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Computational, genetic and biochemic...

Jovanovic, Oliver Svetozar.

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Computational, genetic and biochemical analysis of broad host-range plasmid RK2.

Record Type:	Language materials, printed : Monograph/item
Title/Author:	Computational, genetic and biochemical analysis of broad host-range plasmid RK2./
Author:	Jovanovic, Oliver Svetozar.
Description:	162 p.
Notes:	Adviser: David H. Figurski.
Contained By:	Dissertation Abstracts International63-04B.
Subject:	Biology, Genetics. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3048161
ISBN:	0493624783

Computational, genetic and biochemical analysis of broad host-range plasmid RK2.
Jovanovic, Oliver Svetozar.

Computational, genetic and biochemical analysis of broad host-range plasmid RK2. - 162 p.

Adviser: David H. Figurski.

Thesis (Ph.D.)--Columbia University, 2002.

The computational methods developed here can be more generally applied, and their usefulness in the analysis of other genomes has already been demonstrated.

ISBN: 0493624783Subjects--Topical Terms:

1017730
Biology, Genetics.

Computational, genetic and biochemical analysis of broad host-range plasmid RK2.
LDR:03262nam 2200325 a 45 001 927708
005 20110425
008 110425s2002 eng d
020 $a 0493624783
035 $a (UnM)AAI3048161
035 $a AAI3048161
040 $a UnM $c UnM
100 1 $a Jovanovic, Oliver Svetozar. $3 1251271
245 1 0 $a Computational, genetic and biochemical analysis of broad host-range plasmid RK2.
300 $a 162 p.
500 $a Adviser: David H. Figurski.
500 $a Source: Dissertation Abstracts International, Volume: 63-04, Section: B, page: 1681.
502 $a Thesis (Ph.D.)--Columbia University, 2002.
520 $a The computational methods developed here can be more generally applied, and their usefulness in the analysis of other genomes has already been demonstrated.
520 $a One of the most challenging problems faced by biology in coming years will be the task of successfully analyzing and understanding the exponentially increasing amount of sequence data being generated. As an increasing number of genomes is sequenced, the development of techniques and tools to analyze this mass of data becomes even more critical.
520 $a The broad host-range plasmid RK2, a member of incompatibility group P alpha (IncP alpha), provides a perfect system with which to develop and test such tools. The plasmid is a large, independent replicon whose 60,099 by sequence has been fully determined.
520 $a I therefore set out to test and develop a set of computational techniques with which to analyze the sequence of RK2, then follow the results of the sequence analysis with genetic and biochemical experiments to test the accuracy of the predictions of the analysis. Where currently available software and methodology were lacking, I developed new techniques and software. As my computational analysis began to uncover interesting features, I confirmed their existence genetically and biochemically, and carried out experiments to further elucidate their functions and roles on RK2.
520 $a With this approach, I have been able to demonstrate the following: (1) RK2 encodes a unique single-stranded DNA-binding (SSB) protein. The RK2 SSB is distantly related to the <italic>E. coli</italic> SSB and belongs to a family of IncP alpha SSBs. I found a related family of SSBs on IncP beta plasmids. (2) RK2 encodes a small regulatory RNA, <italic>korE</italic>, which is involved in the regulation of gene expression. (3) RK2 encodes an open reading frame (ORF) whose product has significant similarity (56% identity) to a portion of the TrwC helicase of plasmid R388. (4) Several important RK2 promoters were identified: The <italic>trbA</italic> promoter, the <italic> trbB</italic> promoter and the <italic>korE</italic> promoter. These findings demonstrate the strength of using a combined computational, genetic and biochemical approach, since none of these features had previously been identified by strictly genetic and biochemical approaches.
590 $a School code: 0054.
650 4 $a Biology, Genetics. $3 1017730
650 4 $a Biology, Microbiology. $3 1017734
690 $a 0369
690 $a 0410
710 2 0 $a Columbia University. $3 571054
773 0 $t Dissertation Abstracts International $g 63-04B.
790 $a 0054
790 1 0 $a Figurski, David H., $e advisor
791 $a Ph.D.
792 $a 2002
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3048161