Occurrence of anisakid larvae (Nematoda: Ascardidia) in fishes from Alaska and Idaho

All 25 sablefish ( Anoplopoma fimbria ) examined from two bays near Sitka, Alaska, were infected with anisakid larvae. There were 1 to 11 larvae per infected fish, with worms encysted in the musculature of the body wall of 5 fish and in the liver of 4 fish. For the other hosts the viscera was the site of infection. Chinook salmon ( Onchorhynchus tshawytscha ) from Barrow, Alaska, and Obsidian, Idaho, were also infected with anisakid larvae. These data extend the known northern distribution of the anisakids along the Pacific Coast for sablefish and chinook salmon. The pathogenesis of the migratory pathway of anisakid larvae is described, and comments on human health implications are presented.     

The draft genome of the parasitic nematode Trichinella spiralis

Genome evolution studies for the phylum Nematoda have been limited by focusing on comparisons involving Caenorhabditis elegans. We report a draft genome sequence of Trichinella spiralis, a food-borne zoonotic parasite, which is the most common cause of human trichinellosis. This parasitic nematode is an extant member of a clade that diverged early in the evolution of the phylum, enabling identification of archetypical genes and molecular signatures exclusive to nematodes. We sequenced the 64-Mb nuclear genome, which is estimated to contain 15,808 protein-coding genes, at ～35-fold coverage using whole-genome shotgun and hierarchal map-assisted sequencing. Comparative genome analyses support intrachromosomal rearrangements across the phylum, disproportionate numbers of protein family deaths over births in parasitic compared to a non-parasitic nematode and a preponderance of gene-loss and -gain events in nematodes relative to Drosophila melanogaster. This genome sequence and the identified pan-phylum characteristics will contribute to genome evolution studies of Nematoda as well as strategies to combat global parasites of humans, food animals and crops.     

Variants modulating the expression of a chromosome domain encompassing PLAG1 influence bovine stature

We report mapping of a quantitative trait locus (QTL) with a major effect on bovine stature to a ～780-kb interval using a Hidden Markov Model-based approach that simultaneously exploits linkage and linkage disequilibrium. We re-sequenced the interval in six sires with known QTL genotype and identified 13 clustered candidate quantitative trait nucleotides (QTNs) out of >9,572 discovered variants. We eliminated five candidate QTNs by studying the phenotypic effect of a recombinant haplotype identified in a breed diversity panel. We show that the QTL influences fetal expression of seven of the nine genes mapping to the ～780-kb interval. We further show that two of the eight candidate QTNs, mapping to the PLAG1-CHCHD7 intergenic region, influence bidirectional promoter strength and affect binding of nuclear factors. By performing expression QTL analyses, we identified a splice site variant in CHCHD7 and exploited this naturally occurring null allele to exclude CHCHD7 as single causative gene.     

Chromosome races in Sarcobatus (Sarcobataceae, Caryophyllales)

Sarcobatus Nees., a genus of North American halophytic shrubs, consists of 2 species: S. vermiculatus (Hook.) Torr. ( n = 18, 36), which is widespread in North America, and S. baileyi Cov ( n = 54), endemic to Nevada. Within S. vermiculatus , populations of n = 36 are widely distributed, whereas populations of n = 18 are found only in the Sonoran Desert, northern California, and northwestern Great Plains, locations at the periphery of the species range. Although the chromosome number of n = 18 is apparently a tetraploid, failure to form and n = 27 race intermediate to those of n = 18 and n = 36 suggests than n = 18 S. vermiculatus is of significant age and that it behaves chromosomally as a diploid. Sacrobatus has a long fossil pollen record and endured Pleistocene climatic extremes with little range displacement.     

Records of exotic fishes from Idaho and Wyoming

One exotic poeciliid ( Xiphophorus helleri ) and two cichlids ( Cichlasoma nigrofasciatum and Tilapia mossambica ) are recorded as recently established in thermal springs and their outflows in southern Idaho. Misgurnus anguillicaudatus was collected and is considered as established in the Boise River system. Poecilia mexicana and juvenile hybrid tilapias are recorded from the Bruneau River at Bruneau Hot Springs, Idaho. A reproducing population of X. helleri was found in a spring within the boundaries of Grand Teton National Park, Wyoming. Poecilia reticulata , previously reported from one spring each in Idaho and Wyoming, is recorded from a second spring outflow in Idaho.     

Identification of common variants associated with human hippocampal and intracranial volumes

Identifying genetic variants influencing human brain structures may reveal new biological mechanisms underlying cognition and neuropsychiatric illness. The volume of the hippocampus is a biomarker of incipient Alzheimer's disease and is reduced in schizophrenia, major depression and mesial temporal lobe epilepsy. Whereas many brain imaging phenotypes are highly heritable, identifying and replicating genetic influences has been difficult, as small effects and the high costs of magnetic resonance imaging (MRI) have led to underpowered studies. Here we report genome-wide association meta-analyses and replication for mean bilateral hippocampal, total brain and intracranial volumes from a large multinational consortium. The intergenic variant rs7294919 was associated with hippocampal volume (12q24.22; N = 21,151; P = 6.70 × 10(-16)) and the expression levels of the positional candidate gene TESC in brain tissue. Additionally, rs10784502, located within HMGA2, was associated with intracranial volume (12q14.3; N = 15,782; P = 1.12 × 10(-12)). We also identified a suggestive association with total brain volume at rs10494373 within DDR2 (1q23.3; N = 6,500; P = 5.81 × 10(-7)).     

Bayesian Forecasting for Financial Risk Management,Pre and Post the Global Financial Crisis

Value‐at‐risk (VaR) forecasting via a computational Bayesian framework is considered. A range of parametric models is compared, including standard, threshold nonlinear and Markov switching generalized autoregressive conditional heteroskedasticity (GARCH) specifications, plus standard and nonlinear stochastic volatility models, most considering four error probability distributions: Gaussian, Student‐t, skewed‐t and generalized error distribution. Adaptive Markov chain Monte Carlo methods are employed in estimation and forecasting. A portfolio of four Asia–Pacific stock markets is considered. Two forecasting periods are evaluated in light of the recent global financial crisis. Results reveal that: (i) GARCH models outperformed stochastic volatility models in almost all cases; (ii) asymmetric volatility models were clearly favoured pre crisis, while at the 1% level during and post crisis, for a 1‐day horizon, models with skewed‐t errors ranked best, while integrated GARCH models were favoured at the 5% level; (iii) all models forecast VaR less accurately and anti‐conservatively post crisis. Copyright © 2011 John Wiley & Sons, Ltd.     

Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma

We characterized the mutational landscape of melanoma, the form of skin cancer with the highest mortality rate, by sequencing the exomes of 147 melanomas. Sun-exposed melanomas had markedly more ultraviolet (UV)-like C>T somatic mutations compared to sun-shielded acral, mucosal and uveal melanomas. Among the newly identified cancer genes was PPP6C, encoding a serine/threonine phosphatase, which harbored mutations that clustered in the active site in 12% of sun-exposed melanomas, exclusively in tumors with mutations in BRAF or NRAS. Notably, we identified a recurrent UV-signature, an activating mutation in RAC1 in 9.2% of sun-exposed melanomas. This activating mutation, the third most frequent in our cohort of sun-exposed melanoma after those of BRAF and NRAS, changes Pro29 to serine (RAC1(P29S)) in the highly conserved switch I domain. Crystal structures, and biochemical and functional studies of RAC1(P29S) showed that the alteration releases the conformational restraint conferred by the conserved proline, causes an increased binding of the protein to downstream effectors, and promotes melanocyte proliferation and migration. These findings raise the possibility that pharmacological inhibition of downstream effectors of RAC1 signaling could be of therapeutic benefit.