Showing papers by "Academy of Sciences of the Czech Republic published in 2007"

The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions

Abstract: Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the approximately 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.

Estimation of nuclear DNA content in plants using flow cytometry.

Abstract: Flow cytometry (FCM) using DNA-selective fluorochromes is now the prevailing method for the measurement of nuclear DNA content in plants. Ease of sample preparation and high sample throughput make it generally better suited than other methods such as Feulgen densitometry to estimate genome size, level of generative polyploidy, nuclear replication state and endopolyploidy (polysomaty). Here we present four protocols for sample preparation (suspensions of intact cell nuclei) and describe the analysis of nuclear DNA amounts using FCM. We consider the chemicals and equipment necessary, the measurement process, data analysis, and describe the most frequent problems encountered with plant material such as the interference of secondary metabolites. The purpose and requirement of internal and external standardization are discussed. The importance of using a correct terminology for DNA amounts and genome size is underlined, and its basic principles are explained.

Characterization of human embryonic stem cell lines by the International Stem Cell Initiative

Abstract: The International Stem Cell Initiative characterized 59 human embryonic stem cell lines from 17 laboratories worldwide. Despite diverse genotypes and different techniques used for derivation and maintenance, all lines exhibited similar expression patterns for several markers of human embryonic stem cells. They expressed the glycolipid antigens SSEA3 and SSEA4, the keratan sulfate antigens TRA-1-60, TRA-1-81, GCTM2 and GCT343, and the protein antigens CD9, Thy1 (also known as CD90), tissue- nonspecific alkaline phosphatase and class 1 HLA, as well as the strongly developmentally regulated genes NANOG, POU5F1 (formerly known as OCT4), TDGF1, DNMT3B, GABRB3 and GDF3. Nevertheless, the lines were not identical: differences in expression of several lineage markers were evident, and several imprinted genes showed generally similar allele-specific expression patterns, but some gene-dependent variation was observed. Also, some female lines expressed readily detectable levels of XIST whereas others did not. No significant contamination of the lines with mycoplasma, bacteria or cytopathic viruses was detected.

Riparian vegetation: Degradation, alien plant invasions, and restoration prospects

Abstract: Rivers are conduits for materials and energy; this, the frequent and intense disturbances that these systems experience, and their narrow, linear nature, create problems for conservation of biodiversity and ecosystem functioning in the face of increasing human influence. In most parts of the world, riparian zones are highly modified. Changes caused by alien plants — or environmental changes that facilitate shifts in dominance creating novel ecosystems — are often important agents of perturbation in these systems. Many restoration projects are underway. Objective frameworks based on an understanding of biogeographical processes at different spatial scales (reach, segment, catchment), the specific relationships between invasive plants and resilience and ecosystem functioning, and realistic endpoints are needed to guide sustainable restoration initiatives. This paper examines the biogeography and the determinants of composition and structure of riparian vegetation in temperate and subtropical regions and conceptualizes the components of resilience in these systems. We consider changes to structure and functioning caused by, or associated with, alien plant invasions, in particular those that lead to breached abiotic- or biotic thresholds. These pose challenges when formulating restoration programmes. Pervasive and escalating human-mediated changes to multiple factors and at a range of scales in riparian environments demand innovative and pragmatic approaches to restoration. The application of a new framework accommodating such complexity is demonstrated with reference to a hypothetical riparian ecosystem under three scenarios: (1) system unaffected by invasive plants; (2) system initially uninvaded, but with flood-generated incursion of alien plants and escalating invasion-driven alteration; and (3) system affected by both invasions and engineering interventions. The scheme has been used to derive a decision-making framework for restoring riparian zones in South Africa and could guide similar initiatives in other parts of the world.

Correlation of the highest-energy cosmic rays with nearby extragalactic objects.

Abstract: Using data collected at the Pierre Auger Observatory during the past 3.7 years, we demonstrate that there is a correlation between the arrival directions of cosmic rays with energy above {approx} 6 x 10{sup 19} eV and the positions of active galactic nuclei (AGN) lying within {approx} 75 Mpc. We reject the hypothesis of an isotropic distribution of these cosmic rays at over 99% confidence level from a prescribed a priori test. The correlation we observe is compatible with the hypothesis that the highest energy particles originate from nearby extragalactic sources whose flux has not been significantly reduced by interaction with the cosmic background radiation. AGN or objects having a similar spatial distribution are possible sources.

Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations

Abstract: Standard density functional theory (DFT) is augmented with a damped empirical dispersion term. The damping function is optimized on a small, well balanced set of 22 van der Waals (vdW) complexes and verified on a validation set of 58 vdW complexes. Both sets contain biologically relevant molecules such as nucleic acid bases. Results are in remarkable agreement with reference high-level wave function data based on the CCSD(T) method. The geometries obtained by full gradient optimization are in very good agreement with the best available theoretical reference. In terms of the standard deviation and average errors, results including the empirical dispersion term are clearly superior to all pure density functionals investigated-B-LYP, B3-LYP, PBE, TPSS, TPSSh, and BH-LYP-and even surpass the MP2/cc-pVTZ method. The combination of empirical dispersion with the TPSS functional performs remarkably well. The most critical part of the empirical dispersion approach is the damping function. The damping parameters should be optimized for each density functional/basis set combination separately. To keep the method simple, we optimized mainly a single factor, s(R), scaling globally the vdW radii. For good results, a basis set of at least triple-zeta quality is required and diffuse functions are recommended, since the basis set superposition error seriously deteriorates the results. On average, the dispersion contribution to the interaction energy missing in the DFT functionals examined here is about 15 and 100% for the hydrogen-bonded and stacked complexes considered, respectively.

Understanding of assembly phenomena by aromatic-aromatic interactions: benzene dimer and the substituted systems.

Abstract: Interactions involving aromatic rings are important in molecular/biomolecular assembly and engineering. As a consequence, there have been a number of investigations on dimers involving benzene or other substituted π systems. In this Feature Article, we examine the relevance of the magnitudes of their attractive and repulsive interaction energy components in governing the geometries of several π−π systems. The geometries and the associated binding energies were evaluated at the complete basis set (CBS) limit of coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)] using a least biased scheme for the given data set. The results for the benzene dimer indicate that the floppy T-shaped structure (center-to-center distance: 4.96 A, with an axial benzene off-centered above the facial benzene) is isoenergetic in zero-point-energy (ZPE) corrected binding energy (D0) to the displaced-stacked structure (vertical interplanar distance: 3.54 A). However, the T-shaped structure i...

Chemical identification of individual surface atoms by atomic force microscopy

Abstract: Dynamic force microscopy, which works by detecting the interaction force between the oscillating tip of an atomic force microscope (AFM) and a surface, has been refined to the extent that it can achieve true atomic resolution of insulator, semiconductor and metal surfaces. In a landmark publication in this issue this technique has been used to perform the chemical identification of individual atoms in a multi-element system. The method involves precise quantification of short-range chemical forces between the probed atoms and the AFM tip, and provides a robust and general recognition tool suitable for both cryogenic and room temperature environments. The cover shows a topographic image of a surface alloy made up of silicon (red), tin (blue), and lead atoms (green) in equal proportions on a silicon (111) substrate. This atomic identification method is relevant to a wide range of research areas such as catalysis, materials science and semiconductor technology. Scanning probe microscopy is a versatile and powerful method that uses sharp tips to image, measure and manipulate matter at surfaces with atomic resolution1,2. At cryogenic temperatures, scanning probe microscopy can even provide electron tunnelling spectra that serve as fingerprints of the vibrational properties of adsorbed molecules3,4,5 and of the electronic properties of magnetic impurity atoms6,7, thereby allowing chemical identification. But in many instances, and particularly for insulating systems, determining the exact chemical composition of surfaces or nanostructures remains a considerable challenge. In principle, dynamic force microscopy should make it possible to overcome this problem: it can image insulator, semiconductor and metal surfaces with true atomic resolution8,9,10, by detecting and precisely measuring11,12,13 the short-range forces that arise with the onset of chemical bonding between the tip and surface atoms14,15 and that depend sensitively on the chemical identity of the atoms involved. Here we report precise measurements of such short-range chemical forces, and show that their dependence on the force microscope tip used can be overcome through a normalization procedure. This allows us to use the chemical force measurements as the basis for atomic recognition, even at room temperature. We illustrate the performance of this approach by imaging the surface of a particularly challenging alloy system and successfully identifying the three constituent atomic species silicon, tin and lead, even though these exhibit very similar chemical properties and identical surface position preferences that render any discrimination attempt based on topographic measurements impossible.

Silybin and silymarin--new and emerging applications in medicine.

Abstract: This review critically surveys the literature published mainly within this millennium on the new and emerging applications of silybin (pure, chemically defined substance) and silymarin (flavonoid complex from Silybum marianum - milk thistle seeds). These compounds used so far mostly as hepatoprotectants were shown to have other interesting activities, e.g. anticancer and canceroprotective and also hypocholesterolemic activity. These effects were demonstrated in a large variety of illnesses of different organs, e.g. prostate, lungs, CNS, kidneys, pancreas and also in the skin protection. Besides the cytoprotective activity of silybin mediated by its antioxidative and radical-scavenging properties also new functions based on the specific receptor interaction were discovered. These were studied on the molecular level and modulation of various cell-signaling pathways with silybin was disclosed - e.g. NF-κ B, inhibition of EGFR-MAPK/ERK1/2 signaling, activity upon Rb and E2F proteins, IGF-receptor signaling. Proapoptotic activity of silybin in pre- and/or cancerogenic cells and anti-angiogenic activity of silybin are other important findings that bring silymarin preparations closer to respective application in the cancer treatment. Discovery of the inhibition and modulation of drug transporters, Pglycoproteins, estrogenic receptors, nuclear receptors by silybin and some of its new derivatives contribute further to the better understanding of silybin activity on the molecular level. Silymarin application in veterinary medicine is reviewed as well. Recent works using optically pure silybin diastereomers clearly indicate extreme importance of the use of optically active silybin namely in the receptor studies. Significance of silymarin and its components in the medicine is clearly indicated by an exponential growth of publications on this topic - over 800 papers in the last 5 years.

Energy loss and flow of heavy quarks in Au+Au collisions at sNN=200GeV

Abstract: The PHENIX experiment at the BNL Relativistic Heavy Ion Collider (RHIC) has measured electrons with 0.3 < p(T) < 9 GeV/c at midrapidity (y < 0.35) from heavy-flavor (charm and bottom) decays in Au + Au collisions at root s(NN) = 200 GeV. The nuclear modification factor R-AA relative to p + p collisions shows a strong suppression in central Au + Au collisions, indicating substantial energy loss of heavy quarks in the medium produced at RHIC energies. A large azimuthal anisotropy v(2) with respect to the reaction plane is observed for 0.5 < p(T) < 5 GeV/c indicating substantial heavy-flavor elliptic flow. Both R-AA and v(2) show a p(T) dependence different from those of neutral pions. A comparison to transport models which simultaneously describe R-AA(p(T)) and v(2)(p(T)) suggests that the viscosity to entropy density ratio is close to the conjectured quantum lower bound, i.e., near a perfect fluid.

Carbon-Supported Manganese Oxide Nanoparticles as Electrocatalysts for the Oxygen Reduction Reaction (ORR) in Alkaline Medium: Physical Characterizations and ORR Mechanism

Abstract: MnOx/C and Me-MnOx/C (Me = Ni, Mg) electrocatalysts prepared by chemical deposition of manganese oxide nanoparticles on carbon have been characterized by Transmission Electron Microscopy (TEM), X-ray Diffraction (XRD), and chemical analysis. Their Oxygen Reduction Reaction (ORR) kinetics and mechanism have been investigated in alkaline KOH solutions by using the Rotating Disk Electrode (RDE) and the Rotating Ring-Disk Electrode (RRDE) setups. Doping the MnOx/C nanoparticles with nickel or magnesium divalent cations can considerably improve their oxygen reduction activity. As a result, the Me-MnOx/C electrocatalysts exhibit ORR specific or mass activities close to the benchmark 10 wt % Pt/C from E-TEK. At low ORR current densities, the undoped MnOx/C electrocatalyst displays a reaction order with respect to PO2 and OH- of 1 and −0.5, respectively, while ∂E/∂log i is ca. −59 mV dec-1. The ORR reaction order toward OH- is unchanged with the magnesium doping, while it becomes −2 with the nickel doping. RRDE d...

J/psi production versus centrality, transverse momentum, and rapidity in Au+Au collisions at root S-NN=200 GeV

Abstract: The PHENIX experiment at the BNL Relativistic Heavy Ion Collider (RHIC) has measured J/psi production for rapidities -2.2 < y < 2.2 in Au+Au collisions at root s(NN)=200 GeV. The J/psi invariant yield and nuclear modification factor R-AA as a function of centrality, transverse momentum, and rapidity are reported. A suppression of J/psi relative to binary collision scaling of proton-proton reaction yields is observed. Models which describe the lower energy J/psi data at the CERN Super Proton Synchrotron invoking only J/psi destruction based on the local medium density predict a significantly larger suppression at RHIC and more suppression at midrapidity than at forward rapidity. Both trends are contradicted by our data.

Evolutionary and geographical history of the Leishmania donovani complex with a revision of current taxonomy

Abstract: Leishmaniasis is a geographically widespread severe disease, with an increasing incidence of two million cases per year and 350 million people from 88 countries at risk. The causative agents are species of Leishmania, a protozoan flagellate. Visceral leishmaniasis, the most severe form of the disease, lethal if untreated, is caused by species of the Leishmania donovani complex. These species are morphologically indistinguishable but have been identified by molecular methods, predominantly multilocus enzyme electrophoresis. We have conducted a multifactorial genetic analysis that includes DNA sequences of protein-coding genes as well as noncoding segments, microsatellites, restriction-fragment length polymorphisms, and randomly amplified polymorphic DNAs, for a total of ≈18,000 characters for each of 25 geographically representative strains. Genotype is strongly correlated with geographical (continental) origin, but not with current taxonomy or clinical outcome. We propose a new taxonomy, in which Leishmania infantum and L. donovani are the only recognized species of the L. donovani complex, and we present an evolutionary hypothesis for the origin and dispersal of the species. The genus Leishmania may have originated in South America, but diversified after migration into Asia. L. donovani and L. infantum diverged ≈1 Mya, with further divergence of infraspecific genetic groups between 0.4 and 0.8 Mya. The prevailing mode of reproduction is clonal, but there is evidence of genetic exchange between strains, particularly in Africa.

Non-covalent interactions in biomacromolecules

Abstract: Non-covalent interactions play an important role in chemistry, physics and especially in biodisciplines. They determine the structure of biomacromolecules such as DNA and proteins and are responsible for the molecular recognition process. Theoretical evaluation of interaction energies is difficult; however, perturbation as well as variation (supermolecular) methods are briefly described. Accurate interaction energies can be obtained by complete basis set limit calculations providing a large portion of correlation energy is covered (e.g. by performing CCSD(T) calculations). The role of H-bonding and stacking interactions in the stabilisation of DNA, oligopeptides and proteins is described, and the importance of London dispersion energy is shown.

Reactive oxygen species produced by NADPH oxidase are involved in pollen tube growth.

Abstract: Tip-localized reactive oxygen species (ROS) were detected in growing pollen tubes by chloromethyl dichlorodihydrofluorescein diacetate oxidation, while tip-localized extracellular superoxide production was detected by nitroblue tetrazolium (NBT) reduction. To investigate the origin of the ROS we cloned a fragment of pollen specific tobacco NADPH oxidase (NOX) closely related to a pollen specific NOX from Arabidopsis. Transfection of tobacco pollen tubes with NOX-specific antisense oligodeoxynucleotides (ODNs) resulted in decreased amount of NtNOX mRNA, lower NOX activity and pollen tube growth inhibition. The ROS scavengers and the NOX inhibitor diphenylene iodonium chloride (DPI) inhibited growth and ROS formation in tobacco pollen tube cultures. Exogenous hydrogen peroxide (H2O2) rescued the growth inhibition caused by NOX antisense ODNs. Exogenous CaCl2 increased NBT reduction at the pollen tube tip, suggesting that Ca2+ increases the activity of pollen NOX in vivo. The results show that tip-localized ROS produced by a NOX enzyme is needed to sustain the normal rate of pollen tube growth and that this is likely to be a general mechanism in the control of tip growth of polarized plant cells.

Transverse momentum and centrality dependence of high-pT nonphotonic electron suppression in Au+Au collisions at sNN=200GeV

Abstract: The STAR collaboration at the BNL Relativistic Heavy-Ion Collider (RHIC) reports measurements of the inclusive yield of nonphotonic electrons, which arise dominantly from semileptonic decays of heavy flavor mesons, over a broad range of transverse momenta (1.2

Gas-phase spectroscopy of biomolecular building blocks.

Abstract: Gas-phase spectroscopy lends itself ideally to the study of isolated molecules and provides important data for comparison with theory. In recent years, we have seen enormous progress in the study of biomolecular building blocks in the gas phase. The motivation for such work is threefold: (a) It is important to distinguish between intrinsic molecular properties and properties that result from the biological environment. (b) Gas-phase spectroscopy of clusters provides insights into fundamental interactions and into microsolvation. (c) Gas-phase data support quantum-chemical calculations. This review focuses on the current status of (poly)amino acids and DNA bases. Recent results help elucidate structure and hydrogen-bonded interactions, as well as showcase a successful interplay between theory and experiment.

Electron acceleration in the Van Allen radiation belts by fast magnetosonic waves

Abstract: [1] Local acceleration is required to explain electron flux increases in the outer Van Allen radiation belt during magnetic storms. Here we show that fast magnetosonic waves, detected by Cluster 3, can accelerate electrons between ∼10 keV and a few MeV inside the outer radiation belt. Acceleration occurs via electron Landau resonance, and not Doppler shifted cyclotron resonance, due to wave propagation almost perpendicular to the ambient magnetic field. Using quasi-linear theory, pitch angle and energy diffusion rates are comparable to those for whistler mode chorus, suggesting that these waves are very important for local electron acceleration. Since pitch angle diffusion does not extend into the loss cone, these waves, on their own, are not important for loss to the atmosphere. We suggest that magnetosonic waves, which are generated by unstable proton ring distributions, are an important energy transfer process from the ring current to the Van Allen radiation belts.

Preparation and properties of magnetic nano-and microsized particles for biological and environmental separations

Abstract: The paper presents a critical overview on magnetic nanoparticles and microspheres used as separation media in different fields of chemistry, biochemistry, biology, and environment protection. The preparation of most widely used magnetic iron oxides in appropriate form, their coating or encapsulation in polymer microspheres, and functionalization is discussed in the first part. In the second part, new developments in the main application areas of magnetic composite particles for separation and catalytical purposes are briefly described. They cover separations and isolations of toxic inorganic and organic ions, proteins, and other biopolymers, cells, and microorganisms. Only selected number of relevant papers could be included due to the restricted extent of the review.

Water surface is acidic.

Abstract: Water autoionization reaction 2H2O --> H3O- + OH- is a textbook process of basic importance, resulting in pH = 7 for pure water. However, pH of pure water surface is shown to be significantly lower, the reduction being caused by proton stabilization at the surface. The evidence presented here includes ab initio and classical molecular dynamics simulations of water slabs with solvated H3O+ and OH- ions, density functional studies of (H2O)(48)H+ clusters, and spectroscopic isotopic-exchange data for D2O substitutional impurities at the surface and in the interior of ice nanocrystals. Because H3O+ does, but OH- does not, display preference for surface sites, the H2O surface is predicted to be acidic with pH < 4.8. For similar reasons, the strength of some weak acids, such as carbonic acid, is expected to increase at the surface. Enhanced surface acidity can have a significant impact on aqueous surface chemistry, e.g., in the atmosphere.

Perspectives of Micro/Mesoporous Composites in Catalysis

Abstract: This article covers the recent development in the remarkably growing field of synthesis, characterization and particularly catalytic investigation of zeolite‐based materials combining micro‐ and mesoporous features. New synthetic approaches for preparation of micro/mesoporous composites including recrystallization of originally amorphous matter, utilization of nanocrystalline zeolite seeds and formation of mesoporous zeolite single crystals are the first focus of this article. The advantages and disadvantages of composite materials in comparison with pure micro‐ and mesoporous molecular sieves will be discussed, as well. The relevance of individual experimental techniques for analysis of the composites, i.e., their structure, porosity, chemical composition, morphological features, and so on, are described in the second section of the article. The last Section is focused on the application of micro/mesoporous composites and mesoporous zeolites as catalysts in acid‐catalyzed reactions, oxidation reactions a...