COST Action MARISTEM Training School:

Omics for studying stem cells in model and non-model aquatic invertebrate systems

Organisation of the Training School | Application process | Final schedule

Schedule Week 1 | Week 2 | Week 3 | Week 4 | Week 5

Coordinators:

Ildiko Somorjai (University of St Andrews, UK) Loriano Ballarin (University of Padova, Italy)

Organising committee:

Ute Rothbächer (University of Innsbruck, Austria), Artur Burzynski (Polish Academy of Sciences, Poland), Ana Varela Coelho (ITQB Nova, Portugal), Pedro Martinez (University of Barcelona, Spain), Ildiko Somorjai (University of St Andrews, UK), Loriano Ballarin (University of Padova, Italy)

 

Our mission

Training young researchers is one of the main aims of the COST Action MARISTEM “Stem cells of marine/aquatic invertebrates: from basic research to innovative applications”. This goal is being accomplished through the organization of specific workshops, the support of short-term scientific missions and the provision of training schools.

The training school “Omics for studying stem cells in model and non-model aquatic invertebrate systems” aims to: i) provide trainees with tools in ´omics technology useful for stem cell research; ii) raise the interest of young researchers in studying aquatic invertebrate stem cells, which exhibit characteristics far beyond those seen in their vertebrate counterparts; and iii) establish new contacts among researchers in the field.

Due to COVID-19 restrictions, the training school will be completely virtual, and split into five modules blending theory and practice. Hands-on exercise sessions will be conducted throughout the training school to introduce students to the practical aspects of analysing ´omics data using programming pipelines.
For proteomics and metabolomics data, we will mainly use dedicated available platforms that do not require programming.

Organisation of the Training School

This training school will be held from September 6^th to October 8^th, 2021, broken down into 5 week-long modules on different topics centred around ‘omics technologies for the study of stem cells in aquatic invertebrate, mostly non-model systems. Lectures and online tutorials will be delivered using Zoom, recorded and provided online for the trainees to consult. All students should have internet access and are expected to participate in the entire training course. Although the course runs for 5 weeks, online attendance by students is only required Mondays, 2 hours on Friday mornings as well as in the afternoon of the last Friday of the Training School, on October 8^th. This course is therefore designed to be compatible with the students’ weekly lab work and duties. Certificates of participation will be provided at the end of the training school upon completion of all modules.

This course will cover broad aspects of methodologies, with a focus on adult stem cells (or progenitors) in invertebrates, and include relevant aspects of:

-organising the ideal experiment

-sample preparation

-workflow and (general) methodology

-troubleshooting

-analysis

-discussion about and examples of different invertebrate systems

 

Students will be provided with bibliography as well as information to access materials to prepare for each module. On Mondays, students will have lectures from experts, along with guided practicals. From Tuesday to Thursday, materials and exercises will be available for students to independently study and practice the content learned on Mondays. Time invested here will be at the student’s discretion. On Fridays, the coordinator and tutor(s) will run a virtual 2- hour wrap-up with Q&A session covering all aspects of the module. On the afternoon of Friday October 8^th, a wrap up session and informal “virtual drinks” session will take place. Recorded content will be kept available on the COST Action MARISTEM website after the end of the training school for dissemination across the Action. Certificates of participation will be provided at the end of the training school upon completion of all modules.

 

Application process

25 trainees (students registered for a PhD or postdoctoral researchers at recognised Universities or Institutes for Higher Education) will be invited upon successful application. Course participants must be from EU COST Action member states and affiliated countries in order to be formally recognised as having attended the training course[1]. The application must include 1. A motivation letter from the student (500 words max) and 2. A statement from the supervisor/line manager explaining the suitability of the applicant for the training school. Please send applications to Dr Ildiko Somorjai, imls@st-andrews.ac.uk. The deadline has been extended to July 16th.

 

Final schedule for the Training School

 

 

Week 1: Genomics Module

 

6^th Sept 2021-10^th Sept 2021 See the schedule

Module Organisers: Ute Rothbächer (University of Innsbruck, Austria), Simon Blanchoud (University of Fribourg, Switzerland)

Contact: ute.rothbaecher@uibk.ac.at

 

RATIONALE

‘Reading the genome’ i.e. predicting function from sequence remains one of the greatest challenges. In this module, we will outline some of the efforts to retrieve, assemble and annotate genomic sequences of model and non-model organisms and to learn how to utilize them for experimental design.

Starter Reference: Wei, J., Zhang, J., Lu, Q., Ren, P., Guo, X., Wang, J., Li, X., Chang, Y., Duan, S., Wang, S., Yu, H., Zhang, X., Yang, X., Gao, H., & Dong, B. (2020). Genomic basis of environmental adaptation in the leathery sea squirt (Styela clava). Molecular Ecology Resources, 20, 1414–1431. DOI: 10.1111/1755-0998.13209

 
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Week 2: Transcriptomics Module

 

13^th Sept 2021-10^th Sept 2021 See the schedule

Module Organiser: Artur Burzynski (Institute of Oceanology, Polish Academy of Sciences, Poland)

Contact: aburzynski@iopan.pl

 

RATIONALE

Characterising stem cells is a major challenge in non-model organisms. In this module you will learn how to use transcriptomic data to approach the problem and gain valuable insight from RNA-Seq experiments. The pipeline will include handling of raw Illumina data, their assembly and annotation, with a focus on candidate stem cell markers.

 

Starter reference: Ribeiro, R. P., Ponz-Segrelles, G., Bleidorn, C., & Aguado, M. T. (2019). Comparative transcriptomics in Syllidae (Annelida) indicates that posterior regeneration and regular growth are comparable, while anterior regeneration is a distinct process. BMC Genomics, 20, 1-13. DOI: 10.1186/s12864-019-6223-y

 

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Week 3: Proteomics Module

 

20^th Sept 2021 – 24^th Sept 2021 See the schedule

Module Organisers: Ana Varela Coelho and Luis G Gonçalves (ITQB Nova, Portugal)

Contact: varela@itqb.unl.pt

 

RATIONALE

In this module, you will get an overview of the experimental tools, data treatment and functional interpretation of proteomics data to unravel physiological, biological and metabolic processes in aquatic invertebrates, and how these approaches may be applied to stem cell research.

 

Starter reference:

Shen, M., Di, G., Li, M. et al. (2018) Proteomics studies on the three larval stages of development and metamorphosis of Babylonia areolata. Sci Rep, 8, 6269. doi /10.1038/s41598-018-24645-z

 

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Week 4: Metabolomics Module

 

27^th September 2021 – 1^st October 2021 See the schedule

Module Organisers: Ana Varela Coelho and Luis G Gonçalves (ITQB Nova, Portugal)

Contact: varela@itqb.unl.pt

 

RATIONALE

In this module, you will get an overview of the experimental tools, data treatment and functional interpretation of metabolomics data to unravel physiological, biological and metabolic processes in aquatic invertebrates, and how these approaches may be applied to stem cell research.

 

Starter reference:

Reverter M, Tribalat MA, Pérez T, Thomas OP. (2018) Metabolome variability for two Mediterranean sponge species of the genus Haliclona: specificity, time, and space. Metabolomics, 14, 114. DOI: 10.1007/s11306-018-1401-5.

 

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Week 5: Single Cell Sequencing Module

 

4^th October 2021 – 8^th October 2021 See the schedule

Module Organiser: Pedro Martinez (University of Barcelona, Spain)

Contact: pedro.martinez@ub.edu

 

RATIONALE

The advent of new single cell sequencing technologies is allowing us to understand development and disease in extraordinary detail. In this module, the students will get a good idea of the basic principles that underlie the use of this technology, both practical and theoretical, with a focus on marine animals.

 

Starter Reference: Siebert S, Farrell JA, Cazet JF, Abeykoon Y, Primack AS, Schnitzler CE, Juliano CE. (2019) Stem cell differentiation trajectories in Hydra resolved at single-cell resolution. Science. 365, 341. DOI: 10.1126/science.aav9314

 

 

Please note, the order or specific topics covered within modules may be subject to change. Please contact module organisers for specific queries.

 

 

 

[1] COST Action 16203 MARISTEM member countries: Austria, Belgium, Bosnia and Herzegovina, Croatia, Denmark, France, Germany, Greece, Ireland, Israel, Italy, Latvia, Luxembourg, Malta, Netherlands North Macedonia, Norway, Poland, Portugal, Russia, Serbia, Slovenia, Spain, Switzerland, Turkey, United Kingdom.

 

Please find the schedule attached on the document