STSM Livia Kolesar

Hi, my name is Livia Kolesar and I am a young researcher from the Institute of Animal Physiology of the Slovak Academy of Sciences in Kosice, Slovakia. With the financial support of Methagene COST Action I was able to spend a month at INRA in France and join a very interesting and comprehensive project in Dr. Diego Morgavi’s lab. My host was Dr. Milka Popova. Aim of her project is to predict a genome-scale metabolic network for four ruminal methanogens. Part of this project is and RNA-Seq experiment during which differential gene expression profiles of these methanogens will be obtained. I joined the group for this part of the experiment.

The first work week was shorter due to bank holiday, so was perfect for introduction, training and getting to know the lab. I inoculated a several microbial cultures from stock cultures and from that point I was responsible for them.

The second week we started with trial RNA extraction from cultures that were growing stably. As these were premier RNA extractions from pure cultures, the following next days I conducted a few trial and comparative extractions with slight modifications to assess which works the best for us. After running the collected samples on the Bioanalyzer we were very happy to see that many of the extractions worked out really well: sharp peaks for 16S and 23S rRNA, no DNA contamination, high RIN and concentrations ranging from 100 ng/μl up to 400 ng/μl.

During the second, third and fourth week I was collecting RNA and DNA samples. I repeated many extractions to get an RNA yield that would meet the requirements of sequencing. Works with half of the cultures went well as these were growing stably. Unfortunately, not all the cultures grew as we wished and the work got a bit delayed because of this reason. Eventually I was able to collect RNA samples from 3 out of 4 cultures in two growth stages in at least 5 biological replicates.

In the meantime I was involved in all the discussions regarding the RNA-Seq experiment. At the host lab this was a premier whole transcriptome sequencing experiment so any advice from experienced researchers was highly appreciated and it helped to design the experiment and set the right options and conditions for sequencing. Personally I found this part of my stay the most valuable because we got advice based on real, hands-on experiences and opinions served as a good guideline.

Apart from that I certainly greatly value my whole stay and all the gained knowledge and new experience. I learned a lot - this was my first experience with RNA extractions and RNA sequencing. I am really looking forward to use the gained knowledge and skills in my future experiments. The working environment was calm and friendly and the lab members helpful and supportive. The institute itself is set in a nice and peaceful environment with natural surroundings. I also had the opportunity to travel around in this region and I can only say that the nature of Auvergne is truly beautiful.

I would like to thank Milka Popova for welcoming me and all the information she shared with me, the technicians for their help and patience and Cristina Saro for her help and friendship not only in the lab. I am looking forward meeting them again in the future.

All in all this was a great and valuable visit and I am happy for this opportunity given by the Methagene network.