A functionally defined model for the M2 proton channel of influenza A virus suggests a mechanism for its ion selectivity

The M2 protein from influenza A virus forms proton-selective channels that are essential to viral function and are the target of the drug amantadine. Cys scanning was used to generate a series of mutants with successive substitutions in the transmembrane segment of the protein, and the mutants were expressed in Xenopus laevis oocytes. The effect of the mutations on reversal potential, ion currents, and amantadine resistance were measured. Fourier analysis revealed a periodicity consistent with a four-stranded coiled coil or helical bundle. A three-dimensional model of this structure suggests a possible mechanism for the proton selectivity of the M2 channel of influenza virus.

Enzymatic reaction with unnatural substrates: DNA photolyase (Escherichia coli) recognizes and reverses thymine [2+2] dimers in the DNA strand of a DNA/PNA hybrid duplex

Peptide nucleic acids (PNA) are mimics with normal bases connected to a pseudopeptide chain that obey Watson–Crick rules to form stable duplexes with itself and natural nucleic acids. This has focused attention on PNA as therapeutic or diagnostic reagents. Duplexes formed with PNA mirror some but not all properties of DNA. One fascinating aspect of PNA biochemistry is their reaction with enzymes. Here we show an enzyme reaction that operates effectively on a PNA/DNA hybrid duplex. A DNA oligonucleotide containing a cis, syn-thymine [2+2] dimer forms a stable duplex with PNA. The hybrid duplex is recognized by photolyase, and irradiation of the complex leads to the repair of the thymine dimer. This finding provides insight into the enzyme mechanism and provides a means for the selective repair of thymine photodimers.

Selective Perturbation of Apical Membrane Traffic by Expression of Influenza M2, an Acid-activated Ion Channel, in Polarized Madin–Darby Canine Kidney Cells

The function of acidification along the endocytic pathway is not well understood, in part because the perturbants used to modify compartmental pH have global effects and in some cases alter cytoplasmic pH. We have used a new approach to study the effect of pH perturbation on postendocytic traffic in polarized Madin–Darby canine kidney (MDCK) cells. Influenza M2 is a small membrane protein that functions as an acid-activated ion channel and can elevate the pH of the trans-Golgi network and endosomes. We used recombinant adenoviruses to express the M2 protein of influenza virus in polarized MDCK cells stably transfected with the polymeric immunoglobulin (Ig) receptor. Using indirect immunofluorescence and immunoelectron microscopy, M2 was found to be concentrated at the apical plasma membrane and in subapical vesicles; intracellular M2 colocalized partly with internalized IgA in apical recycling endosomes as well as with the trans-Golgi network marker TGN-38. Expression of M2 slowed the rate of IgA transcytosis across polarized MDCK monolayers. The delay in transport occurred after IgA reached the apical recycling endosome, consistent with the localization of intracellular M2. Apical recycling of IgA was also slowed in the presence of M2, whereas basolateral recycling of transferrin and degradation of IgA were unaffected. By contrast, ammonium chloride affected both apical IgA and basolateral transferrin release. Together, our data suggest that M2 expression selectively perturbs acidification in compartments involved in apical delivery without disrupting other postendocytic transport steps.

A single gene of chloroplast origin codes for mitochondrial and chloroplastic methionyl–tRNA synthetase in Arabidopsis thaliana

One-fifth of the tRNAs used in plant mitochondrial translation is coded for by chloroplast-derived tRNA genes. To understand how aminoacyl–tRNA synthetases have adapted to the presence of these tRNAs in mitochondria, we have cloned an Arabidopsis thaliana cDNA coding for a methionyl–tRNA synthetase. This enzyme was chosen because chloroplast-like elongator tRNAMet genes have been described in several plant species, including A. thaliana. We demonstrate here that the isolated cDNA codes for both the chloroplastic and the mitochondrial methionyl–tRNA synthetase (MetRS). The protein is transported into isolated chloroplasts and mitochondria and is processed to its mature form in both organelles. Transient expression assays using the green fluorescent protein demonstrated that the N-terminal region of the MetRS is sufficient to address the protein to both chloroplasts and mitochondria. Moreover, characterization of MetRS activities from mitochondria and chloroplasts of pea showed that only one MetRS activity exists in each organelle and that both are indistinguishable by their behavior on ion exchange and hydrophobic chromatographies. The high degree of sequence similarity between A. thaliana and Synechocystis MetRS strongly suggests that the A. thaliana MetRS gene described here is of chloroplast origin.

Tetrodotoxin-resistant Na+ currents and inflammatory hyperalgesia

Several mechanisms have been identified that may underlie inflammation-induced sensitization of high-threshold primary afferent neurons, including the modulation of voltage- and Ca2+-dependent ion channels and ion channels responsible for the production of generator potentials. One such mechanism that has recently received a lot of attention is the modulation of a tetrodotoxin (TTX)-resistant voltage-gated Na+ current. Evidence supporting a role for TTX-resistant Na+ currents in the sensitization of primary afferent neurons and inflammatory hyperalgesia is reviewed. Such evidence is derived from studies on the distribution of TTX-resistant Na+ currents among primary afferent neurons and other tissues of the body that suggest that these currents are expressed only in a subpopulation of primary afferent neurons that are likely to be involved in nociception. Data from studies on the biophysical properties of these currents suggest that they are ideally suited to mediate the repetitive discharge associated with prolonged membrane depolarizations. Data from studies on the effects of inflammatory mediators and antinociceptive agents on TTX-resistant Na+ currents suggest that modulation of these currents is an underlying mechanism of primary afferent neuron sensitization. In addition, the second-messenger pathways underlying inflammatory mediator-induced modulation of these currents appear to underlie inflammatory mediator-induced hyperalgesia. Finally, recent antisense studies have also yielded data supporting a role for TTX-resistant Na+ currents in inflammatory hyperalgesia. Although data from these studies are compelling, data presented at the Neurobiology of Pain colloquium raised a number of interesting questions regarding the role of TTX-resistant Na+ currents in inflammatory hyperalgesia; implications of three of these questions are discussed.

Oxygen supply and oxygen-dependent gene expression in differentiating embryonic stem cells.

Blastocyst-derived pluripotent mouse embryonic stem cells can differentiate in vitro to form so-called embryoid bodies (EBs), which recapitulate several aspects of murine embryogenesis. We used this in vitro model to study oxygen supply and consumption as well as the response to reduced oxygenation during the earliest stages of development. EBs were found to grow equally well when cultured at 20% (normoxia) or 1% (hypoxia) oxygen during the first 5 days of differentiation. Microelectrode measurements of pericellular oxygen tension within 13- to 14-day-old EBs (diameter 510-890 micron) done at 20% oxygen revealed efficient oxygenation of the EBs' core region. Confocal laser scanning microscopy analysis of EBs incubated with fluorescent dyes that specifically stain living cells confirmed that the cells within an EB were viable. To determine the EBs' capability to sense low oxygen tension and to specifically respond to low ambient oxygen by modulating gene expression we quantified aldolase A and vascular endothelial growth factor (VEGF) mRNAs, since expression of these genes is upregulated by hypoxia in a variety of cells. Compared with the normoxic controls, we found increased aldolase A and VEGF mRNA levels after exposing 8- to 9-day-old EBs to 1% oxygen. We propose that EBs represent a powerful tool to study oxygen-regulated gene expression during the early steps of embryogenesis, where the preimplantation conceptus resides in a fluid environment with low oxygen tension until implantation and vascularization allow efficient oxygenation.

Primary structure and functional expression of a cGMP-gated potassium channel.

Cyclic nucleotides modulate potassium (K) channel activity in many cells and are thought to act indirectly by inducing channel protein phosphorylation. Herein we report the isolation from rabbit of a gene encoding a K channel (Kcn1) that is specifically activated by cGMP and not by cAMP. Analysis of the deduced amino acid sequence (725 amino acids) indicates that, in addition to a core region that is highly homologous to Shaker K channels, Kcn1 also contains a cysteine-rich region similar to that of ligand-gated ion channels and a cyclic nucleotide-binding region. Northern blot analysis detects gene expression in kidney, aorta, and brain. Kcn1 represents a class of K channels that may be specifically regulated by cGMP and could play an important role in mediating the effects of substances, such as nitric oxide, that increase intracellular cGMP.

Coordinate regulation of Bacillus subtilis peroxide stress genes by hydrogen peroxide and metal ions.

The Bacillus subtilis mrgA gene encodes an abundant DNA-binding protein that protects cells against the lethal effects of H2O2. Transcription of mrgA is induced by H2O2 or by entry into stationary phase when manganese and iron levels are low. We have selected for strains derepressed for transcription of mrgA in the presence of Mn(II). The resulting cis-acting mutants define an operator site just upstream of the mrgA promoter. Similar sequences flank the promoters for the catalase gene, katA, and the heme biosynthesis operon, hemAXCDBL. Like mrgA, transcription of the katA and hem genes is repressed by Mn(II), which thereby potentiates the killing action of H2O2. We identified two classes of trans-acting mutants derepressed for mrgA transcription in the presence of Mn(II): some exhibit a coordinate derepression of MrgA, catalase, heme biosynthesis, and alkyl hydroperoxide reductase and are H2O2 resistant, while others have reduced catalase activity and are H2O2 sensitive. These data indicate that the peroxide stress response of B. subtilis is regulated by a repressor that senses both metal ion levels and H2O2.

Potencial dos biflavonóides de Araucaria angustifolia (Bert.) O. Kuntze como antioxidantes e fotoprotetores

A Araucaria angustifolia é uma conífera endêmica das regiões sul e sudeste do Brasil sendo considerada uma espécie em extinção devido ao extenso extrativismo madeireiro. Atualmente, existem inúmeros projetos visando o reflorestamento e o uso sustentável deste pinheiro. Em vista destes pontos, o estudo das propriedades dos componentes das folhas com o intuito da utilização destes com fins comerciais tornou-se de extrema importância. As suas folhas foram submetidas à extração com solventes e foram identificados seis biflavonóides majoritários, dentre estes a amentoflavona e a ginkgetina, que são apontados como agentes contra inflamações e artrites. A fração rica de biflavonóides (BFF) extraída da araucaria foi testada frente a sua atividade em proteger contra danos em biomoléculas provocadas por espécies reativas de oxigênio, capacidade em quelar metais e proteção contra raios UV. A capacidade do BFF em proteger contra danos provocados por espécies reativas de oxigênio foi comparado com compostos conhecidamente antioxidantes, como o α-tocoferol, Trolox®, quercetina, rutina e com padrões de biflavonóides, a amentoflavona e ginkgetina. O BFF demonstrou que possui uma constante de supressão do 1O2 (50 x 106 M-1s-1), superior ao da quercetina (9 x 106 M-1s-1) e foi o mais eficiente na proteção contra quebras de simples fita em DNA plasmidial, provocado por esta espécie reativa. Ainda em relação à proteção de DNA plasmidial o BFF foi capaz de proteger também contra estes danos provocados através da reação de Fenton, apesar de não demonstrar a mesma eficiência da quercetina que mostrou ser um potente protetor destes danos. O BFF protegeu contra lipoperoxidação em lipossomos de fosfatidilcolina induzida por raios UV e reação de Fenton. Em análises realizadas com espectrometria de massas foi observada a formação de complexos destes biflavonóides com íons metálicos como ferro, cobre e alumínio que possuem um papel importante na formação de radicais livres. Em relação à capacidade fotoprotetora do BFF, este inibiu a formação de dímeros de pirimidina que são apontados como causadores de câncer de pele induzidos, principalmente por radiação UV-B. Esta ação protetora foi superior àquela conferida ao p-metoxicinamato de octila, um conhecido fotoprotetor. Com o intuito de permitir a solubilização do BFF em soluções aquosas e assim, avaliar a ação do BFF em células, incorporou-se o BFF em ciclodextrina. Essa inclusão favoreceu a incorporação de BFF em células CV1-P na concentração aproximada de 0,4 µg/ml após 24 horas de incubação. Essa concentração incorporada não demonstrou ser tóxica para as células no teste com MTT. Assim, o BFF tem despertado grande interesse em relação ao seu potencial na utilização nas mais variadas áreas como cosmética, alimentos e fitoterápicos.

Color representation and interpretation of special effect coatings

A representation of the color gamut of special effect coatings is proposed and shown for six different samples, whose colors were calculated from spectral bidirectional reflectance distribution function (BRDF) measurements at different geometries. The most important characteristic of the proposed representation is that it allows a straightforward understanding of the color shift to be done both in terms of conventional irradiation and viewing angles and in terms of flake-based parameters. A different line was proposed to assess the color shift of special effect coatings on a*,b*-diagrams: the absorption line. Similar to interference and aspecular lines (constant aspecular and irradiation angles, respectively), an absorption line is the locus of calculated color coordinates from measurement geometries with a fixed bistatic angle. The advantages of using the absorption lines to characterize the contributions to the spectral BRDF of the scattering at the absorption pigments and the reflection at interference pigments for different geometries are shown.

Chemical observations in the Red Sea and the inner Gulf of Aden during the International Indian Ocean Expedition 1964/65

The Red Sea has a special place among the adjacent seas of the world. High evaporation, exclusion of its deep water from contact with the Indian Ocean proper and complete absence of continental drainage may result special conditions of the chemistry of the Red Sea. This paper aims to describe and explain the peculiarity of the hydrochemical situation. The influence of the topography, of the inflow and outflow through the straights of Bab el Mandeb, of the evaporation, of the stability of the water layers, and of the circulation will be studied. An attempt is made to estimate the apparent oxygen ultilisation in order to obtain an indication of the biological activity. A further attempt is made toward the quantitative estimation of the circulation of the nutrients and also to obtain some information about transport, dissolution, and precipitation of calcium carbonate. The basis of these investigations are mainly observations of R. V. "Meteor" during the International Indian Ocean Expedition 1964/65. The determination of dissolved oxygen, dissolved inorganic phosphate, nitrate, nitrite, ammonia, pH, alkalinity, silicate as well as salinity and temperature forms the necessary basis for such an investigation of the chemical conditions. In the first chapter the methods and some modifications for the determination of the chemical properties as applied during the I.I.O.E. cruise of R. V. "Meteor" are described. The new methods, as worked out and tested under sea going conditions during several years by the author, are described in more detail. These are the methods for nitrate, silicate, the automatic determination of dissolved inorganic phosphate and silicate, the automated determination of total phosphorus, the in situ recording of the oxygen tension, and the modification for the determination of ammonia, calcium, and dissolved oxygen. With these revised methods more than 18,000 determinations have been carried out during the Indian Ocean cruise. The complete working up of the chemical data of the Indian Ocean Expedition of R. V. "Meteor" is devided into four sections: Contributions 1) to the Chemistry of the Red Sea and the Inner Gulf of Aden, 2) to the Gulf of Aden and the Somali Coast Region, 3) to the Western Indian Coast Region, and 4) to the Persian Gulf and the Straits of Oman. This paper presents the first contribution. The special hydrographical conditions are discussed. It can be shown, that the increase of salinity in the surface waters from the south to the north of the Red Sea is only to about 30 % due to evaporation. The remaining increase is presumed to be due to the admixture of deep water to the surface layers. A special rate for the consumption of oxygen (0.114 ml/ l/a) is derived for the deep water of the Red Sea at 1500 m. Based upon the distribution of the dissolved oxygen along the axii of the Red Sea, a chematic model for the longitudinal circulation of the Red Sea is constructed. This model should be considered as a first approximation and may explain the special distribution of phosphate, nitrate, and silicate. Based upon the evaluation of the residence time of the deep water a dissolution rate for silicate is estimated as 1 mygat/a. It seems possible to calculate residence times of water masses outside the Red Sea from the silicate content. The increase of silicate and the consumption of oxygen lead to residence times of the water below the thermocine of 30 to 48 years. The distribution of oxygen in the Straits of Bab el Mandeb is described and discussed. The rate of consumption of the oxygen in the outflowing Red Sea water is estimated to 8.5 ml/ l/a. This rather high rate is explained with reference to the special conditions in the outflowing water. The Red Sea water is characterized initially by a relative high content of oxygen and a low content of nutrients. The increase in nutrients and the decrease in the oxygen content is a secondary process of the Red Sea water on its way to the Arabian Sea. Based upon the vertical distribution of the dissolved inorganic phosphate vertical exchange coefficients of 1 - 4 g/cm/sec and vertical current speeds of 10**-5 to 10**-4 cm/sec are calculated for some stations in the Red Sea. The distribution of phosphate, silicate, nitrate, nitrite and ammonia for the Red Sea and the Straits of Bab el Mandeb are discussed. The special circulation is evaluated and the balance of the nutrients is estimated by means of the brutto transport. The nutrient deficit is assumed to be balanced by sporadic inflow of intermediate water from the Gulf of Aden. An example for such an inflow has been observed and is demonstrated. The silicate-salinity relationships are a suitable way for characterizing water masses in the Red Sea. Equations for the calculation of the different components from the carbonate system, the ion activities, and the calcium carbonate saturation are evaluated. The influence of temperature and pressure is taken into account. The carbonate saturation is calculated from the determined concentrations of calcium, alkalinity, and the hydrogen ion activity. Saturation values of 320 % are found for the surface layer and of 100% ± 1 for the deep water. The extraordinary equilibrium conditions may explain the constant Ca/Cl ratio and also the sedimentation of undissolved carbonate skelecons even in greater depths. A main sedimentation rate of 2 * 10**-3cm/year is evaluated from a total sedimentation of 10 * 106 to/a of calcium carbonate in the Red Sea. The appendix contains those data, which are not published in the data volume of the I.I.O.E. expedition of R. V. "Meteor".

Vertical profiles of environmental parameters measured from physical, optical and imaging sensors during Tara Oceans expedition 2009-2013

The present data publication provides permanent links to original and updated versions of validated data files. The data files include properties of seawater, particulate matter and dissolved matter from physical, optical and imaging sensors mounted on a vertical sampling system (Rosette) used during the 2009-2013 tara Oceans Expedition. It comprised 2 pairs of conductivity and temperature sensors (SEABIRD components), and a complete set of WEtLabs optical sensors, including chrorophyll and CDOM fluorometers, a 25 cm transmissiometer, and a one-wavelength backscatter meter. In addition, a SATLANTIC ISUS nitrate sensor and a Hydroptic Underwater Vision Profiler (UVP) were mounted on the rosette. In the Arctic Ocean and Arctic Seas (2013), a second oxygen sensor (SBE43) and a four frequency Aquascat acoustic profiler were added. The system was powered on specific Li-Ion batteries and data were self-recorded at 24HZ. Sensors have all been factory calibrated before, during and after the four year program. Oxygen was validated using climatologies (WOA09). Nitrate and Fluorescence data were adjusted with discrete measurements from Niskin bottles mounted on the Rosette, and optical darks were performed monthly on board. A total of 839 quality checked vertical profiles were made during the tara Oceans expedition 2009-2013.

Major and trace element composition of clinopyroxenes from an olivine gabbro of ODP Hole 176-735B (Table 1)

Major and trace element profiles of clinopyroxene grains in oceanic gabbros from ODP Hole 735B have been investigated by a combined in situ analytical study with ion probe, and electron microprobe. In contrast to the homogeneous major element compositions, trace elements (REE, Y, Cr, Sr, and Zr) show continuous core to rim zoning profiles. The observed trace element systematics in clinopyroxene cannot be explained by a simple diffusive exchange between melts and gabbros along grain boundaries. A simultaneous modification of the melt composition is required to generate the zoning, although Rayleigh fractional crystallization modelling could mimic the general shape of the profiles. Simultaneous metasomatism between the cumulate crystal and the porous melt during crystal accumulation is the most likely process to explain the zoning. Deformation during solidification of the crystal mush could have caused squeezing out of the incompatible element enriched residual melts (interstitial liquid). Migration of the melt along grain boundaries might carry these melt out of the system. This process named as synkinematic differentiation or differentiation by deformation (Natland and Dick, 2001, doi:10.1016/S0377-0273(01)00211-6) may act as an important magma evolution mechanism in the oceanic crust, at least at slow-spreading ridges.

(Table A1) CaCO3 contents and Sr/Ca ratios in ODP Leg 130, 138 and 154

Strontium/calcium (Sr/Ca) ratios in bulk and foraminiferal calcite have been used to constrain the history of Sr/Ca in the oceans and to evaluate calcite diagenetic alteration. However bulk Sr/Ca records also may be influenced by differences in Sr uptake and/or in the diagenetic susceptibility of different calcium carbonate sedimentary components. We present data on the sediment size fraction and calcium carbonate distribution in bulk samples, Sr/Ca in a range of sedimentary size components, and Sr/Ca in bulk sediments. Ocean Drilling Program samples from sites on Ontong Java Plateau and Ceara Rise (in the western equatorial Pacific and Atlantic, respectively) and from sites in the eastern equatorial Pacific were selected to represent progressive stages in the diagenetic pathway from the sea floor through a range of burial depths equivalent to sediment ages of ~5.6, ~9.4, and ~37.1 Ma. Samples were subdivided by size to produce a unique data set of size-specific Sr/Ca ratios. Fine fraction (<45 ?m) Sr/Ca ratios are higher than those of all corresponding coarse fractions, indicating that fine nannofossil-dominated calcite has a Sr partition coefficient 1.3-1.5 times greater than that of coarse foraminifera-dominated calcite. Thus, absolute values of bulk Sr/Ca in contemporaneous samples reflect, in part, the ratio of fine to coarse calcite sedimentary components. Sr/Ca values in fine and coarse components also behave differently in their response to pre-burial dissolution and to recrystallization at depth. Coarse size components are sensitive to bottom water carbonate ion undersaturation, and they lose original Sr/Ca differences among contemporary samples over not, vert, similar10 my. In contrast, fine components recrystallize faster in more deeply buried samples. Interpretation of the historical Sr/Ca record is complicated by post-depositional diagenetic artifacts, and thus our data do not provide clear evidence of specific temporal changes in oceanic Sr/Ca ratios over the past 10 million years. This paper represents the first systematic attempt to examine trends in calcite Sr/Ca as a function of sediment size fraction and age.

Irradiation testing of UO₂ : a literature search /

Included are 167 references to unclassified reports and scientific journals on irradiation testing of unalloyed UO₂. Irradiation behavior and effects, heat transfer calculations, fission gas release, post-irradiation examination, and irradiation capsule design are the subject areas covered.