Category Archives: MSc. Plant Biology

I am also learning to code on my own

Last week  I read an interesting article on WIRED about the current need of  biologists who are able to code. The article stressed how more biologists need to learn coding in order to analyze huge data sets, and how most biology curricula in universities lack such topics.

After reading it I could not relate more to it. This is because right now I am working on my master’s thesis in which I need to use R to analyze my data. For those who are not familiar with it, R is a statistics software and programming language widely used in in data analysis. The only “problem”, let’s say,  is that to work on it training is needed because is based on a specific coding language.

This is how my “work space” on R looks like.

However, during my education in Colombia and Sweden I have not had any training whatsoever in coding. From my own perspective I thought coding was a skill only necessary for hard-core software engineers, computer scientists or bioinformaticians, so I never really bothered not taking a course until now, when I face the need to learn how to code  to analyze the data I have generated during my degree project.

As said in the article on WIRED, I am learning these skills on my own -as many other biologists are doing too. Luckily, there are some courses online to learn the basics and manuals to learn  more advanced functions. I followed one online course offered by the University College of London for free .  Additionally, at the Department of Forest Mycology and Plant Pathology (where I’m doing my thesis) we are learning with a group of researchers, master students and PhD students how to use PoppR (Population genetics in R) a package of R to analyze molecular data for population ecology. We are together following the instructions and manuals with our own data sets , which has been a very nice learning experience because together we have been able to compare, discuss, read additional literature and learn topics beyond the mere coding aspect of R.

Today I honestly regret not paying more attention to coding- that I have realized is even fun!  in the past . Nonetheless it is exciting learn such a powerful skill, that will be for sure useful to answer relevant questions in biology.

Best!

Hernán.

 

Where north meets south

I feel very fortunate of having taken part on the European Plant Breeding College, because besides of learning many new things and meeting many interesting people I have had the chance to travel along and getting to know about the culture of the hosting city and country. This time I stayed in Ghent and traveled all round to visit other places no more that 1 hour by train. Those are the perks of being a tiny country, Belgium 😉

Belgium seems like the place where northern Europe meets southern Europe. Where snow meets rain, where Germanic meets the Latin, where beer meets wine, where tidiness meets street-art, responsibility meets spontaneity, and affordable meets expensive. No wonder why Brussels is where the European Parliament is located. I was honestly surprised by the strong cultural and gastronomic identity this place has. Besides this the country has beautiful and photogenic architecture and lively cities with cozy bars and independent stores.

Pretty houses in Ghent.

Ghent is of course my favorite. I loved to stay during two weeks Hostel Uplink, where the organizers of the course decided to locate us. The hostel has nice atmosphere and is located in the heart of the city. However, Antwerp also stole my heart. It is beautiful and authentic. I also visited Bruges, which is so photogenic and charming, Brussels with a good combination between chaos and organization and Leuven is fun town which holds one of the oldest universities in the world.

Antwerp’s Central Station.

Breeding companies in Belgium and The Netherlands

As part of the ISP in Ghent I had the chance to visit different breeding companies in Belgium and The Netherlands. It was a great opportunity to realize about the breeding sector, which is by far one of the biggest in agriculture. Before coming to Ghent, I did not know that these region was well known for hosting some of the biggest breeding companies and seed producers in Europe and the world. Most of these companies started as family companies that have been breeding new plants for generations and managed through generations by the family line.

However, competition is tough and not all companies have survived to Bayer and Monsanto – companies that are by far the biggest in the market and will be soon merged. To coup with this, the companies we visited have had to either focus on very specific niche such as ornamental plants (mostly flowers) or merge with other small companies to be relevant in such a competed field.

We visited Gediflora, a Belgian company that breeds chrysanthemum and is even commercializing chrysanthemum scented Belgian beer; Exotic Plants, a family company which has become the world leader for breeding Bromeliaceas; Bejo a Dutch company that breeds different kinds of vegetables and are world leaders in onion breeding; Royal van Zanten that have specialized in Alstromelia and Redunculus and who happen to have a large extension of their production in Bogotá (!) and Anthura, who are leaders in Anthurium and Phalaenopsis orchids.

 

Hybrid Breeding

On my last post I wrote about the Intensive Study Program In Ghent University. I came all the way from Sweden to learn more about hybrid breeding. But, why is hybrid breeding important?

The whole concept is based on what is known as hybrid vigor. It happens when two parents cross and their progeny is more vigorous than themselves.  For breeding new varieties is extremely helpful due to a few reasons: it is easy to register a new variety created this way, characteristics are easy to stack, it is reproducible, but most importantly it obligates the farmers to buy new seeds every time they want to plant them. That is basically why seed companies have succeeded on making money out of plant breeding.

To make and hybrid it is necessary to create Inbred lines, which are plants mostly homozygous. After two parents are crossed (F0) the resulting seeds (F1)will be completely homogeneous, heterozygote  and hopefully vigorous. These seeds are those that the breeder will sell to the farmer. Why does the farmer have to buy seeds every year? the seeds of the F1 generation (F2 seeds) will be completely different to each other!

 

Intensive Study Program at Ghent University

As part of the European Plant Breeding College (read EPBC: European Plant Breeding College), I got the opportunity to join another intensive course similar to the one at LaSalle Beauvis in France ( read ISP in France: an overview). This course is about Hybrid Breeding and takes place in Ghent University in Belgium, which by the way is such a beautiful city!

Afternoon in Ghent. The hostel is on he picture hast a superb location!

I arrived earlier this week and have had different lectures covering topics such as chromosome engineering, polyploidy, reverse breeding and hybridization. To be honest I did not know that there were such advanced techniques to create new plant varieties. Like, I thought most of the technologies in plant breeding were just marker assisted selection or transformation techniques, but is interesting to know how many different biological alternatives there are to create new varieties.

As in France, students from different universities are attending the course. We are all staying at Upplink Hostel, which has a very good location a very cozy atmosphere. This makes the stay here very nice, because there are many different landmarks at walking distance and interesting people coming every day to the hostel. I have liked it very much so far.

Playing board games in the Hostel after lectures

The course lasts for two weeks and there are going to be many exiting thing coming along the next few days! I will definitely  write about it here 🙂

Cheers,

Hernán.

The peanut project

Yesterday was the defence of the pilot cases from the European Plant Breeding College EPBC (Read EPBC: European Plant Breeding College). The aim of the pilot case was to design an hypothetical breeding program  together with students with different backgrounds from different universities. It started during the Intensive Study Program in France in october (Read The Intensive Study Program at LaSalle-Beauvais and ISP in France: an overview), where 5 different groups were created and topics were chosen. My group was composed by Sibel from Ege University, Bilal from LaSalle-Beaviais, Jorge form Polytechinc University of Valencia, Nicolas from La-Salle Beavis and myself. We decided to create a pilot breeding project for high value peanuts for the EU seed market.

The motivation for the topic was clear:There is a high demand for peanuts from European food companies, an increasing concern about allergies, and opportunities for farmers who are encouraged to grow leguminous plants within EU. Plus, most of peanuts for human consumption in Europe are imported. We thought that there was a need and an opportunity for a high quality variety of peanut adapted to Mediterranean Europe that could meet the requirements of the stakeholders in the market: farmers, food companies and consumers.

The process was not easy, because it was challenging to meet and make decisions after our stay in France. We established communication tools and I assumed the role of Project Manager (hehe), so my role was to organize and try to create a good group dynamic to meet the goals of the project. I think it was amazing how in my group we could complement the skills of each other and in the end we found a synergy between each member strengths, which I believe reflected the focus of the master program each student is following at the moment.

The defence went very good and I am sure that the learning outcome of the project was met. Great job peanut-team!

The peanut team in France

Best,

Hernán.

 

M.Sc. degree project

Time has gone by incredibly fast and it is hard to believe that I already started  with my  degree project. It is considered the last part of the master and I see it indeed as a culmination of this process, because I can acknowledge and apply what I have learnt so far. It is a compulsory course  in the M.Sc. in Plant Biology and it is up to each student to decide how much time and credits it will take.Therefore, I decided to use 45 credits on it to spend more time doing  research than taking courses, because I think it will be more useful for me and my future career.

Before summer I did one research training (read more here) in which I explored possibilities at the Department of Forest Mycology and Plant Pathology. Since I liked the experience and the research I performed there I decided to conitnue where I left for my master’s thesis project. So far it has been going smoothly and hopefully I will soon write more about it.

Cheers,

Hernán.

 

Plant Pathology 15c

Last week I completed another course: Plant Pathology, one of the optional courses that can be taken within the Plant Biology MSc. This course is taught by the department of Forest Mycology and Plant Pathology at SLU, has 15 credits and demands 100% time dedication for 10 weeks.

The course aimed to give a general view on different plant pathogens relevant for agriculture including its taxonomy,  biology and ecology. Furthermore, it dealt with topics such as epidemiology, integrated pest management (IPM) and biological control.

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A rust fungus growing on Rowan leaves. I took the picture.

The topics were assessed with lectures, and theoretical exercises in which scientific articles  were read and discussed.  I found particularly interesting a series of articles published by Molecular Plant Pathology in which plant pathogens are ranked according to their economical or scientific importance (you might like to read The Top 10 Pathogens in Plants).

Besides this, we went on different field excursions to learn how diseases look in planta and collected samples to perform diagnosis in the lab. This last  aspect I found very interesting and important for a future career, because as a biologist myself my knowledge of plant diseases important for agricultural crops is not very broad. Hence, I enjoyed very much going out in the fields, see symptoms and signs to later look into the microscope and give a possible diagnosis.

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Cleistothecia from a fungus under the microscope. I took the picture.

Additionally, the course had laboratory work sessions, a case study and a poster presentation session. Overall, I found the course interesting and important to complement my education. Actually, my interest on this topic is so strong that I am considering to pursue a career as a plant pathologist. But one step at a time.

Do not hesitate to ask or comment below,

Best,

Hernán.