Biochemical and biophysical methods of living systems analysis
Part 1 Biochemistry
Main activity 1 Materials for highly specific adsorption of biomolecules
The activity will develop and test new porous materials for adsorptive separation of organic substances in complex mixtures characterized by highly specific interaction with selected organic substances of biomolecules type. The materials will be tested for applications in the analysis of biomolecules (separation, concentration prior to actual determination) as well as for their removal from aqueous environments (decontamination). The materials will target selected biotic (proteins, nucleic acids, degradation products of living organisms) and abiotic (pesticides, pharmaceuticals) substances. The actual research will start after the completion of the new building.
The activity will be implemented in sub-phases with defined objectives, expected likely outputs, benefits and knowledge:
- Design and synthesis of new materials
- Identification of target molecules - based on research and requirements from practice or medical subtasks, target substances will be selected to be the focus of the research
- Design of adsorbents - the textural and chemical parameters of the required adsorbents will be described; calculations will be performed in VP 3, main activity 2
- Synthesis of adsorbents - materials for testing will be synthesized and their basic characterization will be performed
- Testing new materials
- basic adsorption tests
- optimization of adsorbents
- Advanced testing - optimized adsorbents will be tested towards analytical and environmental applications, i.e. separation of target molecules from mixtures, decontamination tests, flow tests, determination of maximum capacities, scale-up tests, etc. including feedback from potential commercial users
- Publication and potential commercialization of results
- Publication of results
- Potential users of the results - outreach and contractual treatment, potential technology transfer
- Intellectual property treatment
Main activity 2 Analytical use of nanoparticles to study biologically relevant macromolecules in aqueous environments
The activity will be implemented in sub-phases with defined objectives, expected likely outputs, benefits and knowledge:
- Interaction of nanoparticles with biomolecules
- Review of scientific publications to monitor current advances in this field, identification of suitable biomolecules (amino acids, proteins - BSA, HSA, fibrinogen..., nucleic acids - DNA, RNA, etc.) and design of experiments including appropriate techniques to study the interaction.
- Experimentation - Optimization of experiments depending on the measured data. The aim is to describe procedures and techniques for specific biomolecules/groups of biomolecules for reliable characterization of samples after interaction with nanoparticles.
- Publication and potential commercialization of results
- Publication of results
- Potential users of the results - outreach and contractual treatment, potential technology transfer
- Intellectual property treatment
Main activity 3 Preparation of selective adsorbents of biomolecules and their use for immobilization, isolation, quantification and detection of bio medically relevant markers from body fluids and tissues.
The activity builds on activities 1 and 2 and focuses specifically on analysis for medical purposes, and will be implemented in sub-phases with defined objectives, expected likely outputs, benefits and knowledge:
- Investigation of surface modification of porous matrices for immobilization of bio medically relevant molecules
- Theoretical overview of the possibilities of surface modifications of porous matrices (functional groups) and procedures for their realization. Appropriate modification procedures for adsorbent surfaces will be selected with respect to their nature and taking into account the intention to immobilize specific types of biomolecules
- Experimental modification of the surfaces of selected sorbents and verification of the ability to immobilize selected biomolecules
- Introduction and optimization of modification procedures, standardization of immobilization parameters of biomolecules
- Development of new techniques for the isolation and identification of biochemically significant molecules from body fluids (blood, saliva) and tissues
- Theoretical overview of available techniques for isolation and identification of biomolecules and markers determined in clinical practice. Identification and characterization of promising biomarkers with expected routine use in clinical practice.
- Design and conduct immobilization experiments on real biological and clinical samples of body fluids and tissues.
- Standardization and optimization of new techniques for isolation and identification of biomolecules. Evaluation on larger sample sets.
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Analytical use of the developed methods
- Identification and quantification of selected metabolites, determination of enzyme activity and further analyses of samples for VP1 main activities 2, 3, 4, 5 and 7 and VP6 main activity 2
- Publication and potential commercialization of results
- Publication of results
- Potential users of the results - outreach and contractual treatment, potential technology transfer
- Intellectual property treatment
Key activity 4 New study and academic programs
A new specialization NMgr. Analytical Chemistry - extension of the specialization Bioanalytical Chemistry, a new study program Bc. Biochemistry and a new PhD Bioanalytical Chemistry will be accredited.
The activity will be implemented in following phases:
- Accreditation of the new specialization NMgr. Analytical Chemistry - extension of the specialization Bioanalytical Chemistry
- Preparation of the accreditation file
- Submission of the accreditation file and settlement of objections
- Accreditation of the new Bc. Biochemistry study program
- Preparation of the accreditation file
- Submission of the accreditation file and settlement of objections
- Accreditation of the new PhD program Bioanalytical Chemistry
- Preparation of the accreditation file
- Submission of the accreditation file and settlement of objections
Part 2 - Biophysics
Main activity 1 - Structural-functional characteristics of membrane systems and macromolecules
Biophysical methods for studying the structure and function of biological systems (primarily based on optical spectroscopy), which have been mainly developed in the context of photosynthetic apparatus studies, have a broad application potential in other biological and biomedical fields. In this main activity, we will focus on the development of biophysical methods for studying the structure and functional state of biological membranes and biomolecules, particularly in the following areas:
- Methods for studying the properties of the lipid phase in biological membranes,
- Structural-functional analysis of biomolecules and their interactions using fluorescence spectroscopy (including time-resolved fluorescence spectroscopy) and circular dichroism,
- Methods for detecting oxidative damage to biological membranes and its components at the molecular level.
Activity will be accomplished in several stages:
- Study of the influence of lipid phases, lipid/protein ratio, and lipid composition on the structure and function of membrane systems
- Study of the structural-functional properties of proteins and nucleic acids focusing on changes in their (macro-)organization, stability, and flexibility Advanced spectroscopic methods for studying the structural-functional state of macromolecules will be developed during this stage, suitable not only for studying proteins and nucleic acids in plant assimilation apparatus but also in other organisms within the scope of biomedical research.
- Study of the impact of (oxidative) damage to membrane systems (lipid peroxidation) and macromolecules (protein oxidation) on their structural-functional properties
Main activity 2 - New methodical approaches for assessment of oxidative stress in biological systems
Oxidative stress is important factor affecting basic physiological functions as well pathological processes in living organism – its detrimental action can be observed on the molecular, cellular, and even on whole organism level. The response of organism to oxidative stress is the activation of various defensive mechanisms which tend to avoid or limit the extent of oxidative stress or repair already present oxidative damage of nucleic acids, proteins, or biological membranes. An integral part of complex protective processes which are involved in suppression of oxidative stress are low-molecular antioxidants. The actual research of our group deals with the examination of defensive mechanisms which helps plants to cope with the climatic change and related induction of oxidative stress which often accompanies the plant growth in non-optimal conditions. Current knowledge of the importance and exact roles of individual protective mechanisms in the overall plant oxidative stress tolerance is still limited as well as their potential for cross-acclimation (the situation when one environmental stress factor enhances the tolerance of assimilatory apparatus to another one). Within this main activity we intend to develop new methods and approaches allowing thorough examination of oxidative stress as well as of antioxidant defence systems in various biological systems. The research will be divided into several interconnected areas:
- Development of spectroscopic and chromatographic methods suitable for detection and quantification of primary reactive oxygen species (ROS) and products of their interaction with (bio)molecules (lipids, proteins and nucleic acids), i.e. for the determination of oxidative damage extent in various types of biological material (tissues, cells, cell-cultures, sub-cellular parts etc.)
- Examination of changes induced by oxidative stress at the level of gene expression and the study of signalling pathways leading to activation of processes limiting detrimental effects of oxidative stress
- Examination of changes in metabolic profile in biological systems induced by the action of oxidative stress with focus on low-molecular compounds with expected antioxidant properties
Main activity 3 - New study and academic programs
A new habilitation procedure program with the working title "Biophysics and Physics of nanostructures" will be accredited.
The activity will be implemented in partial stages with defined goals, expected probable outputs, benefits and findings
Cooperation with other Research Programs (RPs) and collaborating companies
Due to the very strong interdisciplinary link, the VP2 research team collaborates on some sub-activities with research teams:
Research Program 1 – within the framework of transcriptomic or bioinformatics analyses, we expect cooperation with RP1, further analyzes of structural-functional properties of proteins in the field of molecular biology and nucleic acid genomics will be used
Research Program 3 – use of support for the modelling of intermolecular interactions of macromolecules in biological systems (based on interesting experimental data, main activity 3), modelling of the interaction of adsorbents with target molecules (main activity 2), participation in the accreditation of the new habilitation procedure "Biophysics and Physics of nanostructures"
Research Program 6 – the developed methods of detection of oxidative damage to biological membranes and macromolecules will be used in the experimental part of the hemato-oncology program
In order to prepare the applicability of the research into practice, at the time of the experimental research, at least 2 cooperating companies will be involved, which will participate in the development of new diagnostic tests/analyses.
