Reference genome of Townsend's big-eared bat, Corynorhinus townsendii.

Townsend's big-eared bat, Corynorhinus townsendii, is a cave- and mine-roosting species found largely in western North America. Considered a species of conservation concern throughout much of its range, protection efforts would greatly benefit from understanding patterns of population structure, genetic diversity, and local adaptation. To facilitate such research, we present the first de novo genome assembly of C. townsendii as part of the California Conservation Genomics Project (CCGP). Pacific Biosciences HiFi long reads and Omni-C chromatin-proximity sequencing technologies were used to produce a de novo genome assembly, consistent with the standard CCGP reference genome protocol. This assembly comprises 391 scaffolds spanning 2.1 Gb, represented by a scaffold N50 of 174.6 Mb, a contig N50 of 23.4 Mb, and a benchmarking universal single-copy ortholog (BUSCO) completeness score of 96.6%. This high-quality genome will be a key tool for informed conservation and management of this vulnerable species in California and across its range.

Ten-year projection of white-nose syndrome disease dynamics at the southern leading-edge of infection in North America.

Predicting the emergence and spread of infectious diseases is critical for the effective conservation of biodiversity. White-nose syndrome (WNS), an emerging infectious disease of bats, has resulted in high mortality in eastern North America. Because the fungal causative agent Pseudogymnoascus destructans is constrained by temperature and humidity, spread dynamics may vary by geography. Environmental conditions in the southern part of the continent are different than the northeast, where disease dynamics are typically studied, making it difficult to predict how the disease will manifest. Herein, we modelled WNS pathogen spread in Texas based on cave densities and average dispersal distances of hosts, projecting these results out to 10 years. We parameterized a predictive model of WNS epidemiology and its effects on bat populations with observed cave environmental data. Our model suggests that bat populations in northern Texas will be more affected by WNS mortality than southern Texas. As such, we recommend prioritizing the preservation of large overwintering colonies of bats in north Texas through management actions. Our model illustrates that infectious disease spread and infectious disease severity can become uncoupled over a gradient of environmental variation and highlight the importance of understanding host, pathogen and environmental conditions across a breadth of environments.

Factors Associated with Listing Decisions under the U.S. Endangered Species Act.

Conservation efforts, including authorities outlined in the U.S. Endangered Species Act (ESA) of 1973, are attempting to slow the decline of species. Opinions on the success of the ESA vary widely, due in part to few species historically recovering to the point of delisting. Uncertainty surrounding the ESA relates to listing decisions and ambiguity of terminology within the ESA itself. Our goal was to evaluate the relationship, if any, of species characteristics, population metrics, threat level, and potential non-biological indicators to listing decisions under the ESA by the U.S. Fish and Wildlife Service (Service). We collected data from 143 ESA listing decisions published in the Federal Register from February 2011 to October 2014. Only 33 and 31% of listing decisions included population or range size estimates, respectively. Factors significantly correlated with ESA listing decision included taxonomic group, primary ownership of the species' habitat (federal or non-federal), whether the species is aquatic or terrestrial, and whether the species was part of a single or multiple-species listing decision. Increasing number of listed threats and time as a candidate species correlated positively with being listed as endangered. We have attempted to broadly identify the role both intrinsic (biological) and extrinsic (non-biological) factors play in listing decisions, and the importance of comprehensive data to understanding species distribution and abundance to facilitate more informed listing decisions.

Variation in herpetofauna detection probabilities: implications for study design.

Population monitoring is fundamental for informing management decisions aimed at reducing the rapid rate of global biodiversity decline. Herpetofauna are experiencing declines worldwide and include species that are challenging to monitor. Raw counts and associated metrics such as richness indices are common for monitoring populations of herpetofauna; however, these methods are susceptible to bias as they fail to account for varying detection probabilities. Our goal was to develop a program for efficiently monitoring herpetofauna in southern Texas. Our objectives were to (1) estimate detection probabilities in an occupancy modeling framework using trap arrays for a diverse group of herpetofauna and (2) to evaluate the relative effectiveness of funnel traps, pitfall traps, and cover boards. We collected data with 36 arrays at 2 study sites in 2015 and 2016, for 2105 array-days resulting in 4839 detections of 51 species. We modeled occupancy for 21 species and found support for the hypothesis that detection probability varied over our sampling duration for 10 species and with rainfall for 10 species. For herpetofauna in our study, we found 14 and 12 species were most efficiently captured with funnel traps and pitfall traps, respectively, and no species were most efficiently captured with cover boards. Our results show that using methods that do not account for variations in detection probability are highly subject to bias unless the likelihood of false absences is minimized with exceptionally long capture durations. For monitoring herpetofauna in southern Texas, we recommend using arrays with funnel and pitfall traps and an analytical method such as occupancy modeling that accounts for variation in detection.

Tensions in ethics and policy created by National Precision Medicine Programs.

Precision medicine promises to use genomics and other data-intensive approaches to improve diagnosis and develop new treatments for major diseases, but also raises a range of ethical and governance challenges. Implementation of precision medicine in "real world" healthcare systems blurs the boundary between research and care. This has implications for the meaning and validity of consent, and increased potential for discrimination, among other challenges. Increased sharing of personal information raises concerns about privacy, commercialization, and public trust. This paper considers national precision medicine schemes from the USA, the UK, and Japan, comparing how these challenges manifest in each national context and examining the range of approaches deployed to mitigate the potential undesirable social consequences. There is rarely a "one size" fits all solution to these complex problems, but the most viable approaches are those which take account of cultural preferences and attitudes, available resources, and the wider political landscape in which national healthcare systems are embedded.

Including all voices in international data-sharing governance.

BACKGROUND: Governments, funding bodies, institutions, and publishers have developed a number of strategies to encourage researchers to facilitate access to datasets. The rationale behind this approach is that this will bring a number of benefits and enable advances in healthcare and medicine by allowing the maximum returns from the investment in research, as well as reducing waste and promoting transparency. As this approach gains momentum, these data-sharing practices have implications for many kinds of research as they become standard practice across the world. MAIN TEXT: The governance frameworks that have been developed to support biomedical research are not well equipped to deal with the complexities of international data sharing. This system is nationally based and is dependent upon expert committees for oversight and compliance, which has often led to piece-meal decision-making. This system tends to perpetuate inequalities by obscuring the contributions and the important role of different data providers along the data stream, whether they be low- or middle-income country researchers, patients, research participants, groups, or communities. As research and data-sharing activities are largely publicly funded, there is a strong moral argument for including the people who provide the data in decision-making and to develop governance systems for their continued participation. CONCLUSIONS: We recommend that governance of science becomes more transparent, representative, and responsive to the voices of many constituencies by conducting public consultations about data-sharing addressing issues of access and use; including all data providers in decision-making about the use and sharing of data along the whole of the data stream; and using digital technologies to encourage accessibility, transparency, and accountability. We anticipate that this approach could enhance the legitimacy of the research process, generate insights that may otherwise be overlooked or ignored, and help to bring valuable perspectives into the decision-making around international data sharing.

Valuing height: diagnosis, valuation and the case of idiopathic short stature.

This paper proposes a 'valuographic' approach to diagnosis, exploring how values and valuation practices are implicated in the contested diagnostic category of idiopathic short stature (ISS). ISS describes children who are 'abnormally' short but do not have any other detectable pathology. In the USA growth-promoting hormone therapy has been approved for ISS children, since 2003. However, no other jurisdiction has approved this treatment and the value of ISS as a diagnostic category remains disputed among healthcare professionals. Drawing on qualitative interviews with paediatric endocrinologists in the UK and the US, this study presents a historical snapshot illustrating how the problematisation of ISS as a diagnosis involved multiple registers of value including epistemic, economic and moral calculations of worth. Contestation of the diagnosis was not just about what counts but about what ought to be counted, as respondents' accounts of ISS gave differential weight to a range of types of evidence and methods of assessment. Ultimately what was at stake was not just the value of increased height for short patients, but what it meant to properly practice paediatric endocrinology. Consideration is then given to how a valuographic approach can be applied to sociological studies of diagnosis more broadly.

Iodide Improves Outcome After Acute Myocardial Infarction in Rats and Pigs.

OBJECTIVES: In this study, we tested whether iodide would reduce heart damage in rat and pig models of acute myocardial infarction as a risk analysis for a human trial. DESIGN: Prospective blinded and randomized laboratory animal investigation. SETTING: Animal research laboratories. SUBJECTS: Sexually mature rats and pigs. INTERVENTIONS: Acute myocardial infarction was induced by temporary ligation of the coronary artery followed by reperfusion. Iodide was administered orally in rats or IV in rats and pigs just prior to reperfusion. MEASUREMENTS AND MAIN RESULTS: Damage was assessed by blood cardiac troponin and infarct size; heart function was determined by echocardiography. Blood peroxide scavenging activity was measured enzymatically, and blood thyroid hormone was determined using radioimmune assay. Iodide administration preserved heart function and reduced blood cardiac troponin and infarct size by approximately 45% in pigs and approximately 60% in rats. Iodide administration also increased blood peroxide scavenging activity and maintained thyroid hormone levels. CONCLUSIONS: Iodide administration improved the structure and function of the heart after acute myocardial infarction in rats and pigs.

Patenting Foundational Technologies: Lessons From CRISPR and Other Core Biotechnologies.

In 2012, a new and promising gene manipulation technique, CRISPR-Cas9, was announced that seems likely to be a foundational technique in health care and agriculture. However, patents have been granted. As with other technological developments, there are concerns of social justice regarding inequalities in access. Given the technologies' "foundational" nature and societal impact, it is vital for such concerns to be translated into workable recommendations for policymakers and legislators. Colin Farrelly has proposed a moral justification for the use of patents to speed up the arrival of technology by encouraging innovation and investment. While sympathetic to his argument, this article highlights a number of problems. By examining the role of patents in CRISPR and in two previous foundational technologies, we make some recommendations for realistic and workable guidelines for patenting and licensing.

Cultivation in Space Flight Produces Minimal Alterations in the Susceptibility of Bacillus subtilis Cells to 72 Different Antibiotics and Growth-Inhibiting Compounds.

Past results have suggested that bacterial antibiotic susceptibility is altered during space flight. To test this notion, Bacillus subtilis cells were cultivated in matched hardware, medium, and environmental conditions either in space flight microgravity on the International Space Station, termed flight (FL) samples, or at Earth-normal gravity, termed ground control (GC) samples. The susceptibility of FL and GC samples was compared to 72 antibiotics and growth-inhibitory compounds using the Omnilog phenotype microarray (PM) system. Only 9 compounds were identified by PM screening as exhibiting significant differences (P < 0.05, Student's t test) in FL versus GC samples: 6-mercaptopurine, cesium chloride, enoxacin, lomefloxacin, manganese(II) chloride, nalidixic acid, penimepicycline, rolitetracycline, and trifluoperazine. Testing of the same compounds by standard broth dilution assay did not reveal statistically significant differences in the 50% inhibitory concentrations (IC50s) between FL and GC samples. The results indicate that the susceptibility of B. subtilis cells to a wide range of antibiotics and growth inhibitors is not dramatically altered by space flight.IMPORTANCE This study addresses a major concern of mission planners for human space flight, that bacteria accompanying astronauts on long-duration missions might develop a higher level of resistance to antibiotics due to exposure to the space flight environment. The results of this study do not support that notion.

Responses of a Federally Endangered Songbird to Understory Thinning in Oak-Juniper Woodlands.

Wildlife conservation and management on military lands must be accomplished in the context of military readiness, which often includes ground-based training that is perceived to conflict with wildlife needs and environmental regulations. From 2008‒2012, we examined territory density, pairing success, and fledging success of the federally endangered golden-cheeked warbler (Setophaga chrysoparia; hereafter warbler) in relation to removal of small-diameter trees from the understory of mature oak-juniper (Quercus-Juniperus) woodland at the 87,890 ha Fort Hood Military Reservation in central Texas. Understory thinning created troop maneuver lanes, but left canopy vegetation intact. Warbler density, pairing success, and fledging success were similar across thinned and control sites. We found that warbler pairing and fledging success were best predicted by Ecological site (hereafter Ecosite), an indicator of hardwood tree species composition. Warbler pairing and fledging success were about 1.5 and 1.6 times higher, respectively, for territories dominated by the Low Stony Hill Ecosite than territories dominated by the Redlands Ecosite. Our results indicate that understory thinning for military training purposes did not have a negative effect on warblers at Fort Hood in the manner tested, and suggest that removal of smaller trees from the understory in a way that replicates historic conditions may elicit neutral responses from this forest-dependent songbird. Quantifying wildlife responses to military activities provides the Department of Defense and US Fish and Wildlife Service with data to guide conservation of threatened and endangered species on Department of Defense facilities while maintaining the military mission, and supports wildlife management efforts on other public and private lands.

Between Scylla and Charybdis: reconciling competing data management demands in the life sciences.

BACKGROUND: The widespread sharing of biologicaConcluding Comments: Teaching Responsible Datal and biomedical data is recognised as a key element in facilitating translation of scientific discoveries into novel clinical applications and services. At the same time, twenty-first century states are increasingly concerned that this data could also be used for purposes of bioterrorism. There is thus a tension between the desire to promote the sharing of data, as encapsulated by the Open Data movement, and the desire to prevent this data from 'falling into the wrong hands' as represented by 'dual use' policies. Both frameworks posit a moral duty for life sciences researchers with respect to how they should make their data available. However, Open data and dual use concerns are rarely discussed in concert and their implementation can present scientists with potentially conflicting ethical requirements. DISCUSSION: Both dual use and Open data policies frame scientific data and data dissemination in particular, though different, ways. As such they contain implicit models for how data is translated. Both approaches are limited by a focus on abstract conceptions of data and data sharing. This works to impede consensus-building between the two ethical frameworks. As an alternative, this paper proposes that an ethics of responsible management of scientific data should be based on a more nuanced understanding of the everyday data practices of life scientists. Responsibility for these 'micromovements' of data must consider the needs and duties of scientists as individuals and as collectively-organised groups. Researchers in the life sciences are faced with conflicting ethical responsibilities to share data as widely as possible, but prevent it being used for bioterrorist purposes. In order to reconcile the responsibilities posed by the Open Data and dual use frameworks, approaches should focus more on the everyday practices of laboratory scientists and less on abstract conceptions of data.

Introduction to the article collection 'Translation in healthcare: ethical, legal, and social implications'.

New technologies are transforming and reconfiguring the boundaries between patients, research participants and consumers, between research and clinical practice, and between public and private domains. From personalised medicine to big data and social media, these platforms facilitate new kinds of interactions, challenge longstanding understandings of privacy and consent, and raise fundamental questions about how the translational patient pathway should be organised.This editorial introduces the cross-journal article collection "Translation in healthcare: ethical, legal, and social implications", briefly outlining the genesis of the collection in the 2015 Translation in healthcare conference in Oxford, UK and providing an introduction to the contemporary ethical challenges of translational research in biology and medicine accompanied by a summary of the papers included in this collection.

Selenide Targets to Reperfusing Tissue and Protects It From Injury.

OBJECTIVES: Since blood selenium levels decrease after ischemia and reperfusion injury, and low blood selenium correlates with negative outcome, we designed and performed experiments to determine how selenium distribution is affected by ischemia reperfusion injury. Furthermore, we tested whether different chemical forms of selenium would affect outcome after ischemia and reperfusion injury. We also examined the metabolic effects of selenide administration. DESIGN: Laboratory investigation. SETTING: Animal research laboratory. SUBJECTS: Adult male C57BL/6 mice. INTERVENTIONS: To determine selenium localization, we administered tracer doses of radioactive selenium 75 in the form of selenite or selenide and measured blood and tissue selenium levels after ischemia and reperfusion injury. Anesthetized mice were subjected to myocardial ischemia reperfusion injury (coronary artery occlusion for 60 min followed by 5 min of reperfusion after occlusion was removed) or hindlimb ischemia reperfusion injury (left leg tourniquet for 90 min followed by 5 min reperfusion after tourniquet removal). To determine whether exogenous selenium administration could reduce ischemia reperfusion injury, we synthesized and administered sodium hydroselenide and sodium selenite solutions (0.05-2.4 mg/kg). Solutions were administered at the end of coronary artery occlusion but before reperfusion. In order to determine the metabolic effects of selenide administration, we exposed mice to hydrogen selenide gas (0-5 ppm) mixed into air (20.95% oxygen) for up to 3 hours. MEASUREMENTS AND MAIN RESULTS: In targeting assays, we measured blood and tissue selenium levels. We observed that blood selenium decreases after myocardial ischemia reperfusion and displays an inverse correlation with injury severity; selenium accumulation in heart correlates directly with injury severity. We also measured whether oxidized selenium, selenite, and reduced selenium, selenide, would target to injured heart tissue in myocardial ischemia reperfusion and injured leg muscle in a hindlimb model of ischemia reperfusion. Only selenide targets to injured tissue. We also measured damage after myocardial ischemia reperfusion injury using morphometry, neutrophil accumulation, blood cardiac troponin levels, and echocardiography and observed in all assays that selenide reduced damage to the heart; selenite was not effective. And finally, to assay metabolism, we measured oxygen consumption, carbon dioxide production, and body core temperature before, during, and after hydrogen selenide administration. All measurements indicate that selenide decreases metabolism. CONCLUSIONS: Selenide targets to reperfusing tissue and reduces reperfusion injury perhaps by affecting oxygen metabolism.

The renaissance of bacillosamine and its derivatives: pathway characterization and implications in pathogenicity.

Prokaryote-specific sugars, including N,N'-diacetylbacillosamine (diNAcBac) and pseudaminic acid, have experienced a renaissance in the past decade because of their discovery in glycans related to microbial pathogenicity. DiNAcBac is found at the reducing end of oligosaccharides of N- and O-linked bacterial protein glycosylation pathways of Gram-negative pathogens, including Campylobacter jejuni and Neisseria gonorrhoeae. Further derivatization of diNAcBac results in the nonulosonic acid known as legionaminic acid, which was first characterized in the O-antigen of the lipopolysaccharide (LPS) in Legionella pneumophila. Pseudaminic acid, an isomer of legionaminic acid, is also important in pathogenic bacteria such as Helicobacter pylori because of its occurrence in O-linked glycosylation of flagellin proteins, which plays an important role in flagellar assembly and motility. Here, we present recent advances in the characterization of the biosynthetic pathways leading to these highly modified sugars and investigation of the roles that each plays in bacterial fitness and pathogenicity.

Biochemical analysis and structure determination of bacterial acetyltransferases responsible for the biosynthesis of UDP-N,N'-diacetylbacillosamine.

UDP-N,N'-diacetylbacillosamine (UDP-diNAcBac) is a unique carbohydrate produced by a number of bacterial species and has been implicated in pathogenesis. The terminal step in the formation of this important bacterial sugar is catalyzed by an acetyl-CoA (AcCoA)-dependent acetyltransferase in both N- and O-linked protein glycosylation pathways. This bacterial acetyltransferase is a member of the left-handed ß-helix family and forms a homotrimer as the functional unit. Whereas previous endeavors have focused on the Campylobacter jejuni acetyltransferase (PglD) from the N-linked glycosylation pathway, structural characterization of the homologous enzymes in the O-linked glycosylation pathways is lacking. Herein, we present the apo-crystal structures of the acetyltransferase domain (ATD) from the bifunctional enzyme PglB (Neisseria gonorrhoeae) and the full-length acetyltransferase WeeI (Acinetobacter baumannii). Additionally, a PglB-ATD structure was solved in complex with AcCoA. Surprisingly, this structure reveals a contrasting binding mechanism for this substrate when compared with the AcCoA-bound PglD structure. A comparison between these findings and the previously solved PglD crystal structures illustrates a dichotomy among N- and O-linked glycosylation pathway enzymes. Based upon these structures, key residues in the UDP-4-amino and AcCoA binding pockets were mutated to determine their effect on binding and catalysis in PglD, PglB-ATD, and WeeI. Last, a phylogenetic analysis of the aforementioned acetyltransferases was employed to illuminate the diversity among N- and O-linked glycosylation pathway enzymes.

Systematically searching for and assessing the literature for self-management of chronic pain: a lay users' perspective.

BACKGROUND: The Engaging with older adults in the development of strategies for the self management of chronic pain (EOPIC) study aims to design and develop self management strategies to enable older adults to manage their own pain. Involving older adults in research into chronic pain management will better enable the identification and development of strategies that are more appropriate for their use, but how can perspectives really be utilised to the best possible outcomes? METHOD: Seven older adults were recruited through a local advertising campaign to take part. We also invited participants from the local pain services, individuals who had been involved in earlier phase of the EOPIC study and a previous ESRC funded project. The group undertook library training and research skills training to facilitate searching of the literature and identified sources of material. A grading tool was developed using perceived essential criteria identified by the older adults and material was graded according to the criteria within this scale. RESULTS: Fifty-seven resources from over twenty-eight sources were identified. These materials were identified as being easily accessible, readable and relevant. Many of the web based materials were not always easy to find or readily available so they were excluded by the participants. All but one were UK based. Forty-four items were identified as meeting the key criteria for inclusion in the study. This included five key categories as follows; books, internet, magazines, leaflets, CD's/Tapes. CONCLUSION: This project was able to identify a number of exemplars of self management material along with some general rules regarding the categories identified. We must point out that the materials identified were not age specific, were often locally developed and would need to be adapted to older adults with chronic pain. For copyright issues we have not included them in this paper. The key message is really related to the format rather than the content. However, the group acknowledge that these may vary according to the requirements of each individual older adult and therefore recommend the development of a leaflet to help others in their search for resources. This leaflet has been developed as part of Phase IV of the EOPIC study.