Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “taxonomy assignment”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 181 records · Page 10Linked to original sources
PubMed1986

[DNA-DNA homology and phenotypic characterization of environmental strains of Vibrio parahaemolyticus and Vibrio pelagius].

A taxonomic study by means of DNA homology and the most recent phenetic criteria has been carried out in 11 environmental strains of Vibrio parahaemolyticus and 4 of Vibrio pelagius, previously ascribed to the respective phenons in a numerical taxonomy study. The strains of V. parahaemolyticus showed genetic homogeneity, a guanine plus cytosine content (G + C) of 46% and 61% homology with V. parahaemolyticus type strain ATTC 17802. They exhibited phenetic atypicalities but could be ascribed to the species V. parahaemolyticus. The strains of V. pelagius behaved similarly in regard to the phenotype, but were genetically heterogeneous; they showed a % G + C of 44-46 and were assigned to V. splendidus-V. pelagius homology group.

Base Composition↗
PubMedDate not supplied

Parallel gradualistic evolution of Ordovician trilobites.

There are very few high-resolution studies of the fossil record from which to assess the relative frequency of gradualistic and punctuated evolution. Here I report some of the first detailed evidence of phyletic gradualism in benthic macroinvertebrates, based on a study of approximately 15,000 trilobites from central Wales. Over a period of about three million years, as many as eight lineages underwent a net increase in the number of pygidial ribs, a species-diagnostic character. The end members of most lineages have previously been assigned to different species and, in one case, to different genera. In view of intermediate morphologies and temporary trend reversals, however, practical taxonomic subdivision of each lineage proved impossible. The apparent success of earlier Linnean nomenclature (with its implications of discrete species) could easily have been misinterpreted as evidence of punctuation and stasis, and it is probable that detection of many other gradualistic patterns has been hindered by ready application of binominal taxonomy to fossils.

Animals↗
PubMed1992

Body size and proportions in early hominids.

The discovery of several associated body parts of early hominids whose taxonomic identity is known inspires this study of body size and proportions in early hominids. The approach consists of finding the relationship between various measures of skeletal size and body mass in modern ape and human specimens of known body weight. This effort leads to 78 equations which predict body weight from 95 fossil specimens ranging in geological age between 4 and 1.4 mya. Predicted weights range from 10 kg to over 160 kg, but the partial associated skeletons provide the essential clues as to which predictions are most reliable. Measures of hindlimb joint size are the best and probably those equations based on the human samples are better than those based on all Hominoidea. Using hindlimb joint size of specimens of relatively certain taxonomy and assuming these measures were more like those of modern humans than of apes, the male and female averages are as follows: Australopithecus afarensis, 45 and 29 kg; A. africanus, 41 and 30 kg; A. robustus, 40 and 32 kg; A. boisei, 49 and 34 kg; H. habilis, 52 and 32 kg. These values appear to be consistent with the range of size variation seen in the entire postcranial samples that can be assigned to species. If hominoid (i.e., ape and human combined) proportions are assumed, the males would be 10 to 23 kg larger and the females 4 to 10 kg larger.

Animals↗
PubMed1991

Differentiation of Acanthamoeba strains from infected corneas and the environment by using restriction endonuclease digestion of whole-cell DNA.

Restriction endonuclease digestion of Acanthamoeba whole-cell DNA was used to study the relationship between 33 morphologically identical strains from keratitis cases (30 strains), contact lens storage containers (2 strains), and soil (1 strain). Samples digested with BglII, EcoRI, or HindIII and separated by agarose gel electrophoresis contained detectable mitochondrial DNA restriction fragment length polymorphisms (RFLPs). By comparing RFLPs, the strains could be assigned to seven multiple-strain and three single-strain groups. The largest of these contained nine strains, eight of which were isolated in keratitis cases in various locations worldwide and may indicate a group particularly associated with keratitis. Restriction endonuclease analysis of whole-cell DNA is proposed as a valuable technique for detecting mitochondrial DNA RFLPs in the differentiation of morphologically identical Acanthamoeba strains and may therefore be useful in resolving the complex taxonomy of the genus, which has hitherto been founded on subjective morphological criteria.

Acanthamoeba↗
PubMed2004

Conventional taxonomy obscures deep divergence between Pacific and Atlantic corals.

Only 17% of 111 reef-building coral genera and none of the 18 coral families with reef-builders are considered endemic to the Atlantic, whereas the corresponding percentages for the Indo-west Pacific are 76% and 39%. These figures depend on the assumption that genera and families spanning the two provinces belong to the same lineages (that is, they are monophyletic). Here we show that this assumption is incorrect on the basis of analyses of mitochondrial and nuclear genes. Pervasive morphological convergence at the family level has obscured the evolutionary distinctiveness of Atlantic corals. Some Atlantic genera conventionally assigned to different families are more closely related to each other than they are to their respective Pacific 'congeners'. Nine of the 27 genera of reef-building Atlantic corals belong to this previously unrecognized lineage, which probably diverged over 34 million years ago. Although Pacific reefs have larger numbers of more narrowly distributed species, and therefore rank higher in biodiversity hotspot analyses, the deep evolutionary distinctiveness of many Atlantic corals should also be considered when setting conservation priorities.

Animals↗
PubMed2004

Rhodotorula mucilaginosa, a carotenoid producing yeast strain from a Patagonian high-altitude lake.

The red yeast Rhodotorula mucilaginosa strain CRUB 0138 (previously identified as R. lactosa) was isolated from a high-altitude Patagonian Lake Toncek (1700 m a.s.l.), and assigned with mucilaginosa species. Its biochemical, physiological and molecular features were assessed and compared to R. mucilaginosa PYCC 5166 type strain using a polyphasic approach; in addition, biomass and carotenoid pigment production at different C/N ratios were determined in an incubator shaker. Phenetic characterization by means of 70 current physiological tests including assimilation of aldaric acids and aromatic compounds, and also the ability to grow with amino acids as sole carbon sources, was carried out. According to numerical taxonomy calculations, similarity indexes between R. mucilaginosa CRUB 0138 and PYCC 5166 type strain were 0.86 and 0.77, corresponding to a complete set of physiological tests and MSP-PCR (Mini/Micro Satellite Primed PCR; (GTG)5, M13 and (GAC)5 primers were employed) fingerprinting. Killer activity against 2 native strains, Rhodosporidium kratochvilovae and R. mucilaginosa was detected. Maximum biomass-glucose conversion efficiency (87%) and maximum carotenoid yield (2.32 mg/L) were obtained at C/N = 5 in culture medium containing 10 and 40 g/L glucose, respectively. Different C/N ratios did not influence carotenoid pigment production but low C/N enhanced biomass yield.

Antibiosis↗
PubMed1996

Reliability of diagnosing complicated grief: a preliminary investigation.

Forty experienced mental health providers were asked to diagnose 4 case histories, each involving an aspect of difficult grief embedded in a larger psychopathology context. Half used the full Diagnostic and Statistical Manual of Mental Disorders (3rd ed., rev,; DSM-III-R; American Psychiatric Association, 1987); half used a forced choice from among anxiety, mood, adjustment, and personality disorders. For each case, participants also assigned 1 of 4 complicated grief labels derived from the thanatology literature or the label uncomplicated bereavement taken from the DSM-III-R. Interrater agreement was generally low using the DSM-III-R, regardless of instructional format, despite high reliance on relatively few categories. In contrast, interrater agreement was uniformly high using thanatological classifications. Results are discussed in relation to the growing literature differentiating grief from existing DSM classifications and supporting the argument for a separate taxonomy for grief reactions.

Adjustment Disorders↗
PubMed1988

Comparative studies on the DNA of Pythium species and some possibly related taxa.

DNA from 14 Pythium species, Verrucalvus flavofaciens and Zoophagus insidians was characterized by CsCl-bisbenzimide density gradients in order to investigate its taxonomic potential. A few incomplete analyses were made for other species. All clearly assignable Pythium species produced three DNA bands in the gradient. Pythium undulatum along with Verrucalvus and Zoophagus produced only two bands. Another possible exception, which needs further investigation, is P. vexans. The DNA had a relatively constant banding pattern in CsCl gradients. The small number (eight) of DNA criteria that were available were subjected to cluster analysis to assess the relationships between replicates and species. This restricted database, similar in size to the number of criteria used in morphological taxonomy, provided an independent assessment of the values that have been attached to generic and subgeneric classifications. This approach enabled assessments to be made of relationships between species that have incomplete life-histories and which therefore lack features essential for traditional taxonomic decisions.

Base Composition↗
PubMed2000

Multiple recurrent evolution of trophic types in northeastern Atlantic and Mediterranean seabreams (Sparidae, Percoidei).

Seabreams are among the most valuable fish, not only for small-scale and semiindustrial fisheries but also for aquaculture throughout the Mediterranean. Nevertheless, their phylogenetic relationships are not at all clear. The current taxonomy is based solely on trophic morphology and rests on the assumption that each trophic type evolved only once from a less specialized ancestral condition. We analyzed a 486-bp segment of the mitochondrial 16S rDNA of all 24 seabream species described for the northeastern Atlantic and the Mediterranean to elucidate their generic and subfamily-level relationships. Three major mitochondrial lineages, each comprising species of different feeding strategy and dentition, were found that do not agree with the present taxonomic assignments. Most of the investigated genera were resolved paraphyletically, indicating that the structure and arrangement of oral teeth must have repeatedly evolved from a less specialized ancestral condition. Further, the genus Sparus was resolved as distantly related to the genus Pagrus, in that it was assigned to a different major mitochondrial lineage. Oblada melanura was consistently placed within the Diplodus radiation as sister group to Diplodus puntazzo. Our phylogenetic hypothesis thus suggests multiple independent origins of similar trophic specializations within the Sparidae and indicates that the currently recognized three or four subfamilies need to be redefined.

Animals↗
PubMed2003

Number of ancestral human species: a molecular perspective.

Despite the remarkable developments in molecular biology over the past three decades, anthropological genetics has had only limited impact on systematics in human evolution. Genetics offers the opportunity to objectively test taxonomies based on morphology and may be used to supplement conventional approaches to hominid systematics. Our analyses, examining chromosomes and 46 estimates of genetic distance, indicate there may have been only around 4 species on the direct line to modern humans and 5 species in total. This contrasts with current taxonomies recognising up to 23 species. The genetic proximity of humans and chimpanzees has been used to suggest these species are congeneric. Our analysis of genetic distances between them is consistent with this proposal. It is time that chimpanzees, living humans and all fossil humans be classified in Homo. The creation of new genera can no longer be a solution to the complexities of fossil morphologies. Published genetic distances between common chimpanzees and bonobos, along with evidence for interbreeding, suggest they should be assigned to a single species. The short distance between humans and chimpanzees also places a strict limit on the number of possible evolutionary 'side branches' that might be recognised on the human lineage. All fossil taxa were genetically very close to each other and likely to have been below congeneric genetic distances seen for many mammals. Our estimates of genetic divergence suggest that periods of around 2 million years are required to produce sufficient genetic distance to represent speciation. Therefore, Neanderthals and so-called H. erectus were genetically so close to contemporary H. sapiens they were unlikely to have been separate species. Thus, it is likely there was only one species of human (H. sapiens) for most of the last 2 million years. We estimate the divergence time of H. sapiens from 16 genetic distances to be around 1.7 Ma which is consistent with evidence for the earliest migration out of Africa. These findings call into question the mitochondrial "African Eve" hypothesis based on a far more recent origin for H. sapiens and show that humans did not go through a bottleneck in their recent evolutionary history. Given the large offset in evolutionary rates of molecules and morphology seen in human evolution, Homo species are likely to be characterised by high levels of morphological variation and low levels of genetic variability. Thus, molecular data suggest the limits for intraspecific morphological variation used by many palaeoanthropologists have been set too low. The role of phenotypic plasticity has been greatly underestimated in human evolution. We call into question the use of mtDNA for studies of human evolution. This DNA is under strong selection, which violates the assumption of selective neutrality. This issue should be addressed by geneticists, including a reassessment of its use for molecular clocks. There is a need for greater cooperation between palaeoanthropologists and anthropological geneticists to better understand human evolution and to bring palaeoanthropology into the mainstream of evolutionary biology.

Animals↗
PubMed1982

Dehydrogenase patterns in the taxonomy of Bacteroides.

The malate dehydrogenase (MDH) electrophoretic mobilities of 128 strains of bacteroides belonging to 17 species, including three subspecies of Bacteroides melaninogenicus and two subspecies of Bacteroides ruminicola, were examined. Amongst the pigmented bacteroides, the migration of this enzyme correlated well with recognized taxa, and only one strain, VPI 9085 was clearly different. Other species such as B. oralis, B. buccalis, B. denticola, B. pentosaceus, B. bivius, B. disiens and B. ruminicola were delineated by the combined use of MDH and glutamate dehydrogenase. Forty-three strains belonging to the 'B. fragilis group' differed from the above species in possessing glucose-6-phosphate dehydrogenase and 6-phosphogluconate dehydrogenase, and reference strains as well as fresh isolates were assigned to the correct species by the mobility pattern of these two enzymes. Other properties of MDH such as the pH optima for the oxidation of malate or the reduction of oxaloacetate were of limited taxonomic value. However, the alkaline stability of this enzyme at pH 9, 10 and 11 clearly differentiates the saccharolytic from the non-saccharolytic species of pigmented bacteroides with the latter showing highly stable enzymes with a half life greater than 50 min.

Bacteroides↗
PubMed1976

A taxonomic study of the genus Haemophilus, with the proposal of a new species.

A collection of 426 Haemophilus strains isolated from people with infectious diseases and from the normal flora of mucous membranes in humans and various animal species was studied in an attempt to revise and improve the taxonomy of the genus Haemophilus. The examinations included the determination of a number of biochemical and physiological properties, of which several had not previously been applied to the taxonomy of haemophili. The resulting data reavealed many hitherto unrecognized characters of taxonomic significance and several of the species can now be more accurately defined. The classification presented is supported by the DNA base composition of a large number of representative strains. A diagnostic key to the different taxa is presented. Haemophilus influenzae and H. parainfluenzae have been subdivided into a number of biotypes. It is possible to demonstrate a relationship between the individual biotypes of H. influenzae and the origin of the strains assigned to them. The results indicate that H. aegyptius, H. parahaemolyticus and H. paraphrohaemolyticus do not merit specific status. Four unnamed taxa of V-factor-dependent haemophili have been recognized. The name Haemophilus segnis is proposed for one of these taxa, which consists mainly of strains isolated from the human oral cavity. It is demonstrated that the name H. Ducreyi has been used for different groups of bacteria, and that only one of these groups can legitimately be assigned to the genus Haemophilus. Haemolytic V-factor-dependent strains from swine, previously included in H. parahaemolyticus, are significantly different from strains of human origin and should be named H. pleuropneumoniae. None of the strains from swine and fowls were haemin-dependent. The relationships of these strains to the species H. suis and H. gallinarum, and to H. parasuis and H. paragallinarum are discussed. Haemophilus piscium is shown not to belong to the genus Haemophilus. The taxonomic position of H. aphrophilus is uncertain and its possible relationship to Actinobacillus actinomycetemcomitans requires further study. The positive correlation found between the ecology of the strains studied and their affiliation with the different taxa is discussed.

Animals↗
PubMed2003

Phylogenetic taxonomy of the family Chlorobiaceae on the basis of 16S rRNA and fmo (Fenna-Matthews-Olson protein) gene sequences.

A new taxonomy of the green sulfur bacteria is proposed, based on phylogenetic relationships determined using the sequences of the independent 16S rRNA and fmo (Fenna-Matthews-Olson protein) genes, and supported by the DNA G + C content and sequence signatures. Comparison of the traditional classification system for these bacteria with their phylogenetic relationship yielded a confusing picture, because properties used for classification (such as cell morphology, photosynthetic pigments and substrate utilization) do not concur with their phylogeny. Using the genetic information available, strains and species assigned to the genera Chlorobium, Pelodictyon and Prosthecochloris are considered, and the following changes are proposed. Pelodictyon luteolum is transferred to the genus Chlorobium as Chlorobium luteolum comb. nov. Pelodictyon clathratiforme and Pelodictyon phaeoclathratiforme are transferred to the genus Chlorobium and combined into one species, Chlorobium clathratiforme comb. nov. The name Pelodictyon will become a synonym of Chlorobium. Strains known as Chlorobium limicola subsp. thiosulfatophilum that have a low DNA G + C content (52-52.5 mol%) are treated as strains of Chlorobium limicola; those with a high DNA G + C content (58.1 mol%) are transferred to Chlorobaculum gen. nov., as Chlorobaculum thiosulfatiphilum sp. nov. Chlorobium tepidum is transferred to Chlorobaculum tepidum comb. nov., and defined as the type species of the genus Chlorobaculum. Strains assigned to Chlorobium phaeobacteroides, but phylogenetically distant from the type strain of this species, are assigned to Chlorobium limicola and to Chlorobaculum limnaeum sp. nov. Strains known as Chlorobium vibrioforme subsp. thiosulfatophilum are transferred to Chlorobaculum parvum sp. nov. Chlorobium chlorovibrioides is transferred to 'Chlorobaculum chlorovibrioides' comb. nov. The type strain of Chlorobium vibrioforme is phylogenetically related to Prosthecochloris, and is therefore transferred to this genus as Prosthecochloris vibrioformis comb. nov. Consequently, the name Chlorobium vibrioforme will become a synonym of Prosthecochloris vibrioformis, and other strains that were assigned to this species are now considered to belong to Chlorobium luteolum, Chlorobium phaeovibrioides and 'Chlorobaculum chlorovibrioides', according to their phylogenetic relatedness.

Bacterial Proteins↗
PubMedDate not supplied

Development and content validity testing of a comprehensive classification of diagnoses for pediatric nurse practitioners.

Pediatric nurse practitioners (PNPs) need an integrated, comprehensive classification that includes nursing, disease, and developmental diagnoses to effectively describe their practice. No such classification exists. Further, methodologic studies to help evaluate the content validity of any nursing taxonomy are unavailable. A conceptual framework was derived. Then 178 diagnoses from the North American Nursing Diagnosis Association (NANDA) 1986 list, selected diagnoses from the International Classification of Diseases, the Diagnostic and Statistical Manual, Third Revision, and others were selected. This framework identified and listed, with definitions, three domains of diagnoses: Developmental Problems, Diseases, and Daily Living Problems. The diagnoses were ranked using a 4-point scale (4 = highly related to 1 = not related) and were placed into the three domains. The rating scale was assigned by a panel of eight expert pediatric nurses. Diagnoses that were assigned to the Daily Living Problems domain were then sorted into the 11 Functional Health patterns described by Gordon (1987). Reliability was measured using proportions of agreement and Kappas. Content validity of the groups created was measured using indices of content validity and average congruency percentages. The experts used a new method to sort the diagnoses in a new way that decreased overlaps among the domains. The Developmental and Disease domains were judged reliable and valid. The Daily Living domain of nursing diagnoses showed marginally acceptable validity with acceptable reliability. Six Functional Health Patterns were judged reliable and valid, mixed results were determined for four categories, and the Coping/Stress Tolerance category was judged reliable but not valid using either test. There were considerable differences between the panel's, Gordon's (1987), and NANDA's clustering of NANDA diagnoses. This study defines the diagnostic practice of nurses from a holistic, patient-centered perspective. It is the first study to use quantitative methods to test a diagnostic classification system for nursing. The classification model could also be adapted for other nurse specialties.

Humans↗
PubMedDate not supplied

[Comparative characteristics of the Bdellovibrio strains isolated from river water and sewage].

The morphology, the host ranges, the resistance to pteridine and the nucleotide composition of DNA were compared in 12 newly isolated and 10 collection strains of Bdellovibrio. The significance of properties used for the taxonomy of these organisms was evaluated. The host ranges of Bdellovibrio strains are heterogeneous with respect to the taxonomy of host bacteria. The specificity of the parasite depends to a significant degree on the host bacterium in which it grows. All the strains including Bd. starrii which was described earlier as a pteridine resistant species are sensitive to pteridine. Therefore, such properties as the host range action and the response to pteridine cannot be used for diagnostics of Bdellovibrio species. The strains were found to be very heterogeneous with regard to the nucleotide composition of the DNA. Eight out of the 12 newly isolated strains were assigned to the species Bd, bacteriovorus.

Bdellovibrio↗
PubMed1991

Pestiviruses--taxonomic perspectives.

The history of pestivirus taxonomy is surprisingly consistent: almost 30 years ago it was recognized that pestiviruses are structurally akin to flaviviruses, and recent nucleotide sequence data have confirmed this resemblance at the level of genome organization. For other enveloped positive stranded RNA viruses with ikosahedral nucleocapsids e.g. equine arteritis and lactate dehydrogenase virus of mice a taxonomic dilemma is encountered; while virions resemble ("non-arthropod-borne") togaviruses, the replication via a nested set of subgenomic RNAs is corona and torovirus-like. Pestiviruses, flaviviruses and the hepatitis C virus group have been assigned generic status in the Flaviviridae family.

Animals↗
PubMed1973

Determination of natural host taxonomy of RNA tumor viruses by molecular hybridization: application to RD-114, a candidate human virus.

The lysogenic bacteriophages and the RNA tumor viruses have in common the ability to add their genetic information to the genome of their host cells. The biological similarity extends further; data summarized here indicate that they both possess homology to the DNA of their uninfected indigenous hosts. Sharing of common sequences with normal host DNA has been established with avian, murine, feline, and primate oncornaviruses. This finding provides a method for determining the taxonomic position of the natural host of any new RNA tumor virus isolated. Application of this approach to RD-114 revealed extensive hybridization to normal cat DNA and little, if any, hybridization to human DNA. We conclude that the data assign a feline origin rather than a human origin to RD-114.

Animals↗
PubMed1973

Taxonomy of marine bacteria: Beneckea parahaemolytica and Beneckea alginolytica.

A collection of 169 strains, including 91 obtained from cases of gastroenteritis and 41 from localized tissue infections and infections of the eye and ear, was submitted to an extensive nutritional, physiological, and morphological characterization. The nutritional and physiological data obtained from these strains, as well as data for strains of other species of the genus Beneckea, were submitted to a numerical analysis which grouped the strains into clusters on the basis of phenotypic similarity. Strains from cases of gastroenteritis formed a group of three clusters which linked at a similarity value of 68%. These three clusters could not, however, be separated from each other by universally positive or negative traits, and on the basis of their overall phenotypic similarity were assigned to a single species, B. parahaemolytica. The majority of the strains from human, nonenteric sources segregated into two distinct clusters, one designated B. alginolytica and the other unassigned with respect to species (group C-2). B. parahaemolytica, B. alginolytica, and group C-2 could be readily distinguished from one another as well as from the remaining species of the genus Beneckea by multiple, unrelated, phenotypic traits. Activities of selected enzymes of glucose and gluconate catabolism in cell-free extracts of B. parahaemolytica, B. alginolytica, and group C-2 suggested that these organisms utilized glucose primarily via the Embden-Meyerhof pathway and gluconate primarily via the Entner-Doudoroff pathway. Similar results were observed in the other members of the genus Beneckea.

Bacteria↗