1. Current Biological Approaches for Radiation Research Aleksandra Ristić Fira University of Belgrade - Vinča Institute of Nuclear Sciences, Belgrade, Serbia LNS

2. On the basis of time, radiobiological response is conventionally separated into the physical, chemical and biological stages. It is obvious that radiation physics comes before radiation chemistry. The knowledge, concepts and methodology of radiation chemistry are the guidelines to radiation biology. In such a way bridging basic science and translational biomedicine is enabled.

3. Translational research has lately become an extremely popular expression in the world of biomedical research. Essentially, this kind of research aims to “translate” existing knowledge about basic sciences into techniques and tools for treating human diseases. With its focus on multi-disciplinary collaboration, translational research has the potential to advance applied science. This has been attempted particularly in medicine with translational medicine, research that aims to move “from bench to bedside” or from laboratory experiments through clinical trials to patient point-of-care applications.

4. Spatio-temporal radiation biology represents an original approach to investigate radiation damage. This is a wide and new interdisciplinary research domain, bringing together: - novel developments of spatially or temporally defined radiation sources; - recent progresses in simulations of energy (dose) deposition; - study of early free radical events, molecular biology, genomics and proteomics, biomarker detections, advanced molecular or sub-cellular imaging; - innovative radiation therapies of cancers. The aspects of spatio-temporal radiation biology in general cover several orders of magnitude, usually from femtosecond (10 −15 s) and sub-micrometric scales.

5. Investigations are characterized by multi-scale settings that extend from an initial energy deposition in living targets to biomedical and clinical consequences of ionizing radiations. Spatial aspects take place within a broad angstrom-centimeter range and concern radiation-induced native ionization clusters, damages of targeted biomolecular architectures, cells and tissues. Temporal responses of living matter to an initial energy deposition occur over several orders of magnitude. (Melka et al., Mutation Research, 2010)

6. Radiation-induced ionizations may act directly on the cellular component molecules or indirectly on water molecules, causing water-derived radicals. Radicals react with nearby molecules in a very short time, resulting in breakage of chemical bonds or oxidation of the affected molecules. Radiation biochemistry, is beginning after ionization and excitation processes are completed (in the first seconds after radiation exposure).

7. DNA radiation injuries: Base pair deletion Cross-linking injuries Single Strand Break (SSB) Double Strand Break (DSB) Multiple (complex) lesions

8. There is an important role of free radicals (produced in secondary responses) in biological processes initiated by radiation on much longer timescale. Free radicals are now widely recognized to be important components of cell signaling processes.

9. Standard model for radiation effects in cells based on direct DNA damage leading to downstream biological responses. (K.M. Prise, Occup. Med., (2006), 56(3): 156-161)

10. Cellular mechanisms are in place that can repair most of radiation injuries to the DNA. Repair process is: - time sensitive - cell cycle dependent - dose rate dependent - dose dependent - radiation type dependent Repair of Radiation Injury

11. Different cell death modalities induced by ionizing radiation and the factors involved in this processes. (L. Minafra and V. Bravata, Transl.Cancer Res. 2014;3(1):32-47)

15. How to study different biological pathways?

16. U.S. Department of Energy Genomes to Life Program Genes, proteins and molecular mechanisms

17. Ahn et al (2006), PLoS Medicine. 3(7):209.

18. What is genomics? Genomics is the study of the genomes of organisms (to determine the entire DNA sequence of organisms and fine- scale genetic mapping). The knowledge of full genomes has created the possibility for the field of functional genomics, mainly concerned with patterns of gene expression during various conditions.

19. Techniques: - Northern blots - In situ hybridization - Microarray - Microchip

21. Transformation of genomic information into biological function K. Sreekumaran Nair et.al, American Journal of Physiology - Endocrinology and Metabolism 2004

22. Study of the full set of proteins in a cell type or tissue, and the changes during various conditions, is called proteomics. Proteins are vital parts of living organisms, as they are the main components of the physiological metabolic pathways of the cells. What is proteomics?

23. Why study proteomics? The genome/transcriptome is important but not sufficient to model and predict biological systems. Post-transcriptional modifications such as phosphorylation, proteolytic cleavages, etc. often regulate protein activities. The quantity of protein in a cell, tissue or organism is not always regulated by mRNA. Instead, translation and degradation play critical roles in determining the abundance of protein.

25. Major applications of proteomics 1.Protein profiling (large scale identification of proteins) 2.Comparative proteomics (quantitative proteomics): - target identification and biomarker discovery. 3.Functional proteomics: - antibody arrays to monitor proteins involved in various functions, e.g. the immune system. Process for proteomics 1.Protein separation - gel based, liquid chromatography (LC) based 2. Mass spectrometry - MALDI/TOF, MS/MS 3.Bioinformatics / protein sequence database - SwissProt, NCBI Sample preparation required 1.Remove major proteins (e.g. serum albumin, immunoglobulines,…); 2. Concentrate minor components.

27. What is Epigenetics? Epigenetics implies features that are “on top of” or “in addition to” genetics. It is generally used to refer to changes in gene expression that takes place without a change in the DNA sequence. Epigenetic changes can result from various molecular modifications, but the most extensively studied and best understood are: 1.DNA methylation, which takes place at the carbon-5 position of cytosine in CpG dinucleotide; 2. changes to chromatin packaging of DNA by posttranslational histone modifications. Both of these mechanisms can have a profound effect on gene expression, including the silencing of the gene. Other epigenetic mechanisms that are less well understood include regulation of gene expression by noncoding RNAs, including micro RNAs and mechanisms that control the higher level organization of chromatin within the nucleus.

28. There is increasing evidence from animal studies that prenatal and early postnatal environmental factors can result in altered epigenetic programming and subsequent changes in the risk of developing disease later in life. Environmental factors studied to date include nutritional supplements, xenobiotic chemicals and exposure to ionizing radiation. The radiation studies showed that exposure of adult male or female mice led to trans- generational genome instability in the progeny, resulting from a significant loss of DNA methylation in somatic tissue. In addition, there is some evidence from animal studies that epigenetic alterations may be inherited trans-generationally, thereby affecting the health of future generations. (L. Minafra and V. Bravata, Transl.Cancer Res. 2014;3(1):32-47)

29. Transcription Mediated Amplification (TMA) Component System