MetaCRAST: reference-guided extraction of CRISPR spacers from unassembled metagenomes.

PubMed

Moller, Abraham G; Liang, Chun

2017-01-01

Clustered regularly interspaced short palindromic repeat (CRISPR) systems are the adaptive immune systems of bacteria and archaea against viral infection. While CRISPRs have been exploited as a tool for genetic engineering, their spacer sequences can also provide valuable insights into microbial ecology by linking environmental viruses to their microbial hosts. Despite this importance, metagenomic CRISPR detection remains a major challenge. Here we present a reference-guided CRISPR spacer detection tool ( Meta genomic C RISPR R eference- A ided S earch T ool-MetaCRAST) that constrains searches based on user-specified direct repeats (DRs). These DRs could be expected from assembly or taxonomic profiles of metagenomes. We compared the performance of MetaCRAST to those of two existing metagenomic CRISPR detection tools-Crass and MinCED-using both real and simulated acid mine drainage (AMD) and enhanced biological phosphorus removal (EBPR) metagenomes. Our evaluation shows MetaCRAST improves CRISPR spacer detection in real metagenomes compared to the de novo CRISPR detection methods Crass and MinCED. Evaluation on simulated metagenomes show it performs better than de novo tools for Illumina metagenomes and comparably for 454 metagenomes. It also has comparable performance dependence on read length and community composition, run time, and accuracy to these tools. MetaCRAST is implemented in Perl, parallelizable through the Many Core Engine (MCE), and takes metagenomic sequence reads and direct repeat queries (FASTA or FASTQ) as input. It is freely available for download at https://github.com/molleraj/MetaCRAST.

Current and future resources for functional metagenomics

PubMed Central

Lam, Kathy N.; Cheng, Jiujun; Engel, Katja; Neufeld, Josh D.; Charles, Trevor C.

2015-01-01

Functional metagenomics is a powerful experimental approach for studying gene function, starting from the extracted DNA of mixed microbial populations. A functional approach relies on the construction and screening of metagenomic libraries—physical libraries that contain DNA cloned from environmental metagenomes. The information obtained from functional metagenomics can help in future annotations of gene function and serve as a complement to sequence-based metagenomics. In this Perspective, we begin by summarizing the technical challenges of constructing metagenomic libraries and emphasize their value as resources. We then discuss libraries constructed using the popular cloning vector, pCC1FOS, and highlight the strengths and shortcomings of this system, alongside possible strategies to maximize existing pCC1FOS-based libraries by screening in diverse hosts. Finally, we discuss the known bias of libraries constructed from human gut and marine water samples, present results that suggest bias may also occur for soil libraries, and consider factors that bias metagenomic libraries in general. We anticipate that discussion of current resources and limitations will advance tools and technologies for functional metagenomics research. PMID:26579102

Current and future resources for functional metagenomics.

PubMed

Lam, Kathy N; Cheng, Jiujun; Engel, Katja; Neufeld, Josh D; Charles, Trevor C

2015-01-01

Functional metagenomics is a powerful experimental approach for studying gene function, starting from the extracted DNA of mixed microbial populations. A functional approach relies on the construction and screening of metagenomic libraries-physical libraries that contain DNA cloned from environmental metagenomes. The information obtained from functional metagenomics can help in future annotations of gene function and serve as a complement to sequence-based metagenomics. In this Perspective, we begin by summarizing the technical challenges of constructing metagenomic libraries and emphasize their value as resources. We then discuss libraries constructed using the popular cloning vector, pCC1FOS, and highlight the strengths and shortcomings of this system, alongside possible strategies to maximize existing pCC1FOS-based libraries by screening in diverse hosts. Finally, we discuss the known bias of libraries constructed from human gut and marine water samples, present results that suggest bias may also occur for soil libraries, and consider factors that bias metagenomic libraries in general. We anticipate that discussion of current resources and limitations will advance tools and technologies for functional metagenomics research.

Scalability of Comparative Analysis, Novel Algorithms and Tools (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Mavrommatis, Kostas

2017-12-22

DOE JGI's Kostas Mavrommatis, chair of the Scalability of Comparative Analysis, Novel Algorithms and Tools panel, at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

MIPE: A metagenome-based community structure explorer and SSU primer evaluation tool

PubMed Central

Zhou, Quan

2017-01-01

An understanding of microbial community structure is an important issue in the field of molecular ecology. The traditional molecular method involves amplification of small subunit ribosomal RNA (SSU rRNA) genes by polymerase chain reaction (PCR). However, PCR-based amplicon approaches are affected by primer bias and chimeras. With the development of high-throughput sequencing technology, unbiased SSU rRNA gene sequences can be mined from shotgun sequencing-based metagenomic or metatranscriptomic datasets to obtain a reflection of the microbial community structure in specific types of environment and to evaluate SSU primers. However, the use of short reads obtained through next-generation sequencing for primer evaluation has not been well resolved. The software MIPE (MIcrobiota metagenome Primer Explorer) was developed to adapt numerous short reads from metagenomes and metatranscriptomes. Using metagenomic or metatranscriptomic datasets as input, MIPE extracts and aligns rRNA to reveal detailed information on microbial composition and evaluate SSU rRNA primers. A mock dataset, a real Metagenomics Rapid Annotation using Subsystem Technology (MG-RAST) test dataset, two PrimerProspector test datasets and a real metatranscriptomic dataset were used to validate MIPE. The software calls Mothur (v1.33.3) and the SILVA database (v119) for the alignment and classification of rRNA genes from a metagenome or metatranscriptome. MIPE can effectively extract shotgun rRNA reads from a metagenome or metatranscriptome and is capable of classifying these sequences and exhibiting sensitivity to different SSU rRNA PCR primers. Therefore, MIPE can be used to guide primer design for specific environmental samples. PMID:28350876

Sequencing Single Cell Microbial Genomes with Microfluidic Amplifications Tools (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Quake, Steve

2018-02-02

Stanford University's Steve Quake on "Sequencing Single Cell Microbial Genomes with Microfluidic Amplification Tools" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Sequencing Single Cell Microbial Genomes with Microfluidic Amplifications Tools (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Quake, Steve

2011-10-12

Stanford University's Steve Quake on "Sequencing Single Cell Microbial Genomes with Microfluidic Amplification Tools" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Bambus 2: scaffolding metagenomes.

PubMed

Koren, Sergey; Treangen, Todd J; Pop, Mihai

2011-11-01

Sequencing projects increasingly target samples from non-clonal sources. In particular, metagenomics has enabled scientists to begin to characterize the structure of microbial communities. The software tools developed for assembling and analyzing sequencing data for clonal organisms are, however, unable to adequately process data derived from non-clonal sources. We present a new scaffolder, Bambus 2, to address some of the challenges encountered when analyzing metagenomes. Our approach relies on a combination of a novel method for detecting genomic repeats and algorithms that analyze assembly graphs to identify biologically meaningful genomic variants. We compare our software to current assemblers using simulated and real data. We demonstrate that the repeat detection algorithms have higher sensitivity than current approaches without sacrificing specificity. In metagenomic datasets, the scaffolder avoids false joins between distantly related organisms while obtaining long-range contiguity. Bambus 2 represents a first step toward automated metagenomic assembly. Bambus 2 is open source and available from http://amos.sf.net. mpop@umiacs.umd.edu. Supplementary data are available at Bioinformatics online.

Bambus 2: scaffolding metagenomes

PubMed Central

Koren, Sergey; Treangen, Todd J.; Pop, Mihai

2011-01-01

Motivation: Sequencing projects increasingly target samples from non-clonal sources. In particular, metagenomics has enabled scientists to begin to characterize the structure of microbial communities. The software tools developed for assembling and analyzing sequencing data for clonal organisms are, however, unable to adequately process data derived from non-clonal sources. Results: We present a new scaffolder, Bambus 2, to address some of the challenges encountered when analyzing metagenomes. Our approach relies on a combination of a novel method for detecting genomic repeats and algorithms that analyze assembly graphs to identify biologically meaningful genomic variants. We compare our software to current assemblers using simulated and real data. We demonstrate that the repeat detection algorithms have higher sensitivity than current approaches without sacrificing specificity. In metagenomic datasets, the scaffolder avoids false joins between distantly related organisms while obtaining long-range contiguity. Bambus 2 represents a first step toward automated metagenomic assembly. Availability: Bambus 2 is open source and available from http://amos.sf.net. Contact: mpop@umiacs.umd.edu Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:21926123

Comprehensive benchmarking and ensemble approaches for metagenomic classifiers.

PubMed

McIntyre, Alexa B R; Ounit, Rachid; Afshinnekoo, Ebrahim; Prill, Robert J; Hénaff, Elizabeth; Alexander, Noah; Minot, Samuel S; Danko, David; Foox, Jonathan; Ahsanuddin, Sofia; Tighe, Scott; Hasan, Nur A; Subramanian, Poorani; Moffat, Kelly; Levy, Shawn; Lonardi, Stefano; Greenfield, Nick; Colwell, Rita R; Rosen, Gail L; Mason, Christopher E

2017-09-21

One of the main challenges in metagenomics is the identification of microorganisms in clinical and environmental samples. While an extensive and heterogeneous set of computational tools is available to classify microorganisms using whole-genome shotgun sequencing data, comprehensive comparisons of these methods are limited. In this study, we use the largest-to-date set of laboratory-generated and simulated controls across 846 species to evaluate the performance of 11 metagenomic classifiers. Tools were characterized on the basis of their ability to identify taxa at the genus, species, and strain levels, quantify relative abundances of taxa, and classify individual reads to the species level. Strikingly, the number of species identified by the 11 tools can differ by over three orders of magnitude on the same datasets. Various strategies can ameliorate taxonomic misclassification, including abundance filtering, ensemble approaches, and tool intersection. Nevertheless, these strategies were often insufficient to completely eliminate false positives from environmental samples, which are especially important where they concern medically relevant species. Overall, pairing tools with different classification strategies (k-mer, alignment, marker) can combine their respective advantages. This study provides positive and negative controls, titrated standards, and a guide for selecting tools for metagenomic analyses by comparing ranges of precision, accuracy, and recall. We show that proper experimental design and analysis parameters can reduce false positives, provide greater resolution of species in complex metagenomic samples, and improve the interpretation of results.

Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing.

PubMed

Thoendel, Matthew; Jeraldo, Patricio R; Greenwood-Quaintance, Kerryl E; Yao, Janet Z; Chia, Nicholas; Hanssen, Arlen D; Abdel, Matthew P; Patel, Robin

2016-08-01

Metagenomic whole genome sequencing for detection of pathogens in clinical samples is an exciting new area for discovery and clinical testing. A major barrier to this approach is the overwhelming ratio of human to pathogen DNA in samples with low pathogen abundance, which is typical of most clinical specimens. Microbial DNA enrichment methods offer the potential to relieve this limitation by improving this ratio. Two commercially available enrichment kits, the NEBNext Microbiome DNA Enrichment Kit and the Molzym MolYsis Basic kit, were tested for their ability to enrich for microbial DNA from resected arthroplasty component sonicate fluids from prosthetic joint infections or uninfected sonicate fluids spiked with Staphylococcus aureus. Using spiked uninfected sonicate fluid there was a 6-fold enrichment of bacterial DNA with the NEBNext kit and 76-fold enrichment with the MolYsis kit. Metagenomic whole genome sequencing of sonicate fluid revealed 13- to 85-fold enrichment of bacterial DNA using the NEBNext enrichment kit. The MolYsis approach achieved 481- to 9580-fold enrichment, resulting in 7 to 59% of sequencing reads being from the pathogens known to be present in the samples. These results demonstrate the usefulness of these tools when testing clinical samples with low microbial burden using next generation sequencing. Copyright © 2016 Elsevier B.V. All rights reserved.

Identifying biologically relevant differences between metagenomic communities.

PubMed

Parks, Donovan H; Beiko, Robert G

2010-03-15

Metagenomics is the study of genetic material recovered directly from environmental samples. Taxonomic and functional differences between metagenomic samples can highlight the influence of ecological factors on patterns of microbial life in a wide range of habitats. Statistical hypothesis tests can help us distinguish ecological influences from sampling artifacts, but knowledge of only the P-value from a statistical hypothesis test is insufficient to make inferences about biological relevance. Current reporting practices for pairwise comparative metagenomics are inadequate, and better tools are needed for comparative metagenomic analysis. We have developed a new software package, STAMP, for comparative metagenomics that supports best practices in analysis and reporting. Examination of a pair of iron mine metagenomes demonstrates that deeper biological insights can be gained using statistical techniques available in our software. An analysis of the functional potential of 'Candidatus Accumulibacter phosphatis' in two enhanced biological phosphorus removal metagenomes identified several subsystems that differ between the A.phosphatis stains in these related communities, including phosphate metabolism, secretion and metal transport. Python source code and binaries are freely available from our website at http://kiwi.cs.dal.ca/Software/STAMP CONTACT: beiko@cs.dal.ca Supplementary data are available at Bioinformatics online.

MetaQUAST: evaluation of metagenome assemblies.

PubMed

Mikheenko, Alla; Saveliev, Vladislav; Gurevich, Alexey

2016-04-01

During the past years we have witnessed the rapid development of new metagenome assembly methods. Although there are many benchmark utilities designed for single-genome assemblies, there is no well-recognized evaluation and comparison tool for metagenomic-specific analogues. In this article, we present MetaQUAST, a modification of QUAST, the state-of-the-art tool for genome assembly evaluation based on alignment of contigs to a reference. MetaQUAST addresses such metagenome datasets features as (i) unknown species content by detecting and downloading reference sequences, (ii) huge diversity by giving comprehensive reports for multiple genomes and (iii) presence of highly relative species by detecting chimeric contigs. We demonstrate MetaQUAST performance by comparing several leading assemblers on one simulated and two real datasets. http://bioinf.spbau.ru/metaquast aleksey.gurevich@spbu.ru Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Toward Accurate and Quantitative Comparative Metagenomics

PubMed Central

Nayfach, Stephen; Pollard, Katherine S.

2016-01-01

Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. PMID:27565341

Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes.

PubMed

Olson, Nathan D; Treangen, Todd J; Hill, Christopher M; Cepeda-Espinoza, Victoria; Ghurye, Jay; Koren, Sergey; Pop, Mihai

2017-08-07

Metagenomic samples are snapshots of complex ecosystems at work. They comprise hundreds of known and unknown species, contain multiple strain variants and vary greatly within and across environments. Many microbes found in microbial communities are not easily grown in culture making their DNA sequence our only clue into their evolutionary history and biological function. Metagenomic assembly is a computational process aimed at reconstructing genes and genomes from metagenomic mixtures. Current methods have made significant strides in reconstructing DNA segments comprising operons, tandem gene arrays and syntenic blocks. Shorter, higher-throughput sequencing technologies have become the de facto standard in the field. Sequencers are now able to generate billions of short reads in only a few days. Multiple metagenomic assembly strategies, pipelines and assemblers have appeared in recent years. Owing to the inherent complexity of metagenome assembly, regardless of the assembly algorithm and sequencing method, metagenome assemblies contain errors. Recent developments in assembly validation tools have played a pivotal role in improving metagenomics assemblers. Here, we survey recent progress in the field of metagenomic assembly, provide an overview of key approaches for genomic and metagenomic assembly validation and demonstrate the insights that can be derived from assemblies through the use of assembly validation strategies. We also discuss the potential for impact of long-read technologies in metagenomics. We conclude with a discussion of future challenges and opportunities in the field of metagenomic assembly and validation. © The Author 2017. Published by Oxford University Press.

Toward Accurate and Quantitative Comparative Metagenomics.

PubMed

Nayfach, Stephen; Pollard, Katherine S

2016-08-25

Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. Copyright © 2016 Elsevier Inc. All rights reserved.

Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes.

PubMed

Papudeshi, Bhavya; Haggerty, J Matthew; Doane, Michael; Morris, Megan M; Walsh, Kevin; Beattie, Douglas T; Pande, Dnyanada; Zaeri, Parisa; Silva, Genivaldo G Z; Thompson, Fabiano; Edwards, Robert A; Dinsdale, Elizabeth A

2017-11-28

Microbiome/host interactions describe characteristics that affect the host's health. Shotgun metagenomics includes sequencing a random subset of the microbiome to analyze its taxonomic and metabolic potential. Reconstruction of DNA fragments into genomes from metagenomes (called metagenome-assembled genomes) assigns unknown fragments to taxa/function and facilitates discovery of novel organisms. Genome reconstruction incorporates sequence assembly and sorting of assembled sequences into bins, characteristic of a genome. However, the microbial community composition, including taxonomic and phylogenetic diversity may influence genome reconstruction. We determine the optimal reconstruction method for four microbiome projects that had variable sequencing platforms (IonTorrent and Illumina), diversity (high or low), and environment (coral reefs and kelp forests), using a set of parameters to select for optimal assembly and binning tools. We tested the effects of the assembly and binning processes on population genome reconstruction using 105 marine metagenomes from 4 projects. Reconstructed genomes were obtained from each project using 3 assemblers (IDBA, MetaVelvet, and SPAdes) and 2 binning tools (GroopM and MetaBat). We assessed the efficiency of assemblers using statistics that including contig continuity and contig chimerism and the effectiveness of binning tools using genome completeness and taxonomic identification. We concluded that SPAdes, assembled more contigs (143,718 ± 124 contigs) of longer length (N50 = 1632 ± 108 bp), and incorporated the most sequences (sequences-assembled = 19.65%). The microbial richness and evenness were maintained across the assembly, suggesting low contig chimeras. SPAdes assembly was responsive to the biological and technological variations within the project, compared with other assemblers. Among binning tools, we conclude that MetaBat produced bins with less variation in GC content (average standard deviation: 1

EBI metagenomics in 2016 - an expanding and evolving resource for the analysis and archiving of metagenomic data

PubMed Central

Mitchell, Alex; Bucchini, Francois; Cochrane, Guy; Denise, Hubert; Hoopen, Petra ten; Fraser, Matthew; Pesseat, Sebastien; Potter, Simon; Scheremetjew, Maxim; Sterk, Peter; Finn, Robert D.

2016-01-01

EBI metagenomics (https://www.ebi.ac.uk/metagenomics/) is a freely available hub for the analysis and archiving of metagenomic and metatranscriptomic data. Over the last 2 years, the resource has undergone rapid growth, with an increase of over five-fold in the number of processed samples and consequently represents one of the largest resources of analysed shotgun metagenomes. Here, we report the status of the resource in 2016 and give an overview of new developments. In particular, we describe updates to data content, a complete overhaul of the analysis pipeline, streamlining of data presentation via the website and the development of a new web based tool to compare functional analyses of sequence runs within a study. We also highlight two of the higher profile projects that have been analysed using the resource in the last year: the oceanographic projects Ocean Sampling Day and Tara Oceans. PMID:26582919

Environmental Metagenomics: The Data Assembly and Data Analysis Perspectives

NASA Astrophysics Data System (ADS)

Kumar, Vinay; Maitra, S. S.; Shukla, Rohit Nandan

2015-03-01

Novel gene finding is one of the emerging fields in the environmental research. In the past decades the research was focused mainly on the discovery of microorganisms which were capable of degrading a particular compound. A lot of methods are available in literature about the cultivation and screening of these novel microorganisms. All of these methods are efficient for screening of microbes which can be cultivated in the laboratory. Microorganisms which live in extreme conditions like hot springs, frozen glaciers, acid mine drainage, etc. cannot be cultivated in the laboratory, this is because of incomplete knowledge about their growth requirements like temperature, nutrients and their mutual dependence on each other. The microbes that can be cultivated correspond only to less than 1 % of the total microbes which are present in the earth. Rest of the 99 % of uncultivated majority remains inaccessible. Metagenomics transcends the culture requirements of microbes. In metagenomics DNA is directly extracted from the environmental samples such as soil, seawater, acid mine drainage etc., followed by construction and screening of metagenomic library. With the ongoing research, a huge amount of metagenomic data is accumulating. Understanding this data is an essential step to extract novel genes of industrial importance. Various bioinformatics tools have been designed to analyze and annotate the data produced from the metagenome. The Bio-informatic requirements of metagenomics data analysis are different in theory and practice. This paper reviews the tools that are available for metagenomic data analysis and the capability such tools—what they can do and their web availability.

MG-Digger: An Automated Pipeline to Search for Giant Virus-Related Sequences in Metagenomes

PubMed Central

Verneau, Jonathan; Levasseur, Anthony; Raoult, Didier; La Scola, Bernard; Colson, Philippe

2016-01-01

The number of metagenomic studies conducted each year is growing dramatically. Storage and analysis of such big data is difficult and time-consuming. Interestingly, analysis shows that environmental and human metagenomes include a significant amount of non-annotated sequences, representing a ‘dark matter.’ We established a bioinformatics pipeline that automatically detects metagenome reads matching query sequences from a given set and applied this tool to the detection of sequences matching large and giant DNA viral members of the proposed order Megavirales or virophages. A total of 1,045 environmental and human metagenomes (≈ 1 Terabase) were collected, processed, and stored on our bioinformatics server. In addition, nucleotide and protein sequences from 93 Megavirales representatives, including 19 giant viruses of amoeba, and 5 virophages, were collected. The pipeline was generated by scripts written in Python language and entitled MG-Digger. Metagenomes previously found to contain megavirus-like sequences were tested as controls. MG-Digger was able to annotate 100s of metagenome sequences as best matching those of giant viruses. These sequences were most often found to be similar to phycodnavirus or mimivirus sequences, but included reads related to recently available pandoraviruses, Pithovirus sibericum, and faustoviruses. Compared to other tools, MG-Digger combined stand-alone use on Linux or Windows operating systems through a user-friendly interface, implementation of ready-to-use customized metagenome databases and query sequence databases, adjustable parameters for BLAST searches, and creation of output files containing selected reads with best match identification. Compared to Metavir 2, a reference tool in viral metagenome analysis, MG-Digger detected 8% more true positive Megavirales-related reads in a control metagenome. The present work shows that massive, automated and recurrent analyses of metagenomes are effective in improving knowledge about

Challenges and opportunities in understanding microbial communities with metagenome assembly (accompanied by IPython Notebook tutorial)

DOE PAGES

Howe, Adina; Chain, Patrick S. G.

2015-07-09

Metagenomic investigations hold great promise for informing the genetics, physiology, and ecology of environmental microorganisms. Current challenges for metagenomic analysis are related to our ability to connect the dots between sequencing reads, their population of origin, and their encoding functions. Assembly-based methods reduce dataset size by extending overlapping reads into larger contiguous sequences (contigs), providing contextual information for genetic sequences that does not rely on existing references. These methods, however, tend to be computationally intensive and are again challenged by sequencing errors as well as by genomic repeats. While numerous tools have been developed based on these methodological concepts, theymore » present confounding choices and training requirements to metagenomic investigators. To help with accessibility to assembly tools, this review also includes an IPython Notebook metagenomic assembly tutorial. This tutorial has instructions for execution any operating system using Amazon Elastic Cloud Compute and guides users through downloading, assembly, and mapping reads to contigs of a mock microbiome metagenome. Despite its challenges, metagenomic analysis has already revealed novel insights into many environments on Earth. As software, training, and data continue to emerge, metagenomic data access and its discoveries will to grow.« less

Challenges and opportunities in understanding microbial communities with metagenome assembly (accompanied by IPython Notebook tutorial)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Howe, Adina; Chain, Patrick S. G.

Metagenomic investigations hold great promise for informing the genetics, physiology, and ecology of environmental microorganisms. Current challenges for metagenomic analysis are related to our ability to connect the dots between sequencing reads, their population of origin, and their encoding functions. Assembly-based methods reduce dataset size by extending overlapping reads into larger contiguous sequences (contigs), providing contextual information for genetic sequences that does not rely on existing references. These methods, however, tend to be computationally intensive and are again challenged by sequencing errors as well as by genomic repeats. While numerous tools have been developed based on these methodological concepts, theymore » present confounding choices and training requirements to metagenomic investigators. To help with accessibility to assembly tools, this review also includes an IPython Notebook metagenomic assembly tutorial. This tutorial has instructions for execution any operating system using Amazon Elastic Cloud Compute and guides users through downloading, assembly, and mapping reads to contigs of a mock microbiome metagenome. Despite its challenges, metagenomic analysis has already revealed novel insights into many environments on Earth. As software, training, and data continue to emerge, metagenomic data access and its discoveries will to grow.« less

Fizzy: feature subset selection for metagenomics.

PubMed

Ditzler, Gregory; Morrison, J Calvin; Lan, Yemin; Rosen, Gail L

2015-11-04

Some of the current software tools for comparative metagenomics provide ecologists with the ability to investigate and explore bacterial communities using α- & β-diversity. Feature subset selection--a sub-field of machine learning--can also provide a unique insight into the differences between metagenomic or 16S phenotypes. In particular, feature subset selection methods can obtain the operational taxonomic units (OTUs), or functional features, that have a high-level of influence on the condition being studied. For example, in a previous study we have used information-theoretic feature selection to understand the differences between protein family abundances that best discriminate between age groups in the human gut microbiome. We have developed a new Python command line tool, which is compatible with the widely adopted BIOM format, for microbial ecologists that implements information-theoretic subset selection methods for biological data formats. We demonstrate the software tools capabilities on publicly available datasets. We have made the software implementation of Fizzy available to the public under the GNU GPL license. The standalone implementation can be found at http://github.com/EESI/Fizzy.

Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing

PubMed Central

Tsai, Yu-Chih; Deming, Clayton; Segre, Julia A.; Kong, Heidi H.; Korlach, Jonas

2016-01-01

ABSTRACT Deep metagenomic shotgun sequencing has emerged as a powerful tool to interrogate composition and function of complex microbial communities. Computational approaches to assemble genome fragments have been demonstrated to be an effective tool for de novo reconstruction of genomes from these communities. However, the resultant “genomes” are typically fragmented and incomplete due to the limited ability of short-read sequence data to assemble complex or low-coverage regions. Here, we use single-molecule, real-time (SMRT) sequencing to reconstruct a high-quality, closed genome of a previously uncharacterized Corynebacterium simulans and its companion bacteriophage from a skin metagenomic sample. Considerable improvement in assembly quality occurs in hybrid approaches incorporating short-read data, with even relatively small amounts of long-read data being sufficient to improve metagenome reconstruction. Using short-read data to evaluate strain variation of this C. simulans in its skin community at single-nucleotide resolution, we observed a dominant C. simulans strain with moderate allelic heterozygosity throughout the population. We demonstrate the utility of SMRT sequencing and hybrid approaches in metagenome quantitation, reconstruction, and annotation. PMID:26861018

MPD: a pathogen genome and metagenome database

PubMed Central

Zhang, Tingting; Miao, Jiaojiao; Han, Na; Qiang, Yujun; Zhang, Wen

2018-01-01

Abstract Advances in high-throughput sequencing have led to unprecedented growth in the amount of available genome sequencing data, especially for bacterial genomes, which has been accompanied by a challenge for the storage and management of such huge datasets. To facilitate bacterial research and related studies, we have developed the Mypathogen database (MPD), which provides access to users for searching, downloading, storing and sharing bacterial genomics data. The MPD represents the first pathogenic database for microbial genomes and metagenomes, and currently covers pathogenic microbial genomes (6604 genera, 11 071 species, 41 906 strains) and metagenomic data from host, air, water and other sources (28 816 samples). The MPD also functions as a management system for statistical and storage data that can be used by different organizations, thereby facilitating data sharing among different organizations and research groups. A user-friendly local client tool is provided to maintain the steady transmission of big sequencing data. The MPD is a useful tool for analysis and management in genomic research, especially for clinical Centers for Disease Control and epidemiological studies, and is expected to contribute to advancing knowledge on pathogenic bacteria genomes and metagenomes. Database URL: http://data.mypathogen.org PMID:29917040

The MG-RAST Metagenomics Database and Portal in 2015

DOE PAGES

Wilke, Andreas; Bischof, Jared; Gerlach, Wolfgang; ...

2015-12-09

MG-RAST (http://metagenomics.anl.gov) is an opensubmission data portal for processing, analyzing, sharing and disseminating metagenomic datasets. Currently, the system hosts over 200 000 datasets and is continuously updated. The volume of submissions has increased 4-fold over the past 24 months, now averaging 4 terabasepairs per month. In addition to several new features, we report changes to the analysis workflow and the technologies used to scale the pipeline up to the required throughput levels. Lastly, to show possible uses for the data from MG-RAST, we present several examples integrating data and analyses from MG-RAST into popular third-party analysis tools or sequence alignmentmore » tools.« less

Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes

PubMed Central

Nayfach, Stephen; Bradley, Patrick H.; Wyman, Stacia K.; Laurent, Timothy J.; Williams, Alex; Eisen, Jonathan A.; Pollard, Katherine S.; Sharpton, Thomas J.

2015-01-01

Shotgun metagenomic DNA sequencing is a widely applicable tool for characterizing the functions that are encoded by microbial communities. Several bioinformatic tools can be used to functionally annotate metagenomes, allowing researchers to draw inferences about the functional potential of the community and to identify putative functional biomarkers. However, little is known about how decisions made during annotation affect the reliability of the results. Here, we use statistical simulations to rigorously assess how to optimize annotation accuracy and speed, given parameters of the input data like read length and library size. We identify best practices in metagenome annotation and use them to guide the development of the Shotgun Metagenome Annotation Pipeline (ShotMAP). ShotMAP is an analytically flexible, end-to-end annotation pipeline that can be implemented either on a local computer or a cloud compute cluster. We use ShotMAP to assess how different annotation databases impact the interpretation of how marine metagenome and metatranscriptome functional capacity changes across seasons. We also apply ShotMAP to data obtained from a clinical microbiome investigation of inflammatory bowel disease. This analysis finds that gut microbiota collected from Crohn’s disease patients are functionally distinct from gut microbiota collected from either ulcerative colitis patients or healthy controls, with differential abundance of metabolic pathways related to host-microbiome interactions that may serve as putative biomarkers of disease. PMID:26565399

Signal Processing for Metagenomics: Extracting Information from the Soup

PubMed Central

Rosen, Gail L.; Sokhansanj, Bahrad A.; Polikar, Robi; Bruns, Mary Ann; Russell, Jacob; Garbarine, Elaine; Essinger, Steve; Yok, Non

2009-01-01

Traditionally, studies in microbial genomics have focused on single-genomes from cultured species, thereby limiting their focus to the small percentage of species that can be cultured outside their natural environment. Fortunately, recent advances in high-throughput sequencing and computational analyses have ushered in the new field of metagenomics, which aims to decode the genomes of microbes from natural communities without the need for cultivation. Although metagenomic studies have shed a great deal of insight into bacterial diversity and coding capacity, several computational challenges remain due to the massive size and complexity of metagenomic sequence data. Current tools and techniques are reviewed in this paper which address challenges in 1) genomic fragment annotation, 2) phylogenetic reconstruction, 3) functional classification of samples, and 4) interpreting complementary metaproteomics and metametabolomics data. Also surveyed are important applications of metagenomic studies, including microbial forensics and the roles of microbial communities in shaping human health and soil ecology. PMID:20436876

Random whole metagenomic sequencing for forensic discrimination of soils.

PubMed

Khodakova, Anastasia S; Smith, Renee J; Burgoyne, Leigh; Abarno, Damien; Linacre, Adrian

2014-01-01

Here we assess the ability of random whole metagenomic sequencing approaches to discriminate between similar soils from two geographically distinct urban sites for application in forensic science. Repeat samples from two parklands in residential areas separated by approximately 3 km were collected and the DNA was extracted. Shotgun, whole genome amplification (WGA) and single arbitrarily primed DNA amplification (AP-PCR) based sequencing techniques were then used to generate soil metagenomic profiles. Full and subsampled metagenomic datasets were then annotated against M5NR/M5RNA (taxonomic classification) and SEED Subsystems (metabolic classification) databases. Further comparative analyses were performed using a number of statistical tools including: hierarchical agglomerative clustering (CLUSTER); similarity profile analysis (SIMPROF); non-metric multidimensional scaling (NMDS); and canonical analysis of principal coordinates (CAP) at all major levels of taxonomic and metabolic classification. Our data showed that shotgun and WGA-based approaches generated highly similar metagenomic profiles for the soil samples such that the soil samples could not be distinguished accurately. An AP-PCR based approach was shown to be successful at obtaining reproducible site-specific metagenomic DNA profiles, which in turn were employed for successful discrimination of visually similar soil samples collected from two different locations.

Fizzy. Feature subset selection for metagenomics

DOE PAGES

Ditzler, Gregory; Morrison, J. Calvin; Lan, Yemin; ...

2015-11-04

Background: Some of the current software tools for comparative metagenomics provide ecologists with the ability to investigate and explore bacterial communities using α– & β–diversity. Feature subset selection – a sub-field of machine learning – can also provide a unique insight into the differences between metagenomic or 16S phenotypes. In particular, feature subset selection methods can obtain the operational taxonomic units (OTUs), or functional features, that have a high-level of influence on the condition being studied. For example, in a previous study we have used information-theoretic feature selection to understand the differences between protein family abundances that best discriminate betweenmore » age groups in the human gut microbiome. Results: We have developed a new Python command line tool, which is compatible with the widely adopted BIOM format, for microbial ecologists that implements information-theoretic subset selection methods for biological data formats. We demonstrate the software tools capabilities on publicly available datasets. Conclusions: We have made the software implementation of Fizzy available to the public under the GNU GPL license. The standalone implementation can be found at http://github.com/EESI/Fizzy.« less

In-depth resistome analysis by targeted metagenomics.

PubMed

Lanza, Val F; Baquero, Fernando; Martínez, José Luís; Ramos-Ruíz, Ricardo; González-Zorn, Bruno; Andremont, Antoine; Sánchez-Valenzuela, Antonio; Ehrlich, Stanislav Dusko; Kennedy, Sean; Ruppé, Etienne; van Schaik, Willem; Willems, Rob J; de la Cruz, Fernando; Coque, Teresa M

2018-01-15

Antimicrobial resistance is a major global health challenge. Metagenomics allows analyzing the presence and dynamics of "resistomes" (the ensemble of genes encoding antimicrobial resistance in a given microbiome) in disparate microbial ecosystems. However, the low sensitivity and specificity of available metagenomic methods preclude the detection of minority populations (often present below their detection threshold) and/or the identification of allelic variants that differ in the resulting phenotype. Here, we describe a novel strategy that combines targeted metagenomics using last generation in-solution capture platforms, with novel bioinformatics tools to establish a standardized framework that allows both quantitative and qualitative analyses of resistomes. We developed ResCap, a targeted sequence capture platform based on SeqCapEZ (NimbleGene) technology, which includes probes for 8667 canonical resistance genes (7963 antibiotic resistance genes and 704 genes conferring resistance to metals or biocides), and 2517 relaxase genes (plasmid markers) and 78,600 genes homologous to the previous identified targets (47,806 for antibiotics and 30,794 for biocides or metals). Its performance was compared with metagenomic shotgun sequencing (MSS) for 17 fecal samples (9 humans, 8 swine). ResCap significantly improves MSS to detect "gene abundance" (from 2.0 to 83.2%) and "gene diversity" (26 versus 14.9 genes unequivocally detected per sample per million of reads; the number of reads unequivocally mapped increasing up to 300-fold by using ResCap), which were calculated using novel bioinformatic tools. ResCap also facilitated the analysis of novel genes potentially involved in the resistance to antibiotics, metals, biocides, or any combination thereof. ResCap, the first targeted sequence capture, specifically developed to analyze resistomes, greatly enhances the sensitivity and specificity of available metagenomic methods and offers the possibility to analyze genes

RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets.

PubMed

Scheuch, Matthias; Höper, Dirk; Beer, Martin

2015-03-03

Fuelled by the advent and subsequent development of next generation sequencing technologies, metagenomics became a powerful tool for the analysis of microbial communities both scientifically and diagnostically. The biggest challenge is the extraction of relevant information from the huge sequence datasets generated for metagenomics studies. Although a plethora of tools are available, data analysis is still a bottleneck. To overcome the bottleneck of data analysis, we developed an automated computational workflow called RIEMS - Reliable Information Extraction from Metagenomic Sequence datasets. RIEMS assigns every individual read sequence within a dataset taxonomically by cascading different sequence analyses with decreasing stringency of the assignments using various software applications. After completion of the analyses, the results are summarised in a clearly structured result protocol organised taxonomically. The high accuracy and performance of RIEMS analyses were proven in comparison with other tools for metagenomics data analysis using simulated sequencing read datasets. RIEMS has the potential to fill the gap that still exists with regard to data analysis for metagenomics studies. The usefulness and power of RIEMS for the analysis of genuine sequencing datasets was demonstrated with an early version of RIEMS in 2011 when it was used to detect the orthobunyavirus sequences leading to the discovery of Schmallenberg virus.

New Hydrocarbon Degradation Pathways in the Microbial Metagenome from Brazilian Petroleum Reservoirs

PubMed Central

Sierra-García, Isabel Natalia; Correa Alvarez, Javier; Pantaroto de Vasconcellos, Suzan; Pereira de Souza, Anete; dos Santos Neto, Eugenio Vaz; de Oliveira, Valéria Maia

2014-01-01

Current knowledge of the microbial diversity and metabolic pathways involved in hydrocarbon degradation in petroleum reservoirs is still limited, mostly due to the difficulty in recovering the complex community from such an extreme environment. Metagenomics is a valuable tool to investigate the genetic and functional diversity of previously uncultured microorganisms in natural environments. Using a function-driven metagenomic approach, we investigated the metabolic abilities of microbial communities in oil reservoirs. Here, we describe novel functional metabolic pathways involved in the biodegradation of aromatic compounds in a metagenomic library obtained from an oil reservoir. Although many of the deduced proteins shared homology with known enzymes of different well-described aerobic and anaerobic catabolic pathways, the metagenomic fragments did not contain the complete clusters known to be involved in hydrocarbon degradation. Instead, the metagenomic fragments comprised genes belonging to different pathways, showing novel gene arrangements. These results reinforce the potential of the metagenomic approach for the identification and elucidation of new genes and pathways in poorly studied environments and contribute to a broader perspective on the hydrocarbon degradation processes in petroleum reservoirs. PMID:24587220

Bayesian mixture analysis for metagenomic community profiling.

PubMed

Morfopoulou, Sofia; Plagnol, Vincent

2015-09-15

Deep sequencing of clinical samples is now an established tool for the detection of infectious pathogens, with direct medical applications. The large amount of data generated produces an opportunity to detect species even at very low levels, provided that computational tools can effectively profile the relevant metagenomic communities. Data interpretation is complicated by the fact that short sequencing reads can match multiple organisms and by the lack of completeness of existing databases, in particular for viral pathogens. Here we present metaMix, a Bayesian mixture model framework for resolving complex metagenomic mixtures. We show that the use of parallel Monte Carlo Markov chains for the exploration of the species space enables the identification of the set of species most likely to contribute to the mixture. We demonstrate the greater accuracy of metaMix compared with relevant methods, particularly for profiling complex communities consisting of several related species. We designed metaMix specifically for the analysis of deep transcriptome sequencing datasets, with a focus on viral pathogen detection; however, the principles are generally applicable to all types of metagenomic mixtures. metaMix is implemented as a user friendly R package, freely available on CRAN: http://cran.r-project.org/web/packages/metaMix sofia.morfopoulou.10@ucl.ac.uk Supplementary data are available at Bionformatics online. © The Author 2015. Published by Oxford University Press.

Activity screening of environmental metagenomic libraries reveals novel carboxylesterase families

DOE Office of Scientific and Technical Information (OSTI.GOV)

Popovic, Ana; Hai, Tran; Tchigvintsev, Anatoly

Metagenomics has made accessible an enormous reserve of global biochemical diversity. In order to tap into this vast resource of novel enzymes, we have screened over one million clones from metagenome DNA libraries derived from sixteen different environments for carboxylesterase activity and identified 714 positive hits. Here, we validated the esterase activity of 80 selected genes, which belong to 17 different protein families including unknown and cyclase-like proteins. Three metagenomic enzymes exhibited lipase activity, and seven proteins showed polyester depolymerization activity against polylactic acid and polycaprolactone. Detailed biochemical characterization of four new enzymes revealed their substrate preference, whereas their catalyticmore » residues were identified using site-directed mutagenesis. The crystal structure of the metal-ion dependent esterase MGS0169 from the amidohydrolase superfamily revealed a novel active site with a bound unknown ligand. Thus, activity-centered metagenomics has revealed diverse enzymes and novel families of microbial carboxylesterases, whose activity could not have been predicted using bioinformatics tools.« less

Activity screening of environmental metagenomic libraries reveals novel carboxylesterase families

DOE PAGES

Popovic, Ana; Hai, Tran; Tchigvintsev, Anatoly; ...

2017-03-08

Metagenomics has made accessible an enormous reserve of global biochemical diversity. In order to tap into this vast resource of novel enzymes, we have screened over one million clones from metagenome DNA libraries derived from sixteen different environments for carboxylesterase activity and identified 714 positive hits. Here, we validated the esterase activity of 80 selected genes, which belong to 17 different protein families including unknown and cyclase-like proteins. Three metagenomic enzymes exhibited lipase activity, and seven proteins showed polyester depolymerization activity against polylactic acid and polycaprolactone. Detailed biochemical characterization of four new enzymes revealed their substrate preference, whereas their catalyticmore » residues were identified using site-directed mutagenesis. The crystal structure of the metal-ion dependent esterase MGS0169 from the amidohydrolase superfamily revealed a novel active site with a bound unknown ligand. Thus, activity-centered metagenomics has revealed diverse enzymes and novel families of microbial carboxylesterases, whose activity could not have been predicted using bioinformatics tools.« less

Culture-independent discovery of natural products from soil metagenomes.

PubMed

Katz, Micah; Hover, Bradley M; Brady, Sean F

2016-03-01

Bacterial natural products have proven to be invaluable starting points in the development of many currently used therapeutic agents. Unfortunately, traditional culture-based methods for natural product discovery have been deemphasized by pharmaceutical companies due in large part to high rediscovery rates. Culture-independent, or "metagenomic," methods, which rely on the heterologous expression of DNA extracted directly from environmental samples (eDNA), have the potential to provide access to metabolites encoded by a large fraction of the earth's microbial biosynthetic diversity. As soil is both ubiquitous and rich in bacterial diversity, it is an appealing starting point for culture-independent natural product discovery efforts. This review provides an overview of the history of soil metagenome-driven natural product discovery studies and elaborates on the recent development of new tools for sequence-based, high-throughput profiling of environmental samples used in discovering novel natural product biosynthetic gene clusters. We conclude with several examples of these new tools being employed to facilitate the recovery of novel secondary metabolite encoding gene clusters from soil metagenomes and the subsequent heterologous expression of these clusters to produce bioactive small molecules.

Strain-Level Metagenomic Analysis of the Fermented Dairy Beverage Nunu Highlights Potential Food Safety Risks

PubMed Central

Walsh, Aaron M.; Crispie, Fiona; Daari, Kareem; O'Sullivan, Orla; Martin, Jennifer C.; Arthur, Cornelius T.; Claesson, Marcus J.; Scott, Karen P.

2017-01-01

ABSTRACT The rapid detection of pathogenic strains in food products is essential for the prevention of disease outbreaks. It has already been demonstrated that whole-metagenome shotgun sequencing can be used to detect pathogens in food but, until recently, strain-level detection of pathogens has relied on whole-metagenome assembly, which is a computationally demanding process. Here we demonstrated that three short-read-alignment-based methods, i.e., MetaMLST, PanPhlAn, and StrainPhlAn, could accurately and rapidly identify pathogenic strains in spinach metagenomes that had been intentionally spiked with Shiga toxin-producing Escherichia coli in a previous study. Subsequently, we employed the methods, in combination with other metagenomics approaches, to assess the safety of nunu, a traditional Ghanaian fermented milk product that is produced by the spontaneous fermentation of raw cow milk. We showed that nunu samples were frequently contaminated with bacteria associated with the bovine gut and, worryingly, we detected putatively pathogenic E. coli and Klebsiella pneumoniae strains in a subset of nunu samples. Ultimately, our work establishes that short-read-alignment-based bioinformatics approaches are suitable food safety tools, and we describe a real-life example of their utilization. IMPORTANCE Foodborne pathogens are responsible for millions of illnesses each year. Here we demonstrate that short-read-alignment-based bioinformatics tools can accurately and rapidly detect pathogenic strains in food products by using shotgun metagenomics data. The methods used here are considerably faster than both traditional culturing methods and alternative bioinformatics approaches that rely on metagenome assembly; therefore, they can potentially be used for more high-throughput food safety testing. Overall, our results suggest that whole-metagenome sequencing can be used as a practical food safety tool to prevent diseases or to link outbreaks to specific food products. PMID

Strain-Level Metagenomic Analysis of the Fermented Dairy Beverage Nunu Highlights Potential Food Safety Risks.

PubMed

Walsh, Aaron M; Crispie, Fiona; Daari, Kareem; O'Sullivan, Orla; Martin, Jennifer C; Arthur, Cornelius T; Claesson, Marcus J; Scott, Karen P; Cotter, Paul D

2017-08-15

The rapid detection of pathogenic strains in food products is essential for the prevention of disease outbreaks. It has already been demonstrated that whole-metagenome shotgun sequencing can be used to detect pathogens in food but, until recently, strain-level detection of pathogens has relied on whole-metagenome assembly, which is a computationally demanding process. Here we demonstrated that three short-read-alignment-based methods, i.e., MetaMLST, PanPhlAn, and StrainPhlAn, could accurately and rapidly identify pathogenic strains in spinach metagenomes that had been intentionally spiked with Shiga toxin-producing Escherichia coli in a previous study. Subsequently, we employed the methods, in combination with other metagenomics approaches, to assess the safety of nunu, a traditional Ghanaian fermented milk product that is produced by the spontaneous fermentation of raw cow milk. We showed that nunu samples were frequently contaminated with bacteria associated with the bovine gut and, worryingly, we detected putatively pathogenic E. coli and Klebsiella pneumoniae strains in a subset of nunu samples. Ultimately, our work establishes that short-read-alignment-based bioinformatics approaches are suitable food safety tools, and we describe a real-life example of their utilization. IMPORTANCE Foodborne pathogens are responsible for millions of illnesses each year. Here we demonstrate that short-read-alignment-based bioinformatics tools can accurately and rapidly detect pathogenic strains in food products by using shotgun metagenomics data. The methods used here are considerably faster than both traditional culturing methods and alternative bioinformatics approaches that rely on metagenome assembly; therefore, they can potentially be used for more high-throughput food safety testing. Overall, our results suggest that whole-metagenome sequencing can be used as a practical food safety tool to prevent diseases or to link outbreaks to specific food products. Copyright �

Reconstructing the Genomic Content of Microbiome Taxa through Shotgun Metagenomic Deconvolution

PubMed Central

Carr, Rogan; Shen-Orr, Shai S.; Borenstein, Elhanan

2013-01-01

Metagenomics has transformed our understanding of the microbial world, allowing researchers to bypass the need to isolate and culture individual taxa and to directly characterize both the taxonomic and gene compositions of environmental samples. However, associating the genes found in a metagenomic sample with the specific taxa of origin remains a critical challenge. Existing binning methods, based on nucleotide composition or alignment to reference genomes allow only a coarse-grained classification and rely heavily on the availability of sequenced genomes from closely related taxa. Here, we introduce a novel computational framework, integrating variation in gene abundances across multiple samples with taxonomic abundance data to deconvolve metagenomic samples into taxa-specific gene profiles and to reconstruct the genomic content of community members. This assembly-free method is not bounded by various factors limiting previously described methods of metagenomic binning or metagenomic assembly and represents a fundamentally different approach to metagenomic-based genome reconstruction. An implementation of this framework is available at http://elbo.gs.washington.edu/software.html. We first describe the mathematical foundations of our framework and discuss considerations for implementing its various components. We demonstrate the ability of this framework to accurately deconvolve a set of metagenomic samples and to recover the gene content of individual taxa using synthetic metagenomic samples. We specifically characterize determinants of prediction accuracy and examine the impact of annotation errors on the reconstructed genomes. We finally apply metagenomic deconvolution to samples from the Human Microbiome Project, successfully reconstructing genus-level genomic content of various microbial genera, based solely on variation in gene count. These reconstructed genera are shown to correctly capture genus-specific properties. With the accumulation of metagenomic

MetaGenomic Assembly by Merging (MeGAMerge)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Scholz Chien-Chi Lo, Matthew B.

2015-08-03

"MetaGenomic Assembly by Merging" (MeGAMerge)Is a novel method of merging of multiple genomic assembly or long read data sources for assembly by use of internal trimming/filtering of data, followed by use of two 3rd party tools to merge data by overlap based assembly.

WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequencing data.

PubMed

Devlin, Joseph C; Battaglia, Thomas; Blaser, Martin J; Ruggles, Kelly V

2018-06-25

Exploration of large data sets, such as shotgun metagenomic sequence or expression data, by biomedical experts and medical professionals remains as a major bottleneck in the scientific discovery process. Although tools for this purpose exist for 16S ribosomal RNA sequencing analysis, there is a growing but still insufficient number of user-friendly interactive visualization workflows for easy data exploration and figure generation. The development of such platforms for this purpose is necessary to accelerate and streamline microbiome laboratory research. We developed the Workflow Hub for Automated Metagenomic Exploration (WHAM!) as a web-based interactive tool capable of user-directed data visualization and statistical analysis of annotated shotgun metagenomic and metatranscriptomic data sets. WHAM! includes exploratory and hypothesis-based gene and taxa search modules for visualizing differences in microbial taxa and gene family expression across experimental groups, and for creating publication quality figures without the need for command line interface or in-house bioinformatics. WHAM! is an interactive and customizable tool for downstream metagenomic and metatranscriptomic analysis providing a user-friendly interface allowing for easy data exploration by microbiome and ecological experts to facilitate discovery in multi-dimensional and large-scale data sets.

Open resource metagenomics: a model for sharing metagenomic libraries.

PubMed

Neufeld, J D; Engel, K; Cheng, J; Moreno-Hagelsieb, G; Rose, D R; Charles, T C

2011-11-30

Both sequence-based and activity-based exploitation of environmental DNA have provided unprecedented access to the genomic content of cultivated and uncultivated microorganisms. Although researchers deposit microbial strains in culture collections and DNA sequences in databases, activity-based metagenomic studies typically only publish sequences from the hits retrieved from specific screens. Physical metagenomic libraries, conceptually similar to entire sequence datasets, are usually not straightforward to obtain by interested parties subsequent to publication. In order to facilitate unrestricted distribution of metagenomic libraries, we propose the adoption of open resource metagenomics, in line with the trend towards open access publishing, and similar to culture- and mutant-strain collections that have been the backbone of traditional microbiology and microbial genetics. The concept of open resource metagenomics includes preparation of physical DNA libraries, preferably in versatile vectors that facilitate screening in a diversity of host organisms, and pooling of clones so that single aliquots containing complete libraries can be easily distributed upon request. Database deposition of associated metadata and sequence data for each library provides researchers with information to select the most appropriate libraries for further research projects. As a starting point, we have established the Canadian MetaMicroBiome Library (CM(2)BL [1]). The CM(2)BL is a publicly accessible collection of cosmid libraries containing environmental DNA from soils collected from across Canada, spanning multiple biomes. The libraries were constructed such that the cloned DNA can be easily transferred to Gateway® compliant vectors, facilitating functional screening in virtually any surrogate microbial host for which there are available plasmid vectors. The libraries, which we are placing in the public domain, will be distributed upon request without restriction to members of both the

Open resource metagenomics: a model for sharing metagenomic libraries

PubMed Central

Neufeld, J.D.; Engel, K.; Cheng, J.; Moreno-Hagelsieb, G.; Rose, D.R.; Charles, T.C.

2011-01-01

Both sequence-based and activity-based exploitation of environmental DNA have provided unprecedented access to the genomic content of cultivated and uncultivated microorganisms. Although researchers deposit microbial strains in culture collections and DNA sequences in databases, activity-based metagenomic studies typically only publish sequences from the hits retrieved from specific screens. Physical metagenomic libraries, conceptually similar to entire sequence datasets, are usually not straightforward to obtain by interested parties subsequent to publication. In order to facilitate unrestricted distribution of metagenomic libraries, we propose the adoption of open resource metagenomics, in line with the trend towards open access publishing, and similar to culture- and mutant-strain collections that have been the backbone of traditional microbiology and microbial genetics. The concept of open resource metagenomics includes preparation of physical DNA libraries, preferably in versatile vectors that facilitate screening in a diversity of host organisms, and pooling of clones so that single aliquots containing complete libraries can be easily distributed upon request. Database deposition of associated metadata and sequence data for each library provides researchers with information to select the most appropriate libraries for further research projects. As a starting point, we have established the Canadian MetaMicroBiome Library (CM2BL [1]). The CM2BL is a publicly accessible collection of cosmid libraries containing environmental DNA from soils collected from across Canada, spanning multiple biomes. The libraries were constructed such that the cloned DNA can be easily transferred to Gateway® compliant vectors, facilitating functional screening in virtually any surrogate microbial host for which there are available plasmid vectors. The libraries, which we are placing in the public domain, will be distributed upon request without restriction to members of both the

Genomics and metagenomics in medical microbiology.

PubMed

Padmanabhan, Roshan; Mishra, Ajay Kumar; Raoult, Didier; Fournier, Pierre-Edouard

2013-12-01

Over the last two decades, sequencing tools have evolved from laborious time-consuming methodologies to real-time detection and deciphering of genomic DNA. Genome sequencing, especially using next generation sequencing (NGS) has revolutionized the landscape of microbiology and infectious disease. This deluge of sequencing data has not only enabled advances in fundamental biology but also helped improve diagnosis, typing of pathogen, virulence and antibiotic resistance detection, and development of new vaccines and culture media. In addition, NGS also enabled efficient analysis of complex human micro-floras, both commensal, and pathological, through metagenomic methods, thus helping the comprehension and management of human diseases such as obesity. This review summarizes technological advances in genomics and metagenomics relevant to the field of medical microbiology. Copyright © 2013 Elsevier B.V. All rights reserved.

Whither or wither geomicrobiology in the era of 'community metagenomics'

USGS Publications Warehouse

Oremland, R.S.; Capone, D.G.; Stolz, J.F.; Fuhrman, J.

2005-01-01

Molecular techniques are valuable tools that can improve our understanding of the structure of microbial communities. They provide the ability to probe for life in all niches of the biosphere, perhaps even supplanting the need to cultivate microorganisms or to conduct ecophysiological investigations. However, an overemphasis and strict dependence on such large information-driven endeavours as environmental metagenomics could overwhelm the field, to the detriment of microbial ecology. We now call for more balanced, hypothesis-driven research efforts that couple metagenomics with classic approaches.

The metagenomic approach and causality in virology

PubMed Central

Castrignano, Silvana Beres; Nagasse-Sugahara, Teresa Keico

2015-01-01

Nowadays, the metagenomic approach has been a very important tool in the discovery of new viruses in environmental and biological samples. Here we discuss how these discoveries may help to elucidate the etiology of diseases and the criteria necessary to establish a causal association between a virus and a disease. PMID:25902566

Metagenomics: Probing pollutant fate in natural and engineered ecosystems.

PubMed

Bouhajja, Emna; Agathos, Spiros N; George, Isabelle F

2016-12-01

Polluted environments are a reservoir of microbial species able to degrade or to convert pollutants to harmless compounds. The proper management of microbial resources requires a comprehensive characterization of their genetic pool to assess the fate of contaminants and increase the efficiency of bioremediation processes. Metagenomics offers appropriate tools to describe microbial communities in their whole complexity without lab-based cultivation of individual strains. After a decade of use of metagenomics to study microbiomes, the scientific community has made significant progress in this field. In this review, we survey the main steps of metagenomics applied to environments contaminated with organic compounds or heavy metals. We emphasize technical solutions proposed to overcome encountered obstacles. We then compare two metagenomic approaches, i.e. library-based targeted metagenomics and direct sequencing of metagenomes. In the former, environmental DNA is cloned inside a host, and then clones of interest are selected based on (i) their expression of biodegradative functions or (ii) sequence homology with probes and primers designed from relevant, already known sequences. The highest score for the discovery of novel genes and degradation pathways has been achieved so far by functional screening of large clone libraries. On the other hand, direct sequencing of metagenomes without a cloning step has been more often applied to polluted environments for characterization of the taxonomic and functional composition of microbial communities and their dynamics. In this case, the analysis has focused on 16S rRNA genes and marker genes of biodegradation. Advances in next generation sequencing and in bioinformatic analysis of sequencing data have opened up new opportunities for assessing the potential of biodegradation by microbes, but annotation of collected genes is still hampered by a limited number of available reference sequences in databases. Although metagenomics

Microprocessor design for GaAs technology

NASA Astrophysics Data System (ADS)

Milutinovic, Veljko M.

Recent advances in the design of GaAs microprocessor chips are examined in chapters contributed by leading experts; the work is intended as reading material for a graduate engineering course or as a practical R&D reference. Topics addressed include the methodology used for the architecture, organization, and design of GaAs processors; GaAs device physics and circuit design; design concepts for microprocessor-based GaAs systems; a 32-bit GaAs microprocessor; a 32-bit processor implemented in GaAs JFET; and a direct coupled-FET-logic E/D-MESFET experimental RISC machine. Drawings, micrographs, and extensive circuit diagrams are provided.

Accessing the Soil Metagenome for Studies of Microbial Diversity▿ †

PubMed Central

Delmont, Tom O.; Robe, Patrick; Cecillon, Sébastien; Clark, Ian M.; Constancias, Florentin; Simonet, Pascal; Hirsch, Penny R.; Vogel, Timothy M.

2011-01-01

Soil microbial communities contain the highest level of prokaryotic diversity of any environment, and metagenomic approaches involving the extraction of DNA from soil can improve our access to these communities. Most analyses of soil biodiversity and function assume that the DNA extracted represents the microbial community in the soil, but subsequent interpretations are limited by the DNA recovered from the soil. Unfortunately, extraction methods do not provide a uniform and unbiased subsample of metagenomic DNA, and as a consequence, accurate species distributions cannot be determined. Moreover, any bias will propagate errors in estimations of overall microbial diversity and may exclude some microbial classes from study and exploitation. To improve metagenomic approaches, investigate DNA extraction biases, and provide tools for assessing the relative abundances of different groups, we explored the biodiversity of the accessible community DNA by fractioning the metagenomic DNA as a function of (i) vertical soil sampling, (ii) density gradients (cell separation), (iii) cell lysis stringency, and (iv) DNA fragment size distribution. Each fraction had a unique genetic diversity, with different predominant and rare species (based on ribosomal intergenic spacer analysis [RISA] fingerprinting and phylochips). All fractions contributed to the number of bacterial groups uncovered in the metagenome, thus increasing the DNA pool for further applications. Indeed, we were able to access a more genetically diverse proportion of the metagenome (a gain of more than 80% compared to the best single extraction method), limit the predominance of a few genomes, and increase the species richness per sequencing effort. This work stresses the difference between extracted DNA pools and the currently inaccessible complete soil metagenome. PMID:21183646

Functional metagenomics to decipher food-microbe-host crosstalk.

PubMed

Larraufie, Pierre; de Wouters, Tomas; Potocki-Veronese, Gabrielle; Blottière, Hervé M; Doré, Joël

2015-02-01

The recent developments of metagenomics permit an extremely high-resolution molecular scan of the intestinal microbiota giving new insights and opening perspectives for clinical applications. Beyond the unprecedented vision of the intestinal microbiota given by large-scale quantitative metagenomics studies, such as the EU MetaHIT project, functional metagenomics tools allow the exploration of fine interactions between food constituents, microbiota and host, leading to the identification of signals and intimate mechanisms of crosstalk, especially between bacteria and human cells. Cloning of large genome fragments, either from complex intestinal communities or from selected bacteria, allows the screening of these biological resources for bioactivity towards complex plant polymers or functional food such as prebiotics. This permitted identification of novel carbohydrate-active enzyme families involved in dietary fibre and host glycan breakdown, and highlighted unsuspected bacterial players at the top of the intestinal microbial food chain. Similarly, exposure of fractions from genomic and metagenomic clones onto human cells engineered with reporter systems to track modulation of immune response, cell proliferation or cell metabolism has allowed the identification of bioactive clones modulating key cell signalling pathways or the induction of specific genes. This opens the possibility to decipher mechanisms by which commensal bacteria or candidate probiotics can modulate the activity of cells in the intestinal epithelium or even in distal organs such as the liver, adipose tissue or the brain. Hence, in spite of our inability to culture many of the dominant microbes of the human intestine, functional metagenomics open a new window for the exploration of food-microbe-host crosstalk.

Swine Fecal Metagenomics

EPA Science Inventory

Metagenomic approaches are providing rapid and more robust means to investigate the composition and functional genetic potential of complex microbial communities. In this study, we utilized a metagenomic approach to further understand the functional diversity of the swine gut. To...

Extremozymes from metagenome: Potential applications in food processing.

PubMed

Khan, Mahejibin; Sathya, T A

2017-06-12

The long-established use of enzymes for food processing and product formulation has resulted in an increased enzyme market compounding to 7.0% annual growth rate. Advancements in molecular biology and recognition that enzymes with specific properties have application for industrial production of infant, baby and functional foods boosted research toward sourcing the genes of microorganisms for enzymes with distinctive properties. In this regard, functional metagenomics for extremozymes has gained attention on the premise that such enzymes can catalyze specific reactions. Hence, metagenomics that can isolate functional genes of unculturable extremophilic microorganisms has expanded attention as a promising tool. Developments in this field of research in relation to food sector are reviewed.

EBI metagenomics--a new resource for the analysis and archiving of metagenomic data.

PubMed

Hunter, Sarah; Corbett, Matthew; Denise, Hubert; Fraser, Matthew; Gonzalez-Beltran, Alejandra; Hunter, Christopher; Jones, Philip; Leinonen, Rasko; McAnulla, Craig; Maguire, Eamonn; Maslen, John; Mitchell, Alex; Nuka, Gift; Oisel, Arnaud; Pesseat, Sebastien; Radhakrishnan, Rajesh; Rocca-Serra, Philippe; Scheremetjew, Maxim; Sterk, Peter; Vaughan, Daniel; Cochrane, Guy; Field, Dawn; Sansone, Susanna-Assunta

2014-01-01

Metagenomics is a relatively recently established but rapidly expanding field that uses high-throughput next-generation sequencing technologies to characterize the microbial communities inhabiting different ecosystems (including oceans, lakes, soil, tundra, plants and body sites). Metagenomics brings with it a number of challenges, including the management, analysis, storage and sharing of data. In response to these challenges, we have developed a new metagenomics resource (http://www.ebi.ac.uk/metagenomics/) that allows users to easily submit raw nucleotide reads for functional and taxonomic analysis by a state-of-the-art pipeline, and have them automatically stored (together with descriptive, standards-compliant metadata) in the European Nucleotide Archive.

Current Advances on Virus Discovery and Diagnostic Role of Viral Metagenomics in Aquatic Organisms

PubMed Central

Munang'andu, Hetron M.; Mugimba, Kizito K.; Byarugaba, Denis K.; Mutoloki, Stephen; Evensen, Øystein

2017-01-01

The global expansion of the aquaculture industry has brought with it a corresponding increase of novel viruses infecting different aquatic organisms. These emerging viral pathogens have proved to be a challenge to the use of traditional cell-cultures and immunoassays for identification of new viruses especially in situations where the novel viruses are unculturable and no antibodies exist for their identification. Viral metagenomics has the potential to identify novel viruses without prior knowledge of their genomic sequence data and may provide a solution for the study of unculturable viruses. This review provides a synopsis on the contribution of viral metagenomics to the discovery of viruses infecting different aquatic organisms as well as its potential role in viral diagnostics. High throughput Next Generation sequencing (NGS) and library construction used in metagenomic projects have simplified the task of generating complete viral genomes unlike the challenge faced in traditional methods that use multiple primers targeted at different segments and VPs to generate the entire genome of a novel virus. In terms of diagnostics, studies carried out this far show that viral metagenomics has the potential to serve as a multifaceted tool able to study and identify etiological agents of single infections, co-infections, tissue tropism, profiling viral infections of different aquatic organisms, epidemiological monitoring of disease prevalence, evolutionary phylogenetic analyses, and the study of genomic diversity in quasispecies viruses. With sequencing technologies and bioinformatics analytical tools becoming cheaper and easier, we anticipate that metagenomics will soon become a routine tool for the discovery, study, and identification of novel pathogens including viruses to enable timely disease control for emerging diseases in aquaculture. PMID:28382024

Metagenomics of Thermophiles with a Focus on Discovery of Novel Thermozymes

PubMed Central

DeCastro, María-Eugenia; Rodríguez-Belmonte, Esther; González-Siso, María-Isabel

2016-01-01

Microbial populations living in environments with temperatures above 50°C (thermophiles) have been widely studied, increasing our knowledge in the composition and function of these ecological communities. Since these populations express a broad number of heat-resistant enzymes (thermozymes), they also represent an important source for novel biocatalysts that can be potentially used in industrial processes. The integrated study of the whole-community DNA from an environment, known as metagenomics, coupled with the development of next generation sequencing (NGS) technologies, has allowed the generation of large amounts of data from thermophiles. In this review, we summarize the main approaches commonly utilized for assessing the taxonomic and functional diversity of thermophiles through metagenomics, including several bioinformatics tools and some metagenome-derived methods to isolate their thermozymes. PMID:27729905

Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold

PubMed Central

Nijkamp, Jurgen F.; Pop, Mihai; Reinders, Marcel J. T.; de Ridder, Dick

2013-01-01

Motivation: Although many tools are available to study variation and its impact in single genomes, there is a lack of algorithms for finding such variation in metagenomes. This hampers the interpretation of metagenomics sequencing datasets, which are increasingly acquired in research on the (human) microbiome, in environmental studies and in the study of processes in the production of foods and beverages. Existing algorithms often depend on the use of reference genomes, which pose a problem when a metagenome of a priori unknown strain composition is studied. In this article, we develop a method to perform reference-free detection and visual exploration of genomic variation, both within a single metagenome and between metagenomes. Results: We present the MaryGold algorithm and its implementation, which efficiently detects bubble structures in contig graphs using graph decomposition. These bubbles represent variable genomic regions in closely related strains in metagenomic samples. The variation found is presented in a condensed Circos-based visualization, which allows for easy exploration and interpretation of the found variation. We validated the algorithm on two simulated datasets containing three respectively seven Escherichia coli genomes and showed that finding allelic variation in these genomes improves assemblies. Additionally, we applied MaryGold to publicly available real metagenomic datasets, enabling us to find within-sample genomic variation in the metagenomes of a kimchi fermentation process, the microbiome of a premature infant and in microbial communities living on acid mine drainage. Moreover, we used MaryGold for between-sample variation detection and exploration by comparing sequencing data sampled at different time points for both of these datasets. Availability: MaryGold has been written in C++ and Python and can be downloaded from http://bioinformatics.tudelft.nl/software Contact: d.deridder@tudelft.nl PMID:24058058

Integrative workflows for metagenomic analysis

PubMed Central

Ladoukakis, Efthymios; Kolisis, Fragiskos N.; Chatziioannou, Aristotelis A.

2014-01-01

The rapid evolution of all sequencing technologies, described by the term Next Generation Sequencing (NGS), have revolutionized metagenomic analysis. They constitute a combination of high-throughput analytical protocols, coupled to delicate measuring techniques, in order to potentially discover, properly assemble and map allelic sequences to the correct genomes, achieving particularly high yields for only a fraction of the cost of traditional processes (i.e., Sanger). From a bioinformatic perspective, this boils down to many GB of data being generated from each single sequencing experiment, rendering the management or even the storage, critical bottlenecks with respect to the overall analytical endeavor. The enormous complexity is even more aggravated by the versatility of the processing steps available, represented by the numerous bioinformatic tools that are essential, for each analytical task, in order to fully unveil the genetic content of a metagenomic dataset. These disparate tasks range from simple, nonetheless non-trivial, quality control of raw data to exceptionally complex protein annotation procedures, requesting a high level of expertise for their proper application or the neat implementation of the whole workflow. Furthermore, a bioinformatic analysis of such scale, requires grand computational resources, imposing as the sole realistic solution, the utilization of cloud computing infrastructures. In this review article we discuss different, integrative, bioinformatic solutions available, which address the aforementioned issues, by performing a critical assessment of the available automated pipelines for data management, quality control, and annotation of metagenomic data, embracing various, major sequencing technologies and applications. PMID:25478562

A user's guide to quantitative and comparative analysis of metagenomic datasets.

PubMed

Luo, Chengwei; Rodriguez-R, Luis M; Konstantinidis, Konstantinos T

2013-01-01

Metagenomics has revolutionized microbiological studies during the past decade and provided new insights into the diversity, dynamics, and metabolic potential of natural microbial communities. However, metagenomics still represents a field in development, and standardized tools and approaches to handle and compare metagenomes have not been established yet. An important reason accounting for the latter is the continuous changes in the type of sequencing data available, for example, long versus short sequencing reads. Here, we provide a guide to bioinformatic pipelines developed to accomplish the following tasks, focusing primarily on those developed by our team: (i) assemble a metagenomic dataset; (ii) determine the level of sequence coverage obtained and the amount of sequencing required to obtain complete coverage; (iii) identify the taxonomic affiliation of a metagenomic read or assembled contig; and (iv) determine differentially abundant genes, pathways, and species between different datasets. Most of these pipelines do not depend on the type of sequences available or can be easily adjusted to fit different types of sequences, and are freely available (for instance, through our lab Web site: http://www.enve-omics.gatech.edu/). The limitations of current approaches, as well as the computational aspects that can be further improved, will also be briefly discussed. The work presented here provides practical guidelines on how to perform metagenomic analysis of microbial communities characterized by varied levels of diversity and establishes approaches to handle the resulting data, independent of the sequencing platform employed. © 2013 Elsevier Inc. All rights reserved.

Excitation and De-Excitation Mechanisms of Er-Doped GaAs and A1GaAs.

DTIC Science & Technology

1992-12-01

AD-A258 814 EXCITATION AND DE -EXCITATION MECHANISMS OF Er-DOPED GaAs AND A1GaAs DISSERTATION David W. Elsaesser, Captain, USAF DTICY. ft £ICTE’’ )AN...0 8 1993U -o Wo- .%Approved for public release; Distribution unlimited 93 1 04 022 AFIT/DS/ENP/92-5 EXCITATION AND DE -EXCITATION MECHANISMS OF Er...public release; Distribution unlimited AFIT/DS/ENP/92D-005 EXCITATION AND DE -EXCITATION MECHANISMS OF Er-DOPED GaAs AND A1GaAs 4 toFlor -- David W

GaAs Computer Technology

DTIC Science & Technology

1992-01-07

AD-A259 259 FASTC-ID FOREIGN AEROSPACE SCIENCE AND TECHNOLOGY CENTER GaAs COMPUTER TECHNOLOGY (1) by Wang Qiao-yu 93-00999 Distrir bution t,,,Nm ted...FASTC- ID(RS)T-0310-92 HUMAN TRANSLATION FASTC-ID(RS)T-0310-92 7 January 1993 GaAs COMPUTER TECHNOLOGY (1) By: Wang Qiao-yu English pages: 6 Source...the best quality copy available. j C] " ------ GaAs Computer Technology (1) Wang Qiao-yu (Li-Shan Microelectronics Institute) Abstract: The paper

IMG/M: integrated genome and metagenome comparative data analysis system

DOE PAGES

Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken; ...

2016-10-13

The Integrated Microbial Genomes with Microbiome Samples (IMG/M: https://img.jgi.doe.gov/m/) system contains annotated DNA and RNA sequence data of (i) archaeal, bacterial, eukaryotic and viral genomes from cultured organisms, (ii) single cell genomes (SCG) and genomes from metagenomes (GFM) from uncultured archaea, bacteria and viruses and (iii) metagenomes from environmental, host associated and engineered microbiome samples. Sequence data are generated by DOE's Joint Genome Institute (JGI), submitted by individual scientists, or collected from public sequence data archives. Structural and functional annotation is carried out by JGI's genome and metagenome annotation pipelines. A variety of analytical and visualization tools provide support formore » examining and comparing IMG/M's datasets. IMG/M allows open access interactive analysis of publicly available datasets, while manual curation, submission and access to private datasets and computationally intensive workspace-based analysis require login/password access to its expert review(ER) companion system (IMG/M ER: https://img.jgi.doe.gov/ mer/). Since the last report published in the 2014 NAR Database Issue, IMG/M's dataset content has tripled in terms of number of datasets and overall protein coding genes, while its analysis tools have been extended to cope with the rapid growth in the number and size of datasets handled by the system.« less

IMG/M: integrated genome and metagenome comparative data analysis system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken

The Integrated Microbial Genomes with Microbiome Samples (IMG/M: https://img.jgi.doe.gov/m/) system contains annotated DNA and RNA sequence data of (i) archaeal, bacterial, eukaryotic and viral genomes from cultured organisms, (ii) single cell genomes (SCG) and genomes from metagenomes (GFM) from uncultured archaea, bacteria and viruses and (iii) metagenomes from environmental, host associated and engineered microbiome samples. Sequence data are generated by DOE's Joint Genome Institute (JGI), submitted by individual scientists, or collected from public sequence data archives. Structural and functional annotation is carried out by JGI's genome and metagenome annotation pipelines. A variety of analytical and visualization tools provide support formore » examining and comparing IMG/M's datasets. IMG/M allows open access interactive analysis of publicly available datasets, while manual curation, submission and access to private datasets and computationally intensive workspace-based analysis require login/password access to its expert review(ER) companion system (IMG/M ER: https://img.jgi.doe.gov/ mer/). Since the last report published in the 2014 NAR Database Issue, IMG/M's dataset content has tripled in terms of number of datasets and overall protein coding genes, while its analysis tools have been extended to cope with the rapid growth in the number and size of datasets handled by the system.« less

IMG/M: integrated genome and metagenome comparative data analysis system

PubMed Central

Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken; Palaniappan, Krishna; Szeto, Ernest; Pillay, Manoj; Ratner, Anna; Huang, Jinghua; Andersen, Evan; Huntemann, Marcel; Varghese, Neha; Hadjithomas, Michalis; Tennessen, Kristin; Nielsen, Torben; Ivanova, Natalia N.; Kyrpides, Nikos C.

2017-01-01

The Integrated Microbial Genomes with Microbiome Samples (IMG/M: https://img.jgi.doe.gov/m/) system contains annotated DNA and RNA sequence data of (i) archaeal, bacterial, eukaryotic and viral genomes from cultured organisms, (ii) single cell genomes (SCG) and genomes from metagenomes (GFM) from uncultured archaea, bacteria and viruses and (iii) metagenomes from environmental, host associated and engineered microbiome samples. Sequence data are generated by DOE's Joint Genome Institute (JGI), submitted by individual scientists, or collected from public sequence data archives. Structural and functional annotation is carried out by JGI's genome and metagenome annotation pipelines. A variety of analytical and visualization tools provide support for examining and comparing IMG/M's datasets. IMG/M allows open access interactive analysis of publicly available datasets, while manual curation, submission and access to private datasets and computationally intensive workspace-based analysis require login/password access to its expert review (ER) companion system (IMG/M ER: https://img.jgi.doe.gov/mer/). Since the last report published in the 2014 NAR Database Issue, IMG/M's dataset content has tripled in terms of number of datasets and overall protein coding genes, while its analysis tools have been extended to cope with the rapid growth in the number and size of datasets handled by the system. PMID:27738135

Metagenome Assembly at the DOE JGI (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Chain, Patrick

2018-01-25

Patrick Chain of DOE JGI at LANL, Co-Chair of the Metagenome-specific Assembly session, on Metagenome Assembly at the DOE JGIat the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

GaAs shallow-homojunction solar cells

NASA Technical Reports Server (NTRS)

Fan, J. C. C.

1981-01-01

The feasibility of fabricating space resistant, high efficiency, light weight, low cost GaAs shallow homojunction solar cells for space application is investigated. The material preparation of ultrathin GaAs single crystal layers, and the fabrication of efficient GaAs solar cells on bulk GaAs substrates are discussed. Considerable progress was made in both areas, and conversion efficiency about 16% AMO was obtained using anodic oxide as a single layer antireflection coating. A computer design shows that even better cells can be obtained with double layer antireflection coating. Ultrathin, high efficiency solar cells were obtained from GaAs films prepared by the CLEFT process, with conversion efficiency as high as 17% at AMI from a 10 micrometers thick GaAs film. A organometallic CVD was designed and constructed.

Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer.

PubMed

Yu, Jun; Feng, Qiang; Wong, Sunny Hei; Zhang, Dongya; Liang, Qiao Yi; Qin, Youwen; Tang, Longqing; Zhao, Hui; Stenvang, Jan; Li, Yanli; Wang, Xiaokai; Xu, Xiaoqiang; Chen, Ning; Wu, William Ka Kei; Al-Aama, Jumana; Nielsen, Hans Jørgen; Kiilerich, Pia; Jensen, Benjamin Anderschou Holbech; Yau, Tung On; Lan, Zhou; Jia, Huijue; Li, Junhua; Xiao, Liang; Lam, Thomas Yuen Tung; Ng, Siew Chien; Cheng, Alfred Sze-Lok; Wong, Vincent Wai-Sun; Chan, Francis Ka Leung; Xu, Xun; Yang, Huanming; Madsen, Lise; Datz, Christian; Tilg, Herbert; Wang, Jian; Brünner, Nils; Kristiansen, Karsten; Arumugam, Manimozhiyan; Sung, Joseph Jao-Yiu; Wang, Jun

2017-01-01

To evaluate the potential for diagnosing colorectal cancer (CRC) from faecal metagenomes. We performed metagenome-wide association studies on faecal samples from 74 patients with CRC and 54 controls from China, and validated the results in 16 patients and 24 controls from Denmark. We further validated the biomarkers in two published cohorts from France and Austria. Finally, we employed targeted quantitative PCR (qPCR) assays to evaluate diagnostic potential of selected biomarkers in an independent Chinese cohort of 47 patients and 109 controls. Besides confirming known associations of Fusobacterium nucleatum and Peptostreptococcus stomatis with CRC, we found significant associations with several species, including Parvimonas micra and Solobacterium moorei. We identified 20 microbial gene markers that differentiated CRC and control microbiomes, and validated 4 markers in the Danish cohort. In the French and Austrian cohorts, these four genes distinguished CRC metagenomes from controls with areas under the receiver-operating curve (AUC) of 0.72 and 0.77, respectively. qPCR measurements of two of these genes accurately classified patients with CRC in the independent Chinese cohort with AUC=0.84 and OR of 23. These genes were enriched in early-stage (I-II) patient microbiomes, highlighting the potential for using faecal metagenomic biomarkers for early diagnosis of CRC. We present the first metagenomic profiling study of CRC faecal microbiomes to discover and validate microbial biomarkers in ethnically different cohorts, and to independently validate selected biomarkers using an affordable clinically relevant technology. Our study thus takes a step further towards affordable non-invasive early diagnostic biomarkers for CRC from faecal samples. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Exploring neighborhoods in the metagenome universe.

PubMed

Aßhauer, Kathrin P; Klingenberg, Heiner; Lingner, Thomas; Meinicke, Peter

2014-07-14

The variety of metagenomes in current databases provides a rapidly growing source of information for comparative studies. However, the quantity and quality of supplementary metadata is still lagging behind. It is therefore important to be able to identify related metagenomes by means of the available sequence data alone. We have studied efficient sequence-based methods for large-scale identification of similar metagenomes within a database retrieval context. In a broad comparison of different profiling methods we found that vector-based distance measures are well-suitable for the detection of metagenomic neighbors. Our evaluation on more than 1700 publicly available metagenomes indicates that for a query metagenome from a particular habitat on average nine out of ten nearest neighbors represent the same habitat category independent of the utilized profiling method or distance measure. While for well-defined labels a neighborhood accuracy of 100% can be achieved, in general the neighbor detection is severely affected by a natural overlap of manually annotated categories. In addition, we present results of a novel visualization method that is able to reflect the similarity of metagenomes in a 2D scatter plot. The visualization method shows a similarly high accuracy in the reduced space as compared with the high-dimensional profile space. Our study suggests that for inspection of metagenome neighborhoods the profiling methods and distance measures can be chosen to provide a convenient interpretation of results in terms of the underlying features. Furthermore, supplementary metadata of metagenome samples in the future needs to comply with readily available ontologies for fine-grained and standardized annotation. To make profile-based k-nearest-neighbor search and the 2D-visualization of the metagenome universe available to the research community, we included the proposed methods in our CoMet-Universe server for comparative metagenome analysis.

Exploring Neighborhoods in the Metagenome Universe

PubMed Central

Aßhauer, Kathrin P.; Klingenberg, Heiner; Lingner, Thomas; Meinicke, Peter

2014-01-01

The variety of metagenomes in current databases provides a rapidly growing source of information for comparative studies. However, the quantity and quality of supplementary metadata is still lagging behind. It is therefore important to be able to identify related metagenomes by means of the available sequence data alone. We have studied efficient sequence-based methods for large-scale identification of similar metagenomes within a database retrieval context. In a broad comparison of different profiling methods we found that vector-based distance measures are well-suitable for the detection of metagenomic neighbors. Our evaluation on more than 1700 publicly available metagenomes indicates that for a query metagenome from a particular habitat on average nine out of ten nearest neighbors represent the same habitat category independent of the utilized profiling method or distance measure. While for well-defined labels a neighborhood accuracy of 100% can be achieved, in general the neighbor detection is severely affected by a natural overlap of manually annotated categories. In addition, we present results of a novel visualization method that is able to reflect the similarity of metagenomes in a 2D scatter plot. The visualization method shows a similarly high accuracy in the reduced space as compared with the high-dimensional profile space. Our study suggests that for inspection of metagenome neighborhoods the profiling methods and distance measures can be chosen to provide a convenient interpretation of results in terms of the underlying features. Furthermore, supplementary metadata of metagenome samples in the future needs to comply with readily available ontologies for fine-grained and standardized annotation. To make profile-based k-nearest-neighbor search and the 2D-visualization of the metagenome universe available to the research community, we included the proposed methods in our CoMet-Universe server for comparative metagenome analysis. PMID:25026170

A Novel Prosthetic Joint Infection Pathogen, Mycoplasma salivarium, Identified by Metagenomic Shotgun Sequencing.

PubMed

Thoendel, Matthew; Jeraldo, Patricio; Greenwood-Quaintance, Kerryl E; Chia, Nicholas; Abdel, Matthew P; Steckelberg, James M; Osmon, Douglas R; Patel, Robin

2017-07-15

Defining the microbial etiology of culture-negative prosthetic joint infection (PJI) can be challenging. Metagenomic shotgun sequencing is a new tool to identify organisms undetected by conventional methods. We present a case where metagenomics was used to identify Mycoplasma salivarium as a novel PJI pathogen in a patient with hypogammaglobulinemia. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

Discovery of new cellulases from the metagenome by a metagenomics-guided strategy.

PubMed

Yang, Chao; Xia, Yu; Qu, Hong; Li, An-Dong; Liu, Ruihua; Wang, Yubo; Zhang, Tong

2016-01-01

Energy shortage has become a global problem. Production of biofuels from renewable biomass resources is an inevitable trend of sustainable development. Cellulose is the most abundant and renewable resource in nature. Lack of new cellulases with unique properties has become the bottleneck of the efficient utilization of cellulose. Environmental metagenomes are regarded as huge reservoirs for a variety of cellulases. However, new cellulases cannot be obtained easily by functional screening of metagenomic libraries. In this work, a metagenomics-guided strategy for obtaining new cellulases from the metagenome was proposed. Metagenomic sequences of DNA extracted from the anaerobic beer lees converting consortium enriched at thermophilic conditions were assembled, and 23 glycoside hydrolase (GH) sequences affiliated with the GH family 5 were identified. Among the 23 GH sequences, three target sequences (designated as cel7482, cel3623 and cel36) showing low identity with those known GHs were chosen as the putative cellulase genes to be functionally expressed in Escherichia coli after PCR cloning. The three cellulases were classified into endo-β-1,4-glucanases by product pattern analysis. The recombinant cellulases were more active at pH 5.5 and within a temperature range of 60-70 °C. Computer-assisted 3D structure modeling indicated that the active residues in the active site of the recombinant cellulases were more similar to each other compared with non-active site residues. The recombinant cel7482 was extremely tolerant to 2 M NaCl, suggesting that cel7482 may be a halotolerant cellulase. Moreover, the recombinant cel7482 was shown to have an ability to resist three ionic liquids (ILs), which are widely used for cellulose pretreatment. Furthermore, active cel7482 was secreted by the twin-arginine translocation (Tat) pathway of Bacillus subtilis 168 into the culture medium, which facilitates the subsequent purification and reduces the formation of inclusion body in

Metagenomic ventures into outer sequence space.

PubMed

Dutilh, Bas E

Sequencing DNA or RNA directly from the environment often results in many sequencing reads that have no homologs in the database. These are referred to as "unknowns," and reflect the vast unexplored microbial sequence space of our biosphere, also known as "biological dark matter." However, unknowns also exist because metagenomic datasets are not optimally mined. There is a pressure on researchers to publish and move on, and the unknown sequences are often left for what they are, and conclusions drawn based on reads with annotated homologs. This can cause abundant and widespread genomes to be overlooked, such as the recently discovered human gut bacteriophage crAssphage. The unknowns may be enriched for bacteriophage sequences, the most abundant and genetically diverse component of the biosphere and of sequence space. However, it remains an open question, what is the actual size of biological sequence space? The de novo assembly of shotgun metagenomes is the most powerful tool to address this question.

A Graph-Centric Approach for Metagenome-Guided Peptide and Protein Identification in Metaproteomics

PubMed Central

Tang, Haixu; Li, Sujun; Ye, Yuzhen

2016-01-01

Metaproteomic studies adopt the common bottom-up proteomics approach to investigate the protein composition and the dynamics of protein expression in microbial communities. When matched metagenomic and/or metatranscriptomic data of the microbial communities are available, metaproteomic data analyses often employ a metagenome-guided approach, in which complete or fragmental protein-coding genes are first directly predicted from metagenomic (and/or metatranscriptomic) sequences or from their assemblies, and the resulting protein sequences are then used as the reference database for peptide/protein identification from MS/MS spectra. This approach is often limited because protein coding genes predicted from metagenomes are incomplete and fragmental. In this paper, we present a graph-centric approach to improving metagenome-guided peptide and protein identification in metaproteomics. Our method exploits the de Bruijn graph structure reported by metagenome assembly algorithms to generate a comprehensive database of protein sequences encoded in the community. We tested our method using several public metaproteomic datasets with matched metagenomic and metatranscriptomic sequencing data acquired from complex microbial communities in a biological wastewater treatment plant. The results showed that many more peptides and proteins can be identified when assembly graphs were utilized, improving the characterization of the proteins expressed in the microbial communities. The additional proteins we identified contribute to the characterization of important pathways such as those involved in degradation of chemical hazards. Our tools are released as open-source software on github at https://github.com/COL-IU/Graph2Pro. PMID:27918579

Microbial Metagenomics: Beyond the Genome

NASA Astrophysics Data System (ADS)

Gilbert, Jack A.; Dupont, Christopher L.

2011-01-01

Metagenomics literally means “beyond the genome.” Marine microbial metagenomic databases presently comprise ˜400 billion base pairs of DNA, only ˜3% of that found in 1 ml of seawater. Very soon a trillion-base-pair sequence run will be feasible, so it is time to reflect on what we have learned from metagenomics. We review the impact of metagenomics on our understanding of marine microbial communities. We consider the studies facilitated by data generated through the Global Ocean Sampling expedition, as well as the revolution wrought at the individual laboratory level through next generation sequencing technologies. We review recent studies and discoveries since 2008, provide a discussion of bioinformatic analyses, including conceptual pipelines and sequence annotation and predict the future of metagenomics, with suggestions of collaborative community studies tailored toward answering some of the fundamental questions in marine microbial ecology.

Use of simulated data sets to evaluate the fidelity of metagenomic processing methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mavromatis, K; Ivanova, N; Barry, Kerrie

2007-01-01

Metagenomics is a rapidly emerging field of research for studying microbial communities. To evaluate methods presently used to process metagenomic sequences, we constructed three simulated data sets of varying complexity by combining sequencing reads randomly selected from 113 isolate genomes. These data sets were designed to model real metagenomes in terms of complexity and phylogenetic composition. We assembled sampled reads using three commonly used genome assemblers (Phrap, Arachne and JAZZ), and predicted genes using two popular gene-finding pipelines (fgenesb and CRITICA/GLIMMER). The phylogenetic origins of the assembled contigs were predicted using one sequence similarity-based ( blast hit distribution) and twomore » sequence composition-based (PhyloPythia, oligonucleotide frequencies) binning methods. We explored the effects of the simulated community structure and method combinations on the fidelity of each processing step by comparison to the corresponding isolate genomes. The simulated data sets are available online to facilitate standardized benchmarking of tools for metagenomic analysis.« less

Metagenomic analyses of the late Pleistocene permafrost - additional tools for reconstruction of environmental conditions

NASA Astrophysics Data System (ADS)

Rivkina, Elizaveta; Petrovskaya, Lada; Vishnivetskaya, Tatiana; Krivushin, Kirill; Shmakova, Lyubov; Tutukina, Maria; Meyers, Arthur; Kondrashov, Fyodor

2016-04-01

A comparative analysis of the metagenomes from two 30 000-year-old permafrost samples, one of lake-alluvial origin and the other from late Pleistocene Ice Complex sediments, revealed significant differences within microbial communities. The late Pleistocene Ice Complex sediments (which have been characterized by the absence of methane with lower values of redox potential and Fe2+ content) showed a low abundance of methanogenic archaea and enzymes from both the carbon and nitrogen cycles, but a higher abundance of enzymes associated with the sulfur cycle. The metagenomic and geochemical analyses described in the paper provide evidence that the formation of the sampled late Pleistocene Ice Complex sediments likely took place under much more aerobic conditions than lake-alluvial sediments.

Mining virulence genes using metagenomics.

PubMed

Belda-Ferre, Pedro; Cabrera-Rubio, Raúl; Moya, Andrés; Mira, Alex

2011-01-01

When a bacterial genome is compared to the metagenome of an environment it inhabits, most genes recruit at high sequence identity. In free-living bacteria (for instance marine bacteria compared against the ocean metagenome) certain genomic regions are totally absent in recruitment plots, representing therefore genes unique to individual bacterial isolates. We show that these Metagenomic Islands (MIs) are also visible in bacteria living in human hosts when their genomes are compared to sequences from the human microbiome, despite the compartmentalized structure of human-related environments such as the gut. From an applied point of view, MIs of human pathogens (e.g. those identified in enterohaemorragic Escherichia coli against the gut metagenome or in pathogenic Neisseria meningitidis against the oral metagenome) include virulence genes that appear to be absent in related strains or species present in the microbiome of healthy individuals. We propose that this strategy (i.e. recruitment analysis of pathogenic bacteria against the metagenome of healthy subjects) can be used to detect pathogenicity regions in species where the genes involved in virulence are poorly characterized. Using this approach, we detect well-known pathogenicity islands and identify new potential virulence genes in several human pathogens.

Metagenomic frameworks for monitoring antibiotic resistance in aquatic environments.

PubMed

Port, Jesse A; Cullen, Alison C; Wallace, James C; Smith, Marissa N; Faustman, Elaine M

2014-03-01

High-throughput genomic technologies offer new approaches for environmental health monitoring, including metagenomic surveillance of antibiotic resistance determinants (ARDs). Although natural environments serve as reservoirs for antibiotic resistance genes that can be transferred to pathogenic and human commensal bacteria, monitoring of these determinants has been infrequent and incomplete. Furthermore, surveillance efforts have not been integrated into public health decision making. We used a metagenomic epidemiology-based approach to develop an ARD index that quantifies antibiotic resistance potential, and we analyzed this index for common modal patterns across environmental samples. We also explored how metagenomic data such as this index could be conceptually framed within an early risk management context. We analyzed 25 published data sets from shotgun pyrosequencing projects. The samples consisted of microbial community DNA collected from marine and freshwater environments across a gradient of human impact. We used principal component analysis to identify index patterns across samples. We observed significant differences in the overall index and index subcategory levels when comparing ecosystems more proximal versus distal to human impact. The selection of different sequence similarity thresholds strongly influenced the index measurements. Unique index subcategory modes distinguished the different metagenomes. Broad-scale screening of ARD potential using this index revealed utility for framing environmental health monitoring and surveillance. This approach holds promise as a screening tool for establishing baseline ARD levels that can be used to inform and prioritize decision making regarding management of ARD sources and human exposure routes. Port JA, Cullen AC, Wallace JC, Smith MN, Faustman EM. 2014. Metagenomic frameworks for monitoring antibiotic resistance in aquatic environments. Environ Health Perspect 122:222–228; http://dx.doi.org/10.1289/ehp

A Primer on Metagenomics

PubMed Central

Wooley, John C.; Godzik, Adam; Friedberg, Iddo

2010-01-01

Metagenomics is a discipline that enables the genomic study of uncultured microorganisms. Faster, cheaper sequencing technologies and the ability to sequence uncultured microbes sampled directly from their habitats are expanding and transforming our view of the microbial world. Distilling meaningful information from the millions of new genomic sequences presents a serious challenge to bioinformaticians. In cultured microbes, the genomic data come from a single clone, making sequence assembly and annotation tractable. In metagenomics, the data come from heterogeneous microbial communities, sometimes containing more than 10,000 species, with the sequence data being noisy and partial. From sampling, to assembly, to gene calling and function prediction, bioinformatics faces new demands in interpreting voluminous, noisy, and often partial sequence data. Although metagenomics is a relative newcomer to science, the past few years have seen an explosion in computational methods applied to metagenomic-based research. It is therefore not within the scope of this article to provide an exhaustive review. Rather, we provide here a concise yet comprehensive introduction to the current computational requirements presented by metagenomics, and review the recent progress made. We also note whether there is software that implements any of the methods presented here, and briefly review its utility. Nevertheless, it would be useful if readers of this article would avail themselves of the comment section provided by this journal, and relate their own experiences. Finally, the last section of this article provides a few representative studies illustrating different facets of recent scientific discoveries made using metagenomics. PMID:20195499

Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples.

PubMed

Yu, Feiqiao Brian; Blainey, Paul C; Schulz, Frederik; Woyke, Tanja; Horowitz, Mark A; Quake, Stephen R

2017-07-05

Metagenomics and single-cell genomics have enabled genome discovery from unknown branches of life. However, extracting novel genomes from complex mixtures of metagenomic data can still be challenging and represents an ill-posed problem which is generally approached with ad hoc methods. Here we present a microfluidic-based mini-metagenomic method which offers a statistically rigorous approach to extract novel microbial genomes while preserving single-cell resolution. We used this approach to analyze two hot spring samples from Yellowstone National Park and extracted 29 new genomes, including three deeply branching lineages. The single-cell resolution enabled accurate quantification of genome function and abundance, down to 1% in relative abundance. Our analyses of genome level SNP distributions also revealed low to moderate environmental selection. The scale, resolution, and statistical power of microfluidic-based mini-metagenomics make it a powerful tool to dissect the genomic structure of microbial communities while effectively preserving the fundamental unit of biology, the single cell.

Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software

PubMed Central

Sczyrba, Alexander; Hofmann, Peter; Belmann, Peter; Koslicki, David; Janssen, Stefan; Dröge, Johannes; Gregor, Ivan; Majda, Stephan; Fiedler, Jessika; Dahms, Eik; Bremges, Andreas; Fritz, Adrian; Garrido-Oter, Ruben; Jørgensen, Tue Sparholt; Shapiro, Nicole; Blood, Philip D.; Gurevich, Alexey; Bai, Yang; Turaev, Dmitrij; DeMaere, Matthew Z.; Chikhi, Rayan; Nagarajan, Niranjan; Quince, Christopher; Meyer, Fernando; Balvočiūtė, Monika; Hansen, Lars Hestbjerg; Sørensen, Søren J.; Chia, Burton K. H.; Denis, Bertrand; Froula, Jeff L.; Wang, Zhong; Egan, Robert; Kang, Dongwan Don; Cook, Jeffrey J.; Deltel, Charles; Beckstette, Michael; Lemaitre, Claire; Peterlongo, Pierre; Rizk, Guillaume; Lavenier, Dominique; Wu, Yu-Wei; Singer, Steven W.; Jain, Chirag; Strous, Marc; Klingenberg, Heiner; Meinicke, Peter; Barton, Michael; Lingner, Thomas; Lin, Hsin-Hung; Liao, Yu-Chieh; Silva, Genivaldo Gueiros Z.; Cuevas, Daniel A.; Edwards, Robert A.; Saha, Surya; Piro, Vitor C.; Renard, Bernhard Y.; Pop, Mihai; Klenk, Hans-Peter; Göker, Markus; Kyrpides, Nikos C.; Woyke, Tanja; Vorholt, Julia A.; Schulze-Lefert, Paul; Rubin, Edward M.; Darling, Aaron E.; Rattei, Thomas; McHardy, Alice C.

2018-01-01

In metagenome analysis, computational methods for assembly, taxonomic profiling and binning are key components facilitating downstream biological data interpretation. However, a lack of consensus about benchmarking datasets and evaluation metrics complicates proper performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on datasets of unprecedented complexity and realism. Benchmark metagenomes were generated from ~700 newly sequenced microorganisms and ~600 novel viruses and plasmids, including genomes with varying degrees of relatedness to each other and to publicly available ones and representing common experimental setups. Across all datasets, assembly and genome binning programs performed well for species represented by individual genomes, while performance was 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 the family level. Parameter settings substantially impacted performances, underscoring the importance of program reproducibility. While highlighting current challenges in computational metagenomics, the CAMI results provide a roadmap for software selection to answer specific research questions. PMID:28967888

Loeffler 4.0: Diagnostic Metagenomics.

PubMed

Höper, Dirk; Wylezich, Claudia; Beer, Martin

2017-01-01

A new world of possibilities for "virus discovery" was opened up with high-throughput sequencing becoming available in the last decade. While scientifically metagenomic analysis was established before the start of the era of high-throughput sequencing, the availability of the first second-generation sequencers was the kick-off for diagnosticians to use sequencing for the detection of novel pathogens. Today, diagnostic metagenomics is becoming the standard procedure for the detection and genetic characterization of new viruses or novel virus variants. Here, we provide an overview about technical considerations of high-throughput sequencing-based diagnostic metagenomics together with selected examples of "virus discovery" for animal diseases or zoonoses and metagenomics for food safety or basic veterinary research. © 2017 Elsevier Inc. All rights reserved.

Experimental Design and Bioinformatics Analysis for the Application of Metagenomics in Environmental Sciences and Biotechnology.

PubMed

Ju, Feng; Zhang, Tong

2015-11-03

Recent advances in DNA sequencing technologies have prompted the widespread application of metagenomics for the investigation of novel bioresources (e.g., industrial enzymes and bioactive molecules) and unknown biohazards (e.g., pathogens and antibiotic resistance genes) in natural and engineered microbial systems across multiple disciplines. This review discusses the rigorous experimental design and sample preparation in the context of applying metagenomics in environmental sciences and biotechnology. Moreover, this review summarizes the principles, methodologies, and state-of-the-art bioinformatics procedures, tools and database resources for metagenomics applications and discusses two popular strategies (analysis of unassembled reads versus assembled contigs/draft genomes) for quantitative or qualitative insights of microbial community structure and functions. Overall, this review aims to facilitate more extensive application of metagenomics in the investigation of uncultured microorganisms, novel enzymes, microbe-environment interactions, and biohazards in biotechnological applications where microbial communities are engineered for bioenergy production, wastewater treatment, and bioremediation.

International Standards for Genomes, Transcriptomes, and Metagenomes

PubMed Central

Mason, Christopher E.; Afshinnekoo, Ebrahim; Tighe, Scott; Wu, Shixiu; Levy, Shawn

2017-01-01

Challenges and biases in preparing, characterizing, and sequencing DNA and RNA can have significant impacts on research in genomics across all kingdoms of life, including experiments in single-cells, RNA profiling, and metagenomics (across multiple genomes). Technical artifacts and contamination can arise at each point of sample manipulation, extraction, sequencing, and analysis. Thus, the measurement and benchmarking of these potential sources of error are of paramount importance as next-generation sequencing (NGS) projects become more global and ubiquitous. Fortunately, a variety of methods, standards, and technologies have recently emerged that improve measurements in genomics and sequencing, from the initial input material to the computational pipelines that process and annotate the data. Here we review current standards and their applications in genomics, including whole genomes, transcriptomes, mixed genomic samples (metagenomes), and the modified bases within each (epigenomes and epitranscriptomes). These standards, tools, and metrics are critical for quantifying the accuracy of NGS methods, which will be essential for robust approaches in clinical genomics and precision medicine. PMID:28337071

GaAs MOEMS Technology

DOE Office of Scientific and Technical Information (OSTI.GOV)

SPAHN, OLGA B.; GROSSETETE, GRANT D.; CICH, MICHAEL J.

2003-03-01

Many MEMS-based components require optical monitoring techniques using optoelectronic devices for converting mechanical position information into useful electronic signals. While the constituent piece-parts of such hybrid opto-MEMS components can be separately optimized, the resulting component performance, size, ruggedness and cost are substantially compromised due to assembly and packaging limitations. GaAs MOEMS offers the possibility of monolithically integrating high-performance optoelectronics with simple mechanical structures built in very low-stress epitaxial layers with a resulting component performance determined only by GaAs microfabrication technology limitations. GaAs MOEMS implicitly integrates the capability for radiation-hardened optical communications into the MEMS sensor or actuator component, a vitalmore » step towards rugged integrated autonomous microsystems that sense, act, and communicate. This project establishes a new foundational technology that monolithically combines GaAs optoelectronics with simple mechanics. Critical process issues addressed include selectivity, electrochemical characteristics, and anisotropy of the release chemistry, and post-release drying and coating processes. Several types of devices incorporating this novel technology are demonstrated.« less

An Agile Functional Analysis of Metagenomic Data Using SUPER-FOCUS.

PubMed

Silva, Genivaldo Gueiros Z; Lopes, Fabyano A C; Edwards, Robert A

2017-01-01

One of the main goals in metagenomics is to identify the functional profile of a microbial community from unannotated shotgun sequencing reads. Functional annotation is important in biological research because it enables researchers to identify the abundance of functional genes of the organisms present in the sample, answering the question, "What can the organisms in the sample do?" Most currently available approaches do not scale with increasing data volumes, which is important because both the number and lengths of the reads provided by sequencing platforms keep increasing. Here, we present SUPER-FOCUS, SUbsystems Profile by databasE Reduction using FOCUS, an agile homology-based approach using a reduced reference database to report the subsystems present in metagenomic datasets and profile their abundances. SUPER-FOCUS was tested with real metagenomes, and the results show that it accurately predicts the subsystems present in the profiled microbial communities, is computationally efficient, and up to 1000 times faster than other tools. SUPER-FOCUS is freely available at http://edwards.sdsu.edu/SUPERFOCUS .

Metagenomic Frameworks for Monitoring Antibiotic Resistance in Aquatic Environments

PubMed Central

Port, Jesse A.; Cullen, Alison C.; Wallace, James C.; Smith, Marissa N.

2013-01-01

Background: High-throughput genomic technologies offer new approaches for environmental health monitoring, including metagenomic surveillance of antibiotic resistance determinants (ARDs). Although natural environments serve as reservoirs for antibiotic resistance genes that can be transferred to pathogenic and human commensal bacteria, monitoring of these determinants has been infrequent and incomplete. Furthermore, surveillance efforts have not been integrated into public health decision making. Objectives: We used a metagenomic epidemiology–based approach to develop an ARD index that quantifies antibiotic resistance potential, and we analyzed this index for common modal patterns across environmental samples. We also explored how metagenomic data such as this index could be conceptually framed within an early risk management context. Methods: We analyzed 25 published data sets from shotgun pyrosequencing projects. The samples consisted of microbial community DNA collected from marine and freshwater environments across a gradient of human impact. We used principal component analysis to identify index patterns across samples. Results: We observed significant differences in the overall index and index subcategory levels when comparing ecosystems more proximal versus distal to human impact. The selection of different sequence similarity thresholds strongly influenced the index measurements. Unique index subcategory modes distinguished the different metagenomes. Conclusions: Broad-scale screening of ARD potential using this index revealed utility for framing environmental health monitoring and surveillance. This approach holds promise as a screening tool for establishing baseline ARD levels that can be used to inform and prioritize decision making regarding management of ARD sources and human exposure routes. Citation: Port JA, Cullen AC, Wallace JC, Smith MN, Faustman EM. 2014. Metagenomic frameworks for monitoring antibiotic resistance in aquatic environments

Comparative analysis of metagenomes of Italian top soil improvers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gigliucci, Federica, E-mail: Federica.gigliucci@li

Biosolids originating from Municipal Waste Water Treatment Plants are proposed as top soil improvers (TSI) for their beneficial input of organic carbon on agriculture lands. Their use to amend soil is controversial, as it may lead to the presence of emerging hazards of anthropogenic or animal origin in the environment devoted to food production. In this study, we used a shotgun metagenomics sequencing as a tool to perform a characterization of the hazards related with the TSIs. The samples showed the presence of many virulence genes associated to different diarrheagenic E. coli pathotypes as well as of different antimicrobial resistance-associatedmore » genes. The genes conferring resistance to Fluoroquinolones was the most relevant class of antimicrobial resistance genes observed in all the samples tested. To a lesser extent traits associated with the resistance to Methicillin in Staphylococci and genes conferring resistance to Streptothricin, Fosfomycin and Vancomycin were also identified. The most represented metal resistance genes were cobalt-zinc-cadmium related, accounting for 15–50% of the sequence reads in the different metagenomes out of the total number of those mapping on the class of resistance to compounds determinants. Moreover the taxonomic analysis performed by comparing compost-based samples and biosolids derived from municipal sewage-sludges treatments divided the samples into separate populations, based on the microbiota composition. The results confirm that the metagenomics is efficient to detect genomic traits associated with pathogens and antimicrobial resistance in complex matrices and this approach can be efficiently used for the traceability of TSI samples using the microorganisms’ profiles as indicators of their origin. - Highlights: • Sludge- and green- based biosolids analysed by metagenomics. • Biosolids may introduce microbial hazards in the food chain. • Metagenomics enables tracking biosolids’ sources.« less

Metagenomic Assembly: Overview, Challenges and Applications

PubMed Central

Ghurye, Jay S.; Cepeda-Espinoza, Victoria; Pop, Mihai

2016-01-01

Advances in sequencing technologies have led to the increased use of high throughput sequencing in characterizing the microbial communities associated with our bodies and our environment. Critical to the analysis of the resulting data are sequence assembly algorithms able to reconstruct genes and organisms from complex mixtures. Metagenomic assembly involves new computational challenges due to the specific characteristics of the metagenomic data. In this survey, we focus on major algorithmic approaches for genome and metagenome assembly, and discuss the new challenges and opportunities afforded by this new field. We also review several applications of metagenome assembly in addressing interesting biological problems. PMID:27698619

Reducing inherent biases introduced during DNA viral metagenome analyses of municipal wastewater

EPA Science Inventory

Metagenomics is a powerful tool for characterizing viral composition within environmental samples, but sample and molecular processing steps can bias the estimation of viral community structure. The objective of this study is to understand the inherent variability introduced when...

LEC GaAs for integrated circuit applications

NASA Technical Reports Server (NTRS)

Kirkpatrick, C. G.; Chen, R. T.; Homes, D. E.; Asbeck, P. M.; Elliott, K. R.; Fairman, R. D.; Oliver, J. D.

1984-01-01

Recent developments in liquid encapsulated Czochralski techniques for the growth of semiinsulating GaAs for integrated circuit applications have resulted in significant improvements in the quality and quantity of GaAs material suitable for device processing. The emergence of high performance GaAs integrated circuit technologies has accelerated the demand for high quality, large diameter semiinsulating GaAs substrates. The new device technologies, including digital integrated circuits, monolithic microwave integrated circuits and charge coupled devices have largely adopted direct ion implantation for the formation of doped layers. Ion implantation lends itself to good uniformity and reproducibility, high yield and low cost; however, this technique also places stringent demands on the quality of the semiinsulating GaAs substrates. Although significant progress was made in developing a viable planar ion implantation technology, the variability and poor quality of GaAs substrates have hindered progress in process development.

Design and implementation of GaAs HBT circuits with ACME

NASA Technical Reports Server (NTRS)

Hutchings, Brad L.; Carter, Tony M.

1993-01-01

GaAs HBT circuits offer high performance (5-20 GHz) and radiation hardness (500 Mrad) that is attractive for space applications. ACME is a CAD tool specifically developed for HBT circuits. ACME implements a novel physical schematic-capture design technique where designers simultaneously view the structure and physical organization of a circuit. ACME's design interface is similar to schematic capture; however, unlike conventional schematic capture, designers can directly control the physical placement of both function and interconnect at the schematic level. In addition, ACME provides design-time parasitic extraction, complex wire models, and extensions to Multi-Chip Modules (MCM's). A GaAs HBT gate-array and semi-custom circuits have been developed with ACME; several circuits have been fabricated and found to be fully functional .

Finding and identifying the viral needle in the metagenomic haystack: trends and challenges

PubMed Central

Soueidan, Hayssam; Schmitt, Louise-Amélie; Candresse, Thierry; Nikolski, Macha

2015-01-01

Collectively, viruses have the greatest genetic diversity on Earth, occupy extremely varied niches and are likely able to infect all living organisms. Viral infections are an important issue for human health and cause considerable economic losses when agriculturally important crops or husbandry animals are infected. The advent of metagenomics has provided a precious tool to study viruses by sampling them in natural environments and identifying the genomic composition of a sample. However, reaching a clear recognition and taxonomic assignment of the identified viruses has been hampered by the computational difficulty of these problems. In this perspective paper we examine the trends in current research for the identification of viral sequences in a metagenomic sample, pinpoint the intrinsic computational difficulties for the identification of novel viral sequences within metagenomic samples, and suggest possible avenues to overcome them. PMID:25610431

Technical Report: Benchmarking for Quasispecies Abundance Inference with Confidence Intervals from Metagenomic Sequence Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

McLoughlin, K.

2016-01-22

The software application “MetaQuant” was developed by our group at Lawrence Livermore National Laboratory (LLNL). It is designed to profile microbial populations in a sample using data from whole-genome shotgun (WGS) metagenomic DNA sequencing. Several other metagenomic profiling applications have been described in the literature. We ran a series of benchmark tests to compare the performance of MetaQuant against that of a few existing profiling tools, using real and simulated sequence datasets. This report describes our benchmarking procedure and results.

Design optimization of GaAs betavoltaic batteries

NASA Astrophysics Data System (ADS)

Chen, Haiyanag; Jiang, Lan; Chen, Xuyuan

2011-06-01

GaAs junctions are designed and fabricated for betavoltaic batteries. The design is optimized according to the characteristics of GaAs interface states and the diffusion length in the depletion region of GaAs carriers. Under an illumination of 10 mCi cm-2 63Ni, the open circuit voltage of the optimized batteries is about ~0.3 V. It is found that the GaAs interface states induce depletion layers on P-type GaAs surfaces. The depletion layer along the P+PN+ junction edge isolates the perimeter surface from the bulk junction, which tends to significantly reduce the battery dark current and leads to a high open circuit voltage. The short circuit current density of the optimized junction is about 28 nA cm-2, which indicates a carrier diffusion length of less than 1 µm. The overall results show that multi-layer P+PN+ junctions are the preferred structures for GaAs betavoltaic battery design.

An application of statistics to comparative metagenomics

PubMed Central

Rodriguez-Brito, Beltran; Rohwer, Forest; Edwards, Robert A

2006-01-01

Background Metagenomics, sequence analyses of genomic DNA isolated directly from the environments, can be used to identify organisms and model community dynamics of a particular ecosystem. Metagenomics also has the potential to identify significantly different metabolic potential in different environments. Results Here we use a statistical method to compare curated subsystems, to predict the physiology, metabolism, and ecology from metagenomes. This approach can be used to identify those subsystems that are significantly different between metagenome sequences. Subsystems that were overrepresented in the Sargasso Sea and Acid Mine Drainage metagenome when compared to non-redundant databases were identified. Conclusion The methodology described herein applies statistics to the comparisons of metabolic potential in metagenomes. This analysis reveals those subsystems that are more, or less, represented in the different environments that are compared. These differences in metabolic potential lead to several testable hypotheses about physiology and metabolism of microbes from these ecosystems. PMID:16549025

An application of statistics to comparative metagenomics.

PubMed

Rodriguez-Brito, Beltran; Rohwer, Forest; Edwards, Robert A

2006-03-20

Metagenomics, sequence analyses of genomic DNA isolated directly from the environments, can be used to identify organisms and model community dynamics of a particular ecosystem. Metagenomics also has the potential to identify significantly different metabolic potential in different environments. Here we use a statistical method to compare curated subsystems, to predict the physiology, metabolism, and ecology from metagenomes. This approach can be used to identify those subsystems that are significantly different between metagenome sequences. Subsystems that were overrepresented in the Sargasso Sea and Acid Mine Drainage metagenome when compared to non-redundant databases were identified. The methodology described herein applies statistics to the comparisons of metabolic potential in metagenomes. This analysis reveals those subsystems that are more, or less, represented in the different environments that are compared. These differences in metabolic potential lead to several testable hypotheses about physiology and metabolism of microbes from these ecosystems.

Tracking cashew economically important diseases in the West African region using metagenomics

PubMed Central

Monteiro, Filipa; Romeiras, Maria M.; Figueiredo, Andreia; Sebastiana, Mónica; Baldé, Aladje; Catarino, Luís; Batista, Dora

2015-01-01

During the last decades, agricultural land-uses in West Africa were marked by dramatic shifts in the coverage of individual crops. Nowadays, cashew (Anacardium occidentale L.) is one of the most export-oriented horticulture crops, notably in Guinea-Bissau. Relying heavily on agriculture to increase their income, developing countries have been following a strong trend of moving on from traditional farming systems toward commercial production. Emerging infectious diseases, driven either by adaptation to local conditions or inadvertent importation of plant pathogens, are able to cause tremendous cashew production losses, with economic and social impact of which, in developing countries is often underestimated. Presently, plant genomics with metagenomics as an emergent tool, presents an enormous potential to better characterize diseases by providing extensive knowledge on plant pathogens at a large scale. In this perspective, we address metagenomics as a promising genomic tool to identify cashew fungal associated diseases as well as to discriminate the causal pathogens, aiming at obtaining tools to help design effective strategies for disease control and thus promote the sustainable production of cashew in West African Region. PMID:26175748

Tracking cashew economically important diseases in the West African region using metagenomics.

PubMed

Monteiro, Filipa; Romeiras, Maria M; Figueiredo, Andreia; Sebastiana, Mónica; Baldé, Aladje; Catarino, Luís; Batista, Dora

2015-01-01

During the last decades, agricultural land-uses in West Africa were marked by dramatic shifts in the coverage of individual crops. Nowadays, cashew (Anacardium occidentale L.) is one of the most export-oriented horticulture crops, notably in Guinea-Bissau. Relying heavily on agriculture to increase their income, developing countries have been following a strong trend of moving on from traditional farming systems toward commercial production. Emerging infectious diseases, driven either by adaptation to local conditions or inadvertent importation of plant pathogens, are able to cause tremendous cashew production losses, with economic and social impact of which, in developing countries is often underestimated. Presently, plant genomics with metagenomics as an emergent tool, presents an enormous potential to better characterize diseases by providing extensive knowledge on plant pathogens at a large scale. In this perspective, we address metagenomics as a promising genomic tool to identify cashew fungal associated diseases as well as to discriminate the causal pathogens, aiming at obtaining tools to help design effective strategies for disease control and thus promote the sustainable production of cashew in West African Region.

GaAs Monolithic Microwave Subsystem Technology Base

DTIC Science & Technology

1980-01-01

To provide a captive source of reliable, high-quality GaAs substrates, a new crystal growth and substrate preparation facility which utilizes a high...Symp. GaAs and Related Compounds, Inst. Phys. Conf. Ser. 24, 6. 20. Wood, Woodcock and Harris (1978) GaAs and Related Compounds, Inst. Phys. Conf

Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples

PubMed Central

Yu, Feiqiao Brian; Blainey, Paul C; Schulz, Frederik; Woyke, Tanja; Horowitz, Mark A; Quake, Stephen R

2017-01-01

Metagenomics and single-cell genomics have enabled genome discovery from unknown branches of life. However, extracting novel genomes from complex mixtures of metagenomic data can still be challenging and represents an ill-posed problem which is generally approached with ad hoc methods. Here we present a microfluidic-based mini-metagenomic method which offers a statistically rigorous approach to extract novel microbial genomes while preserving single-cell resolution. We used this approach to analyze two hot spring samples from Yellowstone National Park and extracted 29 new genomes, including three deeply branching lineages. The single-cell resolution enabled accurate quantification of genome function and abundance, down to 1% in relative abundance. Our analyses of genome level SNP distributions also revealed low to moderate environmental selection. The scale, resolution, and statistical power of microfluidic-based mini-metagenomics make it a powerful tool to dissect the genomic structure of microbial communities while effectively preserving the fundamental unit of biology, the single cell. DOI: http://dx.doi.org/10.7554/eLife.26580.001 PMID:28678007

Comparison of methods for library construction and short read annotation of shellfish viral metagenomes.

PubMed

Wei, Hong-Ying; Huang, Sheng; Wang, Jiang-Yong; Gao, Fang; Jiang, Jing-Zhe

2018-03-01

The emergence and widespread use of high-throughput sequencing technologies have promoted metagenomic studies on environmental or animal samples. Library construction for metagenome sequencing and annotation of the produced sequence reads are important steps in such studies and influence the quality of metagenomic data. In this study, we collected some marine mollusk samples, such as Crassostrea hongkongensis, Chlamys farreri, and Ruditapes philippinarum, from coastal areas in South China. These samples were divided into two batches to compare two library construction methods for shellfish viral metagenome. Our analysis showed that reverse-transcribing RNA into cDNA and then amplifying it simultaneously with DNA by whole genome amplification (WGA) yielded a larger amount of DNA compared to using only WGA or WTA (whole transcriptome amplification). Moreover, higher quality libraries were obtained by agarose gel extraction rather than with AMPure bead size selection. However, the latter can also provide good results if combined with the adjustment of the filter parameters. This, together with its simplicity, makes it a viable alternative. Finally, we compared three annotation tools (BLAST, DIAMOND, and Taxonomer) and two reference databases (NCBI's NR and Uniprot's Uniref). Considering the limitations of computing resources and data transfer speed, we propose the use of DIAMOND with Uniref for annotating metagenomic short reads as its running speed can guarantee a good annotation rate. This study may serve as a useful reference for selecting methods for Shellfish viral metagenome library construction and read annotation.

Beyond Biodiversity: Fish Metagenomes

PubMed Central

Ardura, Alba; Planes, Serge; Garcia-Vazquez, Eva

2011-01-01

Biodiversity and intra-specific genetic diversity are interrelated and determine the potential of a community to survive and evolve. Both are considered together in Prokaryote communities treated as metagenomes or ensembles of functional variants beyond species limits. Many factors alter biodiversity in higher Eukaryote communities, and human exploitation can be one of the most important for some groups of plants and animals. For example, fisheries can modify both biodiversity and genetic diversity (intra specific). Intra-specific diversity can be drastically altered by overfishing. Intense fishing pressure on one stock may imply extinction of some genetic variants and subsequent loss of intra-specific diversity. The objective of this study was to apply a metagenome approach to fish communities and explore its value for rapid evaluation of biodiversity and genetic diversity at community level. Here we have applied the metagenome approach employing the Barcoding target gene COI as a model sequence in catch from four very different fish assemblages exploited by fisheries: freshwater communities from the Amazon River and northern Spanish rivers, and marine communities from the Cantabric and Mediterranean seas. Treating all sequences obtained from each regional catch as a biological unit (exploited community) we found that metagenomic diversity indices of the Amazonian catch sample here examined were lower than expected. Reduced diversity could be explained, at least partially, by overexploitation of the fish community that had been independently estimated by other methods. We propose using a metagenome approach for estimating diversity in Eukaryote communities and early evaluating genetic variation losses at multi-species level. PMID:21829636

Beyond biodiversity: fish metagenomes.

PubMed

Ardura, Alba; Planes, Serge; Garcia-Vazquez, Eva

2011-01-01

Biodiversity and intra-specific genetic diversity are interrelated and determine the potential of a community to survive and evolve. Both are considered together in Prokaryote communities treated as metagenomes or ensembles of functional variants beyond species limits.Many factors alter biodiversity in higher Eukaryote communities, and human exploitation can be one of the most important for some groups of plants and animals. For example, fisheries can modify both biodiversity and genetic diversity (intra specific). Intra-specific diversity can be drastically altered by overfishing. Intense fishing pressure on one stock may imply extinction of some genetic variants and subsequent loss of intra-specific diversity. The objective of this study was to apply a metagenome approach to fish communities and explore its value for rapid evaluation of biodiversity and genetic diversity at community level. Here we have applied the metagenome approach employing the barcoding target gene coi as a model sequence in catch from four very different fish assemblages exploited by fisheries: freshwater communities from the Amazon River and northern Spanish rivers, and marine communities from the Cantabric and Mediterranean seas.Treating all sequences obtained from each regional catch as a biological unit (exploited community) we found that metagenomic diversity indices of the Amazonian catch sample here examined were lower than expected. Reduced diversity could be explained, at least partially, by overexploitation of the fish community that had been independently estimated by other methods.We propose using a metagenome approach for estimating diversity in Eukaryote communities and early evaluating genetic variation losses at multi-species level.

New Passivation Methods of GaAs.

DTIC Science & Technology

1980-01-01

Fabrication of Thin Nitride Layers on GaAs 33 - 35 CHAPTER 7 Passivation of InGaAsP 36 - 37 CHAPTER 8 Emulsions on GaAs Surfaces 38 - 42 APPENDIX...not yet given any useful results. The deposition of SiO2 by using emulsions is pursued and first results on the possibility of GaAs doping are...glycol-tartaric acid based aqueous solution was used in order to anodically oxidise the gate notch after the source and drain ohmic contacts were formed

Windshield splatter analysis with the Galaxy metagenomic pipeline

PubMed Central

Kosakovsky Pond, Sergei; Wadhawan, Samir; Chiaromonte, Francesca; Ananda, Guruprasad; Chung, Wen-Yu; Taylor, James; Nekrutenko, Anton

2009-01-01

How many species inhabit our immediate surroundings? A straightforward collection technique suitable for answering this question is known to anyone who has ever driven a car at highway speeds. The windshield of a moving vehicle is subjected to numerous insect strikes and can be used as a collection device for representative sampling. Unfortunately the analysis of biological material collected in that manner, as with most metagenomic studies, proves to be rather demanding due to the large number of required tools and considerable computational infrastructure. In this study, we use organic matter collected by a moving vehicle to design and test a comprehensive pipeline for phylogenetic profiling of metagenomic samples that includes all steps from processing and quality control of data generated by next-generation sequencing technologies to statistical analyses and data visualization. To the best of our knowledge, this is also the first publication that features a live online supplement providing access to exact analyses and workflows used in the article. PMID:19819906

The metagenomic data life-cycle: standards and best practices

PubMed Central

ten Hoopen, Petra; Finn, Robert D.; Bongo, Lars Ailo; Corre, Erwan; Meyer, Folker; Mitchell, Alex; Pelletier, Eric; Pesole, Graziano; Santamaria, Monica; Willassen, Nils Peder

2017-01-01

Abstract Metagenomics data analyses from independent studies can only be compared if the analysis workflows are described in a harmonized way. In this overview, we have mapped the landscape of data standards available for the description of essential steps in metagenomics: (i) material sampling, (ii) material sequencing, (iii) data analysis, and (iv) data archiving and publishing. Taking examples from marine research, we summarize essential variables used to describe material sampling processes and sequencing procedures in a metagenomics experiment. These aspects of metagenomics dataset generation have been to some extent addressed by the scientific community, but greater awareness and adoption is still needed. We emphasize the lack of standards relating to reporting how metagenomics datasets are analysed and how the metagenomics data analysis outputs should be archived and published. We propose best practice as a foundation for a community standard to enable reproducibility and better sharing of metagenomics datasets, leading ultimately to greater metagenomics data reuse and repurposing. PMID:28637310

The metagenomic data life-cycle: standards and best practices

DOE Office of Scientific and Technical Information (OSTI.GOV)

ten Hoopen, Petra; Finn, Robert D.; Bongo, Lars Ailo

Metagenomics data analyses from independent studies can only be compared if the analysis workflows are described in a harmonised way. In this overview, we have mapped the landscape of data standards available for the description of essential steps in metagenomics: (1) material sampling, (2) material sequencing (3) data analysis and (4) data archiving & publishing. Taking examples from marine research, we summarise essential variables used to describe material sampling processes and sequencing procedures in a metagenomics experiment. These aspects of metagenomics dataset generation have been to some extent addressed by the scientific community but greater awareness and adoption is stillmore » needed. We emphasise the lack of standards relating to reporting how metagenomics datasets are analysed and how the metagenomics data analysis outputs should be archived and published. We propose best practice as a foundation for a community standard to enable reproducibility and better sharing of metagenomics datasets, leading ultimately to greater metagenomics data reuse and repurposing.« less

A better sequence-read simulator program for metagenomics.

PubMed

Johnson, Stephen; Trost, Brett; Long, Jeffrey R; Pittet, Vanessa; Kusalik, Anthony

2014-01-01

There are many programs available for generating simulated whole-genome shotgun sequence reads. The data generated by many of these programs follow predefined models, which limits their use to the authors' original intentions. For example, many models assume that read lengths follow a uniform or normal distribution. Other programs generate models from actual sequencing data, but are limited to reads from single-genome studies. To our knowledge, there are no programs that allow a user to generate simulated data following non-parametric read-length distributions and quality profiles based on empirically-derived information from metagenomics sequencing data. We present BEAR (Better Emulation for Artificial Reads), a program that uses a machine-learning approach to generate reads with lengths and quality values that closely match empirically-derived distributions. BEAR can emulate reads from various sequencing platforms, including Illumina, 454, and Ion Torrent. BEAR requires minimal user input, as it automatically determines appropriate parameter settings from user-supplied data. BEAR also uses a unique method for deriving run-specific error rates, and extracts useful statistics from the metagenomic data itself, such as quality-error models. Many existing simulators are specific to a particular sequencing technology; however, BEAR is not restricted in this way. Because of its flexibility, BEAR is particularly useful for emulating the behaviour of technologies like Ion Torrent, for which no dedicated sequencing simulators are currently available. BEAR is also the first metagenomic sequencing simulator program that automates the process of generating abundances, which can be an arduous task. BEAR is useful for evaluating data processing tools in genomics. It has many advantages over existing comparable software, such as generating more realistic reads and being independent of sequencing technology, and has features particularly useful for metagenomics work.

MBMC: An Effective Markov Chain Approach for Binning Metagenomic Reads from Environmental Shotgun Sequencing Projects.

PubMed

Wang, Ying; Hu, Haiyan; Li, Xiaoman

2016-08-01

Metagenomics is a next-generation omics field currently impacting postgenomic life sciences and medicine. Binning metagenomic reads is essential for the understanding of microbial function, compositions, and interactions in given environments. Despite the existence of dozens of computational methods for metagenomic read binning, it is still very challenging to bin reads. This is especially true for reads from unknown species, from species with similar abundance, and/or from low-abundance species in environmental samples. In this study, we developed a novel taxonomy-dependent and alignment-free approach called MBMC (Metagenomic Binning by Markov Chains). Different from all existing methods, MBMC bins reads by measuring the similarity of reads to the trained Markov chains for different taxa instead of directly comparing reads with known genomic sequences. By testing on more than 24 simulated and experimental datasets with species of similar abundance, species of low abundance, and/or unknown species, we report here that MBMC reliably grouped reads from different species into separate bins. Compared with four existing approaches, we demonstrated that the performance of MBMC was comparable with existing approaches when binning reads from sequenced species, and superior to existing approaches when binning reads from unknown species. MBMC is a pivotal tool for binning metagenomic reads in the current era of Big Data and postgenomic integrative biology. The MBMC software can be freely downloaded at http://hulab.ucf.edu/research/projects/metagenomics/MBMC.html .

Automatic Tool for Local Assembly Structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Whole community shotgun sequencing of total DNA (i.e. metagenomics) and total RNA (i.e. metatranscriptomics) has provided a wealth of information in the microbial community structure, predicted functions, metabolic networks, and is even able to reconstruct complete genomes directly. Here we present ATLAS (Automatic Tool for Local Assembly Structures) a comprehensive pipeline for assembly, annotation, genomic binning of metagenomic and metatranscriptomic data with an integrated framework for Multi-Omics. This will provide an open source tool for the Multi-Omic community at large.

FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies.

PubMed

Kim, Jiwoong; Kim, Min Soo; Koh, Andrew Y; Xie, Yang; Zhan, Xiaowei

2016-10-10

Given the lack of a complete and comprehensive library of microbial reference genomes, determining the functional profile of diverse microbial communities is challenging. The available functional analysis pipelines lack several key features: (i) an integrated alignment tool, (ii) operon-level analysis, and (iii) the ability to process large datasets. Here we introduce our open-sourced, stand-alone functional analysis pipeline for analyzing whole metagenomic and metatranscriptomic sequencing data, FMAP (Functional Mapping and Analysis Pipeline). FMAP performs alignment, gene family abundance calculations, and statistical analysis (three levels of analyses are provided: differentially-abundant genes, operons and pathways). The resulting output can be easily visualized with heatmaps and functional pathway diagrams. FMAP functional predictions are consistent with currently available functional analysis pipelines. FMAP is a comprehensive tool for providing functional analysis of metagenomic/metatranscriptomic sequencing data. With the added features of integrated alignment, operon-level analysis, and the ability to process large datasets, FMAP will be a valuable addition to the currently available functional analysis toolbox. We believe that this software will be of great value to the wider biology and bioinformatics communities.

Phosphine Functionalization GaAs(111)A Surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Traub, M.; Biteen, J; Michalak, D

Phosphorus-functionalized GaAs surfaces have been prepared by exposure of Cl-terminated GaAs(111)A surfaces to triethylphosphine (PEt3) or trichlorophosphine (PCl3), or by the direct functionalization of the native-oxide terminated GaAs(111)A surface with PCl3. The presence of phosphorus on each functionalized surface was confirmed by X-ray photoelectron spectroscopy. High-resolution, soft X-ray photoelectron spectroscopy was used to evaluate the As and Ga 3d regions of such surfaces. On PEt3 treated surfaces, the Ga 3d spectra exhibited a bulk Ga peak as well as peaks that were shifted to 0.35, 0.92 and 1.86 eV higher binding energy. These peaks were assigned to residual Cl-terminated Gamore » surface sites, surficial Ga2O and surficial Ga2O3, respectively. For PCl3-treated surfaces, the Ga 3d spectra displayed peaks ascribable to bulk Ga(As), Ga2O, and Ga2O3, as well as a peak shifted 0.30 eV to higher binding energy relative to the bulk signal. A peak corresponding to Ga(OH)3, observed on the Cl-terminated surface, was absent from all of the phosphine-functionalized surfaces. After reaction of the Cl-terminated GaAs(111)A surface with PCl3 or PEt3, the As 3d spectral region was free of As oxides and As0. Although native oxide-terminated GaAs surfaces were free of As oxides after reaction with PCl3, such surfaces contained detectable amounts of As0. Photoluminescence measurements indicted that phosphine-functionalized surfaces prepared from Cl-terminated GaAs(111)A surfaces had better electrical properties than the native-oxide capped GaAs(111)A surface, while the native-oxide covered surface treated with PCl3 showed no enhancement in PL intensity.« less

Nitridation of porous GaAs by an ECR ammonia plasma

NASA Astrophysics Data System (ADS)

Naddaf, M.; Hullavarad, S. S.; Ganesan, V.; Bhoraskar, S. V.

2006-02-01

The effect of surface porosity of GaAs on the nature of growth of GaN, by use of plasma nitridation of GaAs, has been investigated. Porous GaAs samples were prepared by anodic etching of n-type (110) GaAs wafers in HCl solution. Nitridation of porous GaAs samples were carried out by using an electron-cyclotron resonance-induced ammonia plasma. The formation of mixed phases of GaN was investigated using the grazing angle x-ray diffraction method. A remarkable improvement in the intensity of photoluminescence (PL) compared with that of GaN synthesized by direct nitriding of GaAs surface has been observed. The PL intensity of nitrided porous GaAs at the temperature of 380 °C was found to be about two orders of magnitude higher as compared with the directly nitrided GaAs at the temperature of 500 °C. The changes in the morphology of nitrided porous GaAs have been investigated using both scanning electron microscopy and atomic force microscopy.

Human milk metagenome: a functional capacity analysis

PubMed Central

2013-01-01

Background Human milk contains a diverse population of bacteria that likely influences colonization of the infant gastrointestinal tract. Recent studies, however, have been limited to characterization of this microbial community by 16S rRNA analysis. In the present study, a metagenomic approach using Illumina sequencing of a pooled milk sample (ten donors) was employed to determine the genera of bacteria and the types of bacterial open reading frames in human milk that may influence bacterial establishment and stability in this primal food matrix. The human milk metagenome was also compared to that of breast-fed and formula-fed infants’ feces (n = 5, each) and mothers’ feces (n = 3) at the phylum level and at a functional level using open reading frame abundance. Additionally, immune-modulatory bacterial-DNA motifs were also searched for within human milk. Results The bacterial community in human milk contained over 360 prokaryotic genera, with sequences aligning predominantly to the phyla of Proteobacteria (65%) and Firmicutes (34%), and the genera of Pseudomonas (61.1%), Staphylococcus (33.4%) and Streptococcus (0.5%). From assembled human milk-derived contigs, 30,128 open reading frames were annotated and assigned to functional categories. When compared to the metagenome of infants’ and mothers’ feces, the human milk metagenome was less diverse at the phylum level, and contained more open reading frames associated with nitrogen metabolism, membrane transport and stress response (P < 0.05). The human milk metagenome also contained a similar occurrence of immune-modulatory DNA motifs to that of infants’ and mothers’ fecal metagenomes. Conclusions Our results further expand the complexity of the human milk metagenome and enforce the benefits of human milk ingestion on the microbial colonization of the infant gut and immunity. Discovery of immune-modulatory motifs in the metagenome of human milk indicates more exhaustive analyses of the

The Amordad database engine for metagenomics.

PubMed

Behnam, Ehsan; Smith, Andrew D

2014-10-15

Several technical challenges in metagenomic data analysis, including assembling metagenomic sequence data or identifying operational taxonomic units, are both significant and well known. These forms of analysis are increasingly cited as conceptually flawed, given the extreme variation within traditionally defined species and rampant horizontal gene transfer. Furthermore, computational requirements of such analysis have hindered content-based organization of metagenomic data at large scale. In this article, we introduce the Amordad database engine for alignment-free, content-based indexing of metagenomic datasets. Amordad places the metagenome comparison problem in a geometric context, and uses an indexing strategy that combines random hashing with a regular nearest neighbor graph. This framework allows refinement of the database over time by continual application of random hash functions, with the effect of each hash function encoded in the nearest neighbor graph. This eliminates the need to explicitly maintain the hash functions in order for query efficiency to benefit from the accumulated randomness. Results on real and simulated data show that Amordad can support logarithmic query time for identifying similar metagenomes even as the database size reaches into the millions. Source code, licensed under the GNU general public license (version 3) is freely available for download from http://smithlabresearch.org/amordad andrewds@usc.edu Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Accurate read-based metagenome characterization using a hierarchical suite of unique signatures

PubMed Central

Freitas, Tracey Allen K.; Li, Po-E; Scholz, Matthew B.; Chain, Patrick S. G.

2015-01-01

A major challenge in the field of shotgun metagenomics is the accurate identification of organisms present within a microbial community, based on classification of short sequence reads. Though existing microbial community profiling methods have attempted to rapidly classify the millions of reads output from modern sequencers, the combination of incomplete databases, similarity among otherwise divergent genomes, errors and biases in sequencing technologies, and the large volumes of sequencing data required for metagenome sequencing has led to unacceptably high false discovery rates (FDR). Here, we present the application of a novel, gene-independent and signature-based metagenomic taxonomic profiling method with significantly and consistently smaller FDR than any other available method. Our algorithm circumvents false positives using a series of non-redundant signature databases and examines Genomic Origins Through Taxonomic CHAllenge (GOTTCHA). GOTTCHA was tested and validated on 20 synthetic and mock datasets ranging in community composition and complexity, was applied successfully to data generated from spiked environmental and clinical samples, and robustly demonstrates superior performance compared with other available tools. PMID:25765641

Metagenomic Analysis of Viruses in Feces from Unsolved Outbreaks of Gastroenteritis in Humans

PubMed Central

Moore, Nicole E.; Wang, Jing; Hewitt, Joanne; Croucher, Dawn; Williamson, Deborah A.; Paine, Shevaun; Yen, Seiha; Greening, Gail E.

2014-01-01

The etiology of an outbreak of gastroenteritis in humans cannot always be determined, and ∼25% of outbreaks remain unsolved in New Zealand. It is hypothesized that novel viruses may account for a proportion of unsolved cases, and new unbiased high-throughput sequencing methods hold promise for their detection. Analysis of the fecal metagenome can reveal the presence of viruses, bacteria, and parasites which may have evaded routine diagnostic testing. Thirty-one fecal samples from 26 gastroenteritis outbreaks of unknown etiology occurring in New Zealand between 2011 and 2012 were selected for de novo metagenomic analysis. A total data set of 193 million sequence reads of 150 bp in length was produced on an Illumina MiSeq. The metagenomic data set was searched for virus and parasite sequences, with no evidence of novel pathogens found. Eight viruses and one parasite were detected, each already known to be associated with gastroenteritis, including adenovirus, rotavirus, sapovirus, and Dientamoeba fragilis. In addition, we also describe the first detection of human parechovirus 3 (HPeV3) in Australasia. Metagenomics may thus provide a useful audit tool when applied retrospectively to determine where routine diagnostic processes may have failed to detect a pathogen. PMID:25339401

From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems.

PubMed

Garza, Daniel R; Dutilh, Bas E

2015-11-01

Microorganisms and the viruses that infect them are the most numerous biological entities on Earth and enclose its greatest biodiversity and genetic reservoir. With strength in their numbers, these microscopic organisms are major players in the cycles of energy and matter that sustain all life. Scientists have only scratched the surface of this vast microbial world through culture-dependent methods. Recent developments in generating metagenomes, large random samples of nucleic acid sequences isolated directly from the environment, are providing comprehensive portraits of the composition, structure, and functioning of microbial communities. Moreover, advances in metagenomic analysis have created the possibility of obtaining complete or nearly complete genome sequences from uncultured microorganisms, providing important means to study their biology, ecology, and evolution. Here we review some of the recent developments in the field of metagenomics, focusing on the discovery of genetic novelty and on methods for obtaining uncultured genome sequences, including through the recycling of previously published datasets. Moreover we discuss how metagenomics has become a core scientific tool to characterize eco-evolutionary patterns of microbial ecosystems, thus allowing us to simultaneously discover new microbes and study their natural communities. We conclude by discussing general guidelines and challenges for modeling the interactions between uncultured microorganisms and viruses based on the information contained in their genome sequences. These models will significantly advance our understanding of the functioning of microbial ecosystems and the roles of microbes in the environment.

GaAs VLSI technology and circuit elements for DSP

NASA Astrophysics Data System (ADS)

Mikkelson, James M.

1990-10-01

Recent progress in digital GaAs circuit performance and complexity is presented to demonstrate the current capabilities of GaAs components. High density GaAs process technology and circuit design techniques are described and critical issues for achieving favorable complexity speed power and cost tradeoffs are reviewed. Some DSP building blocks are described to provide examples of what types of DSP systems could be implemented with present GaAs technology. DIGITAL GaAs CIRCUIT CAPABILITIES In the past few years the capabilities of digital GaAs circuits have dramatically increased to the VLSI level. Major gains in circuit complexity and power-delay products have been achieved by the use of silicon-like process technologies and simple circuit topologies. The very high speed and low power consumption of digital GaAs VLSI circuits have made GaAs a desirable alternative to high performance silicon in hardware intensive high speed system applications. An example of the performance and integration complexity available with GaAs VLSI circuits is the 64x64 crosspoint switch shown in figure 1. This switch which is the most complex GaAs circuit currently available is designed on a 30 gate GaAs gate array. It operates at 200 MHz and dissipates only 8 watts of power. The reasons for increasing the level of integration of GaAs circuits are similar to the reasons for the continued increase of silicon circuit complexity. The market factors driving GaAs VLSI are system design methodology system cost power and reliability. System designers are hesitant or unwilling to go backwards to previous design techniques and lower levels of integration. A more highly integrated system in a lower performance technology can often approach the performance of a system in a higher performance technology at a lower level of integration. Higher levels of integration also lower the system component count which reduces the system cost size and power consumption while improving the system reliability

Metagenomic applications in environmental monitoring and bioremediation

DOE PAGES

Techtmann, Stephen M.; Hazen, Terry C.

2016-01-01

With the rapid advances in sequencing technology, the cost of sequencing has dramatically dropped and the scale of sequencing projects has increased accordingly. This has provided the opportunity for the routine use of sequencing techniques in the monitoring of environmental microbes. While metagenomic applications have been routinely applied to better understand the ecology and diversity of microbes, their use in environmental monitoring and bioremediation is increasingly common. In this review we seek to provide an overview of some of the metagenomic techniques used in environmental systems biology, addressing their application and limitation. We will also provide several recent examples ofmore » the application of metagenomics to bioremediation. We discuss examples where microbial communities have been used to predict the presence and extent of contamination, examples of how metagenomics can be used to characterize the process of natural attenuation by unculturable microbes, as well as examples detailing the use of metagenomics to understand the impact of biostimulation on microbial communities.« less

Metagenomic applications in environmental monitoring and bioremediation.

PubMed

Techtmann, Stephen M; Hazen, Terry C

2016-10-01

With the rapid advances in sequencing technology, the cost of sequencing has dramatically dropped and the scale of sequencing projects has increased accordingly. This has provided the opportunity for the routine use of sequencing techniques in the monitoring of environmental microbes. While metagenomic applications have been routinely applied to better understand the ecology and diversity of microbes, their use in environmental monitoring and bioremediation is increasingly common. In this review we seek to provide an overview of some of the metagenomic techniques used in environmental systems biology, addressing their application and limitation. We will also provide several recent examples of the application of metagenomics to bioremediation. We discuss examples where microbial communities have been used to predict the presence and extent of contamination, examples of how metagenomics can be used to characterize the process of natural attenuation by unculturable microbes, as well as examples detailing the use of metagenomics to understand the impact of biostimulation on microbial communities.

Viral Metagenomics on Blood-Feeding Arthropods as a Tool for Human Disease Surveillance

PubMed Central

Brinkmann, Annika; Nitsche, Andreas; Kohl, Claudia

2016-01-01

Surveillance and monitoring of viral pathogens circulating in humans and wildlife, together with the identification of emerging infectious diseases (EIDs), are critical for the prediction of future disease outbreaks and epidemics at an early stage. It is advisable to sample a broad range of vertebrates and invertebrates at different temporospatial levels on a regular basis to detect possible candidate viruses at their natural source. However, virus surveillance systems can be expensive, costly in terms of finances and resources and inadequate for sampling sufficient numbers of different host species over space and time. Recent publications have presented the concept of a new virus surveillance system, coining the terms “flying biological syringes”, “xenosurveillance” and “vector-enabled metagenomics”. According to these novel and promising surveillance approaches, viral metagenomics on engorged mosquitoes might reflect the viral diversity of numerous mammals, birds and humans, combined in the mosquitoes’ blood meal during feeding on the host. In this review article, we summarize the literature on vector-enabled metagenomics (VEM) techniques and its application in disease surveillance in humans. Furthermore, we highlight the combination of VEM and “invertebrate-derived DNA” (iDNA) analysis to identify the host DNA within the mosquito midgut. PMID:27775568

Single Cell and Metagenomic Assemblies: Biology Drives Technical Choices and Goals (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Stepanauskas, Ramunas

2018-02-06

DOE JGI's Tanja Woyke, chair of the Single Cells and Metagenomes session, delivers an introduction, followed by Bigelow Laboratory's Ramunas Stepanauskas on "Single Cell and Metagenomic Assemblies: Biology Drives Technical Choices and Goals" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Three-dimensional lattice rotation in GaAs nanowire growth on hydrogen-silsesquioxane covered GaAs (001) using molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Tran, Dat Q.; Pham, Huyen T.; Higashimine, Koichi; Oshima, Yoshifumi; Akabori, Masashi

2018-05-01

We report on crystallographic behaviors of inclined GaAs nanowires (NWs) self-crystallized on GaAs (001) substrate. The NWs were grown on hydrogen-silsesquioxane (HSQ) covered substrates using molecular beam epitaxy (MBE). Commonly, the epitaxial growth of GaAs < 111>B (B-polar) NWs is prominently observed on GaAs (001); however, we yielded a remarkable number of epitaxially grown GaAs < 111>A (A-polar) NWs in addition to the majorly obtained B-polar NWs. Such NW orientations are always accompanied by a typical inclined angle of 35° from (001) plane. NWs with another inclined angle of 74° were additionally observed and attributed to be < 111>-oriented, not in direct epitaxial relation with the substrate. Such 74° NWs' existence is related to first-order three-dimensional (3D) lattice rotation taking place at the very beginning of the growth. It turns out that spatially 60° lattice rotation around < 111> directions at GaAs seeds is essentially in charge of A- and B-polar 74° NWs. Transmission electron microscope observations reveal a high density of twinning in the B-polar NWs and twin-free characteristic in the A-polar NWs.

Molecular Diagnosis of Orthopedic-Device-Related Infection Directly from Sonication Fluid by Metagenomic Sequencing

PubMed Central

Sanderson, Nicholas D.; Atkins, Bridget L.; Brent, Andrew J.; Cole, Kevin; Foster, Dona; McNally, Martin A.; Oakley, Sarah; Peto, Leon; Taylor, Adrian; Peto, Tim E. A.; Crook, Derrick W.; Eyre, David W.

2017-01-01

ABSTRACT Culture of multiple periprosthetic tissue samples is the current gold standard for microbiological diagnosis of prosthetic joint infections (PJI). Additional diagnostic information may be obtained through culture of sonication fluid from explants. However, current techniques can have relatively low sensitivity, with prior antimicrobial therapy and infection by fastidious organisms influencing results. We assessed if metagenomic sequencing of total DNA extracts obtained direct from sonication fluid can provide an alternative rapid and sensitive tool for diagnosis of PJI. We compared metagenomic sequencing with standard aerobic and anaerobic culture in 97 sonication fluid samples from prosthetic joint and other orthopedic device infections. Reads from Illumina MiSeq sequencing were taxonomically classified using Kraken. Using 50 derivation samples, we determined optimal thresholds for the number and proportion of bacterial reads required to identify an infection and confirmed our findings in 47 independent validation samples. Compared to results from sonication fluid culture, the species-level sensitivity of metagenomic sequencing was 61/69 (88%; 95% confidence interval [CI], 77 to 94%; for derivation samples 35/38 [92%; 95% CI, 79 to 98%]; for validation samples, 26/31 [84%; 95% CI, 66 to 95%]), and genus-level sensitivity was 64/69 (93%; 95% CI, 84 to 98%). Species-level specificity, adjusting for plausible fastidious causes of infection, species found in concurrently obtained tissue samples, and prior antibiotics, was 85/97 (88%; 95% CI, 79 to 93%; for derivation samples, 43/50 [86%; 95% CI, 73 to 94%]; for validation samples, 42/47 [89%; 95% CI, 77 to 96%]). High levels of human DNA contamination were seen despite the use of laboratory methods to remove it. Rigorous laboratory good practice was required to minimize bacterial DNA contamination. We demonstrate that metagenomic sequencing can provide accurate diagnostic information in PJI. Our findings

Challenges and Opportunities of Airborne Metagenomics

PubMed Central

Behzad, Hayedeh; Gojobori, Takashi; Mineta, Katsuhiko

2015-01-01

Recent metagenomic studies of environments, such as marine and soil, have significantly enhanced our understanding of the diverse microbial communities living in these habitats and their essential roles in sustaining vast ecosystems. The increase in the number of publications related to soil and marine metagenomics is in sharp contrast to those of air, yet airborne microbes are thought to have significant impacts on many aspects of our lives from their potential roles in atmospheric events such as cloud formation, precipitation, and atmospheric chemistry to their major impact on human health. In this review, we will discuss the current progress in airborne metagenomics, with a special focus on exploring the challenges and opportunities of undertaking such studies. The main challenges of conducting metagenomic studies of airborne microbes are as follows: 1) Low density of microorganisms in the air, 2) efficient retrieval of microorganisms from the air, 3) variability in airborne microbial community composition, 4) the lack of standardized protocols and methodologies, and 5) DNA sequencing and bioinformatics-related challenges. Overcoming these challenges could provide the groundwork for comprehensive analysis of airborne microbes and their potential impact on the atmosphere, global climate, and our health. Metagenomic studies offer a unique opportunity to examine viral and bacterial diversity in the air and monitor their spread locally or across the globe, including threats from pathogenic microorganisms. Airborne metagenomic studies could also lead to discoveries of novel genes and metabolic pathways relevant to meteorological and industrial applications, environmental bioremediation, and biogeochemical cycles. PMID:25953766

Metagenomics and novel gene discovery

PubMed Central

Culligan, Eamonn P; Sleator, Roy D; Marchesi, Julian R; Hill, Colin

2014-01-01

Metagenomics provides a means of assessing the total genetic pool of all the microbes in a particular environment, in a culture-independent manner. It has revealed unprecedented diversity in microbial community composition, which is further reflected in the encoded functional diversity of the genomes, a large proportion of which consists of novel genes. Herein, we review both sequence-based and functional metagenomic methods to uncover novel genes and outline some of the associated problems of each type of approach, as well as potential solutions. Furthermore, we discuss the potential for metagenomic biotherapeutic discovery, with a particular focus on the human gut microbiome and finally, we outline how the discovery of novel genes may be used to create bioengineered probiotics. PMID:24317337

Survey of (Meta)genomic Approaches for Understanding Microbial Community Dynamics.

PubMed

Sharma, Anukriti; Lal, Rup

2017-03-01

Advancement in the next generation sequencing technologies has led to evolution of the field of genomics and metagenomics in a slim duration with nominal cost at precipitous higher rate. While metagenomics and genomics can be separately used to reveal the culture-independent and culture-based microbial evolution, respectively, (meta)genomics together can be used to demonstrate results at population level revealing in-depth complex community interactions for specific ecotypes. The field of metagenomics which started with answering "who is out there?" based on 16S rRNA gene has evolved immensely with the precise organismal reconstruction at species/strain level from the deeply covered metagenome data outweighing the need to isolate bacteria of which 99% are de facto non-cultivable. In this review we have underlined the appeal of metagenomic-derived genomes in providing insights into the evolutionary patterns, growth dynamics, genome/gene-specific sweeps, and durability of environmental pressures. We have demonstrated the use of culture-based genomics and environmental shotgun metagenome data together to elucidate environment specific genome modulations via metagenomic recruitments in terms of gene loss/gain, accessory and core-genome extent. We further illustrated the benefit of (meta)genomics in the understanding of infectious diseases by deducing the relationship between human microbiota and clinical microbiology. This review summarizes the technological advances in the (meta)genomic strategies using the genome and metagenome datasets together to increase the resolution of microbial population studies.

Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw

USGS Publications Warehouse

MacKelprang, R.; Waldrop, M.P.; Deangelis, K.M.; David, M.M.; Chavarria, K.L.; Blazewicz, S.J.; Rubin, E.M.; Jansson, J.K.

2011-01-01

Permafrost contains an estimated 1672????????Pg carbon (C), an amount roughly equivalent to the total currently contained within land plants and the atmosphere. This reservoir of C is vulnerable to decomposition as rising global temperatures cause the permafrost to thaw. During thaw, trapped organic matter may become more accessible for microbial degradation and result in greenhouse gas emissions. Despite recent advances in the use of molecular tools to study permafrost microbial communities, their response to thaw remains unclear. Here we use deep metagenomic sequencing to determine the impact of thaw on microbial phylogenetic and functional genes, and relate these data to measurements of methane emissions. Metagenomics, the direct sequencing of DNA from the environment, allows the examination of whole biochemical pathways and associated processes, as opposed to individual pieces of the metabolic puzzle. Our metagenome analyses reveal that during transition from a frozen to a thawed state there are rapid shifts in many microbial, phylogenetic and functional gene abundances and pathways. After one week of incubation at 5 ??C, permafrost metagenomes converge to be more similar to each other than while they are frozen. We find that multiple genes involved in cycling of C and nitrogen shift rapidly during thaw. We also construct the first draft genome from a complex soil metagenome, which corresponds to a novel methanogen. Methane previously accumulated in permafrost is released during thaw and subsequently consumed by methanotrophic bacteria. Together these data point towards the importance of rapid cycling of methane and nitrogen in thawing permafrost. ?? 2011 Macmillan Publishers Limited. All rights reserved.

Marine metagenomics: strategies for the discovery of novel enzymes with biotechnological applications from marine environments

PubMed Central

Kennedy, Jonathan; Marchesi, Julian R; Dobson, Alan DW

2008-01-01

Metagenomic based strategies have previously been successfully employed as powerful tools to isolate and identify enzymes with novel biocatalytic activities from the unculturable component of microbial communities from various terrestrial environmental niches. Both sequence based and function based screening approaches have been employed to identify genes encoding novel biocatalytic activities and metabolic pathways from metagenomic libraries. While much of the focus to date has centred on terrestrial based microbial ecosystems, it is clear that the marine environment has enormous microbial biodiversity that remains largely unstudied. Marine microbes are both extremely abundant and diverse; the environments they occupy likewise consist of very diverse niches. As culture-dependent methods have thus far resulted in the isolation of only a tiny percentage of the marine microbiota the application of metagenomic strategies holds great potential to study and exploit the enormous microbial biodiversity which is present within these marine environments. PMID:18717988

The electronic and optical properties of quaternary GaAs1-x-y N x Bi y alloy lattice-matched to GaAs: a first-principles study.

PubMed

Ma, Xiaoyang; Li, Dechun; Zhao, Shengzhi; Li, Guiqiu; Yang, Kejian

2014-01-01

First-principles calculations based on density functional theory have been performed for the quaternary GaAs1-x-y N x Bi y alloy lattice-matched to GaAs. Using the state-of-the-art computational method with the Heyd-Scuseria-Ernzerhof (HSE) hybrid functional, electronic, and optical properties were obtained, including band structures, density of states (DOSs), dielectric function, absorption coefficient, refractive index, energy loss function, and reflectivity. It is found that the lattice constant of GaAs1-x-y N x Bi y alloy with y/x =1.718 can match to GaAs. With the incorporation of N and Bi into GaAs, the band gap of GaAs1-x-y N x Bi y becomes small and remains direct. The calculated optical properties indicate that GaAs1-x-y N x Bi y has higher optical efficiency as it has less energy loss than GaAs. In addition, it is also found that the electronic and optical properties of GaAs1-x-y N x Bi y alloy can be further controlled by tuning the N and Bi compositions in this alloy. These results suggest promising applications of GaAs1-x-y N x Bi y quaternary alloys in optoelectronic devices.

Design and fabrication of GaAs OMIST photodetector

NASA Astrophysics Data System (ADS)

Kang, Xuejun; Lin, ShiMing; Liao, Qiwei; Gao, Junhua; Liu, Shi'an; Cheng, Peng; Wang, Hongjie; Zhang, Chunhui; Wang, Qiming

1998-08-01

We designed and fabricated GaAs OMIST (Optical-controlled Metal-Insulator-Semiconductor Thyristor) device. Using oxidation of AlAs layer that is grown by MBE forms the Ultra- Thin semi-Insulating layer (UTI) of the GAAS OMIST. The accurate control and formation of high quality semi-insulating layer (AlxOy) are the key processes for fabricating GaAs OMIST. The device exhibits a current-controlled negative resistance region in its I-V characteristics. When illuminated, the major effect of optical excitation is the reduction of the switching voltage. If the GaAs OMIST device is biased at a voltage below its dark switching voltage Vs, sufficient incident light can switch OMIST from high impedance low current 'off' state to low impedance high current 'on' state. The absorbing material of OMIST is GaAS, so if the wavelength of incident light within 600 to approximately 850 nm can be detected effectively. It is suitable to be used as photodetector for digital optical data process. The other attractive features of GaAs OMIST device include suitable conducted current, switching voltage and power levels for OEIC, high switch speed and high sensitivity to light or current injection.

Rapid and efficient method to extract metagenomic DNA from estuarine sediments.

PubMed

Shamim, Kashif; Sharma, Jaya; Dubey, Santosh Kumar

2017-07-01

Metagenomic DNA from sediments of selective estuaries of Goa, India was extracted using a simple, fast, efficient and environment friendly method. The recovery of pure metagenomic DNA from our method was significantly high as compared to other well-known methods since the concentration of recovered metagenomic DNA ranged from 1185.1 to 4579.7 µg/g of sediment. The purity of metagenomic DNA was also considerably high as the ratio of absorbance at 260 and 280 nm ranged from 1.88 to 1.94. Therefore, the recovered metagenomic DNA was directly used to perform various molecular biology experiments viz. restriction digestion, PCR amplification, cloning and metagenomic library construction. This clearly proved that our protocol for metagenomic DNA extraction using silica gel efficiently removed the contaminants and prevented shearing of the metagenomic DNA. Thus, this modified method can be used to recover pure metagenomic DNA from various estuarine sediments in a rapid, efficient and eco-friendly manner.

Metagenomic Sequencing for Surveillance of Food- and Waterborne Viral Diseases.

PubMed

Nieuwenhuijse, David F; Koopmans, Marion P G

2017-01-01

A plethora of viruses can be transmitted by the food- and waterborne route. However, their recognition is challenging because of the variety of viruses, heterogeneity of symptoms, the lack of awareness of clinicians, and limited surveillance efforts. Classical food- and waterborne viral disease outbreaks are mainly caused by caliciviruses, but the source of the virus is often not known and the foodborne mode of transmission is difficult to discriminate from human-to-human transmission. Atypical food- and waterborne viral disease can be caused by viruses such as hepatitis A and hepatitis E. In addition, a source of novel emerging viruses with a potential to spread via the food- and waterborne route is the repeated interaction of humans with wildlife. Wildlife-to-human adaptation may give rise to self- limiting outbreaks in some cases, but when fully adjusted to the human host can be devastating. Metagenomic sequencing has been investigated as a promising solution for surveillance purposes as it detects all viruses in a single protocol, delivers additional genomic information for outbreak tracing, and detects novel unknown viruses. Nevertheless, several issues must be addressed to apply metagenomic sequencing in surveillance. First, sample preparation is difficult since the genomic material of viruses is generally overshadowed by host- and bacterial genomes. Second, several data analysis issues hamper the efficient, robust, and automated processing of metagenomic data. Third, interpretation of metagenomic data is hard, because of the lack of general knowledge of the virome in the food chain and the environment. Further developments in virus-specific nucleic acid extraction methods, bioinformatic data processing applications, and unifying data visualization tools are needed to gain insightful surveillance knowledge from suspect food samples.

Metagenomic Sequencing for Surveillance of Food- and Waterborne Viral Diseases

PubMed Central

Nieuwenhuijse, David F.; Koopmans, Marion P. G.

2017-01-01

A plethora of viruses can be transmitted by the food- and waterborne route. However, their recognition is challenging because of the variety of viruses, heterogeneity of symptoms, the lack of awareness of clinicians, and limited surveillance efforts. Classical food- and waterborne viral disease outbreaks are mainly caused by caliciviruses, but the source of the virus is often not known and the foodborne mode of transmission is difficult to discriminate from human-to-human transmission. Atypical food- and waterborne viral disease can be caused by viruses such as hepatitis A and hepatitis E. In addition, a source of novel emerging viruses with a potential to spread via the food- and waterborne route is the repeated interaction of humans with wildlife. Wildlife-to-human adaptation may give rise to self- limiting outbreaks in some cases, but when fully adjusted to the human host can be devastating. Metagenomic sequencing has been investigated as a promising solution for surveillance purposes as it detects all viruses in a single protocol, delivers additional genomic information for outbreak tracing, and detects novel unknown viruses. Nevertheless, several issues must be addressed to apply metagenomic sequencing in surveillance. First, sample preparation is difficult since the genomic material of viruses is generally overshadowed by host- and bacterial genomes. Second, several data analysis issues hamper the efficient, robust, and automated processing of metagenomic data. Third, interpretation of metagenomic data is hard, because of the lack of general knowledge of the virome in the food chain and the environment. Further developments in virus-specific nucleic acid extraction methods, bioinformatic data processing applications, and unifying data visualization tools are needed to gain insightful surveillance knowledge from suspect food samples. PMID:28261185

Characteristics of GaAs with inverted thermal conversion

NASA Technical Reports Server (NTRS)

Kang, C. H.; Lagowski, J.; Gatos, H. C.

1987-01-01

GaAs crystals exhibiting inverted thermal conversion (ITC) of resistivity were investigated in conjunction with standard semiinsulating (SI) GaAs regarding characteristics important in device processing. It was established that dislocation density and Si implant activation are unaffected by transformation to the ITC state. However, in ITC GaAs the controlled increase of the EL2 (native midgap donor) concentration during annealing makes it possible to attain resistivities one order of magnitude greater (e.g., about 10 to the 9th ohm cm of 300 K) than those attained in standard SI GaAs (e.g., 10 to the 7th-10 to the 8th ohm cm).

Challenges and opportunities of airborne metagenomics.

PubMed

Behzad, Hayedeh; Gojobori, Takashi; Mineta, Katsuhiko

2015-05-06

Recent metagenomic studies of environments, such as marine and soil, have significantly enhanced our understanding of the diverse microbial communities living in these habitats and their essential roles in sustaining vast ecosystems. The increase in the number of publications related to soil and marine metagenomics is in sharp contrast to those of air, yet airborne microbes are thought to have significant impacts on many aspects of our lives from their potential roles in atmospheric events such as cloud formation, precipitation, and atmospheric chemistry to their major impact on human health. In this review, we will discuss the current progress in airborne metagenomics, with a special focus on exploring the challenges and opportunities of undertaking such studies. The main challenges of conducting metagenomic studies of airborne microbes are as follows: 1) Low density of microorganisms in the air, 2) efficient retrieval of microorganisms from the air, 3) variability in airborne microbial community composition, 4) the lack of standardized protocols and methodologies, and 5) DNA sequencing and bioinformatics-related challenges. Overcoming these challenges could provide the groundwork for comprehensive analysis of airborne microbes and their potential impact on the atmosphere, global climate, and our health. Metagenomic studies offer a unique opportunity to examine viral and bacterial diversity in the air and monitor their spread locally or across the globe, including threats from pathogenic microorganisms. Airborne metagenomic studies could also lead to discoveries of novel genes and metabolic pathways relevant to meteorological and industrial applications, environmental bioremediation, and biogeochemical cycles. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Low-temperature photoluminescence study of thin epitaxial GaAs films on Ge substrates

NASA Astrophysics Data System (ADS)

Brammertz, Guy; Mols, Yves; Degroote, Stefan; Motsnyi, Vasyl; Leys, Maarten; Borghs, Gustaaf; Caymax, Matty

2006-05-01

reduced intensity. We tentatively explain this observation by Si or Ge clustering at antiphase boundaries, which eliminates the effects of the Ga-Ga and As-As bonds. This assumption is confirmed by the fact that, at 77 K, the ratio between the intensity of the IB peak at 1.17 eV to the intensity of the peak at 1.04 eV is smaller than 1.4 for all films containing APDs, whereas it is larger than 1.4 for all films without APDs. This shows stronger clustering of Si or Ge in the material with APDs. For future electronic applications, Ge diffusion into the GaAs will have to be reduced. PL analysis will be a rapid tool for studying the Ge diffusion into the GaAs thin films.

Electrodeposition of Metal on GaAs Nanowires

NASA Astrophysics Data System (ADS)

Liu, Chao; Einabad, Omid; Watkins, Simon; Kavanagh, Karen

2010-10-01

Copper (Cu) electrical contacts to freestanding gallium arsenide (GaAs) nanowires have been fabricated via electrodeposition. The nanowires are zincblende (111) oriented grown epitaxially on n-type Si-doped GaAs (111)B substrates by gold-catalyzed Vapor Liquid Solid (VLS) growth in a metal organic vapour phase epitaxy (MOVPE) reactor. The epitaxial electrodeposition process, based on previous work with bulk GaAs substrates, consists of a substrate oxide pre-etch in dilute ammonium-hydroxide carried out prior to galvanostatic electrodeposition in a pure Cu sulphate aqueous electrolyte at 20-60^oC. For GaAs nanowires, we find that Cu or Fe has a preference for growth on the gold catalyst avoiding the sidewalls. After removing gold, both metals still prefer to grow only on top of the nanowire, which has the largest potential field.

BusyBee Web: metagenomic data analysis by bootstrapped supervised binning and annotation

PubMed Central

Kiefer, Christina; Fehlmann, Tobias; Backes, Christina

2017-01-01

Abstract Metagenomics-based studies of mixed microbial communities are impacting biotechnology, life sciences and medicine. Computational binning of metagenomic data is a powerful approach for the culture-independent recovery of population-resolved genomic sequences, i.e. from individual or closely related, constituent microorganisms. Existing binning solutions often require a priori characterized reference genomes and/or dedicated compute resources. Extending currently available reference-independent binning tools, we developed the BusyBee Web server for the automated deconvolution of metagenomic data into population-level genomic bins using assembled contigs (Illumina) or long reads (Pacific Biosciences, Oxford Nanopore Technologies). A reversible compression step as well as bootstrapped supervised binning enable quick turnaround times. The binning results are represented in interactive 2D scatterplots. Moreover, bin quality estimates, taxonomic annotations and annotations of antibiotic resistance genes are computed and visualized. Ground truth-based benchmarks of BusyBee Web demonstrate comparably high performance to state-of-the-art binning solutions for assembled contigs and markedly improved performance for long reads (median F1 scores: 70.02–95.21%). Furthermore, the applicability to real-world metagenomic datasets is shown. In conclusion, our reference-independent approach automatically bins assembled contigs or long reads, exhibits high sensitivity and precision, enables intuitive inspection of the results, and only requires FASTA-formatted input. The web-based application is freely accessible at: https://ccb-microbe.cs.uni-saarland.de/busybee. PMID:28472498

Comparative Viral Metagenomics of Environmental Samples from Korea

PubMed Central

Kim, Min-Soo; Whon, Tae Woong

2013-01-01

The introduction of metagenomics into the field of virology has facilitated the exploration of viral communities in various natural habitats. Understanding the viral ecology of a variety of sample types throughout the biosphere is important per se, but it also has potential applications in clinical and diagnostic virology. However, the procedures used by viral metagenomics may produce technical errors, such as amplification bias, while public viral databases are very limited, which may hamper the determination of the viral diversity in samples. This review considers the current state of viral metagenomics, based on examples from Korean viral metagenomic studies-i.e., rice paddy soil, fermented foods, human gut, seawater, and the near-surface atmosphere. Viral metagenomics has become widespread due to various methodological developments, and much attention has been focused on studies that consider the intrinsic role of viruses that interact with their hosts. PMID:24124407

GaAs Solar Cell Radiation Handbook

NASA Technical Reports Server (NTRS)

Anspaugh, B. E.

1996-01-01

The handbook discusses the history of GaAs solar cell development, presents equations useful for working with GaAs solar cells, describes commonly used instrumentation techniques for assessing radiation effects in solar cells and fundamental processes occurring in solar cells exposed to ionizing radiation, and explains why radiation decreases the electrical performance of solar cells. Three basic elements required to perform solar array degradation calculations: degradation data for GaAs solar cells after irradiation with 1 MeV electrons at normal incidence; relative damage coefficients for omnidirectional electron and proton exposure; and the definition of the space radiation environment for the orbit of interest, are developed and used to perform a solar array degradation calculation.

Crystal growth of device quality GaAs in space

NASA Technical Reports Server (NTRS)

Gatos, H. C.; Lagowski, J.

1979-01-01

The optimization of space processing of GaAs is described. The detailed compositional, structural, and electronic characterization of GaAs on a macro- and microscale and the relationships between growth parameters and the properties of GaAs are among the factors discussed. The key parameters limiting device performance are assessed.

Antibiotic Resistome: Improving Detection and Quantification Accuracy for Comparative Metagenomics.

PubMed

Elbehery, Ali H A; Aziz, Ramy K; Siam, Rania

2016-04-01

The unprecedented rise of life-threatening antibiotic resistance (AR), combined with the unparalleled advances in DNA sequencing of genomes and metagenomes, has pushed the need for in silico detection of the resistance potential of clinical and environmental metagenomic samples through the quantification of AR genes (i.e., genes conferring antibiotic resistance). Therefore, determining an optimal methodology to quantitatively and accurately assess AR genes in a given environment is pivotal. Here, we optimized and improved existing AR detection methodologies from metagenomic datasets to properly consider AR-generating mutations in antibiotic target genes. Through comparative metagenomic analysis of previously published AR gene abundance in three publicly available metagenomes, we illustrate how mutation-generated resistance genes are either falsely assigned or neglected, which alters the detection and quantitation of the antibiotic resistome. In addition, we inspected factors influencing the outcome of AR gene quantification using metagenome simulation experiments, and identified that genome size, AR gene length, total number of metagenomics reads and selected sequencing platforms had pronounced effects on the level of detected AR. In conclusion, our proposed improvements in the current methodologies for accurate AR detection and resistome assessment show reliable results when tested on real and simulated metagenomic datasets.

Stable isotope probing in the metagenomics era: a bridge towards improved bioremediation

PubMed Central

Uhlik, Ondrej; Leewis, Mary-Cathrine; Strejcek, Michal; Musilova, Lucie; Mackova, Martina; Leigh, Mary Beth; Macek, Tomas

2012-01-01

Microbial biodegradation and biotransformation reactions are essential to most bioremediation processes, yet the specific organisms, genes, and mechanisms involved are often not well understood. Stable isotope probing (SIP) enables researchers to directly link microbial metabolic capability to phylogenetic and metagenomic information within a community context by tracking isotopically labeled substances into phylogenetically and functionally informative biomarkers. SIP is thus applicable as a tool for the identification of active members of the microbial community and associated genes integral to the community functional potential, such as biodegradative processes. The rapid evolution of SIP over the last decade and integration with metagenomics provides researchers with a much deeper insight into potential biodegradative genes, processes, and applications, thereby enabling an improved mechanistic understanding that can facilitate advances in the field of bioremediation. PMID:23022353

Identification of fungi in shotgun metagenomics datasets

PubMed Central

Donovan, Paul D.; Gonzalez, Gabriel; Higgins, Desmond G.

2018-01-01

Metagenomics uses nucleic acid sequencing to characterize species diversity in different niches such as environmental biomes or the human microbiome. Most studies have used 16S rRNA amplicon sequencing to identify bacteria. However, the decreasing cost of sequencing has resulted in a gradual shift away from amplicon analyses and towards shotgun metagenomic sequencing. Shotgun metagenomic data can be used to identify a wide range of species, but have rarely been applied to fungal identification. Here, we develop a sequence classification pipeline, FindFungi, and use it to identify fungal sequences in public metagenome datasets. We focus primarily on animal metagenomes, especially those from pig and mouse microbiomes. We identified fungi in 39 of 70 datasets comprising 71 fungal species. At least 11 pathogenic species with zoonotic potential were identified, including Candida tropicalis. We identified Pseudogymnoascus species from 13 Antarctic soil samples initially analyzed for the presence of bacteria capable of degrading diesel oil. We also show that Candida tropicalis and Candida loboi are likely the same species. In addition, we identify several examples where contaminating DNA was erroneously included in fungal genome assemblies. PMID:29444186

Beyond research: a primer for considerations on using viral metagenomics in the field and clinic.

PubMed

Hall, Richard J; Draper, Jenny L; Nielsen, Fiona G G; Dutilh, Bas E

2015-01-01

Powered by recent advances in next-generation sequencing technologies, metagenomics has already unveiled vast microbial biodiversity in a range of environments, and is increasingly being applied in clinics for difficult-to-diagnose cases. It can be tempting to suggest that metagenomics could be used as a "universal test" for all pathogens without the need to conduct lengthy serial testing using specific assays. While this is an exciting prospect, there are issues that need to be addressed before metagenomic methods can be applied with rigor as a diagnostic tool, including the potential for incidental findings, unforeseen consequences for trade and regulatory authorities, privacy and cultural issues, data sharing, and appropriate reporting of results to end-users. These issues will require consideration and discussion across a range of disciplines, with inclusion of scientists, ethicists, clinicians, diagnosticians, health practitioners, and ultimately the public. Here, we provide a primer for consideration on some of these issues.

Characterisation of semi-insulating GaAs

NASA Technical Reports Server (NTRS)

Walukiewicz, W.; Pawlowicz, L.; Lagowski, J.; Gatos, H. C.

1982-01-01

Hole and electron mobilities as functions of temperature and ionised impurity concentration are calculated for GaAs. It is shown that these calculations, when used to analyse electrical properties of semi-insulating GaAs, enable an assessment of the Fermi energy position and ionised impurity concentration to be made. In contrast to previous work, the analysis does not require any phenomenological assumptions.

Technology requirements for GaAs photovoltaic arrays

NASA Technical Reports Server (NTRS)

Scott-Monck, J.; Rockey, D.

1981-01-01

An analysis based on percent GaAs solar cell weight and cost is performed to assess the utility of this cell for future space missions. It is shown that the GaAs substrate cost and the end-of-life (EOL) advantage the cell can provide over the space qualified silicon solar cell are the dominant factors determining potential use. Examples are presented to show that system level advantages resulting from reduction in solar panel area may warrant the use of GaAs at its current weight and projected initial cost provided the EOL advantage over silicon is at least 20 percent.

Crystal Growth of Device Quality Gaas in Space

NASA Technical Reports Server (NTRS)

Gatos, H. C.

1985-01-01

The GaAs research evolves about these key thrust areas. The overall program combines: (1) studies of crystal growth on novel approaches to engineering of semiconductor material (i.e., GaAs and related compounds); (2) investigation and correlation of materials properties and electronic characteristics on a macro- and microscale; and (3) investigation of electronic properties and phenomena controlling device applications and device performance. This effort is aimed at the essential ground-based program which would insure successful experimentation with and eventually processing of GaAs in near zero gravity environment. It is believed that this program addresses in a unique way materials engineering aspects which bear directly on the future exploitation of the potential of GaAs and related materials in device and systems applications.

Crystal growth of device quality GaAs in space

NASA Technical Reports Server (NTRS)

Gatos, H. C.; Lagowski, J.

1984-01-01

The crystal growth, device processing and device related properties and phenomena of GaAs are investigated. Our GaAs research evolves about these key thrust areas. The overall program combines: (1) studies of crystal growth on novel approaches to engineering of semiconductor materials (i.e., GaAs and related compounds); (2) investigation and correlation of materials properties and electronic characteristics on a macro- and microscale; (3) investigation of electronic properties and phenomena controlling device applications and device performance. The ground based program is developed which would insure successful experimentation with and eventually processing of GaAs in a near zero gravity environment.

Genome signature analysis of thermal virus metagenomes reveals Archaea and thermophilic signatures.

PubMed

Pride, David T; Schoenfeld, Thomas

2008-09-17

Metagenomic analysis provides a rich source of biological information for otherwise intractable viral communities. However, study of viral metagenomes has been hampered by its nearly complete reliance on BLAST algorithms for identification of DNA sequences. We sought to develop algorithms for examination of viral metagenomes to identify the origin of sequences independent of BLAST algorithms. We chose viral metagenomes obtained from two hot springs, Bear Paw and Octopus, in Yellowstone National Park, as they represent simple microbial populations where comparatively large contigs were obtained. Thermal spring metagenomes have high proportions of sequences without significant Genbank homology, which has hampered identification of viruses and their linkage with hosts. To analyze each metagenome, we developed a method to classify DNA fragments using genome signature-based phylogenetic classification (GSPC), where metagenomic fragments are compared to a database of oligonucleotide signatures for all previously sequenced Bacteria, Archaea, and viruses. From both Bear Paw and Octopus hot springs, each assembled contig had more similarity to other metagenome contigs than to any sequenced microbial genome based on GSPC analysis, suggesting a genome signature common to each of these extreme environments. While viral metagenomes from Bear Paw and Octopus share some similarity, the genome signatures from each locale are largely unique. GSPC using a microbial database predicts most of the Octopus metagenome has archaeal signatures, while bacterial signatures predominate in Bear Paw; a finding consistent with those of Genbank BLAST. When using a viral database, the majority of the Octopus metagenome is predicted to belong to archaeal virus Families Globuloviridae and Fuselloviridae, while none of the Bear Paw metagenome is predicted to belong to archaeal viruses. As expected, when microbial and viral databases are combined, each of the Octopus and Bear Paw metagenomic contigs

Supernormal hardness increase of dilute Ga(As, N) thin films

NASA Astrophysics Data System (ADS)

Berggren, Jonas; Hanke, Michael; Luna, Esperanza; Trampert, Achim

2017-03-01

Hardness of epitaxial GaAs1-xNx films on GaAs(001) with different film thicknesses, varying from 80 to 700 nm, and nitrogen compositions x between zero (pure GaAs) and 0.031, were studied by means of nano-indentation. As a result, a disproportionate and monotonic increase by 17% in hardness was proved in the dilute range from GaAs to GaAs0.969N0.031. We are tracing this observation to solid solution strengthening, an extrinsic effect based on dislocation pinning due to interstitial nitrogen. On the other hand, intrinsic effects related to different electronegativities of As and N (i.e., altered bonding conditions) could be ruled out. Furthermore, in tensilely strained GaAs1-xNx layers, the appearance of cracks acts as the main strain relieving mechanism. A correlation between cracking and hardness reduction is investigated and discussed as a further relaxation pathway.

Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes

PubMed Central

Aziz, Ramy K.; Dwivedi, Bhakti; Akhter, Sajia; Breitbart, Mya; Edwards, Robert A.

2015-01-01

Phages are the most abundant biological entities on Earth and play major ecological roles, yet the current sequenced phage genomes do not adequately represent their diversity, and little is known about the abundance and distribution of these sequenced genomes in nature. Although the study of phage ecology has benefited tremendously from the emergence of metagenomic sequencing, a systematic survey of phage genes and genomes in various ecosystems is still lacking, and fundamental questions about phage biology, lifestyle, and ecology remain unanswered. To address these questions and improve comparative analysis of phages in different metagenomes, we screened a core set of publicly available metagenomic samples for sequences related to completely sequenced phages using the web tool, Phage Eco-Locator. We then adopted and deployed an array of mathematical and statistical metrics for a multidimensional estimation of the abundance and distribution of phage genes and genomes in various ecosystems. Experiments using those metrics individually showed their usefulness in emphasizing the pervasive, yet uneven, distribution of known phage sequences in environmental metagenomes. Using these metrics in combination allowed us to resolve phage genomes into clusters that correlated with their genotypes and taxonomic classes as well as their ecological properties. We propose adding this set of metrics to current metaviromic analysis pipelines, where they can provide insight regarding phage mosaicism, habitat specificity, and evolution. PMID:26005436

Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes

DOE PAGES

Aziz, Ramy K.; Dwivedi, Bhakti; Akhter, Sajia; ...

2015-05-08

Phages are the most abundant biological entities on Earth and play major ecological roles, yet the current sequenced phage genomes do not adequately represent their diversity, and little is known about the abundance and distribution of these sequenced genomes in nature. Although the study of phage ecology has benefited tremendously from the emergence of metagenomic sequencing, a systematic survey of phage genes and genomes in various ecosystems is still lacking, and fundamental questions about phage biology, lifestyle, and ecology remain unanswered. To address these questions and improve comparative analysis of phages in different metagenomes, we screened a core set ofmore » publicly available metagenomic samples for sequences related to completely sequenced phages using the web tool, Phage Eco-Locator. We then adopted and deployed an array of mathematical and statistical metrics for a multidimensional estimation of the abundance and distribution of phage genes and genomes in various ecosystems. Experiments using those metrics individually showed their usefulness in emphasizing the pervasive, yet uneven, distribution of known phage sequences in environmental metagenomes. Using these metrics in combination allowed us to resolve phage genomes into clusters that correlated with their genotypes and taxonomic classes as well as their ecological properties. By adding this set of metrics to current metaviromic analysis pipelines, where they can provide insight regarding phage mosaicism, habitat specificity, and evolution.« less

Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aziz, Ramy K.; Dwivedi, Bhakti; Akhter, Sajia

Phages are the most abundant biological entities on Earth and play major ecological roles, yet the current sequenced phage genomes do not adequately represent their diversity, and little is known about the abundance and distribution of these sequenced genomes in nature. Although the study of phage ecology has benefited tremendously from the emergence of metagenomic sequencing, a systematic survey of phage genes and genomes in various ecosystems is still lacking, and fundamental questions about phage biology, lifestyle, and ecology remain unanswered. To address these questions and improve comparative analysis of phages in different metagenomes, we screened a core set ofmore » publicly available metagenomic samples for sequences related to completely sequenced phages using the web tool, Phage Eco-Locator. We then adopted and deployed an array of mathematical and statistical metrics for a multidimensional estimation of the abundance and distribution of phage genes and genomes in various ecosystems. Experiments using those metrics individually showed their usefulness in emphasizing the pervasive, yet uneven, distribution of known phage sequences in environmental metagenomes. Using these metrics in combination allowed us to resolve phage genomes into clusters that correlated with their genotypes and taxonomic classes as well as their ecological properties. By adding this set of metrics to current metaviromic analysis pipelines, where they can provide insight regarding phage mosaicism, habitat specificity, and evolution.« less

Doping assessment in GaAs nanowires.

PubMed

Goktas, N Isik; Fiordaliso, E M; LaPierre, R R

2018-06-08

Semiconductor nanowires (NWs) are a candidate technology for future optoelectronic devices. One of the critical issues in NWs is the control of impurity doping for the formation of p-n junctions. In this study, beryllium (p-type dopant) and tellurium (n-type dopant) in self-assisted GaAs NWs was studied. The GaAs NWs were grown on (111) Si by molecular beam epitaxy using the self-assisted method. The dopant incorporation in the self-assisted GaAs NWs was investigated using Raman spectroscopy, photoluminescence, secondary ion mass spectrometry and electron holography. Be-doped NWs showed similar carrier concentration as compared to thin film (TF) standards. However, Te-doped NWs showed at least a one order of magnitude lower carrier concentration as compared to TF standards. Dopant incorporation mechanisms in NWs are discussed.

Doping assessment in GaAs nanowires

NASA Astrophysics Data System (ADS)

Isik Goktas, N.; Fiordaliso, E. M.; LaPierre, R. R.

2018-06-01

Semiconductor nanowires (NWs) are a candidate technology for future optoelectronic devices. One of the critical issues in NWs is the control of impurity doping for the formation of p–n junctions. In this study, beryllium (p-type dopant) and tellurium (n-type dopant) in self-assisted GaAs NWs was studied. The GaAs NWs were grown on (111) Si by molecular beam epitaxy using the self-assisted method. The dopant incorporation in the self-assisted GaAs NWs was investigated using Raman spectroscopy, photoluminescence, secondary ion mass spectrometry and electron holography. Be-doped NWs showed similar carrier concentration as compared to thin film (TF) standards. However, Te-doped NWs showed at least a one order of magnitude lower carrier concentration as compared to TF standards. Dopant incorporation mechanisms in NWs are discussed.

Using populations of human and microbial genomes for organism detection in metagenomes

DOE PAGES

Ames, Sasha K.; Gardner, Shea N.; Marti, Jose Manuel; ...

2015-04-29

Identifying causative disease agents in human patients from shotgun metagenomic sequencing (SMS) presents a powerful tool to apply when other targeted diagnostics fail. Numerous technical challenges remain, however, before SMS can move beyond the role of research tool. Accurately separating the known and unknown organism content remains difficult, particularly when SMS is applied as a last resort. The true amount of human DNA that remains in a sample after screening against the human reference genome and filtering nonbiological components left from library preparation has previously been underreported. In this study, we create the most comprehensive collection of microbial and reference-freemore » human genetic variation available in a database optimized for efficient metagenomic search by extracting sequences from GenBank and the 1000 Genomes Project. The results reveal new human sequences found in individual Human Microbiome Project (HMP) samples. Individual samples contain up to 95% human sequence, and 4% of the individual HMP samples contain 10% or more human reads. In conclusion, left unidentified, human reads can complicate and slow down further analysis and lead to inaccurately labeled microbial taxa and ultimately lead to privacy concerns as more human genome data is collected.« less

Using populations of human and microbial genomes for organism detection in metagenomes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ames, Sasha K.; Gardner, Shea N.; Marti, Jose Manuel

Identifying causative disease agents in human patients from shotgun metagenomic sequencing (SMS) presents a powerful tool to apply when other targeted diagnostics fail. Numerous technical challenges remain, however, before SMS can move beyond the role of research tool. Accurately separating the known and unknown organism content remains difficult, particularly when SMS is applied as a last resort. The true amount of human DNA that remains in a sample after screening against the human reference genome and filtering nonbiological components left from library preparation has previously been underreported. In this study, we create the most comprehensive collection of microbial and reference-freemore » human genetic variation available in a database optimized for efficient metagenomic search by extracting sequences from GenBank and the 1000 Genomes Project. The results reveal new human sequences found in individual Human Microbiome Project (HMP) samples. Individual samples contain up to 95% human sequence, and 4% of the individual HMP samples contain 10% or more human reads. In conclusion, left unidentified, human reads can complicate and slow down further analysis and lead to inaccurately labeled microbial taxa and ultimately lead to privacy concerns as more human genome data is collected.« less

MetaDP: a comprehensive web server for disease prediction of 16S rRNA metagenomic datasets.

PubMed

Xu, Xilin; Wu, Aiping; Zhang, Xinlei; Su, Mingming; Jiang, Taijiao; Yuan, Zhe-Ming

2016-01-01

High-throughput sequencing-based metagenomics has garnered considerable interest in recent years. Numerous methods and tools have been developed for the analysis of metagenomic data. However, it is still a daunting task to install a large number of tools and complete a complicated analysis, especially for researchers with minimal bioinformatics backgrounds. To address this problem, we constructed an automated software named MetaDP for 16S rRNA sequencing data analysis, including data quality control, operational taxonomic unit clustering, diversity analysis, and disease risk prediction modeling. Furthermore, a support vector machine-based prediction model for intestinal bowel syndrome (IBS) was built by applying MetaDP to microbial 16S sequencing data from 108 children. The success of the IBS prediction model suggests that the platform may also be applied to other diseases related to gut microbes, such as obesity, metabolic syndrome, or intestinal cancer, among others (http://metadp.cn:7001/).

The Challenge and Potential of Metagenomics in the Clinic

PubMed Central

Mulcahy-O’Grady, Heidi; Workentine, Matthew L.

2016-01-01

resistance identified from the sequencing data. All of these applications rely on sophisticated computational tools, and we also discuss the importance of skilled bioinformatic support for the implementation and use of metagenomics in the clinic. PMID:26870044

Dereplication, Aggregation and Scoring Tool (DAS Tool) v1.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

SIEBER, CHRISTIAN

Communities of uncultivated microbes are critical to ecosystem function and microorganism health, and a key objective of metagenomic studies is to analyze organism-specific metabolic pathways and reconstruct community interaction networks. This requires accurate assignment of genes to genomes, yet existing binning methods often fail to predict a reasonable number of genomes and report many bins of low quality and completeness. Furthermore, the performance of existing algorithms varies between samples and biotypes. Here, we present a dereplication, aggregation and scoring strategy, DAS Tool, that combines the strengths of a flexible set of established binning algorithms. DAS Tools applied to a constructedmore » community generated more accurate bins than any automated method. Further, when applied to samples of different complexity, including soil, natural oil seeps, and the human gut, DAS Tool recovered substantially more near-complete genomes than any single binning method alone. Included were three genomes from a novel lineage . The ability to reconstruct many near-complete genomes from metagenomics data will greatly advance genome-centric analyses of ecosystems.« less

Genome signature analysis of thermal virus metagenomes reveals Archaea and thermophilic signatures

PubMed Central

Pride, David T; Schoenfeld, Thomas

2008-01-01

Background Metagenomic analysis provides a rich source of biological information for otherwise intractable viral communities. However, study of viral metagenomes has been hampered by its nearly complete reliance on BLAST algorithms for identification of DNA sequences. We sought to develop algorithms for examination of viral metagenomes to identify the origin of sequences independent of BLAST algorithms. We chose viral metagenomes obtained from two hot springs, Bear Paw and Octopus, in Yellowstone National Park, as they represent simple microbial populations where comparatively large contigs were obtained. Thermal spring metagenomes have high proportions of sequences without significant Genbank homology, which has hampered identification of viruses and their linkage with hosts. To analyze each metagenome, we developed a method to classify DNA fragments using genome signature-based phylogenetic classification (GSPC), where metagenomic fragments are compared to a database of oligonucleotide signatures for all previously sequenced Bacteria, Archaea, and viruses. Results From both Bear Paw and Octopus hot springs, each assembled contig had more similarity to other metagenome contigs than to any sequenced microbial genome based on GSPC analysis, suggesting a genome signature common to each of these extreme environments. While viral metagenomes from Bear Paw and Octopus share some similarity, the genome signatures from each locale are largely unique. GSPC using a microbial database predicts most of the Octopus metagenome has archaeal signatures, while bacterial signatures predominate in Bear Paw; a finding consistent with those of Genbank BLAST. When using a viral database, the majority of the Octopus metagenome is predicted to belong to archaeal virus Families Globuloviridae and Fuselloviridae, while none of the Bear Paw metagenome is predicted to belong to archaeal viruses. As expected, when microbial and viral databases are combined, each of the Octopus and Bear Paw

Data on partial polyhydroxyalkanoate synthase genes (phaC) mined from Aaptos aaptos marine sponge-associated bacteria metagenome.

PubMed

Amelia, Tan Suet May; Amirul, Al-Ashraf Abdullah; Bhubalan, Kesaven

2018-02-01

We report data associated with the identification of three polyhydroxyalkanoate synthase genes (phaC) isolated from the marine bacteria metagenome of Aaptos aaptos marine sponge in the waters of Bidong Island, Terengganu, Malaysia. Our data describe the extraction of bacterial metagenome from sponge tissue, measurement of purity and concentration of extracted metagenome, polymerase chain reaction (PCR)-mediated amplification using degenerate primers targeting Class I and II phaC genes, sequencing at First BASE Laboratories Sdn Bhd, and phylogenetic analysis of identified and known phaC genes. The partial nucleotide sequences were aligned, refined, compared with the Basic Local Alignment Search Tool (BLAST) databases, and released online in GenBank. The data include the identified partial putative phaC and their GenBank accession numbers, which are Rhodocista sp. phaC (MF457754), Pseudomonas sp. phaC (MF437016), and an uncultured bacterium AR5-9d_16 phaC (MF457753).

Exploiting HPC Platforms for Metagenomics: Challenges and Opportunities (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Canon, Shane

2018-01-24

DOE JGI's Zhong Wang, chair of the High-performance Computing session, gives a brief introduction before Berkeley Lab's Shane Canon talks about "Exploiting HPC Platforms for Metagenomics: Challenges and Opportunities" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

GaAs photoconductive semiconductor switch

DOEpatents

Loubriel, Guillermo M.; Baca, Albert G.; Zutavern, Fred J.

1998-01-01

A high gain, optically triggered, photoconductive semiconductor switch (PCSS) implemented in GaAs as a reverse-biased pin structure with a passivation layer above the intrinsic GaAs substrate in the gap between the two electrodes of the device. The reverse-biased configuration in combination with the addition of the passivation layer greatly reduces surface current leakage that has been a problem for prior PCSS devices and enables employment of the much less expensive and more reliable DC charging systems instead of the pulsed charging systems that needed to be used with prior PCSS devices.

MetaSort untangles metagenome assembly by reducing microbial community complexity

PubMed Central

Ji, Peifeng; Zhang, Yanming; Wang, Jinfeng; Zhao, Fangqing

2017-01-01

Most current approaches to analyse metagenomic data rely on reference genomes. Novel microbial communities extend far beyond the coverage of reference databases and de novo metagenome assembly from complex microbial communities remains a great challenge. Here we present a novel experimental and bioinformatic framework, metaSort, for effective construction of bacterial genomes from metagenomic samples. MetaSort provides a sorted mini-metagenome approach based on flow cytometry and single-cell sequencing methodologies, and employs new computational algorithms to efficiently recover high-quality genomes from the sorted mini-metagenome by the complementary of the original metagenome. Through extensive evaluations, we demonstrated that metaSort has an excellent and unbiased performance on genome recovery and assembly. Furthermore, we applied metaSort to an unexplored microflora colonized on the surface of marine kelp and successfully recovered 75 high-quality genomes at one time. This approach will greatly improve access to microbial genomes from complex or novel communities. PMID:28112173

PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures

PubMed Central

Lipinski, Leszek; Dziembowski, Andrzej

2018-01-01

Abstract Plasmids are mobile genetics elements that play an important role in the environmental adaptation of microorganisms. Although plasmids are usually analyzed in cultured microorganisms, there is a need for methods that allow for the analysis of pools of plasmids (plasmidomes) in environmental samples. To that end, several molecular biology and bioinformatics methods have been developed; however, they are limited to environments with low diversity and cannot recover large plasmids. Here, we present PlasFlow, a novel tool based on genomic signatures that employs a neural network approach for identification of bacterial plasmid sequences in environmental samples. PlasFlow can recover plasmid sequences from assembled metagenomes without any prior knowledge of the taxonomical or functional composition of samples with an accuracy up to 96%. It can also recover sequences of both circular and linear plasmids and can perform initial taxonomical classification of sequences. Compared to other currently available tools, PlasFlow demonstrated significantly better performance on test datasets. Analysis of two samples from heavy metal-contaminated microbial mats revealed that plasmids may constitute an important fraction of their metagenomes and carry genes involved in heavy-metal homeostasis, proving the pivotal role of plasmids in microorganism adaptation to environmental conditions. PMID:29346586

Structure of high-index GaAs surfaces - the discovery of the stable GaAs(2511) surface

NASA Astrophysics Data System (ADS)

Jacobi, K.; Geelhaar, L.; Márquez, J.

We present a brief overview of surface structures of high-index GaAs surfaces, putting emphasis on recent progress in our own laboratory. By adapting a commercial scanning tunneling microscope (STM) to our molecular beam epitaxy and ultra high vacuum analysis chamber system, we have been able to atomically resolve the GaAs( {1} {1} {3})B(8 ×1), (114)Aα2(2×1), (137), (3715), and (2511) surface structures. In cooperation with P. Kratzer and M. Scheffler from the Theory Department of the Fritz-Haber Institute we determined the structure of some of these surfaces by comparing total-energy calculations and STM image simulations with the atomically resolved STM images. We present the results for the {112}, {113}, and {114} surfaces. Then we describe what led us to proceed into the inner parts of the stereographic triangle and to discover the hitherto unknown stable GaAs(2511) surface.

Electrode pattern design for GaAs betavoltaic batteries

NASA Astrophysics Data System (ADS)

Haiyang, Chen; Jianhua, Yin; Darang, Li

2011-08-01

The sensitivities of betavoltaic batteries and photovoltaic batteries to series and parallel resistance are studied. Based on the study, an electrode pattern design principle of GaAs betavoltaic batteries is proposed. GaAs PIN junctions with and without the proposed electrode pattern are fabricated and measured under the illumination of 63Ni. Results show that the proposed electrode can reduce the backscattering and shadowing for the beta particles from 63Ni to increase the GaAs betavoltaic battery short circuit currents effectively but has little impact on the fill factors and ideal factors.

GaAs core--shell nanowires for photovoltaic applications.

PubMed

Czaban, Josef A; Thompson, David A; LaPierre, Ray R

2009-01-01

We report the use of Te as an n-type dopant in GaAs core-shell p-n junction nanowires for use in photovoltaic devices. Te produced significant change in the morphology of GaAs nanowires grown by the vapor-liquid-solid process in a molecular beam epitaxy system. The increase in radial growth of nanowires due to the surfactant effect of Te had a significant impact on the operating characteristics of photovoltaic devices. A decrease in solar cell efficiency occurred when the Te-doped GaAs growth duration was increased.

RCN4GSC workshop report: managing data at the interface of biodiversity and (meta)genomics, March 2011

USDA-ARS?s Scientific Manuscript database

The Genomic Standards Consortium (GSC) is an international working body with the mission of working towards richer descriptions of genomic and metagenomic data through the development of standards and tools for supporting the consistent documentation of contextual information about sequences. Becaus...

Strain/species identification in metagenomes using genome-specific markers

PubMed Central

Tu, Qichao; He, Zhili; Zhou, Jizhong

2014-01-01

Shotgun metagenome sequencing has become a fast, cheap and high-throughput technology for characterizing microbial communities in complex environments and human body sites. However, accurate identification of microorganisms at the strain/species level remains extremely challenging. We present a novel k-mer-based approach, termed GSMer, that identifies genome-specific markers (GSMs) from currently sequenced microbial genomes, which were then used for strain/species-level identification in metagenomes. Using 5390 sequenced microbial genomes, 8 770 321 50-mer strain-specific and 11 736 360 species-specific GSMs were identified for 4088 strains and 2005 species (4933 strains), respectively. The GSMs were first evaluated against mock community metagenomes, recently sequenced genomes and real metagenomes from different body sites, suggesting that the identified GSMs were specific to their targeting genomes. Sensitivity evaluation against synthetic metagenomes with different coverage suggested that 50 GSMs per strain were sufficient to identify most microbial strains with ≥0.25× coverage, and 10% of selected GSMs in a database should be detected for confident positive callings. Application of GSMs identified 45 and 74 microbial strains/species significantly associated with type 2 diabetes patients and obese/lean individuals from corresponding gastrointestinal tract metagenomes, respectively. Our result agreed with previous studies but provided strain-level information. The approach can be directly applied to identify microbial strains/species from raw metagenomes, without the effort of complex data pre-processing. PMID:24523352

Cost-benefit analysis of introducing next-generation sequencing (metagenomic) pathogen testing in the setting of pyrexia of unknown origin.

PubMed

Chai, Jia Hui; Lee, Chun Kiat; Lee, Hong Kai; Wong, Nicholas; Teo, Kahwee; Tan, Chuen Seng; Thokala, Praveen; Tang, Julian Wei-Tze; Tambyah, Paul Anantharajah; Oh, Vernon Min Sen; Loh, Tze Ping; Yoong, Joanne

2018-01-01

Pyrexia of unknown origin (PUO) is defined as a temperature of >38.3°C that lasts for >3 weeks, where no cause can be found despite appropriate investigation. Existing protocols for the work-up of PUO can be extensive and costly, motivating the application of recent advances in molecular diagnostics to pathogen testing. There have been many reports describing various analytical methods and performance of metagenomic pathogen testing in clinical samples but the economics of it has been less well studied. This study pragmatically evaluates the feasibility of introducing metagenomic testing in this setting by assessing the relative cost of clinically-relevant strategies employing this investigative tool under various cost and performance scenarios using Singapore as a demonstration case, and assessing the price and performance benchmarks, which would need to be achieved for metagenomic testing to be potentially considered financially viable relative to the current diagnostic standard. This study has some important limitations: we examined only impact of introducing the metagenomic test to the overall diagnostic cost and excluded costs associated with hospitalization and makes assumptions about the performance of the routine diagnostic tests, limiting the cost of metagenomic test, and the lack of further work-up after positive pathogen detection by the metagenomic test. However, these assumptions were necessary to keep the model within reasonable limits. In spite of these, the simplified presentation lends itself to the illustration of the key insights of our paper. In general, we find the use of metagenomic testing as second-line investigation is effectively dominated, and that use of metagenomic testing at first-line would typically require higher rates of detection or lower cost than currently available in order to be justifiable purely as a cost-saving measure. We conclude that current conditions do not warrant a widespread rush to deploy metagenomic testing to

Understanding and Curing Structural Defects in Colloidal GaAs Nanocrystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Srivastava, Vishwas; Liu, Wenyong; Janke, Eric M.

2017-02-22

Nearly three decades since the first report on the synthesis of colloidal GaAs nanocrystals (NCs), the preparation and properties of this material remain highly controversial. Traditional synthetic routes either fail to produce the GaAs phase or result in materials that do not show expected optical properties such as excitonic transitions. In this work, we demonstrate a variety of synthetic routes toward crystalline GaAs NCs. By using a combination of Raman, EXAFS and transient absorption spectroscopies, we conclude that unusual optical properties of 2 colloidal GaAs NCs can be related to the presence of vacancies and lattice disorder. We introduce novelmore » molten salt based annealing approach to alleviate these structural defects and show the emergence of size-dependent excitonic transitions in colloidal GaAs quantum dots.« less

GaAs homojunction solar cell development

NASA Technical Reports Server (NTRS)

Flood, D. J.; Swartz, C. K.; Hart, R. E., Jr.

1980-01-01

The Lincoln Laboratory n(+)/p/p(+) GaAs shallow homojunction cell structure was successfully demonstrated on 2 by 2 cm GaAs substrates. Air mass zero efficiencies of the seven cells produced to date range from 13.6 to 15.6 percent. Current voltage (I-V) characteristics, spectral response, and measurements were made on all seven cells. Preliminary analysis of 1 MeV electron radiation damage data indicate excellent radiation resistance for these cells.

Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids

NASA Astrophysics Data System (ADS)

Jungbluth, Sean P.; Amend, Jan P.; Rappé, Michael S.

2017-03-01

The global deep subsurface biosphere is one of the largest reservoirs for microbial life on our planet. This study takes advantage of new sampling technologies and couples them with improvements to DNA sequencing and associated informatics tools to reconstruct the genomes of uncultivated Bacteria and Archaea from fluids collected deep within the Juan de Fuca Ridge subseafloor. Here, we generated two metagenomes from borehole observatories located 311 meters apart and, using binning tools, retrieved 98 genomes from metagenomes (GFMs). Of the GFMs, 31 were estimated to be >90% complete, while an additional 17 were >70% complete. Phylogenomic analysis revealed 53 bacterial and 45 archaeal GFMs, of which nearly all were distantly related to known cultivated isolates. In the GFMs, abundant Bacteria included Chloroflexi, Nitrospirae, Acetothermia (OP1), EM3, Aminicenantes (OP8), Gammaproteobacteria, and Deltaproteobacteria, while abundant Archaea included Archaeoglobi, Bathyarchaeota (MCG), and Marine Benthic Group E (MBG-E). These data are the first GFMs reconstructed from the deep basaltic subseafloor biosphere, and provide a dataset available for further interrogation.

Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids.

PubMed

Jungbluth, Sean P; Amend, Jan P; Rappé, Michael S

2017-03-28

The global deep subsurface biosphere is one of the largest reservoirs for microbial life on our planet. This study takes advantage of new sampling technologies and couples them with improvements to DNA sequencing and associated informatics tools to reconstruct the genomes of uncultivated Bacteria and Archaea from fluids collected deep within the Juan de Fuca Ridge subseafloor. Here, we generated two metagenomes from borehole observatories located 311 meters apart and, using binning tools, retrieved 98 genomes from metagenomes (GFMs). Of the GFMs, 31 were estimated to be >90% complete, while an additional 17 were >70% complete. Phylogenomic analysis revealed 53 bacterial and 45 archaeal GFMs, of which nearly all were distantly related to known cultivated isolates. In the GFMs, abundant Bacteria included Chloroflexi, Nitrospirae, Acetothermia (OP1), EM3, Aminicenantes (OP8), Gammaproteobacteria, and Deltaproteobacteria, while abundant Archaea included Archaeoglobi, Bathyarchaeota (MCG), and Marine Benthic Group E (MBG-E). These data are the first GFMs reconstructed from the deep basaltic subseafloor biosphere, and provide a dataset available for further interrogation.

Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids

PubMed Central

Jungbluth, Sean P.; Amend, Jan P.; Rappé, Michael S.

2017-01-01

The global deep subsurface biosphere is one of the largest reservoirs for microbial life on our planet. This study takes advantage of new sampling technologies and couples them with improvements to DNA sequencing and associated informatics tools to reconstruct the genomes of uncultivated Bacteria and Archaea from fluids collected deep within the Juan de Fuca Ridge subseafloor. Here, we generated two metagenomes from borehole observatories located 311 meters apart and, using binning tools, retrieved 98 genomes from metagenomes (GFMs). Of the GFMs, 31 were estimated to be >90% complete, while an additional 17 were >70% complete. Phylogenomic analysis revealed 53 bacterial and 45 archaeal GFMs, of which nearly all were distantly related to known cultivated isolates. In the GFMs, abundant Bacteria included Chloroflexi, Nitrospirae, Acetothermia (OP1), EM3, Aminicenantes (OP8), Gammaproteobacteria, and Deltaproteobacteria, while abundant Archaea included Archaeoglobi, Bathyarchaeota (MCG), and Marine Benthic Group E (MBG-E). These data are the first GFMs reconstructed from the deep basaltic subseafloor biosphere, and provide a dataset available for further interrogation. PMID:28350381

Fast and sensitive taxonomic classification for metagenomics with Kaiju

PubMed Central

Menzel, Peter; Ng, Kim Lee; Krogh, Anders

2016-01-01

Metagenomics emerged as an important field of research not only in microbial ecology but also for human health and disease, and metagenomic studies are performed on increasingly larger scales. While recent taxonomic classification programs achieve high speed by comparing genomic k-mers, they often lack sensitivity for overcoming evolutionary divergence, so that large fractions of the metagenomic reads remain unclassified. Here we present the novel metagenome classifier Kaiju, which finds maximum (in-)exact matches on the protein-level using the Burrows–Wheeler transform. We show in a genome exclusion benchmark that Kaiju classifies reads with higher sensitivity and similar precision compared with current k-mer-based classifiers, especially in genera that are underrepresented in reference databases. We also demonstrate that Kaiju classifies up to 10 times more reads in real metagenomes. Kaiju can process millions of reads per minute and can run on a standard PC. Source code and web server are available at http://kaiju.binf.ku.dk. PMID:27071849

Fast and sensitive taxonomic classification for metagenomics with Kaiju.

PubMed

Menzel, Peter; Ng, Kim Lee; Krogh, Anders

2016-04-13

Metagenomics emerged as an important field of research not only in microbial ecology but also for human health and disease, and metagenomic studies are performed on increasingly larger scales. While recent taxonomic classification programs achieve high speed by comparing genomic k-mers, they often lack sensitivity for overcoming evolutionary divergence, so that large fractions of the metagenomic reads remain unclassified. Here we present the novel metagenome classifier Kaiju, which finds maximum (in-)exact matches on the protein-level using the Burrows-Wheeler transform. We show in a genome exclusion benchmark that Kaiju classifies reads with higher sensitivity and similar precision compared with current k-mer-based classifiers, especially in genera that are underrepresented in reference databases. We also demonstrate that Kaiju classifies up to 10 times more reads in real metagenomes. Kaiju can process millions of reads per minute and can run on a standard PC. Source code and web server are available at http://kaiju.binf.ku.dk.

Meta4: a web application for sharing and annotating metagenomic gene predictions using web services.

PubMed

Richardson, Emily J; Escalettes, Franck; Fotheringham, Ian; Wallace, Robert J; Watson, Mick

2013-01-01

Whole-genome shotgun metagenomics experiments produce DNA sequence data from entire ecosystems, and provide a huge amount of novel information. Gene discovery projects require up-to-date information about sequence homology and domain structure for millions of predicted proteins to be presented in a simple, easy-to-use system. There is a lack of simple, open, flexible tools that allow the rapid sharing of metagenomics datasets with collaborators in a format they can easily interrogate. We present Meta4, a flexible and extensible web application that can be used to share and annotate metagenomic gene predictions. Proteins and predicted domains are stored in a simple relational database, with a dynamic front-end which displays the results in an internet browser. Web services are used to provide up-to-date information about the proteins from homology searches against public databases. Information about Meta4 can be found on the project website, code is available on Github, a cloud image is available, and an example implementation can be seen at.

Gate Drain Underlapped-PNIN-GAA-TFET for Comprehensively Upgraded Analog/RF Performance

NASA Astrophysics Data System (ADS)

Madan, Jaya; Chaujar, Rishu

2017-02-01

This work integrates the merits of gate-drain underlapping (GDU) and N+ source pocket on cylindrical gate all around tunnel FET (GAA-TFET) to form GDU-PNIN-GAA-TFET. It is analysed that the source pocket located at the source-channel junction narrows the tunneling barrier width at the tunneling junction and thereby enhances the ON-state current of GAA-TFET. Further, it is obtained that the GDU resists the extension of carrier density (built-up under the gated region) towards the drain side (under the underlapped length), thereby suppressing the ambipolar current and reducing the parasitic capacitances of GAA-TFET. Consequently, the amalgamated merits of both engineering schemes are obtained in GDU-PNIN-GAA-TFET that thus conquers the greatest challenges faced by TFET. Thus, GDU-PNIN-GAA-TFET results in an up-gradation in the overall performance of GAA-TFET. Moreover, it is realised that the RF figure of merits FOMs such as cut-off frequency (fT) and maximum oscillation frequency (fMAX) are also considerably improved with integration of source pocket on GAA-TFET. Thus, the improved analog and RF performance of GDU-PNIN-GAA-TFET makes it ideal for low power and high-speed applications.

Phase diagrams for understanding gold-seeded growth of GaAs and InAs nanowires

NASA Astrophysics Data System (ADS)

Ghasemi, Masoomeh; Johansson, Jonas

2017-04-01

Phase diagrams are useful tools to study the phase equilibria of nanowire materials systems because the growth of nanowires is accompanied by phase formation and phase transition. We have modeled the phase equilibria of the As-Au-Ga ternary system by means of the CALPHAD method. This method is a well-established semi-empirical technique for thermodynamic modeling in which Gibbs energy functions with free parameters are defined for all phases in a system followed by adjusting these parameters to the experimental data. Using the resulting As-Au-Ga thermodynamic database, four vertical cuts of this ternary system are calculated and all show good agreement with experiments. This ternary system is particularly useful for predicting the state of the Au seed alloys when growing GaAs nanowires and we discuss such predictions. Similar calculations are performed for Au-seeded InAs nanowires. We show that the vapor-liquid-solid (VLS) growth fails for InAs nanowires, while GaAs nanowires can grow from a liquid particle. Our calculations are in agreement with experimental data on the growth of Au-seeded GaAs and InAs nanowires.

Tentacle: distributed quantification of genes in metagenomes.

PubMed

Boulund, Fredrik; Sjögren, Anders; Kristiansson, Erik

2015-01-01

In metagenomics, microbial communities are sequenced at increasingly high resolution, generating datasets with billions of DNA fragments. Novel methods that can efficiently process the growing volumes of sequence data are necessary for the accurate analysis and interpretation of existing and upcoming metagenomes. Here we present Tentacle, which is a novel framework that uses distributed computational resources for gene quantification in metagenomes. Tentacle is implemented using a dynamic master-worker approach in which DNA fragments are streamed via a network and processed in parallel on worker nodes. Tentacle is modular, extensible, and comes with support for six commonly used sequence aligners. It is easy to adapt Tentacle to different applications in metagenomics and easy to integrate into existing workflows. Evaluations show that Tentacle scales very well with increasing computing resources. We illustrate the versatility of Tentacle on three different use cases. Tentacle is written for Linux in Python 2.7 and is published as open source under the GNU General Public License (v3). Documentation, tutorials, installation instructions, and the source code are freely available online at: http://bioinformatics.math.chalmers.se/tentacle.

Shotgun metagenomic data streams: surfing without fear

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berendzen, Joel R

2010-12-06

Timely information about bio-threat prevalence, consequence, propagation, attribution, and mitigation is needed to support decision-making, both routinely and in a crisis. One DNA sequencer can stream 25 Gbp of information per day, but sampling strategies and analysis techniques are needed to turn raw sequencing power into actionable knowledge. Shotgun metagenomics can enable biosurveillance at the level of a single city, hospital, or airplane. Metagenomics characterizes viruses and bacteria from complex environments such as soil, air filters, or sewage. Unlike targeted-primer-based sequencing, shotgun methods are not blind to sequences that are truly novel, and they can measure absolute prevalence. Shotgun metagenomicmore » sampling can be non-invasive, efficient, and inexpensive while being informative. We have developed analysis techniques for shotgun metagenomic sequencing that rely upon phylogenetic signature patterns. They work by indexing local sequence patterns in a manner similar to web search engines. Our methods are laptop-fast and favorable scaling properties ensure they will be sustainable as sequencing methods grow. We show examples of application to soil metagenomic samples.« less

Lateral epitaxial overgowth of GaAs by organometallic chemical vapor deposition

NASA Technical Reports Server (NTRS)

Gale, R. P.; Mcclelland, R. W.; Fan, J. C. C.; Bozler, C. O.

1982-01-01

Lateral epitaxial overgrowth of GaAs by organometallic chemical vapor deposition has been demonstrated. Pyrolytic decomposition of trimethylgallium and arsine, without the use of HCl, was used to deposit GaAs on substrates prepared by coating (110) GaAs wafers with SiO2, then using photolithography to open narrow stripes in the oxide. Lateral overgrowth was seeded by epitaxial deposits formed on the GaAs surfaces exposed by the stripe openings. The extent of lateral overgrowth was investigated as a function of stripe orientation and growth temperature. Ratios of lateral to vertical growth rates greater than five have been obtained. The lateral growth is due to surface-kinetic control for the two-dimensional growth geometry studied. A continuous epitaxial GaAs layer 3 microns thick has been grown over a patterned mask on a GaAs substrate and then cleaved from the substrate.

Insights into resistome and stress responses genes in Bubalus bubalis rumen through metagenomic analysis.

PubMed

Reddy, Bhaskar; Singh, Krishna M; Patel, Amrutlal K; Antony, Ancy; Panchasara, Harshad J; Joshi, Chaitanya G

2014-10-01

Buffalo rumen microbiota experience variety of diets and represents a huge reservoir of mobilome, resistome and stress responses. However, knowledge of metagenomic responses to such conditions is still rudimentary. We analyzed the metagenomes of buffalo rumen in the liquid and solid phase of the rumen biomaterial from river buffalo adapted to varying proportion of concentrate to green or dry roughages, using high-throughput sequencing to know the occurrence of antibiotics resistance genes, genetic exchange between bacterial population and environmental reservoirs. A total of 3914.94 MB data were generated from all three treatments group. The data were analysed with Metagenome rapid annotation system tools. At phyla level, Bacteroidetes were dominant in all the treatments followed by Firmicutes. Genes coding for functional responses to stress (oxidative stress and heat shock proteins) and resistome genes (resistance to antibiotics and toxic compounds, phages, transposable elements and pathogenicity islands) were prevalent in similar proportion in liquid and solid fraction of rumen metagenomes. The fluoroquinolone resistance, MDR efflux pumps and Methicillin resistance genes were broadly distributed across 11, 9, and 14 bacterial classes, respectively. Bacteria responsible for phages replication and prophages and phage packaging and rlt-like streptococcal phage genes were mostly assigned to phyla Bacteroides, Firmicutes and proteaobacteria. Also, more reads matching the sigma B genes were identified in the buffalo rumen. This study underscores the presence of diverse mechanisms of adaptation to different diet, antibiotics and other stresses in buffalo rumen, reflecting the proportional representation of major bacterial groups.

Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing.

PubMed

Noyes, Noelle R; Weinroth, Maggie E; Parker, Jennifer K; Dean, Chris J; Lakin, Steven M; Raymond, Robert A; Rovira, Pablo; Doster, Enrique; Abdo, Zaid; Martin, Jennifer N; Jones, Kenneth L; Ruiz, Jaime; Boucher, Christina A; Belk, Keith E; Morley, Paul S

2017-10-17

Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for environmental surveillance of antimicrobial resistance and pathogenic microorganisms is also increasing. In published metagenomic datasets, the total of all resistance- and virulence-related sequences accounts for < 1% of all sequenced DNA, leading to limitations in detection of low-abundance resistome-virulome elements. This study describes the extent and composition of the low-abundance portion of the resistome-virulome, using a bait-capture and enrichment system that incorporates unique molecular indices to count DNA molecules and correct for enrichment bias. The use of the bait-capture and enrichment system significantly increased on-target sequencing of the resistome-virulome, enabling detection of an additional 1441 gene accessions and revealing a low-abundance portion of the resistome-virulome that was more diverse and compositionally different than that detected by more traditional metagenomic assays. The low-abundance portion of the resistome-virulome also contained resistance genes with public health importance, such as extended-spectrum betalactamases, that were not detected using traditional shotgun metagenomic sequencing. In addition, the use of the bait-capture and enrichment system enabled identification of rare resistance gene haplotypes that were used to discriminate between sample origins. These results demonstrate that the rare resistome-virulome contains valuable and unique information that can be utilized for both surveillance and population genetic investigations of resistance. Access to the rare resistome-virulome using the bait-capture and enrichment system validated in this study can greatly advance our understanding of microbiome-resistome dynamics.

GaAs photoconductive semiconductor switch

DOEpatents

Loubriel, G.M.; Baca, A.G.; Zutavern, F.J.

1998-09-08

A high gain, optically triggered, photoconductive semiconductor switch (PCSS) implemented in GaAs as a reverse-biased pin structure with a passivation layer above the intrinsic GaAs substrate in the gap between the two electrodes of the device is disclosed. The reverse-biased configuration in combination with the addition of the passivation layer greatly reduces surface current leakage that has been a problem for prior PCSS devices and enables employment of the much less expensive and more reliable DC charging systems instead of the pulsed charging systems that needed to be used with prior PCSS devices. 5 figs.

Evaluating the Quantitative Capabilities of Metagenomic Analysis Software.

PubMed

Kerepesi, Csaba; Grolmusz, Vince

2016-05-01

DNA sequencing technologies are applied widely and frequently today to describe metagenomes, i.e., microbial communities in environmental or clinical samples, without the need for culturing them. These technologies usually return short (100-300 base-pairs long) DNA reads, and these reads are processed by metagenomic analysis software that assign phylogenetic composition-information to the dataset. Here we evaluate three metagenomic analysis software (AmphoraNet--a webserver implementation of AMPHORA2--, MG-RAST, and MEGAN5) for their capabilities of assigning quantitative phylogenetic information for the data, describing the frequency of appearance of the microorganisms of the same taxa in the sample. The difficulties of the task arise from the fact that longer genomes produce more reads from the same organism than shorter genomes, and some software assign higher frequencies to species with longer genomes than to those with shorter ones. This phenomenon is called the "genome length bias." Dozens of complex artificial metagenome benchmarks can be found in the literature. Because of the complexity of those benchmarks, it is usually difficult to judge the resistance of a metagenomic software to this "genome length bias." Therefore, we have made a simple benchmark for the evaluation of the "taxon-counting" in a metagenomic sample: we have taken the same number of copies of three full bacterial genomes of different lengths, break them up randomly to short reads of average length of 150 bp, and mixed the reads, creating our simple benchmark. Because of its simplicity, the benchmark is not supposed to serve as a mock metagenome, but if a software fails on that simple task, it will surely fail on most real metagenomes. We applied three software for the benchmark. The ideal quantitative solution would assign the same proportion to the three bacterial taxa. We have found that AMPHORA2/AmphoraNet gave the most accurate results and the other two software were under

Metagenomics workflow analysis of endophytic bacteria from oil palm fruits

NASA Astrophysics Data System (ADS)

Tanjung, Z. A.; Aditama, R.; Sudania, W. M.; Utomo, C.; Liwang, T.

2017-05-01

Next-Generation Sequencing (NGS) has become a powerful sequencing tool for microbial study especially to lead the establishment of the field area of metagenomics. This study described a workflow to analyze metagenomics data of a Sequence Read Archive (SRA) file under accession ERP004286 deposited by University of Sao Paulo. It was a direct sequencing data generated by 454 pyrosequencing platform originated from oil palm fruits endophytic bacteria which were cultured using oil-palm enriched medium. This workflow used SortMeRNA to split ribosomal reads sequence, Newbler (GS Assembler and GS Mapper) to assemble and map reads into genome reference, BLAST package to identify and annotate contigs sequence, and QualiMap for statistical analysis. Eight bacterial species were identified in this study. Enterobacter cloacae was the most abundant species followed by Citrobacter koseri, Seratia marcescens, Latococcus lactis subsp. lactis, Klebsiella pneumoniae, Citrobacter amalonaticus, Achromobacter xylosoxidans, and Pseudomonas sp. respectively. All of these species have been reported as endophyte bacteria in various plant species and each has potential as plant growth promoting bacteria or another application in agricultural industries.

DOE JGI Quality Metrics; Approaches to Scaling and Improving Metagenome Assembly (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Copeland, Alex; Brown, C. Titus

2011-10-13

DOE JGI's Alex Copeland on "DOE JGI Quality Metrics" and Michigan State University's C. Titus Brown on "Approaches to Scaling and Improving Metagenome Assembly" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

DOE JGI Quality Metrics; Approaches to Scaling and Improving Metagenome Assembly (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Copeland, Alex; Brown, C. Titus

2018-04-27

DOE JGI's Alex Copeland on "DOE JGI Quality Metrics" and Michigan State University's C. Titus Brown on "Approaches to Scaling and Improving Metagenome Assembly" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Panel fabrication utilizing GaAs solar cells

NASA Technical Reports Server (NTRS)

Mardesich, N.

1984-01-01

The development of the GaAs solar cells for space applications is described. The activities in the fabrication of GaAs solar panels are outlined. Panels were fabricated while introducing improved quality control, soldering laydown and testing procedures. These panels include LIPS II, San Marco Satellite, and a low concentration panel for Rockwells' evaluation. The panels and their present status are discussed.

MetaABC--an integrated metagenomics platform for data adjustment, binning and clustering.

PubMed

Su, Chien-Hao; Hsu, Ming-Tsung; Wang, Tse-Yi; Chiang, Sufeng; Cheng, Jen-Hao; Weng, Francis C; Kao, Cheng-Yan; Wang, Daryi; Tsai, Huai-Kuang

2011-08-15

MetaABC is a metagenomic platform that integrates several binning tools coupled with methods for removing artifacts, analyzing unassigned reads and controlling sampling biases. It allows users to arrive at a better interpretation via series of distinct combinations of analysis tools. After execution, MetaABC provides outputs in various visual formats such as tables, pie and bar charts as well as clustering result diagrams. MetaABC source code and documentation are available at http://bits2.iis.sinica.edu.tw/MetaABC/ CONTACT: dywang@gate.sinica.edu.tw; hktsai@iis.sinica.edu.tw Supplementary data are available at Bioinformatics online.

Effective Analysis of NGS Metagenomic Data with Ultra-Fast Clustering Algorithms (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Li, Weizhong

2018-02-12

San Diego Supercomputer Center's Weizhong Li on "Effective Analysis of NGS Metagenomic Data with Ultra-fast Clustering Algorithms" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Identifying Differentially Abundant Metabolic Pathways in Metagenomic Datasets

NASA Astrophysics Data System (ADS)

Liu, Bo; Pop, Mihai

Enabled by rapid advances in sequencing technology, metagenomic studies aim to characterize entire communities of microbes bypassing the need for culturing individual bacterial members. One major goal of such studies is to identify specific functional adaptations of microbial communities to their habitats. Here we describe a powerful analytical method (MetaPath) that can identify differentially abundant pathways in metagenomic data-sets, relying on a combination of metagenomic sequence data and prior metabolic pathway knowledge. We show that MetaPath outperforms other common approaches when evaluated on simulated datasets. We also demonstrate the power of our methods in analyzing two, publicly available, metagenomic datasets: a comparison of the gut microbiome of obese and lean twins; and a comparison of the gut microbiome of infant and adult subjects. We demonstrate that the subpathways identified by our method provide valuable insights into the biological activities of the microbiome.

Metagenomic studies of the Red Sea.

PubMed

Behzad, Hayedeh; Ibarra, Martin Augusto; Mineta, Katsuhiko; Gojobori, Takashi

2016-02-01

Metagenomics has significantly advanced the field of marine microbial ecology, revealing the vast diversity of previously unknown microbial life forms in different marine niches. The tremendous amount of data generated has enabled identification of a large number of microbial genes (metagenomes), their community interactions, adaptation mechanisms, and their potential applications in pharmaceutical and biotechnology-based industries. Comparative metagenomics reveals that microbial diversity is a function of the local environment, meaning that unique or unusual environments typically harbor novel microbial species with unique genes and metabolic pathways. The Red Sea has an abundance of unique characteristics; however, its microbiota is one of the least studied among marine environments. The Red Sea harbors approximately 25 hot anoxic brine pools, plus a vibrant coral reef ecosystem. Physiochemical studies describe the Red Sea as an oligotrophic environment that contains one of the warmest and saltiest waters in the world with year-round high UV radiations. These characteristics are believed to have shaped the evolution of microbial communities in the Red Sea. Over-representation of genes involved in DNA repair, high-intensity light responses, and osmoregulation were found in the Red Sea metagenomic databases suggesting acquisition of specific environmental adaptation by the Red Sea microbiota. The Red Sea brine pools harbor a diverse range of halophilic and thermophilic bacterial and archaeal communities, which are potential sources of enzymes for pharmaceutical and biotechnology-based application. Understanding the mechanisms of these adaptations and their function within the larger ecosystem could also prove useful in light of predicted global warming scenarios where global ocean temperatures are expected to rise by 1-3°C in the next few decades. In this review, we provide an overview of the published metagenomic studies that were conducted in the Red Sea, and

GaAs Photovoltaics on Polycrystalline Ge Substrates

NASA Technical Reports Server (NTRS)

Wilt, David M.; Pal, AnnaMaria T.; McNatt, Jeremiah S.; Wolford, David S.; Landis, Geoffrey A.; Smith, Mark A.; Scheiman, David; Jenkins, Phillip P.; McElroy Bruce

2007-01-01

High efficiency III-V multijunction solar cells deposited on metal foil or even polymer substrates can provide tremendous advantages in mass and stowage, particularly for planetary missions. As a first step towards that goal, poly-crystalline p/i/n GaAs solar cells are under development on polycrystalline Ge substrates. Organo Metallic Vapor Phase Epitaxy (OMVPE) parameters for pre-growth bake, nucleation and deposition have been examined. Single junction p/i/n GaAs photovoltaic devices, incorporating InGaP front and back window layers, have been grown and processed. Device performance has shown a dependence upon the thickness of a GaAs buffer layer deposited between the Ge substrate and the active device structure. A thick (2 m) GaAs buffer provides for both increased average device performance as well as reduced sensitivity to variations in grain size and orientation. Illumination under IR light (lambda > 1 micron), the cells showed a Voc, demonstrating the presence of an unintended photoactive junction at the GaAs/Ge interface. The presence of this junction limited the efficiency to approx.13% (estimated with an anti-refection coating) due to the current mismatch and lack of tunnel junction interconnect.

BioCreative Workshops for DOE Genome Sciences: Text Mining for Metagenomics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Cathy H.; Hirschman, Lynette

The objective of this project was to host BioCreative workshops to define and develop text mining tasks to meet the needs of the Genome Sciences community, focusing on metadata information extraction in metagenomics. Following the successful introduction of metagenomics at the BioCreative IV workshop, members of the metagenomics community and BioCreative communities continued discussion to identify candidate topics for a BioCreative metagenomics track for BioCreative V. Of particular interest was the capture of environmental and isolation source information from text. The outcome was to form a “community of interest” around work on the interactive EXTRACT system, which supported interactive taggingmore » of environmental and species data. This experiment is included in the BioCreative V virtual issue of Database. In addition, there was broad participation by members of the metagenomics community in the panels held at BioCreative V, leading to valuable exchanges between the text mining developers and members of the metagenomics research community. These exchanges are reflected in a number of the overview and perspective pieces also being captured in the BioCreative V virtual issue. Overall, this conversation has exposed the metagenomics researchers to the possibilities of text mining, and educated the text mining developers to the specific needs of the metagenomics community.« less

Comparisons of single event vulnerability of GaAs SRAMS

NASA Astrophysics Data System (ADS)

Weatherford, T. R.; Hauser, J. R.; Diehl, S. E.

1986-12-01

A GaAs MESFET/JFET model incorporated into SPICE has been used to accurately describe C-EJFET, E/D MESFET and D MESFET/resistor GaAs memory technologies. These cells have been evaluated for critical charges due to gate-to-drain and drain-to-source charge collection. Low gate-to-drain critical charges limit conventional GaAs SRAM soft error rates to approximately 1E-6 errors/bit-day. SEU hardening approaches including decoupling resistors, diodes, and FETs have been investigated. Results predict GaAs RAM cell critical charges can be increased to over 0.1 pC. Soft error rates in such hardened memories may approach 1E-7 errors/bit-day without significantly reducing memory speed. Tradeoffs between hardening level, performance and fabrication complexity are discussed.

Scalable metagenomic taxonomy classification using a reference genome database

PubMed Central

Ames, Sasha K.; Hysom, David A.; Gardner, Shea N.; Lloyd, G. Scott; Gokhale, Maya B.; Allen, Jonathan E.

2013-01-01

Motivation: Deep metagenomic sequencing of biological samples has the potential to recover otherwise difficult-to-detect microorganisms and accurately characterize biological samples with limited prior knowledge of sample contents. Existing metagenomic taxonomic classification algorithms, however, do not scale well to analyze large metagenomic datasets, and balancing classification accuracy with computational efficiency presents a fundamental challenge. Results: A method is presented to shift computational costs to an off-line computation by creating a taxonomy/genome index that supports scalable metagenomic classification. Scalable performance is demonstrated on real and simulated data to show accurate classification in the presence of novel organisms on samples that include viruses, prokaryotes, fungi and protists. Taxonomic classification of the previously published 150 giga-base Tyrolean Iceman dataset was found to take <20 h on a single node 40 core large memory machine and provide new insights on the metagenomic contents of the sample. Availability: Software was implemented in C++ and is freely available at http://sourceforge.net/projects/lmat Contact: allen99@llnl.gov Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23828782

Prediction of dislocation generation during Bridgman growth of GaAs crystals

NASA Technical Reports Server (NTRS)

Tsai, C. T.; Yao, M. W.; Chait, Arnon

1992-01-01

Dislocation densities are generated in GaAs single crystals due to the excessive thermal stresses induced by temperature variations during growth. A viscoplastic material model for GaAs, which takes into account the movement and multiplication of dislocations in the plastic deformation, is developed according to Haasen's theory. The dislocation density is expressed as an internal state variable in this dynamic viscoplastic model. The deformation process is a nonlinear function of stress, strain rate, dislocation density and temperature. The dislocation density in the GaAs crystal during vertical Bridgman growth is calculated using a nonlinear finite element model. The dislocation multiplication in GaAs crystals for several temperature fields obtained from thermal modeling of both the GTE GaAs experimental data and artificially designed data are investigated.

Prediction of dislocation generation during Bridgman growth of GaAs crystals

NASA Astrophysics Data System (ADS)

Tsai, C. T.; Yao, M. W.; Chait, Arnon

1992-11-01

Dislocation densities are generated in GaAs single crystals due to the excessive thermal stresses induced by temperature variations during growth. A viscoplastic material model for GaAs, which takes into account the movement and multiplication of dislocations in the plastic deformation, is developed according to Haasen's theory. The dislocation density is expressed as an internal state variable in this dynamic viscoplastic model. The deformation process is a nonlinear function of stress, strain rate, dislocation density and temperature. The dislocation density in the GaAs crystal during vertical Bridgman growth is calculated using a nonlinear finite element model. The dislocation multiplication in GaAs crystals for several temperature fields obtained from thermal modeling of both the GTE GaAs experimental data and artificially designed data are investigated.

Zooplankton community analysis in the Changjiang River estuary by single-gene-targeted metagenomics

NASA Astrophysics Data System (ADS)

Cheng, Fangping; Wang, Minxiao; Li, Chaolun; Sun, Song

2014-07-01

DNA barcoding provides accurate identification of zooplankton species through all life stages. Single-gene-targeted metagenomic analysis based on DNA barcode databases can facilitate longterm monitoring of zooplankton communities. With the help of the available zooplankton databases, the zooplankton community of the Changjiang (Yangtze) River estuary was studied using a single-gene-targeted metagenomic method to estimate the species richness of this community. A total of 856 mitochondrial cytochrome oxidase subunit 1 (cox1) gene sequences were determined. The environmental barcodes were clustered into 70 molecular operational taxonomic units (MOTUs). Forty-two MOTUs matched barcoded marine organisms with more than 90% similarity and were assigned to either the species (similarity>96%) or genus level (similarity<96%). Sibling species could also be distinguished. Many species that were overlooked by morphological methods were identified by molecular methods, especially gelatinous zooplankton and merozooplankton that were likely sampled at different life history phases. Zooplankton community structures differed significantly among all of the samples. The MOTU spatial distributions were influenced by the ecological habits of the corresponding species. In conclusion, single-gene-targeted metagenomic analysis is a useful tool for zooplankton studies, with which specimens from all life history stages can be identified quickly and effectively with a comprehensive database.

Using populations of human and microbial genomes for organism detection in metagenomes.

PubMed

Ames, Sasha K; Gardner, Shea N; Marti, Jose Manuel; Slezak, Tom R; Gokhale, Maya B; Allen, Jonathan E

2015-07-01

Identifying causative disease agents in human patients from shotgun metagenomic sequencing (SMS) presents a powerful tool to apply when other targeted diagnostics fail. Numerous technical challenges remain, however, before SMS can move beyond the role of research tool. Accurately separating the known and unknown organism content remains difficult, particularly when SMS is applied as a last resort. The true amount of human DNA that remains in a sample after screening against the human reference genome and filtering nonbiological components left from library preparation has previously been underreported. In this study, we create the most comprehensive collection of microbial and reference-free human genetic variation available in a database optimized for efficient metagenomic search by extracting sequences from GenBank and the 1000 Genomes Project. The results reveal new human sequences found in individual Human Microbiome Project (HMP) samples. Individual samples contain up to 95% human sequence, and 4% of the individual HMP samples contain 10% or more human reads. Left unidentified, human reads can complicate and slow down further analysis and lead to inaccurately labeled microbial taxa and ultimately lead to privacy concerns as more human genome data is collected. © 2015 Ames et al.; Published by Cold Spring Harbor Laboratory Press.

Viral Metagenomics on Animals as a Tool for the Detection of Zoonoses Prior to Human Infection?

PubMed Central

Temmam, Sarah; Davoust, Bernard; Berenger, Jean-Michel; Raoult, Didier; Desnues, Christelle

2014-01-01

Many human viral infections have a zoonotic, i.e., wild or domestic animal, origin. Several zoonotic viruses are transmitted to humans directly via contact with an animal or indirectly via exposure to the urine or feces of infected animals or the bite of a bloodsucking arthropod. If a virus is able to adapt and replicate in its new human host, human-to-human transmissions may occur, possibly resulting in an epidemic, such as the A/H1N1 flu pandemic in 2009. Thus, predicting emerging zoonotic infections is an important challenge for public health officials in the coming decades. The recent development of viral metagenomics, i.e., the characterization of the complete viral diversity isolated from an organism or an environment using high-throughput sequencing technologies, is promising for the surveillance of such diseases and can be accomplished by analyzing the viromes of selected animals and arthropods that are closely in contact with humans. In this review, we summarize our current knowledge of viral diversity within such animals (in particular blood-feeding arthropods, wildlife and domestic animals) using metagenomics and present its possible future application for the surveillance of zoonotic and arboviral diseases. PMID:24918293

Metagenomics: A Call for Bringing a New Science into the Classroom (While It's Still New)

ERIC Educational Resources Information Center

Jurkowski, Anne; Reid, Ann H.; Labov, Jay B.

2007-01-01

This article describes the emerging field of metagenomics, a potent new tool that vastly expands the ability of scientists to study the myriad capabilities of microbial communities and the as yet unrecognized relationships and interactions of microbes with other forms of life and the environment. The birth of this exciting new field provides the…

Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity.

PubMed

Rodriguez-R, Luis M; Gunturu, Santosh; Tiedje, James M; Cole, James R; Konstantinidis, Konstantinos T

2018-01-01

Estimations of microbial community diversity based on metagenomic data sets are affected, often to an unknown degree, by biases derived from insufficient coverage and reference database-dependent estimations of diversity. For instance, the completeness of reference databases cannot be generally estimated since it depends on the extant diversity sampled to date, which, with the exception of a few habitats such as the human gut, remains severely undersampled. Further, estimation of the degree of coverage of a microbial community by a metagenomic data set is prohibitively time-consuming for large data sets, and coverage values may not be directly comparable between data sets obtained with different sequencing technologies. Here, we extend Nonpareil, a database-independent tool for the estimation of coverage in metagenomic data sets, to a high-performance computing implementation that scales up to hundreds of cores and includes, in addition, a k -mer-based estimation as sensitive as the original alignment-based version but about three hundred times as fast. Further, we propose a metric of sequence diversity ( N d ) derived directly from Nonpareil curves that correlates well with alpha diversity assessed by traditional metrics. We use this metric in different experiments demonstrating the correlation with the Shannon index estimated on 16S rRNA gene profiles and show that N d additionally reveals seasonal patterns in marine samples that are not captured by the Shannon index and more precise rankings of the magnitude of diversity of microbial communities in different habitats. Therefore, the new version of Nonpareil, called Nonpareil 3, advances the toolbox for metagenomic analyses of microbiomes. IMPORTANCE Estimation of the coverage provided by a metagenomic data set, i.e., what fraction of the microbial community was sampled by DNA sequencing, represents an essential first step of every culture-independent genomic study that aims to robustly assess the sequence

Metagenomics of Bacterial Diversity in Villa Luz Caves with Sulfur Water Springs

PubMed Central

Artacho, Alejandro; Bautista, José S.; Méndez, Roberto; Gamboa, María T.; Gamboa, Jesús R.; Gómez-Cruz, Rodolfo

2018-01-01

New biotechnology applications require in-depth preliminary studies of biodiversity. The methods of massive sequencing using metagenomics and bioinformatics tools offer us sufficient and reliable knowledge to understand environmental diversity, to know new microorganisms, and to take advantage of their functional genes. Villa Luz caves, in the southern Mexican state of Tabasco, are fed by at least 26 groundwater inlets, containing 300–500 mg L−1 H2S and <0.1 mg L−1 O2. We extracted environmental DNA for metagenomic analysis of collected samples in five selected Villa Luz caves sites, with pH values from 2.5 to 7. Foreign organisms found in this underground ecosystem can oxidize H2S to H2SO4. These include: biovermiculites, a bacterial association that can grow on the rock walls; snottites, that are whitish, viscous biofilms hanging from the rock walls, and sacks or bags of phlegm, which live within the aquatic environment of the springs. Through the emergency food assistance program (TEFAP) pyrosequencing, a total of 20,901 readings of amplification products from hypervariable regions V1 and V3 of 16S rRNA bacterial gene in whole and pure metagenomic DNA samples were generated. Seven bacterial phyla were identified. As a result, Proteobacteria was more frequent than Acidobacteria. Finally, acidophilic Proteobacteria was detected in UJAT5 sample. PMID:29361802

De-MetaST-BLAST: A Tool for the Validation of Degenerate Primer Sets and Data Mining of Publicly Available Metagenomes

PubMed Central

Gulvik, Christopher A.; Effler, T. Chad; Wilhelm, Steven W.; Buchan, Alison

2012-01-01

Development and use of primer sets to amplify nucleic acid sequences of interest is fundamental to studies spanning many life science disciplines. As such, the validation of primer sets is essential. Several computer programs have been created to aid in the initial selection of primer sequences that may or may not require multiple nucleotide combinations (i.e., degeneracies). Conversely, validation of primer specificity has remained largely unchanged for several decades, and there are currently few available programs that allows for an evaluation of primers containing degenerate nucleotide bases. To alleviate this gap, we developed the program De-MetaST that performs an in silico amplification using user defined nucleotide sequence dataset(s) and primer sequences that may contain degenerate bases. The program returns an output file that contains the in silico amplicons. When De-MetaST is paired with NCBI’s BLAST (De-MetaST-BLAST), the program also returns the top 10 nr NCBI database hits for each recovered in silico amplicon. While the original motivation for development of this search tool was degenerate primer validation using the wealth of nucleotide sequences available in environmental metagenome and metatranscriptome databases, this search tool has potential utility in many data mining applications. PMID:23189198

Crystal growth of device quality GaAs in space

NASA Technical Reports Server (NTRS)

Gatos, H. C.; Lagowski, J.

1983-01-01

GaAs device technology has recently reached a new phase of rapid advancement, made possible by the improvement of the quality of GaAs bulk crystals. At the same time, the transition to the next generation of GaAs integrated circuits and optoelectronic systems for commercial and government applications hinges on new quantum steps in three interrelated areas: crystal growth, device processing and device-related properties and phenomena. Special emphasis is placed on the establishment of quantitative relationships among crystal growth parameters-material properties-electronic properties and device applications. The overall program combines studies of crystal growth on novel approaches to engineering of semiconductor material (i.e., GaAs and related compounds); investigation and correlation of materials properties and electronic characteristics on a macro- and microscale; and investigation of electronic properties and phenomena controlling device applications and device performance.

Sidewall GaAs tunnel junctions fabricated using molecular layer epitaxy

PubMed Central

Ohno, Takeo; Oyama, Yutaka

2012-01-01

In this article we review the fundamental properties and applications of sidewall GaAs tunnel junctions. Heavily impurity-doped GaAs epitaxial layers were prepared using molecular layer epitaxy (MLE), in which intermittent injections of precursors in ultrahigh vacuum were applied, and sidewall tunnel junctions were fabricated using a combination of device mesa wet etching of the GaAs MLE layer and low-temperature area-selective regrowth. The fabricated tunnel junctions on the GaAs sidewall with normal mesa orientation showed a record peak current density of 35 000 A cm-2. They can potentially be used as terahertz devices such as a tunnel injection transit time effect diode or an ideal static induction transistor. PMID:27877466

Metagenomic analysis of microbial communities yields insight into impacts of nanoparticle design

NASA Astrophysics Data System (ADS)

Metch, Jacob W.; Burrows, Nathan D.; Murphy, Catherine J.; Pruden, Amy; Vikesland, Peter J.

2018-01-01

Next-generation DNA sequencing and metagenomic analysis provide powerful tools for the environmentally friendly design of nanoparticles. Herein we demonstrate this approach using a model community of environmental microbes (that is, wastewater-activated sludge) dosed with gold nanoparticles of varying surface coatings and morphologies. Metagenomic analysis was highly sensitive in detecting the microbial community response to gold nanospheres and nanorods with either cetyltrimethylammonium bromide or polyacrylic acid surface coatings. We observed that the gold-nanoparticle morphology imposes a stronger force in shaping the microbial community structure than does the surface coating. Trends were consistent in terms of the compositions of both taxonomic and functional genes, which include antibiotic resistance genes, metal resistance genes and gene-transfer elements associated with cell stress that are relevant to public health. Given that nanoparticle morphology remained constant, the potential influence of gold dissolution was minimal. Surface coating governed the nanoparticle partitioning between the bioparticulate and aqueous phases.

Activity-Based Screening of Metagenomic Libraries for Hydrogenase Enzymes.

PubMed

Adam, Nicole; Perner, Mirjam

2017-01-01

Here we outline how to identify hydrogenase enzymes from metagenomic libraries through an activity-based screening approach. A metagenomic fosmid library is constructed in E. coli and the fosmids are transferred into a hydrogenase deletion mutant of Shewanella oneidensis (ΔhyaB) via triparental mating. If a fosmid exhibits hydrogen uptake activity, S. oneidensis' phenotype is restored and hydrogenase activity is indicated by a color change of the medium from yellow to colorless. This new method enables screening of 48 metagenomic fosmid clones in parallel.

Heteroepitaxial growth of GaAs on (100) Ge/Si using migration enhanced epitaxy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tanoto, H.; Loke, W. K.; Yoon, S. F.

In this paper, heteroepitaxial growth of GaAs on nominal (100) Ge/Si substrate was investigated. The root-mean square surface roughness of the sample where the first few monolayers of the GaAs were nucleated by migration enhanced epitaxy (MEE) is four times smaller compared to the sample without such a process, indicating better surface planarity. From the (004) x-ray diffraction rocking curve measurement, the full width at half maximum of the GaAs layer nucleated by MEE is 40% lower compared to that of the GaAs layer without such a process, indicating better crystal quality. Furthermore, it was found that the sample wheremore » the GaAs layer was nucleated by MEE experienced early relaxation. As the MEE process promotes two-dimensional growth, the GaAs layer where nucleation was initiated by such a process has fewer islandlike formations. This leads to a pseudomorphically grown GaAs layer, which experiences higher strain compared to the GaAs layer with more islandlike formations, where most relaxation occurs on the free surface of the islands. Therefore, for the same layer thickness, the GaAs layer on (100) Ge/Si substrate where nucleation was initiated by MEE relaxed first.« less

Evaluation method for the potential functionome harbored in the genome and metagenome

PubMed Central

2012-01-01

Background One of the main goals of genomic analysis is to elucidate the comprehensive functions (functionome) in individual organisms or a whole community in various environments. However, a standard evaluation method for discerning the functional potentials harbored within the genome or metagenome has not yet been established. We have developed a new evaluation method for the potential functionome, based on the completion ratio of Kyoto Encyclopedia of Genes and Genomes (KEGG) functional modules. Results Distribution of the completion ratio of the KEGG functional modules in 768 prokaryotic species varied greatly with the kind of module, and all modules primarily fell into 4 patterns (universal, restricted, diversified and non-prokaryotic modules), indicating the universal and unique nature of each module, and also the versatility of the KEGG Orthology (KO) identifiers mapped to each one. The module completion ratio in 8 phenotypically different bacilli revealed that some modules were shared only in phenotypically similar species. Metagenomes of human gut microbiomes from 13 healthy individuals previously determined by the Sanger method were analyzed based on the module completion ratio. Results led to new discoveries in the nutritional preferences of gut microbes, believed to be one of the mutualistic representations of gut microbiomes to avoid nutritional competition with the host. Conclusions The method developed in this study could characterize the functionome harbored in genomes and metagenomes. As this method also provided taxonomical information from KEGG modules as well as the gene hosts constructing the modules, interpretation of completion profiles was simplified and we could identify the complementarity between biochemical functions in human hosts and the nutritional preferences in human gut microbiomes. Thus, our method has the potential to be a powerful tool for comparative functional analysis in genomics and metagenomics, able to target unknown

Evaluation method for the potential functionome harbored in the genome and metagenome.

PubMed

Takami, Hideto; Taniguchi, Takeaki; Moriya, Yuki; Kuwahara, Tomomi; Kanehisa, Minoru; Goto, Susumu

2012-12-12

One of the main goals of genomic analysis is to elucidate the comprehensive functions (functionome) in individual organisms or a whole community in various environments. However, a standard evaluation method for discerning the functional potentials harbored within the genome or metagenome has not yet been established. We have developed a new evaluation method for the potential functionome, based on the completion ratio of Kyoto Encyclopedia of Genes and Genomes (KEGG) functional modules. Distribution of the completion ratio of the KEGG functional modules in 768 prokaryotic species varied greatly with the kind of module, and all modules primarily fell into 4 patterns (universal, restricted, diversified and non-prokaryotic modules), indicating the universal and unique nature of each module, and also the versatility of the KEGG Orthology (KO) identifiers mapped to each one. The module completion ratio in 8 phenotypically different bacilli revealed that some modules were shared only in phenotypically similar species. Metagenomes of human gut microbiomes from 13 healthy individuals previously determined by the Sanger method were analyzed based on the module completion ratio. Results led to new discoveries in the nutritional preferences of gut microbes, believed to be one of the mutualistic representations of gut microbiomes to avoid nutritional competition with the host. The method developed in this study could characterize the functionome harbored in genomes and metagenomes. As this method also provided taxonomical information from KEGG modules as well as the gene hosts constructing the modules, interpretation of completion profiles was simplified and we could identify the complementarity between biochemical functions in human hosts and the nutritional preferences in human gut microbiomes. Thus, our method has the potential to be a powerful tool for comparative functional analysis in genomics and metagenomics, able to target unknown environments containing various

Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond.

PubMed

Hiraoka, Satoshi; Yang, Ching-Chia; Iwasaki, Wataru

2016-09-29

Metagenomic approaches are now commonly used in microbial ecology to study microbial communities in more detail, including many strains that cannot be cultivated in the laboratory. Bioinformatic analyses make it possible to mine huge metagenomic datasets and discover general patterns that govern microbial ecosystems. However, the findings of typical metagenomic and bioinformatic analyses still do not completely describe the ecology and evolution of microbes in their environments. Most analyses still depend on straightforward sequence similarity searches against reference databases. We herein review the current state of metagenomics and bioinformatics in microbial ecology and discuss future directions for the field. New techniques will allow us to go beyond routine analyses and broaden our knowledge of microbial ecosystems. We need to enrich reference databases, promote platforms that enable meta- or comprehensive analyses of diverse metagenomic datasets, devise methods that utilize long-read sequence information, and develop more powerful bioinformatic methods to analyze data from diverse perspectives.

FY11 Report on Metagenome Analysis using Pathogen Marker Libraries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gardner, Shea N.; Allen, Jonathan E.; McLoughlin, Kevin S.

2011-06-02

A method, sequence library, and software suite was invented to rapidly assess whether any member of a pre-specified list of threat organisms or their near neighbors is present in a metagenome. The system was designed to handle mega- to giga-bases of FASTA-formatted raw sequence reads from short or long read next generation sequencing platforms. The approach is to pre-calculate a viral and a bacterial "Pathogen Marker Library" (PML) containing sub-sequences specific to pathogens or their near neighbors. A list of expected matches comparing every bacterial or viral genome against the PML sequences is also pre-calculated. To analyze a metagenome, readsmore » are compared to the PML, and observed PML-metagenome matches are compared to the expected PML-genome matches, and the ratio of observed relative to expected matches is reported. In other words, a 3-way comparison among the PML, metagenome, and existing genome sequences is used to quickly assess which (if any) species included in the PML is likely to be present in the metagenome, based on available sequence data. Our tests showed that the species with the most PML matches correctly indicated the organism sequenced for empirical metagenomes consisting of a cultured, relatively pure isolate. These runs completed in 1 minute to 3 hours on 12 CPU (1 thread/CPU), depending on the metagenome and PML. Using more threads on the same number of CPU resulted in speed improvements roughly proportional to the number of threads. Simulations indicated that detection sensitivity depends on both sequencing coverage levels for a species and the size of the PML: species were correctly detected even at ~0.003x coverage by the large PMLs, and at ~0.03x coverage by the smaller PMLs. Matches to true positive species were 3-4 orders of magnitude higher than to false positives. Simulations with short reads (36 nt and ~260 nt) showed that species were usually detected for metagenome coverage above 0.005x and coverage in the PML above 0

Application of metagenomic techniques in mining enzymes from microbial communities for biofuel synthesis.

PubMed

Xing, Mei-Ning; Zhang, Xue-Zhu; Huang, He

2012-01-01

Feedstock for biofuel synthesis is transitioning to lignocelluosic biomass to address criticism over competition between first generation biofuels and food production. As microbial catalysis is increasingly applied for the conversion of biomass to biofuels, increased import has been placed on the development of novel enzymes. With revolutionary advances in sequencer technology and metagenomic sequencing, mining enzymes from microbial communities for biofuel synthesis is becoming more and more practical. The present article highlights the latest research progress on the special characteristics of metagenomic sequencing, which has been a powerful tool for new enzyme discovery and gene functional analysis in the biomass energy field. Critical enzymes recently developed for the pretreatment and conversion of lignocellulosic materials are evaluated with respect to their activity and stability, with additional explorations into xylanase, laccase, amylase, chitinase, and lipolytic biocatalysts for other biomass feedstocks. Copyright © 2012 Elsevier Inc. All rights reserved.

MetaStorm: A Public Resource for Customizable Metagenomics Annotation

PubMed Central

Arango-Argoty, Gustavo; Singh, Gargi; Heath, Lenwood S.; Pruden, Amy; Xiao, Weidong; Zhang, Liqing

2016-01-01

Metagenomics is a trending research area, calling for the need to analyze large quantities of data generated from next generation DNA sequencing technologies. The need to store, retrieve, analyze, share, and visualize such data challenges current online computational systems. Interpretation and annotation of specific information is especially a challenge for metagenomic data sets derived from environmental samples, because current annotation systems only offer broad classification of microbial diversity and function. Moreover, existing resources are not configured to readily address common questions relevant to environmental systems. Here we developed a new online user-friendly metagenomic analysis server called MetaStorm (http://bench.cs.vt.edu/MetaStorm/), which facilitates customization of computational analysis for metagenomic data sets. Users can upload their own reference databases to tailor the metagenomics annotation to focus on various taxonomic and functional gene markers of interest. MetaStorm offers two major analysis pipelines: an assembly-based annotation pipeline and the standard read annotation pipeline used by existing web servers. These pipelines can be selected individually or together. Overall, MetaStorm provides enhanced interactive visualization to allow researchers to explore and manipulate taxonomy and functional annotation at various levels of resolution. PMID:27632579

MetaStorm: A Public Resource for Customizable Metagenomics Annotation.

PubMed

Arango-Argoty, Gustavo; Singh, Gargi; Heath, Lenwood S; Pruden, Amy; Xiao, Weidong; Zhang, Liqing

2016-01-01

Metagenomics is a trending research area, calling for the need to analyze large quantities of data generated from next generation DNA sequencing technologies. The need to store, retrieve, analyze, share, and visualize such data challenges current online computational systems. Interpretation and annotation of specific information is especially a challenge for metagenomic data sets derived from environmental samples, because current annotation systems only offer broad classification of microbial diversity and function. Moreover, existing resources are not configured to readily address common questions relevant to environmental systems. Here we developed a new online user-friendly metagenomic analysis server called MetaStorm (http://bench.cs.vt.edu/MetaStorm/), which facilitates customization of computational analysis for metagenomic data sets. Users can upload their own reference databases to tailor the metagenomics annotation to focus on various taxonomic and functional gene markers of interest. MetaStorm offers two major analysis pipelines: an assembly-based annotation pipeline and the standard read annotation pipeline used by existing web servers. These pipelines can be selected individually or together. Overall, MetaStorm provides enhanced interactive visualization to allow researchers to explore and manipulate taxonomy and functional annotation at various levels of resolution.

Long-term radiation effects on GaAs solar cell characteristics

NASA Technical Reports Server (NTRS)

Heinbockel, J. H.; Doviak, M. J.

1978-01-01

This report investigates preliminary design considerations which should be considered for a space experiment involving Gallium Arsenide (GaAs) solar cells. The electron radiation effects on GaAs solar cells were conducted in a laboratory environment, and a statistical analysis of the data is presented. In order to augment the limited laboratory data, a theoretical investigation of the effect of radiation on GaAs solar cells is also developed. The results of this study are empirical prediction equations which can be used to estimate the actual damage of electrical characteristics in a space environment. The experimental and theoretical studies also indicate how GaAs solar cell parameters should be designed in order to withstand the effects of electron radiation damage.

GaAs thin films and methods of making and using the same

DOEpatents

Boettcher, Shannon; Ritenour, Andrew; Boucher, Jason; Greenaway, Ann

2016-06-14

Disclosed herein are embodiments of methods for making GaAs thin films, such as photovoltaic GaAs thin films. The methods disclosed herein utilize sources, precursors, and reagents that do not produce (or require) toxic gas and that are readily available and relatively low in cost. In some embodiments, the methods are readily scalable for industrial applications and can provide GaAs thin films having properties that are at least comparable to or potentially superior to GaAs films obtained from conventional methods.

High-efficiency thin-film GaAs solar cells, phase2

NASA Technical Reports Server (NTRS)

Yeh, Y. C. M.

1981-01-01

Thin GaAs epi-layers with good crystallographic quality were grown using a (100) Si-substrate on which a thin Ge epi-interlayer was grown by CVD from germane. Both antireflection-coated metal oxide semiconductor (AMOS) and n(+)/p homojunction structures were studied. The AMOS cells were fabricated on undoped-GaAs epi-layers deposited on bulk poly-Ge substrates using organo-metallic CVD film-growth, with the best achieved AM1 conversion efficiency being 9.1%. Both p-type and n(+)-type GaAs growth were optimized using 50 ppm dimethyl zinc and 1% hydrogen sulfide, respectively. A direct GaAs deposition method in fabricating ultra-thin top layer, epitaxial n(+)/p shallow homojunction solar cells on (100) GaAs substrates (without anodic thinning) was developed to produce large area (1 sq/cm) cells, with 19.4% AM1 conversion efficiency achieved. Additionally, an AM1 conversion efficiency of 18.4% (17.5% with 5% grid coverage) was achieved for a single crystal GaAs n(+)/p cell grown by OM-CVD on a Ge wafer.

Marine Metagenome as A Resource for Novel Enzymes.

PubMed

Alma'abadi, Amani D; Gojobori, Takashi; Mineta, Katsuhiko

2015-10-01

More than 99% of identified prokaryotes, including many from the marine environment, cannot be cultured in the laboratory. This lack of capability restricts our knowledge of microbial genetics and community ecology. Metagenomics, the culture-independent cloning of environmental DNAs that are isolated directly from an environmental sample, has already provided a wealth of information about the uncultured microbial world. It has also facilitated the discovery of novel biocatalysts by allowing researchers to probe directly into a huge diversity of enzymes within natural microbial communities. Recent advances in these studies have led to a great interest in recruiting microbial enzymes for the development of environmentally-friendly industry. Although the metagenomics approach has many limitations, it is expected to provide not only scientific insights but also economic benefits, especially in industry. This review highlights the importance of metagenomics in mining microbial lipases, as an example, by using high-throughput techniques. In addition, we discuss challenges in the metagenomics as an important part of bioinformatics analysis in big data. Copyright © 2015 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

Deciphering viral presences: two novel partial giant viruses detected in marine metagenome and in a mine drainage metagenome.

PubMed

Andreani, Julien; Verneau, Jonathan; Raoult, Didier; Levasseur, Anthony; La Scola, Bernard

2018-04-10

Nucleo-cytoplasmic large DNA viruses are doubled stranded DNA viruses capable of infecting eukaryotic cells. Since the discovery of Mimivirus and Pandoravirus, there has been no doubt about their extraordinary features compared to "classic" viruses. Recently, we reported the expansion of the proposed family Pithoviridae, with the description of Cedratvirus and Orpheovirus, two new viruses related to Pithoviruses. Studying the major capsid protein of Orpheovirus, we detected a homologous sequence in a mine drainage metagenome. The in-depth exploration of this metagenome, using the MG-Digger program, enabled us to retrieve up to 10 contigs with clear evidence of viral sequences. Moreover, phylogenetic analyses further extended our screening with the discovery in another marine metagenome of a second virus closely related to Orpheovirus IHUMI-LCC2. This virus is a misidentified virus confused with and annotated as a Rickettsiales bacterium. It presents a partial genome size of about 170 kbp.

Metagenomics: A new horizon in cancer research

PubMed Central

Banerjee, Joyita; Mishra, Neetu; Dhas, Yogita

2015-01-01

Metagenomics has broadened the scope of targeting microbes responsible for inducing various types of cancers. About 16.1% of cancers are associated with microbial infection. Metagenomics is an equitable way of identifying and studying micro-organisms within their habitat. In cancer research, this approach has revolutionized the way of identifying, analyzing and targeting the microbial diversity present in the tissue specimens of cancer patients. The genomic analyses of these micro-organisms through next generation sequencing techniques invariably facilitate in recognizing the microbial population in biopsies and their evolutionary relationships with each other. In this review an attempt has been made to generate current metagenomic view on cancer microbiota. Different types of micro-organisms have been found to be linked to various types of cancers, thus, contributing significantly in understanding the disease at molecular level. PMID:26110115

Consensus statement: Virus taxonomy in the age of metagenomics.

PubMed

Simmonds, Peter; Adams, Mike J; Benkő, Mária; Breitbart, Mya; Brister, J Rodney; Carstens, Eric B; Davison, Andrew J; Delwart, Eric; Gorbalenya, Alexander E; Harrach, Balázs; Hull, Roger; King, Andrew M Q; Koonin, Eugene V; Krupovic, Mart; Kuhn, Jens H; Lefkowitz, Elliot J; Nibert, Max L; Orton, Richard; Roossinck, Marilyn J; Sabanadzovic, Sead; Sullivan, Matthew B; Suttle, Curtis A; Tesh, Robert B; van der Vlugt, René A; Varsani, Arvind; Zerbini, F Murilo

2017-03-01

The number and diversity of viral sequences that are identified in metagenomic data far exceeds that of experimentally characterized virus isolates. In a recent workshop, a panel of experts discussed the proposal that, with appropriate quality control, viruses that are known only from metagenomic data can, and should be, incorporated into the official classification scheme of the International Committee on Taxonomy of Viruses (ICTV). Although a taxonomy that is based on metagenomic sequence data alone represents a substantial departure from the traditional reliance on phenotypic properties, the development of a robust framework for sequence-based virus taxonomy is indispensable for the comprehensive characterization of the global virome. In this Consensus Statement article, we consider the rationale for why metagenomic sequence data should, and how it can, be incorporated into the ICTV taxonomy, and present proposals that have been endorsed by the Executive Committee of the ICTV.

Ensemble-based classification approach for micro-RNA mining applied on diverse metagenomic sequences.

PubMed

ElGokhy, Sherin M; ElHefnawi, Mahmoud; Shoukry, Amin

2014-05-06

computational tool for miRNA prediction in genomic or metagenomic data. It has been applied on three metagenomic samples from different environments (mine drainage, groundwater and marine metagenomic sequences). The prediction results provide a set of extremely potential miRNA hairpins for cloning prediction methods. Among the ensemble prediction obtained results there are pre-miRNA candidates that have been validated using miRbase while they have not been recognized by some of the base classifiers.

Influence of arsenic flow on the crystal structure of epitaxial GaAs grown at low temperatures on GaAs (100) and (111)A substrates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Galiev, G. B.; Klimov, E. A.; Vasiliev, A. L.

The influence of arsenic flow in a growth chamber on the crystal structure of GaAs grown by molecular-beam epitaxy at a temperature of 240°C on GaAs (100) and (111)A substrates has been investigated. The flow ratio γ of arsenic As4 and gallium was varied in the range from 16 to 50. GaAs films were either undoped, or homogeneously doped with silicon, or contained three equidistantly spaced silicon δ-layers. The structural quality of the annealed samples has been investigated by transmission electron microscopy. It is established for the first time that silicon δ-layers in “low-temperature” GaAs serve as formation centers ofmore » arsenic precipitates. Their average size, concentration, and spatial distribution are estimated. The dependence of the film structural quality on γ is analyzed. Regions 100–150 nm in size have been revealed in some samples and identified (by X-ray microanalysis) as pores. It is found that, in the entire range of γ under consideration, GaAs films on (111)A substrates have a poorer structural quality and become polycrystalline beginning with a thickness of 150–200 nm.« less

Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples

PubMed Central

White, James Robert; Nagarajan, Niranjan; Pop, Mihai

2009-01-01

Numerous studies are currently underway to characterize the microbial communities inhabiting our world. These studies aim to dramatically expand our understanding of the microbial biosphere and, more importantly, hope to reveal the secrets of the complex symbiotic relationship between us and our commensal bacterial microflora. An important prerequisite for such discoveries are computational tools that are able to rapidly and accurately compare large datasets generated from complex bacterial communities to identify features that distinguish them. We present a statistical method for comparing clinical metagenomic samples from two treatment populations on the basis of count data (e.g. as obtained through sequencing) to detect differentially abundant features. Our method, Metastats, employs the false discovery rate to improve specificity in high-complexity environments, and separately handles sparsely-sampled features using Fisher's exact test. Under a variety of simulations, we show that Metastats performs well compared to previously used methods, and significantly outperforms other methods for features with sparse counts. We demonstrate the utility of our method on several datasets including a 16S rRNA survey of obese and lean human gut microbiomes, COG functional profiles of infant and mature gut microbiomes, and bacterial and viral metabolic subsystem data inferred from random sequencing of 85 metagenomes. The application of our method to the obesity dataset reveals differences between obese and lean subjects not reported in the original study. For the COG and subsystem datasets, we provide the first statistically rigorous assessment of the differences between these populations. The methods described in this paper are the first to address clinical metagenomic datasets comprising samples from multiple subjects. Our methods are robust across datasets of varied complexity and sampling level. While designed for metagenomic applications, our software can also be applied

Growth and characteristics of p-type doped GaAs nanowire

NASA Astrophysics Data System (ADS)

Li, Bang; Yan, Xin; Zhang, Xia; Ren, Xiaomin

2018-05-01

The growth of p-type GaAs nanowires (NWs) on GaAs (111) B substrates by metal-organic chemical vapor deposition (MOCVD) has been systematically investigated as a function of diethyl zinc (DEZn) flow. The growth rate of GaAs NWs was slightly improved by Zn-doping and kink is observed under high DEZn flow. In addition, the I–V curves of GaAs NWs has been measured and the p-type dope concentration under the II/III ratio of 0.013 and 0.038 approximated to 1019–1020 cm‑3. Project supported by the National Natural Science Foundation of China (Nos. 61376019, 61504010, 61774021) and the Fund of State Key Laboratory of Information Photonics and Optical Communications (Beijing University of Posts and Telecommunications), China (Nos. IPOC2017ZT02, IPOC2017ZZ01).

Multiband corrections for the semi-classical simulation of interband tunneling in GaAs tunnel junctions

NASA Astrophysics Data System (ADS)

Louarn, K.; Claveau, Y.; Hapiuk, D.; Fontaine, C.; Arnoult, A.; Taliercio, T.; Licitra, C.; Piquemal, F.; Bounouh, A.; Cavassilas, N.; Almuneau, G.

2017-09-01

The aim of this study is to investigate the impact of multiband corrections on the current density in GaAs tunnel junctions (TJs) calculated with a refined yet simple semi-classical interband tunneling model (SCITM). The non-parabolicity of the considered bands and the spin-orbit effects are considered by using a recently revisited SCITM available in the literature. The model is confronted to experimental results from a series of molecular beam epitaxy grown GaAs TJs and to numerical results obtained with a full quantum model based on the non-equilibrium Green’s function formalism and a 6-band k.p Hamiltonian. We emphasize the importance of considering the non-parabolicity of the conduction band by two different measurements of the energy-dependent electron effective mass in N-doped GaAs. We also propose an innovative method to compute the non-uniform electric field in the TJ for the SCITM simulations, which is of prime importance for a successful operation of the model. We demonstrate that, when considering the multiband corrections and this new computation of the non-uniform electric field, the SCITM succeeds in predicting the electrical characteristics of GaAs TJs, and are also in agreement with the quantum model. Besides the fundamental study of the tunneling phenomenon in TJs, the main benefit of this SCITM is that it can be easily embedded into drift-diffusion software, which are the most widely-used simulation tools for electronic and opto-electronic devices such as multi-junction solar cells, tunnel field-effect transistors, or vertical-cavity surface-emitting lasers.

Sulfur doping of GaAs with (NH4)2Sx solution

NASA Astrophysics Data System (ADS)

Lee, Jong-Lam

1999-01-01

A novel technique for sulfur doping to GaAs was demonstrated. The surface of GaAs was treated with (NH4)2Sx solution, subsequent to annealing using either furnace or rapid thermal processing. Sulfur atoms adsorbed at the surface of GaAs during the (NH4)2Sx treatment diffuse into GaAs during the annealing. The diffusion profiles of sulfur in both types of annealing treatments show a concave shape from the GaAs surface. Diffusion constants of sulfur determined using the Boltzmann-Matano technique increase with the decrease of sulfur concentration via the depth from the surface of GaAs. This suggests that immobile sulfur donor SAs+ forms at the near surface interacts with a Ga divacancy, and results in the production of mobile As interstitials, IAs. The IAs moves fast toward the inside of GaAs and kickout the SAs+ donor, producing a fast diffusing species of interstitial S atoms. The diffusion coefficients of sulfur determined are 2.5×10-14 cm2/s at 840 °C and 5×10-12 cm2/s at 900 °C. The sulfur doping technique is applied to the fabrication of metal-semiconductor field-effect transistors (MESFETs). The MESFETs with 1.0 μm gate length exhibit transconductance of 190 mS/mm, demonstrating the applicability of this technique to the formation of active channel layer of MESFETs.

Effect of Changing Treatment Disinfectants on the Microbiology of Distributed Water and Pipe Biofilm Communities using Conventional and Metagenomic Approaches

EPA Science Inventory

The purpose of this research was to add to our knowledge of chlorine and monochloramine disinfectants, with regards to effects on the microbial communities in distribution systems. A whole metagenome-based approach using sophisticated molecular tools (e.g., next generation sequen...

Comparing viral metagenomics methods using a highly multiplexed human viral pathogens reagent

PubMed Central

Li, Linlin; Deng, Xutao; Mee, Edward T.; Collot-Teixeira, Sophie; Anderson, Rob; Schepelmann, Silke; Minor, Philip D.; Delwart, Eric

2014-01-01

Unbiased metagenomic sequencing holds significant potential as a diagnostic tool for the simultaneous detection of any previously genetically described viral nucleic acids in clinical samples. Viral genome sequences can also inform on likely phenotypes including drug susceptibility or neutralization serotypes. In this study, different variables of the laboratory methods often used to generate viral metagenomics libraries on the efficiency of viral detection and virus genome coverage were compared. A biological reagent consisting of 25 different human RNA and DNA viral pathogens was used to estimate the effect of filtration and nuclease digestion, DNA/RNA extraction methods, pre-amplification and the use of different library preparation kits on the detection of viral nucleic acids. Filtration and nuclease treatment led to slight decreases in the percentage of viral sequence reads and number of viruses detected. For nucleic acid extractions silica spin columns improved viral sequence recovery relative to magnetic beads and Trizol extraction. Pre-amplification using random RT-PCR while generating more viral sequence reads resulted in detection of fewer viruses, more overlapping sequences, and lower genome coverage. The ScriptSeq library preparation method retrieved more viruses and a greater fraction of their genomes than the TruSeq and Nextera methods. Viral metagenomics sequencing was able to simultaneously detect up to 22 different viruses in the biological reagent analyzed including all those detected by qPCR. Further optimization will be required for the detection of viruses in biologically more complex samples such as tissues, blood, or feces. PMID:25497414

Relation between trinucleotide GAA repeat length and sensory neuropathy in Friedreich's ataxia.

PubMed

Santoro, L; De Michele, G; Perretti, A; Crisci, C; Cocozza, S; Cavalcanti, F; Ragno, M; Monticelli, A; Filla, A; Caruso, G

1999-01-01

To verify if GAA expansion size in Friedreich's ataxia could account for the severity of sensory neuropathy. Retrospective study of 56 patients with Friedreich's ataxia selected according to homozygosity for GAA expansion and availability of electrophysiological findings. Orthodromic sensory conduction velocity in the median nerve was available in all patients and that of the tibial nerve in 46 of them. Data of sural nerve biopsy and of a morphometric analysis were available in 12 of the selected patients. The sensory action potential amplitude at the wrist (wSAP) and at the medial malleolus (m mal SAP) and the percentage of myelinated fibres with diameter larger than 7, 9, and 11 microm in the sural nerve were correlated with disease duration and GAA expansion size on the shorter (GAA1) and larger (GAA2) expanded allele in each pair. Pearson's correlation test and stepwise multiple regression were used for statistical analysis. A significant inverse correlation between GAA1 size and wSAP, m mal SAP, and percentage of myelinated fibres was found. Stepwise multiple regression showed that GAA1 size significantly affects electrophysiological and morphometric data, whereas duration of disease has no effect. The data suggest that the severity of the sensory neuropathy is probably genetically determined and that it is not progressive.

Comparison of photoemission characteristics between square and circular wire array GaAs photocathodes.

PubMed

Deng, Wenjuan; Peng, Xincun; Zou, Jijun; Wang, Weilu; Liu, Yun; Zhang, Tao; Zhang, Yijun; Zhang, Daoli

2017-11-10

Two types of negative electron affinity gallium arsenide (GaAs) wire array photocathodes were fabricated by reactive ion etching and inductively coupled plasma etching of bulk GaAs material. High density GaAs wire arrays with high periodicity and good morphology were verified using scanning electron microscopy, and photoluminescence spectra confirmed the wire arrays had good crystalline quality. Reflection spectra showed that circular GaAs wire arrays had superior light trapping compared with square ones. However, after Cs/O activation, the square GaAs wire array photocathodes showed enhanced spectral response. The integral sensitivity of the square wire array photocathodes was approximately 2.8 times that of the circular arrays.

ATLAS (Automatic Tool for Local Assembly Structures) - A Comprehensive Infrastructure for Assembly, Annotation, and Genomic Binning of Metagenomic and Metaranscripomic Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, Richard A.; Brown, Joseph M.; Colby, Sean M.

ATLAS (Automatic Tool for Local Assembly Structures) is a comprehensive multiomics data analysis pipeline that is massively parallel and scalable. ATLAS contains a modular analysis pipeline for assembly, annotation, quantification and genome binning of metagenomics and metatranscriptomics data and a framework for reference metaproteomic database construction. ATLAS transforms raw sequence data into functional and taxonomic data at the microbial population level and provides genome-centric resolution through genome binning. ATLAS provides robust taxonomy based on majority voting of protein coding open reading frames rolled-up at the contig level using modified lowest common ancestor (LCA) analysis. ATLAS provides robust taxonomy based onmore » majority voting of protein coding open reading frames rolled-up at the contig level using modified lowest common ancestor (LCA) analysis. ATLAS is user-friendly, easy install through bioconda maintained as open-source on GitHub, and is implemented in Snakemake for modular customizable workflows.« less

Metagenomics: The Next Culture-Independent Game Changer

PubMed Central

Forbes, Jessica D.; Knox, Natalie C.; Ronholm, Jennifer; Pagotto, Franco; Reimer, Aleisha

2017-01-01

A trend towards the abandonment of obtaining pure culture isolates in frontline laboratories is at a crossroads with the ability of public health agencies to perform their basic mandate of foodborne disease surveillance and response. The implementation of culture-independent diagnostic tests (CIDTs) including nucleic acid and antigen-based assays for acute gastroenteritis is leaving public health agencies without laboratory evidence to link clinical cases to each other and to food or environmental substances. This limits the efficacy of public health epidemiology and surveillance as well as outbreak detection and investigation. Foodborne outbreaks have the potential to remain undetected or have insufficient evidence to support source attribution and may inadvertently increase the incidence of foodborne diseases. Next-generation sequencing of pure culture isolates in clinical microbiology laboratories has the potential to revolutionize the fields of food safety and public health. Metagenomics and other ‘omics’ disciplines could provide the solution to a cultureless future in clinical microbiology, food safety and public health. Data mining of information obtained from metagenomics assays can be particularly useful for the identification of clinical causative agents or foodborne contamination, detection of AMR and/or virulence factors, in addition to providing high-resolution subtyping data. Thus, metagenomics assays may provide a universal test for clinical diagnostics, foodborne pathogen detection, subtyping and investigation. This information has the potential to reform the field of enteric disease diagnostics and surveillance and also infectious diseases as a whole. The aim of this review will be to present the current state of CIDTs in diagnostic and public health laboratories as they relate to foodborne illness and food safety. Moreover, we will also discuss the diagnostic and subtyping utility and concomitant bias limitations of metagenomics and comparable

n-Type Doping of Vapor-Liquid-Solid Grown GaAs Nanowires.

PubMed

Gutsche, Christoph; Lysov, Andrey; Regolin, Ingo; Blekker, Kai; Prost, Werner; Tegude, Franz-Josef

2011-12-01

In this letter, n-type doping of GaAs nanowires grown by metal-organic vapor phase epitaxy in the vapor-liquid-solid growth mode on (111)B GaAs substrates is reported. A low growth temperature of 400°C is adjusted in order to exclude shell growth. The impact of doping precursors on the morphology of GaAs nanowires was investigated. Tetraethyl tin as doping precursor enables heavily n-type doped GaAs nanowires in a relatively small process window while no doping effect could be found for ditertiarybutylsilane. Electrical measurements carried out on single nanowires reveal an axially non-uniform doping profile. Within a number of wires from the same run, the donor concentrations ND of GaAs nanowires are found to vary from 7 × 10(17) cm(-3) to 2 × 10(18) cm(-3). The n-type conductivity is proven by the transfer characteristics of fabricated nanowire metal-insulator-semiconductor field-effect transistor devices.

Caught in the middle with multiple displacement amplification: the myth of pooling for avoiding multiple displacement amplification bias in a metagenome.

PubMed

Marine, Rachel; McCarren, Coleen; Vorrasane, Vansay; Nasko, Dan; Crowgey, Erin; Polson, Shawn W; Wommack, K Eric

2014-01-30

Shotgun metagenomics has become an important tool for investigating the ecology of microorganisms. Underlying these investigations is the assumption that metagenome sequence data accurately estimates the census of microbial populations. Multiple displacement amplification (MDA) of microbial community DNA is often used in cases where it is difficult to obtain enough DNA for sequencing; however, MDA can result in amplification biases that may impact subsequent estimates of population census from metagenome data. Some have posited that pooling replicate MDA reactions negates these biases and restores the accuracy of population analyses. This assumption has not been empirically tested. Using mock viral communities, we examined the influence of pooling on population-scale analyses. In pooled and single reaction MDA treatments, sequence coverage of viral populations was highly variable and coverage patterns across viral genomes were nearly identical, indicating that initial priming biases were reproducible and that pooling did not alleviate biases. In contrast, control unamplified sequence libraries showed relatively even coverage across phage genomes. MDA should be avoided for metagenomic investigations that require quantitative estimates of microbial taxa and gene functional groups. While MDA is an indispensable technique in applications such as single-cell genomics, amplification biases cannot be overcome by combining replicate MDA reactions. Alternative library preparation techniques should be utilized for quantitative microbial ecology studies utilizing metagenomic sequencing approaches.

SPHINX--an algorithm for taxonomic binning of metagenomic sequences.

PubMed

Mohammed, Monzoorul Haque; Ghosh, Tarini Shankar; Singh, Nitin Kumar; Mande, Sharmila S

2011-01-01

Compared with composition-based binning algorithms, the binning accuracy and specificity of alignment-based binning algorithms is significantly higher. However, being alignment-based, the latter class of algorithms require enormous amount of time and computing resources for binning huge metagenomic datasets. The motivation was to develop a binning approach that can analyze metagenomic datasets as rapidly as composition-based approaches, but nevertheless has the accuracy and specificity of alignment-based algorithms. This article describes a hybrid binning approach (SPHINX) that achieves high binning efficiency by utilizing the principles of both 'composition'- and 'alignment'-based binning algorithms. Validation results with simulated sequence datasets indicate that SPHINX is able to analyze metagenomic sequences as rapidly as composition-based algorithms. Furthermore, the binning efficiency (in terms of accuracy and specificity of assignments) of SPHINX is observed to be comparable with results obtained using alignment-based algorithms. A web server for the SPHINX algorithm is available at http://metagenomics.atc.tcs.com/SPHINX/.

Photovoltaic Properties of p-Doped GaAs Nanowire Arrays Grown on n-Type GaAs(111)B Substrate

PubMed Central

2010-01-01

We report on the molecular beam epitaxy growth of Au-assisted GaAs p-type-doped NW arrays on the n-type GaAs(111)B substrate and their photovoltaic properties. The samples are grown at different substrate temperature within the range from 520 to 580 °C. It is shown that the dependence of conversion efficiency on the substrate temperature has a maximum at the substrate temperature of 550 °C. For the best sample, the conversion efficiency of 1.65% and the fill factor of 25% are obtained. PMID:20672038

Two-Photon Pumped Synchronously Mode-Locked Bulk GaAs Laser

NASA Astrophysics Data System (ADS)

Cao, W. L.; Vaucher, A. M.; Ling, J. D.; Lee, C. H.

1982-04-01

Pulses 7 picoseconds or less in duration have been generated from a bulk GaAs crystal by a synchronous mode-locking technique. The GaAs crystal was optically pumped by two-photon absorption of the emission from a mode-locked Nd:glass laser. Two-photon absorption as the means of excitation increases the volume of the gain medium by increasing the pene-tration depth of the pump intensity, enabling generation of intra-cavity pulses with peak power in the megawatt range. Tuning of the wavelength of the GaAs emission is achieved by varying the temperature. A tuning range covering 840 nm to 885 nm has been observed over a temperature range from 97°K to 260°K. The intensity of the GaAs emission has also been observed to decrease as the temperature of the crystal is increased.

Interface demarcation in GaAs by current pulsing

NASA Technical Reports Server (NTRS)

Matthiesen, D. H.; Kafalas, J. A.; Duchene, G. A.; Bellows, A. H.

1990-01-01

GTE Laboratories is currently conducting a program to investigate the effect of convection in the melt on the properties of bulk grown gallium arsenide (GaAs). In addition to extensive ground based experimentation, a Get Away Special growth system has been developed to grow two GaAs crystals aboard the Space Shuttle, each with a one inch diameter. In order to perform a complete segregation analysis of the crystals grown in space, it is necessary to measure the interface shape and growth rate as well as the spatial distribution of the selenium dopant. The techniques for interface demarcation in selenium doped GaAs by current pulsing have been developed at GTE Laboratories and successful interface demarcation has been achieved for current pulses ranging from 20 to 90 amps, in both single crystal and polycrystalline regions.

Microwave GaAs Integrated Circuits On Quartz Substrates

NASA Technical Reports Server (NTRS)

Siegel, Peter H.; Mehdi, Imran; Wilson, Barbara

1994-01-01

Integrated circuits for use in detecting electromagnetic radiation at millimeter and submillimeter wavelengths constructed by bonding GaAs-based integrated circuits onto quartz-substrate-based stripline circuits. Approach offers combined advantages of high-speed semiconductor active devices made only on epitaxially deposited GaAs substrates with low-dielectric-loss, mechanically rugged quartz substrates. Other potential applications include integration of antenna elements with active devices, using carrier substrates other than quartz to meet particular requirements using lifted-off GaAs layer in membrane configuration with quartz substrate supporting edges only, and using lift-off technique to fabricate ultrathin discrete devices diced separately and inserted into predefined larger circuits. In different device concept, quartz substrate utilized as transparent support for GaAs devices excited from back side by optical radiation.

MinION™ nanopore sequencing of environmental metagenomes: a synthetic approach

PubMed Central

Watson, Mick; Minot, Samuel S.; Rivera, Maria C.; Franklin, Rima B.

2017-01-01

averaging 5700 bp with up to 98% assignment accuracy at the species level. The observed community proportions for “equal” and “rare” synthetic libraries were close to the known proportions, deviating from 0.1% to 10% across all tests. For a 20-species mock community with staggered contributions, a sequencing run detected all but 3 species (each included at <0.05% of DNA in the total mixture), 91% of reads were assigned to the correct species, 93% of reads were assigned to the correct genus, and >99% of reads were assigned to the correct family. Conclusions: At the current level of output and sequence quality (just under 4 × 103 2D reads for a synthetic metagenome), MinION sequencing followed by Kraken or One Codex analysis has the potential to provide rapid and accurate metagenomic analysis where the consortium is comprised of a limited number of taxa. Important considerations noted in this study included: high sensitivity of the MinION platform to the quality of input DNA, high variability of sequencing results across libraries and flow cells, and relatively small numbers of 2D reads per analysis limit. Together, these limited detection of very rare components of the microbial consortia, and would likely limit the utility of MinION for the sequencing of high-complexity metagenomic communities where thousands of taxa are expected. Furthermore, the limitations of the currently available data analysis tools suggest there is considerable room for improvement in the analytical approaches for the characterization of microbial communities using long reads. Nevertheless, the fact that the accurate taxonomic assignment of high-quality reads generated by MinION is approaching 99.5% and, in most cases, the inferred community structure mirrors the known proportions of a synthetic mixture warrants further exploration of practical application to environmental metagenomics as the platform continues to develop and improve. With further improvement in sequence throughput and error

Oral Metagenomic Biomarkers in Rheumatoid Arthritis

DTIC Science & Technology

2017-09-01

AWARD NUMBER: W81XWH-15-1-0320 TITLE: Oral Metagenomic Biomarkers in Rheumatoid Arthritis PRINCIPAL INVESTIGATOR: Edward K Chan CONTRACTING... Rheumatoid Arthritis 5a. CONTRACT NUMBER 5b. GRANT NUMBER W81XWH-15-1-0320 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Edward K Chan 5d. PROJECT NUMBER...individuals with  rheumatoid   arthritis  (RA). The goal is to test the  hypothesis that oral microbiome and metagenomic analyses will allow us to identify new

Studies of molecular-beam epitaxy growth of GaAs on porous Si substrates

NASA Technical Reports Server (NTRS)

Mii, Y. J.; Kao, Y. C.; Wu, B. J.; Wang, K. L.; Lin, T. L.; Liu, J. K.

1988-01-01

GaAs has been grown on porous Si directly and on Si buffer layer-porous Si substrates by molecular-beam epitaxy. In the case of GaAs growth on porous Si, transmission electron microscopy (TEM) reveals that the dominant defects in GaAs layers grown on porous Si are microtwins and stacking faults, which originate from the GaAs/porous Si interface. GaAs is found to penetrate into the porous Si layers. By using a thin Si buffer layer (50 nm), GaAs penetration diminishes and the density of microtwins and stacking faults is largely reduced and localized at the GaAs/Si buffer interface. However, there is a high density of threading dislocations remaining. Both Si (100) aligned and four degree tilted substrates have been examined in this study. TEM results show no observable effect of the tilted substrates on the quality of the GaAs epitaxial layer.

Metagenomics approach to the study of the gut microbiome structure and function in zebrafish Danio rerio fed with gluten formulated diet.

PubMed

Koo, Hyunmin; Hakim, Joseph A; Powell, Mickie L; Kumar, Ranjit; Eipers, Peter G; Morrow, Casey D; Crowley, Michael; Lefkowitz, Elliot J; Watts, Stephen A; Bej, Asim K

2017-04-01

In this study, we report the gut microbial composition and predictive functional profiles of zebrafish, Danio rerio, fed with a control formulated diet (CFD), and a gluten formulated diet (GFD) using a metagenomics approach and bioinformatics tools. The microbial communities of the GFD-fed D. rerio displayed heightened abundances of Legionellales, Rhizobiaceae, and Rhodobacter, as compared to the CFD-fed counterparts. Predicted metagenomics of microbial communities (PICRUSt) in GFD-fed D. rerio showed KEGG functional categories corresponding to bile secretion, secondary bile acid biosynthesis, and the metabolism of glycine, serine, and threonine. The CFD-fed D. rerio exhibited KEGG functional categories of bacteria-mediated cobalamin biosynthesis, which was supported by the presence of cobalamin synthesizers such as Bacteroides and Lactobacillus. Though these bacteria were absent in GFD-fed D. rerio, a comparable level of the cobalamin biosynthesis KEGG functional category was observed, which could be contributed by the compensatory enrichment of Cetobacterium. Based on these results, we conclude D. rerio to be a suitable alternative animal model for the use of a targeted metagenomics approach along with bioinformatics tools to further investigate the relationship between the gluten diet and microbiome profile in the gut ecosystem leading to gastrointestinal diseases and other undesired adverse health effects. Copyright © 2017. Published by Elsevier B.V.

Ray Meta: scalable de novo metagenome assembly and profiling

PubMed Central

2012-01-01

Voluminous parallel sequencing datasets, especially metagenomic experiments, require distributed computing for de novo assembly and taxonomic profiling. Ray Meta is a massively distributed metagenome assembler that is coupled with Ray Communities, which profiles microbiomes based on uniquely-colored k-mers. It can accurately assemble and profile a three billion read metagenomic experiment representing 1,000 bacterial genomes of uneven proportions in 15 hours with 1,024 processor cores, using only 1.5 GB per core. The software will facilitate the processing of large and complex datasets, and will help in generating biological insights for specific environments. Ray Meta is open source and available at http://denovoassembler.sf.net. PMID:23259615

Fabrication, testing and reliability modeling of copper/titanium-metallized GaAs MESFETs and HEMTs for low-noise applications

NASA Astrophysics Data System (ADS)

Feng, Ting

Today, GaAs based field effect transistors (FETs) have been used in a broad range of high-speed electronic military and commercial applications. However, their reliability still needs to be improved. Particularly the hydrogen induced degradation is a large remaining issue in the reliability of GaAs FETs, because hydrogen can easily be incorporated into devices during the crystal growth and virtually every device processing step. The main objective of this research work is to develop a new gate metallization system in order to reduce the hydrogen induced degradation from the gate region for GaAs based MESFETs and HEMTs. Cu/Ti gate metallization has been introduced into the GaAs MESFETs and HEMTs in our work in order to solve the hydrogen problem. The purpose of the use of copper is to tie up the hydrogen atoms and prevent hydrogen penetration into the device active region as well as to keep a low gate resistance for low noise applications. In this work, the fabrication technology of GaAs MESFETs and AlGaAs/GaAs HEMTs with Cu/Ti metallized gates have been successfully developed and the fabricated Cu/Ti FETs have shown comparable DC performance with similar Au-based GaAs FETs. The Cu/Ti FETs were subjected to temperature accelerated testing at NOT under 5% hydrogen forming gas and the experimental results show the hydrogen induced degradation has been reduced for the Cu/Ti FETs compared to commonly used AuPtTi based GaAs FETs. A long-term reliability testing for Cu/Ti FETs has also been carried out at 200°C and up to 1000hours and testing results show Cu/Ti FETs performed with adequate reliability. The failure modes were found to consist of a decrease in drain saturation current and pinch-off voltage and an increase in source ohmic contact resistance. Material characterization tools including Rutherford backscattering spectroscopy and a back etching technique were used in Cu/Ti GaAs FETs, and pronounced gate metal copper in-diffusion and intermixing compounds at the

MetaCAA: A clustering-aided methodology for efficient assembly of metagenomic datasets.

PubMed

Reddy, Rachamalla Maheedhar; Mohammed, Monzoorul Haque; Mande, Sharmila S

2014-01-01

A key challenge in analyzing metagenomics data pertains to assembly of sequenced DNA fragments (i.e. reads) originating from various microbes in a given environmental sample. Several existing methodologies can assemble reads originating from a single genome. However, these methodologies cannot be applied for efficient assembly of metagenomic sequence datasets. In this study, we present MetaCAA - a clustering-aided methodology which helps in improving the quality of metagenomic sequence assembly. MetaCAA initially groups sequences constituting a given metagenome into smaller clusters. Subsequently, sequences in each cluster are independently assembled using CAP3, an existing single genome assembly program. Contigs formed in each of the clusters along with the unassembled reads are then subjected to another round of assembly for generating the final set of contigs. Validation using simulated and real-world metagenomic datasets indicates that MetaCAA aids in improving the overall quality of assembly. A software implementation of MetaCAA is available at https://metagenomics.atc.tcs.com/MetaCAA. Copyright © 2014 Elsevier Inc. All rights reserved.

Metagenome assembly through clustering of next-generation sequencing data using protein sequences.

PubMed

Sim, Mikang; Kim, Jaebum

2015-02-01

The study of environmental microbial communities, called metagenomics, has gained a lot of attention because of the recent advances in next-generation sequencing (NGS) technologies. Microbes play a critical role in changing their environments, and the mode of their effect can be solved by investigating metagenomes. However, the difficulty of metagenomes, such as the combination of multiple microbes and different species abundance, makes metagenome assembly tasks more challenging. In this paper, we developed a new metagenome assembly method by utilizing protein sequences, in addition to the NGS read sequences. Our method (i) builds read clusters by using mapping information against available protein sequences, and (ii) creates contig sequences by finding consensus sequences through probabilistic choices from the read clusters. By using simulated NGS read sequences from real microbial genome sequences, we evaluated our method in comparison with four existing assembly programs. We found that our method could generate relatively long and accurate metagenome assemblies, indicating that the idea of using protein sequences, as a guide for the assembly, is promising. Copyright © 2015 Elsevier B.V. All rights reserved.

Advanced GaAs Process Modeling. Volume 1

DTIC Science & Technology

1989-05-01

COSATI CODES 18 . SUBJECT TERMS (Continue on reverse if necessary and identify by block number) FIELD GROUP SUB-GROUP Gallium Arsenide, MESFET, Process...Background 9 3.2 Model Calculations 10 3.3 Conclusions 17 IV. ION-IMPLANTATION INTO GaAs PROFILE DETERMINATION 18 4.1 Ion Implantation Profile...Determination in GaAs 18 4.1.1. Background 18 4.1.2. Experimental Measurements 20 4.1.3. Results 22 4.1.3.1 Ion-Energy Dependence 22 4.1.3.2. Tilt and Rotation

Longitudinal Metagenomic Analysis of Hospital Air Identifies Clinically Relevant Microbes.

PubMed

King, Paula; Pham, Long K; Waltz, Shannon; Sphar, Dan; Yamamoto, Robert T; Conrad, Douglas; Taplitz, Randy; Torriani, Francesca; Forsyth, R Allyn

2016-01-01

We describe the sampling of sixty-three uncultured hospital air samples collected over a six-month period and analysis using shotgun metagenomic sequencing. Our primary goals were to determine the longitudinal metagenomic variability of this environment, identify and characterize genomes of potential pathogens and determine whether they are atypical to the hospital airborne metagenome. Air samples were collected from eight locations which included patient wards, the main lobby and outside. The resulting DNA libraries produced 972 million sequences representing 51 gigabases. Hierarchical clustering of samples by the most abundant 50 microbial orders generated three major nodes which primarily clustered by type of location. Because the indoor locations were longitudinally consistent, episodic relative increases in microbial genomic signatures related to the opportunistic pathogens Aspergillus, Penicillium and Stenotrophomonas were identified as outliers at specific locations. Further analysis of microbial reads specific for Stenotrophomonas maltophilia indicated homology to a sequenced multi-drug resistant clinical strain and we observed broad sequence coverage of resistance genes. We demonstrate that a shotgun metagenomic sequencing approach can be used to characterize the resistance determinants of pathogen genomes that are uncharacteristic for an otherwise consistent hospital air microbial metagenomic profile.

Rare-earth gate oxides for GaAs MOSFET application

NASA Astrophysics Data System (ADS)

Kwon, Kwang-Ho; Yang, Jun-Kyu; Park, Hyung-Ho; Kim, Jongdae; Roh, Tae Moon

2006-08-01

Rare-earth oxide films for gate dielectric on n-GaAs have been investigated. The oxide films were e-beam evaporated on S-passivated GaAs, considering interfacial chemical bonding state and energy band structure. Rare-earth oxides such as Gd 2O 3, (Gd xLa 1- x) 2O 3, and Gd-silicate were employed due to high resistivity and no chemical reaction with GaAs. Structural and bonding properties were characterized by X-ray photoemission, absorption, and diffraction. The electrical characteristics of metal-oxide-semiconductor (MOS) diodes were correlated with material properties and energy band structures to guarantee the feasibility for MOS field effect transistor (FET) application. Gd 2O 3 films were grown epitaxially on S-passivated GaAs (0 0 1) at 400 °C. The passivation induced a lowering of crystallization temperature with an epitaxial relationship of Gd 2O 3 (4 4 0) and GaAs (0 0 1). A better lattice matching relation between Gd 2O 3 and GaAs substrate was accomplished by the substitution of Gd with La, which has larger ionic radius. The in-plane relationship of (Gd xLa 1- x) 2O 3 (4 4 0) with GaAs (0 0 1) was found and the epitaxial films showed an improved crystalline quality. Amorphous Gd-silicate film was synthesized by the incorporation of SiO 2 into Gd 2O 3. These amorphous Gd-silicate films excluded defect traps or current flow path due to grain boundaries and showed a relatively larger energy band gap dependent on the contents of SiO 2. Energy band parameters such as Δ EC, Δ EV, and Eg were effectively controlled by the film composition.

Failure Mechanisms of GaAs Transistors - A Literature Survey

DTIC Science & Technology

1990-03-01

doping profile cannot be as sharp as with epitaxial methods. This is the result of the statistics of the implantation and the general diffusion that...Speed GaAs Logic Gates 5.1 GaAs PLANAR TRANSITOR STRUCTURES USED IN IC’S Some planar transistor structures used in IC’s with examples of the

Antibiotic resistance genes across a wide variety of metagenomes.

PubMed

Fitzpatrick, David; Walsh, Fiona

2016-02-01

The distribution of potential clinically relevant antibiotic resistance (AR) genes across soil, water, animal, plant and human microbiomes is not well understood. We aimed to investigate if there were differences in the distribution and relative abundances of resistance genes across a variety of ecological niches. All sequence reads (human, animal, water, soil, plant and insect metagenomes) from the MG-RAST database were downloaded and assembled into a local sequence database. We show that there are many reservoirs of the basic form of resistance genes e.g. blaTEM, but the human and mammalian gut microbiomes contain the widest diversity of clinically relevant resistance genes using metagenomic analysis. The human microbiomes contained a high relative abundance of resistance genes, while the relative abundances varied greatly in the marine and soil metagenomes, when datasets with greater than one million genes were compared. While these results reflect a bias in the distribution of AR genes across the metagenomes, we note this interpretation with caution. Metagenomics analysis includes limits in terms of detection and identification of AR genes in complex and diverse microbiome population. Therefore, if we do not detect the AR gene is it in fact not there or just below the limits of our techniques? © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Tolerance of GaAs as an original substrate for HVPE growth of free standing GaN

NASA Astrophysics Data System (ADS)

Suzuki, Mio; Sato, T.; Suemasu, T.; Hasegawa, F.

2004-09-01

In order to investigate possibility of thick GaN growth on a GaAs substrate by halide vapar phase epitaxy (HVPE), GaN was grown on GaAs(111)/Ti wafer with Ti deposited by E-gun. It was found that surface treatment of the GaAs substrate by HF solution deteriorated greatly the tolerence of GaAs and that Ti can protected GaAs from erosion by NH3. By depositing Ti on GaAs(111)A surface, a millor-like GaN layer could be grown at 1000 °C for 1 hour without serious deterioration of the original GaAs substrate. By increasing the growth rate, a thick free standing GaN will be obtained with GaAs as an original substrate in near future.

Photon counting microstrip X-ray detectors with GaAs sensors

NASA Astrophysics Data System (ADS)

Ruat, M.; Andrä, M.; Bergamaschi, A.; Barten, R.; Brückner, M.; Dinapoli, R.; Fröjdh, E.; Greiffenberg, D.; Lopez-Cuenca, C.; Lozinskaya, A. D.; Mezza, D.; Mozzanica, A.; Novikov, V. A.; Ramilli, M.; Redford, S.; Ruder, C.; Schmitt, B.; Shi, X.; Thattil, D.; Tinti, G.; Tolbanov, O. P.; Tyazhev, A.; Vetter, S.; Zarubin, A. N.; Zhang, J.

2018-01-01

High-Z sensors are increasingly used to overcome the poor efficiency of Si sensors above 15 keV, and further extend the energy range of synchrotron and FEL experiments. Detector-grade GaAs sensors of 500 μm thickness offer 98% absorption efficiency at 30 keV and 50% at 50 keV . In this work we assess the usability of GaAs sensors in combination with the MYTHEN photon-counting microstrip readout chip developed at PSI. Different strip length and pitch are compared, and the detector performance is evaluated in regard of the sensor material properties. Despite increased leakage current and noise, photon-counting strips mounted with GaAs sensors can be used with photons of energy as low as 5 keV, and exhibit excellent linearity with energy. The charge sharing is doubled as compared to silicon strips, due to the high diffusion coefficient of electrons in GaAs.

Laser Induced Electrodeposition on Polyimide and GaAs Substrates

DTIC Science & Technology

1983-10-01

6 3.1 Laser Gold Plating on Undoped Ga As Substrate ........... 6 3.1.1 Deposit Formation...22 iv LIST OF ILLUSTRATIONS Figure Page 1. Experimental Set-Up . . . . . .................. 4 2. Laser Gold Pla’ting Undoped GaAs (100...9 3. Laser Gold Plating Undoped GaAs (100) Deposit Resistance Measurement ......................... .10 4. Laser Gold Plating on Polyimide

Investigation of ZnSe-coated silicon substrates for GaAs solar cells

NASA Technical Reports Server (NTRS)

Huber, Daniel A.; Olsen, Larry C.; Dunham, Glen; Addis, F. William

1993-01-01

Studies are being carried out to determine the feasibility of using ZnSe as a buffer layer for GaAs solar cells grown on silicon. This study was motivated by reports in the literature indicating ZnSe films had been grown by metallorganic chemical vapor deposition (MOCVD) onto silicon with EPD values of 2 x 10(exp 5) cm(sup -2), even though the lattice mismatch between silicon and ZnSe is 4.16 percent. These results combined with the fact that ZnSe and GaAs are lattice matched to within 0.24 percent suggest that the prospects for growing high efficiency GaAs solar cells onto ZnSe-coated silicon are very good. Work to date has emphasized development of procedures for MOCVD growth of (100) ZnSe onto (100) silicon wafers, and subsequent growth of GaAs films on ZnSe/Si substrates. In order to grow high quality single crystal GaAs with a (100) orientation, which is desirable for solar cells, one must grow single crystal (100) ZnSe onto silicon substrates. A process for growth of (100) ZnSe was developed involving a two-step growth procedure at 450 C. Single crystal, (100) GaAs films were grown onto the (100) ZnSe/Si substrates at 610 C that are adherent and specular. Minority carrier diffusion lengths for the GaAs films grown on ZnSe/Si substrates were determined from photoresponse properties of Al/GaAs Schottky barriers. Diffusion lengths for n-type GaAs films are currently on the order of 0.3 microns compared to 2.0 microns for films grown simultaneously by homoepitaxy.

Cathodoluminescence Characterization of Ion Implanted GaAs.

DTIC Science & Technology

1980-03-01

technique that can be used to characterize the semiconductor device "in situ" before further processing can save the Air Force valuable time as well...Patterson Air Force Base,Ohio i! i ill i I ;Wow AFIT/DS/PH/80- I.i1I LEVELOO CATHODOLUMINESCENCE CHARACTERIZATION OF ION IPLANTED GaAs D I SSERUrAT ION...CATODOLUMINESCENCE CHARACTERIZATION .’ a .... OF ION IMPLANTED GaAs’ - .. .. Dtriy’ t’ c:’/ A’: t 1. - Cc;-,P by an i’or Milton L one B.S., M.S. Major USAF Approved

Amplification in Double Heterostructure GaAs Lasers.

DTIC Science & Technology

1981-03-15

done, for example, in the book by Siegman . When the laser signal which is to be amplified is a single mode, it is important to include the possibility...k A’AD-A097 862 AEROSPACE CORP EL SEGUNDO CA ELECTRONICS RESEARCH LAP) P 5 20/5 I AMPLIFICATION IN DOUBLE HETEROSTRUCTURE GAAS LASERS .(U IMAR al E...GARMIRE, M CHANG F04701-80-C-0081I UNCLASSIFIED TR GO81(6930 03)-2 SD-TA8-30 NL Amplification in Double Heterostructure GaAs Lasers E. GARMIRE nd M

GaAs Surface Passivation for Device Applications.

DTIC Science & Technology

1981-12-01

Ga203.’" . QI. a) / b) x 2.5 •• 24 21 18 As3d a) b) x 2. / 0 II 2 46 43 40 BINDING ENERGY (eV) Fig. 3 XPS spectra from a Ga2O3 covered GaAs surface of Ga...wU 24 21 Gas 18 SAs3d As2O3 ) .. 46 43 40 BINDING ENERGY (e) Fig. 4 XPS spectra from a AsJ03- Ga2O3 covered GaAs surface of Ga 3d (upper panel) and As

Inverted thermal conversion - GaAs, a new alternative material for integrated circuits

NASA Technical Reports Server (NTRS)

Lagowski, J.; Gatos, H. C.; Kang, C. H.; Skowronski, M.; Ko, K. Y.

1986-01-01

A new type of GaAs is developed which exhibits inverted thermal conversion (ITC); i.e., it converts from conducting to semiinsulating upon annealing at about 850 C. In device fabrication, its low resistivity prior to high-temperature processing differentiates ITC GaAs from the standard semiinsulating GaAs. The ITC characteristics are obtained through control of the concentration of the midgap donor EL2 based on heat treatment and crystal-growth modification. Thus EL2 does not exist in the conducting state of ITC GaAs. Conversion to the semiinsulating state during 850 C annealing is caused by the formation of EL2.

Dynamics of reflection high-energy electron diffraction intensity oscillations during molecular beam epitaxial growth of GaAs on (111)B GaAs substrates

NASA Astrophysics Data System (ADS)

Yen, M. Y.; Haas, T. W.

1990-06-01

We have observed intensity oscillations in reflection high-energy electron diffraction during molecular beam epitaxial growth of GaAs on (111)B GaAs substrates. These oscillations only exist over a narrow range of growth conditions and their behavior is strongly dependent on the migration kinetics of group III and the molecular dissociative reaction of group V elements.

Metagenomes from two microbial consortia associated with Santa Barbara seep oil.

PubMed

Hawley, Erik R; Malfatti, Stephanie A; Pagani, Ioanna; Huntemann, Marcel; Chen, Amy; Foster, Brian; Copeland, Alexander; del Rio, Tijana Glavina; Pati, Amrita; Jansson, Janet R; Gilbert, Jack A; Tringe, Susannah Green; Lorenson, Thomas D; Hess, Matthias

2014-12-01

The metagenomes from two microbial consortia associated with natural oils seeping into the Pacific Ocean offshore the coast of Santa Barbara (California, USA) were determined to complement already existing metagenomes generated from microbial communities associated with hydrocarbons that pollute the marine ecosystem. This genomics resource article is the first of two publications reporting a total of four new metagenomes from oils that seep into the Santa Barbara Channel. Copyright © 2014 Elsevier B.V. All rights reserved.

Integration of GaAs vertical-cavity surface emitting laser on Si by substrate removal

NASA Astrophysics Data System (ADS)

Yeh, Hsi-Jen J.; Smith, John S.

1994-03-01

The successful integration of strained quantum well InGaAs vertical-cavity surface-emitting lasers (VCSELs) on both Si and Cu substrates was described using a GaAs substrate removal technique. The GaAs VCSEL structure was metallized and bonded to the Si substrate after growth. The GaAs substrate was then removed by selective chemical wet etching. Finally, the bonded GaAs film metallized on the top (emitting) side and separate lasers were defined. This is the first time a VCSEL had been integrated on a Si substrate with its substrate removed. The performance enhancement of GaAs VCSELs bonded on good thermal conductors are demonstrated.

Metagenomic Analysis of the Ferret Fecal Viral Flora

PubMed Central

Smits, Saskia L.; Raj, V. Stalin; Oduber, Minoushka D.; Schapendonk, Claudia M. E.; Bodewes, Rogier; Provacia, Lisette; Stittelaar, Koert J.; Osterhaus, Albert D. M. E.; Haagmans, Bart L.

2013-01-01

Ferrets are widely used as a small animal model for a number of viral infections, including influenza A virus and SARS coronavirus. To further analyze the microbiological status of ferrets, their fecal viral flora was studied using a metagenomics approach. Novel viruses from the families Picorna-, Papilloma-, and Anelloviridae as well as known viruses from the families Astro-, Corona-, Parvo-, and Hepeviridae were identified in different ferret cohorts. Ferret kobu- and hepatitis E virus were mainly present in human household ferrets, whereas coronaviruses were found both in household as well as farm ferrets. Our studies illuminate the viral diversity found in ferrets and provide tools to prescreen for newly identified viruses that potentially could influence disease outcome of experimental virus infections in ferrets. PMID:23977082

Genetic variability of psychrotolerant Acidithiobacillus ferrivorans revealed by (meta)genomic analysis.

PubMed

González, Carolina; Yanquepe, María; Cardenas, Juan Pablo; Valdes, Jorge; Quatrini, Raquel; Holmes, David S; Dopson, Mark

2014-11-01

Acidophilic microorganisms inhabit low pH environments such as acid mine drainage that is generated when sulfide minerals are exposed to air. The genome sequence of the psychrotolerant Acidithiobacillus ferrivorans SS3 was compared to a metagenome from a low temperature acidic stream dominated by an A. ferrivorans-like strain. Stretches of genomic DNA characterized by few matches to the metagenome, termed 'metagenomic islands', encoded genes associated with metal efflux and pH homeostasis. The metagenomic islands were enriched in mobile elements such as phage proteins, transposases, integrases and in one case, predicted to be flanked by truncated tRNAs. Cus gene clusters predicted to be involved in copper efflux and further Cus-like RND systems were predicted to be located in metagenomic islands and therefore, constitute part of the flexible gene complement of the species. Phylogenetic analysis of Cus clusters showed both lineage specificity within the Acidithiobacillus genus as well as niche specificity associated with an acidic environment. The metagenomic islands also contained a predicted copper efflux P-type ATPase system and a polyphosphate kinase potentially involved in polyphosphate mediated copper resistance. This study identifies genetic variability of low temperature acidophiles that likely reflects metal resistance selective pressures in the copper rich environment. Copyright © 2014 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Metagenomics and the protein universe

PubMed Central

Godzik, Adam

2011-01-01

Metagenomics sequencing projects have dramatically increased our knowledge of the protein universe and provided over one-half of currently known protein sequences; they have also introduced a much broader phylogenetic diversity into the protein databases. The full analysis of metagenomic datasets is only beginning, but it has already led to the discovery of thousands of new protein families, likely representing novel functions specific to given environments. At the same time, a deeper analysis of such novel families, including experimental structure determination of some representatives, suggests that most of them represent distant homologs of already characterized protein families, and thus most of the protein diversity present in the new environments are due to functional divergence of the known protein families rather than the emergence of new ones. PMID:21497084

MetaVelvet: An Extension of Velvet Assembler to de novo Metagenome Assembly from Short Sequence Reads (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Sakakibara, Yasumbumi

2018-02-13

Keio University's Yasumbumi Sakakibara on "MetaVelvet: An Extension of Velvet Assembler to de novo Metagenome Assembly from Short Sequence Reads" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

MetaVelvet: An Extension of Velvet Assembler to de novo Metagenome Assembly from Short Sequence Reads (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sakakibara, Yasumbumi

2011-10-13

Keio University's Yasumbumi Sakakibara on "MetaVelvet: An Extension of Velvet Assembler to de novo Metagenome Assembly from Short Sequence Reads" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Genomic and metagenomic technologies to explore the antibiotic resistance mobilome.

PubMed

Martínez, José L; Coque, Teresa M; Lanza, Val F; de la Cruz, Fernando; Baquero, Fernando

2017-01-01

Antibiotic resistance is a relevant problem for human health that requires global approaches to establish a deep understanding of the processes of acquisition, stabilization, and spread of resistance among human bacterial pathogens. Since natural (nonclinical) ecosystems are reservoirs of resistance genes, a health-integrated study of the epidemiology of antibiotic resistance requires the exploration of such ecosystems with the aim of determining the role they may play in the selection, evolution, and spread of antibiotic resistance genes, involving the so-called resistance mobilome. High-throughput sequencing techniques allow an unprecedented opportunity to describe the genetic composition of a given microbiome without the need to subculture the organisms present inside. However, bioinformatic methods for analyzing this bulk of data, mainly with respect to binning each resistance gene with the organism hosting it, are still in their infancy. Here, we discuss how current genomic methodologies can serve to analyze the resistance mobilome and its linkage with different bacterial genomes and metagenomes. In addition, we describe the drawbacks of current methodologies for analyzing the resistance mobilome, mainly in cases of complex microbiotas, and discuss the possibility of implementing novel tools to improve our current metagenomic toolbox. © 2016 New York Academy of Sciences.

Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis.

PubMed

Wen, Chengping; Zheng, Zhijun; Shao, Tiejuan; Liu, Lin; Xie, Zhijun; Le Chatelier, Emmanuelle; He, Zhixing; Zhong, Wendi; Fan, Yongsheng; Zhang, Linshuang; Li, Haichang; Wu, Chunyan; Hu, Changfeng; Xu, Qian; Zhou, Jia; Cai, Shunfeng; Wang, Dawei; Huang, Yun; Breban, Maxime; Qin, Nan; Ehrlich, Stanislav Dusko

2017-07-27

The assessment and characterization of the gut microbiome has become a focus of research in the area of human autoimmune diseases. Ankylosing spondylitis is an inflammatory autoimmune disease and evidence showed that ankylosing spondylitis may be a microbiome-driven disease. To investigate the relationship between the gut microbiome and ankylosing spondylitis, a quantitative metagenomics study based on deep shotgun sequencing was performed, using gut microbial DNA from 211 Chinese individuals. A total of 23,709 genes and 12 metagenomic species were shown to be differentially abundant between ankylosing spondylitis patients and healthy controls. Patients were characterized by a form of gut microbial dysbiosis that is more prominent than previously reported cases with inflammatory bowel disease. Specifically, the ankylosing spondylitis patients demonstrated increases in the abundance of Prevotella melaninogenica, Prevotella copri, and Prevotella sp. C561 and decreases in Bacteroides spp. It is noteworthy that the Bifidobacterium genus, which is commonly used in probiotics, accumulated in the ankylosing spondylitis patients. Diagnostic algorithms were established using a subset of these gut microbial biomarkers. Alterations of the gut microbiome are associated with development of ankylosing spondylitis. Our data suggest biomarkers identified in this study might participate in the pathogenesis or development process of ankylosing spondylitis, providing new leads for the development of new diagnostic tools and potential treatments.

Comparative fecal metagenomics unveils unique functional capacity of the swine gut

PubMed Central

2011-01-01

Background Uncovering the taxonomic composition and functional capacity within the swine gut microbial consortia is of great importance to animal physiology and health as well as to food and water safety due to the presence of human pathogens in pig feces. Nonetheless, limited information on the functional diversity of the swine gut microbiome is available. Results Analysis of 637, 722 pyrosequencing reads (130 megabases) generated from Yorkshire pig fecal DNA extracts was performed to help better understand the microbial diversity and largely unknown functional capacity of the swine gut microbiome. Swine fecal metagenomic sequences were annotated using both MG-RAST and JGI IMG/M-ER pipelines. Taxonomic analysis of metagenomic reads indicated that swine fecal microbiomes were dominated by Firmicutes and Bacteroidetes phyla. At a finer phylogenetic resolution, Prevotella spp. dominated the swine fecal metagenome, while some genes associated with Treponema and Anareovibrio species were found to be exclusively within the pig fecal metagenomic sequences analyzed. Functional analysis revealed that carbohydrate metabolism was the most abundant SEED subsystem, representing 13% of the swine metagenome. Genes associated with stress, virulence, cell wall and cell capsule were also abundant. Virulence factors associated with antibiotic resistance genes with highest sequence homology to genes in Bacteroidetes, Clostridia, and Methanosarcina were numerous within the gene families unique to the swine fecal metagenomes. Other abundant proteins unique to the distal swine gut shared high sequence homology to putative carbohydrate membrane transporters. Conclusions The results from this metagenomic survey demonstrated the presence of genes associated with resistance to antibiotics and carbohydrate metabolism suggesting that the swine gut microbiome may be shaped by husbandry practices. PMID:21575148

Lightweight, Light-Trapped, Thin GaAs Solar Cells for Spacecraft Applications.

DTIC Science & Technology

1995-10-05

improve the efficiency of this type of cell. 2 The high efficiency and light weight of the cover glass supported GaAs solar cell can have a significant...is a 3-mil cover glass and 1-mil silicone adhesive on the front surface of the GaAs solar cell. Power Output 3000 400 -{ 2400 { N 300 S18200 W/m2...the ultra-thin, light-trapped GaAs solar ceill 3. Incorporate light trapping. 0 external quantum efficiency at 850 nm increased by 5.2% 4. Develop

The mismatch repair system protects against intergenerational GAA repeat instability in a Friedreich ataxia mouse model.

PubMed

Ezzatizadeh, Vahid; Pinto, Ricardo Mouro; Sandi, Chiranjeevi; Sandi, Madhavi; Al-Mahdawi, Sahar; Te Riele, Hein; Pook, Mark A

2012-04-01

Friedreich ataxia (FRDA) is an autosomal recessive neurodegenerative disorder caused by a dynamic GAA repeat expansion mutation within intron 1 of the FXN gene. Studies of mouse models for other trinucleotide repeat (TNR) disorders have revealed an important role of mismatch repair (MMR) proteins in TNR instability. To explore the potential role of MMR proteins on intergenerational GAA repeat instability in FRDA, we have analyzed the transmission of unstable GAA repeat expansions from FXN transgenic mice which have been crossed with mice that are deficient for Msh2, Msh3, Msh6 or Pms2. We find in all cases that absence of parental MMR protein not only maintains transmission of GAA expansions and contractions, but also increases GAA repeat mutability (expansions and/or contractions) in the offspring. This indicates that Msh2, Msh3, Msh6 and Pms2 proteins are not the cause of intergenerational GAA expansions or contractions, but act in their canonical MMR capacity to protect against GAA repeat instability. We further identified differential modes of action for the four MMR proteins. Thus, Msh2 and Msh3 protect against GAA repeat contractions, while Msh6 protects against both GAA repeat expansions and contractions, and Pms2 protects against GAA repeat expansions and also promotes contractions. Furthermore, we detected enhanced occupancy of Msh2 and Msh3 proteins downstream of the FXN expanded GAA repeat, suggesting a model in which Msh2/3 dimers are recruited to this region to repair mismatches that would otherwise produce intergenerational GAA contractions. These findings reveal substantial differences in the intergenerational dynamics of expanded GAA repeat sequences compared with expanded CAG/CTG repeats, where Msh2 and Msh3 are thought to actively promote repeat expansions. Copyright © 2012 Elsevier Inc. All rights reserved.

The mismatch repair system protects against intergenerational GAA repeat instability in a Friedreich ataxia mouse model

PubMed Central

Ezzatizadeh, Vahid; Pinto, Ricardo Mouro; Sandi, Chiranjeevi; Sandi, Madhavi; Al-Mahdawi, Sahar; te Riele, Hein; Pook, Mark A.

2013-01-01

Friedreich ataxia (FRDA) is an autosomal recessive neurodegenerative disorder caused by a dynamic GAA repeat expansion mutation within intron 1 of the FXN gene. Studies of mouse models for other trinucleotide repeat (TNR) disorders have revealed an important role of mismatch repair (MMR) proteins in TNR instability. To explore the potential role of MMR proteins on intergenerational GAA repeat instability in FRDA, we have analyzed the transmission of unstable GAA repeat expansions from FXN transgenic mice which have been crossed with mice that are deficient for Msh2, Msh3, Msh6 or Pms2. We find in all cases that absence of parental MMR protein not only maintains transmission of GAA expansions and contractions, but also increases GAA repeat mutability (expansions and/or contractions) in the offspring. This indicates that Msh2, Msh3, Msh6 and Pms2 proteins are not the cause of intergenerational GAA expansions or contractions, but act in their canonical MMR capacity to protect against GAA repeat instability. We further identified differential modes of action for the four MMR proteins. Thus, Msh2 and Msh3 protect against GAA repeat contractions, while Msh6 protects against both GAA repeat expansions and contractions, and Pms2 protects against GAA repeat expansions and also promotes contractions. Furthermore, we detected enhanced occupancy of Msh2 and Msh3 proteins downstream of the FXN expanded GAA repeat, suggesting a model in which Msh2/3 dimers are recruited to this region to repair mismatches that would otherwise produce intergenerational GAA contractions. These findings reveal substantial differences in the intergenerational dynamics of expanded GAA repeat sequences compared with expanded CAG/CTG repeats, where Msh2 and Msh3 are thought to actively promote repeat expansions. PMID:22289650

Oxygen in GaAs - Direct and indirect effects

NASA Technical Reports Server (NTRS)

Gatos, H. C.; Skowronski, M.; Pawlowicz, L.; Lagowski, J.

1984-01-01

Oxygen has profound effects on the key electronic properties and point defects of GaAs crystals. Thus, when added in the growth system, it decreases the free electron concentration and enhances the concentration of deep donors in the resulting crystals. Both of these effects are highly beneficial for achieving semi-insulating material and have been utilized for that purpose. They have been attributed to the tendency of oxygen to getter silicon impurities during crystal growth. Only recently, it has been found that oxygen in GaAs introduces also a midgap level, ELO, with essentially the same activation energy as EL2 but with four times greater electron capture cross section. The present report reassesses the electrical and optical properties of the midgap levels in GaAs crystals grown by the horizontal Bridgman (HB) and the Czochralski-LEC techniques. Emphasis is placed on the identification of the specific effects of ELO.

Optoelectronic simulation of GaAs solar cells with angularly selective filters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kraus, Tobias, E-mail: tobias.kraus@ise.fraunhofer.de; Höhn, Oliver; Hauser, Hubert

We discuss the influence of angularly selective filters on thin film gallium arsenide solar cells. For this reason, the detailed balance model was refined to fit our needs with respect to Auger recombination, reflection, transmission, and realistic absorption. For calculating real systems, an approach was made to include optical effects of angularly selective filters into electron-hole dynamic equations implemented in PC1D, a one dimensional solar cell calculation tool. With this approach, we find a relative V{sub oc} increase of 5% for an idealized 100 nm GaAs cell, including Auger recombination.

Performance and temperature dependencies of proton irradiated n/p GaAs and n/p silicon cells

NASA Technical Reports Server (NTRS)

Weinberg, I.; Swartz, C. K.; Hart, R. E., Jr.

1985-01-01

The n/p homojunction GaAs cell is found to be more radiation resistant than p/nheteroface GaAs under 10 MeV proton irradiation. Both GaAs cell types outperform conventional silicon n/p cells under the same conditions. An increase temperature dependency of maximum power for the GaAs n/p cells is attributed largely to differences in Voc between the two GaAs cell types. These results and diffusion length considerations are consistent with the conclusion that p-type GaAs is more radiation resistant than n-type and therefore that the n/p configuration is possibly favored for use in the space radiation environment. However, it is concluded that additional work is required in order to choose between the two GaAs cell configurations.

GaAs Spectrometer for Electron Spectroscopy at Europa

NASA Astrophysics Data System (ADS)

Lioliou, G.; Barnett, A. M.

2016-12-01

We propose a GaAs based electron spectrometer for a hypothetical future mission orbiting Europa. Previous observations at Europa's South Pole with the Hubble Space Telescope of hydrogen Lyman-α and oxygen OI 130.4 nm emissions were consistent with water vapor plumes [Roth et al., 2014, Science 343, 171]. Future observations and analysis of plumes on Europa could provide information about its subsurface structure and the distribution of liquid water within its icy shells [Rhoden at al. 2015, Icarus 253, 169]. In situ low energy (1keV - 100keV) electron spectroscopy along with UV imaging either in situ or with the Hubble Space Telescope Wide Field Camera 3 or similar would allow verification of the auroral observations being due to electron impact excitation of water vapor plumes. The proposed spectrometer includes a novel GaAs p+-i-n+ photodiode and a custom-made charge-sensitive preamplifier. The use of an early prototype GaAs detector for direct electron spectroscopy has already been demonstrated in ground based applications [Barnett et al., 2012, J. Instrum. 7, P09012]. Based on previous radiation hardness measurements of GaAs, the expected duration of the mission without degradation of the detector performance is estimated to be 4 months. Simulations and laboratory experiments characterising the detection performance of the proposed system are presented.

Photo-recovery of electron-irradiated GaAs solar cells

NASA Technical Reports Server (NTRS)

Meulenberg, Andrew

1995-01-01

The first long-term (3000 hours) UV testing of unirradiated and 1 MeV electron-irradiated GaAs solar cells, with multilayer-coated coverslides to reduce solar array operating temperature, has produced some unexpected and important results. Two results, independent of the coverslide coatings, are of particular importance in terms of the predictability of GaAs solar-array lifetime in space: ( 1) The GaAs/Ge solar cells used for this series of tests displayed a much higher radiation degradation than that predicted based on JPL Solar Cell Radiation Handbook data. Covered cells degraded more in Isc than did bare cells. Short-term illumination at 60 C did not produce significant recovery (-1%) of the radiation damage. (2) However, electron radiation damage to these GaAs solar celIs anneals at 40 C when exposed to approximately 1 sun AM0 UV light sources for extended periods. The effect appears to be roughly linear with time (-1% of lsc per 1000 UVSH), is large (greater than or equal to 3%), and has not yet saturated (at 3000 hours). This photo-recovery of radiation damage to GaAs solar cells is a new effect and potentially important to the spacecraft community. The figure compares the effects of extended UV on irradiated and unirradiated GaAs solar cells with INTELSAT-6 Si cells. The effect and its generality, the extent of and conditions for photo-recovery, and the implications of such recovery for missions in radiation environments have not yet been determined.

Defect interactions in GaAs single crystals

NASA Technical Reports Server (NTRS)

Gatos, H. C.; Lagowski, J.

1984-01-01

The two-sublattice structural configuration of GaAs and deviations from stoichiometry render the generation and interaction of electrically active point defects (and point defect complexes) critically important for device applications and very complex. Of the defect-induced energy levels, those lying deep into the energy band are very effective lifetime ""killers". The level 0.82 eV below the condition band, commonly referred to as EL2, is a major deep level, particularly in melt-grown GaAs. This level is associated with an antisite defect complex (AsGa - VAS). Possible mechanisms of its formation and its annihilation were further developed.

MeCorS: Metagenome-enabled error correction of single cell sequencing reads

DOE PAGES

Bremges, Andreas; Singer, Esther; Woyke, Tanja; ...

2016-03-15

Here we present a new tool, MeCorS, to correct chimeric reads and sequencing errors in Illumina data generated from single amplified genomes (SAGs). It uses sequence information derived from accompanying metagenome sequencing to accurately correct errors in SAG reads, even from ultra-low coverage regions. In evaluations on real data, we show that MeCorS outperforms BayesHammer, the most widely used state-of-the-art approach. MeCorS performs particularly well in correcting chimeric reads, which greatly improves both accuracy and contiguity of de novo SAG assemblies.

Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances.

PubMed

Xu, Jianping

2006-06-01

Microbial ecology examines the diversity and activity of micro-organisms in Earth's biosphere. In the last 20 years, the application of genomics tools have revolutionized microbial ecological studies and drastically expanded our view on the previously underappreciated microbial world. This review first introduces the basic concepts in microbial ecology and the main genomics methods that have been used to examine natural microbial populations and communities. In the ensuing three specific sections, the applications of the genomics in microbial ecological research are highlighted. The first describes the widespread application of multilocus sequence typing and representational difference analysis in studying genetic variation within microbial species. Such investigations have identified that migration, horizontal gene transfer and recombination are common in natural microbial populations and that microbial strains can be highly variable in genome size and gene content. The second section highlights and summarizes the use of four specific genomics methods (phylogenetic analysis of ribosomal RNA, DNA-DNA re-association kinetics, metagenomics, and micro-arrays) in analysing the diversity and potential activity of microbial populations and communities from a variety of terrestrial and aquatic environments. Such analyses have identified many unexpected phylogenetic lineages in viruses, bacteria, archaea, and microbial eukaryotes. Functional analyses of environmental DNA also revealed highly prevalent, but previously unknown, metabolic processes in natural microbial communities. In the third section, the ecological implications of sequenced microbial genomes are briefly discussed. Comparative analyses of prokaryotic genomic sequences suggest the importance of ecology in determining microbial genome size and gene content. The significant variability in genome size and gene content among strains and species of prokaryotes indicate the highly fluid nature of prokaryotic

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

DOE PAGES

Kang, Dongwan D.; Froula, Jeff; Egan, Rob; ...

2015-01-01

Grouping large genomic fragments assembled from shotgun metagenomic sequences to deconvolute complex microbial communities, or metagenome binning, enables the study of individual organisms and their interactions. Because of the complex nature of these communities, existing metagenome binning methods often miss a large number of microbial species. In addition, most of the tools are not scalable to large datasets. Here we introduce automated software called MetaBAT that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency for accurate metagenome binning. MetaBAT outperforms alternative methods in accuracy and computational efficiency on both synthetic and real metagenome datasets. Lastly, it automatically formsmore » hundreds of high quality genome bins on a very large assembly consisting millions of contigs in a matter of hours on a single node. MetaBAT is open source software and available at https://bitbucket.org/berkeleylab/metabat.« less

Heterojunction photovoltaics using GaAs nanowires and conjugated polymers.

PubMed

Ren, Shenqiang; Zhao, Ni; Crawford, Samuel C; Tambe, Michael; Bulović, Vladimir; Gradecak, Silvija

2011-02-09

We demonstrate an organic/inorganic solar cell architecture based on a blend of poly(3-hexylthiophene) (P3HT) and narrow bandgap GaAs nanowires. The measured increase of device photocurrent with increased nanowire loading is correlated with structural ordering within the active layer that enhances charge transport. Coating the GaAs nanowires with TiO(x) shells passivates nanowire surface states and further improves the photovoltaic performance. We find that the P3HT/nanowire cells yield power conversion efficiencies of 2.36% under white LED illumination for devices containing 50 wt % of TiO(x)-coated GaAs nanowires. Our results constitute important progress for the use of nanowires in large area solution processed hybrid photovoltaic cells and provide insight into the role of structural ordering in the device performance.

Phylogenetic convolutional neural networks in metagenomics.

PubMed

Fioravanti, Diego; Giarratano, Ylenia; Maggio, Valerio; Agostinelli, Claudio; Chierici, Marco; Jurman, Giuseppe; Furlanello, Cesare

2018-03-08

Convolutional Neural Networks can be effectively used only when data are endowed with an intrinsic concept of neighbourhood in the input space, as is the case of pixels in images. We introduce here Ph-CNN, a novel deep learning architecture for the classification of metagenomics data based on the Convolutional Neural Networks, with the patristic distance defined on the phylogenetic tree being used as the proximity measure. The patristic distance between variables is used together with a sparsified version of MultiDimensional Scaling to embed the phylogenetic tree in a Euclidean space. Ph-CNN is tested with a domain adaptation approach on synthetic data and on a metagenomics collection of gut microbiota of 38 healthy subjects and 222 Inflammatory Bowel Disease patients, divided in 6 subclasses. Classification performance is promising when compared to classical algorithms like Support Vector Machines and Random Forest and a baseline fully connected neural network, e.g. the Multi-Layer Perceptron. Ph-CNN represents a novel deep learning approach for the classification of metagenomics data. Operatively, the algorithm has been implemented as a custom Keras layer taking care of passing to the following convolutional layer not only the data but also the ranked list of neighbourhood of each sample, thus mimicking the case of image data, transparently to the user.

Transient GaAs plasmonic metasurfaces at terahertz frequencies

DOE PAGES

Yang, Yuanmu; Kamaraju, N.; Campione, Salvatore; ...

2016-12-09

Here we demonstrate the ultrafast formation of terahertz (THz) metasurfaces through all-optical creation of spatially modulated carrier density profiles in a deep-subwavelength GaAs film. The switch-on of the transient plasmon mode, governed by the GaAs effective electron mass and electron–phonon interactions, is revealed by structured-optical pump THz probe spectroscopy, on a time scale of 500 fs. By modulating the carrier density using different pump fluences, we observe a wide tuning of the electric dipole resonance of the transient GaAs metasurface from 0.5 THz to 1.7 THz. Furthermore, we numerically demonstrate that the metasurface presented here can be generalized to moremore » complex architectures for realizing functionalities such as perfect absorption, leading to a 30 dB modulation depth. In conclusion, the platform also provides a pathway to achieve ultrafast manipulation of infrared beams in the linear and, potentially, nonlinear regime.« less

The single-species metagenome: subtyping Staphylococcus aureus core genome sequences from shotgun metagenomic data

PubMed Central

Li, Ben; Petit III, Robert A.; Qin, Zhaohui S.; Darrow, Lyndsey

2016-01-01

In this study we developed a genome-based method for detecting Staphylococcus aureus subtypes from metagenome shotgun sequence data. We used a binomial mixture model and the coverage counts at >100,000 known S. aureus SNP (single nucleotide polymorphism) sites derived from prior comparative genomic analysis to estimate the proportion of 40 subtypes in metagenome samples. We were able to obtain >87% sensitivity and >94% specificity at 0.025X coverage for S. aureus. We found that 321 and 149 metagenome samples from the Human Microbiome Project and metaSUB analysis of the New York City subway, respectively, contained S. aureus at genome coverage >0.025. In both projects, CC8 and CC30 were the most common S. aureus clonal complexes encountered. We found evidence that the subtype composition at different body sites of the same individual were more similar than random sampling and more limited evidence that certain body sites were enriched for particular subtypes. One surprising finding was the apparent high frequency of CC398, a lineage often associated with livestock, in samples from the tongue dorsum. Epidemiologic analysis of the HMP subject population suggested that high BMI (body mass index) and health insurance are possibly associated with S. aureus carriage but there was limited power to identify factors linked to carriage of even the most common subtype. In the NYC subway data, we found a small signal of geographic distance affecting subtype clustering but other unknown factors influence taxonomic distribution of the species around the city. PMID:27781166

Metagenomic sequence of saline desert microbiota from wild ass sanctuary, Little Rann of Kutch, Gujarat, India.

PubMed

Patel, Rajesh; Mevada, Vishal; Prajapati, Dhaval; Dudhagara, Pravin; Koringa, Prakash; Joshi, C G

2015-03-01

We report Metagenome from the saline desert soil sample of Little Rann of Kutch, Gujarat State, India. Metagenome consisted of 633,760 sequences with size 141,307,202 bp and 56% G + C content. Metagenome sequence data are available at EBI under EBI Metagenomics database with accession no. ERP005612. Community metagenomics revealed total 1802 species belonged to 43 different phyla with dominating Marinobacter (48.7%) and Halobacterium (4.6%) genus in bacterial and archaeal domain respectively. Remarkably, 18.2% sequences in a poorly characterized group and 4% gene for various stress responses along with versatile presence of commercial enzyme were evident in a functional metagenome analysis.

The YNP Metagenome Project: Environmental Parameters Responsible for Microbial Distribution in the Yellowstone Geothermal Ecosystem

PubMed Central

Inskeep, William P.; Jay, Zackary J.; Tringe, Susannah G.; Herrgård, Markus J.; Rusch, Douglas B.

2013-01-01

The Yellowstone geothermal complex contains over 10,000 diverse geothermal features that host numerous phylogenetically deeply rooted and poorly understood archaea, bacteria, and viruses. Microbial communities in high-temperature environments are generally less diverse than soil, marine, sediment, or lake habitats and therefore offer a tremendous opportunity for studying the structure and function of different model microbial communities using environmental metagenomics. One of the broader goals of this study was to establish linkages among microbial distribution, metabolic potential, and environmental variables. Twenty geochemically distinct geothermal ecosystems representing a broad spectrum of Yellowstone hot-spring environments were used for metagenomic and geochemical analysis and included approximately equal numbers of: (1) phototrophic mats, (2) “filamentous streamer” communities, and (3) archaeal-dominated sediments. The metagenomes were analyzed using a suite of complementary and integrative bioinformatic tools, including phylogenetic and functional analysis of both individual sequence reads and assemblies of predominant phylotypes. This volume identifies major environmental determinants of a large number of thermophilic microbial lineages, many of which have not been fully described in the literature nor previously cultivated to enable functional and genomic analyses. Moreover, protein family abundance comparisons and in-depth analyses of specific genes and metabolic pathways relevant to these hot-spring environments reveal hallmark signatures of metabolic capabilities that parallel the distribution of phylotypes across specific types of geochemical environments. PMID:23653623

GaAs QWIP Array Containing More Than a Million Pixels

NASA Technical Reports Server (NTRS)

Jhabvala, Murzy; Choi, K. K.; Gunapala, Sarath

2005-01-01

A 1,024 x 1,024-pixel array of quantum-well infrared photodetectors (QWIPs) has been built on a 1.8 x 1.8- cm GaAs chip. In tests, the array was found to perform well in detecting images at wavelengths from 8 to 9 m in operation at temperatures between 60 and 70 K. The largest-format QWIP prior array that performed successfully in tests contained 512 x 640 pixels. There is continuing development effort directed toward satisfying actual and anticipated demands to increase numbers of pixels and pixel sizes in order to increase the imaging resolution of infrared photodetector arrays. A 1,024 x 1,024-pixel and even larger formats have been achieved in the InSb and HgCdTe material systems, but photodetector arrays in these material systems are very expensive and manufactured by fewer than half a dozen large companies. In contrast, GaAs-photodetector-array technology is very mature, and photodetectors in the GaAs material system can be readily manufactured by a wide range of industrial technologists, by universities, and government laboratories. There is much similarity between processing in the GaAs industry and processing in the pervasive silicon industry. With respect to yield and cost, the performance of GaAs technology substantially exceeds that of InSb and HgCdTe technologies. In addition, GaAs detectors can be designed to respond to any portion of the wavelength range from 3 to about 16 micrometers - a feature that is very desirable for infrared imaging. GaAs QWIP arrays, like the present one, have potential for use as imaging sensors in infrared measuring instruments, infrared medical imaging systems, and infrared cameras.

Metagenomic Taxonomy-Guided Database-Searching Strategy for Improving Metaproteomic Analysis.

PubMed

Xiao, Jinqiu; Tanca, Alessandro; Jia, Ben; Yang, Runqing; Wang, Bo; Zhang, Yu; Li, Jing

2018-04-06

Metaproteomics provides a direct measure of the functional information by investigating all proteins expressed by a microbiota. However, due to the complexity and heterogeneity of microbial communities, it is very hard to construct a sequence database suitable for a metaproteomic study. Using a public database, researchers might not be able to identify proteins from poorly characterized microbial species, while a sequencing-based metagenomic database may not provide adequate coverage for all potentially expressed protein sequences. To address this challenge, we propose a metagenomic taxonomy-guided database-search strategy (MT), in which a merged database is employed, consisting of both taxonomy-guided reference protein sequences from public databases and proteins from metagenome assembly. By applying our MT strategy to a mock microbial mixture, about two times as many peptides were detected as with the metagenomic database only. According to the evaluation of the reliability of taxonomic attribution, the rate of misassignments was comparable to that obtained using an a priori matched database. We also evaluated the MT strategy with a human gut microbial sample, and we found 1.7 times as many peptides as using a standard metagenomic database. In conclusion, our MT strategy allows the construction of databases able to provide high sensitivity and precision in peptide identification in metaproteomic studies, enabling the detection of proteins from poorly characterized species within the microbiota.

Spin-lattice relaxation of optically polarized nuclei in p -type GaAs

NASA Astrophysics Data System (ADS)

Kotur, M.; Dzhioev, R. I.; Vladimirova, M.; Cherbunin, R. V.; Sokolov, P. S.; Yakovlev, D. R.; Bayer, M.; Suter, D.; Kavokin, K. V.

2018-04-01

Spin-lattice relaxation of the nuclear spin system in p -type GaAs is studied using a three-stage experimental protocol including optical pumping and measuring the difference of the nuclear spin polarization before and after a dark interval of variable length. This method allows us to measure the spin-lattice relaxation time T1 of optically pumped nuclei "in the dark," that is, in the absence of illumination. The measured T1 values fall into the subsecond time range, being three orders of magnitude shorter than in earlier studied n -type GaAs. The drastic difference is further emphasized by magnetic-field and temperature dependencies of T1 in p -GaAs, showing no similarity to those in n -GaAs. This unexpected behavior finds its explanation in the spatial selectivity of the optical pumping in p -GaAs, that is only efficient in the vicinity of shallow donors, together with the quadrupole relaxation of nuclear spins, which is induced by electric fields within closely spaced donor-acceptor pairs. The developed theoretical model explains the whole set of experimental results.

Multilayer self-organization of InGaAs quantum wires on GaAs surfaces

NASA Astrophysics Data System (ADS)

Wang, Zhiming M.; Kunets, Vasyl P.; Xie, Yanze Z.; Schmidbauer, Martin; Dorogan, Vitaliy G.; Mazur, Yuriy I.; Salamo, Gregory J.

2010-12-01

Molecular-Beam Epitaxy growth of multiple In 0.4Ga 0.6As layers on GaAs (311)A and GaAs (331)A has been investigated by Atomic Force Microscopy and Photoluminescence. On GaAs (311)A, uniformly distributed In 0.4Ga 0.6As quantum wires (QWRs) with wider lateral separation were achieved, presenting a significant improvement in comparison with the result on single layer [H. Wen, Z.M. Wang, G.J. Salamo, Appl. Phys. Lett. 84 (2004) 1756]. On GaAs (331)A, In 0.4Ga 0.6As QWRs were revealed to be much straighter than in the previous report on multilayer growth [Z. Gong, Z. Niu, Z. Fang, Nanotechnology 17 (2006) 1140]. These observations are discussed in terms of the strain-field interaction among multilayers, enhancement of surface mobility at high temperature, and surface stability of GaAs (311)A and (331)A surfaces.

Evaluation of the Cow Rumen Metagenome: Assembly by Single Copy Gene Analysis and Single Cell Genome Assemblies (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Sczyrba, Alex

2018-02-13

DOE JGI's Alex Sczyrba on "Evaluation of the Cow Rumen Metagenome" and "Assembly by Single Copy Gene Analysis and Single Cell Genome Assemblies" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Evaluation of the Cow Rumen Metagenome: Assembly by Single Copy Gene Analysis and Single Cell Genome Assemblies (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sczyrba, Alex

2011-10-13

DOE JGI's Alex Sczyrba on "Evaluation of the Cow Rumen Metagenome" and "Assembly by Single Copy Gene Analysis and Single Cell Genome Assemblies" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

MinION™ nanopore sequencing of environmental metagenomes: a synthetic approach.

PubMed

Brown, Bonnie L; Watson, Mick; Minot, Samuel S; Rivera, Maria C; Franklin, Rima B

2017-03-01

to 98% assignment accuracy at the species level. The observed community proportions for “equal” and “rare” synthetic libraries were close to the known proportions, deviating from 0.1% to 10% across all tests. For a 20-species mock community with staggered contributions, a sequencing run detected all but 3 species (each included at <0.05% of DNA in the total mixture), 91% of reads were assigned to the correct species, 93% of reads were assigned to the correct genus, and >99% of reads were assigned to the correct family. Conclusions: At the current level of output and sequence quality (just under 4 × 103 2D reads for a synthetic metagenome), MinION sequencing followed by Kraken or One Codex analysis has the potential to provide rapid and accurate metagenomic analysis where the consortium is comprised of a limited number of taxa. Important considerations noted in this study included: high sensitivity of the MinION platform to the quality of input DNA, high variability of sequencing results across libraries and flow cells, and relatively small numbers of 2D reads per analysis limit. Together, these limited detection of very rare components of the microbial consortia, and would likely limit the utility of MinION for the sequencing of high-complexity metagenomic communities where thousands of taxa are expected. Furthermore, the limitations of the currently available data analysis tools suggest there is considerable room for improvement in the analytical approaches for the characterization of microbial communities using long reads. Nevertheless, the fact that the accurate taxonomic assignment of high-quality reads generated by MinION is approaching 99.5% and, in most cases, the inferred community structure mirrors the known proportions of a synthetic mixture warrants further exploration of practical application to environmental metagenomics as the platform continues to develop and improve. With further improvement in sequence throughput and error rate reduction

Implementation and Performance of GaAs Digital Signal Processing ASICs

NASA Technical Reports Server (NTRS)

Whitaker, William D.; Buchanan, Jeffrey R.; Burke, Gary R.; Chow, Terrance W.; Graham, J. Scott; Kowalski, James E.; Lam, Barbara; Siavoshi, Fardad; Thompson, Matthew S.; Johnson, Robert A.

1993-01-01

The feasibility of performing high speed digital signal processing in GaAs gate array technology has been demonstrated with the successful implementation of a VLSI communications chip set for NASA's Deep Space Network. This paper describes the techniques developed to solve some of the technology and implementation problems associated with large scale integration of GaAs gate arrays.

Paths to light trapping in thin film GaAs solar cells.

PubMed

Xiao, Jianling; Fang, Hanlin; Su, Rongbin; Li, Kezheng; Song, Jindong; Krauss, Thomas F; Li, Juntao; Martins, Emiliano R

2018-03-19

It is now well established that light trapping is an essential element of thin film solar cell design. Numerous light trapping geometries have already been applied to thin film cells, especially to silicon-based devices. Less attention has been paid to light trapping in GaAs thin film cells, mainly because light trapping is considered less attractive due to the material's direct bandgap and the fact that GaAs suffers from strong surface recombination, which particularly affects etched nanostructures. Here, we study light trapping structures that are implemented in a high-bandgap material on the back of the GaAs active layer, thereby not perturbing the integrity of the GaAs active layer. We study photonic crystal and quasi-random nanostructures both by simulation and by experiment and find that the photonic crystal structures are superior because they exhibit fewer but stronger resonances that are better matched to the narrow wavelength range where GaAs benefits from light trapping. In fact, we show that a 1500 nm thick cell with photonic crystals achieves the same short circuit current as an unpatterned 4000 nm thick cell. These findings are significant because they afford a sizeable reduction in active layer thickness, and therefore a reduction in expensive epitaxial growth time and cost, yet without compromising performance.

Luminescence and Electroluminescence of Nd, Tm and Yb Doped GaAs and some II-Vi Compounds

DTIC Science & Technology

1994-02-28

from the bandgap discontinuity (as was proposed in my publications [1,2]). Also, by using superlattice structure A1GaAs / GaAs: Er / AlGaAs, we could...n ipact ightemiting evic 10 3. The AlGaAs/GaAs: Er/A1GaAs superlattice structure. For the first time we designed the unipolar n’ - superlattice - n...structure as shown in Figure 5. The GaAs: Er/Alo.45Gao.55As superlattice was grown by MBE on an n’ GaAs: Si substrate. It consisted of 60 periods of

Crystal growth of GaAs in space

NASA Technical Reports Server (NTRS)

Gatos, H. C.; Lagowski, J.; Pawlowicz, L. M.; Dabkowski, F.; Li, C. J.

1984-01-01

It is shown that stoichiometry variations in the GaAs melt during growth constitute the most critical parameter regarding defect formations and their interactions; this defect structure determines all relevant characteristics of GaAs. Convection in the melt leads to stoichiometric variations. Growth in axial magnetic fields reduces convection and permits the study of defect structure. In order to control stoichiometry in space and to accommodate expansion during solidification, a partially confined configuration was developed. A triangular prism is employed to contain the growth melt. This configuration permits the presence of the desired vapor phase in contact with the melt for controlling the melt stoichiometry.

EBI metagenomics—a new resource for the analysis and archiving of metagenomic data

PubMed Central

Hunter, Sarah; Corbett, Matthew; Denise, Hubert; Fraser, Matthew; Gonzalez-Beltran, Alejandra; Hunter, Christopher; Jones, Philip; Leinonen, Rasko; McAnulla, Craig; Maguire, Eamonn; Maslen, John; Mitchell, Alex; Nuka, Gift; Oisel, Arnaud; Pesseat, Sebastien; Radhakrishnan, Rajesh; Rocca-Serra, Philippe; Scheremetjew, Maxim; Sterk, Peter; Vaughan, Daniel; Cochrane, Guy; Field, Dawn; Sansone, Susanna-Assunta

2014-01-01

Metagenomics is a relatively recently established but rapidly expanding field that uses high-throughput next-generation sequencing technologies to characterize the microbial communities inhabiting different ecosystems (including oceans, lakes, soil, tundra, plants and body sites). Metagenomics brings with it a number of challenges, including the management, analysis, storage and sharing of data. In response to these challenges, we have developed a new metagenomics resource (http://www.ebi.ac.uk/metagenomics/) that allows users to easily submit raw nucleotide reads for functional and taxonomic analysis by a state-of-the-art pipeline, and have them automatically stored (together with descriptive, standards-compliant metadata) in the European Nucleotide Archive. PMID:24165880

Environmental Viral Metagenomics Analyses in Aquaculture: Applications in Epidemiology and Disease Control

PubMed Central

Munang’andu, Hetron M.

2016-01-01

Studies on the epidemiology of viral diseases in aquaculture have for a long time depended on isolation of viruses from infected aquatic organisms. The role of aquatic environments in the epidemiology of viral diseases in aquaculture has not been extensively expounded mainly because of the lack of appropriate tools for environmental studies on aquatic viruses. However, the upcoming of metagenomics analyses opens great avenues in which environmental samples can be used to study the epidemiology of viral diseases outside their host species. Hence, in this review I have shown that epidemiological factors that influence the composition of viruses in different aquatic environments include ecological factors, anthropogenic activities and stocking densities of cultured organisms based on environmental metagenomics studies carried out this far. Ballast water transportation and global trade of aquatic organisms are the most common virus dispersal process identified this far. In terms of disease control for outdoor aquaculture systems, baseline data on viruses found in different environments intended for aquaculture use can be obtained to enable the design of effective disease control strategies. And as such, high-risk areas having a high specter of pathogenic viruses can be identified as an early warning system. As for the control of viral diseases for indoor recirculation aquaculture systems (RAS), the most effective disinfection methods able to eliminate pathogenic viruses from water used in RAS can be identified. Overall, the synopsis I have put forth in this review shows that environmental samples can be used to study the epidemiology of viral diseases in aquaculture using viral metagenomics analysis as an overture for the design of rational disease control strategies. PMID:28018317

A model for proton-irradiated GaAs solar cells

NASA Technical Reports Server (NTRS)

Wilson, J. W.; Walker, G. H.; Outlaw, R. A.; Stock, L. V.

1982-01-01

A simple model for proton radiation damage in GaAs heteroface solar cells is developed. The model includes the effects of spatial nonuniformity of low energy proton damage. Agreement between the model and experimental proton damage data for GaAs heteroface solar cells is satisfactory. An extension of the model to include angular isotropy, as is appropriate for protons in space, is shown to result in significantly less cell damage than for normal proton incidence.

High efficiency thin-film GaAs solar cells

NASA Technical Reports Server (NTRS)

Stirn, R. J.

1977-01-01

Several oxidation techniques are discussed which have been found to increase the open circuit (V sub oc) of metal-GaAs Schottky barrier solar cells, the oxide chemistry, attempts to measure surface state parameters, the evolving characteristics of the solar cell as background contamination (has been decreased, but not eliminated), results of focused Nd/YAG laser beam recrystallization of Ge films evaporated onto tungsten, and studies of AMOS solar cells fabricated on sliced polycrystalline GaAs wafers. Also discussed are projected materials availability and costs for GaAs thin-film solar cells.

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

PubMed Central

2013-01-01

We describe MetAMOS, an open source and modular metagenomic assembly and analysis pipeline. MetAMOS represents an important step towards fully automated metagenomic analysis, starting with next-generation sequencing reads and producing genomic scaffolds, open-reading frames and taxonomic or functional annotations. MetAMOS can aid in reducing assembly errors, commonly encountered when assembling metagenomic samples, and improves taxonomic assignment accuracy while also reducing computational cost. MetAMOS can be downloaded from: https://github.com/treangen/MetAMOS. PMID:23320958

Under-detection of endospore-forming Firmicutes in metagenomic data

DOE PAGES

Filippidou, Sevasti; Junier, Thomas; Wunderlin, Tina; ...

2015-04-25

Microbial diversity studies based on metagenomic sequencing have greatly enhanced our knowledge of the microbial world. However, one caveat is the fact that not all microorganisms are equally well detected, questioning the universality of this approach. Firmicutes are known to be a dominant bacterial group. Several Firmicutes species are endospore formers and this property makes them hardy in potentially harsh conditions, and thus likely to be present in a wide variety of environments, even as residents and not functional players. While metagenomic libraries can be expected to contain endospore formers, endospores are known to be resilient to many traditional methodsmore » of DNA isolation and thus potentially undetectable. In this study we evaluated the representation of endospore-forming Firmicutes in 73 published metagenomic datasets using two molecular markers unique to this bacterial group ( spo0A and gpr). Both markers were notably absent in well-known habitats of Firmicutes such as soil, with spo0A found only in three mammalian gut microbiomes. A tailored DNA extraction method resulted in the detection of a large diversity of endospore-formers in amplicon sequencing of the 16S rRNA and spo0A genes. However, shotgun classification was still poor with only a minor fraction of the community assigned to Firmicutes. Thus, removing a specific bias in a molecular workflow improves detection in amplicon sequencing, but it was insufficient to overcome the limitations for detecting endospore-forming Firmicutes in whole-genome metagenomics. In conclusion, this study highlights the importance of understanding the specific methodological biases that can contribute to improve the universality of metagenomic approaches.« less

Under-detection of endospore-forming Firmicutes in metagenomic data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Filippidou, Sevasti; Junier, Thomas; Wunderlin, Tina

Microbial diversity studies based on metagenomic sequencing have greatly enhanced our knowledge of the microbial world. However, one caveat is the fact that not all microorganisms are equally well detected, questioning the universality of this approach. Firmicutes are known to be a dominant bacterial group. Several Firmicutes species are endospore formers and this property makes them hardy in potentially harsh conditions, and thus likely to be present in a wide variety of environments, even as residents and not functional players. While metagenomic libraries can be expected to contain endospore formers, endospores are known to be resilient to many traditional methodsmore » of DNA isolation and thus potentially undetectable. In this study we evaluated the representation of endospore-forming Firmicutes in 73 published metagenomic datasets using two molecular markers unique to this bacterial group ( spo0A and gpr). Both markers were notably absent in well-known habitats of Firmicutes such as soil, with spo0A found only in three mammalian gut microbiomes. A tailored DNA extraction method resulted in the detection of a large diversity of endospore-formers in amplicon sequencing of the 16S rRNA and spo0A genes. However, shotgun classification was still poor with only a minor fraction of the community assigned to Firmicutes. Thus, removing a specific bias in a molecular workflow improves detection in amplicon sequencing, but it was insufficient to overcome the limitations for detecting endospore-forming Firmicutes in whole-genome metagenomics. In conclusion, this study highlights the importance of understanding the specific methodological biases that can contribute to improve the universality of metagenomic approaches.« less

Temporal behavior of RHEED intensity oscillations during molecular beam epitaxial growth of GaAs and AlGaAs on (111)B GaAs substrates

NASA Astrophysics Data System (ADS)

Yen, Ming Y.; Haas, T. W.

1990-10-01

We present the temporal behavior of intensity oscillations in reflection high-energy electron diffraction (RHEED) during molecular beam epitaxial (MBE) growth of GaAs and A1GaAs on (1 1 1)B GaAs substrates. The RHEED intensity oscillations were examined as a function of growth parameters in order to provide the insight into the dynamic characteristics and to identify the optimal condition for the two-dimensional layer-by-layer growth. The most intense RHEED oscillation was found to occur within a very narrow temperature range which seems to optimize the surface migration kinetics of the arriving group III elements and the molecular dissodiative reaction of the group V elements. The appearance of an initial transient of the intensity upon commencement of the growth and its implications are described.

Metagenomic gene annotation by a homology-independent approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Froula, Jeff; Zhang, Tao; Salmeen, Annette

2011-06-02

Fully understanding the genetic potential of a microbial community requires functional annotation of all the genes it encodes. The recently developed deep metagenome sequencing approach has enabled rapid identification of millions of genes from a complex microbial community without cultivation. Current homology-based gene annotation fails to detect distantly-related or structural homologs. Furthermore, homology searches with millions of genes are very computational intensive. To overcome these limitations, we developed rhModeller, a homology-independent software pipeline to efficiently annotate genes from metagenomic sequencing projects. Using cellulases and carbonic anhydrases as two independent test cases, we demonstrated that rhModeller is much faster than HMMERmore » but with comparable accuracy, at 94.5percent and 99.9percent accuracy, respectively. More importantly, rhModeller has the ability to detect novel proteins that do not share significant homology to any known protein families. As {approx}50percent of the 2 million genes derived from the cow rumen metagenome failed to be annotated based on sequence homology, we tested whether rhModeller could be used to annotate these genes. Preliminary results suggest that rhModeller is robust in the presence of missense and frameshift mutations, two common errors in metagenomic genes. Applying the pipeline to the cow rumen genes identified 4,990 novel cellulases candidates and 8,196 novel carbonic anhydrase candidates.In summary, we expect rhModeller to dramatically increase the speed and quality of metagnomic gene annotation.« less

Unbiased Taxonomic Annotation of Metagenomic Samples

PubMed Central

Fosso, Bruno; Pesole, Graziano; Rosselló, Francesc

2018-01-01

Abstract The classification of reads from a metagenomic sample using a reference taxonomy is usually based on first mapping the reads to the reference sequences and then classifying each read at a node under the lowest common ancestor of the candidate sequences in the reference taxonomy with the least classification error. However, this taxonomic annotation can be biased by an imbalanced taxonomy and also by the presence of multiple nodes in the taxonomy with the least classification error for a given read. In this article, we show that the Rand index is a better indicator of classification error than the often used area under the receiver operating characteristic (ROC) curve and F-measure for both balanced and imbalanced reference taxonomies, and we also address the second source of bias by reducing the taxonomic annotation problem for a whole metagenomic sample to a set cover problem, for which a logarithmic approximation can be obtained in linear time and an exact solution can be obtained by integer linear programming. Experimental results with a proof-of-concept implementation of the set cover approach to taxonomic annotation in a next release of the TANGO software show that the set cover approach further reduces ambiguity in the taxonomic annotation obtained with TANGO without distorting the relative abundance profile of the metagenomic sample. PMID:29028181

Phylogenetic screening of a bacterial, metagenomic library using homing endonuclease restriction and marker insertion

PubMed Central

Yung, Pui Yi; Burke, Catherine; Lewis, Matt; Egan, Suhelen; Kjelleberg, Staffan; Thomas, Torsten

2009-01-01

Metagenomics provides access to the uncultured majority of the microbial world. The approaches employed in this field have, however, had limited success in linking functional genes to the taxonomic or phylogenetic origin of the organism they belong to. Here we present an efficient strategy to recover environmental DNA fragments that contain phylogenetic marker genes from metagenomic libraries. Our method involves the cleavage of 23S ribsosmal RNA (rRNA) genes within pooled library clones by the homing endonuclease I-CeuI followed by the insertion and selection of an antibiotic resistance cassette. This approach was applied to screen a library of 6500 fosmid clones derived from the microbial community associated with the sponge Cymbastela concentrica. Several fosmid clones were recovered after the screen and detailed phylogenetic and taxonomic assignment based on the rRNA gene showed that they belong to previously unknown organisms. In addition, compositional features of these fosmid clones were used to classify and taxonomically assign a dataset of environmental shotgun sequences. Our approach represents a valuable tool for the analysis of rapidly increasing, environmental DNA sequencing information. PMID:19767618

ELIXIR pilot action: Marine metagenomics - towards a domain specific set of sustainable services.

PubMed

Robertsen, Espen Mikal; Denise, Hubert; Mitchell, Alex; Finn, Robert D; Bongo, Lars Ailo; Willassen, Nils Peder

2017-01-01

Metagenomics, the study of genetic material recovered directly from environmental samples, has the potential to provide insight into the structure and function of heterogeneous microbial communities.  There has been an increased use of metagenomics to discover and understand the diverse biosynthetic capacities of marine microbes, thereby allowing them to be exploited for industrial, food, and health care products. This ELIXIR pilot action was motivated by the need to establish dedicated data resources and harmonized metagenomics pipelines for the marine domain, in order to enhance the exploration and exploitation of marine genetic resources. In this paper, we summarize some of the results from the ELIXIR pilot action "Marine metagenomics - towards user centric services".

DFT algorithms for bit-serial GaAs array processor architectures

NASA Technical Reports Server (NTRS)

Mcmillan, Gary B.

1988-01-01

Systems and Processes Engineering Corporation (SPEC) has developed an innovative array processor architecture for computing Fourier transforms and other commonly used signal processing algorithms. This architecture is designed to extract the highest possible array performance from state-of-the-art GaAs technology. SPEC's architectural design includes a high performance RISC processor implemented in GaAs, along with a Floating Point Coprocessor and a unique Array Communications Coprocessor, also implemented in GaAs technology. Together, these data processors represent the latest in technology, both from an architectural and implementation viewpoint. SPEC has examined numerous algorithms and parallel processing architectures to determine the optimum array processor architecture. SPEC has developed an array processor architecture with integral communications ability to provide maximum node connectivity. The Array Communications Coprocessor embeds communications operations directly in the core of the processor architecture. A Floating Point Coprocessor architecture has been defined that utilizes Bit-Serial arithmetic units, operating at very high frequency, to perform floating point operations. These Bit-Serial devices reduce the device integration level and complexity to a level compatible with state-of-the-art GaAs device technology.

Effects of surface passivation on twin-free GaAs nanosheets.

PubMed

Arab, Shermin; Chi, Chun-Yung; Shi, Teng; Wang, Yuda; Dapkus, Daniel P; Jackson, Howard E; Smith, Leigh M; Cronin, Stephen B

2015-02-24

Unlike nanowires, GaAs nanosheets exhibit no twin defects, stacking faults, or dislocations even when grown on lattice mismatched substrates. As such, they are excellent candidates for optoelectronic applications, including LEDs and solar cells. We report substantial enhancements in the photoluminescence efficiency and the lifetime of passivated GaAs nanosheets produced using the selected area growth (SAG) method with metal organic chemical vapor deposition (MOCVD). Measurements are performed on individual GaAs nanosheets with and without an AlGaAs passivation layer. Both steady-state photoluminescence and time-resolved photoluminescence spectroscopy are performed to study the optoelectronic performance of these nanostructures. Our results show that AlGaAs passivation of GaAs nanosheets leads to a 30- to 40-fold enhancement in the photoluminescence intensity. The photoluminescence lifetime increases from less than 30 to 300 ps with passivation, indicating an order of magnitude improvement in the minority carrier lifetime. We attribute these enhancements to the reduction of nonradiative recombination due to the compensation of surface states after passivation. The surface recombination velocity decreases from an initial value of 2.5 × 10(5) to 2.7 × 10(4) cm/s with passivation.

High-efficiency, radiation-resistant GaAs space cells

NASA Technical Reports Server (NTRS)

Bertness, K. A.; Ristow, M. Ladle; Grounner, M.; Kuryla, M. S.; Werthen, J. G.

1991-01-01

Although many GaAs solar cells are intended for space applicatons, few measurements of cell degradation after radiation are available, particularly for cells with efficiencies exceeding 20 percent (one-sun, AMO). Often the cell performance is optimized for the highest beginning-of-life (BOL) efficiency, despite the unknown effect of such design on end-of-life (EOL) efficiencies. The results of a study of the radiation effects on p-n GaAs cells are presented. The EOL efficiency of GaAs space cell can be increased by adjusting materials growth parameters, resulting in a demonstration of 16 percent EOL efficiency at one-sun, AMO. Reducing base doping levels to below 3 x 10(exp 17)/cu m and decreasing emitter thickness to 0.3 to 0.5 micron for p-n cells led to significant improvements in radiation hardness as measured by EOL/BOL efficiency ratios for irradiation of 10(exp -15)/sq cm electrons at 1 MeV. BOL efficiency was not affected by changes in emitter thickness but did improve with lower base doping.

A potential source for cellulolytic enzyme discovery and environmental aspects revealed through metagenomics of Brazilian mangroves

PubMed Central

2013-01-01

The mangroves are among the most productive and biologically important environments. The possible presence of cellulolytic enzymes and microorganisms useful for biomass degradation as well as taxonomic and functional aspects of two Brazilian mangroves were evaluated using cultivation and metagenomic approaches. From a total of 296 microorganisms with visual differences in colony morphology and growth (including bacteria, yeast and filamentous fungus), 179 (60.5%) and 117 (39.5%) were isolated from the Rio de Janeiro (RJ) and Bahia (BA) samples, respectively. RJ metagenome showed the higher number of microbial isolates, which is consistent with its most conserved state and higher diversity. The metagenomic sequencing data showed similar predominant bacterial phyla in the BA and RJ mangroves with an abundance of Proteobacteria (57.8% and 44.6%), Firmicutes (11% and 12.3%) and Actinobacteria (8.4% and 7.5%). A higher number of enzymes involved in the degradation of polycyclic aromatic compounds were found in the BA mangrove. Specific sequences involved in the cellulolytic degradation, belonging to cellulases, hemicellulases, carbohydrate binding domains, dockerins and cohesins were identified, and it was possible to isolate cultivable fungi and bacteria related to biomass decomposition and with potential applications for the production of biofuels. These results showed that the mangroves possess all fundamental molecular tools required for building the cellulosome, which is required for the efficient degradation of cellulose material and sugar release. PMID:24160319

Influence of GaAs substrate properties on the congruent evaporation temperature

NASA Astrophysics Data System (ADS)

Spirina, A. A.; Nastovjak, A. G.; Shwartz, N. L.

2018-03-01

High-temperature annealing of GaAs(111)A and GaAs(111)B substrates under Langmuir evaporation conditions was studied using Monte Carlo simulation. The maximal value of the congruent evaporation temperature was estimated. The congruent evaporation temperature was demonstrated to be dependent on the surface orientation and concentration of surface defects.

Metagenomic Analyses Reveal That Energy Transfer Gene Abundances Can Predict the Syntrophic Potential of Environmental Microbial Communities.

PubMed

Oberding, Lisa; Gieg, Lisa M

2016-01-05

Hydrocarbon compounds can be biodegraded by anaerobic microorganisms to form methane through an energetically interdependent metabolic process known as syntrophy. The microorganisms that perform this process as well as the energy transfer mechanisms involved are difficult to study and thus are still poorly understood, especially on an environmental scale. Here, metagenomic data was analyzed for specific clusters of orthologous groups (COGs) related to key energy transfer genes thus far identified in syntrophic bacteria, and principal component analysis was used in order to determine whether potentially syntrophic environments could be distinguished using these syntroph related COGs as opposed to universally present COGs. We found that COGs related to hydrogenase and formate dehydrogenase genes were able to distinguish known syntrophic consortia and environments with the potential for syntrophy from non-syntrophic environments, indicating that these COGs could be used as a tool to identify syntrophic hydrocarbon biodegrading environments using metagenomic data.

Metagenomic Analyses Reveal That Energy Transfer Gene Abundances Can Predict the Syntrophic Potential of Environmental Microbial Communities

PubMed Central

Oberding, Lisa; Gieg, Lisa M.

2016-01-01

Hydrocarbon compounds can be biodegraded by anaerobic microorganisms to form methane through an energetically interdependent metabolic process known as syntrophy. The microorganisms that perform this process as well as the energy transfer mechanisms involved are difficult to study and thus are still poorly understood, especially on an environmental scale. Here, metagenomic data was analyzed for specific clusters of orthologous groups (COGs) related to key energy transfer genes thus far identified in syntrophic bacteria, and principal component analysis was used in order to determine whether potentially syntrophic environments could be distinguished using these syntroph related COGs as opposed to universally present COGs. We found that COGs related to hydrogenase and formate dehydrogenase genes were able to distinguish known syntrophic consortia and environments with the potential for syntrophy from non-syntrophic environments, indicating that these COGs could be used as a tool to identify syntrophic hydrocarbon biodegrading environments using metagenomic data. PMID:27681901

Taxonomic and functional assignment of cloned sequences from high Andean forest soil metagenome.

PubMed

Montaña, José Salvador; Jiménez, Diego Javier; Hernández, Mónica; Angel, Tatiana; Baena, Sandra

2012-02-01

Total metagenomic DNA was isolated from high Andean forest soil and subjected to taxonomical and functional composition analyses by means of clone library generation and sequencing. The obtained yield of 1.7 μg of DNA/g of soil was used to construct a metagenomic library of approximately 20,000 clones (in the plasmid p-Bluescript II SK+) with an average insert size of 4 Kb, covering 80 Mb of the total metagenomic DNA. Metagenomic sequences near the plasmid cloning site were sequenced and them trimmed and assembled, obtaining 299 reads and 31 contigs (0.3 Mb). Taxonomic assignment of total sequences was performed by BLASTX, resulting in 68.8, 44.8 and 24.5% classification into taxonomic groups using the metagenomic RAST server v2.0, WebCARMA v1.0 online system and MetaGenome Analyzer v3.8 software, respectively. Most clone sequences were classified as Bacteria belonging to phlya Actinobacteria, Proteobacteria and Acidobacteria. Among the most represented orders were Actinomycetales (34% average), Rhizobiales, Burkholderiales and Myxococcales and with a greater number of sequences in the genus Mycobacterium (7% average), Frankia, Streptomyces and Bradyrhizobium. The vast majority of sequences were associated with the metabolism of carbohydrates, proteins, lipids and catalytic functions, such as phosphatases, glycosyltransferases, dehydrogenases, methyltransferases, dehydratases and epoxide hydrolases. In this study we compared different methods of taxonomic and functional assignment of metagenomic clone sequences to evaluate microbial diversity in an unexplored soil ecosystem, searching for putative enzymes of biotechnological interest and generating important information for further functional screening of clone libraries.

Formation of embedded plasmonic Ga nanoparticle arrays and their influence on GaAs photoluminescence

NASA Astrophysics Data System (ADS)

Kang, M.; Jeon, S.; Jen, T.; Lee, J.-E.; Sih, V.; Goldman, R. S.

2017-07-01

We introduce a novel approach to the seamless integration of plasmonic nanoparticle (NP) arrays into semiconductor layers and demonstrate their enhanced photoluminescence (PL) efficiency. Our approach utilizes focused ion beam-induced self-assembly of close-packed arrays of Ga NPs with tailorable NP diameters, followed by overgrowth of GaAs layers using molecular beam epitaxy. Using a combination of PL spectroscopy and electromagnetic computations, we identify a regime of Ga NP diameter and overgrown GaAs layer thickness where NP-array-enhanced absorption in GaAs leads to enhanced GaAs near-band-edge (NBE) PL efficiency, surpassing that of high-quality epitaxial GaAs layers. As the NP array depth and size are increased, the reduction in spontaneous emission rate overwhelms the NP-array-enhanced absorption, leading to a reduced NBE PL efficiency. This approach provides an opportunity to enhance the PL efficiency of a wide variety of semiconductor heterostructures.

Self-assembled InAs quantum dot formation on GaAs ring-like nanostructure templates

PubMed Central

Strom, NW; Wang, Zh M; AbuWaar, ZY; Mazur, Yu I; Salamo, GJ

2007-01-01

The evolution of InAs quantum dot (QD) formation is studied on GaAs ring-like nanostructures fabricated by droplet homo-epitaxy. This growth mode, exclusively performed by a hybrid approach of droplet homo-epitaxy and Stransky-Krastanor (S-K) based QD self-assembly, enables one to form new QD morphologies that may find use in optoelectronic applications. Increased deposition of InAs on the GaAs ring first produced a QD in the hole followed by QDs around the GaAs ring and on the GaAs (100) surface. This behavior indicates that the QDs prefer to nucleate at locations of high monolayer (ML) step density.

GaAs quantum dots in a GaP nanowire photodetector

NASA Astrophysics Data System (ADS)

Kuyanov, P.; McNamee, S. A.; LaPierre, R. R.

2018-03-01

We report the structural, optical and electrical properties of GaAs quantum dots (QDs) embedded along GaP nanowires. The GaP nanowires contained p-i-n junctions with 15 consecutively grown GaAs QDs within the intrinsic region. The nanowires were grown by molecular beam epitaxy using the self-assisted vapor-liquid-solid process. The crystal structure of the NWs alternated between twinned ZB and WZ as the composition along the NW alternated between the GaP barriers and the GaAs QDs, respectively, leading to a polytypic structure with a periodic modulation of the NW sidewall facets. Photodetector devices containing QDs showed absorption beyond the bandgap of GaP in comparison to nanowires without QDs. Voltage-dependent measurements suggested a field emission process of carriers from the QDs.

GaAs optoelectronic neuron arrays

NASA Technical Reports Server (NTRS)

Lin, Steven; Grot, Annette; Luo, Jiafu; Psaltis, Demetri

1993-01-01

A simple optoelectronic circuit integrated monolithically in GaAs to implement sigmoidal neuron responses is presented. The circuit integrates a light-emitting diode with one or two transistors and one or two photodetectors. The design considerations for building arrays with densities of up to 10,000/sq cm are discussed.

Recovering complete and draft population genomes from metagenome datasets

DOE PAGES

Sangwan, Naseer; Xia, Fangfang; Gilbert, Jack A.

2016-03-08

Assembly of metagenomic sequence data into microbial genomes is of fundamental value to improving our understanding of microbial ecology and metabolism by elucidating the functional potential of hard-to-culture microorganisms. Here, we provide a synthesis of available methods to bin metagenomic contigs into species-level groups and highlight how genetic diversity, sequencing depth, and coverage influence binning success. Despite the computational cost on application to deeply sequenced complex metagenomes (e.g., soil), covarying patterns of contig coverage across multiple datasets significantly improves the binning process. We also discuss and compare current genome validation methods and reveal how these methods tackle the problem ofmore » chimeric genome bins i.e., sequences from multiple species. Finally, we explore how population genome assembly can be used to uncover biogeographic trends and to characterize the effect of in situ functional constraints on the genome-wide evolution.« less

Recovering complete and draft population genomes from metagenome datasets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sangwan, Naseer; Xia, Fangfang; Gilbert, Jack A.

Assembly of metagenomic sequence data into microbial genomes is of fundamental value to improving our understanding of microbial ecology and metabolism by elucidating the functional potential of hard-to-culture microorganisms. Here, we provide a synthesis of available methods to bin metagenomic contigs into species-level groups and highlight how genetic diversity, sequencing depth, and coverage influence binning success. Despite the computational cost on application to deeply sequenced complex metagenomes (e.g., soil), covarying patterns of contig coverage across multiple datasets significantly improves the binning process. We also discuss and compare current genome validation methods and reveal how these methods tackle the problem ofmore » chimeric genome bins i.e., sequences from multiple species. Finally, we explore how population genome assembly can be used to uncover biogeographic trends and to characterize the effect of in situ functional constraints on the genome-wide evolution.« less

Investigation of high efficiency GaAs solar cells

NASA Technical Reports Server (NTRS)

Olsen, Larry C.; Dunham, Glen; Addis, F. W.; Huber, Dan; Linden, Kurt

1989-01-01

Investigations of basic mechanisms which limit the performance of high efficiency GaAs solar cells are discussed. P/N heteroface structures have been fabricated from MOCVD epiwafers. Typical AM1 efficiencies are in the 21 to 22 percent range, with a SERI measurement for one cell being 21.5 percent. The cells are nominally 1.5 x 1.5 cm in size. Studies have involved photoresponse, T-I-V analyses, and interpretation of data in terms of appropriate models to determine key cell parameters. Results of these studies are utilized to determine future approaches for increasing GaAs solar cell efficiencies.

Metagenomic Functional Potential Predicts Degradation Rates of a Model Organophosphorus Xenobiotic in Pesticide Contaminated Soils

PubMed Central

Jeffries, Thomas C.; Rayu, Smriti; Nielsen, Uffe N.; Lai, Kaitao; Ijaz, Ali; Nazaries, Loic; Singh, Brajesh K.

2018-01-01

Chemical contamination of natural and agricultural habitats is an increasing global problem and a major threat to sustainability and human health. Organophosphorus (OP) compounds are one major class of contaminant and can undergo microbial degradation, however, no studies have applied system-wide ecogenomic tools to investigate OP degradation or use metagenomics to understand the underlying mechanisms of biodegradation in situ and predict degradation potential. Thus, there is a lack of knowledge regarding the functional genes and genomic potential underpinning degradation and community responses to contamination. Here we address this knowledge gap by performing shotgun sequencing of community DNA from agricultural soils with a history of pesticide usage and profiling shifts in functional genes and microbial taxa abundance. Our results showed two distinct groups of soils defined by differing functional and taxonomic profiles. Degradation assays suggested that these groups corresponded to the organophosphorus degradation potential of soils, with the fastest degrading community being defined by increases in transport and nutrient cycling pathways and enzymes potentially involved in phosphorus metabolism. This was against a backdrop of taxonomic community shifts potentially related to contamination adaptation and reflecting the legacy of exposure. Overall our results highlight the value of using holistic system-wide metagenomic approaches as a tool to predict microbial degradation in the context of the ecology of contaminated habitats. PMID:29515526

Bacterial diversity of the American sand fly Lutzomyia intermedia using high-throughput metagenomic sequencing.

PubMed

Monteiro, Carolina Cunha; Villegas, Luis Eduardo Martinez; Campolina, Thais Bonifácio; Pires, Ana Clara Machado Araújo; Miranda, Jose Carlos; Pimenta, Paulo Filemon Paolucci; Secundino, Nagila Francinete Costa

2016-08-31

Parasites of the genus Leishmania cause a broad spectrum of diseases, collectively known as leishmaniasis, in humans worldwide. American cutaneous leishmaniasis is a neglected disease transmitted by sand fly vectors including Lutzomyia intermedia, a proven vector. The female sand fly can acquire or deliver Leishmania spp. parasites while feeding on a blood meal, which is required for nutrition, egg development and survival. The microbiota composition and abundance varies by food source, life stages and physiological conditions. The sand fly microbiota can affect parasite life-cycle in the vector. We performed a metagenomic analysis for microbiota composition and abundance in Lu. intermedia, from an endemic area in Brazil. The adult insects were collected using CDC light traps, morphologically identified, carefully sterilized, dissected under a microscope and the females separated into groups according to their physiological condition: (i) absence of blood meal (unfed = UN); (ii) presence of blood meal (blood-fed = BF); and (iii) presence of developed ovaries (gravid = GR). Then, they were processed for metagenomics with Illumina Hiseq Sequencing in order to be sequence analyzed and to obtain the taxonomic profiles of the microbiota. Bacterial metagenomic analysis revealed differences in microbiota composition based upon the distinct physiological stages of the adult insect. Sequence identification revealed two phyla (Proteobacteria and Actinobacteria), 11 families and 15 genera; 87 % of the bacteria were Gram-negative, while only one family and two genera were identified as Gram-positive. The genera Ochrobactrum, Bradyrhizobium and Pseudomonas were found across all of the groups. The metagenomic analysis revealed that the microbiota of the Lu. intermedia female sand flies are distinct under specific physiological conditions and consist of 15 bacterial genera. The Ochrobactrum, Bradyrhizobium and Pseudomonas were the common genera. Our results detailing

Captured metagenomics: large-scale targeting of genes based on ‘sequence capture’ reveals functional diversity in soils

PubMed Central

Manoharan, Lokeshwaran; Kushwaha, Sandeep K.; Hedlund, Katarina; Ahrén, Dag

2015-01-01

Microbial enzyme diversity is a key to understand many ecosystem processes. Whole metagenome sequencing (WMG) obtains information on functional genes, but it is costly and inefficient due to large amount of sequencing that is required. In this study, we have applied a captured metagenomics technique for functional genes in soil microorganisms, as an alternative to WMG. Large-scale targeting of functional genes, coding for enzymes related to organic matter degradation, was applied to two agricultural soil communities through captured metagenomics. Captured metagenomics uses custom-designed, hybridization-based oligonucleotide probes that enrich functional genes of interest in metagenomic libraries where only probe-bound DNA fragments are sequenced. The captured metagenomes were highly enriched with targeted genes while maintaining their target diversity and their taxonomic distribution correlated well with the traditional ribosomal sequencing. The captured metagenomes were highly enriched with genes related to organic matter degradation; at least five times more than similar, publicly available soil WMG projects. This target enrichment technique also preserves the functional representation of the soils, thereby facilitating comparative metagenomics projects. Here, we present the first study that applies the captured metagenomics approach in large scale, and this novel method allows deep investigations of central ecosystem processes by studying functional gene abundances. PMID:26490729

A Delphi Technology Foresight Study: Mapping Social Construction of Scientific Evidence on Metagenomics Tests for Water Safety

PubMed Central

Birko, Stanislav; Dove, Edward S.; Özdemir, Vural

2015-01-01

Access to clean water is a grand challenge in the 21st century. Water safety testing for pathogens currently depends on surrogate measures such as fecal indicator bacteria (e.g., E. coli). Metagenomics concerns high-throughput, culture-independent, unbiased shotgun sequencing of DNA from environmental samples that might transform water safety by detecting waterborne pathogens directly instead of their surrogates. Yet emerging innovations such as metagenomics are often fiercely contested. Innovations are subject to shaping/construction not only by technology but also social systems/values in which they are embedded, such as experts’ attitudes towards new scientific evidence. We conducted a classic three-round Delphi survey, comprised of 107 questions. A multidisciplinary expert panel (n = 24) representing the continuum of discovery scientists and policymakers evaluated the emergence of metagenomics tests. To the best of our knowledge, we report here the first Delphi foresight study of experts’ attitudes on (1) the top 10 priority evidentiary criteria for adoption of metagenomics tests for water safety, (2) the specific issues critical to governance of metagenomics innovation trajectory where there is consensus or dissensus among experts, (3) the anticipated time lapse from discovery to practice of metagenomics tests, and (4) the role and timing of public engagement in development of metagenomics tests. The ability of a test to distinguish between harmful and benign waterborne organisms, analytical/clinical sensitivity, and reproducibility were the top three evidentiary criteria for adoption of metagenomics. Experts agree that metagenomic testing will provide novel information but there is dissensus on whether metagenomics will replace the current water safety testing methods or impact the public health end points (e.g., reduction in boil water advisories). Interestingly, experts view the publics relevant in a “downstream capacity” for adoption of

MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit

PubMed Central

Li, Junhua; Chen, Weineng; Chen, Hua; Mende, Daniel R.; Arumugam, Manimozhiyan; Pan, Qi; Liu, Binghang; Qin, Junjie; Wang, Jun; Bork, Peer

2012-01-01

MOCAT is a highly configurable, modular pipeline for fast, standardized processing of single or paired-end sequencing data generated by the Illumina platform. The pipeline uses state-of-the-art programs to quality control, map, and assemble reads from metagenomic samples sequenced at a depth of several billion base pairs, and predict protein-coding genes on assembled metagenomes. Mapping against reference databases allows for read extraction or removal, as well as abundance calculations. Relevant statistics for each processing step can be summarized into multi-sheet Excel documents and queryable SQL databases. MOCAT runs on UNIX machines and integrates seamlessly with the SGE and PBS queuing systems, commonly used to process large datasets. The open source code and modular architecture allow users to modify or exchange the programs that are utilized in the various processing steps. Individual processing steps and parameters were benchmarked and tested on artificial, real, and simulated metagenomes resulting in an improvement of selected quality metrics. MOCAT can be freely downloaded at http://www.bork.embl.de/mocat/. PMID:23082188

MOCAT: a metagenomics assembly and gene prediction toolkit.

PubMed

Kultima, Jens Roat; Sunagawa, Shinichi; Li, Junhua; Chen, Weineng; Chen, Hua; Mende, Daniel R; Arumugam, Manimozhiyan; Pan, Qi; Liu, Binghang; Qin, Junjie; Wang, Jun; Bork, Peer

2012-01-01

MOCAT is a highly configurable, modular pipeline for fast, standardized processing of single or paired-end sequencing data generated by the Illumina platform. The pipeline uses state-of-the-art programs to quality control, map, and assemble reads from metagenomic samples sequenced at a depth of several billion base pairs, and predict protein-coding genes on assembled metagenomes. Mapping against reference databases allows for read extraction or removal, as well as abundance calculations. Relevant statistics for each processing step can be summarized into multi-sheet Excel documents and queryable SQL databases. MOCAT runs on UNIX machines and integrates seamlessly with the SGE and PBS queuing systems, commonly used to process large datasets. The open source code and modular architecture allow users to modify or exchange the programs that are utilized in the various processing steps. Individual processing steps and parameters were benchmarked and tested on artificial, real, and simulated metagenomes resulting in an improvement of selected quality metrics. MOCAT can be freely downloaded at http://www.bork.embl.de/mocat/.

Metagenomics analysis of microbial communities associated with a traditional rice wine starter culture (Xaj-pitha) of Assam, India.

PubMed

Bora, Sudipta Sankar; Keot, Jyotshna; Das, Saurav; Sarma, Kishore; Barooah, Madhumita

2016-12-01

This is the first report on the microbial diversity of xaj-pitha, a rice wine fermentation starter culture through a metagenomics approach involving Illumine-based whole genome shotgun (WGS) sequencing method. Metagenomic DNA was extracted from rice wine starter culture concocted by Ahom community of Assam and analyzed using a MiSeq ® System. A total of 2,78,231 contigs, with an average read length of 640.13 bp, were obtained. Data obtained from the use of several taxonomic profiling tools were compared with previously reported microbial diversity studies through the culture-dependent and culture-independent method. The microbial community revealed the existence of amylase producers, such as Rhizopus delemar, Mucor circinelloides, and Aspergillus sp. Ethanol producers viz., Meyerozyma guilliermondii, Wickerhamomyces ciferrii, Saccharomyces cerevisiae, Candida glabrata, Debaryomyces hansenii, Ogataea parapolymorpha, and Dekkera bruxellensis, were found associated with the starter culture along with a diverse range of opportunistic contaminants. The bacterial microflora was dominated by lactic acid bacteria (LAB). The most frequent occurring LAB was Lactobacillus plantarum, Lactobacillus brevis, Leuconostoc lactis, Weissella cibaria, Lactococcus lactis, Weissella para mesenteroides, Leuconostoc pseudomesenteroides, etc. Our study provided a comprehensive picture of microbial diversity associated with rice wine fermentation starter and indicated the superiority of metagenomic sequencing over previously used techniques.

Response of GaAs charge storage devices to transient ionizing radiation

NASA Astrophysics Data System (ADS)

Hetherington, D. L.; Klem, J. F.; Hughes, R. C.; Weaver, H. T.

Charge storage devices in which non-equilibrium depletion regions represent stored charge are sensitive to ionizing radiation. This results since the radiation generates electron-hole pairs that neutralize excess ionized dopant charge. Silicon structures, such as dynamic RAM or CCD cells are particularly sensitive to radiation since carrier diffusion lengths in this material are often much longer than the depletion width, allowing collection of significant quantities of charge from quasi-neutral sections of the device. For GaAs the situation is somewhat different in that minority carrier diffusion lengths are shorter than in silicon, and although mobilities are higher, we expect a reduction of radiation sensitivity as suggested by observations of reduced quantum efficiency in GaAs solar cells. Dynamic memory cells in GaAs have potential increased retention times. In this paper, we report the response of a novel GaAs dynamic memory element to transient ionizing radiation. The charge readout technique is nondestructive over a reasonable applied voltage range and is more sensitive to stored charge than a simple capacitor.

Enhancement of conductance of GaAs sub-microwires under external stimuli

NASA Astrophysics Data System (ADS)

Qu, Xianlin; Deng, Qingsong; Zheng, Kun

2018-03-01

Semiconductors with one dimension on the micro-nanometer scale have many unique physical properties that are remarkably different from those of their bulk counterparts. Moreover, changes in the external field will further modulate the properties of the semiconductor micro-nanomaterials. In this study, we used focused ion beam technology to prepare freestanding ⟨111⟩-oriented GaAs sub-microwires from a GaAs substrate. The effects of laser irradiation and bending or buckling deformation induced by compression on the electrical transport properties of an individual GaAs sub-microwire were studied. The experimental results indicate that both laser irradiation and bending deformation can enhance their electrical transport properties, the laser irradiation resulted in a conductance enhancement of ˜30% compared to the result with no irradiation, and in addition, bending deformation changed the conductance by as much as ˜180% when the average strain was approximately 1%. The corresponding mechanisms are also discussed. This study provides beneficial insight into the fabrication of electronic and optoelectronic devices based on GaAs micro/nano-wires.

The rumen microbial metagenome associated with high methane production in cattle.

PubMed

Wallace, R John; Rooke, John A; McKain, Nest; Duthie, Carol-Anne; Hyslop, Jimmy J; Ross, David W; Waterhouse, Anthony; Watson, Mick; Roehe, Rainer

2015-10-23

Methane represents 16 % of total anthropogenic greenhouse gas emissions. It has been estimated that ruminant livestock produce ca. 29 % of this methane. As individual animals produce consistently different quantities of methane, understanding the basis for these differences may lead to new opportunities for mitigating ruminal methane emissions. Metagenomics is a powerful new tool for understanding the composition and function of complex microbial communities. Here we have applied metagenomics to the rumen microbial community to identify differences in the microbiota and metagenome that lead to high- and low-methane-emitting cattle phenotypes. Four pairs of beef cattle were selected for extreme high and low methane emissions from 72 animals, matched for breed (Aberdeen-Angus or Limousin cross) and diet (high or medium concentrate). Community analysis was carried out by qPCR of 16S and 18S rRNA genes and by alignment of Illumina HiSeq reads to the GREENGENES database. Total genomic reads were aligned to the KEGG genes databasefor functional analysis. Deep sequencing produced on average 11.3 Gb per sample. 16S rRNA gene abundances indicated that archaea, predominantly Methanobrevibacter, were 2.5× more numerous (P = 0.026) in high emitters, whereas among bacteria Proteobacteria, predominantly Succinivibrionaceae, were 4-fold less abundant (2.7 vs. 11.2 %; P = 0.002). KEGG analysis revealed that archaeal genes leading directly or indirectly to methane production were 2.7-fold more abundant in high emitters. Genes less abundant in high emitters included acetate kinase, electron transport complex proteins RnfC and RnfD and glucose-6-phosphate isomerase. Sequence data were assembled de novo and over 1.5 million proteins were annotated on the subsequent metagenome scaffolds. Less than half of the predicted genes matched matched a domain within Pfam. Amongst 2774 identified proteins of the 20 KEGG orthologues that correlated with methane emissions, only 16 showed

Crystal growth of device quality GaAs in space

NASA Technical Reports Server (NTRS)

Gatos, H. C.; Lagowski, J.

1985-01-01

The present program has been aimed at solving the fundamental and technological problems associated with Crystal Growth of Device Quality in Space. The initial stage of the program was devoted strictly to ground-based research. The unsolved problems associated with the growth of bulk GaAs in the presence of gravitational forces were explored. Reliable chemical, structural and electronic characterization methods were developed which would permit the direct relation of the salient materials parameters (particularly those affected by zero gravity conditions) to the electronic characteristics of single crystal GaAs, in turn to device performance. These relationships are essential for the development of optimum approaches and techniques. It was concluded that the findings on elemental semiconductors Ge and Si regarding crystal growth, segregation, chemical composition, defect interactions, and materials properties-electronic properties relationships are not necessarily applicable to GaAs (and to other semiconductor compounds). In many instances totally unexpected relationships were found to prevail.

Blueish green photoluminescence from nitrided GaAs(100) surfaces

NASA Astrophysics Data System (ADS)

Shimaoka, Goro; Udagawa, Takashi

1999-04-01

Optical and structural studies were made on the Si-doped (100)GaAs surfaces nitrided at a temperature between 650° and 750°C for 15 min in the flowing NH 3 gas. The wavelength of photoluminescence (PL) spectra were observed to be shortened from 820 nm of the GaAs nitrided at 650°C with increasing nitridation temperature. Blueish green PL with wavelengths of approx. 490 nm and 470 nm were emitted from the nitrided surfaces at 700° and 750°C, respectively. Results of AES and SIMS indicated that the surfaces are nitrided as GaAs 1- xN x, (0< x≤1) alloy layer, and the nitrided region also tended to increase as the temperature raised. High-resolution transmission electron microscopic (HRTEM), transmission electron diffraction (TED) and energy dispersive X-ray (EDX) results showed that films peeled off from the nitrided surfaces consisted mainly of hexagonal, wurtzite-type gallium nitride (GaN) with stacking faults and microtwins.

GaAs High Breakdown Voltage Front and Back Side Processed Schottky Detectors for X-Ray Detection

DTIC Science & Technology

2007-11-01

front and back side processed, unintentionally doped bulk gallium -arsenic (GaAs) Schottky detectors and determined that GaAs detectors with a large...a few materials that fulfill these requirements are gallium -arsenic (GaAs) and cadmium-zinc-tellurium (CdZnTe or CZT). They are viable alternative...Whitehill, C.; Pospíšil, S.; Wilhem, I.; Doležal, Z.; Juergensen, H.; Heuken, M. Development of low-pressure vapour -phase epitaxial GaAs for medical imaging

The effects of variable sample biomass on comparative metagenomics.

PubMed

Chafee, Meghan; Maignien, Loïs; Simmons, Sheri L

2015-07-01

Longitudinal studies that integrate samples with variable biomass are essential to understand microbial community dynamics across space or time. Shotgun metagenomics is widely used to investigate these communities at the functional level, but little is known about the effects of combining low and high biomass samples on downstream analysis. We investigated the interacting effects of DNA input and library amplification by polymerase chain reaction on comparative metagenomic analysis using dilutions of a single complex template from an Arabidopsis thaliana-associated microbial community. We modified the Illumina Nextera kit to generate high-quality large-insert (680 bp) paired-end libraries using a range of 50 pg to 50 ng of input DNA. Using assembly-based metagenomic analysis, we demonstrate that DNA input level has a significant impact on community structure due to overrepresentation of low-GC genomic regions following library amplification. In our system, these differences were largely superseded by variations between biological replicates, but our results advocate verifying the influence of library amplification on a case-by-case basis. Overall, this study provides recommendations for quality filtering and de-replication prior to analysis, as well as a practical framework to address the issue of low biomass or biomass heterogeneity in longitudinal metagenomic surveys. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Room temperature lasing of GaAs quantum wire vertical-cavity surface-emitting lasers grown on (7 7 5) B GaAs substrates by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Higuchi, Y.; Osaki, S.; Kitada, T.; Shimomura, S.; Takasuka, Y.; Ogura, M.; Hiyamizu, S.

2006-06-01

Self-organized GaAs/(GaAs) 4(AlAs) 2 quantum wires (QWRs) grown on (7 7 5) B-oriented GaAs substrates by molecular beam epitaxy have been applied to an active region of vertical-cavity surface-emitting lasers (VCSELs). The (7 7 5) B GaAs QWR-VCSEL with an aperture diameter of 3 μm lased at a wavelength of 765 nm with a threshold current of 0.38 mA at room temperature. This is the first demonstration of laser operation of the QWR-VCSEL by current injection. The light output was linearly polarized in the direction parallel to the QWRs due to the optical anisotropy of the self-organized (7 7 5) B GaAs QWRs.

Growth and characterization of molecular beam epitaxial GaAs layers on porous silicon

NASA Technical Reports Server (NTRS)

Lin, T. L.; Liu, J. K.; Sadwick, L.; Wang, K. L.; Kao, Y. C.

1987-01-01

GaAs layers have been grown on porous silicon (PS) substrates with good crystallinity by molecular beam epitaxy. In spite of the surface irregularity of PS substrates, no surface morphology deterioration was observed on epitaxial GaAs overlayers. A 10-percent Rutherford backscattering spectroscopy minimum channeling yield for GaAs-on-PS layers as compared to 16 percent for GaAs-on-Si layers grown under the same condition indicates a possible improvement of crystallinity when GaAs is grown on PS. Transmission electron microscopy reveals that the dominant defects in the GaAs-on-PS layers are microtwins and stacking faults, which originate from the GaAs/PS interface. GaAs is found to penetrate into the PS layers. n-type GaAs/p-type PS heterojunction diodes were fabricated with good rectifying characteristics.

Deconvoluting simulated metagenomes: the performance of hard- and soft- clustering algorithms applied to metagenomic chromosome conformation capture (3C)

PubMed Central

DeMaere, Matthew Z.

2016-01-01

Background Chromosome conformation capture, coupled with high throughput DNA sequencing in protocols like Hi-C and 3C-seq, has been proposed as a viable means of generating data to resolve the genomes of microorganisms living in naturally occuring environments. Metagenomic Hi-C and 3C-seq datasets have begun to emerge, but the feasibility of resolving genomes when closely related organisms (strain-level diversity) are present in the sample has not yet been systematically characterised. Methods We developed a computational simulation pipeline for metagenomic 3C and Hi-C sequencing to evaluate the accuracy of genomic reconstructions at, above, and below an operationally defined species boundary. We simulated datasets and measured accuracy over a wide range of parameters. Five clustering algorithms were evaluated (2 hard, 3 soft) using an adaptation of the extended B-cubed validation measure. Results When all genomes in a sample are below 95% sequence identity, all of the tested clustering algorithms performed well. When sequence data contains genomes above 95% identity (our operational definition of strain-level diversity), a naive soft-clustering extension of the Louvain method achieves the highest performance. Discussion Previously, only hard-clustering algorithms have been applied to metagenomic 3C and Hi-C data, yet none of these perform well when strain-level diversity exists in a metagenomic sample. Our simple extension of the Louvain method performed the best in these scenarios, however, accuracy remained well below the levels observed for samples without strain-level diversity. Strain resolution is also highly dependent on the amount of available 3C sequence data, suggesting that depth of sequencing must be carefully considered during experimental design. Finally, there appears to be great scope to improve the accuracy of strain resolution through further algorithm development. PMID:27843713

ZnSe Window Layers for GaAs and GaInP2 Solar Cells

NASA Technical Reports Server (NTRS)

Olsen, Larry C.

1997-01-01

This report concerns studies of the use of n-type ZnSe as a window layer for n/p GaAs and GaInP2 solar cells. Emphasis was placed in this phase of the project on characterizing the interface between n-type ZnSe films grown on epi-GaAs films grown onto single crystal GaAs. Epi-GaAs and heteroepitaxial ZnSe films were grown by MOCVD with a Spire 50OXT Reactor. After growing epitaxial GaAs films on single crystal GaAs wafers, well-oriented crystalline ZnSe films were grown by MOCVD. ZnSe films were grown with substrate temperatures ranging from 250 C to 450 C. Photoluminescence studies carried out by researchers at NASA Lewis determined that the surface recombination velocity at a GaAs surface was significantly reduced after the deposition of a heteroepitaxial layer of ZnSe. The optimum temperature for ZnSe deposition appears to be on the order of 350 C.

A retrospective metagenomics approach to studying Blastocystis.

PubMed

Andersen, Lee O'Brien; Bonde, Ida; Nielsen, Henrik Bjørn; Stensvold, Christen Rune

2015-07-01

Blastocystis is a common single-celled intestinal parasitic genus, comprising several subtypes. Here, we screened data obtained by metagenomic analysis of faecal DNA for Blastocystis by searching for subtype-specific genes in coabundance gene groups, which are groups of genes that covary across a selection of 316 human faecal samples, hence representing genes originating from a single subtype. The 316 faecal samples were from 236 healthy individuals, 13 patients with Crohn's disease (CD) and 67 patients with ulcerative colitis (UC). The prevalence of Blastocystis was 20.3% in the healthy individuals and 14.9% in patients with UC. Meanwhile, Blastocystis was absent in patients with CD. Individuals with intestinal microbiota dominated by Bacteroides were much less prone to having Blastocystis-positive stool (Matthew's correlation coefficient = -0.25, P < 0.0001) than individuals with Ruminococcus- and Prevotella-driven enterotypes. This is the first study to investigate the relationship between Blastocystis and communities of gut bacteria using a metagenomics approach. The study serves as an example of how it is possible to retrospectively investigate microbial eukaryotic communities in the gut using metagenomic datasets targeting the bacterial component of the intestinal microbiome and the interplay between these microbial communities. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

De novo assembly of highly polymorphic metagenomic data using in situ generated reference sequences and a novel BLAST-based assembly pipeline.

PubMed

Lin, You-Yu; Hsieh, Chia-Hung; Chen, Jiun-Hong; Lu, Xuemei; Kao, Jia-Horng; Chen, Pei-Jer; Chen, Ding-Shinn; Wang, Hurng-Yi

2017-04-26

. Both PDR and BBAP independently increased the assembly efficiency and accuracy of highly polymorphic data, and assembly performances were further improved when used together. BBAP also provides nucleotide frequency information. Together, PDR and BBAP provide powerful tools for metagenomic data studies.

Maskless micro/nanofabrication on GaAs surface by friction-induced selective etching

PubMed Central

2014-01-01

In the present study, a friction-induced selective etching method was developed to produce nanostructures on GaAs surface. Without any resist mask, the nanofabrication can be achieved by scratching and post-etching in sulfuric acid solution. The effects of the applied normal load and etching period on the formation of the nanostructure were studied. Results showed that the height of the nanostructure increased with the normal load or the etching period. XPS and Raman detection demonstrated that residual compressive stress and lattice densification were probably the main reason for selective etching, which eventually led to the protrusive nanostructures from the scratched area on the GaAs surface. Through a homemade multi-probe instrument, the capability of this fabrication method was demonstrated by producing various nanostructures on the GaAs surface, such as linear array, intersecting parallel, surface mesas, and special letters. In summary, the proposed method provided a straightforward and more maneuverable micro/nanofabrication method on the GaAs surface. PMID:24495647

The ZnSe(110) puzzle - Comparison with GaAs(110)

NASA Technical Reports Server (NTRS)

Duke, C. B.; Paton, A.; Kahn, A.; Tu, D.-W.

1984-01-01

The surface structure of monocrystalline ZnSe(110) and of 4-5-nm-thick ZnSe(110) layers epitaxially grown on GaAs(110) is investigated by means of elastic LEED and AES; the results are analyzed using the computer programs and R-factor methods of Duke et al. (1981 and 1983), presented in graphs and tables, and compared to those for GaAs(110). Significant differences are attributed to bond-length-conserving outward rotation of Se and inward rotation of Zn in the top layer, with an angle of 4 deg between the actual plane of the cation-anion chain and the truncated bulk surface. The R intensities measured for ZnSe(110) and GaAs(110) are given as Rx = 0.22 and RI = 0.21 and Rx = 0.24 and RI = 0.16, respectively.

First tests of Timepix detectors based on semi-insulating GaAs matrix of different pixel size

NASA Astrophysics Data System (ADS)

Zaťko, B.; Kubanda, D.; Žemlička, J.; Šagátová, A.; Zápražný, Z.; Boháček, P.; Nečas, V.; Mora, Y.; Pichotka, M.; Dudák, J.

2018-02-01

In this work, we have focused on Timepix detectors coupled with the semi-insulating GaAs material sensor. We used undoped bulk GaAs material with the thickness of 350 μm. We prepared and tested four pixelated detectors with 165 μm and 220 μm pixel size with two versions of technology preparation, without and with wet chemically etched trenches around each pixel. We have carried out adjustment of GaAs Timepix detectors to optimize their performance. The energy calibration of one GaAs Timepix detector in Time-over-threshold mode was performed with the use of 241Am and 133Ba radioisotopes. We were able to detect γ-photons with the energy up to 160 keV. The X-ray imaging quality of GaAs Timepix detector was tested with X-ray source using various samples. After flat field we obtained very promising imaging performance of tested GaAs Timepix detectors.

Bioactive compounds synthesized by non-ribosomal peptide synthetases and type-I polyketide synthases discovered through genome-mining and metagenomics.

PubMed

Nikolouli, Katerina; Mossialos, Dimitris

2012-08-01

Non-ribosomal peptide synthetases (NRPS) and type-I polyketide synthases (PKS-I) are multimodular enzymes involved in biosynthesis of oligopeptide and polyketide secondary metabolites produced by microorganisms such as bacteria and fungi. New findings regarding the mechanisms underlying NRPS and PKS-I evolution illustrate how microorganisms expand their metabolic potential. During the last decade rapid development of bioinformatics tools as well as improved sequencing and annotation of microbial genomes led to discovery of novel bioactive compounds synthesized by NRPS and PKS-I through genome-mining. Taking advantage of these technological developments metagenomics is a fast growing research field which directly studies microbial genomes or specific gene groups and their products. Discovery of novel bioactive compounds synthesized by NRPS and PKS-I will certainly be accelerated through metagenomics, allowing the exploitation of so far untapped microbial resources in biotechnology and medicine.

Performance and temperature dependencies of proton irradiated n/p and p/n GaAs and n/p silicon cells

NASA Technical Reports Server (NTRS)

Weinberg, I.; Swartz, C. K.; Hart, R. E., Jr.

1985-01-01

n/p homojunction GaAs cells are found to be more radiation resistant than p/n heteroface GaAs under 10 MeV proton irradiation. Both GaAs cell types outperform conventional silicon n/p cells under the same conditions. An increased temperature dependency of maximum power for the GaAs n/p cells is attributed to differences in Voc between the two GaAs cell types. These results and diffusion length considerations are consistent with the conclusion that p-type GaAs is more radiation resistant than n-type and therefore that the n/p configuration is possibly favored for use in the space radiation environment. However, it is concluded that additional work is required in order to choose between the two GaAs cell configurations.

ELIXIR pilot action: Marine metagenomics – towards a domain specific set of sustainable services

PubMed Central

Robertsen, Espen Mikal; Denise, Hubert; Mitchell, Alex; Finn, Robert D.; Bongo, Lars Ailo; Willassen, Nils Peder

2017-01-01

Metagenomics, the study of genetic material recovered directly from environmental samples, has the potential to provide insight into the structure and function of heterogeneous microbial communities.  There has been an increased use of metagenomics to discover and understand the diverse biosynthetic capacities of marine microbes, thereby allowing them to be exploited for industrial, food, and health care products. This ELIXIR pilot action was motivated by the need to establish dedicated data resources and harmonized metagenomics pipelines for the marine domain, in order to enhance the exploration and exploitation of marine genetic resources. In this paper, we summarize some of the results from the ELIXIR pilot action “Marine metagenomics – towards user centric services”. PMID:28620454

GaAs laser diode pumped Nd:YAG laser

NASA Technical Reports Server (NTRS)

Conant, L. C.; Reno, C. W.

1974-01-01

A 1.5-mm by 3-cm neodymium-ion doped YAG laser rod has been side pumped using a GaAs laser diode array tuned to the 8680-A absorption line, achieving a multimode average output power of 120 mW for a total input power of 20 W to the final-stage laser diode drivers. The pumped arrangement was designed to take advantage of the high brightness of a conventional GaAs array as a linear source by introducing the pump light through a slit into a close-wrapped gold coated pump cavity. This cavity forms an integrating chamber for the pump light.

Effects of ultrathin oxides in conducting MIS structures on GaAs

NASA Technical Reports Server (NTRS)

Childs, R. B.; Ruths, J. M.; Sullivan, T. E.; Fonash, S. J.

1978-01-01

Schottky barrier-type GaAs baseline devices (semiconductor surface etched and then immediately metalized) and GaAs conducting metal oxide-semiconductor devices are fabricated and characterized. The baseline surfaces (no purposeful oxide) are prepared by a basic or an acidic etch, while the surface for the MIS devices are prepared by oxidizing after the etch step. The metallizations used are thin-film Au, Ag, Pd, and Al. It is shown that the introduction of purposeful oxide into these Schottky barrier-type structures examined on n-type GaAs modifies the barrier formation, and that thin interfacial layers can modify barrier formation through trapping and perhaps chemical reactions. For Au- and Pd-devices, enhanced photovoltaic performance of the MIS configuration is due to increased barrier height.

Xander: employing a novel method for efficient gene-targeted metagenomic assembly

DOE PAGES

Wang, Qiong; Fish, Jordan A.; Gilman, Mariah; ...

2015-08-05

Here, metagenomics can provide important insight into microbial communities. However, assembling metagenomic datasets has proven to be computationally challenging. Current methods often assemble only fragmented partial genes. We present a novel method for targeting assembly of specific protein-coding genes. This method combines a de Bruijn graph, as used in standard assembly approaches, and a protein profile hidden Markov model (HMM) for the gene of interest, as used in standard annotation approaches. These are used to create a novel combined weighted assembly graph. Xander performs both assembly and annotation concomitantly using information incorporated in this graph. We demonstrate the utility ofmore » this approach by assembling contigs for one phylogenetic marker gene and for two functional marker genes, first on Human Microbiome Project (HMP)-defined community Illumina data and then on 21 rhizosphere soil metagenomic datasets from three different crops totaling over 800 Gbp of unassembled data. We compared our method to a recently published bulk metagenome assembly method and a recently published gene-targeted assembler and found our method produced more, longer, and higher quality gene sequences. In conclusion, xander combines gene assignment with the rapid assembly of full-length or near full-length functional genes from metagenomic data without requiring bulk assembly or post-processing to find genes of interest. HMMs used for assembly can be tailored to the targeted genes, allowing flexibility to improve annotation over generic annotation pipelines.« less

Xander: employing a novel method for efficient gene-targeted metagenomic assembly.

PubMed

Wang, Qiong; Fish, Jordan A; Gilman, Mariah; Sun, Yanni; Brown, C Titus; Tiedje, James M; Cole, James R

2015-01-01

Metagenomics can provide important insight into microbial communities. However, assembling metagenomic datasets has proven to be computationally challenging. Current methods often assemble only fragmented partial genes. We present a novel method for targeting assembly of specific protein-coding genes. This method combines a de Bruijn graph, as used in standard assembly approaches, and a protein profile hidden Markov model (HMM) for the gene of interest, as used in standard annotation approaches. These are used to create a novel combined weighted assembly graph. Xander performs both assembly and annotation concomitantly using information incorporated in this graph. We demonstrate the utility of this approach by assembling contigs for one phylogenetic marker gene and for two functional marker genes, first on Human Microbiome Project (HMP)-defined community Illumina data and then on 21 rhizosphere soil metagenomic datasets from three different crops totaling over 800 Gbp of unassembled data. We compared our method to a recently published bulk metagenome assembly method and a recently published gene-targeted assembler and found our method produced more, longer, and higher quality gene sequences. Xander combines gene assignment with the rapid assembly of full-length or near full-length functional genes from metagenomic data without requiring bulk assembly or post-processing to find genes of interest. HMMs used for assembly can be tailored to the targeted genes, allowing flexibility to improve annotation over generic annotation pipelines. This method is implemented as open source software and is available at https://github.com/rdpstaff/Xander_assembler.

Pooled assembly of marine metagenomic datasets: enriching annotation through chimerism.

PubMed

Magasin, Jonathan D; Gerloff, Dietlind L

2015-02-01

Despite advances in high-throughput sequencing, marine metagenomic samples remain largely opaque. A typical sample contains billions of microbial organisms from thousands of genomes and quadrillions of DNA base pairs. Its derived metagenomic dataset underrepresents this complexity by orders of magnitude because of the sparseness and shortness of sequencing reads. Read shortness and sequencing errors pose a major challenge to accurate species and functional annotation. This includes distinguishing known from novel species. Often the majority of reads cannot be annotated and thus cannot help our interpretation of the sample. Here, we demonstrate quantitatively how careful assembly of marine metagenomic reads within, but also across, datasets can alleviate this problem. For 10 simulated datasets, each with species complexity modeled on a real counterpart, chimerism remained within the same species for most contigs (97%). For 42 real pyrosequencing ('454') datasets, assembly increased the proportion of annotated reads, and even more so when datasets were pooled, by on average 1.6% (max 6.6%) for species, 9.0% (max 28.7%) for Pfam protein domains and 9.4% (max 22.9%) for PANTHER gene families. Our results outline exciting prospects for data sharing in the metagenomics community. While chimeric sequences should be avoided in other areas of metagenomics (e.g. biodiversity analyses), conservative pooled assembly is advantageous for annotation specificity and sensitivity. Intriguingly, our experiment also found potential prospects for (low-cost) discovery of new species in 'old' data. dgerloff@ffame.org Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs.

PubMed

Eloe-Fadrosh, Emiley A; Paez-Espino, David; Jarett, Jessica; Dunfield, Peter F; Hedlund, Brian P; Dekas, Anne E; Grasby, Stephen E; Brady, Allyson L; Dong, Hailiang; Briggs, Brandon R; Li, Wen-Jun; Goudeau, Danielle; Malmstrom, Rex; Pati, Amrita; Pett-Ridge, Jennifer; Rubin, Edward M; Woyke, Tanja; Kyrpides, Nikos C; Ivanova, Natalia N

2016-01-27

Analysis of the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum ('Candidatus Kryptonia') found exclusively in high-temperature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic 'blind spot' because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestyle with conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery.

Probability of twin formation on self-catalyzed GaAs nanowires on Si substrate

PubMed Central

2012-01-01

We attempted to control the incorporation of twin boundaries in self-catalyzed GaAs nanowires (NWs). Self-catalyzed GaAs NWs were grown on a Si substrate under various arsenic pressures using molecular beam epitaxy and the vapor-liquid-solid method. When the arsenic flux is low, wurtzite structures are dominant in the GaAs NWs. On the other hand, zinc blende structures become dominant as the arsenic flux rises. We discussed this phenomenon on the basis of thermodynamics and examined the probability of twin-boundary formation in detail. PMID:23043754

MALINA: a web service for visual analytics of human gut microbiota whole-genome metagenomic reads.

PubMed

Tyakht, Alexander V; Popenko, Anna S; Belenikin, Maxim S; Altukhov, Ilya A; Pavlenko, Alexander V; Kostryukova, Elena S; Selezneva, Oksana V; Larin, Andrei K; Karpova, Irina Y; Alexeev, Dmitry G

2012-12-07

MALINA is a web service for bioinformatic analysis of whole-genome metagenomic data obtained from human gut microbiota sequencing. As input data, it accepts metagenomic reads of various sequencing technologies, including long reads (such as Sanger and 454 sequencing) and next-generation (including SOLiD and Illumina). It is the first metagenomic web service that is capable of processing SOLiD color-space reads, to authors' knowledge. The web service allows phylogenetic and functional profiling of metagenomic samples using coverage depth resulting from the alignment of the reads to the catalogue of reference sequences which are built into the pipeline and contain prevalent microbial genomes and genes of human gut microbiota. The obtained metagenomic composition vectors are processed by the statistical analysis and visualization module containing methods for clustering, dimension reduction and group comparison. Additionally, the MALINA database includes vectors of bacterial and functional composition for human gut microbiota samples from a large number of existing studies allowing their comparative analysis together with user samples, namely datasets from Russian Metagenome project, MetaHIT and Human Microbiome Project (downloaded from http://hmpdacc.org). MALINA is made freely available on the web at http://malina.metagenome.ru. The website is implemented in JavaScript (using Ext JS), Microsoft .NET Framework, MS SQL, Python, with all major browsers supported.

Construction and screening of marine metagenomic libraries.

PubMed

Weiland, Nancy; Löscher, Carolin; Metzger, Rebekka; Schmitz, Ruth

2010-01-01

Marine microbial communities are highly diverse and have evolved during extended evolutionary processes of physiological adaptations under the influence of a variety of ecological conditions and selection pressures. They harbor an enormous diversity of microbes with still unknown and probably new physiological characteristics. Besides, the surfaces of marine multicellular organisms are typically covered by a consortium of epibiotic bacteria and act as barriers, where diverse interactions between microorganisms and hosts take place. Thus, microbial diversity in the water column of the oceans and the microbial consortia on marine tissues of multicellular organisms are rich sources for isolating novel bioactive compounds and genes. Here we describe the sampling, construction of large-insert metagenomic libraries from marine habitats and exemplarily one function based screen of metagenomic clones.

Meta-Storms: efficient search for similar microbial communities based on a novel indexing scheme and similarity score for metagenomic data.

PubMed

Su, Xiaoquan; Xu, Jian; Ning, Kang

2012-10-01

It has long been intriguing scientists to effectively compare different microbial communities (also referred as 'metagenomic samples' here) in a large scale: given a set of unknown samples, find similar metagenomic samples from a large repository and examine how similar these samples are. With the current metagenomic samples accumulated, it is possible to build a database of metagenomic samples of interests. Any metagenomic samples could then be searched against this database to find the most similar metagenomic sample(s). However, on one hand, current databases with a large number of metagenomic samples mostly serve as data repositories that offer few functionalities for analysis; and on the other hand, methods to measure the similarity of metagenomic data work well only for small set of samples by pairwise comparison. It is not yet clear, how to efficiently search for metagenomic samples against a large metagenomic database. In this study, we have proposed a novel method, Meta-Storms, that could systematically and efficiently organize and search metagenomic data. It includes the following components: (i) creating a database of metagenomic samples based on their taxonomical annotations, (ii) efficient indexing of samples in the database based on a hierarchical taxonomy indexing strategy, (iii) searching for a metagenomic sample against the database by a fast scoring function based on quantitative phylogeny and (iv) managing database by index export, index import, data insertion, data deletion and database merging. We have collected more than 1300 metagenomic data from the public domain and in-house facilities, and tested the Meta-Storms method on these datasets. Our experimental results show that Meta-Storms is capable of database creation and effective searching for a large number of metagenomic samples, and it could achieve similar accuracies compared with the current popular significance testing-based methods. Meta-Storms method would serve as a suitable

Modified energetics and growth kinetics on H-terminated GaAs (110)

NASA Astrophysics Data System (ADS)

Galiana, B.; Benedicto, M.; Díez-Merino, L.; Lorbek, S.; Hlawacek, G.; Teichert, C.; Tejedor, P.

2013-10-01

Atomic hydrogen modification of the surface energy of GaAs (110) epilayers, grown at high temperatures from molecular beams of Ga and As4, has been investigated by friction force microscopy (FFM). The reduction of the friction force observed with longer exposures to the H beam has been correlated with the lowering of the surface energy originated by the progressive de-relaxation of the GaAs (110) surface occurring upon H chemisorption. Our results indicate that the H-terminated GaAs (110) epilayers are more stable than the As-stabilized ones, with the minimum surface energy value of 31 meV/Å2 measured for the fully hydrogenated surface. A significant reduction of the Ga diffusion length on the H-terminated surface irrespective of H coverage has been calculated from the FFM data, consistent with the layer-by-layer growth mode and the greater As incorporation coefficient determined from real-time reflection high-energy electron diffraction studies. Arsenic incorporation through direct dissociative chemisorption of single As4 molecules mediated by H on the GaAs (110) surface has been proposed as the most likely explanation for the changes in surface kinetics observed.

Surface segregation and the Al problem in GaAs quantum wells

NASA Astrophysics Data System (ADS)

Chung, Yoon Jang; Baldwin, K. W.; West, K. W.; Shayegan, M.; Pfeiffer, L. N.

2018-03-01

Low-defect two-dimensional electron systems (2DESs) are essential for studies of fragile many-body interactions that only emerge in nearly-ideal systems. As a result, numerous efforts have been made to improve the quality of modulation-doped AlxGa1 -xAs /GaAs quantum wells (QWs), with an emphasis on purifying the source material of the QW itself or achieving better vacuum in the deposition chamber. However, this approach overlooks another crucial component that comprises such QWs, the AlxGa1 -xAs barrier. Here we show that having a clean Al source and hence a clean barrier is instrumental to obtain a high-quality GaAs 2DES in a QW. We observe that the mobility of the 2DES in GaAs QWs declines as the thickness or Al content of the AlxGa1 -xAs barrier beneath the QW is increased, which we attribute to the surface segregation of oxygen atoms that originate from the Al source. This conjecture is supported by the improved mobility in the GaAs QWs as the Al cell is cleaned out by baking.

Intracellular screen to identify metagenomic clones that induce or inhibit a quorum-sensing biosensor.

PubMed

Williamson, Lynn L; Borlee, Bradley R; Schloss, Patrick D; Guan, Changhui; Allen, Heather K; Handelsman, Jo

2005-10-01

The goal of this study was to design and evaluate a rapid screen to identify metagenomic clones that produce biologically active small molecules. We built metagenomic libraries with DNA from soil on the floodplain of the Tanana River in Alaska. We extracted DNA directly from the soil and cloned it into fosmid and bacterial artificial chromosome vectors, constructing eight metagenomic libraries that contain 53,000 clones with inserts ranging from 1 to 190 kb. To identify clones of interest, we designed a high throughput "intracellular" screen, designated METREX, in which metagenomic DNA is in a host cell containing a biosensor for compounds that induce bacterial quorum sensing. If the metagenomic clone produces a quorum-sensing inducer, the cell produces green fluorescent protein (GFP) and can be identified by fluorescence microscopy or captured by fluorescence-activated cell sorting. Our initial screen identified 11 clones that induce and two that inhibit expression of GFP. The intracellular screen detected quorum-sensing inducers among metagenomic clones that a traditional overlay screen would not. One inducing clone carries a LuxI homologue that directs the synthesis of an N-acyl homoserine lactone quorum-sensing signal molecule. The LuxI homologue has 62% amino acid sequence identity to its closest match in GenBank, AmfI from Pseudomonas fluorescens, and is on a 78-kb insert that contains 67 open reading frames. Another inducing clone carries a gene with homology to homocitrate synthase. Our results demonstrate the power of an intracellular screen to identify functionally active clones and biologically active small molecules in metagenomic libraries.

Analysis of composition-based metagenomic classification.

PubMed

Higashi, Susan; Barreto, André da Motta Salles; Cantão, Maurício Egidio; de Vasconcelos, Ana Tereza Ribeiro

2012-01-01

An essential step of a metagenomic study is the taxonomic classification, that is, the identification of the taxonomic lineage of the organisms in a given sample. The taxonomic classification process involves a series of decisions. Currently, in the context of metagenomics, such decisions are usually based on empirical studies that consider one specific type of classifier. In this study we propose a general framework for analyzing the impact that several decisions can have on the classification problem. Instead of focusing on any specific classifier, we define a generic score function that provides a measure of the difficulty of the classification task. Using this framework, we analyze the impact of the following parameters on the taxonomic classification problem: (i) the length of n-mers used to encode the metagenomic sequences, (ii) the similarity measure used to compare sequences, and (iii) the type of taxonomic classification, which can be conventional or hierarchical, depending on whether the classification process occurs in a single shot or in several steps according to the taxonomic tree. We defined a score function that measures the degree of separability of the taxonomic classes under a given configuration induced by the parameters above. We conducted an extensive computational experiment and found out that reasonable values for the parameters of interest could be (i) intermediate values of n, the length of the n-mers; (ii) any similarity measure, because all of them resulted in similar scores; and (iii) the hierarchical strategy, which performed better in all of the cases. As expected, short n-mers generate lower configuration scores because they give rise to frequency vectors that represent distinct sequences in a similar way. On the other hand, large values for n result in sparse frequency vectors that represent differently metagenomic fragments that are in fact similar, also leading to low configuration scores. Regarding the similarity measure, in

Large Signal Modeling and Analysis of the GaAs MESFET.

DTIC Science & Technology

1986-07-09

various dimensions and physical parameters. A powerful computer aided design system can be developed by automating the circuit element and parameter...circuit model of the GaAs MESFET to aid in the designs of microwave MESFET circuits. The circuit elements of this model are obtained either directly...34. -. ’ Abstract The purpose of this work is to develop a large signal signal lumped circuit model of the GaAs MESFET to aid In the designs of microwave MESFET

Structural and electronic properties of isovalent boron atoms in GaAs

NASA Astrophysics Data System (ADS)

Krammel, C. M.; Nattermann, L.; Sterzer, E.; Volz, K.; Koenraad, P. M.

2018-04-01

Boron containing GaAs, which is grown by metal organic vapour phase epitaxy, is studied at the atomic level by cross-sectional scanning tunneling microscopy (X-STM) and spectroscopy (STS). In topographic X-STM images, three classes of B related features are identified, which are attributed to individual B atoms on substitutional Ga sites down to the second layer below the natural {110} cleavage planes. The X-STM contrast of B atoms below the surface reflects primarily the structural modification of the GaAs matrix by the small B atoms. However, B atoms in the cleavage plane have in contrast to conventional isovalent impurities, such as Al and In, a strong influence on the local electronic structure similar to donors or acceptors. STS measurements show that B in the GaAs {110} surfaces gives rise to a localized state short below the conduction band (CB) edge while in bulk GaAs, the B impurity state is resonant with the CB. The analysis of BxGa1-xAs/GaAs quantum wells reveals a good crystal quality and shows that the incorporation of B atoms in GaAs can be controlled along the [001] growth direction at the atomic level. Surprisingly, the formation of the first and fourth nearest neighbor B pairs, which are oriented along the <110 > directions, is strongly suppressed at a B concentration of 1% while the third nearest neighbor B pairs are found more than twice as often than expected for a completely spatially random pattern.

The soil microbiome — from metagenomics to metaphenomics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jansson, Janet K.; Hofmockel, Kirsten S.

Soil microorganisms carry out important processes, including support of plant growth and cycling of carbon and other nutrients. However, the majority of soil microbes have not yet been isolated and their functions are largely unknown. Although metagenomic sequencing reveals microbial identities and functional gene information, it includes DNA from microbes with vastly varying physiological states. Therefore, metagenomics is only predictive of community functional potential. We posit that the next frontier lies in understanding the metaphenome, the product of the combined genetic potential of the microbiome and available resources. Here in this paper we describe examples of opportunities towards gaining understandingmore » of the soil metaphenome.« less

Kraken: ultrafast metagenomic sequence classification using exact alignments

PubMed Central

2014-01-01

Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences. Previous programs designed for this task have been relatively slow and computationally expensive, forcing researchers to use faster abundance estimation programs, which only classify small subsets of metagenomic data. Using exact alignment of k-mers, Kraken achieves classification accuracy comparable to the fastest BLAST program. In its fastest mode, Kraken classifies 100 base pair reads at a rate of over 4.1 million reads per minute, 909 times faster than Megablast and 11 times faster than the abundance estimation program MetaPhlAn. Kraken is available at http://ccb.jhu.edu/software/kraken/. PMID:24580807

The soil microbiome — from metagenomics to metaphenomics

DOE PAGES

Jansson, Janet K.; Hofmockel, Kirsten S.

2018-02-15

Soil microorganisms carry out important processes, including support of plant growth and cycling of carbon and other nutrients. However, the majority of soil microbes have not yet been isolated and their functions are largely unknown. Although metagenomic sequencing reveals microbial identities and functional gene information, it includes DNA from microbes with vastly varying physiological states. Therefore, metagenomics is only predictive of community functional potential. We posit that the next frontier lies in understanding the metaphenome, the product of the combined genetic potential of the microbiome and available resources. Here in this paper we describe examples of opportunities towards gaining understandingmore » of the soil metaphenome.« less

Laboratory procedures to generate viral metagenomes.

PubMed

Thurber, Rebecca V; Haynes, Matthew; Breitbart, Mya; Wegley, Linda; Rohwer, Forest

2009-01-01

This collection of laboratory protocols describes the steps to collect viruses from various samples with the specific aim of generating viral metagenome sequence libraries (viromes). Viral metagenomics, the study of uncultured viral nucleic acid sequences from different biomes, relies on several concentration, purification, extraction, sequencing and heuristic bioinformatic methods. No single technique can provide an all-inclusive approach, and therefore the protocols presented here will be discussed in terms of hypothetical projects. However, care must be taken to individualize each step depending on the source and type of viral-particles. This protocol is a description of the processes we have successfully used to: (i) concentrate viral particles from various types of samples, (ii) eliminate contaminating cells and free nucleic acids and (iii) extract, amplify and purify viral nucleic acids. Overall, a sample can be processed to isolate viral nucleic acids suitable for high-throughput sequencing in approximately 1 week.

Giant and reversible enhancement of the electrical resistance of GaAs1-xNx by hydrogen irradiation

NASA Astrophysics Data System (ADS)

Alvarez, J.; Kleider, J.-P.; Trotta, R.; Polimeni, A.; Capizzi, M.; Martelli, F.; Mariucci, L.; Rubini, S.

2011-08-01

The electrical properties of untreated and hydrogen-irradiated GaAs1-xNx are investigated by conductive-probe atomic force microscopy (CP-AFM). After hydrogen irradiation, the resistance R of GaAs1-xNx increases by more than three orders of magnitude while that of a N-free GaAs reference slightly decreases. Thermal annealing at 550 °C of H-irradiated GaAs1-xNx restores the pristine electrical properties of the as-grown sample thus demonstrating that this phenomenon is fully reversible. These effects are attributed to the nitrogen-hydrogen complexes that passivate N in GaAs1-xNx (thus restoring the energy gap of N-free GaAs) and, moreover, reduce the carrier scattering time by more than one order of magnitude. This opens up a route to the fabrication of planar conductive/resistive/conductive heterostructures with submicrometer spatial resolution, which is also reported here.

A Metagenomic Approach to Cyanobacterial Genomics

PubMed Central

Alvarenga, Danillo O.; Fiore, Marli F.; Varani, Alessandro M.

2017-01-01

Cyanobacteria, or oxyphotobacteria, are primary producers that establish ecological interactions with a wide variety of organisms. Although their associations with eukaryotes have received most attention, interactions with bacterial and archaeal symbionts have also been occurring for billions of years. Due to these associations, obtaining axenic cultures of cyanobacteria is usually difficult, and most isolation efforts result in unicyanobacterial cultures containing a number of associated microbes, hence composing a microbial consortium. With rising numbers of cyanobacterial blooms due to climate change, demand for genomic evaluations of these microorganisms is increasing. However, standard genomic techniques call for the sequencing of axenic cultures, an approach that not only adds months or even years for culture purification, but also appears to be impossible for some cyanobacteria, which is reflected in the relatively low number of publicly available genomic sequences of this phylum. Under the framework of metagenomics, on the other hand, cumbersome techniques for achieving axenic growth can be circumvented and individual genomes can be successfully obtained from microbial consortia. This review focuses on approaches for the genomic and metagenomic assessment of non-axenic cyanobacterial cultures that bypass requirements for axenity. These methods enable researchers to achieve faster and less costly genomic characterizations of cyanobacterial strains and raise additional information about their associated microorganisms. While non-axenic cultures may have been previously frowned upon in cyanobacteriology, latest advancements in metagenomics have provided new possibilities for in vitro studies of oxyphotobacteria, renewing the value of microbial consortia as a reliable and functional resource for the rapid assessment of bloom-forming cyanobacteria. PMID:28536564

Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection.

PubMed

Schlaberg, Robert; Chiu, Charles Y; Miller, Steve; Procop, Gary W; Weinstock, George

2017-06-01

- Metagenomic sequencing can be used for detection of any pathogens using unbiased, shotgun next-generation sequencing (NGS), without the need for sequence-specific amplification. Proof-of-concept has been demonstrated in infectious disease outbreaks of unknown causes and in patients with suspected infections but negative results for conventional tests. Metagenomic NGS tests hold great promise to improve infectious disease diagnostics, especially in immunocompromised and critically ill patients. - To discuss challenges and provide example solutions for validating metagenomic pathogen detection tests in clinical laboratories. A summary of current regulatory requirements, largely based on prior guidance for NGS testing in constitutional genetics and oncology, is provided. - Examples from 2 separate validation studies are provided for steps from assay design, and validation of wet bench and bioinformatics protocols, to quality control and assurance. - Although laboratory and data analysis workflows are still complex, metagenomic NGS tests for infectious diseases are increasingly being validated in clinical laboratories. Many parallels exist to NGS tests in other fields. Nevertheless, specimen preparation, rapidly evolving data analysis algorithms, and incomplete reference sequence databases are idiosyncratic to the field of microbiology and often overlooked.

Testing a GaAs cathode in SRF gun

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, E.; Kewisch, J.; Ben-Zvi, I.

RF electron guns with a strained superlattice GaAs cathode are expected to generate polarized electron beams of higher brightness and lower emittance than do DC guns, due to their higher field gradient at the cathode's surface and lower cathode temperature. We plan to install a bulk GaAs:Cs in a SRF gun to evaluate the performance of both the gun and the cathode in this environment. The status of this project is: In our 1.3 GHz 1/2 cell SRF gun, the vacuum can be maintained at nearly 10{sup -12} Torr because of cryo-pumping at 2K. With conventional activation of bulk GaAs,more » we obtained a QE of 10% at 532 nm, with lifetime of more than 3 days in the preparation chamber and have shown that it can survive in transport from the preparation chamber to the gun. The beam line has been assembled and we are exploring the best conditions for baking the cathode under vacuum. We report here the progress of our test of the GaAs cathode in the SRF gun. Future particle accelerators, such as eRHIC and the ILC require high-brightness, high-current polarized electrons. Strained superlattice GaAs:Cs has been shown to be an efficient cathode for producing polarized electrons. Activation of GaAs with Cs,O(F) lowers the electron affinity and makes it energetically possible for all the electrons, excited into the conduction band that drift or diffuse to the emission surface, to escape into the vacuum. Presently, all operating polarized electron sources, such as the CEBAF, are DC guns. In these devices, the excellent ultra-high vacuum extends the lifetime of the cathode. However, the low field gradient on the photocathode's emission surface of the DC guns limits the beam quality. The higher accelerating gradients, possible in the RF guns, generate a far better beam. Until recently, most RF guns operated at room temperature, limiting the vacuum to {approx}10{sup -9} Torr. This destroys the GaAs's NEA surface. The SRF guns combine the excellent vacuum conditions of DC guns and the

Design of quantum efficiency measurement system for variable doping GaAs photocathode

NASA Astrophysics Data System (ADS)

Chen, Liang; Yang, Kai; Liu, HongLin; Chang, Benkang

2008-03-01

To achieve high quantum efficiency and good stability has been a main direction to develop GaAs photocathode recently. Through early research, we proved that variable doping structure is executable and practical, and has great potential. In order to optimize variable doping GaAs photocathode preparation techniques and study the variable doping theory deeply, a real-time quantum efficiency measurement system for GaAs Photocathode has been designed. The system uses FPGA (Field-programmable gate array) device, and high speed A/D converter to design a high signal noise ratio and high speed data acquisition card. ARM (Advanced RISC Machines) core processor s3c2410 and real-time embedded system are used to obtain and show measurement results. The measurement precision of photocurrent could reach 1nA, and measurement range of spectral response curve is within 400~1000nm. GaAs photocathode preparation process can be real-time monitored by using this system. This system could easily be added other functions to show the physic variation of photocathode during the preparation process more roundly in the future.

Metagenomic Characterization of the Human Intestinal Microbiota in Fecal Samples from STEC-Infected Patients

PubMed Central

Gigliucci, Federica; von Meijenfeldt, F. A. Bastiaan; Knijn, Arnold; Michelacci, Valeria; Scavia, Gaia; Minelli, Fabio; Dutilh, Bas E.; Ahmad, Hamideh M.; Raangs, Gerwin C.; Friedrich, Alex W.; Rossen, John W. A.; Morabito, Stefano

2018-01-01

The human intestinal microbiota is a homeostatic ecosystem with a remarkable impact on human health and the disruption of this equilibrium leads to an increased susceptibility to infection by numerous pathogens. In this study, we used shotgun metagenomic sequencing and two different bioinformatic approaches, based on mapping of the reads onto databases and on the reconstruction of putative draft genomes, to investigate possible changes in the composition of the intestinal microbiota in samples from patients with Shiga Toxin-producing E. coli (STEC) infection compared to healthy and healed controls, collected during an outbreak caused by a STEC O26:H11 infection. Both the bioinformatic procedures used, produced similar result with a good resolution of the taxonomic profiles of the specimens. The stool samples collected from the STEC infected patients showed a lower abundance of the members of Bifidobacteriales and Clostridiales orders in comparison to controls where those microorganisms predominated. These differences seemed to correlate with the STEC infection although a flexion in the relative abundance of the Bifidobacterium genus, part of the Bifidobacteriales order, was observed also in samples from Crohn's disease patients, displaying a STEC-unrelated dysbiosis. The metagenomics also allowed to identify in the STEC positive samples, all the virulence traits present in the genomes of the STEC O26 that caused the outbreak as assessed through isolation of the epidemic strain and whole genome sequencing. The results shown represent a first evidence of the changes occurring in the intestinal microbiota of children in the course of STEC infection and indicate that metagenomics may be a promising tool for the culture-independent clinical diagnosis of the infection. PMID:29468143

Recovery of a Medieval Brucella melitensis Genome Using Shotgun Metagenomics

PubMed Central

Kay, Gemma L.; Sergeant, Martin J.; Giuffra, Valentina; Bandiera, Pasquale; Milanese, Marco; Bramanti, Barbara

2014-01-01

ABSTRACT Shotgun metagenomics provides a powerful assumption-free approach to the recovery of pathogen genomes from contemporary and historical material. We sequenced the metagenome of a calcified nodule from the skeleton of a 14th-century middle-aged male excavated from the medieval Sardinian settlement of Geridu. We obtained 6.5-fold coverage of a Brucella melitensis genome. Sequence reads from this genome showed signatures typical of ancient or aged DNA. Despite the relatively low coverage, we were able to use information from single-nucleotide polymorphisms to place the medieval pathogen genome within a clade of B. melitensis strains that included the well-studied Ether strain and two other recent Italian isolates. We confirmed this placement using information from deletions and IS711 insertions. We conclude that metagenomics stands ready to document past and present infections, shedding light on the emergence, evolution, and spread of microbial pathogens. PMID:25028426

Epitaxial lateral overgrowth of GaAs: effect of doping on LPE growth behaviour

NASA Astrophysics Data System (ADS)

Zytkiewicz, Z. R.; Dobosz, D.; Pawlowska, M.

1999-05-01

Results of epitaxial lateral overgrowth (ELO) of GaAs on (001) GaAs substrates by liquid phase epitaxy are reported. We show that by introducing Si, Sn or Te impurities to the Ga-As solution the vertical growth rate is reduced while the lateral growth rate is significantly enhanced, which leads to a growth habit modification. Furthermore, the impurity incorporation into the growing layer is different on the upper and side surfaces of the ELO, reflecting the fundamental differences between the lateral and vertical growth modes. This phenomenon can be applied for studying the temporal development of ELO layers.

Electric field effects on the optical properties of buckled GaAs monolayer

NASA Astrophysics Data System (ADS)

Bahuguna, Bhagwati Prasad; Saini, L. K.; Sharma, Rajesh O.

2018-04-01

Buckled GaAs monolayer has a direct band gap semiconductor with energy gap of 1.31 eV in the absence of electric field. When we applied transverse electric field, the value of band gap decreases with increasing of electric field strength. In our previous work [1], it is observed that the buckled GaAs monolayer becomes metallic at 1.3 V/Å. In the present work, we investigate the optical properties such as photon energy-dependent dielectric functions, extinction coefficient, refractive index, absorption spectrum and reflectivity of buckled GaAs monolayer in the semiconducting phase i.e. absence of external electric field and metallic phase i.e. presence of external electric field using density functional theory.

Biotechnological applications of functional metagenomics in the food and pharmaceutical industries.

PubMed

Coughlan, Laura M; Cotter, Paul D; Hill, Colin; Alvarez-Ordóñez, Avelino

2015-01-01

Microorganisms are found throughout nature, thriving in a vast range of environmental conditions. The majority of them are unculturable or difficult to culture by traditional methods. Metagenomics enables the study of all microorganisms, regardless of whether they can be cultured or not, through the analysis of genomic data obtained directly from an environmental sample, providing knowledge of the species present, and allowing the extraction of information regarding the functionality of microbial communities in their natural habitat. Function-based screenings, following the cloning and expression of metagenomic DNA in a heterologous host, can be applied to the discovery of novel proteins of industrial interest encoded by the genes of previously inaccessible microorganisms. Functional metagenomics has considerable potential in the food and pharmaceutical industries, where it can, for instance, aid (i) the identification of enzymes with desirable technological properties, capable of catalyzing novel reactions or replacing existing chemically synthesized catalysts which may be difficult or expensive to produce, and able to work under a wide range of environmental conditions encountered in food and pharmaceutical processing cycles including extreme conditions of temperature, pH, osmolarity, etc; (ii) the discovery of novel bioactives including antimicrobials active against microorganisms of concern both in food and medical settings; (iii) the investigation of industrial and societal issues such as antibiotic resistance development. This review article summarizes the state-of-the-art functional metagenomic methods available and discusses the potential of functional metagenomic approaches to mine as yet unexplored environments to discover novel genes with biotechnological application in the food and pharmaceutical industries.

Biotechnological applications of functional metagenomics in the food and pharmaceutical industries

PubMed Central

Coughlan, Laura M.; Cotter, Paul D.; Hill, Colin; Alvarez-Ordóñez, Avelino

2015-01-01

Microorganisms are found throughout nature, thriving in a vast range of environmental conditions. The majority of them are unculturable or difficult to culture by traditional methods. Metagenomics enables the study of all microorganisms, regardless of whether they can be cultured or not, through the analysis of genomic data obtained directly from an environmental sample, providing knowledge of the species present, and allowing the extraction of information regarding the functionality of microbial communities in their natural habitat. Function-based screenings, following the cloning and expression of metagenomic DNA in a heterologous host, can be applied to the discovery of novel proteins of industrial interest encoded by the genes of previously inaccessible microorganisms. Functional metagenomics has considerable potential in the food and pharmaceutical industries, where it can, for instance, aid (i) the identification of enzymes with desirable technological properties, capable of catalyzing novel reactions or replacing existing chemically synthesized catalysts which may be difficult or expensive to produce, and able to work under a wide range of environmental conditions encountered in food and pharmaceutical processing cycles including extreme conditions of temperature, pH, osmolarity, etc; (ii) the discovery of novel bioactives including antimicrobials active against microorganisms of concern both in food and medical settings; (iii) the investigation of industrial and societal issues such as antibiotic resistance development. This review article summarizes the state-of-the-art functional metagenomic methods available and discusses the potential of functional metagenomic approaches to mine as yet unexplored environments to discover novel genes with biotechnological application in the food and pharmaceutical industries. PMID:26175729

Nuclear spin warm up in bulk n -GaAs

NASA Astrophysics Data System (ADS)

Kotur, M.; Dzhioev, R. I.; Vladimirova, M.; Jouault, B.; Korenev, V. L.; Kavokin, K. V.

2016-08-01

We show that the spin-lattice relaxation in n -type insulating GaAs is dramatically accelerated at low magnetic fields. The origin of this effect, which cannot be explained in terms of well-known diffusion-limited hyperfine relaxation, is found in the quadrupole relaxation, induced by fluctuating donor charges. Therefore, quadrupole relaxation, which governs low field nuclear spin relaxation in semiconductor quantum dots, but was so far supposed to be harmless to bulk nuclei spins in the absence of optical pumping, can be studied and harnessed in the much simpler model environment of n -GaAs bulk crystal.

46 CFR Sec. 7 - Operation under current GAA/MSTS Southeast Asia Program.

Code of Federal Regulations, 2013 CFR

2013-10-01

... provisions of NSA Order 35 (OPR-2) to the particular circumstances of the present GAA/MSTS Southeast Asia... General Agency operations not related to the current GAA/MSTS Southeast Asia Program, NSA Order 35 (OPR-2... lieu of those appearing in sections 3 and 4 of NSA Order 35 (OPR-2). Continental United States ports do...

46 CFR Sec. 7 - Operation under current GAA/MSTS Southeast Asia Program.

Code of Federal Regulations, 2012 CFR

2012-10-01

... provisions of NSA Order 35 (OPR-2) to the particular circumstances of the present GAA/MSTS Southeast Asia... General Agency operations not related to the current GAA/MSTS Southeast Asia Program, NSA Order 35 (OPR-2... lieu of those appearing in sections 3 and 4 of NSA Order 35 (OPR-2). Continental United States ports do...

46 CFR Sec. 7 - Operation under current GAA/MSTS Southeast Asia Program.

Code of Federal Regulations, 2010 CFR

2010-10-01

... provisions of NSA Order 35 (OPR-2) to the particular circumstances of the present GAA/MSTS Southeast Asia... General Agency operations not related to the current GAA/MSTS Southeast Asia Program, NSA Order 35 (OPR-2... lieu of those appearing in sections 3 and 4 of NSA Order 35 (OPR-2). Continental United States ports do...

46 CFR Sec. 7 - Operation under current GAA/MSTS Southeast Asia Program.

Code of Federal Regulations, 2014 CFR

2014-10-01

... provisions of NSA Order 35 (OPR-2) to the particular circumstances of the present GAA/MSTS Southeast Asia... General Agency operations not related to the current GAA/MSTS Southeast Asia Program, NSA Order 35 (OPR-2... lieu of those appearing in sections 3 and 4 of NSA Order 35 (OPR-2). Continental United States ports do...

46 CFR Sec. 7 - Operation under current GAA/MSTS Southeast Asia Program.

Code of Federal Regulations, 2011 CFR

2011-10-01

... provisions of NSA Order 35 (OPR-2) to the particular circumstances of the present GAA/MSTS Southeast Asia... General Agency operations not related to the current GAA/MSTS Southeast Asia Program, NSA Order 35 (OPR-2... lieu of those appearing in sections 3 and 4 of NSA Order 35 (OPR-2). Continental United States ports do...

deFUME: Dynamic exploration of functional metagenomic sequencing data.

PubMed

van der Helm, Eric; Geertz-Hansen, Henrik Marcus; Genee, Hans Jasper; Malla, Sailesh; Sommer, Morten Otto Alexander

2015-07-31

Functional metagenomic selections represent a powerful technique that is widely applied for identification of novel genes from complex metagenomic sources. However, whereas hundreds to thousands of clones can be easily generated and sequenced over a few days of experiments, analyzing the data is time consuming and constitutes a major bottleneck for experimental researchers in the field. Here we present the deFUME web server, an easy-to-use web-based interface for processing, annotation and visualization of functional metagenomics sequencing data, tailored to meet the requirements of non-bioinformaticians. The web-server integrates multiple analysis steps into one single workflow: read assembly, open reading frame prediction, and annotation with BLAST, InterPro and GO classifiers. Analysis results are visualized in an online dynamic web-interface. The deFUME webserver provides a fast track from raw sequence to a comprehensive visual data overview that facilitates effortless inspection of gene function, clustering and distribution. The webserver is available at cbs.dtu.dk/services/deFUME/and the source code is distributed at github.com/EvdH0/deFUME.

GaAs Solar Cell Radiation Handbook

NASA Technical Reports Server (NTRS)

Anspaugh, B. E.

1996-01-01

History of GaAs solar cell development is provided. Photovoltaic equations are described along with instrumentation techniques for measuring solar cells. Radiation effects in solar cells, electrical performance, and spacecraft flight data for solar cells are discussed. The space radiation environment and solar array degradation calculations are addressed.

Protein Structure Determination using Metagenome sequence data

PubMed Central

Ovchinnikov, Sergey; Park, Hahnbeom; Varghese, Neha; Huang, Po-Ssu; Pavlopoulos, Georgios A.; Kim, David E.; Kamisetty, Hetunandan; Kyrpides, Nikos C.; Baker, David

2017-01-01

Despite decades of work by structural biologists, there are still ~5200 protein families with unknown structure outside the range of comparative modeling. We show that Rosetta structure prediction guided by residue-residue contacts inferred from evolutionary information can accurately model proteins that belong to large families, and that metagenome sequence data more than triples the number of protein families with sufficient sequences for accurate modeling. We then integrate metagenome data, contact based structure matching and Rosetta structure calculations to generate models for 614 protein families with currently unknown structures; 206 are membrane proteins and 137 have folds not represented in the PDB. This approach provides the representative models for large protein families originally envisioned as the goal of the protein structure initiative at a fraction of the cost. PMID:28104891

Interface dynamics and crystal phase switching in GaAs nanowires

NASA Astrophysics Data System (ADS)

Jacobsson, Daniel; Panciera, Federico; Tersoff, Jerry; Reuter, Mark C.; Lehmann, Sebastian; Hofmann, Stephan; Dick, Kimberly A.; Ross, Frances M.

2016-03-01

Controlled formation of non-equilibrium crystal structures is one of the most important challenges in crystal growth. Catalytically grown nanowires are ideal systems for studying the fundamental physics of phase selection, and could lead to new electronic applications based on the engineering of crystal phases. Here we image gallium arsenide (GaAs) nanowires during growth as they switch between phases as a result of varying growth conditions. We find clear differences between the growth dynamics of the phases, including differences in interface morphology, step flow and catalyst geometry. We explain these differences, and the phase selection, using a model that relates the catalyst volume, the contact angle at the trijunction (the point at which solid, liquid and vapour meet) and the nucleation site of each new layer of GaAs. This model allows us to predict the conditions under which each phase should be observed, and use these predictions to design GaAs heterostructures. These results could apply to phase selection in other nanowire systems.

Periodic annealing of radiation damage in GaAs solar cells

NASA Technical Reports Server (NTRS)

Loo, R. Y.; Knechtli, R. C.; Kamath, G. S.

1980-01-01

Continuous annealing of GaAs solar cells is compared with periodic annealing to determine their relative effectiveness in minimizing proton radiation damage. It is concluded that continuous annealing of the cells in space at 150 C can effectively reduce the proton radiation damage to the GaAs solar cells. Periodic annealing is most effective if it can be initiated at relatively low fluences (approximating continuous annealing), especially if low temperatures of less than 200 C are to be used. If annealing is started only after the fluence of the damaging protons has accumulated to a high value 10 to the 11th power sq/pcm), effective annealing is still possible at relatively high temperatures. Finally, since electron radiation damage anneals even more easily than proton radiation damage, substantial improvements in GaAs solar cell life can be achieved by incorporating the proper annealing capabilities in solar panels for practical space missions where both electron and proton radiation damage have to be minimized.

Interface dynamics and crystal phase switching in GaAs nanowires.

PubMed

Jacobsson, Daniel; Panciera, Federico; Tersoff, Jerry; Reuter, Mark C; Lehmann, Sebastian; Hofmann, Stephan; Dick, Kimberly A; Ross, Frances M

2016-03-17

Controlled formation of non-equilibrium crystal structures is one of the most important challenges in crystal growth. Catalytically grown nanowires are ideal systems for studying the fundamental physics of phase selection, and could lead to new electronic applications based on the engineering of crystal phases. Here we image gallium arsenide (GaAs) nanowires during growth as they switch between phases as a result of varying growth conditions. We find clear differences between the growth dynamics of the phases, including differences in interface morphology, step flow and catalyst geometry. We explain these differences, and the phase selection, using a model that relates the catalyst volume, the contact angle at the trijunction (the point at which solid, liquid and vapour meet) and the nucleation site of each new layer of GaAs. This model allows us to predict the conditions under which each phase should be observed, and use these predictions to design GaAs heterostructures. These results could apply to phase selection in other nanowire systems.

Heterologous viral expression systems in fosmid vectors increase the functional analysis potential of metagenomic libraries.

PubMed

Terrón-González, L; Medina, C; Limón-Mortés, M C; Santero, E

2013-01-01

The extraordinary potential of metagenomic functional analyses to identify activities of interest present in uncultured microorganisms has been limited by reduced gene expression in surrogate hosts. We have developed vectors and specialized E. coli strains as improved metagenomic DNA heterologous expression systems, taking advantage of viral components that prevent transcription termination at metagenomic terminators. One of the systems uses the phage T7 RNA-polymerase to drive metagenomic gene expression, while the other approach uses the lambda phage transcription anti-termination protein N to limit transcription termination. A metagenomic library was constructed and functionally screened to identify genes conferring carbenicillin resistance to E. coli. The use of these enhanced expression systems resulted in a 6-fold increase in the frequency of carbenicillin resistant clones. Subcloning and sequence analysis showed that, besides β-lactamases, efflux pumps are not only able contribute to carbenicillin resistance but may in fact be sufficient by themselves to convey carbenicillin resistance.

GaSb thermophotovoltaic cells grown on GaAs by molecular beam epitaxy using interfacial misfit arrays

DOE Office of Scientific and Technical Information (OSTI.GOV)

Juang, Bor-Chau, E-mail: bcjuang@ucla.edu; Laghumavarapu, Ramesh B.; Foggo, Brandon J.

There exists a long-term need for foreign substrates on which to grow GaSb-based optoelectronic devices. We address this need by using interfacial misfit arrays to grow GaSb-based thermophotovoltaic cells directly on GaAs (001) substrates and demonstrate promising performance. We compare these cells to control devices grown on GaSb substrates to assess device properties and material quality. The room temperature dark current densities show similar characteristics for both cells on GaAs and on GaSb. Under solar simulation the cells on GaAs exhibit an open-circuit voltage of 0.121 V and a short-circuit current density of 15.5 mA/cm{sup 2}. In addition, the cells on GaAsmore » substrates maintain 10% difference in spectral response to those of the control cells over a large range of wavelengths. While the cells on GaSb substrates in general offer better performance than the cells on GaAs substrates, the cost-savings and scalability offered by GaAs substrates could potentially outweigh the reduction in performance. By further optimizing GaSb buffer growth on GaAs substrates, Sb-based compound semiconductors grown on GaAs substrates with similar performance to devices grown directly on GaSb substrates could be realized.« less

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

PubMed Central

Abubucker, Sahar; Segata, Nicola; Goll, Johannes; Schubert, Alyxandria M.; Izard, Jacques; Cantarel, Brandi L.; Rodriguez-Mueller, Beltran; Zucker, Jeremy; Thiagarajan, Mathangi; Henrissat, Bernard; White, Owen; Kelley, Scott T.; Methé, Barbara; Schloss, Patrick D.; Gevers, Dirk; Mitreva, Makedonka; Huttenhower, Curtis

2012-01-01

Microbial communities carry out the majority of the biochemical activity on the planet, and they play integral roles in processes including metabolism and immune homeostasis in the human microbiome. Shotgun sequencing of such communities' metagenomes provides information complementary to organismal abundances from taxonomic markers, but the resulting data typically comprise short reads from hundreds of different organisms and are at best challenging to assemble comparably to single-organism genomes. Here, we describe an alternative approach to infer the functional and metabolic potential of a microbial community metagenome. We determined the gene families and pathways present or absent within a community, as well as their relative abundances, directly from short sequence reads. We validated this methodology using a collection of synthetic metagenomes, recovering the presence and abundance both of large pathways and of small functional modules with high accuracy. We subsequently applied this method, HUMAnN, to the microbial communities of 649 metagenomes drawn from seven primary body sites on 102 individuals as part of the Human Microbiome Project (HMP). This provided a means to compare functional diversity and organismal ecology in the human microbiome, and we determined a core of 24 ubiquitously present modules. Core pathways were often implemented by different enzyme families within different body sites, and 168 functional modules and 196 metabolic pathways varied in metagenomic abundance specifically to one or more niches within the microbiome. These included glycosaminoglycan degradation in the gut, as well as phosphate and amino acid transport linked to host phenotype (vaginal pH) in the posterior fornix. An implementation of our methodology is available at http://huttenhower.sph.harvard.edu/humann. This provides a means to accurately and efficiently characterize microbial metabolic pathways and functional modules directly from high-throughput sequencing reads

Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing.

PubMed

Fang, Chao; Zhong, Huanzi; Lin, Yuxiang; Chen, Bing; Han, Mo; Ren, Huahui; Lu, Haorong; Luber, Jacob M; Xia, Min; Li, Wangsheng; Stein, Shayna; Xu, Xun; Zhang, Wenwei; Drmanac, Radoje; Wang, Jian; Yang, Huanming; Hammarström, Lennart; Kostic, Aleksandar D; Kristiansen, Karsten; Li, Junhua

2018-03-01

More extensive use of metagenomic shotgun sequencing in microbiome research relies on the development of high-throughput, cost-effective sequencing. Here we present a comprehensive evaluation of the performance of the new high-throughput sequencing platform BGISEQ-500 for metagenomic shotgun sequencing and compare its performance with that of 2 Illumina platforms. Using fecal samples from 20 healthy individuals, we evaluated the intra-platform reproducibility for metagenomic sequencing on the BGISEQ-500 platform in a setup comprising 8 library replicates and 8 sequencing replicates. Cross-platform consistency was evaluated by comparing 20 pairwise replicates on the BGISEQ-500 platform vs the Illumina HiSeq 2000 platform and the Illumina HiSeq 4000 platform. In addition, we compared the performance of the 2 Illumina platforms against each other. By a newly developed overall accuracy quality control method, an average of 82.45 million high-quality reads (96.06% of raw reads) per sample, with 90.56% of bases scoring Q30 and above, was obtained using the BGISEQ-500 platform. Quantitative analyses revealed extremely high reproducibility between BGISEQ-500 intra-platform replicates. Cross-platform replicates differed slightly more than intra-platform replicates, yet a high consistency was observed. Only a low percentage (2.02%-3.25%) of genes exhibited significant differences in relative abundance comparing the BGISEQ-500 and HiSeq platforms, with a bias toward genes with higher GC content being enriched on the HiSeq platforms. Our study provides the first set of performance metrics for human gut metagenomic sequencing data using BGISEQ-500. The high accuracy and technical reproducibility confirm the applicability of the new platform for metagenomic studies, though caution is still warranted when combining metagenomic data from different platforms.

Disruption of Higher Order DNA Structures in Friedreich’s Ataxia (GAA)n Repeats by PNA or LNA Targeting

PubMed Central

Bergquist, Helen; Rocha, Cristina S. J.; Álvarez-Asencio, Rubén; Nguyen, Chi-Hung; Rutland, Mark. W.; Smith, C. I. Edvard; Good, Liam; Nielsen, Peter E.; Zain, Rula

2016-01-01

Expansion of (GAA)n repeats in the first intron of the Frataxin gene is associated with reduced mRNA and protein levels and the development of Friedreich’s ataxia. (GAA)n expansions form non-canonical structures, including intramolecular triplex (H-DNA), and R-loops and are associated with epigenetic modifications. With the aim of interfering with higher order H-DNA (like) DNA structures within pathological (GAA)n expansions, we examined sequence-specific interaction of peptide nucleic acid (PNA) with (GAA)n repeats of different lengths (short: n=9, medium: n=75 or long: n=115) by chemical probing of triple helical and single stranded regions. We found that a triplex structure (H-DNA) forms at GAA repeats of different lengths; however, single stranded regions were not detected within the medium size pathological repeat, suggesting the presence of a more complex structure. Furthermore, (GAA)4-PNA binding of the repeat abolished all detectable triplex DNA structures, whereas (CTT)5-PNA did not. We present evidence that (GAA)4-PNA can invade the DNA at the repeat region by binding the DNA CTT strand, thereby preventing non-canonical-DNA formation, and that triplex invasion complexes by (CTT)5-PNA form at the GAA repeats. Locked nucleic acid (LNA) oligonucleotides also inhibited triplex formation at GAA repeat expansions, and atomic force microscopy analysis showed significant relaxation of plasmid morphology in the presence of GAA-LNA. Thus, by inhibiting disease related higher order DNA structures in the Frataxin gene, such PNA and LNA oligomers may have potential for discovery of drugs aiming at recovering Frataxin expression. PMID:27846236

Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs

PubMed Central

Eloe-Fadrosh, Emiley A.; Paez-Espino, David; Jarett, Jessica; Dunfield, Peter F.; Hedlund, Brian P.; Dekas, Anne E.; Grasby, Stephen E.; Brady, Allyson L.; Dong, Hailiang; Briggs, Brandon R.; Li, Wen-Jun; Goudeau, Danielle; Malmstrom, Rex; Pati, Amrita; Pett-Ridge, Jennifer; Rubin, Edward M.; Woyke, Tanja; Kyrpides, Nikos C.; Ivanova, Natalia N.

2016-01-01

Analysis of the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum (‘Candidatus Kryptonia') found exclusively in high-temperature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic ‘blind spot' because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestyle with conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery. PMID:26814032

Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs

DOE PAGES

Eloe-Fadrosh, Emiley A.; Paez-Espino, David; Jarett, Jessica; ...

2016-01-27

Analysis of the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum (' Candidatus Kryptonia') found exclusively in higherature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic 'blind spot' because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestylemore » with conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery.« less

Applications of metagenomics for industrial bioproducts

USDA-ARS?s Scientific Manuscript database

Recent progress in mining the rich genetic resource of non-culturable microbes has led to the discovery of new genes, enzymes, and natural products. The impact of metagenomics is witnessed in the development of commodity and fine chemicals, agrochemicals and pharmaceuticals where the benefit of enz...

Preparation of fosmid libraries and functional metagenomic analysis of microbial community DNA.

PubMed

Martínez, Asunción; Osburne, Marcia S

2013-01-01

One of the most important challenges in contemporary microbial ecology is to assign a functional role to the large number of novel genes discovered through large-scale sequencing of natural microbial communities that lack similarity to genes of known function. Functional screening of metagenomic libraries, that is, screening environmental DNA clones for the ability to confer an activity of interest to a heterologous bacterial host, is a promising approach for bridging the gap between metagenomic DNA sequencing and functional characterization. Here, we describe methods for isolating environmental DNA and constructing metagenomic fosmid libraries, as well as methods for designing and implementing successful functional screens of such libraries. © 2013 Elsevier Inc. All rights reserved.

Genovo: De Novo Assembly for Metagenomes

NASA Astrophysics Data System (ADS)

Laserson, Jonathan; Jojic, Vladimir; Koller, Daphne

Next-generation sequencing technologies produce a large number of noisy reads from the DNA in a sample. Metagenomics and population sequencing aim to recover the genomic sequences of the species in the sample, which could be of high diversity. Methods geared towards single sequence reconstruction are not sensitive enough when applied in this setting. We introduce a generative probabilistic model of read generation from environmental samples and present Genovo, a novel de novo sequence assembler that discovers likely sequence reconstructions under the model. A Chinese restaurant process prior accounts for the unknown number of genomes in the sample. Inference is made by applying a series of hill-climbing steps iteratively until convergence. We compare the performance of Genovo to three other short read assembly programs across one synthetic dataset and eight metagenomic datasets created using the 454 platform, the largest of which has 311k reads. Genovo's reconstructions cover more bases and recover more genes than the other methods, and yield a higher assembly score.

A comparison of GaAs and Si hybrid solar power systems

NASA Technical Reports Server (NTRS)

Heinbockel, J. H.; Roberts, A. S., Jr.

1977-01-01

Five different hybrid solar power systems using silicon solar cells to produce thermal and electric power are modeled and compared with a hybrid system using a GaAs cell. Among the indices determined are capital cost per unit electric power plus mechanical power, annual cost per unit electric energy, and annual cost per unit electric plus mechanical work. Current costs are taken to be $35,000/sq m for GaAs cells with an efficiency of 15% and $1000/sq m for Si cells with an efficiency of 10%. It is shown that hybrid systems can be competitive with existing methods of practical energy conversion. Limiting values for annual costs of Si and GaAs cells are calculated to be 10.3 cents/kWh and 6.8 cents/kWh, respectively. Results for both systems indicate that for a given flow rate there is an optimal operating condition for minimum cost photovoltaic output. For Si cell costs of $50/sq m optimal performance can be achieved at concentrations of about 10; for GaAs cells costing 1000/sq m, optimal performance can be obtained at concentrations of around 100. High concentration hybrid systems offer a distinct cost advantage over flat systems.

Taxonomic and functional metagenomic profiling of gastrointestinal tract microbiome of the farmed adult turbot (Scophthalmus maximus).

PubMed

Xing, Mengxin; Hou, Zhanhui; Yuan, Jianbo; Liu, Yuan; Qu, Yanmei; Liu, Bin

2013-12-01

Metagenomics combined with 16S rRNA gene sequence analyses was applied to unveil the taxonomic composition and functional diversity of the farmed adult turbot gastrointestinal (GI) microbiome. Proteobacteria and Firmicutes which existed in both GI content and mucus were dominated in the turbot GI microbiome. 16S rRNA gene sequence analyses also indicated that the turbot GI tract may harbor some bacteria which originated from associated seawater. Functional analyses indicated that the clustering-based subsystem and many metabolic subsystems were dominant in the turbot GI metagenome. Compared with other gut metagenomes, quorum sensing and biofilm formation was overabundant in the turbot GI metagenome. Genes associated with quorum sensing and biofilm formation were found in species within Vibrio, including Vibrio vulnificus, Vibrio cholerae and Vibrio parahaemolyticus. In farmed fish gut metagenomes, the stress response and protein folding subsystems were over-represented and several genes concerning antibiotic and heavy metal resistance were also detected. These data suggested that the turbot GI microbiome may be affected by human factors in aquaculture. Additionally, iron acquisition and the metabolism subsystem were more abundant in the turbot GI metagenome when compared with freshwater fish gut metagenome, suggesting that unique metabolic potential may be observed in marine animal GI microbiomes. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Basic mechanisms study for MIS solar cell structures on GaAs

NASA Technical Reports Server (NTRS)

Fonash, S. J.

1978-01-01

The solar cell structure examined is the MIS configuration on (n) GaAs. The metal room temperature oxide/(n) GaAs materials system was studied. Metals with electronegativities varying from 2.4 (Au) to 1.5 (Al) were used as the upper electrode. The thinnest metallization that did not interfere with the measurement techniques (by introducing essentially transmission line series resistance problems across a device) was used. Photovoltaic response was not optimized.

Chemical beam epitaxy of GaAs1-xNx using MMHy and DMHy precursors, modeled by ab initio study of GaAs(100) surfaces stability over As2, H2 and N2

NASA Astrophysics Data System (ADS)

Valencia, Hubert; Kangawa, Yoshihiro; Kakimoto, Koichi

2017-06-01

Using ab initio calculations, a simple model for GaAs1-xNx vapor-phase epitaxy on (100) surface of GaAs was created. By studying As2 and H2 molecules adsorptions and As/N atom substitutions on (100) GaAs surfaces, we obtain a relative stability diagram of all stable surfaces under varying As2, H2, and N2 conditions. We previously proved that this model could describe the vapor-phase epitaxy of GaAs1-x Nx with simple, fully decomposed, precursors. In this paper, we show that in more complex reaction conditions using monomethylhydrazine (MMHy), and dimethylhydrazine (DMHy), it is still possible to use our model to obtain an accurate description of the temperature and pressure stability domains for each surfaces, linked to chemical beam epitaxy (CBE) growth conditions. Moreover, the different N-incorporation regimes observed experimentally at different temperature can be explain and predict by our model. The use of MMHy and DMHy precursors can also be rationalized. Our model should then help to better understand the conditions needed to obtain an high quality GaAs1-xNx using vapor-phase epitaxy.

Photoelectrochemical Water Oxidation by GaAs Nanowire Arrays Protected with Atomic Layer Deposited NiO x Electrocatalysts

NASA Astrophysics Data System (ADS)

Zeng, Joy; Xu, Xiaoqing; Parameshwaran, Vijay; Baker, Jon; Bent, Stacey; Wong, H.-S. Philip; Clemens, Bruce

2018-02-01

Photoelectrochemical (PEC) hydrogen production makes possible the direct conversion of solar energy into chemical fuel. In this work, PEC photoanodes consisting of GaAs nanowire (NW) arrays were fabricated, characterized, and then demonstrated for the oxygen evolution reaction (OER). Uniform and periodic GaAs nanowire arrays were grown on a heavily n-doped GaAs substrates by metal-organic chemical vapor deposition selective area growth. The nanowire arrays were characterized using cyclic voltammetry and impedance spectroscopy in a non-aqueous electrochemical system using ferrocene/ferrocenium (Fc/Fc+) as a redox couple, and a maximum oxidation photocurrent of 11.1 mA/cm2 was measured. GaAs NW arrays with a 36 nm layer of nickel oxide (NiO x ) synthesized by atomic layer deposition were then used as photoanodes to drive the OER. In addition to acting as an electrocatalyst, the NiO x layer served to protect the GaAs NWs from oxidative corrosion. Using this strategy, GaAs NW photoanodes were successfully used for the oxygen evolution reaction. This is the first demonstration of GaAs NW arrays for effective OER, and the fabrication and protection strategy developed in this work can be extended to study any other nanostructured semiconductor materials systems for electrochemical solar energy conversion.

BeerDeCoded: the open beer metagenome project.

PubMed

Sobel, Jonathan; Henry, Luc; Rotman, Nicolas; Rando, Gianpaolo

2017-01-01

Next generation sequencing has radically changed research in the life sciences, in both academic and corporate laboratories. The potential impact is tremendous, yet a majority of citizens have little or no understanding of the technological and ethical aspects of this widespread adoption. We designed BeerDeCoded as a pretext to discuss the societal issues related to genomic and metagenomic data with fellow citizens, while advancing scientific knowledge of the most popular beverage of all. In the spirit of citizen science, sample collection and DNA extraction were carried out with the participation of non-scientists in the community laboratory of Hackuarium, a not-for-profit organisation that supports unconventional research and promotes the public understanding of science. The dataset presented herein contains the targeted metagenomic profile of 39 bottled beers from 5 countries, based on internal transcribed spacer (ITS) sequencing of fungal species. A preliminary analysis reveals the presence of a large diversity of wild yeast species in commercial brews. With this project, we demonstrate that coupling simple laboratory procedures that can be carried out in a non-professional environment with state-of-the-art sequencing technologies and targeted metagenomic analyses, can lead to the detection and identification of the microbial content in bottled beer.

BeerDeCoded: the open beer metagenome project

PubMed Central

Sobel, Jonathan; Henry, Luc; Rotman, Nicolas; Rando, Gianpaolo

2017-01-01

Next generation sequencing has radically changed research in the life sciences, in both academic and corporate laboratories. The potential impact is tremendous, yet a majority of citizens have little or no understanding of the technological and ethical aspects of this widespread adoption. We designed BeerDeCoded as a pretext to discuss the societal issues related to genomic and metagenomic data with fellow citizens, while advancing scientific knowledge of the most popular beverage of all. In the spirit of citizen science, sample collection and DNA extraction were carried out with the participation of non-scientists in the community laboratory of Hackuarium, a not-for-profit organisation that supports unconventional research and promotes the public understanding of science. The dataset presented herein contains the targeted metagenomic profile of 39 bottled beers from 5 countries, based on internal transcribed spacer (ITS) sequencing of fungal species. A preliminary analysis reveals the presence of a large diversity of wild yeast species in commercial brews. With this project, we demonstrate that coupling simple laboratory procedures that can be carried out in a non-professional environment with state-of-the-art sequencing technologies and targeted metagenomic analyses, can lead to the detection and identification of the microbial content in bottled beer. PMID:29123645

Monolithic optical integrated control circuitry for GaAs MMIC-based phased arrays

NASA Technical Reports Server (NTRS)

Bhasin, K. B.; Ponchak, G. E.; Kascak, T. J.

1985-01-01

Gallium arsenide (GaAs) monolithic microwave integrated circuits (MMIC's) show promise in phased-array antenna applications for future space communications systems. Their efficient usage will depend on the control of amplitude and phase signals for each MMIC element in the phased array and in the low-loss radiofrequency feed. For a phased array contining several MMIC elements a complex system is required to control and feed each element. The characteristics of GaAs MMIC's for 20/30-GHz phased-array systems are discussed. The optical/MMIC interface and the desired characteristics of optical integrated circuits (OIC's) for such an interface are described. Anticipated fabrication considerations for eventual full monolithic integration of optical integrated circuits with MMIC's on a GaAs substrate are presented.

Nitride surface passivation of GaAs nanowires: impact on surface state density.

PubMed

Alekseev, Prokhor A; Dunaevskiy, Mikhail S; Ulin, Vladimir P; Lvova, Tatiana V; Filatov, Dmitriy O; Nezhdanov, Alexey V; Mashin, Aleksander I; Berkovits, Vladimir L

2015-01-14

Surface nitridation by hydrazine-sulfide solution, which is known to produce surface passivation of GaAs crystals, was applied to GaAs nanowires (NWs). We studied the effect of nitridation on conductivity and microphotoluminescence (μ-PL) of individual GaAs NWs using conductive atomic force microscopy (CAFM) and confocal luminescent microscopy (CLM), respectively. Nitridation is found to produce an essential increase in the NW conductivity and the μ-PL intensity as well evidence of surface passivation. Estimations show that the nitride passivation reduces the surface state density by a factor of 6, which is of the same order as that found for GaAs/AlGaAs nanowires. The effects of the nitride passivation are also stable under atmospheric ambient conditions for six months.

Metagenomics, metaMicrobesOnline and Kbase Data Integration (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Dehal, Paramvir

2018-02-06

Berkeley Lab's Paramvir Dehal on "Managing and Storing large Datasets in MicrobesOnline, metaMicrobesOnline and the DOE Knowledgebase" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Soil Bacterial Community Shifts after Chitin Enrichment: An Integrative Metagenomic Approach

PubMed Central

Jacquiod, Samuel; Franqueville, Laure; Cécillon, Sébastien; M. Vogel, Timothy; Simonet, Pascal

2013-01-01

Chitin is the second most produced biopolymer on Earth after cellulose. Chitin degrading enzymes are promising but untapped sources for developing novel industrial biocatalysts. Hidden amongst uncultivated micro-organisms, new bacterial enzymes can be discovered and exploited by metagenomic approaches through extensive cloning and screening. Enrichment is also a well-known strategy, as it allows selection of organisms adapted to feed on a specific compound. In this study, we investigated how the soil bacterial community responded to chitin enrichment in a microcosm experiment. An integrative metagenomic approach coupling phylochips and high throughput shotgun pyrosequencing was established in order to assess the taxonomical and functional changes in the soil bacterial community. Results indicate that chitin enrichment leads to an increase of Actinobacteria, γ-proteobacteria and β-proteobacteria suggesting specific selection of chitin degrading bacteria belonging to these classes. Part of enriched bacterial genera were not yet reported to be involved in chitin degradation, like the members from the Micrococcineae sub-order (Actinobacteria). An increase of the observed bacterial diversity was noticed, with detection of specific genera only in chitin treated conditions. The relative proportion of metagenomic sequences related to chitin degradation was significantly increased, even if it represents only a tiny fraction of the sequence diversity found in a soil metagenome. PMID:24278158

High purity low dislocation GaAs single crystals

NASA Technical Reports Server (NTRS)

Chen, R. T.; Holmes, D. E.; Kirkpatrick, C. G.

1982-01-01

Recent advances in GaAs bulk crystal growth using the LEC (liquid encapsulated Czochralski) technique are described. The dependence of the background impurity concentration and the dislocation density distribution on the materials synthesis and growth conditions were investigated. Background impurity concentrations as low as 4 x 10 to the 15th power were observed in undoped LEC GaAs. The dislocation density in selected regions of individual ingots was very low, below the 3000 cm .3000/sq cm threshold. The average dislocation density over a large annular ring on the wafers fell below the 10000/sq cm level for 3 inch diameter ingots. The diameter control during the program advanced to a diameter variation along a 3 inch ingot less than 2 mm.

Insertion of GaAs MMICs into EW systems

NASA Astrophysics Data System (ADS)

Schineller, E. R.; Pospishil, A.; Grzyb, J.

1989-09-01

Development activities on a microwave/mm-wave monolithic IC (MIMIC) program are described, as well as the methodology for inserting these GaAs IC chips into several EW systems. The generic EW chip set developed on the MIMIC program consists of 23 broadband chip types, including amplifiers, oscillators, mixers, switches, variable attenuators, power dividers, and power combiners. These chips are being designed for fabrication using the multifunction self-aligned gate process. The benefits from GaAs IC insertion are quantified by a comparison of hardware units fabricated with existing MIC and digital ECL technology and the same units manufactured with monolithic technology. It is found that major improvements in cost, reliability, size, weight, and performance can be realized. Examples illustrating the methodology for technology insertion are presented.

Highly efficient single-junction GaAs thin-film solar cell on flexible substrate.

PubMed

Moon, Sunghyun; Kim, Kangho; Kim, Youngjo; Heo, Junseok; Lee, Jaejin

2016-07-20

There has been much interest in developing a thin-film solar cell because it is lightweight and flexible. The GaAs thin-film solar cell is a top contender in the thin-film solar cell market in that it has a high power conversion efficiency (PCE) compared to that of other thin-film solar cells. There are two common structures for the GaAs solar cell: n (emitter)-on-p (base) and p-on-n. The former performs better due to its high collection efficiency because the electron diffusion length of the p-type base region is much longer than the hole diffusion length of the n-type base region. However, it has been limited to fabricate highly efficient n-on-p single-junction GaAs thin film solar cell on a flexible substrate due to technical obstacles. We investigated a simple and fast epitaxial lift-off (ELO) method that uses a stress originating from a Cr/Au bilayer on a 125-μm-thick flexible substrate. A metal combination of AuBe/Pt/Au is employed as a new p-type ohmic contact with which an n-on-p single-junction GaAs thin-film solar cell on flexible substrate was successfully fabricated. The PCE of the fabricated single-junction GaAs thin-film solar cells reached 22.08% under air mass 1.5 global illumination.

SEMICONDUCTOR TECHNOLOGY: GaAs surface wet cleaning by a novel treatment in revolving ultrasonic atomization solution

NASA Astrophysics Data System (ADS)

Zaijin, Li; Liming, Hu; Ye, Wang; Ye, Yang; Hangyu, Peng; Jinlong, Zhang; Li, Qin; Yun, Liu; Lijun, Wang

2010-03-01

A novel process for the wet cleaning of GaAs surface is presented. It is designed for technological simplicity and minimum damage generated within the GaAs surface. It combines GaAs cleaning with three conditions consisting of (1) removal of thermodynamically unstable species and (2) surface oxide layers must be completely removed after thermal cleaning, and (3) a smooth surface must be provided. Revolving ultrasonic atomization technology is adopted in the cleaning process. At first impurity removal is achieved by organic solvents; second NH4OH:H2O2:H2O = 1:1:10 solution and HCl: H2O2:H2O = 1:1:20 solution in succession to etch a very thin GaAs layer, the goal of the step is removing metallic contaminants and forming a very thin oxidation layer on the GaAs wafer surface; NH4OH:H2O = 1:5 solution is used as the removed oxide layers in the end. The effectiveness of the process is demonstrated by the operation of the GaAs wafer. Characterization of the oxide composition was carried out by X-ray photoelectron spectroscopy. Metal-contamination and surface morphology was observed by a total reflection X-ray fluorescence spectroscopy and atomic force microscope. The research results show that the cleaned surface is without contamination or metal contamination. Also, the GaAs substrates surface is very smooth for epitaxial growth using the rotary ultrasonic atomization technology.

Radiation testing of GaAs on CRRES and LIPS experiment

NASA Technical Reports Server (NTRS)

Trumble, T. M.; Masloski, K.

1984-01-01

The radiation damage of solar cells has become a prime concern to the U.S. Air Force due to longer satellite lifetime requirements. Flight experiments were undertaken on the Navy Living Plume Shield (LPS) satellite and the NASA/Air Force Combined Release and Radiation Effects Satellite (CRRES) to complement existing radiation testing. Each experiment, the rationale behind it, and its approach and status are presented. The effect of space radiation on gallium arsenide (GaAs) solar cells was the central parameter investigated. Specifications of the GaAs solar cells are given.

Core-level photoemission investigation of atomic-fluorine adsorption on GaAs(110)

NASA Astrophysics Data System (ADS)

McLean, A. B.; Terminello, L. J.; McFeely, F. R.

1989-12-01

The adsorption of atomic F on the cleaved GaAs(110) surface has been studied with use of high-resolution core-level photoelectron spectroscopy by exposing the GaAs(110) surfaces to XeF2, which adsorbs dissociatively, leaving atomic F behind. This surface reaction produces two chemically shifted components in the Ga 3d core-level emission which are attributed to an interfacial monofluoride and a stable trifluoride reaction product, respectively. The As 3d core level develops only one chemically shifted component and from its exposure-dependent behavior it is attributed to an interfacial monofluoride. Least-squares analysis of the core-level line shapes revealed that (i) the F bonds to both the anion and the cation , (ii) the GaF3 component (characteristic of strong interfacial reaction) and the surface core-level shifted component (characteristic of a well ordered, atomically clean surface) are present together over a relatively large range of XeF2 exposures, and (iii) it is the initial disruption of the GaAs(110) surface that is the rate-limiting step in this surface reaction. These results are compared with similar studies of Cl and O adsorption on GaAs(110).

Self-catalyzed GaAs nanowires on silicon by hydride vapor phase epitaxy.

PubMed

Dong, Zhenning; André, Yamina; Dubrovskii, Vladimir G; Bougerol, Catherine; Leroux, Christine; Ramdani, Mohammed R; Monier, Guillaume; Trassoudaine, Agnès; Castelluci, Dominique; Gil, Evelyne

2017-03-24

Gold-free GaAs nanowires on silicon substrates can pave the way for monolithic integration of photonic nanodevices with silicon electronic platforms. It is extensively documented that the self-catalyzed approach works well in molecular beam epitaxy but is much more difficult to implement in vapor phase epitaxies. Here, we report the first gallium-catalyzed hydride vapor phase epitaxy growth of long (more than 10 μm) GaAs nanowires on Si(111) substrates with a high integrated growth rate up to 60 μm h -1 and pure zincblende crystal structure. The growth is achieved by combining a low temperature of 600 °C with high gaseous GaCl/As flow ratios to enable dechlorination and formation of gallium droplets. GaAs nanowires exhibit an interesting bottle-like shape with strongly tapered bases, followed by straight tops with radii as small as 5 nm. We present a model that explains the peculiar growth mechanism in which the gallium droplets nucleate and rapidly swell on the silicon surface but then are gradually consumed to reach a stationary size. Our results unravel the necessary conditions for obtaining gallium-catalyzed GaAs nanowires by vapor phase epitaxy techniques.

Enhanced second-harmonic generation from resonant GaAs gratings.

PubMed

de Ceglia, D; D'Aguanno, G; Mattiucci, N; Vincenti, M A; Scalora, M

2011-03-01

We theoretically study second harmonic generation in nonlinear, GaAs gratings. We find large enhancement of conversion efficiency when the pump field excites the guided mode resonances of the grating. Under these circumstances the spectrum near the pump wavelength displays sharp resonances characterized by dramatic enhancements of local fields and favorable conditions for second-harmonic generation, even in regimes of strong linear absorption at the harmonic wavelength. In particular, in a GaAs grating pumped at 1064 nm, we predict second-harmonic conversion efficiencies approximately 5 orders of magnitude larger than conversion rates achievable in either bulk or etalon structures of the same material.

Scanning microwave microscopy applied to semiconducting GaAs structures

NASA Astrophysics Data System (ADS)

Buchter, Arne; Hoffmann, Johannes; Delvallée, Alexandra; Brinciotti, Enrico; Hapiuk, Dimitri; Licitra, Christophe; Louarn, Kevin; Arnoult, Alexandre; Almuneau, Guilhem; Piquemal, François; Zeier, Markus; Kienberger, Ferry

2018-02-01

A calibration algorithm based on one-port vector network analyzer (VNA) calibration for scanning microwave microscopes (SMMs) is presented and used to extract quantitative carrier densities from a semiconducting n-doped GaAs multilayer sample. This robust and versatile algorithm is instrument and frequency independent, as we demonstrate by analyzing experimental data from two different, cantilever- and tuning fork-based, microscope setups operating in a wide frequency range up to 27.5 GHz. To benchmark the SMM results, comparison with secondary ion mass spectrometry is undertaken. Furthermore, we show SMM data on a GaAs p-n junction distinguishing p- and n-doped layers.

Theoretical and experimental study of highly textured GaAs on silicon using a graphene buffer layer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alaskar, Yazeed; Arafin, Shamsul; Lin, Qiyin

2015-09-01

A novel heteroepitaxial growth technique, quasi-van der Waals epitaxy, promises the ability to deposit three-dimensional GaAs materials on silicon using two-dimensional graphene as a buffer layer by overcoming the lattice and thermal expansion mismatch. In this study, density functional theory (DFT) simulations were performed to understand the interactions at the GaAs/graphene hetero-interface as well as the growth orientations of GaAs on graphene. To develop a better understanding of the molecular beam epitaxy-grown GaAs films on graphene, samples were characterized by x-ray diffraction (..theta..-2..theta.. scan, ..omega..-scan, grazing incidence XRD and pole figure measurement) and transmission electron microscopy. The realizations of smoothmore » GaAs films with a strong (111) oriented fiber-texture on graphene/silicon using this deposition technique are a milestone towards an eventual demonstration of the epitaxial growth of GaAs on silicon, which is necessary for integrated photonics application.« less

Reflection high energy electron diffraction study of nitrogen plasma interactions with a GaAs (100) surface

NASA Astrophysics Data System (ADS)

Hauenstein, R. J.; Collins, D. A.; Cai, X. P.; O'Steen, M. L.; McGill, T. C.

1995-05-01

Effect of a nitrogen electron-cyclotron-resonance (ECR) microwave plasma on near-surface composition, crystal structure, and morphology of the As-stabilized GaAs (100) surface is investigated with the use of digitally image-processed in situ reflection high energy electron diffraction. Nitridation is performed on molecular beam epitaxially (MBE) grown GaAs surfaces near 600 °C under typical conditions for ECR microwave plasma-assisted MBE growth of GaN films on GaAs. Brief plasma exposures (≊3-5 s) are shown to result in a specular, coherently strained, relatively stable, GaN film approximately one monolayer in thickness, which can be commensurately overgrown with GaAs while longer exposures (up to 1 min) result in incommensurate zincblende epitaxial GaN island structures. Specular and nonspecular film formations are explained in terms of N-for-As surface and subsurface anion exchange reactions, respectively. Commensurate growth of ultrathin buried GaN layers in GaAs is achieved.

Simultaneous virus identification and characterization of severe unexplained pneumonia cases using a metagenomics sequencing technique.

PubMed

Zou, Xiaohui; Tang, Guangpeng; Zhao, Xiang; Huang, Yan; Chen, Tao; Lei, Mingyu; Chen, Wenbing; Yang, Lei; Zhu, Wenfei; Zhuang, Li; Yang, Jing; Feng, Zhaomin; Wang, Dayan; Wang, Dingming; Shu, Yuelong

2017-03-01

Many viruses can cause respiratory diseases in humans. Although great advances have been achieved in methods of diagnosis, it remains challenging to identify pathogens in unexplained pneumonia (UP) cases. In this study, we applied next-generation sequencing (NGS) technology and a metagenomic approach to detect and characterize respiratory viruses in UP cases from Guizhou Province, China. A total of 33 oropharyngeal swabs were obtained from hospitalized UP patients and subjected to NGS. An unbiased metagenomic analysis pipeline identified 13 virus species in 16 samples. Human rhinovirus C was the virus most frequently detected and was identified in seven samples. Human measles virus, adenovirus B 55 and coxsackievirus A10 were also identified. Metagenomic sequencing also provided virus genomic sequences, which enabled genotype characterization and phylogenetic analysis. For cases of multiple infection, metagenomic sequencing afforded information regarding the quantity of each virus in the sample, which could be used to evaluate each viruses' role in the disease. Our study highlights the potential of metagenomic sequencing for pathogen identification in UP cases.

Fermi level pinning at epitaxial Si on GaAs(100) interfaces

NASA Astrophysics Data System (ADS)

Silberman, J. A.; de Lyon, T. J.; Woodall, J. M.

1991-12-01

GaAs Schottky barrier contacts and metal-insulator-semiconductor structures that include thin epitaxial Si interfacial layers operate in a manner consistent with an unpinned Fermi level at the GaAs interface. These findings raise the question of whether this effect is an intrinsic property of the epitaxial GaAs(100)-Si interface. We have used x-ray photoemission spectroscopy to monitor the Fermi level position during in situ growth of thin epitaxial Si layers. In particular, films formed on heavily doped n- and p-type substrates were compared so as to use the large depletion layer fields available with high impurity concentration as a field-effect probe of the interface state density. The results demonstrate that epitaxial bonding at the interface alone is insufficient to eliminate Fermi level pinning, indicating that other mechanisms affect the interfacial charge balance in the devices that utilize Si interlayers.

Sequence-based screening for self-sufficient P450 monooxygenase from a metagenome library.

PubMed

Kim, B S; Kim, S Y; Park, J; Park, W; Hwang, K Y; Yoon, Y J; Oh, W K; Kim, B Y; Ahn, J S

2007-05-01

Cytochrome P450 monooxygenases (CYPs) are useful catalysts for oxidation reactions. Self-sufficient CYPs harbour a reductive domain covalently connected to a P450 domain and are known for their robust catalytic activity with great potential as biocatalysts. In an effort to expand genetic sources of self-sufficient CYPs, we devised a sequence-based screening system to identify them in a soil metagenome. We constructed a soil metagenome library and performed sequence-based screening for self-sufficient CYP genes. A new CYP gene, syk181, was identified from the metagenome library. Phylogenetic analysis revealed that SYK181 formed a distinct phylogenic line with 46% amino-acid-sequence identity to CYP102A1 which has been extensively studied as a fatty acid hydroxylase. The heterologously expressed SYK181 showed significant hydroxylase activity towards naphthalene and phenanthrene as well as towards fatty acids. Sequence-based screening of metagenome libraries is expected to be a useful approach for searching self-sufficient CYP genes. The translated product of syk181 shows self-sufficient hydroxylase activity towards fatty acids and aromatic compounds. SYK181 is the first self-sufficient CYP obtained directly from a metagenome library. The genetic and biochemical information on SYK181 are expected to be helpful for engineering self-sufficient CYPs with broader catalytic activities towards various substrates, which would be useful for bioconversion of natural products and biodegradation of organic chemicals.

GaAs VLSI for aerospace electronics

NASA Technical Reports Server (NTRS)

Larue, G.; Chan, P.

1990-01-01

Advanced aerospace electronics systems require high-speed, low-power, radiation-hard, digital components for signal processing, control, and communication applications. GaAs VLSI devices provide a number of advantages over silicon devices including higher carrier velocities, ability to integrate with high performance optical devices, and high-resistivity substrates that provide very short gate delays, good isolation, and tolerance to many forms of radiation. However, III-V technologies also have disadvantages, such as lower yield compared to silicon MOS technology. Achieving very large scale integration (VLSI) is particularly important for fast complex systems. At very short gate delays (less than 100 ps), chip-to-chip interconnects severely degrade circuit clock rates. Complex systems, therefore, benefit greatly when as many gates as possible are placed on a single chip. To fully exploit the advantages of GaAs circuits, attention must be focused on achieving high integration levels by reducing power dissipation, reducing the number of devices per logic function, and providing circuit designs that are more tolerant to process and environmental variations. In addition, adequate noise margin must be maintained to ensure a practical yield.

Functional Metagenomic Investigations of Microbial Communities in a Shallow-Sea Hydrothermal System

PubMed Central

Tang, Kai; Liu, Keshao; Jiao, Nianzhi; Zhang, Yao; Chen, Chen-Tung Arthur

2013-01-01

Little is known about the functional capability of microbial communities in shallow-sea hydrothermal systems (water depth of <200 m). This study analyzed two high-throughput pyrosequencing metagenomic datasets from the vent and the surface water in the shallow-sea hydrothermal system offshore NE Taiwan. This system exhibited distinct geochemical parameters. Metagenomic data revealed that the vent and the surface water were predominated by Epsilonproteobacteria (Nautiliales-like organisms) and Gammaproteobacteria ( Thiomicrospira -like organisms), respectively. A significant difference in microbial carbon fixation and sulfur metabolism was found between the vent and the surface water. The chemoautotrophic microorganisms in the vent and in the surface water might possess the reverse tricarboxylic acid cycle and the Calvin−Bassham−Benson cycle for carbon fixation in response to carbon dioxide highly enriched in the environment, which is possibly fueled by geochemical energy with sulfur and hydrogen. Comparative analyses of metagenomes showed that the shallow-sea metagenomes contained some genes similar to those present in other extreme environments. This study may serve as a basis for deeply understanding the genetic network and functional capability of the microbial members of shallow-sea hydrothermal systems. PMID:23940820

Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics

PubMed Central

Eiler, Alexander; Zaremba-Niedzwiedzka, Katarzyna; Martínez-García, Manuel; McMahon, Katherine D; Stepanauskas, Ramunas; Andersson, Siv G E; Bertilsson, Stefan

2014-01-01

Little is known about the diversity and structuring of freshwater microbial communities beyond the patterns revealed by tracing their distribution in the landscape with common taxonomic markers such as the ribosomal RNA. To address this gap in knowledge, metagenomes from temperate lakes were compared to selected marine metagenomes. Taxonomic analyses of rRNA genes in these freshwater metagenomes confirm the previously reported dominance of a limited subset of uncultured lineages of freshwater bacteria, whereas Archaea were rare. Diversification into marine and freshwater microbial lineages was also reflected in phylogenies of functional genes, and there were also significant differences in functional beta-diversity. The pathways and functions that accounted for these differences are involved in osmoregulation, active transport, carbohydrate and amino acid metabolism. Moreover, predicted genes orthologous to active transporters and recalcitrant organic matter degradation were more common in microbial genomes from oligotrophic versus eutrophic lakes. This comparative metagenomic analysis allowed us to formulate a general hypothesis that oceanic- compared with freshwater-dwelling microorganisms, invest more in metabolism of amino acids and that strategies of carbohydrate metabolism differ significantly between marine and freshwater microbial communities. PMID:24118837

A new structure for comparing surface passivation materials of GaAs solar cells

NASA Technical Reports Server (NTRS)

Desalvo, Gregory C.; Barnett, Allen M.

1989-01-01

The surface recombination velocity (S sub rec) for bare GaAs is typically as high as 10 to the 6th power to 10 to the 7th power cm/sec, which dramatically lowers the efficiency of GaAs solar cells. Early attempts to circumvent this problem by making an ultra thin junction (xj less than .1 micron) proved unsuccessful when compared to lowering S sub rec by surface passivation. Present day GaAs solar cells use an GaAlAs window layer to passivate the top surface. The advantages of GaAlAs in surface passivation are its high bandgap energy and lattice matching to GaAs. Although GaAlAs is successful in reducing the surface recombination velocity, it has other inherent problems of chemical instability (Al readily oxidizes) and ohmic contact formation. The search for new, more stable window layer materials requires a means to compare their surface passivation ability. Therefore, a device structure is needed to easily test the performance of different passivating candidates. Such a test device is described.

Covalent attachment of TAT peptides and thiolated alkyl molecules on GaAs surfaces.

PubMed

Cho, Youngnam; Ivanisevic, Albena

2005-07-07

Four TAT peptide fragments were used to functionalize GaAs surfaces by adsorption from solution. In addition, two well-studied alkylthiols, mercaptohexadecanoic acid (MHA) and 1-octadecanethiol (ODT) were utilized as references to understand the structure of the TAT peptide monolayer on GaAs. The different sequences of TAT peptides were employed in recognition experiments where a synthetic RNA sequence was tested to verify the specific interaction with the TAT peptide. The modified GaAs surfaces were characterized by atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and Fourier transform infrared reflection absorption spectroscopy (FT-IRRAS). AFM studies were used to compare the surface roughness before and after functionalization. XPS allowed us to characterize the chemical composition of the GaAs surface and conclude that the monolayers composed of different sequences of peptides have similar surface chemistries. Finally, FT-IRRAS experiments enabled us to deduce that the TAT peptide monolayers have a fairly ordered and densely packed alkyl chain structure. The recognition experiments showed preferred interaction of the RNA sequence toward peptides with high arginine content.

Structures, Properties and Defects of SrTiO3/GaAs Hetero-interfaces

NASA Astrophysics Data System (ADS)

Hong, Liang; Bhatnagar, Kunal; Droopad, Ravi; Öğüt, Serdar; Klie, Robert

SrTiO3 thin film can be epitaxially grown on GaAs substrate and used as a platform for growing other oxides to create functional metal-oxide-semiconductor devices, where a high-quality SrTiO3/GaAs interface is essential. We studied the structural and electronic properties of SrTiO3/GaAs hetero-interfaces at atomic level using scanning transmission electron microscopy and first-principles calculations. Our results suggest the preferred termination of GaAs (001) is significantly dependent on the oxygen concentration in the first oxide layer. The favorable interface structure is characterized as oxygen-deficient SrO in contact with arsenic and is observed in both experiment and simulation. The electronic properties are calculated and found to be tunable by interfacial defects such as oxygen, gallium and arsenic vacancies. This work was supported by the National Science Foundation (Grant No. DMR-1408427). This work made use of instruments in the Electron Microscopy Service and the High Performance Computing Clusters at University of Illinois at Chicago.

Introduction to Metagenomics at DOE JGI (Opening Remarks for the Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Kyrpides, Nikos [DOE JGI

2018-05-30

After a quick introduction by DOE JGI Director Eddy Rubin, DOE JGI's Nikos Kyrpides delivers the opening remarks at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Mining the metagenome of activated biomass of an industrial wastewater treatment plant by a novel method.

PubMed

Sharma, Nandita; Tanksale, Himgouri; Kapley, Atya; Purohit, Hemant J

2012-12-01

Metagenomic libraries herald the era of magnifying the microbial world, tapping into the vast metabolic potential of uncultivated microbes, and enhancing the rate of discovery of novel genes and pathways. In this paper, we describe a method that facilitates the extraction of metagenomic DNA from activated sludge of an industrial wastewater treatment plant and its use in mining the metagenome via library construction. The efficiency of this method was demonstrated by the large representation of the bacterial genome in the constructed metagenomic libraries and by the functional clones obtained. The BAC library represented 95.6 times the bacterial genome, while, the pUC library represented 41.7 times the bacterial genome. Twelve clones in the BAC library demonstrated lipolytic activity, while four clones demonstrated dioxygenase activity. Four clones in pUC library tested positive for cellulase activity. This method, using FTA cards, not only can be used for library construction, but can also store the metagenome at room temperature.

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.

PubMed

Nielsen, H Bjørn; Almeida, Mathieu; Juncker, Agnieszka Sierakowska; Rasmussen, Simon; Li, Junhua; Sunagawa, Shinichi; Plichta, Damian R; Gautier, Laurent; Pedersen, Anders G; Le Chatelier, Emmanuelle; Pelletier, Eric; Bonde, Ida; Nielsen, Trine; Manichanh, Chaysavanh; Arumugam, Manimozhiyan; Batto, Jean-Michel; Quintanilha Dos Santos, Marcelo B; Blom, Nikolaj; Borruel, Natalia; Burgdorf, Kristoffer S; Boumezbeur, Fouad; Casellas, Francesc; Doré, Joël; Dworzynski, Piotr; Guarner, Francisco; Hansen, Torben; Hildebrand, Falk; Kaas, Rolf S; Kennedy, Sean; Kristiansen, Karsten; Kultima, Jens Roat; Léonard, Pierre; Levenez, Florence; Lund, Ole; Moumen, Bouziane; Le Paslier, Denis; Pons, Nicolas; Pedersen, Oluf; Prifti, Edi; Qin, Junjie; Raes, Jeroen; Sørensen, Søren; Tap, Julien; Tims, Sebastian; Ussery, David W; Yamada, Takuji; Renault, Pierre; Sicheritz-Ponten, Thomas; Bork, Peer; Wang, Jun; Brunak, Søren; Ehrlich, S Dusko

2014-08-01

Most current approaches for analyzing metagenomic data rely on comparisons to reference genomes, but the microbial diversity of many environments extends far beyond what is covered by reference databases. De novo segregation of complex metagenomic data into specific biological entities, such as particular bacterial strains or viruses, remains a largely unsolved problem. Here we present a method, based on binning co-abundant genes across a series of metagenomic samples, that enables comprehensive discovery of new microbial organisms, viruses and co-inherited genetic entities and aids assembly of microbial genomes without the need for reference sequences. We demonstrate the method on data from 396 human gut microbiome samples and identify 7,381 co-abundance gene groups (CAGs), including 741 metagenomic species (MGS). We use these to assemble 238 high-quality microbial genomes and identify affiliations between MGS and hundreds of viruses or genetic entities. Our method provides the means for comprehensive profiling of the diversity within complex metagenomic samples.

Accelerated GaAs growth through MOVPE for low-cost PV applications

NASA Astrophysics Data System (ADS)

Ubukata, Akinori; Sodabanlu, Hassanet; Watanabe, Kentaroh; Koseki, Shuichi; Yano, Yoshiki; Tabuchi, Toshiya; Sugaya, Takeyoshi; Matsumoto, Koh; Nakano, Yoshiaki; Sugiyama, Masakazu

2018-05-01

The high growth rate of epitaxial GaAs was investigated using a novel horizontal metalorganic vapor phase epitaxy (MOVPE) reactor, from the point of view of realizing low-cost photovoltaic (PV) solar cells. The GaAs growth rate exhibited an approximately linear relationship with the amount of trimethylgalium (TMGa) supplied, up to a rate of 90 μm/h. The distribution of growth rate was observed for a two-inch wafer, along the flow direction, and the normalized profile of the distribution was found to be independent of the precursor input, from 20 to 70 μm/h. These tendencies indicated that significant parasitic prereaction did not occur in the gaseous phase, for this range of growth rate. GaAs p-n single-junction solar cells were successfully fabricated at growth rates of 20, 60, and 80 μm/h. The conversion efficiency of the cell grown at 80 μm/h was comparable to that of the 20 μm/h cell, indicating the good quality and properties of GaAs. The epitaxial growth exhibited good uniformity, as evidenced by the uniformity of the cell performance across the wafer, from the center to the edge. The result indicated the potential of high-throughput MOVPE for low-cost production, not only for PV devices but also for other semiconductor applications.

Divacancy complexes induced by Cu diffusion in Zn-doped GaAs

NASA Astrophysics Data System (ADS)

Elsayed, M.; Krause-Rehberg, R.; Korff, B.; Ratschinski, I.; Leipner, H. S.

2013-08-01

Positron annihilation spectroscopy was applied to investigate the nature and thermal behavior of defects induced by Cu diffusion in Zn-doped p-type GaAs crystals. Cu atoms were intentionally introduced in the GaAs lattice through thermally activated diffusion from a thin Cu capping layer at 1100 °C under defined arsenic vapor pressure. During isochronal annealing of the obtained Cu-diffused GaAs in the temperature range of 450-850 K, vacancy clusters were found to form, grow and finally disappear. We found that annealing at 650 K triggers the formation of divacancies, whereas further increasing in the annealing temperature up to 750 K leads to the formation of divacancy-copper complexes. The observations suggest that the formation of these vacancy-like defects in GaAs is related to the out-diffusion of Cu. Two kinds of acceptors are detected with a concentration of about 1016 - 1017 cm-3, negative ions and arsenic vacancy copper complexes. Transmission electron microscopy showed the presence of voids and Cu precipitates which are not observed by positron measurements. The positron binding energy to shallow traps is estimated using the positron trapping model. Coincidence Doppler broadening spectroscopy showed the presence of Cu in the immediate vicinity of the detected vacancies. Theoretical calculations suggested that the detected defect is VGaVAs-2CuGa.

Aging behavior of Au-based ohmic contacts to GaAs

NASA Technical Reports Server (NTRS)

Fatemi, Navid S.

1989-01-01

Gold based alloys, commonly used as ohmic contacts for solar cells, are known to react readily with GaAs. It is shown that the contact interaction with the underlying GaAs can continue even at room temperature upon aging, altering both the electrical characteristics of the contacts and the nearby pn junction. Au-Ge-Ni as-deposited (no heat-treatment) contacts made to thin emitter (0.15 microns) GaAs diodes have shown severe shunting of the pn junction upon aging for several months at room temperature. The heat-treated contacts, despite showing degradation in contact resistance, did not affect the underlying pn junction. Au-Zn-Au contacts to p-GaAs emitter (0.2 microns) diodes, however, showed slight improvement in contact resistance upon 200 C isothermal annealing for several months, without degrading the pn junction. The effect of aging on electrical characteristics of the as-deposited and heat-treated contacts and the nearby pn junction, as well as on the surface morphology of the contacts are presented.

Aging behavior of Au-based ohmic contacts to GaAs

NASA Technical Reports Server (NTRS)

Fatemi, Navid S.

1988-01-01

Gold based alloys, commonly used as ohmic contacts for solar cells, are known to react readily with GaAs. It is shown that the contact interaction with the underlying GaAs can continue even at room temperature upon aging, altering both the electrical characteristics of the contacts and the nearby pn junction. Au-Ge-Ni as-deposited (no heat treatment) contacts made to thin emitter (0.15 micrometer) GaAs diodes have shown severe shunting of the pn junction upon aging for several months at room temperature. The heat-treated contacts, despite showing degradation in contact resistance did not affect the underlying pn junction. Au-Zn-Au contacts to p-GaAs emitter (0.2 micrometer) diodes, however, showed slight improvement in contact resistance upon 200 C isothermal annealing for several months, without degrading the pn junction. The effect of aging on electrical characteristics of the as-deposited and heat-treated contacts and the nearby pn junction, as well as on the surface morphology of the contacts are presented.

Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches

PubMed Central

Hayes, Stephen; Mahony, Jennifer; Nauta, Arjen; van Sinderen, Douwe

2017-01-01