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Laboratory of DNA Sequencing and Oligonucleotide Synthesis

Head: Doctor Robert Gromadka

 

 


Paramecium tetraurelia genomics

Group leader: Dr. Robert Gromadka
Staff: Prof. Joanna Rytka, Dr. Jacek Nowak, M.Sc. Julita Gruchota, M.Sc. Kamila Maliszewska

 

Main Research Area:
Functional analysis of newly discovered genes of the Paramecium tetraurelia.
Currently we are screening the Paramecium tetraurelia megabase chromosome for early autogamy-specific genes. We are performing a functional RNAi-based screening of the effect of inactivating their expression. RNA interference is obtained by the method of "feeding", with bacteria which produce double-stranded RNA.

 

The organism:
Paramecium tetraurelia

Eukaryota; Alveolata; Ciliophora; Oligohymenophorea; Peniculida; Paramecium

Paramecium is a very large eukaryotic cell (120 micrometers) covered with vibrating cilia. The Ciliates have separate germinal and somatic lineages within a single cytoplasmic unit. These cells possess indeed two nuclei. A germinal nucleus (the micronucleus) is diploid, transcriptionally inactive, contains heterochromatin responsible for the transmission of genetic information via sexual processes. A somatic nucleus (the macronucleus) ensures expression of this information. The macronucleus is derived from the zygotic germlinenucleus by programmed DNA rearrangements, is polyploid, has no genetic continuity, consists only of euchromatin, and is the seat of all transcriptional activity.

 

Collaboration:
The European Group of Research (Groupement de Recherches Européen or GDRE) called "Paramecium Genomics" was created for 4 years on July 1st 2002 by the CNRS to promote Parameciuim Genome sequencing, annotation and functional analysis. It has now been renewed for 4 years starting January 1st 2006. The GDRE, coordinated by Jean Cohen at the Centre de Génétique Moléculaire in Gif-sur-Yvette, France, groups six laboratories in France, three in Germany and three in Poland. GDRE web site: http://paramecium.cgm.cnrs-gif.fr/gdre.php

 

Research grants: 

2007-2010 "Identification and characterization of genes involved in process of autogamy of the ciliate Paramecium
                   tetraurelia",
(Ministry of Sciences and Higher Education)
2003-2006 "Genome sequencing and functional analysis of genes of the ciliate Paramecium tetraurelia by application

                    of posttranscryptional silencing of genes used interferring RNA (RNAi)", (Ministry of Sciences
                    and Higher Education)

 

Selected publications:

  1. Aury J.M., Jaillon O., Duret L., Noel B., Jubin C., Porcel B.M., Segurens B., Daubin V., Anthouard V., Aiach N., Arnaiz O., Billaut A., Beisson J., Blanc I., Bouhouche K., Camara F., Duharcourt S., Guigo R., Gogendeau D., Katinka M., Keller A.M., Kissmehl R., Klotz C., Koll F., Le Mouel A., Lepere G., Malinsky S., Nowacki M., Nowak J.K., Plattner H., Poulain J., Ruiz F., Serrano V., Zagulski M., Dessen P., Bétermier M., Weissenbach J., Scarpelli C., Schächter V., Sperling L., Meyer E., Cohen J., Wincker P. Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature (2006) 444: 171-178
  2. Zagulski M., Nowak J.K., Le Mouel A., Nowacki M., Migdalski A., Gromadka R., Noel B., Blanc I., Dessen P., Wincker P., Keller A.M., Cohen J., Meyer E., Sperling L. High coding density on the largest Paramecium tetraurelia somatic chromosome. Curr Biol. 2004; 14:1397-1404.
Useful links:
Paramecium genomics - CNRS Gif-sur-Yvette
Paramecium tetraurelia - Genoscope
Paramecioum tetraurelia Megabase Chromosome - IBB Warsaw
Paramecium Wiki

 


Methodology of genomic sequencing
Head: Prof. Włodzimierz Zagórski-Ostoja
Group leader: Dr. Robert Gromadka
Staff: Dr. Piotr Dzierzbicki, M.Sc. Beata Babińska, M.Sc. Małgorzata Filipiak, M.Sc. Jan Gawor, M.Sc. Ewa Kalińska, M.Sc. Helena Kossowska, M.Sc. Anna Trzemecka, M.Sc. Karolina Wylot

 

The aim of laboratory are massive sequencing of genomic DNA and functional genomics. We provide annotation of newly discovered sequences and functional analysis of particular genes. Our competency include classical and molecular genetics of bacteria, yeast and ciliate. Our laboratory is equipped in high throughput sequencers for classic sequencing by Sangers’s method and since 2008 it was installed and works in full-range genomic sequencer GS FLX Titanium (454) from Roche company. The staff were engaged in sequencing of chromosomes from Saccharomyces cerevisiae  then first chromosome and full genome of Paramecium tetraurelia. Currently the laboratory is engaged in the national project of sequencing of a part one potato’s chromosome in framework of The Potato Genome Sequencing Consortium (PGSC). We do sequencing for researcher groups from our institute and for  cooperators from others scientific institutes. We have experience in sequencing for diagnostic purpose. More info at laboratory web page www.oligo.pl