Portrait picture

Contact details

Stefano Berri

School of Computing
room 7.27 E. C. Stoner Building
University Of Leeds
LS2 9JT, Leeds. UK

tel: +44 (0) 113 24 34699

email: s.berri@leeds.ac.uk

Current Position

I currently have a post-doc position within the biosystems group at the School of Computing in Leeds, under the supervision of Dr Netta Cohen. Together with graduate student Jordan H. Boyle and Dr Behrooz Esmaeili, we are interested in understanding and modelling locomotion of the nematode worm Caenorhabditis elegans

My role in the group

I perform behavioural experiments on C. elegans and write custom programs to analyse the large set of data produced from recorded movies. The aim is to test predictions of a mathematical model of the neuronal control of locomotion that we are developing. At the same time I provide new ideas and insight to refine the model and make it as biologically meaningful as possible. Experiments are performed on campus in Prof. Ian A. Hope's lab.. I set up experiments to record the behaviour of different mutants and transformed lines in a series of environment.

The skeletonizer

In early stage of my post doc I developed a "skeletonizer", a computer program to obtain the mid-body line of a worm from every frame of a movie of free moving worms. I presented a poster describing it at the 16th International C. elegans meeting. I have subsequently written a program to record position of the motorized stage we use to keep the worm in the microscope field of view

Here you can see a movie showing the result for a small clip. Blue points represent 25 equally distant points along the worm body. The big red dot represents the head, the black dot the Centre of Mass location and the blue segment the direction of motion.

Swimming-crawling transition

C. elegans is capable of two apparently different behaviours: it can swimm in water and crawl on agar surface. To understand how a small nervous system of merely 302 neurons can produce these two behaviours, I recorded worms in a range of gelatine media with increasing visco-elasticity: from water, where the worm swimms, to a thick gel where the worm crawls. I then extracted data using the skeletonizer. I calculated and plotted a series of statistics, including wavelength, frequency and amplitude.

Swimming to crawling transition

Results show that swimming and crawling are actually two snapshots of a single modulted behaviour. All intermediate behaviours can, infact, be observed.

In the following movie (mpg file, 1.4 Mb or , , ) you can see worms swimming/crawling in four different environments with increasing gelatin concentration and thereby visco-elasticity.

four worm in four different media

These results are now published on HFSP journal

Stefano Berri, Jordan H. Boyle, Manlio Tassieri, Ian A. Hope and Netta Cohen. Forward locomotion of the nematode C. elegans is achieved through modulation of a single gait. 2009. Adv. Online Pub. HFSP J. (dowload pdf )

The University of Leeds made a press release that was picked and used to make this rather funny video: Dance of the Supermodel Worm


Ph.D.

I obtained the Ph.D. degree at the Department of Biomolecular Sciences and Biotechnology, University of Milan with a thesis titled "Phylogenetic and Functional Characterization of WRKY Genes in Rice" (download the pdf - 5.1 MB).

WRKY genes encode for zinc finger transcription factors. Initially believed to be plant specific, they have an ancient origin, but got lost in the fungi and animal kingdom. However, WRKY genes experienced an incredible evolutionary success in the plant kingdom where successive duplication events originated a wide gene family that includes up to 74 members in Arabidopsis and 104 in rice. I analysed the phylogenetic origin of rice and Arabidopsis WRKY genes and performed a gene family wide transcriptome analysis using custom oligo microarray. We assessed transcription regulation of rice WRKY genes upon infection with the fungus Magnaporthe grisea and during osmotic stress. Results indicate that phylogenetically unrelated genes are co-regulated during the early response to stress. We extended and confirmed our findings in Arabidopsis, where a much wider set of microarray is publicly available.

Rice WRKY microarray analysis Arabidopsis WRKY co-regulation network





Publications in peer reviewed journals

Berri S, Boyle JH, Tassieri M, Hope IA, Cohen N. "Forward locomotion of the nematode C. elegans is achieved through modulation of a single gait." HFSP J. 2009 Jun;3(3):186-93.
PMID: 19639043, DOI: 10.2976/1.3082260

Berri S, Abbruscato P, Faivre-Rampant O, Brasileiro AC, Fumasoni I, Satoh K, Kikuchi S, Mizzi L, Morandini P, Pe ME, Piffanelli P. "Characterization of WRKY co-regulatory networks in rice and Arabidopsis." BMC Plant Biol. 2009 Sep 22;9(1):120.
PMID: 19772648, DOI: 10.1186/1471-2229-9-120

van Enckevort LJ, Droc G, Piffanelli P, Greco R, Gagneur C, Weber C, González VM, Cabot P, Fornara F, Berri S, Miro B, Lan P, Rafel M, Capell T, Puigdomènech P, Ouwerkerk PB, Meijer AH, Pe' E, Colombo L, Christou P, Guiderdoni E, Pereira A. "EU-OSTID: a collection of transposon insertional mutants for functional genomics in rice." Plant Mol Biol. 2005 Sep;59(1):99-110
PMID: 16217605, DOI: 10.1007/s11103-005-8532-6