IZKF Technology Platform Overview by liaoqinmei

VIEWS: 4 PAGES: 30

									Chronic Disease

      Technology Platform
      Interdisciplinary Center
      for Clinical Research
      of the Medical Faculty Münster
 
                           State-of-the-Art Technologies
                               IZKF Technology Platform




                                            CONTENTS


1. Aims                                                                      1

2. Introduction                                                              2

3. Overview                                                                  3

4. Integrated Functional Genomics (IFG) - Genomics Facility                  4

5. Integrated Functional Genomics (IFG) - Proteomics Facility                8

6. Integrated Functional Genomics (IFG) - Bioinformatics Facility            12

7. Transgenic Animal Models (TRAM)                                           16

8. Small Animal PET (SmAP)                                                   18

9. Optical Imaging for Functional and Molecular in vivo Diagnostics (OPTI)   20

10. Ultrasound Imaging of Small Animals (ECHO)                               22

11. Small Animal MRI (SAMRI)                                                 24

12. Terms of Use                                                             26
        State-of-the-Art Technologies
        State-of-the-Art Technologies
           IZKF Technology Platform
           IZKF Technology Platform




Our Goal                                              > Specialists in the field assist researchers
                                                        from the stage of project conception to its
The rapid advancement in the field of biological
                                                        completion thus ensuring maximum efficien-
and biomedical research has facilitated an in-
                                                        cy.
depth understanding of cellular and molecular
processes in health and disease. This has given
rise to the need for researchers to have access       > Researchers have open access to a large in-

to efficient high throughput services that are          strument pool consisting of expensive high-

too cost- and labor-intensive for single univer-        end equipment that has increased the versa-

sity institutions. The Interdisciplinary Center for     tile nature of the technology available to the

Clinical Research (IZKF) Münster operates sev-          institutions of the Medical Faculty.

eral Core Units, which are a valuable resource
for an effective research environment.                > The Core Units operate on a cost recovery ba-
                                                        sis and charges reflect the actual expenses
Principal Aims                                          for consumables and service contracts.

> The Core Units specialize in providing State-
  of-the-Art skilled technical and instrument         Moreover, the Core Units promote translational

  support for the Medical Faculty of the Univer-      research by interacting closely with academia

  sity of Münster, extramural faculty, external       and industry, ensuring that the technology

  non-affiliated institutions as well as indus-       available is continuously updated. Lectures,

  trial researchers, at affordable rates.             workshops and practical courses are organized
                                                      on a regular basis to keep users informed about
                                                      current developments.


                                                      This information folder provides an overview
                                                      of the different facilities, their technical equip-
                                                      ment and methodological support services
                                                      available to researchers.


                                                      Contact and more information
                                                      IZKF Scientific Office
                                                      Albert-Schweitzer-Campus 1, Gebäude D3,
                                                      48149 Münster
                                                      Tel.: +49 (251) 83-58695
                                                      Fax: +49 (251) 83-52946
                                                      Mail: izkf.muenster@uni-muenster.de                   >1
                      State-of-the-Art Technologies

                                 IZKF Technology Platform




The IZKF Münster Technology Platform provides users with state-of-the-art ex-
pertise and equipment in four main technological areas, each of which consist
of several highly specialised Core Units (CU). The IZKF Scientific Office coordi-
nates and supports these Core Units and oversees their smooth operation.


  Integrated Functional                                          Transgenic Animal
       Genomics                                                       Models


          Small Animal                                           Optical and Molecular
          Phenotyping                                                  Imaging




                   Proteomics             TRAM                OPTI


                      01001011         Coordination
                      10001000
                      10100110              &
                      10010001         Management
     Genomics    Bioinformatics                               SmAP        SAMRI




                                     Cardiovascular
                                     Physiology starting in
                                     2012                     ECHO



Our information folder aims to provide users with an overview of the services
offered by the Core Units. For special experimental paradigms not listed, users
are requested to contact the Head of the respective Core Unit. It is manda-
tory for all users to strictly abide with the Terms of Use of the Core Units. The
IZKF Scientific Office provides information on prices and issues invoices for
services carried out. Users are advised to include costs for CU services in their
grant applications.
The logos on the upper right hand corner are specific to each CU, enabling
the easy identification of leaflets that have been updated. In addition, news
regarding novel technologies will be communicated to users via a newsletter.
As a user of our Technology Platform, we would appreciate your feedback on
our Technology Platform and urge you to contact the IZKF Scientific Office if you
have any concerns or constructive suggestions involving any of our facilities.



                                                                                         >2
                           IZKF Technology Platform
                                   Overview



The Core Unit Integrated Functional Genomics (IFG) is a multidisciplinary
technology platform that pursues an integrated approach to understanding
gene expression profiling and protein analysis in order to identify genes,
proteins and peptides in complex samples. The bioinformatics unit uses
mathematical, statistical and computing methods in the acquisition, stor-
age, analysis and interpretation of data arising from genomic and proteomic
projects. The ultimate aim is to relate gene and protein expression patterns
to pathways, pathways to networks and networks to function in order to gain
new insight into biological and disease circuits and develop therapeutic strat-
egies. The automation of high-end molecular biology methods necessitates
complex state-of-the-art instrumentation and technology. The IFG provides
open access to this leading edge technology that is continuously validated
according to the experimental needs of researchers, coordinates interdisci-
plinary research projects and organises workshops. The IFG hosts the Annual
Münster Conference on Single Cell and Molecule Analysis. This conference
monitors the state-of-the-art in the field of nanoanalytics.

Transgenic animal models are a key tool to study the pathogenesis of various
diseases and to test therapeutic strategies for human diseases. Since 1996
the IZKF supports the Core Unit TRAM, thus providing centralised services to
all members of the Medical Faculty, WWU Münster at reduced costs.

Small animal phenotyping is the logical choice for the analysis of human
cardiovascular diseases in mouse models. This platform consists of an unit
that carries out the ultrasound analysis of the murine cardiovascular sys-
tem (ECHO). A new core unit to study cardiovascular physiology will be es-
tablished in January 2012.

The Optical and molecular imaging platform carries out non-invasive imag-
ing techniques that aim to understand the molecular processes in small
rodent models of human diseases at the intracellular level and in vivo by
determining the bio-distribution of various radiolabelled tracer molecules
(SmAP) and fluorochromes (OPTI). This platform was complemented by the
CU Small animal MRI (SAMRI) in 2010, enabling High Throughput morpho-
logical and functional MRI scans to be carried out.




                                                                                  >3
Integrated Functional Genomics (IFG)
Genomics Facility



The field of genomics emerged from the        terial is pure enough to be used in down-
initiation of various genome projects, and    stream applications like PCR and genetic
the resulting knowledge created the field     fingerprinting. The P.A.L.M. Micro Laser
of functional genomics, concerned with        system is housed in a separate room and
analysing gene expression, epigenetics,       is available to all users of the Genomics
mutations and genetic variation, to name      unit.
a few. The Genomics facility offers its
customers a wide range of services from       Quantitative real-time PCR
single-cell microdissection, real-time        Real-time PCR continues to be the stand-
PCR, various microarrays to Next-Gener-       ard technology for gene expression stud-
ation Sequencing (NGS). In addition to        ies. The 7900HT system (Applied Biosys-
providing the full service package from       tems) detects and quantitates nucleic
experimental design to the final steps of     acids sequences in 384-well plates. This
data interpretation, technical training is    system supports applications such as
offered to enable self-service handling of    gene expression, SNP genotyping, path-
the equipment.                                ogen detection, viral load analysis and
                                              miRNA quantification.
                   Laser capture micro-
                   dissection                 The 7900 HT system is available for self-
                   Laser capture micro-       service after a demonstration by the
                   dissection (LCM) is
                                              Genomics team.
                   a unique technique
                   that enables RNA and                                   TaqMan® Low
DNA to be isolated from pure specimens                                    Density Arrays
of specific groups of cells or even single                                The 7900HT sys-
cells devoid of contaminating adjacent                                    tem has an in-
tissue. LCM can be performed on a vari-
                                                                          t e r cha n gea bl e
ety of tissue samples including frozen tis-
                                              block for TaqMan® Custom Array Cards.
sue sections and paraffin sections. Using
                                              These are 384-well micro fluidic cards
this method a sufficient number of cells
                                              that enable 384 real-time PCR reactions
can also be collected from archival brain
                                              to be performed simultaneously without
tissue (Hasselblatt et al., 2006). This ma-
                                              the need for liquid handling robots.




Laser capture microdissection workflow                Courtesy of P.A.L.M. Microlaser Technologies




                                                                                                     >4
Integrated Functional Genomics (IFG)
Genomics Facility



This low- to medium- throughput micro          for many species like human, mouse, rat,
fluidic card allows for 1-8 samples to be      Arabidopsis, C. elegans, chicken, Dros-
run in parallel against 12-384 TaqMan®         ophila, E. coli, maize, rice, S. aureus,
Gene Expression Assay targets that are         Xenophus, yeast, zebrafish etc.
pre-loaded into each of the wells on           The Genomics unit offers a complete
the card. The TaqMan® Custom Array is          gene expression analysis service from
completely customizable. Over 50,000           controlling RNA integrity to supplying the
TaqMan® Gene Expression Assays de-             raw data. A basic or extensive analysis of
signed for human, mouse, rat genes, and        the data is carried out by the IFG bioinfor-
miRNAs are available. Additionally, pre-       matics facility.
configured TaqMan® Gene Signature Ar-
rays for human ABC transporters, human         GenePix® microarray scanner
angiogenesis, human apoptosis, human,          The GenePix® 4000B microarray scan-
mouse or rat GPCR, human and mouse             ner coupled with GenePix® Pro Micro-
Alzheimer, rat and human inflammation          array Image Analysis Software and Acu-
etc. can be used.                              ity® microarray informatics software,
                                               sets the highest standards in the ac-
Affymetrix microarrays
                                               quisition and analysis of data from all
Affymetrix arrays enable the simultane-
                                               types of arrays, including nucleic acids,
ous detection of mRNA abundance of
                                               proteins, tissues, and cells. The Gene-
thousands of target genes to determine
                                               Pix® 4000B scanner acquires data at
whether they have been switched “on” or
                                               user-selectable resolutions between
“off” in a biological or pathological state.
                                               5–100 microns, allowing optimization
                                               of image resolution and file size for
                                               each experiment. The scanner features
                                               non-confocal optics, simultaneously
                                               2-channel scanning with 532 nm and
                                               635 nm lasers, and is usable for stand-
                                               ard microscope slides (e.g. Agilent mi-
                                               croarrays). It is available for self-service
                                               use.
Affymetrix GeneChip

The Affymetrix platform enables:
• DNA Copy Number Analysis
• Genome-Wide Genotyping
• Re-Sequencing Analysis
• Targeted Genotyping Analysis
• 3´IVT Expression Analysis
• Gene Regulation Analysis
• miRNA Analysis
                                               Genepix 4000B Array-Scanner
• Whole-Transcriptome Analysis




                                                                                              >5
Integrated Functional Genomics (IFG)
Genomics Facility



Next Generation Sequencing                   Eukaryotes as well as Prokaryotes such
The Next-Generation Sequencing (NGS)         as:
technology is the most up-to-date tech-      • Whole genome (Re-)Sequencing,
nology available in genomic science.         • Targeted Resequencing,
Thus, the IFG is proud to offer this tech-   • SNP Detection,
nology to its customers.
                                             • Structural Variant Detection,
Our 5500xl SOLiD™ System (Applied
                                             • Whole Transcriptome Analysis,
Biosystems®/LifeTechnologies®)
                                             • Gene Expression Analysis,
provides the combination of accuracy,
sensitivity, and cost effectiveness to       • Small RNA Analysis,
support large translational research         • Chromatin Immunoprecipitation
                                             Sequencing,
studies. It helps to ensure optimal pro-
ductivity with two flexible FlowChips,       • Methylation Analysis
embedded quality controls, and project        using
scalability. The system’s two configura-     • Fragment Libraries (single or
ble microfluidic FlowChips process up        paired end) or
to 12 independent samples and the            • Mate-paired Libraries
intelligent barcoding kits multiplex up
                                              in
to hundreds of samples in a single run.
                                             • Single-sample or
However, also projects with small sam-
ple numbers can be run at a reasonable       • Multiplex Design.
cost due to the flexible design. Pay-Per-
                                             The NGS service provided by the IFG
Lane Sequencing and independent run
                                             comprises the project design support,
lanes tailor the system to any project
                                             quality control (QC) of the customer-
scale.
                                             provided samples, library preparation,
                                             further QC steps, library quantification,
                                             sequencing run supervision, and vali-
                                             dation of the raw data. The raw data will
                                             be handed out to the customer who is
                                             free to use the IFG Bioinformatics ser-
                                             vice for secondary and tertiary analysis.




5500xl SOLiD™ System
With the 5500xl Genetic Analyzer, the
customer is empowered to discover
rare genetic events or sub-populations
of somatic mutations at an unprec-
edented pace. The industry-leading ac-
curacy of the 5500xl Genetic Analyzer
enables detection of significant biolog-     Covaris S-series High Performance
ical variation for applications for          Sample Preparation System



                                                                                         >6
Integrated Functional Genomics (IFG)
Genomics Facility




             WORKFLOW                         Bioinformatics support
                                              The Genomics team works closely with
 Meeting with the Genomics & Bioinfor-
 matics team to discuss experimental de-
                                              the Bioinformatics team offering cus-
 sign, sample preparation and pricing         tomers of the IFG professional scale
                                              bioinformatics solutions. In addition
                                              to standard services the bioinformatics
 Researcher fills out the mandatory Order     team supports specific requests with in-
 Form                                         dividual bioinformatics solutions tailored
                                              to the specific needs of the customers.

 - Sample submission                          Representative Publications
 - Quality control of RNA / DNA               Schmitz KJ, Helwig J, Bertram S, Sheu SY, Suttorp
                                              AC, Seggewiss J, Willscher E, Walz MK, Worm K,
 - Customer feedback                          Schmid KW (2011) Differential expression of
                                              microRNA-675, microRNA-139-3p and microR-
                                              NA-335 in benign and malignant adrenocortical
                                              tumours. J Clin Pathol 64: 529-535.
 Microarray or High Throughput Sequenc-
 ing experiments are carried out              Grundmeier M, Tuchscherr L, Brück M, Viemann
                                              D, Roth J, Willscher E, Becker K, Peters G, Löffler B
                                              (2010) Staphylococcal strains vary greatly in their
                                              ability to induce an inflammatory response in en-
 Raw or analysed data will be handed over     dothelial cells. J Infect Dis 201: 871-80.
 to the customer as a hard copy
                                              Hasselblatt M, Mertsch S, Koos B et al. (2009)
                                              TWIST-1 is overexpressed in neoplastic choroid
                                              plexus epithelial cells and promotes proliferation
 Please acknowledge the IFG Genomics /        and invasion. Cancer Res 69: 2219-2223.
 Bioinformatics Departments if the data       Edemir B, Kurian SM, Eisenacher M et al. (2008)
 generated by us is used in a publication     Activation of counter-regulatory mechanisms in a
 and notify us when the manuscript is         rat renal acute rejection model. BMC Genomics
 published                                    9: 71.
                                              Hasselblatt M, Bohm C, Tatenhorst L et al. (2006)
                                              Identification of novel diagnostic markers for
                                              choroid plexus tumors: A microarray-based ap-
                                              proach. Am J Surg Pathol 30: 66-74.




Contact
                                                                                                      IZKF Münster (08/2011)




                  Dr. rer. nat. Jochen Seggewiß
                  Integrated Functional Genomics (IFG)
                  Röntgenstraße 21
                                                  Tel: +49 (251) 83 - 57168
                  48149 Münster
                                                  Fax: +49 (251) 83 - 57255
                  http://ifg-izkf.uni-muenster.de jochen.seggewiss@ifg.uni-muenster.de



                                                                                                                               >7
Integrated Functional Genomics (IFG)
Proteomics Facility




Proteins are the principal effectors in       Protein expression analysis
cellular function and the target of most      The The unit offers a choice of gel-based
pharmacological strategies. The goal of       or MS-based differential analysis. The
the proteomics facility is to provide cost-   entire pipeline for the DiGE technol-
effective access to sophisticated tech-       ogy (Differential Gel Electrophoresis) is
nology for modern proteomics analysis         available. This is an advanced system
in a central facility. Special emphasis is    solution based on 2D-PAGE (separation
placed on assisting researchers in de-        of proteins according to their isoelectric
signing and evaluating their research         point (pI) and molecular weight), which
projects and includes extra features such     enables the quantification of protein
as advanced manual and bioinformatic          expression profiles of two samples (e.g.
data mining.                                  normal vs disease state) in a reproduci-
                                              ble and statistically relevant manner. The
Biomolecular mass spectromery                 methodology eliminates gel-to-gel vari-
Mass spectrometers are available (Q-TOF       ance and represents the state-of-the-art
Premier, ESI/AP-MALDI (IR/UV) ion trap,       in gel-based expression analysis. DiGE
MALDI-TOF), which can be flexibly used        gels are scanned with the Typhoon 9400
for different types of experiments such as    three-laser scanner, which is also versa-
the determination of molecular weights        tile for use in other applications such as
of biomolecules regardless of their size.     modification-directed staining. Regulat-
Soft ionization techniques allow the anal-    ed proteins are subsequently identified
ysis of intact proteins and labile modifi-    using LC-MS/MS.
cations. Procedures have been devel-
                                              A dedicated MS-based approach using Q-
oped to monitor enzymatic or chemical
                                              TOF Premier MSE technology allows label-
reactions or to fingerprint biological flu-
                                              free absolute and relative quantification
ids. Not only proteins and peptides can
                                              of proteins. It promises comprehensive
be investigated; the analysis of certain
                                              data with high reproducibility and re-
types of drugs (e.g. Imatinib), fatty acids
                                              duced sample handling. Even less sam-
or other substances in complex mixtures
                                              ple is needed (~2 µg compared to 500
is also possible.
                                              µg for DiGE) and the data can be stored
Protein identification                        indefinitely for later mining. The identi-
The analysis of proteins pre-separated        fication of hundreds of protein compo-
by electrophoretic or chromatographic         nents of one proteome is automatically
means is one of the main service tasks.       performed. The results of the analysis in-
Reversed-phase      nanochromatography        clude not only the fold changes in regula-
coupled to high-end mass spectrometry         tion but also provide clear insights about
(LC-MS; nanoUPLC/Q-TOF Premier) allows        the magnitude of proteome differences
confident assignment of proteins after        and regulatory factors using principal
enzymatic digestion. Protein modifica-        component analysis (PCA)- see Bioinfor-
tions such as phosphorylation, isoforms       matics section).
and unknown sequences are accessible
in specially designed experiments.




                                                                                           >8
Integrated Functional Genomics (IFG)
Proteomics Facility



Protein separation and gel electro-            tions and functions. Using protein arrays,
phoresis                                       efficient and sensitive high-throughput
The unit assists in the preparation of tis-    analysis of thousands of proteins can be
sue homogenates or cell lysates. 1D- and       achieved simultaneously. Protein arrays
2D-electrophoresis can be performed            such as the FAST slides can be analysed
with customer samples. Moreover, the           with two microarray scanners. Protein
fractionation of proteins in the liquid        arrays are commercially available for cy-
phase based on their pI is possible, e.g.      tokine and biomarker analysis as well as
to exclude dominant proteins for subpro-       autoimmune diagnostics.
teome analysis. Quality control of protein     Bioinformatics for proteomics and
separations is carried out with a minia-
                                               profiling
turized capillary electrophoresis lab-on-
                                               It has become increasingly necessary to
a-chip system. This method serves to rap-
                                               evaluate and visualize proteomic or mass
idly diagnose separation procedures or
                                               spectrometric data with statistical meth-
sample quality. Biological fluids such as
                                               ods. A number of procedures have been
urine, cell extracts or whey can be evalu-
                                               established for that purpose:
ated for their protein content.
                                               Protein expression analysis using
                                               DIGE
                                               The DeCyder software applies a gel com-
                                               parison method that introduces zero
                                               statistical error, offering reliable data
                                               and analysis. Co-detection, background
                                               subtraction, normalization, and quanti-
                                               fication of spots in images are improved
                                               based on a warping function. The soft-

Pre-fractionation of protein mixtures for
sub-proteome analysis

Profiling of biofluids
LC-MS profiles are excellent means to
study biological changes. In particular,
urine profiles of low-to-medium molecu-
lar weight compounds have been shown
to reflect health or hormonal status. Rep-
licate samples are compared with statis-
tical tools such as PCA and the results are
evaluated further for biomarkers.              ware provides multivariate statistics
                                               tools and enables the combined analysis
Protein arrays                                 of different datasets, aiding the biologi-
Protein arrays are increasingly used to
                                               cal interpretation of results by matching
miniaturize interaction experiments.
                                               with data retrieved from public and local
They serve to detect proteins, study their
                                               databases.
expression levels, as well as their interac-



                                                                                            >9
Integrated Functional Genomics (IFG)
Proteomics Facility




Protein expression analysis using LC-
MSE
The expression module of ProteinLynx-
GlobalMiner 2.5 assists in the statistical
evaluation of LC-MS runs of proteome
digest replicate runs. Both relative and
absolute quantification is possible with-
out the need for sample labeling. Experi-
mental data are further mined using tools
such as Principal component analysis.

Principal component analysis (PCA)
PCA (SimcaP, RapidMiner) as a linear
dimensionality reduction algorithm,
which projects high dimensional
data (replicate runs with hundreds to        Pathway analysis
thousands of data points) to lower           The information about regulated
dimensional subspace spanned by              proteins is further processed identifying
the principal eigenvectors and assist        relationships, mechanisms, functions,
investigators in finding major differences   and pathways of relevance using
in their samples. It is an important step    Ingenuity software. It delivers an
preceding biomarker assignment both          assessment of signaling and metabolic
in proteomics and the analysis of LC-MS      pathways, molecular networks, and
profiles of urine or other biofluids         biological processes that are most
                                             significantly perturbed in the dataset of
Exploratory analysis and data visu-          interest.
alisation
VisuMap software allows
understanding data that
otherwise resists easy in-
terpretation.

It provides a novel insight
into the patterns, relation-
ships and correlations be-
hind the data. In particu-
lar, relational perspective
mapping and advanced
clustering algorithms for
high dimensional data
like self-organizing map,
affinity propagation, k-
mean clustering are of
great value for analysis of
LC-MS data.



                                                                                         >10
Integrated Functional Genomics (IFG)
Proteomics Facility




Protein Histidine Phosphatase (PHP)

     1   GHHHHHHHHH HSSGHIEGRH MAVADLALIP DVDIDSDGVF KYVLIRVHSA
     51 PRSGAPAAES KEIVRGYKWA EYHADIYDKV SGDMQKQGCD CECLGGGRIS
     101 HQSQDKKIHV YGYSMAYGPA QHAISTEKIK AKYPDYEVTW ANDGY


PHP was discovered by the late                      König S (2011) Urine molecular profiling distin-
Prof. Susanne Klumpp and studied                    guishes health and disease: New ways in diag-
                                                    nostics? Test case UPLC-MS. Exp Rev Mol Diagn
extensively* in her group at the Institute          11: 383-391.
of Pharmaceutical and Medical Chemistry             Wang W, Ackermann D, Mehlich A-M, König S
at the WWU, Münster. As a result of                 (2010) False labelling due to quenching failure of
                                                    N-hydroxysuccinimide-ester coupled dyes. Prot-
earlier collaborations, the IFG continues           eomics 7: 1525-2529.
to provide PHP for research purposes.               Hasche A, Ferenz KB, Rose K, König S, Humpf H-U,
*Klumpp S, Krieglstein J (2009) Reversible          Klumpp S, Krieglstein J (2010) Binding of ATP to
Phosphorylation of Histidine Residues in Proteins   nerve growth factor: Characterization and rele-
                                                    vance for bioactivity. Neurochemistry Intern 56:
from Vertebrates. Sci Sig 10: 2(61):pe13            276-284.
                                                    Hohenester UM, Ludwig K, Krieglstein J, König S
The following products are available on             (2010) Stepchild phosphohistidine: Acid-labile
request:                                            phosphorylation becomes accessible by func-
                                                    tional proteomics. Anal Bioanal Chem 8: 3209-
1. Dry recombinant PHP supplied in                  3212.
aliquots of 1 mg (or as required)
2. Glycerol culture of recombinant
PHP supplied in aliquots of 1 ml (or as
                                                     Open access
required)
                                                     Instrumentation such as array scan-
Additional publications and further                  ners, gel imagers and PAGE equipment
information  can     be  found   at                  are available for customer’s use.
http://php. uni-muenster.de
                                                     Getting started
Representative Publications                          Users can provide tissue, cells or pro-
Kummer MP, Hermes M, Hammerschmidt T et              tein mixtures for analysis and are ad-
al. (2011) Nitration of Tyr10 critically enhances    vised to contact the proteomics staff
amyloid beta aggregation and plaque formation.       who will be pleased to assist in ex-
Neuron. (In press)                                   perimental design and to discuss the
Kriegeskorte A & König S, Sander G et al. (2011)     parameters that samples have to fulfill
Small colony variants of Staphylococcus aureus       to ensure smooth processing and ex-
reveal distinct protein profiles. Proteomics 11:
                                                     cellent results.
2476-2490.




Contact
                                                                                                       IZKF Münster (07/2011)




                     Prof. Dr. rer. nat. Simone König
                     Integrated Functional Genomics (IFG)
                     Röntgenstraße 21                                Tel: +49 (251) 83 - 57164
                     48149 Münster                                   Fax: +49 (251) 83 - 57255

                     http://ifg-izkf.uni-muenster.de                 koenigs@uni-muenster.de




                                                                                                                                >11
Integrated Functional Genomics (IFG)                                                        01001011
                                                                                            10001000
Bioinformatics Facility                                                                     10100110
                                                                                            10010001



The Bioinformatics Group provides cus-        platform useful for many applications.
tomers of the IFG with standard and           These include variant discovery by
advanced statistical solutions for their      resequencing targeted regions of interest
Microarray, Real-Time PCR and Next Gen-       or whole genomes, de novo assemblies of
eration Sequencing projects.                  bacterial and lower eukaryotic genomes,
                                              cataloguing the transcriptomes of cells,
Especially the analysis of data from a
                                              tissues and organisms (RNA–seq),
whole genome association study or a
                                              genome-wide profiling of epigenetic
NGS sequencing project requires pro-
                                              marks and chromatin structure using
fessional scale bioinformatics. We offer
                                              other seq-based methods (ChIP–seq)
standard assembly, alignment, mapping
                                              and species classification and/or gene
genotyping and annotation services and
                                              discovery by metagenomics studies.
in addition we can support specific re-
                                              We use a flexible software pipeline ar-
quests with individual bioinformatics
                                              chitecture based on Bioscope®, which
solutions in close collaboration with cus-
                                              enables maximum flexibility and ease of
tomers and scientists.
                                              use for performing high throughput data
Next Generation Sequencing (NGS)              analysis for the SOLiD™ instrument data.
                        The next-genera-      It provides the following features:
                        tion sequencing
                                              Alignment and Mapping
                        (NGS) technolo-
                                              Various bioinformatics tools are used
                        gies constitute
                                                                        for the assem-
                        various    strate-
                                                                        bly (Velvet) and
                        gies that rely on
                                                                        the alignment
a combination of template preparation,
                                              (BFAST, BWA, Bowtie) and are intelligent-
sequencing and imaging, and genome
                                              ly linked up to form project-specific pipe-
alignment and assembly methods. The
                                              lines. After the NGS raw data has been
arrival of NGS technologies on the market
                                              generated, the color space reads are
has changed the way we think about sci-
                                              aligned to a known reference sequence
entific approaches in basic, applied and
clinical research.                            or assembled de novo.

We offer individual solutions for the anal-   SNP detection
ysis of NGS data from our Life technolo-      We use the diBayes software package
gies SOLiD 5500 System and other plat-        which allows sensitive and specific SNP
forms (e.g. Roche 454, Illumina HiSeq or      detection even at moderate to low cov-
GA). We provide a NGS data service from                                   erage. It al-
the primary basic analysis with quality                                   lows varying
checks and base calling to the advanced                                   the levels of
analysis with assembly, mapping, clus-        stringency and provides full control over
tering, annotation and visualization in       many filters for customization to fit par-
close collaboration with our customers.       ticular experimental designs.
NGS applications
The production of large numbers
of low-cost reads makes the NGS



                                                                                                       >12
01001011   Integrated Functional Genomics (IFG)
10001000
10100110   Bioinformatics Facility
10010001



           Structural variants detection                 ing technical and biological replicates) in
           All sequence variants other than single-      small groups up to whole genome associ-
           nucleotide variants, including insertions     ation studies with hundreds or thousands
           or deletions, inversions, segmental du-       of samples in a case-control design.
           plications and copy-number differences        Primary and advanced analysis
           can be detected by the use of the special     Our Bioinformatics facility provides users
           Applied Biosystems software (AB Large         with data from a primary analysis (qual-
           and Small InDel tools, Inversion and CNV      ity, .CEL, .CHP, .CNT and exported text
           tools).                                       and Excel-files) using the Affymetrix tools
           Whole transcriptome analysis                  (Genotyping and Expression Console,
                                                         GTC-Browser and Chromosome Analysis
            The Whole Transcriptome Analysis (WTA)
                                                         Suite). In addition we provide results
           toolset (Bowtie, TopHat, and Cufflinks)
                                                         and data from a more comprehensive
           aligns the reads to a reference genome.
                                                         and complete microarray data analysis
           Using the mapping results, it counts the
                                                         in which we use the commercial Partek®
           number of tags aligned with exons, and
                                                         Genomics Suite, Ingenuity® Pathway
           can convert the BAM file to the WIG for-
                                                         Analysis (IPA) and S-Plus (TIBCO® Spot-
           mat to view the coverage in a genome
                                                         fire S-Plus) scripts from our own software
           browser (UCSC, IGV). The Expression
                                                         development. For the advanced (second-
           analysis includes statistical tests and the
                                                         ary) analysis, which we coordinate in
           calculation of p-values and fold changes.
                                                         close collaboration with our customers
           WTA also supports experiments in fusion
                                                         we offer:
           detection. A fusion junction is a section
           of transcribed RNA that maps to an exon       Expression analysis
           from one gene followed by an exon from        This includes quality checks (background
           another gene. It occurs as the result of a    adjustment, outlier detection), normali-
           translocation, deletion, or chromosomal       zation (standard, quantile and lowess
           inversion. A fusion junction excludes         normalization), two group comparisons
           exon- exon boundaries that arise from al-     to identify genes which show differential
           ternative splicing for a gene.                expression (robust two sample t tests, F
                                                                       tests comparing the mean
           The Affymetrix platform
                                                                       square of two varieties, fold
           Our Affymetrix® Microarray technology
                                                                       changes,      Mann-Whitney-
           platform is a powerful tool for genomic
                                                                       Wilcoxon rank sum tests),
           RNA and DNA analysis. Each study com-
                                                                       multiplicity adjustments for
           prises multiple arrays with thousands of
                                                                       the p-values (FWER: Holm-
           transcripts or millions of markers (geno-
                                                                       Bonferroni, FDR: Benjamini-
                          types, SNPs, CNV and
                                                                       Hochberg), multiple group
                          LOH marker) in groups
                                                                       comparisons (ANOVA, basic
                          corresponding to differ-
                                                                       linear and nonlinear mod-
                          ent experimental settings.
                                                                       els and Neural Networks),
                          Conditions range from sin-
                                                                       pattern discovery (hierar-
           gle factor designs (treatments or tissue
                                                                       chical and model based
           types, times, benign-adverse in complex
                                                         (two-way) clustering), principal compo-
           diseases) with only a view arrays (includ-



                                                                                                       >13
Integrated Functional Genomics (IFG)                                                       01001011
                                                                                           10001000
Bioinformatics Facility                                                                    10100110
                                                                                           10010001



nents and factor analysis (Biplots, mul-      minor allele frequencies), calculations of
tidimensional scaling and gene shav-          Odds ratios (case vs. control) with FWER
ing), class prediction (linear discriminant   and FDR control of the p-values for al-
                  and nearest neighbors       lele and genotype frequencies in differ-
                  analysis, classification    ent inheritance models, pairwise LD and
                  trees, Neural Networks,     haplotype analysis, phenotype-genotype
                  risk analysis and ROC       association (susceptibility between
                  curves) and annotation      genotypes and disease) and relative risk
                  with genomic informa-       analysis using Logistic Regression (ad-
tion including pathway analysis using the     justed Odds ratios) and Neural Network
IPA Pathway Analysis software.                models.

Analysis of Whole Genome Associa-             Copy Number Variation (CNV) and
tion Studies (WGAS)                           Loss of Heterozygosity (LOH) analy-
WGAS are used in population genetics          sis
to identify single nucleotide polymor-        Chromosomal abnormalities (allelic im-
phism (SNPs and their genotypes) which        balance, deletions, gains, Uniparental
can serve as marker sets in complex dis-      Disomies (UPDs)) with structural changes
eases. A sufficient power requires a large    in the DNA play a major role in cancer
sample size, often 500 samples (arrays)                         and cytogenetic re-
and more in each of two groups within a                         search. Amplification
case-control design. A typical WGA study                        of oncogenes and
comprises three stages: screening (geno-                        loss of tumor sup-
typing of ~106 SNPs using SNP 6.0 ar-                           pressor genes can
                  rays), replication of the   be detected by homozygous deletion or
                  most promising SNPs in      loss of heterozygosity (LOH). Affymetrix
                  matched cases and con-      SNP 6.0 arrays with 906.600 SNPs and
                  trols and verification of   946.000 CNV oligos and the Cytogenetics
                  replicated association      Copy Number Assay (CytoScan HD) with
                  signals in a larger co-     750.000 genotype-able SNPs and 1.8
hort using an independent method (e.g.        million non-polymorphic probes allows
TaqMan).                                      the user to perform a high-resolution
We provide full bioinformatics user sup-      genome-wide analysis of chromosomal
port from the study design (sample size       aberrations.
and power calculations) during the whole      Registered users can download the Chro-
execution of the study (quality control       mosome Analysis Sweet from Affymetrix
with reports from each array batch) to the    to analyze and compare the .cel files
final genotype analysis of the TaqMan ex-     from different experiments and to display
periments.                                    chromosomal abnormalities in a user-
This includes quality checks (call rates,     friendly viewer.
identification of genotyping errors, Men-     We use Parteks Genomics Suite’s to de-
del checks, tests for deviations from Har-    tect, display, and report regions of am-
dy-Weinberg equilibrium and control of        plification or deletions on the genome.




                                                                                                      >14
01001011   Integrated Functional Genomics (IFG)
10001000
10100110   Bioinformatics Facility
10010001



           After identification of regions with signifi-
                                                            Getting started
           cant copy number changes (CNV) or LOH,
           gene lists can be created and exported,          After consultation with the customer
                                                            or scientist we perform a basic (prima-
           and corresponding gene or exon expres-           ry) or more comprehensive (second-
           sion data can be seamlessly linked to the        ary) analysis of the raw data. Micro-
           mapping array data if available.                 array data (.CEL, .CHP, .CNT, .CSV and
                                                            .XLS files) can be obtained on CDs or
           On user inquiry we develop special S-            DVDs. The raw data from NGS experi-
           Plus scripts e.g. to display LOH and CNV         ments (.CSFASTA, .QUAL files) and the
                                                            data from a secondary analysis (.BAM,
           regions from several case-control or tu-
                                                            .SAM, .GFF, .BAI, .BED and .CSFASTA.
           mor vs. normal tissue experiments in one         MA files) can be obtained on external
           (publication quality) graphic or to detect       2TeraByte HardDisks. Alternatively all
           significant marker regions by comparing          data can be downloaded from the IFG
                                                            FTP-server.
           the discordant Chi-square distributions
           (McNemar’s chi-square test) of markers
           in case-control experiments.                    Representative Publications
           Real-time PCR analysis                          Schmitz KJ, Helwig J, Bertram S, Sheu SY, Suttorp
                                                           AC, Seggewiss J, Willscher E, Walz MK, Worm K,
           We carry out quality controls of the input      Schmid KW (2011) Differential expression of
           data to detect and filter errors that oc-       microRNA-675, microRNA-139-3p and microR-
                                                           NA-335 in benign and malignant adrenocortical
           curred during the experiment. Embed-            tumours. J Clin Pathol 64: 529-535.
           ded methods permit endogenous genes,            Grundmeier M, Tuchscherr L, Brück M et al.
           which are optimal for normalisation, to         (2010) Staphylococcal strains vary greatly in their
                                                           ability to induce an inflammatory response in en-
           be determined. The applied software pro-        dothelial cells. J Infect Dis. 201: 871-80.
           vides relative quantification analysis of       Mees ST, Mardin WA, Wendel C et al. (2010)
           differential expression data, combining         EP300--a miRNA-regulated metastasis suppres-
                                                           sor gene in ductal adenocarcinomas of the pan-
           interactive visualisation with advanced         creas. Int J Cancer 126: 114-124.
           statistics and data mining.                     Mees ST, Mardin WA, Sielker S et al. (2009) In-
                                                           volvement of CD40 targeting miR-224 and miR-
                                                           486 on the progression of pancreatic ductal ade-
                                                           nocarcinomas. Ann Surg Oncol 16: 2339-2350.




                               Dr. rer. nat. Andreas Huge
                               Integrated Functional Genomics (IFG)
                               Röntgenstraße 21                    Tel: +49 (251) 83 - 52207
                               48149 Münster                       Fax: +49 (251) 83 - 57255
                                                                   a.huge@uni-muenster.de
                                                                                                                 IZKF Münster (07/2011)




                               Dr. rer. nat. Reinhard Voss
                               Integrated Functional Genomics (IFG)
                                                                  Tel: +49 (251) 83 - 58964
                               Röntgenstraße 21
                                                                  Fax: +49 (251) 83 - 57255
                               48149 Münster
                                                                  voss@uni-muenster.de
                               http://ifg-izkf.uni-muenster.de




                                                                                                                                          >15
Transgenic Animal Models (TRAM)




Mice are physiologically similar to hu-       The animal house is equipped with indi-
mans, thus making them ideal organisms        vidually ventilated cages and is operated
to model human diseases. This is made         under specific pathogen free (SPF) condi-
possible by recent advances in transgen-      tions. Mice are housed under sterile con-
ic technologies. Transgenic mice are cre-     ditions until they can be transferred to
ated by integrating foreign DNA into the      the care of the customer.
germ line of mice. The pathogenesis and
therapeutic strategies of various human       Generation of conventional/
diseases can be studied in transgenic         conditional “knock-out”, “knock-in”
mice carrying the respective disease          and “chromosome engineered” mice
causing genes. Another major advance-         We offer the following services for each
ment in the development of mouse mod-         step of targeted mice production:
els of human diseases was the gene
                                              • Targeting vector design includes bio-
knockout. This technology makes it pos-
                                                informatics analysis and cloning strat-
sible to introduce certain mutations into
                                                egy design. For genomic sequences
endogenous genes and transmit these
                                                that are difficult to clone we provide
through the mouse germ line.
                                                alternative strategies.

Since 1996 this unit has provided a cen-
                                              • Embryonic stem (ES) cell line genera-
tralised service to produce regular trans-
                                                tion from the desired mouse lines, in-
genic mice, BAC (bacterial artificial chro-
                                                cluding karyotype analysis and char-
mosome) transgenic animals, as well as
                                                acterisation of ES cell for the germ-line
a variety of gene-targeted (conventional
                                                competence.
or conditional), and chromosome-engi-
neered mice. The unit aims to reduce the
                                              • ES cell electroporation and process-
work load and the costs of its customers.
                                                ing (expansion, analysis and freezing)
Methods for transgenic/targeting DNA
                                                of individual ES colonies. Screening of
constructs design (conventional and PCR
                                                ES cells for positive targeting events
cloning) and DNA recombineering in E.coli
                                                is performed with the help of nested
have been developed. Related services
                                                PCR and Southern blot analysis. All
such as embryo cryo-preservation and
                                                positively targeted colonies are sub-
strain re-derivation are also available.
                                                jected to karyotype analysis.

The unit is fully equipped for:
                                              • Blastocyst injections of positively
1) Molecular biology procedures such as
                                                targeted ES colonies into B6D2F1
   cloning, mutagenesis etc.
                                                hybrids, as well as tetraploid blasto-
2) Cell culture                                 cysts, with production either chimae-
3) Microinjection with 2 complete setups        ras or 100% ES derived animals.
   for pronuclear and blastocyst injec-
   tions.




                                                                                            >16
Transgenic Animal Models (TRAM)




Generation of transgenic mice                     Disease models created in mice:
DNA constructs are purified and in-               › Renal development and function
jected into both pronuclei of the FVB/n           › Arterial hypertension with endothelial
mouse oocytes. 150-200 oocytes are                  and smooth muscle control
routinely injected per construct. DNA in-         › Cardiac hypertrophy and Insufficiency
jected into the pronucleus integrates into        › Skin sensitivity
chromosome(s) and is transmitted to the           › Hypervolemic arterial hypertension
germ line. Injections are repeated in case
                                                  › Neuropsychiatric disease and
they do not result in positive transgenic           behaviour
animals. Services also include Southern
                                                  › Role of S100A9 in inflammatory
blot analysis of tail biopsy DNA as well            mechanisms
as pronuclear injections of BAC DNA con-
                                                  › Autosomal dominant polycystic
structs.                                            kidney disease (PKD2)
                                                  › Model for the Prader Willi syndrome
                                                    (PWS)

                                                  Representative Publications
                                                  Hartmann M, Skryabin BV, Müller T et al. (2008)
                                                  Alternative splicing of the guanylyl cyclase-A
                                                  receptor modulates atrial natriuretic peptide
                                                  signaling. J Biol Chem 283: 28313-28320.
                                                  Skryabin BV, Gubar LV, Seeger B et al. (2007)
                                                  Deletion of the MBII-85 sno RNA gene cluster
Pronuclei Injection
                                                  in mice results in postnatal growth retardation.
                                                  PLoS Genet 3: e235.
Re-derivation of mouse colonies
                                                  Dworniczak B, Skryabin B, Tcinda S et al. (2007)
In order to produce infection-free animal         Inducible Cre/loxP recombination in the mouse
models, mouse lines are held in a specific        proximal tubule. Nephron Exp Nephrol 106: e11-
                                                  20.
pathogen free (SPF) environment. Embry-
os can be stored for a long period of time
by transferring them from a “contaminat-           Getting started
ed” environment to SPF conditions.                 The investigator is requested to meet
                                                   with the facility staff to design the
                                                   project. Forms to initiate service can
Long-term storage of mouse sperm                   be downloaded from the website. In-
Mouse sperm is obtained and frozen with            formation about costs and issuing in-
                                                   voices are given by the IZKF Scientific
consecutive in vitro fertilisation proce-
                                                   Office.
dures.
Contact
                                                                                                     IZKF Münster (12/2009)




                      Univ.-Prof. Dr. rer. phil. Jürgen Brosius
                      Institute of Experimental Pathology (ZMBE)
                      Von-Esmarch-Str. 56                 Tel: +49 (251) 83 - 52133
                      48149 Münster                       Fax: +49 (251) 83 - 58512

                      http://tram-izkf.uni-muenster.de    RNA.world@uni-muenster.de




                                                                                                                              >17
Small Animal PET (SmAP)




Molecular imaging covers a broad spec-       cm) are available (quadHIDAC®, Oxford
trum of applications ranging from imag-      Positrons Ltd., Oxford, UK). In coopera-
ing of single cells or even subcellular      tion with the Department of Nuclear Med-
structures in vitro to clinical diagnostic   icine and the SFB 656 “Molecular Cardio-
imaging in patients in vivo. The aim of      vascular Imaging” this core unit is able to
this core unit is the non-invasive phe-      offer a wide range of different molecular
notypisation of wild type, surgical and      imaging probes ranging from whole-body
transgenic animal models using highly        measurement of perfusion and metabo-
sensitive and high resolution dedicated      lism down to cell imaging and imaging of
small animal imaging technology. The CU      targets involved in oncological, inflam-
offers both scientific expertise and tech-   matory, neurological, cardiovascular and
nology access.                               other diseases.

Small animal positron emission               Small animal single photon emission
tomography (PET)                             tomography (SPECT)
PET is a highly sensitive, quantitative      Recently a dedicated multi-pinhole
imaging modality capable of assessing        SPECT/CT system for animals having a
molecular dynamics in vivo with nano-/       sub-millimeter resolution and good sen-
picomolar sensitivity. Within SmAP two       sitivity was installed (NanoSPECT/CT,
dedicated high resolution small animal       Bioscan, US). The SPECT methodology is
PET scanners with sub-milliliter resolu-     basically a gamma camera system that-
tion and a large field of view (28 cm * 16   provides tomographic images. Since this
                                                                     technology     is
                                                                     the most com-
                                                                     mon molecular
                                                                     imaging tool in
                                                                     patients a diver-
                                                                     sity of tracers/
                                                                     tracer kits are
                                                                     clinically avail-
                                                                     able, which can
                                                                     be directly used
                                                                      in small animal
                                                                      SPECT. This will
                                                                      substantially
                                                                      broaden     the
                                                                      spectrum of mo-
                                                                      lecular targets
                                                                      and methodol-
                                                                      ogy.




                                                                                           >18
Small Animal PET (SmAP)




                                               Ex-vivo autoradiography and
                                               biodistribution
                                               Beside in vivo studies, questions con-
                                               cerning biodistribution and metabolism
                                               can be answered by high-resolution ex-
                                               vivo autoradiography (Biospace Micro-
                                               Imager®, 40 µm resolution) and tissue
                                               counting studies.

                                               Statistics
Tc-99m-Tetrofosmin myocardial perfusion        In the last three years 4279 PET and CT
imaging. Diagnostics for myocardial            measurements have been carried out on
schemia/infarction (normal perfusion)          mouse (87%) and rat (13%) models of
                                               human disease.
Small animal computed tomography               Representative Publications
(CT)                                           Bunk EC, Stelzer S, Hermann S, Schäfers M,
CT is an anatomic imaging modality with a      Schlatt S, Schwamborn JC (2011) Cellular organi-
                                               zation of adult neurogenesis in the Common Mar-
very high spatial resolution. The core unit    moset. Aging Cell 10:28-38
houses a dedicated small animal high-
                                               Reuter S, Schnöckel U, Edemir B, Schröter R,
resolution CT device with a resolution         Kentrup D, Pavenstädt H, Schober O, Schlatter E,
down to 15 µm for in vivo and ex vivo          Gabriëls G, Schäfers M (2010) Potential of nonin-
                                               vasive serial assessment of acute renal allograft
applications (Siemens Inveon®). SmAP           rejection by 18F-FDG PET to monitor treatment ef-
uses this method primarily to provide          ficiency. J Nucl Med 51:1644-52.
anatomical information in correlation          Law MP, Schäfers K, Kopka K, Wagner S, Schober
to the distribution of specific molecular      O, Schäfers M (2010) Molecular imaging of car-
                                               diac sympathetic innervation by 11C-mHED and
imaging probes in PET and SPECT. In            PET: from man to mouse? J Nucl Med 51:1269-76.
general, small animal CT alone offers a
                                               Büscher K, Judenhofer MS, Kuhlmann MT, Her-
spectrum of applications similar to CT in      mann S, Wehrl HF, Schäfers KP, Schäfers M,
the clinical setting.                          Pichler BJ, Stegger L (2010) Isochronous assess-
                                               ment of cardiac metabolism and function in mice
                                               using hybrid PET/MRI. J Nucl Med 51:1277-84.

Contact



                    Univ.-Prof. Dr. med. Michael Schäfers
                    European Institute for Molecular Imaging
                                                             Tel: +49 (251) 83 - 49301
                    Technologiehof Münster, Building L1
                                                             Fax: +49 (251) 83 - 49313
                    Mendelstraße 11
                    48149 Münster                            schafmi@uni-muenster.de

                    Dr. med. Sven Hermann
                                                                                                  IZKF Münster (07/2011)




                    European Institute for Molecular Imaging
                    Technologiehof Münster, Building L1
                    Mendelstraße 11                          Tel: +49 (251) 83 - 49303
                    48149 Münster                            Fax: +49 (251) 83 - 49313
                    http://smap-izkf.uni-muenster.de          shermann@uni-muenster.de



                                                                                                                           >19
Optical Imaging for Functional and Molecular
in vivo Diagnostics (OPTI)



Small animal optical imaging allows             cutaneous tumors. In addition to in vivo
quantitative data on key diseases and           imaging, the system is suitable for in situ,
therapeutic response profiles to be gen-        and ex-vivo fluorescence applications,
erated in vivo. Fluorescence imaging in         e.g. biodistribution studies. A wide range
the near-infrared range (700-900 nm),           of filter sets are available that are suited
also called „optical window“, is char-          for different fluorochromes or fluorescent
acterised by low absorbance through             proteins.
oxy-and-deoxy-hemoglobin (i.e. good tis-
sue penetration) as well as low levels of
autofluorescence, yielding high contrast
to noise ratios. Thus, even picomolar
amounts of fluorochromes can sensitive-
ly be detected without ionising radiation
(permitting continuous or repeated expo-        In vivo and ex vivo FRI images:
sures) so that molecular structures can         alpha(v)beta(3) expression of artherioscle-
                                                rotic plaques.
be resolved in vivo using this technique.
With the available fluorescence imaging
systems - in combination with near-infra-
red emitting fluorophors tailored to spe-
cific biological applications - biological
targets and pathways can be monitored
and quantified even in deeper tissue sec-
tions. Beside the access to two state-of-
the-art optical in vivo imaging methods,
                                                Biodistribution study
the core unit offers scientific expertise for
experimental design and data analysis in
optical imaging.                                Fluorescence mediated tomograph
                                                In comparison to 2D techniques, fluores-
Fluorescence reflectance imager                 cence mediated tomography (FMT) offers
A fluorescence reflectance imaging (FRI)        superior quantification accuracy and can
system is available on-site for fast and        yield three-dimensional determination of
convenient acquisition of 2D fluoresence        contrast agent uptake. Two state-of-the-
images. The Kodak In-vivo Imaging Station       art FMT systems for small animal imaging
FX Pro combines advanced multispectral          are installed in the core unit to yield 3D
fluorescence, luminescence, digital x-ray       quantitative tomographic images of small
and radioisotopic imaging in a single sys-      animals. Data can be acquired at two dif-
tem. Thus, multichannel and multimodal          ferent wavelengths: Excitation: 670 nm/
imaging capabilities are available. The         Emission: 700 nm and Excitation: 745
system is ideal for rapid evaluation of su-     nm/Emission: 780 nm. Co-registration of
perficially located processes such as sub-      FMT data and e.g. MRT data is possible.




                                                                                               >20
Optical Imaging for Functional and Molecular
in vivo Diagnostics (OPTI)




White light image and FMT reconstructions of in vivo fluorescence signals indicating tumor-
driven angiogenesis.

Contrast agents                                 Representative Publications
In addition to commercially available           Eisenblätter M, Höltke C, Persigehl T, Bremer C
                                                (2010) Optical techniques for the molecular ima-
fluorescent contrast agents, the core unit      ging of angiogenesis. Eur J Nucl Med Mol Imaging
offers access to different fluorescence         37 Suppl 1: S127-137.

imaging probes that were developed in           Larmann J, Frenzel T, Hahnenkamp A, et al. (2010)
                                                In vivo fluorescence-mediated tomography for
cooperation with the Department of Clini-       quantification of urokinase receptor-dependent
                                                leukocyte trafficking in inflammation. Anesthesi-
cal Radiology, the Department of Nuclear
                                                ology 113: 610-618.
Medicine and the Collaborative Research         Eisenblätter M, Ehrchen JM, et al (2009) In-vivo
Centre SFB 656 (MoBil) „Molecular Car-          optical imaging of cellular inflammatory response
                                                in granuloma formation using fluoresence la-
diovascular Imaging“ at the University          belled macrophages. J Nucl Med 50: 1676-1682.
of Münster. In detail, markers of tissue
                                                 Getting started
perfusion, targeted probes for imaging
angiogenesis and MMP-expression are              The investigator is requested to meet
                                                 with the facility staff to discuss specific
available.
                                                 needs and to design the project.
                                                 Information about costs and issuing
                                                 invoices are given by the IZKF Scientific
                                                 office.
Contact
                                                                                                    IZKF Münster (07/2011)




                   Prof. Dr. med. Christoph Bremer
                   Department of Clinical Radiology
                   Albert-Schweitzer-Campus 1, Gebäude A16
                                                                 Tel: +49 (251) 83 - 56146
                   48149 Münster
                                                                 Fax: +49 (251) 83 - 52067
                   http://opti-izkf.uni-muenster.de              optiizkf@uni-muenster.de



                                                                                                                             >21
Ultrasound Imaging of Small Animals (ECHO)




The Core Unit ECHO was established to        the wide spectrum of ultrasonic imaging
provide high-resolution ultra-sound im-      techniques. Computer-assisted steering
aging for morphological and functional       and high-temporal real time ultrasound
analysis in murine models. The core unit     microscopy allow image-guided injec-
is equipped with high-end ultrasound         tions for model-induction (e.g. tumor
technology and provides a wide range         models), advanced therapeutic strate-
of services using diagnostic ultrasound      gies (stem-cells, gene-therapy) or mere
equipment and ultrasound microscopes.        local drug delivery.


Small animal ultrasound: Imaging             Service
and therapy                                  Services include follow-up studies in vari-
A major focus of the core unit is small      ous cardiovascular and tumor models.
animal phenotypisation of transgenic         On special demand multimodal imaging
murine models. Non-invasive morpho-          combining other IZKF imaging platforms
logical and functional analysis of cardio-   can be arranged. The core unit integrates
vascular structures (heart and vessels)      our expertise and resources in small ani-
are provided for fetal, adolescent and       mal imaging and therapy with leading
adult rodents. Supplementary to basic ul-    researchers in this field to create new
trasound imaging, simultaneous record-       opportunities and directions for study-
ing of other physiological parameters        ing a large range of animal models. Team
(e.g. ECG, blood-pressure) is provided.      members have long standing expertise in
Advanced imaging techniques such as          mouse handling and physiologic moni-
molecular imaging of a large range of        toring. Databases supporting networking,
vascular epitopes, inflammation imaging      data handling and biostatistics round off
and tissue-perfusion imaging complete        the spectrum of services provided.




Small animal phenotypisation by ultrasound. A wide spectrum of imaging modalities:
Ultrasound microscopy allows studying fetal mice in-utero, blood flow even in cerebral
arteries, inflammation by targeted ultrasound contrast agents and comparison with
other imaging modalities by 3D acquisition.



                                                                                           >22
Ultrasound Imaging of Small Animals (ECHO)




Computer controlled injection of tumor cells into e.g. pancreas (left) or liver (right).
Follow up of induced tumors is feasible by ultrasound and provides highly accurate 3D
tumor volumes.

Representative Publications
Di Marco GS, Reuter S, Kentrup D, Ting L, Ting L,   Stypmann J, Engelen MA, Troatz C, Rotheburger
Grabner A, Jacobi AM, Pavenstadt H, Baba HA,        M, Eckardt L, Tiemann K (2009). Echocardio-
Tiemann* K, Brand* M (2010) Cardioprotective        graphic assessment of global left ventricular
effect of calcineurin inhibition in an animal mo-   function in mice. Laboratory Animals 43: 127-
del of renal disease. Eur Heart J. Epub ahead of    137.
print. *= equal contribution
Dreischaluck J, Schwoppe C, Spieker T, Kessler T,   Getting started
Tiemann K, Liersch R, Schliemann C, Kreuter M,
Kolkmeyer A, Hintelmann H, Mesters RM, Berdel       The investigator is requested to meet
WE (2010) Vascular infarction by subcutaneous       with the facility staff to discuss specific
application of tissue factor targeted to tumor
                                                    needs and to design the project.
vessels with NGR-peptides: activity and toxicity
profile. Int J Oncol 37: 1389-1397.                 Information about costs and issuing
                                                    invoices are given by IZKF Scientific
                                                    Office.




Contact
                                                                                                    IZKF Münster (07/2011)




                       PD Dr. med. Jörg Stypmann
                       Department of Cardiology and Angiology
                       Albert-Schweitzer-Campus 1, Gebäude A1
                       48149 Münster                       Tel: +49 (251) 83 - 44906
                                                              Fax: +49 (251) 83 - 47864
                       http://echo-izkf.uni-muenster.de       Stypmann@ukmuenster.de



                                                                                                                             >23
Small Animal MRI (SAMRI)




Magnetic Resonance Imaging (MRI) is an
extremely versatile pre-clinical diagnos-
tic technique. Besides morphological
imaging, MRI allows for functional and
metabolic imaging in non-invasive longi-
tudinal studies, aiming at both phenotyp-
ing or molecular imaging in mice, rats, or
guinea pigs.

MRI - A tool in pre-clinical research
With 3D spatial resolutions approaching
10 µm in fixed specimens and 50 µm in
                                             9.4 T Biospec with cryoprobe
vivo MR microscopy provides valuable
information for phenotyping novel trans-
genic animals either in utero, during de-
velopment, or following disease onset.
Additional functional parameters such as
cardiac volumes in models of heart dis-
ease or tumor tissue characterisation in
cancer models are readily available from
standard measurement protocols.
Cell tracking MRI allows for visualisation
of labeled tumor cells or grafted stem       3D reconstruction of the murine thorax
cells over a time course of several weeks.
                                             Infrastructure
Morphological and functional data is
complemented by metabolic information,       The core unit SAMRI is equipped with a
which is available from MR spectroscopy      state-of-the-art small animal MRI sys-
measurements, providing metabolic data       tem (Bruker Biospec 94/20), operating
with sub-millimeter resolution.              at a magnetic field strength of 9.4 tesla.
Furthermore, fMRI is a valuable tool in      Dedicated probes for mice and rats and
neurophysiological research, detecting       high-performance microscopy gradient
either the hemodynamic response of           systems provide optimum preconditions-
neural activity via the BOLD (blood          for numerous applications. Installation
oxygen level dependent) effect, or           of a CryoProbe (Helium-cooled detector)
activity of Ca2+-channels via MEMRI          affords highest sensitivity for ultimate
(Manganese-enhanced MRI). Since fMRI         temporal of spatial resolution. For cardiac
is a non-invasive techniques these data      MRI and fMRI studies ECG and transcuta-
can be collected over a time course and      neous blood gas monitoring devices are
compared to behavior experiments in the      available.
same animal.




                                                                                           >24
Small Animal MRI (SAMRI)




                                                 Sagittal image of the mouse brain
                                                 in vivo

   Morphological imaging of the mouse
   heart in vivo




                                                 Coronal image of the mouse brain
                                                 in vivo
                                              Representative Publications
                                              Hoerr V, Purea A, Faber C (2010) NMR Separation
  Morphological imaging of the zebra          of intra- and extracellular compounds based on
  finch brain in vitro                        intermolecular coherences. Biophys J 99: 2336-
                                              2343.
Service
                                              Weiss K, Melkus G, Jakob P, Faber C (2009) Quan-
SAMRI offers a number of routine proto-       titative in vivo 1H spectroscopic imaging of me-
                                              tabolites in the early postnatal mouse brain at
cols for high resolution morphological        17.6 T. Magn Reson Mater Phy 22: 53-62.
imaging, as well as protocols for function-   Schneider JT, Faber C (2008) BOLD Imaging in the
                                              Mouse Brain using a TurboCRAZED Sequence at
al parameters in cardiac, developmental
                                              High Magnetic Fields. Magn Reson Med 60: 850-
or oncological models. Protocols for fMRI     859.
studies or cell tracking applications are
devised on demand. MR spectroscopy             Getting started
protocols can be established in coopera-       The investigator is requested to meet
tion with the interested user. To allow for    with the facility staff to discuss specific
                                               needs and to design the project.
a wide range of applications, including
                                               Information about costs and issuing
infection models, the MR-system is in-         invoices are given by IZKF Scientific
stalled in a S2-laboratory.                    Office.

Contact
                                                                                                IZKF Münster (07/2011)




                    Univ.-Prof. Dr. rer. nat. Cornelius Faber
                    Department of Clinical Radiology
                    Albert-Schweitzer-Campus 1, Gebäude A1
                    48149 Münster                             Tel: +49 (251) 83 - 57608
                                                              Fax: +49 (251) 83 - 52067
                                                              faberc@uni-muenster.de



                                                                                                                         >25
TERMS OF USE                                                                  sible	to	carry	out	a	scientific	cooperation	that	exceeds	the	
                                                                              routine	 service	 character.	 These	 exceptions	 have	 to	 be	
I.   The Terms of Use of the Core Units of the IZKF Münster                   justified	in	the	application	and	require	the	permission	of	
     serves to provide information for all users and to imple-                the	IZKF	Board	of	Directors.	Costs	for	consumables	have	to	
     ment the statutes of the IZKF.                                           be	reimbursed.	Additional	user	charges	do	not	apply.	All	
                                                                              publications	resulting	from	a	scientific	cooperation	should	
II.		 The	IZKF	Scientific	Office	acting	on	behalf	of	the	Board	of	
                                                                              acknowledge	the	IZKF	Münster	on	the	title	page	under	the	
     Directors	 is	 responsible	 for	 all	 administrative	 coordina-
                                                                              authors’ address.
     tion.

                                                                          6.		 In	this	context	it	is	not	possible	to	consider	routine	investi-
1.		 The	Core	units	should	be	exclusively	utilized	for	research	              gations	as	a	scientific	cooperation	and	these	services	are	
     purposes.                                                                liable	for	fees.

2.		 Priority	access	will	be	given	to	all	members	of	the	IZKF	and	        7.		 All	members	of	the	research	groups	are	responsible	for	the	
     the	 Medical	 Faculty.	The	 heads	 of	 the	 Core	 Units	 should	         correct	operation	and	handling	of	the	equipment.	General	
     ensure	 that	 orders	 are	 processed	 in	 a	 timely	 manner.	 In	        lab	safety	rules	have	to	be	observed.
     order	to	enable	optimal	planning	it	is	mandatory	for	inves-
                                                                          8.		 The	equipment	belonging	to	the	IZKF	Münster	cannot	be	
     tigators	to	make	an	appointment.
                                                                              relocated.	 Experiment-based	 relocation	 of	 equipment	 is	
3.		 Use	of	the	Core	Units	by	researchers	from	other	faculties,	              only	possible	after	obtaining	prior	consent	from	the	IZKF	
     universities	or	industrial	clients	is	invariably	possible	fol-           Scientific	Office.
     lowing	 submission	 of	 a	 written	 application.	 Cooperation	
                                                                          9.		 The	researchers	of	the	Core	Units	are	obligated	to	handle	
     with	other	universities	and	industrial	clients	necessitates	
                                                                              the	results	and	data	in	a	strictly	confidential	manner,	and	
     the	signing	of	a	contract	e.g.	MTA	with	the	UKM	or	WWU	
                                                                              cannot	 duplicate,	 publish	 or	 use	 the	 data	 for	 any	 other	
     Münster,	 in	 order	 to	 protect	 the	 ownership	 rights	 of	 the	
                                                                              purposes.	Exceptions	to	this	rule	have	to	be	documented	
     data acquired.
                                                                              in	writing.
4.		 Members	 of	 the	 Medical	 Faculty	 will	 be	 charged	 for	 con-
                                                                          10.	 Users	of	the	services	affirm	that	the	Core	Units	of	the	IZKF	
     sumables.	Members	of	other	Natural	Sciences	Faculties	of	
                                                                              Münster	take	no	responsibility	for	contaminated	samples.	
     the	WWU	Münster	will	be	charged	additional	costs	(partial	
                                                                              Users	 also	 take	 complete	 responsibility	 for	 all	 data	 /	 re-
     cost	recovery	expenses	for	service	contracts).	All	external	
                                                                              sults	with	respect	to	safety,	completeness	and	confidenti-
     users	have	to	pay	service	fees	including	value-added	tax	
                                                                              ality.	
     (VAT),	as	outlined	in	the	respective	price	lists.

5.		 Scientific	cooperation	between	the	head	of	a	facility	and	             These	Terms	of	Use	were	passed	by	the	IZKF	Board	of	Direc-
     other	scientists	is	solely	intended	for	the	advancement	of	            tors	on	06.	November	2007	and	take	effect	immediately.
     methods	 and	 technology.	 In	 exceptional	 cases	 it	 is	 pos-
                                                                                                                                                    >26

								
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