To see the other types of publications on this topic, follow the link: Genome comparison.
Dissertations / Theses on the topic 'Genome comparison'
Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles
Consult the top 50 dissertations / theses for your research on the topic 'Genome comparison.'
Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.
You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.
Browse dissertations / theses on a wide variety of disciplines and organise your bibliography correctly.
1
Mok, Kwai-lung. "Computational discovery of cis-regulatory modules in human genome by genome comparison." Click to view the E-thesis via HKUTO, 2008. http://sunzi.lib.hku.hk/hkuto/record/b40203621.
Full text
2
Mok, Kwai-lung, and 莫貴龍. "Computational discovery of cis-regulatory modules in human genome by genome comparison." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2008. http://hub.hku.hk/bib/B40203621.
Full text
3
Dörr, Daniel [Verfasser]. "Gene family-free genome comparison / Daniel Dörr." Bielefeld : Universitätsbibliothek Bielefeld, 2016. http://d-nb.info/1096457229/34.
Full text
4
Zerbino, Daniel Robert. "Genome assembly and comparison using de Bruijn graphs." Thesis, University of Cambridge, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.611752.
Full text
5
Sturgill, David Matthew. "Comparative Genome Analysis of Three Brucella spp. and a Data Model for Automated Multiple Genome Comparison." Thesis, Virginia Tech, 2003. http://hdl.handle.net/10919/10163.
Full textAbstract:
Comparative analysis of multiple genomes presents many challenges ranging from management of information about thousands of local similarities to definition of features by combination of evidence from multiple analyses and experiments. This research represents the development stage of a database-backed pipeline for comparative analysis of multiple genomes. The genomes of three recently sequenced species of Brucella were compared and a superset of known and hypothetical coding sequences was identified to be used in design of a discriminatory genomic cDNA array for comparative functional genomics experiments. Comparisons were made of coding regions from the public, annotated sequence of B. melitensis (GenBank) to the annotated sequence of B. suis (TIGR) and to the newly-sequenced B. abortus (personal communication, S. Halling, National Animal Disease Center, USDA).
A systematic approach to analysis of multiple genome sequences is described including a data model for storage of defined features is presented along with necessary descriptive information such as input parameters and scores from the methods used to define features. A collection of adjacency relationships between features is also stored, creating a unified database that can be mined for patterns of features which repeat among or within genomes.
The biological utility of the data model was demonstrated by a detailed analysis of the multiple genome comparison used to create the sample data set. This examination of genetic differences between three Brucella species with different virulence patterns and host preferences enabled investigation of the genomic basis of virulence. In the B. suis genome, seventy-one differentiating genes were found, including a contiguous 17.6 kb region unique to the species. Although only one unique species-specific gene was identified in the B. melitensis genome and none in the B. abortus genome, seventy-nine differentiating genes were found to be present in only two of the three Brucella species. These differentiating features may be significant in explaining differences in virulence or host specificity. RT-PCR analysis was performed to determine whether these genes are transcribed in vitro. Detailed comparisons were performed on a putative B. suis pathogenicity island (PAI). An overview of these genomic differences and discussion of their significance in the context of host preference and virulence is presented.Master of Science
6
Garg, Kavita. "Genome-wide comparison of evolutionarily conserved alternative and constitutive splice sites /." Thesis, Connect to this title online; UW restricted, 2006. http://hdl.handle.net/1773/10260.
Full text
7
Wang, Hao. "THE POTENTIAL INDUCING PATTERN OF THE FLAX GENOME." Case Western Reserve University School of Graduate Studies / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=case1532609009820723.
Full text
8
Vorster, Barend Juan. "Using whole genome comparison to detect sequence similarities between plants and microbes." Electronic thesis, 2007. http://upetd.up.ac.za/thesis/available/etd-01192009-142048.
Full text
9
Bennett, Helen Victoria. "Giardia lamblia : a genome comparison of three reference strains using microarray technology." Thesis, Royal Holloway, University of London, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.538294.
Full text
10
Lantermann, Alexandra. "Comparison of Genome-Wide Nucleosome Positioning Mechanisms in Schizosaccharomyces pombe and Saccharomyces cerevisiae." Diss., lmu, 2010. http://nbn-resolving.de/urn:nbn:de:bvb:19-118784.
Full text
11
Choudhuri, Jomuna Veronica. "Bioinformatics approaches to large scale genome comparison, including the identification of conserved noncoding regions." [S.l. : s.n.], 2003. http://deposit.ddb.de/cgi-bin/dokserv?idn=968573630.
Full text
12
Frank, Anna Carolin. "Lifestyle and Genome Evolution in Vector-Borne Bacteria : A Comparison of Three Bartonella Species." Doctoral thesis, Uppsala universitet, Molekylär evolution, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-5913.
Full textAbstract:
Bacterial genomes provide records of the molecular processes associated with emergence and evolution of different bacterial lifestyles. This thesis is based on whole-genome comparisons within the genus Bartonella, an excellent model system for studies of host- and vector-specificity and infection outcome in animal-associated bacteria. The louse-borne human specialist and trench fever agent Bartonella quintana was contrasted to the flea-borne generalist relatives Bartonella henselae and Bartonella grahamii, which cause asymptomatic infection in cat and mouse respectively. While B. henselae is commonly isolated from humans, and causes cat scratch disease, there is only one reported case of B. grahamii human infection. The gene complements of the three species are nested like Russian dolls with the smaller genome (B. quintana) being entirely contained in the medium sized (B. henselae), which in turned is contained in the largest (B. grahamii). Size differences reflect differences in the horizontally and vertically acquired gene content, and in the number of genus- and species- specific genes, owing to differential impact of bacteriophages and plasmids, and to different degrees of genome decay. These processes can be attributed to the three distinct lifestyles. Comparisons with other alpha-proteobacteria suggest that the Bartonella genus as a whole evolved from plant-associated species, and that horizontal transfer, in particular of genes involved in interaction with the host, played a key role in the transition to animal intracellular lifestyle. The long-term genome decay associated with this lifestyle is most advanced in the host-restricted B. quintana. The broad host-range species B. grahamii has the largest genome and the largest proportion of auxiliary DNA of the three, probably because it has access to a larger gene pool. In encodes all the known pathogenicity determinants found in the genomes of B. henselae and B. quintana, suggesting that these genes primarily evolved to facilitate colonization in the reservoir host.
13
Rieber, Nora [Verfasser], and Roland [Akademischer Betreuer] Eils. "Performance comparison of four human whole-genome sequencing technologies / Nora Rieber. Betreuer: Roland Eils." Heidelberg : Universitätsbibliothek Heidelberg, 2013. http://d-nb.info/1061054527/34.
Full text
14
Zhao, Zhiyu. "Robust and Efficient Algorithms for Protein 3-D Structure Alignment and Genome Sequence Comparison." ScholarWorks@UNO, 2008. http://scholarworks.uno.edu/td/851.
Full textAbstract:
Sequence analysis and structure analysis are two of the fundamental areas of bioinformatics research. This dissertation discusses, specifically, protein structure related problems including protein structure alignment and query, and genome sequence related problems including haplotype reconstruction and genome rearrangement. It first presents an algorithm for pairwise protein structure alignment that is tested with structures from the Protein Data Bank (PDB). In many cases it outperforms two other well-known algorithms, DaliLite and CE. The preliminary algorithm is a graph-theory based approach, which uses the concept of \stars" to reduce the complexity of clique-finding algorithms. The algorithm is then improved by introducing \double-center stars" in the graph and applying a self-learning strategy. The updated algorithm is tested with a much larger set of protein structures and shown to be an improvement in accuracy, especially in cases of weak similarity. A protein structure query algorithm is designed to search for similar structures in the PDB, using the improved alignment algorithm. It is compared with SSM and shows better performance with lower maximum and average Q-score for missing proteins. An interesting problem dealing with the calculation of the diameter of a 3-D sequence of points arose and its connection to the sublinear time computation is discussed. The diameter calculation of a 3-D sequence is approximated by a series of sublinear time deterministic, zero-error and bounded-error randomized algorithms and we have obtained a series of separations about the power of sublinear time computations. This dissertation also discusses two genome sequence related problems. A probabilistic model is proposed for reconstructing haplotypes from SNP matrices with incomplete and inconsistent errors. The experiments with simulated data show both high accuracy and speed, conforming to the theoretically provable e ciency and accuracy of the algorithm. Finally, a genome rearrangement problem is studied. The concept of non-breaking similarity is introduced. Approximating the exemplar non-breaking similarity to factor n1..f is proven to be NP-hard. Interestingly, for several practical cases, several polynomial time algorithms are presented.
15
Chen, Daidi. "Genetic studies on pleiotropic polyoxin resistant mutants of Bipolaris maydis." Kyoto University, 2018. http://hdl.handle.net/2433/232359.
Full textAbstract:
Kyoto University (京都大学)0048
新制・課程博士
博士(農学)
甲第21158号
農博第2284号
新制||農||1060(附属図書館)
学位論文||H30||N5132(農学部図書室)
京都大学大学院農学研究科地域環境科学専攻
(主査)教授 田中 千尋, 教授 本田 与一, 教授 宮川 恒
学位規則第4条第1項該当
16
Darby, Jake. "Comparison of complete mitochondrial genome sequence between different ethnic groups from Southern Africa / by Jake Darby." Thesis, North-West University, 2004. http://hdl.handle.net/10394/533.
Full textAbstract:
The human mitochondrial genome is a 16,569 base pair double-stranded deoxyribonucleic
acid (DNA) molecule located in the mitochondrion. The mitochondria1 genome sequence is
conserved, maternally inherited and undergoes no recombination, making its evaluation
ideal for evolutionary studies. Certain alterations in the genome are unique to specific
human populations and haplogroups. The genetic background, or haplogroup of an
individual, may act in concert with disease associated mutations. The ethnicity of an
individual is often utilised as an indicator of haplogroup.
During this investigation the full mitochondrial sequence of 10 individuals belonging to
three ethnic Southern African populations, namely three Xhosa, three Zulu and four
Tswana individuals, was generated. The complete nucleotide sequences were compared
to one another in order to determine the genetic relationship between individuals.
Sequences were also evaluated against the 2001 revised Cambridge reference sequence
(RCRS) to detect novel alterations as well as alterations present in all individuals
analysed.
A total of 222 alterations (207 previously reported, 15 unreported) were detected relative to
the RCRS. Five length alterations and 207 nucleotide substitutions were detected.
Ninety-eight alterations were detected only once, and 115 were detected in at least two
individuals. Haplogroup analysis clustered individuals into haplogroups LO, L2 and L3. No
clear correlation between haplogroup assignment and ethnic origin could be observed.
The distribution of shared alterations between individuals was in agreement with the
haplogroup clustering.
Ethnicity can therefore not be utilised as an indicator of haplogroup in the context of the
current study. To investigate the association between disease presentation and
haplogroup, individuals will have to be randomly sampled and then haplogrouped.
Reasons to substantiate the lack of association between ethnicity and haplogroups include
the occurrence of gene flow between populations, inaccurate ethnic and incomplete
haplogroup classification and populations not being sufficiently divergent.Thesis (M.Sc. (Biochemistry))--North-West University, Potchefstroom Campus, 2005.
17
MENNI, CRISTINA. "Population stratification in genome-wide association studies: a comparison among different multivariate analysis methods for dimensionality reduction." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2011. http://hdl.handle.net/10281/19317.
Full textAbstract:
INTRODUCTION:
Genome-wide association studies (GWAS) are large-scale association mapping using SNPs, making no assumptions on the genomic location of the causal variant. They hold substantial promise for unraveling the genetic basis of common human diseases. A well known problem with such studies is population stratification (PS), a form of confounding which arises when there are two or more strata in the study population, and both the risk of disease and the frequency of marker alleles differ between strata. It therefore may appear that the risk of disease is related to the marker alleles when in fact it is not.
Many statistical methods were developed to account for PS so that association studies could proceed even in the presence of structure and for GWAS, linear principal components analysis (PCA) represents a sort of gold-standard. PCA uses genotype data to extract continuous (principal) axis of variation, which can be used to adjust for association attributable to ancestry along each axis. The assumption underlying PCA, however, is that the variable under studies are continuous and so SNPs are quantified by fixing for each marker a reference and a variant allele and by counting the number of mutations. This implies that the distance between homozygous wild type and heterozygous is the same as the distance between heterozygous and homozygous mutant and it thus implies an additive model of inheritance. This model is very conservative, is very static and most importantly it is not necessarily the correct one.
AIM: The aim of this thesis is to treat SNPs as ordinal qualitative variables. This means that there is a distance between homozygous wild type, heterozygous and homozygous mutant, but that the distance between each pair is not necessarily the same. So, we no longer assume any model of inheritance and can potentially better capture some information that linear PCA misses out.
METHODS: We apply a multivariate technique to reduce dimensionality in the presence of non-metric data known as non linear principal components analysis (NLPCA, also known as PRINCALS: Principal components analysis by means of alternating least squares). PRINCALS belongs to “Gifi’ s system”, a unified theoretical framework under which many well known descriptive multivariate techniques are organised.
We apply both PCA and PRINCALS to a sample dataset of 90 individuals belonging to three very distinct subpopulations and 1,000 randomly chosen uncorrelated SNPs and compare the results graphically, using Procrustean superimposition approach and the test Protest and finally with a scenarios analysis.
RESULTS: When we compare the performances of PCA and PRINCALS, we find that the two methods yield similar scores for markers with a low/null genotypic variability across the study sample, while scores differ as the level of genotypic variability increases. This suggests that the two methods capture intra-subject variability differently. Procrustes analysis and scenarios analysis confirm this. Indeed, the matrix of principal components obtained with PCA and the matrix of dimensions obtained with PRINCALS are shown to be statistically different by the test PROTEST and, in the scenarios analysis, we find that, as the level of PS increases, PRINCALS appears to outperform PCA.
CONCLUSION: PCA and PRINCALS behave differently. Validation analyses are needed to confirm these results.
18
Patil, Kaustubh Raosaheb Verfasser], and Alice [Akademischer Betreuer] [McHardy. "Genome signature based sequence comparison for taxonomic assignment and tree inference / Kaustubh Raosaheb Patil. Betreuer: Alice Carolyn McHardy." Saarbrücken : Saarländische Universitäts- und Landesbibliothek, 2013. http://d-nb.info/1052952178/34.
Full text
19
Pereira, Vivian Mayumi Yamassaki. "Reconstrução filogenética de procariotos com base em famílias de genes homólogos." Universidade de São Paulo, 2017. http://www.teses.usp.br/teses/disponiveis/100/100131/tde-28052017-221803/.
Full textAbstract:
A comparação de genomas é uma importante tarefa na qual a bioinformática pode ser aplicada, uma vez que ela permite a identificação de genes patogênicos, o que, por sua vez, pode auxiliar a combater ou a prevenir o surgimento de doenças. A partir da comparação de genomas, também é possível realizar a análise filogenética, que permite entender as relações evolutivas entre diferentes organismos. Em genomas de bactérias, essa análise geralmente é realizada com base no gene 16S rRNA. Entretanto, apesar de ser amplamente utilizado, filogenias com base nesse gene podem ter dificuldades para diferenciar organismos muito próximos evolutivamente. Essa importância da comparação de genomas e a necessidade de uma metodologia que permita distinguir organismos evolutivamente próximos na análise filogenética motivaram este trabalho, que teve como objetivo implementar ferramentas computacionais para identificar genes homólogos em genomas e, com base nesses genes, gerar filogenias e analisar se é possível distinguir os organismos evolutivamente próximos nessas filogenias. Para tanto, as ferramentas desenvolvidas para identificação de genes homólogos recebem resultados de alinhamentos e os filtram, de modo que dois genes são considerados homólogos se o alinhamento entre eles satisfizer os limiares definidos. Após a identificação das famílias de genes homólogos, tabelas são geradas com informações a respeito dos genes homólogos em cada genoma e, com base nessas tabelas, é possível gerar matrizes de distância e utilizar métodos de agrupamento hierárquico para a geração da filogenia ou realizar alinhamentos múltiplos com os genes identificados para posterior reconstrução filogenética. Além disso, também é possível representar os genes e famílias de genes homólogos por meio de um grafo, que pode auxiliar na escolha dos limiares para filtrar os alinhamentos. Para demonstrar e analisar a aplicabilidade das ferramentas desenvolvidas e das abordagens adotadas, experimentos foram realizados utilizando genomas de bactérias do gênero Xanthomonas, que contém um grande grupo de bactérias que causam doenças em plantas. Os resultados obtidos foram então comparados com filogenias de referência e com resultados de outros experimentos realizados. Essas comparações demonstraram que as famílias de genes homólogos podem ser úteis para distinguir genomas de organismos muito próximos evolutivamente, apesar de que essa abordagem apresentou dificuldades para separar os grupos de genomas mais distantes. Em contrapartida, na filogenia gerada a partir da região 16S rRNA, foi possível diferenciar esses organismos mais distantes, mas não foi possível distinguir os organismos muito próximos. Por fim, os experimentos realizados fornecem indícios de que as ferramentas desenvolvidas e as abordagens adotadas podem ser úteis para diferenciar genomas muito próximos evolutivamente de outros procariotos além das bactérias estudadas neste trabalhoGenome comparison is an important task on which bioinformatics can be used because it allows the identification of pathogen genes which can aid the combat of diseases and to avoid the emerging of new ones. Genome comparison also allows the phylogenetic analysis which provides the understanding of evolutional relations of different organisms. In bacterial genomes, this analysis is commonly based on 16S rRNA gene. Unfortunately, it can present some difficulties to distinguish closely related organisms. This importance of genome comparison and the necessity of a methodology to distinguish organisms that are closely related motivated this study, which aimed the development of computational tools to identify homologous genes in genomes, to use these genes to reconstruct phylogenies and to analyze if it is possible to distinguish closely related organisms on these phylogenies. To achieve this purpose, the developed tools to identify homologous genes receive the alignments results and filter it, such that two genes are homologous if their alignment satisfies the thresholds. After the identification of homologous gene families, the tools generates tables with information about the homologous genes presents in each genome and with these tables it is possible to create distance matrix to be used by hierarchical clustering methods to generate phylogenies or it is possible to perform multiple alignments with the identified genes to accomplish a phylogenetic reconstruction. Besides that, it is possible to represent the genes and homologous gene families in a graph, which can aid the choice of the thresholds to filter the alignments. To demonstrate and analyze the applicability of the developed tools and the approaches chosen in this study, experiments were performed using genomes of the bacterial genus Xanthomonas, which include a group of phytopathogenic bacteria. The results obtained were compared with reference phylogenies and with results of other experiments. These comparisons showed that homologous gene families can be used to differentiate closely related organisms, despite the fact that it presented difficulties to distinguish the groups of genomes that were evolutionarily far from each other. On the other hand, the phylogeny based on 16S rRNA region allows to distinguish the groups of genomes that were distant, but it was not possible to differentiate closely related organisms. As a conclusion, the experiments performed give pieces of evidence that the developed tools and the approaches adopted can be useful to distinguish genomes of closely related organisms of other prokaryotes besides the bacterias considered in this study
20
Mokotoane, Ralengopeng Nick. "Complete genome comparison of the recent and historic field strains of African horse sickness virus isolated over four decades." Diss., University of Pretoria, 2016. http://hdl.handle.net/2263/60271.
Full textAbstract:
African horse sickness (AHS), caused by the African horse sickness virus (AHSV), is an economically important disease of equids. Outbreaks of the disease usually have a devastating effect on the susceptible equine populations. Due to the severity of AHS in horses, the economical impact and ability to spread rapidly, the disease has been listed by the World Organisation for Animal Health (OIE) as a notifiable disease. Nine serotypes of the virus have been identified. Transmission is mediated by biting midges of the genus Culicoides. Despite the fact that a cell culture-attenuated live virus vaccine is commercially available, AHS outbreaks occur annually in endemic regions. Several shortcomings of the vaccine itself and its application have been identified that may explain the occurrence of outbreaks.
In this study, we sought to evaluate the level of genetic divergence between the AHSV reference strains that the current polyvalent vaccine was based on and recent field isolates. The effectivity of the vaccine to induce complete protective immunity against current circulating strains is, thus, an additional concern and warranted further investigation. Similarly, the current serological diagnostic assays to detect virus or antibodies to the virus in the recent field isolates or horse sera respectively, are based on the reference isolates. Towards accomplishing the above mentioned goal, a panel of recent AHSV field strains, isolated between 1994 and 2009, were selected for comparative analysis to the reference strains isolated in the 1960s. The complete, segmented double stranded RNA (dsRNA) genomes of nine recent field isolates of AHSV, representing serotypes 1 to 9, were characterised. Ultra-deep sequencing data of cDNA copies of the genome segments were generated. Consensus nucleotide sequences of each of the ten segments of each isolate were successfully assembled. Sequence data analysis showed that each virus isolate not only contained single serotype of AHSV, but was also free from other contaminating equine dsRNA viruses, such as equine encephalosis virus (EEV). The sequence data also confirmed the serotypes of the virus, as previously determined by virus neutralisation (VN) assays and reverse-transcription polymerase chain reaction (RT-PCR).
Intra-serotype comparative sequence analyses of the corresponding segments of the reference and recent field strains showed a maximum variability of 28% and 9% on nucleotide and amino acid level, respectively. The most variable genome segments were S2 encoding viral protein 2 (VP2), followed by S10 encoding non-structural protein 3 (NS3) and S6 encoding viral protein 5 (VP5). Therefore, these segments of the AHSV-9 reference and recent strains were further investigated. Comparative analysis of VP2 of the AHSV-9 reference strain with those of more recent field strains revealed a number of dissimilar amino acid mutations within, or adjacent to, known epitope-containing regions. In addition, significant changes were observed in the amino terminus. Some of the mutations correlated with altered predicted secondary structure and/or antigenicity profiles. Similar analysis of AHSV-9 VP5 indicated that the region between residue 101 and 201 was variable, although the overall predicted secondary structure appeared to be conserved. Our results indicated that the hydrophobic domain regions 1 (HD-1) and 2 (HD-2) respectively, in S10 (NS3), previously reported to play an important role in the function of NS3, remained conserved.Dissertation (MSc)--University of Pretoria, 2016.
Veterinary Tropical Diseases
MSc
Unrestricted
21
Li, Xing Xing Li. "Viral structural proteins, genome, and in vivo replication : a comparison between nuclear and cytoplasmic types of Adoxophyes orana granulosis virus /." [S.l.] : [s.n.], 1993. http://e-collection.ethbib.ethz.ch/show?type=diss&nr=10326.
Full text
22
Perisic, Tatjana. "Epigenetic control of GLT-1 gene activity and its modulation by psychoactive drugs in comparison to genome-wide drug effects." Diss., lmu, 2012. http://nbn-resolving.de/urn:nbn:de:bvb:19-143931.
Full text
23
Gross, Arnd, Anke Tonjes, Peter Kovacs, Krishna Veeramah, Peter Ahnert, Nab Roshyara, Christian Gieger, et al. "Population-genetic comparison of the Sorbian isolate population in Germany with the German KORA population using genome-wide SNP arrays." BioMed Central, 2011. http://hdl.handle.net/10150/610390.
Full textAbstract:
BACKGROUND:The Sorbs are an ethnic minority in Germany with putative genetic isolation, making the population interesting for disease mapping. A sample of N = 977 Sorbs is currently analysed in several genome-wide meta-analyses. Since genetic differences between populations are a major confounding factor in genetic meta-analyses, we compare the Sorbs with the German outbred population of the KORA F3 study (N = 1644) and other publically available European HapMap populations by population genetic means. We also aim to separate effects of over-sampling of families in the Sorbs sample from effects of genetic isolation and compare the power of genetic association studies between the samples.RESULTS:The degree of relatedness was significantly higher in the Sorbs. Principal components analysis revealed a west to east clustering of KORA individuals born in Germany, KORA individuals born in Poland or Czech Republic, Half-Sorbs (less than four Sorbian grandparents) and Full-Sorbs. The Sorbs cluster is nearest to the cluster of KORA individuals born in Poland. The number of rare SNPs is significantly higher in the Sorbs sample. FST between KORA and Sorbs is an order of magnitude higher than between different regions in Germany. Compared to the other populations, Sorbs show a higher proportion of individuals with runs of homozygosity between 2.5 Mb and 5 Mb. Linkage disequilibrium (LD) at longer range is also slightly increased but this has no effect on the power of association studies.Oversampling of families in the Sorbs sample causes detectable bias regarding higher FST values and higher LD but the effect is an order of magnitude smaller than the observed differences between KORA and Sorbs. Relatedness in the Sorbs also influenced the power of uncorrected association analyses.CONCLUSIONS:Sorbs show signs of genetic isolation which cannot be explained by over-sampling of relatives, but the effects are moderate in size. The Slavonic origin of the Sorbs is still genetically detectable.Regarding LD structure, a clear advantage for genome-wide association studies cannot be deduced. The significant amount of cryptic relatedness in the Sorbs sample results in inflated variances of Beta-estimators which should be considered in genetic association analyses.
24
Yamamoto, Takehiro, Yuki Moriya, Norio Suzuki, and Chikako Morinaga. "Identification of tandem organization of soluble guanylyl cyclase α_1 and β_1 subunit genes in the Japanese pufferfish (Fugu rubripes) genome: comparison with their human homologues." Laboratory of Freshwater Fish Stocks Bioscience and Biotechnology Center Nagoya University, 2007. http://hdl.handle.net/2237/13831.
Full text
25
Kalapanulak, Saowalak. "High quality genome-scale metabolic network reconstruction of Mycobacterium tuberculosis and comparison with human metabolic network : application for drug targets identification." Thesis, University of Edinburgh, 2009. http://hdl.handle.net/1842/3925.
Full textAbstract:
Mycobacterium tuberculosis (Mtb), a pathogenic bacterium, is the causative agent in the vast majority of human tuberculosis (TB) cases. Nearly one-third of the world’s population has been affected by TB and annually two million deaths result from the disease. Because of the high cost of medication for a long term treatment with multiple drugs and the increase of multidrug-resistant Mtb strains, faster-acting drugs and more effective vaccines are urgently demanded. Several metabolic pathways of Mtb are attractive for identifying novel drug targets against TB. Hence, a high quality genome-scale metabolic network of Mtb (HQMtb) was reconstructed to investigate its whole metabolism and explore for new drug targets. The HQMtb metabolic network was constructed using an unbiased approach by extracting gene annotation information from various databases and consolidating the data with information from literature. The HQMtb consists of 686 genes, 607 intracellular reactions, 734 metabolites and 471 E.C. numbers, 27 of which are incomplete. The HQMtb was compared with two recently published Mtb metabolic models, GSMN-TB by Beste et al. and iNJ661 model by Jamshidi and Palsson. Due to the different reconstruction methods used, the three models have different characteristics. The 68 new genes and 80 new E.C. numbers were found only in the HQMtb and resulting in approximately 52 new metabolic reactions located in various metabolic pathways, for example biosynthesis of steroid, fatty acid metabolism, and TCA cycle. Through a comparison of HQMtb with a previously published human metabolic network (EHMN) in terms of protein signatures, 42 Mtb metabolic genes were proposed as new drug targets based on two criteria: (a) their protein functional sites do not match with any human protein functional sites; (b) they are essential genes. Interestingly, 13 of them are found in a list of current validated drug targets. Among all proposed drug targets, Rv0189c, Rv3001c and Rv3607c are of interest to be tested in the laboratory because they were also proposed as drug target candidates from two research groups using different methods.
26
Eraclio, G. "POLYPHASIC APPROACH TO STUDY THE EMERGING PATHOGEN LACTOCOCCUS GARVIEAE." Doctoral thesis, Università degli Studi di Milano, 2015. http://hdl.handle.net/2434/333486.
Full textAbstract:
This Ph.D. thesis research project aims to increase knowledge on emerging and opportunistic pathogens in food, to improve the current systems of management and control of food safety. During the project, the attention was focused on the study of Lactococcus garvieae, the aetiological agent of a hemorrhagic septicemia in aquaculture, but recently recognized as an opportunistic human pathogen.
In the first part of the research, strains of L. garvieae coming from different niches were studied through a Multi Locus Sequence Typing approach and genome analysis and comparison. Data highlighted a high level of genetic heterogeneity within the species and the separation in two main genomic lineages, with the presence of a third lineage that might be considered the ancestor branch, and the evolutionary intermediate between Lactococcus lactis and L. garvieae main clusters. Moreover, the analysis of 11 sequenced genomes of L. garvieae and their comparison with L. lactis genomic sequences provided a first insight in the core and pan-genome of L. garvieae. The core genome, consisting of 1341 genes, contains genes related to virulence factors; about 70% of the total core genes were also conserved in the analysed Lactococcus genomes, suggesting a common ancestor. A dispensable genome constitute by many genes, could explain the cosmopolitan lifestyle of L. garvieae species.
Subsequently to better clarify the polymorphic character of these strains, insertion sequences distribution and temperate bacteriophages were studied as mechanisms involved in genome plasticity.
Insertion sequences (ISs) were found in many analysed genomes and a substantial homology to the Lactococcus lactis elements was found, suggesting the movement of ISs between these two phylogenetically closely related species. Moreover, five new elements occurring in Lactococcus garvieae where for the first time described. All the ISs are inserted in non-coding regions and their possible involvement in chromosomal rearrangement was described.
The 50% of the 45 strains of L. garvieae, coming from different ecological niches, showed the presence of inducible temperate phages, belonging to Siphoviridae family; their differences in tail length and capside width group them in two morphotypes.
Sequencing of a prophage from a dairy L. garvieae strain and in silico analysis of fourteen sequenced L. garvieae strains, revealed 7 complete phages disseminated along six genomes. The phage genomes have a length on average with other lactococcal phages, ranging from 30 to 40 kb; genome comparison revealed in some case homology with other L. lactis phages. Interestingly only one phage genome has a %GC similar to L. garvieae species: the other genomes showed a GC value similar to that of L. lactis. These findings led us to hypothesize that the phages infecting L. garvieae originated from L. lactis, highlighting that the latter species might have appeared long time ago in the environment.
Being Lactococcus garvieae one of the most important pathogen in aquaculture sector, in the last part of this research, we isolated virulent phages to use in future strategies of phage therapy. Eleven lytic phages were isolated, and they showed a narrow lytic spectrum, in some case specific to few hosts. These results highlighted the importance of design a specific phage cocktail to improve the efficiency of phage therapy.
Moreover, the genome sequencing of one of these phages showed homology with other L. lactis phages (c2 and Q54), suggesting that phages infecting different lactococcal species may have a common ancestor.
27
Huang, Xiufeng. "Immunogenetics of acute anterior uveitis and comparison to ankylosing spondylitis." Thesis, Queensland University of Technology, 2021. https://eprints.qut.edu.au/213839/1/Xiufeng_Huang_Thesis.pdf.
Full textAbstract:
This thesis comprehensively applies genome-wide association study, Mendelian randomization analyses, and cytokine proteomics to investigate the genetic basis and immunopathogenic mechanisms of acute anterior uveitis (AAU). Multiple susceptibility loci, environmental risk factors, and potential biomarkers are identified, and a polygenic risk score for AAU developed. These findings provide novel insights into the immunogenetics in AAU, and contribute to clinical translational studies.
28
Sawada, Ryusuke, Runcong Ke, Toshiyuki Tsuji, Masashi Sonoyama, and Shigeki Mitaku. "Ratio of membrane proteins in total proteomes of prokaryota." THE BIOPHYSICAL SOCIETY OF JAPAN, 2007. http://hdl.handle.net/2237/9298.
Full text
29
Bradwell, Katie. "Genomic comparisons and genome architecture of divergent Trypanosoma species." VCU Scholars Compass, 2016. http://scholarscompass.vcu.edu/etd/4598.
Full textAbstract:
Virulent Trypanosoma cruzi, and the non-pathogenic Trypanosoma conorhini and Trypanosoma rangeli are protozoan parasites with divergent lifestyles. T. cruzi and T. rangeli are endemic to Latin America, whereas T. conorhini is tropicopolitan. Reduviid bug vectors spread these parasites to mammalian hosts, within which T. rangeli and T. conorhini replicate extracellularly, while T. cruzi has intracellular stages. Firstly, this work compares the genomes of these parasites to understand their differing phenotypes. Secondly, genome architecture of T. cruzi is examined to address the effect of a complex hybridization history, polycistronic transcription, and genome plasticity on this organism, and study its highly repetitive nature and cryptic genome organization. Whole genome sequencing, assembly and comparison, as well as chromosome-scale genome mapping were employed. This study presents the first comprehensive whole-genome maps of Trypanosoma, and the first T. conorhini strain ever sequenced. Original contributions vii to knowledge include the ~21-25 Mbp assembled genomes of the less virulent T. cruzi G, T. rangeli AM80, and T. conorhini 025E, containing ~10,000 to 13,000 genes, and the ~36 Mbp genome assembly of highly virulent T. cruzi CL with ~24,000 genes. The T. cruzi strains exhibited ~74% identity to proteins of T. rangeli or T. conorhini. T. rangeli and T. conorhini displayed greater complex carbohydrate metabolic capabilities, and contained fewer retrotransposons and multigene family copies, e.g. mucins, DGF-1, and MASP, compared to T. cruzi. Although all four genomes appear highly syntenic, T. rangeli and T. conorhini exhibited greater karyotype conservation. T. cruzi genome architecture studies revealed 66 maps varying from 0.13 to 2.4 Mbp. At least 2.6% of the genome comprises highly repetitive repeat regions, and 7.4% exhibits repetitive regions barren of labels. The 66 putative chromosomes identified are likely diploid. However, 20 of these maps contained regions of up to 1.25 Mbp of homology to at least one other map, suggestive of widespread segmental duplication or an ancient hybridization event that resulted in a genome with significant redundancy. Assembled genomes of these parasites closely reflect their phylogenetic relationships and give a greater context for understanding their divergent lifestyles. Genome mapping provides insight on the genomic evolution of these parasites.
30
Pitt, Alison Patricia. "Comparison of Middle Eastern Bedouin genotypes with previously studies populations using polymorphic Alu insertions." University of Western Australia. Centre for Forensic Science, 2009. http://theses.library.uwa.edu.au/adt-WU2009.0119.
Full textAbstract:
[Truncated abstract] Polymorphic Alu insertions (POALINs) are known to contribute to the variation and genetic diversity of the human genome. In this report specific POALINs of the Major Histocompatibility Complex (MHC) were studied. Previous population studies on the MHC POALINs have focused on individuals of African, European and Asian descent. In this study, we expand the research by studying a new and previously uncharacterised population, focusing on the Bedouin from the Middle East. Specifically we report on the individual insertion frequencies of four POALINs within the MHC class I region of this population. POALINs are members of a young Alu subfamily that have only recently been inserted into the human genome. POALINs are either present or absent at particular sites. Individuals that share the inserted (or deleted) polymorphism inherited the insertion (or deletion) from a common ancestor, making Alu alleles identical by decent. In population genetics a comparison of the resulting products from each population can then be done by comparing the lengths of the PCR products in a series of unrelated individuals and may also detect polymorphisms with regard to the presence or absence of the Alu repeats. As a direct result of their abundance and sequence identity, they promote genetic recombination events that are responsible for large-scale deletions, duplication and translocations. The deletions occur mostly in the A-T rich regions and have found to be unlikely to have been created independently of the insertions of the Alu elements (Callinan et al, 2005) The easy genotyping of the POALINs has proven to be very valuable as lineage markers for the study of human population genetics, pedigree and forensics as well as genomic diversity and evolution. POALINs have been used in a range of applications, primarily focusing on anthropological analysis of human populations. As a result of its ease of use and its utility as a marker in human evolutions studies, combining the POALINs along with other markers used in forensics could lead to improved identity testing in forensic science. More specifically, in combination with more traditional markers, race specific genotypes and haplotypes could be used for profiling crime scene samples. ... This is supported by previously reported molecular data using various types of genetic markers. In a study using six separate Alu genes, Antunez-de-Mayolo et al were able to generate a phylogenetic tree, in which the biogeographical groups followed a pattern. The biogeographical groups started with African populations that were found to relate closely to the hypothetical ancestral African population. The African populations were then followed in order by Southwest Asian populations, European populations which include Middle Eastern groups (Antunez-de-Mayolo et al, 2002). This study shows the similarities and differences between the frequencies of the Middle Eastern Bedouin and the rest of the compared populations. Though no clear results were determined, the information from the POALINs along with information provided from other genetic markers can lead to further research on the Bedouin population and the improvement of the forensic population database in order to accurately test individual ethnic background of samples to be analysed.
31
Perisic, Tatjana [Verfasser], and Florian [Akademischer Betreuer] Holsboer. "Epigenetic control of GLT-1 gene activity and its modulation by psychoactive drugs in comparison to genome-wide drug effects / Tatjana Perisic. Betreuer: Florian Holsboer." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2012. http://d-nb.info/102343556X/34.
Full text
32
Mitchell, Candice Melissa. "Morphologic and genomic characterisation of the koala Chlamydia pneumoniae strain." Thesis, Queensland University of Technology, 2010. https://eprints.qut.edu.au/33259/1/Candice_Mitchell_Thesis.pdf.
Full textAbstract:
Chlamydia pneumoniae is a common human and animal pathogen associated with a wide range of upper and lower respiratory tract infections. In more recent years there has been increasing evidence to suggest a link between C. pneumoniae and chronic diseases in humans, including atherosclerosis, stroke and Alzheimer’s disease. C. pneumoniae human strains show little genetic variation, indicating that the human-derived strain originated from a common ancestor in the recent past. Despite extensive information on the genetics and morphology processes of the human strain, knowledge concerning many other hosts (including marsupials, amphibians, reptiles and equines) remains virtually unexplored. The koala (Phascolarctos cinereus) is a native Australian marsupial under threat due to habitat loss, predation and disease. Koalas are very susceptible to chlamydial infections, most commonly affecting the conjunctiva, urogenital tract and/or respiratory tract. To address this gap in the literature, the present study (i) provides a detailed description of the morphologic and genomic architecture of the C. pneumoniae koala (and human) strain, and shows that the koala strain is microscopically, developmentally and genetically distinct from the C. pneumoniae human strain, and (ii) examines the genetic relationship of geographically diverse C. pneumoniae isolates from human, marsupial, amphibian, reptilian and equine hosts, and identifies two distinct lineages that have arisen from animal-to-human cross species transmissions. Chapter One of this thesis explores the scientific problem and aims of this study, while Chapter Two provides a detailed literature review of the background in this field of work. Chapter Three, the first results chapter, describes the morphology and developmental stages of C. pneumoniae koala isolate LPCoLN, as revealed by fluorescence and transmission electron microscopy. The profile of this isolate, when cultured in HEp-2 human epithelial cells, was quite different to the human AR39 isolate. Koala LPCoLN inclusions were larger; the elementary bodies did not have the characteristic pear-shaped appearance, and the developmental cycle was completed within a shorter period of time (as confirmed by quantitative real-time PCR). These in vitro findings might reflect biological differences between koala LPCoLN and human AR39 in vivo. Chapter Four describes the complete genome sequence of the koala respiratory pathogen, C. pneumoniae LPCoLN. This is the first animal isolate of C. pneumoniae to be fully-sequenced. The genome sequence provides new insights into genomic ‘plasticity’ (organisation), evolution and biology of koala LPCoLN, relative to four complete C. pneumoniae human genomes (AR39, CWL029, J138 and TW183). Koala LPCoLN contains a plasmid that is not shared with any of the human isolates, there is evidence of gene loss in nucleotide salvage pathways, and there are 10 hot spot genomic regions of variation that were previously not identified in the C. pneumoniae human genomes. Sequence (partial-length) from a second, independent, wild koala isolate (EBB) at several gene loci confirmed that the koala LPCoLN isolate was representative of a koala C. pneumoniae strain. The combined sequence data provides evidence that the C. pneumoniae animal (koala LPCoLN) genome is ancestral to the C. pneumoniae human genomes and that human infections may have originated from zoonotic infections. Chapter Five examines key genome components of the five C. pneumoniae genomes in more detail. This analysis reveals genomic features that are shared by and/or contribute to the broad ecological adaptability and evolution of C. pneumoniae. This analysis resulted in the identification of 65 gene sequences for further analysis of intraspecific variation, and revealed some interesting differences, including fragmentation, truncation and gene decay (loss of redundant ancestral traits). This study provides valuable insights into metabolic diversity, adaptation and evolution of C. pneumoniae. Chapter Six utilises a subset of 23 target genes identified from the previous genomic comparisons and makes a significant contribution to our understanding of genetic variability among C. pneumoniae human (11) and animal (6 amphibian, 5 reptilian, 1 equine and 7 marsupial hosts) isolates. It has been shown that the animal isolates are genetically diverse, unlike the human isolates that are virtually clonal. More convincing evidence that C. pneumoniae originated in animals and recently (in the last few hundred thousand years) crossed host species to infect humans is provided in this study. It is proposed that two animal-to-human cross species events have occurred in the context of the results, one evident by the nearly clonal human genotype circulating in the world today, and the other by a more animal-like genotype apparent in Indigenous Australians. Taken together, these data indicate that the C. pneumoniae koala LPCoLN isolate has morphologic and genomic characteristics that are distinct from the human isolates. These differences may affect the survival and activity of the C. pneumoniae koala pathogen in its natural host, in vivo. This study, by utilising the genetic diversity of C. pneumoniae, identified new genetic markers for distinguishing human and animal isolates. However, not all C. pneumoniae isolates were genetically diverse; in fact, several isolates were highly conserved, if not identical in sequence (i.e. Australian marsupials) emphasising that at some stage in the evolution of this pathogen, there has been an adaptation/s to a particular host, providing some stability in the genome. The outcomes of this study by experimental and bioinformatic approaches have significantly enhanced our knowledge of the biology of this pathogen and will advance opportunities for the investigation of novel vaccine targets, antimicrobial therapy, or blocking of pathogenic pathways.
33
Turlapaty, Sandhya. "Implementation and Performance Comparison of Some Heuristic Algorithms for Block Sorting." UNF Digital Commons, 2018. https://digitalcommons.unf.edu/etd/816.
Full textAbstract:
An implementation framework has been developed in this thesis for a well-known APX-hard combinatorial optimization problem known as Block Sorting. The motivation for the study of this problem comes from applications such as computational biology and optical character recognition. While existing Block Sorting research has been theoretically focused on the development and analysis of several approximation algorithms for Block Sorting, little or no work has been carried out thus far on the implementation of the proposed approximation algorithms. The conceptualization of an implementation framework and illustrating its use by experimenting with the existing approximation algorithms will provide means for discovering newer approaches to handling this important problem. As the main contribution, the research in this thesis provides a new greedy algorithm for Block Sorting in which each block move either reduces the number of blocks by two or three blocks, or reduces by one the number of reversals or inversions in the orig- inal permutation. Experimental results for all algorithms are also provided along with a comparison of their performance using the number of block moves and approximation ratios as performance metrics when sorting permutations of a given order, and as the order of permutations is varied. Preliminary results from the experimentation were shared at the 2017 IEEE 17th International Conference on Bioinformatics and Bioengineering (BIBE) [1]. To the best of our knowledge, this is the first work that has been focused on the implementation and experimental performance analysis of any algorithm for Block Sorting. We believe the results presented in this thesis will be useful for researchers and practitioners working in this area.
34
Santos, Almeida Alexandre Miguel. "Evolutionary insights into the host--specific adaptation and pathogenesis of group B Streptococcus Persistence of a dominant bovine lineage of group B Streptococcus reveals genomic signatures of host adaptation Whole-Genome Comparison Uncovers Genomic Mutations between Group B Streptococci Sampled from Infected Newborns and Their Mothers." Thesis, Paris 6, 2017. http://www.theses.fr/2017PA066029/document.
Full textAbstract:
Streptococcus agalactiae (streptocoque du groupe B, SGB) est un commensal fréquent des voies intestinale et génito-urinaire dans la population humaine mais constitue une des causes principales d'infections néonatales. Dans le même temps, SGB est connu comme pathogène vétérinaire, responsable de mastites bovines à l'origine de pertes économiques importantes dans plusieurs pays comme le Portugal. L'objectif de ma thèse était d'analyser au niveau génomique les bases de l'adaptation spécifique de SGB à ses hôtes humains et bovins et de l'établissement des lignées plus pathogènes. La comparaison des profils génomiques des souches isolées de nouveau-nés infectés et de leurs mères nous a permis de montrer que la transmission de SGB de mère à enfant est accompagnée dans certains cas par l'acquisition de mutations pathoadaptives. Par ailleurs, l'analyse des séquences génomiques de plus de 600 souches appartenant au complexe clonal (CC) 17, hypervirulent et spécifique à l'hôté humain, nous a permis de caractériser les forces évolutives agissant sur ce complexe. Finalement, l'étude de la colonisation des fermes laitières portugaises par un seul clone CC61 depuis plus de 20 ans a mis en évidence que la régulation spécifique de l'import du fer/manganèse est une stratégie d'adaptation récurrente dans l’environnement bovin. En conclusion, les résultats que nous présentons améliorent notre compréhension de l'adaptation chez les espèces hôte-généralistes, en apportant des idées utiles qui pourront spécifiquement aider à améliorer le contrôle et le traitement des infections de SGB mondialementStreptococcus agalactiae (group B Streptococcus, GBS) is a commensal of the intestinal and genitourinary tracts in the human population, while also a leading cause of neonatal infections. Likewise, GBS remains a serious concern in many countries as frequently responsible for bovine mastitis. Therefore, the purpose of my PhD project was to use state-of-the-art whole-genome approaches to decipher the host-specific adaptation and pathogenesis of GBS in both humans and bovines. By comparing the genomic profile of strains from infected newborns and their mothers we showed that the transmission of GBS from mother to child is accompanied in particular instances by the acquisition of specific pathoadaptive mutations. Moreover, from the study of the evolutionary forces acting on the human-specific and hypervirulent clonal complex (CC) 17, we reveal that various systems can evolve to improve the ability of GBS to survive in the human host. Functions related to metabolism, cell adhesion, regulation and immune evasion were among the most preferentially affected in GBS strains from human origin. Conversely, colonization of Portuguese dairy farms by one single CC61 clone for over 20 years highlighted that the specific regulation of iron/manganese uptake is a recurrent adaptive strategy in the bovine environment
35
Benamar, Samia. "Utilisation d'outils bio-informatiques pour l'étude de pathogènes émergents." Thesis, Aix-Marseille, 2017. http://www.theses.fr/2017AIXM0197.
Full textAbstract:
La recherche en bactériologie et virologie est à la fois de nature cognitive et appliquée. Elle consiste à fédérer et mettre en place une capacité de recherche multidisciplinaire et pouvoir l'intégrer sur un champ très vaste de microorganismes et de maladies. Les nouvelles avancées conceptuelles et technologiques dans le domaine de la génomique, notamment les avancées dans les techniques à haut débit (séquençage, PCR...) permettent actuellement d’avoir rapidement des génomes bactériens et viraux entiers, ou seulement sur quelques gènes d’une grande population. Les progrès dans ce domaine permettent l’accès à ces informations en évitant une combinaison de plusieurs méthodologies, et à moindre coûts. Dans notre travail de thèse, nous avons été porté à analyser et traiter les données de deux études genomiques et métagenomiques, mettant en évidence avantages, limites et attentes liés à ces techniques. La première étude porte sur l'analyse génomique de nouveaux virus géants et chlamydia infectant Vermamoeba vermiformis. La deuxième étude concerne le pyroséquençage 16S de microbiote intestinal de nouveau-nés atteint de l'entérocolite nécrosante. Pour le premier projet du travail de thèse, nous avons analysé les génomes de trois nouvelles espèces de Chlamydiae et onze virus giants (premiers membres de deux probables nouvelles familles) qui se multiplient naturellement dans Vermamoeba vermiformis. L'objectif étant de mettre en évidence les caractéristiques génétiques spécifiques à ces micro-organismes. La deuxième partie a été consacrée à l'analyse des données de pyroséquençage 16S des selles de nouveau-nés atteints de l'entérocolite nécrosanteResearch in bacteriology and virology is both cognitive and applied. It involves federating and developing a multidisciplinary research capacity and being able to integrate it into a very broad field of microorganisms and diseases. New genomic and conceptual advances in genomics, including advances in high-throughput techniques, now permit rapid bacterial and viral genomes, or only a few genes of a large population. Progress in this area allows access to this information by avoiding a combination of several methodologies and at lower costs. In our thesis work, we were led to analyze and process the data of two genomic and metagenomic studies, highlighting advantages, limitations and expectations related to these techniques. The first study focuses on the genomic analysis of new giant viruses and chlamydia infecting Vermamoeba vermiformis. The second study concerns the 16S pyrosequencing of intestinal microbiota of neonates with necrotizing enterocolitis. The first project of the thesis work analyzed the genomes of three new species of Chlamydiae and eleven giant viruses (first members of two probable new families) which naturally multiply in Vermamoeba vermiformis. The objective is to highlight the genetic characteristics specific to these microorganisms. The second part was devoted to the analysis of 16S pyrosequencing data from neonatal enterocolitis neonatal stools. The goal was to identify an agent responsible for this disease
36
Frouin, Eléonore. "Taxonomic and functional exploration of the biosphere of serpentinizing hydrothermal systems by metagenomics." Thesis, Aix-Marseille, 2018. http://www.theses.fr/2018AIXM0507/document.
Full textAbstract:
Les systèmes hydrothermaux associés à la serpentinisation sont anoxiques et riches en $H_2$, $CH_4$ et molécules organiques. Ces composants alimentent des micro-organismes qui colonisent les systèmes serpentinisés, et ce en dépit d’un pH élevé et de faibles concentrations en accepteurs d'électrons et en carbone dissous. Dans ce travail, les communautés microbiennes ont été étudiées en se focalisant sur Prony, un écosystème serpentinisé côtier de Nouvelle-Calédonie, puis, en comparant différents écosystèmes serpentinisés, pour faire émerger des similarités taxonomiques et fonctionnelles. À Prony, nos analyses de métabarcoding ont mis en évidence l'importance d’une biosphère rare. L'analyse de métagénomes a permis de reconstruire 82 génomes procaryotes. Un de ces génomes est phylogénétiquement proche des espèces du genre Serpentinomonas, bactéries chimiolithotrophes isolées du site serpentinisé The Cedars, qui détiennent le record d’alcalophilie. Ces espèces et d'autres phylotypes, tels que les taxons affiliés aux Lost City Methanosarcinales, ont été trouvés dans plusieurs sites serpentinisés et pourraient contribuer à la définition d'une signature biologique des phénomènes de serpentinisation. En ciblant spécifiquement les métabolismes enrichis dans les milieux serpentinisés, nous avons pu mettre en évidence l'importance du métabolisme de l'hydrogène, des mécanismes cellulaires de réponse aux stress et d’une voie de dégradation des phosphonates, reposant sur l’activité d'une C-P lyase. Cette voie métabolique, qui a un rôle clé dans l'assimilation du phosphore et la libération de molécules organiques, vient enrichir les modèles écologiques des systèmes serpentinisésSerpentinizing hydrothermal systems are anoxic and enriched in $H_2$, $CH_4$ and organic molecules. These compounds support microbes that colonize serpentinizing systems, despite high pH and low concentrations of electron acceptors and dissolved inorganic carbon. In this work, two axes were explored to study the microbial communities. On the one hand, we focused on Prony, a coastal serpentinizing site in New Caledonia, and on the other hand we compared different serpentinizing systems to reveal taxonomic and functional similarities. At Prony, our metabarcoding analyses highlighted the importance of the rare biosphere. Moreover, 82 prokaryotic genomes were successfully reconstructed using five metagenomes from Prony. One of these genomes was phylogenetically close to the species of the genus Serpentinomonas, chemolithotrophic bacteria isolated at the serpentinizing site The Cedars that are capable of growth up to pH 12.5. These species, and other phylotypes, such as taxa affiliated with Lost City Methanosarcinales were identified in several serpentinizing sites and could contribute to the definition of a biological signature associated with serpentinization. By specifically targeting enriched metabolisms in serpentinizing environments, we highlighted key functions associated with hydrogen metabolism and environmental stress response mechanisms. The comparison of serpentinizing metagenomes revealed the importance of a phosphonate degradative pathway, based on the activity of a C-P lyase. This metabolic pathway, which plays a key role in the uptake of phosphorus and the release of organic molecules, was integrated into the ecological models of serpentinizing systems
37
Wetterbom, Anna. "Genome and Transcriptome Comparisons between Human and Chimpanzee." Doctoral thesis, Uppsala universitet, Genomik, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-112893.
Full textAbstract:
The chimpanzee is humankind’s closest living relative and the two species diverged ~6 million years ago. Comparative studies of the human and chimpanzee genomes and transcriptomes are of great interest to understand the molecular mechanisms of speciation and the development of species-specific traits. The aim of this thesis is to characterize differences between the two species with regard to their genome sequences and the resulting transcript profiles. The first two papers focus on indel divergence and in particular, indels causing premature termination codons (PTCs) in 8% of the chimpanzee genes. The density of PTC genes is correlated with both the distance to the telomere and the indel divergence. Many PTC genes have several associated transcripts and since not all are affected by the PTC we propose that PTCs may affect the pattern of expressed isoforms. In the third paper, we investigate the transcriptome divergence in cerebellum, heart and liver, using high-density exon arrays. The results show that gene expression differs more between tissues than between species. Approximately 15% of the genes are differentially expressed between species, and half of the genes show different splicing patterns. We identify 28 cassette exons which are only included in one of the species, often in a tissue-specific manner. In the fourth paper, we use massive parallel sequencing to study the chimpanzee transcriptome in frontal cortex and liver. We estimate gene expression and search for novel transcribed regions (TRs). The majority of TRs are located close to genes and possibly extend the annotations. A subset of TRs are not found in the human genome. The brain transcriptome differs substantially from that of the liver and we identify a subset of genes enriched with TRs in frontal cortex. In conclusion, this thesis provides evidence of extensive genomic and transcriptomic variability between human and chimpanzee. The findings provide a basis for further studies of the underlying differences affecting phenotypic divergence between human and chimpanzee.
38
Beck, Johannes Christian. "Analysis of diurnal gene regulation and metabolic diversity in Synechocystis sp. PCC 6803 and other phototrophic cyanobacteria." Doctoral thesis, Humboldt-Universität zu Berlin, 2018. http://dx.doi.org/10.18452/19240.
Full textAbstract:
Cyanobakterien sind meist photoautotroph lebende Prokaryoten, welche nahezu alle Biotope der Welt besiedeln. Sie gehören zu den wichtigsten Produzenten der weltweiten Nahrungskette. Um sich auf den täglichen Wechsel von Tag und Nacht einzustellen, besitzen Cyanobakterien eine innere Uhr, bestehend aus den Proteinen KaiA, KaiB und KaiC, deren biochemische Interaktionen zu einem 24-stündigen Rhythmus von Phosphorylierung und Dephosphorylierung führen. Die circadiane Genexpression im Modellorganismus Synechocystis sp. PCC 6803 habe ich mittels drei verschiedener Zeitserienexperimente untersucht, wobei ich einen genauen Zeitplan der Genaktivierung in einer Tag-Nacht-Umgebung, aber keine selbsterhaltenden Rhythmen entdecken konnte. Allerdings beobachtete ich einen überaus starken Anstieg der ribosomalen RNA in der Dunkelheit.
Aufgrund ihrer hohen Wachstumsraten und der geringen Anforderungen an die Umwelt bilden Cyanobakterien eine gute Grundlage für die nachhaltige Erzeugung von Biokraftstoffen, für einen industriellen Einsatz sind aber weitere Optimierung und ein verbessertes Verständnis des Metabolismus von Nöten. Hierfür habe ich die Orthologie von verschiedenen Cyanobakterien sowie die Konservierung von Genen und Stoffwechselwegen untersucht. Mit einer neu entwickelten Methode konnte ich gemeinsam vorkommende Gene identifizieren und zeigen, dass diese Gene häufig an einem gemeinsamen biologischen Prozess beteiligt sind, und damit bisher unbekannte Beziehungen aufdecken. Zusätzlich zu den diskutierten Modulen habe ich den SimilarityViewer entwickelt, ein grafisches Computerprogramm für die Identifizierung von gemeinsam vorkommenden Partnern für jedes beliebige Gen. Des Weiteren habe ich für alle Organismen automatische Rekonstruktionen des Stoffwechsels erstellt und konnte zeigen, dass diese die Synthese von gewünschten Stoffen gut vorhersagen, was hilfreich für zukünftige Forschung am Metabolismus von Cyanobakterien sein wird.Cyanobacteria are photoautotrophic prokaryotes populating virtually all habitats on the surface of the earth. They are one of the prime producers for the global food chain. To cope with the daily alternation of light and darkness, cyanobacteria harbor a circadian clock consisting of the three proteins KaiA, KaiB, and KaiC, whose biochemical interactions result in a phosphorylation cycle with a period of approximately 24 hours. I conducted three time-series experiments in the model organism Synechocystis sp. PCC 6803, which revealed a tight diurnal schedule of gene activation. However, I could not identify any self-sustained oscillations. On the contrary, I observed strong diurnal accumulation of ribosomal RNAs during dark periods, which challenges common assumptions on the amount of ribosomal RNAs. Due to their high growth rates and low demand on their environment, cyanobacteria emerged as a viable option for sustainable production of biofuels. For an industrialized production, however, optimization of growth and comprehensive knowledge of the cyanobacterial metabolism is inevitable. To address this issue, I analyzed the orthology of multiple cyanobacteria and studied the conservation of genes and metabolic pathways. Systematic analysis of genes shared by similar subsets of organisms indicates high rates of functional relationship in such co-occurring genes. I designed a novel approach to identify modules of co-occurring genes, which exhibit a high degree of functional coherence and reveal unknown functional relationships between genes. Complementing the precomputed modules, I developed the SimilarityViewer, a graphical toolbox that facilitates further analysis of co-occurrence with respect to specific cyanobacterial genes of interest. Simulations of automatically generated metabolic reconstructions revealed the biosynthetic capacities of individual cyanobacterial strains, which will assist future research addressing metabolic engineering of cyanobacteria.
39
Puterová, Janka. "Porovnání eukaryotních genomů." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2015. http://www.nusl.cz/ntk/nusl-264943.
Full textAbstract:
Main motive of this master thesis was the need of good bioinformatics tools for genome comparison and improvement of one of the existing tools - RepeatExplorer. This work offers an overview of transposable elements in DNA, existing tools for identification and analysis of repetitions in sequenced genomes, summary of currently used genome sequencing methods. This work describes shortcomings of RepeatExplorer tool with focus on comparative analysis of genomes. Two solutions to remove these problems were designed and implemented. The first solution is designed for comparing pairs of genomes. The principle of this solution is based on comparison of similarity of distribution of contigs coverages using Kolmogorov-Smirnov test, thanks to which we are able to determine different parts in the genomes.The second solution, which is used to compare multiple genomes, is based on the method of mapping reads from compared genomes to the reference genome contigs and provides contigs coverage graphs, by which we are able to determine the variability of the repeats.Their functionality was verified on real NGS data of organism Silene latifolia.
40
Batzoglou, Serafim. "Computational genomics : mapping, comparison, and annotation of genomes." Thesis, Massachusetts Institute of Technology, 2000. http://hdl.handle.net/1721.1/8629.
Full textAbstract:
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2000.Includes bibliographical references (leaves 180-191).
The field of genomics provides many challenges to computer scientists and mathematicians. The area of computational genomics has been expanding recently, and the timely application of computer science in this field is proving to be an essential component of the large international effort in genomics. In this thesis we address key issues in the different stages of genome research: planning of a genome sequencing project, obtaining and assembling sequence information, and ultimately study, cross-species comparison, and annotation of finished genomic sequence. We present applications of computational techniques to the above areas: (1) In relation to the early stages of a genome project, we address physical mapping, and we present results on the theoretical problem of finding minimum superstrings of hypergraphs, a combinatorial problem motivated by physical mapping. We also present a statistical and simulation study of "walking with clone-end sequences", an important method for sequencing a large genome.
(cont.) (2) Turning to the problem of obtaining the finished genomic sequence, we present ARACHNE, a prototype software system for assembling sequence data that are derived from sequencing a genome with the "shotgun" method. (3) Finally, we turn to the computational analysis of finished genomic sequence. We present GLASS, a software system for obtaining global pairwise alignments of orthologous finished sequences. We finally use GLASS to perform a comparative structure and sequence analysis of orthologous human and mouse genomic regions, and develop ROSETTA, the first cross-species comparison-based system for the prediction of protein coding regions in genomic sequences.
by Serafin Batzoglou.
Ph.D.
41
Tang, Haibao, Eric Lyons, Brent Pedersen, James Schnable, Andrew Paterson, and Michael Freeling. "Screening synteny blocks in pairwise genome comparisons through integer programming." BioMed Central, 2011. http://hdl.handle.net/10150/610221.
Full textAbstract:
BACKGROUND:It is difficult to accurately interpret chromosomal correspondences such as true orthology and paralogy due to significant divergence of genomes from a common ancestor. Analyses are particularly problematic among lineages that have repeatedly experienced whole genome duplication (WGD) events. To compare multiple "subgenomes" derived from genome duplications, we need to relax the traditional requirements of "one-to-one" syntenic matchings of genomic regions in order to reflect "one-to-many" or more generally "many-to-many" matchings. However this relaxation may result in the identification of synteny blocks that are derived from ancient shared WGDs that are not of interest. For many downstream analyses, we need to eliminate weak, low scoring alignments from pairwise genome comparisons. Our goal is to objectively select subset of synteny blocks whose total scores are maximized while respecting the duplication history of the genomes in comparison. We call this "quota-based" screening of synteny blocks in order to appropriately fill a quota of syntenic relationships within one genome or between two genomes having WGD events.RESULTS:We have formulated the synteny block screening as an optimization problem known as "Binary Integer Programming" (BIP), which is solved using existing linear programming solvers. The computer program QUOTA-ALIGN performs this task by creating a clear objective function that maximizes the compatible set of synteny blocks under given constraints on overlaps and depths (corresponding to the duplication history in respective genomes). Such a procedure is useful for any pairwise synteny alignments, but is most useful in lineages affected by multiple WGDs, like plants or fish lineages. For example, there should be a 1:2 ploidy relationship between genome A and B if genome B had an independent WGD subsequent to the divergence of the two genomes. We show through simulations and real examples using plant genomes in the rosid superorder that the quota-based screening can eliminate ambiguous synteny blocks and focus on specific genomic evolutionary events, like the divergence of lineages (in cross-species comparisons) and the most recent WGD (in self comparisons).CONCLUSIONS:The QUOTA-ALIGN algorithm screens a set of synteny blocks to retain only those compatible with a user specified ploidy relationship between two genomes. These blocks, in turn, may be used for additional downstream analyses such as identifying true orthologous regions in interspecific comparisons. There are two major contributions of QUOTA-ALIGN: 1) reducing the block screening task to a BIP problem, which is novel2) providing an efficient software pipeline starting from all-against-all BLAST to the screened synteny blocks with dot plot visualizations. Python codes and full documentations are publicly available http://github.com/tanghaibao/quota-alignment webcite. QUOTA-ALIGN program is also integrated as a major component in SynMap http://genomevolution.com/CoGe/SynMap.pl webcite, offering easier access to thousands of genomes for non-programmers.
42
Ong, Wai, Trang Vu, Klaus Lovendahl, Jenna Llull, Margrethe Serres, Margaret Romine, and Jennifer Reed. "Comparisons of Shewanella strains based on genome annotations, modeling, and experiments." BioMed Central, 2014. http://hdl.handle.net/10150/610105.
Full textAbstract:
BACKGROUND:Shewanella is a genus of facultatively anaerobic, Gram-negative bacteria that have highly adaptable metabolism which allows them to thrive in diverse environments. This quality makes them an attractive bacterial target for research in bioremediation and microbial fuel cell applications. Constraint-based modeling is a useful tool for helping researchers gain insights into the metabolic capabilities of these bacteria. However, Shewanella oneidensis MR-1 is the only strain with a genome-scale metabolic model constructed out of 21 sequenced Shewanella strains.RESULTS:In this work, we updated the model for Shewanella oneidensis MR-1 and constructed metabolic models for three other strains, namely Shewanella sp. MR-4, Shewanella sp. W3-18-1, and Shewanella denitrificans OS217 which span the genus based on the number of genes lost in comparison to MR-1. We also constructed a Shewanella core model that contains the genes shared by all 21 sequenced strains and a few non-conserved genes associated with essential reactions. Model comparisons between the five constructed models were done at two levels - for wildtype strains under different growth conditions and for knockout mutants under the same growth condition. In the first level, growth/no-growth phenotypes were predicted by the models on various carbon sources and electron acceptors. Cluster analysis of these results revealed that the MR-1 model is most similar to the W3-18-1 model, followed by the MR-4 and OS217 models when considering predicted growth phenotypes. However, a cluster analysis done based on metabolic gene content revealed that the MR-4 and W3-18-1 models are the most similar, with the MR-1 and OS217 models being more distinct from these latter two strains. As a second level of comparison, we identified differences in reaction and gene content which give rise to different functional predictions of single and double gene knockout mutants using Comparison of Networks by Gene Alignment (CONGA). Here, we showed how CONGA can be used to find biomass, metabolic, and genetic differences between models.CONCLUSIONS:We developed four strain-specific models and a general core model that can be used to do various in silico studies of Shewanella metabolism. The developed models provide a platform for a systematic investigation of Shewanella metabolism to aid researchers using Shewanella in various biotechnology applications.
43
Tvedte, Eric S. "Genome evolution in parasitic wasps: comparisons of sexual and asexual species." Diss., University of Iowa, 2018. https://ir.uiowa.edu/etd/6516.
Full textAbstract:
The fate of any lineage is contingent on the rate at which its genome changes over time. Genome dynamics are influenced by patterns of mutation and recombination. Mutations as the raw force of variation can be acted on independently during exchanges of homologous genetic regions via meiotic recombination. While molecular evolution in sexual lineages is impacted by both mutation and recombination, asexual lineage fate is primarily influenced by the mutation rate; recombination is often altered or absent in asexuals. Although multiple studies show accelerated mutation accumulation in asexual lineages that have lost recombination, virtually nothing is known about rate patterns when meiosis is retained. Here, I use parasitic wasps in genus Diachasma to investigate genome evolution in a recently-derived asexual lineage. I provide evidence that asexual Diachasma possess a canonical set of meiosis genes as well as high levels of genomic homozygosity. Taken together, these observations support an active, albeit modified, form of meiosis in this asexual lineage. In addition, I present the first documentation of accelerated mutation accumulation in the nuclear genome of a naturally-occurring, meiotically- reproducing organism. If harmful, these mutations could impede asexual lineage persistence and contribute strong support for the long-term benefits of sex.
44
Dousseaud, Peggy Marie Madeleine. "A comparative genomic analysis of hydrocarbon synthesis in Desulfovibrio sp." Thesis, University of Exeter, 2018. http://hdl.handle.net/10871/34379.
Full textAbstract:
To fulfil global energy demand and to mitigate economical, geopolitical and ecological challenges associated with fossil fuel utilisation, the energy sector is moving towards greater use of sustainable and environmentally friendly energy sources, including biofuels. The ideal transport biofuel would be hydrocarbons that are identical to fossil petroleum. However, to date characterised hydrocarbon biosynthetic pathways include a decarbonylation or decarboxylation reaction, which involves the loss of one carbon resulting in odd-numbered carbon chain hydrocarbons. This carbon loss decreases carbon efficiency for alkane production, which reduces microbial fuel economic competitiveness. Therefore, it is key that new pathways for alkane production are identified. The sulphate-reducing bacteria genus Desulfovibrio was previously reported to synthesise even-numbered carbon chain alkanes, which suggests an alternative route for alkane production without carbon loss. This investigation aimed to verify Desulfovibrio alkane biosynthesis and characterise the possible synthetic pathway. Ten Desulfovibrio strains, representing seven species, were screened for alkane synthesis using isotopically labelled growth media. The ability to produce alkanes within the Desulfovibrio genus was confirmed and was shown to be strain-specific under a set of culture conditions. The biogenic alkanes detected were octadecane (C18), nonadecane (C19) and eicosane (C20), with a predominance of even-numbered carbon chain alkanes. Fatty acid analysis of Desulfovibrio strains showed an alkane biosynthetic pathway was unlikely to involve a decarbonylation or decarboxylation step. A novel hypothesis was therefore proposed that alkane biosynthesis by Desulfovibrio follows a metabolic route, which has not previously been characterised, involving a series of reduction reactions from the fatty acid pool. The characterisation of the putative Desulfovibrio hydrogenation pathway for alkane biosynthesis was undertaken via a target-directed genome mining approach. The genomic DNA of nine Desulfovibrio spp. was purified, sequenced, de novo assembled and annotated. Seven of these nine genomes are unpublished to date. No homologs of previously characterised alkane biosynthetic enzymes from bacteria were in silico identified in the genomes and proteomes of alkane producing Desulfovibrio spp., suggesting that Desulfovibrio alkane biosynthetic pathway is likely to be catalysed by currently uncharacterised enzymes. The 16S rRNA-based phylogeny of Desulfovibrio spp. supported the hypothesis that the Desulfovibrio alkane biosynthetic pathway was acquired by a common ancestral strain via horizontal gene transfer. The ability of Desulfovibrio to produce alkanes was therefore hypothesised to be due to the presence of recruited genes encoding enzymes involved in alkane synthesis. A comparative genomic analysis intersecting six-alkane producing and four non-alkane producing Desulfovibrio genomes resulted in the in silico identification of 33 hypothetical proteins considered with high confidence to be exclusive to alkane producing Desulfovibrio strains. A novel hypothetical Desulfovibrio alkane biosynthetic pathway was proposed involving a V-type ATPase, an uncharacterised protein, named as a putative reductase in this investigation, and a putative methyltransferase, which were predicted to be exclusive to alkane producing Desulfovibrio spp. The inorganic phosphates resulting from the ATP hydrolysis catalysed by the V-type ATPase would be involved in a reaction with fatty alcohols to form alkyl phosphates, which are putative activated intermediates required for the hydrogenation route from fatty alcohols to alkanes. The putative reductase and the methyltransferase, predicted to share similar structural features with known alkane-binding proteins, would subsequently reduce alkyl phosphates to alkanes and to iso-alkanes respectively. Empirical investigation of the candidate molecular basis function in Desulfovibrio alkane biosynthesis was undertaken. The Desulfovibrio alkane biosynthetic pathway remains to be fully characterised.
45
Dickens, Nicholas J. "Comparisons of proteins and genomes by integrating bioinformatics data." Thesis, University of Oxford, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.496848.
Full text
46
Kastenmüller, Gabriele. "In silico prediction and comparison of metabolic capabilities in sequenced genomes /." München : Hut, 2009. http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&doc_number=018929163&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA.
Full text
47
Xue, Jianli. "Comparison of ascovirus and baculovirus genomes and their replication and gene expression strategies." Miami University / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=miami1312568903.
Full text
48
Li, Alice Hoy Lam. "Identification of virulence determinants of Mycobacterium tuberculosis via genetic comparisons of a virulent and an attenuated strain of Mycobacterium tuberculosis." Thesis, University of British Columbia, 2008. http://hdl.handle.net/2429/596.
Full textAbstract:
Candidate virulence genes were sought through the genetic analyses of two strains of Mycobacterium tuberculosis, one virulent, H37Rv, one attenuated, H37Ra. Derived from the same parent, H37, genomic differences between strains were first examined via two-dimensional DNA technologies: two-dimensional bacterial genome display, and bacterial comparative genomic hybridisation. The two-dimensional technologies were optimised for mycobacterial use, but failed to yield reproducible genomic differences between the two strains. Expression differences between strains during their infection of murine bone-marrow-derived macrophages were then assessed using Bacterial Artificial Chromosome Fingerprint Arrays. This technique successfully identified expression differences between intracellular M. tuberculosis H37Ra and H37Rv, and six candidate genes were confirmed via quantitative real-time PCR for their differential expression at 168 hours post-infection. Genes identified to be upregulated in the attenuated H37Ra were frdB, frdC, and frdD. Genes upregulated in the virulent H37Rv were pks2, aceE, and Rv1571. Further qPCR analysis of these genes at 4 and 96h post-infection revealed that the frd operon (encoding for the fumarate reductase enzyme complex or FRD) was expressed at higher levels in the virulent H37Rv at earlier time points while the expression of aceE and pks2 was higher in the virulent strain throughout the course of infection. Assessment of frd transcripts in oxygen-limited cultures of M. tuberculosis H37Ra and H37Rv showed that the attenuated strain displayed a lag in frdA and frdB expression at the onset of culture when compared to microaerophilic cultures of H37Rv and aerated cultures of H37Ra. Furthermore, inhibition of the fumarate reductase complex in intracellular bacteria resulted in a significant reduction of intracellular growth. Microarray technology was also applied in the expression analysis of intracellular bacteria at 168h post-infection. Forty-eight genes were revealed to be differentially expressed between the H37Ra and H37Rv strains, and a subset were further analysed via qPCR to confirm and validate the microarray data. phoP was expressed at a lower level in the attenuated M. tuberculosis H37Ra, whereas members of the phoPR regulon were up-regulated in the virulent H37Rv. Additionally, a group of genes (Rv3616c-Rv3613c) that may associate with the region of difference 1 were also up-regulated in the virulent H37Rv.
49
De, Maayer Pieter. "Genome comparisons to identify selected pathogenicity factors of a plant-associated Pantoea ananatis strain." Thesis, University of Pretoria, 2010. http://hdl.handle.net/2263/30849.
Full textAbstract:
Pantoea ananatis is a ubiquitous organism found in almost every environment on
earth. It has been implicated in diseases of a wide range of agronomic crops
worldwide, including onion, maize, rice and pineapple, as well as a human disease. In
South Africa, P. ananatis causes blight and dieback of Eucalyptus, resulting in severe
losses of this important forestry resource. Nevertheless, little is known about the
pathogenicity mechanisms utilised by this pathogen to cause disease in this host.
The whole genome of a highly virulent Eucalyptus-pathogenic P. ananatis strain,
LMG20103, was sequenced. This genome sequence was subsequently mined to
identify a vast array of genes encoding putative pathogenicity determinants.
Comparative genomics revealed that it has evolved to be able to thrive in a wide range
of environments and that this strain carries pathogenicity determinants that may allow
it to infect hosts in both the animal and plant Kingdom. Interestingly, no Type II and
III secretion systems, which form a major part of the pathogenicity arsenal of many
plant pathogenic bacteria are present in P. ananatis. However, three loci on the
genome encode three distinct copies of the Type VI secretion system, which has
recently been demonstrated to play an important role in diseases caused by many
plant- and animal-pathogenic bacteria. In silico analysis of these secretion systems
showed that they likely secrete several pathogenicity effectors which may have a role
in P. ananatis infection of both plant and animal hosts. Another putative
pathogenicity determinant identified from the genome, the exopolysaccharide
ananatan, was experimentally demonstrated to play a role in disease expression on
both onion seedlings and pineapple fruit. This was done through the production of a
library of mutants which encompasses all the genes on the P. ananatis genome.
Genome sequencing enabled the identification of all the putative pathogenicity factors
of P. ananatis LMG20103 and the use of the mutant library and post-genomic
techniques has and will allow the functional characterization of many of these
pathogenicity determinants. By this means, the mechanisms underlying the disease
caused by P. ananatis on Eucalyptus and other hosts can be better understood. With
this information, more directed and effective strategies for the control of this pathogen
and its diseases can be developed.Thesis (PhD)--University of Pretoria, 2010.
Microbiology and Plant Pathology
Unrestricted
50
Moss, Stephen Paul. "The development of computational methods for large-scale comparisons and analyses of genome evolution." Thesis, University of Hull, 2015. http://hydra.hull.ac.uk/resources/hull:13083.
Full textAbstract:
The last four decades have seen the development of a number of experimental methods for the deduction of the whole genome sequences of an ever-increasing number of organisms. These sequences have in the first instance, allowed their investigators the opportunity to examine the molecular primary structure of areas of scientific interest, but with the increased sampling of organisms across the phylogenetic tree and the improved quality and coverage of genome sequences and their associated annotations, the opportunity to undertake detailed comparisons both within and between taxonomic groups has presented itself. The work described in this thesis details the application of comparative bioinformatics analyses on inter- and intra-genomic datasets, to elucidate those genomic changes, which may underlie organismal adaptations and contribute to changes in the complexity of genome content and structure over time. The results contained herein demonstrate the power and flexibility of the comparative approach, utilising whole genome data, to elucidate the answers to some of the most pressing questions in the biological sciences today. As the volume of genomic data increases, both as a result of increased sampling of the tree of life and due to an increase in the quality and throughput of the sequencing methods, it has become clear that there is a necessity for computational analyses of these data. Manual analysis of this volume of data, which can extend beyond petabytes of storage space, is now impossible. Automated computational pipelines are therefore required to retrieve, categorise and analyse these data. Chapter two discusses the development of a computational pipeline named the Genome Comparison and Analysis Toolkit (GCAT). The pipeline was developed using the Perl programming language and is tightly integrated with the Ensembl Perl API allowing for the retrieval and analyses of their rich genomic resources. In the first instance the pipeline was tested for its robustness by retrieving and describing various components of genomic architecture across a number of taxonomic groups. Additionally, the need for programmatically independent means of accessing data and in particular the need for Semantic Web based protocols and tools for the sharing of genomics resources is highlighted. This is not just for the requirements of researchers, but for improved communication and sharing between computational infrastructure. A prototype Ensembl REST web service was developed in collaboration with the European Bioinformatics Institute (EBI) to provide a means of accessing Ensembl’s genomic data without having to rely on their Perl API. A comparison of the runtime and memory usage of the Ensembl Perl API and prototype REST API were made relative to baseline raw SQL queries, which highlights the overheads inherent in building wrappers around the SQL queries. Differences in the efficiency of the approaches were highlighted, and the importance of investing in the development of Semantic Web technologies as a tool to improve access to data for the wider scientific community are discussed. Data highlighted in chapter two led to the identification of relative differences in the intron structure of a number of organisms including teleost fish. Chapter three encompasses a published, peer-reviewed study. Inter-genomic comparisons were undertaken utilising the 5 available teleost genome sequences in order to examine and describe their intron content. The number and sizes of introns were compared across these fish and a frequency distribution of intron size was produced that identified a novel expansion in the Zebrafish lineage of introns in the size range of approximately 500-2,000 bp. Further hypothesis driven analyses of the introns across the whole distribution of intron sizes identified that the majority, but not all of the introns were largely comprised of repetitive elements. It was concluded that the introns in the Zebrafish peak were likely the result of an ancient expansion of repetitive elements that had since degraded beyond the ability of computational algorithms to identify them. Additional sampling throughout the teleost fish lineage will allow for more focused phylogenetically driven analyses to be undertaken in the future. In chapter four phylogenetic comparative analyses of gene duplications were undertaken across primate and rodent taxonomic groups with the intention of identifying significantly expanded or contracted gene families. Changes in the size of gene families may indicate adaptive evolution. A larger number of expansions, relative to time since common ancestor, were identified in the branch leading to modern humans than in any other primate species. Due to the unique nature of the human data in terms of quantity and quality of annotation, additional analyses were undertaken to determine whether the expansions were methodological artefacts or real biological changes. Novel approaches were developed to test the validity of the data including comparisons to other highly annotated genomes. No similar expansion was seen in mouse when comparing with rodent data, though, as assemblies and annotations were updated, there were differences in the number of significant changes, which brings into question the reliability of the underlying assembly and annotation data. This emphasises the importance of an understanding that computational predictions, in the absence of supporting evidence, may be unlikely to represent the actual genomic structure, and instead be more an artefact of the software parameter space. In particular, significant shortcomings are highlighted due to the assumptions and parameters of the models used by the CAFE gene family analysis software. We must bear in mind that genome assemblies and annotations are hypotheses that themselves need to be questioned and subjected to robust controls to increase the confidence in any conclusions that can be drawn from them. In addition functional genomics analyses were undertaken to identify the role of significantly changed genes and gene families in primates, testing against a hypothesis that would see the majority of changes involving immune, sensory or reproductive genes. Gene Ontology (GO) annotations were retrieved for these data, which enabled highlighting the broad GO groupings and more specific functional classifications of these data. The results showed that the majority of gene expansions were in families that may have arisen due to adaptation, or were maintained due to their necessary involvement in developmental and metabolic processes. Comparisons were made to previously published studies to determine whether the Ensembl functional annotations were supported by the de-novo analyses undertaken in those studies. The majority were not, with only a small number of previously identified functional annotations being present in the most recent Ensembl releases. The impact of gene family evolution on intron evolution was explored in chapter five, by analysing gene family data and intron characteristics across the genomes of 61 vertebrate species. General descriptive statistics and visualisations were produced, along with tests for correlation between change in gene family size and the number, size and density of their associated introns. There was shown to be very little impact of change in gene family size on the underlying intron evolution. Other, non-family effects were therefore considered. These analyses showed that introns were restricted to euchromatic regions, with heterochromatic regions such as the centromeres and telomeres being largely devoid of any such features. A greater involvement of spatial mechanisms such as recombination, GC-bias across GC-rich isochores and biased gene conversion was thus proposed to play more of a role, though depending largely on population genetic and life history traits of the organisms involved. Additional population level sequencing and comparative analyses across a divergent group of species with available recombination maps and life history data would be a useful future direction in understanding the processes involved.