Biology subjects

Pant, A.

Publications and source records attributed to Pant, A..

25 records · Page 2Linked to original sources

bioRxiv2021

The endophilin curvature-sensitive motif requires electrostatic guidance to recycle synaptic vesicles in vivo

Curvature-sensing mechanisms assist proteins in executing particular actions on various membrane organelles. Here, we investigated the functional specificity of curvature-sensing amphipathic motifs through the study of endophilin, an endocytic protein for synaptic vesicle recycling. We generated chimeric endophilin proteins by replacing the endophilin amphipathic motif H0 with other curvature-sensing amphipathic motifs. We found that the role of amphipathic motifs cannot simply be extrapolated from the identity of their parental proteins. For example, the amphipathic motif of the nuclear pore complex protein NUP133 functionally replaced the synaptic role of endophilin H0. Interestingly, non-functional endophilin chimeras had similar defects - producing fewer synaptic vesicles but more endosomes - indicating that the curvature-sensing motifs in these chimeras have a common deficiency at reforming synaptic vesicles. Finally, we converted non-functional endophilin chimeras into functional proteins by changing the cationic property of amphipathic motifs, setting a precedent for reprogramming the functional specificity of curvature-sensing motifs in vivo.

cell biology↗

bioRxiv2021

Knockout of murine Lyplal1 confers sex-specific protection against diet-induced obesity

Human genome-wide association studies found SNPs near LYPLAL1 that have sex-specific effects on fat distribution and metabolic traits. To determine whether altering LYPLAL1 affects obesity and metabolic disease we created and characterized a mouse knockout of Lyplal1. Here we show that CRISPR-Cas9 whole-body Lyplal1 knockout (KO) mice fed a high fat, high sucrose (HFHS) diet showed sex-specific differences in weight gain and fat accumulation. Female, not male, KO mice weighed less than WT mice, had reduced body fat percentage, white fat mass, and adipocyte diameter not accounted for by changes in metabolic rate. Female, but not male, KO mice had increased serum triglycerides, decreased aspartate, and alanine aminotransferase. Lyplal1 KO mice of both sexes have reduced liver triglycerides and steatosis. These diet-specific effects resemble the effects of SNPs near LYPLAL1 in humans, suggesting that LYPLAL1 has an evolutionary conserved sex-specific effect on adiposity. This murine model can be used to study this novel gene-by-sex-by-diet interaction to elucidate the metabolic effects of LYPLAL1 on human obesity.

biochemistry↗

bioRxiv2021

Perturbation of transmembrane 6 superfamily member 2 expression alters lipid metabolism in a human liver cell line

BackgroundNonalcoholic fatty liver disease (NAFLD) is caused by accumulation of excess lipids in hepatocytes. Genome wide association studies have identified strong association of NAFLD with non-synonymous E167K amino acid mutation in transmembrane 6 superfamily member 2 (TM6SF2) protein. The E167K mutation affects TM6SF2 stability and its carriers display increased hepatic lipids levels and lower serum triglycerides. While similar phenotype is evident in mice with TM6SF2 knockdown, effects of TM6SF2 on hepatic lipid metabolism is not completely understood. MethodsHere, we overexpressed wild-type or E167K variant of TM6SF2 or knocked down TM6SF2 expression in lipid-treated Huh-7 cells and used biochemical assays, untargeted lipidomic analysis, RNAseq transcriptome analysis and high-throughput fluorescent imaging to determine changes in lipid metabolism. ResultsBoth knockdown and E167K overexpression increased acylglyceride levels which was decreased by wild-type TM6SF2 overexpression. Further, mean intensity of individual lipid droplets was increased by E167K overexpression and knockdown while wild-type TM6SF2 had no effects. We also observed lipid chain remodeling for acylglycerides by TM6SF2 knockdown leading to a relative increase in species with shorter and more saturated side chains. RNA sequencing revealed differential expression of several lipid metabolizing genes, including genes belonging to AKR1 family and lipases, primarily in cells with TM6SF2 knockdown. ConclusionTaken together, our data shows that overexpression of TM6SF2 gene or its loss-of-function changes hepatic lipid species composition and expression of lipid metabolizing genes. Further, overexpression of E167K variant and TM6SF2 knockdown similarly increased hepatic lipid accumulation and lipid droplets profile further confirming a loss-of-function effect for variant.

cell biology↗

bioRxiv2021

Machine learning algorithms in big data analyses identify determinants of insulin gene transcription

Machine learning (ML)-workflows enable unprejudiced/robust evaluation of complex datasets. Here, we analyzed over 490,000,000 data points to compare 10 different ML-workflows in a large (N=11,652) training dataset of human pancreatic single-cell (sc-)transcriptomes to identify genes associated with the presence or absence of insulin transcript(s). Prediction accuracy/sensitivity of each ML-workflow were tested in a separate validation dataset (N=2,913). Ensemble ML-workflows, in particular Random Forest ML-algorithm delivered high predictive power (AUC=0.83) and sensitivity (0.98), compared to other algorithms. The transcripts identified through these analyses also demonstrated significant correlation with insulin in bulk RNA-seq data from human islets. The top-10 features, (including IAPP, ADCYAP1, LDHA and SST) common to the three Ensemble ML-workflows were significantly dysregulated in scRNA-seq datasets from Ire-1{beta}-/- mice that demonstrate dedifferentiation of pancreatic {beta}-cells in a model of type 1 diabetes (T1D) and in pancreatic single cells from individuals with type 2 Diabetes (T2D). Our findings provide direct comparison of ML-workflows in big data analyses, identify key determinants of insulin transcription and provide workflows for future analyses.

genetics↗

bioRxiv2020

CYCLODEXTRIN DERIVATIVE ENHANCES THE OPHTHALMIC DELIVERY OF POORLY SOLUBLE AZITHROMYCIN.

Azithromycin (AZM), a macrolide antibiotic used for the treatment of Chlamydial conjunctivitis, is less effective for the treatment of this disease due to its poor bioavailability (38%). Various alternatives have been developed for improving the physico-chemical properties (i.e., solubility) of the AZM without much success. To overcome the problems associated with AZM, an inclusion complex employing a modified cyclodextrin i.e., sulfobutylether-{beta}-cyclodextrin (SBE-{beta}-CD) was prepared and characterized by phase solubility studies, pXRD and FTIR techniques. The results portrayed the formation of the inclusion complex of AZM with sulfobutylether {beta}-cyclodextrin (SBE-{beta}-CD) in 1:2 molar stoichiometric ratios. This inclusion complex was later incorporated into a polymer matrix to prepare an in situ gel. Various combinations of carbopol 934P and hydroxypropyl methylcellulose (HPMC K4M) polymers were used and evaluated by rheological and in vitro drug release studies. The optimized formulation (F4), containing carbopol 934P 0.2% (w/v) and HPMC K4M 0.2% (w/v), was evaluated for clarity, pH, gelling capacity, drug content, rheological properties, in vitro drug release pattern, ocular irritation test and antimicrobial efficacy. Finally, owing to the improved antimicrobial efficacy and increased residence time, AZM:SBE-{beta}-CD in situ gel was found to be a promising formulation for the efficient treatment of bacterial ocular disease.

microbiology↗

bioRxiv2020

Repairing neural damage in a C. elegans chemosensory circuit using genetically engineered synapses

Neuronal loss can considerably diminish neural circuit function, impairing normal behavior by disrupting information flow in the circuit. We reasoned that by rerouting the flow of information in the damaged circuit it may be possible to offset these negative outcomes. We examined this possibility using the well-characterized chemosensory circuit of the nematode worm C. elegans. In this circuit, a main sensory neuron class sends parallel outputs to several interneuron classes. We found that the removal of one of these interneuron classes impairs chemotaxis to attractive odors, revealing a prominent path for information flow in the circuit. To alleviate these deficiencies, we sought to reinforce a remaining neural pathway. We used genetically engineered electrical synapses for this purpose, and observed the successful recovery of chemotaxis performance. However, we were surprised to find that the recovery was largely mediated by inadvertently formed left-right lateral electrical connections within individual neuron classes. Our analysis suggests that these additional electrical synapses help restore circuit function by amplifying weakened neuronal signals in the damaged circuit. These results demonstrate the power of genetically engineered synapses to regulate information flow and signal intensity in damaged neural circuits.

neuroscience↗

bioRxiv2018

Asparagine availability is an essential limiting factor for poxvirus protein synthesis

Virus actively interfaces with host metabolism because viral replication relies on host cells to provide nutrients and energy. For efficient viral replication in culture, vaccinia virus (VACV; the prototype poxvirus) prefers glutamine to glucose, to the extent that in glutamine-free medium, VACV replication is inefficient. Remarkably, VACV replication can be fully rescued from glutamine depletion by asparagine supplementation. By global metabolic profiling, genetic and chemical intervening of asparagine supply, we provide evidence demonstrating that the requirement of asparagine for efficient viral replication accounts for VACVs preference of glutamine to glucose, rather than because glutamine is superior to glucose in feeding the tricarboxylic acid (TCA) cycle. Further, we show that asparagine availability is a critical factor for efficient viral protein synthesis. Our study highlights that the asparagine metabolism, whose regulation has been evolutionarily tailored in mammalian cells, presents a critical barrier to poxvirus replication, suggesting new directions of anti-viral strategy development.

microbiology↗