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You searched for subject:(nextgeneration sequencing). Showing records 1 – 3 of 3 total matches.

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University of Wollongong

1. Tsatsaronis, James Anthony. Characterisation of group A streptococcal innate immune resistance and host response mechanisms.

Degree: PhD, 2014, University of Wollongong

Group A Streptococcus (GAS, Streptococcus pyogenes) is a Gram-positive bacterial pathogen responsible for life-threatening, invasive human diseases, including necrotising fasciitis and streptococcal toxic shock syndrome. In the last 30 years, a global increase in the rates of severe and fatal forms of GAS infection has been noted. Coinciding with this epidemiological trend has been a pandemic spread of particularly hypervirulent GAS, notably a clone of the M1T1 serotype. Studies investigating this serotype highlight the unique genetic makeup of M1T1 GAS and its interactions with the host innate immune response as key elements coordinating the virulence of this serotype. Phage-mediated horizontal gene transfer and selective pressure exerted by polymorphonuclear leukocytes (PMNs) for mutations in the control of virulence regulator operon (covRS) bestow M1T1 GAS with enhanced pathogenic capacity. However, isolates of virulent GAS also occur in genetic backgrounds lacking phageencoded factors, such as sda1, and other M1T1-specific core genomic elements necessary for covRS mutation. In this study, high-throughput next-generation sequencing was utilised to generate a draft genome sequence of NS88.2, an emm98.1 GAS isolate exhibiting a hypervirulent and PMN resistant phenotype. The multi-locus sequence type (MLST) was determined from the NS88.2 draft genome sequence, which was compared to fully sequenced GAS strains by whole genome BLAST alignment. NS88.2 was found to have a MLST sequence type of 205, and regions of nucleotide sequence divergence between NS88.2 and other GAS included the multiple gene regulator (MGA) and fibronectin, collagen and T-antigen (FCT) loci. The NS88.2 MGA locus showed low sequence similarity to GAS of other emm-types, and the FCT locus corresponded to an FCT type 3. A ~30 kb region containing putative prophagelike elements constituted the majority of NS88.2 novel sequence data, however interrogation of these elements did not reveal novel genes with obvious roles in modulating PMN responses. Bioinformatic prediction of genes encoding cell surface and secreted proteins was conducted, and identified 10 putative cell surface proteins and 190 putative proteins with secretion signal peptides. The addition of this genome draft to public databases will facilitate other studies of GAS genome biology, and further in-depth analyses of the NS88.2 isolate described here. The phage-encoded extracellular DNase streptodornase 1 (Sda1) has previously been shown as essential for M1T1 GAS acquisition of covRS mutations. Mutations of covRS in M1T1 GAS bestow hypervirulent and PMN resistant qualities. These phenotypes are also observed in the NS88.2 isolate, which encodes a truncated, non-functional covS gene, but not the sda1 gene. In this study, NS88.2 and derivative strains with intact covS (NS88.2rep) or reverse complemented inactive covS (NS88.2covS) were examined to determine potential novel mechanisms by which these strains interact with the innate immune…

Subjects/Keywords: Streptococcus pyogenes; neutrophils; innate immunity; nextgeneration sequencing; apoptosis; oncosis

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APA (6th Edition):

Tsatsaronis, J. A. (2014). Characterisation of group A streptococcal innate immune resistance and host response mechanisms. (Doctoral Dissertation). University of Wollongong. Retrieved from 060102 Bioinformatics, 060501 Bacteriology, 110707 Innate Immunity, 110801 Medical Bacteriology ; https://ro.uow.edu.au/theses/4125

Chicago Manual of Style (16th Edition):

Tsatsaronis, James Anthony. “Characterisation of group A streptococcal innate immune resistance and host response mechanisms.” 2014. Doctoral Dissertation, University of Wollongong. Accessed April 19, 2021. 060102 Bioinformatics, 060501 Bacteriology, 110707 Innate Immunity, 110801 Medical Bacteriology ; https://ro.uow.edu.au/theses/4125.

MLA Handbook (7th Edition):

Tsatsaronis, James Anthony. “Characterisation of group A streptococcal innate immune resistance and host response mechanisms.” 2014. Web. 19 Apr 2021.

Vancouver:

Tsatsaronis JA. Characterisation of group A streptococcal innate immune resistance and host response mechanisms. [Internet] [Doctoral dissertation]. University of Wollongong; 2014. [cited 2021 Apr 19]. Available from: 060102 Bioinformatics, 060501 Bacteriology, 110707 Innate Immunity, 110801 Medical Bacteriology ; https://ro.uow.edu.au/theses/4125.

Council of Science Editors:

Tsatsaronis JA. Characterisation of group A streptococcal innate immune resistance and host response mechanisms. [Doctoral Dissertation]. University of Wollongong; 2014. Available from: 060102 Bioinformatics, 060501 Bacteriology, 110707 Innate Immunity, 110801 Medical Bacteriology ; https://ro.uow.edu.au/theses/4125


West Virginia University

2. Ramachandran, Dhanushya. TRANSPOSABLE ELEMENT DIVERSITY, DIVERGENCE, AND CONTRIBUTION TO GENOME EVOLUTION IN PLANTS.

Degree: PhD, Biology, 2018, West Virginia University

Subjects/Keywords: Transposable elements; genome evolution; plants; polyploidy; copy number; nextgeneration sequencing

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Ramachandran, D. (2018). TRANSPOSABLE ELEMENT DIVERSITY, DIVERGENCE, AND CONTRIBUTION TO GENOME EVOLUTION IN PLANTS. (Doctoral Dissertation). West Virginia University. Retrieved from https://doi.org/10.33915/etd.7236 ; https://researchrepository.wvu.edu/etd/7236

Chicago Manual of Style (16th Edition):

Ramachandran, Dhanushya. “TRANSPOSABLE ELEMENT DIVERSITY, DIVERGENCE, AND CONTRIBUTION TO GENOME EVOLUTION IN PLANTS.” 2018. Doctoral Dissertation, West Virginia University. Accessed April 19, 2021. https://doi.org/10.33915/etd.7236 ; https://researchrepository.wvu.edu/etd/7236.

MLA Handbook (7th Edition):

Ramachandran, Dhanushya. “TRANSPOSABLE ELEMENT DIVERSITY, DIVERGENCE, AND CONTRIBUTION TO GENOME EVOLUTION IN PLANTS.” 2018. Web. 19 Apr 2021.

Vancouver:

Ramachandran D. TRANSPOSABLE ELEMENT DIVERSITY, DIVERGENCE, AND CONTRIBUTION TO GENOME EVOLUTION IN PLANTS. [Internet] [Doctoral dissertation]. West Virginia University; 2018. [cited 2021 Apr 19]. Available from: https://doi.org/10.33915/etd.7236 ; https://researchrepository.wvu.edu/etd/7236.

Council of Science Editors:

Ramachandran D. TRANSPOSABLE ELEMENT DIVERSITY, DIVERGENCE, AND CONTRIBUTION TO GENOME EVOLUTION IN PLANTS. [Doctoral Dissertation]. West Virginia University; 2018. Available from: https://doi.org/10.33915/etd.7236 ; https://researchrepository.wvu.edu/etd/7236

3. Pandey, Ashutosh Kumar. Functional Analysis of Genomic Variation and Impact on Molecular and Higher Order Phenotypes.

Degree: PhD, Biomedical Sciences, 2015, University of Tennessee Health Science Center

Reverse genetics methods, particularly the production of gene knockouts and knockins, have revolutionized the understanding of gene function. High throughput sequencing now makes it practical to exploit reverse genetics to simultaneously study functions of thousands of normal sequence variants and spontaneous mutations that segregate in intercross and backcross progeny generated by mating completely sequenced parental lines. To evaluate this new reverse genetic method we resequenced the genome of one of the oldest inbred strains of mice—DBA/2J—the father of the large family of BXD recombinant inbred strains. We analyzed ~100X wholegenome sequence data for the DBA/2J strain, relative to C57BL/6J, the reference strain for all mouse genomics and the mother of the BXD family. We generated the most detailed picture of molecular variation between the two mouse strains to date and identified 5.4 million sequence polymorphisms, including, 4.46 million single nucleotide polymorphisms (SNPs), 0.94 million intersections/deletions (indels), and 20,000 structural variants. We systematically scanned massive databases of molecular phenotypes and ~4,000 classical phenotypes to detect linked functional consequences of sequence variants. In majority of cases we successfully recovered known genotype-to-phenotype associations and in several cases we linked sequence variants to novel phenotypes (Ahr, Fh1, Entpd2, and Col6a5). However, our most striking and consistent finding is that apparently deleterious homozygous SNPs, indels, and structural variants have undetectable or very modest additive effects on phenotypes. Advisors/Committee Members: Robert W. Williams, Ph.D..

Subjects/Keywords: BXD; complex traits; DBA/2J; nextgeneration sequencing; PheWAS; reverse genetics; Genetic Phenomena; Genetic Processes; Medical Genetics; Medical Sciences; Medicine and Health Sciences

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Pandey, A. K. (2015). Functional Analysis of Genomic Variation and Impact on Molecular and Higher Order Phenotypes. (Doctoral Dissertation). University of Tennessee Health Science Center. Retrieved from https://dc.uthsc.edu/dissertations/359

Chicago Manual of Style (16th Edition):

Pandey, Ashutosh Kumar. “Functional Analysis of Genomic Variation and Impact on Molecular and Higher Order Phenotypes.” 2015. Doctoral Dissertation, University of Tennessee Health Science Center. Accessed April 19, 2021. https://dc.uthsc.edu/dissertations/359.

MLA Handbook (7th Edition):

Pandey, Ashutosh Kumar. “Functional Analysis of Genomic Variation and Impact on Molecular and Higher Order Phenotypes.” 2015. Web. 19 Apr 2021.

Vancouver:

Pandey AK. Functional Analysis of Genomic Variation and Impact on Molecular and Higher Order Phenotypes. [Internet] [Doctoral dissertation]. University of Tennessee Health Science Center; 2015. [cited 2021 Apr 19]. Available from: https://dc.uthsc.edu/dissertations/359.

Council of Science Editors:

Pandey AK. Functional Analysis of Genomic Variation and Impact on Molecular and Higher Order Phenotypes. [Doctoral Dissertation]. University of Tennessee Health Science Center; 2015. Available from: https://dc.uthsc.edu/dissertations/359

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