Consumer experiences of food environments during the Covid-19 pandemic: global insights from a rapid online survey of individuals from 119 countries

This study investigates consumer experiences of food environments and food acquisition practices during the Covid-19 pandemic. Our rapid assessment online survey featured a convenience sample of 2015 individuals from 119 countries, spanning Western Europe, North America, Latin America, Asia-Pacific, and Africa. Data collection took place in April 2020 during the second month of the pandemic. Participants were recruited via existing networks of the United Nations System Standing Committee on Nutrition, through social media, and by snowballing. The majority of participants were female (71.9%), from low- and middle-income countries (51.0%), and working in nutrition or healthcare (39.3%). Qualitative thematic analysis and descriptive statistics reveal a series of common global experiences related to food availability and accessibility, food prices and affordability, food acquisition practices, and food preparation and consumption. The importance of community food participation, food sharing, and resource allocation are highlighted, along with increasing awareness of healthy diets and food waste. We identify ten synergistic policy entry points to: 1) build resilient and equitable food environments resistant to stresses and shocks; 2) harness positive dietary-related behaviors manifested during the pandemic; and, 3) mitigate the projected nutrition crisis and promote sustainable healthy diets for all

Novel real-time PCR species identification assays for British and Irish bats and their application to a non-invasive survey of bat roosts in Ireland

Detection and monitoring of extant bat populations are crucial for conservation success. Non-invasive genetic analysis of bat droppings collected at roosts could be very useful in this respect as a rapid, cost‐efficient monitoring tool. We developed species‐specific real-time PCR assays for 18 British and Irish bat species to enable non‐invasive, large‐scale distribution monitoring, which were then applied to a field survey in Ireland. One hundred and sixty-four DNA samples were collected from 95 bat roosts, of which 73% of samples were identified to species, and the resident bat species were identified at 89% of roosts. However, identification success varied between roost types, ranging from 22% for underground sites to 92% for bat boxes. This panel of DNA tests will be especially useful in cases where roosts contain multiple species, where the number of bats present is small, or bats are otherwise difficult to directly observe. The methodology could be applied to the surveillance of proposed development sites, post development mitigation measures, distribution surveys, bat box schemes and the evaluation of agri-environmental bat box schemes

Resource competition drives an invasion-replacement event among shrew species on an island

Invasive mammals are responsible for the majority of native species extinctions on islands. While most of these extinction events will be due to novel interactions between species (e.g. exotic predators and naive prey), it is more unusual to find incidences where a newly invasive species causes the decline/extinction of a native species on an island when they normally coexist elsewhere in their overlapping mainland ranges. We investigated if resource competition between two insectivorous small mammals was playing a significant role in the rapid replacement of the native pygmy shrew Sorex minutus in the presence of the recently invading greater white-toothed shrew Crocidura russula on the island of Ireland. We used DNA metabarcoding of gut contents from >300 individuals of both species to determine each species' diet and measured the body size (weight and length) during different stages of the invasion in Ireland (before, during and after the species come into contact with one another) and on a French island where both species have long coexisted (acting as a natural ‘control’ site). Dietary composition, niche width and overlap and body size were compared in these different stages. The body size of the invasive C. russula and composition of its diet changes between when it first invades an area and after it becomes established. During the initial stages of the invasion, individual shrews are larger and consume larger sized invertebrate prey species. During later stages of the invasion, C. russula switches to consuming smaller prey taxa that are more essential for the native species. As a result, the level of interspecific dietary overlap increases from between 11% and 14% when they first come into contact with each other to between 39% and 46% after the invasion. Here we show that an invasive species can quickly alter its dietary niche in a new environment, ultimately causing the replacement of a native species. In addition, the invasive shrew could also be potentially exhausting local resources of larger invertebrate species. These subsequent changes in terrestrial invertebrate communities could have severe impacts further downstream on ecosystem functioning and services

Genetic evidence further elucidates the history and extent of badger introductions from Great Britain into Ireland

The colonization of Ireland by mammals has been the subject of extensive study using genetic methods and forms a central problem in understanding the phylogeography of European mammals after the Last Glacial Maximum. Ireland exhibits a depauperate mammal fauna relative to Great Britain and continental Europe, and a range of natural and anthropogenic processes have given rise to its modern fauna. Previous Europe-wide surveys of the European badger (Meles meles) have found conflicting microsatellite and mitochondrial DNA evidence in Irish populations, suggesting Irish badgers have arisen from admixture between human imported British and Scandinavian animals. The extent and history of contact between British and Irish badger populations remains unclear. We use comprehensive genetic data from Great Britain and Ireland to demonstrate that badgers in Ireland's northeastern and southeastern counties are genetically similar to contemporary British populations. Simulation analyses suggest this admixed population arose in Ireland 600–700 (CI 100–2600) years before present most likely through introduction of British badgers by people. These findings add to our knowledge of the complex colonization history of Ireland by mammals and the central role of humans in facilitating it

The population and landscape genetics of the European badger (Meles meles) in Ireland

Publication history: Accepted - 27 July 2018; Published - 12 September 2018.The population genetic structure of free-ranging species is expected to reflect landscape-level effects. Quantifying the role of these factors and their relative contribution often has important implications for wildlife management. The population genetics of the European badger (Meles meles) have received considerable attention, not least because the species acts as a potential wildlife reservoir for bovine tuberculosis (bTB) in Britain and Ireland. Herein, we detail the most comprehensive population and landscape genetic study of the badger in Ireland to date—comprised of 454 Irish badger samples, genotyped at 14 microsatellite loci. Bayesian and multivariate clustering methods demonstrated continuous clinal variation across the island, with potentially distinct differentiation observed in Northern Ireland. Landscape genetic analyses identified geographic distance and elevation as the primary drivers of genetic differentiation, in keeping with badgers exhibiting high levels of philopatry. Other factors hypothesized to affect gene flow, including earth worm habitat suitability, land cover type, and the River Shannon, had little to no detectable effect. By providing a more accurate picture of badger population structure and the factors effecting it, these data can guide current efforts to manage the species in Ireland and to better understand its role in bTB.DAFM - Department of Food Agriculture and the Marine, Republic of Ireland; Department of Agriculture Environment and Rural Affairs for Northern Ireland (DAERA-NI

Evidence of decline of malaria in the general hospital of Libreville, Gabon from 2000 to 2008

BACKGROUND: Substantial decline in malaria transmission, morbidity and mortality has been reported in several countries where new malaria control strategies have been implemented. In Gabon, the national malaria policy changed in 2003, according to the WHO recommendations. The trend in malaria morbidity was evaluated among febrile children before and after their implementation in Libreville, the capital city of Gabon. METHODS: From August 2000 to December 2008, febrile paediatric outpatients and inpatients, under 11 years of age, were screened for malaria by microscopic examination at the Malaria Clinical Research Unit (MCRU) located in the largest public hospital in Gabon. Climatic data were also collected. RESULTS: In total, 28,092 febrile children were examined; those under five years always represented more than 70%. The proportion of malaria-positive slides was 45% in 2000, and declined to 15% in 2008. The median age of children with a positive blood smear increased from 24(15-48) to 41(21-72) months over the study period (p < 0.01). Rainfall patterns had no impact on the decline observed throughout the study period. CONCLUSION: The decrease of malaria prevalence among febrile children during the last nine years is observed following the introduction of new strategies of malaria cases management, and may announce epidemiological changes. Moreover, preventive measures must be extended to children older than five years

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

The DNA Toolbox: Development and optimisation of molecular techniques to identify red squirrels (Sciurus vulgaris)

The red squirrel (Sciurus vulgaris) has seen a population decline in Ireland and Britain over the last 100 years since the introduction of the North American grey squirrel (Sciurus carolineneis). The decline has been attributed to a number of factors including habitat loss and direct competition with the invasive grey squirrel. As a result, there is a growing need to monitor the distribution of both species for conservation management. Squirrels can be surveyed non-invasively using hair-tubes, and the species can be identified by microscopic identification of individual hairs. To increase the information obtained from non-invasive surveys a suite of DNA tools to identify both squirrel species from non-invasive DNA samples were developed in this study. This involved the design of real-time PCR assays designed to amplify short DNA fragments of red and grey squirrel DNA. A molecular dietary study of pine marten (Martes martes) scats using the species-specific assays to detect squirrel DNA in the pine marten diet was also conducted. Methods to determine the gender of squirrels were investigated by testing the utility of a range of Y-chromosome markers. A panel of previously published microsatellite DNA markers were screened and optimised to identify individual red squirrels. The techniques were applied to a hair-tube study in County Waterford, South East Ireland, where individual red squirrels were identified. Additional samples were collected from subpopulations throughout Ireland, and a remnant red squirrel population in mid Wales where the genetic variability of the populations were assessed using microsatellite genotyping and mitochondrial DNA sequencing. The combination of these tools can be used for non-invasive monitoring and translocation projects of the red squirrel

Development of novel real-time TaqMan®PCR assays for the species and sex identification of otter (Lutra lutra) and their application to noninvasive genetic monitoring

Developing strategies to maintain biodiversity requires baseline information on the current status of each individual species. The development of genetic techniques and their application to noninvasively collected samples have the potential to yield information on the structure of elusive animal populations and so are important tools in conservation management. Using DNA isolated from faecal samples can be challenging owing to low quantity and quality. This study, however, presents the development of novel real-time polymerase chain reaction assays using fluorescently labelled TaqMan® MGB probes enabling species and sex identification of Eurasian otter (Lutra lutra) spraints (faeces). These assays can also be used in determining an optimum microsatellite panel and can be employed as cost-saving screening tools for downstream genetic testing including microsatellite genotyping and haplotype analysis. The techniques are shown to work efficiently with L. lutra DNA isolated from tissue, hair, spraint, blood and anal jelly samples

Effects of virtual reality locomotion techniques on distance estimations

Mental representations of geographic space are based on knowledge of spatial elements and the spatial relation between these elements. Acquiring such mental representations of space requires assessing distances between pairs of spatial elements. In virtual reality (VR) applications, locomotion techniques based on real-world movement are constrained by the size of the available room and the used room scale tracking system. Therefore, many VR applications use additional locomotion techniques such as artificial locomotion (continuous forward movement) or teleporting ("jumping" from one location to another). These locomotion techniques move the user through virtual space based on controller input. However, it has not yet been investigated how different established controller-based locomotion techniques affect distance estimations in VR. In an experiment, we compared distance estimations between artificial locomotion and teleportation before and after a training phase. The results showed that distance estimations in both locomotion conditions improved after the training. Additionally, distance estimations were found to be more accurate when teleportation locomotion was used