A Parallel Computational Approach for String Matching- A Novel Structure with Omega Model

In r e cent day2019;s parallel string matching problem catch the attention of so many researchers because of the importance in different applications like IRS, Genome sequence, data cleaning etc.,. While it is very easily stated and many of the simple algorithms perform very well in practice, numerous works have been published on the subject and research is still very active. In this paper we propose a omega parallel computing model for parallel string matching. The algorithm is designed to work on omega model pa rallel architecture where text is divided for parallel processing and special searching at division point is required for consistent and complete searching. This algorithm reduces the number of comparisons and parallelization improves the time efficiency. Experimental results show that, on a multi - processor system, the omega model implementation of the proposed parallel string matching algorithm can reduce string matching time

Evolutionary genomics of dynamic sex chromosomes in the Salicaceae

Identifying the sex-determination region (SDR) and other genomic features of sex chromosomes are of great importance in the studies of the evolution of sex. However, the process of accurately identifying the size and location of the SDR is often difficult, even when a genomic sequence is available. This usually is hindered by large repetitive elements and a lack of recombination in the SDR. In this thesis, I assemble sex chromosomes with whole genomic sequencing data, identify SDRs and explore their genomic features in two sister species from the Salicaceae family. I also develop an interpretation of the lability of the sex configuration in the two species. In Chapter 2, I use quantitative trait locus mapping and a genome-wide association study to characterize the genomic composition of the SDR in a reference genome derived a female Salix purpurea clone. I show that the SDR in S. purpurea has a female heterogametic (ZW) system on chromosome 15. The SDR is inferred to be between 5 to 7 Mb long and overlapping with the centromere. This SDR has several classic features like reduced recombination and high structural polymorphism. Intriguingly, chromosome 19 contains sex-associated markers, which raises the possibility of a translocation of the SDR within the Salicaceae lineage. In Chapter 3, I improve the quality of assembly of sex chromosomes in S. purpurea with long-reads sequencing data and a modified map. Using an improved assembly of the SDR, I show that two consecutive palindromes span over a region of 200 kb, with conspicuous 20 kb stretches of highly conserved homologous sequences among the four arms in the female-specific regions of the SDR. Comparison to the genome of a closely related species S. suchowensis provides evidence for gene conversion occurring among the palindrome arms. The hypothesis of the translocation of the SDR within the Salicaceae could not be rejected. In Chapter 4, I use a similar strategy from Chapter 3 to study the SDR of a male Populus trichocarpa clone. I show that the SDR in P. trichocarpa has a male heterogametic (XY) system on chromosome 19. A cluster of inverted repeats that are homologous with a response regulator gene is present in the male-specific region in the SDR. This research provides important genomic resources for futures studies in these two species as well as the evolution of SDRs in the Salicaceae

LOCAL AND GLOBAL GENE REGULATION ANALYSIS OF THE AUTOINDUCER-2 MEDIATED QUORUM SENSING MECHANISM IN ESCHERICHIA COLI

The term `quorum sensing' (QS) is used to define a population density based communication mechanism which uses chemical signal molecules called autoinducers to trigger unique and varied changes in gene expression. Although several communication methods have been identified in bacteria that are unique to a particular species, one type of signal molecule, autoinducer-2 (AI-2) is linked to interspecies communication, indicating its potential as a universal signal for cueing a QS response among multiple bacterial types. In E. coli, AI-2 acts as an effector by binding to the QS repressor LsrR. As a result, LsrR unbinds and relieves repression of the lsr regulon, stimulating a subsequent QS gene expression cascade. In this dissertation, LsrR structure and in vitro binding activity are examined. Genomic binding and DNA microarray analyses are conducted and three novel sites putatively regulated by LsrR, yegE-udk, mppA and yihF, are revealed. Two cAMP receptor protein (CRP) binding locations in intergenic region of the lsr regulon are also confirmed. The role of each CRP site in divergent expression is qualified, indicating the lsr intergenic region to be a class III CRP-dependent promoter. Also, four specific DNA binding sites for LsrR in the lsr intergenic region are proposed, and reliance upon simultaneous binding to these various sites and the resulting effects on LsrR repression is presented. Finally, a complex model for regulation of the lsr regulon is depicted incorporating LsrR, CRP, DNA looping, and a predicted secondary layer of repression by an integration host factor (IHF)-like protein. Further understanding of this QS genetic mechanism may potentially be used for inhibiting bacterial proliferation and infection, modifying the natural genetic system to elicit alternate desired responses, or extracted and applied to a highly customizable and sensitive in vitro biosensor

Within-Genome Evolution of REPINs: a New Family of Miniature Mobile DNA in Bacteria

Repetitive sequences are a conserved feature of many bacterial genomes. While first reported almost thirty years ago, and frequently exploited for genotyping purposes, little is known about their origin, maintenance, or processes affecting the dynamics of within-genome evolution. Here, beginning with analysis of the diversity and abundance of short oligonucleotide sequences in the genome of Pseudomonas fluorescens SBW25, we show that over-represented short sequences define three distinct groups (GI, GII, and GIII) of repetitive extragenic palindromic (REP) sequences. Patterns of REP distribution suggest that closely linked REP sequences form a functional replicative unit: REP doublets are over-represented, randomly distributed in extragenic space, and more highly conserved than singlets. In addition, doublets are organized as inverted repeats, which together with intervening spacer sequences are predicted to form hairpin structures in ssDNA or mRNA. We refer to these newly defined entities as REPINs (REP doublets forming hairpins) and identify short reads from population sequencing that reveal putative transposition intermediates. The proximal relationship between GI, GII, and GIII REPINs and specific REP-associated tyrosine transposases (RAYTs), combined with features of the putative transposition intermediate, suggests a mechanism for within-genome dissemination. Analysis of the distribution of REPs in a range of RAYT–containing bacterial genomes, including Escherichia coli K-12 and Nostoc punctiforme, show that REPINs are a widely distributed, but hitherto unrecognized, family of miniature non-autonomous mobile DNA

Doctor of Philosophy

dissertationA small but growing number of bacteria and phages are known to contain linear, hairpin-ended genomes. The hairpin "protelomeres" are created by the action of a dedicated enzyme known as protelomerase that acts on a palindromic DNA target sequence. Phage protelomerases are typically longer than their bacterial counterparts and contain an additional far C-terminal region of limited sequence conservation. Studies of the protelomerase of the Klebsiella oxytoca phage ΦKO2 have shown that although the far C-terminal region is not required to produce hairpin ends, truncation of the region has a drastic effect on enzyme kinetics. To date, no other studies have been reported on the far C-terminal region of this or any other protelomerase. We present the solution structures of the far C-terminal regions of two phage protelomerases. The regions form homologous, compact structures that adopt a fold similar to the canonical double-stranded RNA-binding domain and have been called the far C-terminal domains. Sequence alignment and secondary structure predictions show that all known and putative phage protelomerases contain C-terminal regions which will almost certainly form homologous domains. A sequence comparison of these proteins with all known protelomerases is presented, along with an analysis of the sequence and structure of proteins which adopt a similar fold. Based on structure homology and comparative sequence conservation of key binding regions, we propose that the domain belongs to the growing family of three stranded β-sheet DNA-binding proteins that is a subclass of the double-stranded RNA-binding domain superfamily

Dagstuhl Reports : Volume 1, Issue 2, February 2011

Online Privacy: Towards Informational Self-Determination on the Internet (Dagstuhl Perspectives Workshop 11061) : Simone Fischer-Hübner, Chris Hoofnagle, Kai Rannenberg, Michael Waidner, Ioannis Krontiris and Michael Marhöfer Self-Repairing Programs (Dagstuhl Seminar 11062) : Mauro Pezzé, Martin C. Rinard, Westley Weimer and Andreas Zeller Theory and Applications of Graph Searching Problems (Dagstuhl Seminar 11071) : Fedor V. Fomin, Pierre Fraigniaud, Stephan Kreutzer and Dimitrios M. Thilikos Combinatorial and Algorithmic Aspects of Sequence Processing (Dagstuhl Seminar 11081) : Maxime Crochemore, Lila Kari, Mehryar Mohri and Dirk Nowotka Packing and Scheduling Algorithms for Information and Communication Services (Dagstuhl Seminar 11091) Klaus Jansen, Claire Mathieu, Hadas Shachnai and Neal E. Youn