Removal of divalent cations induces structural transitions in red clover necrotic mosaic virus, revealing a potential mechanism for RNA release

The structure of Red clover necrotic mosaic virus (RCNMV), an icosahedral plant virus, was resolved to 8.5 A by cryoelectron microscopy. The virion capsid has prominent surface protrusions and subunits with a clearly defined shell and protruding domains. The structures of both the individual capsid protein (CP) subunits and the entire virion capsid are consistent with other species in the Tombusviridae family. Within the RCNMV capsid, there is a clearly defined inner cage formed by complexes of genomic RNA and the amino termini of CP subunits. An RCNMV virion has approximately 390 +/- 30 Ca2+ ions bound to the capsid and 420 +/- 25 Mg2+ ions thought to be in the interior of the capsid. Depletion of both Ca2+ and Mg2+ ions from RCNMV leads to significant structural changes, including (i) formation of 11- to 13-A-diameter channels that extend through the capsid and (ii) significant reorganization within the interior of the capsid. Genomic RNA within native capsids containing both Ca2+ and Mg2+ ions is extremely resistant to nucleases, but depletion of both of these cations results in nuclease sensitivity, as measured by a significant reduction in RCNMV infectivity. These results indicate that divalent cations play a central role in capsid dynamics and suggest a mechanism for the release of viral RNA in low-divalent-cation environments such as those found within the cytoplasm of a cell.     

The enzymes of a marine bacterial isolate from the brown alga <Emphasis Type="Italic">Sargassum polycystum</Emphasis> agardh, 1821, that catalyzes the transformation of polyanionic oligo-and polysaccharides

A search for enzymes involved in the degradation of polyanionic polysaccharides (fucoidans and alginic acid) was conducted among bacterial epiphytes of the brown alga Sargassum polycystum that grows in the territorial waters of the Socialist Republic of Vietnam. Two resistant bacterial strains, F10 and F14, have been isolated from the algal microflora that degrade the thallus of the alga under laboratory conditions. These bacterial strains differed in the morphological, physiological, and biochemical characteristics and in the composition of enzymes. The strains were studied for the ability to synthesize intracellular oligo-and polysaccharide hydrolases and alginate lyases. The optimal conditions for the growth of bacterial strain F14 and the biosynthesis of fucoidanase and polymannuronate-specific alginate lyase were determined. The partially purified alginate lyase was stable at a temperature up to 40°C and had an optimal pH 6.0 and an optimal temperature 35°C.     

Occurrence and diversity of mesophilic Shewanella strains isolated from the North-West Pacific Ocean

Although bacteria of the genus Shewanella belong to one of the readily cultivable groups of "Gammaproteobacteria", little is known about the occurrence and abundance of these microorganisms in the marine ecosystem. Studies revealed that of 654 isolates obtained from marine invertebrates (ophiuroid Amphiopholis kochii, sipuncula Phascolosoma japonicum, and holothurian Apostichopus japonicus, Cucumaria japonica), seawater and sediments of the North-West Pacific Ocean (i.e. the Sea of Japan and Iturup Is, Kurile Islands), 10.7% belonged to the genus Shewanella. The proportion of viable Shewanella species varied from 4% to 20% depending on the source of isolation. From the isolation study, representative strains of different phenotypes (from seventy presumptive Shewanella strains) were selected for detailed characterization using phenotypic, chemotaxonomic, and phylogenetic testing. 16S rDNA sequence-based phylogenetic analysis confirmed the results of tentative identification and placed the majority of these strains within only a few species of the genus Shewanella with 98-99% of 16S rDNA sequences identity mainly with S. japonica and S. colwelliana, suggesting that the strains studied might belong to these species. Numerically dominant strains of S. japonica were metabolically active and produced proteinases (gelatinases, caseinases), lipases, amylases, agarases, and alginases. Shewanella strains studied demonstrated weak antimicrobial and antifungal activities that might be an indication of their passive role in the colonization on living and non-living surfaces.     

Stability of global magnetohydrodynamic modes in the L-5 compact torsatron

Global magnetohydrodynamic (MHD) modes in free-boundary plasma equilibrium configurations of the L-5 six-period compact torsatron (project of the Prokhorov General Physics Institute, Russian Academy of Sciences; G. M. Batanov et al., Plasma Dev. Operat. 11, 161 (2003)) have been investigated using the CAS3D code. It is shown that global internal ideal MHD modes can be found reliably only in Mercier unstable plasmas. In all cases under study, they are intrinsically ballooning in nature, i.e., the disturbance at the inner side of the torus is significantly lower in value than that at the outer side. Besides internal modes localized near low-order rational magnetic surfaces, external modes that are localized near the free plasma boundary and are not associated with any rational magnetic surface inside the plasma (the so-called peeling modes) have been found. In contrast to a tokamak with the same aspect ratio, in which pressure-gradient edge-localized modes are ballooning in nature, the peeling modes in the 3D currentless magnetic configuration investigated in the present work are quasi-cylindrical in the flux coordinate system. The problem of plasma boundary destruction under the action of magnetic fields generated by plasma currents is also briefly discussed.     

Antifungal compounds produced by bacterial populations of the Sea SpongeVerongia sp.

The taxonomic structure and some metabolic features of the bacterial populations of the sea spongeVerongia sp were studied. Twenty-three symbiotrophic strains were isolated into axenic cultures and identified. These wereProteobacteria of the generaPseudoalteromonas andVibrio (about 52%), firmicutes with low G+C content (up to 22%), and bacteria of the generaFlavobacterium/Cytophaga/Bacteroides (13% of the strains studied). The strain KMM 3427, identified asBacillus subtilis, synthesized the secondary metabolite 2-p-hydroxyphenylalcohol (tyrosol), which is known to be an antifungal compound and may perform the function of chemical defence inVerongia sp.     

Synthesis Aitd Properties of C'-Methylhuclsosides and Their Phosphoric Esters

Abstract

A brief review on the synthesis and properties of C'-inethylnucleooides is given.     

Collisionless fast-particle confinement in high-β W7-X equilibria

Fast-particle collisionless confinement in Wendelstein 7-X is revisited exploring the configurational space given by the currents in the modular and auxiliary coils and a two-parameter pressure profile. Preliminary results indicate that at 〈β〉 ∼ 0.04 the core-plasma loss cone usually present in stellarators can be approximately eliminated.     

Synthesis and Properties of Some 2′-O-d-Ribofuranosyl-nucleosides

Abstract

A high yield preparation of 9-(2-O-β-d-ribofuranosyl-β-d-ribofuranosyl)-adenine and its pyrimidine analogues has been achieved and their physico-chemical properties were investigated.     

Substrate properties of C′-methyl UTP derivatives in T7 RNA polymerase reactions. Evidence for N-type NTP conformation

The number of synthetic UTP analogues containing methyl groups in different positions of the ribose moiety were tested as substrates for T7 RNA polymerase (T7 RNAP). Two of these compounds (containing substituents in the 5′ position) were shown to be weak substrates of T7 RNAP. 3′Me-UTP was neither substrate nor inhibitor of T7 RNAP while 2′Me-UTP was shown to terminate RNA chain synthesis. Conformational analysis of the analogues and parent nucleotide using the force-field method indicates that the allowed conformation of UTP during its incorporation into the growing RNA chain by T7 RNAP is limited to the χ angle range of 192–256° of N-type conformation.     

Crosslinking of Chitosan with Dialdehyde Derivatives of Nucleosides and Nucleotides. Mechanism and Comparison with Glutaraldehyde

In medical and pharmaceutical applications, chitosan is used as a component of hydrogels–macromolecular networks swollen in water. Chemical hydrogels are formed by covalent links between the crosslinking reagents and amino functionalities of chitosan. To date, the most commonly used chitosan crosslinkers are dialdehydes, such as glutaraldehyde (GA). We have developed novel GA like crosslinkers with additional functional groups–dialdehyde derivatives of uridine (oUrd) and nucleotides (oUMP and oAMP)–leading to chitosan-based biomaterials with new properties. The process of chitosan crosslinking was investigated in details and compared to crosslinking with GA. The rates of crosslinking with oUMP, oAMP, and GA were essentially the same, though much higher than in the case of oUrd. The remarkable difference in the crosslinking properties of nucleoside and nucleotide dialdehydes can be clearly attributed to the presence of the phosphate group in nucleotides that participates in the gelation process through ionic interactions with the amino groups of chitosan. Using NMR spectroscopy, we have not observed the formation of aldimine bonds. It can be concluded that the real number of crosslinks needed to cause gelation of chitosan chains may be less than 1%.