Biology subjects

Cooke, M.

Publications and source records attributed to Cooke, M..

11 recordsLinked to original sources

bioRxiv2026

NC4touch: An open-source networked touchscreen apparatus for rodent behavioral testing

In recent years, rodent touchscreen-based paradigms have gained popularity for their flexible task design, automated data collection and improved standardization. These devices minimize experimenter intervention and contribute to more replicable and reliable research. However, the high costs and proprietary hardware / software associated with commercially available systems present a financial barrier for smaller labs or researchers with limited resources. To address this issue, we developed "NC4Touch", an open-source scalable, modular rodent testing apparatus. It features three independent touchscreens and a feeding port for easy use in a wide array of tests comparable to those available with standard operant chambers, with the added benefit that visual stimuli can be highly customized. The system includes a user-friendly graphical interface that offers real-time control, task customization, video recording, and data management. We demonstrate its effectiveness in a visual discrimination task using both rats and mice. Several devices can be operated in parallel from the same computer and user interface, allowing high- throughput data collection. We provide detailed assembly instructions for the hardware and well- documented and easily-configurable software. We hope that the affordable open-source nature of NC4Touch will expand the scope of behavioral testing, allowing researchers to overcome traditional financial barriers and create a more collaborative community. Significance StatementTouchscreen-based testing is a powerful tool for assessing cognition in rodent models, however commercial systems remain cost-prohibitive for many researchers. NC4Touch is a rodent touchscreen apparatus that provides an open-source, customizable, and affordable alternative that enables high-throughput, cognitive testing in both mice and rats. By lowering financial barriers and promoting hackability, this system enables greater accessibility and collaboration in research.

animal behavior and cognition↗

bioRxiv2026

The ω subunit stabilizes transcribing RNA polymerase to balance processivity and collision resolution

The ubiquitous subunit of RNA polymerase (RNAP), {omega}/RPB6, is traditionally viewed as an assembly chaperone or bacterial {sigma}-factor competition modulator. This study redefines the role of Escherichia coli {omega}, encoded by the rpoZ gene. Unexpectedly,{Delta} rpoZ strain does not exhibit major defects in {sigma}S-dependent stress responses, indicating its primary function lies elsewhere. Our CRISPRi screen suggested that losing {omega} may promote survival during transcription-replication conflicts. Consistently, we show that loss of {omega} sensitizes RNAP to termination, reduces RNAP processivity, and suppresses toxic effects of DNA-damaging agents in strains lacking functional DksA, Rho, or SeqA; DksA and Rho promote the release of stalled RNAP from nucleic acids, while SeqA prevents aberrant replication initiation. These findings suggest that loss of {omega} facilitates the removal of stalled RNAP, preventing catastrophic replisome collisions. We propose that {omega}/RPB6 homologs may balance RNAP processivity with controlled release to preserve genome integrity across all domains of life.

genetics↗

bioRxiv2023

The roles of GpsB and DivIVA in Staphylococcus aureus growth and division

The spheroid bacterium S. aureus is often used as a model of morphogenesis due to its apparent simple cell cycle. S. aureus has many cell division proteins that are conserved across bacteria alluding to common functions. However, despite intensive study we still do not know the roles of many of these components. Here we have examined the functions of the paralogues DivIVA and GpsB in the S. aureus cell cycle. Cells lacking gpsB display a more spherical phenotype than wild type, associated with a decrease in peripheral cell wall peptidoglycan synthesis. This correlates with an increased localisation of penicillin binding proteins at the developing septum, notably PBPs 2 and 3. Our results highlight the role of GpsB as an apparent regulator of cell morphogenesis in S. aureus.

microbiology↗

bioRxiv2022

Towards a General Approach for Bat Echolocation Detection and Classification

O_LIAcoustic monitoring is a scalable approach for assessing bat populations, yet automating the detection and classification of bat echolocation calls remains challenging, particularly in data-scarce regions. Although deep learning (DL) is increasingly applied to this task, most existing approaches repurpose computer-vision architectures and generate a single prediction per spectrogram clip, offering limited robustness to variable background noise and potentially constraining generality across regions and species assemblages. C_LIO_LIHere, we develop BatDetect2, an open-source DL pipeline for the joint detection and classification of bat echolocation calls. BatDetect2 builds on a 2D convolutional architecture and incorporates two targeted modifications: (i) a temporal self-attention layer designed to capture long-range structure across call sequences, and (ii) convolutional layers augmented with frequency coordinates to explicitly encode frequency information directly. We evaluate model generality using five diverse datasets from four different regions: UK, Mexico, Australia, and Brazil, and conduct ablation analyses using a UK dataset spanning 17 bat species. We further assess whether a trained model can detect echolocation calls from species absent from the training data. C_LIO_LIBatDetect2 consistently outperforms a traditional call-parameter extraction baseline across all datasets and evaluation metrics. Ablation analyses show that the inclusion of temporal self-attention yields a substantial species classification performance gain, increasing mean Average Precision (mAP) from 0.83 to 0.88, while frequency-coordinate augmentation provides no measurable benefit. When applied to novel species assemblages without retraining, model detection performance varies across datasets, with Average Precision ranging from 0.60 to 0.98. C_LIO_LIOverall, BatDetect2 demonstrates strong and transferable performance across acoustically and taxonomically diverse regions. By jointly detecting and classifying all bat calls present in each input clip, the pipeline provides a practical and extensible tool for passive acoustic monitoring. The full training pipeline and a pretrained UK model are released through the open-source Python package batdetect2, enabling practitioners to develop and deploy models using their own data. C_LI

ecology↗

bioRxiv2022

Protein kinase C alpha is a central node for tumorigenic transcriptional networks in human prostate cancer

Aberrant expression of protein kinase C (PKC) isozymes is a hallmark of cancer. The different members of the PKC family control cellular events associated with cancer development and progression. Whereas the classical/conventional PKC isozyme has been linked to tumor suppression in most cancer types, here we demonstrate that this kinase is required for the mitogenic activity of aggressive human prostate cancer cells displaying aberrantly high PKC expression. Immunohistochemical analysis showed abnormal up-regulation of PKC in human primary prostate tumors. Interestingly, silencing PKC expression from aggressive prostate cancer cells impairs cell cycle progression, proliferation and invasion, as well as their tumorigenic activity in a mouse xenograft model. Mechanistic analysis revealed that PKC exerts a profound control of gene expression, particularly over genes and transcriptional networks associated with cell cycle progression and E2F transcription factors. PKC RNAi depletion from PC3 prostate cancer cells led to reduced expression of pro-inflammatory cytokine and epithelial-to-mesenchymal transition (EMT) genes, as well as a prominent down-regulation in the expression of the immune checkpoint ligand PD-L1. This PKC-dependent gene expression profile was corroborated in a human prostate cancer database. Our studies established PKC as a multifunctional kinase that plays pleiotropic roles in prostate cancer, particularly by controlling genetic networks associated with tumor growth and progression. The identification of PKC as a pro-tumorigenic kinase in human prostate cancer provides strong rationale for developing therapeutic approaches towards targeting PKC or its effectors. IMPLICATIONSOur findings implicate PKC as a major node for transcriptional regulation of tumorigenic pathways in prostate cancer.

cancer biology↗

bioRxiv2022

Modulation of RNA polymerase processivity affects double-strand break repair in the presence of a DNA-end binding protein

Homologous recombination is the predominant double-strand DNA break repair pathway in Escherichia coli. A recent report of non-homologous end joining involving the Ku-like Gam protein of bacteriophage Mu (MuGam) has sparked interest in understanding the functions of DNA end-binding proteins in bacteria. MuGam binds to DNA ends, but how it interferes with DNA repair or transcription in live bacteria remains elusive. In E. coli, RNA polymerase secondary channel interactors, such as the Gre factors, play a role in coordinating transcription with DNA replication and break repair. Here we show that MuGam inhibits break repair by slowing down DNA resection and impeding recombination in living cells. Loss of GreA restores break repair in the presence of MuGam by allowing for increased DNA resection due to a potential release of MuGam from the DNA. Using MuGam as a DNA break sensor, we found that breaks are generated when translation is inhibited, more so in the presence of GreA, supporting the model where transcription-translation uncoupling increases transcription/replication collisions. Significantly, this work reveals that modulation of RNA polymerase can impact DNA break repair in presence of a Ku-like protein.

molecular biology↗

bioRxiv2021

Non-destructive extraction of DNA from preserved tissues in medical collections

Museum and medically fixed material are valuable samples for the study of historical soft tissues and represent a pathogen-specific source for retrospective molecular investigations. However, current methods for the molecular analysis are inherently destructive, posing a dilemma between performing a study with the available technology thus damaging the sample - or conserving the material for future investigations. Here we present an unprecedented non-destructive alternative that facilitates the genetic analysis of fixed wet tissues while avoiding tissue damage. We extracted DNA from the fixed tissues as well as their embedding fixative solution, to quantify the DNA that was transferred to the liquid component. Our results prove that human ancient DNA can be retrieved from the fixative material of stored medical specimens and provide new options for the sampling of valuable curated collections. Method summaryWe compared the metagenomic content of historical tissues and their embedding liquid to retrieve DNA from the host and specified pathogens based on the diagnosis of the sample. We applied ancient DNA research techniques, including in-solution hybridization capture with DNA baits for human mitochondrial DNA, Mycobacterium tuberculosis, Mycobacterium leprae, and Treponema pallidum.

genetics↗

bioRxiv2020

Mechanisms of protein kinase C epsilon down-regulation by transforming growth factor-beta in lung cancer cells

Protein kinase C epsilon (PKC{varepsilon}), a diacylglycerol (DAG)/phorbol ester-regulated PKC isoform, has been widely linked to oncogenesis and metastasis. PKC{varepsilon} plays important roles in the regulation of motility and invasiveness in non-small cell lung cancer (NSCLC). We previously reported that this kinase becomes prominently down-regulated upon TGF-{beta}-induced epithelial-to-mesenchymal transition (EMT), which leads to prominent phenotypic changes. While the phorbol ester PMA causes down-regulation of PKC, {delta} and {varepsilon} within hours, TGF-{beta} requires at least 4 days to reduce the expression levels of PKC{varepsilon} without affecting the expression of other PKCs, an effect that parallels the acquisition of a mesenchymal phenotype. Despite the prominent transcriptional component involved in EMT, we found that PKC{varepsilon} down-regulation does not involve changes in PKC{varepsilon} mRNA levels and was entirely independent of transcriptional activation of the PRKCE gene. Further mechanistic analysis revealed that the reduction in PKC{varepsilon} expression is dependent on proteasomal and endolysosomal pathways, but independent of autophagy processing mechanisms. Site-directed mutagenesis of Lys312 and Lys321 in PKC{varepsilon} prevented its down-regulation in response to either TGF-{beta} or the phorbol ester PMA. The shift in PKC{varepsilon} isozyme levels depending on cell plasticity underscores relevant functional consequences by modulating the expression of this oncogenic/metastatic kinase and highlights key roles of protein stability mechanisms in the control of PKC{varepsilon} phenotypic outcomes.

cell biology↗

bioRxiv2020

Requirement for PKC epsilon in KRAS-driven lung tumorigenesis

ABSTRACTNon-small cell lung cancer (NSCLC), the most frequent subtype of lung cancer, remains a highly lethal malignancy and one of the leading causes of cancer deaths worldwide. Mutant KRAS is the prevailing oncogenic driver of lung adenocarcinoma, the most common histological form of NSCLC. In this study, we examined the role of PKCε, an oncogenic kinase highly expressed in NSCLC and other cancers, in KRAS-driven tumorigenesis. Notably, database analysis revealed an association between PKCε expression and poor outcome in lung adenocarcinoma patients specifically having KRAS mutation. By generating a PKCε-deficient, conditionally activatable allele of oncogenic Kras (LSL-KrasG12D;PKCε−/− mice) we were able to demonstrate the requirement of PKCε for Kras-driven lung tumorigenesis in vivo, which is consistent with the impaired transformed growth observed in PKCε-deficient KRAS-dependent NSCLC cells. Moreover, PKCε-knockout mice were found to be less susceptible to lung tumorigenesis induced by benzo[a]pyrene, a carcinogen that induces mutations in Kras. Mechanistic analysis using RNA-Seq revealed little overlapping for PKCε and KRAS in the control of genes/biological pathways relevant in NSCLC, suggesting that a permissive role of PKCε in KRAS-driven lung tumorigenesis may involve non-redundant mechanisms. Our results thus highlight the relevance and potential of targeting PKCε for lung cancer therapeutics.Competing Interest StatementThe authors have declared no competing interest.View Full Text

cancer biology↗

bioRxiv2017

Secondary Osteons Scale Allometrically In Mammalian Humerus And Femur

Intra-cortical bone remodelling is a cell-driven process that replaces existing bone tissue with new bone tissue in the bone cortex, leaving behind histological features called secondary osteons. While the scaling of bone dimensions on a macroscopic scale is well known, less is known about how the spatial dimensions of secondary osteons vary in relation to the adult body size of the species. We measured the cross-sectional area of individual intact secondary osteons and their central Haversian canals in transverse sections from 40 stylopodal bones of 39 mammalian species. Scaling analysis of our data shows that mean osteonal resorption area (negative allometry, exponent 0.23, R2 0.54, p < 0.005) and Haversian canal area (negative allometry, exponent 0.34, R2 0.45, p < 0.005) are significantly related to body mass, independent of phylogeny. This study is the most comprehensive of its kind to date, and allows us to describe overall trends in the scaling behaviour of secondary osteon dimensions, supporting the inference that osteonal resorption area may be limited by the need to avoid fracture in smaller mammalian species, but the need to maintain osteocyte viability in larger mammalian species.

zoology↗

bioRxiv2017

Polygenic prediction of the phenome, across ancestry, in emerging adulthood

BackgroundIdentifying genetic relationships between complex traits in emerging adulthood can provide useful etiological insights into risk for psychopathology. College-age individuals are under-represented in genomic analyses thus far, and the majority of work has focused on clinical disorder or cognitive abilities rather than normal-range behavioral outcomes.\n\nMethodsThis study examined a sample of emerging adults 18-22 years of age (N = 5,947) to construct an atlas of polygenic risk for 33 traits predicting relevant phenotypic outcomes. Twenty-eight hypotheses were tested based on the previous literature on samples of European ancestry, and the availability of rich assessment data allowed for polygenic predictions across 55 psychological and medical phenotypes.\n\nResultsPolygenic risk for schizophrenia in emerging adults predicted anxiety, depression, nicotine use, trauma, and family history of psychological disorders. Polygenic risk for neuroticism predicted anxiety, depression, phobia, panic, neuroticism, and was correlated with polygenic risk for cardiovascular disease.\n\nConclusionsThese results demonstrate the extensive impact of genetic risk for schizophrenia, neuroticism, and major depression on a range of health outcomes in early adulthood. Minimal cross-ancestry replication of these phenomic patterns of polygenic influence underscores the need for more genome-wide association studies of non-European populations.

genomics↗