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Combinatorial optimization algorithms for (pseudo)alignment in bioinformatics
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Luka Borozan The field of bioinformatics is a fast growing interdisciplinary field with a strong contribution from mathematics and computer science. This thesis will deal with mathematical problems and algorithmic challenges from that field. Its first focus will be the comparison of hierarchic structures, mainly phylogenetic trees, which is used to explain various biological processes such as the evolution of the species. We will study mathematical models and algorithmic techniques which quantify the...
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Compaction of nucleic acids
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Sanjin Marion Packing of nucleic acids inside (naturally occurring) confined spaces presents an intriguing problem of compacting a long and highly charged polymer into a small space possibly crowded with other particles (proteins). For example, viruses have a large amount of genomic information that is encoded in nucleic acids packed in small spaces resulting in high densities of matter. The arising interactions are coupled to the confinement giving a more complex phase diagram than expected in bulk. In...
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Constraints on neutrino oscillation parameters implied by OPERA experiment data
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Budimir Kliček The OPERA experiment in the CNGS beam was designed to measure the appearance of tau neutrinos in the high purity muon neutrino beam. The physical run lasted for five years in the period 2008 - 2012 with the total accumulated CNGS intensity of 1.797 · 10^20 protons-on-target. The primary goal was achieved by observing five tau neutrino candidate events, which corresponds to the significance of the ν_τ observation of more than 5 σ. In addition to this, constraints on │Δm^2_32│ mass...
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Construction of molecular tools based on CRISPR/Cas9 system for epigenetic modulation of gene expression
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Vanja Tadić Repurposing of platforms for targeted genome engineering, zinc finger nucleases (ZFNs),
transcription activator-like nucleases (TALENs) and especially CRISPR/Cas9 system, has enabled
targeted manipulation of epigenetic marks and new insights into epigenetic regulatory mechanisms. In
this work, I have fused the catalytic domain of human TET1 (Ten-Eleven Translocation 1) protein Cterminally
to the catalytically inactive Cas9 (dCas9) from Streptococcus pyogenes to create the dCas9-
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Cosmic evolution of active galactic nuclei detected in the radio waveband
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Bruno Šlaus A major topic in the field of astrophysics is understanding the evolution of the Universe through cosmic time. Throughout the evolution of the Universe and galaxies, among the most interesting objects are galaxies containing active, super-massive black holes in their galactic centers, called active galactic nuclei (AGN). We model the evolution of AGN by constructing their radio luminosity functions. We use radio surveys of varying area and depth, namely the deep COSMOS survey of 1,916 AGN...
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Crosstalk of gene polymorphisms with RNA and protein phenotypic characteristics
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Marina Rudan Both RNA and protein molecules can misfold into non-functional conformations. Since DNA is transcribed into RNA to direct the biosynthesis of proteins, functional cells require the maintenance of DNA, RNA and protein homeostasis. Here, it is explored whether DNA polymorphisms can impact upon RNA and protein conformation to the extent of displaying phenotypic changes. It has been found that this is a multifaceted process. Mutation-induced protein conformational ...
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DIVERSITY OF DIATOM AND BACTERIAL COMMUNITIES ASSOCIATED
WITH LOGGERHEAD SEA TURTLES (CARETTA CARETTA)
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Klara Filek Loggerhead sea turtles are ancient marine reptiles inhabiting the oceans worldwide. They are
colonized by microorganisms both in the gastrointestinal tract and on their carapace and skin.
In this thesis that consists of four scientific publications, the loggerhead sea turtle-associated
diatom and bacterial communities were investigated by high-throughput sequencing of
chloroplast rbcL gene and 16S rRNA gene, and cultivation. The culture-independent approach
has shown that loggerheads...
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DOMAIN-SPECIFIC INTERACTIONS OF BPM1 WITH DMS3 AND RDM1 IN RNADIRECTED DNA METHYLATION
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Mateja Jagić BPM1 protein belongs to the MATH-BTB protein family, characterized as adaptors of CUL3-
dependent E3 ubiquitin ligase complex responsible for recognizing and directing substrates for
proteasomal degradation. An initial mass spectrometry experiment identified a key component of
the RdDM, the DMS3 protein, as a potential BPM1 partner. Since RdDM is the major epigenetic
mechanism responsible for de novo DNA methylation in plants, the goal of this work was to further
investigate the role of...
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DOPRINOS DNA BARKODIRANJA ISTRAŽIVANJIMA BIORAZNOLIKOSTI GLJIVA HRVATSKE
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Ana Pošta Cilj doktorske disertacije bio je rješavanje znanstvenih problema u sistematici gljiva metodama integrativne taksonomije koja objedinjuje evaluaciju molekularnih, morfoloških i ekoloških obilježja gljivljih organizama. Poseban naglasak stavljen je na vrednovanje znanstvenog doprinosa DNA barkodiranja u otkrivanju, razgraničenju i identifikaciji srodnih vrsta u različitim skupinama nadzemnih gljiva iz odjeljaka Ascomycota i Basidiomycota. Prikazan je znanstveni opis tri vrste nove za...
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Defekti i nanostrukture u metalnim oksidima pogodnim za organske solarne ćelije
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Daniel Meljanac Da bi tanki film metalnog oksida ušao u upotrebu kao prozirni i vodljivi sloj za solarne ćelije, način njegovog formiranja mora garantirati vrhunske performanse ostvarene na jednostavan način i sa perspektivom jednostavnog povećavanja proizvodne skale. Hipoteza rada je da se ovo može postići preciznim podešavanjem procesa formiranja i jednostavnim postupcima naknadne obrade. Posebnost organskih solarnih ćelija je mala difuziona dužina fotogeneriranih nosilaca naboja (kratko vrijeme...
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