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DEPARTMENT OF MOLECULAR BIOLOGY
The Department of Molecular Biology was established in 1989 with the aim of furthering biological research at the molecular level and establishing a study curriculum in molecular biology. In spring 2004, the Department moved into its new premises, which provide excellent conditions for research and laboratory teaching. Research in the Department comprises about ten scientific research projects funded by the Ministry of Science, Education and Sport of the Republic of Croatia. Several researchers also participate in prestigious internationally funded research projects. Molecular biology research is carried out on both plant and animal models, with research topics ranging from developmental biology, genomics and biomedicine to proteomics, computational biology and bioinformatics. The Department houses the electron microscopy core facility.
In the field of plant and animal biology, there are four main areas of research.
1) Studying the structure, organisation and evolution of the genome at the chromosomal and molecular levels (repetitive DNA – satellite DNA and retrotransposons, rRNAgenes). This research includes the application of retrotransposons in targeted gene inactivation (gene targeting) that is based on homologous recombination.
2) Research in the area of developmental biology and regulation of secondary metabolism is directed at the identification and functional characterisation of genes associated with embryogenic plant development, and at determining the regulation and biosynthesis mechanisms of phenolic secondary metabolites.
3) Research of the chromatin dynamics and geneplasticity relates to the analysis of epigenetic modifications that alter the structure and function of individual genome areas (primarily rDNA chromatin). Research interests are focused on the plasticity of plant genomes exposed to stress. In situ (natural) populations are studied, and the alterations in the methylation status of certain genome areas of those plants, which cause the formation of epialleles (rDNA epialleles) are investigated. Research is also focused on the three-dimensional organisation of active and inactive rDNA chromatin within the interphase nucleus.
4) Research of plant proteomes is aimed at obtaining a better understanding of the development processes in plants, and of plant responses to abiotic stress. Through the use of tissue and cell cultures and cell transformation using Agrobacteriumstrains, stable biological systems have been achieved and are the starting material for cell fractioning, protein extraction and quantification, enzymes and secondary metabolites.
In the field of toxicology, research is focused on the extent to which stress caused by heavy metals and model genotoxicants, as well as the abiotic stress damage the DNA molecule and/or cause its epigenetic modification (changes in methylation patterns), thus impacting the mechanisms of gene expression regulation. Analysis of biochemical parameters (lipid peroxidation, oxidative damage of proteins, activation of antioxidant systems) is employed to investigate the ties between oxidative damage to plants and the quantity of heavy metals accumulated over agiven time period.
Research is also ongoing in four areas in the field of biomedicine.
1) Investigating the influence of ultraviolet radiation on the DNA molecule and guiding the cell in programmed cell death (apoptosis); apoptotic pathways induced by UV radiation and the impacts on important physiological functions using the FADD cell knockout model, and inparticular, studying the relationship between the membrane and mitochondrial mechanisms of apoptotic signalling pathways.
2) Molecular research of the Hepatitis C virus has, for the first time in Croatia, described in detail the genotypes and subtypes present within the Croatian population, and thus enabled accurate comparison with strains in other geographical areas. Studies are performed to compare the course of the disease with the evolution and changes to the virus, and biochemically describe the viral RNA polymerase as well as its mutants, all for the purpose of designing better therapy and preventive vaccines.
3) Research on the regulationof cell proliferation and cell death in chronic myeloproliferative diseases is investigated by analysing the expression and activity of proteins in colonies of progenitor cells in the bone marrow of affected patients.
4) Investigation of the role of poly(ADP-ribolysation), as a post-translational protein modification in the response of animal cells to damages and in tumour-generating processes.
In the fields of bioinformatics and computational biology, information technology methods, machine learning and statistics are applied on high-throughput experimental data in several projects aimed at discovering the fundamental principles of life at the genomic level.
1) Metagenomics is the analysis of vast quantities of genomic data obtained by DNA sequencing samples taken directly from microbial environments, for the purpose of investigating genetic diversity, adaptation and evolution of genetic information at the level of entire ecosystems.
2) Development of programming tools for the analysis, display and contextual integration of data obtained from microarray (or similar genomic) experiments.
3) Application of machine learning methods in predictingepigenetic signals in the regulation of eukaryotic transcription (in cooperation with the Max Planck Institute for Molecular Genetics in Berlin, Germany).
4) Development and experimental verification of predictive models for exonic splicing enhancers, in cooperation with the International Centre for Genetic Engineering and Biotechnology (ICGEB) in Trieste, Italy.
5) Computer predictions of protein interaction sites directly from primary sequence, without the need for structural data.
6) Classification of protein folding patterns using statistical and machine learning methods.
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