A high pressure cell for dynamic light scattering up to 2kbars with conservation of plane of polarization

We report on a high pressure cell with six optical windows which can be used up to 2 kbars for laser light scattering applications at scattering angles of 45 degrees , 90 degrees , and 135 degrees of liquid samples in a temperature range between -20 and 150 degrees C. The pressure transmitting medium is compressed nitrogen. The window material used is SF57 NSK, a glass with an extremely low stress optical coefficient in the order of about 10(-5) which allows thus to maintain the plane of polarization even under the action of high pressure. In order to demonstrate the functioning of the cell we show Rayleigh-Brillouin spectra of poly(methylphenylsiloxane) at different polarizations and pressures

Waves of genomic hitchhikers shed light on the evolution of gamebirds (Aves: Galliformes) : research article

Background The phylogenetic tree of Galliformes (gamebirds, including megapodes, currassows, guinea fowl, New and Old World quails, chicken, pheasants, grouse, and turkeys) has been considerably remodeled over the last decades as new data and analytical methods became available. Analyzing presence/absence patterns of retroposed elements avoids the problems of homoplastic characters inherent in other methodologies. In gamebirds, chicken repeats 1 (CR1) are the most prevalent retroposed elements, but little is known about the activity of their various subtypes over time. Ascertaining the fixation patterns of CR1 elements would help unravel the phylogeny of gamebirds and other poorly resolved avian clades. Results We analyzed 1,978 nested CR1 elements and developed a multidimensional approach taking advantage of their transposition in transposition character (TinT) to characterize the fixation patterns of all 22 known chicken CR1 subtypes. The presence/absence patterns of those elements that were active at different periods of gamebird evolution provided evidence for a clade (Cracidae + (Numididae + (Odontophoridae + Phasianidae))) not including Megapodiidae; and for Rollulus as the sister taxon of the other analyzed Phasianidae. Genomic trace sequences of the turkey genome further demonstrated that the endangered African Congo Peafowl (Afropavo congensis) is the sister taxon of the Asian Peafowl (Pavo), rejecting other predominantly morphology-based groupings, and that phasianids are monophyletic, including the sister taxa Tetraoninae and Meleagridinae. Conclusions The TinT information concerning relative fixation times of CR1 subtypes enabled us to efficiently investigate gamebird phylogeny and to reconstruct an unambiguous tree topology. This method should provide a useful tool for investigations in other taxonomic groups as well

Unexpected Effect of Internal Degrees of Freedom on Transverse Phonons in Supercooled Liquids

We show experimentally that in a supercooled liquid composed of molecules with internal degrees of freedom the internal modes contribute to the frequency dependent shear viscosity and damping of transverse phonons, which results in an additional broadening of the transverse Brillouin lines. Earlier, only the effect of internal modes on the frequency dependent bulk viscosity and damping of longitudinal phonons was observed and explained theoretically in the limit of weak coupling of internal degrees of freedom to translational motion. A new theory is needed to describe this new effect. We also demonstrate, that the contributions of structural relaxation and internal processes to the width of the Brillouin lines can be separated by measurements under high pressure

Morphologie einiger Zweigsänger (Aves: Sylviidae) Nordasiens

Morphologische Daten von Zweigsängern Sylviidae sind nur spärlich publiziert. Basierend auf Beringungstätigkeit in drei Regionen Nordasiens (Ussurien, Baikalsee und Zentralkasachstan) präsentieren wir Flügellängen, Teilfederlängen der achten Handschwinge, Tarsuslängen, Schwanzlängen und Gewichtsmessungen von 27 Zweigsängerarten aus 6 Gattungen. Außerdem zeigen wir flügelmorphologische Profile basierend auf Einzelfedermessungen des Handflügels für 15 Arten aus 5 Gattungen. Von allen untersuchten Arten zeigte der Koreabuschsänger Cettia canturians den rundesten Handflügel, während der Wanderlaubsänger Phylloscopus borealis den spitzesten Handflügel (mit langen Handschwingen 6-8) zeigte. Für einige Arten waren Tests auf Unterschiede in den Messwerten zwischen den Regionen möglich. Wander- und Dunkellaubsänger Phylloscopus fuscatus unterschieden sich nicht zwischen den Fangorten, während am Baikalsee gefangene Gelbbrauenlaubsänger Phylloscopus inornatus kleiner, aber schwerer waren als Individuen aus Ussurien. Auch Klappergrasmücken Sylvia curruca unterschieden sich in Tarsus- und Schwanzlängen, aber nicht in Flügelmorphologie zwischen den Fangregionen Baikalsee und Zentralkasachstan. Die präsentierten Ergebnisse zeigen, wie innerhalb relativ kurzer Fangzeiträume interessante morphologische Daten gesammelt werden können.Data on the morphology of warblers belonging to the family Sylviidae have only scarcely been published. Here we present data on maximum wing chord, length of the 8th primary, tarsus length, tail length and body weight of 27 species (from 6 genera) of Sylviidae. The data are based on ringing activities in three regions of Northern Eurasia (Ussuriland, Lake Baikal and Central Kazakhstan). For 15 species (from 5 genera) we also show wing tip profiles based on measurement of individual feathers of the outer wing. Of all species studied, the Korean Bush Warbler Cettia canturians showed the bluntest wing tip, while the arctic warbler Phylloscopus borealis showed the most pointed wing (with long primaries 6-8). For a number of species we compared morphological measurements between regions. Arctic and Dusky Warblers Phylloscopus fuscatus did not differ in measurements between sites, while Yellow-browed Warblers Phylloscopus inornatus caught at Lake Baikal were smaller but heavier than individuals caught in Ussuriland. Furthermore, Lesser Whitethroats Sylvia curruca differed in tarsus and tail length, but not in wing morphology between Lake Baikal and Central Kazakhstan. The results show how interesting morphological data can be collected within relative short periods of ringing activity

Charakterisierung der gravitropen Signaltransduktionin <i>Helianthus annuus</i> L. über Genexpressionsanalysen nach Auxin-und Gravistimulation

Die gravitrope Krümmungsreaktion in höheren Pflanzen als Antwort auf eine veränderte Orientierung zum gegebenen Schwerkraftvektor ist geprägt von einer asymmetrischen Verteilung des Pflanzenwuchsstoffes Auxin. Daher scheint Auxin ein wichtiges Element in der Signalweiterleitung des Schwerkraftreizes vom Ort der Schwerkraftwahrnehmung bis zum Ort der gravitropen Antwort zu sein. Auf molekularer Ebene ist die Signaltransduktion allerdings noch weitgehend ungeklärt. Ziel dieser Arbeit war es daher, die gravitrop regulierten Prozesse auf der Basis differentiell exprimierter Gene zu analysieren. In einem parallelen Versuchsansatz anhand gravistimulierter und Auxin-stimulierter Pflanzen wurde der Zusammenhang von Auxin im Gravitropismus bzw. die Abhängigkeit der gravitrop regulierten Gene von Auxin untersucht. Die Gravistimulationsexperimente erfolgten durch Kippen sieben Tage alter Sonnenblumenhypokotyle um 45°, während die Auxinstimulation durch Applikation von Indol-3-Essigsäure an Hypokotylprotoplasten vorgenommen wurde. Aufgrund der stärkeren Krümmungsreaktion sowie der höheren Auxin-abhängigen PM/H+-ATPase-Aktivität im apika-len Hypokotylabschnitt wurden die Hypokotyle in den jeweiligen Experimenten in einen apikalen und basalen Bereich unterteilt, um eine detailliertere Bestimmung des gravisensitiven Pflanzengewebes zu gewährleisten. Für die Genexpressionsanalysen wurde die Methode der Differential Display (DD)-RT-PCR herangezogen, die einen Vergleich zwischen mehreren Populationen gleichzeitig erlaubt, ohne die vorherige Kenntnis der zu untersuchenden Gensequenzen vorauszusetzen. Dabei basiert die Technik auf der Amplifikation von cDNA-Fragmenten unterschiedlicher Länge mittels Zufallsprimer. Die Auftrennung der Fragmente zur Identifizierung differentieller Expressionsraten erfolgte anschließend mit einer Kapillarelektrophorese (ABI310). Nach der Gravistimulation konnten fünf Gene isoliert werden, die in ihrer Expression jeweils gravitrop hochreguliert wurden. Dazu gehörten die GTPase Ran, eine Calcium-abhängige Proteinkinase, das Histon H2B, Cytochrom c und eine Xylosyltransferase. Nach der Auxinstimulation konnten vier Gene isoliert werden, die eine herunterregulier-te Expression zeigten. Hierzu gehörten der Translations-Initiations-Faktor eIF1, eine Histondeacetylase, das Histon H3 sowie eine Fruktose-1,6-bisphosphat Aldolase. Ein Vergleich in Bezug auf die Induzierbarkeit der identifizierten Gene durch Auxin und Gravistimulation zeigte für Ran und eIF1 eine negative Korrelation und für Cytochrom c und die Xylosyltransferase eine positive Korrelation. Durch die Segmentierung der Sonnenblumenhypokotyle konnte anhand der Verteilung der differentiell exprimierten Gene sowie der Rate der Transkriptionsänderung der apikale Hypokotylbereich als das sensitivere Gewebe erkannt werden. Die Genexpression wurde neben der Gravistimulation von ganzen Hypokotylen ebenfalls in Hypokotylprotoplasten unter simulierten und realen Mikrogravitationsbedingungen untersucht. Dadurch konnte gezeigt werden, dass sowohl die Umorientierung nach Kippen der Pflanzen als auch die Bedingungen unter Mikrogravitation dieselben Reaktionen auf Transkriptionsebene in den Pflanzen hervorruft. Die positiv korrelierenden Ergebnisse nach den Gravistimulationsexperimenten in den Hypokotylen und in den Protoplasten zeigen zudem, dass Protoplasten als Modellsystem für Genexpressionsanalysen geeignet und die Ergebnisse auf intakte Pflanzen übertragbar sind.Characterization of the gravitropic signal transduction pathway in Helianthus annuus L. via gene expression analysis after auxin- and gravistimulation Gravity triggers a biochemical pathway, which determines the orientation of plant organs. Although signal transduction pathways following graviperception are still unclear, auxin has been proposed to be responsible for the bending reaction of the gravistimulated plant organs through its asymmetric distribution. Beside auxin as one element of the signal transduction chain linking gravi-perception to gravi-response, little is known about the molecular mechanisms involved in gravitropism. In order to gain further insight into the link between auxin and gravity the expression profiles of mRNA in etiolated sunflower (Helianthus annuus L.) seedlings were analyzed. Therefore, comparative gene expression studies with parallel auxin- and gravistimulation experiments have been established. Gravistimulation was performed by tilting of sunflower hypocotyls for different time intervals and has been supplemented by simulated (fast clinorotation) and real microgravity conditions during flight experiments (sounding rocket TEXUS40) with isolated hypocotyl protoplasts. Also auxin stimulation was achieved by application of exogenous IAA to hypocotyl protoplasts. While there is evidence for a differential sensitivity of apical and basal hypocotyl protoplasts for auxin as measured by PM/H+-ATPase activity, a separate investigation of apical and basal hypocotyl segments provided a more detailed determination of the real gravitropic sensitive tissue. Screening of mRNA profiles was done by Differential Display (DD) RT-PCR, which is one gene expression profiling technique that does not require prior knowledge of any sequences. Furthermore, DDRT-PCR supplies an approach to identify differentially expressed genes in more than one population by comparing several cell populations or variables simultaneously. Thereby the principle is based on the amplification of a numerousness of randomly primed cDNA-fragments of different lengths. Using capillary electrophoresis (ABI310) to separate the fluorophor-labeled cDNA fragments revealed the expression of genes predominantly involved in signal transduction, the regulatory machinery of translation and transcription, metabolism and cell wall. Gravistimulation identified the small GTPase Ran, a calmodulin like domain protein kinase (CDPK), histone H2B, beta-6-xylosyltransferase and electron carrier protein cytochrome c, which all were gravity inducible proteins. In contrast, the isolated genes after auxin stimulation like translation initiation factor eIF1, histone deacetylase (HDAC), histone H3 and fructose-1,6-bisphosphat aldolase (FBPA) were all suppressed by auxin. All of the auxin inducible partial gene fragments showed no apparent homology with known DNA-sequences in the gene databases. Comparing the inducibility of the identified genes by gravistimulation and auxin stimulation revealed a negative correlation for Ran and eIF1 and a positive correlation for cytochrome c and xylosyltransferase, whereas a correlation for CDPK, Histone H3 and H2B, HDAC and FBPA between gravity and auxin-induction has still to be investigated. Differing expression rates were mostly identified in apical segments, which indicate the apical segment as the more sensitive tissue concerning gravitropism and auxin. Moreover, the results obtained with protoplasts after µg-stimulation by clinorotation and TEXUS-flight and by tilting of entire hypocotyls established a positive correlation. Regarding the clearly increase of Ran-mRNA in all experiments, the comparability of protoplasts and whole plants on transcription level was shown

Raf-1 kinase associates with Hepatitis C virus NS5A and regulates viral replication

AbstractHepatitis C virus (HCV) is a positive-strand RNA virus that frequently causes persistent infection associated with severe liver disease. HCV nonstructural protein 5A (NS5A) is essential for viral replication. Here, the kinase Raf-1 was identified as a novel cellular binding partner of NS5A, binding to the C-terminal domain of NS5A. Raf-1 colocalizes with NS5A in the HCV replication complex. The interaction of NS5A with Raf-1 results in increased Raf-1 phosphorylation at serine 338. Integrity of Raf-1 is crucial for HCV replication: inhibition of Raf-1 by the small-molecule inhibitor BAY43-9006 or downregulation of Raf-1 by siRNA attenuates viral replication

Photoswitchable Azo- and Diazocine-Functionalized Derivatives of the VEGFR-2 Inhibitor Axitinib

In this study, we aimed at the application of the concept of photopharmacology to the approved vascular endothelial growth factor receptor (VEGFR)-2 kinase inhibitor axitinib. In a previous study, we found out that the photoisomerization of axitinib's stilbene-like double bond is unidirectional in aqueous solution due to a competing irreversible [2+2]-cycloaddition. Therefore, we next set out to azologize axitinib by means of incorporating azobenzenes as well as diazocine moieties as photoresponsive elements. Conceptually, diazocines (bridged azobenzenes) show favorable photoswitching properties compared to standard azobenzenes because the thermodynamically stable Z-isomer usually is bioinactive, and back isomerization from the bioactive E-isomer occurs thermally. Here, we report on the development of different sulfur-diazocines and carbon-diazocines attached to the axitinib pharmacophore that allow switching the VEGFR-2 activity reversibly. For the best sulfur-diazocine, we could verify in a VEGFR-2 kinase assay that the Z-isomer is biologically inactive (IC50 >> 10,000 nM), while significant VEGFR-2 inhibition can be observed after irradiation with blue light (405 nm), resulting in an IC50 value of 214 nM. In summary, we could successfully develop reversibly photoswitchable kinase inhibitors that exhibit more than 40-fold differences in biological activities upon irradiation. Moreover, we demonstrate the potential advantage of diazocine photoswitches over standard azobenzenes

Analyzing the influence of kinase inhibitors on DNA repair by differential proteomics of chromatin-interacting proteins and nuclear phospho-proteins

The combination of radiotherapy and pharmacological inhibition of cellular signal transduction pathways offers promising strategies for enhanced cancer cell inactivation. However, the molecular effects of kinase inhibitors especially on DNA damage detection and repair after X-irradiation have to be understood to facilitate the development of efficient and personalized treatment regimens. Therefore, we applied differential proteomics for analyzing inhibitor-induced changes in either chromatin-bound or phosphorylated nuclear proteins. The effect of the multi kinase inhibitor sorafenib on DNA repair, chromatin binding and phosphorylation of nuclear proteins was analyzed in UT-SCC 42B head and neck cancer cells using metabolic labeling based differential proteomics (SILAC). Sorafenib significantly inhibited DNA repair but failed to significantly affect chromatin interactions of 90 quantified proteins. In contrast, analyzing nuclear phospho-proteins following sorafenib treatment, we detected quantitative changes in 9 out of 59 proteins, including DNA-repair proteins. In conclusion, the analysis of nuclear phospho-proteins by differential proteomics is an effective tool for determining the molecular effects of kinase inhibitors on X-irradiated cells. Analyzing chromatin binding might be less promising

Trade integration and trade imbalances in the European Union: a network perspective

peer reviewedWe study the ever more integrated and ever more unbalanced trade relationships between European countries. To better capture the complexity of economic networks, we propose two global measures that assess the trade integration and the trade imbalances of the European countries. These measures are the network (or indirect) counterparts to traditional (or direct) measures such as the trade-to-GDP (Gross Domestic Product) and trade deficit-to-GDP ratios. Our indirect tools account for the European inter-country trade structure and follow (i) a decomposition of the global trade flow into elementary flows that highlight the long-range dependencies between exporting and importing economies and (ii) the commute-time distance for trade integration,which measures the impact of a perturbation in the economy of a country on another country, possibly through intermediate partners by domino effect. Our application addresses the impact of the launch of the Euro. We find that the indirect imbalance measures better identify the countries ultimately bearing deficits and surpluses, by neutralizing the impact of trade transit countries, such as the Netherlands. Among others, we find that ultimate surpluses of Germany are quite concentrated in only three partners. We also show that for some countries, the direct and indirect measures of trade integration diverge, thereby revealing that these countries (e.g. Greece and Portugal) trade to a smaller extent with countries considered as central in the European Union network