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At least 109 records · Page 6Linked to original sources

Identification of Carnobacterium species by restriction fragment length polymorphism of the 16S-23S rRNA gene intergenic spacer region and species-specific PCR.

The genus Carnobacterium is currently divided into the following eight species: Carnobacterium piscicola, C. divergens, C. gallinarum, C. mobile, C. funditum, C. alterfunditum, C. inhibens, and C. viridans. An identification tool for the rapid differentiation of these eight Carnobacterium species was developed, based on the 16S-23S ribosomal DNA (rDNA) intergenic spacer region (ISR). PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of this 16S-23S rDNA ISR was performed in order to obtain restriction profiles for all of the species. Three PCR amplicons, which were designated small ISR (S-ISR), medium ISR (M-ISR), and large ISR (L-ISR), were obtained for all Carnobacterium species. The L-ISR sequence revealed the presence of two tRNA genes, tRNA(Ala) and tRNA(Ile), which were separated by a spacer region that varied from 24 to 38 bp long. This region was variable among the species, allowing the design of species-specific primers. These primers were tested and proved to be species specific. The identification method based on the 16S-23S rDNA ISR, using PCR-RFLP and specific primers, is very suitable for the rapid low-cost identification and discrimination of all of the Carnobacterium species from other phylogenetically related lactic acid bacteria.

Animals↗

Physical localisation of repetitive DNA sequences in Alstroemeria: karyotyping of two species with species-specific and ribosomal DNA.

Fluorescence in situ hybridization (FISH) was used to localise two species-specific repetitive DNA sequences, A001-I and D32-13, and two highly conserved 25S and 5S rDNA sequences on the metaphase chromosomes of two species of Alstroemeria. The Chilean species, Alstroemeria aurea (2n = 16), has abundant constitutive heterochromatin, whereas the Brazilian species, Alstroemeria inodora, has hardly any heterochromatin. The A. aurea specific A001-I probe hybridized specifically to the C-band regions on all chromosomes. The FISH patterns on A. inodora chromosomes using species-specific probe D32-13 resembled the C-banding pattern and the A001-I pattern on A. aurea chromosomes. There were notable differences in number and distribution of rDNA sites between the two species. The 25S rDNA probe revealed 16 sites in A. aurea that closely colocalised with A001-I sites and 12 in A. inodora that were predominantly detected in the centromeric regions. FISH karyotypes of the two Alstroemeria species were constructed accordingly, enabling full identification of all individual chromosomes. These FISH karyotypes will be useful for monitoring the chromosomes of both Alstroemeria species in hybrids and backcross derivatives.

Brazil↗

Insecticide species sensitivity distributions: importance of test species selection and relevance to aquatic ecosystems.

Single-species acute toxicity data and (micro)mesocosm data were collated for 16 insecticides. These data were used to investigate the importance of test-species selection in constructing species sensitivity distributions (SSDs) and the ability of estimated hazardous concentrations (HCs) to protect freshwater aquatic ecosystems. A log-normal model was fitted to a minimum of six data points, and the resulting distribution was used to estimate lower (95% confidence), median (50% confidence), and upper (5% confidence) 5% HC (HC5) values. Species sensitivity distributions for specific taxonomic groups (vertebrates, arthropods, nonarthropod invertebrates), habitats (saltwater, freshwater, lentic, lotic), and geographical regions (Palaearctic, Nearctic, temperate, tropical) were compared. The taxonomic composition of the species assemblage used to construct the SSD does have a significant influence on the assessment of hazard, but the habitat and geographical distribution of the species do not. Moreover, SSDs constructed using species recommended in test guidelines did not differ significantly from those constructed using nonrecommended species. Hazardous concentrations estimated using laboratory-derived acute toxicity data for freshwater arthropods (i.e., the most sensitive taxonomic group) were compared to the response of freshwater ecosystems exposed to insecticides. The sensitivity distributions of freshwater arthropods were similar for both field and laboratory exposure, and the lower HC5 (95% protection with 95% confidence) estimate was protective of adverse ecological effects in freshwater ecosystems. The corresponding median HC5 (95% protection level with 50% confidence) was generally protective of single applications of insecticide but not of continuous or multiple applications. In the latter cases, a safety factor of at least five should be applied to the median HC5.

Analysis of Variance↗

Analysis of result variability from high-density oligonucleotide arrays comparing same-species and cross-species hybridizations.

There exists a significant limitation in the variety of organismsfor which microarrays have been developed because of a lack of genomic sequence data. A near-term solution to this limitation is to use microarrays designed for one species to analyze RNA samples from closely related species. The assumption is that conservation of gene sequences between species will be sufficient to generate a reasonable amount of good-quality data. While there have been relatively few published reports describing the use of microarrays for cross-species hybridizations, this technique is potentially a powerful tool for understanding genomics in model organisms such as nonhuman primates. Here we describe the analysis and comparison of hybridization characteristics and data variability from a set of cross-species (rhesus macaque) and same-species (human) hybridization experiments using human high-density Affymetrix oligonucleotide arrays. The data reveal that a large fraction of probe sets are effective at transcript detection in the cross-species hybridization, validating the application of cross-species hybridizations for nonhuman primate genomics research.

Analysis of Variance↗

[Species and species diversity in relation with restoration and persistence of degraded ecosystem functions].

Species diversity is an important character of an ecosystem, and keeps it to function. Species diversity and their communities provide human with essential ecosystem services, including nutrient cycling, biological productivity, trophic function, etc. Species diversity is tightly related with the ecosystem's ability to withstand stress and disturbance. Increasing biodiversity could enhance system stability. Compared to individual species and species number, functional group and functional diversity impose larger impact on system functioning, and are good approaches used to measure stability and to predict community change. Several forms with which the species act on ecosystem functioning were proposed and discussed in this paper. Understanding the relationship between species diversity and ecosystem function could guide the practice of restoring degraded ecosystem and maintaining its functions. Particularly, it provides basic ecological theories for "species assemblage" at initial stage of restoration.

Ecosystem↗

[Genomic structure of the autotetraploid oat species Avena macrostachya inferred from comparative analysis of the ITS1 and ITS2 sequences: on the oat karyotype evolution during the early stages of the Avena species divergence].

To examine the genomic structure of Avena macrostachya, internal transcribed spacers, ITS1 and ITS2, as well as nuclear 5.8S tRNA genes from three oat species with AsAs karyotype (A. wiestii, A. hirtula, and A. atlantica), and those from A. longiglumis (AlAl), A. canariensis (AcAc), A. ventricosa (CvCv), A. pilosa, and A. clauda (CpCp) were sequenced. All species of the genus Avena examined represented a monophyletic group (bootstrap index = 98), within which two branches, i.e., species with A- and C-genomes, were distinguished (bootstrap indices = 100). The subject of our study, A. macrostachya, albeit belonging to the phylogenetic branch of C-genome oat species (karyotype with submetacentic and subacrocentric chromosomes), has preserved an isobrachyal karyotype, (i.e., that containing metacentric chromosomes), probably typical of the common Avena ancestor. It was suggested to classify the A. macrostachya genome as a specific form of C-genome, Cm-genome. Among the species from other genera studied, Arrhenatherum elatius was found to be the closest to Avena in ITS1 and ITS structure. Phylogenetic relationships between Avena and Helictotrichon remain intriguingly uncertain. The HPR389153 sequence from H. pratense genome was closest to the ITS1 sequences specific to the Avena A-genomes (p-distance = 0.0237), while the differences of this sequence from the ITS1 of A. macrostachya reached 0.1221. On the other hand, HAD389117 from H. adsurgens was close to the ITS1 specific to Avena C-genomes (p-distance = 0.0189), while its differences from the A-genome specific ITS1 sequences reached 0.1221. It seems likely that the appearance of highly polyploid (2n = 12-21x) species of H. pratense and H. adsurgens could be associated with interspecific hybridization involving Mediterranean oat species carrying A- and C-genomes. A hypothesis on the pathways of Avena chromosomes evolution during the early stages the oat species divergence is proposed.

Avena↗

Adipocyte insulin-binding species: the size and subunit composition of the larger binding species.

Several investigators have reported that there are both large and small insulin-binding proteins in plasma membranes; the larger protein demonstrates nonlinear Scatchard binding, and the smaller protein has linear binding. We now present evidence that the larger insulin-binding species consists of four proteins of different sizes. Rat epididymal adipocyte plasma membranes were prebound with 125I-insulin and then exposed to 1 mM disuccinimidyl suberate for 15 min at 2 degrees C. The membranes were solubilized in 0.1% Triton X-100 and applied to a Sepharose 6B column. Peaks of radioactivity from the column were dialyzed, lyophilized, and analyzed by dodecyl-sulphate gel electrophoresis (5%, 100/l; mono/bisacrylamide). Autoradiograms of the gels were scanned with a densitometer. The Sepharose chromatogram revealed four radioactive peaks: peak 1 at column void volume; peak 2, Kav = 0.27; peak 3, Kav = 0.77; and peak 4, Kav = 1.09. Dodecyl sulphate electrophoresis of fractions in peak 2 demonstrated four bands on autoradiography; peak 1 did not enter the gel and peaks 3 and 4 ran with the dye front. Molecular weight estimates of the four insulin-binding species in peak 2 were 600, 500, 420, and 350 K. On dithiothreitol reduction each insulin-binding species yielded subunits of Mr approximately equal to 135 and 18 K. The three largest binding species demonstrated an additional 45-K dalton protein on dithiothreitol reduction, and the 500-K and 420-K binding species also yielded a 49-K dalton protein. These results suggest that the large insulin-binding protein in rat epididymal adipocytes contains several insulin-binding species, and that these insulin-binding species differ in the number of and the type of subunits they contain. In addition, it may be postulated that the nonlinear Scatchard binding associated with the larger binding protein is a consequence of the heterogeneity of the insulin-binding species in this Sepharose peak.

Adipose Tissue↗

Species-specific detection of three human-pathogenic microsporidial species from the genus Encephalitozoon via fluorogenic 5' nuclease PCR assays.

This study describes fluorogenic 5' nuclease PCR assays suitable for rapid, sensitive, high-throughput detection of the human-pathogenic microsporidial species Encephalitozoon hellem, E. cuniculi and E.intestinalis. The assays utilize species-specific primer sets and a genus-specific dual fluorescent-labeled probe that anneals to a region within the Encephalitozoon 16S rRNA gene. The assay design theoretically permits the probe to be used either with one set of primers for species-level determination or with a combination of all three primer sets for a genus-level screening of samples. The linear range of all three species-specific calibration curves that were developed using serial ten-fold dilutions of genomic DNA isolated from hemacytometer counted spores was determined to be between 10(4) and 10(-1) spores per PCR sample. The coefficients of variation were < or =5.2% over the entire 5-log span of each calibration curve. When DNA isolated from flow cytometric enumerated spores from each of the three Encephalitozoon species was used to evaluate the quantitative capability of the species' respective calibration curves, the results from 34 out of 36 (94%) samples were within 2 standard deviations. The species-specificity of each assay was confirmed using DNA isolated from 10(4) spores from each of the other two Encephalitozoon species as well as DNA extracted from numerous other protozoa, algae and bacteria.

Animals↗

Patterns in the co-occurrence of fish species in streams: the role of site suitability, morphology and phylogeny versus species interactions.

A number of studies at large scales have pointed out that abiotic factors and recolonization dynamics appear to be more important than biotic interactions in structuring stream-fish assemblages. In contrast, experimental and field studies at small scales show the importance of competition among stream fishes. However, given the highly variable nature of stream systems over time, competition may not be intense enough to generate large-scale complementary distributions via competitive exclusion. Complementary distribution is a recurrent pattern observed in fish communities across stream gradients, though it is not clear which instances of this pattern are due to competitive interactions and which to individual species' requirements. In this study, I introduce a series of null models developed to provide a more robust evaluation of species associations by facilitating the distinction between different processes that may shape species distributions and community assembly. These null models were applied to test whether conspicuous patterns in species co-occurrences are more consistent with their differences in habitat use, morphological features and/or phylogenetic constraints, or with species interactions in fish communities in the streams of a watershed in eastern Brazil. I concluded that patterns in species co-occurrences within the studied system are driven by common species-habitat relationships and species interactions may not play a significant role in structuring these communities. I suggest that large-scale studies, where adequate designs and robust analytical tools are applied, can contribute substantially to understanding the importance of different types of processes in structuring stream-fish communities.

Animals↗

Selection of species-specific DNA probes which detect strain restriction polymorphism in four Bifidobacterium species.

Randomly cloned fragments (in a size range 1 to 2.5 kb) of DNA from Bifidobacterium longum ATCC 15707, B. adolescentis CIP 64.59T, B. bifidum CIP 64.65 and B. animalis ATCC 25527 were used as hybridization probes to characterize strains of these species and distinguish them from closely related Bifidobacterium species. The fragments were screened for hybridization with native DNA from 41 different Bifidobacterium strains. For each species, a fragment hybridizing specifically with DNA from strains of the same species was isolated. Each fragment was then hybridized with restriction digests in order to study the genome polymorphism. In some of the tested B. longum strains including strain ATCC 15707, the species-specific fragment L6/45 hybridized with 2 fragments instead of one as expected. Sequence of the fragment revealed the presence of an ORF which had an amino acid sequence similar to the site-specific recombinases of lambda integrase family. Moreover, Southern analysis demonstrated that at least 3 copies of this fragment are present in the chromosome of B. longum ATCC 15707 and in some other B. longum strains. The species-specific fragment A6/17 of B. adolescentis hybridized with the same restriction fragment on the eight strains of this species tested. The B. bifidum-specific fragment hybridized with different DNA restriction fragments according to the strain. The restriction fragment an1 from B. animalis ATCC 25527 hybridized with the same restriction fragment from strain B. animalis ATCC 27536. However, these two strains could be differentiated by another restriction pattern. Thus, hybridization results highlight the genetic polymorphism which exists among Bifidobacterium strains of the same species.

Base Sequence↗

Evidence for subdivision of the root-endophyte Phialocephala fortinii into cryptic species and recombination within species.

The genetic structure of the root-endophyte Phialocephala fortinii was analyzed in three study sites using 11 single-copy RFLP probes. A total of 541 strains isolated from surface-sterilized, fine roots (diameter 0.5-3 mm) of Norway spruce (Picea abies) were examined. The average gene diversity (H) was high in all three study sites. Cluster analysis showed that up to four well-separated clusters of multi-locus haplotypes were present within the sites. Significant population subdivision was detected among these clusters, suggesting that groups of multi-locus haplotypes were reproductively isolated and that P. fortinii is a species complex composed of several cryptic species. This hypothesis was supported by ISSR-PCR which showed clusters consistent with those of the multi-locus haplotypes identified by RFLP analysis. In contrast, ITS sequence analysis did not allow to separate the species as clearly. The index of association (IA) did not deviate significantly from zero within any cryptic species, suggesting that recombination occurs within these species. Cryptic species occurred sympatrically. Thalli of two cryptic species were detected in the same 5-mm-long root segment in one instance. No significant differentiation was observed among populations of the same cryptic species in forest stands located approximately 5 km from each other. This finding is consistent with significant gene flow over this spatial scale. In addition, several isolates with both identical multi-locus haplotype and identical ISSR fingerprint were found at each study site indicating genotype flow or a recent common history between study sites.

Ascomycota↗

Metazoan parasite species richness and genetic variation among freshwater fish species: cause or consequence?

The factors responsible for the maintenance of genetic variation among natural populations remain a mystery. Recent models of host-parasite co-evolution assume that parasites exert frequency-dependent selection on their hosts by favouring rare alleles that may confer resistance against infection. We tested this prediction in a comparative analysis that sought relationships between levels of genetic variation and the number of metazoan parasite species exploiting each host species. We used data on 40 species of North American freshwater fishes. After controlling for sampling effort and phylogenetic influences, we found no relationship between genetic polymorphism and parasite species richness among fish species. However, we found a marginal negative correlation between parasite species richness and heterozygosity. This result goes against the prediction that increased selective pressure by parasites should be associated with higher levels of genetic variation. Instead, it suggests that parasites may be colonising host species showing low levels of genetic variation with greater success than genetically more variable host species.

Animals↗

Feeding characteristics of two tintinnid ciliate species on phytoplankton including harmful species: effects of prey size on ingestion rates and selectivity.

The feeding abilities of two tintinnid ciliates, Favella ehrenbergii and Favella taraikaensis, on 10 species of flagellates including harmful marine algae were examined under single prey conditions, and selective feeding of F. taraikaensis on two species of algae of different sizes was investigated under mixed prey conditions. Ingestion rates calculated from the rate of increases of auto-fluorescent particles inside food vacuoles in individuals ranged from 0.5 to 22.1 cells ind(-1) h(-1) for F. ehrenbergii and from 0.8 to 44.9 cells ind(-1) h(-1) for F. taraikaensis on nine species of prey algae. Significant ingestion rates of both Favella species could not be detected on Heterosigma akashiwo, although some individuals of both species were observed ingesting H. akashiwo in the initial incubation period. The relationship between prey cell volume and ingestion rate could be expressed mathematically for both Favella species, indicating that it is possible to estimate the potential feeding activity of each Favella species on specific algae using an equation, and may be applicable to evaluate the food value of prey alga for both Favella species. When F. taraikensis was fed mixtures of H. circularisquama and Pavlova lutheri, significant ingestion rates of H. circularisquama by F. taraikaensis could not be measured when H. circularisquama accounted for less than 20% of the other prey biomass. However, clear selectivity for H. circularisquama was observed when H. circularisquama reached and exceeded 34% of the other prey biomass. Under mixed prey conditions, it is likely that the selectivity of F. taraikaensis is stronger for larger prey compared to prey algae with a size near the lower limit on which F. taraikaensis can feed.

Journal Article↗

The crossroads of molecular, typological and biological species concepts: two new species of Gyrodactylus Nordmann, 1832 (Monogenea: Gyrodactylidae).

Nucleotide sequences of nuclear ribosomal DNA internal transcribed spacers (ITS) were used to confirm morphological identification of Gyrodactylus species in Fennoscandia. Three pairs of morphologically similar or cryptic species are compared in this study. G. branchicus Malmberg, 1964 and G. rarus Wegener, 1910, hosted by the sticklebacks Gasterosteus aculeatus L. and Pungitius pungitius (L.), respectively, displayed a genetic divergence of 0.9-1.3% along 774 nucleotides of ITS (Jukes & Cantor distance). G. branchicus isolates from the Baltic, White Sea and Scottish North Sea were invariable, but a Belgian North Sea population with a 0.4% divergence in ITS sequence has been collected. The species status of G. branchicus and G. rarus is supported by host-specificity in sympatric habitats and consistent morphological difference in the marginal hook sickles. Among Gyrodactylus on burbot Lota lota (L.) specimens were collected with their 792 bp long ITS sequences differing by 8.5%. This has led to the splitting of G. lotae Gusev, 1953 into two species, G. lotae and G. alexgusevi n. sp. The species are morphologically separable, and a similar range of variation was found in both the anchors and the marginal hooks in other collections and in the original description. Among G. macronychus-like parasites of minnow Phoxinus phoxinus (L.), divergent ITS sequences indicate two cryptic species. By comparison with the type-specimens, one was identified as G. macronychus Malmberg, 1957; the other is here designated as G. jussii n. sp., differing by 21.8% in 950-973 bp long ITS. The consequences of these findings for the species concept and species identification of Gyrodactylus are discussed.

Animals↗

Equilibria amongst different molybdenum (V)-containing species from sulphite oxidase. Evidence for a halide ligand of molybdenum in the low-pH species.

The interaction of chloride, fluoride and phosphate ions with the molybdenum centre of sulphite oxidase in the pH range 6.2 to 9.6 has been studied by e.p.r. of Mo(V) in the enzyme reduced by sulphite. Detailed studies were made from e.p.r. spectra recorded at about 120K and more limited studies from spectra of liquid samples at about 295K and also from enzyme activity measurements. Interconversion between low-pH and high-pH Mo(V) e.p.r. signal-giving species [described by Lamy, Gutteridge & Bray (1980) Biochem. J. 185, 397-403] is influenced by chloride concentration, a 10-fold increase in concentration (in the range of about 1 mM to 100 mM) causing an increase of about 1 pH unit in the apparent pK for the conversion. This suggests that chloride is a constituent of the low-pH species. In support of this, high concentrations of fluoride modified the e.p.r. spectrum. Partial conversion to a Mo(V) species, in which F- has presumably replaced Cl- and showing hyperfine coupling of A(19F)av. 0.5mT, is indicated. It is proposed that interconversion between high-pH and low-pH species is of the form: (formula; see text) No evidence that Cl- is essential for enzymic activity was found. Data relating to equilibria amongst low-pH, high-pH and also the phosphate species are presented. Depending on pH and on concentrations of Cl- and H2PO4-, one, two, or all three species may be present. Qualitatively, under appropriate conditions, the phosphate species tends to replace some or all of the low-pH species. Quantitative analysis by a computer procedure permitted an appropriate scheme to be deduced and equilibrium constants to be evaluated. Studies on the e.p.r. signals at 295K indicated that similar equilibria applied in liquid solution, but with some changes in the values of the constants. The structure of the molybdenum centre in its various states and the nature of the enzymic reaction are discussed.

Chlorides↗

Species pattern of phosphatidylinositol from lung surfactant and a comparison of the species pattern of phosphatidylinositol and phosphatidylglycerol synthesized de novo in lung microsomal fractions.

1. Phosphatidylinositol (PI) is a minor component of lung surfactant which may be able to replace the functionally important phosphatidylglycerol (PG) [Beppu, Clements & Goerke (1983) J. Appl. Physiol. 55, 496-502] without disturbing lung function. The dipalmitoyl species is one of the main species for both PI (14.4%) and PG (16.9%). Besides the C16:0--C16:0 species, the C16:0--C18:0, C16:0--C18:1, C16:0--C18:2 and C18:0--C18:1 species showed comparable proportions in the PG and PI fractions. These similarities of the species patterns and the acidic character of both phospholipids could explain why surfactant PG may be replaced by PI. 2. PI and PG were radiolabelled by incubation of microsomal fractions with [14C]glycerol 3-phosphate (Gro3P). For 11 out of 14 molecular species of PI and PG we measured comparable proportions of radioactivity. The radioactivity of these 11 species accounted together for more than 80% of the total. The addition of inositol to the incubation system decreased the incorporation in vitro of Gro3P into PG and CDP-DG (diacylglycerol) of lung microsomes (microsomal fractions), but did not change the distribution of radioactivity among the molecular species of PG. These results supported the idea that both acidic surfactant phospholipids may be synthesized de novo from a common CDP-DG pool in lung microsomes.

Acylation↗

Molecular species composition of the major phospholipids in brain and retina from rainbow trout (Salmo gairdneri). Occurrence of high levels of di-(n-3)polyunsaturated fatty acid species.

The molecular-species compositions of the diacyl classes of the major phospholipids from the brain and retina of rainbow trout (Salmo gairdneri) were determined. A total of 46 possible species was identified. Didocosahexaenoyl species were major components of phosphatidylcholine (PC), phosphatidylethanolamine (PE) and phosphatidylserine (PS) from retina, comprising 14.1, 41.3 and 28.3% of the respective totals. This species was also abundant in PE and PS from brain, accounting for 14.9 and 19.9% of the totals respectively. Small amounts of di-polyunsaturated fatty acid species [C22:6(n-3) with C20:5(n-3), and C22:6(n-3) with C22:5(n-3)] were also found in these phospholipids. Phosphatidylinositol (PI) from both tissues contained no di-polyunsaturated fatty acid species. Retinal PI contained 40.1% C18:0-C20:4(n-6) with 14.9% of C18:0-C20:5(n-3); brain PI contained 42.3% of C18:0-C20:5 and 10.4% of C18:0-C20:4 species. Brain PC contained a substantial amount of nervonic acid-containing species with the pair C18:1-C24:1/C24:1-C18:1 comprising 8.9% of the total.

Animals↗

Immigration and extinction probabilities for individual species: relation to incidence functions and species colonization curves.

We develop a dynamic model of island biogeography based on immigration and extinction probabilities of individual species rather than on the usual biogeographic parameters of the number of species immigrating or going extinct per unit time. In the real world, these probabilities vary enormously among species, and three field studies suggest lognormal distributions. Based on such distributions of individual probabilities, our model proceeds by calculating the conditional probability of species occurrence--the likelihood that a given species will occur on a given island--as a function of total species number on the island. The model succeeds in predicting two observed features of species communities; (i) staggered, sigmoidally-shaped incidence functions ("differing area requirements of different species") and (ii) concave immigration and extinction curves.

Animals↗