Biomedical subjects

Bhaskar D Kulkarni

Publications and source records attributed to Bhaskar D Kulkarni.

5 recordsLinked to original sources

PubMed2005

A support vector machine-based method for predicting the propensity of a protein to be soluble or to form inclusion body on overexpression in Escherichia coli.

MOTIVATION: Inclusion body formation has been a major deterrent for overexpression studies since a large number of proteins form insoluble inclusion bodies when overexpressed in Escherichia coli. The formation of inclusion bodies is known to be an outcome of improper protein folding; thus the composition and arrangement of amino acids in the proteins would be a major influencing factor in deciding its aggregation propensity. There is a significant need for a prediction algorithm that would enable the rational identification of both mutants and also the ideal protein candidates for mutations that would confer higher solubility-on-overexpression instead of the presently used trial-and-error procedures. RESULTS: Six physicochemical properties together with residue and dipeptide-compositions have been used to develop a support vector machine-based classifier to predict the overexpression status in E.coli. The prediction accuracy is approximately 72% suggesting that it performs reasonably well in predicting the propensity of a protein to be soluble or to form inclusion bodies. The algorithm could also correctly predict the change in solubility for most of the point mutations reported in literature. This algorithm can be a useful tool in screening protein libraries to identify soluble variants of proteins.

Algorithms↗

PubMed2005

Identification of coding and non-coding sequences using local Holder exponent formalism.

MOTIVATION: Accurate prediction of genes in genomes has always been a challenging task for bioinformaticians and computational biologists. The discovery of existence of distinct scaling relations in coding and non-coding sequences has led to new perspectives in the understanding of the DNA sequences. This has motivated us to exploit the differences in the local singularity distributions for characterization and classification of coding and non-coding sequences. RESULTS: The local singularity density distribution in the coding and non-coding sequences of four genomes was first estimated using the wavelet transform modulus maxima methodology. Support vector machines classifier was then trained with the extracted features. The trained classifier is able to provide an average test accuracy of 97.7%. The local singularity features in a DNA sequence can be exploited for successful identification of coding and non-coding sequences. CONTACT: Available on request from bd.kulkarni@ncl.res.in.

Algorithms↗

PubMed2003

Artificial neural networks for prediction of mycobacterial promoter sequences.

A multilayered feed-forward ANN architecture trained using the error-back-propagation (EBP) algorithm has been developed for predicting whether a given nucleotide sequence is a mycobacterial promoter sequence. Owing to the high prediction capability ( congruent with 97%) of the developed network model, it has been further used in conjunction with the caliper randomization (CR) approach for determining the structurally/functionally important regions in the promoter sequences. The results obtained thereby indicate that: (i) upstream region of -35 box, (ii) -35 region, (iii) spacer region and, (iv) -10 box, are important for mycobacterial promoters. The CR approach also suggests that the -38 to -29 region plays a significant role in determining whether a given sequence is a mycobacterial promoter. In essence, the present study establishes ANNs as a tool for predicting mycobacterial promoter sequences and determining structurally/functionally important sub-regions therein.

Base Sequence↗

PubMed2003

Statistical analysis of the physico-chemical data on the coastal waters of Cochin.

Measurements of temperature, salinity, dissolved oxygen, nitrogen as ammonia, nitrate and nitrite, and phosphate along with chlorophyll were carried out at three stations on the coastal waters of Cochin, south west India, at two-levels of the water column over a period of five years. The data set has been factorised using principal component analysis (PCA) for extracting linear relationships existing among a set of variables. A graphical display of the scores generated from the PCA was done by means of boxplots and biplots, which helped in the interpretation of the data. The major factors conditioning the system are related to the input of fresh water from the estuary of the Periyar river and the high organic load of the bottom sediment in the coastal area which results in a reducing environment, as reflected in the parameters of dissolved oxygen, ammoniacal-nitrogen and nitrite-nitrogen. Another factor which contributes to the variation in the system is related to the unloading activity in the port area. The present approach presents a logical way to interpret the complex data of the physico-chemical measurements.

Ammonia↗

PubMedDate not supplied

Genetic programming assisted stochastic optimization strategies for optimization of glucose to gluconic acid fermentation.

This article presents two hybrid strategies for the modeling and optimization of the glucose to gluconic acid batch bioprocess. In the hybrid approaches, first a novel artificial intelligence formalism, namely, genetic programming (GP), is used to develop a process model solely from the historic process input-output data. In the next step, the input space of the GP-based model, representing process operating conditions, is optimized using two stochastic optimization (SO) formalisms, viz., genetic algorithms (GAs) and simultaneous perturbation stochastic approximation (SPSA). These SO formalisms possess certain unique advantages over the commonly used gradient-based optimization techniques. The principal advantage of the GP-GA and GP-SPSA hybrid techniques is that process modeling and optimization can be performed exclusively from the process input-output data without invoking the detailed knowledge of the process phenomenology. The GP-GA and GP-SPSA techniques have been employed for modeling and optimization of the glucose to gluconic acid bioprocess, and the optimized process operating conditions obtained thereby have been compared with those obtained using two other hybrid modeling-optimization paradigms integrating artificial neural networks (ANNs) and GA/SPSA formalisms. Finally, the overall optimized operating conditions given by the GP-GA method, when verified experimentally resulted in a significant improvement in the gluconic acid yield. The hybrid strategies presented here are generic in nature and can be employed for modeling and optimization of a wide variety of batch and continuous bioprocesses.

Artificial Intelligence↗