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PubMed1983

Neurotoxins from the venoms of the sea snakes Hydrophis ornatus and Hydrophis lapemoides.

The main neurotoxic components, toxins Hydrophis ornatus a and Hydrophis lapemoides a, were isolated from the venoms of the sea snakes Hydrophis ornatus and Hydrophis lapemoides respectively. The amino acid sequence of toxin Hydrophis ornatus a was deduced to be identical with that of toxin Astrotia stokesii a [Maeda & Tamiya (1978) Biochem. J. 175, 507-517] on the basis of identity of the tryptic peptide 'map' and the amino acid composition of each peptide. The amino acid sequence of toxin Hydrophis lapemoides a was determined mainly on the basis of identity of the amino acid compositions, mobilities on paper electrophoresis and migration positions on paper chromatography of the tryptic peptides with those of other sea-snake toxins whose sequences are known. Both toxins Hydrophis ornatus a and Hydrophis lapemoides a consisted of 60 amino acid residues and there were six amino acid replacements between them. The taxonomy of sea snakes in the Hydrophis ornatus complex has long been confused, and the above snakes were originally assigned to taxa that proved to be inconsistent with the relationships indicated by the neurotoxin amino acid sequences obtained. A subsequent re-examination of the specimens revealed an error in the original identifications and demonstrated the value of the protein amino acid sequences in systematic and phylogenetic studies. The isolation procedure and results of amino acid analysis of the tryptic peptides have been deposited as Supplementary Publication SUP 50121 (8 pages) with the British Library Lending Division, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies may be obtained as indicated in Biochem. J. (1983) 209, 5.

Amino Acid Sequence↗
PubMed2004

Dissection of phylogenetic relationships among 19 rapidly growing Mycobacterium species by 16S rRNA, hsp65, sodA, recA and rpoB gene sequencing.

The current classification of non-pigmented and late-pigmenting rapidly growing mycobacteria (RGM) capable of producing disease in humans and animals consists primarily of three groups, the Mycobacterium fortuitum group, the Mycobacterium chelonae-abscessus group and the Mycobacterium smegmatis group. Since 1995, eight emerging species have been tentatively assigned to these groups on the basis of their phenotypic characters and 16S rRNA gene sequence, resulting in confusing taxonomy. In order to assess further taxonomic relationships among RGM, complete sequences of the 16S rRNA gene (1483-1489 bp), rpoB (3486-3495 bp) and recA (1041-1056 bp) and partial sequences of hsp65 (420 bp) and sodA (441 bp) were determined in 19 species of RGM. Phylogenetic trees based upon each gene sequence, those based on the combined dataset of the five gene sequences and one based on the combined dataset of the rpoB and recA gene sequences were then compared using the neighbour-joining, maximum-parsimony and maximum-likelihood methods after using the incongruence length difference test. Combined datasets of the five gene sequences comprising nearly 7000 bp and of the rpoB+recA gene sequences comprising nearly 4600 bp distinguished six phylogenetic groups, the M. chelonae-abscessus group, the Mycobacterium mucogenicum group, the M. fortuitum group, the Mycobacterium mageritense group, the Mycobacterium wolinskyi group and the M. smegmatis group, respectively comprising four, three, eight, one, one and two species. The two protein-encoding genes rpoB and recA improved meaningfully the bootstrap values at the nodes of the different groups. The species M. mucogenicum, M. mageritense and M. wolinskyi formed new groups separated from the M. chelonae-abscessus, M. fortuitum and M. smegmatis groups, respectively. The M. mucogenicum group was well delineated, in contrast to the M. mageritense and M. wolinskyi groups. For phylogenetic organizations derived from the hsp65 and sodA gene sequences, the bootstrap values at the nodes of a few clusters were <70 %. In contrast, phylogenetic organizations obtained from the 16S rRNA, rpoB and recA genes were globally similar to that inferred from combined datasets, indicating that the rpoB and recA genes appeared to be useful tools in addition to the 16S rRNA gene for the investigation of evolutionary relationships among RGM species. Moreover, rpoB gene sequence analysis yielded bootstrap values higher than those observed with recA and 16S rRNA genes. Also, molecular signatures in the rpoB and 16S rRNA genes of the M. mucogenicum group showed that it was a sister group of the M. chelonae-abscessus group. In this group, M. mucogenicum ATCC 49650(T) was clearly distinguished from M. mucogenicum ATCC 49649 with regard to analysis of the five gene sequences. This was in agreement with phenotypic and biochemical characteristics and suggested that these strains are representatives of two closely related, albeit distinct species.

Bacterial Proteins↗
PubMed2001

Phylogenetic analysis of partial sequences of elongation factor 1alpha identifies major groups of lice (Insecta: Phthiraptera).

As a first attempt to use molecular data to resolve the relationships between the four suborders of lice and within the suborder Ischnocera, we sequenced a 347-bp fragment of the elongation factor 1alpha gene of 127 lice (Insecta: Phthiraptera) as well as outgroup taxa from the order Psocoptera. A number of well-supported monophyletic groups were found but the relationships among many of these groups could not be resolved. While it is probable that multiple substitutions at high divergences and ancient radiation over a short period of time have contributed to the problem, we attribute most of this lack of resolution to the high ratio of taxa to characters. Nevertheless, the sequence data unequivocally support a number of important relationships that are at variance with the conclusions of morphological taxonomy. These include the sister group relationship of Chelopistes and Oxylipeurus, two lice occupying different ecological niches on the same host, which have previously been assigned to different families. These results provide evidence in support of the hypothesis that lice have speciated in situ on the host in response to niche specialization and that this has given rise to convergent morphologies in the lice of different host groups which share similar ecological niches. We discuss our attempts to overcome the limitations of this large data set, including the use of leaf stability analysis, a new method for analyzing the stability of taxa in a phylogenetic tree, and examine a number of hypotheses of relationships based on both traditional taxonomy and host associations.

Animals↗
PubMed2005

Characterization and subgrouping of Campylobacter concisus strains using protein profiles, conventional biochemical testing and antibiotic susceptibility.

OBJECTIVE: To characterize and subgroup clinical strains of Campylobacter concisus isolated from patients with gastrointestinal disease. METHODS: A total of 109 C. concisus isolates from 98 patients obtained between June 1997 and December 1998 were analysed using protein profiles, conventional biochemical tube tests, ApiCampy, and susceptibility patterns by Neosensitabs and E-test. RESULTS: Two groups were identified by using protein profiles. One resembled the ATCC 33237 type strain of oral origin, and a second group differing from it, particularly in the high molecular weight zone. Considerable diversity exists in the lower molecular range of the gels, also within assigned subgroups. Biochemical testing showed differences between the groups in the ability to reduce nitrate, ApiCampy testing also yielded differences between the two assigned groups, although reactions were highly heterogeneous. Resistance to erythromycin, ciprofloxacin, ampicillin, ceftriaxone and tetracycline occurred in 3%, 13%, 7%, 11% and 0% of the isolates when using Neosensitabs. The E-test yielded comparable results 7%, 5%, 0%, 2% and 3%, respectively. CONCLUSION: Results indicate that C. concisus can be assigned to two broad groups based on differences in protein profiles. No distinct phenotypic marker was identified. Susceptibility patterns are not suitable for discrimination between the two assigned groups. Further studies using a polyphasic approach including the application of genetic methods are needed to assess the complex taxonomy of this potential pathogen.

Bacterial Proteins↗
PubMed2006

Phylogeny of finescale shiners of the genus Lythrurus (Cypriniformes: Cyprinidae) inferred from four mitochondrial genes.

We infer the phylogenetic relationships of finescale shiners of the genus Lythrurus, a group of 11 species of freshwater minnows widely distributed in eastern North America, using DNA sequences from the ND2 (1047 bp), ATPase8 and 6 (823 bp), and ND3 (421 bp) mitochondrial protein-coding genes. The topologies resulting from maximum parsimony, Bayesian, and maximum likelihood tree building methods are broadly congruent, with two distinct clades within the genus: the L. umbratilis clade (L. umbratilis + L. lirus + (L. fasciolaris + (L. ardens, L. matutinus))) and the L. bellus clade (L. fumeus + L. snelsoni + (L. roseipinnis + (L. atrapiculus + (L. bellus, L. algenotus)))). Support is weak at the base of several clades, but strongly supported nodes differ significantly from prior investigations. In particular, our results confirm and extend earlier studies recovering two clades within Lythrurus corresponding to groups with largely "northern" and "southern" geographic distributions. Several species in this genus are listed in the United States as threatened or of special concern due to habitat degradation or limited geographic ranges. In this study, populations assigned to L. roseipinnis show significant genetic divergence suggesting that there is greater genetic diversity within this species than its current taxonomy reflects. A full accounting of the biodiversity of the genus awaits further study.

Animals↗
PubMed1998

A taxonomy of adolescent health: development of the adolescent health profile-types.

OBJECTIVES: The aim of this study was to develop a taxonomy of health profile-types that describe adolescents' patterns of health as self-reported on a health status questionnaire. The intent was to be able to assign individuals to mutually exclusive and exhaustive groups that characterize the important aspects of their health and need for health services. METHODS: Cluster analytic empirical methods and clinically based conceptual methods were used to identify patterns of health in samples of adolescents from schools and from clinics that serve adolescents with chronic conditions and acute illnesses. Individuals with similar patterns of scores across multiple domains were assigned to the same profile-type. Results from the empirical and conceptually based methods were integrated to produce a practical system for assigning youths to profile-types. RESULTS: Four domains of health (Satisfaction, Discomfort, Risks and Resilience) were used to group individuals into 13 distinct profile-types. The profile-types were characterized primarily by the number of domains in which health is poor, identifying the unique combinations of problems that characterize different subgroups of adolescents. CONCLUSIONS: This method of reporting the information available on health status surveys is potentially a more informative way of identifying and classifying the health needs of subgroups in the population than is available from global scores or multiple scale scores. The reliability and validity of this taxonomy of health profile-types for the purposes of planning and evaluating health services must be demonstrated. That is the purpose of the accompanying study.

Acute Disease↗
PubMed1996

Molecular phylogenetic analysis of Cyclospora, the human intestinal pathogen, suggests that it is closely related to Eimeria species.

A coccidian organism assigned to the genus Cyclospora has been increasingly recognized in association with prolonged diarrhea in humans throughout the world. Confusion surrounds the taxonomy of this fastidious organism, despite the availability of morphology and sporulation characteristics. The small subunit rRNA coding region from cyclosporan oocysts purified from a human fecal specimen was amplified and sequenced. The same sequence was present in specimens from 8 other patients with cyclosporan oocysts but absent in specimens from asymptomatic subjects and from cryptosporidiosis patients. Phylogenetic analysis of rDNA sequences reveals that the human-associated Cyclospora is closely related to members of the Eimeria genus. These results allow predictions concerning Cyclospora host specificity, life cycle, and epidemiology as well as the development of a specific polymerase chain reaction-based diagnostic assay.

Animals↗
PubMed1997

Numerical taxonomy applied to Leonhard's classification of endogenous psychoses.

Among the existing classifications in the field of psychiatry, Leonhard's comprises 35 forms of endogenous psychoses, allowing a more precise differentiation. Computerassisted mathematical methods of numerical taxonomy, frequently used in other fields of biological sciences, were used to check its coherence, definitely proving its taxonomic validity. Numerical values were assigned to signs and symptoms described by Leonhard, taking into account their frequency and diagnostical importance. The resulting data matrix was processed, obtaining the dissimilitude coefficients and the main components which validate Leonhard classification. This method can be applied to other psychiatric classifications validating them or displaying their weaknesses.

Humans↗
PubMed1995

Occupational adaptation model of professional development as applied to level II fieldwork.

OBJECTIVE: The purpose of this study was to test the validity of a model of professional development that was based on occupational adaptation. This model proposes that students have three classes of adaptive response behaviors available for use: primitive, transitional, and mature. METHOD: Eight Level II fieldwork students were assigned to the Department of Veterans Affairs Medical Center, Dallas, Texas, for 12 weeks. Experienced fieldwork supervisors at the medical center developed a taxonomy of behavioral statements consistent with the developmental model's three classes of adaptive response behaviors. This taxonomy was converted to a student log in which supervisors rated the frequency with which the Level II fieldwork students exhibited these behaviors. RESULTS: The patterns of behaviors, which were represented graphically for each of the students, generally supported the predictions of the model. Students demonstrated all three classes of behaviors. Primitive and transitional behaviors emerged when the students experienced increased or unusual demands, even when the students' model behavior was mature. Students temporarily reverted to lower level behaviors when faced with situations that they perceived as too difficult or as too unfamiliar. CONCLUSION: This model of professional development facilitates an understanding of students' development during their transition from classroom to practice setting. Generalization to other settings will require validation of the student log.

Adaptation, Psychological↗
PubMed1980

[On the taxonomy of Actinobacillus, Haemophilus, and Pasteurella: DNA base composition, respiratory quinones, and biochemical reactions of representative collection cultures (author's transl)].

In a comparative study, 63 collection cultures representing 38 nomenspecies of, or assigned to, the genera Actinobacillus, Haemophilus, or Pasteurella were characterized by phenotypical features and deoxyribonucleic acid base composition. The latter was calculated from the thermal denaturation point. Biochemical reactions were tested in differential media commonly used for Enterobacteriaceae, and two test procedures were compared: (i) pure cultures with haematin and nicotine adenine dinucleotide added, where necessary, and (ii) xenocultures with an asaccharolytic Acinetobacter strain (ST 661/60). Furthermore, the respiratory quinones, and the effect of fumarate on oxygen-limited growth were considered. On the basis of these and some additional physiological and morphological criteria, a definition of the Actinobacillus-Haemophilus-Pasteurella group as a whole was established which appears to rank as a family. Several misclassified species, i.e. the so-called Actinobacillus actinoides, Haemophilus piscium, Haemophilus vaginalis, Pasteurella anatipestifer, and the organisms of the Bovine Lymphangitis group were eliminated, and the position of so-called Pasteurella piscicida was questioned. Some principles of subdivision of the group, and some of the practical identification procedures were discussed.

Actinobacillus↗
PubMedDate not supplied

Phase II evaluation of clinical coding schemes: completeness, taxonomy, mapping, definitions, and clarity. CPRI Work Group on Codes and Structures.

OBJECTIVE: To compare three potential sources of controlled clinical terminology (READ codes version 3.1, SNOMED International, and Unified Medical Language System (UMLS) version 1.6) relative to attributes of completeness, clinical taxonomy, administrative mapping, term definitions and clarity (duplicate coding rate). METHODS: The authors assembled 1929 source concept records from a variety of clinical information taken from four medical centers across the United States. The source data included medical as well as ample nursing terminology. The source records were coded in each scheme by an investigator and checked by the coding scheme owner. The codings were then scored by an independent panel of clinicians for acceptability. Codes were checked for definitions provided with the scheme. Codes for a random sample of source records were analyzed by an investigator for "parent" and "child" codes within the scheme. Parent and child pairs were scored by an independent panel of medical informatics specialists for clinical acceptability. Administrative and billing code mapping from the published scheme were reviewed for all coded records and analyzed by independent reviewers for accuracy. The investigator for each scheme exhaustively searched a sample of coded records for duplications. RESULTS: SNOMED was judged to be significantly more complete in coding the source material than the other schemes (SNOMED* 70%; READ 57%; UMLS 50%; *p < .00001). SNOMED also had a richer clinical taxonomy judged by the number of acceptable first-degree relatives per coded concept (SNOMED* 4.56, UMLS 3.17; READ 2.14, *p < .005). Only the UMLS provided any definitions; these were found for 49% of records which had a coding assignment. READ and UMLS had better administrative mappings (composite score: READ* 40.6%; UMLS* 36.1%; SNOMED 20.7%, *p < .00001), and SNOMED had substantially more duplications of coding assignments (duplication rate: READ 0%; UMLS 4.2%; SNOMED* 13.9%, *p < .004) associated with a loss of clarity. CONCLUSION: No major terminology source can lay claim to being the ideal resource for a computer-based patient record. However, based upon this analysis of releases for April 1995, SNOMED International is considerably more complete, has a compositional nature and a richer taxonomy. Is suffers from less clarity, resulting from a lack of syntax and evolutionary changes in its coding scheme. READ has greater clarity and better mapping to administrative schemes (ICD-10 and OPCS-4), is rapidly changing and is less complete. UMLS is a rich lexical resource, with mappings to many source vocabularies. It provides definitions for many of its terms. However, due to the varying granularities and purposes of its source schemes, it has limitations for representation of clinical concepts within a computer-based patient record.

Abstracting and Indexing↗
PubMed1996

A scanning electron microscopy study of Taxus leaves as related to taxonomy.

Scanning electron microscopy, when applied to the surfaces of the needles of Taxus spp. (yew) revealed features that appear useful in the taxonomy of this tree species which yields the important anticancer drug, taxol. For instance, all of the four North American species have 3-5 rows of stomata on one-half of the abaxial leaf surface, whereas all of the others, including those from Europe and Asia, have 7-10 rows of stomata. The appearance of individual or fused papilliform epidermal cells and their arrangement on the leaf surface also is a feature that varies between species. Patterns of wax formation appeared on all species of yew examined but none could characteristically be assigned to a given species. Wax pattern variation was dependent upon age, environment, and probably to some extent, species differences. This study may provide some additional useful and reliable indicators in Taxus taxonomy.

Microscopy, Electron, Scanning↗
PubMed2005

Opinion: Re-evaluating prokaryotic species.

There is no widely accepted concept of species for prokaryotes, and assignment of isolates to species is based on measures of phenotypic or genome similarity. The current methods for defining prokaryotic species are inadequate and incapable of keeping pace with the levels of diversity that are being uncovered in nature. Prokaryotic taxonomy is being influenced by advances in microbial population genetics, ecology and genomics, and by the ease with which sequence data can be obtained. Here, we review the classical approaches to prokaryotic species definition and discuss the current and future impact of multilocus nucleotide-sequence-based approaches to prokaryotic systematics. We also consider the potential, and difficulties, of assigning species status to biologically or ecologically meaningful sequence clusters.

Bacteria↗
PubMed2005

Dissection efficiency during laparoscopic oesophageal dissection.

Advanced techniques in laparoscopic surgery have led to an increased need for appropriate training in instrument handling and dissection. Recent developments in computer video technology have facilitated critical analysis of surgical technique. Video deconstruction of oesophageal hiatal dissection during six laparoscopic fundoplication procedures was undertaken. The procedures were performed by surgeons with a wide range of surgical experience, and the investigators analysing performance were blinded to their level of training. Sequential five-second video segments were analysed in detail by 3 investigators. A taxonomy list was developed to describe individual types of movement. The number and time per movement was assessed and a degree of efficiency was assigned. An efficient movement was defined as one that advances the dissection towards a recognised goal. The total oesophageal dissection time varied from 10 minutes (min) to 25 min (mean 16 min). The mean number of actions performed was 173 (range 120-272). A mean of 7 min was spent separating tissues (range 5-13), with 6 min spent grasping and positioning tissue (range 3-8). The amount of time spent in inefficient movement varied from 3 to 14 min (mean 7 min). The greatest variation between operators was seen in the efficiency of tissue separation when using dissecting instruments. Inexperienced operators spent a lot more time performing additional movements such as scope cleaning, observation and instrument exchange. This technique of video deconstruction can identify key areas for improvement. This could be used for trainee assessment and to provide constructive feedback. Future development in this area could enhance training in advanced laparoscopic techniques.

Journal Article↗
PubMed1977

Macrolide antibiotics M-4365 produced by Micromonospora. I. Taxonomy, production, isolation, characterization and properties.

A series of basic 16-membered macrolide antibiotics, M-4365 A1, A2, A3, G1, G2 and G3, were isolated from the culture broth of strain MCRL 0940 which is assigned to be a new species of Micromonospora and for which the name Micromonospora capillata sp. nov. is proposed. Among these antibiotics, M-4365 A2 and G2 showed strong inhibitory activity against Gram-positive and Gram-negative bacteria.

Aminoglycosides↗
PubMed1984

Penitricin, a new class of antibiotic produced by Penicillium aculeatum. I. Taxonomy of the producer strain and fermentation.

A novel antibiotic, penitricin (Ro 09-0804) was discovered in the culture filtrate of a fungal strain NR 5165. Taxonomic studies of the producing organism resulted in its assignment to Penicillium aculeatum. Further examination on penitricin production by other strains of this species and related taxa revealed that penitricin was produced by several other strains of P. aculeatum, but not by any available strains of the closely similar species, P. verruculosum. It was also found that copper ion was essential for production of penitricin.

Anti-Bacterial Agents↗
PubMedDate not supplied

[Concepts of taxonomy and concepts of biodiversity: the problem of interaction].

There is, or there should be, an interaction between concepts of taxonomy and biodiversity. On the one hand, taxonomy develops some general and particular classificatory paradigms, which own diversity is to be taken into account to understand the nature of variety of natural kinds. On the other hand, analysis of the properties of biodiversity may put forward nontrivial problems for taxonomy that cannot be deduced directly from its own statements. From the point view of taxonomy, it is argued that the current concept of biodiversity based entirely on the species concept is deeply rooted in reductionistic view of nature. It is outdated epistemologically and should be replaced by the modern taxonomic concept of the hierarchical phylogenetic pattern. Operationally, the latter presumes a possibility for each species to be assigned a certain "phylogenetic weight", according to its phylogenetic uniqueness. From the point view of biodiversity, it is argued that the global biodiversity is a three component entity, as it includes, in addition to phylogenetic and ecological hierarchies, a biomorphic hierarchy, as well. This calls for taxonomy to elaborate the general principles of classification of biomorphs.

Classification↗