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.

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

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?

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

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

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

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

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 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.

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,…

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.

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).

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

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.

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

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.

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

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

Mapping of bacterial genomes to combat infectious diseases

Do understudied animals contain hidden species?

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

How do balanced lethal systems originate and persist in nature?

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…

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.

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…

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.

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

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.

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. The available expertise extends…

Throughout all domains of life, from bacteria and archaea to eukaryotes, genomes adopt well-organized three-dimensional structures that can change in space and time to accommodate preferred transcriptional programs for environmental adaptation, the maintenance of cellular identity and differentiation…

The mission of the Plant Science research programme is to contribute to the sustainable production of high quality crops, flowers and high-value bio-based products. This is realised by generating fundamental knowledge of basic biological processes related to development of plants and their interaction…

The CIGR comprises research groups from the Leiden Institute of Chemistry (LIC), the Leiden Academic Centre for Drug Research (LACDR) and the Leiden Institue of Physics (LION).

This dissertation is part of a broader research project that revolves around unraveling the evolution of balanced lethal systems.