Advanced Course

Integrated Multi-Omics approaches for Improvement of Industrial Microbes

Course description

The advanced course Integrated Multi-Omics approaches for Improvement of Industrial Microbes aims to offers a coherent overview of current state of the art omics technologies, bridging the different cellular levels, i.e. metabolomics, fluxomics, transcriptomics and proteomics. It will be shown how integrated application of these technologies provides holistic, quantitative insights in cellular physiology. Finally, it will be demonstrated how targets for (further) improvement of industrial microbes can be identified through integration of omics data with modelling approaches.

To be announced 2021

Delft University of Technology, the Netherlands

A limited number of fellowships is available for PhD students (reduced fee).

THE COURSE

Advanced Course Integrated Multi-Omics approaches for Improvement of Industrial Microbes

This intensive, activating, one-week course aims at providing fundamental and applied knowledge in the field. To this end, the course is set up as an alternating program of expert lectures and exercises.

Especially, the course offers a coherent overview of current state of the art omics technologies, bridging the different cellular levels, i.e. metabolomics, fluxomics, transcriptomics and proteomics. It will be shown how integrated application of these technologies provides holistic, quantitative insights in cellular physiology. Finally, it will be demonstrated how targets for (further) improvement of industrial microbes can be identified through integration of omics data with modelling approaches.

The day themes are:
Day 1 – Omics technologies: Overview and state of the art.
Day 2 – Mass spectrometry based proteomics & metabolomics techniques
Day 3 – Fluxomics & Modelling approaches
Day 4 – Integration of omics data & Modelling approaches
Day 5 – Future perspectives

Lectures

Attention will be on a variety of themes:

  • Genome sequencing and analysis
  • Transcriptomics (incl. RNA sequencing)
  • Proteomics
  • Bioinformatics
  • Novel molecular tools and automated strain construction
  • Rapid sampling and quantitative analysis
  • Metabolite quantification and validation using
  • Isotope Dilution Mass Spectrometry, IDMS
  • Estimation of extra- and intracellular rates from experimental data
  • Kinetic modeling and approaches to handle parameter identification problems
  • Genomics in strain improvement (incl. metabolic and evolutionary engineering)

Exercises

Several exercises will be performed to familiarize the participants with the theory and practice and to illustrate the utility and utilization of bioinformatics, quantitative metabolomics and metabolic modeling. Especially, the participants will focus on analysis of next-generation sequence data, massive data handling, statistics, interpretation and visualisation of multi-omics data.

Study load

The course (including preparatory materials) is valued 41 hours of work.

Who should attend?

This Advanced Course is aimed at participants from industry, universities and research institutions who want to update and extend their theoretical knowledge and practical insight in multi-omics and modeling. The course is intended for postgraduates (MSc, PDEng, PhD), with a sound background in microbiology, microbial physiology, biotechnology, biochemistry or biochemical engineering, with a basic working knowledge in some of the other disciplines and an affinity to applied mathematics.

Course registration

Please register clicking the tab Register to attend the course. Deadline for application is 5 October 2020. Applicants will be handled in order of the date of receipt.

PROGRAMME

Preliminary Programme 2021

(with names as far as speakers accepted)

Monday, to be announced 2021
Theme: Omics technologies: Overview and state of the art
08.45 Registration
09.00 Short introduction on Surfaces and BioTech Delft Vincent Renken
09.10 Introduction, including motivation for multi-omix analysis Aljoscha Wahl
09.30 Genome insights in plant, microbial and fungal genomes using long-read sequencing technologies Alexander Wittenberg
10.30 Break
10.45 Introduction to genome analyses Marcel van den Broek, Raúl A. Ortiz-Merino
11.45 Genome analyses I Marcel van den Broek, Raúl A. Ortiz-Merino
12:30 Group picture and lunch
13.30 Genome analyses II Marcel van den Broek, Raúl A. Ortiz-Merino
17.30 RNA sequencing and transcriptomics Eduard Kerkhoven
18.30 Social drink and buffet
 
Tuesday, to be announced 2021
Theme: Mass spectrometry based proteomics & metabolomics techniques
09.00 Genome analyses III Marcel van den Broek, Raúl A. Ortiz-Merino
12.00 Break
12.15 Mass Spectrometry technologies – fundamentals Martin Pabst
13.00 Lunch
14.00 Large-scale proteomics approaches Martin Pabst
14.45 Break
15.00 Multi-omics to steer industrial metabolic pathway engineering and product development Maurien Olsthoorn
15.45 State-of-the-art metabolomics Walter van Gulik
16.45  Break
 17:00 Experimental design for quantitative metabolomics (with tracer stories) Aljoscha Wahl
Wednesday, to be announced 2021
Theme: Fluxomics & Modelling approaches
09.00 Exercise with open source tools Aljoscha Wahl
11.15 Break
11.30 Genome-scale modelling for in-silico analysis of metabolism Bas Teusink
12.30 Lunch
13.30 Continuation: Exercise with open source tools Aljoscha Wahl
14.30 Industrial applications (including 13 MFA) Aljoscha Wahl
15:30 Break
15:45 E. Coli resource allocation  (experimental) Greg Bokinsky
16:45 Resource allocation modelling (S. cerevisiae, E. coli) Aljoscha Wahl
Thursday, to be announced 2021
Theme: Integration of omics data & Modelling approaches
09.00 Regulatory functions of the metabolomics network Frank Bruggeman
10.00 Break
10.15 Kinetic modelling approaches – open source tools (Copasi) Aljoscha Wahl, Walter van Gulik
12.30 Lunch
13.30 Continuation: Kinetic modelling approaches – open source tools Aljoscha Wahl
15.15 Break
15:30 Multi omics in industrial environment (with examples) Liang Wu
16:30 Radical Empiricism to improve microbe performance Stefan de Kok
17:30 Evolution of Orbitrap mass spectrometry instrumentation Samy Memmi
19:00 Course dinner
Friday, to be announced 2021
Theme: Future perspectives
09.30 Machine learning for industrial biotechnology Hector Garcia Martin
10.30 Break
10.40 Leveraging cell-to-cell heterogeneity to gain functional insight into microbial metabolism and physiology Johan van Heerden
11.30 Ex vivo expansion of erythroblasts: Media and culture condition optimization using untargeted metabolomics Joan Gallego Murillo
12.30 Lunch
13.30 Cell culture proteomics Jeroen Demmers
14.30 Single cell proteomics Samy Memmi
15.30 Panel discussion, Evaluation, Drinks
LOCATION

The course will be held at:

Faculty of Applied Sciences (building 58)
Department of Biotechnology
Delft University of Technology
Van der Maasweg 9
2629 HZ Delft
The Netherlands
P +31 (0)15 278 1922
F +31 (0)15 278 2355
E BiotechDelft@tudelft.nl
W http://www.biotechnologycourses.nl


FEE

Deadline for registration is to be announced 2021

The course fee is:

Early Bird €2.500,-*
Regular Fee €2.750,-
PhD Students €1.250,-**

*To be eligible for the reduced early bird fee you need to register before to be announced 2021. If this date is exceeded, the regular fee applies.

**A limited number of fellowships is available for PhD students. To apply, please include a copy of your registration as a PhD student from your university.

The fee includes course materials, lunches and the buffets and the course dinners as indicated on the program. The fee does not cover other meals or lodging. Hotel accommodation can be arranged at your request.

The course fee is preferably paid by bank transfer. Payment by PayPal is possible. TU Delft employees can use their internal (project) code.

Preparatory texts will be sent one month before start of the course and after receipt of the course fee. The complete set of course books will be supplied at the start of the course.

In the event of your cancellation before to be announced 2021, a full refund will be granted. After this date, a 25% fee charge can be made.

Delay of payment past the final deadline as indicated on the invoice may result in cancellation of entry to the course. Re-entry is only possible in case of vacancies and the regular fee will be applied. Payment terms and deadlines will be indicated on the invoice and/or provided in an e-mail after registration, but the course fee should always be paid before the start of the course.

When the number of participants is too low to have a fruitful course, the Institute BioTech Delft will cancel the event no later than six weeks before the start of the course. The course fee will be reimbursed within three weeks after cancellation. In case a speaker will not be able to present his/her lecture, due to unforeseen circumstances, BioTech Delft will arrange an equivalent replacement.

BROCHURES

Not yet available

Expected end of January 2020 

LECTURERS

Course board

Dr. Jean-Marc Daran

Industrial Microbiology, Department of Biotechnology, Delft University of Technology, the Netherlands

Dr. Walter van Gulik

Cell Systems Engineering, Department of Biotechnology, Delft University of Technology, the Netherlands

Dr. Martin Pabst

Cell Systems Engineering, Delft University of Technology, Department of Biotechnology, Delft, the Netherlands

Dr. Aljoscha Wahl

Aljoscha Wahl is assistant professor at TU Delft with a focus on fluxomics and metabolomics in eukaryotic microorganisms. He studies the interactions of metabolism and its regulation under dynamic environmental conditions. Dr. Wahl contributes to experimental and computational approaches for (1) 13C flux analysis under metabolic dynamic conditions, (2) compartmentalized fluxomics and metabolomics using intracellular sensor reactions, (3) transport system studies. He teaches several master courses at TUD and was active in the iGEM competition (supervisor of the TUD team and organization of the European Jamboree). In addition, he is member of the editorial board of Applied and Environmental Microbiology (AEM).

Guest lecturers

Greg Bokinsky

Department of Bionanoscience Delft University of Technology
Delft, the Netherlands

Marcel van den Broek

Industrial Microbial Biotechnology
Delft University of Technology
Delft, the Netherlands

Johan van Heerden

Raúl A. Ortiz Merino

Industrial Microbial Biotechnology
Delft University of Technology
Delft, the Netherlands

Eduard Kerkhoven

Stefan de Kok

Zymergen
Emeryvill, USA

Hector Garcia Martin

Joan Gallego Murillo

Bioprocess Engineering
Delft University of Technology
Delft, the Netherlands

Maurien Olsthoorn

Corporate Science Fellow, Analysis & Characterization
DSM, Delft, the Netherlands

Jeroen Demmers

Bas Teusink

Vrije Universiteit Amsterdam
Systems Bioinformatics group (AIMMS)
Amsterdam, the Netherlands

Liang Wu

DSM, Delft, The Netherlands

Alexander Wittenberg

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