Genome-wide SNP identification in Fraxinus linking genetic characteristics to tolerance of Agrilus planipennis

Ash (Fraxinus spp.) is one of the most widely distributed tree genera in North America. Populations of ash in the United States and Canada have been decimated by the introduced pest Agrilus planipennis (Coleoptera: Buprestidae; emerald ash borer), having negative impacts on both forest ecosystems and economic interests. The majority of trees succumb to attack by A. planipennis, but some trees have been found to be tolerant to infestation despite years of exposure. Restriction site-associated DNA (RAD) sequencing was used to sequence ash individuals, both tolerant and susceptible to A. planipennis attack, in order to identify single nucleotide polymorphism (SNP) patterns related to tolerance and health declines. de novo SNPs were called using SAMtools and, after filtering criteria were implemented, a set of 17,807 SNPs were generated. Principal component analysis (PCA) of SNPs aligned individual trees into clusters related to geography; however, five tolerant trees clustered together despite geographic location. A subset of 32 outlier SNPs identified within this group, as well as a subset of 17 SNPs identified based on vigor rating, are potential candidates for the selection of host tolerance. Understanding the mechanisms of host tolerance through genome-wide association has the potential to restore populations with cultivars that are able to withstand A. planipennis infestation. This study was successful in using RAD-sequencing in order to identify SNPs that could contribute to tolerance of A. planipennis. This was a first step toward uncovering the genetic basis for host tolerance to A. planipennis. Future studies are needed to identify the functionality of the loci where these SNPs occur and how they may be related to tolerance of A. planipennis attack

Hamiltonian evolutions of twisted gons in \RP^n

In this paper we describe a well-chosen discrete moving frame and their associated invariants along projective polygons in \RP^n, and we use them to write explicit general expressions for invariant evolutions of projective $N$-gons. We then use a reduction process inspired by a discrete Drinfeld-Sokolov reduction to obtain a natural Hamiltonian structure on the space of projective invariants, and we establish a close relationship between the projective $N$-gon evolutions and the Hamiltonian evolutions on the invariants of the flow. We prove that {any} Hamiltonian evolution is induced on invariants by an evolution of $N$-gons - what we call a projective realization - and we give the direct connection. Finally, in the planar case we provide completely integrable evolutions (the Boussinesq lattice related to the lattice $W_3$-algebra), their projective realizations and their Hamiltonian pencil. We generalize both structures to $n$-dimensions and we prove that they are Poisson. We define explicitly the $n$-dimensional generalization of the planar evolution (the discretization of the $W_n$-algebra) and prove that it is completely integrable, providing also its projective realization

Spatial patterns and environmental constraints on ecosystem services at a catchment scale

Improved understanding and prediction of the fundamental environmental controls on ecosystem service supply across the landscape will help to inform decisions made by policy makers and land-water managers. To evaluate this issue for a local catchment case study, we explored metrics and spatial patterns of service supply for water quality regulation, agriculture production, carbon storage, and biodiversity for the Macronutrient Conwy catchment. Methods included using ecosystem models such as LUCI and JULES, integration of national scale field survey datasets, earth observation products and plant trait databases, to produce finely resolved maps of species richness and primary production. Analyses were done with both 1x1 km gridded and subcatchment data. A common single gradient characterised catchment scale ecosystem services supply with agricultural production and carbon storage at opposing ends of the gradient as reported for a national-scale assessment. Species diversity was positively related to production due to the below national average productivity levels in the Conwy combined with the unimodal relationship between biodiversity and productivity at the national scale. In contrast to the national scale assessment, a strong reduction in water quality as production increased was observed in these low productive systems. Various soil variables were tested for their predictive power of ecosystem service supply. Soil carbon, nitrogen, their ratio and soil pH all had double the power of rainfall and altitude, each explaining around 45% of variation but soil pH is proposed as a potential metric for ecosystem service supply potential as it is a simple and practical metric which can be carried out in the field with crowd-sourcing technologies now available. The study emphasises the importance of considering multiple ecosystem services together due to the complexity of covariation at local and national scales, and the benefits of exploiting a wide range of metrics for each service to enhance data robustness

Fermi Large Area Telescope Constraints on the Gamma-ray Opacity of the Universe

The Extragalactic Background Light (EBL) includes photons with wavelengths from ultraviolet to infrared, which are effective at attenuating gamma rays with energy above ~10 GeV during propagation from sources at cosmological distances. This results in a redshift- and energy-dependent attenuation of the gamma-ray flux of extragalactic sources such as blazars and Gamma-Ray Bursts (GRBs). The Large Area Telescope onboard Fermi detects a sample of gamma-ray blazars with redshift up to z~3, and GRBs with redshift up to z~4.3. Using photons above 10 GeV collected by Fermi over more than one year of observations for these sources, we investigate the effect of gamma-ray flux attenuation by the EBL. We place upper limits on the gamma-ray opacity of the Universe at various energies and redshifts, and compare this with predictions from well-known EBL models. We find that an EBL intensity in the optical-ultraviolet wavelengths as great as predicted by the "baseline" model of Stecker et al. (2006) can be ruled out with high confidence.Comment: 42 pages, 12 figures, accepted version (24 Aug.2010) for publication in ApJ; Contact authors: A. Bouvier, A. Chen, S. Raino, S. Razzaque, A. Reimer, L.C. Reye

\u3ci\u3eFundulus\u3c/i\u3e as the premier teleost model in environmental biology: Opportunities for new insights using genomics

A strong foundation of basic and applied research documents that the estuarine fish Fundulus heteroclitus and related species are unique laboratory and field models for understanding how individuals and populations interact with their environment. In this paper we summarize an extensive body of work examining the adaptive responses of Fundulus species to environmental conditions, and describe how this research has contributed importantly to our understanding of physiology, gene regulation, toxicology, and ecological and evolutionary genetics of teleosts and other vertebrates. These explorations have reached a critical juncture at which advancement is hindered by the lack of genomic resources for these species. We suggest that a more complete genomics toolbox for F. heteroclitus and related species will permit researchers to exploit the power of this model organism to rapidly advance our understanding of fundamental biological and pathological mechanisms among vertebrates, as well as ecological strategies and evolutionary processes common to all living organisms

Prediction of absolute risk of fragility fracture at 10 years in a Spanish population: validation of the WHO FRAX ™ tool in Spain

<p>Abstract</p> <p>Background</p> <p>Age-related bone loss is asymptomatic, and the morbidity of osteoporosis is secondary to the fractures that occur. Common sites of fracture include the spine, hip, forearm and proximal humerus. Fractures at the hip incur the greatest morbidity and mortality and give rise to the highest direct costs for health services. Their incidence increases exponentially with age.</p> <p>Independently changes in population demography, the age - and sex- specific incidence of osteoporotic fractures appears to be increasing in developing and developed countries. This could mean more than double the expected burden of osteoporotic fractures in the next 50 years.</p> <p>Methods/Design</p> <p>To assess the predictive power of the WHO FRAX™ tool to identify the subjects with the highest absolute risk of fragility fracture at 10 years in a Spanish population, a predictive validation study of the tool will be carried out. For this purpose, the participants recruited by 1999 will be assessed. These were referred to scan-DXA Department from primary healthcare centres, non hospital and hospital consultations. Study population: Patients attended in the national health services integrated into a FRIDEX cohort with at least one Dual-energy X-ray absorptiometry (DXA) measurement and one extensive questionnaire related to fracture risk factors. Measurements: At baseline bone mineral density measurement using DXA, clinical fracture risk factors questionnaire, dietary calcium intake assessment, history of previous fractures, and related drugs. Follow up by telephone interview to know fragility fractures in the 10 years with verification in electronic medical records and also to know the number of falls in the last year. The absolute risk of fracture will be estimated using the FRAX™ tool from the official web site.</p> <p>Discussion</p> <p>Since more than 10 years ago numerous publications have recognised the importance of other risk factors for new osteoporotic fractures in addition to low BMD. The extension of a method for calculating the risk (probability) of fractures using the FRAX™ tool is foreseeable in Spain and this would justify a study such as this to allow the necessary adjustments in calibration of the parameters included in the logarithmic formula constituted by FRAX™.</p

Genomic and molecular analyses identify molecular subtypes of pancreatic cancer recurrence

Pancreatic cancer (PC) remains a highly lethal malignancy, and most patients with localized disease that undergo surgical resection still succumb to recurrent disease. Pattern of recurrence after pancreatectomy is heterogenous, with some studies illustrating that site of recurrence can be associated with prognosis.1 Another study suggested that tumors that develop local and distant recurrence can be regarded as a homogenous disease with similar outcomes.2 Here we investigate novel molecular determinants of recurrence pattern after pancreatectomy for PC

Onchocerciasis: The Pre-control Association between Prevalence of Palpable Nodules and Skin Microfilariae

*Background*: The prospect of eliminating onchocerciasis from Africa by mass treatment with ivermectin has been rejuvenated following recent successes in foci in Mali, Nigeria and Senegal. Elimination prospects depend strongly on local transmission conditions and therefore on pre-control infection levels. Pre-control infection levels in Africa have been mapped largely by means of nodule palpation of adult males, a relatively crude method for detecting infection. We investigated how informative pre-control nodule prevalence data are for estimating the pre-control prevalence of

Assessment of parental contributions to fast- and slow-growing progenies in the sea bream Sparus aurata L. using a new multiplex PCR

Molecular tools to assist breeding programs in the gilthead sea bream (Sparus aurata L.) are scarce. A new multiplex PCR technique (OVIDORPLEX), which amplifies nine known microsatellite markers, was developed in this work. This multiplex system showed a high mean heterozygosity (>0.800) and a high mean number of alleles per marker (>14) when tested in two sea bream broodstocks (A: 40 breeders and B: 38 breeders). We tested this multiplex PCR for inferring parentage in a Spanish hatchery that graded the animals by size as part of their management procedure. The progeny of the broodstock were divided into fast- and slow-growth groups. Parentage studies revealed that this management procedure entailed a global reduction of the breeders' representation in progeny and that breeders' contributions were significantly unequal. Due to this, effective sample sizes fell to N ê¿13-14 for fast- and N ê¿18-24 for slow-growth progeny groups. These results imply a 3 to 4% rate of inbreeding per generation in the fast-growth group, which is more important to hatchery managers than the slow group. Not all the progeny were evaluated in this experiment (due to the discarding steps), and thus it is difficult to know if the phenotypic performance showed by the fast-growing progeny will be heritable. However, there were genetic differences between the differentiated growth progeny groups (fast vs. slow, F ST values=0.016 to 0.023; P<0.01). We also identified breeders with significantly different contributions to the fast- (10 breeders) or to the slow- (15 breeders) growth progeny groups. Our results demonstrated that this new multiplex PCR could be useful for quantitative programs (breeding programs, detection of QTL, inbreeding control or reconstruction of fish genealogies) to improve the aquaculture of the gilthead sea bream (S. aurata). © 2011 Elsevier B.V.This work was carried out in collaboration with the fish farm Granja Marina Safor, S.L. (Gandia, Valencia, Spain) and the hatchery Piscicultura Marina Mediterranea, S.L. (Burriana, Castellon, Spain). It was financed by JACUMAR (the PROGENSA project) and the Spanish Ministry of Science and Innovation (MICINN; National Program of Resources and Food and Agriculture Technologies, AGL2006-13411-C03-00, SELECTSPARUS, and AGL2007-64040-C03-00, SELECTBREAM, including European Regional Development Funds). V. Gallego was supported by a FPI scholarship financed by MICINN; C. Garcia-Fernandez was supported by a FPU scholarship financed by MICINN; and I. Mazzeo was supported by a FPI scholarship financed by Generalitat Valenciana. We are indebted to three anonymous referees and the journal editor for valuable comments.Borrell, YJ.; Gallego Albiach, V.; García Fernández, C.; Mazzeo ., I.; Pérez Igualada, LM.; Asturiano Nemesio, JF.; Carleos, CE.... (2011). Assessment of parental contributions to fast- and slow-growing progenies in the sea bream Sparus aurata L. using a new multiplex PCR. Aquaculture. 314(1-4):58-65. https://doi.org/10.1016/j.aquaculture.2011.01.028S58653141-

Sulfur isotope evolution in sulfide ores from Western Alps: Assessing the influence of subduction-related metamorphism

Sulfides entering subduction zones can play an important role in the release of sulfur and metals to the mantle wedge and contribute to the formation of volcanic arc-associated ores. Fractionation of stable sulfur isotopes recorded by sulfides during metamorphism can provide evidence of fluid-rock interactions during metamorphism and give insights on sulfur mobilization. A detailed microtextural and geochemical study was performed on mineralized samples from two ocean floor-related sulfide deposits (Servette and Beth-Ghinivert) in high-pressure units of the Italian Western Alps, which underwent different metamorphic evolutions. The combination of microtextural investigations with d34S values from in situ ion probe analyses within individual pyrite and chalcopyrite grains allowed evaluation of the effectiveness of metamorphism in modifying the isotopic record and mobilizing sulfur and metals and have insights on fluid circulation within the slab. Textures and isotopic compositions inherited from the protolith are recorded at Beth-Ghinivert, where limited metamorphic recrystallization is attributed to limited interaction with metamorphic fluids. Isotopic modification by metamorphic processes occurred only at the submillimeter scale at Servette, where local interactions with infiltrating hydrothermal fluid are recorded by metamorphic grains. Notwithstanding the differences recorded by the two deposits, neither underwent intensive isotopic reequilibration or records evidence of intense fluid-rock interaction and S mobilization during metamorphism. Therefore, subducted sulfide deposits dominated by pyrite and chalcopyrite are unlikely to release significant quantities of sulfur to the mantle wedge and to arc magmatism sources at metamorphic grades below the lower eclogite facies