Vr 2: a new apple scab resistance gene

Reports from several European countries of the breakdown of the Vf resistance, the most frequently used source of resistance in breeding programs against apple scab, emphasize the urgency of diversifying the basis of apple scab resistance and pyramiding different apple scab resistances with the use of their associated molecular markers. GMAL 2473 is an apple scab resistant selection thought to carry the resistance gene Vr. We report the identification by BSA of three AFLP markers and one RAPD marker associated with the GMAL 2473 resistance gene. SSRs associated with the resistance gene were found by (1) identifying the linkage group carrying the apple scab resistance and (2) testing the SSRs previously mapped in the same region. One such SSR, CH02c02a, mapped on linkage group 2, co-segregates with the resistance gene. GMAL 2473 was tested with molecular markers associated with other apple scab resistance genes, and accessions carrying known apple scab resistance genes were tested with the SSR linked to the resistance gene found in GMAL 2473. The results indicate that GMAL 2473 does not carry Vr, and that a new apple scab resistance gene, named Vr 2, has been identifie

Detection of the fire blight biocontrol agent Bacillus subtilis BD170 (Biopro®) in a Swiss apple orchard

Fire blight, caused by Erwinia amylovora, is a major disease threat to apple, pear and other pome fruit worldwide. The disease is widespread in Europe and has recently become established in Switzerland. Antibiotics are the most effective controls used in North America but these are not permitted for agricultural use in most European countries. A newly registered biological control product Biopro®, based on the antagonist Bacillus subtilis strain BD170, is being used as an alternative strategy for fire blight management. A specific molecular marker was developed for monitoring the spread of this agent on blossoms after Biopro® spray application in a Swiss apple orchard throughout the bloom period for 2years. Direct spraying resulted in efficient primary colonisation of pistils in flowers that were open at the time of treatment. Subsequent bacterial dissemination (secondary colonisation) of flowers that were closed or at bud stage at the time of treatment was observed but was found to be dependent on the timing of treatments relative to bloom stage in the orchard. Foraging honeybees were shown to be disseminators of Biopro®. We also report detection of the biocontrol agent in honey collected from hives where bees were exposed by placing Biopro® at the entrance or in the hatching nest and from hives that were simply placed in sprayed orchard

Gross Domestic Product (GDP) and productivity of schizophrenia trials: an ecological study

The 5000 randomised controlled trials (RCTs) in the Cochrane Schizophrenia Group's database affords an opportunity to research for variables related to the differences between nations of their output of schizophrenia trials. Ecological study – investigating the relationship between four economic/demographic variables and number of schizophrenia RCTs per country. The variable with closest correlation was used to predict the expected number of studies. GDP closely correlated with schizophrenia trial output, with 76% of the total variation about the Y explained by the regression line (r = 0.87, 95% CI 0.79 to 0.92, r2 = 0.76). Many countries have a strong tradition of schizophrenia trials, exceeding their predicted output. All nations with no identified trial output had GDPs that predicted zero trial activity. Several nations with relatively small GDPs are, nevertheless, highly productive of trials. Some wealthy countries seem either not to have produced the expected number of randomised trials or not to have disseminated them to the English-speaking world. This hypothesis-generating study could not investigate causal relationships, but suggests, that for those seeking all relevant studies, expending effort searching the scientific literature of Germany, Italy, France, Brazil and Japan may be a good investment

A geometric study of the dispersionless Boussinesq type equation

We discuss the dispersionless Boussinesq type equation, which is equivalent to the Benney-Lax equation, being a system of equations of hydrodynamical type. This equation was discussed in . The results include: a description of local and nonlocal Hamiltonian and symplectic structures, hierarchies of symmetries, hierarchies of conservation laws, recursion operators for symmetries and generating functions of conservation laws (cosymmetries). Highly interesting are the appearances of operators that send conservation laws and symmetries to each other but are neither Hamiltonian, nor symplectic. These operators give rise to a noncommutative infinite-dimensional algebra of recursion operators

The catalase gene differentiates between some strains of Staphylococcus aureus ssp. anaerobius

Staphylococcus aureus ssp anaerobius strain S10 was isolated from an outbreak of sheep abscess disease. Sequence of the catalase gene of this strain showed 99 % identity to the catalase gene (katB) sequence of the reference strain (S. aureus ssp. anaerobius strain MVF213) with mismatching of three base pairs. An important substitution located 1036 nucleotides upstream of the initiation codon from "C" in katB to "T" in the catalase gene of strain S10 originated a stop codon. The deduced protein (345 amino acids) is 105 amino acids shorter than that of katB. Partial sequence of the catalase gene of other 8 local isolates in addition to another reference strain (DSM 20714/ATCC 35844) revealed the same mutations in all local (African) strains, whereas the sequence of the reference (European) strain was typical to that of katB. Sequence of the catalase gene of S. aureus ssp. anaerobius strain S10 was deposited in GenBank under accession no. EU281993

Microsatellite markers spanning the apple ( Malus x domestica Borkh.) genome

A new set of 148 apple microsatellite markers has been developed and mapped on the apple reference linkage map Fiesta x Discovery. One-hundred and seventeen markers were developed from genomic libraries enriched with the repeats GA, GT, AAG, AAC and ATC; 31 were developed from EST sequences. Markers derived from sequences containing dinucleotide repeats were generally more polymorphic than sequences containing trinucleotide repeats. Additional eight SSRs from published apple, pear, and Sorbus torminalis SSRs, whose position on the apple genome was unknown, have also been mapped. The transferability of SSRs across Maloideae species resulted in being efficient with 41% of the markers successfully transferred. For all 156 SSRs, the primer sequences, repeat type, map position, and quality of the amplification products are reported. Also presented are allele sizes, ranges, and number of SSRs found in a set of nine cultivars. All this information and those of the previous CH-SSR series can be searched at the apple SSR database ( http://www.hidras.unimi.it ) to which updates and comments can be added. A large number of apple ESTs containing SSR repeats are available and should be used for the development of new apple SSRs. The apple SSR database is also meant to become an international platform for coordinating this effort. The increased coverage of the apple genome with SSRs allowed the selection of a set of 86 reliable, highly polymorphic, and overall the apple genome well-scattered SSRs. These SSRs cover about 85% of the genome with an average distance of one marker per 15c

The evolution of gene regulation underlying sex determination in turtles

Understanding genome-wide responses to environmental conditions during embryogenesis is essential for discerning the evolution of developmental plasticity and canalization, two processes generating phenotypic variation targeted by natural selection. One case of developmental plasticity is environmental sex determination (ESD) where environmental cues (such as temperature) during development direct gonadal phenotype. Sex determination can also be canalized (such as with sex chromosomes) where genetic signals instead direct development. Intriguingly, sex determination has evolved repeatedly in vertebrates, and numerous lineages often make use of similar gene players. However, the full genetic architecture of vertebrate sexual development is unknown. Emerging evidence indicates changes have occurred in both up- and downstream factors of sexual development networks. Additionally, studies point to key roles for epigenomic regulation in integrating environmental signals during development. These elements of conservation despite sex determination diversity are fascinating, thus this dissertation asks, what changes in the genetic wiring can explain this simultaneous mechanistic diversification alongside genetic and developmental conservation? Additionally, as this turnover is associated with transitions between ESD and GSD we ask, how and when are environmental signals communicated into genetic and developmental signals and how are they ignored when environmental sensitivity is lost? A comparative perspective of turtle lineages (where sex determination has evolved repeatedly) allows contrast of proxy-ancestral temperature-dependent sex determination (TSD, Chrysemys picta) to derived GSD (Apalone spinifera, ZZ/ZW sex chromosomes). Over three studies we focused on changes in gene expression, gene regulation, and genomic environmental sensitivity to learn how environmental signals integrate into the genome (or not) during development and how developmental plasticity and canalization contribute to biodiversity. This dissertation significantly expanded the genomic resources available for turtles and implemented novel application of multiple methodological approaches that facilitated deeper synthesis and interpretation of these resources. Among the significant findings revealed were the retention of substantial transcriptomic thermal plasticity in GSD turtles that has persisted >145 Myr since the evolution of sex chromosomes, representing plasticity in GSD species that may be co-opted during future adaptive shifts. Additionally, this dissertation expanded molecular models of sex determination through the identification of the primary cilium as a likely critical organelle involved in the sensing and integration of environmental cues during sexual development that may co-evolve with sex determination. Finally, it was the first to attempt genome-wide chromatin studies in turtles, which revealed the presence of bivalent domains that may contribute to establishing the bipotential state of the early gonad. This dissertation has expanded our understanding of the molecular mechanisms underlying vertebrate sex determination and provides a rich source of novel observations to drive future studies in this area. This research sheds light on the gene expression, gene regulation, and environmental sensitivity that not only underly these mechanisms of sex determination but also reveal how these mechanisms evolved contributing to the vast biodiversity in sex determination observed throughout vertebrates

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

The iPlant Collaborative (iPlant) is a United States National Science Foundation (NSF) funded project that aims to create an innovative, comprehensive, and foundational cyberinfrastructure in support of plant biology research (PSCIC, 2006). iPlant is developing cyberinfrastructure that uniquely enables scientists throughout the diverse fields that comprise plant biology to address Grand Challenges in new ways, to stimulate and facilitate cross-disciplinary research, to promote biology and computer science research interactions, and to train the next generation of scientists on the use of cyberinfrastructure in research and education. Meeting humanity's projected demands for agricultural and forest products and the expectation that natural ecosystems be managed sustainably will require synergies from the application of information technologies. The iPlant cyberinfrastructure design is based on an unprecedented period of research community input, and leverages developments in high-performance computing, data storage, and cyberinfrastructure for the physical sciences. iPlant is an open-source project with application programming interfaces that allow the community to extend the infrastructure to meet its needs. iPlant is sponsoring community-driven workshops addressing specific scientific questions via analysis tool integration and hypothesis testing. These workshops teach researchers how to add bioinformatics tools and/or datasets into the iPlant cyberinfrastructure enabling plant scientists to perform complex analyses on large datasets without the need to master the command-line or high-performance computational services

Search for the standard model Higgs boson decaying to a bb pair in events with one charged lepton and large missing transverse energy using the full CDF data set

We present a search for the standard model Higgs boson produced in association with a W boson in sqrt(s) = 1.96 TeV p-pbar collision data collected with the CDF II detector at the Tevatron corresponding to an integrated luminosity of 9.45 fb-1. In events consistent with the decay of the Higgs boson to a bottom-quark pair and the W boson to an electron or muon and a neutrino, we set 95% credibility level upper limits on the WH production cross section times the H->bb branching ratio as a function of Higgs boson mass. At a Higgs boson mass of 125 GeV/c2 we observe (expect) a limit of 4.9 (2.8) times the standard model value.Comment: Submitted to Phys. Rev. Lett (v2 contains clarifications suggested by PRL