Metabolism of phenanthrene by the marine cyanobacterium Agmenellum quadruplicatum PR-6.

Under photoautotrophic growth conditions, the marine cyanobacterium Agmenellum quadruplicatum PR-6 metabolized phenanthrene to form trans-9,10-dihydroxy-9,10-dihydrophenanthrene (phenanthrene trans-9,10-dihydrodiol) and 1-methoxyphenanthrene as the major ethyl acetate-extractable metabolites. Small amounts of phenanthrols were also formed. The metabolites were purified by high-pressure liquid chromatography and identified from their UV, infrared, mass, and proton magnetic resonance spectral properties. A. quadruplicatum PR-6 formed phenanthrene trans-9,10-dihydrodiol with a 22% enantiomeric excess of the (-)-9S,10S-enantiomer. Incorporation experiments with 18O2 showed that one atom of oxygen from O2 was incorporated into the dihydrodiol. Toxicity studies, using an algal lawn bioassay, indicated that 9-phenanthrol and 9,10-phenanthrenequinone inhibit the growth of A. quadruplicatum PR-6.     

Evidence for an NIH shift in oxidation of naphthalene by the marine cyanobacterium Oscillatoria sp. strain JCM.

The marine cyanobacterium Oscillatoria sp. strain JCM oxidized naphthalene predominantly to 1-naphthol. Experiments with [1-2H]naphthalene and [2-2H]naphthalene indicated that 1-naphthol was formed with 68 and 74% retention of deuterium, respectively. No significant isotope effect was observed when the organism was incubated with a 1:1 mixture of naphthalene and [2H8]naphthalene. The results indicate that 1-naphthol is formed through a naphthalene 1,2-oxide intermediate, which rearranges spontaneously via an NIH shift mechanism.     

The taxonomic name resolution service: an online tool for automated standardization of plant names

Background

The digitization of biodiversity data is leading to the widespread application of taxon names that are superfluous, ambiguous or incorrect, resulting in mismatched records and inflated species numbers. The ultimate consequences of misspelled names and bad taxonomy are erroneous scientific conclusions and faulty policy decisions. The lack of tools for correcting this ‘names problem’ has become a fundamental obstacle to integrating disparate data sources and advancing the progress of biodiversity science.

Results

The TNRS, or Taxonomic Name Resolution Service, is an online application for automated and user-supervised standardization of plant scientific names. The TNRS builds upon and extends existing open-source applications for name parsing and fuzzy matching. Names are standardized against multiple reference taxonomies, including the Missouri Botanical Garden's Tropicos database. Capable of processing thousands of names in a single operation, the TNRS parses and corrects misspelled names and authorities, standardizes variant spellings, and converts nomenclatural synonyms to accepted names. Family names can be included to increase match accuracy and resolve many types of homonyms. Partial matching of higher taxa combined with extraction of annotations, accession numbers and morphospecies allows the TNRS to standardize taxonomy across a broad range of active and legacy datasets.

Conclusions

We show how the TNRS can resolve many forms of taxonomic semantic heterogeneity, correct spelling errors and eliminate spurious names. As a result, the TNRS can aid the integration of disparate biological datasets. Although the TNRS was developed to aid in standardizing plant names, its underlying algorithms and design can be extended to all organisms and nomenclatural codes. The TNRS is accessible via a web interface at http://tnrs.iplantcollaborative.org/ and as a RESTful web service and application programming interface. Source code is available at https://github.com/iPlantCollaborativeOpenSource/TNRS/.     

Metabolism of phenanthrene by the marine cyanobacterium Agmenellum quadruplicatum PR-6.

Under photoautotrophic growth conditions, the marine cyanobacterium Agmenellum quadruplicatum PR-6 metabolized phenanthrene to form trans-9,10-dihydroxy-9,10-dihydrophenanthrene (phenanthrene trans-9,10-dihydrodiol) and 1-methoxyphenanthrene as the major ethyl acetate-extractable metabolites. Small amounts of phenanthrols were also formed. The metabolites were purified by high-pressure liquid chromatography and identified from their UV, infrared, mass, and proton magnetic resonance spectral properties. A. quadruplicatum PR-6 formed phenanthrene trans-9,10-dihydrodiol with a 22% enantiomeric excess of the (-)-9S,10S-enantiomer. Incorporation experiments with 18O2 showed that one atom of oxygen from O2 was incorporated into the dihydrodiol. Toxicity studies, using an algal lawn bioassay, indicated that 9-phenanthrol and 9,10-phenanthrenequinone inhibit the growth of A. quadruplicatum PR-6.     

Additive, dominant, and epistatic effects for maize grain yield in acid and non-acid soils

Acid soils severely reduce maize (Zea mays L.) yield in the tropics. Breeding for tolerance to soil acidity provides a permanent, environmentally friendly, and inexpensive solution to the problem. This study was carried out to determine the relative importance of additive, dominant, and epistatic effects on maize grain-yields in different tropical genotypes. Divergent selection in three populations (SA4, SA5, and SA7) provided inbred lines tolerant or sensitive to acid soils. The tolerant and sensitive lines from each population were used to obtain the F₁, F₂, F₃, back-crosses, second back-crosses, and selfed back-cross generations. In addition, the tolerant lines from SA4 and SA5 were crossed with a sensitive line from the Tuxpeño Sequía population, from which the same generations were also derived. All generations from each of the five sets of crosses were evaluated in three acid-soil environments and one non-acid-soil environment. A generation-mean analysis was performed on each set for yield. The sequential sum of squares associated with additive, dominance, and digenic epistatic effects were used to estimate the relative importance of each genetic effect. Epistasis was not important in any set in the non-acid-soil environment, with dominance accounting for 80.76% of the total variation among generation means across sets. In acid-soil environments, epistasis was more important. The relative importance of digenic epistasis was greater in those evaluations with large experimental errors. The tolerant line from population SA5 was prone to severe root lodging, suggesting a very poor root system. Apparently, the tolerance to soil acidity in this line is not associated with a large root system.     

Response of left ventricular diastolic filling to graded exercise relative to the lactate threshold

During incremental exercise, the left ventricular ejection fraction increases up to the intensity of the anaerobic threshold and tends to level off at higher exercise intensities. Since there is a correlation between the response of peak filling rate and ejection fraction to exercise, this study was conducted to determine whether the response of left ventricular diastolic function is similar to the response of systolic function relative to lactate threshold. Twelve healthy men performed two exercise tests on a cycle ergometer. In the first test, lactate threshold and maximal power output were determined. In the second exercise test, gated radionuclide ventriculography was performed at rest, at the lactate threshold intensity, and at peak exercise to measure ejection fraction and peak filling rate. Ejection fraction increased significantly from rest [mean (SD): 62 (5)%] to lactate threshold [76 (7) %] and did not change significantly from lactate threshold to peak exercise [77 (7)%]. Likewise, peak filling rate (normalized for stroke counts) increased from resting [6.1 (0.9)V _s · s^–1] to lactate threshold [9.4 (1.8)V _s · s^–1] and did not change significantly from lactate threshold to peak exercise [9.6 (2.9)V _s · s^–1]. There was no correlation between the change in peak filling rate and the change in ejection fraction from rest to lactate threshold. Thus, during incremental exercise, left ventricular diastolic function responds qualitatively similar to systolic function.     

Evidence for an NIH shift in oxidation of naphthalene by the marine cyanobacterium Oscillatoria sp. strain JCM.

The marine cyanobacterium Oscillatoria sp. strain JCM oxidized naphthalene predominantly to 1-naphthol. Experiments with [1-2H]naphthalene and [2-2H]naphthalene indicated that 1-naphthol was formed with 68 and 74% retention of deuterium, respectively. No significant isotope effect was observed when the organism was incubated with a 1:1 mixture of naphthalene and [2H8]naphthalene. The results indicate that 1-naphthol is formed through a naphthalene 1,2-oxide intermediate, which rearranges spontaneously via an NIH shift mechanism.