With molecular approaches we determined a deficiency in screening protocol and presence of a single nucleotide polymorphism (SNP) in GM maize TC1507. After our publication the discussion was open at the EU level how to harmonize screening analyses and how the observed deficiency would be systemically corrected. Paper is one in a series of papers published by the members of the program team in the field of GMOs. Because of their international recognition and many years of experience in GMO testing, development of real-time PCR methods, implementation of quality system requirements, validations and verification of methods, and measurement uncertainty they were invited to write a book on GMO detection in the series Springer Briefs in Food, Health and Nutrition: Žel et al. (2012) »How to reliably test for GMOs?« They invited the colleagues from the European Union Joint Research Centre which hosts the European Union Reference Laboratory for GM Food and Feed and chairs the European Network of GMO Laboratories to join the authorship. This Brief provides the current state-of-the-art on all key topics involved in GMO testing and is a source of detailed practical information for laboratories. Special focus is given to qualitative and quantitative real-time PCR analysis relevant to all areas where detection and identification rely on nucleic acid-based methods. The following topics, important for testing laboratories, are also discussed: organization of the laboratory, focusing on aspects of the quality system and methods for testing, validation and verification of methods, and measurement uncertainty. The Brief also discusses the new challenges of GMOs and novel modified organisms, using new technologies, and the possible solutions for GMO detection, including bioinformatics tools. Finally, legislation on GMOs and sources of information on GMOs are provided, which are relevant not only to testing laboratories, but to anyone interested in GMOs.
COBISS.SI-ID: 2059087
NIB Department of biotechnology and systems biology in cooperation with the Jožef Stefan Institute (JSI) have developed a brand new web application, that allows researchers new insights into the inner workings of agro-economically important plant species (potato, tomato, rice, cacao tree, sugar beet, tobacco) and the model species Arabidopsis on a gene level, which eases the intepretation of next generation data sets and knowledge transfer from a model species to crops. Connecting the application with other various computer tools additionally allows for more complex studies and dynamic updates of the plant defense response model, with the end goal of improving crops against various stressors.
COBISS.SI-ID: 2966607
Background Variations in testing for Clostridium difficile infection can hinder patients' care, increase the risk of transmission, and skew epidemiological data. We aimed to measure the underdiagnosis of C difficile infection across Europe. Methods We did a questionnaire-based study at 482 participating hospitals across 20 European countries. Hospitals were questioned about their methods and testing policy for C difficile infection during the periods September, 2011, to August, 2012, and September, 2012, to August, 2013. On one day in winter, 2012-13 (December, 2012, or January, 2013), and summer, 2013 (July or August), every hospital sent all diarrhoeal samples submitted to their microbiology laboratory to a national coordinating laboratory for standardised testing of C difficile infection. Our primary outcome measures were the rates of testing for and cases of C difficile infection per 10 000 patient bed-days. Results of local and national C difficile infection testing were compared with each other. If the result was positive at the national laboratory but negative at the local hospital, the result was classified as undiagnosed C difficile infection. We compared differences in proportions with the Mann-Whitney test, or McNemar's test if data were matched. Findings During the study period, participating hospitals reported a mean of 65*8 tests (country range 4*6-223*3) for C difficile infection per 10 000 patient-bed days and a mean of 7*0 cases (country range 0*7-28*7) of C difficile infection per 10 000 patient-bed days. Only two-fifths of hospitals reported using optimum methods for testing of C difficile infection (defined by European guidelines), although the number of participating hospitals using optimum methods increased during the study period, from 152 (32%) of 468 in 2011-12 to 205 (48%) of 428 in 2012-13. Across all 482 European hospitals on the two sampling days, 148 (23%) of 641 samples positive for C difficile infection (as determined by the national laboratory) were not diagnosed by participating hospitals because of an absence of clinical suspicion, equating to about 74 missed diagnoses per day. Interpretation A wide variety of testing strategies for C difficile infection are used across Europe. Absence of clinical suspicion and suboptimum laboratory diagnostic methods mean that an estimated 40 000 inpatients with C difficile infection are potentially undiagnosed every year in 482 European hospitals. Funding Astellas Pharmaceuticals Europe.
COBISS.SI-ID: 512464440
We investigated a leaf transcriptome of grapevine infected with phytoplasma "Bois noir". The results show that many genes involved in photosynthesis, biotic stress and sugar signaling are differentially expressed. Based on the results we designed a model of interaction between "Bois noir" and grapevine plant. The paper is part of the broad research of the biology and epidemiology of phytoplasmas and is also associated with the role of the program team in development of new molecular methods for detection of phytoplasmas that cause severe diseases in economically important plants.
COBISS.SI-ID: 2103375
A quarantine bacterium Erwinia amylovora causes a major disease of pomes fruit trees worldwide. The members of the program team have been involved in its investigation since the first outbreak of fire blight on pears in 2003. Besides the research on its biology, they also developed molecular assays for its effective detection based on the real-time PCR. In this paper we described a molecular typing system of E. amylovora based on variable number of tandem repeats (VNTR) analysis. With a Multiple-Locus VNTR Analysis (MLVA) we identified previously unresolved population structure within outbreaks. Knowledge of such structure can increase our understanding on how plant diseases emerge and spread over a given geographical region.
COBISS.SI-ID: 2982991