Biology subjects

Prakash, R.

Publications and source records attributed to Prakash, R..

15 recordsLinked to original sources

bioRxiv2026

No Effect of Exercise Timing on Daily Glycaemia Despite Shifts in Acute Glucose Dynamics in Participants with Normal Glucose Tolerance: A Randomised Crossover Trial

Exercise is a well-established modulator of glucose regulation, but whether the time of day it is performed matters for healthy, free-living adults remains unresolved. In a randomised crossover trial, 29 healthy adults completed a single 30-minute bout of moderate-intensity exercise in the morning (07:00-10:00) and in the evening (16:00-19:00), with continuous glucose monitoring and wrist-worn activity tracking used to capture responses over an 8-day free-living protocol. Evening exercise produced a significantly greater acute reduction in blood glucose (P < 0.001) compared to morning exercise, but this did not translate into consistent differences in overall daily mean glycaemic exposure, whether measured over the calendar day or over a window aligned with exercise onset. Evening exercise was linked to greater within-day glycaemic variability than morning exercise, with the clearest evidence coming from the circadian-aligned analysis (day x timing interaction, SD: P = 0.00939; CV: P = 0.00766). Appetite rose after exercise in both conditions, with no difference by time of day. Taken together, these results show that exercise timing does not change how much glucose exposure a healthy adult accumulates over a day, but it does change the shape of the glucose response around the exercise bout itself, a distinction only visible when glucose is examined at a finer temporal resolution than daily averages allow.

physiology↗

bioRxiv2026

Certified Design Regions under Parametric Plant Uncertainty with Application to Antithetic Integral Feedback

Kinetic parameters in engineered biomolecular circuits are typically known only within intervals and are not precisely tunable; controller synthesis is therefore naturally posed over sets of gains rather than at a single nominal design. We formulate robust controller tuning under parametric plant uncertainty as a universally quantified set-inversion problem: given a plant-parameter box, compute the controller gains that stabilize every plant in the box. Robust stability is decided by Hurwitz sign conditions, which are bounded over the joint gain-parameter domain using validated range enclosures, yielding machine-checkable certificates of local exponential stability of the deterministic equilibrium. Numerical experiments show that the certified region depends strongly on the range enclosure. For an antithetic integral feedback (AIF) controller acting on a two-species gene-expression cascade, a tensor-product Bernstein enclosure certifies 83.2% of the design plane at bisection tolerance epsilon=0.05 with 324 terminal boxes, whereas four baseline enclosures certify between 50.9% and 58.9% on the same paving. For a fifth-order loop, the certified fraction increases from 34.4% to 73.8%, and the certified and excluded terminal boxes confine the robustly stabilizing area to a window of about 2.1 percentage points. Finally, for a refining variant of the algorithm in which the plant box is refined alongside the design box, the undecided area satisfies |U(epsilon)|=O(epsilon) under a non-degeneracy assumption on the stability boundary.

synthetic biology↗

bioRxiv2026

Oxaliplatin and 5-Fluorouracil induce p53-p21-pRb-associated cell cycle arrest and a transient senescence-like phenotype in patient-derived low-grade serous ovarian cancer cells

Objectives Low grade serous ovarian cancer (LGSOC) is characterized by frequent TP53 wild type status and limited responsiveness to conventional chemotherapy. This study investigated the cytotoxic effects of oxaliplatin combined with 5-fluorouracil on patient derived LGSOC cells. Results Clinically relevant concentrations of oxaliplatin and 5-fluorouracil had minimal effects on LGSOC cell viability but markedly reduced cellular proliferation and clonogenic recovery. Combined treatment induced pronounced accumulation of cells in the G0/G1 phase of the cell cycle and increased expression of p53 and p21, accompanied by reduced pRB phosphorylation, consistent with activation of the p53-p21-pRb pathway. Oxaliplatin plus 5-fluorouracil also increased senescence-associated beta-galactosidase activity, cellular enlargement and flattening, and reactive oxygen species production, supporting a senescence-like phenotype. However, after drug withdrawal, treated cells progressively regained proliferative capacity, indicating that the senescence phenotype was transient rather than fully irreversible. Together, these findings show that oxaliplatin plus 5-fluorouracil primarily arrest rather than kill LGSOC cells and induces a transient senescence-like phenotype and G0/G1-phase arrest by activating the p53-p21-pRb pathway.

cancer biology↗

bioRxiv2026

The combination of nelfinavir and cisplatin drives lytic cell death through a caspase-8/caspase-3/GSDME axis in platinum-resistant ovarian cancer cells

PurposeCisplatin (CDDP) is the most active chemotherapy for ovarian cancer; primary or acquired resistance signals a poor prognosis. Nelfinavir (NFV), an HIV protease inhibitor, has demonstrated anti-tumor activity in multiple cancer models, but its interaction with CDDP in ovarian cancer has yet to be demonstrated. In this work, we addressed whether the combination of CDDP and NFV provides treatment advantage in platinum (Pt)-resistant ovarian cancer cells. MethodsDrug synergy between NFV and CDDP was assessed using cell vitality assays and Loewe additivity modelling. Apoptotic and pyroptotic signalling were evaluated by immunoblotting, mitochondrial membrane potential analysis, and lactate dehydrogenase (LDH) release, and caspase inhibition. Transcriptomic changes were assessed by bulk mRNA sequencing followed by differential gene expression analysis and gene set enrichment analysis. ResultsNFV synergized with CDDP to reduce the viability of Pt-resistant ovarian cancer cells, promoting a regulated lytic cell death phenotype involving apoptotic and pyroptotic features. Combination treatment induced caspase-8 and caspase-3 activation, and downstream gasdermin E (GSDME) processing. Inhibition of caspase-3 significantly attenuated cell death, and caspase-8 inhibition rescued viability and prevented Bid cleavage, caspase-3 activation, and GSDME cleavage. These effects occurred in the context of enhanced endoplasmic reticulum stress, increased DNA damage with reduced DNA repair, and impaired Akt-driven survival signalling. ConclusionsOur findings establish that NFV synergizes with CDDP in killing Pt-resistant ovarian cancer cells by promoting a caspase-8-dependent apoptotic-to-secondary pyroptotic response, supporting further investigation of NFV as a potential drug to be repurposed to increase the efficacy of Pt-based therapy.

cancer biology↗

bioRxiv2026

Mutational and functional heterogeneity of homology-directed repair deficiency and clinical implications

Homology-directed repair deficiency (HRd) encompasses mutations in multiple genes yet is treated clinically as a single entity. Here, through parallel analyses of isogenic knockouts of multiple HR pathway genes, integrating multi-omic analyses with genome-wide CRISPR-Cas9-dependency and resistance screens, we show that HRd is not a single entity but exists along a molecular and functional continuum. BRCA1, BRCA2, PALB2, RAD51C, and RAD51D mutants shared many HRd-associated mutational signatures, while RAD51B, BRIP1, CDK12 exhibited distinct genomic patterns. Functional heterogeneity was equally apparent: synthetic lethal interactions including CIP2A and a novel dependency on PRDX1 were penetrant across most HRd genotypes, whereas FANCM dependency was linked to HRd subtypes characterized by tandem duplications. PARPi resistance screens in distinct HRd contexts uncovered BRIP1 and RECQL5 as new BRCA2-specific resistance genes. HRd is thus a complex continuum, underscoring why modernizing the molecular taxonomy utilizing all genomic features available per patient is crucial to informing precision interventions.

genomics↗

bioRxiv2026

Certified Steady-State Parameter-Interval Design for Uncertain Biomolecular Models using a Global Shaving Contractor

The design of parameter intervals that provably enforce steady-state specifications in biomolecular circuits is challenging due to nonlinear reaction kinetics, parametric uncertainty, and the under-determined nature of steady-state constraints. Most validated approaches either rely on recursive subdivision (set inversion) or may stall due to dependency effects when applied directly in parameter space, limiting scalability in moderate to high dimensions. This paper introduces a global shaving contractor that contracts an initial parameter box by repeatedly applying certified interval-exclusion tests against a prescribed steady-state set. The proposed procedure returns a guaranteed outer enclosure of the feasible parameter set and provides finite-termination guarantees, along with worst-case bounds on the number of inclusion-function evaluations. Case studies spanning low-dimensional motifs and a sixteen-parameter integral-feedback model, including bistability specifications for a CRISPRi toggle switch, demonstrate substantial contraction of design domains without subdivision. The resulting certificates support uncertainty-aware circuit tuning, rigorous parameter screening, and robust design workflows in systems & synthetic biology and related nonlinear dynamical-system design problems.

synthetic biology↗

bioRxiv2025

Robustness of a Bistable Biomolecular PositiveFeedback Circuit to Global Parametric Perturbations

Achieving robustness to multi-parametric perturbations where all parameters can change at the same time is challenging because the controller would also face the same disturbance as the plant. For nonlinear positive feedback, an important mechanism for cell fate determination in biomolecular contexts, quantitative aspects of robustness to such perturbations are generally unclear. Here we used mathematical methods of control and dynamical systems, interval analysis, and a benchmark model of a bistable biomolecular positive feedback circuit to address this. We confirmed that such perturbations can change the qualitative behaviour of the system extinguishing bistability. We obtained a quantitative relation between the relative variation in the stable steady state and the unstable steady state in terms of the relative changes in the parameters. We showed how the deviation in the trajectories near the unstable steady state due to multi-parametric perturbations could diverge almost exponentially after an initial transient, which could have a significant impact on the bistable switching dynamics. We found that the size of the eigenvalue for the unstable steady state was greater than that for the stable steady state, and proved this for certain parameters using a rigorous numerical construction. We noted a tradeoff between enhancing the parameter space of bistability and the increased sensitivity in the bistable dynamics due to parametric perturbations. We obtained rigorous bounds on the entire transient response for multi-parametric perturbations. These results provide a quantitative insight into the robustness of a bistable biomolecular positive feedback circuit to multi-parametric perturbations.

systems biology↗

bioRxiv2024

A novel miniaturized filamentous phagemid as a gene delivery vehicle to target mammalian cells

The filamentous phage M13 is a single-stranded DNA phage with several attractive characteristics for gene delivery, including a capsid amenable to the display of foreign peptides, and a simple well-characterized genome that is easy to genetically modify. Previously, we constructed a DNA minivector based on M13 (a miniphagemid), which minimized the inflammatory bacterial and phage DNA content in the vector. In general, DNA minivectors, devoid of their prokaryotic components have shown improved gene transfer and safety. We examined the miniphagemids capacity for in vitro transgene delivery to target cells through phage display of epidermal growth factor to target its cognate receptor. The absence of the prokaryotic backbone and smaller vector size conferred by the miniphagemid was associated with improved transgene expression for purified single-stranded phagemid DNA and phagemid virion particles. We further engineered this system to enhance packaging of DNA minivectors by deletion of the packaging signal within the helper plasmid, used to produce miniphagemids, and observed improved phage-mediated gene expression in mammalian cells. Overall, here, we present a set of novel transgene delivery vectors that combine cell-targeting ligand display and vector minimization. This platform showcases the flexibility of M13 as a gene delivery tool with immense therapeutic potential.

molecular biology↗

bioRxiv2024

An E. coli-based platform for the production and assembly of anellovirus vectors

Gene therapy offers immense potential for treating various diseases, including cancer, immunodeficiencies, and cardiovascular conditions. The efficacy of gene therapy (GT) largely depends on the vector used for gene delivery. Viral vectors, while effective, pose risks including insertional mutagenesis, immune responses, and high manufacturing costs. Non-viral vectors, although safer and easier to produce, often exhibit lower transfection efficiency and weaker transgene expression. This highlights the need for novel, more efficient vectors. Among emerging strategies, bacteriophages are gaining attention as promising GT delivery vehicles due to their adaptability and safety profile. Filamentous phages like M13 have demonstrated potential as targeted gene delivery vectors. This study proposes constructing a single-stranded DNA (ssDNA) phage-based vector incorporating a eukaryotic gene cassette. By leveraging Ff phage replication mechanisms in E. coli, the study explores encapsidating ssDNA within anellovirus capsids. These small, ssDNA viruses, known for their ability to transfect diverse tissues, offer a safer alternative to conventional viral vectors. Through successful expression and assembly of anellovirus capsid proteins, ssDNA viral particles were produced ex vivo. This innovative E. coli-based anellovirus-phagemid system provides a promising, cost-effective platform for developing next-generation viral vectors in gene therapy.

molecular biology↗

bioRxiv2024

Design of Parameter Intervals to Meet Steady-State Specifications in Biomolecular Circuits using Interval Analysis

It is often desired, in the analysis or the design of biomolecular circuits, to search for parameters that satisfy certain specifications, such as on the number of the steady states or on their magnitudes. These problems are challenging because of the presence of multiple parameters, the nonlinear mapping between the parameters and the steady states, as well as the specifications themselves, such as when multiple steady states are desired. Typically, exact analytical solutions are limited and numerical approaches, if they converge, may not capture all solutions. We used Interval Analysis versions of Bisection and Constraint Propagation to obtain rigorous and guaranteed estimates of circuit parameters for the design problem. We established criteria that rule out the existence of design solutions in a given parameter space. We presented algorithms to rigorously bound all solutions and developed variants that enclosed the solutions as accurately as required. These theoretical results were illustrated on benchmark feedback and feedforward circuits. These results should aid in the analysis and design of biomolecular circuits as well as in other contexts with similar modelling frameworks. The rigorous nature of the results may be particularly useful for resource optimization and safety criticality in synthetic biology applications, such as in therapeutic applications and drug delivery.

synthetic biology↗

bioRxiv2021

Brain structure and function predict adherence to an exercise intervention in older adults

Individualized and precision medicine approaches to exercise for cognitive and brain health in aging have the potential to improve intervention efficacy. Predicting adherence to an exercise intervention in older adults prior to its commencement will allow for adaptive and optimized approaches that could save time (no need to demonstrate failure before changing course) and money (cost of de-implementing approaches that do not work for certain individuals) which ultimately could improve health outcomes (e.g., preventative medicine approaches prior to the onset of symptoms). Individual differences in brain structure and function in older adults are potential proxies of brain and brain reserve or maintenance and may provide strong predictions of adherence. We hypothesized that brain-based measures would predict adherence to a six-month randomized controlled trial of exercise in older adults, alone and in combination with psychosocial, cognitive and health measures. In 131 older adults (aged 65.79 {+/-} 4.65 years, 63% female) we found, using regularized elastic net regression within a nested cross-validation framework, that brain structure (cortical thickness and cortical surface area) in somatosensory, inferior temporal, and inferior frontal regions and functional connectivity (degree count) in primary information processing (somatosensory, visual), executive control, default, and attentional networks, predicted exercise adherence (R2 = 0.15, p < 0.001). Traditional survey and clinical measures such as gait and walking self-efficacy, biological sex and perceived stress also predicted adherence (R2 = 0.06, p = 0.001) but a combined multimodal model achieved the highest predictive strength (R2 = 0.22, p <0.001). Neuroimaging features alone can predict adherence to a structured group-based exercise intervention in older adults which suggests there is substantial utility of these measures for future research into precision medicine approaches. The best performing model contained multimodal features suggesting that each modality provided independent relevant information in the prediction of exercise adherence.

neuroscience↗

bioRxiv2020

CoronaHiT: large scale multiplexing of SARS-CoV-2 genomes using Nanopore sequencing

The COVID-19 pandemic has spread to almost every country in the world since it started in China in late 2019. Controlling the pandemic requires a multifaceted approach including whole genome sequencing to support public health interventions at local and national levels. One of the most widely used methods for sequencing is the ARTIC protocol, a tiling PCR approach followed by Oxford Nanopore sequencing (ONT) of up to 96 samples at a time. There is a need, however, for a flexible, platform agnostic, method that can provide multiple throughput options depending on changing requirements as the pandemic peaks and troughs. Here we present CoronaHiT, a method capable of multiplexing up to 96 small genomes on a single MinION flowcell or >384 genomes on Illumina NextSeq, using transposase mediated addition of adapters and PCR based addition of barcodes to ARTIC PCR products. We demonstrate the method by sequencing 95 and 59 SARS-CoV-2 genomes for routine and rapid outbreak response runs, respectively, on Nanopore and Illumina platforms and compare to the standard ARTIC LoCost nanopore method. Of the 154 samples sequenced using the three approaches, genomes with [≥] 90% coverage (GISAID criteria) were generated for 64.3% of samples for ARTIC LoCost, 71.4% for CoronaHiT-ONT, and 76.6% for CoronaHiT-Illumina and have almost identical clustering on a maximum likelihood tree. In conclusion, we demonstrate that CoronaHiT can multiplex up to 96 SARS-CoV-2 genomes per MinION flowcell and that Illumina sequencing can be performed on the same libraries, which will allow significantly higher throughput. CoronaHiT provides increased coverage for higher Ct samples, thereby increasing the number of high quality genomes that pass the GISAID QC threshold. This protocol will aid the rapid expansion of SARS-CoV-2 genome sequencing globally, to help control the pandemic.

genomics↗

bioRxiv2019

Prevalence and Determinants of Caesarean Section in South and South-east Asian Women

BackgroundCaesarean section is considered a preferable and safe method of delivery. In the last decade, its prevalence has increased in both developed and developing countries. In the context of developing countries viz., South Asia (the highest populated region) and South-east Asia (the third highest populated region), the preference for, and variation in, caesarean section delivery and its associated maternal socioeconomic characteristics are still to be determined.\n\nObjectiveTo study the magnitude of caesarean delivery in the South and South-east Asian countries, by correlating the maternal socioeconomic characteristics with the preference for caesarean sections.\n\nMethodologyData on ever-married women of nine developing countries of South and South-east Asia viz., Vietnam, India, Maldives, Timor-Leste, Nepal, Indonesia, Pakistan, Bangladesh and Cambodia, from Demographic and Health Survey has considered. Both bivariate and multivariate binary logistic regression models were used to estimate the probability that a woman undergoes caesarean section and to assess the influence of maternal socioeconomic characteristics towards the preference for caesarean section.\n\nConclusionIn seven urban and four rural regions of nine South and South-East Asian countries, a significant inclination towards the caesarean delivery above the more recent outdate WHO recommended optimal range of 10-15% or the more recent study by top researchers of 19% has been found. The analysis confirmed that the prevalence of caesarean section and its associated maternal socioeconomic characteristics varied widely among these nine South and South-East Asian countries.

scientific communication and education↗

bioRxiv2019

Differential Requirements for the RAD51 Paralogs in Genome Repair and Maintenance in Human Cells

Deficiency in several of the classical human RAD51 paralogs [RAD51B, RAD51C, RAD51D, XRCC2 and XRCC3] is associated with cancer predisposition and Fanconi anemia. To investigate their functions, isogenic disruption mutants for each were generated in non-transformed MCF10A mammary epithelial cells and in transformed U2OS and HEK293 cells. In U2OS and HEK293 cells, viable ablated clones were readily isolated for each RAD51 paralog; in contrast, with the exception of RAD51B, RAD51 paralogs are cell-essential in MCF10A cells. Underlining their importance for genomic stability, mutant cell lines display variable growth defects, impaired sister chromatid recombination, reduced levels of stable RAD51 nuclear foci, and hypersensitivity to mitomycin C and olaparib. Altogether these observations underscore the contributions of RAD51 paralogs in diverse DNA repair processes, and demonstrate essential differences in different cell types. Finally, this study will provide useful reagents to analyze patient-derived mutations and to investigate mechanisms of chemotherapeutic resistance deployed by cancers.

cell biology↗

bioRxiv2017

Shu complex SWS1-SWSAP1 is required for mouse meiotic recombination in concert with the BRCA2 C terminus

Homology recognition and DNA-strand invasion ensure faithful homolog pairing and segregation during the first meiotic division1. RAD51 and DMC1 recombinases catalyze these steps2, with BRCA2 promoting their assembly into nuclear foci3. The recently identified human SWS1-SWSAP1 complex, related to the Shu complex in yeast, promotes RAD51 focus formation in cell lines4,5. We show here that mouse SWS1-SWSAP1 is critical for meiotic homologous recombination (HR) by promoting the assembly of RAD51 and DMC1 on early recombination intermediates. Absence of the complex perturbs meiotic progression in males and females and both sexes are sterile, although a fraction of meiocytes form crossovers. Remarkably, loss of the DNA damage checkpoint kinase CHK2 rescues fertility specifically in females without rescuing crossover numbers. Unlike the Shu complex, the BRCA2 C terminus (known to be required for RAD51 stabilization6,7) is dispensible for RAD51 and DMC1 focus formation. However, concomitant loss of the BRCA2 C terminus aggravates the meiotic defects in Shu mutant spermatocytes. These results point to a complex interplay of factors that ensure recombinase function and hence meiotic progression in the mouse.

genetics↗