Biology subjects

Swain, P.

Publications and source records attributed to Swain, P..

8 recordsLinked to original sources

bioRxiv2025

Sex differences in durability following heavy intensity cycling exercise in trained athletes

The ability to withstand impairments in key physiological variables during prolonged exercise, known as durability, is emerging as an important factor in cycling performance. While females possess physiological characteristics that could confer enhanced durability relative to males, little is known about potential sex differences. 32 trained cyclists (16 males and 16 females) performed an incremental exercise test to exhaustion in visit 1. In visit 2 they performed 90 minutes of heavy intensity cycling (HVY) at 110% of gas exchange threshold (GET), followed by another incremental test. During HVY, pulmonary gas exchange ([V]O2 and [V]CO2) ventilation ([V]E), heart rate (HR), rating of perceived exertion (RPE), near-infrared spectroscopy and electromyography were recorded, and blood lactate (BLa) was collected. Before and after HVY, maximal voluntary contraction (MVIC), voluntary activation (VA) and potentiated twitches (100Hz, 10Hz, Qtw{middle dot}pot) of the knee extensors were assessed. Power at GET (-16{+/-}15% vs -2{+/-}13%) and respiratory compensation point (-13{+/-}10% vs -6{+/-}9%) decreased more in males than females (P[≤]0.049). All aspects of neuromuscular function decreased from pre to post (all P<0.001), without sex differences (P[≥]0.096). During HVY, HR, [V]O2 (%peak), relative energy expenditure increased more in males (P[≤]0.008), whereas respiratory exchange ratio decreased more in females (P=0.001). BLa was higher in males than females (P=0.030). Muscle oxygen extraction was lower (P=0.004) and tissue saturation index higher for females (P<0.001). The smaller reductions exhibited by females in submaximal thresholds, associated with lesser derangements to oxidative efficiency, highlight the need to consider sex-specific training prescription and pacing strategies for long duration events. Key PointsO_LIDurability, as measured by the reduction in incremental exercise test outcomes, is relatively unexplored in females compared to males, despite physiological sex differences that might confer a female advantage. C_LIO_LIAfter 90 minutes of heavy intensity cycling, males demonstrated greater reductions in the power outputs associated with gas exchange threshold and respiratory compensation point. C_LIO_LIThe maximal rate of oxygen consumption and incremental test peak power output decreased similarly in both sexes. C_LIO_LIThese changes are associated with greater carbohydrate metabolism and losses of efficiency in males, whereas no sex differences were observed in neuromuscular fatigue. C_LI

physiology↗

bioRxiv2024

Role of protein-protein interactions on model chromatin organization

The three-dimensional organization of chromatin is influenced by DNA-binding proteins, through specific and non-specific interactions. However, the role of DNA sequence and interaction between binding proteins in influencing chromatin structure is not yet fully understood. By employing a simple polymer-based model of chromatin, that explicitly considers sequence-dependent binding of proteins to DNA and protein-protein interactions, we elucidate a mechanism for chromatin organization. We find that: (1) Tuning of protein-protein interaction and protein concentration is sufficient to either promote or inhibit the compartmentalization of chromatin. (2) The presence of chromatin acts as a nucleating site for the condensation of the proteins at a density lower than in isolated protein systems. (3) The exponents describing the spatial distance between the different parts of the chromatin, and their contact probabilities are strongly influenced by both sequence and the protein-protein attraction. Our findings have the potential application of re-interpreting data obtained from various chromosome conformation capture technologies, thereby laying the groundwork for advancing our understanding of chromatin organization.

biophysics↗

bioRxiv2024

Decoding the role of DNA sequence on protein-DNA co-condensation

The eukaryotic genome is organized within the cell nucleus through three-dimensional compaction. The physical principles that govern genome organization in vivo remain less understood. Phase separation of protein and DNA has emerged as an attractive mechanism for reshaping chromatin and compacting the genome. In vitro studies have shed light on the biophysical principles of protein-DNA condensates driven by protein-protein and protein-DNA interactions. However, the role of DNA sequence and its impact on protein-DNA condensation remains elusive. Guided by experiments, this paper presents a simple polymer-based model of protein-mediated DNA condensation that explicitly incorporates the influence of DNA sequence on protein binding. Using coarse-grained Brownian dynamics simulations, we demonstrate that, in the case of a homogeneous DNA, only one condensate forms in equilibrium. In sharp contrast, DNA sequence heterogeneity can result in the coexistence of multiple condensates, giving rise to the formation of structures resembling pearl-necklaces. Interestingly, we observe that protein binding affinity of interfacial DNA governs the capillary forces arising from the protein-DNA condensates. To demonstrate the usefulness of our modeling framework, we compare the simulation results against published data for co-condensation of Dps, Sox2, and HP1. We find that while Dps exhibits sequence-independent binding, DNA sequence heterogeneity dictates the co-condensation of Sox2 and HP1 with DNA. Overall, the framework developed here can be harnessed to gain mechanistic insights into the role of DNA sequence on protein-DNA co-condensation and pave the way for developing a deeper understanding of genome organisation.

biophysics↗

bioRxiv2022

Calculating ATP production rates from oxidative phosphorylation and glycolysis during cell activation

Oxidative phosphorylation and glycolysis are the dominant ATP-generating pathways in mammalian metabolism. The balance between these two pathways is often shifted to execute cell-specific functions in response to stimuli that promote activation, proliferation, or differentiation. However, measurement of these metabolic switches has remained mostly qualitative, making it difficult to discriminate between healthy, physiological changes in energy transduction or compensatory responses due to metabolic dysfunction. We therefore developed a broadly applicable method to calculate ATP production rates from oxidative phosphorylation and glycolysis using Seahorse XF Analyzer data. We quantified the bioenergetic changes observed during macrophage polarization as well as cancer cell adaptation to in vitro culture conditions. Additionally, we detected substantive changes in ATP utilization upon neuronal depolarization and T cell receptor activation that are not evident from steady-state ATP measurements. This method generates a single readout that allows the direct comparison of ATP produced from oxidative phosphorylation and glycolysis in live cells. Additionally, the manuscript provides a framework for tailoring the calculations to specific cell systems or experimental conditions.

biochemistry↗

bioRxiv2020

Exogenously applied ABA induced changes in physio-biochemical attributes in selected rice varieties under osmotic stress

Drought is the most catastrophic abiotic stress that affect plant growth and development. Plant initiates alterations at physiological, biochemical and molecular levels to combat deleterious effects of drought in which abscisic acid, play a pivotal role. The present investigation was conducted to investigate how abscisic acid modulates different biochemical traits under osmotic stress. Twenty-one days old seedlings were exposed to osmotic stress, exogenously applied abscisic acid and the combination of both osmotic stress and abscisic acid to study the influence of abscisic acid on biochemical traits under moisture stress. The results reveals that abscisic acid has no influence on leaf water potential, however, it has active role in increasing osmolytes like proline. {Delta}1-pyrroline-5-carboxylate reductase and proline dehydrogenase remained unresponsiveness to ABA that indicates ABA-independent regulation of these two enzymes but the activity of {Delta}1-pyrroline-5-carboxylate synthesase and Ornithine-{delta}-aminotransferase was enhanced (3 fold) in response to abscisic acid. Antioxidative enzymes increased (catalase-2.5 fold; peroxidase-3 fold and SOD-6 fold) in response to abscisic acid and osmotic stress, gave an insight of the regulation of these traits under the influence of abscisic acid. Aldehyde oxidase remained unresponsive to abscisic acid but showed enhanced expression when both abscisic acid and osmotic stress was applied suggest its ABA-independent regulation. The information provided here has significance in understanding the regulation of different catabolite that play important role in drought tolerance and can be implemented for the development of drought-tolerant varieties.

plant biology↗

bioRxiv2020

Phenological, Physiological and yield markers as efficient tools to identify drought tolerant rice genotypes in Eastern India

Rice production is severely threatened by drought stress in Eastern India. To develop drought tolerant varieties, selection of donors for breeding programme is crucial. Twenty one selected rice genotypes including both tolerant and sensitive to drought were grown under well-watered and drought stress conditions in dry seasons of two successive years of 2017 and 2018. Leaf water potential, relative water content displayed significant difference among the genotypes during vegetative screening. At reproductive stage drought screening, days to 50% flowering was delayed in all genotypes except N22 and Anjali (showed early flowering) however grain yield and other yield related traits decreased significantly compared to well watered condition. Correlation analysis of phenological and yield related traits with grain yield revealed that tiller numbers and panicle numbers are highly correlated with grain yield both under well-watered and water stress conditions and contributes maximum towards grain yield. The dendrogram grouped Mahamaya, Sahabhagidhan, Poornima, IBD 1, Hazaridhan, Samleshwari and Danteshwari into one cluster which performed better under water stress conditions and had grain yield more than 1.69 tha-1. Sahabhagidhan, Poornima, Vandana, and N22 displayed tolerance to drought both under vegetative and reproductive conditions which could be a good selection for the breeders to develop drought tolerant rice cultivars for eastern region of India.

plant biology↗

bioRxiv2020

Identification of QTLs for high grain yield and component traits in New Plant Types of rice

A panel of 60 genotypes consisting of New Plant Types (NPTs) along with indica, tropical and temperate japonica genotypes were phenotypically evaluated for four seasons in irrigated situation for grain yield per se and component traits. Twenty NPT genotypes were found to be promising with an average grain yield of 5.45 to 8.8 t/ha. A total of 85 SSR markers were used in the study to identify QTLs associated with grain yield per se and related traits. Sixty-six (77.65%) markers were found to be polymorphic. The PIC values varied from 0.516 to 0.92 with an average of 0.704. A moderate level of genetic diversity (0.39) was detected among genotypes. Variation to the tune of 8% within genotypes, 68% among the genotypes within the population and 24% among the populations were observed (AMOVA). The association analysis using GLM and MLM models led to the identification of 30 and 10 SSR markers were associated with 70 and 16 QTLs, respectively. Thirty novel QTLs linked with 16 SSRs were identified to be associated with eleven traits, namely, tiller number (qTL-6.1, qTL-11.1, qTL-4.1), panicle length (qPL-1.1, qPL-5.1, qPL-7.1, qPL-8.1), flag leaf length (qFLL-8.1, qFLL-9.1), flag leaf width (qFLW-6.2, qFLW-5.1, qFLW-8.1, qFLW-7.1), total no. of grains (qTG-2.2, qTG-a7.1), thousand-grain weight (qTGW-a1.1, qTGW-a9.2, qTGW-5.1, qTGW-8.1), fertile grains (qFG-7.1), seed length-breadth ratio (qSlb-3.1), plant height (qPHT-6.1, qPHT-9.1), days to 50% flowering (qFD-1.1) and grain yield per se (qYLD-5.1, qYLD-6.1a, qYLD-11.1). This information could be useful for identification of highly potential parents for development of transgressive segregants. Moreover, super rice genotypes could be developed through pyramiding of these QTLS for important yield traits for prospective increment in yield potentiality and breaking yield ceiling.

plant biology↗

bioRxiv2018

Cell boundary confinement sets the size and position of the E. coli chromosome

While the spatiotemporal structure of the genome is crucial to its biological function, many basic questions remain unanswered on the morphology and segregation of chromosomes. Here, we experimentally show in Escherichia coli that spatial confinement plays a dominant role in determining both the chromosome size and position. In non-dividing cells with lengths up to 10 times normal, single chromosomes are observed to expand more than 4 fold in size, an effect only modestly influenced by deletions of various nucleoid-associated proteins. Chromosomes show pronounced internal dynamics but exhibit a robust positioning where single nucleoids reside strictly at mid-cell, while two nucleoids self-organize at [1/4] and [3/4] cell positions. Molecular dynamics simulations of model chromosomes recapitulate these phenomena and indicate that these observations can be attributed to depletion effects induced by cytosolic crowders. These findings highlight boundary confinement as a key causal factor that needs to be considered for understanding chromosome organization.

biophysics↗