Promotores: J.N. Kok, H.J. Hoogeboom

Identification and characterization of components of DNA repair pathways and their role in Agrobacterium T-DNA integration and repair of CRISPR/Cas induced DSBs.

The type-IV secretion system (T4SS) is a machinery able to transfer DNA and proteins between bacteria and in certain cases also to eukaryotic cells.

Our DNA molecules are packaged by proteins in compact structures. The aim of this project is to understand how modern gene editing techniques nevertheless get access to their target in the DNA.

Promotor: R.D. Gill, F. Taroni

Promotor: D. Bouwmeester, Co-promotor: D. Kraft

The genetic information of all living organisms is contained in their DNA. Cells modify the degree of DNA compaction by epigenetics, which largely determines what genes are read out and which genes are transcriptionally silent.

What is the most effective way to eliminate tumour cells? The DNA repair mechanism could play an important role in increasing the effectiveness of chemotherapy in the fight against cancerous cells. If we are to influence this mechanism, we need fundamental knowledge about how the mechanism works.

Bacteria often experience external challenges, such as changes in environmental conditions or attacks by bacteriophages.

Promotor: P. J. J. Hooykaas Co-promotor: B. S de Pater

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).

Inactivating mutations in BRCA1 or BRCA2 genes predispose to several types of cancer.

Leiden physicist Maarten Kruithof has discovered how our DNA is infallibly able to fold itself and to unfold again. In his dissertation he demonstrates how DNA is folded in a single long, very flexible spiral.

This project aims to assess the risk of spread of antimicrobial resistance genes in the environment derived from currently used synthetic biology approaches in the field of drug discovery.

Single-celled organisms have stiffer DNA than multicellular lifeforms like humans and rice. Theoretical physicists managed to simulate the folding in full genomes for the first time to reach this conclusion. Publication in Biophysical Journal on February 7.

Lecture, Areal Histories

In an Advance Online Publication biophysicist John van Noort and others show using magnetic tweezers that DNA is folded in compliant helices of chromatin. This allows enzymes access to the DNA needed for gene expression. Van Noort's research group made the discovery in close partnership with researchers…

Schneider

Theoretical physicist Helmut Schiessel receives an NWO Projectruimte grant of 390,000 euro. He will use this budget to hire a postdoc and a PhD student to continue his research on flexibility of double stranded DNA.

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.

Why do opposites attract? According to Karin van der Tuin, researcher at Leiden University Medical Center (LUMC), it could be because of your DNA. The more you differ from one another, the better. She will be testing her ideas at the Lowlands festival Lowlands, where she will subject visitors to DNA…

Researching DNA material for genetic disorders using the most powerful apparatus. This is what GenomeScan, a company on the Leiden Bio Science Park, does. Master's student Konstantina Konstantinopoulou is doing an internship there. 'It's a world where developments happen really rapidly so it's a fantastic…

The DNA of young people is regulated to express the right genes at the right time. With the passing of years, the regulation of the DNA gradually gets disrupted, which is an important cause of ageing. A study of over 3,000 people shows that this is not true for everyone: there are people whose DNA appears…

Leiden and Jülich researchers discovered an elegant and simple approach to improve the sensitivity of graphene biosensors. These so-called ‘next generation graphene electronic biochemical sensor devices’ are able to detect very low amounts of HIV DNA thanks to their very low electronic noise.

The main purpose of DNAmarkerpoint is to better understand the ecology, evolution and biodiversity through the study of ancient- and modern DNA.

Leiden theoretical physicists have proven that not only the genetic information in DNA determines who we are, but also DNA’s mechanics. Helmut Schiessel and his group simulated many DNA sequences and found a correlation between mechanical cues and the way DNA is folded. Publication in PLoS One.

The way DNA folds, largely determines which genes are read out. John van Noort and his group have quantified how easily rolled-up DNA parts stack. This costs less energy than previously assumed. Publication in Biophysical Journal.

PhD student Willem Noteborn has investigated supramolecular structures. These can be useful for the loading of medicines and signalling molecules regarding, for example, cellular differentiation. In his thesis, he describes the functioning of these structures.

Researchers from Biomon have used DNA-techniques to find 40 different species of fish in the river Dommel. This technique is capable of detecting more species than conventional methods of measuring.

Self-assembly is an abundant process in nature and is vital to many processes in living organisms.

Conference

How do forensic scientists deal with complex DNA-evidence found at crime scenes? Giulia Cereda developed new statistical models to analyse them. PhD defense 12 January.

A group of single-celled organisms organises its DNA in a similar way to higher organisms such as plants, animals, and fungi. However, the way packaged DNA is read out differs between the two related groups, Bram Henneman discovered. PhD defence on 5 December.

According to a new study by an international team of researchers from the Caribbean, Europe and North America, the Caribbean was settled by several successive population dispersals that originated on the American mainland.

Large carnivores and humans, along with their livestock, have co-existed for thousands of years. However, human population growth and an increase in economic activities are modifying the landscape for large carnivores and their prey.

How do our cells keep DNA stored away? To find out, biochemist Remus Dame received a 3 million euro Science-Groot grant. Leiden University will share the grant with TU Delft, VU Amsterdam and the Hubrecht Institute.

In the largest study of ancient DNA ever conducted, an international team of scientists has revealed the complex story behind one of the defining periods in European prehistory. The study is published this week in the journal Nature.

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?

PhD Defence

Promotor: J.N. Kok, P.E. Slagboom Co-promotor: J.F.J. Laros

Dynamics of material, social and ideological relationships in the pre-Columbian insular Caribbean

Lancering

In human cells, a meter-long DNA is condensed inside a micrometer-sized cell nucleus. Simultaneously, the genetic code must remain accessible for its replication and transcription to functional proteins.

The way genes are folded determines their activity in our body. Leiden biophysicists are now the first to unravel this structure molecule-by-molecule. Publication on December 1st in Nature’s Scientific Reports.

Leiden physicists and chemists have managed to bring two graphene layers so close together that an electric current spontaneously jumps across. In the future this could enable scientists to study the edges of graphene and use them for sequencing DNA with a precision beyond existing technologies. Publication…