The Structural Basis for the Integrity of Adenovirus Ad3 Dodecahedron

During the viral life cycle adenoviruses produce excess capsid proteins. Human adenovirus serotype 3 (Ad3) synthesizes predominantly an excess of free pentons, the complexes of pentameric penton base and trimeric fiber proteins, which are responsible for virus penetration. In infected cells Ad3 pentons spontaneously assemble into dodecahedral virus-like nano-particles containing twelve pentons. They also form in insect cells during expression in the baculovirus system. Similarly, in the absence of fiber protein dodecahedric particles built of 12 penton base pentamers can be produced. Both kinds of dodecahedra show remarkable efficiency of intracellular penetration and can be engineered to deliver several millions of foreign cargo molecules to a single target cell. For this reason, they are of great interest as a delivery vector. In order to successfully manipulate this potential vector for drug and/or gene delivery, an understanding of the molecular basis of vector assembly and integrity is critical. Crystallographic data in conjunction with site-directed mutagenesis and biochemical analysis provide a model for the molecular determinants of dodecamer particle assembly and the requirements for stability. The 3.8 Å crystal structure of Ad3 penton base dodecamer (Dd) shows that the dodecahedric structure is stabilized by strand-swapping between neighboring penton base molecules. Such N-terminal strand-swapping does not occur for Dd of Ad2, a serotype which does not form Dd under physiological conditions. This unique stabilization of the Ad3 dodecamer is controlled by residues 59–61 located at the site of strand switching, the residues involved in putative salt bridges between pentamers and by the disordered N-terminus (residues 1–47), as confirmed by site directed mutagenesis and biochemical analysis of mutant and wild type protein. We also provide evidence that the distal N-terminal residues are externally exposed and available for attaching cargo.     

Pollen‐based biomes for Beringia 18,000, 6000 and 0 14C yr bp†

The objective biomization method developed by Prentice et al. (1996) for Europe was extended using modern pollen samples from Beringia and then applied to fossil pollen data to reconstruct palaeovegetation patterns at 6000 and 18,000 ¹⁴C yr bp . The predicted modern distribution of tundra, taiga and cool conifer forests in Alaska and north‐western Canada generally corresponds well to actual vegetation patterns, although sites in regions characterized today by a mosaic of forest and tundra vegetation tend to be preferentially assigned to tundra. Siberian larch forests are delimited less well, probably due to the extreme under‐representation of Larix in pollen spectra. The biome distribution across Beringia at 6000 ¹⁴C yr bp was broadly similar to today, with little change in the northern forest limit, except for a possible northward advance in the Mackenzie delta region. The western forest limit in Alaska was probably east of its modern position. At 18,000 ¹⁴C yr bp the whole of Beringia was covered by tundra. However, the importance of the various plant functional types varied from site to site, supporting the idea that the vegetation cover was a mosaic of different tundra types.     

Present-day and mid-Holocene biomes reconstructed from pollen and plant macrofossil data from the former Soviet Union and Mongolia

Fossil pollen data supplemented by tree macrofossil records were used to reconstruct the vegetation of the Former Soviet Union and Mongolia at 6000 years. Pollen spectra were assigned to biomes using the plant-functional-type method developed by Prentice et al . (1996). Surface pollen data and a modern vegetation map provided a test of the method. This is the first time such a broad-scale vegetation reconstruction for the greater part of northern Eurasia has been attempted with objective techniques. The new results confirm previous regional palaeoenvironmental studies of the mid-Holocene while providing a comprehensive synopsis and firmer conclusions. West of the Ural Mountains temperate deciduous forest extended both northward and southward from its modern range. The northern limits of cool mixed and cool conifer forests were also further north than present. Taiga was reduced in European Russia, but was extended into Yakutia where now there is cold deciduous forest. The northern limit of taiga was extended (as shown by increased Picea pollen percentages, and by tree macrofossil records north of the present-day forest limit) but tundra was still present in north-eastern Siberia. The boundary between forest and steppe in the continental interior did not shift substantially, and dry conditions similar to present existed in western Mongolia and north of the Aral Sea.     

Novel antifungal α-hairpinin peptide from Stellaria media seeds: structure, biosynthesis, gene structure and evolution

Plant defense against disease is a complex multistage system involving initial recognition of the invading pathogen, signal transduction and activation of specialized genes. An important role in pathogen deterrence belongs to so-called plant defense peptides, small polypeptide molecules that present antimicrobial properties. Using multidimensional liquid chromatography, we isolated a novel antifungal peptide named Sm-AMP-X (33 residues) from the common chickweed (Stellaria media) seeds. The peptide sequence shows no homology to any previously described proteins. The peculiar cysteine arrangement (C¹X₃C²X_nC³X₃C⁴), however, allocates Sm-AMP-X to the recently acknowledged α-hairpinin family of plant defense peptides that share the helix-loop-helix fold stabilized by two disulfide bridges C¹–C⁴ and C²–C³. Sm-AMP-X exhibits high broad-spectrum activity against fungal phytopathogens. We further showed that the N- and C-terminal “tail” regions of the peptide are important for both its structure and activity. The truncated variants Sm-AMP-X1 with both disulfide bonds preserved and Sm-AMP-X2 with only the internal S–S-bond left were progressively less active against fungi and presented largely disordered structure as opposed to the predominantly helical conformation of the full-length antifungal peptide. cDNA and gene cloning revealed that Sm-AMP-X is processed from a unique multimodular precursor protein that contains as many as 12 tandem repeats of α-hairpinin-like peptides. Structure of the sm-amp-x gene and two related pseudogenes sm-amp-x-ψ1 and sm-amp-x-ψ2 allows tracing the evolutionary scenario that led to generation of such a sophisticated precursor protein. Sm-AMP-X is a new promising candidate for engineering disease resistance in plants.     

Tuning the insertion properties of pHLIP

The pH (low) insertion peptide (pHLIP) has exceptional characteristics: at neutral pH it is an unstructured monomer in solution or when bound to lipid bilayer surfaces, and it inserts across a lipid bilayer as a monomeric alpha-helix at acidic pH. The peptide targets acidic tissues in vivo and may be useful in cancer biology for delivery of imaging or therapeutic molecules to acidic tumors. To find ways to vary its useful properties, we have designed and analyzed pHLIP sequence variants. We find that each of the Asp residues in the transmembrane segment is critical for solubility and pH-dependent membrane insertion of the peptide. Changing both of the Asp residues in the transmembrane segment to Glu, inserting an additional Asp into the transmembrane segment, or replacing either of the Asp residues with Ala leads to aggregation and/or loss of pH-dependent membrane insertion of the peptide. However, variants with either of the Asp residues changed to Glu remained soluble in an aqueous environment and inserted into the membrane at acidic pH with a higher pK_app of membrane insertion.     

Breaking of nonlinear cylindrical plasma oscillations

Nonlinear axisymmetric cylindrical plasma oscillations are investigated analytically and numerically. It is shown that the breaking of strongly nonlinear oscillations is attributed to a singularity in the electron density and occurs several periods after the onset of an off-axis density maximum. For weakly nonlinear conditions, an analytic dependence of the breaking time of the oscillations on their amplitude is obtained based on the effect of intersection of electron trajectories and is shown to agree with numerical results.     

A leaderless mRNA can bind to mammalian 80S ribosomes and direct polypeptide synthesis in the absence of translation initiation factors

Translation initiation in eukaryotic cells is known to be a complex multistep process which involves numerous protein factors. Here we demonstrate that leaderless mRNAs with initiator Met-tRNA can bind directly to 80S mammalian ribosomes in the absence of initiation factors and that the complexes thus formed are fully competent for the subsequent steps of polypeptide synthesis. We show that the canonical 48S pathway of eukaryotic translation initiation has no obvious advantage over the 80S pathway of translation initiation on leaderless mRNAs and suggest that, in the presence of competing mRNAs containing a leader, the latter mechanism will be preferred. The direct binding of the leaderless mRNA to the 80S ribosome was precluded when such an mRNA was supplied with a 5' leader, irrespective of whether it was in a totally single-stranded conformation or was prone to base pairing. The striking similarity between the mechanisms of binding of leaderless mRNAs with mammalian 80S or bacterial 70S ribosomes gives support to the idea that the alternative mode of translation initiation used by leaderless mRNAs represents a relic from early steps in the evolution of the translation apparatus.     

Structural chromosome organisation and radiation-induced interchromosomal aberrations

The quantitative prediction of the biological effects of radiation is one of the actual tasks of radiobiology. The experimental study may be impossible under certain conditions (low doses, complex radiation fields, etc). The development of theoretical tools is required to predict biological and medical consequence of the irradiation of cell and organism. The effect under the consideration in the present paper is chromosome aberrations (CA) induced by low and high LET radiation. One of the most uncertain factors in CA prediction is the impact of chromosomal and nuclear architecture. In the present study the quantitative evaluation of the mechanisms of CA induction are discussed in the framework of the biophysical modelling technique taking into account interphase chromosomes structure in the nucleus of living (human) cell. We show that the surface contacts mechanism of interchromosomal aberrations (interchange) formation does not explain the observed ratio of simple/complex interchanges induced by both low and high LET radiation. The chromatin structure repositioning following irradiation is proposed as a possible mechanism involved in the formation of the complex aberrations.     

Na+-transporting ATPase in the plasma membrane of halotolerant microalga Dunaliella maritima operates as a Na+ uniporter

A fraction of inside-out membrane vesicles enriched in plasma membranes (PM) was isolated from Dunaliella maritima cells. Attempts were made to reveal ATP-driven Na⁺-dependent H⁺ efflux from the PM vesicles to external medium, as detected by alkalization of the vesicle lumen. In parallel experiments, ATP-dependent Na⁺ uptake and electric potential generation in PM vesicles were investigated. The alkalization of the vesicle lumen was monitored with an impermeant pH-sensitive optical probe pyranine (8-hydroxy-1,3,6-pyrenetrisulfonic acid), which was loaded into vesicles during the isolation procedure. Sodium uptake was measured with ²²Na⁺ radioactive label. The generation of electric potential in PM vesicles (positive inside) was recorded with a voltage-sensitive probe oxonol VI. Appreciable Na⁺-and ATP-dependent alkalization of vesicle lumen was only observed in the presence of a protonophore CCCP (carbonyl cyanide-chlorophenylhydrazone). In parallel experiments, CCCP accelerated the ATP-dependent ²²Na⁺ uptake and abolished the electric potential generated by the Na⁺-ATPase at the vesicle membrane. A permeant anion NO^? ₃ accelerated ATP-dependent ²²Na⁺ uptake and promoted dissipation of the electric potential like CCCP did. At the same time, NO^? ₃ inhibited the ATP-and Na⁺-dependent alkalization of the vesicle lumen. The results clearly show that the ATP-and Na⁺-dependent H⁺ efflux from PM vesicles of D. maritima is driven by the electric potential generated at the vesicle membrane by the Na⁺-ATPase. Hence, the Na⁺-transporting ATPase of D. maritima carries only one ion species, i.e., Na⁺. Proton is not involved as a counter-ion in the catalytic cycle of this enzyme.     

Gene silencing of serine proteases affects melanization of Sephadex beads in Anopheles gambiae

Serine proteases play an important role in activation of prophenoloxidase (proPO), a critical enzyme in the production of melanin. We tested the effect of knockdown of gene expression for five clip domain serine proteases on melanization of abiotic targets in Anopheles gambiae. Knockdown of CLIPB4 resulted in a striking lack of melanization of Sephadex beads while knockdown of CLIPB8 caused a strong shift towards incompletely melanized beads. Knockdown of CLIPB1, B9 and B10 had lesser effects. CLIPB4 and CLIPB8 are strong candidates for activating enzymes in the proPO enzymatic cascade.