Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling
Cindy J. Castelle,Kelly C. Wrighton,Brian C. Thomas,Laura A. Hug,Christopher T. Brown,Michael J. Wilkins,Kyle R. Frischkorn,Susannah G. Tringe,Andrea Singh,Lye Meng Markillie,Ronald C. Taylor,Kenneth H. Williams,Jillian F. Banfield +12 more
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TLDR
This study sequenced DNA from complex sediment and planktonic consortia from an aquifer adjacent to the Colorado River and reconstructed the first complete genomes for Archaea using cultivation-independent methods, which dramatically expand genomic sampling of the domain Archaea and clarify taxonomic designations within a major superphylum.About:
This article is published in Current Biology.The article was published on 2015-03-16 and is currently open access. It has received 463 citations till now. The article focuses on the topics: Nanohaloarchaea & Phylum.read more
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Previously uncharacterized rectangular bacteria in the dolphin mouth
Natasha K. Dudek,Natasha K. Dudek,Natasha K. Dudek,Jesús G. Galaz-Montoya,Handuo Shi,Megan L. Mayer,Megan L. Mayer,Cristina Danita,Arianna I. Celis,Gong-Her Wu,Barry Behr,Kerwyn Casey Huang,Wah Chiu,Wah Chiu,David A. Relman +14 more
TL;DR: The rectangular cell-like units (RCUs) as discussed by the authors were found in the mouths of bottlenose dolphins and DNA staining revealed multiple paired bands that suggested cells in the act of dividing along the longitudinal axis.
Journal ArticleDOI
Archaeal lipolytic enzymes: Current developments and further prospects
TL;DR: In this paper , a review on the current knowledge and future avenues of investigation on lipolytic enzymes sourced from the underexploited archaeal domain is presented.
Journal ArticleDOI
The Prodigal Compound: Return of Ribosyl 1,5-Bisphosphate as an Important Player in Metabolism.
TL;DR: All aspects of PRibP metabolism are described, with emphasis on the biochemical, genetic, and physiological aspects of the enzymes that produce or utilizePRibP.
Posted ContentDOI
Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments
Satoshi Hiraoka,Miho Hirai,Yohei Matsui,Akiko Makabe,Hiroaki Minegishi,Miwako Tsuda,Juliarni,Eugenio Rastelli,Roberto Danovaro,Cinzia Corinaldesi,Tomo Kitahashi,Eiji Tasumi,Manabu Nishizawa,Ken Takai,Hidetaka Nomaki,Takuro Nunoura +15 more
TL;DR: Trans-trenches analysis highlights intra- and inter-trench distributions of microbial assemblages and geochemistry in surface seafloor sediments, providing novel insights into ultra-deep-sea microbial ecology, one of the last frontiers on the authors' planet.
References
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Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
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Fast gapped-read alignment with Bowtie 2
TL;DR: Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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TL;DR: MUSCLE is a new computer program for creating multiple alignments of protein sequences that includes fast distance estimation using kmer counting, progressive alignment using a new profile function the authors call the log-expectation score, and refinement using tree-dependent restricted partitioning.
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A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.
Stéphane Guindon,Olivier Gascuel +1 more
TL;DR: This work has used extensive and realistic computer simulations to show that the topological accuracy of this new method is at least as high as that of the existing maximum-likelihood programs and much higher than the performance of distance-based and parsimony approaches.
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RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
TL;DR: UNLABELLED RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML) that has been used to compute ML trees on two of the largest alignments to date.
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