Grey seal predation mortality on three depleted stocks in the West of Scotland : what are the implications for stock assessments?

The decrease in groundfish stocks in the North Atlantic since the mid-1900s coupled with increases in grey seal populations is responsible for an enduring controversy between fishers and conservationists regarding the role seals have played in stock declines. We used a Bayesian state-space model to investigate stock trends in the presence of grey seals and associated MSY reference points in the West of Scotland. This study provides new estimates of seal predation mortality on haddock and whiting and updates the estimates for cod, which together form the traditional main components of the mixed demersal fishery in this area. Grey seal predation mortality is greatest on cod resulting in estimates of total natural mortality higher than those used in the current ICES assessments. Seal predation mortality is low for haddock and whiting. Considering seal predation in stock assessments changes the scale of biomass and fishing mortality estimates for the three stocks. The estimates of F0.1 and FMSY are sensitive to seal predation for cod and whiting but not for haddock. In all cases MSY decreases with increased seal predation

Genomes, expression profiles, and diversity of mitochondria of the White-footed Deermouse Peromyscus leucopus, reservoir of Lyme disease and other zoonoses.

The cricetine rodents Peromyscus leucopus and P. maniculatus are key reservoirs for several zoonotic diseases in North America. We determined the complete circular mitochondrial genome sequences of representatives of 3 different stock colonies of P. leucopus, one stock colony of P. maniculatus and two wild populations of P. leucopus. The genomes were syntenic with that of the murids Mus musculus and Rattus norvegicus. Phylogenetic analysis confirmed that these two Peromyscus species are sister taxa in a clade with P. polionotus and also uncovered a distinction between P. leucopus populations in the eastern and the central United States. In one P. leucopus lineage four extended regions of mitochondrial pseudogenes were identified in the nuclear genome. RNA-seq analysis revealed transcription of the entire genome and differences from controls in the expression profiles of mitochondrial genes in the blood, but not in liver or brain, of animals infected with the zoonotic pathogen Borrelia hermsii. PCR and sequencing of the D-loop of the mitochondrion identified 32 different haplotypes among 118 wild P. leucopus at a Connecticut field site. These findings help to further establish P. leucopus as a model organism for studies of emerging infectious diseases, ecology, and in other disciplines

Bioeconomic modelling of grey seal predation impacts on the West of Scotland demersal fisheries

The role grey seals have played in the performance of fisheries is controversial and a cause of much debate between fishers and conservationists. Most studies focus on the effects of seal damage to gears or fish and on prey population abundance but little attention is given to the consequences of the latter for the fisheries. We develop a model that quantifies the economic impact of grey seal predation on the West of Scotland demersal fisheries that traditionally targeted cod, haddock and whiting. Three contrasting fishing strategy scenarios are examined to assess impacts on equilibrium fleet revenues under different levels of seal predation. These include status quo fishing mortality (SQF, steady state with constant fishing mortality), open access fishing (bioeconomic equilibrium, BE) and the maximum economic yield (MEY). In all scenarios, cod emerges as the key stock. Large whitefish trawlers are most sensitive to seal predation due to their higher cod revenues but seal impacts are minor at the aggregate fishery level. Scenarios that consider dynamic fleet behaviour also show the greatest effects of seal predation. Results are sensitive to the choice of seal foraging model where a type II functional response increases sensitivity to seal predation. The cost to the fishery for each seal is estimated

Accurate and Rapid Identification of the Burkholderia pseudomallei Near-Neighbour, Burkholderia ubonensis, Using Real-Time PCR

Burkholderia ubonensis is an environmental bacterium belonging to the Burkholderia cepacia complex (Bcc), a group of genetically related organisms that are associated with opportunistic but generally nonfatal infections in healthy individuals. In contrast, the near-neighbour species Burkholderia pseudomallei causes melioidosis, a disease that can be fatal in up to 95% of cases if left untreated. B. ubonensis is frequently misidentified as B. pseudomallei from soil samples using selective culturing on Ashdown’s medium, reflecting both the shared environmental niche and morphological similarities of these species. Additionally, B. ubonensis shows potential as an important biocontrol agent in B. pseudomallei-endemic regions as certain strains possess antagonistic properties towards B. pseudomallei. Current methods for characterising B. ubonensis are laborious, time-consuming and costly, and as such this bacterium remains poorly studied. The aim of our study was to develop a rapid and inexpensive real-time PCR-based assay specific for B. ubonensis. We demonstrate that a novel B. ubonensis-specific assay, Bu550, accurately differentiates B. ubonensis from B. pseudomallei and other species that grow on selective Ashdown’s agar. We anticipate that Bu550 will catalyse research on B. ubonensis by enabling rapid identification of this organism from Ashdown’s-positive colonies that are not B. pseudomallei

Emerging Themes from the ESA Symposium Entitled “Pollinator Nutrition: Lessons from Bees at Individual to Landscape Levels”

Pollinator populations are declining (Biesmeijer et al., 2006; Brodschneider et al., 2018; Cameron et al., 2011; Goulson, Lye, & Darvill, 2008; Kulhanek et al., 2017; National Research Council, 2007; Oldroyd, 2007), and both anecdotal and experimental evidence suggest that limited access to high quality forage might play a role (Carvell, Meek, Pywell, Goulson, & Nowakowski, 2007; Deepa et al., 2017; Goulson, Nicholls, Botias, & Rotheray, 2015; Potts et al., 2003, 2010; Vanbergen & The Insect Pollinators Initiative, 2013; Vaudo, Tooker, Grozinger, & Patch, 2015; Woodard, 2017). Multiple researchers are earnestly addressing this topic in a diverse array of insect-pollinator systems. As research continues to be published, increased communication among scientists studying the topic of nutrition is essential for improving pollinator health

OGLE-2005-BLG-071Lb, the Most Massive M-Dwarf Planetary Companion?

We combine all available information to constrain the nature of OGLE-2005-BLG-071Lb, the second planet discovered by microlensing and the first in a high-magnification event. These include photometric and astrometric measurements from Hubble Space Telescope, as well as constraints from higher order effects extracted from the ground-based light curve, such as microlens parallax, planetary orbital motion and finite-source effects. Our primary analysis leads to the conclusion that the host of Jovian planet OGLE-2005-BLG-071Lb is an M dwarf in the foreground disk with mass M= 0.46 +/- 0.04 Msun, distance D_l = 3.3 +/- 0.4 kpc, and thick-disk kinematics v_LSR ~ 103 km/s. From the best-fit model, the planet has mass M_p = 3.8 +/- 0.4 M_Jup, lies at a projected separation r_perp = 3.6 +/- 0.2 AU from its host and so has an equilibrium temperature of T ~ 55 K, i.e., similar to Neptune. A degenerate model less favored by \Delta\chi^2 = 2.1 (or 2.2, depending on the sign of the impact parameter) gives similar planetary mass M_p = 3.4 +/- 0.4 M_Jup with a smaller projected separation, r_\perp = 2.1 +/- 0.1 AU, and higher equilibrium temperature T ~ 71 K. These results from the primary analysis suggest that OGLE-2005-BLG-071Lb is likely to be the most massive planet yet discovered that is hosted by an M dwarf. However, the formation of such high-mass planetary companions in the outer regions of M-dwarf planetary systems is predicted to be unlikely within the core-accretion scenario. There are a number of caveats to this primary analysis, which assumes (based on real but limited evidence) that the unlensed light coincident with the source is actually due to the lens, that is, the planetary host. However, these caveats could mostly be resolved by a single astrometric measurement a few years after the event.Comment: 51 pages, 12 figures, 3 tables, Published in Ap

The current understanding of precision medicine and personalised medicine in selected research disciplines:study protocol of a systematic concept analysis

INTRODUCTION: The terms ‘precision medicine’ and ‘personalised medicine’ have become key terms in health-related research and in science-related public communication. However, the application of these two concepts and their interpretation in various disciplines are heterogeneous, which also affects research translation and public awareness. This leads to confusion regarding the use and distinction of the two concepts. Our aim is to provide a snapshot of the current understanding of these concepts. METHODS AND ANALYSIS: Our study will use Rodgers’ evolutionary concept analysis to systematically examine the current understanding of the concepts ‘precision medicine’ and ‘personalised medicine’ in clinical medicine, biomedicine (incorporating genomics and bioinformatics), health services research, physics, chemistry, engineering, machine learning and artificial intelligence, and to identify their respective attributes (clusters of characteristics) and surrogate and related terms. A systematic search of the literature will be conducted for 2016–2022 using databases relevant to each of these disciplines: ACM Digital Library, CINAHL, Cochrane Library, F1000Research, IEEE Xplore, PubMed/Medline, Science Direct, Scopus and Web of Science. These are among the most representative databases for the included disciplines. We will examine similarities and differences in definitions of ‘precision medicine’ and ‘personalised medicine’ in the respective disciplines and across (sub)disciplines, including attributes of each term. This will enable us to determine how these two concepts are distinguished. ETHICS AND DISSEMINATION: Following ethical and research standards, we will comprehensively report the methodology for a systematic analysis following Rodgers’ concept analysis method. Our systematic concept analysis will contribute to the clarification of the two concepts and distinction in their application in given settings and circumstances. Such a broad concept analysis will contribute to non-systematic syntheses of the concepts, or occasional systematic reviews on one of the concepts that have been published in specific disciplines, in order to facilitate interdisciplinary communication, translational medical research and implementation science

Common genetic variants, acting additively, are a major source of risk for autism

Abstract Background Autism spectrum disorders (ASD) are early onset neurodevelopmental syndromes typified by impairments in reciprocal social interaction and communication, accompanied by restricted and repetitive behaviors. While rare and especially de novo genetic variation are known to affect liability, whether common genetic polymorphism plays a substantial role is an open question and the relative contribution of genes and environment is contentious. It is probable that the relative contributions of rare and common variation, as well as environment, differs between ASD families having only a single affected individual (simplex) versus multiplex families who have two or more affected individuals. Methods By using quantitative genetics techniques and the contrast of ASD subjects to controls, we estimate what portion of liability can be explained by additive genetic effects, known as narrow-sense heritability. We evaluate relatives of ASD subjects using the same methods to evaluate the assumptions of the additive model and partition families by simplex/multiplex status to determine how heritability changes with status. Results By analyzing common variation throughout the genome, we show that common genetic polymorphism exerts substantial additive genetic effects on ASD liability and that simplex/multiplex family status has an impact on the identified composition of that risk. As a fraction of the total variation in liability, the estimated narrow-sense heritability exceeds 60% for ASD individuals from multiplex families and is approximately 40% for simplex families. By analyzing parents, unaffected siblings and alleles not transmitted from parents to their affected children, we conclude that the data for simplex ASD families follow the expectation for additive models closely. The data from multiplex families deviate somewhat from an additive model, possibly due to parental assortative mating. Conclusions Our results, when viewed in the context of results from genome-wide association studies, demonstrate that a myriad of common variants of very small effect impacts ASD liability.http://deepblue.lib.umich.edu/bitstream/2027.42/112370/1/13229_2012_Article_55.pd