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!

Project description

The session with children will be initiated with a short presentation introducing children to the world of plant biology, highlighting the importance of plants for our existence. We will broaden the awareness of ‘dependencies’ through the examples of the food chain and hunger, and their impact on our existence. Next, through discussion and experiments, we will learn together how plants produce oxygen, how they grow, and what we can do to ensure good growing conditions for our plants. We will demonstrate how plants direct themselves to a light source, which light colours and intensities they require, and how the needs of plants are the same as ours: eat, drink, breath and grow. These needs will be presented in the way to appreciate how many physical laws are obeyed by plants in order to grow towards the sun and protect themselves against damaging conditions, such as extensive light.

We designed a range of public materials that educate and promote these topics. These include our ‘open access’ presentation (available for after the workshops) and a ‘keep-sake’ flyer (available for download) detailing experiments we performed together.

Where can you hear us?

On Monday, 16th of March we will be conducting workshops as part of the Fraserburgh Science Fair [pdf, width=75%, height = 75%]http://biomatematyka.pl/wp-content/uploads/2015/03/NSEW_2015_Fraserburgh.pdf[/pdf]

On Tuesday and Wednesday, 17-18th of March we will be hosted by Aberdeen Biodiversity Centre.

On Saturday, 21st of March we will support Discovery Day in the Satrosphere Science Centre in Aberdeen.

A personal manual to your own plant lab

Plants in our life

Did you know that plants are our main source of life? They filter our air by consuming toxic CO2. Together with the water they drink from the ground, plants can convert energy captured from sunlight into sugars, for us to eat, and oxygen, for us to breath.

This process is known as photosynthesis:

photosynthesis
image-243

Besides serving us as the main source of energy in the form of fruits or vegetables, plant products are essential resource for human well-being. They include wood, oils, pigments, fibers. Even our technology is driven by plants as coal and petroleum are fossil substances of plant origin.

Sensing the surrounding

Plants live in an ever changing and, at times, a challenging environment, which can dramatically interfere with the process of photosynthesis. Within one day sunny dry conditions can become dark and wet. It is fascinating how plants are able to sense and adapt to such changes. When water becomes available, plants quickly take it up, and when sunlight becomes too intense, plants protect themselves. You have probably also observed that plants grow towards light. However, did you ever wonder what mechanisms govern their behaviour? Have you ever wanted to see plants produce oxygen? Here we suggest a few experiments you can do at home to enable you to witness and understand the science of how plants sense their environment.

Experiment Nr 1: Osmosis

Download PDF.

Like us, plants need water to survive. They use osmosis to absorb it together with nutrients from the soil. By definition, osmosis is the movement of water molecules from an area of high water concentration to an area of low water concentration through a partially permeable membrane.

The cell membrane of the root hair cell acts as partially permeable membrane and because the cell sap inside the vacuole has low water concentration water passes from the soil into the root hair. The concentration of the sap in the vacuole is now weaker as there is a high concentration of water. Water will now pass from this area to the next cell with lower concentration and will continue to move along the cells of the root up the xylem to the leaf.

By colouring the water in which the plant sits in, we can observe how petal turns colour and that water in fact travels up a plant’s xylem.

Experiment Nr 2: Fluorescence

Download PDF.

Since plants need light to carry out photosynthesis, if we provide the plant with light, it should be able to make more oxygen and sugar, right? Not at all!

Actually, plants cannot cope with too much light! To deal with the excess light energy, they release the surplus energy by re-emitting tiny red signal called fluorescence, which is normally invisible to our eyes.

In an experiment, we show how plants protect themselves by re-emitting a part of the UV-light shone on them in the darkness, where photosynthesis process was blocked.

Experiment Nr 3: Gravitropism

Download PDF.

It is a general feature of all higher plants that roots grow in the direction of gravitational pull (i.e., downward) and stems grow in the opposite direction. When the seed is in the soil, it is dark and not easy to find where the surface is. Plants can sense gravity to help the germinated seeds change shoot growth to the ‘upwards’ direction and root growth ‘downwards’. Growth movement in response to gravity is called gravitropism.

To investigate gravitropism in shoots and plant movement towards the light you can built the onion tower that at the end of the experiment may serve as a supply of onion greens for whole family.

Experiment Nr 4: Oxygen production

Download PDF.

Would you like to witness how plant absorbs CO2 and produces oxygen, using quite similar set up as famous scientists Joseph Priestley?

Alone in a sealed jar, with no source of oxygen a burned candle would produce hot carbon dioxide that would accumulate at the top of the jar, pushing down other gases like oxygen and eventually stifles the flame.

Remembering that plants breath the CO2 and produce oxygen in turn, place a plant and candle under a large jar and after a month light up the candle inside to observe that level of oxygen produced inside is sufficient to allow the candle to continue to burn.

 

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!

Are plants like scientists?

In a collaboration with Dr Ahmad Mannan from the University of Aberdeen, with the support from the European project AccliPhot, CEPLAS Cluster of Excellence on Plant Sciences and Aberdeen Biodiversity Centre, we have prepared a project inviting children to the exciting world of plant biology. We blur the lines between different scientific fields so as to raise awareness of the ubiquity of the laws of physics. Through presentations and live experiments, we will demonstrate how plants adapt to various physical perturbations for survival. Moreover, to encourage continued interest outside the classroom, we have designed a set of simple plant experiments that children will be able to repeat on their own.

The objective

of our project is to encourage cross disciplinary thinking, share knowledge, and inaugurate an interest in biophysics. As interdisciplinary researchers we believe that there is no simple division across the fields of science. As such, we wish to disseminate this thought to the next generation of potential scientists by inviting them to view different aspects of life and science in a combined way. In particular, blurring the lines between biology and physics will show how these disciplines intertwine. We believe we can achieve this goal by introducing children to the basic laws of nature, using plants as our examples.

We would like to thank

Yashka Smith, Marie Fish, Heather Doran, Leann Tait, Mark Paterson, Peter Nurick, Adam Price, Stephanie Schelder and Andreas Burkart for their support, valuable comments and ideas altogether allowing us to present the project to more than 200 children.

Contact

If you would like to leave us some comment regarding the project or give us a feedback after one of the sessions please contact don’t hesitate to contact one of us: Anna or Ahmad.

Read more about the workshop

Download educational materials

Follow step by step experiments we performed together during the workshop

 

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.