BACKGROUND Profiling of microbial communities via metagenomic shotgun sequencing has enabled researches to gain unprecedented insight into microbial community structure and the functional roles of community members. This study describes a method and basic analysis for a metagenomic adaptation of the double digest restriction site associated DNA sequencing (ddRADseq) protocol for reduced represe...

In this work we describe a novel, rapid and simple microscale procedure for identification of restriction endonuclease activity in bacteria lysates, which contain high levels of non-specific DNA nucleases.

A DNA fragment carrying the thrP region of Escherichia coli has been identified and characterized. Starting from a secondary site lysogen of bacteriophage h, where the position of the prophage is either within thrP or between thrP and thr structural genes (Gardner et al., 1974; Gardner & Smith, 1975) it has been possible to isolate transducing phages which carry bacterial DNA from either side o...

For promoter studies the cloning, subcloning and transfer to different plasmid vectors usually requires use of restriction enzymes and ligation reactions. One obstacle is the nucleotide polymorphisms of eukaryotic genomic DNA, which has the consequence that a sequence often differs from published sequences. Therefore sequencing, rigorous restriction enzyme analysis or introduction of suitable s...

The marine photosynthetic dinoflagellates Dinophysis Ehrenb. species are obligate mixotrophs that require both light and the ciliate prey Myrionecta rubra (= Mesodinium rubrum) for long-term survival. Despite rapid progress on the study of Dinophysis using laboratory cultures, however, whether it has its own permanent plastids or kleptoplastids (i.e., stolen plastids from its ciliate prey) is n...

Restriction-modification systems are widespread genetic elements that protect bacteria from bacteriophage infections by recognizing and cleaving heterologous DNA at short, well-defined sequences called restriction sites. Bioinformatic evidence shows that restriction sites are significantly underrepresented in bacteriophage genomes, presumably because bacteriophages with fewer restriction sites ...

Type II restriction-modification (R-M) systems encode a restriction endonuclease that cleaves DNA at specific sites, and a methyltransferase that modifies same sites protecting them from restriction endonuclease cleavage. Type II R-M systems benefit bacteria by protecting them from bacteriophages. Many type II R-M systems are plasmid-based and thus capable of horizontal transfer. Upon the entry...

The Candida parapsilosis complex is composed of Candida parapsilosis sensu stricto, Candida orthopsilosis, Candida metapsilosis, and the closely related species Lodderomyces elongisporus. An exon-primed intron-crossing PCR assay was developed here to distinguish the members of the species complex on the basis of the distinct sizes of amplicons, and Candida orthopsilosis and Candida metapsilosis...

Restriction enzyme analysis of PCR-amplified 16S rRNA genes was used to distinguish among clinical isolates of Actinobacillus actinomycetemcomitans, Haemophilus aphrophilus, and Haemophilus paraphrophilus which were originally identified by conventional phenotypic methods. This PCR-based method is a reliable and rapid alternative to conventional methods for identification of these bacterial spe...

Bacteriophage T4 cytosine-containing DNA is cleaved at a single site by the restriction endonuclease, Bam H1. The site lies within the late region of the T4 genome, close to, or within, gene 8, one of the structural genes of the phage particle baseplate.