By Antoine Sambou
Faculty of Science University of Copenhagen
Photo by Julien Dumercq, LabEx COTE
I am Antoine Sambou. I am from Senegal and PhD student in department of Geosciences and Natural Resource Management former department of forest and landscape, Faculty of Science University of Copenhagen. My PhD project is about “Vegetation change, tree diversity and food security in the Sahel: A case from the salinity-affected Fatick province in Senegal”.
This research has an interdisciplinary approach involving ecological, remote sensing and social science approaches. This justifies the particular interest to attend the Ecology and Society: Biodiversity and Global Change Summer School organised by LabEx COTE in Bordeaux from 22nd to 26 Th June 2015.
This course was beneficial for me and fulfilled my expectations. It was a good experience to learn interdisciplinary in approaching ecological problems. The necessity to combine natural, social and civil sciences to better understand the biodiversity loss and conservation was largely developed during the course.
I would like to thank LabEx COTE for organising summer school.
Photo by Antoine Sambou
To see the (Black) Forest for the trees: Black Forest Summer School 2015 on NGS data for phylogenetics
Young sequencing scientists secluded in the Black Forest (14 to 17 September 2015)
Report by Prof. Dr. Stefan Rensing, University of Marburg
During the lectures and workshops of this international summer school, young scientists developed their skills and knowledge in applied bioinformatics. Five of the sixty participants had the opportunity to give a short presentation, while most displayed their work in posters. The topics presented ranged from the analysis of mutants in model organisms via biodiversity research using current sequencing methods to phylogenetic analyses.
The prizes for the poster and talk competition went to Cologne, Bochum and Frankfurt
The young researchers mainly came from Germany, but there were also participants from Switzerland, the United Kingdom, Norway, Portugal, France, Turkey, Slovakia, Iran and Canada. The prize for the best poster went to Sebastian Hess from Cologne for his contribution, "Molecular mechanisms during food acquisition and gliding locomotion in viridiraptorid amoeboflagellates - a transcriptomic study of Orciraptor agilis (Cercozoa, Rhizaria)", to Domink Terfehr from Bochum for his work, “Uncovering the cephalosporin C precursor metabolism of Acremonium chrysogenum using functional genomics“, and to Stefan Simm from Frankfurt for “The composition of the cyanobacterial core- and pan-genomes“.
Tobias Gabriel from Cologne received the prize for best presentation with his contribution "Computational and Genetic Analysis of Perennialism in Arabis alpina".
A lot of time for scientific exchange
Four of the young scientists were able to attend the workshop thanks to the fellowship they were awarded by the DBG. This is what they liked about the event:
- "I would characterize poster sessions as very successful; there were a lot of discussions about and around the posters. During the BFSS 2015 I found answers on many of my questions. As it usually happens with good scientific events I got even more additional questions to look for answers now.” (Nataliya Rybalka, Göttingen)
- "As a first year master student , I really appreciated the explanations of different stages in the process of NGS data generation." (Stina Krsmanovic, Tromsö, Norwegen)
- "(...), a perfect place to forget about daily and mundane preoccupations and dedicate one’s mind to the acquisition of new scientific skills. The summer school was extremely well organized.” (Sergio Munoz, Halifax, Canada).
- "I was also able to speak further to some of the speakers and to get a lot of advice as well as methods and tools to analyse my own data and that will help me to complete further my work and plan my future experiments.” (Sonia Pereira, Instituto Gulbenkian de Ciencia, Portugal)
A particularity of this workshop was its seclusion close to the highest peaks of the Black Forest; the ideal setting for constructive interaction. Its venue, the performance training center “Herzogenhorn”, was much appreciated. The intense scientific exchange was not only limited to the participants, but extended to the invited speakers and the company representatives. The whole programme and the abstracts can be downloaded on the workshop website.
A highlight was the presentation by invited speaker Korbinian Schneeberger about the “Co-occurrence of transposon activity and lack of symmetric CG methylation in the genome of a close relative of Arabidopsis”. The participants were given an insight into which type of analyses can be carried out with NGS methods. They also appreciated the talks given by all seven invited workshop speakers on NGS and phylogenetics, covering the topics of data processing, mapping, metagenomic and network analyses, RNA sequencing, phylogenetics and SNPs. Furthermore, during three introductory lectures, the participants learned about the preparation of NGS data and associated terminology, the difference between prokaryotes and eukaryotes in relation to NGS, and the principals of molecular phylogenetics.
The results of the evaluation of the workshop showed that the participants were very satisfied with the scientific content and the exchange with the other scientists. The workshops and poster sessions were also thought to be very good and the venue and surroundings were rated very positively (see graph). Considering its huge success (it was already booked out 6 weeks before the registration deadline), another workshop of this kind will certainly be organised in the future.
Workshop website: http://plantco.de/BFSS2015/
Photos by RensingLab
Integrated AdapCAR and EVOLTREE summer school on ‘Global change and the evolutionary potential of forest trees’
By Cristina Rosique
Centre for Ecology and Hydrology, UK
This summer school took place in Iceland on 26 and 27 August 2015. Every student had to give a 5 minute presentation on a paper assigned to them and then lead a discussion. I presented a review (Alberto et al. 2013) and throughout the day I was very active in the discussions. It was a very productive day to think and learn a lot, especially from Sally Aitken’s lectures. On the last day of the summer school, we were taught how to use the software ASReml to analyse data from provenance&progeny trials.
Photos by Cristina Rosique
Before the summer school, I attended the ADAPCAR conference and on the second day I gave a short talk of 15 minutes, presenting my PhD project and showing a few preliminary results. I also presented a poster with some other results. The conference was very interesting and a very good chance to talk to other people and get feedback on my work. The third day was a field trip where they took us to see some forests and some poplar plantations.
By the workshop organisers
The Workshop on Forest Genetic Monitoring was held in Thessaloniki, Greece, at Hotel Philippion from 28th February to 4th of March 2015. It was organised as a part of EUFORINNO project dedicated to increase and promote scientific excellence of the Slovenian Forestry Institute and raise awareness of forest science in Europe. The course was opened by prof. dr. Hojka Kraigher, project coordinator, and the lecturers: prof. dr. Phil Aravanopoulos, dr. Evi Alizoti, dr. Eleni Abraham, dr. Barbara Fussi, dr. Gregor Božič, dr. Michail Orfanoudakis, dr. Tine Grebenc, Boris Rantaša, dr. Darius Kavaliauskas and dr. Monika Konnert.
The very best and informative lectures were accompanied by lively discussions, and many scientific and professional network ties were formed between scientists and professionals working in forest genetic monitoring and biodiversity studies from the EU and the Balkan countries.
On Wednesday, 4th of March 2015, a joint field trip of the EUFORINNO and LIFEGENMON projects was organised by the Forest Genetic Laboratory of the Aristotle University of Thessaloniki team with the cooperation of The Decentralized Administration of Macedonia – Thrace in order to visit two potential forest genetic monitoring plots for Abies borisii-regis (Bulgarian fir) in the south side of Mt. Olympus in the region of Kallipefki. The field trip which amounted up to the distance of 125 km took the participants from Thessaloniki through the foothills of the eastern Mt. Olympus massif to the final destination.
All of the EUFORINNO workshop participants visited the plots, discussed advantages and disadvantages of selecting proposed locations for forest genetic monitoring plot and their relative importance, taking into account the specifics of the visited locations. The introductions on both sites were given by George Rousakis of the local Forest Service and prof. dr. Phil Aravanopoulos. An active exchange of opinions and thoughts took place and useful suggestions were made regarding the criteria for choosing the most appropriate Forest Genetic Monitoring Plot in a particular region.
After visiting the proposed locations, the workshop participants had lunch at a local restaurant with excellent local food and amazing views. After a short walk in the village, the workshop came to an end and the workshop participants travelled home to their respective countries.
Photo by SFI
By Patricia González-Dízz
Centre for Ecology and Hydrology, UK
I attended the Approximate Bayesian Computation (ABC) workshop carried out at Uppsala University (Sweden), from 24th to 25th March 2015, as part of the EVOLTREE training courses.
I’m a PhD student from the Centre of Ecology and Hydrology and EVOLTREE member. I am currently studying the effects of past demographic events on the current genetic diversity of forest tree species. To do that, ABC is a very powerful and useful tool; however, learning to manage these techniques by yourself is sometimes not an easy task. The workshop in ABC was a great opportunity to learn and discuss with other researchers and students about the ABC framework, procedure, and aims and advantage of these analyses.
The course was led by Daniel Wegmann, who is a great speaker and has amazing knowledge on ABC methods, coalescent theory and population genetics, among others. It was perfectly organised in two days, starting with a more general introduction to the ABC analyses and then going deeper in practical sessions with real examples. The experience was intensive and useful, allowing me to improve my knowledge of ABC analyses, by asking experts about very specific and applied questions from my specific work and obtaining really useful suggestions.
Thanks to the EVOLTREE financial support, I was able to cover all the expenses during my stay in Uppsala. I’m really glad to have been part of this workshop, and I would like to thank EVOLTREE, the speaker and the organisers for their great job during the workshop! I really recommend the EVOLTREE training courses!
Photos by Patricia Gonzalez Diaz
To see the (Black) Forest for the trees: Black Forest Summer School 2016 on NGS data for phylogenetics – Young sequencing scientists secluded in the Black Forest
(13 to 17 September 2016)
Organised by the University of Marburg
Workshop on cork oak woodlands: an ecosystem in the edge of climate change
Organised by: University of Lisbon, School of Agriculture (ISA), Portugal
By Gediminas Jasinevicius, European Forest Institute and Eduardo Batista, Wageningen University
The cork oak woodlands are important in the Mediterranean region; culturally, economically and environmentally. In Portugal there are more than one million hectares of evergreen cork oak woodlands. However, this unique ecosystem started to shrink mainly due to the severe climate conditions, especially droughts caused by the global climate change. In order to sustain this woodlands, scientific knowledge on cork oak adaptation to the climate change is needed.
The University of Lisbon (School of Agriculture) organised an EVOLTREE workshop on cork oak woodlands (6-9 of September 2016). Over 20 participants from different research organisations shared their knowledge on cork oak management, genetic variability and climate change threats. A one-day field trip to the cork oak woodland “Companhia das Lezírias” enriched understanding about oak management and ongoing research projects.
In summary, the workshop was timely and very well organised.
Photos by Gediminas Jasinevicius (EFI)