Biology subjects

Sekar, K.

Publications and source records attributed to Sekar, K..

6 recordsLinked to original sources

bioRxiv2023

Multi-region spatial transcriptome analysis reveals cellular networks and pathways associated with hepatocellular carcinoma recurrence

Hepatocellular carcinomas (HCC) are driven by various etiologies and molecular diversity at presentation. Patient prognosis post-surgery is generally dismal, and the majority respond poorly to adjuvant targeted and/or immuno-therapies. Tumours are an ecosystem comprised of organization and interaction between different cell types that may contribute to clinically significant outcomes, such as disease recurrence. To better understand this phenomenon, we leveraged on a local cohort of patients with or without recurrence to generate spatial transcriptome profiles from multiple sectors from each tumour. We identified widespread gene expression intra- and inter tumour heterogeneity observed across the tumour sectors. Our analysis also revealed the cell type enrichment and localization, and ligand-receptor interactions identify a specific subset of endothelial cell enriched in primary tumours of patients with recurrence. Altogether, this study describes the spatial gene expression landscape in HCC patients associated with disease recurrence.

cancer biology↗

bioRxiv2022

Identification of potential antifibrinolytic compounds against kringle-1 and serine protease domain of plasminogen and kringle-2 domain of tissue-type plasminogen activator using combined virtual screening, molecular docking, and molecular dynamics simulation approaches.

The zymogen protease Plasminogen (Plg) and its active form plasmin (Plm) carry out important functions in the blood clot disintegration (breakdown of fibrin fibres) process. Inhibition of plasmin effectively reduces fibrinolysis to circumvent heavy bleeding. Currently, available Plm inhibitor tranexamic acid (TXA) that is used to treat severe hemorrhages is associated with an increased incidence of seizures which in turn were traced to gamma-aminobutyric acid antagonistic activity (GABAa) in addition to having multiple side effects. Fibrinolysis can be suppressed by targeting the three important protein domains: kringle-1 and serine protease domain of plasminogen and kringle-2 domain of tissue plasminogen activator. In the present study, combined approaches of structure-based virtual screening and molecular docking using Schrodinger Glide, AutoDock Vina, and ParDock/BAPPL+ were employed to identify potential hits from the ZINC database. Thereafter, the drug-likeness properties of the top three leads for each protein target were evaluated using Discovery Studio. Subsequently, a molecular dynamics simulation of 200ns for each protein-ligand complex was performed in GROMACS. The identified ligands are found to impart higher rigidity and stability to the protein-ligand complexes. Furthermore, the results were validated by performing the principal component analysis (PCA), and calculation of binding free energy using the Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach. The identified ligands occupy smaller phase space, form stable clusters and exhibit stronger non-bonded interactions. Thus, our findings can be useful for the development of promising anti-fibrinolytic agents. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/512028v2_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@b762fforg.highwire.dtl.DTLVardef@1c47591org.highwire.dtl.DTLVardef@1028dc1org.highwire.dtl.DTLVardef@a884ad_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2019

Structural and functional characterization of oligomeric states of proteins in RecFOR pathway

RecFOR pathway is the principal repair pathway for double strand break and single strand gap repair in Thermus thermophilus. RecF and RecR exist as monomer and dimer in solution, interestingly; they undergo condition-dependent dimerization and tetramerization, respectively during the DNA break repair. However, their importance in protein-protein and protein-DNA interactions remains elusive. In this study, the three-dimensional crystal structures of the wild type RecF and RecR proteins are determined. Thereafter, the structural information is used to mutate the interface residues to cysteine to stabilize the dimeric and tetrameric states of the RecF and RecR proteins, respectively. A comparative study for their interactions with other cognate proteins and ssDNA in native and SSB (single strand binding protein) bound states was performed. RecF or RecFR complex displays a negligible affinity towards ssDNA. Conversely, the RecF mutants and its complexes with wild type RecR showed affinity towards ssDNA, suggesting, distinct modes of interaction of RecF and RecFR complex for ssDNA binding. In the presence of RecO, the stabilized tetrameric RecR showed a lower binding affinity for ssDNA as compared to the SSB bound ssDNA, indicating the importance of tetrameric RecR in stabilizing the RecOR complex on the SSB coated ssDNA. This provides an insight into the reduction of the binding affinity of SSB proteins with the ssDNA, which in turn enhances the recruitment of RecA for strand exchange.

biophysics↗

bioRxiv2019

Bacterial glycogen provides short-term benefits in changing environments

Changing nutritional conditions challenge microbes and shape their evolutionary optimization. Here we investigated the role of glycogen in dynamic physiological adaptation of Escherichia coli to fluctuating nutrients following carbon starvation using real-time metabolomics. We found significant metabolic activity remaining after the depletion of environmental glucose that was linked to a rapid utilization of intracellular glycogen. Glycogen was depleted by 80% within minutes of glucose starvation and similarly replenished within minutes of glucose availability. These fast timescales of glycogen utilization correspond to the short-term benefits that glycogen provided to cells undergoing various physiological transitions. Cells capable of utilizing glycogen exhibited shorter lag times than glycogen mutants when starved between different carbon sources. The ability to utilize glycogen was also important for the transition between planktonic and biofilm lifestyles and enabled increased glucose uptake during pulses of limited glucose availability. While wild-type and mutant strains exhibited comparable growth rates in steady environments, mutants deficient in glycogen utilization grew more poorly in environments that fluctuated on minute-scales between carbon availability and starvation. Altogether, these results highlight an underappreciated role of glycogen to rapidly provide carbon and energy in changing environments, thereby increasing survival and competition capabilities in fluctuating and nutrient poor conditions.

microbiology↗

bioRxiv2019

Lipid digestion and autophagy are critical energy providers during acute glucose depletion in Saccharomyces cerevisiae

The ability to tolerate and thrive in diverse environments is paramount to all living organisms, and many organisms spend a large part of their lifetime in starvation. Upon acute glucose starvation, yeast cells undergo drastic physiological and metabolic changes and reestablish a constant - though lower - level of energy production within minutes. The molecules that are rapidly metabolized to fuel energy production under these conditions are unknown. Here, we combine metabolomics and genetics, to characterize the cells response to acute glucose depletion and identify pathways that ensure survival during starvation. We show that the ability to respire is essential for maintaining the energy status and to ensure viability during starvation. Measuring the cells immediate metabolic response, we find that central metabolites drastically deplete and that the intracellular AMP to ATP ratio strongly increases within 20-30 seconds. Furthermore, we detect changes in both amino acid and lipid metabolite levels. Consistent with this, bulk autophagy, a process that frees amino acids, as well as lipid degradation via {beta}-oxidation contribute in parallel to energy maintenance upon acute starvation. In addition, both these pathways ensure long-term survival during starvation. Thus, our results identify bulk autophagy and {beta}-oxidation as important energy providers during acute glucose starvation.

systems biology↗

bioRxiv2018

Synthesis and degradation of FtsZ determines the first cell division in starved bacteria

In natural environments, microbes are typically non-dividing. Such quiescent cells manage fleeting nutrients and gauge when intra- and extracellular resources permit division. Quantitative prediction of the division event as a function of nutritional status is currently achieved through phenomenological models for nutrient-rich, exponentially growing cultures. Such models, however, cannot predict the first division of cells under limiting nutrient availability. To address this, we analyzed the metabolic capability of starved Escherichia coli that were fed pulsed glucose at defined frequencies. Real-time metabolomics and microfluidic single-cell microscopy revealed unexpected, rapid protein and nucleic acid synthesis already in non-dividing cells. Additionally, the lag time to first division shortened as pulsing frequency increased. Here, we demonstrate that the first division from a non-dividing state occurs when the facilitating protein FtsZ reaches division-supporting concentration. A dynamic model quantitatively relates lag time to FtsZ synthesis from nutrient pulses and its protease-dependent degradation. Consistent with model predictions, lag time shortened when FtsZ synthesis was supplemented or protease inhibitors were added. Lag time prolonged when ftsZ was repressed or FtsZ degradation rate was increased. Thus, we provide a basis to quantitatively predict bacterial division using information about molecular determinants and the nutrient input.

microbiology↗