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Reaction Primers (reaction + primer)

Distribution by Scientific Domains
Life Sciences100%

Kinds of Reaction Primers

  • chain reaction primer
    		•
  • polymerase chain reaction primer
    		•

    Selected Abstracts

    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]

    Prokaryotic diversity and metabolically active microbial populations in sediments from an active mud volcano in the Gulf of Mexico

    ENVIRONMENTAL MICROBIOLOGY, Issue 10 2006
    Robert J. Martinez
    Summary In this study, ribosomes and genomic DNA were extracted from three sediment depths (0,2, 6,8 and 10,12 cm) to determine the vertical changes in the microbial community composition and identify metabolically active microbial populations in sediments obtained from an active seafloor mud volcano site in the northern Gulf of Mexico. Domain-specific Bacteria and Archaea 16S polymerase chain reaction primers were used to amplify 16S rDNA gene sequences from extracted DNA. Complementary 16S ribosomal DNA (crDNA) was obtained from rRNA extracted from each sediment depth that had been subjected to reverse transcription polymerase chain reaction amplification. Twelve different 16S clone libraries, representing the three sediment depths, were constructed and a total of 154 rDNA (DNA-derived) and 142 crDNA (RNA-derived) Bacteria clones and 134 rDNA and 146 crDNA Archaea clones obtained. Analyses of the 576 clones revealed distinct differences in the composition and patterns of metabolically active microbial phylotypes relative to sediment depth. For example, ,- Proteobacteria rDNA clones dominated the 0,2 cm clone library whereas ,-Proteobacteria dominated the 0,2 cm crDNA library suggesting , to be among the most active in situ populations detected at 0,2 cm. Some microbial lineages, although detected at a frequency as high as 9% or greater in the total DNA library (i.e. Actinobacteria, ,- Proteobacteria), were markedly absent from the RNA-derived libraries suggesting a lack of in situ activity at any depth in the mud volcano sediments. This study is one of the first to report the composition of the microbial assemblages and physiologically active members of archaeal and bacterial populations extant in a Gulf of Mexico submarine mud volcano. [source]

    Development and application of polymerase chain reaction primers based on fhcD for environmental detection of methanopterin-linked C1 -metabolism in bacteria

    ENVIRONMENTAL MICROBIOLOGY, Issue 8 2005
    Marina G. Kalyuzhnaya
    Summary In this work we describe development and testing of a novel pair of environmental primers targeting fhcD, a conserved gene in the H4MTP-linked C1 -transfer pathway, and demonstrate that these primers enable confident detection of a broad variety of fhcD genes originating from phylogenetically diverse bacteria. The new primer pair was employed to analyse fhcD diversity in Lake Washington sediment, uncovering the presence of 40 fhcD phylotypes. Based on phylogenetic analyses, the phylotypes identified were affiliated with ,-, ,- and ,-proteobacteria, and Planctomycetes, while a number of sequences formed deep branches suggesting the presence of unknown groups of microorganisms. To assess the physiological potential and the possible substrate repertoire of the fhcD- containing species in Lake Washington, we conducted enrichments of natural populations on a variety of C1 substrates, and observed specific shifts in community structure in response to different C1 substrates. A specific shift in community structure was also observed in the presence of humic acids suggesting that C1 transfer metabolism linked to H4MPT may be part of the degradation pathway for this natural polymer, possibly involving formaldehyde production. Overall, our data suggest that C1 oxidation reactions linked to H4MPT are much more widespread in natural environments than previously thought. [source]

    Novel polymerase chain reaction primers for the specific detection of bacterial copper P-type ATPases gene sequences in environmental isolates and metagenomic DNA

    LETTERS IN APPLIED MICROBIOLOGY, Issue 6 2010
    R. De la Iglesia
    Abstract Aims:, In the last decades, the worldwide increase in copper wastes release by industrial activities like mining has driven environmental metal contents to toxic levels. For this reason, the study of the biological copper-resistance mechanisms in natural environments is important. Therefore, an appropriate molecular tool for the detection and tracking of copper-resistance genes was developed. Methods and Results:, In this work, we designed a PCR primer pair to specifically detect copper P-type ATPases gene sequences. These PCR primers were tested in bacterial isolates and metagenomic DNA from intertidal marine environments impacted by copper pollution. As well, T-RFLP fingerprinting of these gene sequences was used to compare the genetic composition of such genes in microbial communities, in normal and copper-polluted coastal environments. New copper P-type ATPases gene sequences were found, and a high degree of change in the genetic composition because of copper exposure was also determined. Conclusions:, This PCR based method is useful to track bacterial copper-resistance gene sequences in the environment. Significance and Impact of the Study:, This study is the first to report the design and use of a PCR primer pair as a molecular marker to track bacterial copper-resistance determinants, providing an excellent tool for long-term analysis of environmental communities exposed to metal pollution. [source]

    Genetic drift outweighs balancing selection in shaping post-bottleneck major histocompatibility complex variation in New Zealand robins (Petroicidae)

    MOLECULAR ECOLOGY, Issue 12 2004
    HILARY C. MILLER
    Abstract The Chatham Island black robin, Petroica traversi, is a highly inbred, endangered passerine with extremely low levels of variation at hypervariable neutral DNA markers. In this study we investigated variation in major histocompatibility complex (MHC) class II genes in both the black robin and its nonendangered relative, the South Island robin Petroica australis australis. Previous studies have shown that Petroica have at least four expressed class II B MHC genes. In this study, the sequences of introns flanking exon 2 of these loci were characterized to design primers for peptide-binding region (PBR) sequence analysis. Intron sequences were comprised of varying numbers of repeated units, with highly conserved regions immediately flanking exon 2. Polymerase chain reaction primers designed to this region amplified three or four sequences per black robin individual, and eight to 14 sequences per South Island robin individual. MHC genes are fitness-related genes thought to be under balancing selection, so they may be more likely to retain variation in bottlenecked populations. To test this, we compared MHC variation in the black robin with artificially bottlenecked populations of South Island robin, and with their respective source populations, using restriction fragment length polymorphism analyses and DNA sequencing of the PBR. Our results indicate that the black robin is monomorphic at class II B MHC loci, while both source and bottlenecked populations of South Island robin have retained moderate levels of variation. Comparison of MHC variation with minisatellite DNA variation indicates that genetic drift outweighs balancing selection in determining MHC diversity in the bottlenecked populations. However, balancing selection appears to influence MHC diversity over evolutionary timescales, and the effects of gene conversion are evident. [source]

    Polymerase chain reaction primers for polymorphic microsatellite loci in the invasive toad species Bufo marinus

    MOLECULAR ECOLOGY, Issue 11 2000
    D. Tikel
    [source]

    Molecular methods for arthropod bloodmeal identification and applications to ecological and vector-borne disease studies

    MOLECULAR ECOLOGY RESOURCES, Issue 1 2009
    REBEKAH J. KENT
    Abstract DNA-based methods have greatly enhanced the sensitivity and specificity of hematophagous arthropod bloodmeal identification. A variety of methods have been applied to study the blood-feeding behaviour of mosquitoes, ticks, black flies and other blood-feeding arthropods as it relates to host,parasite interactions and pathogen transmission. Overviews of the molecular techniques used for bloodmeal identification, their advantages, disadvantages and applications are presented for DNA sequencing, group-specific polymerase chain reaction primers, restriction fragment length polymorphism, real-time polymerase chain reaction, heteroduplex analysis, reverse line-blot hybridization and DNA profiling. Technical challenges to bloodmeal identification including digestion and analysis of mixed bloodmeals are discussed. Analysis of bloodmeal identification results remains a challenge to the field, particularly with regard to incorporation of vertebrate census and ecology data. Future research directions for molecular analysis of arthropod bloodmeals are proposed. [source]

    Characterization of polymorphic microsatellite markers in the Dalmatian wall lizard Podarcis melisellensis (Squamata: Lacertidae)

    MOLECULAR ECOLOGY RESOURCES, Issue 1 2009
    K. HUYGHE
    Abstract We describe polymerase chain reaction primers and amplification conditions for 13 highly polymorphic microsatellite DNA loci isolated from the Dalmatian wall lizard, Podarcis melisellensis. The number of alleles per locus ranged from 12 to 41, with levels of observed heterozygosity between 0.62 and 0.94. Most of these loci were successfully cross-amplified in the closely related species P. sicula, but levels of polymorphism were always lower. [source]

    Non-invasive genetic identification of small mammal species using real-time polymerase chain reaction

    MOLECULAR ECOLOGY RESOURCES, Issue 6 2008
    S. MORAN
    Abstract DNA identification of non-invasive samples is a potentially useful tool for monitoring small mammal species. Here we describe a novel method for identifying five small mammal species: wood mouse, bank vole, common shrew, pygmy shrew and water shrew. Species-specific real-time polymerase chain reaction primers were designed to amplify fragments of the mitochondrial cytochrome b gene from hair and scat samples. We also amplified nuclear DNA from scats, demonstrating their potential as a source of DNA for population genetic studies. [source]

    Isolation and characterization of microsatellite loci in the deep-sea marine fish, the roundnose grenadier (Coryphaenoides rupestris)

    MOLECULAR ECOLOGY RESOURCES, Issue 5 2008
    HALVOR KNUTSEN
    Abstract We developed polymerase chain reaction primers for eight dinucleotide microsatellite loci in the marine deep sea fish, roundnose grenadier (Coryphaenoides rupestris). All markers were obtained from a partial genomic DNA library, and characterized in 90 unrelated individuals from one putative population sampled on the Mid-Atlantic Ridge. The number of alleles ranged from two to 61 with an average of 21 per locus. The observed heterozygosity levels ranged from 0.301 to 0.987 with an average of 0.672. Several of the markers amplified multiple alleles from either the Atlantic cod (Gadus morhua) or the deep-sea fish roughhead grenadier (Macrourus berglax). [source]

    Primers and polymerase chain reaction conditions for DNA barcoding teleost fish based on the mitochondrial cytochrome b and nuclear rhodopsin genes

    MOLECULAR ECOLOGY RESOURCES, Issue 5 2007
    RAFAEL G. SEVILLA
    Abstract This report describes a set of 21 polymerase chain reaction primers and amplification conditions developed to barcode practically any teleost fish species according to their mitochondrial cytochrome b and nuclear rhodopsin gene sequences. The method was successfully tested in more than 200 marine fish species comprising the main Actinopterygii family groups. When used in phylogenetic analyses, its combination of two genes with different evolutionary rates serves to identify fish at the species level. We provide a flow diagram indicating our validated polymerase chain reaction amplification conditions for barcoding and species identification applications as well as population structure or haplotyping analyses, adaptable to high-throughput analyses. [source]