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C. elegans: from genome editing to imaging – Course and Conference Office

EMBO Practical Course

C. elegans: from genome editing to imaging

Overview

Registration is not yet open for this event. If you are interested in receiving more information please register your interest.

Course overview

C. elegans is a popular experimental model that combines transparency, reproducible anatomy, traceable cell lineage, sequenced genome and facile genetics, allowing to dissect animal development, physiology, and behaviour across scales of genes, cells and tissues. This 7-day course will present experimental practices in C. elegans research, while introducing historic and up-to-date findings in various research topics.

Each day includes lectures, practicals, student poster presentations and interactive discussions with faculty. Various methodologies commonly employed in C. elegans research will be presented in parallel practicals with rotating student groups by relevant experts. These experimental techniques span forward and reverse genetics, genome editing, lineaging, imaging approaches for live and fixed samples using light and electron microscopy, computational image analysis and other useful web resources. Meanwhile, lectures by internationally established researchers will present a variety of C. elegans research topics, spanning studies of the genome and epigenome, through cell cycle and death, to tissue specification, connectivity, and function. A combination of senior and junior speakers will ensure a balanced view of pioneer breakthroughs and recent advances in the topics presented as well as the students’ interactions with researchers of different topics and career levels.

Audience

This practical course will be aimed at early career scientists, mostly postdocs and advanced graduate students with an interest in C. elegans. We will target both, participants with little or no prior experience in working with C. elegans who want to use this model organism to advance their research, as well as experienced C. elegans researchers who want to expand their tool set. The course will cover state-of-the-art techniques that are – or will become – essential for a broad range of research topics and we will therefore target participants with diverse research interests.

Modules/resources

The course lectures and practical modules develop in three axes of genes, cells, tissues. It will cover the following modules:

Lectures:

  • Genome and epigenome: structure, function, silencing, environment interactions
  • Cell cycle, division, symmetry breaking, cell biomechanics
  • Cell death and degeneration in development, aging (and genome instability) in disease
  • Tissue specification, transcriptome dynamics, morphogenesis
  • Tissue morphogenesis, cell lineage tracing and forces
  • Tissue assembly, connectivity, activity, cell interactions

Practicals:

  • Web resources for C.elegans research
  • C. elegans handling and genetic manipulations
  • Imaging (fixed/live) cells and molecules
  • Image analysis (deconvolution, EM image analysis, optogenetics, tracing, and lineaging approaches)

Learning outcomes

After this course you should know:

  • The advantages of C. elegans for your research
  • Handling and maintenance of C. elegans
  • Staging and C. elegans life cycle
  • Designing and performing forward and reverse genetics experiments
  • Principles of generating transgenic animals
  • The potential of C. elegans imaging – from live imaging to high-resolution imaging, EM, and optogenetics
  • Options for analysis of light and EM images, optogenetics, cell tracing

What past participants say about the course

“The c.elegans from genome editing to imaging is one of the best C.elegans practical courses and I would strongly recommend C.elegans researchers in their early careers to attend this course.” – Somarani Dash, Institute of advanced study in science and technology, Guwahati, Assam, India.

“This course far exceeded my expectations: it was the perfect mixture of theory, hands-onexperiments and networking. An incredible opportunity not only to learn but also to meet peoplefrom all over the world. ” – Antonella Lavatellai, Centre for Research in Agricultural Genomics, Barcelona, Spain.

The course has a recommendation rate of 100% from previous attendees.

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

Speakers

Speakers, trainers, and staff

Scientific organisers

Pavak Shah

University of California, Los Angeles

USA

Event organisers

Maria Bacadare

Maria Bacadare

Course and Conference Manager

EMBL Heidelberg

Germany

Swetlana Krez

Training Lab Technician

EMBL Heidelberg

Germany

Preliminary Programme

Are you on social media? Post using #EMBOCelegans and don’t forget to tag @EMBLEvents.

  • 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 (Onboarding) – Monday 29 May 2024
Time (Europe/Berlin)SpeakerLocation
14:30 – 16:00Onboarding session (access to eCampus learning platform), introduction on Zoom
– introduction to the course
– materials to be used and expectations from the participants
– overview of the tools used during the course
EMBL eCampus
Day 1 – Sunday 9 June 2024
Time (Europe/Berlin)SpeakerLocation
09:45 – 10:00Bus from hotel to EMBL ATC EntranceISG Hotel bus stop
10:00 – 10:30Health and safety briefingCourtyard Room A & B
10:30 – 13:30Optional Bootcamp A or B
Option A: Basic C. elegans methodology: maintenance, propagation, decontamination

Trainers: Simone Köhler – EMBL Heidelberg, Germany
Georgia Rapti – EMBL Heidelberg, Germany
Cristina Piñeiro López – EMBL Heidelberg, Germany
Francesca Caroti – EMBL Heidelberg, Germany
Option B: Basic principles for image analysis
Trainer: Pavak Shah – University of California, Los Angeles, USA
13:45 – 14:00Bus from EMBL ATC Entrance to hotel ATC Entrance
15:00 – 15:30ISG Hotel registrationISG Hotel
15:30 – 15:45Welcome
Simone Köhler – EMBL Heidelberg, Germany
Georgia Rapti – EMBL Heidelberg, Germany
ISG Hotel
15:45 – 16:15Flash talks (1 min per participant)ISG Hotel
16:15 – 17:15Challenges & expectations for the course (all participants)ISG Hotel
17:15 – 17:30Coffee breakISG Hotel
17:30 – 17:45Course overview
Simone Köhler – EMBL Heidelberg, Germany
Georgia Rapti – EMBL Heidelberg, Germany
ISG Hotel
17:45 – 18:45Introduction to useful web resources and databases for C.elegans research
Introduction on responsible conduct of research

Simone Köhler – EMBL Heidelberg, Germany
Georgia Rapti – EMBL Heidelberg, Germany
ISG Hotel
18:45 – 19:00BreakISG Hotel
19:00DinnerISG Hotel
Day 2 – Monday 10 June 2024
Time (Europe/Berlin)SpeakerLocation
08:40 – 08:50Bus to EMBL ATC EntranceISG Hotel bus stop
08:55 – 09:00Overview of the dayCourtyard Room A & B
09:00 – 09:30Lecture: Functional organisation of the nucleus
Susan Gasser – University of Lausanne and ISREC Foundation, Switzerland
Courtyard Room A & B
09:30 – 09:45Q&A after the lectureCourtyard Room A & B
09:45 – 10:15Lecture: Genome silencing
Christian Frøkjær-Jensen – King Abdullah University, Saudi Arabia
Courtyard Room A & B
10:15 – 10:30Q&A after the lectureCourtyard Room A & B
10:30 – 11:00Coffee breakCourtyard Room A & B
11:00 – 11:30Lecture: Evolution of C. elegans
Marie-Anne Félix – Institut Biologie Ecole Normale Superieure, France
Courtyard Room A & B
11:30 – 11:45Q&A after the lectureCourtyard Room A & B
11:45 – 12:15Health and safety briefingCourtyard Room A & B
12:15 – 13:15Lunch breakEMBL Canteen
13:15 – 19:30Practical: Methods of genome manipulation
Station 1: Screening RNAi / mutagenesis
Trainer: Francesca Caroti – EMBL Heidelberg, Germany
Georgia Rapti – EMBL Heidelberg, Germany
Station 2: Transgenesis (sample preparation, injection)
Trainer: Simone Köhler – EMBL Heidelberg, Germany
Cristina Piñeiro López – EMBL Heidelberg, Germany
Station 3: Design for CRISPRs, MoSCIs, arrays
Trainer: Christian Frœkjær-Jensen – King Abdullah University, Saudi Arabia
Alex Paix – EMBL Heidelberg, Germany
Station 4: In silico Lineaging / Transcriptomics – design, analysis
Trainer: Priya Sivaramakrishnan – University of Pennsylvania, USA
helper on site
19:30 – 20:30Dinner with guided discussion on “Publishing” and “Grant writing”EMBL Canteen
20:30Bus to ISG HotelATC Entrance
Day 3 – Tuesday 11 June 2024
Time (Europe/Berlin)SpeakerLocation
08:40 – 08:55Bus to EMBL ATC EntranceISG Hotel bus stop
08:55 – 09:00Overview of the dayCourtyard Room A & B
09:00 – 09:30Lecture: Self-organization in meiosis
Simone Köhler – EMBL Heidelberg, Germany
Courtyard Room A & B
09:30 – 09:45Q&A after the lectureCourtyard Room A & B
09:45 – 10:15Lecture: Cell fate and the cell cycle of the early embryo
Pavak Shah – University of California, Los Angeles, USA
Courtyard Room A & B
10:15 – 10:30Q&A after the lectureCourtyard Room A & B
10:30 – 11:00Coffee breakCourtyard Room A & B
11:00 – 12:45Practical: Methods of genome manipulation
Station 1: Screening RNAi / mutagenesis
Trainer: Francesca Caroti – EMBL Heidelberg, Germany
Georgia Rapti – EMBL Heidelberg, Germany
Station 2: Transgenesis (sample preparation, injection)
Trainer: Simone Köhler – EMBL Heidelberg, Germany
Cristina Piñeiro López – EMBL Heidelberg, Germany
Station 3: Design for CRISPRs, MoSCIs, arrays
Trainer: Christian Frœkjær-Jensen – King Abdullah University, Saudi Arabia
Alex Paix – EMBL Heidelberg, Germany
Station 4: In silico Lineaging / Transcriptomics – design, analysis
Trainer: Priya Sivaramakrishnan – University of Pennsylvania, USA
helper on site
12:45 – 13:45Lunch break with guided discussion on “Choosing a postdoc”, “Getting a research PI position”EMBL Canteen
13:45 – 16:45Practical: Imaging cells and molecules
Station 1: Live imaging and Lineaging
Trainer: Francesca Caroti – EMBL Heidelberg, Germany
Georgia Rapti – EMBL Heidelberg, Germany
Pavak Shah – University of California, Los Angeles, USA
Station 2: Expansion Microscopy
Trainer: Yangning Lu – MIT McGovern Institute, USA
Simone Köhler – EMBL Heidelberg, Germany
Cristina Piñeiro López – EMBL Heidelberg, Germany
Station 3: Basics in Optogenetics
Trainer: Inka Busack – Biotechnology Center, Germany
helper
Station 4: Electron Microscopy
Trainer: Mandy Boermel – EMBL Heidelberg, Germany
Rachel Mellwig – EMBL Heidelberg, Germany
Paolo Ronchi – EMBL Heidelberg, Germany
16:45 – 17:15Coffee breakCourtyard Room A & B
17:15 – 17:45Lecture: Expansion microscopy of C. elegans
Ed Boyden – MIT McGovern Institute, USA (Virtual Speaker)
Courtyard Room A & B
17:45 – 18:00Q&A after the lectureCourtyard Room A & B
18:00 – 18:15Coffee breakCourtyard Room A & B
18:15 – 19:15Poster session 1 (odd numbers)Helix A
19:15 – 20:45Dinner with poster networking (All posters)Helix A
20:45Bus to ISG HotelATC Entrance
Day 4 – Wednesday 12 June 2024
Time (Europe/Berlin)SpeakerLocation
08:40 – 08:55Bus to EMBL ATC EntranceISG Hotel bus stop
08:55 – 09:00Overview of the dayCourtyard Room A & B
09:00 – 09:30Lecture: Cell division and differentiation
Sander van den Heuvel – Utrecht University, The Netherland
Courtyard Room A & B
09:30 – 09:45Q&A after the lectureCourtyard Room A & B
09:45 – 10:15Lecture: Genotype-to-phenotype relationship
Michalis Barkoulas – Imperial College, UK
Courtyard Room A & B
10:15 – 10:30Q&A after the lectureCourtyard Room A & B
10:30 – 10:45Coffee breakCourtyard Room A & B
10:45 – 11:15Lecture: Molecular Promotion of Healthy Aging
Monica Driscoll – Rutgers University, USA
Courtyard Room A & B
11:15 – 11:30Q&A after the lectureCourtyard Room A & B
10:30 – 11:30Poster session 2 (even numbers)Helix A
11:30 – 12:30Lunch break with guided discussion on “Science policy & communication”, “Choosing a postdoc”EMBL Canteen
12:30 – 19:00Practical: Imaging cells and molecules
Station 1: Live imaging and Lineaging
Trainer: Francesca Caroti – EMBL Heidelberg, Germany
Georgia Rapti – EMBL Heidelberg, Germany
Pavak Shah – University of California, Los Angeles, USA
Station 2: Expansion Microscopy
Trainer: Yangning Lu – MIT McGovern Institute, USA
Simone Köhler – EMBL Heidelberg, Germany
Cristina Piñeiro López – EMBL Heidelberg, Germany
Station 3: Basics in Optogenetics
Trainer: Inka Busack – Biotechnology Center, Germany
helper
Station 4: Electron Microscopy
Trainer: Mandy Boermel – EMBL Heidelberg, Germany
Rachel Mellwig – EMBL Heidelberg, Germany
Paolo Ronchi – EMBL Heidelberg, Germany
19:00 – 20:30Dinner with poster networking (All posters)Helix A
20:30Bus to ISG HotelATC Entrance
Day 5 – Thursday 13 June 2024
Time (Europe/Berlin)SpeakerLocation
08:40 – 08:55Bus to EMBL ATC EntranceISG Hotel bus stop
08:55 – 09:00Overview of the dayCourtyard Room A & B
09:00 – 12:00Practical: Imaging cells and molecules – Part 3: 1 of 4 stations. Students rotate in 4 independent stations of 3 h each, all stations provided for 2 days, 2 trainers per station; 4 students per station)

Station 1: Live imaging and Lineaging
Trainer: Francesca Caroti – EMBL Heidelberg, Germany
Georgia Rapti – EMBL Heidelberg, Germany
Pavak Shah – University of California, Los Angeles, USA
Station 2: Expansion Microscopy
Trainer: Yangning Lu – MIT McGovern Institute, USA
Simone Köhler – EMBL Heidelberg, Germany
Cristina Piñeiro López – EMBL Heidelberg, Germany
Station 3: Basics in Optogenetics
Trainer: Inka Busack – Biotechnology Center, Germany
helper
Station 4: Electron Microscopy
Trainer: Mandy Boermel – EMBL Heidelberg, Germany
Rachel Mellwig – EMBL Heidelberg, Germany
Paolo Ronchi – EMBL Heidelberg, Germany
12:00 – 13:00Lunch break with guided discussion on “Starting a junior PI position”, “Positions in PUI institutions”EMBL Canteen
13:00 – 16:00Practical: Advanced image analysis tools (Part 1)
Station 1: Deconvolution
Trainer: Marko Lampe – EMBL Heidelberg, Germany
Station 3: Lineage tracing & analysis
Trainer: Pavak Shah – University of California, Los Angeles, USA
Station 4: Image analysis for optogenetics
Trainer: Inka Busack – Biotechnology Center, Germany
Station 5: Analysis of EM imaging
Trainer: Ben Mulcahy – Lunenfeld-Tanenbaum Research Institute, Canada (Virtual speaker)
16:00 – 16:30Coffee breakCourtyard Room A & B
16:30 – 17:00Lecture: Signal transduction during C. elegans development
Alex Hajnal – University of Zurich, Switzerland (Virtual speaker)
Courtyard Room A & B
17:00 – 17:15Q&A after the lectureCourtyard Room A & B
17:15 – 17:45Lecture: Neurogenetics of sensory behaviors
Piali Sengupta – Brandeis University, USA (Virtual Speaker)
Courtyard Room A & B
17:45 – 18:00Q&A after the lectureCourtyard Room A & B
18:00 – 18:30Coffee breakCourtyard Room A & B
18:30 – 19:00Lecture: Cytoskeletal assembly and dynamics in neurodevelopment
Dhanya Cheerambathur The University of Edinburgh, UK
Courtyard Room A & B
19:00 – 19:15Q&A after the lectureCourtyard Room A & B
19:15 – 20:15DinnerEMBL Canteen
20:15Bus to ISG HotelATC Entrance
Day 6 – Friday 14 June 2024
Time (Europe/Berlin)SpeakerLocation
08:40 – 08:55Bus to EMBL ATC EntranceISG Hotel bus stop
08:55 – 09:00Overview of the dayCourtyard Room A & B
09:00 – 12:00Practical: Advanced image analysis tools (Part 2)
Station 1: Deconvolution
Trainer: Marko Lampe – EMBL Heidelberg, Germany
Station 2: Automated membrane tracing
Trainer: Zhongying Zhao
Station 3: Lineage tracing & analysis
Trainer: Pavak Shah – University of California, Los Angeles, USA
Station 4: Image analysis for optogenetics
Trainer: Inka Busack – Biotechnology Center, Germany
12:00 – 13:00LunchEMBL Canteen
13:00 – 13:30Lecture: Generation of neuronal diversity
Oliver Hobert – Columbia University, USA
Courtyard Room A & B
13:30 – 13:45Q&A after the lectureCourtyard Room A & B
13:45 – 14:15Coffee breakCourtyard Room A & B
14:15 – 16:45Practical: Advanced image analysis tools (Part 3)
Station 1: Deconvolution
Trainer: Marko Lampe – EMBL Heidelberg, Germany
Station 2: Automated membrane tracing
Trainer: Zhongying Zhao – Hong Kong Baptist University, Hong Kong (Virtual speaker)
Station 3: Lineage tracing & analysis
Trainer: Pavak Shah – University of California, Los Angeles, USA
Station 4: Image analysis for optogenetics
Trainer: Inka Busack – Biotechnology Center, Germany
Station 5: Analysis of EM imaging
Trainer: Ben Mulcahy – Lunenfeld-Tanenbaum Research Institute, Canada (Virtual speaker)
16:45 – 17:15Coffee breakCourtyard Room A & B
17:15 – 17:30Bus to downtownATC Entrance
17:30 – 19:00Free evening
19:00Dinner downtown
Day 7 – Saturday 15 June 2024
Time (Europe/Berlin)SpeakerLocation
09:40 – 09:55Bus to EMBL ATC EntranceISG Hotel bus stop
09:55 – 10:00Overview of the dayCourtyard Room A & B
10:00 – 10:30Lecture: Optogenetic manipulation of tissue activity
Henrik Bringmann – Biotechnology Center, Germany
Courtyard Room A & B
10:30 – 10:45Q&A after the lectureCourtyard Room A & B
10:45 – 11:15Coffee breakCourtyard Room A & B
11:15 – 11:45Lecture: Glia & neuron interactions in nervous system assembly
Georgia Rapti – EMBL Heidelberg, Germany
Courtyard Room A & B
11:45 – 12:00Q&A after the lectureCourtyard Room A & B
12:00 – 12:30Feedback session and closing remarksCourtyard Room A & B
12:30Bus from EMBL to Heidelberg city center/train station or Walk to ISGATC Entrance

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Sponsorship opportunities

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

Warning

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Please also note that:

  • EMBL never provides attendee lists for purchase. Any offers of such are fraudulent.
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  • 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: 9 - 15 Jun 2024

Location: EMBL Heidelberg

Venue: EMBL Advanced Training Centre

Organisers:

  • Henrik Bringmann
    Biotechnology Center, Germany
    • Simone Köhler
      EMBL Heidelberg, Germany

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

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