Biology subjects

Moore, M.

Publications and source records attributed to Moore, M..

At least 19 recordsLinked to original sources

bioRxiv2026

PCR-based assays for determining mating status in field-weathered Ceratitis capitata with enhanced precision across conventional, quantitative, and droplet digital platforms

Accurately determining the mating status of the agricultural fruit fly pest Ceratitis capitata, commonly known as Medfly, is essential for timely and effective eradication efforts. To overcome the limitations of subjective DAPI-based staining assessments of females captured in Jackson dry traps and Multilure liquid traps, we developed a multi-tier molecular diagnostic method that unequivocally detects mating status using DNA probes targeting the male-specific Y114 locus on the Y-chromosome of the species. Our protocol integrates morphological evaluation with increasingly sensitive molecular assays through the following steps: 1) A preliminary quality assessment of the specimens physical condition, DNA preservation, and mating status using conventional PCR followed by agarose electrophoresis (cPCR); 2) Quantification and real-time detection of sperm presence via quantitative PCR (qPCR); and 3) Detection of trace sperm amounts through droplet digital PCR (ddPCR). This PCR-based framework is designed for samples collected in the field, enabling accurate analysis of specimens exposed to adverse environmental conditions and varying levels of preservation after 2- and 3-weeks weathering times in traps. It allows quantitative determination of mating status even when sperm concentrations are extremely low, such as during transient copulation, and achieves detection limits down to approximately 14 spermatozoa in a mated female. By accounting for variable specimen quality and the performance characteristics of each molecular platform, this tiered approach ensures highly sensitive and unequivocal detection of mated females. The methodology can be used to assist eradication efforts across the C. capitata geographic range through the timely detection of mated females, halting their expansion and establishment into novel regions reducing control and eradication costs.

genetics↗

bioRxiv2026

Physiological limits of localized hypothermia in the human cochlea: The role of vascular heat transport

PurposeMild therapeutic hypothermia (MTH) preserves cochlear function in animal models and is now entering early-phase human trials for hearing preservation. However, the extent to which the human cochlea can actually be cooled, and the mechanisms underlying MTH, remain unclear, in part because blood perfusion is expected to oppose localized cooling. In this study we evaluated the impact of blood flow on human cochlear temperature exposed to the MTH device using a combined experimental and computational approach. MethodsTemperature measurements were obtained from a human cadaver skull exposed to a commercial MTH device. These data were used to validate a three-dimensional bioheat transfer model incorporating realistic skull anatomy. The validated model was subsequently extended to include physiological blood perfusion in the internal carotid artery; a major heat source located near the cochlea. Finally, the in silico model was further expanded to incorporate the surrounding skin and brain tissues. ResultsIncorporating blood flow in internal carotid artery substantially altered predicted cochlear temperature distributions, highlighting the importance of localized vascular heat transport in the human cochlea during MTH. Although cochlear cooling was attenuated in the presence of perfusion, the therapeutic effects of MTH may not depend solely on the magnitude of local intracochlear temperature reduction. Additional mechanisms, such as reduced facial surface temperature, may also contribute to its efficacy. ConclusionThe validated in silico model provides a physiologically realistic framework for evaluating human cochlear thermal responses, investigating MTH mechanisms, and optimizing temperature-based strategies for hearing preservation.

bioengineering↗

bioRxiv2026

Preclinical translation of Neurofibromatosis type 1 (NF1) exon 17 skipping using targeted U7-SnRNA packaged into engineered AAV serotypes.

To facilitate the translation of NF1 exon 17 skipping as a mutation-specific therapy for Neurofibromatosis type 1 into in vivo testing, we have continued to develop more efficient antisense oligonucleotides (ASOs), humanized mouse models, and explored multiple delivery platforms including an adeno-associated virus (AAV)-U7-SnRNA vector approach. We evaluated both biodistribution and exon skipping efficacy of a U7-SnRNA targeting NF1 exon 17 with an SFFV-driven cassette containing T2A-linked Luciferase (Luc) and eGFP packaged in AAV-9, AAV-F and AAV-B1 capsids. We show that AAV-F is superior to AAV-9 and AAV-B1 for mouse brain delivery based on DNA transduction, GFP expression, and luciferase activity, but AAV-B1 delivers 2-4 fold more to sciatic nerve (SCN). In terms of exon skipping, AAV-F appears to induce the most skipping in liver and optic nerve (ON), while AAV-B1 mediates highest skipping in the liver, SCN, and ON. The identification of AAV serotypes that allow efficient transduction and delivery of transgenes to the mouse CNS and PNS is impactful for preclinical research in murine models of other diseases. Furthermore, this is both the first report of NF1 exon skipping efficacy in vivo and the first successful application of an U7-SnRNA for the restoration of functional neurofibromin for NF1. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/734312v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@34b7eborg.highwire.dtl.DTLVardef@116c11aorg.highwire.dtl.DTLVardef@dfb251org.highwire.dtl.DTLVardef@341cb5_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2026

Colorful connections: pigment-based plumage and breeding condition are associated with gut microbiome variation in the Common Yellowthroat

Carotenoid- and melanin-based plumage coloration traits are key signals in avian communication and sexual selection as they are often thought to provide "honest" information about individual condition and fitness. These traits arise through distinct but interconnected physiological and genetic pathways. Recent work suggests that there may be a link between host-associated gut microbiota and the functional pathways leading to pigment-based plumage coloration, but this remains largely unexplored in wild populations. To address this gap, we tested whether variation in plumage coloration, as well as breeding condition, is associated with gut microbiome variation in wild populations of male Common Yellowthroats (Parulidae: Geothlypis trichas). We quantified multiple plumage coloration traits and characterized gut microbiome bacterial diversity using 16S rRNA metabarcoding. Through a comprehensive modeling framework, we found that individuals with brighter, more orange-tinted breast feathers and smaller cloacal protuberances (a proxy for breeding condition) exhibited higher gut microbiome diversity. At the taxonomic level, Methylobacterium-Methylorubrum, a carotenoid-producing bacteria, showed strong associations with multiple plumage traits, including mask area, breast feather hue, and saturation. Our results demonstrate that gut microbiome diversity is associated with variation in carotenoid-based coloration traits and breeding condition in Common Yellowthroats. More broadly, these results highlight the potential for host-microbiome interactions to shape phenotypic variation through physiological pathways in wild animal populations.

ecology↗

bioRxiv2026

A citywide metagenomic analysis reveals surface-specific microbiome and resistome patterns in outdoor urban environments across Liverpool, UK.

Urbanisation is rapidly increasing worldwide, with increasing attention focused on its consequences for human populations and the environment. Despite the importance of outdoor urban environments for biodiversity and human wellbeing, their microbial ecology remains poorly characterised, particularly in relation to emerging microbial threats including antimicrobial resistance (AMR). Here, we present a citywide metagenomic study of outdoor public surfaces across Liverpool, United Kingdom, examining microbial community composition, diversity, and antimicrobial resistance gene (ARG) distribution across five distinct surface types. We show that patterns of human activity and surface use strongly influence both microbial community structure and AMR signatures in outdoor urban environments. Touchpoints were enriched for human-associated taxa and exhibited the highest overall resistome burdens, whereas Pathway and Waterside niches showed no strong taxonomic enrichment and exhibited low ARG prevalence. Refuse surfaces showed mixed patterns, characterised by sporadic but occasionally high-abundance ARG detections. Soil harboured the most distinct microbial communities but showed minimal ARG prevalence, which may partly reflect the limited representation of environmental taxa in current ARG databases. This study provides a baseline for understanding how urban infrastructure and behaviour shape microbial and resistance landscapes, and highlights the value of outdoor metagenomic surveillance for future environmental and public health research.

microbiology↗

bioRxiv2025

Arabidopsis DXO1 is an evolutionarily diverged homolog that impacts ribosome loading and mRNA surveillance

The Rai1/Dxo1/DXO protein family are involved in eukaryotic 5'-end RNA quality control by hydrolyzing non-canonical mRNA cap structures, such as the NAD+ 5'-cap. The plant DXO1 ortholog shows distinct biochemical properties, compared to its fungal and mammalian counterparts, and only minor phenotypic traits can be attributed to its NAD+-decapping (deNADding) activity. On the other hand, the chloroplast and growth defects observed in dxo1 null mutants appear linked to the presence of a serine-rich domain at its N-terminus. Here, we report that plant DXO1 is a distinct ortholog that likely diverged earlier than its fungal and mammalian counterparts. We attribute this to the presence of a serine-rich N-terminal domain, which is found almost exclusively in plants and likely arose during the emergence of angiosperms. Degradome profiling revealed that Arabidopsis DXO1 contributes to mRNA surveillance, via examination of exon junction complex and ribosome footprints, and this activity is reliant on the presence of the serine-rich N-terminal domain in Arabidopsis. Furthermore, polysome profiling revealed that plants lacking DXO1 have severe ribosome loading defects, which may explain the loss of mRNA surveillance and alterations in pre-rRNA processing. Taken together, our data leads us to propose a model whereby Arabidopsis DXO1 is involved in 5'-end RNA quality control, which is critical for ribosome loading that impacts translational fidelity and translation-dependent mRNA surveillance.

plant biology↗

bioRxiv2025

High-throughput screening and structure-guided design of small molecules enable modulation of SAL-PAP stress signaling

Chloroplasts sense environmental stress and activate chloroplast-to-nucleus retrograde signalling, reprogramming nuclear gene expression to drive plant acclimation. One such pathway is regulated by the chloroplastic phosphatase, SAL, which hydrolyses the nucleotide signal 3-phosphoadenosine 5-phosphate (PAP). In Arabidopsis thaliana, genetic loss of AtSAL1 elevates PAP and enhances stress tolerance but causes pleiotropic growth defects, complicating the interpretation of the role of PAP in cellular signalling. To uncouple stress signalling from genetic pleiotropy, we conducted a high-throughput in vitro screen of 13,000 small molecules and identified V20, a competitive inhibitor of AtSAL1 with three-fold greater potency than the known Li inhibitor. Structural analoguing of V20 and biochemical assays defined key pharmacophore features required for inhibition, including an ortho-halogenated aromatic ring, hydrogen-bond donor capacity at the triazole carboxamide, and electron-withdrawing substitutions that enhance {pi}-{pi} stacking with aromatic residues. Accelerated molecular dynamics simulations using a new high-resolution crystal structure revealed two previously uncharacterised V20 binding pockets adjacent to the catalytic site. V20 binding induces conformational changes which restrict substrate access to the catalytic site. Exogenous application of V20 to Arabidopsis led to increased PAP accumulation, activated PAP-responsive gene expression and enhanced oxidative tolerance, demonstrating cellular uptake and in vivo efficacy in the energy organelles, chloroplasts and mitochondria, where AtSAL1 is localised. Collectively, our findings reveal new insights into the regulatory domains of SAL enzymatic activity for control of PAP-mediated signalling and establish a proof-of-concept for targeted chemical modulation of SAL activity, which offers novel strategies to selectively manipulate chloroplast-to-nucleus retrograde signalling in plants. Significance StatementWe applied drug discovery strategies to test 13,000 small molecules for inhibition of AtSAL1, a key regulator of plant stress signalling from chloroplasts. Using biochemical assays, chemical analogues and molecular dynamic simulations, we defined the structural-activity relationship of a lead compound, V20, and elucidated its inhibitory mechanism. Application of V20 to plant leaves elevated the levels of AtSAL1s natural substrate, PAP (a chloroplast stress signalling molecule), activated stress-responsive genes and improved oxidative stress tolerance in Arabidopsis. This on-demand activation of SAL-PAP chloroplast signalling avoids pleotropic effects observed in loss-of-function mutants. Our approach provides a new strategy to study chloroplast-mediated cellular signaling pathways that are crucial for plant acclimation to stressful environmental conditions such as excessive sunlight.

plant biology↗

bioRxiv2025

Scalable transcription factor mapping uncovers the regulatory dynamics of natural and synthetic transcription factors in human T cell states

Heterogeneous T cell states are critical in immune responses and have been explored by CRISPR-based and synthetic domain-swapped transcription factor (TF) screens, yielding novel insights and immunotherapeutics. However, a scalable strategy to map TFs in primary human T cells is lacking, which limits our understanding of the functions of critical TFs. We therefore adapted a transposon-based TF mapping strategy termed Calling Cards for primary human CD8 T cells, applying it to five key TFs with undefined binding sites in this cell type: TOX, TOX2, TCF7, SOX4, and RBPJ. To derive biological insights from these data, we developed an analytical framework to integrate TF binding with multi-omic sequencing data, revealing convergence of TOX and TCF7 binding at dynamic enhancers of memory CD8 T cells. We then identified TF co-bound gene programs related to memory and exhaustion states in addition to putative gene targets of known and unappreciated TF roles, including TOX binding at critical genes of both exhaustion and terminal effector memory differentiation. To further scale our TF analysis platform, we modified Calling Cards to create TFlex: a method uniquely suited for multiplexed mapping of paralogous TFs. We applied TFlex to simultaneously map eight natural and domain-swapped TFs in primary human CD8 T cells, which demonstrated that domain-swapped TFs display emergent behavior in binding site selection and transcriptional effects on target genes that cannot be estimated as the sum of their constituent domains. Collectively, our data highlight the importance of scalable TF mapping in primary human T cells to elucidate TF function and the transcriptional regulation of cell states.

immunology↗

bioRxiv2025

Droplet-based Random Barcode Transposon-site Sequencing (Droplet RB-TnSeq) to characterize phage-host interactions

Bacteriophages (phages), the most abundant self-replicating entities on Earth, are central to microbial ecology and hold promise as therapies against antibiotic-resistant pathogens. However, the molecular determinants of phage adaptation to hosts remain poorly defined. While bulk genetic screens such as transposon sequencing are high throughput, running all mutants in mixed populations biases outcomes toward phage receptor discovery. Competition among resistant mutants and the escalating multiplicity of infection (MOI) from additional phages released from lysed cells often mask moderately acting host factors--such as inner-membrane and energy-transduction systems supporting DNA entry, surface modifiers, and regulators of host defense. To overcome these limitations, we developed droplet-based random barcode transposon-site sequencing (Droplet RB-TnSeq), which encapsulates single barcoded mutant cells with defined phage titers. Applying this method to Escherichia coli infected with phages T4 and N4, we reproducibly recovered known determinants (ompC for T4 and nfrA/B for N4) and identified additional contributors, including membrane proteins, polysaccharide modifiers, signaling modules, and several uncharacterized genes. Notably, mutations in chbR/C/F, ygaZ/H, and yfbO/L were found to confer resistance to N4, validated by plaque assays and complementation. Droplet RB-TnSeq thus enables genome-wide dissection of host factors beyond receptor-level interactions under well-controlled infection conditions.

microbiology↗

bioRxiv2025

An evaluation of screening methods for the detection of extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae in environmental samples from healthcare settings

Drug-resistant infections with extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-E) are increasingly problematic, especially in healthcare settings. ESBL-E infections lead to a worse treatment outcome and often require escalating antibiotic treatment to reserve antibiotics such as carbapenems. Understanding how these bacteria are transmitted within healthcare settings is complex and not well understood, but it is a requirement for effective infection prevention and control strategies. To what extent environmental ESBL-E reservoirs contribute to transmission is unclear. To accurately capture these reservoirs, laboratory processing of environmental samples needs to be optimised to reliably detect ESBL-E, which is challenging because they can be scarce and part of complex microbial communities. Here, we assessed screening methods for the detection of ESBL-producing Escherichia coli (ESBL-Ec) and Klebsiella pneumoniae (ESBL-Kp) from environmental swabs taken from healthcare settings, testing different swab types, pre-enrichment conditions and selective agars. We show that a pre-enrichment of 18 hours significantly increased the recovery of 3GC-resistant gram-negatives. The choice of selective agar impacted the number of ESBL-Ec and ESBL-Kp detected. This also affected the number of samples requiring additional species confirmation, which is costly and time-consuming. For our use case and by considering additional factors such as cost and practical aspects, Membrane Lactose Glucuronide Agar supplemented with cefotaxime performed best for the combined detection of ESBL-Ec and ESBL-Kp. Our work will guide environmental surveillance of ESBL-E by providing optimised methods for laboratory processing of environmental samples from healthcare settings.

microbiology↗

bioRxiv2025

AAV delivery of RNA editing machinery rescues SUDEP and seizure phenotype in a mouse model of Dravet Syndrome

Dravet syndrome (DS) is a severe childhood genetic epilepsy, caused by de novo heterozygous mutations in SCN1A, resulting in a loss-of-function of the voltage-gated sodium ion channel, Nav1.1. Nav1.1 is expressed in the brain, and at a lower level, in the heart. DS manifests in the first year of life. Patients exhibit tonic-clonic seizures, febrile seizures, cognitive decline, developmental delays, ataxia, and sudden unexpected death from epilepsy (SUDEP). We have developed a novel AAV-F mediated CRISPR-Cas-inspired RNA targeting system (CIRTS) preclinical treatment to increase endogenous Scn1a and ameliorate the disease phenotype in a clinically-relevant heterozygous loss-of-function mouse model of DS. We designed novel guide RNAs (gRNAs) to target the long non-coding RNA, (or natural antisense transcript) of Scn1a to increase the expression of Scn1a mRNA in DS mice. We show that intracerebroventricular and intravenous administration of AAV-F-CIRTS-gRNA9 to target the brain and the heart to neonatal Scn1a+/-mice resulted in a significant increase in survival, and a reduction in SUDEP, febrile seizures and seizure duration. These findings provide proof-of-concept evidence that an AAV-F-CIRTS mediated therapy hold promise as a potential treatment for DS.

neuroscience↗

bioRxiv2025

CACNA1C TS-II variants alter single-cell dynamics in computational models of cortical pyramidal cells

Timothy Syndrome (TS) is a rare multi-system disorder and a monogenic calcium channelopathy. Previous computational work on this disorder has focused on the myocardium, ignoring the effects of TS on neural development and its strong association with autism spectrum disorder. Variation in the TS-causative gene, CACNA1C, is indeed also associated with a variety of complex neurodevelopmental and neuropsychiatric disorders. We apply computational methods, drawing on experimental data, to understand the mechanisms of calcium dysregulation in TS, and validate our findings in four well-established multi-compartmental neuronal models. CACNA1C encodes the L-type voltage-gated calcium channel, Cav1.2, which modulates neuronal excitability and several activity-dependent pathways. We investigate two mutations in CACNA1C causative of TS type II, Cav1.2G406R and Cav1.2G402S. Both variants show a loss of voltage-dependent inactivation and changes in their voltage dependence of activation. We incorporate the altered steady-state activity of these variants with additional morphological data indicating a significant increase in activity-dependent dendritic retraction of layer II/III pyramidal cells in TS mutant neurones. Our findings replicate experimental work suggesting that increased Ca2+ flux reduces firing frequency but does not affect the rheobase current for action potential initiation. Furthermore, models expressing dendritic Cav1.2 current show altered apical-somatic signal integration in mutant neurones. All models with shortened dendrite morphology show hyperexcitability, denoted by reduced rheobase current and increased responsiveness to current injection compared to their full-length counterparts. Importantly, our approach identifies robust and testable predictions on the impacts of TS on single-cell dynamics. We also discuss the broader implications of our findings for other Ca2+-related neurodevelopmental and neuropsychiatric disorders.

neuroscience↗

bioRxiv2025

SAMP-Score: A morphology-based machine learning classification method for screening pro-senescence compounds in p16 positive cancer cells

BackgroundSenescence identification is rendered challenging due to a lack of universally available biomarkers. This represents a bottleneck in efforts to develop pro-senescence therapeutics - agents designed to induce the arrest of cellular proliferation associated with a senescence response in cancer cells for therapeutic gain. This is particularly true in contexts such as basal-like breast cancer (BLBC), which often express high levels of widely reported senescence hallmarks, which has led to the designation of these subtypes as senescence marker positive (Sen-Mark+). Unfortunately, these are often cancers with the most limited treatment options, where novel pro-senescence compounds would be of potential clinical utility. ResultsTo address these challenges, we have developed SAMP-Score, a machine learning classification tool for identifying senescence induction in Sen-Mark+ cancers. This technique builds upon our previous observation that senescent cells develop distinct senescence-associated morphological profiles (SAMPs), which can be assessed readily in traditionally challenging contexts for senescence identification, including high-throughput screens. ConclusionsThrough application of SAMP-Score, we have identified QM5928, a novel pro-senescence compound, that is able to induce senescence in a variety of Sen-Mark+ cancers and has potential utility as a tool molecule to explore the mechanisms and pathways through which senescence induction occurs in these cells.

cancer biology↗

bioRxiv2025

Organellar data sets confirm overall angiosperm relationships if problematic RNA-edit sites are accounted for in mitochondrial genomes

PremisePlastid-based data sets continue to play a major role in our understanding of early flowering-plant relationships, although organellar genomes of major lineages outside the monocots and eudicots remain under-sampled. A tendency of mitochondrial RNA-edit sites to mislead phylogenetic analysis in mixed transcriptomic/genomic data sets needs attention in angiosperm-wide studies, which only rarely consider mitochondrial genomes. MethodsWe compared mitochondrial- vs. plastid-based phylogenomic inferences, examined the effect of removing putative RNA-edit sites from mitochondrial data, and performed combined organellar analysis (plastid plus filtered mitochondrial genomes). We expanded taxon sampling for multiple angiosperm lineages for phylogenomic analysis using both organellar genomes, representing several poorly sampled lineages (in particular Degeneriaceae, Trimeniaceae) with smaller (few-gene) data sets. ResultsPlastid-based inferences recover well-supported relationships that align with and build upon previous studies, and recover well-supported internal relationships for two ANA-grade families (Hydatellaceae, Trimeniaceae) sampled for nearly all species. By contrast, unfiltered mitochondrial inferences of angiosperm phylogeny are generally poorly supported, and recover anomalous relationships compared to plastid-based inferences. However, removing putative mitochondrial RNA-edit sites dramatically reduces inter-organellar conflict and improves overall branch support. ConclusionsWe accounted for phylogenomic discordance between the two organellar genomes regarding overall angiosperm-wide relationships and filled in taxonomic gaps (poorly sampled lineages). Removing RNA edit sites substantially improves congruence in interorganellar inferences by effectively correcting a systematic bias in mitochondrial data. Uncertain relationships persist among five major mesangiosperm lineages in plastid-based inferences, but a clade comprising Chloranthales, Ceratophyllales and eudicots is well supported by filtered mitochondrial data.

plant biology↗

bioRxiv2025

The adenovirus E4orf1 protein initiates a feedback loop involving insulin and growth factor receptors, AKT, and NF-κB, leading to abnormal DNA content in infected cells

Abnormal DNA levels, such as aneuploidy and polyploidy, can indicate cellular transformation and cancer; however, the mechanisms remain poorly understood. All tumor viruses inherently cause abnormal DNA content in cells due to their oncogenes. During infections, adenovirus (Ad) oncogenes--early region 1A (E1A), early region 4 open reading frame 3 (E4orf3), and E4 open reading frame 1 (E4orf1)--promote the abnormal buildup of cellular DNA. Previous studies have described how E1A and E4orf3 lead infected cells to accumulate abnormal DNA content; however, the role of E4orf1 remains speculative. In this study, we generated cells that express E4orf1 to investigate its role in abnormal DNA content. The E4orf1-expressing cells initially exhibited no increase in DNA content compared to the control group. However, after Ad infection, they displayed higher ploidy levels. To detail how E4orf1 influences ploidy levels in Ad-infected cells, we employed pharmacological agents that target E4orf1 signaling. Our results indicate that E4orf1 enhances signaling from insulin and growth factor receptors to AKT and NF-{kappa}B, creating a feedback loop that elevates levels of cellular DNA in Ad-infected cells. Author SummaryThe early region 4 open reading frame 1 of adenovirus (E4orf1) is recognized for its ability to initiate signals that convert normal cells into cancerous ones. In the initial stages of cancer, cells exhibit DNA content that exceeds the typical levels seen during the G2 and M phases of the cell cycle. This study demonstrates that E4orf1 can trigger a feedback loop involving EGFR, INSR, IGF1R, AKT, and NF-kB, which is both dependent on and independent of PI3 kinase and leads to the accumulation of abnormal DNA content.

cancer biology↗

bioRxiv2025

Increased mRNA translation delays lung adenocarcinoma initiation and exposes a therapeutic vulnerability to MEK inhibitors

Although protein synthesis inhibitors are being evaluated as anti-cancer agents, the dynamics of mRNA translation in early tumorigenesis are still poorly understood. We report that deletion of the mRNA-translation repressor, eIF4A2 in early KRAS-driven lung adenocarcinoma leads to a dysregulated protein synthesis landscape characterised by a strongly upregulated secretome, enlarged secretory compartments, increased oxidative metabolism and acquisition of senescence-like characteristics. Paradoxically, this overdriven protein synthesis landscape delays tumorigenesis and leads to appearance of clusters of non-proliferative, p21-positive KRAS-expressing cells in the lung. Administration of rapamycin to reduce mRNA translation suppresses senescence and restores tumorigenesis following eIF4A2 deletion. Importantly, some eIF4A2 knockout cells overcome senescence to form tumours that exhibit enhanced MAP-kinase signalling and, in contrast to eIF4A2+/+ lesions, these may be eradicated by administration of a MEK inhibitor. Thus, dysregulated mRNA translation exposes a potential therapeutic vulnerability in KRAS-driven lung adenocarcinoma by forcing cancer cells to rely on MEK signalling. Statement of significanceThe requirement for anabolism in cancers has led to the search for inhibitors of mRNA translation as anti-cancer agents. However, we report that increased rates of mRNA translation promote a senescence-like phenotype in KRAS-driven lung cancer which delays tumorigenesis and renders the resulting tumours sensitive to MEK inhibition.

cancer biology↗

bioRxiv2025

Priming of retrograde signaling in wheat across multiple natural environments reveal how responses to dynamic stimuli can be integrated to alter yield, yield stability and water productivity

O_LIChloroplast-to-nucleus retrograde signaling enables rapid stress responses in plants, but whether these signals accumulate to affect crop performance across entire growing seasons under field conditions remains unknown. C_LIO_LIWe generated wheat mutants with targeted deletions in specific SAL gene copies from two distinct homeologous groups (TaSAL1 and TaSAL2), creating lines with enhanced stress signal responsiveness. We tested these lines across 15 field trials spanning diverse Australian environments with varying temperatures, rainfall, and irrigation regimes, measuring physiological responses, yield, biomass, and water productivity. C_LIO_LILines with TaSAL2 gene deletions showed 4-8% yield improvements with enhanced water productivity, while TaSAL1 deletions reduced yields. The TaSAL2 mutants maintained superior photosynthetic function under drought stress, showed improved relative water content, and demonstrated enhanced yield stability across environments. Canopy temperature measurements revealed dynamic stomatal regulation, with increased closure during midday stress periods but normal aperture under benign conditions. Significantly, specific SAL modifications enhanced photosynthetic efficiency and stress resilience without traditional yield penalties. C_LIO_LITargeted modification of specific SAL homeologous groups can simultaneously improve both yield and stress tolerance in wheat. This demonstrates that retrograde signaling integrates environmental information across the plant lifecycle, and highlights the importance of locus-specific targeting and multi-environment field validation for crop modifications. C_LI

plant biology↗

bioRxiv2024

Natural Language Prompts Guide the Design of Novel Functional Protein Sequences

The advent of natural language interaction with machines has ushered in new innovations in text-guided generation of images, audio, video, and more. In this arena, we introduce Biological Multi-Modal Model (BioM3), as a novel framework for designing functional proteins via natural language prompts. This framework integrates natural language with protein design through a three-stage process: aligning protein and text representations in a joint embedding space learned using contrastive learning, refinement of the text embeddings, and conditional generation of protein sequences via a discrete autoregressive diffusion model. BioM3 synthe-sizes protein sequences with detailed descriptions of the protein structure, lineage, and function from text annotations to enable the conditional generation of novel sequences with desired attributes through natural language prompts. We present in silico validation of the model predictions for subcellular localization prediction, reaction classification, remote homology detection, scaffold in-painting, and structural plausibility, and in vivo and in vitro experimental tests of natural language prompt-designed synthetic analogs of Src-homology 3 (SH3) domain proteins that mediate signaling in the Sho1 osmotic stress response pathway in bakers yeast. BioM3 possesses state-of-the-art performance in zero-shot prediction and homology detection tasks, and generates proteins with native-like tertiary folds and wild-type levels of experimentally assayed function.

synthetic biology↗