Theses and Dissertations


Alka Tiwari

Issuing Body

Mississippi State University


Shan, Xueyan

Committee Member

Ma, Din-Pow

Committee Member

Williams, W. Paul

Committee Member

Brown, Ashli

Committee Member

Perkins, Andy D.

Date of Degree


Document Type

Dissertation - Open Access


Molecular Biology

Degree Name

Doctor of Philosophy


College of Agriculture and Life Sciences


Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology


Plant breeders have focused on improving maize resistance to Aspergillus flavus infection and aflatoxin accumulation by breeding with genotypes having the desirable traits. Various maize inbred lines have been developed for the breeding of resistance. Identification of differentially expressed proteins among such maize inbred lines will facilitate the development of gene markers and expedite the breeding process. Computational biology and proteomics approaches on the investigation of differentially expressed proteins were explored in this research. The major research objectives included 1) application of computational methods in homology and comparative modeling to study 3D protein structures and identify single nucleotide polymorphisms (SNPs) involved in changes of protein structures and functions, which can in turn increase the efficiency of the development of DNA markers; 2) investigation of methods on total protein profiling including purification, separation, visualization, and computational analysis at the proteome level. Special research goals were set on the development of open source computational methods using Matlab image processing tools to quantify and compare protein expression levels visualized by 2D protein electrophoresis gel techniques.