Yield losses caused by late blight (Phytophthora infestans (Mont.) de Bary) in potato crops in Ireland

peer-reviewedField experiments, using foliage blight susceptible cultivars, were conducted at Oak Park, Carlow from 1983 to 2007 to determine the loss in potato production caused by crop infection with Phytophthora infestans. In each of the 25 years an untreated control was compared with protectant and with systemic fungicide programmes to determine the effect of late blight on the defoliation percentage at the end of the season, the area under the disease progress curve, marketable tuber yield, total tuber yield and yield of blighted tubers. The earliest date of first recorded late blight was 22 June and the latest was 15 September, but in 15 of the 25 years, blight was first recorded between 17 July and 13 August. Disease reached epidemic proportions in all but 4 of the years. Yields varied considerably among years. The mean loss in total yield from not using a fungicide was 10.1 t/ha. Differences in yield were significant across the 25 seasons. No overall increase in aggressiveness of the pathogen could be detected over the 25-year period

Potato Breeding at Oak Park 2000-2006

End of project reportThe potato breeding programme at Oak Park was started in the 1960's and has consisted of a number of distinct phases. In the first phase the focus was on the evaluation of the main domestic and foreign varieties for suitability for the Irish market. This was followed by a breeding programme for the domestic market, with particular emphasis on the production of a blight resistant replacement for Kerr’s Pink. The emphasis then switched to breeding for the export market, with the focus on the UK and Mediterranean markets. Since then the breeding programme has been focused on both the domestic, processing and export markets. The process of breeding, testing and multiplying a new potato variety from the making of the initial cross until the new variety can be commercially grown takes about 15 years (see Appendix 1). This report covers the period 2001-2006 (RMIS NO 4720).Irish Potato Marketing Ltd.National Development Pla

Matrix metalloproteinase inhibitors: Present achievements and future prospects

Matrix metalloproteinases (MMPs) are a class of structurally related enzymes that function in the degradation of extracellular matrix proteins that constitute the pericellular connective tissue and play an important role in both normal and pathological tissue remodelling. Increased MMP activity is detected in a wide range of cancers and seems correlated to their invasive and metastatic potential. MMPs thus seem an attractive target for both diagnostic and therapeutic purposes. Several synthetic matrix metalloproteinase inhibitors (MMPIs) are currently being developed. Preclinical studies are promising as they suggest inhibition of several steps in the metastatic process. Marimastat is the first MMPI to enter comparative phase III trials after early clinical trials established the safety profile. Clinical trials will need to be specifically designed to optimally evaluate the therapeutic potential of this novel class of cytostatic drugs. Safety studies should consider the markedly different toxicity profile and determine the range of biologically active dosage, while efficacy studies should be performed in selected clinical settings with appropriate end-points. We review the present achievements in preclinical and clinical studies with MMPIs, discuss specific considerations for appropriate study design and reflect on the future prospects of this novel class of agents

Genetic Analysis of Irish Populations of Phytophthora Infestans

End of Project ReportPhytophthora infestans (Mont.) de Bary, the causal agent of potato late blight is best known for its role in the great Irish famine of 1845-1849 which resulted in the deaths of over 1 million people. Since then, the disease has become established in all potato growing countries and is the most important pathogen of potatoes worldwide. The appearance of resistance to the phenylamide fungicides in the late 1970’s indicated that populations of P. infestans were changing. An antiresistance strategy was developed for growers in an effort to reduce the spread of resistant strains. Subsequently the A2 mating type of the fungus was discovered in 1989 promoting fears that a super strain of the fungus could evolve through sexual reproduction. Populations of the fungus have been monitored from 1981 to 1998 for levels of phenylamide resistance and since 1988 for the A2 mating type. Physiological race surveys were conducted in 1983 and 1996. Prior to the 1980s no reliable methods were available for adequate identification of genotypes. Development of molecular markers specific to P. infestans has made this possible and a survey was conducted on isolates from the 1996 population. Results confirm that the anti-resistance strategy for phenylamide based fungicides has been effective in preventing the build up of metalaxyl resistant populations of P. infestans. During the 1990’s the distribution of phenylamide resistance has remained stable at about 50% of crops tested compared to a high of over 80 % in 1981. The level of A2 in the population has also fallen from a high of 35% of isolates tested in 1989 to a static level of 3-4 % in the 1990’s. Physiological race composition has become much more complex since 1983 and 16 different physiological races were found in Ireland in 1996. The population was dominated by race 3.4.7.10.11 which accounted for over 54% of isolates tested. This change has taken place without a corresponding change to varieties with a complex Rgene base. Twelve different genotypes of the fungus were uncovered using the multilocus probe RG57. Races of the fungus were independent of genotype. One particular genotype IE-2 was predominantly associated with phenylamide resistance. The low population diversity discovered suggests that sexual reproduction between A1 and A2 types has not been a major factor in disease epidemiology to date. Super strains similar to those identified in the USA could not be confirmed. The overall level of variation in the Irish isolates of Phytophthora infestans would confirm that the population has become progressively more diverse during the last forty years. However, the population is much less complex than that found in the highland tropics of central Mexico.Teagasc Walsh Fellowship Programm

The Reverse Transcription Signature of N-\u3csub\u3e1\u3c/sub\u3e-Methyladenosine in RNA-Seq is Sequence Dependent

The combination of Reverse Transcription (RT) and high-throughput sequencing has emerged as a powerful combination to detect modified nucleotides in RNA via analysis of either abortive RT-products or of the incorporation of mismatched dNTPs into cDNA. Here we simultaneously analyze both parameters in detail with respect to the occurrence of N-1-methyladenosine (m1A) in the template RNA. This naturally occurring modification is associated with structural effects, but it is also known as a mediator of antibiotic resistance in ribosomal RNA. In structural probing experiments with dimethylsulfate, m1A is routinely detected by RT-arrest. A specifically developed RNA-Seq protocol was tailored to the simultaneous analysis of RT-arrest and misincorporation patterns. By application to a variety of native and synthetic RNA preparations, we found a characteristic signature of m1A, which, in addition to an arrest rate, features misincorporation as a significant component. Detailed analysis suggests that the signature depends on RNA structure and on the nature of the nucleotide 3’ of m1A in the template RNA, meaning it is sequence dependent. The RT-signature ofm1Awas used for inspection and confirmation of suspected modification sites and resulted in the identification of hitherto unknown m1A residues in trypanosomal tRNA

Relationship Between Baseline Prostate-specific Antigen on Cancer Detection and Prostate Cancer Death:Long-term Follow-up from the European Randomized Study of Screening for Prostate Cancer

Background: The European Association of Urology guidelines recommend a risk-based strategy for prostate cancer screening based on the first prostate-specific antigen (PSA) level and age. Objective: To analyze the impact of the first PSA level on prostate cancer (PCa) detection and PCa-specific mortality (PCSM) in a population-based screening trial (repeat screening every 2–4 yr). Design, setting, and participants: We evaluated 25 589 men aged 55–59 yr, 16 898 men aged 60–64 yr, and 12 936 men aged 65–69 yr who attended at least one screening visit in the European Randomized Study of Screening for Prostate Cancer (ERSPC) trial (screening arm: repeat PSA testing every 2–4 yr and biopsy in cases with elevated PSA; control arm: no active screening offered) during 16-yr follow-up (FU). Outcome measurements and statistical analysis: We assessed the actuarial probability for any PCa and for clinically significant (cs)PCa (Gleason ≥7). Cox proportional-hazards regression was performed to assess whether the association between baseline PSA and PCSM was comparable for all age groups. A Lorenz curve was computed to assess the association between baseline PSA and PCSM for men aged 60–61 yr. Results and limitations: The overall actuarial probability at 16 yr ranged from 12% to 16% for any PCa and from 3.7% to 5.7% for csPCa across the age groups. The actuarial probability of csPCa at 16 yr ranged from 1.2–1.5% for men with PSA &lt;1.0 ng/ml to 13.3–13.8% for men with PSA ≥3.0 ng/ml. The association between baseline PSA and PCSM differed marginally among the three age groups. A Lorenz curve for men aged 60–61 yr showed that 92% of lethal PCa cases occurred among those with PSA above the median (1.21 ng/ml). In addition, for men initially screened at age 60–61 yr with baseline PSA &lt;2 ng/ml, further continuation of screening is unlikely to be beneficial after the age of 68–70 yr if PSA is still &lt;2 ng/ml. No case of PCSM emerged in the subsequent 8 yr (up to age 76–78 yr). A limitation is that these results may not be generalizable to an opportunistic screening setting or to contemporary clinical practice. Conclusions: In all age groups, baseline PSA can guide decisions on the repeat screening interval. Baseline PSA of &lt;1.0 ng/ml for men aged 55–69 yr is a strong indicator to delay or stop further screening. Patient summary: In prostate cancer screening, the patient's baseline PSA (prostate-specific antigen) level can be used to guide decisions on when to repeat screening. The PSA test when used according to current knowledge is valuable in helping to reduce the burden of prostate cancer.</p

Search for direct production of charginos and neutralinos in events with three leptons and missing transverse momentum in √s = 7 TeV pp collisions with the ATLAS detector

A search for the direct production of charginos and neutralinos in final states with three electrons or muons and missing transverse momentum is presented. The analysis is based on 4.7 fb−1 of proton–proton collision data delivered by the Large Hadron Collider and recorded with the ATLAS detector. Observations are consistent with Standard Model expectations in three signal regions that are either depleted or enriched in Z-boson decays. Upper limits at 95% confidence level are set in R-parity conserving phenomenological minimal supersymmetric models and in simplified models, significantly extending previous results

Jet size dependence of single jet suppression in lead-lead collisions at sqrt(s(NN)) = 2.76 TeV with the ATLAS detector at the LHC

Measurements of inclusive jet suppression in heavy ion collisions at the LHC provide direct sensitivity to the physics of jet quenching. In a sample of lead-lead collisions at sqrt(s) = 2.76 TeV corresponding to an integrated luminosity of approximately 7 inverse microbarns, ATLAS has measured jets with a calorimeter over the pseudorapidity interval |eta| < 2.1 and over the transverse momentum range 38 < pT < 210 GeV. Jets were reconstructed using the anti-kt algorithm with values for the distance parameter that determines the nominal jet radius of R = 0.2, 0.3, 0.4 and 0.5. The centrality dependence of the jet yield is characterized by the jet "central-to-peripheral ratio," Rcp. Jet production is found to be suppressed by approximately a factor of two in the 10% most central collisions relative to peripheral collisions. Rcp varies smoothly with centrality as characterized by the number of participating nucleons. The observed suppression is only weakly dependent on jet radius and transverse momentum. These results provide the first direct measurement of inclusive jet suppression in heavy ion collisions and complement previous measurements of dijet transverse energy imbalance at the LHC.Comment: 15 pages plus author list (30 pages total), 8 figures, 2 tables, submitted to Physics Letters B. All figures including auxiliary figures are available at http://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/HION-2011-02

Measurements of Higgs boson production and couplings in diboson final states with the ATLAS detector at the LHC

Measurements are presented of production properties and couplings of the recently discovered Higgs boson using the decays into boson pairs, H →γ γ, H → Z Z∗ →4l and H →W W∗ →lνlν. The results are based on the complete pp collision data sample recorded by the ATLAS experiment at the CERN Large Hadron Collider at centre-of-mass energies of √s = 7 TeV and √s = 8 TeV, corresponding to an integrated luminosity of about 25 fb−1. Evidence for Higgs boson production through vector-boson fusion is reported. Results of combined fits probing Higgs boson couplings to fermions and bosons, as well as anomalous contributions to loop-induced production and decay modes, are presented. All measurements are consistent with expectations for the Standard Model Higgs boson

Standalone vertex finding in the ATLAS muon spectrometer

A dedicated reconstruction algorithm to find decay vertices in the ATLAS muon spectrometer is presented. The algorithm searches the region just upstream of or inside the muon spectrometer volume for multi-particle vertices that originate from the decay of particles with long decay paths. The performance of the algorithm is evaluated using both a sample of simulated Higgs boson events, in which the Higgs boson decays to long-lived neutral particles that in turn decay to bbar b final states, and pp collision data at √s = 7 TeV collected with the ATLAS detector at the LHC during 2011