Vendian-Cambrian tidal and sabkha facies of the Siberian platform

Summary The Vendian-Cambrian interval on the Siberian Platform contains thick carbonate and evaporite sequences formed in extensive shallow-water basins. The carbonate sequences are characterized by a cyclic composition. Finegrained dolomites, undulated algal dolomites, flat pebble conglomerates, storm breccias and solution-collapse breccias form the base of each cycle. These rocks are characterized by an increased clay content which can be high enough to form argillites. Short sedimentation breaks reflected by mudcracks or silicification horizons are present as well as small cross-bedded tidal channels. Peloidal grainstones with algal overgrowth dominate in the central parts of the cycles. These members are often recrystallized and dolomitized. Micritic dolomites, undulous laminated dolomites, storm breccias and columnar stromatolites with abundant mud cracks form the upper members of the cycles. These sequences are free of clay but contain abundant anhydrite crystals and nodules. In the uppermost parts of some cycles massive layered anhydrite beds are present. The cycles vary in thickness, but usually they are between 15 and 20 m thick. The lower cycle member documents extreme shallow-water deposits. They formed in tidal and partially also supratidal zones not far from the mainland, from where fine clayey material was washed in. These parts of the sequence reflect a slow transgression. The central member of a cycle was deposited during the maximal transgression in a shallow basin with normal salinity and rather active hydrodynamics. Sedimentation of the upper part of the cycles reflects a regression stage (tidal and especially sabkha environments). The final layered anhydrite beds formed most probably in relict lakes on the sabkha plain. During sea-level falls some sequences of the central parts of the cycles were subaerially exposed and underwent partial dolomitization. The Vendian-Cambrian sabkhas are partly comparable with their recent counterparts.     

Lasioglossins LLIII affect the morphogenesis of Candida albicans and reduces the duration of experimental vaginal candidiasis in mice

Lasioglossins are a group of peptides with identified antimicrobial activity. The inhibitory effects of two synthetic lasioglossin derivatives, LLIII and D‐isomeric variant LLIII‐D, on morphological changes in Candida albicans in vitro and the effect of local administration of LLIII during experimental murine candidiasis were investigated. C. albicans blastoconidia were grown in the presence of lasioglossin LLIII or LLIII‐D at concentrations of 11.5 μM and 21 μM, respectively, for 1, 2 and 3 days and their viability determined by flow cytometry using eosin Y staining. Morphological changes were examined by light and fluorescent microscopy. The Candida‐inhibitory effect of daily intravaginal administration of 0.7 or 1.4 μg of LLIII was assessed in mice with experimentally‐induced vaginal candidiasis. LLIII and LLIII‐D lasioglossins exhibited candidacidal activity in vitro (>76% after 24 hr and >84% after 48 hr of incubation). After 72 hr incubation of Candida with low concentration of lasioglossins, an increase in viability was detected, probably due to a Candida antimicrobial peptides evasion strategy. Furthermore, lasioglossins inhibited temperature‐induced morphotype changes toward hyphae and pseudohyphae with sporadic occurrence of atypical cells with two or enlarged nuclei, suggesting interference with mitosis or cytokinesis. Local application of LLIII reduced the duration of experimental candidiasis with no evidence of adverse effects. Lasioglossin LLIII is a promising candidate for development as an antimicrobial drug for treating the vaginal candidiasis.

     

Birds girdling activity on exotic tree species as a form of adaptive behavior?

Four tree species in the Kostelec n. ?. l. arboretum (Czech Republic) have been repeatedly damaged by Dendrocopos medius. The unique aspect of this otherwise common behavior called girdling consists in regularly visiting the same trees every spring, although there are more than 1.200 tree species within the arboretum. We monitored transpiration, leaf phenology and the chemical composition of the xylem sap of girdled and nongirdled trees. Spectral analysis revealed slightly higher amounts of sugars, especially saccharose, in Cladrastis Raf. as the most regularly girdled tree among other conditions, comparing girdled to non-girdled trees. Higher transpiration rates were not confirmed in connection with girdling—quite the opposite—Cladrastis Raf. as the most highly favored tree for girdling showed the lowest transpiration rates (in average 6 kg water per day within spring months) compared to other non-girdled trees. We presume that the birds do not choose a particular tree on the basis of any visible or chemical traits but they examine many trees within their territory. Afterwards they probably remember the position of trees whose xylem sap starts to flow early in the spring compared to other trees, as their transpiration stream is enriched with sweet organic substances that represent an advantage for the forthcoming nesting period.     

High Resolution NMR-based Model for the Structure of a scFv-IL-1�� Complex: POTENTIAL FOR NMR AS A KEY TOOL IN THERAPEUTIC ANTIBODY DESIGN AND DEVELOPMENT*

Monoclonal antibodies have recently started to deliver on their promise as highly specific and active drugs; however, a more effective, knowledge-based approach to the selection, design, and optimization of potential therapeutic antibodies is currently limited by the surprising lack of detailed structural information for complexes formed with target proteins. Here we show that complexes formed with minimal antigen binding single chain variable fragments (scFv) reliably reflect all the features of the binding interface present in larger Fab fragments, which are commonly used as therapeutics, and report the development of a robust, reliable, and relatively rapid approach to the determination of high resolution models for scFv-target protein complexes. This NMR spectroscopy-based approach combines experimental determination of the interaction surfaces and relative orientations of the scFv and target protein, with NMR restraint-driven, semiflexible docking of the proteins to produce a reliable and highly informative model of the complex. Experience with scFvs and Fabs targeted at a number of secreted regulatory proteins suggests that the approach will be applicable to many therapeutic antibodies targeted at proteins, and its application is illustrated for a potential therapeutic antibody targeted at the cytokine IL-1β. The detailed structural information that can be obtained by this approach has the potential to have a major impact on the rational design and development of an increasingly important class of biological pharmaceuticals.     

Antibody array analysis with label-based detection and resolution of protein size

Elements from DNA microarray analysis, such as sample labeling and micro-spotting of capture reagents, have been successfully adapted to multiplex measurements of soluble cytokines. Application in cell biology is hampered by the lack of mono-specific antibodies and the fact that many proteins occur in complexes. Here, we incorporated a principle from Western blotting and resolved protein size as an additional parameter. Proteins from different cellular compartments were labeled and separated by size exclusion chromatography into 20 fractions. All were analyzed with replicate antibody arrays. The elution profiles of all antibody targets were compiled to color maps that resemble Western blots with bands of antibody reactivity across the size separation range (670-10 kDa). A new solid phase designed for processing in microwell plates was developed to handle the large number of samples. Antibodies were bound to protein G-coupled microspheres surface-labeled with 300 combinations of four fluorescent dyes. Fluorescence from particle color codes and the protein label were measured by high-speed flow cytometry. Cytoplasmic protein kinases were detected as bands near predictable elution points. For proteins with atypical elution characteristics or multiple contexts, two or more antibodies were used as internal references of specificity. Membrane proteins eluted near the void volume, and additional bands corresponding to intracellular forms were detected for several targets. Elution profiles of cyclin-dependent kinases (cdks), cyclins, and cyclin-dependent kinase inhibitors, were compatible with their occurrence in complexes that vary with the cell cycle phase and subcellular localization. A two-dimensional platform circumvents the need for mono-specific capture antibodies and extends the utility of antibody array analysis to studies of protein complexes.     

Complete genome sequence of the haloaromatic acid-degrading bacterium Achromobacter xylosoxidans A8

Achromobacter xylosoxidans strain A8 was isolated from soil contaminated with polychlorinated biphenyls. It can use 2-chlorobenzoate and 2,5-dichlorobenzoate as sole sources of carbon and energy. This property makes it a good starting microorganism for further development toward a bioremediation tool. The genome of A. xylosoxidans consists of a 7-Mb chromosome and two large plasmids (98 kb and 248 kb). Besides genes for the utilization of xenobiotic organic substrates, it contains genes associated with pathogenesis, toxin production, and resistance. Here, we report the complete genome sequence.     

Structure of the tandem MA-3 region of Pdcd4 protein and characterization of its interactions with eIF4A and eIF4G: molecular mechanisms of a tumor suppressor

One of the key regulatory points of translation initiation is recruitment of the 43S preinitation complex to the 5' mRNA cap by the eIF4F complex (eIF4A, eIF4E, and eIF4G). The tumor suppressor protein Pdcd4 has been shown to inhibit cap-dependent translation by interacting tightly with the RNA helicase eIF4A via its tandem MA-3 domains. The NMR studies reported here reveal a fairly extensive and well defined interface between the two MA-3 domains in solution, which appears to be stabilized by a network of interdomain salt bridges and hydrogen bonds, and reveals a unique orientation of the two domains. Characterization of the stoichiometry of the Pdcd4-eIF4A complex suggests that under physiological conditions Pdcd4 binds to a single molecule of eIF4A, which involves contacts with both Pdcd4 MA-3 domains. We also show that contacts mediated by a conserved acidic patch on the middle MA-3 domain of Pdcd4 are essential for forming a tight complex with eIF4A in vivo, whereas the equivalent region of the C-terminal MA-3 domain appears to have no role in complex formation in vivo. The formation of a 1:1 eIF4A-Pdcd4 complex in solution is consistent with the reported presence in vivo of only one molecule of eIF4A in the eIF4F complex. Pdcd4 has also been reported to interact directly with the middle region of eIF4G, however, we were unable to obtain any evidence for even a weak, transient direct interaction.