Biology subjects

McClure, S.

Publications and source records attributed to McClure, S..

9 recordsLinked to original sources

bioRxiv2026

Mining Microbial Transcriptomes to Engineer Cell-Based Bacterial Biosensors in Gut-Resident Bacteroidaceae

The gastrointestinal tract is rich in metabolic, immune, and microbiome-derived signals that can inform the design of live biotherapeutics and diagnosis of intestinal disorders. Engineered cell-based biosensors can tap into this molecular information and report on their environment, yet their development in gut-resident symbionts has been limited by a lack of validated sensor systems. Here, we present a generalizable pipeline that leverages bacterial transcriptional profiling to identify environment-responsive systems for biosensor engineering. Candidate Sensors Systems (CSSs) mined from healthy, disease, and in vitro transcriptomes were assembled into a barcoded library in Bacteroidaceae chassis and screened in high-throughput in vivo to identify responsive promoters. A unique Bacteroidales ECF-type sigma factor operon with ties to sphingolipid metabolism and flux was highly responsive in chemically-induced colitis models. The biosensor responded robustly to disease and returned to baseline upon recovery, establishing an in vivo-driven strategy for discovering functional biosensors in non-model gut-resident bacteria.

synthetic biology↗

bioRxiv2026

Dopamine dynamics in human anterior cingulate cortex during Pavlovian-instrumental conflict

Dopamine is believed to modulate not only instrumental learning about the link between states, actions, and outcomes but also reflexive behaviours, such as a Pavlovian bias to approach in rewarding states and freeze in aversive ones. We studied these dual roles in the human brain, by combining intracranial dopamine recordings from the anterior cingulate cortex (ACC)-- a region implicated in behavioural and cognitive control -- with a motivational Go/NoGo task involving conflict between instrumental and Pavlovian action selection. We found evidence that dopamine in the ACC is involved in evaluating whether Pavlovian responding should guide behaviour. This computational motif was observed across multiple task events, including in response to rewards and punishments, and in analyses based on a reinforcement learning model. Our results indicate that dopamine supports learning at the more abstract level of behavioural policies in addition to the more concrete levels of states and actions.

neuroscience↗

bioRxiv2025

Engineering butyrate-producing Lachnospiraceae to treat metabolic disease

Engineering native gut bacteria offers a route to persistent, programmable therapeutics, yet many dominant taxa remain genetically intractable. Lachnospiraceae are a prevalent and abundant family in the human gut microbiome, possessing metabolic functions generally associated with health1. Despite their promise as engineered live biotherapeutics, genetic manipulation of Lachnospiraceae remains challenging. Here, we develop a modular toolkit for Lachnospiraceae engineering, including constitutive and inducible expression and chromosomal integration systems. Applying this toolkit to the native commensal Coprococcus comes, we program secretion of the mammalian cytokine interleukin-22 (IL-22) in the mouse intestinal tract where it elicits ileal transcriptional responses consistent with cytokine signaling. In a mouse model of metabolic associated steatotic liver disease, IL-22-secreting C. comes improves glucose homeostasis and attenuates hepatic steatosis. This work demonstrates that a native Lachnospiraceae chassis can be genetically programmed to modulate host metabolic and immune physiology. The toolkit provides a generalizable foundation for Lachnospiraceae-derived microbiome therapeutics and for probing causal links between Lachnospiraceae gene programs and host phenotypes.

synthetic biology↗

bioRxiv2024

Nanoparticle-Supported, Rapid, and Electronic Detection of SARS-CoV-2 Antibodies and Antigens at Attomolar Level

Major challenges remain to precisely detect low-abundance proteins from diverse biofluids in a rapid and cost-effective manner. Here we present a gold nanoparticle (AuNP)-supported, rapid electronic detection (NasRED) platform with sub-femtomolar sensitivity and high specificity. Surface-functionalized AuNPs act as multivalent detectors to recognize target antigens and antibodies through high-affinity binding, subsequently forming aggregates precipitated in a microcentrifuge tube and producing a solution color change. The optical extinction of residual floating AuNPs is digitized using a customized circuitry incorporating inexpensive optoelectronic elements and feedback mechanisms for stabilized readout. Uniquely, NasRED introduces active fluidic forces through engineered centrifugation and vortex agitation, effectively promoting protein detection at low concentrations and accelerating signal generation. Using SARS-CoV-2 as a demonstration, NasRED enables detection of both antibodies and antigens from a small sample volume (6 {micro}L), distinguishes the viral antigens from those of human coronaviruses, and delivers test results in a short time (as fast as <15 min). The limits of detection (LoDs) for antibody detection are approximately 49 aM (7 fg/mL) in phosphate-buffered saline, or >3,000 times more sensitive than Enzyme-Linked Immunosorbent Assay (ELISA), [~]76 aM (11 fg/mL) in human pooled serum and in the femtomolar range in diluted whole blood. For nucleocapsid protein detection, NasRED LoDs are [~]190 aM (10 fg/mL) in human saliva and [~]2 fM (100 fg/mL) in nasal fluid. Unlike laboratory-based ELISA platforms, NasRED is a one-pot, in-solution assay that eliminates the needs for washing, labeling, expensive instrumentation or highly trained operators. With low reagent costs and a compact system footprint, this modular digital platform is well-suited for accurate, near-patient diagnosis and screening of a wide range of infectious and chronic diseases.

microbiology↗

bioRxiv2023

MGAT5 (GnTase-V) products are overexpressed in primary osteoblastic osteogenic sarcoma

It is well documented that MGAT5 (Glycosyltransferase V) products are over expressed in carcinomas and likely accelerate metastasis by promoting neoangiogenesis. We now report a similar over expression in primary osteoblastic osteogenic sarcoma and demonstrate new intratumoural blood vessels. Expansion of the tumours is by osteoclastic resorption of both trabecular and cortical bone with the latter by cutting channels similar to physiological cutting cones. Osteoclasts, adjacent capillaries, and related mast cells also overexpress MGAT5 products and we speculate that this facilitates neoangiogenesis.

pathology↗

bioRxiv2022

Aspects of the glycome of endochondral ossification

Comparatively little is known about the glycome (the set of glycans and glycoconjugates made by the cell, tissue or organism) of bone and cartilage. The glycome has a high-density coding capacity and is important in post-translational modification. Lectin histochemistry provides insights into the glycome and we applied this technique to an ectopic ossification site in human bronchial cartilages. Our results show that cartilage matrix at the site of erosion by chondroclasts has a limited but definite glycoprofile. In contrast, bone matrix does not express many lectin ligands. Chondroclasts have an extensive glycoprofile similar to that of, but not identical to, osteoclasts. N and O glycans are both expressed in the zone of presumptive mineralization and are relevant to that process. Bone trabecular lining cells communicate with osteocytes via intracanalicular processes and some lectin ligands were expressed by these three components. Mast cells and angiogenesis were prominent. Since cartilage normally resists vascular penetration by the secretion of antiangiogenesis factors it is postulated that the hypertrophic chondrocytes in the mineralization zone produce proteases which inhibit antiangiogenesis and facilitate angiogenesis by mast cells.

molecular biology↗

bioRxiv2020

Frontoparietal dynamics and value accumulation in intertemporal choice

Intertemporal choice requires choosing between a smaller reward available after a shorter time delay and a larger reward available after a longer time delay. Previous studies suggest that intertemporal preferences are formed by generating a subjective value of the monetary rewards that depends on reward amount and the associated time delay. Neuroimaging results indicate that this subjective value is tracked by ventral medial prefrontal cortex (vmPFC) and ventral striatum. Subsequently, an accumulation process, subserved by a network including dorsal medial frontal cortex (dmFC), dorsal lateral prefrontal cortex (dlPFC) and posterior parietal cortex (pPC), selects a choice based on the subjective values. The mechanisms of how value accumulation interacts with subjective valuation to make a choice, and how brain regions communicate during decision making are undetermined. We developed and performed an EEG experiment that parametrically manipulated the probability of preferring delayed larger rewards. A computational model equipped with time and reward information transformation, selective attention, and stochastic value accumulation mechanisms was constructed and fit to choice and response time data using a hierarchical Bayesian approach. Phase-based functional connectivity between putative dmFC and pPC was found to be associated with stimulus processing and to resemble the reconstructed accumulation dynamics from the best performing computational model across experimental conditions. By combining computational modeling and phase-based functional connectivity, our results suggest an association between value accumulation, choice competition, and frontoparietal connectivity in intertemporal choice. Author summaryIntertemporal choice is a prominent experimental assay for impulsivity. Behavior in the task involves several cognitive functions including valuation, action selection and self-control. It is unknown how these different functions are temporally implemented during the course of decision making. In the current study, we combined formal computational models of intertemporal choice with a phase-based EEG measure of activity across brain regions to show that functional connectivity between dmFC and pPC reflects cognitive mechanisms of both visual stimulus processing and choice value accumulation. The result supports the notion that dynamic interaction between frontopatietal regions instantiates the critical value accumulation process in intertemporal choice.

neuroscience↗

bioRxiv2018

Causal Evidence for the Dependence of the Magnitude Effect on Dorsolateral Prefrontal Cortex

Impulsivity refers to the tendency to insufficiently consider alternatives or to overvalue rewards that are available immediately. Impulsivity is a hallmark of human decision making with well documented health and financial ramifications. Numerous contextual changes and framing manipulations powerfully influence impulsivity. One of the most robust such phenomenon is the finding that people are more patient as the values of choice options are increased. This magnitude effect has been related to cognitive control mechanisms in the dorsal lateral prefrontal cortex (dlPFC). We used repetitive transcranial magnetic stimulation (rTMS) to transiently disrupt dlPFC neural activity. This manipulation dramatically reduced the magnitude effect, establishing causal evidence that the magnitude effect depends on dlPFC.

neuroscience↗

bioRxiv2017

Beyond Reward Prediction Errors: Human Striatum Updates Rule Values During Learning

Humans naturally group the world into coherent categories defined by membership rules. Rules can be learned implicitly by building stimulus-response associations using reinforcement learning (RL) or by using explicit reasoning. We tested if the striatum, in which activation reliably scales with reward prediction error, would track prediction errors in a task that required explicit rule generation. Using functional magnetic resonance imaging during a categorization task, we show that striatal responses to feedback scale with a \"surprise\" signal derived from a Bayesian rule-learning model and are inconsistent with RL prediction error. We also find that striatum and caudal inferior frontal sulcus (cIFS) are involved in updating the likelihood of discriminative rules. We conclude that the striatum, in cooperation with the cIFS, is involved in updating the values assigned to categorization rules when people learn using explicit reasoning.

neuroscience↗