Vaughn Iverson

Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota

Mystery of an Unextreme Microbe Metagenomics has given us glimpses into the huge diversity of microorganisms that are the engines of Earths elemental cycling. These kinds of surveys can supply a good idea of the dominant organisms in ecosystems, but, because the majority of environmental microbes are difficult to culture and the most abundant organisms swamp metagenomes, it is difficult to discern the functional significance of other contributors. Iverson et al. (p. 587) sampled the Puget Sound and developed methods to reconstruct individual genomes from metagenomes, which allowed closure of a genome from the enigmatic marine group II Euryarchaeota. This Archaean is evidently motile, shows signs of extensive gene-swapping with bacteria, and offers some hints to the origin of proteorhodopsin—a molecule that some marine bacteria use to harvest energy from sunlight. Reconstruction of whole genomes from a complex microbial community has revealed an evolutionary surprise. Ecosystems are shaped by complex communities of mostly unculturable microbes. Metagenomes provide a fragmented view of such communities, but the ecosystem functions of major groups of organisms remain mysterious. To better characterize members of these communities, we developed methods to reconstruct genomes directly from mate-paired short-read metagenomes. We closed a genome representing the as-yet uncultured marine group II Euryarchaeota, assembled de novo from 1.7% of a metagenome sequenced from surface seawater. The genome describes a motile, photo-heterotrophic cell focused on degradation of protein and lipids and clarifies the origin of proteorhodopsin. It also demonstrates that high-coverage mate-paired sequence can overcome assembly difficulties caused by interstrain variation in complex microbial communities, enabling inference of ecosystem functions for uncultured members.

Whole-genome expression profiling of the marine diatom Thalassiosira pseudonana identifies genes involved in silicon bioprocesses

Formation of complex inorganic structures is widespread in nature. Diatoms create intricately patterned cell walls of inorganic silicon that are a biomimetic model for design and generation of three-dimensional silica nanostructures. To date, only relatively simple silica structures can be generated in vitro through manipulation of known diatom phosphoproteins (silaffins) and long-chain polyamines. Here, we report the use of genome-wide transcriptome analyses of the marine diatom Thalassiosira pseudonana to identify additional candidate gene products involved in the biological manipulation of silicon. Whole-genome oligonucleotide tiling arrays and tandem mass spectrometry identified transcripts for >8,000 genes, ≈3,000 of which were not previously described and included noncoding and antisense RNAs. Gene-specific expression profiles detected a set of 75 genes induced only under low concentrations of silicon but not under low concentrations of nitrogen or iron, alkaline pH, or low temperatures. Most of these induced gene products were predicted to contain secretory signals and/or transmembrane domains but displayed no homology to known proteins. Over half of these genes were newly discovered, identified only through the use of tiling arrays. Unexpectedly, a common set of 84 genes were induced by both silicon and iron limitations, suggesting that biological manipulation of silicon may share pathways in common with iron or, alternatively, that iron may serve as a required cofactor for silicon processes. These results provide insights into the transcriptional and translational basis for the biological generation of elaborate silicon nanostructures by these ecologically important microbes.

Real-time H.24-AVC codec on Intel architectures

The impressive coding efficiency of H.264-AVC comes at the expense of significantly increased algorithm complexity compared to existing standards, which has limited the availability of cost-effective, high-performance solutions. We present a design overview and implementation details of the compliant code optimized for the Intel/sup /spl reg// Pentium/sup /spl reg//4 Pentium/sup /spl reg//M and Xscale/spl trade/ microarchitectures, including results for encoder rate-distortion performance and encoder/decoder execution speed on the above processors. These results demonstrate that high-quality, real-time H.264/AVC recording and playback are achievable on todays PC (desktop and notebook) platforms and that real-time playback on handheld (mobile phone/portable media player) platforms can also be achieved, with both implemented as optimized software for these general-purpose processor architectures.

A fast method for combining palettes of color quantized images

The authors consider the use of a vector quantization algorithm-the pairwise nearest neighbor algorithm-as a means of quickly combining the palettes of multiple images into a single shared palette that can be used for simultaneous display. This approach yields an efficient and practical method of managing palettes that adds little distortion to the images being displayed. The implementation and results of this work are described.<<ETX>>

Sexual ancestors generated an obligate asexual and globally dispersed clone within the model diatom species Thalassiosira pseudonana

Sexual reproduction roots the eukaryotic tree of life, although its loss occurs across diverse taxa. Asexual reproduction and clonal lineages persist in these taxa despite theoretical arguments suggesting that individual clones should be evolutionarily short-lived due to limited phenotypic diversity. Here, we present quantitative evidence that an obligate asexual lineage emerged from a sexual population of the marine diatom Thalassiosira pseudonana and rapidly expanded throughout the world’s oceans. Whole genome comparisons identified two lineages with characteristics expected of sexually reproducing strains in Hardy-Weinberg equilibrium. A third lineage displays genomic signatures for the functional loss of sexual reproduction followed by a recent global colonization by a single ancestral genotype. Extant members of this lineage are genetically differentiated and phenotypically plastic, potentially allowing for rapid adaptation when they are challenged by natural selection. Such mechanisms may be expected to generate new clones within marginal populations of additional unicellular species, facilitating the exploration and colonization of novel environments, aided by exponential growth and ease of dispersal.