What are the principles of genome folding and dynamics in bacteria?

The facility develops and applies advanced, high-throughput methods for genomic research.

The four possible segments A, T, C and G that link together to form DNA molecules, and with their ordering encode genetic information, are not only different in name, but also in their physical and chemical properties.

How did toxin genes evolve from harmless physiological genes?

Promotor: M. Ubbink, Co-Promotor: R. T. Dame

The CIGR brings together a diverse range of unique expertise in genome research rooted in biology, chemistry and physics. Members of the CIGR investigate genome folding and genome transactions. An important aspect is direct as well as long term relevance for medicine.

In this thesis I highlight the applications of Oxford Nanopore Technologies (ONT) sequencing. This technique is a relatively new approach in the sequencing field, where nanopores are embedded in a membrane, DNA molecules are pulled through nanopores and an electrical current serving as the sequencing…

All crested and marbled newts (the genus Triturus) suffer from an unusual genetic abnormality, called a balanced lethal system, that kills exactly half of their offspring. How can a trait so disadvantageous have survived millions of years of natural selection?

Is translocation of nucleases possible via Agrobacterium T4SS and is it efficient enough for mutagenesis?

Increasing the efficiency of gene targeting (GT) as a genome editing tool in plants has been an important goal in plant biotechnology.

Streptomyces are filamentous bacteria that produce more than two-thirds of known antibiotics.

This thesis pioneers diatom molecular identification and quantification through genome-scale methods, with four key aims: (i) reviewing DNA/RNA sequencing methods in aquatic biomonitoring to highlight their strengths and limitations;

Promotor: G.P. van Wezel, Co-promotor: Y.H. Choi

The research is aimed at development of an efficient gene targeting method that allows controlled integration of DNA at a preselected site in the Trichoderma genome.

Filamentous Actinobacteria, such as Streptomyces, produce a plethora of chemically diverse bioactive metabolites that have found applications across medicine, agriculture and biotechnology.

Can the venom of snakes, scorpions and other animals be sources of new antibiotics?

Leiden evolutionary biologist Maurijn van der Zee has co-operated on an enormous international project to describe the genetic material of the pea aphid Acyrthosiphon pisum. The more than 100 authors involved in the project have published their findings in the online magazine PLoS Biology.

Parkinson's disease is the second most common neurodegenerative disease in the world. One of its symptoms is the loss of dopaminergic neurons in the substantia nigra pars compacta.

Promotor: P.J.J. Hooykaas, Co-Promotor: E.J. van der Zaal

Promotor: Prof.dr. T. Hankemeier, Co-promotor: R.J. Vreeken

All life on earth contains DNA, which is used to store biological information. Organisms compact their DNA in order for it to fit inside their cell(s).

Every organisms in the tree of life faces the same challenge: the length of its DNA exceeds the volume of the cell it needs to fit in. Several strategies have evolved to solve this problem, one of them being the expression of proteins that bind and organize the DNA.

The genomic DNA of every organism is organized and compacted in order to fit inside the cell. This is achieved by the joint action of numerous architectural proteins that aid in folding the genome. Genome folding is tightly interconnected with transcription, with genes in certain regions being silenced,…

Leiden researcher Dr Ben Zonneveld has determined the size of the genome - the amount of DNA per nucleus - of wild tulips. His conclusion is that there are more than 87 wild species. Various possibly new species have been discovered.

An international team from the Netherlands, France, Norway and Austria demonstrate how new sequencing technologies can be used to efficiently generate the genome, DNA, sequence of an endangered animal, the European Eel.

Climate change is a challenge for both current and future generations. New biological resources have to be developed in order to meet the demand for energy as well as the demand for food.

PhD defence

Freek Vonk and Mike Richardson, with many collaborators, have published two snake genomes in two parallel articles in the prestigious journal PNAS. Their new findings provide insight into the co-evolutionary arms race between predator and prey.

DNA carries various forms of information. Out of these forms of information the most well-known is classical genetic information.

The 1st CIGR meeting was held on March 30, 2021, with talks by representatives of all participating groups.

The guardian of our genome, the protein MutS, scans the DNA for spelling errors and makes sure they are corrected. An essential process for our health. Researchers at Leiden University Medical Centre (LUMC) have discovered precisely how this protein works by making MutS visible with cryo-electron microscopy.…

Mapping of bacterial genomes to combat infectious diseases

What are the phylogenetic relationships among the members of speciation bursts?

Identifying natural plant-associated bacteria that provide targeted inhibition of pathogens through the production of antimicrobial peptides.

This month, a paper was published in Nanoscale by scientists from Dr. Alireza Mashaghi group at the Systems Biomedicine and Pharmacology Division in collaboration with the group of Dr. Sander Tans from TU Delft/AMOLF. In this paper, the authors studied how nanoscale spatial confinement affects the fold…

How do balanced lethal systems originate and persist in nature?

Do understudied animals contain hidden species?

This thesis focuses on two processes involved in fighting infections: metabolism and immune cell motility and navigation.

The increasing resistance of pathogenic bacteria to antibiotics necessitates the discovery of new medicines.

Understanding DNA repair mechanisms is essential for advancing plant biotechnology and crop improvement. This study investigates how double-strand breaks (DSBs), induced by CRISPR/Cas systems, are repaired in the model plant Arabidopsis thaliana, and how these processes influence Agrobacterium tumefaciens…

Bacterial biocatalysis constitutes a sustainable alternative for high-value chemicals production by enabling the utilization of renewable feedstocks.

How is Pol θ responsible for T-DNA integration, and how do other DNA double-strand break repair pathways interact with Pol θ? How may we manipulate T-DNA integration to stimulate error-free integration at a predetermined genomic site?

In this thesis, I targeted the orchid genus Lepanthes, one of the six genera of angiosperms that surpasses 1,000 species in the Neotropics, as a study model to investigate the evolutionary processes that promoted species diversifications.