Biology subjects

Kundu, A.

Publications and source records attributed to Kundu, A..

At least 19 recordsLinked to original sources

bioRxiv2026

AntiOxiPred: Predicting Antioxidant Peptides using Machine Learning Techniques and BLAST

Antioxidant peptides (AOPs) offer significant therapeutic potential in counteracting oxidative damage associated with chronic diseases. As AOPs gain market traction in cosmeceuticals, functional foods, and clinical trials for disease intervention, efficient computational methods are essential to accelerate their discovery. In this study, a systematic attempt has been made to develop a highly accurate and reliable method for predicting AOPs from their primary sequences. The dataset comprises 1,511 experimentally validated AOPs and 1,511 randomly generated non-AOPs, partitioned into 2,417 sequences for training and 606 for testing. First, we developed machine learning-based models using one-hot encoded (OHE) representations, sequence-derived compositional features, protein language model (PLM) embeddings, and feature fusion. Our CatBoost model, developed using selected fused features, achieved the best performance, with an AUC of 0.945 and an MCC of 0.788 on the independent testing dataset. An ensemble model combining CatBoost with BLAST achieved a peak AUC of 0.956 on the same testing dataset. Furthermore, our method outperformed existing state-of-the-art predictors when benchmarked on two external validation datasets comprising 150 peptides (75 AOPs and 75 non-AOPs) and 248 peptides (124 AOPs and 124 non-AOPs). AntiOxiPred (https://webs.iiitd.edu.in/raghava/antioxipred/) is freely available as an interactive web server, a standalone package, and a pip-installable tool to support the scientific community.

bioinformatics↗

bioRxiv2026

Urea is a dynamic and functional component of mammalian breast milk

Urea is a constituent of human milk, yet its regulation and interactions with the infant gut microbiome remain unclear. Combining three human cohorts, a controlled mouse model, and complementary microbiome analyses, we show that milk urea increases across lactation, is conserved across mammals, and is not explained by circulating urea levels or maternal diet. Instead, we identify lactation-dependent remodeling of mammary urea-metabolism and transport pathways, including dynamic AQP3 localization in secretory epithelium, indicative of regulated transfer of circulating urea into breast milk. Alongside urea, maternal milk and stool provide complementary reservoirs of urea-metabolizing bacteria that help establish the infant "ureabiome", whose urea-utilization capacity is supported by metagenomics. This maternal-infant axis is context-dependent: infant formulas provide substantially higher urea levels than human milk, while functional assays show that urea supports both commensal and opportunistic bacteria in a concentration-dependent manner. Together, these findings define a maternal nitrogen axis through which lactation can shape the assembly and function of the infant gut microbiome.

microbiology↗

bioRxiv2026

Novel Target Combinations in Lung Squamous Cell Carcinoma proposed by the Emet AI Research Environment and supported by discovery stage experimentation

Early drug discovery is frequently bottlenecked by target identification, a challenge that becomes particularly difficult in complex diseases driven by overlapping, redundant pathways rather than a single dominant driver. Lung squamous cell carcinoma (LUSC) is one such disease: mutationally complex, lacking a dominant actionable target, and marked by a long series of failed single-agent targeted trials. We hypothesized a research environment, capable of reasoning across interconnected datasets, would be well-suited to generate novel, mechanistically grounded therapeutic hypotheses for LUSC. Emet, an AI research environment utilizing a biomedical knowledge graph of more than 1.5 billion triples connected to over 100 specialised biological databases, was paired with an Agentic Research Director that pursues each hypothesis through a graph-of-thoughts search, invoking scoped link-prediction and retrieval tools and committing every round of findings to persistent memory. The top-ranked hypotheses were two-target combinations rather than a single target. The four highest-ranked combinations were advanced to dose-matrix testing in NCI-H520 and SK-MES-1 cells, and two produced combination effects exceeding either single agent; to our knowledge neither of these two pairings had previously been evaluated in LUSC. Dual inhibition of CDC7 (TAK-931) and PKMYT1 (RP-6306) produced statistically significant synergy in both lines that strengthened from day 5 to day 7 (HSA 19.24 to 24.19 in NCI-H520; 11.07 to 13.73 in SK-MES-1). Dual inhibition of USP13 (spautin-1) and PI3K (alpelisib) produced an additive, cell-line-dependent effect, and immunoblotting confirmed the predicted mechanism: time-dependent depletion of MCL-1, c-Myc and SOX-2 driven by the USP13 arm. Agentic reasoning over multi-domain biomedical evidence can therefore nominate testable, mechanism-bearing combination hypotheses that survive experimental scrutiny.

bioinformatics↗

bioRxiv2026

The demonstration of a single origin for nodule evolution, with nodule engineering in a non-nodulating species

The nitrogen-fixing root-nodule symbiosis provides a sustainable source of nitrogen for plants within the Nitrogen (N)-fixing clade (NFC). A debate has raged over whether nodulation evolved once, with many losses or multiple times following a predisposition event. Here we demonstrate that nodule-organogenesis is fully conserved between an actinorhizal nodulator Datisca glomerata and the legume Medicago truncatula, showing entirely conserved programmes for Nodule INception (NIN)-controlled development leading to nodule emergence. Convergent losses of N-fixation within the NFC is associated with loss of NIN and we show the engineering of nodule-like development into strawberry, a non-nodulating member of the NFC, through the repair of NIN-functionality. Similar NIN-engineering resulted in altered-root developmental responses in barley. Our work is consistent with the single-gain hypothesis, where repair of NIN can recapitulate nodules in species within the NFC, demonstrating that understanding the ancestral state of nodulation facilitates its engineering.

plant biology↗

bioRxiv2025

Integrative proteomics and metabolomics map reveals key sectors of defense metabolism in ginger against Pythium myriotylum

Ginger (Zingiber officinale) cultivation is severely threatened by rhizome rot caused by Pythium myriotylum. Hitherto, detail molecular machineries and metabolic pathways of defense against P. myriotylum in edible ginger are elusive. To elucidate the defense mechanisms, we employed integrative quantitative proteomics (TMT labelling) and high resolution untargeted metabolomics to investigate temporal defense responses of ginger during infection. Proteomics analysis revealed enrichment of cellular detoxification and secondary metabolism pathways indicating co-activation of oxidative stress management and its mediated defense metabolite biosynthesis. Key phenylpropanoid enzymes (PAL, C4H, CAD) and LOX, a regulator of jasmonic acid (JA) biosynthesis, were significantly up-regulated, correlating JA signaling with secondary metabolic defenses. Metabolomics profiling confirmed accumulation of phenylpropanoids, flavonoids, and terpenoids, including known antimicrobial metabolites such as gingerol, shogaol, curcumin, and gingerdione, alongside expression of their key regulatory enzyme was also induced. Notably, machine learning identified the monoterpenoid TGA as the top defense-associated metabolite. Functional assays demonstrated strong anti-P. myriotylum activity of TGA, which inhibited mycelial growth and suppressed expression of key pathogenicity-related genes (NIP1, GHs, cellulase). These findings highlight coordinated activation of detoxification and secondary metabolic pathways in ginger defense and establish TGA as a promising bio-control agent against P. myriotylum.

plant biology↗

bioRxiv2025

Discovery and structure-activity relationship analysis of 2-Pyridyl Thienopyrimidine derivatives as promising therapeutic candidates for the treatment of Buruli ulcer

Mycobacterium ulcerans, the bacterium causing Buruli ulcer (BU), can potentially develop resistance to existing antibiotics (rifampicin - clarithromycin/ moxifloxacin), underscoring the need for new antimycobacterial treatments. This study screened the Pathogen Box from Medicines for Malaria Venture (MMV) to identify M. ulcerans inhibitors. Four hit compounds were found, including the 2-(6-methylpyridin-2-yl)-N-(pyrimidin-4-yl)thieno[3,2-d]pyrimidin-4-amine MMV688122 as a novel anti-M. ulcerans chemotype. Synthesis of structural analogues of MMV688122 allowed the identification of 2-(4-methylpyridin-2-yl)-N-(pyrimidin-4-yl)thieno[3,2-d]pyrimidin-4-amine MMV1578877 as the most potent, with submicromolar activity. Importantly, this analogue was non-cytotoxic up to 100 {micro}M in human fibroblasts. Structure-activity relationship (SAR) studies indicated the crucial role of the methylpyridin-2-yl group in inhibiting M. ulcerans and the possibility to replace the thienopyrimidine core by a quinazoline. While MMV1578877 showed better metabolic stability than MMV688122, further improvement and testing in real-world M. ulcerans clinical isolates are still required. Further metabolite identification and SAR data should guide the optimization of this novel chemotype to enable in vivo testing. Author SummaryBuruli ulcer is a neglected tropical disease that causes severe skin ulcers and long-term disability, mostly affecting people in remote African communities. Current treatments rely on antibiotics that are not always effective and may lead to resistance. In this study, we searched for new drug candidates by testing a library of compounds provided by the Medicines for Malaria Venture (MMV). We discovered a promising new chemical family that can kill the bacteria responsible for Buruli ulcer in the lab. One compound, in particular, showed strong activity without harming human cells. This compound also showed better stability and effectiveness. These findings bring us closer to developing a new, safer, and more effective treatment for Buruli ulcer.

pharmacology and toxicology↗

bioRxiv2025

Optimization of Microwave-Assisted Extraction of AntioxidantCompounds from Vitex negundo Leaves using Response SurfaceMethodology

IntroductionPolyphenolic substances are obtained from the leaves of Vitex negundo has gained attention for its therapeutic benefits. ObjectivesTo obtain the maximized antioxidant-rich polyphenolic substances from the Vitex negundo leaves via microwave-assisted extraction (MAE). Material and MethodsBox-Behnken design (BBD) was employed to evaluate the influence of several variables of MAE on the total phenolic content (TPC) and total flavonoid content (TFC) as determined by Folin-Ciocalteu assay method and Aluminum Chloride assay method, and the antioxidant capacity as measured by DPPH and ABTS assay methods, respectively. Response surface methodology (RSM) was used for finding optimal extraction conditions. GC-MS analysis was conducted on the extract. The tocopherol content and anticancer potential were also estimated using HPLC and MTT assay respectively. ResultsThe ideal extraction parameters were found to be 14 minutes, 48 {degrees}C, 65 % (v/v) methanol concentration, and 14 mL of extraction solvent. The optimum experiment conditions produced the TPC and TFC values of 1.46 mg GAE/g extract and 1.06 mg QE/g extract respectively. Furthermore, the DPPH and ABTS assays results showed the optimum values of 53 % and 77 % respectively. 12 bioactive compounds were identified using GC-MS. The amount of tocopherol was found to be 414.87 {micro}g/g. Lastly, the obtained leaf extract was demonstrated its anticancer potential on PC3 cell lines. ConclusionThe findings demonstrated leaf extracts potential as a useful source of polyphenols with strong antioxidant qualities that can be used in a variety of pharmaceutical applications.

plant biology↗

bioRxiv2025

Actin contractility and endocytosis create apico-basal tension gradient in HeLa cells

The functions of the plasma membrane of a cell are coupled to its mechanical state. To understand the players that contribute to the tight regulation of membrane mechanics with its local heterogeneities, the tension of the cell membrane requires to be mapped out from the basal to the apical membrane. In this work, optical-trap-based tension measurements performed at two axial (z) planes per cell reveal an apico-basal gradient, that is understood better on comparison with basal membrane mechanics and membrane compaction measurements by a combination of high resolution microscopy (IRM) and fluorescence lifetime (Flipper-TR) measurements, respectively. While the apico-basal gradient in the apparent tension (low to high) was found to depend on an intact actin cytoskeleton, analysing the colocalization of the cortical actin with the motor protein myosin and the actin-membrane linker ezrin suggested that cytoskeleton contractility is a major determinant of the patterned tension. Tension-sensitive lifetime of Flipper-TR, validated the gradient but failed to catch the dependence on actin due to the dual and opposite effects of tension on lifetime. Finally, measurements utilizing fluorescently tagged transferrin (Tf) demonstrated that the functional state of the membrane also showed similar height dependence. Thus, planes where tension maximized showed a peak in accumulation of Tf colocalizing with clathrin indicative of the presence of more pits. This enabled us to demonstrate that cells exist in tightly regulated patterned tension states that is coupled to their cytoskeleton as well membrane functions like endocytosis. Significance StatementThe cell membrane is protective but also highly dynamic - performing a diverse set of functions usually via membrane shape changes. These functions affect membrane mechanics but are also mechano-regulated. Mapping the state of cell surface mechanics or tension of live cells is therefore of fundamental importance. Interestingly, recent works have suggested that membrane tension can be non-uniform. However, no single tension-measuring technique can truly reach every part of the cell. Our work addresses this issue where we map tension in live HeLa cells using multifarious approaches including the measurement of tether forces, membrane fluctuations, and lipid compaction. We show that at the top/apical surface, the membrane-tension is lower than that at the midplane. The observed gradient resembles that of the state of endocytosis and controlled acto-myosin contractility.

biophysics↗

bioRxiv2025

Distinct filament morphology and membrane tethering features of the dual FtsZs in Odinarchaeota

The deep-branching Asgard archaea have emerged as a model to study Eukaryogenesis as they harbor homologs of many of the major eukaryotic protein families. In this study, we use Candidatus Odinarchaeota FtsZs as representatives to understand the probable origin, evolution, and assembly of the FtsZ-Tubulin protein superfamily in Asgard archaea. We have performed a comparative analysis of the biochemical properties and cytoskeletal assembly of FtsZ1 and FtsZ2, the two FtsZ isoforms in the Odinarchaeota metagenome. Our electron microscopy analysis reveals that OdinFtsZ1 assembles into curved single protofilaments, while OdinFtsZ2 forms stacked spiral ring-like structures. Upon sequence analysis, we identified an N-terminal amphipathic helix in OdinFtsZ1, which mediates direct membrane tethering. In contrast, OdinFtsZ2 is recruited to the membrane by the membrane-anchor OdinSepF via OdinFtsZ2s C-terminal tail. Overall, we report the presence of two distant evolutionary paralogs of FtsZ in Odinarchaeota, with distinct filament assemblies and differing modes of membrane targeting mechanisms, namely direct vs SepF-mediated membrane binding. Our findings highlight the diversity of FtsZ proteins in the transitional archaeal phylum Odinarchaeota, providing valuable insights into the evolution and differentiation of tubulin family proteins.

biochemistry↗

bioRxiv2024

Renal L-2-hydroxyglutarate dehydrogenase activity promotes hypoxia tolerance and mitochondrial metabolism in Drosophila melanogaster

The mitochondrial enzyme L-2-hydroxyglutarate dehydrogenase (L2HGDH) regulates the abundance of L-2-hydroxyglutarate (L-2HG), a potent signaling metabolite capable of influencing chromatin architecture, mitochondrial metabolism, and cell fate decisions. Loss of L2hgdh activity in humans induces ectopic L-2HG accumulation, resulting in neurodevelopmental defects, altered immune cell function, and enhanced growth of clear cell renal cell carcinomas. To better understand the molecular mechanisms that underlie these disease pathologies, we used the fruit fly Drosophila melanogaster to investigate the endogenous functions of L2hgdh. Our studies revealed that while L2hgdh is not essential for growth or viability under standard culture conditions, L2hgdh mutants are hypersensitive to hypoxia and expire during the reoxygenation phase with severe disruptions of mitochondrial metabolism. Moreover, we find that the fly renal system (Malpighian tubules; MTs) is a key site of L2hgdh activity, as L2hgdh mutants that express a rescuing transgene within the MTs survive hypoxia treatment and exhibit normal levels of mitochondrial metabolites. We also demonstrate that even under normoxic conditions, L2hgdh mutant MTs experience significant metabolic stress and are sensitized to aberrant growth upon Egfr activation. Overall, our findings present a model in which renal L2hgdh activity limits systemic L-2HG accumulation, thus indirectly regulating the balance between glycolytic and mitochondrial metabolism, enabling successful recovery from hypoxia exposure, and ensuring renal tissue integrity.

genetics↗

bioRxiv2024

Transcriptome-wide quantitative profiling of PUS7-dependent pseudouridylation by nanopore direct long read RNA sequencing

Understanding the interactions between different RNA modifications is essential for unraveling their biological functions. Here, we report NanoPsiPy, a computational pipeline that employs nanopore direct RNA sequencing to identify pseudouridine ({Psi}) sites and quantify their levels at single-nucleotide resolution. We validated NanoPsiPy by transcriptome-wide profiling of PUS7-dependent {Psi} sites in poly-A RNA and rRNA. NanoPsiPy leverages {Psi}-induced U-to-C basecalling errors in nanopore sequencing data, allowing detection of both low and high stoichiometric {Psi} sites. We identified 8,624 PUS7-dependent {Psi} sites in 1,246 mRNAs encoding proteins associated with ribosome biogenesis, translation, and energy metabolism. Importantly, integrative analysis revealed that PUS7 knockdown increases global mRNA N6-methyladenosine (m6A) and 5-methylcytosine (m5C) levels, suggesting an antagonistic relationship between {Psi} and these modifications. Our study underscores the potential of nanopore direct RNA sequencing in revealing the co-regulation of RNA modifications and the capacity of NanoPsiPy in analyzing pseudouridylation and its impact on other RNA modifications.

cancer biology↗

bioRxiv2023

Formation of clathrin-pits and ATP-independent cholesterol-dependent tubules initiates mechano-regulation on de-adhesion.

Adherent cells ensure membrane homeostasis during de-adhesion by various mechanisms including endocytosis. Although mechano-chemical feedbacks involved in this process have been studied, the step-by-step build-up and resolution of the mechanical changes by endocytosis is not well understood. To investigate this, we study the de-adhesion of HeLa cells using a combination of interference reflection microscopy, optical-trapping and fluorescence experiments. We found that de-adhesion enhanced membrane height fluctuations of the basal membrane in the presence of an intact cortex. A reduction in the tether-force was also noted at the apical side. However, membrane fluctuations reveal phases of an initial drop in effective tension followed by a saturation. The area fractions of early (Rab5-labelled) and recycling (Rab4-labelled) endosomes as well as transferrin-labelled pits close to the basal plasma membrane also transiently increased. On blocking dynamin-dependent scission of endocytic pits, the regulation of fluctuations was not blocked but proceeded uncontrolled. Interestingly, the regulation could not be suppressed by ATP or cholesterol depletion individually but was arrested on depleting both. The data strongly supports pit-formation to be central to the reduction in fluctuations whether in normal or ATP depleted condition. Furthermore, while in normal conditions the contribution of clathrin-mediated endocytosis is clear, under ATP-depleted conditions we propose that cholesterol-dependent pits spontaneously regulate tension. SummaryWe show that during de-adhesion, cell edges retract, creating membrane folds and increasing fluctuations. Cells increase the rate of endocytosis to regulate back their membrane fluctuations. This is achieved by forming invaginations. Dynamin-dependent pathways are majorly involved, while cholesterol-dependent ATP-independent mechanisms also contribute.

biophysics↗

bioRxiv2023

Larger and denser: an optimal design for surface grids of EMG electrodes to identify greater and more representative samples of motor units

The spinal motor neurons are the only neural cells whose individual activity can be non-invasively identified. This is usually done using grids of surface electromyographic (EMG) electrodes and source separation algorithms; an approach called EMG decomposition. In this study, we combined computational and experimental analyses to assess how the design parameters of grids of electrodes influence the number and the properties of the identified motor units. We first computed the percentage of motor units that could be theoretically discriminated within a pool of 200 simulated motor units when decomposing EMG signals recorded with grids of various sizes and interelectrode distances (IED). Increasing the density, the number of electrodes, and the size of the grids, increased the number of motor units that our decomposition algorithm could theoretically discriminate, i.e., up to 83.5% of the simulated pool (range across conditions: 30.5-83.5%). We then identified motor units from experimental EMG signals recorded in six participants with grids of various sizes (range: 2-36 cm2) and IED (range: 4-16 mm). The configuration with the largest number of electrodes and the shortest IED maximized the number of identified motor units (56{+/-}14; range: 39-79) and the percentage of early recruited motor units within these samples (29{+/-}14%). Finally, the number of identified motor units further increased with a prototyped grid of 256 electrodes and an IED of 2 mm. Taken together, our results showed that larger and denser surface grids of electrodes allow to identify a more representative pool of motor units than currently reported in experimental studies. Significance statementThe application of source separation methods to multi-channel EMG signals recorded with grids of electrodes enables users to accurately identify the activity of individual motor units. However, the design parameters of these grids have never been discussed. They are usually arbitrarily fixed, often based on commercial availability. Here, we showed that using larger and denser grids of electrodes than conventionally proposed drastically increases the number of identified motor units. The samples of identified units are more balanced between early- and late-recruited motor units. Thus, these grids provide a more representative sampling of the active motor unit population. Gathering large datasets of motor units using large and dense grids will impact the study of motor control, neuromuscular modelling, and human-machine interfacing.

neuroscience↗

bioRxiv2022

Saccharomyces cerevisiae DJ-1 paralogs maintain genome integrity through glycation repair of nucleic acids and proteins

Reactive carbonyl species (RCS) such as methylglyoxal and glyoxal are potent glycolytic intermediates that extensively damage cellular biomolecules leading to genetic aberration and protein misfolding. Hence, RCS levels are crucial indicators in the progression of various pathological diseases. Besides the glyoxalase system, emerging studies report highly conserved DJ-1/ThiJ/PfpI superfamily proteins as critical regulators of RCS. DJ-1 superfamily proteins, including the human DJ-1, a genetic determinant of Parkinsons disease possess diverse physiological functions paramount for combating multiple stressors. Although S. cerevisiae retains four DJ-1 orthologs (namely Hsp31, Hsp32, Hsp33, and Hsp34), their physiological relevance and collective requirement are still obscure due to their close sequence similarity. Here, we report for the first time that the yeast DJ-1 orthologs function as novel enzymes involved in the preferential scavenge of glyoxal and methylglyoxal, toxic metabolites, and genotoxic agents. At the cellular level, their collective loss induces chronic glycation of the proteome, and nucleic acids, resulting in a spectrum of genetic mutations and reduced mRNA translational efficiency. Furthermore, the Hsp31 paralogs efficiently repair severely glycated macromolecules derived from carbonyl modifications. They also participate in genome maintenance as their absence upregulates DNA damage response pathways when exposed to different genotoxins. Interestingly, yeast DJ-1 orthologs provide robust organellar protection by redistributing into mitochondria to alleviate the glycation damage of mitochondrial DNA and proteins. Taken together, our study uncovers the existence of a novel glycation repair pathway in S. cerevisiae and a possible neuroprotective mechanism of how hDJ-1 confers mitochondrial health during carbonyl stress.

biochemistry↗

bioRxiv2021

TGF-B signaling suppresses TCA cycle metabolism in renal cancer.

The Warburg effect is one of most-well studied metabolic phenomenon in cancer cells. For the most part, these studies have focused on enhanced rates of glycolysis observed in various models. The presumption has been that mitochondrial metabolism is suppressed. However, recent studies indicate that the extent of mitochondrial metabolism is far more heterogeneous in tumors than originally presumed. One tumor type with suppression of mitochondrial metabolism is renal cell carcinoma (RCC). Prior studies indicate that suppressed TCA cycle enzyme mRNA expression is associated with aggressive RCC. Yet, the mechanisms that regulate the TCA cycle in RCC remain uncharacterized. Here, we demonstrate that loss of TCA cycle enzyme expression is retained in RCC metastatic tissues. Moreover, proteomic analysis demonstrates that reduced TCA cycle enzyme expression is far more pronounced in RCC relative to other tumor types. Loss of TCA cycle enzyme expression is correlated with reduced expression of the transcription factor peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1) which is also lost in RCC tissues. PGC-1 re-expression in RCC cells restores the expression of TCA cycle enzymes in vitro and in vivo and leads to enhanced glucose carbon incorporation into TCA cycle intermediates. Mechanistically, TGF-{beta} signaling, in concert with histone deacetylase 7 (HDAC7), suppresses TCA cycle enzyme expression. In turn, pharmacologic inhibition of TGF-{beta} restores expression of TCA cycle enzyme expression and suppresses tumor growth in an orthotopic model of RCC. Taken together, our findings reveal a novel role for the TGF-{beta} /HDAC7 axis in global suppression of TCA cycle enzymes in RCC and provide novel insight into the molecular basis of altered mitochondrial metabolism in this malignancy.

cancer biology↗

bioRxiv2021

Active microrheology using pulsed optical tweezers to probe viscoelasticity of Lamin A towards diagnosis of laminopathies

Lamins are nucleoskeletal proteins of mammalian cells that stabilize the structure and maintain the rigidity of the nucleus. These type V intermediate filament proteins which are predominantly of A and B types provide necessary tensile strength to the nucleus. Single amino acid missense mutations occurring all over the lamin A protein form a cluster of human diseases termed as laminopathies, a few of which principally affect the muscle and cardiac tissues responsible for load bearing functionalities of the body. One such mutation is lamin A350P which causes dilated cardiomyopathy in patients. It is likely that a change from alanine to proline in the -helical 2B rod domain of the protein might severely disrupt the propensity of the filaments to polymerise into functional higher order structures required to form a fully functional lamina with its characteristic elasticity. In this study, we validate for the very first time, the application of active microrheology employing oscillating optical tweezers to investigate any alterations in the visco-elastic parameters of the mutant protein meshwork in vitro, which might translate into possible changes in nuclear plasticity. We confirm our findings from this robust yet fast method by imaging both the wild type and mutant lamins using a super resolution microscope, and observe changes in the mesh size which explain our measured changes in the viscoelastic parameters of the lamins. This method could naturally be extended to conduct microrheological measurements on any intermediate filament protein or any protein endowed with elastic behavior, with minor schematic modifications, thus bearing significant implications in laminopathies and other diseases which are associated with changes in structural rigidity of any cellular organelle. SignificanceLamin A mutations produce an array of diseases termed as laminopathies which are primarily characterized by alteration of elastic behavior of the nucleus which in turn leads to defects in mechanotransduction. This is the first report in the lamin arena which shows a fast, accurate and direct quantification of elastic moduli of lamin A using optical tweezers-based microrheology. This has very significant implications and can be registered to be a robust and universal method that could also be suitably used for probing changes in elastic properties of any proteins or surfactants in a disease scenario such as SARS-Cov2 (Covid-19), which is pandemic at this time.

biophysics↗

bioRxiv2021

Piriformospora indica employs hosts putrescine for growth promotion in plants

Growth promotion by endosymbiont Piriformospora indica has been observed in various plants; however, specific functional metabolites involved in P. indica mediated growth promotion are unknown. A GC-MS based untargeted metabolite analysis was used to identify Solanum lycopersicum metabolites altered during P. indica mediated growth promotion. Metabolomic analysis showed primary metabolites altered and specifically putrescine to be maximally induced in roots during the interaction. P. indica induced putrescine biosynthetic gene SlADC1 in S. lycopersicum and acts via arginine decarboxylase (ADC) mediated pathway. P. indica did not promote growth in Sladc-VIGS (virus induced gene silencing of SlADC gene) lines of S. lycopersicum and when the ADC enzyme was inhibited with an inhibitor, DL--(Difluoromethyl) arginine. In Arabidopsis adc knock-out mutants, P. indica do not promote growth and this response was rescued upon exogenous application of putrescine. Putrescine promoted growth by elevation of auxin (indole-3-acetic acid) and gibberellin (GA4, GA7) levels in S. lycopersicum. Putrescine is also important for P. indica hyphal growth indicating that it is co-adapted by both host and microbe. Hence, we conclude that putrescine is an essential metabolite and its biosynthesis in plants is crucial for P. indica mediated growth promotion and fungal growth.

plant biology↗

bioRxiv2020

Peripheral electrical stimulation augments cerebral collateral circulation if performed within a critical time window.

Ischemic stroke is one of the leading causes of death and disability in the world. Recent advances in acute stroke care have dramatically improved clinicians abilities to reperfuse occluded blood vessels. With these advances, the importance of adjunctive therapies to supplement or complement reperfusion therapy is receiving greater interest. Cerebral collateral circulation is one of such area that is now gaining greater interest in acute stroke care. In this study, we investigate the use of peripheral electrical stimulation to induce functional hyperemia in a mouse animal model in the setting of acute stroke. Using a laser speckle contrast imaging system, we evaluated the use of peripheral electrical stimulation at 1 hour and 3 hours after stroke induction. Results demonstrated that stimulation initiated 1 hour following stroke significantly increase collateral cerebral blood flow, while stimulation at 3 hours after stroke had no appreciable effect. These results suggest that augmentation cerebral collateral circulation may be possible in the setting of acute stroke although there may be a critical time window in which this would have to be initiated.

neuroscience↗