All posts by Anna

Aberdeen and my favourite library

It is not that long time ago when I was a citizen of the Granite City. It’s hard to believe that now I visit it only as a guest researcher. It is my first ‘adult home’, away from my family and friends, place where I made new friendships for a lifetime, place where I started my PhD journey, place where I found a very different myself.

People love it or hate it. You can hear complaints on weather, parochialism, monotony, dullness. What I always see instead is the city sparkling like silver, condensed with the warmest and kind people I have ever had a chance to meet. I’ve learned how to drink whisky and don’t care about the rain at all, how to prepare fish soup on milk and reply to my neighbours when asked far div ye bide?

Now, every time I come back, I point out one thing I miss specially, and this time I’ll write about the library: The Sir Duncan Rice Library. The most modern and adjusted to the needs of students library I had a pleasure to study in. I always thought that I’m not a kind of ‘library’ person. I found it more comfortable to stay at home in my pj’s, allowed to listen to some music and have a snack while studying my notes. The truth was that libraries I’ve been to simply didn’t give me the possibility to feel comfortable. They were either too dark, had no place to sit, not enough sockets for students to plug in their laptops, no space for a discussion or cafeteria to grab an espresso and get a break. The Sir Duncan Rice Library is finally a 21st century space for learning and research I’ve been looking for. It was officially opened the day after I arrived in Aberdeen, almost as if Her Majesty Queen Elizabeth gave me a very personalised gift.

Except of the great collection of books, the study space includes interactive areas for collaborative projects. No more: ‘so where do we meet’ when it comes to a join project. There are also informal areas, such like The Hardback Cafe and the ‘Break-out Room’ where you can enjoy a beautiful view over the city. Each of the seven floors of the library includes sufficient number of PCs and sockets to plug in your own laptop, as well as number of comfortable armchairs and tables. Whenever I’m in Aberdeen I look for few hours to spend in the library, as there is simply no other place like this where I can truly focus and enjoy the fact I can study.

Perspective

Monday, 16th of March

We have finished the first round of workshops conducted as a part of Science Fair in Fraserburgh. We are positively exhausted and look forward for tomorrow’s groups at the Aberdeen Biodiversity Centre. The biggest surprise of the day was how well behaved kids are and how easy it was to work with them.

Tuesday, 17th of March

Groups in Biodiversity Centre were just terrific! Actively participating in question session, interested in the topic. We would love to have more groups like that!

Saturday, 21nd of March

It’s hard to believe that this is the end! Today we have participated in a Discovery Day at Aberdeen Science Centre. We hosted together dozen of pupils who investigated with us how plants adapt to changes in their environment. Five volunteers even performed an osmosis experiment. Here you can see the picture of their experimental set up from 2 pm. Unfortunately the time was not sufficient to allow the colour to pass through the xylem to the pellets. We encourage you to repeat it again at home!

Heard in the seminar room

My seminar/conference notes does not always include only scientific comments. Sometimes they just capture a nice quote, funny parafrase or situational joke. Selection of the recent below:

Answer on the question “Will that work” during the talk on understanding development and diversity of leaf shape

Well, parafrasing Gramsci, thake the “Pessimism of the intellect and optimism of the will” and it should.

About Flux Balance Analysis:

How often have I said to you that when you have eliminated the impossible, whatever remains, however improbable, must be the truth? [Sherlock Holmes in The Sign of the Four]

Model of acclimation publicly available

Institute for Quantitative and Theoretical Biology made available on-line the old photosynthesis model for model organism alga Chlamydomonas reinhardtii and you can now easy download it and play with it! All you need is a working python and scientific packages. I suggest to download Anaconda distribution that comes with all packages needed to smoothly run the model.

We share Python files reproducing the mathematical model described in the paper published by Ebenhoeh et al. 2014, originally developed in MATLAB. The model comprises a set of seven coupled ordinary differential equations and captures the temporal evolution of: PQ, PC, Fd, lumenal H, ATP concentration, NADPH concentration and cross section of PSII.

You can access the model from git repository.

You now have two options: either you download the model as a zip file and use it directly on your computer, or you setup git. Second option is preferred if you would like to be anyhow involved in the development. In this case, I would suggest signing in (free of charge) and cloning the model. So for those who would like to know how to use git, a few simple steps:

*INSTALL GIT INSTRUCTIONS*

If you’re on a Debian-based distribution like myself, try apt-get:

[code language=”bash”]
$ apt-get install git
[/code]

If you are using Windows, an easy way to get Git installed is by installing GitHub for Windows. The installer includes a command line version of Git as well as the GUI and can be downloaded from http://windows.github.com.

If you are using Mac, there are several ways, like simply try to run git from the Terminal the very first time. If you don’t have it installed already, it will prompt you to install it.

*GET THE MODEL COPY ON YOUR COMPUTER*

If you wish to start tracking an existing project in Git, create a new directory of choice, then go to this project directory on your computer and type:

[code language=”bash”]
$ git init
[/code]

You clone a repository with git clone [url]. In our case we copy the url from the right hand side of the website:

[code language=”bash”]
$ git clone https://github.com/QTB-HHU/petcmodel.git
[/code]

You should notice that in the selected directory on your computer you have now all files from the on-line repository. Now, you can construct a branch of the project, for instance named with your name:

[code language=”bash”]
$ git checkout -b Giulio
[/code]

and edit files within this branch. Whatever you will change in the file you need to /add and further /commit. Without going to too many details, we have three stage path from the changing the file to uploading to the github, which helps avoiding publishing mistakes.

You can change a parameter in a file, you can add some simple plotting function. You can do whatever. But whatever you wish to change, you need to type:

[code language=”bash”]
$ git add [name-of-the-changed-file]
$ git commit [name-of-the-changed-file] -m "here-you-can-put-message-with-information-what-you-changed"
[/code]

And what is the coolest part, later you can share it with the others, by sending your project back to the github:

[code language=”bash”]
$ git push origin Giulio
[/code]

*HOW TO USE THE MODEL*

Actually, all you need to know is described in the README file in the repository. The equations are implemented in petcModel.py and their origin is explained in detail in the electronic supplementary material of the publication. If you wish to reproduce for instance the PAM experiment in the darkness, you can easily type:

[code language=”bash”]
python dld.py >/dev/null 2>/dev/null
[/code]

You can also investigate the steady state change in the redox state of the reductant pool under different light conditions, like on the figure below or write your own protocol for an experiment in silco!

I hope that some of you will be interested in playing with the model. Have fun!

CEPLAS association

I am happy to share the news that last month, as the first PhD student in the history, I was accepted to become associated with the Cluster of Excellence on Plant Science (CEPLAS) Graduate School.

Becoming a part of this cluster raises new challenges but also gives new opportunities for collaboration. CEPLAS mission is to contribute new paradigms to solve urgent problems in plant performance and production through exploitation of natural variation and biodiversity. My research project on photosynthetic electron transport chain matches the research programme of Area B of CEPLAS and I believe that I can bring a valuable insight to increasing our understanding of differences between existing types of photosynthesis.

I would encourage you to watch this short video by NationalGeographic, where you can learn why plant science, especially related to breading, is crucial in solving present global challenges.

Scotland, there is still no umbrella for you!

When I moved to Aberdeen, Scotland, I didn’t have big expectations regarding the weather. I imagined dark, rainy days, and I got them (no complains on that, people and whisky compensate weather conditions, but I will write about that some other time). Therefore it’s no surprise that I immediately bought an umbrella. Feeling save and equipped in ‘rain-protector’ I went for the first time to the city centre. The very same day my umbrella got broken. By the wind, of course. Without giving that too many thoughts, I bought my second umbrella. My walk from home to the university lasted for about 40 minutes. My umbrella didn’t survive even half of the way as after 10 minutes it turned inside-out and fabric frigged. When I reached university, soaked in rain, looking truly miserable I have learned the most unbelievable fact from a colleague of mine: ‘Oh, didn’t you know that only tourists carry umbrellas here? That is exactly how we distinguish Aberdonians from the rest!’ And that was actually true. I dig up that there exists dozens of expressions Scots use to describe their windy weather, like ‘Gab o’ May‘, to describe stormy weather at the start of May or ‘skirl‘ which corresponds to the sound of strong wind (you can read more about that here). I finally realized that there was simply no point of buying another umbrella.

Up until today. Scientists from Nanjing University of Aeronautics and Astronautics, China, had designed an umbrella that instead of relying on a metal pole and attached to it fabric, wants to use advantages of an air flow to provide shelter and keep users dry (source) . As the team is currently rising money on the kickstarter website to fund their further research on invisible umbrella (you can take a look into their demo video below), I thought it might solve the problem of carrying an umbrella under heavy rain and wind. Unfortunately, authors inform on their FAQ site that if the speed of wind is high, the natural wind will oppress the air flow generated by the air umbrella and will decrease the scope of sheltering and affect its performance. Also, the market price of the product is predicted to be about $200 and the battery currently lasts only for about 30 minutes, which significantly narrows group of possible clients.

So sorry Scotland, there is still no umbrella that would help Scots to stay dry during the gandiegow.

Cyprus in October

Can you imagine a better solution for the autumn blues than to find yourself on a Mediterranean beach full of sun? Right when Düsseldorf was being taken by dullness and apathy, I was given an amazing opportunity to escape from all the sadness and last week I visited Cyprus!

Before I landed, I thought that my knowledge about Cyprus was limited only to few, basic facts: such as Nicosia being the capital city, or that Cyprus is in fact the third largest Mediterranean island, or that since mid 70s last century it is divided into two parts, separating Greek Cypriots from Turkish one. I was surprised how in the course of my stay I refreshed my memory in history and mythology, finding how much do I actually know about this beautiful country. But something I really didn’t expect, was to be astonished by Cypriot cuisine. I even decided to devote a separate space below to praise its taste.

One of the most fascinating places I have explored during my stay was a salt lake right behind my hotel, that during the summer almost completely dries out. In winter it’s been said it’s a home for flamingos.

 

IMG_20141006_135407
image-74

Cypriot delicacies

Thanks to my lovely Cypriot girlfriends and the owner of lively restaurant in the city centre of Larnaca I had discovered typical island delicacies and learned a bit of Greek. I was even said to have a Cypriot accent!

As my favourite dishes I would classify κολοκούθκια με τα αυκά, which is a simple dish containing fried zuccini and eggs; and famous halloumi cheese that was served as an appetiser. But what I was completely bought with was the taste of Cypriot deserts!

IMG_3076
image-75

Lay summary of my PhD Project

How algae acclimate to changing light conditions

In the process of photosynthesis, organisms are able to absorb Sun light and in a series of reactions convert it into sugars. Those highly energetic molecules are then stored in different forms in photosynthetic organisms such as plants or green algae, and can be used for various purposes, for instance as a source of energy in the form of biofuels.

The way photosynthetic organisms are tuned to capture solar energy amazes researchers. If we could understand better the processes that are involved in capturing and transferring light energy, we could use this knowledge to improve how fast the green algae will grow and how many energetic molecules they will produce. And ultimately, we could improve industrial exploitation of microalgae.

We know that the availability and quality of light influence the photosynthetic efficiency, therefore my task in the project is to help to understand the level of such influences. I am focusing on how mechanisms developed by algae in order to deal with such changes affect the photosynthetic reaction. When algae are lacking light they try to absorb as much light as possible, on the other hand when light is too strong, they ‘waste’ energy to protect themselves against damage.

Based on our current understanding of the photosynthetic reactions I am developing theoretical models of the process that starts with the absorption of light and ends up with the synthesis of ATP: the trading molecule that is necessary for the production of sugars. I am using experimental data to calibrate my model and validate it and any discrepancies between my predictions and observations are considered as a gap in our theoretical understanding and a space for improvement. I hope to contribute to selecting the optimal light conditions for algae growth and to help to understand to what extent we can stimulate the energy transfer by using different light spectra and intensities.