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Method Training Workshops

Theoretical and hands-on experience methodological training will provide basic knowledge, background, application fields, protocols and valuable tips taught by specialists. Depending on their individual research program, MB Train fellows will select training courses from the yearly program to complement their own methodological profile and to cover the entire spectrum of molecular-biochemical, biophysical and cellular biology.
At least two method training courses reflecting the interdisciplinary areas of the CRC (X-ray crystallography, protein mass spectrometry, Fluorescence imaging, Liquid and solid state NMR, Structural Bioinformatics, Single Molecule Spectroscopy and Nanoscopy, Cell biology, etc.) should be attended during the doctorate.

Currently offered courses

2. Transmission Electron Microscopy – A High-Resolution Imaging Technique to Visualize your Specimen at an Ultrastructural Level
This course will deal with the basics of transmission electron microscopy, especially specimen preparation. The participants will gain insight into Negativ Stain and the conventional preparation of biological specimens in the context of immunogold labeling. Furthermore, they will also have hands-on sessions at two different transmission electron microscopes, Zeiss TEM902 and JEOL JEM-2100Plus.

Teacher: Miriam Bäumers
Date: June
min/max number of participants: min. 2; maximum 4. If needed we can offer an additional course.
Email for registration: sfb1208@hhu.de, subject: Transmission Electron Microscopy CAi
Deadline for registration: end of April

3. Scanning Electron Microscopy – A Tool to Study the Surface of your Specimen in Detail
This course will focus on scanning electron microscopy (SEM). To gain insight into SEM, the participants will explore the entire process, from the conventional preparation of a biological sample to image acquisition. Therefore, they will also have hands-on sessions at the ZEISS Supra 55VP.

Teachers: Miriam Bäumers, Steffen Köhler
Date: June
min/max number of participants: min. 2; maximum 4. If needed we can offer an additional course.
Email for registration: sfb1208@hhu.de, subject: Scanning Electron Microscopy CAi
Deadline for registration: end of April

4. Basic & Advanced Fluorescence Microscopy
In this course different fluorescence microscopy techniques will be discussed and introduced. On the first day the theoretical background will be introduced, followed by an introduction to confocal microscopy as the most commonly used technique on the second day. The rest of the second day and possibly the third day is intended to deal with actual projects / challenges of the attendees and possibly to apply more advanced techniques depending on the samples and needs.

Teachers: Dr. Sebastian Hänsch - CAi
Date:  June / July (2x3 days each)
min/max number of participants: max 2x4 person each
Email for registration:  
Deadline for registration: 05.05.2023


Structural studies in modern biology
How can we use structural techniques to explain biological phenomena.  Insight in x-ray crystallography, SAXS, Modelling and Simulations.
Basic hands-on training in X-ray crystallography, SAXS, modeling and simulations.

Topics of the course: 

  • what can the techniques used for
  • introduction and basics for X-ray crystallography, SAXS and Modeling
  • sample quality for X-Ray and SAXS, buffer requirements and limitations.
  • practical sessions about selected topics in X-ray crystallography and SAXS
  • data evaluation and analysis
  • what can you learn from these data
  • introduction to modeling techniques and different tools
  • assessing model quality
  • practical sessions about how to get a protein model
  • presentation of advanced techniques, e.g., docking, MD, QSAR

Lecturers: Sander Smits , Astrid Port, Elisa Constanzi, Jens Reiners, Christoph Gertzen
Date : 12.-16.06.2023, 09:00 a.m. until 17:00 p.m.
Room: 25.41.00.26 (ZIM) and CSS labs (26.24.01.024)
Number of participants: max. 10
Information and Email for registration : https://www.css.hhu.de/en/
Deadline for registration : 15.05.2023


Optogenetics course  - open offer of AG Zurbriggen (open in terms of timing)
Optogenetic approaches enable the control of (sub)cellular processes with light. The possibility to manipulate pathways and cell physiology at highest spatiotemporal resolution, reversibly and with minimised invasiveness is revolutionising neurobiology and cell research. The course will introduce the ECRs into the fundamental concepts and strategies of optogenetics in prokaryotic and eukaryotic biological systems. They will implement in the lab these approaches for the understanding and control of cellular processes in plant and mammalian cells. They will implement LED, laser and digital micro mirror device-based light patterning systems, and evaluate the optogenetic activity in cell culture by confocal microscopy.

Teachers: AG Matias Zurbriggen
Date: 21.-23.08.2023
Min/Max number of participants: 6-10
Email for registration:
Deadline for registration: 22.05.2023
 


Workshop: Basics of 3D Printing and its Applications in Life Sciences

Learning Competencies:
After completing this seminar, students will be able to
· understand the concepts and principles of different 3D printing techniques, their applications in life sciences as well as their limitations
· design objects to be 3D printed by FFF 3D printers
· use (open source) software for preparation of the objects to be printed (=slicing)
· print objects, postprocess them, evaluate them and implement needed changes.

 Description
This seminar will introduce students to 3D printing, designing of objects for 3D printing with a focus on applications in life sciences.  The students will learn the process of the 3D printing based on provided 3D printed objects as well as by designing, printing and postprocessing their own objects. The students will use 3D printing to design objects to help people in their daily routine in the lab. The focus will be mainly on FFF 3D printing technique, other available techniques will be introduced.
The seminar is suitable especially for beginners.

Tools
3D printers: Ultimaker S5 and Prusa MK3S+, including suitable printing materials (=filament) -> supplied by the lecturers
On day 2 and 3, each student is expected to bring and work on their own laptop - slicing and modelling objects for 3D printing. The software for modelling has higher system requirements, otherwise it is laggy or crashes. The system requirements are in the link below: https://www.autodesk.com/support/technical/article/caas/sfdcarticles/sfdcarticles/System-requirements-for-Autodesk-Fusion-360.html

 Software
CAD design software - Autodesk Fusion: student or hobbyist license (free); Slicing software: Cura and Prusaslicer (free)

In the final lesson the students will present the design process, applications and functionality, discuss used settings, critically assess their object and share the lessons learned from their work in a form of an oral presentation (15 min + discussion)
Attendance in all classes, individual work and presenting the outcomes of your work at the end of the course are obligatory to pass this course.

 Schedule
Day 1 - 28.08. - 09:30-12:30 - Introduction to 3D printing
Day 2 - 29.08. - 09:30-12:30 - Principles of slicing, slicing in PrusaSlicer & Cura, introduction to 3D printing materials
Day 3 - 30.08. - 09:30-12:30 - Print quality assesment, principles of 3D printing-optimized design, designing in Fusion360
Day 4 - 08.09. - 09:30-12:30 - Presentation of your projects

 Between 30.08. and 01.09. the students will design their own object (working in pairs) and send it to the lecturers for feedback. Then the students will come in person, have the object revised, slice it and print it (until 07.09.2023). On 08.09.2023, the students will present their designs and printed objects to the group.

Previous courses

GUV Method course

In this course you will learn how to produce synthetic membranes in the form of giant unilamellar vesicles (GUVs). Furthermore we will study the interaction of recombinant proteins with these GUVs, either your own protein, or the ones we currently study.

Teacher(s): Jan Galle, Fabienne Kocher, Sebastian Wintgens
Date: 24.05. -26.05.2023
min/max number of participants: 4-6
Email for registration:
Deadline for registration: 30.04.2022


Courses of Center for Advanced Imaging (CAi)

1. Integrated image analysis and data management with Fiji, CellProfiler and OMERO.
Introduction to image analysis with Fiji, CellProfiler and OMERO.
The course focus is on scientific digital images, image analysis with Fiji and CellProfiler and research data management. More specifically, you will learn how to create and apply series of operation on images with the macro language of Fiji and learn how to analyse in depth images content with CellProfiler. Finally, you will learn how to handle imaging data with OMERO and how connect it to such image analysis tools. For this course, students should have a laptop and are invited to bring an image dataset of their own.

Teachers: Tom Boissonnet, Anna Hamacher, Sebastian Hänsch
Date (3 days, once): Tuesday, 9th to Thursday, 11th of May
Min/Max number of participants: 4-12
Email for registration:
Deadline for registration: 26 th of April, 2023

 

Molecular Dynamics: Hands-On Workshop
Predicting the effects of, e.g., a mutation, a change in the pH, binding of a ligand or to a membrane on the structure, dynamics and function of a protein is possible thanks to molecular dynamics simulations. Anyone with basic molecular biology and physics background and a general interest in computer simulations can learn how to setup and run computational modeling and dynamics. Participants of this course will use popular open source tools and techniques necessary for conducting and analyzing molecular dynamics simulations.

Lecturer(s): Birgit Strodel, Jennifer Loschwitz
Date: 13.-17.03.2023
min/max number of participants: 1/10


Live cell metabolic assay platform - Introduction to Agilent Seahorse XFe96 Analyzer
One hands-on experiment is performed including technical introduction to the Seahorse Analyzer and Data Analysis.
Experimental setup includes application of the Mito Stress Test Kit for testing mitochondrial activity.

Lecturers: Dr. Nahal Brocke-Ahmadinejad, Andre Wolsing, Yulia Schaumkessel
Date: 16./17.03.2023
First day ~3 h second day ~4 h.
min/max number of participants: 2/6


Properties and methods_small GTPases
Prof. Reza Ahmadian will explain the biological activities, mutant phenotypes and biochemical assays for studying the various small GTPases for cellular signaling.
The workshop is interactive, with chalkboard.

Lecturer: Reze Ahmadian
Date: March 6th
Remaining slots: 8


Architecture and function of proteins and other biomolecules -- insights via X-ray crystallography
(Module V530)
Description: This module is designed for students who are curious to understand how the application of X-rays reveals atomic resolution
details in the structures of biomolecules. Students will learn the basics of X-ray crystallography, including the essential steps of
crystal structure determination, from crystallization of macromolecules to generation and validation of structural models. The knowledge
acquired in this module will render them capable of analyzing publications on macromolecular structure and function and
critically assessing methodology and interpretation of results.

Teachers: R. Batra-Safferling, A. Cukkemane, J. Labahn, O.H. Weiergräber
Date: 16.01.-27.01.2023


add-on to V530: Lecture with exercises: Mathematical foundations of X-ray crystallography

Description: This course is designed as an add-on to V530 and will provide additional information on the mathematical background
relevant to X-ray crystallography and related fields. The knowledge acquired will be consolidated by practical exercises.

Teacher: J. Labahn
Date: 30.01.-02.02.2023


Introduction into and fun facts about solid phase peptide synthesis - for chemists, biologists and everyone who is interested
About 70 years ago, solid phase peptide synthesis has revolutionized access to defined biomolecules and since then impacted not only chemistry but also biology and medicine. Fundamental concepts of solid phase peptide synthesis have also enabled the synthesis of oligonucleotides and oligosaccharides - and now are used to even derive molecules that go beyond the natural structures. The 2 hour lecture will introduce key concepts and the general strategy of solid phase synthesis highlighting also some modern developments and trends.

Lecturer: Laura Hartmann
Duration: 2 h Lecture
Date: January 19th, 2023
Location: 26.24.U1.20


Workshop on 3D Printing in Life Sciences
This seminar will introduce 3D printing, designing of objects for 3D printing with a focus on applications in life sciences. You will learn the process of the 3D printing based on provided 3D printed objects as well as by designing, printing and postprocessing their own objects. The students will be encouraged to use 3D printing to design objects to help people in their daily routine in the lab.

The focus will be mainly on FDM/FFF 3D printing technique, other available techniques will be introduced.
The seminar is suitable especially for beginners.

Learning Competencies: After completing this seminar, you will be able to
-understand the concepts and principles of different 3D printing techniques, their applications in life sciences as well as their limitations
-design objects to be 3D printed, choose a suitable 3D printing technology
- use (open source) software for preparation of the objects to be printed (=slicing)
- print objects, postprocess them, evaluate them and implement needed changes.

Tools: 3D printers: Ultimaker S5 and Prusa MK3S+, including suitable printing materials (=filament)
Software: CAD design software - Autodesk Fusion: student or hobbyist license (free)
Slicing software: Cura and Prusaslicer (free)

In the final lesson the students will present the design process, applications and functionality, discuss used settings, critically assess their object and share the lessons learned from their work in a form of an oral presentation (15 min + discussion).

Attendance in all classes, individual work and presenting the outcomes of your work at the end of the course are obligatory to pass this course.

Schedule:
Day 0 - premeeting 19.08.2022:  13:30-14:30 (online; obligatory for participation) 

Day 1 - 22.08.2022 - 13:00-16:00 - (in person, seminar room 26.44.U1.022)
Day 2 - 23.08.2022 - 13:00-16:00 - (online)
Day 3 - 24.08.2022 - 13:00-16:00 - (online)
Day 4 - 06.09.2022 - 14:30-16:30 - (in person, seminar room 26.44.U1.022):

There is a longer break between days 3 and 4 to give everyone time to design their own object, get feedback, revise and have it printed. At the last meeting, the designs and printed objects will be presented to the group.

Registration: guido.grossmann@hhu.de


Visualization of protein structures with Pymol - Introduction

Lecturers: Lutz Schmitt, Sander Smits
Date: 17.12.2021,
from 9-12 am in room 25.41 (ZIM) U1.R22.
Registration: CRC 1208 office (sfb1208@hhu.de)


Basic Electron Microscopy: Negative Staining
This course will deal with the basic knowledge of electron microscopy. You will not only perform negative staining to prepare samples, you will also have hands-on sessions at two different transmission electron microscopes, Zeiss TEM902 and JEOL JEM-2100Plus. We encourage you to bring your own sample. If so, just give us notice.
To make the course as effective as possible the number of participants is limited to a maximum of 4 persons. If there is any demand, we would offer an additional course.

Course 1: 16th -17th of November, 9.30am-  4pm
Course 2: 23rd –24th November, 9.30am - 4pm
Course 3: 25th – 26th November, 9.30am - 4pm

Deadline for registration is: November, 5th (email to: miriam.baeumers@hhu.de)


Molecular Dynamics: Hands-On Workshop
Predicting the effects of, e.g., a mutation, a change in the pH, binding of a ligand or to a membrane on the structure, dynamics and function of a protein is possible thanks to molecular dy-
namics simulations. Anyone with basic molecular biology and physics background and a general interest in computer simulations can setup and run computational modeling and dynamics
“experiments”.
Objectives:
Participants will use popular open source tools and techniques necessary for conducting
successful molecular dynamics experiments.

Who should attend:
Researchers and students interested in learning tools to explore, visualize and understand
biomolecular structures and their functions in three dimensions.

Who will teach:
Members of the Strodel lab: Prof. Birgit Strodel, Anna Jäckering, Lara Scharbert, Moritz Schäffler
14-18 March 2022, 09:30-16:00
Schedule:

09:30 - 11:00 Lectures on the theory of MD simulations
11:00 - 16:00 Hands-On Sessions (Basic Linux commands / Visualization of proteins with VMD /
Setting up and running an MD simulation / Analysis of MD simulations)
Where: Computer room
in the self-study centre (building 26.21)


Online course - Sample preparation and introduction into mass spectrometry - 2nd calendar week 2021
Dr. Nina Prescher, Dr. Anja Stefanski, Prof. Kai Stühler

Subjects & Dates:
Day 1:  13. Jan. 2021 - 4 hours - 10 a.m.–2 p.m. - "Sample preparation for MS analysis"
Day 2:  14. Jan. 2021 - 2 hours - 10 a.m.-12 p.m. - "MS introduction, protein ID"
Day 3:  15. Jan. 2021 -  1 hour -  10 a.m.–11 p.m. - "MS live demo"

Registration: Please contact Dr. Nina Prescher, postdoc in the Z01 project (
The Link for the online course will be send in January by the organizing group.
Registration deadline: 10. January 2021


Due to the restrictions in attendance, no methodology courses will be offered in 2020.


Status: 12 December 2022

"Production of synthetic membranes in the form of giant unilamellar vesicles (GUVs) and interaction studies of recombinant proteins with GUVs "
Sven Gould (Molekulare Evolution) / Johannes Hegemann (Funktionelle Genomforschung der Mikroorganismen)
Thorsten Eierhoff, Jan Galle , Philipp Hanisch

Requirements: No previous experience is required
Objectives:
Theoretical: first approach to the topic of synthetic membranes,
practical: learning basic techniques for the production of GUVs.
Description:
Participants will learn various techniques for making GUVs, as an example of a synthetic membrane model. Using various membrane/ lipid interacting proteins, membrane binding, dynamics, curvature, pore formation, and lipid translocation in GUVs will be studied by confocal microscopy. If possible, participants should also bring their own labeled and functional (!) Proteins (e.g., Alexa488 or fluorescein labeled). Further, it would be helpful to have information about possible lipid interaction partners (e.g., via lipid strip testing).
Dates: 3 days, 9.-11. October 2018
Registration: eierhoff@hhu.de or Jan.Galle@hhu.de
Registration deadline: 21.09.2018
Number of participants: max. 6
Location: 25.12/00.32 and 25.02/00.21

 

Special Mercartor Workshop:
" Nutrient transport regulation" & " Publishing research and research possibilities in Japan"

" Nutrient transport regulation"
- theoretical modeling
- protein translation regulation
- nutrient sensing approaches

" Publishing research and research possibilities in Japan"
- research publication, publication procedures and analysis of an example
- Japanese research infrastructure and funding

Registration via SFB 1208 office (email)

Working with eukaryotic microorganisms (Hands-on course using mainly S. cerevisiae as a model; basic methods course for low level of experience in this field) Dr. Schipper, Dr. Pohlmann, Prof. Dr. Feldbrügge Duration and dates: 3 days, 27.08., 03.09. and 10.09. Location: HHU, Institute for Microbiology Number of participants: max. 12 Registration via SFB office Registration deadline: 03.08.2018


NMR-Workshop
Dr. Philipp Neudecker
This course will give theoretical and practical insights into solution NMR spectroscopy.
No previous experience is required.
* Note that part (three days) of the course will be shared with M4414.
Therefore, the course will be given in german.
Dates: Monday 09.07.2018 - Friday 13.07.2018 , 9 a.m. - 5:30 p.m.
Registration:
Registration deadline: 29.6.2018
Number of participants: 3
Location: FZ Jülich (Shuttle Bus)


"Gene expression, RT-qPCR"
Prof. Petra Bauer
This course addresses to persons that intend using RT-qPCR in their project.
No previous experience is required.
You will learn how to use RT-qPCR and how to analyze and present gene expression data.
* Note that this course is part of M4450.
There is the possibility to participate in the theoretical part and analyze own cDNA samples and qPCR data during or after the course on a flexible basis.
In this case it is not necessary to be present during the week the whole days.

Dates:
Monday 25.06.2018 - Friday 29.06.2018 , 9 a.m. - 5 p.m.
Registration: 
Registration deadline: 20.6.2018
Number of participants:  4
Location: 26.13.02.11

Mercartor Module - Part 2 (practical module)
"Plant Biophysics - Membrane Biophysics"

given by our Mercartor Fellow Prof. Ingo Dreyer, University of TALCA, Chile
Hands-on example for the computational simulation of transport processes; simulations using "Virtual Cell"
08.01. - 12.01.2018, 9 a.m., 26.23.00.26

Mercartor Module - Part 1
"Plant Biophysics - Membrane Biophysics"
given by our Mercartor Fellow Prof. Ingo Dreyer, University of TALCA, Chile
18.12.2017, 9 a.m., 26.23.00.26
19.12.2017, 1:00 p.m., 26.23.00.26

Content of the course in Membrane Biophysics:
· Thermodynamic bases of membrane transport processes
· Ion channels, coupled transporters, pumps
· Experimental techniques for electrophysiology
· Mathematical description of transport processes for computational modeling
· Dynamics of coupled transport processes
· Examples of successful research projects in the addressed fields

CAi course "Image analysis (Fiji / Image J) - beginner course"
Dr. Zobel, Dr. Weidtkamp-Peters, Dr. Hänsch

No previous experience with Fiji is required. You will learn how to use Fiji and how to analyze
your microscope images e. g. automatic object detection and counting as well as batch processing.
It will be possible to analyze your own images during the course.

Dates Beginner Course:
Tuesday 28.11.2017 , 9 a.m. - 5 p.m.
Thursday 30.11.2017, 9 a.m. - 5 p.m.
Registration: SFB office (email)
Registration deadline: 23.11.2017
Number of participants: max. 30
Location: t.b.a.


CAi course "Image analysis (Fiji / Image J) - advanced course"
Dr. Zobel, Dr. Weidtkamp-Peters, Dr. Hänsch

The second course is aimed at advanced users.
This course will deal with advanced plugins and macro programming.
It will be possible to analyze your own images / write your own macros during the course.

Dates Advanced course:
Monday 04.12.2017, 9 a.m. - 5 p.m.
Tuesday 05.12.2017, 9 a.m. - 5 p.m.
Registration: SFB office (email)
Registration deadline: 23.11.2017
Number of participants: max. 30
Location: t.b.a.


Mass spectrometry "Data Analysis"
Prof. Kai Stühler / Dr. Daniel Waldera-Lupa
Duration and dates: 2 days; 26.-27.09.2017, 10:00-17:00
Location: HHU, 25.41.00.61
Numer of participants: max. 18
Registration: Daniel Waldera-Lupa

X-ray course
(shifted from May to October/November 2017)
Prof. Groth / Prof. Schmitt
Duration and dates: t.b.a.
Location: HHU, Institute of Biochemistry and Institute of Biochemical Plant Physiology
Number of participants: min. 8, max. 15
Registration: SFB office (email)
Registration deadline: t.b.a.

Advanced Imaging Methods – Superresolution
(Prerequisite: participation in "„Basic Confocal Imaging“)
Dr. Weidtkamp-Peters, Dr. Hänsch, Dr. Zobel
Duration and dates: 3 days, 04.-06.04.2017
Location: HHU, CAi
Number of participants: max. 6

Lecture Module, overview and discussion of different subjects
2 days, 9 a.m. - 3 / 5 p.m.
Monday, May, 29th
9-11 a.m.  Georg Groth- "Protein purification"
13-15 a.m. Lutz Schmitt - "Non-natural amino acids"
Tursday, May, 30th
9 -11 a.m. Kerstin Schipper / Michael Feldbrügge - "Virtual cloning using CloneManager"
13 - 15 a.m. Andreas Weber  - "Metabolomics/Mass Spectrometry of Small Molecules"
15 - 17 a.m. Karin Meierhoff - "Mutations in plants"

Mercartor Module
Crash Kurs "Plant Biophysics - Membrane Biophysics"
given by our Mercartor Fellow Prof. Ingo Dreyer, University of TALCA, Chile
28.07.2017, 9 a.m., 26.23.00.26
31.07.2017, 1:30 p.m., 26.23.00.26


Working with eukaryotic microorganisms
(Hands-on course using mainly S. cerevisiae as a model; basic methods course for low level of experience in this field)
Dr. Schipper, Dr. Pohlmann, Prof. Dr. Feldbrügge
Duration and dates: 3 days, 04.09., 11.09. and 18.09.2017
Location: HHU, Institute for Microbiology
Number of participants: max. 12
Registration via SFB office
Registration deadline: 04.08.2017

Bioinformatics and Biomolecular Modelling
Prof. Birgit Strodel / Dr. Bogdan Barz
Duration and dates: 3 days; 28.11.-01.12.2016, 09:00-17:00
Location: HHU, 26.42.03.39
Number of participants: min. 3, max. 8
Registration deadline: 02.11.2016

Mass spectrometry and the pitfalls in sample preparation
Prof. Kai Stühler / Dr. Daniel Waldera-Lupa
Duration and dates: 1 day; 14.12.2016, 10:00-16:00
Location: HHU
Registration deadline: 18.11.2016

Basic Confocal Imaging
Dr. Weidtkamp-Peters, Dr. Hänsch, Dr. Zobel
Duration and dates: 2 days, 14.-15.2.2017
Location: HHU, CAi
Number of participants: max. 6
(You can work on your own samples.)

Basic Confocal Imaging
Dr. Weidtkamp-Peters, Dr. Hänsch, Dr. Zobel
Duration and dates: 2 days, 21.-22.2.2017
Location: HHU, CAi
Number of participants: max. 6
(You can work on your own samples.)

Advanced Imaging Methods – Superresolution
(Prerequisite: participation in "„Basic Confocal Imaging“)
Dr. Weidtkamp-Peters, Dr. Hänsch, Dr. Zobel
Duration and dates: 3 days, 28.-30.03.2017
Location: HHU, CAi
Number of participants: max. 6

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