CF1 BIOINFORMATICS

head: vacancy

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The core equipment of the CF1 Module is the latest generation Nvidia DGX-2 supercomputer, enabling the use of state-of-the-art artificial intelligence (AI)-based technologies in the areas of in silico modelling and computational genomics. Research work using the Nvidia DGX-2 supercomputer focuses on developing advanced computational methods that use machine learning algorithms, particularly deep learning, for broad applications in genomics and computational drug design. Nvidia DGX-2 enables the development and widespread use of state-of-the-art tools for predictive analytics, identification and validation of novel therapeutic targets, virtual screening and de novo design of prototype drugs. Additionally, it enables the optimisation of ADME parameters, prediction of ligand-protein interactions, receptor selectivity, investigation of the impact of genetic polymorphisms on drug action and performance of meta-analyses of clinical data to better understand disease aetiology. The technologies and methods used in these computational processes are considered key to the successful development of future drugs, which can significantly reduce the time and cost of the overall process. Complementing the Module are 2.5 PB NAS servers and drives for storing data generated by the HTS high-throughput analysis equipment.

• The EasyMax 102 Advanced small-scale synthesis workstation (Mettler Toledo) is equipped with fully automated systems for real-time monitoring of reaction kinetics, parameter control, recording, analysis and data archiving. The station includes a Detector, IR 702L, 9.5×305 mm for real-time tracking of reaction progress, a laser camera for monitoring crystallisation processes, precision reagent dosing pumps, a cooling cryostat, a hydrogen generator with pressure vessel, and a shielding gas flow controller that enables reactions to be carried out under anaerobic and anhydrous conditions. In addition, the station has a system that ensures unattended collection of representative samples at a specified time in 24-hour mode. Thanks to the station’s extensive equipment, it is possible to carry out chemical reactions over a wide temperature range from -40 °C to 200 °C and pressures from 0 to 60 bar, with a maximum reactor volume of 100

• The process scaling workstation (Radleys Reactor-Ready™ ): for larger scale syntheses is dedicated to optimising and scaling up chemical processes over a wide temperature range (-80°C-180°C) with high precision and accuracy, ensuring reproducibility and repeatability of experiments. The synthesis scale-up kit is equipped with glass reactors (1L, 2L, 5L capacity), an automatic dosing and mixing system, a circulating cryostat, an IR probe and AVA Lab Control control software. With the Larger Scale Synthesis Workstation, it is possible to optimise reaction parameters and chemical processes in a multistage and fully controlled manner with regard to: increasing process efficiency and safety, reducing the amount of reagents and solvents used in the reaction, eliminating the formation of environmentally hazardous by-products, determining the complete mass balance of a given process on a scale of a few grams to several hundred grams.

• The flash chromatograph (PuriFlash XS 520, Interchim) is an automated system for purification and separation of reaction products, ideal for routine applications. The system features a highly efficient gradient pump and an integrated DAD detector (UV-Vis) and a lockable fraction collector. Equipped with columns from 4 g to 330 g.

•  Preparative liquid chromatograph (AutoPurification-Waters) coupled to a single quadrupole mass detector, HPLC-DAD-MS enables rapid and efficient isolation and purification of a variety of organic compounds on analytical and semi-preparative scales. Equipped with a UV detector (190-700 nm range) and a single quadrupole mass detector with electrospray ionisation (ESI, mass range: 30-1250 m/z mass accuracy: ±0.2 Da), and an autosampler and fraction collector (based on a three-way valve with fast switching time for high fractionation efficiency). By combining high-performance liquid chromatography with mass spectrometry, fast and high-throughput mass-oriented purification or purification based on UV detection is possible.

• Opera Phenix Plus (Revvity) – High-throughput confocal microscopy system for precise 3D imaging of samples for screening and cellular analysis. It uses spinning disk confocal technology to minimise image burn-in and cell damage; it is an advanced high-throughput image analysis system that is particularly useful for cell biology research, especially cell-based screening assays. Featuring four-channel fluorescence detection and multi-channel image analysis capabilities, it enables simultaneous monitoring of multiple parameters in real time. Optimised for the analysis of complex biological models such as co-cultures or organoids. The system provides excellent resolution and speed of analysis thanks to spinning disk confocal technology. The ability to perform image acquisition and fluorescence detection in parallel makes Opera Phenix Plus ideal for high throughput screening (HTS). It has an automation option, which increases the efficiency of experiments and allows working with large data sets. The automatic image focus and stable temperature control features ensure optimal conditions for long-term experiments with live cells. With Harmony’s advanced software, the user can perform complex analyses and data visualisations in an intuitive way. Applications in compound, toxicity and pharmacological studies are supported by multifunctional image analysis at the single cell level.

• Biacore S200 (Cytiva) is a platform for the analysis of biomolecular interactions using Surface Plasmon Resonance (SPR) technology. It enables the study of the binding kinetics, affinity and stoichiometry of interactions between proteins, nucleic acids, peptides and other molecules. The instrument offers exceptional sensitivity and accuracy, enabling real-time measurements of very weak interactions, which is crucial for drug and biotherapeutic research. The S200 allows experiments to be performed over a wide temperature range, enabling accurate assessment of the thermodynamics of interactions. The software supporting the experiments provides detailed analysis of kinetic parameters, such as rates of association and dissociation, as well as calculation of binding equilibrium constants (KD). With the ability to study interactions without labelling, it eliminates potential interference from molecule modifications. It enables analysis of interactions at the pM level, making it ideal for drug discovery, bond strength analysis and ligand affinity studies. Built-in automation and a sample management system allow simultaneous analysis of multiple samples, increasing research throughput. The system is widely used in biological drug product research, pharmaceutical research and biomolecular science.

• Dianthus Pico (Nanotemper) for the analysis of protein interactions with small-molecule ligands, using MicroScale Thermophoresis (MST) technology. It monitors fluorescence changes, offering precise real-time measurements – a state-of-the-art device for molecular binding analysis. The device allows for non-contact and label-free evaluation of interactions between molecules, such as proteins, nucleic acids, lipids and other ligands, at low nanomolar and picomolar concentrations. MST technology enables the analysis of changes in the mobility of molecules under the influence of a varying temperature gradient, allowing the precise determination of binding strength between molecular partners. Dianthus offers very fast analysis times, making it ideal for high throughput screening (HTS) in drug research. The system can work with samples under different environmental conditions, such as different buffers, high concentrations of DMSO or detergents, increasing its flexibility in biological analysis. With direct measurement without the need for tracers, Dianthus eliminates the possibility of biasing results due to chemical modifications. The instrument allows for the analysis of large libraries of compounds, making it an ideal tool in drug discovery. The automation of the analysis process allows large volumes of samples to be tested in a short period of time, increasing efficiency in the laboratory.

• Echo 650 (Beckman) is a device that uses acoustic dosing technology to enable precise, non-contact liquid transfer. This technology allows the transfer of very small sample volumes – from nanolitres to microlitres – with extreme accuracy, minimising the risk of contamination and material loss. The Echo 650 is widely used in laboratories involved in compound screening, enzyme assays and sample preparation for sequencing. The system eliminates the need for conventional pipettes and tips, reducing operational costs and waste generation. It enables rapid transfer of samples between microplates, speeding up research processes and increasing throughput in high throughput screening (HTS) laboratories. The Echo 650 is compatible with a wide range of microplate formats, allowing integration with other laboratory systems. The control software allows programming of complex dispensing protocols and monitoring of liquid transfer accuracy in real time. The instrument also supports multilayer transfers and sample mixing, further enhancing its application in complex chemical and biological research. With its high precision sample transfer, the Echo 650 is an indispensable tool for laboratories involved in drug research, biotechnology and genetics.

• Biomek i7 (Beckman Coulter) is a robotic pipetting station designed to automate complex laboratory protocols such as sample preparation for sequencing, screening assays, PCR reactions and other biological and chemical tests. The station features a precision pipetting arm that can handle a wide range of liquid volumes, from microlitres to millilitres, providing exceptional accuracy and repeatability. The Biomek i7 can be integrated with a variety of modules, such as reagent dispensers, incubators or shakers, increasing the flexibility of the instrument. The Biomek software allows the user to program complex protocols, optimising lab work and reducing the risk of human error. With advanced features, the station supports high-throughput research and automated library preparation for sequencing. The ability to work with different microplate formats allows the instrument to be adapted to a wide range of research applications, from screening assays to sample preparation for molecular studies.

• CLARIOstar Plus (BMG LABTECH) is a versatile microplate reader, equipped with an LVF (Linear Variable Filter) monochromator, enabling a choice of wavelengths for measurements such as fluorescence, luminescence, absorbance, FRET and BRET. The instrument provides automatic focusing, CO₂ and O₂ level control through Gas Control, as well as advanced temperature and shaking management. It can work with microplate formats (from 6 to 1536 wells) and supports High Throughput Screening (HTS) assays. The CLARIOstar Plus is also equipped with a 50 microplate feeder, which increases productivity and automation when analysing large volumes of samples. In addition, it offers photo bleaching correction functions and integration with advanced analysis software.

CF3C Laboratory of Proteomics and Mass Spectroscopy

head: Przemysław Mielczarek, PhD

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Mass spectrometry is particularly useful for shotgun proteomic analyses, i.e. the simultaneous determination of thousands of proteins present in very complex biological mixtures, while not losing information about the post-translational modifications of each protein being determined. High-resolution mass spectrometry not only allows unambiguous identification of proteins and peptides, but, in combination with the TIMS ion mobility analyser, allows very detailed characterisation of post-translational modifications, such as glycosylations, with simultaneous differentiation of isomeric glycan residues, i.e. chemical compounds of the same molecular weight but different chemical structure. Measurement by conventional mass spectrometry alone, will not be useful in such cases. Such analyses can be used in in vivo and in vitro models, and particularly in the analysis of peptides found in the central nervous system. Current techniques severely limit the feasibility of quantitative analyses, as they require the use of very expensive isobaric labelling with tracers such as iTraq or TMTpro. The high cost of such analyses greatly limits the performance of such mass-scale determinations. The timsTOF Pro 2 mass spectrometer allows for label-free quantitative analyses, reducing the cost of analysis and requiring no markers. It is possible to perform quantitative analyses of all proteins in a mixture, rather than just one or a few selected proteins, as in the case of targeted analyses using mass spectrometers equipped with quadrupole analysers. Furthermore, this spectrometer is equipped with an ESI-type ion source, which allows direct online nanoLC-MS analyses to be performed thanks to the possibility of combining liquid chromatography directly with the mass spectrometer.

In addition, the laboratory is equipped with its own MASCOT server for searching protein databases. The LC-MALDI system described above, which is equipped in the Proteomics and Mass Spectrometry Laboratory, is designed for advanced proteomic analyses involving the identification of proteins without the need for gel electrophoresis. Using isobaric markers such as iTraq, it is possible to perform quantitative proteomics, simultaneously determining the concentrations of up to thousands of proteins in a single sample. Another application using the high-resolution MALDI-TOF/TOF mass spectrometer is MALDI molecular imaging. During these experiments, the spectrometer allows maps of the imaged tissue to be obtained, presenting areas where substances with specific m/z (mass-to-charge ratio) values are present. This makes it possible to visualise, for example, in which brain structures specific lipids, peptides, neurotransmitters or even whole proteins are present. This strategy is often used to identify brain structures in which specific endogenous compounds are present, but also to search for new biomarkers.

• TimsTOF Pro 2 mass spectrometer with PASEF technology (Bruker) equipped with an Ultimate 3000 capillary liquid chromatograph)  a unique instrument on a global scale, in Poland it is the first installation in a scientific research unit available for commercial use. The instrument is not only a high-resolution mass spectrometer equipped with ESI ionisation, but additionally has a TIMS ion mobility analyser. This solution allows additional structural information on the structure of the compounds under study and, in the case of proteomic studies, significantly improves the quality of the results obtained. Thanks to the high sensitivity and fragmentation of peptides/proteins/molecules using PASEF technology, this spectrometer is the market-leading instrument in shotgun proteomic studies. The combination of this spectrometer with capillary liquid chromatography makes it an analytical instrument with a wide range of applications, not only in the field of proteomics, but also for the analysis of drugs, endogenous compounds and all kinds of quantitative analyses.

• Mass spectrometer ultrafleXtreme (Bruker) is a mass spectrometer that has evolved from the latest technical advances in MALDI-TOF/TOF mass spectrometry. It is the leading model with MALDI-type ionisation offering the best results in proteomic studies, biomarker discovery and MALDI molecular imaging. This spectrometer is an ideal tool for studies involving the following topics : identification of proteins from polyacrylamide gels, identification and quantitative analysis of proteins by LC-MALDI (using isotopic labelling methods, mainly iTRAQ, TMTpro, but also ICAT), advanced biomarker analyses, MALDI imaging of tissues to study the spatial distribution of different types of biologically active compounds, de novo sequencing of peptides.

• Seahorse XF Pro (Agilent)
  This unique instrument enables functional analysis of cellular energy metabolism by automatically measuring two key parameters: Oxygen Consumption Rate (OCR) for mitochondrial respiration and Extracellular Acidification Rate (ECAR) for glycolysis. OCR measurements provide insights into basal respiration, ATP production, proton leak, maximal respiration, and spare respiratory capacity, while ECAR measurements evaluate glycolysis, glycolytic capacity, and glycolytic reserve. The method requires no cell labeling, ensuring minimal interference with the biological system. Detection is performed via optical sensors that do not alter the physiological state of the biological samples.
  The instrument operates in a 96-well plate format and allows the precise addition of up to four different compounds during analysis. It supports measurements on various living cell types, including adherent and suspension cultures, 3D cultures, tissue fragments, and isolated mitochondrial fractions.

• Amersham Typhoon 5  (Cytiva)
  A multifunctional biomolecular imaging scanner for applications such as DIGE-based quantitative proteomics and large-format digital autoradiography (40 x 46 cm). Equipped with five lasers and six emission filters, the system can analyze fluorescence in blue, green, red, infrared, and near-infrared spectra, as well as detect radioactive isotope decays. Typhoon 5 is versatile, capable of analyzing a wide range of samples, including gels, membranes, multiwell culture plates, microscope slides, and tissue preparations.

• Protein Simple Jess  (Biotechne)
  Equipment that fully automates the Western blotting process, from electrophoresis to antibody incubation, washing, detection, and quantitative analysis, all within less than four hours.
  With sensitivity levels in the picogram range, Jess detects proteins even in small sample quantities (<0.6 μg). The automated process enhances reproducibility, which is a real challenge in traditional multi-step methods. Additionally, the system supports the RePlex procedure, which enables the detection of multiple proteins from a single sample preparation, expanding measurement capabilities. Jess also offers chemiluminescent and fluorescent detection, providing flexibility in experimental design.

• HPLC-EDC high performance liquid chromatography kit (Vanquish Core, Thermo Scientific, Decade Elite electrochemical detector, Antec Scietific)
  High-performance liquid chromatography system, based on the Vanquish Core series, designed for pharmaceutical and scientific laboratory applications. Equipped with a high-sensitivity electrochemical detector, it facilitates routine quantification of neurotransmitters (e.g., norepinephrine, dopamine, serotonin, and their metabolites) in microdialysates and tissue homogenates. HPLC-EDC analyses support studies on the effects of novel compounds on biological targets, mechanisms of action, and neurotoxicity. They are also critical for research into psychiatric, neurological, and neurodegenerative disorders.

CF4B Laboratory of Cell Function Imaging

head:  Julita Wesołowska, PhD (tel. +12 3343 709)

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The laboratory’s equipment includes, among other things, a nationally unique Leica Stellaris Dive two-photon microscope designed primarily for electrophysiological studies and in vivo imaging and for recording three-dimensional images of thick (approximately 400 um) tissue sections with high resolution. Thanks to the fully tunable InSight X3 laser (Spectra Physics) in the range 680 – 1300 nm, it is possible to register biological samples that are labelled with standard fluorescent markers, which are commonly used in fluorescence and confocal microscopy. This advanced system allows for ex vivo experiments to be performed on living isolated tissue: a wide range of electrophysiological experiments to study the functionality of nerve cells e.g. patch clamp, photo-release and photostimulation anywhere in the cell, optogenetic experiments, imaging deep into the labelled tissue, which allows images to be recorded in intact cell layers e.g. brain tissue.

In the future, the equipment will also be used to perform experiments on small live transgenic animals to study the direct therapeutic effects of chemical compounds and drugs being studied and designed at CEPHARES.

• Leica Stellaris DIVE two-photon microscope An upright two-photon microscope whose main applications are ex vivo electrophysiological studies (patch clamp, photoactivation, photo-release) and deep tissue imaging. The microscope is equipped with a tunable in the range 680-1300 nm Insight X3 laser (Spectra physics) with a fixed laser beam at 1045 nm. It is equipped with spectral detectors. In future, the system will be upgraded with an in vivo imaging equipment.

• Leica TCS SP8 X confocal microscope Inverted microscope equipped with white light laser and HyD and PMT detectors. Can excite any fluorophore in the range 405 nm – 600 nm, spectral detection, two modes of imaging: wide-field and confocal. The environmental chamber for maintenance of optimal conditions for live-cell imaging, and conducting FRAP, FLIP and FRET experiments.

• Leica THUNDER wide-field microscope with TIRF module. The inverted microscope is equipped with wide-field imaging diodes and lasers at 488 nm and 561 nm (TIRF module), Hamamatsu sCMOS ORCA camera. In addition, the system is equipped with a laser-safety OkoLAB environmental chamber for recording live samples.

CF5B Laboratory of behavioral studies

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The laboratory allows for advanced pre-clinical studies on mouse models of CNS diseases, including genetic models. It is possible to carry out extensive animal behavioural analysis based on basic tests analysing spontaneous locomotor activity (OFT), locomotor coordination (rotarod, CatWalk), anxiety (LDB, EPM), tests to detect depressive behaviour and measure response after antidepressant administration (FST, TST). The laboratory is also equipped to conduct tests to assess working memory (equipment being completed). A hallmark of the laboratory is its work based on the automated analysis of behavioural data using the Nodus EthoVision system. The laboratory is also equipped with two stereotactic administration stations (automatic infusion pump) together with an inhalation anaesthesia system.

In addition, the behavioural laboratory is equipped with the only Promethion Core metabolic cage system in research facilities in the country, which is one of the most advanced tools available on the market for comprehensive metabolic and behavioural analysis of animals in vivo. The system allows animals to be monitored 24/7 , in a setup of two experimental groups of up to eight animals each. Dedicated to mice, however, it has also been retrofitted with rat cages (it is also possible to carry out experiments on rats after prior reconfiguration and appropriate room preparation).

CF5C Breeding of transgenic mice

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The dedicated area of Module CF5 includes 6 modern, air-conditioned rooms for the breeding of transgenic mice, with independent ventilation systems. The rooms can be individually programmed in terms of daily cycle, humidity and temperature. In addition, they are equipped with racks of self-ventilated IVC cages and a portable cage changing station. Access to the zone is restricted to trained personnel only. The transgenic mouse breeding zone of the CF5 Module provides a safe, high standard of maintenance for transgenic animal lines, which can be particularly sensitive to pathogens from the external environment. In terms of animal housing, the zone is operated by the staff of the Animal Facility of the IF PAN.