Crystal structure of a berenil-dodecanucleotide complex: the role of water in sequence-specific ligand binding.

The three-dimensional structure of a complex between the dodecanucleotide d(CGCGAATTCGCG) and the anti-trypanocidal drug berenil, has been determined to a resolution of 2.5 A. The structure has been solved by molecular replacement and refined to an R factor of 0.177. A total of 49 water molecules have been located. The drug is bound at the 5'-AAT-3' region of the oligonucleotide. At one end of the drug the amidinium group is in hydrogen-bonded contact with N3 of the adenine base complementary to the thymine of the AAT. The other amidinium group does not make direct interactions with the DNA. Instead, a water molecule mediates between them. This is in hydrogen-bonded contact with an amidinium nitrogen atom, N3 of the 5' end adenine base and the ring oxygen atom of an adjacent deoxyribose. Molecular mechanics calculations have been performed on this complex, with the drug at various positions along the sequence. These show that the observed position is only 0.8 kcal/mol higher in energy than the best position. It is suggested that there is a broad energy well in the AATT region for this drug, and that water molecules as well as the neighbouring sequence, will determine precise positioning. More general aspects of minor groove binding are discussed.     

15-hydroxyeicosatetraenoic acid stimulates migration of human retinal microvessel endothelium in vitro and neovascularization in vivo

We evaluated 15-hydroxyeicosatetraenoic acid (15-HETE), a major arachidonic acid product of vascular endothelium and leukocytes, for its effect on neovascularization. In a modified Boyden chamber assay, 15-HETE (10⁻⁷ M) sitmulated human retinal microvessel endothelial cell migration by 42 ± 10% (mean ± S.E.M., p<0.01). 12-HETE, a major arachidonic acid metabolite of platelets, had no such effect. Further studies in the rabbit corneal pocket assay revealed that 15-HETE stimulated neovascularization . Concentrations at which the effects were observed are within the range generated by several cell types and are achievable in human serum. 15-HETE stimulation of human endothelial cell migration and neovascularization suggests that it may play a role in vasoproliferative disorders.     

Efficient infection of cells in culture by type O foot-and-mouth disease virus requires binding to cell surface heparan sulfate.

Foot-and-mouth disease virus (FMDV) enters cells by attaching to cellular receptor molecules of the integrin family, one of which has been identified as the RGD-binding integrin alpha(v)beta3. Here we report that, in addition to an integrin binding site, type O strains of FMDV share with natural ligands of alpha(v)beta3 (i.e., vitronectin and fibronectin) a specific affinity for heparin and that binding to the cellular form of this sulfated glycan, heparan sulfate, is required for efficient infection of cells in culture. Binding of the virus to paraformaldehyde-fixed cells was powerfully inhibited by agents such as heparin, that compete with heparan sulfate or by agents that compete for heparan sulfate (platelet factor 4) or that inactivate it (heparinase). Neither chondroitin sulfate, a structurally related component of the extracellular matrix, nor dextran sulfate appreciably inhibited binding. The functional importance of heparan sulfate binding was demonstrated by the facts that (i) infection of live cells by FMDV could also be blocked specifically by heparin, albeit at a much higher concentration of inhibitor; (ii) pretreatment of cells with heparinase reduced the number of plaques formed compared with that for untreated cells; and (iii) mutant cell lines deficient in heparan sulfate expression were unable to support plaque formation by FMDV, even though they remained equally susceptible to another picornavirus, bovine enterovirus. The results show that entry of type O FMDV into cells is a complex process and suggest that the initial contact with the cell surface is made through heparan sulfate.     

Structure and function in the herpes simplex virus 1 RNA-binding protein U(s)11: mapping of the domain required for ribosomal and nucleolar association and RNA binding in vitro.

The herpes simplex virus 1 US11 protein is an RNA-binding regulatory protein that specifically and stably associates with 60S ribosomal subunits and nucleoli and is incorporated into virions. We report that US11/ beta-galactosidase fusion protein expressed in bacteria bound to rRNA from the 60S subunit and not the 40S subunit. This binding reflects the specificity of ribosomal subunit association. Analyses of deletion mutants of the US11 gene showed that specific RNA binding activity, nucleolar localization, and association with 60S ribosomal subunits were found to map to the amino acid sequences of the carboxyl terminus of US11 protein, suggesting that these activities all reflect specific binding of US11 to large subunit rRNA. The carboxyl-terminal half of the protein consists of a regular tripeptide repeat of the sequence RXP and constitutes a completely novel RNA-binding domain. All of the mutant US11 proteins could be incorporated into virus particles, suggesting that the signal for virion incorporation either is at the amino-terminal four amino acids or is redundant in the protein.     

A long-term perspective of dissolved organic carbon transport in Sycamore Creek, Arizona, USA

Dissolved organic carbon (DOC) dynamics were examined over five years (1989–1993) in Sycamore Creek, a Sonoran Desert stream, specifically focusing on DOC concentration in surface and hyporheic waters, and rates of export. In 1989 and 1990, the years of lowest stream discharge (0.08 and 0.04 m³ s^–1 annual mean of daily discharge, respectively), DOC was high, averaging 7.37 and 6.22 mgC l^–1 (weighted annual means). In contrast, from 1991 through 1993, a period of increased flow (1.1, 1.2 and 4.3 m³ s^–1), concentration was significantly lower (P<0.001) with annual mean concentrations of 3.54, 3.49 and 3.39 mgC l^–1. Concentration exhibited little spatial variation between two sampling stations located 6 km apart along the mainstem or between surface and hyporheic waters. Annual export of DOC from Sycamore Creek varied 100-fold over the five-year period from a mean rate of only 24 kgC d^–1 in 1990 to 2100 kgC d^–1 in 1993. Ninety percent of DOC was exported by flows greater than 2.8 m³ s^–1, and 50% during flows greater than 27 m³ s^–1; flows of 2.8 and 24 m³ s^–1 occurred only 9 and 1% of the time. The export of organic matter in Sycamore Creek appears to be coupled to El Niño-Southern Oscillation phenomena. The years of highest export, 1991–1993, had El Niño conditions while 1989 and 1990 had medial conditions.     

The Hypothalamic-Pituitary-Adrenal Axis in Obesity

The hypothalamic-pituitary-adrenal (HPA) axis normally maintains the concentration of Cortisol within a narrow range with a diurnal variation characterized by higher Cortisol concentrations in the morning and reduced levels in the evening. Excessive or deficient secretion of Cortisol is associated with pathologic changes. Obesity has been linked with age, sex and racial alterations in the functioning of the HP A axis which are reviewed. The possible relationship of altered HPA axis activity with the long-term complications of obesity are considered.     

Taxonomy of Pyramimonas obovata and other observations on the subgenus Vestigifera of Pyramimonas (Prasinophyceae, Chlorophyta)

A vestigiferan species commonly referred to as Pyramimonas obovata N. Carter has been redescribed as P. melkonianii sp, nov. Characters of this species and a further six (P. disomata Butcher ex McFadden, Hill et Wetherbee, P. mantoniae Moestrup et Hill, P. mitra Moestrup et Hill. P. moestrupii McFadden, P. aff. nephroidea McFadden, P. orientalis Butcher ex McFadden, Hill et Wetherbee) isolated from South African waters are used to define further the subgenus Vestigifera McFadden. This includes a unique chloroplast shape and basal hyaline region with stellate or cruciform vacuoles, a transitional plate-like structure in the flagellum, and a different microtubular root system. The proximal set of basal body connectives were found to be remarkably symmetrical and like those of the subgenus Trichocystis McFadden, and a duct fibre was found associated with the Id root in all currently investigated species. The validity of the larger body (box and crown) scales as taxonomic markers at a fine level is also questioned.     

Platelet activating factor (PAF) stimulates release of PGI2 from inflamed rabbit gallbladder cell cultures

This study examines the hypothesis that PAF stimulates release of PGI₂ from inflamed rabbit gallbladder explant cell cultures. New Zealand white rabbits underwent bile duct ligation for 72 h (72 h BDL), or sham operation, Sham and 72 h BDL gallbladder explants were placed in culture, and the cells grown to 75% confluence. The cells were exposed to increasing concentrations of PAF for 60 min. The media analyzed for eicosanoid release by EIA and the cells analyzed for cyclooxygenase and prostacyclin synthase content by immunoblot analysis. PAF increased release of 6-keto-PGF_1α from the 72 h BDL gallbladder cell cultures in a dose-related manner which was inhibited by indomethacin preincubation by 90%. The increased 72 h BDL cell release of 6-keto-PGF_1α was not associated with changes in the content of cyclooxygenase or prostacyclin synthase. PAF did not alter eicosanoid release from sham control cell cultures. These data suggest that PAF can only up-regulate endogenous 6-keto-PGF_1α release from the 72 h BDL cells that had been previously stimulated by inflammation. PAF may thus contribute to gallbladder distention and injury by chronic stimulation of inflamed gallbladder PGI₂ release.