The Swammerdam Institute for Life Sciences (SILS), one of the largest institutes of the Faculty of Science, is seeking a PhD candidate, preferentially with prior expertise in analysing and interpreting genome-wide sequencing datasets and skills in molecular biology techniques.

One of the hallmarks of human evolution is the evolutionary expansion of the neocortex, the part of our brain that forms the substrate for the development of human-specific higher cognitive functions. The genomic basis for the increase in size and complexity of the human brain remains elusive, but the availability of an increasing amount of sequenced primate genomes now make it possible to form hypotheses about the evolutionary forces that helped shaping the human brain.

Given the extreme high similarity of genes between primate species, it’s expected that instead of changes in the composition of our genes, major evolutionary changes in brain-development are driven by changes in how our genes are regulated. Most properties of gene-regulation are harboured in the ‘non-coding’ part of our genome, which consists of numerous repetitive DNA sequences called ‘ Transposable elements’ (TEs). These TEs are derived from selfishly replicating viral DNA sequences within our genome, which are relics of ancient retroviruses that once invaded our ancestral genome and which have accumulated in our genome over the course of millions of years of primate evolution. For a long time the non-coding ‘ junk’ DNA was considered to lack a particular function or influence on our genes. We now start to realize that TEs carry viral gene-regulatory properties which can influence how, where and when nearby genes are expressed. One important consequence of the continuing invasion of genomes by TEs is that gene-regulatory networks can become rewired, with new TE insertions adding a new species-specific layer of gene control. Importantly, this extra layer of gene-control can lead to dysregulation of genes when the epigenetic silencing of TEs is disturbed, as is seen in many neurological diseases and cancer.

The PhD candidate will investigate the impact of primate-specific TE invasions on human neuronal gene-regulatory networks: Using state of the art techniques, including human stem cell biology and CRISPR/Cas9 technology, the PhD candidate will investigate the extent to which these viral DNA invasions contributed to what makes us human. In addition, he/she will investigate the mechanism of how transposable elements influence gene expression, focusing in particular on genes important for brain development or genes that have known associations to human neurological diseases.

Master’s degree in a relevant field of biology, genomics, biomedical sciences or equivalent. Candidates should be familiar with molecular biology techniques, and high throughput sequencing (RNA-seq/ChIP-seq) analysis.

The appointment will be on a temporary basis for a period of 4 years (initial appointment will be for a period of 18 months and after satisfactory evaluation it can be extended to a total duration of 4 years) and should lead to a dissertation (PhD thesis). An educational plan will be drafted that includes attendance of courses and (international) meetings. The PhD candidate is also expected to assist in teaching of undergraduates.

Based on a full-time appointment (38 hours per week) the gross monthly salary will range from €2,222 in the first year to €2,840 in the last year. The Collective Labour Agreement (cao) for Dutch universities is applicable.

The position will be filled between February and June 2018.

University of Amsterdam

With over 5,000 employees, 30,000 students and a budget of more than 600 million euros, the University of Amsterdam (UvA) is an intellectual hub within the Netherlands. Teaching and research at the UvA are conducted within seven faculties: Humanities, Social and Behavioural Sciences, Economics and Business, Law, Science, Medicine and Dentistry. Housed on four city campuses in or near the heart of Amsterdam, where disciplines come together and interact, the faculties have close links with thousands of researchers and hundreds of institutions at home and abroad.  

The UvA’s students and employees are independent thinkers, competent rebels who dare to question dogmas and aren’t satisfied with easy answers and standard solutions. To work at the UvA is to work in an independent, creative, innovative and international climate characterised by an open atmosphere and a genuine engagement with the city of Amsterdam and society.

http://www.uva.nl/en/home

Swammerdam Institute for Life Sciences

The Swammerdam Institute for Life Sciences (SILS) is one of the largest institutes of the Faculty of Science. Its approximately 240 scientists and staff members work in 16 research groups that perform excellent research centered on three themes:

1. Cell & Sytems Biology,
2. Neurosciences, and
3. Molecular Life Sciences.

The research group of Frank Jacobs investigates the impact of primate genome evolution on human neuronal gene regulatory networks. In this context we are seeking a PhD candidate, preferentially with prior expertise in analysing and interpreting genome-wide sequencing datasets and skills in molecular biology techniques.

http://sils.uva.nl/