Biology subjects

Chakrabarty, S.

Publications and source records attributed to Chakrabarty, S..

At least 19 recordsLinked to original sources

bioRxiv2026

An Evolutionarily Conserved Ypk1/SGK1 Kinase Pathway Regulates the Unfolded Protein Response by Modulating the Ire1 Protein Abundance

The unfolded protein response (UPR) is a cellular mechanism that maintains protein homeostasis (proteostasis) under conditions of endoplasmic reticulum (ER) stress. The dual kinase/RNase Ire1 is a conserved regulator of the UPR, mediating the unconventional cytosolic splicing of HAC1 mRNA in yeast and XBP1 mRNA in human cells. The resulting spliced HAC1/XBP1 transcript encodes a transcription factor that induces the expression of protein-folding chaperones and stress-responsive genes, thereby restoring proteostasis. In our previous work, we showed that the MAP kinase Slt2 (homolog of human ERKs) contributes to UPR signaling by promoting IRE1 expression through the transcription factor Rlm1 (homolog of human MEF2C). Here, we demonstrate that Hac1 expression is reduced in yeast strains deficient in essential protein kinase Cdc28, Pkc1, Rio2, Tor2, Pkh1, or Ypk1, suggesting that these kinases also serve as UPR regulators. We focused on the kinase Ypk1, the yeast ortholog of human SGK1 (serum/glucocorticoid-regulated kinase 1). We provide genetic and biochemical evidence that Ypk1/SGK1 acts upstream of the Pkc1/PKC{delta} signaling pathway and is required for maintaining IRE1 protein abundance in both yeast and human cells. Collectively, our results identify an evolutionarily conserved Ypk1/SGK1 signaling pathway that regulates the HAC1 and XBP1 mRNA splicing by modulating the Ire1 protein abundance.

genetics↗

bioRxiv2026

Species climate-niche properties suggest that both physiological tolerance and stress dominance shape plant community assembly across a tropical dry ecosystem

Climate influences community assembly by constraining the conditions under which species can persist, but the consistency of macroecological processes across different ecosystems remains unclear. Interspecific variation in climatic niche properties that govern community assembly across climate gradients can be gleaned from species distributions. Species-climate associations, niche properties, and resulting assembly remains poorly understood for plants in tropical dry ecosystems, and among different life-forms. We examined how species-climate associations governed community assembly of four plant life-forms across 60,000 km2 of tropical dry ecosystem in peninsular India. In the 1750 km long Eastern Ghats mountain range, we surveyed vegetation in 2500 20 x 50 m plots. Across the north-south climatic gradient from cool, wet and seasonal sites to warm, dry and less-seasonal sites, from presence-absence data of 1601 species in four life forms (trees, shrubs, herbs, climbers), we performed Bayesian Hierarchical Modelling of Species Communities to predict conditions of occurrence for each species. From this, we derived species climatic niche optima and niche width, and examined the local-level prevalence of niche properties across the climate gradient to glean assembly. Most tree, shrub and climber species associated with warm-dry conditions had wider niches than species associated with cool-wet conditions, which also resulted in assemblages having wider niches at warmer sites. Herbaceous species, by contrast, had narrower niches when associated with warmer conditions, where narrow-niche species dominated the assemblage. In all life-forms, however, assemblages in both warm-dry and cool-humid conditions consisted of species primarily associated with and preferring (having their optima in) those conditions, suggestive of stress dominance. Further evidence for stress dominance in shrubs and climbers came from assemblages in the warmest and coolest sites having low richness and comprising mainly of species with wider niches. Tree richness increased at either end of the gradient, while herb richness increased in warm-dry conditions. Overall, our results suggest that plant life-forms differ in the processes driving assembly across broad climate gradients in a tropical dry ecosystem, but many herbs were specialized to warm-dry climates. To understand life-form-specific responses to environmental gradients in tropical dry ecosystems, future work should incorporate traits and evolutionary history.

ecology↗

bioRxiv2026

A druggable ATP13A3-antizyme switch controls adaptive polyamine uptake in cancer

Cellular polyamine depletion is a promising anticancer strategy, but compensatory polyamine uptake limits efficacy when synthesis is blocked by DFMO (difluoromethylornithine), a clinically approved inhibitor of ornithine decarboxylase. The transporter and feedback mechanism driving this adaptive response have remained unclear. Despite their similar biochemical properties, we identify ATP13A3, rather than ATP13A2, as the principal DFMO-responsive polyamine importer, suggesting that these isoforms regulate distinct polyamine fluxes. Mechanistically, the polyamine sensor antizyme not only restrains polyamine biosynthesis but also selectively inhibits ATP13A3-mediated uptake, a brake that is relieved upon DFMO treatment. This regulatory circuit exposes distinct polyamine-acquisition states across cancers, defining synthesis- and/or uptake-biased subtypes that can shift during disease progression. Melanoma metastasis and vemurafenib resistance evolve toward increased ATP13A3-dependent uptake. The polyamine uptake branch controlled by ATP13A3-antizyme regulation can be pharmacologically blocked by AMXT 1501, which directly inhibits ATP13A3. Together, our findings explain DFMO adaptation through ATP13A3-antizyme control and establish ATP13A3 as a targetable node for polyamine depletion strategies in multiple cancers, supporting ongoing clinical evaluation of combined DFMO/AMXT 1501 therapy.

cell biology↗

bioRxiv2026

Homozygous c.820G>A variant in MGME1 contributes to multi-systemic mitochondrial dysfunction in an Indian patient cohort

Mitochondrial DNA (mtDNA) maintenance disorders arise from defects in mtDNA replication or repair, frequently resulting in extensive deletions or depletion of mtDNA. Mitochondrial genome maintenance exonuclease 1 (MGME1) is a nuclear-encoded nuclease essential for mtDNA replication and genome stability, and biallelic pathogenic variants in MGME1 cause mitochondrial DNA depletion syndrome 11. Here, we report a novel homozygous MGME1 missense variant c.820G>A (p. Ala274Thr) in five affected individuals from unrelated South Indian families presenting with proximal myopathy, chronic progressive external ophthalmoplegia, and cardiac and renal involvement. Patient-derived cells exhibited a significant reduction in mtDNA copy number, consistent with impaired mtDNA maintenance. Mechanistic analyses combining imaging-based and biochemical approaches demonstrated that the MGME1 variant disrupts both mtDNA replication and repair. Functional characterization further revealed defective oxidative phosphorylation and reduced mitochondrial membrane potential, confirming mitochondrial dysfunction. Collectively, our findings establish the pathogenicity of this novel MGME1 variant and expand the clinical and molecular spectrum of MGME1-associated mitochondrial disease, linking impaired mtDNA replication to multisystemic mitochondrial dysfunction. Graphical abstract summarySchematic overview of mitochondrial DNA (mtDNA) replication in wild-type and MGME1 mutant conditions. In wild-type cells, the coordinated activity of the mitochondrial replication machinery (TWNK, POLG, LIG3, TFAM, and MGME1) maintains mtDNA integrity and supports normal oxidative phosphorylation and ATP production. In contrast, the MGME1 mutation disrupts mtDNA replication and processing, leading to replication defects, mtDNA depletion, and mitochondrial dysfunction. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=116 SRC="FIGDIR/small/725852v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@406ce7org.highwire.dtl.DTLVardef@1adc863org.highwire.dtl.DTLVardef@3ef92aorg.highwire.dtl.DTLVardef@585559_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2025

Conformational Diversity and Allosteric Network Enable Multi-Substrate Recognition in Laccase Enzyme

Laccase is a multicopper oxidase with remarkable potential for environmental remediation due to its ability to degrade a wide range of pollutants. However, the molecular origins of its broad substrate scope have remained elusive. Here, through extensive molecular dynamics (MD) simulations coupled with machine learning (ML) based Markov State Model (MSM), we uncover a previously uncharacterized allosteric pathway that governs laccases catalytic activity. This pathway functionally couples the dynamics of two key loops at the active site, and its integrity is crucial for enzymatic efficiency. Our analysis of the apo enzymes conformational free energy landscape reveals that this allostery is part of a cooperative global network, leading to distinct, slowly interconverting conformational states. We demonstrate that different dye substrates bind by selectively recognising these pre-existing states, confirming a conformational selection mechanism. Collectively, these findings provide a dynamic blueprint for laccases functional versatility and offer a general framework for understanding and engineering other multi-substrate enzymes.

biophysics↗

bioRxiv2025

Genetic and environmental factors regulating soybean reproductive stages and their transitions

The reproductive stage of soybean is influenced by the effect of genotype, environment, and their interactions. While days to flowering and days to full maturity have been studied, a systematic and comprehensive study that investigates the variation in days to each stage and the role of maturity-related genes and environmental variables is lacking. Therefore, we studied 508 unique accessions from the USDA germplasm collection from maturity group 0-IV, and a set of 67 near-isogenic lines differing for maturity-related genes. Field experiments and evaluations were conducted in central Iowa, USA. The days to each of the reproductive stages, R1-R8, were recorded. We report considerable variation in the duration of reproductive growth stages between flowering and maturity, which is largely explainable by known flowering and maturity genes as well as environmental variables, day length, and growing degree days. Besides the known maturity-related genes E1, E2, and Dt1, we identified two novel SNPs, such as Glyma.01G180600 and Glyma.10G221300, as potential targets for genetic regulation of reproductive stages. We also captured two other loci, Glyma.08G216800 and Glyma.04G088100 for day length and growing degree days, respectively, that revealed dynamic regulation of environmental gradients on the reproductive stages. Furthermore, we developed a random forest-based genetic maturity model that can predict genetic and environmental effects across a wide range of genotypes. This study broadens the understanding of the factors that contribute to reproductive development, which will help to develop cultivars that combine the optimal combinations of stage durations for a higher seed yield and enhanced resilience.

genetics↗

bioRxiv2025

It's about time! Leaf minimum conductance determines time to reach critical thresholds for leaf dehydration in a seasonal tropical forest

O_LILeaf minimum conductance (gmin) is important in determining plant responses to drought. However, we do not understand how gmin is related to drought tolerance across species, and how important it is in determining the time to reach critical dehydration levels. C_LIO_LIIn 18 coexisting species from a seasonal tropical forest we quantified gmin to test relationships with early, moderate and severe dehydration thresholds associated with tolerance to turgor loss, breakdown of structural integrity, and disruption of cellular function, respectively. We quantified other functional and hydraulic traits to determine the major axes of trait variation in these species. C_LIO_LIVariation in gmin was the primary determinant of the time to reach critical levels of dehydration, and was unrelated to thresholds for early and severe dehydration. Surprisingly, gmin was negatively related to maximum stomatal conductance, but unrelated to other functional and hydraulic traits. C_LIO_LIThese results highlight the importance of avoiding dehydration via minimizing gmin, and suggest that avoidance, tolerance to early, and severe dehydration represent independent strategies for coping with drought. This would allow coexisting species to balance opportunities for carbon gain with costs of physiological breakdown when faced with varying intensities and durations of drought. C_LI

ecology↗

bioRxiv2024

Mitochondrial genome-encoded mitomiRs regulate cellular plasticity and susceptibility to ferroptosis in triple-negative breast cancer

Ferroptosis is a distinct form of regulated cell death promoted by iron-dependent lipid peroxidation. The metabolic plasticity of cancer cells determines their sensitivity to ferroptosis. Although mitochondrial dysfunction contributes to metabolic reprogramming in cancer cells, its role in ferroptosis remains to be identified. We identified that the mitochondrial genome encodes 13 miRNAs (mitomiRs) that are highly expressed in breast cancer cell lines and patient-derived tumor samples. Expression analysis revealed that mitomiRs are upregulated in basal-like triple-negative breast cancer (TNBC) cells compared to mesenchymal stem-like TNBC cells. Interestingly, 11 out of the 13 mitomiRs bind to the 3'UTR of zinc finger E-box-binding homeobox 1 (ZEB1), a transcription factor, involved in epithelial to mesenchymal transition (EMT) in breast cancer. Using mitomiR-3 mimic, inhibitor and sponges, we confirmed that mitomiR-3 indeed regulate ZEB1 expression in TNBC cells. Increased mesenchymal features in TNBC contributed to vulnerability to pro-ferroptotic metabolic reprogramming sensitizing to cell death in in vitro and in vivo models. Some of the challenges associated with pro-ferroptotic drugs includes lack of cancer cell specificity, low targeting ability, normal tissue toxicity contributing to their limited clinical application as cancer therapeutics. Here, we identified mitomiRs which are highly expressed in TNBC subtypes with low expression in normal breast cells making them an ideal candidate for selective inhibition for targeted therapy. Further, we demonstrated that the inhibition of mitomiRs in triple-negative breast cancer cells promote pro-ferroptotic metabolic reprogramming which can be exploited as novel vulnerability for targeted ferroptotic induction in cancer cells avoiding the normal tissue toxicity. Collectively, our results indicate a novel mechanism of mitochondrial miRNA mediated ferroptosis sensitivity in TNBC subtypes which could be exploited to develop potential miRNA-based therapeutics.

cancer biology↗

bioRxiv2024

Unravelling Antibody-Induced Mechanical Stability of Antigen: Insights from Single-Molecule Studies

The intricate nature of antigen-antibody interactions plays a pivotal role in immunological responses. Despite the multitude of ligand-binding sites on antigens, the influence of antibodies on their mechanical stability remains elusive. This study elucidates the impact of IgM, the largest antibody isotype, on the mechanical stability of protein L, a bacterial superantigen, using single-molecule magnetic tweezers and steered molecular dynamics. Our findings reveal a concentration-dependent elevation in mechanical stability induced by IgM, as demonstrated by prolonged unfolding dwell times. Through steered molecular dynamics simulations, we elucidate the distinct mechanical responses of protein L binding interfaces at various IgM complex states, highlighting their synergistic effect on IgM dimer complex stability. Notably, this enhanced response stems from the altered unfolding pathway of protein L upon IgM interaction, providing significant insights into the generic mechanisms governing antibody-induced mechanical stability of antigenic substrates in physiological conditions, shedding light on the underlying folding dynamics and molecular mechanics of antigen-antibody interaction.

biophysics↗

bioRxiv2023

Spinal facilitation of descending motor input

Highly varying patterns of electrostimulation (Dynamic Stimulation, DS) delivered to the dorsal cord through an epidural array with 18 independent electrodes transiently facilitate corticospinal motor responses, even after spinal injury. To partly unravel how corticospinal input are affected by DS, we introduced a corticospinal platform that allows selective cortical stimulation during the multisite acquisition of cord dorsum potentials (CDPs) and the simultaneous supply of DS. Firstly, the epidural interface was validated by the acquisition of the classical multisite distribution of CDPs on the dorsal cord and their input-output profile elicited by pulses delivered to peripheral nerves. Apart from increased EMGs, DS selectively increased excitability of the spinal interneurons that first process corticospinal input, without changing the magnitude of commands descending from the motor cortex, suggesting a novel correlation between muscle recruitment and components of cortically-evoked CDPs. Finally, DS increases excitability of post-synaptic spinal interneurons at the stimulation site and their responsiveness to any residual supraspinal control, thus supporting the use of electrical neuromodulation whenever the motor output is jeopardized by a weak volitional input, due to a partial disconnection from supraspinal structures and/or neuronal brain dysfunctions.

neuroscience↗

bioRxiv2023

Molecular Mechanism of Regulation of RhoA GTPase by Phosphorylation of RhoGDI

Rho-specific guanine dissociation inhibitors (RhoGDIs) play a crucial role in the regulation of Rho family GTPases. They act as negative regulators that prevent the activation of Rho GTPases by forming complexes with the inactive GDP-bound state of GTPase. Release of Rho GTPase from the RhoGDI-bound complex is necessary for Rho GTPase activation. Biochemical studies provide evidence of a "phosphorylation code", where phosphorylation of some specific residues of RhoGDI selectively releases its GTPase partner (RhoA, Rac1, Cdc42 etc.). This work attempts to understand the molecular mechanism behind this phosphorylation code. Using several microseconds long atomistic molecular dynamics (MD) simulations of the wild-type and phosphorylated states of the RhoA-RhoGDI complex, we propose a molecular-interaction-based mechanistic model for the dissociation of the complex. Phosphorylation induces major structural changes, particularly in the positively charged polybasic region (PBR) of RhoA and the negatively charged N-terminal region of RhoGDI that contribute most to the binding affinity. MM-PBSA binding free energy calculations show a significant weakening of interaction on phosphorylation at the RhoA-specific site of RhoGDI. In contrast, phosphorylation at a Rac1-specific site leads to the strengthening of the interaction confirming the presence of a phosphorylation code. RhoA-specific phosphorylation leads to a reduction in the number of contacts between the PBR of RhoA and the N-terminal region of RhoGDI, which manifests reduction of the binding affinity. Using hydrogen bond occupancy analysis and energetic perturbation network, we propose a mechanistic model for the allosteric response, i.e., long range signal propagation from the site of phosphorylation to the PBR and buried geranylgeranyl group in the form of rearrangement and rewiring of hydrogen bonds and salt bridges. Our results highlight the crucial role of specific electrostatic interactions in manifestation of the phosphorylation code.

biophysics↗

bioRxiv2023

MiR-4521 perturbs FOXM1-mediated DNA damage response in breast cancer

Forkhead (FOX) transcription factors are involved in cell cycle control, cellular differentiation, maintenance of tissues, and aging. Mutation or aberrant expression of FOX proteins is associated with developmental disorders and cancers. FOXM1, an oncogenic transcription factor, is a promoter of cell proliferation and accelerated development of breast adenocarcinomas, squamous carcinoma of the head, neck, and cervix, and nasopharyngeal carcinoma. High FOXM1 expression is correlated with chemoresistance in patients treated with doxorubicin and Epirubicin by enhancing the DNA repair in breast cancer cells. Here, we showed that FOXM1 is a direct target of miR-4521 in breast cancer. Overexpression of miR-4521 significantly downregulated FOXM1 expression in breast cancer cells. FOXM1 regulates cell cycle progression and DNA damage response in breast cancer. We showed that miR-4521 expression leads to increased ROS levels and DNA damage in breast cancer cells. FOXM1 plays a critical role in ROS scavenging and promotes stemness which contributes to drug resistance in breast cancer. We observed that breast cancer cells stably expressing miR-4521 lead to cell cycle arrest, impaired FOXM1 mediated DNA damage response leading to increased cell death in breast cancer cells. Additionally, miR-4521-mediated FOXM1 downregulation perturbs cell proliferation, invasion, cell cycle progression, and epithelial-to-mesenchymal progression (EMT) in breast cancer. High FOXM1 expression has been associated with radio and chemoresistance contributing to poor patient survival in multiple cancers, including breast cancer. Our study showed that FOXM1 mediated DNA damage response could be targeted using miR-4521 mimics as a novel therapeutic for breast cancer.

cancer biology↗

bioRxiv2022

Anti-Biofilm Potential of Nanonized Eugenol against Pseudomonas aeruginosa

This study dealt with nanonization of eugenol, a major phytochemical present in basil leaf, which has pharmacological potential as an anti-bacterial agent. Eugenol nanoparticle (ENP) was synthesized by simple ultrasonic cavitation method through emulsification of hydrophobic eugenol into hydrophilic gelatin. Thus, the nanonization process made the water-insoluble eugenol to water-soluble nano-eugenol, making the nano-form bioavailable. The average size of the ENPs was 20-30 nm. Entrapment efficiency of eugenol within gelatin cap was about 80% of the eugenol, that was used as precursor in the nanonization reaction. In vitro release of eugenol from gelatin cap was slow and sustained over a period of five days. The ENP had higher anti-biofilm potency than eugenol for both formation and eradication of biofilm, formed by clinically relevant pathogen Pseudomonas aeruginosa. Minimal biofilm inhibitory concentration and minimal biofilm eradication concentration of ENPs were 2.0 and 4.0 mM respectively. In addition, the measurement of P. aeruginosa biofilm biomass, biofilm pellicle formation, biofilm thickness, amount of biofilm-forming extra-polymeric substance, cell surface hydrophobicity, cell swarming and twitching efficiencies, cellular morphology and biofilm formation in catheter demonstrated that the anti-biofilm efficacy of nano-eugenol was 30-40% higher than that of bulk eugenol. Thus, ENP can be used as a potential drug against pneumonia, a chronic infection in lung caused by P. aeruginosa, which is difficult to treat with antibiotics, due to natural intrinsic resistance of biofilm-formed cells to most antibiotics. The overall actions of ENP have been presented in the figure 1. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=146 SRC="FIGDIR/small/521144v1_fig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@12445e2org.highwire.dtl.DTLVardef@6813aforg.highwire.dtl.DTLVardef@e4779borg.highwire.dtl.DTLVardef@1688a9a_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1:C_FLOATNO Graphical abstract showing overall anti-biofilm action of ENP that is capable to inhibit each and every step of biofilm formation. ENP also carries the potential to destroy EPS and kill the biofilm residing cells by membrane disruption. Bacterial colonization has been found to be prevented significantly on ENP-coated catheter. C_FIG HighlightsO_LINano-formulation of eugenol, an important phytochemical, by ultrasonic cavitation method, which was simple, time-saving, low-cost and eco-friendly. C_LIO_LINanonization made water-insoluble eugenol into water-soluble form with enhanced therapeutic efficacy. C_LIO_LIThe eugenol nanoparticle (ENP) could inhibit formation of biofilm as well as facilitate eradication of pre-formed biofilm of P. aeruginosa. C_LIO_LIBiofilm formation was found to be prevented significantly on ENP-coated catheter. C_LIO_LINano-eugenol may be used as a potential drug against bacterial diseases, caused by pseudomonal biofilm, which are difficult to treat by antibiotics. C_LIO_LINano-formulated eugenol may also be used as an effective anti-fouling agent for biomedical devices like contact lens, pace-maker, materials for organ transplantation etc. to prevent bacterial colonization. C_LI

microbiology↗

bioRxiv2022

A Simplified Model of Motor Control

In general, control of movement is considered to be either cortical, spinal, or purely biomechanical and is studied separately at these levels. To achieve this separation when studying a particular level, variations that may be introduced by the other levels are generally either ignored or restricted. This restriction misrepresents the way movements occur in realistic scenarios and limits the ability to model movements in a biologically inspired manner. In this work, we propose a heuristic model for motor control that conceptually and mathematically accounts for the entire motor process, from target to endpoint. It simulates human arm motion and is able to represent functionally different motion properties by flexibly choosing more or less complex motion paths without built-in optimization or joint constraints. With a novel implementation of hierarchical control, this model successfully overcomes the problem of degrees of freedom in robotics. It can serve as a template for neurocomputational work that currently uses control architectures that do not mirror the human motor control process. The model itself also suggests a maximum threshold for delays in position feedback for effective movement, and that the primary role of position feedback in movement is to overcome the effects of environmental perturbations at the joint level. These findings can inform future efforts to develop biologically inspired motor control techniques for prosthetic devices.

neuroscience↗

bioRxiv2022

Genetic diversity analysis and characterization of Ugandan sorghum

The National Genebank of Uganda houses diverse and rich Sorghum bicolor germplasm collection. This genetic diversity resource is untapped, under-utilized and has not been systematically incorporated into sorghum breeding programs. In this study, we characterized the germplasm collection using whole genome SNP markers. Discriminant analysis of principal components (DAPC) was implemented to study racial ancestry of the accessions in comparison to a global sorghum diversity set and characterize sub-groups and admixture in the Ugandan germplasm. Genetic structure and phylogenetic analysis was conducted to identify distinct genotypes in the Ugandan collection and relationships among groups. Furthermore, in a case study for identification of potentially useful adaptive trait variation for breeding, we performed genome-wide association studies for juvenile cold tolerance. Genomic regions potentially involved in adaptation of Ugandan sorghum varieties to cooler climatic conditions were identified that could be of interest for expansion of sorghum production into temperate latitudes. The study demonstrates how genebank genomics can potentially facilitate effective and efficient usage of valuable, untapped germplasm collections for agronomic trait evaluation and subsequent allele mining.

plant biology↗

bioRxiv2021

Loss of Nuclear DNA ligase III Can Revert PARP Inhibitor Resistance in BRCA1-deficient Cells by Increasing DNA Replication Stress

Inhibitors of poly(ADP-ribose) (PAR) polymerase (PARPi) have entered the clinic for the treatment of homologous recombination (HR)-deficient cancers. Despite the success of this approach, preclinical and clinical research with PARPi has revealed multiple resistance mechanisms, highlighting the need for identification of novel functional biomarkers and combination treatment strategies. Functional genetic screens performed in cells and organoids that acquired resistance to PARPi by loss of 53BP1 identified loss of LIG3 as an enhancer of PARPi toxicity in BRCA1-deficient cells. Enhancement of PARPi toxicity by LIG3 depletion is dependent on BRCA1 deficiency but independent of the loss of 53BP1 pathway. Mechanistically, we show that LIG3 loss promotes formation of MRE11-mediated post-replicative ssDNA gaps in BRCA1-deficient and BRCA1/53BP1 double-deficient cells exposed to PARPi, leading to an accumulation of chromosomal abnormalities. LIG3 depletion also enhances efficacy of PARPi against BRCA1-deficient mammary tumors in mice, suggesting LIG3 as a potential therapeutic target.

cancer biology↗

bioRxiv2021

Quantitative estimates of deciduousness in woody species from a seasonally dry tropical forest are related to leaf functional traits and the timing of leaf flush

Leaf phenology based classification of woody species into discrete evergreen and deciduous categories is widely used in ecology, but these categories hide important variation in leaf phenological behaviour. Few studies have examined the continuous nature of deciduousness and our understanding of variation in quantitative estimates of leaf shedding behaviour and the causes and consequences of this is limited. In this study we monitored leaf phenology in 75 woody species from a seasonally dry tropical forest to quantify three quantitative measures of deciduousness, namely: maximum canopy loss, duration of deciduousness, and average canopy loss. Based on proposed drought tolerance and drought avoidance strategies of evergreen and deciduous species, respectively, we tested whether the quantitative measures of deciduousness were related to leaf functional traits. Additionally, to understand the functional consequences of variation in deciduousness we examined relationships with the timing of leaf flushing and senescing. We found wide and continuous variation in quantitative measures of deciduousness in these coexisting species. Variation in deciduousness was related to leaf function traits, and the timing of leaf flushing. Along a continuous axis ranging from evergreen to deciduous species, increasing deciduousness was associated with more acquisitive leaf functional traits, with lower leaf mass per area and leaf dry matter content, and greater leaf nitrogen content. These results indicate that the continuous nature of deciduousness is an important component of resource acquisition strategies in woody species from seasonally dry forests.

ecology↗

bioRxiv2021

C-bouton components on rat extensor digitorum longus motoneurons are resistant to chronic functional overload

Mammalian motor systems adapt to the demands of their environment. For example, muscle fibre types change in response to increased load or endurance demands. However, for adaptations to be effective, motoneurons must adapt such that their properties match those of the innervated muscle fibres. We used a rat model of chronic functional overload to assess adaptations to both motoneuron size and a key modulatory synapse responsible for amplification of motor output, C-boutons. Overload of Extensor Digitorum Longus (EDL) muscles was induced by removal of their synergists, Tibialis Anterior (TA) muscles. Following 21 days survival, EDL muscles showed an increase in fatigue resistance and a decrease in force output, indicating a shift to a slower phenotype. These changes were reflected by a decrease in motoneuron size. However, C-bouton complexes remained largely unaffected by overload. The C-boutons themselves, quantified by expression of vesicular acetylcholine transporter, were similar in size and density in the control and overload conditions. Expression of the post-synaptic voltage-gated potassium channel (KV2.1) was also unchanged. Small conductance calcium activated potassium channels (SK3) were expressed in most EDL motoneurons, despite this being an almost exclusively fast motor pool. Overload induced a decrease in the proportion of SK3+ cells, however there was no change in density or size of clusters. We propose that reductions in motoneuron size may promote early recruitment of EDL motoneurons, but that C-bouton plasticity is not necessary to increase the force output required in response to muscle overload.

neuroscience↗