Biomedical subjects

Mark W E J Fiers

Publications and source records attributed to Mark W E J Fiers.

6 recordsLinked to original sources

PubMed2006

In plants, highly expressed genes are the least compact.

In both the monocot rice and the dicot Arabidopsis, highly expressed genes have more and longer introns and a larger primary transcript than genes expressed at a low level: higher expressed genes tend to be less compact than lower expressed genes. In animal genomes, it is the other way round. Although the length differences in plant genes are much smaller than in animals, these findings indicate that plant genes are in this respect different from animal genes. Explanations for the relationship between gene configuration and gene expression in animals might be (or might have been) less important in plants. We speculate that selection, if any, on genome configuration has taken a different turn after the divergence of plants and animals.

Animals↗

PubMed2005

DNAVis: interactive visualization of comparative genome annotations.

The software package DNAVis offers a fast, interactive and real-time visualization of DNA sequences and their comparative genome annotations. DNAVis implements advanced methods of information visualization such as linked views, perspective walls and semantic zooming, in addition to the display of heterologous data in dot plot-like matrix views.

Algorithms↗

PubMed2005

Local coexpression domains of two to four genes in the genome of Arabidopsis.

Expression of genes in eukaryotic genomes is known to cluster, but cluster size is generally loosely defined and highly variable. We have here taken a very strict definition of cluster as sets of physically adjacent genes that are highly coexpressed and form so-called local coexpression domains. The Arabidopsis (Arabidopsis thaliana) genome was analyzed for the presence of such local coexpression domains to elucidate its functional characteristics. We used expression data sets that cover different experimental conditions, organs, tissues, and cells from the Massively Parallel Signature Sequencing repository and microarray data (Affymetrix) from a detailed root analysis. With these expression data, we identified 689 and 1,481 local coexpression domains, respectively, consisting of two to four genes with a pairwise Pearson's correlation coefficient larger than 0.7. This number is approximately 1- to 5-fold higher than the numbers expected by chance. A small (5%-10%) yet significant fraction of genes in the Arabidopsis genome is therefore organized into local coexpression domains. These local coexpression domains were distributed over the genome. Genes in such local domains were for the major part not categorized in the same functional category (GOslim). Neither tandemly duplicated genes nor shared promoter sequence nor gene distance explained the occurrence of coexpression of genes in such chromosomal domains. This indicates that other parameters in genes or gene positions are important to establish coexpression in local domains of Arabidopsis chromosomes.

Arabidopsis↗

PubMed2004

Allermatch, a webtool for the prediction of potential allergenicity according to current FAO/WHO Codex alimentarius guidelines.

BACKGROUND: Novel proteins entering the food chain, for example by genetic modification of plants, have to be tested for allergenicity. Allermatch http://allermatch.org is a webtool for the efficient and standardized prediction of potential allergenicity of proteins and peptides according to the current recommendations of the FAO/WHO Expert Consultation, as outlined in the Codex alimentarius. DESCRIPTION: A query amino acid sequence is compared with all known allergenic proteins retrieved from the protein databases using a sliding window approach. This identifies stretches of 80 amino acids with more than 35% similarity or small identical stretches of at least six amino acids. The outcome of the analysis is presented in a concise format. The predictive performance of the FAO/WHO criteria is evaluated by screening sets of allergens and non-allergens against the Allermatch databases. Besides correct predictions, both methods are shown to generate false positive and false negative hits and the outcomes should therefore be combined with other methods of allergenicity assessment, as advised by the FAO/WHO. CONCLUSIONS: Allermatch provides an accessible, efficient, and useful webtool for analysis of potential allergenicity of proteins introduced in genetically modified food prior to market release that complies with current FAO/WHO guidelines.

Allergens↗

PubMed2003

Complete genome sequence of Lactobacillus plantarum WCFS1.

The 3,308,274-bp sequence of the chromosome of Lactobacillus plantarum strain WCFS1, a single colony isolate of strain NCIMB8826 that was originally isolated from human saliva, has been determined, and contains 3,052 predicted protein-encoding genes. Putative biological functions could be assigned to 2,120 (70%) of the predicted proteins. Consistent with the classification of L. plantarum as a facultative heterofermentative lactic acid bacterium, the genome encodes all enzymes required for the glycolysis and phosphoketolase pathways, all of which appear to belong to the class of potentially highly expressed genes in this organism, as was evident from the codon-adaptation index of individual genes. Moreover, L. plantarum encodes a large pyruvate-dissipating potential, leading to various end-products of fermentation. L. plantarum is a species that is encountered in many different environmental niches, and this flexible and adaptive behavior is reflected by the relatively large number of regulatory and transport functions, including 25 complete PTS sugar transport systems. Moreover, the chromosome encodes >200 extracellular proteins, many of which are predicted to be bound to the cell envelope. A large proportion of the genes encoding sugar transport and utilization, as well as genes encoding extracellular functions, appear to be clustered in a 600-kb region near the origin of replication. Many of these genes display deviation of nucleotide composition, consistent with a foreign origin. These findings suggest that these genes, which provide an important part of the interaction of L. plantarum with its environment, form a lifestyle adaptation region in the chromosome.

Biological Transport↗

PubMed2003

What drives plant stress genes?

Currently, there is a lot of interest in the plant stress response. Using large-scale genomics approaches, more and more genes are being identified that are involved in or even regulate this complex process. The recent boost in expression profile analyses for several plant stress responses has enabled the identification of new promoter elements as important factors in establishing the expression regulatory network controlling plant stress response.

Adaptation, Physiological↗