Biology subjects

Spencer, D.

Publications and source records attributed to Spencer, D..

9 recordsLinked to original sources

bioRxiv2026

Microaerobic Copper Stress Redirects Pyruvate Metabolism and Reveals a CopL-linked Nitrogen Response in Staphylococcus aureus.

Copper is both an essential enzyme cofactor and an antimicrobial agent deployed by the host immune system to eradicate micro-organisms. The epidemic community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) lineage USA300 carries mobile genetic elements that encode copX/B and copL, conferring hyper-resistance to copper, but the role of CopL beyond extracellular copper sequestration remains unclear. We have combined RNA sequencing with targeted metabolite assays under microaerobic conditions, more reflective of host environments, to define key copper induced responses in WT and copL mutant strains. Subinhibitory copper exposure in microaerobic conditions triggered a distinctive transcriptional response across multiple biological functions. Unlike previous studies, copper exposure did not induce an oxidative stress response. Instead, classical copper resistance, teichoic acid modification, immune-evasion factors and core metabolic genes were induced, while genes for stress responses, metal homeostasis and virulence were repressed. Gene set enrichment analysis (GSEA) identified regulation by multiple global regulators, e.g. SigB, CodY, CcpA, Agr and Sae. Copper exposure affected metabolism, redirecting pyruvate flux toward acetoin and lactate production rather than acetate, accompanied by coordinated shifts in TCA cycle and amino acid pathways, including glutamate accumulation. Inactivation of copL revealed a distinct adaptive response, with strong induction of nitrogen metabolism genes and nitrite reduction. Together, these data show that copper functions as a regulatory signal, triggering coordinated transcriptional and metabolic remodelling that potentiates S. aureus fitness in the host.

microbiology↗

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↗

bioRxiv2025

Potato dihaploids uncover diverse alleles to facilitate diploid potato breeding

Commercial potato in North America is a clonal autotetraploid crop, which complicates breeding. Efforts are underway to convert potato to a diploid inbred-hybrid crop that is amenable to additional breeding strategies and allows breeders to more quickly respond to demands for crop improvement. With the goal of preserving haplotypes developed over the last 200 years of selection, diploid potato breeding in the US started with the creation of diploids from tetraploid commercial varieties and advanced breeding lines through prickle pollination. This is an effective but slow method which presents a barrier to entry for individual breeding programs. Therefore, we developed 97 publicly available dihaploids (diploids from prickle pollination of tetraploids) as a resource for diploid breeding in the U.S. These clones contain the majority of alleles in the US breeding population for three market classes: chips, russets, and fresh market reds. To facilitate genomic informed breeding, all clones have been resequenced using short read sequencing technology, and we have developed de novo assemblies based on PacBio HiFi long reads for 20 individuals. As an illustration of how these data will be used in breeding, we explored the maturity locus (StCDF1) and identified 15 different alleles. The majority of dihaploids were heterozygous for early and late alleles, resulting in intermediate maturity. Beyond informing breeding, this data facilitates investigations into potato genomics. The dihaploid population is both highly heterozygous and incredibly diverse on a population level. In particular, there is extensive structural diversity, including copy number variation, segregating within the population. This contrasts with a relatively low genome-wide historical recombination rate ({rho}). Taken together, these findings indicate that potato is highly diverse, with much of that diversity found within long linkage blocks.

plant biology↗

bioRxiv2025

Genomic and Immunogenomic Profiling of Extramedullary Acute Myeloid Leukemia Reveals Actionable Clonal Branching and Frequent Immune Editing

Extramedullary acute myeloid leukemia (eAML) is a rare form of myeloid neoplasm characterized by leukemic infiltration outside the bone marrow (BM). Despite its prognostic significance, eAML is often underdiagnosed and poorly characterized at molecular level. We performed a comprehensive genomic and immunogenomic profiling on paired BM and extramedullary specimens from 26 eAML patients, alongside over 400 AML cases without extramedullary involvement and 97 healthy controls. Clonal branching from BM was observed in 38.5% of extramedullary sites, frequently involving actionable mutations in FLT3, IDH2 and NPM1 genes. Both compartments were enriched in RAS pathway mutations and class II HLA losses, suggesting active immunoediting mechanisms driving eAML development. Strikingly all relapsed cases acquired FLT3 aberrations, highlighting therapeutic opportunities. These findings underpin the need for improved detection and routine genomic profiling, including targeted sequencing of suspected extramedullary lesions.

genomics↗

bioRxiv2024

Student experiences with an interactive 3D immersive biotechnology simulation and its impact on motivational beliefs

The development and use of virtual laboratories to augment traditional in-person skills training continues to grow. Virtual labs have been implemented in a number of diverse educational settings, which have many purported benefits including their adaptability, accessibility, and repeatability. However, few studies have evaluated the impact of virtual laboratories outside of academic achievement and skills competencies, especially in biotechnology. In this study, an interdisciplinary team of content experts, video game researchers, instructional designers, and assessment experts developed a 3D immersive simulation designed to teach novice scientists the technical skills necessary to perform sterile mammalian cell culture technique. Unique to the simulation development process is the recreation of an immersive experience through the capture of details in the real-world lab where participants have the freedom of choice in their actions, while receiving immediate feedback on their technical skills as well as procedural execution. However, unlike an in-person laboratory course, students are able to iterate and practice their skills outside of class time and learn from their mistakes. Using a mixed-methods study design, over the course of two semesters we evaluated student attitudes of the simulation and their science motivational beliefs including self-efficacy and science identity after engaging with the simulation prior to the physical laboratory. Our results show that students science identity remained unchanged while their science self-efficacy increased. Furthermore, students had positive perceptions of the benefits of the virtual simulation. These data suggest that the virtual cell culture simulation can be a useful pedagogical training tool to bolster students motivational beliefs that is both accessible and easy to implement.

scientific communication and education↗

bioRxiv2023

The neural activity of auditory conscious perception

Although recent work has made significant headway in understanding the temporal and spatial dynamics of the neural mechanisms of conscious perception, much of that work has focused on visual paradigms. To determine whether there are shared mechanisms for perceptual consciousness across sensory modalities, here we developed a task to test within the auditory domain. Participants (n=31) completed an auditory perceptual threshold task while undergoing intracranial electroencephalography (icEEG) for intractable epilepsy. Intracranial recordings from over 2,800 grey matter electrodes representing widespread cortical coverage were analyzed for power in the high gamma range (40-115 Hz)--a frequency range that reflects local neural activity. For trials that were perceived, we find activity in early auditory regions which is accompanied by activity in the right caudal middle frontal gyrus, and shortly thereafter by activity in non-auditory thalamus. This is followed by a wave of activity that sweeps through the higher auditory association regions and into parietal and frontal cortices, similar to the wave observed in our visual conscious perception paradigm. However, for not perceived trials, we find that significant activity is restricted to early auditory regions (and areas immediately adjacent to the Sylvian fissure). These findings show that the broad anatomical regions of cortical and subcortical networks involved in auditory perception are similar to the networks observed with vision, suggesting shared general mechanisms for conscious perception.

neuroscience↗

bioRxiv2022

Antibody optimization enabled by artificial intelligence predictions of binding affinity and naturalness

Traditional antibody optimization approaches involve screening a small subset of the available sequence space, often resulting in drug candidates with suboptimal binding affinity, developability or immunogenicity. Based on two distinct antibodies, we demonstrate that deep contextual language models trained on high-throughput affinity data can quantitatively predict binding of unseen antibody sequence variants. These variants span a KD range of three orders of magnitude over a large mutational space. Our models reveal strong epistatic effects, which highlight the need for intelligent screening approaches. In addition, we introduce the modeling of "naturalness", a metric that scores antibody variants for similarity to natural immunoglobulins. We show that naturalness is associated with measures of drug developability and immunogenicity, and that it can be optimized alongside binding affinity using a genetic algorithm. This approach promises to accelerate and improve antibody engineering, and may increase the success rate in developing novel antibody and related drug candidates.

bioinformatics↗

bioRxiv2020

Tsetse salivary glycoproteins are modified with paucimannosidic N-glycans, are recognised by C-type lectins and bind to trypanosomes

African sleeping sickness is caused by Trypanosoma brucei, a parasite transmitted by the bite of a tsetse fly. Trypanosome infection induces a severe transcriptional downregulation of tsetse genes encoding for salivary proteins, which reduces its anti-hemostatic and anti-clotting properties. To better understand trypanosome transmission and the possible role of glycans in insect bloodfeeding, we characterized the N-glycome of tsetse saliva glycoproteins. Tsetse salivary N-glycans were enzymatically released, tagged with either 2-aminobenzamide (2-AB) or procainamide, and analyzed by HILIC-UHPLC-FLR coupled online with positive-ion ESI-LC-MS/MS. We found that the N-glycan profiles of T. brucei-infected and naive tsetse salivary glycoproteins are almost identical, consisting mainly (>50%) of highly processed Man3GlcNAc2 in addition to several other paucimannose, high mannose, and few hybrid-type glycans. In overlay assays, these sugars were differentially recognized by the C-type lectins mannose receptor and DC-SIGN. We also show that salivary glycoproteins bind strongly to the surface of transmissible metacyclic trypanosomes. We suggest that although the repertoire of tsetse salivary N-glycans does not change during a trypanosome infection, the interactions with mannosylated glycoproteins may influence parasite transmission into the vertebrate host.

biochemistry↗

bioRxiv2019

Ectopic HCN4 expression drives mTOR-dependent epilepsy

The causative link between focal cortical malformations (FCM) and epilepsy is well-accepted, especially among patients with focal cortical dysplasia type II (FCDII) and tuberous sclerosis complex (TSC). However, the mechanisms underlying seizures remain unclear. Using a mouse model of TSC- and FCDII-associated FCM, we show that FCM neurons are responsible for seizure activity via their unexpected abnormal expression of the hyperpolarization-activated cyclic nucleotide-gated potassium channel isoform 4 (HCN4), which is normally not present in cortical pyramidal neurons after birth. Increasing intracellular cAMP levels, which preferentially affects HCN4 gating relative to the other isoforms, drove repetitive firing of FCM neurons but not that of control pyramidal neurons. Ectopic HCN4 expression was mTOR-dependent, preceded the onset of seizures, and was also found in diseased neurons in tissue resected for epilepsy treatment from TSC and FCDII patients. Finally, blocking HCN4 channel activity in FCM neurons prevented epilepsy in mice. These findings that demonstrate HCN4 acquisition as seizure-genic, identify a novel cAMP-dependent seizure mechanism in TSC and FCDII. Furthermore, the unique expression of HCN4 exclusively in FCM neurons provides opportunities for using HCN4 as a gene therapy target to treat epilepsy in individuals with FCDII or TSC. One Sentence SummaryOur data provide a novel cAMP-dependent mechanism of seizure initiation in focal cortical dysplasia and tuberous sclerosis complex due to the unexpected ectopic expression of HCN4 channels only in diseased neurons. HCN4 channels are thus promising candidates for gene therapy to treat epilepsy generated by mTOR-driven focal malformations.

neuroscience↗