Biology subjects

Srivastava, A.

Publications and source records attributed to Srivastava, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Response to SMAC mimetics in patient-derived models of triple-negative breast cancer relies on RIPK1 activation

Triple-negative breast cancer (TNBC) is a highly metastatic and aggressive breast cancer subtype with limited targeted treatment options. Second mitochondrial activator of caspases (SMAC) mimetics represent a promising therapeutic class for TNBC patients, although they have yet to be approved clinically. Screening a repository of 69 breast cancer patient-derived xenograft organoid (PDxO) lines revealed that approximately 39% were sensitive to the SMAC mimetic birinapant. To define the basis of resistance in lines that did not respond, we compared birinapant-sensitive (S-) and de novo resistant (R-) TNBC PDxOs. Birinapant caused degradation of inhibitor of apoptosis proteins (IAPs) in both groups but failed to induce cell death in R-PDxOs. We determined that R-PDxOs were susceptible to certain types of apoptosis but were specifically resistant to TNFR-mediated cell death, an integral pathway involved in SMAC mimetic response. Moreover, RIPK1 activation via autophosphorylation, a critical event in TNFR-mediated apoptosis, was absent in both R-PDxOs and PDxOs selected for acquired birinapant resistance. Pharmacologic inhibition or degradation of RIPK1 protected S-PDxOs from birinapant-induced cell death, demonstrating that RIPK1 activation is required for response in TNBC. To investigate how to restore RIPK1 activation in R-PDxOs, we discovered that HOIP, an E3 ubiquitin ligase that inhibits RIPK1 autophosphorylation, was more abundant in R-PDxOs compared to S-PDxOs. Inhibiting HOIP activity restored RIPK1 autophosphorylation and sensitized a subset of R-PDxOs to birinapant. Together, these findings identify impaired RIPK1 autophosphorylation as a mechanism of birinapant resistance in TNBC and suggest that RIPK1 activation state may distinguish SMAC mimetic-sensitive and -resistant tumors. Targeting HOIP may provide a strategy to overcome resistance in selected tumors.

cancer biology↗

bioRxiv2026

Toward A Whole-Brain Interface Enabled by High-Resolution Surface Electrophysiology

The goal of building a whole-brain interface - capable of generating a real-time digital representation of the state of the entire central nervous system - has long been framed as a hardware challenge of recording simultaneously from ever-larger numbers of microelectrodes. Advances in high-resolution neural interfaces now enable electrophysiologic interaction with the human nervous system at spatial and temporal resolutions previously unattainable without disrupting tissue architecture or physiology. These capabilities create new opportunities for mechanistic neuroscience, neuroprosthetics, and precision-guided neurosurgery. With the advent of modern microelectrode array technology, however, the whole-brain interface has also become a data challenge. Rather than pursuing large-scale human brain recording purely through a single device placed in a single patient, we demonstrate here that systematic multi-subject aggregation, across brain regions and behavioral paradigms, in a common anatomical framework, can achieve something functionally similar to a whole-brain interface. Here we present an approach to a functional atlas of the human central nervous system derived from high-resolution surface electrophysiology recordings obtained in the first 70 patients implanted with an anatomically conformal, thin-film neural interface positioned in more than 100 locations. The atlas comprises >100,000 electrode deployments and catalogs placement across a broad range of neuroanatomic targets spanning the motor, sensory, language, auditory, and associative domains, as well as brainstem and spinal cord structures that have historically been difficult to access at high electrophysiologic resolution. Across participants, aggregated recordings reveal somatotopic organization, including digit representations that follow a lateral-to-medial ordering consistent with classical homuncular maps, with transitions between adjacent representations occurring over spatial scales of approximately 0.8 - 2.0 mm; canonical frequency-band signatures, such as movement-related beta-band suppression and focal high-gamma (70 - 200 Hz) increases during motor and speech behaviors; and task-modulated population dynamics in both evoked and spontaneous activity across cortical, brainstem, and spinal cord regions. These findings yield insight into patterns of mesoscale electrophysiological dynamics conserved across the entire human central nervous system, suggesting that fine-scale functional organization is preserved across individuals when aligned to common anatomical landmarks. We further demonstrate several applications of these high-resolution recordings, including real-time neural decoding from upper extremity motor cortex to enable real-time neuroprosthetic control, and from ventrolateral cortex to decode cortical correlates of spoken language, facial movements, and complex facial expressions of emotion, supporting initial feasibility of combined verbal and nonverbal communication interfaces. Together, these results establish a paradigm for approaching large-scale interfaces with the human brain, as well as a starting point for a scalable, extensible atlas of human electrophysiologic function designed to accelerate discovery across basic neuroscience, translational research, and clinical neurotechnology.

neuroscience↗

bioRxiv2026

AmyloCore-ML: AI/Machine Learning Enabled Identification of Amyloid Fibril Core Regions Using Protein Language Models

Identification of amyloid forming regions in proteins remains central to understanding of their aggregation behaviour, which are central to various neurodegenerative and systemic disorders. Many predictors have been designed to identify amyloid forming regions, however they may not necessarily identify total residues found in actual disease associated fibril structures. To address this, we formed a sequence-based based predictor-AmyloCore-ML to ascertain structural amyloid-core propensity. The predictor was developed using experimentally determined fibril structures obtained from Amyloid Atlas. Ordered residues in the experimental structures were designated as core, and unresolved sampled from the same proteins as matched controls as non-core. Core and non-core regions were encoded using various physicochemical descriptors and protein language model (PLM) embeddings (ESM-2, ANKH, ProtT5) and evaluated using protein-grouped cross-validation. PLMs consistently outperformed physicochemical descriptors, with the best models reaching AUROC values of ~0.88 and AUPRC values of ~0.85. Locked full-length protein scans further localized experimental cores, with ESM-2/ExtraTrees achieving AUROC 0.833, AUPRC 0.751, and a mean peak distance of 12.4 residues. In comparative benchmarking, our predictor showed better performance metrics than CrossBeta and AggrescanAI. The framework therefore provides residue-resolved prediction of structurally incorporated amyloid-core regions directly from sequence.

bioinformatics↗

bioRxiv2026

SOP-Multi-π: A Two-Site Coarse-Grained Model with Rescaled Aromatic Interactions to Bridge Single-Chain Ensembles and Condensate Phase Behavior of IDPs and Multidomain Proteins

We present SOP-Multi-{pi}, an enhanced version of the two-bead-per-amino-acid resolution Self-Organized Polymer (SOP) model designed to investigate the conformational dynamics of Intrinsically Disordered Proteins (IDPs) and their phase behavior in biomolecular condensates. The original SOP-IDP and SOP-Multi models work well for chains in good solvents that predominantly adopt expanded conformations. However, they fail to reproduce the single-chain properties and phase-separation behavior of IDPs such as hnRNPA1 and its variants, which have a distinct pattern of aromatic residues. We therefore reparameterized the SOP-IDP force field to explicitly capture {pi}-{pi} and cation-{pi} interactions at the coarse-grained (CG) resolution. These interactions are weak but important for biomolecular recognition and for driving and stabilizing biomolecular condensates. Dimensionless rescaling prefactors ({lambda}) were applied exclusively to the aromatic {pi}-{pi} (Phe, Tyr, Trp) and cation-{pi} (Arg/Lys with Phe, Tyr, Trp) pairs. They were optimized iteratively against experimental radii of gyration of the hnRNPA1 low-complexity domain (A1-LCD) and its 16 aromatic and charge mutants. This restored a physically meaningful Tyr > Phe interaction hierarchy, and the Pearson correlation for Rg improved from r = 0.07 (SOP-IDP) to r = 0.83 (RMSD = 0.08 nm). The same parameters, without further tuning, gave r = 0.93 for 34 additional IDPs (24-198 residues) and reproduced Flory scaling ( {nu} ~ 0.588). We back-mapped microsecond-scale CG ensembles to all-atom representations and computed SAXS and Kratky profiles for direct comparison with experiments on IDPs and on the multidomain proteins hnRNPA1, TDP-43, G3BP1, and FUS. In direct-coexistence slab simulations, the model captures the phase behavior of A1-LCD condensates and their variants, with critical temperatures that correlate strongly with experiment (r = 0.88) but are somewhat underestimated in absolute terms. The model is implemented in LAMMPS, and a detailed user manual is provided for setting up single-chain and multi-chain condensate simulations of full-length multidomain proteins.

biophysics↗

bioRxiv2026

A panel of Diversity Outbred mouse embryonic stem cells: enabling the functional characterization of natural genetic variation in vitro

Phenotypic variation in pluripotent stem cells arises largely from genetic variants that impact stability of the pluripotent state, response to differentiation cues, and cell fate diversification. Panels derived from genetic reference populations leverage genetic diversity to map the loci influencing these molecular and cellular traits. Here we describe the first publicly available resource for in vitro systems genetics in Mus musculus: 299 genetically diverse, highly heterozygous embryonic stem cell lines derived from Diversity Outbred mice, with minimal kinship across the panel. We characterize genomic integrity and allelic variation across the panel and describe differences in pluripotency and differentiation networks in embryoid bodies. Mapping the genetic determinants of gene expression differences in response to cadmium exposure in embryoid bodies identified 13 regulatory hotspots, the largest acting on ribosome biogenesis genes. This panel enables mapping of loci and gene-by-environment interactions that influence molecular identity in pluripotent cells and their derived cell types.

systems biology↗

bioRxiv2026

Phosphoinositides protonation states dictate AKT1 binding with membrane

Phosphoinositides are key regulators of membrane-associated signaling, yet their electrostatic properties are commonly represented by a single nominal charge in molecular simulations and structural models. Using the essential protein kinase AKT1 as a model system, we show that phosphoinositide protonation microstates, both the degree and positional placement of protons, govern peripheral membrane-protein recognition. By integrating quantum-mechanics-derived headgroup parameters, microsecond-scale all-atom molecular dynamics, and umbrella-sampling free-energy calculations with the available solid-state NMR-derived lipid populations via Bayesian/Maximum Entropy reweighting, we account explicitly for the thermodynamic ensemble of phosphoinositide proto-nation states. This population-weighted free-energy framework provides a quantitative mechanistic rationale for the strict specificity of wild-type AKT1 toward PI(3, 4, 5)P3 and elucidates how the oncogenic sentry mutation (E17K) alters this specificity to enable high-affinity PIP2 binding. Furthermore, Proximity-based Labeling of Membrane Associated Proteins (PLiMAP) assays experimentally confirm that AKT1 pleckstrin homology domain binding to distinct phosphoinositide species is differentially sensitive to pH. Together, our findings establish a direct connection between phosphoinositide protonation equilibria, binding energetics, and AKT1 lipid specificity. Beyond AKT1, these results demonstrate that the dynamic protonation microstates of anionic phospholipids act as a functional regulatory layer governing peripheral membrane-protein recruitment across diverse cellular microenvironments.

biophysics↗

bioRxiv2026

Morpheus-3D: Structural Diversity-Guided Detection and Localization of Protein Fold Switching

Proteins that reversibly adopt multiple stable folds challenge the classical sequence-structure paradigm, yet their discovery remains limited because fold switching is difficult to detect experimentally and current computational methods fail to resolve the underlying conformationally plastic regions. Here we present Morpheus-3D, a sequence-based framework that quantifies residue-level tertiary structural diversity using entropy profiles derived from the Foldseek 3Di structural alphabet. By capturing variation in tertiary interaction environments rather than secondary structure alone, Morpheus-3D identifies fold-switching proteins while simultaneously localizing the sequence regions responsible for structural transitions. The framework outperforms existing predictors, accurately recovers experimentally characterized switching regions, generalizes to recently discovered natural and engineered fold-switching proteins absent from training, and detects conformational plasticity inaccessible to secondary-structure-based approaches. Application to 57 representative proteomes reveals that fold-switching potential is widespread but enriched in regulatory, pathogenic, and environmentally adaptive lineages. Integration with ancestral sequence reconstruction further un-covers evolutionary trajectories through which conformational plasticity emerges. To make these predictions directly accessible, we implemented Morpheus-3D as an interactive web platform (https://morpheus.slicearrow.com/), in which per-residue entropy profiles, sequence and three-dimensional structure are displayed together and respond as one, allowing predicted fold-switching regions to be mapped onto the structure and exported for downstream analysis. Morpheus-3D provides a scalable framework for discovering metamorphic proteins and investigating the origins, mechanisms, and evolution of structural plasticity directly from sequence.

biophysics↗

bioRxiv2026

Structural basis of K+/H+ antiport in YcgO and its inhibition by unphosphorylated PtsN

Cation-proton antiporters (CPAs) are vital for the maintenance of ionic homeostasis and normal physiology among diverse cell types. Despite recent insights into K+/H+ exchange transporters, the diversity in their structural organization and regulatory mechanisms of K+-specific CPAs are minimally understood. Here, we explore the architecture of an E. coli CPA1 K+/H+ antiporter, YcgO and its inhibition by the unphosphorylated form of PtsN, the terminal protein of a regulatory phosphorelay, using cryoEM structures at 3.4 [A] and 3.2 [A] resolution, respectively. Homodimeric YcgO bound to K+ ions in the occluded conformation, harbors additional linked cytosolic domains, RCK and CorC, to regulate the movement of the transport helices within the YcgO dimer. These domains are the sites of interaction and efflux inhibition by unphosphorylated PtsN, which interacts with the CorC domains with high affinity and allosterically augments inhibitory interactions of CorC with transport helices of YcgO. Inhibition is relieved leading to constitutive activation, upon disrupting the CorC-transport conduit interface. This study illuminates the structural basis of K+ efflux mediated through regulation of a K+/H+ antiporter in E. coli and related prokaryotes via a metabolic network involving a regulatory phosphorelay.

biochemistry↗

bioRxiv2026

Bioactive Spermidine-Crosslinked DNA Hydrogel for rapid homeostasis and accelerated wound healing

Damage to the skin by trauma, burns, or surgical procedures often results in uncontrolled bleeding, which remains a leading cause of preventable death following injury, yet most conventional hemostatic materials are engineered solely to arrest bleeding and often adhere strongly to the wound bed, causing pain, rebleeding, and disruption of newly formed tissue upon removal. Here, we report a DNA hydrogel that structurally mimics neutrophil extracellular traps (NETs) and is crosslinked using a bioactive small molecule with potent autophagy-inducing, cardioprotective, anti-inflammatory, antioxidant, and mitochondria-protective properties, integrating rapid hemostasis with active support for tissue regeneration in a single biomaterial. The DNA network provides an intrinsically biocompatible, biodegradable scaffold capable of recruiting platelets and erythrocytes to achieve rapid clot formation, while the bioactive crosslinker is released as the network degrades, delivering a sustained cytoprotective and anti-inflammatory stimulus directly at the wound site. The hydrogel was characterised physiochemically and evaluated for cytocompatibility, hemolytic potential, hemostatic efficacy, and wound-healing performance in a murine model. Results demonstrate that the bioactive-crosslinked DNA hydrogel achieves rapid, effective hemostasis, while accelerating wound closure and supporting regenerative tissue remodelling. This dual-function platform offers a promising strategy for next-generation wound-care biomaterials that unite immediate bleeding control with accelerated, natural tissue healing.

bioengineering↗

bioRxiv2026

Expanding the Promoter Toolbox for Metabolic Engineering in the Lignocellulolytic Thermophile Anaerocellum bescii

Anaerocellum (formerly Caldicellulosiruptor) bescii, an anaerobic, extremely thermophilic (Topt [~]78 {degrees}C) lignocellulolytic bacterium, is a promising chassis for metabolic engineering and next-generation bioprocessing. Yet, a lack of well-characterized genetic parts in A. bescii has hampered metabolic engineering efforts. Here, using a previously developed hyperthermophilic {beta}-galactosidase reporter system, we screened a diverse panel of putative A. bescii promoter sequences, identifying promoters that drove reporter output across a broad range. For a select subset, we mapped their transcriptional start sites (TSSs) and evaluated ribosome binding site (RBS) regions using chimeric promoter constructs. By constructing truncated promoter variants, we defined functional regions within the widely used, high-expression S-layer protein promoter (Pslp) and engineered a compact 99 bp variant that retained substantial reporter activity. Finally, we demonstrated that these new promoters can be used for metabolic engineering by using two newly characterized promoters to express an established thermostable alcohol dehydrogenase from Thermoclostridium stercorarium to drive ethanol production in A. bescii. Together, this work expands and diversifies the A. bescii genetic toolkit, opening doors to future metabolic engineering efforts in this species.

Synthetic Biology↗

bioRxiv2026

Plasma-derived extracellular vesicles as potential biomarkers and mediators of functional alterations in MELAS

Mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes (MELAS) syndrome is a genetic disorder characterized by progressive neuromuscular and multisystem symptoms. MELAS typically manifests during childhood, can be difficult to diagnose, and has no cure. Extracellular vesicles (EVs) are lipid-enclosed nanoparticles secreted from cells that contain biological cargo and have demonstrated potential as biomarkers. We investigated the potential of plasma-derived EVs as diagnostic biomarkers of MELAS and examined their functional effects on mitochondrial respiration in treated skeletal muscle myotubes. Plasma-derived EVs were isolated from MELAS patients and age- and sex-matched control individuals, and biophysical characteristics and cargo of EVs analyzed. A Mito Stress Test was performed to assess oxygen consumption rate (OCR) in healthy myotubes treated with Control- or MELAS-EVs to determine the functional effects of circulatory EVs. Nine MELAS patients from two families were studied, and the results were categorized by age, sex and mtDNA heteroplasmy level. EV size and zeta potential remained unchanged. However, total EV concentration was higher in MELAS patients, particularly for small-EVs (<200 nm) and in younger patients (<25 years old). Relative protein yield per EV was lower in the MELAS group, especially among female and younger individuals. EV double-stranded DNA (dsDNA) concentration did not differ between MELAS- and Control-EVs overall, but was higher in male MELAS patients. Protein markers typically enriched in small-EVs showed altered expression in MELAS EVs: TSG101 and CD63 were lower, while flotillin-1 was higher compared to Control-EVs. A decrease in basal OCR was shown in cells treated with MELAS-EVs, with a similar response noted in the group treated with EVs from female MELAS patients. Post-treatment analysis showed no differences in oxidative phosphorylation (OXPHOS) subunit levels between cells treated with MELAS- and Control-EVs. In conclusion, plasma-derived EVs show promise as potential biomarkers for MELAS, and circulating EVs in this patient population may contribute to systemic metabolic dysfunction.

Cell Biology↗

bioRxiv2026

STITCH links cellular morphology and gene expression in spatial transcriptomics

In situ spatial (ISS) sequencing can uncover co-variation between cellular morphology and gene expression in vivo. However, a principled and interpretable mathematical representation of morphology has not yet been applied in this context. In particular, current deep learning-based representations of cell images confound a cell's shape with its size. We present an interpretable representation of cellular boundary contours, based on tangent principal component analysis (TPCA) in a Kendall shape manifold, that captures size-independent contour shape features. This approach successfully recovers shape-perturbing genes in an RNAi screen than a previous metric geometry-based approach. We build on TPCA to develop KSTITCH (Kendall Shape-TranscriptomIc Correlation and Harmonization), an approach to reveal covariation between cell morphology with gene expression in ISS datasets. In a Xenium dataset, KSTITCH recovers known morphology-transcriptomic relationships in keratinocytes, macrophages and endothelial cells. Across samples in a melanoma CosMx dataset, KSTITCH reproducibly associates elongated and triangular fibroblasts with proximity to malignant cells and myofibroblast-like transcriptional program. Finally, KSTITCH independently recovers a known link between mesenchymal-like malignant cell states and increased cell area in two melanoma cohorts. KSTITCH can thus yield interpretable morphology-transcriptome relationships across cell types, patients, and spatial transcriptomics platforms. KSTITCH is available at https://github.com/vishakagopalan/kstitch .

bioinformatics↗

bioRxiv2026

Mapping the structural coverage of Arabidopsis thaliana plant developmental proteins: Insights from Experimental and AlphaFold Approaches

BackgroundPlant development is a multifaceted process governed by intricate protein regulatory networks. High-throughput sequencing methods have vastly expanded plant transcriptomic and proteomic datasets, yet there is a large discrepancy between structural information for plant developmental proteins and the UniProt sequence entries. Advances in X-ray crystallography, NMR spectroscopy, and Cryo-EM have enabled the determination of protein complex structures and their dynamics. AI-driven tools like AlphaFold have revolutionized analysis of protein structural intricacies. However, available three-dimensional structural models predominantly prioritize the human proteome and other mammals over plants. Assessing structural coverage of plant developmental proteins is thus essential to identify research gaps, guide structure-function studies, and advance agriculture. ResultsHere, we focus on mapping the structural coverage of developmental proteins in Arabidopsis thaliana. We observed a substantial disparity in the Protein Data Bank (PDB) representation of Arabidopsis thaliana proteins compared to those of Homo sapiens. Our analysis identified 16,389 reviewed UniProt entries, of which only 1,038 have experimentally determined structures. Functional mapping using PlantGSEA revealed 3,485 proteins associated with plant developmental processes; of which only 337 (9.67%) have experimentally determined structures. In contrast, analysis of the AlphaFold database showed that 69.85% of the 39,278 Arabidopsis thaliana UniProt protein entries have predicted structures. Notably, all 3,485 plant developmental proteins (100%) from Arabidopsis thaliana are covered by AlphaFold models. The substantially higher structural coverage provided by AlphaFold for Arabidopsis thaliana, relative to Homo sapiens, highlights the strength of computational approaches in addressing the challenges of structural studies of difficult-to-crystallize proteins. Furthermore, 79.15% of reviewed A. thaliana protein models exhibit high confidence (pLDDT > 70), indicating reliable structural predictions. Although the experimental structural coverage of Arabidopsis thaliana developmental proteins remains limited, AlphaFold has markedly expanded the accessible structural landscape. ConclusionThis study investigated the structural coverage of Arabidopsis thaliana plant developmental proteins, underscoring the critical need for structural studies using both experimental and AlphaFold approaches. It provides research directions for bridging the knowledge gap in understanding molecular mechanisms of plant development.

bioinformatics↗

bioRxiv2026

A phylogeny-guided framework for decoding mechanisms of human endogenous retrovirus regulation in health and disease

Human endogenous retroviruses (HERVs) are remmants of ancient infections which make up to [~]8% of the human genome. Their activity influences development, immunity, and cancer, but studying them has been limited by a key technical challenge: short-read sequencing cannot uniquely assign reads to these highly repetitive elements. Here, we present ERVmancer, a phylogeny-informed method that resolves the read-mapping ambiguity and quantifies HERV expression across scales, from individual loci to entire retroviral clades, depending on mapping confidence. Benchmarking with sample-matched long- and short-read data generated in this study demonsrates that ERVmancer outperforms existing approaches in both sensitivity and specificity. Application of ERVmancer recapitulates known HERV expression patterns in multiple sclerosis and uncovers new biology in breast cancer, including suppression of HERVH-LTR7 by p53. By enabling accurate and scalable quantification of integrated retroviral elements, ERVmancer provides a broadly applicable resource for investigating retroviral mechanisms in health and disease.

bioinformatics↗

bioRxiv2026

Co-expression network analysis reveals repression of Igf2bp2 by REV-ERBβ in skeletal muscle

The circadian clock genes Bmal1 and Nr1d1/2 (REV-ERB/{beta}) regulate skeletal muscle metabolism and homeostasis, yet the precise genes and mechanisms involved remain incompletely understood. Here, we perform Weighted Gene Co-expression Network Analysis (WGCNA) on skeletal muscle circadian transcriptomes with varying Bmal1 operational status to identify genes central to muscle circadian function. The largest WGCNA module, potentially under Bmal1 regulation, contains clock and muscle-specific output genes governed hierarchically by hub genes including Igf2bp2, an RNA-binding protein involved in muscle progenitor growth and maintenance. Igf2bp2 expression is rhythmic in mouse and human muscle and functional experiments in muscle-specific Bmal1 knockout mice show that Igf2bp2 is upregulated by loss of Bmal1 at ZT8 and negatively correlated with Nr1d2, suggesting de-repression through REV-ERB{beta} as a regulatory mechanism. Luciferase reporter experiments in cultured myotubes show that REV-ERB{beta}, but not REV-ERB, represses Igf2bp2 transcription and that repression is mediated by non-canonical GCC motifs in the Igf2bp2 promoter region. Together, these findings uncover a circadian Nr1d2-Igf2bp2 regulatory axis linking transcriptional and post-transcriptional regulation in skeletal muscle, with implications for muscle homeostasis. HighlightsO_LIIgf2bp2 clusters with Nr1d2 (Rev-erb{beta}) in circadian co-expression network C_LIO_LIBmal1 or Rev-erb[a]/{beta} knockout upregulates Igf2bp2 in muscle C_LIO_LIIgf2bp2 is rhythmic in WT muscle but arrhythmic in clock mutant muscle C_LIO_LIREV-ERB{beta} represses Igf2bp2 transcription in myotubes C_LIO_LIREV-ERB{beta} repression requires GCC motifs in the Igf2bp2 promoter C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/724827v1_ufig1.gif" ALT="Figure 1"> View larger version (89K): org.highwire.dtl.DTLVardef@1716a34org.highwire.dtl.DTLVardef@f3a5b1org.highwire.dtl.DTLVardef@33f58org.highwire.dtl.DTLVardef@133e3db_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2026

A Retro-Inverso Peptide that Inhibits Formation and Disrupts Preformed α-Helical Amyloid and Staphylococcus aureus Biofilms

Combatting biofilm-associated methicillin-resistant Staphylococcus aureus (MRSA) infections remains a formidable challenge, largely due to bacterias heightened resistance to antibiotics and evasion of the hosts immune responses. Inhibiting biofilm formation or promoting biofilm dissolution is believed to disrupt the protective matrices and expose bacterial cells to immune clearance or antimicrobial treatments. Cross- helical amyloid fibrils of phenol-soluble modulins are the key structural components of the MRSA biofilm. In this study, we present a novel retro-inverso peptide that successfully inhibits cross- amyloid formation, induces disassembly of pre-formed fibrils of the biofilm-forming modulin peptide, and efficiently disperses MRSA biofilm biomass in a dose-dependent manner. The biophysical studies of the interaction of the designed peptide and modulins have suggested a mechanism for the biofilm disruption. The findings highlight the potential of the proteolytically resistant mirror-image peptide as a promising therapeutic agent for the treatment of biofilm-associated MRSA infections.

biophysics↗

bioRxiv2026

Dissecting the Network Architecture of a Plant Circadian Clock Model: Identifying Key Regulatory Mechanisms and Essential Interactions

Circadian rhythms are self-sustained biological oscillations that coordinate diverse physiological processes in plants, including growth, metabolism, and environmental responses. These rhythms arise from an interconnected transcriptional translational feedback network that integrates multiple entrainment cues such as light and temperature. The plant circadian clock is organized around key regulatory loops involving CCA1, LHY, PRRs, TOC1, ELF4, LUX, and other transcriptional regulators, whose coordinated interactions ensure precise and robust oscillations. In this study, we developed an ordinary differential equation based mathematical model, building upon a previous framework to incorporate additional regulatory modules and transcriptional controls that better reflect experimentally observed behaviour. To elucidate the regulatory organization of this model, we performed a multi-layered computational analysis combining four complementary approaches: (i) period sensitivity analysis to quantify how parameter perturbations influence the systems timing, (ii) phase portrait analysis to visualize dynamic interactions among key components, (iii) knockout analysis to identify parameters essential for sustained rhythmicity, and (iv) network impact analysis using composite weighted network indices to evaluate hierarchical control across the network. Together, these analyses reveal that transcriptional repression, protein degradation, and light-regulated synthesis form the dominant control mechanisms within the circadian system. The results highlight a hierarchical and robust network structure centred on the CCA1/LHY and PRRs feedback loop, with redundant modules ensuring stability under perturbations. Thus, this model provides an improved, biologically consistent framework for dissecting the dynamic architecture of the plant circadian clock and guiding future experimental validation.

systems biology↗

bioRxiv2026

BenchDrop-seq: a microfluidics-free platform for benchtop single-cell long-read RNA sequencing

Single-cell long-read RNA sequencing enables direct measurement of full-length transcripts but has remained difficult to deploy at scale due to reliance on microfluidic barcoding, specialized instrumentation, and high per-cell cost. Here we present BenchDrop-seq, a benchtop platform for single-cell long-read transcriptomics that leverages particle-templated partitioning for single-cell molecular barcoding and couples this workflow to Oxford Nanopore sequencing for full-length transcript capture. By integrating established bead-based partitioning chemistry with long-read sequencing and a dedicated open-source analysis pipeline for barcode recovery, alignment, and transcript quantification, BenchDrop-seq enables isoform-resolved measurements from thousands of individual cells using standard laboratory equipment. We validate the platform in both a homogeneous cell line and a heterogeneous primary tissue, demonstrating high barcode recovery, accurate gene-level quantification, and reproducible detection of cell-type-specific transcript usage that is not readily accessible to short-read assays. Together, BenchDrop-seq establishes a practical and accessible framework for single-cell long-read RNA sequencing, lowering experimental barriers while enabling transcript-level analyses in routine single-cell experiments.

genomics↗