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RNA Gene Sequences (rna + gene_sequence)

Distribution by Scientific Domains
Life Sciences83%

Kinds of RNA Gene Sequences

  • ribosomal rna gene sequence
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    Selected Abstracts

    Integrated polymerase chain reaction-based procedures for the detection and identification of species and subspecies of the Gram-positive bacterial genus Lactococcus

    JOURNAL OF APPLIED MICROBIOLOGY, Issue 2 2002
    Z.Y. Pu
    Aims:,Five species of the Gram-positive bacterial genus Lactococcus (Lactococcus lactis, L. garvieae, L. plantarum, L. piscium and L. raffinolactis) are currently recognized. The aim of this work was to develop a simple approach for the identification of these species, as well as to differentiate the industrially important dairy subspecies L. lactis subsp. lactis and L. lactis subsp. cremoris. Methods and Results:,Methods were devised based on specific polymerase chain reaction (PCR) amplifications that exploit differences in the sequences of the 16S ribosomal RNA genes of each species, followed by restriction enzyme cleavage of the PCR products. The techniques developed were used to characterize industrial cheese starter strains of L. lactis and the results were compared with biochemical phenotype and DNA sequence data. Conclusions:,The PCR primers designed can be used simultaneously, providing a simple scheme for screening unknown isolates. Strains of L. lactis show heterogeneity in the 16S ribosomal RNA gene sequence. Significance and Impact of the Study:,This work provides an integrated set of methods for differentiation and identification of lactococcal species associated with agricultural, veterinary, medical and processed food industries. [source]

    Molecular link of different stages of the trematode host of Neorickettsia risticii to Acanthatrium oregonense

    ENVIRONMENTAL MICROBIOLOGY, Issue 8 2008
    Kathryn E. Gibson
    Summary Neorickettsia risticii, the obligatory intracellular bacterium that causes Potomac horse fever, has been detected in various developmental stages of digenetic trematodes in the environment. Neorickettsia risticii -infected gravid trematodes were identified as Acanthatrium oregonense, based on morphologic keys. However, whether immature trematodes harbouring N. risticii are also A. oregonense was unknown. The objective of this study was to infer the life cycle of N. risticii -positive trematode hosts and transstadial transmission of the bacterium by molecularly characterizing the relationship among adult and immature stages of trematodes confirmed infected with N. risticii. Sequences of 18S ribosomal RNA genes up to 1922 bp in size were obtained from infected adult gravid trematodes, sporocysts and cercariae, and metacercariae. The sequences from the different immature stages of trematode are closely related to those of adult trematodes, some with 100% sequence identity; thus, they likely are life stages of A. oregonense. Comparisons with known 18S ribosomal RNA gene sequences of other digenetic trematodes indicated that all tested stages of the N. risticii -positive trematodes belong to the family Lecithodendriidae, supporting the morphological identification. [source]

    Multiple displacement amplification as a pre-polymerase chain reaction (pre-PCR) to process difficult to amplify samples and low copy number sequences from natural environments

    ENVIRONMENTAL MICROBIOLOGY, Issue 7 2005
    Juan M. Gonzalez
    Summary Microbial assessment of natural biodiversity is usually achieved through polymerase chain reaction (PCR) amplification. Deoxyribonucleic acid (DNA) sequences from natural samples are often difficult to amplify because of the presence of PCR inhibitors or to the low number of copies of specific sequences. In this study, we propose a non-specific preamplification procedure to overcome the presence of inhibitors and to increase the number of copies prior to carrying out standard amplification by PCR. The pre-PCR step is carried out through a multiple displacement amplification (MDA) technique using random hexamers as priming oligonucleotides and ,29 DNA polymerase in an isothermal, whole-genome amplification reaction. Polymerase chain reaction amplification using specific priming oligonucleotides allows the selection of the sequences of interest after a preamplification reaction from complex environmental samples. The procedure (MDA-PCR) has been tested on a natural microbial community from a hypogean environment and laboratory assemblages of known bacterial species, in both cases targeting the small subunit ribosomal RNA gene sequences. Results from the natural community showed successful amplifications using the two steps protocol proposed in this study while standard, direct PCR amplification resulted in no amplification product. Amplifications from a laboratory assemblage by the two-step proposed protocol were successful at bacterial concentrations ,,10-fold lower than standard PCR. Amplifications carried out in the presence of different concentrations of fulvic acids (a soil humic fraction) by the MDA-PCR protocol generated PCR products at concentrations of fulvic acids over 10-fold higher than standard PCR amplifications. The proposed procedure (MDA-PCR) opens the possibility of detecting sequences represented at very low copy numbers, to work with minute samples, as well as to reduce the negative effects on PCR amplifications of some inhibitory substances commonly found in environmental samples. [source]

    Chytrid infections of Daphnia pulicaria: development, ecology, pathology and phylogeny of Polycaryum laeve

    FRESHWATER BIOLOGY, Issue 4 2006
    PIETER T. J. JOHNSON
    Summary 1. We combined ecological surveys, life table studies, microscopy and molecular sequencing to determine the development, ecology, pathology and phylogeny of Polycaryum laeve, an endoparasite of cladocerans. We report the first records of P. laeve from North America, where we have used a polymerase chain reaction primer and microscopic examination to confirm infections in 14 lakes. Infections are highly pathogenic and caused increased mortality, reduced growth, and reproductive castration in Daphnia pulicaria during life table studies. 2. Biweekly data from Allequash Lake (Wisconsin, U.S.A.) throughout 2003 indicated that fecundity and infection prevalence were inversely correlated. Infection prevalence was highest in late winter and early spring (up to 80%) and lowest during late summer. Epidemics were generally followed by sharp declines in host population density (up to 99%). 3. Within the haemocoel of its host, P. laeve forms thick-walled sporangia, which occur systemically in later stages of infection. Fungal thalli associate closely with muscle fibres and connective tissue, leading to degeneration as the infection becomes advanced. Following death of the host, flagellated zoospores are released through an exit papilla on the sporangium. Based on the infection-induced castration of the host and increases in infection prevalence with Daphnia size, we postulate that transmission is horizontal, but may be indirect through an additional host or free-living stage. 4. Molecular and morphological data clearly indicate that P. laeve belongs in the fungal phylum Chytriodiomycota, order Blastocladiales. Based on ribosomal RNA gene sequences and morphological features, we transfer the genus Polycaryum from the Haplosporidia to the Chytridiomycota, and designate a lectotype and epitype for P. laeve. Considering the high prevalence of P. laeve infection within Daphnia populations, the frequency with which we detected infections among lakes, and the keystone importance of large-bodied Daphnia in aquatic food webs, we suggest that P. laeve may exert a regulatory influence on Daphnia populations in lake ecosystems. [source]

    Molecular diversity of arbuscular mycorrhizal fungi and patterns of host association over time and space in a tropical forest

    MOLECULAR ECOLOGY, Issue 12 2002
    R. Husband
    Abstract We have used molecular techniques to investigate the diversity and distribution of the arbuscular mycorrhizal (AM) fungi colonizing tree seedling roots in the tropical forest on Barro Colorado Island (BCI), Republic of Panama. In the first year, we sampled newly emergent seedlings of the understory treelet Faramea occidentalis and the canopy emergent Tetragastris panamensis, from mixed seedling carpets at each of two sites. The following year we sampled surviving seedlings from these cohorts. The roots of 48 plants were analysed using AM fungal-specific primers to amplify and clone partial small subunit (SSU) ribosomal RNA gene sequences. Over 1300 clones were screened for random fragment length polymorphism (RFLP) variation and 7% of these were sequenced. Compared with AM fungal communities sampled from temperate habitats using the same method, the overall diversity was high, with a total of 30 AM fungal types identified. Seventeen of these types have not been recorded previously, with the remainder being similar to types reported from temperate habitats. The tropical mycorrhizal population showed significant spatial heterogeneity and nonrandom associations with the different hosts. Moreover there was a strong shift in the mycorrhizal communities over time. AM fungal types that were dominant in the newly germinated seedlings were almost entirely replaced by previously rare types in the surviving seedlings the following year. The high diversity and huge variation detected across time points, sites and hosts, implies that the AM fungal types are ecologically distinct and thus may have the potential to influence recruitment and host composition in tropical forests. [source]

    Molecular detection of dermatophytes and nondermatophytes in onychomycosis by nested polymerase chain reaction based on 28S ribosomal RNA gene sequences

    BRITISH JOURNAL OF DERMATOLOGY, Issue 5 2009
    M. Ebihara
    Summary Background, Onychomycosis is often caused by dermatophytes, but the role of nondermatophytes is underestimated due to the difficulty of identifying them by conventional direct microscopy and culture. Objectives, This study aims to detect nondermatophytes, as well as dermatophytes, in the nail samples of patients with onychomycosis using a polymerase chain reaction (PCR)-based culture-independent method. Materials and methods, The nested PCR assay targeting the sequence of the 28S ribosomal RNA gene was used to amplify fungal DNAs from 50 microscopy-positive nail specimens. Newly designed primer sets for dermatophyte universal, Trichophyton rubrum, T. mentagrophytes, Aspergillus spp., Scopulariopsis brevicaulis, Fusarium solani, F. oxysporum, F. verticillioides, Candida albicans and C. tropicalis were used after confirmation of their specificity. Results, Forty-seven cases (94%) were positive for fungal DNA, among which dermatophytes were detected in 39 cases (83·0%): T. rubrum in 35 cases (74·5%) and T. mentagrophytes in eight cases (17·0%). Surprisingly, nondermatophytes were detected in 18 cases (38·3%), both dermatophytes and nondermatophytes in 10 cases (21·3%) and nondermatophytes alone in eight cases (17·0%). Aspergillus spp. alone was observed in five cases (10·6%). Conclusions, This study indicates that most of the affected nail plates of patients with onychomycosis were positive for specific fungal DNAs, and suggests that nondermatophytes detected at high rates may be involved in the pathogenesis of onychomycosis. [source]