Planning an adaptive numerical classification

Summary While numerical methods of classification seek to strictly formalise one part of the classificatory process, a human classifier uses a variety of different approaches to obtain a satisfactory organisation of data. In this paper some means of increasing the flexibility of numerical methods are discussed, in particular the possible uses of the taxonomic hierarchy. It is first necessary to show that higher taxonomic units contain ecologically interesting information. Then, using a two parameter classification method a means of progressing from higher to lower taxonomic units, during analysis and in a data dependent manner, is outlined. A similar procedure is possible with nested samples. However, since the value of a classification resides in its ecological interpretation, an automatic classification requires some means of ascribing meanings to classes. While such a semantic analysis seems theoretically possible, its practical attainment presents considerable difficulties.Contribution to the Symposium on Plant species and plant communities, held at Nijmegen, 11–12 November 1976, on the occasion of the 60th birthday of Professor Victor Westhoff.     

Purification and properties of soybean nodule xanthine dehydrogenase

Xanthine dehydrogenase (EC 1.2.1.37), an essential enzyme for ureide metabolism was purified from the cytosol fraction of soybean nodules. The purified xanthine dehydrogenase was shown to be homogeneous by electrophoresis and a pI of 4.7 was determined by isoelectric focusing. The enzyme had a molecular weight of 285,000 and two subunits of molecular weight 141,000 each. The holoenzyme contained 1.7 (±0.7) mol Mo and 8.1 (±2.0) mol Fe/mol enzyme and the enzyme also contained FMN and is thus a molybdoironflavoprotein. Soybean xanthine dehydrogenase is the second enzyme in plants demonstrated to contain Mo and the first xanthine-oxidizing enzyme reported to contain FMN, rather than FAD as the flavin cofactor.     

Vitreous Carbon: A New Material for Making Microtome Knives

The quality of sections obtained by microtomy depends to a large extent on the quality and characteristics of the microtome knife itself. Despite the need for improved microtomy techniques, there have been few significant developments since the introduction of glass and diamond knives in the 1950's. The manufacture of microtome knives from vitreous carbon provides new possibilities for developing both improved methods and improved equipment for specimen sectioning. Vitreous carbon has unique physical properties that lend themselves to the generation of precision cutting edges. Such an edge can be obtained either by breaking a piece of vitreous carbon or by using lapidary techniques. The resultant edge seems well adapted to both thick and thin sectioning. The introduction of vitreous carbon as a sectioning tool offers a significant alternative to metal, glass and diamond knives.     

Characterization of a phosphorylated form of the intermediate filament-aggregating protein filaggrin

Filaggrin and a phosphorylated form of filaggrin, which has been shown by pulse-chase studies to be a precursor form of the protein [Dale, B. A., & Ling, S. Y. (1979) Biochemistry 18, 3539-3546], were compared for functional, biochemical, and physical properties. Filaggrin reacts with keratin filaments to form visible macrofibrils, unlike the precursor which does not. Biochemical and peptide-mapping studies suggest that the two proteins have similar, perhaps identical, amino acid sequences. The major differences between the two proteins are in molecular weight (precursor, 44 200 g/mol; filaggrin, 38 400 g/mol), the existence of oligomeric forms of the precursor, and the presence of phosphate in the precursor (15-20 mol/mol of protein). Phosphoserine was identified in the precursor, but neither phosphothreonine nor phosphotyrosine was observed. The results of proteolytic digests of [32P]phosphate-radiolabeled precursor show that the phosphate is unevenly distributed throughout the molecule and may be localized in approximately 30% of the precursor. A discrete localization of the phosphate in the precursor may block a specific keratin filament combining site and so prevent premature aggregation of these filaments during epidermal differentiation. It is suggested that a specific phosphatase is involved in the dephosphorylation, because several phosphatases of general specificity, including rat epidermal lysosomal acid phosphatase, did not catalyze this conversion.     

Abundance and distribution of hydroids in a mangrove ecosystem at Twin Cays,Belize, Central America

Qualitative and quantitative collecting was undertaken in 1987 to determine the species composition, abundance, and distribution of hydroids in a mangrove system at Twin Cays, Belize. Of 49 species identified, the 5 most frequent were Ventromma halecioides, Nemalecium sp., Clytia hemisphaerica, Dynamena crisioides and Halopteris diaphana. Line-transect census data and qualitative observations showed that the hydroid fauna was sparse in sheltered, still-water areas of the mangal, but relatively abundant and diverse in areas exposed to waves and/or tidal currents. Species composition and relative abundance varied with depth at stations in exposed locations and in tidal creeks and channels. Although Turritopsoides brehmeri is known only from Twin Cays at present, it seems improbable that any of the species is restricted to mangrove ecosystems.     

Characterization of the human epidermal profilaggrin gene. Genomic organization and identification of an S-100-like calcium binding domain at the amino terminus.

Filaggrin is an intermediate filament-associated protein which functions to aggregate keratin intermediate filaments in the stratum corneum of mammalian epidermis. It is synthesized as a large precursor protein, profilaggrin, that consists of multiple filaggrin units and is localized in keratohyalin granules. In this report, we describe the characterization of cosmid genomic clones containing the human profilaggrin gene coding for 11 complete filaggrin repeats of 324 amino acids each. At the amino- and carboxyl-terminal ends of human profilaggrin are leader and tail peptide sequences of 293 and 157 amino acids, respectively, which differ from filaggrin. The leader peptide is composed of two distinct domains: an 81-residue segment which shows significant homology to the S-100 family of EF hand-containing calcium-binding proteins, and a hydrophilic second domain of 212 residues. The gene is divided into three exons, with one intron (approximately 9.6 kilobase pairs) in the 5' noncoding region and a second one of 570 base pairs between the EF hands. The position of intron 2 is identical to that of other members of the S-100-like family. The presence of an S-100-like domain suggests that profilaggrin binds calcium and that the calcium binding domain is functionally significant in the formation of keratohyalin and/or the subsequent processing of profilaggrin to filaggrin, both of which may be calcium-dependent events.     

Subunit analysis of bovine cytochrome c oxidase by reverse phase high performance liquid chromatography

Bovine cytochrome c oxidase subunits were separated by reverse phase high performance liquid chromatography using a C4 column eluted with water and an acetonitrile gradient, both containing 0.1% trifluoroacetic acid. Subunits I and III precipitated in this solvent and could not be analyzed; the remaining eleven subunits were dissociated, denatured, soluble and could be resolved by elution from the column. The protein subunit eluting in each chromatographic peak was identified by a combination of polyacrylamide gel electrophoresis in sodium dodecyl sulfate, NH2-terminal amino acid sequencing, and amino acid analysis. Each subunit produced a single elution peak with the exception of subunit VIc (nomenclature of Kadenbach et al., 1983, Anal. Biochem. 129, 517-521), which eluted from the column as two well-resolved peaks. Sequence analysis showed that the two subunit VIc elution peaks resulted from partial chemical blockage of the alpha-amino serine residue of subunit VIc. The C4 reverse phase HPLC was used to document specific subunit removal from bovine cytochrome c oxidase either by tryptic digestion or by dodecyl maltoside extraction. The described HPLC method for separating cytochrome c oxidase subunits should be applicable for the analysis of other multisubunit proteins, especially other multisubunit membrane protein complexes.