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

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

A unified hyperbolic formulation for viscous fluids and elastoplastic solids

We discuss a unified flow theory which in a single system of hyperbolic partial differential equations (PDEs) can describe the two main branches of continuum mechanics, fluid dynamics, and solid dynamics. The fundamental difference from the classical continuum models, such as the Navier-Stokes for example, is that the finite length scale of the continuum particles is not ignored but kept in the model in order to semi-explicitly describe the essence of any flows, that is the process of continuum particles rearrangements. To allow the continuum particle rearrangements, we admit the deformability of particle which is described by the distortion field. The ability of media to flow is characterized by the strain dissipation time which is a characteristic time necessary for a continuum particle to rearrange with one of its neighboring particles. It is shown that the continuum particle length scale is intimately connected with the dissipation time. The governing equations are represented by a system of first order hyperbolic PDEs with source terms modeling the dissipation due to particle rearrangements. Numerical examples justifying the reliability of the proposed approach are demonstrated.Comment: 6 figure

Intercalative Stacking: A Critical Feature of DNA Charge-Transport Electrochemistry

In electrochemistry experiments on DNA-modified electrodes, features of the redox probe that determine efficient charge transport through DNA-modified surfaces have been explored using methylene blue (MB^+) and Ru(NH_3)_6^(3+) as DNA-binding redox probes. The electrochemistry of these molecules is studied as a function of ionic strength to determine the necessity of tight binding to DNA and the number of electrons involved in the redox reaction; on the DNA surface, MB^+ displays 2e^-/1H^+ electrochemistry (pH 7) and Ru(NH^3)_6^(3+) displays 1e^- electrochemistry. We examine also the effect of electrode surface passivation and the effect of the mode (intercalation or electrostatic) of MB^+ and Ru(NH_3)_6^(3+) binding to DNA to highlight the importance of intercalation for reduction by a DNA-mediated charge-transport pathway. Furthermore, in experiments in which MB^+ is covalently linked to the DNA through a σ-bonded tether and the ionic strength is varied, it is demonstrated that intercalative stacking rather than covalent σ-bonding is essential for efficient reduction of MB^+. The results presented here therefore establish that efficient charge transport to the DNA-binding moiety in DNA films requires intercalative stacking and is mediated by the DNA base pair array

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

Report on the “Trait-based approaches to ocean life” scoping workshop, October 5-8, 2015

"Trait-based Approaches to Ocean Life” Scoping Workshop, October 5-8, 2015, Waterville Valley, NH, USAFrom the introduction: Marine ecosystems are rich and biodiverse, often populated by thousands of competing and interacting species with a vast range of behaviors, forms, and life histories. This great ecological complexity presents a formidable challenge to understanding how marine ecosystems are structured and controlled, but also how they respond to natural and anthropogenic changes. The trait-based approach to ocean life is emerging as a novel framework for understanding the complexity, structure, and dynamics of marine ecosystems, but also their broader significance. Rather than considering species individually, organisms are characterized by essential traits that capture key aspects of diversity. Trait distributions in the ocean emerge through evolution and natural selection, and are mediated by the environment, biological interactions, anthropogenic drivers, and organism behavior. Because trait variations within and across communities lead to variation in the rates of crucial ecosystem functions such as carbon export, this mechanistic approach sheds light on how variability in the environment, including climate change, impacts marine ecosystems, biogeochemical cycles, and associated feedbacks to climate and society.Funding from the National Science Foundation and National Aeronautics and Space Administration), the Simons Foundation, and the Gordon and Betty Moore Foundation