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At least 55 records · Page 3Linked to original sources
PubMed1998

The Middle Pleistocene human tibia from Boxgrove.

The Boxgrove tibia was discovered in 1993, associated with Middle Pleistocene fauna, and Lower Palaeolithic archaeology. The sediments at Boxgrove were deposited during a temperate interglacial episode and ensuing cold stage. They thus represent a wide range of modes and environments of deposition. Archaeological remains have been excavated from all the major stratigraphic units, giving a continuity of occupation for this part of southern England over a 10(4) year timescale, through markedly changing climatic regimes. The stratigraphic, archaeological and sedimentological contexts of the tibia are described, as well as its preservation and morphology. Measurements are given, with discussion of reconstructed bone length, and stature estimates. Comparative measurements are provided for fossil and recent human samples: the large dimensions of its diaphysis place the Boxgrove tibia near or beyond the upper size limits of the comparative samples, but its reconstructed length and estimated stature are less exceptional. The elevated robusticity of the specimen indicates exceptional diaphyseal strength and/or cold adapted body proportions paralleling those of the Neanderthals. Disagreement about the taxonomy of Middle Pleistocene hominids and lack of comparable fossil material make a specific assignment for the Boxgrove tibia problematic. The tibia can only definitely be assigned to non-modern Homo sp., with possible further reference to Homo cf. heidelbergensis (Schoetensack, 1908) on temporal and geographic grounds, if the validity of that species is accepted.

Animals↗
PubMed1993

Chemotaxonomy and molecular taxonomy of some coryneform clinical isolates.

Six reference strains of the genus Brevibacterium as well as fifteen clinical isolates tentatively assigned to the genus using conventional biochemical methods, were the subject of chemotaxonomic and DNA similarity studies. Five of these clinical isolates were assigned either to the genera Aureobacterium, Mycobacterium, Gordona or to Rhodococcus on the basis of their DNA mol% G+C, mycolic acid, amino-acid, sugar and menaquinone contents. Among the ten remaining strains, six were not brevibacteria and only four conformed to the description of the genus Brevibacterium sensu stricto. These strains showed low values of DNA relatedness with Brevibacterium epidermidis ATCC 35514T and Brevibacterium linens ATCC 9174, and could only be described as Brevibacterium spp. The results indicate that studies of chemical markers are essential for the correct identification of brevibacteria.

Bacterial Typing Techniques↗
PubMed2003

Species concepts and species reality: salvaging a Linnaean rank.

The validity of the species category (rank) as a distinct level of biological organization has been questioned. Phenetic, cohesion and monophyletic species concepts do not delimit species-level taxa that are qualitatively distinct from lower or higher taxa: all organisms throughout the tree of life exhibit varying degrees of similarity, cohesion, and monophyly. In contrast, interbreeding concepts delimit species-level taxa characterized by a phenomenon (regular gene flow) not found in higher taxa, making the species category a distinct level of biological organization. Only interbreeding concepts delimit species-level taxa that are all comparable according to a biologically meaningful criterion and qualitatively distinct from entities assigned to other taxonomic categories. Consistent application of interbreeding concepts can result in counterintuitive taxonomies--e.g. many wide polytypic species in plants and narrow cryptic species in animals. However, far from being problematic, such differences are biologically illuminating--reflecting differing barriers to gene flow in different clades. Empirical problems with interbreeding concepts exist, but many of these also apply to other species concepts, whereas others are not as severe as some have argued. A monistic view of species using interbreeding concepts will encounter strong historical inertia, but can save the species category from redundancy with other categories, and thus justify continued recognition of the species category.

Classification↗
PubMed2003

Assessing alternative medicine: methodological and research policy concerns.

OBJECTIVES: Setting funding priorities among research projects for complementary and alternative therapies is especially vulnerable to arbitrary, partisan criteria and opportunistic readings of controversial evidence. This study develops a procedural approach to characterizing, in a transparent and even-handed way, the available evidence on these treatments and demonstrates a simple analytical scheme for prioritizing competing, but typically incommensurable, research projects for public support. METHODS: A simple five-step scheme for categorizing therapies is developed and justified, based on a taxonomy of the study designs used to generate research evidence. Once identified, candidate therapies are assigned to ordered categories along these design criteria and effectively grouped into equivalence classes by type of evidence. Finally, a partial ordering on the therapies is formed within each class by means of secondary screening criteria. RESULTS: Twenty-five candidate therapies are assigned to equivalence classes. The intent, in effect, is to restrict comparisons to those therapies that fall within a particular class of similar study designs. Within-class orderings avoid the problem of having better-known or better-supported therapies crowd out lesser known ones when it comes to allocating dollars for more research. A set of criteria and procedure for prioritizing spending for further research is demonstrated. CONCLUSIONS: Relying on an open, formal procedure for comparing unconventional therapies offers protection against prejudgment in setting funding priorities, especially when weak clinical evidence relates more to a low investment in research than lack of efficacy.

Complementary Therapies↗
PubMed2006

Culturable phylogenetic diversity of the phylum 'Bacteroidetes' from river epilithon and coastal water and description of novel members of the family Flavobacteriaceae: Epilithonimonas tenax gen. nov., sp. nov. and Persicivirga xylanidelens gen. nov., sp. nov.

Members of the phylum 'Bacteroidetes' are important heterotrophs involved in cycling organic carbon in aquatic habitats. Their diversity has been studied by molecular methods in both freshwater and marine habitats and many novel genera and species within this phylum have been characterized in recent years. In this study, we examined the diversity of members of the 'Bacteroidetes' that could be readily isolated on solid media from river epilithon and coastal sea water. Most (93 %) of the 55 isolates confirmed as members of the 'Bacteroidetes' and examined by phylogenetic analysis of 16S rRNA gene sequences belonged to the Flavobacteriaceae. Furthermore, most (62 %) of these were almost certainly members of the genus Flavobacterium and all but one were from river epilithon. Conversely, the sea-water isolates were more widely distributed in clades containing other genera. Some of the isolates were deep-branching within phylogenetic trees and so could not be assigned to putative genera. Two of these deep-branching isolates were characterized by polyphasic taxonomy and are proposed as novel species within two new genera of the family Flavobacteriaceae. These are Epilithonimonas tenax gen. nov., sp. nov. (type strain EP105T = NCIMB 14026T = DSM 16811T) and Persicivirga xylanidelens gen. nov., sp. nov. (type strain SW256T = NCIMB 14027T = DSM 16809T).

Atlantic Ocean↗
PubMedDate not supplied

Development of definitions for taxonomy II.

In the process of placing diagnoses into Taxonomy I, certain inconsistencies became apparent. Inadequate definition of both diagnoses and human response patterns, lack of defining characteristics, and inconsistency in the levels of abstraction within the taxonomic hierarchy made the task of assigning a diagnosis to a taxonomic pattern difficult. Ambiguity in the definitions of the nine patterns resulted in ambiguity in the basic foundation, which affected the entire structure. The Taxonomy Committee, before evaluating the current structure, had to make the following decisions regarding the current human response patterns: (1) Should the nine human response patterns be retained for further taxonomic work? and (2) If they are retained, what should be the first step in examining Taxonomy I-Revised? This second article in a series of four will familiarize the readers with the process and decisions by which Taxonomy II of the North American Nursing Diagnosis Association (NANDA) is evolving through the work of the Taxonomy Committee. This article also will identify the specific problems encountered in the development of Taxonomy I and Taxonomy I-Revised, and describe the steps establishing the validity of the process of formation of the nine human response patterns.

Classification↗
PubMed2004

Genetic diversity of Leptotrichia and description of Leptotrichia goodfellowii sp. nov., Leptotrichia hofstadii sp. nov., Leptotrichia shahii sp. nov. and Leptotrichia wadei sp. nov.

Sixty strains of Gram-negative, anaerobic, rod-shaped bacteria from human sources initially assigned to Leptotrichia buccalis (n=58) and 'Leptotrichia pseudobuccalis' (n=2) have been subjected to polyphasic taxonomy. Full-length 16S rDNA sequencing, DNA-DNA hybridization, RAPD, SDS-PAGE of whole-cell proteins, cellular fatty acid analysis and enzymic/biochemical tests supported the establishment of four novel Leptotrichia species from this collection, Leptotrichia goodfellowii sp. nov. (type strain LB 57(T)=CCUG 32286(T)=CIP 107915(T)), Leptotrichia hofstadii sp. nov. (type strain LB 23(T)=CCUG 47504(T)=CIP 107917(T)), Leptotrichia shahii sp. nov. (type strain LB 37(T)=CCUG 47503(T)=CIP 107916(T)) and Leptotrichia wadei sp. nov. (type strain LB 16(T)=CCUG 47505(T)=CIP 107918(T)). Light and electron microscopy showed that the four novel species were Gram-negative, non-spore-forming and non-motile rods. L. goodfellowii produced arginine dihydrolase, beta-galactosidase, N-acetyl-beta-glucosaminidase, arginine arylamidase, leucine arylamidase and histidine arylamidase. L. shahii produced alpha-arabinosidase. L. buccalis and L. goodfellowii fermented mannose and were beta-galactosidase-6-phosphate positive. L. goodfellowii, L. hofstadii and L. wadei were beta-haemolytic. L. buccalis fermented raffinose. With L. buccalis, L. goodfellowii showed 3.8-5.5 % DNA-DNA relatedness, L. shahii showed 24.5-34.1 % relatedness, L. hofstadii showed 27.3-36.3 % relatedness and L. wadei showed 24.1-35.9 % relatedness. 16S rDNA sequencing demonstrated that L. hofstadii, L. shahii, L. wadei and L. goodfellowii each formed individual clusters with 97, 96, 94 and 92 % similarity, respectively, to L. buccalis.

Base Sequence↗
PubMed1997

Computer aided assignment of motile Aeromonas strains to genospecies level by standard biochemical tests.

A procedure is given for differentiation of motile Aeromonas spp. Based on nine to 12 biochemical properties it allows an assignment of isolated Aeromonas strains first to phenotypes and, in the second step, to hybridization groups (HGs) 1-13 as well as to the genotypically defined species Aer. allosaccharophila and Aer. encheleia. The computer aided classification is carried out according to the principles of numerical taxonomy. Using this differentiation scheme 23 Aeromonas strains, which were isolated from food, and two reference strains were speciated. A total of 16 strains were assigned to Aer. hydrophila, six strains to Aer. caviae and one strain to Aer. sobria. Of the 16 Aer. hydrophile strains, 11 were attached to HG 1, one to HG 2 and four could not be classified clearly as HG 3 or HG 1. All six Aer. caviae isolated were assigned to HG 5 and the Aer. sobria strain was ranked among HG 8. The reference strains were assigned to the same genotypes by this method than by DNA-DNA hybridization assays.

Aeromonas↗
PubMed2000

Species and series boundaries of Solanum series Longipedicellata (Solanaceae) and phenetically similar species in ser. Demissa and ser. Tuberosa: implications for a practical taxonomy of Section Petota.

Species boundaries were assessed by phenetic analyses of morphological data for all species of wild potatoes (SOLANUM: section PETOTA:) assigned to ser. LONGIPEDICELLATA: S. fendleri, S. hjertingii, S. matehualae, S. papita, S. polytrichon, and S. stoloniferum. These six tetraploid species grow in the southeastern United States (S. fendleri) and Mexico (all six species). We also analyzed morphologically similar species in ser. DEMISSA: (S. demissum) and ser. TUBEROSA: (S. avilesii, S. gourlayi, S. verrucosum). We chose S. verrucosum and S. demissum as Mexican representatives, and S. avilesii and S. gourlayi as South American representatives of other series that are difficult to distinguish from ser. LONGIPEDICELLATA: We also analyzed morphologically more dissimilar species in ser. TUBEROSA: (S. berthaultii) and ser. YUNGASENSIA: (S. chacoense). The results support only three species in ser. LONGIPEDICELLATA: (1) S. polytrichon, (2) S. hjertingii + S. matehualae, (3) S. fendleri + S. papita + S. stoloniferum. Solanum avilesii, S. gourlayi, and to a lesser extent S. demissum and S. verrucosum are very similar to members of ser. LONGIPEDICELLATA: and are difficult to distinguish practically from them, despite differences in chromosome numbers and crossability relationships. These data help document and explain the extensive taxonomic difficulty in sect. Petota, highlight conflicts between biological and morphological species concepts, and add to a growing body of evidence that too many wild potato species are recognized.

Journal Article↗
PubMed1990

The family Pasteurellaceae: modern approaches to taxonomy.

Historically, members of the family Pasteurellaceae were classified on the basis of a limited number of phenotypic characteristics. In particular, organisms were assigned to the family on the basis of their requirements for the growth factors hemin and/or nicotinamide adenine dinucleotide and on the basis of their ability to cause disease in vertebrates. More recent genotypic studies have shown that many members of the family Pasteurellaceae have been misclassified. In this paper we review some of the current taxonomic methods which can be used to emend the classification of Haemophilus, Actinobacillus and Pasteurella spp. and suggest some approaches and criteria for restructuring the family Pasteurellaceae.

Animals↗
PubMed2006

PhenoGO: assigning phenotypic context to gene ontology annotations with natural language processing.

Natural language processing (NLP) is a high throughput technology because it can process vast quantities of text within a reasonable time period. It has the potential to substantially facilitate biomedical research by extracting, linking, and organizing massive amounts of information that occur in biomedical journal articles as well as in textual fields of biological databases. Until recently, much of the work in biological NLP and text mining has revolved around recognizing the occurrence of biomolecular entities in articles, and in extracting particular relationships among the entities. Now, researchers have recognized a need to link the extracted information to ontologies or knowledge bases, which is a more difficult task. One such knowledge base is Gene Ontology annotations (GOA), which significantly increases semantic computations over the function, cellular components and processes of genes. For multicellular organisms, these annotations can be refined with phenotypic context, such as the cell type, tissue, and organ because establishing phenotypic contexts in which a gene is expressed is a crucial step for understanding the development and the molecular underpinning of the pathophysiology of diseases. In this paper, we propose a system, PhenoGO, which automatically augments annotations in GOA with additional context. PhenoGO utilizes an existing NLP system, called BioMedLEE, an existing knowledge-based phenotype organizer system (PhenOS) in conjunction with MeSH indexing and established biomedical ontologies. More specifically, PhenoGO adds phenotypic contextual information to existing associations between gene products and GO terms as specified in GOA. The system also maps the context to identifiers that are associated with different biomedical ontologies, including the UMLS, Cell Ontology, Mouse Anatomy, NCBI taxonomy, GO, and Mammalian Phenotype Ontology. In addition, PhenoGO was evaluated for coding of anatomical and cellular information and assigning the coded phenotypes to the correct GOA; results obtained show that PhenoGO has a precision of 91% and recall of 92%, demonstrating that the PhenoGO NLP system can accurately encode a large number of anatomical and cellular ontologies to GO annotations. The PhenoGO Database may be accessed at the following URL: http://www.phenoGO.org

Computational Biology↗
PubMed2003

Phylogeny, taxonomy, genetics and global heritage ranks of an imperilled, freshwater snail genus Lithasia (Pleuroceridae).

Numerous aquatic species are threatened with extinction from habitat elimination or modification. One particularly imperilled group is the freshwater gastropod family Pleuroceridae. Pleurocerids reach their greatest diversity in the southeastern United States, and many species are currently considered extinct, endangered or threatened. One issue hindering efforts to implement conservation management plans for imperilled pleurocerid species is that the taxonomy is in an abysmal state. The taxonomy of pleurocerids is currently based on late 19th- and early 20th-century studies, which used a typological or morphospecies concept. Most biologists today doubt the validity of many of the currently recognized species; however, this does not stop them from assigning conservation ranks in an attempt to determine which species are imperilled or currently stable. We conducted a phylogenetic analysis of the pleurocerid genus Lithasia using morphological and mitochondrial DNA sequence (mtDNA) data in an attempt to delimit species boundaries and test previous taxonomic schemes. We found that the current taxonomy of Lithasia does not reflect species diversity adequately within the genus, with two new undescribed species being discovered. The conservation status ranks of the new, undescribed species are imperilled and would have been overlooked had we relied on the conventional taxonomy. Additionally, the undescribed species' conservation ranks that were previously apparently secure became vulnerable due to being inappropriately assigned as members of formerly widely distributed species instead of the imperilled status they warrant and vice versa, as some taxa that were considered imperilled are now thought to be modestly stable. Our study suggests that conservation ranks should be considered suspect at best in taxonomically poorly known groups until the taxa are reviewed using modern systematic methods.

Animals↗
PubMed1986

Mycolic acid analysis for clinical identification of Mycobacterium avium and related mycobacteria.

We examined the mycolic acid composition of 133 strains belonging to MAIS complex (Mycobacterium avium-M. intracellulare-M. scrofulaceum) and MAIS intermediate strains and the related species M. asiaticum, M. malmoense, M. shimoidei, and M. simiae. The analysis revealed that about 10% of the strains identified as M. avium-M. intracellulare complex by conventional cultural and biochemical tests were in fact M. simiae strains according to their mycolate composition. Of 25 strains previously studied by the International Working Group on Mycobacterial Taxonomy, 2 (MAIS intermediate and M. asiaticum) presented patterns incompatible with the clusters to which they had been assigned. M. malmoense and both M. simiae serovars shared the same pattern with alpha-, alpha'-, and ketomycolates. We describe here the method used to identify the mycolic acid profiles in detail. We found it to be highly reproducible and convenient for use in mycobacterial reference laboratories.

Chromatography, Thin Layer↗
PubMed2007

Stability of an empirical psychosocial taxonomy across type of diabetes and treatment.

AIMS: The aims of the study were (i) to examine whether an empirical psychosocial taxonomy, based on key diabetes-related variables, is independent of type of diabetes and treatment, and (ii) to further establish the external validation of the taxonomy. METHODS: In a cross-sectional study, 82 patients with Type 1 and 86 patients with Type 2 diabetes mellitus were assigned to one of three psychosocial patient profiles based on their Multidimensional Diabetes Questionnaire (MDQ) scores. General psychological and diabetes-specific measures were obtained through self-report and HbA(1c) was measured. RESULTS: Equal proportions of Type 1 and Type 2 patients, and of patients using insulin and oral medication/diet only were classified within each of the three psychosocial profiles. External validation confirmed the validity and distinctiveness of the patients' profiles. The patient profiles were independent of demographic variables, body mass index, duration of diabetes, complexity of treatment, number of complications, social desirability, and major stress levels. CONCLUSIONS: The Psychosocial Taxonomy for Patients with Diabetes provides a new way to categorize individuals who may have more in common than just their type of diabetes and/or its treatment and can help target interventions to individual patients' needs.

Adult↗
PubMed1994

Molecular taxonomy of the yeasts.

The term 'yeast' is often taken as a synonym for Saccharomyces cerevisiae, but the phylogenetic diversity of yeasts is illustrated by their assignment to two taxonomic classes of fungi, the ascomycetes and the basidiomycetes. Subdivision of taxa within their respective classes is usually made from comparisons of morphological and physiological features whose genetic basis is often unknown. Application of molecular comparisons to questions in yeast classification offers an unprecedented opportunity to re-evaluate current taxonomic schemes from the perspective of quantitative genetic differences. This review examines the impact of molecular comparisons, notably rRNA/rDNA sequence divergence, on the current phenotypically defined classification of yeasts. Principal findings include: 1) budding ascomycetous yeasts are monophyletic and represent a sister group to the filamentous ascomycetes, 2) fission yeasts are ancestral to budding and filamentous ascomycetes, 3) the molecular phylogeny of basidiomycetous yeasts is generally congruent with type of hyphal septum, presence or absence of teliospores in the sexual state, and occurrence of cellular xylose.

DNA, Ribosomal↗
PubMed1998

Taxonomy of African horse sickness viruses.

Nine distinct genera are currently recognised within the virus family Reoviridae, which include a total of 63 virus groups or species (species = virus group = electropherotype or serogroup), comprising 214 virus serotypes or subtypes, as well as 20 provisional types or subtypes, most of which (149 + 9 tentative) are assigned to the genus Orbivirus [5, 9, 16]. The 19 species of orbiviruses (serogroups), were established principally on antigenic (serologic) grounds but many of these placements have been supported by molecular analyses. This introductory paper defines the taxonomy and classification of these viruses and establishes guidelines for use in other paper to be presented at this symposium and elsewhere.

African Horse Sickness↗
PubMed1992

Sporeamicin A, a new macrolide antibiotic. I. Taxonomy, fermentation, isolation and characterization.

Sporeamicin A, a novel antibiotic, was isolated from the culture filtrate of an actinomycete. The producing organism, strain L53-18, was taxonomically assigned as a species of the genus Saccaropolyspora. The antibiotic was extracted with chloroform and was then purified by crystallization. It was obtained as colorless prisms from ethanolic solutions. Sporeamicin A exhibited a strong UV absorption peak at 276 nm. The molecular formula of sporeamicin A was determined to be C37H63NO12.

Anti-Bacterial Agents↗
PubMed1994

Bioxalomycins, new antibiotics produced by the marine Streptomyces sp. LL-31F508: taxonomy and fermentation.

An actinomycete strain designated LL-31F508 was isolated from an intertidal sediment sample collected in Key West, Florida. Culture LL-31F508 was assigned to the Streptomyces genus based on the presence of LL-diaminopimelic acid (DAP) in the cell wall and observations of spiny spores using scanning electron microscopy (SEM). Excellent antimicrobial activity against Staphylococcus and Enterococcus spp. were detected in both the supernatant and cell extract samples from fermentations of culture LL-31F508. Production of antibiotic activity peaked at 48-50 hours and closely paralleled cell growth, during which time glucose was more rapidly assimilated than dextrin. A series of new antibiotics called the bioxalomycins was identified as the antibacterial products from fermentations of this culture. Fermentation conditions for production of bioxalomycin alpha differed substantially from those required for production of a related compound, naphthyridinomycin, by the reference culture Streptomyces lusitanus NRRL 8034.

Anti-Bacterial Agents↗