Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved

Global perspectives on observing ocean boundary current systems

Ocean boundary current systems are key components of the climate system, are home to highly productive ecosystems, and have numerous societal impacts. Establishment of a global network of boundary current observing systems is a critical part of ongoing development of the Global Ocean Observing System. The characteristics of boundary current systems are reviewed, focusing on scientific and societal motivations for sustained observing. Techniques currently used to observe boundary current systems are reviewed, followed by a census of the current state of boundary current observing systems globally. Next steps in the development of boundary current observing systems are considered, leading to several specific recommendations

Thermodynamic analysis of algal biocrude production

Although algal biofuels possess great potential, profitable production is quite challenging. Much of this challenge is rooted in the thermodynamic constraints associated with producing fuels with high energy, low entropy, and high exergy from dispersed materials. In this study, a preliminary thermodynamic analysis is presented that calculates the energy, entropy, and exergy of the intermediate products for algal biocrude production. These values are also used in an initial attempt to characterize the thermodynamic efficiency of that system. The production pathway is simplified by assuming ideal solutions throughout. Results for the energy and exergy efficiencies, and the first-order energy and exergy return on investment, of the system are given. The summary finding is that the first-order energy return on investment in the best case considered could be as high as 520, as compared to 1.7 × 10?3 in the experimental unit under development. While this analysis shows that significant improvement may be possible, the ultimate thermodynamic efficiency of algal biofuels likely lies closer to the moderate case examined here, which yielded a first-order energy return on investment of 10. For perspective, the first-order energy return on investment for oil and gas production has been estimated in the literature to be ?35.Center for Electromechanic

Progression of lipid profile and cell structure in a research-scale production pathway for algal biocrude

Although there has been a large research effort associated with individual parts of various algal biofuel production pathways, few studies have tracked changes in product composition throughout an integrated biofuel production process. This study uses microscopy and chromatography to analyze the progression of lipid profile and cell structure of algal cells throughout a research-scale production pathway for biocrude. For the specific processing methods used in this pathway, it is shown that TAG content decreased, while DAG and FFA content increased during processing. The changes in the lipid content corresponded to cell degradation that was observed by SEM and TEM throughout processing. These results demonstrate the dynamic nature of lipid composition in an algal culture used for biofuel production and emphasize the need to monitor changes in lipid profile, as those changes can directly impact biofuel productivity.Center for Electromechanic

Comprehensive Evaluation of Algal Biofuel Production: Experimental and Target Results

Worldwide, algal biofuel research and development efforts have focused on increasing the competitiveness of algal biofuels by increasing the energy and financial return on investments, reducing water intensity and resource requirements, and increasing algal productivity. In this study, analyses are presented in each of these areas—costs, resource needs, and productivity—for two cases: (1) an Experimental Case, using mostly measured data for a lab-scale system, and (2) a theorized Highly Productive Case that represents an optimized commercial-scale production system, albeit one that relies on full-price water, nutrients, and carbon dioxide. For both cases, the analysis described herein concludes that the energy and financial return on investments are less than 1, the water intensity is greater than that for conventional fuels, and the amounts of required resources at a meaningful scale of production amount to significant fractions of current consumption (e.g., nitrogen). The analysis and presentation of results highlight critical areas for advancement and innovation that must occur for sustainable and profitable algal biofuel production can occur at a scale that yields significant petroleum displacement. To this end, targets for energy consumption, production cost, water consumption, and nutrient consumption are presented that would promote sustainable algal biofuel production. Furthermore, this work demonstrates a procedure and method by which subsequent advances in technology and biotechnology can be framed to track progress.Center for Electromechanic