Biology subjects

Quinn, L.

Publications and source records attributed to Quinn, L..

8 recordsLinked to original sources

bioRxiv2026

AN UPDATED POPULATION ESTIMATE FOR NORTHERN GANNETS ACROSS THEIR NORTH-EAST ATLANTIC BREEDING RANGE FOLLOWING THE 2022 OUTBREAK OF HIGH PATHOGENICITY AVIAN INFLUENZA

Northern gannets (Morus bassanus) have been regarded as a seabird success story, due to population increases throughout the 20th and 21st century contrasting with global seabird declines. However, in 2022 gannets experienced a severe outbreak of High Pathogenicity Avian Influenza (HPAI) across their global distribution, leading to an urgent need to reassess their population status. This study presents breeding gannet census numbers for 2023/24 from all colonies across the North-East Atlantic metapopulation (Great Britain, Ireland, the Channel Islands, Iceland, Norway, the Faroe Islands, France, Germany, Russia). Gannet numbers decreased by 17% across the North-East Atlantic metapopulation between the 2013/14 and 2023/24 census from 414,598 to 345,854 apparently occupied sites (AOS), a global decrease of at least 13%. The bulk of the reduction in AOS was driven by the largest colonies (>10,000 AOS) each losing tens of thousands of AOS. These figures likely underestimate the impact of the HPAI outbreak worldwide, since most colonies will have increased between the last census in 2013/14 and the 2022 HPAI outbreak, and the Canadian breeding population was last counted pre-HPAI outbreak. Scotland still holds the largest proportion of both the North-East Atlantic metapopulation (59%), and the world population (46%), while Great Britain, Ireland and the Channel Islands together hold 83% of the North-East Atlantic metapopulation and 64% of the world population. This study not only presents an updated population census for gannets in the North-East Atlantic but illustrates the large-scale impacts of a disease outbreak on a seabird species across its global range and highlights the importance of more regular census efforts to better quantify the demographic consequences of such events.

ecology↗

bioRxiv2026

Psi represses EGFR signalling in the neural stem cell niche to inhibit neuroblast proliferation in the Drosophila brain

In mammals, neural stem cells (NSCs) generate the neurons and glia essential to brain development, while defective NSCs drive brain cancer (glioma). NSC fate is not only controlled cell intrinsically, but also relies on signalling from the cellular microenvironment, or stem cell niche. Defective communication between NSCs and their niche can, therefore, drive stem cell renewal over differentiation to promote glioma. Here, we demonstrate that the orthologue of glioma-driver mutation FUBP1, Drosophila Psi, is essential in the cortex glia, the NSC niche, for preventing NSC overproliferation. We further demonstrate that Psi controls NSC fate through direct transcriptional repression of EGFR ligands, spitz (spi) and gurken (grk); with spi required cell intrinsically to enable proliferative growth of cortex glia, while grk functions cell extrinsically to control NSC fate. These observations highlight the complexity of EGFR function in modulating communication between NSCs and their niche. Our findings demonstrate the importance of understanding the nuances of intrinsic and extrinsic control of NSC fate, mechanisms of cell-cell communication critical to animal development that will provide insight into FUBP1/EGFR-driven glioma.

developmental biology↗

bioRxiv2026

Daily HIV pre-exposure prophylaxis enhances monocyte activation and effector function and reprogrammes cellular metabolism.

BackgroundPre-exposure prophylaxis (PrEP) with tenofovir/emtricitabine (TDF/FTC) is highly effective for HIV prevention. While antiretroviral therapy (ART) is linked to chronic inflammation in people living with HIV, its direct effects on immune phenotype, function, and metabolism in HIV-negative individuals remain unclear. MethodsGay, bisexual, and other men who have sex with men (gbMSM) on daily TDF/FTC PrEP underwent immunophenotyping and single-cell metabolic profiling using SCENITH. Cytokine and chemokine responses were measured ex vivo and after lipopolysaccharide or Mycobacterium tuberculosis stimulation. These were compared with a demographically similar PrEP-naive cohort, with five individuals followed 6-9 months after PrEP initiation. FindingsMonocytes from people taking PrEP (n=15; median 533 days) exhibited higher activation marker expression (HLA-DR, CD14) ex vivo and enhanced IL-1{beta} and TNF after bacterial challenge compared with PrEP-naive individuals (n=11). Longitudinal follow-up indicated that PrEP initiation increased monocyte activation markers (HLA-DR, CD14, CD40, TNFRI/II) and cytokine production (IL-1{beta}, TNF, GM-CSF, IFN-{gamma}, Granzyme B, MIP-1). Reduced glucose dependency was observed in monocytes, CD56dim NK cells and CD4+ T cells 6-9 months after PrEP initiation. InterpretationDaily TDF/FTC promotes monocyte activation, enhances pro-inflammatory responses, and reprogrammes immune cell metabolism, highlighting ARTs potential to modulate immune-mediated inflammatory pathways in HIV-negative individuals. FundingTrinity Translational Medicine Institute, Trinity College Dublin, Dublin, The Association of Physicians of Great Britain and Ireland, Health Research Board Ireland. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=85 SRC="FIGDIR/small/698427v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@d48088org.highwire.dtl.DTLVardef@1428926org.highwire.dtl.DTLVardef@13a4facorg.highwire.dtl.DTLVardef@144d1f1_HPS_FORMAT_FIGEXP M_FIG C_FIG Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSDespite effective viral suppression with antiretroviral therapy (ART), people living with HIV (PLWHIV) experience persistent immune activation and chronic inflammation that increase their risk of age-associated comorbidities. The extent to which ART itself contributes to this dysregulated immune state remains unclear, as HIV infection confounds most studies. Pre-exposure prophylaxis (PrEP) with tenofovir disoproxil fumarate and emtricitabine (TDF/FTC) offers a unique opportunity to examine the direct immunological effects of ART in HIV-negative individuals. However, few studies have explored how PrEP influences immune cell activation, effector function, or cellular metabolism in the absence of viral infection. Added value of this studyThis study is the first to characterise how daily PrEP with TDF/FTC modulates innate immune activation and cellular metabolism independently of HIV infection. We show that PrEP enhances monocyte activation and effector cytokine production while reprogramming metabolic pathways to reduce glucose dependency in monocytes, NK cells, and CD4 T cells. These findings reveal previously unrecognised immunometabolic effects of ART in HIV-negative individuals, providing mechanistic insight into how ART exposure can shape immune homeostasis in the absence of infection. Implications of all the available evidenceOur findings, together with existing data from PLWHIV, suggest that ART itself can remodel immune and metabolic pathways, potentially contributing to both beneficial and detrimental outcomes. ART-induced immunometabolic reprogramming may underlie persistent inflammation and the early onset of comorbidities observed in treated HIV infection, while also enhancing innate responsiveness to bacterial pathogens such as Mycobacterium tuberculosis. Understanding these mechanisms may inform future strategies to optimise ART regimens and mitigate inflammation-associated complications.

immunology↗

bioRxiv2024

Extensive population structure highlights an apparent paradox of stasis in the impala (Aepyceros melampus)

Impalas are unusual among bovids because they have remained morphologically similar over millions of years - a phenomenon referred to as evolutionary stasis. Here, we sequenced 119 whole genomes from the two extant subspecies of impala, the common (Aepyceros melampus melampus) and black-faced (A. m. petersi) impala. We investigated the evolutionary forces working within the species to explore how they might be associated with its evolutionary stasis as a taxon. Despite being one of the most abundant bovid species, we found low genetic diversity overall, and a phylogeographic signal of spatial expansion from southern to eastern Africa. Contrary to expectations under a scenario of evolutionary stasis, we found pronounced genetic structure between and within the two subspecies with indications of ancient, but not recent, gene flow. Black-faced impala and eastern African common impala populations had more runs of homozygosity than common impala in southern Africa, and, using a proxy for genetic load, we found that natural selection is working less efficiently in these populations compared to the southern African populations. Together with the fossil record, our results are consistent with a fixed-optimum model of evolutionary stasis, in which impalas in the southern African core of the range are able to stay near their evolutionary fitness optimum as a generalist ecotone species, whereas eastern African impalas may struggle to do so due to the effects of genetic drift and reduced adaptation to the local habitat, leading to recurrent local extinction in eastern Africa and re-colonization from the South.

evolutionary biology↗

bioRxiv2023

African bush pigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival

Several African mammals exhibit a phylogeographic pattern where closely related taxa are split between West/Central and East/Southern Africa, but their evolutionary relationships and histories remain controversial. Bushpigs (Potamochoerus larvatus) and red river hogs (P. porcus) are recognised as separate species due to morphological distinctions, a perceived lack of interbreeding at contact, and putatively old divergence times, but historically, they were considered conspecific. Moreover, the presence of Malagasy bushpigs as the sole large terrestrial mammal shared with the African mainland raises intriguing questions about its origin and arrival in Madagascar. Analyses of 67 whole genomes revealed a genetic continuum between the two species, with putative signatures of historical gene flow, variable FST values, and a recent divergence time (<500,000 years). Thus, our study challenges key arguments for splitting Potamochoerus into two species and suggests their speciation might be incomplete. Our findings also indicate that Malagasy bushpigs diverged from southern African populations and underwent a limited bottleneck 1,000-5,000 years ago, concurrent with human arrival in Madagascar. These results shed new light on the evolutionary history of an iconic and widespread African genus and provide insight into the longstanding biogeographic puzzle surrounding the bushpigs presence in Madagascar.

evolutionary biology↗

bioRxiv2022

Population Structure and Migration in the Eastern Highlands of Papua New Guinea; a Region Impacted by the kuru Epidemic

Populations of the Eastern Highlands of Papua New Guinea (EHPNG, area 11,157 km2) lived in relative isolation from the rest of the world until the mid-20th century, and the region contains a wealth of linguistic and cultural diversity. Notably, several populations of EHPNG were devastated by an epidemic prion disease, kuru, which at its peak in the mid-twentieth century led to some villages being almost depleted of adult women. Until now, population genetic analyses to learn about genetic diversity, migration, admixture and the impact of the kuru epidemic have been restricted to a small number of variants or samples. Here, we present a population genetic analysis of the region based on genome-wide genotype data of 943 individuals from 21 linguistic groups and 68 villages in EHPNG, including 34 villages in the South Fore linguistic group, which the group most affected by kuru. We find a striking degree of genetic population structure in the relatively small region (average FST between linguistic groups 0.024; area similar to Jamaica). The genetic population structure correlates well with linguistic grouping, with some noticeable exceptions. Also, we find evidence of a series of discrete admixture events that appear to coincide with previously expected introduction dates and movement of the sweet potato in the region. Finally, we find signatures of more recent migration within the EHPNG region and observe a substantial excess of female migration into the heavily kuru-affected South Fore linguistic group (p=0.0017, Chi Squared Test), likely reflecting the sex-bias in incidence of kuru. These data provide an in-depth look at the population genetics of a region devastated by a prion disease epidemic and which was until recently relatively isolated from the rest of the world.

genetics↗

bioRxiv2019

Zymobacter palmae pyruvate decarboxylase is less efficient than that of Zymomonas mobilis for ethanol production in metabolically engineered Synechocystis sp PCC6803

Pyruvate decarboxylase (PDC) from Zymobacter palmae (ZpPDC) has been reported to have a lower Km the Zymomonas mobilis PDC (ZmPDC). ZpPDC was combined with native slr1192 alcohol dehydrogenase (adh) in an attempt to increase ethanol production in the photoautotrophic cyanobacterium Synechocystis sp. PCC 6803 over constructs created with Zmpdc. Native (Zppdc) and codon optimised (ZpOpdc) versions of the ZpPDC were cloned into a construct where the pdc expression was controlled via the psbA2 light inducible promoter from Synechocystis PCC 6803. These constructs were transformed into wildtype Synechocystis PCC 6803. Ethanol levels were then compared with identical constructs containing the Zmpdc. While strains with the Zppdc (UL071) and ZpOpdc (UL072) constructs did produce ethanol, levels were lower compared to a control strain (UL004) expressing the pdc from Zymomonas mobilis. The utilisation of a PDC with a lower Km from Zymobacter palmae did not result in enhanced ethanol production in Synechocystis PCC 6803.

microbiology↗

bioRxiv2019

A simple and efficient CRISPR technique for protein tagging

Genetic knock-in using homology directed repair is an inefficient process, requiring selection of few modified cells and hindering its application to primary cells. Here we describe Homology independent gene Tagging (HiTag), a method to tag a protein of interest by CRISPR in up to 66% transfected cells with one single electroporation. The technique has proven effective in various cell types, can be used to knock in a fluorescent protein for live cell imaging, to modify the cellular location of a target protein and to monitor levels of a protein of interest by a luciferase assay in primary cells.

cell biology↗