorphisms. The work presented in this document has been shown to be a valuable resource for the medical and scientific societies. Acting as a primary source for the consultation of immune gene frequencies in worldwide populations, the database has been widely used in a variety of contexts by scientists, including histocompatibility, immunology, epidemiology, pharmacogenetics and population genetics among many others. In the last year (August 2010 to August 2011), the website was accessed by 15,784 distinct users from 2,758 cities in 136 countries and has been cited in 168 peer-reviewed publications demonstrating its wide international use.
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Moller, Abraham Ghoreishi. "Mapping ecologically important virus-host interactions in geographically diverse solar salterns with metagenomics." Miami University / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=miami1461841762.
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Acuña, Amador Luis Alberto. "Étude bioinformatique des génomes de Porphyromonas." Thesis, Rennes 1, 2017. http://www.theses.fr/2017REN1B054/document.
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Les bactéries du phylum Bacteroidetes, classe Bacteroidia, sont parmi les plus importantes dans microbiotes gastrointestinaux des humains et d'autres mammifères. La bouche, entrée du tube digestif, est un environnement avec des sites anatomiques variés, auxquels s'associent des microbiotes de composition différente. L'union de la gencive et des dents, le sillon gingivo-dentaire ou sulcus, est un site de dépôt d'un biofilm complexe appelé plaque dentaire. Une bactérie de ce phylum, Porphyromonas gingivalis, est capable de perturber le système immunitaire humain et de produire un déséquilibre du biofilm oral également nommée dysbiose. Ceci déclenche la formation de la poche parodontale, un creusement pathologique du sulcus, et l'apparition de la parodontite. D’autres espèces du genre Porphyromonas sont également associées à la parodontite notamment chez les canidés. Les populations de P. gingivalis sont panmictiques et la plasticité de leurs génomes importante. La bioinformatique peut aider à identifier les causes de la mosaïcité des génomes de cette bactérie, à étudier les facteurs de virulence au niveau du genre bactérien pour expliquer l'existence d'espèces pathogènes et d'autres commensales et à décrire la dysbiose liée à la parodontite. La génomique comparative de P. gingivalis a démontré une corrélation entre le nombre de contigs dans les génomes draft de cette espèce et les répétitions génomiques, notamment des séquences d'insertion. Nous avons re-séquencé, re-assemblé et re-annoté trois souches de référence de cette bactérie qui avaient des génomes complets, en utilisant un séquençage en long-read. Nous avons mis en évidence des erreurs d'assemblage sur les trois génomes publiés, que nous avons corrigé. Une étude du pangénome de ces trois souches montre un génome core important. La plasticité de l'espèce serait donc plus dans l'organisation du génome que dans les différentes capacités de codage. Une sous partie du génome core, dont les gènes ont un pourcentage d'identité nucléotidique plus faible que la plupart (génome core variant) est intéressante pour expliquer les différences phénotypiques de ces bactéries. Nous avons étudié la répartition d'un facteur de virulence, les fimbriae, structures d'adhésion, au sein du genre Porphyromonas et lié les loci à la phylogénie et au caractère pathogène des espèces. Finalement, une description de la dysbiose qui a lieu lors d'une parodontite est faite par une analyse du microbiote de patients atteints de parodontite et d'individus sains. Les genres prépondérants lors des deux états sont mis en évidence. Au cours de ces travaux, nous montrons l'importance de la biocuration et sa valeur ajoutée dans les travaux de génomique et bioinformatique en général. Seulement en faisant ce travail lent et lourd de biocuration, les réponses apportées aux questions biologiques seront pertinentes<br>Bacteria of Bacteroidetes phylum, Bacteroidia class, are amongst the more important in gastrointestimal microbiota, either human or from other mammals. The mouth, digestive tube entry, is an environment with varied anatomic sites, each having a particular microbiota with different composition. The union between gingiva and teeth, the gingival sulcus, is a site for biofilm (dental plaque) formation and accumulation. Porphyromonas gingivalis, a bacterium from this phylum, can modulate the inmune system and produce an oral biofilm desequilibrium called dysbiosis. This triggers the formation of a periodontal pocket, a pathological deepening of the gingival sulcus, and the emergence of periodontitis. Other Porphyromonas species are also associated to periodontitis, mainly in canids. P. gingivalis populations are panmictic and their genomes are highly plastic. Bioinformatics can help to identify the causes of this genomic mosaicity, to study Porphyromonas virulence factors in order to explain why some species are pathogens and other are commensal, and to describe the dysbiosis linked to periodontitis. P. gingivalis comparative genomics showed a correlation between the number of contigs in draft genomes and genomic repeats, mainly insertion sequences. We resequenced, reassembled and reannotated three reference strains of this bacterium that already had complete published genomes, using long-read sequencing. We showed that misassemblies were present in the three published genomes, and we corrected them. A pangenome study of the three strains showed that the core genome is preponderant. The species plasticity might be related more to the genome organization than to different coding capacities. A subpart of th core genome, with genes having a nucleotidic identity percentage lower than the majority (variable core genome), is interesting for explaining the phenotypic differences of bacteria. We analysed the repertoire of a virulence factor, fimbriae, adhesion structures, in the Porphyromonas genus to link the loci to phylogeny and pathogenicity of its species. Finally, we described the dysbiosis occuring with periodontitis, analysing gingival microbiota of patients having the illness and healthy individuals. Preponderant genera in both states are highlighted. With this work, we demonstrate the importance of biocuration and its added value for genomic and bioinformatic studies in general. Only with this slow and arduous work, the answers to biological questions will be relevant
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Cocca, Stephanie M. "Phylogenetic analysis, modeling and experimental studies of the Saccharomyces cerevisiae palmitoylated protein kinase gene, ENV7." Thesis, California State University, Long Beach, 2014. http://pqdtopen.proquest.com/#viewpdf?dispub=1527907.
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<p> Env7 is a vacuole membrane-localized protein kinase that is orthologous to the human serine/threonine protein kinase, STK16. It is evolutionarily well-conserved throughout Eukarya, and it has one ortholog in Bacteria. Phylogenetic analyses of sequences homologous to Env7 revealed clades that are inconsistent with established eukaryotic phylogeny, suggesting that both horizontal and vertical gene transmission are responsible for their conservation. Conserved amino acid residues and motifs that are potentially important to Env7's catalytic activity, localization, and interactions with other proteins were also identified and assessed. Additionally, one such conserved motif—the glycine-rich loop—was mutated in an effort to affect ATP binding in Env7. The phenotype resulting from this mutation was a slightly increased number of mutant cells exhibiting multi-lobed vacuoles under normal conditions.</p>
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Suen, Garret. "Understanding prokaryotic diversity in the post-genomics era." Related electronic resource: Current Research at SU : database of SU dissertations, recent titles available, full text:, 2008. http://wwwlib.umi.com/cr/syr/main.
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Groban, Eli S. "The study and engineering of cellular signaling pathways." Diss., Search in ProQuest Dissertations & Theses. UC Only, 2008. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3339232.
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Thesis (Ph.D.)--University of California, San Francisco, 2008.<br>Source: Dissertation Abstracts International, Volume: 69-12, Section: B, page: 7352. Advisers: Matthew P. Jacobson; Christopher A. Voigt.
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Santiago, Marina Joy. "New Genomics Tools and Strategies for Studying Antibiotics and Antibiotic-Resistance in Staphylococcus Aureus." Thesis, Harvard University, 2016. http://nrs.harvard.edu/urn-3:HUL.InstRepos:33493460.
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Staphylococcus aureus is a gram positive coccoid pathogen that causes intractable infections in hospitals and communities around the world, and tens of thousands of people die of these infections every year. In order to combat these antibiotic-resistant infections, we need to better understand the genes involved in resistance to the cell stress caused by antibiotic treatment, which will enable the discovery of new antimicrobials and the development of novel therapeutic strategies. We chose to use an approach to this problem that utilizes a new phage-based high frequency of transposition system. In this work, we adapted this system so that transposon mutant libraries can be made and sequenced using next-generation sequencing (NGS) in any strain of S. aureus. We validated our new platform by performing a temperature screen and identifying mutants that are significantly resistant or sensitive to temperature-stress. Next, we created transposon libraries in two MRSA strains to show that this system can be broadly applied to other S. aureus strains, and we used one of these libraries to identify a new interaction between two genes involved in the secretion of sortase-anchored surface proteins. To better understand antibiotic-resistance, we performed Tn-Seq on transposon libraries treated with a small panel of six different antibiotics to identify intrinsic resistance factors to these antibiotics. We identified two new intrinsic resistance factors, SAOUHSC_01025 and SAOUHSC_01050, that sensitize to many cell envelope targeting antibiotics and may be involved in hemolysin regulation. Finally, we expanded this approach to sequence transposon libraries treated with 25 different antibiotics. Based on these data, we were able to develop methods for predicting the mechanism of action of new antibiotics. These methods involve identifying genes upregulated by transposon insertion and applying machine learning algorithms to identify similarities to a curated panel of well-studied antibiotics with known mechanisms of action. This work will enable many new functional genomics studies in S. aureus, and it will allow us to gain a better understanding of antibiotic resistance in this dangerous pathogen.<br>Chemical Biology
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Kokkonen, Alexander. "Evaluation of next-generation sequencing as a tool for determining the presence of pathogens in clinical samples." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-17374.
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Metagenomic sequencing is an increasingly popular way of determining microbial diversity from environmental and clinical samples. By specifically targeting the 16S rRNA gene found in all bacteria, classifications of pathogens can be determined based on the variable and conserved regions found in the gene. Metagenomic sequencing can therefore highlight the vast difference in microbiological diversity between culture-dependent and culture-independent methods. Today, this has expanded into various next-generation sequencing platforms which can provide massively parallel sequencing of the target fragment. One of these platforms is Ion-torrent, which can be utilized for targeting the 16S rRNA gene and with the help of bioinformatics pipelines be able to classify pathogens using the bacteria’s own variable and conserved regions. The overall aim of the present work is to evaluate the clinical use of Ion-torrent 16S ribosomal RNA sequencing for determining pathogenic species from clinical samples, but also to set up a pipeline for clinical practice. Optimal DNA-extraction and quantification methods were determined towards each evaluated sample-type and DNA-eluates were sent for 16S rRNA Sanger and Next-generation sequencing. The result indicated that the next-generation sequencing shows a concordance in results towards the culturing-based method, but also the importance of experimental design and effective quality trimming of the NGS data. The conclusion of the project is that the Ion-torrent pipeline provided by the Public Health Agency of Sweden shows great promise in determining pathogens from clinical samples. However, there is still a lot of validation and standardisations needed for the successful implementation into a clinical setting.
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Donnelly, Chase P. "Microbial Ecology of South Florida Surface Waters: Examining the Potential for Anthropogenic Influences." Thesis, NSUWorks, 2018. https://nsuworks.nova.edu/occ_stuetd/485.
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South Florida contains one of the largest subtropical wetlands in the world, and yet not much is known about the microbes that live in these surface waters. These microbes play an important role in chemical cycling and maintaining good water quality for both human and ecosystem health. The hydrology of Florida’s surface waters is tightly regulated with the use of canal and levee systems run by the US Army Corps of Engineers and The South Florida Water Management District. These canals run through the Everglades, agriculture, and urban environments to control water levels in Lake Okeechobee, the Water Conservation Areas, and the surrounding farm lands. I hypothesized that there would be noticeable shifts in the microbial communities (also known as “microbiomes”) at the agriculture and urban sites due to anthropogenic influences such as agricultural and sewage runoff. It is also hypothesized that the diversity and stability of these sites will differ from the natural environment Grassy Waters Preserve (GWP), which we studied as a control. The northern section of GWP is a rain-fed Everglades ecosystem with little influence from manmade canal systems, so GWP can represent wetlands before human influences. High-throughput 16s rRNA sequencing was conducted on 112 GWP, canal, and agricultural water samples taken over a one-year period from September 2016 to November 2017. Data were processed in Qiime2 using DADA2 and resulted in 67732 unique taxa. Nineteen metadata factors were measured for 87 of the sampling points to investigate environmental effects. These factors explained 25% (r2=0.25, p=0.002) of the variation between sample locations. Conductivity was found to have the highest effect on microbial diversity (r2=0.078, p=0.002) while latitude and month also significantly influenced the microbial makeup. Urban and agricultural sites were found to have higher stability with lower variation in microbiomes over the course of study. The GWP site was found to have a high seasonality, probably due to its dependence on rain. The most abundant taxa for all sites (urban, agriculture, and control) were; family Spirochaetaceae, phylum Actinobacteria, and family Burkholderiaceae, respectively. Contamination of GWP and canal sites was also investigated using SourceTracker code. Intracoastal waters that receive canal water were found to be heavily influenced in the peak wet season when there is high flow through from the canals. GWP had little influence from farm lands compared to a high influence of agriculture on the urban sites.
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Mehta, Trupthi. "Availability of Fermentable Nutrients Affect Gut Microbiota Composition." Wright State University / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=wright1535384558865901.
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Garbom, Sara. "A strategy to identify novel antimicrobial compounds : a bioinformatics and HTS approach." Doctoral thesis, Umeå : Department of Molecular Biology, Umeå University, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-900.
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Wang, Mengchi. "Probing the Regulation of Elongation Factor P-Mediated Translation." The Ohio State University, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=osu1372761617.
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Mota, Merlo Marina. "Evolutionary evidence of chromosomal rearrangements through SNAP : Selection during Niche AdaPtation." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-449171.
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The Selection during Niche AdaPtation (SNAP) hypothesis aims to explain how the gene order in bacterial chromosomes can change as the result of bacteria adapting to a new environment. It starts with a duplication of a chromosomal segment that includes some genes providing a fitness advantage. The duplication of these genes is preserved by positive selection. However, the rest of the duplicated segment accumulates mutations, including deletions. This results in a rearranged gene order. In this work, we develop a method to identify SNAP in bacterial chromosomes. The method was tested in Salmonella and Bartonella genomes. First, each gene was assigned an orthologous group (OG). For each genus, single-copy panorthologs (SCPos), the OGs that were present in most of the genomes as one copy, were targeted. If these SCPos were present twice or more in a genome, they were used to build duplicated regions within said genome. The resulting regions were visualized and their possible compatibility with the SNAP hypothesis was discussed. Even though the method proved to be effective on Bartonella genomes, it was less efficient on Salmonella. In addition, no strong evidence of SNAP was detected in Salmonella genomes.
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Simon, Philippe. "Undersökning av Nosema hos bin : utbredning och förekomst i Sverige." Thesis, Umeå universitet, Institutionen för ekologi, miljö och geovetenskap, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-163500.
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This report investigates the presence of Nosema in Sweden. Nosema is an intracellular parasite within the order Microsporidia and is considered a global threat. The most recent academic study on the presence of Nosema in Sweden was published in 2013, however in that study no presence of Nosema in the north of Sweden was reported. The aim of this study was to explore the presence of Nosema in Sweden, particularly in the north of Sweden. Samples were gathered from different locations in Sweden, and thereafter analysed (n=74), 54 samples were analysed under microscope. A geographical map was created to establish the range of Nosema on a global perspective. PCR primers and FISH gene probes for molecular identification were evaluated and tested both in SILVA and in an own database created in the bioinformatics software package ‘ARB’. Main findings of the study were that Nosema were detected in two samples in Sweden and that further studies with more sophisticated methods and better sequencing needs to be developed in order to fully investigate the presence of Nosema in the north of Sweden.
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Knowlton, Caitlin N. "Analysis of microbes in Greenland ice cores from periods of high and low atmospheric carbon dioxide levels." Bowling Green State University / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1362670626.
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Brown, Shawn Paul. "Rules and patterns of microbial community assembly." Diss., Kansas State University, 2014. http://hdl.handle.net/2097/18324.
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Doctor of Philosophy<br>Division of Biology<br>Ari M. Jumpponen<br>Microorganisms are critically important for establishing and maintaining ecosystem properties and processes that fuel and sustain higher-trophic levels. Despite the universal importance of microbes, we know relatively little about the rules and processes that dictate how microbial communities establish and assemble. Largely, we rely on assumptions that microbial community establishment follow similar trajectories as plants, but on a smaller scale. However, these assumptions have been rarely validated and when validation has been attempted, the plant-based theoretical models apply poorly to microbial communities. Here, I utilized genomics-inspired tools to interrogate microbial communities at levels near community saturation to elucidate the rules and patterns of microbial community assembly. I relied on a community filtering model as a framework: potential members of the microbial community are filtered through environmental and/or biotic filters that control which taxa can establish, persist, and coexist. Additionally, I addressed whether two different microbial groups (fungi and bacteria) share similar assembly patterns. Similar dispersal capabilities and mechanisms are thought to result in similar community assembly rules for fungi and bacteria. I queried fungal and bacterial communities along a deglaciated primary successional chronosequence to determine microbial successional dynamics and to determine if fungal and bacterial assemblies are similar or follow trajectories similar to plants. These experiments demonstrate that not only do microbial community assembly dynamics not follow plant-based models of succession, but also that fungal and bacterial community assembly dynamics are distinct. We can no longer assume that because fungi and bacteria share small propagule sizes they follow similar trends. Further, additional studies targeting biotic filters (here, snow algae) suggest strong controls during community assembly, possibly because of fungal predation of the algae or because of fungal utilization of algal exudates. Finally, I examined various technical aspects of sequence-based ecological investigations. These studies aimed to improve microbial community data reliability and analyses.
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Stangl, Karen E. "Comparative Proteomic Analysis of Phase-Switch in the Dimorphic Fungus, Penicillium marneffei." Youngstown State University / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=ysu1233446433.
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Gurung, Deepti. "Evolution of Recombination: RecBCD and AddAB in Bacteria." University of Toledo Health Science Campus / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=mco157444538568144.
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Caufield, J. Harry. "Interactomics-Based Functional Analysis: Using Interaction Conservation To Probe Bacterial Protein Functions." VCU Scholars Compass, 2016. http://scholarscompass.vcu.edu/etd/4580.
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The emergence of genomics as a discrete field of biology has changed humanity’s understanding of our relationship with bacteria. Sequencing the genome of each newly-discovered bacterial species can reveal novel gene sequences, though the genome may contain genes coding for hundreds or thousands of proteins of unknown function (PUFs). In some cases, these coding sequences appear to be conserved across nearly all bacteria. Exploring the functional roles of these cases ideally requires an integrative, cross-species approach involving not only gene sequences but knowledge of interactions among their products. Protein interactions, studied at genome scale, extend genomics into the field of interactomics. I have employed novel computational methods to provide context for bacterial PUFs and to leverage the rich genomic, proteomic, and interactomic data available for hundreds of bacterial species.
The methods employed in this study began with sets of protein complexes. I initially hypothesized that, if protein interactions reveal protein functions and interactions are frequently conserved through protein complexes, then conserved protein functions should be revealed through the extent of conservation of protein complexes and their components. The subsequent analyses revealed how partial protein complex conservation may, unexpectedly, be the rule rather than the exception. Next, I expanded the analysis by combining sets of thousands of experimental protein-protein interactions. Progressing beyond the scope of protein complexes into interactions across full proteomes revealed novel evolutionary consistencies across bacteria but also exposed deficiencies among interactomics-based approaches. I have concluded this study with an expansion beyond bacterial protein interactions and into those involving bacteriophage-encoded proteins.
This work concerns emergent evolutionary properties among bacterial proteins. It is primarily intended to serve as a resource for microbiologists but is relevant to any research into evolutionary biology. As microbiomes and their occupants become increasingly critical to human health, similar approaches may become increasingly necessary.
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Hart, Benjamin Randall. "Expanded Functionality of the Bacterial Global Regulator Lrp." University of Toledo Health Science Campus / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=mco1280773330.
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Li, Wei. "INFLUENCE OF ENVIRONMENTAL DRIVERS AND INTERACTIONS ON THE MICROBIAL COMMUNITY STRUCTURE IN PERMANENTLY STRATIFIED MEROMICTIC ANTARCTIC LAKES." Miami University / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=miami1469757316.
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Scott-Elliston, Ayana. "IN SEARCH OF A FUNCTION FOR AN UNCHARACTERIZED CONSERVED PROTEIN IN Streptococcus sanguinis SK36." VCU Scholars Compass, 2017. http://scholarscompass.vcu.edu/etd/4889.
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With the number of fully sequenced bacterial genomes increasing in the past 7 years, it has been discovered that a large percentage of the putative protein coding genes have no known function. This lack of knowledge leaves scientists with an incomplete understanding of bacteria. In this study, conserved hypothetical protein mutants from Streptococcus sanguinis SK36 were screened on solid media with various environmental conditions. From these screens, the candidate protein, SSA_2372, displayed a sensitivity to acidic conditions. Its homolog in Bacillus subtilis 168, BSU00030, also displayed a sensitivity to pH conditions at its acid tolerance extremes unlike its other homolog in Escherichia coli, YbcJ. When the growth rate and cell yield was acquired, the sensitivity was shown to be significant for both SSA_2372 and BSU00030 mutants. Through data mining, it was determined that Firmicutes in this homolog family COG2501 may function as a regulator for recombination protein F.
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Ferrer, Samuel. "STAIRS : Data reduction strategy on genomics." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-383465.
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Background. An enormous accumulation of genomic data has been taking place over the last ten years. This makes the activities of visualization and manual inspection, key steps in trying to understand large datasets containing DNA sequences with millions of letters. This situation has created a gap between data complexity and qualified personnel due to the need of trading between visualization, reduction capacity and exploratory functions, features rarely achieved by existing tools, such as SRA toolkit (https://www.ncbi.nlm.nih.gov/sra/docs/toolkitsoft/), for instance. A novel approach to the problem of genomic analysis and visualization was pursued in this project, by means of STrAtified Interspersed Reduction Structures (STAIRS). Result. Ten weeks of intense work resulted in novel algorithms to compress data, transform it into stairs vectors and align them. Smith–Waterman and Needleman–Wunsch algorithms have been specially modified for this purpose and the application brought about statistical performance and behavioural charts.
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Klug, Hannah. "Comparison and Genetic Analysis of Host Specificity in Cluster BD1 Bacteriophages infecting Streptomyces." Thesis, University of North Texas, 2019. https://digital.library.unt.edu/ark:/67531/metadc1505244/.
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Bacteriophages are viruses that specifically infect bacteria. When a phage infects a bacterium, it attaches itself to the surface of the bacteria and injects its DNA into the intracellular space. The phage DNA hijacks the cellular machinery of the bacteria and forces it to produce phage proteins. Eventually, the bacteria cell bursts or lyses, releasing new phage. The bacteria act as a host for phage reproduction. The ability for a phage to infect multiple bacterial species is known as host range. In siphoviridae bacteriophages, host range is thought to primarily be determined by proteins at the tip of their tail fibers. These proteins act as anti-receptors to specific receptors on the surface of bacteria. In siphoviridae Gram-positive infecting phages, the genes that code these proteins are typically located between the tape measure protein gene and the endolysin gene. It is hypothesized that phages that have similar anti-receptor proteins will have similar host range. In this study, the host ranges of 12 BD1 bacteriophages were tested on 9 different Streptomyces species. In these 12 phages, the genes between the tape measure protein gene and endolysin gene were compared. The 12 phages had high levels of variability in these genes. Five genes in this region had unknown functions and were called position A, B, C, D, and E. Position A-E were BLASTed on NCBI and Phages-DB and their results were recorded. The functions of position A, C, and E remain unknown. The function of position D is most likely a minor tail protein. Position B had BLAST hits for a collagen-like protein and a putative tail fiber protein. Position B was inspected further, and it was found that it contained Gly-X-Y repeats in its amino acid sequence. Position B also had some conservation in its N-terminal amino acid sequence, specifically where the Gly-X-Y repeats were located. Position B had strong conservation in the C-terminal end of its amino acid sequence. Glycine repeats and conservation in the N and C-terminal end of the amino acid sequence are both common factors in known host specificity related genes. There appeared to be no correlation in conservation of position A-E and host range. It was concluded that no single gene can predict a phages host range, but the discovery of collagen repeats could be used as a landmark to find genes related to host surface receptors.
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Moutran, Alexandre. "Modelagem molecular das proteínas captadoras de molibdato (ModA) e oligopeptídeos (OppA) de Xanthomonas axonopodis pv. citri." Universidade de São Paulo, 2009. http://www.teses.usp.br/teses/disponiveis/42/42132/tde-16072009-100344/.
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Sistemas de transporte tipo ABC são responsáveis pelo transporte de uma grande variedade de substâncias dentre elas os oligopeptídeos e molibdato. Neste trabalho estudamos dois sistemas de transportadores do tipo ABC (mod, envolvido na captação de molibdato e o opp na capação de oligopeptídeos) presentes na bactéria Xanthomonas axonopodis pv. citri (Xac). Em particular analisamos a organização genética dos óperons mod e as proteínas ModA e OppA, componentes solúveis localizados no periplasma e responsáveis pela ligação aos substratos. Por meio de técnicas de modelagem molecular, definimos modelos estruturais para as proteínas ModA e OppA. Para a proteína ModA caracterizamos cinco resíduos que compõem a cavidade ligadora e são responsáveis pelas interações com o íon molibdato, assim como a sua similaridade estrutural e sequencial com ortólogos de 3 grupos distintos de bactérias. Para a OppA, descrevemos o seu comportamento na ancoragem de diferentes oligopeptídeos. Avaliamos parâmetros como a extensão da cadeia e estabelecemos uma ordem crescente de afinidade entre os oligopeptídeos com diferente composição residual e a proteína OppA.<br>ABC transport system are responsable for the uptake of a large variety of substrates, including oligopeptides and molybdate. In this work we studied two ABC transporter systems (mod and opp responsable for molybdate and oligopeptide uptake, respectively) present in plant pathogen Xanthomonas axonopodis pv. citri (Xac). We investigated the genetic organization of mod operon and, particularly, structural feature of periplasmic components, ModA and OppA proteins, of the uptake systems. Using molecular modeling techniques, we defined the structural models of both ModA and OppA proteins. Based on the ModA structural model, amino acid residues involved in molybdate interaction were identified. In addition, both the structural and sequence similarities of Xac ModA and other bacterial orthologs with experimentally defined structural organizations were described. Based on the OppA structural model, we applied molecular docking tools to determine the binding specificity for different oligopeptide regarding number and amino acid composition. Collectively, our results represent an important contribution to the study of ABC transporters in an economically relevant phytopathogen bacterial species.
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Yan, Erfu. "BIOSYNTHETIC MECHANISM OF THE ANTIBIOTIC CAPURAMYCIN." UKnowledge, 2018. https://uknowledge.uky.edu/pharmacy_etds/92.
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A-102395 is a member of the capuramycin family of antibiotics which was isolated from the culture broth of Amycolatopsis sp. SANK 60206. A-102339 is structurally classified as a nucleoside antibiotic, which like all members of the capuramycin family, inhibits bacterial MraY (translocase I) with IC50 of 11 nM which is the lowest among the capuramycin family. A semisynthetic derivative of capuramycin is currently in clinical trials as an antituberculosis antibiotic, suggesting high potential for using A-102395 as a starting point for new antibiotic discovery. In contrast to other capuramycins, A-102395 has a unique arylamine-containing polyamide side chain. The biosynthetic gene cluster of A-102395 was previously identified and includes 35 putative open reading frames responsible for biosynthesis and resistance. Presently, there are no reports focused on the biosynthesis of this polyamide chain. Here we present the functional assignment and biochemical characterization of seven proteins, Cpr33-38 and Cpr12, that initiate the biosynthesis of the polyamide.
Functional characterization of Cpr38, which has sequence similarity to the gene products encoded by pabA and pabB from E. coli, revealed that it functions as a 4-amino-4-deoxychorismate (ADC) synthase catalyzing a two-step reaction involving amidohydrolysis of L-Gln with ammonia channeled and incorporated into chorismic acid to generate ADC. Cpr12, encoded by a gene that was originally proposed to be outside the gene cluster and sharing similarity to proteins annotated as ADC lyase, was revealed to catalyze the elimination of pyruvate to form PABA.
Cpr36 is demonstrated to function as a free-standingpeptidyl carrier protein (PCP), which is activated to form holo-protein from the apo-form. Cpr37, which belongs to the adenylation domain protein in the nonribosomal peptide synthase (NRPS), subsequently activates PABA and loads it to holo-Cpr36 Two proteins Cpr34 and Cpr35 work in concert to catalyze decarboxylative condensation between a thioester linked PABA and malonyl-S-acyl carrier protein (ACP) during aromatic polyketide biosynthesis catalyzed by type II polyketide synthases.
Following condensation, Cpr33 acts as 3-oxoacyl-ACP reductase that catalyzes reduction to the β-hydroxythioester intermediate. In this scenario, hydride is predicted to be added to the re face to generate the S configuration resulting in the same stereochemical outcome as other 3-oxoacyl-ACP reductase (FabG) from bacterial type II fatty acid synthases.These findings are critical advancement for interrogating the biosynthesis of the unusual chemical components of the family of antibiotics of capuramycin.
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Howard, Alexander E. "Characterization of DNA Methyltransferase 1-Associated Protein from Phytophthora sojae." Bowling Green State University / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1498172183304139.
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Gerst, Michelle Marie. "Improving methods to isolate bacteria producing antibacterial compounds followed by identification and characterization of select antimicrobials." The Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu1512070391589857.
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English, Suzanne Elizabeth. "Within-host evolution of HIV-1 and the analysis of transmissible diversity." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:df24b49c-fb27-49a3-bd2e-3e38008e9da4.
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The central problem for researchers of HIV-1 evolution is explaining the apparent design of the virus for causing pandemic infection in humans: understanding how HIV-1 spreads is key to halting the pandemic. Current knowledge of how HIV-1 spreads from host to host is based upon experimental observation and indirect inferences informed by theory. The hypothesis of this thesis is that diversity of HIV-1 around the time of transmission is important for viral adaptation to a new human host, rather than intrinsic superiority of particular strains found in infectious fluids from human donor hosts, and that studying recombination is important for understanding this behaviour. To demonstrate the apparent randomness of transmission, I test the null-hypothesis that hard selection accounts for between-host viral divergence in a rare case study of contemporaneous infection. I explain how the experimental data that I have generated and the analyses I have carried out address certain basic assumptions and predictions about HIV-1 transmission and may inform current strategies for vaccine design. Specifically, my approach contributes to the current literature on HIV-1, by investigating an alternative hypothesis to the single virion theory of sexual transmission and by characterizing the role of recombination in a pseudodiploid virus following multiple-infection.
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Nyrén, Karl. "Phylogenetic analysis of secretion systems in Francisellaceae and Legionellales : Investigating events of intracellularization." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-448062.
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Host-adapted bacteria are pathogens that, through evolutionary time and host-adaptive events, acquired the ability to manipulate hosts into assisting their own reproduction and spread. Through these host-adaptive events, free-living pathogens may be rendered unable to reproduce without their host, which is an irreversible step in evolution. Francisellaceae and Legionellales, two orders of Gammaproteobacteria, are cases where host-adaptation has lead to an intracellular lifestyle. Both orders use secretion systems, in combination with effector proteins, to invade and control their hosts. A current view is that Francisellaceae and Legionellales went through host-adaptive events at two separate time points. However, F. hongkongensis, a member of Francisellaceae shares the same secretion system as the order of Legionellales. Additionally, two host-adapted Gammaproteobacteria, Piscirickettsia spp. and Berkiella spp., swaps phylogenetic positions between Legionellales and Francisellaceae depending on methods applied - indicating shared features of Francisellaceae and Legionellales. In this study, we set up a workflow to screen public metagenomic data for candidate host-adaptive bacteria. Using this data, we attempted to assert the phylogenetic position and possibly resolve evolutionary events that occurred in Legionellales, F. hongkongensis, Francisellaceae, Piscirickettsia spp. and Berkiella spp. We successfully acquired 23 candidate host-adapted MAGs by (i) scanning for genes, among reads before assembly, using PhyloMagnet, and (ii) screening for complete secretion systems with MacSyFinder. The phylogenetic results turned out indecisive in the placement ofBerkiella spp. and Piscirickettsia. However, results found in this study indicate that, contrary to previous beliefs, it is possible that it was one intracellularization event of a common ancestor that gave rise to the intracellular lifestyle of Francisellaceae and Legionellales.
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Rozmarynowycz, Mark Jeremy. "Spatio-Temporal Distribution Of Microbial Communities In TheLaurentian Great Lakes." Bowling Green State University / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1416427796.
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Tuttle, Taylor A. "Characterization of the Persistent Cyanobacterial Bloom, Planktothrix, in Sandusky Bay, Lake Erie." Bowling Green State University / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1435180971.
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Pelicaen, Rudy. "Genome-scale metabolic modeling of candidate functional starter cultures for cocoa bean fermentation." Doctoral thesis, Universite Libre de Bruxelles, 2020. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/308886.
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Cocoa bean fermentation is an essential but spontaneous fermentation process to obtain the necessary raw material for the production of cocoa-derived products, among which chocolate. Successful cocoa bean fermentation processes are typically dominated by three microbial groups, namely yeasts, lactic acid bacteria, and acetic acid bacteria. The use of functional starter cultures may allow to gain a better control over the fermentation process. Previously, a number of candidate functional starter cultures have been proposed for the lactic acid bacteria, namely Lactobacillus fermentum 222 and Lactobacillus plantarum 80, and for the acetic acid bacteria, namely Acetobacter pasteurianus 386B, Acetobacter ghanensis LMG 23848T, and Acetobacter senegalensis 108B. The metabolism of bacteria determines an important part of their physiology, and this is recently being investigated by using computational models. The aim of this PhD thesis was to develop such models for the candidate functional starter cultures for the cocoa bean fermentation process and to perform the related computational analysis. The computational models developed were genome-scale metabolic models, which constitute a comprehensive repertoire of metabolic enzymes with their concomitant reactions, and this at genome-scale. The reconstruction of such models requires a combination of high-quality genome re-annotation, comparative genomics, manual curation, and experimental validation. Genome-scale metabolic modeling together with the use of previously published experimental data under cocoa fermentation conditions allowed to contextualize the experimental data and to gain new insights into the metabolic properties of the candidate functional starter cultures. Simulations with the A. pasteurianus 386B genome-scale metabolic model revealed the metabolic roles of lactate and ethanol, the energetic properties of the strains’ aerobic respiratory chain, and the possible functional role of an NAD(P)+ transhydrogenase. Modeling the metabolite dynamics of A. ghanensis LMG 23848T under cocoa fermentation conditions revealed an alternative strategy for its diauxic growth, compared with A. pasteurianus 386B, which was related to a difference in lactate consumption rate and pyruvate overflow. For A. senegalensis 108B, it was shown that, next to lactic acid, also citric acid could sustain its growth in vitro as the sole carbon source. Furthermore, the absence of the glyoxylate cycle predicted from its genome did not correspond with its species description that reports growth on ethanol as the sole carbon source. For L. fermentum 222 and L. plantarum 80, core genome-scale metabolic models allowed to gain insight into the possible metabolic flux distributions as a function of environmental conditions. The modeling also indicated a current lack in knowledge; for example, concerning the presence and consumption of undefined substrates in the complex medium used.In summary, genome-scale metabolic modelling of candidate functional starter cultures for the cocoa bean fermentation process provided useful in silico tools to gain insight into their metabolic properties at a systemic level.<br>La fermentation du cacao est un processus essentiel pour obtenir la matière première nécessaire pour la production de produits dérivés du cacao, comme par exemple le chocolat. Une fermentation de cacao favorable est caractérisée par la domination de trois groupes de microorganismes :les levures, les bactéries lactiques, et les bactéries acétiques. L'utilisation de cultures de départ fonctionnelles permet un meilleur contrôle sur le processus de fermentation. En ce qui concerne les bactéries, de nombreuses cultures "starter" ont été proposées, à savoir Lactobacillus fermentum 222 et Lactobacillus plantarum 80 pour les bactéries lactiques et Acetobacter pasteurianus 386B, Acetobacter ghanensis LMG 23848T, et Acetobacter senegalensis 108B pour les bactéries acétiques. Le métabolisme des bactéries constitue une partie importante de leur physiologie et la recherche actuelle se concentre de plus en plus sur la modélisation du métabolisme et la simulation des flux métaboliques par ordinateur. Cette thèse de doctorat a été consacrée au développement et à l'analyse de tels modèles computationnels pour des cultures fonctionnelles "starter" proposés pour la fermentation du cacao.Les modèles qui ont été développés dans cette thèse sont des modèles métaboliques à l’échelle du génome. La reconstruction du réseau métabolique a entraîné la ré-annotation du génome, une étude de génomique comparative, la curation manuelle des annotations et la validation du modèle par des expériences in vitro. La modélisation nous a permis de contextualiser des données expérimentales déjà publiées pour en obtenir de nouvelles informations concernant les propriétés métaboliques des cultures starter. Des simulations utilisant le modèle métabolique de A. pasteurianus 386B ont clarifié les rôles métaboliques de l’acide lactique et de l’éthanol, les propriétés énergétiques de sa chaîne respiratoire, et ont permis d'assigner un rôle possible à une NAD(P)+ transhydrogénase. La modélisation de la dynamique des métabolites provenant d’un milieu de croissance de A. ghanensis LMG 23848T dans des conditions simulant la fermentation du cacao, a mis en évidence une stratégie alternative de croissance biphasique comparé à A. pasteurianus 386B. Ceci est dû à une différence dans le taux de consommation de l’acide lactique et à l’éventuelle production de pyruvate. Pour A. senegalensis 108B, les expériences ont démontré, tant pour l’acide lactique que pour l’acide citrique, que ces sources de carbone permettaient, à elles seules, la croissance de cette bactérie. L’absence du cycle du glyoxylate chez A. senegalensis 108B ne correspondait pas à la description de cette espèce, laquelle pouvant croître sur l’éthanol comme seule source de carbone. Pour L. fermentum 222 et L. plantarum 80, la modélisation de leur métabolisme du carbone a permis d’explorer les distributions de flux métaboliques en fonction des substrats consommés. Les simulations ont aussi révélé le manque de connaissance que nous avons sur ces bactéries lactiques, telle que la consommation de substrats non identifiés venant du milieu de croissance et qui pourrait influencer leur dynamique de croissance.En résumé, la modélisation métabolique à l’échelle du génome des cultures starter proposées pour la fermentation du cacao a permis le développement d’outils in silico qui peuvent être utilisés pour mieux comprendre le métabolisme global de ces souches.<br>Het cacaoboonfermentatieproces is een essentieel maar spontaan proces dat nodig is om de noodzakelijke grondstof, met name de gefermenteerde cacaobonen, voor de productie van cacao-afgeleide producten, waaronder chocolade, te bekomen. Succesvolle cacaoboonfermentatieprocessen worden typisch gedomineerd door drie microbiële groepen, met name gisten, melkzuurbacteriën en azijnzuurbacteriën. Om meer controle te verkrijgen over het fermentatieproces is het gebruik van functionele starterculturen aangewezen. In vorige studies werd reeds een reeks kandidaat-functionele starterculturen voorgesteld. Voor de melkzuurbacteriën zijn dit Lactobacillus fermentum 222 en Lactobacillus plantarum 80 en voor de azijnzuurbacteriën zijn dit Acetobacter pasteurianus 386B, Acetobacter ghanensis LMG 23848T en Acetobacter senegalensis 108B. Het metabolisme van bacteriën bepaalt in grote mate hun fysiologie, en dit wordt recent onderzocht door middel van computationele modellen. Het ontwikkelen en analyseren van zulke modellen voor de voorgestelde kandidaat-functionele starterculturen vormde het onderwerp van deze doctoraatsthesis.De computationele modellen waarvan sprake waren genoomwijde metabole modellen (GEMs), dewelke het repertoire aan metabole enzymen en de biochemische reacties die zij katalyseren in de bacteriële cellen omvat. De reconstructie van het metabole netwerk op genoomschaal vraagt om een gecombineerde aanpak van hoge-kwaliteit genoomherannotatie, comparatieve genomica en experimentele validatie. De GEMs werden gebruikt om reeds gepubliceerde experimentele data onder cacaofermentatiecondities te contextualiseren en nieuwe inzichten te verkrijgen in de metabole karakteristieken van de kandidaat-functionele starterculturen. Door middel van simulaties met het A. pasteurianus 386B GEM kon de metabole rol van melkzuur en ethanol, en de energetische karakteristieken van de aerobe respiratieketen van deze stam aangetoond worden, alsook de mogelijke metabole functie van een NAD(P)+ transhydrogenase. Het modelleren van de microbiële dynamica van A. ghanensis LMG 23848T onder cacaofermentatiecondities wees op een alternatieve strategie voor de tweevoudige groei van deze stam ten opzichte van de tweevoudige groei van A. pasteurianus 386B onder dezelfde condities, en dit omwille van een verschil in melkzuurconsumptiesnelheid en pyruvaatsecretie. Voor A. senegalensis 108B werd aangetoond dat deze stam, naast melkzuur, ook op citroenzuur als enige koolstofbron kon groeien. De afwezigheid van de glyoxylaatcyclus, voorspeld op basis van het genoom, bij A. senegalensis 108B is in tegenstelling tot de soortbeschrijving, dewelke stipuleert dat deze azijnzuurbacteriesoort in staat is tot groei op ethanol als enige koolstofbron. Voor L. fermentum 222 en L. plantarum 80 leidde de ontwikkeling van GEMs tot nieuwe inzichten in de mogelijke metabole fluxverdelingen, voornamelijk ten aanzien van substraatverbruik. Het modelleren van de microbiële dynamica wees ook op een tekortkoming aan huidige kennis over deze stammen, bijvoorbeeld met betrekking tot het gebruik van ongedefinieerde substraten in een rijk groeimedium.Samenvattend werden door middel van de ontwikkelde GEMs van de kandidaat-functionele starterculturen voor cacaoboonfermentatieprocessen nieuwe inzichten verkregen in hun metabolisme en dit op systeemniveau.<br>Doctorat en Sciences<br>info:eu-repo/semantics/nonPublished
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Muhindi, Stephen W. "Cloning and Sequencing of Mercury Resistance Operons from the Enterobacter sp. YSU and Stenotrophomonas maltophilia OR02." Youngstown State University / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=ysu1525449851977263.
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