Biology subjects

Gray, D.

Publications and source records attributed to Gray, D..

15 recordsLinked to original sources

bioRxiv2026

Speciation, sexual selection, and the macroevolution of cricket mating signals

Animal mating signals can communicate both species-specific recognition information and male phenotypic quality persuasion information to females. Using a comparative framework across an entire clade, we show that mating signal traits specifically associated with conspecific signal recognition show fast initial divergence during speciation, followed by relative stasis at equilibrium, and that this effect is enhanced among species pairs with the potential for gene flow. In contrast, sexually selected persuasion mating signal evolution is not associated with initial species divergence. These results reveal mechanistically how and when rapid mating signal evolution facilitates speciation and challenge the prevailing view that traits experiencing intrapopulation sexual selection are likely to be the major traits which promote interspecific divergence. In particular, the results suggest that the mechanistic link between sexual selection and speciation is ephemeral. We expect that the distinction between recognition and persuasion traits, and the particular importance of divergence in recognition traits for speciation, should be a widespread phenomenon.

evolutionary biology↗

bioRxiv2026

Ecological genomics of a novel host-parasitoid arms-race in nature

Novel antagonistic interactions between species are expected to drive especially rapid coevolution. However, little is known about the genomic basis of such coevolution in nature because novel inter-specific interactions are rarely observed. Here, we study two species that recently came into first contact in Hawaii, the parasitoid fly Ormia ochracea and its cricket host Teleogryllus oceanicus. The fly locates crickets acoustically using their song, and parasitism usually results in host death. In response, protective male-silencing mutations have rapidly spread through cricket populations over the last [~]25 years, imposing novel selective pressure on flies. By integrating population genomic analyses of 358 re-sequenced flies with field surveys of selection imposed by host adaptations, we discover genomic signatures of recent selective sweeps driven by host adaptations, indicative of escalating arms-race dynamics. This evolutionary response is occurring despite severely depleted genetic variation after bottlenecks in Hawaiian fly populations. Comparative analyses suggest that the genomic substrate of modern-day, rapid counter-adaptation in O. ochracea has been under positive selection on intermediate and long-term timescales across parasitoid flies. Our findings thus support predictions of influential arms race coevolution models and illustrate the current and ancient genomic bases of counteradaptation in nature.

evolutionary biology↗

bioRxiv2026

Multidimensional encoding of temporal features underlies song recognition in Floridian Ormia ochracea

Acoustic communication signals often contain complex temporal structure, yet the features underlying signal recognition remain poorly understood, particularly in eavesdropping receivers. The parasitoid fly Ormia ochracea localises host crickets by eavesdropping on their calling songs. In Florida, preferred host songs consist of sound pulses repeated at ~50 pulses/s, and flies exhibit matching preferences. However, it remains unclear whether this preference reflects sensitivity to individual temporal features (e.g., pulse duration, interpulse interval) or to derived temporal relationships (e.g., pulse rate, pulse period, duty cycle) that emerge from their combination. We independently varied pulse duration and interpulse interval across a broad stimulus space and quantified tethered-walking phonotaxis using a switch-following paradigm. Behavioural responses formed a structured tuning surface, with high performance along a diagonal corresponding to 50 pulses/s, as well as elevated responses for a restricted range of pulse durations across a wide range of interpulse intervals. Responses failed to collapse across stimuli sharing the same pulse rate or pulse period, indicating that these features alone do not determine recognition. Instead, behaviour was best explained by the interacting effects of pulse duration and interpulse interval. These results demonstrate that song recognition in O. ochracea is multidimensional, with pulse rate tuning emerging from an underlying feature space rather than a single encoded parameter.

animal behavior and cognition↗

bioRxiv2025

Experience from an HTS campaign: Investigation of susceptibility and rescue of SARS-CoV-2 nsp3 protease assay from metal contamination

Different biochemical assays yield different rates of false positives than others either due to the nature of the enzyme, the technology associated with the assay, or properties of the compounds being screened. Ensuring that the right counter-screens are in place to identify false positives without wasting time and resources on them is of great importance. Herein we describe the results of a high throughput screen (HTS) against non-structural protein 3 (nsp3) protease PLPro, which resulted exclusively in false-positive hits. By triaging hit compounds through purification of metal chelating resin, we identified contamination by either copper or palladium as the most likely source of false positives from the library screening campaign. We then performed a systematic assessment of the vulnerability of nsp3 protease screening to metal contamination and evaluated common additives to combat the inhibitory effects of different metal salts. We further conducted a thorough survey of the literature reports of nsp3 HTS campaigns with a focus on the presence of additives and what metal susceptibility was likely, given the results of our work. We conclude that the majority of reported nsp3 screens are susceptible to copper contamination with a smaller proportion also potentially susceptible to palladium contamination.

biochemistry↗

bioRxiv2025

SAMP-Score: A morphology-based machine learning classification method for screening pro-senescence compounds in p16 positive cancer cells

BackgroundSenescence identification is rendered challenging due to a lack of universally available biomarkers. This represents a bottleneck in efforts to develop pro-senescence therapeutics - agents designed to induce the arrest of cellular proliferation associated with a senescence response in cancer cells for therapeutic gain. This is particularly true in contexts such as basal-like breast cancer (BLBC), which often express high levels of widely reported senescence hallmarks, which has led to the designation of these subtypes as senescence marker positive (Sen-Mark+). Unfortunately, these are often cancers with the most limited treatment options, where novel pro-senescence compounds would be of potential clinical utility. ResultsTo address these challenges, we have developed SAMP-Score, a machine learning classification tool for identifying senescence induction in Sen-Mark+ cancers. This technique builds upon our previous observation that senescent cells develop distinct senescence-associated morphological profiles (SAMPs), which can be assessed readily in traditionally challenging contexts for senescence identification, including high-throughput screens. ConclusionsThrough application of SAMP-Score, we have identified QM5928, a novel pro-senescence compound, that is able to induce senescence in a variety of Sen-Mark+ cancers and has potential utility as a tool molecule to explore the mechanisms and pathways through which senescence induction occurs in these cells.

cancer biology↗

bioRxiv2024

Temperature effects on interspecific eavesdropping in the wild

Mating signals are targets of conspecific signal recognition and sexual selection, but are also subject to abiotic temperature effects and to biotic interspecific eavesdroppers. In crickets, the male calling song becomes faster at warmer temperatures, and female crickets recognition of male song tracks temperature in a coordinated manner, termed temperature coupling. But female crickets are not the only ecologically relevant listeners: some cricket species are parasitized by Ormia ochracea, a parasitoid fly which finds its cricket hosts by eavesdropping on male cricket song. How temperature affects parasitoid fly phonotaxis to song is largely unexplored, with only one previous study conducted under field conditions. Here we explore six possible patterns of thermal effects on fly responses to cricket song, including temperature coupling, using field playbacks of synthetic Gryllus lineaticeps songs designed to be species-typical at various temperatures. We find that temperature does affect fly response, but that the temperature deviation of songs from ambient does not impact numbers of flies caught. We extend this finding by comparing the temperatures of the air and ground to show that temperature coupling is unlikely to be effective given microhabitat variation and differential rates of cooling in the evening hours when flies are most active. Our results can be interpreted more broadly to suggest (i) temperature effects on intraspecific communication systems may be more tightly coupled than are effects on interspecific eavesdropping, and (ii) variation in thermal microhabitats in the field make it difficult to translate laboratory physiological responses to natural selection in the wild. Lay SummaryMating signals and signal recognition change with temperature, and sometimes mating signals are intercepted by predators or parasites. By using playbacks of cricket song in the wild, we show that temperature changes do affect the response of a parasitoid fly to cricket song. However, parasitoid responses are not tightly coupled to temperature induced changes in cricket song, in part due to unpredictable variation in microhabitat temperatures typical of crickets and flies.

animal behavior and cognition↗

bioRxiv2023

A comprehensive analysis of rheumatoid arthritis B cells reveals the importance of CD11c+ve double-negative-2 B cells as the major synovial plasma cell precursor.

B cells are key pathogenic drivers of chronic inflammation in rheumatoid arthritis (RA). There is limited understanding of the relationship between synovial B cell subsets and pathogenic antibody secreting cells (ASCs). This knowledge is crucial for the development of targeted therapies. Here, we combine flow cytometry of circulating B cells with single-cell RNA and paired repertoire sequencing of over 27,000 synovial B cells from patients with established RA. Twelve B cell clusters were identified including previously recognised subsets, and a novel cluster that strongly expressed heat shock proteins. All lineages identified by trajectory analysis contribute to the DN2 B cell population, which is the major precursor to synovial ASCs. This was further supported by B cell receptor (BCR) lineage analysis, which revealed clonal relationships between DN2 cells and ASCs. This study advances our understanding of B cells in RA and reveals the origin of pathogenic ASCs in the RA synovium.

immunology↗

bioRxiv2020

Characterization of protease activity of Nsp3 from SARS-CoV-2 and its in vitro inhibition by nanobodies

Of the 16 non-structural proteins (Nsps) encoded by SARS CoV-2, Nsp3 is the largest and plays important roles in the viral life cycle. Being a large, multidomain, transmembrane protein, Nsp3 has been the most challenging Nsp to characterize. Encoded within Nsp3 is the papain-like protease PLpro domain that cleaves not only the viral protein but also polyubiquitin and the ubiquitin-like modifier ISG15 from host cells. We here compare the interactors of PLpro and Nsp3 and find a largely overlapping interactome. Intriguingly, we find that near full length Nsp3 is a more active protease compared to the minimal catalytic domain of PLpro. Using a MALDI-TOF based assay, we screen 1971 approved clinical compounds and identify five compounds that inhibit PLpro with IC50s in the low micromolar range but showed cross reactivity with other human deubiquitinases and had no significant antiviral activity in cellular SARS-CoV-2 infection assays. We therefore looked for alternative methods to block PLpro activity and engineered competitive nanobodies that bind to PLpro at the substrate binding site with nanomolar affinity thus inhibiting the enzyme. Our work highlights the importance of studying Nsp3 and provides tools and valuable insights to investigate Nsp3 biology during the viral infection cycle.

biochemistry↗

bioRxiv2020

Insights into glycan import by a prominent gut symbiont

In Bacteroidetes, one of the dominant phyla of the mammalian gut, active uptake of large nutrients across the outer membrane is mediated by SusCD protein complexes via a "pedal bin" transport mechanism. However, many features of SusCD function in glycan uptake remain unclear, including ligand binding, the role of the SusD lid and the size limit for substrate transport. Here we characterise the {beta}2,6 fructo-oligosaccharide (FOS) importing SusCD from Bacteroides thetaiotaomicron (Bt1762-Bt1763) to shed light on SusCD function. Co-crystal structures reveal residues involved in glycan recognition and suggest that the large binding cavity can accommodate several substrate molecules, each up to [~]2.5 kDa in size, a finding supported by native mass spectrometry and isothermal titration calorimetry. Mutational studies in vivo provide functional insights into the key structural features of the SusCD apparatus and cryo-EM of the intact dimeric SusCD complex reveals several distinct states of the transporter, directly visualising the dynamics of the pedal bin transport mechanism.

microbiology↗

bioRxiv2020

Rare protein coding variants implicate genes involved in risk of suicide death

Suicide death is a worldwide health crisis, claiming close to 800,000 lives per year. Recent evidence suggests that prediction and prevention challenges may be aided by discoveries of genetic risk factors. Here we focus on the role of rare (MAF <1%), putatively functional single nucleotide polymorphisms (SNPs) in suicide death using the large genetic resources available in the Utah Suicide Genetic Risk Study (USGRS). We conducted a single-variant association analysis of 30,377 rare putatively functional SNPs present on the PsychArray genotyping array in 2,672 USGRS suicides of non-Finnish European (NFE) ancestry and 51,583 publicly available NFE controls from gnomAD, with additional follow-up analyses using an independent control sample of 21,324 NFE controls from the Psychiatric Genomics Consortium. SNPs underwent rigorous quality control, and among SNPs meeting significance thresholds, we considered only those that were validated in sequence data. We identified five novel, high-impact, rare SNPs with significant associations with suicide death (SNAPC1, rs75418419; TNKS1BP1, rs143883793; ADGRF5, rs149197213; PER1, rs145053802; and ESS2, rs62223875). Both PER1 and SNAPC1 have other supporting gene-level evidence of suicide risk, and an association with bipolar disorder has been reported for PER1 and with schizophrenia for PER1, TNKS1BP1, and ESS2. Three genes (PER1, TNKS1BP1, and ADGRF5), with additional genes implicated by GWAS studies on suicidal behavior, showed significant enrichment in immune system, homeostatic and signal transduction processes. Pain, depression, and accidental trauma were the most prevalent phenotypes in electronic medical record data for the categories assessed. These findings suggest an important role for rare variants in suicide risk and provide new insights into the genetic architecture of suicide death. Furthermore, we demonstrate the added utility of careful assessment of genotyping arrays in rare variant discovery.

genetics↗

bioRxiv2019

Rheumatoid arthritis patients express a skewed repertoire of polyclonal, hypomutated B-cell receptors

ObjectivesThe success of B cell depletion therapy in rheumatoid arthritis (RA) therapy testifies to their importance in disease pathogenesis, but the precise B cells mediating this are unclear. For example, it is unknown if RA patients predominantly express a limited number of circulating clonally expanded populations of B cells with highly mutated B cell antigen receptors (BCRs) that would constitute a shared antigen driven response.\n\nMethodsTo address this, we have undertaken the largest study to date utilising next generation sequencing (NGS), to identify the full length of the peripheral blood BCR sequences from the antigen-binding heavy chain. Between 25,000 to 200,000 BCR sequences per patient were analysed from 127 newly diagnosed RA patients, 16 heathy controls, 16 RA patients with established disease and 8 paired blood and synovial samples. This was complemented with B cell subset analysis from an additional 64 RA patients and 22 healthy controls.\n\nResultsRA patients expressed a significantly higher percentage of circulating poorly mutated polyclonal IgG+ve variable heavy (IgG-Vh) BCR sequences, both at the time of diagnosis and following treatment. These sequences resided predominantly within TNF-alpha secreting IgG+veCD27-ve B cells, that were expanded in RA peripheral blood and enriched in the rheumatoid synovium. Surprisingly, peripheral and synovial B cell repertoires of RA patients are quite distinct, sharing very few IgG sequences.\n\nConclusionsThis is the first report to conclusively establish that a substantial component of the peripheral B cell repertoire in RA consists of polyclonal hypomutated IgG+ve BCRs that may play a critical role in driving an autoimmune mediated inflammation.

immunology↗

bioRxiv2019

Drug screening to identify compounds to act as co-therapies for the treatment of pathogenic Burkholderia

Burkholderia pseudomallei is a soil-dwelling organism present throughout the tropics, and is the causative agent of melioidosis, a disease that is believed to kill 89,000 people per year. It is naturally resistant to most currently available antibiotics. The most efficacious treatment for melioidosis requires at least two weeks of intravenous treatment with ceftazidime or meropenem. This places a large treatment burden on the predominantly middle income nations where the majority of disease occurs. We have established a high-throughput assay for compounds that could be used as a co-therapy to potentiate the effect of ceftazidime, using the related non-pathogenic bacterium Burkholderia thailandensis as a surrogate. Optimization of the assay gave a Z factor of 0.68. We screened a library of 61,250 compounds, and identified 29 compounds with a pIC50 (-log10(IC50)) greater than five. Detailed investigation allowed us to down select to six \"best in class\" compounds, which included the licensed drug chloroxine. Co-treatment of B. thailandensis with ceftazidime and chloroxine reduced culturable cell numbers by two orders of magnitude over 48 hours compared to treatment with ceftazidime alone. Hit expansion around chloroxine was performed using commercially available compounds. Minor modifications to the structure abolished activity, suggesting that chloroxine likely acts against a specific target. Finally, preliminary data also demonstrates the utility of chloroxine to act as a co-therapy to potentiate the effect of ceftazidime against B. pseudomallei. This approach successfully identified potential co-therapies for a recalcitrant Gram-negative bacterial species. Our assay could be used more widely to aid in chemotherapy against these bacteria.

microbiology↗

bioRxiv2019

Neocortical inhibitory interneuron subtypes display distinct responses to synchrony and rate of inputs

Populations of neurons in the neocortex can carry information with both the synchrony and the rate of their spikes. However, it is unknown whether distinct subtypes of neurons in the cortical microcircuit are more sensitive to information carried by synchrony versus rate. Here, we address this question using patterned optical stimulation in slices of barrel cortex from transgenic mouse lines labelling distinct interneuron populations: fast-spiking parvalbumin-positive (PV+) and somatostatin-positive (SST+) interneurons. We use optical stimulation of channelrhodopsin-2 (ChR2) expressing excitatory neurons in layer 2/3 in order to encode a random 1-bit signal in either the synchrony or rate of activity in presynaptic cells. We then examine the mutual information between this 1-bit signal and the voltage and spiking responses in PV+ and SST+ interneurons. Generally, we find that both interneuron types carry more information than GFP negative (GFP-) control cells. More specifically, we find that for a synchrony encoding, PV+ interneurons carry more information in the first 5 milliseconds, while both interneuron subtypes carry more information than negative controls in their later response. We also find that for a rate encoding, SST+ interneurons carry more information than either PV+ or negative controls after several milliseconds. These data demonstrate that inhibitory interneuron subtypes in the neocortex have distinct responses to information carried by synchrony versus rates of spiking.

neuroscience↗

bioRxiv2017

Identification of genome-wide significant shared genomic segments in large extended Utah families at high risk for completed suicide

Suicide is the 10th leading cause of death in the US. While environment has undeniable impact, evidence suggests genetic factors play a significant role in completed suicide. We linked a resource of >4,500 DNA samples from completed suicides obtained from the Utah Medical Examiner to genealogical records and medical records data available on over 8 million individuals. This linking has resulted in the identification of high-risk extended families (7-9 generations) with significant familial risk of completed suicide. Familial aggregation across distant relatives minimizes effects of shared environment, provides more genetically homogeneous risk groups, and magnifies genetic risks through familial repetition. We analyzed Illumina PsychArray genotypes from suicide cases in 43 high-risk families, identifying 30 distinct shared genomic segments with genome-wide evidence (p=2.02E-07 to 1.30E-18) of segregation with completed suicide. The 207 genes implicated by the shared regions provide a focused set of genes for further study; 18 have been previously associated with suicide risk. While PsychArray variants do not represent exhaustive variation within the 207 genes, we investigated these for specific segregation within the high-risk families, and for association of variants with predicted functional impact in ~1300 additional Utah suicides unrelated to the discovery families. None of the limited PsychArray variants explained the high-risk family segregation; sequencing of these regions will be needed to discover segregating risk variants, which may be rarer or regulatory. However, additional association tests yielded four significant PsychArray variants (SP110, rs181058279; AGBL2, rs76215382; SUCLA2, rs121908538; APH1B, rs745918508), raising the likelihood that these genes confer risk of completed suicide.

genetics↗

bioRxiv2017

Demography and selection shape transcriptomic divergence in field crickets

Gene flow, demography, and selection can result in similar patterns of genomic variation and disentangling their effects is key to understanding speciation. Here, we assess transcriptomic variation to unravel the evolutionary history of Gryllus rubens and Gryllus texensis, cryptic field cricket species with highly divergent mating behavior. We infer their demographic history and screen their transcriptomes for footprints of selection in the context of the inferred demography. We find strong support for a long history of bidirectional gene flow, which ceased during the late Pleistocene, and a bottleneck in G. rubens consistent with a peripatric origin of this species. Importantly, the demographic history has likely strongly shaped patterns of neutral genetic differentiation (empirical FST distribution). Concordantly, FST based selection detection uncovers a large number of outliers, likely comprising many false positives, echoing recent theoretical insights. Alternative genetic signatures of positive selection, informed by the demographic history of the sibling species, highlighted a smaller set of loci; many of these are candidates for controlling variation in mating behavior. Our results underscore the importance of demography in shaping overall patterns of genetic divergence and highlight that examining both demography and selection facilitates a more complete understanding of genetic divergence during speciation.

evolutionary biology↗