latest news & announcements

An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies

Background: Cost effective next generation sequencing technologies now enable the production of genomic datasets for many novel planktonic eukaryotes, representing an understudied reservoir of genetic diversity. O. tauri is the smallest free-living photosynthetic eukaryote known to date, a coccoid green alga that was first isolated in 1995 in a lagoon by the Mediterranean sea. Its simple features, ease of culture and the sequencing of its 13 Mb haploid nuclear genome have promoted this microalga as a new model organism for cell biology.

Identification of Functionally Related Enzymes by Learning-to-Rank Methods

Enzyme sequences and structures are routinely used in the biological sciences as queries to search for functionally related enzymes in online databases. To this end, one usually departs from some notion of similarity, comparing two enzymes by looking for correspondences in their sequences, structures or surfaces. For a given query, the search operation results in a ranking of the enzymes in the database, from very similar to dissimilar enzymes, while information about the biological function of annotated database enzymes is ignored.

A Functional and Evolutionary Perspective on Transcription Factor Binding in Arabidopsis thaliana

Understanding the mechanisms underlying gene regulation is paramount to comprehend the translation from genotype to phenotype. The two are connected by gene expression, and it is generally thought that variation in transcription factor (TF) function is an important determinant of phenotypic evolution. We analyzed publicly available genome-wide chromatin immunoprecipitation experiments for 27 TFs in Arabidopsis thaliana and constructed an experimental network containing 46,619 regulatory interactions and 15,188 target genes.

The proteome under translational control

A single eukaryotic gene can give rise to a variety of protein forms (proteoforms) as a result of genetic variation and multilevel regulation of gene expression. In addition to alternative splicing, an increasing line of evidence shows that alternative translation contributes to the overall complexity of proteomes. Identifying the repertoire of proteins and micropeptides expressed by alternative selection of (near-)cognate translation initiation sites and different reading frames however remains challenging with contemporary proteomics.

A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites

Next-generation transcriptome sequencing is increasingly integrated with MS to enhance MS-based protein and peptide identification. Recently, a breakthrough in transcriptome analysis was achieved with the development of ribosome profiling (ribo-seq). This technology is based on the deep sequencing of ribosome-protected mRNA fragments, thereby enabling the direct observation of in vivo protein synthesis at the transcript level.

N2N coordinator Prof. Yves Van de Peer is member of Steering committee AOCC (African Orphan Crops Consortium)

This crop is not an orphan anymore: it now has a home

African orphan crop Hibiscus sabdariffa. Photo credit-
Standing before 20 other senior scientists at the World Agroforestry Centre (ICRAF), Dr Wonder Nunekpeka spoke the words on everyone’s mind. “My crop has been an orphan but is not anymore! I will be a father for it.” Breeders of plants such as the edible aroid cocoyam applauded and roared their approval. The fight to combat hunger and preserve Africa’s indigenous foods is on.

Prometheus Research Award for N2N partner Lennart Martens

Prof. Lennart Martens ( Faculty of Medicine and Health Sciences - Department of Biochemistry ) was nominated for his exemplary role in innovative multidisciplinary research, in which he simultaneously explores the boundaries of academic and social engagement.

Within N2N 4 students obtained an IWT PhD grant this year

  • Laura De Clerck & Prof. Dr. Dieter Deforce with the project 'Application of "data-independent acquisition mass spectrometry" for quantification of histone modifications in toxicological screenings'
  • Senne Cornelis & Prof. Dr. Dieter Deforce with the project 'Designing and validating an integrated lab on a chip (LoC) for STR profiling'
  • Ludger Goeminne & Prof. Dr. Lieven Clement, Prof. Dr. Kris Gevaert & Prof. Dr. Klaas Vandepoele with the project 'Differential proteomics on peptide, protein and module level'