The Effects of Fish Trap Mesh Size on Reef Fish Catch off Southeastern Florida

Catch and mesh selectivity of wire-meshed fish traps were tested for eleven different mesh sizes ranging from 13 X 13 mm (0.5 x 0.5") to 76 x 152 mm (3 X 6"). A total of 1,810 fish (757 kg) representing 85 species and 28 families were captured during 330 trap hauls off southeastern Florida from December 1986 to July 1988. Mesh size significantly affected catches. The 1.5" hexagonal mesh caught the most fish by number, weight, and value. Catches tended to decline as meshes got smaller or larger. Individual fish size increased with larger meshes. Laboratory mesh retention experiments showed relationships between mesh shape and size and individual retention for snapper (Lutjanidae), grouper (Serranidae), jack (Carangidae), porgy (Sparidae), and surgeonfish (Acanthuridae). These relationships may be used to predict the effect of mesh sizes on catch rates. Because mesh size and shape greatly influenced catchability, regulating mesh size may provide a useful basis for managing the commercial trap fishery

Active site remodelling of a cyclodipeptide synthase redefines substrate scope

Funding: Wellcome Trust (210486/Z/18/Z), Cunningham Trust (PhD-CT-18-41).Cyclodipeptide synthases (CDPSs) generate a wide range of cyclic dipeptides using aminoacylated tRNAs as substrates. Histidine-containing cyclic dipeptides have important biological activities as anticancer and neuroprotective molecules. Out of the 120 experimentally validated CDPS members, only two are known to accept histidine as a substrate yielding cyclo(His-Phe) and cyclo(His-Pro) as products. It is not fully understood how CDPSs select their substrates, and we must rely on bioprospecting to find new enzymes and novel bioactive cyclic dipeptides. Here, we developed an in vitro system to generate an extensive library of molecules using canonical and non-canonical amino acids as substrates, expanding the chemical space of histidine-containing cyclic dipeptide analogues. To investigate substrate selection we determined the structure of a cyclo(His-Pro)-producing CDPS. Three consecutive generations harbouring single, double and triple residue substitutions elucidated the histidine selection mechanism. Moreover, substrate selection was redefined, yielding enzyme variants that became capable of utilising phenylalanine and leucine. Our work successfully engineered a CDPS to yield different products, paving the way to direct the promiscuity of these enzymes to produce molecules of our choosing.Publisher PDFPeer reviewe

Imported malaria: key messages in an era of elimination.

Despite concerted efforts to eliminate malaria, it remains a major global cause of morbidity and mortality with over 200 million annual cases. Significant gains have been made, with the annual global malaria incidence and mortality halving over the past twenty years, using tools such as long-lasting insecticide-treated bed nets and artemisinin-based therapies. Malaria is also a significant cause of life-threatening imported infection in the UK. It is vital for front line clinical staff involved in the assessment of acutely ill patients to be aware of the need for early diagnostic testing, malaria epidemiology, markers of severe infection and developments in antimalarial treatments to optimise patient management. The difference between a good and poor outcome is early diagnosis and treatment. Many of the challenges faced in the quest for global eradication, such as availability of appropriate diagnostic tests, and drug and insecticide resistance could also have future implications for imported malaria

Modularization for the Cell Ontology

One of the premises of the OBO Foundry is that development of an orthogonal set of ontologies will increase domain expert contributions and logical interoperability, and decrease maintenance workload. For these reasons, the Cell Ontology (CL) is being re-engineered. This process requires the extraction of sub-modules from existing OBO ontologies, which presents a number of practical engineering challenges. These extracted modules may be intended to cover a narrow or a broad set of species. In addition, applications and resources that make use of the Cell Ontology have particular modularization requirements, such as the ability to extract custom subsets or unions of the Cell Ontology with other OBO ontologies. These extracted modules may be intended to cover a narrow or a broad set of species, which presents unique complications.

We discuss some of these requirements, and present our progress towards a customizable simple-to-use modularization tool that leverages existing OWL-based tools and opens up their use for the CL and other ontologies

Post-head-emergence frost in wheat and barley: defining the problem, assessing the damage, and identifying resistance

Radiant frost is a significant production constraint to wheat (Triticum aestivum) and barley (Hordeum vulgare), particularly in regions where spring-habit cereals are grown through winter, maturing in spring. However, damage to winter-habit cereals in reproductive stages is also reported. Crops are particularly susceptible to frost once awns or spikes emerge from the protection of the flag leaf sheath. Post-head-emergence frost (PHEF) is a problem distinct from other cold-mediated production constraints. To date, useful increased PHEF resistance in cereals has not been identified. Given the renewed interest in reproductive frost damage in cereals, it is timely to review the problem. Here we update the extent and impacts of PHEF and document current management options to combat this challenge. We clarify terminology useful for discussing PHEF in relation to chilling and other freezing stresses. We discuss problems characterizing radiant frost, the environmental conditions leading to PHEF damage, and the effects of frost at different growth stages. PHEF resistant cultivars would be highly desirable, to both reduce the incidence of direct frost damage and to allow the timing of crop maturity to be managed to maximize yield potential. A framework of potential adaptation mechanisms is outlined. Clarification of these critical issues will sharpen research focus, improving opportunities to identify genetic sources for improved PHEF resistance

Sockeye at the Boundary: Controversial and Contested Salmon in the Cohen Commission, 2009-2012

In this STS dissertation, I build on the controversy studies literature by opening the black box that is the Cohen Report, thereby illuminating the various forms taken by, and contestations associated with, controversial salmon in the Cohen Commission, 2009-2012, a federal inquiry into the decline of sockeye salmon in the Fraser River of British Columbia, Canada. In this empirical study, I ask: (i) What are the primary sources of controversy in the Fraser River fishery? (ii) What salmon controversies are revealed through the social-life of sockeye, and how do they compare to those depicted in the Cohen Reports overview of the life-cycle of sockeye? (iii) What factors contributed to the (de)legitimation of particular understandings of controversial salmon during the Cohen Commission? To address these questions, I employed a three-phase, multi-method approach which involved (I) collecting qualitative data in the field; (II) creating a map from these data; and (III) using this map to analyze the social lives of various human and non-human actors. My primary research findings (1-9) shed new light on various salmon controversies, including those arising from (1) Indigenous responses to the ongoing experience of colonial violence and dispossession, (2) an ethic of exploitation oriented towards establishing and maintaining dominion over nature, (3) the prevailing view that fish (and fishing) are principally vehicles for economic growth and financial profit, and (4) the local effects of anthropogenic climate change. I also found that (5) these controversies are largely minimized by the Cohen Reports life-cycle overview, which reduces the sockeye life-cycle to a series of physiological transformations loosely connected to the particulars of place. During the Cohen Commission, salmon controversies were (de)legitimated through (6) the boundary work of expertise, (7) the Commissions emphasis on efficiently neutralizing contention, and (8) differing assessments concerning the importance of place. This resulted in the production of a controversial blueprint for closurei.e., the Cohen Reportwhich (9) called for the production of knowledge and ignorance in relation to the impacts of salmon farming, accentuating the importance of attending to generative symmetry, this dissertations foremost contribution to the STS controversy studies literature

Stereoselective synthesis of 2,6-trans-4-oxopiperidines using an acid-mediated 6-endo-trig cyclisation

An acid-mediated 6-endo-trig cyclisation of amine-substituted enones has been developed for the stereoselective synthesis of trans-6-alkyl-2-methyl-4-oxopiperidines. Performed under conditions that prevent removal of the Boc-protecting group or acetal formation, the key cyclisation was found to generate cleanly the 4-oxopiperidine products in high overall yields from a wide range of alkyl substituted enones. The synthetic utility of the trans-6-alkyl-2-methyl-4-oxopiperidines formed from this process was demonstrated with the total synthesis of the quinolizidine alkaloid, (+)-myrtine and the piperidine alkaloid, (–)-solenopsin A

Seeing beyond 2020: an economic evaluation of contemporary and emerging strategies for elimination of Trypanosoma brucei gambiense

Background Trypanosoma brucei (T b) gambiense is targeted to reach elimination as a public health problem by 2020 and full elimination by 2030. To achieve these goals, stakeholders need to consider strategies to accelerate elimination. Hence, we aimed to model several options related to current and emerging methods for case detection, treatment, and vector control across settings to assess cost-eff ectiveness and the probability of elimination. Methods Five intervention strategies were modelled over 30 years for low, moderate, and high transmission settings. Model parameters related to costs, effi cacy, and transmission were based on available evidence and parameter estimation. Outcomes included disability-adjusted life-years (DALYs), costs, and long-term prevalence. Sensitivity analyses were done to calculate the uncertainty of the results. Findings To reach elimination targets for 2020 across all settings, approaches combining case detection, treatment, and vector control would be most eff ective. Elimination in high and moderate transmission areas was probable and costeff ective when strategies included vector control and novel methods, with incremental cost-eff ectiveness ratios (ICERs) ranging from US$400 to$1500 per DALY averted. In low transmission areas, approaches including the newest interventions alone or in combination with tiny targets (vector control) were cost-eff ective, with ICERs of $200 or$1800 per DALY averted, respectively, but only strategies including vector control were likely to lead to elimination. Results of sensitivity analyses showed that allowing for biennial surveillance, reducing vector control maintenance costs, or variations of active surveillance coverage could also be cost-eff ective options for elimination, depending on the setting. Interpretation Although various strategies might lead to elimination of T b gambiense, cost-eff ective approaches will include adoption of emerging technologies and, in some settings, increased surveillance or implementation of vector control

Realising the potential of linked data in healthcare performance assessment efforts in New South Wales, Australia

ABSTRACT Objectives To describe: (1) a stepwise guide to the use of linked data in the development of individual healthcare performance metrics; and (2) the application of these metrics in comprehensive performance assessment efforts at a system, regional and hospital level of analysis. Approach A stepwise guide to the definition and validation of linked-data based indicators was developed following a rapid review of peer reviewed and grey literature and a series of semi-structured interviews with international subject experts. The review and interviews adopted a snowball approach to collect information on the ways in which linked data are currently used in performance measurement efforts. Data collection continued until indicator type saturation was reached. Details about existing applications of linked data in performance reporting were mapped, and used to inform the development of the guide. Indicators were aligned within a conceptual framework that is used to assess healthcare performance in New South Wales, on the basis of accessibility, appropriateness, effectiveness, efficiency, equity and sustainability. Results The guide to indicator development considers the use and contribution of linked data in four stages: defining a cohort; capturing outcomes of interest; risk adjustment; and attribution. A series of vignettes illustrate the various contributions that linked data can make to performance measurement efforts – highlighting the ways in which those data can enhance understanding of complexity and dynamic relationships, and help build a comprehensive picture of performance. Conclusion In performance measurement efforts internationally, linked data are used to strengthen the reliability, accuracy and precision of individual metrics and to inform efforts to assess various dimensions of healthcare performance. In New South Wales, linked data underpin publicly reported performance measures and have the potential to provide in the future whole-of-government and whole-of-system perspectives on health