Greengenes2 unifies microbial data in a single reference tree.

Studies using 16S rRNA and shotgun metagenomics typically yield different results, usually attributed to PCR amplification biases. We introduce Greengenes2, a reference tree that unifies genomic and 16S rRNA databases in a consistent, integrated resource. By inserting sequences into a whole-genome phylogeny, we show that 16S rRNA and shotgun metagenomic data generated from the same samples agree in principal coordinates space, taxonomy and phenotype effect size when analyzed with the same tree.

Perspective on Improving Environmental Monitoring of Biothreats.

For more than a decade, the United States has performed environmental monitoring by collecting and analyzing air samples for a handful of biological threat agents (BTAs) in order to detect a possible biological attack. This effort has faced numerous technical challenges including timeliness, sampling efficiency, sensitivity, specificity, and robustness. The cost of city-wide environmental monitoring using conventional technology has also been a challenge. A large group of scientists with expertise in bioterrorism defense met to assess the objectives and current efficacy of environmental monitoring and to identify operational and technological changes that could enhance its efficacy and cost-effectiveness, thus enhancing its value. The highest priority operational change that was identified was to abandon the current concept of city-wide environmental monitoring because the operational costs were too high and its value was compromised by low detection sensitivity and other environmental factors. Instead, it was suggested that the focus should primarily be on indoor monitoring and secondarily on special-event monitoring because objectives are tractable and these operational settings are aligned with likelihood and risk assessments. The highest priority technological change identified was the development of a reagent-less, real-time sensor that can identify a potential airborne release and trigger secondary tests of greater sensitivity and specificity for occasional samples of interest. This technological change could be transformative with the potential to greatly reduce operational costs and thereby create the opportunity to expand the scope and effectiveness of environmental monitoring.

An amphiphilic approach to nanocrystal quantum dot-titania nanocomposites.

The addition of octylamine-modified poly(acrylic acid) to nanocrystal quantum dots (NQDs) results in robust, alcohol-soluble nanoparticles that can be readily incorporated into titania matrices without large changes in photoluminescence quantum yields. This approach relies on the amphiphilic nature of the polymer to create an NQD-polymer complex in which the alkyl chains interact with the hydrophobic part of the NQD, leaving the polar carboxylic acid groups on the periphery. This procedure is applicable to hydrophobically capped NQDs of a variety of shapes and compositions, making it a truly generalized route to nanocrystal-titania nanocomposites.

Size-correlated spectroscopy and imaging of rare-earth-doped nanocrystals.

Isolated europium-doped metal-oxide nanoparticles were probed by size-correlated high-numerical-aperture (far-field) imaging techniques. A modified Digital Instruments Bioscope atomic force microscope mounted upon a Nikon TE300 inverted microscope was used to interrogate (dry) particles ranging in size from 2 to 150 nm on the surface of a glass or quartz coverslip. These experiments revealed several interesting features of doped-nanoparticle luminescence such as Poissonian occupation statistics, size-dependent luminescence efficiency enhancement for particle sizes of <10 nm, and correlation of interesting transient behavior at particle sizes of <5 nm.

Three-dimensional single molecule rotational diffusion in glassy state polymer films.

Measuring three-dimensional orientational motions of many individual molecules within glassy state poly(methyl methacrylate) has enabled nanoscopic probing of bulk-obscured polymer dynamics. Complementing bulk studies, the measured distributions of nanoscale barriers to rotational motion afforded by our single molecule orientational methods directly probe the spatial heterogeneity and nanoscopic alpha-relaxation dynamics deep within the glassy state.