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September 12, 2013

Sequencing genomes from single cells by polymerase cloning

Genome sequencing currently requires DNA from pools of numerous nearly identical cells (clones), leaving the genome sequences of many difficult-to-culture microorganisms unattainable. We report a sequencing strategy that eliminates culturing of microorganisms by using real-time isothermal amplification to form polymerase clones (plones) from the DNA of single cells. Two Escherichia coli plones, analyzed by Affymetrix… [Read More]

September 12, 2013

Symbiosis insights through metagenomic analysis of a microbial consortium

Symbioses between bacteria and eukaryotes are ubiquitous, yet our understanding of the interactions driving these associations is hampered by our inability to cultivate most host-associated microbes. Here we use a metagenomic approach to describe four co-occurring symbionts from the marine oligochaete Olavius algarvensis, a worm lacking a mouth, gut and nephridia. Shotgun sequencing and metabolic… [Read More]

September 12, 2013

Facile recovery of individual high-molecular-weight, low-copy-number natural plasmids for genomic sequencing

Sequencing of the large (> 50 kb), low-copy-number (< 5 per cell) plasmids that mediate horizontal gene transfer has been hindered by the difficulty and expense of isolating DNA from individual plasmids of this class. We report here that a kit method previously devised for purification of bacterial artificial chromosomes (BACs) can be adapted for... [Read More]

September 12, 2013

Application of sequence-based methods in human microbial ecology

Ecologists studying microbial life in the environment have recognized the enormous complexity of microbial diversity for many years, and the development of a variety of culture-independent methods, many of them coupled with high-throughput DNA sequencing, has allowed this diversity to be explored in ever-greater detail. Despite the widespread application of these new techniques to the… [Read More]

September 12, 2013

Iron nutrition and physiological responses to iron stress in Nitrosomonas europaea

Nitrosomonas europaea, as an ammonia-oxidizing bacterium, has a high Fe requirement and has 90 genes dedicated to Fe acquisition. Under Fe-limiting conditions (0.2 mu M Fe), N. europaea was able to assimilate up to 70% of the available Fe in the medium even though it is unable to produce siderophores. Addition of exogenous siderophores to… [Read More]

September 12, 2013

Physical map-assisted whole-genome shotgun sequence assemblies

We describe a targeted approach to improve the contiguity of whole-genome shotgun sequence (WGS) assemblies at run-time, using information from Bacterial Artificial Chromosome (BAC)-based physical maps. Clone sizes and overlaps derived from clone fingerprints are used for the calculation of length constraints between any two BAC neighbors sharing 40% of their size. These constraints are… [Read More]

September 12, 2013

Computational analysis of the Phanerochaete chrysosporium v2.0 genome database and mass spectrometry identification of peptides in ligninolytic cultures reveal complex mixtures of secreted proteins

The white-rot basidiomycete Phanerochaete chrysosporium employs extracellular enzymes to completely degrade the major polymers of wood: cellulose. hemicellulose, and lignin. Analysis of a total of 10,048 v2.1 gene niodels predicts 769 secreted proteins. a substantial increase over the 268 models identified in the earlier database (v1.0). Within the v2.1 computational secretome,’ 43% showed no significant… [Read More]

September 12, 2013

Lophotrochozoan mitochondrial genomes

Progress in both molecular techniques and phylogenetic methods has challenged many of the interpretations of traditional taxonomy. One example is in the recognition of the animal superphylum Lophotrochozoa (annelids, mollusks, echiurans, platyhelminthes, brachiopods, and other phyla), although the relationships within this group and the inclusion of some phyla remain uncertain. While much of this progress… [Read More]

September 12, 2013

Naked corals: skeleton loss in Scleractinia

Stony corals, which form the framework for modern reefs, are classified as Scleractinia (Cnidaria, Anthozoa, and Hexacorallia) in reference to their external aragonitic skeletons. However, persistent notions, collectively known as the “naked coral” hypothesis, hold that the scleractinian skeleton does not define a natural group. Three main lines of evidence have suggested that some stony… [Read More]

September 12, 2013

Array2BIO: from microarray expression data to functional annotation of co-regulated genes

Background: There are several isolated tools for partial analysis of microarray expression data. To provide an integrative, easy-to-use and automated toolkit for the analysis of Affymetrix microarray expression data we have developed Array2BIO, an application that couples several analytical methods into a single web based utility. Results: Array2BIO converts raw intensities into probe expression values,… [Read More]
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