Retreat September 2018

September 14/15 we had the fourth QTB group retreat, this time in the Eifel in Zweifall. We discussed a broad range of topics including minimal forests, group I introns, minimising genome-scale networks etc. Maybe they get covered here in future posts.

I presented the question how rapid, long-range signals may work in plants. In retrospect, I should have called the topic long-distance information transmission in plants. Animals have a nerval system to integrate the stimuli from various sensing organs, process this information, and trigger an appropriate response. This response often involves a coordinated muscle movement to run away from the danger. How do plants integrate information from external stimuli?

Surely, plants react in a coordinated fashion. If a caterpillar chews on one leaf, other leaves start producing nasty compounds, poisonous or at least with a terrible taste. If a pathogen attacks, also other parts of the plant trigger a defensive response (systemic acquired resistance, SAR). Salt stress triggers all kind of responses throughout the plants, and so does drought. So, how is it working?

In principle, long-range transmission of signals in plants could work in various ways: Transport of signalling molecules through the phloem, volatiles travelling through the air from one part of the plant to another, hydraulic pressure signals, electric signals, etc. But are these signal transmission mechanisms capable of carrying information? Could they be modulated, much in the fashion of spiking frequency in neurons? Are several routes necessary to integrate information?

The recent results by Simon Gilroy have shown that calcium waves travel across Arabidopsis rosettes in only a minute or so, after local wounding. The response was the same for caterpillar chewing or cutting with scissors. Moreover, calcium waves have also been observed triggered by high salt concentration. So what is the role of the calcium wave in transmitting information? Can this signal be used to differentially transmit the different causes of stress? If so, how? If not, what other transmission routes play a role and how are they interlinked?

A great discussion, which may well results in a number of fascinating research projects at QTB!

There is always a first time

Yes, it is true! Things happen all the time but what we remember is our "first time" like the first day at work or the first trip alone. This brings to sharing my first experience of disseminating science at a conference, with a huge audience (~1000 participants), composed of distinguished people from science. It was a great privilege to be part of Plant Biology Europe EPSO/FESPB 2016 Congress held in the beautiful city of Prague, Czech Republic. It is the second year of my PhD, when I got the opportunity to present my work of developing a mathematical framework to understand the biosynthesis of an important plant's secondary metabolite called "Glucosinolates". Glucosinolates are highly diverse-class of bio-active compounds, found in plants like broccoli, mustard and plant-scientist's pet, "Arabidopsis". It facilitates plant's defence against pathogens and also possess anti-cancer properties in humans. A question, "how these diverse class of compounds are produced and regulated?" has been boggling minds of plant-scientists for many years now. Importantly, the link between the genotype and the metabolic phenotype is poorly understood. Aptly using the given honour to speak about my approach of addressing the question, I highlighted the fact "why there is a need of having a theoretical model?". Additionally, with my mathematical model, I explained how the differences at genomic level within a particular species leads to different metabolic phenotypes. It was intimidating to have "Glucosinolate Queen", the lady who pioneered the glucosinolate research, and other distinguished people from the field interested in your way of understanding and doing the research. With the appraisals, comments and suggestions I received, I continue my PhD journey.

Every "first-time" brings a memory and experience and this experience from my first conference talk has surely boosted my enthusiasm for future endeavours. Looking forward to many more first times.

Garrett's perspective on DAAD-RISE meeting in Heidelberg



"On July 2-4, 2015, I attended the 2015 DAAD-RISE Scholarship Holder Meeting in Heidelberg. A variety of social and academic events occurred throughout the meeting, all of which I, a RISE program participant, found helpful. Thursday evening was devoted to a barbecue for the interns, and Friday afternoon and evening were devoted to a city tour and dinner for the interns. Both events provided me with numerous chances to not only relax in the company of fellow interns, but also gather useful and enlightening information about what fellow interns were studying at which universities, what was the project of their internships, and what their plans were for the future. Friday morning was devoted to a presentation of academic and industry opportunities. The presentation was coordinated and hosted by the RISE program, but it included speakers from various places across Germany and abroad. Current professors in German institutions and RISE alumni spoke about opportunities for further study in Germany and opportunities for employment in Germany. Diplomatic staff from the embassies of countries participating in the RISE program delivered speeches that expressed support for and encouraged further participation in exchange programs like those done by the DAAD. The conference closed with 10 minute presentations by various RISE participants that summarized the topic and methods of their research project."


~ Garrett Early

Farewell, Garrett

We said goodbye today to our RISE student, Garrett Early, who joined our group at the end of May to work with me on the project on ultrasensitive signalling pathways. Garrett is a physics student at North Carolina State University (USA) and was awarded with DAAD RISE scholarship that allowed him to travel to Europe and work with us for 10 weeks. RISE is a summer internship program for undergraduate students from the United States, Canada and the UK in the fields of biology, chemistry, physics, earth sciences and engineering that offers unique opportunities for Bachelor students to work with research groups at universities and top research institutions across Germany for a period of 2 to 3 months during the summer.

During his project he was working on developing mathematical "toy model" to understand the robust maintenance of a cellular state of a photosynthetic cell which reacts in an ultrasensitive way to external stimuli. He got aquanted with differential equations based theoretical approach in modelling complex biological systems on the example of photosynthesis. He learned about and tested several kinetic mechanisms to model the balance of small system and trained his programming skills in Python performing small set of simulations. He gave one oral presentation summarising his first month of work and wrote a short report at the end of his internship.

We wish Garrett all the best in his future career and hope he will continue his interest in biology.


From the left: Oliver Ebenhöh (head of the Institute),
Anna Matuszyńska (RISE supervisor) and Garrett Early (RISE student).


First QTB Conference

It finally happened that the whole QTB scientific team, together with the associated members from the University of Aberdeen, met at the international conference. Held for the 5th time in the last 10 years, Metabolic Pathway Analysis 2015 is a conference that has a primary focus on the structural (topological) analysis of metabolic networks, and in particular techniques allied to linear algebra, linear programming and computer modelling. This time organised in Braga, Portugal, attracted, so far, the largest number of participants and offered an insight into novel methods and tools applicable to metabolic pathways, highlighting applications to metabolic engineering and health and plant sciences. Placed in a marvelous Bom Jesus, besides top scientific content, the meeting offered a unique set of architectonic Baroque jewels and one in kind view over the Braga city.

Our work was proudly represented by five poster presenters and a speaker. Dr. Elahe Radmaneshfar presented her work on stochastic modelling of fatty acid synthesis and her collegaue from Aberdeen, Dr. Ahmad Mannan presented his work on the evolutionary footprint in metabolic genes of Arabidopsis thaliana. Our PostDocs from HHU presented work on co-factors inclusion in the dynamic flux analysis (Dr. Antonella Succurro) and results of the ongoing research held with our Irish collaborators, on diatom-bacteria consortia (Dipl.-Biol. Ovidiu Popa). Also our PhD students contributed to the scientific content of the meeting: Suraj Sharma presented his first results of the modelling of glucosinolate metabolism in plants and Anna Matuszynska gave a talk about a reductionist approach to model self-regulation in plants  during the session on the Applications to Photosynthetic organisms and Microbial Communities.

Inspired by the dynamic discussions we are already looking forward for the next MPA conference that will take place in 2017 in Montana, USA!


From the upper left: A. Mannan, O. Popa, S. Sharma;
First raw from the left: E. Radmaneshfar, O. Ebenhöh, A. Succurro, A. Matuszyńska