Pauli Murray in the 1930s: portraits and post-soul eccentricity

In my thesis I follow the qualities in Murray’s life that suggest contrariety and eccentricity. In particular, I trace Murray’s performances in her portraits from the 1930s, which display her racial, gender, and sex reinvention. I illuminate these portraits as markers of Post-Soul Eccentricity to place Murray in a tradition in which her quare performance can be understood and suggest that her offbeat performances were part of her politics invested in Queer World-Making. I locate these ideas in portraits of Pauli Murray’s scrapbook viewed synchronously with her autobiography, Song in A Weary Throat: An American Pilgrimage (1987) and biographical sources

Promoting resilience and biodiversity in tropical agricultural landscapes

Tropical species are facing multiple environmental pressures, whereby agricultural expansion is causing rainforest loss and climate warming is resulting in range shifts to higher elevations. In Southeast Asia, biodiversity is severely threatened by oil palm expansion and much of the remaining lowland rainforest persists within isolated fragments and protected areas (PAs). I assessed the permeability of oil palm plantations to forest dependent species by examining boundary crossing abilities of fruit-feeding butterflies. I showed that crossing was dominated by species that could potentially breed within oil palm plantations, suggesting that plantations may act as dispersal barriers to forest species. Using the PA network on Borneo as a model system, I examined the spatial distribution of climate within PAs in future, and examined the connectedness of PAs along elevation gradients. For the majority (~60-90%) of PAs, which were predominantly situated at low elevation, analogous climates in future will only be available at higher elevation, requiring species to move in order to track cooler climates. However, over half (~60-82%) of these PAs were too isolated for species with poor dispersal abilities to reach cooler, higher elevation PAs. Finally, I used a novel modelling approach based on electrical circuit theory to identify important areas of rainforest connecting PAs along elevation gradients, and showed considerable spatial overlap in expansion routes under contrasting projections of warming. Protected area extent on Borneo will need to increase by approximately one fifth (~17%) to conserve all important rainforest connections between PAs. I conclude that rainforest species may be particularly vulnerable to the impacts of continued agricultural expansion and climate change, as they may be unable to move across fragmented landscapes due to lack of connecting rainforest habitat. Management to improve linkage of PAs and ensure protection of important dispersal routes along elevation gradients should be a conservation priority

Edge effects of oil palm plantations on tropical anuran communities in Borneo

The expansion of industrial agriculture (oil palm) has significantly reduced lowland tropical diversity through direct loss or alteration of habitat, leading to habitat fragmentation and edge effects. Edge effects can have serious impacts on species diversity and community dynamics. To assess the effect of oil palm plantation edges on anuran communities in Sabah, Malaysian Borneo, we surveyed anuran species and measured structural habitat and landscape parameters at 74 sites spread across forest and plantation habitats along the Kinabatangan River. We then evaluated how anuran species richness and assemblage composition varied in relation to these environmental parameters. Relative species richness was higher at forest sites, compared to oil palm plantation sites. Plantation sites were dominated by wide-ranging terrestrial species, and assemblage composition varied mostly in relation to standing surface water. Forest habitats supported both more endemic and arboreal species. Variability on anuran assemblage composition in forest habitats was greatest in relation to distance to forest edge followed by canopy density, which was also partially correlated with forest edge distance. Moreover, anuran species richness in forest habitats declined as proximity to the forest-plantation interface increased, and as canopy density decreased. Our study provides further evidence that oil palm plantations provide little conservation benefit to anurans. Furthermore, oil palm plantations appear to have adverse pervasive impacts on amphibian diversity considerable distances into adjacent forest areas. These findings suggest that in order for small patches or narrow corridors of retained forest in landscapes managed for oil palm to maintain biodiversity values in the long term, their sizes and widths need to adequately account for the considerable influence of edge effects

Supporting decision-making by companies in delivering their climate net-zero and nature recovery commitments: synthesizing current information and identifying research priorities in rainforest restoration

Many companies are making ambitious pledges to achieve positive impacts for climate and nature by financing restoration of carbon- and biodiversity- rich natural habitats. However, companies cannot make evidence-based choices that will deliver successful restoration if the scientific information required to guide investment has not been synthesised in a way that they can use, or there are knowledge gaps. To explore this issue, share information, and identify knowledge gaps and research priorities, we bring together researchers, a conservation NGO and a multinational consumer goods company (Unilever), focusing on Southeast Asian rainforests. These habitats offer significant restoration opportunities for carbon and biodiversity in areas that have been degraded by commercial logging and agriculture. We find that procedures for carbon restoration are much better developed than those for biodiversity, and that new research is urgently needed to deliver evidence-based biodiversity restoration. Companies need to be confident that their actions are fit-for-purpose to meet their environmental pledges. Achieving successful restoration outcomes will require co-designed projects with the potential to deliver positive co-benefits for carbon, biodiversity and local livelihoods

Testing the benefits of conservation set-asides for improved habitat connectivity in tropical agricultural landscapes

Habitat connectivity is important for tropical biodiversity conservation. Expansion of commodity crops, such as oil palm, fragments natural habitat areas, and strategies are needed to improve habitat connectivity in agricultural landscapes. The Roundtable on Sustainable Palm Oil (RSPO) voluntary certification system requires that growers identify and conserve forest patches identified as High Conservation Value Areas (HCVAs) before oil palm plantations can be certified as sustainable. We assessed the potential benefits of these conservation set-asides for forest connectivity. We mapped HCVAs and quantified their forest cover in 2015. To assess their contribution to forest connectivity, we modelled range expansion of forest-dependent populations with five dispersal abilities spanning those representative of poor dispersers (e.g. flightless insects) to more mobile species (e.g. large birds or bats) across 70 plantation landscapes in Borneo. Because only 21% of HCVA area was forested in 2015, these conservation set-asides currently provide few connectivity benefits. Compared to a scenario where HCVAs contain no forest (i.e. a no-RSPO scenario), current HCVAs improved connectivity by ~3% across all dispersal abilities. However, if HCVAs were fully reforested, then overall landscape connectivity could improve by ~16%. Reforestation of HCVAs had the greatest benefit for poor to intermediate dispersers (0.5–3 km per generation), generating landscapes that were up to 2.7 times better connected than landscapes without HCVAs. By contrast, connectivity benefits of HCVAs were low for highly mobile populations under current and reforestation scenarios, because range expansion of these populations was generally successful regardless of the amount of forest cover. Synthesis and applications. The Roundtable on Sustainable Palm Oil (RSPO) requires that High Conservation Value Areas (HCVAs) be set aside to conserve biodiversity, but HCVAs currently provide few connectivity benefits because they contain relatively little forest. However, reforested HCVAs have the potential to improve landscape connectivity for some forest species (e.g. winged insects), and we recommend active management by plantation companies to improve forest quality of degraded HCVAs (e.g. by enrichment planting). Future revisions to the RSPO's Principles and Criteria should also ensure that large (i.e. with a core area >2 km 2) HCVAs are reconnected to continuous tracts of forest to maximize their connectivity benefits

Proximity to forest mediates trade-offs between yields and biodiversity of birds in oil palm smallholdings

There is much debate about how best to mitigate the effects of agricultural expansion on biodiversity, especially in the tropics. Recent studies have emphasized that proximity to natural habitats can enhance farmland biodiversity, yet few studies have examined whether or not such proximity mediates local trade-offs between yields and biodiversity, and hence alters conclusions about the ecological benefits of alternative farming strategies. Here we examine yield-biodiversity trade-offs, focusing on birds in oil palm smallholdings at different distances from remaining areas of forest, including a large forest reserve, in Ghana. We found significantly fewer birds on higher-yielding than lower-yielding farms, in terms of both species richness and abundance. For forest specialist birds (likely to be highly vulnerable to conversion of land to agriculture) we also found a greater trade-off (i.e., lower richness and abundance for a given yield) at farms further from forest, to the extent that increasing distance to the nearest forest from 1 to 10 km had a similar effect as a 3- to 5-fold increase in fruit yield brought about by increased intensification. Our study highlights the importance of accounting for the effects of natural forest in the landscape when considering agricultural policies for biodiversity protection, underlining the importance of a landscape-scale approach to conservation

Incorporating connectivity into conservation planning for the optimal representation of multiple species and ecosystem services

Funding was provided by the Rainforest Trust foundation. Support was also provided by the Sabah Forest Department, Forest Research Centre, the South East Asia Rainforest Research Partnership, the U.N. Development Programme, the Universiti Malaysia Sabah (FRGS0414-STWN-1/2015), PACOS Trust, BC Initiative, the Natural Environment Research Council UK (grant NE/R009597/1), and the Universities of Aberdeen, Montana, and York. We are grateful to the numerous researchers that collected the data used in our analyses, as well as the local communities and government staff who manage forested areas across Sabah.Peer reviewedPostprin

Caveolae in Rabbit Ventricular Myocytes: Distribution and Dynamic Diminution after Cell Isolation

Caveolae are signal transduction centers, yet their subcellular distribution and preservation in cardiac myocytes after cell isolation are not well documented. Here, we quantify caveolae located within 100 nm of the outer cell surface membrane in rabbit single-ventricular cardiomyocytes over 8 h post-isolation and relate this to the presence of caveolae in intact tissue. Hearts from New Zealand white rabbits were either chemically fixed by coronary perfusion or enzymatically digested to isolate ventricular myocytes, which were subsequently fixed at 0, 3, and 8 h post-isolation. In live cells, the patch-clamp technique was used to measure whole-cell plasma membrane capacitance, and in fixed cells, caveolae were quantified by transmission electron microscopy. Changes in cell-surface topology were assessed using scanning electron microscopy. In fixed ventricular myocardium, dual-axis electron tomography was used for three-dimensional reconstruction and analysis of caveolae in situ. The presence and distribution of surface-sarcolemmal caveolae in freshly isolated cells matches that of intact myocardium. With time, the number of surface-sarcolemmal caveolae decreases in isolated cardiomyocytes. This is associated with a gradual increase in whole-cell membrane capacitance. Concurrently, there is a significant increase in area, diameter, and circularity of sub-sarcolemmal mitochondria, indicative of swelling. In addition, electron tomography data from intact heart illustrate the regular presence of caveolae not only at the surface sarcolemma, but also on transverse-tubular membranes in ventricular myocardium. Thus, caveolae are dynamic structures, present both at surface-sarcolemmal and transverse-tubular membranes. After cell isolation, the number of surface-sarcolemmal caveolae decreases significantly within a time frame relevant for single-cell research. The concurrent increase in cell capacitance suggests that membrane incorporation of surface-sarcolemmal caveolae underlies this, but internalization and/or micro-vesicle loss to the extracellular space may also contribute. Given that much of the research into cardiac caveolae-dependent signaling utilizes isolated cells, and since caveolae-dependent pathways matter for a wide range of other study targets, analysis of isolated cell data should take the time post-isolation into account

Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity

The combined impact of common and rare exonic variants in COVID-19 host genetics is currently insufficiently understood. Here, common and rare variants from whole-exome sequencing data of about 4000 SARS-CoV-2-positive individuals were used to define an interpretable machine-learning model for predicting COVID-19 severity. First, variants were converted into separate sets of Boolean features, depending on the absence or the presence of variants in each gene. An ensemble of LASSO logistic regression models was used to identify the most informative Boolean features with respect to the genetic bases of severity. The Boolean features selected by these logistic models were combined into an Integrated PolyGenic Score that offers a synthetic and interpretable index for describing the contribution of host genetics in COVID-19 severity, as demonstrated through testing in several independent cohorts. Selected features belong to ultra-rare, rare, low-frequency, and common variants, including those in linkage disequilibrium with known GWAS loci. Noteworthily, around one quarter of the selected genes are sex-specific. Pathway analysis of the selected genes associated with COVID-19 severity reflected the multi-organ nature of the disease. The proposed model might provide useful information for developing diagnostics and therapeutics, while also being able to guide bedside disease management. © 2021, The Author(s)

Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice