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Highlights from the iMOP session at HUPO 2014

Madrid 2014, Monday, 6th of October, 8.00-9.30:

We had a well-attended meeting (approx 25-30 persons). Unfortunately the invited keynote speaker (Eric Boncam Rudloff), missed his plane, and did not show up. He was scheduled to present his EU project “ AllBIO”. The title of his talk was planned as “AllBIO: Beyond human-centric Bioinformatics Resources”
Despite this disappointment, we had a fruitful session, with presentations from 2 young speakers selected from submitted abstracts, followed by a lively open discussion on community actions within iMOP. New members of the community were encouraged to contact iMOP members by email, so they can be added to our email-group.

Speaker 1: Fabrize Bertile gave a presentation on Brown adipose tissue (BAT) proteomes of voles (Microtus arvalis). The physiological role of BAT on metabolic regulation is still unclear, and M. arvalis was presented as a model system to study obesity and metabolic adaptations to high and low fat diets in animals genetically selected for low and high BAT activity. Changes observed were mainly related to mitochondrial respiration and oxidative stress. The speaker highlighted the shortcomings caused by lack of a fully covered reference genome DB for this species, and also presented how this was overcome by de novo peptide sequence analysis.

Speaker 2: Dorothea Ruthishauer presented a talk on “Chemosensory and odorant-binding proteins from caterpillar saliva, as affected by host plant and immune challenge”. A label-free quantitative proteome study of novel and highly abundant putative chemosensory proteins from the mandibulary glands of the caterpillar Vanessa cardui resulted in identification of more than 1000 predicted proteins in hemolymph and salivary glands, and demonstrated that expression levels of chemosensory and odorant-binding proteins depend both on host plants as well as pathogen challenge to the caterpillar. The authors conclude that both host- and pathogen perception may be mediated by chemosensory proteins produced in the mandibular glands. This was supported by the observations that isoform specific expression levels depend on exposure to bacteria in the food. It was concluded that salivary proteomes are modulated in response to bacteria and their cell wall components, highlighting the relevance for cross species studies for investigating the saliva mediated mechanisms of pathogen recognition. This is equally important in caterpillars, humans and other mammals.

Following topics were discussed at the workshop:

1. The need for improving high quality reference databases: There are still many animal, plants, and bacteria species where access to either the entire genome sequence, or even a well-annotated version suited as reference proteome/genome DB for searching MS data, is still a major bottleneck for proteome research. As highlighted by both speakers of this session, there is an immediate need for providing pipelines to collect high quality reference DBs. We will ask interested partners to contribute to provide these resources. A first step would be to collect suggestions as to which species this list should include.

2. A status paper should be collected, to present the current aims of iMOP. This paper should present ongoing work and reflect the contents of the recent workshops, and summarize the discussions we have had on how to progress with non-human proteomes.

3. The iMOP community needs chairpersons from also plant and bacteria research. This still needs to be implemented.

Action plan:
1. Collecting reference databases: A workgroup will be assembled. This workgroup discuss how to share the workload for providing high quality reference databases for species where genome info is insufficient for searching shotgun MS data. Henning Hermjakob and Eric Deutsch will be consulted for how to approach this task. Emøke will contact Marius Codrea (Bioinformatics at Tubingen University) to ask for advice and his commitment to this task.

2. A status paper on iMOP progress will be submitted to JOP or Proteomics, so that its in print well in time to attract interested participants for the Vancouver 2015 meeting. A.Tholey and E. Bendixen will be in charge of the writing, and will ask for specific contribution from selected iMOP members.

3. Finding two additional chair persons (Plant and Bacteria focus) for the core-group: Josh Heazlewood and Jesus Jorrin have taken on to bring this to action in the plant community. Susana Cristobal and Paola Roncada will take on to chairpersons from the bacteria community.

4. Preparing for Vancouver 2015: Collect ideas for topics and speakers for an iMOP workgroup session at HUPO2015. Moreover, taking contact to the scientific committee members to plan how to include parallel sessions on plant, bacteria and animal proteomes for the HUPO2015 meeting. These sessions will likely contribute to the conference, also in terms of additional members and broader interest in HUPO.

Aarhus, 21th January 2014
iMOP news letter: January 2014:

Dear iMOP colleagues.

The iMOP initiative has been active since 2011, and it is now timely to reconsider the structure, aims, and the next action plans. A re-cap is also timely because our chairman has wished to step down. As Michael Hengartner is now taking over as president for his university (U of Zurich) he will no longer be able to find the time to lead the iMOP initiative. We wish him all the best with the new and very large challenges. We greatly acknowledge Michaels leadership. Thanks to the work and ideas he invested into getting the iMOP initiative off the ground, we are now a rapidly growing community.

Thanks also to the many of you who have attended the iMOP workshops in 2013 (in Yokohama and in St.Malo). The large and active attendance of both these 2013 workshops allowed us to have broad and representative discussions about the future aims and plans for developing iMOP. These discussions led to the currently ongoing reform process of the iMOP organization. We will here provide a summary of the 2013 discussion, and summarize the steps in the current reform process:

 

Summary and consensus from the 2013 iMOP discussions:

1. We want the iMOP initiative to be a broad and open community.

2. A main aim is to reach the species-oriented research fields, where there is interest in proteome approaches, but still limited access to state of the art technologies.

3. We will contribute to the BD-HPP, by providing research on species closely related to studies on human health. These include bacteria, crops, veterinary species, as well as classical model organism.

4. We need to reconsider whether the terminology “model organism” is the best label for what we aim for in iMOP. Much of our scientific interests are within species that greatly impact human health, but not necessarily as “models” for human biology, i.e. bacteria, parasites, and agricultural species (animals as well as plants).

5. Many alternative names have been suggested, including the most popular: iMOP (initiative on MultiOrganism Proteomes) and iPOP (initiative on Pan Organism Proteomes). It is commonly agreed that it would be good to keep the iMOP acronyme, and just exchange the difficult/exclusive word “model” with “multi”.

6. We will reform the leadership structure of iMOP, to include co-chairs who represent each of the main domains within the iMOP community. Most importantly these are: plants, microorganisms, animals, bioinformatics, proteomics standards. Each of these communities have been asked to discuss and suggest suited co-chairs, who will be the responsible links between iMOP and the species-oriented scientific fields.

7. Emøke Bendixen (Aarhus University) has been elected as next chair. She has been active in the core group of iMOP since 2011. She is active in the EuPA EC and The HUPO board, and therefore in a good position to form a solid link to relevant work groups and to a large selection of scientific communities. Her research is mainly in veterinary proteomics, and the use of pig models for the study of human diseases.

8. To maintain continuity, Sabine Schrimpf (U of Zurich) has agreed to continue as main coordinator, and Andreas Tholey (Kiel University) has agreed to remain a co-chair. We are currently waiting for the plant, animal and microbiology and bioinformatics fields, to suggest suited co-chairs. As soon as the new core-group is collected, we will suggest a revised work plan.

9. The next iMOP workshop will run during the HUPO 2014 meeting in Madrid. When submitting your abstract for the upcoming HUPO meeting, please consider whether it is relevant for presentation under the iMOP sessions. More info on this will follow soon, and all ideas/wishes for planning on how to organize the upcoming iMOP sessions are very welcome.

10. We have collected an email distribution list. This includes all names from the original iMOP position-paper (Jones et al., Proteomics. Feb;12(3):340-5) as well those of you who signed up during workshops in 2013. Please send us feedback if you either do not wish to be on this list, or if you miss any colleagues from this list. This is a HUGE help for us.

11. Latest publications from iMOP 2013:
Tholey A, Treitz C, Kussmann M, Bendixen E, Schrimpf SP, Hengartner MO. (2013). Model organism proteomics – from holobionts to human nutrition. Proteomics, 13: 2537 – 2541.

With all the best wishes for a new iMOP year.

Emøke, Sabine and Andreas

 

Emøke Bendixen ebx@mb.au.dk
Sabine Schrimpf sabine.schrimpf@imls.uzh.ch
Andreas Tholey a.tholey@iem.uni-kiel.de