The SFB 688 participates in the "University of Würzburg Graduate Schools" (UWGS).
The IGS initially started with interdsiciplinary programs in biology and medicine, brought together in the "Graduate School of Life Sciences" (GSLS). The graduate school prepares PhD students for a successful career in academia and industry by offering research projects at the forefront of science and a curriculum custom tailored to the needs of each student.
Currently the GSLS offers programs in the following “Classes”: Biomedicine, Infection and Immunity, Integrative Biology, Neuroscience and the MD/PhD program. The SFB is member of the class biomedicine.
Practicals for Doctoral researchers within the GSLS
A1 and B1: Nieswandt
Our group works on plalelet function in hemostasis, thrombosis and inflammatory disease. We use generate and analyse genetic mouse models with defined defects in platelets and immune cells or proteins that interact with these cells. In our laboratory different murine models of thrombotic/inflammatory disease are established, part of which utilized intravital microscopic methods. We offer training in a broad range of technologies, including:
1. mouse handling, genotyping, organ and blood sampling
2. introduction into gene knockout approaches, including ES cells culture
3. basic methodology of (mouse) platelet analysis, including standard aggregometry, whole blood aggregometry, flow cytometry, fluorimetric Ca2+-measurements, biochemical analyses, etc.
4. flow adhesion assays for platelets (and other cell types)
5. DIC and confocal fluorescence microscopy of platelets (and other cell types)
6. mouse models of arterial thrombus formation and inflammation
7. introduction into hybridoma technology (generation of monoclonal antibodies)
8. Scanning electron microscopy (available from 05/2011)
Visits to our laboratory for 1 - 3 days to get an introduction into one or more of these techniques can be arranged at any time during the year upon request.
A2: Dandekar Lab
Our group works on all aspects of bioinformatics. Focus in our SFB688 project is the human platelet and signal cascades and their transduction, including protein-protein interactions, phosphorylations, phosphatases and other modifications. The activation by vWF/GPIb and further events is central for platelet function and a focus as well as inhibitory input and crosstalk. We offer specific courses to learn all involved techniques such as
1. genome annotation
2. sequence analysis
3. domain analysis
4. metabolic modelling
5. analysis of regulatory networks
6. prediction of protein-protein interactions
All of these are provided regularly and for B.Sc. and M.Sc. students.
For PhD students we also offer specific courses, in particular on sequence analysis (including genome and protein structure) for 2 days, end of July (every year), as well as courses for gene expression analysis.
Our group works on the regulation of endothelial permeability and angiogenesis by the cardiac hormone atrial natriuretic peptide (ANP) and its second messenger cyclic GMP. We use, generate and analyse genetic mouse models with deletion of the ANP receptor in endothelial cells or smooth muscle cells. In our laboratory different techniques are used to study physiological and pathological angiogenesis and permeability. We can offer training in the following technologies:
1. mouse handling, genotyping, organ and blood sampling
2. culture of primary endothelial cells from lung and aorta, assays of proliferation and migration
3. mouse models of angiogenesis: hind limb ischemia, postnatal angiogenesis in the retina,
hypoxic neoangiogenesis in the retina
4. mouse models of permeability in the microcirculation of the cremaster muscle
5. analyses of mouse cardiac function in vivo and ex vivo (in isolated perfused mouse working hearts)
6. analysis of vascular contraction and relaxation: isolated vessels mounted in a small vessel myograph
7. measurement of arterial blood pressure in awake and anesthetized mice
8. fluorometric analyses of calcium handling in isolated adult murine cardiomyocytes
A10: Hofmann/Kerkau / Ertl
Our group works on the role of inflammation in cardiac ischemic injury. We analyse genetic mouse models with defined defects in immune cells or proteins. In our laboratory different murine models of cardiac injuries are established. We offer training in a broad range of technologies, including:
1. mouse handling, genotyping, organ and blood sampling
2. cardiac disease models:
a) chronic myocardial infarction
b) ischemia/ reperfusion injury
c) transverse aortic constriction
d) implantation of alzet mini pumps
3. characterisation of mouse disease models
a) invasive hemodynamics
4. general immunohistochemistry
5. collagen measurements
6. standard molecular techniques including real time PCR
7. FACS analysis of the myocardium
Our group works on a novel class of mammalian protein phosphatases that regulate cell adhesion and migration. We have begun to establish genetic mouse models that are conditionally deficient in these phosphatases, and employ a broad range of biochemical, cell biological and microscopic methods to study regulators of cytoskeletal dynamics. We offer training in technologies such as:
1. recombinant protein expression and purification
2. kinase and phosphatase activity assays
3. analysis of Rho-GTPase activities
4. biochemical protein-protein interaction analysis
5. epifluorescence, TIRF and confocal microscopy
6. analysis of actin cytoskeletal dynamics
7. cell adhesion assays
8. time-lapse imaging of motile cells.
Our group is interested in immune mechanisms in atherosclerosis. In order to study the pathophysiology of atherosclerosis, mouse models are employed which spontaneously develop atherosclerotic lesions. We in addition utilize genetic mouse models for studying defined defects in cellular mediators, such as cytokines and transcription factors, to investigate immune cell functions in vascular inflammation. We can offer training in the following fields and help you set up experiments (often on a collaborative basis):
1. real time PCR analysis/ PCR-based gene arrays: quantitative measurements of gene transcription
2. FACS analysis and cell sorting: antibody staining of cell suspensions and flow cytometric analysis; cell sorting
3. immunohistochemistry: organ preparation, processing and embedding of tissue, sectioning (frozen sections, paraffin sections), and histological and immunofluorescence staining
4. mouse models of inflammation, arterial neointimal hyperplasia and atherosclerosis
We are interested in studying cellular signaling pathways that are involved in cardiovascular diseases, especially cardiac hypertrophy and heart failure. For our investigations we employ a broad sprectrum of biochemical, fluorescent and physiological techniques using purified proteins, cell lines, primary cells and transgenic mouse models. We can offer lab visits (1-2 days) to introduce students to some of the methods, including:
1. monitoring of cardiac function in mice using left ventricular cardiac catheterization
2. monitoring of cardiac function in mice using echocardiography
3. preparation and culture of primary cells, e.g. cardiomyocytes and smooth muscle cells
4. analysis of protein function of purified protein or in intact cells using enzyme activity assays
5. measurement of calcium transients and cell contraction of isolated cardiomyocytes using Fura2 and an edge detection system
6. analysis of protein-protein interaction using different FRET techniques
7. analysis of subcellular localization of proteins using different microscopy techniques
B1 and A13: Kleinschnitz/Stoll
Our group works on the interplay between inflammation and thrombosis in a broad range of neurological disease models. To this end, we mainly use rats and mice but also several in vitro models of blood-brain barrier (BBB) damage and neuronal injury. We can offer short term teaching (1-3 days) in the following fields, or assist in setting up experiments (preferentially on a collaborative basis):
1. Animal models of neurologic diseases
a) acute ischemic stroke: Transient and permanent middle cerebral artery occlusion, cortical photothrombosis, embolic stroke models
b) traumatic brain injury: Weight drop model, cortical cryolesion
c) subarachnoidal hemorrhage (in collaboration with the Dept. of Neurosurgery)
d) Experimental Autoimmune Encephalomyelitis (EAE) / Experimental Autoimmune Neuritis (EAN)
e) peripheral nerve injury
e) neurological testing of rats and mice
Please note that the “Grundkurs Tierschutz und Versuchstierkunde” or equivalent certificate is required for hands-on training!
2. In vitro models of BBB damage and neuronal injury
Preparation of neuronal and glial cell cultures, oxygen/glucose deprivation (OGD) models, human and murine cerebral endothelial cell lines, migration assays, surrogate markers for BBB damage (vascular tracers, determination of brain wet/dry weight)
3. Real-time RT PCR and immunohistochemical techniques in brain and nerve tissue
Our group works on developmental control processes, especially Notch signaling, that regulate development of blood vessels and the heart. We use mouse models and in vitro approaches to identify transcriptional control mechanisms and gene regulatory networks that define key steps like angiogenesis, arterial fate determination and homeostasis in later life. We can offer short term teaching/training in the following fields, or assist in setting up experiments (often on a collaborative basis).
In situ hybridization: Analysis of gene expression by RNA in situ hybridization of paraffin sections or whole mount preparation of mouse tissues or embryos. This allows one to visualize gene expression not just globally like in RT-PCR or Northern blots, but ideally even down to the level of single cells. Quantification and sensitivity is usually below that reached by qRT-PCR, but spatial resolution is unmatched. Immunohistochemistry would even allow subcellular resolution, but depends on suitable antibodies, which are often not available.
ES cell manipulation: Mouse embryonic stem cells can be used for the generation of genetically modified mice by transgenesis or recombination. In addition they can be used to recapitulate early embryonic development in vitro and to differentiate these cells into e.g. endothelia or cardiomyocytes. This makes ES cells a very useful resource to study and manipulate developmental programs. Students can learn ES cell handling and procedures to use them experimentally.
Chromatin-IP (ChIP): DNA binding proteins regulate gene expression and DNA packaging. Chromatin-IP is a method to provide evidence of direct DNA binding in vivo. Cells are fixed with a crosslinking agent to preserve DNA-protein interactions. DNA binding proteins are immunoprecipitated from chromatin fragments and bound DNA is released and quantified by PCR. This method can be employed to test for protein binding at promoters or enhancers of individual genes. When used on a large scale this allows mapping of all binding sites in a genome for a given protein using next-generation sequencing (ChIPseq).
B5/Z2 (Physical Institute EP5) Bauer/ Jakob
In our group we analyze biological structures as cells or blood filled vessels in muscle tissue. We develop Magnetic Resonance Imaging techniques to obtain information of the arrangement and density of microscopic structures. We offer training in a broad range of technologies, including:
1. Mouse handling and preparing for the MRI scan.
2. Introduction into MRI techniques.
3. Mathematical modelling of the MRI signal.
Our group works on the development and the validation of radiopharmaceuticals for both human and preclinical applications. Our laboratories offer all modern applications and training opportunities in radiochemistry and radiopharmacy, including the radiolabelling techniques for small molecules, peptides and antibodies, pharmacological formulation of pharmaceuticals for human applications under GMP conditions and GMP-training on work. We also validate animal models, using positron emission tomography (PET) and single photon emission computed tomography (SPECT). In our laboratory different tumor models are established, which are used for the validation of new radiopharmaceuticals. We offer training in a broad range of technologies, including:
1. Cyclotron for the production of different radioisotopes
2. GMP facilities for the production of radiopharmaceuticals and therapeutics
3. Labs for cell cultures equipped with incubators for handling with cells and microscopes
for cell analysis
4. We have also laboratories for organic chemistry for the synthesis of smart molecules for
5. We are working daily with HPLC, TLC-scanners, GC, -spectroscopy, UV for different
6. Autoradiography has been established for ex-vivo tissue and organ analysis
7. µ-PET for molecular imaging on mice and rat models
8. PET-CT and SPECT-CT are also available for molecular imaging in humans