Biology subjects

Bansal, M.

Publications and source records attributed to Bansal, M..

5 recordsLinked to original sources

bioRxiv2018

Microbial metabolite deoxycholic acid controls Clostridium perfringens-induced chicken necrotic enteritis through attenuating cyclooxygenase signaling

Clostridium perfringens-induced necrotic enteritis (NE) has reemerged as a prevalent chicken disease worldwide due to reduced usage of prophylactic antibiotics. The lack of antimicrobial alternative strategies to control NE is mainly due to limited insight into the disease pathogenesis. The aim of this study is to investigate the role of microbiota metabolic product secondary bile acid deoxycholic acid (DCA) on preventing NE. C. perfringens growth was inhibited by 82.8% in 50 M DCA Tryptic Soy Broth. Sequential Eimeria maxima and C. perfringens challenges induced acute NE showed as severe intestinal inflammation and body weight (BW) loss in broiler chickens, while 1.5 g/kg DCA diet dramatically reduced the disease. At the cellular level, DCA alleviated NE-associated ileal epithelial death and reduced lamina propria cell apoptosis. Interestingly, DCA reduced C. perfringens invasion into ileum without altering the bacterial ileal luminal colonization. Molecular analysis showed that DCA reduced inflammatory mediators of Inf{gamma}, Litaf, and Mmp9 mRNA accumulation in ileal tissue. Mechanism studies revealed that C. perfringens induced elevated expression of inflammatory mediators of Inf{gamma}, Litaf, Mmp9, and Ptgs2 (Cyclooxygenase- 2 (COX-2) gene) in chicken splenocytes. Blocking COX signaling by pharmacological inhibitor aspirin attenuated INF{gamma}-induced inflammatory response in the splenocytes. Consistent with the in vitro assay, chickens fed 0.12 g/kg aspirin diet protected the birds against NE-induced ileal inflammation, intestinal cell apoptosis, and BW loss. In conclusion, microbial metabolic product DCA prevents NE-induced ileal inflammation and BW loss through attenuating inflammatory response. These novel findings offer new strategies against C. perfringens-induced diseases.\n\nSignificance StatementWidespread antimicrobial resistance has become a serious challenge to both agricultural and healthcare industries. Withdrawing antimicrobials without effective alternatives exacerbates chicken productivity loss at billions of dollars every year, caused by intestinal diseases, such as coccidiosis-and C. perfringens-induced necrotic enteritis. This study revealed that microbial metabolic product secondary bile acid DCA prevents C. perfringens-induced intestinal disease in chickens through modulating inflammatory COX signaling pathways. Therefore, microbiome and its downstream targets of host inflammatory responses could be used to control NE. These findings have opened new avenues for developing novel antimicrobial free alternatives to prevent or treat C. perfringens-induced diseases.

microbiology↗

bioRxiv2018

Towards a universal structural and energetic model for prokaryotic promoters

With almost no consensus promoter sequence in prokaryotes, recruitment of RNA polymerase (RNAP) to precise transcriptional start sites (TSSs) has remained an unsolved puzzle. Uncovering the underlying mechanism is critical for understanding the principle of gene regulation. We attempted to search the hidden code in ~16500 promoters, of twelve prokaryotes representing two kingdoms, in their structure and energetics. Twenty eight fundamental parameters of DNA structure including backbone angles, base pair axis, inter base pair and intra base pair parameters were used and information was extracted from X-ray crystallography (XRC) data. Three parameters (solvation energy, hydrogen bond energy and stacking energy) were selected for creating energetics profiles using in-house programs. DNA was found to be inherently designed to undergo a change in every parameter undertaken, from some distance upstream of TSSs to adopt a signature state at these locations in all prokaryotes. These signature states might be the universal hidden codes recognised by RNAP. This observation was reiterated when randomly selected promoter sequences (with little sequence conservation) were subjected to structure generation; all developed into very similar three dimensional structures, quite distinct from those of conventional B-DNA and coding sequences. Fine structural details at important motifs (viz. -11, -35, -75 positions relative to TSS) of promoters reveal novel and pointed insights for RNAP interaction at these locations; it could be correlated that how some particular structural changes at -11 region may allow insertion of RNAP amino acids in inter-base pair space as well as facilitate the flipping out of bases from DNA duplex.

genomics↗

bioRxiv2018

Elucidating synergistic dependencies in lung adenocarcinoma by proteome-wide signaling-network analysis

Signaling pathway models are largely based on the compilation of literature data from heterogeneous cellular contexts. Indeed, de novo reconstruction of signaling interactions from large-scale molecular profiling is still lagging, compared to similar efforts in transcriptional and protein-protein interaction networks. To address this challenge, we introduce a novel algorithm for the systematic inference of protein kinase pathways, and applied it to published mass spectrometry-based phosphotyrosine profile data from 250 lung adenocarcinoma (LUAD) samples. The resulting network includes 43 TKs and 415 inferred, LUAD-specific substrates, which were validated at >60% accuracy by SILAC assays, including \"novel substrates of the EGFR and c-MET TKs, which play a critical oncogenic role in lung cancer. This systematic, data-driven model supported drug response prediction on an individual sample basis, including accurate prediction and validation of synergistic EGFR and c-MET inhibitor activity in cells lacking mutations in either gene, thus contributing to current precision oncology efforts.

systems biology↗

bioRxiv2018

Transcriptional deconvolution reveals consistent functional subtypes of pancreatic cancer epithelium and stroma

Bulk tumor tissues comprise intermixed populations of neoplastic cells and multiple lineages of stromal cells. We used laser capture microdissection and RNA sequencing to disentangle the transcriptional programs active in the malignant epithelium and stroma of pancreatic ductal adenocarcinoma (PDA). This led to the development of a new algorithm (ADVOCATE) that accurately predicts the compartment fractions of bulk tumor samples and can computationally purify bulk gene expression data from PDA. We also present novel stromal subtypes, derived from 110 microdissected PDA stroma samples, that were enriched in extracellular matrix- and immune-associated processes. Finally, we applied ADVOCATE to systematically evaluate cross-compartment subtypes spanning four patient cohorts, revealing consistent functional classes and survival associations despite substantial compositional differences.

systems biology↗

bioRxiv2018

Microbiota metabolic product deoxycholic acid controls chicken necrotic enteritis

Necrotic enteritis (NE) caused by Clostridium perfringens infection has reemerged as a prevalent poultry disease worldwide due to reduced usage of prophylactic antibiotics. The lack of alternative antimicrobial strategies to control this disease is mainly due to limited insight into NE pathogenesis, microbiome relationships, and host responses. Here we reported that the metabolic byproduct of microbial metabolism of bile acids to deoxycholic acid (DCA), at as low as 50 M, inhibited 82.8% of C. perfringens growth in Tryptic Soy Broth (P < 0.05). Sequential Eimeria maxima and C. perfringens challenge strongly induced NE, severe intestinal inflammation, and body weight (BW) loss in broiler chickens. These negative effects were diminished by 1.5 g/kg DCA diet. At the cellular level, DCA alleviated NE-associated ileal epithelial death and lamina propria immune cell apoptosis. Interestingly, DCA reduced C. perfringens invasion into villi without significantly altering the bacterial luminal colonization. Molecular analysis showed that DCA reduced inflammatory mediators of Inf{gamma}, Litaf (Tnf), Il1{beta}, and Mmp9 mRNA accumulation in ileal tissue. Mechanically, C. perfringens induced elevated expression of inflammatory cytokines of Inf{gamma}, Litaf, and Ptgs2 (COX-2 gene) in chicken splenocytes. Inhibiting the COX signaling by aspirin attenuated INF{gamma}- or TNFa-induced inflammatory response in the splenocytes. Consistently, chickens fed 0.12 g/kg aspirin diet resisted against NE-induced BW loss, ileal inflammation, and villus apoptosis. In conclusion, microbial metabolic product DCA prevents NE-induced BW loss and ileal inflammation through curbing inflammatory response. These novel findings could serve as a stepping-stone for developing next generation antimicrobial alternatives against NE.

microbiology↗