Browsing by Author "Ramaraj, Thiruvarangan"

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Development and testing of algorithmic solutions for problems in computational genomics and proteomics
(Montana State University - Bozeman, College of Engineering, 2010) Ramaraj, Thiruvarangan; Chairperson, Graduate Committee: Brendan Mumey
This dissertation covers three subjects: (i) computational characterization of Antigen (Ag)-Antibody (Ab) interactions (ii) a novel and effective algorithm to predict the epitope of a protein based on an antibody imprinting technique (iii) a comparison of existing de novo genome assembler algorithms targeted specifically at the assembly of data generated by Illumina (Solexa) short-read sequencing technology, and suggestions for their improvement. The first part focuses on identification, characterization and understanding the ways in which the antibodies and antigens interact. We analyze Epitope/Paratope region using a large dataset of Ag - Ab complex structural data taken from the PDB. Epitope/Paratope regions in our dataset have been characterized in terms of their size, average amino acid residue composition, residue-residue pairing preferences, and residue dispersion in the epitope and paratope regions. This analysis provides a more up-to-date picture of the Ag-Ab interface and provides new insights into the role of residue composition and distribution in Ag-Ab recognition. The above analysis helps in obtaining a refined substitution matrix optimized for antibody imprinting technique and used to improve the effectiveness of the epitope prediction algorithms that have also been developed and are the second focus of the thesis. The third and the final part focus on the de novo genome assembly problems. The genome assembly programs takes the short reads generated by Whole genome shotgun sequencing technology and computationally reconstructs the genome. For the genome assembly problem the connections between read length, read type, repeat complexity, quality score and coverage and how these parameters help in improving or diminishing the capability of the assembly programs to assemble the sequence data were studied in depth. At the end of this experimental process it gives us a better understanding of the impact of the above mentioned parameters on the complexity of genome assembly and helps ascertain margins on these parameters of sequence data that enable efficient and accurate assembly by the programs.
Draft genome sequence of a metabolically diverse Antarctic supraglacial stream organism, Polaromonas sp. strain CG9_12, determined using pacific biosciences single-molecule real-time sequencing technology
(2014-12) Smith, Heidi J.; Foreman, Christine M.; Ramaraj, Thiruvarangan
Polaromonas species are found in a diversity of environments and are particularly common in icy ecosystems. Polaromonas sp. strain CG9_12 is an aerobic, Gram-negative, catalase-positive, white-pigmented bacterium of the Proteobacteria phylum. Here, we present the draft genome sequence of Polaromonas sp. strain CG9_12, isolated from an Antarctic supraglacial stream.
Genome sequence of Janthinobacterium sp. CG23_2, a violacein-producing isolate from an Antarctic supraglacial stream.
(2016-01) Smith, Heidi J.; Foreman, Christine M.; Akiyama, Tatsuya; Franklin, Michael J.; Devitt, N. P.; Ramaraj, Thiruvarangan
Here, we present the draft genome sequence for the violacein-producing Janthinobacterium sp. CG23_2 isolated from an Antarctic supraglacial stream. The genome is ~7.85 Mb, with a G+C content of 63.5%. The genome includes 7,247 candidate protein coding genes, which may provide insight into UV tolerance mechanisms.
Janthinobacterium CG23_2: comparative genome analysis reveals enhanced environmental sensing and transcriptional regulation for adaptation to life in an Antarctic supraglacial stream
(2019-10) Dieser, Markus; Smith, Heidi J.; Ramaraj, Thiruvarangan; Foreman, Christine M.
As many bacteria detected in Antarctic environments are neither true psychrophiles nor endemic species, their proliferation in spite of environmental extremes gives rise to genome adaptations. Janthinobacterium sp. CG23_2 is a bacterial isolate from the Cotton Glacier stream, Antarctica. To understand how Janthinobacterium sp. CG23_2 has adapted to its environment, we investigated its genomic traits in comparison to genomes of 35 published Janthinobacterium species. While we hypothesized that genome shrinkage and specialization to narrow ecological niches would be energetically favorable for dwelling in an ephemeral Antarctic stream, the genome of Janthinobacterium sp. CG23_2 was on average 1.7 ± 0.6 Mb larger and predicted 1411 ± 499 more coding sequences compared to the other Janthinobacterium spp. Putatively identified horizontal gene transfer events contributed 0.92 Mb to the genome size expansion of Janthinobacterium sp. CG23_2. Genes with high copy numbers in the species-specific accessory genome of Janthinobacterium sp. CG23_2 were associated with environmental sensing, locomotion, response and transcriptional regulation, stress response, and mobile elements—functional categories which also showed molecular adaptation to cold. Our data suggest that genome plasticity and the abundant complementary genes for sensing and responding to the extracellular environment supported the adaptation of Janthinobacterium sp. CG23_2 to this extreme environment.