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Measuring translational dynamics by ribosome profiling – Course and Conference Office

EMBO Practical Course

Measuring translational dynamics by ribosome profiling

Overview

Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course.

Course overview

Regulation of translation is key in the control of gene expression, playing a critical role in many biological and pathophysiological settings. In the last decade, methodological advances have provided comprehensive insights into cellular transcriptomes and proteomes, however, the systems-wide analysis of translation remained an unsolved experimental challenge. The advent of ‘ribosome-profiling’ provided the methodological basis for comprehensive transcriptome-wide analyses of translation at sub-codon resolution by the precise and high-throughput determination of ribosomal positions on mRNA. Its application in a variety of organisms yielded novel insights into protein synthesis and its dynamic regulation, significantly advancing our understanding of the post-transcriptional regulation of gene expression.

Audience

The course is aimed at PhD students and early post-doctoral researchers who are entering the field of posttranscriptional regulation of gene expression.

Learning outcomes

The practical course ‘Measuring translational dynamics by ribosome profiling’ aims to:
a) generate a detailed theoretical understanding of ribosome profiling, its variations to address specific aspects of translation and its experimental strengths and limitations,
b) provide hands-on wet-lab training to perform ribosome-profiling experiments with the aim to understand and master the critical steps of the experimental workflow and to train the participants to independently perform and adapt similar experiments in their own laboratories,
c) provide hands-on bioinformatics training on processing the high-throughput sequencing data, the quality control and on the use of specialised tools for data generated by ribosome-profiling.

Speakers, trainers, and staff

Rachel Green

Johns Hopkins University School of Medicine

USA

Yeji Kim

University of Bern

Switzerland

Marina Rodnina

Marina Rodnina

Max Planck Institute for Biophysical Chemistry

Germany

Scientific organisers

Course organisers

Programme

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  • Some pre-course work (such as watching pre-recordings, protocol reading and computational exercises) with estimated time 0-10 hours will be required and will be shared in advance of the course.
  • Some speakers may need to join virtually to give their lecture or Q&A, and the programme is subject to change.
Day 0 – Monday, 13 March 2023
Time (Europe/Berlin)SessionLocation
14:00 – 15:30Onboarding session: Welcome, introduction to material and software testing Virtual
Day 1 – Sunday 26 March 2023
Time (Europe/Berlin)SessionLocation
13:15Bus to EMBL ATCISG Hotel
13:30 – 14:00Registration and light refreshmentsCourtyard A+B
14:00 – 14:30Welcome and house notes and course overview
Pavel Baranov – University College Cork, Ireland
Sebastian Leidel – University of Bern, Switzerland
Jan Medenbach – University of Regensburg, Germany
Elisabeth Zielonka – EMBL Heidelberg, Germany
Courtyard A+B
14:30 – 15:00Ice-Breaking activityCourtyard A+B
15:00 – 15:30Coffee BreakCourtyard A+B
15:30 – 16:00Introduction Lecture: Overview of the course and technology background
Pavel Baranov – University College Cork, Ireland
Sebastian Leidel – University of Bern, Switzerland
Jan Medenbach – University of Regensburg, Germany
Courtyard A+B
16:00 – 17:00Lecture
Jan Medenbach – University of Regensburg, Germany
Courtyard A+B
17:00 – 18:00Lecture
Sebastian Leidel – University of Bern, Switzerland
Courtyard A+B
18:00 – 20:00Flash talks by participants, speakers and trainersCourtyard A+B
20:00Bus to ISG HotelATC Entrance
20:15 – 21:30Dinner & NetworkingISG Hotel

Day 2 – Monday, 27 March 2023
Time (Europe/Berlin)SessionLocation
08:10Bus to EMBL ATCISG Hotel
08:30 – 08:45Laboratory Safety InstructionsCourtyard A+B
08:45 – 09:00Overview of the day & introduction to practical workCourtyard A+B
09:00 – 10:00Practical work: preparation of RPFs –
Native extract preparation

Leon Kleemann – University of Bern, Switzerland
Sebastian Leidel – University of Bern, Switzerland
Jan Medenbach – University of Regensburg, Germany
Andreas Meindl – University of Regensburg, Germany
Elisabeth Zielonka – EMBL Heidelberg, Germany
Training Lab A+B
10:00 – 10:30Coffee BreakCourtyard A+B
10:30 – 11:30Practical work: preparation of RPFs –
Extract quantification, ribonuclease digestion, preparation of gradients
Leon Kleemann – University of Bern, Switzerland
Sebastian Leidel – University of Bern, Switzerland
Jan Medenbach – University of Regensburg, Germany
Andreas Meindl – University of Regensburg, Germany
Elisabeth Zielonka – EMBL Heidelberg, Germany
Training Lab A+B
11:30 – 12:00Practical work: preparation of RPFs –
Start of ultracentrifugation

Leon Kleemann – University of Bern, Switzerland
Sebastian Leidel – University of Bern, Switzerland
Jan Medenbach – University of Regensburg, Germany
Andreas Meindl – University of Regensburg, Germany
Elisabeth Zielonka – EMBL Heidelberg, Germany
Training Lab A+B
12:00 – 13:00Lunch breakEMBL Canteen
13:00 – 15:30Computer Class:
Raw Data processing: assessment of sequence data quality, adaptors removal, removal of rRNA and tRNA reads, PCR duplicates removal using UMIs, read mapping to genomes and transcriptomes

Pavel Baranov – University College Cork, Ireland
Alla Fedorova – University College Cork, Ireland
Jack Tierney – University College Cork, Ireland
Oza Zaheed – University College Cork, Ireland
Computer Training Lab
15:30 – 16:00Coffee BreakCourtyard A+B
16:00 – 17:00Lecture (remote)
Nicholas Ingolia – University of California, Berkeley, USA
Courtyard A+B
17:00 – 19:00Practical work: preparation of RPFs
Gradient fractionation and RNA preparation

Leon Kleemann – University of Bern, Switzerland
Sebastian Leidel – University of Bern, Switzerland
Jan Medenbach – University of Regensburg, Germany
Andreas Meindl – University of Regensburg, Germany
Elisabeth Zielonka – EMBL Heidelberg, Germany
Training Lab A+B
19:00 – 21:00Poster Session & Discussion concurrent finger food dinner and drinksATC Helix A/Rooftop Lounge
21:00Bus to ISG HotelATC Entrance
Day 3 – Tuesday, 28 March 2023
Time (Europe/Berlin)SessionLocation
08:40Bus to EMBL ATCISG Hotel
09:00 – 09:15Overview of the dayCourtyard A+B
09:15 – 11:00Practical work: preparation of RPFs
Size selection of RPFs by PAGE

Leon Kleemann – University of Bern, Switzerland
Sebastian Leidel – University of Bern, Switzerland
Jan Medenbach – University of Regensburg, Germany
Andreas Meindl – University of Regensburg, Germany
Elisabeth Zielonka – EMBL Heidelberg, Germany
Training Lab A+B
11:00 – 11:30Coffee breakCourtyard A+B
11:30 – 12:30Lecture: Translation – A tug war during viral infection
Noam Stern-Ginossar – Weizmann Institute of Science, Israel
Courtyard A+B
12:30 – 13:00Practical work: preparation of RPFs
Gel extraction setup (over-night incubation)
Leon Kleemann – University of Bern, Switzerland
Sebastian Leidel – University of Bern, Switzerland
Jan Medenbach – University of Regensburg, Germany
Andreas Meindl – University of Regensburg, Germany
Elisabeth Zielonka – EMBL Heidelberg, Germany
Training Lab A+B
13:00 – 14:00Lunch breakEMBL Canteen
14:00 – 16:00Computer Class: Quality Assessments: Analysis of read mapping across different functional regions; read length distribution and triplet periodicity, metagen profiles for the assessment of global translation
Pavel Baranov – University College Cork, Ireland
Alla Fedorova – University College Cork, Ireland
Jack Tierney – University College Cork, Ireland
Oza Zaheed – University College Cork, Ireland
Computer Training Lab
16:00 – 16:30Coffee breakCourtyard A+B
16:30 – 17:30Lecture (remote)
Rachel Green – Johns Hopkins University School of Medicine, USA
Courtyard A+B
17:30 – 19:00Interactive discussion round – Responsible conduct of research:
● sources of experimental artifacts
● the technology in different species
● what are the key quality controls?
● parameter space for optimization
Courtyard A+B
19:00 – 21:00Poster Session & Discussion concurrent finger food dinner and drinksATC Helix A/Rooftop Lounge
21:00Bus to ISG HotelATC Entrance
Day 4 – Wednesday, 29 March 2023
Time (Europe/Berlin)SessionLocation
08:40Bus to EMBL ATCISG Hotel
09:00 – 09:15Overview of the dayCourtyard A+B
09:15 – 10:45Practical work: Library Preparation –
Dephosphorylation, linker ligation

Leon Kleemann – University of Bern, Switzerland
Sebastian Leidel – University of Bern, Switzerland
Jan Medenbach – University of Regensburg, Germany
Andreas Meindl – University of Regensburg, Germany
Elisabeth Zielonka – EMBL Heidelberg, Germany
Training Lab A+B
10:45 – 11:15Coffee breakCourtyard A+B
11:15 – 13:15Computer Class:
Goal oriented data analysis: Differential gene expression;

detection of translated ORFs; translational pauses; codon-specific decoding rates
Pavel Baranov – University College Cork, Ireland
Alla Fedorova – University College Cork, Ireland
Jack Tierney – University College Cork, Ireland
Oza Zaheed – University College Cork, Ireland
Computer Training Lab
13:15 – 14:15Lunch breakEMBL Canteen
14:15 – 15:15Lecture: Junk translation, translation of junk and translation that does not make proteins
Pavel Baranov – University College Cork, Ireland
Courtyard A+B
15:15 – 16:15Lecture
Vladimir Benes – EMBL Heidelberg, Germany
Courtyard A+B
16:15 – 16:45Bus downtownATC Entrance
16:45 – 18:45Guided tour of Heidelberg & free time downtown
18:45 – 21:15Course dinner
Day 5 – Thursday, 30 March 2023
Time (Europe/Berlin)SessionLocation
08:40Bus to EMBL ATCISG Hotel
09:00 – 09:15Overview of the dayCourtyard A+B
09:15 – 11:15Practical work: Library preparation
subtractive hybridization, 1st purification (solid phase extraction), reverse transcription

Leon Kleemann – University of Bern, Switzerland
Sebastian Leidel – University of Bern, Switzerland
Jan Medenbach – University of Regensburg, Germany
Andreas Meindl – University of Regensburg, Germany
Elisabeth Zielonka – EMBL Heidelberg, Germany
Training Lab A+B
11:15 – 11:45Coffee breakCourtyard A+B
11:45 – 13:15Practical Work: Library preparation
2nd purification (solid phase extraction), circularization of RT product

Leon Kleemann – University of Bern, Switzerland
Sebastian Leidel – University of Bern, Switzerland
Jan Medenbach – University of Regensburg, Germany
Andreas Meindl – University of Regensburg, Germany
Elisabeth Zielonka – EMBL Heidelberg, Germany
Training Lab A+B
13:15 – 14:15Lunch breakEMBL Canteen
14:15 – 15:15Guided tour of the EMBL genomics core facility (Genecore)Genecore
15:15 – 16:15Practical Work: Library preparation
3rd purification (solid phase extraction), pre-amplification PCR

Leon Kleemann – University of Bern, Switzerland
Sebastian Leidel – University of Bern, Switzerland
Jan Medenbach – University of Regensburg, Germany
Andreas Meindl – University of Regensburg, Germany
Elisabeth Zielonka – EMBL Heidelberg, Germany
Training Lab A+B
16:15 – 16:45Coffee breakCourtyard A+B
16:45 – 17:45Lecture (remote)
Anne Willis – MRC Toxicology, UK
Courtyard A+B
17:45 – 18:15Practical Work: Library preparation –
purification of PCR product

Leon Kleemann – University of Bern, Switzerland
Sebastian Leidel – University of Bern, Switzerland
Jan Medenbach – University of Regensburg, Germany
Andreas Meindl – University of Regensburg, Germany
Elisabeth Zielonka – EMBL Heidelberg, Germany
Training Lab A+B
18:15 – 19:15DinnerEMBL Canteen
19:15 – 20:45Discussion round – Responsible conduct of research:
● protocol optimization
● the technology in different model organisms
● future applications
Courtyard A+B
20:45Bus to ISG HotelATC Entrance
Day 6 – Friday, 31 March 2023
Time (Europe/Berlin)SessionLocation
08:40Bus to EMBL ATCISG Hotel
09:00 – 09:15Overview of the dayCourtyard A+B
09:15 – 10:15Lecture: Translation dynamics and protein folding
Marina Rodnina – MPI Biophysical Chemistry, Germany
Courtyard A+B
10:15 – 10:45Coffee breakCourtyard A+B
10:45 – 11:30Practical Work: Library preparation –
Scouting PCR, preparation of gels

Leon Kleemann – University of Bern, Switzerland
Sebastian Leidel – University of Bern, Switzerland
Jan Medenbach – University of Regensburg, Germany
Andreas Meindl – University of Regensburg, Germany
Elisabeth Zielonka – EMBL Heidelberg, Germany
Training Lab A+B
11:30 – 13:00Computer Class:
The use of public data resources. riboSeq.Org and beyond

Pavel Baranov – University College Cork, Ireland
Alla Fedorova – University College Cork, Ireland
Jack Tierney – University College Cork, Ireland
Oza Zaheed – University College Cork, Ireland
Computer Training Lab
13:00 – 14:00Lunch breakEMBL Canteen
14:00 – 15:30Discussion round: Data analyses artifactsCourtyard A+B
15:30 – 16:00Practical Work: Library preparation
Analysis of PCR products by PAGE

Leon Kleemann – University of Bern, Switzerland
Sebastian Leidel – University of Bern, Switzerland
Jan Medenbach – University of Regensburg, Germany
Andreas Meindl – University of Regensburg, Germany
Elisabeth Zielonka – EMBL Heidelberg, Germany
Training Lab A+B
16:00 – 16:30Coffee breakCourtyard A+B
16:30 – 18:00Practical Work: Library preparation –
Analysis of PCR products by PAGE (continued)
;
final discussion on library preparation
Leon Kleemann – University of Bern, Switzerland
Sebastian Leidel – University of Bern, Switzerland
Jan Medenbach – University of Regensburg, Germany
Andreas Meindl – University of Regensburg, Germany
Elisabeth Zielonka – EMBL Heidelberg, Germany
Training Lab A+B
18:00 – 19:00Open discussion – Responsible conduct of research:
● data analysis bottlenecks and artifacts
● data management
● FAIR principle
● user defined questions
Courtyard A+B
19:00Bus to ISG HotelATC Entrance
19:15 – 21:15Dinner and networkingISG Hotel
Day 7 – Saturday, 1 April 2023
Time (Europe/Berlin)SessionLocation
08:40Bus to EMBL ATCISG Hotel
09:00 – 09:15Overview of the dayCourtyard A+B
09:15 – 10:15Lecture: Ribosome profiling in single cells
Michael VanInsberghe – Hubrecht Institute-KNAW
Courtyard A+B
10:15 – 10:45Coffee breakComputer Training Lab
10:45 – 11:45Computer Class:
Datamining competition I. Identifying evidence of

non-standard translation mechanisms
(student presentations of results)
Pavel Baranov – University College Cork, Ireland
Alla Fedorova – University College Cork, Ireland
Jack Tierney – University College Cork, Ireland
Oza Zaheed – University College Cork, Ireland
Computer Training Lab
11:45 – 12:45Lunch breakEMBL Canteen
12:45 – 15:15Computer Class:
Datamining competition II. Identifying evidence of

non-standard translation mechanisms
(student presentations of results)
Pavel Baranov – University College Cork, Ireland
Alla Fedorova – University College Cork, Ireland
Jack Tierney – University College Cork, Ireland
Oza Zaheed – University College Cork, Ireland
Computer Training Lab
15:15 – 16:15Open discussion and feedbackCourtyard A+B
16:15End of course & bus to main stationATC Entrance

Practical information

Registration fees and motivation letter

The course is limited to 18 participants. For selection purposes, please note that your application will not be considered without a letter of motivation.

Registration

Registration fees include admission, course materials, COVID-19 safety measures, meals and coffee breaks.  
This EMBO course includes accommodation and transportation to and from the ISG Hotel to the venue.

Academia€500
PhD Student€500
Industry€1000

NO visa support letters will be issued until payment of the registration fee is confirmed.

Confirmation and payment

The registration fee should be paid only after acceptance to the course. The results will be announced approximately 2-3 weeks after the application deadline.

Motivation letter submission

After you have logged in and successfully registered, you will receive an email asking you to submit your motivation letter. Click on the link provided and enter your motivation letter in the text box provided. Alternatively you can submit your motivation letter by clicking on the link on the confirmation page directly after registering.

Instructions

  1. Include your relevant skills, experience and qualifications showing why you would be suitable for the course.
  2. Explain why you would like to attend, including what you can contribute and how you think you will benefit from the course.

Please note:

  • The limit of 2000 characters refers to manually typed text and excludes spaces. If an error occurs try using a different web browser (preferably Google Chrome or Mozilla Firefox).
  • If you copy-paste the text into the form, hidden formatting might still be included which may cause the text to exceed the 2,000 character limit resulting in an error message. We recommend you clear all formatting before pasting in the text.
  • If you have special symbols in your text, make sure you are using Unicode characters, otherwise these will not be recognised.

For detailed instructions, please watch our video on how to submit a course motivation letter.

Further details

For further information about registration and motivation letter submission please refer to the FAQ page.

Financial assistance

Financial assistance

Limited financial assistance is provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO in the form of both registration fee waivers and travel grants. Availability is limited to participants attending on-site EMBL Courses and virtual or on-site EMBO Practical Courses in Heidelberg, and will be indicated during the motivation letter submission process.

Your place in the course is only confirmed by paying the registration fee, which is mandatory even when receiving a fee waiver.

Registration fee waiver

The fee waiver will cover the registration sum that you have paid to attend the course.

Travel grant

The travel grant will cover the cost of travel (airfare, train, bus, taxi, accommodation, visa, and/or registration fees*) and is provided up to specified caps which are normally as follows:

– up to €400 for participants travelling to an EMBL Course within Europe.

– up to €1000 for participants travelling to an EMBL Course from outside Europe.

– up to €500 for any participant travelling to an EMBO Practical Course.

– up to €1000 for any participant working in Chile, India, Singapore or Taiwan travelling to an EMBO Practical Course.

– up to €700 for any participant working in Croatia, Czech Republic, Estonia, Greece, Hungary, Italy, Lithuania, Luxembourg, Poland, Slovenia, and Turkey travelling to an EMBO Practical Course.

*Registration fees are only covered for EMBO Practical Courses

The organisers may reduce the grant cap to accommodate more participants. Recipients will be notified of their travel cap amount when they are informed of the outcome of their application. Original receipts must be provided with your signature for all costs incurred within two months of completion of travel. Scanned copies cannot be accepted.

Childcare grant (EMBO Practical Courses only)

For EMBO Practical Course participants with children, there is the possibility to apply for a childcare grant to offset child care costs incurred by participants or speakers when participating at a course. Eligible costs include fees for a babysitter or child-care facility, travel costs for a caregiver, or travel costs for taking the child to the meeting etc. Please note that priority will be given to early-stage researchers. A maximum amount of €500 can be awarded per participant applying for an EMBO childcare grant. 

Boehringer Ingelheim Fonds travel grant

Applies to selected courses only. Availability will be indicated during the motivation letter submission process.

This grant covers costs related to your attendance at the course (registration, travel and accommodation costs). The grant is restricted to PhD students and postdocs who conduct basic biomedical research.

Whether you are eligible to apply for a travel grant, depends on when you received your university entrance qualification (e.g. Abitur, A-Levels, High School Diploma, Final State Examination):

– for PhD and MD students, as well as graduates, the university entrance qualification must not have been obtained more than 11 years ago at the time of the envisaged course

– for postdocs, the university entrance qualification must not have been obtained more than 13 years ago at the time of the envisaged course

Application

You may apply for financial assistance when submitting your motivation letter for courses. In your application, you will be asked to answer questions regarding why your lab cannot fund your attendance and how your attendance will make a difference to your career. Application for financial support will not affect the outcome of your registration application.

For the Boehringer Ingelheim Fonds Travel Grant, there is a pre-application question during the motivation letter submission process, and if selected you will be requested to complete a standard form and documentation consisting of your travel expense estimation.

Selection

The scientific organisers will select the recipients of all financial assistance during the motivation letter selection process. Results will be announced approximately 6-8 weeks before the event start date, however for some events this may be delayed. Selection results do not impact your admission to the course. Selection is based on scientific merit, your current work or study location, the reasons for needing financial support, and the impact this event will have on your career.

Reimbursement

Costs will be reimbursed after the meeting only once a reimbursement form and original receipts (from travel costs) have been received.

Further details

See our list of external funding opportunities and for further information about financial assistance please refer to the FAQ page.

Accommodation and shuttles

Hotel

Accommodation has been pre-booked for you at the ISG Hotel for the default dates of 26 March to 1 April 2023 (6 nights). Please note that the course registration fee includes coverage of accommodation costs in twin rooms, including breakfasts, for your stay at the ISG but that you will be required to pay an additional cost of 31 EUR per night for a single room. This should be paid by you directly to the ISG during your stay. Any additional nights need to be booked and paid for by you. We recommend that all course participants stay at the ISG Hotel which is the dedicated hotel for the course.

Local transport

Shuttle buses will go from the ISG Hotel to EMBL and back, mornings and evenings. A bus schedule and location of the bus stops will be made available prior to the meeting.

Further details

Address: EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

For further information on getting to EMBL Heidelberg visit our Travel Information page.

For enquiries about accommodation and local transportation please refer to the FAQ page.

Event software

Event software

The EMBL eCampus learning platform will be used to collaborate, communicate and network with all of the course participants. All participants will receive information on how to join shortly before the course. We recommend using Chrome, Safari or Mozilla Firefox browsers for eCampus. 

Additional information

Please find additional information including FAQs, terms and conditions, COVID-19 safety policy and travelling to EMBL on our Information for Participants page.

COVID-19 related questions

COVID-19 information for on-site events at EMBL Heidelberg can be found in our COVID-19 FAQs.

Sponsors

Event partners

Event sponsors

Event supporters



Sponsorship opportunities

We offer a variety of event sponsoring possibilities, with the flexibility to select a set sponsorship package or combine individual sponsorship options to suit your event budget. Discounts are available for companies sponsoring multiple events at EMBL Heidelberg. View other events, or contact sponsorship@embl.de for further information.

If you are interested in becoming a media partner of this event, please visit our media partnerships webpage.

Warning

EMBL wishes to warn sponsors of EMBL conferences and courses of fraudulent schemes purporting to offer sponsorship opportunities on behalf of EMBL or affiliated with EMBL officials. One current scam campaign of which we are aware is conducted using the name ‘Judy Eastman’ (judy@gopcontact.a2hosted.com) and entails approaches to sponsors offering sponsorship opportunities on EMBL’s behalf. Please be kindly advised that all relevant communication regarding sponsorship of EMBL conferences, symposia and courses is handled by EMBL directly and is sent from an official EMBL account. EMBL does not work with any external providers on sponsorship acquisition.

Please also note that:

  • EMBL never provides attendee lists for purchase. Any offers of such are fraudulent.
  • EMBL will never call or email you to ask for your credit card details or to request a payment.
  • All payments are on invoice.

Suspicious communications purportedly from, for or on behalf of EMBL should be reported to EMBL at the following email address sponsorship@embl.de.

Media kit

Want to let others know you’re attending this event? Take a look at our shareable media and feel free to use them in your social media channels or presentations.

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Date: 26 Mar - 1 Apr 2023

Location: EMBL Heidelberg

Venue: EMBL Advanced Training Centre


Deadline(s):

Application: Closed


Organisers:

  • Pavel Baranov
    University College Cork, Ireland
    • Sebastian Leidel
      University of Bern, Switzerland

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