Towards finding the linkage between metabolic and age-related disorders using semantic gene data network analysis

Pathway based therapeutic targets identification and development of an interactive database CampyNIBase of Campylobacter jejuni RM1221 through non-redundant protein dataset

The bacterial species Campylobacter jejuni RM1221 (CjR) is the primary cause of campylobacteriosis which poses a global threat for human health. Over the years the efficacy of antibiotic treatment is becoming more fruitless due to the development of multiple drug resistant strains. Therefore, identification of new drug targets is a valuable tool for the development of new treatments for affected patients and can be obtained by targeting essential protein(s) of CjR. We conducted this in silico study in order to identify therapeutic targets by subtractive CjR proteome analysis. The most important proteins of the CjR proteome, which includes chokepoint enzymes, plasmid, virulence and antibiotic resistant proteins were annotated and subjected to subtractive analyses to filter out the CjR essential proteins from duplicate or human homologous proteins. Through the subtractive and characterization analysis we have identified 38 eligible therapeutic targets including 1 potential vaccine target. Also, 12 potential targets were found in interactive network, 5 targets to be dealt with FDA approved drugs and one pathway as potential pathway based drug target. In addition, a comprehensive database 'CampyNIBase' has also been developed. Besides the results of this study, the database is enriched with other information such as 3D models of the identified targets, experimental structures and Expressed Sequence Tag (EST) sequences. This study, including the database might be exploited for future research and the identification of effective therapeutics against campylobacteriosis. URL: (http://nib.portal.gov.bd/site/page/4516e965-8935-4129-8c3f-df95e754c562#Banner).

Exploring Genomic Variants Related to Residual Feed Intake in Local and Commercial Chickens by Whole Genomic Resequencing

Improving feed efficiency is a major goal in poultry production to reduce production costs and increase profitability. The genomic variants and possible molecular mechanisms responsible for residual feed intake (RFI) in chickens, however, remain poorly understood. In this study, using both local and commercial breeds, genome re-sequencing of low RFI and high RFI chickens was performed to elucidate the genomic variants underlying RFI. Results showed that 8,505,214 and 8,479,041 single nucleotide polymorphisms (SNPs) were detected in low and high RFI Beijing-You chickens, respectively; 8,352,008 and 8,372,769 SNPs were detected in low- and high-RFI Cobb chickens, respectively. Through a series of filtering processes, 3746 candidate SNPs assigned to 1137 genes in Beijing-You chickens and 575 candidate SNPs (448 genes) in Cobb chickens were found. The validation of the selected 191 SNPs showed that 46 SNPs were significantly associated with the RFI in an independent population of 779 Cobb chickens, suggesting that the method of screening associated SNPs with whole genome sequencing (WGS) strategy was reasonable. Functions annotation of RFI-related genes indicated that genes in Beijing-You were enriched in lipid and carbohydrate metabolism, as well as the phosphatase and tensin homolog (PTEN) signaling pathway. In Cobb, however, RFI-related genes were enriched in the feed behavior process and cAMP responsive element binding protein (CREB) signaling pathway. For both breeds, organismal development physiological processes were enriched. Correspondingly, NOS1, PHKG1, NEU3 and PIP5K1B were differentially expressed in Beijing-You, while CDC42, CSK, PIK3R3, CAMK4 and PLCB4 were differentially expressed in Cobb, suggesting that these might be key genes that contribute to RFI. The results of the present study identified numerous novel SNPs for RFI, which provide candidate biomarkers for use in the genetic selection for RFI. The study has improved knowledge of the genomic variants and potential biological pathways underlying RFI in chickens.

Finding Potential Therapeutic Targets against Shigella flexneri through Proteome Exploration

Background:Shigella flexneri is a gram negative bacteria that causes the infectious disease “shigellosis.” S. flexneri is responsible for developing diarrhea, fever, and stomach cramps in human. Antibiotics are mostly given to patients infected with shigella. Resistance to antibiotics can hinder its treatment significantly. Upon identification of essential therapeutic targets, vaccine and drug could be effective therapy for the treatment of shigellosis.

Methods: The study was designed for the identification and qualitative characterization for potential drug targets from S. flexneri by using the subtractive proteome analysis. A set of computational tools were used to identify essential proteins those are required for the survival of S. flexneri. Total proteome (13,503 proteins) of S. flexneri was retrieved from NCBI and further analyzed by subtractive channel analysis. After identification of the metabolic proteins we have also performed its qualitative characterization to pave the way for the identification of promising drug targets.

Results: Subtractive analysis revealed that a list of 53 targets of S. flexneri were human non-homologous essential metabolic proteins that might be used for potential drug targets. We have also found that 11 drug targets are involved in unique pathway. Most of these proteins are cytoplasmic, can be used as broad spectrum drug targets, can interact with other proteins and show the druggable properties. The functionality and drug binding site analysis suggest a promising effective way to design the new drugs against S. flexneri.

Conclusion: Among the 53 therapeutic targets identified through this study, 13 were found highly potential as drug targets based on their physicochemical properties whilst only one was found as vaccine target against S. flexneri. The outcome might also be used as module as well as circuit design in systems biology.