Biology subjects

Gunn, J.

Publications and source records attributed to Gunn, J..

8 recordsLinked to original sources

bioRxiv2026

Contribution of the Late Positive Potential to Emotional Memory: A Joint Neuro-Cognitive Approach to Memory Prediction

Emotional events are better remembered than neutral events. The emotional Context Maintenance and Retrieval model (eCMR) explains this effect by simulating preferential encoding of emotional items, implemented by a free parameter that scales the learning rate. Incorporating a neural signal measured during encoding could make the model's account more specific, permitting a prediction not only of average increased recall but also which emotional items are likely to be recalled. We investigated whether the late positive potential (LPP) event-related potential (ERP) effect could provide this item-specific information in a secondary analysis of EEG recorded while 38 participants encoded negative and neutral pictures for an immediate free recall test (Zarubin et al. 2020). First, we established that the LPP effect was modulated by emotion in an early (400-1000 ms) and a late (1000-2000 ms) time window and this modulation was reliable in 73.7% and 50% of the participants respectively. Second, we investigated at what level the LPP was related to subsequent memory. Emotion-enhanced LPP did not covary with emotion-enhanced memory between participants or across lists within participants, but the early LPP specifically predicted memory for emotional items on a single-trial level. Third, we compared eCMR variants to test whether trial-level early LPP should scale learning for both categories or only for emotional items, and whether it could replace or complement a common learning-rate increase for all emotional items. The best-fitting model combined emotion-specific LPP scaling with the common learning-rate increase. The finding that early LPP predicted enhanced recall only for emotional items is difficult to reconcile with accounts on which the LPP reflects attention or stimulus significance more generally, which predict a relationship to memory for neutral items as well. These results pave the way to quantitative prediction of internal recall trajectories by individual participants without requiring behavioural output.

neuroscience↗

bioRxiv2026

Biofilm-Derived Curli and Z-DNA Shape Anti-DNA Antibody Responses During Salmonella Infections

Antibodies to Z-DNA, a non-canonical DNA conformation with a left-handed zigzag backbone, are abundant in the serum of patients with systemic lupus erythematosus (SLE), with levels increasing with disease activity and flares. As SLE is associated with bacterial infections, and as extracellular DNA (eDNA) within biofilms of several bacterial species has been shown to adopt the Z-DNA conformation, bacterial Z-DNA may represent a source of immunogenic Z-DNA in SLE and other related autoimmune conditions. In these studies, we investigated whether eDNA in Salmonella biofilms also contained Z-DNA and whether such Z-DNA could elicit an antibody response. Using antibody-based staining approaches, we observed abundant eDNA in Salmonella enterica serovar Typhimurium (STm) biofilms in both the Z- and canonical B-DNA configurations, consistent with the highly Z-prone nature of the GC-rich Salmonella genome. To assess the functional contribution of these DNA conformations to biofilm integrity, biofilms were treated with DNase I, which lacks enzymatic activity against Z-DNA, or with benzonase, a nonspecific nuclease that degrades both B- and Z-DNA. DNase I treatment applied after biofilm maturation was less effective at thinning biofilms than treatment during early biofilm formation, a pattern also observed with benzonase treatment. Purified curli:DNA complexes contained Z-DNA and, when administered intraperitoneally to mice, elicited robust anti-Z-DNA antibody responses. Similarly, infection with invasive STm induced the production of anti-Z-DNA antibodies in vivo. Moreover, STm infection in mice fed a diet that promotes biofilm development was associated with increased Z-DNA levels in the cecal lumen and elevated anti-DNA antibody responses. Collectively, these findings suggest that Z-DNA, likely formed by extruded Salmonella genomic DNA, and embedded within curli:DNA complexes of STm biofilms, triggers a host immune response and drives anti-Z-DNA antibody production. This work provides mechanistic insight into how bacterial infections and diet-dependent modulation of biofilm formation may contribute to anti-Z-DNA antibody responses in autoimmune diseases like SLE.

immunology↗

bioRxiv2022

QClus: Robust and reliable preprocessing method for human heart snRNA-seq

Single nuclei RNA sequencing (snRNA-seq) remains a challenge for many human tissues, as incomplete removal of background signal masks cell-type-specific signals and interferes with downstream analyses. Here, we present QClus, a droplet-filtering algorithm targeted toward challenging samples, using cardiac tissue as an example. QClus uses specific metrics such as cell-type-specific marker gene expression to cluster nuclei and filter empty and highly contaminated droplets, providing reliable cleaning of samples with varying number of nuclei and contamination levels. In a benchmarking analysis against seven alternative methods across six datasets consisting of 252 samples and over 1.9 million nuclei, QClus achieved the highest quality in the greatest number of samples over all evaluated quality metrics and recorded no processing failures, while robustly retaining numbers of nuclei within the expected range. QClus combines high quality, automation, and robustness with flexibility and user-adjustability, catering to diverse experimental needs and datasets.

genomics↗

bioRxiv2021

Single-cell dissection of live human hearts in ischemic heart disease and heart failure reveals cell-type-specific driver genes and pathways

Ischemic heart disease is globally the leading cause of death. It plays a central role in the electrical and structural remodeling of the right atrium, predisposing to arrhythmias, heart failure, and sudden death. Here, we provide the first dissection of the gene expression changes in the live right atrial tissue, using single-nuclei RNA-seq and spatial transcriptomics. We investigate matched samples of the tissue and pericardial fluid and reveal substantial differences in disease- associated gene expression in all cell types, leading to inflammatory microvascular dysfunction and changes in the tissue composition. Our study demonstrates the importance of creating high- resolution cellular maps and partitioning disease signals beyond epicardial coronary arteries and ischemic left ventricle to identify candidate mechanisms leading to more severe types of human cardiovascular disease. One-Sentence SummarySingle-cell dissection of ex vivo heart biopsies and pericardial fluid in ischemic heart disease and heart failure

molecular biology↗

bioRxiv2021

Neutralizing IFNL3 Autoantibodies in Severe COVID-19 Identified Using Molecular Indexing of Proteins by Self-Assembly

Unbiased antibody profiling can identify the targets of an immune reaction. A number of likely pathogenic autoreactive antibodies have been associated with life-threatening SARS-CoV-2 infection; yet, many additional autoantibodies likely remain unknown. Here we present Molecular Indexing of Proteins by Self Assembly (MIPSA), a technique that produces ORFeome-scale libraries of proteins covalently coupled to uniquely identifying DNA barcodes for analysis by sequencing. We used MIPSA to profile circulating autoantibodies from 55 patients with severe COVID-19 against 11,076 DNA-barcoded proteins of the human ORFeome library. MIPSA identified previously known autoreactivities, and also detected undescribed neutralizing interferon lambda 3 (IFN-{lambda}3) autoantibodies. At-risk individuals with anti-IFN-{lambda}3 antibodies may benefit from interferon supplementation therapies, such as those currently undergoing clinical evaluation. One-Sentence SummaryMolecular Indexing of Proteins by Self Assembly (MIPSA) identifies neutralizing IFNL3 autoantibodies in patients with severe COVID-19. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=144 SRC="FIGDIR/small/432977v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@a3c55aorg.highwire.dtl.DTLVardef@1f1c840org.highwire.dtl.DTLVardef@920bc7org.highwire.dtl.DTLVardef@43633e_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2020

Feasibility and safety of a telemetric pulmonary artery pressure monitoring system in acute and chronic porcine models of pulmonary hypertension.

AimsPulmonary hypertension (PH) is associated with significant morbidity and mortality and leads to progressive right heart failure. In patients with PAH, haemodynamic parameters measured at catheterisation relate to clinical worsening events, in patients with heart failure proactive pulmonary artery pressure based therapeutic intervention reduces hospitalisation. We therefore investigated use of a novel implanted pulmonary artery (PA) pressure monitor to detect clinically relevant changes in pressure in large animal models of pulmonary hypertension (PH). Methods and ResultsPrototype pulmonary artery pressure sensors (Endotronix) were implanted using standard interventional techniques. Acute PH was induced by infusion of thromboxane A2 in domestic swine. Over a physiological range pressure monitors remained concordant to reference catheter (bias -0.43, 95%CI-5.3-4.4). Chronic PH was induced by i.p. injection of monocrotaline. Implanted pressure sensors demonstrated a gradual rise in PA pressure over 30 days (baseline: 20.7+/-0.4 vrs day-30: 31.74+/-1.4, p<0.01). Pressure sensor derived readings matched reference catheter at baseline and day-30. Pressure sensors remained stable and no adverse events were identified by clinical and histological examination. ConclusionsThe development of PA pressure monitors provide long-term haemodynamic data that identified clinically meaningful changes in pulmonary artery pressure. In addition to proactive heart failure management, such devices may be used to optimise or personalize patient therapy, investigate aspects of physiology and pathology essential to the understanding of disease and provide the opportunity to assess therapeutic interventions in clinical studies.

physiology↗

bioRxiv2020

Highly multiplexed oligonucleotide probe-ligation testing enables efficient extraction-free SARS-CoV-2 detection and viral genotyping

The emergence of SARS-CoV-2 has caused the current COVID-19 pandemic with catastrophic societal impact. Because many individuals shed virus for days before symptom onset, and many show mild or no symptoms, an emergent and unprecedented need exists for development and deployment of sensitive and high throughput molecular diagnostic tests. RNA-mediated oligonucleotide Annealing Selection and Ligation with next generation DNA sequencing (RASL-seq) is a highly multiplexed technology for targeted analysis of polyadenylated mRNA, which incorporates sample barcoding for massively parallel analyses. Here we present a more generalized method, capture RASL-seq (“cRASL-seq”), which enables analysis of any targeted pathogen-(and/or host-) associated RNA molecules. cRASL-seq enables highly sensitive (down to ∼1-100 pfu/ml or cfu/ml) and highly multiplexed (up to ∼10,000 target sequences) detection of pathogens. Importantly, cRASL-seq analysis of COVID-19 patient nasopharyngeal (NP) swab specimens does not involve nucleic acid extraction or reverse transcription, steps that have caused testing bottlenecks associated with other assays. Our simplified workflow additionally enables the direct and efficient genotyping of selected, informative SARS-CoV-2 polymorphisms across the entire genome, which can be used for enhanced characterization of transmission chains at population scale and detection of viral clades with higher or lower virulence. Given its extremely low per-sample cost, simple and automatable protocol and analytics, probe panel modularity, and massive scalability, we propose that cRASL-seq testing is a powerful new surveillance technology with the potential to help mitigate the current pandemic and prevent similar public health crises.Competing Interest StatementJ.J.C. and H.B.L. are listed as inventors on a patent describing the cRASL-seq method. H.B.L. has founded a company to license and commercialize oligonucleotide probe ligation related technologies.View Full Text

pathology↗

bioRxiv2019

Relating visual production and recognition of objects in human visual cortex

Drawing is a powerful tool that can be used to convey rich perceptual information about objects in the world. What are the neural mechanisms that enable us to produce a recognizable drawing of an object, and how does this visual production experience influence how this object is represented in the brain? Here we evaluate the hypothesis that producing and recognizing an object recruit a shared neural representation, such that repeatedly drawing the object can enhance its perceptual discriminability in the brain. We scanned participants using fMRI across three phases of a training study: during training, participants repeatedly drew two objects in an alternating sequence on an MR-compatible tablet; before and after training, they viewed these and two other control objects, allowing us to measure the neural representation of each object in visual cortex. We found that: (1) stimulus-evoked representations of objects in visual cortex are recruited during visually cued production of drawings of these objects, even throughout the period when the object cue is no longer present; (2) the object currently being drawn is prioritized in visual cortex during drawing production, while other repeatedly drawn objects are suppressed; and (3) patterns of connectivity between regions in occipital and parietal cortex supported enhanced decoding of the currently drawn object across the training phase, suggesting a potential substrate for learning how to transform perceptual representations into representational actions. Taken together, our study provides novel insight into the functional relationship between visual production and recognition in the brain.\n\nSignificance StatementHumans can produce simple line drawings that capture rich information about their perceptual experiences. However, the mechanisms that support this behavior are not well understood. Here we investigate how regions in visual cortex participate in the recognition of an object and the production of a drawing of it. We find that these regions carry diagnostic information about an object in a similar format both during recognition and production, and that practice drawing an object enhances transmission of information about it to downstream regions. Taken together, our study provides novel insight into the functional relationship between visual production and recognition in the brain.

neuroscience↗