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Practical Palaeoproteomics Summer School
Provider: Faculty of Health and Medical Sciences

Activity no.: 3172-21-00-00 
Enrollment deadline: 01/03/2021
Date and time12.08.2021, at: 09:00 - 20.08.2021, at: 17:00
Regular seats20
Course fee6,480.00 kr.
LecturersEnrico Cappellini
ECTS credits5.00
Contact personAlberto Taurozzi    E-mail address: alberto.taurozzi@sund.ku.dk
Enrolment Handling/Course OrganiserPhD administration     E-mail address: fak-phdkursus@sund.ku.dk

Aim and content
This course is free of charge for PhD students at Danish universities (except Copenhagen Business School), and for PhD students at graduate schools in the other Nordic countries. All other participants must pay the course fee.
Anyone can apply for the course, but if you are not a PhD student at a Danish university, you will be placed on the waiting list until enrollment deadline. This also applies to PhD students from Nordic countries. After the enrollment deadline, available seats will be allocated to applicants on the waiting list.


Learning objectives
A student who has met the objectives of the course will be able to acquire the following knowledge, skills and competencies:

Knowledge:
- Clearly identify the research challenges in palaeontology, paleoanthropology, archaeology and cultural heritage studies that palaeoproteomics can successfully address,
- Understand major decay mechanisms, and therefore better appreciate how extraction protocols are optimised for ancient proteins,
- Authenticate the proteins retrieved from ancient samples and to evaluate the chemical damage affecting them.

Skills:
- Extract protein residues from small quantities of precious or unique fossil, archaeological or artistic specimen preventing contamination,
- Use proteomics software (i.e. MaxQuant and PEAKS) for basic, and in some cases advanced, data exploration and analysis,
- Characterise and quantify the molecular damage affecting proteins in ancient specimens,
- Discover amino acid substitutions exclusively present in extinct organisms as well as chemical modifications caused by diagenesis.

Competencies:
- Judge, and eventually critique, the content of scientific literature describing palaeoproteomics-based research
- Select the most sound approach to process high-throughput tandem MS-based palaeoproteomics data sets
- Analyse ancient proteome sequences in preparation of their phylogenetic interpretation,
- Evaluate the robustness and reliability of palaeoproteomics result, either yours or previously published.


Content
This intensive seven-days summer course will provide the attendees with a detailed introduction to the methods used for mass spectrometry (MS)-based ancient protein sequencing, i.e. palaeoproteomics. The course will focus on the most advanced methodologies and applications of palaeoproteomics to palaeontology, palaeoprimatology and palaeoanthropology. Applications of palaeoproteomics to cultural heritage (CH) studies and conservation will also be described.
The students will actively take part to all the laboratory activities defining the most advanced workflow currently used in a standard palaeoproteomic study. Hands-on sessions (5 days, 7-8 hours each day) will start with preparation of authentic ancient samples for proteomics analysis, continuing with high-resolution tandem MS data production, and concluding with the analysis and the interpretation of the data the students generated themselves.
A series of introductory lectures, attended remotely or in-person (2 days, 5 hours each day), will present: (i) the history of this research field, (ii) the most advanced technologies and methodologies it relies on, and (iii) the most relevant scientific achievements it accomplished.

Indicative programme:
1. 12/8 Day 1: Introductory lectures: history of palaeoproteomics and key discoveries
2. 13/8 Day 2: Introductory lectures (continued): most advanced applications of palaeoproteomics
3. 16/8 Day 3: Sample preparation
4. 17/8 Day 4: Sample preparation (continued) and nanoLC-MS/MS
5. 18/8 Day 5: Lectures: methods that enabled key palaeoproteomics achievements
6. 19/8 Day 6: MS data analysis
7. 20/8 Day 7: Palaeoproteomic data interpretation and reporting


Participants
The target group for this course are PhD students that wish to augment their research through the incorporation of proteomic analysis. The course will be of special interest to those investigating paleontology, paleoanthropology, archaeology or cultural heritage.


Relevance to graduate programmes
• Life, Earth and Environmental Sciences
• Oral Sciences, Forensic Medicine and Bioanthropology
• Immunology and Infectious Diseases


Language
English


Form
Lectures, practical laboratory training, practical data analysis training and exercises.


Course director
Enrico Cappellini: Associate Professor, Globe Institute, University of Copenhagen, ecappellini@sund.ku.dk
Alberto Taurozzi: Postdoc, Globe Institute, University of Copenhagen, alberto.taurozzi@sund.ku.dk


Teachers
Enrico Cappellini: Associate Professor, Globe Institute, University of Copenhagen
Matthew Collins: Professor, Globe Institute, University of Copenhagen
Frido Welker: Associate Professor, Globe Institute, University of Copenhagen
Alberto Taurozzi: Postdoc, Globe Institute, University of Copenhagen
Jesper V. Olsen: Professor, NNF Center for Protein research, University of Copenhagen
Timothy Cleland: Researcher, Museum Conservation Institute, Smithsonian Institution (USA)
Jessica Handy: Lecturer, BioArch, University of York (UK)
Petra Gutenbrunner:Postdoc, Max Plank Institute for Biochemistry, Munich (Germany)


Dates
12-20 August 2021


Course location
The Globe Institute Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, University of Copenhagen Øster Farimagsgade 5, 1353 Copenhagen K, Denmark


Registration
Please register before 1 March 2021.

Seats to PhD students from other Danish universities will be allocated on a first-come, first-served basis and according to the applicable rules.
Applications from other participants will be considered after the last day of enrolment.

Note: All applicants are asked to submit invoice details in case of no-show, late cancellation or obligation to pay the course fee (typically non-PhD students). If you are a PhD student, your participation in the course must be in agreement with your principal supervisor.

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