Systematic development of computational models for the catalytic site in galactose oxidase: impact of outer-sphere residues on the geometric and electronic structures

A systematic in silico approach has been employed to generate sound, experimentally validated active-site models for galactose oxidase (GO) using a hybrid density functional, B(38HF)P86. GO displays three distinct oxidation states: oxidized [Cu(II)-Y*]; semireduced [Cu(II)-Y]; and reduced [Cu(I)-Y]. Only the [Cu(II)-Y*] and the [Cu(I)-Y] states are assumed to be involved in the catalytic cycle, but their structures have not yet been determined. We have developed several models (1-7) for the [Cu(II)-Y*] state that were evaluated by comparison of our computational results with experimental data. An extended model system (6) that includes solvent molecules and second coordination sphere residues (R330, Y405, and W290) is essential to obtain an experimentally correct electronic structure of the active site. The optimized structure of 6 resulted in a five-coordinate Cu site with a protein radical centered on the Tyr-Cys cofactor. We further validated our converged model with the largest model (7) that included additional outer-sphere residues (Q406, H334, Y329, G513, and T580) and water molecules. Adding these residues did not affect significantly the active site's electronic and geometric structures. Using both 6 and 7, we explored the redox dependence of the active-site structure. We obtained four- and three-coordinate Cu sites for [Cu(II)-Y] and [Cu(I)-Y] states, respectively, that corroborate well with the experimental data. The relative energies of these states were validated by a comparison with experimental redox potentials. Collectively, our computational GO models well reproduce the physicochemical characteristics of the individual states, including their redox behaviors.     

Tetrameric restriction enzymes: expansion to the GIY-YIG nuclease family

The GIY-YIG nuclease domain was originally identified in homing endonucleases and enzymes involved in DNA repair and recombination. Many of the GIY-YIG family enzymes are functional as monomers. We show here that the Cfr42I restriction endonuclease which belongs to the GIY-YIG family and recognizes the symmetric sequence 5′-CCGC/GG-3′ (‘/’ indicates the cleavage site) is a tetramer in solution. Moreover, biochemical and kinetic studies provided here demonstrate that the Cfr42I tetramer is catalytically active only upon simultaneous binding of two copies of its recognition sequence. In that respect Cfr42I resembles the homotetrameric Type IIF restriction enzymes that belong to the distinct PD-(E/D)XK nuclease superfamily. Unlike the PD-(E/D)XK enzymes, the GIY-YIG nuclease Cfr42I accommodates an extremely wide selection of metal-ion cofactors, including Mg²⁺, Mn²⁺, Co²⁺, Zn²⁺, Ni²⁺, Cu²⁺ and Ca²⁺. To our knowledge, Cfr42I is the first tetrameric GIY-YIG family enzyme. Similar structural arrangement and phenotypes displayed by restriction enzymes of the PD-(E/D)XK and GIY-YIG nuclease families point to the functional significance of tetramerization.     

Micropropagation of Achillea filipendulina cv. ‘Parker’

Achillea filipendulina (family Asteraceae) is widespread throughout temperate North America. In order to clean stock plants from endemic fungal and bacterial contaminations a method for large-scale propagation of A. filipendulina through meristem culture was sought and found and is described in this paper. The best conditions for propagating A. filipendulina was found to be MS (Murashige and Skoog) salt medium supplemented with 3% sucrose and 1 mg l^–1 IAA (indole-3-acetic acid) plus 2 mg l^–1 BA (6-benzyladenine) under 16 h of cool fluorescent light. Rooted plants were successfully acclimatized within a short time after propagating on this medium. The propagation via tissue culture did not affect plant's presentation. The use of clean stock plants made it possible to increased Israeli production of Achillea from about 150,000 stems a year to about 1,300,000 stems a year.     

Truncated vitronectins: binding to immobilized fibrin and to fibrin clots, and their subsequent interaction with cells.

The plasminogen activator inhibitor-1 (PAI-1) is stabilized in its inhibitory conformation by binding to Vitronectin (Vn). The anchorage of PAI-1 to the fibrin fibers was recently shown to be mediated by Vn, and as such to modulate fibrinolysis. Here we report the mapping of the fibrin binding sites in Vn using truncated recombinant Vns, and show that two segments of Vn are involved: one at its carboxyl terminus (within residues 348-459) and one at its amino terminus (within residues 1-44). This mapping sets the stage for (i) the design of specific inhibitors for the Vn-fibrin interaction; (ii) for studying the role of this interaction in the anchoring of endothelial cells and platelets onto the fibrin clot; and (iii) for getting a deeper insight into the mechanism of the Vn-fibrin interaction in fibrinolysis. (c)2002 Elsevier Science.     

Occurrence of trichothecenes, zearalenone and ochratoxin A in cereals and mixed feed from central Lithuania

A total of 92 samples — 23 winter wheat, 12 summer barley, 5 oats and 52 mixed feed — were collected from a state factory in Kaunas, Lithuania and were analysed for the presence of trichothecenes, zearalenone (ZEN) and ochratoxin A (OA) using gas chromatography with electron capture detection and immunoaffinity column/high performance liquid chromatography with fluorescence and UV detections. Deoxynivalenol (DON), nivalenol (NIV), T-2 toxin and HT-2 toxin were detected at concentrations above 10 μg/kg in 68%, 48%, 38% and 8% of cereal samples, respectively, and in 98%, 88%, 12% and 8% of samples of mixed feed for swine and poultry. More than 10 μg/kg of zearalenone and ochratoxin A were found in 58% and 92% of the mixed feed samples, respectively. The highest concentrations of all analysed trichothecenes in Lithuanian mixed feed and cereal grains, with an exception of T-2 toxin in one oat lot and one sample of mixed feed and OA in two mixed feed samples, were lower than those reported as Lithuanian advisory or tolerance limits.     

Bone remodelling induced by physical stress is prostaglandin E2 mediated

In vitro cultured bone cells were found to be responsive to hormones and physical forces. A simple device has been developed which enables the direct application of physical forces to tissue culture dishes to which cells are firmly attached. The physical forces created a deformation of the dish. It was found that prostaglandin E₂ synthesis underwent a rapid increase, reaching a maximum after 20 min and then declined. Concurrent with the increase in prostaglandin E₂ was an increase in cyclic AMP production, having a maximum around 15 min. The increase in cyclic AMP was blocked by indomethacin, the prostaglandin E₂ synthesis inhibitor, indicating the dependence of cyclic AMP production on the de novo synthesis of prostaglandin E₂. Prostaglandin E₂ added to cells mimicked the effect of physical forces on the production of cyclic AMP. The increase in cyclic AMP resulted from an early rise in adenyl cyclase activity (within 5 min) and a later (10 min) increase in phosphodiesterase activity. The same physical forces also stimulatedthe incorporation of thymidine into DNA after 24 h. On addition of prostaglandin E₂ the increase in DNA synthesis was also mimicked. Pretreatment of the cells with indomethacin abolished the effect of physical forces on DNA synthesis.The results suggest a stimulus receptor mechanism for physical forces which, like hormonal effectors, are mediated by prostaglandins and stimulate cyclic AMP and DNA synthesis.We believe that physical forces stimulate bone remodelling through such a stimulus receptor system, mediated by prostaglandins.     

Postnatal development of uterine response to estradiol-17β in the rat

The gradual acquisition of uterine responsiveness to a single injection of estradiol-17β was studied in rats aged 5–30 days with respect to wet weight and the content of DNA, RNA, and protein. No significant response in any of these parameters was found in 5- or 10-day-old rats. In 15- and 20-day-old rats all the parameters, except DNA content, were elevated by the hormone treatment; only in 30-day-old rats was there a significant increase in DNA content.     

Phylogeny in Echinocereus (Cactaceae) based on combined morphological and molecular evidence: taxonomic implications

Echinocereus is a morphologically diverse genus that includes 64 species grouped into eight taxonomic sections based on morphological traits. In previous molecular phylogenetic analyses, the relationships amongst Echinocereus species were not entirely revealed and useful characters to recognize clades were not provided. The inclusion of several sources of evidence in a phylogenetic analysis is likely to produce more supported hypotheses. Therefore, we performed a combined phylogenetic analysis with a set of 44 morphological characters and six chloroplast DNA sequences. Topologies from parsimony and Bayesian analyses were mostly congruent. However, the relationships of E. poselgeri were not consistent between analyses. A second Bayesian analysis using a long-branch extraction test resulted in a topology with the morphological position of E. poselgeri congruent with that in parsimony analysis. Parsimony and Bayesian analyses corroborated the monophyly of Echinocereus, which included eight monophyletic groups. The combined phylogeny integrated into different clades those taxa that were not determined in previous analyses and changed the relationships of some recognized clades. The clades did not recover the recent infrageneric classification. In the present study, a new sectional classification for Echinocereus is proposed based on the eight recovered clades, which is supported by a combination of morphological and molecular characters. An identification key for sections in the genus is included.     

Utility of ninhydrin reagent for spectrofluorimetric determination of heptaminol in human plasma

For the determination of heptaminol (HEP) in its authentic and dosage form as well as in human plasma, a new simple, sensitive and cheap fluorimetric method of analysis was developed and validated. The presented method is based on the reaction between aliphatic primary amino moiety present in HEP with ninhydrin and phenylacetaldehyde using Torell and Stenhagen buffer at pH 8.2 that yields a highly fluorescent derivative which after excitation at 390 nm showed a fluorescence emission at 464 nm. The effects of various experimental factors on both the development and stability of the fluorescent product was evaluated and optimized. In the concentration range (0.5–6.0 μg/ml), the constructed calibration curve was linear with a good correlation coefficient (0.9997) and the calculated limit of detection (LOD) and limit of quantitation (LOQ) were 0.14 and 0.43 respectively. The presented method was successfully applied for determination of Corasore® tablets and validated according to ICH guidelines.     

Reproductive ecology of <Emphasis Type="Italic">Agave colorata</Emphasis>: the importance of nectar-feeding bats and the germination consequences of self-pollination

Agave colorata is a paniculate agave distributed along the migratory route of the nectar-feeding bat Leptonycteris yerbabuenae. In this paper, we evaluate the importance of nectar-feeding bats in the reproduction of A. colorata in a population in Sonora, Mexico, and describe the germination consequences of self-pollination. We estimated abundance using five plots and set pollination treatments to evaluate the importance of bats. We recorded 14.8?±?6.8 plants/400 m², with a bimodal size distribution. Flowers are protandrous and visited mainly (>?20 visits/plant/30 min) by L. yerbabuenae. Pollination exclusion experiments showed that flowers excluded from diurnal visitors had maximum fruit set values (0.49?±?0.42), while the autonomous self-pollination treatment had the lowest value (0.03?±?0.06). Similarly, the greatest number of viable seeds per fruit was recorded in the diurnal exclusion treatment, while the greatest number of empty seeds was observed in the self-pollination treatment. Fruit set values among untreated plants varied from 32 to 54%, with a mean value of 41.8%. Seeds derived from self-pollination had a narrower window of opportunity for germination compared to seeds derived from nocturnal pollination. Self-pollinated seeds had lower germination, rate of germination or lag time in response to light, osmotic potential and heat shock treatments, compared to other pollination treatments, revealing an inbreeding cost. Overall, our results show that L. yerbabuenae is the likely major pollinator of the studied A. colorata population. However, under pollinator limitation A. colorata may produce seeds by autonomous self-pollination, at a cost expressed as lower germination.