Biology subjects

Panda, S. K.

Publications and source records attributed to Panda, S. K..

13 recordsLinked to original sources

bioRxiv2026

Integrated miRNA-protein profiling of small extracellular vesicle cargo reveals dynamic cargo remodelling during tissue repair in UV-C-damaged C. elegans

Ultraviolet-C (UV-C) radiation is a potent environmental stressor that induces DNA damage, accumulation of reactive oxygen species (ROS), and cellular dysfunction. This also initiates coordinated molecular responses to regulate cellular adaptation and recovery. Small extracellular vesicles (sEVs) have emerged as key mediators of intercellular communication through the selective incorporation of microRNAs (miRNAs), proteins, and lipids. However, the temporal changes of sEV-associated cargo during the progression from UV-C-induced damage to recovery remain uncharacterized. We hypothesised that UV-C exposure induces stage-specific changes in sEV cargo (miRNA and proteins) that promote the transition of cells from damage to the response and recovery phases. To examine this, a time-resolved UV-C exposure model was established using Caenorhabditis elegans (C. elegans). In this paper, we studied 2.5 hours of UV-C exposure, including cellular damage, intracellular ROS levels, and DNA integrity, to define the damage and repair state. Based on these temporal variations, samples were collected: i) immediately after exposure, ii) 6 hours post-exposure, and iii) 16 hours post-exposure were designated as damage, response, and recovery conditions, respectively. sEVs isolated from whole-worm preparations were characterised using biophysical and molecular approaches, followed by miRNA sequencing and proteomic analyses. Integrative analysis further identified miRNA-protein associations and associated them with pathways involved in stress adaptation, metabolism, signal transduction, and cellular homeostasis. Collectively, these findings provide a temporal molecular framework of sEV cargo associated with UV-C-induced damage, response, and recovery in C. elegans. Overall, this study identified candidate molecular signatures and miRNA-protein associations that underlie the temporally selective packaging of sEV-associated cargo following UV-C-induced damage, providing a basis for future tissue-specific and mechanistic investigations.

molecular biology↗

bioRxiv2026

Early Blood Metabolome Remodeling Reveals Metabolic Signatures of Hypoxic-Ischemic Encephalopathy

Hypoxic-ischemic encephalopathy (HIE) is a neonatal brain injury in which a definitive diagnosis within the first 6 hours of life is essential for initiating therapeutic hypothermia and improving neurological outcomes. However, early clinical evaluation and currently available biomarkers lack quantitative specificity during this narrow therapeutic window. We are providing insights into how rapid disturbances in systemic metabolites that regulate cerebral energy metabolism, neurotransmitter cycling, redox balance, and membrane integrity generate a definitive biochemical signature of HIE immediately after birth. We performed quantitative blood-based 1H NMR metabolomics on collected blood samples within [~]1 hour of birth from 81 neonates (HIE, n = 42; non-HIE, n = 39), under optimized handling conditions to preserve metabolic integrity. Metabolite analysis revealed a distinct HIE-associated profile characterized by elevated lactate, alanine, succinate, glutamate, taurine, glycine, choline, and pyroglutamate, alongside significant depletion of glucose and glutamine compared with non-HIE controls (p < 0.05). These coordinated metabolic shifts reflect impaired mitochondrial respiration, enhanced anaerobic glycolysis, excitotoxic amino acid accumulation, altered membrane phospholipid turnover, and oxidative stress. Multivariate analysis demonstrated clear separation between groups (PLS-DA accuracy = 0.83, R{superscript 2}Y = 0.46, Q{superscript 2} = 0.82), with glutamine, lactate, glutamate, and pyroglutamate as key discriminators. Pathway enrichment highlighted perturbations in glycolysis, the glucose-alanine cycle, glutamate-glutamine metabolism, Warburg effect like metabolic reprogramming, and redox homeostasis. Integration into supervised machine-learning models (Random Forest, XGBoost, SVM, KNN) achieved strong diagnostic performance (AUC = 0.97 {+/-} 0.03; sensitivity {approx} 87%). Collectively, this minimally invasive NMR-to-machine-learning framework enables early, mechanistically grounded risk stratification of neonatal HIE within the therapeutic window.

neuroscience↗

bioRxiv2025

FuChi: A cell cycle biosensor for investigating cell-cycle kinetics during avian development.

The ability to monitor the proliferative status of live cells both in vitro and in vivo over time has revolutionised our understanding of development, growth and disease. This was first made possible by fluorescent ubiquitination-based cell cycle indicator (Fucci) technology, which distinguishes specific cell cycle phases through the reciprocal degradation of fluorescently tagged, truncated forms of human CDT1 and GMNN proteins. Fucci genetic systems have been successfully implemented in transgenic mice, zebrafish, and axolotls. To date, no viable, stably expressing Fucci line has been developed in an avian species. Although a range of continuously improving Fucci constructs have been developed in recent years, existing in vivo Fucci models remain limited because they rely on older reporter technology that fails to distinguish cells in S, G2, and M phases or to label cells in early G1. As a result, these models can be challenging to interpret and their utility for continuous cell tracking and precise analysis of cell-cycle dynamics is limited. Here, we introduce FuChi, a multicistronic Fucci-expressing chicken line incorporating a newly optimised reporter construct composed of an mCerulean-tagged Histone H1.0 linker protein fused via a self-cleaving 2A peptide to the tandem Fucci(CA) cell cycle biosensor, with additional epitope tags included for detection in fixed tissues. We show that this system accurately discriminates and permits tracking of cells in G1, S, G2, and M phases both in vitro and in vivo, enabling faithful visualisation of cell cycle status in intact tissues and organs. Using FuChi embryos, we mapped proliferation dynamics across developing tissues, analysed cell cycle states of migrating cells, and performed live imaging of early embryos. These latter experiments revealed that transition from S phase may be a key morphogenetic event during gastrulation as mesendoderm cells egress from the primitive streak to form embryonic structures including the prechordal plate. Pairing this advanced reporter with the intrinsic experimental advantages of the chicken embryo positions FuChi as a premier in vivo system for studying cell-cycle kinetics in development, delivering clear technological improvements over current Fucci models. FuChi chickens provide a powerful new resource for studying embryonic development, organ growth, tissue homeostasis, disease processes, and infection responses.

developmental biology↗

bioRxiv2025

Clostridium novyi type B causes fatal hemorrhagic disease in wild Asian elephants

The population of Asian elephants, an endangered species, is decreasing significantly due to anthropogenic interference in India. Research on Asian elephant disease is largely confined to observations reported from captive populations. The present study explored 11 disease investigation cases whose clinicopathological changes were similar to those of fatal hemorrhagic disease caused by Bacillus anthracis. We used molecular diagnostic approaches such as PCR (polymerase chain reaction), quantitative PCR, 16S metagenomics analysis and whole-metagenome sequencing for identification of the etiological agent responsible for these wild elephant mortalities. 16S metagenomics analysis revealed the presence of Clostridium hemolyticum as the dominant bacteria in all the mortality events. In contrast, flagellin gene-specific identification of all the samples and whole metagenomics analysis of blood samples collected from the ear pinna of a freshly deceased elephant revealed Clostridium novyi type B as the sole pathogenic agent responsible for the death of elephants. This study provides the first evidence of the involvement of Clostridium novyi type B in the death of wild elephants with similar clinical manifestations to anthrax. The current study also provides ample evidence of the need to explore investigations of emerging diseases of wild elephants to conserve these large mammals.

microbiology↗

bioRxiv2022

The Structural Layers of the Porcine Iris Exhibit Inherently Different Biomechanical Properties

PurposeTo isolate the structural components of the ex vivo porcine iris tissue and to determine their biomechanical properties. MethodsThe porcine stroma and dilator tissues were separated, and their dimensions were assessed using optical coherence tomography (OCT). The stroma underwent flow test (n = 32) to evaluate for permeability using Darcys Law ({Delta}P = 2000 Pa, A = 0.0391 mm2), and both tissues underwent stress relaxation experiments ({varepsilon} = 0.5 with initial ramp of {delta}{varepsilon} = 0.1) to evaluate for their viscoelastic behaviours (n = 28). Viscoelasticity was characterised by the parameters {beta} (half width of the Gaussian distribution), {tau}m(mean relaxation time constant), E0 (instantaneous modulus) and E{infty} (equilibrium modulus). ResultsFor the stroma, the hydraulic permeability was 9.49 {+/-} 3.05 x 10-6 mm2/Pa{middle dot}s, and the viscoelastic parameters were {beta} = 2.50 {+/-} 1.40, and {tau}m = 7.43 {+/-} 4.96 s, with the two moduli calculated to be E0= 14.14 {+/-} 6.44 kPa and E{infty} = 6.08 {+/-} 2.74 kPa. For the dilator tissue, the viscoelastic parameters were {beta} = 2.06 {+/-} 1.33 and {tau}m = 1.28 {+/-} 1.27 s, with the two moduli calculated to be E0 = 9.16 {+/-} 3.03 kPa and E{infty} = 5.54 {+/-} 1.98 kPa. ConclusionWe have established a new protocol to evaluate the biomechanical properties of the structural layers of the iris. Overall, the stroma was permeable and exhibited smaller moduli than those of the dilator muscle. An improved characterisation of iris biomechanics may form the basis to further our understanding of angle closure glaucoma.

bioengineering↗

bioRxiv2021

Differing Associations between Optic Nerve Head Strains and Visual Field Loss in Normal- and High-Tension Glaucoma Subjects

PurposeTo study the associations between optic nerve head (ONH) strains under intraocular pressure (IOP) elevation with retinal sensitivity in glaucoma subjects. DesignClinic based cross-sectional study. Participants229 subjects with primary open angle glaucoma (subdivided into 115 high tension glaucoma (HTG) subjects and 114 normal tension glaucoma (NTG) subjects). MethodsFor one eye of each subject, we imaged the ONH using spectral-domain optical coherence tomography (OCT) under the following conditions: (1) primary gaze and (2) primary gaze with acute IOP elevation (to approximately 33 mmHg) achieved through ophthalmodynamometry. A 3-dimensional (3D) strain-mapping algorithm was applied to quantify IOP-induced ONH tissue strain (i.e. deformation) in each ONH. Strains in the pre-lamina tissue (PLT)and the retina, the choroid, the sclera and the lamina cribrosa (LC) were associated (using linear regression) with measures of retinal sensitivity from the 24-2 Humphrey visual field test (Carl Zeiss Meditec, Dublin, CA, USA). This was done globally, then locally according to the regionalization scheme of Garway-Heath et al. Main Outcome MeasuresAssociations between ONH strains and values of retinal sensitivity from visual field testing. ResultsFor HTG subjects, we found that (1) there were significant negative linear associations between ONH strains and retinal sensitivity (p<0.001) (on average, a 1% increase in ONH strains corresponded to a decrease in retinal sensitivity of 1.1 dB), (2) high strain regions co-localized with anatomically-mapped regions of high visual field loss, (3) the strongest negative associations were observed in the superior region and in the PLT. In contrast, for NTG subjects, no significant associations between strains and retinal sensitivity were observed except in the supero-temporal region of the LC. ConclusionWe found significant negative associations between IOP-induced ONH strains and retinal sensitivity in a relatively large glaucoma cohort. Specifically, HTG subjects who experienced higher ONH strains were more likely to exhibit lower retinal sensitivities. Interestingly, this trend was in general less pronounced in NTG subjects, which could suggest a distinct pathophysiology between the two glaucoma subtypes.

bioengineering↗

bioRxiv2021

Transcriptomic analysis revealed reactive oxygen species scavenging mechanisms associated with ferrous iron toxicity in aromatic Keteki Joha rice

Lowland acidic soils with water-logged regions are often affected by ferrous iron (Fe2+) toxicity, a major yield-limiting factor of rice production. The Reactive Oxygen Species (ROS) was hypothesized to be crucial under severe Fe2+ toxicity conditions. However, molecular mechanisms and associated ROS homeostasis genes are still not well-explored. In this study, a comparative RNA-Seq based transcriptome analysis was conducted to understand the Fe2+ toxicity tolerance mechanism in aromatic Keteki Joha. About 69 Fe homeostasis related genes and their homologs were identified, where most of the genes were downregulated. Differentially expressed genes (DEGs) are associated with biological processes-response to stress, stimulus and abiotic stimulus. DEGs involved in the Biosynthesis of amino acids, RNA degradation, Glutathione metabolism etc. were induced, whereas, Phenylpropanoid biosynthesis, Photosynthesis, and Fatty acid elongation were inhibited. The Mitochondrial iron transporter (OsMIT), Vacuolar Iron Transporter 2 (OsVIT2), Ferritin (OsFER), Vacuolar Mugineic Acid Transporter (OsVMT), Phenolic Efflux Zero1 (OsPEZ1), Root Meander Curling (OsRMC), Nicotianamine synthase (OsNAS3), etc. were upregulated in different tissues suggesting the importance of Fe retention and sequestration for detoxification. However, several antioxidants, ROS scavenging genes and abiotic stress-responsive transcription factors indicate ROS homeostasis as one of the most important defense mechanisms under severe Fe2+ toxicity. The CAT, GSH, APX, MDHAR, DHAR, GR were upregulated. Moreover, abiotic stress-responsive transcription factors NAC, MYB, ARF, bZIP, WRKY, C2H2-ZFP were also upregulated. Accordingly, ROS homeostasis has been proposed to be an important defense mechanism under such conditions. Thus, our results will enrich the knowledge of understanding Fe-homeostasis in rice.

genomics↗

bioRxiv2021

Adduction Induces Large Optic Nerve Head Deformations in Subjects with Normal Tension Glaucoma

Purpose: To assess optic nerve head (ONH) deformations and strains during adduction, abduction, and intraocular pressure (IOP) elevation in subjects with high-tension glaucoma (HTG) and normal-tension glaucoma (NTG). Design: Clinic-based cross-sectional study. Participants: 114 HTG subjects and 114 NTG subjects. Methods. We recruited 228 subjects (114 subjects with HTG [pre-treatment IOP > 21mmHg] and 114 with NTG [pre-treatment IOP < 21mmHg]). For each subject, we imaged the ONH using spectral-domain optical coherence tomography (OCT) under the following conditions: (1) primary gaze, (2) 20 degree adduction, (3) 20 degree abduction, and (4) primary gaze with acute IOP elevation (to approximately 33 mmHg) achieved through ophthalmodynamometry. For each OCT volume, we automatically segmented the prelaminar tissue (PLT), the choroid, the sclera and the lamina cribrosa (LC) using a deep learning algorithm. We also digitally aligned the OCT volumes obtained from (2)-(4) to the primary gaze volume (1) before performing digital volume correlation (DVC) analysis to quantify IOP- and gaze-induced ONH tissues three-dimensional displacements and effective strain (a local measure of tissue deformation) for all scenarios. Main Outcome Measures: Three-dimensional ONH displacements and strains. Results: Across all subjects, adduction generated high effective strain (4.2 {+/-} 1.4%) in the ONH tissues with no significant difference (p>0.05) with those induced by IOP elevation (4.5 {+/-} 1.5%); while abduction generated significantly lower (p = 0.014) effective strain (3.8 {+/-} 1.1%). Interestingly, the LC of HTG subjects exhibited significantly higher effective strain than those of NTG subjects under IOP elevation (HTG:4.6 {+/-} 1.7% vs NTG:4.1 {+/-} 1.5%, p = 0.047). Conversely, the LC tissue of NTG subjects exhibited significantly higher effective strain than those of HTG subjects under adduction (NTG: 4.9 {+/-} 1.9% vs HTG: 4.0 {+/-} 1.4%, p = 0.041). Conclusion: We found that adduction produced comparable strains and displacements as IOP elevation. We also found that NTG subjects experienced higher strains due to adduction than HTG subjects, while HTG subjects experienced higher strain due to IOP elevation than NTG subjects - and that these differences were most pronounced in the LC tissue.

bioengineering↗

bioRxiv2021

Changes in Iris Stiffness and Permeability in Primary Angle Closure Glaucoma

PurposeTo evaluate the biomechanical properties of the iris by evaluating iris movement during pupil constriction and to compare such properties between healthy and primary angle-closure glaucoma (PACG) subjects. MethodsA total of 140 subjects were recruited for this study. In a dark room, the anterior segments of one eye per subject were scanned using anterior segment optical coherence tomography (AS-OCT, SS-1000 CASIA, Tomey Corporation, Nagoya, Japan) imaging during induced pupil constriction with an external white light source of 1700 lux. Using a custom segmentation code, we automatically isolated the iris segments from the AS-OCT images, which were then discretized and transformed into a three-dimensional point cloud. For each iris, a finite element (FE) mesh was constructed from the point cloud, and an inverse FE simulation was performed to match the clinically observed iris constriction in the AS-OCT images. Through this optimization process, we were able to identify the elastic modulus and permeability of each iris. ResultsFor all 140 subjects (95 healthy and 45 PACG of Indian/Chinese ethnicity, Age: 60.2{+/-}8.7 for PACG subjects and 57.7{+/-}10.1 for healthy subjects), the simulated deformation pattern of the iris during pupil constriction matched well with OCT images. We found that the iris stiffness was higher in PACG than in healthy controls (24.5{+/-}8.4 kPa vs 17.1{+/-}6.6 kPa with 40 kPa of active stress specified in the sphincter region; p < 0.001), whereas iris permeability was lower (0.41{+/-}0.2 mm2/kPa.s vs 0.55{+/-}0.2 mm2/kPa.s; p = 0.142). ConclusionThis study suggests that the biomechanical properties of the iris in PACG are different from those in healthy controls. An improved understanding of the biomechanical behavior of the iris may have implications for the understanding and management of angle-closure glaucoma.

bioengineering↗

bioRxiv2021

An active finite viscoelastic model for gastric smooth muscle contraction

A coupled electromechanical model to describe the transduction process of cellular electrical activity into mechanical deformation has been presented. The model consolidates a biophysical smooth muscle cell model, a biophysical actin-myosin interaction model, a sliding filament model and a viscoelastic constitutive model to construct an active finite viscoelastic model. The key input to this model is an electrical pulse which then estimates the resulting stress and deformation in the cell. The proposed model was used to recreate experimental observations performed on canine and porcine gastric tissue strips. In all cases, the simulation results were well matched with the experimental data (R2 > 0.9).

biophysics↗

bioRxiv2020

Transcriptomic expression patterns of two contrasting lowland rice varieties reveal high iron stress tolerance

Iron (Fe) toxicity is a major challenge for plant cultivation in acidic water-logged soil environments, where lowland rice is a major staple food crop. Only few studies addressed the molecular characterization of excess Fe tolerance in rice, and these highlight different mechanisms for Fe tolerance in the studied varieties. Here, we screened 16 lowland rice varieties for excess Fe stress growth responses to identify contrasting lines, Fe-tolerant Lachit and -susceptible Hacha. Hacha and Lachit differed in their physiological and morphological responses to excess Fe, including leaf growth, leaf rolling, reactive oxygen species generation, Fe and metal contents. These responses were mirrored by differential gene expression patterns, obtained through RNA-sequencing, and corresponding GO term enrichment in tolerant versus susceptible lines. From the comparative transcriptomic profiles between Lachit and Hacha in response to excess Fe stress, individual genes of the category metal homeostasis, mainly root-expressed, may contribute to the tolerance of Lachit. 22 out of these 35 metal homeostasis genes are present in selection sweep genomic regions, in breeding signatures and/or differentiated during rice domestication. These findings will serve to design targeted Fe tolerance breeding of rice crops. Summary statementLowland rice varieties Hacha and Lachit were selected for contrasting abilities to cope with iron excess stress. Morphological and physiological phenotypes were mirrored by molecular transcriptome changes, indicating altered metal homeostasis in the root as an adaptive tolerance mechanism in Lachit.

plant biology↗

bioRxiv2020

Identifying novel B-cell targets for chronic inflammatory autoimmune disease by screening of chemical probes in a patient-derived cell assay

B-cell secretion of autoantibodies drives autoimmune diseases, including systemic lupus erythematosus and idiopathic inflammatory myositis. Few therapies are presently available for treatment of these patients, often resulting in unsatisfactory effects and helping only some of patients. We developed a screening assay for evaluation of novel targets suspending B-cell maturation into antibody secreting cells, which could contribute to future drug development. The assay was employed for testing 43 high quality chemical probes and compounds inhibiting under-explored protein targets, using primary cells from patients with autoimmune disease. Probes inhibiting bromodomain family proteins and histone methyl transferases demonstrated abrogation of B-cell functions to a degree comparable to a positive control, the JAK inhibitor tofacitinib. Inhibition of each target rendered a specific functional cell and potential disease modifying effect, indicating specific epigenetic protein targets as potential new intervention points for future drug discovery and development efforts.

immunology↗

bioRxiv2019

Physical activity improves sarcopenia in a murine model by enhancing the proliferative potential of muscle stem cells, oxidative capacity of mitochondrial enzymes and expression of Sestrins

Sarcopenia is a major health issue in old age. Underlying molecular mechanisms in its genesis remain unclear and optimal animal models are yet to be established. A novel animal model was developed to identify structural and functional changes in skeletal muscles from sarcopenia. The influence of physical activity on animals of the sarcopenic model with respect to the expression of anti-oxidant proteins, mitochondrial oxidative capacity, and effect on muscle stem cells (MuSCs), were assessed. Male C57Bl/6 mice of different age groups were recruited: Y-Cntrl (young-control), A-Cntrl (aged-control), SAR-model and SAR-INT. SAR-model group was kept in a retrofitted confined cage and was fed with customized protein-restricted diet (14% protein), which is considered as a sarcopenic featured model. SAR-INT served as the intervention group. Three parameters, namely, muscle mass, grip strength, and physical endurance, were used to confirm the sarcopenic state. All physical parameters deteriorated most in SAR-model and it improved in the SAR-INT group. The impact of physical activity on the SAR-INT group was also evidenced by the improved proliferative potential of MuSCs determined by flow cytometric analysis. Compared with the SAR-model, the SAR-INT exhibited significant improvement in the oxidative capacity of mitochondrial enzymes and increased expression of anti-oxidant proteins, sestrins. In conclusion, physical activity improved physical parameters, MuSC proliferative potential, mitochondrial enzyme oxidative capacity and sestrin expression in sarcopenic animals. Hence, SAR-model in mice can serve as a novel sarcopenic model, physical activity provides scope for improvement in sarcopenic population and sestrin molecule can have a potential implication on sarcopenia.

molecular biology↗