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Synthetic biology in action: beyond standard metabolism – Course and Conference Office

EMBO Practical Course

Synthetic biology in action: beyond standard metabolism

Overview

Proof of COVID-19 vaccination or recovery is required to attend this on-site course. Please see EMBL’s COVID-19 safety policy for on-site events.

Course overview

Synthetic Biology (SynBio) has become a rapidly developing area for tackling a large number of challenges in life science research. This is due to a combination of foundational advances in technologies such as large-scale DNA synthesis and new methods that allow integrating such raw synthesis power into engineering approaches, including genome wide small RNA regulation, dCas9-based regulation, and multiplexed genome engineering. Such fresh approaches fuel new types of biotechnological applications with immense impact on both fundamental science and society.

This course will provide the best and most exciting novelties in the field and focus on exploiting tools and concepts of SynBio for multi-scale engineering of bacterial systems. The intensive schedule includes lectures by experts in the field, discussions, poster sessions, and, importantly, an experimental program.

Audience

The course is directed to PhD students and early post-doctoral researchers active in molecular biology, biotechnology, systems biology and bioengineering. The experimental focus will be on microbiological systems.

Modules/resources

  • Bacterial genome engineering using MAGE
  • CRISPR-based gene knock-down in mammalian cells
  • Integration of non-canonical amino acids into proteins
  • Implementation of advanced evolutionary strategies in SynBio

Learning outcomes

The participants will learn about the design and workflow of Synthetic Biology studies and gain understanding about the possibilities and limitations of synthetic biology in different areas.

Speakers and Trainers

Speakers, trainers, and staff

Birgit Wiltschi

University of Natural Resources and Life Sciences, Vienna and acib GmbH

Austria

Scientific organisers

Course organisers

Yvonne Yeboah

Training Laboratory Manager

EMBL Heidelberg

Germany

Programme

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  • Some pre-course work (such as watching pre-recordings, protocol reading and computational exercises) 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.
  • All times in the programme below are shown as the time in Europe/Berlin.
Day 1 – Sunday 11 September 2022
TimeSpeakerLocation
17:00-17:30RegistrationISG Hotel
17:30-18:30Welcome, breaking the ice, and practicalities by organizersISG Hotel
18:30-19:30Inaugural lecture: Synthetic biology: beyond standard metabolism
Sven Panke – ETH Zurich, Switzerland
ISG Hotel
19:30BBQ dinner and networkingISG Hotel
Day 2 – Monday 12 September 2022
Time SpeakerLocation
9:00-9:30Lecture: Overview of the experiments to be run during the course
Sven Panke – ETH Zurich, Switzerland
Courtyard room A&B
9:30-10:00Lecture: Organization of teams, assignment of supervisors lab safety introduction
Yvonne Yeboah – EMBL Heidelberg, Germany
Courtyard room A&B
10:00-11:00Introduction to practical: Separate meetings of lab teams with respective trainersCourtyard room A&B
11:00-11:30Coffee breakFlex Lab A&B
11:30-12:30Lecture: Genome engineering at scale – strategies for genome assembly
Anke Becker – SYNMIKRO Research Center, Germany
Courtyard room A&B
12:30-13:30Lunch breakCanteen
14:00-16:00Practical 1: Genome engineering with Multiplex Automated Genome Engineering (crMAGE, with Cas9 counterselection)
Nico Claassens – Wageningen University, The Netherlands
Practical 2: I Can CRISPR
Masue Marbiah – Imperial College, UK
Practical 3: Engineering polymerases for XNA synthesis. Starting from a wild-type hyperthermophilic enzyme
Paola Handal Marquez – KU Leuven, Belgium
Practical 4: Reprogramming proteins for non-canonical biochemistries
Nicolas Huguenin-Dezot – ETH Zurich, Switzerland
Training Lab B
16:00-16:30Coffee breakFlex Lab A&B
16:30-17:30Lecture: Engineering strategies for synthetic one-carbon metabolism
Nico Claasens – Wageningen University, The Netherlands
Courtyard room A&B
17:30-19:00Practical session 2: Practical in groups continuesTraining Lab B
19:00-20:00DinnerCanteen
20:00-21:30Poster session and discussion I: Posters 1 – 6Helix A / Rooftop Lounge
21:30Bus departure to ISG HotelEMBL
Bus stop

Day 3 – Tuesday 13 September 2022
TimeSpeakerLocation
09:00-11:00Practical session 3: Practical in groups continuesTraining Lab B
11:00-11:30Coffee breakFlex Lab A&B
11:30-12:30Lecture: Micro RNAs and their roles in programming cellular decision making
Velia Siciliano – Italian Institute of Technology, Italy
Courtyard room A&B
12:30-13:30Lunch breakCanteen
14:00-16:00Practical session 4: Practical in groups continuesTraining Lab A&B
16:00-16:30Coffee breakFlex Lab A&B
16:30-17:30Virtual lecture: Cell free synthetic biology
Michael Jewett – Northwestern University, USA
Courtyard room A&B
17:30-19:00Practical session 5: Practical in groups continuesTraining Lab B
19:00-19:30Round table discussion: Update on laboratory workCourtyard room A&B
19:30-20:30 Tapas dinner Rooftop Lounge
20:30-21:30Poster session and discussion II: Posters 7-10Helix A / Rooftop Lounge
21:30Bus departure to ISG HotelEMBL
Bus stop
Day 4 – Wednesday 14 September 2022
TimeSpeakerLocation
09:00-11:00Practical session 6: Practical in groups continuesTraining Lab B
11:00-11:30Coffee breakFlex Lab A&B
11:30-12:30Lecture: Constraint-based modelling for designing biomolecular systems
Jörg Stelling – ETH Zurich, Switzerland
Courtyard room A&B
12:30-13:30Lunch breakCanteen
14:00-16:00Practical session 7: Practical in groups continuesTraining Lab B
16:00-16:30Coffee breakFlex Lab A&B
16:30-17:30Lecture: Updating the biological table of elements
Pablo Nikel – Technical University, Denmark
Courtyard room A&B
17:30-19:00Practical session 8: Practical in groups continuesTraining Lab B
19:00-19:30Round table discussion: Update on laboratory workCourtyard room A&B
19:30-20:30DinnerCanteen
20:30-21:30Poster session and discussion III: Posters 11-16Helix A / Rooftop Lounge
21:30Bus departure to ISG HotelEMBL
Bus stop
Day 5 – Thursday 15 September 2022
TimeSpeakerLocation
09:00-11:00Practical session 9: Practical in groups continuesTraining Lab B
11:00-11:30Coffee breakFlex Lab A&B
11:30-12:30Lecture: Sensing in bioproduction – orchestrating molecular systems
Karen Polizzi – Imperial College London, UK
Courtyard room A&B
12:30-13:30Lunch breakCanteen
14:00-16:00Practical session 10: Practical in groups continuesTraining Lab B
16:00-16:30Coffee breakFlex Lab A&B
16:30-17:30Virtual lecture: Synthetic biology and the revolution of the chemical industry – a company perspective
Reshma Shetty – Ginkgo Bioworks, USA
Courtyard room A&B
17:30-19:00Practical session 11: Practical in groups continuesTraining Lab B
19:00- 19:30Round table discussions: Update on laboratory workCourtyard room A&B
19:30-21:00Ethical session: Pizza Dinner with viewing and discussion of ELSI movie clipsCourtyard room A&B
21:00Bus departure to ISG HotelEMBL
Bus stop
Day 6 – Friday 16 September 2022
TimeSpeakerLocation
09:00-11:00Practical session 12: Practical in groups continuesTraining Lab B
11:00-11:30Coffee breakFlex Lab A&B
11:30-13:00Keynote lecture: Expanding the biological alphabet
Birgit Wiltschi – University of Natural Resources and Life Sciences, Vienna and acib GmbH, Austria
Courtyard room A&B
13:00-14:00Lunch breakCanteen
14:00-16:00Practical session 13: Practical in groups continuesTraining Lab B
16:00-16:30Coffee breakFlex Lab A&B
16:30-18:00Keynote lecture: Beyond standard biochemistry: Tools to expand in vivo chemistry
Kathrin Lang – ETH Zurich, Switzerland
Courtyard room A&B
18:00-19:00Practical session 14: Practical in groups continuesTraining Lab B
19:00-19:30Departure to ISG followed by dinner in downtown HeidelbergEMBL
Bus stop
Day 7 – Saturday 17 September 2022
TimeSpeakerLocation
09:00-11:00Practical session 15: Practical in groups continuesTraining Lab B
11:00-11:30Coffee breakFlex Lab A&B
11:30-12:30Keynote lecture: Manipulating the storage medium: xenonucleic acids
Vitor Pinheiro – KU Leuven, Belgium
Courtyard room A&B
12:30-13:30Lunch breakCanteen
13:30-14:30TBACourtyard room A&B
14:30-17:00Preparation of final reports by individual teamsCourtyard room A&B
17:00Bus departure to ISG Hotel and Heidelberg Neckarmünzplatz – free afternoonEMBL
Bus stop
Day 8 – Sunday 18 September 2022
TimeSpeakerLocation
09:00-11:00Lecture: Presentation of results by individual teamsCourtyard room A&B
11:00-11:30Coffee breakFlex Lab A&B
11:30-12:30Lecture: Logical computations for therapeutic decision making in mammalian cells
Yaakov Benenson – ETH Zurich, Switzerland
Courtyard room A&B
12:30-13:00Wrap-up and farewellCourtyard room A&B
13:15Packed lunch and departure to ISG Hotel, HauptbahnhofEMBL
Bus stop

Practical information

Registration fees and motivation letter

The course is limited to 16 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

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 more detailed information, follow the instructions provided in 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

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 events in Heidelberg and will be indicated during the abstract or motivation letter submission process.

Your place in the meeting 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 or conference.

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, EMBL Conference or EMBO|EMBL Symposium from within Europe.
– up to €1000 for participants travelling to an EMBL Course, EMBL Conference or EMBO|EMBL Symposium from outside Europe.
– up to €500 for any participant travelling to an EMBO Practical Course or EMBO Workshop.
– up to €1000 for any participant working in Chile, India, Singapore or Taiwan travelling to an EMBO Practical Course or EMBO Workshop.

*Registration fees are only covered for EMBO Practical Courses or EMBO Workshops

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 and workshops only)

For EMBO Practical Course or EMBO Workshop 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 or conference. Eligible costs include fees for a baby-sitter or child-care facility, travel costs for a care giver, 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 EUR can be awarded per participant applying for an EMBO Childcare Grant. In order to apply for this grant for EMBO Workshops, you must be registered by the abstract submission deadline.

Boehringer ingelheim fonds travel grant

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

This grant covers costs related to your attendance to 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, and abstract for conferences. 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 or abstract 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 meeting. Selection is based on 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

View our list of external funding opportunities and information on attending a conference as an event reporter.

For further information about financial assistance please refer to the FAQ page.

Accommodation and shuttles

Accommodation has been pre-booked for you at the ISG Hotel for the default dates of 11 to 18 September 2022 (7 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 21 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.

Technical requirements and 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 Supporter:

EMBOPress_only

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 conferences, 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.

Date: 11 - 18 Sep 2022

Location: EMBL Heidelberg


Deadline(s):

Application: Closed


Organisers:


EMBL Courses and Conferences are kindly supported by our Corporate Partnership Programme

Founder partners

Corporate partners

Associate partners

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