Increasing the potency and breadth of an HIV antibody by using structure-based rational design

Antibodies against the CD4 binding site (CD4bs) on the HIV-1 spike protein gp120 can show exceptional potency and breadth. We determined structures of NIH45-46, a more potent clonal variant of VRC01, alone and bound to gp120. Comparisons with VRC01-gp120 revealed that a four-residue insertion in heavy chain complementarity-determining region 3 (CDRH3) contributed to increased interaction between NIH45-46 and the gp120 inner domain, which correlated with enhanced neutralization. We used structure-based design to create NIH45-46(G54W), a single substitution in CDRH2 that increases contact with the gp120 bridging sheet and improves breadth and potency, critical properties for potential clinical use, by an order of magnitude. Together with the NIH45-46-gp120 structure, these results indicate that gp120 inner domain and bridging sheet residues should be included in immunogens to elicit CD4bs antibodies.     

Determination of water-extractable nonstructural carbohydrates, including inulin, in grass samples with high-performance anion exchange chromatography and pulsed amperometric detection

The exact and reliable determination of carbohydrates in plant samples of different origin is of great importance with respect to plant physiology. Additionally, the identification and quantification of carbohydrates are necessary for the evaluation of the impact of these compounds on the biogeochemistry of carbon. To attain this goal, it is necessary to analyze a great number of samples with both high sensitivity and selectivity within a limited time frame. This paper presents a rugged and easy method that allows the isocratic chromatographic determination of 12 carbohydrates and sugar alcohols from one sample within 30 min. The method was successfully applied to a variety of plant materials with particular emphasis on perennial ryegrass samples of the species Lolium perenne. The method was easily extended to the analysis of the polysaccharide inulin after its acidic hydrolysis into the corresponding monomers without the need for substantial change of chromatographic conditions or even the use of enzymes. It therefore offers a fundamental advantage for the analysis of the complex mixture of nonstructural carbohydrates often found in plant samples.     

Patterns of trichothecene production, genetic variability, and virulence to wheat of Fusarium graminearum from smallholder farms in Nepal

Fusarium graminearum causes wheat head blight and contaminates grain with the trichothecenes 4-deoxynivalenol and nivalenol. Sequence analysis of trichothecene genes indicates that nivalenol production is the ancestral trait; however, deoxynivalenol producers occur worldwide and predominate in North and South America and in Europe. Analysis of a large field population (>500 strains) from Nepal identified three groups that were both genetically distinct and polymorphic for trichothecene production: SCAR1 comprising 95% deoxynivalenol producers, SCAR2 comprising 94% nivalenol producers, and SCAR3/5 comprising 34% deoxynivalenol producers/63% nivalenol producers. The ability to cause wheat head blight differed between SCAR groups and trichothecene chemotypes: deoxynivalenol producers were more virulent than nivalenol producers across all three SCAR groups and within the SCAR3/5 genetic background. These data support the hypothesis that production of deoxynivalenol rather than nivalenol confers a selective advantage to this important wheat pathogen.     

Anionenbestimmung in natürlichen wässrigen Lösungen: ein Methodenvergleich von ionenchromatographischen und Continuous-Flow-Verfahren

Analysis of anions in natural waters: a comparison of methods including ionchromatography and continuous-flow-technics Using waters from different compartments of forest ecosystems, standard solutions, moreover samples containing known internal standards, several analytical methods were tested for the comparability of nitrate, sulfate and chloride results in an inter-laboratory study. The analytical instruments were ion chromatographs with and without suppression as well as continuous-flow-analyzers. A cluster analysis showed a strong correlation between the obtained data and the analytical method used for nitrate, and a poorer relation for sulfate. Concerning nitrate-analysis, the IC-systems showed a better detection limit and a higher recovery of standards. Mean standard deviation among all tested analytical methods was calculated to be 15% for nitrate, 10% for sulfate and 14% for chloride. These results represent deviations as they may occur during laboratory routine analyses with a high amount of samples and the need for simultaneous determination of several anions. For the examined anions no significant correlation was obtained between the variation of the analytical results and the dissolved organic carbon concentrations of the samples.     

Erratum

OLGA RIGINA and ALEXANDER BAKLANOV: Trends in sulfur emission-induced effects in northern Europe. Water, Air, and Soil Pollution 105 (1–4): 331–342, 1998. Figure 2 was mistakenly put mirrored. The correct Figure 2 is printed below. SO₂ emission from the Severonickel (at Monchegorsk) and Pechenganickel (at Nickel and Zapolyarni) smelters and total for the Kola Peninsula (after the Murmansk Regional Committee of Nature Protection data). The correct legend for Figure 10 should read: Figure 10. Average annual SO² concentrations μg m^-3) at the monitoring stations Svanvik and Holmfoss in the Russian-Norwegian border area and SO₂ emission from the Pechenganickel smelter (kt yr^-1) for 1980–1995 (updated after Sivertsen et al., 1994).     

A metabolomic approach differentiates between conventional and organic ketchups

The agronomic environments in which tomatoes are cultivated potentially affect the levels of antioxidants and other metabolites in commercial products. In this study, biochemical and metabolomic techniques were used to assess the differences between ketchups produced by organic and conventional systems. An untargeted metabolomic approach using QToF-MS was used to identify those nutrients that have the greatest impact on the overall metabolomic profile of organic ketchups as compared to conventional ones. Individual polyphenols were quantified using LC-ESI-QqQ. This multifaceted approach revealed that the agronomic environment in which tomatoes are grown induces alterations in the content of antioxidant capacity, phenolics, and other metabolites in ketchups. Organic cultivation was found to provide tomatoes and tomato-derived products with a significantly higher content of antioxidant microconstituents, whereas glutamylphenylalanine and N-malonyltryptophan were detected only in conventional ketchups.     

A fast method coupling ultrahigh performance liquid chromatography with diode array detection for flavonoid quantification in citrus fruit extracts

Flavonoids are a widely distributed group of polyphenolic compounds present in an extensive range of edible plants, notably Citrus species. This article reports a rapid, optimized, and validated method for the separation and quantification of flavonoids in three Citrus fruit extracts by ultrahigh performance liquid chromatography (UHPLC) using a photodiode array detector. This new procedure allowed the simultaneous separation and quantification of 11 selected flavonoids in 5.5 min, 8.2 times faster than that by HPLC analysis. The solvent consumption for each individual analysis was also reduced almost 6.2-fold. The most abundant component in the analyzed samples was naringin (299.06-544.36 mg 100 g?1), followed by rutin (116.60-256.33 mg 100 g?1) and quercetin (7.78-251.49 mg 100 g?1). Isoquercitrin was found in a lower proportion (60.05-81.88 mg 100 g?1). The method was completely validated, providing a sensitive analysis for flavonoid detection and showing satisfactory data for all the parameters tested. This methodology is cheaper, more environmentally friendly, and easier to perform than others previously described.     

Field mesocosms for assessing biotic processes in soils: How to avoid side effects

Field mesocosms can overcome the simplicity and deficiencies of laboratory based experimental designs. This study deals with a number of possible side effects of a mesocosm technique that involves deep-freezing of soil monoliths to eliminate soil fauna, wrapping in nets of various mesh-size to control faunal immigration and replanting in the field. We used Berlese-Tullgren sets in the field to directly inoculate mesocosms with microarthropods. After 6 months of exposure, the number of collembolans equalled control level whereas immigration and inoculation of oribatids accounted for only 30% of the control. The number of ciliates, their distribution into feeding groups, and the numbers of nematodes, tardigrades and rotifers were not significantly affected by the elimination of mesofauna. We also did not detect significant treatment specific effects on microclimatic conditions within the litter layer of the mesocosms. Furthermore, we compared the monolith approach with a technique using sieved soil as a time-saving alternative. Water capacity and infiltration rate of mesocosms made of sieved soil did not differ from mesocosms made of monoliths, but NH₄⁺ losses were significantly higher in sieved soil when defaunated by deep-freezing. We conclude that the investigated mesocosm technique has little side effects and recommend the use of monoliths in mesocosm studies.

Résumé

La mise en œuvre de mésocosmes au champ peut être une alternative pour pallier la simplicité et aux imperfections des expérimentations en laboratoire. Cette étude aborde les différents effets secondaires potentiellement générés par une approche en mésocosmes, impliquant successivement i) une défaunation des monolithes de sol par congélation intense, ii) leur enrobage au moyen d'une toile de vide de mailles dans le but de contrôler l'immigration de la faune, iii) leur replacement au champ. À l'aide d'appareils de Berlèse-Tullgren utilisés sur place, les mésocosmes ont été ensuite directement inoculés avec les micro-arthropodes extraits. Après 6 mois d'incubation, l'abondance des collemboles est similaire à celle observée initialement dans le sol témoin alors que l'abondance des oribates, par immigration et inoculation, atteint seulement 30% de l'abondance observée dans le sol témoin. L'élimination de la mésofaune n'a pas affecté le nombre de ciliés et leur distribution dans les différents groupes trophiques, ni le nombre de nématodes, de tardigrades et de rotifères. De même, nous n'avons pas mis en évidence de manière significative d'effets secondaires, spécifiques au prétraitement des monolithes sur les conditions microclimatiques régnant au sein de la couche de litière dans les mésocosmes. L'approche en monolithes de sol est aussi comparée avec une approche par tamisage du sol, en tant que technique alternative permettant un gain de temps. La capacité de rétention en eau et le taux d'infiltration mesurés dans les mésocosmes constitués de sol tamisé et ceux constitués de monolithes de sol ne différent pas, mais les pertes en NH₄⁺ sont significativement plus élevées dans les mésocosmes faits de sol tamisé, après l'étape de défaunation par forte congélation. Nous concluons que la technique mésocosme proposée ici présente peu d'effets secondaires et nous recommandons l'utilisation de monolithes de sol pour des études en mésocosmes.     

Biochemical analysis and in vivo hypoglycemic activity of a grape polyphenol-soybean flour complex

Defatted soybean flour (DSF) can efficiently sorb, concentrate, and stabilize polyphenols, but not sugars, from Concord grape juice, to yield grape polyphenol-enriched DSF. Sorption of grape polyphenols to DSF particles was dependent on the ratio of DSF and grape juice concentrate used, but not time of mixing or pH. Depending on ratios of starting materials, 1 g of grape polyphenol-enriched DSF contained 1.6-10.4 mg of anthocyanins, 7.5-93.1 mg of proanthocyanidins, and 20.5-144.5 mg of total polyphenols. LC-MS analysis of grape juice samples before and after addition and removal of DSF and eluate from grape polyphenol-enriched DSF confirmed that a broad range of grape compounds were sorbed to the DSF matrix. Finally, grape polyphenol-enriched DSF was able to significantly lower blood glucose levels in hyperglycemic C57BL/6J mice. The data indicate that grape polyphenol-enriched DSF can provide a high-protein, low-sugar ingredient for delivery of concentrated grape polyphenolics.