Assembling large, complex environmental metagenomes

The large volumes of sequencing data required to sample complex environments deeply pose new challenges to sequence analysis approaches. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires significant computational resources. We apply two pre-assembly filtering approaches, digital normalization and partitioning, to make large metagenome assemblies more comput\ ationaly tractable. Using a human gut mock community dataset, we demonstrate that these methods result in assemblies nearly identical to assemblies from unprocessed data. We then assemble two large soil metagenomes from matched Iowa corn and native prairie soils. The predicted functional content and phylogenetic origin of the assembled contigs indicate significant taxonomic differences despite similar function. The assembly strategies presented are generic and can be extended to any metagenome; full source code is freely available under a BSD license.Comment: Includes supporting informatio

State of the art nano materials

ABSTRACT: The special issue of ANM2017 is a collection of papers from the 9th series ANM (Advanced Nano Materials) conference, which was held at the University of Aveiro, Portugal, from 19-21 July 2017. State of the art results were discussed by eminent researchers on a wide range of subjects including nanomaterials, graphene materials, polymer nanocomposites, magnetic materials, spintronics materials, hydrogen energy, nanoelectronics and solar energy materials. We thank all the reviewers for their detailed reviews which immensely helped the authors to improve the quality of their papers. Advanced Nano Materials, ANM (https://www.advancednanomaterials-conference.com/) is an annual conference at the University of Aveiro, Portugal and we invite all our colleagues working in the field of energy materials to attend the next ANM.info:eu-repo/semantics/publishedVersio

State of the art energy materials

ABSTRACT: The special issue of AEM2017 is a collection of papers from the second series of AEM (Advanced Energy Materials) conference, which was held at the University of Surrey, England, from 11-13 September 2017. State of the art results were discussed by eminent researchers on a wide range of subjects including battery, fuel cells, catalysis, carbon materials, photovoltaics, biofuels, polymer-based hydrogen storage, hydrogen production by various methods, crystalline porous materials for hydrogen storage. We thank all the reviewers for their detailed reviews which immensely helped the authors to improve the quality of their papers. Advanced Energy Materials, AEM (www.advanced-energymaterialsconference.com) is an annual conference and we invite all our colleagues working in the field of energy materials to attend the next AEM.info:eu-repo/semantics/publishedVersio

Transcriptome of the Caribbean stony coral Porites astreoides from three developmental stages

© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in GigaScience 5 (2016): 33, doi:10.1186/s13742-016-0138-1.Porites astreoides is a ubiquitous species of coral on modern Caribbean reefs that is resistant to increasing temperatures, overfishing, and other anthropogenic impacts that have threatened most other coral species. We assembled and annotated a transcriptome from this coral using Illumina sequences from three different developmental stages collected over several years: free-swimming larvae, newly settled larvae, and adults (>10 cm in diameter). This resource will aid understanding of coral calcification, larval settlement, and host–symbiont interactions. A de novo transcriptome for the P. astreoides holobiont (coral plus algal symbiont) was assembled using 594 Mbp of raw Illumina sequencing data generated from five age-specific cDNA libraries. The new transcriptome consists of 867 255 transcript elements with an average length of 685 bases. The isolated P. astreoides assembly consists of 129 718 transcript elements with an average length of 811 bases, and the isolated Symbiodinium sp. assembly had 186 177 transcript elements with an average length of 1105 bases. This contribution to coral transcriptome data provides a valuable resource for researchers studying the ontogeny of gene expression patterns within both the coral and its dinoflagellate symbiont.Bioinformatic analysis was performed in part on computing resources at the University of Puerto Rico (UPR) Puerto Rico Center for Environmental Neuroscience (PRCEN)’s High Performance Computing Facility, which is supported by: Institutional Development Award Networks of Biomedical Research Excellent (INBRE) grant P20GM103475 from the National Institute of General Medical Sciences, National Institutes of Health; the Institute for Functional Nanomaterials (IFN) award from the Experimental Program to Stimulate Competitive Research (EPSCoR) Track 1 program of the National Science Foundation (NSF); and EPSCoR Track 2 awards for computational nanoscience (EPS 1002410, EPS 1010094). Funding and support of the research was provided by PRCEN thanks to an NSF Centers of Research Excellent in Science and Technology (CREST) award, number HRD-1137725

NASA Planetary Mission Concept Study: Assessing: Dwarf Planet Ceres' past and Present Habitability Potential

The Dawn mission revolutionized our understanding of Ceres during the same decade that has also witnessed the rise of ocean worlds as a research and exploration focus. We will report progress on the Planetary Mission Concept Study (PMCS) on the future exploration of Ceres under the New Frontiers or Flagship program that was selected for NASA funding in October 2019. At the time this writing, the study was just kicked off, hence this abstract reports the study plan as presented in the proposal

The omega-3 fatty acid eicosapentaenoic acid accelerates disease progression in a model of amyotrophic lateral sclerosis.

Amyotrophic lateral sclerosis (ALS) is a progressive fatal neurodegenerative disease characterised by loss of motor neurons that currently has no cure. Omega-3 polyunsaturated fatty acids, such as eicosapentaenoic acid (EPA), have many health benefits including neuroprotective and myoprotective potential. We tested the hypothesis that a high level of dietary EPA could exert beneficial effects in ALS. The dietary exposure to EPA (300 mg/kg/day) in a well-established mouse model of ALS expressing the G93A superoxide dismutase 1 (SOD1) mutation was initiated at a pre-symptomatic or symptomatic stage, and the disease progression was monitored until the end stage. Daily dietary EPA exposure initiated at the disease onset did not significantly alter disease presentation and progression. In contrast, EPA treatment initiated at the pre-symptomatic stage induced a significantly shorter lifespan. In a separate group of animals sacrificed before the end stage, the tissue analysis showed that the vacuolisation detected in G93A-SOD1 mice was significantly increased by exposure to EPA. Although EPA did not alter motor neurone loss, EPA reversed the significant increase in activated microglia and the astrocytic activation seen in G93A-SOD1 mice. The microglia in the spinal cord of G93A-SOD1 mice treated with EPA showed a significant increase in 4-hydroxy-2-hexenal, a highly toxic aldehydic oxidation product of omega-3 fatty acids. These data show that dietary EPA supplementation in ALS has the potential to worsen the condition and accelerate the disease progression. This suggests that great caution should be exerted when considering dietary omega-3 fatty acid supplements in ALS patients

A Spread-Spectrum SQUID Multiplexer

The Transition-Edge Sensors (TES) is a mature, high-resolution x-ray spectrometer technology that provides a much higher efficiency than dispersive spectrometers such as gratings and crystal spectrometers. As larger arrays are developed, time-division multiplexing schemes operating at MHz frequencies are being replaced by microwave SQUID multiplexers using frequency-division multiplexing at GHz frequencies. However, the multiplexing factor achievable with microwave SQUIDs is limited by the high slew rate on the leading edge of x-ray pulses. In this paper, we propose a new multiplexing scheme for high-slew-rate TES x-ray calorimeters: the spread-spectrum SQUID multiplexer, which has the potential to enable higher multiplexing factors, especially in applications with lower photon arrival rates.Comment: 12 pages, 2 figures, Submitted to the Journal of Low Temperature Physics (Proceedings of the 17th International Workshop on Low Temperature Detectors

Breakdown of Lindstedt Expansion for Chaotic Maps

In a previous paper of one of us [Europhys. Lett. 59 (2002), 330--336] the validity of Greene's method for determining the critical constant of the standard map (SM) was questioned on the basis of some numerical findings. Here we come back to that analysis and we provide an interpretation of the numerical results by showing that no contradiction is found with respect to Greene's method. We show that the previous results based on the expansion in Lindstedt series do correspond to the transition value but for a different map: the semi-standard map (SSM). Moreover, we study the expansion obtained from the SM and SSM by suppressing the small divisors. The first case turns out to be related to Kepler's equation after a proper transformation of variables. In both cases we give an analytical solution for the radius of convergence, that represents the singularity in the complex plane closest to the origin. Also here, the radius of convergence of the SM's analogue turns out to be lower than the one of the SSM. However, despite the absence of small denominators these two radii are lower than the ones of the true maps for golden mean winding numbers. Finally, the analyticity domain and, in particular, the critical constant for the two maps without small divisors are studied analytically and numerically. The analyticity domain appears to be an perfect circle for the SSM analogue, while it is stretched along the real axis for the SM analogue yielding a critical constant that is larger than its radius of convergence.Comment: 12 pages, 3 figure