Research

Research in our lab focuses on the relation between genes, brain and behaviour.

Our research combines broad range of approaches ranging from bioinformatics to neurogenetics and molecular biology, aiming to understand how the brain works. We are particularly interested in the circadian clock system, but other behaviours such as aggression, learning and memory, and sleep are also explored in the lab.

Cryptochrome

3D structure of Cryptochrome—a blue light photoreceptor; a natural variation in a single amino acid shown in green, modify the way flies respond to light.

Our main model organism is Drosophila, and our facilities allow the simultaneous screening of behaviour of hundreds individuals. Recently, we have also launched experiments using Nasonia, an emerging model organism that offers exciting opportunities for epigenomic research. The lab is a member of InsecTIME, a Marie-Curie training network focused on studying rhythm mechanisms in insects.

Next generation sequencing, Quantitative trait loci (QTL) mapping and RNAseq gene expression profiling are a few examples for the techniques we use in the lab to study these mechanisms at a genome-wide level.

Our fly collection of strains from various wild populations, is one of the largest collections in Europe,  allow us to study the evolution of genes associated with circadian and seasonal timing, and provide a valuable tool to assess the impact of global climate changes at the genomic level.

Natural occurring variations in circadian clock genes and their functional role

A circadian clock that drives daily rhythms is present in most organisms and is composed of an

cryEurope4.jpg

Frequency distribution of natural alleles of cry in wild populations of Drosophila.

evolutionary conserved genetic network. Our research is aimed to identify molecular adaptations in circadian clock genes and how these adaptations allow the circadian pacemaker to operate at different environments.

For the last ten years we have been studying natural polymorphisms in the timeless gene, encoding a light-sensitive circadian protein. Thispolymorphism generates two length isoforms of the TIMELESS protein via alternative methionine initiators, ls-tim and s-tim. Together with theRosato and Kyriacou groups in Leicester, and the Costa group in Italy, we have shown that ls-tim is a new European allele that has spread extensively in Europe over the past few thousand years due to directional selection. The selective agent turns out to be photoperiod, and two papers have been published in Science on this work (Tauber et al., 2007; Sandrelli et al. 2007). This study, supported by a NERC award, provided the first molecular link between the circadian clock and seasonal timing.

The molecular basis of seasonal timing

Many organism detect the  change in daylength (photoperiod) as a cue to time their seasonal response. The molecular basis of this photoperiodic clock is unknown. One of the fundamental questions in circadian biology is whether this time mechanism is linked to the circadian pacemaker. We are using the photoperiodic diapause response in Drosophila as a model system to test the effect of various clock mutations. We are employing  microarray global profiling and proteomics  to identify genes involved in the seasonal timer.

The circadian clock and the photoperiodic timer of Nasonia

Nasonia Peter Koomen_Mathijs Zweir_University of Groningen.jpg

The parasitic wasp, Nasonia vitripennis exhibits a robust photoperiodic response, which was extensively studied 40 years ago. Nasonia is a typical long-day insect, in which short photoperiods experienced by the females induce diapause in their larval progeny. The photoperiodic timing is entirely maternal since embryos are committed to either diapause or direct development before they are oviposited. What makes the photoperiodic response of this wasp so interesting is the fact that several studies suggest that daylength measurement (photoperiodic timing) requires the circadian clock, and the two timing mechanisms are causally linked.
Recently, the first draft of the complete genome sequence of Nasonia has been completed, providing the opportunity to study the photoperiodic and the circadian clock in this organism at the molecular level. In addition, methods to knockdown genes in this insect have also been recently developed, allowing functional analysis of candidate genes. One of the objectives of this project is to identify the circadian clock genes in Nasonia and then knockdown these genes and test the effect on the photoperiodic response. Another set of experiments is aimed at taking advantage of the available genomic data and perform a genome-wide expression profiling using RNAseq to identify genes that participate in photoperiodic timing. We will also carry experiments to identify the photoreceptor proteins that channel the light input into the circadian and photoperiodic systems.

Molecular basis for chronotypes in Drosophila

It has become apparent in recent years that the human circadian system shows natural variation in terms of the chronotypes that are expressed (eg ‘larks’ versus ‘owls’). Given the underlying conservation of the fly and human circadian mechanism at the molecular level, fly chronotypes represent a potentially powerful model system to study such variation. We are using selected fly lines that have a significant phase difference in adult emergence, but only a small difference in circadian period. We plan to study these ‘chronotypes’ by subjecting them to a modified QTL analysis in order to identify their underlying genetic bases. We shall complement this genomic analysis with global expression profiling using RNAseq. It is hoped that these two approaches may identify all the differences between early and late flies irrespective of whether they originate from changes in the coding or in the regulatory regions of genes. Any candidate genes identified from the genomic and/or expression studies will be subsequently disrupted with the use of mutants or RNAi, to validate their contributions to the chronotype. We shall also generate a number of novel constructs using GAL4/UAS and FLP/FRT , to dissect out the anatomical substrates that underlie the two phenotypes, and to assess the importance of central versus peripheral clocks in generating these phase differences in behaviour. We hope that our results will provide a novel theoretical framework by which to understand the origins of human chronotypes.