technology platform -...

Interdisciplinary Center

for Clinical Research

of the Medical Faculty Münster

Technology Platform

IZKF MÜNSTER

State-of-the-Art Technologies

IZKF Technology Platform

Our Goal

The rapid advancement in the field of biological

and biomedical research has facilitated an in-

depth understanding of cellular and molecular

processes in health and disease. This has given

rise to the need for researchers to have access

to efficient high throughput services that are

too cost- and labor-intensive for single univer-

sity institutions. The Interdisciplinary Center for

Clinical Research (IZKF) Münster operates sev-

eral Core Units, which are a valuable resource

for an effective research environment.

Principal Aims

> The Core Units specialize in providing State-

of-the-Art skilled technical and instrument

support for the Medical Faculty of the Univer-

sity of Münster, extramural faculty, external

non-affiliated institutions as well as indus-

trial researchers, at affordable rates.

> Specialists in the field assist researchers

from the stage of project conception to its

completion thus ensuring maximum efficien-

cy.

> Researchers have open access to a large in-

strument pool consisting of expensive high-

end equipment that has increased the versa-

tile nature of the technology available to the

institutions of the Medical Faculty.

> The Core Units operate on a cost recovery ba-

sis and charges reflect the actual expenses

for consumables and service contracts.

Moreover, the Core Units promote translational

research by interacting closely with academia

and industry, ensuring that the technology

available is continuously updated. Lectures,

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: [email protected]



The IZKF Münster Technology Platform provides users with state-of-the-art

expertise and equipment and currently consists of three highly specialised Core

Units (CU) - Integrated Functional Genomics (IFG), Transgenic Animal Models

(TRAM) and Preclinical Imaging eXperts (PIX). The Core Unit PIX now combines

the expertise of the former IZKF Core Units ECHO, OPTI, SAMRI and SmAP in the

area of multimodal preclinical imaging. The IZKF Scientific Office coordinates

and supports these Core Units and oversees their smooth operation.

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 mandatory

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 Core Unit services in their

grant applications.

The logos on the upper right hand corner are specific to each Core Unit, 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.



Coordination &

Management

Preclinical Imaging eXpertsIntegrated Functional Genomics

TRAM

Transgenic Animal Models

IZKF

Mün

ster

(01/

2013

)

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, storage, 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 strategies. The IFG provides open access to this leading edge technology that is continuously validated according to the experimental needs of researchers, coordinates interdisciplinary research projects and organises workshops. The IFG hosts the Annual Münster Conference on Single Cell and Molecule Analysis that monitors the state-of-the-art in the field of nanoanalytics.

Prof. Dr. Monika Stoll took over the coordination of the IFG in January 2013.

Transgenic animal models (TRAM) 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. Numerous transgenic and knock-out models have been successfully generated by this Core Unit.

Preclinical Imaging eXperts (PIX) is a Core Unit for preclinical imaging that provides access to multimodal imaging technologies for cooperative research in a highly integrated structure. PIX is based on an already existing infrastructure and proven expertise for single preclinical imaging tools, namely magnetic resonance imaging, positron emission tomography, single-photon-emission-tomography, X-ray computed tomography, ultrasound, near-infrared fluorescence imaging, and bioluminescence imaging

PIX offers:• Integrated expertise through a project consulting service to tailor the application of imaging tools to the scientific questions of research partners • Integrated workflow for efficient multimodal imaging and data analysis • Interdisciplinary training for scientists and technicians• Quality control of project management, imaging workflow, data analysis, data logistics and training.

The imaging workshop The Mouse Imaging Academy (MIA) is a special workshop hosted annually by PIX. MIA aims at providing theoretical and practical training for young researchers and students in the field of small animal imaging.

IZKF Technology PlatformOverview

Coordinators

Prof. M. Stoll

Prof. J. Brosius

Dr. S. Hermann

IZKF

Mün

ster

(01/

2013

)

The field of genomics emerged from the

initiation of various genome projects, and

the resulting knowledge created the field

of functional genomics, concerned with

analysing gene expression, epigenetics,

mutations and genetic variation, to name

a few. The Genomics facility offers its

customers a wide range of services from

single-cell microdissection, real-time

PCR, various microarrays to Next-Gener-

ation Sequencing (NGS). In addition to

providing the full service package from

experimental design to the final steps of

data interpretation, technical training is

offered to enable self-service handling of

the equipment.

Laser capture micro-dissectionLaser capture micro-

dissection (LCM) is

a unique technique

that enables RNA and

DNA to be isolated from pure specimens

of specific groups of cells or even single

cells devoid of contaminating adjacent

tissue. LCM can be performed on a vari-

ety of tissue samples including frozen tis-

sue sections and paraffin sections. Using

this method a sufficient number of cells

can also be collected from archival brain

tissue (Hasselblatt et al., 2006). This ma-

terial is pure enough to be used in down-

stream applications like PCR and genetic

fingerprinting. The P.A.L.M. Micro Laser

system is housed in a separate room and

is available to all users of the Genomics

unit.

Quantitative real-time PCRReal-time PCR continues to be the stand-

ard technology for gene expression stud-

ies. The 7900HT system (Applied Biosys-

tems) detects and quantitates nucleic

acids sequences in 384-well plates. This

system supports applications such as

gene expression, SNP genotyping, path-

ogen detection, viral load analysis and

miRNA quantification.

The 7900 HT system is available for self-

service after a demonstration by the

Genomics team.

TaqMan® Low Density ArraysThe 7900HT sys-

tem has an in-

terchangeable

block for TaqMan® Custom Array Cards.

These are 384-well micro fluidic cards

that enable 384 real-time PCR reactions

to be performed simultaneously without

the need for liquid handling robots.

Integrated Functional Genomics (IFG)

Genomics Facility

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

This low- to medium- throughput micro

fluidic card allows for 1-8 samples to be

run in parallel against 12-384 TaqMan®

Gene Expression Assay targets that are

pre-loaded into each of the wells on

the card. The TaqMan® Custom Array is

completely customizable. Over 50,000

TaqMan® Gene Expression Assays de-

signed for human, mouse, rat genes, and

miRNAs are available. Additionally, pre-

configured TaqMan® Gene Signature Ar-

rays for human ABC transporters, human

angiogenesis, human apoptosis, human,

mouse or rat GPCR, human and mouse

Alzheimer, rat and human inflammation

etc. can be used.

Affymetrix microarraysAffymetrix arrays enable the simultane-

ous detection of mRNA abundance of

thousands of target genes to determine

whether they have been switched “on” or

“off” in a biological or pathological state.

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• Whole-Transcriptome Analysis

for many species like human, mouse, rat,

Arabidopsis, C. elegans, chicken, Dros-

ophila, E. coli, maize, rice, S. aureus,

Xenophus, yeast, zebrafish etc.

The Genomics unit offers a complete

gene expression analysis service from

controlling RNA integrity to supplying the

raw data. A basic or extensive analysis of

the data is carried out by the IFG bioinfor-

matics facility.

GenePix® microarray scanner

The GenePix® 4000B microarray scan-ner coupled with GenePix® Pro Micro-array Image Analysis Software and Acu-ity® microarray informatics software, sets the highest standards in the ac-quisition and analysis of data from all types of arrays, including nucleic acids, proteins, tissues, and cells. The Gene-Pix® 4000B scanner acquires data at user-selectable resolutions between 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.

Genepix 4000B Array-Scanner


Genomics Facility

Affymetrix GeneChip

Next Generation Sequencing

The Next-Generation Sequencing (NGS) technology is the most up-to-date tech-nology available in genomic science. Thus, the IFG is proud to offer this tech-nology to its customers.

Our 5500xl SOLiD™ System (Applied Biosystems®/LifeTechnologies®) provides the combination of accuracy, sensitivity, and cost effectiveness to support large translational research studies. It helps to ensure optimal pro-ductivity with two flexible FlowChips, embedded quality controls, and project scalability. The system’s two configura-ble microfluidic FlowChips process up to 12 independent samples and the intelligent barcoding kits multiplex up to hundreds of samples in a single run. However, also projects with small sam-ple numbers can be run at a reasonable cost due to the flexible design. Pay-Per-Lane Sequencing and independent run lanes tailor the system to any project scale.

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-ical variation for applications for

Eukaryotes as well as Prokaryotes such as:

• Whole genome (Re-)Sequencing,

• Targeted Resequencing,

• SNP Detection,

• Structural Variant Detection,

• Whole Transcriptome Analysis,

• Gene Expression Analysis,

• Small RNA Analysis,

• Chromatin Immunoprecipitation Sequencing,

• Methylation Analysis

using

• Fragment Libraries (single or paired end) or

• Mate-paired Libraries

in

• Single-sample or

• Multiplex Design.

The NGS service provided by the IFG comprises the project design support, quality control (QC) of the customer-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

Covaris S-series High Performance Sample Preparation System


Genomics Facility

Bioinformatics support

The Genomics team works closely with the Bioinformatics team offering cus-tomers of the IFG professional scale

bioinformatics solutions. In addition

to standard services the bioinformatics

team supports specific requests with in-

dividual bioinformatics solutions tailored

to the specific needs of the customers.

Representative PublicationsSchmitz KJ, Helwig J, Bertram S, Sheu SY, Suttorp AC, Seggewiss J, Willscher E, Walz MK, Worm K, Schmid KW (2011) Differential expression of microRNA-675, microRNA-139-3p and micro-RNA-335 in benign and malignant adrenocortical tumours. J Clin Pathol 64: 529-535.

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-dothelial cells. J Infect Dis 201: 871-880.

Hasselblatt M, Mertsch S, Koos B et al. (2009) TWIST-1 is overexpressed in neoplastic choroid plexus epithelial cells and promotes proliferation and invasion. Cancer Res 69: 2219-2223.

Edemir B, Kurian SM, Eisenacher M et al. (2008) Activation of counter-regulatory mechanisms in a rat renal acute rejection model. BMC Genomics 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.

Dr. rer. nat. Jochen SeggewißIntegrated Functional Genomics (IFG)

Röntgenstraße 2148149 Münster

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

Contact

Tel: +49 (251) 83 - 57168 Fax: +49 (251) 83 - [email protected] IZ

KF M

ünst

er (0

7/20

11)

WORKFLOW

Meeting with the Genomics & Bioinfor-matics team to discuss experimental de-sign, sample preparation and pricing

Researcher fills out the mandatory Order Form

- Sample submission

- Quality control of RNA / DNA

- Customer feedback

Microarray or High Throughput Sequenc-ing experiments are carried out

Raw or analysed data will be handed over to the customer as a hard copy


Genomics Facility

Please acknowledge the IFG Genomics / Bioinformatics Departments if the data generated by us is used in a publication and notify us when the manuscript is published

Proteins are the principal effectors in

cellular function and the target of most

pharmacological strategies. The goal of

the proteomics facility is to provide cost-

effective access to sophisticated tech-

nology for modern proteomics analysis

in a central facility. Special emphasis is

placed on assisting researchers in de-

signing and evaluating their research

projects and includes extra features such

as advanced manual and bioinformatic

data mining.

Biomolecular mass spectromeryMass spectrometers are available (Q-TOF

Premier, ESI/AP-MALDI (IR/UV) ion trap,

MALDI-TOF), which can be flexibly used

for different types of experiments such as

the determination of molecular weights

of biomolecules regardless of their size.

Soft ionization techniques allow the anal-

ysis of intact proteins and labile modifi-

cations. Procedures have been devel-

oped to monitor enzymatic or chemical

reactions or to fingerprint biological flu-

ids. Not only proteins and peptides can

be investigated; the analysis of certain

types of drugs (e.g. Imatinib), fatty acids

or other substances in complex mixtures

is also possible.

Protein identificationThe analysis of proteins pre-separated

by electrophoretic or chromatographic

means is one of the main service tasks.

Reversed-phase nanochromatography

coupled to high-end mass spectrometry

(LC-MS; nanoUPLC/Q-TOF Premier) allows

confident assignment of proteins after

enzymatic digestion. Protein modifica-

tions such as phosphorylation, isoforms

and unknown sequences are accessible

in specially designed experiments.

Protein expression analysisThe The unit offers a choice of gel-based

or MS-based differential analysis. The

entire pipeline for the DiGE technol-

ogy (Differential Gel Electrophoresis) is

available. This is an advanced system

solution based on 2D-PAGE (separation

of proteins according to their isoelectric

point (pI) and molecular weight), which

enables the quantification of protein

expression profiles of two samples (e.g.

normal vs disease state) in a reproduci-

ble and statistically relevant manner. The

methodology eliminates gel-to-gel vari-

ance and represents the state-of-the-art

in gel-based expression analysis. DiGE

gels are scanned with the Typhoon 9400

three-laser scanner, which is also versa-

tile for use in other applications such as

modification-directed staining. Regulat-

ed proteins are subsequently identified

using LC-MS/MS.

A dedicated MS-based approach using Q-

TOF Premier MSE technology allows label-

free absolute and relative quantification

of proteins. It promises comprehensive

data with high reproducibility and re-

duced sample handling. Even less sam-

ple is needed (~2 µg compared to 500

µg for DiGE) and the data can be stored

indefinitely for later mining. The identi-

fication of hundreds of protein compo-

nents of one proteome is automatically

performed. The results of the analysis in-

clude not only the fold changes in regula-

tion but also provide clear insights about

the magnitude of proteome differences

and regulatory factors using principal

component analysis (PCA)- see Bioinfor-

matics section).


Proteomics Facility

Protein separation and gel electro-phoresisThe unit assists in the preparation of tis-

sue homogenates or cell lysates. 1D- and

2D-electrophoresis can be performed

with customer samples. Moreover, the

fractionation of proteins in the liquid

phase based on their pI is possible, e.g.

to exclude dominant proteins for subpro-

teome analysis. Quality control of protein

separations is carried out with a minia-

turized capillary electrophoresis lab-on-

a-chip system. This method serves to rap-

idly diagnose separation procedures or

sample quality. Biological fluids such as

urine, cell extracts or whey can be evalu-

ated for their protein content.

Profiling of biofluidsLC-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.

Protein arraysProtein arrays are increasingly used to

miniaturize interaction experiments.

They serve to detect proteins, study their

expression levels, as well as their interac-

tions and functions. Using protein arrays,

efficient and sensitive high-throughput

analysis of thousands of proteins can be

achieved simultaneously. Protein arrays

such as the FAST slides can be analysed

with two microarray scanners. Protein

arrays are commercially available for cy-

tokine and biomarker analysis as well as

autoimmune diagnostics.

Bioinformatics for proteomics and profilingIt has become increasingly necessary to

evaluate and visualize proteomic or mass

spectrometric data with statistical meth-

ods. A number of procedures have been

established for that purpose:

Protein expression analysis using DIGEThe 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-

ware provides multivariate statistics

tools and enables the combined analysis

of different datasets, aiding the biologi-

cal interpretation of results by matching

with data retrieved from public and local

databases.

Pre-fractionation of protein mixtures for sub-proteome analysis


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

thousands of data points) to lower

dimensional subspace spanned by

the principal eigenvectors and assist

investigators in finding major differences

in their samples. It is an important step

preceding biomarker assignment both

in proteomics and the analysis of LC-MS

profiles of urine or other biofluids

Exploratory analysis and data visu-alisationVisuMap 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.

Pathway analysisThe information about regulated

proteins is further processed identifying

relationships, mechanisms, functions,

and pathways of relevance using

Ingenuity software. It delivers an

assessment of signaling and metabolic

pathways, molecular networks, and

biological processes that are most

significantly perturbed in the dataset of

interest.


Proteomics Facility

Prof. Dr. rer. nat. Simone KönigIntegrated Functional Genomics (IFG)



Tel: +49 (251) 83 - 57164 Fax: +49 (251) 83 - 57255

[email protected]

Contact

IZKF

Mün

ster

(01/

2013

)

Protein Histidine Phosphatase (PHP)

PHP was discovered by the late

Prof. Susanne Klumpp and studied

extensively* in her group at the Institute

of Pharmaceutical and Medical Chemistry

at the WWU, Münster. As a result of

earlier collaborations, the IFG continues

to provide PHP for research purposes.

*Klumpp S, Krieglstein J (2009) Reversible Phosphorylation of Histidine Residues in Proteins

from Vertebrates. Sci Sig 10: 2(61):pe13

The following products are available on

request:

1. Dry recombinant PHP supplied in aliquots of 1 mg (or as required)

2. Glycerol culture of recombinant PHP supplied in aliquots of 1 ml (or as required)

Additional publications and further

information can be found at

http://php. uni-muenster.de

Representative PublicationsHahn A, Kaufmann JK, Wies E et al. (2012) The ephrin receptor tyrosine kinase A2 is a cellular receptor for Kaposi’s sarcoma-associated herpesvirus Nature Med 18: 961-966.

Tekook M, Fabritz L, Kirchhof P, König S et al. (2012) Gene construction, expression and func-tional testing of an inotropic polypeptide from the venom of the black scorpion Hottentotta ju-daicus. Toxicon 60: 1415-1427.

Hermann A, König S, Lechtenberg M et al. (2012) Polysaccharides and glycoproteins from Boswellia serrata Roxb. and B. carteri Birdw. and identification of a proteolytic plant basic secretory protein. Glycobiology 11: 1424-1439.

Kummer MP, Hermes M, Delekarte A et al. (2011) Nitration of Tyr10 critically enhances amyloid beta aggregation and plaque formation. Neuron 71: 833-844.

Kriegeskorte A & König S, Sander G et al. (2011) Small colony variants of Staphylococcus aureus reveal distinct protein profiles. Proteomics 11: 2476-2490.

König S (2011) Urine molecular profiling distin-guishes health and disease: New ways in diag-nostics? Test case UPLC-MS. Exp Rev Mol Diagn 11: 383-391.

Wang W, Ackermann D, Mehlich A-M, König S (2010) False labelling due to quenching failure of N-hydroxysuccinimide-ester coupled dyes. Prot-eomics 7: 1525-2529.

Hasche A, Ferenz KB, Rose K, König S et al. (2010) Binding of ATP to nerve growth factor: Characterization and relevance for bioactivity. Neurochemistry Intern 56: 276-284.

Instrumentation such as array scan-ners, gel imagers and PAGE equipment are available for customer’s use.

Open access

Users can provide tissue, cells or pro-tein mixtures for analysis and are ad-vised to contact the proteomics staff who will be pleased to assist in ex-perimental design and to discuss the parameters that samples have to fulfill to ensure smooth processing and ex-cellent results.

Getting started

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Proteomics Facility

The Bioinformatics Group provides cus-

tomers of the IFG with standard and

advanced statistical solutions for their

Microarray, Real-Time PCR and Next Gen-

eration Sequencing projects.

Especially the analysis of data from a

whole genome association study or a

NGS sequencing project requires pro-

fessional scale bioinformatics. We offer

standard assembly, alignment, mapping

genotyping and annotation services and

in addition we can support specific re-

quests with individual bioinformatics

solutions in close collaboration with cus-

tomers and scientists.

Next Generation Sequencing (NGS)The next-genera-

tion sequencing

(NGS) technolo-

gies constitute

various strate-

gies that rely on

a combination of template preparation,

sequencing and imaging, and genome

alignment and assembly methods. The

arrival of NGS technologies on the market

has changed the way we think about sci-

entific approaches in basic, applied and

clinical research.

We offer individual solutions for the anal-

ysis of NGS data from our Life technolo-

gies SOLiD 5500 System and other plat-

forms (e.g. Roche 454, Illumina HiSeq or

GA). We provide a NGS data service from

the primary basic analysis with quality

checks and base calling to the advanced

analysis with assembly, mapping, clus-

tering, annotation and visualization in

close collaboration with our customers.

NGS applicationsThe production of large numbers

of low-cost reads makes the NGS

platform useful for many applications.

These include variant discovery by

resequencing targeted regions of interest

or whole genomes, de novo assemblies of

bacterial and lower eukaryotic genomes,

cataloguing the transcriptomes of cells,

tissues and organisms (RNA–seq),

genome-wide profiling of epigenetic

marks and chromatin structure using

other seq-based methods (ChIP–seq)

and species classification and/or gene

discovery by metagenomics studies.

We use a flexible software pipeline ar-

chitecture based on Bioscope®, which

enables maximum flexibility and ease of

use for performing high throughput data

analysis for the SOLiD™ instrument data.

It provides the following features:

Alignment and MappingVarious bioinformatics tools are used

for the assem-

bly (Velvet) and

the alignment

(BFAST, BWA, Bowtie) and are intelligent-

ly linked up to form project-specific pipe-

lines. After the NGS raw data has been

generated, the color space reads are

aligned to a known reference sequence

or assembled de novo.

SNP detection

We use the diBayes software package

which allows sensitive and specific SNP

detection even at moderate to low cov-

erage. It al-

lows varying

the levels of

stringency and provides full control over

many filters for customization to fit par-

ticular experimental designs.


Bioinformatics Facility

01001011100010001010011010010001

Structural variants detection All sequence variants other than single-

nucleotide variants, including insertions

or deletions, inversions, segmental du-

plications and copy-number differences

can be detected by the use of the special

Applied Biosystems software (AB Large

and Small InDel tools, Inversion and CNV

tools).

Whole transcriptome analysis

The Whole Transcriptome Analysis (WTA)

toolset (Bowtie, TopHat, and Cufflinks)

aligns the reads to a reference genome.

Using the mapping results, it counts the

number of tags aligned with exons, and

can convert the BAM file to the WIG for-

mat to view the coverage in a genome

browser (UCSC, IGV). The Expression

analysis includes statistical tests and the

calculation of p-values and fold changes.

WTA also supports experiments in fusion

detection. A fusion junction is a section

of transcribed RNA that maps to an exon

from one gene followed by an exon from

another gene. It occurs as the result of a

translocation, deletion, or chromosomal

inversion. A fusion junction excludes

exon- exon boundaries that arise from al-

ternative splicing for a gene.

The Affymetrix platformOur Affymetrix® Microarray technology

platform is a powerful tool for genomic

RNA and DNA analysis. Each study com-

prises multiple arrays with thousands of

transcripts or millions of markers (geno-

types, SNPs, CNV and

LOH marker) in groups

corresponding to differ-

ent experimental settings.

Conditions range from sin-

gle factor designs (treatments or tissue

types, times, benign-adverse in complex

diseases) with only a view arrays (includ-

ing technical and biological replicates) in

small groups up to whole genome associ-

ation studies with hundreds or thousands

of samples in a case-control design.

Primary and advanced analysisOur Bioinformatics facility provides users

with data from a primary analysis (qual-

ity, .CEL, .CHP, .CNT and exported text

and Excel-files) using the Affymetrix tools

(Genotyping and Expression Console,

GTC-Browser and Chromosome Analysis

Suite). In addition we provide results

and data from a more comprehensive

and complete microarray data analysis

in which we use the commercial Partek®

Genomics Suite, Ingenuity® Pathway

Analysis (IPA) and S-Plus (TIBCO® Spot-

fire S-Plus) scripts from our own software

development. For the advanced (second-

ary) analysis, which we coordinate in

close collaboration with our customers

we offer:

Expression analysisThis includes quality checks (background

adjustment, outlier detection), normali-

zation (standard, quantile and lowess

normalization), two group comparisons

to identify genes which show differential

expression (robust two sample t tests, F

tests comparing the mean

square of two varieties, fold

changes, Mann-Whitney-

Wilcoxon rank sum tests),

multiplicity adjustments for

the p-values (FWER: Holm-

Bonferroni, FDR: Benjamini-

Hochberg), multiple group

comparisons (ANOVA, basic

linear and nonlinear mod-

els and Neural Networks),

pattern discovery (hierar-

chical and model based

(two-way) clustering), principal compo-

01001011100010001010011010010001



nents and factor analysis (Biplots, mul-

tidimensional scaling and gene shav-

ing), class prediction (linear discriminant

and nearest neighbors

analysis, classification

trees, Neural Networks,

risk analysis and ROC

curves) and annotation

with genomic informa-

tion including pathway analysis using the

IPA Pathway Analysis software.

Analysis of Whole Genome Associa-tion Studies (WGAS)WGAS are used in population genetics

to identify single nucleotide polymor-

phism (SNPs and their genotypes) which

can serve as marker sets in complex dis-

eases. A sufficient power requires a large

sample size, often 500 samples (arrays)

and more in each of two groups within a

case-control design. A typical WGA study

comprises three stages: screening (geno-

typing of ~106 SNPs using SNP 6.0 ar-

rays), replication of the

most promising SNPs in

matched cases and con-

trols and verification of

replicated association

signals in a larger co-

hort using an independent method (e.g.

TaqMan).

We provide full bioinformatics user sup-

port from the study design (sample size

and power calculations) during the whole

execution of the study (quality control

with reports from each array batch) to the

final genotype analysis of the TaqMan ex-

periments.

This includes quality checks (call rates,

identification of genotyping errors, Men-

del checks, tests for deviations from Har-

dy-Weinberg equilibrium and control of

minor allele frequencies), calculations of

Odds ratios (case vs. control) with FWER

and FDR control of the p-values for al-

lele and genotype frequencies in differ-

ent inheritance models, pairwise LD and

haplotype analysis, phenotype-genotype

association (susceptibility between

genotypes and disease) and relative risk

analysis using Logistic Regression (ad-

justed Odds ratios) and Neural Network

models.

Copy Number Variation (CNV) and Loss of Heterozygosity (LOH) analy-sisChromosomal abnormalities (allelic im-

balance, deletions, gains, Uniparental

Disomies (UPDs)) with structural changes

in the DNA play a major role in cancer

and cytogenetic re-

search. Amplification

of oncogenes and

loss of tumor sup-

pressor genes can

be detected by homozygous deletion or

loss of heterozygosity (LOH). Affymetrix

SNP 6.0 arrays with 906.600 SNPs and

946.000 CNV oligos and the Cytogenetics

Copy Number Assay (CytoScan HD) with

750.000 genotype-able SNPs and 1.8

million non-polymorphic probes allows

the user to perform a high-resolution

genome-wide analysis of chromosomal

aberrations.

Registered users can download the Chro-

mosome Analysis Sweet from Affymetrix

to analyze and compare the .cel files

from different experiments and to display

chromosomal abnormalities in a user-

friendly viewer.

We use Parteks Genomics Suite’s to de-

tect, display, and report regions of am-

plification or deletions on the genome.



01001011100010001010011010010001

After identification of regions with signifi-

cant copy number changes (CNV) or LOH,

gene lists can be created and exported,

and corresponding gene or exon expres-

sion data can be seamlessly linked to the

mapping array data if available.

On user inquiry we develop special S-

Plus scripts e.g. to display LOH and CNV

regions from several case-control or tu-

mor vs. normal tissue experiments in one

(publication quality) graphic or to detect

significant marker regions by comparing

the discordant Chi-square distributions

(McNemar’s chi-square test) of markers

in case-control experiments.

Real-time PCR analysisWe carry out quality controls of the input

data to detect and filter errors that oc-

curred during the experiment. Embed-

ded methods permit endogenous genes,

which are optimal for normalisation, to

be determined. The applied software pro-

vides relative quantification analysis of

differential expression data, combining

interactive visualisation with advanced

statistics and data mining.

Representative PublicationsSchmitz KJ, Helwig J, Bertram S, Sheu SY, Suttorp AC, Seggewiss J, Willscher E, Walz MK, Worm K, Schmid KW (2011) Differential expression of microRNA-675, microRNA-139-3p and microRNA-335 in benign and malignant adrenocortical tumours. J Clin Pathol 64: 529-535.

Grundmeier M, Tuchscherr L, Brück M et al. (2010) Staphylococcal strains vary greatly in their ability to induce an inflammatory response in endothelial cells. J Infect Dis 201: 871-80.

Mees ST, Mardin WA, Wendel C et al. (2010) EP300--a miRNA-regulated metastasis suppressor gene in ductal adenocarcinomas of the pancreas. Int J Cancer 126: 114-124.

Mees ST, Mardin WA, Sielker S et al. (2009) Involvement of CD40 targeting miR-224 and miR-486 on the progression of pancreatic ductal adenocarcinomas. Ann Surg Oncol 16: 2339-2350.

Getting started

After consultation with the customer or scientist we perform a basic (prima-ry) or more comprehensive (second-ary) analysis of the raw data. Micro-array data (.CEL, .CHP, .CNT, .CSV and .XLS files) can be obtained on CDs or DVDs. The raw data from NGS experi-ments (.CSFASTA, .QUAL files) and the data from a secondary analysis (.BAM, .SAM, .GFF, .BAI, .BED and .CSFASTA.MA files) can be obtained on external 2TeraByte HardDisks. Alternatively all data can be downloaded from the IFG FTP-server.

Dr. rer. nat. Andreas HugeIntegrated Functional Genomics (IFG)


Dr. rer. nat. Reinhard VossIntegrated Functional Genomics (IFG)



Tel: +49 (251) 83 - 52207 Fax: +49 (251) 83 - 57255

[email protected]

Tel: +49 (251) 83 - 58964 Fax: +49 (251) 83 - 57255

[email protected]

01001011100010001010011010010001



IZKF

Mün

ster

(07/

2011

)

Mice are physiologically similar to hu-

mans, thus making them ideal organisms

to model human diseases. This is made

possible by recent advances in transgen-

ic technologies. Transgenic mice are cre-

ated by integrating foreign DNA into the

germ line of mice. The pathogenesis and

therapeutic strategies of various human

diseases can be studied in transgenic

mice carrying the respective disease

causing genes. Another major advance-

ment in the development of mouse mod-

els of human diseases was the gene

knockout. This technology makes it pos-

sible to introduce certain mutations into

endogenous genes and transmit these

through the mouse germ line.

Since 1996 this unit has provided a cen-

tralised service to produce regular trans-

genic mice, BAC (bacterial artificial chro-

mosome) transgenic animals, as well as

a variety of gene-targeted (conventional

or conditional), and chromosome-engi-

neered mice. The unit aims to reduce the

work load and the costs of its custom-

ers. Methods for transgenic/targeting

DNA constructs design (conventional and

PCR cloning) and DNA recombineering in

E.coli have been developed. Related ser-

vices such as embryo cryo-preservation

and strain re-derivation are also avail-

able.

The unit is fully equipped for:1) Molecular biology procedures such as

cloning, mutagenesis etc.

2) Cell culture

3) Microinjection with 2 complete setups

for pronuclear and blastocyst injec-

tions.

The animal house is equipped with indi-

vidually ventilated cages and is operated

under specific pathogen free (SPF) condi-

tions. Mice are housed under sterile con-

ditions until they can be transferred to

the care of the customer.

Generation of conventional/conditional “knock-out”, “knock-in” and “chromosome engineered” miceWe offer the following services for each

step of targeted mice production:

• Targeting vector design includes bio-

informatics analysis and cloning strat-

egy design. For genomic sequences

that are difficult to clone we provide

alternative strategies.

• Embryonic stem (ES) cell line gen-

eration from the desired mouse

lines, including karyotype analysis

and characterisation of ES cell for the

germ-line competence.

• ES cell electroporation and process-

ing (expansion, analysis and freez-

ing) of individual ES colonies. Screen-

ing of ES cells for positive targeting

events is performed with the help of

nested PCR and Southern blot analy-

sis. All positively targeted colonies

are subjected to karyotype analysis.

• Blastocyst injections of positively

targeted ES colonies into B6D2F1

hybrids, as well as tetraploid blasto-

cysts, with production either chimae-

ras or 100% ES derived animals.

Transgenic Animal Models (TRAM)

Generation of transgenic miceDNA constructs are purified and in-

jected into both pronuclei of the FVB/n

mouse oocytes. 150-200 oocytes are

routinely injected per construct. DNA in-

jected into the pronucleus integrates into

chromosome(s) and is transmitted to the

germ line. Injections are repeated in case

they do not result in positive transgenic

animals. Services also include Southern

blot analysis of tail biopsy DNA as well

as pronuclear injections of BAC DNA con-

structs.

Re-derivation of mouse coloniesIn order to produce infection-free animal

models, mouse lines are held in a spe-

cific pathogen free (SPF) environment.

Embryos can be stored for a long period

of time by transferring them from a “con-

taminated” environment to SPF condi-

tions.

Long-term storage of mouse spermMouse sperm is obtained and frozen with

consecutive in vitro fertilisation proce-

dures.

Disease models created in mice:› Renal development and function

› Arterial hypertension with endothelial and smooth muscle control

› Cardiac hypertrophy and Insufficiency

› Skin sensitivity

› Hypervolemic arterial hypertension

› Neuropsychiatric disease and behaviour

› Role of S100A9 in inflammatory mechanisms

› Autosomal dominant polycystic kidney disease (PKD2)

› Model for the Prader Willi syndrome (PWS)

Representative PublicationsHartmann 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 in mice results in postnatal growth retardation. PLoS Genet 3: e235.

Dworniczak B, Skryabin B, Tcinda S et al. (2007) Inducible Cre/loxP recombination in the mouse proximal tubule. Nephron Exp Nephrol 106: e11-

20.The investigator is requested to meet with the facility staff to design the project. Forms to initiate service can be downloaded from the website. In-formation about costs and issuing in-voices are given by the IZKF Scientific Office.

Getting started

Contact

Univ.-Prof. Dr. rer. phil. Jürgen BrosiusInstitute of Experimental Pathology (ZMBE)

Von-Esmarch-Str. 5648149 Münster

http://tram-izkf.uni-muenster.de

Tel: +49 (251) 83 - 52133 Fax: +49 (251) 83 - 58512

[email protected]

Transgenic Animal Models (TRAM)

Pronuclei Injection

IZKF

Mün

ster

(07/

2011

)

Molecular imaging covers a broad spec-

trum of applications ranging from imag-

ing of single cells or even subcellular

structures in vitro to clinical diagnostic

imaging in patients in vivo. The aim of

this core unit is the non-invasive phe-

notypisation of wild type, surgical and

transgenic animal models using highly

sensitive and high resolution dedicated

small animal imaging technology. The CU

offers both scientific expertise and tech-

nology access.

Small animal positron emission tomography (PET)PET is a highly sensitive, quantitative

imaging modality capable of assessing

molecular dynamics in vivo with nano-/

picomolar sensitivity. Within SmAP two

dedicated high resolution small animal

PET scanners with sub-milliliter resolu-

tion and a large field of view (28 cm * 16

cm) are available (quadHIDAC®, Oxford

Positrons Ltd., Oxford, UK). In coopera-

tion with the Department of Nuclear Med-

icine and the SFB 656 “Molecular Cardio-

vascular Imaging” this core unit is able to

offer a wide range of different molecular

imaging probes ranging from whole-body

measurement of perfusion and metabo-

lism down to cell imaging and imaging of

targets involved in oncological, inflam-

matory, neurological, cardiovascular and

other diseases.

Small animal single photon emission tomography (SPECT)

Recently a dedicated multi-pinhole

SPECT/CT system for animals having a

sub-millimeter resolution and good sen-

sitivity was installed (NanoSPECT/CT,

Bioscan, US). The SPECT methodology is

basically a gamma camera system that-

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

s u bs ta n t i a l l y

broaden the

spectrum of mo-

lecular targets

and methodol-

ogy.

PET-CT / SPECT-CT

Preclinical eXpertsImaging

Small animal computed tomography (CT) CT is an anatomic imaging modality with a

very high spatial resolution. The core unit

houses a dedicated small animal high-

resolution CT device with a resolution

down to 15 µm for in vivo and ex vivo

applications (Siemens Inveon®). SmAP

uses this method primarily to provide

anatomical information in correlation

to the distribution of specific molecular

imaging probes in PET and SPECT. In

general, small animal CT alone offers a

spectrum of applications similar to CT in

the clinical setting.

Ex-vivo autoradiography and biodistributionBeside 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.

StatisticsIn the last three years 4279 PET and CT

measurements have been carried out on

mouse (87%) and rat (13%) models of

human disease.

Representative PublicationsClaesener M, Breyholz H-J, Hermann S, Faust A, Wagner S, Schober O, Schafers M, Kopka K (2012) Efficient synthesis of a fluorine-18 labeled biotin derivative. Nucl Med Biol 39: 1189-1194.

Bunk EC, Stelzer S, Hermann S, Schäfers M, Schlatt S, Schwamborn JC (2011) Cellular organi-zation of adult neurogenesis in the Common Mar-moset. Aging Cell 10: 28-38.

Reuter S, Schnöckel U, Edemir B, Schröter R, Kentrup D, Pavenstädt H, Schober O, Schlatter E, Gabriëls G, Schäfers M (2010) Potential of nonin-vasive serial assessment of acute renal allograft rejection by 18F-FDG PET to monitor treatment ef-ficiency. J Nucl Med 51: 1644-1652.

Law MP, Schäfers K, Kopka K, Wagner S, Schober O, Schäfers M (2010) Molecular imaging of car-diac sympathetic innervation by 11C-mHED and PET: from man to mouse? J Nucl Med 51: 1269-1276.

Contact

Univ.-Prof. Dr. med. Michael SchäfersEuropean Institute for Molecular Imaging Technologiehof Münster, Building L1Mendelstraße 1148149 Münster

Tel: +49 (251) 83 - 49301 Fax: +49 (251) 83 - 49313

[email protected]

IZKF

Mün

ster

(01/

2013

)

PET-CT / SPECT-CT

Tc-99m-Tetrofosmin myocardial perfusion

imaging. Diagnostics for myocardial

schemia/infarction (normal perfusion)

Dr. med. Sven HermannEuropean Institute for Molecular Imaging Technologiehof Münster, Building L1Mendelstraße 1148149 Münster

http://smap-izkf.uni-muenster.de

Tel: +49 (251) 83 - 49303 Fax: +49 (251) 83 - 49313

[email protected]


Small animal optical imaging allows

quantitative data on key diseases and

therapeutic response profiles to be gen-

erated in vivo. Fluorescence imaging in

the near-infrared range (700-900 nm),

also called „optical window“, is charac-

terised by low absorbance through oxy-

and-deoxy-hemoglobin (i.e. good tissue

penetration) as well as low levels of au-

tofluorescence, 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-

sures) so that molecular structures can

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,

the core unit offers scientific expertise for

experimental design and data analysis in

optical imaging.

Fluorescence reflectance imagerA fluorescence reflectance imaging (FRI)

system is available on-site for fast and

convenient acquisition of 2D fluores-

ence images. The Kodak In-vivo Imaging

Station FX Pro combines advanced mul-

tispectral fluorescence, luminescence,

digital x-ray and radioisotopic imaging

in a single system. Thus, multichannel

and multimodal imaging capabilities are

available. The system is ideal for rapid

evaluation of superficially located pro-

cesses such as subcutaneous tumors. In

addition to in vivo imaging, the system is

suitable for in situ, and ex-vivo fluores-

cence applications, e.g. biodistribution

studies. A wide range of filter sets are

available that are suited for different fluo-

rochromes or fluorescent proteins.

Fluorescence mediated tomographIn comparison to 2D techniques, fluores-

cence mediated tomography (FMT) offers

superior quantification accuracy and can

yield three-dimensional determination of

contrast agent uptake. Two state-of-the-

art FMT systems for small animal imaging

are installed in the core unit to yield 3D

quantitative tomographic images of small

animals. Data can be acquired at two dif-

ferent wavelengths: Excitation: 670 nm/

Emission: 700 nm and Excitation: 745

nm/Emission: 780 nm. Co-registration of

FMT data and e.g. MRT data is possible.

Optical Imaging

Biodistribution study

In vivo and ex vivo FRI images: alpha(v)beta(3) expression of artherioscle-rotic plaques.


Contrast agentsIn addition to commercially available

fluorescent contrast agents, the core unit

offers access to different fluorescence

imaging probes that were developed in

cooperation with the Department of Clini-

cal Radiology, the Department of Nuclear

Medicine and the Collaborative Research

Centre SFB 656 (MoBil) „Molecular Car-

diovascular Imaging“ at the University

of Münster. In detail, markers of tissue

perfusion, targeted probes for imaging

angiogenesis and MMP-expression are

available.

Representative PublicationsWaschkau B, Faust A, Schafers M, Bremer C (2013) Performance of a new fluorescence-labeled MMP inhibitor to image tumor MMP activity in vivo in comparison to an MMP-activatable probe. Contrast Media Mol Imaging 8: 1-11.

Eisenblätter M, Höltke C, Persigehl T, Bremer C (2010) Optical techniques for the molecular imaging of angiogenesis. Eur J Nucl Med Mol Imaging 37 Suppl 1: S127-137.

Larmann J, Frenzel T, Hahnenkamp A, et al. (2010) In vivo fluorescence-mediated tomography for quantification of urokinase receptor-dependent leukocyte trafficking in inflammation. Anesthesiol 113: 610-618.

Contact

Prof. Dr. med. Christoph Bremer Department of Clinical RadiologyAlbert-Schweitzer-Campus 1, Gebäude A16

48149 Münster

http://opti-izkf.uni-muenster.de

Tel: +49 (251) 83 - 56146Fax: +49 (251) 83 - [email protected]

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

IZKF

Mün

ster

(01/

2013

)

Optical Imaging

Getting startedThe investigator is requested to contact the Facility staff to discuss specific needs and to design the project.

Information about costs and issuing invoices are given by the IZKF Scientific office.


The Core Unit ECHO was established to

provide high-resolution ultra-sound im-

aging for morphological and functional

analysis in murine models. The core unit

is equipped with high-end ultrasound

technology and provides a wide range

of services using diagnostic ultrasound

equipment and ultrasound microscopes.

Small animal ultrasound: Imaging and therapy

A major focus of the core unit is small

animal phenotypisation of transgenic

murine models. Non-invasive morpho-

logical and functional analysis of cardio-

vascular structures (heart and vessels)

are provided for fetal, adolescent and

adult rodents. Supplementary to basic ul-

trasound imaging, simultaneous record-

ing of other physiological parameters

(e.g. ECG, blood-pressure) is provided.

Advanced imaging techniques such as

molecular imaging of a large range of

vascular epitopes, inflammation imaging

and tissue-perfusion imaging complete

the wide spectrum of ultrasonic imaging

techniques. Computer-assisted steering

and high-temporal real time ultrasound

microscopy allow image-guided injec-

tions for model-induction (e.g. tumor

models), advanced therapeutic strate-

gies (stem-cells, gene-therapy) or mere

local drug delivery.

Service

Services include follow-up studies in vari-

ous cardiovascular and tumor models.

On special demand multimodal imaging

combining other IZKF imaging platforms

can be arranged. The core unit integrates

our expertise and resources in small ani-

mal imaging and therapy with leading

researchers in this field to create new

opportunities and directions for study-

ing a large range of animal models. Team

members have long standing expertise in

mouse handling and physiologic moni-

toring. Databases supporting networking,

data handling and biostatistics round off

the spectrum of services provided.

Ultrasound

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.


PD Dr. med. Jörg StypmannDepartment of Cardiology and AngiologyAlbert-Schweitzer-Campus 1, Gebäude A148149 Münster

http://echo-izkf.uni-muenster.de

Contact

Tel: +49 (251) 83 - 44906 Fax: +49 (251) 83 - [email protected]

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.

The investigator is requested to meet with the Facility staff to discuss specific needs and to design the project.

Information about costs and issuing invoices are given by IZKF Scientific Office.

Getting started

Representative PublicationsDi Marco GS, Reuter S, Kentrup D, Ting L, Ting L, Grabner A, Jacobi AM, Pavenstadt H, Baba HA, Tiemann* K, Brand* M (2010) Cardioprotective effect of calcineurin inhibition in an animal model of renal disease. Eur Heart J 32: 1935-1945 . *= equal contribution

Dreischaluck J, Schwoppe C, Spieker T, Kessler T, Tiemann K, Liersch R, Schliemann C, Kreuter M, Kolkmeyer A, Hintelmann H, Mesters RM, Berdel WE (2010) Vascular infarction by subcutaneous application of tissue factor targeted to tumor vessels with NGR-peptides: activity and toxicity profile. Int J Oncol 37: 1389-1397.

Ultrasound

Stypmann J, Engelen MA, Troatz C, Rotheburger M, Eckardt L, Tiemann K (2009) Echocardiographic assessment of global left ventricular function in mice. Laboratory Animals 43: 127-137.


IZKF

Mün

ster

(07/

2011

)

Magnetic Resonance Imaging

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

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

cells over a time course of several weeks.

Morphological and functional data is

complemented by metabolic information,

which is available from MR spectroscopy

measurements, providing metabolic data

with sub-millimeter resolution.

Furthermore, fMRI is a valuable tool in

neurophysiological research, detecting

either the hemodynamic response of

neural activity via the BOLD (blood

oxygen level dependent) effect, or

activity of Ca2+-channels via MEMRI

(Manganese-enhanced MRI). Since fMRI

is a non-invasive techniques these data

can be collected over a time course and

compared to behavior experiments in the

same animal.

Infrastructure

The core unit SAMRI is equipped with a

state-of-the-art small animal MRI sys-

tem (Bruker Biospec 94/20), operating

at a magnetic field strength of 9.4 tesla.

Dedicated probes for mice and rats and

high-performance microscopy gradient

systems provide optimum preconditions-

for numerous applications. Installation

of a CryoProbe (Helium-cooled detector)

affords highest sensitivity for ultimate

temporal of spatial resolution. For cardiac

MRI and fMRI studies ECG and transcuta-

neous blood gas monitoring devices are

available.

9.4 T Biospec with cryoprobe

3D reconstruction of the murine thorax


Service

SAMRI offers a number of routine proto-

cols for high resolution morphological

imaging, as well as protocols for function-

al parameters in cardiac, developmental

or oncological models. Protocols for fMRI

studies or cell tracking applications are

devised on demand. MR spectroscopy

protocols can be established in coopera-

tion with the interested user. To allow for

a wide range of applications, including

infection models, the MR-system is in-

stalled in a S2-laboratory.

Representative PublicationsHoerr V, Purea A, Faber C (2010) NMR Separation of intra- and extracellular compounds based on intermolecular coherences. Biophys J 99: 2336-2343.

Weiss K, Melkus G, Jakob P, Faber C (2009) Quan-titative in vivo 1H spectroscopic imaging of me-tabolites in the early postnatal mouse brain at 17.6 T. Magn Reson Mater Phy 22: 53-62.

Schneider JT, Faber C (2008) BOLD Imaging in the Mouse Brain using a TurboCRAZED Sequence at High Magnetic Fields. Magn Reson Med 60: 850-859.

Getting started

The investigator is requested to meet with the facility staff to discuss specific needs and to design the project.

Information about costs and issuing invoices are given by IZKF Scientific Office.

Contact

Univ.-Prof. Dr. rer. nat. Cornelius FaberDepartment of Clinical RadiologyAlbert-Schweitzer-Campus 1, Gebäude A148149 Münster Tel: +49 (251) 83 - 57608

Fax: +49 (251) 83 - [email protected]

Sagittal image of the mouse brain in vivo

Magnetic Resonance Imaging

Morphological imaging of the mouse heart in vivo

Morphological imaging of the zebra finch brain in vitro

Coronal image of the mouse brain in vivo


IZKF

Mün

ster

(07/

2011

)

TERMS OF USE

I. The Terms of Use of the Core Units of the IZKF Münster

serves to provide information for all users and to imple-

ment the statutes of the IZKF.

II. TheIZKFScientificOfficeactingonbehalfoftheBoardof

Directors is responsible for all administrative coordina-

tion.

1. TheCoreunitsshouldbeexclusivelyutilizedforresearch

purposes.

2. PriorityaccesswillbegiventoallmembersoftheIZKFand

theMedical Faculty.Theheadsof theCoreUnitsshould

ensure thatordersareprocessed ina timelymanner. In

ordertoenableoptimalplanningitismandatoryforinves-

tigatorstomakeanappointment.

3. UseoftheCoreUnitsbyresearchersfromotherfaculties,

universitiesorindustrialclientsisinvariablypossiblefol-

lowing submissionof awritten application. Cooperation

withotheruniversitiesandindustrialclientsnecessitates

thesigningofacontracte.g.MTAwiththeUKMorWWU

Münster, in order to protect the ownership rights of the

data acquired.

4. Membersof theMedicalFacultywillbecharged forcon-

sumables.MembersofotherNaturalSciencesFacultiesof

theWWUMünsterwillbechargedadditionalcosts(partial

costrecoveryexpensesforservicecontracts).Allexternal

usershavetopayservicefeesincludingvalue-addedtax

(VAT),asoutlinedintherespectivepricelists.

5. Scientificcooperationbetweentheheadofafacilityand

otherscientistsissolelyintendedfortheadvancementof

methodsand technology. In exceptional cases it is pos-

sibletocarryoutascientificcooperationthatexceedsthe

routine service character. These exceptions have to be

justifiedintheapplicationandrequirethepermissionof

theIZKFBoardofDirectors.Costsforconsumableshaveto

bereimbursed.Additionaluserchargesdonotapply.All

publicationsresultingfromascientificcooperationshould

acknowledgetheIZKFMünsteronthetitlepageunderthe

authors’ address.

6. Inthiscontextitisnotpossibletoconsiderroutineinvesti-

gationsasascientificcooperationandtheseservicesare

liableforfees.

7. Allmembersoftheresearchgroupsareresponsibleforthe

correctoperationandhandlingoftheequipment.General

labsafetyruleshavetobeobserved.

8. Theequipmentbelongingtothe IZKFMünstercannotbe

relocated. Experiment-based relocation of equipment is

onlypossibleafterobtainingpriorconsent fromthe IZKF

ScientificOffice.

9. TheresearchersoftheCoreUnitsareobligatedtohandle

theresultsanddatainastrictlyconfidentialmanner,and

cannot duplicate, publish or use the data for any other

purposes.Exceptionstothisrulehavetobedocumented

inwriting.

10. UsersoftheservicesaffirmthattheCoreUnitsoftheIZKF

Münstertakenoresponsibilityforcontaminatedsamples.

Usersalso takecomplete responsibility foralldata/ re-

sultswithrespecttosafety,completenessandconfidenti-

ality.

TheseTermsofUsewerepassedbytheIZKFBoardofDirec-

torson06.November2007andtakeeffectimmediately.

Interdisciplinary Center

for Clinical Research

of the Medical Faculty Münster

Technology Platform

IZKF MÜNSTER

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