The β-Arrestins: Multifunctional Regulators of G Protein-coupled Receptors.

PubMed

Smith, Jeffrey S; Rajagopal, Sudarshan

2016-04-22

The β-arrestins (βarrs) are versatile, multifunctional adapter proteins that are best known for their ability to desensitize G protein-coupled receptors (GPCRs), but also regulate a diverse array of cellular functions. To signal in such a complex fashion, βarrs adopt multiple conformations and are regulated at multiple levels to differentially activate downstream pathways. Recent structural studies have demonstrated that βarrs have a conserved structure and activation mechanism, with plasticity of their structural fold, allowing them to adopt a wide array of conformations. Novel roles for βarrs continue to be identified, demonstrating the importance of these dynamic regulators of cellular signaling. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Performance degradation mechanisms and modes in terrestrial photovoltaic arrays and technology for their diagnosis

NASA Technical Reports Server (NTRS)

Noel, G. T.; Sliemers, F. A.; Derringer, G. C.; Wood, V. E.; Wilkes, K. E.; Gaines, G. B.; Carmichael, D. C.

1978-01-01

Accelerated life-prediction test methodologies have been developed for the validation of a 20-year service life for low-cost photovoltaic arrays. Array failure modes, relevant materials property changes, and primary degradation mechanisms are discussed as a prerequisite to identifying suitable measurement techniques and instruments. Measurements must provide sufficient confidence to permit selection among alternative designs and materials and to stimulate widespread deployment of such arrays. Furthermore, the diversity of candidate materials and designs, and the variety of potential environmental stress combinations, degradation mechanisms and failure modes require that combinations of measurement techniques be identified which are suitable for the characterization of various encapsulation system-cell structure-environment combinations.

Genetic Identity in Genebanks: Application of the SolCAP 12K SNP Array in Fingerprinting and Diversity Analysis in the Global In Trust Potato Collection.

PubMed

Ellis, David; Chavez, Oswaldo; Coombs, Joseph J; Soto, Julian V; Gomez, Rene; Douches, David S; Panta, Ana; Silvestre, Rocio; Anglin, Noelle Lynette

2018-05-24

Breeders rely on genetic integrity of material from genebanks, however, mislabeling and errors in original data can occur. Paired samples of original material and their in vitro counterparts from 250 diverse potato landrace accessions from the International Potato Center (CIP), were fingerprinted using the Infinium 12K V2 Potato Array to confirm genetic identity and evaluate genetic diversity. Diploid, triploid, and tetraploid accessions were included representing seven cultivated potato taxa (Hawkes, 1990). Fingerprints between mother field plants and in vitro clones, were used to evaluate identity, relatedness, and ancestry. Clones of the same accession grouped together, however eleven (4.4%) accessions were mismatches genetically. SNP genotypes were used to construct a phylogeny to evaluate inter- and intraspecific relationships and population structure. Data suggests that the triploids evaluated are genetically similar. STRUCTURE analysis identified several putative hybrids and suggests six populations with significant gene flow between. This study provides a model for genetic identity of plant genetic resources collections as mistakes in conservation of these collections and in genebanks is a reality and confirmed identity is critical for breeders and other users of these collections, as well as for quality management programs and to provide insights into the diversity of the accessions evaluated.

Blue reflectance in tarantulas is evolutionarily conserved despite nanostructural diversity

PubMed Central

Hsiung, Bor-Kai; Deheyn, Dimitri D.; Shawkey, Matthew D.; Blackledge, Todd A.

2015-01-01

Slight shifts in arrangement within biological photonic nanostructures can produce large color differences, and sexual selection often leads to high color diversity in clades with structural colors. We use phylogenetic reconstruction, electron microscopy, spectrophotometry, and optical modeling to show an opposing pattern of nanostructural diversification accompanied by unusual conservation of blue color in tarantulas (Araneae: Theraphosidae). In contrast to other clades, blue coloration in phylogenetically distant tarantulas peaks within a narrow 20-nm region around 450 nm. Both quasi-ordered and multilayer nanostructures found in different tarantulas produce this blue color. Thus, even within monophyletic lineages, tarantulas have evolved strikingly similar blue coloration through divergent mechanisms. The poor color perception and lack of conspicuous display during courtship of tarantulas argue that these colors are not sexually selected. Therefore, our data contrast with sexual selection that typically produces a diverse array of colors with a single structural mechanism by showing that natural selection on structural color in tarantulas resulted in convergence on similar color through diverse structural mechanisms. PMID:26702433

Lessons from 455 Fusarium polyketide synthases

USDA-ARS?s Scientific Manuscript database

In fungi, polyketide synthases (PKSs) synthesize a structurally diverse array of secondary metabolites (SMs) with a range of biological activities. The most studied SMs are toxic to animals and/or plants, alter plant growth, have beneficial pharmaceutical activities, and/or are brightly colored pigm...

The Marvels of Electromagnetic Band Gap (EBG) Structures

DTIC Science & Technology

2003-11-01

terminology of "Electromagnetic conference papers and journal articles dealing with Band- gaps (EBG)". Recently, many researchers the characterizations...Band Gap (EBG) Structures 9 utilized to reduce the mutual coupling between Structures: An FDTD/Prony Technique elements of antenna arrays. based on the...Band- Gap of several patents. He has had pioneering research contributions in diverse areas of electromagnetics,Snteructure", Dymposiget o l 21 IE 48

A nonpolymorphic major histocompatibility complex class Ib molecule binds a large array of diverse self-peptides

PubMed Central

1994-01-01

Unlike the highly polymorphic major histocompatibility complex (MHC) class Ia molecules, which present a wide variety of peptides to T cells, it is generally assumed that the nonpolymorphic MHC class Ib molecules may have evolved to function as highly specialized receptors for the presentation of structurally unique peptides. However, a thorough biochemical analysis of one class Ib molecule, the soluble isoform of Qa-2 antigen (H-2SQ7b), has revealed that it binds a diverse array of structurally similar peptides derived from intracellular proteins in much the same manner as the classical antigen-presenting molecules. Specifically, we find that SQ7b molecules are heterodimers of heavy and light chains complexed with nonameric peptides in a 1:1:1 ratio. These peptides contain a conserved hydrophobic residue at the COOH terminus and a combination of one or more conserved residue(s) at P7 (histidine), P2 (glutamine/leucine), and/or P3 (leucine/asparagine) as anchors for binding SQ7b. 2 of 18 sequenced peptides matched cytosolic proteins (cofilin and L19 ribosomal protein), suggesting an intracellular source of the SQ7b ligands. Minimal estimates of the peptide repertoire revealed that at least 200 different naturally processed self-peptides can bind SQ7b molecules. Since Qa-2 molecules associate with a diverse array of peptides, we suggest that they function as effective presenting molecules of endogenously synthesized proteins like the class Ia molecules. PMID:8294869

Analyzing canopy structure in Pacific Northwest old-growth forests with a stand-scale crown model

Treesearch

Robert Van Pelt; Malcolm P. North

1996-01-01

I n forests, the canopy is the locale of critical ecosystem processes such as photosynthesis and evapotranspiration. and it provides essential habitat for a highly diverse array of animals, plants, and other organisms. Despite its importance, the structure of the canopy as a whole has had little quantitative study because limited access makes quantification difficult...

Carbohydrates in diversity-oriented synthesis: challenges and opportunities.

PubMed

Lenci, E; Menchi, G; Trabocchi, A

2016-01-21

Over the last decade, Diversity-Oriented Synthesis (DOS) has become a new paradigm for developing large collections of structurally diverse small molecules as probes to investigate biological pathways, and to provide a larger array of the chemical space. Drug discovery and chemical biology are taking advantage of DOS approaches to exploit highly-diverse and complex molecular platforms, producing advances in both target and ligand discovery. In this view, carbohydrates are attractive building blocks for DOS libraries, due to their stereochemical diversity and high density of polar functional groups, thus offering many possibilities for chemical manipulation and scaffold decoration. This review will discuss research contributions and perspectives on the application of carbohydrate chemistry to explore the accessible chemical space through appendage, stereochemical and scaffold diversity.

Genome Microscale Heterogeneity among Wild Potatoes Revealed by Diversity Arrays Technology Marker Sequences.

PubMed

Traini, Alessandra; Iorizzo, Massimo; Mann, Harpartap; Bradeen, James M; Carputo, Domenico; Frusciante, Luigi; Chiusano, Maria Luisa

2013-01-01

Tuber-bearing potato species possess several genes that can be exploited to improve the genetic background of the cultivated potato Solanum tuberosum. Among them, S. bulbocastanum and S. commersonii are well known for their strong resistance to environmental stresses. However, scant information is available for these species in terms of genome organization, gene function, and regulatory networks. Consequently, genomic tools to assist breeding are meager, and efficient exploitation of these species has been limited so far. In this paper, we employed the reference genome sequences from cultivated potato and tomato and a collection of sequences of 1,423 potato Diversity Arrays Technology (DArT) markers that show polymorphic representation across the genomes of S. bulbocastanum and/or S. commersonii genotypes. Our results highlighted microscale genome sequence heterogeneity that may play a significant role in functional and structural divergence between related species. Our analytical approach provides knowledge of genome structural and sequence variability that could not be detected by transcriptome and proteome approaches.

GeoChip-based analysis of microbial functional gene diversity in a landfill leachate-contaminated aquifer

USGS Publications Warehouse

Lu, Zhenmei; He, Zhili; Parisi, Victoria A.; Kang, Sanghoon; Deng, Ye; Van Nostrand, Joy D.; Masoner, Jason R.; Cozzarelli, Isabelle M.; Suflita, Joseph M.; Zhou, Jizhong

2012-01-01

The functional gene diversity and structure of microbial communities in a shallow landfill leachate-contaminated aquifer were assessed using a comprehensive functional gene array (GeoChip 3.0). Water samples were obtained from eight wells at the same aquifer depth immediately below a municipal landfill or along the predominant downgradient groundwater flowpath. Functional gene richness and diversity immediately below the landfill and the closest well were considerably lower than those in downgradient wells. Mantel tests and canonical correspondence analysis (CCA) suggested that various geochemical parameters had a significant impact on the subsurface microbial community structure. That is, leachate from the unlined landfill impacted the diversity, composition, structure, and functional potential of groundwater microbial communities as a function of groundwater pH, and concentrations of sulfate, ammonia, and dissolved organic carbon (DOC). Historical geochemical records indicate that all sampled wells chronically received leachate, and the increase in microbial diversity as a function of distance from the landfill is consistent with mitigation of the impact of leachate on the groundwater system by natural attenuation mechanisms.

Synthesis of structurally diverse major groove DNA interstrand crosslinks using three different aldehyde precursors

PubMed Central

Mukherjee, Shivam; Guainazzi, Angelo; Schärer, Orlando D.

2014-01-01

DNA interstrand crosslinks (ICLs) are extremely cytotoxic lesions that block essential cellular processes, such as replication and transcription. Crosslinking agents are widely used in cancer chemotherapy and form an array of structurally diverse ICLs. Despite the clinical success of these agents, resistance of tumors to crosslinking agents, for example, through repair of these lesions by the cellular machinery remains a problem. We have previously reported the synthesis of site-specific ICLs mimicking those formed by nitrogen mustards to facilitate the studies of cellular responses to ICL formation. Here we extend these efforts and report the synthesis of structurally diverse major groove ICLs that induce severe, little or no distortion in the DNA. Our approach employs the incorporation of aldehyde precursors of different lengths into complementary strands and ICL formation using a double reductive amination with a variety of amines. Our studies provide insight into the structure and reactivity parameters of ICL formation by double reductive amination and yield a set of diverse ICLs that will be invaluable for exploring structure–activity relationships in ICL repair. PMID:24782532

Quantification of asymmetric microtubule nucleation at sub-cellular structures

PubMed Central

Zhu, Xiaodong; Kaverina, Irina

2012-01-01

Cell polarization is important for multiple physiological processes. In polarized cells, microtubules (MTs) are organized into a spatially polarized array. Generally, in non-differentiated cells, it is assumed that MTs are symmetrically nucleated exclusively from centrosome (microtubule organizing center, MTOC) and then reorganized into the asymmetric array. We have recently identified the Golgi complex as an additional MTOC that asymmetrically nucleates MTs toward one side of the cell. Methods used for alternative MTOC identification include microtubule re-growth after complete drug-induced depolymerization and tracking of growing microtubules using fluorescence labeled MT +TIP binding proteins in living cells. These approaches can be used for quantification of MT nucleation sites at diverse sub-cellular structures. PMID:21773933

An orthologous transcriptional signature differentiates responses towards closely related chemicals in Arabidopsis thaliana and brassica napus

EPA Science Inventory

Herbicides are structurally diverse chemicals that inhibit plant-specific targets, however their off-target and potentially differentiating side-effects are less well defined. In this study, genome-wide expression profiling based on Affymetrix AtH1 arrays was used to identify dis...

Engaging with Molecular Form to Understand Function

ERIC Educational Resources Information Center

Barber, Nicola C.; Stark, Louisa A.

2014-01-01

Cells are bustling factories with diverse and prolific arrays of molecular machinery. Remarkably, this machinery self-organizes to carry out the complex biochemical activities characteristic of life. When Watson and Crick published the structure of DNA, they noted that DNA base pairing creates a double-stranded form that provides a means of…

Spatiotemporal polarization modulation microscopy with a microretarder array

NASA Astrophysics Data System (ADS)

Ding, Changqin; Ulcickas, James R. W.; Simpson, Garth J.

2018-02-01

A patterned microretarder array positioned in the rear conjugate plane of a microscope enables rapid polarizationdependent nonlinear optical microscopy. The pattern introduced to the array results in periodic modulation of the polarization-state of the incident light as a function of position within the field of view with no moving parts or active control. Introduction of a single stationary optical element and a fixed polarizer into the beam of a nonlinear optical microscope enabled nonlinear optical tensor recovery, which informs on local structure and orientation. Excellent agreement was observed between the measured and predicted second harmonic generation (SHG) of z-cut quartz, selected as a test system with well-established nonlinear optical properties. Subsequent studies of spatially varying samples further support the general applicability of this relatively simple strategy for detailed polarization analysis in both conventional and nonlinear optical imaging of structurally diverse samples.

Host population genetic structure and zooxanthellae diversity of two reef-building coral species along the Florida Reef Tract and wider Caribbean

NASA Astrophysics Data System (ADS)

Baums, I. B.; Johnson, M. E.; Devlin-Durante, M. K.; Miller, M. W.

2010-12-01

In preparation for a large-scale coral restoration project, we surveyed host population genetic structure and symbiont diversity of two reef-building corals in four reef zones along the Florida reef tract (FRT). There was no evidence for coral population subdivision along the FRT in Acropora cervicornis or Montastraea faveolata based on microsatellite markers. However, in A. cervicornis, significant genetic differentiation was apparent when extending the analysis to broader scales (Caribbean). Clade diversity of the zooxanthellae differed along the FRT. A. cervicornis harbored mostly clade A with clade D zooxanthellae being prominent in colonies growing inshore and in the mid-channel zones that experience greater temperature fluctuations and receive significant nutrient and sediment input. M. faveolata harbored a more diverse array of symbionts, and variation in symbiont diversity among four habitat zones was more subtle but still significant. Implications of these results are discussed for ongoing restoration and conservation work.

Diversity of Prdm9 Zinc Finger Array in Wild Mice Unravels New Facets of the Evolutionary Turnover of this Coding Minisatellite

PubMed Central

Buard, Jérôme; Rivals, Eric; Dunoyer de Segonzac, Denis; Garres, Charlotte; Caminade, Pierre; de Massy, Bernard; Boursot, Pierre

2014-01-01

In humans and mice, meiotic recombination events cluster into narrow hotspots whose genomic positions are defined by the PRDM9 protein via its DNA binding domain constituted of an array of zinc fingers (ZnFs). High polymorphism and rapid divergence of the Prdm9 gene ZnF domain appear to involve positive selection at DNA-recognition amino-acid positions, but the nature of the underlying evolutionary pressures remains a puzzle. Here we explore the variability of the Prdm9 ZnF array in wild mice, and uncovered a high allelic diversity of both ZnF copy number and identity with the caracterization of 113 alleles. We analyze features of the diversity of ZnF identity which is mostly due to non-synonymous changes at codons −1, 3 and 6 of each ZnF, corresponding to amino-acids involved in DNA binding. Using methods adapted to the minisatellite structure of the ZnF array, we infer a phylogenetic tree of these alleles. We find the sister species Mus spicilegus and M. macedonicus as well as the three house mouse (Mus musculus) subspecies to be polyphyletic. However some sublineages have expanded independently in Mus musculus musculus and M. m. domesticus, the latter further showing phylogeographic substructure. Compared to random genomic regions and non-coding minisatellites, none of these patterns appears exceptional. In silico prediction of DNA binding sites for each allele, overlap of their alignments to the genome and relative coverage of the different families of interspersed repeated elements suggest a large diversity between PRDM9 variants with a potential for highly divergent distributions of recombination events in the genome with little correlation to evolutionary distance. By compiling PRDM9 ZnF protein sequences in Primates, Muridae and Equids, we find different diversity patterns among the three amino-acids most critical for the DNA-recognition function, suggesting different diversification timescales. PMID:24454780

Ligand binding by repeat proteins: natural and designed

PubMed Central

Grove, Tijana Z; Cortajarena, Aitziber L; Regan, Lynne

2012-01-01

Repeat proteins contain tandem arrays of small structural motifs. As a consequence of this architecture, they adopt non-globular, extended structures that present large, highly specific surfaces for ligand binding. Here we discuss recent advances toward understanding the functional role of this unique modular architecture. We showcase specific examples of natural repeat proteins interacting with diverse ligands and also present examples of designed repeat protein–ligand interactions. PMID:18602006

Diversity, genetic mapping, and signatures of domestication in the carrot (Daucus carota L.) genome, as revealed by Diversity Arrays Technology (DArT) markers

USDA-ARS?s Scientific Manuscript database

Carrot is one of the most economically important vegetables worldwide, however, genetic and genomic resources supporting carrot breeding remain limited. We developed a Diversity Arrays Technology (DArT) platform for wild and cultivated carrot and used it to investigate genetic diversity and to devel...

Will concern for biodiversity spell doom to tropical forest management?

Treesearch

A.E. Lugo

1999-01-01

Arguments against active tropical management are analyzed in light of available data and new research that shows tropical forests to be more resilient after disturbances than previously thought. Tropical forest management involves a diverse array of human activity embedded in a complex social and natural environment. Within this milieu, forest structure and composition...

Molecular Basis of Substrate Recognition and Degradation by Human Presequence Protease

PubMed Central

King, John V.; Liang, Wenguang G.; Scherpelz, Kathryn P.; Schilling, Alexander B.; Meredith, Stephen C.; Tang, Wei-Jen

2014-01-01

Summary Human Presequence Protease (hPreP) is an M16 metalloprotease localized in mitochondria. There, hPreP facilitates proteostasis by utilizing a ∼13,300Å3 catalytic chamber to degrade a diverse array of potentially toxic peptides, including mitochondrial presequences and amyloid-β (Aβ), the latter of which contributes to Alzheimer's disease pathogenesis. Here we report crystal structures for hPreP alone and in complex with Aβ, which show that hPreP uses size-exclusion and charge complementation for substrate recognition. These structures also reveal hPreP-specific features that permit a diverse array of peptides, with distinct distributions of charged and hydrophobic residues, to be specifically captured, cleaved, and their amyloidogenic features destroyed. SAXS analysis demonstrates that hPreP in solution exists in dynamic equilibrium between closed and open states, with the former being preferred. Furthermore, Aβ binding induces the closed state and hPreP dimerization. Together, these data reveal the molecular basis for flexible yet specific substrate recognition and degradation by hPreP. PMID:24931469

Small but not isolated: a population genetic survey of the tropical tree Cariniana estrellensis (Lecythidaceae) in a highly fragmented habitat

PubMed Central

Guidugli, M C; Nazareno, A G; Feres, J M; Contel, E P B; Mestriner, M A; Alzate-Marin, A L

2016-01-01

Here, we explore the mating pattern and genetic structure of a tropical tree species, Cariniana estrellensis, in a small population in which progeny arrays (n=399), all adults (n=28) and all seedlings (n=39) were genotyped at nine highly informative microsatellite loci. From progeny arrays we were able to identify the source tree for at least 78% of pollination events. The gene immigration rates, mainly attributable to pollen, were high, varying from 23.5 to 53%. Although gene dispersal over long distance was observed, the effective gene dispersal distances within the small population were relatively short, with mean pollination distances varying from 69.9 to 146.9 m, and seed dispersal distances occurring up to a mean of 119.6 m. Mating system analyses showed that C. estrellensis is an allogamous species (tm=0.999), with both biparental inbreeding (tm−ts=−0.016) and selfing rates (s=0.001) that are not significantly different from zero. Even though the population is small, the presence of private alleles in both seedlings and progeny arrays and the elevated rates of gene immigration indicate that the C. estrellensis population is not genetically isolated. However, genetic diversity expressed by allelic richness was significantly lower in postfragmentation life stages. Although there was a loss of genetic diversity, indicating susceptibility of C. estrellensis to habitat fragmentation, no evidence of inbreeding or spatial genetic structure was observed across generations. Overall, C. estrellensis showed some resilience to negative genetic effects of habitat fragmentation, but conservation strategies are needed to preserve the remaining genetic diversity of this population. PMID:26732014

Measuring the Kinetic and Mechanical Properties of Non-Processive Myosins using Optical Tweezers

PubMed Central

Greenberg, Michael J.; Shuman, Henry; Ostap, E. Michael

2017-01-01

The myosin superfamily of molecular motors utilizes energy from ATP hydrolysis to generate force and motility along actin filaments in a diverse array of cellular processes. These motors are structurally, kinetically, and mechanically tuned to their specific molecular roles in the cell. Optical trapping techniques have played a central role in elucidating the mechanisms by which myosins generate force and in exposing the remarkable diversity of myosin functions. Here, we present thorough methods for measuring and analyzing interactions between actin and non-processive myosins using optical trapping techniques. PMID:27844441

A waveform diversity method for optimizing 3-d power depositions generated by ultrasound phased arrays.

PubMed

Zeng, Xiaozheng Jenny; Li, Jian; McGough, Robert J

2010-01-01

A waveform-diversity-based approach for 3-D tumor heating is compared to spot scanning for hyperthermia applications. The waveform diversity method determines the excitation signals applied to the phased array elements and produces a beam pattern that closely matches the desired power distribution. The optimization algorithm solves the covariance matrix of the excitation signals through semidefinite programming subject to a series of quadratic cost functions and constraints on the control points. A numerical example simulates a 1444-element spherical-section phased array that delivers heat to a 3-cm-diameter spherical tumor located 12 cm from the array aperture, and the results show that waveform diversity combined with mode scanning increases the heated volume within the tumor while simultaneously decreasing normal tissue heating. Whereas standard single focus and multiple focus methods are often associated with unwanted intervening tissue heating, the waveform diversity method combined with mode scanning shifts energy away from intervening tissues where hotspots otherwise accumulate to improve temperature localization in deep-seated tumors.

The diversity of H3 loops determines the antigen-binding tendencies of antibody CDR loops.

PubMed

Tsuchiya, Yuko; Mizuguchi, Kenji

2016-04-01

Of the complementarity-determining regions (CDRs) of antibodies, H3 loops, with varying amino acid sequences and loop lengths, adopt particularly diverse loop conformations. The diversity of H3 conformations produces an array of antigen recognition patterns involving all the CDRs, in which the residue positions actually in contact with the antigen vary considerably. Therefore, for a deeper understanding of antigen recognition, it is necessary to relate the sequence and structural properties of each residue position in each CDR loop to its ability to bind antigens. In this study, we proposed a new method for characterizing the structural features of the CDR loops and obtained the antigen-binding ability of each residue position in each CDR loop. This analysis led to a simple set of rules for identifying probable antigen-binding residues. We also found that the diversity of H3 loop lengths and conformations affects the antigen-binding tendencies of all the CDR loops. © 2016 The Protein Society.

Natural Products as a Source of Alzheimer’s Drug Leads

PubMed Central

Sorribas, Analia; Howes, Melanie-Jayne R.

2016-01-01

This review focuses on recent developments in the use of natural products as therapeutics for Alzheimer’s disease. Compounds span a diverse array of structural classes and are organized according to their mechanism of action, with the focus primarily on the major hypotheses. Overall, the review discusses more than 180 compounds and summarizes 393 references. PMID:21072430

Development of a Medium Density Combined-Species SNP Array for Pacific and European Oysters (Crassostrea gigas and Ostrea edulis).

PubMed

Gutierrez, Alejandro P; Turner, Frances; Gharbi, Karim; Talbot, Richard; Lowe, Natalie R; Peñaloza, Carolina; McCullough, Mark; Prodöhl, Paulo A; Bean, Tim P; Houston, Ross D

2017-07-05

SNP arrays are enabling tools for high-resolution studies of the genetic basis of complex traits in farmed and wild animals. Oysters are of critical importance in many regions from both an ecological and economic perspective, and oyster aquaculture forms a key component of global food security. The aim of our study was to design a combined-species, medium density SNP array for Pacific oyster ( Crassostrea gigas ) and European flat oyster ( Ostrea edulis ), and to test the performance of this array on farmed and wild populations from multiple locations, with a focus on European populations. SNP discovery was carried out by whole-genome sequencing (WGS) of pooled genomic DNA samples from eight C. gigas populations, and restriction site-associated DNA sequencing (RAD-Seq) of 11 geographically diverse O. edulis populations. Nearly 12 million candidate SNPs were discovered and filtered based on several criteria, including preference for SNPs segregating in multiple populations and SNPs with monomorphic flanking regions. An Affymetrix Axiom Custom Array was created and tested on a diverse set of samples ( n = 219) showing ∼27 K high quality SNPs for C. gigas and ∼11 K high quality SNPs for O. edulis segregating in these populations. A high proportion of SNPs were segregating in each of the populations, and the array was used to detect population structure and levels of linkage disequilibrium (LD). Further testing of the array on three C. gigas nuclear families ( n = 165) revealed that the array can be used to clearly distinguish between both families based on identity-by-state (IBS) clustering parental assignment software. This medium density, combined-species array will be publicly available through Affymetrix, and will be applied for genome-wide association and evolutionary genetic studies, and for genomic selection in oyster breeding programs. Copyright © 2017 Gutierrez et al.

Wafer-scale growth of large arrays of perovskite microplate crystals for functional electronics and optoelectronics.

PubMed

Wang, Gongming; Li, Dehui; Cheng, Hung-Chieh; Li, Yongjia; Chen, Chih-Yen; Yin, Anxiang; Zhao, Zipeng; Lin, Zhaoyang; Wu, Hao; He, Qiyuan; Ding, Mengning; Liu, Yuan; Huang, Yu; Duan, Xiangfeng

2015-10-01

Methylammonium lead iodide perovskite has attracted intensive interest for its diverse optoelectronic applications. However, most studies to date have been limited to bulk thin films that are difficult to implement for integrated device arrays because of their incompatibility with typical lithography processes. We report the first patterned growth of regular arrays of perovskite microplate crystals for functional electronics and optoelectronics. We show that large arrays of lead iodide microplates can be grown from an aqueous solution through a seeded growth process and can be further intercalated with methylammonium iodide to produce perovskite crystals. Structural and optical characterizations demonstrate that the resulting materials display excellent crystalline quality and optical properties. We further show that perovskite crystals can be selectively grown on prepatterned electrode arrays to create independently addressable photodetector arrays and functional field effect transistors. The ability to grow perovskite microplates and to precisely place them at specific locations offers a new material platform for the fundamental investigation of the electronic and optical properties of perovskite materials and opens a pathway for integrated electronic and optoelectronic systems.

Wafer-scale growth of large arrays of perovskite microplate crystals for functional electronics and optoelectronics

PubMed Central

Wang, Gongming; Li, Dehui; Cheng, Hung-Chieh; Li, Yongjia; Chen, Chih-Yen; Yin, Anxiang; Zhao, Zipeng; Lin, Zhaoyang; Wu, Hao; He, Qiyuan; Ding, Mengning; Liu, Yuan; Huang, Yu; Duan, Xiangfeng

2015-01-01

Methylammonium lead iodide perovskite has attracted intensive interest for its diverse optoelectronic applications. However, most studies to date have been limited to bulk thin films that are difficult to implement for integrated device arrays because of their incompatibility with typical lithography processes. We report the first patterned growth of regular arrays of perovskite microplate crystals for functional electronics and optoelectronics. We show that large arrays of lead iodide microplates can be grown from an aqueous solution through a seeded growth process and can be further intercalated with methylammonium iodide to produce perovskite crystals. Structural and optical characterizations demonstrate that the resulting materials display excellent crystalline quality and optical properties. We further show that perovskite crystals can be selectively grown on prepatterned electrode arrays to create independently addressable photodetector arrays and functional field effect transistors. The ability to grow perovskite microplates and to precisely place them at specific locations offers a new material platform for the fundamental investigation of the electronic and optical properties of perovskite materials and opens a pathway for integrated electronic and optoelectronic systems. PMID:26601297

Wafer-scale growth of large arrays of perovskite microplate crystals for functional electronics and optoelectronics

DOE PAGES

Wang, Gongming; Li, Dehui; Cheng, Hung -Chieh; ...

2015-10-02

Methylammonium lead iodide perovskite has attracted intensive interest for its diverse optoelectronic applications. However, most studies to date have been limited to bulk thin films that are difficult to implement for integrated device arrays because of their incompatibility with typical lithography processes. We report the first patterned growth of regular arrays of perovskite microplate crystals for functional electronics and optoelectronics. We show that large arrays of lead iodide microplates can be grown from an aqueous solution through a seeded growth process and can be further intercalated with methylammonium iodide to produce perovskite crystals. Structural and optical characterizations demonstrate that themore » resulting materials display excellent crystalline quality and optical properties. We further show that perovskite crystals can be selectively grown on prepatterned electrode arrays to create independently addressable photodetector arrays and functional field effect transistors. Furthermore, the ability to grow perovskite microplates and to precisely place them at specific locations offers a new material platform for the fundamental investigation of the electronic and optical properties of perovskite materials and opens a pathway for integrated electronic and optoelectronic systems.« less

Atomically precise arrays of fluorescent silver clusters: a modular approach for metal cluster photonics on DNA nanostructures.

PubMed

Copp, Stacy M; Schultz, Danielle E; Swasey, Steven; Gwinn, Elisabeth G

2015-03-24

The remarkable precision that DNA scaffolds provide for arraying nanoscale optical elements enables optical phenomena that arise from interactions of metal nanoparticles, dye molecules, and quantum dots placed at nanoscale separations. However, control of ensemble optical properties has been limited by the difficulty of achieving uniform particle sizes and shapes. Ligand-stabilized metal clusters offer a route to atomically precise arrays that combine desirable attributes of both metals and molecules. Exploiting the unique advantages of the cluster regime requires techniques to realize controlled nanoscale placement of select cluster structures. Here we show that atomically monodisperse arrays of fluorescent, DNA-stabilized silver clusters can be realized on a prototypical scaffold, a DNA nanotube, with attachment sites separated by <10 nm. Cluster attachment is mediated by designed DNA linkers that enable isolation of specific clusters prior to assembly on nanotubes and preserve cluster structure and spectral purity after assembly. The modularity of this approach generalizes to silver clusters of diverse sizes and DNA scaffolds of many types. Thus, these silver cluster nano-optical elements, which themselves have colors selected by their particular DNA templating oligomer, bring unique dimensions of control and flexibility to the rapidly expanding field of nano-optics.

Freshwater mussel assemblage structure in a regulated river in the Lower Mississippi river Alluvial Basin, USA

Treesearch

Wendell R. Haag; Melvin L. Warren

2007-01-01

1. This paper documents a diverse, reproducing freshwater mussel community (20 species) in Lower Lake } an impounded, regulated portion of the Little Tallahatchie River below Sardis Dam in Panola Co., Mississippi, USA. 2. Despite being regulated and impounded, the lake has a heterogeneous array of habitats that differ markedly in mussel community attributes...

Fabrication of highly ordered 2D metallic arrays with disc-in-hole binary nanostructures via a newly developed nanosphere lithography

NASA Astrophysics Data System (ADS)

Yang, Xi; Guo, Wei; Wang, Xixi; Liao, Mingdun; Gao, Pingqi; Ye, Jichun

2017-11-01

2D metallic arrays with binary nanostructures derived from a nanosphere lithography (NSL) method have been rarely reported. Here, we demonstrate a novel NSL strategy to fabricate highly ordered 2D gold arrays with disc-in-hole binary (DIHB) nanostructures in large scale by employing a sacrificing layer combined with a three-step lift-off process. The structural parameters of the resultant DIHB arrays, such as periodicity, hole diameter, disc diameter and thicknesses can be facilely controlled by tuning the nanospheres size, etching condition, deposition angle and duration, respectively. Due to the intimate interactions between two subcomponents, the DIHB arrays exhibit both an extraordinary high surface-enhanced Raman scattering enhancement factor up to 5 × 108 and a low sheet resistance down to 1.7 Ω/sq. Moreover, the DIHB array can also be used as a metal catalyzed chemical etching catalytic pattern to create vertically-aligned Si nano-tube arrays for anti-reflectance application. This strategy provides a universal route for synthesizing other diverse binary nanostructures with controlled morphology, and thus expands the applications of the NSL to prepare ordered nanostructures with multi-function.

Genetic diversity and structure of Iberian Peninsula cowpeas compared to world-wide cowpea accessions using high density SNP markers.

PubMed

Carvalho, Márcia; Muñoz-Amatriaín, María; Castro, Isaura; Lino-Neto, Teresa; Matos, Manuela; Egea-Cortines, Marcos; Rosa, Eduardo; Close, Timothy; Carnide, Valdemar

2017-11-21

Cowpea (Vigna unguiculata L. Walp) is an important legume crop due to its high protein content, adaptation to heat and drought and capacity to fix nitrogen. Europe has a deficit of cowpea production. Knowledge of genetic diversity among cowpea landraces is important for the preservation of local varieties and is the basis to obtain improved varieties. The aims of this study were to explore diversity and the genetic structure of a set of Iberian Peninsula cowpea accessions in comparison to a worldwide collection and to infer possible dispersion routes of cultivated cowpea. The Illumina Cowpea iSelect Consortium Array containing 51,128 SNPs was used to genotype 96 cowpea accessions including 43 landraces and cultivars from the Iberian Peninsula, and 53 landraces collected worldwide. Four subpopulations were identified. Most Iberian Peninsula accessions clustered together with those from other southern European and northern African countries. Only one accession belonged to another subpopulation, while two accessions were 'admixed'. A lower genetic diversity level was found in the Iberian Peninsula accessions compared to worldwide cowpeas. The genetic analyses performed in this study brought some insights into worldwide genetic diversity and structure and possible dispersion routes of cultivated cowpea. Also, it provided an in-depth analysis of genetic diversity in Iberian Peninsula cowpeas that will help guide crossing strategies in breeding programs.

A powerful tool for genome analysis in maize: development and evaluation of the high density 600 k SNP genotyping array.

PubMed

Unterseer, Sandra; Bauer, Eva; Haberer, Georg; Seidel, Michael; Knaak, Carsten; Ouzunova, Milena; Meitinger, Thomas; Strom, Tim M; Fries, Ruedi; Pausch, Hubert; Bertani, Christofer; Davassi, Alessandro; Mayer, Klaus Fx; Schön, Chris-Carolin

2014-09-29

High density genotyping data are indispensable for genomic analyses of complex traits in animal and crop species. Maize is one of the most important crop plants worldwide, however a high density SNP genotyping array for analysis of its large and highly dynamic genome was not available so far. We developed a high density maize SNP array composed of 616,201 variants (SNPs and small indels). Initially, 57 M variants were discovered by sequencing 30 representative temperate maize lines and then stringently filtered for sequence quality scores and predicted conversion performance on the array resulting in the selection of 1.2 M polymorphic variants assayed on two screening arrays. To identify high-confidence variants, 285 DNA samples from a broad genetic diversity panel of worldwide maize lines including the samples used for sequencing, important founder lines for European maize breeding, hybrids, and proprietary samples with European, US, semi-tropical, and tropical origin were used for experimental validation. We selected 616 k variants according to their performance during validation, support of genotype calls through sequencing data, and physical distribution for further analysis and for the design of the commercially available Affymetrix® Axiom® Maize Genotyping Array. This array is composed of 609,442 SNPs and 6,759 indels. Among these are 116,224 variants in coding regions and 45,655 SNPs of the Illumina® MaizeSNP50 BeadChip for study comparison. In a subset of 45,974 variants, apart from the target SNP additional off-target variants are detected, which show only a minor bias towards intermediate allele frequencies. We performed principal coordinate and admixture analyses to determine the ability of the array to detect and resolve population structure and investigated the extent of LD within a worldwide validation panel. The high density Affymetrix® Axiom® Maize Genotyping Array is optimized for European and American temperate maize and was developed based on a diverse sample panel by applying stringent quality filter criteria to ensure its suitability for a broad range of applications. With 600 k variants it is the largest currently publically available genotyping array in crop species.

Microscopy and Chemical Inversing Techniques to Determine the Photonic Crystal Structure of Iridescent Beetle Scales in the Cerambycidae Family

NASA Astrophysics Data System (ADS)

Richey, Lauren; Gardner, John; Standing, Michael; Jorgensen, Matthew; Bartl, Michael

2010-10-01

Photonic crystals (PCs) are periodic structures that manipulate electromagnetic waves by defining allowed and forbidden frequency bands known as photonic band gaps. Despite production of PC structures operating at infrared wavelengths, visible counterparts are difficult to fabricate because periodicities must satisfy the diffraction criteria. As part of an ongoing search for naturally occurring PCs [1], a three-dimensional array of nanoscopic spheres in the iridescent scales of the Cerambycidae insects A. elegans and G. celestis has been found. Such arrays are similar to opal gemstones and self-assembled colloidal spheres which can be chemically inverted to create a lattice-like PC. Through a chemical replication process [2], scanning electron microscopy analysis, sequential focused ion beam slicing and three-dimensional modeling, we analyzed the structural arrangement of the nanoscopic spheres. The study of naturally occurring structures and their inversing techniques into PCs allows for diversity in optical PC fabrication. [1] J.W. Galusha et al., Phys. Rev. E 77 (2008) 050904. [2] J.W. Galusha et al., J. Mater. Chem. 20 (2010) 1277.

Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array

USDA-ARS?s Scientific Manuscript database

High-density single nucleotide polymorphism (SNP) genotyping chips are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships among individuals in populations and studying marker-trait associations in mapping experiments. We developed a genotyping array includ...

Growth and Development of Three-Dimensional Plant Form.

PubMed

Whitewoods, Christopher D; Coen, Enrico

2017-09-11

Plants can generate a spectacular array of complex shapes, many of which exhibit elaborate curvature in three dimensions, illustrated for example by orchid flowers and pitcher-plant traps. All of these structures arise through differential growth. Recent findings provide fresh mechanistic insights into how regional cell behaviours may lead to tissue deformations, including anisotropies and curvatures, which shape growing volumes and sheets of cells. Here were review our current understanding of how genes, growth, mechanics, and evolution interact to generate diverse structures. We illustrate problems and approaches with the complex three-dimensional trap of the bladderwort, Utricularia gibba, to show how a multidisciplinary approach can be extended to new model systems to understand how diverse plant shapes can develop and evolve. Copyright © 2017 Elsevier Ltd. All rights reserved.

Water Oxidation Catalysis via Size-Selected Iridium Clusters

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

Halder, Avik; Liu, Cong; LIU, ZHUN

The detailed mechanism and efficacy of four electron electrochemical water oxidation depend critically upon the detailed atomic structure of each catalytic site, which are numerous and diverse in most metal oxides anodes. In order to limit the diversity of sites, arrays of discrete iridium clusters with identical metal atom number (Ir-2, Ir-4, or Ir-8) were deposited in submonolayer coverage on conductive oxide supports, and the electrochemical properties and activity of each was evaluated. Exceptional electroactivity for the oxygen evolving reaction (OER) was observed for all cluster samples in acidic electrolyte. Reproducible cluster-size-dependent trends in redox behavior were also resolved. First-principlesmore » computational models of the individual discrete-size clusters allow correlation of catalytic-site structure and multiplicity with redox behavior.« less

Genetic structure in village dogs reveals a Central Asian domestication origin.

PubMed

Shannon, Laura M; Boyko, Ryan H; Castelhano, Marta; Corey, Elizabeth; Hayward, Jessica J; McLean, Corin; White, Michelle E; Abi Said, Mounir; Anita, Baddley A; Bondjengo, Nono Ikombe; Calero, Jorge; Galov, Ana; Hedimbi, Marius; Imam, Bulu; Khalap, Rajashree; Lally, Douglas; Masta, Andrew; Oliveira, Kyle C; Pérez, Lucía; Randall, Julia; Tam, Nguyen Minh; Trujillo-Cornejo, Francisco J; Valeriano, Carlos; Sutter, Nathan B; Todhunter, Rory J; Bustamante, Carlos D; Boyko, Adam R

2015-11-03

Dogs were the first domesticated species, originating at least 15,000 y ago from Eurasian gray wolves. Dogs today consist primarily of two specialized groups--a diverse set of nearly 400 pure breeds and a far more populous group of free-ranging animals adapted to a human commensal lifestyle (village dogs). Village dogs are more genetically diverse and geographically widespread than purebred dogs making them vital for unraveling dog population history. Using a semicustom 185,805-marker genotyping array, we conducted a large-scale survey of autosomal, mitochondrial, and Y chromosome diversity in 4,676 purebred dogs from 161 breeds and 549 village dogs from 38 countries. Geographic structure shows both isolation and gene flow have shaped genetic diversity in village dog populations. Some populations (notably those in the Neotropics and the South Pacific) are almost completely derived from European stock, whereas others are clearly admixed between indigenous and European dogs. Importantly, many populations--including those of Vietnam, India, and Egypt-show minimal evidence of European admixture. These populations exhibit a clear gradient of short--range linkage disequilibrium consistent with a Central Asian domestication origin.

Genetic structure in village dogs reveals a Central Asian domestication origin

PubMed Central

Shannon, Laura M.; Boyko, Ryan H.; Castelhano, Marta; Corey, Elizabeth; Hayward, Jessica J.; McLean, Corin; White, Michelle E.; Abi Said, Mounir; Anita, Baddley A.; Bondjengo, Nono Ikombe; Calero, Jorge; Galov, Ana; Hedimbi, Marius; Imam, Bulu; Khalap, Rajashree; Lally, Douglas; Masta, Andrew; Oliveira, Kyle C.; Pérez, Lucía; Randall, Julia; Tam, Nguyen Minh; Trujillo-Cornejo, Francisco J.; Valeriano, Carlos; Sutter, Nathan B.; Todhunter, Rory J.; Bustamante, Carlos D.; Boyko, Adam R.

2015-01-01

Dogs were the first domesticated species, originating at least 15,000 y ago from Eurasian gray wolves. Dogs today consist primarily of two specialized groups—a diverse set of nearly 400 pure breeds and a far more populous group of free-ranging animals adapted to a human commensal lifestyle (village dogs). Village dogs are more genetically diverse and geographically widespread than purebred dogs making them vital for unraveling dog population history. Using a semicustom 185,805-marker genotyping array, we conducted a large-scale survey of autosomal, mitochondrial, and Y chromosome diversity in 4,676 purebred dogs from 161 breeds and 549 village dogs from 38 countries. Geographic structure shows both isolation and gene flow have shaped genetic diversity in village dog populations. Some populations (notably those in the Neotropics and the South Pacific) are almost completely derived from European stock, whereas others are clearly admixed between indigenous and European dogs. Importantly, many populations—including those of Vietnam, India, and Egypt—show minimal evidence of European admixture. These populations exhibit a clear gradient of short-range linkage disequilibrium consistent with a Central Asian domestication origin. PMID:26483491

Multiple intermediates on the energy landscape of a 15-HEAT-repeat protein

PubMed Central

Tsytlonok, Maksym; Craig, Patricio O.; Sivertsson, Elin; Serquera, David; Perrett, Sarah; Best, Robert B.; Wolynes, Peter G.; Itzhaki, Laura S.

2014-01-01

Repeat proteins are a special class of modular, non-globular proteins composed of small structural motifs arrayed to form elongated architectures and stabilised solely by short-range contacts. We find a remarkable complexity in the unfolding of the large HEAT repeat protein PR65/A. In contrast to what has been seen for small repeat proteins in which unfolding propagates from one end, the HEAT array of PR65/A ruptures at multiple distant sites, leading to intermediate states with non-contiguous folded subdomains. Kinetic analysis allows us to define a network of intermediates and to delineate the pathways that connect them. There is a dominant sequence of unfolding, reflecting a non-uniform distribution of stability across the repeat array; however the unfolding of certain intermediates is competitive, leading to parallel pathways. Theoretical models accounting for the heterogeneous contact density in the folded structure are able to rationalize the variation in stability across the array. This variation in stability also suggests how folding may direct function in a large repeat protein: The stability distribution enables certain regions to present rigid motifs for molecular recognition while affording others flexibility to broaden the search area as in a fly-casting mechanism. Thus PR65/A uses the two ends of the repeat array to bind diverse partners and thereby coordinate the dephosphorylation of many different substrates and of multiple sites within hyperphosphorylated substrates. PMID:24120762

Variation in species diversity and functional traits of sponge communities near human populations in Bocas del Toro, Panama

PubMed Central

Matterson, Kenan O.; Freeman, Christopher J.; Archer, Stephanie K.; Thacker, Robert W.

2015-01-01

Recent studies have renewed interest in sponge ecology by emphasizing the functional importance of sponges in a broad array of ecosystem services. Many critically important habitats occupied by sponges face chronic stressors that might lead to alterations in their diversity, relatedness, and functional attributes. We addressed whether proximity to human activity might be a significant factor in structuring sponge community composition, as well as potential functional roles, by monitoring sponge diversity and abundance at two structurally similar sites that vary in distance to areas of high coastal development in Bocas Del Toro, Panama. We surveyed sponge communities at each site using belt transects and differences between two sites were compared using the following variables: (1) sponge species richness, Shannon diversity, and inverse Simpson’s diversity; (2) phylogenetic diversity; (3) taxonomic and phylogenetic beta diversity; (4) trait diversity and dissimilarity; and (5) phylogenetic and trait patterns in community structure. We observed significantly higher sponge diversity at Punta Caracol, the site most distant from human development (∼5 km). Although phylogenetic diversity was lower at Saigon Bay, the site adjacent to a large village including many houses, businesses, and an airport, the sites did not exhibit significantly different patterns of phylogenetic relatedness in species composition. However, each site had a distinct taxonomic and phylogenetic composition (beta diversity). In addition, the sponge community at Saigon included a higher relative abundance of sponges with high microbial abundance and high chlorophyll a concentration, whereas the community at Punta Caracol had a more even distribution of these traits, yielding a significant difference in functional trait diversity between sites. These results suggest that lower diversity and potentially altered community function might be associated with proximity to human populations. This study highlights the importance of evaluating functional traits and phylogenetic diversity in addition to common diversity metrics when assessing potential environmental impacts on benthic communities. PMID:26587347

Multi locus analysis of Pristionchus pacificus on La Réunion Island reveals an evolutionary history shaped by multiple introductions, constrained dispersal events and rare out-crossing.

PubMed

Morgan, Katy; McGaughran, Angela; Villate, Laure; Herrmann, Matthias; Witte, Hanh; Bartelmes, Gabi; Rochat, Jacques; Sommer, Ralf J

2012-01-01

Pristionchus pacificus, recently established as a model organism in evolutionary biology, is a cosmopolitan nematode that has a necromenic association with scarab beetles. The diverse array of host beetle species and habitat types occupied by P. pacificus make it a good model for investigating local adaptation to novel environments. Presence of P. pacificus on La Réunion Island, a young volcanic island with a dynamic geological history and a wide variety of ecozones, facilitates such investigation in an island biogeographic setting. Microsatellite data from 20 markers and 223 strains and mitochondrial sequence data from 272 strains reveal rich genetic diversity among La Réunion P. pacificus isolates, shaped by differentially timed introductions from diverse sources and in association with different beetle species. Distinctions between volcanic zones and between arid western and wet eastern climatic zones have likely limited westward dispersal of recently colonized lineages and maintained a genetic distinction between eastern and western clades. The highly selfing lifestyle of P. pacificus contributes to the strong fine-scale population structure detected, with each beetle host harbouring strongly differentiated assemblages of strains. Periodic out-crossing generates admixture between genetically diverse lineages, creating a diverse array of allelic combinations likely to increase the evolutionary potential of the species and facilitate adaptation to local environments and beetle hosts. © 2011 Blackwell Publishing Ltd.

Current Status and Future Prospects of Marine Natural Products (MNPs) as Antimicrobials.

PubMed

Choudhary, Alka; Naughton, Lynn M; Montánchez, Itxaso; Dobson, Alan D W; Rai, Dilip K

2017-08-28

The marine environment is a rich source of chemically diverse, biologically active natural products, and serves as an invaluable resource in the ongoing search for novel antimicrobial compounds. Recent advances in extraction and isolation techniques, and in state-of-the-art technologies involved in organic synthesis and chemical structure elucidation, have accelerated the numbers of antimicrobial molecules originating from the ocean moving into clinical trials. The chemical diversity associated with these marine-derived molecules is immense, varying from simple linear peptides and fatty acids to complex alkaloids, terpenes and polyketides, etc. Such an array of structurally distinct molecules performs functionally diverse biological activities against many pathogenic bacteria and fungi, making marine-derived natural products valuable commodities, particularly in the current age of antimicrobial resistance. In this review, we have highlighted several marine-derived natural products (and their synthetic derivatives), which have gained recognition as effective antimicrobial agents over the past five years (2012-2017). These natural products have been categorized based on their chemical structures and the structure-activity mediated relationships of some of these bioactive molecules have been discussed. Finally, we have provided an insight into how genome mining efforts are likely to expedite the discovery of novel antimicrobial compounds.

Streptococcus pneumoniae Supragenome Hybridization Arrays for Profiling of Genetic Content and Gene Expression.

PubMed

Kadam, Anagha; Janto, Benjamin; Eutsey, Rory; Earl, Joshua P; Powell, Evan; Dahlgren, Margaret E; Hu, Fen Z; Ehrlich, Garth D; Hiller, N Luisa

2015-02-02

There is extensive genomic diversity among Streptococcus pneumoniae isolates. Approximately half of the comprehensive set of genes in the species (the supragenome or pangenome) is present in all the isolates (core set), and the remaining is unevenly distributed among strains (distributed set). The Streptococcus pneumoniae Supragenome Hybridization (SpSGH) array provides coverage for an extensive set of genes and polymorphisms encountered within this species, capturing this genomic diversity. Further, the capture is quantitative. In this manner, the SpSGH array allows for both genomic and transcriptomic analyses of diverse S. pneumoniae isolates on a single platform. In this unit, we present the SpSGH array, and describe in detail its design and implementation for both genomic and transcriptomic analyses. The methodology can be applied to construction and modification of SpSGH array platforms, as well to other bacterial species as long as multiple whole-genome sequences are available that collectively capture the vast majority of the species supragenome. Copyright © 2015 John Wiley & Sons, Inc.

Genome-wide characterization of genetic diversity and population structure in Secale

PubMed Central

2014-01-01

Background Numerous rye accessions are stored in ex situ genebanks worldwide. Little is known about the extent of genetic diversity contained in any of them and its relation to contemporary varieties, since to date rye genetic diversity studies had a very limited scope, analyzing few loci and/ or few accessions. Development of high throughput genotyping methods for rye opened the possibility for genome wide characterizations of large accessions sets. In this study we used 1054 Diversity Array Technology (DArT) markers with defined chromosomal location to characterize genetic diversity and population structure in a collection of 379 rye accessions including wild species, landraces, cultivated materials, historical and contemporary rye varieties. Results Average genetic similarity (GS) coefficients and average polymorphic information content (PIC) values varied among chromosomes. Comparison of chromosome specific average GS within and between germplasm sub-groups indicated regions of chromosomes 1R and 4R as being targeted by selection in current breeding programs. Bayesian clustering, principal coordinate analysis and Neighbor Joining clustering demonstrated that source and improvement status contributed significantly to the structure observed in the analyzed set of Secale germplasm. We revealed a relatively limited diversity in improved rye accessions, both historical and contemporary, as well as lack of correlation between clustering of improved accessions and geographic origin, suggesting common genetic background of rye accessions from diverse geographic regions and extensive germplasm exchange. Moreover, contemporary varieties were distinct from the remaining accessions. Conclusions Our results point to an influence of reproduction methods on the observed diversity patterns and indicate potential of ex situ collections for broadening the genetic diversity in rye breeding programs. Obtained data show that DArT markers provide a realistic picture of the genetic diversity and population structure present in the collection of 379 rye accessions and are an effective platform for rye germplasm characterization and association mapping studies. PMID:25085433

High-throughput genotyping of hop (Humulus lupulus L.) utilising diversity arrays technology (DArT)

USDA-ARS?s Scientific Manuscript database

Implementation of molecular methods in hop breeding is dependent on the availability of sizeable numbers of polymorphic markers and a comprehensive understanding of genetic variation. Diversity Arrays Technology (DArT) is a high-throughput cost-effective method for the discovery of large numbers of...

Diversity in the organization of elastin bundles and intramembranous muscles in bat wings.

PubMed

Cheney, Jorn A; Allen, Justine J; Swartz, Sharon M

2017-04-01

Unlike birds and insects, bats fly with wings composed of thin skin that envelops the bones of the forelimb and spans the area between the limbs, digits, and sometimes the tail. This skin is complex and unusual; it is thinner than typical mammalian skin and contains organized bundles of elastin and embedded skeletal muscles. These elements are likely responsible for controlling the shape of the wing during flight and contributing to the aerodynamic capabilities of bats. We examined the arrangement of two macroscopic architectural elements in bat wings, elastin bundles and wing membrane muscles, to assess the diversity in bat wing skin morphology. We characterized the plagiopatagium and dactylopatagium of 130 species from 17 families of bats using cross-polarized light imaging. This method revealed structures with distinctive relative birefringence, heterogeneity of birefringence, variation in size, and degree of branching. We used previously published anatomical studies and tissue histology to identify birefringent structures, and we analyzed their architecture across taxa. Elastin bundles, muscles, neurovasculature, and collagenous fibers are present in all species. Elastin bundles are oriented in a predominantly spanwise or proximodistal direction, and there are five characteristic muscle arrays that occur within the plagiopatagium, far more muscle than typically recognized. These results inform recent functional studies of wing membrane architecture, support the functional hypothesis that elastin bundles aid wing folding and unfolding, and further suggest that all bats may use these architectural elements for flight. All species also possess numerous muscles within the wing membrane, but the architecture of muscle arrays within the plagiopatagium varies among families. To facilitate present and future discussion of these muscle arrays, we refine wing membrane muscle nomenclature in a manner that reflects this morphological diversity. The architecture of the constituents of the skin of the wing likely plays a key role in shaping wings during flight. © 2017 Anatomical Society.

Designed synthesis of double-stage two-dimensional covalent organic frameworks

PubMed Central

Chen, Xiong; Addicoat, Matthew; Jin, Enquan; Xu, Hong; Hayashi, Taku; Xu, Fei; Huang, Ning; Irle, Stephan; Jiang, Donglin

2015-01-01

Covalent organic frameworks (COFs) are an emerging class of crystalline porous polymers in which organic building blocks are covalently and topologically linked to form extended crystalline polygon structures, constituting a new platform for designing π-electronic porous materials. However, COFs are currently synthesised by a few chemical reactions, limiting the access to and exploration of new structures and properties. The development of new reaction systems that avoid such limitations to expand structural diversity is highly desired. Here we report that COFs can be synthesised via a double-stage connection that polymerises various different building blocks into crystalline polygon architectures, leading to the development of a new type of COFs with enhanced structural complexity and diversity. We show that the double-stage approach not only controls the sequence of building blocks but also allows fine engineering of pore size and shape. This strategy is widely applicable to different polymerisation systems to yield hexagonal, tetragonal and rhombus COFs with predesigned pores and π-arrays. PMID:26456081

Designed synthesis of double-stage two-dimensional covalent organic frameworks

NASA Astrophysics Data System (ADS)

Chen, Xiong; Addicoat, Matthew; Jin, Enquan; Xu, Hong; Hayashi, Taku; Xu, Fei; Huang, Ning; Irle, Stephan; Jiang, Donglin

2015-10-01

Covalent organic frameworks (COFs) are an emerging class of crystalline porous polymers in which organic building blocks are covalently and topologically linked to form extended crystalline polygon structures, constituting a new platform for designing π-electronic porous materials. However, COFs are currently synthesised by a few chemical reactions, limiting the access to and exploration of new structures and properties. The development of new reaction systems that avoid such limitations to expand structural diversity is highly desired. Here we report that COFs can be synthesised via a double-stage connection that polymerises various different building blocks into crystalline polygon architectures, leading to the development of a new type of COFs with enhanced structural complexity and diversity. We show that the double-stage approach not only controls the sequence of building blocks but also allows fine engineering of pore size and shape. This strategy is widely applicable to different polymerisation systems to yield hexagonal, tetragonal and rhombus COFs with predesigned pores and π-arrays.

Genetic Diversity within a Global Panel of Durum Wheat (Triticum durum) Landraces and Modern Germplasm Reveals the History of Alleles Exchange.

PubMed

Kabbaj, Hafssa; Sall, Amadou T; Al-Abdallat, Ayed; Geleta, Mulatu; Amri, Ahmed; Filali-Maltouf, Abdelkarim; Belkadi, Bouchra; Ortiz, Rodomiro; Bassi, Filippo M

2017-01-01

Durum wheat is the 10th most important crop in the world, and its use traces back to the origin of agriculture. Unfortunately, in the last century only part of the genetic diversity available for this species has been captured in modern varieties through breeding. Here, the population structure and genetic diversity shared among elites and landraces collected from 32 countries was investigated. A total of 370 entries were genotyped with Axiom 35K array to identify 8,173 segregating single nucleotide polymorphisms (SNPs). Of these, 500 were selected as highly informative with a PIC value above 0.32 and used to test population structure via DAPC, STRUCTURE, and neighbor joining tree. A total of 10 sub-populations could be identified, six constituted by modern germplasm and four by landraces of different geographical origin. Interestingly, genomic comparison among groups indicated that Middle East and Ethiopia had the lowest level of allelic diversity, while breeding programs and landraces collected outside these regions were the richest in rare alleles. Further, phylogenetic analysis among landraces indicated that Ethiopia might represent a second center of origin of durum wheat, rather than a second domestication site as previously believed. Together, the analyses carried here provide a global picture of the available genetic diversity for this crop and shall guide its targeted use by breeders.

Community Structure of Lithotrophically-Driven Hydrothermal Microbial Mats from the Mariana Arc and Back-Arc

PubMed Central

Hager, Kevin W.; Fullerton, Heather; Butterfield, David A.; Moyer, Craig L.

2017-01-01

The Mariana region exhibits a rich array of hydrothermal venting conditions in a complex geological setting, which provides a natural laboratory to study the influence of local environmental conditions on microbial community structure as well as large-scale patterns in microbial biogeography. We used high-throughput amplicon sequencing of the bacterial small subunit (SSU) rRNA gene from 22 microbial mats collected from four hydrothermally active locations along the Mariana Arc and back-arc to explore the structure of lithotrophically-based microbial mat communities. The vent effluent was classified as iron- or sulfur-rich corresponding with two distinct community types, dominated by either Zetaproteobacteria or Epsilonproteobacteria, respectively. The Zetaproteobacterial-based communities had the highest richness and diversity, which supports the hypothesis that Zetaproteobacteria function as ecosystem engineers creating a physical habitat within a chemical environment promoting enhanced microbial diversity. Gammaproteobacteria were also high in abundance within the iron-dominated mats and some likely contribute to primary production. In addition, we also compare sampling scale, showing that bulk sampling of microbial mats yields higher diversity than micro-scale sampling. We present a comprehensive analysis and offer new insights into the community structure and diversity of lithotrophically-driven microbial mats from a hydrothermal region associated with high microbial biodiversity. Our study indicates an important functional role of for the Zetaproteobacteria altering the mat habitat and enhancing community interactions and complexity. PMID:28970817

The structure and dynamics of tandem WW domains in a negative regulator of notch signaling, Suppressor of deltex.

PubMed

Fedoroff, Oleg Y; Townson, Sharon A; Golovanov, Alexander P; Baron, Martin; Avis, Johanna M

2004-08-13

WW domains mediate protein recognition, usually though binding to proline-rich sequences. In many proteins, WW domains occur in tandem arrays. Whether or how individual domains within such arrays cooperate to recognize biological partners is, as yet, poorly characterized. An important question is whether functional diversity of different WW domain proteins is reflected in the structural organization and ligand interaction mechanisms of their multiple domains. We have determined the solution structure and dynamics of a pair of WW domains (WW3-4) from a Drosophila Nedd4 family protein called Suppressor of deltex (Su(dx)), a regulator of Notch receptor signaling. We find that the binding of a type 1 PPPY ligand to WW3 stabilizes the structure with effects propagating to the WW4 domain, a domain that is not active for ligand binding. Both WW domains adopt the characteristic triple-stranded beta-sheet structure, and significantly, this is the first example of a WW domain structure to include a domain (WW4) lacking the second conserved Trp (replaced by Phe). The domains are connected by a flexible linker, which allows a hinge-like motion of domains that may be important for the recognition of functionally relevant targets. Our results contrast markedly with those of the only previously determined three-dimensional structure of tandem WW domains, that of the rigidly oriented WW domain pair from the RNA-splicing factor Prp40. Our data illustrate that arrays of WW domains can exhibit a variety of higher order structures and ligand interaction mechanisms.

A review of cetacean lung morphology and mechanics.

PubMed

Piscitelli, Marina A; Raverty, Stephen A; Lillie, Margo A; Shadwick, Robert E

2013-12-01

Cetaceans possess diverse adaptations in respiratory structure and mechanics that are highly specialized for an array of surfacing and diving behaviors. Some of these adaptations and air management strategies are still not completely understood despite over a century of study. We have compiled the historical and contemporary knowledge of cetacean lung anatomy and mechanics in regards to normal lung function during ventilation and air management while diving. New techniques are emerging utilizing pulmonary mechanics to measure lung function in live cetaceans. Given the diversity of respiratory adaptations in cetaceans, interpretations of these results should consider species-specific anatomy, mechanics, and behavior. Copyright © 2013 Wiley Periodicals, Inc.

Gold bugs and beyond: a review of iridescence and structural colour mechanisms in beetles (Coleoptera)

PubMed Central

Seago, Ainsley E.; Brady, Parrish; Vigneron, Jean-Pol; Schultz, Tom D.

2008-01-01

Members of the order Coleoptera are sometimes referred to as ‘living jewels’, in allusion to the strikingly diverse array of iridescence mechanisms and optical effects that have arisen in beetles. A number of novel and sophisticated reflectance mechanisms have been discovered in recent years, including three-dimensional photonic crystals and quasi-ordered coherent scattering arrays. However, the literature on beetle structural coloration is often redundant and lacks synthesis, with little interchange between the entomological and optical research communities. Here, an overview is provided for all iridescence mechanisms observed in Coleoptera. Types of iridescence are illustrated and classified into three mechanistic groups: multilayer reflectors, three-dimensional photonic crystals and diffraction gratings. Taxonomic and phylogenetic distributions are provided, along with discussion of the putative functions and evolutionary pathways by which iridescence has repeatedly arisen in beetles. PMID:18957361

Diversity Arrays Technology (DArT) platform for genotyping and mapping in carrot (Daucus carota L.)

USDA-ARS?s Scientific Manuscript database

Carrot is one of the most important root vegetable crops grown worldwide on more than one million hectares. Its progenitor, wild Daucus carota, is a weed commonly occurring across continents in the temperate climatic zone. Diversity Array Technology (DArT) is a microarray-based molecular marker syst...

Characterization of a Wheat Breeders' Array suitable for high-throughput SNP genotyping of global accessions of hexaploid bread wheat (Triticum aestivum).

PubMed

Allen, Alexandra M; Winfield, Mark O; Burridge, Amanda J; Downie, Rowena C; Benbow, Harriet R; Barker, Gary L A; Wilkinson, Paul A; Coghill, Jane; Waterfall, Christy; Davassi, Alessandro; Scopes, Geoff; Pirani, Ali; Webster, Teresa; Brew, Fiona; Bloor, Claire; Griffiths, Simon; Bentley, Alison R; Alda, Mark; Jack, Peter; Phillips, Andrew L; Edwards, Keith J

2017-03-01

Targeted selection and inbreeding have resulted in a lack of genetic diversity in elite hexaploid bread wheat accessions. Reduced diversity can be a limiting factor in the breeding of high yielding varieties and crucially can mean reduced resilience in the face of changing climate and resource pressures. Recent technological advances have enabled the development of molecular markers for use in the assessment and utilization of genetic diversity in hexaploid wheat. Starting with a large collection of 819 571 previously characterized wheat markers, here we describe the identification of 35 143 single nucleotide polymorphism-based markers, which are highly suited to the genotyping of elite hexaploid wheat accessions. To assess their suitability, the markers have been validated using a commercial high-density Affymetrix Axiom ® genotyping array (the Wheat Breeders' Array), in a high-throughput 384 microplate configuration, to characterize a diverse global collection of wheat accessions including landraces and elite lines derived from commercial breeding communities. We demonstrate that the Wheat Breeders' Array is also suitable for generating high-density genetic maps of previously uncharacterized populations and for characterizing novel genetic diversity produced by mutagenesis. To facilitate the use of the array by the wheat community, the markers, the associated sequence and the genotype information have been made available through the interactive web site 'CerealsDB'. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Three-Dimensionally Functionalized Reverse Phase Glycoprotein Array for Cancer Biomarker Discovery and Validation.

PubMed

Pan, Li; Aguilar, Hillary Andaluz; Wang, Linna; Iliuk, Anton; Tao, W Andy

2016-11-30

Glycoproteins have vast structural diversity that plays an important role in many biological processes and have great potential as disease biomarkers. Here, we report a novel functionalized reverse phase protein array (RPPA), termed polymer-based reverse phase glycoprotein array (polyGPA), to capture and profile glycoproteomes specifically, and validate glycoproteins. Nitrocellulose membrane functionalized with globular hydroxyaminodendrimers was used to covalently capture preoxidized glycans on glycoproteins from complex protein samples such as biofluids. The captured glycoproteins were subsequently detected using the same validated antibodies as in RPPA. We demonstrated the outstanding specificity, sensitivity, and quantitative capabilities of polyGPA by capturing and detecting purified as well as endogenous α-1-acid glycoprotein (AGP) in human plasma. We further applied quantitative N-glycoproteomics and the strategy to validate a panel of glycoproteins identified as potential biomarkers for bladder cancer by analyzing urine glycoproteins from bladder cancer patients or matched healthy individuals.

Nano-array integrated monolithic devices: toward rational materials design and multi-functional performance by scalable nanostructures assembly

DOE PAGES

Wang, Sibo; Ren, Zheng; Guo, Yanbing; ...

2016-03-21

We report the scalable three-dimensional (3-D) integration of functional nanostructures into applicable platforms represents a promising technology to meet the ever-increasing demands of fabricating high performance devices featuring cost-effectiveness, structural sophistication and multi-functional enabling. Such an integration process generally involves a diverse array of nanostructural entities (nano-entities) consisting of dissimilar nanoscale building blocks such as nanoparticles, nanowires, and nanofilms made of metals, ceramics, or polymers. Various synthetic strategies and integration methods have enabled the successful assembly of both structurally and functionally tailored nano-arrays into a unique class of monolithic devices. The performance of nano-array based monolithic devices is dictated bymore » a few important factors such as materials substrate selection, nanostructure composition and nano-architecture geometry. Therefore, the rational material selection and nano-entity manipulation during the nano-array integration process, aiming to exploit the advantageous characteristics of nanostructures and their ensembles, are critical steps towards bridging the design of nanostructure integrated monolithic devices with various practical applications. In this article, we highlight the latest research progress of the two-dimensional (2-D) and 3-D metal and metal oxide based nanostructural integrations into prototype devices applicable with ultrahigh efficiency, good robustness and improved functionality. Lastly, selective examples of nano-array integration, scalable nanomanufacturing and representative monolithic devices such as catalytic converters, sensors and batteries will be utilized as the connecting dots to display a roadmap from hierarchical nanostructural assembly to practical nanotechnology implications ranging from energy, environmental, to chemical and biotechnology areas.« less

Nano-array integrated monolithic devices: toward rational materials design and multi-functional performance by scalable nanostructures assembly

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

Wang, Sibo; Ren, Zheng; Guo, Yanbing

We report the scalable three-dimensional (3-D) integration of functional nanostructures into applicable platforms represents a promising technology to meet the ever-increasing demands of fabricating high performance devices featuring cost-effectiveness, structural sophistication and multi-functional enabling. Such an integration process generally involves a diverse array of nanostructural entities (nano-entities) consisting of dissimilar nanoscale building blocks such as nanoparticles, nanowires, and nanofilms made of metals, ceramics, or polymers. Various synthetic strategies and integration methods have enabled the successful assembly of both structurally and functionally tailored nano-arrays into a unique class of monolithic devices. The performance of nano-array based monolithic devices is dictated bymore » a few important factors such as materials substrate selection, nanostructure composition and nano-architecture geometry. Therefore, the rational material selection and nano-entity manipulation during the nano-array integration process, aiming to exploit the advantageous characteristics of nanostructures and their ensembles, are critical steps towards bridging the design of nanostructure integrated monolithic devices with various practical applications. In this article, we highlight the latest research progress of the two-dimensional (2-D) and 3-D metal and metal oxide based nanostructural integrations into prototype devices applicable with ultrahigh efficiency, good robustness and improved functionality. Lastly, selective examples of nano-array integration, scalable nanomanufacturing and representative monolithic devices such as catalytic converters, sensors and batteries will be utilized as the connecting dots to display a roadmap from hierarchical nanostructural assembly to practical nanotechnology implications ranging from energy, environmental, to chemical and biotechnology areas.« less

GeoChip-Based Analysis of the Functional Gene Diversity and Metabolic Potential of Microbial Communities in Acid Mine Drainage▿ †

PubMed Central

Xie, Jianping; He, Zhili; Liu, Xinxing; Liu, Xueduan; Van Nostrand, Joy D.; Deng, Ye; Wu, Liyou; Zhou, Jizhong; Qiu, Guanzhou

2011-01-01

Acid mine drainage (AMD) is an extreme environment, usually with low pH and high concentrations of metals. Although the phylogenetic diversity of AMD microbial communities has been examined extensively, little is known about their functional gene diversity and metabolic potential. In this study, a comprehensive functional gene array (GeoChip 2.0) was used to analyze the functional diversity, composition, structure, and metabolic potential of AMD microbial communities from three copper mines in China. GeoChip data indicated that these microbial communities were functionally diverse as measured by the number of genes detected, gene overlapping, unique genes, and various diversity indices. Almost all key functional gene categories targeted by GeoChip 2.0 were detected in the AMD microbial communities, including carbon fixation, carbon degradation, methane generation, nitrogen fixation, nitrification, denitrification, ammonification, nitrogen reduction, sulfur metabolism, metal resistance, and organic contaminant degradation, which suggested that the functional gene diversity was higher than was previously thought. Mantel test results indicated that AMD microbial communities are shaped largely by surrounding environmental factors (e.g., S, Mg, and Cu). Functional genes (e.g., narG and norB) and several key functional processes (e.g., methane generation, ammonification, denitrification, sulfite reduction, and organic contaminant degradation) were significantly (P < 0.10) correlated with environmental variables. This study presents an overview of functional gene diversity and the structure of AMD microbial communities and also provides insights into our understanding of metabolic potential in AMD ecosystems. PMID:21097602

Long-term balanced fertilization increases the soil microbial functional diversity in a phosphorus-limited paddy soil.

PubMed

Su, Jian-Qiang; Ding, Long-Jun; Xue, Kai; Yao, Huai-Ying; Quensen, John; Bai, Shi-Jie; Wei, Wen-Xue; Wu, Jin-Shui; Zhou, Jizhong; Tiedje, James M; Zhu, Yong-Guan

2015-01-01

The influence of long-term chemical fertilization on soil microbial communities has been one of the frontier topics of agricultural and environmental sciences and is critical for linking soil microbial flora with soil functions. In this study, 16S rRNA gene pyrosequencing and a functional gene array, geochip 4.0, were used to investigate the shifts in microbial composition and functional gene structure in paddy soils with different fertilization treatments over a 22-year period. These included a control without fertilizers; chemical nitrogen fertilizer (N); N and phosphate (NP); N and potassium (NK); and N, P and K (NPK). Based on 16S rRNA gene data, both species evenness and key genera were affected by P fertilization. Functional gene array-based analysis revealed that long-term fertilization significantly changed the overall microbial functional structures. Chemical fertilization significantly increased the diversity and abundance of most genes involved in C, N, P and S cycling, especially for the treatments NK and NPK. Significant correlations were found among functional gene structure and abundance, related soil enzymatic activities and rice yield, suggesting that a fertilizer-induced shift in the microbial community may accelerate the nutrient turnover in soil, which in turn influenced rice growth. The effect of N fertilization on soil microbial functional genes was mitigated by the addition of P fertilizer in this P-limited paddy soil, suggesting that balanced chemical fertilization is beneficial to the soil microbial community and its functions. © 2014 John Wiley & Sons Ltd.

Who Are the Okinawans? Ancestry, Genome Diversity, and Implications for the Genetic Study of Human Longevity From a Geographically Isolated Population

PubMed Central

Hsueh, Wen-Chi; He, Qimei; Willcox, D. Craig; Nievergelt, Caroline M.; Donlon, Timothy A.; Kwok, Pui-Yan; Suzuki, Makoto; Willcox, Bradley J.

2014-01-01

Isolated populations have advantages for genetic studies of longevity from decreased haplotype diversity and long-range linkage disequilibrium. This permits smaller sample sizes without loss of power, among other utilities. Little is known about the genome of the Okinawans, a potential population isolate, recognized for longevity. Therefore, we assessed genetic diversity, structure, and admixture in Okinawans, and compared this with Caucasians, Chinese, Japanese, and Africans from HapMap II, genotyped on the same Affymetrix GeneChip Human Mapping 500K array. Principal component analysis, haplotype coverage, and linkage disequilibrium decay revealed a distinct Okinawan genome—more homogeneity, less haplotype diversity, and longer range linkage disequilibrium. Population structure and admixture analyses utilizing 52 global reference populations from the Human Genome Diversity Cell Line Panel demonstrated that Okinawans clustered almost exclusively with East Asians. Sibling relative risk (λs) analysis revealed that siblings of Okinawan centenarians have 3.11 times (females) and 3.77 times (males) more likelihood of centenarianism. These findings suggest that Okinawans are genetically distinct and share several characteristics of a population isolate, which are prone to develop extreme phenotypes (eg, longevity) from genetic drift, natural selection, and population bottlenecks. These data support further exploration of genetic influence on longevity in the Okinawans. PMID:24444611

Characterization of the macrocyclase involved in the biosynthesis of RiPP cyclic peptides in plants.

PubMed

Chekan, Jonathan R; Estrada, Paola; Covello, Patrick S; Nair, Satish K

2017-06-20

Enzymes that can catalyze the macrocyclization of linear peptide substrates have long been sought for the production of libraries of structurally diverse scaffolds via combinatorial gene assembly as well as to afford rapid in vivo screening methods. Orbitides are plant ribosomally synthesized and posttranslationally modified peptides (RiPPs) of various sizes and topologies, several of which are shown to be biologically active. The diversity in size and sequence of orbitides suggests that the corresponding macrocyclases may be ideal catalysts for production of cyclic peptides. Here we present the biochemical characterization and crystal structures of the plant enzyme PCY1 involved in orbitide macrocyclization. These studies demonstrate how the PCY1 S9A protease fold has been adapted for transamidation, rather than hydrolysis, of acyl-enzyme intermediates to yield cyclic products. Notably, PCY1 uses an unusual strategy in which the cleaved C-terminal follower peptide from the substrate stabilizes the enzyme in a productive conformation to facilitate macrocyclization of the N-terminal fragment. The broad substrate tolerance of PCY1 can be exploited as a biotechnological tool to generate structurally diverse arrays of macrocycles, including those with nonproteinogenic elements.

System-Level Performance of Antenna Arrays in CDMA-Based Cellular Mobile Radio Systems

NASA Astrophysics Data System (ADS)

Czylwik, Andreas; Dekorsy, Armin

2004-12-01

Smart antennas exploit the inherent spatial diversity of the mobile radio channel, provide an antenna gain, and also enable spatial interference suppression leading to reduced intracell as well as intercell interference. Especially, for the downlink of future CDMA-based mobile communications systems, transmit beamforming is seen as a well-promising smart antenna technique. The main objective of this paper is to study the performance of diverse antenna array topologies when applied for transmit beamforming in the downlink of CDMA-based networks. In this paper, we focus on uniform linear array (ULA) and uniform circular array (UCA) topologies. For the ULA, we consider three-sector base stations with one linear array per sector. While recent research on downlink beamforming is often restricted to one single cell, this study takes into account the important impact of intercell interference on the performance by evaluating complete networks. Especially, from the operator perspective, system capacity and system coverage are very essential parameters of a cellular system so that there is a clear necessity of intensive system level investigations. Apart from delivering assessments on the performance of the diverse antenna array topologies, in the paper also different antenna array parameters, such as element spacing and beamwidth of the sector antennas, are optimized. Although we focus on the network level, fast channel fluctuations are taken into account by including them analytically into the signal-to-interference calculation.

Current Status and Future Prospects of Marine Natural Products (MNPs) as Antimicrobials

PubMed Central

Choudhary, Alka; Naughton, Lynn M.; Montánchez, Itxaso

2017-01-01

The marine environment is a rich source of chemically diverse, biologically active natural products, and serves as an invaluable resource in the ongoing search for novel antimicrobial compounds. Recent advances in extraction and isolation techniques, and in state-of-the-art technologies involved in organic synthesis and chemical structure elucidation, have accelerated the numbers of antimicrobial molecules originating from the ocean moving into clinical trials. The chemical diversity associated with these marine-derived molecules is immense, varying from simple linear peptides and fatty acids to complex alkaloids, terpenes and polyketides, etc. Such an array of structurally distinct molecules performs functionally diverse biological activities against many pathogenic bacteria and fungi, making marine-derived natural products valuable commodities, particularly in the current age of antimicrobial resistance. In this review, we have highlighted several marine-derived natural products (and their synthetic derivatives), which have gained recognition as effective antimicrobial agents over the past five years (2012–2017). These natural products have been categorized based on their chemical structures and the structure-activity mediated relationships of some of these bioactive molecules have been discussed. Finally, we have provided an insight into how genome mining efforts are likely to expedite the discovery of novel antimicrobial compounds. PMID:28846659

Invited Article: Mask-modulated lensless imaging with multi-angle illuminations

NASA Astrophysics Data System (ADS)

Zhang, Zibang; Zhou, You; Jiang, Shaowei; Guo, Kaikai; Hoshino, Kazunori; Zhong, Jingang; Suo, Jinli; Dai, Qionghai; Zheng, Guoan

2018-06-01

The use of multiple diverse measurements can make lensless phase retrieval more robust. Conventional diversity functions include aperture diversity, wavelength diversity, translational diversity, and defocus diversity. Here we discuss a lensless imaging scheme that employs multiple spherical-wave illuminations from a light-emitting diode array as diversity functions. In this scheme, we place a binary mask between the sample and the detector for imposing support constraints for the phase retrieval process. This support constraint enforces the light field to be zero at certain locations and is similar to the aperture constraint in Fourier ptychographic microscopy. We use a self-calibration algorithm to correct the misalignment of the binary mask. The efficacy of the proposed scheme is first demonstrated by simulations where we evaluate the reconstruction quality using mean square error and structural similarity index. The scheme is then experimentally tested by recovering images of a resolution target and biological samples. The proposed scheme may provide new insights for developing compact and large field-of-view lensless imaging platforms. The use of the binary mask can also be combined with other diversity functions for better constraining the phase retrieval solution space. We provide the open-source implementation code for the broad research community.

Nuclear export receptor CRM1 recognizes diverse conformations in nuclear export signals.

PubMed

Fung, Ho Yee Joyce; Fu, Szu-Chin; Chook, Yuh Min

2017-03-10

Nuclear export receptor CRM1 binds highly variable nuclear export signals (NESs) in hundreds of different cargoes. Previously we have shown that CRM1 binds NESs in both polypeptide orientations (Fung et al., 2015). Here, we show crystal structures of CRM1 bound to eight additional NESs which reveal diverse conformations that range from loop-like to all-helix, which occupy different extents of the invariant NES-binding groove. Analysis of all NES structures show 5-6 distinct backbone conformations where the only conserved secondary structural element is one turn of helix that binds the central portion of the CRM1 groove. All NESs also participate in main chain hydrogen bonding with human CRM1 Lys568 side chain, which acts as a specificity filter that prevents binding of non-NES peptides. The large conformational range of NES backbones explains the lack of a fixed pattern for its 3-5 hydrophobic anchor residues, which in turn explains the large array of peptide sequences that can function as NESs.

ER sheet persistence is coupled to myosin 1c–regulated dynamic actin filament arrays

PubMed Central

Joensuu, Merja; Belevich, Ilya; Rämö, Olli; Nevzorov, Ilya; Vihinen, Helena; Puhka, Maija; Witkos, Tomasz M.; Lowe, Martin; Vartiainen, Maria K.; Jokitalo, Eija

2014-01-01

The endoplasmic reticulum (ER) comprises a dynamic three-dimensional (3D) network with diverse structural and functional domains. Proper ER operation requires an intricate balance within and between dynamics, morphology, and functions, but how these processes are coupled in cells has been unclear. Using live-cell imaging and 3D electron microscopy, we identify a specific subset of actin filaments localizing to polygons defined by ER sheets and tubules and describe a role for these actin arrays in ER sheet persistence and, thereby, in maintenance of the characteristic network architecture by showing that actin depolymerization leads to increased sheet fluctuation and transformations and results in small and less abundant sheet remnants and a defective ER network distribution. Furthermore, we identify myosin 1c localizing to the ER-associated actin filament arrays and reveal a novel role for myosin 1c in regulating these actin structures, as myosin 1c manipulations lead to loss of the actin filaments and to similar ER phenotype as observed after actin depolymerization. We propose that ER-associated actin filaments have a role in ER sheet persistence regulation and thus support the maintenance of sheets as a stationary subdomain of the dynamic ER network. PMID:24523293

ER sheet persistence is coupled to myosin 1c-regulated dynamic actin filament arrays.

PubMed

Joensuu, Merja; Belevich, Ilya; Rämö, Olli; Nevzorov, Ilya; Vihinen, Helena; Puhka, Maija; Witkos, Tomasz M; Lowe, Martin; Vartiainen, Maria K; Jokitalo, Eija

2014-04-01

The endoplasmic reticulum (ER) comprises a dynamic three-dimensional (3D) network with diverse structural and functional domains. Proper ER operation requires an intricate balance within and between dynamics, morphology, and functions, but how these processes are coupled in cells has been unclear. Using live-cell imaging and 3D electron microscopy, we identify a specific subset of actin filaments localizing to polygons defined by ER sheets and tubules and describe a role for these actin arrays in ER sheet persistence and, thereby, in maintenance of the characteristic network architecture by showing that actin depolymerization leads to increased sheet fluctuation and transformations and results in small and less abundant sheet remnants and a defective ER network distribution. Furthermore, we identify myosin 1c localizing to the ER-associated actin filament arrays and reveal a novel role for myosin 1c in regulating these actin structures, as myosin 1c manipulations lead to loss of the actin filaments and to similar ER phenotype as observed after actin depolymerization. We propose that ER-associated actin filaments have a role in ER sheet persistence regulation and thus support the maintenance of sheets as a stationary subdomain of the dynamic ER network.

Plant lectins: the ties that bind in root symbiosis and plant defense.

PubMed

De Hoff, Peter L; Brill, Laurence M; Hirsch, Ann M

2009-07-01

Lectins are a diverse group of carbohydrate-binding proteins that are found within and associated with organisms from all kingdoms of life. Several different classes of plant lectins serve a diverse array of functions. The most prominent of these include participation in plant defense against predators and pathogens and involvement in symbiotic interactions between host plants and symbiotic microbes, including mycorrhizal fungi and nitrogen-fixing rhizobia. Extensive biological, biochemical, and molecular studies have shed light on the functions of plant lectins, and a plethora of uncharacterized lectin genes are being revealed at the genomic scale, suggesting unexplored and novel diversity in plant lectin structure and function. Integration of the results from these different types of research is beginning to yield a more detailed understanding of the function of lectins in symbiosis, defense, and plant biology in general.

Genetic structure of populations of Legionella pneumophila.

PubMed Central

Selander, R K; McKinney, R M; Whittam, T S; Bibb, W F; Brenner, D J; Nolte, F S; Pattison, P E

1985-01-01

The genetic structure of populations of Legionella pneumophila was defined by an analysis of electrophoretically demonstrable allelic variation at structural genes encoding 22 enzymes in 292 isolates from clinical and environmental sources. Nineteen of the loci were polymorphic, and 62 distinctive electrophoretic types (ETs), representing multilocus genotypes, were identified. Principal coordinates and clustering analyses demonstrated that isolates received as L. pneumophila were a heterogeneous array of genotypes that included two previously undescribed species. For 50 ETs of L. pneumophila (strict sense), mean genetic diversity per locus was 0.312, and diversity was equivalent in ETs represented by isolates recovered from clinical sources and those collected from environmental sources. Cluster analysis revealed four major groups or lineages of ETs in L. pneumophila. Genetic diversity among ETs of the same serotype was, on average, 93% of that in the total sample of ETs. Isolates marked by particular patterns of reactivity to a panel of nine monoclonal antibodies were also genetically heterogeneous, mean diversity within patterns being about 75% of the total. Both Pontiac fever and the pneumonic form of legionellosis may be caused by isolates of the same ET. The genetic structure of L. pneumophila is clonal, and many clones apparently are worldwide in distribution. The fact that L. pneumophila is only 60% as variable as Escherichia coli raises the possibility that isolates recovered from clinical cases and man-made environments are a restricted subset of all clones in the species as a whole. PMID:4030689

Genetic Diversity and Population Structure Analysis of European Hexaploid Bread Wheat (Triticum aestivum L.) Varieties

PubMed Central

Nielsen, Nanna Hellum; Backes, Gunter; Stougaard, Jens; Andersen, Stig Uggerhøj; Jahoor, Ahmed

2014-01-01

Progress in plant breeding is facilitated by accurate information about genetic structure and diversity. Here, Diversity Array Technology (DArT) was used to characterize a population of 94 bread wheat (Triticum aestivum L.) varieties of mainly European origin. In total, 1,849 of 7,000 tested markers were polymorphic and could be used for population structure analysis. Two major subgroups of wheat varieties, GrI and GrII, were identified using the program STRUCTURE, and confirmed by principal component analysis (PCA). These subgroups were largely separated according to origin; GrI comprised varieties from Southern and Eastern Europe, whereas GrII contained mostly modern varieties from Western and Northern Europe. A large proportion of the markers contributing most to the genetic separation of the subgroups were located on chromosome 2D near the Reduced height 8 (Rht8) locus, and PCR-based genotyping suggested that breeding for the Rht8 allele had a major impact on subgroup separation. Consistently, analysis of linkage disequilibrium (LD) suggested that different selective pressures had acted on chromosome 2D in the two subgroups. Our data provides an overview of the allele composition of bread wheat varieties anchored to DArT markers, which will facilitate targeted combination of alleles following DArT-based QTL studies. In addition, the genetic diversity and distance data combined with specific Rht8 genotypes can now be used by breeders to guide selection of crossing parents. PMID:24718292

Genetic diversity and population structure analysis of European hexaploid bread wheat (Triticum aestivum L.) varieties.

PubMed

Nielsen, Nanna Hellum; Backes, Gunter; Stougaard, Jens; Andersen, Stig Uggerhøj; Jahoor, Ahmed

2014-01-01

Progress in plant breeding is facilitated by accurate information about genetic structure and diversity. Here, Diversity Array Technology (DArT) was used to characterize a population of 94 bread wheat (Triticum aestivum L.) varieties of mainly European origin. In total, 1,849 of 7,000 tested markers were polymorphic and could be used for population structure analysis. Two major subgroups of wheat varieties, GrI and GrII, were identified using the program STRUCTURE, and confirmed by principal component analysis (PCA). These subgroups were largely separated according to origin; GrI comprised varieties from Southern and Eastern Europe, whereas GrII contained mostly modern varieties from Western and Northern Europe. A large proportion of the markers contributing most to the genetic separation of the subgroups were located on chromosome 2D near the Reduced height 8 (Rht8) locus, and PCR-based genotyping suggested that breeding for the Rht8 allele had a major impact on subgroup separation. Consistently, analysis of linkage disequilibrium (LD) suggested that different selective pressures had acted on chromosome 2D in the two subgroups. Our data provides an overview of the allele composition of bread wheat varieties anchored to DArT markers, which will facilitate targeted combination of alleles following DArT-based QTL studies. In addition, the genetic diversity and distance data combined with specific Rht8 genotypes can now be used by breeders to guide selection of crossing parents.

COMPUTATIONAL METHODOLOGIES for REAL-SPACE STRUCTURAL REFINEMENT of LARGE MACROMOLECULAR COMPLEXES

PubMed Central

Goh, Boon Chong; Hadden, Jodi A.; Bernardi, Rafael C.; Singharoy, Abhishek; McGreevy, Ryan; Rudack, Till; Cassidy, C. Keith; Schulten, Klaus

2017-01-01

The rise of the computer as a powerful tool for model building and refinement has revolutionized the field of structure determination for large biomolecular systems. Despite the wide availability of robust experimental methods capable of resolving structural details across a range of spatiotemporal resolutions, computational hybrid methods have the unique ability to integrate the diverse data from multimodal techniques such as X-ray crystallography and electron microscopy into consistent, fully atomistic structures. Here, commonly employed strategies for computational real-space structural refinement are reviewed, and their specific applications are illustrated for several large macromolecular complexes: ribosome, virus capsids, chemosensory array, and photosynthetic chromatophore. The increasingly important role of computational methods in large-scale structural refinement, along with current and future challenges, is discussed. PMID:27145875

Natural Allelic Diversity, Genetic Structure and Linkage Disequilibrium Pattern in Wild Chickpea

PubMed Central

Kujur, Alice; Das, Shouvik; Badoni, Saurabh; Kumar, Vinod; Singh, Mohar; Bansal, Kailash C.; Tyagi, Akhilesh K.; Parida, Swarup K.

2014-01-01

Characterization of natural allelic diversity and understanding the genetic structure and linkage disequilibrium (LD) pattern in wild germplasm accessions by large-scale genotyping of informative microsatellite and single nucleotide polymorphism (SNP) markers is requisite to facilitate chickpea genetic improvement. Large-scale validation and high-throughput genotyping of genome-wide physically mapped 478 genic and genomic microsatellite markers and 380 transcription factor gene-derived SNP markers using gel-based assay, fluorescent dye-labelled automated fragment analyser and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass array have been performed. Outcome revealed their high genotyping success rate (97.5%) and existence of a high level of natural allelic diversity among 94 wild and cultivated Cicer accessions. High intra- and inter-specific polymorphic potential and wider molecular diversity (11–94%) along with a broader genetic base (13–78%) specifically in the functional genic regions of wild accessions was assayed by mapped markers. It suggested their utility in monitoring introgression and transferring target trait-specific genomic (gene) regions from wild to cultivated gene pool for the genetic enhancement. Distinct species/gene pool-wise differentiation, admixed domestication pattern, and differential genome-wide recombination and LD estimates/decay observed in a six structured population of wild and cultivated accessions using mapped markers further signifies their usefulness in chickpea genetics, genomics and breeding. PMID:25222488

Outlook for coastal plain forests: a subregional report from the Southern Forest Futures Project

Treesearch

Kier Klepzig; Richard Shelfer; Zanethia Choice

2014-01-01

The U.S. Coastal Plain consists of seven sections: the Northern Atlantic, Eastern Atlantic, Peninsular Florida, Southern Gulf, Middle Gulf-East, Middle Gulf-West, and Western Gulf. It covers a large area, consists of a diverse array of habitats, and supports a diverse array of uses. This report presents forecasts from the Southern Forest Futures Project that are...

Antimicrobial peptides: a new class of antimalarial drugs?

PubMed Central

Vale, Nuno; Aguiar, Luísa; Gomes, Paula

2014-01-01

A range of antimicrobial peptides (AMP) exhibit activity on malaria parasites, Plasmodium spp., in their blood or mosquito stages, or both. These peptides include a diverse array of both natural and synthetic molecules varying greatly in size, charge, hydrophobicity, and secondary structure features. Along with an overview of relevant literature reports regarding AMP that display antiplasmodial activity, this review makes a few considerations about those molecules as a potential new class of antimalarial drugs. PMID:25566072

Wavelength selective switch array employing silica-based waveguide frontend with integrated polarization diversity optics.

PubMed

Sakamaki, Yohei; Shikama, Kota; Ikuma, Yuichiro; Suzuki, Kenya

2017-08-21

We propose a waveguide frontend with integrated polarization diversity optics for a wavelength selective switch (WSS) array with a liquid crystal on silicon switching engine to simplify the free space optics configuration and the alignment process in optical modules. The polarization diversity function is realized by the integration of a waveguide-type polarization beam splitter and a polarization rotating half-wave plate in a beam launcher using silica-based planar lightwave circuit technology. We confirmed experimentally the feasibility of using our proposed waveguide frontend in a two-in-one 1 × 20 WSS. The experimental results show that the fabricated waveguide frontend provides a polarization diversity function without any degradation in optical performance.

Genome-wide distribution of genetic diversity and linkage disequilibrium in a mass-selected population of maritime pine

PubMed Central

2014-01-01

Background The accessibility of high-throughput genotyping technologies has contributed greatly to the development of genomic resources in non-model organisms. High-density genotyping arrays have only recently been developed for some economically important species such as conifers. The potential for using genomic technologies in association mapping and breeding depends largely on the genome wide patterns of diversity and linkage disequilibrium in current breeding populations. This study aims to deepen our knowledge regarding these issues in maritime pine, the first species used for reforestation in south western Europe. Results Using a new map merging algorithm, we first established a 1,712 cM composite linkage map (comprising 1,838 SNP markers in 12 linkage groups) by bringing together three already available genetic maps. Using rigorous statistical testing based on kernel density estimation and resampling we identified cold and hot spots of recombination. In parallel, 186 unrelated trees of a mass-selected population were genotyped using a 12k-SNP array. A total of 2,600 informative SNPs allowed to describe historical recombination, genetic diversity and genetic structure of this recently domesticated breeding pool that forms the basis of much of the current and future breeding of this species. We observe very low levels of population genetic structure and find no evidence that artificial selection has caused a reduction in genetic diversity. By combining these two pieces of information, we provided the map position of 1,671 SNPs corresponding to 1,192 different loci. This made it possible to analyze the spatial pattern of genetic diversity (H e ) and long distance linkage disequilibrium (LD) along the chromosomes. We found no particular pattern in the empirical variogram of H e across the 12 linkage groups and, as expected for an outcrossing species with large effective population size, we observed an almost complete lack of long distance LD. Conclusions These results are a stepping stone for the development of strategies for studies in population genomics, association mapping and genomic prediction in this economical and ecologically important forest tree species. PMID:24581176

Bacterial CRISPR Regions: General Features and their Potential for Epidemiological Molecular Typing Studies.

PubMed

Karimi, Zahra; Ahmadi, Ali; Najafi, Ali; Ranjbar, Reza

2018-01-01

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) loci as novel and applicable regions in prokaryotic genomes have gained great attraction in the post genomics era. These unique regions are diverse in number and sequence composition in different pathogenic bacteria and thereby can be a suitable candidate for molecular epidemiology and genotyping studies. Results:Furthermore, the arrayed structure of CRISPR loci (several unique repeats spaced with the variable sequence) and associated cas genes act as an active prokaryotic immune system against viral replication and conjugative elements. This property can be used as a tool for RNA editing in bioengineering studies. The aim of this review was to survey some details about the history, nature, and potential applications of CRISPR arrays in both genetic engineering and bacterial genotyping studies.

GeoChip-based analysis of the microbial community functional structures in simultaneous desulfurization and denitrification process.

PubMed

Yu, Hao; Chen, Chuan; Ma, Jincai; Liu, Wenzong; Zhou, Jizhong; Lee, Duu-Jong; Ren, Nanqi; Wang, Aijie

2014-07-01

The elemental sulfur (S°) recovery was evaluated in the presence of nitrate in two development models of simultaneous desulfurization and denitrification (SDD) process. At the loading rates of 0.9 kg S/(m³·day) for sulfide and 0.4 kg N/(m³·day) for nitrate, S° conversion rate was 91.1% in denitrifying sulfide removal (DSR) model which was higher than in integrated simultaneous desulfurization and denitrification (ISDD) model (25.6%). A comprehensive analysis of functional diversity, structure and metabolic potential of microbial communities was examined in two models by using functional gene array (GeoChip 2.0). GeoChip data indicated that diversity indices, community structure, and abundance of functional genes were distinct between two models. Diversity indices (Simpson's diversity index (1/D) and Shannon-Weaver index (H')) of all detected genes showed that with elevated influent loading rate, the functional diversity decreased in ISDD model but increased in DSR model. In contrast to ISDD model, the overall abundance of dsr genes was lower in DSR model, while some functional genes targeting from nitrate-reducing sulfide-oxidizing bacteria (NR-SOB), such as Thiobacillus denitrificans, Sulfurimonas denitrificans, and Paracoccus pantotrophus were more abundant in DSR model which were highly associated with the change of S(0) conversion rate obtained in two models. The results obtained in this study provide additional insights into the microbial metabolic mechanisms involved in ISDD and DSR models, which in turn will improve the overall performance of SDD process. Copyright © 2014. Published by Elsevier B.V.

Exploring Biogeochemistry and Microbial Diversity of Extant Microbialites in Mexico and Cuba

PubMed Central

Valdespino-Castillo, Patricia M.; Hu, Ping; Merino-Ibarra, Martín; López-Gómez, Luz M.; Cerqueda-García, Daniel; González-De Zayas, Roberto; Pi-Puig, Teresa; Lestayo, Julio A.; Holman, Hoi-Ying; Falcón, Luisa I.

2018-01-01

Microbialites are modern analogs of ancient microbial consortia that date as far back as the Archaean Eon. Microbialites have contributed to the geochemical history of our planet through their diverse metabolic capacities that mediate mineral precipitation. These mineral-forming microbial assemblages accumulate major ions, trace elements and biomass from their ambient aquatic environments; their role in the resulting chemical structure of these lithifications needs clarification. We studied the biogeochemistry and microbial structure of microbialites collected from diverse locations in Mexico and in a previously undescribed microbialite in Cuba. We examined their structure, chemistry and mineralogy at different scales using an array of nested methods including 16S rRNA gene high-throughput sequencing, elemental analysis, X-Ray fluorescence (XRF), X-Ray diffraction (XRD), Scanning Electron Microscopy-Energy Dispersive Spectroscopy (SEM-EDS), Fourier Transformed Infrared (FTIR) spectroscopy and Synchrotron Radiation-based Fourier Transformed Infrared (SR-FTIR) spectromicroscopy. The resulting data revealed high biological and chemical diversity among microbialites and specific microbe to chemical correlations. Regardless of the sampling site, Proteobacteria had the most significant correlations with biogeochemical parameters such as organic carbon (Corg), nitrogen and Corg:Ca ratio. Biogeochemically relevant bacterial groups (dominant phototrophs and heterotrophs) showed significant correlations with major ion composition, mineral type and transition element content, such as cadmium, cobalt, chromium, copper and nickel. Microbial-chemical relationships were discussed in reference to microbialite formation, microbial metabolic capacities and the role of transition elements as enzyme cofactors. This paper provides an analytical baseline to drive our understanding of the links between microbial diversity with the chemistry of their lithified precipitations. PMID:29666607

Exploring Biogeochemistry and Microbial Diversity of Extant Microbialites in Mexico and Cuba.

PubMed

Valdespino-Castillo, Patricia M; Hu, Ping; Merino-Ibarra, Martín; López-Gómez, Luz M; Cerqueda-García, Daniel; González-De Zayas, Roberto; Pi-Puig, Teresa; Lestayo, Julio A; Holman, Hoi-Ying; Falcón, Luisa I

2018-01-01

Microbialites are modern analogs of ancient microbial consortia that date as far back as the Archaean Eon. Microbialites have contributed to the geochemical history of our planet through their diverse metabolic capacities that mediate mineral precipitation. These mineral-forming microbial assemblages accumulate major ions, trace elements and biomass from their ambient aquatic environments; their role in the resulting chemical structure of these lithifications needs clarification. We studied the biogeochemistry and microbial structure of microbialites collected from diverse locations in Mexico and in a previously undescribed microbialite in Cuba. We examined their structure, chemistry and mineralogy at different scales using an array of nested methods including 16S rRNA gene high-throughput sequencing, elemental analysis, X-Ray fluorescence (XRF), X-Ray diffraction (XRD), Scanning Electron Microscopy-Energy Dispersive Spectroscopy (SEM-EDS), Fourier Transformed Infrared (FTIR) spectroscopy and Synchrotron Radiation-based Fourier Transformed Infrared (SR-FTIR) spectromicroscopy. The resulting data revealed high biological and chemical diversity among microbialites and specific microbe to chemical correlations. Regardless of the sampling site, Proteobacteria had the most significant correlations with biogeochemical parameters such as organic carbon (C org ), nitrogen and C org :Ca ratio. Biogeochemically relevant bacterial groups (dominant phototrophs and heterotrophs) showed significant correlations with major ion composition, mineral type and transition element content, such as cadmium, cobalt, chromium, copper and nickel. Microbial-chemical relationships were discussed in reference to microbialite formation, microbial metabolic capacities and the role of transition elements as enzyme cofactors. This paper provides an analytical baseline to drive our understanding of the links between microbial diversity with the chemistry of their lithified precipitations.

The toxins of Cyanobacteria.

PubMed

Patocka, J

2001-01-01

Cyanobacteria, formerly called "blue-green algae", are simple, primitive photosynthetic microorganism wide occurrence in fresh, brackish and salt waters. Forty different genera of Cyanobacteria are known and many of them are producers of potent toxins responsible for a wide array of human illnesses, aquatic mammal and bird morbidity and mortality, and extensive fish kills. These cyanotoxins act as neurotoxins or hepatotoxins and are structurally and functionally diverse, and many are derived from unique biosynthetic pathways. All known cyanotoxins and their chemical and toxicological characteristics are presented in this article.

Organocatalytic C-H bond arylation of aldehydes to bis-heteroaryl ketones.

PubMed

Toh, Qiao Yan; McNally, Andrew; Vera, Silvia; Erdmann, Nico; Gaunt, Matthew J

2013-03-13

An organocatalytic aldehyde C-H bond arylation process for the synthesis of complex heteroaryl ketones has been developed. By exploiting the inherent electrophilicity of diaryliodonium salts, we have found that a commercial N-heterocyclic carbene catalyst promotes the union of heteroaryl aldehydes and these heteroaromatic electrophile equivalents in good yields. This straightforward catalytic protocol offers access to ketones bearing a diverse array of arene and heteroarene substituents that can subsequently be converted into molecules displaying structural motifs commonly found in medicinal agents.

Biomimetic multifunctional surfaces inspired from animals.

PubMed

Han, Zhiwu; Mu, Zhengzhi; Yin, Wei; Li, Wen; Niu, Shichao; Zhang, Junqiu; Ren, Luquan

2016-08-01

Over millions of years, animals have evolved to a higher intelligent level for their environment. A large number of diverse surface structures on their bodies have been formed to adapt to the extremely harsh environment. Just like the structural diversity existed in plants, the same also applies true in animals. Firstly, this article provides an overview and discussion of the most common functional surface structures inspired from animals, such as drag reduction, noise reduction, anti-adhesion, anti-wear, anti-erosion, anti-fog, water capture, and optical surfaces. Then, some typical characteristics of morphologies, structures, and materials of the animal multifunctional surfaces were discussed. The adaptation of these surfaces to environmental conditions was also analyzed. It mainly focuses on the relationship between their surface functions and their surface structural characteristics. Afterwards, the multifunctional mechanisms or principles of these surfaces were discussed. Models of these structures were provided for the development of structure materials and machinery surfaces. At last, fabrication techniques and existing or potential technical applications inspired from biomimetic multifunctional surfaces in animals were also discussed. The application prospects of the biomimetic functional surfaces are very broad, such as civil field of self-cleaning textile fabrics and non-stick pots, ocean field of oil-water separation, sports field of swimming suits, space development field of lens arrays. Copyright © 2016 Elsevier B.V. All rights reserved.

Vulnerability of coral reef fisheries to a loss of structural complexity.

PubMed

Rogers, Alice; Blanchard, Julia L; Mumby, Peter J

2014-05-05

Coral reefs face a diverse array of threats, from eutrophication and overfishing to climate change. As live corals are lost and their skeletons eroded, the structural complexity of reefs declines. This may have important consequences for the survival and growth of reef fish because complex habitats mediate predator-prey interactions [1, 2] and influence competition [3-5] through the provision of prey refugia. A positive correlation exists between structural complexity and reef fish abundance and diversity in both temperate and tropical ecosystems [6-10]. However, it is not clear how the diversity of available refugia interacts with individual predator-prey relationships to explain emergent properties at the community scale. Furthermore, we do not yet have the ability to predict how habitat loss might affect the productivity of whole reef communities and the fisheries they support. Using data from an unfished reserve in The Bahamas, we find that structural complexity is associated not only with increased fish biomass and abundance, but also with nonlinearities in the size spectra of fish, implying disproportionately high abundances of certain size classes. By developing a size spectrum food web model that links the vulnerability of prey to predation with the structural complexity of a reef, we show that these nonlinearities can be explained by size-structured prey refugia that reduce mortality rates and alter growth rates in different parts of the size spectrum. Fitting the model with data from a structurally complex habitat, we predict that a loss of complexity could cause more than a 3-fold reduction in fishery productivity. Copyright © 2014 Elsevier Ltd. All rights reserved.

Organic vapor discrimination with chemiresistor arrays of temperature modulated tin-oxide nanowires and thiolate-monolayer-protected gold nanoparticles.

PubMed

Scholten, K; Bohrer, F I; Dattoli, E; Lu, W; Zellers, E T

2011-03-25

This paper explores the discrimination of organic vapors with arrays of chemiresistors (CRs) employing interface layers of tin-oxide nanowires (NWs) and thiolate-monolayer-protected gold nanoparticles (MPNs). The former devices use contact-printed mats of NWs on micro-hotplate membranes to bridge a pair of metal electrodes. Oxidation at the NW surface causes changes in charge transport, the temperature dependence of which differs among different vapors, permitting vapor discrimination. The latter devices use solvent cast films of MPNs on interdigital electrodes operated at room temperature. Sorption into the organic monolayers causes changes in film tunneling resistance that differ among different vapors and MPN structures, permitting vapor discrimination. Here, we compare the performance and assess the 'complementarity' of these two types of sensors. Calibrated responses from an NW CR operated at two different temperatures and from a set of four different MPN CRs were generated for three test vapors: n-hexane, toluene, and nitromethane. This pooled data set was then analyzed using principal components regression classification models with varying degrees of random error superimposed on the responses via Monte Carlo simulation in order to estimate the rates of recognition/discrimination for arrays comprising different combinations of sensors. Results indicate that the diversity of most of the dual MPN-CR arrays exceeds that of the dual NW-CR array. Additionally, in assessing all possible arrays of 4-6 CR sensors, the recognition rates of the hybrid arrays (i.e. MPN + NW) were no better than that of the 4-sensor array containing only MPN CRs.

Development and Evaluation of a Genome-Wide 6K SNP Array for Diploid Sweet Cherry and Tetraploid Sour Cherry

PubMed Central

Peace, Cameron; Bassil, Nahla; Main, Dorrie; Ficklin, Stephen; Rosyara, Umesh R.; Stegmeir, Travis; Sebolt, Audrey; Gilmore, Barbara; Lawley, Cindy; Mockler, Todd C.; Bryant, Douglas W.; Wilhelm, Larry; Iezzoni, Amy

2012-01-01

High-throughput genome scans are important tools for genetic studies and breeding applications. Here, a 6K SNP array for use with the Illumina Infinium® system was developed for diploid sweet cherry (Prunus avium) and allotetraploid sour cherry (P. cerasus). This effort was led by RosBREED, a community initiative to enable marker-assisted breeding for rosaceous crops. Next-generation sequencing in diverse breeding germplasm provided 25 billion basepairs (Gb) of cherry DNA sequence from which were identified genome-wide SNPs for sweet cherry and for the two sour cherry subgenomes derived from sweet cherry (avium subgenome) and P. fruticosa (fruticosa subgenome). Anchoring to the peach genome sequence, recently released by the International Peach Genome Initiative, predicted relative physical locations of the 1.9 million putative SNPs detected, preliminarily filtered to 368,943 SNPs. Further filtering was guided by results of a 144-SNP subset examined with the Illumina GoldenGate® assay on 160 accessions. A 6K Infinium® II array was designed with SNPs evenly spaced genetically across the sweet and sour cherry genomes. SNPs were developed for each sour cherry subgenome by using minor allele frequency in the sour cherry detection panel to enrich for subgenome-specific SNPs followed by targeting to either subgenome according to alleles observed in sweet cherry. The array was evaluated using panels of sweet (n = 269) and sour (n = 330) cherry breeding germplasm. Approximately one third of array SNPs were informative for each crop. A total of 1825 polymorphic SNPs were verified in sweet cherry, 13% of these originally developed for sour cherry. Allele dosage was resolved for 2058 polymorphic SNPs in sour cherry, one third of these being originally developed for sweet cherry. This publicly available genomics resource represents a significant advance in cherry genome-scanning capability that will accelerate marker-locus-trait association discovery, genome structure investigation, and genetic diversity assessment in this diploid-tetraploid crop group. PMID:23284615

Gust prediction via artificial hair sensor array and neural network

NASA Astrophysics Data System (ADS)

Pankonien, Alexander M.; Thapa Magar, Kaman S.; Beblo, Richard V.; Reich, Gregory W.

2017-04-01

Gust Load Alleviation (GLA) is an important aspect of flight dynamics and control that reduces structural loadings and enhances ride quality. In conventional GLA systems, the structural response to aerodynamic excitation informs the control scheme. A phase lag, imposed by inertia, between the excitation and the measurement inherently limits the effectiveness of these systems. Hence, direct measurement of the aerodynamic loading can eliminate this lag, providing valuable information for effective GLA system design. Distributed arrays of Artificial Hair Sensors (AHS) are ideal for surface flow measurements that can be used to predict other necessary parameters such as aerodynamic forces, moments, and turbulence. In previous work, the spatially distributed surface flow velocities obtained from an array of artificial hair sensors using a Single-State (or feedforward) Neural Network were found to be effective in estimating the steady aerodynamic parameters such as air speed, angle of attack, lift and moment coefficient. This paper extends the investigation of the same configuration to unsteady force and moment estimation, which is important for active GLA control design. Implementing a Recurrent Neural Network that includes previous-timestep sensor information, the hair sensor array is shown to be capable of capturing gust disturbances with a wide range of periods, reducing predictive error in lift and moment by 68% and 52% respectively. The L2 norms of the first layer of the weight matrices were compared showing a 23% emphasis on prior versus current information. The Recurrent architecture also improves robustness, exhibiting only a 30% increase in predictive error when undertrained as compared to a 170% increase by the Single-State NN. This diverse, localized information can thus be directly implemented into a control scheme that alleviates the gusts without waiting for a structural response or requiring user-intensive sensor calibration.

Characterization of rhizosphere and endophytic bacterial communities from leaves, stems and roots of medicinal Stellera chamaejasme L.

PubMed

Jin, Hui; Yang, Xiao-Yan; Yan, Zhi-Qiang; Liu, Quan; Li, Xiu-Zhuang; Chen, Ji-Xiang; Zhang, Deng-Hong; Zeng, Li-Ming; Qin, Bo

2014-07-01

A diverse array of bacteria that inhabit the rhizosphere and different plant organs play a crucial role in plant health and growth. Therefore, a general understanding of these bacterial communities and their diversity is necessary. Using the 16S rRNA gene clone library technique, the bacterial community structure and diversity of the rhizosphere and endophytic bacteria in Stellera chamaejasme compartments were compared and clarified for the first time. Grouping of the sequences obtained showed that members of the Proteobacteria (43.2%), Firmicutes (36.5%) and Actinobacteria (14.1%) were dominant in both samples. Other groups that were consistently found, albeit at lower abundance, were Bacteroidetes (2.1%), Chloroflexi (1.9%), and Cyanobacteria (1.7%). The habitats (rhizosphere vs endophytes) and organs (leaf, stem and root) structured the community, since the Wilcoxon signed rank test indicated that more varied bacteria inhabited the rhizosphere compared to the organs of the plant. In addition, correspondence analysis also showed that differences were apparent in the bacterial communities associated with these distinct habitats. Moreover, principal component analysis revealed that the profiles obtained from the rhizosphere and roots were similar, whereas leaf and stem samples clustered together on the opposite side of the plot from the rhizosphere and roots. Taken together, these results suggested that, although the communities associated with the rhizosphere and organs shared some bacterial species, the associated communities differed in structure and diversity. Copyright © 2014 Elsevier GmbH. All rights reserved.

Range-azimuth decouple beamforming for frequency diverse array with Costas-sequence modulated frequency offsets

NASA Astrophysics Data System (ADS)

Wang, Zhe; Wang, Wen-Qin; Shao, Huaizong

2016-12-01

Different from the phased-array using the same carrier frequency for each transmit element, the frequency diverse array (FDA) uses a small frequency offset across the array elements to produce range-angle-dependent transmit beampattern. FDA radar provides new application capabilities and potentials due to its range-dependent transmit array beampattern, but the FDA using linearly increasing frequency offsets will produce a range and angle coupled transmit beampattern. In order to decouple the range-azimuth beampattern for FDA radar, this paper proposes a uniform linear array (ULA) FDA using Costas-sequence modulated frequency offsets to produce random-like energy distribution in the transmit beampattern and thumbtack transmit-receive beampattern. In doing so, the range and angle of targets can be unambiguously estimated through matched filtering and subspace decomposition algorithms in the receiver signal processor. Moreover, random-like energy distributed beampattern can also be utilized for low probability of intercept (LPI) radar applications. Numerical results show that the proposed scheme outperforms the standard FDA in focusing the transmit energy, especially in the range dimension.

Development of DArT markers and assessment of diversity in Fusarium oxysporum f. sp. ciceris, wilt pathogen of chickpea (Cicer arietinum L.).

PubMed

Sharma, Mamta; Nagavardhini, Avuthu; Thudi, Mahendar; Ghosh, Raju; Pande, Suresh; Varshney, Rajeev K

2014-06-10

Fusarium oxysporum f. sp. ciceris (Foc), the causal agent of Fusarium wilt of chickpea is highly variable and frequent recurrence of virulent forms have affected chickpea production and exhausted valuable genetic resources. The severity and yield losses of Fusarium wilt differ from place to place owing to existence of physiological races among isolates. Diversity study of fungal population associated with a disease plays a major role in understanding and devising better disease control strategies. The advantages of using molecular markers to understand the distribution of genetic diversity in Foc populations is well understood. The recent development of Diversity Arrays Technology (DArT) offers new possibilities to study the diversity in pathogen population. In this study, we developed DArT markers for Foc population, analysed the genetic diversity existing within and among Foc isolates, compared the genotypic and phenotypic diversity and infer the race scenario of Foc in India. We report the successful development of DArT markers for Foc and their utility in genotyping of Foc collections representing five chickpea growing agro-ecological zones of India. The DArT arrays revealed a total 1,813 polymorphic markers with an average genotyping call rate of 91.16% and a scoring reproducibility of 100%. Cluster analysis, principal coordinate analysis and population structure indicated that the different isolates of Foc were partially classified based on geographical source. Diversity in Foc population was compared with the phenotypic variability and it was found that DArT markers were able to group the isolates consistent with its virulence group. A number of race-specific unique and rare alleles were also detected. The present study generated significant information in terms of pathogenic and genetic diversity of Foc which could be used further for development and deployment of region-specific resistant cultivars of chickpea. The DArT markers were proved to be a powerful diagnostic tool to study the genotypic diversity in Foc. The high number of DArT markers allowed a greater resolution of genetic differences among isolates and enabled us to examine the extent of diversity in the Foc population present in India, as well as provided support to know the changing race scenario in Foc population.

Diversity Arrays Technology (DArT) Marker Platforms for Diversity Analysis and Linkage Mapping in a Complex Crop, the Octoploid Cultivated Strawberry (Fragaria × ananassa)

PubMed Central

Sánchez-Sevilla, José F.; Horvath, Aniko; Botella, Miguel A.; Gaston, Amèlia; Folta, Kevin; Kilian, Andrzej; Denoyes, Beatrice; Amaya, Iraida

2015-01-01

Cultivated strawberry (Fragaria × ananassa) is a genetically complex allo-octoploid crop with 28 pairs of chromosomes (2n = 8x = 56) for which a genome sequence is not yet available. The diploid Fragaria vesca is considered the donor species of one of the octoploid sub-genomes and its available genome sequence can be used as a reference for genomic studies. A wide number of strawberry cultivars are stored in ex situ germplasm collections world-wide but a number of previous studies have addressed the genetic diversity present within a limited number of these collections. Here, we report the development and application of two platforms based on the implementation of Diversity Array Technology (DArT) markers for high-throughput genotyping in strawberry. The first DArT microarray was used to evaluate the genetic diversity of 62 strawberry cultivars that represent a wide range of variation based on phenotype, geographical and temporal origin and pedigrees. A total of 603 DArT markers were used to evaluate the diversity and structure of the population and their cluster analyses revealed that these markers were highly efficient in classifying the accessions in groups based on historical, geographical and pedigree-based cues. The second DArTseq platform took benefit of the complexity reduction method optimized for strawberry and the development of next generation sequencing technologies. The strawberry DArTseq was used to generate a total of 9,386 SNP markers in the previously developed ‘232’ × ‘1392’ mapping population, of which, 4,242 high quality markers were further selected to saturate this map after several filtering steps. The high-throughput platforms here developed for genotyping strawberry will facilitate genome-wide characterizations of large accessions sets and complement other available options. PMID:26675207

The past, present and future of secondary metabolite research in the Dothideomycetes.

PubMed

Muria-Gonzalez, Mariano Jordi; Chooi, Yit-Heng; Breen, Susan; Solomon, Peter S

2015-01-01

The Dothideomycetes represents a large and diverse array of fungi in which prominent plant pathogens are over-represented. Species within the Cochliobolus, Alternaria, Pyrenophora and Mycosphaerella (amongst others) all cause diseases that threaten food security in many parts of the world. Significant progress has been made over the past decade in understanding how some of these pathogens cause disease at a molecular level. It is reasonable to suggest that much of this progress can be attributed to the increased availability of genome sequences. However, together with revealing mechanisms of pathogenicity, these genome sequences have also highlighted the capacity of the Dothideomycetes to produce an extensive array of secondary metabolites, far greater than originally thought. Indeed, it is now clear that we appear to have only scratched the surface to date in terms of the identification of secondary metabolites produced by these fungi. In the first half of this review, we examine the current status of secondary metabolite research in the Dothideomycetes and highlight the diversity of the molecules discovered thus far, in terms of both structure and biological activity. In the second part of this review, we survey the emerging techniques and technologies that will be required to shed light on the vast array of secondary metabolite potential that is encoded within these genomes. Experimental design, analytical chemistry and synthetic biology are all discussed in the context of how they will contribute to this field. © 2014 BSPP AND JOHN WILEY & SONS LTD.

Drugs from the Oceans: Marine Natural Products as Leads for Drug Discovery.

PubMed

Altmann, Karl-Heinz

2017-10-25

The marine environment harbors a vast number of species that are the source of a wide array of structurally diverse bioactive secondary metabolites. At this point in time, roughly 27'000 marine natural products are known, of which eight are (were) at the origin of seven marketed drugs, mostly for the treatment of cancer. The majority of these drugs and also of drug candidates currently undergoing clinical evaluation (excluding antibody-drug conjugates) are unmodified natural products, but synthetic chemistry has played a central role in the discovery and/or development of all but one of the approved marine-derived drugs. More than 1000 new marine natural products have been isolated per year over the last decade, but the pool of new and unique structures is far from exhausted. To fully leverage the potential offered by the structural diversity of marine-produced secondary metabolites for drug discovery will require their broad assessment for different bioactivities and the productive interplay between new fermentation technologies, synthetic organic chemistry, and medicinal chemistry, in order to secure compound supply and enable lead optimization.

Molecular Mechanisms of Fibroblast Growth Factor Signaling in Physiology and Pathology

PubMed Central

Belov, Artur A.; Mohammadi, Moosa

2013-01-01

Fibroblast growth factors (FGFs) signal in a paracrine or endocrine fashion to mediate a myriad of biological activities, ranging from issuing developmental cues, maintaining tissue homeostasis, and regulating metabolic processes. FGFs carry out their diverse functions by binding and dimerizing FGF receptors (FGFRs) in a heparan sulfate (HS) cofactor- or Klotho coreceptor-assisted manner. The accumulated wealth of structural and biophysical data in the past decade has transformed our understanding of the mechanism of FGF signaling in human health and development, and has provided novel concepts in receptor tyrosine kinase (RTK) signaling. Among these contributions are the elucidation of HS-assisted receptor dimerization, delineation of the molecular determinants of ligand–receptor specificity, tyrosine kinase regulation, receptor cis-autoinhibition, and tyrosine trans-autophosphorylation. These structural studies have also revealed how disease-associated mutations highjack the physiological mechanisms of FGFR regulation to contribute to human diseases. In this paper, we will discuss the structurally and biophysically derived mechanisms of FGF signaling, and how the insights gained may guide the development of therapies for treatment of a diverse array of human diseases. PMID:23732477

Molecular mechanisms of fibroblast growth factor signaling in physiology and pathology.

PubMed

Belov, Artur A; Mohammadi, Moosa

2013-06-01

Fibroblast growth factors (FGFs) signal in a paracrine or endocrine fashion to mediate a myriad of biological activities, ranging from issuing developmental cues, maintaining tissue homeostasis, and regulating metabolic processes. FGFs carry out their diverse functions by binding and dimerizing FGF receptors (FGFRs) in a heparan sulfate (HS) cofactor- or Klotho coreceptor-assisted manner. The accumulated wealth of structural and biophysical data in the past decade has transformed our understanding of the mechanism of FGF signaling in human health and development, and has provided novel concepts in receptor tyrosine kinase (RTK) signaling. Among these contributions are the elucidation of HS-assisted receptor dimerization, delineation of the molecular determinants of ligand-receptor specificity, tyrosine kinase regulation, receptor cis-autoinhibition, and tyrosine trans-autophosphorylation. These structural studies have also revealed how disease-associated mutations highjack the physiological mechanisms of FGFR regulation to contribute to human diseases. In this paper, we will discuss the structurally and biophysically derived mechanisms of FGF signaling, and how the insights gained may guide the development of therapies for treatment of a diverse array of human diseases.

Multi-angle ZnO microstructures grown on Ag nanorods array for plasmon-enhanced near-UV-blue light emitter

NASA Astrophysics Data System (ADS)

Pal, Anil Kumar; Bharathi Mohan, D.

2017-10-01

Metal enhanced ultraviolet light emission has been explored in ZnO/Ag hybrid structures prepared by hydrothermal growth of multi-angled ZnO nanorods on slanted Ag nanorods array fabricated by the thermal evaporation technique. Slanted Ag nanorods are realized to be the stacking of non-spherical Ag nanoparticles, resulting in asymmetric surface plasmon resonance spectra. The surface roughness of Ag nanorod array films significantly influences the growth mechanism of ZnO nanorods, leading to the formation of multi-angled ZnO microflowers. ZnO/Ag hybrid structures facilitate the interfacial charge transfer from Ag to ZnO with the realization of negative shift in binding energy of Ag 3d orbitals by ˜0.8 eV. These high quality ZnO nanorods in ZnO/Ag hybrid nanostructures exhibit strong ultraviolet emission in the 383-396 nm region without broad deep level emission, which can be explained by a suitable band diagram. The metal enhanced photoluminescence is witnessed mainly due to interfacial charge transfer with its dependence on surface roughness of bottom layer Ag nanorods, number density of ZnO nanorods and diversity in the interfacial area between Ag and ZnO nanorods. The existence of strong ultraviolet light with minor blue light emission and appearance of CIE shade in strong violet-blue region by ZnO/Ag hybrid structures depict exciting possibilities towards near UV-blue light emitting devices.

Multi-angle ZnO microstructures grown on Ag nanorods array for plasmon-enhanced near-UV-blue light emitter.

PubMed

Pal, Anil Kumar; Mohan, D Bharathi

2017-10-13

Metal enhanced ultraviolet light emission has been explored in ZnO/Ag hybrid structures prepared by hydrothermal growth of multi-angled ZnO nanorods on slanted Ag nanorods array fabricated by the thermal evaporation technique. Slanted Ag nanorods are realized to be the stacking of non-spherical Ag nanoparticles, resulting in asymmetric surface plasmon resonance spectra. The surface roughness of Ag nanorod array films significantly influences the growth mechanism of ZnO nanorods, leading to the formation of multi-angled ZnO microflowers. ZnO/Ag hybrid structures facilitate the interfacial charge transfer from Ag to ZnO with the realization of negative shift in binding energy of Ag 3d orbitals by ∼0.8 eV. These high quality ZnO nanorods in ZnO/Ag hybrid nanostructures exhibit strong ultraviolet emission in the 383-396 nm region without broad deep level emission, which can be explained by a suitable band diagram. The metal enhanced photoluminescence is witnessed mainly due to interfacial charge transfer with its dependence on surface roughness of bottom layer Ag nanorods, number density of ZnO nanorods and diversity in the interfacial area between Ag and ZnO nanorods. The existence of strong ultraviolet light with minor blue light emission and appearance of CIE shade in strong violet-blue region by ZnO/Ag hybrid structures depict exciting possibilities towards near UV-blue light emitting devices.

Bacterial CRISPR Regions: General Features and their Potential for Epidemiological Molecular Typing Studies

PubMed Central

Karimi, Zahra; Ahmadi, Ali; Najafi, Ali; Ranjbar, Reza

2018-01-01

Introduction: CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) loci as novel and applicable regions in prokaryotic genomes have gained great attraction in the post genomics era. Methods: These unique regions are diverse in number and sequence composition in different pathogenic bacteria and thereby can be a suitable candidate for molecular epidemiology and genotyping studies. Results:Furthermore, the arrayed structure of CRISPR loci (several unique repeats spaced with the variable sequence) and associated cas genes act as an active prokaryotic immune system against viral replication and conjugative elements. This property can be used as a tool for RNA editing in bioengineering studies. Conclusion: The aim of this review was to survey some details about the history, nature, and potential applications of CRISPR arrays in both genetic engineering and bacterial genotyping studies. PMID:29755603

Periodically patterned structures for nanoplasmonic and biomedical applications

NASA Astrophysics Data System (ADS)

Peer, Akshit

Periodically patterned nanostructures have imparted profound impact on diverse scientific disciplines. In physics, chemistry, and materials science, artificially engineered photonic crystals have demonstrated an unprecedented ability to control the propagation of photons through light concentration and diffraction. The field of photonic crystals has led to many technical advances in fabricating periodically patterned nanostructures in dielectric/metallic materials and controlling the light-matter interactions at the nanoscale. In the field of biomaterials, it is of great interest to apply our knowledge base of photonic materials and explore how such periodically patterned structures control diverse biological functions by varying the available surface area, which is a key attribute for surface hydrophobicity, cell growth and drug delivery. Here we describe closely related scientific applications of large-scale periodically patterned polymers and metal nanostructures. The dissertation starts with nanoplasmonics for improving photovoltaic devices, where we design and optimize experimentally realizable light-trapping nanostructures using rigorous scattering matrix simulations for enhancing the performance of organic and perovskite solar cells. The use of periodically patterned plasmonic metal cathode in conjunction with polymer microlens array significantly improves the absorption in solar cells, providing new opportunities for photovoltaic device design. We further show the unprecedented ability of nanoplasmonics to concentrate light at the nanoscale by designing a large-area plasmonic nanocup array with frequency-selective optical transmission. The fabrication of nanostructure is achieved by coating non-uniform gold layer over a submicron periodic nanocup array imprinted on polystyrene using soft lithography. The gold nanocup array shows extraordinary optical transmission at a wavelength close to the structure period. The resonance wavelength for transmission can be tuned by changing the period of the gold nanocup array, which opens up new avenues in subwavelength optics for designing optoelectronic devices and biological sensors. We then demonstrate strong exciton-plasmon coupling between non-toxic CuInS2/ZnS quantum dots in solution and plasmonic gold nanocup array. The photoluminescence decay rate of quantum dots can be enhanced by more than an order of magnitude due to the high electric field intensity enhancement inside the plasmonic nanocup cavity. This solution based metal-nanocrystal coupled system has great promise for biological applications such as biosensing and biolabeling. Moving to the area of biomedical applications, we fabricate nanopatterned biopolymers as templates for controlling the release of therapeutic drugs coated on the polymer surface. From careful drug release experiments performed over extended time periods (e.g. eight days), we find that nanopatterned polymers release the drug slower as compared to the flat polymer surfaces. The slow-down in the drug release from nanopatterned surfaces is attributed to increase in the surface hydrophobicity confirmed by the contact angle measurements and microfluidic simulations. This nanoscale drug release control scheme has great promise for improving the performance of drug-eluting stents in cardiac therapies.

Parkinson’s disease and pesticides: a toxicological perspective

PubMed Central

Hatcher, Jaime M.; Pennell, Kurt D.; Miller, Gary W.

2017-01-01

Environmental factors have been shown to contribute to the incidence of Parkinson’s disease (PD). Pesticides, which represent one of the primary classes of environmental agents associated with PD, share the common feature of being intentionally released into the environment to control or eliminate pests. Pesticides consist of multiple classes and subclasses of insecticides, herbicides, rodenticides, fungicides, fumigants and others and exhibit a vast array of chemically diverse structures. In this review we examine the evidence regarding the ability of each of the major pesticide subclasses to increase the incidence of PD. We propose that, from a toxicological perspective, it would be beneficial to identify specific subclasses, common structural features and the propensity for widespread human exposure when considering the potential role in PD, rather than using the overly broad term of ‘pesticides’ to describe this diverse group of chemicals. Furthermore, these chemicals and their environmentally relevant combinations should be evaluated for their ability to promote or accelerate PD and not merely for being singular causative agents. PMID:18453001

Geo-Chip analysis reveals reduced functional diversity of the bacterial community at a dumping site for dredged Elbe sediment.

PubMed

Störmer, Rebecca; Wichels, Antje; Gerdts, Gunnar

2013-12-15

The dumping of dredged sediments represents a major stressor for coastal ecosystems. The impact on the ecosystem function is determined by its complexity not easy to assess. In the present study, we evaluated the potential of bacterial community analyses to act as ecological indicators in environmental monitoring programmes. We investigated the functional structure of bacterial communities, applying functional gene arrays (GeoChip4.2). The relationship between functional genes and environmental factors was analysed using distance-based multivariate multiple regression. Apparently, both the function and structure of the bacterial communities are impacted by dumping activities. The bacterial community at the dumping centre displayed a significant reduction of its entire functional diversity compared with that found at a reference site. DDX compounds separated bacterial communities of the dumping site from those of un-impacted sites. Thus, bacterial community analyses show great potential as ecological indicators in environmental monitoring. Copyright © 2013 Elsevier Ltd. All rights reserved.

Magnetically-guided assembly of microfluidic fibers for ordered construction of diverse netlike modules

NASA Astrophysics Data System (ADS)

Li, Xingfu; Shi, Qing; Wang, Huaping; Sun, Tao; Huang, Qiang; Fukuda, Toshio

2017-12-01

In this paper, a magnetically-guided assembly method is proposed to methodically construct diverse modules with a microfiber-based network for promoting nutrient circulation and waste excretion of cell culture. The microfiber is smoothly spun from the microfluidic device via precise control of the volumetric flow rate, and superparamagnetic nanoparticles within the alginate solution of the microfluidic fiber enable its magnetic response. The magnetized device is used to effectively capture the microfiber using its powerful magnetic flux density and high magnetic field gradient. Subsequently, the dot-matrix magnetic flux density is used to distribute the microfibers in an orderly fashion that depends on the array structure of the magnetized device. Furthermore, the magnetic microfluidic fibers are spatially organized into desired locations and are cross-aligned to form highly interconnected netlike modules in a liquid environment. Therefore, the experimental results herein demonstrate the structural controllability and stability of various modules and establish the effectiveness of the proposed method.

Catalytic diversity in self-propagating peptide assemblies

NASA Astrophysics Data System (ADS)

Omosun, Tolulope O.; Hsieh, Ming-Chien; Childers, W. Seth; Das, Dibyendu; Mehta, Anil K.; Anthony, Neil R.; Pan, Ting; Grover, Martha A.; Berland, Keith M.; Lynn, David G.

2017-08-01

The protein-only infectious agents known as prions exist within cellular matrices as populations of assembled polypeptide phases ranging from particles to amyloid fibres. These phases appear to undergo Darwinian-like selection and propagation, yet remarkably little is known about their accessible chemical and biological functions. Here we construct simple peptides that assemble into well-defined amyloid phases and define paracrystalline surfaces able to catalyse specific enantioselective chemical reactions. Structural adjustments of individual amino acid residues predictably control both the assembled crystalline order and their accessible catalytic repertoire. Notably, the density and proximity of the extended arrays of enantioselective catalytic sites achieve template-directed polymerization of new polymers. These diverse amyloid templates can now be extended as dynamic self-propagating templates for the construction of even more complex functional materials.

United in Diversity: Mechanosensitive Ion Channels in Plants

PubMed Central

Hamilton, Eric S.; Schlegel, Angela M.; Haswell, Elizabeth S.

2015-01-01

Mechanosensitive (MS) ion channels are a common mechanism for perceiving and responding to mechanical force. This class of mechanoreceptors is capable of transducing membrane tension directly into ion flux. In plant systems, MS ion channels have been proposed to play a wide array of roles, from the perception of touch and gravity to the osmotic homeostasis of intracellular organelles. Three families of plant MS ion channels have been identified: the MscS-like (MSL), Mid1-complementing activity (MCA), and two-pore potassium (TPK) families. Channels from these families vary widely in structure and function, localize to multiple cellular compartments, and conduct chloride, calcium, and/or potassium ions. However, they are still likely to represent only a fraction of the MS ion channel diversity in plant systems. PMID:25494462

Unity in diversity: structural and functional insights into the ancient partnerships between plants and fungi.

PubMed

Field, Katie J; Pressel, Silvia

2018-04-26

Contents I. II. III. IV. V. VI. VII. VIII. References SUMMARY: Mycorrhizal symbiosis is an ancient and widespread mutualism between plants and fungi that facilitated plant terrestrialisation > 500 million years ago, with key roles in ecosystem functioning at multiple scales. Central to the symbiosis is the bidirectional exchange of plant-fixed carbon for fungal-acquired nutrients. Within this unifying role of mycorrhizas, considerable diversity in structure and function reflects the diversity of the partners involved. Early diverging plants form mutualisms not only with arbuscular mycorrhizal Glomeromycotina fungi, but also with poorly characterised Mucoromycotina, which may also colonise the roots of 'higher' plants as fine root endophytes. Functional diversity in these symbioses depends on both fungal and plant life histories and is influenced by the environment. Recent studies have highlighted the roles of lipids/fatty acids in plant-to-fungus carbon transport and potential contributions of Glomeromycotina fungi to plant nitrogen nutrition. Together with emerging appreciation of mycorrhizal networks as multi-species resource-sharing systems, these insights are broadening our views on mycorrhizas and their roles in nutrient cycling. It is crucial that the diverse array of biotic and abiotic factors that together shape the dynamics of carbon-for-nutrient exchange between plants and fungi are integrated, in addition to embracing the unfolding and potentially key role of Mucoromycotina fungi in these processes. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Assessment of Genetic Diversity and Structure of Large Garlic (Allium sativum) Germplasm Bank, by Diversity Arrays Technology “Genotyping-by-Sequencing” Platform (DArTseq)

PubMed Central

Egea, Leticia A.; Mérida-García, Rosa; Kilian, Andrzej; Hernandez, Pilar; Dorado, Gabriel

2017-01-01

Garlic (Allium sativum) is used worldwide in cooking and industry, including pharmacology/medicine and cosmetics, for its interesting properties. Identifying redundancies in germplasm blanks to generate core collections is a major concern, mostly in large stocks, in order to reduce space and maintenance costs. Yet, similar appearance and phenotypic plasticity of garlic varieties hinder their morphological classification. Molecular studies are challenging, due to the large and expected complex genome of this species, with asexual reproduction. Classical molecular markers, like isozymes, RAPD, SSR, or AFLP, are not convenient to generate germplasm core-collections for this species. The recent emergence of high-throughput genotyping-by-sequencing (GBS) approaches, like DArTseq, allow to overcome such limitations to characterize and protect genetic diversity. Therefore, such technology was used in this work to: (i) assess genetic diversity and structure of a large garlic-germplasm bank (417 accessions); (ii) create a core collection; (iii) relate genotype to agronomical features; and (iv) describe a cost-effective method to manage genetic diversity in garlic-germplasm banks. Hierarchical-cluster analysis, principal-coordinates analysis and STRUCTURE showed general consistency, generating three main garlic-groups, mostly determined by variety and geographical origin. In addition, high-resolution genotyping identified 286 unique and 131 redundant accessions, used to select a reduced size germplasm-bank core collection. This demonstrates that DArTseq is a cost-effective method to analyze species with large and expected complex genomes, like garlic. To the best of our knowledge, this is the first report of high-throughput genotyping of a large garlic germplasm. This is particularly interesting for garlic adaptation and improvement, to fight biotic and abiotic stresses, in the current context of climate change and global warming. PMID:28775737

Extended diversity analysis of cultivated grapevine Vitis vinifera with 10K genome-wide SNPs.

PubMed

Laucou, Valérie; Launay, Amandine; Bacilieri, Roberto; Lacombe, Thierry; Adam-Blondon, Anne-Françoise; Bérard, Aurélie; Chauveau, Aurélie; de Andrés, Maria Teresa; Hausmann, Ludger; Ibáñez, Javier; Le Paslier, Marie-Christine; Maghradze, David; Martinez-Zapater, José Miguel; Maul, Erika; Ponnaiah, Maharajah; Töpfer, Reinhard; Péros, Jean-Pierre; Boursiquot, Jean-Michel

2018-01-01

Grapevine is a very important crop species that is mainly cultivated worldwide for fruits, wine and juice. Identification of the genetic bases of performance traits through association mapping studies requires a precise knowledge of the available diversity and how this diversity is structured and varies across the whole genome. An 18k SNP genotyping array was evaluated on a panel of Vitis vinifera cultivars and we obtained a data set with no missing values for a total of 10207 SNPs and 783 different genotypes. The average inter-SNP spacing was ~47 kbp, the mean minor allele frequency (MAF) was 0.23 and the genetic diversity in the sample was high (He = 0.32). Fourteen SNPs, chosen from those with the highest MAF values, were sufficient to identify each genotype in the sample. Parentage analysis revealed 118 full parentages and 490 parent-offspring duos, thus confirming the close pedigree relationships within the cultivated grapevine. Structure analyses also confirmed the main divisions due to an eastern-western gradient and human usage (table vs. wine). Using a multivariate approach, we refined the structure and identified a total of eight clusters. Both the genetic diversity (He, 0.26-0.32) and linkage disequilibrium (LD, 28.8-58.2 kbp) varied between clusters. Despite the short span LD, we also identified some non-recombining haplotype blocks that may complicate association mapping. Finally, we performed a genome-wide association study that confirmed previous works and also identified new regions for important performance traits such as acidity. Taken together, all the results contribute to a better knowledge of the genetics of the cultivated grapevine.

Extended diversity analysis of cultivated grapevine Vitis vinifera with 10K genome-wide SNPs

PubMed Central

Launay, Amandine; Bacilieri, Roberto; Lacombe, Thierry; Adam-Blondon, Anne-Françoise; Bérard, Aurélie; Chauveau, Aurélie; de Andrés, Maria Teresa; Maghradze, David; Maul, Erika; Ponnaiah, Maharajah; Töpfer, Reinhard; Péros, Jean-Pierre; Boursiquot, Jean-Michel

2018-01-01

Grapevine is a very important crop species that is mainly cultivated worldwide for fruits, wine and juice. Identification of the genetic bases of performance traits through association mapping studies requires a precise knowledge of the available diversity and how this diversity is structured and varies across the whole genome. An 18k SNP genotyping array was evaluated on a panel of Vitis vinifera cultivars and we obtained a data set with no missing values for a total of 10207 SNPs and 783 different genotypes. The average inter-SNP spacing was ~47 kbp, the mean minor allele frequency (MAF) was 0.23 and the genetic diversity in the sample was high (He = 0.32). Fourteen SNPs, chosen from those with the highest MAF values, were sufficient to identify each genotype in the sample. Parentage analysis revealed 118 full parentages and 490 parent-offspring duos, thus confirming the close pedigree relationships within the cultivated grapevine. Structure analyses also confirmed the main divisions due to an eastern-western gradient and human usage (table vs. wine). Using a multivariate approach, we refined the structure and identified a total of eight clusters. Both the genetic diversity (He, 0.26–0.32) and linkage disequilibrium (LD, 28.8–58.2 kbp) varied between clusters. Despite the short span LD, we also identified some non-recombining haplotype blocks that may complicate association mapping. Finally, we performed a genome-wide association study that confirmed previous works and also identified new regions for important performance traits such as acidity. Taken together, all the results contribute to a better knowledge of the genetics of the cultivated grapevine. PMID:29420602

Assessment of Genetic Diversity and Structure of Large Garlic (Allium sativum) Germplasm Bank, by Diversity Arrays Technology "Genotyping-by-Sequencing" Platform (DArTseq).

PubMed

Egea, Leticia A; Mérida-García, Rosa; Kilian, Andrzej; Hernandez, Pilar; Dorado, Gabriel

2017-01-01

Garlic ( Allium sativum ) is used worldwide in cooking and industry, including pharmacology/medicine and cosmetics, for its interesting properties. Identifying redundancies in germplasm blanks to generate core collections is a major concern, mostly in large stocks, in order to reduce space and maintenance costs. Yet, similar appearance and phenotypic plasticity of garlic varieties hinder their morphological classification. Molecular studies are challenging, due to the large and expected complex genome of this species, with asexual reproduction. Classical molecular markers, like isozymes, RAPD, SSR, or AFLP, are not convenient to generate germplasm core-collections for this species. The recent emergence of high-throughput genotyping-by-sequencing (GBS) approaches, like DArTseq, allow to overcome such limitations to characterize and protect genetic diversity. Therefore, such technology was used in this work to: (i) assess genetic diversity and structure of a large garlic-germplasm bank (417 accessions); (ii) create a core collection; (iii) relate genotype to agronomical features; and (iv) describe a cost-effective method to manage genetic diversity in garlic-germplasm banks. Hierarchical-cluster analysis, principal-coordinates analysis and STRUCTURE showed general consistency, generating three main garlic-groups, mostly determined by variety and geographical origin. In addition, high-resolution genotyping identified 286 unique and 131 redundant accessions, used to select a reduced size germplasm-bank core collection. This demonstrates that DArTseq is a cost-effective method to analyze species with large and expected complex genomes, like garlic. To the best of our knowledge, this is the first report of high-throughput genotyping of a large garlic germplasm. This is particularly interesting for garlic adaptation and improvement, to fight biotic and abiotic stresses, in the current context of climate change and global warming.

Analysis of genetic diversity using SNP markers in oat

USDA-ARS?s Scientific Manuscript database

A large-scale single nucleotide polymorphism (SNP) discovery was carried out in cultivated oat using Roche 454 sequencing methods. DNA sequences were generated from cDNAs originating from a panel of 20 diverse oat cultivars, and from Diversity Array Technology (DArT) genomic complexity reductions fr...

CRISPR Diversity and Microevolution in Clostridium difficile

PubMed Central

Andersen, Joakim M.; Shoup, Madelyn; Robinson, Cathy; Britton, Robert; Olsen, Katharina E.P.; Barrangou, Rodolphe

2016-01-01

Abstract Virulent strains of Clostridium difficile have become a global health problem associated with morbidity and mortality. Traditional typing methods do not provide ideal resolution to track outbreak strains, ascertain genetic diversity between isolates, or monitor the phylogeny of this species on a global basis. Here, we investigate the occurrence and diversity of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated genes (cas) in C. difficile to assess the potential of CRISPR-based phylogeny and high-resolution genotyping. A single Type-IB CRISPR-Cas system was identified in 217 analyzed genomes with cas gene clusters present at conserved chromosomal locations, suggesting vertical evolution of the system, assessing a total of 1,865 CRISPR arrays. The CRISPR arrays, markedly enriched (8.5 arrays/genome) compared with other species, occur both at conserved and variable locations across strains, and thus provide a basis for typing based on locus occurrence and spacer polymorphism. Clustering of strains by array composition correlated with sequence type (ST) analysis. Spacer content and polymorphism within conserved CRISPR arrays revealed phylogenetic relationship across clades and within ST. Spacer polymorphisms of conserved arrays were instrumental for differentiating closely related strains, e.g., ST1/RT027/B1 strains and pathogenicity locus encoding ST3/RT001 strains. CRISPR spacers showed sequence similarity to phage sequences, which is consistent with the native role of CRISPR-Cas as adaptive immune systems in bacteria. Overall, CRISPR-Cas sequences constitute a valuable basis for genotyping of C. difficile isolates, provide insights into the micro-evolutionary events that occur between closely related strains, and reflect the evolutionary trajectory of these genomes. PMID:27576538

RNA Nanotechnology: Engineering, Assembly and Applications in Detection, Gene Delivery and Therapy

PubMed Central

Guo, Peixuan

2010-01-01

Biological macromolecules including DNA, RNA, and proteins, have intrinsic features that make them potential building blocks for the bottom-up fabrication of nanodevices. RNA is unique in nanoscale fabrication due to its amazing diversity of function and structure. RNA molecules can be designed and manipulated with a level of simplicity characteristic of DNA while possessing versatility in structure and function similar to that of proteins. RNA molecules typically contain a large variety of single stranded loops suitable for inter- and intra-molecular interaction. These loops can serve as mounting dovetails obviating the need for external linking dowels in fabrication and assembly. The self-assembly of nanoparticles from RNA involves cooperative interaction of individual RNA molecules that spontaneously assemble in a predefined manner to form a larger two- or three-dimensional structure. Within the realm of self-assembly there are two main categories, namely template and non-template. Template assembly involves interaction of RNA molecules under the influence of specific external sequence, forces, or spatial constraints such as RNA transcription, hybridization, replication, annealing, molding, or replicas. In contrast, non-template assembly involves formation of a larger structure by individual components without the influence of external forces. Examples of non-template assembly are ligation, chemical conjugation, covalent linkage, and loop/loop interaction of RNA, especially the formation of RNA multimeric complexes. The best characterized RNA multiplier and the first to be described in RNA nanotechnological application is the motor pRNA of bacteriophage phi29 which form dimers, trimers, and hexamers, via hand-in-hand interaction. phi29 pRNA can be redesigned to form a variety of structures and shapes including twins, tetramers, rods, triangles, and 3D arrays several microns in size via interaction of programmed helical regions and loops. 3D RNA array formation requires a defined nucleotide number for twisting and a palindromic sequence. Such arrays are unusually stable and resistant to a wide range of temperatures, salt concentrations, and pH. Both the therapeutic siRNA or ribozyme and a receptor-binding RNA aptamer or other ligands have been engineered into individual pRNAs. Individual chimeric RNA building blocks harboring siRNA or other therapeutic molecules have been fabricated subsequently into a trimer through hand-in-hand interaction of the engineered right and left interlocking RNA loops. The incubation of these particles containing the receptor-binding aptamer or other ligands results in the binding and co-entry of trivalent therapeutic particles into cells. Such particles were subsequently shown to modulate the apoptosis of cancer cells in both cell cultures and animal trials. The use of such antigen-free 20–40 nm particles holds promise for the repeated long-term treatment of chronic diseases. Other potentially useful RNA molecules that form multimers include HIV RNA that contain kissing loop to form dimers, tecto-RNA that forms a “jigsaw puzzle,” and the Drosophila bicoid mRNA that forms multimers via “hand-by-arm” interactions. Applications of RNA molecules involving replication, molding, embossing, and other related techniques, have recently been described that allow the utilization of a variety of materials to enhance diversity and resolution of nanomaterials. It should eventually be possible to adapt RNA to facilitate construction of ordered, patterned, or pre-programmed arrays or superstructures. Given the potential for 3D fabrication, the chance to produce reversible self-assembly, and the ability of self-repair, editing and replication, RNA self-assembly will play an increasingly significant role in integrated biological nanofabrication. A random 100-nucleotide RNA library may exist in 1.6 × 1060 varieties with multifarious structure to serve as a vital system for efficient fabrication, with a complexity and diversity far exceeding that of any current nanoscale system. This review covers the basic concepts of RNA structure and function, certain methods for the study of RNA structure, the approaches for engineering or fabricating RNA into nanoparticles or arrays, and special features of RNA molecules that form multimers. The most recent development in exploration of RNA nanoparticles for pathogen detection, drug/gene delivery, and therapeutic application is also introduced in this review. PMID:16430131

Structural characterization of constituents with molecular diversity in fractions from Lysidice brevicalyx by liquid chromatography/diode-array detection/electrospray ionization tandem mass spectrometry and liquid chromatography/nuclear magnetic resonance.

PubMed

Qu, Jing; Hu, You-cai; Li, Jian-bei; Wang, Ying-hong; Zhang, Jin-lan; Abliz, Zeper; Yu, Shi-shan; Liu, Yun-bao

2008-01-01

A combination of electrospray ionization tandem mass spectrometry with high-performance liquid chromatography (HPLC/ESI-MSn), and hyphenation of liquid chromatography to nuclear magnetic resonance spectroscopy (HPLC/NMR), have been extensively utilized for on-line analysis of natural products, analyzing metabolite and drug impurity. In our last paper, we reported an on-line analytical method for structural identification of trace alkaloids in the same class. However, the structural types of the constituents in plants were various, such as flavanoids, terpenoids and steroids. It is important to establish an effective analytical method for on-line structural identification of constituents with molecular diversity in extracts of plants. So, in the present study, the fragmentation patterns of some isolated stilbenes, phloroglucinols and flavanoids from Lysidice rhodostegia were investigated by ESI-MSn. Their fragmentation rules and UV characteristics are summarized, and the relationship between the spectral characteristics, rules and the structures is described. According to the fragmentation rules, NMR and UV spectral characteristics, 24 constituents of different types in the fractions from L. brevicalyx of the same genus were structurally characterized on the basis of HPLC/HRMS, HPLC-UV/ESI-MSn, HPLC/1H NMR and HPLC/1H-1H COSY rapidly. Of these, six (10, 13, 14, 16, 17 and 23) are new compounds and all of them are reported from L. brevicalyx for the first time. The aim is to develop an effective analytical method for on-line structural identification of natural products with molecular diversity in plants, and to guide the rapid and direct isolation of novel compounds by chemical screening.

Structural-functional diversity of the natural oligopeptides.

PubMed

Zamyatnin, Alexander A

2018-03-01

Natural oligopeptides may regulate nearly all vital processes. To date, the chemical structures of many oligopeptides have been identified from >2000 organisms representing all the biological kingdoms. We have considered a number of mathematical (sequence length), chemical, physical, and biological features of an array of natural oligopeptides on the basis of the oligopeptide EROP-Moscow database (http://erop.inbi.ras.ru, 15,351 entries) data. There is the substantial difference of these substances from polypeptide molecules of proteins according to their physicochemical characteristics. These characteristics may be critical for understanding the molecular mechanisms of the action of oligopeptides that lead to the development of physiological effects. Copyright © 2017 Elsevier Ltd. All rights reserved.

Nanoscale array structures suitable for surface enhanced raman scattering and methods related thereto

DOEpatents

Bond, Tiziana C.; Miles, Robin; Davidson, James C.; Liu, Gang Logan

2014-07-22

Methods for fabricating nanoscale array structures suitable for surface enhanced Raman scattering, structures thus obtained, and methods to characterize the nanoscale array structures suitable for surface enhanced Raman scattering. Nanoscale array structures may comprise nanotrees, nanorecesses and tapered nanopillars.

Nanoscale array structures suitable for surface enhanced raman scattering and methods related thereto

DOEpatents

Bond, Tiziana C.; Miles, Robin; Davidson, James C.; Liu, Gang Logan

2015-07-14

Methods for fabricating nanoscale array structures suitable for surface enhanced Raman scattering, structures thus obtained, and methods to characterize the nanoscale array structures suitable for surface enhanced Raman scattering. Nanoscale array structures may comprise nanotrees, nanorecesses and tapered nanopillars.

Nanoscale array structures suitable for surface enhanced raman scattering and methods related thereto

DOEpatents

Bond, Tiziana C; Miles, Robin; Davidson, James; Liu, Gang Logan

2015-11-03

Methods for fabricating nanoscale array structures suitable for surface enhanced Raman scattering, structures thus obtained, and methods to characterize the nanoscale array structures suitable for surface enhanced Raman scattering. Nanoscale array structures may comprise nanotrees, nanorecesses and tapered nanopillars.

Projecting light beams with 3D waveguide arrays

NASA Astrophysics Data System (ADS)

Crespi, Andrea; Bragheri, Francesca

2017-01-01

Free-space light beams with complex intensity patterns, or non-trivial phase structure, are demanded in diverse fields, ranging from classical and quantum optical communications, to manipulation and imaging of microparticles and cells. Static or dynamic spatial light modulators, acting on the phase or intensity of an incoming light wave, are the conventional choices to produce beams with such non-trivial characteristics. However, interfacing these devices with optical fibers or integrated optical circuits often requires difficult alignment or cumbersome optical setups. Here we explore theoretically and with numerical simulations the potentialities of directly using the output of engineered three-dimensional waveguide arrays, illuminated with linearly polarized light, to project light beams with peculiar structures. We investigate through a collection of illustrative configurations the far field distribution, showing the possibility to achieve orbital angular momentum, or to produce elaborate intensity or phase patterns with several singularity points. We also simulate the propagation of the projected beam, showing the possibility to concentrate light. We note that these devices should be at reach of current technology, thus perspectives are open for the generation of complex free-space optical beams from integrated waveguide circuits.

Genome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheep.

PubMed

Al-Mamun, Hawlader Abdullah; Clark, Samuel A; Kwan, Paul; Gondro, Cedric

2015-11-24

Knowledge of the genetic structure and overall diversity of livestock species is important to maximise the potential of genome-wide association studies and genomic prediction. Commonly used measures such as linkage disequilibrium (LD), effective population size (N e ), heterozygosity, fixation index (F ST) and runs of homozygosity (ROH) are widely used and help to improve our knowledge about genetic diversity in animal populations. The development of high-density single nucleotide polymorphism (SNP) arrays and the subsequent genotyping of large numbers of animals have greatly increased the accuracy of these population-based estimates. In this study, we used the Illumina OvineSNP50 BeadChip array to estimate and compare LD (measured by r (2) and D'), N e , heterozygosity, F ST and ROH in five Australian sheep populations: three pure breeds, i.e., Merino (MER), Border Leicester (BL), Poll Dorset (PD) and two crossbred populations i.e. F1 crosses of Merino and Border Leicester (MxB) and MxB crossed to Poll Dorset (MxBxP). Compared to other livestock species, the sheep populations that were analysed in this study had low levels of LD and high levels of genetic diversity. The rate of LD decay was greater in Merino than in the other pure breeds. Over short distances (<10 kb), the levels of LD were higher in BL and PD than in MER. Similarly, BL and PD had comparatively smaller N e than MER. Observed heterozygosity in the pure breeds ranged from 0.3 in BL to 0.38 in MER. Genetic distances between breeds were modest compared to other livestock species (highest F ST = 0.063) but the genetic diversity within breeds was high. Based on ROH, two chromosomal regions showed evidence of strong recent selection. This study shows that there is a large range of genome diversity in Australian sheep breeds, especially in Merino sheep. The observed range of diversity will influence the design of genome-wide association studies and the results that can be obtained from them. This knowledge will also be useful to design reference populations for genomic prediction of breeding values in sheep.

Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome

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

Hodkinson, Brendan P; Gottel, Neil R; Schadt, Christopher Warren

2011-01-01

Although common knowledge dictates that the lichen thallus is formed solely by a fungus (mycobiont) that develops a symbiotic relationship with an alga and/or cyanobacterium (photobiont), the non-photoautotrophic bacteria found in lichen microbiomes are increasingly regarded as integral components of lichen thalli. For this study, comparative analyses were conducted on lichen-associated bacterial communities to test for effects of photobiont-types (i.e. green algal vs. cyanobacterial), mycobiont-types and large-scale spatial distances (from tropical to arctic latitudes). Amplicons of the 16S (SSU) rRNA gene were examined using both Sanger sequencing of cloned fragments and barcoded pyrosequencing. Rhizobiales is typically the most abundant andmore » taxonomically diverse order in lichen microbiomes; however, overall bacterial diversity in lichens is shown to be much higher than previously reported. Members of Acidobacteriaceae, Acetobacteraceae, Brucellaceae and sequence group LAR1 are the most commonly found groups across the phylogenetically and geographically broad array of lichens examined here. Major bacterial community trends are significantly correlated with differences in large-scale geography, photobiont-type and mycobiont-type. The lichen as a microcosm represents a structured, unique microbial habitat with greater ecological complexity and bacterial diversity than previously appreciated and can serve as a model system for studying larger ecological and evolutionary principles.« less

Proteorhodopsins: an array of physiological roles?

PubMed

Fuhrman, Jed A; Schwalbach, Michael S; Stingl, Ulrich

2008-06-01

Metagenomic analyses have revealed widespread and diverse retinal-binding rhodopsin proteins (named proteorhodopsins) among numerous marine bacteria and archaea, which has challenged the notion that solar energy can only enter marine ecosystems by chlorophyll-based photosynthesis. Most marine proteorhodopsins share structural and functional similarities with archaeal bacteriorhodopsins, which generate proton motive force via light-activated proton pumping, thereby ultimately powering ATP production. This suggests an energetic role for proteorhodopsins. However, results from a growing number of investigations do not readily fit this model, which indicates that proteorhodopsins could have a range of physiological functions.

Boron-doped diamond microdisc arrays: electrochemical characterisation and their use as a substrate for the production of microelectrode arrays of diverse metals (Ag, Au, Cu)via electrodeposition.

PubMed

Simm, Andrew O; Banks, Craig E; Ward-Jones, Sarah; Davies, Trevor J; Lawrence, Nathan S; Jones, Timothy G J; Jiang, Li; Compton, Richard G

2005-09-01

A novel boron-doped diamond (BDD) microelectrode array is characterised with electrochemical and atomic force microscopic techniques. The array consists of 40 micron-diameter sized BDD discs which are separated by 250 microns from their nearest neighbour in a hexagonal arrangement. The conducting discs can be electroplated to produce arrays of copper, silver or gold for analytical purposes in addition to operating as an array of BDD-microelectrodes. Proof-of-concept is shown for four separate examples; a gold plated array for arsenic detection, a copper plated array for nitrate analysis, a silver plated array for hydrogen peroxide monitoring and last, cathodic stripping voltammetry for lead at the bare BDD-array.

Fungal prion HET-s as a model for structural complexity and self-propagation in prions.

PubMed

Wan, William; Stubbs, Gerald

2014-04-08

The highly ordered and reproducible structure of the fungal prion HET-s makes it an excellent model system for studying the inherent properties of prions, self-propagating infectious proteins that have been implicated in a number of fatal diseases. In particular, the HET-s prion-forming domain readily folds into a relatively complex two-rung β-solenoid amyloid. The faithful self-propagation of this fold involves a diverse array of inter- and intramolecular structural features. These features include a long flexible loop connecting the two rungs, buried polar residues, salt bridges, and asparagine ladders. We have used site-directed mutagenesis and X-ray fiber diffraction to probe the relative importance of these features for the formation of β-solenoid structure, as well as the cumulative effects of multiple mutations. Using fibrillization kinetics and chemical stability assays, we have determined the biophysical effects of our mutations on the assembly and stability of the prion-forming domain. We have found that a diversity of structural features provides a level of redundancy that allows robust folding and stability even in the face of significant sequence alterations and suboptimal environmental conditions. Our findings provide fundamental insights into the structural interactions necessary for self-propagation. Propagation of prion structure seems to require an obligatory level of complexity that may not be reproducible in short peptide models.

Natural Product Biosynthetic Diversity and Comparative Genomics of the Cyanobacteria.

PubMed

Dittmann, Elke; Gugger, Muriel; Sivonen, Kaarina; Fewer, David P

2015-10-01

Cyanobacteria are an ancient lineage of slow-growing photosynthetic bacteria and a prolific source of natural products with intricate chemical structures and potent biological activities. The bulk of these natural products are known from just a handful of genera. Recent efforts have elucidated the mechanisms underpinning the biosynthesis of a diverse array of natural products from cyanobacteria. Many of the biosynthetic mechanisms are unique to cyanobacteria or rarely described from other organisms. Advances in genome sequence technology have precipitated a deluge of genome sequences for cyanobacteria. This makes it possible to link known natural products to biosynthetic gene clusters but also accelerates the discovery of new natural products through genome mining. These studies demonstrate that cyanobacteria encode a huge variety of cryptic gene clusters for the production of natural products, and the known chemical diversity is likely to be just a fraction of the true biosynthetic capabilities of this fascinating and ancient group of organisms. Copyright © 2015. Published by Elsevier Ltd.

Making a chocolate chip: development and evaluation of a 6K SNP array for Theobroma cacao

PubMed Central

Livingstone, Donald; Royaert, Stefan; Stack, Conrad; Mockaitis, Keithanne; May, Greg; Farmer, Andrew; Saski, Christopher; Schnell, Ray; Kuhn, David; Motamayor, Juan Carlos

2015-01-01

Theobroma cacao, the key ingredient in chocolate production, is one of the world's most important tree fruit crops, with ∼4,000,000 metric tons produced across 50 countries. To move towards gene discovery and marker-assisted breeding in cacao, a single-nucleotide polymorphism (SNP) identification project was undertaken using RNAseq data from 16 diverse cacao cultivars. RNA sequences were aligned to the assembled transcriptome of the cultivar Matina 1-6, and 330,000 SNPs within coding regions were identified. From these SNPs, a subset of 6,000 high-quality SNPs were selected for inclusion on an Illumina Infinium SNP array: the Cacao6kSNP array. Using Cacao6KSNP array data from over 1,000 cacao samples, we demonstrate that our custom array produces a saturated genetic map and can be used to distinguish among even closely related genotypes. Our study enhances and expands the genetic resources available to the cacao research community, and provides the genome-scale set of tools that are critical for advancing breeding with molecular markers in an agricultural species with high genetic diversity. PMID:26070980

An info-gap application to robust design of a prestressed space structure under epistemic uncertainties

NASA Astrophysics Data System (ADS)

Hot, Aurélien; Weisser, Thomas; Cogan, Scott

2017-07-01

Uncertainty quantification is an integral part of the model validation process and is important to take into account during the design of mechanical systems. Sources of uncertainty are diverse but generally fall into two categories: aleatory due to random process and epistemic resulting from a lack of knowledge. This work focuses on the behavior of solar arrays in their stowed configuration. To avoid impacts during launch, snubbers are used to prestress the panels. Since the mechanical properties of the snubbers and the associated preload configurations are difficult to characterize precisely, an info-gap approach is proposed to investigate the influence of such uncertainties on design configurations obtained for different values of safety factors. This eventually allows to revise the typical values of these factors and to reevaluate them with respect to a targeted robustness level. The proposed methodology is illustrated using a simplified finite element model of a solar array.

A perspective on the structural studies of inner membrane electrochemical potential-driven transporters.

PubMed

Lemieux, M Joanne

2008-09-01

Electrochemical potential-driven transporters represent a vast array of proteins with varied substrate specificities. While diverse in size and substrate specificity, they are all driven by electrochemical potentials. Over the past five years there have been increasing numbers of X-ray structures reported for this family of transporters. Structural information is available for five subfamilies of electrochemical potential-driven transporters. No structural information exists for the remaining 91 subfamilies. In this review, the various subfamilies of electrochemical potential-driven transporters are discussed. The seven reported structures for the electrochemical potential-driven transporters and the methods for their crystallization are also presented. With a few exceptions, overall crystallization trends have been very similar for the transporters despite their differences in substrate specificity and topology. Also discussed is why the structural studies on these transporters were successful while others are not as fruitful. With the plethora of transporters with unknown structures, this review provides incentive for crystallization of transporters in the remaining subfamilies for which no structural information exists.

Diversity Arrays Technology (DArT) for whole-genome profiling of barley

PubMed Central

Wenzl, Peter; Carling, Jason; Kudrna, David; Jaccoud, Damian; Huttner, Eric; Kleinhofs, Andris; Kilian, Andrzej

2004-01-01

Diversity Arrays Technology (DArT) can detect and type DNA variation at several hundred genomic loci in parallel without relying on sequence information. Here we show that it can be effectively applied to genetic mapping and diversity analyses of barley, a species with a 5,000-Mbp genome. We tested several complexity reduction methods and selected two that generated the most polymorphic genomic representations. Arrays containing individual fragments from these representations generated DArT fingerprints with a genotype call rate of 98.0% and a scoring reproducibility of at least 99.8%. The fingerprints grouped barley lines according to known genetic relationships. To validate the Mendelian behavior of DArT markers, we constructed a genetic map for a cross between cultivars Steptoe and Morex. Nearly all polymorphic array features could be incorporated into one of seven linkage groups (98.8%). The resulting map comprised ≈385 unique DArT markers and spanned 1,137 centimorgans. A comparison with the restriction fragment length polymorphism-based framework map indicated that the quality of the DArT map was equivalent, if not superior, to that of the framework map. These results highlight the potential of DArT as a generic technique for genome profiling in the context of molecular breeding and genomics. PMID:15192146

Genetic Diversity and Differentiation in Urban and Indigenous Populations of Mexico: Patterns of Mitochondrial DNA and Y-Chromosome Lineages.

PubMed

González-Sobrino, Blanca Z; Pintado-Cortina, Ana P; Sebastián-Medina, Leticia; Morales-Mandujano, Fabiola; Contreras, Alejandra V; Aguilar, Yasnaya E; Chávez-Benavides, Juan; Carrillo-Rodríguez, Aurelio; Silva-Zolezzi, Irma; Medrano-González, Luis

2016-01-01

Aside from the admixture between indigenous people and people from overseas, populations in Mexico changed drastically after the Spanish conquest of the sixteenth century, forming an intricate history that has been underutilized in understanding the genetic population structure of Mexicans. To infer historical processes of isolation, dispersal, and assimilation, we examined the phylogeography of mitochondrial (mt) DNA and Y-chromosome lineages in 3,026 individuals from 10 urban and nine indigenous populations by identifying single nucleotide polymorphisms. A geographic array with a predominance of Amerindian lineages was observed for mtDNA, with northern indigenous populations being divergent from the central and southern indigenous populations; urban populations showed low differentiation with isolation by distance. Y-chromosome variation distinguished urban and indigenous populations through the Amerindian haplogroup Q frequency. The MtDNA and the Y-chromosome together primarily distinguished urban and indigenous populations, with different geographic arrays for both. Gene flow across geographical distance and between the urban and indigenous realms appears to have altered the pre-Hispanic phylogeography in central and southern Mexico, mainly by displacement of women, while maintaining the indigenous isolation in the north, southeast, and Zapotec regions. Most Amerindian mtDNA diversity currently occurs in urban populations and appears to be reduced among indigenous people.

Highly Adaptive Solid-Liquid Interfacing Triboelectric Nanogenerator for Harvesting Diverse Water Wave Energy.

PubMed

Zhao, Xue Jiao; Kuang, Shuang Yang; Wang, Zhong Lin; Zhu, Guang

2018-05-22

Harvesting water wave energy presents a significantly practical route to energy supply for self-powered wireless sensing networks. Here we report a networked integrated triboelectric nanogenerator (NI-TENG) as a highly adaptive means of harvesting energy from interfacing interactions with various types of water waves. Having an arrayed networking structure, the NI-TENG can accommodate diverse water wave motions and generate stable electric output regardless of how random the water wave is. Nanoscaled surface morphology consisting of dense nanowire arrays is the key for obtaining high electric output. A NI-TENG having an area of 100 × 70 mm 2 can produce a stable short-circuit current of 13.5 μA and corresponding electric power of 1.03 mW at a water wave height of 12 cm. This merit promises practical applications of the NI-TENG in real circumstances, where water waves are highly variable and unpredictable. After energy storage, the generated electric energy can drive wireless sensing by autonomously transmitting data at a period less than 1 min. This work proposes a viable solution for powering individual standalone nodes in a wireless sensor network. Potential applications include but are not limited to long-term environment monitoring, marine surveillance, and off-shore navigation.

CRISPR Diversity and Microevolution in Clostridium difficile.

PubMed

Andersen, Joakim M; Shoup, Madelyn; Robinson, Cathy; Britton, Robert; Olsen, Katharina E P; Barrangou, Rodolphe

2016-09-19

Virulent strains of Clostridium difficile have become a global health problem associated with morbidity and mortality. Traditional typing methods do not provide ideal resolution to track outbreak strains, ascertain genetic diversity between isolates, or monitor the phylogeny of this species on a global basis. Here, we investigate the occurrence and diversity of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated genes (cas) in C. difficile to assess the potential of CRISPR-based phylogeny and high-resolution genotyping. A single Type-IB CRISPR-Cas system was identified in 217 analyzed genomes with cas gene clusters present at conserved chromosomal locations, suggesting vertical evolution of the system, assessing a total of 1,865 CRISPR arrays. The CRISPR arrays, markedly enriched (8.5 arrays/genome) compared with other species, occur both at conserved and variable locations across strains, and thus provide a basis for typing based on locus occurrence and spacer polymorphism. Clustering of strains by array composition correlated with sequence type (ST) analysis. Spacer content and polymorphism within conserved CRISPR arrays revealed phylogenetic relationship across clades and within ST. Spacer polymorphisms of conserved arrays were instrumental for differentiating closely related strains, e.g., ST1/RT027/B1 strains and pathogenicity locus encoding ST3/RT001 strains. CRISPR spacers showed sequence similarity to phage sequences, which is consistent with the native role of CRISPR-Cas as adaptive immune systems in bacteria. Overall, CRISPR-Cas sequences constitute a valuable basis for genotyping of C. difficile isolates, provide insights into the micro-evolutionary events that occur between closely related strains, and reflect the evolutionary trajectory of these genomes. © The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Coherent and Noncoherent Joint Processing of Sonar for Detection of Small Targets in Shallow Water.

PubMed

Pan, Xiang; Jiang, Jingning; Li, Si; Ding, Zhenping; Pan, Chen; Gong, Xianyi

2018-04-10

A coherent-noncoherent joint processing framework is proposed for active sonar to combine diversity gain and beamforming gain for detection of a small target in shallow water environments. Sonar utilizes widely-spaced arrays to sense environments and illuminate a target of interest from multiple angles. Meanwhile, it exploits spatial diversity for time-reversal focusing to suppress reverberation, mainly strong bottom reverberation. For enhancement of robustness of time-reversal focusing, an adaptive iterative strategy is utilized in the processing framework. A probing signal is firstly transmitted and echoes of a likely target are utilized as steering vectors for the second transmission. With spatial diversity, target bearing and range are estimated using a broadband signal model. Numerical simulations show that the novel sonar outperforms the traditional phased-array sonar due to benefits of spatial diversity. The effectiveness of the proposed framework has been validated by localization of a small target in at-lake experiments.

High-density percutaneous chronic connector for neural prosthetics

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

Shah, Kedar G.; Bennett, William J.; Pannu, Satinderpall S.

2015-09-22

A high density percutaneous chronic connector, having first and second connector structures each having an array of magnets surrounding a mounting cavity. A first electrical feedthrough array is seated in the mounting cavity of the first connector structure and a second electrical feedthrough array is seated in the mounting cavity of the second connector structure, with a feedthrough interconnect matrix positioned between a top side of the first electrical feedthrough array and a bottom side of the second electrical feedthrough array to electrically connect the first electrical feedthrough array to the second electrical feedthrough array. The two arrays of magnetsmore » are arranged to attract in a first angular position which connects the first and second connector structures together and electrically connects the percutaneously connected device to the external electronics, and to repel in a second angular position to facilitate removal of the second connector structure from the first connector structure.« less

Genome-wide analysis of the diversity and ancestry of Korean dogs.

PubMed

Choi, Bong Hwan; Wijayananda, Hasini I; Lee, Soo Hyun; Lee, Doo Ho; Kim, Jong Seok; Oh, Seok Il; Park, Eung Woo; Lee, Cheul Koo; Lee, Seung Hwan

2017-01-01

There are various hypotheses on dog domestication based on archeological and genetic studies. Although many studies have been conducted on the origin of dogs, the existing literature about the ancestry, diversity, and population structure of Korean dogs is sparse. Therefore, this study is focused on the origin, diversity and population structure of Korean dogs. The study sample comprised four major categories, including non-dogs (coyotes and wolves), ancient, modern and Korean dogs. Selected samples were genotyped using an Illumina CanineHD array containing 173,662 single nucleotide polymorphisms. The genome-wide data were filtered using quality control parameters in PLINK 1.9. Only autosomal chromosomes were used for further analysis. The negative off-diagonal variance of the genetic relationship matrix analysis depicted, the variability of samples in each population. FIS (inbreeding rate within a population) values indicated, a low level of inbreeding within populations, and the patterns were in concordance with the results of Nei's genetic distance analysis. The lowest FST (inbreeding rate between populations) values among Korean and Chinese breeds, using a phylogenetic tree, multi-dimensional scaling, and a TreeMix likelihood tree showed Korean breeds are highly related to Chinese breeds. The Korean breeds possessed a unique and large diversity of admixtures compared with other breeds. The highest and lowest effective population sizes were observed in Korean Jindo Black (485) and Korean Donggyeong White (109), respectively. The historical effective population size of all Korean dogs showed declining trend from the past to present. It is important to take immediate action to protect the Korean dog population while conserving their diversity. Furthermore, this study suggests that Korean dogs have unique diversity and are one of the basal lineages of East Asian dogs, originating from China.

Genome-wide analysis of the diversity and ancestry of Korean dogs

PubMed Central

Lee, Doo Ho; Kim, Jong Seok; Oh, Seok Il; Park, Eung Woo; Lee, Cheul Koo; Lee, Seung Hwan

2017-01-01

There are various hypotheses on dog domestication based on archeological and genetic studies. Although many studies have been conducted on the origin of dogs, the existing literature about the ancestry, diversity, and population structure of Korean dogs is sparse. Therefore, this study is focused on the origin, diversity and population structure of Korean dogs. The study sample comprised four major categories, including non-dogs (coyotes and wolves), ancient, modern and Korean dogs. Selected samples were genotyped using an Illumina CanineHD array containing 173,662 single nucleotide polymorphisms. The genome-wide data were filtered using quality control parameters in PLINK 1.9. Only autosomal chromosomes were used for further analysis. The negative off-diagonal variance of the genetic relationship matrix analysis depicted, the variability of samples in each population. FIS (inbreeding rate within a population) values indicated, a low level of inbreeding within populations, and the patterns were in concordance with the results of Nei’s genetic distance analysis. The lowest FST (inbreeding rate between populations) values among Korean and Chinese breeds, using a phylogenetic tree, multi-dimensional scaling, and a TreeMix likelihood tree showed Korean breeds are highly related to Chinese breeds. The Korean breeds possessed a unique and large diversity of admixtures compared with other breeds. The highest and lowest effective population sizes were observed in Korean Jindo Black (485) and Korean Donggyeong White (109), respectively. The historical effective population size of all Korean dogs showed declining trend from the past to present. It is important to take immediate action to protect the Korean dog population while conserving their diversity. Furthermore, this study suggests that Korean dogs have unique diversity and are one of the basal lineages of East Asian dogs, originating from China. PMID:29182674

Genotyping-by-sequencing highlights original diversity patterns within a European collection of 1191 maize flint lines, as compared to the maize USDA genebank.

PubMed

Gouesnard, Brigitte; Negro, Sandra; Laffray, Amélie; Glaubitz, Jeff; Melchinger, Albrecht; Revilla, Pedro; Moreno-Gonzalez, Jesus; Madur, Delphine; Combes, Valérie; Tollon-Cordet, Christine; Laborde, Jacques; Kermarrec, Dominique; Bauland, Cyril; Moreau, Laurence; Charcosset, Alain; Nicolas, Stéphane

2017-10-01

Genotyping by sequencing is suitable for analysis of global diversity in maize. We showed the distinctiveness of flint maize inbred lines of interest to enrich the diversity of breeding programs. Genotyping-by-sequencing (GBS) is a highly cost-effective procedure that permits the analysis of large collections of inbred lines. We used it to characterize diversity in 1191 maize flint inbred lines from the INRA collection, the European Cornfed association panel, and lines recently derived from landraces. We analyzed the properties of GBS data obtained with different imputation methods, through comparison with a 50 K SNP array. We identified seven ancestral groups within the Flint collection (dent, Northern flint, Italy, Pyrenees-Galicia, Argentina, Lacaune, Popcorn) in agreement with breeding knowledge. Analysis highlighted many crosses between different origins and the improvement of flint germplasm with dent germplasm. We performed association studies on different agronomic traits, revealing SNPs associated with cob color, kernel color, and male flowering time variation. We compared the diversity of both our collection and the USDA collection which has been previously analyzed by GBS. The population structure of the 4001 inbred lines confirmed the influence of the historical inbred lines (B73, A632, Oh43, Mo17, W182E, PH207, and Wf9) within the dent group. It showed distinctly different tropical and popcorn groups, a sweet-Northern flint group and a flint group sub-structured in Italian and European flint (Pyrenees-Galicia and Lacaune) groups. Interestingly, we identified several selective sweeps between dent, flint, and tropical inbred lines that co-localized with SNPs associated with flowering time variation. The joint analysis of collections by GBS offers opportunities for a global diversity analysis of maize inbred lines.

Emergent mechanics of biological structures

PubMed Central

Dumont, Sophie; Prakash, Manu

2014-01-01

Mechanical force organizes life at all scales, from molecules to cells and tissues. Although we have made remarkable progress unraveling the mechanics of life's individual building blocks, our understanding of how they give rise to the mechanics of larger-scale biological structures is still poor. Unlike the engineered macroscopic structures that we commonly build, biological structures are dynamic and self-organize: they sculpt themselves and change their own architecture, and they have structural building blocks that generate force and constantly come on and off. A description of such structures defies current traditional mechanical frameworks. It requires approaches that account for active force-generating parts and for the formation of spatial and temporal patterns utilizing a diverse array of building blocks. In this Perspective, we term this framework “emergent mechanics.” Through examples at molecular, cellular, and tissue scales, we highlight challenges and opportunities in quantitatively understanding the emergent mechanics of biological structures and the need for new conceptual frameworks and experimental tools on the way ahead. PMID:25368421

Solution NMR studies provide structural basis for endotoxin pattern recognition by the innate immune receptor CD14

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

Albright, Seth; Chen Bin; Holbrook, Kristen

CD14 functions as a key pattern recognition receptor for a diverse array of Gram-negative and Gram-positive cell-wall components in the host innate immune response by binding to pathogen-associated molecular patterns (PAMPs) at partially overlapping binding site(s). To determine the potential contribution of CD14 residues in this pattern recognition, we have examined using solution NMR spectroscopy, the binding of three different endotoxin ligands, lipopolysaccharide, lipoteichoic acid, and a PGN-derived compound, muramyl dipeptide to a {sup 15}N isotopically labeled 152-residue N-terminal fragment of sCD14 expressed in Pichia pastoris. Mapping of NMR spectral changes upon addition of ligands revealed that the pattern ofmore » residues affected by binding of each ligand is partially similar and partially different. This first direct structural observation of the ability of specific residue combinations of CD14 to differentially affect endotoxin binding may help explain the broad specificity of CD14 in ligand recognition and provide a structural basis for pattern recognition. Another interesting finding from the observed spectral changes is that the mode of binding may be dynamically modulated and could provide a mechanism for binding endotoxins with structural diversity through a common binding site.« less

Diversity of chimera-like patterns from a model of 2D arrays of neurons with nonlocal coupling

NASA Astrophysics Data System (ADS)

Tian, Chang-Hai; Zhang, Xi-Yun; Wang, Zhen-Hua; Liu, Zong-Hua

2017-06-01

Chimera states have been studied in 1D arrays, and a variety of different chimera states have been found using different models. Research has recently been extended to 2D arrays but only to phase models of them. Here, we extend it to a nonphase model of 2D arrays of neurons and focus on the influence of nonlocal coupling. Using extensive numerical simulations, we find, surprisingly, that this system can show most types of previously observed chimera states, in contrast to previous models, where only one or a few types of chimera states can be observed in each model. We also find that this model can show some special chimera-like patterns such as gridding and multicolumn patterns, which were previously observed only in phase models. Further, we present an effective approach, i.e., removing some of the coupling links, to generate heterogeneous coupling, which results in diverse chimera-like patterns and even induces transformations from one chimera-like pattern to another.

Diverse microbially induced sedimentary structures from 1 Ga lakes of the Diabaig Formation, Torridon Group, northwest Scotland

NASA Astrophysics Data System (ADS)

Callow, Richard H. T.; Battison, Leila; Brasier, Martin D.

2011-08-01

The siliciclastic lacustrine rocks of the ~ 1000 Ma Diabaig Formation, northwest Scotland, contain a remarkable diversity of macroscopic structures on bedding planes that can be compared with various kinds of microbially induced sedimentary structures (MISS). Field sedimentological investigations, combined with laboratory analysis of bedding planes and petrographic study of thin sections have allowed us to characterise a range of depositional environments and document the spectrum of biological structures. MISS are reported from frequently subaerial environments, through commonly submerged facies, and down to permanently sub-wavebase settings. Palaeoenvironmental conditions (water depth, exposure, hydrodynamic energy) control the distribution of MISS within these facies. This demonstrates that mat-forming microbial communities were arguably well adapted to low light levels or periodic exposure. Some MISS from the Diabaig Formation are typical of Precambrian microbial mats, including reticulate fabrics and 'old elephant skin' textures. In addition to these, a number of new and unusual fabrics of putative microbial origin are described, including linear arrays of ridges and grooves (cf. 'Arumberia') and discoidal structures that are comparable with younger Ediacaran fossils such as Beltanelliformis. These observations indicate that benthic microbial ecosystems were thriving in freshwater lake systems ~ 1000 Ma, and indicate how microbially induced sedimentary structures may be applied as facies indicators for Proterozoic lacustrine environments. The discovery of structures closely resembling Ediacaran fossils (cf. Beltanelliformis) also serves to highlight the difficulty of interpreting simple discoidal bedding plane structures as metazoan fossils.

Conservation genetics in Chinese sheep: diversity of fourteen indigenous sheep (Ovis aries) using microsatellite markers.

PubMed

E, Guang-Xin; Zhong, Tao; Ma, Yue-Hui; Gao, Hui-Jiang; He, Jian-Ning; Liu, Nan; Zhao, Yong-Ju; Zhang, Jia-Hua; Huang, Yong-Fu

2016-02-01

The domestic sheep (Ovis aries) has been an economically and culturally important farm animal species since its domestication around the world. A wide array of sheep breeds with abundant phenotypic diversity exists including domestication and selection as well as the indigenous breeds may harbor specific features as a result of adaptation to their environment. The objective of this study was to investigate the population structure of indigenous sheep in a large geographic location of the Chinese mainland. Six microsatellites were genotyped for 611 individuals from 14 populations. The mean number of alleles (±SD) ranged from 7.00 ± 3.69 in Gangba sheep to 10.50 ± 4.23 in Tibetan sheep. The observed heterozygote frequency (±SD) within a population ranged from 0.58 ± 0.03 in Gangba sheep to 0.71 ± 0.03 in Zazakh sheep and Minxian black fur sheep. In addition, there was a low pairwise difference among the Minxian black fur sheep, Mongolian sheep, Gansu alpine merino, and Lanzhou fat-tailed sheep. Bayesian analysis with the program STRUCTURE showed support for 3 clusters, revealing a vague genetic clustering pattern with geographic location. The results of the current study inferred high genetic diversity within these native sheep in the Chinese mainland.

A computational prediction of structure and function of novel homologue of Arabidopsis thaliana Vps51/Vps67 subunit in Corchorus olitorius.

PubMed

Zaman, Aubhishek; Fancy, Nurun Nahar

2012-12-01

Vps mediated vesicular transport is important for transferring macromolecules trapped inside a vesicle. Although highly abundant, Vps shows tremendous sequence variation among diverse array of species. However, this difference in sequence, which seems to also translate into substantial functional variation, is hardly characterized in Corchorus spp. Here, our computational study investigates structural and functional features of one of the Vps subunit namely Vps51/Vps67 in C. olitorius. Broad scale structural characterization revealed novel information about the overall Vps structure and binding sites. Moreover, functional analyses indicate interaction partners which were unexplored to date. Since membrane trafficking is essentially associated with nutrient uptake and chemical de-toxification, characterization of the Vps subunit can well provide us with better insight into important agronomic traits such as stress response, immune response and phytoremediation capacity.

Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array.

PubMed

Hinze, Lori L; Hulse-Kemp, Amanda M; Wilson, Iain W; Zhu, Qian-Hao; Llewellyn, Danny J; Taylor, Jen M; Spriggs, Andrew; Fang, David D; Ulloa, Mauricio; Burke, John J; Giband, Marc; Lacape, Jean-Marc; Van Deynze, Allen; Udall, Joshua A; Scheffler, Jodi A; Hague, Steve; Wendel, Jonathan F; Pepper, Alan E; Frelichowski, James; Lawley, Cindy T; Jones, Don C; Percy, Richard G; Stelly, David M

2017-02-03

Cotton germplasm resources contain beneficial alleles that can be exploited to develop germplasm adapted to emerging environmental and climate conditions. Accessions and lines have traditionally been characterized based on phenotypes, but phenotypic profiles are limited by the cost, time, and space required to make visual observations and measurements. With advances in molecular genetic methods, genotypic profiles are increasingly able to identify differences among accessions due to the larger number of genetic markers that can be measured. A combination of both methods would greatly enhance our ability to characterize germplasm resources. Recent efforts have culminated in the identification of sufficient SNP markers to establish high-throughput genotyping systems, such as the CottonSNP63K array, which enables a researcher to efficiently analyze large numbers of SNP markers and obtain highly repeatable results. In the current investigation, we have utilized the SNP array for analyzing genetic diversity primarily among cotton cultivars, making comparisons to SSR-based phylogenetic analyses, and identifying loci associated with seed nutritional traits. The SNP markers distinctly separated G. hirsutum from other Gossypium species and distinguished the wild from cultivated types of G. hirsutum. The markers also efficiently discerned differences among cultivars, which was the primary goal when designing the CottonSNP63K array. Population structure within the genus compared favorably with previous results obtained using SSR markers, and an association study identified loci linked to factors that affect cottonseed protein content. Our results provide a large genome-wide variation data set for primarily cultivated cotton. Thousands of SNPs in representative cotton genotypes provide an opportunity to finely discriminate among cultivated cotton from around the world. The SNPs will be relevant as dense markers of genome variation for association mapping approaches aimed at correlating molecular polymorphisms with variation in phenotypic traits, as well as for molecular breeding approaches in cotton.

A plasmonic optical fiber patterned by template transfer as a high-performance flexible nanoprobe for real-time biosensing

NASA Astrophysics Data System (ADS)

Jia, Peipei; Yang, Jun

2014-07-01

Surface plasmon resonance (SPR) on metal nanostructures offers a promising route for manipulation and interrogation of light in the subwavelength regime. However, the utility of SPR structures is largely limited by currently used complex nanofabrication methods and relatively sophisticated optical components. Here to relieve these restrictions, plasmonic optical fibers are constructed by transferring periodic metal nanostructures from patterned templates onto endfaces of optical fibers using an epoxy adhesive. Patterned metal structures are generally extended from two-dimensional (2D) nanohole arrays to one-dimensional (1D) nanoslit arrays. By controlling the viscosity of the adhesive layer, diverse surface topographies of metal structures are realized with the same template. We design a special plasmonic fiber that simultaneously implements multimode refractive index sensing (transmission and reflection) with remarkably narrow linewidth (6.6 nm) and high figure of merit (60.7), which are both among the best reported values for SPR sensors. We further demonstrate a real-time immunoassay relying on our plasmonic fiber integrated with a special flow cell. Plasmonic optical fibers also take advantages of excellent stability during fiber bending and capability of spectrum filtering. These features enable our plasmonic fibers to open up an alternative avenue for the general community in biosensing and nanoplasmonics.

A plasmonic optical fiber patterned by template transfer as a high-performance flexible nanoprobe for real-time biosensing.

PubMed

Jia, Peipei; Yang, Jun

2014-08-07

Surface plasmon resonance (SPR) on metal nanostructures offers a promising route for manipulation and interrogation of light in the subwavelength regime. However, the utility of SPR structures is largely limited by currently used complex nanofabrication methods and relatively sophisticated optical components. Here to relieve these restrictions, plasmonic optical fibers are constructed by transferring periodic metal nanostructures from patterned templates onto endfaces of optical fibers using an epoxy adhesive. Patterned metal structures are generally extended from two-dimensional (2D) nanohole arrays to one-dimensional (1D) nanoslit arrays. By controlling the viscosity of the adhesive layer, diverse surface topographies of metal structures are realized with the same template. We design a special plasmonic fiber that simultaneously implements multimode refractive index sensing (transmission and reflection) with remarkably narrow linewidth (6.6 nm) and high figure of merit (60.7), which are both among the best reported values for SPR sensors. We further demonstrate a real-time immunoassay relying on our plasmonic fiber integrated with a special flow cell. Plasmonic optical fibers also take advantages of excellent stability during fiber bending and capability of spectrum filtering. These features enable our plasmonic fibers to open up an alternative avenue for the general community in biosensing and nanoplasmonics.

Electrochemical Deposition of Conformal and Functional Layers on High Aspect Ratio Silicon Micro/Nanowires.

PubMed

Ozel, Tuncay; Zhang, Benjamin A; Gao, Ruixuan; Day, Robert W; Lieber, Charles M; Nocera, Daniel G

2017-07-12

Development of new synthetic methods for the modification of nanostructures has accelerated materials design advances to furnish complex architectures. Structures based on one-dimensional (1D) silicon (Si) structures synthesized using top-down and bottom-up methods are especially prominent for diverse applications in chemistry, physics, and medicine. Yet further elaboration of these structures with distinct metal-based and polymeric materials, which could open up new opportunities, has been difficult. We present a general electrochemical method for the deposition of conformal layers of various materials onto high aspect ratio Si micro- and nanowire arrays. The electrochemical deposition of a library of coaxial layers comprising metals, metal oxides, and organic/inorganic semiconductors demonstrate the materials generality of the synthesis technique. Depositions may be performed on wire arrays with varying diameter (70 nm to 4 μm), pitch (5 μ to 15 μ), aspect ratio (4:1 to 75:1), shape (cylindrical, conical, hourglass), resistivity (0.001-0.01 to 1-10 ohm/cm 2 ), and substrate orientation. Anisotropic physical etching of wires with one or more coaxial shells yields 1D structures with exposed tips that can be further site-specifically modified by an electrochemical deposition approach. The electrochemical deposition methodology described herein features a wafer-scale synthesis platform for the preparation of multifunctional nanoscale devices based on a 1D Si substrate.

Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome

PubMed Central

Johnston, Henry Richard; Hu, Yi-Juan; Gao, Jingjing; O’Connor, Timothy D.; Abecasis, Gonçalo R.; Wojcik, Genevieve L; Gignoux, Christopher R.; Gourraud, Pierre-Antoine; Lizee, Antoine; Hansen, Mark; Genuario, Rob; Bullis, Dave; Lawley, Cindy; Kenny, Eimear E.; Bustamante, Carlos; Beaty, Terri H.; Mathias, Rasika A.; Barnes, Kathleen C.; Qin, Zhaohui S.; Preethi Boorgula, Meher; Campbell, Monica; Chavan, Sameer; Ford, Jean G.; Foster, Cassandra; Gao, Li; Hansel, Nadia N.; Horowitz, Edward; Huang, Lili; Ortiz, Romina; Potee, Joseph; Rafaels, Nicholas; Ruczinski, Ingo; Scott, Alan F.; Taub, Margaret A.; Vergara, Candelaria; Levin, Albert M.; Padhukasahasram, Badri; Williams, L. Keoki; Dunston, Georgia M.; Faruque, Mezbah U.; Gietzen, Kimberly; Deshpande, Aniket; Grus, Wendy E.; Locke, Devin P.; Foreman, Marilyn G.; Avila, Pedro C.; Grammer, Leslie; Kim, Kwang-Youn A.; Kumar, Rajesh; Schleimer, Robert; De La Vega, Francisco M.; Shringarpure, Suyash S.; Musharoff, Shaila; Burchard, Esteban G.; Eng, Celeste; Hernandez, Ryan D.; Pino-Yanes, Maria; Torgerson, Dara G.; Szpiech, Zachary A.; Torres, Raul; Nicolae, Dan L.; Ober, Carole; Olopade, Christopher O; Olopade, Olufunmilayo; Oluwole, Oluwafemi; Arinola, Ganiyu; Song, Wei; Correa, Adolfo; Musani, Solomon; Wilson, James G.; Lange, Leslie A.; Akey, Joshua; Bamshad, Michael; Chong, Jessica; Fu, Wenqing; Nickerson, Deborah; Reiner, Alexander; Hartert, Tina; Ware, Lorraine B.; Bleecker, Eugene; Meyers, Deborah; Ortega, Victor E.; Maul, Pissamai; Maul, Trevor; Watson, Harold; Ilma Araujo, Maria; Riccio Oliveira, Ricardo; Caraballo, Luis; Marrugo, Javier; Martinez, Beatriz; Meza, Catherine; Ayestas, Gerardo; Francisco Herrera-Paz, Edwin; Landaverde-Torres, Pamela; Erazo, Said Omar Leiva; Martinez, Rosella; Mayorga, Alvaro; Mayorga, Luis F.; Mejia-Mejia, Delmy-Aracely; Ramos, Hector; Saenz, Allan; Varela, Gloria; Marina Vasquez, Olga; Ferguson, Trevor; Knight-Madden, Jennifer; Samms-Vaughan, Maureen; Wilks, Rainford J.; Adegnika, Akim; Ateba-Ngoa, Ulysse; Yazdanbakhsh, Maria

2017-01-01

A primary goal of The Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) is to develop an ‘African Diaspora Power Chip’ (ADPC), a genotyping array consisting of tagging SNPs, useful in comprehensively identifying African specific genetic variation. This array is designed based on the novel variation identified in 642 CAAPA samples of African ancestry with high coverage whole genome sequence data (~30× depth). This novel variation extends the pattern of variation catalogued in the 1000 Genomes and Exome Sequencing Projects to a spectrum of populations representing the wide range of West African genomic diversity. These individuals from CAAPA also comprise a large swath of the African Diaspora population and incorporate historical genetic diversity covering nearly the entire Atlantic coast of the Americas. Here we show the results of designing and producing such a microchip array. This novel array covers African specific variation far better than other commercially available arrays, and will enable better GWAS analyses for researchers with individuals of African descent in their study populations. A recent study cataloging variation in continental African populations suggests this type of African-specific genotyping array is both necessary and valuable for facilitating large-scale GWAS in populations of African ancestry. PMID:28429804

Novel fabrication technique of hybrid structure lens array for 3D images

NASA Astrophysics Data System (ADS)

Lee, Junsik; Kim, Junoh; Kim, Cheoljoong; Shin, Dooseub; Koo, Gyohyun; Won, Yong Hyub

2016-03-01

Tunable liquid lens arrays can produce three dimensional images by using electrowetting principle that alters surface tensions by applying voltage. This method has advantages of fast response time and low power consumption. However, it is challenging to fabricate a high fill factor liquid lens array and operate three dimensional images which demand high diopter. This study describes a hybrid structure lens array which has not only a liquid lens array but a solid lens array. A concave-shape lens array is unavoidable when using only the liquid lens array and some voltages are needed to make the lens flat. By placing the solid lens array on the liquid lens array, initial diopter can be positive. To fabricate the hybrid structure lens array, a conventional lithographic process in semiconductor manufacturing is needed. A negative photoresist SU-8 was used as chamber master molds. PDMS and UV adhesive replica molding are done sequentially. Two immiscible liquids, DI water and dodecane, are injected in the fabricated chamber, followed by sealing. The fabricated structure has a 20 by 20 pattern of cylindrical shaped circle array and the aperture size of each lens is 1mm. The thickness of the overall hybrid structure is about 2.8mm. Hybrid structure lens array has many advantages. Solid lens array has almost 100% fill factor and allow high efficiency. Diopter can be increased by more than 200 and negative diopter can be shifted to the positive region. This experiment showed several properties of the hybrid structure and demonstrated its superiority.

Recent Advances in the Structural Mechanisms of DNA Glycosylases

PubMed Central

Brooks, Sonja C.; Adhikary, Suraj; Rubinson, Emily H.; Eichman, Brandt F.

2012-01-01

DNA glycosylases safeguard the genome by locating and excising a diverse array of aberrant nucleobases created from oxidation, alkylation, and deamination of DNA. Since the discovery 28 years ago that these enzymes employ a base flipping mechanism to trap their substrates, six different protein architectures have been identified to perform the same basic task. Work over the past several years has unraveled details for how the various DNA glycosylases survey DNA, detect damage within the duplex, select for the correct modification, and catalyze base excision. Here, we provide a broad overview of these latest advances in glycosylase mechanisms gleaned from structural enzymology, highlighting features common to all glycosylases as well as key differences that define their particular substrate specificities. PMID:23076011

Natural Products from the Lithistida: A Review of the Literature since 2000

PubMed Central

Winder, Priscilla L.; Pomponi, Shirley A.; Wright, Amy E.

2011-01-01

Lithistid sponges are known to produce a diverse array of compounds ranging from polyketides, cyclic and linear peptides, alkaloids, pigments, lipids, and sterols. A majority of these structurally complex compounds have very potent and interesting biological activities. It has been a decade since a thorough review has been published that summarizes the literature on the natural products reported from this amazing sponge order. This review provides an update on the current taxonomic classification of the Lithistida, describes structures and biological activities of 131 new natural products, and discusses highlights from the total syntheses of 16 compounds from marine sponges of the Order Lithistida providing a compilation of the literature since the last review published in 2002. PMID:22363244

Discovery of new antimalarial chemotypes through chemical methodology and library development.

PubMed

Brown, Lauren E; Chih-Chien Cheng, Ken; Wei, Wan-Guo; Yuan, Pingwei; Dai, Peng; Trilles, Richard; Ni, Feng; Yuan, Jing; MacArthur, Ryan; Guha, Rajarshi; Johnson, Ronald L; Su, Xin-zhuan; Dominguez, Melissa M; Snyder, John K; Beeler, Aaron B; Schaus, Scott E; Inglese, James; Porco, John A

2011-04-26

In an effort to expand the stereochemical and structural complexity of chemical libraries used in drug discovery, the Center for Chemical Methodology and Library Development at Boston University has established an infrastructure to translate methodologies accessing diverse chemotypes into arrayed libraries for biological evaluation. In a collaborative effort, the NIH Chemical Genomics Center determined IC(50)'s for Plasmodium falciparum viability for each of 2,070 members of the CMLD-BU compound collection using quantitative high-throughput screening across five parasite lines of distinct geographic origin. Three compound classes displaying either differential or comprehensive antimalarial activity across the lines were identified, and the nascent structure activity relationships (SAR) from this experiment used to initiate optimization of these chemotypes for further development.

The first genetic map of pigeon pea based on diversity arrays technology (DArT) markers.

PubMed

Yang, Shi Ying; Saxena, Rachit K; Kulwal, Pawan L; Ash, Gavin J; Dubey, Anuja; Harper, John D I; Upadhyaya, Hari D; Gothalwal, Ragini; Kilian, Andrzej; Varshney, Rajeev K

2011-04-01

With an objective to develop a genetic map in pigeon pea (Cajanus spp.), a total of 554 diversity arrays technology (DArT) markers showed polymorphism in a pigeon pea F(2) mapping population of 72 progenies derived from an interspecific cross of ICP 28 (Cajanus cajan) and ICPW 94 (Cajanus scarabaeoides). Approximately 13% of markers did not conform to expected segregation ratio. The total number of DArT marker loci segregating in Mendelian manner was 405 with 73.1% (P > 0.001) of DArT markers having unique segregation patterns. Two groups of genetic maps were generated using DArT markers. While the maternal genetic linkage map had 122 unique DArT maternal marker loci, the paternal genetic linkage map has a total of 172 unique DArT paternal marker loci. The length of these two maps covered 270.0 cM and 451.6 cM, respectively. These are the first genetic linkage maps developed for pigeon pea, and this is the first report of genetic mapping in any grain legume using diversity arrays technology.

Genetic diversity and trait genomic prediction in a pea diversity panel.

PubMed

Burstin, Judith; Salloignon, Pauline; Chabert-Martinello, Marianne; Magnin-Robert, Jean-Bernard; Siol, Mathieu; Jacquin, Françoise; Chauveau, Aurélie; Pont, Caroline; Aubert, Grégoire; Delaitre, Catherine; Truntzer, Caroline; Duc, Gérard

2015-02-21

Pea (Pisum sativum L.), a major pulse crop grown for its protein-rich seeds, is an important component of agroecological cropping systems in diverse regions of the world. New breeding challenges imposed by global climate change and new regulations urge pea breeders to undertake more efficient methods of selection and better take advantage of the large genetic diversity present in the Pisum sativum genepool. Diversity studies conducted so far in pea used Simple Sequence Repeat (SSR) and Retrotransposon Based Insertion Polymorphism (RBIP) markers. Recently, SNP marker panels have been developed that will be useful for genetic diversity assessment and marker-assisted selection. A collection of diverse pea accessions, including landraces and cultivars of garden, field or fodder peas as well as wild peas was characterised at the molecular level using newly developed SNP markers, as well as SSR markers and RBIP markers. The three types of markers were used to describe the structure of the collection and revealed different pictures of the genetic diversity among the collection. SSR showed the fastest rate of evolution and RBIP the slowest rate of evolution, pointing to their contrasted mode of evolution. SNP markers were then used to predict phenotypes -the date of flowering (BegFlo), the number of seeds per plant (Nseed) and thousand seed weight (TSW)- that were recorded for the collection. Different statistical methods were tested including the LASSO (Least Absolute Shrinkage ans Selection Operator), PLS (Partial Least Squares), SPLS (Sparse Partial Least Squares), Bayes A, Bayes B and GBLUP (Genomic Best Linear Unbiased Prediction) methods and the structure of the collection was taken into account in the prediction. Despite a limited number of 331 markers used for prediction, TSW was reliably predicted. The development of marker assisted selection has not reached its full potential in pea until now. This paper shows that the high-throughput SNP arrays that are being developed will most probably allow for a more efficient selection in this species.

Diversity and population-genetic properties of copy number variations and multicopy genes in cattle

PubMed Central

Bickhart, Derek M.; Xu, Lingyang; Hutchison, Jana L.; Cole, John B.; Null, Daniel J.; Schroeder, Steven G.; Song, Jiuzhou; Garcia, Jose Fernando; Sonstegard, Tad S.; Van Tassell, Curtis P.; Schnabel, Robert D.; Taylor, Jeremy F.; Lewin, Harris A.; Liu, George E.

2016-01-01

The diversity and population genetics of copy number variation (CNV) in domesticated animals are not well understood. In this study, we analysed 75 genomes of major taurine and indicine cattle breeds (including Angus, Brahman, Gir, Holstein, Jersey, Limousin, Nelore, and Romagnola), sequenced to 11-fold coverage to identify 1,853 non-redundant CNV regions. Supported by high validation rates in array comparative genomic hybridization (CGH) and qPCR experiments, these CNV regions accounted for 3.1% (87.5 Mb) of the cattle reference genome, representing a significant increase over previous estimates of the area of the genome that is copy number variable (∼2%). Further population genetics and evolutionary genomics analyses based on these CNVs revealed the population structures of the cattle taurine and indicine breeds and uncovered potential diversely selected CNVs near important functional genes, including AOX1, ASZ1, GAT, GLYAT, and KRTAP9-1. Additionally, 121 CNV gene regions were found to be either breed specific or differentially variable across breeds, such as RICTOR in dairy breeds and PNPLA3 in beef breeds. In contrast, clusters of the PRP and PAG genes were found to be duplicated in all sequenced animals, suggesting that subfunctionalization, neofunctionalization, or overdominance play roles in diversifying those fertility-related genes. These CNV results provide a new glimpse into the diverse selection histories of cattle breeds and a basis for correlating structural variation with complex traits in the future. PMID:27085184

Making a chocolate chip: development and evaluation of a 6K SNP array for Theobroma cacao.

PubMed

Livingstone, Donald; Royaert, Stefan; Stack, Conrad; Mockaitis, Keithanne; May, Greg; Farmer, Andrew; Saski, Christopher; Schnell, Ray; Kuhn, David; Motamayor, Juan Carlos

2015-08-01

Theobroma cacao, the key ingredient in chocolate production, is one of the world's most important tree fruit crops, with ∼4,000,000 metric tons produced across 50 countries. To move towards gene discovery and marker-assisted breeding in cacao, a single-nucleotide polymorphism (SNP) identification project was undertaken using RNAseq data from 16 diverse cacao cultivars. RNA sequences were aligned to the assembled transcriptome of the cultivar Matina 1-6, and 330,000 SNPs within coding regions were identified. From these SNPs, a subset of 6,000 high-quality SNPs were selected for inclusion on an Illumina Infinium SNP array: the Cacao6kSNP array. Using Cacao6KSNP array data from over 1,000 cacao samples, we demonstrate that our custom array produces a saturated genetic map and can be used to distinguish among even closely related genotypes. Our study enhances and expands the genetic resources available to the cacao research community, and provides the genome-scale set of tools that are critical for advancing breeding with molecular markers in an agricultural species with high genetic diversity. © The Author 2015. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

GUDM: Automatic Generation of Unified Datasets for Learning and Reasoning in Healthcare.

PubMed

Ali, Rahman; Siddiqi, Muhammad Hameed; Idris, Muhammad; Ali, Taqdir; Hussain, Shujaat; Huh, Eui-Nam; Kang, Byeong Ho; Lee, Sungyoung

2015-07-02

A wide array of biomedical data are generated and made available to healthcare experts. However, due to the diverse nature of data, it is difficult to predict outcomes from it. It is therefore necessary to combine these diverse data sources into a single unified dataset. This paper proposes a global unified data model (GUDM) to provide a global unified data structure for all data sources and generate a unified dataset by a "data modeler" tool. The proposed tool implements user-centric priority based approach which can easily resolve the problems of unified data modeling and overlapping attributes across multiple datasets. The tool is illustrated using sample diabetes mellitus data. The diverse data sources to generate the unified dataset for diabetes mellitus include clinical trial information, a social media interaction dataset and physical activity data collected using different sensors. To realize the significance of the unified dataset, we adopted a well-known rough set theory based rules creation process to create rules from the unified dataset. The evaluation of the tool on six different sets of locally created diverse datasets shows that the tool, on average, reduces 94.1% time efforts of the experts and knowledge engineer while creating unified datasets.

GUDM: Automatic Generation of Unified Datasets for Learning and Reasoning in Healthcare

PubMed Central

Ali, Rahman; Siddiqi, Muhammad Hameed; Idris, Muhammad; Ali, Taqdir; Hussain, Shujaat; Huh, Eui-Nam; Kang, Byeong Ho; Lee, Sungyoung

2015-01-01

A wide array of biomedical data are generated and made available to healthcare experts. However, due to the diverse nature of data, it is difficult to predict outcomes from it. It is therefore necessary to combine these diverse data sources into a single unified dataset. This paper proposes a global unified data model (GUDM) to provide a global unified data structure for all data sources and generate a unified dataset by a “data modeler” tool. The proposed tool implements user-centric priority based approach which can easily resolve the problems of unified data modeling and overlapping attributes across multiple datasets. The tool is illustrated using sample diabetes mellitus data. The diverse data sources to generate the unified dataset for diabetes mellitus include clinical trial information, a social media interaction dataset and physical activity data collected using different sensors. To realize the significance of the unified dataset, we adopted a well-known rough set theory based rules creation process to create rules from the unified dataset. The evaluation of the tool on six different sets of locally created diverse datasets shows that the tool, on average, reduces 94.1% time efforts of the experts and knowledge engineer while creating unified datasets. PMID:26147731

Copper(II)-catalyzed amidations of alkynyl bromides as a general synthesis of ynamides and Z-enamides. An intramolecular amidation for the synthesis of macrocyclic ynamides.

PubMed

Zhang, Xuejun; Zhang, Yanshi; Huang, Jian; Hsung, Richard P; Kurtz, Kimberly C M; Oppenheimer, Jossian; Petersen, Matthew E; Sagamanova, Irina K; Shen, Lichun; Tracey, Michael R

2006-05-26

A general and efficient method for the coupling of a wide range of amides with alkynyl bromides is described here. This novel amidation reaction involves a catalytic protocol using copper(II) sulfate-pentahydrate and 1,10-phenanthroline to direct the sp-C-N bond formation, leading to a structurally diverse array of ynamides including macrocyclic ynamides via an intramolecular amidation. Given the surging interest in ynamide chemistry, this atom economical synthesis of ynamides should invoke further attention from the synthetic organic community.

Structural Coloration of a Colloidal Amorphous Array is Intensified by Carbon Nanolayers.

PubMed

Takeoka, Yukikazu; Iwata, Masanori; Seki, Takahiro; Nueangnoraj, Khanin; Nishihara, Hirotomo; Yoshioka, Shinya

2018-04-10

In this study, we introduce the possibility of applying a colloidal amorphous array composed of fine silica particles as a structural-color material to invisible information technology. The appearance of a thick filmlike colloidal amorphous array formed from fine silica particles is considerably influenced by incoherent light scattering across the entire visible region. Therefore, regardless of the diameter of the fine silica particles, the thick colloidal amorphous array exhibits a white color to the naked eye. When carbon is uniformly deposited in the colloidal amorphous array by a pressure-pulsed chemical vapor deposition method, incoherent light scattering in the colloidal amorphous array is suppressed. As a result, coherent light scattering due to the short-range order in the colloidal amorphous array becomes conspicuous and the array exhibits a vivid structural color. As structures, such as letters and pictures, can be drawn using this technology, the colloidal amorphous array as a structural-colored material may also be applicable for invisible information technology.

Comparative ultrastructure of fruit plastids in three genetically diverse genotypes of apple (Malus × domestica Borkh.) during development.

PubMed

Schaeffer, Scott M; Christian, Ryan; Castro-Velasquez, Nohely; Hyden, Brennan; Lynch-Holm, Valerie; Dhingra, Amit

2017-10-01

Comparative ultrastructural developmental time-course analysis has identified discrete stages at which the fruit plastids undergo structural and consequently functional transitions to facilitate subsequent development-guided understanding of the complex plastid biology. Plastids are the defining organelle for a plant cell and are critical for myriad metabolic functions. The role of leaf plastid, chloroplast, is extensively documented; however, fruit plastids-chromoplasts-are poorly understood, especially in the context of the diverse metabolic processes operating in these diverse plant organs. Recently, in a comparative study of the predicted plastid-targeted proteomes across seven plant species, we reported that each plant species is predicted to harbor a unique set of plastid-targeted proteins. However, the temporal and developmental context of these processes remains unknown. In this study, an ultrastructural analysis approach was used to characterize fruit plastids in the epidermal and collenchymal cell layers at 11 developmental timepoints in three genotypes of apple (Malus × domestica Borkh.): chlorophyll-predominant 'Granny Smith', carotenoid-predominant 'Golden Delicious', and anthocyanin-predominant 'Top Red Delicious'. Plastids transitioned from a proplastid-like plastid to a chromoplast-like plastid in epidermis cells, while in the collenchyma cells, they transitioned from a chloroplast-like plastid to a chloro-chromo-amyloplast plastid. Plastids in the collenchyma cells of the three genotypes demonstrated a diverse array of structures and features. This study enabled the identification of discrete developmental stages during which specific functions are most likely being performed by the plastids as indicated by accumulation of plastoglobuli, starch granules, and other sub-organeller structures. Information regarding the metabolically active developmental stages is expected to facilitate biologically relevant omics studies to unravel the complex biochemistry of plastids in perennial non-model systems.

Block Copolymers as Templates for Arrays of Carbon Nanotubes

NASA Technical Reports Server (NTRS)

Bronikowski, Michael; Hunt, Brian

2003-01-01

A method of manufacturing regular arrays of precisely sized, shaped, positioned, and oriented carbon nanotubes has been proposed. Arrays of carbon nanotubes could prove useful in such diverse applications as communications (especially for filtering of signals), biotechnology (for sequencing of DNA and separation of chemicals), and micro- and nanoelectronics (as field emitters and as signal transducers and processors). The method is expected to be suitable for implementation in standard semiconductor-device fabrication facilities.

Performance analysis of structured gradient algorithm. [for adaptive beamforming linear arrays

NASA Technical Reports Server (NTRS)

Godara, Lal C.

1990-01-01

The structured gradient algorithm uses a structured estimate of the array correlation matrix (ACM) to estimate the gradient required for the constrained least-mean-square (LMS) algorithm. This structure reflects the structure of the exact array correlation matrix for an equispaced linear array and is obtained by spatial averaging of the elements of the noisy correlation matrix. In its standard form the LMS algorithm does not exploit the structure of the array correlation matrix. The gradient is estimated by multiplying the array output with the receiver outputs. An analysis of the two algorithms is presented to show that the covariance of the gradient estimated by the structured method is less sensitive to the look direction signal than that estimated by the standard method. The effect of the number of elements on the signal sensitivity of the two algorithms is studied.

Mapping Hispanic-Serving Institutions: A Typology of Institutional Diversity

ERIC Educational Resources Information Center

Núñez, Anne-Marie; Crisp, Gloria; Elizondo, Diane

2016-01-01

Hispanic-Serving Institutions (HSIs), institutions that enroll at least 25% Hispanic students, are institutionally diverse, including a much wider array of institutional types than other Minority-Serving Institutions (MSIs). Furthermore, they have distinctive institutional characteristics from those typically emphasized in institutional typologies…

Method and apparatus for control of a magnetic structure

DOEpatents

Challenger, Michael P.; Valla, Arthur S.

1996-06-18

A method and apparatus for independently adjusting the spacing between opposing magnet arrays in charged particle based light sources. Adjustment mechanisms between each of the magnet arrays and the supporting structure allow the gap between the two magnet arrays to be independently adjusted. In addition, spherical bearings in the linkages to the magnet arrays permit the transverse angular orientation of the magnet arrays to also be adjusted. The opposing magnet arrays can be supported above the ground by the structural support.

Diurnal roosts of male evening bats (Nycticeius humeralis) in diversely managed pine-hardwood forests

Treesearch

Roger W. Perry; Ronald E. Thill

2008-01-01

We examined attributes of 45 roost sites used by 17 adult male evening bats (Nycticeius humeralis) in a diverse forested landscape within the Ouachita Mountains, Arkansas. Bats roosted in a diverse array of substrates, including live or dead Pinus echinata $15 cm diam at breast height (29% of roosts) and small (,10 cm) understory or midstory...

The Physiology of Protein S-acylation

PubMed Central

Chamberlain, Luke H.; Shipston, Michael J.

2015-01-01

Protein S-acylation, the only fully reversible posttranslational lipid modification of proteins, is emerging as a ubiquitous mechanism to control the properties and function of a diverse array of proteins and consequently physiological processes. S-acylation results from the enzymatic addition of long-chain lipids, most typically palmitate, onto intracellular cysteine residues of soluble and transmembrane proteins via a labile thioester linkage. Addition of lipid results in increases in protein hydrophobicity that can impact on protein structure, assembly, maturation, trafficking, and function. The recent explosion in global S-acylation (palmitoyl) proteomic profiling as a result of improved biochemical tools to assay S-acylation, in conjunction with the recent identification of enzymes that control protein S-acylation and de-acylation, has opened a new vista into the physiological function of S-acylation. This review introduces key features of S-acylation and tools to interrogate this process, and highlights the eclectic array of proteins regulated including membrane receptors, ion channels and transporters, enzymes and kinases, signaling adapters and chaperones, cell adhesion, and structural proteins. We highlight recent findings correlating disruption of S-acylation to pathophysiology and disease and discuss some of the major challenges and opportunities in this rapidly expanding field. PMID:25834228

Radio imaging of solar flares using the very large array - New insights into flare process

NASA Technical Reports Server (NTRS)

Kundu, M. R.; Schmahl, E. J.; Vlahos, L.; Velusamy, T.

1982-01-01

An interpretation of VLA observations of microwave bursts is presented in an attempt to distinguish between certain models of flares. The VLA observations provide information about the pre-flare magnetic field topology and the existence of mildly relativistic electrons accelerated during flares. Examples are shown of changes in magnetic field topology in the hour before flares. In one case, new bipolar loops appear to emerge, which is an essential component of the model developed by Heyvaerts et al. (1977). In another case, a quadrupole structure, suggestive of two juxtaposed bipolar loops, appears to trigger the flare. Because of the observed diversity of magnetic field topologies in microwave bursts, it is believed that the magnetic energy must be dissipated in more than one way. The VLA observations are clearly providing means for sorting out the diverse flare models.

Ghettos and enclaves in the cross-place realm: mapping socially bounded spaces across cities.

PubMed

Montgomery, Alesia F

2011-01-01

Since the early Chicago School, urban researchers have used residential proximity to assess contacts within and between racial and ethnic groups. This approach is increasingly limited. Diverse groups use email, social networking sites, instant messaging and mobile phones to communicate across urban zones and distant cities. These practices enable mutual support among far-flung family members and co-ethnics as they engage with an array of institutions throughout their day. Through interviews and observations that include women and men of diverse occupations, races and national origins, the author explores how and why cross-place enclosures of sociality and resources develop. Rather than framing the residential area as the locus of racial/ethnic concentration, the author focuses on cross-place concentrations in the technologically mediated workspace. This study enhances theorization of the structural negotiations, interpersonal pressures and group preferences that produce separate lifeworlds in globalizing cities.

Graphene Nanoplatelet-Polymer Chemiresistive Sensor Arrays for the Detection and Discrimination of Chemical Warfare Agent Simulants.

PubMed

Wiederoder, Michael S; Nallon, Eric C; Weiss, Matt; McGraw, Shannon K; Schnee, Vincent P; Bright, Collin J; Polcha, Michael P; Paffenroth, Randy; Uzarski, Joshua R

2017-11-22

A cross-reactive array of semiselective chemiresistive sensors made of polymer-graphene nanoplatelet (GNP) composite coated electrodes was examined for detection and discrimination of chemical warfare agents (CWA). The arrays employ a set of chemically diverse polymers to generate a unique response signature for multiple CWA simulants and background interferents. The developed sensors' signal remains consistent after repeated exposures to multiple analytes for up to 5 days with a similar signal magnitude across different replicate sensors with the same polymer-GNP coating. An array of 12 sensors each coated with a different polymer-GNP mixture was exposed 100 times to a cycle of single analyte vapors consisting of 5 chemically similar CWA simulants and 8 common background interferents. The collected data was vector normalized to reduce concentration dependency, z-scored to account for baseline drift and signal-to-noise ratio, and Kalman filtered to reduce noise. The processed data was dimensionally reduced with principal component analysis and analyzed with four different machine learning algorithms to evaluate discrimination capabilities. For 5 similarly structured CWA simulants alone 100% classification accuracy was achieved. For all analytes tested 99% classification accuracy was achieved demonstrating the CWA discrimination capabilities of the developed system. The novel sensor fabrication methods and data processing techniques are attractive for development of sensor platforms for discrimination of CWA and other classes of chemical vapors.

Numerical simulation of crosstalk in reduced pitch HgCdTe photon-trapping structure pixel arrays.

PubMed

Schuster, Jonathan; Bellotti, Enrico

2013-06-17

We have investigated crosstalk in HgCdTe photovoltaic pixel arrays employing a photon trapping (PT) structure realized with a periodic array of pillars intended to provide broadband operation. We have found that, compared to non-PT pixel arrays with similar geometry, the array employing the PT structure has a slightly higher optical crosstalk. However, when the total crosstalk is evaluated, the presence of the PT region drastically reduces the total crosstalk; making the use of the PT structure not only useful to obtain broadband operation, but also desirable for reducing crosstalk in small pitch detector arrays.

Mosquito (Diptera: Culicidae) assemblages associated with Nidularium and Vriesea bromeliads in Serra do Mar, Atlantic Forest, Brazil

PubMed Central

2012-01-01

Background The most substantial and best preserved area of Atlantic Forest is within the biogeographical sub-region of Serra do Mar. The topographic complexity of the region creates a diverse array of microclimates, which can affect species distribution and diversity inside the forest. Given that Atlantic Forest includes highly heterogeneous environments, a diverse and medically important Culicidae assemblage, and possible species co-occurrence, we evaluated mosquito assemblages from bromeliad phytotelmata in Serra do Mar (southeastern Brazil). Methods Larvae and pupae were collected monthly from Nidularium and Vriesea bromeliads between July 2008 and June 2009. Collection sites were divided into landscape categories (lowland, hillslope and hilltop) based on elevation and slope. Correlations between bromeliad mosquito assemblage and environmental variables were assessed using multivariate redundancy analysis. Differences in species diversity between bromeliads within each category of elevation were explored using the Renyi diversity index. Univariate binary logistic regression analyses were used to assess species co-occurrence. Results A total of 2,024 mosquitoes belonging to 22 species were collected. Landscape categories (pseudo-F value = 1.89, p = 0.04), bromeliad water volume (pseudo-F = 2.99, p = 0.03) and bromeliad fullness (Pseudo-F = 4.47, p < 0.01) influenced mosquito assemblage structure. Renyi diversity index show that lowland possesses the highest diversity indices. The presence of An. homunculus was associated with Cx. ocellatus and the presence of An. cruzii was associated with Cx. neglectus, Cx. inimitabilis fuscatus and Cx. worontzowi. Anopheles cruzii and An. homunculus were taken from the same bromeliad, however, the co-occurrence between those two species was not statistically significant. Conclusions One of the main findings of our study was that differences in species among mosquito assemblages were influenced by landscape characteristics. The bromeliad factor that influenced mosquito abundance and assemblage structure was fullness. The findings of the current study raise important questions about the role of An. homunculus in the transmission of Plasmodium in Serra do Mar, southeastern Atlantic Forest. PMID:22340486

Mosquito (Diptera: Culicidae) assemblages associated with Nidularium and Vriesea bromeliads in Serra do Mar, Atlantic Forest, Brazil.

PubMed

Marques, Tatiani C; Bourke, Brian P; Laporta, Gabriel Z; Sallum, Maria Anice Mureb

2012-02-16

The most substantial and best preserved area of Atlantic Forest is within the biogeographical sub-region of Serra do Mar. The topographic complexity of the region creates a diverse array of microclimates, which can affect species distribution and diversity inside the forest. Given that Atlantic Forest includes highly heterogeneous environments, a diverse and medically important Culicidae assemblage, and possible species co-occurrence, we evaluated mosquito assemblages from bromeliad phytotelmata in Serra do Mar (southeastern Brazil). Larvae and pupae were collected monthly from Nidularium and Vriesea bromeliads between July 2008 and June 2009. Collection sites were divided into landscape categories (lowland, hillslope and hilltop) based on elevation and slope. Correlations between bromeliad mosquito assemblage and environmental variables were assessed using multivariate redundancy analysis. Differences in species diversity between bromeliads within each category of elevation were explored using the Renyi diversity index. Univariate binary logistic regression analyses were used to assess species co-occurrence. A total of 2,024 mosquitoes belonging to 22 species were collected. Landscape categories (pseudo-F value = 1.89, p = 0.04), bromeliad water volume (pseudo-F = 2.99, p = 0.03) and bromeliad fullness (Pseudo-F = 4.47, p < 0.01) influenced mosquito assemblage structure. Renyi diversity index show that lowland possesses the highest diversity indices. The presence of An. homunculus was associated with Cx. ocellatus and the presence of An. cruzii was associated with Cx. neglectus, Cx. inimitabilis fuscatus and Cx. worontzowi. Anopheles cruzii and An. homunculus were taken from the same bromeliad, however, the co-occurrence between those two species was not statistically significant. One of the main findings of our study was that differences in species among mosquito assemblages were influenced by landscape characteristics. The bromeliad factor that influenced mosquito abundance and assemblage structure was fullness. The findings of the current study raise important questions about the role of An. homunculus in the transmission of Plasmodium in Serra do Mar, southeastern Atlantic Forest.

Assessing the Location of Surface Plasmons Over Nanotriangle and Nanohole Arrays of Different Size and Periodicity

PubMed Central

Correia-Ledo, Debby; Gibson, Kirsty F.; Dhawan, Anuj; Couture, Maxime; Vo-Dinh, Tuan; Graham, Duncan; Masson, Jean-Francois

2012-01-01

The increasing popularity of surface plasmon resonance (SPR) and surface enhanced Raman scattering (SERS) sensor design based on nanotriangle or nanohole arrays, and the possibility to manufacture substrates at the transition between these plasmonic substrates, makes them ideal candidates for the establishment of structure-property relationships. This work features near diffraction-limited Raman images and FDTD simulations of nanotriangle and nanohole arrays substrates, which clearly demonstrate that the localization of the hot spot on these SERS substrates is significantly influenced by the ratio of diameter/periodicity (D/P). The experimental and simulation data reveal that the hot spots are located around nanotriangles (D/P = 1), characteristic of localized SPR. Decreasing the D/P ratio to 0.75-0.7 led to the creation of nanohole arrays, which promoted the excitation of a propagating surface plasmon (SP) delocalized over the metal network. The optimal SERS intensity was consistently achieved at this transition from nanotriangles to nanoholes, for every periodicity (650 nm to 1.5 μm) and excitation wavelength (633 and 785 nm) investigated, despite the presence or absence of a plasmonic band near the laser excitation. Further decreasing the D/P ratio led to excitation of a localized SP located around the rim of nanohole arrays for D/P of 0.5-0.6, in agreement with previous reports. In addition, this manuscript provides the first evidence that the hot spots are positioned inside the hole for D/P of 0.4, with the center being the region of highest electric field and Raman intensity. The compelling experimental evidence and FDTD simulations offer an overall understanding of the plasmonic properties of nanohole arrays as SERS and SPR sensors, which is of significant value in advancing the diversity of applications from such surfaces. PMID:23977402

Coherent and Noncoherent Joint Processing of Sonar for Detection of Small Targets in Shallow Water

PubMed Central

Jiang, Jingning; Li, Si; Ding, Zhenping; Pan, Chen; Gong, Xianyi

2018-01-01

A coherent-noncoherent joint processing framework is proposed for active sonar to combine diversity gain and beamforming gain for detection of a small target in shallow water environments. Sonar utilizes widely-spaced arrays to sense environments and illuminate a target of interest from multiple angles. Meanwhile, it exploits spatial diversity for time-reversal focusing to suppress reverberation, mainly strong bottom reverberation. For enhancement of robustness of time-reversal focusing, an adaptive iterative strategy is utilized in the processing framework. A probing signal is firstly transmitted and echoes of a likely target are utilized as steering vectors for the second transmission. With spatial diversity, target bearing and range are estimated using a broadband signal model. Numerical simulations show that the novel sonar outperforms the traditional phased-array sonar due to benefits of spatial diversity. The effectiveness of the proposed framework has been validated by localization of a small target in at-lake experiments. PMID:29642637

Riboswitches: emerging themes in RNA structure and function.

PubMed

Montange, Rebecca K; Batey, Robert T

2008-01-01

Riboswitches are RNAs capable of binding cellular metabolites using a diverse array of secondary and tertiary structures to modulate gene expression. The recent determination of the three-dimensional structures of parts of six different riboswitches illuminates common features that allow riboswitches to be grouped into one of two types. Type I riboswitches, as exemplified by the purine riboswitch, are characterized by a single, localized binding pocket supported by a largely pre-established global fold. This arrangement limits ligand-induced conformational changes in the RNA to a small region. In contrast, Type II riboswitches, such as the thiamine pyrophosphate riboswitch, contain binding pockets split into at least two spatially distinct sites. As a result, binding induces both local changes to the binding pocket and global architecture. Similar organizational themes are found in other noncoding RNAs, making it possible to begin to build a hierarchical classification of RNA structure based on the spatial organization of their active sites and associated secondary structural elements.

Computational investigation of fullerene-DNA interactions: Implications of fullerene's size and functionalization on DNA structure and binding energetics.

PubMed

Papavasileiou, Konstantinos D; Avramopoulos, Aggelos; Leonis, Georgios; Papadopoulos, Manthos G

2017-06-01

DNA is the building block of life, as it carries the biological information controlling development, function and reproduction of all organisms. However, its central role in storing and transferring genetic information can be severely hindered by molecules with structure altering abilities. Fullerenes are nanoparticles that find a broad spectrum of uses, but their toxicological effects on living organisms upon exposure remain unclear. The present study examines the interactions of a diverse array of fullerenes with DNA, by means of Molecular Dynamics and MM-PBSA methodologies, with special focus on structural deformations that may hint toxicity implications. Our results show that pristine and hydroxylated fullerenes have no unwinding effects upon DNA structure, with the latter displaying binding preference to the DNA major groove, achieved by both direct formation of hydrogen bonds and water molecule mediation. Fluorinated derivatives are capable of penetrating DNA structure, forming intercalative complexes with high binding affinities. Copyright © 2017 Elsevier Inc. All rights reserved.

Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome

PubMed Central

Shedlock, Andrew M.; Botka, Christopher W.; Zhao, Shaying; Shetty, Jyoti; Zhang, Tingting; Liu, Jun S.; Deschavanne, Patrick J.; Edwards, Scott V.

2007-01-01

We report results of a megabase-scale phylogenomic analysis of the Reptilia, the sister group of mammals. Large-scale end-sequence scanning of genomic clones of a turtle, alligator, and lizard reveals diverse, mammal-like landscapes of retroelements and simple sequence repeats (SSRs) not found in the chicken. Several global genomic traits, including distinctive phylogenetic lineages of CR1-like long interspersed elements (LINEs) and a paucity of A-T rich SSRs, characterize turtles and archosaur genomes, whereas higher frequencies of tandem repeats and a lower global GC content reveal mammal-like features in Anolis. Nonavian reptile genomes also possess a high frequency of diverse and novel 50-bp unit tandem duplications not found in chicken or mammals. The frequency distributions of ≈65,000 8-mer oligonucleotides suggest that rates of DNA-word frequency change are an order of magnitude slower in reptiles than in mammals. These results suggest a diverse array of interspersed and SSRs in the common ancestor of amniotes and a genomic conservatism and gradual loss of retroelements in reptiles that culminated in the minimalist chicken genome. PMID:17307883

Measuring diversity in Gossypium hirsutum using the CottonSNP63K Array

USDA-ARS?s Scientific Manuscript database

A CottonSNP63K array and accompanying cluster file has been developed and includes 45,104 intra-specific SNPs and 17,954 inter-specific SNPs for automated genotyping of cotton (Gossypium spp.) samples. Development of the cluster file included genotyping of 1,156 samples, a subset of which were iden...

Mapping transcription factor interactome networks using HaloTag protein arrays.

PubMed

Yazaki, Junshi; Galli, Mary; Kim, Alice Y; Nito, Kazumasa; Aleman, Fernando; Chang, Katherine N; Carvunis, Anne-Ruxandra; Quan, Rosa; Nguyen, Hien; Song, Liang; Alvarez, José M; Huang, Shao-Shan Carol; Chen, Huaming; Ramachandran, Niroshan; Altmann, Stefan; Gutiérrez, Rodrigo A; Hill, David E; Schroeder, Julian I; Chory, Joanne; LaBaer, Joshua; Vidal, Marc; Braun, Pascal; Ecker, Joseph R

2016-07-19

Protein microarrays enable investigation of diverse biochemical properties for thousands of proteins in a single experiment, an unparalleled capacity. Using a high-density system called HaloTag nucleic acid programmable protein array (HaloTag-NAPPA), we created high-density protein arrays comprising 12,000 Arabidopsis ORFs. We used these arrays to query protein-protein interactions for a set of 38 transcription factors and transcriptional regulators (TFs) that function in diverse plant hormone regulatory pathways. The resulting transcription factor interactome network, TF-NAPPA, contains thousands of novel interactions. Validation in a benchmarked in vitro pull-down assay revealed that a random subset of TF-NAPPA validated at the same rate of 64% as a positive reference set of literature-curated interactions. Moreover, using a bimolecular fluorescence complementation (BiFC) assay, we confirmed in planta several interactions of biological interest and determined the interaction localizations for seven pairs. The application of HaloTag-NAPPA technology to plant hormone signaling pathways allowed the identification of many novel transcription factor-protein interactions and led to the development of a proteome-wide plant hormone TF interactome network.

A tandem array of UDP-glycosyltransferases from the UGT73C subfamily glycosylate sapogenins, forming a spectrum of mono- and bisdesmosidic saponins.

PubMed

Erthmann, Pernille Østerbye; Agerbirk, Niels; Bak, Søren

2018-05-01

This study identifies six UGT73Cs all able to glucosylate sapogenins at positions 3 and/or 28 which demonstrates that B. vulgaris has a much richer arsenal of UGTs involved in saponin biosynthesis than initially anticipated. The wild cruciferous plant Barbarea vulgaris is resistant to some insects due to accumulation of two monodesmosidic triterpenoid saponins, oleanolic acid 3-O-β-cellobioside and hederagenin 3-O-β-cellobioside. Insect resistance depends on the structure of the sapogenin aglycone and the glycosylation pattern. The B. vulgaris saponin profile is complex with at least 49 saponin-like metabolites, derived from eight sapogenins and including up to five monosaccharide units. Two B. vulgaris UDP-glycosyltransferases, UGT73C11 and UGT73C13, O-glucosylate sapogenins at positions 3 and 28, forming mainly 3-O-β-D-glucosides. The aim of this study was to identify UGTs responsible for the diverse saponin oligoglycoside moieties observed in B. vulgaris. Twenty UGT genes from the insect resistant genotype were selected and heterologously expressed in Nicotiana benthamiana and/or Escherichia coli. The extracts were screened for their ability to glycosylate sapogenins (oleanolic acid, hederagenin), the hormone 24-epibrassinolide and sapogenin monoglucosides (hederagenin and oleanolic acid 3-O-β-D-glucosides). Six UGTs from the UGT73C subfamily were able to glucosylate both sapogenins and both monoglucosides at positions 3 and/or 28. Some UGTs formed bisdesmosidic saponins efficiently. At least four UGT73C genes were localized in a tandem array with UGT73C11 and possibly UGT73C13. This organization most likely reflects duplication events followed by sub- and neofunctionalization. Indeed, signs of positive selection on several amino acid sites were identified and modelled to be localized on the UGT protein surface. This tandem array is proposed to initiate higher order bisdesmosidic glycosylation of B. vulgaris saponins, leading to the recently discovered saponin structural diversity, however, not directly to known cellobiosidic saponins.

SEM characterization of anatomical variation in chitin organization in insect and arthropod cuticles.

PubMed

Chandran, Rakkiyappan; Williams, Lee; Hung, Albert; Nowlin, Kyle; LaJeunesse, Dennis

2016-03-01

The cuticles of insects and arthropods have some of the most diverse material properties observed in nature, so much so that it is difficult to imagine that all cutciles are primarily composed of the same two materials: a fibrous chitin network and a matrix composed of cuticle proteins. Various factors contribute to the mechanical and optical properties of an insect or arthropod cuticle including the thickness and composition. In this paper, we also identified another factor that may contribute to the optical, surface, and mechanical properties of a cuticle, i.e. the organization of chitin nanofibers and chitin fiber bundles. Self-assembled chitin nanofibers serve as the foundation for all higher order chitin structures in the cuticles of insects and other arthropods via interactions with structural cuticle proteins. Using a technique that enables the characterization of chitin organization in the cuticle of intact insects and arthropod exoskeletons, we demonstrate a structure/function correlation of chitin organization with larger scale anatomical structures. The chitin scaffolds in cuticles display an extraordinarily diverse set of morphologies that may reflect specific mechanical or physical properties. After removal of the proteinaceous and mineral matrix of a cuticle, we observe using SEM diverse nanoscale and micro scale organization of in-situ chitin in the wing, head, eye, leg, and dorsal and ventral thoracic regions of the periodical cicada Magicicada septendecim and in other insects and arthropods. The organization of chitin also appears to have a significant role in the organization of nanoscale surface structures. While microscale bristles and hairs have long been known to be chitin based materials formed as cellular extensions, we have found a nanostructured layer of chitin in the cuticle of the wing of the dog day annual cicada Tibicen tibicens, which may be the scaffold for the nanocone arrays found on the wing. We also use this process to examine the chitin organizations in the fruit fly, Drosophila melanogaster, and the Atlantic brown shrimp, Farfantepenaeus aztecus. Interestingly many of the homologous anatomical structures from diverse arthropods exhibit similar patterns of chitin organization suggesting that a common set of parameters, govern chitin organization. Copyright © 2016 Elsevier Ltd. All rights reserved.

Structural and functional diversity of soil bacterial and fungal communities following woody plant encroachment in the southern Great Plains

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

Hollister, Emily B; Schadt, Christopher Warren; Palumbo, Anthony Vito

In the southern Great Plains (USA), encroachment of grassland ecosystems by Prosopis glandulosa (honey mesquite) is widespread. Mesquite encroachment alters net primary productivity, enhances stores of C and N in plants and soil, and leads to increased levels of soil microbial biomass and activity. While mesquite's impact on the biogeochemistry of the region is well established, it effects on soil microbial diversity and function are unknown. In this study, soils associated with four plant types (C{sub 3} perennial grasses, C{sub 4} midgrasses, C{sub 4} shortgrasses, and mesquite) from a mesquite-encroached mixed grass prairie were surveyed to in an attempt tomore » characterize the structure, diversity, and functional capacity of their soil microbial communities. rRNA gene cloning and sequencing were used in conjunction with the GeoChip functional gene array to evaluate these potential differences. Mesquite soil supported increased bacterial and fungal diversity and harbored a distinct fungal community relative to other plant types. Despite differences in composition and diversity, few significant differences were detected with respect to the potential functional capacity of the soil microbial communities. These results may suggest that a high level of functional redundancy exists within the bacterial portion of the soil communities; however, given the bias of the GeoChip toward bacterial functional genes, potential functional differences among soil fungi could not be addressed. The results of this study illustrate the linkages shared between above- and belowground communities and demonstrate that soil microbial communities, and in particular soil fungi, may be altered by the process of woody plant encroachment.« less

Microfabricated Nanotopological Surfaces for Study of Adhesion-dependent Cell mechanosensitivity**

PubMed Central

Chen, Weiqiang; Sun, Yubing

2014-01-01

Cells display high sensitivity and exhibit diverse responses to the intrinsic nanotopography of the extracellular matrix through their nanoscale cellular sensing machinery. Here, we reported a simple microfabrication method for precise control and spatial patterning of the local nanoroughness on glass surfaces using photolithography and reactive ion etching (RIE). Using RIE-generated nanorough glass surfaces, we demonstrated that local nanoroughness could provide a potent biophysical signal to regulate a diverse array of NIH/3T3 fibroblast behaviors, including cell morphology, adhesion, proliferation and migration. We further showed that cellular responses to nanotopography might be regulated by cell adhesion signaling and actin cytoskeleton remodeling. To further investigate the role of cytoskeleton contractility in nanoroughness sensing, we applied the RIE method to generate nanoroughness on the tops of an array of elastomeric poly-dimethylsiloxane (PDMS) microposts. We utilized the PDMS microposts as force sensors and demonstrated that nanoroughness could indeed regulate the cytoskeleton contractility of NIH/3T3 fibroblasts. Our results suggested that a feedback regulation and mechano-chemical integration mechanism involving adhesion signaling, actin cytoskeleton, and intracellular mechanosensory components might play an important role in regulating mechanosensitive behaviors of NIH/3T3 fibroblasts. The capability to control and further predict cellular responses to nanoroughness might suggest novel methods for developing biomaterials mimicking nanotopographic structures in vivo and suitable local cellular microenvironments for functional tissue engineering. PMID:22887768

A minimalist approach to stereoselective glycosylation with unprotected donors.

PubMed

Le Mai Hoang, Kim; He, Jing-Xi; Báti, Gábor; Chan-Park, Mary B; Liu, Xue-Wei

2017-10-27

Mechanistic study of carbohydrate interactions in biological systems calls for the chemical synthesis of these complex structures. Owing to the specific stereo-configuration at each anomeric linkage and diversity in branching, significant breakthroughs in recent years have focused on either stereoselective glycosylation methods or facile assembly of glycan chains. Here, we introduce the unification approach that offers both stereoselective glycosidic bond formation and removal of protection/deprotection steps required for further elongation. Using dialkylboryl triflate as an in situ masking reagent, a wide array of glycosyl donors carrying one to three unprotected hydroxyl groups reacts with various glycosyl acceptors to furnish the desired products with good control over regioselectivity and stereoselectivity. This approach demonstrates the feasibility of straightforward access to important structural scaffolds for complex glycoconjugate synthesis.

Resistance to malaria through structural variation of red blood cell invasion receptors

PubMed Central

Leffler, Ellen M.; Band, Gavin; Busby, George B.J.; Kivinen, Katja; Le, Quang Si; Clarke, Geraldine M.; Bojang, Kalifa A.; Conway, David J.; Jallow, Muminatou; Sisay-Joof, Fatoumatta; Bougouma, Edith C.; Mangano, Valentina D.; Modiano, David; Sirima, Sodiomon B.; Achidi, Eric; Apinjoh, Tobias O.; Marsh, Kevin; Ndila, Carolyne M.; Peshu, Norbert; Williams, Thomas N.; Drakeley, Chris; Manjurano, Alphaxard; Reyburn, Hugh; Riley, Eleanor; Kachala, David; Molyneux, Malcolm; Nyirongo, Vysaul; Taylor, Terrie; Thornton, Nicole; Tilley, Louise; Grimsley, Shane; Drury, Eleanor; Stalker, Jim; Cornelius, Victoria; Hubbart, Christina; Jeffreys, Anna E.; Rowlands, Kate; Rockett, Kirk A.; Spencer, Chris C.A.; Kwiatkowski, Dominic P.

2017-01-01

The malaria parasite Plasmodium falciparum invades human red blood cells via interactions between host and parasite surface proteins. By analyzing genome sequence data from human populations, including 1269 individuals from sub-Saharan Africa, we identify a diverse array of large copy number variants affecting the host invasion receptor genes GYPA and GYPB. We find that a nearby association with severe malaria is explained by a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which encode a serologically distinct blood group antigen known as Dantu. This variant reduces the risk of severe malaria by 40% and has recently risen in frequency in parts of Kenya, yet it appears to be absent from west Africa. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria. PMID:28522690

A tale of two centromeres--diversity of structure but conservation of function in plants and animals.

PubMed

Birchler, James A; Gao, Zhi; Han, Fangpu

2009-02-01

The structural and functional aspects of two specific centromeres, one drawn from the animal kingdom (Drosophila) and the other from the plant kingdom (maize), are compared. Both cases illustrate an epigenetic component to centromere specification. The observations of neocentromeres in Drosophila and inactive centromeres in maize constitute one line of evidence for this hypothesis. Another common feature is the divisibility of centromere function with reduced stability as the size decreases. The systems differ in that Drosophila has no common sequence repeat at all centromeres, whereas maize has a 150-bp unit present in tandem arrays together with a centromere-specific transposon, centromere retrotransposon maize, present at all primary constrictions. Aspects of centromere structure known only from one or the other system might be common to both, namely, the presence of centromere RNAs in the kinetochore as found in maize and the organization of the centromeric histone 3 in tetrameric nucleosomes.

Three-dimensional fine structure of the organization of microtubules in neurite varicosities by ultra-high voltage electron microscope tomography.

PubMed

Nishida, Tomoki; Yoshimura, Ryoichi; Endo, Yasuhisa

2017-09-01

Neurite varicosities are highly specialized compartments that are involved in neurotransmitter/ neuromodulator release and provide a physiological platform for neural functions. However, it remains unclear how microtubule organization contributes to the form of varicosity. Here, we examine the three-dimensional structure of microtubules in varicosities of a differentiated PC12 neural cell line using ultra-high voltage electron microscope tomography. Three-dimensional imaging showed that a part of the varicosities contained an accumulation of organelles that were separated from parallel microtubule arrays. Further detailed analysis using serial sections and whole-mount tomography revealed microtubules running in a spindle shape of swelling in some other types of varicosities. These electron tomographic results showed that the structural diversity and heterogeneity of microtubule organization supported the form of varicosities, suggesting that a different distribution pattern of microtubules in varicosities is crucial to the regulation of varicosities development.

Resistance to malaria through structural variation of red blood cell invasion receptors.

PubMed

Leffler, Ellen M; Band, Gavin; Busby, George B J; Kivinen, Katja; Le, Quang Si; Clarke, Geraldine M; Bojang, Kalifa A; Conway, David J; Jallow, Muminatou; Sisay-Joof, Fatoumatta; Bougouma, Edith C; Mangano, Valentina D; Modiano, David; Sirima, Sodiomon B; Achidi, Eric; Apinjoh, Tobias O; Marsh, Kevin; Ndila, Carolyne M; Peshu, Norbert; Williams, Thomas N; Drakeley, Chris; Manjurano, Alphaxard; Reyburn, Hugh; Riley, Eleanor; Kachala, David; Molyneux, Malcolm; Nyirongo, Vysaul; Taylor, Terrie; Thornton, Nicole; Tilley, Louise; Grimsley, Shane; Drury, Eleanor; Stalker, Jim; Cornelius, Victoria; Hubbart, Christina; Jeffreys, Anna E; Rowlands, Kate; Rockett, Kirk A; Spencer, Chris C A; Kwiatkowski, Dominic P

2017-06-16

The malaria parasite Plasmodium falciparum invades human red blood cells by a series of interactions between host and parasite surface proteins. By analyzing genome sequence data from human populations, including 1269 individuals from sub-Saharan Africa, we identify a diverse array of large copy-number variants affecting the host invasion receptor genes GYPA and GYPB We find that a nearby association with severe malaria is explained by a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which encode a serologically distinct blood group antigen known as Dantu. This variant reduces the risk of severe malaria by 40% and has recently increased in frequency in parts of Kenya, yet it appears to be absent from west Africa. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria. Copyright © 2017, American Association for the Advancement of Science.

A bio-inspired structural health monitoring system based on ambient vibration

NASA Astrophysics Data System (ADS)

Lin, Tzu-Kang; Kiremidjian, Anne; Lei, Chi-Yang

2010-11-01

A structural health monitoring (SHM) system based on naïve Bayesian (NB) damage classification and DNA-like expression data was developed in this research. Adapted from the deoxyribonucleic acid (DNA) array concept in molecular biology, the proposed structural health monitoring system is constructed utilizing a double-tier regression process to extract the expression array from the structural time history recorded during external excitations. The extracted array is symbolized as the various genes of the structure from the viewpoint of molecular biology and reflects the possible damage conditions prevalent in the structure. A scaled down, six-story steel building mounted on the shaking table of the National Center for Research on Earthquake Engineering (NCREE) was used as the benchmark. The structural response at different damage levels and locations under ambient vibration was collected to support the database for the proposed SHM system. To improve the precision of detection in practical applications, the system was enhanced by an optimization process using the likelihood selection method. The obtained array representing the DNA array of the health condition of the structure was first evaluated and ranked. A total of 12 groups of expression arrays were regenerated from a combination of four damage conditions. To keep the length of the array unchanged, the best 16 coefficients from every expression array were selected to form the optimized SHM system. Test results from the ambient vibrations showed that the detection accuracy of the structural damage could be greatly enhanced by the optimized expression array, when compared to the original system. Practical verification also demonstrated that a rapid and reliable result could be given by the final system within 1 min. The proposed system implements the idea of transplanting the DNA array concept from molecular biology into the field of SHM.

Erwinia amylovora CRISPR Elements Provide New Tools for Evaluating Strain Diversity and for Microbial Source Tracking

PubMed Central

McGhee, Gayle C.; Sundin, George W.

2012-01-01

Clustered regularly interspaced short palindromic repeats (CRISPRs) comprise a family of short DNA repeat sequences that are separated by non repetitive spacer sequences and, in combination with a suite of Cas proteins, are thought to function as an adaptive immune system against invading DNA. The number of CRISPR arrays in a bacterial chromosome is variable, and the content of each array can differ in both repeat number and in the presence or absence of specific spacers. We utilized a comparative sequence analysis of CRISPR arrays of the plant pathogen Erwinia amylovora to uncover previously unknown genetic diversity in this species. A total of 85 E. amylovora strains varying in geographic isolation (North America, Europe, New Zealand, and the Middle East), host range, plasmid content, and streptomycin sensitivity/resistance were evaluated for CRISPR array number and spacer variability. From these strains, 588 unique spacers were identified in the three CRISPR arrays present in E. amylovora, and these arrays could be categorized into 20, 17, and 2 patterns types, respectively. Analysis of the relatedness of spacer content differentiated most apple and pear strains isolated in the eastern U.S. from western U.S. strains. In addition, we identified North American strains that shared CRISPR genotypes with strains isolated on other continents. E. amylovora strains from Rubus and Indian hawthorn contained mostly unique spacers compared to apple and pear strains, while strains from loquat shared 79% of spacers with apple and pear strains. Approximately 23% of the spacers matched known sequences, with 16% targeting plasmids and 5% targeting bacteriophage. The plasmid pEU30, isolated in E. amylovora strains from the western U.S., was targeted by 55 spacers. Lastly, we used spacer patterns and content to determine that streptomycin-resistant strains of E. amylovora from Michigan were low in diversity and matched corresponding streptomycin-sensitive strains from the background population. PMID:22860008

Erwinia amylovora CRISPR elements provide new tools for evaluating strain diversity and for microbial source tracking.

PubMed

McGhee, Gayle C; Sundin, George W

2012-01-01

Clustered regularly interspaced short palindromic repeats (CRISPRs) comprise a family of short DNA repeat sequences that are separated by non repetitive spacer sequences and, in combination with a suite of Cas proteins, are thought to function as an adaptive immune system against invading DNA. The number of CRISPR arrays in a bacterial chromosome is variable, and the content of each array can differ in both repeat number and in the presence or absence of specific spacers. We utilized a comparative sequence analysis of CRISPR arrays of the plant pathogen Erwinia amylovora to uncover previously unknown genetic diversity in this species. A total of 85 E. amylovora strains varying in geographic isolation (North America, Europe, New Zealand, and the Middle East), host range, plasmid content, and streptomycin sensitivity/resistance were evaluated for CRISPR array number and spacer variability. From these strains, 588 unique spacers were identified in the three CRISPR arrays present in E. amylovora, and these arrays could be categorized into 20, 17, and 2 patterns types, respectively. Analysis of the relatedness of spacer content differentiated most apple and pear strains isolated in the eastern U.S. from western U.S. strains. In addition, we identified North American strains that shared CRISPR genotypes with strains isolated on other continents. E. amylovora strains from Rubus and Indian hawthorn contained mostly unique spacers compared to apple and pear strains, while strains from loquat shared 79% of spacers with apple and pear strains. Approximately 23% of the spacers matched known sequences, with 16% targeting plasmids and 5% targeting bacteriophage. The plasmid pEU30, isolated in E. amylovora strains from the western U.S., was targeted by 55 spacers. Lastly, we used spacer patterns and content to determine that streptomycin-resistant strains of E. amylovora from Michigan were low in diversity and matched corresponding streptomycin-sensitive strains from the background population.

Engineering study of the module/array interface for large terrestrial photovoltaic arrays

NASA Technical Reports Server (NTRS)

1977-01-01

Three major areas--structural, electrical, and maintenance--were evaluated. Efforts in the structural area included establishing acceptance criteria for materials and members, determining loading criteria, and analyzing glass modules in various framing system configurations. Array support structure design was addressed briefly. Electrical considerations included evaluation of module characteristics, intermodule connectors, array wiring, converters and lightning protection. Plant maintenance features such as array cleaning, failure detection, and module installation and replacement were addressed.

Bio-Inspired Bright Structurally Colored Colloidal Amorphous Array Enhanced by Controlling Thickness and Black Background.

PubMed

Iwata, Masanori; Teshima, Midori; Seki, Takahiro; Yoshioka, Shinya; Takeoka, Yukikazu

2017-07-01

Inspired by Steller's jay, which displays angle-independent structural colors, angle-independent structurally colored materials are created, which are composed of amorphous arrays of submicrometer-sized fine spherical silica colloidal particles. When the colloidal amorphous arrays are thick, they do not appear colorful but almost white. However, the saturation of the structural color can be increased by (i) appropriately controlling the thickness of the array and (ii) placing the black background substrate. This is similar in the case of the blue feather of Steller's jay. Based on the knowledge gained through the biomimicry of structural colored materials, colloidal amorphous arrays on the surface of a black particle as the core particle are also prepared as colorful photonic pigments. Moreover, a structural color on-off system is successfully built by controlling the background brightness of the colloidal amorphous arrays. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A microtubule bestiary: structural diversity in tubulin polymers.

PubMed

Chaaban, Sami; Brouhard, Gary J

2017-11-01

Microtubules are long, slender polymers of αβ-tubulin found in all eukaryotic cells. Tubulins associate longitudinally to form protofilaments, and adjacent protofilaments associate laterally to form the microtubule. In the textbook view, microtubules are 1) composed of 13 protofilaments, 2) arranged in a radial array by the centrosome, and 3) built into the 9+2 axoneme. Although these canonical structures predominate in eukaryotes, microtubules with divergent protofilament numbers and higher-order microtubule assemblies have been discovered throughout the last century. Here we survey these noncanonical structures, from the 4-protofilament microtubules of Prosthecobacter to the 40-protofilament accessory microtubules of mantidfly sperm. We review the variety of protofilament numbers observed in different species, in different cells within the same species, and in different stages within the same cell. We describe the determinants of protofilament number, namely nucleation factors, tubulin isoforms, and posttranslational modifications. Finally, we speculate on the functional significance of these diverse polymers. Equipped with novel tubulin-purification tools, the field is now prepared to tackle the long-standing question of the evolutionary basis of microtubule structure. © 2017 Chaaban and Brouhard. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Fungal Community Shifts in Structure and Function across a Boreal Forest Fire Chronosequence

PubMed Central

Santalahti, Minna; Pumpanen, Jukka; Köster, Kajar; Berninger, Frank; Raffaello, Tommaso; Jumpponen, Ari; Asiegbu, Fred O.; Heinonsalo, Jussi

2015-01-01

Forest fires are a common natural disturbance in forested ecosystems and have a large impact on the microbial communities in forest soils. The response of soil fungal communities to forest fire is poorly documented. Here, we investigated fungal community structure and function across a 152-year boreal forest fire chronosequence using high-throughput sequencing of the internal transcribed spacer 2 (ITS2) region and a functional gene array (GeoChip). Our results demonstrate that the boreal forest soil fungal community was most diverse soon after a fire disturbance and declined over time. The differences in the fungal communities were explained by changes in the abundance of basidiomycetes and ascomycetes. Ectomycorrhizal (ECM) fungi contributed to the increase in basidiomycete abundance over time, with the operational taxonomic units (OTUs) representing the genera Cortinarius and Piloderma dominating in abundance. Hierarchical cluster analysis by using gene signal intensity revealed that the sites with different fire histories formed separate clusters, suggesting differences in the potential to maintain essential biogeochemical soil processes. The site with the greatest biological diversity had also the most diverse genes. The genes involved in organic matter degradation in the mature forest, in which ECM fungi were the most abundant, were as common in the youngest site, in which saprotrophic fungi had a relatively higher abundance. This study provides insight into the impact of fire disturbance on soil fungal community dynamics. PMID:26341215

Degree-of-Freedom Strengthened Cascade Array for DOD-DOA Estimation in MIMO Array Systems.

PubMed

Yao, Bobin; Dong, Zhi; Zhang, Weile; Wang, Wei; Wu, Qisheng

2018-05-14

In spatial spectrum estimation, difference co-array can provide extra degrees-of-freedom (DOFs) for promoting parameter identifiability and parameter estimation accuracy. For the sake of acquiring as more DOFs as possible with a given number of physical sensors, we herein design a novel sensor array geometry named cascade array. This structure is generated by systematically connecting a uniform linear array (ULA) and a non-uniform linear array, and can provide more DOFs than some exist array structures but less than the upper-bound indicated by minimum redundant array (MRA). We further apply this cascade array into multiple input multiple output (MIMO) array systems, and propose a novel joint direction of departure (DOD) and direction of arrival (DOA) estimation algorithm, which is based on a reduced-dimensional weighted subspace fitting technique. The algorithm is angle auto-paired and computationally efficient. Theoretical analysis and numerical simulations prove the advantages and effectiveness of the proposed array structure and the related algorithm.

Broadband and Wide Field-of-view Plasmonic Metasurface-enabled Waveplates

PubMed Central

Jiang, Zhi Hao; Lin, Lan; Ma, Ding; Yun, Seokho; Werner, Douglas H.; Liu, Zhiwen; Mayer, Theresa S.

2014-01-01

Quasi two-dimensional metasurfaces composed of subwavelength nanoresonator arrays can dramatically alter the properties of light in an ultra-thin planar geometry, enabling new optical functions such as anomalous reflection and refraction, polarization filtering, and wavefront modulation. However, previous metasurface-based nanostructures suffer from low efficiency, narrow bandwidth and/or limited field-of-view due to their operation near the plasmonic resonance. Here we demonstrate plasmonic metasurface-based nanostructures for high-efficiency, angle-insensitive polarization transformation over a broad octave-spanning bandwidth. The structures are realized by optimizing the anisotropic response of an array of strongly coupled nanorod resonators to tailor the interference of light at the subwavelength scale. Nanofabricated reflective half-wave and quarter-wave plates designed using this approach have measured polarization conversion ratios and reflection magnitudes greater than 92% over a broad wavelength range from 640 to 1290 nm and a wide field-of-view up to ±40°. This work outlines a versatile strategy to create metasurface-based photonics with diverse optical functionalities. PMID:25524830

Compendium: Writings on Effective Practices for Culturally and Linguistically Diverse Exceptional Learners.

ERIC Educational Resources Information Center

Ford, Bridgie Alexis, Ed.

Derived from two national multicultural symposia, this compendium focuses on an array of topics that combine research and educational practices for youth from culturally and linguistically diverse backgrounds with disabilities and/or gifts. Specific papers include: (1) "Parent-Involved Social Skill Instruction and the Perceptions of Children…

Nitrogen and crop rotation as drivers of the maize-associated soil microbiome

USDA-ARS?s Scientific Manuscript database

Microbes inhabit an exciting and interesting array of environments, exhibiting striking amounts of diversity and variation. The soil microbiome is one of the most dynamic and diverse microbial environments, where bacteria, fungi, and plant roots all interact to shape food networks and drive ecosyste...

Teaching complex ecological concepts through a demonstration garden Biodiversity, invasions and conservation in practice

USDA-ARS?s Scientific Manuscript database

Biodiversity encompasses the variety within and between species in an environment. Native communities host a diverse array of species and interactions between members. Invasions by non-native species reduce biodiversity and a community’s ability to support diverse assemblages, and are one of the lar...

Teaching Strategies for Diverse Learners in FCS Classrooms

ERIC Educational Resources Information Center

Allison, Barbara N.; Rehm, Marsha L.

2007-01-01

The growing diversity in today's classrooms demands that family and consumer sciences (FCS) teachers be knowledgeable, responsive, and well-prepared to work with a multicultural, multilingual student population. To meet the needs of students from all backgrounds, FCS teachers must use a broad array of research-based strategies that support diverse…

Genetic Diversity and Phenotypic Variation for Drought Resistance in Alfalfa (Medicago sativa L.) Germplasm Collected for Drought Tolerance

USDA-ARS?s Scientific Manuscript database

Drought is a major environmental factor hampering alfalfa productivity worldwide. Gene banks provide an array of trait diversity, frequently consisting of specific seed collection projects that focused on acquiring germplasm adapted to specific traits such as drought tolerance. These subsets provide...

Diverse binding site structures revealed in homology models of polyreactive immunoglobulins

NASA Astrophysics Data System (ADS)

Ramsland, Paul A.; Guddat, Luke W.; Edmundson, Allen B.; Raison, Robert L.

1997-09-01

We describe here computer-assisted homology models of the combiningsite structure of three polyreactive immunoglobulins. Template-based modelsof Fv (VL-VH) fragments were derived forthe surface IgM expressed by the malignant CD5 positive B cells from threepatients with chronic lymphocytic leukaemia (CLL). The conserved frameworkregions were constructed using crystal coordinates taken from highlyhomologous human variable domain structures (Pot and Hil). Complementaritydetermining regions (CDRs) were predicted by grafting loops, taken fromknown immunoglobulin structures, onto the Fv framework models. The CDRtemplates were chosen, where possible, to be of the same length and of highresidue identity or similarity. LCDR1, 2 and 3 as well as HCDR1 and 2 forthe Fv were constructed using this strategy. For HCDR3 prediction, adatabase containing the Cartesian coordinates of 30 of these loops wascompiled from unliganded antibody X-ray crystallographic structures and anHCDR3 of the same length as that of the B CLL Fv was selected as a template.In one case (Yar), the resulting HCDR3 model gave unfavourable interactionswhen incorporated into the Fv model. This HCDR3 was therefore modelled usingan alternative strategy of construction of the loop stems, using apreviously described HCDR3 conformation (Pot), followed by chain closurewith a β-turn. The template models were subjected to positionalrefinement using energy minimisation and molecular dynamics simulations(X-PLOR). An electrostatic surface description (GRASP) did not reveal acommon structural feature within the binding sites of the three polyreactiveFv. Thus, polyreactive immunoglobulins may recognise similar and multipleantigens through a diverse array of binding site structures.

Design structure for in-system redundant array repair in integrated circuits

DOEpatents

Bright, Arthur A.; Crumley, Paul G.; Dombrowa, Marc; Douskey, Steven M.; Haring, Rudolf A.; Oakland, Steven F.; Quellette, Michael R.; Strissel, Scott A.

2008-11-25

A design structure for repairing an integrated circuit during operation of the integrated circuit. The integrated circuit comprising of a multitude of memory arrays and a fuse box holding control data for controlling redundancy logic of the arrays. The design structure provides the integrated circuit with a control data selector for passing the control data from the fuse box to the memory arrays; providing a source of alternate control data, external of the integrated circuit; and connecting the source of alternate control data to the control data selector. The design structure further passes the alternate control data from the source thereof, through the control data selector and to the memory arrays to control the redundancy logic of the memory arrays.

Comparative ultrastructure of fruit plastids in three genetically diverse genotypes of apple (Malus × domestica Borkh.) during development

PubMed Central

Schaeffer, Scott M.; Christian, Ryan; Castro-Velasquez, Nohely; Hyden, Brennan; Lynch-Holm, Valerie

2017-01-01

Plastids are the defining organelle for a plant cell and are critical for myriad metabolic functions. The role of leaf plastid, chloroplast, is extensively documented; however, fruit plastids—chromoplasts—are poorly understood, especially in the context of the diverse metabolic processes operating in these diverse plant organs. Recently, in a comparative study of the predicted plastid-targeted proteomes across seven plant species, we reported that each plant species is predicted to harbor a unique set of plastid-targeted proteins. However, the temporal and developmental context of these processes remains unknown. In this study, an ultrastructural analysis approach was used to characterize fruit plastids in the epidermal and collenchymal cell layers at 11 developmental timepoints in three genotypes of apple (Malus × domestica Borkh.): chlorophyll-predominant ‘Granny Smith’, carotenoid-predominant ‘Golden Delicious’, and anthocyanin-predominant ‘Top Red Delicious’. Plastids transitioned from a proplastid-like plastid to a chromoplast-like plastid in epidermis cells, while in the collenchyma cells, they transitioned from a chloroplast-like plastid to a chloro-chromo-amyloplast plastid. Plastids in the collenchyma cells of the three genotypes demonstrated a diverse array of structures and features. This study enabled the identification of discrete developmental stages during which specific functions are most likely being performed by the plastids as indicated by accumulation of plastoglobuli, starch granules, and other sub-organeller structures. Information regarding the metabolically active developmental stages is expected to facilitate biologically relevant omics studies to unravel the complex biochemistry of plastids in perennial non-model systems. PMID:28698906

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

Guo, Yiming; Fredrickson, Daniel C.

Intermetallic crystal structures offer an enormous structural diversity, with an endless array of structural motifs whose connection to stability and physical properties are often mysterious. Making sense of the often complex crystal structures that arise here, developing a clear structural description, and identifying connections to other phases can be laborious and require an encyclopedic knowledge of structure types. In this Article, we present PRINCEPS, an algorithm based on a new coordination environment projection scheme that facilitates the structural analysis and comparison of such crystal structures. We demonstrate the potential of this approach by applying it to the complex Ce-Ni-Si ternarymore » system, whose 17 binary and 21 ternary phases would present a daunting challenge to one seeking to understand the system by manual inspection (but has nonetheless been well-described through the heroic efforts of previous researchers). With the help of PRINCEPS, most of the ternary phases in this system can be rationalized as intergrowths of simple structural fragments, and grouped into a handful of structural series (with some outliers). Lastly, these results illustrate how the PRINCEPS approach can be used to organize a vast collection of crystal structures into structurally meaningful families, and guide the description of complex atomic arrangements.« less

Conventional and Unconventional Antimicrobials from Fish, Marine Invertebrates and Micro-algae

PubMed Central

Smith, Valerie J.; Desbois, Andrew P.; Dyrynda, Elisabeth A.

2010-01-01

All eukaryotic organisms, single-celled or multi-cellular, produce a diverse array of natural anti-infective agents that, in addition to conventional antimicrobial peptides, also include proteins and other molecules often not regarded as part of the innate defences. Examples range from histones, fatty acids, and other structural components of cells to pigments and regulatory proteins. These probably represent very ancient defence factors that have been re-used in new ways during evolution. This review discusses the nature, biological role in host protection and potential biotechnological uses of some of these compounds, focusing on those from fish, marine invertebrates and marine micro-algae. PMID:20479976

Biological applications of nanobiotechnology.

PubMed

de Morais, Michele Greque; Martins, Vilásia Guimarães; Steffens, Daniela; Pranke, Patricia; da Costa, Jorge Alberto Vieira

2014-01-01

Nanotechnology is a multidisciplinary field that covers a vast and diverse array of devices derived from engineering, physics, chemistry, and biology. Nanotechnology has opened up by rapid advances in science and technology, creating new opportunities for advances in the fields of medicine, electronics, foods, and the environment. Nanoscale structures and materials (nanoparticles, nanowires, nanofibers, nanotubes) have been explored in many biological applications (biosensing, biological separation, molecular imaging, anticancer therapy) because their novel properties and functions differ drastically from their bulk counterparts. Their high volume/surface ratio, improved solubility, and multifunctionality open many new possibilities. The objective of this review is to describe the potential benefits and impacts of the nanobiotechnology in different areas.

Photovoltaic array space power plus diagnostics experiment

NASA Technical Reports Server (NTRS)

Guidice, Donald A.

1990-01-01

The objective of the Photovoltaic Array Space Power Plus Diagnostics (PASP Plus) experiment is to measure the effects of the interaction of the low- to mid-altitude space environment on the performance of a diverse set of small solar-cell arrays (planar and concentrator, representative of present and future military technologies) under differing conditions of velocity-vector orientation and simulated (by biasing) high-voltage operation. Solar arrays to be tested include Si and GaAs planar arrays and several types of GaAs concentrator arrays. Diagnostics (a Langmuir probe and a pressure gauge) and a transient pulse monitor (to measure radiated and conducted EMI during arcing) will be used to determine the impact of the environment on array operation to help verify various interactions models. Results from a successful PASP Plus flight will furnish answers to important interactions questions and provide inputs for design and test standards for photovoltaic space-power subsystems.

High-rate synthetic aperture communications in shallow water.

PubMed

Song, H C; Hodgkiss, W S; Kuperman, W A; Akal, T; Stevenson, M

2009-12-01

Time reversal communication exploits spatial diversity to achieve spatial and temporal focusing in complex ocean environments. Spatial diversity can be provided easily by a vertical array in a waveguide. Alternatively, spatial diversity can be obtained from a virtual horizontal array generated by two elements, a transmitter and a receiver, due to relative motion between them, referred to as a synthetic aperture. This paper presents coherent synthetic aperture communication results from at-sea experiments conducted in two different frequency bands: (1) 2-4 kHz and (2) 8-20 kHz. Case (1) employs binary-phase shift-keying modulation, while case (2) involves up to eight-phase shift keying modulation with a data rate of 30 kbits/s divided by the number of transmissions (diversity) to be accumulated. The receiver utilizes time reversal diversity combining followed by a single channel equalizer, with frequent channel updates to accommodate the time-varying channel due to coupling of space and time in the presence of motion. Two to five consecutive transmissions from a source moving at 4 kts over 3-6 km range in shallow water are combined successfully after Doppler compensation, confirming the feasibility of coherent synthetic aperture communications using time reversal.

Preparation of arrays of long carbon nanotubes using catalyst structure

DOEpatents

Zhu, Yuntian T.; Arendt, Paul; Li, Qingwen; Zhang, Xiefie

2016-03-22

A structure for preparing an substantially aligned array of carbon nanotubes include a substrate having a first side and a second side, a buffer layer on the first side of the substrate, a catalyst on the buffer layer, and a plurality of channels through the structure for allowing a gaseous carbon source to enter the substrate at the second side and flow through the structure to the catalyst. After preparing the array, a fiber of carbon nanotubes may be spun from the array. Prior to spinning, the array can be immersed in a polymer solution. After spinning, the polymer can be cured.

Wild yeast harbor a variety of distinct amyloid structures with strong prion-inducing capabilities

PubMed Central

Westergard, Laura; True, Heather L.

2014-01-01

Summary Variation in amyloid structures profoundly influences a wide array of pathological phenotypes in mammalian protein conformation disorders and dominantly inherited phenotypes in yeast. Here, we describe, for the first time, naturally occurring, self-propagating, structural variants of a prion protein isolated from wild strains of the yeast Saccharomyces cerevisiae. Variants of the [RNQ+] prion propagating in a variety of wild yeast differ biochemically, in their intracellular distributions, and in their ability to promote formation of the [PSI+] prion. [PSI+] is an epigenetic regulator of cellular phenotype and adaptability. Strikingly, we find that most natural [RNQ+] variants induced [PSI+] at high frequencies and the majority of [PSI+] variants elicited strong cellular phenotypes. We hypothesize that the presence of an efficient [RNQ+] template primes the cell for [PSI+] formation in order to induce [PSI+] in conditions where it would be advantageous. These studies utilize naturally occurring structural variants to expand our understanding of the consequences of diverse prion conformations on cellular phenotypes. PMID:24673812

Spatio-Temporal Equalizer for a Receiving-Antenna Feed Array

NASA Technical Reports Server (NTRS)

Mukai, Ryan; Lee, Dennis; Vilnrotter, Victor

2010-01-01

A spatio-temporal equalizer has been conceived as an improved means of suppressing multipath effects in the reception of aeronautical telemetry signals, and may be adaptable to radar and aeronautical communication applications as well. This equalizer would be an integral part of a system that would also include a seven-element planar array of receiving feed horns centered at the focal point of a paraboloidal antenna that would be nominally aimed at or near the aircraft that would be the source of the signal that one seeks to receive (see Figure 1). This spatio-temporal equalizer would consist mostly of a bank of seven adaptive finite-impulse-response (FIR) filters one for each element in the array - and the outputs of the filters would be summed (see Figure 2). The combination of the spatial diversity of the feedhorn array and the temporal diversity of the filter bank would afford better multipath-suppression performance than is achievable by means of temporal equalization alone. The seven-element feed array would supplant the single feed horn used in a conventional paraboloidal ground telemetry-receiving antenna. The radio-frequency telemetry signals re ceiv ed by the seven elements of the array would be digitized, converted to complex baseband form, and sent to the FIR filter bank, which would adapt itself in real time to enable reception of telemetry at a low bit error rate, even in the presence of multipath of the type found at many flight test ranges.

Patterns of taxonomic, phylogenetic diversity during a long-term succession of forest on the Loess Plateau, China: insights into assembly process

PubMed Central

Chai, Yongfu; Yue, Ming; Liu, Xiao; Guo, Yaoxin; Wang, Mao; Xu, Jinshi; Zhang, Chenguang; Chen, Yu; Zhang, Lixia; Zhang, Ruichang

2016-01-01

Quantifying the drivers underlying the distribution of biodiversity during succession is a critical issue in ecology and conservation, and also can provide insights into the mechanisms of community assembly. Ninety plots were established in the Loess Plateau region of northern Shaanxi in China. The taxonomic and phylogenetic (alpha and beta) diversity were quantified within six succession stages. Null models were used to test whether phylogenetic distance observed differed from random expectations. Taxonomic beta diversity did not show a regular pattern, while phylogenetic beta diversity decreased throughout succession. The shrub stage occurred as a transition from phylogenetic overdispersion to clustering either for NRI (Net Relatedness Index) or betaNRI. The betaNTI (Nearest Taxon Index) values for early stages were on average phylogenetically random, but for the betaNRI analyses, these stages were phylogenetically overdispersed. Assembly of woody plants differed from that of herbaceous plants during late community succession. We suggest that deterministic and stochastic processes respectively play a role in different aspects of community phylogenetic structure for early succession stage, and that community composition of late succession stage is governed by a deterministic process. In conclusion, the long-lasting evolutionary imprints on the present-day composition of communities arrayed along the succession gradient. PMID:27272407

Patterns of taxonomic, phylogenetic diversity during a long-term succession of forest on the Loess Plateau, China: insights into assembly process.

PubMed

Chai, Yongfu; Yue, Ming; Liu, Xiao; Guo, Yaoxin; Wang, Mao; Xu, Jinshi; Zhang, Chenguang; Chen, Yu; Zhang, Lixia; Zhang, Ruichang

2016-06-08

Quantifying the drivers underlying the distribution of biodiversity during succession is a critical issue in ecology and conservation, and also can provide insights into the mechanisms of community assembly. Ninety plots were established in the Loess Plateau region of northern Shaanxi in China. The taxonomic and phylogenetic (alpha and beta) diversity were quantified within six succession stages. Null models were used to test whether phylogenetic distance observed differed from random expectations. Taxonomic beta diversity did not show a regular pattern, while phylogenetic beta diversity decreased throughout succession. The shrub stage occurred as a transition from phylogenetic overdispersion to clustering either for NRI (Net Relatedness Index) or betaNRI. The betaNTI (Nearest Taxon Index) values for early stages were on average phylogenetically random, but for the betaNRI analyses, these stages were phylogenetically overdispersed. Assembly of woody plants differed from that of herbaceous plants during late community succession. We suggest that deterministic and stochastic processes respectively play a role in different aspects of community phylogenetic structure for early succession stage, and that community composition of late succession stage is governed by a deterministic process. In conclusion, the long-lasting evolutionary imprints on the present-day composition of communities arrayed along the succession gradient.

Antibiotic resistance and population structure of cystic fibrosis Pseudomonas aeruginosa isolates from a Spanish multi-centre study.

PubMed

López-Causapé, Carla; de Dios-Caballero, Juan; Cobo, Marta; Escribano, Amparo; Asensio, Óscar; Oliver, Antonio; Del Campo, Rosa; Cantón, Rafael; Solé, Amparó; Cortell, Isidoro; Asensio, Oscar; García, Gloria; Martínez, María Teresa; Cols, María; Salcedo, Antonio; Vázquez, Carlos; Baranda, Félix; Girón, Rosa; Quintana, Esther; Delgado, Isabel; de Miguel, María Ángeles; García, Marta; Oliva, Concepción; Prados, María Concepción; Barrio, María Isabel; Pastor, María Dolores; Olveira, Casilda; de Gracia, Javier; Álvarez, Antonio; Escribano, Amparo; Castillo, Silvia; Figuerola, Joan; Togores, Bernat; Oliver, Antonio; López, Carla; de Dios Caballero, Juan; Tato, Marta; Máiz, Luis; Suárez, Lucrecia; Cantón, Rafael

2017-09-01

The first Spanish multi-centre study on the microbiology of cystic fibrosis (CF) was conducted from 2013 to 2014. The study involved 24 CF units from 17 hospitals, and recruited 341 patients. The aim of this study was to characterise Pseudomonas aeruginosa isolates, 79 of which were recovered from 75 (22%) patients. The study determined the population structure, antibiotic susceptibility profile and genetic background of the strains. Fifty-five percent of the isolates were multi-drug-resistant, and 16% were extensively-drug-resistant. Defective mutS and mutL genes were observed in mutator isolates (15.2%). Considerable genetic diversity was observed by pulsed-field gel electrophoresis (70 patterns) and multi-locus sequence typing (72 sequence types). International epidemic clones were not detected. Fifty-one new and 14 previously described array tube (AT) genotypes were detected by AT technology. This study found a genetically unrelated and highly diverse CF P. aeruginosa population in Spain, not represented by the epidemic clones widely distributed across Europe, with multiple combinations of virulence factors and high antimicrobial resistance rates (except for colistin). Copyright © 2017 Elsevier B.V. and International Society of Chemotherapy. All rights reserved.

Guided Lamb wave based 2-D spiral phased array for structural health monitoring of thin panel structures

NASA Astrophysics Data System (ADS)

Yoo, Byungseok

2011-12-01

In almost all industries of mechanical, aerospace, and civil engineering fields, structural health monitoring (SHM) technology is essentially required for providing the reliable information of structural integrity of safety-critical structures, which can help reduce the risk of unexpected and sometimes catastrophic failures, and also offer cost-effective inspection and maintenance of the structures. State of the art SHM research on structural damage diagnosis is focused on developing global and real-time technologies to identify the existence, location, extent, and type of damage. In order to detect and monitor the structural damage in plate-like structures, SHM technology based on guided Lamb wave (GLW) interrogation is becoming more attractive due to its potential benefits such as large inspection area coverage in short time, simple inspection mechanism, and sensitivity to small damage. However, the GLW method has a few critical issues such as dispersion nature, mode conversion and separation, and multiple-mode existence. Phased array technique widely used in all aspects of civil, military, science, and medical industry fields may be employed to resolve the drawbacks of the GLW method. The GLW-based phased array approach is able to effectively examine and analyze complicated structural vibration responses in thin plate structures. Because the phased sensor array operates as a spatial filter for the GLW signals, the array signal processing method can enhance a desired signal component at a specific direction while eliminating other signal components from other directions. This dissertation presents the development, the experimental validation, and the damage detection applications of an innovative signal processing algorithm based on two-dimensional (2-D) spiral phased array in conjunction with the GLW interrogation technique. It starts with general backgrounds of SHM and the associated technology including the GLW interrogation method. Then, it is focused on the fundamentals of the GLW-based phased array approach and the development of an innovative signal processing algorithm associated with the 2-D spiral phased sensor array. The SHM approach based on array responses determined by the proposed phased array algorithm implementation is addressed. The experimental validation of the GLW-based 2-D spiral phased array technology and the associated damage detection applications to thin isotropic plate and anisotropic composite plate structures are presented.

Design principles of hair-like structures as biological machines

PubMed Central

2018-01-01

Hair-like structures are prevalent throughout biology and frequently act to sense or alter interactions with an organism's environment. The overall shape of a hair is simple: a long, filamentous object that protrudes from the surface of an organism. This basic design, however, can confer a wide range of functions, owing largely to the flexibility and large surface area that it usually possesses. From this simple structural basis, small changes in geometry, such as diameter, curvature and inter-hair spacing, can have considerable effects on mechanical properties, allowing functions such as mechanosensing, attachment, movement and protection. Here, we explore how passive features of hair-like structures, both individually and within arrays, enable diverse functions across biology. Understanding the relationships between form and function can provide biologists with an appreciation for the constraints and possibilities on hair-like structures. Additionally, such structures have already been used in biomimetic engineering with applications in sensing, water capture and adhesion. By examining hairs as a functional mechanical unit, geometry and arrangement can be rationally designed to generate new engineering devices and ideas. PMID:29848593

Structural basis of cargo recognitions for class V myosins

PubMed Central

Wei, Zhiyi; Liu, Xiaotian; Yu, Cong; Zhang, Mingjie

2013-01-01

Class V myosins (MyoV), the most studied unconventional myosins, recognize numerous cargos mainly via the motor’s globular tail domain (GTD). Little is known regarding how MyoV-GTD recognizes such a diverse array of cargos specifically. Here, we solved the crystal structures of MyoVa-GTD in its apo-form and in complex with two distinct cargos, melanophilin and Rab interacting lysosomal protein-like 2. The apo-MyoVa-GTD structure indicates that most mutations found in patients with Griscelli syndrome, microvillus inclusion disease, or cancers or in “dilute” rodents likely impair the folding of GTD. The MyoVa-GTD/cargo complex structure reveals two distinct cargo-binding surfaces, one primarily via charge–charge interaction and the other mainly via hydrophobic interactions. Structural and biochemical analysis reveal the specific cargo-binding specificities of various isoforms of mammalian MyoV as well as very different cargo recognition mechanisms of MyoV between yeast and higher eukaryotes. The MyoVa-GTD structures resolved here provide a framework for future functional studies of vertebrate class V myosins. PMID:23798443

Cone Photoreceptor Structure in Patients With X-Linked Cone Dysfunction and Red-Green Color Vision Deficiency.

PubMed

Patterson, Emily J; Wilk, Melissa; Langlo, Christopher S; Kasilian, Melissa; Ring, Michael; Hufnagel, Robert B; Dubis, Adam M; Tee, James J; Kalitzeos, Angelos; Gardner, Jessica C; Ahmed, Zubair M; Sisk, Robert A; Larsen, Michael; Sjoberg, Stacy; Connor, Thomas B; Dubra, Alfredo; Neitz, Jay; Hardcastle, Alison J; Neitz, Maureen; Michaelides, Michel; Carroll, Joseph

2016-07-01

Mutations in the coding sequence of the L and M opsin genes are often associated with X-linked cone dysfunction (such as Bornholm Eye Disease, BED), though the exact color vision phenotype associated with these disorders is variable. We examined individuals with L/M opsin gene mutations to clarify the link between color vision deficiency and cone dysfunction. We recruited 17 males for imaging. The thickness and integrity of the photoreceptor layers were evaluated using spectral-domain optical coherence tomography. Cone density was measured using high-resolution images of the cone mosaic obtained with adaptive optics scanning light ophthalmoscopy. The L/M opsin gene array was characterized in 16 subjects, including at least one subject from each family. There were six subjects with the LVAVA haplotype encoded by exon 3, seven with LIAVA, two with the Cys203Arg mutation encoded by exon 4, and two with a novel insertion in exon 2. Foveal cone structure and retinal thickness was disrupted to a variable degree, even among related individuals with the same L/M array. Our findings provide a direct link between disruption of the cone mosaic and L/M opsin variants. We hypothesize that, in addition to large phenotypic differences between different L/M opsin variants, the ratio of expression of first versus downstream genes in the L/M array contributes to phenotypic diversity. While the L/M opsin mutations underlie the cone dysfunction in all of the subjects tested, the color vision defect can be caused either by the same mutation or a gene rearrangement at the same locus.

Large-Scale Noniridescent Structural Color Printing Enabled by Infiltration-Driven Nonequilibrium Colloidal Assembly.

PubMed

Bai, Ling; Mai, Van Cuong; Lim, Yun; Hou, Shuai; Möhwald, Helmuth; Duan, Hongwei

2018-03-01

Structural colors originating from interaction of light with intricately arranged micro-/nanostructures have stimulated considerable interest because of their inherent photostability and energy efficiency. In particular, noniridescent structural color with wide viewing angle has been receiving increasing attention recently. However, no method is yet available for rapid and large-scale fabrication of full-spectrum structural color patterns with wide viewing angles. Here, infiltration-driven nonequilibrium assembly of colloidal particles on liquid-permeable and particle-excluding substrates is demonstrated to direct the particles to form amorphous colloidal arrays (ACAs) within milliseconds. The infiltration-assisted (IFAST) colloidal assembly opens new possibilities for rapid manufacture of noniridescent structural colors of ACAs and straightforward structural color mixing. Full-spectrum noniridescent structural colors are successfully produced by mixing primary structural colors of red, blue, and yellow using a commercial office inkjet printer. Rapid fabrication of large-scale structural color patterns with sophisticated color combination/layout by IFAST printing is realized. The IFAST technology is versatile for developing structural color patterns with wide viewing angles, as colloidal particles, inks, and substrates are flexibly designable for diverse applications. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Genetic diversity of K-antigen gene clusters of Escherichia coli and their molecular typing using a suspension array.

PubMed

Yang, Shuang; Xi, Daoyi; Jing, Fuyi; Kong, Deju; Wu, Junli; Feng, Lu; Cao, Boyang; Wang, Lei

2018-04-01

Capsular polysaccharides (CPSs), or K-antigens, are the major surface antigens of Escherichia coli. More than 80 serologically unique K-antigens are classified into 4 groups (Groups 1-4) of capsules. Groups 1 and 4 contain the Wzy-dependent polymerization pathway and the gene clusters are in the order galF to gnd; Groups 2 and 3 contain the ABC-transporter-dependent pathway and the gene clusters consist of 3 regions, regions 1, 2 and 3. Little is known about the variations among the gene clusters. In this study, 9 serotypes of K-antigen gene clusters (K2ab, K11, K20, K24, K38, K84, K92, K96, and K102) were sequenced and correlated with their CPS chemical structures. On the basis of sequence data, a K-antigen-specific suspension array that detects 10 distinct CPSs, including the above 9 CPSs plus K30, was developed. This is the first report to catalog the genetic features of E. coli K-antigen variations and to develop a suspension array for their molecular typing. The method has a number of advantages over traditional bacteriophage and serum agglutination methods and lays the foundation for straightforward identification and detection of additional K-antigens in the future.

Management of New England northern hardwoods, spruce-fir, and eastern white pine for neotropical migratory birds

Treesearch

Richard M. DeGraaf; Mariko Yamasaki; William B. Leak

1993-01-01

Habitat management for neotropical migratory birds must be based upon land capability, vegetation, successional patterns, response to treatments, landscape diversity, and speciedhabitat relationships. Neotropical migratory birds use diverse arrays of aquatic, early successional, and forest habitats. Management of neotropical migratory birds involves enhancement of...

Ecological consequences of the MPB epidemic for habitats and populations of wildlife [Chapter 5

Treesearch

Beth Hahn; Vicki Saab; Barbara Bentz; Rachel Loehman; Bob Keane

2014-01-01

Wildlife biologists must balance a diverse array of ecological and social considerations in managing species and habitats. The challenges of managing species and habitats in dynamic landscapes are influenced by diverse factors, including natural disturbances, vegetation development, and anthropogenic-mediated changes, such as climate change, management activities, and...

Digital Media Production to Support Literacy for Secondary Students with Diverse Learning Abilities

ERIC Educational Resources Information Center

Leach, April Marie

2017-01-01

Producing digital media is a hands-on, inquiry-based mindful process that naturally embeds Universal Design for Learning (UDL) principles into literacy instruction, providing options for learning and assessment for a wide array of students with diverse learning abilities. Video production learning experiences acknowledge the cognitive talents of…

We see more than we can report: "cost free" color phenomenality outside focal attention.

PubMed

Bronfman, Zohar Z; Brezis, Noam; Jacobson, Hilla; Usher, Marius

2014-07-01

The distinction between access consciousness and phenomenal consciousness is a subject of intensive debate. According to one view, visual experience overflows the capacity of the attentional and working memory system: We see more than we can report. According to the opposed view, this perceived richness is an illusion-we are aware only of information that we can subsequently report. This debate remains unresolved because of the inevitable reliance on report, which is limited in capacity. To bypass this limitation, this study utilized color diversity-a unique summary statistic-which is sensitive to detailed visual information. Participants were shown a Sperling-like array of colored letters, one row of which was precued. After reporting a letter from the cued row, participants estimated the color diversity of the noncued rows. Results showed that people could estimate the color diversity of the noncued array without a cost to letter report, which suggests that color diversity is registered automatically, outside focal attention, and without consuming additional working memory resources. © The Author(s) 2014.

Optimal apparent damping as a function of the bandwidth of an array of vibration absorbers.

PubMed

Vignola, Joseph; Glean, Aldo; Judge, John; Ryan, Teresa

2013-08-01

The transient response of a resonant structure can be altered by the attachment of one or more substantially smaller resonators. Considered here is a coupled array of damped harmonic oscillators whose resonant frequencies are distributed across a frequency band that encompasses the natural frequency of the primary structure. Vibration energy introduced to the primary structure, which has little to no intrinsic damping, is transferred into and trapped by the attached array. It is shown that, when the properties of the array are optimized to reduce the settling time of the primary structure's transient response, the apparent damping is approximately proportional to the bandwidth of the array (the span of resonant frequencies of the attached oscillators). Numerical simulations were conducted using an unconstrained nonlinear minimization algorithm to find system parameters that result in the fastest settling time. This minimization was conducted for a range of system characteristics including the overall bandwidth of the array, the ratio of the total array mass to that of the primary structure, and the distributions of mass, stiffness, and damping among the array elements. This paper reports optimal values of these parameters and demonstrates that the resulting minimum settling time decreases with increasing bandwidth.

1,2,4,5-Benzenetetracarboxylic acid: a versatile hydrogen bonding template for controlling the regioselective topochemical synthesis of head-to-tail photodimers from stilbazole derivatives.

PubMed

Ortega, Gabriela; Hernández, Jesús; González, Teresa; Dorta, Romano; Briceño, Alexander

2018-05-16

The crystal engineering of hydrogen bonded organic assemblies based on 1,2,4,5-benzenetetracarboxylic acid (H4bta) and stilbazole derivatives (1-10) is exploited to provide regio-controlled [2 + 2] photocycloadditions in the solid state. Single crystal X-ray diffraction analyses have revealed that all the arrays are built-up from the self-assembly of the (H2bta)2- dianion with two stilbazolium cations via O-HO- and N+-HO- charge-assisted H-bonding synthons: (4-Hstilbazolium+)2(H2bta2-). The dianion displays an interesting diversity of H-bonding motifs. Such structural flexibility allowed us to obtain four structure-types defined by the preferential formation of intramolecular or intermolecular hydrogen bonds between carboxylate-carboxylic groups. In these ionic assemblies two predominant structural H-bonding patterns were observed. The first pattern is characterised by the formation of intramolecular H-bonds in the dianion, leading to discrete assemblies based on ternary arrays. The second hydrogen pattern consists of 2-D hydrogen networks built-up from the self-assembly of anions via intermolecular H-bonds that are linked to the cations. Two additional examples, in which the dianion is self-assembled in two types of ribbons, were also observed. Another supramolecular feature predominant in all these arrays is the stacking of the cations in a head-to-tail fashion, which is controlled via cation-π interactions. These arrays are photoactive in the solid state upon UV-irradiation leading to the regioselective synthesis of rctt-cyclobutane head-to-tail-isomers in high to quantitative yield. In this work, the template tolerance either to steric or electronic effects by changing the number or positions of the supramolecular interactions exerted by distinctive functional groups was also explored. In addition, assemblies bearing 2-chloro (7 and 8) and 3-chloro-4-stilbazole (1 and 9) crystallize in two different crystalline forms, leading to novel examples of supramolecular isomers with similar solid state reactivity.

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

Arendt, Paul N.; DePaula, Ramond F.; Zhu, Yuntian T.

An array of carbon nanotubes is prepared by exposing a catalyst structure to a carbon nanotube precursor. Embodiment catalyst structures include one or more trenches, channels, or a combination of trenches and channels. A system for preparing the array includes a heated surface for heating the catalyst structure and a cooling portion that cools gas above the catalyst structure. The system heats the catalyst structure so that the interaction between the precursor and the catalyst structure results in the formation of an array of carbon nanotubes on the catalyst structure, and cools the gas near the catalyst structure and alsomore » cools any carbon nanotubes that form on the catalyst structure to prevent or at least minimize the formation of amorphous carbon. Arrays thus formed may be used for spinning fibers of carbon nanotubes.« less

Structure, dynamics and biophysics of the cytoplasmic protein–protein complexes of the bacterial phosphoenolpyruvate: Sugar phosphotransferase system

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

Clore, G. Marius; Venditti, Vincenzo

2013-10-01

The bacterial phosphotransferase system (PTS) couples phosphoryl transfer, via a series of bimolecular protein–protein interactions, to sugar transport across the membrane. The multitude of complexes in the PTS provides a paradigm for studying protein interactions, and for understanding how the same binding surface can specifically recognize a diverse array of targets. Fifteen years of work aimed at solving the solution structures of all soluble protein–protein complexes of the PTS has served as a test bed for developing NMR and integrated hybrid approaches to study larger complexes in solution and to probe transient, spectroscopically invisible states, including encounter complexes. We reviewmore » these approaches, highlighting the problems that can be tackled with these methods, and summarize the current findings on protein interactions.« less

Screening combinatorial arrays of inorganic materials with spectroscopy or microscopy

DOEpatents

Schultz, Peter G.; Xiang, Xiaodong; Goldwasser, Isy

2004-02-03

Methods and apparatus for the preparation and use of a substrate having an array of diverse materials in predefined regions thereon. A substrate having an array of diverse materials thereon is generally prepared by delivering components of materials to predefined regions on a substrate, and simultaneously reacting the components to form at least two materials. Materials which can be prepared using the methods and apparatus of the present invention include, for example, covalent network solids, ionic solids and molecular solids. More particularly, materials which can be prepared using the methods and apparatus of the present invention include, for example, inorganic materials, intermetallic materials, metal alloys, ceramic materials, organic materials, organometallic materials, non-biological organic polymers, composite materials (e.g., inorganic composites, organic composites, or combinations thereof), etc. Once prepared, these materials can be screened for useful properties including, for example, electrical, thermal, mechanical, morphological, optical, magnetic, chemical, or other properties. Thus, the present invention provides methods for the parallel synthesis and analysis of novel materials having useful properties.

Polymer arrays from the combinatorial synthesis of novel materials

DOEpatents

Schultz, Peter G.; Xiang, Xiao-Dong; Goldwasser, Isy; Briceno, Gabriel; Sun, Xiao-Dong

2004-09-21

Methods and apparatus for the preparation and use of a substrate having an array of diverse materials in predefined regions thereon. A substrate having an array of diverse materials thereon is generally prepared by delivering components of materials to predefined regions on a substrate, and simultaneously reacting the components to form at least two materials. Materials which can be prepared using the methods and apparatus of the present invention include, for example, covalent network solids, ionic solids and molecular solids. More particularly, materials which can be prepared using the methods and apparatus of the present invention include, for example, inorganic materials, intermetallic materials, metal alloys, ceramic materials, organic materials, organometallic materials, non-biological organic polymers, composite materials (e.g., inorganic composites, organic composites, or combinations thereof), etc. Once prepared, these materials can be screened for useful properties including, for example, electrical, thermal, mechanical, morphological, optical, magnetic, chemical, or other properties. Thus, the present invention provides methods for the parallel synthesis and analysis of novel materials having useful properties.

Synthesis and screening combinatorial arrays of zeolites

DOEpatents

Schultz, Peter G.; Xiang, Xiaodong; Goldwasser, Isy

2003-11-18

Methods and apparatus for the preparation and use of a substrate having an array of diverse materials in predefined regions thereon. A substrate having an array of diverse materials thereon is generally prepared by delivering components of materials to predefined regions on a substrate, and simultaneously reacting the components to form at least two materials. Materials which can be prepared using the methods and apparatus of the present invention include, for example, covalent network solids, ionic solids and molecular solids. More particularly, materials which can be prepared using the methods and apparatus of the present invention include, for example, inorganic materials, intermetallic materials, metal alloys, ceramic materials, organic materials, organometallic materials, non-biological organic polymers, composite materials (e.g., inorganic composites, organic composites, or combinations thereof), etc. Once prepared, these materials can be screened for useful properties including, for example, electrical, thermal, mechanical, morphological, optical, magnetic, chemical, or other properties. Thus, the present invention provides methods for the parallel synthesis and analysis of novel materials having useful properties.

Comparison of Aperture Averaging and Receiver Diversity Techniques for Free Space Optical Links in Presence of Turbulence and Various Weather Conditions

NASA Astrophysics Data System (ADS)

Kaur, Prabhmandeep; Jain, Virander Kumar; Kar, Subrat

2014-12-01

In this paper, we investigate the performance of a Free Space Optic (FSO) link considering the impairments caused by the presence of various weather conditions such as very clear air, drizzle, haze, fog, etc., and turbulence in the atmosphere. Analytic expression for the outage probability is derived using the gamma-gamma distribution for turbulence and accounting the effect of weather conditions using the Beer-Lambert's law. The effect of receiver diversity schemes using aperture averaging and array receivers on the outage probability is studied and compared. As the aperture diameter is increased, the outage probability decreases irrespective of the turbulence strength (weak, moderate and strong) and weather conditions. Similar effects are observed when the number of direct detection receivers in the array are increased. However, it is seen that as the desired level of performance in terms of the outage probability decreases, array receiver becomes the preferred choice as compared to the receiver with aperture averaging.

Micro-Ring Structures Stabilize Microdroplets to Enable Long Term Spheroid Culture in 384 Hanging Drop Array Plates

PubMed Central

Hsiao, Amy Y.; Tung, Yi-Chung; Kuo, Chuan-Hsien; Mosadegh, Bobak; Bedenis, Rachel; Pienta, Kenneth J.; Takayama, Shuichi

2012-01-01

Using stereolithography, 20 different structural variations comprised of millimeter diameter holes surrounded by trenches, plateaus, or micro-ring structures were prepared and tested for their ability to stably hold arrays of microliter sized droplets within the structures over an extended period of time. The micro-ring structures were the most effective in stabilizing droplets against mechanical and chemical perturbations. After confirming the importance of micro-ring structures using rapid prototyping, we developed an injection molding tool for mass production of polystyrene 3D cell culture plates with an array of 384 such micro-ring surrounded through-hole structures. These newly designed and injection molded polystyrene 384 hanging drop array plates with micro-rings were stable and robust against mechanical perturbations as well as surface fouling-facilitated droplet spreading making them capable of long term cell spheroid culture of up to 22 days within the droplet array. This is a significant improvement over previously reported 384 hanging drop array plates which are susceptible to small mechanical shocks and could not reliably maintain hanging drops for longer than a few days. With enhanced droplet stability, the hanging drop array plates with micro-ring structures provide better platforms and open up new opportunities for high-throughput preparation of microscale 3D cell constructs for drug screening and cell analysis. PMID:22057945

Micro-ring structures stabilize microdroplets to enable long term spheroid culture in 384 hanging drop array plates.

PubMed

Hsiao, Amy Y; Tung, Yi-Chung; Kuo, Chuan-Hsien; Mosadegh, Bobak; Bedenis, Rachel; Pienta, Kenneth J; Takayama, Shuichi

2012-04-01

Using stereolithography, 20 different structural variations comprised of millimeter diameter holes surrounded by trenches, plateaus, or micro-ring structures were prepared and tested for their ability to stably hold arrays of microliter sized droplets within the structures over an extended period of time. The micro-ring structures were the most effective in stabilizing droplets against mechanical and chemical perturbations. After confirming the importance of micro-ring structures using rapid prototyping, we developed an injection molding tool for mass production of polystyrene 3D cell culture plates with an array of 384 such micro-ring surrounded through-hole structures. These newly designed and injection molded polystyrene 384 hanging drop array plates with micro-rings were stable and robust against mechanical perturbations as well as surface fouling-facilitated droplet spreading making them capable of long term cell spheroid culture of up to 22 days within the droplet array. This is a significant improvement over previously reported 384 hanging drop array plates which are susceptible to small mechanical shocks and could not reliably maintain hanging drops for longer than a few days. With enhanced droplet stability, the hanging drop array plates with micro-ring structures provide better platforms and open up new opportunities for high-throughput preparation of microscale 3D cell constructs for drug screening and cell analysis.

Investigating microbial colonization in actively forming hydrothermal deposits using thermocouple arrays

NASA Astrophysics Data System (ADS)

Tivey, M. K.; Reysenbach, A. L.; Hirsch, M.; Steinberg, J.; Flores, G. E.

2010-12-01

Investigations of microbial colonization of very young hydrothermal deposits were carried out in 2009 at hydrothermal vents in the Lau Basin (SW Pacific), and in Guaymas Basin, Gulf of California, with a test deployment at the Rainbow vent field on the Mid-Atlantic Ridge in 2008. Our method entailed razing active chimneys and placing arrays of temperature probes (8 titanium-encased probes with their tips placed within a titanium cage) over the active flow. The chimneys that grew back through each array, encasing the temperature probe tips, were recovered after 2 to 15 days, along with temperature records. Molecular phylogenetic methods are being used to reveal the members of the microbial communities that developed in each chimney of known age and thermal history. A total of 15 array deployments were made at 10 vents in 6 different vent fields. Similar morphology beehives (with porous fine-grained interiors and steep temperature gradients across the outermost more-consolidated “wall”) formed at 2 of the 3 vents in Guaymas Basin (in 2 and 5 days at one vent and 3 and 15 days at a second), and at one vent each in the Kilo Moana (in 3 days), Tahi Moana (in 2.5 days), and Tui Malila (in 3 and 8 days) vent fields in the Lau Basin. In contrast, open conduit, thin walled chimneys grew within arrays at the Mariner vent field, Lau Basin, at 3 different vents (in 3 days at one vent, in 3 and 11 days at a second vent, and in 13 days at a third vent). A lower temperature (<280C) diffuser/spire with a filamentous biofilm formed in 15 days in an array at a hydrocarbon-rich vent in the Guaymas Basin. A similar biofilm formed after 6 days within an array placed earlier at this same vent, with little mineralization. Preliminary diversity data from the 6 and 15 day Guaymas deployments show an increased diversity of bacteria with time with initial colonizers being primarily sulfur-oxidizing Epsilonproteobacteria, with members of the Aquificales and Deltaproteobacteria appearing in the 15 day deposit. In contrast, the Archaea showed very little change in diversity over time, with members of the genera Thermococcus and Methanocaldococcus present in all samples analyzed, irrespective of location and timing of sampling. This is very different from a 72-hour test array deployment done in 2008 at Rainbow vent field, where the deposited soft material was colonized only by the sulfate-reducing archaeum, Archaeoglobus. These samples (8 beehives, 4 open conduit smokers, one diffuser spire, from chimneys of known composition, plus less consolidated biofilm material) are all of known age, and fluids were collected from 7 of the 10 vents. This suite of samples will allow comparisons to data from 2003 (Page et al., 2008, Env. Micr.), study of the potential impact of fluid chemistry, mineralogy/texture, and time on microbial diversity, and testing of hypotheses about microbial colonization and succession.

An Approach for Smart Antenna Testbed

NASA Astrophysics Data System (ADS)

Kawitkar, R. S.; Wakde, D. G.

2003-07-01

The use of wireless, mobile, personal communications services are expanding rapidly. Adaptive or "Smart" antenna arrays can increase channel capacity through spatial division. Adaptive antennas can also track mobile users, improving both signal range and quality. For these reasons, smart antenna systems have attracted widespread interest in the telecommunications industry for applications to third generation wireless systems.This paper aims to design and develop an advanced antennas testbed to serve as a common reference for testing adaptive antenna arrays and signal combining algorithms, as well as complete systems. A flexible suite of off line processing software should be written using matlab to perform system calibration, test bed initialization, data acquisition control, data storage/transfer, off line signal processing and analysis and graph plotting. The goal of this paper is to develop low complexity smart antenna structures for 3G systems. The emphasis will be laid on ease of implementation in a multichannel / multi-user environment. A smart antenna test bed will be developed, and various state-of-the-art DSP structures and algorithms will be investigated.Facing the soaring demand for mobile communications, the use of smart antenna arrays in mobile communications systems to exploit spatial diversity to further improve spectral efficiency has recently received considerable attention. Basically, a smart antenna array comprises a number of antenna elements combined via a beamforming network (amplitude and phase control network). Some of the benefits that can be achieved by using SAS (Smart Antenna System) include lower mobile terminal power consumption, range extension, ISI reduction, higher data rate support, and ease of integration into the existing base station system. In terms of economic benefits, adaptive antenna systems employed at base station, though increases the per base station cost, can increase coverage area of each cell site, thereby reducing the total system cost dramatically - often by more than 50% without compromising the system performance. The testbed can be employed to illustrate enhancement of system capacity and service quality in wireless communications.

Operation Manual for the Intensity Based Interrogation of Fibre Bragg Grating Arrays on Vibrating Structures

DTIC Science & Technology

2011-01-01

based demodulation approach for the measurement of strains, induced by structural vibrations, using Fiber Bragg Gratings ( FBG ). This companion...provide the Frequency Response Functions from a series of FBG arrays attached to a vibrating structure. RELEASE LIMITATION Approved for... FBG arrays attached to a vibrating structure. Both this technical note and its companion technical report are formal contributions to an

Local phylogenetic divergence and global evolutionary convergence of skull function in reef fishes of the family Labridae.

PubMed

Westneat, Mark W; Alfaro, Michael E; Wainwright, Peter C; Bellwood, David R; Grubich, Justin R; Fessler, Jennifer L; Clements, Kendall D; Smith, Lydia L

2005-05-22

The Labridae is one of the most structurally and functionally diversified fish families on coral and rocky reefs around the world, providing a compelling system for examination of evolutionary patterns of functional change. Labrid fishes have evolved a diverse array of skull forms for feeding on prey ranging from molluscs, crustaceans, plankton, detritus, algae, coral and other fishes. The species richness and diversity of feeding ecology in the Labridae make this group a marine analogue to the cichlid fishes. Despite the importance of labrids to coastal reef ecology, we lack evolutionary analysis of feeding biomechanics among labrids. Here, we combine a molecular phylogeny of the Labridae with the biomechanics of skull function to reveal a broad pattern of repeated convergence in labrid feeding systems. Mechanically fast jaw systems have evolved independently at least 14 times from ancestors with forceful jaws. A repeated phylogenetic pattern of functional divergence in local regions of the labrid tree produces an emergent family-wide pattern of global convergence in jaw function. Divergence of close relatives, convergence among higher clades and several unusual 'breakthroughs' in skull function characterize the evolution of functional complexity in one of the most diverse groups of reef fishes.

Comparisons between mammalian and artificial olfaction based on arrays of carbon black-polymer composite vapor detectors.

PubMed

Lewis, Nathan S

2004-09-01

Arrays of broadly cross-reactive vapor sensors provide a man-made implementation of an olfactory system, in which an analyte elicits a response from many receptors and each receptor responds to a variety of analytes. Pattern recognition methods are then used to detect analytes based on the collective response of the sensor array. With the use of this architecture, arrays of chemically sensitive resistors made from composites of conductors and insulating organic polymers have been shown to robustly classify, identify, and quantify a diverse collection of organic vapors, even though no individual sensor responds selectively to a particular analyte. The properties and functioning of these arrays are inspired by advances in the understanding of biological olfaction, and in turn, evaluation of the performance of the man-made array provides suggestions regarding some of the fundamental odor detection principles of the mammalian olfactory system.

Noncontact Microembossing Technology for Fabricating Thermoplastic Optical Polymer Microlens Array Sheets

PubMed Central

Chang, Xuefeng; Ge, Xiaohong; Li, Hui

2014-01-01

Thermoplastic optical polymers have replaced traditional optical glass for many applications, due to their superior optical performance, mechanical characteristics, low cost, and efficient production process. This paper investigates noncontact microembossing technology used for producing microlens arrays made out of PMMA (polymethyl methacrylate), PS (polyStyrene), and PC (polycarbonate) from a quartz mold, with microhole arrays. An array of planoconvex microlenses are formed because of surface tension caused by applying pressure to the edge of a hole at a certain glass transition temperature. We studied the principle of noncontact microembossing techniques using finite element analysis, in addition to the thermal and mechanical properties of the three polymers. Then, the independently developed hot-embossing equipment was used to fabricate microlens arrays on PMMA, PS, and PC sheets. This is a promising technique for fabricating diverse thermoplastic optical polymer microlens array sheets, with a simple technological process and low production costs. PMID:25162063

Decreasing Abundance, Increasing Diversity and Changing Structure of the Wild Bee Community (Hymenoptera: Anthophila) along an Urbanization Gradient

PubMed Central

Fortel, Laura; Henry, Mickaël; Guilbaud, Laurent; Guirao, Anne Laure; Kuhlmann, Michael; Mouret, Hugues; Rollin, Orianne; Vaissière, Bernard E.

2014-01-01

Background Wild bees are important pollinators that have declined in diversity and abundance during the last decades. Habitat destruction and fragmentation associated with urbanization are reported as part of the main causes of this decline. Urbanization involves dramatic changes of the landscape, increasing the proportion of impervious surface while decreasing that of green areas. Few studies have investigated the effects of urbanization on bee communities. We assessed changes in the abundance, species richness, and composition of wild bee community along an urbanization gradient. Methodology/Principal Findings Over two years and on a monthly basis, bees were sampled with colored pan traps and insect nets at 24 sites located along an urbanization gradient. Landscape structure within three different radii was measured at each study site. We captured 291 wild bee species. The abundance of wild bees was negatively correlated with the proportion of impervious surface, while species richness reached a maximum at an intermediate (50%) proportion of impervious surface. The structure of the community changed along the urbanization gradient with more parasitic species in sites with an intermediate proportion of impervious surface. There were also greater numbers of cavity-nesting species and long-tongued species in sites with intermediate or higher proportion of impervious surface. However, urbanization had no effect on the occurrence of species depending on their social behavior or body size. Conclusions/Significance We found nearly a third of the wild bee fauna known from France in our study sites. Indeed, urban areas supported a diverse bee community, but sites with an intermediate level of urbanization were the most speciose ones, including greater proportion of parasitic species. The presence of a diverse array of bee species even in the most urbanized area makes these pollinators worthy of being a flagship group to raise the awareness of urban citizens about biodiversity. PMID:25118722

Decreasing abundance, increasing diversity and changing structure of the wild bee community (Hymenoptera: Anthophila) along an urbanization gradient.

PubMed

Fortel, Laura; Henry, Mickaël; Guilbaud, Laurent; Guirao, Anne Laure; Kuhlmann, Michael; Mouret, Hugues; Rollin, Orianne; Vaissière, Bernard E

2014-01-01

Wild bees are important pollinators that have declined in diversity and abundance during the last decades. Habitat destruction and fragmentation associated with urbanization are reported as part of the main causes of this decline. Urbanization involves dramatic changes of the landscape, increasing the proportion of impervious surface while decreasing that of green areas. Few studies have investigated the effects of urbanization on bee communities. We assessed changes in the abundance, species richness, and composition of wild bee community along an urbanization gradient. Over two years and on a monthly basis, bees were sampled with colored pan traps and insect nets at 24 sites located along an urbanization gradient. Landscape structure within three different radii was measured at each study site. We captured 291 wild bee species. The abundance of wild bees was negatively correlated with the proportion of impervious surface, while species richness reached a maximum at an intermediate (50%) proportion of impervious surface. The structure of the community changed along the urbanization gradient with more parasitic species in sites with an intermediate proportion of impervious surface. There were also greater numbers of cavity-nesting species and long-tongued species in sites with intermediate or higher proportion of impervious surface. However, urbanization had no effect on the occurrence of species depending on their social behavior or body size. We found nearly a third of the wild bee fauna known from France in our study sites. Indeed, urban areas supported a diverse bee community, but sites with an intermediate level of urbanization were the most speciose ones, including greater proportion of parasitic species. The presence of a diverse array of bee species even in the most urbanized area makes these pollinators worthy of being a flagship group to raise the awareness of urban citizens about biodiversity.

Reduced signal crosstalk multi neurotransmitter image sensor by microhole array structure

NASA Astrophysics Data System (ADS)

Ogaeri, Yuta; Lee, You-Na; Mitsudome, Masato; Iwata, Tatsuya; Takahashi, Kazuhiro; Sawada, Kazuaki

2018-06-01

A microhole array structure combined with an enzyme immobilization method using magnetic beads can enhance the target discernment capability of a multi neurotransmitter image sensor. Here we report the fabrication and evaluation of the H+-diffusion-preventing capability of the sensor with the array structure. The structure with an SU-8 photoresist has holes with a size of 24.5 × 31.6 µm2. Sensors were prepared with the array structure of three different heights: 0, 15, and 60 µm. When the sensor has the structure of 60 µm height, 48% reduced output voltage is measured at a H+-sensitive null pixel that is located 75 µm from the acetylcholinesterase (AChE)-immobilized pixel, which is the starting point of H+ diffusion. The suppressed H+ immigration is shown in a two-dimensional (2D) image in real time. The sensor parameters, such as height of the array structure and measuring time, are optimized experimentally. The sensor is expected to effectively distinguish various neurotransmitters in biological samples.

Frequency Diverse Array Receiver Architectures

DTIC Science & Technology

2015-06-29

completely associated with FDA, the Hybrid MIMO phased array (HMPAR) concept presented in [18] developed the basic beam patern synthesis theory for an...20], that analyzed beam paterns of chirp waveforms with slightly 6 different starting frequencies. In [21] and [11] they investigated using FDA for...forward-looking radar GMTI benefits. This research showed the ability of the range-dependent energy distribution characteristics of the FDA beam patern

Thermal Management of Quantum Cascade Lasers in an individually Addressable Array Architecture

DTIC Science & Technology

2016-02-08

Thermal Management of Quantum Cascade Lasers in an Individually Addressable Monolithic Array Architecture Leo Missaggia, Christine Wang, Michael...power laser systems in the mid-to-long-infrared wavelength range. By virtue of their demonstrated watt-level performance and wavelength diversity...quantum cascade laser (QCL) and amplifier devices are an excellent choice of emitter for those applications. To realize the power levels of interest

Differential progression of structural and functional alterations in distinct retinal ganglion cell types in a mouse model of glaucoma.

PubMed

Della Santina, Luca; Inman, Denise M; Lupien, Caroline B; Horner, Philip J; Wong, Rachel O L

2013-10-30

Intraocular pressure (IOP) elevation is a principal risk factor for glaucoma. Using a microbead injection technique to chronically raise IOP for 15 or 30 d in mice, we identified the early changes in visual response properties of different types of retinal ganglion cells (RGCs) and correlated these changes with neuronal morphology before cell death. Microbead-injected eyes showed reduced optokinetic tracking as well as cell death. In such eyes, multielectrode array recordings revealed that four RGC types show diverse alterations in their light responses upon IOP elevation. OFF-transient RGCs exhibited a more rapid decline in both structural and functional organizations compared with other RGCs. In contrast, although the light-evoked responses of OFF-sustained RGCs were perturbed, the dendritic arbor of this cell type remained intact. ON-transient and ON-sustained RGCs had normal functional receptive field sizes but their spontaneous and light-evoked firing rates were reduced. ON- and OFF-sustained RGCs lost excitatory synapses across an otherwise structurally normal dendritic arbor. Together, our observations indicate that there are changes in spontaneous activity and light-evoked responses in RGCs before detectable dendritic loss. However, when dendrites retract, we found corresponding changes in receptive field center size. Importantly, the effects of IOP elevation are not uniformly manifested in the structure and function of diverse RGC populations, nor are distinct RGC types perturbed within the same time-frame by such a challenge.

Use of molecular markers aids in the development of diverse inbred backcross lines in beit alpha cucumber (Cucumis sativus L.)

USDA-ARS?s Scientific Manuscript database

Beit Alpha cucumber (Cucumis sativus L.) is a Mediterranean fresh-market type with a relatively narrow genetic base. To broaden its base for plant improvement, 42 diverse accessions were compared employing a previously defined standard marker array to choose wide-based parental lines for use in bac...

Use of molecular markers aids in the development of diverse inbred backcross lines in Beit Alpha cucumber (Cucumis sativus L.)

USDA-ARS?s Scientific Manuscript database

Beit Alpha cucumber (Cucumis sativus L.) is a Mediterranean fresh-market type with a relatively narrow genetic base. To broaden its base for plant improvement, 42 diverse accessions were compared employing a previously defined standard marker array to choose wide-based parental lines for use in bac...

Gaps or Bridges in Multicultural Teacher Education: A Q Study of Attitudes toward Student Diversity

ERIC Educational Resources Information Center

Yang, Yan; Montgomery, Diane

2013-01-01

This paper highlights Q methodology as an appropriate research technique for capturing attitudes and demonstrates the use of Q method to study the attitudes of preservice teachers and teacher educators toward student diversity. A total of 43 participants from a comprehensive American university sorted 47 Q-statements. Two array groups emerged that…

Beyond the Eye: Molecular Evolution of Extraocular Photoreception.

PubMed

Porter, Megan L

2016-11-01

The molecular mechanisms used by biological systems to detect light are diverse, with at least 10 classes of photosensor proteins and additional photosensitive domains characterized. At least six of these protein classes-Type I microbial opsins, Type II animal opsins, cryptochromes, gustatory-related receptors (GRRs), transient receptor potential A1 ion channels, and euglenoid photoactivated adenylyl cylases-can be considered as playing a role in extraocular systems (e.g., expressed outside of the eye in organisms with a visual system). These six classes of extraocular photosensor proteins consist of four broad groups: (1) seven transmembrane proteins, (2) cryptochromes, (3) ion channels, and (4) adenylyl cyclases. The light-driven functions of these extraocular photoreceptors are diverse, ranging from circadian entrainment to phototactic behavior. There are surprising similarities in structural motifs, with at least three independent families-the GRRs and Types I and II opsins-evolving a seven transmembrane helical tertiary structure for light sensing. When considering all of the photosensitive proteins, particularly those in microbial lineages, an image of evolutionary flexibility is emerging, with examples of fusion proteins from multiple types of photosensors and photosensitive domains shared among diverse arrays of proteins. In general, large questions remain for most of these photosensor proteins about exactly how the protein evolved light sensitivity, how light interacts with the protein, and how the photosensitive protein is transducing the signal. © The Author 2016. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Development of a Wireless Unified-Maintenance System for the Structural Health Monitoring of Civil Structures

PubMed Central

Son, Byungjik; Jeon, Seunggon

2018-01-01

A disaster preventive structural health monitoring (SHM) system needs to be equipped with the following abilities: First, it should be able to simultaneously measure diverse types of data (e.g., displacement, velocity, acceleration, strain, load, temperature, humidity, etc.) for accurate diagnosis. Second, it also requires standalone power supply to guarantee its immediate response in crisis (e.g., sudden interruption of normal AC power in disaster situations). Furthermore, it should be capable of prompt processing and realtime wireless communication of a huge amount of data. Therefore, this study is aimed at developing a wireless unified-maintenance system (WUMS) that would satisfy all the requirements for a disaster preventive SHM system of civil structures. The WUMS is designed to measure diverse types of structural responses in realtime based on wireless communication, allowing users to selectively use WiFi RF band and finally working in standalone mode by means of the field-programmable gate array (FPGA) technology. To verify its performance, the following tests were performed: (i) A test to see how far communication is possible in open field, (ii) a test on a shaker to see how accurate responses are, (iii) a modal test on a bridge to see how exactly characteristic real-time dynamic responses are of structures. The test results proved that the WUMS was able to secure stable communication far up to nearly 800 m away by acquiring wireless responses in realtime accurately, when compared to the displacement and acceleration responses which were acquired through wired communication. The analysis of dynamic characteristics also showed that the wireless acceleration responses in real-time represented satisfactorily the dynamic properties of structures. Therefore, the WUMS is proved valid as a SHM, and its outstanding performance is also proven. PMID:29747403

Development of a Wireless Unified-Maintenance System for the Structural Health Monitoring of Civil Structures.

PubMed

Heo, Gwanghee; Son, Byungjik; Kim, Chunggil; Jeon, Seunggon; Jeon, Joonryong

2018-05-09

A disaster preventive structural health monitoring (SHM) system needs to be equipped with the following abilities: First, it should be able to simultaneously measure diverse types of data (e.g., displacement, velocity, acceleration, strain, load, temperature, humidity, etc.) for accurate diagnosis. Second, it also requires standalone power supply to guarantee its immediate response in crisis (e.g., sudden interruption of normal AC power in disaster situations). Furthermore, it should be capable of prompt processing and realtime wireless communication of a huge amount of data. Therefore, this study is aimed at developing a wireless unified-maintenance system (WUMS) that would satisfy all the requirements for a disaster preventive SHM system of civil structures. The WUMS is designed to measure diverse types of structural responses in realtime based on wireless communication, allowing users to selectively use WiFi RF band and finally working in standalone mode by means of the field-programmable gate array (FPGA) technology. To verify its performance, the following tests were performed: (i) A test to see how far communication is possible in open field, (ii) a test on a shaker to see how accurate responses are, (iii) a modal test on a bridge to see how exactly characteristic real-time dynamic responses are of structures. The test results proved that the WUMS was able to secure stable communication far up to nearly 800 m away by acquiring wireless responses in realtime accurately, when compared to the displacement and acceleration responses which were acquired through wired communication. The analysis of dynamic characteristics also showed that the wireless acceleration responses in real-time represented satisfactorily the dynamic properties of structures. Therefore, the WUMS is proved valid as a SHM, and its outstanding performance is also proven.

Preliminary space station solar array structural design study

NASA Technical Reports Server (NTRS)

Dorsey, J. T.; Bush, H. G.; Mikulas, M. M., Jr.

1984-01-01

Structurally efficient ways to support the large solar arrays (3,716 square meters which are currently considered for space station use) are examined. An erectable truss concept is presented for the on orbit construction of winged solar arrays. The means for future growth, maintenance, and repair are integrally designed into this concept. Results from parametric studies, which highlight the physical and structural differences between various configuration options are presented. Consideration is given to both solar blanket and hard panel arrays.

Preliminary space station solar array structural design study

NASA Astrophysics Data System (ADS)

Dorsey, J. T.; Bush, H. G.; Mikulas, M. M., Jr.

Structurally efficient ways to support the large solar arrays (3,716 square meters which are currently considered for space station use) are examined. An erectable truss concept is presented for the on orbit construction of winged solar arrays. The means for future growth, maintenance, and repair are integrally designed into this concept. Results from parametric studies, which highlight the physical and structural differences between various configuration options are presented. Consideration is given to both solar blanket and hard panel arrays.

Development of Low Cost Satellite Communications System for Helicopters and General Aviation

NASA Technical Reports Server (NTRS)

Farazian, K.; Abbe, B.; Divsalar, D.; Raphaeli, D.; Tulintseff, A.; Wu, T.; Hinedi, S.

1994-01-01

In this paper, the development of low-cost satellite communications (SATCOM) system for helicopters and General Aviation (GA) aircrafts is described. System design and standards analysis have been conducted to meet the low-cost, light-weight, small-size and low-power system requirements for helicopters and GA aircraft environments. Other specific issues investigated include coding schemes, spatial diversity, and antenna arraying techniques. Coding schemes employing Channel State Information (CSI) and inverleaving have been studied in order to mitigate severe banking angle fading and the periodic RF signal blockage due to the helicopter rotor blades. In addition, space diversity and antenna arraying techniques have been investigated to further reduce the fading effects and increase the link margin.

Geckoprinting: assembly of microelectronic devices on unconventional surfaces by transfer printing with isolated gecko setal arrays

PubMed Central

Jeong, Jaeyoung; Kim, Juho; Song, Kwangsun; Autumn, Kellar; Lee, Jongho

2014-01-01

Developing electronics in unconventional forms provides opportunities to expand the use of electronics in diverse applications including bio-integrated or implanted electronics. One of the key challenges lies in integrating semiconductor microdevices onto unconventional substrates without glue, high pressure or temperature that may cause damage to microdevices, substrates or interfaces. This paper describes a solution based on natural gecko setal arrays that switch adhesion mechanically on and off, enabling pick and place manipulation of thin microscale semiconductor materials onto diverse surfaces including plants and insects whose surfaces are usually rough and irregular. A demonstration of functional ‘geckoprinted’ microelectronic devices provides a proof of concept of our results in practical applications. PMID:25056216

Population genomics of Fusarium graminearum reveals signatures of divergent evolution within a major cereal pathogen

PubMed Central

2018-01-01

The cereal pathogen Fusarium graminearum is the primary cause of Fusarium head blight (FHB) and a significant threat to food safety and crop production. To elucidate population structure and identify genomic targets of selection within major FHB pathogen populations in North America we sequenced the genomes of 60 diverse F. graminearum isolates. We also assembled the first pan-genome for F. graminearum to clarify population-level differences in gene content potentially contributing to pathogen diversity. Bayesian and phylogenomic analyses revealed genetic structure associated with isolates that produce the novel NX-2 mycotoxin, suggesting a North American population that has remained genetically distinct from other endemic and introduced cereal-infecting populations. Genome scans uncovered distinct signatures of selection within populations, focused in high diversity, frequently recombining regions. These patterns suggested selection for genomic divergence at the trichothecene toxin gene cluster and thirteen additional regions containing genes potentially involved in pathogen specialization. Gene content differences further distinguished populations, in that 121 genes showed population-specific patterns of conservation. Genes that differentiated populations had predicted functions related to pathogenesis, secondary metabolism and antagonistic interactions, though a subset had unique roles in temperature and light sensitivity. Our results indicated that F. graminearum populations are distinguished by dozens of genes with signatures of selection and an array of dispensable accessory genes, suggesting that FHB pathogen populations may be equipped with different traits to exploit the agroecosystem. These findings provide insights into the evolutionary processes and genomic features contributing to population divergence in plant pathogens, and highlight candidate genes for future functional studies of pathogen specialization across evolutionarily and ecologically diverse fungi. PMID:29584736

Habitat heterogeneity and associated microbial community structure in a small-scale floodplain hyporheic flow path.

PubMed

Lowell, Jennifer L; Gordon, Nathan; Engstrom, Dale; Stanford, Jack A; Holben, William E; Gannon, James E

2009-10-01

The Nyack floodplain is located on the Middle Fork of the Flathead River, an unregulated, pristine, fifth-order stream in Montana, USA, bordering Glacier National Park. The hyporheic zone is a nutritionally heterogeneous floodplain component harboring a diverse array of microbial assemblages essential in fluvial biogeochemical cycling, riverine ecosystem productivity, and trophic interactions. Despite these functions, microbial community structure in pristine hyporheic systems is not well characterized. The current study was designed to assess whether physical habitat heterogeneity within the hyporheic zone of the Nyack floodplain was sufficient to drive bacterial beta diversity between three different hyporheic flow path locations. Habitat heterogeneity was assessed by measuring soluble reactive phosphorous, nitrate, dissolved organic carbon, dissolved oxygen, and soluble total nitrogen levels seasonally at surface water infiltration, advection, and exfiltration zones. Significant spatial differences were detected in dissolved oxygen and nitrate levels, and seasonal differences were detected in dissolved oxygen, nitrate, and dissolved organic carbon levels. Denaturing gradient gel electrophoresis (DGGE) and cell counts indicated that bacterial diversity increased with abundance, and DGGE fingerprints covaried with nitrate levels where water infiltrated the hyporheic zone. The ribosomal gene phylogeny revealed that hyporheic habitat heterogeneity was sufficient to drive beta diversity between bacterial assemblages. Phylogenetic (P) tests detected sequence disparity between the flow path locations. Small distinct lineages of Firmicutes, Actinomycetes, Planctomycetes, and Acidobacteria defined the infiltration zone and alpha- and beta-proteobacterial lineages delineated the exfiltration and advection zone communities. These data suggest that spatial habitat heterogeneity drives hyporheic microbial community development and that attempts to understand functional differences between bacteria inhabiting nutritionally heterogeneous hyporheic environments might begin by focusing on the biology of these taxa.

Genetic Diversity and Population Structure of Whitebark Pine (Pinus albicaulis Engelm.) in Western North America

PubMed Central

Liu, Jun-Jun; Sniezko, Richard; Murray, Michael; Wang, Ning; Chen, Hao; Zamany, Arezoo; Sturrock, Rona N.; Savin, Douglas; Kegley, Angelia

2016-01-01

Whitebark pine (WBP, Pinus albicaulis Engelm.) is an endangered conifer species due to heavy mortality from white pine blister rust (WPBR, caused by Cronartium ribicola) and mountain pine beetle (Dendroctonus ponderosae). Information about genetic diversity and population structure is of fundamental importance for its conservation and restoration. However, current knowledge on the genetic constitution and genomic variation is still limited for WBP. In this study, an integrated genomics approach was applied to characterize seed collections from WBP breeding programs in western North America. RNA-seq analysis was used for de novo assembly of the WBP needle transcriptome, which contains 97,447 protein-coding transcripts. Within the transcriptome, single nucleotide polymorphisms (SNPs) were discovered, and more than 22,000 of them were non-synonymous SNPs (ns-SNPs). Following the annotation of genes with ns-SNPs, 216 ns-SNPs within candidate genes with putative functions in disease resistance and plant defense were selected to design SNP arrays for high-throughput genotyping. Among these SNP loci, 71 were highly polymorphic, with sufficient variation to identify a unique genotype for each of the 371 individuals originating from British Columbia (Canada), Oregon and Washington (USA). A clear genetic differentiation was evident among seed families. Analyses of genetic spatial patterns revealed varying degrees of diversity and the existence of several genetic subgroups in the WBP breeding populations. Genetic components were associated with geographic variables and phenotypic rating of WPBR disease severity across landscapes, which may facilitate further identification of WBP genotypes and gene alleles contributing to local adaptation and quantitative resistance to WPBR. The WBP genomic resources developed here provide an invaluable tool for further studies and for exploitation and utilization of the genetic diversity preserved within this endangered conifer and other five-needle pines. PMID:27992468

Semiconductor wire array structures, and solar cells and photodetectors based on such structures

DOEpatents

Kelzenberg, Michael D.; Atwater, Harry A.; Briggs, Ryan M.; Boettcher, Shannon W.; Lewis, Nathan S.; Petykiewicz, Jan A.

2014-08-19

A structure comprising an array of semiconductor structures, an infill material between the semiconductor materials, and one or more light-trapping elements is described. Photoconverters and photoelectrochemical devices based on such structure also described.

Making RISC.

PubMed

Kawamata, Tomoko; Tomari, Yukihide

2010-07-01

It is well established that 20- to 30-nt small RNAs, including small interfering RNAs, microRNAs and Piwi-interacting RNAs, play crucial roles in regulating gene expression and control a surprisingly diverse array of biological processes. These small RNAs cannot work alone: they must form effector ribonucleoprotein complexes - RNA-induced silencing complexes (RISCs) - to exert their function. Thus, RISC assembly is a key process in small RNA-mediated silencing. Recent biochemical analyses of RISC assembly, together with new structural studies of Argonaute, the core protein component of RISC, suggest a revised view of how mature RISC, which contains single-stranded guide RNA, is built from small RNAs that are born double-stranded. Copyright 2010 Elsevier Ltd. All rights reserved.

The complete sequence of the mitochondrial genome of Arctic fox (Alopex lagopus).

PubMed

Yan, Shou-Qing; Guo, Peng-Cheng; Yue, Yuan; Li, Wan-Hong; Bai, Chun-Yan; Li, Yu-Mei; Sun, Jin-Hai; Zhao, Zhi-Hui

2016-11-01

In the present study, the complete mitochondrial genome sequence of Arctic fox (Alopex lagopus) was determined for the first time. It has a total length of 16,656 bp, and contains 13 protein-coding genes, 22 tRNA genes, 2 ribosome RNA genes and 1 control region. The nucleotide composition is 31.3% for A, 26.2% for C, 14.8% for G and 27.7% for T, respectively. The D-loop region located between tRNA Pro and tRNA Phe contains a (ACACGTACACGCAT) 18 tandem repeat array. The data will be useful for the investigation of the genetic structure and diversity in the natural and farmed population of Arctic foxes.

Leak Detection in Spacecraft Using a 64-Element Multiplexed Passive Array to Monitor Structure-Borne Noise

NASA Astrophysics Data System (ADS)

Holland, Stephen D.; Song, Jun-Ho; Chimenti, D. E.; Roberts, Ron

2006-03-01

We demonstrate an array sensor method intended to locate leaks in manned spacecraft using leak-generated, structure-borne ultrasonic noise. We have developed and tested a method for sensing and processing leak noise to reveal the leak location involving the use of a 64-element phased-array. Cross-correlations of ultrasonic noise waveforms from a leak into vacuum have been used with a phased-array analysis to find the direction from the sensor to the leak. This method measures the propagation of guided ultrasonic Lamb waves passing under the PZT array sensor in the spacecraft skin structure. This paper will describe the custom-designed array with integrated electronics, as well as the performance of the array in prototype applications. We show that this method can be used to successfully locate leaks to within a few millimeters on a 0.6-m square aluminum plate.

Structural basis for an inositol pyrophosphate kinase surmounting phosphate crowding

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

Wang, Huanchen; Falck, J.R.; Hall, Traci M. Tanaka

2012-01-11

Inositol pyrophosphates (such as IP7 and IP8) are multifunctional signaling molecules that regulate diverse cellular activities. Inositol pyrophosphates have 'high-energy' phosphoanhydride bonds, so their enzymatic synthesis requires that a substantial energy barrier to the transition state be overcome. Additionally, inositol pyrophosphate kinases can show stringent ligand specificity, despite the need to accommodate the steric bulk and intense electronegativity of nature's most concentrated three-dimensional array of phosphate groups. Here we examine how these catalytic challenges are met by describing the structure and reaction cycle of an inositol pyrophosphate kinase at the atomic level. We obtained crystal structures of the kinase domainmore » of human PPIP5K2 complexed with nucleotide cofactors and either substrates, product or a MgF{sub 3}{sup -} transition-state mimic. We describe the enzyme's conformational dynamics, its unprecedented topological presentation of nucleotide and inositol phosphate, and the charge balance that facilitates partly associative in-line phosphoryl transfer.« less

Trimeric HIV-1-Env Structures Define Glycan Shields from Clades A, B and G

PubMed Central

Stewart-Jones, Guillaume B. E.; Soto, Cinque; Lemmin, Thomas; Chuang, Gwo-Yu; Druz, Aliaksandr; Kong, Rui; Thomas, Paul V.; Wagh, Kshitij; Zhou, Tongqing; Behrens, Anna-Janina; Bylund, Tatsiana; Choi, Chang W.; Davison, Jack R.; Georgiev, Ivelin S.; Joyce, M. Gordon; Do Kwon, Young; Pancera, Marie; Taft, Justin; Yang, Yongping; Zhang, Baoshan; Shivatare, Sachin S.; Shivatare, Vidya S.; Lee, Chang-Chun D.; Wu, Chung-Yi; Bewley, Carole A.; Burton, Dennis R.; Koff, Wayne C.; Connors, Mark; Crispin, Max; Baxa, Ulrich; Korber, Bette T.; Wong, Chi-Huey; Mascola, John R.; Kwong, Peter D.

2017-01-01

The HIV-1-envelope (Env) trimer is covered by a glycan shield of ~90 N-linked oligosaccharides, which comprises roughly half its mass and is a key component of HIV evasion from humoral immunity. To understand how antibodies can overcome the barriers imposed by the glycan shield, we crystallized fully glycosylated Env trimers from clades A, B and G, visualizing the shield at 3.4-3.7 Å resolution. These structures reveal the HIV-1-glycan shield to comprise a network of interlocking oligosaccharides, substantially ordered by glycan crowding, which encase the protein component of Env and enable HIV-1 to avoid most antibody-mediated neutralization. The revealed features delineate a taxonomy of N-linked glycan-glycan interactions. Crowded and dispersed glycans are differently ordered, conserved, processed and recognized by antibody. The structures, along with glycan-array binding and molecular dynamics, reveal a diversity in oligosaccharide affinity and a requirement for accommodating glycans amongst known broadly neutralizing antibodies that target the glycan-shielded trimer. PMID:27114034

Total variation approach for adaptive nonuniformity correction in focal-plane arrays.

PubMed

Vera, Esteban; Meza, Pablo; Torres, Sergio

2011-01-15

In this Letter we propose an adaptive scene-based nonuniformity correction method for fixed-pattern noise removal in imaging arrays. It is based on the minimization of the total variation of the estimated irradiance, and the resulting function is optimized by an isotropic total variation approach making use of an alternating minimization strategy. The proposed method provides enhanced results when applied to a diverse set of real IR imagery, accurately estimating the nonunifomity parameters of each detector in the focal-plane array at a fast convergence rate, while also forming fewer ghosting artifacts.

When lithography meets self-assembly: a review of recent advances in the directed assembly of complex metal nanostructures on planar and textured surfaces

NASA Astrophysics Data System (ADS)

Hughes, Robert A.; Menumerov, Eredzhep; Neretina, Svetlana

2017-07-01

One of the foremost challenges in nanofabrication is the establishment of a processing science that integrates wafer-based materials, techniques, and devices with the extraordinary physicochemical properties accessible when materials are reduced to nanoscale dimensions. Such a merger would allow for exacting controls on nanostructure positioning, promote cooperative phenomenon between adjacent nanostructures and/or substrate materials, and allow for electrical contact to individual or groups of nanostructures. With neither self-assembly nor top-down lithographic processes being able to adequately meet this challenge, advancements have often relied on a hybrid strategy that utilizes lithographically-defined features to direct the assembly of nanostructures into organized patterns. While these so-called directed assembly techniques have proven viable, much of this effort has focused on the assembly of periodic arrays of spherical or near-spherical nanostructures comprised of a single element. Work directed toward the fabrication of more complex nanostructures, while still at a nascent stage, has nevertheless demonstrated the possibility of forming arrays of nanocubes, nanorods, nanoprisms, nanoshells, nanocages, nanoframes, core-shell structures, Janus structures, and various alloys on the substrate surface. In this topical review, we describe the progress made in the directed assembly of periodic arrays of these complex metal nanostructures on planar and textured substrates. The review is divided into three broad strategies reliant on: (i) the deterministic positioning of colloidal structures, (ii) the reorganization of deposited metal films at elevated temperatures, and (iii) liquid-phase chemistry practiced directly on the substrate surface. These strategies collectively utilize a broad range of techniques including capillary assembly, microcontact printing, chemical surface modulation, templated dewetting, nanoimprint lithography, and dip-pen nanolithography and employ a wide scope of chemical processes including redox reactions, alloying, dealloying, phase separation, galvanic replacement, preferential etching, template-mediated reactions, and facet-selective capping agents. Taken together, they highlight the diverse toolset available when fabricating organized surfaces of substrate-supported nanostructures.

Dewetting-mediated pattern formation in nanoparticle assemblies

NASA Astrophysics Data System (ADS)

Stannard, Andrew

2011-03-01

The deposition of nanoparticles from solution onto solid substrates is a diverse subfield of current nanoscience research. Complex physical and chemical processes underpin the self-assembly and self-organization of colloidal nanoparticles at two-phase (solid-liquid, liquid-air) interfaces and three-phase (solid-liquid-air) contact lines. This review discusses key recent advances made in the understanding of nonequilibrium dewetting processes of nanoparticle-containing solutions, detailing how such an apparently simple experimental system can give rise to such a strikingly varied palette of two-dimensional self-organized nanoparticle array morphologies. Patterns discussed include worm-like domains, cellular networks, microscale rings, and fractal-like fingering structures. There remain many unresolved issues regarding the role of the solvent dewetting dynamics in assembly processes of this type, with a significant focus on how dewetting can be coerced to produce nanoparticle arrays with desirable characteristics such as long-range order. In addition to these topics, methods developed to control nanofluid dewetting through routes such as confining the geometries of drying solutions, depositing onto pre-patterned heterogeneous substrates, and post-dewetting pattern evolution via local or global manipulation are covered.

Dewetting-mediated pattern formation in nanoparticle assemblies.

PubMed

Stannard, Andrew

2011-03-02

The deposition of nanoparticles from solution onto solid substrates is a diverse subfield of current nanoscience research. Complex physical and chemical processes underpin the self-assembly and self-organization of colloidal nanoparticles at two-phase (solid-liquid, liquid-air) interfaces and three-phase (solid-liquid-air) contact lines. This review discusses key recent advances made in the understanding of nonequilibrium dewetting processes of nanoparticle-containing solutions, detailing how such an apparently simple experimental system can give rise to such a strikingly varied palette of two-dimensional self-organized nanoparticle array morphologies. Patterns discussed include worm-like domains, cellular networks, microscale rings, and fractal-like fingering structures. There remain many unresolved issues regarding the role of the solvent dewetting dynamics in assembly processes of this type, with a significant focus on how dewetting can be coerced to produce nanoparticle arrays with desirable characteristics such as long-range order. In addition to these topics, methods developed to control nanofluid dewetting through routes such as confining the geometries of drying solutions, depositing onto pre-patterned heterogeneous substrates, and post-dewetting pattern evolution via local or global manipulation are covered.

Characterization and Optimization Design of the Polymer-Based Capacitive Micro-Arrayed Ultrasonic Transducer

NASA Astrophysics Data System (ADS)

Chiou, De-Yi; Chen, Mu-Yueh; Chang, Ming-Wei; Deng, Hsu-Cheng

2007-11-01

This study constructs an electromechanical finite element model of the polymer-based capacitive micro-arrayed ultrasonic transducer (P-CMUT). The electrostatic-structural coupled-field simulations are performed to investigate the operational characteristics, such as collapse voltage and resonant frequency. The numerical results are found to be in good agreement with experimental observations. The study of influence of each defined parameter on the collapse voltage and resonant frequency are also presented. To solve some conflict problems in diversely physical fields, an integrated design method is developed to optimize the geometric parameters of the P-CMUT. The optimization search routine conducted using the genetic algorithm (GA) is connected with the commercial FEM software ANSYS to obtain the best design variable using multi-objective functions. The results show that the optimal parameter values satisfy the conflicting objectives, namely to minimize the collapse voltage while simultaneously maintaining a customized frequency. Overall, the present result indicates that the combined FEM/GA optimization scheme provides an efficient and versatile approach of optimization design of the P-CMUT.

Global assessment of genomic variation in cattle by genome resequencing and high-throughput genotyping

PubMed Central

2011-01-01

Background Integration of genomic variation with phenotypic information is an effective approach for uncovering genotype-phenotype associations. This requires an accurate identification of the different types of variation in individual genomes. Results We report the integration of the whole genome sequence of a single Holstein Friesian bull with data from single nucleotide polymorphism (SNP) and comparative genomic hybridization (CGH) array technologies to determine a comprehensive spectrum of genomic variation. The performance of resequencing SNP detection was assessed by combining SNPs that were identified to be either in identity by descent (IBD) or in copy number variation (CNV) with results from SNP array genotyping. Coding insertions and deletions (indels) were found to be enriched for size in multiples of 3 and were located near the N- and C-termini of proteins. For larger indels, a combination of split-read and read-pair approaches proved to be complementary in finding different signatures. CNVs were identified on the basis of the depth of sequenced reads, and by using SNP and CGH arrays. Conclusions Our results provide high resolution mapping of diverse classes of genomic variation in an individual bovine genome and demonstrate that structural variation surpasses sequence variation as the main component of genomic variability. Better accuracy of SNP detection was achieved with little loss of sensitivity when algorithms that implemented mapping quality were used. IBD regions were found to be instrumental for calculating resequencing SNP accuracy, while SNP detection within CNVs tended to be less reliable. CNV discovery was affected dramatically by platform resolution and coverage biases. The combined data for this study showed that at a moderate level of sequencing coverage, an ensemble of platforms and tools can be applied together to maximize the accurate detection of sequence and structural variants. PMID:22082336

Cone Photoreceptor Structure in Patients With X-Linked Cone Dysfunction and Red-Green Color Vision Deficiency

PubMed Central

Patterson, Emily J.; Wilk, Melissa; Langlo, Christopher S.; Kasilian, Melissa; Ring, Michael; Hufnagel, Robert B.; Dubis, Adam M.; Tee, James J.; Kalitzeos, Angelos; Gardner, Jessica C.; Ahmed, Zubair M.; Sisk, Robert A.; Larsen, Michael; Sjoberg, Stacy; Connor, Thomas B.; Dubra, Alfredo; Neitz, Jay; Hardcastle, Alison J.; Neitz, Maureen; Michaelides, Michel; Carroll, Joseph

2016-01-01

Purpose Mutations in the coding sequence of the L and M opsin genes are often associated with X-linked cone dysfunction (such as Bornholm Eye Disease, BED), though the exact color vision phenotype associated with these disorders is variable. We examined individuals with L/M opsin gene mutations to clarify the link between color vision deficiency and cone dysfunction. Methods We recruited 17 males for imaging. The thickness and integrity of the photoreceptor layers were evaluated using spectral-domain optical coherence tomography. Cone density was measured using high-resolution images of the cone mosaic obtained with adaptive optics scanning light ophthalmoscopy. The L/M opsin gene array was characterized in 16 subjects, including at least one subject from each family. Results There were six subjects with the LVAVA haplotype encoded by exon 3, seven with LIAVA, two with the Cys203Arg mutation encoded by exon 4, and two with a novel insertion in exon 2. Foveal cone structure and retinal thickness was disrupted to a variable degree, even among related individuals with the same L/M array. Conclusions Our findings provide a direct link between disruption of the cone mosaic and L/M opsin variants. We hypothesize that, in addition to large phenotypic differences between different L/M opsin variants, the ratio of expression of first versus downstream genes in the L/M array contributes to phenotypic diversity. While the L/M opsin mutations underlie the cone dysfunction in all of the subjects tested, the color vision defect can be caused either by the same mutation or a gene rearrangement at the same locus. PMID:27447086

Biodiversity, functional processes, and the ecological consequences of fragmentation in Southwestern grasslands

Treesearch

Michele Merola-Zwartjes

2004-01-01

Concern over accelerating extinction rates and loss of species diversity on a global scale was the subject of E.O. Wilson's seminal volume Biodiversity (Wilson 1988). This work essentially transformed the term "biodiversity" into a household word as a short-hand for species diversity--or more simply, the full array and variety of living organisms on...

Construction and in vivo assembly of a catalytically proficient and hyperthermostable de novo enzyme.

PubMed

Watkins, Daniel W; Jenkins, Jonathan M X; Grayson, Katie J; Wood, Nicola; Steventon, Jack W; Le Vay, Kristian K; Goodwin, Matthew I; Mullen, Anna S; Bailey, Henry J; Crump, Matthew P; MacMillan, Fraser; Mulholland, Adrian J; Cameron, Gus; Sessions, Richard B; Mann, Stephen; Anderson, J L Ross

2017-08-25

Although catalytic mechanisms in natural enzymes are well understood, achieving the diverse palette of reaction chemistries in re-engineered native proteins has proved challenging. Wholesale modification of natural enzymes is potentially compromised by their intrinsic complexity, which often obscures the underlying principles governing biocatalytic efficiency. The maquette approach can circumvent this complexity by combining a robust de novo designed chassis with a design process that avoids atomistic mimicry of natural proteins. Here, we apply this method to the construction of a highly efficient, promiscuous, and thermostable artificial enzyme that catalyzes a diverse array of substrate oxidations coupled to the reduction of H 2 O 2 . The maquette exhibits kinetics that match and even surpass those of certain natural peroxidases, retains its activity at elevated temperature and in the presence of organic solvents, and provides a simple platform for interrogating catalytic intermediates common to natural heme-containing enzymes.Catalytic mechanisms of enzymes are well understood, but achieving diverse reaction chemistries in re-engineered proteins can be difficult. Here the authors show a highly efficient and thermostable artificial enzyme that catalyzes a diverse array of substrate oxidations coupled to the reduction of H 2 O 2 .

Gene-for-gene disease resistance: bridging insect pest and pathogen defense.

PubMed

Kaloshian, Isgouhi

2004-12-01

Active plant defense, also known as gene-for-gene resistance, is triggered when a plant resistance (R) gene recognizes the intrusion of a specific insect pest or pathogen. Activation of plant defense includes an array of physiological and transcriptional reprogramming. During the past decade, a large number of plant R genes that confer resistance to diverse group of pathogens have been cloned from a number of plant species. Based on predicted protein structures, these genes are classified into a small number of groups, indicating that structurally related R genes recognize phylogenetically distinct pathogens. An extreme example is the tomato Mi-1 gene, which confers resistance to potato aphid (Macrosiphum euphorbiae), whitefly (Bemisia tabaci), and root-knot nematodes (Meloidogyne spp.). While Mi-1 remains the only cloned insect R gene, there is evidence that gene-for-gene type of plant defense against piercing-sucking insects exists in a number of plant species.

Chemoenzymatic assembly of mammalian O-mannose glycans.

PubMed

Cao, Hongzhi; Meng, Caicai; Sasmal, Aniruddha; Zhang, Yan; Gao, Tian; Liu, Chang-Cheng; Khan, Naazneen; Varki, Ajit; Wang, Fengshan

2018-05-26

O-Mannose glycans account up to 30% of total O-glycans in brain. Previous synthesis and functional studies only focused on the Core M3 O-mannose glycans of α-dystroglycan which are a causative factor for various muscular diseases. In this study, a highly efficient chemoenzymatic strategy was developed that enabled the first collective synthesis of 63 Core M1 and Core M2 O-mannose glycans. This chemoenzymatic strategy features the gram-scale chemical synthesis of 5 judiciously designed core structures, and the diversity-oriented modification of the core structures with 3 enzyme modules to provide 58 complex O-mannose glycans in a linear sequence that does not exceed 4 steps. The binding profiles of synthetic O-mannose glycans with a panel of lectins, antibodies and brain proteins were also explored using the printed O-mannose glycan array. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Increasing diversity in the geosciences through the AfricaArray geophysics field course

NASA Astrophysics Data System (ADS)

Vallejo, G.; Emry, E.; Galindo, B. L.; Carranza, V.; Gomez, C. D.; Ortiz, K.; Castro, J. G.; Guandique, J.; Falzone, C.; Webb, S. J.; Manzi, M.; Mngadi, S. B.; Stephens, K.; Chinamora, B.; Whitehead, R.; de Villiers, D. P.; Tshitlho, K.; Delhaye, R. P.; Smith, J. A.; Nyblade, A.

2014-12-01

For the past nine years, the AfricaArray diversity program, sponsored by industry, the National Science Foundation, and several partnering universities have supported outstanding U.S. STEM underrepresented minority undergraduates to gain field experience in near-surface geophysical techniques during an 8-week summer program at Penn State University and the University of Witwatersrand (Wits). The AfricaArray geophysics field school, which is run by Wits, has been teaching field-based geophysics to African students for over a decade. In the first 2-3 weeks of the program, the U.S. students are given basic instruction in near-surface geophysics, South African geology, and South African history and culture. The students then join the Wits AfricaArray geophysics field school - working alongside Wits students and students from several other African universities to map the shallow subsurface in prospective areas of South Africa for platinum mining. In addition to the primary goals of collecting and interpreting gravity, magnetic, resistivity, seismic refraction, seismic reflection, and EM data, students spend time mapping geologic units and gathering information on the physical properties of the rocks in the region (i.e. seismic velocity, density, and magnetic susceptibility). Subsurface targets include mafic dikes, faults, the water table, and overburden thickness. Upon returning to the U.S., students spend 2-3 weeks finalizing their project reports and presentations. The program has been effective at not only providing students with fundamental skills in applied geophysics, but also in fostering multicultural relationships, preparing students for graduate work in the geosciences, and attracting STEM students into the geosciences. Student presenters will discuss their experiences gained through the field school and give their impressions about how the program works towards the goal of increasing diversity in the geosciences in the U.S.

Nanoskiving: A new method for nanofabrication

NASA Astrophysics Data System (ADS)

Xu, Qiaobing

"Nanoskiving" is the name we have given to a technique for the fabrication of nanostructures by combining deposition of thin films on a topographically patterned polymeric substrate using physical vapor methods and sectioning with an ultramicrotome. Ultramicrotomy was originally developed as a tool for sectioning biological specimens for analysis by optical or electron microscopy. The imaging of biological specimens requires the ability to slice mum to sub-mum thick sections and the imaging is done through the thinnest dimension of the section. Nanoskiving utilizes an ultramicrotome because of its ability to section sub-100 nm slices reproducibly. In this thesis, I will describe the fabrication by nanoskiving of the diverse nanostructures and their applications in electronics and optics. Nanoskiving is experimentally simple, and requires little in the way of facilities (for example, access to a cleanroom or a high-resolution e-beam writer is unnecessary). It is applicable to many classes of structures and materials with which conventional methods of nanofabrication (e.g. EUV or X-ray photolithography, e-beam lithography (EBL) focused ion-beam (FIB)) fail. This method begins with the deposition of thin metallic films on an epoxy substrate by e-beam evaporation or sputtering. After embedding the thin metallic film in an epoxy matrix, sectioning (in a plane perpendicular or parallel to the metal film) with an ultramicrotome generates nanometer-thick sections of epoxy containing metallic nanostructures. The cross-section of the metal wires embedded in the resulting thin epoxy sections is controlled by the thickness of the evaporated metal film (which can be as small as 20 nm), and the thickness of the sections cut by the microtome (as small as 30 nm, using a standard 35° diamond knife). The embedded nanostructures can be transferred to, and positioned on planar or curved substrates by manipulating the thin polymer film. Removal of the epoxy matrix by etching with an oxygen plasma generates free-standing metallic nanostructures. Chapter 1 is an overview of nanoskiving---a technique that combines thin-film deposition of metal on a topographically contoured substrate with sectioning using an ultramicrotome---as a method of fabricating nanostructures. Nanoskiving provides a simple and convenient procedure to produce arrays (over areas of mm2 to cm2) of structures with cross-sectional dimensions in the thirty-nanometer regime embedded in epoxy. The ability to control the dimensions of nanostructures, combined with the ability to manipulate and position them, enables the fabrication of nanostructures with geometries that are difficult to prepare by other methods. Two classes of applications--- in optics and in electronics---demonstrate the utility of nanostructures fabricated by nanoskiving. Chapter 2 shows the fabrication by nanoskiving of complex nanostructures that are difficult or impossible to achieve by other nanofabrication methods. These include multilayer structures, structures on curved surfaces, structures that span gaps, structures in less familiar materials, structures with high-aspect ratios, and large-area structures comprising two-dimensional periodic arrays. Chapter 3 demonstrates the Fabrication patterned arrays of gold structures (for example, rings) with wall thickness of 40 nm, and with high aspect ratios up to 25. Chapter 4 introduces the fabrication by nanoskiving of gold nanowires of uniform, controllable length, width, and height, and describes a systematic study of the dependence of the surface plasmon resonance on the geometry of these wires. Chapter 5 describes the fabrication of arrays of closed and open, loop-shaped nanostructures over mm2 area by nanoskiving. These arrays of metallic structures serve as frequency-selective surfaces at mid-infrared wavelengths. Chapter 6 describes a procedure to fabricate an array of nanoelectrodes that can be addressed from the back face of the slab of epoxy resin.

Infrared-Bolometer Arrays with Reflective Backshorts

NASA Technical Reports Server (NTRS)

Miller, Timothy M.; Abrahams, John; Allen, Christine A.

2011-01-01

Integrated circuits that incorporate square arrays of superconducting-transition- edge bolometers with optically reflective backshorts are being developed for use in image sensors in the spectral range from far infrared to millimeter wavelengths. To maximize the optical efficiency (and, thus, sensitivity) of such a sensor at a specific wavelength, resonant optical structures are created by placing the backshorts at a quarter wavelength behind the bolometer plane. The bolometer and backshort arrays are fabricated separately, then integrated to form a single unit denoted a backshort-under-grid (BUG) bolometer array. In a subsequent fabrication step, the BUG bolometer array is connected, by use of single-sided indium bump bonding, to a readout device that comprises mostly a superconducting quantum interference device (SQUID) multiplexer circuit. The resulting sensor unit comprising the BUG bolometer array and the readout device is operated at a temperature below 1 K. The concept of increasing optical efficiency by use of backshorts at a quarter wavelength behind the bolometers is not new. Instead, the novelty of the present development lies mainly in several features of the design of the BUG bolometer array and the fabrication sequence used to implement the design. Prior to joining with the backshort array, the bolometer array comprises, more specifically, a square grid of free-standing molybdenum/gold superconducting-transition-edge bolometer elements on a 1.4- m-thick top layer of silicon that is part of a silicon support frame made from a silicon-on-insulator wafer. The backshort array is fabricated separately as a frame structure that includes support beams and contains a correspond - ing grid of optically reflective patches on a single-crystal silicon substrate. The process used to fabricate the bolometer array includes standard patterning and etching steps that result in the formation of deep notches in the silicon support frame. These notches are designed to interlock with the support beams on the backshort-array structure to provide structural support and precise relative positioning. The backshort-array structure is inserted in the silicon support frame behind the bolometer array, and the notches in the frame serve to receive the support beams of the backshort-array structure and thus determine the distance between the backshort and bolometer planes. The depth of the notches and, thus, the distance between the backshort and bolometer planes, can be tailored to a value between 25 to 300 m adjusting only a few process steps. The backshort array is designed so as not to interfere with the placement of indium bumps for subsequent indium bump-bonding to the multiplexing readout circuitry

Innate Immune Complexity in the Purple Sea Urchin: Diversity of the Sp185/333 System

PubMed Central

Smith, L. Courtney

2012-01-01

The California purple sea urchin, Strongylocentrotus purpuratus, is a long-lived echinoderm with a complex and sophisticated innate immune system. There are several large gene families that function in immunity in this species including the Sp185/333 gene family that has ∼50 (±10) members. The family shows intriguing sequence diversity and encodes a broad array of diverse yet similar proteins. The genes have two exons of which the second encodes the mature protein and has repeats and blocks of sequence called elements. Mosaics of element patterns plus single nucleotide polymorphisms-based variants of the elements result in significant sequence diversity among the genes yet maintains similar structure among the members of the family. Sequence of a bacterial artificial chromosome insert shows a cluster of six, tightly linked Sp185/333 genes that are flanked by GA microsatellites. The sequences between the GA microsatellites in which the Sp185/333 genes and flanking regions are located, are much more similar to each other than are the sequences outside the microsatellites suggesting processes such as gene conversion, recombination, or duplication. However, close linkage does not correspond with greater sequence similarity compared to randomly cloned and sequenced genes that are unlikely to be linked. There are three segmental duplications that are bounded by GAT microsatellites and include three almost identical genes plus flanking regions. RNA editing is detectible throughout the mRNAs based on comparisons to the genes, which, in combination with putative post-translational modifications to the proteins, results in broad arrays of Sp185/333 proteins that differ among individuals. The mature proteins have an N-terminal glycine-rich region, a central RGD motif, and a C-terminal histidine-rich region. The Sp185/333 proteins are localized to the cell surface and are found within vesicles in subsets of polygonal and small phagocytes. The coelomocyte proteome shows full-length and truncated proteins, including some with missense sequence. Current results suggest that both native Sp185/333 proteins and a recombinant protein bind bacteria and are likely important in sea urchin innate immunity. PMID:22566951

Microbial community functional structure in response to antibiotics in pharmaceutical wastewater treatment systems.

PubMed

Zhang, Yu; Xie, Jianping; Liu, Miaomiao; Tian, Zhe; He, Zhili; van Nostrand, Joy D; Ren, Liren; Zhou, Jizhong; Yang, Min

2013-10-15

It is widely demonstrated that antibiotics in the environment affect microbial community structure. However, direct evidence regarding the impacts of antibiotics on microbial functional structures in wastewater treatment systems is limited. Herein, a high-throughput functional gene array (GeoChip 3.0) in combination with quantitative PCR and clone libraries were used to evaluate the microbial functional structures in two biological wastewater treatment systems, which treat antibiotic production wastewater mainly containing oxytetracycline. Despite the bacteriostatic effects of antibiotics, the GeoChip detected almost all key functional gene categories, including carbon cycling, nitrogen cycling, etc., suggesting that these microbial communities were functionally diverse. Totally 749 carbon-degrading genes belonging to 40 groups (24 from bacteria and 16 from fungi) were detected. The abundance of several fungal carbon-degrading genes (e.g., glyoxal oxidase (glx), lignin peroxidase or ligninase (lip), manganese peroxidase (mnp), endochitinase, exoglucanase_genes) was significantly correlated with antibiotic concentrations (Mantel test; P < 0.05), showing that the fungal functional genes have been enhanced by the presence of antibiotics. However, from the fact that the majority of carbon-degrading genes were derived from bacteria and diverse antibiotic resistance genes were detected in bacteria, it was assumed that many bacteria could survive in the environment by acquiring antibiotic resistance and may have maintained the position as a main player in nutrient removal. Variance partitioning analysis showed that antibiotics could explain 24.4% of variations in microbial functional structure of the treatment systems. This study provides insights into the impacts of antibiotics on microbial functional structure of a unique system receiving antibiotic production wastewater, and reveals the potential importance of the cooperation between fungi and bacteria with antibiotic resistance in maintaining the stability and performance of the systems. Copyright © 2013 Elsevier Ltd. All rights reserved.

On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires.

PubMed

Silas, Sukrit; Makarova, Kira S; Shmakov, Sergey; Páez-Espino, David; Mohr, Georg; Liu, Yi; Davison, Michelle; Roux, Simon; Krishnamurthy, Siddharth R; Fu, Becky Xu Hua; Hansen, Loren L; Wang, David; Sullivan, Matthew B; Millard, Andrew; Clokie, Martha R; Bhaya, Devaki; Lambowitz, Alan M; Kyrpides, Nikos C; Koonin, Eugene V; Fire, Andrew Z

2017-07-11

Cas1 integrase is the key enzyme of the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas adaptation module that mediates acquisition of spacers derived from foreign DNA by CRISPR arrays. In diverse bacteria, the cas1 gene is fused (or adjacent) to a gene encoding a reverse transcriptase (RT) related to group II intron RTs. An RT-Cas1 fusion protein has been recently shown to enable acquisition of CRISPR spacers from RNA. Phylogenetic analysis of the CRISPR-associated RTs demonstrates monophyly of the RT-Cas1 fusion, and coevolution of the RT and Cas1 domains. Nearly all such RTs are present within type III CRISPR-Cas loci, but their phylogeny does not parallel the CRISPR-Cas type classification, indicating that RT-Cas1 is an autonomous functional module that is disseminated by horizontal gene transfer and can function with diverse type III systems. To compare the sequence pools sampled by RT-Cas1-associated and RT-lacking CRISPR-Cas systems, we obtained samples of a commercially grown cyanobacterium- Arthrospira platensis Sequencing of the CRISPR arrays uncovered a highly diverse population of spacers. Spacer diversity was particularly striking for the RT-Cas1-containing type III-B system, where no saturation was evident even with millions of sequences analyzed. In contrast, analysis of the RT-lacking type III-D system yielded a highly diverse pool but reached a point where fewer novel spacers were recovered as sequencing depth was increased. Matches could be identified for a small fraction of the non-RT-Cas1-associated spacers, and for only a single RT-Cas1-associated spacer. Thus, the principal source(s) of the spacers, particularly the hypervariable spacer repertoire of the RT-associated arrays, remains unknown. IMPORTANCE While the majority of CRISPR-Cas immune systems adapt to foreign genetic elements by capturing segments of invasive DNA, some systems carry reverse transcriptases (RTs) that enable adaptation to RNA molecules. From analysis of available bacterial sequence data, we find evidence that RT-based RNA adaptation machinery has been able to join with CRISPR-Cas immune systems in many, diverse bacterial species. To investigate whether the abilities to adapt to DNA and RNA molecules are utilized for defense against distinct classes of invaders in nature, we sequenced CRISPR arrays from samples of commercial-scale open-air cultures of Arthrospira platensis , a cyanobacterium that contains both RT-lacking and RT-containing CRISPR-Cas systems. We uncovered a diverse pool of naturally occurring immune memories, with the RT-lacking locus acquiring a number of segments matching known viral or bacterial genes, while the RT-containing locus has acquired spacers from a distinct sequence pool for which the source remains enigmatic. Copyright © 2017 Silas et al.

Structural-electrical coupling optimisation for radiating and scattering performances of active phased array antenna

NASA Astrophysics Data System (ADS)

Wang, Congsi; Wang, Yan; Wang, Zhihai; Wang, Meng; Yuan, Shuai; Wang, Weifeng

2018-04-01

It is well known that calculating and reducing of radar cross section (RCS) of the active phased array antenna (APAA) are both difficult and complicated. It remains unresolved to balance the performance of the radiating and scattering when the RCS is reduced. Therefore, this paper develops a structure and scattering array factor coupling model of APAA based on the phase errors of radiated elements generated by structural distortion and installation error of the array. To obtain the optimal radiating and scattering performance, an integrated optimisation model is built to optimise the installation height of all the radiated elements in normal direction of the array, in which the particle swarm optimisation method is adopted and the gain loss and scattering array factor are selected as the fitness function. The simulation indicates that the proposed coupling model and integrated optimisation method can effectively decrease the RCS and that the necessary radiating performance can be simultaneously guaranteed, which demonstrate an important application value in engineering design and structural evaluation of APAA.

Method of forming pointed structures

NASA Technical Reports Server (NTRS)

Pugel, Diane E. (Inventor)

2011-01-01

A method of forming an array of pointed structures comprises depositing a ferrofluid on a substrate, applying a magnetic field to the ferrofluid to generate an array of surface protrusions, and solidifying the surface protrusions to form the array of pointed structures. The pointed structures may have a tip radius ranging from approximately 10 nm to approximately 25 micron. Solidifying the surface protrusions may be carried out at a temperature ranging from approximately 10 degrees C. to approximately 30 degrees C.

STS-74/MIR Photogrammetric Appendage Structural Dynamics Experiment Preliminary Data Analysis

NASA Technical Reports Server (NTRS)

Gilbert, Michael G.; Welch, Sharon S.; Pappa, Richard S.; Demeo, Martha E.

1997-01-01

The Photogrammetric Appendage Structural Dynamics Experiment was designed, developed, and flown to demonstrate and prove measurement of the structural vibration response of a Russian Space Station Mir solar array using photogrammetric methods. The experiment flew on the STS-74 Space Shuttle mission to Mir in November 1995 and obtained video imagery of solar array structural response to various excitation events. The video imagery has been digitized and triangulated to obtain response time history data at discrete points on the solar array. This data has been further processed using the Eigensystem Realization Algorithm modal identification technique to determine the natural vibration frequencies, damping, and mode shapes of the solar array. The results demonstrate that photogrammetric measurement of articulating, nonoptically targeted, flexible solar arrays and appendages is a viable, low-cost measurement option for the International Space Station.

Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp.

PubMed Central

Hulse-Kemp, Amanda M.; Lemm, Jana; Plieske, Joerg; Ashrafi, Hamid; Buyyarapu, Ramesh; Fang, David D.; Frelichowski, James; Giband, Marc; Hague, Steve; Hinze, Lori L.; Kochan, Kelli J.; Riggs, Penny K.; Scheffler, Jodi A.; Udall, Joshua A.; Ulloa, Mauricio; Wang, Shirley S.; Zhu, Qian-Hao; Bag, Sumit K.; Bhardwaj, Archana; Burke, John J.; Byers, Robert L.; Claverie, Michel; Gore, Michael A.; Harker, David B.; Islam, Md S.; Jenkins, Johnie N.; Jones, Don C.; Lacape, Jean-Marc; Llewellyn, Danny J.; Percy, Richard G.; Pepper, Alan E.; Poland, Jesse A.; Mohan Rai, Krishan; Sawant, Samir V.; Singh, Sunil Kumar; Spriggs, Andrew; Taylor, Jen M.; Wang, Fei; Yourstone, Scott M.; Zheng, Xiuting; Lawley, Cindy T.; Ganal, Martin W.; Van Deynze, Allen; Wilson, Iain W.; Stelly, David M.

2015-01-01

High-throughput genotyping arrays provide a standardized resource for plant breeding communities that are useful for a breadth of applications including high-density genetic mapping, genome-wide association studies (GWAS), genomic selection (GS), complex trait dissection, and studying patterns of genomic diversity among cultivars and wild accessions. We have developed the CottonSNP63K, an Illumina Infinium array containing assays for 45,104 putative intraspecific single nucleotide polymorphism (SNP) markers for use within the cultivated cotton species Gossypium hirsutum L. and 17,954 putative interspecific SNP markers for use with crosses of other cotton species with G. hirsutum. The SNPs on the array were developed from 13 different discovery sets that represent a diverse range of G. hirsutum germplasm and five other species: G. barbadense L., G. tomentosum Nuttal × Seemann, G. mustelinum Miers × Watt, G. armourianum Kearny, and G. longicalyx J.B. Hutchinson and Lee. The array was validated with 1,156 samples to generate cluster positions to facilitate automated analysis of 38,822 polymorphic markers. Two high-density genetic maps containing a total of 22,829 SNPs were generated for two F2 mapping populations, one intraspecific and one interspecific, and 3,533 SNP markers were co-occurring in both maps. The produced intraspecific genetic map is the first saturated map that associates into 26 linkage groups corresponding to the number of cotton chromosomes for a cross between two G. hirsutum lines. The linkage maps were shown to have high levels of collinearity to the JGI G. raimondii Ulbrich reference genome sequence. The CottonSNP63K array, cluster file and associated marker sequences constitute a major new resource for the global cotton research community. PMID:25908569

Standing spin-wave mode structure and linewidth in partially disordered hexagonal arrays of perpendicularly magnetized sub-micron Permalloy discs

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

Ross, N., E-mail: rossn2282@gmail.com; Kostylev, M., E-mail: mikhail.kostylev@uwa.edu.au; Stamps, R. L.

2014-09-21

Standing spin wave mode frequencies and linewidths in partially disordered perpendicular magnetized arrays of sub-micron Permalloy discs are measured using broadband ferromagnetic resonance and compared to analytical results from a single, isolated disc. The measured mode structure qualitatively reproduces the structure expected from the theory. Fitted demagnetizing parameters decrease with increasing array disorder. The frequency difference between the first and second radial modes is found to be higher in the measured array systems than predicted by theory for an isolated disc. The relative frequencies between successive spin wave modes are unaffected by reduction of the long-range ordering of discs inmore » the array. An increase in standing spin wave resonance linewidth at low applied magnetic fields is observed and grows more severe with increased array disorder.« less

Diversity and interactions of microbial functional genes under differing environmental conditions: insights from a membrane bioreactor and an oxidation ditch.

PubMed

Xia, Yu; Hu, Man; Wen, Xianghua; Wang, Xiaohui; Yang, Yunfeng; Zhou, Jizhong

2016-01-08

The effect of environmental conditions on the diversity and interactions of microbial communities has caused tremendous interest in microbial ecology. Here, we found that with identical influents but differing operational parameters (mainly mixed liquor suspended solid (MLSS) concentrations, solid retention time (SRT) and dissolved oxygen (DO) concentrations), two full-scale municipal wastewater treatment systems applying oxidation ditch (OD) and membrane bioreactor (MBR) processes harbored a majority of shared genes (87.2%) but had different overall functional gene structures as revealed by two datasets of 12-day time-series generated by a functional gene array-GeoChip 4.2. Association networks of core carbon, nitrogen and phosphorus cycling genes in each system based on random matrix theory (RMT) showed different topological properties and the MBR nodes showed an indication of higher connectivity. MLSS and DO were shown to be effective in shaping functional gene structures of the systems by statistical analyses. Higher MLSS concentrations resulting in decreased resource availability of the MBR system were thought to promote positive interactions of important functional genes. Together, these findings show the differences of functional potentials of some bioprocesses caused by differing environmental conditions and suggest that higher stress of resource limitation increased positive gene interactions in the MBR system.

Diversity and interactions of microbial functional genes under differing environmental conditions: insights from a membrane bioreactor and an oxidation ditch

NASA Astrophysics Data System (ADS)

Xia, Yu; Hu, Man; Wen, Xianghua; Wang, Xiaohui; Yang, Yunfeng; Zhou, Jizhong

2016-01-01

The effect of environmental conditions on the diversity and interactions of microbial communities has caused tremendous interest in microbial ecology. Here, we found that with identical influents but differing operational parameters (mainly mixed liquor suspended solid (MLSS) concentrations, solid retention time (SRT) and dissolved oxygen (DO) concentrations), two full-scale municipal wastewater treatment systems applying oxidation ditch (OD) and membrane bioreactor (MBR) processes harbored a majority of shared genes (87.2%) but had different overall functional gene structures as revealed by two datasets of 12-day time-series generated by a functional gene array-GeoChip 4.2. Association networks of core carbon, nitrogen and phosphorus cycling genes in each system based on random matrix theory (RMT) showed different topological properties and the MBR nodes showed an indication of higher connectivity. MLSS and DO were shown to be effective in shaping functional gene structures of the systems by statistical analyses. Higher MLSS concentrations resulting in decreased resource availability of the MBR system were thought to promote positive interactions of important functional genes. Together, these findings show the differences of functional potentials of some bioprocesses caused by differing environmental conditions and suggest that higher stress of resource limitation increased positive gene interactions in the MBR system.

Diversity and interactions of microbial functional genes under differing environmental conditions: insights from a membrane bioreactor and an oxidation ditch

PubMed Central

Xia, Yu; Hu, Man; Wen, Xianghua; Wang, Xiaohui; Yang, Yunfeng; Zhou, Jizhong

2016-01-01

The effect of environmental conditions on the diversity and interactions of microbial communities has caused tremendous interest in microbial ecology. Here, we found that with identical influents but differing operational parameters (mainly mixed liquor suspended solid (MLSS) concentrations, solid retention time (SRT) and dissolved oxygen (DO) concentrations), two full-scale municipal wastewater treatment systems applying oxidation ditch (OD) and membrane bioreactor (MBR) processes harbored a majority of shared genes (87.2%) but had different overall functional gene structures as revealed by two datasets of 12-day time-series generated by a functional gene array-GeoChip 4.2. Association networks of core carbon, nitrogen and phosphorus cycling genes in each system based on random matrix theory (RMT) showed different topological properties and the MBR nodes showed an indication of higher connectivity. MLSS and DO were shown to be effective in shaping functional gene structures of the systems by statistical analyses. Higher MLSS concentrations resulting in decreased resource availability of the MBR system were thought to promote positive interactions of important functional genes. Together, these findings show the differences of functional potentials of some bioprocesses caused by differing environmental conditions and suggest that higher stress of resource limitation increased positive gene interactions in the MBR system. PMID:26743465

Geological Evolution of the Ganiki Planitia Quadrangle (V14) on Venus

NASA Technical Reports Server (NTRS)

Grosfils, E. B.; Drury, D. E.; Hurwitz, D. M.; Kastl, B.; Long, s. M.; Richards, J. W.; Venechuk, E. M.

2005-01-01

The Ganiki Planitia quadrangle (25-50degN, 180-210degE) is located north of Atla Regio, south of Vinmara Planitia, and southeast of Atalanta Planitia. The region contains a diverse array of volcanic-, tectonic- and impact-derived features, and the objectives for the ongoing mapping effort are fivefold: 1) explore the formation and evolution of radiating dike swarms within the region, 2) use the diverse array of volcanic deposits to further test the neutral buoyancy hypothesis proposed to explain the origin of reservoir-derived features, 3&4) unravel the volcanic and tectonic evolution in this area, and 5) explore the implications of 1-4 for resurfacing mechanisms. Here we summarize our onging analysis of the material unit stratigraphy in the quadrangle, data central to meeting the aforementioned objectives successfully.

The design of low cost structures for extensive ground arrays

NASA Technical Reports Server (NTRS)

Franklin, H. A.; Leonard, R. S.

1980-01-01

The development of conceptual designs of solar array support structures and their foundations including considerations of the use of concrete, steel, aluminum, or timber are reported. Some cost trends were examined by varying selected parameters to determine optimum configurations. Detailed civil/structural design criteria were developed. Using these criteria, eight detailed designs for support structures and foundations were developed and cost estimates were made. As a result of the study wind was identified as the major loading experienced by these low height structures, whose arrays are likely to extend over large tracts of land. Proper wind load estimating is considered essential to developing realistic structural designs and achieving minimum cost support structures. Wind tunnel testing of a conceptual array field was undertaken and some of the resulting wind design criteria are presented. The SPS rectenna system designs may be less sensitive to wind load estimates, but consistent design criteria remain important.

Systems and methods for the combinatorial synthesis of novel materials

DOEpatents

Wu, Xin Di; Wang, Youqi; Goldwasser, Isy

2000-01-01

Methods and apparatus for the preparation of a substrate having an array of diverse materials in predefined regions thereon. A substrate having an array of diverse materials thereon is generally prepared by depositing components of target materials to predefined regions on the substrate, and, in some embodiments, simultaneously reacting the components to form at least two resulting materials. In particular, the present invention provides novel masking systems and methods for applying components of target materials onto a substrate in a combinatorial fashion, thus creating arrays of resulting materials that differ slightly in composition, stoichiometry, and/or thickness. Using the novel masking systems of the present invention, components can be delivered to each site in a uniform distribution, or in a gradient of stoichiometries, thicknesses, compositions, etc. Resulting materials which can be prepared using the methods and apparatus of the present invention include, for example, covalent network solids, ionic solids and molecular solids. Once prepared, these resulting materials can be screened sequentially, or in parallel, for useful properties including, for example, electrical, thermal, mechanical, morphological, optical, magnetic, chemical and other properties.

How hollow melanosomes affect iridescent colour production in birds

PubMed Central

Eliason, Chad M.; Bitton, Pierre-Paul; Shawkey, Matthew D.

2013-01-01

Developmental constraints and trade-offs can limit diversity, but organisms have repeatedly evolved morphological innovations that overcome these limits by expanding the range and functionality of traits. Iridescent colours in birds are commonly produced by melanin-containing organelles (melanosomes) organized into nanostructured arrays within feather barbules. Variation in array type (e.g. multilayers and photonic crystals, PCs) is known to have remarkable effects on plumage colour, but the optical consequences of variation in melanosome shape remain poorly understood. Here, we used a combination of spectrophotometric, experimental and theoretical methods to test how melanosome hollowness—a morphological innovation largely restricted to birds—affects feather colour. Optical analyses of hexagonal close-packed arrays of hollow melanosomes in two species, wild turkeys (Meleagris gallopavo) and violet-backed starlings (Cinnyricinclus leucogaster), indicated that they function as two-dimensional PCs. Incorporation of a larger dataset and optical modelling showed that, compared with solid melanosomes, hollow melanosomes allow birds to produce distinct colours with the same energetically favourable, close-packed configurations. These data suggest that a morphological novelty has, at least in part, allowed birds to achieve their vast morphological and colour diversity. PMID:23902909

Multilocus Phylogeography and Species Delimitation in the Cumberland Plateau Salamander, Plethodon kentucki: Incongruence among Data Sets and Methods

PubMed Central

Kuchta, Shawn R.; Brown, Ashley D.; Converse, Paul E.; Highton, Richard

2016-01-01

Species are a fundamental unit of biodiversity, yet can be challenging to delimit objectively. This is particularly true of species complexes characterized by high levels of population genetic structure, hybridization between genetic groups, isolation by distance, and limited phenotypic variation. Previous work on the Cumberland Plateau Salamander, Plethodon kentucki, suggested that it might constitute a species complex despite occupying a relatively small geographic range. To examine this hypothesis, we sampled 135 individuals from 43 populations, and used four mitochondrial loci and five nuclear loci (5693 base pairs) to quantify phylogeographic structure and probe for cryptic species diversity. Rates of evolution for each locus were inferred using the multidistribute package, and time calibrated gene trees and species trees were inferred using BEAST 2 and *BEAST 2, respectively. Because the parameter space relevant for species delimitation is large and complex, and all methods make simplifying assumptions that may lead them to fail, we conducted an array of analyses. Our assumption was that strongly supported species would be congruent across methods. Putative species were first delimited using a Bayesian implementation of the GMYC model (bGMYC), Geneland, and Brownie. We then validated these species using the genealogical sorting index and BPP. We found substantial phylogeographic diversity using mtDNA, including four divergent clades and an inferred common ancestor at 14.9 myr (95% HPD: 10.8–19.7 myr). By contrast, this diversity was not corroborated by nuclear sequence data, which exhibited low levels of variation and weak phylogeographic structure. Species trees estimated a far younger root than did the mtDNA data, closer to 1.0 myr old. Mutually exclusive putative species were identified by the different approaches. Possible causes of data set discordance, and the problem of species delimitation in complexes with high levels of population structure and introgressive hybridization, are discussed. PMID:26974148

Optimal design of aperiodic, vertical silicon nanowire structures for photovoltaics.

PubMed

Lin, Chenxi; Povinelli, Michelle L

2011-09-12

We design a partially aperiodic, vertically-aligned silicon nanowire array that maximizes photovoltaic absorption. The optimal structure is obtained using a random walk algorithm with transfer matrix method based electromagnetic forward solver. The optimal, aperiodic structure exhibits a 2.35 times enhancement in ultimate efficiency compared to its periodic counterpart. The spectral behavior mimics that of a periodic array with larger lattice constant. For our system, we find that randomly-selected, aperiodic structures invariably outperform the periodic array.

Ka-band MMIC subarray technology program (Ka-Mist)

NASA Technical Reports Server (NTRS)

Pottenger, Warren

1995-01-01

The broad objective of this program was to demonstrate a proof of concept insertion of Monolithic Microwave Integrated Circuit (MMIC) device technology into an innovative (tile architecture) active phased array antenna application supporting advanced EHF communication systems. Ka-band MMIC arrays have long been considered as having high potential for increasing the capability of space, aircraft, and land mobile communication systems in terms of scan performance, data rate, link margin, and flexibility while offering a significant reduction in size, weight, and power consumption. Insertion of MMIC technology into antenna systems, particularly at millimeter wave frequencies using low power and low noise amplifiers in close proximity to the radiating elements, offers a significant improvement in the array transmit efficiency, receive system noise figure, and overall array reliability. Application of active array technology also leads to the use of advanced beamforming techniques that can improve beam agility, diversity, and adaptivity to complex signal environments.

Colorimetric sensor array for determination and identification of toxic industrial chemicals.

PubMed

Feng, Liang; Musto, Christopher J; Kemling, Jonathan W; Lim, Sung H; Zhong, Wenxuan; Suslick, Kenneth S

2010-11-15

A low-cost yet highly sensitive colorimetric sensor array for the detection and identification of toxic industrial chemicals (TICs) has been developed. The sensor consists of a disposable array of cross-responsive nanoporous pigments whose colors are changed by diverse chemical interactions with analytes. Clear differentiation among 20 different TICs has been easily achieved at both their IDLH (immediately dangerous to life or health) concentration within 2 min of exposure and PEL (permissible exposure limit) concentration within 5 min of exposure with no errors or misclassifications. Detection limits are generally well below the PEL (in most cases below 5% of PEL) and are typically in the low ppb range. The colorimetric sensor array is not responsive to changes in humidity or temperature over a substantial range. The printed arrays show excellent batch to batch reproducibility and long shelf life (greater than 3 months).

PhylArray: phylogenetic probe design algorithm for microarray.

PubMed

Militon, Cécile; Rimour, Sébastien; Missaoui, Mohieddine; Biderre, Corinne; Barra, Vincent; Hill, David; Moné, Anne; Gagne, Geneviève; Meier, Harald; Peyretaillade, Eric; Peyret, Pierre

2007-10-01

Microbial diversity is still largely unknown in most environments, such as soils. In order to get access to this microbial 'black-box', the development of powerful tools such as microarrays are necessary. However, the reliability of this approach relies on probe efficiency, in particular sensitivity, specificity and explorative power, in order to obtain an image of the microbial communities that is close to reality. We propose a new probe design algorithm that is able to select microarray probes targeting SSU rRNA at any phylogenetic level. This original approach, implemented in a program called 'PhylArray', designs a combination of degenerate and non-degenerate probes for each target taxon. Comparative experimental evaluations indicate that probes designed with PhylArray yield a higher sensitivity and specificity than those designed by conventional approaches. Applying the combined PhyArray/GoArrays strategy helps to optimize the hybridization performance of short probes. Finally, hybridizations with environmental targets have shown that the use of the PhylArray strategy can draw attention to even previously unknown bacteria.

Fabrication and characterization of nano-gas sensor arrays

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

Hassan, H. S., E-mail: hassan.shokry@gmail.com; Kashyout, A. B., E-mail: hady8@yahoo.com; Morsi, I., E-mail: drimanmorsi@yahoo.com

2015-03-30

A novel structures of Nanomaterials gas sensors array constructed using ZnO, and ZnO doped with Al via sol-gel technique. Two structure arrays are developed; the first one is a double sensor array based on doping with percentages of 1% and 5%. The second is a quadrature sensor array based on several doping ratios concentrations (0%, 1%, 5% and 10%). The morphological structures of prepared ZnO were revealed using scanning electron microscope (SEM). X-ray diffraction (XRD) patterns reveal a highly crystallized wurtzite structure and used for identifying phase structure and chemical state of both ZnO and ZnO doped with Al undermore » different preparation conditions and different doping ratios. Chemical composition of Al-doped ZnO nanopowders was performed using energy dispersive x-ray (EDS) analysis. The electrical characteristics of the sensor are determined by measuring the two terminal sensor’s output resistance for O{sub 2}, H{sub 2} and CO{sub 2} gases as a function of temperature.« less

Microbial Diversity and Bioremediation of a Hydrocarbon-Contaminated Aquifer (Vega Baja, Puerto Rico)

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

Rodriguez-Martinex, Enid M.; Perez, Ernie; Schadt, Christopher Warren

2006-01-01

Hydrocarbon contamination of groundwater resources has become a major environmental and human health concern in many parts of the world. Our objectives were to employ both culture and culture-independent techniques to characterize the dynamics of microbial community structure within a fluidized bed reactor used to bioremediate a diesel-contaminated groundwater in a tropical environment. Under normal operating conditions, 97 to 99% of total hydrocarbons were removed with only 14 min hydraulic retention time. Over 25 different cultures were isolated from the treatment unit (96% which utilized diesel constituents as sole carbon source). Approximately 20% of the isolates were also capable ofmore » complete denitrification to nitrogen gas. Sequence analysis of 16S rDNA demonstrated ample diversity with most belonging to the {infinity}, {beta} and {gamma} subdivision of the Proteobacteria, Bacilli, and Actinobacteria groups. Moreover, the genetic constitution of the microbial community was examined at multiple time points with a Functional Gene Array (FGA) containing over 12,000 probes for genes involved in organic degradation and major biogeochemical cycles. Total community DNA was extracted and amplified using an isothermal {phi}29 polymerase-based technique, labeled with Cy5 dye, and hybridized to the arrays in 50% formimide overnight at 50 C. Cluster analysis revealed comparable profiles over the course of treatment suggesting the early selection of a very stable microbial community. A total of 270 genes for organic contaminant degradation (including naphthalene, toluene [aerobic and anaerobic], octane, biphenyl, pyrene, xylene, phenanthrene, and benzene); and 333 genes involved in metabolic activities (nitrite and nitrous oxide reductases [nirS, nirK, and nosZ], dissimilatory sulfite reductases [dsrAB], potential metal reducing C-type cytochromes, and methane monooxygenase [pmoA]) were repeatedly detected. Genes for degradation of MTBE, nitroaromatics and chlorinated compounds were also present, indicating a broad catabolic potential of the treatment unit. FGA's demonstrated the early establishment of a diverse community with concurrent aerobic and anaerobic processes contributing to the bioremediation process.« less

Microbial Diversity and Bioremediation of aHydrocarbon-Contaminated Aquifer (Vega Baja, Puerto Rico)

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

Rodriguez-Martinez, E.M.; Perez, Ernie X.; Schadt, ChristopherW.

2006-09-30

Hydrocarbon contamination of groundwater resources hasbecome a major environmental and human health concern in many parts ofthe world. Our objectives were to employ both culture andculture-independent techniques to characterize the dynamics of microbialcommunity structure within a fluidized bed reactor used to bioremediate adiesel-contaminated groundwater in a tropical environment. Under normaloperating conditions, 97 to 99 percent of total hydrocarbons were removedwith only 14 min hydraulic retention time. Over 25 different cultureswere isolated from the treatment unit (96 percent which utilized dieselconstituents as sole carbon source). Approximately 20 percent of theisolates were also capable of complete denitrification to nitrogen gas.Sequence analysis ofmore » 16S rDNA demonstrated ample diversity with mostbelonging to the infinity, beta and gamma subdivision of theProteobacteria, Bacilli, and Actinobacteria groups. Moreover, the geneticconstitution of the microbial community was examined at multiple timepoints with a Functional Gene Array (FGA) containing over 12,000 probesfor genes involved in organic degradation and major biogeochemicalcycles. Total community DNA was extracted and amplified using anisothermal phi29 polymerase-based technique, labeled with Cy5 dye, andhybridized to the arrays in 50 percent formimide overnight at 50 degreesC. Cluster analysis revealed comparable profiles over the course oftreatment suggesting the early selection of a very stable microbialcommunity. A total of 270 genes for organic contaminant degradation(including naphthalene, toluene [aerobic and anaerobic], octane,biphenyl, pyrene, xylene, phenanthrene, and benzene); and 333 genesinvolved in metabolic activities (nitrite and nitrous oxide reductases[nirS, nirK, and nosZ], dissimilatory sulfite reductases [dsrAB],potential metal reducing C-type cytochromes, and methane monooxygenase[pmoA]) were repeatedly detected. Genes for degradation of MTBE,nitroaromatics and chlorinated compounds werealso present, indicating abroad catabolic potential of the treatment unit. FGA's demonstrated theearly establishment of a diverse community with concurrent aerobic andanaerobic processes contributing to the bioremediationprocess.« less

Assessing the Diversity of Halimeda spp. on Pulley Ridge Mesophotic Reefs

NASA Astrophysics Data System (ADS)

Luzader, R. K.; Baco-Taylor, A.

2016-02-01

The Florida reef system contains an array of organisms that contribute to the development of the reef structure. These include calcifying green macroalgae of the genus Halimeda, which provides important ecosystem services by stabilizing the reefs through calcification. Halimeda is one of several groups of shallow water reef taxa with a depth range that extends into the mesophotic zone. It has been hypothesized the mesophotic reefs may serve as refugia for shallow water taxa impacted by climate change and other anthropogenic stressors. To test this hypothesis, in 2012-2015, the mesophotic reefs of Pulley Ridge and Dry Tortugas were sampled to assess genetic connectivity to the shallow water reefs of the Florida Keys. A diverse array of Halimeda species were represented on Pulley Ridge. Halimeda species are known to be difficult to identify and delineate morphologically and the taxonomy of Halimeda species has been revised several times based on molecular data. Thus, before connectivity of mesophotic Halimeda to shallow populations can be assessed, our first goal is to determine whether there is overlap of any of the Halimeda species between the mesophotic and shallow reefs, and then to determine if any of the species are present in sufficient abundance for population genetics. We sequenced portions of two chloroplast genes commonly used for algal phylogenetics and barcoding, tufA and rbcL, for at least 5 individuals of each morphotype collected on Dry Tortugas and the Pulley Ridge mesophotic reefs. Preliminary results suggest that Halimeda tuna, the species previously reported as the dominant Halimeda species on Pulley Ridge, was relatively uncommon. Morphological results and comparison of initial genetic results to sequences in GenBank suggest that H. goreaui is abundant at the Dry Tortugas site and H. fragilis, H. copiosa and H. discoidea are common on Pulley Ridge, indicating greater Halimeda diversity in the mesophotic reef system than previously documented.

Microbial Diversity and Bioremediation of a Hydrocarbon-Contaminated Aquifer (Vega Baja, Puerto Rico)

PubMed Central

Rodríguez-Martínez, Enid M.; Pérez, Ernie X.; Schadt, Christopher W.; Zhou, Jizhong; Massol-Deyá, Arturo A.

2006-01-01

Hydrocarbon contamination of groundwater resources has become a major environmental and human health concern in many parts of the world. Our objectives were to employ both culture and culture-independent techniques to characterize the dynamics of microbial community structure within a fluidized bed reactor used to bioremediate a diesel-contaminated groundwater in a tropical environment. Under normal operating conditions, 97 to 99% of total hydrocarbons were removed with only 14 min hydraulic retention time. Over 25 different cultures were isolated from the treatment unit (96% which utilized diesel constituents as sole carbon source). Approximately 20% of the isolates were also capable of complete denitrification to nitrogen gas. Sequence analysis of 16S rDNA demonstrated ample diversity with most belonging to the ∝, β and γ subdivision of the Proteobacteria, Bacilli, and Actinobacteria groups. Moreover, the genetic constitution of the microbial community was examined at multiple time points with a Functional Gene Array (FGA) containing over 12,000 probes for genes involved in organic degradation and major biogeochemical cycles. Total community DNA was extracted and amplified using an isothermal φ29 polymerase-based technique, labeled with Cy5 dye, and hybridized to the arrays in 50% formimide overnight at 50°C. Cluster analysis revealed comparable profiles over the course of treatment suggesting the early selection of a very stable microbial community. A total of 270 genes for organic contaminant degradation (including naphthalene, toluene [aerobic and anaerobic], octane, biphenyl, pyrene, xylene, phenanthrene, and benzene); and 333 genes involved in metabolic activities (nitrite and nitrous oxide reductases [nirS, nirK, and nosZ], dissimilatory sulfite reductases [dsrAB], potential metal reducing C-type cytochromes, and methane monooxygenase [pmoA]) were repeatedly detected. Genes for degradation of MTBE, nitroaromatics and chlorinated compounds were also present, indicating a broad catabolic potential of the treatment unit. FGA’s demonstrated the early establishment of a diverse community with concurrent aerobic and anaerobic processes contributing to the bioremediation process. PMID:16968977

Unexpected diversity during community succession in the apple flower microbiome.

PubMed

Shade, Ashley; McManus, Patricia S; Handelsman, Jo

2013-02-26

Despite its importance to the host, the flower microbiome is poorly understood. We report a culture-independent, community-level assessment of apple flower microbial diversity and dynamics. We collected flowers from six apple trees at five time points, starting before flowers opened and ending at petal fall. We applied streptomycin to half of the trees when flowers opened. Assessment of microbial diversity using tag pyrosequencing of 16S rRNA genes revealed that the apple flower communities were rich and diverse and dominated by members of TM7 and Deinococcus-Thermus, phyla about which relatively little is known. From thousands of taxa, we identified six successional groups with coherent dynamics whose abundances peaked at different times before and after bud opening. We designated the groups Pioneer, Early, Mid, Late, Climax, and Generalist communities. The successional pattern was attributed to a set of prevalent taxa that were persistent and gradually changing in abundance. These taxa had significant associations with other community members, as demonstrated with a cooccurrence network based on local similarity analysis. We also detected a set of less-abundant, transient taxa that contributed to general tree-to-tree variability but not to the successional pattern. Communities on trees sprayed with streptomycin had slightly lower phylogenetic diversity than those on unsprayed trees but did not differ in structure or succession. Our results suggest that changes in apple flower microbial community structure are predictable over the life of the flower, providing a basis for ecological understanding and disease management. Flowering plants (angiosperms) represent a diverse group of an estimated 400,000 species, and their successful cultivation is essential to agriculture. Yet fundamental knowledge of flower-associated microbiotas remains largely unknown. Even less well understood are the changes that flower microbial communities experience through time. Flowers are particularly conducive to comprehensive temporal studies because they are, by nature, ephemeral organs. Here, we present the first culture-independent time series of bacterial and archaeal communities associated with the flowers of apple, an economically important crop. We found unexpected diversity on apple flowers, including a preponderance of taxa affiliated with Deinococcus-Thermus and TM7, phyla that are understudied but thought to be tolerant to an array of environmental stresses. Our results also suggest that changes in microbial community structure on the apple flower may be predictable over the life of the flower, providing the basis for ecological understanding and disease management.

Integrated Avalanche Photodiode arrays

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

Harmon, Eric S.

2017-04-18

The present disclosure includes devices for detecting photons, including avalanche photon detectors, arrays of such detectors, and circuits including such arrays. In some aspects, the detectors and arrays include a virtual beveled edge mesa structure surrounded by resistive material damaged by ion implantation and having side wall profiles that taper inwardly towards the top of the mesa structures, or towards the direction from which the ion implantation occurred. Other aspects are directed to masking and multiple implantation and/or annealing steps. Furthermore, methods for fabricating and using such devices, circuits and arrays are disclosed.

Integrated avalanche photodiode arrays

DOEpatents

Harmon, Eric S.

2015-07-07

The present disclosure includes devices for detecting photons, including avalanche photon detectors, arrays of such detectors, and circuits including such arrays. In some aspects, the detectors and arrays include a virtual beveled edge mesa structure surrounded by resistive material damaged by ion implantation and having side wall profiles that taper inwardly towards the top of the mesa structures, or towards the direction from which the ion implantation occurred. Other aspects are directed to masking and multiple implantation and/or annealing steps. Furthermore, methods for fabricating and using such devices, circuits and arrays are disclosed.

Seismic Source Scaling and Discrimination in Diverse Tectonic Environments

DTIC Science & Technology

2009-09-30

3349-3352. Imanishi, K., W. L. Ellsworth, and S. G. Prejean (2004). Earthquake source parameters determined by the SAFOD Pilot Hole seismic array ... seismic discrimination by performing a thorough investigation of* earthquake source scaling using diverse, high-quality datascts from varied tectonic...these corrections has a direct impact on our ability to identify clandestine explosions in the broad regional areas characterized by low seismicity

Michigan`s forests 1993: An analysis. Forest Service resource bulletin

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

Schmidt, T.L.; Spencer, J.S.; Bertsch, R.

1997-02-04

Michigan`s forests are abundant, diverse, healthy, productive, and expanding. These forests make important contributions to the quality of life by providing a wide array of benefits, including wildlife habitat, biological diversity, outdoor recreation, improved air and water quality, and economic resources such as the estimated $12 billion of value added and 200,000 jobs annually supported by forest-based industries/tourism/recreation.

Efficient structures for geosynchronous spacecraft solar arrays. Phase 1, 2 and 3

NASA Astrophysics Data System (ADS)

Adams, L. R.; Hedgepeth, J. M.

1981-09-01

Structural concepts for deploying and supporting lightweight solar-array blankets for geosynchronous electrical power are evaluated. It is recommended that the STACBEAM solar-array system should be the object of further study and detailed evaluation. The STACBEAM system provides high stiffness at low mass, and with the use of a low mass deployment mechanism, full structural properties can be maintained throughout deployment. The stowed volume of the STACBEAM is acceptably small, and its linear deployment characteristic allows periodic attachments to the solar-array blanket to be established in the stowed configuration and maintained during deployment.

Efficient structures for geosynchronous spacecraft solar arrays. Phase 1, 2 and 3

NASA Technical Reports Server (NTRS)

Adams, L. R.; Hedgepeth, J. M.

1981-01-01

Structural concepts for deploying and supporting lightweight solar-array blankets for geosynchronous electrical power are evaluated. It is recommended that the STACBEAM solar-array system should be the object of further study and detailed evaluation. The STACBEAM system provides high stiffness at low mass, and with the use of a low mass deployment mechanism, full structural properties can be maintained throughout deployment. The stowed volume of the STACBEAM is acceptably small, and its linear deployment characteristic allows periodic attachments to the solar-array blanket to be established in the stowed configuration and maintained during deployment.

Characterisation of cuticular nanostructures on surfaces of insects by atomic force microscopy: mining evolution for smart structures

NASA Astrophysics Data System (ADS)

Watson, Gregory S.; Blach, Jolanta A.

2002-11-01

The optical properties of insect nano-structures have been extensively studied. In particular, nano-scale ordered arrays have been reported from studies of the corneal surfaces of some insects and of insect wings showing anti-reflective properties. These arrays have been ascribed to evolutionary adaptation and survival value arising from increased visual capacity and better camouflage against predators. In this study we show that the Atomic Force Microscope (AFM) can effectively reveal and quantify the three dimensional structures of nano-arrays on moth eyes and cicada wings. It is also shown that the arrays present an ideal surface for in situ characterisation of the AFM probe/tip. In addition, a new structure is presented which has been discovered on a termite wing. The structure is similar to that found on the cicada wing, but has a much larger 'lattice parameter' for the ordered array. The function(s) of the array is unknown at present. It could be effective as an anti-reflective coating, but would then be active in the infra-red region of the light spectrum. Alternatively, it may confer evolutionary advantage by virtue of its mechanical strength, or it may improve the aerodynamics of flying. The study demonstrates that natural selection may be a rich source of 'smart' structures.

THz radiation from two electron-beams interaction within a bi-grating and a sub-wavelength holes array composite sandwich structure.

PubMed

Zhang, Yaxin; Zhou, Y; Dong, L

2013-09-23

Two electron-beams' interaction in a sandwich structure composed of a bi-grating and a sub-wavelength holes array is suggested to generate THz radiation in this paper. It shows that this system takes advantage of both bi-grating and sub-wavelength holes array structures. The results demonstrate that surface waves on a bi-grating can couple with mimicking surface plasmons of a sub-wavelength holes array so that the wave-coupling is strong and the field intensity is high in this structure. Moreover, compared with the interaction in the bi-grating structure and sub-wavelength holes array structure, respectively, it shows that in this composite system the two electron-beams' interaction is more efficient and the modulation depth and radiation intensity have been enhanced significantly. The modulation depth and efficiency can reach 22% and 4%, respectively, and the starting current density is only 12 A/cm². This radiation system may provide good opportunities for development of multi-electron beam-driven THz radiation sources.

Thermally-Induced Structural Disturbances of Rigid Panel Solar Arrays

NASA Technical Reports Server (NTRS)

Johnston, John D.; Thornton, Earl A.

1997-01-01

The performance of a significant number of spacecraft has been impacted negatively by attitude disturbances resulting from thermally-induced motions of flexible structures. Recent examples of spacecraft affected by these disturbances include the Hubble Space Telescope (HST) and the Upper Atmosphere Research Satellite (UARS). Thermally-induced structural disturbances occur as the result of rapid changes in thermal loading typically initiated as a satellite exits or enters the Earth's shadow. Temperature differences in flexible appendages give rise to structural deformations, which in turn result in disturbance torques reacting back on the spacecraft. Structures which have proven susceptible to these disturbances include deployable booms and solar arrays. This paper investigates disturbances resulting from thermally-induced deformations of rigid panel solar arrays. An analytical model for the thermal-structural response of the solar array and the corresponding disturbance torque are presented. The effect of these disturbances on the attitude dynamics of a simple spacecraft is then investigated using a coupled system of governing equations which includes the effects of thermally-induced deformations. Numerical results demonstrate the effect of varying solar array geometry on the dynamic response of the system.

The application of structural reliability techniques to plume impingement loading of the Space Station Freedom Photovoltaic Array

NASA Technical Reports Server (NTRS)

Yunis, Isam S.; Carney, Kelly S.

1993-01-01

A new aerospace application of structural reliability techniques is presented, where the applied forces depend on many probabilistic variables. This application is the plume impingement loading of the Space Station Freedom Photovoltaic Arrays. When the space shuttle berths with Space Station Freedom it must brake and maneuver towards the berthing point using its primary jets. The jet exhaust, or plume, may cause high loads on the photovoltaic arrays. The many parameters governing this problem are highly uncertain and random. An approach, using techniques from structural reliability, as opposed to the accepted deterministic methods, is presented which assesses the probability of failure of the array mast due to plume impingement loading. A Monte Carlo simulation of the berthing approach is used to determine the probability distribution of the loading. A probability distribution is also determined for the strength of the array. Structural reliability techniques are then used to assess the array mast design. These techniques are found to be superior to the standard deterministic dynamic transient analysis, for this class of problem. The results show that the probability of failure of the current array mast design, during its 15 year life, is minute.

Do rewardless orchids show a positive relationship between phenotypic diversity and reproductive success?

PubMed

Smithson, Ann; Juillet, Nicolas; Macnair, Mark R; Gigord, Luc D B

2007-02-01

Among rewardless orchids, pollinator sampling behavior has been suggested to drive a positive relationship between population phenotypic variability and absolute reproductive success, and hence population fitness. We tested this hypothesis by constructing experimental arrays using the rewardless orchid Dactylorhiza sambucina, which is dimorphic for corolla color. We found no evidence that polymorphic arrays had higher mean reproductive success than monomorphic arrays for pollinia removal, pollen deposition, or fruit set. For pollinia removal, monomorphic yellow arrays had significantly greater reproductive success, and monomorphic red the least. A tendency for yellow arrays to have higher pollen deposition was also found. We argue that differential population fitness was most likely to reflect differential numbers of pollinators attracted to arrays, through preferential long-distance attraction to arrays with yellow inflorescences. Correlative studies of absolute reproductive success in 52 populations of D. sambucina supported our experimental results. To our knowledge this is the first study to suggest that attraction of a greater number of pollinators to rewardless orchids may be of greater functional importance to population fitness, and thus ecology and conservation, than are the behavioral sequences of individual pollinators.

1-D Metal Nanobead Arrays within Encapsulated Nanowires via a Red-Ox-Induced Dewetting: Mechanism Study by Atom-Probe Tomography.

PubMed

Sun, Zhiyuan; Tzaguy, Avra; Hazut, Ori; Lauhon, Lincoln J; Yerushalmi, Roie; Seidman, David N

2017-12-13

Metal nanoparticle arrays are excellent candidates for a variety of applications due to the versatility of their morphology and structure at the nanoscale. Bottom-up self-assembly of metal nanoparticles provides an important complementary alternative to the traditional top-down lithography method and makes it possible to assemble structures with higher-order complexity, for example, nanospheres, nanocubes, and core-shell nanostructures. Here we present a mechanism study of the self-assembly process of 1-D noble metal nanoparticles arrays, composed of Au, Ag, and AuAg alloy nanoparticles. These are prepared within an encapsulated germanium nanowire, obtained by the oxidation of a metal-germanium nanowire hybrid structure. The resulting structure is a 1-D array of equidistant metal nanoparticles with the same diameter, the so-called nanobead (NB) array structure. Atom-probe tomography and transmission electron microscopy were utilized to investigate the details of the morphological and chemical evolution during the oxidation of the encapsulated metal-germanium nanowire hybrid-structures. The self-assembly of nanoparticles relies on the formation of a metal-germanium liquid alloy and the migration of the liquid alloy into the nanowire, followed by dewetting of the liquid during shape-confined oxidation where the liquid column breaks-up into nanoparticles due to the Plateau-Rayleigh instability. Our results demonstrate that the encapsulating oxide layer serves as a structural scaffold, retaining the overall shape during the eutectic liquid formation and demonstrates the relationship between the oxide mechanical properties and the final structural characteristics of the 1-D arrays. The mechanistic details revealed here provide a versatile tool-box for the bottom-up fabrication of 1-D arrays nanopatterning that can be modified for multiple applications according to the RedOx properties of the material system components.

Continental-shelf Scale Passive Ocean AcousticWaveguide Remote Sensing of Marine Mammals and other Submerged Objects including Detection, Localization, and Classification

NASA Astrophysics Data System (ADS)

Wang, Delin

In this thesis, we develop the basics of the Passive Ocean Acoustic Waveguide Remote Sensing (POAWRS) technique for the instantaneous continental-shelf scale detection, localization and species classification of marine mammal vocalizations. POAWRS uses a large-aperture, densely sampled coherent hydrophone array system with orders of magnitude higher array gain to enhance signal-to-noise ratios (SNR) by coherent beamforming, enabling detection of underwater acoustic signals either two orders of magnitude more distant in range or lower in SNR than a single hydrophone. The ability to employ coherent spatial processing of signals with the POAWRS technology significantly improves areal coverage, enabling detection of oceanic sound sources over instantaneous wide areas spanning 100 km or more in diameter. The POAWRS approach was applied to analyze marine mammal vocalizations from diverse species received on a 160-element Office Naval Research Five Octave Research Array (ONR-FORA) deployed during their feeding season in Fall 2006 in the Gulf of Maine. The species-dependent temporal-spatial distribution of marine mammal vocalizations and correlation to the prey fish distributions have been determined. Furthermore, the probability of detection regions, source level distributions and pulse compression gains of the vocalization signals from diverse marine mammal species have been estimated. We also develop an approach for enhancing the angular resolution and improving bearing estimates of acoustic signals received on a coherent hydrophone array with multiple-nested uniformly-spaced subapertures, such as the ONR-FORA, by nonuniform array beamforming. Finally we develop a low-cost non-oil-filled towable prototype hydrophone array that consists of eight hydrophone elements with real-time data acquisition and 100 m tow cable. The approach demonstrated here will be applied in the development of a full 160 element POAWRS-type low-cost coherent hydrophone array system in the future.

Solid state image sensing arrays

NASA Technical Reports Server (NTRS)

Sadasiv, G.

1972-01-01

The fabrication of a photodiode transistor image sensor array in silicon, and tests on individual elements of the array are described along with design for a scanning system for an image sensor array. The spectral response of p-n junctions was used as a technique for studying the optical-absorption edge in silicon. Heterojunction structures of Sb2S3- Si were fabricated and a system for measuring C-V curves on MOS structures was built.

Application of the Solubility Parameter Concept to the Design of Chemiresistor Arrays

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

Eastman, M.P.; Hughes, R.C.; Jenkins, M.W.

1999-01-11

Arrays of unheated chemically sensitive resistors (chemiresistors) can serve as extremely small, low-power-consumption sensors with simple read-out electronics. We report here results on carbon-loaded polymer composites, as well as polymeric ionic conductors, as chemiresistor sensors. We use the volubility parameter concept to understand and categorize the chemiresistor responses and, in particular, we compare chemiresistors fabricated from polyisobutylene (PIB) to results from PIB-coated acoustic wave sensors. One goal is to examine the possibility that a small number of diverse chemiresistors can sense all possible solvents-the "Universal Solvent Sensor Array". keywords: chemiresistor, volubility parameter, chemical sensor

Synthesis and high catalytic properties of mesoporous Pt nanowire array by novel conjunct template method

NASA Astrophysics Data System (ADS)

Zhong, Yi; Xu, Cai-Ling; Kong, Ling-Bin; Li, Hu-Lin

2008-12-01

A novel conjunct template method for fabricating mesoporous Pt nanowire array through direct current (DC) electrodeposition of Pt into the pores of anodic aluminum oxide (AAO) template on Ti/Si substrate from hexagonal structured lyotropic liquid crystalline phase is demonstrated in this paper. The morphology and structure of as-prepared Pt nanowire array are characterized by field emission scanning electron microscopy (FESEM), transmission electron microscopy (TEM) and X-ray diffraction (XRD). The electrocatalytic properties of Pt nanowire array for methanol are also investigated in detail. The results indicate that Pt nanowire array has the unique mesoporous structure of approximate 40-50 nm in diameter, which resulted in the high surface area and greatly improved electrocatalytic activity for methanol. The mesoporous Pt nanowire array synthesized by the new conjunct template method has a very promising application in portable fuel cell power sources.

Hydrostar Thermal and Structural Deformation Analyses of Antenna Array Concept

NASA Technical Reports Server (NTRS)

Amundsen, Ruth M.; Hope, Drew J.

1998-01-01

The proposed Hydrostar mission used a large orbiting antenna array to demonstrate synthetic aperture technology in space while obtaining global soil moisture data. In order to produce accurate data, the array was required to remain as close as possible to its perfectly aligned placement while undergoing the mechanical and thermal stresses induced by orbital changes. Thermal and structural analyses for a design concept of this antenna array were performed. The thermal analysis included orbital radiation calculations, as well as parametric studies of orbit altitude, material properties and coating types. The thermal results included predicted thermal distributions over the array for several cases. The structural analysis provided thermally-driven deflections based on these cases, as well as based on a 1-g inertial load. In order to minimize the deflections of the array in orbit, the use of XN70, a carbon-reinforced polycyanate composite, was recommended.

Magnetic characteristics of CoPd and FePd antidot arrays on nanoperforated Al2O3 templates

NASA Astrophysics Data System (ADS)

Maximenko, A.; Fedotova, J.; Marszałek, M.; Zarzycki, A.; Zabila, Y.

2016-02-01

Hard magnetic antidot arrays show promising results in context of designing of percolated perpendicular media. In this work the technology of magnetic FePd and CoPd antidot arrays fabrication is presented and correlation between surface morphology, structure and magnetic properties is discussed. CoPd and FePd antidot arrays were fabricated by deposition of Co/Pd and Fe/Pd multilayers (MLs) on porous anodic aluminum oxide templates with bowl-shape cell structure with inclined intercellular regions. FePd ordered L10 structure was obtained by successive vacuum annealing at elevated temperatures (530 °C) and confirmed by XRD analysis. Systematic analysis of magnetization curves evidenced perpendicular magnetic anisotropy of CoPd antidot arrays, while FePd antidot arrays revealed isotropic magnetic anisotropy with increased out-of-plane magnetic contribution. MFM images of antidots showed more complicated contrast, with alternating magnetic dots oriented parallel and antiparallel to tip magnetization moment.

Betavoltaic effect in titanium dioxide nanotube arrays under build-in potential difference

NASA Astrophysics Data System (ADS)

Zhang, Qiang; Chen, Ranbin; San, Haisheng; Liu, Guohua; Wang, Kaiying

2015-05-01

We report the fabrication of sandwich-type metal/TiO2 nanotube (TNT) array/metal structures as well as their betavoltaic effects under build-in voltage through contact potential difference. The sandwiched structure is integrated by immobilized TNT arrays on Ti foil with radioisotope 63Ni planar source on Ni substrate (Ni-63Ni/TNT array/Ti). Under irradiation of the 63Ni source with activity of 8 mCi, the structure (TNT diameter ∼ 130 nm, length ∼ 11 μm) presents optimum energy conversion efficiency of 7.30% with open-circuit voltage of 1.54 V and short-circuit current of 12.43 nA. The TNT arrays exhibit a highly potential for developing betavoltaic batteries due to its wide band gap and nanotube array configuration. The TNT-betavoltaic concept offers a facile solution for micro/nano electronics with high efficiency and long life-time instead of conventional planar junction-type batteries.

High-density SNP assay development for genetic analysis in maritime pine (Pinus pinaster).

PubMed

Plomion, C; Bartholomé, J; Lesur, I; Boury, C; Rodríguez-Quilón, I; Lagraulet, H; Ehrenmann, F; Bouffier, L; Gion, J M; Grivet, D; de Miguel, M; de María, N; Cervera, M T; Bagnoli, F; Isik, F; Vendramin, G G; González-Martínez, S C

2016-03-01

Maritime pine provides essential ecosystem services in the south-western Mediterranean basin, where it covers around 4 million ha. Its scattered distribution over a range of environmental conditions makes it an ideal forest tree species for studies of local adaptation and evolutionary responses to climatic change. Highly multiplexed single nucleotide polymorphism (SNP) genotyping arrays are increasingly used to study genetic variation in living organisms and for practical applications in plant and animal breeding and genetic resource conservation. We developed a 9k Illumina Infinium SNP array and genotyped maritime pine trees from (i) a three-generation inbred (F2) pedigree, (ii) the French breeding population and (iii) natural populations from Portugal and the French Atlantic coast. A large proportion of the exploitable SNPs (2052/8410, i.e. 24.4%) segregated in the mapping population and could be mapped, providing the densest ever gene-based linkage map for this species. Based on 5016 SNPs, natural and breeding populations from the French gene pool exhibited similar level of genetic diversity. Population genetics and structure analyses based on 3981 SNP markers common to the Portuguese and French gene pools revealed high levels of differentiation, leading to the identification of a set of highly differentiated SNPs that could be used for seed provenance certification. Finally, we discuss how the validated SNPs could facilitate the identification of ecologically and economically relevant genes in this species, improving our understanding of the demography and selective forces shaping its natural genetic diversity, and providing support for new breeding strategies. © 2015 John Wiley & Sons Ltd.

Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome

PubMed Central

2013-01-01

Background There is growing evidence for the prevalence of copy number variation (CNV) and its role in phenotypic variation in many eukaryotic species. Here we use array comparative genomic hybridization to explore the extent of this type of structural variation in domesticated barley cultivars and wild barleys. Results A collection of 14 barley genotypes including eight cultivars and six wild barleys were used for comparative genomic hybridization. CNV affects 14.9% of all the sequences that were assessed. Higher levels of CNV diversity are present in the wild accessions relative to cultivated barley. CNVs are enriched near the ends of all chromosomes except 4H, which exhibits the lowest frequency of CNVs. CNV affects 9.5% of the coding sequences represented on the array and the genes affected by CNV are enriched for sequences annotated as disease-resistance proteins and protein kinases. Sequence-based comparisons of CNV between cultivars Barke and Morex provided evidence that DNA repair mechanisms of double-strand breaks via single-stranded annealing and synthesis-dependent strand annealing play an important role in the origin of CNV in barley. Conclusions We present the first catalog of CNVs in a diploid Triticeae species, which opens the door for future genome diversity research in a tribe that comprises the economically important cereal species wheat, barley, and rye. Our findings constitute a valuable resource for the identification of CNV affecting genes of agronomic importance. We also identify potential mechanisms that can generate variation in copy number in plant genomes. PMID:23758725

Surveying the CGM and IGM across 4 orders of magnitude in environmental density

NASA Astrophysics Data System (ADS)

Burchett, Joseph

2017-08-01

Environment matters when it comes to galaxy evolution, and the mechanisms driving this evolution are reflected in the diffuse gas residing within the large-scale structures enveloping the cosmic galaxy population. QSO absorption lines effectively probe the circumgalactic medium (CGM) and intragroup and intracluster media, and work thus far hints at profound environmental effects on the CGM. However, sample sizes remain small, and a unifying picture of the gas characteristics across diverse environments has yet to emerge. Within the Sloan Digital Sky Survey, we have identified a sample volume containing a remarkable diversity in large-scale environment with an array of voids, >10,000 groups, several filaments, and 5 clusters, including the Coma Supercluster and CfA Great Wall. Leveraging the Hubble Spectroscopic Legacy Archive (HSLA), we propose a study using >360 background QSOs probing this volume to study the effects of large-scale environment on CGM and intergalactic medium (IGM) gas. The z = 0.019-0.028 spectroscopic galaxy sample is uniformly complete to galaxies L > 0.03 L* and, with the HSLA, produces 200 galaxy/sightline pairs within 300-kpc impact parameters across a wide range of environmental densities and structures.Upon quantifying the galaxy environment and identifying/measuring the QSO absorption lines at z = 0.019-0.028, we will pursue the following primary science goals:1. Constrain the CGM/IGM physical conditions across four orders of magnitude in galaxy density2. Compare ionic abundances and ionization states in the CGM of galaxies in filaments vs. voids3. Statistically investigate the IGM/CGM gas properties from structure to structure

Root trait diversity, molecular marker diversity, and trait-marker associations in a core collection of Lupinus angustifolius.

PubMed

Chen, Yinglong; Shan, Fucheng; Nelson, Matthew N; Siddique, Kadambot Hm; Rengel, Zed

2016-06-01

Narrow-leafed lupin (Lupinus angustifolius L.) is the predominant grain legume crop in southern Australia, contributing half of the total grain legume production of Australia. Its yield in Australia is hampered by a range of subsoil constraints. The adaptation of lupin genotypes to subsoil constraints may be improved by selecting for optimal root traits from new and exotic germplasm sources. We assessed root trait diversity and genetic diversity of a core collection of narrow-leafed lupin (111 accessions) using 191 Diversity Arrays Technology (DArT) markers. The genetic relationship among accessions was determined using the admixture model in STRUCTURE. Thirty-eight root-associated traits were characterized, with 21 having coefficient of variation values >0.5. Principal coordinate analysis and cluster analysis of the DArT markers revealed broad diversity among the accessions. An ad hoc statistics calculation resulted in 10 distinct populations with significant differences among and within them (P < 0.001). The mixed linear model test in TASSEL showed a significant association between all root traits and some DArT markers, with the numbers of markers associated with an individual trait ranging from 2 to 13. The percentage of phenotypic variation explained by any one marker ranged from 6.4 to 21.8%, with 15 associations explaining >10% of phenotypic variation. The genetic variation values ranged from 0 to 7994, with 23 associations having values >240. Root traits such as deeper roots and lateral root proliferation at depth would be useful for this species for improved adaptation to drier soil conditions. This study offers opportunities for discovering useful root traits that can be used to increase the yield of Australian cultivars across variable environmental conditions. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Root trait diversity, molecular marker diversity, and trait-marker associations in a core collection of Lupinus angustifolius

PubMed Central

Chen, Yinglong; Shan, Fucheng; Nelson, Matthew N; Siddique, Kadambot HM; Rengel, Zed

2016-01-01

Narrow-leafed lupin (Lupinus angustifolius L.) is the predominant grain legume crop in southern Australia, contributing half of the total grain legume production of Australia. Its yield in Australia is hampered by a range of subsoil constraints. The adaptation of lupin genotypes to subsoil constraints may be improved by selecting for optimal root traits from new and exotic germplasm sources. We assessed root trait diversity and genetic diversity of a core collection of narrow-leafed lupin (111 accessions) using 191 Diversity Arrays Technology (DArT) markers. The genetic relationship among accessions was determined using the admixture model in STRUCTURE. Thirty-eight root-associated traits were characterized, with 21 having coefficient of variation values >0.5. Principal coordinate analysis and cluster analysis of the DArT markers revealed broad diversity among the accessions. An ad hoc statistics calculation resulted in 10 distinct populations with significant differences among and within them (P < 0.001). The mixed linear model test in TASSEL showed a significant association between all root traits and some DArT markers, with the numbers of markers associated with an individual trait ranging from 2 to 13. The percentage of phenotypic variation explained by any one marker ranged from 6.4 to 21.8%, with 15 associations explaining >10% of phenotypic variation. The genetic variation values ranged from 0 to 7994, with 23 associations having values >240. Root traits such as deeper roots and lateral root proliferation at depth would be useful for this species for improved adaptation to drier soil conditions. This study offers opportunities for discovering useful root traits that can be used to increase the yield of Australian cultivars across variable environmental conditions. PMID:27049020

PRINCEPS: A computer-based approach to the structural description and recognition of trends within structural databases, and its application to the Ce-Ni-Si System

DOE PAGES

Guo, Yiming; Fredrickson, Daniel C.

2016-04-01

Intermetallic crystal structures offer an enormous structural diversity, with an endless array of structural motifs whose connection to stability and physical properties are often mysterious. Making sense of the often complex crystal structures that arise here, developing a clear structural description, and identifying connections to other phases can be laborious and require an encyclopedic knowledge of structure types. In this Article, we present PRINCEPS, an algorithm based on a new coordination environment projection scheme that facilitates the structural analysis and comparison of such crystal structures. We demonstrate the potential of this approach by applying it to the complex Ce-Ni-Si ternarymore » system, whose 17 binary and 21 ternary phases would present a daunting challenge to one seeking to understand the system by manual inspection (but has nonetheless been well-described through the heroic efforts of previous researchers). With the help of PRINCEPS, most of the ternary phases in this system can be rationalized as intergrowths of simple structural fragments, and grouped into a handful of structural series (with some outliers). Lastly, these results illustrate how the PRINCEPS approach can be used to organize a vast collection of crystal structures into structurally meaningful families, and guide the description of complex atomic arrangements.« less

High thermoelectric properties of (Sb, Bi)2Te3 nanowire arrays by tilt-structure engineering

NASA Astrophysics Data System (ADS)

Tan, Ming; Hao, Yanming; Deng, Yuan; Chen, Jingyi

2018-06-01

In this paper, we present an innovative tilt-structure design concept for (Sb, Bi)2Te3 nanowire array assembled by high-quality nanowires with well oriented growth, utilizing a simple vacuum thermal evaporation technique. The unusual tilt-structure (Sb, Bi)2Te3 nanowire array with a tilted angle of 45° exhibits a high thermoelectric dimensionless figure-of-merit ZT = 1.72 at room temperature. The relatively high ZT value in contrast to that of previously reported (Sb, Bi)2Te3 materials and the vertical (Sb, Bi)2Te3 nanowire arrays evidently reveals the crucial role of the unique tilt-structure in favorably influencing carrier and phonon transport properties, resulting in a significantly improved ZT value. The transport mechanism of such tilt-structure is proposed and investigated. This method opens a new approach to optimize nano-structure in thin films for next-generation thermoelectric materials and devices.

Ultrahigh density array of vertically aligned small-molecular organic nanowires on arbitrary substrates.

PubMed

Starko-Bowes, Ryan; Pramanik, Sandipan

2013-06-18

In recent years π-conjugated organic semiconductors have emerged as the active material in a number of diverse applications including large-area, low-cost displays, photovoltaics, printable and flexible electronics and organic spin valves. Organics allow (a) low-cost, low-temperature processing and (b) molecular-level design of electronic, optical and spin transport characteristics. Such features are not readily available for mainstream inorganic semiconductors, which have enabled organics to carve a niche in the silicon-dominated electronics market. The first generation of organic-based devices has focused on thin film geometries, grown by physical vapor deposition or solution processing. However, it has been realized that organic nanostructures can be used to enhance performance of above-mentioned applications and significant effort has been invested in exploring methods for organic nanostructure fabrication. A particularly interesting class of organic nanostructures is the one in which vertically oriented organic nanowires, nanorods or nanotubes are organized in a well-regimented, high-density array. Such structures are highly versatile and are ideal morphological architectures for various applications such as chemical sensors, split-dipole nanoantennas, photovoltaic devices with radially heterostructured "core-shell" nanowires, and memory devices with a cross-point geometry. Such architecture is generally realized by a template-directed approach. In the past this method has been used to grow metal and inorganic semiconductor nanowire arrays. More recently π-conjugated polymer nanowires have been grown within nanoporous templates. However, these approaches have had limited success in growing nanowires of technologically important π-conjugated small molecular weight organics, such as tris-8-hydroxyquinoline aluminum (Alq3), rubrene and methanofullerenes, which are commonly used in diverse areas including organic displays, photovoltaics, thin film transistors and spintronics. Recently we have been able to address the above-mentioned issue by employing a novel "centrifugation-assisted" approach. This method therefore broadens the spectrum of organic materials that can be patterned in a vertically ordered nanowire array. Due to the technological importance of Alq3, rubrene and methanofullerenes, our method can be used to explore how the nanostructuring of these materials affects the performance of aforementioned organic devices. The purpose of this article is to describe the technical details of the above-mentioned protocol, demonstrate how this process can be extended to grow small-molecular organic nanowires on arbitrary substrates and finally, to discuss the critical steps, limitations, possible modifications, trouble-shooting and future applications.

International Space Station 2A Array Modal Analysis

NASA Technical Reports Server (NTRS)

Laible, Michael; Fitzpatrick, Kristin; Grygier, Michael

2012-01-01

On December 9th 2009, the International Space Station (ISS) 2A solar array mast experienced prolonged longeron shadowing during a Soyuz undocking. Analytical reconstruction of induced thermal and dynamic structural loads showed an exceedance of the mast buckling limit. Possible structural damage to the solar array mast could have occurred during this event. A Low fidelity video survey of the 2A mast showed no obvious damage of the mast longerons or battens. The decision was made to conduct an on-orbit dynamic test of the 2A array on December 18th, 2009. The test included thruster pluming on the array while photogrammetry data was recorded. The test was similar to other Dedicated Thruster Firings (DTFs) that were performed to measure structural frequency and damping of a solar array. Results of the DTF indicated lower frequency mast modes than model predictions, thus leading to speculation of mast damage. A detailed nonlinear analysis was performed on the 2A array model to assess possible solutions to modal differences. The setup of the parametric nonlinear trade study included the use of a detailed array model and the reduced mass and stiffness matrices of the entire ISS being applied to the array interface. The study revealed that the array attachment structure is nonlinear and thus was the source of error in the model prediction of mast modes. In addition, a detailed study was performed to determine mast mode sensitivity to mast longeron damage. This sensitivity study was performed to assess if the ISS program has sufficient instrumentation for mast damage detection.

Biologically Inspired Micro-Flight Research

NASA Technical Reports Server (NTRS)

Raney, David L.; Waszak, Martin R.

2003-01-01

Natural fliers demonstrate a diverse array of flight capabilities, many of which are poorly understood. NASA has established a research project to explore and exploit flight technologies inspired by biological systems. One part of this project focuses on dynamic modeling and control of micro aerial vehicles that incorporate flexible wing structures inspired by natural fliers such as insects, hummingbirds and bats. With a vast number of potential civil and military applications, micro aerial vehicles represent an emerging sector of the aerospace market. This paper describes an ongoing research activity in which mechanization and control concepts for biologically inspired micro aerial vehicles are being explored. Research activities focusing on a flexible fixed- wing micro aerial vehicle design and a flapping-based micro aerial vehicle concept are presented.

Silyl Glyoxylates. Conception and Realization of Flexible Conjunctive Reagents for Multicomponent Coupling

PubMed Central

Boyce, Gregory R.; Greszler, Stephen N.; Linghu, Xin; Malinowski, Justin T.; Nicewicz, David A.; Satterfield, Andrew D.; Schmitt, Daniel C.; Steward, Kimberly M.

2012-01-01

This Perspective describes the discovery and development of silyl glyoxylates, a new family of conjunctive reagents for use in multicomponent coupling reactions. The selection of the nucleophilic and electrophilic components determines whether the silyl glyoxylate reagent will function as a synthetic equivalent to the dipolar glycolic acid synthon, the glyoxylate anion synthon, or the α-keto ester homoenolate synthon. The ability to select for any of these reaction modes has translated to excellent structural diversity in the derived three- and four-component coupling adducts. Preliminary findings on the development of catalytic reactions using these reagents are detailed, as are the design and discovery of new reactions directed toward particular functional group arrays embedded within bioactive natural products. PMID:22414181

Construction of RNA nanocages by re-engineering the packaging RNA of Phi29 bacteriophage

NASA Astrophysics Data System (ADS)

Hao, Chenhui; Li, Xiang; Tian, Cheng; Jiang, Wen; Wang, Guansong; Mao, Chengde

2014-05-01

RNA nanotechnology promises rational design of RNA nanostructures with wide array of structural diversities and functionalities. Such nanostructures could be used in applications such as small interfering RNA delivery and organization of in vivo chemical reactions. Though having impressive development in recent years, RNA nanotechnology is still quite limited and its programmability and complexity could not rival the degree of its closely related cousin: DNA nanotechnology. Novel strategies are needed for programmed RNA self-assembly. Here, we have assembled RNA nanocages by re-engineering a natural, biological RNA motif: the packaging RNA of phi29 bacteriophage. The resulting RNA nanostructures have been thoroughly characterized by gel electrophoresis, cryogenic electron microscopy imaging and dynamic light scattering.

An expanding universe of small proteins.

PubMed

Hobbs, Errett C; Fontaine, Fanette; Yin, Xuefeng; Storz, Gisela

2011-04-01

Historically, small proteins (sproteins) of less than 50 amino acids, in their final processed forms or genetically encoded as such, have been understudied. However, both serendipity and more recent focused efforts have led to the identification of a number of new sproteins in both Gram-negative and Gram-positive bacteria. Increasing evidence demonstrates that sproteins participate in a wide array of cellular processes and exhibit great diversity in their mechanisms of action, yet general principles of sprotein function are emerging. This review highlights examples of sproteins that participate in cell signaling, act as antibiotics and toxins, and serve as structural proteins. We also describe roles for sproteins in detecting and altering membrane features, acting as chaperones, and regulating the functions of larger proteins. Published by Elsevier Ltd.

Organized energetic composites based on micro and nanostructures and methods thereof

DOEpatents

Gash, Alexander E.; Han, Thomas Yong-Jin; Sirbuly, Donald J.

2012-09-04

An ordered energetic composite structure according to one embodiment includes an ordered array of metal fuel portions; and an oxidizer in gaps located between the metal fuel portions. An ordered energetic composite structure according to another embodiment includes at least one metal fuel portion having an ordered array of nanopores; and an oxidizer in the nanopores. A method for forming an ordered energetic composite structure according to one embodiment includes forming an ordered array of metal fuel portions; and depositing an oxidizer in gaps located between the metal fuel portions. A method for forming an ordered energetic composite structure according to another embodiment includes forming an ordered array of nanopores in at least one metal fuel portion; and depositing an oxidizer in the nanopores.

Limited genetic diversity among Sarcocystis neurona strains infecting southern sea otters precludes distinction between marine and terrestrial isolates

PubMed Central

Wendte, J.M.; Miller, M.A.; Nandra, A.K.; Peat, S.M.; Crosbie, P.R.; Conrad, P.A.; Grigg, M.E.

2010-01-01

Sarcocystis neurona is an apicomplexan parasite identified as a cause of fatal neurological disease in the threatened southern sea otter (Enhydra lutris nereis). In an effort to characterize virulent S. neurona strains circulating in the marine ecosystem, this study developed a range of markers relevant for molecular genotyping. Highly conserved sequences within the 18S ribosomal gene array, the plastid-encoded RNA polymerase (RPOb) and the cytochrome c oxidase subunit 1 mitochondrial gene (CO1) were assessed for their ability to distinguish isolates at the genus and species level. For within-species comparisons, five surface antigens (SnSAG1-SnSAG5) and one high resolution microsatellite marker (Sn9) were developed as genotyping markers to evaluate intra-strain diversity. Molecular analysis at multiple loci revealed insufficient genetic diversity to distinguish terrestrial isolates from strains infecting marine mammals. Furthermore, SnSAG specific primers applied against DNA from the closely related species, Sarcocystis falcatula, lead to the discovery of highly similar orthologs to SnSAG2, 3, and 4, calling into question the specificity of diagnostic tests based on these antigens. The results of this study suggest a population genetic structure for S. neurona similar to that reported for the related parasite, Toxoplasma gondii, dominated by a limited number of successful genotypes. PMID:20071081

Local phylogenetic divergence and global evolutionary convergence of skull function in reef fishes of the family Labridae

PubMed Central

Westneat, Mark W; Alfaro, Michael E; Wainwright, Peter C; Bellwood, David R; Grubich, Justin R; Fessler, Jennifer L; Clements, Kendall D; Smith, Lydia L

2005-01-01

The Labridae is one of the most structurally and functionally diversified fish families on coral and rocky reefs around the world, providing a compelling system for examination of evolutionary patterns of functional change. Labrid fishes have evolved a diverse array of skull forms for feeding on prey ranging from molluscs, crustaceans, plankton, detritus, algae, coral and other fishes. The species richness and diversity of feeding ecology in the Labridae make this group a marine analogue to the cichlid fishes. Despite the importance of labrids to coastal reef ecology, we lack evolutionary analysis of feeding biomechanics among labrids. Here, we combine a molecular phylogeny of the Labridae with the biomechanics of skull function to reveal a broad pattern of repeated convergence in labrid feeding systems. Mechanically fast jaw systems have evolved independently at least 14 times from ancestors with forceful jaws. A repeated phylogenetic pattern of functional divergence in local regions of the labrid tree produces an emergent family-wide pattern of global convergence in jaw function. Divergence of close relatives, convergence among higher clades and several unusual ‘breakthroughs’ in skull function characterize the evolution of functional complexity in one of the most diverse groups of reef fishes. PMID:16024356

Genomic diversity and population structure of three autochthonous Greek sheep breeds assessed with genome-wide DNA arrays.

PubMed

Michailidou, S; Tsangaris, G; Fthenakis, G C; Tzora, A; Skoufos, I; Karkabounas, S C; Banos, G; Argiriou, A; Arsenos, G

2018-06-01

In the present study, genome-wide genotyping was applied to characterize the genetic diversity and population structure of three autochthonous Greek breeds: Boutsko, Karagouniko and Chios. Dairy sheep are among the most significant livestock species in Greece numbering approximately 9 million animals which are characterized by large phenotypic variation and reared under various farming systems. A total of 96 animals were genotyped with the Illumina's OvineSNP50K microarray beadchip, to study the population structure of the breeds and develop a specialized panel of single-nucleotide polymorphisms (SNPs), which could distinguish one breed from the others. Quality control on the dataset resulted in 46,125 SNPs, which were used to evaluate the genetic structure of the breeds. Population structure was assessed through principal component analysis (PCA) and admixture analysis, whereas inbreeding was estimated based on runs of homozygosity (ROHs) coefficients, genomic relationship matrix inbreeding coefficients (F GRM ) and patterns of linkage disequilibrium (LD). Associations between SNPs and breeds were analyzed with different inheritance models, to identify SNPs that distinguish among the breeds. Results showed high levels of genetic heterogeneity in the three breeds. Genetic distances among breeds were modest, despite their different ancestries. Chios and Karagouniko breeds were more genetically related to each other compared to Boutsko. Analysis revealed 3802 candidate SNPs that can be used to identify two-breed crosses and purebred animals. The present study provides, for the first time, data on the genetic background of three Greek indigenous dairy sheep breeds as well as a specialized marker panel that can be applied for traceability purposes as well as targeted genetic improvement schemes and conservation programs.

Structural diversity promotes productivity of mixed, uneven-aged forests in southwestern Germany.

PubMed

Dănescu, Adrian; Albrecht, Axel T; Bauhus, Jürgen

2016-10-01

Forest diversity-productivity relationships have been intensively investigated in recent decades. However, few studies have considered the interplay between species and structural diversity in driving productivity. We analyzed these factors using data from 52 permanent plots in southwestern Germany with more than 53,000 repeated tree measurements. We used basal area increment as a proxy for productivity and hypothesized that: (1) structural diversity would increase tree and stand productivity, (2) diversity-productivity relationships would be weaker for species diversity than for structural diversity, and (3) species diversity would also indirectly impact stand productivity via changes in size structure. We measured diversity using distance-independent indices. We fitted separate linear mixed-effects models for fir, spruce and beech at the tree level, whereas at the stand level we pooled all available data. We tested our third hypothesis using structural equation modeling. Structural and species diversity acted as direct and independent drivers of stand productivity, with structural diversity being a slightly better predictor. Structural diversity, but not species diversity, had a significant, albeit asymmetric, effect on tree productivity. The functioning of structurally diverse, mixed forests is influenced by both structural and species diversity. These sources of trait diversity contribute to increased vertical stratification and crown plasticity, which in turn diminish competitive interferences and lead to more densely packed canopies per unit area. Our research highlights the positive effects of species diversity and structural diversity on forest productivity and ecosystem dynamics.

Seismic array processing and computational infrastructure for improved monitoring of Alaskan and Aleutian seismicity and volcanoes

NASA Astrophysics Data System (ADS)

Lindquist, Kent Gordon

We constructed a near-real-time system, called Iceworm, to automate seismic data collection, processing, storage, and distribution at the Alaska Earthquake Information Center (AEIC). Phase-picking, phase association, and interprocess communication components come from Earthworm (U.S. Geological Survey). A new generic, internal format for digital data supports unified handling of data from diverse sources. A new infrastructure for applying processing algorithms to near-real-time data streams supports automated information extraction from seismic wavefields. Integration of Datascope (U. of Colorado) provides relational database management of all automated measurements, parametric information for located hypocenters, and waveform data from Iceworm. Data from 1997 yield 329 earthquakes located by both Iceworm and the AEIC. Of these, 203 have location residuals under 22 km, sufficient for hazard response. Regionalized inversions for local magnitude in Alaska yield Msb{L} calibration curves (logAsb0) that differ from the Californian Richter magnitude. The new curve is 0.2\\ Msb{L} units more attenuative than the Californian curve at 400 km for earthquakes north of the Denali fault. South of the fault, and for a region north of Cook Inlet, the difference is 0.4\\ Msb{L}. A curve for deep events differs by 0.6\\ Msb{L} at 650 km. We expand geographic coverage of Alaskan regional seismic monitoring to the Aleutians, the Bering Sea, and the entire Arctic by initiating the processing of four short-period, Alaskan seismic arrays. To show the array stations' sensitivity, we detect and locate two microearthquakes that were missed by the AEIC. An empirical study of the location sensitivity of the arrays predicts improvements over the Alaskan regional network that are shown as map-view contour plots. We verify these predictions by detecting an Msb{L} 3.2 event near Unimak Island with one array. The detection and location of four representative earthquakes illustrates the expansion of geographic coverage from array processing. Measurements at the arrays of systematic azimuth residuals, between 5sp° and 50sp° from 203 Aleutian events, reveal significant effects of heterogeneous structure on wavefields. Finally, algorithms to automatically detect earthquakes in continuous array data are demonstrated with the detection of an Aleutian earthquake.

Semiconductor nanowire devices: Novel morphologies and applications to electrogenic biological systems

NASA Astrophysics Data System (ADS)

Timko, Brian Paul

The interface between nanoscale semiconductors and biological systems represents a powerful means for molecular-scale, two-way communication between these two diverse yet complementary systems. In this thesis, I present a general methodology for the synthesis of semiconductor nanowires with rationally-defined material composition and geometry. Specifically, I demonstrate that this technique can be used to fabricate silicon nanowires, hollow nanostructures (e.g. nanotubes, nanocones and branched tubular networks), and Ge/Si heterostructures that exhibit 1D hole gasses. Using bottom-up assembly techniques, nanostructures are subsequently built into arrays containing up to tens of nanowire field-effect transistors (NW-FETs) that exhibit exquisite sensitivity to local charges. Significantly, this robust assembly technique enables integration of disparate materials (e.g. n- and p-type silicon nanowires) on virtually any type of substrate. These arrays are particularly useful for integration with biological systems. I will demonstrate that at the single-cell level, silicon nanowire device arrays can be integrated with mammalian neurons. Discrete hybrid structures enable neuronal stimulation and recording at the axon, dendrite, or soma with high sensitivity and spatial resolution, while aligned arrays containing up to 50 devices can be used to measure the speed and temporal evolution of signals or to interact with a single cell as multiple inputs and outputs. I analyze the shape and magnitude of reported signals, and place within the context of previously reported results. Hybrid interfaces can also be extended to entire organs such as embryonic chicken hearts. NW-FET signals are synchronized with the beating heart, and the signal amplitude is directly related to the device sensitivity. Multiplexed measurements made from NW-FET arrays further show that signal propagation across the myocardium can be mapped, with a potential resolution significantly better than microelectrode techniques. I exploit the unique capability of the bottom-up approach to fabricate NW-FET arrays on flexible and transparent plastic substrates, and demonstrate that these novel device arrays enable signal recording in a number of conformations as well as registration of devices to the heart surface. Taken together, these findings demonstrate that nanowire device arrays are a robust platform for studying electrically-active systems at the single-cell or whole-tissue level, and could enable fundamental studies of cellular-level biophysics, real-time drug assays, and novel implants.

Rapid Assessment of Contaminants and Interferences in Mass Spectrometry Data Using Skyline

NASA Astrophysics Data System (ADS)

Rardin, Matthew J.

2018-04-01

Proper sample preparation in proteomic workflows is essential to the success of modern mass spectrometry experiments. Complex workflows often require reagents which are incompatible with MS analysis (e.g., detergents) necessitating a variety of sample cleanup procedures. Efforts to understand and mitigate sample contamination are a continual source of disruption with respect to both time and resources. To improve the ability to rapidly assess sample contamination from a diverse array of sources, I developed a molecular library in Skyline for rapid extraction of contaminant precursor signals using MS1 filtering. This contaminant template library is easily managed and can be modified for a diverse array of mass spectrometry sample preparation workflows. Utilization of this template allows rapid assessment of sample integrity and indicates potential sources of contamination. [Figure not available: see fulltext.

Synaptic molecular imaging in spared and deprived columns of mouse barrel cortex with array tomography

PubMed Central

Weiler, Nicholas C; Collman, Forrest; Vogelstein, Joshua T; Burns, Randal; Smith, Stephen J

2014-01-01

A major question in neuroscience is how diverse subsets of synaptic connections in neural circuits are affected by experience dependent plasticity to form the basis for behavioral learning and memory. Differences in protein expression patterns at individual synapses could constitute a key to understanding both synaptic diversity and the effects of plasticity at different synapse populations. Our approach to this question leverages the immunohistochemical multiplexing capability of array tomography (ATomo) and the columnar organization of mouse barrel cortex to create a dataset comprising high resolution volumetric images of spared and deprived cortical whisker barrels stained for over a dozen synaptic molecules each. These dataset has been made available through the Open Connectome Project for interactive online viewing, and may also be downloaded for offline analysis using web, Matlab, and other interfaces. PMID:25977797

Synaptic molecular imaging in spared and deprived columns of mouse barrel cortex with array tomography.

PubMed

Weiler, Nicholas C; Collman, Forrest; Vogelstein, Joshua T; Burns, Randal; Smith, Stephen J

2014-01-01

A major question in neuroscience is how diverse subsets of synaptic connections in neural circuits are affected by experience dependent plasticity to form the basis for behavioral learning and memory. Differences in protein expression patterns at individual synapses could constitute a key to understanding both synaptic diversity and the effects of plasticity at different synapse populations. Our approach to this question leverages the immunohistochemical multiplexing capability of array tomography (ATomo) and the columnar organization of mouse barrel cortex to create a dataset comprising high resolution volumetric images of spared and deprived cortical whisker barrels stained for over a dozen synaptic molecules each. These dataset has been made available through the Open Connectome Project for interactive online viewing, and may also be downloaded for offline analysis using web, Matlab, and other interfaces.

Non-invasive measurement of thyroid hormone in feces of a diverse array of avian and mammalian species.

PubMed

Wasser, Samuel K; Azkarate, Jurgi Cristòbal; Booth, Rebecca K; Hayward, Lisa; Hunt, Kathleen; Ayres, Katherine; Vynne, Carly; Gobush, Kathleen; Canales-Espinosa, Domingo; Rodríguez-Luna, Ernesto

2010-08-01

We developed and validated a non-invasive thyroid hormone measure in feces of a diverse array of birds and mammals. An I(131) radiolabel ingestion study in domestic dogs coupled with High Pressure Liquid Chromatography (HPLC) analysis, showed that peak excretion in feces occurred at 24-48h post-ingestion, with I(131)-labelled thyroid hormone metabolites excreted primarily as triiodothyronine (T3) and relatively little thyroxine (T4), at all excretion times examined. The immunoreactive T3 profile across these same HPLC fractions closely corresponded with the I(131) radioactive profile. By contrast, the T4 immunoreactive profile was disproportionately high, suggesting that T4 excretion included a high percentage of T4 stores. We optimized and validated T3 and T4 extraction and assay methods in feces of wild northern spotted owls, African elephants, howler monkeys, caribou, moose, wolf, maned wolf, killer whales and Steller sea lions. We explained 99% of the variance in high and low T3 concentrations derived from species-specific sample pools, after controlling for species and the various extraction methods tested. Fecal T3 reflected nutritional deficits in two male and three female howler monkeys held in captivity for translocation from a highly degraded habitat. Results suggest that thyroid hormone can be accurately and reliably measured in feces, providing important indices for environmental physiology across a diverse array of birds and mammals. Copyright 2010 Elsevier Inc. All rights reserved.

Evaluation of Bovine High-Density SNP Genotyping Array in Indigenous Dairy Cattle Breeds.

PubMed

Dash, S; Singh, A; Bhatia, A K; Jayakumar, S; Sharma, A; Singh, S; Ganguly, I; Dixit, S P

2018-04-03

In total 52 samples of Sahiwal ( 19 ), Tharparkar ( 17 ), and Gir ( 16 ) were genotyped by using BovineHD SNP chip to analyze minor allele frequency (MAF), genetic diversity, and linkage disequilibrium among these cattle. The common SNPs of BovineHD and 54K SNP Chips were also extracted and evaluated for their performance. Only 40%-50% SNPs of these arrays was found informative for genetic analysis in these cattle breeds. The overall mean of MAF for SNPs of BovineHD SNPChip was 0.248 ± 0.006, 0.241 ± 0.007, and 0.242 ± 0.009 in Sahiwal, Tharparkar and Gir, respectively, while that for 54K SNPs was on lower side. The average Reynold's genetic distance between breeds ranged from 0.042 to 0.055 based on BovineHD Beadchip, and from 0.052 to 0.084 based on 54K SNP Chip. The estimates of genetic diversity based on HD and 54K chips were almost same and, hence, low density chip seems to be good enough to decipher genetic diversity of these cattle breeds. The linkage disequilibrium started decaying (r 2  < 0.2) at 140 kb inter-marker distance and, hence, a 20K low density customized SNP array from HD chip could be designed for genomic selection in these cattle else the 54K Bead Chip as such will be useful.

Combination of RNAseq and SNP nanofluidic array reveals the center of genetic diversity of cacao pathogen Moniliophthora roreri in the upper Magdalena Valley of Colombia and its clonality

USDA-ARS?s Scientific Manuscript database

Moniliophthora roreri is the fungal pathogen that causes frosty pod rot (FPR) disease of Theobroma cacao L., the source of chocolate. FPR occurs in most of the cacao producing countries in the Western Hemisphere, causing yield losses up to 80%. Genetic diversity within the FPR pathogen population ma...

Diversity and evolution of centromere repeats in the maize genome.

PubMed

Bilinski, Paul; Distor, Kevin; Gutierrez-Lopez, Jose; Mendoza, Gabriela Mendoza; Shi, Jinghua; Dawe, R Kelly; Ross-Ibarra, Jeffrey

2015-03-01

Centromere repeats are found in most eukaryotes and play a critical role in kinetochore formation. Though centromere repeats exhibit considerable diversity both within and among species, little is understood about the mechanisms that drive centromere repeat evolution. Here, we use maize as a model to investigate how a complex history involving polyploidy, fractionation, and recent domestication has impacted the diversity of the maize centromeric repeat CentC. We first validate the existence of long tandem arrays of repeats in maize and other taxa in the genus Zea. Although we find considerable sequence diversity among CentC copies genome-wide, genetic similarity among repeats is highest within these arrays, suggesting that tandem duplications are the primary mechanism for the generation of new copies. Nonetheless, clustering analyses identify similar sequences among distant repeats, and simulations suggest that this pattern may be due to homoplasious mutation. Although the two ancestral subgenomes of maize have contributed nearly equal numbers of centromeres, our analysis shows that the majority of all CentC repeats derive from one of the parental genomes, with an even stronger bias when examining the largest assembled contiguous clusters. Finally, by comparing maize with its wild progenitor teosinte, we find that the abundance of CentC likely decreased after domestication, while the pericentromeric repeat Cent4 has drastically increased.

Challenges and the state of the technology for printed sensor arrays for structural monitoring

NASA Astrophysics Data System (ADS)

Joshi, Shiv; Bland, Scott; DeMott, Robert; Anderson, Nickolas; Jursich, Gregory

2017-04-01

Printed sensor arrays are attractive for reliable, low-cost, and large-area mapping of structural systems. These sensor arrays can be printed on flexible substrates or directly on monitored structural parts. This technology is sought for continuous or on-demand real-time diagnosis and prognosis of complex structural components. In the past decade, many innovative technologies and functional materials have been explored to develop printed electronics and sensors. For example, an all-printed strain sensor array is a recent example of a low-cost, flexible and light-weight system that provides a reliable method for monitoring the state of aircraft structural parts. Among all-printing techniques, screen and inkjet printing methods are well suited for smaller-scale prototyping and have drawn much interest due to maturity of printing procedures and availability of compatible inks and substrates. Screen printing relies on a mask (screen) to transfer a pattern onto a substrate. Screen printing is widely used because of the high printing speed, large selection of ink/substrate materials, and capability of making complex multilayer devices. The complexity of collecting signals from a large number of sensors over a large area necessitates signal multiplexing electronics that need to be printed on flexible substrate or structure. As a result, these components are subjected to same deformation, temperature and other parameters for which sensor arrays are designed. The characteristics of these electronic components, such as transistors, are affected by deformation and other environmental parameters which can lead to erroneous sensed parameters. The manufacturing and functional challenges of the technology of printed sensor array systems for structural state monitoring are the focus of this presentation. Specific examples of strain sensor arrays will be presented to highlight the technical challenges.

Graphene-Based Chemical Vapor Sensors for Electronic Nose Applications

NASA Astrophysics Data System (ADS)

Nallon, Eric C.

An electronic nose (e-nose) is a biologically inspired device designed to mimic the operation of the olfactory system. The e-nose utilizes a chemical sensor array consisting of broadly responsive vapor sensors, whose combined response produces a unique pattern for a given compound or mixture. The sensor array is inspired by the biological function of the receptor neurons found in the human olfactory system, which are inherently cross-reactive and respond to many different compounds. The use of an e-nose is an attractive approach to predict unknown odors and is used in many fields for quantitative and qualitative analysis. If properly designed, an e-nose has the potential to adapt to new odors it was not originally designed for through laboratory training and algorithm updates. This would eliminate the lengthy and costly R&D costs associated with materiel and product development. Although e-nose technology has been around for over two decades, much research is still being undertaken in order to find new and more diverse types of sensors. Graphene is a single-layer, 2D material comprised of carbon atoms arranged in a hexagonal lattice, with extraordinary electrical, mechanical, thermal and optical properties due to its 2D, sp2-bonded structure. Graphene has much potential as a chemical sensing material due to its 2D structure, which provides a surface entirely exposed to its surrounding environment. In this configuration, every carbon atom in graphene is a surface atom, providing the greatest possible surface area per unit volume, so that electron transport is highly sensitive to adsorbed molecular species. Graphene has gained much attention since its discovery in 2004, but has not been realized in many commercial electronics. It has the potential to be a revolutionary material for use in chemical sensors due to its excellent conductivity, large surface area, low noise, and versatile surface for functionalization. In this work, graphene is incorporated into a chemiresistor device and used as a chemical sensor, where its resistance is temporarily modified while exposed to chemical compounds. The inherent, broad selective nature of graphene is demonstrated by testing a sensor against a diverse set of volatile organic compounds and also against a set of chemically similar compounds. The sensor exhibits excellent selectivity and is capable of achieving high classification accuracies. The kinetics of the sensor's response are further investigated revealing a relationship between the transient behavior of the response curve and physiochemical properties of the compounds, such as the molar mass and vapor pressure. This kinetic information is also shown to provide important information for further pattern recognition and classification, which is demonstrated by increased classification accuracy of very similar compounds. Covalent modification of the graphene surface is demonstrated by means of plasma treatment and free radical exchange, and sensing performance compared to an unmodified graphene sensor. Finally, the first example of a graphene-based, cross-reactive chemical sensor array is demonstrated by applying various polymers as coatings over an array of graphene sensors. The sensor array is tested against a variety of compounds, including the complex odor of Scotch whiskies, where it is capable of perfect classification of 10 Scotch whiskey variations.

Method of varying a characteristic of an optical vertical cavity structure formed by metalorganic vapor phase epitaxy

DOEpatents

Hou, Hong Q.; Coltrin, Michael E.; Choquette, Kent D.

2001-01-01

A process for forming an array of vertical cavity optical resonant structures wherein the structures in the array have different detection or emission wavelengths. The process uses selective area growth (SAG) in conjunction with annular masks of differing dimensions to control the thickness and chemical composition of the materials in the optical cavities in conjunction with a metalorganic vapor phase epitaxy (MOVPE) process to build these arrays.

Pollen flow in fragmented landscapes maintains genetic diversity following stand-replacing disturbance in a neotropical pioneer tree, Vochysia ferruginea Mart.

PubMed

Davies, S J; Cavers, S; Finegan, B; White, A; Breed, M F; Lowe, A J

2015-08-01

In forests with gap disturbance regimes, pioneer tree regeneration is typically abundant following stand-replacing disturbances, whether natural or anthropogenic. Differences in pioneer tree density linked to disturbance regime can influence pollinator behaviour and impact on mating patterns and genetic diversity of pioneer populations. Such mating pattern shifts can manifest as higher selfing rates and lower pollen diversity in old growth forest populations. In secondary forest, where more closely related pollen donors occur, an increase in biparental inbreeding is a potential problem. Here, we investigate the consequences of secondary forest colonisation on the mating patterns and genetic diversity of open-pollinated progeny arrays for the long-lived, self-compatible pioneer tree, Vochysia ferruginea, at two Costa Rican sites. Five microsatellite loci were screened across adult and seed cohorts from old growth forest with lower density, secondary forest with higher density, and isolated individual trees in pasture. Progeny from both old growth and secondary forest contexts were predominantly outcrossed (tm=1.00) and experienced low levels of biparental inbreeding (tm-ts=0.00-0.04). In contrast to predictions, our results indicated that the mating patterns of V. ferruginea are relatively robust to density differences between old growth and secondary forest stands. In addition, we observed that pollen-mediated gene flow possibly maintained the genetic diversity of open-pollinated progeny arrays in stands of secondary forest adults. As part of a natural resource management strategy, we suggest that primary forest remnants should be prioritised for conservation to promote restoration of genetic diversity during forest regeneration.

Out-of-Plane Designed Soft Metasurface for Tunable Surface Plasmon Polariton.

PubMed

Liu, Xin; Huang, Zhao; Zhu, Chengkai; Wang, Li; Zang, Jianfeng

2018-02-14

Reliable and repeatable tunability gives functional diversity for reconfigurable plasmonics devices, while reversible and large mechanical deformation enabled by soft materials provides a new way for the global or partial regulation of metadevices. Here, we demonstrate a soft metasurface with an out-of-plane design for tuning the energy of surface plasmon polaritons (SPPs) bloch wave using theory, simulation, and experiments. Our metasurface is composed of two-layered gold nanoribbon arrays (2GNRs) on a soft substrate. The out-of-plane coupling mechanism is systematically analyzed in terms of separation height effect. Moreover, by harnessing mechanical deformation, continuously tunable plasmonic resonance has been achieved in the visible and near-infrared ranges. We further studied the angle-dependent reflection spectra of our metastructure. Compared with its planar counterpart, our soft and two-layered metastructure exhibits diverse tunability and significant field enhancement by out-of-plane interactions. Our approach in designing soft metasurface with out-of-plane structures can be extended to more-complex photonic devices and finds prominent applications such as biosensing, high-density plasmonic circuits, surface-enhanced luminescence, and surface-enhanced Raman scattering.

Krüppel-like factors: three fingers in control.

PubMed

Swamynathan, Shivalingappa K

2010-04-01

Krüppel-like factors (KLFs), members of the zinc-finger family of transcription factors capable of binding GC-rich sequences, have emerged as critical regulators of important functions all over the body. They are characterised by a highly conserved C-terminal DNA-binding motif containing three C2H2 zinc-finger domains, with variable N-terminal regulatory domains. Currently, there are 17 KLFs annotated in the human genome. In spite of their structural similarity to one another, the genes encoding different KLFs are scattered all over the genome. By virtue of their ability to activate and/or repress the expression of a large number of genes, KLFs regulate a diverse array of developmental events and cellular processes, such as erythropoiesis, cardiac remodelling, adipogenesis, maintenance of stem cells, epithelial barrier formation, control of cell proliferation and neoplasia, flow-mediated endothelial gene expression, skeletal and smooth muscle development, gluconeogenesis, monocyte activation, intestinal and conjunctival goblet cell development, retinal neuronal regeneration and neonatal lung development. Characteristic features, nomenclature, evolution and functional diversities of the human KLFs are reviewed here.

Cationic antimicrobial peptides in penaeid shrimp.

PubMed

Tassanakajon, Anchalee; Amparyup, Piti; Somboonwiwat, Kunlaya; Supungul, Premruethai

2011-08-01

Penaeid shrimp aquaculture has been consistently affected worldwide by devastating diseases that cause a severe loss in production. To fight a variety of harmful microbes in the surrounding environment, particularly at high densities (of which intensive farming represents an extreme example), shrimps have evolved and use a diverse array of antimicrobial peptides (AMPs) as part of an important first-line response of the host defense system. Cationic AMPs in penaeid shrimps composed of penaeidins, crustins, and anti-lipopolysaccharide factors are comprised of multiple classes or isoforms and possess antibacterial and antifungal activities against different strains of bacteria and fungi. Shrimp AMPs are primarily expressed in circulating hemocytes, which is the main site of the immune response, and hemocytes expressing AMPs probably migrate to infection sites to fight against pathogen invasion. Indeed, most AMPs are produced as early as the nauplii developmental stage to protect shrimp larvae from infections. In this review, we discuss the sequence diversity, expression, gene structure, and antimicrobial activities of cationic AMPs in penaeid shrimps. The information available on antimicrobial activities indicates that these shrimp AMPs have potential therapeutic applications in the control of disease problems in aquaculture.

Genome-wide analysis of the structural genes regulating defense phenylpropanoid metabolism in Populus

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

Tschaplinski, Timothy J; Tsai, Chung-Jui; Harding, Scott A

Salicin-based phenolic glycosides, hydroxycinnamate derivatives and flavonoid-derived condensed tannins comprise up to one-third of Populus leaf dry mass. Genes regulating the abundance and chemical diversity of these substances have not been comprehensively analysed in tree species exhibiting this metabolically demanding level of phenolic metabolism. Here, shikimate-phenylpropanoid pathway genes thought to give rise to these phenolic products were annotated from the Populus genome, their expression assessed by semiquantitative or quantitative reverse transcription polymerase chain reaction (PCR), and metabolic evidence for function presented. Unlike Arabidopsis, Populus leaves accumulate an array of hydroxycinnamoyl-quinate esters, which is consistent with broadened function of the expandedmore » hydroxycinnamoyl-CoA transferase gene family. Greater flavonoid pathway diversity is also represented, and flavonoid gene families are larger. Consistent with expanded pathway function, most of these genes were upregulated during wound-stimulated condensed tannin synthesis in leaves. The suite of Populus genes regulating phenylpropanoid product accumulation should have important application in managing phenolic carbon pools in relation to climate change and global carbon cycling.« less

A Reconfigurable Instrument System for Nuclear and Particle Physics Experiments

NASA Astrophysics Data System (ADS)

Sang, Ziru; Li, Feng; Jiang, Xiao; Jin, Ge

2014-04-01

We developed a reconfigurable nuclear instrument system (RNIS) that could satisfy the requirements of diverse nuclear and particle physics experiments, and the inertial confinement fusion diagnostic. Benefiting from the reconfigurable hardware structure and digital pulse processing technology, RNIS shakes off the restrictions of cumbersome crates and miscellaneous modules. It retains all the advantages of conventional nuclear instruments and is more flexible and portable. RNIS is primarily composed of a field programmable hardware board and relevant PC software. Separate analog channels are designed to provide different functions, such as amplifiers, ADC, fast discriminators and Schmitt discriminators for diverse experimental purposes. The high-performance field programmable gate array could complete high-precision time interval measurement, histogram accumulation, counting, and coincidence anticoincidence measurement. To illustrate the prospects of RNIS, a series of applications to the experiments are described in this paper. The first, for which RNIS was originally developed, involves nuclear energy spectrum measurement with a scintillation detector and photomultiplier. The second experiment applies RNIS to a G-M tube counting experiment, and in the third, it is applied to a quantum communication experiment through reconfiguration.

Rational protein design: developing next-generation biological therapeutics and nanobiotechnological tools.

PubMed

Wilson, Corey J

2015-01-01

Proteins are the most functionally diverse macromolecules observed in nature, participating in a broad array of catalytic, biosensing, transport, scaffolding, and regulatory functions. Fittingly, proteins have become one of the most promising nanobiotechnological tools to date, and through the use of recombinant DNA and other laboratory methods we have produced a vast number of biological therapeutics derived from human genes. Our emerging ability to rationally design proteins (e.g., via computational methods) holds the promise of significantly expanding the number and diversity of protein therapies and has opened the gateway to realizing true and uncompromised personalized medicine. In the last decade computational protein design has been transformed from a set of fundamental strategies to stringently test our understanding of the protein structure-function relationship, to practical tools for developing useful biological processes, nano-devices, and novel therapeutics. As protein design strategies improve (i.e., in terms of accuracy and efficiency) clinicians will be able to leverage individual genetic data and biological metrics to develop and deliver personalized protein therapeutics with minimal delay. © 2014 Wiley Periodicals, Inc.

Drawing lines and borders: how the dehiscent fruit of Arabidopsis is patterned.

PubMed

Dinneny, José R; Yanofsky, Martin F

2005-01-01

The advent of fruits marked a key innovation in the evolution of flowering plants and helped generate a diverse array of mechanisms for seed dispersal. In the model plant, Arabidopsis thaliana, seed dispersal occurs through a process known as "pod-shatter" in which the fruit structure falls to pieces upon light mechanical pressures. This dispersal mechanism is dependent on the careful patterning of tissues in the fruit, which perform diverse functions that enable the fruit to open at maturation. Using the genetic power of Arabidopsis, many of the molecular components that help specify these tissues have been identified. Studies of the interactions among these genes have revealed a regulatory network that limits processes such as cell-cell separation and lignification to discreet regions of the fruit. Knowledge of these processes in a model fruit creates a foundation on which to build an understanding of the evolution of fruit form in other species and provides tools to engineer shatter-resistant seed pods to prevent crop loss in plants of agronomic importance such as canola. Copyright 2004 Wiley Periodicals, Inc.

Polymer nanoimprinting using an anodized aluminum mold for structural coloration

NASA Astrophysics Data System (ADS)

Kikuchi, Tatsuya; Nishinaga, Osamu; Natsui, Shungo; Suzuki, Ryosuke O.

2015-06-01

Polymer nanoimprinting of submicrometer-scale dimple arrays with structural coloration was demonstrated. Highly ordered aluminum dimple arrays measuring 530-670 nm in diameter were formed on an aluminum substrate via etidronic acid anodizing at 210-270 V and subsequent anodic oxide dissolution. The nanostructured aluminum surface led to bright structural coloration with a rainbow spectrum, and the reflected wavelength strongly depends on the angle of the specimen and the period of the dimple array. The reflection peak shifts gradually with the dimple diameter toward longer wavelength, reaching 800 nm in wavelength at 670 nm in diameter. The shape of the aluminum dimple arrays were successfully transferred to a mercapto-ester ultra-violet curable polymer via self-assembled monolayer coating and polymer replications using a nanoimprinting technique. The nanostructured polymer surfaces with positively and negatively shaped dimple arrays also exhibited structural coloration based on the periodic nanostructure, and reflected light mostly in the visible region, 400-800 nm. This nanostructuring with structural coloration can be easily realized by simple techniques such as anodizing, SAM coating, and nanoimprinting.

Characterization of electronic structures from CdS/Si nanoheterostructure array based on silicon nanoporous pillar array

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

Li, Yong, E-mail: liyong@pdsu.edu.cn; Song, Xiao Yan; Song, Yue Li

2016-02-15

Highlights: • CdS/Si nanoheterostructure array has been fabricated through a CBD method. • The electronic properties have been investigated by the I–V and C–V techniques. • The onset voltages, characteristic frequency and built-in potential are investigated. • The electronic structures can be tuned through the annealing treatments. - Abstract: The electronic properties of heterostructures are very important to its applications in the field of optoelectronic devices. Understanding and control of electronic properties are very necessary. CdS/Si nanoheterostructure array have been fabricated through growing CdS nanocrystals on the silicon nanoporous pillar array using a chemical bath deposition method. The electronic propertiesmore » of CdS nanoheterostructure array have been investigated by the current–voltage, complex impedance spectroscopy and capacitance–voltage techniques. The onset voltages, characteristic frequency and built-in potential are gradually increased with increasing the annealing temperature. It is indicated that the electronic structures of CdS/Si nanoheterostructure array can be tuned through the annealing treatments.« less

Ancient and Recent Duplications Support Functional Diversity of Daphnia Opsins.

PubMed

Brandon, Christopher S; Greenwold, Matthew J; Dudycha, Jeffry L

2017-01-01

Daphnia pulex has the largest known family of opsins, genes critical for photoreception and vision in animals. This diversity may be functionally redundant, arising from recent processes, or ancient duplications may have been preserved due to distinct functions and independent contributions to fitness. We analyzed opsins in D. pulex and its distant congener Daphnia magna. We identified 48 opsins in the D. pulex genome and 32 in D. magna. We inferred the complement of opsins in the last common ancestor of all Daphnia and evaluated the history of opsin duplication and loss. We further analyzed sequence variation to assess possible functional diversification among Daphnia opsins. Much of the opsin expansion occurred before the D. pulex-D. magna split more than 145 Mya, and both Daphnia lineages preserved most ancient opsins. More recent expansion occurred in pteropsins and long-wavelength visual opsins in both species, particularly D. pulex. Recent duplications were not random: the same ancestral genes duplicated independently in each modern species. Most ancient and some recent duplications involved differentiation at residues known to influence spectral tuning of visual opsins. Arthropsins show evidence of gene conversion between tandemly arrayed paralogs in functionally important domains. Intron-exon gene structure was generally conserved within clades inferred from sequences, although pteropsins showed substantial intron size variation. Overall, our analyses support the hypotheses that diverse opsins are maintained due to diverse functional roles in photoreception and vision, that functional diversification is both ancient and recent, and that multiple evolutionary processes have influenced different types of opsins.

The Design of Distributed Micro Grid Energy Storage System

NASA Astrophysics Data System (ADS)

Liang, Ya-feng; Wang, Yan-ping

2018-03-01

Distributed micro-grid runs in island mode, the energy storage system is the core to maintain the micro-grid stable operation. For the problems that it is poor to adjust at work and easy to cause the volatility of micro-grid caused by the existing energy storage structure of fixed connection. In this paper, an array type energy storage structure is proposed, and the array type energy storage system structure and working principle are analyzed. Finally, the array type energy storage structure model is established based on MATLAB, the simulation results show that the array type energy storage system has great flexibility, which can maximize the utilization of energy storage system, guarantee the reliable operation of distributed micro-grid and achieve the function of peak clipping and valley filling.

Towards Integrated Marmara Strong Motion Network

NASA Astrophysics Data System (ADS)

Durukal, E.; Erdik, M.; Safak, E.; Ansal, A.; Ozel, O.; Alcik, H.; Mert, A.; Kafadar, N.; Korkmaz, A.; Kurtulus, A.

2009-04-01

Istanbul has a 65% chance of having a magnitude 7 or above earthquake within the next 30 years. As part of the preparations for the future earthquake, strong motion networks have been installed in and around Istanbul. The Marmara Strong Motion Network, operated by the Department of Earthquake Engineering of Kandilli Observatory and Earthquake Research Institute, encompasses permanent systems outlined below. It is envisaged that the networks will be run by a single entity responsible for technical management and maintanence, as well as for data management, archiving and dissemination through dedicated web-based interfaces. • Istanbul Earthquake Rapid Response and Early Warning System - IERREWS (one hundred 18-bit accelerometers for rapid response; ten 24-bit accelerometers for early warning) • IGDAŞ Gas Shutoff Network (100 accelerometers to be installed in 2010 and integrated with IERREWS) • Structural Monitoring Arrays - Fatih Sultan Mehmet Suspension Bridge (1200m-long suspension bridge across the Bosphorus, five 3-component accelerometers + GPS sensors) - Hagia Sophia Array (1500-year-old historical edifice, 9 accelerometers) - Süleymaniye Mosque Array (450-year-old historical edifice,9 accelerometers) - Fatih Mosque Array (237-year-old historical edifice, 9 accelerometers) - Kanyon Building Array (high-rise office building, 5 accelerometers) - Isbank Tower Array (high-rise office building, 5 accelerometers) - ENRON Array (power generation facility, 4 acelerometers) - Mihrimah Sultan Mosque Array (450-year-old historical edifice,9 accelerometers + tiltmeters, to be installed in 2009) - Sultanahmet Mosque Array, (390-year-old historical edifice, 9 accelerometers + tiltmeters, to be installed in 2009) • Special Arrays - Atakoy Vertical Array (four 3-component accelerometers at 25, 50, 75, and 150 m depths) - Marmara Tube Tunnel (1400 m long submerged tunnel, 128 ch. accelerometric data, 24 ch. strain data, to be installed in 2010) - Air-Force Academy Array (72 ch. dense accelerometric array to be installed in 2010) - Gemlik Array (a dense basin array of 8 stations, to be installed in 2010) The objectives of these systems and networks are: (1) to produce rapid earthquake intensity, damage and loss assessment information after an earthquake (in the case of IERREWS), (2) to monitor conditions of structural systems, (3) to develop real-time data processing, analysis, and damage detection and location tools (in the case of structural networks) after an extreme event, (4) to assess spatial properties of strong ground motion and ground strain, and to characterise basin response (in the case of special arrays), (5) to investigate site response and wave propagation (in the case of vertical array). Ground motion data obtained from these strong motion networks have and are being used for investigations of attenuation, spatial variation (coherence), simulation benchmarking, source modeling, site response, seismic microzonation, system identification and structural model verification and structural health control. In addition to the systems and networks outlined above there are two temporary networks: KIMNET - a dense urban noise and microtremor network consisting of 50 broadband stations expected to be operational in mid 2009, and SOSEWIN - a 20-station, self-organizing structural integrated array at Ataköy in Istanbul.

Test Structures For Bumpy Integrated Circuits

NASA Technical Reports Server (NTRS)

Buehler, Martin G.; Sayah, Hoshyar R.

1989-01-01

Cross-bridge resistors added to comb and serpentine patterns. Improved combination of test structures built into integrated circuit used to evaluate design rules, fabrication processes, and quality of interconnections. Consist of meshing serpentines and combs, and cross bridge. Structures used to make electrical measurements revealing defects in design or fabrication. Combination of test structures includes three comb arrays, two serpentine arrays, and cross bridge. Made of aluminum or polycrystalline silicon, depending on material in integrated-circuit layers evaluated. Aluminum combs and serpentine arrays deposited over steps made by polycrystalline silicon and diffusion layers, while polycrystalline silicon versions of these structures used to cross over steps made by thick oxide layer.

Dielectrophoretic systems without embedded electrodes

DOEpatents

Cummings, Eric B [Livermore, CA; Singh, Anup K [San Francisco, CA

2006-03-21

Method and apparatus for dielectrophoretic separation of particles in a fluid based using array of insulating structures arranged in a fluid flow channel. By utilizing an array of insulating structures, a spatially inhomogeneous electric field is created without the use of the embedded electrodes conventionally employed for dielectrophoretic separations. Moreover, by using these insulating structures a steady applied electric field has been shown to provide for dielectrophoresis in contrast to the conventional use of an alternating electric field. In a uniform array of posts, dielectrophoretic effects have been produced flows having significant pressure-driven and electrokinetic transport. Above a threshold applied electric field, filaments of concentrated and rarefied particles appear in the flow as a result of dielectrophoresis. Above a higher threshold applied voltage, dielectrophoresis produces zones of highly concentrated and immobilized particles. These patterns are strongly influenced by the angle of the array of insulating structures with respect to the mean applied electric field and the shape of the insulating structures.

Localization of multiple defects using the compact phased array (CPA) method

NASA Astrophysics Data System (ADS)

Senyurek, Volkan Y.; Baghalian, Amin; Tashakori, Shervin; McDaniel, Dwayne; Tansel, Ibrahim N.

2018-01-01

Array systems of transducers have found numerous applications in detection and localization of defects in structural health monitoring (SHM) of plate-like structures. Different types of array configurations and analysis algorithms have been used to improve the process of localization of defects. For accurate and reliable monitoring of large structures by array systems, a high number of actuator and sensor elements are often required. In this study, a compact phased array system consisting of only three piezoelectric elements is used in conjunction with an updated total focusing method (TFM) for localization of single and multiple defects in an aluminum plate. The accuracy of the localization process was greatly improved by including wave propagation information in TFM. Results indicated that the proposed CPA approach can locate single and multiple defects with high accuracy while decreasing the processing costs and the number of required transducers. This method can be utilized in critical applications such as aerospace structures where the use of a large number of transducers is not desirable.

Structural cost optimization of photovoltaic central power station modules and support structure

NASA Technical Reports Server (NTRS)

Sutton, P. D.; Stolte, W. J.; Marsh, R. O.

1979-01-01

The results of a comprehensive study of photovoltaic module structural support concepts for photovoltaic central power stations and their associated costs are presented. The objective of the study has been the identification of structural cost drivers. Parametric structural design and cost analyses of complete array systems consisting of modules, primary support structures, and foundations were performed. Area related module cost was found to be constant with design, size, and loading. A curved glass module concept was evaluated and found to have the potential to significantly reduce panel structural costs. Conclusions of the study are: array costs do not vary greatly among the designs evaluated; panel and array costs are strongly dependent on design loading; and the best support configuration is load dependent

Students' Spatial Structuring of 2D Arrays of Squares.

ERIC Educational Resources Information Center

Battista, Michael T.; Clements, Douglas H.; Arnoff, Judy; Battista, Kathryn; Van Auken Borrow, Caroline

1998-01-01

Defines spatial structuring as the mental operation of constructing an organization or form for an object/set of objects. Examines in detail students' structuring and enumeration of two-dimensional rectangular arrays of squares. Concludes that many students do not see row-by-column structure. Describes various levels of sophistication in students'…

Supporting Structures for Flat Solar-Cell Arrays

NASA Technical Reports Server (NTRS)

Wilson, A. H.

1986-01-01

Strong supporting structures for flat solar photovoltaic arrays built with such commonly available materials as wood and galvanized steel sheet. Structures resist expected static loads from snow and ice as well as dynamic loads from winds and even Earthquake vibrations. Supporting structure uses inexpensive materials. Parts prefabricated to minimize assembly work in field.

Optical parameters of ITO/TPD/Alq3/Al luminescent structures, containing arrays of CdSe/ZnS colloidal quantum dots

NASA Astrophysics Data System (ADS)

Mikhailov, I. I.; Tarasov, S. A.; Lamkin, I. A.; Tadtaev, P. O.; Kozlovich, L. I.; Solomonov, A. V.; Stepanov, E. M.

2016-08-01

The luminescent organic ITO/TPD/Alq3/Al structures and CdSe/ZnS quantum dots (QD) arrays were created. Electrical and optical properties of the samples were examined. The luminescence of the layers and QD arrays was shown in the range of wavelengths from 400 to 680 nm. Luminescent structures with phosphors corresponding to the emission standards with CRI>98 and with color temperature of 5500 K and 6504 K were created.

Diversity and evolution of myxozoan minicollagens and nematogalectins.

PubMed

Shpirer, Erez; Chang, E Sally; Diamant, Arik; Rubinstein, Nimrod; Cartwright, Paulyn; Huchon, Dorothée

2014-09-29

Myxozoa are a diverse group of metazoan parasites with a very simple organization, which has for decades eluded their evolutionary origin. Their most prominent and characteristic feature is the polar capsule: a complex intracellular structure of the myxozoan spore, which plays a role in host infection. Striking morphological similarities have been found between myxozoan polar capsules and nematocysts, the stinging structures of cnidarians (corals, sea anemones and jellyfish) leading to the suggestion that Myxozoa and Cnidaria share a more recent common ancestry. This hypothesis has recently been supported by phylogenomic evidence and by the identification of a nematocyst specific minicollagen gene in the myxozoan Tetracapsuloides bryosalmonae. Here we searched genomes and transcriptomes of several myxozoan taxa for the presence of additional cnidarian specific genes and characterized these genes within a phylogenetic context. Illumina assemblies of transcriptome or genome data of three myxozoan species (Enteromyxum leei, Kudoa iwatai, and Sphaeromyxa zaharoni) and of the enigmatic cnidarian parasite Polypodium hydriforme (Polypodiozoa) were mined using tBlastn searches with nematocyst-specific proteins as queries. Several orthologs of nematogalectins and minicollagens were identified. Our phylogenetic analyses indicate that myxozoans possess three distinct minicollagens. We found that the cnidarian repertoire of nematogalectins is more complex than previously thought and we identified additional members of the nematogalectin family. Cnidarians were found to possess four nematogalectin/ nematogalectin-related genes, while in myxozoans only three genes could be identified. Our results demonstrate that myxozoans possess a diverse array of genes that are taxonomically restricted to Cnidaria. Characterization of these genes provide compelling evidence that polar capsules and nematocysts are homologous structures and that myxozoans are highly degenerate cnidarians. The diversity of minicollagens was higher than previously thought, with the presence of three minicollagen genes in myxozoans. Our phylogenetic results suggest that the different myxozoan sequences are the results of ancient divergences within Cnidaria and not of recent specializations of the polar capsule. For both minicollagen and nematogalectin, our results show that myxozoans possess less gene copies than their cnidarian counter parts, suggesting that the polar capsule gene repertoire was simplified with their reduced body plan.

A versatile palindromic amphipathic repeat coding sequence horizontally distributed among diverse bacterial and eucaryotic microbes

PubMed Central

2010-01-01

Background Intragenic tandem repeats occur throughout all domains of life and impart functional and structural variability to diverse translation products. Repeat proteins confer distinctive surface phenotypes to many unicellular organisms, including those with minimal genomes such as the wall-less bacterial monoderms, Mollicutes. One such repeat pattern in this clade is distributed in a manner suggesting its exchange by horizontal gene transfer (HGT). Expanding genome sequence databases reveal the pattern in a widening range of bacteria, and recently among eucaryotic microbes. We examined the genomic flux and consequences of the motif by determining its distribution, predicted structural features and association with membrane-targeted proteins. Results Using a refined hidden Markov model, we document a 25-residue protein sequence motif tandemly arrayed in variable-number repeats in ORFs lacking assigned functions. It appears sporadically in unicellular microbes from disparate bacterial and eucaryotic clades, representing diverse lifestyles and ecological niches that include host parasitic, marine and extreme environments. Tracts of the repeats predict a malleable configuration of recurring domains, with conserved hydrophobic residues forming an amphipathic secondary structure in which hydrophilic residues endow extensive sequence variation. Many ORFs with these domains also have membrane-targeting sequences that predict assorted topologies; others may comprise reservoirs of sequence variants. We demonstrate expressed variants among surface lipoproteins that distinguish closely related animal pathogens belonging to a subgroup of the Mollicutes. DNA sequences encoding the tandem domains display dyad symmetry. Moreover, in some taxa the domains occur in ORFs selectively associated with mobile elements. These features, a punctate phylogenetic distribution, and different patterns of dispersal in genomes of related taxa, suggest that the repeat may be disseminated by HGT and intra-genomic shuffling. Conclusions We describe novel features of PARCELs (Palindromic Amphipathic Repeat Coding ELements), a set of widely distributed repeat protein domains and coding sequences that were likely acquired through HGT by diverse unicellular microbes, further mobilized and diversified within genomes, and co-opted for expression in the membrane proteome of some taxa. Disseminated by multiple gene-centric vehicles, ORFs harboring these elements enhance accessory gene pools as part of the "mobilome" connecting genomes of various clades, in taxa sharing common niches. PMID:20626840

Channel microband electrode arrays for mechanistic electrochemistry. Two-dimensional voltammetry:  transport-limited currents.

PubMed

Alden, J A; Feldman, M A; Hill, E; Prieto, F; Oyama, M; Coles, B A; Compton, R G; Dobson, P J; Leigh, P A

1998-05-01

A channel electrode array, with electrodes ranging in size from the millimeter to the submicrometer scale, is used for the amperometric interrogation of mechanistically complex electrode processes. In this way, the transport-limited current, measured as a function of both electrode size and electrolyte flow rate (convection), is shown to provide a highly sensitive probe of mechanism and kinetics. The application of "two-dimensional voltammetry" to diverse electrode processes, including E, ECE, ECEE, EC', and DISP2 reactions, is reported.

Geochemical and petrographic data for intrusions peripheral to the Big Timber Stock, Crazy Mountains, Montana

USGS Publications Warehouse

du Bray, Edward A.; Van Gosen, Bradley S.

2015-01-01

The Paleocene Fort Union Formation hosts a compositionally diverse array of Eocene plugs, dikes, and sills arrayed around the Eocene Big Timber stock in the Crazy Mountains of south-central Montana. The geochemistry and petrography of the sills have not previously been characterized or interpreted. The purpose of this report is (1) to present available geochemical and petrographic data for several dozen samples of these rocks and (2) to provide a basic interpretive synthesis of these data.

A wideband software reconfigurable modem

NASA Astrophysics Data System (ADS)

Turner, J. H., Jr.; Vickers, H.

A wideband modem is described which provides signal processing capability for four Lx-band signals employing QPSK, MSK and PPM waveforms and employs a software reconfigurable architecture for maximum system flexibility and graceful degradation. The current processor uses a 2901 and two 8086 microprocessors per channel and performs acquisition, tracking, and data demodulation for JITDS, GPS, IFF and TACAN systems. The next generation processor will be implemented using a VHSIC chip set employing a programmable complex array vector processor module, a GP computer module, customized gate array modules, and a digital array correlator. This integrated processor has application to a wide number of diverse system waveforms, and will bring the benefits of VHSIC technology insertion into avionic antijam communications systems.

Piezoresistive cantilever array sensor for consolidated bioprocess monitoring

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

Kim, Seonghwan Sam; Rahman, Touhidur; Senesac, Larry R

2009-01-01

Cellulolytic microbes occur in diverse natural niches and are being screened for industrial modification and utility. A microbe for Consolidated bioprocessing (CBP) development can rapidly degrade pure cellulose and then ferment the resulting sugars into fuels. To identify and screen for novel microbes for CBP, we have developed a piezoresistive cantilever array sensor which is capable of simultaneous monitoring of glucose and ethanol concentration changes in a phosphate buffer solution. 4-mercaptophenylboronic acid (4-MPBA) and polyethyleneglycol (PEG)-thiol are employed to functionalize each piezoresistive cantilever for glucose and ethanol sensing, respectively. Successful concentration measurements of glucose and ethanol with minimal interferences aremore » obtained with our cantilever array sensor.« less

Diversity in GABAergic signaling.

PubMed

Vogt, Kaspar

2015-01-01

GABA(A) receptor-mediated synaptic transmission is responsible for inhibitory control of neural function in the brain. Recent progress has shown that GABA(A) receptors also provide a wide range of additional functions beyond simple inhibition. This diversity of functions is mediated by a large variety of different interneuron classes acting on a diverse population of receptor subtypes. Here, I will focus on an additional source of GABAergic signaling diversity, caused by the highly variable ion signaling mechanism of GABA(A) receptors. In concert with the other two sources of GABAergic heterogeneity, this variability in signaling allows for a wide array of GABAergic effects that are crucial for the development of the brain and its function. © 2015 Elsevier Inc. All rights reserved.

Enhanced Circular Dichroism of Gold Bilayered Slit Arrays Embedded with Rectangular Holes.

PubMed

Zhang, Hao; Wang, Yongkai; Luo, Lina; Wang, Haiqing; Zhang, Zhongyue

2017-01-01

Gold bilayered slit arrays with rectangular holes embedded into the metal surface are designed to enhance the circular dichroism (CD) effect of gold bilayered slit arrays. The rectangular holes in these arrays block electric currents and generate localized surface plasmons around these holes, thereby strengthening the CD effect. The CD enhancement factor depends strongly on the rotational angle and the structural parameters of the rectangular holes; this factor can be enhanced further by drilling two additional rectangular holes into the metal surfaces of the arrays. These results help facilitate the design of chiral structures to produce a strong CD effect and large electric fields.

Design, optimization, and analysis of a self-deploying PV tent array

NASA Astrophysics Data System (ADS)

Collozza, Anthony J.

1991-06-01

A tent shaped PV array was designed and the design was optimized for maximum specific power. In order to minimize output power variation a tent angle of 60 deg was chosen. Based on the chosen tent angle an array structure was designed. The design considerations were minimal deployment time, high reliability, and small stowage volume. To meet these considerations the array was chosen to be self-deployable, form a compact storage configuration, using a passive pressurized gas deployment mechanism. Each structural component of the design was analyzed to determine the size necessary to withstand the various forces to which it would be subjected. Through this analysis the component weights were determined. An optimization was performed to determine the array dimensions and blanket geometry which produce the maximum specific power for a given PV blanket. This optimization was performed for both lunar and Martian environmental conditions. Other factors such as PV blanket types, structural material, and wind velocity (for Mars array), were varied to determine what influence they had on the design point. The performance specifications for the array at both locations and with each type of PV blanket were determined. These specifications were calculated using the Arimid fiber composite as the structural material. The four PV blanket types considered were silicon, GaAs/Ge, GaAsCLEFT, and amorphous silicon. The specifications used for each blanket represented either present day or near term technology. For both the Moon and Mars the amorphous silicon arrays produced the highest specific power.

Nano-Array Integrated Structured Catalysts: A New Paradigm upon Conventional Wash-Coated Monolithic Catalysts?

DOE PAGES

Weng, Junfei; Lu, Xingxu; Gao, Pu-Xian

2017-08-28

The monolithic catalyst, namely the structured catalyst, is one of the important categories of catalysts used in various fields, especially in catalytic exhaust after-treatment. Despite its successful application in conventional wash-coated catalysts in both mobile and stationary catalytic converters, washcoat-based technologies are facing multi-fold challenges, including: (1) high Pt-group metals (PGM) material loading being required, driving the market prices; (2) less-than ideal distribution of washcoats in typically square-shaped channels associated with pressure drop sacrifice; and (3) far from clear correlations between macroscopic washcoat structures and their catalytic performance. To tackle these challenges, the well-defined nanostructure array (nano-array)-integrated structured catalysts whichmore » we invented and developed recently have been proven to be a promising class of cost-effective and efficient devices that may complement or substitute wash-coated catalysts. This new type of structured catalysts is composed of honeycomb-structured monoliths, whose channel surfaces are grown in situ with a nano-array forest made of traditional binary transition metal oxide support such as Al 2O 3, CeO 2, Co 3O 4, MnO 2, TiO 2, and ZnO, or newer support materials including perovskite-type ABO3 structures, for example LaMnO 3, LaCoO 3, LaNiO, and LaFeO 3. The integration strategy parts from the traditional washcoat technique. Instead, an in situ nanomaterial assembly method is utilized, such as a hydro (solva-) thermal synthesis approach, in order to create sound structure robustness, and increase ease and complex-shaped substrate adaptability. Specifically, the critical fabrication procedures for nano-array structured catalysts include deposition of seeding layer, in situ growth of nano-array, and loading of catalytic materials. The generic methodology utilization in both the magnetic stirring batch process and continuous flow reactor synthesis offers the nano-array catalysts with great potential to be scaled up readily and cost-effectively. The tunability of the structure and catalytic performance could be achieved through morphology and geometry adjustment and guest atoms and defect manipulation, as well as composite nano-array catalyst manufacture. Excellent stabilities under various conditions were also present compared to conventional wash-coated catalysts.« less

Nano-Array Integrated Structured Catalysts: A New Paradigm upon Conventional Wash-Coated Monolithic Catalysts?

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

Weng, Junfei; Lu, Xingxu; Gao, Pu-Xian

The monolithic catalyst, namely the structured catalyst, is one of the important categories of catalysts used in various fields, especially in catalytic exhaust after-treatment. Despite its successful application in conventional wash-coated catalysts in both mobile and stationary catalytic converters, washcoat-based technologies are facing multi-fold challenges, including: (1) high Pt-group metals (PGM) material loading being required, driving the market prices; (2) less-than ideal distribution of washcoats in typically square-shaped channels associated with pressure drop sacrifice; and (3) far from clear correlations between macroscopic washcoat structures and their catalytic performance. To tackle these challenges, the well-defined nanostructure array (nano-array)-integrated structured catalysts whichmore » we invented and developed recently have been proven to be a promising class of cost-effective and efficient devices that may complement or substitute wash-coated catalysts. This new type of structured catalysts is composed of honeycomb-structured monoliths, whose channel surfaces are grown in situ with a nano-array forest made of traditional binary transition metal oxide support such as Al 2O 3, CeO 2, Co 3O 4, MnO 2, TiO 2, and ZnO, or newer support materials including perovskite-type ABO3 structures, for example LaMnO 3, LaCoO 3, LaNiO, and LaFeO 3. The integration strategy parts from the traditional washcoat technique. Instead, an in situ nanomaterial assembly method is utilized, such as a hydro (solva-) thermal synthesis approach, in order to create sound structure robustness, and increase ease and complex-shaped substrate adaptability. Specifically, the critical fabrication procedures for nano-array structured catalysts include deposition of seeding layer, in situ growth of nano-array, and loading of catalytic materials. The generic methodology utilization in both the magnetic stirring batch process and continuous flow reactor synthesis offers the nano-array catalysts with great potential to be scaled up readily and cost-effectively. The tunability of the structure and catalytic performance could be achieved through morphology and geometry adjustment and guest atoms and defect manipulation, as well as composite nano-array catalyst manufacture. Excellent stabilities under various conditions were also present compared to conventional wash-coated catalysts.« less

Design, Fabrication and Characterization of a Low-Impedance 3D Electrode Array System for Neuro-Electrophysiology

PubMed Central

Kusko, Mihaela; Craciunoiu, Florea; Amuzescu, Bogdan; Halitzchi, Ferdinand; Selescu, Tudor; Radoi, Antonio; Popescu, Marian; Simion, Monica; Bragaru, Adina; Ignat, Teodora

2012-01-01

Recent progress in patterned microelectrode manufacturing technology and microfluidics has opened the way to a large variety of cellular and molecular biosensor-based applications. In this extremely diverse and rapidly expanding landscape, silicon-based technologies occupy a special position, given their statute of mature, consolidated, and highly accessible areas of development. Within the present work we report microfabrication procedures and workflows for 3D patterned gold-plated microelectrode arrays (MEA) of different shapes (pyramidal, conical and high aspect ratio), and we provide a detailed characterization of their physical features during all the fabrication steps to have in the end a reliable technology. Moreover, the electrical performances of MEA silicon chips mounted on standardized connector boards via ultrasound wire-bonding have been tested using non-destructive electrochemical methods: linear sweep and cyclic voltammetry, impedance spectroscopy. Further, an experimental recording chamber package suitable for in vitro electrophysiology experiments has been realized using custom-design electronics for electrical stimulus delivery and local field potential recording, included in a complete electrophysiology setup, and the experimental structures have been tested on newborn rat hippocampal slices, yielding similar performance compared to commercially available MEA equipments. PMID:23208555

Invasive plants transform the three-dimensional structure of rain forests

PubMed Central

Asner, Gregory P.; Hughes, R. Flint; Vitousek, Peter M.; Knapp, David E.; Kennedy-Bowdoin, Ty; Boardman, Joseph; Martin, Roberta E.; Eastwood, Michael; Green, Robert O.

2008-01-01

Biological invasions contribute to global environmental change, but the dynamics and consequences of most invasions are difficult to assess at regional scales. We deployed an airborne remote sensing system that mapped the location and impacts of five highly invasive plant species across 221,875 ha of Hawaiian ecosystems, identifying four distinct ways that these species transform the three-dimensional (3D) structure of native rain forests. In lowland to montane forests, three invasive tree species replace native midcanopy and understory plants, whereas one understory invader excludes native species at the ground level. A fifth invasive nitrogen-fixing tree, in combination with a midcanopy alien tree, replaces native plants at all canopy levels in lowland forests. We conclude that this diverse array of alien plant species, each representing a different growth form or functional type, is changing the fundamental 3D structure of native Hawaiian rain forests. Our work also demonstrates how an airborne mapping strategy can identify and track the spread of certain invasive plant species, determine ecological consequences of their proliferation, and provide detailed geographic information to conservation and management efforts. PMID:18316720

Trimeric HIV-1-Env Structures Define Glycan Shields from Clades A, B, and G.

PubMed

Stewart-Jones, Guillaume B E; Soto, Cinque; Lemmin, Thomas; Chuang, Gwo-Yu; Druz, Aliaksandr; Kong, Rui; Thomas, Paul V; Wagh, Kshitij; Zhou, Tongqing; Behrens, Anna-Janina; Bylund, Tatsiana; Choi, Chang W; Davison, Jack R; Georgiev, Ivelin S; Joyce, M Gordon; Kwon, Young Do; Pancera, Marie; Taft, Justin; Yang, Yongping; Zhang, Baoshan; Shivatare, Sachin S; Shivatare, Vidya S; Lee, Chang-Chun D; Wu, Chung-Yi; Bewley, Carole A; Burton, Dennis R; Koff, Wayne C; Connors, Mark; Crispin, Max; Baxa, Ulrich; Korber, Bette T; Wong, Chi-Huey; Mascola, John R; Kwong, Peter D

2016-05-05

The HIV-1-envelope (Env) trimer is covered by a glycan shield of ∼90 N-linked oligosaccharides, which comprises roughly half its mass and is a key component of HIV evasion from humoral immunity. To understand how antibodies can overcome the barriers imposed by the glycan shield, we crystallized fully glycosylated Env trimers from clades A, B, and G, visualizing the shield at 3.4-3.7 Å resolution. These structures reveal the HIV-1-glycan shield to comprise a network of interlocking oligosaccharides, substantially ordered by glycan crowding, that encase the protein component of Env and enable HIV-1 to avoid most antibody-mediated neutralization. The revealed features delineate a taxonomy of N-linked glycan-glycan interactions. Crowded and dispersed glycans are differently ordered, conserved, processed, and recognized by antibody. The structures, along with glycan-array binding and molecular dynamics, reveal a diversity in oligosaccharide affinity and a requirement for accommodating glycans among known broadly neutralizing antibodies that target the glycan-shielded trimer. Copyright © 2016 Elsevier Inc. All rights reserved.

“Click, Click, Cyclize”: A DOS Approach to Sultams Utilizing Vinyl Sulfonamide Linchpins

PubMed Central

Zhou, Aihua; Rayabarapu, Dinesh; Hanson, Paul R.

2009-01-01

A diversity-oriented synthesis (DOS) strategy termed “Click, Click, Cyclize” is reported. This approach relies on functional group (FG) pairing between a vinyl sulfonamide and an array of functional groups to synthesize skeletally diverse sultams. Several FG pairing pathways on central tertiary vinyl sulfonamide linchpins have been developed including intramolecular Heck, aza-Michael, ring-closing enyne metathesis, Pauson—Khand, and chemoselective oxidation/Baylis—Hillman reactions. PMID:19115841

A Large Maize (Zea mays L.) SNP Genotyping Array: Development and Germplasm Genotyping, and Genetic Mapping to Compare with the B73 Reference Genome

PubMed Central

Ganal, Martin W.; Durstewitz, Gregor; Polley, Andreas; Bérard, Aurélie; Buckler, Edward S.; Charcosset, Alain; Clarke, Joseph D.; Graner, Eva-Maria; Hansen, Mark; Joets, Johann; Le Paslier, Marie-Christine; McMullen, Michael D.; Montalent, Pierre; Rose, Mark; Schön, Chris-Carolin; Sun, Qi; Walter, Hildrun; Martin, Olivier C.; Falque, Matthieu

2011-01-01

SNP genotyping arrays have been useful for many applications that require a large number of molecular markers such as high-density genetic mapping, genome-wide association studies (GWAS), and genomic selection. We report the establishment of a large maize SNP array and its use for diversity analysis and high density linkage mapping. The markers, taken from more than 800,000 SNPs, were selected to be preferentially located in genes and evenly distributed across the genome. The array was tested with a set of maize germplasm including North American and European inbred lines, parent/F1 combinations, and distantly related teosinte material. A total of 49,585 markers, including 33,417 within 17,520 different genes and 16,168 outside genes, were of good quality for genotyping, with an average failure rate of 4% and rates up to 8% in specific germplasm. To demonstrate this array's use in genetic mapping and for the independent validation of the B73 sequence assembly, two intermated maize recombinant inbred line populations – IBM (B73×Mo17) and LHRF (F2×F252) – were genotyped to establish two high density linkage maps with 20,913 and 14,524 markers respectively. 172 mapped markers were absent in the current B73 assembly and their placement can be used for future improvements of the B73 reference sequence. Colinearity of the genetic and physical maps was mostly conserved with some exceptions that suggest errors in the B73 assembly. Five major regions containing non-colinearities were identified on chromosomes 2, 3, 6, 7 and 9, and are supported by both independent genetic maps. Four additional non-colinear regions were found on the LHRF map only; they may be due to a lower density of IBM markers in those regions or to true structural rearrangements between lines. Given the array's high quality, it will be a valuable resource for maize genetics and many aspects of maize breeding. PMID:22174790

Self-organized TiO2 nanotube arrays in the photocatalytic degradation of methylene blue under UV light irradiation

NASA Astrophysics Data System (ADS)

Chung, Eun Hyuk; Baek, Seong Rim; Yu, Seong Mi; Kim, Jong Pil; Hong, Tae Eun; Kim, Hyun Gyu; Bae, Jong-Seong; Jeong, Euh Duck; Khan, F. Nawaz; Jung, Ok-sang

2015-04-01

Nanostructured titanium dioxide (NTiO2) is known to possess efficient photocatalytic activity and to have diverse applications in many fields due to its chemical stability, high surface area/volume ratio, high transmittance, and high refractive index in the visible and the near-ultraviolet regions. These facts prompted us to develop TiO2 nanotube (TiO2 NT) arrays through electrochemical anodic oxidation involving different electrolytes comprised of phosphoric acid — hydrofluoric acid aqueous systems by varying the voltage and the time. The annealing temperature of the nanotubes, TiO2 NTs, were varied to modify the surface morphology and were characterized by using X-ray diffraction and scanning electron microscopy. Scanning electron microscopy and X-ray diffraction results showed that the samples had uniform morphologies and good crystalline structures of the anatase phase at lower annealing temperatures and of the rutile phase at higher annealing temperatures. A secondary-ion mass-spectrometry analysis was used to investigate the surface atoms and to conduct a depth profile analysis of the TiO2 NTs. The efficiency of the photocatalytic activity of the TiO2 NT arrays in degrading methylene blue (MB) was investigated under UV-Vis light irradiation. The maximum photocatalytic activity was achieved for the samples with lower annealing temperatures due to their being in the anatase phase and having a higher surface area and a smaller crystal size, which play important roles in the degradation of organic pollutants.

Examination of time-reversal acoustics in shallow water and applications to noncoherent underwater communications.

PubMed

Smith, Kevin B; Abrantes, Antonio A M; Larraza, Andres

2003-06-01

The shallow water acoustic communication channel is characterized by strong signal degradation caused by multipath propagation and high spatial and temporal variability of the channel conditions. At the receiver, multipath propagation causes intersymbol interference and is considered the most important of the channel distortions. This paper examines the application of time-reversal acoustic (TRA) arrays, i.e., phase-conjugated arrays (PCAs), that generate a spatio-temporal focus of acoustic energy at the receiver location, eliminating distortions introduced by channel propagation. This technique is self-adaptive and automatically compensates for environmental effects and array imperfections without the need to explicitly characterize the environment. An attempt is made to characterize the influences of a PCA design on its focusing properties with particular attention given to applications in noncoherent underwater acoustic communication systems. Due to the PCA spatial diversity focusing properties, PC arrays may have an important role in an acoustic local area network. Each array is able to simultaneously transmit different messages that will focus only at the destination receiver node.

An Analysis of Artificial Reef Fish Community Structure along the Northwestern Gulf of Mexico Shelf: Potential Impacts of “Rigs-to-Reefs” Programs

PubMed Central

Ajemian, Matthew J.; Wetz, Jennifer J.; Shipley-Lozano, Brooke; Shively, J. Dale; Stunz, Gregory W.

2015-01-01

Artificial structures are the dominant complex marine habitat type along the northwestern Gulf of Mexico (GOM) shelf. These habitats can consist of a variety of materials, but in this region are primarily comprised of active and reefed oil and gas platforms. Despite being established for several decades, the fish communities inhabiting these structures remain poorly investigated. Between 2012 and 2013 we assessed fish communities at 15 sites using remotely operated vehicles (ROVs). Fish assemblages were quantified from standing platforms and an array of artificial reef types (Liberty Ships and partially removed or toppled platforms) distributed over the Texas continental shelf. The depth gradient covered by the surveys (30–84 m) and variability in structure density and relief also permitted analyses of the effects of these characteristics on fish richness, diversity, and assemblage composition. ROVs captured a variety of species inhabiting these reefs from large transient piscivores to small herbivorous reef fishes. While structure type and relief were shown to influence species richness and community structure, major trends in species composition were largely explained by the bottom depth where these structures occurred. We observed a shift in fish communities and relatively high diversity at approximately 60 m bottom depth, confirming trends observed in previous studies of standing platforms. This depth was also correlated with some of the largest Red Snapper captured on supplementary vertical longline surveys. Our work indicates that managers of artificial reefing programs (e.g., Rigs-to-Reefs) in the GOM should carefully consider the ambient environmental conditions when designing reef sites. For the Texas continental shelf, reefing materials at a 50–60 m bottom depth can serve a dual purpose of enhancing diving experiences and providing the best potential habitat for relatively large Red Snapper. PMID:25954943

Using in-cell SHAPE-Seq and simulations to probe structure–function design principles of RNA transcriptional regulators

PubMed Central

Takahashi, Melissa K.; Watters, Kyle E.; Gasper, Paul M.; Abbott, Timothy R.; Carlson, Paul D.; Chen, Alan A.

2016-01-01

Antisense RNA-mediated transcriptional regulators are powerful tools for controlling gene expression and creating synthetic gene networks. RNA transcriptional repressors derived from natural mechanisms called attenuators are particularly versatile, though their mechanistic complexity has made them difficult to engineer. Here we identify a new structure–function design principle for attenuators that enables the forward engineering of new RNA transcriptional repressors. Using in-cell SHAPE-Seq to characterize the structures of attenuator variants within Escherichia coli, we show that attenuator hairpins that facilitate interaction with antisense RNAs require interior loops for proper function. Molecular dynamics simulations of these attenuator variants suggest these interior loops impart structural flexibility. We further observe hairpin flexibility in the cellular structures of natural RNA mechanisms that use antisense RNA interactions to repress translation, confirming earlier results from in vitro studies. Finally, we design new transcriptional attenuators in silico using an interior loop as a structural requirement and show that they function as desired in vivo. This work establishes interior loops as an important structural element for designing synthetic RNA gene regulators. We anticipate that the coupling of experimental measurement of cellular RNA structure and function with computational modeling will enable rapid discovery of structure–function design principles for a diverse array of natural and synthetic RNA regulators. PMID:27103533

ABSTRACT PRESENTATION--PHARMACEUTICALS AS ENVIRONMENTAL CONTAMINATS: AN OVERVIEW OF THE SCIENCE

EPA Science Inventory

Pharmaceuticals comprise a large and diverse array of contaminants that can occur in the environmentfrom the combined activities and actions of multitudes of individuals as well as from veterinary andagricultural use.

Subwavelength grating enabled on-chip ultra-compact optical true time delay line

PubMed Central

Wang, Junjia; Ashrafi, Reza; Adams, Rhys; Glesk, Ivan; Gasulla, Ivana; Capmany, José; Chen, Lawrence R.

2016-01-01

An optical true time delay line (OTTDL) is a basic photonic building block that enables many microwave photonic and optical processing operations. The conventional design for an integrated OTTDL that is based on spatial diversity uses a length-variable waveguide array to create the optical time delays, which can introduce complexities in the integrated circuit design. Here we report the first ever demonstration of an integrated index-variable OTTDL that exploits spatial diversity in an equal length waveguide array. The approach uses subwavelength grating waveguides in silicon-on-insulator (SOI), which enables the realization of OTTDLs having a simple geometry and that occupy a compact chip area. Moreover, compared to conventional wavelength-variable delay lines with a few THz operation bandwidth, our index-variable OTTDL has an extremely broad operation bandwidth practically exceeding several tens of THz, which supports operation for various input optical signals with broad ranges of central wavelength and bandwidth. PMID:27457024

The Next Generation of Space Cells for Diverse Environments

NASA Technical Reports Server (NTRS)

Bailey, Sheila; Landis, Geoffrey; Raffaelle, Ryne

2002-01-01

Future science, military and commercial space missions are incredibly diverse. Military and commercial missions range from large arrays of hundreds of kilowatt to small arrays of ten watts in various Earth orbits. While science missions also have small to very large power needs there are additional unique requirements to provide power for near-sun missions and planetary exploration including orbiters, landers and rovers both to the inner planets and the outer planets with a major emphasis in the near term on Mars. These mission requirements demand cells for low intensity, low temperature applications, high intensity, high temperature applications, dusty environments and often high radiation environments. This paper discusses mission requirements, the current state of the art of space solar cells, and a variety of both evolving thin-film cells as well as new technologies that may impact the future choice of space solar cells for a specific mission application.

Surface Diversity

NASA Image and Video Library

2016-03-17

This enhanced color view of Pluto's surface diversity was created by merging Ralph/Multispectral Visible Imaging Camera (MVIC) color imagery (650 meters per pixel) with Long Range Reconnaissance Imager panchromatic imagery (230 meters per pixel). At lower right, ancient, heavily cratered terrain is coated with dark, reddish tholins. At upper right, volatile ices filling the informally named Sputnik Planum have modified the surface, creating a chaos-like array of blocky mountains. Volatile ice also occupies a few nearby deep craters, and in some areas the volatile ice is pocked with arrays of small sublimation pits. At left, and across the bottom of the scene, gray-white CH4 ice deposits modify tectonic ridges, the rims of craters, and north-facing slopes. The scene in this image is 260 miles (420 kilometers) wide and 140 miles (225 kilometers) from top to bottom; north is to the upper left. http://photojournal.jpl.nasa.gov/catalog/PIA20534

Subwavelength grating enabled on-chip ultra-compact optical true time delay line.

PubMed

Wang, Junjia; Ashrafi, Reza; Adams, Rhys; Glesk, Ivan; Gasulla, Ivana; Capmany, José; Chen, Lawrence R

2016-07-26

An optical true time delay line (OTTDL) is a basic photonic building block that enables many microwave photonic and optical processing operations. The conventional design for an integrated OTTDL that is based on spatial diversity uses a length-variable waveguide array to create the optical time delays, which can introduce complexities in the integrated circuit design. Here we report the first ever demonstration of an integrated index-variable OTTDL that exploits spatial diversity in an equal length waveguide array. The approach uses subwavelength grating waveguides in silicon-on-insulator (SOI), which enables the realization of OTTDLs having a simple geometry and that occupy a compact chip area. Moreover, compared to conventional wavelength-variable delay lines with a few THz operation bandwidth, our index-variable OTTDL has an extremely broad operation bandwidth practically exceeding several tens of THz, which supports operation for various input optical signals with broad ranges of central wavelength and bandwidth.

Effect of Increasing Nitrogen Deposition on Soil Microbial Communities

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

Xiao, Shengmu; Xue, Kai; He, Zhili

2010-05-17

Increasing nitrogen deposition, increasing atmospheric CO2, and decreasing biodiversity are three main environmental changes occurring on a global scale. The BioCON (Biodiversity, CO2, and Nitrogen) ecological experiment site at the University of Minnesota's Cedar Creek Ecosystem Science Reserve started in 1997, to better understand how these changes would affect soil systems. To understand how increasing nitrogen deposition affects the microbial community diversity, heterogeneity, and functional structure impact soil microbial communities, 12 samples were collected from the BioCON plots in which nitrogenous fertilizer was added to simulate the effect of increasing nitrogen deposition and 12 samples from without added fertilizer. DNAmore » from the 24 samples was extracted using a freeze-grind protocol, amplified, labeled with a fluorescent dye, and then hybridized to GeoChip, a functional gene array containing probes for genes involved in N, S and C cycling, metal resistance and organic contaminant degradation. Detrended correspondence analysis (DCA) of all genes detected was performed to analyze microbial community patterns. The first two axes accounted for 23.5percent of the total variation. The samples fell into two major groups: fertilized and non-fertilized, suggesting that nitrogenous fertilizer had a significant impact on soil microbial community structure and diversity. The functional gene numbers detected in fertilized samples was less that detected in non-fertilizer samples. Functional genes involving in the N cycling were mainly discussed.« less

How could discharge management affect Florida spring fish assemblage structure?

PubMed

Work, Kirsten; Codner, Keneil; Gibbs, Melissa

2017-08-01

Freshwater bodies are increasingly affected by reductions in water quantity and quality and by invasions of exotic species. To protect water quantity and maintain the ecological integrity of many water bodies in central Florida, a program of adopting Minimum Flows and Levels (MFLs) has begun for both lentic and lotic waters. The purpose of this study was to determine whether there were relationships between discharge and stage, water quality, and biological parameters for Volusia Blue Spring, a first magnitude spring (discharge > 380,000 m 3 day -1 or 100 mgd) for which an MFL program was adopted in 2006. Over the course of fourteen years, we assessed fish density and diversity weekly, monthly, or seasonally with seine and snorkel counts. We evaluated annual changes in the assemblages for relationships with water quantity and quality. Low discharge and dissolved oxygen combined with high stage and conductivity produced a fish population with a lower density and diversity in 2014 than in previous years. Densities of fish taxonomic/functional groups also were low in 2014 and measures of water quantity were significant predictors of fish assemblage structure. As a result of the strong relationships between variation in discharge and an array of chemical and biological characteristics of the spring, we conclude that maintaining the historical discharge rate is important for preserving the ecological integrity of Volusia Blue Spring. Copyright © 2017 Elsevier Ltd. All rights reserved.

Functional gene diversity of soil microbial communities from five oil-contaminated fields in China.

PubMed

Liang, Yuting; Van Nostrand, Joy D; Deng, Ye; He, Zhili; Wu, Liyou; Zhang, Xu; Li, Guanghe; Zhou, Jizhong

2011-03-01

To compare microbial functional diversity in different oil-contaminated fields and to know the effects of oil contaminant and environmental factors, soil samples were taken from typical oil-contaminated fields located in five geographic regions of China. GeoChip, a high-throughput functional gene array, was used to evaluate the microbial functional genes involved in contaminant degradation and in other major biogeochemical/metabolic processes. Our results indicated that the overall microbial community structures were distinct in each oil-contaminated field, and samples were clustered by geographic locations. The organic contaminant degradation genes were most abundant in all samples and presented a similar pattern under oil contaminant stress among the five fields. In addition, alkane and aromatic hydrocarbon degradation genes such as monooxygenase and dioxygenase were detected in high abundance in the oil-contaminated fields. Canonical correspondence analysis indicated that the microbial functional patterns were highly correlated to the local environmental variables, such as oil contaminant concentration, nitrogen and phosphorus contents, salt and pH. Finally, a total of 59% of microbial community variation from GeoChip data can be explained by oil contamination, geographic location and soil geochemical parameters. This study provided insights into the in situ microbial functional structures in oil-contaminated fields and discerned the linkages between microbial communities and environmental variables, which is important to the application of bioremediation in oil-contaminated sites.

Functional gene diversity of soil microbial communities from five oil-contaminated fields in China

PubMed Central

Liang, Yuting; Van Nostrand, Joy D; Deng, Ye; He, Zhili; Wu, Liyou; Zhang, Xu; Li, Guanghe; Zhou, Jizhong

2011-01-01

To compare microbial functional diversity in different oil-contaminated fields and to know the effects of oil contaminant and environmental factors, soil samples were taken from typical oil-contaminated fields located in five geographic regions of China. GeoChip, a high-throughput functional gene array, was used to evaluate the microbial functional genes involved in contaminant degradation and in other major biogeochemical/metabolic processes. Our results indicated that the overall microbial community structures were distinct in each oil-contaminated field, and samples were clustered by geographic locations. The organic contaminant degradation genes were most abundant in all samples and presented a similar pattern under oil contaminant stress among the five fields. In addition, alkane and aromatic hydrocarbon degradation genes such as monooxygenase and dioxygenase were detected in high abundance in the oil-contaminated fields. Canonical correspondence analysis indicated that the microbial functional patterns were highly correlated to the local environmental variables, such as oil contaminant concentration, nitrogen and phosphorus contents, salt and pH. Finally, a total of 59% of microbial community variation from GeoChip data can be explained by oil contamination, geographic location and soil geochemical parameters. This study provided insights into the in situ microbial functional structures in oil-contaminated fields and discerned the linkages between microbial communities and environmental variables, which is important to the application of bioremediation in oil-contaminated sites. PMID:20861922

Contrasting microbial functional genes in two distinct saline-alkali and slightly acidic oil-contaminated sites.

PubMed

Liang, Yuting; Zhao, Huihui; Zhang, Xu; Zhou, Jizhong; Li, Guanghe

2014-07-15

To compare the functional gene structure and diversity of microbial communities in saline-alkali and slightly acidic oil-contaminated sites, 40 soil samples were collected from two typical oil exploration sites in North and South China and analyzed with a comprehensive functional gene array (GeoChip 3.0). The overall microbial pattern was significantly different between the two sites, and a more divergent pattern was observed in slightly acidic soils. Response ratio was calculated to compare the microbial functional genes involved in organic contaminant degradation and carbon, nitrogen, phosphorus, and sulfur cycling. The results indicated a significantly low abundance of most genes involved in organic contaminant degradation and in the cycling of nitrogen and phosphorus in saline-alkali soils. By contrast, most carbon degradation genes and all carbon fixation genes had similar abundance at both sites. Based on the relationship between the environmental variables and microbial functional structure, pH was the major factor influencing the microbial distribution pattern in the two sites. This study demonstrated that microbial functional diversity and heterogeneity in oil-contaminated environments can vary significantly in relation to local environmental conditions. The limitation of nitrogen and phosphorus and the low degradation capacity of organic contaminant should be carefully considered, particularly in most oil-exploration sites with saline-alkali soils. Copyright © 2014 Elsevier B.V. All rights reserved.

Formation of precise 2D Au particle arrays via thermally induced dewetting on pre-patterned substrates

PubMed Central

Ji, Ran

2011-01-01

Summary The fabrication of precise 2D Au nanoparticle arrays over a large area is presented. The technique was based on pre-patterning of the substrate before the deposition of a thin Au film, and the creation of periodic particle arrays by subsequent dewetting induced by annealing. Two types of pre-patterned substrates were used: The first comprised an array of pyramidal pits and the second an array of circular holes. For the dewetting of Au films on the pyramidal pit substrate, the structural curvature-driven diffusion cooperates with capillarity-driven diffusion, resulting in the formation of precise 2D particle arrays for films within a structure dependent thickness-window. For the dewetting of Au films on the circular hole substrate, the periodic discontinuities in the films, induced by the deposition, can limit the diffusion paths and lead to the formation of one particle per individual separated region (holes or mesas between holes), and thus, result in the evolution of precise 2D particle arrays. The influence of the pre-patterned structures and the film thickness is analyzed and discussed. For both types of pre-patterned substrate, the Au film thickness had to be adjusted in a certain thickness-window in order to achieve the precise 2D particle arrays. PMID:21977445

SELF CALIBRATED STMR ARRAY FOR MATERIAL CHARACTERIZATION AND SHM OF ORTHOTROPIC PLATE-LIKE STRUCTURES

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

Vishnuvardhan, J.; Muralidharan, Ajith; Balasubramaniam, Krishnan

A full ring STMR array patch had been used for Structural Health Monitoring (SHM) of anisotropic materials where the elastic moduli, correspond to the virgin sample, were used in the calculations. In the present work an in-situ SHM has been successfully demonstrated using a novel compact sensor patch (Double ring single quadrant small footprint STMR array) through simultaneous reconstruction of the elastic moduli, material symmetry, orientation of principal planes and defect imaging. The direct received signals were used to measure Lamb wave velocities, which were used in a slowness based reconstructed algorithm using Genetic Algorithm to reconstruct the elastic moduli,more » material symmetry and orientation of principal planes. The measured signals along with the reconstructed elastic moduli were used in the phased addition algorithm for imaging the damages present on the structure. To show the applicability of the method, simulations were carried out with the double ring single quadrant STMR array configuration to image defects and are compared with the images obtained using simulation data of the full ring STMR array configuration. The experimental validation has been carried out using 3.15 mm quasi-isotropic graphite-epoxy composite. The double ring single quadrant STMR array has advantages over the full ring STMR array as it can carry out in-situ SHM with limited footprint on the structure.« less

Investigation of CuInSe2 nanowire arrays with core-shell structure electrodeposited at various duty cycles into anodic alumina templates

NASA Astrophysics Data System (ADS)

Cheng, Yu-Song; Wang, Na-Fu; Tsai, Yu-Zen; Lin, Jia-Jun; Houng, Mau-Phon

2017-02-01

Copper indium selenide (CuInSe2) nanowire (NW) arrays were prepared at various electrolyte duty cycles by filling anodic alumina templates through the pulsed electrodeposition technique. X-ray diffraction and scanning electron microscopy (SEM) images showed that the nucleation mechanism of CuInSe2 NW arrays was affected by the electrodeposition duty cycle. Moreover, SEM images showed that the diameter and length of the NWs were 80 nm and 2 μm, respectively. Furthermore, PEDOT/CuInSe2 NW core-shell arrays were fabricated using surfactant-modified CuInSe2 NW surfaces showing the lotus effect. Transmission electron microscopy images confirmed that a core-shell structure was achieved. Current-voltage plots revealed that the CuInSe2 NW arrays were p-type semiconductors; moreover, the core-shell structure improved the diode ideality factor from 3.91 to 2.63.

Concept Definition Study for In-Space Structural Characterization of a Lightweight Solar Array

NASA Technical Reports Server (NTRS)

Woods-Vedeler, Jessica A.; Pappa, Richard S.; Jones, Thomas W.; Spellman, Regina; Scott, Willis; Mockensturm, Eric M.; Liddle, Donn; Oshel, Ed; Snyder, Michael

2002-01-01

A Concept Definition Study (CDS) was conducted to develop a proposed "Lightweight High-Voltage Stretched-Lens Concentrator Solar Array Experiment" under NASA's New Millennium Program Space Technology-6 (NMP ST-6) activity. As part of a multi-organizational team, NASA Langley Research Center's role in this proposed experiment was to lead Structural Characterization of the solar array during the flight experiment. In support of this role, NASA LaRC participated in the CDS to de.ne an experiment for static, dynamic, and deployment characterization of the array. In this study, NASA LaRC traded state-of-the-art measurement approaches appropriate for an in-space, STS-based flight experiment, provided initial analysis and testing of the lightweight solar array and lens elements, performed a lighting and photogrammetric simulation in conjunction with JSC, and produced an experiment concept definition to meet structural characterization requirements.

Using in-cell SHAPE-Seq and simulations to probe structure-function design principles of RNA transcriptional regulators.

PubMed

Takahashi, Melissa K; Watters, Kyle E; Gasper, Paul M; Abbott, Timothy R; Carlson, Paul D; Chen, Alan A; Lucks, Julius B

2016-06-01

Antisense RNA-mediated transcriptional regulators are powerful tools for controlling gene expression and creating synthetic gene networks. RNA transcriptional repressors derived from natural mechanisms called attenuators are particularly versatile, though their mechanistic complexity has made them difficult to engineer. Here we identify a new structure-function design principle for attenuators that enables the forward engineering of new RNA transcriptional repressors. Using in-cell SHAPE-Seq to characterize the structures of attenuator variants within Escherichia coli, we show that attenuator hairpins that facilitate interaction with antisense RNAs require interior loops for proper function. Molecular dynamics simulations of these attenuator variants suggest these interior loops impart structural flexibility. We further observe hairpin flexibility in the cellular structures of natural RNA mechanisms that use antisense RNA interactions to repress translation, confirming earlier results from in vitro studies. Finally, we design new transcriptional attenuators in silico using an interior loop as a structural requirement and show that they function as desired in vivo. This work establishes interior loops as an important structural element for designing synthetic RNA gene regulators. We anticipate that the coupling of experimental measurement of cellular RNA structure and function with computational modeling will enable rapid discovery of structure-function design principles for a diverse array of natural and synthetic RNA regulators. © 2016 Takahashi et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Low-cost solar array structure development

NASA Astrophysics Data System (ADS)

Wilson, A. H.

1981-06-01

Early studies of flat-plate arrays have projected costs on the order of $50/square meter for installed array support structures. This report describes an optimized low-cost frame-truss structure that is estimated to cost below $25/square meter, including all markups, shipping an installation. The structure utilizes a planar frame made of members formed from light-gauge galvanized steel sheet and is supposed in the field by treated-wood trusses that are partially buried in trenches. The buried trusses use the overburden soil to carry uplift wind loads and thus to obviate reinforced-concrete foundations. Details of the concept, including design rationale, fabrication and assembly experience, structural testing and fabrication drawings are included.

Low-cost solar array structure development

NASA Technical Reports Server (NTRS)

Wilson, A. H.

1981-01-01

Early studies of flat-plate arrays have projected costs on the order of $50/square meter for installed array support structures. This report describes an optimized low-cost frame-truss structure that is estimated to cost below $25/square meter, including all markups, shipping an installation. The structure utilizes a planar frame made of members formed from light-gauge galvanized steel sheet and is supposed in the field by treated-wood trusses that are partially buried in trenches. The buried trusses use the overburden soil to carry uplift wind loads and thus to obviate reinforced-concrete foundations. Details of the concept, including design rationale, fabrication and assembly experience, structural testing and fabrication drawings are included.

Reception of Multiple Telemetry Signals via One Dish Antenna

NASA Technical Reports Server (NTRS)

Mukai, Ryan; Vilnrotter, Victor

2010-01-01

A microwave aeronautical-telemetry receiver system includes an antenna comprising a seven-element planar array of receiving feed horns centered at the focal point of a paraboloidal dish reflector that is nominally aimed at a single aircraft or at multiple aircraft flying in formation. Through digital processing of the signals received by the seven feed horns, the system implements a method of enhanced cancellation of interference, such that it becomes possible to receive telemetry signals in the same frequency channel simultaneously from either or both of two aircraft at slightly different angular positions within the field of view of the antenna, even in the presence of multipath propagation. The present system is an advanced version of the system described in Spatio- Temporal Equalizer for a Receiving-Antenna Feed Array NPO-43077, NASA Tech Briefs, Vol. 34, No. 2 (February 2010), page 32. To recapitulate: The radio-frequency telemetry signals received by the seven elements of the array are digitized, converted to complex baseband form, and sent to a spatio-temporal equalizer that consists mostly of a bank of seven adaptive finite-impulse-response (FIR) filters (one for each element in the array) plus a unit that sums the outputs of the filters. The combination of the spatial diversity of the feedhorn array and the temporal diversity of the filter bank affords better multipath suppression performance than is achievable by means of temporal equalization alone. The FIR filter bank adapts itself in real time to enable reception of telemetry at a low bit error rate, even in the presence of frequency-selective multipath propagation like that commonly found at flight-test ranges. The combination of the array and the filter bank makes it possible to constructively add multipath incoming signals to the corresponding directly arriving signals, thereby enabling reductions in telemetry bit-error rates.

DNA Microarray Profiling of a Diverse Collection of Nosocomial Methicillin-Resistant Staphylococcus aureus Isolates Assigns the Majority to the Correct Sequence Type and Staphylococcal Cassette Chromosome mec (SCCmec) Type and Results in the Subsequent Identification and Characterization of Novel SCCmec-SCCM1 Composite Islands

PubMed Central

Brennan, Orla M.; Deasy, Emily C.; Rossney, Angela S.; Kinnevey, Peter M.; Ehricht, Ralf; Monecke, Stefan; Coleman, David C.

2012-01-01

One hundred seventy-five isolates representative of methicillin-resistant Staphylococcus aureus (MRSA) clones that predominated in Irish hospitals between 1971 and 2004 and that previously underwent multilocus sequence typing (MLST) and staphylococcal cassette chromosome mec (SCCmec) typing were characterized by spa typing (175 isolates) and DNA microarray profiling (107 isolates). The isolates belonged to 26 sequence type (ST)-SCCmec types and subtypes and 35 spa types. The array assigned all isolates to the correct MLST clonal complex (CC), and 94% (100/107) were assigned an ST, with 98% (98/100) correlating with MLST. The array assigned all isolates to the correct SCCmec type, but subtyping of only some SCCmec elements was possible. Additional SCCmec/SCC genes or DNA sequence variation not detected by SCCmec typing was detected by array profiling, including the SCC-fusidic acid resistance determinant Q6GD50/fusC. Novel SCCmec/SCC composite islands (CIs) were detected among CC8 isolates and comprised SCCmec IIA-IIE, IVE, IVF, or IVg and a ccrAB4-SCC element with 99% DNA sequence identity to SCCM1 from ST8/t024-MRSA, SCCmec VIII, and SCC-CI in Staphylococcus epidermidis. The array showed that the majority of isolates harbored one or more superantigen (94%; 100/107) and immune evasion cluster (91%; 97/107) genes. Apart from fusidic acid and trimethoprim resistance, the correlation between isolate antimicrobial resistance phenotype and the presence of specific resistance genes was ≥97%. Array profiling allowed high-throughput, accurate assignment of MRSA to CCs/STs and SCCmec types and provided further evidence of the diversity of SCCmec/SCC. In most cases, array profiling can accurately predict the resistance phenotype of an isolate. PMID:22869569

Field ionization characteristics of an ion source array for neutron generators

NASA Astrophysics Data System (ADS)

Bargsten Johnson, B.; Schwoebel, P. R.; Resnick, P. J.; Holland, C. E.; Hertz, K. L.; Chichester, D. L.

2013-11-01

A new deuterium ion source is being developed to improve the performance of existing compact neutron generators. The ion source is a microfabricated array of metal tips with an integrated gate (i.e., grid) and produces deuterium ions by field ionizing (or field desorbing) a supply of deuterium gas. Deuterium field ion currents from arrays at source temperatures of 77 K and 293 K are studied. Ion currents from single etched-wire tips operating under the same conditions are used to help understand array results. I-F characteristics of the arrays were found to follow trends similar to those of the better understood single etched-wire tip results; however, the fields achieved by the arrays are limited by electrical breakdown of the structure. Neutron production by field ionization at 293 K was demonstrated for the first time from microfabricated array structures with integrated gates.

Find structural aspects of anthozoan desmocyte development (phylum Cnidaria).

PubMed

Tidball, J G

1982-01-01

The fine structural changes associated with the differentiation of skeletogenic cells into cells specialized in binding soft tissues onto skeletal structures are described in the gorgonian coral, Leptogorgia virgulata (Lam.). These binding cells are called desmocytes. The sequence of events in desmocyte development includes: growth of the plasma membrane, invagination of the mesoglea-end of the cell, expansion of the axis-end of the cell, loss of organelles involved in skeletogenesis, proliferation of double vesicles and transformation of double vesicles into cytoskeletal rods. Double vesicles appear either cup-shaped or as a vesicle within a vesicle in sectioned material. These observations of desmocyte development are compared to previous light microscopical observations desmocyte development in diverse forms of anthozoans. Similarities in desmocyte development throughout the class include invagination of the differentiating cell, formation of a pectinate mesogleal margin and formation of an array of cytoskeletal rods at the axis-end of the cell. Comparison with available information on the development and fine structure of desmocytes in the cnidarian classes Scyphozoa and Hydrozoa shows these similarities do not extend across class boundaries and, therefore, common ancestry between the three classes of cnidarian desmocytes seems remote if, indeed, such an ancestral cell existed at all.

Aluminum-based one- and two-dimensional micro fin array structures: high-throughput fabrication and heat transfer testing

NASA Astrophysics Data System (ADS)

Primeaux, Philip A.; Zhang, Bin; Zhang, Xiaoman; Miller, Jacob; Meng, W. J.; KC, Pratik; Moore, Arden L.

2017-02-01

Microscale fin array structures were replicated onto surfaces of aluminum 1100 and aluminum 6061 alloy (Al1100/Al6061) sheet metals through room-temperature instrumented roll molding. Aluminum-based micro fin arrays were replicated at room temperature, and the fabrication process is one with high throughput and low cost. One-dimensional (1D) micro fin arrays were made through one-pass rolling, while two-dimensional (2D) micro fin arrays were made by sequential 90° cross rolling with the same roller sleeve. For roll molding of 1D micro fins, fin heights greater than 600 µm were achieved and were shown to be proportional to the normal load force per feature width. At a given normal load force, the fin height was further shown to scale inversely with the hardness of the sheet metal. For sequential 90° cross rolling, morphologies of roll molded 2D micro fin arrays were examined, which provided clues to understand how plastic deformation occurred under cross rolling conditions. A series of pool boiling experiments on low profile Al micro fin array structures were performed within Novec 7100, a widely used commercial dielectric coolant. Results for both horizontal and vertical surface orientations show that roll molded Al micro fin arrays can increase heat flux at fixed surface temperature as compared to un-patterned Al sheet. The present results further suggest that many factors beyond just increased surface area can influence heat transfer performance, including surface finish and the important multiphase transport mechanisms in and around the fin geometry. These factors must also be considered when designing and optimizing micro fin array structures for heat transfer applications.

Physiogenomic analysis of the Puerto Rican population.

PubMed

Ruaño, Gualberto; Duconge, Jorge; Windemuth, Andreas; Cadilla, Carmen L; Kocherla, Mohan; Villagra, David; Renta, Jessica; Holford, Theodore; Santiago-Borrero, Pedro J

2009-04-01

Admixture in the population of the island of Puerto Rico is of general interest with regards to pharmacogenetics to develop comprehensive strategies for personalized healthcare in Latin Americans. This research was aimed at determining the frequencies of SNPs in key physiological, pharmacological and biochemical genes to infer population structure and ancestry in the Puerto Rican population. A noninterventional, cross-sectional, retrospective study design was implemented following a controlled, stratified-by-region, random sampling protocol. The sample was based on birthrates in each region of the island of Puerto Rico, according to the 2004 National Birth Registry. Genomic DNA samples from 100 newborns were obtained from the Puerto Rico Newborn Screening Program in dried-blood spot cards. Genotyping using a physiogenomic array was performed for 332 SNPs from 196 cardiometabolic and neuroendocrine genes. Population structure was examined using a Bayesian clustering approach as well as by allelic dissimilarity as a measure of allele sharing. The Puerto Rican sample was found to be broadly heterogeneous. We observed three main clusters in the population, which we hypothesize to reflect the historical admixture in the Puerto Rican population from Amerindian, African and European ancestors. We present evidence for this interpretation by comparing allele frequencies for the three clusters with those for the same SNPs available from the International HapMap project for Asian, African and European populations. Our results demonstrate that population analysis can be performed with a physiogenomic array of cardiometabolic and neuroendocrine genes to facilitate the translation of genome diversity into personalized medicine.

Online screening of nitric oxide scavengers in natural products using high performance liquid chromatography coupled with tandem diode array and fluorescence detection.

PubMed

Li, Dapeng; Wang, Ting; Guo, Yujie; Hu, Yuanjia; Yu, Boyang; Qi, Jin

2015-12-18

Nitric oxide (NO) is an important cellular signaling molecule with extensive physiological and pathophysiological effects. NO scavengers have the potential to treat inflammation, septic shock and other related diseases, and numerous examples have been chemically synthesized or isolated from natural products. The chemical diversity of natural products, however, means that a huge effort is necessary to efficiently screen and identify bioactive compounds, especially NO scavengers. In this article, we propose an effective analytical method to screen for NO scavengers in three natural products using an online system that couples high performance liquid chromatography with tandem diode array and fluorescence detection (HPLC-DAD-FLD). Eighteen compounds from radix of Scutellaria baicalensis Georgi and green tea displayed significant NO scavenging activity whereas components of Pueraria lobata (Willd.) Ohwi had no discernable activity. The structures of the active compounds were elucidated using Agilent Accurate-Mass Q-TOF LC/MS system. Preliminary analysis of structure-activity relationships indicated that, in flavonoids, a 2,3-double bond and a 3-H atom or a 3-OH group are essential for activity. In tannins, poly-hydroxyl groups are important for NO scavenging activity. Method validation indicated that the newly developed method is both reliable and repeatable. The online method that we present provides a simple, rapid and effective way to identify and characterize NO scavengers present in natural products. Copyright © 2015 Elsevier B.V. All rights reserved.

Structural properties of templated Ge quantum dot arrays: impact of growth and pre-pattern parameters

NASA Astrophysics Data System (ADS)

Tempeler, J.; Danylyuk, S.; Brose, S.; Loosen, P.; Juschkin, L.

2018-07-01

In this study we analyze the impact of process and growth parameters on the structural properties of germanium (Ge) quantum dot (QD) arrays. The arrays were deposited by molecular-beam epitaxy on pre-patterned silicon (Si) substrates. Periodic arrays of pits with diameters between 120 and 20 nm and pitches ranging from 200 nm down to 40 nm were etched into the substrate prior to growth. The structural perfection of the two-dimensional QD arrays was evaluated based on SEM images. The impact of two processing steps on the directed self-assembly of Ge QD arrays is investigated. First, a thin Si buffer layer grown on a pre-patterned substrate reshapes the pre-pattern pits and determines the nucleation and initial shape of the QDs. Subsequently, the deposition parameters of the Ge define the overall shape and uniformity of the QDs. In particular, the growth temperature and the deposition rate are relevant and need to be optimized according to the design of the pre-pattern. Applying this knowledge, we are able to fabricate regular arrays of pyramid shaped QDs with dot densities up to 7.2 × 1010 cm‑2.

Fabrication of a 3D micro/nano dual-scale carbon array and its demonstration as the microelectrodes for supercapacitors

NASA Astrophysics Data System (ADS)

Jiang, Shulan; Shi, Tielin; Gao, Yang; Long, Hu; Xi, Shuang; Tang, Zirong

2014-04-01

An easily accessible method is proposed for the fabrication of a 3D micro/nano dual-scale carbon array with a large surface area. The process mainly consists of three critical steps. Firstly, a hemispherical photoresist micro-array was obtained by the cost-effective nanoimprint lithography process. Then the micro-array was transformed into hierarchical structures with longitudinal nanowires on the microstructure surface by oxygen plasma etching. Finally, the micro/nano dual-scale carbon array was fabricated by carbonizing these hierarchical photoresist structures. It has also been demonstrated that the micro/nano dual-scale carbon array can be used as the microelectrodes for supercapacitors by the electrodeposition of a manganese dioxide (MnO2) film onto the hierarchical carbon structures with greatly enhanced electrochemical performance. The specific gravimetric capacitance of the deposited micro/nano dual-scale microelectrodes is estimated to be 337 F g-1 at the scan rate of 5 mV s-1. This proposed approach of fabricating a micro/nano dual-scale carbon array provides a facile way in large-scale microstructures’ manufacturing for a wide variety of applications, including sensors and on-chip energy storage devices.

Structural properties of templated Ge quantum dot arrays: impact of growth and pre-pattern parameters.

PubMed

Tempeler, J; Danylyuk, S; Brose, S; Loosen, P; Juschkin, L

2018-07-06

In this study we analyze the impact of process and growth parameters on the structural properties of germanium (Ge) quantum dot (QD) arrays. The arrays were deposited by molecular-beam epitaxy on pre-patterned silicon (Si) substrates. Periodic arrays of pits with diameters between 120 and 20 nm and pitches ranging from 200 nm down to 40 nm were etched into the substrate prior to growth. The structural perfection of the two-dimensional QD arrays was evaluated based on SEM images. The impact of two processing steps on the directed self-assembly of Ge QD arrays is investigated. First, a thin Si buffer layer grown on a pre-patterned substrate reshapes the pre-pattern pits and determines the nucleation and initial shape of the QDs. Subsequently, the deposition parameters of the Ge define the overall shape and uniformity of the QDs. In particular, the growth temperature and the deposition rate are relevant and need to be optimized according to the design of the pre-pattern. Applying this knowledge, we are able to fabricate regular arrays of pyramid shaped QDs with dot densities up to 7.2 × 10 10 cm -2 .

Metagenomic evidence for metabolism of trace atmospheric gases by high-elevation desert Actinobacteria

PubMed Central

Lynch, Ryan C.; Darcy, John L.; Kane, Nolan C.; Nemergut, Diana R.; Schmidt, Steve K.

2014-01-01

Previous surveys of very dry Atacama Desert mineral soils have consistently revealed sparse communities of non-photosynthetic microbes. The functional nature of these microorganisms remains debatable given the harshness of the environment and low levels of biomass and diversity. The aim of this study was to gain an understanding of the phylogenetic community structure and metabolic potential of a low-diversity mineral soil metagenome that was collected from a high-elevation Atacama Desert volcano debris field. We pooled DNA extractions from over 15 g of volcanic material, and using whole genome shotgun sequencing, observed only 75–78 total 16S rRNA gene OTUs3%. The phylogenetic structure of this community is significantly under dispersed, with actinobacterial lineages making up 97.9–98.6% of the 16S rRNA genes, suggesting a high degree of environmental selection. Due to this low diversity and uneven community composition, we assembled and analyzed the metabolic pathways of the most abundant genome, a Pseudonocardia sp. (56–72% of total 16S genes). Our assembly and binning efforts yielded almost 4.9 Mb of Pseudonocardia sp. contigs, which accounts for an estimated 99.3% of its non-repetitive genomic content. This genome contains a limited array of carbohydrate catabolic pathways, but encodes for CO2 fixation via the Calvin cycle. The genome also encodes complete pathways for the catabolism of various trace gases (H2, CO and several organic C1 compounds) and the assimilation of ammonia and nitrate. We compared genomic content among related Pseudonocardia spp. and estimated rates of non-synonymous and synonymous nucleic acid substitutions between protein coding homologs. Collectively, these comparative analyses suggest that the community structure and various functional genes have undergone strong selection in the nutrient poor desert mineral soils and high-elevation atmospheric conditions. PMID:25566214

Metagenomes from High-Temperature Chemotrophic Systems Reveal Geochemical Controls on Microbial Community Structure and Function

PubMed Central

Inskeep, William P.; Rusch, Douglas B.; Jay, Zackary J.; Herrgard, Markus J.; Kozubal, Mark A.; Richardson, Toby H.; Macur, Richard E.; Hamamura, Natsuko; Jennings, Ryan deM.; Fouke, Bruce W.; Reysenbach, Anna-Louise; Roberto, Frank; Young, Mark; Schwartz, Ariel; Boyd, Eric S.; Badger, Jonathan H.; Mathur, Eric J.; Ortmann, Alice C.; Bateson, Mary; Geesey, Gill; Frazier, Marvin

2010-01-01

The Yellowstone caldera contains the most numerous and diverse geothermal systems on Earth, yielding an extensive array of unique high-temperature environments that host a variety of deeply-rooted and understudied Archaea, Bacteria and Eukarya. The combination of extreme temperature and chemical conditions encountered in geothermal environments often results in considerably less microbial diversity than other terrestrial habitats and offers a tremendous opportunity for studying the structure and function of indigenous microbial communities and for establishing linkages between putative metabolisms and element cycling. Metagenome sequence (14–15,000 Sanger reads per site) was obtained for five high-temperature (>65°C) chemotrophic microbial communities sampled from geothermal springs (or pools) in Yellowstone National Park (YNP) that exhibit a wide range in geochemistry including pH, dissolved sulfide, dissolved oxygen and ferrous iron. Metagenome data revealed significant differences in the predominant phyla associated with each of these geochemical environments. Novel members of the Sulfolobales are dominant in low pH environments, while other Crenarchaeota including distantly-related Thermoproteales and Desulfurococcales populations dominate in suboxic sulfidic sediments. Several novel archaeal groups are well represented in an acidic (pH 3) Fe-oxyhydroxide mat, where a higher O2 influx is accompanied with an increase in archaeal diversity. The presence or absence of genes and pathways important in S oxidation-reduction, H2-oxidation, and aerobic respiration (terminal oxidation) provide insight regarding the metabolic strategies of indigenous organisms present in geothermal systems. Multiple-pathway and protein-specific functional analysis of metagenome sequence data corroborated results from phylogenetic analyses and clearly demonstrate major differences in metabolic potential across sites. The distribution of functional genes involved in electron transport is consistent with the hypothesis that geochemical parameters (e.g., pH, sulfide, Fe, O2) control microbial community structure and function in YNP geothermal springs. PMID:20333304

Design and development of conformal antenna composite structure

NASA Astrophysics Data System (ADS)

Xie, Zonghong; Zhao, Wei; Zhang, Peng; Li, Xiang

2017-09-01

In the manufacturing process of the common smart skin antenna, the adhesive covered on the radiating elements of the antenna led to severe deviation of the resonant frequency, which degraded the electromagnetic performance of the antenna. In this paper, a new component called package cover was adopted to prevent the adhesive from covering on the radiating elements of the microstrip antenna array. The package cover and the microstrip antenna array were bonded together as packaged antenna which was then embedded into the composite sandwich structure to develop a new structure called conformal antenna composite structure (CACS). The geometric parameters of the microstrip antenna array and the CACS were optimized by the commercial software CST microwave studio. According to the optimal results, the microstrip antenna array and the CACS were manufactured and tested. The experimental and numerical results of electromagnetic performance showed that the resonant frequency of the CACS was close to that of the microstrip antenna array (with error less than 1%) and the CACS had a higher gain (about 2 dB) than the microstrip antenna array. The package system would increase the electromagnetic radiating energy at the design frequency nearly 66%. The numerical model generated by CST microwave studio in this study could successfully predict the electromagnetic performance of the microstrip antenna array and the CACS with relatively good accuracy. The mechanical analysis results showed that the CACS had better flexural property than the composite sandwich structure without the embedment of packaged antenna. The comparison of the electromagnetic performance for the CACS and the MECSSA showed that the package system was useful and effective.

A review of chemosensation and related behavior in aquatic insects.

PubMed

Crespo, José G

2011-01-01

Insects that are secondarily adapted to aquatic environments are able to sense odors from a diverse array of sources. The antenna of these insects, as in all insects, is the main chemosensory structure and its input to the brain allows for integration of sensory information that ultimately ends in behavioral responses. Only a fraction of the aquatic insect orders have been studied with respect to their sensory biology and most of the work has centered either on the description of the different types of sensilla, or on the behavior of the insect as a whole. In this paper, the literature is exhaustively reviewed and ways in which antennal morphology, brain structure, and associated behavior can advance better understanding of the neurobiology involved in processing of chemosensory information are discussed. Moreover, the importance of studying such group of insects is stated, and at the same time it is shown that many interesting questions regarding olfactory processing can be addressed by looking into the changes that aquatic insects undergo when leaving their aquatic environment.

Functional Hydrogel Materials Inspired by Amyloid

NASA Astrophysics Data System (ADS)

Schneider, Joel

2012-02-01

Protein assembly resulting in the formation of amyloid fibrils, assemblies rich in cross beta-sheet structure, is normally thought of as a deleterious event associated with disease. However, amyloid formation is also involved in a diverse array of normal biological functions such as cell adhesion, melanin synthesis, insect defense mechanism and modulation of water surface tension by fungi and bacteria. These findings indicate that Nature has evolved to take advantage of large, proteinaceous fibrillar assemblies to elicit function. We are designing functional materials, namely hydrogels, from peptides that self-assembled into fibrillar networks, rich in cross beta-sheet structure. These gels can be used for the direct encapsulation and delivery of small molecule-, protein- and cell-based therapeutics. Loaded gels exhibit shear-thinning/self-healing mechanical properties enabling their delivery via syringe. In addition to their use for delivery, we have found that some of these gels display antibacterial activity. Although cytocompatible towards mammalian cells, the hydrogels can kill a broad spectrum of bacteria on contact.

Basic science and surgical treatment options for articular cartilage injuries of the knee.

PubMed

Tetteh, Elizabeth S; Bajaj, Sarvottam; Ghodadra, Neil S

2012-03-01

The complex structure of articular cartilage allows for diverse knee function throughout range of motion and weight bearing. However, disruption to the structural integrity of the articular surface can cause significant morbidity. Due to an inherently poor regenerative capacity, articular cartilage defects present a treatment challenge for physicians and therapists. For many patients, a trial of nonsurgical treatment options is paramount prior to surgical intervention. In instances of failed conservative treatment, patients can undergo an array of palliative, restorative, or reparative surgical procedures to treat these lesions. Palliative methods include debridement and lavage, while restorative techniques include marrow stimulation. For larger lesions involving subchondral bone, reparative procedures such as osteochondral grafting or autologous chondrocyte implantation are considered. Clinical success not only depends on the surgical techniques but also requires strict adherence to rehabilitation guidelines. The purpose of this article is to review the basic science of articular cartilage and to provide an overview of the procedures currently performed at our institution for patients presenting with symptomatic cartilage lesions.

Emerging Paradigm of Intracellular Targeting of G Protein-Coupled Receptors.

PubMed

Chaturvedi, Madhu; Schilling, Justin; Beautrait, Alexandre; Bouvier, Michel; Benovic, Jeffrey L; Shukla, Arun K

2018-05-04

G protein-coupled receptors (GPCRs) recognize a diverse array of extracellular stimuli, and they mediate a broad repertoire of signaling events involved in human physiology. Although the major effort on targeting GPCRs has typically been focused on their extracellular surface, a series of recent developments now unfold the possibility of targeting them from the intracellular side as well. Allosteric modulators binding to the cytoplasmic surface of GPCRs have now been described, and their structural mechanisms are elucidated by high-resolution crystal structures. Furthermore, pepducins, aptamers, and intrabodies targeting the intracellular face of GPCRs have also been successfully utilized to modulate receptor signaling. Moreover, small molecule compounds, aptamers, and synthetic intrabodies targeting β-arrestins have also been discovered to modulate GPCR endocytosis and signaling. Here, we discuss the emerging paradigm of intracellular targeting of GPCRs, and outline the current challenges, potential opportunities, and future outlook in this particular area of GPCR biology. Copyright © 2018 Elsevier Ltd. All rights reserved.

Structure and dynamics of cationic membrane peptides and proteins: Insights from solid-state NMR

PubMed Central

Hong, Mei; Su, Yongchao

2011-01-01

Many membrane peptides and protein domains contain functionally important cationic Arg and Lys residues, whose insertion into the hydrophobic interior of the lipid bilayer encounters significant energy barriers. To understand how these cationic molecules overcome the free energy barrier to insert into the lipid membrane, we have used solid-state NMR spectroscopy to determine the membrane-bound topology of these peptides. A versatile array of solid-state NMR experiments now readily yields the conformation, dynamics, orientation, depth of insertion, and site-specific protein–lipid interactions of these molecules. We summarize key findings of several Arg-rich membrane peptides, including β-sheet antimicrobial peptides, unstructured cell-penetrating peptides, and the voltage-sensing helix of voltage-gated potassium channels. Our results indicate the central role of guanidinium-phosphate and guanidinium-water interactions in dictating the structural topology of these cationic molecules in the lipid membrane, which in turn account for the mechanisms of this functionally diverse class of membrane peptides. PMID:21344534

Simulating Food Web Dynamics along a Gradient: Quantifying Human Influence

PubMed Central

Jordán, Ferenc; Gjata, Nerta; Mei, Shu; Yule, Catherine M.

2012-01-01

Realistically parameterized and dynamically simulated food-webs are useful tool to explore the importance of the functional diversity of ecosystems, and in particular relations between the dynamics of species and the whole community. We present a stochastic dynamical food web simulation for the Kelian River (Borneo). The food web was constructed for six different locations, arrayed along a gradient of increasing human perturbation (mostly resulting from gold mining activities) along the river. Along the river, the relative importance of grazers, filterers and shredders decreases with increasing disturbance downstream, while predators become more dominant in governing eco-dynamics. Human activity led to increased turbidity and sedimentation which adversely impacts primary productivity. Since the main difference between the study sites was not the composition of the food webs (structure is quite similar) but the strengths of interactions and the abundance of the trophic groups, a dynamical simulation approach seemed to be useful to better explain human influence. In the pristine river (study site 1), when comparing a structural version of our model with the dynamical model we found that structurally central groups such as omnivores and carnivores were not the most important ones dynamically. Instead, primary consumers such as invertebrate grazers and shredders generated a greater dynamical response. Based on the dynamically most important groups, bottom-up control is replaced by the predominant top-down control regime as distance downstream and human disturbance increased. An important finding, potentially explaining the poor structure to dynamics relationship, is that indirect effects are at least as important as direct ones during the simulations. We suggest that our approach and this simulation framework could serve systems-based conservation efforts. Quantitative indicators on the relative importance of trophic groups and the mechanistic modeling of eco-dynamics could greatly contribute to understanding various aspects of functional diversity. PMID:22768346

Emergent Rotational Symmetries in Disordered Magnetic Domain Patterns

NASA Astrophysics Data System (ADS)

Su, Run; Seu, Keoki A.; Parks, Daniel; Kan, Jimmy J.; Fullerton, Eric E.; Roy, Sujoy; Kevan, Stephen D.

2011-12-01

Uniaxial systems often form labyrinthine domains that exhibit short-range order but are macroscopically isotropic and would not be expected to exhibit precise symmetries. However, their underlying frustration results in a multitude of metastable configurations of comparable energy, and driving such a system externally might lead to pattern formation. We find that soft x-ray speckle diffraction patterns of the labyrinthine domains in CoPd/IrMn heterostructures reveal a diverse array of hidden rotational symmetries about the magnetization axis, thereby suggesting an unusual form of emergent order in an otherwise disordered system. These symmetries depend on applied magnetic field, magnetization history, and scattering wave vector. Maps of rotational symmetry exhibit intriguing structures that can be controlled by manipulating the applied magnetic field in concert with the exchange bias condition.

Emergent rotational symmetries in disordered magnetic domain patterns.

PubMed

Su, Run; Seu, Keoki A; Parks, Daniel; Kan, Jimmy J; Fullerton, Eric E; Roy, Sujoy; Kevan, Stephen D

2011-12-16

Uniaxial systems often form labyrinthine domains that exhibit short-range order but are macroscopically isotropic and would not be expected to exhibit precise symmetries. However, their underlying frustration results in a multitude of metastable configurations of comparable energy, and driving such a system externally might lead to pattern formation. We find that soft x-ray speckle diffraction patterns of the labyrinthine domains in CoPd/IrMn heterostructures reveal a diverse array of hidden rotational symmetries about the magnetization axis, thereby suggesting an unusual form of emergent order in an otherwise disordered system. These symmetries depend on applied magnetic field, magnetization history, and scattering wave vector. Maps of rotational symmetry exhibit intriguing structures that can be controlled by manipulating the applied magnetic field in concert with the exchange bias condition. © 2011 American Physical Society

Biodistribution mechanisms of therapeutic monoclonal antibodies in health and disease.

PubMed

Tabrizi, Mohammad; Bornstein, Gadi Gazit; Suria, Hamza

2010-03-01

The monoclonal antibody market continues to witness an impressive rate of growth and has become the leading source of expansion in the biologic segment within the pharmaceutical industry. Currently marketed monoclonal antibodies target a diverse array of antigens. These antigens are distributed in a variety of tissues such as tumors, lungs, synovial fluid, psoriatic plaques, and lymph nodes. As the concentration of drug at the proximity of the biological receptor determines the magnitude of the observed pharmacological responses, a significant consideration in effective therapeutic application of monoclonal antibodies is a thorough understanding of the processes that regulate antibody biodistribution. Monoclonal antibody distribution is affected by factors such as molecular weight, blood flow, tissue and tumor heterogeneity, structure and porosity, target antigen density, turnover rate, and the target antigen expression profile.

Design and synthesis of imidazopyridine analogues as inhibitors of phosphoinositide 3-kinase signaling and angiogenesis.

PubMed

Kim, Okseon; Jeong, Yujeong; Lee, Hyunseung; Hong, Sun-Sun; Hong, Sungwoo

2011-04-14

Phosphatidylinositol 3-kinase α (PI3Kα) is an important regulator of intracellular signaling pathways, controlling remarkably diverse arrays of physiological processes. Because the PI3K pathway is frequently up-regulated in human cancers, the inhibition of PI3Kα can be a promising approach to cancer therapy. In this study, we have designed and synthesized a new series of imidazo[1,2-a]pyridine derivatives as PI3Kα inhibitors through the fragment-growing strategy. By varying groups at the 3- and 6-positions of imidazo[1,2-a]pyridines, we studied the structure-activity relationships (SAR) profiles and identified a series of potent PI3Kα inhibitors. Representative derivatives showed good activity in cellular proliferation and apoptosis assays. Moreover, these inhibitors exhibited noteworthy antiangiogenic activity.

Development and mapping of DArT markers within the Festuca - Lolium complex

PubMed Central

Kopecký, David; Bartoš, Jan; Lukaszewski, Adam J; Baird, James H; Černoch, Vladimír; Kölliker, Roland; Rognli, Odd Arne; Blois, Helene; Caig, Vanessa; Lübberstedt, Thomas; Studer, Bruno; Shaw, Paul; Doležel, Jaroslav; Kilian, Andrzej

2009-01-01

Background Grasses are among the most important and widely cultivated plants on Earth. They provide high quality fodder for livestock, are used for turf and amenity purposes, and play a fundamental role in environment protection. Among cultivated grasses, species within the Festuca-Lolium complex predominate, especially in temperate regions. To facilitate high-throughput genome profiling and genetic mapping within the complex, we have developed a Diversity Arrays Technology (DArT) array for five grass species: F. pratensis, F. arundinacea, F. glaucescens, L. perenne and L. multiflorum. Results The DArTFest array contains 7680 probes derived from methyl-filtered genomic representations. In a first marker discovery experiment performed on 40 genotypes from each species (with the exception of F. glaucescens for which only 7 genotypes were used), we identified 3884 polymorphic markers. The number of DArT markers identified in every single genotype varied from 821 to 1852. To test the usefulness of DArTFest array for physical mapping, DArT markers were assigned to each of the seven chromosomes of F. pratensis using single chromosome substitution lines while recombinants of F. pratensis chromosome 3 were used to allocate the markers to seven chromosome bins. Conclusion The resources developed in this project will facilitate the development of genetic maps in Festuca and Lolium, the analysis on genetic diversity, and the monitoring of the genomic constitution of the Festuca × Lolium hybrids. They will also enable marker-assisted selection for multiple traits or for specific genome regions. PMID:19832973

Generation of tunable radially polarized array beams by controllable coherence

NASA Astrophysics Data System (ADS)

Wang, Jing; Zhang, Jipeng; Zhu, Shijun; Li, Zhenhua

2017-05-01

In this paper, a new method for converting a single radial polarization beam into an arbitrary radially polarized array (RPA) beam such as a radial or rectangular symmetry array in the focal plane by modulating a periodic correlation structure is introduced. The realizability conditions for such source and the beam condition for radiation generated by such source are derived. It is illustrated that both the amplitude and the polarization are controllable by means of initial correlation structure and coherence parameter. Furthermore, by designing the source correlation structure, a tunable NUST-shaped RPA beam is demonstrated, which can find widespread applications in micro-nano engineering. Such a method for generation of arbitrary vector array beams is useful in beam shaping and optical tweezers.

Stand structural diversity rather than species diversity enhances aboveground carbon storage in secondary subtropical forests in Eastern China

NASA Astrophysics Data System (ADS)

Ali, Arshad; Yan, En-Rong; Chen, Han Y. H.; Chang, Scott X.; Zhao, Yan-Tao; Yang, Xiao-Dong; Xu, Ming-Shan

2016-08-01

Stand structural diversity, typically characterized by variances in tree diameter at breast height (DBH) and total height, plays a critical role in influencing aboveground carbon (C) storage. However, few studies have considered the multivariate relationships of aboveground C storage with stand age, stand structural diversity, and species diversity in natural forests. In this study, aboveground C storage, stand age, tree species, DBH and height diversity indices, were determined across 80 subtropical forest plots in Eastern China. We employed structural equation modelling (SEM) to test for the direct and indirect effects of stand structural diversity, species diversity, and stand age on aboveground C storage. The three final SEMs with different directions for the path between species diversity and stand structural diversity had a similar goodness of fit to the data. They accounted for 82 % of the variation in aboveground C storage, 55-59 % of the variation in stand structural diversity, and 0.1 to 9 % of the variation in species diversity. Stand age demonstrated strong positive total effects, including a positive direct effect (β = 0.41), and a positive indirect effect via stand structural diversity (β = 0.41) on aboveground C storage. Stand structural diversity had a positive direct effect on aboveground C storage (β = 0.56), whereas there was little total effect of species diversity as it had a negative direct association with, but had a positive indirect effect, via stand structural diversity, on aboveground C storage. The negligible total effect of species diversity on aboveground C storage in the forests under study may have been attributable to competitive exclusion with high aboveground biomass, or a historical logging preference for productive species. Our analyses suggested that stand structural diversity was a major determinant for variations in aboveground C storage in the secondary subtropical forests in Eastern China. Hence, maintaining tree DBH and height diversity through silvicultural operations might constitute an effective approach for enhancing aboveground C storage in these forests.

Population-Level Metrics of Trophic Structure Based on Stable Isotopes and Their Application to Invasion Ecology

PubMed Central

Jackson, Michelle C.; Donohue, Ian; Jackson, Andrew L.; Britton, J. Robert; Harper, David M.; Grey, Jonathan

2012-01-01

Biological invasions are a significant driver of human-induced global change and many ecosystems sustain sympatric invaders. Interactions occurring among these invaders have important implications for ecosystem structure and functioning, yet they are poorly understood. Here we apply newly developed metrics derived from stable isotope data to provide quantitative measures of trophic diversity within populations or species. We then use these to test the hypothesis that sympatric invaders belonging to the same functional feeding group occupy a smaller isotopic niche than their allopatric counterparts. Two introduced, globally important, benthic omnivores, Louisiana swamp crayfish (Procambarus clarkii) and carp (Cyprinus carpio), are sympatric in Lake Naivasha, Kenya. We applied our metrics to an 8-year data set encompassing the establishment of carp in the lake. We found a strong asymmetric interaction between the two invasive populations, as indicated by inverse correlations between carp abundance and measures of crayfish trophic diversity. Lack of isotopic niche overlap between carp and crayfish in the majority of years indicated a predominantly indirect interaction. We suggest that carp-induced habitat alteration reduced the diversity of crayfish prey, resulting in a reduction in the dietary niche of crayfish. Stable isotopes provide an integrated signal of diet over space and time, offering an appropriate scale for the study of population niches, but few isotope studies have retained the often insightful information revealed by variability among individuals in isotope values. Our population metrics incorporate such variation, are robust to the vagaries of sample size and are a useful additional tool to reveal subtle dietary interactions among species. Although we have demonstrated their applicability specifically using a detailed temporal dataset of species invasion in a lake, they have a wide array of potential ecological applications. PMID:22363724

Population-level metrics of trophic structure based on stable isotopes and their application to invasion ecology.

PubMed

Jackson, Michelle C; Donohue, Ian; Jackson, Andrew L; Britton, J Robert; Harper, David M; Grey, Jonathan

2012-01-01

Biological invasions are a significant driver of human-induced global change and many ecosystems sustain sympatric invaders. Interactions occurring among these invaders have important implications for ecosystem structure and functioning, yet they are poorly understood. Here we apply newly developed metrics derived from stable isotope data to provide quantitative measures of trophic diversity within populations or species. We then use these to test the hypothesis that sympatric invaders belonging to the same functional feeding group occupy a smaller isotopic niche than their allopatric counterparts. Two introduced, globally important, benthic omnivores, Louisiana swamp crayfish (Procambarus clarkii) and carp (Cyprinus carpio), are sympatric in Lake Naivasha, Kenya. We applied our metrics to an 8-year data set encompassing the establishment of carp in the lake. We found a strong asymmetric interaction between the two invasive populations, as indicated by inverse correlations between carp abundance and measures of crayfish trophic diversity. Lack of isotopic niche overlap between carp and crayfish in the majority of years indicated a predominantly indirect interaction. We suggest that carp-induced habitat alteration reduced the diversity of crayfish prey, resulting in a reduction in the dietary niche of crayfish. Stable isotopes provide an integrated signal of diet over space and time, offering an appropriate scale for the study of population niches, but few isotope studies have retained the often insightful information revealed by variability among individuals in isotope values. Our population metrics incorporate such variation, are robust to the vagaries of sample size and are a useful additional tool to reveal subtle dietary interactions among species. Although we have demonstrated their applicability specifically using a detailed temporal dataset of species invasion in a lake, they have a wide array of potential ecological applications.

Rapid evaluation of the durability of cortical neural implants using accelerated aging with reactive oxygen species

PubMed Central

Takmakov, Pavel; Ruda, Kiersten; Phillips, K Scott; Isayeva, Irada S; Krauthamer, Victor; Welle, Cristin G

2017-01-01

Objective A challenge for implementing high bandwidth cortical brain–machine interface devices in patients is the limited functional lifespan of implanted recording electrodes. Development of implant technology currently requires extensive non-clinical testing to demonstrate device performance. However, testing the durability of the implants in vivo is time-consuming and expensive. Validated in vitro methodologies may reduce the need for extensive testing in animal models. Approach Here we describe an in vitro platform for rapid evaluation of implant stability. We designed a reactive accelerated aging (RAA) protocol that employs elevated temperature and reactive oxygen species (ROS) to create a harsh aging environment. Commercially available microelectrode arrays (MEAs) were placed in a solution of hydrogen peroxide at 87 °C for a period of 7 days. We monitored changes to the implants with scanning electron microscopy and broad spectrum electrochemical impedance spectroscopy (1 Hz–1 MHz) and correlated the physical changes with impedance data to identify markers associated with implant failure. Main results RAA produced a diverse range of effects on the structural integrity and electrochemical properties of electrodes. Temperature and ROS appeared to have different effects on structural elements, with increased temperature causing insulation loss from the electrode microwires, and ROS concentration correlating with tungsten metal dissolution. All array types experienced impedance declines, consistent with published literature showing chronic (>30 days) declines in array impedance in vivo. Impedance change was greatest at frequencies <10 Hz, and smallest at frequencies 1 kHz and above. Though electrode performance is traditionally characterized by impedance at 1 kHz, our results indicate that an impedance change at 1 kHz is not a reliable predictive marker of implant degradation or failure. Significance ROS, which are known to be present in vivo, can create structural damage and change electrical properties of MEAs. Broad-spectrum electrical impedance spectroscopy demonstrates increased sensitivity to electrode damage compared with single-frequency measurements. RAA can be a useful tool to simulate worst-case in vivo damage resulting from chronic electrode implantation, simplifying the device development lifecycle. PMID:25627426

Uniform circular array for structural health monitoring of composite structures

NASA Astrophysics Data System (ADS)

Stepinski, Tadeusz; Engholm, Marcus

2008-03-01

Phased array with all-azimuth angle coverage would be extremely useful in structural health monitoring (SHM) of planar structures. One method to achieve the 360° coverage is to use uniform circular arrays (UCAs). In this paper we present the concept of UCA adapted for SHM applications. We start from a brief presentation of UCA beamformers based on the principle of phase mode excitation. UCA performance is illustrated by the results of beamformer simulations performed for the narrowband and wideband ultrasonic signals. Preliminary experimental results obtained with UCA used for the reception of ultrasonic signals propagating in an aluminum plate are also presented.

An Optoelectronic Nose for Detection of Toxic Gases

PubMed Central

Lim, Sung H.; Feng, Liang; Kemling, Jonathan W.; Musto, Christopher J.; Suslick, Kenneth S.

2009-01-01

We have developed a simple colorimetric sensor array (CSA) for the detection of a wide range of volatile analytes and applied it to the detection of toxic gases. The sensor consists of a disposable array of cross-responsive nanoporous pigments whose colors are changed by diverse chemical interactions with analytes. Although no single chemically responsive pigment is specific for any one analyte, the pattern of color change for the array is a unique molecular fingerprint. Clear differentiation among 19 different toxic industrial chemicals (TICs) within two minutes of exposure at IDLH (immediately dangerous to life or health) concentration has been demonstrated. Quantification of each analyte is easily accomplished based on the color change of the array, and excellent detection limits have been demonstrated, generally below the PELs (permissible exposure limits). Identification of the TICs was readily achieved using a standard chemometric approach, i.e., hierarchical clustering analysis (HCA), with no misclassifications over 140 trials. PMID:20160982

Design principles for wave plate metasurfaces using plasmonic L-shaped nanoantennas

NASA Astrophysics Data System (ADS)

Tahir, Asad A.; Schulz, Sebastian A.; De Leon, Israel; Boyd, Robert W.

2017-03-01

Plasmonic L-shaped antennas are an important building block of metasurfaces and have been used to fabricate ultra-thin wave plates. In this work we present principles that can be used to design wave plates at a wavelength of choice and for diverse application requirements using arrays of L-shaped plasmonic antennas. We derive these design principles by studying the behavior of the vast parameter space of these antenna arrays. We show that there are two distinct regimes: a weak inter-particle coupling and a strong inter-particle coupling regime. We describe the behavior of the antenna array in each regime with regards to wave plate functionality, without resorting to approximate theoretical models. Our work is the first to explain these design principles and serves as a guide for designing wave plates for specific application requirements using plasmonic L-shaped antenna arrays.

An optoelectronic nose for the detection of toxic gases.

PubMed

Lim, Sung H; Feng, Liang; Kemling, Jonathan W; Musto, Christopher J; Suslick, Kenneth S

2009-10-01

We have developed a simple colorimetric sensor array that detects a wide range of volatile analytes and then applied it to the detection of toxic gases. The sensor consists of a disposable array of cross-responsive nanoporous pigments with colours that are changed by diverse chemical interactions with analytes. Although no single chemically responsive pigment is specific for any one analyte, the pattern of colour change for the array is a unique molecular fingerprint. Clear differentiation among 19 different toxic industrial chemicals (TICs) within two minutes of exposure at concentrations immediately dangerous to life or health were demonstrated. Based on the colour change of the array, quantification of each analyte was accomplished easily, and excellent detection limits were achieved, generally below the permissible exposure limits. Different TICs were identified readily using a standard chemometric approach (hierarchical clustering analysis), with no misclassifications over 140 trials.

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

Mosher, J.C.; Leahy, R.M.

A new method for source localization is described that is based on a modification of the well known multiple signal classification (MUSIC) algorithm. In classical MUSIC, the array manifold vector is projected onto an estimate of the signal subspace, but errors in the estimate can make location of multiple sources difficult. Recursively applied and projected (RAP) MUSIC uses each successively located source to form an intermediate array gain matrix, and projects both the array manifold and the signal subspace estimate into its orthogonal complement. The MUSIC projection is then performed in this reduced subspace. Using the metric of principal angles,more » the authors describe a general form of the RAP-MUSIC algorithm for the case of diversely polarized sources. Through a uniform linear array simulation, the authors demonstrate the improved Monte Carlo performance of RAP-MUSIC relative to MUSIC and two other sequential subspace methods, S and IES-MUSIC.« less

Promising Results from Three NASA SBIR Solar Array Technology Development Programs

NASA Technical Reports Server (NTRS)

Eskenazi, Mike; White, Steve; Spence, Brian; Douglas, Mark; Glick, Mike; Pavlick, Ariel; Murphy, David; O'Neill, Mark; McDanal, A. J.; Piszczor, Michael

2005-01-01

Results from three NASA SBIR solar array technology programs are presented. The programs discussed are: 1) Thin Film Photovoltaic UltraFlex Solar Array; 2) Low Cost/Mass Electrostatically Clean Solar Array (ESCA); and 3) Stretched Lens Array SquareRigger (SLASR). The purpose of the Thin Film UltraFlex (TFUF) Program is to mature and validate the use of advanced flexible thin film photovoltaics blankets as the electrical subsystem element within an UltraFlex solar array structural system. In this program operational prototype flexible array segments, using United Solar amorphous silicon cells, are being manufactured and tested for the flight qualified UltraFlex structure. In addition, large size (e.g. 10 kW GEO) TFUF wing systems are being designed and analyzed. Thermal cycle and electrical test and analysis results from the TFUF program are presented. The purpose of the second program entitled, Low Cost/Mass Electrostatically Clean Solar Array (ESCA) System, is to develop an Electrostatically Clean Solar Array meeting NASA s design requirements and ready this technology for commercialization and use on the NASA MMS and GED missions. The ESCA designs developed use flight proven materials and processes to create a ESCA system that yields low cost, low mass, high reliability, high power density, and is adaptable to any cell type and coverglass thickness. All program objectives, which included developing specifications, creating ESCA concepts, concept analysis and trade studies, producing detailed designs of the most promising ESCA treatments, manufacturing ESCA demonstration panels, and LEO (2,000 cycles) and GEO (1,350 cycles) thermal cycling testing of the down-selected designs were successfully achieved. The purpose of the third program entitled, "High Power Platform for the Stretched Lens Array," is to develop an extremely lightweight, high efficiency, high power, high voltage, and low stowed volume solar array suitable for very high power (multi-kW to MW) applications. These objectives are achieved by combining two cutting edge technologies, the SquareRigger solar array structure and the Stretched Lens Array (SLA). The SLA SquareRigger solar array is termed SLASR. All program objectives, which included developing specifications, creating preliminary designs for a near-term SLASR, detailed structural, mass, power, and sizing analyses, fabrication and power testing of a functional flight-like SLASR solar blanket, were successfully achieved.

Non-traditional Infrasound Deployment

NASA Astrophysics Data System (ADS)

McKenna, M. H.; McComas, S.; Simpson, C. P.; Diaz-Alvarez, H.; Costley, R. D.; Hayward, C.; Golden, P.; Endress, A.

2017-12-01

Historically, infrasound arrays have been deployed in rural environments where anthropological noise sources are limited. As interest in monitoring low energy sources at local distances grows in the infrasound community, it will be vital to understand how to monitor infrasound sources in an urban environment. Arrays deployed in urban centers have to overcome the decreased signal-to-noise ratio and reduced amount of real estate available to deploy an array. To advance the understanding of monitoring infrasound sources in urban environments, local and regional infrasound arrays were deployed on building rooftops on the campus at Southern Methodist University (SMU), and data were collected for one seasonal cycle. The data were evaluated for structural source signals (continuous-wave packets), and when a signal was identified, the back azimuth to the source was determined through frequency-wavenumber analysis. This information was used to identify hypothesized structural sources; these sources were verified through direct measurement and dynamic structural analysis modeling. In addition to the rooftop arrays, a camouflaged infrasound sensor was installed on the SMU campus and evaluated to determine its effectiveness for wind noise reduction. Permission to publish was granted by Director, Geotechnical and Structures Laboratory.

Insect Resistance

USDA-ARS?s Scientific Manuscript database

Insect pests exhibit a diverse array of genetic-based responses when interacting with crop systems; these changes can be in response to pathogens, symbiotic microbes, host plants, chemicals, and the environment. Agricultural research has for decades focused on gathering crucial information on the bi...

Source diversity among journals cited in Science Times.

PubMed

Kiernan, Vincent

2016-02-01

A content analysis of The New York Times' Science Times section from 1998 to 2012 found evidence of increased source diversity in use of scientific journals as news sources. Science Times increased the frequency at which it cited journals, the number of different journals that it cited, and the number of disciplines represented by cited journals. The results suggest that online availability of a wide array of scientific journals has changed sourcing behaviors. © The Author(s) 2014.

All-atom four-body knowledge-based statistical potential to distinguish native tertiary RNA structures from nonnative folds.

PubMed

Masso, Majid

2018-09-14

Scientific breakthroughs in recent decades have uncovered the capability of RNA molecules to fulfill a wide array of structural, functional, and regulatory roles in living cells, leading to a concomitantly significant increase in both the number and diversity of experimentally determined RNA three-dimensional (3D) structures. Atomic coordinates from a representative training set of solved RNA structures, displaying low sequence and structure similarity, facilitate derivation of knowledge-based energy functions. Here we develop an all-atom four-body statistical potential and evaluate its capacity to distinguish native RNA 3D structures from nonnative folds based on calculated free energy scores. Atomic four-body nearest-neighbors are objectively identified by their occurrence as tetrahedral vertices in the Delaunay tessellations of RNA structures, and rates of atomic quadruplet interactions expected by chance are obtained from a multinomial reference distribution. Our four-body energy function, referred to as RAMP (ribonucleic acids multibody potential), is subsequently derived by applying the inverted Boltzmann principle to the frequency data, yielding an energy score for each type of atomic quadruplet interaction. Several well-known benchmark datasets reveal that RAMP is comparable with, and often outperforms, existing knowledge- and physics-based energy functions. To the best of our knowledge, this is the first study detailing an RNA tertiary structure-based multibody statistical potential and its comparative evaluation. Copyright © 2018 Elsevier Ltd. All rights reserved.

Improved performance of HgCdTe infrared detector focal plane arrays by modulating light field based on photonic crystal structure

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

Liang, Jian; Hu, Weida, E-mail: wdhu@mail.sitp.ac.cn; Ye, Zhenhua

2014-05-14

An HgCdTe long-wavelength infrared focal plane array photodetector is proposed by modulating light distributions based on the photonic crystal. It is shown that a promising prospect of improving performance is better light harvest and dark current limitation. To optimize the photon field distributions of the HgCdTe-based photonic crystal structure, a numerical method is built by combining the finite-element modeling and the finite-difference time-domain simulation. The optical and electrical characteristics of designed HgCdTe mid-wavelength and long-wavelength photon-trapping infrared detector focal plane arrays are obtained numerically. The results indicate that the photon crystal structure, which is entirely compatible with the large infraredmore » focal plane arrays, can significantly reduce the dark current without degrading the quantum efficiency compared to the regular mesa or planar structure.« less

THz wavefront manipulation based on metal waveguides

NASA Astrophysics Data System (ADS)

Wu, Mengru; Lang, Tingting; Shen, Changyu; Shi, Guohua; Han, Zhanghua

2018-07-01

In this paper, two waveguiding structures for arbitrary wavefront manipulation in the terahertz spectral region were proposed, designed and characterized. The first structure consists of parallel stack copper plates forming an array of parallel-plate waveguides (PPWGs). The second structure is three-dimensional metal rectangular waveguides array. The phase delay of the input wave after passing through the waveguide array is mainly determined by the effective index of the waveguides. Therefore, the waveguide array can be engineered using different core width distribution to generate any desired light beam. Examples, working at the frequency of 0.3 THz show that good focusing phenomenon with different focus lengths and spot sizes were observed, as well as arbitrarily tilted propagation of incident plane waves. The structure introduces a new method to perform wavefront manipulation, and can be utilized in many important applications in terahertz imaging and communication systems.

Stacbeam 2

NASA Astrophysics Data System (ADS)

Adams, L. R.; Vonroos, A.

1985-04-01

An investigation being conducted by Astro Aerospace Corporation (Astro) for Jet Propulsion Laboratory in which efficient structures for geosynchronous spacecraft solar arrays are being developed is discussed. Recent developments in solar blanket technology, including the introduction of ultrathin (50 micrometer) silicon solar cells with conversion efficiencies approaching 15 percent, have resulted in a significant increase in blanket specific power. System specific power depends not only on blanket mass but also on the masses of the support structure and deployment mechanism. These masses must clearly be reduced, not only to minimize launch weight, but also to increase array natural frequency. The solar array system natural frequency should be kept high in order to reduce the demands on the attitude control system. This goal is approached by decreasing system mass, by increasing structural stiffness, and by partitioning the blanket. As a result of this work, a highly efficient structure for deploying a solar array was developed.

Exploitation of "Excess" Data Now Routinely Collected by Large N, Continuously Recorded Oil Exploration Surveys: From Microseismicity to Deep Crustal Imaging

NASA Astrophysics Data System (ADS)

Brown, L. D.

2014-12-01

The rapidly expanding use by the oil and gas industry of "nodal", large channel capacity areal arrays that record continuously for extended periods of time is generating large volumes of data in excess of that needed for the conventional CMP reflection imaging that is the primary goal of such surveys. These excess data, once considered as simply "noise", have recently been recognized to have utility not only for the exploration seismologist but also for addressing a diverse range of phenomena. The most widely recognized use for these "noise" records is surface wave tomographic imaging of near surface velocity structure via seismic interferometry of ambient natural noise. Such results are proving to be of great value in enhancing conventional 3D exploration imagery, but they should be appreciated in their own right for the information they provide on the shallow subsurface to the hydrologist, engineer and tectonicist. Another relatively dramatic application is the delineation of local structure by tracing the propagation of body and surface waves from local and teleseismic events across these dense arrays. Here I would like draw attention to three other promising uses for such data: a) detection and mapping of microseismicity below the detection thresholds of conventional earthquake monitoring networks, especially in areas of low conventional seismicity; b) reflection and refraction imaging of structure using cultural, as opposed to natural, energy sources, and c) systematic mapping of the basement in 3D using the existing exploration sources recorded at travel times longer than that typically harvested for resource purposes. We conclude by emphasizing that these potentially invaluable "extras" are now being recorded routinely around the world, but there is as yet no mechanism in place to ensure they are exploited rather than simply deleted.

Depth-dependent Vertical-to-Horizontal (V/H) Ratios of Free-Field Ground Motion Response Spectra for Deeply Embedded Nuclear Structures

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

Wei, X.; Braverman, J.; Miranda, M.

2015-02-01

This report documents the results of a study to determine the depth-dependent V/H ratios of ground motion response spectra in the free field. The V/H ratios reported herein were developed from a worldwide database of surface and downhole acceleration recordings obtained from 45 vertical array stations. This database was specifically compiled for this project, and includes information from a diversity of active tectonic regions (California, Alaska, Taiwan, Japan), site conditions (rock to soft soil), ground motion intensity levels (PGAs between 0.01 g and 0.50 g), magnitudes (between ML 2.78 and JMA 8.1), epicentral distances (between 3.2 km and 812 km),more » and source depths (between 1.2 km and 112 km), as well as sensors at surface and at a wide range of depths relevant to the project. To study the significance of the depth effect, V/H ratios from all the records were sorted into a number of depth bins relevant to the project, and statistics (average, standard deviation, coefficient of variation, 16th, 50th, and 84th percentiles) of the V/H ratios within each bin were computed. Similar analyses were repeated, controlling for different site conditions, ground motion intensity levels, array locations, and source depths, to study their relative effect on the V/H ratios. Our findings confirm the importance of the depth effect on the V/H ratios. The research findings in this report can be used to provide guidance on the significance of the depth effect, and the extent to which this effect should be considered in the seismic design of deeply embedded SMR structures and NPP structures in general.« less

Flexible Structural-Health-Monitoring Sheets

NASA Technical Reports Server (NTRS)

Qing, Xinlin; Kuo, Fuo

2008-01-01

A generic design for a type of flexible structural-health-monitoring sheet with multiple sensor/actuator types and a method of manufacturing such sheets has been developed. A sheet of this type contains an array of sensing and/or actuation elements, associated wires, and any other associated circuit elements incorporated into various flexible layers on a thin, flexible substrate. The sheet can be affixed to a structure so that the array of sensing and/or actuation elements can be used to analyze the structure in accordance with structural-health-monitoring techniques. Alternatively, the sheet can be designed to be incorporated into the body of the structure, especially if the structure is made of a composite material. Customarily, structural-health monitoring is accomplished by use of sensors and actuators arrayed at various locations on a structure. In contrast, a sheet of the present type can contain an entire sensor/actuator array, making it unnecessary to install each sensor and actuator individually on or in a structure. Sensors of different types such as piezoelectric and fiber-optic can be embedded in the sheet to form a hybrid sensor network. Similarly, the traces for electric communication can be deposited on one or two layers as required, and an entirely separate layer can be employed to shield the sensor elements and traces.

High Aspect Ratio Semiconductor Heterojunction Solar Cells

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

Redwing, Joan; Mallouk, Tom; Mayer, Theresa

2013-05-17

The project focused on the development of high aspect ratio silicon heterojunction (HARSH) solar cells. The solar cells developed in this study consisted of high density vertical arrays of radial junction silicon microwires/pillars formed on Si substrates. Prior studies have demonstrated that vertical Si wire/pillar arrays enable reduced reflectivity and improved light trapping characteristics compared to planar solar cells. In addition, the radial junction structure offers the possibility of increased carrier collection in solar cells fabricated using material with short carrier diffusion lengths. However, the high junction and surface area of radial junction Si wire/pillar array devices can be problematicmore » and lead to increased diode leakage and enhanced surface recombination. This study investigated the use of amorphous hydrogenated Si in the form of a heterojunction-intrinsic-thin layer (HIT) structure as a junction formation method for these devices. The HIT layer structure has widely been employed to reduce surface recombination in planar crystalline Si solar cells. Consequently, it was anticipated that it would also provide significant benefits to the performance of radial junction Si wire/pillar array devices. The overall goals of the project were to demonstrate a HARSH cell with a HIT-type structure in the radial junction Si wire/pillar array configuration and to develop potentially low cost pathways to fabricate these devices. Our studies demonstrated that the HIT structure lead to significant improvements in the open circuit voltage (V oc>0.5) of radial junction Si pillar array devices compared to devices fabricated using junctions formed by thermal diffusion or low pressure chemical vapor deposition (LPCVD). In addition, our work experimentally demonstrated that the radial junction structure lead to improvements in efficiency compared to comparable planar devices for devices fabricated using heavily doped Si that had reduced carrier diffusion lengths. Furthermore, we made significant advances in employing the bottom-up vapor-liquid-solid (VLS) growth technique for the fabrication of the Si wire arrays. Our work elucidated the effects of growth conditions and substrate pattern geometry on the growth of large area Si microwire arrays grown with SiCl4. In addition, we also developed a process to grow p-type Si nanowire arrays using aluminum as the catalyst metal instead of gold. Finally, our work demonstrated the feasibility of growing vertical arrays of Si wires on non-crystalline glass substrates using polycrystalline Si template layers. The accomplishments demonstrated in this project will pave the way for future advances in radial junction wire array solar cells.« less

In Situ Estimation of Applied Biaxial Loads with Lamb Waves (Preprint)

DTIC Science & Technology

2012-07-01

be correct. IV. EXPERIMENTS AND RESULTS Fatigue tests were conducted for an array of six surface-bonded PZT transducers permanently attached to...because of their cumulative effects on the fatigue life of the structures. Waves propagating between array elements are directly affected by applied loads...their cumulative effects on the fatigue life of the structures. Waves propagating between array elements are directly affected by applied loads

Carious Dentine Provides a Habitat for a Complex Array of Novel Prevotella-Like Bacteria

PubMed Central

Nadkarni, Mangala A.; Caldon, C. Elizabeth; Chhour, Kim-Ly; Fisher, Ilana P.; Martin, F. Elizabeth; Jacques, Nicholas A.; Hunter, Neil

2004-01-01

Previous analysis of the microbiology of advanced caries by culture and real-time PCR emphasized the high incidence and abundance of gram-negative anaerobic species, particularly Prevotella-like bacteria. The diversity of Prevotella-like bacteria was further explored by analyzing pooled bacterial DNA from lesions of carious dentine. This was achieved by amplification of a region of the 16S ribosomal DNA with a Prevotella genus-specific forward primer and a universal bacterial reverse primer, followed by cloning and sequencing. Cultured Prevotella species commonly associated with oral tissues constituted only 12% of the Prevotella clones isolated from advanced carious lesions. The remaining 88% consisted of a diverse range of phylotypes. These included five clusters of previously recognized but uncultured oral Prevotella spp. and a major cluster containing Prevotella-like bacteria most closely related to uncharacterized rumen bacteria. Cluster-specific primers were designed, and the numbers of bacteria within clusters were quantified by real-time PCR, confirming the abundance of these organisms. The data indicated that advanced dental caries provides a unique environment for a complex array of novel and uncultured Prevotella and Prevotella-like bacteria which, in some cases, may dominate the diverse polymicrobial community associated with the disease. PMID:15528720

Exploring doxorubicin localization in eluting TiO2 nanotube arrays through fluorescence correlation spectroscopy analysis.

PubMed

De Santo, Ilaria; Sanguigno, Luigi; Causa, Filippo; Monetta, Tullio; Netti, Paolo A

2012-11-07

Drug elution properties of TiO(2) nanotube arrays have been largely investigated by means of solely macroscopic observations. Controversial elution performances have been reported so far and a clear comprehension of these phenomena is still missing as a consequence of a lack of molecular investigation methods. Here we propose a way to discern drug elution properties of nanotubes through the evaluation of drug localization by Fluorescence Correlation Spectroscopy (FCS) analysis. We verified this method upon doxorubicin elution from differently loaded TiO(2) nanotubes. Diverse elution profiles were obtained from nanotubes filled by soaking and wet vacuum impregnation methods. Impregnated nanotubes controlled drug diffusion up to thirty days, while soaked samples completed elution in seven days. FCS analysis of doxorubicin motion in loaded nanotubes clarified that more than 90% of drugs dwell preferentially in inter-nanotube spaces in soaked samples due to decorrelation in a 2D fashion, while a 97% fraction of molecules showed 1D mobility ascribable to displacements along the nanotube vertical axis of wet vacuum impregnated nanotubes. The diverse drug localizations inferred from FCS measurements, together with distinct drug-surface interaction strengths resulting from diverse drug filling techniques, could explain the variability in elution kinetics.

Solvothermal transformation of a calcium oleate precursor into large-sized highly ordered arrays of ultralong hydroxyapatite microtubes.

PubMed

Lu, Bing-Qiang; Zhu, Ying-Jie; Chen, Feng; Qi, Chao; Zhao, Xin-Yu; Zhao, Jing

2014-06-02

Hydroxyapatite (HAP), a well-known member of the calcium phosphate family, is the major inorganic component of bones and teeth in vertebrates. The highly ordered arrays of HAP structures are of great significance for hard tissue repair and for understanding the formation mechanisms of bones and teeth. However, the synthesis of highly ordered HAP structure arrays remains a great challenge. In this work, inspired by the ordered structure of tooth enamel, we have successfully synthesized three-dimensional bulk materials with large sizes (millimeter scale) that are made of highly ordered arrays of ultralong HAP microtubes (HOAUHMs) by solvothermal transformation of calcium oleate precursor. The core-shell-structured oblate sphere consists of a core that is composed of HAP nanorods and a shell that consists of highly ordered HAP microtube arrays. The prepared HOAUHMs are large: 6.0 mm in diameter and up to 1.4 mm in thickness. With increasing solvothermal reaction time, the HOAUHMs grow larger; the microtubes become more uniform and more ordered. This work provides a new synthetic method for synthesizing highly ordered arrays of uniform HAP ultralong microtubes that are promising for biomedical applications. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Patterns in bacterial and archaeal community structure and diversity in western Beaufort Sea sediments and waters

NASA Astrophysics Data System (ADS)

Hamdan, L. J.; Sikaroodi, M.; Coffin, R. B.; Gillevet, P. M.

2010-12-01

A culture-independent phylogenetic study of microbial communities in water samples and sediment cores recovered from the Beaufort Sea slope east of Point Barrow, Alaska was conducted. The goal of the work was to describe community composition in sediment and water samples and determine the influence of local environmental conditions on microbial populations. Archaeal and bacterial community composition was studied using length heterogeneity-polymerase chain reaction (LH-PCR) and multitag pyrosequencing (MTPS). Sediment samples were obtained from three piston cores on the slope (~1000m depth) arrayed along an east-west transect and one core from a depth of approximately 2000m. Discrete water samples were obtained using a CTD-rosette from three locations adjacent to piston core sites. Water sample were selected at three discrete depths within a vertically stratified (density) water column. The microbial community in near surface waters was distinct from the community observed in deeper stratified layers of the water column. Multidimensional scaling analysis (MDS) revealed that water samples from mid and deep stratified layers bore high similarity to communities in cores collected in close proximity. Overall, the highest diversity (bacteria and archaea) was observed in a core which had elevated methane concentration relative to other locations. Geochemical (e.g., bulk organic and inorganic carbon pools, nutrients, metabolites) and physical data (e.g. depth, water content) were used to reveal the abiotic factors structuring microbial communities. The analysis indicates that sediment water content (porosity) and inorganic carbon concentration are the most significant structuring elements on Beaufort shelf sedimentary microbial communities.

The microbially mediated soil organic carbon loss under degenerative succession in an alpine meadow.

PubMed

Zhang, Yuguang; Liu, Xiao; Cong, Jing; Lu, Hui; Sheng, Yuyu; Wang, Xiulei; Li, Diqiang; Liu, Xueduan; Yin, Huaqun; Zhou, Jizhong; Deng, Ye

2017-07-01

Land-cover change has long been recognized as having marked effect on the amount of soil organic carbon (SOC). However, the microbially mediated processes and mechanisms on SOC are still unclear. In this study, the soil samples in a degenerative succession from alpine meadow to alpine steppe meadow in the Qinghai-Tibetan Plateau were analysed using high-throughput technologies, including Illumina sequencing and geochip functional gene arrays. The soil microbial community structure and diversity were significantly (p < .05) different between alpine meadow and alpine steppe meadow; the microbial ɑ-diversity in alpine steppe meadow was significantly (p < .01) higher than in alpine meadow. Molecular ecological network analysis indicated that the microbial community structure in alpine steppe meadow was more complex and tighter than in the alpine meadow. The relative abundance of soil microbial labile carbon degradation genes (e.g., pectin and hemicellulose) was significantly higher in alpine steppe meadow than in alpine meadow, but the relative abundance of soil recalcitrant carbon degradation genes (e.g., chitin and lignin) showed the opposite tendency. The Biolog Ecoplate experiment showed that microbially mediated soil carbon utilization was more active in alpine steppe meadow than in alpine meadow. Consequently, more soil labile carbon might be decomposed in alpine steppe meadow than in alpine meadow. Therefore, the degenerative succession of alpine meadow because of climate change or anthropogenic activities would most likely decrease SOC and nutrients medicated by changing soil microbial community structure and their functional potentials for carbon decomposition. © 2017 John Wiley & Sons Ltd.

Triclosan Exposure Is Associated with Rapid Restructuring of the Microbiome in Adult Zebrafish

PubMed Central

Barton, Carrie L.; Proffitt, Sarah; Tanguay, Robert L.; Sharpton, Thomas J.

2016-01-01

Growing evidence indicates that disrupting the microbial community that comprises the intestinal tract, known as the gut microbiome, can contribute to the development or severity of disease. As a result, it is important to discern the agents responsible for microbiome disruption. While animals are frequently exposed to a diverse array of environmental chemicals, little is known about their effects on gut microbiome stability and structure. Here, we demonstrate how zebrafish can be used to glean insight into the effects of environmental chemical exposure on the structure and ecological dynamics of the gut microbiome. Specifically, we exposed forty-five adult zebrafish to triclosan-laden food for four or seven days or a control diet, and analyzed their microbial communities using 16S rRNA amplicon sequencing. Triclosan exposure was associated with rapid shifts in microbiome structure and diversity. We find evidence that several operational taxonomic units (OTUs) associated with the family Enterobacteriaceae appear to be susceptible to triclosan exposure, while OTUs associated with the genus Pseudomonas appeared to be more resilient and resistant to exposure. We also found that triclosan exposure is associated with topological alterations to microbial interaction networks and results in an overall increase in the number of negative interactions per microbe in these networks. Together these data indicate that triclosan exposure results in altered composition and ecological dynamics of microbial communities in the gut. Our work demonstrates that because zebrafish afford rapid and inexpensive interrogation of a large number of individuals, it is a useful experimental system for the discovery of the gut microbiome’s interaction with environmental chemicals. PMID:27191725

Integrated dynamic analysis simulation of space stations with controllable solar array

NASA Technical Reports Server (NTRS)

Heinrichs, J. A.; Fee, J. J.

1972-01-01

A methodology is formulated and presented for the integrated structural dynamic analysis of space stations with controllable solar arrays and non-controllable appendages. The structural system flexibility characteristics are considered in the dynamic analysis by a synthesis technique whereby free-free space station modal coordinates and cantilever appendage coordinates are inertially coupled. A digital simulation of this analysis method is described and verified by comparison of interaction load solutions with other methods of solution. Motion equations are simulated for both the zero gravity and artificial gravity (spinning) orbital conditions. Closed loop controlling dynamics for both orientation control of the arrays and attitude control of the space station are provided in the simulation by various generic types of controlling systems. The capability of the simulation as a design tool is demonstrated by utilizing typical space station and solar array structural representations and a specific structural perturbing force. Response and interaction load solutions are presented for this structural configuration and indicate the importance of using an integrated type analysis for the predictions of structural interactions.

Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts.

PubMed

Sanford, Jeremy R; Wang, Xin; Mort, Matthew; Vanduyn, Natalia; Cooper, David N; Mooney, Sean D; Edenberg, Howard J; Liu, Yunlong

2009-03-01

Metazoan genes are encrypted with at least two superimposed codes: the genetic code to specify the primary structure of proteins and the splicing code to expand their proteomic output via alternative splicing. Here, we define the specificity of a central regulator of pre-mRNA splicing, the conserved, essential splicing factor SFRS1. Cross-linking immunoprecipitation and high-throughput sequencing (CLIP-seq) identified 23,632 binding sites for SFRS1 in the transcriptome of cultured human embryonic kidney cells. SFRS1 was found to engage many different classes of functionally distinct transcripts including mRNA, miRNA, snoRNAs, ncRNAs, and conserved intergenic transcripts of unknown function. The majority of these diverse transcripts share a purine-rich consensus motif corresponding to the canonical SFRS1 binding site. The consensus site was not only enriched in exons cross-linked to SFRS1 in vivo, but was also enriched in close proximity to splice sites. mRNAs encoding RNA processing factors were significantly overrepresented, suggesting that SFRS1 may broadly influence the post-transcriptional control of gene expression in vivo. Finally, a search for the SFRS1 consensus motif within the Human Gene Mutation Database identified 181 mutations in 82 different genes that disrupt predicted SFRS1 binding sites. This comprehensive analysis substantially expands the known roles of human SR proteins in the regulation of a diverse array of RNA transcripts.

Limited genetic diversity among Sarcocystis neurona strains infecting southern sea otters precludes distinction between marine and terrestrial isolates.

PubMed

Wendte, J M; Miller, M A; Nandra, A K; Peat, S M; Crosbie, P R; Conrad, P A; Grigg, M E

2010-04-19

Sarcocystis neurona is an apicomplexan parasite identified as a cause of fatal neurological disease in the threatened southern sea otter (Enhydra lutris nereis). In an effort to characterize virulent S. neurona strains circulating in the marine ecosystem, this study developed a range of markers relevant for molecular genotyping. Highly conserved sequences within the 18S ribosomal gene array, the plastid-encoded RNA polymerase (RPOb) and the cytochrome c oxidase subunit 1 mitochondrial gene (CO1) were assessed for their ability to distinguish isolates at the genus and species level. For within-species comparisons, five surface antigens (SnSAG1-SnSAG5) and one high resolution microsatellite marker (Sn9) were developed as genotyping markers to evaluate intra-strain diversity. Molecular analysis at multiple loci revealed insufficient genetic diversity to distinguish terrestrial isolates from strains infecting marine mammals. Furthermore, SnSAG specific primers applied against DNA from the closely related species, Sarcocystis falcatula, lead to the discovery of highly similar orthologs to SnSAG2, 3, and 4, calling into question the specificity of diagnostic tests based on these antigens. The results of this study suggest a population genetic structure for S. neurona similar to that reported for the related parasite, Toxoplasma gondii, dominated by a limited number of successful genotypes. Published by Elsevier B.V.

Genome-wide investigation of genetic changes during modern breeding of Brassica napus.

PubMed

Wang, Nian; Li, Feng; Chen, Biyun; Xu, Kun; Yan, Guixin; Qiao, Jiangwei; Li, Jun; Gao, Guizhen; Bancroft, Ian; Meng, Jingling; King, Graham J; Wu, Xiaoming

2014-08-01

Considerable genome variation had been incorporated within rapeseed breeding programs over past decades. In past decades, there have been substantial changes in phenotypic properties of rapeseed as a result of extensive breeding effort. Uncovering the underlying patterns of allelic variation in the context of genome organisation would provide knowledge to guide future genetic improvement. We assessed genome-wide genetic changes, including population structure, genetic relatedness, the extent of linkage disequilibrium, nucleotide diversity and genetic differentiation based on F ST outlier detection, for a panel of 472 Brassica napus inbred accessions using a 60 k Brassica Infinium® SNP array. We found genetic diversity varied in different sub-groups. Moreover, the genetic diversity increased from 1950 to 1980 and then remained at a similar level in China and Europe. We also found ~6-10 % genomic regions revealed high F ST values. Some QTLs previously associated with important agronomic traits overlapped with these regions. Overall, the B. napus C genome was found to have more high F ST signals than the A genome, and we concluded that the C genome may contribute more valuable alleles to generate elite traits. The results of this study indicate that considerable genome variation had been incorporated within rapeseed breeding programs over past decades. These results also contribute to understanding the impact of rapeseed improvement on available genome variation and the potential for dissecting complex agronomic traits.

A photovoltaic catenary-tent array for the Martian surface

NASA Technical Reports Server (NTRS)

Crutchik, M.; Colozza, Anthony J.; Appelbaum, J.

1993-01-01

To provide electrical power during an exploration mission to Mars, a deployable tent-shaped structure with a flexible photovoltaic (PV) blanket is proposed. The array is designed with a self-deploying mechanism utilizing pressurized gas expansion. The structural design for the array uses a combination of cables, beams, and columns to support and deploy the PV blanket. Under the force of gravity a cable carrying a uniform load will take the shape of a catenary curve. A catenary-tent collector is self shadowing which must be taken into account in the solar radiation calculation. The shape and the area of the shadow on the array was calculated and used in the determination of the global radiation on the array. The PV blanket shape and structure dimension were optimized to achieve a configuration which maximizes the specific power (W/kg). The optimization was performed for four types of PV blankets (Si, GaAs/Ge, GaAs CLEFT, and amorphous Si) and four types of structure materials (Carbon composite, Aramid Fiber composite, Aluminum, and Magnesium). The results show that the catenary shape of the PV blanket, which produces the highest specific power, corresponds to zero end angle at the base with respect to the horizontal. The tent angle is determined by the combined effect of the array structure specific mass and the PV blanket output power. The combination of carbon composite structural material and GaAs CLEFT solar cells produce the highest specific power. The study was carried out for two sites on Mars corresponding to the Viking Lander locations. The designs were also compared for summer, winter, and yearly operation.

Terrestrial central station array life-cycle analysis support study

NASA Technical Reports Server (NTRS)

1978-01-01

Plant elements evaluated included designs for module, panel and array structures, as well as balance-of-plant systems. Installation and maintenance procedures and the impact of site environment were also evaluated. In terms of the cost of energy produced, the horizontal array configuration was found to be less expensive than the tandem array at latitudes less than 40 deg. Both of these configurations are less expensive than the rack design. However, the costs of energy for all three configurations are within approximately ?10 percent of each other. For flat plate panels, the seasonally adjusted and tracking array configurations are not economically attractive when compared to the three other designs. Balance-of-plant costs are approximately equal to (goal) module costs. The array structures and foundations are the most expensive items in the balance-of-plant costs.

PEP solar array definition study

NASA Technical Reports Server (NTRS)

1979-01-01

The conceptual design of a large, flexible, lightweight solar array is presented focusing on a solar array overview assessment, solar array blanket definition, structural-mechanical systems definition, and launch/reentry blanket protection features. The overview assessment includes a requirements and constraints review, the thermal environment assessment on the design selection, an evaluation of blanket integration sequence, a conceptual blanket/harness design, and a hot spot analysis considering the effects of shadowing and cell failures on overall array reliability. The solar array blanket definition includes the substrate design, hinge designs and blanket/harness flexibility assessment. The structural/mechanical systems definition includes an overall loads and deflection assessment, a frequency analysis of the deployed assembly, a components weights estimate, design of the blanket housing and tensioning mechanism. The launch/reentry blanket protection task includes assessment of solar cell/cover glass cushioning concepts during ascent and reentry flight condition.

Drying induced upright sliding and reorganization of carbon nanotube arrays

NASA Astrophysics Data System (ADS)

Li, Qingwen; DePaula, Raymond; Zhang, Xiefei; Zheng, Lianxi; Arendt, Paul N.; Mueller, Fred M.; Zhu, Y. T.; Tu, Yi

2006-09-01

Driven by capillary force, wet carbon nanotube (CNT) arrays have been found to reorganize into cellular structures upon drying. During the reorganization process, individual CNTs are firmly attached to the substrate and have to lie down on the substrate at cell bottoms, forming closed cells. Here we demonstrate that by modifying catalyst structures, the adhesion of CNTs to the substrate can be weakened. Upon drying such CNT arrays, CNTs may slide away from their original sites on the surface and self-assemble into cellular patterns with bottoms open. It is also found that the sliding distance of CNTs increases with array height, and drying millimetre tall arrays leads to the sliding of CNTs over a few hundred micrometres and the eventual self-assembly into discrete islands. By introducing regular vacancies in CNT arrays, CNTs may be manipulated into different patterns.