Biology subjects

Shukla, S.

Publications and source records attributed to Shukla, S..

60 records · Page 4Linked to original sources

bioRxiv2020

Proteomics, lipidomics, metabolomics and 16S rDNA sequencing of dental plaque from patients with diabetes and periodontal disease

Oral microbiome influences human health, specifically pre- and type 2 diabetes (Pre-DM/DM) and periodontal diseases (PD), through complex microbial interactions. To explore these relations, we performed 16S rDNA sequencing, metabolomics, lipidomics, and proteomics analyses on supragingival dental plaque collected from individuals with Pre-DM/DM (n=39), Pre-DM/DM and PD (n=37), PD alone (n=11), or neither (n=10). We identified on average 2,790 operational taxonomic units and 2,025 microbial and host proteins per sample and quantified 110 metabolites and 415 lipids. Plaque samples from Pre-DM/DM patients contained higher abundance of Fusobacterium and Tannerella vs. plaques from metabolically healthy. Phosphatidylcholines, plasmenyl-phosphatidylcholines, ceramides containing non-OH fatty acids, and host proteins related to actin filament rearrangement were elevated in plaques from PD vs. non-PD. Cross-omic correlation analysis enabled the detection of a strong association between Lautropia and mono-methyl phophospotidlyethanolamine (PE-NMe), striking because synthesis of PE-NMe is uncommon in oral bacteria. Lipidomics analysis of in vitro cultures of Lautropia mirabilis confirmed the bacterias synthesis of PE-NMe. This comprehensive analysis revealed a novel microbial metabolic pathway and significant associations of host-derived proteins with PD.

systems biology↗

bioRxiv2020

Cellular internalization of Godanti Bhasma (anhydrous CaSO4) induces massive cytoplasmic reversible vacuolation and survival response of mammalian cells.

Bhasmas are Ayurvedic herbo-mineral formulations that have been used since ancient times for therapeutic benefits. Godanti Bhasma (GB) is an anhydrous calcium sulfate preparation processed by heating of gypsum powder with herbal extracts. Thermo-transformation of gypsum into the anhydrous GB was confirmed by Raman and FT-IR spectroscopy. GB particle showed size range of 0.5-5 {micro}m and neutral surface charge. Exposure to mammalian cells with GB particles showed massive vacuolation in their cytoplasm. Interestingly, no vacuolation was observed with parent gypsum particle. The result indicated that the cytoplasmic vacuolation by GB was due to its unique physicochemical property obtained during the thermo-transformation of gypsum. Using lysosomal inhibitors Bafilomycin A1 (BFA1) and Chloroquine (CQ), the process of vacuole formation was suppressed indicating GB induced vacuolation require acidic environment. The GB induced vacuolation was also found to follow dose and time dependent manner. Vacuolation often accompany with the sign of cell death whereas, in our study, massive vacuolation by GB did not induce any cell death. Moreover, GB treated cells survive with massive vacuolar process, which was reversed following post-treatment with vacuole inhibitors in GB treated cells, suggesting normal vacuolar function is essential for cell survival. Treatment of cells with GB was also found to induce translocation of LC3 protein from the nucleus to vacuolar membrane, indicating LC3 associated phagocytosis (LAP) is involved in the vacuolar process. Interestingly, the LAP function was found to be reversed in the cells treated with vacuole inhibitors. Our results provide a mechanistic correlation with GB induced vacuolation and associated LAP function, essential for cell survival. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=164 SRC="FIGDIR/small/930594v3_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@169ed89org.highwire.dtl.DTLVardef@169c339org.highwire.dtl.DTLVardef@900004org.highwire.dtl.DTLVardef@1f13823_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2019

Function of TRIP6 in brain-specific ciliogenesis

TRIP6, a member of the zyxin-family of LIM domain proteins, is a focal adhesion component. trip6 deletion in the mouse revealed, unexpectedly, in view of its ubiquitous expression, a function in the brain: ependymal and choroid plexus epithelial cells were poorly developed, carrying fewer and shorter cilia, and the mice developed hydrocephalus. TRIP6 disruption, via RNAi or inhibition of its homodimerization, in a choroid plexus epithelial cell line, confirmed its function in ciliogenesis. Zyxin-family members carry numerous protein interaction domains. In common with assembly of other multiprotein complexes, ciliogenesis may be facilitated by molecular assembly factors. Super-resolution microscopy demonstrated TRIP6 localization at the pericentriolar material and along the ciliary axoneme. The requirement for homodimerization which doubles its interaction sites, its punctate localization along the axoneme, and its co-localization with other cilia components suggest a scaffold/co-transporter function for TRIP6 in cilia. This is the first discovery of a protein assembly factor essential for mammalian ciliogenesis.

cell biology↗

bioRxiv2019

Asymmetric Tug-of-War leads to Cooperative Transport of a Cargo by Multiple Kinesins

How cargoes move within a crowded cell--over long distances and at speeds that are nearly the same as when moving on an unimpeded pathway--has long been mysterious. Through an in vitro gliding assay, which involves measuring nanometer displacement and piconewtons of force, we have evidence that when kinesins, a cytoplasmic molecular motor, operate in small groups, from 2-10, they can communicate among themselves through an asymmetric tug-of-war by inducing tension (up to 4 pN) on the cargo. Surprisingly, the primary role of approximately one-third of kinesins is to develop tension, which instantaneously slows forward motion but helps increase cargo run length. These hindering kinesins fall off rapidly when experiencing a forward tug. Occasionally, they may be ripped off from their anchors by other driving kinesins working in tandem. Furthermore, with roadblocks on the microtubule, multiple kinesins cooperate to overcome impediments. Hence, kinesin may employ an asymmetric tug-of-war and a cooperative motion to navigate through cellular environment.

biophysics↗

bioRxiv2018

A Novel Uranium Bioremediation Approach using Radioresistance Deinocoocus radiodurans Biofilm

Deinococcus radiodurans, is the most radiation tolerant organism ever known, it has gained importance in recent years as a potential candidate for bioremediation of heavy metals, especially radioactive ones. This study investigates the efficiency of a recombinant D. radiodurans (DR1-bf+) strain with an ability to form biofilm for uranium remediation. The modified Arsenazo III dye method was used to estimate the uranium concentration. Uranyl nitrate aqueous solution is generated during the operation of nuclear fuel reprocessing. The D. radiodurans biofilm (DR1-bf+) grown in the presence of 20 mM Ca2+ showed remarkable ability of uranyl ion removal. DR1-bf+ (+Ca2+) biofilm removed [~]75 {+/-} 2% of 1000 mg/L uranium within 30 minutes post treatment from uranyl nitrate aqueous solution. U removal rate was also found to be directly proportional to biofilm age. This study discusses the ability of D. radiodurans biofilm in uranium removal.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=88 SRC=\"FIGDIR/small/503896_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (34K):\norg.highwire.dtl.DTLVardef@1905462org.highwire.dtl.DTLVardef@93f7f6org.highwire.dtl.DTLVardef@7c6d1dorg.highwire.dtl.DTLVardef@dfb11f_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG

microbiology↗

bioRxiv2018

The landscape of antigen-specific T cells in human cancers

Antigen-specific T cells can be orchestrated to kill cancer cells in immunotherapies but the utilities of the TCR information have not been fully explored. Here, we leveraged previous efforts on tumor TCR repertoire, and developed a novel algorithm to characterize antigen-specific TCR clusters. Joint analysis with gene expression revealed novel regulators for T cell activation. Investigation of single-cell sequencing data revealed a novel subset of tissue-resident memory T cell population with elevated metabolic status. Integrative analysis of TCR clusters with HLA alleles and cancer genomics data identified candidate antigens derived from missense mutations, frameshift indels, and tumor-associated gene overexpression. Predicted antigen HSFX1 was further validated using vaccinated humanized HLA-A*02:01 mice. Finally, high abundant cancer-associated TCRs were observed in the blood repertoire of early breast cancer patients, suggesting new avenues for noninvasive early detection. Thus, our analysis identified cancer-associated T cells with broad utilities in immune monitoring and cancer immunotherapies.

bioinformatics↗