Open Access

Call for proposals is now OPEN

1. Call for projects  

Project RIAT-CZ, funded via the programme Interreg V-A Austria – Czech Republic 2014–2020, is focused on creating synergies between research infrastructures to stimulate innovation in the cross-border region Austria-Czech Republic. In accordance with the project aim, the distributed infrastructure is available at project partner institutions (VBCF, CEITEC MU, CEITEC BUT and FNUSA-ICRC) in open-access regime.
The partner institutions are the most prominent centers operating bio- and nano- research infrastructures in the Czech-Austrian cross-border region:
  •  Vienna Biocenter Core Facilities, GmbH (VBCF)
  •  Central European Institute of Technology (CEITEC-MU and CEITEC-BUT)
  •  International Clinical Research Center (FNUSA-ICRC)

Within the project RIAT-CZ they have developed new services which are now open for scientific projects in the regime of open access as follows:

Type of open access projectRelevant partner institutionsCore Facilities Involved 

Single cell sequencing

Library preparation of up to 90 single cells using the smart-seq 2 protocol and subsequent sequencing on a HiSeq 2500 single read 50 bp lane. Analysis of results including separation and characterization of subpopulations.

CEITEC MU/VBCF

Genomics / Next Generation Sequencing

Protein Quality Assessment Service 

A new service to evaluate the quality of protein samples for subsequent biophysical and biochemical experiments is provided. This service consists of a standard set of analysis techniques, analyzing protein purity, homogeneity and folding state. Introduction of this service should lead to a higher success rate of downstream experiments that require pure and homogeneous proteins.

CEITEC MU/VBCFBiomolecular Interactions & Crystallization / Protein Technologies

Galaxy Workflow tool for NGS and imaging data analysis

Galaxy is a web-based easy-to-use bioinformatics analysis platform. We offer open access to the created installation including training of the involved scientists.

CEITEC MU/VBCFBioinformatics + Genomics / Bioinformatics & Scientific Computing

Data management solutions and making experimental data available through simple web interfaces for experimental labs

Open access to web applications LiteMol suite and ValTrendsDB. The application web pages contain interactive documentation, video guides and user support.

CEITEC MU/VBCFBioinformatics / Bioinformatics & Scientific Computing

Motor function analysis with Motorater system 1

The MotoRater system by TSE-Systems allows for gold-standard gait analysis of mice as they walk across a runway or a ladder. Mice are briefly anesthetized, shaved and points of interest are marked with coloured pens such as the knee, ankle, elbow, etc.., and the mice are trained to walk across a runway or ladder while being videorecorded. Using SimiMotion software we can analyze the movement of each point in the 2D space, looking at the mouse from both sides and from below. The combination of movement and anatomical parameters (distances, angles during the movement, speed, gait pattern,..) is a valuable readout for  injury models and mouse models of e.g. Huntington’s or Parkinson’s disease or other neurodegenerative/neuromuscular disorders.

VBCF/FNUSA-ICRCPreclinical Phenotyping / Animal Center

Pipeline for cognitive function 1

The Intellicage system by TSE-Systems allows for high-throughput screening of homecage behavior and cognitive performance (operant conditioning) in a social group (up to 16 mice simultaneously) with minimal handling by the experimenter. A multitude of conditioning protocols can be programmed using e.g. sucrose rewards or air puffs as negative feedback.

VBCF/FNUSA-ICRCPreclinical Phenotyping / Animal Center

Pipeline for depression/anxiety-like behaviour 1

Using the Intellicage system by TSE-Systems (see also cognitive function pipeline), we can test for anxio-depressive-like behavior using a Vogel-water-lick conflict test in socially grouped mice by testing their reaction to punishment, which is often enhanced in anxio-depressive disorders.

Additionally, we can test the circadian rhythmicity (which often shows deviations in anxio-depressive disorders) by measuring the day and night activity and metabolic parameters in the PhenoMaster metabolic cages by TSE-Systems, and we can test for anhedonia in a sucrose preference test.

VBCF/FNUSA-ICRCPreclinical Phenotyping / Animal Center

Functional imaging at high field

  • Advanced processing of fMRI data
    (available at CEITEC MU/VBCF)

  • Analysis of dynamic connectivity from both human and animal data
    (available at CEITEC MU/VBCF)

  • Acquisition of functional MR images at ultra-high magnetic field strength 15.2 T
    (available at VBCF only)

  • Acquisition of functional MR images with human scanners (3 T)
    (available at CEITEC MU only)

CEITEC MU/VBCFMultimodal and Functional Imaging LaboratoryPreclinical Imaging

High-Resolution Imaging using cryo-electron microscopy

The Electron Microscopy Facility (EM) offers a variety of preparation techniques for biological samples of diverse origin. We examine the complex architecture of macromolecules, cells and tissues at nanometer resolution using state-of-the-art conventional and cryo-techniques for specimen preparation and visualization. Whether you are interested in quick sample screening or high resolution 2D or 3D imaging, we can help. Furthermore, we provide the processing of purified molecules for conventional and cryo-electron microscopy as well sample preparation for scanning electron microscopy.

The main objective of the Cryo-electron Microscopy & Tomography Core Facility is to establish a world-class facility for cryo-electron microscopy accessible also for external users. The centre will provide access to EM instrumentation set up for high-throughput image acquisition for single particle analysis as well as for the acquisition of cellular cryo-electron tomograms. Moreover, it will provide assistance to external users/collaborators in image processing (e.g. 3-D reconstruction, denoising, pattern recognition, segmentation, visualization). External user projects will be selected by peer review on the basis of scientific merit, technical suitability and feasibility. The centre will also offer training enabling non-specialists to develop the necessary skills. The high-end instrumentation and the team of experienced researchers will ensure expert services, user training and the cost-effective use of resources.

CEITEC MU/VBCFCryo-electron Microscopy & Tomography / Electron Microscopy

Improved in situ visualization of regions of interest in eukaryotic cells using HPF and cryo-FIB

This new service will allow researchers to examine the structure of a region of interest within a large biological samples - for example the nucleus of a eukaryotic cell - at high resolution and as close to the native state as possible today. Samples are rapidly frozen by High Pressure Freezing (HPF) and then a region of interest within this sample is "cut out" using a Focused Ion Beam (FIB). Finally the sample is transferred to a transmission electron microscope and the region of interest is examined by cryo-electron microscopy or -tomography to obtain unprecedented new 2D and 3D insights.

CEITEC MU/VBCFCryo-electron Microscopy & Tomography / Electron Microscopy

Custom made nanofabricated substrates for surface modified imaging/spectroscopy

TBD

CEITEC BUT/VBCFNano Research Infrastructure / Advanced Microscopy

High-resolution mechanical characterization of biological matter over various frequency regimes

We provide a correlative approach to obtain high resolution stiffness maps of biological samples under nearly physiological conditions. Mechanical approach given by atomic force microscopy (AFM) combined with optical microscopy (Brillouin microscopy, BFS) provides better view to distribution of elastic properties of living and biosamples.

CEITEC MU/VBCFNanobiotechnology / Advanced Microscopy

Agar-plate screening system

Within the RIAT-CZ project, our PHENObox for side-view crop plant phenotyping was upgraded with a custom designed agar-plate sample holder facilitating semi-automated RGB screening of seedlings and root phenotyping. Corresponding image analysis algorithms were developed by using the LemnaTec software and are available at PlantS (VBCF). 

CEITEC MU/VBCFPlant Sciences (CEITEC) / 
Plant Sciences (VBCF)

Environmental simulation and high-throughput plant phenotyping

Both Plant Sciences core facilities provide access to state-of-the-art and highly specialized plant growth chambers for environmental simulation and phenotyping analyses. 

At CEITEC MU, several chambers are capable of providing exceptional environmental conditions like low and high temperature stress, different light intensities and light spectra and different gas conditions (e.g. CO2 atmosphere). 

The VBCF PlantS Facility offers two of the completed pilot projects in one service. Their phytotrons are designed for simulation of complex global environments within the temperature limits of minus 15 °C and up to plus 30 °C.
In the framework of the RIAT-CZ project, several of the phytotrons were equipped with high-tech LED lights with adjustable light spectrum extending the simulation portfolio. Moreover, one of these phytotrons is equipped with a robotic high-throughput RGB plant phenotyping system. The subsequent analysis of the generated data including data visualization and statistics is done via the PHENOComp tool developed within RIAT-CZ.

CEITEC MU/VBCFPlant Sciences (CEITEC) / 
Plant Sciences (VBCF)

1 Registration for open access projects implemented at FNUSA-ICRC facilities will be started in May 2019.

1.1 Eligible beneficiaries/users

Researchers working at universities and research institutes in the cross-border region (South Moravia, South Bohemia, Vysočina, Oberösterreich, Niederösterreich, Wien). Only external academic users (users from other research institutes and universities than RIAT-CZ partner institutions) can apply for access. This call is NOT eligible for private companies. One user can use more than one access but only in a different area predefined in the table.

1.2 Available equipment and services for this call

The following VBCF core facilities participate in the call:
  •  Bioinformatics & Scientific Computing
  •  Electron Microscopy
  •  Next Generation Sequencing
  •  Plant Sciences
  •  Protein Technologies
  •  Advanced Microscopy
  •  Preclinical Phenotyping
  •  Preclinical Imaging

The following CEITEC core facilities participate in the call:
  •  CEITEC Nano Research Infrastructure (CEITEC BUT)
  •  Biomolecular Interactions and Crystallization
  •  Nanobiotechnology Core Facility
  •  Cryo-electron Microscopy and Tomography
  •  Genomics Core Facility
  •  Multimodal and Functional Imaging Laboratory
  •  Plant Sciences Core Facility
  •  Bioinformatics

The following FNUSA-ICRC core facility participates in the call:
  •  Animal Center

For more information about equipment and services available within this call please read Core Facilities Profile Cards.

1.3 Selection process

The selection process is composed of two steps:
  •  Technical feasibility – heads of the respective CEITEC/VBCF/FNUSA-ICRC core facilities judge the technical feasibility of the submitted research project at their facilities (YES/NO decision).
  •  Financial feasibility – for each access, only a limited amount of support can be provided in respect to the total budget dedicated to the project. Financial feasibility will be evaluated and negotiated individually for each proposal.

All received project proposals to be implemented at CEITEC/VBCF core facilities will be forwarded to the selection process immediately. Assessment of proposals realized at FNUSA-ICRC Animal Center is postponed. If the proposals are evaluated positively, the applicants are invited to conduct their experiments.

1.4 Deadlines and funding

The call is open from 1st October 2018 until the capacity for open accesses will be depleted. All projects must be implemented by 30th August 2019.

Fill in the application form accessible HERE and send by email to lada.fialova@vbcf.ac.at. State “RIAT-CZ proposal” in the subject line.

Project proposals that successfully pass through the selection procedure will be supported by RIAT-CZ project funded via programme Interreg V-A Austria – Czech Republic. Use of the research infrastructures including training and interpretation of the obtained results is provided for free; the users will be obliged to provide his/her own samples in a sufficient quality. The grant does not cover travel & accommodation expenses.


2.   General Conditions of Access

2.1 Intellectual property

Intellectual property generated within the research projects belongs to the user.

2.2 Nature of research and publication of results:

This call intends to support projects of basic and applied research conducted at academic institutions. All research results achieved under this call shall be published.

2.3 Acknowledgments

Publications resulting from the work undertaken at core facilities in the framework of RIAT-CZ project have to contain an acknowledgment according as follows:

RIAT-CZ project (ATCZ40) funded via Interreg V-A Austria – Czech Republic is gratefully acknowledged for the financial support of the measurements at the CF [name of the CF+ name of the institution].

A similar acknowledgment should be included during conference presentations, including the proceedings, and at other public presentations.

Users shall notify RIAT-CZ project managers of all publications resulting from this open access call. A PDF file and reference details of a publication as soon as it has been published are necessary. Please indicate the type of publication: Scientific Journal, Book, Patent, Proceedings, an article on www, other. These publications should also carry the acknowledgment given above.

2.4 Safety requirements

Users must comply with all relevant health and occupational safety rules.

Users who carry potentially dangerous materials and/or equipment must notify the CF Head and host organization.

All visitors bringing material, including samples or equipment are advised that such equipment or material remains entirely in the responsibility of the visitors concerned.

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