Filtering method for obtaining stock indices by shark species from species-combined logbook data in tuna longline fisheries

ABSTRACT:   A method of filtering logbook data to obtain estimates of catch per unit effort (CPUE) for sharks has been proposed which simultaneously addresses the issues of under-reporting and the lack of species-specific catch records in historical data. Logbook catch data from vessels with high shark reporting rates are used to represent catch rates for the abundant blue shark Prionace glauca and low reporting vessels' data are used for the main commercially valuable species, the shortfin mako Isurus oxyrinchus . Logbook reporting rate filter (RRF) levels are evaluated through analytical and model-based comparisons to species-specific logbook records available since 1994 and shipboard observer data. At the high reporting rates, the ≥ 80% filter avoids large numbers of false zeros and provides the best fit to observer data for blue shark. At the low reporting rates, the ≤ 40% filter best matches the observer data for makos, but this filter level includes large numbers of false zeros and sharks of other species. The ≤ 20% filter produces a dataset that is better targeted to mako catches but considerably under-estimates CPUE relative to observer records. For these reasons, other means of estimating mako catch rates are suggested for further research.     

Parental effects on the performance of cultivated × wild species hybrids in potato

Valuable genetic diversity in diploid wild Solanum species can be accessed through crosses to haploids (2n = 2×) of the tetraploid cultivated potato, Solanum tuberosum. Haploid-wild species hybrids segregate for the ability to tuberize in the field. In addition, they vary in male fertility, vine size, stolon length, and tuber size. In this study, three haploids were crossed with nine diploid wild Solanum species and 27 hybrid families were evaluated in the field for two years. The proportion of male fertile hybrid clones varied depending on the wild species parent. A large effect of the female parent was detected for vine size, stolon length, tuber size, percent tuberization, and percent plants selected for agronomic quality. An exceptional haploid (US-W4) was identified for the production of agronomically desirable haploid-wild species hybrids. In hybrids derived from US-W4, differences among wild species parents were observed for agronomic quality. Superior hybrids were produced by S. berthaultii and S. microdontum. Reciprocal crosses were evaluated for a subset of families. When the wild species was used as the female parent, male fertility was restored, but tuberization and tuber size were reduced. Careful selection of both haploid and wild species parents can result in a large proportion of fertile, agronomically desirable hybrid offspring.     

Chondrules with peculiar REE patterns: implications for solar nebular condensation at high C/O

Rare earth element (REE) data from two ordinary chondrite chondrules show distinct negative chondrite-normalized concentration anomalies of samarium, europium, and ytterbium. The peculiar patterns may be the result of REE gas/solid fractionation at an oxygen fugacity lower than has been assumed for the canonical solar nebula. We suggest that the two ordinary chondrite chondrules acquired the fractionated REE patterns by incorporation of highly reduced, ultrarefractory condensates in their precursors. This interpretation implies that high-temperature condensation processes occurred in nebular environments with a strong deficit in oxygen, such as regions with an enhanced carbon/oxygen ratio.     

A decision-analytic approach to the optimal allocation of resources for endangered species consultation

The resources available to support conservation work, whether time or money, are limited. Decision makers need methods to help them identify the optimal allocation of limited resources to meet conservation goals, and decision analysis is uniquely suited to assist with the development of such methods. In recent years, a number of case studies have been described that examine optimal conservation decisions under fiscal constraints; here we develop methods to look at other types of constraints, including limited staff and regulatory deadlines. In the US, Section Seven consultation, an important component of protection under the federal Endangered Species Act, requires that federal agencies overseeing projects consult with federal biologists to avoid jeopardizing species. A benefit of consultation is negotiation of project modifications that lessen impacts on species, so staff time allocated to consultation supports conservation. However, some offices have experienced declining staff, potentially reducing the efficacy of consultation. This is true of the US Fish and Wildlife Service’s Washington Fish and Wildlife Office (WFWO) and its consultation work on federally-threatened bull trout (Salvelinus confluentus). To improve effectiveness, WFWO managers needed a tool to help allocate this work to maximize conservation benefits. We used a decision-analytic approach to score projects based on the value of staff time investment, and then identified an optimal decision rule for how scored projects would be allocated across bins, where projects in different bins received different time investments. We found that, given current staff, the optimal decision rule placed 80% of informal consultations (those where expected effects are beneficial, insignificant, or discountable) in a short bin where they would be completed without negotiating changes. The remaining 20% would be placed in a long bin, warranting an investment of seven days, including time for negotiation. For formal consultations (those where expected effects are significant), 82% of projects would be placed in a long bin, with an average time investment of 15 days. The WFWO is using this decision-support tool to help allocate staff time. Because workload allocation decisions are iterative, we describe a monitoring plan designed to increase the tool’s efficacy over time. This work has general application beyond Section Seven consultation, in that it provides a framework for efficient investment of staff time in conservation when such time is limited and when regulatory deadlines prevent an unconstrained approach.     

A real-time PCR assay to detect the Panton Valentine Leukocidin toxin in staphylococci: screening Staphylococcus schleiferi subspecies coagulans strains from companion animals

Recent reports suggest that methicillin-resistant strains of Staphylococcus schleiferi subspecies coagulans are now commonly isolated from dogs. Given the association of a potentially mobile SCCmec type IV element with lysogenic phage-encoded Panton Valentine Leukocidin (PVL) toxin genes in community-acquired methicillin-resistant Staphylococcus aureus strains we hypothesized that methicillin-resistant S. schleiferi ssp. coagulans strains may also encode PVL toxin genes. Forty S. schleiferi ssp. coagulans strains isolated from companion animals were studied. Susceptibility to oxacillin was determined by broth microdilution and all isolates were screened by PCR for the presence of the mecA gene. SCCmec typing was performed on 14 isolates. A real-time PCR assay was developed for the detection of the PVL genes using a SmartCycler. Pulsed-field gel electrophoresis (PFGE) was performed to determine whether S. schleiferi ssp. coagulans strains were homogeneous. Twenty-eight of the 40 isolates (70%) were resistant to oxacillin and 26/28 possessed the mecA gene by PCR. SCCmec IV was identified in seven strains; the other seven isolates were not typable by this technique. All 40 strains were negative for the PVL toxin gene. PFGE showed a heterogeneous population and 13 different profiles were determined. In conclusion, this study showed that PVL toxin genes were not detected in a heterogeneous population of methicillin-resistant S. schleiferi ssp. coagulans strains isolated from companion animals.     

Putative transmission of Mycobacterium tuberculosis infection from a human to a dog

A 3.5-year-old Yorkshire Terrier was evaluated for anorexia and vomiting; infection with Mycobacterium tuberculosis was diagnosed by use of histology, bacteriologic culture, and polymerase chain reaction (PCR) assay on various tissues. The dog was living with a human with an established M. tuberculosis infection. Findings were unique in that diagnosis of M. tuberculosis infection was obtained via PCR techniques, and isolates from the owner and dog were matched via restriction fragment length polymorphism fingerprinting. Dogs infected with M. tuberculosis from humans are most commonly infected via the respiratory tract. Clinical signs in dogs are variable and depend on the integrity of the immune system and the degree of dissemination. Diagnosis can often be obtained through histopathology and bacteriologic culture; additional diagnostic techniques are also available. Treatment of a dog with confirmed M. tuberculosis infection is controversial, and at least 6 months of multidrug treatment is required.     

Optimization of a Staphylococcus aureus adhesion assay for equine corneocytes

Meticillin-resistant Staphylococcus aureus (MRSA) causes serious skin and soft-tissue infections of humans and animals. Multiple strains of MRSA have been characterized, and one in particular, designated as strain USA 500, causes infections predominantly of horses and the people who work with them. The purpose of this study was to optimize an assay which could subsequently be used to compare the relative avidity of different S. aureus strains for equine corneocytes. Corneocytes were collected from the perineal skin of 10 healthy horses onto adhesive discs. The discs were then incubated at 37°C with an S. aureus field strain at each of three concentrations [10(7), 10(8) and 10(9) colony forming units (CFU)/mL] and for each of three incubation periods (45, 90 and 180 min). After standardized rinsing and staining procedures, discs were examined at ×1,000 magnification and areas containing confluent corneocytes photographed. The percentage of surface area occupied by adherent bacteria was analysed using image processing and analysis software. Significant colour space image processing was required to distinguish bacteria from the ubiquitous melanin granules present within equine corneocytes. Objective and subjective methods were used to determine optimal conditions for specific adherence without introducing confounding factors. A bacterial concentration of 10(8) CFU/mL incubated with corneocytes for 45 min produced maximal bacterial adhesion with the least amount of interbacterial clumping. Future studies should utilize these conditions for optimal assay performance.     

Effects of 2 different medetomidine infusion rates on selected neurohormonal and metabolic parameters in dogs

The effects of 2 different 8-hour continuous rate infusions (CRIs) of medetomidine on epinephrine, norepinephrine, cortisol, glucose, and insulin levels were investigated in 6 healthy dogs. Each dog received both treatments and a control as follows: MED1 = 2 μg/kg bodyweight (BW) loading dose followed by 1 μg/kg BW per hour CRI; MED2 = 4 μg/kg BW loading dose followed by 2 μg/kg BW per hour CRI; and CONTROL = saline bolus followed by a saline CRI. Both infusion rates of medetomidine decreased norepinephrine levels throughout the infusion compared to CONTROL. While norepinephrine levels tended to be lower with the MED2 treatment compared to the MED1, this difference was not significant. No differences in epinephrine, cortisol, glucose, or insulin were documented among any of the treatments at any time point. At the low doses used in this study, both CRIs of medetomidine decreased norepinephrine levels over the 8-hour infusion period, while no effects were observed on epinephrine, cortisol, glucose, and insulin.