Model Differencing for Textual DSLs

The syntactic and semantic comparison of models is important for understanding and supporting their evolution. In this paper we present TMDIFF, a technique for semantically comparing models that are represented as text. TMDIFF incorporates the referential structure of a language, which is determined by symbolic names and language-specific scoping rules. Furthermore, it employs a novel technique for matching entities existing in source and target versions of a model, and finds entities that are added or removed. As a result, TMDIFF is fully language parametric, and brings the benefits of model differencing to textual languages

Isolation and characterization of microsatellite loci from two inbreeding bark beetle species (Coccotrypes)

We developed 14 microsatellite markers in Coccotrypes carpophagus and 14 in C. dactyliperda. These loci will be used for studying genetic structure and the level of inbreeding in populations in the Canary Islands and Madeira. As a result of long-term inbreeding, genetic variability is relatively low in these bark beetle species. We found one to five alleles per locus in 29 C. carpophagus and 41 C. dactyliperda from various localities. Eleven of the markers developed for C. carpophagus amplified in C. dactyliperda and seven of the markers developed for C. dactyliperda amplified in C. carpophagus

Determinants of Homodimerization Specificity in Histidine Kinases

Two-component signal transduction pathways consisting of a histidine kinase and a response regulator are used by prokaryotes to respond to diverse environmental and intracellular stimuli. Most species encode numerous paralogous histidine kinases that exhibit significant structural similarity. Yet in almost all known examples, histidine kinases are thought to function as homodimers. We investigated the molecular basis of dimerization specificity, focusing on the model histidine kinase EnvZ and RstB, its closest paralog in Escherichia coli. Direct binding studies showed that the cytoplasmic domains of these proteins each form specific homodimers in vitro. Using a series of chimeric proteins, we identified specificity determinants at the base of the four-helix bundle in the dimerization and histidine phosphotransfer domain. Guided by molecular coevolution predictions and EnvZ structural information, we identified sets of residues in this region that are sufficient to establish homospecificity. Mutating these residues in EnvZ to the corresponding residues in RstB produced a functional kinase that preferentially homodimerized over interacting with EnvZ. EnvZ and RstB likely diverged following gene duplication to yield two homodimers that cannot heterodimerize, and the mutants we identified represent possible evolutionary intermediates in this process.National Institutes of Health (U.S.) (Award GM067681)National Science Foundation (U.S.) (CAREER Grant)National Science Foundation (U.S.). Graduate Research Fellowshi

Polymorphisms in the methylenetetrahydrofolate reductase (MTHFR) gene, intakes of folate and related B vitamins and colorectal cancer : a case-control study in a population with relatively low folate intake

Peer reviewedPublisher PD

Kennis als gereedschap om schade te beperken

Slakken, emelten en ritnaalden zijn al op veel percelen suikerbieten waargenomen. Ze veroorzaken plantwegval. Hierdoor moesten enkele telers hun percelen zelfs overzaaien. Ieder jaar zorgen bodemplagen voor schade. Met meer kennis hierover heeft een teler meer gereedschappen in handen om schade te beperken en de opbrengst te verhogen

The Complete Chloroplast Genome of 17 Individuals of Pest Species Jacobaea vulgaris: SNPs, Microsatellites and Barcoding Markers for Population and Phylogenetic Studies

Invasive individuals from the pest species Jacobaea vulgaris show different allocation patterns in defence and growth compared with native individuals. To examine if these changes are caused by fast evolution, it is necessary to identify native source populations and compare these with invasive populations. For this purpose, we are in need of intraspecific polymorphic markers. We therefore sequenced the complete chloroplast genomes of 12 native and 5 invasive individuals of J. vulgaris with next generation sequencing and discovered single-nucleotide polymorphisms (SNPs) and microsatellites. This is the first study in which the chloroplast genome of that many individuals within a single species was sequenced. Thirty-two SNPs and 34 microsatellite regions were found. For none of the individuals, differences were found between the inverted repeats. Furthermore, being the first chloroplast genome sequenced in the Senecioneae clade, we compared it with four other members of the Asteraceae family to identify new regions for phylogentic inference within this clade and also within the Asteraceae family. Five markers (ndhC-trnV, ndhC-atpE, rps18-rpl20, clpP and psbM-trnD) contained parsimony-informative characters higher than 2%. Finally, we compared two procedures of preparing chloroplast DNA for next generation sequencing

Begeleidende rapportage Schema Bodemplagen

De bodem is een reservoir van insecten, waarvan een deel verantwoordelijk is voor economische schade in akkerbouw- en vollegrondsgroentegewassen. Bij de meeste zogenaamde bodeminsecten leeft alleen het volwassen stadium bovengronds; andere stadia leven voornamelijk in de bodem. Daarnaast zijn er veel plaaginsecten die de bodem gebruiken als schuilplaats om een ongunstige periode van het jaar (zoals de winter) door te brengen. Daardoor functioneert de bodem voor veel bodemplagen als een brug van het ene teeltseizoen naar het andere. Doordat de plagen zich kunnen verbergen in de bodem of in het ondergrondse plantenweefsel zijn ze in die levensfase moeilijk te bestrijden. Inzicht in biologische en ecologische aspecten van deze insectenplagen is noodzakelijk om ze doelgericht te beheersen of te bestrijden. Een overzichtelijk bodemplagenschema biedt een degelijke basis voor een milieuvriendelijke en duurzame aanpak van bodemgerelateerde plagen