Synthesis of conformationally restricted nucleic acid fragments using ring-closing alkene and enyne metathesis reactions

In the aim of constructing conformationally restricted nucleic acid fragments for the recognition of secondary RNA structures, we have synthesized different mono- and dinucleotides containing extra rings. These rings were prepared by ring-closing alkene or enyne metathesis reactions from nucleotide substrates in which double or triple bonds have been introduced.     

Interlocking and knotting of ring nucleoli in amphibian oocytes

Various configurations of interlocking and knotting of ring nucleoli from amphibian oocytes have been identified in material taken from 2 females of Eurycea bislineata and one female of Plethodon cinereus. The simplest configuration is a simple interlock between 2 rings of similar or different lengths. More complex interlocks have been seen, in which 3 rings are linked together in such a way that they cannot be extended into a chain. A third configuration involves complex knotting of single long rings. It is suggested that the interlocked configurations arise through the replication of rings of DNA that have low levels of supercoiling, and that the knotted rings arise by misjoining of the ends of linear molecules that have become wound around one another. Models are suggested in support of these proposals and the significance of interlocking of ring nucleoli in relation to the mechanism of gene amplification is discussed.     

Dynamic apical surface rings in superficial layer cells of koi Cyprinus carpio scale epidermis

This study examined the novel ring‐shaped structures found in the apical surface of individual cells of the scale epidermis of koi Cyprinus carpio. These apical rings are highly dynamic structures with lifetimes ranging from a few to several minutes. While several ring forms were observed, the predominant ring morphology is circular or oval. Two distinct ring forms were identified and designated type I and type II. Type I rings have a well‐defined outer border that encircles the surface microridges. Type II rings are smooth‐surfaced, dinner‐plate‐like structures with membranous folds or compressed microridges in the centre. Type II rings appear less frequently than type I rings. Type I rings form spontaneously, arising from swollen or physically interrupted microridges but without initially perturbing the encircled microridges. After persisting for up to several minutes the ring closes in a centripetal movement to form a circular or irregular‐shaped structure, the terminal disc. The terminal disc eventually disappears, leaving behind a submembranous vesicle‐like structure, the terminal body. Type I rings can undergo multiple cycles of formation and closing. Recycling epidermal apical rings form through centrifugal expansion from the terminal disc followed by apparent contraction back to the disc structure, whereupon the cycle may repeat or cease. The findings demonstrate a novel skin surface structure in fishes and are discussed with respect to communication with the external aqueous environment.     

Tubulin rings: Curved filaments with limited flexibility and two modes of association

Tubulin rings have been previously identified as composed of linear polymers of tubulin subunits, equivalent to a protofilament in the microtubule wall but in a curved rather than a straight conformation. We have examined and measured a number of different ring structures obtained under different conditions. The preferred curvature is indicated by a single ring of 380 Å outside diameter. Radially double rings consist of two coplanar rings of 460 Å and 350 Å outside diameter, held together by a pattern of eight identical contacts between the 40 Å subunits in the inner and outer rings. In some circumstances a larger ring, 570 Å diameter, can be added to the outside, or a smaller ring, 240 Å diameter, may be added to the inside of the radially double ring, in both cases repeating the pattern of eight radial contacts. The distortion of the filament from its relaxed 380 Å diameter curvature apparently can be made without disrupting the longitudinal bond between subunits in the filament, but must be stabilized by the energy of the radial contacts. All of these rings (single and radially double and triple) are observed to associate axially to form pairs or in some cases larger stacks. The radially double rings or an axially associated pair of these (quadruple ring) may also associate to form crystals. These are thin plates, up to 100 μm in extent and several μm thick which have been of limited use so far in diffraction studies because of irregularities in the packing of adjacent rings.     

Validation of age readings from otoliths of juvenile roundnose grenadier, Coryphaenoides rupestris, a deep-water macrourid fish

Validation of the ageing of deep-water fish is difficult and there are only a few instances where the rings on the otoliths have been shown to be laid down annually. Roundnose grenadier have been fished commercially in the North Atlantic since the 1960s and the adult fish have frequently been aged by counting the rings in otoliths or scales. All the ageing was done on the assumption that the rings in the otoliths or scales were annual. Between 1975 and 1992, the Scottish Association for Marine Science carried out seasonal trawling surveys in the Rockall Trough using a fine-meshed trawl, and collected otoliths from a wide size range of roundnose grenadier. An examination of the growing edge of otoliths from juvenile fish from these collections suggests that the rings in the otoliths are laid down annually. The broader, opaque zones which represent the growth phase were dominant between September and March. The thinner, hyaline zones were dominant between April and July. The apparent delay in the growth phase compared with most shallow-water species is discussed in relation to the availability of mesopelagic prey.     

LSm proteins form heptameric rings that bind to RNA via repeating motifs

Members of the LSm family of proteins share the Sm fold--a closed barrel comprising five anti-parallel beta strands with an alpha helix stacked on the top. The fold forms a subunit of hexameric or heptameric rings of approximately 7nm in diameter. Interactions between neighboring subunits center on an anti-parallel interaction of the fourth and fifth beta strands. In the lumen of the ring, the subunits have the same spacing as nucleotides in RNA, enabling the rings to bind to single-stranded RNA via a repeating motif. Eubacteria and archaea build homohexamers and homoheptamers, respectively, whereas eukaryotes use >18 LSm paralogs to build at least six different heteroheptameric rings. The four different rings in the nucleus that permanently bind small nuclear RNAs and function in pre-mRNA maturation are called Sm rings. The two different rings that transiently bind to RNAs and, thereby, assist in the degradation of mRNA in the cytoplasm and the maturation of a wide spectrum of RNAs in the nucleus are called LSm rings.     

Conformations and interactions of excited stales. I. Model compounds for polymers

From observations on model compounds having two or more benzene rings and structures analogous to high polymers of interest (polystyrene and aromatic polypeptides), we conclude that interactions of pairs of benzene rings sufficiently strong to cause observable excimer emission requires that these rings be separated by no more than 2–3 A. and that they be in an approximately parallel-stacked, face-to-face arrangement. If a molecule does not have such a configuration of its aromatic rings in its ground-state conformation, strong excimer emission can still occur provided there is a conformation with the appropriate ring configuration which can be attained within the radiative lifetime of the excited state.     

Are periodic (intra-annual) tangential bands of vessels in diffuse-porous tree species the equivalent of flood rings in ring-porous species? Reproducibility and cause

Tree rings from ring-porous species have often been used as flood proxy. Many ring-porous species produce characteristic flood rings in response to stem submersion during vessel formation. Flood rings have earlywood vessels that are more numerous and/or of smaller cross-sectional area than “normal” rings. This study aimed at determining if diffuse-porous balsam poplar and trembling aspen, like ring-porous black ash, produce anatomically distinct annual tree rings in response to flooding. More specifically, we asked (i) if periodic tangential bands of vessels (hereafter PTBV) could be as easily identified/quantified as flood rings and (ii) if PTBV could be associated with spring flooding. Sampling of black ash, balsam poplar and trembling aspen trees took place along a flood exposure gradient in the floodplain of Lake Duparquet in northwestern Québec. Two observers recorded flood rings and PTBV. Consistency between observers was greatest when identifying flood rings. In both diffuse-porous species, PTBV occurred less abundantly than flood rings in black ash. They also occurred less often in balsam poplar than in trembling aspen. Years in which PTBV were initiated early in the growing season were associated with years in which flood rings occurred. Like flood rings, early occurring PTBV were more abundant in springs characterized by high mean river discharge, extensive snow cover, cold temperatures and heavy precipitation. Early-occurring PTBV dominated in flooded sites and late-occurring ones dominated in the control site. However, PTBV of the late-types were also observed in both flood exposures indicating that spring flood may not be the only factor modulating their formation. While flood rings seem to be associated with a change in the transport of growth regulators resulting from stem submergence and excess water, PTBV may be reflective of rhythmic alterations in the transport of growth regulators resulting from either water excess or deficit. Despite promising findings, many questions remain before PTBV in riparian diffuse-porous species can be widely used as a flood proxy. Why do species and individual trees differ in their ability to record them? What is the full range of environmental conditions triggering PTBV’s formation especially in unflooded sites and in the late growing season?     

The role of stacking interactions in clonidine binding

Stacking interactions of the clonidine aromatic ring with that of Phe or Tyr in the α₂-adrenoreceptor and Tyr in the tetrodotoxin-resistant sodium channel pore have been studied. Ab initio quantum-chemical calculations for a model system of two parallel aromatic rings have been performed with the GAMESS software using the 6-31G* basis set in the framework of the second-order Muller-Plesset perturbation theory with full geometry optimization without symmetry constraints. The parallel shifted conformation of two aromatic rings was found to be energetically most favorable. The 2′,6′-chlorination of one of the benzene rings enhances the stacking interaction, somewhat increases the shift of these rings, and possibly improves the hypotensive and analgesic functions of clonidine owing to an increase in the binding energy. The 4-fluorination of the clonidine ring can increase its analgesic effect but practically excludes its hypotensive activity.     

Evolutionary diversification of the Sm family of RNA-associated proteins

The Sm family of proteins is closely associated with RNA metabolism throughout all life. These proteins form homomorphic and heteromorphic rings consisting of six or seven subunits with a characteristic central pore, the presence of which is critical for binding U-rich regions of single-stranded RNA. Eubacteria and Archaea typically carry one or two forms of Sm proteins and assemble one homomorphic ring per Sm protein. Eukaryotes typically carry 16 or more Sm proteins that assemble to form heteromorphic rings which lie at the center of a number of critical RNA-associated small nuclear ribonucleoproteins (snRNPs). High Sm protein diversity and heteromorphic Sm rings are features stretching back to the origin of eukaryotes; very deep phylogenetic divisions among existing Sm proteins indicate simultaneous evolution across essentially all existing eukaryotic life. Two basic forms of heteromorphic Sm rings are found in eukaryotes. Fixed Sm rings are highly stable and static and are assembled around an RNA cofactor. Flexible Sm rings also stabilize and chaperone RNA but assemble in the absence of an RNA substrate and, more significantly, associate with and dissociate from RNA substrates more freely than fixed rings. This suggests that the conformation of flexible Sm rings might be modified in some specific manner to facilitate association and dissociation with RNA. Diversification of eukaryotic Sm proteins may have been initiated by gene transfers and/or genome clashes that accompanied the origin of the eukaryotic cell itself, with further diversification driven by a greater need for steric specificity within increasingly complex snRNPs.     

Internal structure of the starch granule revealed by AFM

Atomic force microscopy images of sectioned native corn starch granules show evidence of the well-known radial organisation of the starch macromolecules, with the less-ordered hilum region near to the centre. Native granules show blocks 400-500 nm in size that span the growth rings. Lintnerised starch granules, where a mild acid hydrolysis has been used to remove the amorphous and less crystalline parts of the granule, clearly show smaller 'blocklets' within the rings approximately 10-30 nm in size. This level of organisation within the growth rings corresponds to the blocklet or superhelix structures that have been proposed in the literature for the association or clustering of amylopectin helices. Mechanical property imaging techniques have provided enhanced contrast to view this morphology, and shown the deformability of the starch structure under contact mode imaging conditions.     

Negative-stain electron microscopy of inside-out FtsZ rings reconstituted on artificial membrane tubules show ribbons of protofilaments

FtsZ, the primary cytoskeletal element of the Z ring, which constricts to divide bacteria, assembles into short, one-stranded filaments in vitro. These must be further assembled to make the Z ring in bacteria. Conventional electron microscopy (EM) has failed to image the Z ring or resolve its substructure. Here we describe a procedure that enabled us to image reconstructed, inside-out FtsZ rings by negative-stain EM, revealing the arrangement of filaments. We took advantage of a unique lipid that spontaneously forms 500 nm diameter tubules in solution. We optimized conditions for Z-ring assembly with fluorescence light microscopy and then prepared specimens for negative-stain EM. Reconstituted FtsZ rings, encircling the tubules, were clearly resolved. The rings appeared as ribbons of filaments packed side by side with virtually no space between neighboring filaments. The rings were separated by variable expanses of empty tubule as seen by light microscopy or EM. The width varied considerably from one ring to another, but each ring maintained a constant width around its circumference. The inside-out FtsZ rings moved back and forth along the tubules and exchanged subunits with solution, similarly to Z rings reconstituted outside or inside tubular liposomes. FtsZ from Escherichia coli and Mycobacterium tuberculosis assembled rings of similar structure, suggesting a universal structure across bacterial species. Previous models for the Z ring in bacteria have favored a structure of widely scattered filaments that are not in contact. The ribbon structure that we discovered here for reconstituted inside-out FtsZ rings provides what to our knowledge is new evidence that the Z ring in bacteria may involve lateral association of protofilaments.     

The role of stacking interactions in the mechanisms of clonidine binding

The stacking interactions of the clonidine aromatic ring with the aromatic rings of Phe or Tyr of alpha2-adrenoreceptor and Tyr aromatic ring of the pore of the tetradotoxin-resistant channel have been investigated. Ab initio quantum chemical calculations for a model system of two parallel aromatic rings were performed by GAMESS software with 6-31G** basis set in the framework of the Moller-Plesset second-order perturbation theory with full geometry optimization without any symmetry. It was shown that the parallel shifted conformation of two aromatic rings is energetically most favorable. The 2,6-chlorination of one of the benzene rings leads to the amplification of the stacking interaction, an increase in the relative shift of the rings and possible growth of both the hypotensive and analgetic functions of clonidine due to the increase in the binding energy. The 4-fluoridization of the clonidine benzene ring can amplify its analgetic function but practically excludes its hypotensive action.     

Achiasmatic meiosis and complex heterozygosity in female cyclopoid copepods (Copepoda,Crustacea)

In Mesocyclops edax S.A. Forbes, 2n=14, a North American copepod, the females are heterozygous for several interchanges leading to the formation of large rings of chromosomes (rings of 14, or of 12 plus 1 bivalent) at meiotic metaphase, comparable to those of the plant Oenothera, although no chiasmata are present. The chromosomes are more or less metacentric and have large terminal H-segments. In the rings homologous arms are held together by connecting fibers which insert close to the euchromatin-heterochromatin junctions. Coordinated orientation of the zigzag type seems to be the role.     

Influence of the nucleoid on placement of FtsZ and MinE rings in Escherichia coli

We previously presented evidence that replicating but unsegregated nucleoids, along with the Min system, act as topological inhibitors to restrict assembly of the FtsZ ring (Z ring) to discrete sites in the cell. To test if nonreplicating nucleoids have similar exclusion effects, we examined Z rings in dnaA (temperature sensitive) mutants. Z rings were excluded from centrally localized nucleoids and were often observed at nucleoid edges. Cells with nonreplicating nucleoids formed filaments, some of which contained large nucleoid-free areas in which Z rings were positioned at regular intervals. Because MinE may protect FtsZ from the action of the MinC inhibitor in these nucleoid-free zones, we examined the localization of a MinE-green fluorescent protein (GFP) fusion with respect to Z rings and nucleoids. Like Z rings, MinE-GFP appeared to localize independently of nucleoid position, forming rings at regular intervals in nucleoid-free regions. Unlike FtsZ, however, MinE-GFP often localized on top of nucleoids, replicating or not, suggesting that MinE is relatively insensitive to the nucleoid inhibition effect. These data suggest that both replicating and nonreplicating nucleoids are capable of topologically excluding Z rings but not MinE.     

Clathrate hydrates are poor models of biomolecule hydration

Clathrate hydrates form the basis of a general model of biomolecule hydration. In clathrate hydrate crystal structures, the size of hydrogen-bonded water rings is highly constrained to five members. The clathrate hydrate model predicts that the size of water rings near biomolecule surfaces is similarly constrained to five members. This report describes a test of this model of biomolecule hydration. We have demonstrated that five-membered water rings are not a general feature of protein or nucleic acid hydration. The clathrate hydrate model appears to be inappropriate for biomolecules. © 1996 John Wiley & Sons, Inc.     

Differential inhibition of hepatic ferrochelatase by the isomers of N-ethylprotoporphyrin IX

The four isomers of N-ethylprotoporphyrin IX have been synthesized. The two isomers with the N-ethyl group on pyrrole rings A or B inhibit rat liver ferrochelatase as effectively as the corresponding N-methyl analogues, whereas those with the N-ethyl moiety on rings C or D are 30–100 times less effective. The ability of N-alkyl porphyrins to inhibit ferrochelatase thus depends not only on the size of the N-alkyl group but also on its precise location on the porphyrin face.     

Unique and overlapping roles for ZipA and FtsA in septal ring assembly in Escherichia coli

ZipA and FtsA are essential division proteins in Escherichia coli that are recruited to the division site by interaction with FtsZ. Utilizing a newly isolated temperature-sensitive mutation in zipA we have more fully characterized the role of ZipA. We confirmed that ZipA is not required for Z ring formation; however, we found that ZipA, like FtsA, is required for recruitment of FtsK and therefore all downstream division proteins. In the absence of FtsA or ZipA Z rings formed; however, in the absence of both, new Z rings were unable to form and preformed Z rings were destabilized. Consistent with this, we found that an FtsZ mutant unable to interact with both ZipA and FtsA was unable to assemble into Z rings. These results demonstrate that ZipA and FtsA are both required for recruitment of additional division proteins to the Z ring, but either one is capable of supporting formation and stabilization of Z rings.     

Acute O-GlcNAcylation prevents inflammation-induced vascular dysfunction

Acute increases in cellular protein O-linked N-acetyl-glucosamine (O-GlcNAc) modification (O-GlcNAcylation) have been shown to have protective effects in the heart and vasculature. We hypothesized that d-glucosamine (d-GlcN) and Thiamet-G, two agents that increase protein O-GlcNAcylation via different mechanisms, inhibit TNF-α-induced oxidative stress and vascular dysfunction by suppressing inducible nitric oxide (NO) synthase (iNOS) expression. Rat aortic rings were incubated for 3h at 37°C with d-GlcN or its osmotic control l-glucose (l-Glc) or with Thiamet-G or its vehicle control (H(2)O) followed by the addition of TNF-α or vehicle (H(2)O) for 21 h. After incubation, rings were mounted in a myograph to assess arterial reactivity. Twenty-four hours of incubation of aortic rings with TNF-α resulted in 1) a hypocontractility to 60 mM K(+) solution and phenylephrine, 2) blunted endothelium-dependent relaxation responses to ACh and substance P, and 3) unaltered relaxing response to the Ca(2+) ionophore A-23187 and the NO donor sodium nitroprusside compared with aortic rings cultured in the absence of TNF-α. d-GlcN and Thiamet-G pretreatment suppressed the TNF-α-induced hypocontractility and endothelial dysfunction. Total protein O-GlcNAc levels were significantly higher in aortic segments treated with d-GlcN or Thiamet-G compared with controls. Expression of iNOS protein was increased in TNF-α-treated rings, and this was attenuated by pretreatment with either d-GlcN or Thiamet-G. Dense immunostaining for nitrotyrosylated proteins was detected in the endothelium and media of the aortic wall, suggesting enhanced peroxynitrite production by iNOS. These findings demonstrate that acute increases in protein O-GlcNAcylation prevent TNF-α-induced vascular dysfunction, at least in part, via suppression of iNOS expression.     

Vascular effects of some opioid receptor agonists.

Opioid peptides have been implicated in shock-associated hypotension. Our aim was to find out whether opioid agonists have direct vasodilator actions on vascular smooth muscle. The study was conducted on rat abdominal aortic rings. In rings precontracted with either norepinephrine, prostaglandin F2 alpha, or high potassium Krebs (HPK), the effects of the opioid agonists tested (morphine, U50488H, ethylketocyclazocine (EKC), and bremazocine) depended on the precontracting agent used. HPK-precontracted rings were relaxed by all agonists tested. In norepinephrine-precontracted rings, all caused contraction at low concentrations and relaxation at high concentrations except bremazocine, which caused only relaxation. In prostaglandin F2 alpha-precontracted rings, U50488H produced contraction at low concentrations and relaxation at high concentrations while EKC caused only relaxation and morphine or bremazocine caused only contraction. All relaxant responses were endothelium-independent and were antagonized by verapamil but not by a number of antagonists including naloxone. MR2266, propranolol, diphenhydramine, cimetidine, and indomethacin. They may reflect calcium channel blockade. Morphine-induced vasoconstriction was antagonized by high concentrations of of naloxone or mepyramine and may be due to release of histamine by a naloxone-sensitive mechanism. We conclude that (a) the opioid agonists tested exert direct actions on vascular smooth muscle; (b) the nature of the response depended not only on the agonist used and its concentration but also on the agent used to precontract the tissue; and (c) it is unlikely that direct actions of endogenous opioids contribute to the shock-associated hypotension because high doses were needed to elicit them.