Method facilities

MF 1 - Joint Microbiome Facility

The Joint Microbiome Facility (JMF) was established in 2018 and currently consists of 4 scientists and 3 laboratory technical assistants, and operates state-of-the-art DNA/RNA sequencing facilities both at the Medical University of Vienna and the University of Vienna. The JMF offers individualized consulting and services in study design, sample processing, sequencing, bioinformatic analyses, and data interpretation to both clinical and environmental microbiome researchers. Additionally, the
JMF is experienced in benchmarking existing approaches and developing new technological and analytical strategies. The JMF performs DNA/RNA extraction from diverse sample types, amplicon sequencing (e.g., 16S/18S rRNA gene, ITS, functional gene markers), full-length primer-free rRNA profiling, and metagenomic and metatranscriptomic sequencing using Illumina and Oxford Nanopore technologies. In parallel to these well-established services, the JMF is also developing and implementing amplicon approaches that allow for absolute, fully integrate ultra-high throughput long read sequencing and activity-based sequencing approaches based on incorporation of bioorthogonal or isotope-labeled nucleotides.

2 Technician positions (Pjevac) - both filled


MF 2 - Bioanalytics and Environmental Mass Spectrometry Facility

We perform environmental trace analysis and cover the full analytical circle starting from sampling and sample preparation (digestion, extraction and preconcentration) to data acquisition and analysis. We currently run Gas- and liquid chromatographic, separation coupled to triple quadrupole, tandem mass spectrometry, inductively coupled plasma optical emission spectrometry (ICP-OES) for high-throughput analysis (ppb-range) of main and trace elements in a wide variety of matrices and single quadrupole inductively coupled plasma mass spectrometry (ICP-MS) for ultratrace analysis (ppt-range) of main and trace metals and metalloids, triple quadrupole inductively coupled plasma mass spectrometry (ICP-MS/MS) for ultratrace analysis of metals, metalloids, sulfur and phosphorus at ppt levels for the analysis of rare earth elements at ppq levels. 

Technician position (Hofmann) - filled          Postdoc/High Level Technician position (Birner-Grünberger) - filled 

PhD position (Birner-Grünberger)

MF 3+4 - Fluorescence In Situ Hybridization & Single-Cell Transcriptomics Facility

Fluorescence in situ hybridization (FISH) with rRNA-targeted probes is a gold standard technique for the identification and visualization of microorganisms in environmental and clinical samples. This facility will make FISH, advanced confocal and super-resolution fluorescence microscopy, and digital image analysis techniques available for the projects in the cluster. For selected projects, highly multiplexed FISH and multicolor imaging techniques for the parallel identification of hundreds of microbial species in complex samples will be adopted. For spatially structured microbiomes, 2D and 3D image analysis will extract important information, such as the spatial arrangement patterns of microbial populations.
Analyzing single-cell gene expression patterns within natural environments offers exciting opportunities to better understand microbial interactions and responses to perturbation. This facility will leverage signal amplification and multicolor imaging techniques to establish an mRNA-targeted FISH approach for spatially-resolved single-cell transcriptomics, which will be applied to detect selected gene transcripts directly in complex microbial communities.

Technician position (Wagner) - filled          Postdoc position (Daims) - filled


MF 5 - Stable Isotope Facility

The Stable Isotope Laboratory for Environmental Research (SILVER) provides high-end stable isotope ratio mass spectrometry (IRMS) techniques for light elements (H/D, 13C/12C, 15N/14N and 18O/16O) for bulk and compound-specific measurements. The facility holds five IRMS coupled to elemental analyzer, high temperature pyrolysis unit, gas- and liquid chromatography systems, and headspace gas preparation systems, as well as high resolution Orbitrap mass spectrometer with UPLC. SILVER specializes in (i) tracing isotopes into biomarkers (e.g. DNA, proteins, and lipids), (ii) isotope pool-dilution approaches, to estimate gross biogeochemical process rates, (iii) measuring stable isotopes at their natural abundance, and (iv) fluxomics approaches based on isotope labeling. The services encompass advice on experimental approaches and evaluation of results, measurement execution, and help with development of new methods. 

Technician position (Wanek) - filled


MF 6 - Chemical Imaging Facility

The chemical imaging support will be coordinated by Michael Wagner and Bernhard Lendl. CoE projects will utilize a well-established NanoSIMS facility (unique in Austria), several spontaneous Raman microspectroscopy instruments coupled to fluorescence microscopes as well as multiple cutting-edge nano-infrared spectrometers: high-speed scanning probe IR, mid-infrared photothermal (MIP) microscopy enabling fast single-cell imaging and analysis of cell-on-chip systems.
Furthermore, the projects will have access to our unique microfluidic-based Raman sorting device that realizes sorting thousands of microbial cells based on their isotopic composition or other chemical features. High-throughput single-cell isotope imaging in microbiome samples will be possible using our custom-made Stimulated Raman Scattering (SRS) microscope providing quantification of the deuterium content of FISH-identified microbial cells at unprecedented speed. Within the CoE, a novel SRS-based device for high-throughput sorting of microbial cells and liquid AFM-IR for life cells will be developed and applied for microbiome research. 

Postdoc position (Lendl) - filled        PhD position (Lendl)


MF 7 - Microfluidics and Lab/Organ-on-a-Chip Facility

This methods facility contributes its rapid prototyping technologies, microfluidics, CFD simulations and optical and electrical biosensing systems as well as bio-functionalization strategies to develop (portable) multifunctional lab-on-a-chip systems for cell culture and analysis. Following the global trend of miniaturization, automation and integration the Lab-on-a-Chip laboratories maintain a range of rapid prototyping technologies and micromachining tools to develop computer-controlled microanalysis platforms, biochips, biosensors, micropumps and micro-degassers. We are equipped to fabricate devices based on micromachining, lithography, soft- and hard polymer replication techniques such as casting, hot embossing and micro-injection molding as well as various 3D printing techniques for fabrication of microdevices and microfluidic components facilitating controlled cell-to-cell interactions between roots, fungal hyphae, and bacteria.

Technician position (Ertl) - filled     PhD position (Ertl)


MF 8 - Protein Characterization Facility

Genes of particular interest revealed by the CoE microbiome projects will be heterologously expressed (or native proteins and complexes purified directly from bacterial cultures)and their structures analyzed using integrative structural biology approaches. Kristina Djinovic-Carugo (University of Vienna) will coordinate these efforts for cytoplasmic proteins. Djinovic lab has access to a blend of complementary molecular biophysics and structural biology techniques and is equipped for protein expression and purification. Leonid Sazanov (ISTA) will focus on selected membrane proteins. The Sazanov lab at ISTA has access to state-of-the-art cryo-EM facilities including a high-end 300 kV TEM Titan Krios for collection of high-resolution datasets, a 200 kV TEM Glacios for optimisation of cryo-EM grids and preliminary data collection, and cryo-FIB/SEM Aquilos for preparation of samples for cryogenic electron tomography.
In addition, Ruth Birner-Grünberger (Technische Universität Wien) will support selected projects with her expertise on enzyme discovery and profiling. These experimental approaches will be complemented by Thomas Rattei (University of Vienna) with in-silico predictions, e.g., on secreted proteins by microbiome members using deep learning models trained on sequence and structural features.

Postdoc position (Djinovic Carugo) - filled          Postdoc position (Sazanov) - filled


MF 9 - Atomic Force Microscopy Facility

The atomic force microscopy (AFM) facility is equipped with 4 conventional AFMs, 1 fast-scanning AFM, 1 high-speed AFM, and 1 correlative AFM/Fluorescence Microscopy device to provide the following measurement modes.
AFM: Topographical and mechanical imaging in physiological environments to resolve ultrastructure, mechanics, molecular and cellular interactions at spatial dimensions from 1 nm to 100 µm in physiological environments with minute time resolution. 
High-speed Bio-AFM (HS-AFM): Filming molecular dynamics, conformational changes, and interaction of molecules in physiological environments with sub-nm spatial and 50 ms time resolution. 
Molecular Recognition Force Spectroscopy (MRFS): Studying molecular interactions at the single-molecule level to achieve interaction forces and energies. 
Cellular Recognition Force Spectroscopy (CRFS): Decipher interactions between microbes and hosts/biotic/abiotic surfaces on the cellular and molecular level. 
Topography and RECognition (TREC) Imaging: Localization and distribution of receptor binding sites on cells with nanometer resolution. 
Fluorescence Microscopy: Assisting AFM in a combined AFM/Fluorescence microscope.

Postdoc position (Hinterdorfer)- filled


MF 10 - Life Science Compute Cluster

The Life Science Compute Cluster (LiSC) is available to all members of the Cluster of Excellence. It consists of data storage and high-performance computing facilities, and a user helpdesk. Parallel file systems with a total capacity of 1 PB are used for high-performance storage of original and derived data. Backups are performed on separate storage in a different location. The high-performance computing nodes provide >3,000 CPU cores and 30 GPUs and are used via a job scheduling system. In order to facilitate easy and reproducible access to all relevant state-of-the-art scientific software, the LiSC provides a helpdesk to its users. The helpdesk not only supports users in case of problems with scientific computing, statistics and data analysis, but also takes installation requests for software versions. The LiSC is connected to further high-performance-computing facilities, namely the Vienna Scientific Cluster, allowing users straightforward access to additional computing power, if needed. 

Technician position (Rattei)          Postdoc position (Rattei) - filled