Chinook salmon Oncorhynchus tshawytscha support important subsistence and commercial fisheries throughout the Yukon River. Low returns and diverse user groups have made management of these fisheries ...contentious and have necessitated information on the origin of the spawning migration and harvest. Here we compare estimates of individual assignment and stock composition derived from genetic and radiotelemetry data collected from the same Chinook salmon. Radiotelemetry and genetic individual assignments were highly concordant. Agreement between methods for individual assignment was 79% to region and 93% to country when using the most probable genetic criterion, improving to 94% for region and 98% for country when using the ≥95% probability genetic criterion; however, under the more stringent criterion, fewer individuals could be assigned. Further analysis showed that estimates of stock composition based on radiotelemetry and genetic methods were within 6% of each other and were not significantly different. The concordance between estimates of individual assignment and stock composition from the radiotelemetry and genetic methods indicates that both methods are credible tools for fishery assessment of Yukon River Chinook salmon. Received October 14, 2011; accepted April 17, 2012
Single-nucleotide polymorphisms from western Alaska Larson, Wesley A; Seeb, James E; Pascal, Carita E ...
Canadian journal of fisheries and aquatic sciences,
05/2014, Letnik:
71, Številka:
5
Journal Article
Recenzirano
Genetic stock identification (GSI), an important tool for fisheries management that relies upon the ability to differentiate stocks of interest, can be difficult when populations are closely related. ...Here we genotyped 11850 single-nucleotide polymorphisms (SNPs) from existing DNA sequence data available in five closely related populations of Chinook salmon (Oncorhynchus tshawytscha) from western Alaska. We then converted a subset of 96 of these SNPs displaying high differentiation into high-throughput genotyping assays. These 96 SNPs (RAD96) and 191 SNPs developed previously (CTC191) were screened in 28 populations from western Alaska. Regional assignment power was evaluated for five different SNP panels, including a panel containing the 96 SNPs with the highest F.sub.ST across the CTC191 and RAD96 panels (F.sub.ST96). Assignment tests indicated that SNPs in the RAD96 were more useful for GSI than those in the CTC191 and that increasing the number of reporting groups in western Alaska from one to three was feasible with the F.sub.ST96. Our approach represents an efficient way to discover SNPs for GSI and should be applicable to other populations and species.
Background Left ventricle (LV) remodeling after anterior wall myocardial infarction leads to increased LV volumes, myocardial stress, and, ultimately, heart failure (HF). Patients have high morbidity ...and mortality risk, and treatment remains limited. Percutaneous ventricular restoration (PVR) therapy using the Parachute device, a fluoropolymer membrane stretched over a nitinol conical frame, is a novel approach to partition off the damaged myocardium. In the European and United States PARACHUTE feasibility trials, the observed rates of death or rehospitalization for HF were <17% at 12 months. These data compare favorably with historical data and support the need of a randomized trial to determine the clinical efficacy of PVR on outcomes for patients with ischemic HF. Objective To determine the safety and efficacy of PVR utilizing a LV partitioning device, Parachute, in a randomized clinical trial compared with optimal medical therapy. Methods This US pivotal trial is approved by the Food and Drug Administration (ClinicalTrials.gov Identifier: NCT01286116) and will randomly assign (1:1) 478 patients with New York Heart Association class III-IV ischemic HF, akinetic or dyskinetic LV wall abnormality, and ejection fraction between 15% and 35% to optimal medical therapy (control) versus Parachute device implantation in approximately 65 hospitals. The primary endpoint is death or rehospitalization for worsening HF. Sample size calculation assumes constant hazards and follow-up ≥12 months using an event-driven trial design. Conclusions We reported the rational and design of the first multicenter randomized trial to test the efficacy of PVR using the Parachute device to treat patients with ischemic HF and dilated LV.
Wildlife managers and researchers often need to estimate the relative contributions of distinct populations in a mixture of organisms. Increasingly, there is interest in comparing these mixture ...contributions across space or time. Comparisons usually just check for overlap in the interval estimates for each population contribution from each mixture. This method inflates Type I error rates, has limited power due to its focus on marginal comparisons, and employs a fundamentally inappropriate measure of mixture difference. Given the difficulty of defining an appropriate measure of mixture difference, a powerful alternative is to compare mixtures using a likelihood ratio test. In applications where the standard asymptotic theory does not hold, the null reference distribution can be obtained through parametric bootstrapping. In addition to testing simple hypotheses, a likelihood ratio framework encourages modeling the change in mixture contributions as a function of covariates. The method is demonstrated with an analysis of potential sampling bias in the estimation of population contributions to the commercial sockeye salmon (Oncorhynchus nerka) fishery in Upper Cook Inlet, Alaska.
Baraitser-Winter, Fryns-Aftimos and cerebrofrontofacial syndrome types 1 and 3 have recently been associated with heterozygous gain-of-function mutations in one of the two ubiquitous cytoplasmic ...actin-encoding genes ACTB and ACTG1 that encode β- and γ-actins. We present detailed phenotypic descriptions and neuroimaging on 36 patients analyzed by our group and six cases from the literature with a molecularly proven actinopathy (9 ACTG1 and 33 ACTB). The major clinical anomalies are striking dysmorphic facial features with hypertelorism, broad nose with large tip and prominent root, congenital non-myopathic ptosis, ridged metopic suture and arched eyebrows. Iris or retinal coloboma is present in many cases, as is sensorineural deafness. Cleft lip and palate, hallux duplex, congenital heart defects and renal tract anomalies are seen in some cases. Microcephaly may develop with time. Nearly all patients with ACTG1 mutations, and around 60% of those with ACTB mutations have some degree of pachygyria with anteroposterior severity gradient, rarely lissencephaly or neuronal heterotopia. Reduction of shoulder girdle muscle bulk and progressive joint stiffness is common. Early muscular involvement, occasionally with congenital arthrogryposis, may be present. Progressive, severe dystonia was seen in one family. Intellectual disability and epilepsy are variable in severity and largely correlate with CNS anomalies. One patient developed acute lymphocytic leukemia, and another a cutaneous lymphoma, indicating that actinopathies may be cancer-predisposing disorders. Considering the multifaceted role of actins in cell physiology, we hypothesize that some clinical manifestations may be partially mutation specific. Baraitser-Winter cerebrofrontofacial syndrome is our suggested designation for this clinical entity.
We examined genetic diversity patterns among 55 collections of Chum Salmon from the northeastern Pacific Ocean using 89 single nucleotide polymorphisms (SNPs). The distribution of Chum Salmon samples ...extended from the Nass River along the coast of British Columbia and along the coast of Washington as far south as the Columbia River. Chum Salmon represented three previously defined run-groups: fall (primarily), summer, and winter. Genetic variation at SNP loci, as measured by F ST, ranged from 0.002 to 0.279 over all collections and averaged 0.062 over all loci. Similar to the genetic patterns detected with microsatellites and allozymes, genetic variation followed a regional structure along geographic distance, with genetic diversity being highest in the north and decreasing southward, then increasing in and near the Columbia River. Within Puget Sound, Washington, genetic variation was structured further according to run timing (fall, summer, and winter) and shared ancestry. Simulations indicated that this suite of SNPs is powerful for identifying regional components in a Chum Salmon mixed fishery. Because of the transferability of SNP data, the growing SNP baseline for Chum Salmon will be useful for multiple agencies managing Chum Salmon around the Pacific Rim. Received December 19, 2014; accepted May 20, 2015
Detecting Specific Populations in Mixtures Reynolds, Joel Howard; Templin, William David
Environmental biology of fishes,
03/2004, Letnik:
69, Številka:
1-4
Journal Article
Recenzirano
Mixed stock analysis (MSA) estimates the relative contributions of distinct populations in a mixture of organisms. Increasingly, MSA is used to judge the presence or absence of specific populations ...in specific mixture samples. This is commonly done by inspecting the bootstrap confidence interval of the contribution of interest. This method has a number of statistical deficiencies, including almost zero power to detect small contributions even if the population has perfect identifiability. We introduce a more powerful method based on the likelihood ratio test and compare both methods in a simulation demonstration using a 17 population baseline of sockeye salmon, Oncorhynchus nerka, from the Kenai River, Alaska, watershed. Power to detect a nonzero contribution will vary with the population(s) identifiability relative to the rest of the baseline, the contribution size, mixture sample size, and analysis method. The demonstration shows that the likelihood ratio method is always more powerful than the bootstrap method, the two methods only being equal when both display 100% power. Power declines for both methods as contribution declines, but it declines faster and goes to zero for the bootstrap method. Power declines quickly for both methods as population identifiability declines, though the likelihood ratio test is able to capitalize on the presence of 'perfect identification' characteristics, such as private alleles. Given the baseline-specific nature of detection power, researchers are encouraged to conduct a priori power analyses similar to the current demonstration when planning their applications.
We analyzed the demographic, clinical, laboratory and histologic features of 13 patients who were diagnosed as having polyarteritis nodosa associated with hepatitis B virus infection over a 12‐year ...period, 1974 to 1985. All 13 patients were Yupik Eskimos and resided in southwest Alaska, an area hyperendemic for hepatitis B virus infection. The annual incidence of hepatitis B virus‐associated polyarteritis nodosa for this population is 7.7 cases per 100,000 population. All patients presented with multisystem disease, and all had biopsy or angiographic findings consistent with polyarteritis nodosa. All 13 were positive for hepatitis B surface antigen and hepatitis B e antigen at diagnosis. Two untreated patients and two of five patients who received corticosteroids died, vs. none of six who received corticosteroids plus cyclophosphamide. None of the patients who survived the initial bout of polyarteritis nodosa has relapsed after a mean follow‐up of 55 months, but all have become chronic HBsAg carriers. In eight patients, clinical or serologic evidence indicated that polyarteritis nodosa followed recent hepatitis B virus infection. We concluded that hepatitis B virus‐associated polyarteritis nodosa is a serious, life‐threatening complication that occurs early in the course of hepatitis B virus infection, is ameliorated by immunosuppressive therapy and can be prevented by hepatitis B vaccine.
The reaction of ferrous bleomycin with dioxygen is reexamined to clarify whether radical species derived from molecular oxygen are generated. Detection of low levels of spin-trapped oxyradicals ...confirm the production of OH during this reaction when bleomycin is present in excess, but not when iron and drug concentrations are equal. In phosphate buffer, hydroxyl radicals continue to be spin trapped for at least 15 min after Fe(II)bleomycin has been oxidized to Fe(III)bleomycin. In HEPES buffer, detection of a HEPES radical in the absence of spin trap over the same period independently supports the conclusion that reactive radicals are present after the initial oxidation of Fe(II)bleomycin is complete. When glutathione is included in the aerobic reaction mixture, thiyl radical species are spin trapped. The reaction of Fe(III)bleomycin with cysteine produces thiyl radical without spin-trapped hydroxyl radical.
The Yukon River is one of the largest producers of chum salmon (Oncorhynchus keta) in western Alaska. Management of Yukon River chum salmon is complex. One of the current concerns is overharvesting ...of the fall-run component. An earlier and typically more abundant summer-run type spawns in the lower to middle reaches of the drainage, whereas the genetically distinct fall-run type spawns in the middle to upper reaches in Alaska and Canada. Juvenile chum salmon migrate from the Yukon River in the spring and are found in the pelagic waters on the eastern Bering Sea shelf during summer and fall months. We genetically analyzed juvenile chum salmon caught on the eastern Bering Sea shelf during the 2003–2007 Bering-Aleutian Salmon International Surveys. Juvenile chum salmon were predominately from coastal western Alaska and upper/middle Yukon River populations. The relative proportions of fall and summer Yukon chum salmon varied considerably across years. The proportion of fall-run chum salmon in the juvenile collections was positively correlated with the proportion of fall-run chum salmon in the adult returns to the Yukon River, suggesting that the brood-year strength of Yukon River summer and fall-run chum salmon is determined early in the first year of life.
PDF
