Gilbert Berben

Bio: Gilbert Berben is an academic researcher from European Union. The author has contributed to research in topics: European union & Detection of genetically modified organisms. The author has an hindex of 24, co-authored 70 publications receiving 2716 citations. Previous affiliations of Gilbert Berben include Netherlands Organisation for Applied Scientific Research.

The complete DNA sequence of yeast chromosome III.

Abstract: The entire DNA sequence of chromosome III of the yeast Saccharomyces cerevisiae has been determined. This is the first complete sequence analysis of an entire chromosome from any organism. The 315-kilobase sequence reveals 182 open reading frames for proteins longer than 100 amino acids, of which 37 correspond to known genes and 29 more show some similarity to sequences in databases. Of 55 new open reading frames analysed by gene disruption, three are essential genes; of 42 non-essential genes that were tested, 14 show some discernible effect on phenotype and the remaining 28 have no overt function.

The YDp plasmids: A uniform set of vectors bearing versatile gene disruption cassettes for Saccharomyces cerevisiae

Abstract: The YDp plasmids (Yeast Disruption plasmids) are pUC9 vectors bearing a set of yeast gene disruption cassettes, all uniform in structure and differing only in the selectable marker used (HIS3, LEU2, LYS2, TRP1 or URA3). The markers, surrounded by translational termination codons, are embedded in the slightly modified sequence of the pUC9 multiple cloning sites.

Guidelines for validation of qualitative real-time PCR methods

Abstract: As for many areas of molecular testing, detection of Genetically Modified Organisms (GMO) relies on the real-time Polymerase Chain Reaction (qPCR) technology. Due to the increasing number of GMO, a screening approach using qualitative screening methods has become an integrated part of GMO detection. However, specific guidelines for the validation of these methods are lacking. Here, a pragmatic approach to conduct in-house and inter-laboratory validation studies for GMO screening methods, is proposed. Such guidelines could be adapted to other areas where qualitative qPCR methods are used for molecular testing allowing to implement easily a more reliable screening phase where necessary.

Effective PCR detection of animal species in highly processed animal byproducts and compound feeds

Abstract: In this paper we present a polymerase chain reaction (PCR)-based method for detecting meat and bone meal (MBM) in compound feedingstuffs. By choosing adequate DNA targets from an appropriate localisation in the genome, the real-time PCR method developed here proved to be robust to severe heat treatment of the MBM, showing high sensitivity in the detection of MBM. The method developed here permits the specific detection of processed pig and cattle materials treated at 134 °C in various feed matrices down to a limit of detection of about 0.1%. This technique has also been successfully applied to well-characterised MBM samples heated to as high as 141 °C, as well as to various blind feed samples with very low MBM contents. Finally, the method also passed several official European ring trials.

Methods of detection, species identification and quantification of processed animal proteins in feedingstuffs

Abstract: 1. IntroductionThe outbreak of bovine spongiform encephalopathy (BSE) urged the European Union to take several decisions in order to avoid the transmission of its most probable causal agent through the food chain. At present, with exceptions for fish meal, processed animal proteins (PAPs) including meat and bone meals (MBM) are banned from use as feed ingredients for all farmed animals. Moreover, the use of PAPs is controlled within the European Union through several regulations. Regulation (EC) n°999/2001 prohibits explicitly the feeding of mammalian proteins to ruminants, whereas Regulation (EC) n°1774/2002 introduced several provisions, which are mainly:– the ban of feeding animals with proteins from the same species (ban of intra-species recycling),– the classification of animal by-products (ABPs) into 3 categories reflecting different safety levels and including the risk due to transmissible spongiform encephalopathy (TSE).Only material from category 3, i.e. that originates from animals fit for human consumption could be used to feed farm animals. Enforcing these regulations required analytical methods capable to allow species-specific identification. The lack of such methods led to the introduction of an extended feed ban for all farmed animals by amending Regulation (EC) n°999/2001 through Commission Regulation (EC) n°1234/2003. Nevertheless, with the present feed ban, fish meal is the only source of PAPs authorized for pig and poultry feed. The decline in the BSE epid

Initial sequencing and analysis of the human genome.

Abstract: The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

The European commission

Abstract: 2 1 The innovative transport systems and the CityMobil project 10 1.1 The research questions 10 2 The state of art in the field of automatic transport systems 12 2.1 Case studies and demand studies for innovative transport systems 12 3 The design and implementation of surveys 14 3.1 Definition of experimental design 14 3.2 Questionnaire design and delivery 16 3.3 First analyses on the collected sample 18 4 Calibration of Logit Multionomial demand models 21 4.1 Methodology 21 4.2 Calibration of the “full” model. 22 4.3 Calibration of the “final” model 24 4.4 The demand analysis through the final Multinomial Logit model 25 5 The analysis of interaction between the demand and socioeconomic attributes 31 5.1 Methodology 31 5.2 Application of Mixed Logit models to the demand 31 5.3 Analysis of the interactions between demand and socioeconomic attributes through Mixed Logit models 32 5.4 Mixed Logit model and interaction between age and the demand for the CTS 38 5.5 Demand analysis with Mixed Logit model 39 6 Final analyses and conclusions 45 6.1 Comparison between the results of the analyses 45 6.2 Conclusions 48 6.3 Answers to the research questions and future developments 52

Life with 6000 Genes

Abstract: The genome of the yeast Saccharomyces cerevisiae has been completely sequenced through a worldwide collaboration. The sequence of 12,068 kilobases defines 5885 potential protein-encoding genes, approximately 140 genes specifying ribosomal RNA, 40 genes for small nuclear RNA molecules, and 275 transfer RNA genes. In addition, the complete sequence provides information about the higher order organization of yeast's 16 chromosomes and allows some insight into their evolutionary history. The genome shows a considerable amount of apparent genetic redundancy, and one of the major problems to be tackled during the next stage of the yeast genome project is to elucidate the biological functions of all of these genes.

Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications.

Abstract: A set of yeast strains based on Saccharomyces cerevisiae S288C in which commonly used selectable marker genes are deleted by design based on the yeast genome sequence has been constructed and analysed. These strains minimize or eliminate the homology to the corresponding marker genes in commonly used vectors without significantly affecting adjacent gene expression. Because the homology between commonly used auxotrophic marker gene segments and genomic sequences has been largely or completely abolished, these strains will also reduce plasmid integration events which can interfere with a wide variety of molecular genetic applications. We also report the construction of new members of the pRS400 series of vectors, containing the kanMX, ADE2 and MET15 genes.