Community-Based Natural Resource Management in the Western United States: A Pilot Study of Capacity

32 pagesThis paper was made possible by grants from the Ford Foundation, U.S. Endowment for Forestry and Communities, and U.S.D.A. Rural Development

Interaction generalisation and demographic feedbacks drive the resilience of plant–insect networks to extinctions

Understanding the processes driving ecological resilience, that is the extent to which systems retain their structure while absorbing perturbations, is a central challenge for theoretical and applied ecologists. Plant–insect assemblages are well-suited for the study of ecological resilience as they are species-rich and encompass a variety of ecological interactions that correspond to essential ecosystem functions. Mechanisms affecting community response to perturbations depend on both the natural history and structure of ecological interactions. Natural history attributes of the interspecific interactions, for example whether they are mutualistic or antagonistic, may affect the ecological resilience by controlling the demographic feedbacks driving ecological dynamics at the community level. Interaction generalisation may also affect resilience, by defining opportunities for interaction rewiring, the extent to which species are able to switch interactions in fluctuating environments. These natural history attributes may also interact with network structure to affect ecological resilience. Using adaptive network models, we investigated the resilience of plant–pollinator and plant–herbivore networks to species loss. We specifically investigated how fundamental natural history differences between these systems, namely the demographic consequences of the interaction and their level of generalisation—mediating rewiring opportunities—affect the resilience of dynamic ecological networks to extinctions. We also create a general benchmark for the effect of network structure on resilience simulating extinctions on theoretical networks with controlled structures. When network structure was static, pollination networks were less resilient than herbivory networks; this is related to their high levels of nestedness and the reciprocally positive feedbacks that define mutualisms, which made co-extinction cascades more likely and longer in plant–pollinator assemblages. When considering interaction rewiring, the high generalisation and the structure of pollination networks boosted their resilience to extinctions, which approached those of herbivory networks. Simulation results using theoretical networks suggested that the empirical structure of herbivory networks may protect them from collapse. Elucidating the ecological and evolutionary processes driving interaction rewiring is key to understanding the resilience of plant–insect assemblages. Accounting for rewiring requires ecologists to combine natural history with network models that incorporate feedbacks between species abundances, traits and interactions. This combination will elucidate how perturbations propagate at community level, reshaping biodiversity structure and ecosystem functions

Population ecology and conservation of aeglids (Crustacea: Decapoda: Aeglidae) in caves from the Alto Ribeira karstic area, São Paulo

Exploratory field surveys were carried out in 2009 to estimate the population size of three troglobitic (Aegla microphthalma from Santana Cave, A. cavernicola from Areias de Baixo Cave and A. leptochela from Paiva Cave) and one troglophile aeglid species (A. marginata from Paiva Cave and Barra Bonita Cave) from the karst region of the Alto Ribeira by means of visual census (all caves) and markrecapture technique (Paiva Cave only). Results were compared with previous population size data obtained in 1994 for the same species and respective localities. A. marginata was no longer found at the Barra Bonita Cave and no A. microphthalma specimens were eye-spotted at the Santana Cave. Thirteen specimens of A. cavernicola were found at the Areias de Baixo Cave. Only Paiva Cave provided enough number of individuals of the co-existing aeglids A. leptochela and A. marginata produced significant population size estimates, which indicated a sharp decline of the cave dwelling population size of both species as compared to previous dataInvestigações de campo realizadas em 2009 objetivaram a determinação do tamanho populacional de três espécies troglóbias (Aegla microphthalma da Caverna Santana, A. cavernicola da Caverna Areias de Baixo e A. leptochela da Gruta dos Paiva) e uma troglófila (A. marginata de duas localidades: Gruta dos Paiva e Gruta Barra Bonita) de eglídeos da região cárstica do Alto Ribeira, por meio das técnicas de censo visual (todas as cavernas) e marcação-e-recaptura (apenas na Gruta dos Paiva). Os resultados foram comparados com dados populacionais anteriores obtidos em 1994 para as mesmas espécies e localidades. Aegla marginata não mais foi encontrada na Gruta Barra Bonita e nenhum exemplar de A. microphthalma foi tampouco avistado na Caverna Santana. Apenas treze exemplares de A. cavernicola foram observados na Caverna Areias de Baixo. Apenas na Gruta dos Paiva foi coletado número suficiente de indivíduos das espécies sintópicas, A. leptochela e A. marginata, que permitisse estimar o tamanho da população destes eglídeos. Os valores obtidos indicam que houve um drástico declínio populacional destas espécies no interior da caverna em comparação com dados pretéritos

Characterisation of the transcriptome and proteome of SARS-CoV-2 reveals a cell passage induced in-frame deletion of the furin-like cleavage site from the spike glycoprotein

Background SARS-CoV-2 is a recently emerged respiratory pathogen that has significantly impacted global human health. We wanted to rapidly characterise the transcriptomic, proteomic and phosphoproteomic landscape of this novel coronavirus to provide a fundamental description of the virus’s genomic and proteomic potential. Methods We used direct RNA sequencing to determine the transcriptome of SARS-CoV-2 grown in Vero E6 cells which is widely used to propagate the novel coronavirus. The viral transcriptome was analysed using a recently developed ORF-centric pipeline. Allied to this, we used tandem mass spectrometry to investigate the proteome and phosphoproteome of the same virally infected cells. Results Our integrated analysis revealed that the viral transcripts (i.e. subgenomic mRNAs) generally fitted the expected transcription model for coronaviruses. Importantly, a 24 nt in-frame deletion was detected in over half of the subgenomic mRNAs encoding the spike (S) glycoprotein and was predicted to remove a proposed furin cleavage site from the S glycoprotein. Tandem mass spectrometry identified over 500 viral peptides and 44 phosphopeptides in virus-infected cells, covering almost all proteins predicted to be encoded by the SARS-CoV-2 genome, including peptides unique to the deleted variant of the S glycoprotein. Conclusions Detection of an apparently viable deletion in the furin cleavage site of the S glycoprotein, a leading vaccine target, shows that this and other regions of SARS-CoV-2 proteins may readily mutate. The furin site directs cleavage of the S glycoprotein into functional subunits during virus entry or exit and likely contributes strongly to the pathogenesis and zoonosis of this virus. Our data emphasises that the viral genome sequence should be carefully monitored during the growth of viral stocks for research, animal challenge models and, potentially, in clinical samples. Such variations may result in different levels of virulence, morbidity and mortality

The Free Fatty Acid-Binding Pocket is a Conserved Hallmark in Pathogenic β-Coronavirus Spike Proteins from SARS-CoV to Omicron

As coronavirus disease 2019 (COVID-19) persists, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) emerge, accumulating spike (S) glycoprotein mutations. S receptor binding domain (RBD) comprises a free fatty acid (FFA)–binding pocket. FFA binding stabilizes a locked S conformation, interfering with virus infectivity. We provide evidence that the pocket is conserved in pathogenic β-coronaviruses (β-CoVs) infecting humans. SARS-CoV, MERS-CoV, SARS-CoV-2, and VOCs bind the essential FFA linoleic acid (LA), while binding is abolished by one mutation in common cold–causing HCoV-HKU1. In the SARS-CoV S structure, LA stabilizes the locked conformation, while the open, infectious conformation is devoid of LA. Electron tomography of SARS-CoV-2–infected cells reveals that LA treatment inhibits viral replication, resulting in fewer deformed virions. Our results establish FFA binding as a hallmark of pathogenic β-CoV infection and replication, setting the stage for FFA-based antiviral strategies to overcome COVID-19

Catalogue of parasites and diseases of the common cockle Cerastoderma edule

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Support for UNRWA's survival

The United Nations Relief and Works Agency for Palestine Refugees in the Near East (UNRWA) provides life-saving humanitarian aid for 5·4 million Palestine refugees now entering their eighth decade of statelessness and conflict. About a third of Palestine refugees still live in 58 recognised camps. UNRWA operates 702 schools and 144 health centres, some of which are affected by the ongoing humanitarian disasters in Syria and the Gaza Strip. It has dramatically reduced the prevalence of infectious diseases, mortality, and illiteracy. Its social services include rebuilding infrastructure and homes that have been destroyed by conflict and providing cash assistance and micro-finance loans for Palestinians whose rights are curtailed and who are denied the right of return to their homeland

"If we use the strength of diversity among researchers we can only improve the quality and impact of our research": Issues of equality, diversity, inclusion, and transparency in the process of applying for research funding

This paper sets out the recommendations that have emerged from a six-month-long exploration and discussion of the processes that take place before research is submitted for funding: the ‘pre-award’ environment. Our work concentrated on how this environment is experienced by researchers at all career stages and from a variety of backgrounds, demographics, and disciplines, as well as by research managers and research support professionals. In the later stages of our exploration, representatives from research funders were also involved in the discussions. The primary component of this project was an analysis of pre-award activities and processes at UK universities, using information collated from workshops with researchers and research management and support staff. The findings of this analysis were presented as a workflow diagram, which was then used to surface issues relating to equality, diversity, inclusion, and transparency in context. The workflow diagram and the issues highlighted by it were used to structure discussions at a symposium for a range of research stakeholders, held in Bristol, UK, in January 2023. The recommendations set out in this paper are drawn from discussions that took place at that event. This paper is not an exhaustive landscape analysis, nor a review of existing research and practice in the area of pre-award processes or of recent thinking on the topics of equality, diversity, and inclusion (EDI). Instead, it aims to summarise and encapsulate the suggestions put forward by the stakeholders during the symposium. These recommendations, from experienced professionals working in the field, are based on their encounters with the issues raised in the project. They do not solely relate to those working on pre-award processes, but may also apply to funders, policymakers, university leaders, and professional associations, since many of the challenges flagged in our research are systemic and cultural, and reach far beyond the research office