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Fachschaftsinitiative Biomedizin

Workshops

You always wanted to know how microinjection and genetic manipulation of oocytes, professional pipetting, microarray-based genomic hybridization or ChIP-Sequencing works? Or what it's like to conduct research with different animal models like mouse, zebrafish, fly or worm? Here, all available workshops provided by research groups of the Julius Maximilian University are listed. If you are interested in participating in one ore two of them, you can state so in the registration form. Requirements for participation are indicated if necessary.

[01] Transgenic mouse models: The transition from in vitro functional studies to a complex organism

Organizer: Professor Dr. Michael Bösl

Institute/Department: Department of Experimental Biomedicine I

Abstract: We will briefly touch the artificial reproductive technologies (ARTs), necessary to manage a modern mouse facility and will focus on micromanipulation of preimplantation mouse embryos in order to modify the genome.

Location: Zentrum für Experimentelle Molekulare Medizin (ZEMM), Building E7, Lab 4.02, basement, Zinklesweg 10, 97078 Würzburg

Max. number of participants: 4

Session: 1. Session

Remark: You may bring your own labcoat

[02] Electron microscopy of biological complexes

Organizer: Professor Dr. Bettina Böttcher

Institute/Department: Department of Biochemistry, Rudolf Virchow Center, Kryo-Elektronenmikroskopie

Abstract: Electron cryo microscopy has become the method of choice for structure determination of biological complexes. In this workshop we will use negative staining to look at 1-2 complexes at room temperature. This simple technique is typically used for quickly evaluating samples for their suitability for subsequent cryo-EM.

Location: Rudolf-Virchow-Zentrum, building D15 - atrium of RVZ for pick-up (rooms 00.225-EM; 00.229 Prep), Josef-Schneider Straße 2, 97080 Würzburg

Max. number of participants: 4

Session: 1. Session, 2. Session

[CANCELED] Quantification of DNA-damage with the Comet-Assay

Organizer: Professor Dr. Helga Stopper

Institute/Department: Institute of Pharmacology and Toxicology, Department of Toxicology

Abstract: Mutagenic acitivites of chemicals are important for regulatory agencies and basic research. The Comet-Assay is a simple method for quantification of DNA damage. With microscopy based image analysis the percentage of damaged DNA per nucleus is evaluated in a series of treated cells.

Location: Department of Toxicology, Room 215, Versbacher Str. 9, 97078 Würzburg

Max. number of participants: 4

Session: 1. Session

[04] Deciphering Chromatin Association of Myc by ChIP-sequencing: A hands on workshop

Organizer: Dr. Elmar Wolf

Institute/Department: Department for Biochemistry and Molecular Biology

Abstract: Chromatin immunoprecipitation followed by Deep sequencing is a method to investigate Chromatin binding of transcription factors genome-wide. We will perform some of the key steps of a ChIP-sequencing experiments together and everybody will analyze an existing dataset to get a first impression of the bio-informatics analysis.

Location: Biozentrum, part B, level 3, room will be anounced soon, Am Hubland,  Campus Süd, 97074 Würzburg

Max. number of participants: 8

Session: 1. Session, 2. Session

[05] Analysing cardiac myocyte function

Organizer: Prof. Dr. Christoph Maack / Dr. Michael Kohlhaas / Dr. Alexander Nickel / Dr. Vasco Sequeira

Institute/Department: Comprehensive Heart Failure Center (CHFC), Department for Translational Science

Abstract: The processes of excitation-contraction (EC) coupling in cardiac myocytes are key for the function of the heart and consume large amounts of energy, which needs to be replenished by oxidative phosphorylation in mitochondria. In heart failure, the processes of EC coupling and also mitochondrial energetics are substantially disturbed. In our laboratory, we are specialized to analyse the close interplay of EC coupling with mitochondrial energetics in normal and diseased cardiac myocytes. This hand-on workshop will introduce the students into key techniques for the analysis of EC coupling and mitochondrial function.

Location: Comprehensive Heart Failure Center (CHFC), Building A15, Level 2, room A15.0.303, South wing, Am Schwarzenberg 15, 97078 Würzburg

Max. number of participants: 20

Session: 1. Session, 2. Session

[06] The power of whole-exome sequencing for genetic variant detection in hearing loss patients

Organizer: Julia Doll / Michaela Hofrichter / Caroline Lekszas / Professor Dr. Thomas Haaf

Institute/Department: Institute of Human Genetics

Abstract: Hearing loss (HL) belongs to one of the most common sensory disorders in humans and is characterized by its extremely heterogeneous appearance. About 1-2 in 1000 newborns are affected at birth. The majority of disease-causing mutations occur in the exome – the 2 percent of the human genome that encodes proteins. Thus, whole-exome sequencing has been established both in academic research and as a clinical diagnostic tool to investigate already known and novel genetic variants.

Location: Biozentrum, room A106, Am Hubland, Campus Süd, 97074 Würzburg

Max. number of participants: 8

Session: 1. Session, 2. Session

[07] Imaging calcium in cultured cells and neurons

Organizer: PD. Dr. Robert Blum

Institute/Department: Institute for Clinical Neurobiology

Abstract: In this workshop, we will visualize calcium dynamics of neurons. Changes in cytosolic calcium will be visualized with synthetic calcium indicators and genetically encoded calcium indicators (GCamps). An upright microscope will be used to image spontaneous and induced calcium activity. Finally, we will discuss different strategies to analyze calcium transients with the help of open source computational tools.

Location: Institute for Clinical Neurobiology, building E4, room 2.31, Versbacher Str. 5, 97078 Würzburg

Max. number of participants: 4

Session: 1. Session, 2. Session

[08] Drosophila as a model organism in neuroscience – from genes to behaviour

Organizer: Professor Dr. Erich Buchner

Institute/Department: Institute for Clinical Neurobiology

Abstract: Drosophila has a small brain yet a rich behavioral repertoire. Genetics allows manipulating molecules and cells, the functional consequences for the system can be studied by quantitative behavioral analysis. You will prepare brains of transgenic flies to image cell-specific GFP expression by (confocal) fluorescence microscopy and perform rapid iterative negative geotaxis (RING) experiments to quantify motor deficiencies of mutants.

Location: Institute for Clinical Neurobiology (E4), room 0.02, Versbacher Str. 5, 97078 Würzburg

Max. number of participants: 4

Session: 2. Session

[09] Ion channels at work

Organizer: Professor Dr. Carmen Villmann

Institute/Department: Institute for Clinical Neurobiology

Abstract: Students will get an introduction into the patch-clamp technique used to functionally analyze various types of ion channels. We will show the organization of an electrophysiology setup and demonstrate functional recordings from transfected cells and primary neurons. We use this technique to identify pathomechanisms of various neurological diseases, which are in focus of our research, associated with impaired function of either ligand-gated ion channels or voltage-gated ion channels.

Location: Institute for Clinical Neurobiology, building E4, 1. floor, Raum 1.03.1, Versbacher Str. 5, 97078 Würzburg

Max. number of participants: 4

Session: 1. Session

[10] Time-lapse imaging of extracellular vesicle release

Organizer: Dr. Ann Wehman

Institute/Department: Rudolf Virchow Center

Abstract: Extracellular vesicles are released by all cell types, carry signals, and sculpt membranes. To understand their biogenesis, we use fluorescent reporters and live imaging in genetically modified worms (C. elegans). In the workshop, participants will learn how advanced imaging techniques can be combined with genetic techniques to learn about membrane dynamics in vivo.

Location: Rudolf-Virchow-Zentrum für Experimentelle Biomedizin, room D15.02.209, Josef-Schneider-Straße 2, Haus D15, 97080 Würzburg

Max. number of participants: 8

Session: 1. Session, 2. Session

*CANCELED* [11] Methods of microarray-based genomic hybridization (array CGH)

Organizer: Professor Dr. Eva Klopocki

Institute/Department: Institute for Human Genetics

Abstract: Microarray-based genomic hybridization/ molecular karyotyping allow genome-wide detection of copy number variants (losses and gains). The aim of this workshop is to give an introduction to this technology as well as exercises on copy number variant (CNV) interpretation and classification. We will use genome browsers and databases i.e. DECIPHER, DGV, etc. and students work on illustrative cases from diagnostic laboratories as well as research cases.

Location: Institute for Human Genetics, Biozentrum, CIP-Pool, room will be announced soon, Am Hubland,  Campus Süd, 97074 Würzburg

Max. number of participants: 16

Session: 2. Session

[12] 3D printing at the micron scale

Organizer: Professor Dr. Paul Dalton

Institute/Department: Department for Functional Materials in Medicine and Dentistry

Abstract: Melt processing has been used for decades to manufacture medical materials including 3D printed implants. This lecture will describe a little-known, solvent-free 3D printing technology that uses polymers relevant for medical implants. Melt electrowriting (MEW) generates small filament diameter structures in the low-micron resolutions where the application of a high voltage stabilizes a molten jet at low flow rates, resulting in small fiber diameters that can be direct written and used for biomedical research.

Location: Department for Functional Materials in Medicine and Dentistry, room will be announced soon, Röntgenring 11, 97070 Würzburg

Max. number of participants: 8

Session: 2. Session

[13] Translational bioinformatics: from data to computational models and new therapeutic approaches

Organizer: Dr. Meik Kunz, Johannes Vey, Maximilian Fuchs

Institute/Department: Department of Bioinformatics

Abstract: The area of Big Data is producing large amounts of data in biomedicine. Bioinformatics allow to find pattern and correlations to better understand such data. This workshop gives an overview of typical bioinformatics methods such as statistical analysis, machine learning and functional network analysis and simulations.

Location: Biologie Kursgebäude 80, CIP-Pool, Emil-Fischer-Straße, Campus Nord, 97074 Würzburg

Max. number of participants: 20

Session: 1. Session

[14] Human Genetics in Fish ??? - How fish can be used to model diseases.

Organizer: Dr. Daniel Liedtke

Institute/Department: Institute for Human Genetics, Biozentrum

Abstract: Identification of potential inherited disease-causing mutations in patients is nowadays boosted by advanced diagnostic techniques, but often functional investigations are lacking. For efficient examination the best suited in vivo system has to be chosen. Besides rodents, zebrafish have recently been established as a comprehensive vertebrate model species, due to their optical clarity and easy handling. The hands-on workshop will introduce participants in the usage of small laboratory fish as animal models for human diseases. Besides a short introduction into the topic, participants will have the possibility to investigate embryonic development live, visit our aquatic facilities and participate in several small experiments featuring zebrafish.

Location: Biozentrum, Foyer (room A106), Am Hubland, Campus Süd,  97074 Würzburg

Max. number of participants: 12

Session: 1. Session, 2. Session

[15] Liquid Handling: basis, modern pipetting systems and special applications

Organizer: Dr. Hans von Besser

Organization: Eppendorf 

Abstract: In the first part the technological basis of pipetting and dispensing will be presented. Limits of air cushion pipettes and the advantages of electronic Xplorer® and positive displacement pipettes (Multipette®) will be figured out. Several factors (environmental, physical) have a significant impact on the accuracy of the pipetting results. Best practice of liquid handling is important in many applications like e.g. qPCR. In the second part (hands-on) several pipetting tasks will give you the opportunity to compare the advantages of air cushion pipettes vs. positive displacement pipettes.

Location: Biozentrum, Biochemistry course room, Am Hubland, Campus Süd, 97074 Würzburg

Max. number of participants: 8

Session: 1. Session

[16] Nanopore sequencing

Organizer: Jun.-Prof Redmond Smyth

Institute/Department: Helmholtz Institute for RNA-based Infection Research (HIRI)

Abstract: Students will get an introduction into nucleic acid sequencing using the portable MinION sequencer. This USB-sized sequencer is set to revolutionize biology, and offers real-time sequencing by measuring changes in electrical current as molecules pass through nanopores. In this workshop, we will demonstrate this technology, and show how it can be used to rapidly obtain sequencing data from biological samples, such as the human pathogens HIV and Influenza.

Location: Helmholtz Institute for RNA-based Infection Research (HIRI), room will be anounced soon, Building D15, Josef-Schneider-Str. 2, 97080 Würzburg

Max. number of participants: 4

Session: 2. Session

[17] Understanding cellular identities using single-cell RNA-seq

Organizer: Dr. Antoine-Emmanuel Saliba

Institute/Department: Helmholtz Institute for RNA-based Infection Research (HIRI)

Abstract: Single-cell RNA-sequencing is totally changing our understanding of cellular identities. With this technique, one can fingerprint thousands of information per single-cell and understand individually the physiology of each of them. In this workshop, the students will learn how to analyse and visualize single-cell RNA-sequencing data. As an example, we will dissect immune cells in the liver and try to reach the most comprehensive view on the diversity of cells being present.

Location: Helmholtz Institute for RNA-based Infection Research (HIRI), room will be announced soon, Building D15, Josef-Schneider-Str. 2, 97080 Würzburg

Max. number of participants: 6

Session: 1. Session

[18] Design and testing of CRISPR technologies

Organizer: Prof. Dr. Chase Beisel

Institute/Department: Helmholtz Institute for RNA-based Infection Research (HIRI)

Abstract: Students will get an introduction to CRISPR-Cas systems and how they can be harnessed as biomolecular tools for genome editing and high-throughput genetic screens. Basic biomolecular research is undergoing a revolution with the advent of these tools, and they have become standards in every molecular biology research group. As part of the experiment, students will learn how to design guide RNAs that direct DNA cleavage of different CRISPR nucleases. They will also test their designs using cell-free transcription-translation systems.

Location: Helmholtz Institute for RNA-based Infection Research (HIRI), room will be anounced soon, Building D15, Josef-Schneider-Str. 2, 97080 Würzburg

Max. number of participants: 4

Session: 1. Session

[19] From bone marrow to platelet biogenesis and function

Organizer: Prof. Dr. Harald Schulze

Institute/Department: Institute of Experimental Biomedicine, Chair I

Abstract: All blood cells are generated by progenitor cells in the bone marrow. Hematopoietic stem cells can differentiate to megakaryocytes that become the immediate precursors of blood platelets. Megakaryocytes in the bone marrow are rare cells and not easy to visualize. We will provide inside by confocal laser scanning microscopy to detect these cells in the context of capillaries in the bone marrow. In addition, we will characterize blood platelets by flow cytometry to study their receptor expression and how they react towards distinct agonists. The release of internal dense granules is monitored online by a kinetic assay. Finally, we will demonstrate how these data are analyzed using different modules of the processing software FlowJo.

Location: Rudolf-Virchow-Zentrum für Experimentelle Biomedizin, seminar room (3rd floor), Josef-Schneider-Straße 2, Haus D16, 97080 Würzburg

Max. number of participants: 4

Session: 2. Session

[20] Micro-Tomography resolving the structure of biomaterials

Organizer: Dr. Simon Zabler

Institute/Department: Institute of Physics, Chair of X-ray Microscopy LRM

Abstract: Students and researchers at LRM develop cutting edge three-dimensional X-ray imaging techniques based on Micro- and Nano Computed Tomography CT. Biological samples can thus be scanned at a resolution of several micrometer, e.g. resolving the structure of small animals and plants, which are made of bone, dentin, and wood. We invite you to LRM labs to get a hands-on experience with our technology and the people working on the instrument as well as on the development of 3D imaging software.

Location: Institute of Physics, Lab & seminar room, Josef-Martin Weg 63, Campus Nord, 97074 Würzburg

Max. number of participants: 10

Session: 2. Session

[21] Small-angle X-ray Scattering for resolving the ultrastructure of biomaterials

Organizer: Bernhard Schummer

Institute/Department: Institute of Physics, Chair of X-ray Microscopy LRM

Abstract: Students and researchers at LRM developed the Small (and Wide) Angle X-ray Scattering SAXS /WAXS beamline which allows for recording scattering patterns from nanometer to micrometer biological structures. The students will work on the beamline, preparing samples, measuring SAXS profiles and analyzing the data as well as discussing results with researches at LRM /Fraunhofer. The workshop provides a basic insight and hands-on experience on the techniques SAXS and WAXS.

Location:  Institute of Physics, Lab & seminar room, Josef-Martin Weg 63, Campus Nord, 97074 Würzburg

Max. number of participants: 10

Session: 2. Session