High Microbial Diversity Despite Extremely Low Biomass in a Deep Karst Aquifer.

Despite the importance of karst aquifers as a source of drinking water, little is known about the role of microorganisms in maintaining the quality of this water. One of the limitations in exploring the microbiology of these environments is access, which is usually limited to wells and surface springs. In this study, we compared the microbiology of the Madison karst aquifer sampled via the potentiometric lakes of Wind Cave with surface sampling wells and a spring. Our data indicated that only the Streeter Well (STR), which is drilled into the same hydrogeologic domain as the Wind Cave Lakes (WCL), allowed access to water with the same low biomass (1.56-9.25 × 103 cells mL-1). Filtration of ∼300 L of water from both of these sites through a 0.2 µm filter allowed the collection of sufficient cells for DNA extraction, PCR amplification of 16S rRNA gene sequences, and identification through pyrosequencing. The results indicated that bacteria (with limited archaea and no detectable eukaryotic organisms) dominated both water samples; however, there were significant taxonomic differences in the bacterial populations of the samples. The STR sample was dominated by a single phylotype within the Gammaproteobacteria (Order Acidithiobacillales), which dramatically reduced the overall diversity and species richness of the population. In WCL, despite less organic carbon, the bacterial population was significantly more diverse, including significant contributions from the Gammaproteobacteria, Firmicutes, Chloroflexi, Actinobacteria, Planctomycetes, Fusobacter, and Omnitrophica phyla. Comparisons with similar oligotrophic environments suggest that karst aquifers have a greater species richness than comparable surface environs. These data also demonstrate that Wind Cave provides a unique opportunity to sample a deep, subterranean aquifer directly, and that the microbiology of such aquifers may be more complex than previously anticipated.

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.

Methods for assembly, taxonomic profiling and binning are key to interpreting metagenome data, but a lack of consensus about benchmarking complicates performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on highly complex and realistic data sets, generated from ∼700 newly sequenced microorganisms and ∼600 novel viruses and plasmids and representing common experimental setups. Assembly and genome binning programs performed well for species represented by individual genomes but were substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below family level. Parameter settings markedly affected performance, underscoring their importance for program reproducibility. The CAMI results highlight current challenges but also provide a roadmap for software selection to answer specific research questions.

Bioboxes: standardised containers for interchangeable bioinformatics software.

Software is now both central and essential to modern biology, yet lack of availability, difficult installations, and complex user interfaces make software hard to obtain and use. Containerisation, as exemplified by the Docker platform, has the potential to solve the problems associated with sharing software. We propose bioboxes: containers with standardised interfaces to make bioinformatics software interchangeable.

The genome of Pseudomonas fluorescens strain R124 demonstrates phenotypic adaptation to the mineral environment.

Microbial adaptation to environmental conditions is a complex process, including acquisition of positive traits through horizontal gene transfer or the modification of existing genes through duplication and/or mutation. In this study, we examined the adaptation of a Pseudomonas fluorescens isolate (R124) from the nutrient-limited mineral environment of a silica cave in comparison with P. fluorescens isolates from surface soil and the rhizosphere. Examination of metal homeostasis gene pathways demonstrated a high degree of conservation, suggesting that such systems remain functionally similar across chemical environments. The examination of genomic islands unique to our strain revealed the presence of genes involved in carbohydrate metabolism, aromatic carbon metabolism, and carbon turnover, confirmed through phenotypic assays, suggesting the acquisition of potentially novel mechanisms for energy metabolism in this strain. We also identified a twitching motility phenotype active at low-nutrient concentrations that may allow alternative exploratory mechanisms for this organism in a geochemical environment. Two sets of candidate twitching motility genes are present within the genome, one on the chromosome and one on a plasmid; however, a plasmid knockout identified the functional gene as being present on the chromosome. This work highlights the plasticity of the Pseudomonas genome, allowing the acquisition of novel nutrient-scavenging pathways across diverse geochemical environments while maintaining a core of functional stress response genes.

Measurement of the anisotropic thermal conductivity of the porcine cornea.

Accurate thermal models for the cornea of the eye support the development of thermal techniques for reshaping the cornea and other scientific purposes. Heat transfer in the cornea must be quantified accurately so that a thermal treatment does not destroy the endothelial layer, which cannot regenerate, and yet is responsible for maintaining corneal transparency. We developed a custom apparatus to measure the thermal conductivity of ex vivo porcine corneas perpendicular to the surface and applied a commercial apparatus to measure thermal conductivity parallel to the surface. We found that corneal thermal conductivity is 14% anisotropic at the normal state of corneal hydration. Small numbers of ex vivo feline and human corneas had a thermal conductivity perpendicular to the surface that was indistinguishable from the porcine corneas. Aqueous humor from ex vivo porcine, feline, and human eyes had a thermal conductivity nearly equal to that of water. Including the anisotropy of corneal thermal conductivity will improve the predictive power of thermal models of the eye.

Genomer--a Swiss army knife for genome scaffolding.

The increasing accessibility and reduced costs of sequencing has made genome analysis accessible to more and more researchers. Yet there remains a steep learning curve in the subsequent computational steps required to process raw reads into a database-deposited genome sequence. Here we describe "Genomer," a tool to simplify the manual tasks of finishing and uploading a genome sequence to a database. Genomer can format a genome scaffold into the common files required for submission to GenBank. This software also simplifies updating a genome scaffold by allowing a human-readable YAML format file to be edited instead of large sequence files. Genomer is written as a command line tool and is an effort to make the manual process of genome scaffolding more robust and reproducible. Extensive documentation and video tutorials are available at http://next.gs.

Scaffolder - software for manual genome scaffolding.

BACKGROUND: The assembly of next-generation short-read sequencing data can result in a fragmented non-contiguous set of genomic sequences. Therefore a common step in a genome project is to join neighbouring sequence regions together and fill gaps. This scaffolding step is non-trivial and requires manually editing large blocks of nucleotide sequence. Joining these sequences together also hides the source of each region in the final genome sequence. Taken together these considerations may make reproducing or editing an existing genome scaffold difficult. METHODS: The software outlined here, "Scaffolder," is implemented in the Ruby programming language and can be installed via the RubyGems software management system. Genome scaffolds are defined using YAML - a data format which is both human and machine-readable. Command line binaries and extensive documentation are available. RESULTS: This software allows a genome build to be defined in terms of the constituent sequences using a relatively simple syntax. This syntax further allows unknown regions to be specified and additional sequence to be used to fill known gaps in the scaffold. Defining the genome construction in a file makes the scaffolding process reproducible and easier to edit compared with large FASTA nucleotide sequences. CONCLUSIONS: Scaffolder is easy-to-use genome scaffolding software which promotes reproducibility and continuous development in a genome project. Scaffolder can be found at http://next.gs.

Evolutionary systems biology of amino acid biosynthetic cost in yeast.

Every protein has a biosynthetic cost to the cell based on the synthesis of its constituent amino acids. In order to optimise growth and reproduction, natural selection is expected, where possible, to favour the use of proteins whose constituents are cheaper to produce, as reduced biosynthetic cost may confer a fitness advantage to the organism. Quantifying the cost of amino acid biosynthesis presents challenges, since energetic requirements may change across different cellular and environmental conditions. We developed a systems biology approach to estimate the cost of amino acid synthesis based on genome-scale metabolic models and investigated the effects of the cost of amino acid synthesis on Saccharomyces cerevisiae gene expression and protein evolution. First, we used our two new and six previously reported measures of amino acid cost in conjunction with codon usage bias, tRNA gene number and atomic composition to identify which of these factors best predict transcript and protein levels. Second, we compared amino acid cost with rates of amino acid substitution across four species in the genus Saccharomyces. Regardless of which cost measure is used, amino acid biosynthetic cost is weakly associated with transcript and protein levels. In contrast, we find that biosynthetic cost and amino acid substitution rates show a negative correlation, but for only a subset of cost measures. In the economy of the yeast cell, we find that the cost of amino acid synthesis plays a limited role in shaping transcript and protein expression levels compared to that of translational optimisation. Biosynthetic cost does, however, appear to affect rates of amino acid evolution in Saccharomyces, suggesting that expensive amino acids may only be used when they have specific structural or functional roles in protein sequences. However, as there appears to be no single currency to compute the cost of amino acid synthesis across all cellular and environmental conditions, we conclude that a systems approach is necessary to unravel the full effects of amino acid biosynthetic cost in complex biological systems.

Modified GFAP promoter auto-regulates tet-activator expression for increased transactivation and reduced tTA-associated toxicity.

Transactivator tTA is a necessary component of the tetracycline-regulated inducible gene system. While several transgenic animals have been described that express tTA in the central nervous system (CNS), their tTA levels are often limited, presumably due to toxic effects. We evaluated methods for auto-regulating tTA levels in astrocytes by modifying the transgenic promoter human GFAP (hGFAP). The hGFAP promoter carrying a single copy of the tet-operon in place of a native enhancer element (GFAPtetO1) drove expression of tTA at low levels during un-stimulated, basal condition. However the same promoter auto-induced expression of tTA to significant levels after tetracycline withdrawal. Glial cell-specificity of the promoter remained uncompromised during both basal and induced conditions. Transgenic rats were developed using the auto-inducible GFAPtetO1 promoter that expressed tTA mRNA to high levels in the brain. Expression was widespread within the CNS but enriched in astrocyte-rich regions including the cerebellum. Primary cerebellar astrocytes from GFAPtetO1 rats transfected with 07LacZ produced substantially greater inducibility of reporter gene compared to GFAP-tTA transgenic rats. Finally, GFAPtetO1 rats exhibited severe motor/gait deficit when bred to homozygosity. This phenotype was attributable to developmental abnormalities of the cerebellum and was completely abrogated by doxycycline administration. These results suggest that developmental toxicity resulting from tTA expression can be circumvented and tTA transgenics with high transactivation potential can be developed using the auto-activation strategy. Promoter modification presented here may be useful in developing highly inducible transgenic strategies without loss in tissue-specificity.