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Surface Science Reports
Trace elemental analysis by laser-induced breakdown spectroscopy – Biological applications
Kaiser, J.; Novotný, K.; Martin, M.; Hrdlička, A.; Malina, R.; Hartl, M.; Adam, V.; Kizek, R.
CEITEC Research Group: X-ray Micro CT and Nano CT, Smart Nanodevices
Research Programme 1: Advanced Nanotechnologies and Microtechnologies
Summary
Laser-Induced Breakdown Spectroscopy (LIBS) is a sensitive optical technique capable of fast multi-elemental analysis of solid, gaseous and liquid samples. Since the late 1980s LIBS became visible in the analytical atomic spectroscopy scene; its applications having been developed continuously since then. In this paper, the use of LIBS for trace element determination in different matrices is reviewed. The main emphasis is on spatially resolved analysis of microbiological, plant and animal samples.
ACS Nano
Guided assembly of gold colloidal nanoparticles on silicon substrates prepatterned by charged particle beams
Kolíbal M.; Konečný M.; Ligmajer F.; Škoda D.; Vystavěl T.; Zlámal J.; Varga P.; Šikola T.
CEITEC Research Group: Fabrication and Characterisation of Nanostructures
Research Programme 1: Advanced Nanotechnologies and Microtechnologies
Summary
Colloidal gold nanoparticles represent technological building blocks which are easy to fabricate while keeping full control of their shape and dimensions. We report on a simple two-step maskless process to assemble gold nanoparticles from a water colloidal solution at specific sites of a silicon surface. First, the silicon substrate covered by native oxide is exposed to a charged particle beam (ions or electrons) and then immersed in a HF-modified solution of colloidal nanoparticles. The irradiation of the native oxide layer by a low-fluence charged particle beam causes changes in the type of surface-terminating groups, while the large fluences induce even more profound modification of surface composition. Hence, by a proper selection of the initial substrate termination, solution pH, and beam fluence, either positive or negative deposition of the colloidal nanoparticles can be achieved.
Physical Review B
Antiferrodistortive phase transition in EuTiO3
Goian, V.; Kamba, S.; Pacherová, O.; Drahokoupil, J.; Palainus, L.; Dušek, M.; Rohlíček, J.; Savinov, M.; Laufek, F.; Schranz, W.; Fuith, A.; Kachlík, M.; Maca, K.; Shkabko, A.; Sagarna, L.; Weidenkaff, A.; Belik, A.A.
CEITEC Research Group: Advanced Ceramics Materials
Research Programme 2: Advanced Materials
Summary
X-ray diffraction, dynamical mechanical analysis, and infrared reflectivity studies revealed an antiferrodistortive phase transition in EuTiO3 ceramics. Near 300 K, the perovskite structure changes from cubic Pm3m to tetragonal I4/mcm due to antiphase tilting of oxygen octahedra along the c axis (a0a0c− in Glazer notation). The phase transition is analogous to SrTiO3. However, some ceramics as well as single crystals of EuTiO3 show different infrared reflectivity spectra bringing evidence of a different crystal structure. In such samples, electron diffraction revealed an incommensurate tetragonal structure with modulation wave vector q ≈ 0.38 a∗. Extra phonons in samples with modulated structure are activated in the IR spectra due to folding of the Brillouin zone. We propose that defects such as Eu3+ and oxygen vacancies strongly influence the temperature of the phase transition to antiferrodistortive phase as well as the tendency to incommensurate modulation in EuTiO3.
The EMBO Journal
In vivo SELEX reveals novel sequence and structural determinants of Nrd1-Nab3-Sen1-dependent transcription termination
Porrua, O.; Hobor, F.; Boulay, J.; Kubicek, K.; D’Aubenton-Carafa, Y.; Kanth Gudipati, R.; Stefl, R.; Libri, D.
CEITEC Research Group: Structural Biology of Gene Regulation
Research Programme 3: Structural Biology
Summary
The Nrd1-Nab3-Sen1 (NNS) complex pathway is responsible for transcription termination of cryptic unstable transcripts and sn/snoRNAs. The NNS complex recognizes short motifs on the nascent RNA, but the presence of these sequences alone is not sufficient to define a functional terminator. We generated a homogeneous set of several hundreds of artificial, NNS-dependent terminators with an in vivo selection approach. Analysis of these terminators revealed novel and extended sequence determinants for transcription termination and NNS complex binding as well as supermotifs that are critical for termination. Biochemical and structural data revealed that affinity and specificity of RNA recognition by Nab3p relies on induced fit recognition implicating an α-helical extension of the RNA recognition motif. Interestingly, the same motifs can be recognized by the NNS or the mRNA termination complex depending on their position relative to the start of transcription, suggesting that they function as general transcriptional insulators to prevent interference between the non-coding and the coding yeast transcriptomes.
Nucleic Acids Research
Polymorphism of human telomeric quadruplex structure controlled by DNA concentration: a Raman study
Palacky, J.; Vorlickova, M.; Kejnovska, I.; Mojzes, P.
CEITEC Research Group: CD Spectroscopy of Nucleic Acids and Proteins
Research Programme 3: Structural Biology
Summary:
DNA concentration ha sbeen recently suggested to be the reason why different arrangements are revealed for K+-stabilized human telomere quadruplexes by experimental methods requiring DNA concentrations differing by orders of magnitude. As Raman spectroscopy can be applied to DNA samples ranging from those accessible by absorption and CD spectroscopies up to extremely concentrated solutions, gels and even crystals; it has been used here to clarify polymorphism of a core human telomeric sequence G3(TTAG3)3 in the presence of K+ and Na+ ions throughout wide range of DNA concentrations. We demonstrate that the K+-structure of G3(TTAG3)3 at low DNA concentration is close to the antiparallel fold of Na+-stabilized quadruplex. On the increase of G3(TTAG3)3 concentration, a gradual transition from antiparallel to intramolecular parallel arrangement was observed, but only for thermodynamically equilibrated K+-stabilized samples. The transition is synergically supported by increased K+ concentration. However, even for extremely high G3(TTAG3)3 and K+concentrations, an intramolecular antiparallel quadruplex is spontaneously formed from desalted non-quadruplex single-strand after addition of K+ ions. Thermal destabilization or long dwell time are necessary to induce interquadruplex transition. On the contrary, Na+-stabilized G3(TTAG3)3 retains its antiparallel folding regardless of the extremely high DNA and/or Na+ concentrations, thermal destabilization or annealing.
Science
53BP1 Regulates DSB Repair Using Rif1 to Control 5′ End Resection
Zimmermann, M.; Lottersberger, F.; Buonomo, S.B.; Sfeir, A.; de Lange, T.
CEITEC Research Group: Chromatin Molecular Complexes
Research Programme 4: Genomics and Proteomics of Plant Systems
Summary
The choice between double-strand break (DSB) repair by either homology-directed repair (HDR) or nonhomologous end joining (NHEJ) is tightly regulated. Defects in this regulation can induce genome instability and cancer. 53BP1 is critical for the control of DSB repair, promoting NHEJ, and inhibiting the 5′ end resection needed for HDR. Using dysfunctional telomeres and genome-wide DSBs, we identify Rif1 as the main factor used by 53BP1 to impair 5′ end resection. Rif1 inhibits resection involving CtIP, BLM, and Exo1; limits accumulation of BRCA1/BARD1 complexes at sites of DNA damage; and defines one of the mechanisms by which 53BP1 causes chromosomal abnormalities in Brca1-deficient cells. These data establish Rif1 as an important contributor to the control of DSB repair by 53BP1.
Plant Physiology
Proteome Analysis in Arabidopsis Reveals Shoot- and Root-Specific Targets of Cytokinin Action and Differential Regulation of Hormonal Homeostasis
Žd’árská, M.; Zatloukalová, P.; Benitez, M.; Šedo, O.; Potěšil, D.; Novák, O.; Svačinová, J.; Pešek, B.; Malbeck, J.; Vašíčková, J.; Zdráhal, Z.; Hejátko, J.
CEITEC Research Group: Functional Genomics and Proteomics of Plants
Research Programme 4: Genomics and Proteomics of Plant Systems
Summary
The plant hormones cytokinins (CKs) regulate multiple developmental and physiological processes in Arabidopsis (Arabidopsis thaliana). Responses to CKs vary in different organs and tissues (e.g. the response to CKs has been shown to be opposite in shoot and root samples). However, the tissue-specific targets of CKs and the mechanisms underlying such specificity remain largely unclear. Here, we show that the Arabidopsis proteome responds with strong tissue and time specificity to the aromatic CK 6-benzylaminopurine (BAP) and that fast posttranscriptional and/or posttranslational regulation of protein abundance is involved in the contrasting shoot and root proteome responses to BAP. We demonstrate that BAP predominantly regulates proteins involved in carbohydrate and energy metabolism in the shoot as well as protein synthesis and destination in the root. Furthermore, we found that BAP treatment affects endogenous hormonal homeostasis, again with strong tissue specificity. In the shoot, BAP up-regulates the abundance of proteins involved in abscisic acid (ABA) biosynthesis and the ABA response, whereas in the root, BAP rapidly and strongly up-regulates the majority of proteins in the ethylene biosynthetic pathway. This was further corroborated by direct measurements of hormone metabolites, showing that BAP increases ABA levels in the shoot and 1-aminocyclopropane-1-carboxylic acid, the rate-limiting precursor of ethylene biosynthesis, in the root. In support of the physiological importance of these findings, we identified the role of proteins mediating BAP-induced ethylene production, METHIONINE SYNTHASE1 and ACC OXIDASE2, in the early root growth response to BAP.
Clinica Chimica Acta
Hyperphenylalaninemia in the Czech Republic: Genotype–phenotype correlations and in silico analysis of novel missense mutations
Réblová, K.; Hrubá, Z.; Procházková, D.; Pazdírková, R.; Pouchlá, S.; Fajkusová, L.
CEITEC Research Group: Inherited Diseases I – Genetic Research
Research Programme 5: Molecular Medicine
Summary
Hyperphenylalaninemia (HPA) is one of the most common inherited metabolic disorders caused by deficiency of the enzyme phenylalanine hydroxylase (PAH). HPA is associated with mutations in the PAH gene, which leads to reduced protein stability and/or impaired catalytic function. Currently, almost 700 different disease-causing mutations have been described. The impact of mutations on enzyme activity varies ranging from classical PKU, mild PKU, to non-PKU HPA phenotype.
Pharmacology & Therapeutics
Endocannabinoid system and mood disorders: Priming a target for new therapies
Micale V.; Di Marzo V.; Sulcova A.; Wotjak C.T.; Drago F.
CEITEC Research Group: Experimental and Applied Neuropsychopharmacology
Research Programme 6: Brain and Mind Research
Summary:
The endocannabinoid system (ECS), comprising two G protein-coupled receptors (the cannabinoid receptors 1 and 2 [CB1 and CB2] for marijuana’s psychoactive principle ∆9-tetrahydrocannabinol [∆9-THC]), their endogenous small lipid ligands (namely anandamide [AEA] and 2-arachidonoylglycerol [2-AG], also known as endocannabinoids), and the proteins for endocannabinoid biosynthesis and degradation, has been suggested as a pro-homeostatic and pleiotropic signaling system activated in a time- and tissue-specific way during physiopathological conditions. In the brain activation of this system modulates the release of excitatory and inhibitory neurotransmitters and of cytokines from glial cells. As such, the ECS is strongly involved in neuropsychiatric disorders, particularly in affective disturbances such as anxiety and depression. It has been proposed that synthetic molecules that inhibit endocannabinoid degradation can exploit the selectivity of endocannabinoid action, thus activating cannabinoid receptors only in those tissues where there is perturbed endocannabinoid turnover due to the disorder, and avoiding the potential side effects of direct CB1 and CB2 activation. However, the realization that endocannabinoids, and AEA in particular, also act at other molecular targets, and that these mediators can be deactivated by redundant pathways, has recently led to question the efficacy of such approach, thus opening the way to new multi-target therapeutic strategies, and to the use of non-psychotropic cannabinoids, such as cannabidiol (CBD), which act via several parallel mechanisms, including indirect interactions with the ECS. The state of the art of the possible therapeutic use of endocannabinoid deactivation inhibitors and phytocannabinoids in mood disorders is discussed in this review article.
Human Brain Mapping
Brain Functional Connectivity of Male Patients in Remission after the First Episode of Schizophrenia
Kasparek, T.; Prikryl, R.; Rehulova, J.; Marecek, R.; Mikl, M.; Prikrylova, H.; Vanicek, J.; Ceskova, E.
CEITEC Research Group: Behavioural and Social Neuroscience
Research Programme 6: Brain and Mind research
Summary:
Objectives: Abnormal task-related activation and connectivity is present in schizophrenia. The aim of this study was the analysis of functional networks in schizophrenia patients in remission after the first episode. Experimental design: Twenty-nine male patients in remission after the first episode of schizophrenia and 22 healthy controls underwent examination by functional magnetic resonance during verbal fluency tasks (VFT). The functional connectivity of brain networks was analysed using independent component analysis. Results: The patients showed lower activation of the salience network during VFT. They also showed lower deactivation of the default mode network (DMN) during VFT processing. Spectral analysis of the component time courses showed decreased power in slow frequencies of signal fluctuations in the salience and DMNs and increased power in higher frequencies in the left frontoparietal cortex reflecting higher fluctuations of the network activity. Moreover, there was decreased similarity of component time courses in schizophrenia—the patients had smaller negative correlation between VFT activated and deactivated networks, and smaller positive correlations between DMN subcomponents. Conclusions: There is still an abnormal functional connectivity of several brain networks in remission after the first episode of schizophrenia. The effect of different treatment modalities on brain connectivity, together with temporal dynamics of this functional abnormality should be the objective of further studies to assess its potential as a marker of disease stabilization.
Environmental microbiology
Vancomycin-resistant enterococci in rooks (Corvus frugilegus) wintering throughout Europe
Oravcova, V.; Ghosh, A.; Zurek, L.; Bardon, J.; Guenther, S.; Cizek, A.; Literak, I.
CEITEC Research Group: Molecular Bacteriology
Research Programme 7: Molecular Veterinary Medicine
Summary:
This study’s aims were to assess the prevalence of, and to characterize, vancomycin-resistant enterococci (VRE) from rooks (Corvus frugilegus) wintering in Europe during 2010/2011. Faeces samples were cultivated selectively for VRE and characterized. Pulsed-field gel electrophoresis and multilocus sequence typing (MLST) were used to examine epidemiologic relationships of vanA-containing VRE. The vanA-carrying VRE were tested in vitro for mobility of vancomycin resistance traits. Eight VRE harboured the vanA and ermB genes. Seven vanA-carrying VRE originated from the Czech Republic and one from Germany. All vanA-carrying VRE were identified as E. faecium. Based on MLST analysis, six vanA-positive isolates were grouped as ST92 type, one isolate belonged to ST121, and the remaining one was described as a novel type ST671. Seven out of eight isolates were able to transfer the vancomycin resistance trait via filter mating with a transfer rate of 8.95±3.25 x10-7 transconjugants per donor. In conclusion, wintering rooks in some European countries may disseminate clinically important enterococci and pose a risk for environmental contamination.
PNAS – Proceedings of the National Academy of Sciences of the United States of America
Mechanistic basis of infertility of mouse intersubspecific hybrids
Bhattacharyya, T.; Gregorova, S.; Mihola, O.; Anger, M.; Sebestova, J.; Denny, P.; Simecek, P.; Forejt, J.
CEITEC Research Group: Mammalian Reproduction
Research Programme 7: Molecular Veterinary Medicine
Summary
According to the Dobzhansky–Muller model, hybrid sterility is a consequence of the independent evolution of related taxa resulting in incompatible genomic interactions of their hybrids. The model implies that the incompatibilities evolve randomly, unless a particular gene or nongenic sequence diverges much faster than the rest of the genome. Here we propose that asynapsis of heterospecific chromosomes in meiotic prophase provides a recurrently evolving trigger for the meiotic arrest of interspecific F1 hybrids. We observed extensive asynapsis of chromosomes and disturbance of the sex body in >95% of pachynemas of Mus m. musculus × Mus m. domesticus sterile F1 males. Asynapsis was not preceded by a failure of double-strand break induction, and the rate of meiotic crossing over was not affected in synapsed chromosomes. DNA double-strand break repair was delayed or failed in unsynapsed autosomes, and misexpression of chromosome X and chromosome Y genes was detected in single pachynemas and by genome-wide expression profiling. Oocytes of F1 hybrid females showed the same kind of synaptic problems but with the incidence reduced to half. Most of the oocytes with pachytene asynapsis were eliminated before birth. We propose the heterospecific pairing of homologous chromosomes as a pre-existing condition of asynapsis in interspecific hybrids. The asynapsis may represent a universal mechanistic basis of F1 hybrid sterility manifested by pachytene arrest. It is tempting to speculate that a fast-evolving subset of the noncoding genomic sequence important for chromosome pairing and synapsis may be the culprit.
