Course description
The advanced course Integrated Multi-Omics approaches for Improvement of Industrial Microbes aims to offer 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.
1 – 5 November 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 11 October 2021. Applicants will be handled in order of the date of receipt.
PROGRAMME
Programme 2021
| Monday, 1 November 2021 Theme: Omics technologies: Overview and state of the art |
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| 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, 2 November 2021 Theme: Mass spectrometry based proteomics & metabolomics techniques |
||
| 09.00 | Genome analyses III | Marcel van den Broek, Raúl A. Ortiz-Merino |
| 12.30 | Lunch | |
| 13.30 | Technology – Mass Spectrometry | Martin Pabst |
| 14.30 | High resolution proteomics approaches | Martin Pabst |
| 15.30 | Break | |
| 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, 3 November 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, 4 November 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, Maurien Oudshoorn |
| 16:30 | Radical Empiricism to improve microbe performance | Stefan de Kok |
| 17:30 | Evolution of Orbitrap mass spectrometry instrumentation | To Be Announced |
| 19:00 | Course dinner | |
| Friday, 5 November 2021 Theme: Future perspectives |
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| 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 Sebastián Gallego Murillo |
| 12.30 | Lunch | |
| 13.30 | Cell culture proteomics | Jeroen Demmers |
| 14.30 | Single cell proteomics To Be Announced | To Be Announced |
| 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 https://www.biotechnologycourses.nl
FEE
Deadline for registration is 11 October 2021
The course fee is:
| Early Bird | €2.500,-* |
| Regular Fee | €2.750,- |
| Small and medium-sized enterprises (SME/Startups/scaleups) | €1.750,-** |
| Small and medium-sized enterprises (SME/Startups/scaleups) of Biotech Campus Delft | €1.250,-** |
| PhD Students | €1.250,-** |
*To be eligible for the reduced early bird fee you need to register before 23 August 2021. If this date is exceeded, the regular fee applies.
**A limited number of fellowships is available for PhD students and SME’s (small/medium enterprise). Fellowships will be available on a first-come-first-serve basis. To apply as to one of these fellowships, please include a copy either of your registration as a PhD student from your university or a proof of the SME-status of the company you work at.
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 6 September 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
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
REGISTER
Please register for the Advanced Course Integrated Multi-Omics approaches for Improvement of Industrial Microbes
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