The list of national projects SAS

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Institute: Centre of Biosciences SAS (Institute of Animal Biochemistry and Genetics)

Establishment of methodology of bovine ovarian tissue cryopreservation for the purposes of the gene banking
Etablovanie techník kryouchovania ovariálného tkaniva hovädzieho dobytka pre účely génovej banky
Program: SRDA
Project leader: RNDr. Antalíková Jana PhD.
Annotation:The number of females of Pinzgau cattle breeds in Slovakia according to FAO database is around 2000 units, what is considered as a critical state within the animal genetic resources. Moreover, in Slovakia there are no frozen embryos of Pinzgau cattle yet, which represents history, landscaping and indispensable part of mountainous and mountain foothill areas of Slovakia. One solution to this problem is the cryopreservation of rare biological material, which will play an important role in addressing the issue of preservation of animal genetic resources. Cryopreservation of ovaries, their surface tissues or ovarian follicles represents the future main source of female gametes. In frame of this methodology the oocytes isolated from frozen-thawed ovarian fragments will be selected for the quality, in vitro matured, fertilized with a bull semen and resultant zygotes will be cultured to reach higher preimplantation stages of embryoa (blastocysts, expanded blastocysts). These results will be compared with the embryo development obtained from the oocyte culture from fresh (noncryopreserved) ovarian follicles. These methodical approaches will be performed on biological material (ovaries) acquired from slaughtered cows at local abattoirs. Since our workplace already deals with the task of animal genetic resource preservation at the in situ and ex citu levels, we have all the conditions to solve this task.
Duration: 1.7.2016 - 30.6.2020

Characterization of novel genes involved in meiotic chromosome segregation.
Charakterizácia nových génov potrebných pre meiotickú segregáciu chromozómov.
Program: SASPRO
Project leader: Mgr. Bágeľová Poláková Silvia PhD.
Annotation:Sexual reproduction is primarily dependent on meiosis, a special type of cell division, in which the number of sets of chromosomes is reduced to half the original number. It is absolutely essential that the halving of chromosome sets is achieved accurately, because errors in this process can lead to various genetic diseases such as Down Syndrome in humans. The aim of my research project is to understand the molecular mechanisms underlying this reduction of the chromosome sets using the fission yeast S. pombe, which is an excellent model organism for studying meiosis. To identify novel genes required for proper segregation of chromosomes during meiosis, I screened a collection of S. pombe knock-out mutants. Out of 3.400 screened mutants, 238 mutants showed chromosome missegregation. At least 30 of these mutants represent novel genes, which have not yet been implicated in meiosis. The functional analysis of two of these proteins Mal3 and Mto1 has been recently published (Polakova et al., 2014). The results of this screening clearly demonstrate that many of the key regulators of meiotic chromosome segregation have not yet been described, and thus open exciting possibilities for future research projects. I have accorded the highest priority to the mutants defective in meiotic recombination, cell cycle regulation and karyogamy because these processes are of fundamental importance from yeast to human cells. I apply a combination of classical molecular and genetic techniques with a multidisciplinary approach such as live-cell imaging, protein complex analysis by mass spectrometry, and high performance liquid chromatography tandem mass spectrometry (HPLC-MS/MS) to decipher the molecular functions of the identified proteins. This research will also lend itself to an expansion of its scope by building upon the idea that many of the identified proteins required for meiosis play important roles in mitosis, and may have significant implications for the diagnosis and treatment of cancer.
Duration: 1.4.2015 - 31.3.2018

Japanese quail chorioallantoic membrane as in vivo model for testing hypericin induced fluorescence diagnosis of tumor lesions
Chorioalantoická membrána embrya prepelice japonskej ako in vivo model na testovanie hypericínom indukovanej fluorescenčnej diagnostiky nádorových lézií
Program: VEGA
Project leader: RNDr. Bilčík Boris PhD.
Annotation:Cancer of the oral cavity is one of the most common forms of malignancy, with rather poor survival. Early diagnosis and precise localization is crucial, however, oral tumors are mostly superficial and its margins can be difficult to visualize under white light. Promising approach is photodynamic diagnosis (or drug induced fluorescence imaging). The aim of our proposal is to evaluate model for diagnosis and treatment of squamocellular carcinoma using quail chorioallantoic membrane (CAM) and a plant-based photosensitiser hypericin (Hyp). The combination of high-resolution fluorescence imaging systems and image analysis will enable more precise visualization of the tumor margins and differentiate tumors, pre-cancerous and inflammatory tissues.
Duration: 1.1.2015 - 31.12.2017

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Interakcie mitochondrií a jadier v procese speciácie.
Program: VEGA
Project leader: Mgr. Bágeľová Poláková Silvia PhD.
Duration: 1.1.2016 - 31.12.2019

Yeast phosphatidylinositol transfer proteins: lipid homeostasis and resistance to azole antimycotics.
Kvasinkové fosfatidylinozitol transferové proteíny: homeostáza lipidov a rezistencia k azolovým antimykotikám
Program: VEGA
Project leader: RNDr. Griač Peter CSc.
Annotation:Phosphatidylinositol transfer proteins (PITPs) were found in all eukaryotic organisms where studied. PITPs in mammals are involved in multiple important metabolic pathways and in transmission of nerve signals. In yeasts they form a heterogenous group with different sub-cellular localizations and multiple, mostly unknown, roles in cell physiology. One of these proteins, Pdr16, is involved in the development of yeast resistance to azole antimycotics. The other one, Sfh1p, is supposed to play role in sphingolipid biosynthesis and intracellular signaling. The present project aims to investigate the mechanisms by which PITPs are involved in maintaining optimal lipid composition of eukaryotic cell membranes and their role in the development of azole resistance. Basic knowledge will be obtained using the model organism, yeast Saccharomyces cerevisiae. Our findings will be applied to study PITPs relationship to azole resistance in the opportunistic pathogen Candida albicans.
Duration: 1.1.2015 - 31.12.2018

Unravelling the mechanisms of post-translational regulation of RNA splicing factors in maintenance of genome integrity
Objasnenie mechanizmov posttranslačnej regulácie faktorov zostrihu RNA pri udržiavaní stability genómu
Program: SRDA
Project leader: Mgr. Bágeľová Poláková Silvia PhD.
Annotation:Several mutations in RNA biogenesis factors have been implicated in human cancers. Early studies linked RNA processing defects with genome instability phenotypes such as hyper-mutation and hyper-recombination. Since then, recent functional genomic studies have implicated several more aspects of RNA processing in genome instability and revealed that virtually every major aspect of RNA processing is potentially mutable to a genome instability phenotype and in some cases are coupling RNA processing defects to increased RNA:DNA hybrid- mediated R-loop formation, which in turn constitute a major source of genome instability across species. Despite it is now clear that RNA processing defects could destabilize genomes, the molecular mechanism of post-translational regulations of RNA processing and its connections to genome instability are not clear. Our project is aimed at a detailed analysis of the regulatory role of phosphorylation for functions of splicing factors that co-purified with the recently identified spliceosome-associated Nrl1 protein of fission yeast S. pombe. We showed Nrl1 protein be involved in suppression of accumulation of genome threating RNA:DNA hybrids, structures formed during RNA processing. The experimental approaches include protein purifications and phospho proteomics analysis, which will help us to identify post-translational modifications of splicing factors. Analysis of phenotypes of phospho mutants of splicing factors employ fluorescence/live-cell microscopy, analysis of splicing defects of these mutants using RT-PCR or transcriptome sequencing, followed by analysis of their sensitivity to DNA damaging agents and analysis of their defects in DNA repair pathways. The obtained data should bring especially completely new information concerning the regulatory roles of post-translational modifications associated with the defects of RNA processing leading to genome instability that may be important as possible targets for anti-cancer therapy.
Duration: 1.9.2017 - 31.8.2021

Damaging behaviour and the welfare of laying hens
Poškodzujúce správanie a welfare nosníc
Program: VEGA
Project leader: RNDr. Košťál Ľubor CSc.
Annotation:The European laying hen industry is changing dramatically. After the EU ban on battery cages in 2012 laying hens were moved to large flocks in non-cage systems or furnished cages. Although this transition was led by an intention to offer animals greater opportunities to move and display their species-specific behaviour, is also poses an increased risk for damaging behaviour (feather pecking, aggressive behavior, cannibalism). Many EU countries practice beak trimming in laying hens in order to minimize the damaging behavior consequences. Since this mutilation causes chronic pain, there is an increased demand to ban the beak trimming. Another problem associated with the free movement of hens is the increased incidence of keel bone fractures. The aim of this project is to contribute to the understanding of factors influencing the development of damaging behavior and other problems associated with the changes in housing systems and to find the solutions for industry in collaboration with international consortia.
Duration: 1.1.2017 - 31.12.2020

Tetraspanins and partner molecules presence in the reproductive system of cattle, their participation in gamete interaction.
Prítomnosť tetraspanínov a partnerských molekúl v rozmnožovacej sústave hovädzieho dobytka a ich účasť v interakcii gamét.
Program: VEGA
Project leader: RNDr. Antalíková Jana PhD.
Annotation:Fertilization in mammals is complicated and a complex process, which includes amount of molecules on oocytes and sperm. Their identification is not complete yet, and their function and cooperation is not understood. The aim of the proposed project is to study tetraspanins (focusing on CD9, CD81 molecules) and their partner molecules within the multi-molecular "tetraspanin web" on oocytes and sperm of cattle. Using monoclonal antibodies, the biochemical and immunochemical analysis will be performed and study of the role of this molecule in reproduction-related processes using in vitro fertilization experiments will be performed.
Duration: 1.1.2016 - 31.12.2019

Regeneration of specific brain regions of adult songbirds studied by in vivo magnetic resonance
Regenerácia špecifických regiónov mozgu dospelých spevavcov skúmaná pomocou in vivo magnetickej rezonancie
Program: VEGA
Project leader: Mgr. Niederová Ľubica PhD.
Annotation:Neurodegenerative diseases represent a major problem recently because their occurrence rises with increasing age of human population. Neurogenesis, generation of new neurons, is intensively studied for treatment of neurodegeneration. The rate of neuronal regeneration can be influenced also by dopamine receptors (DRs) activity. However, the precise mechanism how DRs affect generation of new neurons after brain damage is unclear. The aim of this project is to study the mechanism and to investigate the rate of this regeneration using in vivo magnetic resonance – MRI. We will use a model of songbirds which learn their songs from other birds and the song learning and production are controlled by specialized brain areas. We will damage a specific striatal region important for song learning. This injury and the following regeneration will provide the advantage of precise examinantion of behavioral subsequences of both processes. Our results should add to understanding the brain regeneration mechanism after injury.
Duration: 1.1.2014 - 31.12.2017

Study of mitochondrial lipids in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe.
Štúdium mitochondriálnych lipidov v kvasinkách Saccharomyces cerevisiae a Schizosaccharomyces pombe.
Program: VEGA
Project leader: Mgr. Balážová Mária PhD.
Annotation:Optimal membranes lipid composition is essential for their function and the proper functioning of the cell. The maintenance of biomembranes lipid composition is a dynamic process involving lipid synthesis, degradation, transport, and remodeling. Aim of the project is to study mitochondrial phospholipids in two yeasts, Saccharomyces cerevisiae and Schizosaccharomyces pombe. Mitochondrial membranes contain specific anionic phospholipid, cardiolipin (CL) and its precursor, phosphatidylglycerol (PG). The project is oriented to the study of regulatory mechanisms involved in CL biosynthesis. In the yeast S. cerevisiae the experiments will be aimed to understand the function of PG specific phospholipase C, Pgc1p. In Sch. pombe we plan to identify and analyze CL synthase. Using the comparative analysis of novel regulatory mechanisms of the CL biosynthetic pathway we will contribute to the understanding of the mechanisms by which eukaryotic cells sustain the optimal lipid composition of mitochondrial membranes.
Duration: 1.1.2014 - 31.12.2017

Learning and neuronal plasticity in songbirds
Učenie a nervová plasticita spevavcov
Program: SRDA
Project leader: Mgr. Niederová Ľubica PhD.
Annotation:Learning and plasticity in adult brain are important topics of the current neurobiological research. In the proposed project we focus on the study of neuroplasticity at regeneration of the striatal part of basal ganglia that control learned vocal communication. Birdsong is a form of learned vocal communication and although language has a unique cognitive architecture, birdsong has many parallels with human language. Therefore, the songbird model is often used in neuroscience studies. The present project is based on our previous results where we found that the striatal vocal nucleus in songbirds regenerates after injury and this regeneration is associated with song changes. The aim of the project is to elucidate the role of newborn neurons incorporated into the injured striatum in the relation to the learned vocal communication. We will study this role both via correlation studies comparing song variability and the rate of brain regeneration (measured by MRI) and via examining the effect of neurogenesis rate manipulation on song. We will focus on the changes in both song tempo and stuttering-like song with abnormal syllable repetition. Further, we will study the mechanism how striatum affects motor pathway necessary for song production. Particularly, we will investigate the repaired brain connectivity. Last, we will explore cognitive abilities of songbirds in relation to the changes in song after brain injury. These results will add to the knowledge of functional integration of the newborn neurons into brain circuitry and to the understanding of the role of neurogenesis in the regulation of behavior.
Duration: 1.7.2016 - 30.6.2020

The role of lipid droplets in the biotechnology of squalene production in yeast
Úloha lipidových partikúl v biotechnologickej produkcii skvalénu kvasinkami
Program: VEGA
Project leader: RNDr. Hapala Ivan CSc.
Annotation:Lipid droplets are dynamic organelles participating in the accumulation of neutral lipids as energy source or stores of simple lipid components for membrane biogenesis. The project is aimed at the role of yest lipid droplets in the accumulation of a high-value lipid squalene. Squalene is produced as the precursor in sterol biosynthesis and due to its physico-chemical properties it finds broad applications in food industry, cosmetics and pharmacology.Limited natural resources open the way for yeast as an alternative organism for squalene production. Genetic modification of squalene epoxidase (Erg1p) will be used in the project to increase squalene levels in yeast. The main aim of the project will be the identification of facors affecting the storage capacity of lipid droplets for squalene (genes affecting lipid droplet biogenesis,lipid and protein composition)and the potential lipotoxicity of squalene if the storage capacity of lipid droplets is exceeded.
Duration: 1.1.2016 - 31.12.2019

The role of organelle interactions in lipid homeostasis
Úloha medziorganelových interakcií v lipidovej homeostáze
Program: SRDA
Project leader: RNDr. Hapala Ivan CSc.
Annotation:Lipids are obligatory constituents of all living organisms serving as structural components of biomembranes,energy storage or signalling molecules. Despite the structural diversity of lipids and variability of environmental conditions affecting membrane functions, lipid composition of individual cell membranes is remarkably stable. This implies the existence of efficient homeostatic mechanisms maintaining optimal lipid composition in eukaryotic cells. These mechanisms are involved in the tightly regulated interplay between lipid biosynthesis, intracellular lipid trafficking, and lipid remodelling or degradation. Using the yeast Saccharomyces cerevisiae as a model eukaryotic cell the project is aimed at answering the question how interactions between intracellular organelles contribute to maintenance of lipid homeostasis. We will focus on three aspects of the problem of the lipid homeostatic mechanisms related to interorganelle interactions: 1) involvement of phosphatidyl inositol transfer proteins in maintaining membrane phospholipid composition; 2) the role of interactions between mitochondria and other intracellular organelles in the homeostasis of phosphatidylglycerol; and 3) the role of lipid droplets in ergosterol biosynthesis and sterol esterification.
Duration: 1.7.2016 - 30.6.2020

Towards highly seletive cancer treatment: Endogenous lipoprotein-DARPin complexes as a new generation of targeted drug delivery vehicles
Vysoko selektívna liečba nádorových ochorení: komplexy endogénnych lipoproteínov s DARPinmi ako nová generácia transportných systémov pre cielený transport liečiv
Program: SRDA
Project leader: RNDr. Bilčík Boris PhD.
Annotation:Cancer chemotherapy generally exhibits a restricted therapeutic index. One of the underlying reasons is the lack of selective accumulation of drugs in cancer tissue. Thus, delivering anticancer drugs to a tumor in therapeutically effective concentrations, whilst sparing healthy tissue, is essential for the efficient treatment of solid cancer. The DARLIK project's ultimate goal is to develop a new technology for drug delivery resulting in a significantly improved selectivity of drug accumulation in cancer tissue and efficacy of chemotherapy. The proposed drug delivery vehicle (DARLINK) is a result of an original and innovative combination of a targeting scaffold protein, known as a Designed Ankyrin Repeat Protein (DARPin), and a lipoprotein-based drug carrier (LDL vehicle). It represents an emerging generation of targeted drug delivery systems, which will lead to a breakthrough in cancer treatment due to its optimal size as well as strong and selective binding to tumor- expressed receptors and capability to transport hundreds of drug molecules per vehicle. Moreover, DARLIK can be tailored to the mutated cancer cell receptors of individual patients, thus contributing to personalized medicine. This breakthrough nano-medical engineering technology is based on the unique expertise of the consortium, which consists of a trans-disciplinary knowledge in protein engineering, display technology, organic and polymer chemistry, biophotonics, cell biology, nanotechnology, computational modeling and medicine.
Duration: 1.7.2016 - 30.6.2020

Development of novel diagnostic method for clinical oncology based on the interaction of DNA aptamers with proteins
Vývoj progresívnej diagnostickej metódy pre klinickú onkológiu založenej na interakcii DNA aptamérov s proteínmi
Program: SRDA
Project leader: Ing. Poturnayová Alexandra PhD.
Annotation:The project is focused on the development of novel diagnostic method for clinical oncology based on the interaction of DNA aptamers with membrane proteins. For this purpose the extensive basic research will be performed with focus on the study of the mechanisms of interaction DNA aptamers with model proteins incorporated into the supported lipid membranes as well as with tumor markers at the surface of the cell cultures. The progressive biophysical methods will be applied such as acoustic thickness shear mode method, atomic force misroscopy, single molecule force spectroscopy, fluorescence resonance energy transfer and others. The exprienced teams composed of senior scientists, young researchers and PhD students from Faculty of Mathematics, Physics and Informatics of Comenius University in Bratislava and from two Research Institutes of the Slovak Academy of Sciences – Institute of Animal Biochemistry and Genetics and Cancer Research Institute will be involved in the project. We assume that will obtain new knowledge on the mechanisms of interaction of DNA aptamers with membrane proteins depending on the lipid composition as well as with tumor markers at the surface of cell cultures depending on the type of the tumor and the progress of dissease.
Duration: 1.7.2015 - 30.6.2019

The total number of projects: 15