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1st edition of the HaemMetabolome Newsletter
 



Newsletter 1
February 2017
Welcome to the first edition of the HaemMetabolome newsletter, aimed at keeping you up to date with everything that is happening with the project. Funded by the Research Executive Agency of the European Comission, HaemMetabolome aims to characterise the metabolism of blood cancer cells in the hope of identifying potential therapeutics for patients with haematological malignancies. Composed of 9 partners, it brings together a team of experts from the UK, Spain, Netherlands and Germany in the fields of blood cancer and metabolomics. Included are a number of prestigious universities, as well as 3 successful bio-pharmaceutical companies. As an innovative training network (ITN), the research conducted within HaemMetabolome will be carried out by 10 early stage researchers as they train in basic and translational research to attain their PhDs.
Meet the Fellows.....


Nuria Vilaplana Lopera
 

Nuria is a chemist (University of Barcelona, 2015) and studied a molecular biotechnology master (University of Barcelona, 2016). She loves travelling, cooking and cinema.
 



Grigorios Papatzikas
 
       

Greg is a molecular biologist (Democritus University of Thrace, 2011) and he also has a master in public health and health care management (University of Crete, 2014). He worked as a researcher in a pharmaceutical company and also as a geneticist in an in vitro fertilisation company. Greg is an amazing ski instructor and enjoys all kinds of cultural activities.




Gaelle Vanderstichelen


 
Gaelle studied biology in the University of Mons (2012) and also a biochemistry, molecular and cell biology master (2014) in the same university. She worked in a cell therapy company specialised in bone retrieval. Gaelle is passionate about nature, ethology and gastronomy.
 
Ines Baptista
 
        

Ines graduated with a degree in Biomedical Science at the University of Algarve (2012) and did a masters in Oncobiology at the same university (2015). She loves watching TV series and movies. She is a game geek and loves cultural travelling.


Effrosyni Karakitsou
 
         


Effi did her B.Sc in Applied Mathematics and Physics at the National Technical University of Athens (2012) and performed her Master on Systems Biology at the University of Surrey (2015). She has also worked as a bioinformatician developing computational tools for decision support systems for clinical cytopathology at the University hospital “ATTIKON”. Beside her mathematical brain, she is great at contemporary dance and aerial acrobatics. She also likes playing the classical guitar and doing yoga.
 
Miriam Contreras Mostazo


Miriam is a biologist (University of Salamanca, 2013). She performed her Master degree in Molecular Biology and Genetics at the University of Iceland (2015). During her Master, she was also working for Stofnfiskur Company as a research scientist. She is a very active girl who loves sports, food and people. She is passionate about travelling and music.

Islam Alshamleh


Sam is a stem cell biologist. He did his Bachelors degree in medical laboratory sciences at An-Najah University (Palestine, 2014). Then he worked at the blood bank of An-Najah Hospital. In 2016, he graduated from Newcastle University (UK) with a master by research degree (MRes) in stem cells and regenerative medicine. His research was about using induced pluripotent stem cells technology in disease modelling.
Sam is an excellent swimmer and he has a real passion for travel and hiking.


Johanna Krietz


 
Johanna did her B.Sc. at the University of Applied Sciences (Rheinbach, Germany) and spent her final year at the Robert Gordon University (Aberdeen, Scotland). During her undergraduate studies she gained a pronounced understanding in proteomics, genomics, biotechnological and biomedical research.  In 2014 she graduated with a double degree from both universities.
Johanna continued her studies at the Robert Gordon University with the key focus being the bioremediation of cyanobacterial toxins. She graduated with a M.Phil. in 2016.
Beside her love for travelling and experiencing different cultures, she enjoys spending time outdoors, experimenting with different art activities and testing all kind of sports.


Ayşegül Erdem


Ayşegül studied Biology (Hacettepe University, 2013) and she has a Master’s degree in Molecular Mechanisms of Disease (Radboud University & University of Cambridge, 2015). During her Master’s studies she focused on different biological mechanisms involved in leukaemia development. Her current PhD project explores key metabolic pathways in different Acute Myeloid Leukaemia  subtypes. Next to her work as a researcher she enjoys travelling, summer festivals, 60s music and contemporary art.
 
Alan Cunningham

        

Alan trained as a medical laboratory scientist with a focus in haematology and blood transfusion at the Dublin Institute of Technology. Following a year in a hospital blood transfusion lab, he undertook a M.Sc in Regenerative Medicine at the National University of Ireland, Galway. He then worked as a Marie Curie research associate at the University of Birmingham before commencing his PhD. An avid follower of politics and current affairs, he also enjoys cycling, fishing and is really interested in food.







 
BEAR Cloud: a powerful computational tool for HaemMetabolome         
                                                       
On October 21st 2016, the University of Birmingham and the Centre of Computational Biology (CCB) launched a new private cloud for computationally intensive research.
The Research Computing Team designed and built this cloud as the next generation of resources for Birmingham Environment for Academic Research (BEAR). Dubbed the BEAR Cloud, it is not a server for hosting web pages. It complements the BlueBEAR High Performance Computing Cluster (HPC) with the ability for researchers to request large memory or multi-core count systems. The Cloud is available to researchers at the University of Birmingham and provides access to different computing resources. In it, a researcher can benefit from a single large instance (virtual machine) all the way up to a secure HPC cluster.
CCB is one of the associate partners in the HaemMetabolome project. Foreseeing the diversity and complexity of the data this project is going to generate, we decided to take advantage of the above next-generation computational tool. In order to overcome the computational power and storage demands of data, we created a new Virtual Machine (VM) in BEAR Cloud. This VM is powered by an 18-Core CPU with 120GB of RAM. This gives us enough power to handle and analyse all the data-sets this project will generate. Software tools for data mining, visualisation, and statistical analysis have also been installed in this VM. Finally, we managed to secure for HaemMetabolome a 20TB space to compute, store, and back up all this data. 
The BEAR Cloud is a powerful new technology, which will help to process and analyse the HaemMetabolome data-sets with the most efficient and effective way.
 
For more information visit:

https://intranet.birmingham.ac.uk/it/teams/infrastructure/research/bear/bear-cloud/index.aspx

Grigorios Papatzikas
PhD candidate in HaemMetabolome                   

                 
HaemMetabolome 1st Training School in Barcelona
Alan's thoughts on the meeting
 
The inaugural HaemMetabolome workshop took place in Barcelona in January and was a great success. We kicked off with a really nice talk from Professor Schuringa introducing haematopoietic stem cells, haematological malignancy and the work of our lab. Professor Guenther followed with a presentation on metabololomics and specifically NMR, the possibilities and the limitations. Then we had well-polished introductory talks by the fellows with a hearty 3 course Spanish lunch in between. It was great to hear about the focus of everyones project and how they are progressing. Then we had some hands on training in metabolomic flux simulations for the fellows, using software developed by the computational biology teams  at the University of Barcelona. It was cool being able to simulate the metabolic effects of conditions such as gene knockouts or hypoxia and would be nice to be able to apply these simulations to our own data. We ended the day at a nearby restaurant with some nice tapas.
 
The next day we had more two more talks on haematological malignancy and NMR by Professors Hubert Serve and Harold Schwalbe, respectively. Dr. Johannas Coy discussed his finding of the TKTL1 gene and the important role it plays in cancer, as well as his other business focuses. The fellows then resumed our metabolic flux simulation training while the PIs held management discussions

With one day to spare before flying back to the Netherlands, I managed to squeeze in a few attractions around the city, spending almost three hours visiting Park Güell, before going to Sagrada Familia and walking around the city.  A couple of beers and some more tapas ended the trip nicely.
 
It was great meeting all the fellows and partners who attended. The Cascante lab did a great job organising the event. Thank you for the hospitality. 

   
                           Park Güell                                               Sagrada Familia                           
What's going on with the Fellows?..........
Ayşegeül's Secondments

In 2016, we already saw a commencement of research secondments.  Ayşegül has been in Barcelona now twice to perform some significant experiments for her project. As a principle of Marie Curie academic partnerships, she mentioned the advantage of double supervision for various aspects of her project lines. This has also afforded her the chance to enjoy the nice cultural atmosphere of Barcelona both in winter and summer during her short visits.


                 

                 
Sam's visit to the University of Birmingham
 
Sam recently did a research secondment at the University of Birmingham in Prof. Guenther's group. He received intensive training in NMR technology and its applications in metabolomics (metabolic fluxes). What he found most interesting in the Birmingham group was the quality of their research and the close supervision and assistance afforded, besides the very social and wonderful group members. 
Sam believes that having the chance to work with other groups, in renowned institutions, during his PhD is one of the great things about being a Marie Curie fellow. 

 
Getting to grips with new languages
 
Already a year into her project, Ayşegül has progressed to the second stage of the Dutch language course. From Ayşegül - "Having some background in German grammar made it easier for me to be able to start and learn Dutch. Although I do still struggle with the Dutch pronunciation at the second stage, I really enjoy using common Dutch idioms and expressions already in my daily life!"

Alan is in the last month of a beginners Dutch course and is having a lot of fun. He now knows the basic greetings & introductions, can count and most importantly can order a beer! He plans on continuing to the next level as soon as this one is completed.

Because of his interest in integrating in the German society, Sam started learning German in the first month he arrived in Germany and now he is in A2 level. He believes it is the best way to get to know the culture and open prospects for his future career in Germany.

Efi started using Duolingo last week and signed up for another online Spanish course. 

It will be great to see how this progresses over the next few years. 
Effrosyni (Efi) is currently in Birmingham
 
Right after the first HaemMetabolome meeting in Barcelona I came to the lab of Jean-Baptiste Cazier at the University of Birmingham to start my secondment. The main purpose of my stay here will be to get support and training on the computational analysis of expression data. And I am very happy to say that this is exactly what I am receiving. The researchers and post-docs here have strong programming skills and are really willing to share their knowledge. The campus is really beautiful, especially the main building of the university (Aston Webb building) built in 1900 which is truly amazing. I am enjoying my time in Birmingham and the opportunity to work in such a welcoming and supporting environment.
Paper share: Editors literature picks
Alan
Shafat MS, Oellerich T, Mohr S, et al. Leukemic blasts program bone marrow adipocytes to generate a pro-tumoral microenvironment. Blood. 2017
Huang, A., Ju, H.-Q., Liu, K., Zhan, G., Liu, D., Wen, S., Garcia-Manero, G., Huang, P., Hu, Y., 2016. Metabolic alterations and drug sensitivity of tyrosine kinase inhibitor resistant leukemia cells with a FLT3/ITD mutation. Cancer Lett. 377, 149–157. doi:10.1016/j.canlet.2016.04.040
Oze, Hiroki, et al. Impact of medium volume and oxygen concentration in the incubator on pericellular oxygen concentration and differentiation of murine chondrogenic cell culture. In Vitro Cellular & Developmental Biology-Animal, 2012, 48.2: 123-130. doi:10.1007/s11626-011-9479-3
Zhanf, Kuan, et al. Dissolved oxygen concentration in the medium during cell culture: Defects and improvements. Cell biology international. 2016, 40.3: 354-360. doi:10.1002/cbin.10570
Project Management
  • We would like to thank all of the Cascante lab for their work in hosting the 1st HaemMetabolome workshop and for their superb hospitality.
  • Please let Karen Atkins know about all articles and posters so they can be showcased on the project website. Remember that all HaemMetabolome related publications need to acknowledge funding.
HaemMetabolome Outreach and Communication
Website


The HaemMetabolome site is currently being updated. If any ESRs or Partners attend any interesting events, present posters or have any exciting project news, please get in touch with Karen Atkins. Any suggestions of new sections for the website would also be very welcome.
Social Media


Our social networking is in its early stages but updates will now be made regularly through Facebook and Twitter, so please send your news and achievements in for sharing. Twitter and Facebook provide a great opportunity to showcase researcher achievements and connect with others in the HaemMetabolome network. Please follow/like & share the project through the links below. 
Outreach and dissemination is an important aspect of Marie Curie ITNs. Fellows are encouraged to get involved in open science days, give public talks, give science demonstrations to kids, such as teaching DNA extractions from fruit etc.

Another outreach example is PubhD, where PhD students have 10 minutes to explain their PhD without any visual aids and to an audience with often little knowledge of your field. As the name suggests, a perk is that they are hosted in a pub and the speaker is afforded a free drink. One occurs monthly at the Victoria pub in Birmingham (http://pubhdbirmingham.strikingly.com/) and assistance on setting up one in your own city is available through the website - https://pubhd.wordpress.com/ 
Twitter
Facebook
Website
The next HaemMetabolome newsletter will be published in August 2017. If you have any news that you would like to be included, please get in touch with Karen Atkins (K.L.Atkins@bham.ac.uk). 
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