Biology subjects

Saxena, G.

Publications and source records attributed to Saxena, G..

6 recordsLinked to original sources

bioRxiv2024

Quantifying the ~75-95% of Peptides in DIA-MS Datasets that were not Previously Quantified

We demonstrate an algorithm termed GoldenHaystack (GH) that, compared to the leading DIA-MS algorithm, (a) quantifies and identifies with better FDR accuracy the peptides found in FASTA search spaces ([~]5-25% of analytes in DIA-MS datasets), (b) quantifies the remaining [~]75-95% of analytes that were previously unquantified, and (c) runs [~]40-200x faster (or [~]1-10x faster than the LC-MS). Specifically, without a FASTA or spectral library, GH can deconvolute and accurately quantify chimeric LC-MS spectra. The central idea that enables this claim is: for sufficiently sized projects (e.g., [≥] [~]50 LC-MS files), pairs of peptides that co-elute in one subset of LC-MS files do not exactly co-elute in a different subset of files. GH thus analyzes a project holistically: it uses multi-partite matching to match fragment ions across all samples, separates and regroups the fragment ions into unique analyte signatures, reduces stochastic noise, and then quantifies those unique analyte signatures.

bioinformatics↗

bioRxiv2024

Insights into the role of phosphorylation on microtubule crosslinking by PRC1

The mitotic spindle is composed of distinct networks of microtubules, including interpolar bundles that can bridge sister kinetochore fibers and bundles that organize the spindle midzone in anaphase. The crosslinking protein PRC1 can mediate such interactions between antiparallel microtubules. PRC1 is a substrate of mitotic kinases including CDK/cyclin-B, suggesting that it can be phosphorylated in metaphase and dephosphorylated in anaphase. How these biochemical changes to specific residues regulate its function and ability to organize bundles is not known. Here, we perform biophysical analyses on microtubule networks crosslinked by two PRC1 constructs, one a wild-type reflecting a dephosphorylated state, and one phosphomimetic construct with two threonine to glutamic acid substitutions near PRC1s microtubule binding domain. We find that the wild-type construct builds longer and larger bundles that form more rapidly and are much less resistant to mechanical disruption than the phosphomimetic PRC1. Interestingly, microtubule pairs organized by both constructs behave similarly within the same assays. Our results suggest that phosphorylation of PRC1 in metaphase would tune the protein to stabilize smaller and more flexible bundles, while removal of these PTMs in anaphase would favor the assembly of larger more mechanically robust bundles to resist chromosome and pole separation forces at the spindle midzone.

biophysics↗

bioRxiv2020

Integrative systems approach reveals dynamics of microbiome-metal-ion axis in mesocosms representing tropical urban freshwater canal ecosystem

Freshwater ecosystems of tropical urban canals systems (TrUCS), are highly dynamic and experience constant pressures from interspersed effects of land-use and rain. The dynamic nature of TrUCS ecosystems presents a unique opportunity to unravel the signature interactions between the macro-organisms (top-down), sedimentary microbial communities (SedMICs), their functioning and the geochemical environment (bottom-up). A systems level understanding of the molecular and mechanistic basis of the highly dynamic behaviour that leads to specific ecosystem outcomes, is currently lacking. Therefore, a research framework to identify the direct link between top-down and bottom-up ecological effects on SedMICs in a highly dynamic urban canal sedimentary system is needed. Here, we present a framework of integrated multi-dimensional data across system-level biotic and abiotic ecological descriptors, such as environmental variables and active SedMICs. We followed the ecosystem shifts after a natural disturbance (rain) in two different anthropogenic disturbance (land-use) regimes. Shifts in profiles of metabolically active community were conserved across different land-use types, indicating resilience to perturbation is an intrinsic property of the TrUCs ecosystem. Three distinct phases, which were dominated sequentially by autotrophy, anoxic-heterotrophy and oxic-heterotrophy, were identified within these shifts. The first two phases were influenced by the bottom-up effects of specific metal-ion combinations of nitrates and sulfates with magnesium, aluminum and iron, and the third phase was triggered by top-down influences of bioturbation. This generalized systems-level approach, which provides an ecosystem-centric understanding of TrUCS and integrates them in sustainable management practices, can also be extended to other freshwater ecosystems.

ecology↗

bioRxiv2020

A Simultaneous Methylome and Proteome Quantitative Workflow for Complex Samples

Proteoforms containing post-translational modifications (PTMs) represent a degree of functional diversity only harnessed through analytically precise simultaneous quantification of multiple PTMs. Here we present a method to accurately differentiate an unmodified peptide from its PTM-containing counterpart through data-independent acquisition-mass spectrometry, leveraging small precursor mass windows to physically separate modified peptidoforms from each other during MS2 acquisition. We utilize a lysine and arginine PTM-enriched peptide assay library and site localization algorithm to simultaneously localize and quantify seven PTMs including mono-, di-, and tri-methylation, acetylation, and succinylation in addition to total protein quantification in a single MS run without the need to enrich experimental samples. To evaluate biological relevance, this method was applied to liver lysate from differentially methylated non-alcoholic steatohepatitis (NASH) mouse models. We report altered methylation and acetylation together with total protein changes drive the novel hypothesis of a regulatory function of PTMs in protein synthesis and mRNA stability in NASH. Graphical Abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

systems biology↗

bioRxiv2019

Morpho-anatomical variation and their phylogenetic implications in native and exotic species of Pinus growing in the Indian Himalayas.

Pine is native to all continents and some oceanic islands of the northern hemisphere, chiefly in boreal, temperate or mountainous tropical regions; reaching its southernmost distribution below the equator in Southeast Asia. Pinus is divided into two subgenera, Strobus, and Pinus by the number of vascular bundles present in the needles. Comprehensive and detailed anatomy of needles in ten species of Pinus using nine anatomical traits was carried out. These morphological and anatomical traits supported the classification of the genus up to section level. It was observed that number of needles per fascicle varied along with other related traits such as thickness and width of vascular bundles, the diameter of resin ducts, the thickness of epidermis and thickness and width of endodermal cells that show remarkable variations among different species selected for the present study. The data can be used as a tool for identification and classification of Pinus upto genus and species level. We also found that similarity and differences in leaf anatomical traits supported the molecular phylogeny of Pinus conducted by several researchers.

plant biology↗

bioRxiv2019

Mathematical modeling of the role of α-synuclein and dopamine in cell death in Parkinson’s disease provides the molecular basis to the toxicity of different point mutations

Different types of -synuclein and non-{beta}-amyloid component (NAC) peptides have been shown to induce cell death, with varying degree of toxicity, in various in vitro experiments. Oxidative stress has also been associated and proved to be involved in the pathogenesis of neuronal cell death in Parkinsons disease. Oxidative stress has been shown to accelerate the aggregation of -synuclein in vitro and in resent studies -synuclein has been shown to increase oxidative stress. Thus it seems like a vicious cycle, one promoting the other.\n\nIn this present work we have modeled the -synuclein pathway to increase cytoplasmic Dopamine concentration, and thereby increasing the Reactive Oxygen Species (ROS) level of the cell, which consequently results in cell death. This model relates the -synuclein concentration with the fractional cell survival and provides insight of crucial reaction(s) of -synuclein which promote cell death. It predicts the toxicity of the type of -synuclein and also explains the pattern of cell death with increasing concentration of -synuclein. First we modeled a part of the pathway i.e. from dopamine to cell death. The results were compared with experimental data available for PC12 neuronal cell line. Then modeling of full pathway was done and the results were compared with experimental data available for Human neuroblastoma SH-SY5Y cells. It is predicted from this model that higher the auto catalysis of dopamine, higher is the cell death. Interestingly, the model predicts that NAC (1-18) not only hinders the vesicles coming from Endoplasmic Reticulum, to fuse with Golgi bodies, but also reduces the synthesis of Dopamine and the formation of vesicles from Endoplasmic Reticulum. The model is generalized and can predict the toxicity of any protein which impedes the early secretary pathway in dopaminergic cells and also the cell survival pattern with increasing concentration of the protein.

systems biology↗