Biology subjects

Banik, S.

Publications and source records attributed to Banik, S..

7 recordsLinked to original sources

bioRxiv2026

Subcellular pharmacology of a novel cell-permeable fluorescent phosphodiesterase inhibitor using advanced fluorescence microscopy

Direct visualisation of drug-target engagement within living cells remains a major challenge. Here we develop a cell-permeable fluorogenic analogue of the phosphodiesterase 4 (PDE4) inhibitor rolipram (MAN193), generated by conjugation to fluorescein diacetate. Following intracellular activation, the probe functions as a near-neutral PDE4 antagonist and enables direct visualisation of endogenous PDE4 populations. Using advanced fluorescence spectroscopy imaging approaches, including molecular brightness analysis and fluorescence anisotropy imaging, we demonstrate rolipram-displaceable binding of the analogue to cytosolic PDE4 and resolve thesubcellular distribution of binding sites. We further show that the probe enables visualisation of untagged PDE4 at focal adhesion complexes in cardiomyocyte-like cells. Together these findings establish fluorogenic drug conjugation combined with quantitative spectroscopy imaging as a generalisable strategy to map intracellular drug-target engagement with subcellular resolution, providing an effective framework for interrogating the spatial pharmacology of small molecules in living systems.

biophysics↗

bioRxiv2024

Improved protein binder design using -pairing targeted RFdiffusion

Despite recent advances in the computational design of protein binders, designing proteins that bind with high affinity to polar protein targets remains an outstanding problem. Here we show that RFdiffusion can be conditioned to efficiently generate protein scaffolds that form geometrically matched extended beta-sheets with target protein edge beta-strands in which polar groups on the target are nearly perfectly complemented with hydrogen bonding groups on the design. We use this approach to design binders against a set of therapeutically relevant polar targets (KIT, PDGFR[a], ALK-2, ALK-3, FCRL5, and NRP1) and find that beta-strand-targeted design yields higher affinities and success rates than unconditioned RFdiffusion. All by all binding experiments show that the designs have affinities ranging from 137 pM to mid nM for their targets and essentially no off target binding despite the sharing of beta-strand interactions, likely reflecting the precise customization of interacting beta-strand geometry and additional designed binder-target interactions. A co-crystal structure of one such design in complex with the KIT receptor is nearly identical to the computational design model confirming the accuracy of the design approach. The ability to robustly generate binders displaying high affinity and specificity to polar interaction surfaces with exposed beta-strands considerably increases the range and capabilities of computational binder design.

biochemistry↗

bioRxiv2023

Characterization of B646L (p72) gene and the resistance pattern of African swine fever Virus tolerant to indigenous Doom Pig breeds of India

African Swine Fever (ASF) has affected all pig breeds in North-East India since 2020, except Doom pigs, a unique indigenous breed from Assam and the closest progenitor to Indian wild pigs, resulting in significant economic losses for pig farmers in the region. Based on the complete sequences of the B646L (p72) gene, it has been determined that the virus responsible for the outbreak is ASFV genotype II. The further characterization of three complete sequences of the B646L (p72) gene established 100% identical with other existing sequences of different parts of the world as well as confirmed that there is no co-circulation of different genotypes of ASFV in India except genotype II. Present studies also corroborate that MYD88, LDHB and IFIT1 were important genes of the immune system involved in the pathogenesis of ASFV. The differential expression patterns of these genes in ASFV-infected survived, and healthy Doom breed pigs, compared to healthy control pigs, were studied to distinguish the expression pattern at different stages. The hardiness and ability of the Doom pig to withstand common pig diseases, along with its genetic resemblance to wild pigs, make it an ideal candidate for studying tolerance to ASFV infection. So, the present study investigates the natural resistance to ASF in Doom pigs from an endemic area in North-East India to support the proposition that Doom pigs can co-exist with virulent ASFVs recently break in North-East India. The results of this study also provide important molecular insights into the regulation of the ASFV-tolerant gene. ImportanceStudying the natural resistance to African Swine Fever (ASF) in Doom pigs from North-East India holds crucial importance. ASF has inflicted significant economic losses on pig farmers in the region, necessitating the identification and comprehension of factors contributing to resistance and tolerance in specific pig breeds such as Doom pigs. Understanding the molecular mechanisms and genetic factors associated with ASFV tolerance could help in breeding programs and the selection of resilient pig breeds, ultimately aiding in disease control efforts.

microbiology↗

bioRxiv2023

Mass spectrometric analysis and biostimulatory effects of boar seminal gel, saliva and semen in pigs

The present study aimed to identify novel biostimulatory compounds in boar seminal gel (SG), saliva and semen using Gas chromatography-mass spectrometry (GC-MS). SG alone and its combined application with saliva (SG+saliva) and semen (SG+semen) also studied to train young boars. SG alone and SG+Saliva investigated for estrus induction in gilts and sows. Distilled water (DW) exposure was kept as control. SG, saliva and semen screened for total 105, 96 and 89 compounds. The highest concentration was of alkanes followed by sugar alcohols, then hydrocarbons, amino acids and fatty acids. Elaidic acid is the novel compound identified in pigs. Other compounds were tridecenol, undecane, hexadecone, eicosane, tetracosane etc. Further, young males (64.86%) were able to get trained. Significant higher (p<0.05) number of males got trained in exposure to SG (80%), SG+saliva (75%) and SG+semen (75%) than control. The time (hrs) taken by young boars to get trained on exposure to combination of SG+saliva (244{+/-}22.19) and SG+semen (216{+/-}13.14) was lesser (p<0.05) than SG (356{+/-}61.85) alone. Interval (hrs) for exhibition of different sexual behaviour by males on exposure to SG, saliva and semen was lesser (p<0.05) than control. Estrus was induced in 61.25% of females. Significant (p<0.05) higher number of females showed estrus response to exposure of SG (72.72%) and SG+saliva (69.23%) than control. Interval taken to exhibit estrus was lesser (p<0.05) in females exposed to SG+saliva (201.88{+/-}12.66) than SG (262.14{+/-}20.06) alone. Interval (hrs) for exhibition of different sexual behaviour by females on exposure to SG+saliva was lesser (p<0.05) than control. In conclusion, novel compounds with biostimulatory properties have been identified in boar SG, saliva and semen. The combined exposure of SG with saliva and semen have more intense biostimulation effect than SG alone. Such compounds and biostimulatory effects can be exploited for augmenting reproductive efficiency in pigs.

animal behavior and cognition↗

bioRxiv2023

Hormonal Interventions for optimizing reproductive efficiency in pigs at Farmers field

ObjectiveOptimizing reproductive efficiency in terms of estrus induction and production performance using simplified hormonal intervention using GnRH, gonadotropins and progesterone at farmers field conditions to bred animals with superior quality semen and also to reduce the maintenance cost. MethodThe present study was planned for optimizing reproductive efficiency using four different easily available hormonal agents with simplified protocols at farmers field. A total of 126 females were used in the study. Hormonal protocols I, II, III and IV using GnRH + (PMSG+ hCG), (PMSG+ hCG), PMSG alone and prepared progesterone gel respectively were used for estrus induction in gilts and sows. ResultsThe estrus induction/rate was (77.77%, 81.36%, 78.57% and 50% respectively. The corresponding figures for interval (hrs) of heat exhibition from hormonal administration (121.33{+/-}4.93, 121.54{+/-}3.60, 78.52{+/-}4.52 and 192{+/-}24), conception rate (%) (72.22%, 81.25%, 68.18% and 33.33%) farrowing rate (55.55%, 68.29%, 68.18% and 33.33 %), total litter size at birth (7.2{+/-}0.64, 7.90{+/-}0.47, 8.90{+/-}0.47 and 7.00{+/-}0) and hormonal cost (Rs.) per animal (570, 335, 280 and 250 Rs.) were respectively. The easier to use protocol was III followed by II, I and IV. ConclusionIt was found that protocol II and III are effective and easier so can be used for optimizing reproductive efficiency in pigs at farmers field.

physiology↗

bioRxiv2023

Metagenomic analysis of Pigs' faecal microbiome and its functional response associated with dietary fibre

Pig husbandry is the most valued and economically sustainable husbandry in the livestock farming system. The performance and productivity of the pig are chiefly dependent on the nutritional factor steered by gut beneficial bacteria. The swine gut microbiome has a direct relationship with feed efficiency. As a consequence, identifying microbial taxonomy and functional capacity is critical for proper nutrient digestion. In the present investigation, eighteen grower pigs aged 3 months and weighing 30{+/-}0.55 kg were allocated into three different groups using a randomized block layout and supplemented with QPM maize fodder of 0, 5, and 10% to the basal diet by substituting (wt/wt on DM) the maize grains, and named as T0, T1, and T2 to probe the increase in gut beneficial bacteria found in the faecal contents. For comparison with T0, T1, and T2, a random faecal sample designated R was collected from six grower pigs of the same age group and bodyweight fed a maize-soya bean-based diet. The experiment is being carried out to investigate the effect of various maize fodder levels on the metagenomic profiles of pig gut microbiota using the 16S rRNA gene. All of the experimental diets were iso-nitrogenous, with protein content ranging from 18.37 to 18.63 per cent. The data generated by 16S rRNA amplicon analysis was 68, 56, 61, and 39 Mb in R, T0, T1, and T2 samples, respectively. From taxonomic distribution, bacterial phyla namely Firmicutes, Bacteroidetes, Proteobacteria, and Spirochetes are found in descending order of relative abundance in the R, T0, and T1 groups, respectively, while Spirochaetes, Proteobacteria, Fibrobacteres, Bacteroidetes, and Firmicutesare found in descending order of relative abundance in the T2 group. The relative profusion of Fibrobacter succinogenes is 0.89% and 16.84% in the T1 and T2 groups. According to the findings, a higher level of maize fodder in the diet of grower pigs promotes the growth of fibre-degrading bacteria in the gut microbiota, particularly Fibrobacter succinogenes. Moreover, feeding green maize has decreased the population of methanobacteria in the gut of pigs, which in turn has limited the production of methane.

genomics↗

bioRxiv2019

Spreading of a virulence lipid into host membranes promotes mycobacterial pathogenesis

Several virulence lipids populate the outer cell wall of pathogenic mycobacteria (Jackson, 2014). Phthiocerol dimycocerosate (PDIM), one of the most abundant outer membrane lipids (Anderson, 1929), plays important roles in both defending against host antimicrobial programs (Camacho et al., 2001; Cox et al., 1999; Murry et al., 2009) and in evading these programs altogether (Cambier et al., 2014a; Rousseau et al., 2004). Immediately following infection, mycobacteria rely on PDIM to evade toll-like receptor (TLR)-dependent recruitment of bactericidal monocytes which can clear infection (Cambier et al., 2014b). To circumvent the limitations in using genetics to understand virulence lipid function, we developed a chemical approach to introduce a clickable, semi-synthetic PDIM onto the cell wall of Mycobacterium marinum. Upon infection of zebrafish, we found that PDIM rapidly spreads into host epithelial membranes, and that this spreading inhibits TLR activation. PDIMs ability to spread into epithelial membranes correlated with its enhanced fluidity afforded by its methyl-branched mycocerosic acids. Additionally, PDIMs affinity for cholesterol promoted its occupation of epithelial membranes; treatment of zebrafish with statins, cholesterol synthesis inhibitors, decreased spreading and provided protection from infection. This work establishes that interactions between host and pathogen lipids influence mycobacterial infectivity and suggests the use of statins as tuberculosis preventive therapy by inhibiting PDIM spread.

microbiology↗