The competition between methyl viologen and monodehydroascorbate radical as electron acceptors in spinach thylakoids and intact chloroplasts

In spinach thylakoids prepared from intact chloroplasts by shocking in the presence of ascorbate to preserve the operation of ascorbate peroxidase, the rate of oxygen uptake with methyl viologen as acceptor decreased in response to the addition of H₂O₂. Such a decrease was not observed in the presence of KCN or when the thylakoids lost ascorbate peroxidase activity. Illumination of intact chloroplasts in the presence of H₂O₂ and methyl viologen showed an initial rate of oxygen exchange, which is intermediate between the initial rate of oxygen evolution in the presence of H₂O₂ alone and steady-state oxygen uptake in the presence of methyl viologen. The data showed that monodehydroascorbate radical generated in ascorbate peroxidase reaction could compete with methyl viologen for electrons supplied by the electron transport chain in both thylakoids and intact chloroplasts. During the illumination of intact chloroplasts the rate of oxygen uptake increased. The presence of nigericin swiftly led to steady-state oxygen uptake, and to a clear-cut 1:1 relationship between the electron transport rate estimated from fluorescence assay and the electron transport rate determined from oxygen uptake, taking the stoichiometry 1O₂:4e. The increase in oxygen uptake was attributed to the cessation of monodehydroascorbate radical generation brought about by consumption of intrachloroplast ascorbate in the peroxidase reactions, and the effects of nigericin were explained by acceleration of such consumption. The competition between methyl viologen and monodehydroascorbate radical in the intact chloroplasts was estimated under various conditions.     

DNA damage causes TP53-dependent coupling of self-renewal and senescence pathways in embryonal carcinoma cells

Comment on: Wu R, et al. Clin Cancer Res 2011; 17:7359–72     

Intracellular Neural Recording with Pure Carbon Nanotube Probes

The computational complexity of the brain depends in part on a neuron’s capacity to integrate electrochemical information from vast numbers of synaptic inputs. The measurements of synaptic activity that are crucial for mechanistic understanding of brain function are also challenging, because they require intracellular recording methods to detect and resolve millivolt- scale synaptic potentials. Although glass electrodes are widely used for intracellular recordings, novel electrodes with superior mechanical and electrical properties are desirable, because they could extend intracellular recording methods to challenging environments, including long term recordings in freely behaving animals. Carbon nanotubes (CNTs) can theoretically deliver this advance, but the difficulty of assembling CNTs has limited their application to a coating layer or assembly on a planar substrate, resulting in electrodes that are more suitable for in vivo extracellular recording or extracellular recording from isolated cells. Here we show that a novel, yet remarkably simple, millimeter-long electrode with a sub-micron tip, fabricated from self-entangled pure CNTs can be used to obtain intracellular and extracellular recordings from vertebrate neurons in vitro and in vivo. This fabrication technology provides a new method for assembling intracellular electrodes from CNTs, affording a promising opportunity to harness nanotechnology for neuroscience applications.     

Nucleus-independent chemical shift criterion for aromaticity in π-extended tetraoxa[8]circulenes

Recently synthesized π-extended symmetrical tetraoxa[8]circulenes that exhibit electroluminescent properties were calculated at the density functional theory (DFT) level using the quantum theory of atoms in molecules (QTAIM) approach to electron density distribution analysis. Nucleus-independent chemical shift (NICS) indices were used to characterize the aromaticity of the studied molecules. The tetraoxa[8]circulene molecules were found to consist of two antiaromatic perimeters (according to the Hückel “4n” antiaromaticity rule) that include 8 and 24 π-electrons. Conversely, NICS calculations demonstrated the existence of a common π-extended system (distributed like a flat ribbon) in the studied tetraoxa[8]circulene molecules. Thus, these symmetrical tetraoxa[8]circulene molecules provide examples of diatropic systems characterized by the presence of induced diatropic ring currents.

Ceruloplasmin: Macromolecular Assemblies with Iron-Containing Acute Phase Proteins

Copper-containing ferroxidase ceruloplasmin (Cp) forms binary and ternary complexes with cationic proteins lactoferrin (Lf) and myeloperoxidase (Mpo) during inflammation. We present an X-ray crystal structure of a 2Cp-Mpo complex at 4.7 Å resolution. This structure allows one to identify major protein–protein interaction areas and provides an explanation for a competitive inhibition of Mpo by Cp and for the activation of p-phenylenediamine oxidation by Mpo. Small angle X-ray scattering was employed to construct low-resolution models of the Cp-Lf complex and, for the first time, of the ternary 2Cp-2Lf-Mpo complex in solution. The SAXS-based model of Cp-Lf supports the predicted 1∶1 stoichiometry of the complex and demonstrates that both lobes of Lf contact domains 1 and 6 of Cp. The 2Cp-2Lf-Mpo SAXS model reveals the absence of interaction between Mpo and Lf in the ternary complex, so Cp can serve as a mediator of protein interactions in complex architecture. Mpo protects antioxidant properties of Cp by isolating its sensitive loop from proteases. The latter is important for incorporation of Fe³⁺ into Lf, which activates ferroxidase activity of Cp and precludes oxidation of Cp substrates. Our models provide the structural basis for possible regulatory role of these complexes in preventing iron-induced oxidative damage.     

Microbial Synthesis of Nanoparticles: Mechanisms,Characteristics, and Applications

Cadmium sulfide (CdS) and zinc sulfide (ZnS) biogenic nanoparticles (NPs) were produced by microbial synthesis using bacteria of different taxonomic groups: Gram-negative (Shewanella oneidensis MR-1) and Gram-positive (Bacillus subtilis 168) bacteria in a liquid medium under aerobic conditions in the presence of salts of the respective metals and sulfur. It was shown that the stabilization of nanoparticles in aqueous suspensions is due to the presence of certain protein molecules of the outer membrane of cells, that is, proteins of the families of various receptors, porins, and flagellin, on the nanoparticle (NP) surface. The effect of the protein coating on stability, luminescence, zeta-potential, hydrodynamics diameter and other physiochemical characteristics of nanoparticles was studied. Decolorization of methylene blue dye under the exposure to UV irradiation was used as a model to demonstrate the photocatalytic properties of NPsCdS. This opens the possibility of using biogenic nanoparticles in photocatalysis for industrial wastewater treatment.

     

In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes

DNA methylation is one of the most important epigenetic alterations involved in the control of gene expression. Bisulfite sequencing of genomic DNA is currently the only method to study DNA methylation patterns at single-nucleotide resolution. Hence, next-generation sequencing of bisulfite-converted DNA is the method of choice to investigate DNA methylation profiles at the genome-wide scale. Nevertheless, whole genome sequencing for analysis of human methylomes is expensive, and a method for targeted gene analysis would provide a good alternative in many cases where the primary interest is restricted to a set of genes.Here, we report the successful use of a custom Agilent SureSelect Target Enrichment system for the hybrid capture of bisulfite-converted DNA. We prepared bisulfite-converted next-generation sequencing libraries, which are enriched for the coding and regulatory regions of 174 ADME genes (i.e. genes involved in the metabolism and distribution of drugs). Sequencing of these libraries on Illumina’s HiSeq2000 revealed that the method allows a reliable quantification of methylation levels of CpG sites in the selected genes, and validation of the method using pyrosequencing and the Illumina 450K methylation BeadChips revealed good concordance.     

Eye movements in the process of reading as an indicator of development of reading skill

The parameters of oculomotor activity were investigated using the video recording method when texts of different complexity were read by pupils with various reading skill levels. The parameters of eye movements and their determination have been described. It has been shown that the total reading time, the average duration of fixations, and the total number of regressions decrease, and the amplitude of progressive and regressive saccades increases as the reading skill is formed, which testifies to the perfection of the mechanisms of implementing the cognitive processes that form the basis of reading.     

Early Miocene herpetofaunas from the Greek localities of Aliveri and Karydia – bridging a gap in the knowledge of amphibians and reptiles from the early Neogene of southeastern Europe

Abstract

We here describe new remains of amphibians and reptiles from the early Miocene (MN 4) of two different Greek localities, Aliveri and Karydia. The newly described material consists of urodelans, alytids, indeterminate anurans, turtles, crocodylians, lacertids, indeterminate scincomorphs, anguids, colubrids, viperids, and indeterminate snakes. The presence of the frog Latonia cf. gigantea in Greece is documented for the first time. Additionally, the presence of viperids in Aliveri implies a much wider distribution for these snakes during the early Miocene of Europe. Of special interest is the presence of a peculiar colubrid that seems to possess a hitherto unknown vertebral structure, which is herein defined as the ‘paracentral ridge’. Although incomplete, the new material has important taxonomic and biogeographic implications, as it enhances our understanding of southeastern European herpetofaunas from the early Miocene, a time period that was characterised by major dispersal and extinction events and climatic change that affected the whole continent.