The brighter side of soils: quantum dots track organic nitrogen through fungi and plants.

Soil microorganisms mediate many nutrient transformations that are central in terrestrial cycling of carbon and nitrogen. However, uptake of organic nutrients by microorganisms is difficult to study in natural systems. We assessed quantum dots (fluorescent nanoscale semiconductors) as a new tool to observe uptake and translocation of organic nitrogen by fungi and plants. We conjugated quantum dots to the amino groups of glycine, arginine, and chitosan and incubated them with Penicillium fungi (a saprotroph) and annual bluegrass (Poa annua) inoculated with arbuscular mycorrhizal fungi. As experimental controls, we incubated fungi and bluegrass samples with substrate-free quantum dots as well as unbound quantum dot substrate mixtures. Penicillium fungi, annual bluegrass, and arbuscular mycorrhizal fungi all showed uptake and translocation of quantum dot-labeled organic nitrogen, but no uptake of quantum dot controls. Additionally, we observed quantum dot-labeled organic nitrogen within soil hyphae, plant roots, and plant shoots using field imaging techniques. This experiment is one of the first to demonstrate direct uptake of organic nitrogen by arbuscular mycorrhizal fungi

Amino Acid Uptake in Arbuscular Mycorrhizal Plants

We examined the extent to which arbuscular mycorrhizal (AM) fungi root improved the acquisition of simple organic nitrogen (ON) compounds by their host plants. In a greenhouse-based study, we used quantum dots (fluorescent nanoparticles) to assess uptake of each of the 20 proteinaceous amino acids by AM-colonized versus uncolonized plants. We found that AM colonization increased uptake of phenylalanine, lysine, asparagine, arginine, histidine, methionine, tryptophan, and cysteine; and reduced uptake of aspartic acid. Arbuscular mycorrhizal colonization had the greatest effect on uptake of amino acids that are relatively rare in proteins. In addition, AM fungi facilitated uptake of neutral and positively-charged amino acids more than negatively-charged amino acids. Overall, the AM fungi used in this study appeared to improve access by plants to a number of amino acids, but not necessarily those that are common or negatively-charged

The Burkholderia Genome Database: facilitating flexible queries and comparative analyses

Summary: As the genome sequences of multiple strains of a given bacterial species are obtained, more generalized bacterial genome databases may be complemented by databases that are focused on providing more information geared for a distinct bacterial phylogenetic group and its associated research community. The Burkholderia Genome Database represents a model for such a database, providing a powerful, user-friendly search and comparative analysis interface that contains features not found in other genome databases. It contains continually updated, curated and tracked information about Burkholderia cepacia complex genome annotations, plus other Burkholderia species genomes for comparison, providing a high-quality resource for its targeted cystic fibrosis research community

InnateDB: facilitating systems-level analyses of the mammalian innate immune response

Although considerable progress has been made in dissecting the signaling pathways involved in the innate immune response, it is now apparent that this response can no longer be productively thought of in terms of simple linear pathways. InnateDB (www.innatedb.ca) has been developed to facilitate systems-level analyses that will provide better insight into the complex networks of pathways and interactions that govern the innate immune response. InnateDB is a publicly available, manually curated, integrative biology database of the human and mouse molecules, experimentally verified interactions and pathways involved in innate immunity, along with centralized annotation on the broader human and mouse interactomes. To date, more than 3500 innate immunity-relevant interactions have been contextually annotated through the review of 1000 plus publications. Integrated into InnateDB are novel bioinformatics resources, including network visualization software, pathway analysis, orthologous interaction network construction and the ability to overlay user-supplied gene expression data in an intuitively displayed molecular interaction network and pathway context, which will enable biologists without a computational background to explore their data in a more systems-oriented manner

Identification of the Regulatory Logic Controlling Salmonella Pathoadaptation by the SsrA-SsrB Two-Component System

Sequence data from the past decade has laid bare the significance of horizontal gene transfer in creating genetic diversity in the bacterial world. Regulatory evolution, in which non-coding DNA is mutated to create new regulatory nodes, also contributes to this diversity to allow niche adaptation and the evolution of pathogenesis. To survive in the host environment, Salmonella enterica uses a type III secretion system and effector proteins, which are activated by the SsrA-SsrB two-component system in response to the host environment. To better understand the phenomenon of regulatory evolution in S. enterica, we defined the SsrB regulon and asked how this transcription factor interacts with the cis-regulatory region of target genes. Using ChIP-on-chip, cDNA hybridization, and comparative genomics analyses, we describe the SsrB-dependent regulon of ancestral and horizontally acquired genes. Further, we used a genetic screen and computational analyses integrating experimental data from S. enterica and sequence data from an orthologous regulatory system in the insect endosymbiont, Sodalis glossinidius, to identify the conserved yet flexible palindrome sequence that defines DNA recognition by SsrB. Mutational analysis of a representative promoter validated this palindrome as the minimal architecture needed for regulatory input by SsrB. These data provide a high-resolution map of a regulatory network and the underlying logic enabling pathogen adaptation to a host

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data