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PubMed2004

Nocardiopsis alkaliphila sp. nov., a novel alkaliphilic actinomycete isolated from desert soil in Egypt.

An alkaliphilic actinomycete strain, designated YIM 80379T, was isolated from a soil sample collected from the eastern desert of Egypt and subjected to polyphasic taxonomy. The strain produced substrate and aerial mycelia on different media, with an optimum pH for growth of 9.5-10 and scarce or no growth at pH 7. Strain YIM 80379T contained meso-diaminopimelic acid, no diagnostic sugars, type PIII phospholipids and MK-10(H6) and MK-10(H8) as the predominant menaquinones. All of these characters assign isolate YIM 80379T consistently to the genus Nocardiopsis. This was confirmed by 16S rDNA analysis. It can be differentiated from all Nocardiopsis species with validly published names by phenotypic characteristics, phylogenetic analysis and DNA-DNA hybridization results. On the basis of polyphasic evidence, a novel species, Nocardiopsis alkaliphila sp. nov., is proposed. The type strain of the species is YIM 80379T (=CCTCC AA001031T=DSM 44657T).

Actinomycetales↗
PubMedDate not supplied

Mycoplasma hominis: historical outline and taxonomy.

Although known as a separate group of organisms since 1898, the isolation in 1937 of a human genital mycoplasma represented the first observation of the association of this group of organisms with humans, a discovery that provided the impetus for extensive investigations of the interactions of mycoplasmas with the human host. These studies showed that mycoplasmas were frequent inhabitants of the mucous membranes of the urogenital and upper respiratory tracts. In early studies of human mycoplasmas, they were not speciated but were assigned to this group of organisms almost exclusively on the basis of cultural characteristics. However, differentiation between groups of human genital and oral mycoplasmas based on cultural, morphologic, biochemical, and serologic properties was achieved in 1953. A few years later formal proposals for the establishment of three human species of Mycoplasma (including Mycoplasma hominis) were made, along with suggestions for a new classification and nomenclature of the mycoplasmas. Serologic, genetic, and other data clearly show that M. hominis does constitute a relatively heterogeneous group of organisms. However, although this heterogeneity has practical implications for identification of isolates of M. hominis and for demonstration of antibodies to M. hominis, further studies are necessary to justify formal recognition of a taxonomic subdivision of M. hominis into distinct serovars. Investigations of the role of M. hominis as a potential human pathogen date back to the very first years of its discovery.(ABSTRACT TRUNCATED AT 250 WORDS)

Bacteriology↗
PubMed2002

An Assessment of Athletic Training Students' Clinical-Placement Hours.

OBJECTIVE: To establish a time profile to determine how athletic training students use their time in clinical placements and to determine the effects of academic standing, sex, sport type, and risk of injury associated with a sport during athletic training students' clinical placements on instructional, clinical, unengaged, managerial, and active learning time. DESIGN AND SETTING: Subjects were enrolled in clinical placements within National Collegiate Athletic Association Division I athletics, intramural sports, and a local high school. Students were individually videotaped for approximately 4 hours. SUBJECTS: A total of 20 undergraduate athletic training students (17 women, 3 men) from a Committee on Accreditation of Allied Health Education Programs (CAAHEP)-accredited athletic training education program. MEASUREMENTS: We created a conceptual behavioral time framework to examine athletic training students' use of clinical-placement time with the performance domains associated with the 1999 National Athletic Trainers' Association Board of Certification Role Delineation Study. Students' use of time was analyzed with the Behavior Evaluation Strategies and Taxonomies software. RESULTS: Students spent 7% of their overall clinical-placement time in instructional activities, 23% in clinical activities, 10% in managerial activities, and 59% in unengaged activities. Using multiple 3 x 3 factorial analyses of variance, we found that advanced students were engaged in significantly more active learning and clinical time compared with novice and intermediate students. Students assigned to sports in which injuries predominately occur in the upper extremities (upper extremity sports) spent significantly more clinical-placement time unengaged compared with students assigned to sports in which injuries predominantly occur in the lower extremities (lower extremity sports) or in both upper and lower extremities (mixed extremity sports). CONCLUSIONS: In this exploratory study, we examined only the clinical-placement component of 1 athletic training program; therefore, it may not be accurate to generalize the results for all CAAHEP-accredited programs. However, these results can be used by athletic training educators to examine the amount of time students are actually engaged in specific domains of athletic training, to determine the domains in which skills are most commonly being performed, to identify the relationships between the students and clinical instructors or supervisors, and to develop clinical placements in which students learn and practice clinical and educational competencies.

Journal Article↗
PubMed2003

A taxonomy of obstacles to breast examinations in African American women.

The purpose of this study was to describe and classify the barriers to breast self-examinations (BSE) and mammography in African American women. A total of 125 African American women were recruited from historically black colleges, churches and community organizations in Nashville, Tennessee. Their responses to a comprehensive open- and closed-ended questionnaire about barriers to BSE and mammography were coded using a hierarchical coding system and analyzed according to participants' stage of behavior change assignment. On the average, each woman reported 3.1 barriers to BSE (2.5 psychological and 0.6 environmental) and 2.5 barriers to mammography (1.5 psychological and 1.0 environmental). Barriers cited included fear of finding cancer, forgetting, lack of time, lack of knowledge, competing demands, costs, pain, emotional consequences, cultural attitudes towards medicine, uncertainty about benefits and laziness. For BSE, the number of psychological barriers exceeded environmental barriers, while for mammography, the number of psychological and environmental barriers was similar. For BSE, but not mammography, psychological barriers appeared most important for women in the precontemplation, contemplation and preparation stages of behavior change. Overcoming barriers to BSE and mammography could increase early detection rates in African American women. Interventions based on stage of change theory may be especially applicable.

Black or African American↗
PubMed1998

Intergenic transcribed spacer PCR ribotyping for differentiation of Saccharomyces species and interspecific hybrids.

The taxonomy of the genus Saccharomyces has undergone significant changes recently with the use of genotypic rather than phenotypic methods for the identification of strains to the species level. The sequence of rRNA genes has been utilized for the identification of a variety of fungi to the species level. This methodology, applied to species of Saccharomyces, allows unknown Saccharomyces isolates to be assigned to the type strains. It was the aim of the present study to assess whether typing of the intergenic spacer region by using restriction fragment length polymorphisms of PCR products (intergenic transcribed spacer PCR [ITS-PCR] ribotyping) could distinguish among type strains of the 10 accepted species of Saccharomyces and further to assess if this method could distinguish strains that were interspecific hybrids. Cellular DNA, isolated after the lysis of protoplasts, was amplified by PCR using ITS1 and ITS4 primers, purified by liquid chromatography, and digested with restriction endonucleases. Ribotyping patterns using the restriction enzymes MaeI and HaeIII could distinguish all species of Saccharomyces from each other, as well as from Candida glabrata, Candida albicans, and Blastomyces dermatitidis. The only exception to this was the inability to distinguish between Saccharomyces bayanus and S. pastorianus (S. carlsbergensis). Furthermore, interspecific hybrids resulting from the mating of sibling species of Saccharomyces were shown to share the ITS-PCR ribotyping patterns of both parental species. It should now be possible, by this simple PCR-based technique, to accurately identify these strains to the species level, thereby allowing an increase in our understanding of the characteristics required by these interspecific hybrids for their particular ecological niches.

DNA, Fungal↗
PubMed1984

The kingdom Protista and its 45 phyla.

Because most recent treatments of the protists ('lower' eukaryotes comprising the kingdom PROTISTA Haeckel, 1866) have been preoccupied with either a 'phylogenetic-tree' approach or a discussion of the impact of possible endosymbiotic origins of major intracellular organelles, the overall systematics of the group, from taxonomic and nomenclatural points of view, has been almost totally neglected. As a result, confusion over contained phyla, their places in a classification scheme, and even their names (and authorships) is growing; the situation could become chaotic. The principal objective of the present paper is to recognize the taxonomic interrelationships among all protist groups; and it includes the specific proposal that some 45 phyla, defined and characterized, be assigned to 18 supraphyletic assemblages within the kingdom PROTISTA (itself redefined and contrasted with the other eukaryotic kingdoms recognized here: ANIMALIA, PLANTAE and FUNGI). Vernacular terms are employed for identification of the 18 assemblages, but defensible formal names are proposed at the level of phylum. None is presented as new: authorship-and-date credits are given to preceding workers on the taxonomy of the many groups involved. By presenting taxonomic characterizations as well as relevant nomenclatural data for each taxon described, a comprehensive scheme of overall higher-level classification within the kingdom emerges that may be considered to serve as a solid base or 'taking-off point' for future discussions. The 18 supraphyletic groups and their phyla (in parentheses and including authorships and dates of their formal names) are as follows: I. The rhizopods (phyla Karyoblastea Margulis, 1974; Amoebozoa Lühe, 1913; Acrasia Van Tieghem, 1880; Eumycetozoa Zopf, 1885; Plasmodiophorea Zopf, 1885; Granuloreticulosa De Saedeleer, 1934; incertae sedis Xenophyophora Schulze, 1904). II. The mastigomycetes (Hypochytridiomycota Sparrow, 1959; Oomycota Winter, 1897; incert. sed. Chytridiomycota Sparrow, 1959). III. The chlorobionts (Chlorophyta Pascher, 1914; Prasinophyta Christensen, 1962; Conjugatophyta Engler, 1892; Charophyta Rabenhorst, 1863; incert. sed. Glaucophyta Bohlin, 1901). IV. The euglenozoa (Euglenophyta Pascher, 1931; Kinetoplastidea Honigberg, 1963; incert. sed. Pseudociliata Corliss & Lipscomb, 1982). V. The rhodophytes (Rhodophyta Rabenhorst, 1863). VI. The cryptomonads (Cryptophyta Pascher, 1914). VII. The choanoflagellates (Choanoflagellata Kent, 1880).(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed2004

Molecular and phenotypic characterization of nonmotile Gram-negative bacteria associated with spoilage of freshwater fish.

AIMS: Characterization of nonmotile bacteria associated with freshwater fish spoilage and that phenotypically resembled Psychrobacter spp. METHODS AND RESULTS: A population of 44 nonmotile Gram-negative rods could not be assigned to the genus Psychrobacter on the basis of a definitive test (transformation assay). Conventional and commercial phenotypic systems did not help in identification. A second extensive phenotypic analysis using different temperatures and media confirmed these isolates as nonmotile although electron microscopic examination showed that all but two had one to four polar flagella and other appendages. On the basis of numerical taxonomy, this population was divided into six clusters, one of them consisting of five fluorescent strains. Sequencing of fluorescent and non fluorescent representative strains from each cluster demonstrated that strains from five clusters had between 97.8 and 98.8% sequence homology with Pseudomonas fragi IFO 3458. This and an unknown strain from deep sea were the closest organisms (80.9% sequence homology) to one aflagellated representative strain of the remaining cluster. CONCLUSIONS: Oxidase-positive, nonmotile, nonfermenter Gram-negative rods isolated from freshwater fish can be wrongly ascribed to the genus Psychrobacter. SIGNIFICANCE AND IMPACT OF THE STUDY: Molecular methods are necessary for the identification of environmental isolates and species with an incomplete phenotypic description. This work emphasizes the need for a sound description of Ps. fragi based on molecular and phenotypic characterization.

Animals↗
PubMed2026

Two Saccharopolyspora isolates from archaeological excavation sites: polyphasic taxonomy, biosynthetic potential, bioactivity profiling and description of Saccharopolyspora antiqui sp. nov.

Archaeological excavation sites represent underexplored microbial habitats with the potential to recover taxonomically and biotechnologically valuable actinomycetes. In this study, two Saccharopolyspora strains, 5N708T and 5N102, were isolated from soil samples collected from the Gaziantep-Doliche-Dülük and Bitlis-Ahlat-Selçuklu Cemetery archaeological excavation sites in Türkiye. A polyphasic taxonomic approach, including 16S rRNA gene sequencing, phylogenetic and phylogenomic analyses, average nucleotide identity, digital DNA-DNA hybridization, phenotypic characterization, and chemotaxonomic analyses, showed that strain 5N708T represents a novel species of the genus Saccharopolyspora, for which the name Saccharopolyspora antiqui sp. nov. is proposed, whereas strain 5N102 was assigned to Saccharopolyspora elongata. Both isolates were further evaluated for their antimicrobial, antioxidant, and cytotoxic activities, and their biosynthetic potential was investigated by genome mining. Both strains showed activity against Staphylococcus aureus, with strain 5N708T producing the larger inhibition zone. Strain 5N102 exhibited markedly stronger antioxidant activity than strain 5N708T in radical scavenging, ferric reducing antioxidant power, and reducing power assays. In contrast, strain 5N708T showed more promising cytotoxic activity, with relative selectivity toward MIA PaCa-2 pancreatic cancer cells compared with HEK293 cells after prolonged incubation. Genome mining revealed multiple biosynthetic gene clusters in both isolates, supporting their capacity to produce secondary metabolites. These findings indicate that archaeological soils are promising reservoirs of taxonomically novel and biologically active Saccharopolyspora strains.

Saccharopolyspora↗
PubMed2001

The main biological determinants of tumor line taxonomy elucidated by a principal component analysis of microarray data.

By using principal components analysis (PCA) we demonstrate here that the information relevant to tumor line classification linked to the activity of 1375 genes expressed in 60 tumor cell lines can be reproduced by only five independent components. These components can be interpreted as cell motility and migration, cellular trafficking and endo/exocytosis, and epithelial character. PCA, at odds with cluster analysis methods routinely used in microarray analysis, allows for the participation of individual genes to multiple biochemical pathways, while assigning to each cell line a quantitative score reflecting fundamental biological functions.

Cell Movement↗
PubMed1999

A re-evaluation of the taxonomy of Paracoccus denitrificans and a proposal for the combination Paracoccus pantotrophus comb. nov.

Comparison of both 16S rRNA coding sequences and DNA-DNA hybridization of ten strains of alpha-subclass of Proteobacteria currently classified as strains of Paracoccus denitrificans has shown that they fall into two groups which are distinct from each other at the species level. Comparison with published data on the cytochrome c profiles and other 16S rRNA coding sequences in the literature has confirmed these observations and enabled several other strains also to be assigned to these two groups. Group A comprises strains ATCC 17741T (the type strain of P. denitrificans), LMD 22.21T, DSM 413T, ATCC 19367, ATCC 13543, DSM 1404, DSM 1405, Pd 1222 (a genetic modification of DSM 413T) and NCIMB 8944. Group B comprises ATCC 35512T (the original type strain of Thiosphaera pantotropha), LMD 82.5T, LMD 92.63, DSM 65, LMG 4218, IAM 12479, JCM 6892, DSM 11072, DSM 11073 and DSM 11104. In light of these findings, it is proposed that: (1) strains of group A are retained as P. denitrificans, with ATCC 17741T as the type strain of the type species; and (2) all strains of group B are assigned to the new species combination Paracoccus pantotrophus comb. nov., with strain ATCC 35512T as the type strain. Comparative 16S rRNA sequence analysis and DNA-DNA hybridization of strains of Paracoccus versutus confirm that this species is distinct from both P. denitrificans and P. pantotrophus, but that its nearest phylogenetic neighbour is P. pantotrophus.

Cytochrome c Group↗
PubMed2005

Application of a recN sequence similarity analysis to the identification of species within the bacterial genus Geobacillus.

Full-length recN and 16S rRNA gene sequences were determined for a collection of 68 strains from the thermophilic Gram-positive genus Geobacillus, members of which have been isolated from geographically and ecologically diverse locations. Phylogenetic treeing methods clustered the isolates into nine sequence similarity groups, regardless of which gene was used for analysis. Several of these groups corresponded unambiguously to known Geobacillus species, whereas others contained two or more type strains from species with validly published names, highlighting a need for a re-assessment of the taxonomy for this genus. For taxonomic analysis of bacteria related at a genus, species or subspecies level, recN sequence comparisons had a resolving power nearly an order or magnitude greater than 16S rRNA gene comparisons. Mutational saturation rendered recN comparisons much less powerful than 16S rRNA gene comparisons for analysis of higher taxa, however. Analysis of recN sequences should prove a powerful tool for assigning strains to species within Geobacillus, and perhaps within other genera as well.

Bacillaceae↗
PubMed2003

Phylogeny of the genus Nocardia based on reassessed 16S rRNA gene sequences reveals underspeciation and division of strains classified as Nocardia asteroides into three established species and two unnamed taxons.

Conventional identification of Nocardia in the routine laboratory remains problematic due to a paucity of reliable phenotypic tests and due to the yet-unresolved taxonomy of strains classified as belonging to the species Nocardia asteroides, which comprises the type strain and isolates with drug pattern types II and VI. The 16S rRNA gene of 74 representative strains of the genus Nocardia, encompassing 25 established species, was sequenced in order to provide a molecular basis for accurate species identification and with the aim of reassessing the phylogeny of taxons assigned to the species N. asteroides. The result of this phylogenetic analysis confirms that the interspecies heterogeneity of closely related nocardial species can be considerably low (a sequence divergence of only 0.5% was found between N. paucivorans and N. brevicatena). We observed a sequence microheterogeneity (sequence divergence of fewer than five bases) in 8 of 11 species of which more than one strain in the species was studied. At least 10 taxons were found that merit description as new species. Strains previously classified as N. asteroides fell into five distinct phylogenetic groups: the type strain cluster (N. asteroides sensu strictu), N. abscessus, N. cyriacigeorgica, and two clusters closely related to N. carnea or N. flavorosea. The strains within the latter two groups probably represent new species, pending further genetic and phenotypic evaluation. Restricted phenotypic data revealed that N. abscessus, N. cyriacigeorgica, and the two Nocardia species taxons are equivalent to drug patterns I, VI, and II, respectively. In the future, these data will help in finding species-specific markers after adoption of a more precise nomenclature for isolates closely related to N. asteroides and unravel confusing phenotypic data obtained in the past for unresolved groups of strains that definitely belong to separate taxons from a phylogenetic point of view.

DNA, Bacterial↗
PubMed2007

Adaptive radiation in African weakly electric fish (Teleostei: Mormyridae: Campylomormyrus): a combined molecular and morphological approach.

We combined multiple molecular markers and geometric morphometrics to revise the current taxonomy and to build a phylogenetic hypothesis for the African weakly electric fish genus Campylomormyrus. Genetic data (2039 bp DNA sequence of mitochondrial cytochrome b and nuclear S7 genes) on 106 specimens support the existence of at least six species occurring in sympatry. We were able to further confirm these species by microsatellite analysis at 16 unlinked nuclear loci and landmark-based morphometrics. We assigned them to nominal taxa by comparisons to type specimens of all Campylomormyrus species recognized so far. Additionally, we showed that the shape of the elongated trunk-like snout is the major source of morphological differentiation among them. This finding suggests that the radiation of this speciose genus might have been driven by adaptation to different food sources.

Adaptation, Biological↗
PubMed2006

Myxozoan genera: definition and notes on taxonomy, life-cycle terminology and pathogenic species.

A list of myxozoan genera is presented in the current taxonomical scheme. These genera are defined; their type species and most important pathogens along with their hosts are listed. Simultaneously, definitions of actinospore stages representing sexual stages of the myxosporean life cycle are given; altogether, 17 actinospore collective groups with 180 types have been described. Life cycles of the two classes of the phylum Myxozoa, Malacosporea and Myxosporea, are briefly outlined with specification of the appropriate terms. Up to now, 4 malacosporean and 2,180 myxosporean species assigned to a total of 62 genera, have been established. The surviving classification of myxosporeans, based on spore morphology, is discussed in the context of the still fragmentary data resulting from SSU rDNA sequence analyses. The main task for the future is a rigorous, detailed morphological description combined with molecular techniques in establishment of new species and in revision of the existing ones. Establishment of a classification acceptable from morphological, biological and phylogenetical viewpoints is necessary.

Animals↗
PubMed1982

A survey of the structures of mycolic acids in Corynebacterium and related taxa.

Acid methanolysates of 104 strains of coryneform and related bacteria were examined for mycolic acids by thin-layer chromatography and mass spectrometry. The mycolic acids of Corynebacterium sensu stricto strains were not uniform in size and structure, and considerable variation existed within the approximate limiting range of C22 to C36. Two species, Corynebacterium bovis and 'Corynebacterium mycetoides', were particularly distinctive; the former had exceptionally low molecular weight mycolic acids (C22 to C32), whereas the latter contained major amounts of mycolates with a side-chain possessing an odd number of carbon atoms. Caseobacter polymorphus contained mycolic acids of a similar size (C30 to C36) to those of true corynebacteria. The mycolates of organisms assigned to the genus Rhodococcus were generally larger (C30 to C56), although a clear distinction between two corynebacteria and rhodococci cannot presently be made by analysis of mycolic acids alone. Strains labelled 'Arthrobacter roseoparaffinus', Corynebacterium equi and Corynebacterium hoagii contained mycolic esters with molecular weights 'intermediate' in size between those of true corynebacteria and rhodococci. The mycolic acid data correlate well with other major trends in coryneform taxonomy and support earlier suggestions that they are of value in the classification of the group.

Arthrobacter↗
PubMed1998

Signal transduction inhibitors, hibarimicins, A, B, C, D and G produced by Microbispora. I. Taxonomy, fermentation, isolation and physico-chemical and biological properties.

Strain TP-AO121 which produces a complex of novel tyrosine kinase inhibitors designated hibarimicins A, B, C, D and G was considered to be a new subspecies of Microbispora rosea, and the name, Microbispora rosea subsp. hibaria, was proposed. Hibarimicins A, B, C and D specifically inhibited the src tyrosine kinase activity without affecting protein kinase A or protein kinase C. They also showed in vitro anti-Gram-positive bacterial and antitumor activities. The molecular formulae of hibarimicins A, B, C, D and G were assigned to be C85H112O37, C85H112O37, C83H110O36, C85H112O38, and C85H112O39 respectively.

Actinomycetales↗
PubMed1981

Dna-Dna hybridization of Rhodopseudomonas capsulata, Rhodopseudomonas sphaeroides and Rhodopseudomonas sulfidophila strains.

The genetic relatedness of 21 Rhodopseudomonas strains has been studied by means of DNA-DNA hybridization. All strains included in the study belonged to the subgroup of the genus Rhodopseudomonas which is characterized by a short-rod to coccus morphology, a vesicular intracytoplasmic membrane system and carotenoids of the spheroidene group. Mol percentages guanine + cytosine ranged from 64 to 73, most strains having values between 68 and 72. With few exceptions, the hybridization data obtained were in agreement with the subdivision in three (or possibly four) species on the basis of classical taxonomy. Strain SCJ, formerly considered to be a somewhat atypical R. capsulata strain, is most probably R. sphaeroides strain and two out of seven strains that were received as R. sulfidophila did not fit in this species on the basis of the hybridization data. The results also showed that two undesignated strains that were previously thought to be related to R. capsulata (Hansen et al. 1975) cannot be assigned to this species and may be representatives of another species. The seven strains that required approximately 2.5% NaCl in the medium and that had been designated R. sulfidophila were found to synthesize far higher levels of bacteriochlorophyll during fully aerobic growth in the dark than the purple bacteria studied thus far.

DNA, Bacterial↗
PubMed2003

Classifying the precancers: a metadata approach.

BACKGROUND: During carcinogenesis, precancers are the morphologically identifiable lesions that precede invasive cancers. In theory, the successful treatment of precancers would result in the eradication of most human cancers. Despite the importance of these lesions, there has been no effort to list and classify all of the precancers. The purpose of this study is to describe the first comprehensive taxonomy and classification of the precancers. As a novel approach to disease classification, terms and classes were annotated with metadata (data that describes the data) so that the classification could be used to link precancer terms to data elements in other biological databases. METHODS: Terms in the UMLS (Unified Medical Language System) related to precancers were extracted. Extracted terms were reviewed and additional terms added. Each precancer was assigned one of six general classes. The entire classification was assembled as an XML (eXtensible Mark-up Language) file. A Perl script converted the XML file into a browser-viewable HTML (HyperText Mark-up Language) file. RESULTS: The classification contained 4700 precancer terms, 568 distinct precancer concepts and six precancer classes: 1) Acquired microscopic precancers; 2) acquired large lesions with microscopic atypia; 3) Precursor lesions occurring with inherited hyperplastic syndromes that progress to cancer; 4) Acquired diffuse hyperplasias and diffuse metaplasias; 5) Currently unclassified entities; and 6) Superclass and modifiers. CONCLUSION: This work represents the first attempt to create a comprehensive listing of the precancers, the first attempt to classify precancers by their biological properties and the first attempt to create a pathologic classification of precancers using standard metadata (XML). The classification is placed in the public domain, and comment is invited by the authors, who are prepared to curate and modify the classification.

Decision Support Systems, Clinical↗