Research Institute of Biology of Southern Federal University

1. НИИ биологии ЮФУ Research Institute of Biology of Southern Federal University Adress: 344090, 194/1 Stachkiave., Rostov-on-Don, Russian Federation Web adress: http://niib.sfedu.ru/ Contacts: e-mail niib@sfedu.ru Director: Doctor of biological sciences, Prof. Tatiana P. Shkurat, e-mail: tshkurat@yandex.ru

3. Laboratory of industrial microorganisms The head of the laboratory: MarinaSazykina, e-mail: samara@sfedu.ru Research areas of interest and their summary: • Research of different mechanisms of oil components microbial degradation and the role of reactive oxygen species in this process: the possibility of non-enzymatic oxidation of various oil components with free-radical mechanism is shown. Studies are being conducted to identify the nature of ROS, their participation in oil transformation and the mechanisms of free radical generation in the oil-degrading microorganisms. • Investigation of the biological effects of newly synthesized drugs: use of lux-based biosensors can be used to evaluate the biological activity of newly synthesized drugs - their toxicity, mechanisms of action, adaptogenic properties, etc.. • Monitoring of environmental pollution by bacterial lux-based biosensors: toxicity investigation is conducted with the help of bacterial lux-based biosensors which can be natural or genetically engineered strains. These are specific, highly sensitive express test systems for detection of various physical and chemical factors. In genetically engineered bacterial biosensors lux-genes responsible for bioluminescence are under the control of specific promotors. These test systems are useful for assessing toxicity of various ecosystems with genotoxins, heavy metals, substances of oxidizing nature, etc.

4. Laboratory of industrial microorganisms Research Projects • “The study of mechanisms of action and extreme negative anthropogenic environmental factors with cell biosensors“, 2012-2013; order of the Ministry of Education and Science of the Russian Federation; • "Development of fundamental principles of biotechnology-based extreme-tolerant microorganisms“, 2012-2013; order of the Ministry of Education and Science of the Russian Federation; • "Research of ecotoxicological parameters and bacterial contamination of waste water in Rostov-on-Don and Munich“, 2012-2013; Federal Targeted Programme; • «Study of adaptogenic effect of low molecular weight organic cations with bacterial biosensors», 2012-2013; Russian Foundation for Fundamental Research; • "Research of ecotoxicological parameters and bacterial contamination of waste water in Rostov-on-Don and Munich“, 2012-2013; Federal Target Programme; • “Monitoring of environmental pollution by bacterial lux-based biosensors", 2009-2011; Analytical Departmental Target Programme; • «Research in the field of micro-and nanostructures based on oxide, organic and biological materials, the development of production technologies of promising sensor systems based on new physical principles in the center of scientific equipment for collective use" High Technology», 2009-2010; Federal Targeted Programme; • "The study of free-radical mechanisms of biodegradation of hydrocarbons", 2009-2011, Analytical Departmental Target Programme; • Institute of Hygiene and Medical Microbiology, Max von Pettenkofer Munich University LMU, Laboratory ofFunctionalGenomics; • University of Kastamonu,Faculty of Fisheries, Turkey. Collaborative laboratories:

5. Laboratory of engineering ecology The head of the laboratory: Vladimir Lysenko, e-mail: vs958@yandex.ru Research areas of interest and their summary: • Preproject studies on ecological, geochemical and geophysical characteristics and risks in the fields of house building and industrial engineering: the laboratory staff carry out ecological monitoring, geological and geochemical prospecting within Rostov, Krasnodar and Stavropol regions designated for house building and industrial engineering, that is completed with the issue of necessary sertificates. The laboratory have a variety of equipment and instrumentation calibrated and certified at the established order; Carrying out lab works on plant physiology using resources of laboratory of engineering ecology • Studies on light reactions of plant photosynthesis under normal environment and ecological stress: arrangement of electron transport chain of thylakoids in normal and chlorophyll-deficient plant tissues is studying using chlorophyll fluorescence and photoacoustic methods. Recently it has been discovered in the laboratory that chloroplasts of stomata guard cells are possessed an unique, previously unknown type of photosynthesis when cyclic electron transport simultaneously occurring in guard cell thylakoids around photosystems I and II under blue light, whereas linear electron transport is absent or insufficient.

6. Laboratory of engineering ecology Research Projects State research contract "Studies on distributional and developmental patterns of Don river basin vegetation in conditions of fragmentation and making of a multilevel biomonitoring model”. (Sci. Res. work 5.5676.2011 at 2012-2-13) Collaborative laboratories: Southern Scientific Centre of Russian Academy of Sciences

7. Experimental mutagenesis laboratory The head of the laboratory: Vladimir Chistyakov, e-mail: Vladimirchi@sfedu.ru Research areas of interest and their summary: • Antimutagenic activity of antioxidants; • Geroprotectors; • Environmental genotoxicity • Substances that protect DNA against damage exhibit the system adaptogenic effect. They can enhance regeneration and stimulate the immune system, slow the aging process. These types of activities are of interest to pharmacology. Using of bacterial biosensors makes measurement of genotoxicity environment faster and more accurate. First working conference of biomedical project “Skulachev ions”, Moscow, 2007 Whipped cream with probiotics

8. Experimental mutagenesis laboratory Research Projects • "Skulachev ions“, 2007-2010; Extra-budgetary funds; • «Research of the biological effects of UV radiation with 300-400 nm wavelength with the help of bacterial lux-based biosensors", 2009-2011; Analytical Departmental Target Programm, Project № 2.1.1/5628; • «Study of antioxidant properties of bacterial carotenoids“, 2009-2011; Analytical Departmental Target Programm, Project № 2.1.1/5630; • "Development of laboratory technology of deinoxanthin production“, 2009-2010 , Foundation for Assistance to Small Innovative Enterprises in science and technology, the program «UMNIK», Project № 8170/12632; • "Development of antioxidant complex to protect against UV radiation“, 2010-2011, Foundation for Assistance to Small Innovative Enterprises in Science and Technology, the programm «UMNIK», Project № 8694r/13153. Collaborative laboratories: • Mitoengineering Centre of MSU, Russia; • Central Research Laboratory of Rostov State Medical University, Russia; • Laboratory of mutagenesis of Research Centre for Medical Genetics” of Russian Academy of Medical Sciences (FSBI “RCMG”); • Institute of Hygiene and Medical Microbiology, Max von Pettenkofer Munich University LMU, Laboratory ofFunctionalGenomics; • University of Kastamonu,Faculty of Fisheries, Turkey.

9. Laboratory of biomedicine The head of the laboratory: AnzhelaAleksandrova, e-mail: aalexsandrova@sfedu.ru Research areas of interest and their summary: • Physiology and pathophysiology of the human reproductive system: the aim of many of our research projects is to characterize the dynamics of hormones, growth factors and other members of a set of signaling pathways involved in the development of the human reproductive system. As far as many harsh genetic disorders are the etiologic cause of reproductive disorders we perform not only postgenomic analyses, but also classical and molecular cytogenetic tests. Moreover, our lab identifies regional reference ranges for numerous biochemical markers and carries out reproductive health screening programs in Rostov region. • Physiology and pathophysiology of human embryogenesis: many types of pregnancy complications are within the scope of the lab, including early pregnancy disorders, uterine cervical incompetence, pre-eclampsia, myomas, fetal and neonatal hypo- and hypertrophy, placental insufficiency and antenatal death. All the kinds of embryogenesis disorders are investigated using pathway-oriented systemic approaches – from metabolome and to epigenome. Additionallywe perform complex microbiological testing in physiologic and complicated gestation cases, in both mothers and neonates. • Interactomics of human oxidative status:  we created interactive oxidative status interactome map (OSIM) - a manually curated multi-omics integrative scheme of molecular interactions and expression control in pro- and antioxidant systems of human cells. Our experimental work in this area is aimed at both suggesting novel diagnostic and therapeutic approaches, and revealing the molecular mechanisms of the oxidative status function.

10. Laboratory of biomedicine Research Projects • “Analysis of polymorphisms and DNA methylation in genes involved in the trophoblast invasion and the formation of the syncytium at different gestation terms and pregnancy conditions in humans”, DAAD; • “ Developing the technology for human reproductive function monitoring using novel genomic and post-genomic markers”, Federal targeted program; • “Developing the system to monitor the health state in teachers and students of schools and universities in Rostov region using molecular genetic and biochemical markers”, Analytical institutional program; • “Systemic bioinformatic analysis of the human cellular tissue-specific oxidative status interactome”, Federal targeted program; • “Developing analytical approach for the individual assessment of the pregnancy/embryogenesis progress”, Grant; • “The association of the mtDNA mutational load and carotid atherosclerosis in humans” • ”Analyzing prognostic genomic and post-genomic markers in human embryogenesis”, Global work order; • “Investigating the molecular mechanisms of the biological effects of allantoin”, Global work order; • “Investigating the effects of the low intensity infrared laser radiation on animal somatic tissues in oxidative stress conditions”, Global work order; • “Global project on the application of Skulachev ions”, Non-budgetary financing; • “Identifying season- and age-dependent regional reference ranges of prostate-specific antigen and carbohydrate antigen CA 15-3”, Non-budgetary financing; • “Identifying season- and age-dependent regional reference ranges of mammary gland disease markers M20 and M22 prostate-specific antigen and carbohydrate antigen CA 15-3”, Non-budgetary financing. • Saarland University, Germany • Research Centre of Medical Genetics of the Russian Academy of Medical Sciences, Russia • Russian research institute of atherosclerosis Collaborative laboratories:

11. Laboratory of human genetics The head of the laboratory: Elena Mashkina, e-mail: lenmash@mail.ru Research areas of interest and their summary: • Reproductivegenetics: investigation of candidate genes associated with pregnancy loss on the early embryonic development; the study of genetic factors associated with sterility and disturbance of reproductive function in men. • Population genetics: analysis of genetic structure of Rostov region population; association genetic factors with heart diseases

12. Laboratory of human genetics Research Projects • “Investigation of frequency polymorphisms MTHFR, MTRR genes in women with recurrent pregnancy loss”, VBS; • “Cytological features blood cells of men and women with disturbance of reproductive function. Design of test systems for predictive diagnostics of newborn”, Grant; • “Design of a screening system of reproductive health of boys in puberty based on genetic and biochemical markers’, VBS; • “Molecular genetic analysis of cytokines genes and disturbance of reproductive function”, FCP; • “Molecular genetic analysis of gene repair and cell cycle control for miscarriage”, RFFI. Collaborative laboratories: • Saarland University, Germany • Research Centre of Medical Genetics of the Russian Academy of Medical Sciences

13. Reproductive and developmental biology laboratory The head of the laboratory: Tatiana Shkurat, e-mail: tshkurat@yandex.ru Research areas of interest and their summary: • Bioinformatic screening of the binding transcription sites in the regulatory regions of genes: we focuse on bioinformatics search for new regulatory structures in the non-coding DNA, located around the patterns of gene expression levels changed significantly in response to oxidative stress using supercomputers. Hypothesized that all of the genes increase the expression in response to oxidative stress may have the same motifs in non-coding DNA. • Structural and functional annotation of non-coding DNA: non-coding DNA sequences are considered to be a new challenge for molecular genetics, genomics, transcriptomics and proteomics. • It is not yet fully understood how the regulatory information is encoded in DNA in order to define the positions of enhancers, silencers and other distantly operating regulatory elements. Systematic analysis of the transcription profile provides us with the data on regulatory mechanisms and screening for the linked scenario of coding and non-coding DNA interactions that are basically important for understanding of system biology and molecular pathogenesis of a variety of human diseases. • Evolutionary and phylogenetic analysis: comparative analysis of growth hormones genes and intergenic regions features within the genomes of different mammalian species.

14. Reproductive and developmental biology laboratory Research Projects “Development of bioinformatic technology of search for the related scenarios in the organization of non-coding DNA and protein-coding DNA within human and animal genomes”, State contract № 14.740.11.0006; "Development and testing of new FIAV method for rapid identification of allelic gene variants“, State contract № 02.740.11.5015 • Univerity of Aveiro, Portugal • Saarland University, Germany • Vavilov Institute of General Genetics, Russian Academy of Sciences, Russia Collaborative laboratories:

15. Analytical research laboratory The head of the laboratory: Irina Sherstneva, e-mail: ailniib@mail.ru Research areas of interest and their summary: The analytical research laboratory is accredited on the right of the quantitative chemical analysis of theenvironment: we providequantitativechemicalanalysisofnatural water, wastewater, soils, air of a working zone, air of a sanitary protection zone, industrial bursts, industrial wastes, transformer oils. The laboratory works on the basis of paid service agreements. Collaborative laboratories: • Departmentofenvironmentalinnovation of Southern Federal University

16. Radiobiology and Ecological Genetics laboratory The head of the laboratory: Elena Shimanskaya, e-mail: shimamed@yandex.ru Research areas of interest and their summary: • Development and introduction to practice of integrated methods of assessment of surface air genotoxicity with bryo- and lichenoflora: The method was tested with complex long-term monitoring of Rostov-on-Don, the oil and gas complex of the Stavropol Region, Territories of geomagnetic faults of the Main Caucasian Ridge and areas adjacent to the Rostov nuclear power station; • Conducting of radiation and genetic monitoring of 30 km zone of Volgodonsk nuclear power station and gas industry of the Stavropol region: we investigate the impact of multi-component pollution on the human genome using total genotoxic activity of air, water, soil samples etc., conduct classical genetic experiments to assess gene and chromosome mutations; • Monitoring of human impact on ecosystems and their components using biogeocenotic methods. Development of human impact bioindication methods using techniques of soil and zoological research on biological biosensors, based on testing of microarthropods as subjects for monitoring at the level of the complex species within anthropogenic ecosystems. We study mechanisms for improving soil fertility by stimulating chernozem soil interactions in the system: soil - crop - herbivores - insecticides - activators of soil fertility - soil microflora - soil animal population on biocenotic level, depending on soil and climatic conditions.

17. Radiobiology and Ecological Genetics laboratory Research Projects • “Research of genotype-environment interaction pattern in natural and anthropogenic ecosystems”, 2009-2011 , State research contract № 01200951806; • “The study of the distribution and development of vegetation in the Don basin in fragmentation conditions and development of multilevel biomonitoring model”, 2012-2014, State research contract № 5.5676.2011. Field work of the laboratory personnel, Northern Caucasus region

18. Laboratory of Biodiversity The head of the laboratory: Olga Demina, e-mail: demina@sfedu.ru Research areas of interest and their summary: • Biodiversity; • phytosociology; • study of the natural flora; • palynology. • Our laboratory concentrates on the study of vegetation of Don basin and the North-West Caucasus at the organismal, populational and phytocenotic levels of organization. We also conduct aeropalynologic monitoring of Rostov-on-Don and Rostov Region.

19. Laboratory of Biodiversity Research Projects • «Sustainable Integrated Land Use of Eurasian Steppe»,  Project financed by EU; • Pilot project "Virtual Encyclopedia of Key Steppes" (Don basin steppes) of the Global Thematic Group "Holarctic Steppes" of the Commission on Ecosystem Management of the International Union for Conservation of Nature (IUCN / CEM), Project financed by EU; • “The study of the distribution and development of vegetation in the Don basin in fragmentation conditions and development of multilevel biomonitoring model”, 2012-2014, State research contract № 5.5676.2011; • "Landscape Mapping the territory of “Utrish " State Nature Reserve”, State contract; • "Geobotanical mapping of Anapa district forest area of “Utrish” State Nature Reserve”, State contract; • "Supplement to the vascular flora of “Utrish” State Nature Reserve” , State contract.

20. Every year more than 50 bachelor’s and master’s degree students practice in the laboratories of the Research institute

21. Adress: 344090, 194/1 Stachkiave., Rostov-on-Don, Russian Federation Web adress: http://niib.sfedu.ru/ Contacts: e-mail niib@sfedu.ru Director: Doctor of biological sciences, Prof. Tatiana P. Shkurat, e-mail: tshkurat@yandex.ru