Information Theory and Multivariate Techniques for Analyzing DNA Sequence Data: An Example from Tomato Genes

oai:nepjol.info:article/3867DNA and amino acid sequences are alphabetic symbols having no underlying metric. Use of information theory is one of the solutions for sequence metric problems. The reflection of DNA sequence complexity in phenotype stability might be useful for crop improvement. Shannon-Weaver index (Shannon Entropy, H\u27) and mutual information (MI) index were estimated from DNA sequences of 22 genes, consisted of two gene families of tomato, namely disease resistance and fruit quality. Main objective was use of information theory and multivariate techniques to understand diversity among genes and relate the sequence complexity with phenotypes. The normalized H\u27 value ranged from 0.429 to 0.461. The highest diversity was observed in the gene Crtr-B (beta carotene hydroxylase). Two principal components which accounted for 36.65% variation placed these genes into four groups. Groupings of these genes by both principal component and cluster analyses showed clearly the similarity at phenotypes levels within cluster. Sequences similarity among genes was observed within a family. Diversity assessment of genes applying information theory should link to understand the sequences complexity with respect to gene stability for example stability of resistance gene.Key words: Diversity analysis; DNA sequences; principal component analysis; tomato genesNepal Journal of Biotechnology, 2011, Vol. 1, No. 1 pp.1-

In vitro cultivation and regeneration of Solanum melongena (L.) using stem, root and leaf explants

The treatment combinations was BAP (0, 2.0, 3.0 and 4.0 mg/L) and NAA (0, 0.1, 0.5, and 1.0 mg/L). The rate of callus formation varied in different treatments. The highest amount of callus (48.66%) was produced on MS medium containing 2.0 mg/l BAP and 0.5 mg/l NAA from stem and 8.2 days required for callus induction. The number of shoot regenerated through callus from stem containing 2.0 mg/l BAP and 0.5 mg/l NAA was 3.4 (23.287%) and days required for 38.8 days. Key words: Regeneration; BAP; NAA. Nepal Journal of Biotechnology. Jan. 2011, Vol. 1, No. 1 : 49-5

Development of PCR assay for targeting partial lipL21 and lipL41 gene of leptospira

Leptospirosis is a bacterial zoonotic disease caused by spirochetes of the genus Leptospira that affects human and a wide range of animals. The direct method of diagnosis of leptospirosis, has been so far by culture isolation but it is time consuming and potentially biohazardous. Another traditional method is the detection of antibodies (Serological tests) which is also a time consuming method and fails to identify the infecting serovar. To overcome these limitations associated with the cultivation and serology, we developed PCR assay targeting partial lipL21 gene and lipL41 gene of Leptospires using in-house designed P28/29 and P30/31 primers, with a product size of 385bp and 427bp. The amplicons were subjected to restriction enzyme digestion using RsaI, Pvu II and HindIII for product of P28/29 and ClaI, TaqI and RsaI were used for product of P30/31. The protocols were standardized and the assay targeting the partial lipL21 and lipL41 gene was found to be specific for eight pathogenic Leptospires out of nine leptospires tested. The products were then cloned in pGEMT Easy vector and sequenced to facilitate further studies. PCR could detect the target bacterial gene without any ambiguity and showed good efficiency in detection of targeted species in the sample. This simple, rapid and cost-effective method can be applicable in a prediction system to prevent disease outbreak by these Leptospira species and can be considered as an effective tool for disease diagnosis of Leptospira species. Key words: PCR; lipL21; lipL41; Molecular Diagnostics; Transformation. Nepal Journal of Biotechnology. Jan. 2011, Vol. 1, No. 1 : 22-3

Race for Excellence

Nepal Journal of Biotechnology. Jan. 2011, Vol. 1, No.

Biotechnology Growth Partnership: A Potential Flagship Program in S&T

Nepal Journal of Biotechnology. Jan. 2011, Vol. 1, No. 1 : 55-5

Analysis of KatG Ser315Thr Mutation in Multidrug Resistant Mycobacterium tuberculosis and SLC11A1 Polymorphism in Multidrug Resistance Tuberculosis in Central Development Region of Nepal Using PCR-RFLP Technique: A Pilot Study

Ser315Thr mutations in genes encoding the mycobacteria catalase-peroxidase (KatG) has been associated with the major resistance to isoniazid (INH) in Mycobacterium tuberculosis (MTB). Also G/C polymorphisms in INT4 region of the solute carrier family 11 member 1 gene (SLC11A1) and susceptibility towards tuberculosis (TB) has been demonstrated worldwide. 24 drug resistant MTB culture positive samples and 24 whole?blood samples were collected from different TB patients of Central Development Region of Nepal in 2009. A Polymerase Chain Reaction (PCR) - Restriction Fragment Length Polymorphism (RFLP) assay was carried out in order to investigate Ser315Thr KatG mutation and G/C polymorphism in INT4 region. 4 (16.67%) samples out of 24 MTB culture samples demonstrated the Ser315Thr KatG mutation whereas none of the 24 whole blood samples were found to contain G/C polymorphism in INT4. Though no significant correlation could be found between INT4 polymorphism and TB susceptibility, overall scenario of Nepal cannot be drawn from this data. Molecular diagnostic technique such as PCR-RFLP can be used in a robust scale to carry out base line studies in the TB population of Nepal. Key words: Multi?drug resistance; Tuberculosis; PCR; RFLP Nepal Journal of Biotechnology. Jan. 2011, Vol. 1, No. 1 : 14-2

Information Theory and Multivariate Techniques for Analyzing DNA Sequence Data: An Example from Tomato Genes

oai:nepjol:article/3867DNA and amino acid sequences are alphabetic symbols having no underlying metric. Use of information theory is one of the solutions for sequence metric problems. The reflection of DNA sequence complexity in phenotype stability might be useful for crop improvement. Shannon-Weaver index (Shannon Entropy, H') and mutual information (MI) index were estimated from DNA sequences of 22 genes, consisted of two gene families of tomato, namely disease resistance and fruit quality. Main objective was use of information theory and multivariate techniques to understand diversity among genes and relate the sequence complexity with phenotypes. The normalized H' value ranged from 0.429 to 0.461. The highest diversity was observed in the gene Crtr-B (beta carotene hydroxylase). Two principal components which accounted for 36.65% variation placed these genes into four groups. Groupings of these genes by both principal component and cluster analyses showed clearly the similarity at phenotypes levels within cluster. Sequences similarity among genes was observed within a family. Diversity assessment of genes applying information theory should link to understand the sequences complexity with respect to gene stability for example stability of resistance gene.Key words: Diversity analysis; DNA sequences; principal component analysis; tomato genesNepal Journal of Biotechnology, 2011, Vol. 1, No. 1 pp.1-

Molecular differences between GM- and non-GM crops over-estimated?

Peer reviewed contribution available on the following websites:Public Research Initiative: www.pubresreg.orgEuropean Federation of Biotechnology: http://www.efb-central.org/Nepal Journal of Biotechnology. Jan. 2011, Vol. 1, No. 1 : 31-4