Biology subjects

Agarwal, P.

Publications and source records attributed to Agarwal, P..

At least 19 recordsLinked to original sources

bioRxiv2026

Machine learning guided design of strong transcriptional activation domains

Artificial intelligence has accelerated the design of structured proteins, but it remains difficult to design functional intrinsically disordered proteins because of weak structural constraints and poorly defined sequence-to-function relationships1. Activation domains (ADs), transcription factor regions that recruit coactivators, are an excellent test case for the de novo design of intrinsically disordered sequences. ADs are one of the oldest groups of functional intrinsically disordered sequences2 and designed ADs have applications in synthetic biology, biotechnology, and agriculture. We computationally generated 500,000 candidate sequences that resembled known ADs and predicted AD function with extant machine learning models, including three neural networks. From high-scoring sequences, we selected 18,750 for experimental validation in yeast. Surprisingly, >90% of the 16,770 well-measured sequences function as ADs. Sequences predicted to be active by multiple models were stronger, motivating development of a fast and accurate consensus AD predictor, MADRIGAL. A number of our designed ADs retain functionality across fungi, plants, and human cells. This work illustrates a generalizable paradigm for incorporating sequence-to-function models into the design loop to efficiently generate functional intrinsically disordered sequences.

synthetic biology↗

bioRxiv2026

Smartphone-Validated Portable Paper-Based Device Integrated with an Electropolymerized Molecularly Imprinted Polymer for Serotonin Detection in Serum Samples

Accurate and decentralized quantification of serotonin, also known as 5-hydroxytryptamine (5-HT), in biological fluids is critically important for the diagnosis, prognosis, and therapeutic monitoring of neurological and psychiatric disorders. However, conventional analytical methods generally rely on centralized laboratory infrastructure, skilled personnel, and labor-intensive sample processing, which restrict their applicability in rapid near-patient and point-of-care settings. Herein, we report a portable molecularly imprinted polymer (MIP)-based electrochemical sensing platform for selective and on-site detection of serotonin using screen-printed carbon electrodes (SPCEs). The biomimetic recognition interface was fabricated through direct electropolymerization of a polydopamine recognition layer in the presence of serotonin as the template molecule, followed by template extraction to generate complementary recognition cavities for selective rebinding. The sensor fabrication parameters, including monomer concentration, electropolymerization cycles, template-to-monomer stoichiometry, and electrolyte pH, were systematically optimized to achieve improved sensitivity, selectivity, and signal stability. Under optimized conditions, the MIP/SPCE sensor exhibited a broad linear response from 10 pM -10 {micro}M in phosphate buffer, with a correlation coefficient of R2 = 0.974 and an ultralow limit of detection of 0.16 pM. The analytical applicability of the platform was further validated in spiked artificial serum, where the sensor achieved an LOD of 0.12 pM, satisfactory recovery values of 88.66-96.02%, and acceptable precision with RSD values [≤] 8.43% (n=3), confirming its reliability in a complex biological matrix. The developed sensor demonstrated excellent selectivity toward serotonin against physiologically relevant interferents, maintaining signal retention between 99% and 101%. In addition, the platform showed high operational repeatability with an RSD of 0.45%, good inter-electrode reproducibility with an RSD of 6.3%, and long-term storage stability, retaining 90-110% of its initial response over 28 days. Importantly, cross-platform validation using a smartphone-coupled potentiostat demonstrated strong analytical agreement with laboratory-grade instrumentation, as evidenced by R2 = 0.9967 and a slope of 1.023. These findings establish the proposed MIP/SPCE platform as a simple, low-cost, portable, and smartphone-compatible electrochemical device for field-deployable serotonin monitoring in clinically relevant samples.

bioengineering↗

bioRxiv2026

Biofunctional 2D Graphitic Carbon Nitride-Hydrogel Heterointerfaces for Electrochemical Detection of Interleukin-6 toward Septic Cardiomyopathy Diagnostics in Clinical Biofluids

Interleukin-6 (IL-6) is a key pro-inflammatory cytokine closely associated with sepsis progression and septic cardiomyopathy (SCM), a severe clinical condition characterized by acute cardiac dysfunction and high mortality in critically ill patients. Rapid and sensitive monitoring of IL-6 in clinical biofluids is therefore crucial for early diagnosis, disease prognosis, and timely therapeutic intervention in emergency healthcare settings. Herein, we report a biofunctional, label-free electrochemical aptasensor based on a graphitic carbon nitride-incorporated chitosan hydrogel-modified gold screen-printed electrode (MCH/Apt-IL-6/g-C3N4@CS/Au-SPE) for ultrasensitive detection of IL-6 in clinical biofluids. The electroactive g-C3N4@CS hydrogel heterointerface was engineered via electrostatic interactions between the negatively charged surface functionalities of two-dimensional graphitic carbon nitride (g-C3N4) and the protonated amino groups (-NH3+) of chitosan (CS), yielding a porous, conductive, and biocompatible sensing matrix with enhanced aptamer immobilization and accelerated electron-transfer kinetics. Biocompatibility evaluation using MTT assay and confocal fluorescence imaging demonstrated that the hydrogel maintained excellent cellular compatibility at 5 mg/mL, preserving normal cytoskeletal organization, mitochondrial integrity, and nuclear morphology, while higher concentrations induced cellular stress responses. Under optimized experimental conditions, the developed aptasensor exhibited outstanding analytical performance with an ultrawide linear detection range from 1 fg/mL to 10 ng/mL, a high sensitivity of 2.162 A/[log10(ng/mL)] cm-2, a low detection limit of 0.460 pg/mL, and excellent linearity (R2 = 0.979). In addition, the sensor demonstrated remarkable selectivity toward common biological interferents, including ascorbic acid, cysteine, glucose, glycine, and urea, together with excellent reproducibility (RSD = 1.139%). Validation studies performed in spiked human serum samples further confirmed the reliability and practical applicability of the proposed sensing platform for rapid clinical analysis. Owing to its label-free detection strategy, disposable electrode format, high sensitivity, and favorable biocompatibility, the developed g-C3N4-hydrogel heterointerface-based aptasensor represents a promising next-generation platform for early septic cardiomyopathy diagnostics, inflammatory biomarker monitoring, and point-of-care electrochemical biosensing applications.

bioengineering↗

bioRxiv2026

Targeting intracellular mycobacteria using novel antibiotic-loaded nanoparticles

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a significant global health challenge. Currently treatment of drug-sensitive TB, involves a six-month regimen consisting of a combination of four anti-TB drugs, with drug-resistant TB requiring over two years of treatment and additional drugs. As toxicity of anti-TB drugs often leads to poor compliance, disease relapse and the emergence of drug-resistant strains, new strategies to reduce drug toxicity and shorten treatment duration are critical. We report nanocarrier-based drug delivery systems targeting macrophages, which primarily support replication and survival of Mtb. We have developed mannose-functionalized nanoparticles that bind to mannose receptors on macrophages and feature a pH-sensitive core which releases an encapsulated drug in the acidic lysosomal environment of macrophages. Rifampicin (RIF), a main anti-TB drug currently in use clinically, was encapsulated within the nanoparticles. We demonstrate that antibiotic-containing nanocarriers efficiently accumulated in macrophages without causing toxicity. Encapsulated RIF showed enhanced efficacy against both BCG and Mtb in primary macrophages. Biodistribution studies in mice revealed that the nanoparticles have extended circulation time and do not induce toxicity. In addition, the encapsulated RIF showed better targeting of mycobacteria when compared to free RIF in a murine model of mycobacterial infection. Such an enhanced bacterial killing using mannose-functionalised nanocarriers loaded with the key anti-TB drug rifampicin offers excellent potential for TB therapy.

microbiology↗

bioRxiv2026

Green Synthesis of Fluorescent Carbon Quantum Dots from Bearberry Extract via Hydrothermal and Microwave-Assisted Routes: Comparative Physicochemical Characterisation, Antioxidant Activity, and Biocompatibility Evaluation

Producing photoluminescent nanomaterials with controllable surface chemistry and predictable biological activity remains one of the outstanding problems in green nanoscience. The present study shows that, even when the same bearberry (Arctostaphylos uva-ursi) extract precursor is used, the mode of energy delivery during synthesis plays a determining role in shaping the surface composition, photophysical properties, and biological activity of the resulting carbon quantum dots (CQDs). Hydrothermal processing at 160 {degrees}C for 6 h yielded CQDs with an average particle size of 7.13 nm. Surface characterisation indicated abundant hydroxyl- and carbonyl-containing functionalities, while XPS analysis showed a comparatively higher proportion of graphitic sp2 carbon (43.06%). These structural features were accompanied by strong DPPH free-radical scavenging activity. Microwave-assisted synthesis, by contrast, yields 9.65 nm particles carrying a substantially greater surface carboxylate content (O-C=O: 19.06%), a higher fluorescence quantum yield, and enhanced intracellular uptake statistically significant in retinal epithelial cells at 200 {micro}g/mL (p < 0.001) and showing concentration-dependent accumulation in zebrafish larvae from 100 {micro}g/mL onwards (p < 0.05). XPS C 1s deconvolution, interpreted alongside FTIR difference spectroscopy, points to incomplete decarboxylation under microwave conditions as the primary mechanistic origin of these divergent properties. Cytocompatibility was uncompromised for both formulations across the full concentration range tested (10-250 {micro}g/mL) in RPE-1 and HeLa cells, with no statistically significant loss of viability at any concentration. Taken together, these results define a synthesis-route-encoded structure-property relationship that permits rational selection between an antioxidant-optimised and an imaging-optimised CQD formulation from the same green precursor feedstock.

bioengineering↗

bioRxiv2025

Biocompatibility assessment of SilkMA-Gelatin ink tuned for 3D extrusion bioprinting

3D bioprinting applications have led to the development of multifunctional scaffolds that are biocompatible, overcoming shear stress to provide structural integrity. We report the isolation of silk fibroin (SF) using calcium chloride (CaCl2), which was further developed into an ink comprising silkMA and gelatin, demonstrating effective cytocompatibility and biocompatibility when 3D printed using an extrusion-based 3D bioprinter. Rheological characterization of SilkMA-Gelatin showed an improved viscosity and printability of the formulation as compared to an unmodified silk-gelatin composition. SilkMA-gelatin was bioprinted with NIH3T3 cells and demonstrated enhanced viability and proliferation, highlighting its cytocompatibility and ability to support a favourable 3D microenvironment. In vivo biocompatibility of the 3D bioprinted SilkMA-Gelatin was evaluated in Wistar rats, where 3D printed scaffolds maintained structural stability for up to 1 month, with no inflammatory response, progressive cell infiltration, and re-epithelialization. Serum biochemistry analysis, including ALP, ALT, LDH, and Urea (BUN), remained within normal physiological ranges, further confirming systemic safety. Based on the findings, the optimized SilkMA-gelatin ink proves to be highly effective in fabricating cell-laden structures that are stable, exhibit enhanced cytocompatibility and biocompatibility, and offer promising potential for advanced tissue regeneration applications. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=172 SRC="FIGDIR/small/687334v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@1fad3dcorg.highwire.dtl.DTLVardef@6b2d3aorg.highwire.dtl.DTLVardef@6655b8org.highwire.dtl.DTLVardef@85d894_HPS_FORMAT_FIGEXP M_FIG Schematic overview of 3D bioprinting in wound healing and biomedical applications C_FIG

bioengineering↗

bioRxiv2025

The staphylococcal type VII secretion system delays macrophage cell death through modulating multiple cell death pathways

The major human pathogen Staphylococcus aureus is a facultatively intracellular bacterium that can replicate and survive within a range of host cells including macrophages. While macrophage-mediated immune modulation is pivotal in S. aureus pathogenesis, bacterial manipulation of macrophage pathways remains poorly understood. The specialised type VII secretion system (T7SSb) is an important virulence-associated factor and immune modulator during staphylococcal infection, although, unlike its mycobacterial counterparts, its role in controlling staphylococcal-macrophage interactions remains unclear. Employing high-resolution time-lapse imaging, we demonstrated an induction of cell death corpses or pore-induced cellular traps (PITs) during S. aureus infection of macrophages in vitro, with a higher number of PITs forming in macrophages infected with S. aureus lacking EssC ({Delta}essC), a central T7SS transporter. Interestingly, {Delta}essC-infected macrophages displayed increased bacterial escape compared to wild type (WT)-infected cells, implicating a role for T7SS in delaying macrophage cell death. {Delta}essC-infected macrophages were also efferocytosed less compared to WT in vitro. We investigated the induction of cell death signalling markers in WT and {Delta}essC-infected macrophages and demonstrated that the T7SS delayed the induction of key cell death pathways, necroptosis and pyroptosis. A dual RNAseq analysis of WT- and {Delta}essC-infected macrophages further indicated a T7SS-dependent increase in ferroptosis later in infection, along with modulation of chemokines. We demonstrated that individual T7SS effectors, EsxA and EsxC, which were induced within macrophages, could individually delay macrophage cell death. Furthermore, in a murine skin infection model, we showed that effector and transporter mutants have distinct S. aureus infection outcomes. Our findings suggest for the first time a key role for T7SSb proteins in controlling macrophage cell death, which impacts staphylococcal survival within the host during infection. ImportanceStaphylococcus aureus is a major hospital and community associated pathogen which causes an array of infections. S. aureus can survive within immune cells, which may provide a niche for this pathogen to both persist and disseminate. Here we report a role for the staphylococcal type VII secretion system b, which secretes effectors that have been associated with bacterial virulence, in delaying macrophage cell death induced in response to this pathogen. T7SS functions through interfering with inflammatory cell death pathways, impacting the local cellular and immune environment. Our findings thus highlight a protective role for this system in macrophages, distinct to functions reported for the mycobacterial T7SS, and may implicate similar functions for T7SS proteins from related pathogens. Controlling macrophage cell death could be a critical mechanism by which S. aureus modulates the local immune responses, enabling its survival within the host,

microbiology↗

bioRxiv2025

Progressive decoding of DNA-stored JPEG data with on-the-fly error correction

DNA storage is a developing field that uses DNA to archive digital data owing to its superior information density and stability. Although DNA storage has been performed on a significant scale, challenges arise from the synthesis and sequencing of data-encoded oligonucleotides. Synthesis of DNA introduces significant noise into the process. Consequently, high-read-quality sequencers are often required, making the process expensive and lack scalability. Error correction codes are used within the DNA storage pipeline to provide resilience to noise at a cost of additional redundancy and decoding complexity. Given such constraints and challenges, the main objective we seek to deliver is a time- and storage-efficient image coding strategy. We introduce a novel DNA-based progressive JPEG decoder with on-the-fly error-correcting & rendering capability. This system can progressively decode an image while also correcting for errors as they occur. It modifies standard JPEG encoding methods to store data in localized chunks and uses adapted Raptor error-correction codes to improve the speed and quality of partial decoding. We optimize and evaluated the method under varying levels of simulated errors, as well as show how different parts of the pipeline improve real-time decoding capability. We also test the pipeline in a real-world wet-lab experiment. We present the first progressive image decoding schema aimed at realizing real-time rendering of DNA-stored images.

bioinformatics↗

bioRxiv2025

Scm3 interacts with the N-terminal tail of Cse4 to regulate kinetochore assembly in budding yeast

The kinetochore is a multiprotein complex formed at the centromeres and is essential for the faithful chromosome segregation. In most of the organisms the kinetochore is assembled on a specialized centromeric nucleosome where histone H3 is replaced by a variant, named CENP-A. In budding yeast, the CENP-A homolog, Cse4 is recruited to the centromeric nucleosome through an interaction between its C-terminal domain and a specific chaperone, named Scm3. Interestingly, following Cse4 recruitment during S phase, Scm3 persists at the centromeres throughout the cell cycle. Recent in vitro studies have reported that Scm3 also interacts with N-terminal of Cse4 (N-C) that in turn facilitates a better interaction of Ame1-Okp1 (AO) of COMA subcomplex with N-C, which promotes kinetochore assembly. In this work, using genetic and biochemical assays we provide in vivo evidence of the interaction between Scm3 and N-C. Additionally, by artificially tethering Scm3, we show that their association has the potential to stabilize a missegregating chromosome with inactive centromere, perhaps by forming an active kinetochore at an ectopic site. We propose that at the centromeres, Scm3 has two jobs in tandem - Cse4 deposition and stabilization of N-C, which together culminates into proper kinetochore assembly. This work has clinical significance as both CENP-A and its chaperone are known to be upregulated in human cells under disease states which can predispose the cells to aneuploidy due to increased chances of forming ectopic kinetochores.

cell biology↗

bioRxiv2025

Decoding Rice Seed Storage Proteins: From Gene Identification to Structural Prediction

Rice seed storage proteins (SSPs) serve as the primary source of dietary protein, energy, and nutrition; however, our understanding of these proteins remains limited, hindering efforts aimed at enhancing grain nutritional quality. To address this, we conducted a comprehensive genome-wide analysis of rice SSPs, encompassing phylogenetic relationships, domain and motif characterization, promoter cis-element mapping, expression profiling, and 3D structural modeling. Through homology- and domain-based searches, we identified 65 SSP-encoding genes, including 19 previously uncharacterized members. Phylogenetic analysis and domain comparisons revealed evolutionary proximity between albumins and prolamins; and between globulins and glutelins. Albumins, glutelins and prolamins clustered tandemly implying that duplication has driven SSP expansion. Transcriptomic evidence indicated that albumins, globulins, and glutelins were transcriptionally active from S2 seed development stage, whereas prolamins initiated expression from S3 stage. Promoter analysis revealed several seed-specific cis-regulatory elements, with CAATBOX1, EBOXBNNAPA, and DOFCOREZM being the most prevalent. Structural modeling showed that albumins and prolamins predominantly adopted -helical conformations, whereas globulins and glutelins were enriched in {beta}-strands and coils. This integrated analysis offers valuable insights into the classification, evolution, regulation, and structure of rice SSPs, providing a foundational resource for advancing grain nutritional improvement strategies.

plant biology↗

bioRxiv2025

Tagging and harvesting of developing rice spikelets to demarcate grain developmental stages

PremiseIn rice, grain is the major sink for nutrient storage and is a rich source of carbohydrates, seed storage proteins, lipids, minerals, and vitamins, making it a principal food source for over half of the worlds population. Grain development in rice generally spans over a month and has been divided into five stages, S1-S5, depending upon various morphological and physiological changes occurring in the developing seed. To completely understand the process, rice grain development needs to be examined at each stage. However, there are no detailed protocols available to demarcate grain developmental stages. Methods and ResultsThis protocol describes how to tag and harvest the developing rice spikelets. The process starts with anthesis and continues till seed maturation, demarcating the five stages of rice grain development. Seeds are collected, labelled, and stored for use in molecular experiments. Using this protocol, we were able to identify and distinguish different seed developmental stages as observed by histochemical screening. ConclusionThis is an easy, efficient, and cost-effective method. This protocol ensures the collection of the entire panel of rice seed developmental stages. The stored tissue can later be used for various molecular biology based experiments.

plant biology↗

bioRxiv2025

A switch in collagen expression regulates cessation of distal tip cell migration in C. elegans

Development of the C. elegans gonad requires precise regulation of cell migration. The distal tip cell (DTC) guides the elongation of the gonad into its final U-shaped structure before halting in adulthood. How cessation of elongation is regulated remains unknown. Here, we analyze an RNA-seq data set isolated from stage-specific DTCs to uncover the temporal gene expression dynamics underlying this process. Collagens emerged as the most enriched gene family during the transition from migratory larval stages to adulthood. We identify distinct temporal waves of collagen expression, culminating in a core adult-specific module that coincides with migration cessation. Functional analysis by RNAi depletion revealed that many collagens upregulated in adulthood are required for timely migration arrest, while others affect gonad shape. Perturbation of collagen remodeling enzymes phenocopied these effects. Our findings uncover a stage-specific collagen program in the DTC and suggest that terminal migration arrest is actively reinforced by matrix remodeling.

developmental biology↗

bioRxiv2025

Stage-specific transcriptomics of a leader cell reveals cell machineries driving collective invasion

Collective cell invasion underlies organ development, epithelial repair, and cancer metastasis. "Leader cells" remodel extracellular matrix, sense guidance cues, reorganize their cytoskeleton, and coordinate follower cells, but the molecular programs enabling these functions remain unclear. Here, we present a stage-specific transcriptomic dataset of the C. elegans gonadal leader cell, the distal tip cell (DTC), which invades basement membrane and guides germ cells to form U-shaped gonadal arms. Comparing invasive larval-stage DTCs with non-invasive adult-stage DTCs defines the molecular signature of an actively invading leader cell in vivo. Our dataset recapitulates known regulators of gonad morphogenesis and reveals numerous uncharacterized genes with potential roles in leader cell activity. As proof of concept, we identify vesicular trafficking proteins as enriched in invading DTCs, and demonstrate their importance for gonad development using endogenous tagging and DTC-specific RNAi. We also catalog diverse DTC-specific knockdown phenotypes. This resource establishes a molecular framework for leader cell activity and a platform to investigate conserved mechanisms of invasive migration.

developmental biology↗

bioRxiv2025

Interpretable biophysical neural networks of transcriptional activation domains separate roles of protein abundance and coactivator binding

Deep neural networks have improved the accuracy of many difficult prediction tasks in biology, but it remains challenging to interpret these networks and learn molecular mechanisms. Here, we address the interpretability challenges associated with predicting transcriptional activation domains from protein sequence. Activation domains, regions within transcription factors that drive gene expression, were traditionally difficult to predict due to their sequence diversity and poor conservation. Multiple deep neural networks can now accurately predict activation domains, but these predictors are difficult to interpret. With the goal of interpretability, we designed simple neural networks that incorporated biophysical models of activation domains. The simplicity of these neural networks allowed us to visualize their parameters and directly interpret what the networks learned. The biophysical neural networks revealed two new ways that arrangement (i.e. the sequence grammar) of activation domain controlled function: 1) hydrophobic residues both increase activation domain strength and decrease protein abundance, and 2) acidic residues control both activation domain strength and protein abundance. Notably, the biophysical neural networks helped us to recognize the same signatures in complex interpreters of the deeper neural networks. We demonstrate how combining biophysical and deep neural networks maximizes both prediction accuracy and interpretability to yield insights into biological mechanisms.

systems biology↗

bioRxiv2025

MYD88 mutations in clonal hematopoiesis promote inflammation and hematopoietic stem cell expansion

Clonal hematopoiesis of indeterminate potential (CHIP) is characterized by expansion of mutant hematopoietic stem and progenitor cells (HSPCs) and an increased risk of chronic diseases and cancers. While mutations in DNMT3A, TET2, and ASXL1 are common in CHIP, the contribution of less frequent gene mutations is not well understood. Here, we report MYD88 mutations, including lymphoma-associated and novel variants in blood cells of the general population and newly diagnosed solid cancer patients. MYD88 CHIP mutations in HSPCs activate NF-{kappa}B, indicating a gain-of-function activity. Modeling MYD88 CHIP in mice, Myd88L252P (equivalent of human L265P) expression resulted in a competitive fitness advantage of HSPCs. Myd88L252P HSPCs exhibit a myeloid cell bias and inflammation, leading to hematologic disease. Single-cell RNA sequencing indicated that Myd88L252P expands distinct hematopoietic and immune cell clusters and activates immune-related pathways in HSPCs. An IRAK1/4 inhibitor suppressed MYD88-dependent NF-{kappa}B activation and reversed Myd88L252P cell expansion. Overall, MYD88 mutations contribute to CHIP by inducing innate immune pathways in HSPCs and inflammatory disease.

cancer biology↗

bioRxiv2025

The cellular mammalian clock regulates Staphylococcus aureus invasion in epithelial cells

An endogenous biological clock, the circadian clock, coordinates life with the 24-hour day/night environmental cycle. In mammals, a central pacemaker in the suprachiasmatic nucleus of the hypothalamus coordinates timing between peripheral clocks and with the environment and, for example, modulates immune responses to infections. However, its role in controlling bacterial infections at a cellular level is not understood. Here, we investigate the role of the host cellular clock during infection by a highly drug-resistant human pathogen, Staphylococcus aureus. Our findings revealed that S. aureus invasion into epithelial cells was dependent on the host circadian phase. Interestingly, cells deficient in BMAL1, a transcriptional activator and an essential clock protein, demonstrated increased bacterial uptake compared to parental A549 cells. The BMAL1-knockdown (KD) cells showed significant induction of GP340, a receptor of the S. aureus adhesin, SraP. An S. aureus sraP mutant did not exhibit rhythmic uptake into A549 cells or an increased uptake into BMAL1-KD compared to parental A549 cells. Of note, other bacterial adhesin mutants showed rhythmic and higher uptake in BMAL1-KD cells. Hence, we report that S. aureus epithelial cell invasion is clock-modulated and mediated through the S. aureus SraP-GP340 pathway, suggesting potential for host clock-directed therapy against this pathogen.

microbiology↗

bioRxiv2025

ANARCII: A Generalised Language Model for Antigen Receptor Numbering

Antigen receptor numbering allows the rapid delineation of the antigen-binding regions of antibody and T cell receptor (TCR) sequences, from sequence alone. It also allows the comparison of the vast diversity of antigen receptors in a consistent frame of reference. Numbering of antigen receptors is currently achieved by aligning sequences to a reference set. This approach may result in different numbering, depending on the reference set used or may fail to number query sequences derived from new species or rare sequence types. To address this problem, we have built a new numbering method (ANARCII) which requires no alignment step and is based on a Seq2Seq language model. Our results show that ANARCII can deal with the complexity that arises in experimentally collected sequencing data and generalise to sequences which are highly dissimilar to those in training. In test sets designed to contain challenging and ambiguous sequence patterns ANARCII numbering was identical to existing methods for over 99.99% of conserved residues and over 99.94% for complete CDR regions. The lightweight architecture allows numbering of over 90,000 sequences per minute on a single A100 GPU. Furthermore, the ANARCII package can be conditioned to fit rare sequence types and provide new training data for fine-tuning. We demonstrate that fine-tuned versions of ANARCII can correctly number other immunoglobulin domains such as TCRs and VNARs. Our model is freely available as a web tool (https://github.com/oxpig/ANARCII), as well as a package for high throughput numbering of next generation sequencing data (https://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/sabpred/anarcii/).

bioinformatics↗

bioRxiv2024

Reproductive experience drives changes in behavior and physiology in male California mice (Peromyscus californicus)

Paternal experience improves memory and reduces anxiety-like behavior in males, but it is unclear whether these changes are due to mating, siring offspring, or caregiving behavior. Likewise, paternal males have larger testes, a measure of sperm production, but again, the effects of siring and caregiving experience are difficult to disentangle. We examined behavioral and physiological outcomes in three groups of male mice: 1) virgins, 2) males paired with sterile females ( non-fathers), and 3) experienced fathers (Experiment 1). Compared to virgins and non-fathers, experienced fathers exhibited increased recognition memory (novel object recognition) and decreased anxiety-like behavior (elevated plus maze). Virgin males, however, had smaller testes and fewer sperm compared to non-fathers. We then compared the same traits in three additional groups of male mice: 1) non-fathers, 2) non-fathers with experience caring for unrelated pups ( pup-sensitized non-fathers), and 3) first-time fathers, to determine whether the behavioral and physiological observations in Experiment 1 were due to siring offspring or caregiving, and how rapidly these changes occur (Experiment 2). Recognition memory and anxiety-like behavior did not differ among these three groups, suggesting that caring for a single litter does not recapitulate the behavioral changes observed in experienced fathers (Experiment 1). Despite equal mating opportunity, we observed larger testes in first-time fathers compared to non-fathers, suggesting that investment in sperm production may be more plastic than behavioral changes. Finally, we compared pup interactions in pup-sensitized non-fathers and first-time fathers. While pup-sensitized non-fathers were slower to approach pups than first-time fathers, they spent more time grooming pups, whereas first-time fathers invested more time in nest building, suggesting different caregiving behaviors in pup-sensitized males and biological fathers. Taken together, our study revealed that mating, siring, and caregiving experience contributes to changes in memory, anxiety-like behavior, and reproductive investment in males of a biparental species.

animal behavior and cognition↗