Biology subjects

Sarkar, K.

Publications and source records attributed to Sarkar, K..

10 recordsLinked to original sources

bioRxiv2026

Who rests with whom? Sex composition and group demography shape resting associations in free-ranging dogs

Free-ranging dogs frequently rest near conspecifics, but the demographic factors structuring their resting associations remain poorly understood. We quantified dyadic resting associations in 26 free-ranging dog groups in West Bengal, India, observed between 2019 and 2023. Association strength was estimated from scan based resting co-occurrences using the Half-Weight Index. We tested whether dyadic association strength varied with dyad sex composition, dyad life stage composition, group size, and group sex ratio using a generalised additive model for location, scale and shape that accounted for group identity and repeated occurrence of individuals across dyads. Male-male dyads had lower association strengths than female-female dyads, whereas mixed-sex dyads did not differ from female-female dyads. Association strength decreased with increasing group size but increased as the male-to-female ratio within the group increased, while life-stage composition had no detectable effect. Individual level network metrics, including strength, reach, clustering coefficient, affinity, and eigenvector centrality, did not vary with sex or season. Mixed-sex pairs were also frequently represented among the strongest dyadic associations within groups. These findings indicate that resting associations in free-ranging dogs vary with dyad sex composition and group demography. Further opportunity-controlled analyses are required to determine whether the prominence of mixed-sex dyads reflects preferential association rather than group composition alone.

animal behavior and cognition↗

bioRxiv2024

Influence of metal ions on the isothermal self-assembly of DNA nanostructures

DNA nanostructures are typically assembled by thermal annealing in buffers containing magnesium. We demonstrate the assembly of DNA nanostructures at constant temperatures ranging from 4 {degrees}C to 50 {degrees}C in solutions containing different metal ions. The choice of metal ions and the assembly temperature influence the isothermal assembly of several DNA motifs and designed three-dimensional DNA crystals. Molecular dynamics simulations show more fluctuations of the DNA structure in select monovalent ions (Na+ and K+) compared to divalent ions (Mg2+ and Ca2+). A key highlight is the successful assembly of DNA motifs in nickel-containing buffer at temperatures below 40 {degrees}C, otherwise unachievable at higher temperatures, or using an annealing protocol. DNA nanostructures isothermally assembled in different ions do not affect the viability of fibroblasts, myoblasts, and myotubes and or the immune response in myoblasts. The use of ions other than the typically-used magnesium holds key potential in biological and materials science applications that require minimal amounts of magnesium.

bioengineering↗

bioRxiv2024

Mitochondrial calcium uniporter regulates human fibroblast-like synoviocytes invasion via altering mitochondrial dynamics and dictates rheumatoid arthritis pathogenesis

Rheumatoid arthritis (RA) is characterized by the aggressive migration and invasion of fibroblast-like synoviocytes (FLS) into cartilage and bone, a process that is significantly influenced by mitochondrial calcium uptake. This study highlights the critical role of mitochondrial calcium uniporter (MCU) in regulating FLS migration and mitochondrial dynamics, and its potential as a therapeutic target in RA. Notably, RA-FLS exhibited increased MCU expression and mitochondrial dysfunction compared to controls. Treatment with Ru360, a potent MCU inhibitor significantly reduced RA-FLS migration, calcium influx, and mitochondrial reactive oxygen species (ROS) levels, while restoring mitochondrial morphology and enhancing ATP production. Further analysis of MCU complex expression revealed elevated levels of MCU and other regulatory subunits (EMRE, MICU1, MICU2) in RA-FLS compared to controls, indicating mitochondrial dysfunction in RA. Mechanistically, MCU inhibition altered gene expression related to cytoskeletal dynamics, focal adhesion, and metabolic pathways. In human RA-FLS, MCU inhibition suppressed migration and invasion both in vitro and in vivo. The interaction between MCU and Miro1, essential for mitochondrial transport, was validated, and its disruption impaired FLS migration. Our findings highlight MCU as a promising therapeutic target to inhibit FLS migration and ameliorate RA progression.

immunology↗

bioRxiv2024

Curtailed CaSR expression in peripheral blood mononuclear cells is associated with hypertension

The calcium-sensing receptor (CaSR) is a GPCR family member. CaSR is abundantly expressed in the parathyroid gland and controls calcium homeostasis. There are no particular discoveries involving CaSR expression in hypertensive peripheral blood mononuclear cells. We investigated lower CaSR expression in hypertensive human and animal models. Nitric oxide (NO) has an important role in vascular function. Impaired NO production disrupts CaSR-mediated fine adjustment of the intra- and extracellular [Ca2+] gradients. According to the law Ca2+ transportation through Ca channels maintains its connection from the circulatory micro-vascular bed to interstitial space, influenced by capillary and interstitial fluid hydrostatic pressure, as well as oncotic pressure. In that situation, the alterations in Ca2+ microenvironment and dynamics remain unknown. CaSR on circulatory mononuclear cells may detect changes in the Ca2+ microenvironment in the ISF of endothelial cells-VSMC and endothelium lining in hypertension. In this experiment, the decreased expression of CaSR revealed a molecular sensor in the presence of elevated blood pressure.

biochemistry↗

bioRxiv2022

Oo-site: A dashboard to visualize gene expression during Drosophila oogenesis reveals meiotic entry is regulated post-transcriptionally

Determining how stem cell differentiation is controlled has important implications for understanding the etiology of degenerative disease and designing regenerative therapies. In vivo analyses of stem cell model systems have revealed regulatory paradigms for stem cell self-renewal and differentiation. The germarium of the female Drosophila gonad, which houses both germline and somatic stem cells, is one such model system. Bulk mRNA sequencing (RNA-seq), single-cell (sc) RNA-seq, and bulk translation efficiency of mRNAs are available for stem cells and their differentiating progeny within the Drosophila germarium. However, visualizing those data is hampered by the lack of a tool to spatially map gene expression and translational data in the germarium. Here, we have developed Oo-site (https://www.ranganlab.com/Oo-site), a tool for visualizing bulk RNA-seq, scRNA-seq, and translational efficiency data during different stages of germline differentiation, that makes these data accessible to non-bioinformaticians. Using this tool, we recapitulated previously reported expression patterns of developmentally regulated genes and discovered that meiotic genes, such as those that regulate the synaptonemal complex, are regulated at the level of translation.

developmental biology↗

bioRxiv2021

A feedback loop between heterochromatin and the nucleopore complex controls germ-cell to oocyte transition during Drosophila oogenesis

Germ cells differentiate into oocytes that become totipotent upon fertilization. How the highly specialized oocyte acquires this distinct cell fate is poorly understood. During Drosophila oogenesis, H3K9me3 histone methyltransferase SETDB1 translocates from the cytoplasm to the nucleus of germ cells concurrent with oocyte specification. Here, we discovered that nuclear SETDB1 is required to silence a cohort of differentiation-promoting genes by mediating their heterochromatinization. Intriguingly, SETDB1 is also required for the upregulation of 18 of the ~30 nucleoporins (Nups) that comprise the nucleopore complex (NPC). NPCs in turn anchor SETDB1-dependent heterochromatin at the nuclear periphery to maintain H3K9me3 and gene silencing in the egg chambers. Aberrant gene expression due to loss of SETDB1 or Nups results in loss of oocyte identity, cell death and sterility. Thus, a feedback loop between heterochromatin and NPCs promotes transcriptional reprogramming at the onset of oocyte specification that is critical to establish oocyte identity.

developmental biology↗

bioRxiv2021

A Synthetic Genetic Reversible Feynman Gate in a Single E.coli Cell and its Application in Bacterial to Mammalian Cell Information Transfer

Reversible computing is a nonconventional form of computing where the inputs and outputs are mapped in a unique one-to-one fashion. Reversible logic gates in single living cells have not been demonstrated. Here, we created a synthetic genetic reversible Feynman gate in a single E.coli cell. The inputs were extracellular chemicals, IPTG and aTc and the outputs were two fluorescence proteins EGFP and E2-Crimson. We developed a simple mathematical model and simulation to capture the essential features of the genetic Feynman gate and experimentally demonstrated that the behavior of the circuit was ultrasensitive and predictive. We showed an application by creating an intercellular Feynman gate, where input information from bacteria was computed and transferred to HeLa cells through shRNAs delivery and the output signals were observed as silencing of native AKT1 and CTNNB1 genes in HeLa cells. Given that one-to-one input-output mapping, such reversible genetic systems might have applications in diagnostics and sensing, where compositions of multiple input chemicals could be estimated from the outputs.

synthetic biology↗

bioRxiv2021

A single layer artificial neural network type architecture with molecular engineered bacteria for complex conventional and reversible computing

Here, we adapted the basic concept of artificial neural networks (ANN) and experimentally demonstrate a broadly applicable single layer ANN type architecture with molecular engineered bacteria to perform complex irreversible computing like multiplexing, de-multiplexing, encoding, decoding, majority functions, and reversible computing like Feynman and Fredkin gates. The encoder and majority functions and reversible computing were experimentally implemented within living cells for the first time. We created molecular-devices, which worked as artificial neuro-synapses in bacteria, where input chemical signals were linearly combined and processed through a non-linear activation function to produce fluorescent protein outputs. To create such molecular devices, we established a set of rules by corelating truth tables, mathematical equations of ANN, and molecular-device design, which unlike molecular computing, does not require circuit diagram and the equation directly correlates the design of the molecular-device. To our knowledge this is the first adaptation of ANN type architecture with engineered cells. This work may have significance in new platform for biomolecular computing, reversible computing and in transforming living cells as ANN-enabled hardware.

synthetic biology↗

bioRxiv2021

Engineered Bacteria Computationally Solve Chemically Generated 2X2 Maze Problems

Maze generating and solving are challenging problems in mathematics and computing. Here we generated simple 2X2 maze problems applying four chemicals and created a set of engineered bacteria, which in a mixed population worked as a computational solver for any such problem. The input-output matrices of a mathematical maze were mapped through a truth table, where the 1 and 0 logic values of four chemical inputs determined the sixteen different 2X2 maze problems on a chemical space. Our engineered bacteria, which consisted of six different genetic logic circuits and distributed among six cell populations processed the chemical information and solved the problems by expressing or not expressing four different fluorescent proteins according to the input-output matrices. The three available solutions were visualized by glowing bacteria and for the thirteen cases, where there was no solution no bacteria glowed. This work may have significance in cell based computing and synthetic biology.

synthetic biology↗

bioRxiv2019

MSL3 coordinates a transcriptional and translational meiotic program in female Drosophila

Gamete formation from germline stem cells (GSCs) is essential for sexual reproduction. However, the regulation of GSC differentiation and meiotic entry are incompletely understood. Set2, which deposits H3K36me3 modifications, is required for differentiation of GSCs during Drosophila oogenesis. We discovered that the H3K36me3 reader Male-specific lethal 3 (MSL3) and the histone acetyltransferase complex Ada2a-containing (ATAC) cooperate with Set2 to regulate entry into meiosis in female Drosophila. MSL3 expression is restricted to the mitotic and early meiotic stages of the female germline, where it promotes transcription of genes encoding synaptonemal complex components and a germline enriched ribosomal protein S19 paralog, RpS19b. RpS19b upregulation is required for translation of Rbfox1, a known meiotic cell cycle entry factor. Thus, MSL3 is a master regulator of meiosis, coordinating the expression of factors required for recombination and GSC differentiation. We find that MSL3 is expressed during mouse spermatogenesis, suggesting a conserved function during meiosis.

developmental biology↗