Linkage between site characterization program and performance and design data needs

The basis for identifying site-specific data needs for the Yucca Mountain site was a thorough review and evaluation of the regulatory requirements for a geologic repository. The US Nuclear Regulatory Commission`s (NRC) regulation governing disposal of high-level waste in a geologic repository utilizes a multiple barrier approach that includes reliance on both engineered and natural elements. Given an understanding of the regulatory requirements, the next step was to identify the natural features of the site and the components of the engineered barriers considered most likely to make significant contributions to isolation of waste at Yucca Mountain. The intent was to develop a site testing program that focused on understanding those natural site characteristics and processes most likely to contribute to waste isolation; and providing site data necessary to design and assess the performance of engineered barriers. 3 refs., 3 figs

Molecular Characterization of a Fus3/Kss1 Type MAPK from Puccinia striiformis f. sp. tritici, PsMAPK1

Puccinia striiformis f. sp. tritici (Pst) is an obligate biotrophic fungus that causes the destructive wheat stripe rust disease worldwide. Due to the lack of reliable transformation and gene disruption method, knowledge about the function of Pst genes involved in pathogenesis is limited. Mitogen-activated protein kinase (MAPK) genes have been shown in a number of plant pathogenic fungi to play critical roles in regulating various infection processes. In the present study, we identified and characterized the first MAPK gene PsMAPK1 in Pst. Phylogenetic analysis indicated that PsMAPK1 is a YERK1 MAP kinase belonging to the Fus3/Kss1 class. Single nucleotide polymerphisms (SNPs) and insertion/deletion were detected in the coding region of PsMAPK1 among six Pst isolates. Real-time RT-PCR analyses revealed that PsMAPK1 expression was induced at early infection stages and peaked during haustorium formation. When expressed in Fusarium graminearum, PsMAPK1 partially rescued the map1 mutant in vegetative growth and pathogenicity. It also partially complemented the defects of the Magnaporthe oryzae pmk1 mutant in appressorium formation and plant infection. These results suggest that F. graminearum and M. oryzae can be used as surrogate systems for functional analysis of well-conserved Pst genes and PsMAPK1 may play a role in the regulation of plant penetration and infectious growth in Pst

Self organising maps for visualising and modelling

The paper describes the motivation of SOMs (Self Organising Maps) and how they are generally more accessible due to the wider available modern, more powerful, cost-effective computers. Their advantages compared to Principal Components Analysis and Partial Least Squares are discussed. These allow application to non-linear data, are not so dependent on least squares solutions, normality of errors and less influenced by outliers. In addition there are a wide variety of intuitive methods for visualisation that allow full use of the map space. Modern problems in analytical chemistry include applications to cultural heritage studies, environmental, metabolomic and biological problems result in complex datasets. Methods for visualising maps are described including best matching units, hit histograms, unified distance matrices and component planes. Supervised SOMs for classification including multifactor data and variable selection are discussed as is their use in Quality Control. The paper is illustrated using four case studies, namely the Near Infrared of food, the thermal analysis of polymers, metabolomic analysis of saliva using NMR, and on-line HPLC for pharmaceutical process monitoring

A Novel High-Affinity Sucrose Transporter Is Required for Virulence of the Plant Pathogen Ustilago maydis

A novel, high-affinity sucrose transporter identified in the plasma membrane of the plant pathogen Ustilago maydis is essential for fungal virulence and successful infection of maize

Transcriptome profiling of the rice blast fungus during invasive plant infection and in vitro stresses

<p>Abstract</p> <p>Background</p> <p>Rice blast is the most threatening disease to cultivated rice. <it>Magnaporthe oryzae</it>, its causal agent, is likely to encounter environmental challenges during invasive growth in its host plants that require shifts in gene expression to establish a compatible interaction. Here, we tested the hypothesis that gene expression patterns during <it>in planta </it>invasive growth are similar to <it>in vitro </it>stress conditions, such as nutrient limitation, temperature up shift and oxidative stress, and determined which condition most closely mimicked that of <it>in planta </it>invasive growth. Gene expression data were collected from these <it>in vitro </it>experiments and compared to fungal gene expression during the invasive growth phase at 72 hours post-inoculation in compatible interactions on two grass hosts, rice and barley.</p> <p>Results</p> <p>We identified 4,973 genes that were differentially expressed in at least one of the <it>in planta </it>and <it>in vitro </it>stress conditions when compared to fungal mycelia grown in complete medium, which was used as reference. From those genes, 1,909 showed similar expression patterns between at least one of the <it>in vitro </it>stresses and rice and/or barley. Hierarchical clustering of these 1,909 genes showed three major clusters in which <it>in planta </it>conditions closely grouped with the nutrient starvation conditions. Out of these 1,909 genes, 55 genes and 129 genes were induced and repressed in all treatments, respectively. Functional categorization of the 55 induced genes revealed that most were either related to carbon metabolism, membrane proteins, or were involved in oxidoreduction reactions. The 129 repressed genes showed putative roles in vesicle trafficking, signal transduction, nitrogen metabolism, or molecular transport.</p> <p>Conclusions</p> <p>These findings suggest that <it>M. oryzae </it>is likely primarily coping with nutrient-limited environments at the invasive growth stage 72 hours post-inoculation, and not with oxidative or temperature stresses.</p

Empirical Evaluation of Bone Extraction Protocols

The application of high-resolution analytical techniques to characterize ancient bone proteins requires clean, efficient extraction to obtain high quality data. Here, we evaluated many different protocols from the literature on ostrich cortical bone and moa cortical bone to evaluate their yield and relative purity using the identification of antibody-antigen complexes on enzyme-linked immunosorbent assay and gel electrophoresis. Moa bone provided an ancient comparison for the effectiveness of bone extraction protocols tested on ostrich bone. For the immunological part of this study, we focused on collagen I, osteocalcin, and hemoglobin because collagen and osteocalcin are the most abundant proteins in the mineralized extracellular matrix and hemoglobin is common in the vasculature. Most of these procedures demineralize the bone first, and then the remaining organics are chemically extracted. We found that the use of hydrochloric acid, rather than ethylenediaminetetraacetic acid, for demineralization resulted in the cleanest extractions because the acid was easily removed. In contrast, the use of ethylenediaminetetraacetic acid resulted in smearing upon electrophoretic separation, possibly indicating these samples were not as pure. The denaturing agents sodium dodecyl sulfate, urea, and guanidine HCl have been used extensively for the solubilization of proteins in non-biomineralized tissue, but only the latter has been used on bone. We show that all three denaturing agents are effective for extracting bone proteins. One additional method tested uses ammonium bicarbonate as a solubilizing buffer that is more appropriate for post-extraction analyses (e.g., proteomics) by removing the need for desalting. We found that both guanidine HCl and ammonium bicarbonate were effective for extracting many bone proteins, resulting in similar electrophoretic patterns. With the increasing use of proteomics, a new generation of scientists are now interested in the study of proteins from not only extant bone but also from ancient bone

Differences in energy balance-related behaviours in European preschool children: The ToyBox-study

Background: The aim of the current study was to compare levels of energy balance-related behaviours (physical activity, sedentary behaviour, and dietary behaviours (more specifically water consumption, sugar-sweetened beverage consumption and unhealthy snacking)) in four- to six-year-old preschoolers from six European countries (Belgium, Bulgaria, Germany, Greece, Poland, and Spain) within the ToyBox cross-sectional study. Methods: A sample of 4,045 preschoolers (4.77 ± 0.43 years; 52.2% boys) had valid physical activity data (steps per day), parents of 8,117 preschoolers (4.78 ± 0.46 years; 53.0% boys) completed a parental questionnaire with questions on sedentary behaviours (television viewing, computer use, and quiet play), and parents of 7,244 preschoolers (4.77 ± 0.44 years; 52.0% boys) completed a food frequency questionnaire with questions on water consumption, sugar-sweetened beverage consumption and unhealthy snacking. Results: The highest levels of physical activity were found in Spain (12,669 steps/day on weekdays), while the lowest levels were found in Bulgaria and Greece (9,777 and 9,656 steps/day on weekdays, respectively). German preschoolers spent the least amount of time in television viewing (43.3 min/day on weekdays), while Greek preschoolers spent the most time in television viewing (88.5 min/day on weekdays). A considerable amount of time was spent in quiet play in all countries, with the highest levels in Poland (104.9 min/day on weekdays), and the lowest levels in Spain (60.4 min/day on weekdays). Belgian, German, and Polish preschoolers had the lowest intakes of water and the highest intakes of sugar-sweetened beverages. The intake of snacks was the highest in Belgian preschoolers (73.1 g/day) and the lowest in Greek preschoolers (53.3 g/day). Conclusions: Across six European countries, differences in preschoolers'' energy balance-related behaviours were found. Future interventions should target European preschoolers '' energy balance- related behaviours simultaneously, but should apply country-specific adaptations

Effect and process evaluation of a kindergarten-based, family-involved cluster randomised controlled trial in six European countries on four- to six-year-old children's steps per day: The ToyBox-study

Background: The ToyBox-intervention is a theory- and evidence-based intervention delivered in kindergartens to improve four- to six-year-old children''s energy balance-related behaviours and prevent obesity. The current study aimed to (1) examine the effect of the ToyBox-intervention on increasing European four- to six-year-old children'' steps per day, and (2) examine if a higher process evaluation score from teachers and parents was related to a more favourable effect on steps per day. Methods: A sample of 2438 four- to six-year-old children (51.9% boys, mean age 4.75±0.43years) from 6 European countries (Belgium, Bulgaria, Germany, Greece, Poland and Spain) wore a motion sensor (pedometer or accelerometer) for a minimum of two weekdays and one weekend day both at baseline and follow-up to objectively measure their steps per day. Kindergarten teachers implemented the physical activity component of the ToyBox-intervention for 6 weeks in total, with a focus on (1) environmental changes in the classroom, (2) the child performing the actual behaviour and (3) classroom activities. Children''s parents received newsletters, tip cards and posters. To assess intervention effects, multilevel repeated measures analyses were conducted for the total sample and the six intervention countries separately. In addition, process evaluation questionnaires were used to calculate a total process evaluation score (with implementation and satisfaction as a part of the overall score) for teachers and parents which was then linked with the physical activity outcomes. Results: No significant intervention effects on four- to six-year-old children'' steps per weekday, steps per weekend day and steps per average day were found, both in the total sample and in the country-specific samples (all p>0.05). In general, the intervention effects on steps per day were least favourable in four- to six-year-old children with a low teachers process evaluation score and most favourable in four- to six-year-old children with a high teachers process evaluation score. No differences in intervention effects were found for a low, medium or high parents'' process evaluation score. Conclusion: The physical activity component of the ToyBox-intervention had no overall effect on four- to six-year-old children'' steps per day. However, the process evaluation scores showed that kindergarten teachers that implemented the physical activity component of the ToyBox-intervention as planned and were satisfied with the physical activity component led to favourable effects on children''s steps per day. Strategies to motivate, actively involve and engage the kindergarten teachers and parents/caregivers are needed to induce larger effects

No evidence that protein truncating variants in BRIP1 are associated with breast cancer risk: implications for gene panel testing.

BACKGROUND: BRCA1 interacting protein C-terminal helicase 1 (BRIP1) is one of the Fanconi Anaemia Complementation (FANC) group family of DNA repair proteins. Biallelic mutations in BRIP1 are responsible for FANC group J, and previous studies have also suggested that rare protein truncating variants in BRIP1 are associated with an increased risk of breast cancer. These studies have led to inclusion of BRIP1 on targeted sequencing panels for breast cancer risk prediction. METHODS: We evaluated a truncating variant, p.Arg798Ter (rs137852986), and 10 missense variants of BRIP1, in 48 144 cases and 43 607 controls of European origin, drawn from 41 studies participating in the Breast Cancer Association Consortium (BCAC). Additionally, we sequenced the coding regions of BRIP1 in 13 213 cases and 5242 controls from the UK, 1313 cases and 1123 controls from three population-based studies as part of the Breast Cancer Family Registry, and 1853 familial cases and 2001 controls from Australia. RESULTS: The rare truncating allele of rs137852986 was observed in 23 cases and 18 controls in Europeans in BCAC (OR 1.09, 95% CI 0.58 to 2.03, p=0.79). Truncating variants were found in the sequencing studies in 34 cases (0.21%) and 19 controls (0.23%) (combined OR 0.90, 95% CI 0.48 to 1.70, p=0.75). CONCLUSIONS: These results suggest that truncating variants in BRIP1, and in particular p.Arg798Ter, are not associated with a substantial increase in breast cancer risk. Such observations have important implications for the reporting of results from breast cancer screening panels.The COGS project is funded through a European Commission's Seventh Framework Programme grant (agreement number 223175 - HEALTH-F2-2009-223175). BCAC is funded by Cancer Research UK [C1287/A10118, C1287/A12014] and by the European Community´s Seventh Framework Programme under grant agreement number 223175 (grant number HEALTH-F2-2009-223175) (COGS). Funding for the iCOGS infrastructure came from: the European Community's Seventh Framework Programme under grant agreement n° 223175 (HEALTH-F2-2009-223175) (COGS), Cancer Research UK (C1287/A10118, C1287/A 10710, C12292/A11174, C1281/A12014, C5047/A8384, C5047/A15007, C5047/A10692, C8197/A16565), the National Institutes of Health (CA128978) and Post-Cancer GWAS initiative (1U19 CA148537, 1U19 16 CA148065 and 1U19 CA148112 - the GAME-ON initiative), the Department of Defense (W81XWH-10-1- 0341), the Canadian Institutes of Health Research (CIHR) for the CIHR Team in Familial Risks of Breast Cancer, Komen Foundation for the Cure, the Breast Cancer Research Foundation, and the Ovarian Cancer Research Fund. This study made use of data generated by the Wellcome Trust Case Control consortium. Funding for the project was provided by the Wellcome Trust under award 076113. The results published here are in part based upon data generated by The Cancer Genome Atlas Project established by the National Cancer Institute and National Human Genome Research Institute.This is the author accepted manuscript. The final version is available from BMJ Group at http://dx.doi.org/10.1136/jmedgenet-2015-103529