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At least 235 records · Page 13Linked to original sources
PubMed1997

Comparison of use of phenotypic and genotypic characteristics for identification of species of the anamorph genus Candida and related teleomorph yeast species.

A total of 49 type and neotype isolates and 32 clinical isolates of the anamorph genus Candida and related teleomorph genera were obtained from different culture collections and clinical laboratories. Isolates were subjected to two phenotypic methods of identification, Vitek yeast biochemical card (YBC) and API ID 32C, both based on carbohydrate assimilation, and one genotypic method, PCR fingerprinting, based on the detection of DNA polymorphisms between minisatellite-specific sequences with the primer M13 (5' GAGGGTGGCGGTTCT 3'). The correct identification of a strain at the Centraalbureau voor Schimmelcultures was used as the gold standard for the identification of an isolate. When the study was restricted to species included in the respective biochemical databases, the Vitek YBC and API ID 32C systems performed adequately with positive identification rates of 87.3 and 76.8%, respectively. When uncommon species were added to the study, several of which are not included in the databases, the identification efficiencies were 76.5 and 77.5%, respectively. By comparison, all isolates were correctly identified by PCR fingerprinting, with 63 reference species profiles in the databank. Sufficient polymorphisms among the total set of banding patterns were observed, with adequate similarity in the major patterns obtained from a given species, to allow each isolate to be assigned unambiguously to a particular species. In addition, variations in minor bands allowed for differentiation to the strain level. PCR fingerprinting was found to be rapid, reproducible, and more cost-effective than either biochemical approach. Our results provide reference laboratories with an improved identification method for yeasts based on genotypic rather than phenotypic markers.

Base Sequence↗
PubMed1998

Species-specific plasmid sequences for PCR identification of the three species of Borrelia burgdorferi sensu lato involved in Lyme disease.

Species-specific sequences were shown to be carried by plasmids of the three main species of Borrelia burgdorferi sensu lato involved in Lyme disease. Libraries of the 16-, 33-, and 25-kb plasmids of B. burgdorferi sensu stricto, Borrelia garinii, and Borrelia afzelii, respectively, were then built and used to isolate species-specific sequences. After sequencing of the cloned inserts, three sets of primers were designed. They were shown to determine species-specific PCR amplification products. The sensitivities of the PCR assay with these primers were 100 spirochetes for B. burgdorferi sensu stricto and 1,000 spirochetes for B. garinii and B. afzelii. The usefulness of these primers for the identification of species in biological samples (tick, serum, and cerebrospinal fluid samples) was ascertained.

Base Sequence↗
PubMed2004

Detection of four Plasmodium species in blood from humans by 18S rRNA gene subunit-based and species-specific real-time PCR assays.

There have been reports of increasing numbers of cases of malaria among migrants and travelers. Although microscopic examination of blood smears remains the "gold standard" in diagnosis, this method suffers from insufficient sensitivity and requires considerable expertise. To improve diagnosis, a multiplex real-time PCR was developed. One set of generic primers targeting a highly conserved region of the 18S rRNA gene of the genus Plasmodium was designed; the primer set was polymorphic enough internally to design four species-specific probes for P. falciparum, P. vivax, P. malarie, and P. ovale. Real-time PCR with species-specific probes detected one plasmid copy of P. falciparum, P. vivax, P. malariae, and P. ovale specifically. The same sensitivity was achieved for all species with real-time PCR with the 18S screening probe. Ninety-seven blood samples were investigated. For 66 of them (60 patients), microscopy and real-time PCR results were compared and had a crude agreement of 86% for the detection of plasmodia. Discordant results were reevaluated with clinical, molecular, and sequencing data to resolve them. All nine discordances between 18S screening PCR and microscopy were resolved in favor of the molecular method, as were eight of nine discordances at the species level for the species-specific PCR among the 31 samples positive by both methods. The other 31 blood samples were tested to monitor the antimalaria treatment in seven patients. The number of parasites measured by real-time PCR fell rapidly for six out of seven patients in parallel to parasitemia determined microscopically. This suggests a role of quantitative PCR for the monitoring of patients receiving antimalaria therapy.

Animals↗
PubMed2005

Rapid identification of Candida species and other clinically important yeast species by flow cytometry.

Two rapid diagnostic assays, utilizing two different Luminex flow cytometry methods, were developed for identification of clinically important ascomycetous yeast species. Direct hybridization and allele-specific primer extension methods were both successful in establishing a DNA-based assay that can rapidly and accurately identify Candida albicans, Candida krusei, Candida parapsilosis, Candida glabrata, and Candida tropicalis as well as other clinical species. The direct hybridization assay was designed to identify a total of 19 ascomycetous yeast species, and the allele-specific primer extension assay was designed to identify a total of 34 species. Probes were validated against 438 strains representing 303 species. From culture to identification, the allele-specific primer extension method takes 8 h and the direct hybridization method takes less than 5 h to complete. These assays represent comprehensive, rapid tests that are well suited for the clinical laboratory.

Candida↗
PubMed2006

Use of PCR to demonstrate presence of adenovirus species B, C, or F as well as coinfection with two adenovirus species in children with flu-like symptoms.

Adenovirus (AdV) respiratory infections have usually been associated with species B, C, and E. In this study, we detected 9.4% of AdVs by PCR in 500 nasal swabs from 319 children with influenza-like symptoms. AdV typing by PCR with specific probes showed species C, B, and F as well as coinfection with two species. Coinfection with two AdV species and the presence of species F in respiratory samples are novel findings that should be further investigated.

Adenovirus Infections, Human↗
PubMed2002

Search for species-specific mating signal in courtship songs of sympatric sibling species, Drosophila ananassae and D. pallidosa.

Sexual isolation is one of the most important mechanisms that may lead to speciation. Drosophila ananassae and D. pallidosa are useful for the study of sexual isolation, because of their sympatric distribution and no postmating isolation between them. Courtship songs are considered to play a crucial role in sexual isolation between D. ananassae and D. pallidosa. We recorded and analyzed male courtship songs of D. ananassae and D. pallidosa for eight and four geographical strains, respectively. Courtship behaviors of the two species were consistent with those previously described, however, male's middle leg shaking, which had not before been described, was observed in both species. Males sing by wing vibration only during courtship. Their song oscillograms were distinct between species, but those of conspecific strains were very similar, in spite of their different geographical derivation. We found species-specificity in burst length, pulse length, cycle number in a pulse, and frequency spectra of bursts; these results suggest that these song parameters may play a role in mate recognition that enforces their sexual isolation. The specific values of interpulse interval, cycle number in a pulse and intrapulse frequency were involved with the determination of specificity in frequency spectra of bursts. We discussed the possibility that the specific frequency spectra of bursts are recognized by females as the species-specific signal rather than each parameter individually.

Animals↗
PubMed1998

A diagnostic polymerase chain reaction assay for species A and D of the Anopheles Dirus (Diptera: Culicidae) species complex based on ribosomal DNA second internal transcribed spacer sequence.

A polymerase chain reaction assay based on differences in the internal transcribed spacer regions of ribosomal DNA was developed for distinguishing 2 members of the Anopheles dirus sibling species complex. This assay distinguished An. dirus species A from species D by producing diagnostic bands, 374 base pairs (bp) in length for species A and 663 bp in length for species D. Both laboratory colonies and field collections from Hainan and Yunnan provinces of China were identified with 100% accuracy.

Amino Acid Sequence↗
PubMed2002

Genetic divergence within the Drosophila mayaguana subcluster, a closely related triad of Caribbean species in the repleta species group.

The mayaguana triad of the Drosophila repleta species group includes D. mayaguana, D. straubae, and D. parisiena, the latter two of which are very similar when examined morphologically. Many morphological characters used to define these taxa are quantitative and overlap substantially among some forms--it is only through suites of such characters that species can be identified. We apply Population Aggregation Analysis and tree building methods to five rapidly evolving gene regions--the mitochondrial AT rich region and the nuclear acetylcholinesterase, hunchback, mastermind, and vestigial loci to test the morphological species delineations within the morphocryptic mayaguana triad. We find that D. mayaguana is diagnosable using DNA sequences, but the other two species form a non-diagnosable paraphyletic assemblage. A single ecological factor, oviposition substrate, is an important diagnostic character distinguishing D. straubae from D. parisiena, highlighting the importance of examining a diverse array of data (morphological, molecular, ecological, and behavioral) when defining species limits.

Animals↗
PubMed1995

[Genetic structure and origin of the tetraploid toad Bufo danatensis Pisanetz, 1978 (Amphibia, Bufonidae) from Central Asia. Biochemical polymorphism and comparison of the level of heterozygosity of diploid species with tetraploid species].

Comparison of individual variation at 24 biochemical loci in members of the species complex of Palearctic green toads showed that the heterozygosity of the tetraploid species Bufo danatensis (Hobs + 0.45) was significantly higher than that of the diploid species B. viridis, B. sp., and B. raddei (Hobs = 0.009 - 0.103). Such difference can be explained only by a hybrid origin of the tetraploid species. Individual electrophoretic variability of the polyploid toad species is associated with an allelic variation that is manifested in constantly heterozygous spectra as the gene dosage effect. At the population level, this phenomenon found in Pamir toads is caused by irregular meiosis in founders of the population or by directional changes in gene regulation. Genotypic distributions in zones of contact of the diploid and tetraploid taxons demonstrate the possibility of restricted introgressive hybridization.

Animals↗
PubMed2006

A morphologically ill-founded powdery mildew species, Pleochaeta indica, is recognized as a phylogenetic species based on the analysis of the nuclear ribosomal DNA sequences.

Morphological characteristics of a powdery mildew fungus found on Celtis australis in the Indian Himalayas coincided with those of Pleochaeta indica, described from this tree species in India, as well with those of P. shiraiana, known to infect C. australis and other plant species in Asia. This suggested that the original description of P. indica based on morphological patterns was not well founded and this taxon could be reduced to synonymy with P. shiraiana. However, phylogenetic analyses of the rDNA 28S and ITS sequences determined in some Indian Pleochaeta specimens from C. australis showed that this fungus is closely related, but not identical to P. shiraiana infecting C. sinensis in Japan which served as the basis of the original description of P. shiraiana. Molecular clock analysis of the ITS region and that of the 28S rDNA indicated that the split between the Japanese P. shiraiana infecting C. sinensis and Pleochaeta sp. infecting C. australis in India may have occurred 2.0-8.5 million years ago in the Pliocene and may have coincided with the formation of the Himalayan mountains and the global cooling of the Earth during the late Tertiary. Thus, P. indica is recognized in this study as a distinct phylogenetic species, although our morphological study showed that its description as a morphological species was not well founded. This is a striking example of a cryptic species which is genetically different from close relatives but cannot be distinguished from them based on morphology.

Ascomycota↗
PubMedDate not supplied

Characterization of Sarcocystis species in domestic animals using a PCR-RFLP analysis of variation in the 18S rRNA gene: a cost-effective and simple technique for routine species identification.

Thirteen restriction endonucleases were used to investigate nuclotide sequence variation in the 18S rRNA DNA of 88 individuals from ten Sarcocystis taxa collected as cysts from their intermediate hosts, swine, cattle and water buffalo. A DNA sequence of approximately 900 bp was used. A total of 26 electromorphs were detected. The electromorphs were sorted into seven different haplotypes that coincided with the six named species and an unidentified species from cattle. These findings support those of our morphological examinations, which suggested that the taxa resembling Sarcocystis hirsuta, S. hominis, both found in water buffalo, and S. sinensis found in cattle, are not new species but are in fact S. hirsuta and S. hominis as found in cattle, and S. sinensis as found in water buffalo; this finding supports the idea that these species can utilize both cattle and water buffalo as intermediate hosts and are not restricted to one or the other host group as previously thought. PCR-RFLP resolved by agarose gel electrophoresis is shown to be an easy and rapid method of discriminating between these species.

Animals↗
PubMed1999

Trends in species distribution and susceptibility to fluconazole among blood stream isolates of Candida species in the United States.

National surveillance of blood stream infections (BSI) attributable to Candida spp. has been limited to date. Recent studies have suggested in increase in the proportion of BSI attributable to non-Candida albicans species and have also raised concerns regarding the emergence of antifungal resistance among Candida spp. The increased utilization of broad-spectrum antifungal agents and the recognition of Candida spp. as prominent pathogens with the potential for developing antifungal resistance, emphasize the need for ongoing surveillance of antifungal susceptibility patterns. In this investigation trends in species distribution and susceptibility to fluconazole among BSI isolates of Candida spp. referred to our laboratory by United States hospitals were evaluated over the 7-year period from 1992 to 1998. A total of 1579 BSI isolates from more than 50 medical centers were processed. Overall, C. albicans accounted for 52% of isolates followed by C. glabrata (18%), C. parapsilosis (15%), C. tropicalis (11%), and C. krusei (2%). The proportion of BSI isolates that were C. albicans ranged from 45% in 1992 to 60% in 1998. Among the non-C. albicans isolates, C. glabrata succeeded C. parapsilosis as the most common species beginning in 1995. Overall, the susceptibility of all Candida species (C. albicans plus all other species) to fluconazole remained stable (MIC90, 16 micrograms/mL). The fluconazole MIC90 for C. albicans was 0.5-2.0 micrograms/ml for all years studied except 1995 (8.0 micrograms/mL) and was 1.0 microgram/mL overall. The present study suggests a continued prominent role of C. albicans as a cause of BSI, and a constant level of susceptibility of Candida BSI isolates to fluconazole over 7 years. These data should serve as a baseline for future surveillance efforts for anti-fungal agents tested against yeast BSI isolates.

Antifungal Agents↗
PubMed2003

Phytophthora pseudosyringae sp. nov., a new species causing root and collar rot of deciduous tree species in Europe.

In several studies of oak decline in Europe, a semi-papillate homothallic Phytophthora taxon was consistently isolated, together with other Phytophthora species, from rhizosphere soil samples. It was also found associated with necrotic fine roots and stem necroses of Fagus sylvatica and Alnus glutinosa. Due to morphological and physiological similarities, the semi-papillate isolates were previously identified as P. syringae by various authors. The morphology, physiology and pathogenicity against fine roots of Quercus robur, Q. petraea and F. sylvatica, bark of A. glutinosa, leaves of Ilex aquifolium and apple fruits of this Phytophthora species are described and compared with those of related and similar Phytophthora species, namely P. ilicis, P. psychrophila, P. quercina, P. citricola and P. syringae. The phylogenetic placement on the basis of ITS and mtDNA sequence data was also examined. Isolates of this taxon produce colonies with stellate to rosaceous growth patterns and limited aerial mycelium on various agar media. Antheridia are predominantly paragynous. In water culture catenulate hyphal swellings and semi-papillate caducous sporangia, that are usually limoniform, ellipsoid or ovoid, are formed abundandly, mostly in lax or dense sympodia. This taxon is a moderately slow growing, low temperature species with optimum and maximum temperatures around 20 and 25 degrees C, respectively. Tested isolates are moderately aggressive to fine roots of oaks and beech, highly aggressive to holly leaves and apple fruits, and slightly pathogenic to alder bark. Thirteen tested isolates had an identical and distinct ITS sequence which was more similar to that of P. ilicis and P. psychrophila than any other known taxa. On the basis of their unique combination of morphological characters, colony growth patterns, cardinal temperatures for growth, growth rates, pathogenicity to oaks, beech, alder, apple and holly, their host range, and ITS and mtDNA sequences the semi-papillate caducous Phytophthora isolates from oaks, beech and alder are clearly separated from related and similar Phytophthora spp., and described as a new species, P. pseudosyringae sp. nov.

Alnus↗
PubMed2004

Nominal species of the genus Gyrodactylus von Nordmann 1832 (Monogenea: Gyrodactylidae), with a list of principal host species.

The total diversity of the monogenean genus Gyrodactylus is evaluated. There are 409 potentially valid species names within the genus, recorded from c. 400 host species. Five species have been placed within Fundulotrema and an additional 51 Gyrodactylus species names represent synonyms, nomina nuda or have been reassigned to other non-viviparous monogenean genera. While the majority of Gyrodactylus species (59%) are recorded from single hosts, some have a much broader broad range.

Animals↗
PubMed2003

Cold- and light-induced changes of metabolite and antioxidant levels in two high mountain plant species Soldanella alpina and Ranunculus glacialis and a lowland species Pisum sativum.

Leaves of the two cold-acclimated alpine plant species Ranunculus glacialis and Soldanella alpina and, for comparison, of the non-acclimated lowland species Pisum sativum were illuminated with high light intensity at low temperature. The light- and cold-induced changes of antioxidants and of the major carbon and phosphate metabolites were analysed to examine which metabolic pathways might be limiting in non-acclimated pea leaves and whether alpine plants are able to circumvent such limitation. During illumination at low temperature pea leaves accumulated high quantities of sucrose, glucose-6-phosphate, fructose-6-phosphate, mannose-6-phosphate and phosphoglycerate (PGA) whereas ATP/ADP-ratios decreased. Although the PGA content also increased in leaves of R. glacialis the other metabolites did not accumulate and ATP/ADP-ratios remained fairly constant in either alpine species. These data indicate a inorganic phosphate (Pi)-limitation in the chloroplasts of pea leaves but not in the alpine species. However, the total phosphate pool and the percentage of free Pi were highest in pea and did not change during illumination in cold. In contrast, free Pi contents declined markedly in R. glacialis leaves, suggesting that Pi is available for metabolism in this species. In S. alpina leaves contents of ascorbate and glutathione doubled in light and cold, while the contents of sugars did not increase. Obviously, S. alpina leaves can use assimilated carbon for ascorbate synthesis, rather than for the synthesis of sugars. A high capacity for ascorbate synthesis might prevent the accumulation of mannose-6-phosphate and Pi-limitation.

Journal Article↗
PubMed2000

Species-specific oligonucleotide probes for macroalgae: molecular discrimination of two marine fouling species of Enteromorpha (Ulvophyceae).

The green seaweeds Enteromorpha intestinalis and E. compressa are important fouling organisms commonly found in polluted and nutrient-enriched marine and brackish water habitats, where they are used in environmental monitoring. Discrimination of the two species is extremely difficult because of overlapping morphological characters. In this study a quick molecular method for species identification was developed based on the nuclear rDNA ITS2 sequence data of 54 E. intestinalis samples and 20 E. compressa samples from a wide geographical range. Oligonucleotide probes were designed for species-specific hybridization to dot-blots of the PCR-amplified ITS1, 5.8S gene and ITS2 fragment of both E. intestinalis and E. compressa. Specificity of the oligonucleotide probes was confirmed by tests with taxonomically diverse species that could morphologically be confused with E. intestinalis or E. compressa. This is the first use of species-specific probes for macroalgae. The restriction endonuclease NruI digested specifically the amplified PCR product from E. compressa into two fragments detectable on agarose gels, but no suitable restriction sites were identifiable in the PCR product of E. intestinalis.

Base Sequence↗
PubMed2006

Helminths in Mesaspis monticola (Squamata: Anguidae) from Costa Rica, with the description of a new species of Entomelas (Nematoda: Rhabdiasidae) and a new species of Skrjabinodon (Nematoda: Pharyngodonidae).

Entomelas duellmani n. sp. (Rhabditida: Rhabdiasidae) from the lungs and Skrjabinodon cortagoensis n. sp. (Oxyurida: Pharyngodonidae) from the intestines of Mesaspis monticola (Sauria: Anguidae) are described and illustrated. E. duellmani is the sixth species assigned to the genus and is the third species described from the Western Hemisphere. It is easily separated from other neotropical species in the genus by pre-equatorial position of its vulva. Skrjabinodon cartagoensis is the 24th species assigned to the genus and differs from other neotropical species in the genus by female tail morphology.

Animals↗
PubMed1971

Regional Coexistence of Species and Competition between Rare Species.

A model is developed for the coexistence and exclusion of species over a region of similar habitable patches. Since the balance of local extinction and colonization would leave some patches unoccupied even without competitors, species may coexist even when all the patches are the same. Regional competition coefficients are found when species affect the local extinction or migration rates of each other. Rare species can regulate each other and even exclude other species completely.

Journal Article↗