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Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP)
Identification
Hosting Legal Entity
Jožef Stefan Institute (JSI)
Address:
39, Jamova cesta, Ljubljana, PO: SI-1000, Central (Slovenia)
Location
39, Jamova cesta, Ljubljana, PO: SI-1000, Central (Slovenia)
Structure
Type Of RI
Distributed
Coordinating Country
Slovenia
Status
Status
Current Status:
Under construction since 2010
Scientific Description
Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins CIPKEBIP is a non-profit research institution. CIPKeBiP will connect the top available expertise, knowhow, and technology of Slovenian research laboratories in protein science, thus emphasizing biomedical relevance of the applied project (priority health and life sciences). The Centre is coordinated by the Department of Biochemistry and Molecular and Structural Biology at JSI, the leading edge of Slovenian biochemical science, and includes institutions from central and northeastern region of Slovenia as well as small, medium and large industrial entities. Using the Centre of Excellence grant as the start-up money we have established a research infrastructure and scientific platforms which enable us to:-identify molecular carriers and pathways underlying physiological and pathological processes;-monitor molecules, their position, transfer and transformations in biological processes;-characterize their biochemical and biophysical properties and structure;-and exploit the gained knowledge for commercial purposes. The platforms are: -High resolution and super-resolution light microscopy for visualization of molecules and their interactions in cells or in tissues and organisms.-Mass spectroscopy for analysis of protein composition in complex samples and analysis and identification of individual biological molecules and their modifications.-Protein and structure production platform for analysis of molecular mechanisms from biochemical to atomic resolution studies (3D crystal structures, kinetics of interactions and properties of biologically active molecules - proteins and small organic molecules).-Platform for development of biologically active organic molecules based on biological and chemical synthesis. -Computational analysis of complex biological and other experimental data with the purpose of descriptive and predictive modeling, knowledge extraction and integration, as well as optimization of experimental approaches and technological processes.The founding members of CIPKeBip are:- Jožef Stefan Institute- AciesBio d.o.o.- University of Ljubljana, Medical Faculty, Institute of Pathophysiology- University of Ljubljana, Biotechnical faculty- University Medical Centre Ljubljana- Jenko d.o.o.- University of Maribor, Medical Faculty- Institute of Public Health Maribor.

RI Keywords
Adaptive immune response mechanisms, Gut microbiota, Structural biology, Endosomal hydrolases, Surface proteins of pathogens, Systems biology
Classifications
RI Category
Bio-informatics Facilities
Data Mining and Analysis (Methodological) Centers, including statistical analysis
Analytical Facilities
Genomic, Transcriptomic, Proteomics and Metabolomics Facilities
Structural Biology Facilities
Systems Biology/Computational Biology Facilities
Scientific Domain
Biological and Medical Sciences
Chemistry and Material Sciences
Information Science and Technology
Services
Support of educational programs at Universities and Jozef Stefan International Postgraduate school, researchers from Academia, researchers from industry and researchers from SMEs

CIPKEBIP research equipment and CIPKEBIP researchers who are involved in educational programs and with the other researchers from Academia industry in different kind of research projects and programs directly and indirectly support them.

Access to research equipment, technology and knowledge

CIPKEBIP research infrastructure is divided into 5 platforms where combination of knowledge, technology and equipment lead to new findings: 1. High resolution and super-resolution light microscopy for visualization of molecules and their interactions in cells or in tissues and organisms. 2. Mass spectroscopy for analysis of protein composition in complex samples and analysis and identification of individual biological molecules and their modifications. 3. Protein and structure production platform for analysis of molecular mechanisms from biochemical to atomic resolution studies (3D crystal structures, kinetics of interactions and properties of biologically active molecules - proteins and small organic molecules). 4. Platform for development of biologically active organic molecules based on biological and chemical synthesis. 5. Computational analysis of complex biological and other experimental data with the purpose of descriptive and predictive modeling, knowledge extraction and integration, as well as optimization of experimental approaches and technological processes.

Training

CIPKEBIP is involved at the national level in the program of early stage researchers - 4 year doctoral study financed by Slovenian Research Agency. First researcher has started training in November 2011. The second one has started in November 2012.

Equipment
Nano-HPLC instrument

Nanoflow HPLC unit is used for low flow chromatographic analysis (10-1000 nL/min). It is connected directly to the ESI source of mass spectrometer: Thermo Scientific Orbitrap Velos. Nanoflow HLPC unit is equiped with vacum degasser and temperature regulated autosampler (1-10 uL injection volumes). Product: EASY-nLC II LC-446, Thermo Scientific.

Multi-functional spectrophotometer for microtiter plates

The microplate monochromator reader is used at multiple levels of our research: for basic qualitative and quantitative spectral analysis of macromolecules, analysis of the changes in various cellular processes in living cells and analysis of specific interactions between macromolecules. Product: Multi-functional spectrophotometer for microtiter plates, Tecan.

Shaking incubators

Production of proteins and synthetic bio-active molecules - System for cultivation of microorganisms and cell cultures, includes a series of shakers andincubators. Products: INFORS Multitron II (two-deck), Labcaire Microbiological Safety Cabinet, On-or-under bench incubator shaker Innova 42R with added refrigerator, Low temperature incubator, Orbital shaker.

System for parallel synthesis

System is used for automated parallel chemical synthesis on a smaller scale. It includes an instrument for monitoring of the reaction progress and analysis. System allows precise regulation conditions for synthesis (temperature, Ph, pressure). Product: Easy max Mettler and React IR45FTIR InSitu, Mettler Toledo.

Real-time PCR device with HRM option

Real time PCR is used for detection of genes or gene regions within the genome and in the quantitative form also for analysis of gene expression. Melting curve analysis of amplified fragments is used for detection of mutations in amplified products, for genotyping or for analysis of metilation. High resolution melting is further upgrade that enables much more exact analysis and alsodetection of single mutations. Product: ROTOR-GENE Q, 5-PLEX HRM (High Resolution Melt) option.

Nonlinear acustooptical modulator

Acustooptical beamsplitter (AOBS) with spectral detectors is used to interfere with physiological processes in intact tissues and organs. The basis of this microscope enables spatially limited interference within single cells in biological samples of bigger dimensions. Handling of the laser beam used for photolysis or depletion of stimulated emission can be relatively slow to enable long-term spatially resolved manipulation of the cellular processes or in high speed mode, which enables triggering of transient sub-millisecond events. The basis of laser light manipulation is electrooptical modulator that can precisely set the duration and power of the laser light in the focal point. Product: Acoustooptical beamsplitter (AOBS) with spectral detectors, Leica.

Heart Imaging

Instrument is diagnostic ultrasound system used for heart visualization/imaging and the assesmet of cardiac function. System includes standard ultrasound configuration with several different probes for heart examination and additional software equipment for data retrieval and analysis. Product: ProSound ALPHA 7 Premier, ALOKA.

High performance cluster computer

High performance cluster computer is used for complex analysis of data.

Laboratory scale bioreactor (20L), pilot bioreactors (100 and 150L)

Production of proteins and synthetic bio-active molecules - System for cultivation of microorganisms and cell cultures, includes a series of bioreactors that will allow parallel cultivation of a larger number of MO and CC cultures on a different volume scale (from a 20 to 150 liters), allowing precise regulation and optimization of growth and expression conditions (temperature, pH, aeration, feeding and mixing speed) and providing the conditions for sterile work, and preventing the release of genetically modified organisms into the environment. Products: Fermenter BIOSTAT Dplus 150L for microbial fermentation and cell culture, Fermenter BIOSTAT D-DCU II 100L, Fermenter BIOSTAT Cplus 20L, Sartorius Stedim Systems GmbH.

System for macromolecular crystal structure determination

System for macromolecular crystal structure determination is composed of x-ray generator, detector system, computers and software, maintenance and support, and accessories for crystallization, crystal storage and handling. Product: X8 PROTEUM, Bruker.

Nano-optical microscopy with technology STED

Research equipment Nano-optical microscopy with technology STED represents the most advanced technology in the field of optical microscopy, comprising of most advanced optics, mechanics and electronics. This equipment allows the observation of live objects at resolution of 35 to 40 nm. The key parts of the system consist of the upright and inverted microscopes with stable body to prevent long term focus drifts. These are to be mounted on an antivibrational table with a Faraday cage to enable use o electrical equipment in optical measurements. Laser scanning module with electronics, pulse lasers with long (tunable) wavelength, lasers and diodes for excitation of probes, software equipment for data acquisition and data analysis (permitting own software implementation). This equipment represents the-state-of-the-art European invention with the origins in 2000 and has recently seen wide applications in biological experimentations (see Nature comment June 4th, 2009). In addition to the key instrumentation one needs to acquire bench top centrifuge, CO2 incubator with a chamber to be mounted onto the stage of the microscope, freezer/refrigerator and a routine inverted microscope. Product: Ti:Saphire laser, Microscope with laser diode 405 nm CW, Components for fluorescence signal manipulation, The supercontinuum triple laser fo the microscope, Superresolution combined light microscopy, Carl Zeiss Inc.

LC-MS system

LC-MS system is used for identification, structural confirmation and quantitative determination of small compounds. The system is composed of a HPLC system, equipped with a pump, autosampler and UV/VIS detector. Mass detector is equipped with triple stage quadrupole and with two different H-ESI-II and APCI ionization probes. Product: TSQ Quatum Access MAX/Accela 1250, Thermo Scientific.

High-pressure HPLC system

HPLC system for high-pressure liquid chromatography is used for analytics of special organic compounds: difficult-volatile and thermolabile compounds.

Laboratory chemical reactors from 100 to 500 ml

Set of chemical reactors from 100 to 500 ml are used for the synthesis of small molecules.They allow a wide range of reactions in terms of volumes (100 to 500 ml), temperatures (-90 ° C to + 200 ° C) and pressure (from vacuum to 150 B).

High performance HPLC

High performance HPLC is used for analysis of small molecules. Product: Agilent 1260, Agilent Technologies.

System for isolation of recombinant proteins

Automated protein purification workstation AKTAexpress (GE Healthcare) is chromatographic system designed for automated two-step protein purification on affinity columns and desalting and size exclusion columns. The system capacity is purification of 8 proteins in a single day. Product: ÄKTAexpress Single System, ÄKTA.

High resolution mass spectrometer

High resolution mass spectrometer is used for the identification of proteins and their posttranslational modifications. It enables molecular mass determination of intact proteins and protein complexes. Product: Mass spectrometer ULTRAFLEXTREME tm maldi tof, Bruker.

Isothermal titration calorimetry

Protein microcalorimetry is based on measurements of heat that is released or consumed during the interaction between protein and ligand.

Preparative HPLC system

HPLC System is used for micro-separation and analysis of complex biological samples. System includes the following modular components: a pump, detector, column heater, automatic capture of samples and fractions collector. For the protein purification different kind of centrifuges are needed for quality separation of the cells from media. Products: Preparative HPLC system (Waters), Cooling centrifuge for volumes to 500 ml, Centrifugal evaporator, Rotary evaporator R-215.

Upright nonlinear microscope

An upright nonlinear microscope is used to monitor and quantification of physiological processes in intact tissues and organs. The basis of this microscope enables mounting of biological samples of bigger dimensions and at the same time utilizes deep-penetrating infrared laser light to excite fluorescence. Handling of the laser beam used for fluorescence excitation can be relatively slow to improve the high spatially resolved morphological images or monitoring of relatively slow physiological processes. On the other hand we can move the laser beam over the sample using a high speed mode, which enables monitoring of the physiological processes with millisecond time resolution. The detector side consists of a classical system of high gain photodiodes with a possibility of spectral resolution. The major advance in detection of the faintest signals of fluorescence or bioluminescence comes from the direct mounting the system of non-descanned high resolution photodiodes. Product: System for non-linear nanoscopy in tandem configuration, Leica.

Inverted fluorescence microscope with the incubation chamber

To preserve the characteristics of cells observed under the microscope these cells must be kept under optimal and controlled conditions, i.e. temperature, CO2 level (5%) and humidity must be controlled and maintained. Therefore, special incubation chamber together with control units must be mounted on the platform of the microscope, adjusted to the microscope type. Incubation chamber must enable optimal growing milieu for the cells, on the other hand it must allow the operator to access the sample as well as to perform all the necessary manipulation with the microscope. Temperature control is achieved with warm, filtered air, circulating from the separated heater unit into the acrylic enclosure where it is continuously circulated. Product: Inverted fluorescence microscope Olympus IX81 with the incubation chamber (from Solent Scientific) attached to the platform of the Olympus microscope, Olympus.

Flow Cytometry

Flow Cytometry is usedfor determination of sequencing of proteins. Product: Procise 492A, Applied Biosystems.

Flow cytometry with a routine inverted microscope

Flow cytometry with a routine inverted microscope is used to measure and analyse physical and chemical characteristics of individual cells as they travel in suspension one by one through sensor. As the cells pass through the laser (488nm, 633nm), the fluorochromes attached to the cells absorb light and then emit a specific color of light depending on the type of fluorochrome. The color detectors collect the different colors of light emitted by the fluorochromes. Light bounced off at small angles is called forward scatter and is proprotional to cell size. Light bounced off in other directions is called side scatter and correlate with cytoplasmic granularity of a cell. Product: FACSCanto II Flow Cytometry, BD.

Date of last update: 05/06/2013
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