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PubMed1986

[Taxonomy and systematics of pathogenic microorganisms].

The modern state of the problem of the systematics of microorganisms is analyzed and the data on the taxonomy of bacteria belonging to the family Enterobacteriaceae are presented. The importance of studies on the taxonomy of microorganisms is emphasized. These studies play a vital role in the development of diagnostic preparations and techniques for the identification of infective agents, as well as in the realization of epidemiological surveillance. Much attention is given to the works of Soviet microbiologists, discussing such problems as the unification of the classification scheme of dysentery bacteria, the intraspecific taxonomy of Francisella tularensis, the systematic position of Allomonas and the antigenic scheme of Hafnia, included into Bergey's Determinative Bacteriology, edition IX (1984).

DNA, Bacterial↗

PubMed1989

Problems in taxonomy of streptomycetes.

The bacterial species concept has different bearings. It is used to define "natural" entities with low intra-group variation, but also to serve more subjective purposes. One of problems in Streptomyces taxonomy is that it applies the species concept in both ways, i.e. both to clarify natural relationships and to protect potential (bio)technological inventions. The latter usage has introduced a streptomycetal "technospecies" which may require definition and description in other terms and by other tools than the "nomentaxospecies" which represent a more objective approach to Streptomyces taxonomy. Genetic engineering creates "man-made" microorganisms which are characterized by completely different sets of criteria as compared to their natural counterparts, which may imply needs for different taxonomies for both kinds of organisms. However, since they may occur side by side in one environment both "man-made" and "natural" streptomycetes have to be identified and classified by the same methods and tools, but in such a way which allows their separation.

Streptomyces↗

PubMed1986

[Determination of the optimal method of numerical taxonomy].

A great number of numeric taxonomy methods, varying in the techniques of coding signs, similarity calculations and group analysis, as well as the insufficiency of criteria for the evaluation of numeric taxonomy methods, permitted us to propose the quantitative approach to the evaluation of the optimum method of numeric taxonomy. The dendrograms obtained by different methods were compared by calculating the measure of "proximity" which was assumed to be the sum of distances between divisions on different grouping levels.

Bacteria↗

PubMed1981

[The application of a numerical method to the taxonomy of the genus Leishmania Ross, 1903,--The recognition of 146 original lines in the Old World. Use of allozymic characters. Epidemiological and phyletic significance (author's transl)].

Using enzyme characters determined by starch gel electrophoresis, the authors have applied the method of Numerical Taxonomy to the genus Leishmania Ross, 1903. Eight isoenzymes (PGI, ME, PGM, GOT, G-6-PDH, 6-PGDH, MDH and IDH) of 146 Old World strains are examined. 35 electromorphs, corresponding to equivalent number of isoenzymes, are identified by this method, and then grouped into 14 zymodemes. These zymodemes were used as Operational Taxonomy Units (OTU) and pairs were compared, using Jaccard's index of similarity. A matrix of association was constructed using these indices and it forms the basis for the taxonomic scheme elaborated. The final relationships are exhibited in the agglomerative dendrogram, constructed using complete linkage. The separation into phylons is confirmed by correspondence analysis. It is concluded that the original lines fall into five groups corresponding to the complexes Leishmania donovani, Leishmania tropica, Leishmania major, Leishmania aethiopica and cf. Leishmania tarentolae. The phylons as recognised by Numerical Taxonomy, can be equated with the taxa of traditional systematics. The phyletic significance of the individualized phylons is then provided by a genetic approach. Thus, it is possible to compute the genetic distances of Nei with allozyme frequency values of 0,0.5 and 1. The new dendrogram is similar to the previous one: Leishmania major constitutes an homogeneous taxon, long isolated from the others. Leishmania donovani and Leishmania tropica have retained a nonnegligible amount of genetic similarity, attesting both a common origin and a more recent evolutionary divergence.

Animals↗

PubMed1996

Taxonomy of high-risk situations for alcohol relapse: evolution and development of a cognitive-behavioral model.

The purpose of this paper is to provide an historical overview of the development of the taxonomy of high-risk situations for relapse in patients receiving abstinence-based treatment for alcoholism. Research conducted during the 1970s on determinants of relapse is briefly reviewed, beginning with a preliminary analysis of relapse patterns in alcoholics treated with aversion therapy. Theoretical foundations underlying the development of the taxonomy are then discussed with an emphasis on social-learning theory and its implications for cognitive-behavioral interventions for relapse prevention. Findings supporting the efficacy of coping-skills training for high-risk relapse situations, based on a prospective treatment outcome study for inpatient alcoholics, are also presented in support of the clinical validity of the relapse model. The paper concludes with a description of the refined and extended taxonomy of high-risk situations and the associated cognitive-behavioral model of relapse described in the Marlatt & Gordon (1985) text on relapse prevention.

Adaptation, Psychological↗

PubMed2004

Taxonomy as a contextualist views it.

The Henriques' article, "Psychology Defined" (this issue), reflects an underlying philosophy of science that emphasizes coherence as its truth criterion. The taxonomic efforts that result are of unknown value when viewed from other philosophical positions. From the point of view of functional contextualism, the primary metric of successful science is not coherence per se, but the precision, scope, and depth of the analysis as a means of predicting and influencing psychological phenomena. Henriques presents neither data nor specific research proposals that would allow even the beginning application of such a metric. Thus, the proposed taxonomy has no known value when viewed contextualistically. Since the practical goals of clinical psychology are very similar to those of functional contextualism, clinical psychologists interested in making a practical difference will have few current empirical reasons to be attracted to this taxonomy.

Animals↗

PubMed1998

Molecular tests of phylogenetic taxonomies: a general procedure and example using four subfamilies of the lizard family Iguanidae.

A general procedure is described for examining when results of molecular phylogenetic analyses warrant formal revision of taxonomies constructed using morphological characters. We illustrate this procedure with tests of monophyly for four subfamilies in the lizard family Iguanidae using 1561 aligned base positions (838 phylogenetically informative) of mitochondrial DNA sequences, representing coding regions for eight tRNAs, ND2, and portions of ND1 and COI. Ten new sequences ranging in length from 1732 to 1751 bases are compared with 12 previously reported sequences and 67 morphological characters (54 phylogenetically informative) from the literature. New morphological character states are provided for Sator. Phylogenies derived from the molecular and combined data are in agreement but both conflict with phylogenetic inferences from the morphological data alone. Strong support is found for the monophyly of the subfamilies Crotaphytinae and Phrynosomatinae. Monophyly of the Iguaninae is weakly supported in each analysis. All analyses suggest that the Tropidurinae is not monophyletic but the hypothesis of monophyly cannot be rejected. A phylogenetic taxonomy is proposed in which the Tropidurinae* is maintained as a metataxon (denoted with an asterisk), for which monophyly has not been demonstrated. Within the Phrynosomatinae, the close relationship of Sator and Sceloporus is questioned and an alternative hypothesis in which Sator is the sister taxon to a clade comprising Petrosaurus, Sceloporus, and Urosaurus is presented. Statistical tests of monophyly provide a powerful way to evaluate support for taxonomic groupings. Use of the metataxon prevents premature taxonomic rearrangements where support is lacking.

Animals↗

PubMed1992

Specific infectivity and host resistance have predicated potyviral and pathotype nomenclature but relate less to taxonomy.

The names of potyviruses and viral-strains have represented the occurrence of predominant pathotypes on predominant crop genotypes. Thus virus nomenclature, but not viral taxonomy, has been decisively influenced by plant-genotype susceptibility and indirectly by host genetic resistance. REsistance to infection (i.e., host range) continues to serve a practical role in differentiating recognized viruses. Plant genes that confer disease tolerance or viral resistance remain a principal means of viral pathotype differentiation, as well as a principal control measure against major viral pathogens. Degrees of genetic diversity among isolates of recognized viruses should not be underestimated, and any system of viral taxonomy should be prepared for flexibility at the species level.

Immunity, Innate↗

PubMed1992

The recombinative nature of potyviruses: implications for setting up true phylogenetic taxonomy.

Sequence comparisons reveal that positive-strand RNA viruses not only evolve by divergence from common ancestors but also by interviral recombination. A considerable number of these viruses, exemplified by the family Potyviridae, can in fact, be regarded as successful products of a number of recombination events. It is concluded that the recombinative character of RNA viruses will hamper any attempt to set up a true phylogenetic taxonomy. It is advisable, therefore, to avoid the introduction of any taxon higher-than-family in virus taxonomy.

Picornaviridae↗

PubMed1990

The problem of the taxonomy of the fusiform bacillus of acute necrotizing ulcerative gingivitis (Vincent's gingivitis).

The characteristic microscopic appearance of the fusospirochaetal complex in smears from patients with acute necrotizing ulcerative gingivitis has long been regarded as virtually pathognomonic of the disease. Unfortunately there is considerable confusion surrounding the taxonomy of the fusiform organism in the fusospirochaetal complex. The conflicting views appear to be irreconcilable and a re-evaluation of the taxonomy of oral fusiforms is urgently required.

Bacteroidaceae↗

PubMed2003

A comparative sequence analysis to revise the current taxonomy of the family Coronaviridae.

The Coronaviridae family, comprising the Coronavirus and Torovirus genera, is part of the Nidovirales order that also includes two other families, Arteriviridae and Roniviridae. Based on genetic and serological relationships, groups 1, 2 and 3 were previously recognized in the Coronavirus genus. In this report we present results of comparative sequence analysis of the spike (S), envelope (E), membrane (M), and nucleoprotein (N) structural proteins, and the two most conserved replicase domains, putative RNA-dependent RNA polymerase (RdRp) and RNA helicase (HEL), aimed at a revision of the Coronaviridae taxonomy. The results of pairwise comparisons involving structural and replicase proteins of the Coronavirus genus were consistent and produced percentages of sequence identities that were distributed in discontinuous clusters. Inter-group pairwise scores formed a single cluster in the lowest percentile. No homologs of the N and E proteins have been found outside coronaviruses, and the only (very) distant homologs of S and M proteins were identified in toroviruses. Intragroup sequence conservation was higher, although for some pairs, especially those from the most diverse group 1, scores were close or even overlapped with those from the intergroup comparisons. Phylogenetic analysis of six proteins using a neighbor-joining algorithm confirmed three coronavirus groups. Comparative sequence analysis of RdRp and HEL domains were extended to include arterivirus and ronivirus homologs. The pairwise scores between sequences of the genera Coronavirus and Torovirus (22-25% and 21-25%) were found to be very close to or overlapped with the value ranges (12 to 22% and 17 to 25%) obtained for interfamily pairwise comparisons, but were much smaller than values derived from pairwise comparisons within the Coronavirus genus (63-71% and 59-67%). Phylogenetic analysis confirmed toroviruses and coronaviruses to be separated by a large distance that is comparable to those between established nidovirus families. Based on comparison of these scores with those derived from analysis of separate ranks of several multi-genera virus families, like the Picornaviridae, a revision of the Coronaviridae taxonomy is proposed. We suggest the Coronavirus and Torovirus genera to be re-defined as two subfamilies within the Coronavirdae or two families within Nidovirales, and the current three informal coronavirus groups to be converted into three genera within the Coronaviridae.

Conserved Sequence↗

PubMed2005

Managing risk: a taxonomy of error in health policy.

This paper discusses the current initiatives on error and adverse events within healthcare, with a particular focus on the NHS, within the context of health policy. One of the key features of the paper is the proposal for an emergent taxonomy of the medical error literature, developed from the ideologies and rationales that underpin their approaches. This taxonomy provides details of three categories--empiricists, organisational rationalists and reformers of professional culture--and these act as an organising framework for the exploration of the potential consequences of current policy on errors and adverse events. This discussion highlights the tension between optimising health outcomes for patients and managing the health system as effectively as possible. In particular, the inherent tension between explicit managerial formulations of risk and implicit risk management strategies associated with medical professionalism are considered.

Classification↗

PubMed2000

General characteristics of Pinus spp. seed fatty acid compositions, and importance of delta5-olefinic acids in the taxonomy and phylogeny of the genus.

The delta5-unsaturated polymethylene-interrupted fatty acid (delta5-UPIFA) contents and profiles of gymnosperm seeds are useful chemometric data for the taxonomy and phylogeny of that division, and these acids may also have some biomedical or nutritional applications. We recapitulate here all data available on pine (Pinus; the largest genus in the family Pinaceae) seed fatty acid (SFA) compositions, including 28 unpublished compositions. This overview encompasses 76 species, subspecies, and varieties, which is approximately one-half of all extant pines officially recognized at these taxon levels. Qualitatively, the SFA from all pine species analyzed so far are identical. The genus Pinus is coherently united--but this qualitative feature can be extended to the whole family Pinaceae--by the presence of delta5-UPIFA with C18 [taxoleic (5,9-18:2) and pinolenic (5,9,12-18:3) acids] and C20 chains [5,11-20:2, and sciadonic (5,11,14-20:3) acids]. Not a single pine species was found so far with any of these acids missing. Linoleic acid is almost always, except in a few cases, the prominent SFA, in the range 40-60% of total fatty acids. The second habitual SFA is oleic acid, from 12 to 30%. Exceptions, however, occur, particularly in the Cembroides subsection, where oleic acid reaches ca. 45%, a value higher than that of linoleic acid. Alpha-linolenic acid, on the other hand, is a minor constituent of pine SFA, almost always less than 1%, but that would reach 2.7% in one species (P. merkusii). The sum of saturated acids [16:0 (major) and 18:0 (minor) acids principally] is most often less than 10% of total SFA, and anteiso-17:0 acid is present in all species in amounts up to 0.3%. Regarding C18 delta5-UPIFA, taxoleic acid reaches a maximum of 4.5% of total SFA, whereas pinolenic acid varies from 0.1 to 25.3%. The very minor coniferonic (5,9,12,15-18:4) acid is less than 0.2% in all species. The C20 elongation product of pinolenic acid, bishomo-pinolenic (7,11,14-20:3) acid, is a frequent though minor SFA constituent (maximum, 0.7%). When considering C20 delta5-UPIFA, a difference is noted between the subgenera Strobus and Pinus. In the former subgenus, 5,11-20:2 and sciadonic acids are < or =0.3 and < or =1.9%, respectively, whereas in the latter subgenus, they are most often > or =0.3 and > or =2.0%, respectively. The highest values for 5,11-20:2 and sciadonic acids are 0.5% (many species) and 7.0% (P. pinaster). The 5,11,14,17-20:4 (juniperonic) acid is present occasionally in trace amounts. The highest level of total delta5-UPIFA is 30-31% (P. sylvestris), and the lowest level is 0.6% (P. monophylla). Uniting as well as discriminating features that may complement the knowledge about the taxonomy and phylogeny of pines are emphasized.

Cycadopsida↗

PubMed1984

A clinical taxonomy for the categorization of pragmatic language functions in normal preschool children.

The present study assessed the pragmatic language skills in normal preschool children. A specially designed taxonomy was used to classify the subjects' responses. Findings revealed (1) high reliability in the use of the taxonomy; (2) a decrease in the inappropriate responses used by children with an increase in age; (3) generally, inappropriate responses were confined to the same categories across age levels. Findings are discussed relative to patterns of pragmatic language development as a function of age.

Child, Preschool↗

PubMed1980

Delimitation of Trypanosoma cruzi zymodemes by numerical taxonomy.

Based on the absence or presence of 24 isoenzyme characters, Brazilian Trypanosoma cruzi stocks can be separated by methods of numerical taxonomy into three principal, distinct groups; these groups correspond to the three T. cruzi zymodemes previously reported from north Brazil. A distinction is drawn between taxonomy, which may be of zoological interest only, and identification of medically important groups according to one or a few distinguishing characters.

Animals↗

PubMed1989

The taxonomy of invertebrate neurons: a plea for a new field.

It is generally accepted that the 'identified cell' concept and its practical application are responsible for the appeal of invertebrate preparations (and perhaps in the near future of certain vertebrate preparations too) for general neurobiology. The considerable number of neurons contained in many such preparations, and the number of investigations to which they are subjected, has led to a minor crisis: it is increasingly hard to determine whether a given neuron has been previously described, and if so, under what name. The taxonomy of identified interneurons requires a far more serious and rigorous approach than has so far been the rule. The main proposals made in this article are for the application of the normal procedural rules of classical organism taxonomy, which are highly applicable to the neural situation, and for a standardized nomenclature. Also recommended is the establishment of networked computer data bases for each of the popular invertebrate preparations (e.g. locusts, leeches) and of international committees for their supervision, and the increased use of confocal fluorescence microscopy to increase the amount of anatomical data which can be gathered from a normal physiological preparation.

Animals↗

PubMed1988

The taxonomy of social support: an ethnographic analysis among adolescent mothers.

Current approaches to assessing the health-related functions of social support are based on a theoretical frame of reference regarding the taxonomic structure of social networks. Nearly all previous work addresses the issue of social network taxonomies from an etic (i.e. objective, outside) rather than emic (i.e. subjective) perspective. Because of this, we intensively studied 5 unmarried adolescent mothers over the year following the delivery of their firstborn infants, utilizing ethnographic methods to elicit detailed portrayals of their personal, subjective taxonomies of social network support. Ranked in order of successful adaptation to parenthood, the young women with the best outcomes displayed a richer, more differentiated view of their social networks' taxonomic structure and regarded individual network members as more diverse in their capacity to provide broad, multi-faceted support. A common element among all subjects was the tendency to discriminate among categories of network members according to the stability and continuity perceived in individual relationships.

Adolescent↗

PubMed1988

Present state of lactic acid bacteria phage taxonomy.

Recent developments in molecular taxonomy of bacteriophages of lactobacilli and lactic streptococci are presented. DNA homology appears to be the most valid criterion in studying phage taxonomy. For each bacterial species, phages can be classified in a few families according to this criterion. A fair correspondence is observed between the groups differentiated by DNA-DNA hybridization and those differenciated by protein composition. In 2 bacterial species, a close relatedness between some virulent and temperate phages has been demonstrated. The presence of homologous sequences in the genome of various phages may play an important role in their evolution. For future taxonomic studies, some phages representative of DNA homology groups are proposed as reference phages.

Bacteriophages↗