LIV
Next generation sequencing (NGS)
Head: Prof. Dr. Adam Grundhoff
The technology makes it possible to analyze the genetic basis of complex virus-host interactions, such as those that play a role in the establishment of chronic infections, the adaptation of viruses to new hosts, the emergence of resistance or the development of virus-related cancers. In addition, known as well as highly modified or unknown infectious agents can be identified in clinical samples.
Microscopy and Image Analysis
Head: Prof. Dr. Kay Grünewald
The Microscopy and Image Analysis technology platform uses various electron microscopy techniques such as cryo, transmission and environmental scanning electron microscopy as well as innovative light and fluorescence microscopy to visualize virus-infected cell and tissue systems.
The analysis spectrum ranges from the structural elucidation of the course of virus pathogenesis in intact cells and tissues to the in situ visualization of dynamic and molecular interactions between virus components and cellular macromolecules. The technology platform is part of the LIV Research Department Structural Cell Biology of Viruses and complements the structural and systems biology research focus of the department at the CSSB both methodologically and thematically. At the same time, the NIKON Center of Excellence is located in this technology platform.
Bioinformatics / Scientific Computing / Viral Data Science
The Viral Data Science research field links the overarching priority topics as well as the technology platforms and scientific computing IT infrastructures of the LIV. It promotes the development of expertise for processing innovative scientific questions in complex biological systems and enables the implementation of central approaches for the integrative analysis of systemic data. The term Viral Data Science encompasses all steps involved in extracting knowledge from large amounts of data, from the collection, storage and processing to the computer-aided interpretation (data mining) of the data using advanced algorithms (machine learning, deep learning). Examples include the systemic analysis of high-dimensional flow cytometry, mass spectrometry and sequence data to correlate immunological parameters with viral evolution and host adaptation, or the linking of genomic and proteomic data sets to investigate geno-phenotype relationships during the pathogenesis of viral diseases.
Flow Cytometry/
FACS
Head: Prof. Dr. Marcus Altfeld
With the Flow Cytometry/FACS technology platform, the LIV offers interested researchers access to state-of-the-art devices for fluorescence-based analysis and sorting of cells (FACS = Fluorescence Activated Cell Sorting).
Small Animal Models
In animal husbandry, laboratory animals and breeding animals are kept on the basis of current guidelines and legal principles of animal welfare, genetic engineering and hygiene as well as the latest scientific findings. This includes close hygiene monitoring, veterinary care and restrictive access regulations to animal facilities.
BNITM
BSL-3 Insectarium
For studies on vector competence of mosquitoes with tropical viruses up to risk level 3, including characterization of vector and transmission controls using the microbiome and the immune response of mosquitoes, testing of novel virostatics and drugs against mosquito-borne viruses in natural transmission models.
The BSL-4 high security laboratory
Basis for the diagnosis of risk group 4 viruses, the World Health Organization Collaboration Centre, the European Mobile Laboratories, research collaborations on highly pathogenic viruses in Africa and experimental research on pathogenesis, vaccines, therapeutics and diagnostics.
Mobile Laboratory
The mobile laboratories are used to support scientific analyses in the run-up to and during the implementation of measures in the event of outbreaks of infectious diseases caused by viral pathogens abroad.
Bioinformatics
Supports projects involving extensive DNA/RNA sequencing and bioinformatic analyses and advises researchers in the planning phase of projects.
Next-Generation Sequencing Core Facility
The unit offers research groups, diagnostics and external partners a cost-effective NGS pipeline for various sample types. Viral components of the microbiome are analyzed using metagenomics and metatranscriptomics approaches. Single-cell sequencing can capture molecular reads of cell activity in multiple dimensions, including gene expression, cell surface proteins, immunoclonotype, antigen specificity and chromatin accessibility.
Flow cytometry
The unit offers measurement methods that enable rapid analysis of larger cell populations. After instruction in the devices, the flow cytometers can be used for preparative and analytical procedures. In addition to assistance with problems, the service unit also offers prior methodological advice.
Animal husbandry
In animal husbandry, laboratory animals and breeding animals are kept on the basis of current guidelines and legal principles of animal welfare, genetic engineering and hygiene as well as the latest scientific findings. This includes close hygiene monitoring, veterinary care and restrictive access regulations to animal facilities.
Microscopy and Image Analysis
Support is provided primarily for projects in molecular parasitology and virology, as well as selective clarification of diagnostic issues. Since the establishment of a joint Leibniz Center for Infection (LCI) Imaging Platform with the Leibniz Institute of Virology (LIV) in 2020, the BNITM device has been installed there.
WHO Collaborating Center (WHO-CC)
As a cooperation center, the virology department is an important contact for the WHO for the diagnosis of rare and dangerous viral diseases. The WHO-CC offers special diagnostics and advice on imported cases of tropical viral infections throughout Europe.
National Reference Center for Tropical Infectious Pathogens (NRC)
The NRC offers specific diagnostic services for a broad spectrum of viral, bacterial and parasitic infections that are not provided by routine laboratories. It supports the RKI in clarifying epidemiological correlations in cases of outbreaks of infection in Germany and provides reference material to other laboratories for interlaboratory tests or for the evaluation of diagnostic procedures.
FZB
High-performance computing for OMICS data analysis and AI
The Data Science Group provides high-performance computing infrastructure for the analysis and storage of large research data. The focus here is on molecular high-throughput data, so-called OMICS data, in particular from sequencing. The infrastructure includes computers with 64 cores and 2 TB RAM. An NVIDIA H100 GPU is available for hardware-accelerated AI applications, which is used for protein structure prediction and for processing nanopore sequencing data, among other things. In addition to local, fast-connected SSD hard disks for analysis, an OMICS data storage system with one petabyte of storage capacity is also available.
Histology
We carry out histological work on animal models and human tissues generated in FZB projects. In addition to advice on pre-analysis, we process tissue for embedding in kerosene, production of sections, histological staining, immunohistochemistry and archiving of block material. Frozen sections are also part of our activities. We work closely with BMB Nord in the field of archiving. We are happy to advise the various RGs on the planning and implementation of histological analyses, as well as further investigations such as transcriptomics, multispectral IHC, nanostring and spatial transcriptomics.
In the field of infection, we are particularly interested in the multispectral immunohistochemical analysis of pathophysiological events in tuberculosis granulomas as well as transcriptome studies within different model systems and cohorts, with the aim of developing host-directed therapies.
Center for Clinical Studies
The study center is the interface between basic science and patient care in the clinic and the affiliated care center. Its expertise lies in the planning, organization and implementation of clinical studies. The spectrum includes translational research projects in close cooperation with basic scientists, collaborative studies of pneumological and infectiological associations and drug studies of the pharmaceutical industry.
The focus is on communicable and non-communicable diseases of the respiratory tract. One focus is clinical tuberculosis research. There is a close connection to research groups at the FZB for conducting international clinical studies and biomarker analyses (transcription-, PCR-, ELISA/ELISPOT-based analyses of samples for clinical studies). Other studies concern asthma, allergy, COPD, pneumonia, weaning and other pneumological diseases.
Pulmonary Clinic MVZ Borstel
The pulmonology practice at the MVZ of the Borstel Research Center offers diagnosis and treatment of all common and rare lung diseases. The focus is on the management of asthma - especially severe asthma - chronic bronchitis and pulmonary emphysema (COPD), chronic cough, “pulmonary fibrosis” and other so-called “interstitial lung diseases”, infectious lung diseases (tuberculosis, diseases caused by non-tuberculous mycobacteria, bronchiectasis), lung cancer and sleep-related breathing disorders (“sleep apnea”). In cooperation with the Clinical Study Center, patients are included in clinical studies.
BioMaterialBank Nord (BMB Nord)
BioMaterialBank Nord (BMB Nord) supports biomedical research in respiratory medicine. BMB Nord obtains, processes, collects, stores and manages biomaterial samples such as blood, tissue and cells from test subjects participating in studies at its member institutions. The biomaterial samples are analyzed by scientists. In this way, the BMB North acts as an interface between patient care and basic science. In addition, it advises scientists in the planning of translational research projects in the field of respiratory medicine. Upon request, it provides research groups with clinical information in pseudonymized form. By analyzing this information, conclusions can be drawn about diseases and their progression, which makes it possible to improve diagnostics and therapy. The focus of BioMaterialBank North is on communicable and non-communicable diseases of the respiratory tract and lungs.
Clinical advice service for doctors on tuberculosis and diseases caused by non-tuberculous mycobacteria (TBinfo)
The clinical infrastructure (ClinTB) at the German Center for Infection Research (DZIF) offers a round-the-clock telephone consultation service for questions about tuberculosis and diseases caused by non-tuberculous mycobacteria (TBinfo). Complicated treatment situations are discussed weekly on Fridays at 15:00-16:00 in the TBinfo Board with experienced experts before recommendations are made (T 04537 188-0).
Diagnostic mycobacteriology at the National Reference Center for Mycobacteria
Together with Molecular and Experimental Mycobacteriology, Diagnostic Mycobacteriology is responsible for the National Reference Center for Mycobacteria. The focus of Diagnostic Mycobacteriology is the mycobacteriological examination of submitted patient material and cultures. The range of methods includes all relevant areas of mycobacterial diagnostics (rapid molecular biological detection, differentiation of mycobacterial species, microbiological susceptibility testing, also according to the EUCAST reference method) and, in collaboration with Molecular Mycobacteriology, the fine typing of tuberculosis bacteria of the Mycobacterium tuberculosis complex (Mtbk) and non-tuberculous mycobacteria (e.g. resistance prediction, resistance detection). e.g. resistance prediction, phylogeny, genome analysis). In addition, it offers an advisory service on the diagnosis and treatment of mycobacterioses for treating physicians, laboratories and the public health service.
Cellular microbiology
Cellular Microbiology analyzes host-pathogen interactions in primary cell cultures and mice under BSL2 and 3 safety conditions with the following pathogens: Mycobacterium tuberculosis (TB), Klebsiella pneumoniae, Stenotrophomonas maltophilia, Candida albicans, influenza, SARS-CoV-NL63. For this purpose it uses
- In vitro infection models in primary cells (macrophages, neutrophils; mouse, human (BSL2, 3)
- M. tuberculosis, S. maltophilia, P. aeruginosa, C. albicans reporter strains
- Intracellular pathogen transport in host cells, live cell microscopy (BSL2 and 3), cell death assays
- Air-Liquid-Interface cultures with lung epithelial cells for mixed biofilm studies
- Aerosol TB infection model in granuloma-necrosis-developing susceptible mice for testing nanocarrier-packaged antibiotics
- Histology, immunohistology, FACS (BSL2 and 3), Bioplex, RNAseq, in vivo and in vitro imaging under BSL3 conditions (IVIS)Bakteriophagen-Sammlung
- Microbiome and mycetome analyses (16s-RNA/DNA, metagenomics, ITS, FISH, bioinformatics)
Bioanalytical Chemistry
Our research group combines expertise in mass spectrometry (MS) and nuclear magnetic resonance spectroscopy (NMR), which allows us to investigate metabolic processes in both biological model systems and clinical samples. We are specialized in the analysis of lipids, glycoconjugates and cell wall components. We offer LC-MS based quantification of drugs in relation to research into new formulations and therapeutic strategies. Furthermore, we can perform MS-based protein characterization.
Host-Microbe Interactome (Liaison group at the CSSB)
Mycobacteria utilize host lipids, such as fatty acids and sterols, as the main source of energy and carbon during chronic infection. The research focus of the Host-Microbe Interactome Unit is to decipher the molecular mechanisms by which pathogenic mycobacteria influence lipid metabolism and intracellular lipid transport pathways of the host cell. The application of functional lipids to analyze lipid dynamics during different stages of infection is combined with state-of-the-art microscopy methods and lipid biochemical methods such as mass spectrometric lipidomics.
- In vitro infection models (BSL2): immortalized BMDMs (mouse), transdifferentiated human macrophages (CEBRA), Dictyostelium discoideum, Mycobacterium marinum
- In vitro systems for the identification of lipid ligands and interaction partners including functional lipids
- High-resolution microscopy: live cell microscopy, correlative light and electron microscopy (2D and 3D), expansion microscopy
- Lipid extraction and thin-layer chromatography
Fluorescence Cytometry
Fluorescence cytometry provides modern equipment in the field of microscopy and flow cytometry for both program areas of the center. In addition to maintenance and care of the equipment, the focus is on training and advice on experimental planning and evaluation. For complex methods, cooperation with research groups takes place.
A Leica TCS SP5 confocal laser scanning microscope with five lasers (including deconvolution software) is available for microscopy. An Olympus IX-81 inverted fluorescence microscope can also be used for live cell analyses.
Several analyzers (6x) with 8-21 color parameters are available for flow cytometry, including a FACSymphony A1 with Small Particle Detector (SPD) for analyzing the smallest particles down to 60 nm.
Cell sorting is offered with a BD FACSAria IIIu (four excitation lasers, 13 fluorescence channels, safety level 2 sorting thanks to bioBUBBLE) or with the FACSDiscover S8 with CellView image technology (6-way sorting with 78 spectral and up to three fluorescent visual detectors).
Several flow cytometers are available in the genetic engineering laboratory of safety level 3, including a MACSQuant10 (three lasers, eight fluorescence channels) and a BioRad S3 cell sorter (two lasers, four fluorescence channels).
Microbial Interface Biology: Rapid and relevant test systems to identify new drugs against pathogenic mycobacteria
In recent years, the research group has focused on the development of various in vitro test systems for the rapid identification and characterization of the efficacy of new anti-TB lead structures. The direct effect on the pathogen is tested in 96- and 384-well plates. The systems allow us to analyze small and medium-sized compound libraries for new anti-TB compounds.
Following the characterization of a possible cytotoxic effect of the compounds on host cells (primary macrophages), the effect of the new compounds on the replication of intracellular bacteria will be investigated, in particular M. tuberculosis-infected human macrophages will be analyzed to identify promising anti-TB lead structures. Using a recently acquired high-content imaging system, we are also able to identify compounds that target the host rather than the bacteria in order to identify compounds for host-targeted therapeutic approaches.
Host determinants in lung infections
The group is investigating the influence of biological sex and viral co-infection on the immune response against tuberculosis in mice and primary cell cultures under BSL2 and BSL3 conditions:
- Aerosol TB infection model with Mycobacterium tuberculosis H37Rv and HN878 in immunocompetent C57BL/6, immunodeficient RAG2 KO and other KO strains
- Influenza, MCMV (mainly as co-infection)
- BCG vaccination in the mouse model
- Germ load determination, histology, immunohistology, flow cytometry, multiplex cytokine/chemokine/immunoglobulin assays, qPCR
- In vitro infection models in primary cells (macrophages; B cells; mouse, human)
- Hormone treatments (in vitro)
- High content screening of Mtb-infected human macrophages (Opera Phenix)
Biophysics
The Biophysics group is dedicated to the structure-function analysis of
bacterial and human membranes, their interaction with natural and
synthetic antimicrobial peptides and membrane-active substances of
pathogens. We carry out experiments on whole cells and, above all, on
very well-defined membrane reconstitution models. A range of biophysical
methods are available for this purpose:
- Atomic force microscopyScanning electron microscopy
- Electrophysiology
- Film balance
- Microfluidics
- ITC
- DLS
- Fluorescence spectroscopy
- X-ray synchrotron experiments
- In addition, we have the possibility to produce and characterize aerosols.
