Our Institute shares an extensive structure of Service-facilities to support our Research Groups. Sharing and bundling our resources allows us to staff our facilities with dedicated experts and acquire state-of-the-art instrumentation, all of which is available to our scientists at the click of a button. New to a field? To further support the multidisciplinary nature of our research, we provide training and guidance tailored to your needs.
Our Service-facilities operate in four technology areas: model systems, imaging, biomolecules, and omics. To identify the specific Service-facility for addressing your request, choose the area that matches best and use the fold-out menu to reach the relevant service. Cannot find what you need? Each technology area has a dedicated Head that oversees the complete portfolio of services, technologies, and expertises. Simply reach out by mail or rocketchat and we get you there!
The BIOMOLECULES technology area provides services related to proteins, lipids, metabolites, and antibodies plus nanobodies. We provide technologies for the generation, characterization, and detection of biomolecules. BIOMOLECULES is your technology area of choice if you aim to study a limited number of biomolecules. For analyzing a complex repertoire of biomolecules, such as lipids, metabolites, DNA, or RNA, from a single cell, tissue, organism, or population, we refer you to the OMICS technology area.
The expression vector contains a promoter and the open reading frame coding for your target protein. The design of the expression vector lies the basis for a successful protein purification. It involves a multitude of initial decisions to be made concerning your expression host, purification-, characterization-, and imaging strategies. We maintain a large portfolio of expression vectors, generate custom vectors tailored to your needs, and offer training and guidance in cloning and design.
The quality and quantity of the protein produced will depend strongly on the expression host used. Next to supporting bacterial expression, we offer exponentially growing cultures of insect cells (TNI and Sf9) and mammalian cells (HEK293) and baculovirus and bacmam-virus preparations, respectively, as an economic alternative to transfection. For rapidly assessing the quality and quantity of the protein produced prior to purification, we established protein quality control pipelines.
The first step in protein purification is cell disruption to free your target protein. Following this, affinity chromatography based on a purification tag attached to your protein, often allows significant purification of the protein of interest. This step is often followed by one or more additional purification or polishing steps using a chromatography system. As a final step, the quality of the protein is quickly assessed by determining its melting point and/or mass homogeneity.
IMAGE my sample
We offer upright wide-field system for histology imaging of stained samples (e.g. hematoxylin-eosin staining), as well as laser scanning confocal systems and spinning disk confocal systems to image broad range of fixed samples. If you need to image fixed samples please contact the Light Microscopy Facility.
For automated and high-throughput imaging of fixed samples in multi-well well plates please contact the Technology Development Studio.
We offer several setups for live cell imaging, including wide-field systems, quantitative phase imaging, spinning disk confocal, light sheet microscopy, laser scanning confocal and two-photon microscopy. We also offer various environmental chambers, objective heaters and gas mixing units to keep desirable concentration of gasses. Most of the setups are available at the Light Microscopy Facility.
Setups for automated high-throughput live cell imaging in multi-well plates are available at the Technology Development Studio.
The Advanced Imaging Facility offers high speed volumetric imaging of live cells using the lattice light sheet, as well as single objective light sheet technology – SCAPE (Scanned Confocally Aligned Planar Excitation).
Various setups for photomanipulation, photoconversion, laser ablation and FLUCS ( Focused Light Induced Cytoplasmic Streaming) are available at the Light Microscopy Facility.
Should your imaging experiments require high time resolution in ranges of dozens frames per second, then we have several spinning disk setups and TIRF (Total Internal Reflection fluorescence) setup available at that the Light Microscopy Facility.
The Advanced Imaging Facility offers high speed volumetric imaging of live cells using the lattice light sheet, as well as single objective light sheet technology – SCAPE (Scanned Confocally Aligned Planar Excitation).
Imaging of thicker samples live and fixed (in a range of several hundreds of micrometers) can be done with two-photon systems. Imaging of thicker fixed samples can be also performed on specialized light sheet setup optimized for imaging of cleared samples. Cleared samples can also be imaged on laser scanning confocal microscopes, as well as on spinning disk microscopes. If you wish to use these setups, please contact the Light Microscopy Facility.
For automated and high-throughput imaging of fixed and cleared samples in multi-well well plates please contact the Technology Development Studio.
For long-term live imaging of 3D cell cultures and organoids which can last for several days we offer spinning disk confocal setups and inverted light sheet setup at the Light Microscopy Facility.
For automated and high-troughput imaging of growing organoids in multi-well well plates please contact the Technology Development Studio.
Should your imaging experiments require improved spatial resolution beyond diffraction limit of 200 nanometers, then we can support you with setup for Structured Illumination (SIM), pixel reassignment technology – Airy scan on Zeiss laser scanning confocal systems, or SoRa spinning disk scan head. For single molecule localization microscopy we offer STORM (Stochastic Optical Reconstruction Microscopy) setup. If you wish to use these setups, please contact the Light Microscopy Facility.
For single molecule imaging and for single molecule localization microscopy we offer TIRF (Total Internal Reflection Fluorescence) setup that is also capable to perform STORM (Stochastic Optical Reconstruction Microscopy). Setup is available at the Light Microscopy Facility.
To measure dry mass of the cells we offer Quantitative phase imaging setup with low-coherence illumination - Q-Phase. If you wish to use such setup, please contact Light Microscopy Facility.
Laser capture micro dissection is used to cut out subcellular or cellular regions of interest (ranging from hundreds of micrometers to few micrometers) from larger samples. First, it acquires microscopy images of samples and then users select regions of interest which can be automatically cut out by UV laser and transferred to test tubes. Samples in test tubes can be used for downstream OMICs applications, such as proteomics or lipidomics methods. If you wish to use this technology, please contact the Light Microscopy Facility.
We use automated microscopy (mainly the YOKOGAWA CV7000) which allows unbiased imaging capability in a series of modality: brightfield, epifluorescence and spinning disk confocal mode. We can image structures in 2D and 3D. A new automated microscope (the Zeiss Cell Discoverer) will be installed in the second quarter of 2022
contact: tds-clinic@mpi-cbg.de
We can image samples arrayed in any multi-well format: from slides to lower density 6, 24 and 48 well format to higher density 96, 384 and 1536 format.
contact: tds-clinic@mpi-cbg.de
We can image the samples with a wide range of resolutions: 4x, 10x, 20x, 40x and 60. We can use 4 different laser sources (405, 488, 561 and 647 nm) to image a wide range of fluorophores. This makes us able to perform imaging at different scales of organizations of the cellular systems: from small organisms (Zebrafish or C.Elegans), to tissue and cellular level (cell lines, primary cells, organoids and tissue slices) to subcellular structures (nuclei, mitochondria, endosomal vesicles etc).
contact: tds-clinic@mpi-cbg.de
Images can be acquired from fixed as well from live samples, as the microscope is equipped with an incubator with C02, temperature and humidity control
contact: tds-clinic@mpi-cbg.de
Acquisitions can be performed using automation of big batches of plates in an unsupervised manner, either for fixed and live samples.
contact: tds-clinic@mpi-cbg.de
In case of samples seeded with low density in the wells we can perform low resolution imaging to identify objects of interest using image analysis, followed by higher resolution imaging to increase effective sampling of the structures of interest (e.g spheroids or organoids)
contact: tds-clinic@mpi-cbg.de
The Electron microscopy Facility offers fast and easy preparation of samples by staining with salts of heavy metals. This approach can be used to investigate large proteins or as part of a more complex projects.
The Electron microscopy Facility offers high pressure freezing for room temperature TEM (Transmission Electron Microscopy). High pressure freezing allows to maintain near-native state of the biological samples. Samples are then embedded into plastic to be further handled and imaged at room temperature.
The Electron microscopy Facility offers imaging of large volumes of samples of the thickness from several micrometers up to 100 µm. Samples are fixed with high pressure freezing and subsequently embedded into plastic with special addition of heavy metals to increase contrast. Very large areas of a size of many micrometers and volumes can be imaged by special microscopes: FIB-SEM (combined Focused Ion Beam in a Scanning Electron Microscope) or SBF-SEM (Serial Block Face Scanning Electron Microscope).
The Electron microscopy Facility can support your CLEM experiments by arresting living tissue at a desired timepoint by snap-freezing. CLEM studies then involve light microscopy and electron microscopy of the same region(s) of interest. Thanks to high pressure freezing we can keep samples in near-native state. They can be then imaged by light microscopy in 2D and 3D in their frozen state and subsequently the same (!) areas can be imaged by TEM (Transmission Electron Microscopy) in 2D and 3D. This approach combines the strength of light and electron microscopy techniques. In the area of CLEM we closely collaborate with the Light Microscopy Facility.
The Electron microscopy Facility offers snap-freezing of biological materials up to the thickness of 100-200 nm. Samples are frozen within milliseconds and maintained in a perfect near-native state. If they are sufficiently thin, then they can be directly imaged in 2D and 3D directly while still in their frozen state. To image these samples we use cryo TEM (Transmission Electron Microscopy) tomography.
An image can be considered as a combination of information from the sample and distortion/noise added due to the properties of optical system. The Scientific Computing Facility can offer you data restoration techniques such as deconvolution aim to restore the raw image information from the mixture of sample data and noise. This is especially important if you need accurate intensity measurements. We guide you to the right mathematical operations to improve the overall contrast and signal-to-noise ratio of your image data.
Samples that cannot be fit onto the field of view are acquired as tile images (with certain overlap). Light-sheet imaging allows the acquisition of 3D image stacks of whole tissues, organisms, and organoids from multiple views or rotation angles. Such images have to be reconstructed before analysis. In the case of tile images, the data is reconstructed using stitching which is the registration of the tiles next to each other by using the common overlapping information. In the case of light-sheet multi-view images, the registration and fusion of data help to reconstruct images of sample from the various views. All these data reconstruction approaches are supported by the Scientific Computing Facility.
Object detection and segmentation are the most important part of any image analysis task. The goal of segmentation is to identify accurate outlines of your regions of interest (ROIs). These could be anything from individual cells, nuclei, sub-cellular structures and protein spots. Available methods comprise classical image processing (thresholding, watershed), shallow machine learning (random forests, SVM, clustering) and deep learning (convolutional neural networks). The choice depends on the quality of your data in terms of resolution, the signal-to-noise ratio and the complexity of the structure of interest. Automated workflows for object detection and segmentation are important for unbiased and reproducible extraction of quantitative measurements and are part of the varied services which the Scientific Computing Facility offers to the institute.
Object classification has many applications in molecular cell biology, medicine, and drug discovery. For example, studying the effect of a protein on different cell components, identifying cell types and groups, identifying cell-phase, etc. Traditionally, such tasks were done manually taking many hours to go through each image and mark objects belonging to various categories. To ease this process, the Scientific Computing Facility will assist you with accurate machine-learning and deep-learning approaches to automate the classification in a robust and efficient way.
Biological systems are inherently dynamic. Tracking has been useful to study many biological processes at sub-cellular levels as well as to understand cell motility, migration, and development. Tracking is also important to study the dynamic and functional properties of many proteins. Advances in optical technologies have now made it possible to resolve the smallest of the features and follow them over time. Reliable methods for segmentation and tracking allow us to unravel the spatial and temporal relationships that exist in complex biological environments. They are available for you at the Scientific Computing Facility.
The goal of bio-image analysis is to quantify biological structures to understand their underlying processes and functions. The most common parameters that are measured are size, intensity, and density. In the case of tracking, parameters related to motion such as velocity, lifetime, displacement, etc. are measured. An efficient analysis can only be achieved on the foundation of a robust experiment plan and the correct translation of the experiment hypothesis into the bio-image analysis task. The Scientific Computing Facility will assist you with this task and will provide support for taking measurements as well as down-stream analysis of measured properties.
Building meaningful visualization is essential to reveal insights from complex structures and processes and communicate your research to the wider community. The Scientific Computing Facility will assist you with finding the right viewing and rendering technologies to visualize complex biological systems in multidimensional space.
Flow cytometry is utilized to analyse and enrich for single-cells, certain cell types, or populations of interest, out of which the biomolecules are extracted subsequently. Our instrument park of cytometers includes cell sorters and a spectral analyser. We assist in project design and optimization, provide staining protocols, operate and maintain the cytometers, and train users on our user machines.
Laser capture micro dissection is used to cut out subcellular or cellular regions of interest (ranging from hundreds of micrometers to few micrometers) from larger objects. First, it acquires microscopy images of samples and then users select regions of interest which can be automatically cut out by UV laser and transferred to test tubes. Samples in test tubes can be used for downstream OMICs applications, such as proteomics or lipidomics methods.
The extraction of biomolecules such as DNA, RNA, or proteins from cellular regions, cells, organs, or whole organisms is the key step towards a successful OMICs analysis. The read-out (or technology) of choice defines the requirements on the integrity, input amount, and purity of the sample of interest. We offer a broad range of extraction protocols for biomolecules and provide state of the art quality measures.
The analysis of high-quality, annotated genomes is the basis to answer many biological questions and to genetically engineer a model system of choice. A combination of different state of the art sequencing technologies with a sophisticated assembly and annotation pipeline leads to almost complete and highly accurate genome assemblies at chromosomal resolution. We provide this genome assembly portfolio and combine it with an annotation pipeline that makes use of short- and long-read transcriptome data.
Nowadays, resequencing of complete genomes or genomic regions of interest are tools to identify differences and to compare whole genomes. Targeting a region of interest could be performed, for example by PCR-based amplification or alternatively by capturing these regions making use of CRISPR/Cas9 based protocols or microfluidics, followed by next generation sequencing and analysis. Thus, depending on your biological question in combination with the input sample we will assist you to define the best enrichment strategy.
Epigenetic marks are chemical modifications of DNA and histone proteins and have been shown to regulate activation or silencing of genes. ChIPSeq is using antibodies against histone modifications and sequencing to identify these genome wide patterns. State of the art long read sequencing technologies allow the direct read-out of nucleic acid marks across a genome, whereas bisulfite sequencing indirectly detects methyl-marks in genomes. We will help and consult, which epigenetic applications or combination of applications would help the investigation of regulatory relationships in cells and tissues.
Sequence variation in genomes could be due to changes at the nucleotide level (single nucleotide polymorphisms, SNPs). SNPs are identified by re-sequencing of complete genomes or of target regions. Large structural variants such as insertions, deletion, or inversions are observed at the genome level and could be identified by sequencing of contiguous and long fragments making use of state of the art long-read technologies. We offer different solutions to detects nucleotide or structural variants in whole genomes or regions of interest.
Validation of transcriptomics results via relative quantification PCR (qPCR) analysis of particular transcripts is a standardized method of backing up and highlighting data. We offer qPCR service as a comprehensive package from experiment design, to primer design and optimization, to running the qPCR reactions and analyzing the data.
The quantification and profiling of gene expression patterns are one of the key objectives in transcriptomics studies. Typical analyses of bulk RNA-Seq data include the detection of differentially expressed genes as well as enrichment analysis on pathways and other defined gene sets. Single cell RNA-Seq data further allow you to detect individual cell populations and/or to unravel the trajectories of underlying differentiation processes. On the more mechanistic side, transcriptome data also reveal insights into alternative splicing and the detection of novel transcript isoforms. We have the expertise and tools to assist you with all these analyses to get comprehensive insights into your sample’s transcriptome.
Quantitative proteomics is performed as a bottom-up approach using liquid chromatography and tandem mass spectrometry on peptides obtained via proteolytic digestion of complex protein extracts. The spectra are matched to source peptides by database searching software and constellation of peptides identifies the corresponding protein or protein group. Intensities of peptide peaks are used to estimate the relative abundance of the proteins in the series of biological experiments. While relative abundance measures are the most common methodology, we also support absolute quantification of proteins to obtain their molar concentrations by the methods developed in-house.
Differential abundance analyses based on data of relative or absolute quantification of individual proteins can be performed on the full proteome level. Our team has the know-how and software tools to support proteomics screens and expand them to characterization of proteomes in organisms with unknown genomes.