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Journal of the American Chemical Society
Higly Adaptable Two-Dimensional Metal-Organic Coordination Networks on Metal Surfaces
Kley, S. Ch.; Čechal, J.; Kumagai, T.; Schramm, F.; Ruben, M.; Stepanow, S.; Kern, K.
CEITEC Research Group: Fabrication and Characterisation of Nanostructures
Research Programme 1: Advanced Nanotechnologies and Microtechnologies
Summary
The formation of extended two-dimensional metal−organic coordination networks (2D-MOCNs) showing high adaptability to surface step edges and structural defects is revealed by scanning tunneling microscopy. Rod-like 4,4′-di-(1,4-buta-1,3-diynyl)-benzoic acid (BDBA) and iron atoms assemble into extended 2D-MOCNs on Au(111) and Ag(100) surfaces. Independent from the chosen substrate and its surface symmetry the MOCN grows continuously over multiple surface terraces through mutual inphase structure adaptation of network domains at step edges as well as on terraces. The adaptability of the MOCNs is mainly ascribed to the high degree of conformational flexibility of the butadiynyl functionality of the ligand. Despite their flexibility, the MOCNs exhibit considerable robustness against annealing at high temperatures. The findings show that mesoscale self-assembled functional architectures with a high degree of substrate error tolerance can be realized with metal coordination networks.
International Journal of Fatigue
Casting defects and high temperature fatigue life of IN 713LC superalloy
Kunz, L.; Lukáš, P.; Konečná, R.; Fintová, S.
CEITEC Research Group: Advanced Metallic Materials and Metal Based Composited
Research Programme 2: Advanced Materials
Summary
High-cycle high temperature fatigue life of a superalloy IN 713LC in as cast state and after hot isostatic pressing was experimentally determined for symmetrical cycling and cycling with tensile mean stress of 300 MPa. Fatigue tests were conducted at 800 °C in laboratory air. It has been found that the hot isostatic pressing improves the fatigue life. Large casting defects are sites of fatigue crack initiation in both states of the alloy. The hot isostatic pressing reduces the size of casting defects, however the broad scatter band of the lifetime data remains. Determination of casting defects size by optical microscopy on metallographic sections and an analysis of the size distribution by extreme value statistics indicates two types of defects: (i) small isolated defects and (ii) defect clusters consisting of complicated interconnected shrinkages in the three-dimensional space. The size distribution of both types of defects follows the extreme value statistics. This enables to estimate the maximum size of a defect likely to occur in a defined volume. The predicted maximum defect size in a volume of a fatigue specimen reasonable corresponds to the size of defect observed on the fracture surface of failed specimen.
Journal of Chemical Information and Modeling
SiteBinder: An Improved Approach for Comparing Multiple Protein Structural Motifs
Sehnal, D.; Varekova; Svobodova, R. S.; Huber, H. J .; Geidl, S.; Ionescu, C. M.; Wimmerova, M.; Koca, J.
CEITEC Research Group: Computational Chemistry
Research Programme 3: Structural Biology
Summary
There is a paramount need to develop new techniques and tools that will extract as much information as possible from the ever growing repository of protein 3D structures. We report here on the development of a software tool for the multiple superimposition of large sets of protein structural motifs. Our superimposition methodology performs a systematic search for the atom pairing that provides the best fit. During this search, the RMSD values for all chemically relevant pairings are calculated by quaternion algebra. The number of evaluated pairings is markedly decreased by using PDB annotations for atoms. This approach guarantees that the best: fit will be found and can be applied even when sequence similarity is low or does not exist at all. We have implemented this methodology in the Web application SiteBinder, which is able to process up to thousands of protein structural motifs in a very short time, and which provides an intuitive and user-friendly interface. Our benchmarking analysis has shown the robustness, efficiency, and versatility of our methodology and its implementation by the successful superimposition of 1000 experimentally determined structures for each of 32 eukaryotic linear motifs. We also demonstrate the applicability of SiteBinder using three case studies. We first compared the structures of 61 PA-ILL sugar binding sites containing nine different sugars, and we found that the sugar binding sites of PA-IIL and its mutants have a conserved structure despite their binding different sugars. We then superimposed. over 300 zinc finger central motifs and revealed that the molecular structure in the vicinity of the Zn atom is highly conserved. Finally, we superimposed 12 BH3 domains from pro-apoptotic proteins. Our findings come to support the hypothesis that there is a structural basis for the functional segregation of BH3-only proteins into activators and enablers.
Analysis of the Nse3/MAGE-binding Domain of the Nse4/EID Family Proteins
Guerineau M.; Kriz Z.; Bednarova K.; Kozakova L.; Janos P.; Palecek J.
CEITEC Research Group: Chromatin Molecular Complexes
Research Program 4: Genomics and Proteomics of Plant Systems
Summary
The SMC (structural maintenance of chromosomes) complexes are conserved in all eukaryotes and play crucial roles in chromosome maintenance. The SMC5-6 complex is comprised of 6 subunits assembled into two sub-complexes. The Nse1, Nse3 and Nse4 subunits interact with each other and form one of the SMC5-6 sub-complexes. Interestingly, Nse3/MAGEG1 is the founding member of the MAGE (melanoma-associated antigen) mammalian protein family and Nse4 is related to the EID (E1A-like inhibitor of differentiation) family of proteins. We have shown that human MAGE proteins can interact with NSE4/EID proteins through their characteristic conserved hydrophobic pocket. Using mutagenesis and protein-protein interaction analyses, we have identified a conserved Nse3/MAGE-binding domain of the Nse4/EID proteins. In addition, docking and molecular dynamic simulations enabled us to generate a structure model for EID-MAGE heterodimer. The conservation of the interacting surfaces suggest tight co-evolution of both Nse4/EID and Nse3/MAGE protein families.
Journal of Experimental Botany
Developmetal silencing of the AtTERT gene is associated with increased H3K27me3 loading and maintenance of its euchromatic environment
Ogrocká, A.; Sýkorová, E.; Fajkus, J.; Fojtová, M.
CEITEC Research Group: Chromatin Molecular Complexes
Research Program 4: Genomics and Proteomics of Plant Systems
Summary
Telomerase is an enzyme responsible for the maintenance of telomeres, specialized nucleoprotein structures at the ends of linear chromosomes, and its activity is precisely regulated during development. In animal model organisms, involvement of epigenetic mechanisms (DNA methylation and histone modifications determining chromatin structure) in the complex process of regulation of telomerase activity has been reported. In this work, telomerase activity and transcription in plant tissues was correlated to the epigenetic state of telomerase promoter. Our discovery that (i) DNA methylation is not involved in developmental regulation of telomerase promoter and (ii) euchromatic nature of the AtTERT chromatin is maintained even in telomerase-negative tissues may reflect the totipotency, unique attribute of plants, and represents another interesting difference in plant and animal telomere biology.
HMGB1 gene knockout in mouse embryonic fibroblasts results in reduced telomerase activity and telomere dysfunction
Polanská, E.; Dobšáková, Z.; Dvořáčková, M.; Fajkus, J; Štros, M.
CEITEC Research Group: Chromatin Molecular Complexes
Research Program 4: Genomics and Proteomics of Plant Systems
Summary
Telomere DNA repeats are added onto chromosome ends by telomerase, consisting of two main components: a catalytic protein subunit (telomerase reverse trancriptase, TERT), and an RNA subunit (telomerase RNA, TR). We found HMGB1 (a chromatin-associated protein acting as a DNA chaperone in transcription, replication, recombination, and repair) can modulate cellular activity of telomerase. Knockout of the HMGB1 gene (HMGB1 KO) in mouse embryonic fibroblasts (MEFs) results in chromosomal abnormalities, emerging DNA damage signals at telomeres, and telomere shortening. HMGB1 KO MEFs also exhibit much lower telomerase activity than the wild-type MEFs. orrespondingly, enhanced telomerase activity is observed upon overexpression of HMGB1 in MEFs. HMGB1 physically interacts with both TERT and TR, as well as with active telomerase complex in vitro. However, direct interaction of HMGB1 with telomerase is most likely not accountable for the observed higher telomerase activity in HMGB1-containing cells, as revealed from the inability of purified HMGB1 protein to stimulate telomerase activity in vitro. While no transcriptional silencing of TERT is observed in HMGB1 KO MEFs, levels of TR are diminished (~3-fold), providing possible explanation for the observed lower telomerase activity in HMGB1 KO cells. Interestingly, knockout of the related HMGB2 gene elevates telomerase activity (~3-fold) in MEFs, suggesting that the two closely related proteins of the HMGB family, HMGB1 and HMGB2, have opposite effects on telomerase activity in the cell. The ability of HMGB1 to modulate cellular activity of telomerase and to maintain telomere integrity can help to understand some aspects of the protein involvement in chromosome stability and cancer.
Iowa Gambling Task in patients with early-onset
Parkinson’s disease: strategy analysis
Gescheidt, T.; Czekoova, K.; Urbanek, T.; Marecek, R.; Mikl, M.; Kubıkova, R.; Telecka, S.; Andrlova, H.; Husarova, I.; Bares, M.
CEITEC Research Group: Behavioural and Social Neuroscience
Research Program 6: Brain and Mind Research
Summary
The aim of our study was to analyse decision making in early-onset Parkinson’s disease (PD) patients performing the Iowa Gambling Task (IGT). We compared 19 patients with early-onset PD (B45 years) on dopaminergic medication (no evidence of depression, dementia, executive dysfunction according to the Tower of London test and the Stroop test, or pathological gambling) with 20 age-matched controls. A computer version of the IGT was employed. The PD patients achieved slightly lower IGT scores than the control group. A detailed analysis based on ‘shift frequencies’ between the individual decks showed that the patients tended to change their preferences for the decks more frequently, with a higher preference for the ‘disadvantageous’ deck B. Control subjects seemed to develop a more effective strategy. These differences could be caused by the poorer ability of the patients to develop any strategy at all. We observed changes in decision making during IGT performance in patients with earlyonset PD, although they had no executive dysfunction as measured by established neuropsychological tests. The more detailed analysis employed in the present study could lead to a more accurate study of IGT performance and application of IGT in clinical practice.
Unveiling the mystery of de´ja` vu: The structural anatomy of de´ja` vu
Brazdil, M.; Marecek, R.; Urbanek, T.; Kasparek, T.; Mikl, M.; Rektor, I.; Zeman, A.
CEITEC Research Group: Behavioural and Social Neuroscience
Research Program 6: Brain and Mind Research
Summary
De´ ja` vu (DV) is a widespread, fascinating and mysterious human experience. It occurs both in health and in disease, notably as an aura of temporal lobe epilepsy. This feeling of inappropriate familiarity has attracted interest from psychologists and neuroscientists for over a century, but still there is no widely agreed explanation for the phenomenon of non-pathological DV. Here we investigated differences in brain morphology between healthy subjects with and without DV using a novel multivariate neuroimaging technique, Source-Based Morphometry. The analysis revealed a set of cortical (predominantly mesiotemporal) and subcortical regions in which there was significantly less gray matter in subjects reporting DV. In these regions gray matter volume was inversely correlated with the frequency of DV. Our results demonstrate a structural correlate of DV in healthy individuals for the first time and support a neurological explanation for the phenomenon. We hypothesis that the observed local gray matter decrease in subjects experiencing DV reflects an alteration of hippocampal function and postnatal neurogenesis with resulting changes of volume in remote brain regions.
Pharmacology, Biochemistry and Behavior
Differential effects of modafinil, methamphetamine, and MDMA on agonistic behavior in male mice
Machalova, A.; Slais, K.; Vrskova, D.; Sulcova, A.
CEITEC Research Group: Experimental and Applied Neuropsychopharmacology
Research Program 6: Brain and Mind Research
Summary
The results of this study present behavioral profiles of acute effects of modafinil, methamphetamine, and MDMA (ecstasy) in male mice that differ in some parameters of agonistic behavior. The model allowed us to observe different responses to administered drugs, apparent especially in categories of affective behavioral activities (sociable, timid, aggressive) and in locomotor behavior, which varied between predominantly aggressive and timid mice. Agonistic behavior was not affected by modafinil as markedly as by MET and MDMA treatment; however, it was the only drug tested that increased aggression in timid mice. This should be taken into account in the individualized set up of neuroscience experiments, regarding the individual behavioral and neurochemical background of tested subjects. Such an approach may contribute substantially to translation of our knowledge from animal to individualized human treatment.
Poststroke delirium incidence and outcomes: Validation of the Confusion Assessment Method for the Intensive Care Unit (CAM-ICU)
Mitasova, A.; Kostalova, M.; Bednarik, J.; Michalcakova, R.; Kasparek, T.; Balabanova; P.; Dusek, L.; Vohanka, S.; Ely, E. W.
CEITEC Research Group: Applied Neuroscience
Research Program 6: Brain and Mind Research
Summary
We evaluated epidemiology of poststroke delirium and validated a tool for delirium assessment: the Czech version of the Confusion Assessment Method for the Intensive Care Unit (CAM-ICU). An episode of delirium based on reference Diagnostic and Statistical Manual assessment was detected in 55 patients with stroke (42.6%). The CAM-ICU demonstrated a sensitivity of 76% (95% confidence interval [CI] 55% to 91%), a specificity of 98% (95% CI 93% to 100%), an overall accuracy of 94% (95% CI 88% to 97%), and high interrater reliability (κ = 0.94; 95% CI 0.83-1.0).
Default Mode Network and Extrastriate Visual Resting State Network in Patients with Parkinson’s Disease Dementia
Rektorova, I.; Krajcovicova, L.; Marecek, R.; Mikl, M.
CEITEC Research Group: Applied Neuroscience
Research Program 6: Brain and Mind Research
Summary
Aims: Using fMRI, we evaluated the default mode network (DMN) and the extrastriate visual resting state network (ESVRSN) in 14 patients with Parkinson’s disease dementia (PDD) as compared with 18 patients with Parkinson’s disease (PD) without dementia and 18 healthy controls (HC). Methods: We analyzed the seed-based functional connectivity of both resting state data and deactivations during a visual complex scene-encoding task. Results: Using the posterior cingulate cortex/precuneus as a seed for the DMN analysis, we observed significant decreases of connectivity in the right inferior frontal gyrus in PDD as compared to PD and HC. Using the caudate nucleus as a seed for the ESV-RSN analysis, we found significant decreases of connectivity in the left and right inferior occipital gyrus in PDD as compared to HC. Conclusion: Differences in functional connectivity patterns between PDD and PD/HC were observed in areas known to be engaged in stimulus-driven reorienting of attention and in visual processing.
Aneuploidy Detection in Pigs Using Comparative Genomic Hybridization: From the Oocytes to Blastocysts
Hornak, M.; Oracova, E.; Hulinska, P.; Urbankova,L.; Rubes, J.
CEITEC Research Group: Animal Cytogenomics
Research Programme 7: Molecular Veterinary Medicine
Summary
Data on the frequency of aneuploidy in farm animals are lacking and there is the need for a reliable technique which is capable of detecting all chromosomes simultaneously in a single cell. With the employment of comparative genomic hybridization coupled with the whole genome amplification technique, this study brings new information regarding the aneuploidy of individual chromosomes in pigs. Focus is directed on in vivo porcine blastocysts and late morulas, 4.7% of which were found to carry chromosomal abnormality. Further, ploidy abnormalities were examined using FISH in a sample of porcine embryos. True polyploidy was relatively rare (1.6%), whilst mixoploidy was presented in 46.8% of embryos, however it was restricted to only a small number of cells per embryo. The combined data indicates that aneuploidy is not a prevalent cause of embryo mortality in pigs.
Journal of Antimicrobial Chemotherapy
Escherichia coli with extended-spectrum beta-lactamase and plasmid-mediated quinolone resistance genes in great cormorants and mallards in Central Europe
Tausova, D.; Dolejska, M.; Cizek, A.; Hanusova, L.; Hrusakova, J.; Svoboda, O.; Camlik, G.; Literak, I.
CEITEC Research Group: Molecular Bacteriology
Research Programme 7: Molecular Veterinary Medicine
Summary
The emergence of multidrug-resistant bacteria in the natural environment constitutes a serious risk to domestic animal and human health. It can be presumed that resistant bacteria colonizing wild cormorants and mallards originated in aquatic environment. Faecal Escherichia coli strains were isolated from great cormorants and mallards, which are commonly occurring waterbirds in Europe, and studied for resistance to cephalosporins and fluoroquinolones. Ten ESBL (extended spectrum beta-lactamase)-producing E. coli with the blaCTX-M-15 or blaCTX-M-27 gene were isolated from eight great cormorants (1.6%, n=499). The blaCTX-M genes were harboured by plasmids of F and I1 incompatibility groups. CTX-M-27-producing isolates were identified as the epidemiologically important B2-O25b-ST131 clone which has high virulence potential all over the world and represents a great public health problem. This is the first detection of a CTX-M-27 ESBL type in an O25b-ST131 isolate in Europe. Eight E. coli isolates with plasmid-mediated quinolone resistance (PMQR) genes [six aac(6′)-Ib-cr, and two qnrS1] were detected in six great cormorants (1.2%). Seventeen strains with qnrS1 were detected in 17 mallards (6%, n=305). The PMQR genes were located on plasmids of incompatibility groups F, N or X2. ESBL and PMQR genes were found on conjugative plasmids, enabling the horizontal spread of resistance. Both great cormorants and mallards can spread epidemiologically important antimicrobial resistant E. coli isolates to water bodies throughout Europe.
EVROPSKÁ UNIE
