Biology subjects

Kumar, R.

Publications and source records attributed to Kumar, R..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Water stress adaptive responses in plants require movement of ABA and AB-aldehyde from vascular to target tissues

Vascular plants rapidly coordinate root and shoot responses to water stress. Abscisic acid (ABA) mediates these adaptations; however, it remains unclear which cells produce ABA, whether ABA synthesis shifts during stress, and whether ABA movement is required for its adaptive functions. Here, we map ABA biosynthesis at cellular resolution in Arabidopsis and report that water-stress adaptive responses in roots and shoots require movement of ABA and its precursor AB-aldehyde from vascular tissues to target cells. We suggest that ABA accumulation arises from two parallel routes: (i) ABA synthesized in the vasculature via ABA2 and AAO3, then moving to guard cells, and (ii) phloem-derived AB-aldehyde being converted to ABA in the epidermis or bundle sheath by AAO1 and AAO2. Finally, we predict that tightly packed cells beneath leaf veins facilitate efficient ABA delivery to guard cells, an anatomical arrangement that has enabled angiosperms to evolve the use of ABA to rapidly close stomata.

plant biology↗

bioRxiv2026

TAOK3 inhibition constrains invasion, potentiates paclitaxel, and reprograms the tumor microenvironment toward anti-tumor immunity in cervical cancer

TAOK3 is a lesser-studied MAPK family serine/threonine kinase our group has shown to be targeted by HPV integration, suggesting a potential role in driving invasive cervical cancer (ICC). Here, we profiled TAOK3 expression in patient tumors, metastases, and cervical cancer models and localized TAOK3 within a tumor epithelial subpopulation by integrating two single-cell RNA-seq datasets. Functional consequences of TAOK3 loss were assessed with siRNA and CRISPRi in cell lines and 3D spheroids. In vivo effects were evaluated in intracervical xenografts with species-specific RNA-seq to resolve tumor versus microenvironmental responses. TAOK3 mRNA/protein were elevated in primary and metastatic ICC and primarily localized to a keratin-positive epithelial subset (T3epi) enriched for cadherin/S100 binding, vesicle/endocytic pathways, and leading-edge programs. TAOK3 silencing reprogrammed transcriptomes and proteomes toward reduced WNT/cell-cycle and motility signaling, altered endocytosis and cytoskeleton organization, and reshaped phospho-networks linked to chromatin remodeling and ERBB2-ERBB3/cytoskeletal kinase activity. Functionally, TAOK3 inhibition prolonged G2/M, suppressed invasion, and enhanced sensitivity to low dose paclitaxel. Prolonged inactivation induced methuosis-like cell death with extracellular ATP release. In xenografts, TAOK3 knockdown reduced tumor burden, downregulated KRT14--a leader cell marker--within the human tumor compartment, and enriched microenvironmental pathways for immune activation, with a specific decrease in CD206+ M2 macrophages. TAOK3 delineates an invasion-competent epithelial state in ICC and coordinates cell-cycle control, cytoskeleton-membrane dynamics, and tumor-immune crosstalk. Genetic or pharmacologic TAOK3 inhibition constrains tumor growth, potentiates paclitaxel, and remodels the microenvironment toward anti-tumor immunity, supporting TAOK3 as a potential therapeutic target and biomarker in ICC. Statement of SignificanceTAOK3 marks an invasion-competent epithelial subpopulation in cervical cancer. TAOK3 inhibition slows tumor growth, enhances chemoresponse, and reduces M2 macrophages, revealing TAOK3 as a potential therapeutic target and biomarker for patient stratification.

cancer biology↗

bioRxiv2026

Analyte-Class-Dependent Electrophoretic Organization Enables Single-Run Proteome-Metabolome Analysis by CE-ESI-MS

Dual proteome-metabolome measurements from limited samples typically require sample splitting or sequential analyses using electrospray ionization mass spectrometry (ESI-MS). Here we show that capillary electrophoresis (CE) can avoid that tradeoff by organizing predominantly singly charged small molecules and multiply charged peptides into partially resolved, analyte-class-dependent regions of migration time-m/z space. Leveraging this intrinsic electrophoretic organization together with charge- and m/z-resolved precursor selection, we developed a single-run CE-ESI-MS workflow that combines single-vial sample processing with class-resolved tandem MS acquisition. In a HeLa digest spiked with 17 amino acids, the integrated analysis detected all amino acids while preserving proteomic depth relative to a dedicated proteomics run, yielding 1,221 versus 1,227 cumulative protein groups. Applied to identified single Xenopus laevis blastomeres, the method provided matched readouts of 86 metabolite features together with 1,097 and 1,083 protein groups from D1.1 and V1.1 cells, respectively. The paired measurements resolved cell-type-dependent molecular differences and mapped protein and metabolite changes into shared pathway context. These results establish analyte-class-dependent electrophoretic organization coupled to class-resolved MS acquisition as an analytical basis for single-run proteome-metabolome analysis by CE-ESI-MS in material-limited samples.

biochemistry↗

bioRxiv2026

Hepatobiliary Progenitor-like Reprogramming in Liver Metastases

Metastatic progression requires cancer cells to adapt to the unique constraints of distant organ microenvironments, yet the mechanisms that drive organ-specific adaptations remain poorly understood. Here, we show that the liver actively rewrites metastatic cancer cell identity, driving tumor cells toward a hepatobiliary progenitor-like state. Through integrated transcriptomic, proteomic, metabolomic, and epigenomic analyses of patient-derived rapid-autopsy samples and experimental models, we identify this state as selectively enriched in liver metastases. It is characterized by co-activation of hepatic and biliary/progenitor regulators HNF4A and SOX9 and is observed across multiple epithelial cancers, indicating a conserved response to the hepatic niche. Mechanistically, hepatocyte-derived TGF-{beta} and hypoxia converge to activate a HIF-1-ACLY axis, increasing nuclear acetyl-coenzyme A availability and histone acetylation at hepatic lineage regulatory elements to drive hepatobiliary reprogramming. This coordinated niche-response program can be captured transcriptionally and is associated with inferior overall survival. Disruption of this pathway suppresses hepatic reprogramming and impairs liver metastatic fitness. These findings identify the liver as an active determinant of metastatic cell fate, linking microenvironmental signaling to metabolic and chromatin remodeling programs that enable lineage plasticity. More broadly, they reveal organ-specific reprogramming as a fundamental principle of metastasis and a therapeutic vulnerability in liver metastases.

cancer biology↗

bioRxiv2026

FALCON: Closed-Loop Multi-Objective Optimization of Lipid Nanoparticles for Cell-Selective mRNA Delivery

Efficient, cell type-selective delivery of genetic payloads remains a central challenge in the development of gene and cell therapies. Lipid nanoparticles (LNPs) offer a versatile delivery platform, but their optimization is hindered by reliance on brute-force screening methods that are laborious, resource-intensive, and focus on single targets. Here, we present FALCON (Framework for Active Learning-driven Compositional Optimization of Nanoparticles), a closed-loop pipeline that leverages iterative screening, surrogate modeling, and multi-objective optimization to accelerate LNP compositional design. In B cell-targeted validation experiments, FALCON-optimized LNPs achieved a 1.8-fold increase in splenic B cell transfection in vivo compared with reference compositions. When optimized for selectivity, FALCON LNPs displayed an 84-fold improvement in selective transfection of splenic B cells over off-target liver populations and enabled spleen-tropic behavior across factorial panels of varying ionizable and helper lipid chemistries. In vaccine studies, these LNPs induced higher IgG2c antibody titers and a more Th1-biased immune profile. FALCON was also deployed to optimize LNPs for myeloid cell-selective delivery, achieving enhanced in vivo selectivity following systemic administration both across and within spleen and liver compartments. Our results establish FALCON as a useful tool for data-driven design of LNP compositions for precision gene delivery.

bioengineering↗

bioRxiv2026

SPARK: A Systems-level Computational Framework for Reconstructing Transcriptomic State Organisation in Lung Adenocarcinoma

Lung adenocarcinoma (LUAD) exhibits substantial molecular heterogeneity, which complicates tumour stratification and limits the ability of mutation-centric models to capture tumour behaviour and predict patient outcomes. This study investigates whether coordinated transcriptomic programs can provide a systems-level representation of tumour states. Bulk RNA-sequencing data from the TCGA-LUAD cohort were analysed to reconstruct pathway-level transcriptomic organisation using a stability-optimised network framework (SPARK). This analysis identified eight transcriptomic modules representing coordinated biological processes active across tumours. Module activity scores were subsequently used to derive a composite Transcriptomic Risk Score through elastic-net Cox proportional hazards modelling. The resulting risk score showed a significant association with overall survival in the discovery cohort and improved prognostic discrimination beyond clinical variables. An independent evaluation in the CPTAC-LUAD cohort confirmed the prognostic signal and preserved risk stratification across patient groups. Unsupervised clustering of module activity further revealed three transcriptomic patient groups characterised by distinct biological programs, genomic alteration patterns, and survival outcomes. Single-cell analysis also demonstrated that the identified transcriptomic modules reflect coordinated organisation of the tumour-immune-stromal ecosystem across cellular compartments. Together, these findings suggest that LUAD heterogeneity can be organised into coordinated transcriptomic programs with measurable clinical relevance, providing a systems-level framework for representing tumour molecular states.

bioinformatics↗

bioRxiv2026

Exploiting NDH-2 Vulnerability: Quinolines as Antitubercular Agents

Mycobacterium tuberculosis possesses a flexible metabolic system helping it to survive inside the host. The type II NADH dehydrogenase, composed of Ndh and NdhA, essential for bacilli, is a promising drug target. Based on ATP depletion values, two quinoline scaffolds were shortlisted after screening of a library of drug like molecules. Structurally, both 64-9C and 64-9D carry ester moieties at the 5- and 8-positions of the quinoline core, respectively. Ease to re-synthesise 64-9D resulted in synthesis of a focused library of compounds, with MIC values of 0.25-4 g/mL, consistent with ATP depletion. These compounds exhibited bactericidal activity against non-replicating mycobacteria, and showed potent efficacy against multidrug-resistant isolates. Altered, intracellular NADH/NAD+ ratio and reduced respiration was indicative of oxidative phosphorylation inhibition. Inhibition of the purified recombinant NDH protein uncompetitively, SNPs in gene encoding NDH-2 for selected one step mutants and, molecular modelling of 4FQN and 2FQN validated NDH-2 as a target for these compounds. The derivative 2FQN exhibited dose-dependent bactericidal efficacy in mice, underscoring the potential of the series as a promising anti-tuberculosis candidates.

microbiology↗

bioRxiv2026

Steroid Hormone-Induced LIF Regulates Vasoactive Mediators During Implantation and Decidualization in the Golden Hamster

Embryo implantation is early and complex stage of pregnancy begins when competent blastocyst makes a physiological attachment to receptive endometrium. Expression of numerous molecules are essential for initiation of pregnancy. leukemia inhibitory factor (LIF) is essential cytokines required for priming uterus to make it receptive for implantation. In mice, the ovarian estrogen regulated expression of LIF is absolutely required for implantation. Golden hamster showed ovarian estrogen independent process of embryo implantation. Hence, the regulation of LIF in uterus of golden hamster during early pregnancy is still ambiguous. In this study, we explored the possible regulation of LIF by uterine factor and their spatio-temporal localization and expression in the uterus of golden hamster during early pregnancy and pseudopregnancy. We further demonstrated their ability to activate prostaglandin synthesizing enzymes to achieve successful pregnancy. We used immunohistochemistry, quantitative and semiquantitative PCR to achieve the objectives. We observed the expression of LIF in all the day of early pregnancy and pseudopregnancy in the uterus of hamster. Their m-RNA was found to be upregulated around the day of implantation and decidualization. LIF showed high expression in D3 pseudopregnancy. LIF was found to be regulated by estrogen in ovariectomized uterus and significantly reduced expression of LIF was observed in letrozole treated uterine horn. Downregulated expression of prostaglandin synthesizing enzymes was observed in anti-LIF antibody treated uterus. Together, these findings highlights that uterine factor regulated LIF mediate their action via activating prostaglandin synthesizing enzymes to make uterus receptive for successful early pregnancy in hamster. HighlightO_LIExpression of LIF in uterus during pregnancy in golden hamster is independent from the presence of blastocyst C_LIO_LILIF is regulated by estrogen in ovariectomized hamster C_LIO_LIExpression of LIF mRNA is downregulated in letrozole treated uterine horn in day 5 of pregnancy indicating the possibility of their regulation by uterine estrogen in golden hamster C_LIO_LIProstaglandin synthesizing enzyme and LIF might be associated with the activation of inflammatory signals which are essential for successful establishment of early pregnancy in golden hamster. C_LI

physiology↗

bioRxiv2026

The CCCH-type zinc-finger PfMD3 promotes translation for malaria parasite transmission

Sexual maturation and fertility of the malaria causing parasite, Plasmodium spp., is critical to transmission between hosts. This developmental process involves an intricate gene expression regulatory network that drives gametocyte commitment, development, and the production of male and female gametes. Here, we characterized the role of the CCCH-type zinc-finger protein Plasmodium falciparum Male Development 3 (PfMD3) in the formation of gametes. Genetic disruption of PfMD3 revealed a male fertility defect that decreased infectivity to mosquitoes. Molecular characterization of PfMD3 revealed its binding to mRNA transcripts associated with male gamete development through a specific RNA sequence. Gametocyte proteins encoded by these PfMD3-bound transcripts decreased significantly in PfMD3 knockout parasites, suggesting that PfMD3 impacts translation. In addition to RNA-binding, PfMD3 also interacts with proteins involved in mRNA processing and nuclear export that influence translational regulation. This study establishes PfMD3 as an RNA-binding protein that impacts lineage-specific translation and male gamete fertility.

molecular biology↗

bioRxiv2026

AE-PocketMiner Uses Attention to Simultaneously Predict Cryptic Pockets and Their Allosteric Coupling

Finding and targeting cryptic pockets could dramatically expand the druggable proteome. However, discovering these sites remains challenging since they are only open a fraction of the time. It is also difficult to predict the functional relevance of a cryptic site as this often requires insight into allostery. Here we introduce attention enabled (AE-)PocketMiner, an artificial intelligence (AI) method that uses a graph neural network with an attention mechanism to simultaneously predict the locations of cryptic pockets and their allosteric coupling to the rest of the protein from a single input structure. We show that AE-PocketMiner outperforms past methods for identifying cryptic pockets and recapitulates known allosteric interactions. Moreover, we experimentally confirm newly predicted cryptic pockets and mutations that allosterically control pocket opening. AE-PocketMiner thus provides a powerful framework for multiple steps of the drug discovery process--including pocket identification, prioritization, and assay design--that will help expand the druggable proteome.

biophysics↗

bioRxiv2026

Elevated Expression of MALAT1 Contributes to the Survival of Drug-Tolerant Persister Cells Following Targeted Therapy in Lung Adenocarcinoma

Lung adenocarcinomas frequently harbour actionable oncogenic mutations that are vulnerable to treatment with targeted therapies. While responses to targeted therapies are often initially dramatic, relapse is almost inevitable and prevents durable responses in advanced-stage patients. Relapse is, in part, caused by drug tolerant persister cells (DTPs) which are able to survive treatment by entering a reversible, dormant state. Although long non-coding RNAs (lncRNAs) regulate processes thought to allow DTPs to survive and become stably resistant, the potential roles of lncRNAs in DTPs are largely unknown. In this study, we sought to investigate the expression of lncRNAs in in vitro DTP models of lung adenocarcinoma. We found that the lncRNAs Metastasis-Associated Lung Adenocarcinoma Transcript 1 (MALAT1) and Nuclear Paraspeckle Assembly Transcript 1 (NEAT1) were enriched in DTPs and that knocking down MALAT1 enhanced the effect of targeted therapies in both EGFR- and KRAS-mutant DTP models. To better understand pathways that MALAT1 might regulate in DTPs, bulk RNA-sequencing was performed and several pathways that may contribute to the actions of MALAT1 in DTPs were identified. Overall, our work describes a role for the lncRNA MALAT1 in DTPs in NSCLC and suggests that MALAT1 may be a novel target for the prevention of drug tolerance and subsequent resistance to targeted therapy in NSCLC.

cancer biology↗

bioRxiv2026

Synthetic lethality of fungal catabolite repressors reveals essential coupling of carbon repression with mitochondrial and ribosomal gene expression

Carbon catabolite repression (CCR) enables fungi to preferentially utilize favorable carbon sources through global transcriptional control. In filamentous fungi, CCR is classically attributed to the C2H2 zinc-finger repressor Mig1/CreA; however, residual repression following Mig1 disruption suggests additional regulatory layers in Talaromyces pinophilus (previously called Penicillium funiculosum NCIM1228). Here, we identify Mig3, a previously uncharacterized, Eurotiales-specific C2H2 transcription factor that functions redundantly with Mig1 in CCR. Mig3 contains conserved N-terminal zinc-finger motifs and a fungal transcription factor middle homology region and binds canonical Mig1 response elements with higher DNA affinity. Genetic analyses reveal that simultaneous loss of Mig1 and Mig3 is synthetically lethal, indicating an essential shared function beyond carbon repression. Integrative transcriptomic, chromatin immunoprecipitation sequencing, and proteomic analyses demonstrate that Mig1 and Mig3 directly regulate genes encoding mitochondrial and ribosomal components, including key factors involved in oxidative phosphorylation, while repressing genes required for alternative carbon metabolism. Loss of either repressor compromises expression of respiratory and ribosomal genes and confers hypersensitivity to mitochondrial and ribosomal inhibitors. In addition, both repressors physically associate with mitochondrial, ribosomal, and central metabolic proteins, suggesting coordination of transcriptional and post-transcriptional regulatory mechanisms. Together, our findings redefine fungal catabolite repressors as metabolic gatekeepers that couple CCR to mitochondrial and ribosome biogenesis, thereby controlling the metabolic switch between core cellular growth processes and enzyme secretion.

microbiology↗

bioRxiv2026

Coordinated immune architecture underlies durable survival in pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) is characterised by profound immune dysfunction and limited response to immunotherapy. Although tertiary lymphoid structures (TLSs) are associated with improved outcomes, most studies focus on their presence or density, providing limited insight into how their organisation contributes to tumour control. Here, we analyse a unique cohort of treatment-naive PDAC patients enriched for exceptionally rare long-term survivors (LTS, n = 23; >5-year survival) alongside more common short-term survivors (STS, n = 24), enabling direct interrogation of mechanisms underlying durable tumour control. We develop a multi-scale spatial framework integrating multiplex imaging, computational modelling, and transcriptomics to quantify TLS architecture. By modelling TLSs as higher-order immune assemblies, we define their structural states, spatial organisation, assembly rules and tissue context-dependency within the tumour microenvironment. We show that long-term survival is associated with organised, spatially integrated TLSs exhibiting coordinated B and T cell zoning, whereas short-term survival is characterised by disorganised, Treg-enriched, and spatially isolated TLSs, despite similar immune cell abundance. These architectural differences align with transcriptional programmes: LTS tumours display coordinated lymphoid and NF-{kappa}B-driven chemokine signalling, while STS tumours exhibit inflammation uncoupled from immune organisation. Together, these findings demonstrate that durable anti-tumour immunity in PDAC is defined by coordinated transcriptional, cellular, and spatial organisation, rather than immune presence alone. This study provides a blueprint for structure-informed strategies to reprogram the tumour microenvironment and improve outcomes in PDAC. Statement of significanceIntegrating multiplex imaging, computational modelling and transcriptomics in treatment-naive PDAC enriched for exceptional survivors shows that durable tumour control is associated with organised TLS architecture rather than immune abundance alone, providing a framework for immune-architecture-based biomarkers and therapeutic reprogramming.

cancer biology↗

bioRxiv2026

Activation of the mRNA Decay-Associated DEAD-Box ATPase Dhh1 Requires Deadenylation and Decapping Factors

The DEAD-box ATPase Dhh1 (DDX6 in humans) is a general activator of 5-3 mRNA decay that acts between the deadenylation and decapping steps of the pathway, although the exact mechanism of its action remains unclear. Dhh1 has been shown to interact with the MIF4G domain of the central scaffold protein of the Ccr4-Not deadenylase complex, Not1, as well as the decapping activator Edc3. Although structures have been published of Dhh1 in complex with Not1MIF4G or an Edc3 peptide, the impact of these interactions on the catalytic cycle of Dhh1 are unknown. Here, we show Edc3 enhances ATP and RNA binding by Dhh1, whereas Not1MIF4G promotes the catalytic step of ATP hydrolysis. Additionally, the modulation of Dhh1 activity by Edc3 requires a more extensive set of interaction motifs and interfaces than was previously recognized. While the effect of either Not1MIF4G or Edc3 on the ATPase activity of Dhh1 is modest, together both proteins increase Dhh1 activity over 200-fold. The fact that Dhh1 biochemical activity is cooperatively tuned by deadenylation and decapping factors suggests that Dhh1 may coordinate deadenylation and decapping in the 5-3 mRNA decay pathway through changes in its ATP-coupled RNA binding affinity during its catalytic cycle. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=75 SRC="FIGDIR/small/721454v2_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@12a38e2org.highwire.dtl.DTLVardef@fcb87forg.highwire.dtl.DTLVardef@1b4c77dorg.highwire.dtl.DTLVardef@194fc1d_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2026

Agroforestry reshapes soil bacterial communities to enhance Ricinus communis oil quality and bioactivity over monocropping: comparative metagenomics and culture-dependent insights

An agroforestry (AF) system improves crop quality, ecosystem services, and microbial resilience, but its effects on oilseed bioactivity and soil microbiomes are still underexplored. This study compared AF and monocropping systems for castor (Ricinus communis L.) grown in Rajasthan, India, to evaluate plant productivity, seed oil composition, antimicrobial properties, and soil bacterial communities. AF enhanced seed morphology and germination. Castor oil from agroforestry had a 2.4-fold higher phenolic content, 2% more ricinoleic acid, and lower levels of oleic and linoleic acids compared to monocropping, confirmed by infrared spectroscopy and gas chromatography, along with increased expression of the RcDGAT2 gene involved in fatty acid biosynthesis. This led to improved antimicrobial activity against Bacillus mobilis and Pseudomonas fluorescens. Full-length 16S rRNA gene sequencing on the Nanopore platform identified 17 bacterial phyla in soil microbiomes, with Proteobacteria and Firmicutes as the dominant phyla. While alpha diversity was similar, AF soils showed distinct taxonomic shifts, enriching bacteria such as Alkalimonas, Aureimonas, Blastopirellula, Glutamicibacter, Rhizobium, Rhizomicrobium, and Rhodovulum, linked to nutrient cycling and plant growth promotion. Isolated rhizospheric/root endophytic Bacillus safensis and Enterobacter cloacae from AF castor exhibited plant growth-promoting traits via biochemical tests and whole-genome sequencing; their oil biosynthesis genes likely contribute to host oil quality by enhancing precursor supply and phenolic pathways. These isolates enhanced the growth of the model plant Arabidopsis thaliana. In summary, AF enhances the bioactivity of castor oil and microbial functions by modulating plant-soil-microbe interactions, thereby supporting sustainable crop quality and soil health.

microbiology↗

bioRxiv2026

Identification of the novel inhibitors against M. tuberculosis ESX-1 secretion system EccA1 enzyme using virtual screening, docking and dynamics simulation techniques

The M. tuberculosis ESX-1 secretion system EccA1 enzyme is involved in the secretion of virulence factors and is essential for virulence and bacterial survival within the phagosome. Development of the small molecular inhibitors abolishing EccA1 function can yield new antivirulence drugs. In this study, we modeled the full-length EccA1 (573 residues, Mw [~]62.4 kDa) structure, which contains N-terminal TPR domain and a C-terminal CbxX/CfqX type ATPase domain. We have identified five ZINC compounds having binding energy i. e. Z1 (ZINC000004513760, -43.45 kcal/mol), Z2 (ZINC000000001793, -49.56 kcal/mol), Z3 (ZINC000005390388, -55.83 kcal/mol), Z4 (ZINC000257294577, -52.33 kcal/mol), Z5 (ZINC000004824264, -44.44 kcal/mol) through virtual screening of the ZINC compounds targeting C-terminal ATPase pocket of EccA1. The Z1-Z5 compounds were compared with ADP substrate having binding energy (Adenosine diphosphate, -35.00 kcal/mol), p97 ATPase inhibitors i.e. NMS873 (3-[3-cyclopentylsulfanyl-5-[[3-methyl-4-(4 methylsulfonylphenyl)phenoxy]methyl]-1,2,4-triazol-4-yl]pyridine, -48.68 kcal/mol), and CB5083 (1-[4-(benzylamino)-5H,7H,8H-pyrano[4,3-d]pyrimidin-2-yl]-2-methyl-1H-indole-4-carboxamide, -50.88 kcal/mol) against EccA1. The Z1-Z5 compounds exhibited good Absorption, Distribution, Metabolism, and/or Excretion properties (ADMTE). Pharmacokinetic properties and Lipinskys rule of five for Z1-Z5 compounds showed drug-like properties. 100 ns dynamics simulation analysis on EccA1 complexed with (i) Z1-Z5 compounds (ii) ADP substrate and (iii) NMS873 and CB5083 inhibitors showed high stability and biologically relevant conformation during dynamics simulation. These data indicate that Z1-Z5 compounds may act as potential inhibitors against EccA1 and provide avenues for new antivirulence drug development after in vitro and in vivo clinical trials.

bioinformatics↗

bioRxiv2026

Cellular hydraulics ensures robust endothelial-to-haematopoietic transition

Haematopoietic stem and progenitor cells (HSPCs) emerge from specialised haemogenic endothelial cells (HECs) in the ventral wall of the dorsal aorta (VDA) through a process known as endothelial-to-haematopoietic transition (EHT). During EHT, elongated HECs undergo actomyosin-driven rounding and extrusion, a mechanically demanding transformation that requires cell integrity to be maintained. Here, we identify an osmo-hydraulic volume-regulation mechanism that enables HECs to adapt to and withstand this mechanical challenge. Haemodynamic forces increase Piezo-dependent calcium ion activity in ventral endothelial cells, while Piezo activation promotes HEC swelling. Combined genetic and pharmacological analyses support a pathway in which Piezo-mediated swelling triggers VRAC-dependent osmolyte efflux and Aqp1a.1-mediated water efflux to reduce HEC volume. Disrupting either osmolyte or water efflux causes excessive HEC swelling, compromises HEC integrity and reduces HSPC production. Together, our findings establish osmo-hydraulic volume regulation as a mechanism that preserves cellular robustness during EHT and support a model in which aquaporins act as pressure-relief valves, dissipating intracellular hydrostatic pressure to sustain HEC survival and definitive haematopoiesis.

cell biology↗

bioRxiv2026

Suppression of upstream ORF translation is not a widespread mechanism of translational stimulation by yeast helicase Ded1

Ded1 is an essential DEAD-box helicase in yeast that broadly stimulates translation initiation and is critical for mRNAs with structured 5UTRs. We have evaluated the proposal that Ded1 stimulates translation primarily by preventing initiation at upstream ORFs (uORFs) associated with stable secondary structures. By Ribo-Seq analysis under experimental conditions designed to suppress artifactual 5UTR translation, we found that reduced translation of the main open-reading-frames (mORFs) in native mRNAs is generally not accompanied by increased 5UTR translation in ded1 mutant cells, and that the presence of translated uORFs in yeast mRNAs generally does not confer heightened dependence on Ded1 for efficient translation of mORFs. Results from a high-throughput reporter assay examining native 5UTRs reinforce the importance of Ded1 in initiation from structured 5 UTRs and show that impairing Ded1 has minimal effects on translational repression by uORFs. Our results demonstrate that, in cells growing vegetatively in rich medium, translational stimulation by suppression of inhibitory uORFs is restricted to a minority of Ded1 targets, and that unwinding of 5 UTR secondary structures per se is the principal mechanism for Ded1 stimulation of translation initiation.

genomics↗