Soft Computing Approach for Optimization of siRNA Efficiency Prediction for Post-transcriptional Gene Silencing

Post-transcriptional gene silencing by RNA interference is mediated by small interfering RNA called siRNA. This gene silencing mechanism can be exploited therapeutically to a wide variety of disease-associated targets, especially in AIDS, neurodegenerative diseases, cholesterol and cancer on mice with the hope of extending these approaches to treat humans. Over the recent past, a significant amount of work has been undertaken to understand the gene silencing mediated by exogenous siRNA. The design of efficient exogenous siRNA sequences is challenging because of many issues related to siRNA. While designing efficient siRNA, target mRNAs must be selected such that their corresponding siRNAs are likely to be efficient against that target and unlikely to accidentally silence other transcripts due to sequence similarity. So before doing gene silencing by siRNAs, it is essential to analyze their off-target effects in addition to their inhibition efficiency against a particular target. Hence designing exogenous siRNA with good knock-down efficiency and target specificity is an area of concern to be addressed. Some methods have been developed already by considering both inhibition efficiency and off-target possibility of siRNA against agene. Out of these methods, only a few have achieved good inhibition efficiency, specificity and sensitivity. The main focus of this thesis is to develop computational methods to optimize the efficiency of siRNA in terms of “inhibition capacity and off-target possibility” against target mRNAs with improved efficacy, which may be useful in the area of gene silencing and drug design for tumor development. This study aims to investigate the currently available siRNA prediction approaches and to devise a better computational approach to tackle the problem of siRNA efficacy by inhibition capacity and off-target possibility. The strength and limitations of the available approaches are investigated and taken into consideration for making improved solution. Thus the approaches proposed in this study extend some of the good scoring previous state of the art techniques by incorporating machine learning and statistical approaches and thermodynamic features like whole stacking energy to improve the prediction accuracy, inhibition efficiency, sensitivity and specificity. Here, we propose one Support Vector Machine (SVM) model, and two Artificial Neural Network (ANN) models for siRNA efficiency prediction. In SVM model, the classification property is used to classify whether the siRNA is efficient or inefficient in silencing a target gene. The first ANNmodel, named siRNA Designer, is used for optimizing the inhibition efficiency of siRNA against target genes. The second ANN model, named Optimized siRNA Designer, OpsiD, produces efficient siRNAs with high inhibition efficiency to degrade target genes with improved sensitivity-specificity, and identifies the off-target knockdown possibility of siRNA against non-target genes. The models are trained and tested against a large data set of siRNA sequences. The validations are conducted using Pearson Correlation Coefficient, Mathews Correlation Coefficient, Receiver Operating Characteristic analysis, Accuracy of prediction, Sensitivity and Specificity. It is found that the approach, OpsiD, is capable of predicting the inhibition capacity of siRNA against a target mRNA with improved results over the state of the art techniques. Also we are able to understand the influence of whole stacking energy on efficiency of siRNA. The model is further improved by including the ability to identify the “off-target possibility” of predicted siRNA on non-target genes. Thus the proposed model, OpsiD, can predict optimized siRNA by considering both “inhibition efficiency on target genes and off-target possibility on non-target genes”, with improved inhibition efficiency, specificity and sensitivity. Since we have taken efforts to optimize the siRNA efficacy in terms of “inhibition efficiency and offtarget possibility”, we hope that the risk of “off-target effect” while doing gene silencing in various bioinformatics fields can be overcome to a great extent. These findings may provide new insights into cancer diagnosis, prognosis and therapy by gene silencing. The approach may be found useful for designing exogenous siRNA for therapeutic applications and gene silencing techniques in different areas of bioinformatics.

Studies on Soft Bycatch Reduction Devices for Selective Trawling

Trawling, though an efficient method of fishing, is known to be one of the most non-selective methods of fish capture. The bulk of the wild caught penaeid shrimps landed in India are caught by trawling.In addition to shrimps, the trawler fleet also catches considerable amount of non-shrimp resources. The term bycatch means that portion of the catch other than target species caught while fishing, which are either retained or discarded. Bycatch discards is a serious problem leading to the depletion of the resources and negative impacts on biodiversity. In order to minimize this problem, trawling has to be made more selective by incorporating Bycatch Reduction Devices (BRDs). There are several advantages in using BRDs in shrimp trawling. BRDs reduce the negative impacts of shrimp trawling on marine community. Fishers could benefit economically from higher catch value due to improved catch quality, shorter sorting time, lower fuel costs, and longer tow duration. Adoption of BRDs by fishers would forestall criticism by conservation groups against trawling.

Study of cyclohexanol decomposition reaction over the ferrospinels, A1−xCuxFe2O4 (A=Ni or Co and x=0, 0.3, 0.5, 0.7 and 1), prepared by ‘soft’ chemical methods

Preparation of simple and mixed ferrospinels of nickel, cobalt and copper and their sulphated analogues by the room temperature coprecipitation method yielded fine particles with high surface areas. Study of the vapour phase decomposition of cyclohexanol at 300 °C over all the ferrospinel systems showed very good conversions yielding cyclohexene by dehydration and/or cyclohexanone by dehydrogenation, as the major products. Sulphation very much enhanced the dehydration activity over all the samples. A good correlation was obtained between the dehydration activities of the simple ferrites and their weak plus medium strength acidities (usually of the Brφnsted type) determined independently by the n-butylamine adsorption and ammonia-TPD methods. Mixed ferrites containing copper showed a general decrease in acidities and a drastic decrease in dehydration activities. There was no general correlation between the basicity parameters obtained by electron donor studies and the ratio of dehydrogenation to dehydration activities. There was a leap in the dehydrogenation activities in the case of all the ferrospinel samples containing copper. Along with the basic properties, the redox properties of copper ion have been invoked to account for this added activity.

Surface properties and catalytic activity of ferrospinels of nickel, cobalt and copper, prepared by soft chemical methods

Ferrospinels of nickel, cobalt and copper and their sulphated analogues were prepared by the room temperature coprecipitation route to yield samples with high surface areas. The intrinsic acidity among the ferrites was found to decrease in the order: cobalt> nickel> copper. Sulphation caused an increase in the number of weak and medium strong acid sites, whereas the strong acid sites were left unaffected. Electron donor studies revealed that copper ferrite has both the highest proportion of strong sites and the lowest proportion of weak basic sites. All the ferrite samples proved to be good catalysts for the benzoy lation of toluene with benzoyl chloride. copper and cobalt ferrites being much more active than nickel ferrite. The catalytic activity for benzoylation was not much influenced by sulphation, but it increased remarkably with calcination temperature of the catalyst. Surface Lewis acid sites, provided by the octahedral cations on the spinel surface, are suggested to be responsible for the catalytic activity for the benzoylation reaction.

“Reconstruction of Gene Regulatory Network from Expression Profile of Plasma RNA Data of Colorectal Cancer Patients using Soft Computing Techniques”

Microarray data analysis is one of data mining tool which is used to extract meaningful information hidden in biological data. One of the major focuses on microarray data analysis is the reconstruction of gene regulatory network that may be used to provide a broader understanding on the functioning of complex cellular systems. Since cancer is a genetic disease arising from the abnormal gene function, the identification of cancerous genes and the regulatory pathways they control will provide a better platform for understanding the tumor formation and development. The major focus of this thesis is to understand the regulation of genes responsible for the development of cancer, particularly colorectal cancer by analyzing the microarray expression data. In this thesis, four computational algorithms namely fuzzy logic algorithm, modified genetic algorithm, dynamic neural fuzzy network and Takagi Sugeno Kang-type recurrent neural fuzzy network are used to extract cancer specific gene regulatory network from plasma RNA dataset of colorectal cancer patients. Plasma RNA is highly attractive for cancer analysis since it requires a collection of small amount of blood and it can be obtained at any time in repetitive fashion allowing the analysis of disease progression and treatment response.