Biology subjects

Corcoran, J.

Publications and source records attributed to Corcoran, J..

10 recordsLinked to original sources

bioRxiv2026

Differences in interactions between brain regions across personality types while learning in zebrafish (Danio rerio)

Learning is an important process for survival. Many studies find that variation in learning ability is related to personality type. Bold individuals generally learn faster than shy, however, the underlying neural mechanisms are not well understood. Potential mechanisms for differences in learning speed are variation in neurotransmitter activity, specifically dopamine and serotonin, and functional connectivity across the brain. In this study we quantified the number of generally active, active dopaminergic, and active serotonergic neurons using immunohistochemistry across 12 brain regions at two timepoints in bold and shy zebrafish undergoing an associative learning task. There were no interactions between treatment and personality type in any of the cell count measures suggesting that individual region activity and neurotransmitter activity do not explain learning differences. However, analyses of general neural activity networks revealed that the connection from the posterior zone of the dorsal telencephalon (olfactory cortex homolog) to lateral zone of the dorsal telencephalon (hippocampus homolog) was positive in bold but negative in shy fish undergoing learning. Overall, the results suggest that differences in activity involving reward processing in the brain may explain differences in reward learning between personality types.

neuroscience↗

bioRxiv2026

Kaposi's sarcoma-associated herpesvirus forms and maintains R-loops at origins of lytic replication

GC-rich sequences are abundant in human herpesviruses genomes. GC-rich regions can form three-stranded RNA:DNA hybrid structures called R-loops. Though these hybrid structures serve important biological roles at telomeres or during cellular DNA synthesis, unscheduled or prolonged R-loop formation causes DNA damage and genome instability. For this reason, several mechanisms exist to resolve R-loops including endoribonucleases RNaseH1 (constitutively expressed) and RNaseH2A (cell cycle-regulated) which degrade the RNA portion of the R-loop. The Kaposi's sarcoma-associated herpesvirus (KSHV) origins of lytic replication (OriLyts) contain multiple cis-acting elements that are required for viral DNA replication including the production of GC-rich and repetitive transcripts, T1.4 (OriLyt-L) and kaposin (OriLyt-R). We previously showed that R-loops form at both OriLyts and that deleting kaposin repeats or decreasing their GC-rich content prevented R-loop formation at OriLyt-R, reduced genome amplification after primary infection and caused defects in latency establishment. To define the contribution that R-loops play in KSHV replication, we overexpressed RNaseH1, reasoning that excess RNaseH1 would resolve both OriLyt R-loops. However, RNaseH1 protein levels decreased following KSHV reactivation in both iSLK and BCBL-1 cell lines. Using co-transfection, we discovered that the KSHV viral replication and transcription activator protein, RTA, mediated RNaseH1 protein decreases in a E3 ligase domain-dependent manner without impacting levels of its cognate RNA transcript. We attempted to construct an RTA-resistant yet functional version of RNaseH1 by site-directed mutagenesis of lysine residues individually or in combination, yet these constructs remain susceptible to RTA-mediated protein decreases. An amino terminally tagged RNaseH1 displayed reduced susceptibility to RTA, suggesting that RTA may target the N-terminus of RNaseH1 for ubiquitination. However, overexpression of the cell-cycle regulated endonuclease, RNaseH2, exhibited RTA resistance, suggesting RNaseH2 may be a tool that will effectively resolve R-loops during KSHV infection. KSHV is not the only herpesvirus to encode a protein that reduces RNaseH1 levels, as co-expression of RTA homologs from the related gamma-herpesviruses EBV and MHV-68 likewise decreased steady-state levels of RNaseH1 protein. We propose that RTA-mediated RNaseH1 degradation is conserved strategy to ensure R-loop persistence during gamma-herpesvirus infection, underscoring the importance of these structures.

microbiology↗

bioRxiv2026

Human coronavirus nucleocapsid proteins have disparate innate immune evasion abilities

During infection, coronaviruses produce abundant double-stranded RNA (dsRNA) which can induce antiviral innate immune responses such as the interferon, 2-5-oligoadenylate synthetase (OAS)/RNase L, and protein kinase R (PKR) pathways. Coronaviruses must antagonize these dsRNA responses for successful replication. The SARS-CoV-2 nucleocapsid (N) protein plays a central role in evasion of dsRNA responses, interacting with dsRNA to block interferon-{beta} production and the activation of OAS/RNase L and PKR. Despite intensive study of SARS-CoV-2 N, our understanding of the innate immune evasion abilities of N proteins produced by other human coronaviruses (HCoVs) remains incomplete. Here, we provide a comprehensive comparison of HCoV N proteins expressed in a human lung cell line and show that their abilities to block dsRNA-induced innate immune responses differ. Highly pathogenic HCoV N proteins inhibited the production of interferon-{beta} mRNA and activation of OAS/RNase L, while common cold HCoV N proteins did not. While most HCoV N proteins inhibited PKR phosphorylation, HCoV-OC43 N did not, an observation that correlated with high levels of PKR activation observed during HCoV-OC43 infection. The ability of HCoV N proteins to antagonize PKR required colocalization with dsRNA, yet the overall decrease in PKR phosphorylation mediated by N was not due to sequestration of dsRNA away from PKR. Rather, N colocalized with dsRNA and PKR at dsRNA-induced foci (dRIFs) and inhibited PKR phosphorylation within dRIFs. Sarbecovirus N proteins also relocalized PKR to G3BP1 foci, suggesting that these N proteins can inhibit PKR using two distinct mechanisms. Collectively, our work reveals an unexpected level of functional and mechanistic diversity among the innate immune evasion abilities of human coronavirus N proteins. These findings challenge existing presumptions that observations made in one coronavirus can be extrapolated to others, because even conserved essential proteins such as N can exhibit considerable functional heterogeneity.

microbiology↗

bioRxiv2025

Stress Coping Style Alters Functional Brain Network Activity to Acute Stressor

Consistent individual differences in behavior (e.g., personality types, stress coping styles) are a common occurrence across animal taxa. One hypothesis poses that the resulting constraints for within-individual behavioral variation may also lead to constraints for the evolution of behavior. With stress coping styles seen across taxa, it suggests a common underlying proximate mechanism. In this study we investigated neural activity patterns across the brain by quantifying immediate early gene expression in individuals with alternative stress coping styles in response to an acute stressor in zebrafish (Danio rerio). While immediate early gene expression levels of individual brain regions in the aversive brain network were similar across groups, functional network activity differed. There were several differences across groups including interactions between the basolateral amygdala and hippocampal homologs. One brain area that had many different connections across groups was the central gray. There were many differences involving central gray activity between proactive and reactive fish at baseline suggesting that baseline activity may prime for the reaction to stress. Collectively, baseline brain activity can predict behaviors, suggesting that these differences in brain interactions at baseline may be important for biasing behavioral responses to stressors that characterizes a stress coping style. Significance StatementIt is well known that individuals cope with stress in different ways but the underlying mechanisms are not well understood. In this study we investigate how different brain regions interact under stress in animals of different stress coping styles. We investigated activity patterns across several brain regions in fish with a passive or active response to stress. We used an innovative statistical method that allowed us to compare how the brain regions function together under stress. The central gray was the most different between proactive and reactive groups, suggesting that this region is important for biasing the response to stressors. Further baseline functional connectivity differed the most between groups, suggesting that activity at baseline is important for biasing the response to stress mainly through connections with the central gray. Ultimately, functional neural network activity better explains stress behaviors than individual brain activity.

neuroscience↗

bioRxiv2025

Evaluating anaesthetics for improving scientific research and welfare using larval zebrafish

Establishing anaesthesia for ensuring both animal welfare and compatibility with protocols required for different areas of scientific research is vital. Zebrafish (Danio rerio) are one of the most used animal models in research; however, little is known about the appropriateness of anaesthetic used for this species, especially for embryo-larval life stages. Using a combination of whole-brain functional imaging, quantification of cardiovascular performance, and behaviour, we explore the efficacy and tolerability of six widely used fish anaesthetics (2-phenoxyethanol, benzocaine, etomidate, MS222, isoeugenol and quinaldine sulfate) in larval zebrafish. We show that MS222 and quinaldine sulfate are the most suitable for achieving deep anaesthesia, while etomidate is better suited for studies focused on the cardiovascular system. Only quinaldine sulfate was found to be aversive. Our findings aid researchers for selecting the most suitable anaesthetic compounds and concentrations for their specific research goals, and the refinement of studies using anaesthesia in larval zebrafish.

physiology↗

bioRxiv2025

Coronavirus M proteins disperse the trans-Golgi network and inhibit anterograde protein trafficking in the secretory pathway

Coronaviruses (CoVs) encode Spike, Membrane (M), and Envelope (E) transmembrane proteins that are translated and processed at the endoplasmic reticulum (ER) and traverse the secretory pathway to converge at sites of virus assembly. Three transmembrane ER resident proteins, activating transcription factor 6 (ATF6), inositol-requiring enzyme 1 (IRE1), and PKR-like endoplasmic reticulum kinase (PERK), sense the accumulation of unfolded proteins in the ER and initiate the unfolded protein response (UPR) to increase ER protein folding capacity. We observed UPR modulation by numerous CoV proteins, including Spike, which broadly activated all three arms of the UPR. By contrast, M selectively inhibited the ATF6 arm of the UPR, either when it was activated by CoV proteins like Spike, or when it was activated by chemical stimuli of ER stress; however, M was unable to inhibit Spike-mediated activation of IRE1 or PERK. ATF6 inhibition was conserved amongst all human CoV M proteins. Amongst the UPR sensors, ATF6 has a unique activation mechanism whereby ER stress triggers translocation to the Golgi where ATF6 is processed by resident proteases to release the ATF6-N bZIP transcription factor. Because M had no effect on the function of the ATF6-N transcription factor, we reasoned that it may act upstream by inhibiting ATF6 trafficking in the secretory pathway. Indeed, we observed that ectopically expressed M inhibited several processes that require ER-to-Golgi transport, including sterol regulatory element binding protein-2 (SREBP2)-mediated activation of sterol responses and stimulator of interferon response cGAMP interactor 1 (STING1)-mediated activation of interferon responses. M also inhibited the secretion of a soluble Gaussia luciferase reporter protein. Using a Retention Using Selective Hooks (RUSH) cargo sorting assay, we observed that M accumulated in the cis-Golgi and inhibited further anterograde transport of a transmembrane reporter protein beyond this compartment, while dispersing the trans-Golgi network (TGN). We also observed a conserved TGN dispersal phenotype in cells infected with SARS-CoV-2, hCoV-OC43, or hCoV-229E. We determined that M is present in both detergent resistant and detergent soluble membranes and that M increased cholesterol abundance at the cis-Golgi. Together, these observations suggest that CoV M proteins disrupt the TGN and impede normal anterograde traffic in the canonical secretory pathway, potentially by increasing cholesterol levels at the cis-Golgi . Because CoV egress does not require the TGN, this mechanism could allow the virus to selectively interfere with host responses to infection without impeding egress of nascent virions. IMPORTANCEMany viruses encode proteins that limit host antiviral responses. Coronaviruses encode a remarkably diverse array of proteins that antagonize host responses at discrete steps including the detection of viral products, signal transduction, host mRNA processing and nuclear export, and protein synthesis. Here, we describe a new form of viral antagonism of host antiviral responses by remodelling the secretory pathway, dispersing a distal portion of the Golgi network and causing accumulation of proteins early in the Golgi. This is achieved by an abundant viral structural transmembrane glycoprotein M, which is best known for its role as the central player in the assembly of new viruses. This newly discovered function of M allows it to limit host antiviral responses that depend on trafficking in the late secretory pathway, while maintaining its role in virus assembly in the early secretory pathway.

microbiology↗

bioRxiv2024

Bold zebrafish (danio rerio) learn faster in an associative learning task

Animals differ in their ability to learn. One potential factor contributing to learning differences is personality types. We investigated the relationship between learning and the bold-shy continuum by comparing performance of bold and shy zebrafish in conditioned place preference (CPP) and 2 choice tasks. Bold fish learned significantly faster than the shy fish but there were no differences in their final performance. When tested in the 2 choice task, we found no clear evidence of learning, however bold fish made more initial choices than shy fish. Overall,our study suggests that bold fish tend to be faster learners when compared to shy fish. The lack of differences in the final change in behavior suggests that the learning difference is due to neophobic tendencies and resulting initial interactions with the learning stimulus.

animal behavior and cognition↗

bioRxiv2022

Thiopurines inhibit coronavirus Spike protein processing and incorporation into progeny virions

There is an outstanding need for broadly acting antiviral drugs to combat emerging viral diseases. Here, we report that thiopurines inhibit the replication of the betacoronaviruses HCoV-OC43 and SARS-CoV-2, and to a lesser extent, the alphacoronavirus HCoV-229E. 6-Thioguanine (6-TG) disrupted early stages of infection, limiting synthesis of full-length and subgenomic HCoV RNAs. Furthermore, consistent with our previous report on the effects of thiopurines on influenza A virus glycoproteins, we observed that 6-TG inhibited accumulation of Spike glycoproteins from diverse HCoVs. Specifically, 6-TG treatment decreased the accumulation of Spike proteins and increased their electrophoretic mobility, consistent with Spike migration following the enzymatic removal of N-linked oligosaccharides with Peptide:N-glycosidase F (PNGaseF). SARS-CoV-2 virus-like particles (VLPs) harvested from 6-TG-treated cells were deficient in Spike. 6-TG treatment had a similar effect on lentiviruses pseudotyped with SARS-CoV-2 Spike; lentiviruses could be harvested from cell supernatants but were deficient in Spike and unable to infect human cells bearing ACE2 receptors. Together, these findings from complementary ectopic expression and infection models strongly indicate that defective Spike trafficking and processing is an outcome of 6-TG treatment. At low micromolar doses, the primary known mode of action of 6-TG is selective inhibition of the small GTPase Rac1. However, we observed that selective chemical inhibitors of the small GTPases Rac1, CDC42 and Rho had no effect on Spike processing and accumulation. The GTPase agonist ML099 countered the effects of 6-TG, suggesting that an unknown GTPase could be the relevant 6-TG-target protein involved in regulating Spike processing and accumulation. Overall, these findings provide important clues about the mechanism of action of a candidate antiviral that can broadly target HCoVs and suggest that small GTPases are promising targets for host-targeted antivirals. AUTHOR SUMMARYThe COVID-19 pandemic has ignited efforts to repurpose existing drugs as safe and effective antivirals. Rather than directly inhibiting viral enzymes, host-targeted antivirals inhibit host cell processes to indirectly impede viral replication and/or stimulate antiviral responses. Here, we describe a new antiviral mechanism of action for the FDA-approved thiopurine 6-thioguanine. We demonstrate that this thiopurine is a pro-drug that must be metabolized by host enzymes to gain antiviral activity. We show that it can inhibit the replication of several human coronaviruses, including SARS-CoV-2, at least in part by interfering with the processing and accumulation of Spike glycoproteins, thereby impeding assembly of infectious progeny viruses. We provide evidence implicating host cell GTPase enzymes in the antiviral mechanism of action.

microbiology↗

bioRxiv2021

A viral protein utilizes the NDP52/CALCOCO2 selective autophagy receptor to disassemble processing bodies

Kaposis sarcoma-associated herpesvirus (KSHV) causes the inflammatory and angiogenic endothelial cell neoplasm, Kaposis sarcoma (KS). We previously demonstrated that expression of the KSHV protein, Kaposin B (KapB), promoted inflammation via the disassembly of cytoplasmic ribonucleoprotein granules called processing bodies (PBs). Processing bodies (PBs) modify gene expression by silencing or degrading labile messenger RNAs (mRNAs) including many transcripts that encode inflammatory or angiogenic proteins that are associated with KS disease. Although our work implicated PB disassembly as one of the causes of inflammation during KSHV infection, the precise mechanism used by KapB to elicit PB disassembly was unclear. Here we reveal a new connection between the degradative process of autophagy and PB disassembly. We show that both latent KSHV infection and KapB expression enhanced autophagic flux via the phosphorylation of the autophagy regulatory protein, Beclin 1. KapB was necessary for this effect, as infection with a recombinant virus that does not express the KapB protein did not induce Beclin 1 phosphorylation or autophagic flux. Moreover, we reveal that PB disassembly mediated by KSHV or KapB depended on canonical autophagy genes and the selective autophagy receptor NDP52/CALCOCO2 and that the PB scaffolding protein, Pat1b, co-immunoprecipitated with NDP52. These studies reveal a new role for autophagy and the selective autophagy receptor NDP52 in promoting PB turnover and the concomitant synthesis of inflammatory molecules during KSHV infection. Author SummaryKaposis sarcoma-associated herpesvirus (KSHV) is the causative agent of the inflammatory, endothelial cell cancer, Kaposis Sarcoma (KS). KSHV induces a pro-tumourigenic inflammatory environment which aids in the establishment and maintenance of the KS lesion. Processing bodies (PBs) are cellular structures that dampen inflammatory gene expression by suppression or decay of their cognate RNA molecules. We previously showed that the viral protein KapB caused PB disappearance during KSHV infection, identifying a new pathway used by KSHV to elicit inflammation. Now, we show that KSHV and KapB hijack the cellular degradative process of autophagy to promote PB disassembly and increase inflammatory gene expression. This places autophagy as central to the regulation of inflammation by KSHV and illustrates another remarkable strategy used by these viruses to create a tumourigenic microenvironment.

microbiology↗

bioRxiv2019

Identifying Novel Candidates for Re-Purposing as Potential Therapeutic Agents for Alzheimer’s disease

The current paper describes the identification of novel candidate compounds for repositioning as treatments for Alzheimers disease (AD) from the CMAP library. Candidate compounds were identified based on inverse correlation with transcriptome signatures developed from meta-analyses of Alzheimer RNA expression studies using the SPIED platform. The 78 compounds with a significant inverse correlation were taken forward into an in vitro programme using 6 well validated screening assays relevant to potential treatment targets in AD. Nineteen pf the compounds were hits in at least 2 of these assays. A description of each of these compounds is presented.

neuroscience↗