Biology subjects

Cooke, S. F.

Publications and source records attributed to Cooke, S. F..

6 recordsLinked to original sources

bioRxiv2025

Simultaneous measurements of translation rate and transcriptome in single bacterial cells by scTR-seq uncovers linked regulation within a specialized active cell population.

Cell-to-cell variation within clonal bacterial populations provides bacterial communities important advantages including opportunities for bet-hedging and metabolic division of labor. In recent years the extent of bacterial heterogeneity has been documented both at the transcriptome level and with physiological measurements of cell growth rate and translation rate. However, methods that link physiological parameters to a single cells full transcriptomic state are lacking, making it difficult to identify the regulatory mechanisms that couple physiology and transcriptional output. Here we introduce a method that combines click-chemistry enabled labeling of nascent polypeptides to measure translation rates in single cells alongside microfluidic encapsulation and single cell transcriptomic measurements, providing a tandem measurement of translation rate and transcriptome in thousands of single Bacillus subtilis cells. In a culture experiencing nutrient limitation, we identified a subpopulation of cells with a higher rate of protein translation that uniquely overexpresses genes for several metabolic processes including acetoin production and arginine synthesis. Using a genetic approach informed by the gene expression in this subpopulation, we identified a regulatory mechanism that couples the increase in protein abundance of a transcriptional regulator AlsR with expression of alsR regulated genes in this subpopulation.

microbiology↗

bioRxiv2025

A human electrophysiological biomarker of Fragile X Syndrome is shared in V1 of Fmr1 KO mice and caused by loss of FMRP in cortical excitatory neurons

Predicting clinical therapeutic outcomes from preclinical animal studies remains an obstacle to developing treatments for neuropsychiatric disorders. Electrophysiological biomarkers analyzed consistently across species could bridge this divide. In humans, alpha oscillations in the resting state electroencephalogram (rsEEG) are altered in many disorders, but these disruptions have not yet been characterized in animal models. Here, we employ a uniform analytical method to show in males with fragile X syndrome (FXS) that the slowed alpha oscillations observed in adults are also present in children and in visual cortex of adult and juvenile Fmr1-/y mice. We find that alpha-like oscillations in mice reflect the differential activity of two classes of inhibitory interneurons, but the phenotype is caused by deletion of Fmr1 specifically in cortical excitatory neurons. These results provide a framework for studying alpha oscillation disruptions across species, advance understanding of a critical rsEEG signature in the human brain and inform the cellular basis for a putative biomarker of FXS.

neuroscience↗

bioRxiv2025

Targeting MDM2 homodimer and heterodimer disruption with DRx-098D in TP53 wild-type and mutant cancer cells

Novel pharmacological strategies capable of inhibiting pro-oncogenic MDM2 beyond its p53-dependent functions represents an increasingly attractive therapeutic strategy to treating solid and haematological cancers that are depdendent upon MDM2/MDMX, regardless of TP53 mutational status. Utilising a novel first-in-class cell-penetrating peptide disruptor of MDM2 homo- and heterodimerisation (DRx-098D), we demonstrate the anti-proliferative effect of blocking MDM2 dimerisation against a a panel of human cancer cell lines that are TP53 wild-type, mutant or null. DRx-098D elicits its anti-cancer activity via a differentiated mechanism vs. Idasanutlin (a Phase III clinical candidate MDM2-p53 small molecule inhibitor), inducing significantly superior growth inhibition against TP53 null HCT116 cells. Our preliminary data highlight, for the first time, the potential therapeutic utility of exploiting MDM2 dimerisation in TP53 wild-type and mutant cancers.

cancer biology↗

bioRxiv2023

Electrophysiological signatures of visual recognition memory across all layers of mouse V1

In mouse primary visual cortex (V1), familiar stimuli evoke significantly altered responses when compared to novel stimuli. This stimulus-selective response plasticity (SRP) was described originally as an increase in the magnitude of visual evoked potentials (VEPs) elicited in layer (L) 4 by familiar phase-reversing grating stimuli. SRP is dependent on NMDA receptors (NMDAR) and has been hypothesized to reflect potentiation of thalamocortical synapses in L4. However, recent evidence indicates that the synaptic modifications that manifest as SRP do not occur on L4 principal cells. To shed light on where and how SRP is induced and expressed, the present study had three related aims: (1) to confirm that NMDAR are required specifically in glutamatergic principal neurons of V1, (2) to investigate the consequences of deleting NMDAR specifically in L6, and (3) to use translaminar electrophysiological recordings to characterize SRP expression in different layers of V1. We find that knockout of NMDAR in L6 principal neurons disrupts SRP. Current-source density analysis of the VEP depth profile shows augmentation of short latency current sinks in layers 3, 4 and 6 in response to phase reversals of familiar stimuli. Multiunit recordings demonstrate that increased peak firing occurs to in response to phase reversals of familiar stimuli across all layers, but that activity between phase reversals is suppressed. Together, these data reveal important aspects of the underlying phenomenology of SRP and generate new hypotheses for the expression of experience-dependent plasticity in V1. Significance StatementRepeated exposure to stimuli that portend neither reward nor punishment leads to behavioral habituation, enabling organisms to dedicate attention to novel or otherwise significant features of the environment. The neural basis of this process, which is so often dysregulated in neurological and psychiatric disorders, remains poorly understood. Learning and memory of stimulus familiarity can be studied in mouse visual cortex by measuring electrophysiological responses to simple phase-reversing grating stimuli. The current study advances knowledge of this process by documenting changes in visual evoked potentials, neuronal spiking activity, and oscillations in the local field potentials across all layers of mouse visual cortex. In addition, we identify a key contribution of a specific population of neurons in layer 6 of visual cortex.

neuroscience↗

bioRxiv2020

Visual recognition is heralded by shifts in local field potential oscillations and inhibitory networks in primary visual cortex

Learning to recognize and filter familiar, irrelevant sensory stimuli eases the computational burden on the cerebral cortex. Inhibition is a candidate mechanism in this filtration process, and oscillations in the cortical local field potential (LFP) serve as markers of the engagement of different inhibitory neurons. We show here that LFP oscillatory activity in visual cortex is profoundly altered as male and female mice learn to recognize an oriented grating stimulus--low frequency ([~]15 Hz peak) power sharply increases while high frequency ([~]65 Hz peak) power decreases. These changes report recognition of the familiar pattern, as they disappear when the stimulus is rotated to a novel orientation. Two-photon imaging of neuronal activity reveals that parvalbumin-expressing inhibitory neurons disengage with familiar stimuli and reactivate to novelty, whereas somatostatin-expressing inhibitory neurons show opposing activity patterns. We propose a model in which the balance of two interacting interneuron circuits shifts as novel stimuli become familiar. Significance StatementHabituation, familiarity and novelty detection are fundamental cognitive processes that enable organisms to adaptively filter meaningless stimuli and focus attention on potentially important elements of their environment. We have shown that this process can be studied fruitfully in the mouse primary visual cortex by using simple grating stimuli for which novelty and familiarity are defined by orientation, and by measuring stimulus-evoked and continuous local field potentials. Altered event-related and spontaneous potentials, and deficient habituation, are well-documented features of several neurodevelopmental psychiatric disorders. The paradigm described here will be valuable to interrogate the origins of these signals and the meaning of their disruption more deeply.

neuroscience↗

bioRxiv2020

The immediate early gene Arc is not required for hippocampal long-term potentiation.

The immediate early gene Arc is critical for maintenance of long-term memory. How Arc mediates this process remains unclear, but it has been proposed to sustain Hebbian synaptic potentiation, which is a key component of memory encoding. This form of plasticity is modelled experimentally by induction of long-term potentiation (LTP), which increases Arc mRNA and protein expression. However, mechanistic data implicates Arc in the endocytosis of AMPA-type glutamate receptors and the weakening of synapses. Here, we took a comprehensive approach to determine if Arc is necessary for hippocampal LTP. We find that Arc is not required for LTP maintenance and must regulate memory storage through alternative mechanisms.

neuroscience↗