Are marine algal bloom terminated by viruses?

A new study by Lehan et al. brings a new insight in the algal bloom termination process. Combining satellite images and Lagrangian and Eulerean approach with in situ measurements, this research group demonstrated that bloom termination for the microalga Emiliania huxleyi was not driven by nutrient limitation but by viral infection.

This study shows a novel approach in studying algal bloom, which might lead to new interesting developments in understanding the role of marine viruses in the ocean.

Here you will find the link to the paper:

http://www.sciencedirect.com/science/article/pii/S0960982214009099

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Ocean models: Will we ever been able to add viruses to them? A summer school to learn how to use ocean models.

Various people asked me what was my interest in an oceanography modeling course if my PhD is on molecular biology. Well, the answer is very simple, my PhD is NOT only molecular biology but is an interdisciplinary project. I am working on marine viruses but since I know that they play key roles in ecosystems, I see the necessity to include these “entities” or particles (or… really we do need to decide what “they” are) into models. I know we are still far away from the incorporation of viruses into models, both to investigate biogeochemical cycles or algal bloom termination, but I hope that one day I will be able to use the knowledge gained in this course to collaborate with great researchers to include viruses in ocean models.

But lets talk about the course… I have to say I am glad I took it, even if it meant putting my work on standby for two weeks. The course was very well organized, this was in fact the second edition and I am sure that there will be a third one soon. Hopefully the next time this course will be run, it will include more international students – even from Europe, I know that flying to South Africa is very expensive but being able to see what this great team is achieving as well as learning oceanography close to some very important oceanography systems. It is priceless. The course was organized by the marine research institute (Ma-Re, UCT) in collaboration with the International Centre for Education, the Marine and Atmospheric Sciences over Africa (ICEMASA) and the Institute for Research and Development (IRD, France) with the title “Modelling the Marine Ecosystem from the Ocean to the Fish” (here’s the link for more information: http://ma-re.uct.ac.za/modelling-the-marine-ecosystem-from-the-ocean-to-the-fish/). Amazing lectures took us into the world of ocean modeling, trying to guide us first through the physical component (I am seriously thanking my background for being able to follow easily this part) and then moving slowly into more practical, at least from my point of view, type of modeling including: coupled physical –biogeochemical modelling, trophic interactions modeling and fish spatial population dynamics (to mention only a few examples). One of the key points raised was the importance, when running specific models, to normalize our data, specifically if we plan to run comparisons and the important of proper parameterization. At the end of the course I am sure of one thing, we were given a great tool, even if as an overview. We were guided through a very intricate and difficult world, but all the lecturers were impressively good at guiding us and giving us enough tools to help us choose the right model based on the type of research and the main goal of a project. What I will never forget now is the definition of a model, and it kind of makes sense finally, so I believe I’ll have to share it now: “A model can be easily defined as a set of mathematical formulations that we can use to solve physical processes in order to describe the state the ocean”.

In easy words a bunch of coupled mathematical/physical equations that will help us untangle various process in the ocean, and yes, maybe one day help us add the viruses as a variable (we live in a virus world!!!).

During the course we were not only subjected to hours and hours of lectures but the best part was being able to try different tools. I am not going to talk about them, I don’t have the skills and it will go beyond the role of this blog but if you are curious and want to know more about them here are the names and the links:

  1. ROMS: Regional Ocean Modeling System. This is an open source program but, at the moment, it requires MATLAB which for me is a shame, since I believe in open source programs and I truly hope that it will be adapt for Python.
  1. OSMOSE: http://www.meece.eu/library/OSMOSE/osmose.html . Object oriented simulator of marine ecosystem; it is limited to biogeochemical models.
  1. ICHTHYOP: “free Java tool designed to study the effects of physical and biological factors on ichthyoplankton dynamics” http://www.ichthyop.org
  1. APECOSM: http://meece.eu/library/APECOSM/apecosm.html . Apex predator ecosystem model, a mechanistic model of biodiversity.
  1. ECOPATH-ECOSIM: http://www.ecopath.org a whole ecosystem model that structures the ecosystem into components, with ECOSIM as a dynamic version of ECOPATH.

And if you are interested in the lecturers here are some links:

  1. Yunne Shin (http://www.unesco.org/new/en/natural-sciences/ioc-oceans/priority-areas/gender-equality/women-marine-scientists-share-their-stories/yunne-jai-shin-shares-her-story/ ) lecturer and coordinator of the course.
  2. Julie Deshayes (http://www.whoi.edu/hpb/Site.do?id=6472)
  3. Steven Herbette (http://www.researchgate.net/profile/Steven_Herbette)
  4. Eric Machu (http://annuaire.ifremer.fr/cv/18438/en/)
  5. Oliver Maury (http://www.researchgate.net/profile/Olivier_Maury2)
  6. Stephane Pous (http://www.researchgate.net/profile/Stephane_Pous)

And finally a photo of the student and some lecturers:

IMG_0377

Bioinformatics unseminar in Cape Town

I have to admit that when I moved to Cape Town I felt disoriented, because being a bioinformatician in a new country I had no idea how to get in touch with bioinformatician here. So I started using twitter and I also decided to write a blog. I realised that creating connections it’s all about not feeling alone and being able to communicate.

At the beginning, no matter how hard I’ve tried, I felt that I was the only one in this area working on bioinformatics, even though I knew that this wasn’t true; then I realized that I needed some ideas to meet other bioinformaticians.

Fortunately, one day, one of my colleagues at the university told me about a CUB meeting: an unseminar where people that do bioinformatics in the Cape Town area meet (http://thecubhub.wordpress.com). I was very excited and scared at the same time at the idea to meet this group and I almost skip the meeting, but eventually I took courage and I went. It was their second meeting and “whoa!” – I was so surprise to meet so many people that work in different bioinformatics areas! Talking with some of them I realised they had my same feelings and it was the start for a great opportunity of making new friends. This meeting was in Stellenbosh and it was amazingly organised: there were interesting talks sessions and wine was served. Once there I felt happy to have gone beyond my fears.

The meeting introduction was brief and very useful: we were supposed to explain what we do like we will to a five year old… and it wasn’t easy! This was of great help to me since I’ve always though I was explaining in easy words what I do and … ops… I wasn’t.

On the 1st of October I took part at the 4th CUB meeting (the 2nd for me, because I was in Zurich for a conference during the 3rd meeting) and again I have to say it was impressive. This time they applied the “speed dating” concept through skype: we had to talk for five minutes with a stranger and tell him about our research. It was absolutely terrifying at first but it turned out to be an awesome experience.

I can’t wait for the next meeting to see what the organisers will come out with. I feel that I am learning a lot from these meetings: first of all I am getting in touch with the bioinformatics community; secondly I have the opportunity to explain what I do in different ways. Explaining science and research to a heterogeneous public, from kids to scientists or just to a curious person it has to be done in an appropriate way. It is fundamental that scientists learn how to explain their work and discoveries to the global public in a complete but simple way, avoiding the not-competent people to distort information.

Now you will be asking why I am sharing this or why you should read my blog.

Well, after that first meeting I felt so much better, there was a bioinformatics community around me and I was able to share a conversation about my project and get advice from different angles of the field. I am also learning that twitter and blogs are a great way to get in touch with people within specific communities.

If you are in a new country and you are not sure if there is a bioinformatics community next to you or, even if you just want to understand more, check via twitter or contact the HUB (http://www.hub-hub.de/wiki/index.php?title=HUB_-_Heidelberg_Unseminars_in_Bioinformatics) community and start a new adventure in your area. The community will grow and improve the experience of other people!

Are we getting close to study virus- host interactions without the need to culture them?

A new interesting paper from Matt Sullivan group: http://elifesciences.org/content/early/2014/08/29/eLife.03125

Despite the development of new technologies, cultivation bottleneck remain a critical issue in the study of virus-host interactions, especially when dealing with environmental samples. Focusing on uncultivable bacteria from a marine Oxygen Minimum Zone, here Roux et al combine metagenomic with single-cell genomic sequencing to explore virus-host interactions, therefore bypassing the problem of not being able to culture certain hosts. Application of various bioinformatics tools reveals the presence of a novel Microviridae genus, in addition to an unexpected co-infection of ssDNA Microviridae with a dsDNA phage. A three-year time scale sample comparison highlights evolution in the viral population. Finally, focusing on the DsrC gene (a component of the sulphur metabolism) reveals the biological role of the viral gene in the bacteria community.

Learn to code in Python at the first African Software Carpentry Bootcamp at eResearch Africa 2014

A great opportunity for everyone in South Africa!
Following online courses it’s great and gave the opportunity to students, researchers and everyone interested, all around the world to be updated and learn. Nevertheless it is also important to have a “human contact” with the possibility to ask questions directly to a teacher in a smaller class.
So if you are interested have a look at it!

Cape Unseminars in Bioinformatics

http://www.eresearch.uct.ac.za/news/learn-code-python-first-african-software-carpentry-bootcamp-eresearch-africa-2014

What is a Software Carpentry boot camp?

We help researchers to become more productive by teaching software development skills that enable more to be done, in less time, and with less pain.

What will be taught?

We will cover skills including version control, task automation, good programming practice (Python) and automated testing. These skills enable researchers to optimise their time and provide them with a secure basis to optimise and parallelise their code.  The course will be tailored to suit the level of expertise of registered participants.

Who will be the Instructors:

·      Jonah Duckles (University of Oklahoma, USA)

·      James Hetherington (University College London, UK)

·      JC Leyder (ESA’s European Space Astronomy Centre, Spain)

·      David Merand (University of the Witwatersrand, South Africa)

Who should attend: The course is aimed at postgraduate students, post-docs and other researchers affiliated with South African or African…

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To start … A little bit about me

I was born in Sardinia, an island in the middle of the Mediterranean Sea. Growing up on an island I was always interested in the sea. My curiosity and love for the marine environment led to my PhD project in South Africa on the study of marine viral diversity in the Southern Hemisphere. It’s a multi-disciplinary project involving marine biology, molecular biology and bioinformatics. To get there I started with a BSc in Applied Bio-Ecology (curriculum Marine Biology) where I did my thesis research on corals. Specifically the purpose was to understand how different species interact (such as sponges, other corals, fish…) and how the bionomical association would impact Corallium rubrum growth as well as the fishery interactions. I analysed ROV (Remotely operated underwater vehicle) images and went on fishing boats to collect samples, this was hard but also very rewarding. I was also able to see for myself the issues of fisheries and how the community interact with researchers. I learnt that we have to learn to talk to each other in comprehensive ways, without diminishing anyone work and trying to be open minded in other people views because is only through understanding the needs of the community that we can all understand the ecological problems. This experience inspired me so much that I decided to work on Cephalopod (octopus & squid) reproduction for my MSc in Marine Biology. The project consisted of analysing the correlation between maturity stages and growth, reproduction and the impact of fisheries on their life cycle. I participated in weekly boat sampling trips tagging cephalopods to enable fishermen to identify the best time of year to sustainably fish. Both species that I worked with were very susceptible to environmental changes; small changes in their geographical range will change the stock size and their life cycles. After graduation I decided that I wasn’t ready for a PhD so I started a post-graduate internship at the University of Cagliari in a public health laboratory (Molecular and clinical department) where we were researching microorganisms from water, air and food matrixes. During all these projects I developed an understanding of the impact of environmental change on the marine ecosystem. For example changes in water temperature, increases in environmental pollutants (e.g. TBT and other anti-fouling substances), how these variables with unsustainable fisheries can impact the geographic range of biota. After the end of that experience, I started a second internship at the clinical laboratory in Brotzu hospital (Cagliari, Italy); my goal was to learn new techniques to improve my laboratory skills (in the meantime I had pass the Italian examination to work as professional biologist, and I am now a qualified biologist). The internship was interrupted after only a month, because I got selected for a one-year masters on bioinformatics (2nd level vocational master) with the University of Cagliari & the CRS4. During this experience I was able to spend three months in the UK at the Marine Biological Association (Dr Declan Schroeder’s cellular and molecular group) to develop my final project on marine viruses, specifically on transcriptomic data from an algae virus. This last experience grew my passion for bioinformatics and allowed me to learn work with Next Generation Sequencing data, working with small genomes (especially from viruses). I was always interested in microorganisms from water and I have tried to incorporate them into my past research, I was especially curious on their effect in the community considering both in the human-health and economical perspective. Unfortunately I was unable to follow this path until I started the PhD with the University of Cape Town on viral diversity on surface seawater. Furthering my knowledge of viruses and how to analyse them, learning new technics, of both molecular biology and bioinformatics, has became a key point for my PhD.

This was the path that brought me from an Italian island to South Africa in order to achieve my goal of working on viruses in the marine environment.