Scaffolder - Software for Reproducible Genome Scaffolding.

Background: Assembly of short-read sequencing data can result in a fragmented non-contiguous series of genomic sequences. Therefore a common step in a genome project is to join neighboring sequence regions together and fill gaps in the assembly using additional sequences. This scaffolding step, however, 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 build 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 to define the scaffold. This syntax further allows unknown regions to be defined, and adds additional sequences to fill gaps in the scaffold. Defining the genome construction in a file makes the scaffolding process reproducible and easier to edit compared with FASTA nucleotide sequence.

Conclusions: Scaffolder is easy-to-use genome scaffolding software. This tool promotes reproducibility and continuous development in a genome project. Scaffolder can be found at http://next.gs

Systems biology of energetic and atomic costs in the yeast transcriptome, proteome, and metabolome

Proteins vary in their cost to the cell and natural selection may favour the use of proteins that are cheaper to produce. We develop a novel approach to estimate the amino acid biosynthetic cost based on genome-scale metabolic models, and directly investigate the effects of biosynthetic cost on transcriptomic, proteomic and metabolomic data in _Saccharomyces cerevisiae_. We find that our systems approach to formulating biosynthetic cost produces a novel measure that explains similar levels of variation in gene expression compared with previously reported cost measures. Regardless of the measure used, the cost of amino acid synthesis is weakly associated with transcript and protein levels, independent of codon usage bias. In contrast, energetic costs explain a large proportion of variation in levels of free amino acids. In the economy of the yeast cell, there appears to be no single currency to compute the cost of amino acid synthesis, and thus a systems approach is necessary to uncover the full effects of amino acid biosynthetic cost in complex biological systems that vary with cellular and environmental conditions

Structural disorder, magnetism, and electrical and thermoelectric properties of pyrochlore Nd2Ru2O7

Polycrystalline Nd2Ru2O7 samples have been prepared and examined using a combination of structural, magnetic, and electrical and thermal transport studies. Analysis of synchrotron X-ray and neutron diffraction patterns suggests some site disorder on the A-site in the pyrochlore sublattice: Ru substitutes on the Nd-site up to 7.0(3)%, regardless of the different preparative conditions explored. Intrinsic magnetic and electrical transport properties have been measured. Ru 4d spins order antiferromagnetically at 143 K as seen both in susceptibility and specific heat, and there is a corresponding change in the electrical resistivity behaviour. A second antiferromagnetic ordering transition seen below 10 K is attributed to ordering of Nd 4f spins. Nd2Ru2O7 is an electrical insulator, and this behaviour is believed to be independent of the Ru-antisite disorder on the Nd site. The electrical properties of Nd2Ru2O7 are presented in the light of data published on all A2Ru2O7 pyrochlores, and we emphasize the special structural role that Bi3+ ions on the A-site play in driving metallic behaviour. High-temperature thermoelectric properties have also been measured. When considered in the context of known thermoelectric materials with useful figures-of-merit, it is clear that Nd2Ru2O7 has excessively high electrical resistivity which prevents it from being an effective thermoelectric. A method for screening candidate thermoelectrics is suggested.Comment: 19 pages, 10 figure

Charge Photoinjection in Intercalated and Covalently Bound [Re(CO)_(3)(dppz)(py)]^(+)–DNA Constructs Monitored by Time-Resolved Visible and Infrared Spectroscopy

The complex [Re(CO)_(3)(dppz)(py′-OR)]+ (dppz = dipyrido[3,2-a:2′,3′-c]phenazine; py′-OR = 4-functionalized pyridine) offers IR sensitivity and can oxidize DNA directly from the excited state, making it a promising probe for the study of DNA-mediated charge transport (CT). The behavior of several covalent and noncovalent Re–DNA constructs was monitored by time-resolved IR (TRIR) and UV/visible spectroscopies, as well as biochemical methods, confirming the long-range oxidation of DNA by the excited complex. Optical excitation of the complex leads to population of MLCT and at least two distinct intraligand states. Experimental observations that are consistent with charge injection from these excited states include similarity between long-time TRIR spectra and the reduced state spectrum observed by spectroelectrochemistry, the appearance of a guanine radical signal in TRIR spectra, and the eventual formation of permanent guanine oxidation products. The majority of reactivity occurs on the ultrafast time scale, although processes dependent on slower conformational motions of DNA, such as the accumulation of oxidative damage at guanine, are also observed. The ability to measure events on such disparate time scales, its superior selectivity in comparison to other spectroscopic techniques, and the ability to simultaneously monitor carbonyl ligand and DNA IR absorption bands make TRIR a valuable tool for the study of CT in DNA

Establishing Pine Monocultures and Mixed Pine-Hardwood Stands on Reclaimed Surface Mined Land in Eastern Kentucky: Implications for Forest Resilience in a Changing Climate

Surface mining and mine reclamation practices have caused significant forest loss and forest fragmentation in Appalachia. Shortleaf pine (Pinus echinata) is threatened by a variety of stresses, including diseases, pests, poor management, altered fire regimes, and climate change, and the species is the subject of a widescale restoration effort. Surface mines may present opportunity for shortleaf pine restoration; however, the survival and growth of shortleaf pine on these harsh sites has not been critically evaluated. This paper presents first-year survival and growth of native shortleaf pine planted on a reclaimed surface mine, compared to non-native loblolly pine (Pinus taeda), which has been highly successful in previous mined land reclamation plantings. Pine monoculture plots are also compared to pine-hardwood polyculture plots to evaluate effects of planting mix on tree growth and survival, as well as soil health. Initial survival of shortleaf pine is low (42%), but height growth is similar to that of loblolly pine. No differences in survival or growth were observed between monoculture and polyculture treatments. Additional surveys in coming years will address longer-term growth and survival patterns of these species, as well as changes to relevant soil health endpoints, such as soil carbon

Biophysical Aspects of Resource Acquisition and Competition in Algal Mixotrophs

Mixotrophic organisms combine autotrophic and heterotrophic nutrition and are abundant in both freshwater and marine environments. Recent observations indicate that mixotrophs constitute a large fraction of the biomass, bacterivory, and primary production in oligotrophic environments. While mixotrophy allows greater flexibility in terms of resource acquisition, any advantage must be traded off against an associated increase in metabolic costs, which appear to make mixotrophs uncompetitive relative to obligate autotrophs and heterotrophs. Using an idealized model of cell physiology and community competition, we identify one mechanism by which mixotrophs can effectively outcompete specialists for nutrient elements. At low resource concentrations, when the uptake of nutrients is limited by diffusion toward the cell, the investment in cell membrane transporters can be minimized. In this situation, mixotrophs can acquire limiting elements in both organic and inorganic forms, outcompeting their specialist competitors that can utilize only one of these forms. This advantage can be enough to offset as much as a twofold increase in additional metabolic costs incurred by mixotrophs. This mechanism is particularly relevant for the maintenance of mixotrophic populations and productivity in the highly oligotro phic subtropical oceans.United States. National Aeronautics and Space AdministrationGordon and Betty Moore Foundatio

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

Bioboxes: standardised containers for interchangeable bioinformatics software

Belmann P, Dröge J, Bremges A, McHardy AC, Sczyrba A, Barton MD. Bioboxes: standardised containers for interchangeable bioinformatics software. GigaScience. 2015;4(1): 47.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

Vacuum Polarization and Energy Conditions at a Planar Frequency Dependent Dielectric to Vacuum Interface

The form of the vacuum stress-tensor for the quantized scalar field at a dielectric to vacuum interface is studied. The dielectric is modeled to have an index of refraction that varies with frequency. We find that the stress-tensor components, derived from the mode function expansion of the Wightman function, are naturally regularized by the reflection and transmission coefficients of the mode at the boundary. Additionally, the divergence of the vacuum energy associated with a perfectly reflecting mirror is found to disappear for the dielectric mirror at the expense of introducing a new energy density near the surface which has the opposite sign. Thus the weak energy condition is always violated in some region of the spacetime. For the dielectric mirror, the mean vacuum energy density per unit plate area in a constant time hypersurface is always found to be positive (or zero) and the averaged weak energy condition is proven to hold for all observers with non-zero velocity along the normal direction to the boundary. Both results are found to be generic features of the vacuum stress-tensor and not necessarily dependent of the frequency dependence of the dielectric.Comment: 16 pages, 4 figures, Revtex style Minor typographic corrections to equations and tex