Services and Facilities MPI-CBG

Jussi Helppi Speaker of Services and Facilities

Head of Biomedical Services MPI-CBG

Imaging and HTS

Light Microscopy (Jan Peychl)

Electron Microscopy (Jean-Marc Verbavatz)

TDS/Screening (Marc Bickle)

FACS (Ina Nüsslein)

Biochemistry

Antibody Facility (Patrick Keller, MSD)

Protein Expression (David Drechsel)

Chromatography (Barbara Borgonovo)

Mass Spectrometry (Anna Shevchenko)

DNA, RNA and Associated Technologies

DNA sequencing and Genotyping (Sylke Winkler)

DNA Microarray (Julia Jarrells)

TransgeneOmics (BACs) (Mihail Sarov)

Information Technology

IT Coordination (Jeff Oegema)

IT Infrastructure (Matt Boes)

Scientific Computing (Ian Henry) Bioinformatics, Scientific Software Development, Image Processing

Photolab (Franziska Friedrich)

Scientific Administration

Information Office (Florian Frisch)

Library (Silke Thüm)

Grants Office (Birgit Knepper–Nicolai)

International Office (Carolyn Fritzsche)

Laboratory Management (Deborah Newby)

Budget Office (Kristina Oertel/Susanne Hoesel)

Technology Transfer (Ivan Baines/ Tobias Mahn)

Model Systems

Biomedical Services (Jussi Helppi)

Transgenic Core Facility (Ronald Naumann)

Fish Unit (Evelyn Lehmann)

Services and Facilities at MPI-CBG

Services and Facilities

Genomics (DNA, RNA and

Associated Technologies)

DNA Sequencing and TILLING Leader: Sylke Winkler

Services Offered: Sanger DNA Sequencing, Primer Walking, Template Preparation, Fragment Analysis, high-throughput sequencing of DNA templates, expertise in Zebrafish genomics and genetics

Collaborative Projects: screens for sequence variants in genetic model organisms (collaborative

TILLING project in zebrafish and fly)

EcoTILLING and AFLP genotyping of Aspen populations

Optimization of ENU mutagenesis and sperm freezing in zebrafish

Equipment / tools:

- Capillary DNA sequencers for small and large-scale

applications

- Automated liquid handling for PCR and sequencing

(384well format)

- PCR capacity (96- and 384well)

- Automated large-scale sequence analysis

(Polyphred)

“The DNA Sequencing Facility provides high-quality sequencing results, quick turnaround times, and professional support for small and large-scale projects.”

Genotyping Collaboration between DNA Sequencing and the BMS

Service offered:

• routine preparation of genomic DNA from mouse tails

• routine PCR-based detection of knock-out or knock-in genotypes in mice

• design and establishment of PCR-based genotyping strategies for new mouse

mutants (together with TCF)

• establishment of highly sensitive PCR-based pathogen detection assays (together

with BMS)

“The Genotyping Facility performs routine genotyping of mouse mutants and establishes and optimizes genotyping strategies”

DNA Microarray Leader: Julia Jarrells / Britta Schilling

Microarray-based Methods: • Gene Expression Analysis • miRNA Analysis • ChIP-on-chip Analysis • aCGH

Services: • Experimental design • Choice of the most suitable microarray design • Quality control of input samples • Microarray Analysis • Data analysis to identify lists of genes of interest • Validation of microarray results with qRT-PCR • Custom array design with Agilent eArray tool • Array-based and solution-based targeted enrichment for Next Generation Sequencing • Any type of array processing, e.g. protein, peptide, antibody, lipid, glycan, etc.

Equipment: • Peqlab NanoDrop ND-1000 • Agilent 2100 Bioanalyzer • Agilent Microarray Scanner • Hybridization Oven • Mx 3000P qRT-PCR machines • GeneSpring Software

TransgeneOmics (Technology Development) Leader: Mihail Sarov

Protein tagging technology

Mission: High throughput genome engineering for protein function exploration

Central storage and distribution

Genome wide resources Biobanking

C. elegans Cell culture Drosophila

Tools and technology development Web based resource exploration tools

Services and Facilities

Imaging and HTS

Light Microscopy Leader: Jan Peychl

“Our mission is to provide access to state of the art biological imaging techniques and instruments along with vision towards future trends. We assist through consultation, training, and project collaborations”

Statistics for 2011:

Hours of usage: ~ 45,000

Number of users: ~ 250

• Laser scanning confocal systems • Spinning disk confocal systems

• Two photon systems

• Wide-field systems

• TIRF systems

• Super-resolution light microscopy systems

FACS Leader: Ina Nuesslein

“The FACS Facility provides instrumentation, education and expertise for all your flow cytometry needs.”

Services Offered

ANALYSIS: • Cell cycle analysis • Apoptosis • Expression of surface and intracellular proteins • High throughput analysis

CELL SORTING: • sorting of cell populations into

phenotypic, biochemical and molecular subsets

• single cell sort into 96 well plates • Sorting of dissociated tissue

EQUIPMENT: • FACSAria cell sorter • Calibur Analyser • FacScan

Electron Microscopy Facility Leader: Jean-Marc Verbavatz

“The EM Facility provides resources, technology and expertise for the investigation of ultrastructure and subcellular localization”

Service: Sample preparation (for cell culture, worms, flies, fish, mice) after cryo-immobilisation (HPF) or chemical fixation; sectioning; contrasting; immunolocalisation; electron tomography and 3D reconstruction; Correlative light electron microscopy (CLEM)

Facility: Support and training in microtome, TEM usage and EM methods, cell morphology and data interpretation

Plans: Enlarge repertoire, data archive, antibody and sample library, EM network setup

Electron Tomography negative staining Immunogold labelling Tecnai G2 F30

HT Technology Development Studio Leader: Marc Bickle

“The major goal of the HT-TDS is to provide expertise in

high-throughput functional and chemical genomics

screening applications using state-of-the-art cell-based imaging technology”

Expertise: assay development, automated image analysis, statistics and High-Content Imaging applications (lab

automation, siRNA transfection, compound screening, automated plate preparation, automated microscopy,

image analysis, statistics, data management), small scale optimizations of RNAi and antibody stainings in 96 well

format

Equipment: Flexible liquid handling work stations, microtiter plate reader, automated microscopy systems OPERA,

ArrayScan VTI, BD Pathway, image analysis software

Interests: Application of automated image-based screening at the sub-cellular level

Identification of new gene functions and phenotypes after depletion or knock-down

Identification of new chemical or biological entities that induce equivalent phenotypes

Unbiased, statistically robust acquisition of imaging data

Services and Facilities

Biochemistry

Antibody Facility Leader: Patrick Keller

“The Antibody Facility provides a centralized resource and state-of-the-art technology for the production, purification and labeling of polyclonal and monoclonal antibodies”

Service: rabbit polyclonal antibodies mouse monoclonal antibodies growth and storage of hybridoma cell lines purification of monoclonal antibodies from cell culture affinity purification of antibodies labeling of antibodies

Research:

-cloning of Ig genes

(with Protein Expression)

-recombinant antibody production

(with Protein Expression)

Protein Expression and Purification Leader: David Drechsel

“An institute resource providing expertise, tools and reagents for recombinant protein over-expression and purification”

Research and Development :

• Modification of the Baculovirus genome for improved expression in insect and other cells

• Affinity purification of tubulin

• Cell-Free expression

Service • Cells, vectors and reagents for expression in

insect (baculovirus), HEK293 (transient), and bacterial cells (E. coli)

• Soluble Fragment Screen • Expression & Affinity Purification • Reagents available in Stores

Facility • Advice, protocols, Instruments and

reagents for protein expression, purification and biochemistry

Chromatography Leader: Barbara Borgonovo

“The Chromatography facility provides information and assistance to help protein purification and analysis”

Service • We offer active support, advice and training

Facility • We provide columns, resins, protocols • Five fully automated liquid chromatography

systems • Reagents through the Stores

b_xtract #1 RT: 0.50 AV: 1 NL: 2.92E5T: FTMS + p NSI Full ms [440.11-6502.86]

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Mass Spectrometry Facility Leader: Anna Shevchenko

“ The MS service facility supports proteomic efforts in MPI-CBG

and Biopolis Dresden” We offer:

• Protein identification and quantification

• Small- to medium-scale proteomic screens

• Analysis of PTMs

• Determination of the molecular weight for small

molecules

• Gel running service

• 1D and 2-D gel electrophoresis equipment to let,

protocols, advice

• Consulting in planning of proteomic experiments

Research focus: Proteomics in organisms with unsequenced

genomes

Analysis of archeological samples

Instruments and software: 5 mass spectrometers of different types, 4 nano-

HPLC, 3 automated ionsorces

software licenses: MASCOT, Scaffold, Progenesis

Services and Facilities

Model Systems

Biomedical Services (BMS) Leader: Jussi Helppi

“Our mission is to help our users to excel in scientific research by

offering an easy access to full scale mouse service by highly motivated staff”

Our core values: Humane Care, Excellence, Customer Service, Teamwork, Growth

Service: Animal Husbandry, Technical & Experimental Service, Health Monitoring, Import & Export of Animals, Quarantine, Training…

Facility: Expert in Transgenic Mouse Colony Management and Facility Management

Research: Mouse Ethology, Effects of Environmental Conditions on Mouse Breeding Behaviour

Key elements of BMS:

State-of-the-art facility with multiple barriers & labs

Highly trained and motivated staff

Individually Ventilated Cages (IVC)

Interactive computerised database (PyRAT)

Transgenic Core Facility (TCF) Leader: Ronald Naumann

Service:

• cleaning, freezing and thawing of mouse embryos

• in-vitro-fertilisation

• ES-cell injection into morulae or blastocysts

• DNA pronuclear injection of plasmids, BAC’s and YAC’s

• production of tetraploid mouse embryos

• ovary transplantation

• mouse sperm freezing and cryo-storage

• electroporation service of mouse embryonic stem cells, as well as selection, picking and backup into 96 – well plates

Facility-User: • Internal mouse groups and external mouse groups in

Germany and Europe

Research: • pronuclear injection into mongolian gerbil oocytos

• refinements to increase the efficiency of K/O and transgenic mouse production

• transplantation with old ovary tissue as a rescue method of mouse strains that have been lost

“The Transgenic Core Facility provides a centralized resource and state-of-the-art technology in production of Knock-Out (-In) mice and transgenic mice”

The Fish Facility provides a full scientific service and husbandry of zebrafish in accordance with animal welfare by highly motivated staff.

Scope: The zebrafish model system offers some advantages over higher vertebrates to answer questions in

science. In the last years, several mutagenesis screens have been performed, focusing on many different developmental processes. It have been screens performed to identify genes and pathways which are

important for development and function of body system.

Fish Unit Leader: Evelyn Lehmann

The Fish Facility has the following tasks: - organization of the breeding and husbandry of mutants, transgenes and wild-type lines - the assurance of the hygiene and health status of animals - reproduction - training - scientific Service - sperm freezing & in vitro fertilization - import and export - quarantine

Services and Facilities

Information Technology

IT Coordination Jeff Oegema (Scionics GmbH)

• Strategic coordination across the IT Service Center (Bioinformatics, Bioinformatics Walk-In

Service, Software Engineering, and the Computer Department)

• Long term budget and technical planning for IT related issues

• Responsible for alignment of the IT Service Center with the scientific goals of the MPI-CBG

• Creation of IT Strategy and Policy Decisions

• Represent the MPI-CBG in collaborations and interactions with other Institutes on IT issues

IT Service Center

Bioinformatics Scientific Computing Computer Infrastructure

“It is our goal to provide innovative services and not just basic support. We are dedicated to providing fast and flexible solutions to aid in the advancement of scientific research. We will continue to study and progress in our own discipline so that we can supply the latest technology to the Institute community.”

Walk-in Service:

• Daily support requirements

Expertise offered:

º Networking

º Computer Ordering and Advice

º E-mail

º Applications

º Hardware

º Installations

º Printers

º Applications

º Web support

º High-Performance Computing

Infrastructure Design and

Implementation:

• UNIX Backbone

º A large quantity of storage space

º A backup and fileserving structure capable

of handling hundreds of terabytes of data

• Network

º Gigabit/10GigE redundant LAN

º Redundant 150Mbit Internet Connection

º Institute-wide 802.11n Wireless Network

• Clients

º Seamless integration of Macintosh, PC,

and UNIX clients

º Hardware and instrument integration for

research purposes

IT Infrastucture Leader: Matt Boes (Scionics GmbH)

IT is a necessity in the research world, and is now connected to all parts of modern science. The MPI-CBG firmly believes in providing and promoting modern, capable, and flexible IT in order to facilitate cutting-edge scientific research.

Scientific Computing Leader: Ian Henry (Scionics GmbH)

“The Scientific Computing Facility aims to provide a common interface point to assist researchers in the tackling of scientific questions involving computational analysis, data

handling and image processing”

Scientific Software

Development

Bioinformatics

Image Processing

Bioinformatics

Typical Service Requests: 1. Sequence Analysis

Protein sequence analysis & functional prediction DNA/RNA sequence analysis

2. Evolutionary Analysis Phylogenetic tree construction Orthologue/Paralogue searching

3. Structural Analysis Protein/RNA structure prediction

4. High Throughput Data Analysis Next generation sequencing analysis Custom microarray design Annotation and analysis of screening hit-lists

5. Custom Code Development Scripting and small tools (R/Python) Data mining and workflow management using KNIME Plugin development for Geneious Custom algorithm development upon request

“The Bioinformatics Service aims to provide a high-quality, efficient and friendly service to aid scientists with all their bioinformatics needs, from small scale to genome wide analysis”

Scientific Software Development

Services Offered:

Design, deployment and maintenance of software applications for

Display, management, and analysis of scientific data

Management of high-volume scientific research data including genomic information, microscope image data and movies, and related metadata

Guidance, support and training to:

Help scientists to improve research code and turn it into distributable applications and packages

Work with researchers to improve algorithms and parallelization of code to improve code efficiency and processing speed

Help scientists port code to an HPC environment and queuing system

Ensuring that software created within the Institute is of the highest quality, reliability and correctness.

“Scientific Development designs, constructs, and deploys scientific applications within the MPI-CBG. We also help to ensure that software created within the Institute is of the

highest quality, reliability and correctness”

Image Processing

Maintain a high-quality infrastructure of software programs, documentation, and experience in common tasks.

Train individuals and groups.

Develop tools where appropriate

Supported software: Fiji (ImageJ) + plugins BioImageXD Huygens SoftWorX Cell Profiler Imaris/Volocity

Image Processing/Analysis techniques

3D Reconstruction/Visualization Segmentation Image Registration / Tile Stitching Object Motion Tracking / Kymographs Co-localization Analysis De-convolution, Super Resolution Reconstruction, etc.

“Image processing will provide expertise and guidance in the correct use of appropriate image processing/analysis techniques to analyze biological image data”

Photolab (provided by Scionics Computer Innovation GmbH) Franziska Friedrich

Photography/Video Digital Imaging

Conference Service Overview of provided services:

• Creating and editing scientific images, presentations, posters

• High quality printing of scientific posters and figures

• Studio and on location photography

• Audiovisual support of seminars and conferences

• Book binding, laminating

• Digital video shooting and editing

• Scanning of slides and prints including retouching

• Maintenance of the in-house X-ray machines

• and more…