Translating the terrestrial mitigation hierarchy to marine megafauna by‐catch

In terrestrial and coastal systems, the mitigation hierarchy is widely and increasingly used to guide actions to ensure that no net loss of biodiversity ensues from development. We develop a conceptual model which applies this approach to the mitigation of marine megafauna by‐catch in fisheries, going from defining an overarching goal with an associated quantitative target, through avoidance, minimization, remediation to offsetting. We demonstrate the framework's utility as a tool for structuring thinking and exposing uncertainties. We draw comparisons between debates ongoing in terrestrial situations and in by‐catch mitigation, to show how insights from each could inform the other; these are the hierarchical nature of mitigation, out‐of‐kind offsets, research as an offset, incentivizing implementation of mitigation measures, societal limits and uncertainty. We explore how economic incentives could be used throughout the hierarchy to improve the achievement of by‐catch goals. We conclude by highlighting the importance of clear agreed goals, of thinking beyond single species and individual jurisdictions to account for complex interactions and policy leakage, of taking uncertainty explicitly into account and of thinking creatively about approaches to by‐catch mitigation in order to improve outcomes for conservation and fishers. We suggest that the framework set out here could be helpful in supporting efforts to improve by‐catch mitigation efforts and highlight the need for a full empirical application to substantiate this.     

Simrank: Rapid and sensitive general-purpose k-mer search tool

Background  

Terabyte-scale collections of string-encoded data are expected from consortia efforts such as the Human Microbiome Project . Intra- and inter-project data similarity searches are enabled by rapid k-mer matching strategies. Software applications for sequence database partitioning, guide tree estimation, molecular classification and alignment acceleration have benefited from embedded k-mer searches as sub-routines. However, a rapid, general-purpose, open-source, flexible, stand-alone k-mer tool has not been available.     

Demonstration of primary cilia and acetylated α-tubulin in fish endothelial,epithelial and fibroblast cell lines

Primary cilia (PC) were demonstrated for the first time in fish endothelial, epithelial and fibroblast cell lines through immunofluorescence staining with the monoclonal antibody, 6-11B-1, against acetylated α-tubulin. The study was carried out with eight recently developed cell lines from the walleye, Sander vitreus (Mitchill). These were three fibroblast-like cell lines, WE-cfin11f, WE-skin11f and WE-liver3 from, respectively, the caudal fin, skin and liver, and three epithelial-like cell lines, WE-cfin11e, WE-spleen6 and WErpe from, respectively, the caudal fin, spleen and retina. Also, endothelial-like WEBA from the bulbus arteriosus and glial-like WE-brain5 from the brain were used. Immunocytochemistry revealed strong staining for acetylated α-tubulin in mitotic spindles and midbodies for all cell lines, and in PC for all cell lines except WE-skin11f. Staining of cytoplasmic microtubules (fibrils) was absent in three cell lines, including WEBA, but present in the others, especially WE-skin11f, which might have obscured PC detection in these cells. Tubacin, an inhibitor of histone deacetylase 6, induced cytoplasmic fibrils in WEBA and the intensity of their staining in WE-cfin11f. These results suggest that the cell lines might differ in their deacetylase activities, making them useful for studying this tubulin modification in teleosts, as well as for studying PC.     

Marine mortality in the river? Atlantic salmon smolts under high predation pressure in the last kilometres of a river monitored for stock assessment

The River Bush (Northern Ireland) is an index river for the estimation of Atlantic salmon, Salmo salar L., stock size, population dynamics and marine survival rates. Marine survival estimates are based on the number of smolts counted at a trap 3.5 km upstream of the river outlet. The survival from release to coastal inshore waters for acoustic‐tagged smolts released at the Bushmills trap varied between 32% and 68%, with both year and brightness during river exit playing a significant role in explaining the variations in survival. This constitutes an important survival bottleneck. Contrary to true marine mortality, this significant loss of smolts in the river and nearshore environments could be reduced by focused management actions. More studies on other rivers, where smolts are enumerated above the head of tide, could further partition smolt and post‐smolt mortality, help differentiate true marine survival and help understand fluctuations in adult returns.     

Testing the yield of a pilot‐scale bubble column photobioreactor for cultivation of the microalga Rhodomonas salina as feed for intensive calanoid copepod cultures

A dual column photobioreactor (PBR) (2 × 47 L) with mixed CO₂/air bubbling was tested for cultivation of the microalga Rhodomonas salina as food for live feed copepods. In the continuous growth phase, the cell density was relatively stable at 2.40 ± 0.13 × 10⁶ cells/ml at an average dilution rate of 0.46 ± 0.02 per day throughout the 30‐day experiment. The produced algae had a high content of both total fatty acids (TFA) and free amino acids (FAA). Especially, the harvested algae contained a high proportion of poly‐unsaturated fatty acids that made up 80% of the TFA and of essential amino acids (35% of all FAA), implicating desirable components as feed for copepods. The current PBR was sufficient to feed a culture of the calanoid copepod Acartia tonsa at a density of 2,500 adult/L in ca. 500 L culture with a daily yield of approximately 17 × 10⁶ eggs. To be able to sustain the integrated copepods production, the suggested volume of the algae cultures should be ca. 20% of the copepod culture volume.     

Selective haddock (Melanogrammus aeglefinus) trawling: Avoiding cod (Gadus morhua) bycatch

The critical condition of the North Sea cod stocks has resulted in restrictions on not only cod, but also haddock and other species that are caught together with cod. Thus full exploitation of the haddock stock is unachievable unless cod can be excluded from the haddock catch. We designed a selective trawl based on the behavioral differences between haddock and cod as they enter a trawl, i.e., cod stay close to the seabed whereas haddock rise above it. The trawl's fishing line is raised ～60 cm above the seabed to allow cod to escape beneath the trawl while haddock are retained. To collect the escapees, three sampling bags were attached beneath the raised fishing line. The selective haddock trawl reduced the total catch of cod by 55% during the day and 82% at night, and 99% of the marketable haddock was caught during the day and 89% at night. Cod escape rates were highly length dependent: smaller cod escaped the trawl in greater numbers than did larger individuals. Whiting, saithe, lemon sole, and plaice were included in the analysis.     

Effect of Herbicide Treatment on Host Plant Quality for a Leaf-Eating Beetle

The effect of sub-lethal chlorsulfuron treatment of the annual weed Polygonum convolvulus L. on growth and survival of the folivorous beetle Gastrophysa polygoni L. was studied in a controlled environment. Treated and untreated plants were used in whole plant bioassays and in feeding experiments with excised leaves. Direct insect toxicity of the herbicide was studied by use of a Potter Spray Tower. The herbicide was non-toxic to the larvae when applied topically. Larvae fed excised leaves from treated plants did not differ from larvae fed leaves from control plants in terms of developmental time, weight or survival. This suggests that the treatment did not affect the nutritional value of the plant or at least that the beetles could compensate for any such changes. Chlorsulfuron reduced survival of larvae living on whole plants treated with sub-lethal dosages (8 to 67% of the recommended field rate). The mortality of larvae in whole plant experiments was dependent on herbicide dosage and herbivore load. Mortality ranged from approximately 20% on control plants to a maximum of 80% on plants sustaining the highest dosages and herbivore loads. It is argued that the beetles' response to chlorsulfuron-treated plants could be caused by a herbivore-induced plant response enhanced by the action of chlorsulfuron.     

Diagnostic Features of Clinical Neurologic Feline Infectious Peritonitis

Feline infectious peritonitis (FIP) is a fatal Arthus-type immune response of cats to infection with FIP virus, a mutant of the ubiquitous feline enteric coronavirus (FECV). The disease may occur systemically or in any single organ system, and primary neurologic disease is a common subset of such manifestations. We examined 16 domestic cats with clinical neurologic FIP and 8 control cats with nonneurologic FIP, with the intention of identifying the ante-and postmortem diagnostic tests that most contribute to accurate diagnosis. Of the 16 cats with neurologic FIP, 15 were less than 2 years of age and all 16 originated from large multiplecat households. The most useful antemortem indicators of disease were positive anti-coronavirus IgG titer in cerebrospinal fluid, high serum total protein concentration, and findings on magnetic resonance imaging suggesting periventricular contrast enhancement, ventricular dilatation, and hydrocephalus. Postmortem diagnosis was facilitated by FIP monoclonal antibody staining of affected tissue and coronavirus-specific polymerase chain reaction. Most cats with neurologic and ocular forms of FIP had patchy, focal lesions, suggesting that recently developed technologies described in this report may be useful for evaluation of cats with suspected FIP.     

Genetic analysis of resistance to nematodes in inbred maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.) and maize hybrids

Nematodes cause substantial grain yield loss in susceptible maize (Zea mays L.) cultivars. This study was conducted to estimate general combining ability (GCA), specific combining ability (SCA) and genetic effects associated with nematode resistance in maize. The 30 F ₁ hybrids generated from a 6 × 6 diallel and two local checks were evaluated in 2009 at three sites in Uganda. A split plot design was used with nematode treatments serving as whole plots and the hybrids as subplots but arranged in an 8 × 4 spatially adjusted alpha-lattice design. The experiment was replicated three times. Results showed GCA to be important for the reduction of P. zeae and Meloidogyne spp. densities and increase of root mass, with a contribution of 72 to 93% of the phenotypic variance. Inbreds MP709 and CML206 had the highest GCA for Pratylenchus zeae resistance, whereas for grain yield, it was CML444, CML312 and CML395 that were outstanding. The SCA influenced plant height and grain yield under nematode infestation, contributing 43 and 58% of the phenotypic variance, respectively. Observed reciprocal differences due to maternal effects also played a role in influencing the grain yield under nematode infestation. Overdominance genetic effects explained the non-additive variance recorded for the plant height, grain yield, number of root lesions, and P. zeae and Meloidogyne spp. densities under nematode infestation. The parents MP709, CML206, 5057, and CML444 contributed most of the dominant genes for the P. zeae resistance in all their crosses. The parent CML444 contributed most of the dominant genes for improved grain yield in all of its crosses. The high GCA effects among some parents support their utility in breeding of widely adapted nematode-resistant cultivars. The dominant genes and SCA effects would favour pedigree and various sib tests to improve grain yield under nematode pressure.     

Strain-specific vital rates in four Acartia tonsa cultures II: Life history traits and biochemical contents of eggs and adults

The need of copepods as live feed is increasing in aquaculture because of the limitations of traditionally used preys, and this increases the demand for an easy and sustainable large-scale production of copepods. In this study, 4 strains of the copepod Acartia tonsa Dana, 1849 were compared in a common garden experiment to identify a strain with life history traits essential for sustainable mass cultivation of copepods and to identify a strain which produces preys with a highly valuable chemical composition. The strains originated from 4 coastal sites in Øresund, Denmark (DIFRES), Kiel, Germany (KIEL), Turkey Point, Florida, USA, and Mobile Bay, Alabama, USA. Stage development and mortality were analysed at 17 °C, 34 ppt. When the copepods reached adulthood, individual females were isolated to determine the egg production and hatching success. The biochemical contents of both eggs and adults were evaluated for all strains. The DIFRES and Alabama strains had both shorter generation time (13.7 and 14.6 d^− 1, respectively) and lower mortality (4.0 and 5.7% d^− 1, respectively) than other strains, making them attractive for mass cultivation. Strain-specific patterns were observed in egg production, with highest productivity observed in the DIFRES strain. Hatching success of the eggs ranged from 47.3 to 83.6% in the DIFRES, Kiel and Alabama strains, but showed reduced hatching in the Florida strain (1.6 to 7.2%). The strains had similar total free amino acids (FAA) content in the eggs in comparison to their dry weight (6–8%). In general, the FAA pattern of the eggs was dominated by Proline, while the females had a more diffuse FAA pattern. The fatty acid ratio between DHA and EPA in the eggs was lowest for the Florida strain (0.82) and highest in the Alabama strain (1.48), and adults had even higher ratios (2.1 to 2.45). Apart from the low DHA/EPA ratio in the Florida eggs, we find that all the strains met nutritional values needed for the first feeding of marine finfish larvae. However, essential criteria for mass cultivation such as fast development, low mortality and high egg production led us to recommend the use of the DIFRES strain of A. tonsa under the present growth conditions. A study to optimize the copepod cultivation to meet industry's criteria should include deliberate selection pressure on copepod to promote the needed traits for first feeding of finfish larvae.