Biology subjects

Goswami, P.

Publications and source records attributed to Goswami, P..

8 recordsLinked to original sources

bioRxiv2026

Production of a resilient biosurfactant using agro-wastes and Paenibacillus dendritiformis isolated from petroleum-contaminated soil: a break-even analysis at pilot scale

Wastes from mustard oil mills and dairy were used as partial replacement of pure reagents in modified Bushnell and Haas broth media for production of biosurfactant by Paenibacillus dendritiformis isolated from petroleum-contaminated soil. The process was optimised by construction of a response model using Taguchi experimental design, leading to a 28.23% increase in performance characteristics and a 13.23 % increase in yield of biosurfactant. The optimized production medium consisted of carbon @7.9 %, nitrogen @ 1.1% and agitation rate 180 r.p.m. This was provided by adding glucose @ 2%, ammonium nitrate @0.2%, mustard oil seed meal @10% and whey@ 10% in modified Bushnell Haas broth. The biosurfactant produced retained its properties during exposure to a wide range of pH values (5-11), high temperatures (up to 121C), high salinities of up to 5% and also five -fold concentration. Approximately three- fold increase in yield of the biosurfactant (25g/L to 68.5g/L) was obtained upon scaling-up the production from 100ml to 1500 ml in a lab scale fermenter with agitation @ 150r.p.m. and D.O. levels maintained at 6mg/L. Power calculations and the cost thereof was calculated (Rs 10.24 /L) and summed up with the cost of raw materials Rs 8.40/L and found to be Rs 18.64/L of product .Since 68.5g product is present in 1L, the cost is calculated to be Rs 271/- per kg. Comparison with selling price of currently used chemical surfactants like Linear Alkyl Benzene sulphonic acid (LAB) and sodium Lauryl sulphate and Sodium Lauryl ether sulphate (SLS and SLES) reveals that prices of these products varies from Rs 120 to 600 per kg depending on manufacturer and quality, order quantity. From the above studies it can be seen that production and use of this multiutility biosurfactant has, besides a clear advantage over chemically produced surfactants in terms of sustainability, a fairly good comparison with selling price of currently used chemical surfactants. The present study on the production costs (excluding capital costs) successfully demonstrates a break even analysis into the production of biosurfactants.

microbiology↗

bioRxiv2026

Remodelling of chromatin architecture and super-enhancer landscape in lamin A/C depleted HGSOC

Lamins are nuclear intermediate filament proteins that maintain nuclear architecture through interactions with the chromatin. The A- and B-type lamins tether the genome at the peripheral lamina underlying the inner nuclear membrane in the form of heterochromatic lamina-associated domains (LADs). However, LADs associated with A-type lamins are confined not only to lamina but also to the nuclear core, thereby pointing to their distinct and multifarious roles in chromatin organisation and regulation. Previous studies involving lamin B1 depletion depicted the detachment of LADs from the nuclear periphery, accompanied by alteration of chromatin distribution while preserving the topologically associating domains (TADs) in structurally intact form. In this piece of work, we have shown, for the first time in HGSOC, the effects of lamin A/C knockdown on chromatin organisation, which was characterised by significant detethering of gene-poor chromatin from the periphery along with active (A) to inactive (B) compartment switching. This was associated with a rewiring of oncogenic super-enhancer elements corroborated by the differential gene expression profile. Overall analysis tipped the scale in favour of reduced cellular proliferation upon lamin A/C knockdown. This finding was strengthened by the observed proliferative potential of spheroids ex vivo and tumours in a mouse xenograft model.

cancer biology↗

bioRxiv2026

Quantitative Deciphering of Mammalian Histamine Receptors through Mathematical Genomics

Histamine receptors (HRH1-HRH4) are G-protein coupled receptors (GPCRs) that mediate essential physiological functions, including neurotransmission, gastric acid secretion, immune regulation, and presynaptic autoregulation. Despite their importance, systematic comparative analyses across mammalian histamine receptor sequences remain scarce. In this study, we performed a comprehensive evaluation of HRH1-HRH4 across multiple mammalian species, integrating sequence homology, invariant residue mapping, amino acid substitutions, compositional frequencies, Shannon entropy, polystring distributions, intrinsic disorder profiling, and phylogenetic clustering. HRH2 and HRH1 were highly conserved among primates, HRH3 showed strong cohesion within rodents, while HRH4 exhibited pronounced divergence consistent with immune-related specialization. Invariant residues localized to transmembrane helices and activation motifs (D107, W428/Y431, NPxxY), underscoring strict evolutionary constraints on ligand binding, receptor stability, and G-protein coupling. Substitutions were confined to non-essential lipid-facing and loop regions, predominantly conservative in nature, enabling diversification without disrupting the GPCR fold. Amino acid frequency and entropy analyses revealed hydrophobic dominance with subtype-specific enrichment of polar residues, while disorder profiling identified HRH1 as the most dynamic and HRH2 as the most structurally constrained. Polystring analysis highlighted conserved motifs (WWW, PP) alongside subtype- and species-specific repeats, reflecting evolutionary strategies balancing receptor stability with adaptive flexibility. Phylogenetic clustering confirmed subtype-specific cohesion, with HRH3 and HRH4 forming compact clades, HRH1 showing moderate dispersion, and HRH2 forming the most isolated cluster. Collectively, these findings demonstrate that mammalian histamine receptor evolution is governed by conserved biophysical cores and selective variability, offering insights into structural conservation, functional diversification, and translational relevance for drug design and model selection.

bioinformatics↗

bioRxiv2024

Analysis of FAIMS for the Study of Affinity-Purified Protein Complexes Using the Orbitrap Ascend Tribrid Mass Spectrometer

In this study, we analyzed the combination of affinity purification mass spectrometry (AP-MS) with high-field asymmetric waveform ion mobility spectrometry (FAIMS), integrated between nanoLC-MS and an Orbitrap Ascend Tribrid Mass Spectrometer. Our primary objective was to evaluate the application of the FAIMS interface for detecting affinity purified SAP25 protein complexes with enhanced sensitivity and robustness. As a result, we observed that nanoLC-FAIMS-MS (with FAIMS) significantly improved the sensitivity and detection limits at the protein level, peptide level and significantly reduced chemical contaminants compared to nanoLC-MS alone without FAIMS (No FAIMS). This FAIMS configuration resulted in 42% and 92% increases for the total proteins and unique proteins, respectively, and 44% and 88% increases for total peptides and unique peptides compared to the No FAIMS configuration. Our in-depth comparison of FAIMS and No FAIMS shows that FAIMS outperforms by significantly reducing the missing value by <15% in datasets and plays a significant role in filtering chemical contaminants. Our findings highlight the potential of FAIMS with Orbitrap Ascend Tribrid Mass Spectrometer to enhance the depth of AP-MS analysis. The data were deposited with the MASSIVE repository with the identifier MSV000096548.

systems biology↗

bioRxiv2024

The under-recognized dominance of magnetosome gene cluster-containing bacteria in oxygen-stratified freshwater ecosystems

Magnetotactic bacteria (MTB) capable of magnetosome organelle biomineralization and magnetotaxis are widespread in chemically stratified aquatic environments. Conventionally, it has long been considered that the overall abundance of MTB in microbiota is not very high and that Magnetococcia is the most frequently identified and predominant MTB members. However, the diversity and distribution of MTB in chemically stratified environments remain elusive due to the lack of large-scale systematic analyses. Here we conduct a comprehensive survey of genomes containing magnetosome gene clusters (MGCs), a group of genes responsible for magnetosome biomineralization and magnetotaxis, in 267 metagenomes from 38 oxygen-stratified freshwater environments. A total of 63 MGC-containing genomes belonging to eight bacterial phyla are reconstructed, including the newly identified Myxococcota. We discover an unexpectedly high relative abundance of putative MTB (up to 15.4% of metagenomic reads) in hypoxic and anoxic water columns, in which Deltaproteobacteria, rather than traditionally considered Magnetococcia, are the most ubiquitous and predominant MGC-containing bacteria. Our analysis reveals a depth-specific taxonomy and function of MGC-containing bacteria in stratified water columns shaped by physicochemical conditions. These findings underscore the unrecognized ecophysiological importance of MTB in freshwater ecosystems.

microbiology↗

bioRxiv2024

Distinct regions within SAP25 recruit O-linked glycosylation, DNA demethylation, and ubiquitin ligase and hydrolase activities to the Sin3/HDAC complex

Epigenetic control of gene expression is crucial for maintaining gene regulation. Sin3 is an evolutionarily conserved repressor protein complex mainly associated with histone deacetylase (HDAC) activity. A large number of proteins are part of Sin3/HDAC complexes, and the function of most of these members remains poorly understood. SAP25, a previously identified Sin3A associated protein of 25 kDa, has been proposed to participate in regulating gene expression programs involved in the immune response but the exact mechanism of this regulation is unclear. SAP25 is not expressed in HEK293 cells, which hence serve as a natural knockout system to decipher the molecular functions uniquely carried out by this Sin3/HDAC subunit. Using molecular, proteomic, protein engineering, and interaction network approaches, we show that SAP25 interacts with distinct enzymatic and regulatory protein complexes in addition to Sin3/HDAC. While the O-GlcNAc transferase (OGT) and the TET1 /TET2/TET3 methylcytosine dioxygenases have been previously linked to Sin3/HDAC, in HEK293 cells, these interactions were only observed in the affinity purification in which an exogenously expressed SAP25 was the bait. Additional proteins uniquely recovered from the Halo-SAP25 pull-downs included the SCF E3 ubiquitin ligase complex SKP1/FBXO3/CUL1 and the ubiquitin carboxyl-terminal hydrolase 11 (USP11), which have not been previously associated with Sin3/HDAC. Finally, we use mutational analysis to demonstrate that distinct regions of SAP25 participate in its interaction with USP11, OGT/TETs, and SCF(FBXO3).) These results suggest that SAP25 may function as an adaptor protein to coordinate the assembly of different enzymatic complexes to control Sin3/HDAC-mediated gene expression.

biochemistry↗

bioRxiv2023

Swi4-dependent SWI4 transcription couples cell size to cell cycle commitment

Growth-dependent accumulation of the limiting SBF transcription factor, composed of Swi4 and Swi6, occurs in G1 phase in budding yeast and is limiting for commitment to division, termed Start. Here we measure size-dependence of Swi4 protein copy number under different genetic contexts using the scanning number and brightness technique. Mutation of SBF binding sites in the SWI4 promoter or disruption of SBF activation resulted in [~]33-50% decrease in Swi4 accumulation rate and concordantly increased cell size at Start. Ectopic inducible expression of Swi4 in G1 phase cells increased production of Swi4 from the endogenous promoter, upregulated transcription of the G1/S regulon, and accelerated Start. Despite the potential for Swi4 positive feedback, G1 phase Swi4 accumulation was linear unless the Whi5 transcriptional repressor was inactivated. A threshold model in which Swi4 titrates SBF binding sites in G1/S promoters predicted the effects of nutrients, ploidy, and G1/S regulatory mutations on cell size. These results exemplify how transcription factor auto-production can contribute to a cell state transition.

cell biology↗

bioRxiv2022

SARS-CoV-2 Infects Peripheral and Central Neurons of Mice Before Viremia, Facilitated by Neuropilin-1

Neurological symptoms associated with COVID-19, acute and long-term, suggest SARS-CoV-2 affects both central and peripheral nervous systems. Although studies have shown olfactory and hematogenous entry into the brain and neuroinflammation, little attention has been paid to the susceptibility of the peripheral nervous system to infection or to alternative routes of CNS invasion. We show that neurons in the central and peripheral nervous system are susceptible to productive infection with SARS-CoV-2. Infection of K18-hACE2 mice, wild-type mice, golden Syrian hamsters, and primary neuronal cultures demonstrate viral RNA, protein, and infectious virus in peripheral nervous system neurons and satellite glial cells, spinal cord, and specific brain regions. Moreover, neuropilin-1 facilitates SARS-CoV-2 neuronal infection. Our data show that SARS-CoV-2 rapidly invades and establishes a productive infection in the peripheral and central nervous system via direct invasion of neurons prior to viremia, which may underlie some cognitive and sensory symptoms associated with COVID-19.

neuroscience↗