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  • 1
    Publication Date: 2006-12-23
    Description: Novel, low-abundance microbial species can be easily overlooked in standard polymerase chain reaction (PCR)-based surveys. We used community genomic data obtained without PCR or cultivation to reconstruct DNA fragments bearing unusual 16S ribosomal RNA (rRNA) and protein-coding genes from organisms belonging to novel archaeal lineages. The organisms are minor components of all biofilms growing in pH 0.5 to 1.5 solutions within the Richmond Mine, California. Probes specific for 16S rRNA showed that the fraction less than 0.45 micrometers in diameter is dominated by these organisms. Transmission electron microscope images revealed that the cells are pleomorphic with unusual folded membrane protrusions and have apparent volumes of 〈0.006 cubic micrometer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baker, Brett J -- Tyson, Gene W -- Webb, Richard I -- Flanagan, Judith -- Hugenholtz, Philip -- Allen, Eric E -- Banfield, Jillian F -- New York, N.Y. -- Science. 2006 Dec 22;314(5807):1933-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17185602" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; *Biofilms ; California ; Cell Membrane/ultrastructure ; DNA Transposable Elements ; DNA, Archaeal ; Databases, Genetic ; *Ecosystem ; *Euryarchaeota/genetics/physiology/ultrastructure ; Genes, Archaeal ; Genes, rRNA ; *Genome, Archaeal ; Hydrogen-Ion Concentration ; Microscopy, Electron, Transmission ; Mining ; Molecular Sequence Data ; Oligonucleotide Probes ; Phylogeny ; Pyrophosphatases/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; Temperature
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2015-11-17
    Description: Single Molecule, Real-Time (SMRT ® ) Sequencing (Pacific Biosciences, Menlo Park, CA, USA) provides the longest continuous DNA sequencing reads currently available. However, the relatively high error rate in the raw read data requires novel analysis methods to deconvolute sequences derived from complex samples. Here, we present a workflow of novel computer algorithms able to reconstruct viral variant genomes present in mixtures with an accuracy of 〉QV50. This approach relies exclusively on Continuous Long Reads (CLR), which are the raw reads generated during SMRT Sequencing. We successfully implement this workflow for simultaneous sequencing of mixtures containing up to forty different 〉9 kb HIV-1 full genomes. This was achieved using a single SMRT Cell for each mixture and desktop computing power. This novel approach opens the possibility of solving complex sequencing tasks that currently lack a solution.
    Keywords: Polymorphism/mutation detection
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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