Characterization and Transferable Utility of Microsatellite Markers in the Wild and Cultivated Arachis Species.

PubMed

Huang, Li; Wu, Bei; Zhao, Jiaojiao; Li, Haitao; Chen, Weigang; Zheng, Yanli; Ren, Xiaoping; Chen, Yuning; Zhou, Xiaojing; Lei, Yong; Liao, Boshou; Jiang, Huifang

2016-01-01

Microsatellite or simple sequence repeat (SSR) is one of the most widely distributed molecular markers that have been widely utilized to assess genetic diversity and genetic mapping for important traits in plants. However, the understanding of microsatellite characteristics in Arachis species and the currently available amount of high-quality SSR markers remain limited. In this study, we identified 16,435 genome survey sequences SSRs (GSS-SSRs) and 40,199 expressed sequence tag SSRs (EST-SSRs) in Arachis hypogaea and its wild relative species using the publicly available sequence data. The GSS-SSRs had a density of 159.9-239.8 SSRs/Mb for wild Arachis and 1,015.8 SSR/Mb for cultivated Arachis, whereas the EST-SSRs had the density of 173.5-384.4 SSR/Mb and 250.9 SSRs/Mb for wild and cultivated Arachis, respectively. The trinucleotide SSRs were predominant across Arachis species, except that the dinucleotide accounted for most in A. hypogaea GSSs. From Arachis GSS-SSR and EST-SSR sequences, we developed 2,589 novel SSR markers that showed a high polymorphism in six diverse A. hypogaea accessions. A genetic linkage map that contained 540 novel SSR loci and 105 anchor SSR loci was constructed by case of a recombinant inbred lines F6 population. A subset of 82 randomly selected SSR markers were used to screen 39 wild and 22 cultivated Arachis accessions, which revealed a high transferability of the novel SSRs across Arachis species. Our results provided informative clues to investigate microsatellite patterns across A. hypogaea and its wild relative species and potentially facilitate the germplasm evaluation and gene mapping in Arachis species.

Discovery and mapping of single feature polymorphisms in wheat using Affymetrix arrays

PubMed Central

Bernardo, Amy N; Bradbury, Peter J; Ma, Hongxiang; Hu, Shengwa; Bowden, Robert L; Buckler, Edward S; Bai, Guihua

2009-01-01

Background Wheat (Triticum aestivum L.) is a staple food crop worldwide. The wheat genome has not yet been sequenced due to its huge genome size (~17,000 Mb) and high levels of repetitive sequences; the whole genome sequence may not be expected in the near future. Available linkage maps have low marker density due to limitation in available markers; therefore new technologies that detect genome-wide polymorphisms are still needed to discover a large number of new markers for construction of high-resolution maps. A high-resolution map is a critical tool for gene isolation, molecular breeding and genomic research. Single feature polymorphism (SFP) is a new microarray-based type of marker that is detected by hybridization of DNA or cRNA to oligonucleotide probes. This study was conducted to explore the feasibility of using the Affymetrix GeneChip to discover and map SFPs in the large hexaploid wheat genome. Results Six wheat varieties of diverse origins (Ning 7840, Clark, Jagger, Encruzilhada, Chinese Spring, and Opata 85) were analyzed for significant probe by variety interactions and 396 probe sets with SFPs were identified. A subset of 164 unigenes was sequenced and 54% showed polymorphism within probes. Microarray analysis of 71 recombinant inbred lines from the cross Ning 7840/Clark identified 955 SFPs and 877 of them were mapped together with 269 simple sequence repeat markers. The SFPs were randomly distributed within a chromosome but were unevenly distributed among different genomes. The B genome had the most SFPs, and the D genome had the least. Map positions of a selected set of SFPs were validated by mapping single nucleotide polymorphism using SNaPshot and comparing with expressed sequence tags mapping data. Conclusion The Affymetrix array is a cost-effective platform for SFP discovery and SFP mapping in wheat. The new high-density map constructed in this study will be a useful tool for genetic and genomic research in wheat. PMID:19480702

Identification of Simple Sequence Repeats in Chloroplast Genomes of Magnoliids Through Bioinformatics Approach.

PubMed

Srivastava, Deepika; Shanker, Asheesh

2016-12-01

Basal angiosperms or Magnoliids is an important clade of commercially important plants which mainly include spices and edible fruits. In this study, 17 chloroplast genome sequences belonging to clade Magnoliids were screened for the identification of chloroplast simple sequence repeats (cpSSRs). Simple sequence repeats or microsatellites are short stretches of DNA up to 1-6 base pair in length. These repeats are ubiquitous and play important role in the development of molecular markers and to study the mapping of traits of economic, medical or ecological interest. A total of 479 SSRs were detected, showing average density of 1 SSR/6.91 kb. Depending on the repeat units, the length of SSRs ranged from 12 to 24 bp for mono-, 12 to 18 bp for di-, 12 to 26 bp for tri-, 12 to 24 bp for tetra-, 15 bp for penta- and 18 bp for hexanucleotide repeats. Mononucleotide repeats were the most frequent (207, 43.21 %) followed by tetranucleotide repeats (130, 27.13 %). Penta- and hexanucleotide repeats were least frequent or absent in these chloroplast genomes.

Development, characterization and cross species amplification of polymorphic microsatellite markers from expressed sequence tags of turmeric (Curcuma longa L.).

PubMed

Siju, S; Dhanya, K; Syamkumar, S; Sasikumar, B; Sheeja, T E; Bhat, A I; Parthasarathy, V A

2010-02-01

Expressed sequence tags (ESTs) from turmeric (Curcuma longa L.) were used for the screening of type and frequency of Class I (hypervariable) simple sequence repeats (SSRs). A total of 231 microsatellite repeats were detected from 12,593 EST sequences of turmeric after redundancy elimination. The average density of Class I SSRs accounts to one SSR per 17.96 kb of EST. Mononucleotides were the most abundant class of microsatellite repeat in turmeric ESTs followed by trinucleotides. A robust set of 17 polymorphic EST-SSRs were developed and used for evaluating 20 turmeric accessions. The number of alleles detected ranged from 3 to 8 per loci. The developed markers were also evaluated in 13 related species of C. longa confirming high rate (100%) of cross species transferability. The polymorphic microsatellite markers generated from this study could be used for genetic diversity analysis and resolving the taxonomic confusion prevailing in the genus.

Construction of an ultra-high density consensus genetic map, and enhancement of the physical map from genome sequencing in Lupinus angustifolius.

PubMed

Zhou, Gaofeng; Jian, Jianbo; Wang, Penghao; Li, Chengdao; Tao, Ye; Li, Xuan; Renshaw, Daniel; Clements, Jonathan; Sweetingham, Mark; Yang, Huaan

2018-01-01

An ultra-high density genetic map containing 34,574 sequence-defined markers was developed in Lupinus angustifolius. Markers closely linked to nine genes of agronomic traits were identified. A physical map was improved to cover 560.5 Mb genome sequence. Lupin (Lupinus angustifolius L.) is a recently domesticated legume grain crop. In this study, we applied the restriction-site associated DNA sequencing (RADseq) method to genotype an F 9 recombinant inbred line population derived from a wild type × domesticated cultivar (W × D) cross. A high density linkage map was developed based on the W × D population. By integrating sequence-defined DNA markers reported in previous mapping studies, we established an ultra-high density consensus genetic map, which contains 34,574 markers consisting of 3508 loci covering 2399 cM on 20 linkage groups. The largest gap in the entire consensus map was 4.73 cM. The high density W × D map and the consensus map were used to develop an improved physical map, which covered 560.5 Mb of genome sequence data. The ultra-high density consensus linkage map, the improved physical map and the markers linked to genes of breeding interest reported in this study provide a common tool for genome sequence assembly, structural genomics, comparative genomics, functional genomics, QTL mapping, and molecular plant breeding in lupin.

Construction of an Integrated High Density Simple Sequence Repeat Linkage Map in Cultivated Strawberry (Fragaria × ananassa) and its Applicability

PubMed Central

Isobe, Sachiko N.; Hirakawa, Hideki; Sato, Shusei; Maeda, Fumi; Ishikawa, Masami; Mori, Toshiki; Yamamoto, Yuko; Shirasawa, Kenta; Kimura, Mitsuhiro; Fukami, Masanobu; Hashizume, Fujio; Tsuji, Tomoko; Sasamoto, Shigemi; Kato, Midori; Nanri, Keiko; Tsuruoka, Hisano; Minami, Chiharu; Takahashi, Chika; Wada, Tsuyuko; Ono, Akiko; Kawashima, Kumiko; Nakazaki, Naomi; Kishida, Yoshie; Kohara, Mitsuyo; Nakayama, Shinobu; Yamada, Manabu; Fujishiro, Tsunakazu; Watanabe, Akiko; Tabata, Satoshi

2013-01-01

The cultivated strawberry (Fragaria× ananassa) is an octoploid (2n = 8x = 56) of the Rosaceae family whose genomic architecture is still controversial. Several recent studies support the AAA′A′BBB′B′ model, but its complexity has hindered genetic and genomic analysis of this important crop. To overcome this difficulty and to assist genome-wide analysis of F. × ananassa, we constructed an integrated linkage map by organizing a total of 4474 of simple sequence repeat (SSR) markers collected from published Fragaria sequences, including 3746 SSR markers [Fragaria vesca expressed sequence tag (EST)-derived SSR markers] derived from F. vesca ESTs, 603 markers (F. × ananassa EST-derived SSR markers) from F. × ananassa ESTs, and 125 markers (F. × ananassa transcriptome-derived SSR markers) from F. × ananassa transcripts. Along with the previously published SSR markers, these markers were mapped onto five parent-specific linkage maps derived from three mapping populations, which were then assembled into an integrated linkage map. The constructed map consists of 1856 loci in 28 linkage groups (LGs) that total 2364.1 cM in length. Macrosynteny at the chromosome level was observed between the LGs of F. × ananassa and the genome of F. vesca. Variety distinction on 129 F. × ananassa lines was demonstrated using 45 selected SSR markers. PMID:23248204

Supramolecular polymerization of a prebiotic nucleoside provides insights into the creation of sequence-controlled polymers.

PubMed

Wang, Jun; Bonnesen, Peter V; Rangel, E; Vallejo, E; Sanchez-Castillo, Ariadna; James Cleaves Ii, H; Baddorf, Arthur P; Sumpter, Bobby G; Pan, Minghu; Maksymovych, Petro; Fuentes-Cabrera, Miguel

2016-01-04

Self-assembly of a nucleoside on Au(111) was studied to ascertain whether polymerization on well-defined substrates constitutes a promising approach for making sequence-controlled polymers. Scanning tunneling microscopy and density functional theory were used to investigate the self-assembly on Au(111) of (RS)-N(9)-(2,3-dihydroxypropyl)adenine (DHPA), a plausibly prebiotic nucleoside analog of adenosine. It is found that DHPA molecules self-assemble into a hydrogen-bonded polymer that grows almost exclusively along the herringbone reconstruction pattern, has a two component sequence that is repeated over hundreds of nanometers, and is erasable with electron-induced excitation. Although the sequence is simple, more complicated ones are envisioned if two or more nucleoside types are combined. Because polymerization occurs on a substrate in a dry environment, the success of each combination can be gauged with high-resolution imaging and accurate modeling techniques. These characteristics make nucleoside self-assembly on a substrate an attractive approach for designing sequence-controlled polymers. Further, by choosing plausibly prebiotic nucleosides, insights may be provided into how nature created the first sequence-controlled polymers capable of storing information. Such insights, in turn, can inspire new ways of synthesizing sequence-controlled polymers.

Draft Sequences of the Radish (Raphanus sativus L.) Genome

PubMed Central

Kitashiba, Hiroyasu; Li, Feng; Hirakawa, Hideki; Kawanabe, Takahiro; Zou, Zhongwei; Hasegawa, Yoichi; Tonosaki, Kaoru; Shirasawa, Sachiko; Fukushima, Aki; Yokoi, Shuji; Takahata, Yoshihito; Kakizaki, Tomohiro; Ishida, Masahiko; Okamoto, Shunsuke; Sakamoto, Koji; Shirasawa, Kenta; Tabata, Satoshi; Nishio, Takeshi

2014-01-01

Radish (Raphanus sativus L., n = 9) is one of the major vegetables in Asia. Since the genomes of Brassica and related species including radish underwent genome rearrangement, it is quite difficult to perform functional analysis based on the reported genomic sequence of Brassica rapa. Therefore, we performed genome sequencing of radish. Short reads of genomic sequences of 191.1 Gb were obtained by next-generation sequencing (NGS) for a radish inbred line, and 76,592 scaffolds of ≥300 bp were constructed along with the bacterial artificial chromosome-end sequences. Finally, the whole draft genomic sequence of 402 Mb spanning 75.9% of the estimated genomic size and containing 61,572 predicted genes was obtained. Subsequently, 221 single nucleotide polymorphism markers and 768 PCR-RFLP markers were used together with the 746 markers produced in our previous study for the construction of a linkage map. The map was combined further with another radish linkage map constructed mainly with expressed sequence tag-simple sequence repeat markers into a high-density integrated map of 1,166 cM with 2,553 DNA markers. A total of 1,345 scaffolds were assigned to the linkage map, spanning 116.0 Mb. Bulked PCR products amplified by 2,880 primer pairs were sequenced by NGS, and SNPs in eight inbred lines were identified. PMID:24848699

Developing expressed sequence tag libraries and the discovery of simple sequence repeat markers for two species of raspberry (Rubus L.)

USDA-ARS?s Scientific Manuscript database

Background: Due to a relatively high level of codominant inheritance and transferability within and among taxonomic groups, simple sequence repeat (SSR) markers are important elements in comparative mapping and delineation of genomic regions associated with traits of economic importance. Expressed S...

Chromosome arm-specific BAC end sequences permit comparative analysis of homoeologous chromosomes and genomes of polyploid wheat

PubMed Central

2012-01-01

Background Bread wheat, one of the world’s staple food crops, has the largest, highly repetitive and polyploid genome among the cereal crops. The wheat genome holds the key to crop genetic improvement against challenges such as climate change, environmental degradation, and water scarcity. To unravel the complex wheat genome, the International Wheat Genome Sequencing Consortium (IWGSC) is pursuing a chromosome- and chromosome arm-based approach to physical mapping and sequencing. Here we report on the use of a BAC library made from flow-sorted telosomic chromosome 3A short arm (t3AS) for marker development and analysis of sequence composition and comparative evolution of homoeologous genomes of hexaploid wheat. Results The end-sequencing of 9,984 random BACs from a chromosome arm 3AS-specific library (TaaCsp3AShA) generated 11,014,359 bp of high quality sequence from 17,591 BAC-ends with an average length of 626 bp. The sequence represents 3.2% of t3AS with an average DNA sequence read every 19 kb. Overall, 79% of the sequence consisted of repetitive elements, 1.38% as coding regions (estimated 2,850 genes) and another 19% of unknown origin. Comparative sequence analysis suggested that 70-77% of the genes present in both 3A and 3B were syntenic with model species. Among the transposable elements, gypsy/sabrina (12.4%) was the most abundant repeat and was significantly more frequent in 3A compared to homoeologous chromosome 3B. Twenty novel repetitive sequences were also identified using de novo repeat identification. BESs were screened to identify simple sequence repeats (SSR) and transposable element junctions. A total of 1,057 SSRs were identified with a density of one per 10.4 kb, and 7,928 junctions between transposable elements (TE) and other sequences were identified with a density of one per 1.39 kb. With the objective of enhancing the marker density of chromosome 3AS, oligonucleotide primers were successfully designed from 758 SSRs and 695 Insertion Site Based Polymorphisms (ISBPs). Of the 96 ISBP primer pairs tested, 28 (29%) were 3A-specific and compared to 17 (18%) for 96 SSRs. Conclusion This work reports on the use of wheat chromosome arm 3AS-specific BAC library for the targeted generation of sequence data from a particular region of the huge genome of wheat. A large quantity of sequences were generated from the A genome of hexaploid wheat for comparative genome analysis with homoeologous B and D genomes and other model grass genomes. Hundreds of molecular markers were developed from the 3AS arm-specific sequences; these and other sequences will be useful in gene discovery and physical mapping. PMID:22559868

An integrated genetic linkage map of watermelon and genetic diversity based on single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers

USDA-ARS?s Scientific Manuscript database

Watermelon (Citrullus lanatus var. lanatus) is an important vegetable fruit throughout the world. A high number of single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers should provide large coverage of the watermelon genome and high phylogenetic resolution of germplasm acces...

Highly Informative Simple Sequence Repeat (SSR) Markers for Fingerprinting Hazelnut

USDA-ARS?s Scientific Manuscript database

Simple sequence repeat (SSR) or microsatellite markers have many applications in breeding and genetic studies of plants, including fingerprinting of cultivars and investigations of genetic diversity, and therefore provide information for better management of germplasm collections. They are repeatab...

Mapping Simple Repeated DNA Sequences in Heterochromatin of Drosophila Melanogaster

PubMed Central

Lohe, A. R.; Hilliker, A. J.; Roberts, P. A.

1993-01-01

Heterochromatin in Drosophila has unusual genetic, cytological and molecular properties. Highly repeated DNA sequences (satellites) are the principal component of heterochromatin. Using probes from cloned satellites, we have constructed a chromosome map of 10 highly repeated, simple DNA sequences in heterochromatin of mitotic chromosomes of Drosophila melanogaster. Despite extensive sequence homology among some satellites, chromosomal locations could be distinguished by stringent in situ hybridizations for each satellite. Only two of the localizations previously determined using gradient-purified bulk satellite probes are correct. Eight new satellite localizations are presented, providing a megabase-level chromosome map of one-quarter of the genome. Five major satellites each exhibit a multichromosome distribution, and five minor satellites hybridize to single sites on the Y chromosome. Satellites closely related in sequence are often located near one another on the same chromosome. About 80% of Y chromosome DNA is composed of nine simple repeated sequences, in particular (AAGAC)(n) (8 Mb), (AAGAG)(n) (7 Mb) and (AATAT)(n) (6 Mb). Similarly, more than 70% of the DNA in chromosome 2 heterochromatin is composed of five simple repeated sequences. We have also generated a high resolution map of satellites in chromosome 2 heterochromatin, using a series of translocation chromosomes whose breakpoints in heterochromatin were ordered by N-banding. Finally, staining and banding patterns of heterochromatic regions are correlated with the locations of specific repeated DNA sequences. The basis for the cytochemical heterogeneity in banding appears to depend exclusively on the different satellite DNAs present in heterochromatin. PMID:8375654

Predicting Fish Densities in Lotic Systems: a Simple Modeling Approach

EPA Science Inventory

Fish density models are essential tools for fish ecologists and fisheries managers. However, applying these models can be difficult because of high levels of model complexity and the large number of parameters that must be estimated. We designed a simple fish density model and te...

T1 weighted brain images at 7 Tesla unbiased for Proton Density, T2* contrast and RF coil receive B1 sensitivity with simultaneous vessel visualization.

PubMed

Van de Moortele, Pierre-François; Auerbach, Edwards J; Olman, Cheryl; Yacoub, Essa; Uğurbil, Kâmil; Moeller, Steen

2009-06-01

At high magnetic field, MR images exhibit large, undesirable signal intensity variations commonly referred to as "intensity field bias". Such inhomogeneities mostly originate from heterogeneous RF coil B(1) profiles and, with no appropriate correction, are further pronounced when utilizing rooted sum of square reconstruction with receive coil arrays. These artifacts can significantly alter whole brain high resolution T(1)-weighted (T(1)w) images that are extensively utilized for clinical diagnosis, for gray/white matter segmentation as well as for coregistration with functional time series. In T(1) weighted 3D-MPRAGE sequences, it is possible to preserve a bulk amount of T(1) contrast through space by using adiabatic inversion RF pulses that are insensitive to transmit B(1) variations above a minimum threshold. However, large intensity variations persist in the images, which are significantly more difficult to address at very high field where RF coil B(1) profiles become more heterogeneous. Another characteristic of T(1)w MPRAGE sequences is their intrinsic sensitivity to Proton Density and T(2)(*) contrast, which cannot be removed with post-processing algorithms utilized to correct for receive coil sensitivity. In this paper, we demonstrate a simple technique capable of producing normalized, high resolution T(1)w 3D-MPRAGE images that are devoid of receive coil sensitivity, Proton Density and T(2)(*) contrast. These images, which are suitable for routinely obtaining whole brain tissue segmentation at 7 T, provide higher T(1) contrast specificity than standard MPRAGE acquisitions. Our results show that removing the Proton Density component can help in identifying small brain structures and that T(2)(*) induced artifacts can be removed from the images. The resulting unbiased T(1)w images can also be used to generate Maximum Intensity Projection angiograms, without additional data acquisition, that are inherently registered with T(1)w structural images. In addition, we introduce a simple technique to reduce residual signal intensity variations induced by transmit B(1) heterogeneity. Because this approach requires two 3D images, one divided with the other, head motion could create serious problems, especially at high spatial resolution. To alleviate such inter-scan motion problems, we developed a new sequence where the two contrast acquisitions are interleaved within a single scan. This interleaved approach however comes with greater risk of intra-scan motion issues because of a longer single scan time. Users can choose between these two trade offs depending on specific protocols and patient populations. We believe that the simplicity and the robustness of this double contrast based approach to address intensity field bias at high field and improve T(1) contrast specificity, together with the capability of simultaneously obtaining angiography maps, advantageously counter balance the potential drawbacks of the technique, mainly a longer acquisition time and a moderate reduction in signal to noise ratio.

T1 weighted Brain Images at 7 Tesla Unbiased for Proton Density, T2* contrast and RF Coil Receive B1 Sensitivity with Simultaneous Vessel Visualization

PubMed Central

Van de Moortele, Pierre-François; Auerbach, Edwards J.; Olman, Cheryl; Yacoub, Essa; Uğurbil, Kâmil; Moeller, Steen

2009-01-01

At high magnetic field, MR images exhibit large, undesirable signal intensity variations commonly referred to as “intensity field bias”. Such inhomogeneities mostly originate from heterogeneous RF coil B1 profiles and, with no appropriate correction, are further pronounced when utilizing rooted sum of square reconstruction with receive coil arrays. These artifacts can significantly alter whole brain high resolution T1-weighted (T1w) images that are extensively utilized for clinical diagnosis, for gray/white matter segmentation as well as for coregistration with functional time series. In T1 weighted 3D-MPRAGE sequences, it is possible to preserve a bulk amount of T1 contrast through space by using adiabatic inversion RF pulses that are insensitive to transmit B1 variations above a minimum threshold. However, large intensity variations persist in the images, which are significantly more difficult to address at very high field where RF coil B1 profiles become more heterogeneous. Another characteristic of T1w MPRAGE sequences is their intrinsic sensitivity to Proton Density and T2* contrast, which cannot be removed with post-processing algorithms utilized to correct for receive coil sensitivity. In this paper, we demonstrate a simple technique capable of producing normalized, high resolution T1w 3D-MPRAGE images that are devoid of receive coil sensitivity, Proton Density and T2* contrast. These images, which are suitable for routinely obtaining whole brain tissue segmentation at 7 Tesla, provide higher T1 contrast specificity than standard MPRAGE acquisitions. Our results show that removing the Proton Density component can help identifying small brain structures and that T2* induced artifacts can be removed from the images. The resulting unbiased T1w images can also be used to generate Maximum Intensity Projection angiograms, without additional data acquisition, that are inherently registered with T1w structural images. In addition, we introduce a simple technique to reduce residual signal intensity variations induced by Transmit B1 heterogeneity. Because this approach requires two 3D images, one divided with the other, head motion could create serious problems, especially at high spatial resolution. To alleviate such inter-scan motion problems, we developed a new sequence where the two contrast acquisitions are interleaved within a single scan. This interleaved approach however comes with greater risk of intra-scan motion issues because of a longer single scan time. Users can choose between these two trade offs depending on specific protocols and patient populations. We believe that the simplicity and the robustness of this double contrast based approach to address intensity field bias at high field and improve T1 contrast specificity, together with the capability of simultaneously obtaining angiography maps, advantageously counter balance the potential drawbacks of the technique, mainly a longer acquisition time and a moderate reduction in signal to noise ratio. PMID:19233292

High-density, microsphere-based fiber optic DNA microarrays.

PubMed

Epstein, Jason R; Leung, Amy P K; Lee, Kyong Hoon; Walt, David R

2003-05-01

A high-density fiber optic DNA microarray has been developed consisting of oligonucleotide-functionalized, 3.1-microm-diameter microspheres randomly distributed on the etched face of an imaging fiber bundle. The fiber bundles are comprised of 6000-50000 fused optical fibers and each fiber terminates with an etched well. The microwell array is capable of housing complementary-sized microspheres, each containing thousands of copies of a unique oligonucleotide probe sequence. The array fabrication process results in random microsphere placement. Determining the position of microspheres in the random array requires an optical encoding scheme. This array platform provides many advantages over other array formats. The microsphere-stock suspension concentration added to the etched fiber can be controlled to provide inherent sensor redundancy. Examining identical microspheres has a beneficial effect on the signal-to-noise ratio. As other sequences of interest are discovered, new microsphere sensing elements can be added to existing microsphere pools and new arrays can be fabricated incorporating the new sequences without altering the existing detection capabilities. These microarrays contain the smallest feature sizes (3 microm) of any DNA array, allowing interrogation of extremely small sample volumes. Reducing the feature size results in higher local target molecule concentrations, creating rapid and highly sensitive assays. The microsphere array platform is also flexible in its applications; research has included DNA-protein interaction profiles, microbial strain differentiation, and non-labeled target interrogation with molecular beacons. Fiber optic microsphere-based DNA microarrays have a simple fabrication protocol enabling their expansion into other applications, such as single cell-based assays.

Hierarchy and extremes in selections from pools of randomized proteins

PubMed Central

Boyer, Sébastien; Biswas, Dipanwita; Kumar Soshee, Ananda; Scaramozzino, Natale; Nizak, Clément; Rivoire, Olivier

2016-01-01

Variation and selection are the core principles of Darwinian evolution, but quantitatively relating the diversity of a population to its capacity to respond to selection is challenging. Here, we examine this problem at a molecular level in the context of populations of partially randomized proteins selected for binding to well-defined targets. We built several minimal protein libraries, screened them in vitro by phage display, and analyzed their response to selection by high-throughput sequencing. A statistical analysis of the results reveals two main findings. First, libraries with the same sequence diversity but built around different “frameworks” typically have vastly different responses; second, the distribution of responses of the best binders in a library follows a simple scaling law. We show how an elementary probabilistic model based on extreme value theory rationalizes the latter finding. Our results have implications for designing synthetic protein libraries, estimating the density of functional biomolecules in sequence space, characterizing diversity in natural populations, and experimentally investigating evolvability (i.e., the potential for future evolution). PMID:26969726

Hierarchy and extremes in selections from pools of randomized proteins.

PubMed

Boyer, Sébastien; Biswas, Dipanwita; Kumar Soshee, Ananda; Scaramozzino, Natale; Nizak, Clément; Rivoire, Olivier

2016-03-29

Variation and selection are the core principles of Darwinian evolution, but quantitatively relating the diversity of a population to its capacity to respond to selection is challenging. Here, we examine this problem at a molecular level in the context of populations of partially randomized proteins selected for binding to well-defined targets. We built several minimal protein libraries, screened them in vitro by phage display, and analyzed their response to selection by high-throughput sequencing. A statistical analysis of the results reveals two main findings. First, libraries with the same sequence diversity but built around different "frameworks" typically have vastly different responses; second, the distribution of responses of the best binders in a library follows a simple scaling law. We show how an elementary probabilistic model based on extreme value theory rationalizes the latter finding. Our results have implications for designing synthetic protein libraries, estimating the density of functional biomolecules in sequence space, characterizing diversity in natural populations, and experimentally investigating evolvability (i.e., the potential for future evolution).

Human proinsulin C-peptide from a precursor overexpressed in Pichia pastoris.

PubMed

Huang, Yang-Bin; Li, Jiang; Gao, Xin; Sun, Jiu-Ru; Lu, Yi; Feng, Tao; Fei, Jian; Cui, Da-Fu; Xia, Qi-Chang; Ren, Jun; Zhang, You-Shang

2006-08-01

In this article we report the production of human proinsulin C-peptide with 31 amino acid residues from a precursor overexpressed in Pichia pastoris. A C-peptide precursor expression plasmid containing nine C-peptide genes in tandem was constructed and used to transform P. pastoris. Transformants with a high copy number of the C-peptide precursor gene integrated into the chromosome of P. pastoris were selected. In high-density fermentation in a 300 liter fermentor using a simple culture medium composed mainly of salt and methanol, the C-peptide precursor was overexpressed to a level of 2.28 g per liter. A simple procedure was established to purify the expression product from the culture medium. The purified C-peptide precursor was converted into C-peptide by trypsin and carboxypeptidase B joint digestion. The yield of C-peptide with a purity of 96% was 730 mg per liter of culture. The purified C-peptide was characterized by mass spectrometry, N- and C-terminal amino acid sequencing, and sodium dodecylsulfate-polyacrylamide gel electrophoresis.

Genome-Wide Characterization and Linkage Mapping of Simple Sequence Repeats in Mei (Prunus mume Sieb. et Zucc.)

PubMed Central

Sun, Lidan; Yang, Weiru; Zhang, Qixiang; Cheng, Tangren; Pan, Huitang; Xu, Zongda; Zhang, Jie; Chen, Chuguang

2013-01-01

Because of its popularity as an ornamental plant in East Asia, mei (Prunus mume Sieb. et Zucc.) has received increasing attention in genetic and genomic research with the recent shotgun sequencing of its genome. Here, we performed the genome-wide characterization of simple sequence repeats (SSRs) in the mei genome and detected a total of 188,149 SSRs occurring at a frequency of 794 SSR/Mb. Mononucleotide repeats were the most common type of SSR in genomic regions, followed by di- and tetranucleotide repeats. Most of the SSRs in coding sequences (CDS) were composed of tri- or hexanucleotide repeat motifs, but mononucleotide repeats were always the most common in intergenic regions. Genome-wide comparison of SSR patterns among the mei, strawberry (Fragaria vesca), and apple (Malus×domestica) genomes showed mei to have the highest density of SSRs, slightly higher than that of strawberry (608 SSR/Mb) and almost twice as high as that of apple (398 SSR/Mb). Mononucleotide repeats were the dominant SSR motifs in the three Rosaceae species. Using 144 SSR markers, we constructed a 670 cM-long linkage map of mei delimited into eight linkage groups (LGs), with an average marker distance of 5 cM. Seventy one scaffolds covering about 27.9% of the assembled mei genome were anchored to the genetic map, depending on which the macro-colinearity between the mei genome and Prunus T×E reference map was identified. The framework map of mei constructed provides a first step into subsequent high-resolution genetic mapping and marker-assisted selection for this ornamental species. PMID:23555708

Survey and analysis of simple sequence repeats in the Laccaria bicolor genome, with development of microsatellite markers

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

Labbe, Jessy L; Murat, Claude; Morin, Emmanuelle

It is becoming clear that simple sequence repeats (SSRs) play a significant role in fungal genome organization, and they are a large source of genetic markers for population genetics and meiotic maps. We identified SSRs in the Laccaria bicolor genome by in silico survey and analyzed their distribution in the different genomic regions. We also compared the abundance and distribution of SSRs in L. bicolor with those of the following fungal genomes: Phanerochaete chrysosporium, Coprinopsis cinerea, Ustilago maydis, Cryptococcus neoformans, Aspergillus nidulans, Magnaporthe grisea, Neurospora crassa and Saccharomyces cerevisiae. Using the MISA computer program, we detected 277,062 SSRs in themore » L. bicolor genome representing 8% of the assembled genomic sequence. Among the analyzed basidiomycetes, L. bicolor exhibited the highest SSR density although no correlation between relative abundance and the genome sizes was observed. In most genomes the short motifs (mono- to trinucleotides) were more abundant than the longer repeated SSRs. Generally, in each organism, the occurrence, relative abundance, and relative density of SSRs decreased as the repeat unit increased. Furthermore, each organism had its own common and longest SSRs. In the L. bicolor genome, most of the SSRs were located in intergenic regions (73.3%) and the highest SSR density was observed in transposable elements (TEs; 6,706 SSRs/Mb). However, 81% of the protein-coding genes contained SSRs in their exons, suggesting that SSR polymorphism may alter gene phenotypes. Within a L. bicolor offspring, sequence polymorphism of 78 SSRs was mainly detected in non-TE intergenic regions. Unlike previously developed microsatellite markers, these new ones are spread throughout the genome; these markers could have immediate applications in population genetics.« less

Supramolecular polymerization of a prebiotic nucleoside provides insights into the creation of sequence-controlled polymers

DOE PAGES

Wang, Jun; Bonnesen, Peter V; Rangel, E.; ...

2016-01-04

The self-assembly of a nucleoside on Au(111) was studied to ascertain whether polymerization on well-defined substrates constitutes a promising approach for making sequence-controlled polymers. Scanning tunneling microscopy and density functional theory were used to investigate the self-assembly on Au(111) of (RS)-N9-(2,3-dihydroxypropyl)adenine (DHPA), a plausibly prebiotic nucleoside analog of adenosine. It is found that DHPA molecules self-assemble into a hydrogen-bonded polymer that grows almost exclusively along the herringbone reconstruction pattern, has a two component sequence that is repeated over hundreds of nanometers, and is erasable with electron-induced excitation. Although the sequence is simple, more complicated ones are envisioned if two ormore » more nucleoside types are combined. Because polymerization occurs on a substrate in a dry environment, the success of each combination can be gauged with high-resolution imaging and accurate modeling techniques. The resulting characteristics make nucleoside self-assembly on a substrate an attractive approach for designing sequence-controlled polymers. Moreover, by choosing plausibly prebiotic nucleosides, insights may be provided into how nature created the first sequence-controlled polymers capable of storing information. Such insights, in turn, can inspire new ways of synthesizing sequence-controlled polymers.« less

Supramolecular polymerization of a prebiotic nucleoside provides insights into the creation of sequence-controlled polymers

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

Wang, Jun; Bonnesen, Peter V; Rangel, E.

The self-assembly of a nucleoside on Au(111) was studied to ascertain whether polymerization on well-defined substrates constitutes a promising approach for making sequence-controlled polymers. Scanning tunneling microscopy and density functional theory were used to investigate the self-assembly on Au(111) of (RS)-N9-(2,3-dihydroxypropyl)adenine (DHPA), a plausibly prebiotic nucleoside analog of adenosine. It is found that DHPA molecules self-assemble into a hydrogen-bonded polymer that grows almost exclusively along the herringbone reconstruction pattern, has a two component sequence that is repeated over hundreds of nanometers, and is erasable with electron-induced excitation. Although the sequence is simple, more complicated ones are envisioned if two ormore » more nucleoside types are combined. Because polymerization occurs on a substrate in a dry environment, the success of each combination can be gauged with high-resolution imaging and accurate modeling techniques. The resulting characteristics make nucleoside self-assembly on a substrate an attractive approach for designing sequence-controlled polymers. Moreover, by choosing plausibly prebiotic nucleosides, insights may be provided into how nature created the first sequence-controlled polymers capable of storing information. Such insights, in turn, can inspire new ways of synthesizing sequence-controlled polymers.« less

Genic Microsatellite Markers in Brassica rapa: Development, Characterization, Mapping, and Their Utility in Other Cultivated and Wild Brassica Relatives

PubMed Central

Ramchiary, Nirala; Nguyen, Van Dan; Li, Xiaonan; Hong, Chang Pyo; Dhandapani, Vignesh; Choi, Su Ryun; Yu, Ge; Piao, Zhong Yun; Lim, Yong Pyo

2011-01-01

Genic microsatellite markers, also known as functional markers, are preferred over anonymous markers as they reveal the variation in transcribed genes among individuals. In this study, we developed a total of 707 expressed sequence tag-derived simple sequence repeat markers (EST-SSRs) and used for development of a high-density integrated map using four individual mapping populations of B. rapa. This map contains a total of 1426 markers, consisting of 306 EST-SSRs, 153 intron polymorphic markers, 395 bacterial artificial chromosome-derived SSRs (BAC-SSRs), and 572 public SSRs and other markers covering a total distance of 1245.9 cM of the B. rapa genome. Analysis of allelic diversity in 24 B. rapa germplasm using 234 mapped EST-SSR markers showed amplification of 2 alleles by majority of EST-SSRs, although amplification of alleles ranging from 2 to 8 was found. Transferability analysis of 167 EST-SSRs in 35 species belonging to cultivated and wild brassica relatives showed 42.51% (Sysimprium leteum) to 100% (B. carinata, B. juncea, and B. napus) amplification. Our newly developed EST-SSRs and high-density linkage map based on highly transferable genic markers would facilitate the molecular mapping of quantitative trait loci and the positional cloning of specific genes, in addition to marker-assisted selection and comparative genomic studies of B. rapa with other related species. PMID:21768136

Cosmic Star Formation: A Simple Model of the SFRD(z)

NASA Astrophysics Data System (ADS)

Chiosi, Cesare; Sciarratta, Mauro; D’Onofrio, Mauro; Chiosi, Emanuela; Brotto, Francesca; De Michele, Rosaria; Politino, Valeria

2017-12-01

We investigate the evolution of the cosmic star formation rate density (SFRD) from redshift z = 20 to z = 0 and compare it with the observational one by Madau and Dickinson derived from recent compilations of ultraviolet (UV) and infrared (IR) data. The theoretical SFRD(z) and its evolution are obtained using a simple model that folds together the star formation histories of prototype galaxies that are designed to represent real objects of different morphological type along the Hubble sequence and the hierarchical growing of structures under the action of gravity from small perturbations to large-scale objects in Λ-CDM cosmogony, i.e., the number density of dark matter halos N(M,z). Although the overall model is very simple and easy to set up, it provides results that mimic results obtained from highly complex large-scale N-body simulations well. The simplicity of our approach allows us to test different assumptions for the star formation law in galaxies, the effects of energy feedback from stars to interstellar gas, the efficiency of galactic winds, and also the effect of N(M,z). The result of our analysis is that in the framework of the hierarchical assembly of galaxies, the so-called time-delayed star formation under plain assumptions mainly for the energy feedback and galactic winds can reproduce the observational SFRD(z).

High-Throughput Density Measurement Using Magnetic Levitation.

PubMed

Ge, Shencheng; Wang, Yunzhe; Deshler, Nicolas J; Preston, Daniel J; Whitesides, George M

2018-06-20

This work describes the development of an integrated analytical system that enables high-throughput density measurements of diamagnetic particles (including cells) using magnetic levitation (MagLev), 96-well plates, and a flatbed scanner. MagLev is a simple and useful technique with which to carry out density-based analysis and separation of a broad range of diamagnetic materials with different physical forms (e.g., liquids, solids, gels, pastes, gums, etc.); one major limitation, however, is the capacity to perform high-throughput density measurements. This work addresses this limitation by (i) re-engineering the shape of the magnetic fields so that the MagLev system is compatible with 96-well plates, and (ii) integrating a flatbed scanner (and simple optical components) to carry out imaging of the samples that levitate in the system. The resulting system is compatible with both biological samples (human erythrocytes) and nonbiological samples (simple liquids and solids, such as 3-chlorotoluene, cholesterol crystals, glass beads, copper powder, and polymer beads). The high-throughput capacity of this integrated MagLev system will enable new applications in chemistry (e.g., analysis and separation of materials) and biochemistry (e.g., cellular responses under environmental stresses) in a simple and label-free format on the basis of a universal property of all matter, i.e., density.

High density bit transition requirements versus the effects on BCH error correcting code. [bit synchronization

NASA Technical Reports Server (NTRS)

Ingels, F. M.; Schoggen, W. O.

1982-01-01

The design to achieve the required bit transition density for the Space Shuttle high rate multiplexes (HRM) data stream of the Space Laboratory Vehicle is reviewed. It contained a recommended circuit approach, specified the pseudo random (PN) sequence to be used and detailed the properties of the sequence. Calculations showing the probability of failing to meet the required transition density were included. A computer simulation of the data stream and PN cover sequence was provided. All worst case situations were simulated and the bit transition density exceeded that required. The Preliminary Design Review and the critical Design Review are documented. The Cover Sequence Generator (CSG) Encoder/Decoder design was constructed and demonstrated. The demonstrations were successful. All HRM and HRDM units incorporate the CSG encoder or CSG decoder as appropriate.

Similarities in the chromosomal distribution of AG and AC repeats within and between Drosophila, human and barley chromosomes.

PubMed

Cuadrado, A; Jouve, N

2007-01-01

Two simple sequence repeats (SSRs), AG and AC, were mapped directly in the metaphase chromosomes of man and barley (Hordeum vulgare L.), and in the metaphase and polytene chromosomes of Drosophila melanogaster. To this end, synthetic oligonucleotides corresponding to (AG)(12) and (AC)(8) were labelled by the random primer technique and used as probes in fluorescent in situ hybridisation (FISH) under high stringency and strict washing conditions. The distribution and intensity of the signals for the repeat sequences were found to be characteristic of the chromosomes and genomes of the three species analysed. The AC repeat sites were uniformly dispersed along the euchromatic segments of all three genomes; in fact, they were largely excluded from the heterochromatin. The Drosophila genome showed a high density of AC sequences on the X chromosome in both mitotic and polytene nuclei. In contrast, the AG repeats were associated with the euchromatic regions of the polytene chromosomes (and in high density on the X chromosome), but were only seen in specific heterochromatic regions in the mitotic chromosomes of all three species. In Drosophila, the AG repeats were exclusively distributed on the tips of the Y chromosome and near the centromere on both arms of chromosome 2. In barley and man, AG repeats were associated with the centromeres (of all chromosomes) and nucleolar organizer regions, respectively. The conserved chromosome distribution of AC within and between these three phylogenetically distant species, and the association of AG in specific chromosome regions with structural or functional properties, suggests that long clusters of these repeats may have some, as yet unknown, role. Copyright (c) 2007 S. Karger AG, Basel.

A framework linkage map of perennial ryegrass based on SSR markers

Treesearch

G.P. Gill; P.L. Wilcox; D.J. Whittaker; R.A. Winz; P. Bickerstaff; Craig E. Echt; J. Kent; M.O. Humphreys; K.M. Elborough; R.C. Gardner

2006-01-01

A moderate-density linkage map for Lolium perenne L. has been constructed based on 376 simple sequence repeat (SSR) markers. Approximately one third ( 124) of the SSR markers were developed from GeneThresher libraries that preferentially select genomic DNA clones from the gene-rich unmethylated portion of the genome. The remaining SSR marker loci...

Using microsatellites to understand the physical distribution of recombination on soybean chromosomes.

PubMed

Ott, Alina; Trautschold, Brian; Sandhu, Devinder

2011-01-01

Soybean is a major crop that is an important source of oil and proteins. A number of genetic linkage maps have been developed in soybean. Specifically, hundreds of simple sequence repeat (SSR) markers have been developed and mapped. Recent sequencing of the soybean genome resulted in the generation of vast amounts of genetic information. The objectives of this investigation were to use SSR markers in developing a connection between genetic and physical maps and to determine the physical distribution of recombination on soybean chromosomes. A total of 2,188 SSRs were used for sequence-based physical localization on soybean chromosomes. Linkage information was used from different maps to create an integrated genetic map. Comparison of the integrated genetic linkage maps and sequence based physical maps revealed that the distal 25% of each chromosome was the most marker-dense, containing an average of 47.4% of the SSR markers and 50.2% of the genes. The proximal 25% of each chromosome contained only 7.4% of the markers and 6.7% of the genes. At the whole genome level, the marker density and gene density showed a high correlation (R(2)) of 0.64 and 0.83, respectively with the physical distance from the centromere. Recombination followed a similar pattern with comparisons indicating that recombination is high in telomeric regions, though the correlation between crossover frequency and distance from the centromeres is low (R(2) = 0.21). Most of the centromeric regions were low in recombination. The crossover frequency for the entire soybean genome was 7.2%, with extremes much higher and lower than average. The number of recombination hotspots varied from 1 to 12 per chromosome. A high correlation of 0.83 between the distribution of SSR markers and genes suggested close association of SSRs with genes. The knowledge of distribution of recombination on chromosomes may be applied in characterizing and targeting genes.

Overlay improvement by exposure map based mask registration optimization

NASA Astrophysics Data System (ADS)

Shi, Irene; Guo, Eric; Chen, Ming; Lu, Max; Li, Gordon; Li, Rivan; Tian, Eric

2015-03-01

Along with the increased miniaturization of semiconductor electronic devices, the design rules of advanced semiconductor devices shrink dramatically. [1] One of the main challenges of lithography step is the layer-to-layer overlay control. Furthermore, DPT (Double Patterning Technology) has been adapted for the advanced technology node like 28nm and 14nm, corresponding overlay budget becomes even tighter. [2][3] After the in-die mask registration (pattern placement) measurement is introduced, with the model analysis of a KLA SOV (sources of variation) tool, it's observed that registration difference between masks is a significant error source of wafer layer-to-layer overlay at 28nm process. [4][5] Mask registration optimization would highly improve wafer overlay performance accordingly. It was reported that a laser based registration control (RegC) process could be applied after the pattern generation or after pellicle mounting and allowed fine tuning of the mask registration. [6] In this paper we propose a novel method of mask registration correction, which can be applied before mask writing based on mask exposure map, considering the factors of mask chip layout, writing sequence, and pattern density distribution. Our experiment data show if pattern density on the mask keeps at a low level, in-die mask registration residue error in 3sigma could be always under 5nm whatever blank type and related writer POSCOR (position correction) file was applied; it proves random error induced by material or equipment would occupy relatively fixed error budget as an error source of mask registration. On the real production, comparing the mask registration difference through critical production layers, it could be revealed that registration residue error of line space layers with higher pattern density is always much larger than the one of contact hole layers with lower pattern density. Additionally, the mask registration difference between layers with similar pattern density could also achieve under 5nm performance. We assume mask registration excluding random error is mostly induced by charge accumulation during mask writing, which may be calculated from surrounding exposed pattern density. Multi-loading test mask registration result shows that with x direction writing sequence, mask registration behavior in x direction is mainly related to sequence direction, but mask registration in y direction would be highly impacted by pattern density distribution map. It proves part of mask registration error is due to charge issue from nearby environment. If exposure sequence is chip by chip for normal multi chip layout case, mask registration of both x and y direction would be impacted analogously, which has also been proved by real data. Therefore, we try to set up a simple model to predict the mask registration error based on mask exposure map, and correct it with the given POSCOR (position correction) file for advanced mask writing if needed.

High density FTA plates serve as efficient long-term sample storage for HLA genotyping.

PubMed

Lange, V; Arndt, K; Schwarzelt, C; Boehme, I; Giani, A S; Schmidt, A H; Ehninger, G; Wassmuth, R

2014-02-01

Storage of dried blood spots (DBS) on high-density FTA(®) plates could constitute an appealing alternative to frozen storage. However, it remains controversial whether DBS are suitable for high-resolution sequencing of human leukocyte antigen (HLA) alleles. Therefore, we extracted DNA from DBS that had been stored for up to 4 years, using six different methods. We identified those extraction methods that recovered sufficient high-quality DNA for reliable high-resolution HLA sequencing. Further, we confirmed that frozen whole blood samples that had been stored for several years can be transferred to filter paper without compromising HLA genotyping upon extraction. Concluding, DNA derived from high-density FTA(®) plates is suitable for high-resolution HLA sequencing, provided that appropriate extraction protocols are employed. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Assembly-history dynamics of a pitcher-plant protozoan community in experimental microcosms.

PubMed

Kadowaki, Kohmei; Inouye, Brian D; Miller, Thomas E

2012-01-01

History drives community assembly through differences both in density (density effects) and in the sequence in which species arrive (sequence effects). Density effects arise from predictable population dynamics, which are free of history, but sequence effects are due to a density-free mechanism, arising solely from the order and timing of immigration events. Few studies have determined how components of immigration history (timing, number of individuals, frequency) alter local dynamics to determine community assembly, beyond addressing when immigration history produces historically contingent assembly. We varied density and sequence effects independently in a two-way factorial design to follow community assembly in a three-species aquatic protozoan community. A superior competitor, Colpoda steinii, mediated alternative community states; early arrival or high introduction density allowed this species to outcompete or suppress the other competitors (Poterioochromonas malhamensis and Eimeriidae gen. sp.). Multivariate analysis showed that density effects caused greater variation in community states, whereas sequence effects altered the mean community composition. A significant interaction between density and sequence effects suggests that we should refine our understanding of priority effects. These results highlight a practical need to understand not only the "ingredients" (species) in ecological communities but their "recipes" as well.

An Exploration into Fern Genome Space.

PubMed

Wolf, Paul G; Sessa, Emily B; Marchant, Daniel Blaine; Li, Fay-Wei; Rothfels, Carl J; Sigel, Erin M; Gitzendanner, Matthew A; Visger, Clayton J; Banks, Jo Ann; Soltis, Douglas E; Soltis, Pamela S; Pryer, Kathleen M; Der, Joshua P

2015-08-26

Ferns are one of the few remaining major clades of land plants for which a complete genome sequence is lacking. Knowledge of genome space in ferns will enable broad-scale comparative analyses of land plant genes and genomes, provide insights into genome evolution across green plants, and shed light on genetic and genomic features that characterize ferns, such as their high chromosome numbers and large genome sizes. As part of an initial exploration into fern genome space, we used a whole genome shotgun sequencing approach to obtain low-density coverage (∼0.4X to 2X) for six fern species from the Polypodiales (Ceratopteris, Pteridium, Polypodium, Cystopteris), Cyatheales (Plagiogyria), and Gleicheniales (Dipteris). We explore these data to characterize the proportion of the nuclear genome represented by repetitive sequences (including DNA transposons, retrotransposons, ribosomal DNA, and simple repeats) and protein-coding genes, and to extract chloroplast and mitochondrial genome sequences. Such initial sweeps of fern genomes can provide information useful for selecting a promising candidate fern species for whole genome sequencing. We also describe variation of genomic traits across our sample and highlight some differences and similarities in repeat structure between ferns and seed plants. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Comparison of liquid-state anomalies in Stillinger-Weber models of water, silicon, and germanium

NASA Astrophysics Data System (ADS)

Dhabal, Debdas; Chakravarty, Charusita; Molinero, Valeria; Kashyap, Hemant K.

2016-12-01

We use molecular dynamics simulations to compare and contrast the liquid-state anomalies in the Stillinger-Weber models of monatomic water (mW), silicon (Si), and germanium (Ge) over a fairly wide range of temperatures and densities. The relationships between structure, entropy, and mobility, as well as the extent of the regions of anomalous behavior, are discussed as a function of the degree of tetrahedrality. We map out the cascade of density, structural, pair entropy, excess entropy, viscosity, and diffusivity anomalies for these three liquids. Among the three liquids studied here, only mW displays anomalies in the thermal conductivity, and this anomaly is evident only at very low temperatures. Diffusivity and viscosity, on the other hand, show pronounced anomalous regions for the three liquids. The temperature of maximum density of the three liquids shows re-entrant behavior consistent with either singularity-free or liquid-liquid critical point scenarios proposed to explain thermodynamic anomalies. The order-map, which shows the evolution of translational versus tetrahedral order in liquids, is different for Ge than for Si and mW. We find that although the monatomic water reproduces several thermodynamic and dynamic properties of rigid-body water models (e.g., SPC/E, TIP4P/2005), its sequence of anomalies follows, the same as Si and Ge, the silica-like hierarchy: the region of dynamic (diffusivity and viscosity) anomalies encloses the region of structural anomalies, which in turn encloses the region of density anomaly. The hierarchy of the anomalies based on excess entropy and Rosenfeld scaling, on the other hand, reverses the order of the structural and dynamic anomalies, i.e., predicts that the three Stillinger-Weber liquids follow a water-like hierarchy of anomalies. We investigate the scaling of diffusivity, viscosity, and thermal conductivity with the excess entropy of the liquid and find that for dynamical properties that present anomalies there is no universal scaling of the reduced property with excess entropy for the whole range of temperatures and densities. Instead, Rosenfeld's scaling holds for all the three liquids at high densities and high temperatures, although deviations from simple exponential dependence are observed for diffusivity and viscosity at lower temperatures and intermediate densities. The slope of the scaling of transport properties obtained for Ge is comparable to that obtained for simple liquids, suggesting that this low tetrahedrality liquid, although it stabilizes a diamond crystal, is already close to simple liquid behavior for certain properties.

Comparison of liquid-state anomalies in Stillinger-Weber models of water, silicon, and germanium.

PubMed

Dhabal, Debdas; Chakravarty, Charusita; Molinero, Valeria; Kashyap, Hemant K

2016-12-07

We use molecular dynamics simulations to compare and contrast the liquid-state anomalies in the Stillinger-Weber models of monatomic water (mW), silicon (Si), and germanium (Ge) over a fairly wide range of temperatures and densities. The relationships between structure, entropy, and mobility, as well as the extent of the regions of anomalous behavior, are discussed as a function of the degree of tetrahedrality. We map out the cascade of density, structural, pair entropy, excess entropy, viscosity, and diffusivity anomalies for these three liquids. Among the three liquids studied here, only mW displays anomalies in the thermal conductivity, and this anomaly is evident only at very low temperatures. Diffusivity and viscosity, on the other hand, show pronounced anomalous regions for the three liquids. The temperature of maximum density of the three liquids shows re-entrant behavior consistent with either singularity-free or liquid-liquid critical point scenarios proposed to explain thermodynamic anomalies. The order-map, which shows the evolution of translational versus tetrahedral order in liquids, is different for Ge than for Si and mW. We find that although the monatomic water reproduces several thermodynamic and dynamic properties of rigid-body water models (e.g., SPC/E, TIP4P/2005), its sequence of anomalies follows, the same as Si and Ge, the silica-like hierarchy: the region of dynamic (diffusivity and viscosity) anomalies encloses the region of structural anomalies, which in turn encloses the region of density anomaly. The hierarchy of the anomalies based on excess entropy and Rosenfeld scaling, on the other hand, reverses the order of the structural and dynamic anomalies, i.e., predicts that the three Stillinger-Weber liquids follow a water-like hierarchy of anomalies. We investigate the scaling of diffusivity, viscosity, and thermal conductivity with the excess entropy of the liquid and find that for dynamical properties that present anomalies there is no universal scaling of the reduced property with excess entropy for the whole range of temperatures and densities. Instead, Rosenfeld's scaling holds for all the three liquids at high densities and high temperatures, although deviations from simple exponential dependence are observed for diffusivity and viscosity at lower temperatures and intermediate densities. The slope of the scaling of transport properties obtained for Ge is comparable to that obtained for simple liquids, suggesting that this low tetrahedrality liquid, although it stabilizes a diamond crystal, is already close to simple liquid behavior for certain properties.

Metagenomic survey of bacterial diversity in the atmosphere of Mexico City using different sampling methods.

PubMed

Serrano-Silva, N; Calderón-Ezquerro, M C

2018-04-01

The identification of airborne bacteria has traditionally been performed by retrieval in culture media, but the bacterial diversity in the air is underestimated using this method because many bacteria are not readily cultured. Advances in DNA sequencing technology have produced a broad knowledge of genomics and metagenomics, which can greatly improve our ability to identify and study the diversity of airborne bacteria. However, researchers are facing several challenges, particularly the efficient retrieval of low-density microorganisms from the air and the lack of standardized protocols for sample collection and processing. In this study, we tested three methods for sampling bioaerosols - a Durham-type spore trap (Durham), a seven-day recording volumetric spore trap (HST), and a high-throughput 'Jet' spore and particle sampler (Jet) - and recovered metagenomic DNA for 16S rDNA sequencing. Samples were simultaneously collected with the three devices during one week, and the sequencing libraries were analyzed. A simple and efficient method for collecting bioaerosols and extracting good quality DNA for high-throughput sequencing was standardized. The Durham sampler collected preferentially Cyanobacteria, the HST Actinobacteria, Proteobacteria and Firmicutes, and the Jet mainly Proteobacteria and Firmicutes. The HST sampler collected the largest amount of airborne bacterial diversity. More experiments are necessary to select the right sampler, depending on study objectives, which may require monitoring and collecting specific airborne bacteria. Copyright © 2017 Elsevier Ltd. All rights reserved.

Comparison of 74-MHz interplanetary scintillation and IMP 7 observations of the solar wind during 1973

NASA Technical Reports Server (NTRS)

Coles, W. A.; Harmon, J. K.; Lazarus, A. J.; Sullivan, J. D.

1978-01-01

Solar wind velocities measured by earth-orbiting spacecraft are compared with velocities determined from interplanetary scintillation (IPS) observations for 1973, a period when high-velocity streams were prevalent. The spacecraft and IPS velocities agree well in the mean and are highly correlated. No simple model for the distribution of enhanced turbulence within streams is sufficient to explain the velocity comparison results for the entire year. Although a simple proportionality between density fluctuation level and bulk density is consistent with IPS velocities for some periods, some streams appear to have enhanced turbulence in the high-velocity region, where the density is low.

Role of moisture and density of sand for microwave enhancement of thermal detection of buried mines

NASA Astrophysics Data System (ADS)

Swiderski, Waldemar; Hlosta, Pawel; Jarzemski, Jozef; Szugajew, Leszek; Usowicz, Jerzy

2012-06-01

The main disadvantage of applying the IRT method is presence of plenty false indications in thermograms. A simple use of IRT equipment with better temperature resolution would not help in distinguishing the mines, since noise comes not from a camera, but from soil surface. Recognizing the role of moisture and density of sand and possibilities to express it quantitatively plays an important role. In our model of thermal properties of the soil the volumetric unit of the soil consists of mineral and organic particles, as well as water and air. All needed parameters can be calculated. Calculations of thermal signatures of the underground objects were made basing on 3D-heat equation for the sinus type heating of 3D model and cooling by convection. Measurements were made for field and laboratory stand-ups, using methodologies typical for "single-shot" measurements as well as analyses of transient processes based on sequence of thermograms. Results of simulations and measurements confirm expectation tha that high level of "radiant noises" is caused mainly by differences in the moisture and sand density levels.

Development of chromosome-specific markers with high polymorphism for allotetraploid cotton based on genome-wide characterization of simple sequence repeats in diploid cottons (Gossypium arboreum L. and Gossypium raimondii Ulbrich).

PubMed

Lu, Cairui; Zou, Changsong; Zhang, Youping; Yu, Daoqian; Cheng, Hailiang; Jiang, Pengfei; Yang, Wencui; Wang, Qiaolian; Feng, Xiaoxu; Prosper, Mtawa Andrew; Guo, Xiaoping; Song, Guoli

2015-02-06

Tetraploid cotton contains two sets of homologous chromosomes, the At- and Dt-subgenomes. Consequently, many markers in cotton were mapped to multiple positions during linkage genetic map construction, posing a challenge to anchoring linkage groups and mapping economically-important genes to particular chromosomes. Chromosome-specific markers could solve this problem. Recently, the genomes of two diploid species were sequenced whose progenitors were putative contributors of the At- and Dt-subgenomes to tetraploid cotton. These sequences provide a powerful tool for developing chromosome-specific markers given the high level of synteny among tetraploid and diploid cotton genomes. In this study, simple sequence repeats (SSRs) on each chromosome in the two diploid genomes were characterized. Chromosome-specific SSRs were developed by comparative analysis and proved to distinguish chromosomes. A total of 200,744 and 142,409 SSRs were detected on the 13 chromosomes of Gossypium arboreum L. and Gossypium raimondii Ulbrich, respectively. Chromosome-specific SSRs were obtained by comparing SSR flanking sequences from each chromosome with those from the other 25 chromosomes. The average was 7,996 per chromosome. To confirm their chromosome specificity, these SSRs were used to distinguish two homologous chromosomes in tetraploid cotton through linkage group construction. The chromosome-specific SSRs and previously-reported chromosome markers were grouped together, and no marker mapped to another homologous chromosome, proving that the chromosome-specific SSRs were unique and could distinguish homologous chromosomes in tetraploid cotton. Because longer dinucleotide AT-rich repeats were the most polymorphic in previous reports, the SSRs on each chromosome were sorted by motif type and repeat length for convenient selection. The primer sequences of all chromosome-specific SSRs were also made publicly available. Chromosome-specific SSRs are efficient tools for chromosome identification by anchoring linkage groups to particular chromosomes during genetic mapping and are especially useful in mapping of qualitative-trait genes or quantitative trait loci with just a few markers. The SSRs reported here will facilitate a number of genetic and genomic studies in cotton, including construction of high-density genetic maps, positional gene cloning, fingerprinting, and genetic diversity and comparative evolutionary analyses among Gossypium species.

High-density genetic map using whole-genome re-sequencing for fine mapping and candidate gene discovery for disease resistance in peanut

USDA-ARS?s Scientific Manuscript database

High-density genetic linkage maps are essential for fine mapping QTLs controlling disease resistance traits, such as early leaf spot (ELS), late leaf spot (LLS), and Tomato spotted wilt virus (TSWV). With completion of the genome sequences of two diploid ancestors of cultivated peanut, we could use ...

Use of a Tea Infuser to Submerge Low-Density Dry Ice

ERIC Educational Resources Information Center

Fictorie, Carl P.; Vitz, Ed

2004-01-01

A simple tea infuser is obtained and been used as a container for the dry ice to simulate the effect from high-density dry ice. The tea infuser is a simple, low cost device to allow instructors with access to dry ice makers to effectively use the interesting demonstration.

Abundance and Characterization of Perfect Microsatellites on the Cattle Y Chromosome.

PubMed

Ma, Zhi-Jie

2017-07-03

Microsatellites or simple sequence repeats (SSRs) are found in most organisms and play an important role in genomic organization and function. To characterize the abundance of SSRs (1-6 base-pairs [bp]) on the cattle Y chromsome, the relative frequency and density of perfect or uninterrupted SSRs based on the published Y chromosome sequence were examined. A total of 17,273 perfect SSRs were found, with total length of 324.78 kb, indicating that approximately 0.75% of the cattle Y chromosome sequence (43.30 Mb) comprises perfect SSRs, with an average length of 18.80 bp. The relative frequency and density were 398.92 loci/Mb and 7500.62 bp/Mb, respectively. The proportions of the six classes of perfect SSRs were highly variable on the cattle Y chromosome. Mononucleotide repeats had a total number of 8073 (46.74%) and an average length of 15.45 bp, and were the most abundant SSRs class, while the percentages of di-, tetra-, tri-, penta-, and hexa-nucleotide repeats were 22.86%, 11.98%, 11.58%, 6.65%, and 0.19%, respectively. Different classes of SSRs varied in their repeat number, with the highest being 42 for dinucleotides. Results reveal that repeat categories A, AC, AT, AAC, AGC, GTTT, CTTT, ATTT, and AACTG predominate on the Y chromosome. This study provides insight into the organization of cattle Y chromosome repetitive DNA, as well as information useful for developing more polymorphic cattle Y-chromosome-specific SSRs.

Construction and analysis of a high-density genetic linkage map in cabbage (Brassica oleracea L. var. capitata)

PubMed Central

2012-01-01

Background Brassica oleracea encompass a family of vegetables and cabbage that are among the most widely cultivated crops. In 2009, the B. oleracea Genome Sequencing Project was launched using next generation sequencing technology. None of the available maps were detailed enough to anchor the sequence scaffolds for the Genome Sequencing Project. This report describes the development of a large number of SSR and SNP markers from the whole genome shotgun sequence data of B. oleracea, and the construction of a high-density genetic linkage map using a double haploid mapping population. Results The B. oleracea high-density genetic linkage map that was constructed includes 1,227 markers in nine linkage groups spanning a total of 1197.9 cM with an average of 0.98 cM between adjacent loci. There were 602 SSR markers and 625 SNP markers on the map. The chromosome with the highest number of markers (186) was C03, and the chromosome with smallest number of markers (99) was C09. Conclusions This first high-density map allowed the assembled scaffolds to be anchored to pseudochromosomes. The map also provides useful information for positional cloning, molecular breeding, and integration of information of genes and traits in B. oleracea. All the markers on the map will be transferable and could be used for the construction of other genetic maps. PMID:23033896

Strategies for Achieving High Sequencing Accuracy for Low Diversity Samples and Avoiding Sample Bleeding Using Illumina Platform

PubMed Central

Mitra, Abhishek; Skrzypczak, Magdalena; Ginalski, Krzysztof; Rowicka, Maga

2015-01-01

Sequencing microRNA, reduced representation sequencing, Hi-C technology and any method requiring the use of in-house barcodes result in sequencing libraries with low initial sequence diversity. Sequencing such data on the Illumina platform typically produces low quality data due to the limitations of the Illumina cluster calling algorithm. Moreover, even in the case of diverse samples, these limitations are causing substantial inaccuracies in multiplexed sample assignment (sample bleeding). Such inaccuracies are unacceptable in clinical applications, and in some other fields (e.g. detection of rare variants). Here, we discuss how both problems with quality of low-diversity samples and sample bleeding are caused by incorrect detection of clusters on the flowcell during initial sequencing cycles. We propose simple software modifications (Long Template Protocol) that overcome this problem. We present experimental results showing that our Long Template Protocol remarkably increases data quality for low diversity samples, as compared with the standard analysis protocol; it also substantially reduces sample bleeding for all samples. For comprehensiveness, we also discuss and compare experimental results from alternative approaches to sequencing low diversity samples. First, we discuss how the low diversity problem, if caused by barcodes, can be avoided altogether at the barcode design stage. Second and third, we present modified guidelines, which are more stringent than the manufacturer’s, for mixing low diversity samples with diverse samples and lowering cluster density, which in our experience consistently produces high quality data from low diversity samples. Fourth and fifth, we present rescue strategies that can be applied when sequencing results in low quality data and when there is no more biological material available. In such cases, we propose that the flowcell be re-hybridized and sequenced again using our Long Template Protocol. Alternatively, we discuss how analysis can be repeated from saved sequencing images using the Long Template Protocol to increase accuracy. PMID:25860802

M13-Tailed Simple Sequence Repeat (SSR) Markers in Studies of Genetic Diversity and Population Structure of Common Oat Germplasm.

PubMed

Onyśk, Agnieszka; Boczkowska, Maja

2017-01-01

Simple Sequence Repeat (SSR) markers are one of the most frequently used molecular markers in studies of crop diversity and population structure. This is due to their uniform distribution in the genome, the high polymorphism, reproducibility, and codominant character. Additional advantages are the possibility of automatic analysis and simple interpretation of the results. The M13 tagged PCR reaction significantly reduces the costs of analysis by the automatic genetic analyzers. Here, we also disclose a short protocol of SSR data analysis.

VAR2CSA signatures of high Plasmodium falciparum parasitemia in the placenta.

PubMed

Rovira-Vallbona, Eduard; Monteiro, Isadora; Bardají, Azucena; Serra-Casas, Elisa; Neafsey, Daniel E; Quelhas, Diana; Valim, Clarissa; Alonso, Pedro; Dobaño, Carlota; Ordi, Jaume; Menéndez, Clara; Mayor, Alfredo

2013-01-01

Plasmodium falciparum infected erythrocytes (IE) accumulate in the placenta through the interaction between Duffy-binding like (DBL) domains of parasite-encoded ligand VAR2CSA and chondroitin sulphate-A (CSA) receptor. Polymorphisms in these domains, including DBL2X and DBL3X, may affect their antigenicity or CSA-binding affinity, eventually increasing parasitemia and its adverse effects on pregnancy outcomes. A total of 373 DBL2X and 328 DBL3X sequences were obtained from transcripts of 20 placental isolates infecting Mozambican women, resulting in 176 DBL2X and 191 DBL3X unique sequences at the protein level. Sequence alignments were divided in segments containing combinations of correlated polymorphisms and the association of segment sequences with placental parasite density was tested using Bonferroni corrected regression models, taking into consideration the weight of each sequence in the infection. Three DBL2X and three DBL3X segments contained signatures of high parasite density (P<0.003) that were highly prevalent in the parasite population (49-91%). Identified regions included a flexible loop that contributes to DBL3X-CSA interaction and two DBL3X motifs with evidence of positive natural selection. Limited antibody responses against signatures of high parasite density among malaria-exposed pregnant women could not explain the increased placental parasitemia. These results suggest that a higher binding efficiency to CSA rather than reduced antigenicity might provide a biological advantage to parasites with high parasite density signatures in VAR2CSA. Sequences contributing to high parasitemia may be critical for the functional characterization of VAR2CSA and the development of tools against placental malaria.

A Simple Method for Determination of the Density of Granular Materials

ERIC Educational Resources Information Center

Tsutsumanova, G. G.; Kirilov, K. M.; Russev, S. C.

2012-01-01

A simple experiment using low cost equipment for the determination of the density of granular materials, without immersing them in a liquid, is presented. It is based only on the ideal gas state equation, so it is a good experimental task for undergraduate and high school students. (Contains 2 tables and 5 figures.)

The puzzling spectrum of HD 94509. Sounding out the extremes of Be shell star spectral morphology

NASA Astrophysics Data System (ADS)

Cowley, C. R.; Przybilla, N.; Hubrig, S.

2015-06-01

Context. The spectral features of HD 94509 are highly unusual, adding an extreme to the zoo of Be and shell stars. The shell dominates the spectrum, showing lines typical for spectral types mid-A to early-F, while the presence of a late/mid B-type central star is indicated by photospheric hydrogen line wings and helium lines. Numerous metallic absorption lines have broad wings but taper to narrow cores. They cannot be fit by Voigt profiles. Aims: We describe and illustrate unusual spectral features of this star, and make rough calculations to estimate physical conditions and abundances in the shell. Furthermore, the central star is characterized. Methods: We assume mean conditions for the shell. An electron density estimate is made from the Inglis-Teller formula. Excitation temperatures and column densities for Fe i and Fe ii are derived from curves of growth. The neutral H column density is estimated from high Paschen members. The column densities are compared with calculations made with the photoionization code Cloudy. Atmospheric parameters of the central star are constrained employing non-LTE spectrum synthesis. Results: Overall chemical abundances are close to solar. Column densities of the dominant ions of several elements, as well as excitation temperatures and the mean electron density are well accounted for by a simple model. Several features, including the degree of ionization, are less well described. Conclusions: HD 94509 is a Be star with a stable shell, close to the terminal-age main sequence. The dynamical state of the shell and the unusually shaped, but symmetric line profiles, require a separate study.

Sunflower Hybrid Breeding: From Markers to Genomic Selection

PubMed Central

Dimitrijevic, Aleksandra; Horn, Renate

2018-01-01

In sunflower, molecular markers for simple traits as, e.g., fertility restoration, high oleic acid content, herbicide tolerance or resistances to Plasmopara halstedii, Puccinia helianthi, or Orobanche cumana have been successfully used in marker-assisted breeding programs for years. However, agronomically important complex quantitative traits like yield, heterosis, drought tolerance, oil content or selection for disease resistance, e.g., against Sclerotinia sclerotiorum have been challenging and will require genome-wide approaches. Plant genetic resources for sunflower are being collected and conserved worldwide that represent valuable resources to study complex traits. Sunflower association panels provide the basis for genome-wide association studies, overcoming disadvantages of biparental populations. Advances in technologies and the availability of the sunflower genome sequence made novel approaches on the whole genome level possible. Genotype-by-sequencing, and whole genome sequencing based on next generation sequencing technologies facilitated the production of large amounts of SNP markers for high density maps as well as SNP arrays and allowed genome-wide association studies and genomic selection in sunflower. Genome wide or candidate gene based association studies have been performed for traits like branching, flowering time, resistance to Sclerotinia head and stalk rot. First steps in genomic selection with regard to hybrid performance and hybrid oil content have shown that genomic selection can successfully address complex quantitative traits in sunflower and will help to speed up sunflower breeding programs in the future. To make sunflower more competitive toward other oil crops higher levels of resistance against pathogens and better yield performance are required. In addition, optimizing plant architecture toward a more complex growth type for higher plant densities has the potential to considerably increase yields per hectare. Integrative approaches combining omic technologies (genomics, transcriptomics, proteomics, metabolomics and phenomics) using bioinformatic tools will facilitate the identification of target genes and markers for complex traits and will give a better insight into the mechanisms behind the traits. PMID:29387071

Liquid-liquid critical point in a simple analytical model of water.

PubMed

Urbic, Tomaz

2016-10-01

A statistical model for a simple three-dimensional Mercedes-Benz model of water was used to study phase diagrams. This model on a simple level describes the thermal and volumetric properties of waterlike molecules. A molecule is presented as a soft sphere with four directions in which hydrogen bonds can be formed. Two neighboring waters can interact through a van der Waals interaction or an orientation-dependent hydrogen-bonding interaction. For pure water, we explored properties such as molar volume, density, heat capacity, thermal expansion coefficient, and isothermal compressibility and found that the volumetric and thermal properties follow the same trends with temperature as in real water and are in good general agreement with Monte Carlo simulations. The model exhibits also two critical points for liquid-gas transition and transition between low-density and high-density fluid. Coexistence curves and a Widom line for the maximum and minimum in thermal expansion coefficient divides the phase space of the model into three parts: in one part we have gas region, in the second a high-density liquid, and the third region contains low-density liquid.

Liquid-liquid critical point in a simple analytical model of water

NASA Astrophysics Data System (ADS)

Urbic, Tomaz

2016-10-01

A statistical model for a simple three-dimensional Mercedes-Benz model of water was used to study phase diagrams. This model on a simple level describes the thermal and volumetric properties of waterlike molecules. A molecule is presented as a soft sphere with four directions in which hydrogen bonds can be formed. Two neighboring waters can interact through a van der Waals interaction or an orientation-dependent hydrogen-bonding interaction. For pure water, we explored properties such as molar volume, density, heat capacity, thermal expansion coefficient, and isothermal compressibility and found that the volumetric and thermal properties follow the same trends with temperature as in real water and are in good general agreement with Monte Carlo simulations. The model exhibits also two critical points for liquid-gas transition and transition between low-density and high-density fluid. Coexistence curves and a Widom line for the maximum and minimum in thermal expansion coefficient divides the phase space of the model into three parts: in one part we have gas region, in the second a high-density liquid, and the third region contains low-density liquid.

Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing

PubMed Central

2012-01-01

Background Genetic mapping and QTL detection are powerful methodologies in plant improvement and breeding. Construction of a high-density and high-quality genetic map would be of great benefit in the production of superior grapes to meet human demand. High throughput and low cost of the recently developed next generation sequencing (NGS) technology have resulted in its wide application in genome research. Sequencing restriction-site associated DNA (RAD) might be an efficient strategy to simplify genotyping. Combining NGS with RAD has proven to be powerful for single nucleotide polymorphism (SNP) marker development. Results An F1 population of 100 individual plants was developed. In-silico digestion-site prediction was used to select an appropriate restriction enzyme for construction of a RAD sequencing library. Next generation RAD sequencing was applied to genotype the F1 population and its parents. Applying a cluster strategy for SNP modulation, a total of 1,814 high-quality SNP markers were developed: 1,121 of these were mapped to the female genetic map, 759 to the male map, and 1,646 to the integrated map. A comparison of the genetic maps to the published Vitis vinifera genome revealed both conservation and variations. Conclusions The applicability of next generation RAD sequencing for genotyping a grape F1 population was demonstrated, leading to the successful development of a genetic map with high density and quality using our designed SNP markers. Detailed analysis revealed that this newly developed genetic map can be used for a variety of genome investigations, such as QTL detection, sequence assembly and genome comparison. PMID:22908993

Communication: Simple liquids' high-density viscosity

NASA Astrophysics Data System (ADS)

Costigliola, Lorenzo; Pedersen, Ulf R.; Heyes, David M.; Schrøder, Thomas B.; Dyre, Jeppe C.

2018-02-01

This paper argues that the viscosity of simple fluids at densities above that of the triple point is a specific function of temperature relative to the freezing temperature at the density in question. The proposed viscosity expression, which is arrived at in part by reference to the isomorph theory of systems with hidden scale invariance, describes computer simulations of the Lennard-Jones system as well as argon and methane experimental data and simulation results for an effective-pair-potential model of liquid sodium.

The Star Formation Histories of Disk Galaxies: The Live, the Dead, and the Undead

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

Oemler, Augustus Jr; Dressler, Alan; Abramson, Louis E.

We reexamine the properties of local galaxy populations using published surveys of star formation, structure, and gas content. After recalibrating star formation measures, we are able to reliably measure specific star formation rates well below that of the so-called “main sequence” of star formation versus mass. We find an unexpectedly large population of quiescent galaxies with star formation rates intermediate between the main sequence and passive populations and with disproportionately high star formation rates. We demonstrate that a tight main sequence is a natural outcome of most histories of star formation and has little astrophysical significance but that the quiescentmore » population requires additional astrophysics to explain its properties. Using a simple model for disk evolution based on the observed dependence of star formation on gas content in local galaxies, and assuming simple histories of cold gas inflow, we show that the evolution of galaxies away from the main sequence can be attributed to the depletion of gas due to star formation after a cutoff of gas inflow. The quiescent population is composed of galaxies in which the density of disk gas has fallen below a threshold for star formation probably set by disk stability. The evolution of galaxies beyond the quiescent state to gas exhaustion and the end of star formation requires another process, probably wind-driven mass loss. The environmental dependence of the three galaxy populations is consistent with recent numerical modeling, which indicates that cold gas inflows into galaxies are truncated at earlier epochs in denser environments.« less

PSSRdb: a relational database of polymorphic simple sequence repeats extracted from prokaryotic genomes.

PubMed

Kumar, Pankaj; Chaitanya, Pasumarthy S; Nagarajaram, Hampapathalu A

2011-01-01

PSSRdb (Polymorphic Simple Sequence Repeats database) (http://www.cdfd.org.in/PSSRdb/) is a relational database of polymorphic simple sequence repeats (PSSRs) extracted from 85 different species of prokaryotes. Simple sequence repeats (SSRs) are the tandem repeats of nucleotide motifs of the sizes 1-6 bp and are highly polymorphic. SSR mutations in and around coding regions affect transcription and translation of genes. Such changes underpin phase variations and antigenic variations seen in some bacteria. Although SSR-mediated phase variation and antigenic variations have been well-studied in some bacteria there seems a lot of other species of prokaryotes yet to be investigated for SSR mediated adaptive and other evolutionary advantages. As a part of our on-going studies on SSR polymorphism in prokaryotes we compared the genome sequences of various strains and isolates available for 85 different species of prokaryotes and extracted a number of SSRs showing length variations and created a relational database called PSSRdb. This database gives useful information such as location of PSSRs in genomes, length variation across genomes, the regions harboring PSSRs, etc. The information provided in this database is very useful for further research and analysis of SSRs in prokaryotes.

The dark nemesis of galaxy formation: why hot haloes trigger black hole growth and bring star formation to an end

NASA Astrophysics Data System (ADS)

Bower, Richard G.; Schaye, Joop; Frenk, Carlos S.; Theuns, Tom; Schaller, Matthieu; Crain, Robert A.; McAlpine, Stuart

2017-02-01

Galaxies fall into two clearly distinct types: `blue-sequence' galaxies which are rapidly forming young stars, and `red-sequence' galaxies in which star formation has almost completely ceased. Most galaxies more massive than 3 × 1010 M⊙ follow the red sequence, while less massive central galaxies lie on the blue sequence. We show that these sequences are created by a competition between star formation-driven outflows and gas accretion on to the supermassive black hole at the galaxy's centre. We develop a simple analytic model for this interaction. In galaxies less massive than 3 × 1010 M⊙, young stars and supernovae drive a high-entropy outflow which is more buoyant than any tenuous corona. The outflow balances the rate of gas inflow, preventing high gas densities building up in the central regions. More massive galaxies, however, are surrounded by an increasingly hot corona. Above a halo mass of ˜1012 M⊙, the outflow ceases to be buoyant and star formation is unable to prevent the build-up of gas in the central regions. This triggers a strongly non-linear response from the black hole. Its accretion rate rises rapidly, heating the galaxy's corona, disrupting the incoming supply of cool gas and starving the galaxy of the fuel for star formation. The host galaxy makes a transition to the red sequence, and further growth predominantly occurs through galaxy mergers. We show that the analytic model provides a good description of galaxy evolution in the EAGLE hydrodynamic simulations. So long as star formation-driven outflows are present, the transition mass scale is almost independent of subgrid parameter choice.

Fueling Future with Algal Genomics

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

Grigoriev, Igor

Algae constitute a major component of fundamental eukaryotic diversity, play profound roles in the carbon cycle, and are prominent candidates for biofuel production. The US Department of Energy Joint Genome Institute (JGI) is leading the world in algal genome sequencing (http://jgi.doe.gov/Algae) and contributes of the algal genome projects worldwide (GOLD database, 2012). The sequenced algal genomes offer catalogs of genes, networks, and pathways. The sequenced first of its kind genomes of a haptophyte E.huxleyii, chlorarachniophyte B.natans, and cryptophyte G.theta fill the gaps in the eukaryotic tree of life and carry unique genes and pathways as well as molecular fossils ofmore » secondary endosymbiosis. Natural adaptation to conditions critical for industrial production is encoded in algal genomes, for example, growth of A.anophagefferens at very high cell densities during the harmful algae blooms or a global distribution across diverse environments of E.huxleyii, able to live on sparse nutrients due to its expanded pan-genome. Communications and signaling pathways can be derived from simple symbiotic systems like lichens or complex marine algae metagenomes. Collectively these datasets derived from algal genomics contribute to building a comprehensive parts list essential for algal biofuel development.« less

Genotyping by Sequencing Using Specific Allelic Capture to Build a High-Density Genetic Map of Durum Wheat

PubMed Central

Holtz, Yan; Ardisson, Morgane; Ranwez, Vincent; Besnard, Alban; Leroy, Philippe; Poux, Gérard; Roumet, Pierre; Viader, Véronique; Santoni, Sylvain; David, Jacques

2016-01-01

Targeted sequence capture is a promising technology which helps reduce costs for sequencing and genotyping numerous genomic regions in large sets of individuals. Bait sequences are designed to capture specific alleles previously discovered in parents or reference populations. We studied a set of 135 RILs originating from a cross between an emmer cultivar (Dic2) and a recent durum elite cultivar (Silur). Six thousand sequence baits were designed to target Dic2 vs. Silur polymorphisms discovered in a previous RNAseq study. These baits were exposed to genomic DNA of the RIL population. Eighty percent of the targeted SNPs were recovered, 65% of which were of high quality and coverage. The final high density genetic map consisted of more than 3,000 markers, whose genetic and physical mapping were consistent with those obtained with large arrays. PMID:27171472

Toward allotetraploid cotton genome assembly: integration of a high-density molecular genetic linkage map with DNA sequence information

PubMed Central

2012-01-01

Background Cotton is the world’s most important natural textile fiber and a significant oilseed crop. Decoding cotton genomes will provide the ultimate reference and resource for research and utilization of the species. Integration of high-density genetic maps with genomic sequence information will largely accelerate the process of whole-genome assembly in cotton. Results In this paper, we update a high-density interspecific genetic linkage map of allotetraploid cultivated cotton. An additional 1,167 marker loci have been added to our previously published map of 2,247 loci. Three new marker types, InDel (insertion-deletion) and SNP (single nucleotide polymorphism) developed from gene information, and REMAP (retrotransposon-microsatellite amplified polymorphism), were used to increase map density. The updated map consists of 3,414 loci in 26 linkage groups covering 3,667.62 cM with an average inter-locus distance of 1.08 cM. Furthermore, genome-wide sequence analysis was finished using 3,324 informative sequence-based markers and publicly-available Gossypium DNA sequence information. A total of 413,113 EST and 195 BAC sequences were physically anchored and clustered by 3,324 sequence-based markers. Of these, 14,243 ESTs and 188 BACs from different species of Gossypium were clustered and specifically anchored to the high-density genetic map. A total of 2,748 candidate unigenes from 2,111 ESTs clusters and 63 BACs were mined for functional annotation and classification. The 337 ESTs/genes related to fiber quality traits were integrated with 132 previously reported cotton fiber quality quantitative trait loci, which demonstrated the important roles in fiber quality of these genes. Higher-level sequence conservation between different cotton species and between the A- and D-subgenomes in tetraploid cotton was found, indicating a common evolutionary origin for orthologous and paralogous loci in Gossypium. Conclusion This study will serve as a valuable genomic resource for tetraploid cotton genome assembly, for cloning genes related to superior agronomic traits, and for further comparative genomic analyses in Gossypium. PMID:23046547

Capturing chloroplast variation for molecular ecology studies: a simple next generation sequencing approach applied to a rainforest tree

PubMed Central

2013-01-01

Background With high quantity and quality data production and low cost, next generation sequencing has the potential to provide new opportunities for plant phylogeographic studies on single and multiple species. Here we present an approach for in silicio chloroplast DNA assembly and single nucleotide polymorphism detection from short-read shotgun sequencing. The approach is simple and effective and can be implemented using standard bioinformatic tools. Results The chloroplast genome of Toona ciliata (Meliaceae), 159,514 base pairs long, was assembled from shotgun sequencing on the Illumina platform using de novo assembly of contigs. To evaluate its practicality, value and quality, we compared the short read assembly with an assembly completed using 454 data obtained after chloroplast DNA isolation. Sanger sequence verifications indicated that the Illumina dataset outperformed the longer read 454 data. Pooling of several individuals during preparation of the shotgun library enabled detection of informative chloroplast SNP markers. Following validation, we used the identified SNPs for a preliminary phylogeographic study of T. ciliata in Australia and to confirm low diversity across the distribution. Conclusions Our approach provides a simple method for construction of whole chloroplast genomes from shotgun sequencing of whole genomic DNA using short-read data and no available closely related reference genome (e.g. from the same species or genus). The high coverage of Illumina sequence data also renders this method appropriate for multiplexing and SNP discovery and therefore a useful approach for landscape level studies of evolutionary ecology. PMID:23497206

A genome-wide BAC-end sequence survey provides first insights into sweetpotato (Ipomoea batatas (L.) Lam.) genome composition.

PubMed

Si, Zengzhi; Du, Bing; Huo, Jinxi; He, Shaozhen; Liu, Qingchang; Zhai, Hong

2016-11-21

Sweetpotato, Ipomoea batatas (L.) Lam., is an important food crop widely grown in the world. However, little is known about the genome of this species because it is a highly heterozygous hexaploid. Gaining a more in-depth knowledge of sweetpotato genome is therefore necessary and imperative. In this study, the first bacterial artificial chromosome (BAC) library of sweetpotato was constructed. Clones from the BAC library were end-sequenced and analyzed to provide genome-wide information about this species. The BAC library contained 240,384 clones with an average insert size of 101 kb and had a 7.93-10.82 × coverage of the genome, and the probability of isolating any single-copy DNA sequence from the library was more than 99%. Both ends of 8310 BAC clones randomly selected from the library were sequenced to generate 11,542 high-quality BAC-end sequences (BESs), with an accumulative length of 7,595,261 bp and an average length of 658 bp. Analysis of the BESs revealed that 12.17% of the sweetpotato genome were known repetitive DNA, including 7.37% long terminal repeat (LTR) retrotransposons, 1.15% Non-LTR retrotransposons and 1.42% Class II DNA transposons etc., 18.31% of the genome were identified as sweetpotato-unique repetitive DNA and 10.00% of the genome were predicted to be coding regions. In total, 3,846 simple sequences repeats (SSRs) were identified, with a density of one SSR per 1.93 kb, from which 288 SSRs primers were designed and tested for length polymorphism using 20 sweetpotato accessions, 173 (60.07%) of them produced polymorphic bands. Sweetpotato BESs had significant hits to the genome sequences of I. trifida and more matches to the whole-genome sequences of Solanum lycopersicum than those of Vitis vinifera, Theobroma cacao and Arabidopsis thaliana. The first BAC library for sweetpotato has been successfully constructed. The high quality BESs provide first insights into sweetpotato genome composition, and have significant hits to the genome sequences of I. trifida and more matches to the whole-genome sequences of Solanum lycopersicum. These resources as a robust platform will be used in high-resolution mapping, gene cloning, assembly of genome sequences, comparative genomics and evolution for sweetpotato.

Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.).

PubMed

Zhang, Zhen; Shang, Haihong; Shi, Yuzhen; Huang, Long; Li, Junwen; Ge, Qun; Gong, Juwu; Liu, Aiying; Chen, Tingting; Wang, Dan; Wang, Yanling; Palanga, Koffi Kibalou; Muhammad, Jamshed; Li, Weijie; Lu, Quanwei; Deng, Xiaoying; Tan, Yunna; Song, Weiwu; Cai, Juan; Li, Pengtao; Rashid, Harun or; Gong, Wankui; Yuan, Youlu

2016-04-11

Upland Cotton (Gossypium hirsutum) is one of the most important worldwide crops it provides natural high-quality fiber for the industrial production and everyday use. Next-generation sequencing is a powerful method to identify single nucleotide polymorphism markers on a large scale for the construction of a high-density genetic map for quantitative trait loci mapping. In this research, a recombinant inbred lines population developed from two upland cotton cultivars 0-153 and sGK9708 was used to construct a high-density genetic map through the specific locus amplified fragment sequencing method. The high-density genetic map harbored 5521 single nucleotide polymorphism markers which covered a total distance of 3259.37 cM with an average marker interval of 0.78 cM without gaps larger than 10 cM. In total 18 quantitative trait loci of boll weight were identified as stable quantitative trait loci and were detected in at least three out of 11 environments and explained 4.15-16.70 % of the observed phenotypic variation. In total, 344 candidate genes were identified within the confidence intervals of these stable quantitative trait loci based on the cotton genome sequence. These genes were categorized based on their function through gene ontology analysis, Kyoto Encyclopedia of Genes and Genomes analysis and eukaryotic orthologous groups analysis. This research reported the first high-density genetic map for Upland Cotton (Gossypium hirsutum) with a recombinant inbred line population using single nucleotide polymorphism markers developed by specific locus amplified fragment sequencing. We also identified quantitative trait loci of boll weight across 11 environments and identified candidate genes within the quantitative trait loci confidence intervals. The results of this research would provide useful information for the next-step work including fine mapping, gene functional analysis, pyramiding breeding of functional genes as well as marker-assisted selection.

Simple gain probability functions for large reflector antennas of JPL/NASA

NASA Technical Reports Server (NTRS)

Jamnejad, V.

2003-01-01

Simple models for the patterns as well as their cumulative gain probability and probability density functions of the Deep Space Network antennas are developed. These are needed for the study and evaluation of interference from unwanted sources such as the emerging terrestrial system, High Density Fixed Service, with the Ka-band receiving antenna systems in Goldstone Station of the Deep Space Network.

Construction and development of an auto-regulatory gene expression system in Bacillus subtilis.

PubMed

Guan, Chengran; Cui, Wenjing; Cheng, Jintao; Zhou, Li; Guo, Junling; Hu, Xu; Xiao, Guoping; Zhou, Zhemin

2015-09-21

Bacillus subtilis is an all-important Gram-positive bacterium of valuable biotechnological utility that has been widely used to over-produce industrially and pharmaceutically relevant proteins. There are a variety of expression systems in terms of types of transcriptional patterns, among which the auto-inducible and growth-phase-dependent promoters are gaining increasing favor due to their inducer-independent feature, allowing for the potential to industrially scale-up. To expand the applicability of the auto-inducible expression system, a novel auto-regulatory expression system coupled with cell density was constructed and developed in B. subtilis using the quorum-sensing related promoter srfA (PsrfA). The promoter of the srf operon was used to construct an expression plasmid with the green fluorescent protein (GFP) downstream of PsrfA. The expression displayed a cell-density-dependent pattern in that GFP had a fairly low expression level at the early exponential stage and was highly expressed at the late exponential as well as the stationary stages. Moreover, the recombinant system had a similar expression pattern in wild-type B. subtilis 168, WB600, and WB800, as well as in B. subtilis 168 derivative strain 1681, with the complete deletion of PsrfA, indicating the excellent compatibility of this system. Noticeably, the expression strength of PsrfA was enhanced by optimizing the -10 and -35 core sequence by substituting both sequences with consensus sequences. Importantly, the expression pattern was successfully developed in an auto-regulatory cell-density coupling system by the simple addition of glucose in which GFP could not be strongly expressed until glucose was depleted, resulting in a greater amount of the GFP product and increased cell density. The expression system was eventually tested by the successful over-production of aminopeptidase to a desired level. The auto-regulatory cell density coupling system that is mediated by PsrfA is a novel expression system that has an expression pattern that is split between cell-growth and over-expression, leading to an increase in cell density and elevating the overall expression levels of heterologously expressed proteins. The broad applicability of this system and inducer-free expression property in B. subtilis facilitate the industrial scale-up and medical applications for the over-production of a variety of desired proteins.

Analysis on the DNA Fingerprinting of Aspergillus Oryzae Mutant Induced by High Hydrostatic Pressure

NASA Astrophysics Data System (ADS)

Wang, Hua; Zhang, Jian; Yang, Fan; Wang, Kai; Shen, Si-Le; Liu, Bing-Bing; Zou, Bo; Zou, Guang-Tian

2011-01-01

The mutant strains of aspergillus oryzae (HP300a) are screened under 300 MPa for 20 min. Compared with the control strains, the screened mutant strains have unique properties such as genetic stability, rapid growth, lots of spores, and high protease activity. Random amplified polymorphic DNA (RAPD) and inter simple sequence repeats (ISSR) are used to analyze the DNA fingerprinting of HP300a and the control strains. There are 67.9% and 51.3% polymorphic bands obtained by these two markers, respectively, indicating significant genetic variations between HP300a and the control strains. In addition, comparison of HP300a and the control strains, the genetic distances of random sequence and simple sequence repeat of DNA are 0.51 and 0.34, respectively.

Insights Into Upland Cotton (Gossypium hirsutum L.) Genetic Recombination Based on 3 High-Density Single-Nucleotide Polymorphism and a Consensus Map Developed Independently With Common Parents. Genomics Insights

USDA-ARS?s Scientific Manuscript database

High-density linkage maps are vital to supporting the correct placement of scaffolds and gene sequences on chromosomes and fundamental to contemporary organismal research and scientific approaches to genetic improvement; high-density linkage maps are especially important in paleopolyploids with exce...

Structural alphabets derived from attractors in conformational space

PubMed Central

2010-01-01

Background The hierarchical and partially redundant nature of protein structures justifies the definition of frequently occurring conformations of short fragments as 'states'. Collections of selected representatives for these states define Structural Alphabets, describing the most typical local conformations within protein structures. These alphabets form a bridge between the string-oriented methods of sequence analysis and the coordinate-oriented methods of protein structure analysis. Results A Structural Alphabet has been derived by clustering all four-residue fragments of a high-resolution subset of the protein data bank and extracting the high-density states as representative conformational states. Each fragment is uniquely defined by a set of three independent angles corresponding to its degrees of freedom, capturing in simple and intuitive terms the properties of the conformational space. The fragments of the Structural Alphabet are equivalent to the conformational attractors and therefore yield a most informative encoding of proteins. Proteins can be reconstructed within the experimental uncertainty in structure determination and ensembles of structures can be encoded with accuracy and robustness. Conclusions The density-based Structural Alphabet provides a novel tool to describe local conformations and it is specifically suitable for application in studies of protein dynamics. PMID:20170534

Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L.

PubMed Central

2012-01-01

Background In the last 30 years, a number of DNA fingerprinting methods such as RFLP, RAPD, AFLP, SSR, DArT, have been extensively used in marker development for molecular plant breeding. However, it remains a daunting task to identify highly polymorphic and closely linked molecular markers for a target trait for molecular marker-assisted selection. The next-generation sequencing (NGS) technology is far more powerful than any existing generic DNA fingerprinting methods in generating DNA markers. In this study, we employed a grain legume crop Lupinus angustifolius (lupin) as a test case, and examined the utility of an NGS-based method of RAD (restriction-site associated DNA) sequencing as DNA fingerprinting for rapid, cost-effective marker development tagging a disease resistance gene for molecular breeding. Results Twenty informative plants from a cross of RxS (disease resistant x susceptible) in lupin were subjected to RAD single-end sequencing by multiplex identifiers. The entire RAD sequencing products were resolved in two lanes of the 16-lanes per run sequencing platform Solexa HiSeq2000. A total of 185 million raw reads, approximately 17 Gb of sequencing data, were collected. Sequence comparison among the 20 test plants discovered 8207 SNP markers. Filtration of DNA sequencing data with marker identification parameters resulted in the discovery of 38 molecular markers linked to the disease resistance gene Lanr1. Five randomly selected markers were converted into cost-effective, simple PCR-based markers. Linkage analysis using marker genotyping data and disease resistance phenotyping data on a F8 population consisting of 186 individual plants confirmed that all these five markers were linked to the R gene. Two of these newly developed sequence-specific PCR markers, AnSeq3 and AnSeq4, flanked the target R gene at a genetic distance of 0.9 centiMorgan (cM), and are now replacing the markers previously developed by a traditional DNA fingerprinting method for marker-assisted selection in the Australian national lupin breeding program. Conclusions We demonstrated that more than 30 molecular markers linked to a target gene of agronomic trait of interest can be identified from a small portion (1/8) of one sequencing run on HiSeq2000 by applying NGS based RAD sequencing in marker development. The markers developed by the strategy described in this study are all co-dominant SNP markers, which can readily be converted into high throughput multiplex format or low-cost, simple PCR-based markers desirable for large scale marker implementation in plant breeding programs. The high density and closely linked molecular markers associated with a target trait help to overcome a major bottleneck for implementation of molecular markers on a wide range of germplasm in breeding programs. We conclude that application of NGS based RAD sequencing as DNA fingerprinting is a very rapid and cost-effective strategy for marker development in molecular plant breeding. The strategy does not require any prior genome knowledge or molecular information for the species under investigation, and it is applicable to other plant species. PMID:22805587

Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L.

PubMed

Yang, Huaan; Tao, Ye; Zheng, Zequn; Li, Chengdao; Sweetingham, Mark W; Howieson, John G

2012-07-17

In the last 30 years, a number of DNA fingerprinting methods such as RFLP, RAPD, AFLP, SSR, DArT, have been extensively used in marker development for molecular plant breeding. However, it remains a daunting task to identify highly polymorphic and closely linked molecular markers for a target trait for molecular marker-assisted selection. The next-generation sequencing (NGS) technology is far more powerful than any existing generic DNA fingerprinting methods in generating DNA markers. In this study, we employed a grain legume crop Lupinus angustifolius (lupin) as a test case, and examined the utility of an NGS-based method of RAD (restriction-site associated DNA) sequencing as DNA fingerprinting for rapid, cost-effective marker development tagging a disease resistance gene for molecular breeding. Twenty informative plants from a cross of RxS (disease resistant x susceptible) in lupin were subjected to RAD single-end sequencing by multiplex identifiers. The entire RAD sequencing products were resolved in two lanes of the 16-lanes per run sequencing platform Solexa HiSeq2000. A total of 185 million raw reads, approximately 17 Gb of sequencing data, were collected. Sequence comparison among the 20 test plants discovered 8207 SNP markers. Filtration of DNA sequencing data with marker identification parameters resulted in the discovery of 38 molecular markers linked to the disease resistance gene Lanr1. Five randomly selected markers were converted into cost-effective, simple PCR-based markers. Linkage analysis using marker genotyping data and disease resistance phenotyping data on a F8 population consisting of 186 individual plants confirmed that all these five markers were linked to the R gene. Two of these newly developed sequence-specific PCR markers, AnSeq3 and AnSeq4, flanked the target R gene at a genetic distance of 0.9 centiMorgan (cM), and are now replacing the markers previously developed by a traditional DNA fingerprinting method for marker-assisted selection in the Australian national lupin breeding program. We demonstrated that more than 30 molecular markers linked to a target gene of agronomic trait of interest can be identified from a small portion (1/8) of one sequencing run on HiSeq2000 by applying NGS based RAD sequencing in marker development. The markers developed by the strategy described in this study are all co-dominant SNP markers, which can readily be converted into high throughput multiplex format or low-cost, simple PCR-based markers desirable for large scale marker implementation in plant breeding programs. The high density and closely linked molecular markers associated with a target trait help to overcome a major bottleneck for implementation of molecular markers on a wide range of germplasm in breeding programs. We conclude that application of NGS based RAD sequencing as DNA fingerprinting is a very rapid and cost-effective strategy for marker development in molecular plant breeding. The strategy does not require any prior genome knowledge or molecular information for the species under investigation, and it is applicable to other plant species.

SNP Discovery by Illumina-Based Transcriptome Sequencing of the Olive and the Genetic Characterization of Turkish Olive Genotypes Revealed by AFLP, SSR and SNP Markers

PubMed Central

Kaya, Hilal Betul; Cetin, Oznur; Kaya, Hulya; Sahin, Mustafa; Sefer, Filiz; Kahraman, Abdullah; Tanyolac, Bahattin

2013-01-01

Background The olive tree (Olea europaea L.) is a diploid (2n = 2x = 46) outcrossing species mainly grown in the Mediterranean area, where it is the most important oil-producing crop. Because of its economic, cultural and ecological importance, various DNA markers have been used in the olive to characterize and elucidate homonyms, synonyms and unknown accessions. However, a comprehensive characterization and a full sequence of its transcriptome are unavailable, leading to the importance of an efficient large-scale single nucleotide polymorphism (SNP) discovery in olive. The objectives of this study were (1) to discover olive SNPs using next-generation sequencing and to identify SNP primers for cultivar identification and (2) to characterize 96 olive genotypes originating from different regions of Turkey. Methodology/Principal Findings Next-generation sequencing technology was used with five distinct olive genotypes and generated cDNA, producing 126,542,413 reads using an Illumina Genome Analyzer IIx. Following quality and size trimming, the high-quality reads were assembled into 22,052 contigs with an average length of 1,321 bases and 45 singletons. The SNPs were filtered and 2,987 high-quality putative SNP primers were identified. The assembled sequences and singletons were subjected to BLAST similarity searches and annotated with a Gene Ontology identifier. To identify the 96 olive genotypes, these SNP primers were applied to the genotypes in combination with amplified fragment length polymorphism (AFLP) and simple sequence repeats (SSR) markers. Conclusions/Significance This study marks the highest number of SNP markers discovered to date from olive genotypes using transcriptome sequencing. The developed SNP markers will provide a useful source for molecular genetic studies, such as genetic diversity and characterization, high density quantitative trait locus (QTL) analysis, association mapping and map-based gene cloning in the olive. High levels of genetic variation among Turkish olive genotypes revealed by SNPs, AFLPs and SSRs allowed us to characterize the Turkish olive genotype. PMID:24058483

Simple chained guide trees give high-quality protein multiple sequence alignments

PubMed Central

Boyce, Kieran; Sievers, Fabian; Higgins, Desmond G.

2014-01-01

Guide trees are used to decide the order of sequence alignment in the progressive multiple sequence alignment heuristic. These guide trees are often the limiting factor in making large alignments, and considerable effort has been expended over the years in making these quickly or accurately. In this article we show that, at least for protein families with large numbers of sequences that can be benchmarked with known structures, simple chained guide trees give the most accurate alignments. These also happen to be the fastest and simplest guide trees to construct, computationally. Such guide trees have a striking effect on the accuracy of alignments produced by some of the most widely used alignment packages. There is a marked increase in accuracy and a marked decrease in computational time, once the number of sequences goes much above a few hundred. This is true, even if the order of sequences in the guide tree is random. PMID:25002495

Magnetic flux density measurement with balanced steady state free precession pulse sequence for MREIT: a simulation study.

PubMed

Minhas, Atul S; Woo, Eung Je; Lee, Soo Yeol

2009-01-01

Magnetic Resonance Electrical Impedance Tomography (MREIT) utilizes the magnetic flux density B(z), generated due to current injection, to find conductivity distribution inside an object. This B(z) can be measured from MR phase images using spin echo pulse sequence. The SNR of B(z) and the sensitivity of phase produced by B(z) in MR phase image are critical in deciding the resolution of MREIT conductivity images. The conventional spin echo based data acquisition has poor phase sensitivity to current injection. Longer scan time is needed to acquire data with higher SNR. We propose a balanced steady state free precession (b-SSFP) based pulse sequence which is highly sensitive to small off-resonance phase changes. A procedure to reconstruct B(z) from MR signal obtained with b-SSFP sequence is described. Phases for b-SSFP signals for two conductivity phantoms of TX 151 and Gelatin are simulated from the mathematical models of b-SSFP signal. It was observed that the phase changes obtained from b-SSFP pulse sequence are highly sensitive to current injection and hence would produce higher magnetic flux density. However, the b-SSFP signal is dependent on magnetic field inhomogeneity and the signal deteriorated highly for small offset from resonance frequency. The simulation results show that the b-SSFP sequence can be utilized for conductivity imaging of a local region where magnetic field inhomogeneity is small. A proper shimming of magnet is recommended before using the b-SSFP sequence.

A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat

PubMed Central

2013-01-01

Background As for other major crops, achieving a complete wheat genome sequence is essential for the application of genomics to breeding new and improved varieties. To overcome the complexities of the large, highly repetitive and hexaploid wheat genome, the International Wheat Genome Sequencing Consortium established a chromosome-based strategy that was validated by the construction of the physical map of chromosome 3B. Here, we present improved strategies for the construction of highly integrated and ordered wheat physical maps, using chromosome 1BL as a template, and illustrate their potential for evolutionary studies and map-based cloning. Results Using a combination of novel high throughput marker assays and an assembly program, we developed a high quality physical map representing 93% of wheat chromosome 1BL, anchored and ordered with 5,489 markers including 1,161 genes. Analysis of the gene space organization and evolution revealed that gene distribution and conservation along the chromosome results from the superimposition of the ancestral grass and recent wheat evolutionary patterns, leading to a peak of synteny in the central part of the chromosome arm and an increased density of non-collinear genes towards the telomere. With a density of about 11 markers per Mb, the 1BL physical map provides 916 markers, including 193 genes, for fine mapping the 40 QTLs mapped on this chromosome. Conclusions Here, we demonstrate that high marker density physical maps can be developed in complex genomes such as wheat to accelerate map-based cloning, gain new insights into genome evolution, and provide a foundation for reference sequencing. PMID:23800011

Terminator oligo blocking efficiently eliminates rRNA from Drosophila small RNA sequencing libraries.

PubMed

Wickersheim, Michelle L; Blumenstiel, Justin P

2013-11-01

A large number of methods are available to deplete ribosomal RNA reads from high-throughput RNA sequencing experiments. Such methods are critical for sequencing Drosophila small RNAs between 20 and 30 nucleotides because size selection is not typically sufficient to exclude the highly abundant class of 30 nucleotide 2S rRNA. Here we demonstrate that pre-annealing terminator oligos complimentary to Drosophila 2S rRNA prior to 5' adapter ligation and reverse transcription efficiently depletes 2S rRNA sequences from the sequencing reaction in a simple and inexpensive way. This depletion is highly specific and is achieved with minimal perturbation of miRNA and piRNA profiles.

HYBRIDCHECK: software for the rapid detection, visualization and dating of recombinant regions in genome sequence data.

PubMed

Ward, Ben J; van Oosterhout, Cock

2016-03-01

HYBRIDCHECK is a software package to visualize the recombination signal in large DNA sequence data set, and it can be used to analyse recombination, genetic introgression, hybridization and horizontal gene transfer. It can scan large (multiple kb) contigs and whole-genome sequences of three or more individuals. HYBRIDCHECK is written in the r software for OS X, Linux and Windows operating systems, and it has a simple graphical user interface. In addition, the r code can be readily incorporated in scripts and analysis pipelines. HYBRIDCHECK implements several ABBA-BABA tests and visualizes the effects of hybridization and the resulting mosaic-like genome structure in high-density graphics. The package also reports the following: (i) the breakpoint positions, (ii) the number of mutations in each introgressed block, (iii) the probability that the identified region is not caused by recombination and (iv) the estimated age of each recombination event. The divergence times between the donor and recombinant sequence are calculated using a JC, K80, F81, HKY or GTR correction, and the dating algorithm is exceedingly fast. By estimating the coalescence time of introgressed blocks, it is possible to distinguish between hybridization and incomplete lineage sorting. HYBRIDCHECK is libré software and it and its manual are free to download from http://ward9250.github.io/HybridCheck/. © 2015 John Wiley & Sons Ltd.

Genetic linkage map and QTL identification for adventitious rooting traits in red gum eucalypts.

PubMed

Sumathi, Murugan; Bachpai, Vijaya Kumar Waman; Mayavel, A; Dasgupta, Modhumita Ghosh; Nagarajan, Binai; Rajasugunasekar, D; Sivakumar, Veerasamy; Yasodha, Ramasamy

2018-05-01

The eucalypt species, Eucalyptus tereticornis and Eucalyptus camaldulensis , show tolerance to drought and salinity conditions, respectively, and are widely cultivated in arid and semiarid regions of tropical countries. In this study, genetic linkage map was developed for interspecific cross E. tereticornis  ×  E. camaldulensis using pseudo-testcross strategy with simple sequence repeats (SSRs), intersimple sequence repeats (ISSRs), and sequence-related amplified polymorphism (SRAP) markers. The consensus genetic map comprised totally 283 markers with 84 SSRs, 94 ISSRs, and 105 SRAP markers on 11 linkage groups spanning 1163.4 cM genetic distance. Blasting the SSR sequences against E. grandis sequences allowed an alignment of 64% and the average ratio of genetic-to-physical distance was 1.7 Mbp/cM, which strengths the evidence that high amount of synteny and colinearity exists among eucalypts genome. Blast searches also revealed that 37% of SSRs had homologies with genes, which could potentially be used in the variety of downstream applications including candidate gene polymorphism. Quantitative trait loci (QTL) analysis for adventitious rooting traits revealed six QTL for rooting percent and root length on five chromosomes with interval and composite interval mapping. All the QTL explained 12.0-14.7% of the phenotypic variance, showing the involvement of major effect QTL on adventitious rooting traits. Increasing the density of markers would facilitate the detection of more number of small-effect QTL and also underpinning the genes involved in rooting process.

Anomalous evolution of Ar metastable density with electron density in high density Ar discharge

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

Park, Min; Chang, Hong-Young; You, Shin-Jae

2011-10-15

Recently, an anomalous evolution of argon metastable density with plasma discharge power (electron density) was reported [A. M. Daltrini, S. A. Moshkalev, T. J. Morgan, R. B. Piejak, and W. G. Graham, Appl. Phys. Lett. 92, 061504 (2008)]. Although the importance of the metastable atom and its density has been reported in a lot of literature, however, a basic physics behind the anomalous evolution of metastable density has not been clearly understood yet. In this study, we investigated a simple global model to elucidate the underlying physics of the anomalous evolution of argon metastable density with the electron density. Onmore » the basis of the proposed simple model, we reproduced the anomalous evolution of the metastable density and disclosed the detailed physics for the anomalous result. Drastic changes of dominant mechanisms for the population and depopulation processes of Ar metastable atoms with electron density, which take place even in relatively low electron density regime, is the clue to understand the result.« less

Construction of a high-density high-resolution genetic map and its integration with BAC-based physical map in channel catfish

USDA-ARS?s Scientific Manuscript database

Construction of genetic linkage map is essential for genetic and genomic studies. Recent advances in sequencing and genotyping technologies made it possible to generate high-density and high-resolution genetic linkage maps, especially for the organisms lacking extensive genomic resources. In the pre...

Tracking flow of leukocytes in blood for drug analysis

NASA Astrophysics Data System (ADS)

Basharat, Arslan; Turner, Wesley; Stephens, Gillian; Badillo, Benjamin; Lumpkin, Rick; Andre, Patrick; Perera, Amitha

2011-03-01

Modern microscopy techniques allow imaging of circulating blood components under vascular flow conditions. The resulting video sequences provide unique insights into the behavior of blood cells within the vasculature and can be used as a method to monitor and quantitate the recruitment of inflammatory cells at sites of vascular injury/ inflammation and potentially serve as a pharmacodynamic biomarker, helping screen new therapies and individualize dose and combinations of drugs. However, manual analysis of these video sequences is intractable, requiring hours per 400 second video clip. In this paper, we present an automated technique to analyze the behavior and recruitment of human leukocytes in whole blood under physiological conditions of shear through a simple multi-channel fluorescence microscope in real-time. This technique detects and tracks the recruitment of leukocytes to a bioactive surface coated on a flow chamber. Rolling cells (cells which partially bind to the bioactive matrix) are detected counted, and have their velocity measured and graphed. The challenges here include: high cell density, appearance similarity, and low (1Hz) frame rate. Our approach performs frame differencing based motion segmentation, track initialization and online tracking of individual leukocytes.

Radial chromatin positioning is shaped by local gene density, not by gene expression

PubMed Central

2009-01-01

G- and R-bands of metaphase chromosomes are characterized by profound differences in gene density, CG content, replication timing, and chromatin compaction. The preferential localization of gene-dense, transcriptionally active, and early replicating chromatin in the nuclear interior and of gene-poor, later replicating chromatin at the nuclear envelope has been demonstrated to be evolutionary-conserved in various cell types. Yet, the impact of different local chromatin features on the radial nuclear arrangement of chromatin is still not well understood. In particular, it is not known whether radial chromatin positioning is preferentially shaped by local gene density per se or by other related parameters such as replication timing or transcriptional activity. The interdependence of these distinct chromatin features on the linear deoxyribonucleic acid (DNA) sequence precludes a simple dissection of these parameters with respect to their importance for the reorganization of the linear DNA organization into the distinct radial chromatin arrangements observed in the nuclear space. To analyze this problem, we generated probe sets of pooled bacterial artificial chromosome (BAC) clones from HSA 11, 12, 18, and 19 representing R/G-band-assigned chromatin, segments with different gene density and gene loci with different expression levels. Using multicolor 3D flourescent in situ hybridization (FISH) and 3D image analysis, we determined their localization in the nucleus and their positions within or outside the corresponding chromosome territory (CT). For each BAC data on local gene density within 2- and 10-Mb windows, as well as GC (guanine and cytosine) content, replication timing and expression levels were determined. A correlation analysis of these parameters with nuclear positioning revealed regional gene density as the decisive parameter determining the radial positioning of chromatin in the nucleus in contrast to band assignment, replication timing, and transcriptional activity. We demonstrate a polarized distribution of gene-dense vs gene-poor chromatin within CTs with respect to the nuclear border. Whereas we confirm previous reports that a particular gene-dense and transcriptionally highly active region of about 2 Mb on 11p15.5 often loops out from the territory surface, gene-dense and highly expressed sequences were not generally found preferentially at the CT surface as previously suggested. PMID:17333233

Accuracy of dynamical-decoupling-based spectroscopy of Gaussian noise

NASA Astrophysics Data System (ADS)

Szańkowski, Piotr; Cywiński, Łukasz

2018-03-01

The fundamental assumption of dynamical-decoupling-based noise spectroscopy is that the coherence decay rate of qubit (or qubits) driven with a sequence of many pulses, is well approximated by the environmental noise spectrum spanned on frequency comb defined by the sequence. Here we investigate the precise conditions under which this commonly used spectroscopic approach is quantitatively correct. To this end we focus on two representative examples of spectral densities: the long-tailed Lorentzian, and finite-ranged Gaussian—both expected to be encountered when using the qubit for nanoscale nuclear resonance imaging. We have found that, in contrast to Lorentz spectrum, for which the corrections to the standard spectroscopic formulas can easily be made negligible, the spectra with finite range are more challenging to reconstruct accurately. For Gaussian line shape of environmental spectral density, direct application of the standard dynamical-decoupling-based spectroscopy leads to erroneous attribution of long-tail behavior to the reconstructed spectrum. Fortunately, artifacts such as this, can be completely avoided with the simple extension to standard reconstruction method.

Appliation of rad-sequencing to linkage mapping in citrus

USDA-ARS?s Scientific Manuscript database

High density linkage maps can be developed for modest cost using high-throughput DNA sequencing to genotype a defined fraction (representation) of the genome. We developed linkage maps in two citrus populations using the RAD (Restriction site Associated DNA) genotyping method which involves restrict...

Increasing Classroom Compliance: Using a High-Probability Command Sequence with Noncompliant Students

ERIC Educational Resources Information Center

Axelrod, Michael I.; Zank, Amber J.

2012-01-01

Noncompliance is one of the most problematic behaviors within the school setting. One strategy to increase compliance of noncompliant students is a high-probability command sequence (HPCS; i.e., a set of simple commands in which an individual is likely to comply immediately prior to the delivery of a command that has a lower probability of…

Identification of QTLs for 14 Agronomically Important Traits in Setaria italica Based on SNPs Generated from High-Throughput Sequencing

PubMed Central

Zhang, Kai; Fan, Guangyu; Zhang, Xinxin; Zhao, Fang; Wei, Wei; Du, Guohua; Feng, Xiaolei; Wang, Xiaoming; Wang, Feng; Song, Guoliang; Zou, Hongfeng; Zhang, Xiaolei; Li, Shuangdong; Ni, Xuemei; Zhang, Gengyun; Zhao, Zhihai

2017-01-01

Foxtail millet (Setaria italica) is an important crop possessing C4 photosynthesis capability. The S. italica genome was de novo sequenced in 2012, but the sequence lacked high-density genetic maps with agronomic and yield trait linkages. In the present study, we resequenced a foxtail millet population of 439 recombinant inbred lines (RILs) and developed high-resolution bin map and high-density SNP markers, which could provide an effective approach for gene identification. A total of 59 QTL for 14 agronomic traits in plants grown under long- and short-day photoperiods were identified. The phenotypic variation explained ranged from 4.9 to 43.94%. In addition, we suggested that there may be segregation distortion on chromosome 6 that is significantly distorted toward Zhang gu. The newly identified QTL will provide a platform for sequence-based research on the S. italica genome, and for molecular marker-assisted breeding. PMID:28364039

Identification of QTLs for 14 Agronomically Important Traits in Setaria italica Based on SNPs Generated from High-Throughput Sequencing.

PubMed

Zhang, Kai; Fan, Guangyu; Zhang, Xinxin; Zhao, Fang; Wei, Wei; Du, Guohua; Feng, Xiaolei; Wang, Xiaoming; Wang, Feng; Song, Guoliang; Zou, Hongfeng; Zhang, Xiaolei; Li, Shuangdong; Ni, Xuemei; Zhang, Gengyun; Zhao, Zhihai

2017-05-05

Foxtail millet ( Setaria italica ) is an important crop possessing C4 photosynthesis capability. The S. italica genome was de novo sequenced in 2012, but the sequence lacked high-density genetic maps with agronomic and yield trait linkages. In the present study, we resequenced a foxtail millet population of 439 recombinant inbred lines (RILs) and developed high-resolution bin map and high-density SNP markers, which could provide an effective approach for gene identification. A total of 59 QTL for 14 agronomic traits in plants grown under long- and short-day photoperiods were identified. The phenotypic variation explained ranged from 4.9 to 43.94%. In addition, we suggested that there may be segregation distortion on chromosome 6 that is significantly distorted toward Zhang gu. The newly identified QTL will provide a platform for sequence-based research on the S. italica genome, and for molecular marker-assisted breeding. Copyright © 2017 Zhang et al.

A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits

PubMed Central

Wenzl, Peter; Li, Haobing; Carling, Jason; Zhou, Meixue; Raman, Harsh; Paul, Edie; Hearnden, Phillippa; Maier, Christina; Xia, Ling; Caig, Vanessa; Ovesná, Jaroslava; Cakir, Mehmet; Poulsen, David; Wang, Junping; Raman, Rosy; Smith, Kevin P; Muehlbauer, Gary J; Chalmers, Ken J; Kleinhofs, Andris; Huttner, Eric; Kilian, Andrzej

2006-01-01

Background Molecular marker technologies are undergoing a transition from largely serial assays measuring DNA fragment sizes to hybridization-based technologies with high multiplexing levels. Diversity Arrays Technology (DArT) is a hybridization-based technology that is increasingly being adopted by barley researchers. There is a need to integrate the information generated by DArT with previous data produced with gel-based marker technologies. The goal of this study was to build a high-density consensus linkage map from the combined datasets of ten populations, most of which were simultaneously typed with DArT and Simple Sequence Repeat (SSR), Restriction Enzyme Fragment Polymorphism (RFLP) and/or Sequence Tagged Site (STS) markers. Results The consensus map, built using a combination of JoinMap 3.0 software and several purpose-built perl scripts, comprised 2,935 loci (2,085 DArT, 850 other loci) and spanned 1,161 cM. It contained a total of 1,629 'bins' (unique loci), with an average inter-bin distance of 0.7 ± 1.0 cM (median = 0.3 cM). More than 98% of the map could be covered with a single DArT assay. The arrangement of loci was very similar to, and almost as optimal as, the arrangement of loci in component maps built for individual populations. The locus order of a synthetic map derived from merging the component maps without considering the segregation data was only slightly inferior. The distribution of loci along chromosomes indicated centromeric suppression of recombination in all chromosomes except 5H. DArT markers appeared to have a moderate tendency toward hypomethylated, gene-rich regions in distal chromosome areas. On the average, 14 ± 9 DArT loci were identified within 5 cM on either side of SSR, RFLP or STS loci previously identified as linked to agricultural traits. Conclusion Our barley consensus map provides a framework for transferring genetic information between different marker systems and for deploying DArT markers in molecular breeding schemes. The study also highlights the need for improved software for building consensus maps from high-density segregation data of multiple populations. PMID:16904008

Access to Barrier Perches Improves Behavior Repertoire in Broilers

PubMed Central

Ventura, Beth A.; Siewerdt, Frank; Estevez, Inma

2012-01-01

Restriction of behavioral opportunities and uneven use of space are considerable welfare concerns in modern broiler production, particularly when birds are kept at high densities. We hypothesized that increased environmental complexity by provision of barrier perches would help address these issues by encouraging perching and enhancing use of the pen space across a range of stocking densities. 2,088 day-old broiler chicks were randomly assigned to one of the following barrier and density treatment combinations over four replications: simple barrier, complex barrier, or control (no barrier) and low (8 birds/m2), moderate (13 birds/m2), or high (18 birds/m2) density. Data were collected on focal birds via instantaneous scan sampling from 2 to 6 weeks of age. Mean estimates per pen for percent of observations seen performing each behavior, as well as percent of observations in the pen periphery vs. center, were quantified and submitted to an analysis of variance with week as the repeated measure. Barrier perches, density and age affected the behavioral time budget of broilers. Both simple and complex barrier perches effectively stimulated high perching rates. Aggression and disturbances were lower in both barrier treatments compared to controls (P<0.05). Increasing density to 18 birds/m2 compared to the lower densities suppressed activity levels, with lower foraging (P<0.005), decreased perching (P<0.0001) and increased sitting (P = 0.001) earlier in the rearing period. Disturbances also increased at higher densities (P<0.05). Use of the central pen area was higher in simple barrier pens compared to controls (P<0.001), while increasing density above 8 birds/m2 suppressed use of the central space (P<0.05). This work confirms some negative effects of increasing density and suggests that barrier perches have the potential to improve broiler welfare by encouraging activity (notably by providing accessible opportunities to perch), decreasing aggression and disturbances, and promoting more even distribution of birds throughout the pen space. PMID:22299026

Colloidal polymers with controlled sequence and branching constructed from magnetic field assembled nanoparticles.

PubMed

Bannwarth, Markus B; Utech, Stefanie; Ebert, Sandro; Weitz, David A; Crespy, Daniel; Landfester, Katharina

2015-03-24

The assembly of nanoparticles into polymer-like architectures is challenging and usually requires highly defined colloidal building blocks. Here, we show that the broad size-distribution of a simple dispersion of magnetic nanocolloids can be exploited to obtain various polymer-like architectures. The particles are assembled under an external magnetic field and permanently linked by thermal sintering. The remarkable variety of polymer-analogue architectures that arises from this simple process ranges from statistical and block copolymer-like sequencing to branched chains and networks. This library of architectures can be realized by controlling the sequencing of the particles and the junction points via a size-dependent self-assembly of the single building blocks.

CMOS Active-Pixel Image Sensor With Simple Floating Gates

NASA Technical Reports Server (NTRS)

Fossum, Eric R.; Nakamura, Junichi; Kemeny, Sabrina E.

1996-01-01

Experimental complementary metal-oxide/semiconductor (CMOS) active-pixel image sensor integrated circuit features simple floating-gate structure, with metal-oxide/semiconductor field-effect transistor (MOSFET) as active circuit element in each pixel. Provides flexibility of readout modes, no kTC noise, and relatively simple structure suitable for high-density arrays. Features desirable for "smart sensor" applications.

The force distribution probability function for simple fluids by density functional theory.

PubMed

Rickayzen, G; Heyes, D M

2013-02-28

Classical density functional theory (DFT) is used to derive a formula for the probability density distribution function, P(F), and probability distribution function, W(F), for simple fluids, where F is the net force on a particle. The final formula for P(F) ∝ exp(-AF(2)), where A depends on the fluid density, the temperature, and the Fourier transform of the pair potential. The form of the DFT theory used is only applicable to bounded potential fluids. When combined with the hypernetted chain closure of the Ornstein-Zernike equation, the DFT theory for W(F) agrees with molecular dynamics computer simulations for the Gaussian and bounded soft sphere at high density. The Gaussian form for P(F) is still accurate at lower densities (but not too low density) for the two potentials, but with a smaller value for the constant, A, than that predicted by the DFT theory.

Multiplexed microsatellite recovery using massively parallel sequencing

Treesearch

T.N. Jennings; B.J. Knaus; T.D. Mullins; S.M. Haig; R.C. Cronn

2011-01-01

Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of...

Kangaroo – A pattern-matching program for biological sequences

PubMed Central

2002-01-01

Background Biologists are often interested in performing a simple database search to identify proteins or genes that contain a well-defined sequence pattern. Many databases do not provide straightforward or readily available query tools to perform simple searches, such as identifying transcription binding sites, protein motifs, or repetitive DNA sequences. However, in many cases simple pattern-matching searches can reveal a wealth of information. We present in this paper a regular expression pattern-matching tool that was used to identify short repetitive DNA sequences in human coding regions for the purpose of identifying potential mutation sites in mismatch repair deficient cells. Results Kangaroo is a web-based regular expression pattern-matching program that can search for patterns in DNA, protein, or coding region sequences in ten different organisms. The program is implemented to facilitate a wide range of queries with no restriction on the length or complexity of the query expression. The program is accessible on the web at http://bioinfo.mshri.on.ca/kangaroo/ and the source code is freely distributed at http://sourceforge.net/projects/slritools/. Conclusion A low-level simple pattern-matching application can prove to be a useful tool in many research settings. For example, Kangaroo was used to identify potential genetic targets in a human colorectal cancer variant that is characterized by a high frequency of mutations in coding regions containing mononucleotide repeats. PMID:12150718

A Practical Workshop for Generating Simple DNA Fingerprints of Plants

ERIC Educational Resources Information Center

Rouziere, A.-S.; Redman, J. E.

2011-01-01

Gel electrophoresis DNA fingerprints offer a graphical and visually appealing illumination of the similarities and differences between DNA sequences of different species and individuals. A polymerase chain reaction (PCR) and restriction digest protocol was designed to give high-school students the opportunity to generate simple fingerprints of…

Repliscan: a tool for classifying replication timing regions.

PubMed

Zynda, Gregory J; Song, Jawon; Concia, Lorenzo; Wear, Emily E; Hanley-Bowdoin, Linda; Thompson, William F; Vaughn, Matthew W

2017-08-07

Replication timing experiments that use label incorporation and high throughput sequencing produce peaked data similar to ChIP-Seq experiments. However, the differences in experimental design, coverage density, and possible results make traditional ChIP-Seq analysis methods inappropriate for use with replication timing. To accurately detect and classify regions of replication across the genome, we present Repliscan. Repliscan robustly normalizes, automatically removes outlying and uninformative data points, and classifies Repli-seq signals into discrete combinations of replication signatures. The quality control steps and self-fitting methods make Repliscan generally applicable and more robust than previous methods that classify regions based on thresholds. Repliscan is simple and effective to use on organisms with different genome sizes. Even with analysis window sizes as small as 1 kilobase, reliable profiles can be generated with as little as 2.4x coverage.

Hippocampal Replay is Not a Simple Function of Experience

PubMed Central

Gupta, Anoopum S.; van der Meer, Matthijs A. A.; Touretzky, David S.; Redish, A. David

2015-01-01

Summary Replay of behavioral sequences in the hippocampus during sharp-wave-ripple-complexes (SWRs) provides a potential mechanism for memory consolidation and the learning of knowledge structures. Current hypotheses imply that replay should straightforwardly reflect recent experience. However, we find these hypotheses to be incompatible with the content of replay on a task with two distinct behavioral sequences (A&B). We observed forward and backward replay of B even when rats had been performing A for >10 minutes. Furthermore, replay of non-local sequence B occurred more often when B was infrequently experienced. Neither forward nor backward sequences preferentially represented highly-experienced trajectories within a session. Additionally, we observed the construction of never-experienced novel-path sequences. These observations challenge the idea that sequence activation during SWRs is a simple replay of recent experience. Instead, replay reflected all physically available trajectories within the environment, suggesting a potential role in active learning and maintenance of the cognitive map. PMID:20223204

Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus.

PubMed

Li, Fagen; Zhou, Changpin; Weng, Qijie; Li, Mei; Yu, Xiaoli; Guo, Yong; Wang, Yu; Zhang, Xiaohong; Gan, Siming

2015-01-01

Dense genetic maps, along with quantitative trait loci (QTLs) detected on such maps, are powerful tools for genomics and molecular breeding studies. In the important woody genus Eucalyptus, the recent release of E. grandis genome sequence allows for sequence-based genomic comparison and searching for positional candidate genes within QTL regions. Here, dense genetic maps were constructed for E. urophylla and E. tereticornis using genomic simple sequence repeats (SSR), expressed sequence tag (EST) derived SSR, EST-derived cleaved amplified polymorphic sequence (EST-CAPS), and diversity arrays technology (DArT) markers. The E. urophylla and E. tereticornis maps comprised 700 and 585 markers across 11 linkage groups, totaling at 1,208.2 and 1,241.4 cM in length, respectively. Extensive synteny and colinearity were observed as compared to three earlier DArT-based eucalypt maps (two maps with E. grandis × E. urophylla and one map of E. globulus) and with the E. grandis genome sequence. Fifty-three QTLs for growth (10-56 months of age) and wood density (56 months) were identified in 22 discrete regions on both maps, in which only one colocalizaiton was found between growth and wood density. Novel QTLs were revealed as compared with those previously detected on DArT-based maps for similar ages in Eucalyptus. Eleven to 585 positional candidate genes were obained for a 56-month-old QTL through aligning QTL confidence interval with the E. grandis genome. These results will assist in comparative genomics studies, targeted gene characterization, and marker-assisted selection in Eucalyptus and the related taxa.

Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus

PubMed Central

Weng, Qijie; Li, Mei; Yu, Xiaoli; Guo, Yong; Wang, Yu; Zhang, Xiaohong; Gan, Siming

2015-01-01

Dense genetic maps, along with quantitative trait loci (QTLs) detected on such maps, are powerful tools for genomics and molecular breeding studies. In the important woody genus Eucalyptus, the recent release of E. grandis genome sequence allows for sequence-based genomic comparison and searching for positional candidate genes within QTL regions. Here, dense genetic maps were constructed for E. urophylla and E. tereticornis using genomic simple sequence repeats (SSR), expressed sequence tag (EST) derived SSR, EST-derived cleaved amplified polymorphic sequence (EST-CAPS), and diversity arrays technology (DArT) markers. The E. urophylla and E. tereticornis maps comprised 700 and 585 markers across 11 linkage groups, totaling at 1,208.2 and 1,241.4 cM in length, respectively. Extensive synteny and colinearity were observed as compared to three earlier DArT-based eucalypt maps (two maps with E. grandis × E. urophylla and one map of E. globulus) and with the E. grandis genome sequence. Fifty-three QTLs for growth (10–56 months of age) and wood density (56 months) were identified in 22 discrete regions on both maps, in which only one colocalizaiton was found between growth and wood density. Novel QTLs were revealed as compared with those previously detected on DArT-based maps for similar ages in Eucalyptus. Eleven to 585 positional candidate genes were obained for a 56-month-old QTL through aligning QTL confidence interval with the E. grandis genome. These results will assist in comparative genomics studies, targeted gene characterization, and marker-assisted selection in Eucalyptus and the related taxa. PMID:26695430

PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics.

PubMed

Azuara, Cyril; Lindahl, Erik; Koehl, Patrice; Orland, Henri; Delarue, Marc

2006-07-01

We describe a new way to calculate the electrostatic properties of macromolecules which eliminates the assumption of a constant dielectric value in the solvent region, resulting in a Generalized Poisson-Boltzmann-Langevin equation (GPBLE). We have implemented a web server (http://lorentz.immstr.pasteur.fr/pdb_hydro.php) that both numerically solves this equation and uses the resulting water density profiles to place water molecules at preferred sites of hydration. Surface atoms with high or low hydration preference can be easily displayed using a simple PyMol script, allowing for the tentative prediction of the dimerization interface in homodimeric proteins, or lipid binding regions in membrane proteins. The web site includes options that permit mutations in the sequence as well as reconstruction of missing side chain and/or main chain atoms. These tools are accessible independently from the electrostatics calculation, and can be used for other modeling purposes. We expect this web server to be useful to structural biologists, as the knowledge of solvent density should prove useful to get better fits at low resolution for X-ray diffraction data and to computational biologists, for whom these profiles could improve the calculation of interaction energies in water between ligands and receptors in docking simulations.

Sequenced sorghum mutant library- an efficient platform for discovery of causal gene mutations

USDA-ARS?s Scientific Manuscript database

Ethyl methanesulfonate (EMS) efficiently generates high-density mutations in genomes. We applied whole-genome sequencing to 256 phenotyped mutant lines of sorghum (Sorghum bicolor L. Moench) to 16x coverage. Comparisons with the reference sequence revealed >1.8 million canonical EMS-induced G/C to A...

Mapping axonal density and average diameter using non-monotonic time-dependent gradient-echo MRI

NASA Astrophysics Data System (ADS)

Nunes, Daniel; Cruz, Tomás L.; Jespersen, Sune N.; Shemesh, Noam

2017-04-01

White Matter (WM) microstructures, such as axonal density and average diameter, are crucial to the normal function of the Central Nervous System (CNS) as they are closely related with axonal conduction velocities. Conversely, disruptions of these microstructural features may result in severe neurological deficits, suggesting that their noninvasive mapping could be an important step towards diagnosing and following pathophysiology. Whereas diffusion based MRI methods have been proposed to map these features, they typically entail the application of powerful gradients, which are rarely available in the clinic, or extremely long acquisition schemes to extract information from parameter-intensive models. In this study, we suggest that simple and time-efficient multi-gradient-echo (MGE) MRI can be used to extract the axon density from susceptibility-driven non-monotonic decay in the time-dependent signal. We show, both theoretically and with simulations, that a non-monotonic signal decay will occur for multi-compartmental microstructures - such as axons and extra-axonal spaces, which were here used as a simple model for the microstructure - and that, for axons parallel to the main magnetic field, the axonal density can be extracted. We then experimentally demonstrate in ex-vivo rat spinal cords that its different tracts - characterized by different microstructures - can be clearly contrasted using the MGE-derived maps. When the quantitative results are compared against ground-truth histology, they reflect the axonal fraction (though with a bias, as evident from Bland-Altman analysis). As well, the extra-axonal fraction can be estimated. The results suggest that our model is oversimplified, yet at the same time evidencing a potential and usefulness of the approach to map underlying microstructures using a simple and time-efficient MRI sequence. We further show that a simple general-linear-model can predict the average axonal diameters from the four model parameters, and map these average axonal diameters in the spinal cords. While clearly further modelling and theoretical developments are necessary, we conclude that salient WM microstructural features can be extracted from simple, SNR-efficient multi-gradient echo MRI, and that this paves the way towards easier estimation of WM microstructure in vivo.

Mapping axonal density and average diameter using non-monotonic time-dependent gradient-echo MRI.

PubMed

Nunes, Daniel; Cruz, Tomás L; Jespersen, Sune N; Shemesh, Noam

2017-04-01

White Matter (WM) microstructures, such as axonal density and average diameter, are crucial to the normal function of the Central Nervous System (CNS) as they are closely related with axonal conduction velocities. Conversely, disruptions of these microstructural features may result in severe neurological deficits, suggesting that their noninvasive mapping could be an important step towards diagnosing and following pathophysiology. Whereas diffusion based MRI methods have been proposed to map these features, they typically entail the application of powerful gradients, which are rarely available in the clinic, or extremely long acquisition schemes to extract information from parameter-intensive models. In this study, we suggest that simple and time-efficient multi-gradient-echo (MGE) MRI can be used to extract the axon density from susceptibility-driven non-monotonic decay in the time-dependent signal. We show, both theoretically and with simulations, that a non-monotonic signal decay will occur for multi-compartmental microstructures - such as axons and extra-axonal spaces, which were here used as a simple model for the microstructure - and that, for axons parallel to the main magnetic field, the axonal density can be extracted. We then experimentally demonstrate in ex-vivo rat spinal cords that its different tracts - characterized by different microstructures - can be clearly contrasted using the MGE-derived maps. When the quantitative results are compared against ground-truth histology, they reflect the axonal fraction (though with a bias, as evident from Bland-Altman analysis). As well, the extra-axonal fraction can be estimated. The results suggest that our model is oversimplified, yet at the same time evidencing a potential and usefulness of the approach to map underlying microstructures using a simple and time-efficient MRI sequence. We further show that a simple general-linear-model can predict the average axonal diameters from the four model parameters, and map these average axonal diameters in the spinal cords. While clearly further modelling and theoretical developments are necessary, we conclude that salient WM microstructural features can be extracted from simple, SNR-efficient multi-gradient echo MRI, and that this paves the way towards easier estimation of WM microstructure in vivo. Copyright © 2017 Elsevier Inc. All rights reserved.

In-vivo measurement of relationship between applied current amplitude and current density magnitude from 10 mA to 110 mA.

PubMed

DeMonte, Tim P; Wang, Dinghui; Ma, Weijing; Gao, Jia-Hong; Joy, Michael L G

2009-01-01

Current density imaging (CDI) is a magnetic resonance imaging (MRI) technique used to quantitatively measure current density vectors throughout the volume of an object/subject placed in the MRI system. Electrical current pulses are applied externally to the object/subject and are synchronized with the MRI sequence. In this work, CDI is used to measure average current density magnitude in the torso region of an in-vivo piglet for applied current pulse amplitudes ranging from 10 mA to 110 mA. The relationship between applied current amplitude and current density magnitude is linear in simple electronic elements such as wires and resistors; however, this relationship may not be linear in living tissue. An understanding of this relationship is useful for research in defibrillation, human electro-muscular incapacitation (e.g. TASER(R)) and other bioelectric stimulation devices. This work will show that the current amplitude to current density magnitude relationship is slightly nonlinear in living tissue in the range of 10 mA to 110 mA.

Molecular evidence of hybridization in sympatric populations of the Enantia jethys complex (Lepidoptera: Pieridae).

PubMed

Jasso-Martínez, Jovana M; Machkour-M'Rabet, Salima; Vila, Roger; Rodríguez-Arnaiz, Rosario; Castañeda-Sortibrán, América Nitxin

2018-01-01

Hybridization events are frequently demonstrated in natural butterfly populations. One interesting butterfly complex species is the Enantia jethys complex that has been studied for over a century; many debates exist regarding the species composition of this complex. Currently, three species that live sympatrically in the Gulf slope of Mexico (Enantia jethys, E. mazai, and E. albania) are recognized in this complex (based on morphological and molecular studies). Where these species live in sympatry, some cases of interspecific mating have been observed, suggesting hybridization events. Considering this, we employed a multilocus approach (analyses of mitochondrial and nuclear sequences: COI, RpS5, and Wg; and nuclear dominant markers: inter-simple sequence repeat (ISSRs) to study hybridization in sympatric populations from Veracruz, Mexico. Genetic diversity parameters were determined for all molecular markers, and species identification was assessed by different methods such as analyses of molecular variance (AMOVA), clustering, principal coordinate analysis (PCoA), gene flow, and PhiPT parameters. ISSR molecular markers were used for a more profound study of hybridization process. Although species of the Enantia jethys complex have a low dispersal capacity, we observed high genetic diversity, probably reflecting a high density of individuals locally. ISSR markers provided evidence of a contemporary hybridization process, detecting a high number of hybrids (from 17% to 53%) with significant differences in genetic diversity. Furthermore, a directional pattern of hybridization was observed from E. albania to other species. Phylogenetic study through DNA sequencing confirmed the existence of three clades corresponding to the three species previously recognized by morphological and molecular studies. This study underlines the importance of assessing hybridization in evolutionary studies, by tracing the lineage separation process that leads to the origin of new species. Our research demonstrates that hybridization processes have a high occurrence in natural populations.

Forming-free and self-rectifying resistive switching of the simple Pt/TaOx/n-Si structure for access device-free high-density memory application

NASA Astrophysics Data System (ADS)

Gao, Shuang; Zeng, Fei; Li, Fan; Wang, Minjuan; Mao, Haijun; Wang, Guangyue; Song, Cheng; Pan, Feng

2015-03-01

The search for self-rectifying resistive memories has aroused great attention due to their potential in high-density memory applications without additional access devices. Here we report the forming-free and self-rectifying bipolar resistive switching behavior of a simple Pt/TaOx/n-Si tri-layer structure. The forming-free phenomenon is attributed to the generation of a large amount of oxygen vacancies, in a TaOx region that is in close proximity to the TaOx/n-Si interface, via out-diffusion of oxygen ions from TaOx to n-Si. A maximum rectification ratio of ~6 × 102 is obtained when the Pt/TaOx/n-Si devices stay in a low resistance state, which originates from the existence of a Schottky barrier between the formed oxygen vacancy filament and the n-Si electrode. More importantly, numerical simulation reveals that the self-rectifying behavior itself can guarantee a maximum crossbar size of 212 × 212 (~44 kbit) on the premise of 10% read margin. Moreover, satisfactory switching uniformity and retention performance are observed based on this simple tri-layer structure. All of these results demonstrate the great potential of this simple Pt/TaOx/n-Si tri-layer structure for access device-free high-density memory applications.The search for self-rectifying resistive memories has aroused great attention due to their potential in high-density memory applications without additional access devices. Here we report the forming-free and self-rectifying bipolar resistive switching behavior of a simple Pt/TaOx/n-Si tri-layer structure. The forming-free phenomenon is attributed to the generation of a large amount of oxygen vacancies, in a TaOx region that is in close proximity to the TaOx/n-Si interface, via out-diffusion of oxygen ions from TaOx to n-Si. A maximum rectification ratio of ~6 × 102 is obtained when the Pt/TaOx/n-Si devices stay in a low resistance state, which originates from the existence of a Schottky barrier between the formed oxygen vacancy filament and the n-Si electrode. More importantly, numerical simulation reveals that the self-rectifying behavior itself can guarantee a maximum crossbar size of 212 × 212 (~44 kbit) on the premise of 10% read margin. Moreover, satisfactory switching uniformity and retention performance are observed based on this simple tri-layer structure. All of these results demonstrate the great potential of this simple Pt/TaOx/n-Si tri-layer structure for access device-free high-density memory applications. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr06406b

A ddRAD-based genetic map and its integration with the genome assembly of Japanese eel (Anguilla japonica) provides insights into genome evolution after the teleost-specific genome duplication

PubMed Central

2014-01-01

Background Recent advancements in next-generation sequencing technology have enabled cost-effective sequencing of whole or partial genomes, permitting the discovery and characterization of molecular polymorphisms. Double-digest restriction-site associated DNA sequencing (ddRAD-seq) is a powerful and inexpensive approach to developing numerous single nucleotide polymorphism (SNP) markers and constructing a high-density genetic map. To enrich genomic resources for Japanese eel (Anguilla japonica), we constructed a ddRAD-based genetic map using an Ion Torrent Personal Genome Machine and anchored scaffolds of the current genome assembly to 19 linkage groups of the Japanese eel. Furthermore, we compared the Japanese eel genome with genomes of model fishes to infer the history of genome evolution after the teleost-specific genome duplication. Results We generated the ddRAD-based linkage map of the Japanese eel, where the maps for female and male spanned 1748.8 cM and 1294.5 cM, respectively, and were arranged into 19 linkage groups. A total of 2,672 SNP markers and 115 Simple Sequence Repeat markers provide anchor points to 1,252 scaffolds covering 151 Mb (13%) of the current genome assembly of the Japanese eel. Comparisons among the Japanese eel, medaka, zebrafish and spotted gar genomes showed highly conserved synteny among teleosts and revealed part of the eight major chromosomal rearrangement events that occurred soon after the teleost-specific genome duplication. Conclusions The ddRAD-seq approach combined with the Ion Torrent Personal Genome Machine sequencing allowed us to conduct efficient and flexible SNP genotyping. The integration of the genetic map and the assembled sequence provides a valuable resource for fine mapping and positional cloning of quantitative trait loci associated with economically important traits and for investigating comparative genomics of the Japanese eel. PMID:24669946

A ddRAD-based genetic map and its integration with the genome assembly of Japanese eel (Anguilla japonica) provides insights into genome evolution after the teleost-specific genome duplication.

PubMed

Kai, Wataru; Nomura, Kazuharu; Fujiwara, Atushi; Nakamura, Yoji; Yasuike, Motoshige; Ojima, Nobuhiko; Masaoka, Tetsuji; Ozaki, Akiyuki; Kazeto, Yukinori; Gen, Koichiro; Nagao, Jiro; Tanaka, Hideki; Kobayashi, Takanori; Ototake, Mitsuru

2014-03-26

Recent advancements in next-generation sequencing technology have enabled cost-effective sequencing of whole or partial genomes, permitting the discovery and characterization of molecular polymorphisms. Double-digest restriction-site associated DNA sequencing (ddRAD-seq) is a powerful and inexpensive approach to developing numerous single nucleotide polymorphism (SNP) markers and constructing a high-density genetic map. To enrich genomic resources for Japanese eel (Anguilla japonica), we constructed a ddRAD-based genetic map using an Ion Torrent Personal Genome Machine and anchored scaffolds of the current genome assembly to 19 linkage groups of the Japanese eel. Furthermore, we compared the Japanese eel genome with genomes of model fishes to infer the history of genome evolution after the teleost-specific genome duplication. We generated the ddRAD-based linkage map of the Japanese eel, where the maps for female and male spanned 1748.8 cM and 1294.5 cM, respectively, and were arranged into 19 linkage groups. A total of 2,672 SNP markers and 115 Simple Sequence Repeat markers provide anchor points to 1,252 scaffolds covering 151 Mb (13%) of the current genome assembly of the Japanese eel. Comparisons among the Japanese eel, medaka, zebrafish and spotted gar genomes showed highly conserved synteny among teleosts and revealed part of the eight major chromosomal rearrangement events that occurred soon after the teleost-specific genome duplication. The ddRAD-seq approach combined with the Ion Torrent Personal Genome Machine sequencing allowed us to conduct efficient and flexible SNP genotyping. The integration of the genetic map and the assembled sequence provides a valuable resource for fine mapping and positional cloning of quantitative trait loci associated with economically important traits and for investigating comparative genomics of the Japanese eel.

High-Resolution Whole-Genome Sequencing Reveals That Specific Chromatin Domains from Most Human Chromosomes Associate with Nucleoli

PubMed Central

van Koningsbruggen, Silvana; Gierliński, Marek; Schofield, Pietá; Martin, David; Barton, Geoffey J.; Ariyurek, Yavuz; den Dunnen, Johan T.

2010-01-01

The nuclear space is mostly occupied by chromosome territories and nuclear bodies. Although this organization of chromosomes affects gene function, relatively little is known about the role of nuclear bodies in the organization of chromosomal regions. The nucleolus is the best-studied subnuclear structure and forms around the rRNA repeat gene clusters on the acrocentric chromosomes. In addition to rDNA, other chromatin sequences also surround the nucleolar surface and may even loop into the nucleolus. These additional nucleolar-associated domains (NADs) have not been well characterized. We present here a whole-genome, high-resolution analysis of chromatin endogenously associated with nucleoli. We have used a combination of three complementary approaches, namely fluorescence comparative genome hybridization, high-throughput deep DNA sequencing and photoactivation combined with time-lapse fluorescence microscopy. The data show that specific sequences from most human chromosomes, in addition to the rDNA repeat units, associate with nucleoli in a reproducible and heritable manner. NADs have in common a high density of AT-rich sequence elements, low gene density and a statistically significant enrichment in transcriptionally repressed genes. Unexpectedly, both the direct DNA sequencing and fluorescence photoactivation data show that certain chromatin loci can specifically associate with either the nucleolus, or the nuclear envelope. PMID:20826608

High-resolution whole-genome sequencing reveals that specific chromatin domains from most human chromosomes associate with nucleoli.

PubMed

van Koningsbruggen, Silvana; Gierlinski, Marek; Schofield, Pietá; Martin, David; Barton, Geoffey J; Ariyurek, Yavuz; den Dunnen, Johan T; Lamond, Angus I

2010-11-01

The nuclear space is mostly occupied by chromosome territories and nuclear bodies. Although this organization of chromosomes affects gene function, relatively little is known about the role of nuclear bodies in the organization of chromosomal regions. The nucleolus is the best-studied subnuclear structure and forms around the rRNA repeat gene clusters on the acrocentric chromosomes. In addition to rDNA, other chromatin sequences also surround the nucleolar surface and may even loop into the nucleolus. These additional nucleolar-associated domains (NADs) have not been well characterized. We present here a whole-genome, high-resolution analysis of chromatin endogenously associated with nucleoli. We have used a combination of three complementary approaches, namely fluorescence comparative genome hybridization, high-throughput deep DNA sequencing and photoactivation combined with time-lapse fluorescence microscopy. The data show that specific sequences from most human chromosomes, in addition to the rDNA repeat units, associate with nucleoli in a reproducible and heritable manner. NADs have in common a high density of AT-rich sequence elements, low gene density and a statistically significant enrichment in transcriptionally repressed genes. Unexpectedly, both the direct DNA sequencing and fluorescence photoactivation data show that certain chromatin loci can specifically associate with either the nucleolus, or the nuclear envelope.

Fuzzy cluster analysis of simple physicochemical properties of amino acids for recognizing secondary structure in proteins.

PubMed Central

Mocz, G.

1995-01-01

Fuzzy cluster analysis has been applied to the 20 amino acids by using 65 physicochemical properties as a basis for classification. The clustering products, the fuzzy sets (i.e., classical sets with associated membership functions), have provided a new measure of amino acid similarities for use in protein folding studies. This work demonstrates that fuzzy sets of simple molecular attributes, when assigned to amino acid residues in a protein's sequence, can predict the secondary structure of the sequence with reasonable accuracy. An approach is presented for discriminating standard folding states, using near-optimum information splitting in half-overlapping segments of the sequence of assigned membership functions. The method is applied to a nonredundant set of 252 proteins and yields approximately 73% matching for correctly predicted and correctly rejected residues with approximately 60% overall success rate for the correctly recognized ones in three folding states: alpha-helix, beta-strand, and coil. The most useful attributes for discriminating these states appear to be related to size, polarity, and thermodynamic factors. Van der Waals volume, apparent average thickness of surrounding molecular free volume, and a measure of dimensionless surface electron density can explain approximately 95% of prediction results. hydrogen bonding and hydrophobicity induces do not yet enable clear clustering and prediction. PMID:7549882

High-density ddRAD linkage and yield-related QTL mapping delimits a chromosomal region responsible for oil content in rapeseed (Brassica napus L.).

PubMed

Chen, Jun; Wang, Bo; Zhang, Yueli; Yue, Xiaopeng; Li, Zhaohong; Liu, Kede

2017-06-01

Rapeseed ( Brassica napus L.) is one of the most important oil crops almost all over the world. Seed-related traits, including oil content (OC), silique length (SL), seeds per silique (SS), and seed weight (SW), are primary targets for oil yield improvement. To dissect the genetic basis of these traits, 192 recombinant inbred lines (RILs) were derived from two parents with distinct oil content and silique length. High-density linkage map with a total length of 1610.4 cM were constructed using 1,329 double-digestion restriction site associated DNA (ddRAD) markers, 107 insertion/deletions (INDELs), and 90 well-distributed simple sequence repeats (SSRs) markers. A total of 37 consensus quantitative trait loci (QTLs) were detected for the four traits, with individual QTL explained 3.1-12.8% of the phenotypic variations. Interestingly, one OC consensus QTL ( cqOCA10b ) on chromosome A10 was consistently detected in all three environments, and explained 9.8% to 12.8% of the OC variation. The locus was further delimited into an approximately 614 kb genomic region, in which the flanking markers could be further evaluated for marker-assisted selection in rapeseed OC improvement and the candidate genes targeted for map-based cloning and genetic manipulation.

Asymmetric simple exclusion process with position-dependent hopping rates: Phase diagram from boundary-layer analysis.

PubMed

Mukherji, Sutapa

2018-03-01

In this paper, we study a one-dimensional totally asymmetric simple exclusion process with position-dependent hopping rates. Under open boundary conditions, this system exhibits boundary-induced phase transitions in the steady state. Similarly to totally asymmetric simple exclusion processes with uniform hopping, the phase diagram consists of low-density, high-density, and maximal-current phases. In various phases, the shape of the average particle density profile across the lattice including its boundary-layer parts changes significantly. Using the tools of boundary-layer analysis, we obtain explicit solutions for the density profile in different phases. A detailed analysis of these solutions under different boundary conditions helps us obtain the equations for various phase boundaries. Next, we show how the shape of the entire density profile including the location of the boundary layers can be predicted from the fixed points of the differential equation describing the boundary layers. We discuss this in detail through several examples of density profiles in various phases. The maximal-current phase appears to be an especially interesting phase where the boundary layer flows to a bifurcation point on the fixed-point diagram.

Asymmetric simple exclusion process with position-dependent hopping rates: Phase diagram from boundary-layer analysis

NASA Astrophysics Data System (ADS)

Mukherji, Sutapa

2018-03-01

In this paper, we study a one-dimensional totally asymmetric simple exclusion process with position-dependent hopping rates. Under open boundary conditions, this system exhibits boundary-induced phase transitions in the steady state. Similarly to totally asymmetric simple exclusion processes with uniform hopping, the phase diagram consists of low-density, high-density, and maximal-current phases. In various phases, the shape of the average particle density profile across the lattice including its boundary-layer parts changes significantly. Using the tools of boundary-layer analysis, we obtain explicit solutions for the density profile in different phases. A detailed analysis of these solutions under different boundary conditions helps us obtain the equations for various phase boundaries. Next, we show how the shape of the entire density profile including the location of the boundary layers can be predicted from the fixed points of the differential equation describing the boundary layers. We discuss this in detail through several examples of density profiles in various phases. The maximal-current phase appears to be an especially interesting phase where the boundary layer flows to a bifurcation point on the fixed-point diagram.

Nucleic acid arrays and methods of synthesis

DOEpatents

Sabanayagam, Chandran R.; Sano, Takeshi; Misasi, John; Hatch, Anson; Cantor, Charles

2001-01-01

The present invention generally relates to high density nucleic acid arrays and methods of synthesizing nucleic acid sequences on a solid surface. Specifically, the present invention contemplates the use of stabilized nucleic acid primer sequences immobilized on solid surfaces, and circular nucleic acid sequence templates combined with the use of isothermal rolling circle amplification to thereby increase nucleic acid sequence concentrations in a sample or on an array of nucleic acid sequences.

Development of expressed sequence tag-simple sequence repeat markers for genetic characterization and population structure analysis of Praxelis clematidea (Asteraceae).

PubMed

Wang, Q Z; Huang, M; Downie, S R; Chen, Z X

2016-05-23

Invasive plants tend to spread aggressively in new habitats and an understanding of their genetic diversity and population structure is useful for their management. In this study, expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed for the invasive plant species Praxelis clematidea (Asteraceae) from 5548 Stevia rebaudiana (Asteraceae) expressed sequence tags (ESTs). A total of 133 microsatellite-containing ESTs (2.4%) were identified, of which 56 (42.1%) were hexanucleotide repeat motifs and 50 (37.6%) were trinucleotide repeat motifs. Of the 24 primer pairs designed from these 133 ESTs, 7 (29.2%) resulted in significant polymorphisms. The number of alleles per locus ranged from 5 to 9. The relatively high genetic diversity (H = 0.2667, I = 0.4212, and P = 100%) of P. clematidea was related to high gene flow (Nm = 1.4996) among populations. The coefficient of population differentiation (GST = 0.2500) indicated that most genetic variation occurred within populations. A Mantel test suggested that there was significant correlation between genetic distance and geographical distribution (r = 0.3192, P = 0.012). These results further support the transferability of EST-SSR markers between closely related genera of the same family.

A high-density SNP genetic map consisting of a complete set of homologous groups in autohexaploid sweetpotato (Ipomoea batatas)

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

Shirasawa, Kenta; Tanaka, Masaru; Takahata, Yasuhiro

Sweetpotato (Ipomoea batatas) is an autohexaploid species with 90 chromosomes (2n = 6x = 90) and a basic chromosome number of 15, and is therefore regarded as one of the most challenging species for high-density genetic map construction. Here, we used single nucleotide polymorphisms (SNPs) identified by double-digest restriction site-associated DNA sequencing based on next-generation sequencing technology to construct a map for sweetpotato. We then aligned the sequence reads onto the reference genome sequence of I. trifida, a likely diploid ancestor of sweetpotato, to detect SNPs. In addition, to simplify analysis of the complex genetic mode of autohexaploidy, we usedmore » an S1 mapping population derived from self-pollination of a single parent. As a result, 28,087 double-simplex SNPs showing a Mendelian segregation ratio in the S1 progeny could be mapped onto 96 linkage groups (LGs), covering a total distance of 33,020.4 cM. Based on the positions of the SNPs on the I. trifida genome, the LGs were classified into 15 groups, each with roughly six LGs and six small extra groups. The molecular genetic techniques used in this study are applicable to high-density mapping of other polyploid plant species, including important crops.« less

A high-density SNP genetic map consisting of a complete set of homologous groups in autohexaploid sweetpotato (Ipomoea batatas)

DOE PAGES

Shirasawa, Kenta; Tanaka, Masaru; Takahata, Yasuhiro; ...

2017-03-10

Sweetpotato (Ipomoea batatas) is an autohexaploid species with 90 chromosomes (2n = 6x = 90) and a basic chromosome number of 15, and is therefore regarded as one of the most challenging species for high-density genetic map construction. Here, we used single nucleotide polymorphisms (SNPs) identified by double-digest restriction site-associated DNA sequencing based on next-generation sequencing technology to construct a map for sweetpotato. We then aligned the sequence reads onto the reference genome sequence of I. trifida, a likely diploid ancestor of sweetpotato, to detect SNPs. In addition, to simplify analysis of the complex genetic mode of autohexaploidy, we usedmore » an S1 mapping population derived from self-pollination of a single parent. As a result, 28,087 double-simplex SNPs showing a Mendelian segregation ratio in the S1 progeny could be mapped onto 96 linkage groups (LGs), covering a total distance of 33,020.4 cM. Based on the positions of the SNPs on the I. trifida genome, the LGs were classified into 15 groups, each with roughly six LGs and six small extra groups. The molecular genetic techniques used in this study are applicable to high-density mapping of other polyploid plant species, including important crops.« less

SSR_pipeline: a bioinformatic infrastructure for identifying microsatellites from paired-end Illumina high-throughput DNA sequencing data

USGS Publications Warehouse

Miller, Mark P.; Knaus, Brian J.; Mullins, Thomas D.; Haig, Susan M.

2013-01-01

SSR_pipeline is a flexible set of programs designed to efficiently identify simple sequence repeats (e.g., microsatellites) from paired-end high-throughput Illumina DNA sequencing data. The program suite contains 3 analysis modules along with a fourth control module that can automate analyses of large volumes of data. The modules are used to 1) identify the subset of paired-end sequences that pass Illumina quality standards, 2) align paired-end reads into a single composite DNA sequence, and 3) identify sequences that possess microsatellites (both simple and compound) conforming to user-specified parameters. The microsatellite search algorithm is extremely efficient, and we have used it to identify repeats with motifs from 2 to 25bp in length. Each of the 3 analysis modules can also be used independently to provide greater flexibility or to work with FASTQ or FASTA files generated from other sequencing platforms (Roche 454, Ion Torrent, etc.). We demonstrate use of the program with data from the brine fly Ephydra packardi (Diptera: Ephydridae) and provide empirical timing benchmarks to illustrate program performance on a common desktop computer environment. We further show that the Illumina platform is capable of identifying large numbers of microsatellites, even when using unenriched sample libraries and a very small percentage of the sequencing capacity from a single DNA sequencing run. All modules from SSR_pipeline are implemented in the Python programming language and can therefore be used from nearly any computer operating system (Linux, Macintosh, and Windows).

SSR_pipeline: a bioinformatic infrastructure for identifying microsatellites from paired-end Illumina high-throughput DNA sequencing data.

PubMed

Miller, Mark P; Knaus, Brian J; Mullins, Thomas D; Haig, Susan M

2013-01-01

SSR_pipeline is a flexible set of programs designed to efficiently identify simple sequence repeats (e.g., microsatellites) from paired-end high-throughput Illumina DNA sequencing data. The program suite contains 3 analysis modules along with a fourth control module that can automate analyses of large volumes of data. The modules are used to 1) identify the subset of paired-end sequences that pass Illumina quality standards, 2) align paired-end reads into a single composite DNA sequence, and 3) identify sequences that possess microsatellites (both simple and compound) conforming to user-specified parameters. The microsatellite search algorithm is extremely efficient, and we have used it to identify repeats with motifs from 2 to 25 bp in length. Each of the 3 analysis modules can also be used independently to provide greater flexibility or to work with FASTQ or FASTA files generated from other sequencing platforms (Roche 454, Ion Torrent, etc.). We demonstrate use of the program with data from the brine fly Ephydra packardi (Diptera: Ephydridae) and provide empirical timing benchmarks to illustrate program performance on a common desktop computer environment. We further show that the Illumina platform is capable of identifying large numbers of microsatellites, even when using unenriched sample libraries and a very small percentage of the sequencing capacity from a single DNA sequencing run. All modules from SSR_pipeline are implemented in the Python programming language and can therefore be used from nearly any computer operating system (Linux, Macintosh, and Windows).

Comparative fine mapping of the Wax 1 (W1) locus in hexaploid wheat.

PubMed

Lu, Ping; Qin, Jinxia; Wang, Guoxin; Wang, Lili; Wang, Zhenzhong; Wu, Qiuhong; Xie, Jingzhong; Liang, Yong; Wang, Yong; Zhang, Deyun; Sun, Qixin; Liu, Zhiyong

2015-08-01

By applying comparative genomics analyses, a high-density genetic linkage map of the Wax 1 ( W1 ) locus was constructed as a framework for map-based cloning. Glaucousness is described as the scattering effect of visible light from wax deposited on the cuticle of plant aerial organs. In wheat, the wax on leaves and stems is mainly controlled by two sets of genes: glaucousness loci (W1 and W2) and non-glaucousness loci (Iw1 and Iw2). Bulked segregant analysis (BSA) and simple sequence repeat (SSR) mapping showed that Wax1 (W1) is located on chromosome arm 2BS between markers Xgwm210 and Xbarc35. By applying comparative genomics analyses, colinearity genomic regions of the W1 locus on wheat 2BS were identified in Brachypodium distachyon chromosome 5, rice chromosome 4 and sorghum chromosome 6, respectively. Four STS markers were developed using the Triticum aestivum cv. Chinese Spring 454 contig sequences and the International Wheat Genome Sequencing Consortium (IWGSC) survey sequences. W1 was mapped into a 0.93 cM genetic interval flanked by markers XWGGC3197 and XWGGC2484, which has synteny with genomic regions of 56.5 kb in Brachypodium, 390 kb in rice and 31.8 kb in sorghum. The fine genetic map can serve as a framework for chromosome landing, physical mapping and map-based cloning of the W1 in wheat.

High-throughput sequencing of forensic genetic samples using punches of FTA cards with buccal swabs.

PubMed

Kampmann, Marie-Louise; Buchard, Anders; Børsting, Claus; Morling, Niels

2016-01-01

Here, we demonstrate that punches from buccal swab samples preserved on FTA cards can be used for high-throughput DNA sequencing, also known as massively parallel sequencing (MPS). We typed 44 reference samples with the HID-Ion AmpliSeq Identity Panel using washed 1.2 mm punches from FTA cards with buccal swabs and compared the results with those obtained with DNA extracted using the EZ1 DNA Investigator Kit. Concordant profiles were obtained for all samples. Our protocol includes simple punch, wash, and PCR steps, reducing cost and hands-on time in the laboratory. Furthermore, it facilitates automation of DNA sequencing.

Development of a high-density intra-specific linkage map of lettuce using genotyping by sequencing (GBS)

USDA-ARS?s Scientific Manuscript database

Genotyping by sequencing (GBS) has been developed as an affordable application of next-generation sequencing for the purposes of discovering and genotyping SNPs in a variety of crop species and populations. In this study we employed a double restriction enzyme digestion protocol (HindIII and NlaIII)...

Loblolly pine SSR markers for shortleaf pine genetics

Treesearch

C. Dana Nelson; Sedley Josserand; Craig S. Echt; Jeff Koppelman

2007-01-01

Simple sequence repeats (SSR) are highly informative DNA-based markers widely used in population genetic and linkage mapping studies. We have been developing PCR primer pairs for amplifying SSR markers for loblolly pine (Pinus taeda L.) using loblolly pine DNA and EST sequence data as starting materials. Fifty primer pairs known to reliably amplify...

The spatial distribution of fixed mutations within genes coding for proteins

NASA Technical Reports Server (NTRS)

Holmquist, R.; Goodman, M.; Conroy, T.; Czelusniak, J.

1983-01-01

An examination has been conducted of the extensive amino acid sequence data now available for five protein families - the alpha crystallin A chain, myoglobin, alpha and beta hemoglobin, and the cytochromes c - with the goal of estimating the true spatial distribution of base substitutions within genes that code for proteins. In every case the commonly used Poisson density failed to even approximate the experimental pattern of base substitution. For the 87 species of beta hemoglobin examined, for example, the probability that the observed results were from a Poisson process was the minuscule 10 to the -44th. Analogous results were obtained for the other functional families. All the data were reasonably, but not perfectly, described by the negative binomial density. In particular, most of the data were described by one of the very simple limiting forms of this density, the geometric density. The implications of this for evolutionary inference are discussed. It is evident that most estimates of total base substitutions between genes are badly in need of revision.

Density dependence in demography and dispersal generates fluctuating invasion speeds

PubMed Central

Li, Bingtuan; Miller, Tom E. X.

2017-01-01

Density dependence plays an important role in population regulation and is known to generate temporal fluctuations in population density. However, the ways in which density dependence affects spatial population processes, such as species invasions, are less understood. Although classical ecological theory suggests that invasions should advance at a constant speed, empirical work is illuminating the highly variable nature of biological invasions, which often exhibit nonconstant spreading speeds, even in simple, controlled settings. Here, we explore endogenous density dependence as a mechanism for inducing variability in biological invasions with a set of population models that incorporate density dependence in demographic and dispersal parameters. We show that density dependence in demography at low population densities—i.e., an Allee effect—combined with spatiotemporal variability in population density behind the invasion front can produce fluctuations in spreading speed. The density fluctuations behind the front can arise from either overcompensatory population growth or density-dependent dispersal, both of which are common in nature. Our results show that simple rules can generate complex spread dynamics and highlight a source of variability in biological invasions that may aid in ecological forecasting. PMID:28442569

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.

On the joint spectral density of bivariate random sequences. Thesis Technical Report No. 21

NASA Technical Reports Server (NTRS)

Aalfs, David D.

1995-01-01

For univariate random sequences, the power spectral density acts like a probability density function of the frequencies present in the sequence. This dissertation extends that concept to bivariate random sequences. For this purpose, a function called the joint spectral density is defined that represents a joint probability weighing of the frequency content of pairs of random sequences. Given a pair of random sequences, the joint spectral density is not uniquely determined in the absence of any constraints. Two approaches to constraining the sequences are suggested: (1) assume the sequences are the margins of some stationary random field, (2) assume the sequences conform to a particular model that is linked to the joint spectral density. For both approaches, the properties of the resulting sequences are investigated in some detail, and simulation is used to corroborate theoretical results. It is concluded that under either of these two constraints, the joint spectral density can be computed from the non-stationary cross-correlation.

Genetic diversity studies and identification of SSR markers associated with Fusarium wilt (Fusarium udum) resistance in cultivated pigeonpea (Cajanus cajan).

PubMed

Singh, A K; Rai, V P; Chand, R; Singh, R P; Singh, M N

2013-01-01

Genetic diversity and identification of simple sequence repeat markers correlated with Fusarium wilt resistance was performed in a set of 36 elite cultivated pigeonpea genotypes differing in levels of resistance to Fusarium wilt. Twenty-four polymorphic sequence repeat markers were screened across these genotypes, and amplified a total of 59 alleles with an average high polymorphic information content value of 0.52. Cluster analysis, done by UPGMA and PCA, grouped the 36 pigeonpea genotypes into two main clusters according to their Fusarium wilt reaction. Based on the Kruskal-Wallis ANOVA and simple regression analysis, six simple sequence repeat markers were found to be significantly associated with Fusarium wilt resistance. The phenotypic variation explained by these markers ranged from 23.7 to 56.4%. The present study helps in finding out feasibility of prescreened SSR markers to be used in genetic diversity analysis and their potential association with disease resistance.

Phonotactics, Neighborhood Activation, and Lexical Access for Spoken Words

PubMed Central

Vitevitch, Michael S.; Luce, Paul A.; Pisoni, David B.; Auer, Edward T.

2012-01-01

Probabilistic phonotactics refers to the relative frequencies of segments and sequences of segments in spoken words. Neighborhood density refers to the number of words that are phonologically similar to a given word. Despite a positive correlation between phonotactic probability and neighborhood density, nonsense words with high probability segments and sequences are responded to more quickly than nonsense words with low probability segments and sequences, whereas real words occurring in dense similarity neighborhoods are responded to more slowly than real words occurring in sparse similarity neighborhoods. This contradiction may be resolved by hypothesizing that effects of probabilistic phonotactics have a sublexical focus and that effects of similarity neighborhood density have a lexical focus. The implications of this hypothesis for models of spoken word recognition are discussed. PMID:10433774

Genome Wide Characterization of Simple Sequence Repeats in Cucumber

USDA-ARS?s Scientific Manuscript database

The whole genome sequence of the cucumber cultivar Gy14 was recently sequenced at 15× coverage with the Roche 454 Titanium technology. The microsatellite DNA sequences (simple sequence repeats, SSRs) in the assembled scaffolds were computationally explored and characterized. A total of 112,073 SSRs ...

Investigating ChaMPlane X-Ray Sources in the Galactic Bulge with Magellan LDSS2 Spectra

NASA Astrophysics Data System (ADS)

Koenig, Xavier; Grindlay, Jonathan E.; van den Berg, Maureen; Laycock, Silas; Zhao, Ping; Hong, JaeSub; Schlegel, Eric M.

2008-09-01

We have carried out optical and X-ray spectral analyses on a sample of 136 candidate optical counterparts of X-ray sources found in five Galactic bulge fields included in our Chandra Multiwavelength Plane Survey. We use a combination of optical spectral fitting and quantile X-ray analysis to obtain the hydrogen column density toward each object, and a three-dimensional dust model of the Galaxy to estimate the most probable distance in each case. We present the discovery of a population of stellar coronal emission sources, likely consisting of pre-main-sequence, young main-sequence, and main-sequence stars, as well as a component of active binaries of RS CVn or BY Dra type. We identify one candidate quiescent low-mass X-ray binary with a subgiant companion; we note that this object may also be an RS CVn system. We report the discovery of three new X-ray-detected cataclysmic variables (CVs) in the direction of the Galactic center (at distances lesssim2 kpc). This number is in excess of predictions made with a simple CV model based on a local CV space density of lesssim10-5 pc-3, and a scale height ~200 pc. We discuss several possible reasons for this observed excess.

A simple, rapid, high-fidelity and cost-effective PCR-based two-step DNA synthesis method for long gene sequences.

PubMed

Xiong, Ai-Sheng; Yao, Quan-Hong; Peng, Ri-He; Li, Xian; Fan, Hui-Qin; Cheng, Zong-Ming; Li, Yi

2004-07-07

Chemical synthesis of DNA sequences provides a powerful tool for modifying genes and for studying gene function, structure and expression. Here, we report a simple, high-fidelity and cost-effective PCR-based two-step DNA synthesis (PTDS) method for synthesis of long segments of DNA. The method involves two steps. (i) Synthesis of individual fragments of the DNA of interest: ten to twelve 60mer oligonucleotides with 20 bp overlap are mixed and a PCR reaction is carried out with high-fidelity DNA polymerase Pfu to produce DNA fragments that are approximately 500 bp in length. (ii) Synthesis of the entire sequence of the DNA of interest: five to ten PCR products from the first step are combined and used as the template for a second PCR reaction using high-fidelity DNA polymerase pyrobest, with the two outermost oligonucleotides as primers. Compared with the previously published methods, the PTDS method is rapid (5-7 days) and suitable for synthesizing long segments of DNA (5-6 kb) with high G + C contents, repetitive sequences or complex secondary structures. Thus, the PTDS method provides an alternative tool for synthesizing and assembling long genes with complex structures. Using the newly developed PTDS method, we have successfully obtained several genes of interest with sizes ranging from 1.0 to 5.4 kb.

Evolutionary Influenced Interaction Pattern as Indicator for the Investigation of Natural Variants Causing Nephrogenic Diabetes Insipidus

PubMed Central

Labudde, Dirk

2015-01-01

The importance of short membrane sequence motifs has been shown in many works and emphasizes the related sequence motif analysis. Together with specific transmembrane helix-helix interactions, the analysis of interacting sequence parts is helpful for understanding the process during membrane protein folding and in retaining the three-dimensional fold. Here we present a simple high-throughput analysis method for deriving mutational information of interacting sequence parts. Applied on aquaporin water channel proteins, our approach supports the analysis of mutational variants within different interacting subsequences and finally the investigation of natural variants which cause diseases like, for example, nephrogenic diabetes insipidus. In this work we demonstrate a simple method for massive membrane protein data analysis. As shown, the presented in silico analyses provide information about interacting sequence parts which are constrained by protein evolution. We present a simple graphical visualization medium for the representation of evolutionary influenced interaction pattern pairs (EIPPs) adapted to mutagen investigations of aquaporin-2, a protein whose mutants are involved in the rare endocrine disorder known as nephrogenic diabetes insipidus, and membrane proteins in general. Furthermore, we present a new method to derive new evolutionary variations within EIPPs which can be used for further mutagen laboratory investigations. PMID:26180540

Evolutionary Influenced Interaction Pattern as Indicator for the Investigation of Natural Variants Causing Nephrogenic Diabetes Insipidus.

PubMed

Grunert, Steffen; Labudde, Dirk

2015-01-01

The importance of short membrane sequence motifs has been shown in many works and emphasizes the related sequence motif analysis. Together with specific transmembrane helix-helix interactions, the analysis of interacting sequence parts is helpful for understanding the process during membrane protein folding and in retaining the three-dimensional fold. Here we present a simple high-throughput analysis method for deriving mutational information of interacting sequence parts. Applied on aquaporin water channel proteins, our approach supports the analysis of mutational variants within different interacting subsequences and finally the investigation of natural variants which cause diseases like, for example, nephrogenic diabetes insipidus. In this work we demonstrate a simple method for massive membrane protein data analysis. As shown, the presented in silico analyses provide information about interacting sequence parts which are constrained by protein evolution. We present a simple graphical visualization medium for the representation of evolutionary influenced interaction pattern pairs (EIPPs) adapted to mutagen investigations of aquaporin-2, a protein whose mutants are involved in the rare endocrine disorder known as nephrogenic diabetes insipidus, and membrane proteins in general. Furthermore, we present a new method to derive new evolutionary variations within EIPPs which can be used for further mutagen laboratory investigations.

A sequence-dependent rigid-base model of DNA

NASA Astrophysics Data System (ADS)

Gonzalez, O.; Petkevičiutė, D.; Maddocks, J. H.

2013-02-01

A novel hierarchy of coarse-grain, sequence-dependent, rigid-base models of B-form DNA in solution is introduced. The hierarchy depends on both the assumed range of energetic couplings, and the extent of sequence dependence of the model parameters. A significant feature of the models is that they exhibit the phenomenon of frustration: each base cannot simultaneously minimize the energy of all of its interactions. As a consequence, an arbitrary DNA oligomer has an intrinsic or pre-existing stress, with the level of this frustration dependent on the particular sequence of the oligomer. Attention is focussed on the particular model in the hierarchy that has nearest-neighbor interactions and dimer sequence dependence of the model parameters. For a Gaussian version of this model, a complete coarse-grain parameter set is estimated. The parameterized model allows, for an oligomer of arbitrary length and sequence, a simple and explicit construction of an approximation to the configuration-space equilibrium probability density function for the oligomer in solution. The training set leading to the coarse-grain parameter set is itself extracted from a recent and extensive database of a large number of independent, atomic-resolution molecular dynamics (MD) simulations of short DNA oligomers immersed in explicit solvent. The Kullback-Leibler divergence between probability density functions is used to make several quantitative assessments of our nearest-neighbor, dimer-dependent model, which is compared against others in the hierarchy to assess various assumptions pertaining both to the locality of the energetic couplings and to the level of sequence dependence of its parameters. It is also compared directly against all-atom MD simulation to assess its predictive capabilities. The results show that the nearest-neighbor, dimer-dependent model can successfully resolve sequence effects both within and between oligomers. For example, due to the presence of frustration, the model can successfully predict the nonlocal changes in the minimum energy configuration of an oligomer that are consequent upon a local change of sequence at the level of a single point mutation.

A sequence-dependent rigid-base model of DNA.

PubMed

Gonzalez, O; Petkevičiūtė, D; Maddocks, J H

2013-02-07

A novel hierarchy of coarse-grain, sequence-dependent, rigid-base models of B-form DNA in solution is introduced. The hierarchy depends on both the assumed range of energetic couplings, and the extent of sequence dependence of the model parameters. A significant feature of the models is that they exhibit the phenomenon of frustration: each base cannot simultaneously minimize the energy of all of its interactions. As a consequence, an arbitrary DNA oligomer has an intrinsic or pre-existing stress, with the level of this frustration dependent on the particular sequence of the oligomer. Attention is focussed on the particular model in the hierarchy that has nearest-neighbor interactions and dimer sequence dependence of the model parameters. For a Gaussian version of this model, a complete coarse-grain parameter set is estimated. The parameterized model allows, for an oligomer of arbitrary length and sequence, a simple and explicit construction of an approximation to the configuration-space equilibrium probability density function for the oligomer in solution. The training set leading to the coarse-grain parameter set is itself extracted from a recent and extensive database of a large number of independent, atomic-resolution molecular dynamics (MD) simulations of short DNA oligomers immersed in explicit solvent. The Kullback-Leibler divergence between probability density functions is used to make several quantitative assessments of our nearest-neighbor, dimer-dependent model, which is compared against others in the hierarchy to assess various assumptions pertaining both to the locality of the energetic couplings and to the level of sequence dependence of its parameters. It is also compared directly against all-atom MD simulation to assess its predictive capabilities. The results show that the nearest-neighbor, dimer-dependent model can successfully resolve sequence effects both within and between oligomers. For example, due to the presence of frustration, the model can successfully predict the nonlocal changes in the minimum energy configuration of an oligomer that are consequent upon a local change of sequence at the level of a single point mutation.

Liquid density analysis of sucrose and alcoholic beverages using polyimide guided Love-mode acoustic wave sensors

NASA Astrophysics Data System (ADS)

Turton, Andrew; Bhattacharyya, Debabrata; Wood, David

2006-02-01

A liquid density sensor using Love-mode acoustic waves has been developed which is suitable for use in the food and drinks industries. The sensor has an open flat surface allowing immersion into a sample and simple cleaning. A polyimide waveguide layer allows cheap and simple fabrication combined with a robust chemically resistant surface. The low shear modulus of polyimide allows thin guiding layers giving a high sensitivity. A dual structure with a smooth reference device exhibiting viscous coupling with the wave, and a patterned sense area to trap the liquid causing mass loading, allows discrimination of the liquid density from the square root of the density-viscosity product (ρη)0.5. Frequency shift and insertion loss change were proportional to (ρη)0.5 with a non-linear response due to the non-Newtonian nature of viscous liquids at high frequencies. Measurements were made with sucrose solutions up to 50% and different alcoholic drinks. A maximum sensitivity of 0.13 µg cm-3 Hz-1 was achieved, with a linear frequency response to density. This is the highest liquid density sensitivity obtained for acoustic mode sensors to the best of our knowledge.

A Simple and Efficient Method for Assembling TALE Protein Based on Plasmid Library

PubMed Central

Xu, Huarong; Xin, Ying; Zhang, Tingting; Ma, Lixia; Wang, Xin; Chen, Zhilong; Zhang, Zhiying

2013-01-01

DNA binding domain of the transcription activator-like effectors (TALEs) from Xanthomonas sp. consists of tandem repeats that can be rearranged according to a simple cipher to target new DNA sequences with high DNA-binding specificity. This technology has been successfully applied in varieties of species for genome engineering. However, assembling long TALE tandem repeats remains a big challenge precluding wide use of this technology. Although several new methodologies for efficiently assembling TALE repeats have been recently reported, all of them require either sophisticated facilities or skilled technicians to carry them out. Here, we described a simple and efficient method for generating customized TALE nucleases (TALENs) and TALE transcription factors (TALE-TFs) based on TALE repeat tetramer library. A tetramer library consisting of 256 tetramers covers all possible combinations of 4 base pairs. A set of unique primers was designed for amplification of these tetramers. PCR products were assembled by one step of digestion/ligation reaction. 12 TALE constructs including 4 TALEN pairs targeted to mouse Gt(ROSA)26Sor gene and mouse Mstn gene sequences as well as 4 TALE-TF constructs targeted to mouse Oct4, c-Myc, Klf4 and Sox2 gene promoter sequences were generated by using our method. The construction routines took 3 days and parallel constructions were available. The rate of positive clones during colony PCR verification was 64% on average. Sequencing results suggested that all TALE constructs were performed with high successful rate. This is a rapid and cost-efficient method using the most common enzymes and facilities with a high success rate. PMID:23840477

A simple and efficient method for assembling TALE protein based on plasmid library.

PubMed

Zhang, Zhiqiang; Li, Duo; Xu, Huarong; Xin, Ying; Zhang, Tingting; Ma, Lixia; Wang, Xin; Chen, Zhilong; Zhang, Zhiying

2013-01-01

DNA binding domain of the transcription activator-like effectors (TALEs) from Xanthomonas sp. consists of tandem repeats that can be rearranged according to a simple cipher to target new DNA sequences with high DNA-binding specificity. This technology has been successfully applied in varieties of species for genome engineering. However, assembling long TALE tandem repeats remains a big challenge precluding wide use of this technology. Although several new methodologies for efficiently assembling TALE repeats have been recently reported, all of them require either sophisticated facilities or skilled technicians to carry them out. Here, we described a simple and efficient method for generating customized TALE nucleases (TALENs) and TALE transcription factors (TALE-TFs) based on TALE repeat tetramer library. A tetramer library consisting of 256 tetramers covers all possible combinations of 4 base pairs. A set of unique primers was designed for amplification of these tetramers. PCR products were assembled by one step of digestion/ligation reaction. 12 TALE constructs including 4 TALEN pairs targeted to mouse Gt(ROSA)26Sor gene and mouse Mstn gene sequences as well as 4 TALE-TF constructs targeted to mouse Oct4, c-Myc, Klf4 and Sox2 gene promoter sequences were generated by using our method. The construction routines took 3 days and parallel constructions were available. The rate of positive clones during colony PCR verification was 64% on average. Sequencing results suggested that all TALE constructs were performed with high successful rate. This is a rapid and cost-efficient method using the most common enzymes and facilities with a high success rate.

A reference genetic map of C. clementina hort. ex Tan.; citrus evolution inferences from comparative mapping

PubMed Central

2012-01-01

Background Most modern citrus cultivars have an interspecific origin. As a foundational step towards deciphering the interspecific genome structures, a reference whole genome sequence was produced by the International Citrus Genome Consortium from a haploid derived from Clementine mandarin. The availability of a saturated genetic map of Clementine was identified as an essential prerequisite to assist the whole genome sequence assembly. Clementine is believed to be a ‘Mediterranean’ mandarin × sweet orange hybrid, and sweet orange likely arose from interspecific hybridizations between mandarin and pummelo gene pools. The primary goals of the present study were to establish a Clementine reference map using codominant markers, and to perform comparative mapping of pummelo, sweet orange, and Clementine. Results Five parental genetic maps were established from three segregating populations, which were genotyped with Single Nucleotide Polymorphism (SNP), Simple Sequence Repeats (SSR) and Insertion-Deletion (Indel) markers. An initial medium density reference map (961 markers for 1084.1 cM) of the Clementine was established by combining male and female Clementine segregation data. This Clementine map was compared with two pummelo maps and a sweet orange map. The linear order of markers was highly conserved in the different species. However, significant differences in map size were observed, which suggests a variation in the recombination rates. Skewed segregations were much higher in the male than female Clementine mapping data. The mapping data confirmed that Clementine arose from hybridization between ‘Mediterranean’ mandarin and sweet orange. The results identified nine recombination break points for the sweet orange gamete that contributed to the Clementine genome. Conclusions A reference genetic map of citrus, used to facilitate the chromosome assembly of the first citrus reference genome sequence, was established. The high conservation of marker order observed at the interspecific level should allow reasonable inferences of most citrus genome sequences by mapping next-generation sequencing (NGS) data in the reference genome sequence. The genome of the haploid Clementine used to establish the citrus reference genome sequence appears to have been inherited primarily from the ‘Mediterranean’ mandarin. The high frequency of skewed allelic segregations in the male Clementine data underline the probable extent of deviation from Mendelian segregation for characters controlled by heterozygous loci in male parents. PMID:23126659

High-density carbon nanotube buckypapers with superior transport and mechanical properties.

PubMed

Zhang, Ling; Zhang, Guang; Liu, Changhong; Fan, Shoushan

2012-09-12

High-density buckypapers were obtained by using well-aligned carbon nanotube arrays. The density of the buckypapers was as high as 1.39 g cm(-3), which is close to the ultimate density of ideal buckypapers. Then we measured the transport and mechanical properties of the buckypapers. Our results demonstrated that its electrical and thermal conductivities could be almost linearly improved by increasing its density. In particular, its superior thermal conductivity is nearly twice that of common metals, which enables it a lightweight and more efficient heat-transfer materials. The Young's modulus of the buckypapers could reach a magnitude over 2 GPa, which is greatly improved compared with previous reported results. In view of this, our work provided a simple and convenient method to prepare high-density buckypapers with excellent transport and mechanical properties.

Efficient self-assembly of DNA-functionalized fluorophores and gold nanoparticles with DNA functionalized silicon surfaces: the effect of oligomer spacers

PubMed Central

Milton, James A.; Patole, Samson; Yin, Huabing; Xiao, Qiang; Brown, Tom; Melvin, Tracy

2013-01-01

Although strategies for the immobilization of DNA oligonucleotides onto surfaces for bioanalytical and top-down bio-inspired nanobiofabrication approaches are well developed, the effect of introducing spacer molecules between the surface and the DNA oligonucleotide for the hybridization of nanoparticle–DNA conjugates has not been previously assessed in a quantitative manner. The hybridization efficiency of DNA oligonucleotides end-labelled with gold nanoparticles (1.4 or 10 nm diameter) with DNA sequences conjugated to silicon surfaces via hexaethylene glycol phosphate diester oligomer spacers (0, 1, 2, 6 oligomers) was found to be independent of spacer length. To quantify both the density of DNA strands attached to the surfaces and hybridization with the surface-attached DNA, new methodologies have been developed. Firstly, a simple approach based on fluorescence has been developed for determination of the immobilization density of DNA oligonucleotides. Secondly, an approach using mass spectrometry has been created to establish (i) the mean number of DNA oligonucleotides attached to the gold nanoparticles and (ii) the hybridization density of nanoparticle–oligonucleotide conjugates with the silicon surface–attached complementary sequence. These methods and results will be useful for application with nanosensors, the self-assembly of nanoelectronic devices and the attachment of nanoparticles to biomolecules for single-molecule biophysical studies. PMID:23361467

Detecting very low allele fraction variants using targeted DNA sequencing and a novel molecular barcode-aware variant caller.

PubMed

Xu, Chang; Nezami Ranjbar, Mohammad R; Wu, Zhong; DiCarlo, John; Wang, Yexun

2017-01-03

Detection of DNA mutations at very low allele fractions with high accuracy will significantly improve the effectiveness of precision medicine for cancer patients. To achieve this goal through next generation sequencing, researchers need a detection method that 1) captures rare mutation-containing DNA fragments efficiently in the mix of abundant wild-type DNA; 2) sequences the DNA library extensively to deep coverage; and 3) distinguishes low level true variants from amplification and sequencing errors with high accuracy. Targeted enrichment using PCR primers provides researchers with a convenient way to achieve deep sequencing for a small, yet most relevant region using benchtop sequencers. Molecular barcoding (or indexing) provides a unique solution for reducing sequencing artifacts analytically. Although different molecular barcoding schemes have been reported in recent literature, most variant calling has been done on limited targets, using simple custom scripts. The analytical performance of barcode-aware variant calling can be significantly improved by incorporating advanced statistical models. We present here a highly efficient, simple and scalable enrichment protocol that integrates molecular barcodes in multiplex PCR amplification. In addition, we developed smCounter, an open source, generic, barcode-aware variant caller based on a Bayesian probabilistic model. smCounter was optimized and benchmarked on two independent read sets with SNVs and indels at 5 and 1% allele fractions. Variants were called with very good sensitivity and specificity within coding regions. We demonstrated that we can accurately detect somatic mutations with allele fractions as low as 1% in coding regions using our enrichment protocol and variant caller.

High-Throughput Analysis of T-DNA Location and Structure Using Sequence Capture.

PubMed

Inagaki, Soichi; Henry, Isabelle M; Lieberman, Meric C; Comai, Luca

2015-01-01

Agrobacterium-mediated transformation of plants with T-DNA is used both to introduce transgenes and for mutagenesis. Conventional approaches used to identify the genomic location and the structure of the inserted T-DNA are laborious and high-throughput methods using next-generation sequencing are being developed to address these problems. Here, we present a cost-effective approach that uses sequence capture targeted to the T-DNA borders to select genomic DNA fragments containing T-DNA-genome junctions, followed by Illumina sequencing to determine the location and junction structure of T-DNA insertions. Multiple probes can be mixed so that transgenic lines transformed with different T-DNA types can be processed simultaneously, using a simple, index-based pooling approach. We also developed a simple bioinformatic tool to find sequence read pairs that span the junction between the genome and T-DNA or any foreign DNA. We analyzed 29 transgenic lines of Arabidopsis thaliana, each containing inserts from 4 different T-DNA vectors. We determined the location of T-DNA insertions in 22 lines, 4 of which carried multiple insertion sites. Additionally, our analysis uncovered a high frequency of unconventional and complex T-DNA insertions, highlighting the needs for high-throughput methods for T-DNA localization and structural characterization. Transgene insertion events have to be fully characterized prior to use as commercial products. Our method greatly facilitates the first step of this characterization of transgenic plants by providing an efficient screen for the selection of promising lines.

Single Nucleotide Polymorphism Markers for Genetic Mapping in Drosophila melanogaster

PubMed Central

Hoskins, Roger A.; Phan, Alexander C.; Naeemuddin, Mohammed; Mapa, Felipa A.; Ruddy, David A.; Ryan, Jessica J.; Young, Lynn M.; Wells, Trent; Kopczynski, Casey; Ellis, Michael C.

2001-01-01

For nearly a century, genetic analysis in Drosophila melanogaster has been a powerful tool for analyzing gene function, yet Drosophila lacks the molecular genetic mapping tools that recently have revolutionized human, mouse, and plant genetics. Here, we describe the systematic characterization of a dense set of molecular markers in Drosophila by using a sequence tagged site-based physical map of the genome. We identify 474 biallelic markers in standard laboratory strains of Drosophila that span the genome. Most of these markers are single nucleotide polymorphisms and sequences for these variants are provided in an accessible format. The average density of the new markers is one per 225 kb on the autosomes and one per megabase on the X chromosome. We include in this survey a set of P-element strains that provide additional use for high-resolution mapping. We show one application of the new markers in a simple set of crosses to map a mutation in the hedgehog gene to an interval of <1 Mb. This new map resource significantly increases the efficiency and resolution of recombination mapping and will be of immediate value to the Drosophila research community. PMID:11381036

Query-seeded iterative sequence similarity searching improves selectivity 5–20-fold

PubMed Central

Li, Weizhong; Lopez, Rodrigo

2017-01-01

Abstract Iterative similarity search programs, like psiblast, jackhmmer, and psisearch, are much more sensitive than pairwise similarity search methods like blast and ssearch because they build a position specific scoring model (a PSSM or HMM) that captures the pattern of sequence conservation characteristic to a protein family. But models are subject to contamination; once an unrelated sequence has been added to the model, homologs of the unrelated sequence will also produce high scores, and the model can diverge from the original protein family. Examination of alignment errors during psiblast PSSM contamination suggested a simple strategy for dramatically reducing PSSM contamination. psiblast PSSMs are built from the query-based multiple sequence alignment (MSA) implied by the pairwise alignments between the query model (PSSM, HMM) and the subject sequences in the library. When the original query sequence residues are inserted into gapped positions in the aligned subject sequence, the resulting PSSM rarely produces alignment over-extensions or alignments to unrelated sequences. This simple step, which tends to anchor the PSSM to the original query sequence and slightly increase target percent identity, can reduce the frequency of false-positive alignments more than 20-fold compared with psiblast and jackhmmer, with little loss in search sensitivity. PMID:27923999

Typing of artiodactyl MHC-DRB genes with the help of intronic simple repeated DNA sequences.

PubMed

Schwaiger, F W; Buitkamp, J; Weyers, E; Epplen, J T

1993-02-01

An efficient oligonucleotide typing method for the highly polymorphic MHC-DRB genes is described for artiodactyls like cattle, sheep and goat. By means of the polymerase chain reaction, the second exon of MHC-DRB is amplified as well as part of the adjacent intron containing a mixed simple repeat sequence. Using this primer combination we were able to amplify the MHC-DRB exons 2 and adjacent introns from all of the investigated 10 species of the family of Bovidae and giraffes. Therefore, the DRB genes of novel artiodactyl species can also be readily studied. Oligonucleotide probes specific for the polymorphisms of ungulate DRB genes are used with which sequences differing in at least one single base can be distinguished. Exonic polymorphism was found to be correlated with the allele lengths and the patterns of the repeat structures. Hence oligonucleotide probes specific for different simple repeats and polymorphic positions serve also for typing across species barriers. The strict correlation of sequence length and exonic polymorphism permits a preselection of specific oligonucleotides for hybridization. Thus more than 20 alleles can already be differentiated from each of the three species.

Experiment and mathematical model for the heat transfer in water around 4 °C

NASA Astrophysics Data System (ADS)

Ogawa, Naohisa; Kaneko, Fumitoshi

2017-03-01

Water, which is the habitat for a variety of living creatures, has a maximum density at 4.0 °C. This crucial property is considered to play a very important role in the biology of a lake and also has a close relationship with the areas of environmentology and geoscience. It would be desirable for students to confirm this important property of water themselves by carrying out simple experiments. However, it is not easy to detect the maximum density at 4.0 °C because the temperature dependence of the water density is very small close to its freezing point. For example, the density of water is 0.999 975 g cm-3 at 4.0 °C and 0.999 850 g cm-3 at 0.1 °C. The aim in this manuscript is to demonstrate a simple experiment to detect 4.0 °C as the temperature of maximum density, in which the time dependence of the water temperature is measured at several different depths by chilling the water surface. This is a simple experiment that can also be performed by high school students. We also present a mathematical model that can explain the results of this experiment.

Genotyping-by-Sequencing derived High-Density Linkage Map and its Application to QTL Mapping of Flag Leaf Traits in Bread Wheat

USDA-ARS?s Scientific Manuscript database

Hard red winter wheat parents ‘Harry’ (drought tolerant) and ‘Wesley’ (drought susceptible) was used to develop a recombinant inbred population to identify genomic regions associated with drought and adaptation. To precisely map genomic regions high-density linkage maps are a prerequisite. In this s...

Development and evaluation of a high density genotyping 'Axiom_Arachis' array with 58K SNPs for accelerating genetics and breeding in groundnut

USDA-ARS?s Scientific Manuscript database

Single nucleotide polymorphisms (SNPs) are the most abundant DNA sequence variation in the genomes which can be used to associate genotypic variation to the phenotype. Therefore, availability of a high-density SNP array with uniform genome coverage can advance genetic studies and breeding applicatio...

Application of multi-criteria decision analysis in prediction of groundwater resources potential: A case of Oke-Ana, Ilesa Area Southwestern, Nigeria

NASA Astrophysics Data System (ADS)

Akinlalu, A. A.; Adegbuyiro, A.; Adiat, K. A. N.; Akeredolu, B. E.; Lateef, W. Y.

2017-06-01

Groundwater Potential of Oke-Ana area southwestern Nigeria have been evaluated using the integration of electrical resistivity method, remote sensing and geographic information systems. The effect of five hydrogeological indices, namely lineament density, drainage density, lithology, overburden thickness and aquifer layer resistivity on groundwater occurrence was established. Multi-criteria decision analysis technique was employed to assign weight to each of the index using the concept of analytical hierarchy process. The assigned weight was normalized and consistency ratio was established. In order to evaluate the groundwater potential of Oke-Ana, sixty-seven (67) vertical electrical sounding points were occupied. Ten curve types were delineated in the study area. The curve types vary from simple three layer A and H-type curves to the more complex four, five and six layer AA, HA, KH, QH, AKH, HKH, KHA and KHKH curves. Four subsurface geo-electric sequences of top soil, weathered layer, partially weathered/fractured basement and the fresh basement were delineated in the area. The analytical process assisted in classifying Oke-Ana into, low, medium and high groundwater potential zones. Validation of the model from well information and two aborted boreholes suggest 70% agreement.

Using specific length amplified fragment sequencing to construct the high-density genetic map for Vitis (Vitis vinifera L. × Vitis amurensis Rupr.).

PubMed

Guo, Yinshan; Shi, Guangli; Liu, Zhendong; Zhao, Yuhui; Yang, Xiaoxu; Zhu, Junchi; Li, Kun; Guo, Xiuwu

2015-01-01

In this study, 149 F1 plants from the interspecific cross between 'Red Globe' (Vitis vinifera L.) and 'Shuangyou' (Vitis amurensis Rupr.) and the parent were used to construct a molecular genetic linkage map by using the specific length amplified fragment sequencing technique. DNA sequencing generated 41.282 Gb data consisting of 206,411,693 paired-end reads. The average sequencing depths were 68.35 for 'Red Globe,' 63.65 for 'Shuangyou,' and 8.01 for each progeny. In all, 115,629 high-quality specific length amplified fragments were detected, of which 42,279 were polymorphic. The genetic map was constructed using 7,199 of these polymorphic markers. These polymorphic markers were assigned to 19 linkage groups; the total length of the map was 1929.13 cm, with an average distance of 0.28 cm between each maker. To our knowledge, the genetic maps constructed in this study contain the largest number of molecular markers. These high-density genetic maps might form the basis for the fine quantitative trait loci mapping and molecular-assisted breeding of grape.

Daytime Sleep Enhances Consolidation of the Spatial but Not Motoric Representation of Motor Sequence Memory

PubMed Central

Albouy, Geneviève; Fogel, Stuart; Pottiez, Hugo; Nguyen, Vo An; Ray, Laura; Lungu, Ovidiu; Carrier, Julie; Robertson, Edwin; Doyon, Julien

2013-01-01

Motor sequence learning is known to rely on more than a single process. As the skill develops with practice, two different representations of the sequence are formed: a goal representation built under spatial allocentric coordinates and a movement representation mediated through egocentric motor coordinates. This study aimed to explore the influence of daytime sleep (nap) on consolidation of these two representations. Through the manipulation of an explicit finger sequence learning task and a transfer protocol, we show that both allocentric (spatial) and egocentric (motor) representations of the sequence can be isolated after initial training. Our results also demonstrate that nap favors the emergence of offline gains in performance for the allocentric, but not the egocentric representation, even after accounting for fatigue effects. Furthermore, sleep-dependent gains in performance observed for the allocentric representation are correlated with spindle density during non-rapid eye movement (NREM) sleep of the post-training nap. In contrast, performance on the egocentric representation is only maintained, but not improved, regardless of the sleep/wake condition. These results suggest that motor sequence memory acquisition and consolidation involve distinct mechanisms that rely on sleep (and specifically, spindle) or simple passage of time, depending respectively on whether the sequence is performed under allocentric or egocentric coordinates. PMID:23300993

Next Generation Mapping of Enological Traits in an F2 Interspecific Grapevine Hybrid Family

PubMed Central

Sun, Qi; Manns, David C.; Sacks, Gavin L.; Mansfield, Anna Katharine; Luby, James J.; Londo, Jason P.; Reisch, Bruce I.; Cadle-Davidson, Lance E.; Fennell, Anne Y.

2016-01-01

In winegrapes (Vitis spp.), fruit quality traits such as berry color, total soluble solids content (SS), malic acid content (MA), and yeast assimilable nitrogen (YAN) affect fermentation or wine quality, and are important traits in selecting new hybrid winegrape cultivars. Given the high genetic diversity and heterozygosity of Vitis species and their tendency to exhibit inbreeding depression, linkage map construction and quantitative trait locus (QTL) mapping has relied on F1 families with the use of simple sequence repeat (SSR) and other markers. This study presents the construction of a genetic map by single nucleotide polymorphisms identified through genotyping-by-sequencing (GBS) technology in an F2 mapping family of 424 progeny derived from a cross between the wild species V. riparia Michx. and the interspecific hybrid winegrape cultivar, ‘Seyval’. The resulting map has 1449 markers spanning 2424 cM in genetic length across 19 linkage groups, covering 95% of the genome with an average distance between markers of 1.67 cM. Compared to an SSR map previously developed for this F2 family, these results represent an improved map covering a greater portion of the genome with higher marker density. The accuracy of the map was validated using the well-studied trait berry color. QTL affecting YAN, MA and SS related traits were detected. A joint MA and SS QTL spans a region with candidate genes involved in the malate metabolism pathway. We present an analytical pipeline for calling intercross GBS markers and a high-density linkage map for a large F2 family of the highly heterozygous Vitis genus. This study serves as a model for further genetic investigations of the molecular basis of additional unique characters of North American hybrid wine cultivars and to enhance the breeding process by marker-assisted selection. The GBS protocols for identifying intercross markers developed in this study can be adapted for other heterozygous species. PMID:26974672

A note on coarse-grained gravity-flow deposits within proterozoic lacustrine sedimentary rocks, Transvaal sequence, South Africa

NASA Astrophysics Data System (ADS)

Eriksson, P. G.

A widely developed, thin, coarse-matrix conglomerate occurs within early Proterozoic lacustrine mudrocks in the Transvaal Sequence, South Africa. The poorly sorted tabular chert clasts, alternation of a planar clast fabric with disorientated zones, plus normal and inverse grading in the former rock type suggest deposition by density-modified grain-flow and high density turbidity currents. The lower fan-delta slope palæenvironment inferred for the conglomerate is consistent with the lacustrine interpretation for the enclosing mudrock facies. This intracratonic setting contrasts with the marine environment generally associated with density-modified grain-flow deposits.

Friction on the Bond and the Vibrational Relaxation in Simple Liquids.

NASA Astrophysics Data System (ADS)

Mishra, Bimalendu Kumar

In chapter 1, the energy relaxation of a stiff Morse oscillator dissolved in a simple LJ fluid is calculated using a reversible integrator (r-RESPA) in molecular dynamics generated from the Trotter factorization of the classical propagator. We compare the "real" relaxation from full MD simulations with that predicted by the Generalized Langevin Equation (GLE) with memory friction determined from the full Molecular Dynamics for a series of fluid densities. It is found that the GLE gives very good agreement with MD for the vibrational energy relaxation for this nonlinear oscillator far from equilibrium only for high density fluids, but reduced densities rho < 0.5 the energy relaxation from the MD simulation becomes considered slower than that from the GLE. An analysis of the statistical properties of the random force shows that as the density is lowered the non-Gaussian behavior of the random force becomes more prominent. This behavior is consistent with a simple model in which the oscillator undergoes generalized Langevin dynamics between strong binary collisions with solvent atoms. In chapter 2, molecular hydrodynamics is used to calculate the memory friction on the intramolecular vibrational coordinate of a homonuclear diatomic molecule dissolved in a simple liquid. The predicted memory friction is then compared to recent computer experiments. Agreement with the experimental memory functions is obtained when the linearized hydrodynamics is modified to include gaussian viscoelasticity and compressibility. The hydrodynamic friction on the bond appears to agree qualitatively very well, although quantitative agreement is not found at high frequencies. Various limits of the hydrodynamic friction are discussed.

Construction of a high-density genetic map for grape using specific length amplified fragment (SLAF) sequencing

PubMed Central

Guo, Yinshan; Xing, Huiyang; Zhao, Yuhui; Liu, Zhendong; Li, Kun; Guo, Xiuwu

2017-01-01

Genetic maps are important tools in plant genomics and breeding. We report a large-scale discovery of single nucleotide polymorphisms (SNPs) using the specific length amplified fragment sequencing (SLAF-seq) technique for the construction of high-density genetic maps for two elite wine grape cultivars, ‘Chardonnay’ and ‘Beibinghong’, and their 130 F1 plants. A total of 372.53 M paired-end reads were obtained after preprocessing. The average sequencing depth was 33.81 for ‘Chardonnay’ (the female parent), 48.20 for ‘Beibinghong’ (the male parent), and 12.66 for the F1 offspring. We detected 202,349 high-quality SLAFs of which 144,972 were polymorphic; 10,042 SNPs were used to construct a genetic map that spanned 1,969.95 cM, with an average genetic distance of 0.23 cM between adjacent markers. This genetic map contains the largest molecular marker number of the grape maps so far reported. We thus demonstrate that SLAF-seq is a promising strategy for the construction of high-density genetic maps; the map that we report here is a good potential resource for QTL mapping of genes linked to major economic and agronomic traits, map-based cloning, and marker-assisted selection of grape. PMID:28746364

A high-density genetic map and QTL analysis of agronomic traits in foxtail millet [Setaria italica (L.) P. Beauv.] using RAD-seq.

PubMed

Wang, Jun; Wang, Zhilan; Du, Xiaofen; Yang, Huiqing; Han, Fang; Han, Yuanhuai; Yuan, Feng; Zhang, Linyi; Peng, Shuzhong; Guo, Erhu

2017-01-01

Foxtail millet (Setaria italica), a very important grain crop in China, has become a new model plant for cereal crops and biofuel grasses. Although its reference genome sequence was released recently, quantitative trait loci (QTLs) controlling complex agronomic traits remains limited. The development of massively parallel genotyping methods and next-generation sequencing technologies provides an excellent opportunity for developing single-nucleotide polymorphisms (SNPs) for linkage map construction and QTL analysis of complex quantitative traits. In this study, a high-throughput and cost-effective RAD-seq approach was employed to generate a high-density genetic map for foxtail millet. A total of 2,668,587 SNP loci were detected according to the reference genome sequence; meanwhile, 9,968 SNP markers were used to genotype 124 F2 progenies derived from the cross between Hongmiaozhangu and Changnong35; a high-density genetic map spanning 1648.8 cM, with an average distance of 0.17 cM between adjacent markers was constructed; 11 major QTLs for eight agronomic traits were identified; five co-dominant DNA markers were developed. These findings will be of value for the identification of candidate genes and marker-assisted selection in foxtail millet.

A high-density genetic map and QTL analysis of agronomic traits in foxtail millet [Setaria italica (L.) P. Beauv.] using RAD-seq

PubMed Central

Wang, Zhilan; Du, Xiaofen; Yang, Huiqing; Han, Fang; Han, Yuanhuai; Yuan, Feng; Zhang, Linyi; Peng, Shuzhong; Guo, Erhu

2017-01-01

Foxtail millet (Setaria italica), a very important grain crop in China, has become a new model plant for cereal crops and biofuel grasses. Although its reference genome sequence was released recently, quantitative trait loci (QTLs) controlling complex agronomic traits remains limited. The development of massively parallel genotyping methods and next-generation sequencing technologies provides an excellent opportunity for developing single-nucleotide polymorphisms (SNPs) for linkage map construction and QTL analysis of complex quantitative traits. In this study, a high-throughput and cost-effective RAD-seq approach was employed to generate a high-density genetic map for foxtail millet. A total of 2,668,587 SNP loci were detected according to the reference genome sequence; meanwhile, 9,968 SNP markers were used to genotype 124 F2 progenies derived from the cross between Hongmiaozhangu and Changnong35; a high-density genetic map spanning 1648.8 cM, with an average distance of 0.17 cM between adjacent markers was constructed; 11 major QTLs for eight agronomic traits were identified; five co-dominant DNA markers were developed. These findings will be of value for the identification of candidate genes and marker-assisted selection in foxtail millet. PMID:28644843

Plant genotyping using fluorescently tagged inter-simple sequence repeats (ISSRs): basic principles and methodology.

PubMed

Prince, Linda M

2015-01-01

Inter-simple sequence repeat PCR (ISSR-PCR) is a fast, inexpensive genotyping technique based on length variation in the regions between microsatellites. The method requires no species-specific prior knowledge of microsatellite location or composition. Very small amounts of DNA are required, making this method ideal for organisms of conservation concern, or where the quantity of DNA is extremely limited due to organism size. ISSR-PCR can be highly reproducible but requires careful attention to detail. Optimization of DNA extraction, fragment amplification, and normalization of fragment peak heights during fluorescent detection are critical steps to minimizing the downstream time spent verifying and scoring the data.

The undatables: Quantifying uncertainty in a highly expanded Late Glacial-Holocene sediment sequence recovered from the deepest Baltic Sea basin—IODP Site M0063

NASA Astrophysics Data System (ADS)

Obrochta, S. P.; Andrén, T.; Fazekas, S. Z.; Lougheed, B. C.; Snowball, I.; Yokoyama, Y.; Miyairi, Y.; Kondo, R.; Kotilainen, A. T.; Hyttinen, O.; Fehr, A.

2017-03-01

Laminated, organic-rich silts and clays with high dissolved gas content characterize sediments at IODP Site M0063 in the Landsort Deep, which at 459 m is the deepest basin in the Baltic Sea. Cores recovered from Hole M0063A experienced significant expansion as gas was released during the recovery process, resulting in high sediment loss. Therefore, during operations at subsequent holes, penetration was reduced to 2 m per 3.3 m core, permitting expansion into 1.3 m of initially empty liner. Fully filled liners were recovered from Holes B through E, indicating that the length of recovered intervals exceeded the penetrated distance by a factor of >1.5. A typical down-core logarithmic trend in gamma density profiles, with anomalously low-density values within the upper ˜1 m of each core, suggests that expansion primarily occurred in this upper interval. Thus, we suggest that a simple linear correction is inappropriate. This interpretation is supported by anisotropy of magnetic susceptibility data that indicate vertical stretching in the upper ˜1.5 m of expanded cores. Based on the mean gamma density profiles of cores from Holes M0063C and D, we obtain an expansion function that is used to adjust the depth of each core to conform to its known penetration. The variance in these profiles allows for quantification of uncertainty in the adjusted depth scale. Using a number of bulk 14C dates, we explore how the presence of multiple carbon source pathways leads to poorly constrained radiocarbon reservoir age variability that significantly affects age and sedimentation rate calculations.

Intermittency in the Helimak, a simple magnetic torus

NASA Astrophysics Data System (ADS)

Taylor, E. I.; Rowan, W. L.; Gentle, K. W.; Horton, W.; Bernard, T.

2017-10-01

Irregularly-spaced, large-amplitude bursts are observed in the Helimak plasma turbulence with sufficient definition to investigate their physical basis and possibly improve understanding of the induced particle transport. The Helimak is an experimental realization of a sheared cylindrical slab that generates and heats a plasma with microwaves and confines it in a helical magnetic field. Although it is MHD stable, the plasma is always in a nonlinearly saturated state of microturbulence. The intermittency in this turbulence manifests itself in highly skewed PDFs of the normalized electron density. Cross-conditional averaging exposes large amplitude structures propagating down the density gradient at a few hundred meters per second. Introduction of a radial electric field via bias plates appears to suppress these intermittent transport events (ITEs) for Er pointing down the density gradient. In addition, the cross-conditionally averaged waveforms are relatively unchanged as connection length is varied. Within certain regimes, our measurements are consistent with the predictions of a stochastic model that represents the plasma fluctuations as a random sequence of burst events. Furthermore, we attempt to gain insight into the physical origin of these ITEs by searching for similar statistical behavior in fluid and gyrokinetic simulations. This material is based upon work supported by the U.S. Department of Energy Office of Science, Office of Fusion Energy Sciences under Award Number DE-FG02- 04ER5476.

Symmetric supercapacitor: Sulphurized graphene and ionic liquid.

PubMed

Shaikh, Jasmin S; Shaikh, Navajsharif S; Kharade, Rohini; Beknalkar, Sonali A; Patil, Jyoti V; Suryawanshi, Mahesh P; Kanjanaboos, Pongsakorn; Hong, Chang Kook; Kim, Jin Hyeok; Patil, Pramod S

2018-10-01

Symmetric supercapacitor is advanced over simple supercapacitor device due to their stability over a large potential window and high energy density. Graphene is a desired candidate for supercapacitor application since it has a high surface area, good electronic conductivity and high electro chemical stability. There is a pragmatic use of ionic liquid electrolyte for supercapacitor due to its stability over a large potential window, good ionic conductivity and eco-friendly nature. For high performance supercapacitor, the interaction between ionic liquid electrolyte and graphene are crucial for better charge transportation. In respect of this, a three-dimensional (3D) nanoporous honeycomb shaped sulfur embedded graphene (S-graphene) has been synthesized by simple chemical method. Here, the fabrication of high performance symmetric supercapacitor is done by using S-graphene as an electrode and [BMIM-PF 6 ] as an electrolyte. The particular architecture of S-graphene benefited to reduce the ion diffusion resistance, providing the large surface area for charge transportation and efficient charge storage. The S-graphene and ionic liquid-based symmetric supercapacitor device showed the large potential window of 3.2 V with high energy density 124 Wh kg -1 at 0.2 A g -1 constant applied current density. Furthermore, this device shows good cycling performance (stability) with a capacitive retention of 95% over 20,000 cycles at a higher current density of 2 A g -1 . Copyright © 2018 Elsevier Inc. All rights reserved.

Ultra high vacuum broad band high power microwave window

DOEpatents

Nguyen-Tuong, V.; Dylla, H.F. III

1997-11-04

An improved high vacuum microwave window has been developed that utilizes high density polyethylene coated on two sides with SiOx, SiNx, or a combination of the two. The resultant low dielectric and low loss tangent window creates a low outgassing, low permeation seal through which broad band, high power microwave energy may be passed. No matching device is necessary and the sealing technique is simple. The features of the window are broad band transmission, ultra-high vacuum compatibility with a simple sealing technique, low voltage standing wave ratio, high power transmission and low cost. 5 figs.

Ultra high vacuum broad band high power microwave window

DOEpatents

Nguyen-Tuong, Viet; Dylla, III, Henry Frederick

1997-01-01

An improved high vacuum microwave window has been developed that utilizes high density polyethylene coated on two sides with SiOx, SiNx, or a combination of the two. The resultant low dielectric and low loss tangent window creates a low outgassing, low permeation seal through which broad band, high power microwave energy may be passed. No matching device is necessary and the sealing technique is simple. The features of the window are broad band transmission, ultra-high vacuum compatibility with a simple sealing technique, low voltage standing wave ratio, high power transmission and low cost.

A simple method for semi-random DNA amplicon fragmentation using the methylation-dependent restriction enzyme MspJI.

PubMed

Shinozuka, Hiroshi; Cogan, Noel O I; Shinozuka, Maiko; Marshall, Alexis; Kay, Pippa; Lin, Yi-Han; Spangenberg, German C; Forster, John W

2015-04-11

Fragmentation at random nucleotide locations is an essential process for preparation of DNA libraries to be used on massively parallel short-read DNA sequencing platforms. Although instruments for physical shearing, such as the Covaris S2 focused-ultrasonicator system, and products for enzymatic shearing, such as the Nextera technology and NEBNext dsDNA Fragmentase kit, are commercially available, a simple and inexpensive method is desirable for high-throughput sequencing library preparation. MspJI is a recently characterised restriction enzyme which recognises the sequence motif CNNR (where R = G or A) when the first base is modified to 5-methylcytosine or 5-hydroxymethylcytosine. A semi-random enzymatic DNA amplicon fragmentation method was developed based on the unique cleavage properties of MspJI. In this method, random incorporation of 5-methyl-2'-deoxycytidine-5'-triphosphate is achieved through DNA amplification with DNA polymerase, followed by DNA digestion with MspJI. Due to the recognition sequence of the enzyme, DNA amplicons are fragmented in a relatively sequence-independent manner. The size range of the resulting fragments was capable of control through optimisation of 5-methyl-2'-deoxycytidine-5'-triphosphate concentration in the reaction mixture. A library suitable for sequencing using the Illumina MiSeq platform was prepared and processed using the proposed method. Alignment of generated short reads to a reference sequence demonstrated a relatively high level of random fragmentation. The proposed method may be performed with standard laboratory equipment. Although the uniformity of coverage was slightly inferior to the Covaris physical shearing procedure, due to efficiencies of cost and labour, the method may be more suitable than existing approaches for implementation in large-scale sequencing activities, such as bacterial artificial chromosome (BAC)-based genome sequence assembly, pan-genomic studies and locus-targeted genotyping-by-sequencing.

in silico Whole Genome Sequencer & Analyzer (iWGS): a computational pipeline to guide the design and analysis of de novo genome sequencing studies

USDA-ARS?s Scientific Manuscript database

The availability of genomes across the tree of life is highly biased toward vertebrates, pathogens, human disease models, and organisms with relatively small and simple genomes. Recent progress in genomics has enabled the de novo decoding of the genome of virtually any organism, greatly expanding it...

Current density imaging sequence for monitoring current distribution during delivery of electric pulses in irreversible electroporation.

PubMed

Serša, Igor; Kranjc, Matej; Miklavčič, Damijan

2015-01-01

Electroporation is gaining its importance in everyday clinical practice of cancer treatment. For its success it is extremely important that coverage of the target tissue, i.e. treated tumor, with electric field is within the specified range. Therefore, an efficient tool for the electric field monitoring in the tumor during delivery of electroporation pulses is needed. The electric field can be reconstructed by the magnetic resonance electric impedance tomography method from current density distribution data. In this study, the use of current density imaging with MRI for monitoring current density distribution during delivery of irreversible electroporation pulses was demonstrated. Using a modified single-shot RARE sequence, where four 3000 V and 100 μs long pulses were included at the start, current distribution between a pair of electrodes inserted in a liver tissue sample was imaged. Two repetitions of the sequence with phases of refocusing radiofrequency pulses 90° apart were needed to acquire one current density image. For each sample in total 45 current density images were acquired to follow a standard protocol for irreversible electroporation where 90 electric pulses are delivered at 1 Hz. Acquired current density images showed that the current density in the middle of the sample increased from first to last electric pulses by 60%, i.e. from 8 kA/m2 to 13 kA/m2 and that direction of the current path did not change with repeated electric pulses significantly. The presented single-shot RARE-based current density imaging sequence was used successfully to image current distribution during delivery of short high-voltage electric pulses. The method has a potential to enable monitoring of tumor coverage by electric field during irreversible electroporation tissue ablation.

High-Capacity Cathode Material with High Voltage for Li-Ion Batteries

DOE PAGES

Shi, Ji -Lei; Xiao, Dong -Dong; Ge, Mingyuan; ...

2018-01-15

Electrochemical energy storage devices with a high energy density are an important technology in modern society, especially for electric vehicles. The most effective approach to improve the energy density of batteries is to search for high-capacity electrode materials. According to the concept of energy quality, a high-voltage battery delivers a highly useful energy, thus providing a new insight to improve energy density. Based on this concept, a novel and successful strategy to increase the energy density and energy quality by increasing the discharge voltage of cathode materials and preserving high capacity is proposed. The proposal is realized in high-capacity Li-richmore » cathode materials. The average discharge voltage is increased from 3.5 to 3.8 V by increasing the nickel content and applying a simple after-treatment, and the specific energy is improved from 912 to 1033 Wh kg-1. The current work provides an insightful universal principle for developing, designing, and screening electrode materials for high energy density and energy quality.« less

High-Capacity Cathode Material with High Voltage for Li-Ion Batteries

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

Shi, Ji -Lei; Xiao, Dong -Dong; Ge, Mingyuan

Electrochemical energy storage devices with a high energy density are an important technology in modern society, especially for electric vehicles. The most effective approach to improve the energy density of batteries is to search for high-capacity electrode materials. According to the concept of energy quality, a high-voltage battery delivers a highly useful energy, thus providing a new insight to improve energy density. Based on this concept, a novel and successful strategy to increase the energy density and energy quality by increasing the discharge voltage of cathode materials and preserving high capacity is proposed. The proposal is realized in high-capacity Li-richmore » cathode materials. The average discharge voltage is increased from 3.5 to 3.8 V by increasing the nickel content and applying a simple after-treatment, and the specific energy is improved from 912 to 1033 Wh kg-1. The current work provides an insightful universal principle for developing, designing, and screening electrode materials for high energy density and energy quality.« less

Development of Genomic Simple Sequence Repeats (SSR) by Enrichment Libraries in Date Palm.

PubMed

Al-Faifi, Sulieman A; Migdadi, Hussein M; Algamdi, Salem S; Khan, Mohammad Altaf; Al-Obeed, Rashid S; Ammar, Megahed H; Jakse, Jerenj

2017-01-01

Development of highly informative markers such as simple sequence repeats (SSR) for cultivar identification and germplasm characterization and management is essential for date palms genetic studies. The present study documents the development of SSR markers and assesses genetic relationships of commonly grown date palm (Phoenix dactylifera L.) cultivars in different geographical regions of Saudi Arabia. A total of 93 novel simple sequence repeat (SSR) markers were screened for their ability to detect polymorphism in date palm. Around 71% of genomic SSRs are dinucleotide, 25% trinucleotide, 3% tetranucleotide, and 1% pentanucleotide motives and show 100% polymorphism. The Unweighted Pair Group Method with Arithmetic Mean (UPGMA) cluster analysis illustrates that cultivars trend to group according to their class of maturity, region of cultivation, and fruit color. Analysis of molecular variations (AMOVA) reveals genetic variation among and within cultivars of 27% and 73%, respectively, according to the geographical distribution of the cultivars. Developed microsatellite markers are of additional value to date palm characterization, tools which can be used by researchers in population genetics, cultivar identification, as well as genetic resource exploration and management. The cultivars tested exhibited a significant amount of genetic diversity and could be suitable for successful breeding programs. Genomic sequences generated from this study are available at the National Center for Biotechnology Information (NCBI), Sequence Read Archive (Accession numbers. LIBGSS_039019).

Defect reaction network in Si-doped InAs. Numerical predictions.

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

Schultz, Peter A.

This Report characterizes the defects in the def ect reaction network in silicon - doped, n - type InAs predicted with first principles density functional theory. The reaction network is deduced by following exothermic defect reactions starting with the initially mobile interstitial defects reacting with common displacement damage defects in Si - doped InAs , until culminating in immobile reaction p roducts. The defect reactions and reaction energies are tabulated, along with the properties of all the silicon - related defects in the reaction network. This Report serves to extend the results for the properties of intrinsic defects in bulkmore » InAs as colla ted in SAND 2013 - 2477 : Simple intrinsic defects in InAs : Numerical predictions to include Si - containing simple defects likely to be present in a radiation - induced defect reaction sequence . This page intentionally left blank« less

Identification and characterization of 43 microsatellite markers derived from expressed sequence tags of the sea cucumber ( Apostichopus japonicus)

NASA Astrophysics Data System (ADS)

Jiang, Qun; Li, Qi; Yu, Hong; Kong, Lingfeng

2011-06-01

The sea cucumber Apostichopus japonicus is a commercially and ecologically important species in China. A total of 3056 potential unigenes were generated after assembling 7597 A. japonicus expressed sequence tags (ESTs) downloaded from Gen-Bank. Two hundred and fifty microsatellite-containing ESTs (8.18%) and 299 simple sequence repeats (SSRs) were detected. The average density of SSRs was 1 per 7.403 kb of EST after redundancy elimination. Di-nucleotide repeat motifs appeared to be the most abundant type with a percentage of 69.90%. Of the 126 primer pairs designed, 90 amplified the expected products and 43 showed polymorphism in 30 individuals tested. The number of alleles per locus ranged from 2 to 26 with an average of 7.0 alleles, and the observed and expected heterozygosities varied from 0.067 to 1.000 and from 0.066 to 0.959, respectively. These new EST-derived microsatellite markers would provide sufficient polymorphism for population genetic studies and genome mapping of this sea cucumber species.

From Lévy to Brownian: a computational model based on biological fluctuation.

PubMed

Nurzaman, Surya G; Matsumoto, Yoshio; Nakamura, Yutaka; Shirai, Kazumichi; Koizumi, Satoshi; Ishiguro, Hiroshi

2011-02-03

Theoretical studies predict that Lévy walks maximizes the chance of encountering randomly distributed targets with a low density, but Brownian walks is favorable inside a patch of targets with high density. Recently, experimental data reports that some animals indeed show a Lévy and Brownian walk movement patterns when forage for foods in areas with low and high density. This paper presents a simple, Gaussian-noise utilizing computational model that can realize such behavior. We extend Lévy walks model of one of the simplest creature, Escherichia coli, based on biological fluctuation framework. We build a simulation of a simple, generic animal to observe whether Lévy or Brownian walks will be performed properly depends on the target density, and investigate the emergent behavior in a commonly faced patchy environment where the density alternates. Based on the model, animal behavior of choosing Lévy or Brownian walk movement patterns based on the target density is able to be generated, without changing the essence of the stochastic property in Escherichia coli physiological mechanism as explained by related researches. The emergent behavior and its benefits in a patchy environment are also discussed. The model provides a framework for further investigation on the role of internal noise in realizing adaptive and efficient foraging behavior.

Geometrical optics analysis of atmospheric turbulence

NASA Astrophysics Data System (ADS)

Wu, Chensheng; Davis, Christopher C.

2013-09-01

2D phase screen methods have been frequently applied to estimate atmospheric turbulence in free space optic communication and imaging systems. In situations where turbulence is "strong" enough to cause severe discontinuity of the wavefront (small Fried coherence length), the transmitted optic signal behaves more like "rays" rather than "waves". However, to achieve accurate simulation results through ray modeling requires both a high density of rays and a large number of eddies. Moreover, their complicated interactions require significant computational resources. Thus, we introduce a 3D ray model based on simple characteristics of turbulent eddies regardless of their particular geometry. The observed breakup of a beam wave into patches at a receiver and the theoretical description indicates that rays passing through the same sequence of turbulent eddies show "group" behavior whose wavefront can still be regarded as continuous. Thus, in our approach, we have divided the curved trajectory of rays into finite line segments and intuitively related their redirections to the refractive property of large turbulent eddies. As a result, our proposed treatment gives a quick and effective high-density ray simulation of a turbulent channel which only requires knowledge of the magnitude of the refractive index deviations. And our method points out a potential correction in reducing equivalent Cn2 by applying adaptive optics. This treatment also shows the possibility of extending 2D phase screen simulations into more general 3D treatments.

High-throughput analysis of T-DNA location and structure using sequence capture

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

Inagaki, Soichi; Henry, Isabelle M.; Lieberman, Meric C.

Agrobacterium-mediated transformation of plants with T-DNA is used both to introduce transgenes and for mutagenesis. Conventional approaches used to identify the genomic location and the structure of the inserted T-DNA are laborious and high-throughput methods using next-generation sequencing are being developed to address these problems. Here, we present a cost-effective approach that uses sequence capture targeted to the T-DNA borders to select genomic DNA fragments containing T-DNA—genome junctions, followed by Illumina sequencing to determine the location and junction structure of T-DNA insertions. Multiple probes can be mixed so that transgenic lines transformed with different T-DNA types can be processed simultaneously,more » using a simple, index-based pooling approach. We also developed a simple bioinformatic tool to find sequence read pairs that span the junction between the genome and T-DNA or any foreign DNA. We analyzed 29 transgenic lines of Arabidopsis thaliana, each containing inserts from 4 different T-DNA vectors. We determined the location of T-DNA insertions in 22 lines, 4 of which carried multiple insertion sites. Additionally, our analysis uncovered a high frequency of unconventional and complex T-DNA insertions, highlighting the needs for high-throughput methods for T-DNA localization and structural characterization. Transgene insertion events have to be fully characterized prior to use as commercial products. As a result, our method greatly facilitates the first step of this characterization of transgenic plants by providing an efficient screen for the selection of promising lines.« less

High-throughput analysis of T-DNA location and structure using sequence capture

DOE PAGES

Inagaki, Soichi; Henry, Isabelle M.; Lieberman, Meric C.; ...

2015-10-07

Agrobacterium-mediated transformation of plants with T-DNA is used both to introduce transgenes and for mutagenesis. Conventional approaches used to identify the genomic location and the structure of the inserted T-DNA are laborious and high-throughput methods using next-generation sequencing are being developed to address these problems. Here, we present a cost-effective approach that uses sequence capture targeted to the T-DNA borders to select genomic DNA fragments containing T-DNA—genome junctions, followed by Illumina sequencing to determine the location and junction structure of T-DNA insertions. Multiple probes can be mixed so that transgenic lines transformed with different T-DNA types can be processed simultaneously,more » using a simple, index-based pooling approach. We also developed a simple bioinformatic tool to find sequence read pairs that span the junction between the genome and T-DNA or any foreign DNA. We analyzed 29 transgenic lines of Arabidopsis thaliana, each containing inserts from 4 different T-DNA vectors. We determined the location of T-DNA insertions in 22 lines, 4 of which carried multiple insertion sites. Additionally, our analysis uncovered a high frequency of unconventional and complex T-DNA insertions, highlighting the needs for high-throughput methods for T-DNA localization and structural characterization. Transgene insertion events have to be fully characterized prior to use as commercial products. As a result, our method greatly facilitates the first step of this characterization of transgenic plants by providing an efficient screen for the selection of promising lines.« less

Genotyping and Molecular Identification of Date Palm Cultivars Using Inter-Simple Sequence Repeat (ISSR) Markers.

PubMed

Ayesh, Basim M

2017-01-01

Molecular markers are credible for the discrimination of genotypes and estimation of the extent of genetic diversity and relatedness in a set of genotypes. Inter-simple sequence repeat (ISSR) markers rapidly reveal high polymorphic fingerprints and have been used frequently to determine the genetic diversity among date palm cultivars. This chapter describes the application of ISSR markers for genotyping of date palm cultivars. The application involves extraction of genomic DNA from the target cultivars with reliable quality and quantity. Subsequently the extracted DNA serves as a template for amplification of genomic regions flanked by inverted simple sequence repeats using a single primer. The similarity of each pair of samples is measured by calculating the number of mono- and polymorphic bands revealed by gel electrophoresis. Matrices constructed for similarity and genetic distance are used to build a phylogenetic tree and cluster analysis, to determine the molecular relatedness of cultivars. The protocol describes 3 out of 9 tested primers consistently amplified 31 loci in 6 date palm cultivars, with 28 polymorphic loci.

IV INTERNATIONAL CONFERENCE ON ATOM AND MOLECULAR PULSED LASERS (AMPL'99): Critical electron density in a self-contained copper vapour laser in the restricted pulse repetition rate

NASA Astrophysics Data System (ADS)

Yakovlenko, Sergei I.

2000-06-01

One of the mechanisms of the inversion breaking in copper vapour lasers caused by a high prepulse electron density is considered. Inversion breaking occurs at a critical electron density Ne cr. If the prepulse electron density exceeds Ne cr, the electron temperature Te cr cannot reach, during a plasma heating pulse, the temperature of ~2eV required for lasing. A simple estimate of Ne cr is made.

Analysis of High Temporal and Spatial Observations of Hurricane Joaquin During TCI-15

NASA Technical Reports Server (NTRS)

Creasey, Robert; Elsberry, Russell L.; Velden, Chris; Cecil, Daniel J.; Bell, Michael; Hendricks, Eric A.

2016-01-01

Objectives: Provide an example of why analysis of high density soundings across Hurricane Joaquin also require highly accurate center positions; Describe technique for calculating 3-D zero-wind center positions from the highly accurate GPS positions of sequences of High-Density Sounding System (HDSS) soundings as they fall from 10 km to the ocean surface; Illustrate the vertical tilt of the vortex above 4-5 km during two center passes through Hurricane Joaquin on 4 October 2015.

Museum genomics: low-cost and high-accuracy genetic data from historical specimens.

PubMed

Rowe, Kevin C; Singhal, Sonal; Macmanes, Matthew D; Ayroles, Julien F; Morelli, Toni Lyn; Rubidge, Emily M; Bi, Ke; Moritz, Craig C

2011-11-01

Natural history collections are unparalleled repositories of geographical and temporal variation in faunal conditions. Molecular studies offer an opportunity to uncover much of this variation; however, genetic studies of historical museum specimens typically rely on extracting highly degraded and chemically modified DNA samples from skins, skulls or other dried samples. Despite this limitation, obtaining short fragments of DNA sequences using traditional PCR amplification of DNA has been the primary method for genetic study of historical specimens. Few laboratories have succeeded in obtaining genome-scale sequences from historical specimens and then only with considerable effort and cost. Here, we describe a low-cost approach using high-throughput next-generation sequencing to obtain reliable genome-scale sequence data from a traditionally preserved mammal skin and skull using a simple extraction protocol. We show that single-nucleotide polymorphisms (SNPs) from the genome sequences obtained independently from the skin and from the skull are highly repeatable compared to a reference genome. © 2011 Blackwell Publishing Ltd.

Strain rates, stress markers and earthquake clustering (Invited)

NASA Astrophysics Data System (ADS)

Fry, B.; Gerstenberger, M.; Abercrombie, R. E.; Reyners, M.; Eberhart-Phillips, D. M.

2013-12-01

The 2010-present Canterbury earthquakes comprise a well-recorded sequence in a relatively low strain-rate shallow crustal region. We present new scientific results to test the hypothesis that: Earthquake sequences in low-strain rate areas experience high stress drop events, low-post seismic relaxation, and accentuated seismic clustering. This hypothesis is based on a physical description of the aftershock process in which the spatial distribution of stress accumulation and stress transfer are controlled by fault strength and orientation. Following large crustal earthquakes, time dependent forecasts are often developed by fitting parameters defined by Omori's aftershock decay law. In high-strain rate areas, simple forecast models utilizing a single p-value fit observed aftershock sequences well. In low-strain rate areas such as Canterbury, assumptions of simple Omori decay may not be sufficient to capture the clustering (sub-sequence) nature exhibited by the punctuated rise in activity following significant child events. In Canterbury, the moment release is more clustered than in more typical Omori sequences. The individual earthquakes in these clusters also exhibit somewhat higher stress drops than in the average crustal sequence in high-strain rate regions, suggesting the earthquakes occur on strong Andersonian-oriented faults, possibly juvenile or well-healed . We use the spectral ratio procedure outlined in (Viegas et al., 2010) to determine corner frequencies and Madariaga stress-drop values for over 800 events in the sequence. Furthermore, we will discuss the relevance of tomographic results of Reyners and Eberhart-Phillips (2013) documenting post-seismic stress-driven fluid processes following the three largest events in the sequence as well as anisotropic patterns in surface wave tomography (Fry et al., 2013). These tomographic studies are both compatible with the hypothesis, providing strong evidence for the presence of widespread and hydrated regional upper crustal cracking parallel to sub-parallel to the dominant transverse failure plane in the sequence. Joint interpretation of the three separate datasets provide a positive first attempt at testing our fundamental hypothesis.

De Novo Transcriptome Sequencing Reveals Important Molecular Networks and Metabolic Pathways of the Plant, Chlorophytum borivilianum

PubMed Central

Kalra, Shikha; Puniya, Bhanwar Lal; Kulshreshtha, Deepika; Kumar, Sunil; Kaur, Jagdeep; Ramachandran, Srinivasan; Singh, Kashmir

2013-01-01

Chlorophytum borivilianum, an endangered medicinal plant species is highly recognized for its aphrodisiac properties provided by saponins present in the plant. The transcriptome information of this species is limited and only few hundred expressed sequence tags (ESTs) are available in the public databases. To gain molecular insight of this plant, high throughput transcriptome sequencing of leaf RNA was carried out using Illumina's HiSeq 2000 sequencing platform. A total of 22,161,444 single end reads were retrieved after quality filtering. Available (e.g., De-Bruijn/Eulerian graph) and in-house developed bioinformatics tools were used for assembly and annotation of transcriptome. A total of 101,141 assembled transcripts were obtained, with coverage size of 22.42 Mb and average length of 221 bp. Guanine-cytosine (GC) content was found to be 44%. Bioinformatics analysis, using non-redundant proteins, gene ontology (GO), enzyme commission (EC) and kyoto encyclopedia of genes and genomes (KEGG) databases, extracted all the known enzymes involved in saponin and flavonoid biosynthesis. Few genes of the alkaloid biosynthesis, along with anticancer and plant defense genes, were also discovered. Additionally, several cytochrome P450 (CYP450) and glycosyltransferase unique sequences were also found. We identified simple sequence repeat motifs in transcripts with an abundance of di-nucleotide simple sequence repeat (SSR; 43.1%) markers. Large scale expression profiling through Reads per Kilobase per Million mapped reads (RPKM) showed major genes involved in different metabolic pathways of the plant. Genes, expressed sequence tags (ESTs) and unique sequences from this study provide an important resource for the scientific community, interested in the molecular genetics and functional genomics of C. borivilianum. PMID:24376689

De Novo transcriptome sequencing reveals important molecular networks and metabolic pathways of the plant, Chlorophytum borivilianum.

PubMed

Kalra, Shikha; Puniya, Bhanwar Lal; Kulshreshtha, Deepika; Kumar, Sunil; Kaur, Jagdeep; Ramachandran, Srinivasan; Singh, Kashmir

2013-01-01

Chlorophytum borivilianum, an endangered medicinal plant species is highly recognized for its aphrodisiac properties provided by saponins present in the plant. The transcriptome information of this species is limited and only few hundred expressed sequence tags (ESTs) are available in the public databases. To gain molecular insight of this plant, high throughput transcriptome sequencing of leaf RNA was carried out using Illumina's HiSeq 2000 sequencing platform. A total of 22,161,444 single end reads were retrieved after quality filtering. Available (e.g., De-Bruijn/Eulerian graph) and in-house developed bioinformatics tools were used for assembly and annotation of transcriptome. A total of 101,141 assembled transcripts were obtained, with coverage size of 22.42 Mb and average length of 221 bp. Guanine-cytosine (GC) content was found to be 44%. Bioinformatics analysis, using non-redundant proteins, gene ontology (GO), enzyme commission (EC) and kyoto encyclopedia of genes and genomes (KEGG) databases, extracted all the known enzymes involved in saponin and flavonoid biosynthesis. Few genes of the alkaloid biosynthesis, along with anticancer and plant defense genes, were also discovered. Additionally, several cytochrome P450 (CYP450) and glycosyltransferase unique sequences were also found. We identified simple sequence repeat motifs in transcripts with an abundance of di-nucleotide simple sequence repeat (SSR; 43.1%) markers. Large scale expression profiling through Reads per Kilobase per Million mapped reads (RPKM) showed major genes involved in different metabolic pathways of the plant. Genes, expressed sequence tags (ESTs) and unique sequences from this study provide an important resource for the scientific community, interested in the molecular genetics and functional genomics of C. borivilianum.

Remarkably Divergent Regions Punctuate the Genome Assembly of the Caenorhabditis elegans Hawaiian Strain CB4856

PubMed Central

Thompson, Owen A.; Snoek, L. Basten; Nijveen, Harm; Sterken, Mark G.; Volkers, Rita J. M.; Brenchley, Rachel; van’t Hof, Arjen; Bevers, Roel P. J.; Cossins, Andrew R.; Yanai, Itai; Hajnal, Alex; Schmid, Tobias; Perkins, Jaryn D.; Spencer, David; Kruglyak, Leonid; Andersen, Erik C.; Moerman, Donald G.; Hillier, LaDeana W.; Kammenga, Jan E.; Waterston, Robert H.

2015-01-01

The Hawaiian strain (CB4856) of Caenorhabditis elegans is one of the most divergent from the canonical laboratory strain N2 and has been widely used in developmental, population, and evolutionary studies. To enhance the utility of the strain, we have generated a draft sequence of the CB4856 genome, exploiting a variety of resources and strategies. When compared against the N2 reference, the CB4856 genome has 327,050 single nucleotide variants (SNVs) and 79,529 insertion–deletion events that result in a total of 3.3 Mb of N2 sequence missing from CB4856 and 1.4 Mb of sequence present in CB4856 but not present in N2. As previously reported, the density of SNVs varies along the chromosomes, with the arms of chromosomes showing greater average variation than the centers. In addition, we find 61 regions totaling 2.8 Mb, distributed across all six chromosomes, which have a greatly elevated SNV density, ranging from 2 to 16% SNVs. A survey of other wild isolates show that the two alternative haplotypes for each region are widely distributed, suggesting they have been maintained by balancing selection over long evolutionary times. These divergent regions contain an abundance of genes from large rapidly evolving families encoding F-box, MATH, BATH, seven-transmembrane G-coupled receptors, and nuclear hormone receptors, suggesting that they provide selective advantages in natural environments. The draft sequence makes available a comprehensive catalog of sequence differences between the CB4856 and N2 strains that will facilitate the molecular dissection of their phenotypic differences. Our work also emphasizes the importance of going beyond simple alignment of reads to a reference genome when assessing differences between genomes. PMID:25995208

CIDR

Science.gov Websites

NIH CIDR Program Studies For whole exome sequencing projects, we pretest all samples using a high -density SNP array (>200,000 markers). For custom targeted sequencing, we pretest all samples using a 96 pretest samples using a 96 SNP GoldenGate assay. This extensive pretesting allows us to unambiguously tie

Comparison of double-locus sequence typing (DLST) and multilocus sequence typing (MLST) for the investigation of Pseudomonas aeruginosa populations.

PubMed

Cholley, Pascal; Stojanov, Milos; Hocquet, Didier; Thouverez, Michelle; Bertrand, Xavier; Blanc, Dominique S

2015-08-01

Reliable molecular typing methods are necessary to investigate the epidemiology of bacterial pathogens. Reference methods such as multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) are costly and time consuming. Here, we compared our newly developed double-locus sequence typing (DLST) method for Pseudomonas aeruginosa to MLST and PFGE on a collection of 281 isolates. DLST was as discriminatory as MLST and was able to recognize "high-risk" epidemic clones. Both methods were highly congruent. Not surprisingly, a higher discriminatory power was observed with PFGE. In conclusion, being a simple method (single-strand sequencing of only 2 loci), DLST is valuable as a first-line typing tool for epidemiological investigations of P. aeruginosa. Coupled to a more discriminant method like PFGE or whole genome sequencing, it might represent an efficient typing strategy to investigate or prevent outbreaks. Copyright © 2015 Elsevier Inc. All rights reserved.

Investigation of sequential properties of snoring episodes for obstructive sleep apnoea identification.

PubMed

Cavusoglu, M; Ciloglu, T; Serinagaoglu, Y; Kamasak, M; Erogul, O; Akcam, T

2008-08-01

In this paper, 'snore regularity' is studied in terms of the variations of snoring sound episode durations, separations and average powers in simple snorers and in obstructive sleep apnoea (OSA) patients. The goal was to explore the possibility of distinguishing among simple snorers and OSA patients using only sleep sound recordings of individuals and to ultimately eliminate the need for spending a whole night in the clinic for polysomnographic recording. Sequences that contain snoring episode durations (SED), snoring episode separations (SES) and average snoring episode powers (SEP) were constructed from snoring sound recordings of 30 individuals (18 simple snorers and 12 OSA patients) who were also under polysomnographic recording in Gülhane Military Medical Academy Sleep Studies Laboratory (GMMA-SSL), Ankara, Turkey. Snore regularity is quantified in terms of mean, standard deviation and coefficient of variation values for the SED, SES and SEP sequences. In all three of these sequences, OSA patients' data displayed a higher variation than those of simple snorers. To exclude the effects of slow variations in the base-line of these sequences, new sequences that contain the coefficient of variation of the sample values in a 'short' signal frame, i.e., short time coefficient of variation (STCV) sequences, were defined. The mean, the standard deviation and the coefficient of variation values calculated from the STCV sequences displayed a stronger potential to distinguish among simple snorers and OSA patients than those obtained from the SED, SES and SEP sequences themselves. Spider charts were used to jointly visualize the three parameters, i.e., the mean, the standard deviation and the coefficient of variation values of the SED, SES and SEP sequences, and the corresponding STCV sequences as two-dimensional plots. Our observations showed that the statistical parameters obtained from the SED and SES sequences, and the corresponding STCV sequences, possessed a strong potential to distinguish among simple snorers and OSA patients, both marginally, i.e., when the parameters are examined individually, and jointly. The parameters obtained from the SEP sequences and the corresponding STCV sequences, on the other hand, did not have a strong discrimination capability. However, the joint behaviour of these parameters showed some potential to distinguish among simple snorers and OSA patients.

Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV)

PubMed Central

Martin, Andrew C. R.

2014-01-01

The JavaScript Sequence Alignment Viewer (JSAV) is designed as a simple-to-use JavaScript component for displaying sequence alignments on web pages. The display of sequences is highly configurable with options to allow alternative coloring schemes, sorting of sequences and ’dotifying’ repeated amino acids. An option is also available to submit selected sequences to another web site, or to other JavaScript code. JSAV is implemented purely in JavaScript making use of the JQuery and JQuery-UI libraries. It does not use any HTML5-specific options to help with browser compatibility. The code is documented using JSDOC and is available from http://www.bioinf.org.uk/software/jsav/. PMID:25653836

Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV).

PubMed

Martin, Andrew C R

2014-01-01

The JavaScript Sequence Alignment Viewer (JSAV) is designed as a simple-to-use JavaScript component for displaying sequence alignments on web pages. The display of sequences is highly configurable with options to allow alternative coloring schemes, sorting of sequences and 'dotifying' repeated amino acids. An option is also available to submit selected sequences to another web site, or to other JavaScript code. JSAV is implemented purely in JavaScript making use of the JQuery and JQuery-UI libraries. It does not use any HTML5-specific options to help with browser compatibility. The code is documented using JSDOC and is available from http://www.bioinf.org.uk/software/jsav/.

Not all transmembrane helices are born equal: Towards the extension of the sequence homology concept to membrane proteins

PubMed Central

2011-01-01

Background Sequence homology considerations widely used to transfer functional annotation to uncharacterized protein sequences require special precautions in the case of non-globular sequence segments including membrane-spanning stretches composed of non-polar residues. Simple, quantitative criteria are desirable for identifying transmembrane helices (TMs) that must be included into or should be excluded from start sequence segments in similarity searches aimed at finding distant homologues. Results We found that there are two types of TMs in membrane-associated proteins. On the one hand, there are so-called simple TMs with elevated hydrophobicity, low sequence complexity and extraordinary enrichment in long aliphatic residues. They merely serve as membrane-anchoring device. In contrast, so-called complex TMs have lower hydrophobicity, higher sequence complexity and some functional residues. These TMs have additional roles besides membrane anchoring such as intra-membrane complex formation, ligand binding or a catalytic role. Simple and complex TMs can occur both in single- and multi-membrane-spanning proteins essentially in any type of topology. Whereas simple TMs have the potential to confuse searches for sequence homologues and to generate unrelated hits with seemingly convincing statistical significance, complex TMs contain essential evolutionary information. Conclusion For extending the homology concept onto membrane proteins, we provide a necessary quantitative criterion to distinguish simple TMs (and a sufficient criterion for complex TMs) in query sequences prior to their usage in homology searches based on assessment of hydrophobicity and sequence complexity of the TM sequence segments. Reviewers This article was reviewed by Shamil Sunyaev, L. Aravind and Arcady Mushegian. PMID:22024092

Gravity survey and regional geology of the Prince William Sound epicentral region, Alaska: Chapter C in The Alaska earthquake, March 27, 1964: regional effects

USGS Publications Warehouse

Case, J.E.; Barnes, D.F.; Plafker, George; Robbins, S.L.

1966-01-01

Sedimentary and volcanic rocks of Mesozoic and early Tertiary age form a roughly arcuate pattern in and around Prince William Sound, the epicentral region of the Alaska earthquake of 1964. These rocks include the Valdez Group, a predominantly slate and graywacke sequence of Jurassic and Cretaceous age, and the Orca Group, a younger sequence of early Tertiary age. The Orca consists of a lower unit of dense-average 2.87 g per cm3 (grams per cubic centimeter) pillow basalt and greenstone intercalated with sedimentary rocks and an upper unit of lithologically variable sandstone interbedded with siltstone or argillite. Densities of the clastic rocks in both the Valdez and Orca Groups average about 2.69 g per cm3. Granitic rocks of relatively low density (2.62 g per cm3) cut the Valdez and Orca Groups at several localities. Both the Valdez and the Orca Groups were complexly folded and extensively faulted during at least three major episodes of deformation: an early period of Cretaceous or early Tertiary orogeny, a second orogeny that probably culminated in late Eocene or early Oligocene time and was accompanied or closely followed by emplacement of granitic batholiths, and a third episode of deformation that began in late Cenozoic time and continued intermittently to the present. About 500 gravity stations were established in the Prince William Sound region in conjunction with postearthquake geologic investigations. Simple Bouguer anomaly contours trend approximately parallel to the arcuate geologic structure around the sound. Bouguer anomalies decrease northward from +40 mgal (milligals) at the southwestern end of Montague Island to -70 mgal at College and Harriman Fiords. Most of this change may be interpreted as a regional gradient caused by thickening of the continental crust. Superimposed on the gradient is a prominent gravity high of as much as 65 mgal that extends from Elrington Island on the southwest, across Knight and Glacier Islands to the Ellamar Peninsula and Valdez on the northeast. This high coincides with the wide belt of greenstone and pillow basalt of the Orca Group and largely reflects the high density of these volcanic rocks. A large low in the east-central part of the sound is inferred to have a composite origin, and results from the combined effects of low-density sedimentary and granitic rocks. The Prince William Sound gravity high extends southwest-northeast without major horizontal offset for more than 100 miles. Thus the belt of volcanic rocks causing the high constitutes a major virtually continuous, geologic element of south-central Alaska.

Robust optical flow using adaptive Lorentzian filter for image reconstruction under noisy condition

NASA Astrophysics Data System (ADS)

Kesrarat, Darun; Patanavijit, Vorapoj

2017-02-01

In optical flow for motion allocation, the efficient result in Motion Vector (MV) is an important issue. Several noisy conditions may cause the unreliable result in optical flow algorithms. We discover that many classical optical flows algorithms perform better result under noisy condition when combined with modern optimized model. This paper introduces effective robust models of optical flow by using Robust high reliability spatial based optical flow algorithms using the adaptive Lorentzian norm influence function in computation on simple spatial temporal optical flows algorithm. Experiment on our proposed models confirm better noise tolerance in optical flow's MV under noisy condition when they are applied over simple spatial temporal optical flow algorithms as a filtering model in simple frame-to-frame correlation technique. We illustrate the performance of our models by performing an experiment on several typical sequences with differences in movement speed of foreground and background where the experiment sequences are contaminated by the additive white Gaussian noise (AWGN) at different noise decibels (dB). This paper shows very high effectiveness of noise tolerance models that they are indicated by peak signal to noise ratio (PSNR).

Textural and mineralogical study of sandstones from the onshore Gulf of Alaska Tertiary Province, southern Alaska

USGS Publications Warehouse

Winkler, Gary R.; McLean, Hugh; Plafker, George

1976-01-01

Petrographic examination of 74 outcrop samples of Paleocene through Pliocene age from the onshore Gulf of Alaska Tertiary Province indicates that sandstones of the province characteristically are texturally immature and mineralogically unstable. Diagenetic alteration of framework grains throughout the stratigraphic sequence has produced widespread zeolite cement or phyllosilicate grain coatings and pseudomatrix. Multiple deformation and deep burial of the older Tertiary sequence--the Orca Group, the shale of Haydon Peak, and the Kulthieth and Tokun Formations--caused extensive alteration and grain interpenetration, resulting in low porosity values. Less intense deformation and intermediate depth of burial of the younger Tertiary sequence--the Katalla, Poul Creek, Redwood, and Yakataga Formations--has resulted in a greater range in textural properties. Most sandstone samples in the younger Tertiary sequence are poorly sorted, tightly packed, and have strongly appressed framework grains, but some are less tightly packed and contain less matrix. Soft and mineralogically unstable framework grains have undergone considerable alteration, reducing pore space even in the youngest rocks. Measurements of porosity, permeability, grain density, and sonic velocity of outcrop samples of the younger Tertiary sequence indicate a modest up-section improvement in sandstone reservoir characteristics. Nonetheless porosity and permeability values typically are below 16 percent and 15 millidarcies respectively and grain densities are consistently high, about 2.7 gm/cc. Low permeability and porosity values, and high grain densities and sonic velocities appear to be typical of most outcrop areas throughout the onshore Gulf of Alaska Tertiary Province.

Construction of a high-density linkage map and mapping quantitative trait loci for somatic embryogenesis using leaf petioles as explants in upland cotton (Gossypium hirsutum L.).

PubMed

Xu, Zhenzhen; Zhang, Chaojun; Ge, Xiaoyang; Wang, Ni; Zhou, Kehai; Yang, Xiaojie; Wu, Zhixia; Zhang, Xueyan; Liu, Chuanliang; Yang, Zuoren; Li, Changfeng; Liu, Kun; Yang, Zhaoen; Qian, Yuyuan; Li, Fuguang

2015-07-01

The first high-density linkage map was constructed to identify quantitative trait loci (QTLs) for somatic embryogenesis (SE) in cotton ( Gossypium hirsutum L.) using leaf petioles as explants. Cotton transformation is highly limited by only a few regenerable genotypes and the lack of understanding of the genetic and molecular basis of somatic embryogenesis (SE) in cotton (Gossypium hirsutum L.). To construct a more saturated linkage map and further identify quantitative trait loci (QTLs) for SE using leaf petioles as explants, a high embryogenesis frequency line (W10) from the commercial Chinese cotton cultivar CRI24 was crossed with TM-1, a genetic standard upland cotton with no embryogenesis frequency. The genetic map spanned 2300.41 cM in genetic distance and contained 411 polymorphic simple sequence repeat (SSR) loci. Of the 411 mapped loci, 25 were developed from unigenes identified for SE in our previous study. Six QTLs for SE were detected by composite interval mapping method, each explaining 6.88-37.07% of the phenotypic variance. Single marker analysis was also performed to verify the reliability of QTLs detection, and the SSR markers NAU3325 and DPL0209 were detected by the two methods. Further studies on the relatively stable and anchoring QTLs/markers for SE in an advanced population of W10 × TM-1 and other cross combinations with different SE abilities may shed light on the genetic and molecular mechanism of SE in cotton.

Using specific length amplified fragment sequencing to construct the high-density genetic map for Vitis (Vitis vinifera L. × Vitis amurensis Rupr.)

PubMed Central

Guo, Yinshan; Shi, Guangli; Liu, Zhendong; Zhao, Yuhui; Yang, Xiaoxu; Zhu, Junchi; Li, Kun; Guo, Xiuwu

2015-01-01

In this study, 149 F1 plants from the interspecific cross between ‘Red Globe’ (Vitis vinifera L.) and ‘Shuangyou’ (Vitis amurensis Rupr.) and the parent were used to construct a molecular genetic linkage map by using the specific length amplified fragment sequencing technique. DNA sequencing generated 41.282 Gb data consisting of 206,411,693 paired-end reads. The average sequencing depths were 68.35 for ‘Red Globe,’ 63.65 for ‘Shuangyou,’ and 8.01 for each progeny. In all, 115,629 high-quality specific length amplified fragments were detected, of which 42,279 were polymorphic. The genetic map was constructed using 7,199 of these polymorphic markers. These polymorphic markers were assigned to 19 linkage groups; the total length of the map was 1929.13 cm, with an average distance of 0.28 cm between each maker. To our knowledge, the genetic maps constructed in this study contain the largest number of molecular markers. These high-density genetic maps might form the basis for the fine quantitative trait loci mapping and molecular-assisted breeding of grape. PMID:26089826

Nanopore Technology: A Simple, Inexpensive, Futuristic Technology for DNA Sequencing.

PubMed

Gupta, P D

2016-10-01

In health care, importance of DNA sequencing has been fully established. Sanger's Capillary Electrophoresis DNA sequencing methodology is time consuming, cumbersome, hence become more expensive. Lately, because of its versatility DNA sequencing became house hold name, and therefore, there is an urgent need of simple, fast, inexpensive, DNA sequencing technology. In the beginning of this century efforts were made, and Nanopore DNA sequencing technology was developed; still it is infancy, nevertheless, it is the futuristic technology.

Construction of an SNP-based high-density linkage map for flax (Linum usitatissimum L.) using specific length amplified fragment sequencing (SLAF-seq) technology.

PubMed

Yi, Liuxi; Gao, Fengyun; Siqin, Bateer; Zhou, Yu; Li, Qiang; Zhao, Xiaoqing; Jia, Xiaoyun; Zhang, Hui

2017-01-01

Flax is an important crop for oil and fiber, however, no high-density genetic maps have been reported for this species. Specific length amplified fragment sequencing (SLAF-seq) is a high-resolution strategy for large scale de novo discovery and genotyping of single nucleotide polymorphisms. In this study, SLAF-seq was employed to develop SNP markers in an F2 population to construct a high-density genetic map for flax. In total, 196.29 million paired-end reads were obtained. The average sequencing depth was 25.08 in male parent, 32.17 in the female parent, and 9.64 in each F2 progeny. In total, 389,288 polymorphic SLAFs were detected, from which 260,380 polymorphic SNPs were developed. After filtering, 4,638 SNPs were found suitable for genetic map construction. The final genetic map included 4,145 SNP markers on 15 linkage groups and was 2,632.94 cM in length, with an average distance of 0.64 cM between adjacent markers. To our knowledge, this map is the densest SNP-based genetic map for flax. The SNP markers and genetic map reported in here will serve as a foundation for the fine mapping of quantitative trait loci (QTLs), map-based gene cloning and marker assisted selection (MAS) for flax.

Simple Electrolyzer Model Development for High-Temperature Electrolysis System Analysis Using Solid Oxide Electrolysis Cell

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

JaeHwa Koh; DuckJoo Yoon; Chang H. Oh

2010-07-01

An electrolyzer model for the analysis of a hydrogen-production system using a solid oxide electrolysis cell (SOEC) has been developed, and the effects for principal parameters have been estimated by sensitivity studies based on the developed model. The main parameters considered are current density, area specific resistance, temperature, pressure, and molar fraction and flow rates in the inlet and outlet. Finally, a simple model for a high-temperature hydrogen-production system using the solid oxide electrolysis cell integrated with very high temperature reactors is estimated.

Comparison of Dixon Sequences for Estimation of Percent Breast Fibroglandular Tissue

PubMed Central

Ledger, Araminta E. W.; Scurr, Erica D.; Hughes, Julie; Macdonald, Alison; Wallace, Toni; Thomas, Karen; Wilson, Robin; Leach, Martin O.; Schmidt, Maria A.

2016-01-01

Objectives To evaluate sources of error in the Magnetic Resonance Imaging (MRI) measurement of percent fibroglandular tissue (%FGT) using two-point Dixon sequences for fat-water separation. Methods Ten female volunteers (median age: 31 yrs, range: 23–50 yrs) gave informed consent following Research Ethics Committee approval. Each volunteer was scanned twice following repositioning to enable an estimation of measurement repeatability from high-resolution gradient-echo (GRE) proton-density (PD)-weighted Dixon sequences. Differences in measures of %FGT attributable to resolution, T1 weighting and sequence type were assessed by comparison of this Dixon sequence with low-resolution GRE PD-weighted Dixon data, and against gradient-echo (GRE) or spin-echo (SE) based T1-weighted Dixon datasets, respectively. Results %FGT measurement from high-resolution PD-weighted Dixon sequences had a coefficient of repeatability of ±4.3%. There was no significant difference in %FGT between high-resolution and low-resolution PD-weighted data. Values of %FGT from GRE and SE T1-weighted data were strongly correlated with that derived from PD-weighted data (r = 0.995 and 0.96, respectively). However, both sequences exhibited higher mean %FGT by 2.9% (p < 0.0001) and 12.6% (p < 0.0001), respectively, in comparison with PD-weighted data; the increase in %FGT from the SE T1-weighted sequence was significantly larger at lower breast densities. Conclusion Although measurement of %FGT at low resolution is feasible, T1 weighting and sequence type impact on the accuracy of Dixon-based %FGT measurements; Dixon MRI protocols for %FGT measurement should be carefully considered, particularly for longitudinal or multi-centre studies. PMID:27011312

A simple model of hohlraum power balance and mitigation of SRS

DOE PAGES

Albright, Brian J.; Montgomery, David S.; Yin, Lin; ...

2016-04-01

A simple energy balance model has been obtained for laser-plasma heating in indirect drive hohlraum plasma that allows rapid temperature scaling and evolution with parameters such as plasma density and composition. Furthermore, this model enables assessment of the effects on plasma temperature of, e.g., adding high-Z dopant to the gas fill or magnetic fields.

A low-density culture method of cerebellar granule neurons with paracrine support applicable for the study of neuronal morphogenesis.

PubMed

Kubota, Kenta; Seno, Takeshi; Konishi, Yoshiyuki

2013-11-20

Cerebellar granule neuronal cultures have been used to study the molecular mechanisms underlying neuronal functions, including neuronal morphogenesis. However, a limitation of this system is the difficulty to analyze isolated neurons because these are required to be maintained at a high density. Therefore, in the present study, we aimed to develop a simple and cost-effective method for culturing low-density cerebellar granule neurons. Cerebellar granule cells at two different densities (low- and high-density) were co-cultivated in order for the low-density culture to be supported by the paracrine signals from the high-density culture. This method enabled morphology analysis of isolated cerebellar granule neurons without astrocytic feeder cultures or supplements such as B27. Using this method, we investigated the function of a polarity factor. Studies using hippocampal neurons suggested that glycogen synthase kinase-3 (GSK-3) is an essential regulator of neuronal polarity, and inhibition of GSK-3 results in the formation of multiple axons. Pharmacological inhibitors for GSK-3 (6-bromoindirubin-3'-oxime and lithium chloride) did not cause the formation of multiple axons of cerebellar granule neurons but significantly reduced their length. Consistent results were obtained by introducing kinase-dead form of GSK-3 beta (K85A). These results indicated that GSK-3 is not directly involved in the control of neuronal polarity in cerebellar granule neurons. Overall, this study provides a simple method for culturing low-density cerebellar granule neurons and insights in to the neuronal-type dependent function of GSK-3 in neuronal morphogenesis. © 2013 Elsevier B.V. All rights reserved.

Automated side-chain model building and sequence assignment by template matching.

PubMed

Terwilliger, Thomas C

2003-01-01

An algorithm is described for automated building of side chains in an electron-density map once a main-chain model is built and for alignment of the protein sequence to the map. The procedure is based on a comparison of electron density at the expected side-chain positions with electron-density templates. The templates are constructed from average amino-acid side-chain densities in 574 refined protein structures. For each contiguous segment of main chain, a matrix with entries corresponding to an estimate of the probability that each of the 20 amino acids is located at each position of the main-chain model is obtained. The probability that this segment corresponds to each possible alignment with the sequence of the protein is estimated using a Bayesian approach and high-confidence matches are kept. Once side-chain identities are determined, the most probable rotamer for each side chain is built into the model. The automated procedure has been implemented in the RESOLVE software. Combined with automated main-chain model building, the procedure produces a preliminary model suitable for refinement and extension by an experienced crystallographer.

Genome-wide characterization and selection of expressed sequence tag simple sequence repeat primers for optimized marker distribution and reliability in peach

USDA-ARS?s Scientific Manuscript database

Expressed sequence tag (EST) simple sequence repeats (SSRs) in Prunus were mined, and flanking primers designed and used for genome-wide characterization and selection of primers to optimize marker distribution and reliability. A total of 12,618 contigs were assembled from 84,727 ESTs, along with 34...

Exploiting genotyping by sequencing to characterize the genomic structure of the American cranberry through high-density linkage mapping

USDA-ARS?s Scientific Manuscript database

The application of genotyping by sequencing (GBS) approaches, combined with data imputation methodologies, is narrowing the genetic knowledge gap between major and understudied, minor crops. GBS is an excellent tool to characterize the genomic structure of recently domesticated (~200 years) and unde...

Data series embedding and scale invariant statistics.

PubMed

Michieli, I; Medved, B; Ristov, S

2010-06-01

Data sequences acquired from bio-systems such as human gait data, heart rate interbeat data, or DNA sequences exhibit complex dynamics that is frequently described by a long-memory or power-law decay of autocorrelation function. One way of characterizing that dynamics is through scale invariant statistics or "fractal-like" behavior. For quantifying scale invariant parameters of physiological signals several methods have been proposed. Among them the most common are detrended fluctuation analysis, sample mean variance analyses, power spectral density analysis, R/S analysis, and recently in the realm of the multifractal approach, wavelet analysis. In this paper it is demonstrated that embedding the time series data in the high-dimensional pseudo-phase space reveals scale invariant statistics in the simple fashion. The procedure is applied on different stride interval data sets from human gait measurements time series (Physio-Bank data library). Results show that introduced mapping adequately separates long-memory from random behavior. Smaller gait data sets were analyzed and scale-free trends for limited scale intervals were successfully detected. The method was verified on artificially produced time series with known scaling behavior and with the varying content of noise. The possibility for the method to falsely detect long-range dependence in the artificially generated short range dependence series was investigated. (c) 2009 Elsevier B.V. All rights reserved.

Formation of Bipolar Lobes by Jets

NASA Astrophysics Data System (ADS)

Soker, Noam

2002-04-01

I conduct an analytical study of the interaction of jets, or a collimated fast wind (CFW), with a previously blown asymptotic giant branch (AGB) slow wind. Such jets (or CFWs) are supposedly formed when a compact companion, a main-sequence star, or a white dwarf accretes mass from the AGB star, forms an accretion disk, and blows two jets. This type of flow, which I think shapes bipolar planetary nebulae (PNs), requires three-dimensional gasdynamical simulations, which are limited in the parameter space they can cover. By imposing several simplifying assumptions, I derive simple expressions which reproduce some basic properties of lobes in bipolar PNs and which can be used to guide future numerical simulations. I quantitatively apply the results to two proto-PNs. I show that the jet interaction with the slow wind can form lobes which are narrow close to, and far away from, the central binary system, and which are wider somewhere in between. Jets that are recollimated and have constant cross section can form cylindrical lobes with constant diameter, as observed in several bipolar PNs. Close to their source, jets blown by main-sequence companions are radiative; only further out they become adiabatic, i.e., they form high-temperature, low-density bubbles that inflate the lobes.

Molecular Identification of Date Palm Cultivars Using Random Amplified Polymorphic DNA (RAPD) Markers.

PubMed

Al-Khalifah, Nasser S; Shanavaskhan, A E

2017-01-01

Ambiguity in the total number of date palm cultivars across the world is pointing toward the necessity for an enumerative study using standard morphological and molecular markers. Among molecular markers, DNA markers are more suitable and ubiquitous to most applications. They are highly polymorphic in nature, frequently occurring in genomes, easy to access, and highly reproducible. Various molecular markers such as restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP), simple sequence repeats (SSR), inter-simple sequence repeats (ISSR), and random amplified polymorphic DNA (RAPD) markers have been successfully used as efficient tools for analysis of genetic variation in date palm. This chapter explains a stepwise protocol for extracting total genomic DNA from date palm leaves. A user-friendly protocol for RAPD analysis and a table showing the primers used in different molecular techniques that produce polymorphisms in date palm are also provided.

Draft Genome Sequence of Thermoanaerobacter sp. Strain A7A, Reconstructed from a Metagenome Obtained from a High-Temperature Hydrocarbon Reservoir in the Bass Strait, Australia

PubMed Central

Li, Dongmei; Greenfield, Paul; Rosewarne, Carly P.

2013-01-01

The draft genome sequence of Thermoanaerobacter sp. strain A7A was reconstructed from a metagenome of a microbial consortium obtained from the Tuna oil field in the Gippsland Basin, Australia. The organism is a strict anaerobe that is predicted to ferment a range of simple sugars and undertake sulfur reduction. PMID:24029756

Plasmonic SERS nanochips and nanoprobes for medical diagnostics and bio-energy applications

NASA Astrophysics Data System (ADS)

Ngo, Hoan T.; Wang, Hsin-Neng; Crawford, Bridget M.; Fales, Andrew M.; Vo-Dinh, Tuan

2017-02-01

The development of rapid, easy-to-use, cost-effective, high accuracy, and high sensitive DNA detection methods for molecular diagnostics has been receiving increasing interest. Over the last five years, our laboratory has developed several chip-based DNA detection techniques including the molecular sentinel-on-chip (MSC), the multiplex MSC, and the inverse molecular sentinel-on-chip (iMS-on-Chip). In these techniques, plasmonic surface-enhanced Raman scattering (SERS) Nanowave chips were functionalized with DNA probes for single-step DNA detection. Sensing mechanisms were based on hybridization of target sequences and DNA probes, resulting in a distance change between SERS reporters and the Nanowave chip's gold surface. This distance change resulted in change in SERS intensity, thus indicating the presence and capture of the target sequences. Our techniques were single-step DNA detection techniques. Target sequences were detected by simple delivery of sample solutions onto DNA probe-functionalized Nanowave chips and SERS signals were measured after 1h - 2h incubation. Target sequence labeling or washing to remove unreacted components was not required, making the techniques simple, easy-to-use, and cost effective. The usefulness of the techniques for medical diagnostics was illustrated by the detection of genetic biomarkers for respiratory viral infection and of dengue virus 4 DNA.

Learning Orthographic Structure With Sequential Generative Neural Networks.

PubMed

Testolin, Alberto; Stoianov, Ivilin; Sperduti, Alessandro; Zorzi, Marco

2016-04-01

Learning the structure of event sequences is a ubiquitous problem in cognition and particularly in language. One possible solution is to learn a probabilistic generative model of sequences that allows making predictions about upcoming events. Though appealing from a neurobiological standpoint, this approach is typically not pursued in connectionist modeling. Here, we investigated a sequential version of the restricted Boltzmann machine (RBM), a stochastic recurrent neural network that extracts high-order structure from sensory data through unsupervised generative learning and can encode contextual information in the form of internal, distributed representations. We assessed whether this type of network can extract the orthographic structure of English monosyllables by learning a generative model of the letter sequences forming a word training corpus. We show that the network learned an accurate probabilistic model of English graphotactics, which can be used to make predictions about the letter following a given context as well as to autonomously generate high-quality pseudowords. The model was compared to an extended version of simple recurrent networks, augmented with a stochastic process that allows autonomous generation of sequences, and to non-connectionist probabilistic models (n-grams and hidden Markov models). We conclude that sequential RBMs and stochastic simple recurrent networks are promising candidates for modeling cognition in the temporal domain. Copyright © 2015 Cognitive Science Society, Inc.

From Lévy to Brownian: A Computational Model Based on Biological Fluctuation

PubMed Central

Nurzaman, Surya G.; Matsumoto, Yoshio; Nakamura, Yutaka; Shirai, Kazumichi; Koizumi, Satoshi; Ishiguro, Hiroshi

2011-01-01

Background Theoretical studies predict that Lévy walks maximizes the chance of encountering randomly distributed targets with a low density, but Brownian walks is favorable inside a patch of targets with high density. Recently, experimental data reports that some animals indeed show a Lévy and Brownian walk movement patterns when forage for foods in areas with low and high density. This paper presents a simple, Gaussian-noise utilizing computational model that can realize such behavior. Methodology/Principal Findings We extend Lévy walks model of one of the simplest creature, Escherichia coli, based on biological fluctuation framework. We build a simulation of a simple, generic animal to observe whether Lévy or Brownian walks will be performed properly depends on the target density, and investigate the emergent behavior in a commonly faced patchy environment where the density alternates. Conclusions/Significance Based on the model, animal behavior of choosing Lévy or Brownian walk movement patterns based on the target density is able to be generated, without changing the essence of the stochastic property in Escherichia coli physiological mechanism as explained by related researches. The emergent behavior and its benefits in a patchy environment are also discussed. The model provides a framework for further investigation on the role of internal noise in realizing adaptive and efficient foraging behavior. PMID:21304911

Spectroscopy and atomic physics of highly ionized Cr, Fe, and Ni for tokamak plasmas

NASA Technical Reports Server (NTRS)

Feldman, U.; Doschek, G. A.; Cheng, C.-C.; Bhatia, A. K.

1980-01-01

The paper considers the spectroscopy and atomic physics for some highly ionized Cr, Fe, and Ni ions produced in tokamak plasmas. Forbidden and intersystem wavelengths for Cr and Ni ions are extrapolated and interpolated using the known wavelengths for Fe lines identified in solar-flare plasmas. Tables of transition probabilities for the B I, C I, N I, O I, and F I isoelectronic sequences are presented, and collision strengths and transition probabilities for Cr, Fe, and Ni ions of the Be I sequence are given. Similarities of tokamak and solar spectra are discussed, and it is shown how the atomic data presented may be used to determine ion abundances and electron densities in low-density plasmas.

Comparative performance of high-density oligonucleotide sequencing and dideoxynucleotide sequencing of HIV type 1 pol from clinical samples.

PubMed

Günthard, H F; Wong, J K; Ignacio, C C; Havlir, D V; Richman, D D

1998-07-01

The performance of the high-density oligonucleotide array methodology (GeneChip) in detecting drug resistance mutations in HIV-1 pol was compared with that of automated dideoxynucleotide sequencing (ABI) of clinical samples, viral stocks, and plasmid-derived NL4-3 clones. Sequences from 29 clinical samples (plasma RNA, n = 17; lymph node RNA, n = 5; lymph node DNA, n = 7) from 12 patients, from 6 viral stock RNA samples, and from 13 NL4-3 clones were generated by both methods. Editing was done independently by a different investigator for each method before comparing the sequences. In addition, NL4-3 wild type (WT) and mutants were mixed in varying concentrations and sequenced by both methods. Overall, a concordance of 99.1% was found for a total of 30,865 bases compared. The comparison of clinical samples (plasma RNA and lymph node RNA and DNA) showed a slightly lower match of base calls, 98.8% for 19,831 nucleotides compared (protease region, 99.5%, n = 8272; RT region, 98.3%, n = 11,316), than for viral stocks and NL4-3 clones (protease region, 99.8%; RT region, 99.5%). Artificial mixing experiments showed a bias toward calling wild-type bases by GeneChip. Discordant base calls are most likely due to differential detection of mixtures. The concordance between GeneChip and ABI was high and appeared dependent on the nature of the templates (directly amplified versus cloned) and the complexity of mixes.

Tailoring sphere density for high pressure physical property measurements on liquids

NASA Astrophysics Data System (ADS)

Secco, R. A.; Tucker, R. F.; Balog, S. P.; Rutter, M. D.

2001-04-01

We present a new method of tailoring the density of a sphere for use as a probe in high pressure-temperature physical property experiments on liquids. The method consists of a composite sphere made of an inner, high density, metallic, spherical core and an exterior, low density, refractory, spherical shell or mantle. Micromechanical techniques are used to fabricate the composite sphere. We describe a relatively simple mechanical device that can grind hemispherical recesses as small as 200 μm in diameter in sapphire and as small as 500 μm in diameter in ruby hemispheres. Examples of composite spheres made with a Pt or WC core and Al2O3 shell used in metallic liquids pressurized to 16 GPa and 1900 K are shown.

HTSstation: a web application and open-access libraries for high-throughput sequencing data analysis.

PubMed

David, Fabrice P A; Delafontaine, Julien; Carat, Solenne; Ross, Frederick J; Lefebvre, Gregory; Jarosz, Yohan; Sinclair, Lucas; Noordermeer, Daan; Rougemont, Jacques; Leleu, Marion

2014-01-01

The HTSstation analysis portal is a suite of simple web forms coupled to modular analysis pipelines for various applications of High-Throughput Sequencing including ChIP-seq, RNA-seq, 4C-seq and re-sequencing. HTSstation offers biologists the possibility to rapidly investigate their HTS data using an intuitive web application with heuristically pre-defined parameters. A number of open-source software components have been implemented and can be used to build, configure and run HTS analysis pipelines reactively. Besides, our programming framework empowers developers with the possibility to design their own workflows and integrate additional third-party software. The HTSstation web application is accessible at http://htsstation.epfl.ch.

HTSstation: A Web Application and Open-Access Libraries for High-Throughput Sequencing Data Analysis

PubMed Central

David, Fabrice P. A.; Delafontaine, Julien; Carat, Solenne; Ross, Frederick J.; Lefebvre, Gregory; Jarosz, Yohan; Sinclair, Lucas; Noordermeer, Daan; Rougemont, Jacques; Leleu, Marion

2014-01-01

The HTSstation analysis portal is a suite of simple web forms coupled to modular analysis pipelines for various applications of High-Throughput Sequencing including ChIP-seq, RNA-seq, 4C-seq and re-sequencing. HTSstation offers biologists the possibility to rapidly investigate their HTS data using an intuitive web application with heuristically pre-defined parameters. A number of open-source software components have been implemented and can be used to build, configure and run HTS analysis pipelines reactively. Besides, our programming framework empowers developers with the possibility to design their own workflows and integrate additional third-party software. The HTSstation web application is accessible at http://htsstation.epfl.ch. PMID:24475057

Always look on both sides: Phylogenetic information conveyed by simple sequence repeat allele sequences

USDA-ARS?s Scientific Manuscript database

Simple sequence repeat (SSR) markers are widely used tools for inferences about genetic diversity, phylogeography and spatial genetic structure. Their applications assume that variation among alleles is essentially caused by an expansion or contraction of the number of repeats and that, accessorily,...

Centromere Locations in Brassica A and C Genomes Revealed Through Half-Tetrad Analysis

PubMed Central

Mason, Annaliese S.; Rousseau-Gueutin, Mathieu; Morice, Jérôme; Bayer, Philipp E.; Besharat, Naghmeh; Cousin, Anouska; Pradhan, Aneeta; Parkin, Isobel A. P.; Chèvre, Anne-Marie; Batley, Jacqueline; Nelson, Matthew N.

2016-01-01

Locating centromeres on genome sequences can be challenging. The high density of repetitive elements in these regions makes sequence assembly problematic, especially when using short-read sequencing technologies. It can also be difficult to distinguish between active and recently extinct centromeres through sequence analysis. An effective solution is to identify genetically active centromeres (functional in meiosis) by half-tetrad analysis. This genetic approach involves detecting heterozygosity along chromosomes in segregating populations derived from gametes (half-tetrads). Unreduced gametes produced by first division restitution mechanisms comprise complete sets of nonsister chromatids. Along these chromatids, heterozygosity is maximal at the centromeres, and homologous recombination events result in homozygosity toward the telomeres. We genotyped populations of half-tetrad-derived individuals (from Brassica interspecific hybrids) using a high-density array of physically anchored SNP markers (Illumina Brassica 60K Infinium array). Mapping the distribution of heterozygosity in these half-tetrad individuals allowed the genetic mapping of all 19 centromeres of the Brassica A and C genomes to the reference Brassica napus genome. Gene and transposable element density across the B. napus genome were also assessed and corresponded well to previously reported genetic map positions. Known centromere-specific sequences were located in the reference genome, but mostly matched unanchored sequences, suggesting that the core centromeric regions may not yet be assembled into the pseudochromosomes of the reference genome. The increasing availability of genetic markers physically anchored to reference genomes greatly simplifies the genetic and physical mapping of centromeres using half-tetrad analysis. We discuss possible applications of this approach, including in species where half-tetrads are currently difficult to isolate. PMID:26614742

Centromere Locations in Brassica A and C Genomes Revealed Through Half-Tetrad Analysis.

PubMed

Mason, Annaliese S; Rousseau-Gueutin, Mathieu; Morice, Jérôme; Bayer, Philipp E; Besharat, Naghmeh; Cousin, Anouska; Pradhan, Aneeta; Parkin, Isobel A P; Chèvre, Anne-Marie; Batley, Jacqueline; Nelson, Matthew N

2016-02-01

Locating centromeres on genome sequences can be challenging. The high density of repetitive elements in these regions makes sequence assembly problematic, especially when using short-read sequencing technologies. It can also be difficult to distinguish between active and recently extinct centromeres through sequence analysis. An effective solution is to identify genetically active centromeres (functional in meiosis) by half-tetrad analysis. This genetic approach involves detecting heterozygosity along chromosomes in segregating populations derived from gametes (half-tetrads). Unreduced gametes produced by first division restitution mechanisms comprise complete sets of nonsister chromatids. Along these chromatids, heterozygosity is maximal at the centromeres, and homologous recombination events result in homozygosity toward the telomeres. We genotyped populations of half-tetrad-derived individuals (from Brassica interspecific hybrids) using a high-density array of physically anchored SNP markers (Illumina Brassica 60K Infinium array). Mapping the distribution of heterozygosity in these half-tetrad individuals allowed the genetic mapping of all 19 centromeres of the Brassica A and C genomes to the reference Brassica napus genome. Gene and transposable element density across the B. napus genome were also assessed and corresponded well to previously reported genetic map positions. Known centromere-specific sequences were located in the reference genome, but mostly matched unanchored sequences, suggesting that the core centromeric regions may not yet be assembled into the pseudochromosomes of the reference genome. The increasing availability of genetic markers physically anchored to reference genomes greatly simplifies the genetic and physical mapping of centromeres using half-tetrad analysis. We discuss possible applications of this approach, including in species where half-tetrads are currently difficult to isolate. Copyright © 2016 by the Genetics Society of America.

MR arthrography in chondromalacia patellae diagnosis on a low-field open magnet system.

PubMed

Harman, Mustafa; Ipeksoy, Umit; Dogan, Ali; Arslan, Halil; Etlik, Omer

2003-01-01

The purpose of this study was to compare the diagnostic efficacy conventional MRI and MR arthrography (MRA) in the diagnosis of chondromalacia patella (CP) on a low-field open magnet system (LFOMS), correlated with arthroscopy. Forty-two patients (50 knees) with pain in the anterior part of the knee were prospectively examined with LFOMS, including T1-weighted, proton density-weighted and T2-weighted sequences. All were also examined T1-weighted MRI after intraarticular injection of dilue gadopentetate dimeglumine. Two observers, who reached a consensus interpretation, evaluated each imaging technique independently. Thirty-six of the 50 facets examined had chondromalacia shown by arthroscopy, which was used as the standard of reference. The sensitivity, specificity and accuracy of each imaging technique in the diagnosis of each stage of CP were determined and compared by using the McNemar two-tailed analysis. Arthroscopy showed that 16 facets were normal. Four (30%) of 13 grade 1 lesions were detected with T1. Four lesions (30%) with T2 and three lesions (23%) with proton-weighted images were detected. Seven (53%) of 13 grade 1 lesions were detected with MRA. Grade 2 abnormalities were diagnosed in two (33%) of six facets with proton density-weighted pulse sequences, two (33%) of six facets with T1-weighted pulse sequences, in three (50%) of six facets with T2-weighted pulse sequences, in five (83%) of six facets with MRA sequences. Grade 3 abnormalities were diagnosed in three (71%) of seven facets with proton density- and T1-weighted images, five (71%) of seven facets with T2-weighted pulse sequences, six (85%) of seven facets with MRA sequences. Grade 4 CP was detected with equal sensitivity with T1-, proton density- and T2-weighted pulse sequences, all showing seven (87%) of the eight lesions. MRA again showed these findings in all eight patients. All imaging techniques were insensitive to grade 1 lesions and highly sensitive to grade 4 lesion, so that no significant difference among the techniques could be shown. All imaging technique studied had high specificity and accuracy in the detection and grading of CP; however, MRA was more sensitive than T1-weighted and proton density-weighted MR imaging on a LFOMS. Although the arthrographic techniques were not significantly better than T2-weighted imaging, the number of false-positive diagnosis was greatest with T2-weighted MRI.

SNP discovery by high-throughput sequencing in soybean

PubMed Central

2010-01-01

Background With the advance of new massively parallel genotyping technologies, quantitative trait loci (QTL) fine mapping and map-based cloning become more achievable in identifying genes for important and complex traits. Development of high-density genetic markers in the QTL regions of specific mapping populations is essential for fine-mapping and map-based cloning of economically important genes. Single nucleotide polymorphisms (SNPs) are the most abundant form of genetic variation existing between any diverse genotypes that are usually used for QTL mapping studies. The massively parallel sequencing technologies (Roche GS/454, Illumina GA/Solexa, and ABI/SOLiD), have been widely applied to identify genome-wide sequence variations. However, it is still remains unclear whether sequence data at a low sequencing depth are enough to detect the variations existing in any QTL regions of interest in a crop genome, and how to prepare sequencing samples for a complex genome such as soybean. Therefore, with the aims of identifying SNP markers in a cost effective way for fine-mapping several QTL regions, and testing the validation rate of the putative SNPs predicted with Solexa short sequence reads at a low sequencing depth, we evaluated a pooled DNA fragment reduced representation library and SNP detection methods applied to short read sequences generated by Solexa high-throughput sequencing technology. Results A total of 39,022 putative SNPs were identified by the Illumina/Solexa sequencing system using a reduced representation DNA library of two parental lines of a mapping population. The validation rates of these putative SNPs predicted with low and high stringency were 72% and 85%, respectively. One hundred sixty four SNP markers resulted from the validation of putative SNPs and have been selectively chosen to target a known QTL, thereby increasing the marker density of the targeted region to one marker per 42 K bp. Conclusions We have demonstrated how to quickly identify large numbers of SNPs for fine mapping of QTL regions by applying massively parallel sequencing combined with genome complexity reduction techniques. This SNP discovery approach is more efficient for targeting multiple QTL regions in a same genetic population, which can be applied to other crops. PMID:20701770

Carbon nanofibers (CNFs) supported cobalt- nickel sulfide (CoNi2S4) nanoparticles hybrid anode for high performance lithium ion capacitor.

PubMed

Jagadale, Ajay; Zhou, Xuan; Blaisdell, Douglas; Yang, Sen

2018-01-25

Lithium ion capacitors possess an ability to bridge the gap between lithium ion battery and supercapacitor. The main concern of fabricating lithium ion capacitors is poor rate capability and cyclic stability of the anode material which uses sluggish faradaic reactions to store an electric charge. Herein, we have fabricated high performance hybrid anode material based on carbon nanofibers (CNFs) and cobalt-nickel sulfide (CoNi 2 S 4 ) nanoparticles via simple electrospinning and electrodeposition methods. Porous and high conducting CNF@CoNi 2 S 4 electrode acts as an expressway network for electronic and ionic diffusion during charging-discharging processes. The effect of anode to cathode mass ratio on the performance has been studied by fabricating lithium ion capacitors with different mass ratios. The surface controlled contribution of CNF@CoNi 2 S 4 electrode was 73% which demonstrates its excellent rate capability. Lithium ion capacitor fabricated with CNF@CoNi 2 S 4 to AC mass ratio of 1:2.6 showed excellent energy density of 85.4 Wh kg -1 with the power density of 150 W kg -1 . Also, even at the high power density of 15 kW kg -1 , the cell provided the energy density of 35 Wh kg -1 . This work offers a new strategy for designing high-performance hybrid anode with the combination of simple and cost effective approaches.

A Model Connecting Galaxy Masses, Star Formation Rates, and Dust Temperatures across Cosmic Time

NASA Astrophysics Data System (ADS)

Imara, Nia; Loeb, Abraham; Johnson, Benjamin D.; Conroy, Charlie; Behroozi, Peter

2018-02-01

We investigate the evolution of dust content in galaxies from redshifts z = 0 to z = 9.5. Using empirically motivated prescriptions, we model galactic-scale properties—including halo mass, stellar mass, star formation rate, gas mass, and metallicity—to make predictions for the galactic evolution of dust mass and dust temperature in main-sequence galaxies. Our simple analytic model, which predicts that galaxies in the early universe had greater quantities of dust than their low-redshift counterparts, does a good job of reproducing observed trends between galaxy dust and stellar mass out to z ≈ 6. We find that for fixed galaxy stellar mass, the dust temperature increases from z = 0 to z = 6. Our model forecasts a population of low-mass, high-redshift galaxies with interstellar dust as hot as, or hotter than, their more massive counterparts; but this prediction needs to be constrained by observations. Finally, we make predictions for observing 1.1 mm flux density arising from interstellar dust emission with the Atacama Large Millimeter Array.

UPIC + GO: Zeroing in on informative markers

USDA-ARS?s Scientific Manuscript database

Microsatellites/SSRs (simple sequence repeats) have become a powerful tool in genomic biology because of their broad range of applications and availability. An efficient method recently developed to generate microsatellite-enriched libraries used in combination with high throughput DNA pyrosequencin...

An ultra-high-density bin map facilitates high-throughput QTL mapping of horticultural traits in pepper (Capsicum annuum).

PubMed

Han, Koeun; Jeong, Hee-Jin; Yang, Hee-Bum; Kang, Sung-Min; Kwon, Jin-Kyung; Kim, Seungill; Choi, Doil; Kang, Byoung-Cheorl

2016-04-01

Most agricultural traits are controlled by quantitative trait loci (QTLs); however, there are few studies on QTL mapping of horticultural traits in pepper (Capsicum spp.) due to the lack of high-density molecular maps and the sequence information. In this study, an ultra-high-density map and 120 recombinant inbred lines (RILs) derived from a cross between C. annuum'Perennial' and C. annuum'Dempsey' were used for QTL mapping of horticultural traits. Parental lines and RILs were resequenced at 18× and 1× coverage, respectively. Using a sliding window approach, an ultra-high-density bin map containing 2,578 bins was constructed. The total map length of the map was 1,372 cM, and the average interval between bins was 0.53 cM. A total of 86 significant QTLs controlling 17 horticultural traits were detected. Among these, 32 QTLs controlling 13 traits were major QTLs. Our research shows that the construction of bin maps using low-coverage sequence is a powerful method for QTL mapping, and that the short intervals between bins are helpful for fine-mapping of QTLs. Furthermore, bin maps can be used to improve the quality of reference genomes by elucidating the genetic order of unordered regions and anchoring unassigned scaffolds to linkage groups. © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

A PORTRAIT OF COLD GAS IN GALAXIES AT 60 pc RESOLUTION AND A SIMPLE METHOD TO TEST HYPOTHESES THAT LINK SMALL-SCALE ISM STRUCTURE TO GALAXY-SCALE PROCESSES

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

Leroy, Adam K.; Hughes, Annie; Schruba, Andreas

2016-11-01

The cloud-scale density, velocity dispersion, and gravitational boundedness of the interstellar medium (ISM) vary within and among galaxies. In turbulent models, these properties play key roles in the ability of gas to form stars. New high-fidelity, high-resolution surveys offer the prospect to measure these quantities across galaxies. We present a simple approach to make such measurements and to test hypotheses that link small-scale gas structure to star formation and galactic environment. Our calculations capture the key physics of the Larson scaling relations, and we show good correspondence between our approach and a traditional “cloud properties” treatment. However, we argue thatmore » our method is preferable in many cases because of its simple, reproducible characterization of all emission. Using, low- J {sup 12}CO data from recent surveys, we characterize the molecular ISM at 60 pc resolution in the Antennae, the Large Magellanic Cloud (LMC), M31, M33, M51, and M74. We report the distributions of surface density, velocity dispersion, and gravitational boundedness at 60 pc scales and show galaxy-to-galaxy and intragalaxy variations in each. The distribution of flux as a function of surface density appears roughly lognormal with a 1 σ width of ∼0.3 dex, though the center of this distribution varies from galaxy to galaxy. The 60 pc resolution line width and molecular gas surface density correlate well, which is a fundamental behavior expected for virialized or free-falling gas. Varying the measurement scale for the LMC and M31, we show that the molecular ISM has higher surface densities, lower line widths, and more self-gravity at smaller scales.« less

A Simple Method for High-Performance, Solution-Processed, Amorphous ZrO2 Gate Insulator TFT with a High Concentration Precursor

PubMed Central

Cai, Wei; Zhu, Zhennan; Wei, Jinglin; Fang, Zhiqiang; Zheng, Zeke; Zhou, Shangxiong; Peng, Junbiao; Lu, Xubing

2017-01-01

Solution-processed high-k dielectric TFTs attract much attention since they cost relatively little and have a simple fabrication process. However, it is still a challenge to reduce the leakage of the current density of solution-processed dielectric TFTs. Here, a simple solution method is presented towards enhanced performance of ZrO2 films by intentionally increasing the concentration of precursor. The ZrO2 films not only exhibit a low leakage current density of 10−6 A/cm2 at 10 V and a breakdown field of 2.5 MV/cm, but also demonstrate a saturation mobility of 12.6 cm2·V−1·s−1 and a Ion/Ioff ratio of 106 in DC pulse sputtering IGZO-TFTs based on these films. Moreover, the underlying mechanism of influence of precursor concentration on film formation is presented. Higher concentration precursor results in a thicker film within same coating times with reduced ZrO2/IGZO interface defects and roughness. It shows the importance of thickness, roughness, and annealing temperature in solution-processed dielectric oxide TFT and provides an approach to precisely control solution-processed oxide films thickness. PMID:28825652

A Simple Method for High-Performance, Solution-Processed, Amorphous ZrO₂ Gate Insulator TFT with a High Concentration Precursor.

PubMed

Cai, Wei; Zhu, Zhennan; Wei, Jinglin; Fang, Zhiqiang; Ning, Honglong; Zheng, Zeke; Zhou, Shangxiong; Yao, Rihui; Peng, Junbiao; Lu, Xubing

2017-08-21

Solution-processed high-k dielectric TFTs attract much attention since they cost relatively little and have a simple fabrication process. However, it is still a challenge to reduce the leakage of the current density of solution-processed dielectric TFTs. Here, a simple solution method is presented towards enhanced performance of ZrO₂ films by intentionally increasing the concentration of precursor. The ZrO₂ films not only exhibit a low leakage current density of 10 -6 A/cm² at 10 V and a breakdown field of 2.5 MV/cm, but also demonstrate a saturation mobility of 12.6 cm²·V -1 ·s -1 and a I on /I off ratio of 10⁶ in DC pulse sputtering IGZO-TFTs based on these films. Moreover, the underlying mechanism of influence of precursor concentration on film formation is presented. Higher concentration precursor results in a thicker film within same coating times with reduced ZrO₂/IGZO interface defects and roughness. It shows the importance of thickness, roughness, and annealing temperature in solution-processed dielectric oxide TFT and provides an approach to precisely control solution-processed oxide films thickness.

WebSat--a web software for microsatellite marker development.

PubMed

Martins, Wellington Santos; Lucas, Divino César Soares; Neves, Kelligton Fabricio de Souza; Bertioli, David John

2009-01-01

Simple sequence repeats (SSR), also known as microsatellites, have been extensively used as molecular markers due to their abundance and high degree of polymorphism. We have developed a simple to use web software, called WebSat, for microsatellite molecular marker prediction and development. WebSat is accessible through the Internet, requiring no program installation. Although a web solution, it makes use of Ajax techniques, providing a rich, responsive user interface. WebSat allows the submission of sequences, visualization of microsatellites and the design of primers suitable for their amplification. The program allows full control of parameters and the easy export of the resulting data, thus facilitating the development of microsatellite markers. The web tool may be accessed at http://purl.oclc.org/NET/websat/

High Discharge Energy Density at Low Electric Field Using an Aligned Titanium Dioxide/Lead Zirconate Titanate Nanowire Array.

PubMed

Zhang, Dou; Liu, Weiwei; Guo, Ru; Zhou, Kechao; Luo, Hang

2018-02-01

Polymer-based capacitors with high energy density have attracted significant attention in recent years due to their wide range of potential applications in electronic devices. However, the obtained high energy density is predominantly dependent on high applied electric field, e.g., 400-600 kV mm -1 , which may bring more challenges relating to the failure probability. Here, a simple two-step method for synthesizing titanium dioxide/lead zirconate titanate nanowire arrays is exploited and a demonstration of their ability to achieve high discharge energy density capacitors for low operating voltage applications is provided. A high discharge energy density of 6.9 J cm -3 is achieved at low electric fields, i.e., 143 kV mm -1 , which is attributed to the high relative permittivity of 218.9 at 1 kHz and high polarization of 23.35 µC cm -2 at this electric field. The discharge energy density obtained in this work is the highest known for a ceramic/polymer nanocomposite at such a low electric field. The novel nanowire arrays used in this work are applicable to a wide range of fields, such as energy harvesting, energy storage, and photocatalysis.

A high-density transcript linkage map with 1,845 expressed genes positioned by microarray-based Single Feature Polymorphisms (SFP) in Eucalyptus

PubMed Central

2011-01-01

Background Technological advances are progressively increasing the application of genomics to a wider array of economically and ecologically important species. High-density maps enriched for transcribed genes facilitate the discovery of connections between genes and phenotypes. We report the construction of a high-density linkage map of expressed genes for the heterozygous genome of Eucalyptus using Single Feature Polymorphism (SFP) markers. Results SFP discovery and mapping was achieved using pseudo-testcross screening and selective mapping to simultaneously optimize linkage mapping and microarray costs. SFP genotyping was carried out by hybridizing complementary RNA prepared from 4.5 year-old trees xylem to an SFP array containing 103,000 25-mer oligonucleotide probes representing 20,726 unigenes derived from a modest size expressed sequence tags collection. An SFP-mapping microarray with 43,777 selected candidate SFP probes representing 15,698 genes was subsequently designed and used to genotype SFPs in a larger subset of the segregating population drawn by selective mapping. A total of 1,845 genes were mapped, with 884 of them ordered with high likelihood support on a framework map anchored to 180 microsatellites with average density of 1.2 cM. Using more probes per unigene increased by two-fold the likelihood of detecting segregating SFPs eventually resulting in more genes mapped. In silico validation showed that 87% of the SFPs map to the expected location on the 4.5X draft sequence of the Eucalyptus grandis genome. Conclusions The Eucalyptus 1,845 gene map is the most highly enriched map for transcriptional information for any forest tree species to date. It represents a major improvement on the number of genes previously positioned on Eucalyptus maps and provides an initial glimpse at the gene space for this global tree genome. A general protocol is proposed to build high-density transcript linkage maps in less characterized plant species by SFP genotyping with a concurrent objective of reducing microarray costs. HIgh-density gene-rich maps represent a powerful resource to assist gene discovery endeavors when used in combination with QTL and association mapping and should be especially valuable to assist the assembly of reference genome sequences soon to come for several plant and animal species. PMID:21492453

BASIC: A Simple and Accurate Modular DNA Assembly Method.

PubMed

Storch, Marko; Casini, Arturo; Mackrow, Ben; Ellis, Tom; Baldwin, Geoff S

2017-01-01

Biopart Assembly Standard for Idempotent Cloning (BASIC) is a simple, accurate, and robust DNA assembly method. The method is based on linker-mediated DNA assembly and provides highly accurate DNA assembly with 99 % correct assemblies for four parts and 90 % correct assemblies for seven parts [1]. The BASIC standard defines a single entry vector for all parts flanked by the same prefix and suffix sequences and its idempotent nature means that the assembled construct is returned in the same format. Once a part has been adapted into the BASIC format it can be placed at any position within a BASIC assembly without the need for reformatting. This allows laboratories to grow comprehensive and universal part libraries and to share them efficiently. The modularity within the BASIC framework is further extended by the possibility of encoding ribosomal binding sites (RBS) and peptide linker sequences directly on the linkers used for assembly. This makes BASIC a highly versatile library construction method for combinatorial part assembly including the construction of promoter, RBS, gene variant, and protein-tag libraries. In comparison with other DNA assembly standards and methods, BASIC offers a simple robust protocol; it relies on a single entry vector, provides for easy hierarchical assembly, and is highly accurate for up to seven parts per assembly round [2].

Accurate, high-throughput typing of copy number variation using paralogue ratios from dispersed repeats

PubMed Central

Armour, John A. L.; Palla, Raquel; Zeeuwen, Patrick L. J. M.; den Heijer, Martin; Schalkwijk, Joost; Hollox, Edward J.

2007-01-01

Recent work has demonstrated an unexpected prevalence of copy number variation in the human genome, and has highlighted the part this variation may play in predisposition to common phenotypes. Some important genes vary in number over a high range (e.g. DEFB4, which commonly varies between two and seven copies), and have posed formidable technical challenges for accurate copy number typing, so that there are no simple, cheap, high-throughput approaches suitable for large-scale screening. We have developed a simple comparative PCR method based on dispersed repeat sequences, using a single pair of precisely designed primers to amplify products simultaneously from both test and reference loci, which are subsequently distinguished and quantified via internal sequence differences. We have validated the method for the measurement of copy number at DEFB4 by comparison of results from >800 DNA samples with copy number measurements by MAPH/REDVR, MLPA and array-CGH. The new Paralogue Ratio Test (PRT) method can require as little as 10 ng genomic DNA, appears to be comparable in accuracy to the other methods, and for the first time provides a rapid, simple and inexpensive method for copy number analysis, suitable for application to typing thousands of samples in large case-control association studies. PMID:17175532

Comparative Genome Sequence Analysis of the Bpa/Str Region in Mouse and Man

PubMed Central

Mallon, A.-M.; Platzer, M.; Bate, R.; Gloeckner, G.; Botcherby, M.R.M.; Nordsiek, G.; Strivens, M.A.; Kioschis, P.; Dangel, A.; Cunningham, D.; Straw, R.N.A.; Weston, P.; Gilbert, M.; Fernando, S.; Goodall, K.; Hunter, G.; Greystrong, J.S.; Clarke, D.; Kimberley, C.; Goerdes, M.; Blechschmidt, K.; Rump, A.; Hinzmann, B.; Mundy, C.R.; Miller, W.; Poustka, A.; Herman, G.E.; Rhodes, M.; Denny, P.; Rosenthal, A.; Brown, S.D.M.

2000-01-01

The progress of human and mouse genome sequencing programs presages the possibility of systematic cross-species comparison of the two genomes as a powerful tool for gene and regulatory element identification. As the opportunities to perform comparative sequence analysis emerge, it is important to develop parameters for such analyses and to examine the outcomes of cross-species comparison. Our analysis used gene prediction and a database search of 430 kb of genomic sequence covering the Bpa/Str region of the mouse X chromosome, and 745 kb of genomic sequence from the homologous human X chromosome region. We identified 11 genes in mouse and 13 genes and two pseudogenes in human. In addition, we compared the mouse and human sequences using pairwise alignment and searches for evolutionary conserved regions (ECRs) exceeding a defined threshold of sequence identity. This approach aided the identification of at least four further putative conserved genes in the region. Comparative sequencing revealed that this region is a mosaic in evolutionary terms, with considerably more rearrangement between the two species than realized previously from comparative mapping studies. Surprisingly, this region showed an extremely high LINE and low SINE content, low G+C content, and yet a relatively high gene density, in contrast to the low gene density usually associated with such regions. [The sequence data described in this paper have been submitted to EMBL under the following accession nos.: Mouse Genomic Sequence: Mouse contig A (AL021127), Mouse contig B (AL049866), BAC41M10 (AL136328), PAC303O11(AL136329). Human Genomic Sequence: Human contig 1 (U82671, U82670), Human contig 2 (U82695).] PMID:10854409

THE FIRST FERMI IN A HIGH ENERGY NUCLEAR COLLISION.

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

KRASNITZ,A.

1999-08-09

At very high energies, weak coupling, non-perturbative methods can be used to study classical gluon production in nuclear collisions. One observes in numerical simulations that after an initial formation time, the produced partons are on shell, and their subsequent evolution can be studied using transport theory. At the initial formation time, a simple non-perturbative relation exists between the energy and number densities of the produced partons, and a scale determined by the saturated parton density in the nucleus.

Deriving Sea Surface Salinity and Density Variations from Satellite and Aircraft Microwave Radiometer Measurements: Application to Coastal Plumes Using STARRS

DTIC Science & Technology

2007-11-01

again, with of the prevailing T, S, and, hence, D gradients through the the advent of high-performance spaceborne altimeters (e.g., high- aspect - ratio ... rectangular domains with linear dimensions largely , if not completely, eliminated by the differencing oper- of about 60 km in a 4-h flight. (See...strongest A simple four- quadrant arctangent of the terms in the density in the 00 and 1800 directions, whereas compensation is most ratio would serve our

Genome sequencing in microfabricated high-density picolitre reactors.

PubMed

Margulies, Marcel; Egholm, Michael; Altman, William E; Attiya, Said; Bader, Joel S; Bemben, Lisa A; Berka, Jan; Braverman, Michael S; Chen, Yi-Ju; Chen, Zhoutao; Dewell, Scott B; Du, Lei; Fierro, Joseph M; Gomes, Xavier V; Godwin, Brian C; He, Wen; Helgesen, Scott; Ho, Chun Heen; Ho, Chun He; Irzyk, Gerard P; Jando, Szilveszter C; Alenquer, Maria L I; Jarvie, Thomas P; Jirage, Kshama B; Kim, Jong-Bum; Knight, James R; Lanza, Janna R; Leamon, John H; Lefkowitz, Steven M; Lei, Ming; Li, Jing; Lohman, Kenton L; Lu, Hong; Makhijani, Vinod B; McDade, Keith E; McKenna, Michael P; Myers, Eugene W; Nickerson, Elizabeth; Nobile, John R; Plant, Ramona; Puc, Bernard P; Ronan, Michael T; Roth, George T; Sarkis, Gary J; Simons, Jan Fredrik; Simpson, John W; Srinivasan, Maithreyan; Tartaro, Karrie R; Tomasz, Alexander; Vogt, Kari A; Volkmer, Greg A; Wang, Shally H; Wang, Yong; Weiner, Michael P; Yu, Pengguang; Begley, Richard F; Rothberg, Jonathan M

2005-09-15

The proliferation of large-scale DNA-sequencing projects in recent years has driven a search for alternative methods to reduce time and cost. Here we describe a scalable, highly parallel sequencing system with raw throughput significantly greater than that of state-of-the-art capillary electrophoresis instruments. The apparatus uses a novel fibre-optic slide of individual wells and is able to sequence 25 million bases, at 99% or better accuracy, in one four-hour run. To achieve an approximately 100-fold increase in throughput over current Sanger sequencing technology, we have developed an emulsion method for DNA amplification and an instrument for sequencing by synthesis using a pyrosequencing protocol optimized for solid support and picolitre-scale volumes. Here we show the utility, throughput, accuracy and robustness of this system by shotgun sequencing and de novo assembly of the Mycoplasma genitalium genome with 96% coverage at 99.96% accuracy in one run of the machine.

Analysis of sequence diversity through internal transcribed spacers and simple sequence repeats to identify Dendrobium species.

PubMed

Liu, Y T; Chen, R K; Lin, S J; Chen, Y C; Chin, S W; Chen, F C; Lee, C Y

2014-04-08

The Orchidaceae is one of the largest and most diverse families of flowering plants. The Dendrobium genus has high economic potential as ornamental plants and for medicinal purposes. In addition, the species of this genus are able to produce large crops. However, many Dendrobium varieties are very similar in outward appearance, making it difficult to distinguish one species from another. This study demonstrated that the 12 Dendrobium species used in this study may be divided into 2 groups by internal transcribed spacer (ITS) sequence analysis. Red and yellow flowers may also be used to separate these species into 2 main groups. In particular, the deciduous characteristic is associated with the ITS genetic diversity of the A group. Of 53 designed simple sequence repeat (SSR) primer pairs, 7 pairs were polymorphic for polymerase chain reaction products that were amplified from a specific band. The results of this study demonstrate that these 7 SSR primer pairs may potentially be used to identify Dendrobium species and their progeny in future studies.

Development and characterization of simple sequence repeats for Bipolaris sokiniana and cross transferability to related species

USDA-ARS?s Scientific Manuscript database

Simple sequence repeats (SSR) markers were developed from a small insert genomic library for Bipolaris sorokiniana, a mitosporic fungal pathogen that causes spot blotch and root rot in switchgrass. About 59% of sequenced clones (n=384) harbored various SSR motifs. After eliminating the redundant seq...

Tuning carrier density across Dirac point in epitaxial graphene on SiC by corona discharge

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

Lartsev, Arseniy; Yager, Tom; Lara-Avila, Samuel, E-mail: samuel.lara@chalmers.se

We demonstrate reversible carrier density control across the Dirac point (Δn ∼ 10{sup 13 }cm{sup −2}) in epitaxial graphene on SiC (SiC/G) via high electrostatic potential gating with ions produced by corona discharge. The method is attractive for applications where graphene with a fixed carrier density is needed, such as quantum metrology, and more generally as a simple method of gating 2DEGs formed at semiconductor interfaces and in topological insulators.

Divide and Conquer (DC) BLAST: fast and easy BLAST execution within HPC environments

DOE PAGES

Yim, Won Cheol; Cushman, John C.

2017-07-22

Bioinformatics is currently faced with very large-scale data sets that lead to computational jobs, especially sequence similarity searches, that can take absurdly long times to run. For example, the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST and BLAST+) suite, which is by far the most widely used tool for rapid similarity searching among nucleic acid or amino acid sequences, is highly central processing unit (CPU) intensive. While the BLAST suite of programs perform searches very rapidly, they have the potential to be accelerated. In recent years, distributed computing environments have become more widely accessible andmore » used due to the increasing availability of high-performance computing (HPC) systems. Therefore, simple solutions for data parallelization are needed to expedite BLAST and other sequence analysis tools. However, existing software for parallel sequence similarity searches often requires extensive computational experience and skill on the part of the user. In order to accelerate BLAST and other sequence analysis tools, Divide and Conquer BLAST (DCBLAST) was developed to perform NCBI BLAST searches within a cluster, grid, or HPC environment by using a query sequence distribution approach. Scaling from one (1) to 256 CPU cores resulted in significant improvements in processing speed. Thus, DCBLAST dramatically accelerates the execution of BLAST searches using a simple, accessible, robust, and parallel approach. DCBLAST works across multiple nodes automatically and it overcomes the speed limitation of single-node BLAST programs. DCBLAST can be used on any HPC system, can take advantage of hundreds of nodes, and has no output limitations. Thus, this freely available tool simplifies distributed computation pipelines to facilitate the rapid discovery of sequence similarities between very large data sets.« less

Divide and Conquer (DC) BLAST: fast and easy BLAST execution within HPC environments

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

Yim, Won Cheol; Cushman, John C.

Bioinformatics is currently faced with very large-scale data sets that lead to computational jobs, especially sequence similarity searches, that can take absurdly long times to run. For example, the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST and BLAST+) suite, which is by far the most widely used tool for rapid similarity searching among nucleic acid or amino acid sequences, is highly central processing unit (CPU) intensive. While the BLAST suite of programs perform searches very rapidly, they have the potential to be accelerated. In recent years, distributed computing environments have become more widely accessible andmore » used due to the increasing availability of high-performance computing (HPC) systems. Therefore, simple solutions for data parallelization are needed to expedite BLAST and other sequence analysis tools. However, existing software for parallel sequence similarity searches often requires extensive computational experience and skill on the part of the user. In order to accelerate BLAST and other sequence analysis tools, Divide and Conquer BLAST (DCBLAST) was developed to perform NCBI BLAST searches within a cluster, grid, or HPC environment by using a query sequence distribution approach. Scaling from one (1) to 256 CPU cores resulted in significant improvements in processing speed. Thus, DCBLAST dramatically accelerates the execution of BLAST searches using a simple, accessible, robust, and parallel approach. DCBLAST works across multiple nodes automatically and it overcomes the speed limitation of single-node BLAST programs. DCBLAST can be used on any HPC system, can take advantage of hundreds of nodes, and has no output limitations. Thus, this freely available tool simplifies distributed computation pipelines to facilitate the rapid discovery of sequence similarities between very large data sets.« less

High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions.

PubMed

Krebs, Arnaud R; Dessus-Babus, Sophie; Burger, Lukas; Schübeler, Dirk

2014-09-26

The majority of mammalian promoters are CpG islands; regions of high CG density that require protection from DNA methylation to be functional. Importantly, how sequence architecture mediates this unmethylated state remains unclear. To address this question in a comprehensive manner, we developed a method to interrogate methylation states of hundreds of sequence variants inserted at the same genomic site in mouse embryonic stem cells. Using this assay, we were able to quantify the contribution of various sequence motifs towards the resulting DNA methylation state. Modeling of this comprehensive dataset revealed that CG density alone is a minor determinant of their unmethylated state. Instead, these data argue for a principal role for transcription factor binding sites, a prediction confirmed by testing synthetic mutant libraries. Taken together, these findings establish the hierarchy between the two cis-encoded mechanisms that define the DNA methylation state and thus the transcriptional competence of CpG islands.

Research Techniques Made Simple: Single-Cell RNA Sequencing and its Applications in Dermatology.

PubMed

Wu, Xiaojun; Yang, Bin; Udo-Inyang, Imo; Ji, Suyun; Ozog, David; Zhou, Li; Mi, Qing-Sheng

2018-05-01

RNA sequencing is one of the most highly reliable and reproducible methods of assessing the cell transcriptome. As high-throughput RNA sequencing libraries at the single cell level have recently developed, single cell RNA sequencing has become more feasible and popular in biology research. Single cell RNA sequencing allows investigators to evaluate cell transcriptional profiles at the single cell level. It has become a very useful tool to perform investigations that could not be addressed by other methodologies, such as the assessment of cell-to-cell variation, the identification of rare populations, and the determination of heterogeneity within a cell population. So far, the single cell RNA sequencing technique has been widely applied to embryonic development, immune cell development, and human disease progress and treatment. Here, we describe the history of single cell technology development and its potential application in the field of dermatology. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

MnO2 nanowires-decorated carbon fiber cloth as electrodes for aqueous asymmetric supercapacitor

NASA Astrophysics Data System (ADS)

Hong, Congcong; Wang, Xing; Yu, Houlin; Wu, Huaping; Wang, Jianshan; Liu, Aiping

Manganese dioxide nanowires (MnO2 NWs) anchored on carbon fiber cloth (CFC) were fabricated through a simple hydrothermal reaction and used as integrated electrodes for supercapacitor. The morphology-dependent electrochemical performance of MnO2 NWs was confirmed, yielding good capacitance performance with a high specific capacitance of 3.88Fṡcm‑2 at a charge-discharge current density of 5mAṡcm‑2 and excellent stability of 91.5% capacitance retention after 3000 cycles. Moreover, the composite electrodes were used to fabricate supercapacitors, which showed a high specific capacitance of 194mFṡcm‑2 at a charge-discharge current density of 2mAṡcm‑2 and high energy density of 0.108mWhṡcm‑2 at power density of 2mWṡcm‑2, foreboding its potential application for high-performance supercapacitor.

Improved first-pass spiral myocardial perfusion imaging with variable density trajectories.

PubMed

Salerno, Michael; Sica, Christopher; Kramer, Christopher M; Meyer, Craig H

2013-11-01

To develop and evaluate variable-density spiral first-pass perfusion pulse sequences for improved efficiency and off-resonance performance and to demonstrate the utility of an apodizing density compensation function (DCF) to improve signal-to-noise ratio (SNR) and reduce dark-rim artifact caused by cardiac motion and Gibbs Ringing. Three variable density spiral trajectories were designed, simulated, and evaluated in 18 normal subjects, and in eight patients with cardiac pathology on a 1.5T scanner. By using a DCF, which intentionally apodizes the k-space data, the sidelobe amplitude of the theoretical point spread function (PSF) is reduced by 68%, with only a 13% increase in the full-width at half-maximum of the main-lobe when compared with the same data corrected with a conventional variable-density DCF, and has an 8% higher resolution than a uniform density spiral with the same number of interleaves and readout duration. Furthermore, this strategy results in a greater than 60% increase in measured SNR when compared with the same variable-density spiral data corrected with a conventional DCF (P < 0.01). Perfusion defects could be clearly visualized with minimal off-resonance and dark-rim artifacts. Variable-density spiral pulse sequences using an apodized DCF produce high-quality first-pass perfusion images with minimal dark-rim and off-resonance artifacts, high SNR and contrast-to-noise ratio, and good delineation of resting perfusion abnormalities. Copyright © 2012 Wiley Periodicals, Inc.

[Methodological aspects of evaluation of potential lipid capacity for peroxidation from the serum levels of TBA-active products during iron ion stimulation].

PubMed

Kulikova, A I; Tugusheva, F A; Zubina, I M; Shepilova, I N

2008-05-01

The authors propose a simple and reproducible procedure for using iron ions to stimulate serum lipid peroxidation, with TBA-active products being further determined. The procedure determines the reserve of lipids that can be oxidized during oxidative stress. A combination of direct studies and correlation analysis suggests that low-density lipoproteins and very low-density lipoproteins are the major substrates for lipid peroxidation while high-density lipoproteins show a high resistance to this process. The presented procedure may be used to monitor lipid peroxidation in various conditions and upon various exposures in common laboratory practice.

Pyrosequencing-based validation of a simple cell-suspension polymerase chain reaction assay for Campylobacter with application of high-processivity polymerase and novel internal amplification controls for rapid and specific detection.

PubMed

Oakley, Brian B; Line, J Eric; Berrang, Mark E; Johnson, Jessica M; Buhr, R Jeff; Cox, Nelson A; Hiett, Kelli L; Seal, Bruce S

2012-02-01

Although Campylobacter is an important food-borne human pathogen, there remains a lack of molecular diagnostic assays that are simple to use, cost-effective, and provide rapid results in research, clinical, or regulatory laboratories. Of the numerous Campylobacter assays that do exist, to our knowledge none has been empirically tested for specificity using high-throughput sequencing. Here we demonstrate the power of next-generation sequencing to determine the specificity of a widely cited Campylobacter-specific polymerase chain reaction (PCR) assay and describe a rapid method for direct cell suspension PCR to quickly and easily screen samples for Campylobacter. We present a specific protocol which eliminates the need for time-consuming and expensive genomic DNA extractions and, using a high-processivity polymerase, demonstrate conclusive screening of samples in <1 h. Pyrosequencing results show the assay to be extremely (>99%) sensitive, and spike-back experiments demonstrated a detection threshold of <10(2) CFU mL(-1). Additionally, we present 2 newly designed broad-range bacterial primer sets targeting the 23S rRNA gene that have wide applicability as internal amplification controls. Empirical testing of putative taxon-specific assays using high-throughput sequencing is an important validation step that is now financially feasible for research, regulatory, or clinical applications. Published by Elsevier Inc.

Adenosine stress cardiovascular magnetic resonance with variable-density spiral pulse sequences accurately detects coronary artery disease: initial clinical evaluation.

PubMed

Salerno, Michael; Taylor, Angela; Yang, Yang; Kuruvilla, Sujith; Ragosta, Michael; Meyer, Craig H; Kramer, Christopher M

2014-07-01

Adenosine stress cardiovascular magnetic resonance perfusion imaging can be limited by motion-induced dark-rim artifacts, which may be mistaken for true perfusion abnormalities. A high-resolution variable-density spiral pulse sequence with a novel density compensation strategy has been shown to reduce dark-rim artifacts in first-pass perfusion imaging. We aimed to assess the clinical performance of adenosine stress cardiovascular magnetic resonance using this new perfusion sequence to detect obstructive coronary artery disease. Cardiovascular magnetic resonance perfusion imaging was performed during adenosine stress (140 μg/kg per minute) and at rest on a Siemens 1.5-T Avanto scanner in 41 subjects with chest pain scheduled for coronary angiography. Perfusion images were acquired during injection of 0.1 mmol/kg Gadolinium-diethylenetriaminepentacetate at 3 short-axis locations using a saturation recovery interleaved variable-density spiral pulse sequence. Significant stenosis was defined as >50% by quantitative coronary angiography. Two blinded reviewers evaluated the perfusion images for the presence of adenosine-induced perfusion abnormalities and assessed image quality using a 5-point scale (1 [poor] to 5 [excellent]). The prevalence of obstructive coronary artery disease by quantitative coronary angiography was 68%. The average sensitivity, specificity, and accuracy were 89%, 85%, and 88%, respectively, with a positive predictive value and negative predictive value of 93% and 79%, respectively. The average image quality score was 4.4±0.7, with only 1 study with more than mild dark-rim artifacts. There was good inter-reader reliability with a κ statistic of 0.67. Spiral adenosine stress cardiovascular magnetic resonance results in high diagnostic accuracy for the detection of obstructive coronary artery disease with excellent image quality and minimal dark-rim artifacts. © 2014 American Heart Association, Inc.

Calculation of density of states for modeling photoemission using method of moments

NASA Astrophysics Data System (ADS)

Finkenstadt, Daniel; Lambrakos, Samuel G.; Jensen, Kevin L.; Shabaev, Andrew; Moody, Nathan A.

2017-09-01

Modeling photoemission using the Moments Approach (akin to Spicer's "Three Step Model") is often presumed to follow simple models for the prediction of two critical properties of photocathodes: the yield or "Quantum Efficiency" (QE), and the intrinsic spreading of the beam or "emittance" ɛnrms. The simple models, however, tend to obscure properties of electrons in materials, the understanding of which is necessary for a proper prediction of a semiconductor or metal's QE and ɛnrms. This structure is characterized by localized resonance features as well as a universal trend at high energy. Presented in this study is a prototype analysis concerning the density of states (DOS) factor D(E) for Copper in bulk to replace the simple three-dimensional form of D(E) = (m/π2 h3)p2mE currently used in the Moments approach. This analysis demonstrates that excited state spectra of atoms, molecules and solids based on density-functional theory can be adapted as useful information for practical applications, as well as providing theoretical interpretation of density-of-states structure, e.g., qualitatively good descriptions of optical transitions in matter, in addition to DFT's utility in providing the optical constants and material parameters also required in the Moments Approach.

New solutions with accelerated expansion in string theory

DOE PAGES

Dodelson, Matthew; Dong, Xi; Silverstein, Eva; ...

2014-12-05

We present concrete solutions with accelerated expansion in string theory, requiring a small, tractable list of stress energy sources. We explain how this construction (and others in progress) evades previous no go theorems for simple accelerating solutions. Our solutions respect an approximate scaling symmetry and realize discrete sequences of values for the equation of state, including one with an accumulation point at w = –1 and another accumulating near w = –1/3 from below. In another class of models, a density of defects generates scaling solutions with accelerated expansion. Here, we briefly discuss potential applications to dark energy phenomenology, andmore » to holography for cosmology.« less

Ultrahigh-Density Nanowire Arrays Grown in Self-Assembled Diblock Copolymer Templates

NASA Astrophysics Data System (ADS)

Thurn-Albrecht, T.; Schotter, J.; Kästle, G. A.; Emley, N.; Shibauchi, T.; Krusin-Elbaum, L.; Guarini, K.; Black, C. T.; Tuominen, M. T.; Russell, T. P.

2000-12-01

We show a simple, robust, chemical route to the fabrication of ultrahigh-density arrays of nanopores with high aspect ratios using the equilibrium self-assembled morphology of asymmetric diblock copolymers. The dimensions and lateral density of the array are determined by segmental interactions and the copolymer molecular weight. Through direct current electrodeposition, we fabricated vertical arrays of nanowires with densities in excess of 1.9 × 1011 wires per square centimeter. We found markedly enhanced coercivities with ferromagnetic cobalt nanowires that point toward a route to ultrahigh-density storage media. The copolymer approach described is practical, parallel, compatible with current lithographic processes, and amenable to multilayered device fabrication.

Mapping tree density in forests of the southwestern USA using Landsat 8 data

USGS Publications Warehouse

Humagain, Kamal; Portillo-Quintero, Carlos; Cox, Robert D.; Cain, James W.

2017-01-01

The increase of tree density in forests of the American Southwest promotes extreme fire events, understory biodiversity losses, and degraded habitat conditions for many wildlife species. To ameliorate these changes, managers and scientists have begun planning treatments aimed at reducing fuels and increasing understory biodiversity. However, spatial variability in tree density across the landscape is not well-characterized, and if better known, could greatly influence planning efforts. We used reflectance values from individual Landsat 8 bands (bands 2, 3, 4, 5, 6, and 7) and calculated vegetation indices (difference vegetation index, simple ratios, and normalized vegetation indices) to estimate tree density in an area planned for treatment in the Jemez Mountains, New Mexico, characterized by multiple vegetation types and a complex topography. Because different vegetation types have different spectral signatures, we derived models with multiple predictor variables for each vegetation type, rather than using a single model for the entire project area, and compared the model-derived values to values collected from on-the-ground transects. Among conifer-dominated areas (73% of the project area), the best models (as determined by corrected Akaike Information Criteria (AICc)) included Landsat bands 2, 3, 4, and 7 along with simple ratios, normalized vegetation indices, and the difference vegetation index (R2 values for ponderosa: 0.47, piñon-juniper: 0.52, and spruce-fir: 0.66). On the other hand, in aspen-dominated areas (9% of the project area), the best model included individual bands 4 and 2, simple ratio, and normalized vegetation index (R2 value: 0.97). Most areas dominated by ponderosa, pinyon-juniper, or spruce-fir had more than 100 trees per hectare. About 54% of the study area has medium to high density of trees (100–1000 trees/hectare), and a small fraction (4.5%) of the area has very high density (>1000 trees/hectare). Our results provide a better understanding of tree density for identifying areas in need of treatment and planning for more effective treatment. Our analysis also provides an integrated method of estimating tree density across complex landscapes that could be useful for further restoration planning.

Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants.

PubMed

Taheri, Sima; Lee Abdullah, Thohirah; Yusop, Mohd Rafii; Hanafi, Mohamed Musa; Sahebi, Mahbod; Azizi, Parisa; Shamshiri, Redmond Ramin

2018-02-13

Microsatellites, or simple sequence repeats (SSRs), are one of the most informative and multi-purpose genetic markers exploited in plant functional genomics. However, the discovery of SSRs and development using traditional methods are laborious, time-consuming, and costly. Recently, the availability of high-throughput sequencing technologies has enabled researchers to identify a substantial number of microsatellites at less cost and effort than traditional approaches. Illumina is a noteworthy transcriptome sequencing technology that is currently used in SSR marker development. Although 454 pyrosequencing datasets can be used for SSR development, this type of sequencing is no longer supported. This review aims to present an overview of the next generation sequencing, with a focus on the efficient use of de novo transcriptome sequencing (RNA-Seq) and related tools for mining and development of microsatellites in plants.

HTP-OligoDesigner: An Online Primer Design Tool for High-Throughput Gene Cloning and Site-Directed Mutagenesis.

PubMed

Camilo, Cesar M; Lima, Gustavo M A; Maluf, Fernando V; Guido, Rafael V C; Polikarpov, Igor

2016-01-01

Following burgeoning genomic and transcriptomic sequencing data, biochemical and molecular biology groups worldwide are implementing high-throughput cloning and mutagenesis facilities in order to obtain a large number of soluble proteins for structural and functional characterization. Since manual primer design can be a time-consuming and error-generating step, particularly when working with hundreds of targets, the automation of primer design process becomes highly desirable. HTP-OligoDesigner was created to provide the scientific community with a simple and intuitive online primer design tool for both laboratory-scale and high-throughput projects of sequence-independent gene cloning and site-directed mutagenesis and a Tm calculator for quick queries.

High current proton beams production at Simple Mirror Ion Source 37.

PubMed

Skalyga, V; Izotov, I; Razin, S; Sidorov, A; Golubev, S; Kalvas, T; Koivisto, H; Tarvainen, O

2014-02-01

This paper presents the latest results of high current proton beam production at Simple Mirror Ion Source (SMIS) 37 facility at the Institute of Applied Physics (IAP RAS). In this experimental setup, the plasma is created and the electrons are heated by 37.5 GHz gyrotron radiation with power up to 100 kW in a simple mirror trap fulfilling the ECR condition. Latest experiments at SMIS 37 were performed using a single-aperture two-electrode extraction system. Proton beams with currents up to 450 mA at high voltages below 45 kV were obtained. The maximum beam current density was measured to be 600 mA/cm(2). A possibility of further improvement through the development of an advanced extraction system is discussed.

Mining and validation of pyrosequenced simple sequence repeats (SSRs) from American cranberry (Vaccinium macrocarpon Ait.).

PubMed

Zhu, H; Senalik, D; McCown, B H; Zeldin, E L; Speers, J; Hyman, J; Bassil, N; Hummer, K; Simon, P W; Zalapa, J E

2012-01-01

The American cranberry (Vaccinium macrocarpon Ait.) is a major commercial fruit crop in North America, but limited genetic resources have been developed for the species. Furthermore, the paucity of codominant DNA markers has hampered the advance of genetic research in cranberry and the Ericaceae family in general. Therefore, we used Roche 454 sequencing technology to perform low-coverage whole genome shotgun sequencing of the cranberry cultivar 'HyRed'. After de novo assembly, the obtained sequence covered 266.3 Mb of the estimated 540-590 Mb in cranberry genome. A total of 107,244 SSR loci were detected with an overall density across the genome of 403 SSR/Mb. The AG repeat was the most frequent motif in cranberry accounting for 35% of all SSRs and together with AAG and AAAT accounted for 46% of all loci discovered. To validate the SSR loci, we designed 96 primer-pairs using contig sequence data containing perfect SSR repeats, and studied the genetic diversity of 25 cranberry genotypes. We identified 48 polymorphic SSR loci with 2-15 alleles per locus for a total of 323 alleles in the 25 cranberry genotypes. Genetic clustering by principal coordinates and genetic structure analyzes confirmed the heterogeneous nature of cranberries. The parentage composition of several hybrid cultivars was evident from the structure analyzes. Whole genome shotgun 454 sequencing was a cost-effective and efficient way to identify numerous SSR repeats in the cranberry sequence for marker development.

A simple algorithm for quantifying DNA methylation levels on multiple independent CpG sites in bisulfite genomic sequencing electropherograms.

PubMed

Leakey, Tatiana I; Zielinski, Jerzy; Siegfried, Rachel N; Siegel, Eric R; Fan, Chun-Yang; Cooney, Craig A

2008-06-01

DNA methylation at cytosines is a widely studied epigenetic modification. Methylation is commonly detected using bisulfite modification of DNA followed by PCR and additional techniques such as restriction digestion or sequencing. These additional techniques are either laborious, require specialized equipment, or are not quantitative. Here we describe a simple algorithm that yields quantitative results from analysis of conventional four-dye-trace sequencing. We call this method Mquant and we compare it with the established laboratory method of combined bisulfite restriction assay (COBRA). This analysis of sequencing electropherograms provides a simple, easily applied method to quantify DNA methylation at specific CpG sites.

A Simple and Reliable Setup for Monitoring Corrosion Rate of Steel Rebars in Concrete

PubMed Central

Jibran, Mohammed Abdul Azeem; Azad, Abul Kalam

2014-01-01

The accuracy in the measurement of the rate of corrosion of steel in concrete depends on many factors. The high resistivity of concrete makes the polarization data erroneous due to the Ohmic drop. The other source of error is the use of an arbitrarily assumed value of the Stern-Geary constant for calculating corrosion current density. This paper presents the outcomes of a research work conducted to develop a reliable and low-cost experimental setup and a simple calculation procedure that can be utilised to calculate the corrosion current density considering the Ohmic drop compensation and the actual value of the Stern-Geary constants calculated using the polarization data. The measurements conducted on specimens corroded to different levels indicate the usefulness of the developed setup to determine the corrosion current density with and without Ohmic drop compensation. PMID:24526907

Phase and vacancy behaviour of hard "slanted" cubes

NASA Astrophysics Data System (ADS)

van Damme, R.; van der Meer, B.; van den Broeke, J. J.; Smallenburg, F.; Filion, L.

2017-09-01

We use computer simulations to study the phase behaviour for hard, right rhombic prisms as a function of the angle of their rhombic face (the "slant" angle). More specifically, using a combination of event-driven molecular dynamics simulations, Monte Carlo simulations, and free-energy calculations, we determine and characterize the equilibrium phases formed by these particles for various slant angles and densities. Surprisingly, we find that the equilibrium crystal structure for a large range of slant angles and densities is the simple cubic crystal—despite the fact that the particles do not have cubic symmetry. Moreover, we find that the equilibrium vacancy concentration in this simple cubic phase is extremely high and depends only on the packing fraction and not the particle shape. At higher densities, a rhombic crystal appears as the equilibrium phase. We summarize the phase behaviour of this system by drawing a phase diagram in the slant angle-packing fraction plane.

Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology

USDA-ARS?s Scientific Manuscript database

The dissection of complex traits of economic importance for the pig industry requires the availability of a significant number of genetic markers, such as SNPs. This study was conducted in order to discover thousands of porcine SNPs using next generation sequencing technologies and use those SNPs, a...

A simple index of stand density for Douglas-fir.

Treesearch

R.O. Curtis

1982-01-01

The expression RD = G/(Dg½), where G is basal area and Dg is quadratic mean stand diameter, provides a simple and convenient scale of relative stand density for Douglas-fir, equivalent to other generally accepted diameter-based stand density measures.

High-density genetic map construction and comparative genome analysis in asparagus bean.

PubMed

Huang, Haitao; Tan, Huaqiang; Xu, Dongmei; Tang, Yi; Niu, Yisong; Lai, Yunsong; Tie, Manman; Li, Huanxiu

2018-03-19

Genetic maps are a prerequisite for quantitative trait locus (QTL) analysis, marker-assisted selection (MAS), fine gene mapping, and assembly of genome sequences. So far, several asparagus bean linkage maps have been established using various kinds of molecular markers. However, these maps were all constructed by gel- or array-based markers. No maps based on sequencing method have been reported. In this study, an NGS-based strategy, SLAF-seq, was applied to create a high-density genetic map for asparagus bean. Through SLAF library construction and Illumina sequencing of two parents and 100 F2 individuals, a total of 55,437 polymorphic SLAF markers were developed and mined for SNP markers. The map consisted of 5,225 SNP markers in 11 LGs, spanning a total distance of 1,850.81 cM, with an average distance between markers of 0.35 cM. Comparative genome analysis with four other legume species, soybean, common bean, mung bean and adzuki bean showed that asparagus bean is genetically more related to adzuki bean. The results will provide a foundation for future genomic research, such as QTL fine mapping, comparative mapping in pulses, and offer support for assembling asparagus bean genome sequence.

Measuring the Density of a Sugar Solution: A General Chemistry Experiment Using a Student-Prepared Unknown

ERIC Educational Resources Information Center

Peterson, Karen I.

2008-01-01

The experiment developed in this article addresses the concept of equipment calibration for reducing systematic error. It also suggests simple student-prepared sucrose solutions for which accurate densities are known, but not readily available to students. Densities are measured with simple glassware that has been calibrated using the density of…

Improved First Pass Spiral Myocardial Perfusion Imaging with Variable Density Trajectories

PubMed Central

Salerno, Michael; Sica, Christopher; Kramer, Christopher M.; Meyer, Craig H.

2013-01-01

Purpose To develop and evaluate variable-density (VD) spiral first-pass perfusion pulse sequences for improved efficiency and off-resonance performance and to demonstrate the utility of an apodizing density compensation function (DCF) to improve SNR and reduce dark-rim artifact caused by cardiac motion and Gibbs Ringing. Methods Three variable density spiral trajectories were designed, simulated, and evaluated in 18 normal subjects, and in 8 patients with cardiac pathology on a 1.5T scanner. Results By utilizing a density compensation function (DCF) which intentionally apodizes the k-space data, the side-lobe amplitude of the theoretical PSF is reduced by 68%, with only a 13% increase in the FWHM of the main-lobe as compared to the same data corrected with a conventional VD DCF, and has an 8% higher resolution than a uniform density spiral with the same number of interleaves and readout duration. Furthermore, this strategy results in a greater than 60% increase in measured SNR as compared to the same VD spiral data corrected with a conventional DCF (p<0.01). Perfusion defects could be clearly visualized with minimal off-resonance and dark-rim artifacts. Conclusion VD spiral pulse sequences using an apodized DCF produce high-quality first-pass perfusion images with minimal dark-rim and off-resonance artifacts, high SNR and CNR and good delineation of resting perfusion abnormalities. PMID:23280884

Development of simple sequence repeat markers and diversity analysis in alfalfa (Medicago sativa L.).

PubMed

Wang, Zan; Yan, Hongwei; Fu, Xinnian; Li, Xuehui; Gao, Hongwen

2013-04-01

Efficient and robust molecular markers are essential for molecular breeding in plant. Compared to dominant and bi-allelic markers, multiple alleles of simple sequence repeat (SSR) markers are particularly informative and superior in genetic linkage map and QTL mapping in autotetraploid species like alfalfa. The objective of this study was to enrich SSR markers directly from alfalfa expressed sequence tags (ESTs). A total of 12,371 alfalfa ESTs were retrieved from the National Center for Biotechnology Information. Total 774 SSR-containing ESTs were identified from 716 ESTs. On average, one SSR was found per 7.7 kb of EST sequences. Tri-nucleotide repeats (48.8 %) was the most abundant motif type, followed by di-(26.1 %), tetra-(11.5 %), penta-(9.7 %), and hexanucleotide (3.9 %). One hundred EST-SSR primer pairs were successfully designed and 29 exhibited polymorphism among 28 alfalfa accessions. The allele number per marker ranged from two to 21 with an average of 6.8. The PIC values ranged from 0.195 to 0.896 with an average of 0.608, indicating a high level of polymorphism of the EST-SSR markers. Based on the 29 EST-SSR markers, assessment of genetic diversity was conducted and found that Medicago sativa ssp. sativa was clearly different from the other subspecies. The high transferability of those EST-SSR markers was also found for relative species.

Simple, multiplexed, PCR-based barcoding of DNA enables sensitive mutation detection in liquid biopsies using sequencing.

PubMed

Ståhlberg, Anders; Krzyzanowski, Paul M; Jackson, Jennifer B; Egyud, Matthew; Stein, Lincoln; Godfrey, Tony E

2016-06-20

Detection of cell-free DNA in liquid biopsies offers great potential for use in non-invasive prenatal testing and as a cancer biomarker. Fetal and tumor DNA fractions however can be extremely low in these samples and ultra-sensitive methods are required for their detection. Here, we report an extremely simple and fast method for introduction of barcodes into DNA libraries made from 5 ng of DNA. Barcoded adapter primers are designed with an oligonucleotide hairpin structure to protect the molecular barcodes during the first rounds of polymerase chain reaction (PCR) and prevent them from participating in mis-priming events. Our approach enables high-level multiplexing and next-generation sequencing library construction with flexible library content. We show that uniform libraries of 1-, 5-, 13- and 31-plex can be generated. Utilizing the barcodes to generate consensus reads for each original DNA molecule reduces background sequencing noise and allows detection of variant alleles below 0.1% frequency in clonal cell line DNA and in cell-free plasma DNA. Thus, our approach bridges the gap between the highly sensitive but specific capabilities of digital PCR, which only allows a limited number of variants to be analyzed, with the broad target capability of next-generation sequencing which traditionally lacks the sensitivity to detect rare variants. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

High density lipoproteins: Measurement techniques and potential biomarkers of cardiovascular risk

PubMed Central

Hafiane, Anouar; Genest, Jacques

2015-01-01

Plasma high density lipoprotein cholesterol (HDL) comprises a heterogeneous family of lipoprotein species, differing in surface charge, size and lipid and protein compositions. While HDL cholesterol (C) mass is a strong, graded and coherent biomarker of cardiovascular risk, genetic and clinical trial data suggest that the simple measurement of HDL-C may not be causal in preventing atherosclerosis nor reflect HDL functionality. Indeed, the measurement of HDL-C may be a biomarker of cardiovascular health. To assess the issue of HDL function as a potential therapeutic target, robust and simple analytical methods are required. The complex pleiotropic effects of HDL make the development of a single measurement challenging. Development of laboratory assays that accurately HDL function must be developed validated and brought to high-throughput for clinical purposes. This review discusses the limitations of current laboratory technologies for methods that separate and quantify HDL and potential application to predict CVD, with an emphasis on emergent approaches as potential biomarkers in clinical practice. PMID:26674734

WebSat ‐ A web software for microsatellite marker development

PubMed Central

Martins, Wellington Santos; Soares Lucas, Divino César; de Souza Neves, Kelligton Fabricio; Bertioli, David John

2009-01-01

Simple sequence repeats (SSR), also known as microsatellites, have been extensively used as molecular markers due to their abundance and high degree of polymorphism. We have developed a simple to use web software, called WebSat, for microsatellite molecular marker prediction and development. WebSat is accessible through the Internet, requiring no program installation. Although a web solution, it makes use of Ajax techniques, providing a rich, responsive user interface. WebSat allows the submission of sequences, visualization of microsatellites and the design of primers suitable for their amplification. The program allows full control of parameters and the easy export of the resulting data, thus facilitating the development of microsatellite markers. Availability The web tool may be accessed at http://purl.oclc.org/NET/websat/ PMID:19255650

Structural behavior and dynamics of an anomalous fluid between attractive and repulsive walls: Templating, molding, and superdiffusion

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

Leoni, Fabio; Franzese, Giancarlo

2014-11-07

Confinement can modify the dynamics, the thermodynamics, and the structural properties of liquid water, the prototypical anomalous liquid. By considering a generic model for anomalous liquids, suitable for describing solutions of globular proteins, colloids, or liquid metals, we study by molecular dynamics simulations the effect that an attractive wall with structure and a repulsive wall without structure have on the phases, the crystal nucleation, and the dynamics of the fluid. We find that at low temperatures the large density of the attractive wall induces a high-density, high-energy structure in the first layer (“templating” effect). In turn, the first layer inducesmore » a “molding” effect on the second layer determining a structure with reduced energy and density, closer to the average density of the system. This low-density, low-energy structure propagates further through the layers by templating effect and can involve all the existing layers at the lowest temperatures investigated. Therefore, although the high-density, high-energy structure does not self-reproduce further than the first layer, the structured wall can have a long-range influence thanks to a sequence of templating, molding, and templating effects through the layers. We find that the walls also have an influence on the dynamics of the liquid, with a stronger effect near the attractive wall. In particular, we observe that the dynamics is largely heterogeneous (i) among the layers, as a consequence of the sequence of structures caused by the walls presence, and (ii) within the same layer, due to superdiffusive liquid veins within a frozen matrix of particles near the walls at low temperature and high density. Hence, the partial freezing of the first layer does not correspond necessarily to an effective reduction of the channel's section in terms of transport properties, as suggested by other authors.« less

Structural behavior and dynamics of an anomalous fluid between attractive and repulsive walls: templating, molding, and superdiffusion.

PubMed

Leoni, Fabio; Franzese, Giancarlo

2014-11-07

Confinement can modify the dynamics, the thermodynamics, and the structural properties of liquid water, the prototypical anomalous liquid. By considering a generic model for anomalous liquids, suitable for describing solutions of globular proteins, colloids, or liquid metals, we study by molecular dynamics simulations the effect that an attractive wall with structure and a repulsive wall without structure have on the phases, the crystal nucleation, and the dynamics of the fluid. We find that at low temperatures the large density of the attractive wall induces a high-density, high-energy structure in the first layer ("templating" effect). In turn, the first layer induces a "molding" effect on the second layer determining a structure with reduced energy and density, closer to the average density of the system. This low-density, low-energy structure propagates further through the layers by templating effect and can involve all the existing layers at the lowest temperatures investigated. Therefore, although the high-density, high-energy structure does not self-reproduce further than the first layer, the structured wall can have a long-range influence thanks to a sequence of templating, molding, and templating effects through the layers. We find that the walls also have an influence on the dynamics of the liquid, with a stronger effect near the attractive wall. In particular, we observe that the dynamics is largely heterogeneous (i) among the layers, as a consequence of the sequence of structures caused by the walls presence, and (ii) within the same layer, due to superdiffusive liquid veins within a frozen matrix of particles near the walls at low temperature and high density. Hence, the partial freezing of the first layer does not correspond necessarily to an effective reduction of the channel's section in terms of transport properties, as suggested by other authors.

High-resolution definition of the Vibrio cholerae essential gene set with hidden Markov model–based analyses of transposon-insertion sequencing data

PubMed Central

Chao, Michael C.; Pritchard, Justin R.; Zhang, Yanjia J.; Rubin, Eric J.; Livny, Jonathan; Davis, Brigid M.; Waldor, Matthew K.

2013-01-01

The coupling of high-density transposon mutagenesis to high-throughput DNA sequencing (transposon-insertion sequencing) enables simultaneous and genome-wide assessment of the contributions of individual loci to bacterial growth and survival. We have refined analysis of transposon-insertion sequencing data by normalizing for the effect of DNA replication on sequencing output and using a hidden Markov model (HMM)-based filter to exploit heretofore unappreciated information inherent in all transposon-insertion sequencing data sets. The HMM can smooth variations in read abundance and thereby reduce the effects of read noise, as well as permit fine scale mapping that is independent of genomic annotation and enable classification of loci into several functional categories (e.g. essential, domain essential or ‘sick’). We generated a high-resolution map of genomic loci (encompassing both intra- and intergenic sequences) that are required or beneficial for in vitro growth of the cholera pathogen, Vibrio cholerae. This work uncovered new metabolic and physiologic requirements for V. cholerae survival, and by combining transposon-insertion sequencing and transcriptomic data sets, we also identified several novel noncoding RNA species that contribute to V. cholerae growth. Our findings suggest that HMM-based approaches will enhance extraction of biological meaning from transposon-insertion sequencing genomic data. PMID:23901011

SOMKE: kernel density estimation over data streams by sequences of self-organizing maps.

PubMed

Cao, Yuan; He, Haibo; Man, Hong

2012-08-01

In this paper, we propose a novel method SOMKE, for kernel density estimation (KDE) over data streams based on sequences of self-organizing map (SOM). In many stream data mining applications, the traditional KDE methods are infeasible because of the high computational cost, processing time, and memory requirement. To reduce the time and space complexity, we propose a SOM structure in this paper to obtain well-defined data clusters to estimate the underlying probability distributions of incoming data streams. The main idea of this paper is to build a series of SOMs over the data streams via two operations, that is, creating and merging the SOM sequences. The creation phase produces the SOM sequence entries for windows of the data, which obtains clustering information of the incoming data streams. The size of the SOM sequences can be further reduced by combining the consecutive entries in the sequence based on the measure of Kullback-Leibler divergence. Finally, the probability density functions over arbitrary time periods along the data streams can be estimated using such SOM sequences. We compare SOMKE with two other KDE methods for data streams, the M-kernel approach and the cluster kernel approach, in terms of accuracy and processing time for various stationary data streams. Furthermore, we also investigate the use of SOMKE over nonstationary (evolving) data streams, including a synthetic nonstationary data stream, a real-world financial data stream and a group of network traffic data streams. The simulation results illustrate the effectiveness and efficiency of the proposed approach.

Developing expressed sequence tag libraries and the discovery of simple sequence repeat markers for two species of raspberry (Rubus L.).

PubMed

Bushakra, Jill M; Lewers, Kim S; Staton, Margaret E; Zhebentyayeva, Tetyana; Saski, Christopher A

2015-10-26

Due to a relatively high level of codominant inheritance and transferability within and among taxonomic groups, simple sequence repeat (SSR) markers are important elements in comparative mapping and delineation of genomic regions associated with traits of economic importance. Expressed sequence tags (ESTs) are a source of SSRs that can be used to develop markers to facilitate plant breeding and for more basic research across genera and higher plant orders. Leaf and meristem tissue from 'Heritage' red raspberry (Rubus idaeus) and 'Bristol' black raspberry (R. occidentalis) were utilized for RNA extraction. After conversion to cDNA and library construction, ESTs were sequenced, quality verified, assembled and scanned for SSRs.  Primers flanking the SSRs were designed and a subset tested for amplification, polymorphism and transferability across species. ESTs containing SSRs were functionally annotated using the GenBank non-redundant (nr) database and further classified using the gene ontology database. To accelerate development of EST-SSRs in the genus Rubus (Rosaceae), 1149 and 2358 cDNA sequences were generated from red raspberry and black raspberry, respectively. The cDNA sequences were screened using rigorous filtering criteria which resulted in the identification of 121 and 257 SSR loci for red and black raspberry, respectively. Primers were designed from the surrounding sequences resulting in 131 and 288 primer pairs, respectively, as some sequences contained more than one SSR locus. Sequence analysis revealed that the SSR-containing genes span a diversity of functions and share more sequence identity with strawberry genes than with other Rosaceous species. This resource of Rubus-specific, gene-derived markers will facilitate the construction of linkage maps composed of transferable markers for studying and manipulating important traits in this economically important genus.

High Discharge Energy Density at Low Electric Field Using an Aligned Titanium Dioxide/Lead Zirconate Titanate Nanowire Array

PubMed Central

Zhang, Dou; Liu, Weiwei; Guo, Ru; Zhou, Kechao

2017-01-01

Abstract Polymer‐based capacitors with high energy density have attracted significant attention in recent years due to their wide range of potential applications in electronic devices. However, the obtained high energy density is predominantly dependent on high applied electric field, e.g., 400–600 kV mm−1, which may bring more challenges relating to the failure probability. Here, a simple two‐step method for synthesizing titanium dioxide/lead zirconate titanate nanowire arrays is exploited and a demonstration of their ability to achieve high discharge energy density capacitors for low operating voltage applications is provided. A high discharge energy density of 6.9 J cm−3 is achieved at low electric fields, i.e., 143 kV mm−1, which is attributed to the high relative permittivity of 218.9 at 1 kHz and high polarization of 23.35 µC cm−2 at this electric field. The discharge energy density obtained in this work is the highest known for a ceramic/polymer nanocomposite at such a low electric field. The novel nanowire arrays used in this work are applicable to a wide range of fields, such as energy harvesting, energy storage, and photocatalysis. PMID:29610724

Application of the High Resolution Melting analysis for genetic mapping of Sequence Tagged Site markers in narrow-leafed lupin (Lupinus angustifolius L.).

PubMed

Kamel, Katarzyna A; Kroc, Magdalena; Święcicki, Wojciech

2015-01-01

Sequence tagged site (STS) markers are valuable tools for genetic and physical mapping that can be successfully used in comparative analyses among related species. Current challenges for molecular markers genotyping in plants include the lack of fast, sensitive and inexpensive methods suitable for sequence variant detection. In contrast, high resolution melting (HRM) is a simple and high-throughput assay, which has been widely applied in sequence polymorphism identification as well as in the studies of genetic variability and genotyping. The present study is the first attempt to use the HRM analysis to genotype STS markers in narrow-leafed lupin (Lupinus angustifolius L.). The sensitivity and utility of this method was confirmed by the sequence polymorphism detection based on melting curve profiles in the parental genotypes and progeny of the narrow-leafed lupin mapping population. Application of different approaches, including amplicon size and a simulated heterozygote analysis, has allowed for successful genetic mapping of 16 new STS markers in the narrow-leafed lupin genome.

High Energy Density All Solid State Asymmetric Pseudocapacitors Based on Free Standing Reduced Graphene Oxide-Co3O4 Composite Aerogel Electrodes.

PubMed

Ghosh, Debasis; Lim, Joonwon; Narayan, Rekha; Kim, Sang Ouk

2016-08-31

Modern flexible consumer electronics require efficient energy storage devices with flexible free-standing electrodes. We report a simple and cost-effective route to a graphene-based composite aerogel encapsulating metal oxide nanoparticles for high energy density, free-standing, binder-free flexible pseudocapacitive electrodes. Hydrothermally synthesized Co3O4 nanoparticles are successfully housed inside the microporous graphene aerogel network during the room temperature interfacial gelation at the Zn surface. The resultant three-dimensional (3D) rGO-Co3O4 composite aerogel shows mesoporous quasiparallel layer stack morphology with a high loading of Co3O4, which offers numerous channels for ion transport and a 3D interconnected network for high electrical conductivity. All solid state asymmetric pseudocapacitors employing the composite aerogel electrodes have demonstrated high areal energy density of 35.92 μWh/cm(2) and power density of 17.79 mW/cm(2) accompanied by excellent cycle life.

Highly-Ordered 3D Vertical Resistive Switching Memory Arrays with Ultralow Power Consumption and Ultrahigh Density.

PubMed

Al-Haddad, Ahmed; Wang, Chengliang; Qi, Haoyuan; Grote, Fabian; Wen, Liaoyong; Bernhard, Jörg; Vellacheri, Ranjith; Tarish, Samar; Nabi, Ghulam; Kaiser, Ute; Lei, Yong

2016-09-07

Resistive switching random access memories (RRAM) have attracted great scientific and industrial attention for next generation data storage because of their advantages of nonvolatile properties, high density, low power consumption, fast writing/erasing speed, good endurance, and simple and small operation system. Here, by using a template-assisted technique, we demonstrate a three-dimensional highly ordered vertical RRAM device array with density as high as that of the nanopores of the template (10(8)-10(9) cm(-2)), which can also be fabricated in large area. The high crystallinity of the materials, the large contact area and the intimate semiconductor/electrode interface (3 nm interfacial layer) make the ultralow voltage operation (millivolt magnitude) and ultralow power consumption (picowatt) possible. Our procedure for fabrication of the nanodevice arrays in large area can be used for producing many other different materials and such three-dimensional electronic device arrays with the capability to adjust the device densities can be extended to other applications of the next generation nanodevice technology.

Hi-Plex for Simple, Accurate, and Cost-Effective Amplicon-based Targeted DNA Sequencing.

PubMed

Pope, Bernard J; Hammet, Fleur; Nguyen-Dumont, Tu; Park, Daniel J

2018-01-01

Hi-Plex is a suite of methods to enable simple, accurate, and cost-effective highly multiplex PCR-based targeted sequencing (Nguyen-Dumont et al., Biotechniques 58:33-36, 2015). At its core is the principle of using gene-specific primers (GSPs) to "seed" (or target) the reaction and universal primers to "drive" the majority of the reaction. In this manner, effects on amplification efficiencies across the target amplicons can, to a large extent, be restricted to early seeding cycles. Product sizes are defined within a relatively narrow range to enable high-specificity size selection, replication uniformity across target sites (including in the context of fragmented input DNA such as that derived from fixed tumor specimens (Nguyen-Dumont et al., Biotechniques 55:69-74, 2013; Nguyen-Dumont et al., Anal Biochem 470:48-51, 2015), and application of high-specificity genetic variant calling algorithms (Pope et al., Source Code Biol Med 9:3, 2014; Park et al., BMC Bioinformatics 17:165, 2016). Hi-Plex offers a streamlined workflow that is suitable for testing large numbers of specimens without the need for automation.

Hemorrhagic Fever with Renal Syndrome (Korean Hemorrhagic Fever)

DTIC Science & Technology

1990-06-29

particles were used for a rapid serologic diagnostic test for HFRS. ’te-re were 430 cases of HFRS in Korea in 1989 and large outbreaks of scrub typhus...almost same as in 1988. A simple and rapid serologic diagnostic test for hantavirus infection was developed by high density particle agglutination...infection and HFRS b) serologic relation cif hantaviruses isolated from the different parts of the world c) development of a simple serologic diagnostic

Genomic Definition of Hypervirulent and Multidrug-Resistant Klebsiella pneumoniae Clonal Groups

PubMed Central

Bialek-Davenet, Suzanne; Criscuolo, Alexis; Ailloud, Florent; Passet, Virginie; Jones, Louis; Delannoy-Vieillard, Anne-Sophie; Garin, Benoit; Le Hello, Simon; Arlet, Guillaume; Nicolas-Chanoine, Marie-Hélène; Decré, Dominique

2014-01-01

Multidrug-resistant and highly virulent Klebsiella pneumoniae isolates are emerging, but the clonal groups (CGs) corresponding to these high-risk strains have remained imprecisely defined. We aimed to identify K. pneumoniae CGs on the basis of genome-wide sequence variation and to provide a simple bioinformatics tool to extract virulence and resistance gene data from genomic data. We sequenced 48 K. pneumoniae isolates, mostly of serotypes K1 and K2, and compared the genomes with 119 publicly available genomes. A total of 694 highly conserved genes were included in a core-genome multilocus sequence typing scheme, and cluster analysis of the data enabled precise definition of globally distributed hypervirulent and multidrug-resistant CGs. In addition, we created a freely accessible database, BIGSdb-Kp, to enable rapid extraction of medically and epidemiologically relevant information from genomic sequences of K. pneumoniae. Although drug-resistant and virulent K. pneumoniae populations were largely nonoverlapping, isolates with combined virulence and resistance features were detected. PMID:25341126

Single-Genome Sequencing of Hepatitis C Virus in Donor-Recipient Pairs Distinguishes Modes and Models of Virus Transmission and Early Diversification.

PubMed

Li, Hui; Stoddard, Mark B; Wang, Shuyi; Giorgi, Elena E; Blair, Lily M; Learn, Gerald H; Hahn, Beatrice H; Alter, Harvey J; Busch, Michael P; Fierer, Daniel S; Ribeiro, Ruy M; Perelson, Alan S; Bhattacharya, Tanmoy; Shaw, George M

2016-01-01

Despite the recent development of highly effective anti-hepatitis C virus (HCV) drugs, the global burden of this pathogen remains immense. Control or eradication of HCV will likely require the broad application of antiviral drugs and development of an effective vaccine. A precise molecular identification of transmitted/founder (T/F) HCV genomes that lead to productive clinical infection could play a critical role in vaccine research, as it has for HIV-1. However, the replication schema of these two RNA viruses differ substantially, as do viral responses to innate and adaptive host defenses. These differences raise questions as to the certainty of T/F HCV genome inferences, particularly in cases where multiple closely related sequence lineages have been observed. To clarify these issues and distinguish between competing models of early HCV diversification, we examined seven cases of acute HCV infection in humans and chimpanzees, including three examples of virus transmission between linked donors and recipients. Using single-genome sequencing (SGS) of plasma vRNA, we found that inferred T/F sequences in recipients were identical to viral sequences in their respective donors. Early in infection, HCV genomes generally evolved according to a simple model of random evolution where the coalescent corresponded to the T/F sequence. Closely related sequence lineages could be explained by high multiplicity infection from a donor whose viral sequences had undergone a pretransmission bottleneck due to treatment, immune selection, or recent infection. These findings validate SGS, together with mathematical modeling and phylogenetic analysis, as a novel strategy to infer T/F HCV genome sequences. Despite the recent development of highly effective, interferon-sparing anti-hepatitis C virus (HCV) drugs, the global burden of this pathogen remains immense. Control or eradication of HCV will likely require the broad application of antiviral drugs and the development of an effective vaccine, which could be facilitated by a precise molecular identification of transmitted/founder (T/F) viral genomes and their progeny. We used single-genome sequencing to show that inferred HCV T/F sequences in recipients were identical to viral sequences in their respective donors and that viral genomes generally evolved early in infection according to a simple model of random sequence evolution. Altogether, the findings validate T/F genome inferences and illustrate how T/F sequence identification can illuminate studies of HCV transmission, immunopathogenesis, drug resistance development, and vaccine protection, including sieving effects on breakthrough virus strains. Copyright © 2015 Li et al.

High levels of heterozygosity found for 15 SSR loci in Solanum chacoense

USDA-ARS?s Scientific Manuscript database

Genetic variation is a necessary prerequisite for improving domesticated plants through breeding; without it, breeding progress would be impossible. Genetic variation can be readily ascertained with co-dominant DNA markers, such as simple sequence repeats (SSRs). Twenty-four SSR markers specifically...

Density structure of submarine slump and normal sediments of the first gas production test site at Daini-Atsumi Knoll near Nankai Trough, estimated by LWD logging data

NASA Astrophysics Data System (ADS)

Suzuki, K.; Takayama, T.; Fujii, T.; Yamamoto, K.

2014-12-01

Many geologists have discussed slope instability caused by gas-hydrate dissociation, which could make movable fluid in pore space of sediments. However, physical property changes caused by gas hydrate dissociation would not be so simple. Moreover, during the period of natural gas-production from gas-hydrate reservoir applying depressurization method would be completely different phenomena from dissociation processes in nature, because it could not be caused excess pore pressure, even though gas and water exist. Hence, in all cases, physical properties of gas-hydrate bearing sediments and that of their cover sediments are quite important to consider this phenomena, and to carry out simulation to solve focusing phenomena during gas hydrate dissociation periods. Daini-Atsumi knoll that was the first offshore gas-production test site from gas-hydrate is partially covered by slumps. Fortunately, one of them was penetrated by both Logging-While-Drilling (LWD) hole and pressure-coring hole. As a result of LWD data analyses and core analyses, we have understood density structure of sediments from seafloor to Bottom Simulating Reflector (BSR). The results are mentioned as following. ・Semi-confined slump showed high-density, relatively. It would be explained by over-consolidation that was result of layer-parallel compression caused by slumping. ・Bottom sequence of slump has relative high-density zones. It would be explained by shear-induced compaction along slide plane. ・Density below slump tends to increase in depth. It is reasonable that sediments below slump deposit have been compacting as normal consolidation. ・Several kinds of log-data for estimating physical properties of gas-hydrate reservoir sediments have been obtained. It will be useful for geological model construction from seafloor until BSR. We can use these results to consider geological model not only for slope instability at slumping, but also for slope stability during depressurized period of gas production from gas-hydrate. AcknowledgementThis study was supported by funding from the Research Consortium for Methane Hydrate Resources in Japan (MH21 Research Consortium) planned by the Ministry of Economy, Trade and Industry (METI).

X-Ray Wind Tomography of IGR J17252-3616

NASA Astrophysics Data System (ADS)

Manousakis, Antonios; Walter, Roland

2010-07-01

IGR J17252-3616, a highly absorbed High Mass X-ray Binary (HMXB) with Hydrogen column density NH~(2-4)×1023 cm-2, has been observed with XMM-Newton for about one month. Observations were scheduled in order to cover the orbital-phase space as much as possible. IGR J17252-3616 shows a varying column density NH and Fe Kα line when fit with simple phenomenological models. A refined orbital solution can be derived. Spectral timing analysis allows derivation of the wind properties of the massive star.

Determination of Process Parameters for High-Density, Ti-6Al-4V Parts Using Additive Manufacturing

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

Kamath, C.

In our earlier work, we described an approach for determining the process parameters that re- sult in high-density parts manufactured using the additive-manufacturing process of selective laser melting (SLM). Our approach, which combines simple simulations and experiments, was demon- strated using 316L stainless steel. We have also used the approach successfully for several other materials. This short note summarizes the results of our work in determining process parameters for Ti-6Al-4V using a Concept Laser M2 system.

Portable and Error-Free DNA-Based Data Storage.

PubMed

Yazdi, S M Hossein Tabatabaei; Gabrys, Ryan; Milenkovic, Olgica

2017-07-10

DNA-based data storage is an emerging nonvolatile memory technology of potentially unprecedented density, durability, and replication efficiency. The basic system implementation steps include synthesizing DNA strings that contain user information and subsequently retrieving them via high-throughput sequencing technologies. Existing architectures enable reading and writing but do not offer random-access and error-free data recovery from low-cost, portable devices, which is crucial for making the storage technology competitive with classical recorders. Here we show for the first time that a portable, random-access platform may be implemented in practice using nanopore sequencers. The novelty of our approach is to design an integrated processing pipeline that encodes data to avoid costly synthesis and sequencing errors, enables random access through addressing, and leverages efficient portable sequencing via new iterative alignment and deletion error-correcting codes. Our work represents the only known random access DNA-based data storage system that uses error-prone nanopore sequencers, while still producing error-free readouts with the highest reported information rate/density. As such, it represents a crucial step towards practical employment of DNA molecules as storage media.

Long-term stability of the Io high-temperature plasma torus

NASA Technical Reports Server (NTRS)

Moos, H. W.; Skinner, T. E.; Durrance, S. T.; Feldman, P. D.; Festou, M. C.

1985-01-01

The short wavelength camera of the International Ultraviolet Explorer satellite was used to measure S II 1256, S III 1199, semiforbidden S III 1729, and semiforbidden S IV 1406 emission from the high-temperature region of the Io plasma torus. Observations over a period of five years (1979-1984) indicate that the Io plasma parameters have relatively small variations, particularly in the case of the mixing ratio for the dominant constituent S(++), and electron temperature. A simple three-dimensional model of the plasma torus was used to obtain the ion mixing ratios and the plasma density for each observation. The results are compared with Voyager 1 data for mixing ratio (ion density divided by electron density); ionization balance; and plasma density. The results of the comparison are discussed in detail.

The paradox of MHC-DRB exon/intron evolution: alpha-helix and beta-sheet encoding regions diverge while hypervariable intronic simple repeats coevolve with beta-sheet codons.

PubMed

Schwaiger, F W; Weyers, E; Epplen, C; Brün, J; Ruff, G; Crawford, A; Epplen, J T

1993-09-01

Twenty-one different caprine and 13 ovine MHC-DRB exon 2 sequences were determined including part of the adjacent introns containing simple repetitive (gt)n(ga)m elements. The positions for highly polymorphic DRB amino acids vary slightly among ungulates and other mammals. From man and mouse to ungulates the basic (gt)n(ga)m structure is fixed in evolution for 7 x 10(7) years whereas ample variations exist in the tandem (gt)n and (ga)m dinucleotides and especially their "degenerated" derivatives. Phylogenetic trees for the alpha-helices and beta-pleated sheets of the ungulate DRB sequences suggest different evolutionary histories. In hoofed animals as well as in humans DRB beta-sheet encoding sequences and adjacent intronic repeats can be assembled into virtually identical groups suggesting coevolution of noncoding as well as coding DNA. In contrast alpha-helices and C-terminal parts of the first DRB domain evolve distinctly. In the absence of a defined mechanism causing specific, site-directed mutations, double-recombination or gene-conversion-like events would readily explain this fact. The role of the intronic simple (gt)n(ga)m repeat is discussed with respect to these genetic exchange mechanisms during evolution.

Reentrant and Isostructural Transitions in the Cluster-Crystal Forming GEM-4

NASA Astrophysics Data System (ADS)

Zhang, Kai; Charbonneau, Patrick; Mladek, Bianca

2011-03-01

Systems governed by soft, bounded, purely repulsive interactions show two possible equilibrium behaviors under compression: reentrant melting, as in the Gaussian core model (GCM), or clustering, as in the penetrable sphere model (PSM). The generalized exponential model of power 4 (GEM-4), which is the intermedia of the GCM and PSM with a simple isotropic pair interaction u (r) ~e-r4 , is thought to belong to the second family and was indeed found to form clusters at sufficiently high densities at high temperatures. Here, we present the low-temperature behavior of GEM-4 through Monte Carlo simulations using a specially developed free energy integration scheme. We find the phase behavior to be hybrid between the GCM and the PSM limits, showing a surprisingly rich phase behavior in spite of the simplicity of the interaction form. For instance, S- shaped doubly reentrant phase sequences and evidence of a cascade of critical isostructural transitions between crystals of different average lattice site occupancy are observed. The possible annihilation of lattice sites and accompanying clustering moreover leads to an unusual softening upon compression, which suggest that these materials may have interesting mechanical properties. We discuss possible experimental realizations and challenges of this class of materials.

Evaluation of interpolation techniques for the creation of gridded daily precipitation (1 × 1 km2); Cyprus, 1980-2010

NASA Astrophysics Data System (ADS)

Camera, Corrado; Bruggeman, Adriana; Hadjinicolaou, Panos; Pashiardis, Stelios; Lange, Manfred A.

2014-01-01

High-resolution gridded daily data sets are essential for natural resource management and the analyses of climate changes and their effects. This study aims to evaluate the performance of 15 simple or complex interpolation techniques in reproducing daily precipitation at a resolution of 1 km2 over topographically complex areas. Methods are tested considering two different sets of observation densities and different rainfall amounts. We used rainfall data that were recorded at 74 and 145 observational stations, respectively, spread over the 5760 km2 of the Republic of Cyprus, in the Eastern Mediterranean. Regression analyses utilizing geographical copredictors and neighboring interpolation techniques were evaluated both in isolation and combined. Linear multiple regression (LMR) and geographically weighted regression methods (GWR) were tested. These included a step-wise selection of covariables, as well as inverse distance weighting (IDW), kriging, and 3D-thin plate splines (TPS). The relative rank of the different techniques changes with different station density and rainfall amounts. Our results indicate that TPS performs well for low station density and large-scale events and also when coupled with regression models. It performs poorly for high station density. The opposite is observed when using IDW. Simple IDW performs best for local events, while a combination of step-wise GWR and IDW proves to be the best method for large-scale events and high station density. This study indicates that the use of step-wise regression with a variable set of geographic parameters can improve the interpolation of large-scale events because it facilitates the representation of local climate dynamics.

Evaluating the impact of a wide range of vegetation densities on river channel pattern

NASA Astrophysics Data System (ADS)

Pattison, Ian; Roucou, Ron

2016-04-01

Braided rivers are very dynamic systems which have complex controls over their planform and flow dynamics. Vegetation is one variable which influences channel geometry and pattern, through its effect on local flow hydraulics and the process continuum of sediment erosion-transport-deposition. Furthermore, where in the braided floodplain stable vegetation develops depends on the temporal sequencing of the river discharge i.e. floods. Understanding the effect of vegetation in these highly dynamic systems has multiple consequences for human activity and floodplain management. This paper focusses on the specific role of vegetation density in controlling braided river form and processes. Previous research in this field has been contradictory; with Gran and Paola (2001) finding that increasing vegetation density decreased the number of active channels. In contrast, Coulthard (2005] observed that as vegetation become denser there was an increase in the number of channels. This was hypothesized to be caused by flow separation around vegetation and the development of bars immediately downstream of the plant. This paper reports the results from a set of experiments in a 4m by 1m flume, where discharge, slope and sediment size were kept constant. Artificial grass was used to represent vegetation with a density ranging from 50 plants/m2 to 400 plants/m2. Digital photographs, using a GoPro camera with a fish eye lens, were taken from ~1m above the flume at an interval of 30 seconds during the 3 hour experiment. The experiments showed that as the vegetation density increased from 50 to 150 plants/m2, the number of channel bars developing doubled from 12 to 24. At vegetation densities greater than 150 plants/m2 there was a decline in the number of bars created to a minimum of 8 bars for a density of 400 plants/m2. We attribute these patterns to the effect that the vegetation has on flow hydraulics, sediment transport processes and the spatial patterns of erosion and deposition. We develop a simple conceptual model to explain the observations along the wide range of vegetation densities investigated. At low plant densities, each plant acted independently and caused flow separation and convergence around each plant, similar to in the Coulthard (2005] experiment. At medium densities, individual plants start to interact together with narrow channels developing longitudinally between vegetative bars. Finally at very high densities, there was both lateral and longitudinal interaction between plants meaning that flow was diverted around them forming wandering, meandering channels. In summary, the relationship between vegetation density and channel braiding is more complex than previous thought, taking a parabolic shape, with maximum braiding occurring at medium vegetation densities.

High-speed imaging using 3CCD camera and multi-color LED flashes

NASA Astrophysics Data System (ADS)

Hijazi, Ala; Friedl, Alexander; Cierpka, Christian; Kähler, Christian; Madhavan, Vis

2017-11-01

This paper demonstrates the possibility of capturing full-resolution, high-speed image sequences using a regular 3CCD color camera in conjunction with high-power light emitting diodes of three different colors. This is achieved using a novel approach, referred to as spectral-shuttering, where a high-speed image sequence is captured using short duration light pulses of different colors that are sent consecutively in very close succession. The work presented in this paper demonstrates the feasibility of configuring a high-speed camera system using low cost and readily available off-the-shelf components. This camera can be used for recording six-frame sequences at frame rates up to 20 kHz or three-frame sequences at even higher frame rates. Both color crosstalk and spatial matching between the different channels of the camera are found to be within acceptable limits. A small amount of magnification difference between the different channels is found and a simple calibration procedure for correcting the images is introduced. The images captured using the approach described here are of good quality to be used for obtaining full-field quantitative information using techniques such as digital image correlation and particle image velocimetry. A sequence of six high-speed images of a bubble splash recorded at 400 Hz is presented as a demonstration.

One-dimensional α-MoO3 nanorods for high energy density pseudocapacitor

NASA Astrophysics Data System (ADS)

Dutta, Shibsankar; Pal, Shreyasi; De, Sukanta

2018-04-01

Ultralong α-MoO3 nanorods having length of 500 nm to 1 µm and uniform width of around ˜50 nm have been synthesized by a simple one step hydrothermal route using a molybdenum organic salt precursor. An evaluation of the electrochemical properties of the nanorods was done by cyclic voltammetry (CV), and galvanometric charging- discharging (GCD) test. Because of the high active sites and rapid ion diffusion and electron transport of the electrodes using as prepared nanorods reveals energy density of 65 Wh/kg at a power density of 940 W/ kg and a maximum specific capacitance of 474 F/g. It also shows excellent cycling stability.

SIRW: A web server for the Simple Indexing and Retrieval System that combines sequence motif searches with keyword searches.

PubMed

Ramu, Chenna

2003-07-01

SIRW (http://sirw.embl.de/) is a World Wide Web interface to the Simple Indexing and Retrieval System (SIR) that is capable of parsing and indexing various flat file databases. In addition it provides a framework for doing sequence analysis (e.g. motif pattern searches) for selected biological sequences through keyword search. SIRW is an ideal tool for the bioinformatics community for searching as well as analyzing biological sequences of interest.

Effect of sequencing of complementary feeding in relation to breast-feeding on total intake in infants.

PubMed

Shah, Dheeraj; Singh, Meenakshi; Gupta, Piyush; Faridi, M M A

2014-03-01

The aim of the present study was to evaluate whether the order of complementary feeding in relation to breast-feeding affects breast milk, semisolid, or total energy intake in infants. The present study was designed as a randomized crossover trial. The study was conducted in a tertiary care hospital. The study participants were 25 healthy infants between the ages of 7 and 11 months who were exclusively breast-fed for at least 6 months and were now receiving complementary foods for at least 1 month in addition to breast-feeding. Infants were randomized to follow a sequence of either complementary feeding before breast-feeding (sequence A) or complementary feeding after breast-feeding (sequence B) for the first day (24 hours) of the study period using simple randomization. For the next day, the sequence was reversed for each child. All babies received 3 actively fed complementary food meals per day (morning, afternoon, and evening). A semisolid study diet was prepared in the hospital by cooking rice and pulse with oil using a standard method, ensuring the energy density of at least 0.6 kcal/g. The infants were allowed ad libitum breast-feeding during the observation period. Semisolid intake was directly measured and breast milk intake was quantified by test weighing method. Energy intake from complementary foods was calculated from the product of energy density of the diet served on that day and the total amount consumed. The total energy intake and energy intake from breast milk and complementary foods between the 2 sequences were compared. The mean (standard deviation) energy intake from breast milk during 12 hours of daytime by following sequence A (complementary feeding before breast-feeding) was 132.0 (67.4) kcal in comparison with 135.9 (56.2) kcal in sequence B, which was not statistically different (P = 0.83). The mean (standard deviation) energy consumed from semisolids in sequences A and B was also comparable (88.6 [75.5] kcal vs. 85.5 [89.7] kcal; P = 0.58). The total energy intake during daytime in sequence A was 220.6 (96.2) kcal in comparison with 221.5 (94.0) kcal in sequence B, which was also comparable (P = 0.97). The results related to energy intake through breast milk and total energy intake were not different when insensible losses during feeding were adjusted in both groups. Altering the sequence of complementary feeding in relation to breast-feeding does not affect total energy intake.

Use of Sine Shaped High-Frequency Rhythmic Visual Stimuli Patterns for SSVEP Response Analysis and Fatigue Rate Evaluation in Normal Subjects

PubMed Central

Keihani, Ahmadreza; Shirzhiyan, Zahra; Farahi, Morteza; Shamsi, Elham; Mahnam, Amin; Makkiabadi, Bahador; Haidari, Mohsen R.; Jafari, Amir H.

2018-01-01

Background: Recent EEG-SSVEP signal based BCI studies have used high frequency square pulse visual stimuli to reduce subjective fatigue. However, the effect of total harmonic distortion (THD) has not been considered. Compared to CRT and LCD monitors, LED screen displays high-frequency wave with better refresh rate. In this study, we present high frequency sine wave simple and rhythmic patterns with low THD rate by LED to analyze SSVEP responses and evaluate subjective fatigue in normal subjects. Materials and Methods: We used patterns of 3-sequence high-frequency sine waves (25, 30, and 35 Hz) to design our visual stimuli. Nine stimuli patterns, 3 simple (repetition of each of above 3 frequencies e.g., P25-25-25) and 6 rhythmic (all of the frequencies in 6 different sequences e.g., P25-30-35) were chosen. A hardware setup with low THD rate (<0.1%) was designed to present these patterns on LED. Twenty two normal subjects (aged 23–30 (25 ± 2.1) yrs) were enrolled. Visual analog scale (VAS) was used for subjective fatigue evaluation after presentation of each stimulus pattern. PSD, CCA, and LASSO methods were employed to analyze SSVEP responses. The data including SSVEP features and fatigue rate for different visual stimuli patterns were statistically evaluated. Results: All 9 visual stimuli patterns elicited SSVEP responses. Overall, obtained accuracy rates were 88.35% for PSD and > 90% for CCA and LASSO (for TWs > 1 s). High frequency rhythmic patterns group with low THD rate showed higher accuracy rate (99.24%) than simple patterns group (98.48%). Repeated measure ANOVA showed significant difference between rhythmic pattern features (P < 0.0005). Overall, there was no significant difference between the VAS of rhythmic [3.85 ± 2.13] compared to the simple patterns group [3.96 ± 2.21], (P = 0.63). Rhythmic group had lower within group VAS variation (min = P25-30-35 [2.90 ± 2.45], max = P35-25-30 [4.81 ± 2.65]) as well as least individual pattern VAS (P25-30-35). Discussion and Conclusion: Overall, rhythmic and simple pattern groups had higher and similar accuracy rates. Rhythmic stimuli patterns showed insignificantly lower fatigue rate than simple patterns. We conclude that both rhythmic and simple visual high frequency sine wave stimuli require further research for human subject SSVEP-BCI studies. PMID:29892219

Use of Sine Shaped High-Frequency Rhythmic Visual Stimuli Patterns for SSVEP Response Analysis and Fatigue Rate Evaluation in Normal Subjects.

PubMed

Keihani, Ahmadreza; Shirzhiyan, Zahra; Farahi, Morteza; Shamsi, Elham; Mahnam, Amin; Makkiabadi, Bahador; Haidari, Mohsen R; Jafari, Amir H

2018-01-01

Background: Recent EEG-SSVEP signal based BCI studies have used high frequency square pulse visual stimuli to reduce subjective fatigue. However, the effect of total harmonic distortion (THD) has not been considered. Compared to CRT and LCD monitors, LED screen displays high-frequency wave with better refresh rate. In this study, we present high frequency sine wave simple and rhythmic patterns with low THD rate by LED to analyze SSVEP responses and evaluate subjective fatigue in normal subjects. Materials and Methods: We used patterns of 3-sequence high-frequency sine waves (25, 30, and 35 Hz) to design our visual stimuli. Nine stimuli patterns, 3 simple (repetition of each of above 3 frequencies e.g., P25-25-25) and 6 rhythmic (all of the frequencies in 6 different sequences e.g., P25-30-35) were chosen. A hardware setup with low THD rate (<0.1%) was designed to present these patterns on LED. Twenty two normal subjects (aged 23-30 (25 ± 2.1) yrs) were enrolled. Visual analog scale (VAS) was used for subjective fatigue evaluation after presentation of each stimulus pattern. PSD, CCA, and LASSO methods were employed to analyze SSVEP responses. The data including SSVEP features and fatigue rate for different visual stimuli patterns were statistically evaluated. Results: All 9 visual stimuli patterns elicited SSVEP responses. Overall, obtained accuracy rates were 88.35% for PSD and > 90% for CCA and LASSO (for TWs > 1 s). High frequency rhythmic patterns group with low THD rate showed higher accuracy rate (99.24%) than simple patterns group (98.48%). Repeated measure ANOVA showed significant difference between rhythmic pattern features ( P < 0.0005). Overall, there was no significant difference between the VAS of rhythmic [3.85 ± 2.13] compared to the simple patterns group [3.96 ± 2.21], ( P = 0.63). Rhythmic group had lower within group VAS variation (min = P25-30-35 [2.90 ± 2.45], max = P35-25-30 [4.81 ± 2.65]) as well as least individual pattern VAS (P25-30-35). Discussion and Conclusion: Overall, rhythmic and simple pattern groups had higher and similar accuracy rates. Rhythmic stimuli patterns showed insignificantly lower fatigue rate than simple patterns. We conclude that both rhythmic and simple visual high frequency sine wave stimuli require further research for human subject SSVEP-BCI studies.

Population-genetic nature of copy number variations in the human genome.

PubMed

Kato, Mamoru; Kawaguchi, Takahisa; Ishikawa, Shumpei; Umeda, Takayoshi; Nakamichi, Reiichiro; Shapero, Michael H; Jones, Keith W; Nakamura, Yusuke; Aburatani, Hiroyuki; Tsunoda, Tatsuhiko

2010-03-01

Copy number variations (CNVs) are universal genetic variations, and their association with disease has been increasingly recognized. We designed high-density microarrays for CNVs, and detected 3000-4000 CNVs (4-6% of the genomic sequence) per population that included CNVs previously missed because of smaller sizes and residing in segmental duplications. The patterns of CNVs across individuals were surprisingly simple at the kilo-base scale, suggesting the applicability of a simple genetic analysis for these genetic loci. We utilized the probabilistic theory to determine integer copy numbers of CNVs and employed a recently developed phasing tool to estimate the population frequencies of integer copy number alleles and CNV-SNP haplotypes. The results showed a tendency toward a lower frequency of CNV alleles and that most of our CNVs were explained only by zero-, one- and two-copy alleles. Using the estimated population frequencies, we found several CNV regions with exceptionally high population differentiation. Investigation of CNV-SNP linkage disequilibrium (LD) for 500-900 bi- and multi-allelic CNVs per population revealed that previous conflicting reports on bi-allelic LD were unexpectedly consistent and explained by an LD increase correlated with deletion-allele frequencies. Typically, the bi-allelic LD was lower than SNP-SNP LD, whereas the multi-allelic LD was somewhat stronger than the bi-allelic LD. After further investigation of tag SNPs for CNVs, we conclude that the customary tagging strategy for disease association studies can be applicable for common deletion CNVs, but direct interrogation is needed for other types of CNVs.

The relation between high-density and very-high-density amorphous ice.

PubMed

Loerting, Thomas; Salzmann, Christoph G; Winkel, Katrin; Mayer, Erwin

2006-06-28

The exact nature of the relationship between high-density (HDA) and very-high-density (VHDA) amorphous ice is unknown at present. Here we review the relation between HDA and VHDA, concentrating on experimental aspects and discuss these with respect to the relation between low-density amorphous ice (LDA) and HDA. On compressing LDA at 125 K up to 1.5 GPa, two distinct density steps are observable in the pressure-density curves which correspond to the LDA --> HDA and HDA --> VHDA conversion. This stepwise formation process LDA --> HDA --> VHDA at 125 K is the first unambiguous observation of a stepwise amorphous-amorphous-amorphous transformation sequence. Density values of amorphous ice obtained in situ between 0.3 and 1.9 GPa on isobaric heating up to the temperatures of crystallization show a pronounced change of slope at ca. 0.8 GPa which could indicate formation of a distinct phase. We infer that the relation between HDA and VHDA is very similar to that between LDA and HDA except for a higher activation barrier between the former. We further discuss the two options of thermodynamic phase transition versus kinetic densification for the HDA --> VHDA conversion.

LookSeq: a browser-based viewer for deep sequencing data.

PubMed

Manske, Heinrich Magnus; Kwiatkowski, Dominic P

2009-11-01

Sequencing a genome to great depth can be highly informative about heterogeneity within an individual or a population. Here we address the problem of how to visualize the multiple layers of information contained in deep sequencing data. We propose an interactive AJAX-based web viewer for browsing large data sets of aligned sequence reads. By enabling seamless browsing and fast zooming, the LookSeq program assists the user to assimilate information at different levels of resolution, from an overview of a genomic region to fine details such as heterogeneity within the sample. A specific problem, particularly if the sample is heterogeneous, is how to depict information about structural variation. LookSeq provides a simple graphical representation of paired sequence reads that is more revealing about potential insertions and deletions than are conventional methods.

Modeling of the merging of two colliding field reversed configuration plasmoids

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

Wang, Guanqiong; Wang, Xiaoguang; Li, Lulu

2016-06-15

The field reversed configuration (FRC) is one of the candidate plasma targets for the magneto-inertial fusion, and a high temperature FRC can be formed by using the collision-merging technology. Although the merging process and mechanism of FRC are quite complicated, it is thinkable to build a simple model to investigate the macroscopic equilibrium parameters including the density, the temperature and the separatrix volume, which may play an important role in the collision-merging process of FRC. It is quite interesting that the estimates of the related results based on our simple model are in agreement with the simulation results of amore » two-dimensional magneto-hydrodynamic code (MFP-2D), which has being developed by our group since the last couple of years, while these results can qualitatively fit the results of C-2 experiments by Tri-alpha energy company. On the other hand, the simple model can be used to investigate how to increase the density of the merged FRC. It is found that the amplification of the density depends on the poloidal flux-increase factor and the temperature increases with the translation speed of two plasmoids.« less

Deployment Design of Wireless Sensor Network for Simple Multi-Point Surveillance of a Moving Target

PubMed Central

Tsukamoto, Kazuya; Ueda, Hirofumi; Tamura, Hitomi; Kawahara, Kenji; Oie, Yuji

2009-01-01

In this paper, we focus on the problem of tracking a moving target in a wireless sensor network (WSN), in which the capability of each sensor is relatively limited, to construct large-scale WSNs at a reasonable cost. We first propose two simple multi-point surveillance schemes for a moving target in a WSN and demonstrate that one of the schemes can achieve high tracking probability with low power consumption. In addition, we examine the relationship between tracking probability and sensor density through simulations, and then derive an approximate expression representing the relationship. As the results, we present guidelines for sensor density, tracking probability, and the number of monitoring sensors that satisfy a variety of application demands. PMID:22412326

Superconductivity in dense carbon-based materials

DOE PAGES

Lu, Siyu; Liu, Hanyu; Naumov, Ivan I.; ...

2016-03-08

Guided by a simple strategy in searching of new superconducting materials we predict that high temperature superconductivity can be realized in classes of high-density materials having strong sp 3 chemical bonding and high lattice symmetry. Here, we examine in detail sodalite carbon frameworks doped with simple metals such as Li, Na, and Al. Though such materials share some common features with doped diamond, their doping level is not limited and the density of states at the Fermi level in them can be as high as that in the renowned MgB 2. Altogether, with other factors, this boosts the superconducting temperaturemore » (T c) in the materials investigated to higher levels compared to doped diamond. For example, the superconducting T c of sodalite-like NaC 6 is predicted to be above 100 K. This phase and a series of other sodalite-based superconductors are predicted to be metastable phases but are dynamically stable. In owing to the rigid carbon framework of these and related dense carbon-materials, these doped sodalite-based structures could be recoverable as potentially useful superconductors.« less

Ultrahigh-density nanowire arrays grown in self-assembled diblock copolymer templates.

PubMed

Thurn-Albrecht, T; Schotter, J; Kästle, G A; Emley, N; Shibauchi, T; Krusin-Elbaum, L; Guarini, K; Black, C T; Tuominen, M T; Russell, T P

2000-12-15

We show a simple, robust, chemical route to the fabrication of ultrahigh-density arrays of nanopores with high aspect ratios using the equilibrium self-assembled morphology of asymmetric diblock copolymers. The dimensions and lateral density of the array are determined by segmental interactions and the copolymer molecular weight. Through direct current electrodeposition, we fabricated vertical arrays of nanowires with densities in excess of 1.9 x 10(11) wires per square centimeter. We found markedly enhanced coercivities with ferromagnetic cobalt nanowires that point toward a route to ultrahigh-density storage media. The copolymer approach described is practical, parallel, compatible with current lithographic processes, and amenable to multilayered device fabrication.

Intertwined nanocarbon and manganese oxide hybrid foam for high-energy supercapacitors.

PubMed

Wang, Wei; Guo, Shirui; Bozhilov, Krassimir N; Yan, Dong; Ozkan, Mihrimah; Ozkan, Cengiz S

2013-11-11

Rapid charging and discharging supercapacitors are promising alternative energy storage systems for applications such as portable electronics and electric vehicles. Integration of pseudocapacitive metal oxides with single-structured materials has received a lot of attention recently due to their superior electrochemical performance. In order to realize high energy-density supercapacitors, a simple and scalable method is developed to fabricate a graphene/MWNT/MnO2 nanowire (GMM) hybrid nanostructured foam, via a two-step process. The 3D few-layer graphene/MWNT (GM) architecture is grown on foamed metal foils (nickel foam) via ambient pressure chemical vapor deposition. Hydrothermally synthesized α-MnO2 nanowires are conformally coated onto the GM foam by a simple bath deposition. The as-prepared hierarchical GMM foam yields a monographical graphene foam conformally covered with an intertwined, densely packed CNT/MnO2 nanowire nanocomposite network. Symmetrical electrochemical capacitors (ECs) based on GMM foam electrodes show an extended operational voltage window of 1.6 V in aqueous electrolyte. A superior energy density of 391.7 Wh kg(-1) is obtained for the supercapacitor based on the GMM foam, which is much higher than ECs based on GM foam only (39.72 Wh kg(-1) ). A high specific capacitance (1108.79 F g(-1) ) and power density (799.84 kW kg(-1) ) are also achieved. Moreover, the great capacitance retention (97.94%) after 13 000 charge-discharge cycles and high current handability demonstrate the high stability of the electrodes of the supercapacitor. These excellent performances enable the innovative 3D hierarchical GMM foam to serve as EC electrodes, resulting in energy-storage devices with high stability and power density in neutral aqueous electrolyte. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Highly specific gene silencing in a monocot species by artificial microRNAs derived from chimeric miRNA precursors

DOE PAGES

Carbonell, Alberto; Fahlgren, Noah; Mitchell, Skyler; ...

2015-05-20

Artificial microRNAs (amiRNAs) are used for selective gene silencing in plants. However, current methods to produce amiRNA constructs for silencing transcripts in monocot species are not suitable for simple, cost-effective and large-scale synthesis. Here, a series of expression vectors based on Oryza sativa MIR390 (OsMIR390) precursor was developed for high-throughput cloning and high expression of amiRNAs in monocots. Four different amiRNA sequences designed to target specifically endogenous genes and expressed from OsMIR390-based vectors were validated in transgenic Brachypodium distachyon plants. Surprisingly, amiRNAs accumulated to higher levels and were processed more accurately when expressed from chimeric OsMIR390-based precursors that include distalmore » stem-loop sequences from Arabidopsis thaliana MIR390a (AtMIR390a). In all cases, transgenic plants displayed the predicted phenotypes induced by target gene repression, and accumulated high levels of amiRNAs and low levels of the corresponding target transcripts. Genome-wide transcriptome profiling combined with 5-RLM-RACE analysis in transgenic plants confirmed that amiRNAs were highly specific. Finally, significance Statement A series of amiRNA vectors based on Oryza sativa MIR390 (OsMIR390) precursor were developed for simple, cost-effective and large-scale synthesis of amiRNA constructs to silence genes in monocots. Unexpectedly, amiRNAs produced from chimeric OsMIR390-based precursors including Arabidopsis thaliana MIR390a distal stem-loop sequences accumulated elevated levels of highly effective and specific amiRNAs in transgenic Brachypodium distachyon plants.« less

Large-scale development of SSR markers in tobacco and construction of a linkage map in flue-cured tobacco

PubMed Central

Tong, Zhijun; Xiao, Bingguang; Jiao, Fangchan; Fang, Dunhuang; Zeng, Jianmin; Wu, Xingfu; Chen, Xuejun; Yang, Jiankang; Li, Yongping

2016-01-01

Tobacco (Nicotiana tabacum L.), particularly flue-cured tobacco, is one of the most economically important nonfood crops and is also an important model system in plant biotechnology. Despite its importance, only limited molecular marker resources are available for genome analysis, genetic mapping, and breeding. Simple sequence repeats (SSR) are one of the most widely-used molecular markers, having significant advantages including that they are generally co-dominant, easy to use, abundant in eukaryotic organisms, and produce highly reproducible results. In this study, based on the genome sequence data of flue-cured tobacco (K326), we developed a total of 13,645 mostly novel SSR markers, which were working in a set of eighteen tobacco varieties of four different types. A mapping population of 213 backcross (BC1) individuals, which were derived from an intra-type cross between two flue-cured tobacco varieties, Y3 and K326, was selected for mapping. Based on the newly developed SSR markers as well as published SSR markers, we constructed a genetic map consisting of 626 SSR loci distributed across 24 linkage groups and covering a total length of 1120.45 cM with an average distance of 1.79 cM between adjacent markers, which is the highest density map of flue-cured tobacco till date. PMID:27436948

The SCUBA-2 Cosmology Legacy Survey: galaxies in the deep 850 μm survey, and the star-forming `main sequence'

NASA Astrophysics Data System (ADS)

Koprowski, M. P.; Dunlop, J. S.; Michałowski, M. J.; Roseboom, I.; Geach, J. E.; Cirasuolo, M.; Aretxaga, I.; Bowler, R. A. A.; Banerji, M.; Bourne, N.; Coppin, K. E. K.; Chapman, S.; Hughes, D. H.; Jenness, T.; McLure, R. J.; Symeonidis, M.; Werf, P. van der

2016-06-01

We investigate the properties of the galaxies selected from the deepest 850-μm survey undertaken to date with (Submillimetre Common-User Bolometer Array 2) SCUBA-2 on the James Clerk Maxwell Telescope as part of the SCUBA-2 Cosmology Legacy Survey. A total of 106 sources (>5σ) were uncovered at 850 μm from an area of ≃150 arcmin2 in the centre of the COSMOS/UltraVISTA/Cosmic Assembly Near-infrared Deep Extragalactic Legacy Survey (CANDELS) field, imaged to a typical depth of σ850 ≃ 0.25 mJy. We utilize the available multifrequency data to identify galaxy counterparts for 80 of these sources (75 per cent), and to establish the complete redshift distribution for this sample, yielding bar{z} = 2.38± 0.09. We have also been able to determine the stellar masses of the majority of the galaxy identifications, enabling us to explore their location on the star formation rate:stellar mass (SFR:M*) plane. Crucially, our new deep 850-μm-selected sample reaches flux densities equivalent to SFR ≃ 100 M⊙ yr-1, enabling us to confirm that sub-mm galaxies form the high-mass end of the `main sequence' (MS) of star-forming galaxies at z > 1.5 (with a mean specific SFR of sSFR = 2.25 ± 0.19 Gyr-1 at z ≃ 2.5). Our results are consistent with no significant flattening of the MS towards high masses at these redshifts. However, our results add to the growing evidence that average sSFR rises only slowly at high redshift, resulting in log10sSFR being an apparently simple linear function of the age of the Universe.

Exome Sequencing in Suspected Monogenic Dyslipidemias

PubMed Central

Stitziel, Nathan O.; Peloso, Gina M.; Abifadel, Marianne; Cefalu, Angelo B.; Fouchier, Sigrid; Motazacker, M. Mahdi; Tada, Hayato; Larach, Daniel B.; Awan, Zuhier; Haller, Jorge F.; Pullinger, Clive R.; Varret, Mathilde; Rabès, Jean-Pierre; Noto, Davide; Tarugi, Patrizia; Kawashiri, Masa-aki; Nohara, Atsushi; Yamagishi, Masakazu; Risman, Marjorie; Deo, Rahul; Ruel, Isabelle; Shendure, Jay; Nickerson, Deborah A.; Wilson, James G.; Rich, Stephen S.; Gupta, Namrata; Farlow, Deborah N.; Neale, Benjamin M.; Daly, Mark J.; Kane, John P.; Freeman, Mason W.; Genest, Jacques; Rader, Daniel J.; Mabuchi, Hiroshi; Kastelein, John J.P.; Hovingh, G. Kees; Averna, Maurizio R.; Gabriel, Stacey; Boileau, Catherine; Kathiresan, Sekar

2015-01-01

Background Exome sequencing is a promising tool for gene mapping in Mendelian disorders. We utilized this technique in an attempt to identify novel genes underlying monogenic dyslipidemias. Methods and Results We performed exome sequencing on 213 selected family members from 41 kindreds with suspected Mendelian inheritance of extreme levels of low-density lipoprotein (LDL) cholesterol (after candidate gene sequencing excluded known genetic causes for high LDL cholesterol families) or high-density lipoprotein (HDL) cholesterol. We used standard analytic approaches to identify candidate variants and also assigned a polygenic score to each individual in order to account for their burden of common genetic variants known to influence lipid levels. In nine families, we identified likely pathogenic variants in known lipid genes (ABCA1, APOB, APOE, LDLR, LIPA, and PCSK9); however, we were unable to identify obvious genetic etiologies in the remaining 32 families despite follow-up analyses. We identified three factors that limited novel gene discovery: (1) imperfect sequencing coverage across the exome hid potentially causal variants; (2) large numbers of shared rare alleles within families obfuscated causal variant identification; and (3) individuals from 15% of families carried a significant burden of common lipid-related alleles, suggesting complex inheritance can masquerade as monogenic disease. Conclusions We identified the genetic basis of disease in nine of 41 families; however, none of these represented novel gene discoveries. Our results highlight the promise and limitations of exome sequencing as a discovery technique in suspected monogenic dyslipidemias. Considering the confounders identified may inform the design of future exome sequencing studies. PMID:25632026

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning

PubMed Central

Valouev, Anton; Ichikawa, Jeffrey; Tonthat, Thaisan; Stuart, Jeremy; Ranade, Swati; Peckham, Heather; Zeng, Kathy; Malek, Joel A.; Costa, Gina; McKernan, Kevin; Sidow, Arend; Fire, Andrew; Johnson, Steven M.

2008-01-01

Using the massively parallel technique of sequencing by oligonucleotide ligation and detection (SOLiD; Applied Biosystems), we have assessed the in vivo positions of more than 44 million putative nucleosome cores in the multicellular genetic model organism Caenorhabditis elegans. These analyses provide a global view of the chromatin architecture of a multicellular animal at extremely high density and resolution. While we observe some degree of reproducible positioning throughout the genome in our mixed stage population of animals, we note that the major chromatin feature in the worm is a diversity of allowed nucleosome positions at the vast majority of individual loci. While absolute positioning of nucleosomes can vary substantially, relative positioning of nucleosomes (in a repeated array structure likely to be maintained at least in part by steric constraints) appears to be a significant property of chromatin structure. The high density of nucleosomal reads enabled a substantial extension of previous analysis describing the usage of individual oligonucleotide sequences along the span of the nucleosome core and linker. We release this data set, via the UCSC Genome Browser, as a resource for the high-resolution analysis of chromatin conformation and DNA accessibility at individual loci within the C. elegans genome. PMID:18477713

Self-assembly of 3D Carbon Nanotube Sponges: A Simple and Controllable Way to Build Macroscopic and Ultralight Porous Architectures.

PubMed

Luo, Shu; Luo, Yufeng; Wu, Hengcai; Li, Mengya; Yan, Lingjia; Jiang, Kaili; Liu, Liang; Li, Qunqing; Fan, Shoushan; Wang, Jiaping

2017-01-01

Macroscopic and 3D superaligned CNT (SACNT) sponges are fabricated through a simple, low-cost, controllable, and scalable self-assembly method without using organic binder. Sponges with specific shapes and densities can be achieved. SACNT sponges are ultralight (1-50 mg cm -3 ), highly porous (97.5%-99.9%) with honeycomb-like hierarchical structure, and highly conductive. Using SACNT sponges as templates, various materials with honeycomb-like structure can be obtained for wide applications. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular Landscape of Modified Histones in Drosophila Heterochromatic Genes and Euchromatin-Heterochromatin Transition Zones

PubMed Central

Yasuhara, Jiro C; Wakimoto, Barbara T

2008-01-01

Constitutive heterochromatin is enriched in repetitive sequences and histone H3-methylated-at-lysine 9. Both components contribute to heterochromatin's ability to silence euchromatic genes. However, heterochromatin also harbors hundreds of expressed genes in organisms such as Drosophila. Recent studies have provided a detailed picture of sequence organization of D. melanogaster heterochromatin, but how histone modifications are associated with heterochromatic sequences at high resolution has not been described. Here, distributions of modified histones in the vicinity of heterochromatic genes of normal embryos and embryos homozygous for a chromosome rearrangement were characterized using chromatin immunoprecipitation and genome tiling arrays. We found that H3-di-methylated-at-lysine 9 (H3K9me2) was depleted at the 5′ ends but enriched throughout transcribed regions of heterochromatic genes. The profile was distinct from that of euchromatic genes and suggests that heterochromatic genes are integrated into, rather than insulated from, the H3K9me2-enriched domain. Moreover, the profile was only subtly affected by a Su(var)3–9 null mutation, implicating a histone methyltransferase other than SU(VAR)3–9 as responsible for most H3K9me2 associated with heterochromatic genes in embryos. On a chromosomal scale, we observed a sharp transition to the H3K9me2 domain, which coincided with increased retrotransposon density in the euchromatin-heterochromatin (eu-het) transition zones on the long chromosome arms. Thus, a certain density of retrotransposons, rather than specific boundary elements, may demarcate Drosophila pericentric heterochromatin. We also demonstrate that a chromosome rearrangement that created a new eu-het junction altered H3K9me2 distribution and induced new euchromatic sites of enrichment as far as several megabases away from the breakpoint. Taken together, the findings argue against simple classification of H3K9me as the definitive signature of silenced genes, and clarify roles of histone modifications and repetitive DNAs in heterochromatin. The results are also relevant for understanding the effects of chromosome aberrations and the megabase scale over which epigenetic position effects can operate in multicellular organisms. PMID:18208336

Analysis of simple sequence repeat (SSR) structure and sequence within Epichloë endophyte genomes reveals impacts on gene structure and insights into ancestral hybridization events.

PubMed

Clayton, William; Eaton, Carla Jane; Dupont, Pierre-Yves; Gillanders, Tim; Cameron, Nick; Saikia, Sanjay; Scott, Barry

2017-01-01

Epichloë grass endophytes comprise a group of filamentous fungi of both sexual and asexual species. Known for the beneficial characteristics they endow upon their grass hosts, the identification of these endophyte species has been of great interest agronomically and scientifically. The use of simple sequence repeat loci and the variation in repeat elements has been used to rapidly identify endophyte species and strains, however, little is known of how the structure of repeat elements changes between species and strains, and where these repeat elements are located in the fungal genome. We report on an in-depth analysis of the structure and genomic location of the simple sequence repeat locus B10, commonly used for Epichloë endophyte species identification. The B10 repeat was found to be located within an exon of a putative bZIP transcription factor, suggesting possible impacts on polypeptide sequence and thus protein function. Analysis of this repeat in the asexual endophyte hybrid Epichloë uncinata revealed that the structure of B10 alleles reflects the ancestral species that hybridized to give rise to this species. Understanding the structure and sequence of these simple sequence repeats provides a useful set of tools for readily distinguishing strains and for gaining insights into the ancestral species that have undergone hybridization events.

High-resolution Imaging of PHIBSS z ˜ 2 Main-sequence Galaxies in CO J = 1 → 0

NASA Astrophysics Data System (ADS)

Bolatto, A. D.; Warren, S. R.; Leroy, A. K.; Tacconi, L. J.; Bouché, N.; Förster Schreiber, N. M.; Genzel, R.; Cooper, M. C.; Fisher, D. B.; Combes, F.; García-Burillo, S.; Burkert, A.; Bournaud, F.; Weiss, A.; Saintonge, A.; Wuyts, S.; Sternberg, A.

2015-08-01

We present Karl Jansky Very Large Array observations of the CO J=1-0 transition in a sample of four z˜ 2 main-sequence galaxies. These galaxies are in the blue sequence of star-forming galaxies at their redshift, and are part of the IRAM Plateau de Bure HIgh-z Blue Sequence Survey which imaged them in CO J=3-2. Two galaxies are imaged here at high signal-to-noise, allowing determinations of their disk sizes, line profiles, molecular surface densities, and excitation. Using these and published measurements, we show that the CO and optical disks have similar sizes in main-sequence galaxies, and in the galaxy where we can compare CO J=1-0 and J=3-2 sizes we find these are also very similar. Assuming a Galactic CO-to-H2 conversion, we measure surface densities of {{{Σ }}}{mol}˜ 1200 {M}⊙ pc-2 in projection and estimate {{{Σ }}}{mol}˜ 500-900 {M}⊙ pc-2 deprojected. Finally, our data yields velocity-integrated Rayleigh-Jeans brightness temperature line ratios r31 that are approximately at unity. In addition to the similar disk sizes, the very similar line profiles in J=1-0 and J=3-2 indicate that both transitions sample the same kinematics, implying that their emission is coextensive. We conclude that in these two main-sequence galaxies there is no evidence for significant excitation gradients or a large molecular reservoir that is diffuse or cold and not involved in active star formation. We suggest that r31 in very actively star-forming galaxies is likely an indicator of how well-mixed the star formation activity and the molecular reservoir are.

Detection of possible restriction sites for type II restriction enzymes in DNA sequences.

PubMed

Gagniuc, P; Cimponeriu, D; Ionescu-Tîrgovişte, C; Mihai, Andrada; Stavarachi, Monica; Mihai, T; Gavrilă, L

2011-01-01

In order to make a step forward in the knowledge of the mechanism operating in complex polygenic disorders such as diabetes and obesity, this paper proposes a new algorithm (PRSD -possible restriction site detection) and its implementation in Applied Genetics software. This software can be used for in silico detection of potential (hidden) recognition sites for endonucleases and for nucleotide repeats identification. The recognition sites for endonucleases may result from hidden sequences through deletion or insertion of a specific number of nucleotides. Tests were conducted on DNA sequences downloaded from NCBI servers using specific recognition sites for common type II restriction enzymes introduced in the software database (n = 126). Each possible recognition site indicated by the PRSD algorithm implemented in Applied Genetics was checked and confirmed by NEBcutter V2.0 and Webcutter 2.0 software. In the sequence NG_008724.1 (which includes 63632 nucleotides) we found a high number of potential restriction sites for ECO R1 that may be produced by deletion (n = 43 sites) or insertion (n = 591 sites) of one nucleotide. The second module of Applied Genetics has been designed to find simple repeats sizes with a real future in understanding the role of SNPs (Single Nucleotide Polymorphisms) in the pathogenesis of the complex metabolic disorders. We have tested the presence of simple repetitive sequences in five DNA sequence. The software indicated exact position of each repeats detected in the tested sequences. Future development of Applied Genetics can provide an alternative for powerful tools used to search for restriction sites or repetitive sequences or to improve genotyping methods.

``Sequence space soup'' of proteins and copolymers

NASA Astrophysics Data System (ADS)

Chan, Hue Sun; Dill, Ken A.

1991-09-01

To study the protein folding problem, we use exhaustive computer enumeration to explore ``sequence space soup,'' an imaginary solution containing the ``native'' conformations (i.e., of lowest free energy) under folding conditions, of every possible copolymer sequence. The model is of short self-avoiding chains of hydrophobic (H) and polar (P) monomers configured on the two-dimensional square lattice. By exhaustive enumeration, we identify all native structures for every possible sequence. We find that random sequences of H/P copolymers will bear striking resemblance to known proteins: Most sequences under folding conditions will be approximately as compact as known proteins, will have considerable amounts of secondary structure, and it is most probable that an arbitrary sequence will fold to a number of lowest free energy conformations that is of order one. In these respects, this simple model shows that proteinlike behavior should arise simply in copolymers in which one monomer type is highly solvent averse. It suggests that the structures and uniquenesses of native proteins are not consequences of having 20 different monomer types, or of unique properties of amino acid monomers with regard to special packing or interactions, and thus that simple copolymers might be designable to collapse to proteinlike structures and properties. A good strategy for designing a sequence to have a minimum possible number of native states is to strategically insert many P monomers. Thus known proteins may be marginally stable due to a balance: More H residues stabilize the desired native state, but more P residues prevent simultaneous stabilization of undesired native states.

cyclostratigraphy, sequence stratigraphy and organic matter accumulation mechanism

NASA Astrophysics Data System (ADS)

Cong, F.; Li, J.

2016-12-01

The first member of Maokou Formation of Sichuan basin is composed of well preserved carbonate ramp couplets of limestone and marlstone/shale. It acts as one of the potential shale gas source rock, and is suitable for time-series analysis. We conducted time-series analysis to identify high-frequency sequences, reconstruct high-resolution sedimentation rate, estimate detailed primary productivity for the first time in the study intervals and discuss organic matter accumulation mechanism of source rock under sequence stratigraphic framework.Using the theory of cyclostratigraphy and sequence stratigraphy, the high-frequency sequences of one outcrop profile and one drilling well are identified. Two third-order sequences and eight fourth-order sequences are distinguished on outcrop profile based on the cycle stacking patterns. For drilling well, sequence boundary and four system tracts is distinguished by "integrated prediction error filter analysis" (INPEFA) of Gamma-ray logging data, and eight fourth-order sequences is identified by 405ka long eccentricity curve in depth domain which is quantified and filtered by integrated analysis of MTM spectral analysis, evolutive harmonic analysis (EHA), evolutive average spectral misfit (eASM) and band-pass filtering. It suggests that high-frequency sequences correlate well with Milankovitch orbital signals recorded in sediments, and it is applicable to use cyclostratigraphy theory in dividing high-frequency(4-6 orders) sequence stratigraphy.High-resolution sedimentation rate is reconstructed through the study interval by tracking the highly statistically significant short eccentricity component (123ka) revealed by EHA. Based on sedimentation rate, measured TOC and density data, the burial flux, delivery flux and primary productivity of organic carbon was estimated. By integrating redox proxies, we can discuss the controls on organic matter accumulation by primary production and preservation under the high-resolution sequence stratigraphic framework. Results show that high average organic carbon contents in the study interval are mainly attributed to high primary production. The results also show a good correlation between high organic carbon accumulation and intervals of transgression.

Microsatellite analysis and marker development in garlic: distribution in EST sequence, genetic diversity analysis, and marker transferability across Alliaceae.

PubMed

Barboza, Karina; Beretta, Vanesa; Kozub, Perla C; Salinas, Cecilia; Morgenfeld, Mauro M; Galmarini, Claudio R; Cavagnaro, Pablo F

2018-04-28

Allium vegetables, such as garlic and onion, have understudied genomes and limited molecular resources, hindering advances in genetic research and breeding of these species. In this study, we characterized and compared the simple sequence repeats (SSR) landscape in the transcriptomes of garlic and related Allium (A. cepa, A. fistulosum, and A. tuberosum) and non-Allium monocot species. In addition, 110 SSR markers were developed from garlic ESTs, and they were characterized-along with 112 previously developed SSRs-at various levels, including transferability across Alliaceae species, and their usefulness for genetic diversity analysis. Among the Allium species analyzed, garlic ESTs had the highest overall SSR density, the lowest frequency of trinucleotides, and the highest of di- and tetranucleotides. When compared to more distantly related monocots, outside the Asparagales order, it was evident that ESTs of Allium species shared major commonalities with regards to SSR density, frequency distribution, sequence motifs, and GC content. A significant fraction of the SSR markers were successfully transferred across Allium species, including crops for which no SSR markers have been developed yet, such as leek, shallot, chives, and elephant garlic. Diversity analysis of garlic cultivars with selected SSRs revealed 36 alleles, with 2-5 alleles/locus, and PIC = 0.38. Cluster analysis grouped the accessions according to their flowering behavior, botanical variety, and ecophysiological characteristics. Results from this study contribute to the characterization of Allium transcriptomes. The new SSR markers developed, along with the data from the polymorphism and transferability analyses, will aid in assisting genetic research and breeding in garlic and other Allium.

Transcriptome analysis by strand-specific sequencing of complementary DNA

PubMed Central

Parkhomchuk, Dmitri; Borodina, Tatiana; Amstislavskiy, Vyacheslav; Banaru, Maria; Hallen, Linda; Krobitsch, Sylvia; Lehrach, Hans; Soldatov, Alexey

2009-01-01

High-throughput complementary DNA sequencing (RNA-Seq) is a powerful tool for whole-transcriptome analysis, supplying information about a transcript's expression level and structure. However, it is difficult to determine the polarity of transcripts, and therefore identify which strand is transcribed. Here, we present a simple cDNA sequencing protocol that preserves information about a transcript's direction. Using Saccharomyces cerevisiae and mouse brain transcriptomes as models, we demonstrate that knowing the transcript's orientation allows more accurate determination of the structure and expression of genes. It also helps to identify new genes and enables studying promoter-associated and antisense transcription. The transcriptional landscapes we obtained are available online. PMID:19620212

Transcriptome analysis by strand-specific sequencing of complementary DNA.

PubMed

Parkhomchuk, Dmitri; Borodina, Tatiana; Amstislavskiy, Vyacheslav; Banaru, Maria; Hallen, Linda; Krobitsch, Sylvia; Lehrach, Hans; Soldatov, Alexey

2009-10-01

High-throughput complementary DNA sequencing (RNA-Seq) is a powerful tool for whole-transcriptome analysis, supplying information about a transcript's expression level and structure. However, it is difficult to determine the polarity of transcripts, and therefore identify which strand is transcribed. Here, we present a simple cDNA sequencing protocol that preserves information about a transcript's direction. Using Saccharomyces cerevisiae and mouse brain transcriptomes as models, we demonstrate that knowing the transcript's orientation allows more accurate determination of the structure and expression of genes. It also helps to identify new genes and enables studying promoter-associated and antisense transcription. The transcriptional landscapes we obtained are available online.

Wave induced density modification in RF sheaths and close to wave launchers

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

Van Eester, D., E-mail: d.van.eester@fz-juelich.de; Crombé, K.; Department of Applied Physics, Ghent University, Ghent

2015-12-10

With the return to full metal walls - a necessary step towards viable fusion machines - and due to the high power densities of current-day ICRH (Ion Cyclotron Resonance Heating) or RF (radio frequency) antennas, there is ample renewed interest in exploring the reasons for wave-induced sputtering and formation of hot spots. Moreover, there is experimental evidence on various machines that RF waves influence the density profile close to the wave launchers so that waves indirectly influence their own coupling efficiency. The present study presents a return to first principles and describes the wave-particle interaction using a 2-time scale modelmore » involving the equation of motion, the continuity equation and the wave equation on each of the time scales. Through the changing density pattern, the fast time scale dynamics is affected by the slow time scale events. In turn, the slow time scale density and flows are modified by the presence of the RF waves through quasilinear terms. Although finite zero order flows are identified, the usual cold plasma dielectric tensor - ignoring such flows - is adopted as a first approximation to describe the wave response to the RF driver. The resulting set of equations is composed of linear and nonlinear equations and is tackled in 1D in the present paper. Whereas the former can be solved using standard numerical techniques, the latter require special handling. At the price of multiple iterations, a simple ’derivative switch-on’ procedure allows to reformulate the nonlinear problem as a sequence of linear problems. Analytical expressions allow a first crude assessment - revealing that the ponderomotive potential plays a role similar to that of the electrostatic potential arising from charge separation - but numerical implementation is required to get a feeling of the full dynamics. A few tentative examples are provided to illustrate the phenomena involved.« less

Establishment of a simple and rapid identification method for Listeria spp. by using high-resolution melting analysis, and its application in food industry.

PubMed

Ohshima, Chihiro; Takahashi, Hajime; Phraephaisarn, Chirapiphat; Vesaratchavest, Mongkol; Keeratipibul, Suwimon; Kuda, Takashi; Kimura, Bon

2014-01-01

Listeria monocytogenes is the causative bacteria of listeriosis, which has a higher mortality rate than that of other causes of food poisoning. Listeria spp., of which L. monocytogenes is a member, have been isolated from food and manufacturing environments. Several methods have been published for identifying Listeria spp.; however, many of the methods cannot identify newly categorized Listeria spp. Additionally, they are often not suitable for the food industry, owing to their complexity, cost, or time consumption. Recently, high-resolution melting analysis (HRMA), which exploits DNA-sequence differences, has received attention as a simple and quick genomic typing method. In the present study, a new method for the simple, rapid, and low-cost identification of Listeria spp. has been presented using the genes rarA and ldh as targets for HRMA. DNA sequences of 9 Listeria species were first compared, and polymorphisms were identified for each species for primer design. Species specificity of each HRM curve pattern was estimated using type strains of all the species. Among the 9 species, 7 were identified by HRMA using rarA gene, including 3 new species. The remaining 2 species were identified by HRMA of ldh gene. The newly developed HRMA method was then used to assess Listeria isolates from the food industry, and the method efficiency was compared to that of identification by 16S rDNA sequence analysis. The 2 methods were in coherence for 92.6% of the samples, demonstrating the high accuracy of HRMA. The time required for identifying Listeria spp. was substantially low, and the process was considerably simplified, providing a useful and precise method for processing multiple samples per day. Our newly developed method for identifying Listeria spp. is highly valuable; its use is not limited to the food industry, and it can be used for the isolates from the natural environment.

Establishment of a Simple and Rapid Identification Method for Listeria spp. by Using High-Resolution Melting Analysis, and Its Application in Food Industry

PubMed Central

Ohshima, Chihiro; Takahashi, Hajime; Phraephaisarn, Chirapiphat; Vesaratchavest, Mongkol; Keeratipibul, Suwimon; Kuda, Takashi; Kimura, Bon

2014-01-01

Listeria monocytogenes is the causative bacteria of listeriosis, which has a higher mortality rate than that of other causes of food poisoning. Listeria spp., of which L. monocytogenes is a member, have been isolated from food and manufacturing environments. Several methods have been published for identifying Listeria spp.; however, many of the methods cannot identify newly categorized Listeria spp. Additionally, they are often not suitable for the food industry, owing to their complexity, cost, or time consumption. Recently, high-resolution melting analysis (HRMA), which exploits DNA-sequence differences, has received attention as a simple and quick genomic typing method. In the present study, a new method for the simple, rapid, and low-cost identification of Listeria spp. has been presented using the genes rarA and ldh as targets for HRMA. DNA sequences of 9 Listeria species were first compared, and polymorphisms were identified for each species for primer design. Species specificity of each HRM curve pattern was estimated using type strains of all the species. Among the 9 species, 7 were identified by HRMA using rarA gene, including 3 new species. The remaining 2 species were identified by HRMA of ldh gene. The newly developed HRMA method was then used to assess Listeria isolates from the food industry, and the method efficiency was compared to that of identification by 16S rDNA sequence analysis. The 2 methods were in coherence for 92.6% of the samples, demonstrating the high accuracy of HRMA. The time required for identifying Listeria spp. was substantially low, and the process was considerably simplified, providing a useful and precise method for processing multiple samples per day. Our newly developed method for identifying Listeria spp. is highly valuable; its use is not limited to the food industry, and it can be used for the isolates from the natural environment. PMID:24918440

Resolution of a Protracted Serogroup B Meningococcal Outbreak with Whole-Genome Sequencing Shows Interspecies Genetic Transfer

PubMed Central

Brehony, Carina; O'Connor, Lois; Meyler, Kenneth; Jolley, Keith A.; Bray, James; Bennett, Desiree; Maiden, Martin C. J.; Cunney, Robert

2016-01-01

A carriage study was undertaken (n = 112) to ascertain the prevalence of Neisseria spp. following the eighth case of invasive meningococcal disease in young children (5 to 46 months) and members of a large extended indigenous ethnic minority Traveller family (n = 123), typically associated with high-occupancy living conditions. Nested multilocus sequence typing (MLST) was employed for case specimen extracts. Isolates were genome sequenced and then were assembled de novo and deposited into the Bacterial Isolate Genome Sequencing Database (BIGSdb). This facilitated an expanded MLST approach utilizing large numbers of loci for isolate characterization and discrimination. A rare sequence type, ST-6697, predominated in disease specimens and isolates that were carried (n = 8/14), persisting for at least 44 months, likely driven by the high population density of houses (n = 67/112) and trailers (n = 45/112). Carriage for Neisseria meningitidis (P < 0.05) and Neisseria lactamica (P < 0.002) (2-sided Fisher's exact test) was more likely in the smaller, more densely populated trailers. Meningococcal carriage was highest in 24- to 39-year-olds (45%, n = 9/20). Evidence of horizontal gene transfer (HGT) was observed in four individuals cocolonized by Neisseria lactamica and Neisseria meningitidis. One HGT event resulted in the acquisition of 26 consecutive N. lactamica alleles. This study demonstrates how housing density can drive meningococcal transmission and carriage, which likely facilitated the persistence of ST-6697 and prolonged the outbreak. Whole-genome MLST effectively distinguished between highly similar outbreak strain isolates, including those isolated from person-to-person transmission, and also highlighted how a few HGT events can distort the true phylogenetic relationship between highly similar clonal isolates. PMID:27629899

A High-Density Genetic Map Identifies a Novel Major QTL for Boron Efficiency in Oilseed Rape (Brassica napus L.)

PubMed Central

Wang, Xiaohua; Zhao, Hua; Shi, Lei; Xu, Fangsen

2014-01-01

Low boron (B) seriously limits the growth of oilseed rape (Brassica napus L.), a high B demand species that is sensitive to low B conditions. Significant genotypic variations in response to B deficiency have been observed among B. napus cultivars. To reveal the genetic basis for B efficiency in B. napus, quantitative trait loci (QTLs) for the plant growth traits, B uptake traits and the B efficiency coefficient (BEC) were analyzed using a doubled haploid (DH) population derived from a cross between a B-efficient parent, Qingyou 10, and a B-inefficient parent, Westar 10. A high-density genetic map was constructed based on single nucleotide polymorphisms (SNPs) assayed using Brassica 60 K Infinium BeadChip Array, simple sequence repeats (SSRs) and amplified fragment length polymorphisms (AFLPs). The linkage map covered a total length of 2139.5 cM, with 19 linkage groups (LGs) and an average distance of 1.6 cM between adjacent markers. Based on hydroponic evaluation of six B efficiency traits measured in three separate repeated trials, a total of 52 QTLs were identified, accounting for 6.14–46.27% of the phenotypic variation. A major QTL for BEC, qBEC-A3a, was co-located on A3 with other QTLs for plant growth and B uptake traits under low B stress. Using a subset of substitution lines, qBEC-A3a was validated and narrowed down to the interval between CNU384 and BnGMS436. The results of this study provide a novel major locus located on A3 for B efficiency in B. napus that will be suitable for fine mapping and marker-assisted selection breeding for B efficiency in B. napus. PMID:25375356

Counter-facing plasma guns for efficient extreme ultra-violet plasma light source

NASA Astrophysics Data System (ADS)

Kuroda, Yusuke; Yamamoto, Akiko; Kuwabara, Hajime; Nakajima, Mitsuo; Kawamura, Tohru; Horioka, Kazuhiko

2013-11-01

A plasma focus system composed of a pair of counter-facing coaxial guns was proposed as a long-pulse and/or repetitive high energy density plasma source. We applied Li as the source of plasma for improvement of the conversion efficiency, the spectral purity, and the repetition capability. For operation of the system with ideal counter-facing plasma focus mode, we changed the system from simple coaxial geometry to a multi-channel configuration. We applied a laser trigger to make synchronous multi-channel discharges with low jitter. The results indicated that the configuration is promising to make a high energy density plasma with high spectral efficiency.

Development and validation of new SSR markers from expressed regions in the garlic genome

USDA-ARS?s Scientific Manuscript database

Limited number of simple sequence repeat (SSR) markers is available for the genome of garlic (Allium sativum L.) although SSR markers have become one of the most preferred marker systems because they are typically co-dominant, reproducible, cross species transferable and highly polymorphic. In this ...

New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis.

PubMed

Smith, Michael G; Gianoulis, Tara A; Pukatzki, Stefan; Mekalanos, John J; Ornston, L Nicholas; Gerstein, Mark; Snyder, Michael

2007-03-01

Acinetobacter baumannii has emerged as an important and problematic human pathogen as it is the causative agent of several types of infections including pneumonia, meningitis, septicemia, and urinary tract infections. We explored the pathogenic content of this harmful pathogen using a combination of DNA sequencing and insertional mutagenesis. The genome of this organism was sequenced using a strategy involving high-density pyrosequencing, a novel, rapid method of high-throughput sequencing. Excluding the rDNA repeats, the assembled genome is 3,976,746 base pairs (bp) and has 3830 ORFs. A significant fraction of ORFs (17.2%) are located in 28 putative alien islands, indicating that the genome has acquired a large amount of foreign DNA. Consistent with its role in pathogenesis, a remarkable number of the islands (16) contain genes implicated in virulence, indicating the organism devotes a considerable portion of its genes to pathogenesis. The largest island contains elements homologous to the Legionella/Coxiella Type IV secretion apparatus. Type IV secretion systems have been demonstrated to be important for virulence in other organisms and thus are likely to help mediate pathogenesis of A. baumannii. Insertional mutagenesis generated avirulent isolates of A. baumannii and verified that six of the islands contain virulence genes, including two novel islands containing genes that lacked homology with others in the databases. The DNA sequencing approach described in this study allows the rapid elucidation of the DNA sequence of any microbe and, when combined with genetic screens, can identify many novel genes important for microbial pathogenesis.

Optimization of sequence alignment for simple sequence repeat regions.

PubMed

Jighly, Abdulqader; Hamwieh, Aladdin; Ogbonnaya, Francis C

2011-07-20

Microsatellites, or simple sequence repeats (SSRs), are tandemly repeated DNA sequences, including tandem copies of specific sequences no longer than six bases, that are distributed in the genome. SSR has been used as a molecular marker because it is easy to detect and is used in a range of applications, including genetic diversity, genome mapping, and marker assisted selection. It is also very mutable because of slipping in the DNA polymerase during DNA replication. This unique mutation increases the insertion/deletion (INDELs) mutation frequency to a high ratio - more than other types of molecular markers such as single nucleotide polymorphism (SNPs).SNPs are more frequent than INDELs. Therefore, all designed algorithms for sequence alignment fit the vast majority of the genomic sequence without considering microsatellite regions, as unique sequences that require special consideration. The old algorithm is limited in its application because there are many overlaps between different repeat units which result in false evolutionary relationships. To overcome the limitation of the aligning algorithm when dealing with SSR loci, a new algorithm was developed using PERL script with a Tk graphical interface. This program is based on aligning sequences after determining the repeated units first, and the last SSR nucleotides positions. This results in a shifting process according to the inserted repeated unit type.When studying the phylogenic relations before and after applying the new algorithm, many differences in the trees were obtained by increasing the SSR length and complexity. However, less distance between different linage had been observed after applying the new algorithm. The new algorithm produces better estimates for aligning SSR loci because it reflects more reliable evolutionary relations between different linages. It reduces overlapping during SSR alignment, which results in a more realistic phylogenic relationship.

Introducing High School Students to NMR Spectroscopy through Percent Composition Determination Using Low-Field Spectrometers

ERIC Educational Resources Information Center

Bonjour, Jessica L.; Pitzer, Joy M.; Frost, John A.

2015-01-01

Mole to gram conversions, density, and percent composition are fundamental concepts in first year chemistry at the high school or undergraduate level; however, students often find it difficult to engage with these concepts. We present a simple laboratory experiment utilizing portable nuclear magnetic resonance spectroscopy (NMR) to determine the…

Cellulose Triacetate Dielectric Films For Capacitors

NASA Technical Reports Server (NTRS)

Yen, Shiao-Ping S.; Jow, T. Richard

1994-01-01

Cellulose triacetate investigated for use as dielectric material in high-energy-density capacitors for pulsed-electrical-power systems. Films of cellulose triacetate metalized on one or both sides for use as substrates for electrodes and/or as dielectrics between electrodes in capacitors. Used without metalization as simple dielectric films. Advantages include high breakdown strength and self-healing capability.

Acute Ischemia Induced by High-Density Culture Increases Cytokine Expression and Diminishes the Function and Viability of Highly Purified Human Islets of Langerhans.

PubMed

Smith, Kate E; Kelly, Amy C; Min, Catherine G; Weber, Craig S; McCarthy, Fiona M; Steyn, Leah V; Badarinarayana, Vasudeo; Stanton, J Brett; Kitzmann, Jennifer P; Strop, Peter; Gruessner, Angelika C; Lynch, Ronald M; Limesand, Sean W; Papas, Klearchos K

2017-11-01

Encapsulation devices have the potential to enable cell-based insulin replacement therapies (such as human islet or stem cell-derived β cell transplantation) without immunosuppression. However, reasonably sized encapsulation devices promote ischemia due to high β cell densities creating prohibitively large diffusional distances for nutrients. It is hypothesized that even acute ischemic exposure will compromise the therapeutic potential of cell-based insulin replacement. In this study, the acute effects of high-density ischemia were investigated in human islets to develop a detailed profile of early ischemia induced changes and targets for intervention. Human islets were exposed in a pairwise model simulating high-density encapsulation to normoxic or ischemic culture for 12 hours, after which viability and function were measured. RNA sequencing was conducted to assess transcriptome-wide changes in gene expression. Islet viability after acute ischemic exposure was reduced compared to normoxic culture conditions (P < 0.01). Insulin secretion was also diminished, with ischemic β cells losing their insulin secretory response to stimulatory glucose levels (P < 0.01). RNA sequencing revealed 657 differentially expressed genes following ischemia, with many that are associated with increased inflammatory and hypoxia-response signaling and decreased nutrient transport and metabolism. In order for cell-based insulin replacement to be applied as a treatment for type 1 diabetes, oxygen and nutrient delivery to β cells will need to be maintained. We demonstrate that even brief ischemic exposure such as would be experienced in encapsulation devices damages islet viability and β cell function and leads to increased inflammatory signaling.

Deterministic models for traffic jams

NASA Astrophysics Data System (ADS)

Nagel, Kai; Herrmann, Hans J.

1993-10-01

We study several deterministic one-dimensional traffic models. For integer positions and velocities we find the typical high and low density phases separated by a simple transition. If positions and velocities are continuous variables the model shows self-organized critically driven by the slowest car.

High-throughput sequencing methods to study neuronal RNA-protein interactions.

PubMed

Ule, Jernej

2009-12-01

UV-cross-linking and RNase protection, combined with high-throughput sequencing, have provided global maps of RNA sites bound by individual proteins or ribosomes. Using a stringent purification protocol, UV-CLIP (UV-cross-linking and immunoprecipitation) was able to identify intronic and exonic sites bound by splicing regulators in mouse brain tissue. Ribosome profiling has been used to quantify ribosome density on budding yeast mRNAs under different environmental conditions. Post-transcriptional regulation in neurons requires high spatial and temporal precision, as is evident from the role of localized translational control in synaptic plasticity. It remains to be seen if the high-throughput methods can be applied quantitatively to study the dynamics of RNP (ribonucleoprotein) remodelling in specific neuronal populations during the neurodegenerative process. It is certain, however, that applications of new biochemical techniques followed by high-throughput sequencing will continue to provide important insights into the mechanisms of neuronal post-transcriptional regulation.

A high-density genetic map reveals variation in recombination rate across the genome of Daphnia magna.

PubMed

Dukić, Marinela; Berner, Daniel; Roesti, Marius; Haag, Christoph R; Ebert, Dieter

2016-10-13

Recombination rate is an essential parameter for many genetic analyses. Recombination rates are highly variable across species, populations, individuals and different genomic regions. Due to the profound influence that recombination can have on intraspecific diversity and interspecific divergence, characterization of recombination rate variation emerges as a key resource for population genomic studies and emphasises the importance of high-density genetic maps as tools for studying genome biology. Here we present such a high-density genetic map for Daphnia magna, and analyse patterns of recombination rate across the genome. A F2 intercross panel was genotyped by Restriction-site Associated DNA sequencing to construct the third-generation linkage map of D. magna. The resulting high-density map included 4037 markers covering 813 scaffolds and contigs that sum up to 77 % of the currently available genome draft sequence (v2.4) and 55 % of the estimated genome size (238 Mb). Total genetic length of the map presented here is 1614.5 cM and the genome-wide recombination rate is estimated to 6.78 cM/Mb. Merging genetic and physical information we consistently found that recombination rate estimates are high towards the peripheral parts of the chromosomes, while chromosome centres, harbouring centromeres in D. magna, show very low recombination rate estimates. Due to its high-density, the third-generation linkage map for D. magna can be coupled with the draft genome assembly, providing an essential tool for genome investigation in this model organism. Thus, our linkage map can be used for the on-going improvements of the genome assembly, but more importantly, it has enabled us to characterize variation in recombination rate across the genome of D. magna for the first time. These new insights can provide a valuable assistance in future studies of the genome evolution, mapping of quantitative traits and population genetic studies.

Evaluation of 2-point, 3-point, and 6-point Dixon magnetic resonance imaging with flexible echo timing for muscle fat quantification.

PubMed

Grimm, Alexandra; Meyer, Heiko; Nickel, Marcel D; Nittka, Mathias; Raithel, Esther; Chaudry, Oliver; Friedberger, Andreas; Uder, Michael; Kemmler, Wolfgang; Quick, Harald H; Engelke, Klaus

2018-06-01

The purpose of this study is to evaluate and compare 2-point (2pt), 3-point (3pt), and 6-point (6pt) Dixon magnetic resonance imaging (MRI) sequences with flexible echo times (TE) to measure proton density fat fraction (PDFF) within muscles. Two subject groups were recruited (G1: 23 young and healthy men, 31 ± 6 years; G2: 50 elderly men, sarcopenic, 77 ± 5 years). A 3-T MRI system was used to perform Dixon imaging on the left thigh. PDFF was measured with six Dixon prototype sequences: 2pt, 3pt, and 6pt sequences once with optimal TEs (in- and opposed-phase echo times), lower resolution, and higher bandwidth (optTE sequences) and once with higher image resolution (highRes sequences) and shortest possible TE, respectively. Intra-fascia PDFF content was determined. To evaluate the comparability among the sequences, Bland-Altman analysis was performed. The highRes 6pt Dixon sequences served as reference as a high correlation of this sequence to magnetic resonance spectroscopy has been shown before. The PDFF difference between the highRes 6pt Dixon sequence and the optTE 6pt, both 3pt, and the optTE 2pt was low (between 2.2% and 4.4%), however, not to the highRes 2pt Dixon sequence (33%). For the optTE sequences, difference decreased with the number of echoes used. In conclusion, for Dixon sequences with more than two echoes, the fat fraction measurement was reliable with arbitrary echo times, while for 2pt Dixon sequences, it was reliable with dedicated in- and opposed-phase echo timing. Copyright © 2018 Elsevier B.V. All rights reserved.

Analysis of expressed sequence tags from Prunus mume flower and fruit and development of simple sequence repeat markers

PubMed Central

2010-01-01

Background Expressed Sequence Tag (EST) has been a cost-effective tool in molecular biology and represents an abundant valuable resource for genome annotation, gene expression, and comparative genomics in plants. Results In this study, we constructed a cDNA library of Prunus mume flower and fruit, sequenced 10,123 clones of the library, and obtained 8,656 expressed sequence tag (EST) sequences with high quality. The ESTs were assembled into 4,473 unigenes composed of 1,492 contigs and 2,981 singletons and that have been deposited in NCBI (accession IDs: GW868575 - GW873047), among which 1,294 unique ESTs were with known or putative functions. Furthermore, we found 1,233 putative simple sequence repeats (SSRs) in the P. mume unigene dataset. We randomly tested 42 pairs of PCR primers flanking potential SSRs, and 14 pairs were identified as true-to-type SSR loci and could amplify polymorphic bands from 20 individual plants of P. mume. We further used the 14 EST-SSR primer pairs to test the transferability on peach and plum. The result showed that nearly 89% of the primer pairs produced target PCR bands in the two species. A high level of marker polymorphism was observed in the plum species (65%) and low in the peach (46%), and the clustering analysis of the three species indicated that these SSR markers were useful in the evaluation of genetic relationships and diversity between and within the Prunus species. Conclusions We have constructed the first cDNA library of P. mume flower and fruit, and our data provide sets of molecular biology resources for P. mume and other Prunus species. These resources will be useful for further study such as genome annotation, new gene discovery, gene functional analysis, molecular breeding, evolution and comparative genomics between Prunus species. PMID:20626882

Sequential Effects of High and Low Instructional Guidance on Children's Acquisition of Experimentation Skills: Is It All in the Timing?

ERIC Educational Resources Information Center

Matlen, Bryan J.; Klahr, David

2013-01-01

We report the effect of different sequences of high vs low levels of instructional guidance on children's immediate learning and long-term transfer of simple experimental design procedures and concepts, often called "CVS" (Control of Variables Strategy). Third-grade children (N = 57) received instruction in CVS via one of four possible orderings…

Differentiation of “Candidatus Liberibacter asiaticus” Isolates by Variable-Number Tandem-Repeat Analysis ▿

PubMed Central

Katoh, Hiroshi; Subandiyah, Siti; Tomimura, Kenta; Okuda, Mitsuru; Su, Hong-Ji; Iwanami, Toru

2011-01-01

Four highly polymorphic simple sequence repeat (SSR) loci were selected and used to differentiate 84 Japanese isolates of “Candidatus Liberibacter asiaticus.” The Nei's measure of genetic diversity values for these four SSRs ranged from 0.60 to 0.86. The four SSR loci were also highly polymorphic in four isolates from Taiwan and 12 isolates from Indonesia. PMID:21239554

Fabrication and characterization of active nanostructures

NASA Astrophysics Data System (ADS)

Opondo, Noah F.

Three different nanostructure active devices have been designed, fabricated and characterized. Junctionless transistors based on highly-doped silicon nanowires fabricated using a bottom-up fabrication approach are first discussed. The fabrication avoids the ion implantation step since silicon nanowires are doped in-situ during growth. Germanium junctionless transistors fabricated with a top down approach starting from a germanium on insulator substrate and using a gate stack of high-k dielectrics and GeO2 are also presented. The levels and origin of low-frequency noise in junctionless transistor devices fabricated from silicon nanowires and also from GeOI devices are reported. Low-frequency noise is an indicator of the quality of the material, hence its characterization can reveal the quality and perhaps reliability of fabricated transistors. A novel method based on low-frequency noise measurement to envisage trap density in the semiconductor bandgap near the semiconductor/oxide interface of nanoscale silicon junctionless transistors (JLTs) is presented. Low-frequency noise characterization of JLTs biased in saturation is conducted at different gate biases. The noise spectrum indicates either a Lorentzian or 1/f. A simple analysis of the low-frequency noise data leads to the density of traps and their energy within the semiconductor bandgap. The level of noise in silicon JLT devices is lower than reported values on transistors fabricated using a top-down approach. This noise level can be significantly improved by improving the quality of dielectric and the channel interface. A micro-vacuum electron device based on silicon field emitters for cold cathode emission is also presented. The presented work utilizes vertical Si nanowires fabricated by means of self-assembly, standard lithography and etching techniques as field emitters in this dissertation. To obtain a high nanowire density, hence a high current density, a simple and inexpensive Langmuir Blodgett technique to deposit silica nanoparticles as a mask to etch Si is adopted. Fabrication and characterization of a metal-gated microtriode with a high current density and low operating voltage are presented.

Simple sequence repeat markers that identify Claviceps species and strains

USDA-ARS?s Scientific Manuscript database

Claviceps purpurea is a pathogen that infects most members of the Pooideae subfamily and causes ergot, a floral disease in which the ovary is replaced with a sclerotium. This study was initiated to develop Simple Sequence Repeat (SSRs) markers for rapid identification of C. purpurea. SSRs were desi...

Morphometric analysis of a fresh simple crater on the Moon.

NASA Astrophysics Data System (ADS)

Vivaldi, V.; Ninfo, A.; Massironi, M.; Martellato, E.; Cremonese, G.

In this research we are proposing an innovative method to determine and quantify the morphology of a simple fresh impact crater. Linné is a well preserved impact crater of 2.2 km in diameter, located at 27.7oN 11.8oE, near the western edge of Mare Serenitatis on the Moon. The crater was photographed by the Lunar Orbiter and the Apollo space missions. Its particular morphology may place Linné as the most striking example of small fresh simple crater. Morphometric analysis, conducted on recent high resolution DTM from LROC (NASA), quantitatively confirmed the pristine morphology of the crater, revealing a clear inner layering which highlight a sequence of lava emplacement events.

Modeling of electron cyclotron resonance discharges

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

Meyyappan, M.; Govindan, T.R.

The current trend in plasma processing is the development of high density plasma sources to achieve high deposition and etch rates, uniformity over large ares, and low wafer damage. Here, is a simple model to predict the spatially-averaged plasma characteristics of electron cyclotron resonance (ECR) reactors is presented. The model consists of global conservation equations for species concentration, electron density and energy. A gas energy balance is used to predict the neutral temperature self-consistently. The model is demonstrated for an ECR argon discharge. The predicted behavior of the discharge as a function of system variables agrees well with experimental observations.

High data density temperature measurement for quasi steady-state flows

NASA Technical Reports Server (NTRS)

Mercer, Carolyn R.; Rashidnia, Nasser; Creath, Katherine

1995-01-01

A new optical instrument, the liquid crystal point diffraction interferometer (LCPDI), is used to measure the temperature distribution across a heated chamber filled with silicone oil. Data taken using the LCPDI are compared to equivalent measurements made with a traversing thermocouple and the two data sets show excellent agreement This instrument maintains the compact, robust design of Linnik's point diffraction interferometer and adds to it phase stepping capability for quantitative interferogram analysis. The result is a compact, simple to align, environmentally insensitive interferometer capable of accurately measuring optical wavefronts with very high data density and with automated data reduction.

High Data Density Temperature Measurement for Quasi Steady-State Flows

NASA Technical Reports Server (NTRS)

Mercer, C. R.; Rashidnia, N.; Creath, K.

1996-01-01

A new optical instrument, the liquid crystal point diffraction interferometer (LCPDI), is used to measure the temperature distribution across a heated chamber filled with silicone oil. Data taken using the LCPDI are compared to equivalent measurements made with a traversing thermo-couple and the two data sets show excellent agreement. This instrument maintains the compact, robust design of Linniks point diffraction interferometer and adds to it phase stepping capability for quantitative interferogram analysis. The result is a compact, simple to align, environmentally insensitive interferometer capable of accurately measuring optical wave-fronts with very high data density and with automated data reduction.

Cr2O3 nanoparticles: Advanced electrode materials for high performance pseudocapacitors

NASA Astrophysics Data System (ADS)

Babu, I. Manohara; William, J. Johnson; Muralidharan, G.

2017-05-01

Cr2O3 nanoparticles have been synthesized via simple and facile microwave irradiation method. The structural, morphological and electrochemical performances of Cr2O3 nanoparticles have been studied. Electrochemical analysis indicates the Cr2O3 electrodes to be good pseudocapacitor material with a specific capacitance (122 F g-1 at a constant current of 1 A g-1), high energy density (6.08 W h kg-1), large power density (218.98 W kg-1). These results allow us to state with confidence that new class of electrode materials with good electrochemical performance has been identified.

Continental extension, magmatism and elevation; formal relations and rules of thumb

USGS Publications Warehouse

Lachenbruch, A.H.; Morgan, P.

1990-01-01

To investigate simplified relations between elevation and the extensional, magmatic and thermal processes that influence lithosphere buoyancy, we assume that the lithosphere floats on an asthenosphere of uniform density and has no flexural strength. A simple graph relating elevation to lithosphere density and thickness provides an overview of expectable conditions around the earth and a simple test for consistancy of continental and oceanic lithosphere models. The mass-balance relations yield simple general rules for estimating elevation changes caused by various tectonic, magmatic and thermal processes without referring to detailed models. The rules are general because they depend principally on buoyancy, which under our assumptions is specified by elevation, a known quantity; they do not generally require a knowledge of lithosphere thickness and density. The elevation of an extended terrain contains important information on its tectonic and magmatic history. In the Great Basin where Cenozoic extension is estimated to be 100%, the present high mean elevation ( ~ 1.75 km) probably requires substantial low-density magmatic contributions to the extending lithosphere. The elevation cannot be reasonably explained solely as the buoyant residue of a very high initial terrane, or of a lithosphere that was initially very thick and subsequently delaminated and heated. Even models with a high initial elevation typically call for 10 km or so of accumulated magmatic material of near-crustal density. To understand the evolution of the Great Basin, it is important to determine whether such intruded material is present; some could replenish the stretching crust by underplating and crustal intrusion and some might reside in the upper mantle. The elevation maintained or approached by an intruded extending lithosphere depends on the ratio B of how fast magma is supplied from the asthenosphere ( b km/Ma) to how fast the lithosphere spreads the magma out by extension (?? Ma-1). For a surface maintained 2 1 2km below sea level (e.g., an ocean ridge) B is about 5 km; for continental extension the ratio may be much greater. The frequent association of volcanism with continental extension, the high elevation (and buoyancy) of some appreciably extended terrains, and the oceanic spreading analog all suggest that magmatism may play an important role in continental extension. Better estimates of total extension and elevation change in extended regions can help to identify that role. ?? 1990.

Re-Ranking Sequencing Variants in the Post-GWAS Era for Accurate Causal Variant Identification

PubMed Central

Faye, Laura L.; Machiela, Mitchell J.; Kraft, Peter; Bull, Shelley B.; Sun, Lei

2013-01-01

Next generation sequencing has dramatically increased our ability to localize disease-causing variants by providing base-pair level information at costs increasingly feasible for the large sample sizes required to detect complex-trait associations. Yet, identification of causal variants within an established region of association remains a challenge. Counter-intuitively, certain factors that increase power to detect an associated region can decrease power to localize the causal variant. First, combining GWAS with imputation or low coverage sequencing to achieve the large sample sizes required for high power can have the unintended effect of producing differential genotyping error among SNPs. This tends to bias the relative evidence for association toward better genotyped SNPs. Second, re-use of GWAS data for fine-mapping exploits previous findings to ensure genome-wide significance in GWAS-associated regions. However, using GWAS findings to inform fine-mapping analysis can bias evidence away from the causal SNP toward the tag SNP and SNPs in high LD with the tag. Together these factors can reduce power to localize the causal SNP by more than half. Other strategies commonly employed to increase power to detect association, namely increasing sample size and using higher density genotyping arrays, can, in certain common scenarios, actually exacerbate these effects and further decrease power to localize causal variants. We develop a re-ranking procedure that accounts for these adverse effects and substantially improves the accuracy of causal SNP identification, often doubling the probability that the causal SNP is top-ranked. Application to the NCI BPC3 aggressive prostate cancer GWAS with imputation meta-analysis identified a new top SNP at 2 of 3 associated loci and several additional possible causal SNPs at these loci that may have otherwise been overlooked. This method is simple to implement using R scripts provided on the author's website. PMID:23950724

Rare earth chalcogenide Ce3Te4 as high efficiency high temperature thermoelectric material

NASA Astrophysics Data System (ADS)

Wang, Xiaochun; Yang, Ronggui; Zhang, Yong; Zhang, Peihong; Xue, Yu

2011-05-01

The electronic band structures of Ce3Te4 have been studied using the first-principles density-functional theory calculations. It is found that the density of states of Ce3Te4 has a very high delta-shaped peak appearing 0.21 eV above the Fermi level, which mainly comes from the f orbital electrons of the rare-earth element Ce. Using the simple theory proposed by Mahan and Sofo, [Proc. Natl. Acad. Sci. U.S.A. 93, 7436 (1996)], we obtain an ideal value of zT=13.5 for Ce3Te4 at T=1200 K, suggesting that the rare-earth chalcogenide Ce3Te4 could be a promising high efficiency high temperature thermoelectric material.

Genomic Characterization of DArT Markers Based on High-Density Linkage Analysis and Physical Mapping to the Eucalyptus Genome

PubMed Central

Petroli, César D.; Sansaloni, Carolina P.; Carling, Jason; Steane, Dorothy A.; Vaillancourt, René E.; Myburg, Alexander A.; da Silva, Orzenil Bonfim; Pappas, Georgios Joannis; Kilian, Andrzej; Grattapaglia, Dario

2012-01-01

Diversity Arrays Technology (DArT) provides a robust, high throughput, cost-effective method to query thousands of sequence polymorphisms in a single assay. Despite the extensive use of this genotyping platform for numerous plant species, little is known regarding the sequence attributes and genome-wide distribution of DArT markers. We investigated the genomic properties of the 7,680 DArT marker probes of a Eucalyptus array, by sequencing them, constructing a high density linkage map and carrying out detailed physical mapping analyses to the Eucalyptus grandis reference genome. A consensus linkage map with 2,274 DArT markers anchored to 210 microsatellites and a framework map, with improved support for ordering, displayed extensive collinearity with the genome sequence. Only 1.4 Mbp of the 75 Mbp of still unplaced scaffold sequence was captured by 45 linkage mapped but physically unaligned markers to the 11 main Eucalyptus pseudochromosomes, providing compelling evidence for the quality and completeness of the current Eucalyptus genome assembly. A highly significant correspondence was found between the locations of DArT markers and predicted gene models, while most of the 89 DArT probes unaligned to the genome correspond to sequences likely absent in E. grandis, consistent with the pan-genomic feature of this multi-Eucalyptus species DArT array. These comprehensive linkage-to-physical mapping analyses provide novel data regarding the genomic attributes of DArT markers in plant genomes in general and for Eucalyptus in particular. DArT markers preferentially target the gene space and display a largely homogeneous distribution across the genome, thereby providing superb coverage for mapping and genome-wide applications in breeding and diversity studies. Data reported on these ubiquitous properties of DArT markers will be particularly valuable to researchers working on less-studied crop species who already count on DArT genotyping arrays but for which no reference genome is yet available to allow such detailed characterization. PMID:22984541

High-density fiber-optic DNA random microsphere array.

PubMed

Ferguson, J A; Steemers, F J; Walt, D R

2000-11-15

A high-density fiber-optic DNA microarray sensor was developed to monitor multiple DNA sequences in parallel. Microarrays were prepared by randomly distributing DNA probe-functionalized 3.1-microm-diameter microspheres in an array of wells etched in a 500-microm-diameter optical imaging fiber. Registration of the microspheres was performed using an optical encoding scheme and a custom-built imaging system. Hybridization was visualized using fluorescent-labeled DNA targets with a detection limit of 10 fM. Hybridization times of seconds are required for nanomolar target concentrations, and analysis is performed in minutes.

Construction of high-density bacterial colony arrays and patterns by the ink-jet method.

PubMed

Xu, Tao; Petridou, Sevastioni; Lee, Eric H; Roth, Elizabeth A; Vyavahare, Narendra R; Hickman, James J; Boland, Thomas

2004-01-05

We have developed a method for fabricating bacterial colony arrays and complex patterns using commercially available ink-jet printers. Bacterial colony arrays with a density of 100 colonies/cm(2) were obtained by directly ejecting Escherichia coli (E. coli) onto agar-coated substrates at a rapid arraying speed of 880 spots per second. Adjusting the concentration of bacterial suspensions allowed single colonies of viable bacteria to be obtained. In addition, complex patterns of viable bacteria as well as bacteria density gradients were constructed using desktop printers controlled by a simple software program. Copyright 2003 Wiley Periodicals, Inc.

Artificially Constructed Quorum-Sensing Circuits Are Used for Subtle Control of Bacterial Population Density

PubMed Central

Wang, Zhaoshou; Wu, Xin; Peng, Jianghai; Hu, Yidan; Fang, Baishan; Huang, Shiyang

2014-01-01

Vibrio fischeri is a typical quorum-sensing bacterium for which lux box, luxR, and luxI have been identified as the key elements involved in quorum sensing. To decode the quorum-sensing mechanism, an artificially constructed cell–cell communication system has been built. In brief, the system expresses several programmed cell-death BioBricks and quorum-sensing genes driven by the promoters lux pR and PlacO-1 in Escherichia coli cells. Their transformation and expression was confirmed by gel electrophoresis and sequencing. To evaluate its performance, viable cell numbers at various time periods were investigated. Our results showed that bacteria expressing killer proteins corresponding to ribosome binding site efficiency of 0.07, 0.3, 0.6, or 1.0 successfully sensed each other in a population-dependent manner and communicated with each other to subtly control their population density. This was also validated using a proposed simple mathematical model. PMID:25119347

A High-Density Genetic Map of Tetraploid Salix matsudana Using Specific Length Amplified Fragment Sequencing (SLAF-seq)

PubMed Central

Li, Min; Li, Yujuan; Wang, Ying; Ma, Xiangjian; Zhang, Yuan; Tan, Feng; Wu, Rongling

2016-01-01

As a salt-tolerant arbor tree species, Salix matsudana plays an important role in afforestation and greening in the coastal areas of China. To select superior Salix varieties that adapt to wide saline areas, it is of paramount importance to understand and identify the mechanisms of salt-tolerance at the level of the whole genome. Here, we describe a high-density genetic linkage map of S. matsudana that represents a good coverage of the Salix genome. An intraspecific F1 hybrid population was established by crossing the salt-sensitive “Yanjiang” variety as the female parent with the salt-tolerant “9901” variety as the male parent. This population, along with its parents, was genotyped by specific length amplified fragment sequencing (SLAF-seq), leading to 277,333 high-quality SLAF markers. By marker analysis, we found that both the parents and offspring were tetraploid. The mean sequencing depth was 53.20-fold for “Yanjiang”, 47.41-fold for “9901”, and 11.02-fold for the offspring. Of the SLAF markers detected, 42,321 are polymorphic with sufficient quality for map construction. The final genetic map was constructed using 6,737 SLAF markers, covering 38 linkage groups (LGs). The genetic map spanned 5,497.45 cM in length, with an average distance of 0.82 cM. As a first high-density genetic map of S. matsudana constructed from salt tolerance-varying varieties, this study will provide a foundation for mapping quantitative trait loci that modulate salt tolerance and resistance in Salix and provide important references for molecular breeding of this important forest tree. PMID:27327501

High-density fiber optic biosensor arrays

NASA Astrophysics Data System (ADS)

Epstein, Jason R.; Walt, David R.

2002-02-01

Novel approaches are required to coordinate the immense amounts of information derived from diverse genomes. This concept has influenced the expanded role of high-throughput DNA detection and analysis in the biological sciences. A high-density fiber optic DNA biosensor was developed consisting of oligonucleotide-functionalized, 3.1 mm diameter microspheres deposited into the etched wells on the distal face of a 500 micrometers imaging fiber bundle. Imaging fiber bundles containing thousands of optical fibers, each associated with a unique oligonucleotide probe sequence, were the foundation for an optically connected, individually addressable DNA detection platform. Different oligonucleotide-functionalized microspheres were combined in a stock solution, and randomly dispersed into the etched wells. Microsphere positions were registered from optical dyes incorporated onto the microspheres. The distribution process provided an inherent redundancy that increases the signal-to-noise ratio as the square root of the number of sensors examined. The representative amount of each probe-type in the array was dependent on their initial stock solution concentration, and as other sequences of interest arise, new microsphere elements can be added to arrays without altering the existing detection capabilities. The oligonucleotide probe sequences hybridize to fluorescently-labeled, complementary DNA target solutions. Fiber optic DNA microarray research has included DNA-protein interaction profiles, microbial strain differentiation, non-labeled target interrogation with molecular beacons, and single cell-based assays. This biosensor array is proficient in DNA detection linked to specific disease states, single nucleotide polymorphism (SNP's) discrimination, and gene expression analysis. This array platform permits multiple detection formats, provides smaller feature sizes, and enables sensor design flexibility. High-density fiber optic microarray biosensors provide a fast, reversible format with the detection limit of a few hundred molecules.

High-Density SNP Map Construction and QTL Identification for the Apetalous Character in Brassica napus L.

PubMed Central

Wang, Xiaodong; Yu, Kunjiang; Li, Hongge; Peng, Qi; Chen, Feng; Zhang, Wei; Chen, Song; Hu, Maolong; Zhang, Jiefu

2015-01-01

The apetalous genotype is a morphological ideotype for increasing seed yield and should be of considerable agricultural use; however, only a few studies have focused on the genetic control of this trait in Brassica napus. In the present study, a recombinant inbred line, the AH population, containing 189 individuals was derived from a cross between an apetalous line ‘APL01’ and a normally petalled variety ‘Holly’. The Brassica 60 K Infinium BeadChip Array harboring 52,157 single nucleotide polymorphism (SNP) markers was used to genotype the AH individuals. A high-density genetic linkage map was constructed based on 2,755 bins involving 11,458 SNPs and 57 simple sequence repeats, and was used to identify loci associated with petalous degree (PDgr). The linkage map covered 2,027.53 cM, with an average marker interval of 0.72 cM. The AH map had good collinearity with the B. napus reference genome, indicating its high quality and accuracy. After phenotypic analyses across five different experiments, a total of 19 identified quantitative trait loci (QTLs) distributed across chromosomes A3, A5, A6, A9 and C8 were obtained, and these QTLs were further integrated into nine consensus QTLs by a meta-analysis. Interestingly, the major QTL qPD.C8-2 was consistently detected in all five experiments, and qPD.A9-2 and qPD.C8-3 were stably expressed in four experiments. Comparative mapping between the AH map and the B. napus reference genome suggested that there were 328 genes underlying the confidence intervals of the three steady QTLs. Based on the Gene Ontology assignments of 52 genes to the regulation of floral development in published studies, 146 genes were considered as potential candidate genes for PDgr. The current study carried out a QTL analysis for PDgr using a high-density SNP map in B. napus, providing novel targets for improving seed yield. These results advanced our understanding of the genetic control of PDgr regulation in B. napus. PMID:26779193

High-Density SNP Map Construction and QTL Identification for the Apetalous Character in Brassica napus L.

PubMed

Wang, Xiaodong; Yu, Kunjiang; Li, Hongge; Peng, Qi; Chen, Feng; Zhang, Wei; Chen, Song; Hu, Maolong; Zhang, Jiefu

2015-01-01

The apetalous genotype is a morphological ideotype for increasing seed yield and should be of considerable agricultural use; however, only a few studies have focused on the genetic control of this trait in Brassica napus. In the present study, a recombinant inbred line, the AH population, containing 189 individuals was derived from a cross between an apetalous line 'APL01' and a normally petalled variety 'Holly'. The Brassica 60 K Infinium BeadChip Array harboring 52,157 single nucleotide polymorphism (SNP) markers was used to genotype the AH individuals. A high-density genetic linkage map was constructed based on 2,755 bins involving 11,458 SNPs and 57 simple sequence repeats, and was used to identify loci associated with petalous degree (PDgr). The linkage map covered 2,027.53 cM, with an average marker interval of 0.72 cM. The AH map had good collinearity with the B. napus reference genome, indicating its high quality and accuracy. After phenotypic analyses across five different experiments, a total of 19 identified quantitative trait loci (QTLs) distributed across chromosomes A3, A5, A6, A9 and C8 were obtained, and these QTLs were further integrated into nine consensus QTLs by a meta-analysis. Interestingly, the major QTL qPD.C8-2 was consistently detected in all five experiments, and qPD.A9-2 and qPD.C8-3 were stably expressed in four experiments. Comparative mapping between the AH map and the B. napus reference genome suggested that there were 328 genes underlying the confidence intervals of the three steady QTLs. Based on the Gene Ontology assignments of 52 genes to the regulation of floral development in published studies, 146 genes were considered as potential candidate genes for PDgr. The current study carried out a QTL analysis for PDgr using a high-density SNP map in B. napus, providing novel targets for improving seed yield. These results advanced our understanding of the genetic control of PDgr regulation in B. napus.

Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation.

PubMed

Ralph, Duncan K; Matsen, Frederick A

2016-01-01

VDJ rearrangement and somatic hypermutation work together to produce antibody-coding B cell receptor (BCR) sequences for a remarkable diversity of antigens. It is now possible to sequence these BCRs in high throughput; analysis of these sequences is bringing new insight into how antibodies develop, in particular for broadly-neutralizing antibodies against HIV and influenza. A fundamental step in such sequence analysis is to annotate each base as coming from a specific one of the V, D, or J genes, or from an N-addition (a.k.a. non-templated insertion). Previous work has used simple parametric distributions to model transitions from state to state in a hidden Markov model (HMM) of VDJ recombination, and assumed that mutations occur via the same process across sites. However, codon frame and other effects have been observed to violate these parametric assumptions for such coding sequences, suggesting that a non-parametric approach to modeling the recombination process could be useful. In our paper, we find that indeed large modern data sets suggest a model using parameter-rich per-allele categorical distributions for HMM transition probabilities and per-allele-per-position mutation probabilities, and that using such a model for inference leads to significantly improved results. We present an accurate and efficient BCR sequence annotation software package using a novel HMM "factorization" strategy. This package, called partis (https://github.com/psathyrella/partis/), is built on a new general-purpose HMM compiler that can perform efficient inference given a simple text description of an HMM.

Extraction of High Molecular Weight DNA from Fungal Rust Spores for Long Read Sequencing.

PubMed

Schwessinger, Benjamin; Rathjen, John P

2017-01-01

Wheat rust fungi are complex organisms with a complete life cycle that involves two different host plants and five different spore types. During the asexual infection cycle on wheat, rusts produce massive amounts of dikaryotic urediniospores. These spores are dikaryotic (two nuclei) with each nucleus containing one haploid genome. This dikaryotic state is likely to contribute to their evolutionary success, making them some of the major wheat pathogens globally. Despite this, most published wheat rust genomes are highly fragmented and contain very little haplotype-specific sequence information. Current long-read sequencing technologies hold great promise to provide more contiguous and haplotype-phased genome assemblies. Long reads are able to span repetitive regions and phase structural differences between the haplomes. This increased genome resolution enables the identification of complex loci and the study of genome evolution beyond simple nucleotide polymorphisms. Long-read technologies require pure high molecular weight DNA as an input for sequencing. Here, we describe a DNA extraction protocol for rust spores that yields pure double-stranded DNA molecules with molecular weight of >50 kilo-base pairs (kbp). The isolated DNA is of sufficient purity for PacBio long-read sequencing, but may require additional purification for other sequencing technologies such as Nanopore and 10× Genomics.

A founder large deletion mutation in Xeroderma pigmentosum-Variant form in Tunisia: implication for molecular diagnosis and therapy.

PubMed

Ben Rekaya, Mariem; Laroussi, Nadia; Messaoud, Olfa; Jones, Mariem; Jerbi, Manel; Naouali, Chokri; Bouyacoub, Yosra; Chargui, Mariem; Kefi, Rym; Fazaa, Becima; Boubaker, Mohamed Samir; Boussen, Hamouda; Mokni, Mourad; Abdelhak, Sonia; Zghal, Mohamed; Khaled, Aida; Yacoub-Youssef, Houda

2014-01-01

Xeroderma pigmentosum Variant (XP-V) form is characterized by a late onset of skin symptoms. Our aim is the clinical and genetic investigations of XP-V Tunisian patients in order to develop a simple tool for early diagnosis. We investigated 16 suspected XP patients belonging to ten consanguineous families. Analysis of the POLH gene was performed by linkage analysis, long range PCR, and sequencing. Genetic analysis showed linkage to the POLH gene with a founder haplotype in all affected patients. Long range PCR of exon 9 to exon 11 showed a 3926 bp deletion compared to control individuals. Sequence analysis demonstrates that this deletion has occurred between two Alu-Sq2 repetitive sequences in the same orientation, respectively, in introns 9 and 10. We suggest that this mutation POLH NG_009252.1: g.36847_40771del3925 is caused by an equal crossover event that occurred between two homologous chromosomes at meiosis. These results allowed us to develop a simple test based on a simple PCR in order to screen suspected XP-V patients. In Tunisia, the prevalence of XP-V group seems to be underestimated and clinical diagnosis is usually later. Cascade screening of this founder mutation by PCR in regions with high frequency of XP provides a rapid and cost-effective tool for early diagnosis of XP-V in Tunisia and North Africa.

A Founder Large Deletion Mutation in Xeroderma Pigmentosum-Variant Form in Tunisia: Implication for Molecular Diagnosis and Therapy

PubMed Central

Ben Rekaya, Mariem; Laroussi, Nadia; Messaoud, Olfa; Jones, Mariem; Jerbi, Manel; Bouyacoub, Yosra; Chargui, Mariem; Kefi, Rym; Fazaa, Becima; Boubaker, Mohamed Samir; Boussen, Hamouda; Mokni, Mourad; Abdelhak, Sonia; Zghal, Mohamed; Khaled, Aida; Yacoub-Youssef, Houda

2014-01-01

Xeroderma pigmentosum Variant (XP-V) form is characterized by a late onset of skin symptoms. Our aim is the clinical and genetic investigations of XP-V Tunisian patients in order to develop a simple tool for early diagnosis. We investigated 16 suspected XP patients belonging to ten consanguineous families. Analysis of the POLH gene was performed by linkage analysis, long range PCR, and sequencing. Genetic analysis showed linkage to the POLH gene with a founder haplotype in all affected patients. Long range PCR of exon 9 to exon 11 showed a 3926 bp deletion compared to control individuals. Sequence analysis demonstrates that this deletion has occurred between two Alu-Sq2 repetitive sequences in the same orientation, respectively, in introns 9 and 10. We suggest that this mutation POLH NG_009252.1: g.36847_40771del3925 is caused by an equal crossover event that occurred between two homologous chromosomes at meiosis. These results allowed us to develop a simple test based on a simple PCR in order to screen suspected XP-V patients. In Tunisia, the prevalence of XP-V group seems to be underestimated and clinical diagnosis is usually later. Cascade screening of this founder mutation by PCR in regions with high frequency of XP provides a rapid and cost-effective tool for early diagnosis of XP-V in Tunisia and North Africa. PMID:24877075

The Three-part Structure of a Filament-unrelated Solar Coronal Mass Ejection

NASA Astrophysics Data System (ADS)

Song, H. Q.; Cheng, X.; Chen, Y.; Zhang, J.; Wang, B.; Li, L. P.; Li, B.; Hu, Q.; Li, G.

2017-10-01

Coronal mass ejections (CMEs) often exhibit the typical three-part structure in the corona when observed with white-light coronagraphs, I.e., the bright leading front, dark cavity, and bright core, corresponding to a high-low-high density sequence. As CMEs result from eruptions of magnetic flux ropes (MFRs), which can possess either lower (e.g., coronal-cavity MFRs) or higher (e.g., hot-channel MFRs) density compared to their surroundings in the corona, the traditional opinion regards the three-part structure as the manifestations of coronal plasma pileup (high density), coronal-cavity MFR (low density), and filament (high density) contained in the trailing part of MFR, respectively. In this paper, we demonstrate that filament-unrelated CMEs can also exhibit the classical three-part structure. The observations were made from different perspectives through an event that occurred on 2011 October 4. The CME cavity corresponds to the low-density zone between the leading front and the high-density core, and it is obvious in the low corona and gradually becomes fuzzy when propagating outward. The bright core corresponds to a high-density structure that is suggested to be an erupting MFR. The MFR is recorded from both edge-on and face-on perspectives, exhibiting different morphologies that are due to projection effects. We stress that the zone (MFR) with lower (higher) density in comparison to the surroundings can appear as the dark cavity (bright core) when observed through white-light coronagraphs, which is not necessarily the coronal-cavity MFR (erupted filament).

Measuring the density of a molecular cluster injector via visible emission from an electron beam.

PubMed

Lundberg, D P; Kaita, R; Majeski, R; Stotler, D P

2010-10-01

A method to measure the density distribution of a dense hydrogen gas jet is presented. A Mach 5.5 nozzle is cooled to 80 K to form a flow capable of molecular cluster formation. A 250 V, 10 mA electron beam collides with the jet and produces H(α) emission that is viewed by a fast camera. The high density of the jet, several 10(16) cm(-3), results in substantial electron depletion, which attenuates the H(α) emission. The attenuated emission measurement, combined with a simplified electron-molecule collision model, allows us to determine the molecular density profile via a simple iterative calculation.

Evaluation of genetic diversity amongst Descurainia sophia L. genotypes by inter-simple sequence repeat (ISSR) marker.

PubMed

Saki, Sahar; Bagheri, Hedayat; Deljou, Ali; Zeinalabedini, Mehrshad

2016-01-01

Descurainia sophia is a valuable medicinal plant in family of Brassicaceae. To determine the range of diversity amongst D. sophia in Iran, 32 naturally distributed plants belonging to six natural populations of the Iranian plateau were investigated by inter-simple sequence repeat (ISSR) markers. The average percentage of polymorphism produced by 12 ISSR primers was 86 %. The PIC values for primers ranged from 0.22 to 0.40 and Rp values ranged between 6.5 and 19.9. The relative genetic diversity of the populations was not high (Gst =0.32). However, the value of gene flow revealed by the ISSR marker was high (Nm = 1.03). UPGMA clustering method based on Jaccard similarity coefficient grouped the genotypes into two major clusters. Graph results from Neighbor-Net Network generated after a 1000 bootstrap test using Jaccard coefficient, and STRUCTURE analysis confirmed the UPGMA clustering. The first three PCAs represented 57.31 % of the total variation. The high levels of genetic diversity were observed within populations, which is useful in breeding and conservation programs. ISSR is found to be an eligible marker to study genetic diversity of D. sophia.

Mass density images from the diffraction enhanced imaging technique.

PubMed

Hasnah, M O; Parham, C; Pisano, E D; Zhong, Z; Oltulu, O; Chapman, D

2005-02-01

Conventional x-ray radiography measures the projected x-ray attenuation of an object. It requires attenuation differences to obtain contrast of embedded features. In general, the best absorption contrast is obtained at x-ray energies where the absorption is high, meaning a high absorbed dose. Diffraction-enhanced imaging (DEI) derives contrast from absorption, refraction, and extinction. The refraction angle image of DEI visualizes the spatial gradient of the projected electron density of the object. The projected electron density often correlates well with the projected mass density and projected absorption in soft-tissue imaging, yet the mass density is not an "energy"-dependent property of the object, as is the case of absorption. This simple difference can lead to imaging with less x-ray exposure or dose. In addition, the mass density image can be directly compared (i.e., a signal-to-noise comparison) with conventional radiography. We present the method of obtaining the mass density image, the results of experiments in which comparisons are made with radiography, and an application of the method to breast cancer imaging.

Generation and analysis of expressed sequence tags from a cDNA library of the fruiting body of Ganoderma lucidum

PubMed Central

2010-01-01

Background Little genomic or trancriptomic information on Ganoderma lucidum (Lingzhi) is known. This study aims to discover the transcripts involved in secondary metabolite biosynthesis and developmental regulation of G. lucidum using an expressed sequence tag (EST) library. Methods A cDNA library was constructed from the G. lucidum fruiting body. Its high-quality ESTs were assembled into unique sequences with contigs and singletons. The unique sequences were annotated according to sequence similarities to genes or proteins available in public databases. The detection of simple sequence repeats (SSRs) was preformed by online analysis. Results A total of 1,023 clones were randomly selected from the G. lucidum library and sequenced, yielding 879 high-quality ESTs. These ESTs showed similarities to a diverse range of genes. The sequences encoding squalene epoxidase (SE) and farnesyl-diphosphate synthase (FPS) were identified in this EST collection. Several candidate genes, such as hydrophobin, MOB2, profilin and PHO84 were detected for the first time in G. lucidum. Thirteen (13) potential SSR-motif microsatellite loci were also identified. Conclusion The present study demonstrates a successful application of EST analysis in the discovery of transcripts involved in the secondary metabolite biosynthesis and the developmental regulation of G. lucidum. PMID:20230644

A weighted U-statistic for genetic association analyses of sequencing data.

PubMed

Wei, Changshuai; Li, Ming; He, Zihuai; Vsevolozhskaya, Olga; Schaid, Daniel J; Lu, Qing

2014-12-01

With advancements in next-generation sequencing technology, a massive amount of sequencing data is generated, which offers a great opportunity to comprehensively investigate the role of rare variants in the genetic etiology of complex diseases. Nevertheless, the high-dimensional sequencing data poses a great challenge for statistical analysis. The association analyses based on traditional statistical methods suffer substantial power loss because of the low frequency of genetic variants and the extremely high dimensionality of the data. We developed a Weighted U Sequencing test, referred to as WU-SEQ, for the high-dimensional association analysis of sequencing data. Based on a nonparametric U-statistic, WU-SEQ makes no assumption of the underlying disease model and phenotype distribution, and can be applied to a variety of phenotypes. Through simulation studies and an empirical study, we showed that WU-SEQ outperformed a commonly used sequence kernel association test (SKAT) method when the underlying assumptions were violated (e.g., the phenotype followed a heavy-tailed distribution). Even when the assumptions were satisfied, WU-SEQ still attained comparable performance to SKAT. Finally, we applied WU-SEQ to sequencing data from the Dallas Heart Study (DHS), and detected an association between ANGPTL 4 and very low density lipoprotein cholesterol. © 2014 WILEY PERIODICALS, INC.

MGIS: Managing banana (Musa spp.) genetic resources information and high-throughput genotyping data

USDA-ARS?s Scientific Manuscript database

Unraveling genetic diversity held in genebanks on a large scale is underway, due to the advances in Next-generation sequence-based technologies that produce high-density genetic markers for a large number of samples at low cost. Genebank users should be in a position to identify and select germplasm...

FPGA based control system for space instrumentation

NASA Astrophysics Data System (ADS)

Di Giorgio, Anna M.; Cerulli Irelli, Pasquale; Nuzzolo, Francesco; Orfei, Renato; Spinoglio, Luigi; Liu, Giovanni S.; Saraceno, Paolo

2008-07-01

The prototype for a general purpose FPGA based control system for space instrumentation is presented, with particular attention to the instrument control application software. The system HW is based on the LEON3FT processor, which gives the flexibility to configure the chip with only the necessary HW functionalities, from simple logic up to small dedicated processors. The instrument control SW is developed in ANSI C and for time critical (<10μs) commanding sequences implements an internal instructions sequencer, triggered via an interrupt service routine based on a HW high priority interrupt.

A simple microfluidic Coriolis effect flowmeter for operation at high pressure and high temperature.

PubMed

Harrison, Christopher; Jundt, Jacques

2016-08-01

We describe a microfluidic Coriolis effect flowmeter that is simple to assemble, operates at elevated temperature and pressure, and can be operated with a lock-in amplifier. The sensor has a flow rate sensitivity greater than 2° of phase shift per 1 g/min of mass flow and is benchmarked with flow rates ranging from 0.05 to 2.0 g/min. The internal volume is 15 μl and uses off-the-shelf optical components to measure the tube motion. We demonstrate that fluid density can be calculated from the frequency of the resonating element with proper calibration.

Flow cytometry for enrichment and titration in massively parallel DNA sequencing

PubMed Central

Sandberg, Julia; Ståhl, Patrik L.; Ahmadian, Afshin; Bjursell, Magnus K.; Lundeberg, Joakim

2009-01-01

Massively parallel DNA sequencing is revolutionizing genomics research throughout the life sciences. However, the reagent costs and labor requirements in current sequencing protocols are still substantial, although improvements are continuously being made. Here, we demonstrate an effective alternative to existing sample titration protocols for the Roche/454 system using Fluorescence Activated Cell Sorting (FACS) technology to determine the optimal DNA-to-bead ratio prior to large-scale sequencing. Our method, which eliminates the need for the costly pilot sequencing of samples during titration is capable of rapidly providing accurate DNA-to-bead ratios that are not biased by the quantification and sedimentation steps included in current protocols. Moreover, we demonstrate that FACS sorting can be readily used to highly enrich fractions of beads carrying template DNA, with near total elimination of empty beads and no downstream sacrifice of DNA sequencing quality. Automated enrichment by FACS is a simple approach to obtain pure samples for bead-based sequencing systems, and offers an efficient, low-cost alternative to current enrichment protocols. PMID:19304748

Diatom centromeres suggest a mechanism for nuclear DNA acquisition

DOE PAGES

Diner, Rachel E.; Noddings, Chari M.; Lian, Nathan C.; ...

2017-07-18

Centromeres are essential for cell division and growth in all eukaryotes, and knowledge of their sequence and structure guides the development of artificial chromosomes for functional cellular biology studies. Centromeric proteins are conserved among eukaryotes; however, centromeric DNA sequences are highly variable. We combined forward and reverse genetic approaches with chromatin immunoprecipitation to identify centromeres of the model diatom Phaeodactylum tricornutum. We observed 25 unique centromere sequences typically occurring once per chromosome, a finding that helps to resolve nuclear genome organization and indicates monocentric regional centromeres. Diatom centromere sequences contain low-GC content regions but lack repeats or other conserved sequencemore » features. Native and foreign sequences with similar GC content to P. tricornutum centromeres can maintain episomes and recruit the diatom centromeric histone protein CENH3, suggesting nonnative sequences can also function as diatom centromeres. Thus, simple sequence requirements may enable DNA from foreign sources to persist in the nucleus as extrachromosomal episomes, revealing a potential mechanism for organellar and foreign DNA acquisition.« less

Diatom centromeres suggest a mechanism for nuclear DNA acquisition

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

Diner, Rachel E.; Noddings, Chari M.; Lian, Nathan C.

Centromeres are essential for cell division and growth in all eukaryotes, and knowledge of their sequence and structure guides the development of artificial chromosomes for functional cellular biology studies. Centromeric proteins are conserved among eukaryotes; however, centromeric DNA sequences are highly variable. We combined forward and reverse genetic approaches with chromatin immunoprecipitation to identify centromeres of the model diatom Phaeodactylum tricornutum. We observed 25 unique centromere sequences typically occurring once per chromosome, a finding that helps to resolve nuclear genome organization and indicates monocentric regional centromeres. Diatom centromere sequences contain low-GC content regions but lack repeats or other conserved sequencemore » features. Native and foreign sequences with similar GC content to P. tricornutum centromeres can maintain episomes and recruit the diatom centromeric histone protein CENH3, suggesting nonnative sequences can also function as diatom centromeres. Thus, simple sequence requirements may enable DNA from foreign sources to persist in the nucleus as extrachromosomal episomes, revealing a potential mechanism for organellar and foreign DNA acquisition.« less

Sequence Complexity of Amyloidogenic Regions in Intrinsically Disordered Human Proteins

PubMed Central

Das, Swagata; Pal, Uttam; Das, Supriya; Bagga, Khyati; Roy, Anupam; Mrigwani, Arpita; Maiti, Nakul C.

2014-01-01

An amyloidogenic region (AR) in a protein sequence plays a significant role in protein aggregation and amyloid formation. We have investigated the sequence complexity of AR that is present in intrinsically disordered human proteins. More than 80% human proteins in the disordered protein databases (DisProt+IDEAL) contained one or more ARs. With decrease of protein disorder, AR content in the protein sequence was decreased. A probability density distribution analysis and discrete analysis of AR sequences showed that ∼8% residue in a protein sequence was in AR and the region was in average 8 residues long. The residues in the AR were high in sequence complexity and it seldom overlapped with low complexity regions (LCR), which was largely abundant in disorder proteins. The sequences in the AR showed mixed conformational adaptability towards α-helix, β-sheet/strand and coil conformations. PMID:24594841

Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.

PubMed

Lin, X; Kaul, S; Rounsley, S; Shea, T P; Benito, M I; Town, C D; Fujii, C Y; Mason, T; Bowman, C L; Barnstead, M; Feldblyum, T V; Buell, C R; Ketchum, K A; Lee, J; Ronning, C M; Koo, H L; Moffat, K S; Cronin, L A; Shen, M; Pai, G; Van Aken, S; Umayam, L; Tallon, L J; Gill, J E; Adams, M D; Carrera, A J; Creasy, T H; Goodman, H M; Somerville, C R; Copenhaver, G P; Preuss, D; Nierman, W C; White, O; Eisen, J A; Salzberg, S L; Fraser, C M; Venter, J C

1999-12-16

Arabidopsis thaliana (Arabidopsis) is unique among plant model organisms in having a small genome (130-140 Mb), excellent physical and genetic maps, and little repetitive DNA. Here we report the sequence of chromosome 2 from the Columbia ecotype in two gap-free assemblies (contigs) of 3.6 and 16 megabases (Mb). The latter represents the longest published stretch of uninterrupted DNA sequence assembled from any organism to date. Chromosome 2 represents 15% of the genome and encodes 4,037 genes, 49% of which have no predicted function. Roughly 250 tandem gene duplications were found in addition to large-scale duplications of about 0.5 and 4.5 Mb between chromosomes 2 and 1 and between chromosomes 2 and 4, respectively. Sequencing of nearly 2 Mb within the genetically defined centromere revealed a low density of recognizable genes, and a high density and diverse range of vestigial and presumably inactive mobile elements. More unexpected is what appears to be a recent insertion of a continuous stretch of 75% of the mitochondrial genome into chromosome 2.

Technical Considerations for Reduced Representation Bisulfite Sequencing with Multiplexed Libraries

PubMed Central

Chatterjee, Aniruddha; Rodger, Euan J.; Stockwell, Peter A.; Weeks, Robert J.; Morison, Ian M.

2012-01-01

Reduced representation bisulfite sequencing (RRBS), which couples bisulfite conversion and next generation sequencing, is an innovative method that specifically enriches genomic regions with a high density of potential methylation sites and enables investigation of DNA methylation at single-nucleotide resolution. Recent advances in the Illumina DNA sample preparation protocol and sequencing technology have vastly improved sequencing throughput capacity. Although the new Illumina technology is now widely used, the unique challenges associated with multiplexed RRBS libraries on this platform have not been previously described. We have made modifications to the RRBS library preparation protocol to sequence multiplexed libraries on a single flow cell lane of the Illumina HiSeq 2000. Furthermore, our analysis incorporates a bioinformatics pipeline specifically designed to process bisulfite-converted sequencing reads and evaluate the output and quality of the sequencing data generated from the multiplexed libraries. We obtained an average of 42 million paired-end reads per sample for each flow-cell lane, with a high unique mapping efficiency to the reference human genome. Here we provide a roadmap of modifications, strategies, and trouble shooting approaches we implemented to optimize sequencing of multiplexed libraries on an a RRBS background. PMID:23193365

HOW GALACTIC ENVIRONMENT REGULATES STAR FORMATION

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

Meidt, Sharon E.

2016-02-10

In a new simple model I reconcile two contradictory views on the factors that determine the rate at which molecular clouds form stars—internal structure versus external, environmental influences—providing a unified picture for the regulation of star formation in galaxies. In the presence of external pressure, the pressure gradient set up within a self-gravitating turbulent (isothermal) cloud leads to a non-uniform density distribution. Thus the local environment of a cloud influences its internal structure. In the simple equilibrium model, the fraction of gas at high density in the cloud interior is determined simply by the cloud surface density, which is itselfmore » inherited from the pressure in the immediate surroundings. This idea is tested using measurements of the properties of local clouds, which are found to show remarkable agreement with the simple equilibrium model. The model also naturally predicts the star formation relation observed on cloud scales and at the same time provides a mapping between this relation and the closer-to-linear molecular star formation relation measured on larger scales in galaxies. The key is that pressure regulates not only the molecular content of the ISM but also the cloud surface density. I provide a straightforward prescription for the pressure regulation of star formation that can be directly implemented in numerical models. Predictions for the dense gas fraction and star formation efficiency measured on large-scales within galaxies are also presented, establishing the basis for a new picture of star formation regulated by galactic environment.« less

BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction.

PubMed

Townsley, Brad T; Covington, Michael F; Ichihashi, Yasunori; Zumstein, Kristina; Sinha, Neelima R

2015-01-01

Next Generation Sequencing (NGS) is driving rapid advancement in biological understanding and RNA-sequencing (RNA-seq) has become an indispensable tool for biology and medicine. There is a growing need for access to these technologies although preparation of NGS libraries remains a bottleneck to wider adoption. Here we report a novel method for the production of strand specific RNA-seq libraries utilizing the terminal breathing of double-stranded cDNA to capture and incorporate a sequencing adapter. Breath Adapter Directional sequencing (BrAD-seq) reduces sample handling and requires far fewer enzymatic steps than most available methods to produce high quality strand-specific RNA-seq libraries. The method we present is optimized for 3-prime Digital Gene Expression (DGE) libraries and can easily extend to full transcript coverage shotgun (SHO) type strand-specific libraries and is modularized to accommodate a diversity of RNA and DNA input materials. BrAD-seq offers a highly streamlined and inexpensive option for RNA-seq libraries.

Co3O4 nanowire@NiO nanosheet arrays for high performance asymmetric supercapacitors.

PubMed

Xing, Lei; Dong, Yidi; Hu, Fang; Wu, Xiang; Umar, Ahmad

2018-04-24

Herein, we report a simple and facile sequential hydrothermal process for the synthesis of Co3O4 nanowire@NiO nanosheet arrays (CNAs). The as-synthesized CNAs were characterized in detail using various analytical techniques, which confirmed the high crystallinity, purity, and high-density growth of these nanomaterials. From an application point of view, the as-synthesized CNAs were directly used as supercapacitor electrodes, revealing a specific capacitance of up to 2018 mF cm-2 at a current density of 2 mA cm-2. Furthermore, a flexible asymmetric supercapacitor was fabricated using the as-synthesized CNAs as the anode and activated carbon as the cathode, which revealed a specific capacitance of 134.6 mF cm-2 at a current density of 2 mA cm-2. In addition, the supercapacitor showed excellent capacity retention of 73.5% after 10 000 cycles at a current density of 10 mA cm-2.

High performance, flexible, poly(3,4-ethylenedioxythiophene) supercapacitors achieved by doping redox mediators in organogel electrolytes

NASA Astrophysics Data System (ADS)

Zhang, Huanhuan; Li, Jinyu; Gu, Cheng; Yao, Mingming; Yang, Bing; Lu, Ping; Ma, Yuguang

2016-11-01

The relatively low energy density is now a central issue hindering the development of supercapacitors as energy storage devices. Various approaches are thus developed to enhance the energy density, mainly centering on the fabrication of electrode materials or optimization of cell configurations. Compared with these approaches, modifications in electrolytes are much simple and versatile. Herein, we integrate the wide voltages endowed by organic electrolytes and the additional capacitances brought by redox mediators, to fabricate high energy density supercapacitors. On the basis of this idea, supercapacitors with poly(3,4-ethylenedioxythiophene) (PEDOT) as electrode material exhibit extended operating voltage of 1.5 V, extraordinary capacitance of 363 F g-1 and high energy density of 27.4 Wh kg-1. The redox mediators reported here, ferrocene and 4-oxo-2,2,6,6-tetramethylpiperidinooxy, are the first time being applied in supercapacitors, especially in the gel state. While providing additional faradaic capacitances, they also exhibit synergistic interaction with PEDOT and improve the cycling stability of supercapacitors.

High resolution NMR imaging using a high field yokeless permanent magnet.

PubMed

Kose, Katsumi; Haishi, Tomoyuki

2011-01-01

We measured the homogeneity and stability of the magnetic field of a high field (about 1.04 tesla) yokeless permanent magnet with 40-mm gap for high resolution nuclear magnetic resonance (NMR) imaging. Homogeneity was evaluated using a 3-dimensional (3D) lattice phantom and 3D spin-echo imaging sequences. In the central sphere (20-mm diameter), peak-to-peak magnetic field inhomogeneity was about 60 ppm, and the root-mean-square was 8 ppm. We measured room temperature, magnet temperature, and NMR frequency of the magnet simultaneously every minute for about 68 hours with and without the thermal insulator of the magnet. A simple mathematical model described the magnet's thermal property. Based on magnet performance, we performed high resolution (up to [20 µm](2)) imaging with internal NMR lock sequences of several biological samples. Our results demonstrated the usefulness of the high field small yokeless permanent magnet for high resolution NMR imaging.

Inter-Simple Sequence Repeat Data Reveals High Genetic Diversity in Wild Populations of the Narrowly Distributed Endemic Lilium regale in the Minjiang River Valley of China

PubMed Central

Wu, Zhu-hua; Shi, Jisen; Xi, Meng-li; Jiang, Fu-xing; Deng, Ming-wen; Dayanandan, Selvadurai

2015-01-01

Lilium regale E.H. Wilson is endemic to a narrow geographic area in the Minjiang River valley in southwestern China, and is considered an important germplasm for breeding commercially valuable lily varieties, due to its vigorous growth, resistance to diseases and tolerance for low moisture. We analyzed the genetic diversity of eight populations of L. regale sampled across the entire natural distribution range of the species using Inter-Simple Sequence Repeat markers. The genetic diversity (expected heterozygosity= 0.3356) was higher than those reported for other narrowly distributed endemic plants. The levels of inbreeding (F st = 0.1897) were low, and most of the genetic variability was found to be within (80.91%) than amongpopulations (19.09%). An indirect estimate of historical levels of gene flow (N m =1.0678) indicated high levels of gene flow among populations. The eight analyzed populations clustered into three genetically distinct groups. Based on these results, we recommend conservation of large populations representing these three genetically distinct groups. PMID:25799495

E-microsatellite markers for Centella asiatica (Gotu Kola) genome: validation and cross-transferability in Apiaceae family for plant omics research and development.

PubMed

Sahu, Jagajjit; Das Talukdar, Anupam; Devi, Kamalakshi; Choudhury, Manabendra Dutta; Barooah, Madhumita; Modi, Mahendra Kumar; Sen, Priyabrata

2015-01-01

Abstract Centella asiatica (Gotu Kola) is a plant that grows in tropical swampy regions of the world and has important medicinal and culinary use. It is often considered as part of Ayurvedic medicine, traditional African medicine, and traditional Chinese medicine. The unavailability of genomics resources is significantly impeding its genetic improvement. To date, no attempt has been made to develop Expressed Sequence Tags (ESTs) derived Simple Sequence Repeat (SSR) markers (eSSRs) from the Centella genome. Hence, the present study aimed to develop eSSRs and their further experimental validation and cross-transferability of these markers in different genera of the Apiaceae family to which Centella belongs. An in-house pipeline was developed for the entire analyses by combining bioinformatics tools and perl scripts. A total of 4443 C. asiatica EST sequences from dbEST were processed, which generated 2617 nonredundant high quality EST sequences consisting 441 contigs and 2176 singletons. Out of 1776.5 kb of examined sequences, 417 (15.9%) ESTs containing 686 SSRs were detected with a density of one SSR per 2.59 kb. The gene ontology study revealed 282 functional domains involved in various processes, components, and functions, out of which 64 ESTs were found to have both SSRs and functional domains. Out of 603 designed EST-SSR primers, 18 pairs of primers were selected for validation based on the optimum parameter value. Reproducible amplification was obtained for six primer pairs in C. asiatica that were further tested for cross-transferability in nine other important genera/species of the Apiaceae family. Cross-transferability of the EST-SSR markers among the species were examined and Centella javanica showed highest transferability (83.3%). The study revealed six highly polymorphic EST-SSR primers with an average PIC value of 0.95. In conclusion, these EST-SSR markers hold a big promise for the genomics analysis of Centella asiatica, to facilitate comparative map-based analyses across other related species within the Apiaceae family, and future marker-assisted breeding programs. To the best of our knowledge, this is the first report of development of EST-SSRs in Centella asiatica by in silico approaches, which offers a veritable potential in further use in plant omics research and development.

Draft genome analysis provides insights into the fiber yield, crude protein biosynthesis, and vegetative growth of domesticated ramie (Boehmeria nivea L. Gaud).

PubMed

Liu, Chan; Zeng, Liangbin; Zhu, Siyuan; Wu, Lingqing; Wang, Yanzhou; Tang, Shouwei; Wang, Hongwu; Zheng, Xia; Zhao, Jian; Chen, Xiaorong; Dai, Qiuzhong; Liu, Touming

2017-11-15

Plentiful bast fiber, a high crude protein content, and vigorous vegetative growth make ramie a popular fiber and forage crop. Here, we report the draft genome of ramie, along with a genomic comparison and evolutionary analysis. The draft genome contained a sequence of approximately 335.6 Mb with 42,463 predicted genes. A high-density genetic map with 4,338 single nucleotide polymorphisms (SNPs) was developed and used to anchor the genome sequence, thus, creating an integrated genetic and physical map containing a 58.2-Mb genome sequence and 4,304 molecular markers. A genomic comparison identified 1,075 unique gene families in ramie, containing 4,082 genes. Among these unique genes, five were cellulose synthase genes that were specifically expressed in stem bark, and 3 encoded a WAT1-related protein, suggesting that they are probably related to high bast fiber yield. An evolutionary analysis detected 106 positively selected genes, 22 of which were related to nitrogen metabolism, indicating that they are probably responsible for the crude protein content and vegetative growth of domesticated varieties. This study is the first to characterize the genome and develop a high-density genetic map of ramie and provides a basis for the genetic and molecular study of this crop. © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

QUENCHING STAR FORMATION AT INTERMEDIATE REDSHIFTS: DOWNSIZING OF THE MASS FLUX DENSITY IN THE GREEN VALLEY

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

Goncalves, Thiago S.; Menendez-Delmestre, Karin; Martin, D. Christopher

2012-11-01

The bimodality in galaxy properties has been observed at low and high redshifts, with a clear distinction between star-forming galaxies in the blue cloud and passively evolving objects in the red sequence; the absence of galaxies with intermediate properties indicates that the quenching of star formation and subsequent transition between populations must happen rapidly. In this paper, we present a study of over 100 transiting galaxies in the so-called green valley at intermediate redshifts (z {approx} 0.8). By using very deep spectroscopy with the DEIMOS instrument at the Keck telescope we are able to infer the star formation histories ofmore » these objects and measure the stellar mass flux density transiting from the blue cloud to the red sequence when the universe was half its current age. Our results indicate that the process happened more rapidly and for more massive galaxies in the past, suggesting a top-down scenario in which the massive end of the red sequence is forming first. This represents another aspect of downsizing, with the mass flux density moving toward smaller galaxies in recent times.« less

Nullomers and High Order Nullomers in Genomic Sequences

PubMed Central

Vergni, Davide; Santoni, Daniele

2016-01-01

A nullomer is an oligomer that does not occur as a subsequence in a given DNA sequence, i.e. it is an absent word of that sequence. The importance of nullomers in several applications, from drug discovery to forensic practice, is now debated in the literature. Here, we investigated the nature of nullomers, whether their absence in genomes has just a statistical explanation or it is a peculiar feature of genomic sequences. We introduced an extension of the notion of nullomer, namely high order nullomers, which are nullomers whose mutated sequences are still nullomers. We studied different aspects of them: comparison with nullomers of random sequences, CpG distribution and mean helical rise. In agreement with previous results we found that the number of nullomers in the human genome is much larger than expected by chance. Nevertheless antithetical results were found when considering a random DNA sequence preserving dinucleotide frequencies. The analysis of CpG frequencies in nullomers and high order nullomers revealed, as expected, a high CpG content but it also highlighted a strong dependence of CpG frequencies on the dinucleotide position, suggesting that nullomers have their own peculiar structure and are not simply sequences whose CpG frequency is biased. Furthermore, phylogenetic trees were built on eleven species based on both the similarities between the dinucleotide frequencies and the number of nullomers two species share, showing that nullomers are fairly conserved among close species. Finally the study of mean helical rise of nullomers sequences revealed significantly high mean rise values, reinforcing the hypothesis that those sequences have some peculiar structural features. The obtained results show that nullomers are the consequence of the peculiar structure of DNA (also including biased CpG frequency and CpGs islands), so that the hypermutability model, also taking into account CpG islands, seems to be not sufficient to explain nullomer phenomenon. Finally, high order nullomers could emphasize those features that already make simple nullomers useful in several applications. PMID:27906971

Molecular Identification of Sex in Phoenix dactylifera Using Inter Simple Sequence Repeat Markers.

PubMed

Al-Ameri, Abdulhafed A; Al-Qurainy, Fahad; Gaafar, Abdel-Rhman Z; Khan, Salim; Nadeem, M

2016-01-01

Early sex identification of Date Palm (Phoenix dactylifera L.) at seedling stage is an economically desirable objective, which will significantly increase the profits of seed based cultivation. The utilization of molecular markers at this stage for early and rapid identification of sex is important due to the lack of morphological markers. In this study, a total of two hundred Inter Simple Sequence Repeat (ISSR) primers were screened among male and female Date palm plants to identify putative sex-specific marker, out of which only two primers (IS_A02 and IS_A71) were found to be associated with sex. The primer IS_A02 produced a unique band of size 390 bp and was found clearly in all female plants, while it was absent in all male plants. Contrary to this, the primer IS_A71 produced a unique band of size 380 bp and was clearly found in all male plants, whereas it was absent in all the female plants. Subsequently, these specific fragments were excised, purified, and sequenced for the development of sequence specific markers further in future for the implementation on dioecious Date Palm for sex determination. These markers are efficient, highly reliable, and reproducible for sex identification at the early stage of seedling.

Mode conversion in cold low-density plasma with a sheared magnetic field

DOE PAGES

Dodin, I. Y.; Ruiz, D. E.; Kubo, S.

2017-12-19

Here, a theory is proposed that describes mutual conversion of two electromagnetic modes in cold low-density plasma, specifically, in the high-frequency limit where the ion response is negligible. In contrast to the classic (Landau–Zener-type) theory of mode conversion, the region of resonant coupling in low-density plasma is not necessarily narrow, so the coupling matrix cannot be approximated with its first-order Taylor expansion; also, the initial conditions are set up differently. For the case of strong magnetic shear, a simple method is identified for preparing a two-mode wave such that it transforms into a single-mode wave upon entering high-density plasma. Themore » theory can be used for reduced modeling of wave-power input in fusion plasmas. In particular, applications are envisioned in stellarator research, where the mutual conversion of two electromagnetic modes near the plasma edge is a known issue.« less

Mode conversion in cold low-density plasma with a sheared magnetic field

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

Dodin, I. Y.; Ruiz, D. E.; Kubo, S.

Here, a theory is proposed that describes mutual conversion of two electromagnetic modes in cold low-density plasma, specifically, in the high-frequency limit where the ion response is negligible. In contrast to the classic (Landau–Zener-type) theory of mode conversion, the region of resonant coupling in low-density plasma is not necessarily narrow, so the coupling matrix cannot be approximated with its first-order Taylor expansion; also, the initial conditions are set up differently. For the case of strong magnetic shear, a simple method is identified for preparing a two-mode wave such that it transforms into a single-mode wave upon entering high-density plasma. Themore » theory can be used for reduced modeling of wave-power input in fusion plasmas. In particular, applications are envisioned in stellarator research, where the mutual conversion of two electromagnetic modes near the plasma edge is a known issue.« less

Use of complex hydraulic variables to predict the distribution and density of unionids in a side channel of the Upper Mississippi River

USGS Publications Warehouse

Steuer, J.J.; Newton, T.J.; Zigler, S.J.

2008-01-01

Previous attempts to predict the importance of abiotic and biotic factors to unionids in large rivers have been largely unsuccessful. Many simple physical habitat descriptors (e.g., current velocity, substrate particle size, and water depth) have limited ability to predict unionid density. However, more recent studies have found that complex hydraulic variables (e.g., shear velocity, boundary shear stress, and Reynolds number) may be more useful predictors of unionid density. We performed a retrospective analysis with unionid density, current velocity, and substrate particle size data from 1987 to 1988 in a 6-km reach of the Upper Mississippi River near Prairie du Chien, Wisconsin. We used these data to model simple and complex hydraulic variables under low and high flow conditions. We then used classification and regression tree analysis to examine the relationships between hydraulic variables and unionid density. We found that boundary Reynolds number, Froude number, boundary shear stress, and grain size were the best predictors of density. Models with complex hydraulic variables were a substantial improvement over previously published discriminant models and correctly classified 65-88% of the observations for the total mussel fauna and six species. These data suggest that unionid beds may be constrained by threshold limits at both ends of the flow regime. Under low flow, mussels may require a minimum hydraulic variable (Rez.ast;, Fr) to transport nutrients, oxygen, and waste products. Under high flow, areas with relatively low boundary shear stress may provide a hydraulic refuge for mussels. Data on hydraulic preferences and identification of other conditions that constitute unionid habitat are needed to help restore and enhance habitats for unionids in rivers. ?? 2008 Springer Science+Business Media B.V.

GenoCore: A simple and fast algorithm for core subset selection from large genotype datasets.

PubMed

Jeong, Seongmun; Kim, Jae-Yoon; Jeong, Soon-Chun; Kang, Sung-Taeg; Moon, Jung-Kyung; Kim, Namshin

2017-01-01

Selecting core subsets from plant genotype datasets is important for enhancing cost-effectiveness and to shorten the time required for analyses of genome-wide association studies (GWAS), and genomics-assisted breeding of crop species, etc. Recently, a large number of genetic markers (>100,000 single nucleotide polymorphisms) have been identified from high-density single nucleotide polymorphism (SNP) arrays and next-generation sequencing (NGS) data. However, there is no software available for picking out the efficient and consistent core subset from such a huge dataset. It is necessary to develop software that can extract genetically important samples in a population with coherence. We here present a new program, GenoCore, which can find quickly and efficiently the core subset representing the entire population. We introduce simple measures of coverage and diversity scores, which reflect genotype errors and genetic variations, and can help to select a sample rapidly and accurately for crop genotype dataset. Comparison of our method to other core collection software using example datasets are performed to validate the performance according to genetic distance, diversity, coverage, required system resources, and the number of selected samples. GenoCore selects the smallest, most consistent, and most representative core collection from all samples, using less memory with more efficient scores, and shows greater genetic coverage compared to the other software tested. GenoCore was written in R language, and can be accessed online with an example dataset and test results at https://github.com/lovemun/Genocore.

Dog leukocyte antigen class II-associated genetic risk testing for immune disorders of dogs: simplified approaches using Pug dog necrotizing meningoencephalitis as a model.

PubMed

Pedersen, Niels; Liu, Hongwei; Millon, Lee; Greer, Kimberly

2011-01-01

A significantly increased risk for a number of autoimmune and infectious diseases in purebred and mixed-breed dogs has been associated with certain alleles or allele combinations of the dog leukocyte antigen (DLA) class II complex containing the DRB1, DQA1, and DQB1 genes. The exact level of risk depends on the specific disease, the alleles in question, and whether alleles exist in a homozygous or heterozygous state. The gold standard for identifying high-risk alleles and their zygosity has involved direct sequencing of the exon 2 regions of each of the 3 genes. However, sequencing and identification of specific alleles at each of the 3 loci are relatively expensive and sequencing techniques are not ideal for additional parentage or identity determination. However, it is often possible to get the same information from sequencing only 1 gene given the small number of possible alleles at each locus in purebred dogs, extensive homozygosity, and tendency for disease-causing alleles at each of the 3 loci to be strongly linked to each other into haplotypes. Therefore, genetic testing in purebred dogs with immune diseases can be often simplified by sequencing alleles at 1 rather than 3 loci. Further simplification of genetic tests for canine immune diseases can be achieved by the use of alternative genetic markers in the DLA class II region that are also strongly linked with the disease genotype. These markers consist of either simple tandem repeats or single nucleotide polymorphisms that are also in strong linkage with specific DLA class II genotypes and/or haplotypes. The current study uses necrotizing meningoencephalitis of Pug dogs as a paradigm to assess simple alternative genetic tests for disease risk. It was possible to attain identical necrotizing meningoencephalitis risk assessments to 3-locus DLA class II sequencing by sequencing only the DQB1 gene, using 3 DLA class II-linked simple tandem repeat markers, or with a small single nucleotide polymorphism array designed to identify breed-specific DQB1 alleles.

High-resolution melting analysis for bird sexing: a successful approach to molecular sex identification using different biological samples.

PubMed

Morinha, Francisco; Travassos, Paulo; Seixas, Fernanda; Santos, Nuno; Sargo, Roberto; Sousa, Luís; Magalhães, Paula; Cabral, João A; Bastos, Estela

2013-05-01

High-resolution melting (HRM) analysis is a very attractive and flexible advanced post-PCR method with high sensitivity/specificity for simple, fast and cost-effective genotyping based on the detection of specific melting profiles of PCR products. Next generation real-time PCR systems, along with improved saturating DNA-binding dyes, enable the direct acquisition of HRM data after quantitative PCR. Melting behaviour is particularly influenced by the length, nucleotide sequence and GC content of the amplicons. This method is expanding rapidly in several research areas such as human genetics, reproductive biology, microbiology and ecology/conservation of wild populations. Here we have developed a successful HRM protocol for avian sex identification based on the amplification of sex-specific CHD1 fragments. The melting curve patterns allowed efficient sexual differentiation of 111 samples analysed (plucked feathers, muscle tissues, blood and oral cavity epithelial cells) of 14 bird species. In addition, we sequenced the amplified regions of the CHD1 gene and demonstrated the usefulness of this strategy for the genotype discrimination of various amplicons (CHD1Z and CHD1W), which have small size differences, ranging from 2 bp to 44 bp. The established methodology clearly revealed the advantages (e.g. closed-tube system, high sensitivity and rapidity) of a simple HRM assay for accurate sex differentiation of the species under study. The requirements, strengths and limitations of the method are addressed to provide a simple guide for its application in the field of molecular sexing of birds. The high sensitivity and resolution relative to previous real-time PCR methods makes HRM analysis an excellent approach for improving advanced molecular methods for bird sexing. © 2013 Blackwell Publishing Ltd.

Facile and generalized encapsulations of inorganic nanocrystals with nitrogen-doped carbonaceous coating for multifunctionality

NASA Astrophysics Data System (ADS)

Yang, Yong; Zhang, Jingchao; Wang, Shitong; Xu, Xiaobin; Zhang, Zhicheng; Wang, Pengpeng; Tang, Zilong; Wang, Xun

2015-02-01

A simple strategy toward versatile encapsulations of inorganic nanocrystals, through a green hydrothermal treatment of commercial polyurethane sponge, was developed. This approach enables us to realize a general method to form a surface-adherent, N-doped coating with a controllable thickness for well-defined structures. These composites exhibit active properties in optical applications and energy storage. For example, N-doped carbon encapsulated Fe2O3 nanoboxes show a very high discharge capacity and outstanding cyclability, and the capacity still remained at 1086 mA h g-1 at a current density of 400 mA g-1 after 200 cycles. Our results described here provide a simple surface coating technique to design various functional nanostructures.A simple strategy toward versatile encapsulations of inorganic nanocrystals, through a green hydrothermal treatment of commercial polyurethane sponge, was developed. This approach enables us to realize a general method to form a surface-adherent, N-doped coating with a controllable thickness for well-defined structures. These composites exhibit active properties in optical applications and energy storage. For example, N-doped carbon encapsulated Fe2O3 nanoboxes show a very high discharge capacity and outstanding cyclability, and the capacity still remained at 1086 mA h g-1 at a current density of 400 mA g-1 after 200 cycles. Our results described here provide a simple surface coating technique to design various functional nanostructures. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr07181f

A simple model for estimating a magnetic field in laser-driven coils

DOE PAGES

Fiksel, Gennady; Fox, William; Gao, Lan; ...

2016-09-26

Magnetic field generation by laser-driven coils is a promising way of magnetizing plasma in laboratory high-energy-density plasma experiments. A typical configuration consists of two electrodes—one electrode is irradiated with a high-intensity laser beam and another electrode collects charged particles from the expanding plasma. The two electrodes are separated by a narrow gap forming a capacitor-like configuration and are connected with a conducting wire-coil. The charge-separation in the expanding plasma builds up a potential difference between the electrodes that drives the electrical current in the coil. A magnetic field of tens to hundreds of Teslas generated inside the coil has beenmore » reported. This paper presents a simple model that estimates the magnetic field using simple assumptions. Lastly, the results are compared with the published experimental data.« less

Electron density and plasma dynamics of a colliding plasma experiment

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

Wiechula, J., E-mail: wiechula@physik.uni-frankfurt.de; Schönlein, A.; Iberler, M.

2016-07-15

We present experimental results of two head-on colliding plasma sheaths accelerated by pulsed-power-driven coaxial plasma accelerators. The measurements have been performed in a small vacuum chamber with a neutral-gas prefill of ArH{sub 2} at gas pressures between 17 Pa and 400 Pa and load voltages between 4 kV and 9 kV. As the plasma sheaths collide, the electron density is significantly increased. The electron density reaches maximum values of ≈8 ⋅ 10{sup 15} cm{sup −3} for a single accelerated plasma and a maximum value of ≈2.6 ⋅ 10{sup 16} cm{sup −3} for the plasma collision. Overall a raise of the plasma density by a factor ofmore » 1.3 to 3.8 has been achieved. A scaling behavior has been derived from the values of the electron density which shows a disproportionately high increase of the electron density of the collisional case for higher applied voltages in comparison to a single accelerated plasma. Sequences of the plasma collision have been taken, using a fast framing camera to study the plasma dynamics. These sequences indicate a maximum collision velocity of 34 km/s.« less

THE FORMATION AND EVOLUTION OF YOUNG LOW-MASS STARS WITHIN HALOS WITH HIGH CONCENTRATION OF DARK MATTER PARTICLES

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

Casanellas, Jordi; Lopes, IlIDio, E-mail: jordicasanellas@ist.utl.p, E-mail: ilidio.lopes@ist.utl.p

2009-11-01

The formation and evolution of low-mass stars within dense halos of dark matter (DM) leads to evolution scenarios quite different from the classical stellar evolution. As a result of our detailed numerical work, we describe these new scenarios for a range of DM densities on the host halo, for a range of scattering cross sections of the DM particles considered, and for stellar masses from 0.7 to 3 M {sub sun}. For the first time, we also computed the evolution of young low-mass stars in their Hayashi track in the pre-main-sequence phase and found that, for high DM densities, thesemore » stars stop their gravitational collapse before reaching the main sequence, in agreement with similar studies on first stars. Such stars remain indefinitely in an equilibrium state with lower effective temperatures (|DELTAT{sub eff}|>10{sup 3} K for a star of one solar mass), the annihilation of captured DM particles in their core being the only source of energy. In the case of lower DM densities, these protostars continue their collapse and progress through the main-sequence burning hydrogen at a lower rate. A star of 1 M{sub sun} will spend a time period greater than the current age of the universe consuming all the hydrogen in its core if it evolves in a halo with DM density rho{sub c}hi = 10{sup 9} GeV cm{sup -3}. We also show the strong dependence of the effective temperature and luminosity of these stars on the characteristics of the DM particles and how this can be used as an alternative method for DM research.« less

Evidence of Collisionless Shocks in a Hall Thruster Plume

DTIC Science & Technology

2003-04-25

Triple Langmuir probes and emissive probes are used to measure the electron number density, electron temperature, and plasma potential downstream of a low-power Hall thruster . The results show a high density plasma core with elevated electron temperature and plasma potential along the thruster centerline. These properties are believed to be due to collisionless shocks formed as a result of the ion/ion acoustic instability. A simple model is presented that shows the existence of a collisionless shock to be consistent with the observed phenomena.

High-current fast electron beam propagation in a dielectric target.

PubMed

Klimo, Ondrej; Tikhonchuk, V T; Debayle, A

2007-01-01

Recent experiments demonstrate an efficient transformation of high intensity laser pulse into a relativistic electron beam with a very high current density exceeding 10(12) A cm(-2). The propagation of such a beam inside the target is possible if its current is neutralized. This phenomenon is not well understood, especially in dielectric targets. In this paper, we study the propagation of high current density electron beam in a plastic target using a particle-in-cell simulation code. The code includes both ionization of the plastic and collisions of newborn electrons. The numerical results are compared with a relatively simple analytical model and a reasonable agreement is found. The temporal evolution of the beam velocity distribution, the spatial density profile, and the propagation velocity of the ionization front are analyzed and their dependencies on the beam density and energy are discussed. The beam energy losses are mainly due to the target ionization induced by the self-generated electric field and the return current. For the highest beam density, a two-stream instability is observed to develop in the plasma behind the ionization front and it contributes to the beam energy losses.

High-Density Genetic Linkage Map Construction and Quantitative Trait Locus Mapping for Hawthorn (Crataegus pinnatifida Bunge).

PubMed

Zhao, Yuhui; Su, Kai; Wang, Gang; Zhang, Liping; Zhang, Jijun; Li, Junpeng; Guo, Yinshan

2017-07-14

Genetic linkage maps are an important tool in genetic and genomic research. In this study, two hawthorn cultivars, Qiujinxing and Damianqiu, and 107 progenies from a cross between them were used for constructing a high-density genetic linkage map using the 2b-restriction site-associated DNA (2b-RAD) sequencing method, as well as for mapping quantitative trait loci (QTL) for flavonoid content. In total, 206,411,693 single-end reads were obtained, with an average sequencing depth of 57× in the parents and 23× in the progeny. After quality trimming, 117,896 high-quality 2b-RAD tags were retained, of which 42,279 were polymorphic; of these, 12,951 markers were used for constructing the genetic linkage map. The map contained 17 linkage groups and 3,894 markers, with a total map length of 1,551.97 cM and an average marker interval of 0.40 cM. QTL mapping identified 21 QTLs associated with flavonoid content in 10 linkage groups, which explained 16.30-59.00% of the variance. This is the first high-density linkage map for hawthorn, which will serve as a basis for fine-scale QTL mapping and marker-assisted selection of important traits in hawthorn germplasm and will facilitate chromosome assignment for hawthorn whole-genome assemblies in the future.

A study of high density bit transition requirements versus the effects on BCH error correcting coding

NASA Technical Reports Server (NTRS)

Ingels, F.; Schoggen, W. O.

1981-01-01

Several methods for increasing bit transition densities in a data stream are summarized, discussed in detail, and compared against constraints imposed by the 2 MHz data link of the space shuttle high rate multiplexer unit. These methods include use of alternate pulse code modulation waveforms, data stream modification by insertion, alternate bit inversion, differential encoding, error encoding, and use of bit scramblers. The psuedo-random cover sequence generator was chosen for application to the 2 MHz data link of the space shuttle high rate multiplexer unit. This method is fully analyzed and a design implementation proposed.

Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology

PubMed Central

Ramos, Antonio M.; Crooijmans, Richard P. M. A.; Affara, Nabeel A.; Amaral, Andreia J.; Archibald, Alan L.; Beever, Jonathan E.; Bendixen, Christian; Churcher, Carol; Clark, Richard; Dehais, Patrick; Hansen, Mark S.; Hedegaard, Jakob; Hu, Zhi-Liang; Kerstens, Hindrik H.; Law, Andy S.; Megens, Hendrik-Jan; Milan, Denis; Nonneman, Danny J.; Rohrer, Gary A.; Rothschild, Max F.; Smith, Tim P. L.; Schnabel, Robert D.; Van Tassell, Curt P.; Taylor, Jeremy F.; Wiedmann, Ralph T.; Schook, Lawrence B.; Groenen, Martien A. M.

2009-01-01

Background The dissection of complex traits of economic importance to the pig industry requires the availability of a significant number of genetic markers, such as single nucleotide polymorphisms (SNPs). This study was conducted to discover several hundreds of thousands of porcine SNPs using next generation sequencing technologies and use these SNPs, as well as others from different public sources, to design a high-density SNP genotyping assay. Methodology/Principal Findings A total of 19 reduced representation libraries derived from four swine breeds (Duroc, Landrace, Large White, Pietrain) and a Wild Boar population and three restriction enzymes (AluI, HaeIII and MspI) were sequenced using Illumina's Genome Analyzer (GA). The SNP discovery effort resulted in the de novo identification of over 372K SNPs. More than 549K SNPs were used to design the Illumina Porcine 60K+SNP iSelect Beadchip, now commercially available as the PorcineSNP60. A total of 64,232 SNPs were included on the Beadchip. Results from genotyping the 158 individuals used for sequencing showed a high overall SNP call rate (97.5%). Of the 62,621 loci that could be reliably scored, 58,994 were polymorphic yielding a SNP conversion success rate of 94%. The average minor allele frequency (MAF) for all scorable SNPs was 0.274. Conclusions/Significance Overall, the results of this study indicate the utility of using next generation sequencing technologies to identify large numbers of reliable SNPs. In addition, the validation of the PorcineSNP60 Beadchip demonstrated that the assay is an excellent tool that will likely be used in a variety of future studies in pigs. PMID:19654876

A matrix-based approach to solving the inverse Frobenius-Perron problem using sequences of density functions of stochastically perturbed dynamical systems

NASA Astrophysics Data System (ADS)

Nie, Xiaokai; Coca, Daniel

2018-01-01

The paper introduces a matrix-based approach to estimate the unique one-dimensional discrete-time dynamical system that generated a given sequence of probability density functions whilst subjected to an additive stochastic perturbation with known density.

A matrix-based approach to solving the inverse Frobenius-Perron problem using sequences of density functions of stochastically perturbed dynamical systems.

PubMed

Nie, Xiaokai; Coca, Daniel

2018-01-01

The paper introduces a matrix-based approach to estimate the unique one-dimensional discrete-time dynamical system that generated a given sequence of probability density functions whilst subjected to an additive stochastic perturbation with known density.

Density-controlled, solution-based growth of ZnO nanorod arrays via layer-by-layer polymer thin films for enhanced field emission

NASA Astrophysics Data System (ADS)

Weintraub, Benjamin; Chang, Sehoon; Singamaneni, Srikanth; Han, Won Hee; Choi, Young Jin; Bae, Joonho; Kirkham, Melanie; Tsukruk, Vladimir V.; Deng, Yulin

2008-10-01

A simple, scalable, and cost-effective technique for controlling the growth density of ZnO nanorod arrays based on a layer-by-layer polyelectrolyte polymer film is demonstrated. The ZnO nanorods were synthesized using a low temperature (T = 90 °C), solution-based method. The density-control technique utilizes a polymer thin film pre-coated on the substrate to control the mass transport of the reactant to the substrate. The density-controlled arrays were investigated as potential field emission candidates. The field emission results revealed that an emitter density of 7 nanorods µm-2 and a tapered nanorod morphology generated a high field enhancement factor of 5884. This novel technique shows promise for applications in flat panel display technology.

A Genome-Wide Survey of the Microsatellite Content of the Globe Artichoke Genome and the Development of a Web-Based Database

PubMed Central

Portis, Ezio; Portis, Flavio; Valente, Luisa; Moglia, Andrea; Barchi, Lorenzo; Lanteri, Sergio; Acquadro, Alberto

2016-01-01

The recently acquired genome sequence of globe artichoke (Cynara cardunculus var. scolymus) has been used to catalog the genome’s content of simple sequence repeat (SSR) markers. More than 177,000 perfect SSRs were revealed, equivalent to an overall density across the genome of 244.5 SSRs/Mbp, but some 224,000 imperfect SSRs were also identified. About 21% of these SSRs were complex (two stretches of repeats separated by <100 nt). Some 73% of the SSRs were composed of dinucleotide motifs. The SSRs were categorized for the numbers of repeats present, their overall length and were allocated to their linkage group. A total of 4,761 perfect and 6,583 imperfect SSRs were present in 3,781 genes (14.11% of the total), corresponding to an overall density across the gene space of 32,5 and 44,9 SSRs/Mbp for perfect and imperfect motifs, respectively. A putative function has been assigned, using the gene ontology approach, to the set of genes harboring at least one SSR. The same search parameters were applied to reveal the SSR content of 14 other plant species for which genome sequence is available. Certain species-specific SSR motifs were identified, along with a hexa-nucleotide motif shared only with the other two Compositae species (sunflower (Helianthus annuus) and horseweed (Conyza canadensis)) included in the study. Finally, a database, called “Cynara cardunculus MicroSatellite DataBase” (CyMSatDB) was developed to provide a searchable interface to the SSR data. CyMSatDB facilitates the retrieval of SSR markers, as well as suggested forward and reverse primers, on the basis of genomic location, genomic vs genic context, perfect vs imperfect repeat, motif type, motif sequence and repeat number. The SSR markers were validated via an in silico based PCR analysis adopting two available assembled transcriptomes, derived from contrasting globe artichoke accessions, as templates. PMID:27648830

MAI statistics estimation and analysis in a DS-CDMA system

NASA Astrophysics Data System (ADS)

Alami Hassani, A.; Zouak, M.; Mrabti, M.; Abdi, F.

2018-05-01

A primary limitation of Direct Sequence Code Division Multiple Access DS-CDMA link performance and system capacity is multiple access interference (MAI). To examine the performance of CDMA systems in the presence of MAI, i.e., in a multiuser environment, several works assumed that the interference can be approximated by a Gaussian random variable. In this paper, we first develop a new and simple approach to characterize the MAI in a multiuser system. In addition to statistically quantifying the MAI power, the paper also proposes a statistical model for both variance and mean of the MAI for synchronous and asynchronous CDMA transmission. We show that the MAI probability density function (PDF) is Gaussian for the equal-received-energy case and validate it by computer simulations.

The evolution of galaxies

NASA Technical Reports Server (NTRS)

Gunn, J. E.

1982-01-01

The recent observational evidence on the evolution of galaxies is reviewed and related to the framework of current ideas for galaxy formation from primordial density fluctuations. Recent strong evidence for the evolution of the stellar population in ellipticals is presented, as well as evidence that not all ellipticals behave as predicted by any simple theory. The status of counts of faint galaxies and the implications for the evolution of spirals is discussed, together with a discussion of recent work on the redshift distribution of galaxies at faint magnitudes and a spectroscopic investigation of the Butcher-Oemler blue cluster galaxies. Finally a new picture for the formation and evolution of disk galaxies which may explain most of the features of the Hubble sequence is outlined.

High-rate nano-crystalline Li 4Ti 5O 12 attached on carbon nano-fibers for hybrid supercapacitors

NASA Astrophysics Data System (ADS)

Naoi, Katsuhiko; Ishimoto, Shuichi; Isobe, Yusaku; Aoyagi, Shintaro

A lithium titanate (Li 4Ti 5O 12)-based electrode which can operate at unusually high current density (300 C) was developed as negative electrode for hybrid capacitors. The high-rate Li 4Ti 5O 12 electrode has a unique nano-structure consisting of unusually small nano-crystalline Li 4Ti 5O 12 (ca. 5-20 nm) grafted onto carbon nano-fiber anchors (nc-Li 4Ti 5O 12/CNF). This nano-structured nc-Li 4Ti 5O 12/CNF composite are prepared by simple sol-gel method under ultra-centrifugal force (65,000 N) followed by instantaneous annealing at 900 °C for 3 min. A model hybrid capacitor cell consisting of a negative nc-Li 4Ti 5O 12/CNF composite electrode and a positive activated carbon electrode showed high energy density of 40 Wh L -1 and high power density of 7.5 kW L -1 comparable to conventional EDLCs.

Edge-enriched, porous carbon-based, high energy density supercapacitors for hybrid electric vehicles.

PubMed

Kim, Yong Jung; Yang, Cheol-Min; Park, Ki Chul; Kaneko, Katsumi; Kim, Yoong Ahm; Noguchi, Minoru; Fujino, Takeshi; Oyama, Shigeki; Endo, Morinobu

2012-03-12

Supercapacitors can store and deliver energy by a simple charge separation, and thus they could be an attractive option to meet transient high energy density in operating fuel cells and in electric and hybrid electric vehicles. To achieve such requirements, intensive studies have been carried out to improve the volumetric capacitance in supercapacitors using various types and forms of carbons including carbon nanotubes and graphenes. However, conventional porous carbons are not suitable for use as electrode material in supercapacitors for such high energy density applications. Here, we show that edge-enriched porous carbons are the best electrode material for high energy density supercapacitors to be used in vehicles as an auxiliary powertrain. Molten potassium hydroxide penetrates well-aligned graphene layers vertically and consequently generates both suitable pores that are easily accessible to the electrolyte and a large fraction of electrochemically active edge sites. We expect that our findings will motivate further research related to energy storage devices and also environmentally friendly electric vehicles. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An Efficient Strategy Combining SSR Markers- and Advanced QTL-seq-driven QTL Mapping Unravels Candidate Genes Regulating Grain Weight in Rice

PubMed Central

Daware, Anurag; Das, Sweta; Srivastava, Rishi; Badoni, Saurabh; Singh, Ashok K.; Agarwal, Pinky; Parida, Swarup K.; Tyagi, Akhilesh K.

2016-01-01

Development and use of genome-wide informative simple sequence repeat (SSR) markers and novel integrated genomic strategies are vital to drive genomics-assisted breeding applications and for efficient dissection of quantitative trait loci (QTLs) underlying complex traits in rice. The present study developed 6244 genome-wide informative SSR markers exhibiting in silico fragment length polymorphism based on repeat-unit variations among genomic sequences of 11 indica, japonica, aus, and wild rice accessions. These markers were mapped on diverse coding and non-coding sequence components of known cloned/candidate genes annotated from 12 chromosomes and revealed a much higher amplification (97%) and polymorphic potential (88%) along with wider genetic/functional diversity level (16–74% with a mean 53%) especially among accessions belonging to indica cultivar group, suggesting their utility in large-scale genomics-assisted breeding applications in rice. A high-density 3791 SSR markers-anchored genetic linkage map (IR 64 × Sonasal) spanning 2060 cM total map-length with an average inter-marker distance of 0.54 cM was generated. This reference genetic map identified six major genomic regions harboring robust QTLs (31% combined phenotypic variation explained with a 5.7–8.7 LOD) governing grain weight on six rice chromosomes. One strong grain weight major QTL region (OsqGW5.1) was narrowed-down by integrating traditional QTL mapping with high-resolution QTL region-specific integrated SSR and single nucleotide polymorphism markers-based QTL-seq analysis and differential expression profiling. This led us to delineate two natural allelic variants in two known cis-regulatory elements (RAV1AAT and CARGCW8GAT) of glycosyl hydrolase and serine carboxypeptidase genes exhibiting pronounced seed-specific differential regulation in low (Sonasal) and high (IR 64) grain weight mapping parental accessions. Our genome-wide SSR marker resource (polymorphic within/between diverse cultivar groups) and integrated genomic strategy can efficiently scan functionally relevant potential molecular tags (markers, candidate genes and alleles) regulating complex agronomic traits (grain weight) and expedite marker-assisted genetic enhancement in rice. PMID:27833617

Cultivar identification, pedigree verification, and diversity analysis among Peach (Prunus persica L. Batsch) Cultivars based on Simple Sequence Repeat markers

USDA-ARS?s Scientific Manuscript database

The genetic relationships and pedigree inferences among peach (Prunus persica (L.) Batsch) accessions and breeding lines used in genetic improvement were evaluated using 15 simple sequence repeat (SSR) markers. A total of 80 alleles were detected among the 37 peach accessions with an average of 5.53...

THE USE OF INTER SIMPLE SEQUENCE REPEATS (ISSR) IN DISTINGUISHING NEIGHBORING DOUGLAS-FIR TREES AS A MEANS TO IDENTIFYING TREE ROOTS WITH ABOVE-GROUND BIOMASS

EPA Science Inventory

We are attempting to identify specific root fragments from soil cores with individual trees. We successfully used Inter Simple Sequence Repeats (ISSR) to distinguish neighboring old-growth Douglas-fir trees from one another, while maintaining identity among each tree's parts. W...

High-density magnetoresistive random access memory operating at ultralow voltage at room temperature.

PubMed

Hu, Jia-Mian; Li, Zheng; Chen, Long-Qing; Nan, Ce-Wen

2011-11-22

The main bottlenecks limiting the practical applications of current magnetoresistive random access memory (MRAM) technology are its low storage density and high writing energy consumption. Although a number of proposals have been reported for voltage-controlled memory device in recent years, none of them simultaneously satisfy the important device attributes: high storage capacity, low power consumption and room temperature operation. Here we present, using phase-field simulations, a simple and new pathway towards high-performance MRAMs that display significant improvements over existing MRAM technologies or proposed concepts. The proposed nanoscale MRAM device simultaneously exhibits ultrahigh storage capacity of up to 88 Gb inch(-2), ultralow power dissipation as low as 0.16 fJ per bit and room temperature high-speed operation below 10 ns.

High-density magnetoresistive random access memory operating at ultralow voltage at room temperature

PubMed Central

Hu, Jia-Mian; Li, Zheng; Chen, Long-Qing; Nan, Ce-Wen

2011-01-01

The main bottlenecks limiting the practical applications of current magnetoresistive random access memory (MRAM) technology are its low storage density and high writing energy consumption. Although a number of proposals have been reported for voltage-controlled memory device in recent years, none of them simultaneously satisfy the important device attributes: high storage capacity, low power consumption and room temperature operation. Here we present, using phase-field simulations, a simple and new pathway towards high-performance MRAMs that display significant improvements over existing MRAM technologies or proposed concepts. The proposed nanoscale MRAM device simultaneously exhibits ultrahigh storage capacity of up to 88 Gb inch−2, ultralow power dissipation as low as 0.16 fJ per bit and room temperature high-speed operation below 10 ns. PMID:22109527

Logo2PWM: a tool to convert sequence logo to position weight matrix.

PubMed

Gao, Zhen; Liu, Lu; Ruan, Jianhua

2017-10-03

position weight matrix (PWM) and sequence logo are the most widely used representations of transcription factor binding site (TFBS) in biological sequences. Sequence logo - a graphical representation of PWM, has been widely used in scientific publications and reports, due to its easiness of human perception, rich information, and simple format. Different from sequence logo, PWM works great as a precise and compact digitalized form, which can be easily used by a variety of motif analysis software. There are a few available tools to generate sequence logos from PWM; however, no tool does the reverse. Such tool to convert sequence logo back to PWM is needed to scan a TFBS represented in logo format in a publication where the PWM is not provided or hard to be acquired. A major difficulty in developing such tool to convert sequence logo to PWM is to deal with the diversity of sequence logo images. We propose logo2PWM for reconstructing PWM from a large variety of sequence logo images. Evaluation results on over one thousand logos from three sources of different logo format show that the correlation between the reconstructed PWMs and the original PWMs are constantly high, where median correlation is greater than 0.97. Because of the high recognition accuracy, the easiness of usage, and, the availability of both web-based service and stand-alone application, we believe that logo2PWM can readily benefit the study of transcription by filling the gap between sequence logo and PWM.

An innovative diagnostic technology for the codon mutation C580Y in kelch13 of Plasmodium falciparum with MinION nanopore sequencer.

PubMed

Imai, Kazuo; Tarumoto, Norihito; Runtuwene, Lucky Ronald; Sakai, Jun; Hayashida, Kyoko; Eshita, Yuki; Maeda, Ryuichiro; Tuda, Josef; Ohno, Hideaki; Murakami, Takashi; Maesaki, Shigefumi; Suzuki, Yutaka; Yamagishi, Junya; Maeda, Takuya

2018-05-29

The recent spread of artemisinin (ART)-resistant Plasmodium falciparum represents an emerging global threat to public health. In Southeast Asia, the C580Y mutation of kelch13 (k13) is the dominant mutation of ART-resistant P. falciparum. Therefore, a simple method for the detection of C580Y mutation is urgently needed to enable widespread routine surveillance in the field. The aim of this study is to develop a new diagnostic procedure for the C580Y mutation using loop-mediated isothermal amplification (LAMP) combined with the MinION nanopore sequencer. A LAMP assay for the k13 gene of P. falciparum to detect the C580Y mutation was successfully developed. The detection limit of this procedure was 10 copies of the reference plasmid harboring the k13 gene within 60 min. Thereafter, amplicon sequencing of the LAMP products using the MinION nanopore sequencer was performed to clarify the nucleotide sequences of the gene. The C580Y mutation was identified based on the sequence data collected from MinION reads 30 min after the start of sequencing. Further, clinical evaluation of the LAMP assay in 34 human blood samples collected from patients with P. falciparum malaria in Indonesia revealed a positive detection rate of 100%. All LAMP amplicons of up to 12 specimens were simultaneously sequenced using MinION. The results of sequencing were consistent with those of the conventional PCR and Sanger sequencing protocol. All procedures from DNA extraction to variant calling were completed within 3 h. The C580Y mutation was not found among these 34 P. falciparum isolates in Indonesia. An innovative method combining LAMP and MinION will enable simple, rapid, and high-sensitivity detection of the C580Y mutation of P. falciparum, even in resource-limited situations in developing countries.

High-density genetic map construction and QTLs identification for plant height in white jute (Corchorus capsularis L.) using specific locus amplified fragment (SLAF) sequencing.

PubMed

Tao, Aifen; Huang, Long; Wu, Guifen; Afshar, Reza Keshavarz; Qi, Jianmin; Xu, Jiantang; Fang, Pingping; Lin, Lihui; Zhang, Liwu; Lin, Peiqing

2017-05-08

Genetic mapping and quantitative trait locus (QTL) detection are powerful methodologies in plant improvement and breeding. White jute (Corchorus capsularis L.) is an important industrial raw material fiber crop because of its elite characteristics. However, construction of a high-density genetic map and identification of QTLs has been limited in white jute due to a lack of sufficient molecular markers. The specific locus amplified fragment sequencing (SLAF-seq) strategy combines locus-specific amplification and high-throughput sequencing to carry out de novo single nuclear polymorphism (SNP) discovery and large-scale genotyping. In this study, SLAF-seq was employed to obtain sufficient markers to construct a high-density genetic map for white jute. Moreover, with the development of abundant markers, genetic dissection of fiber yield traits such as plant height was also possible. Here, we present QTLs associated with plant height that were identified using our newly constructed genetic linkage groups. An F 8 population consisting of 100 lines was developed. In total, 69,446 high-quality SLAFs were detected of which 5,074 SLAFs were polymorphic; 913 polymorphic markers were used for the construction of a genetic map. The average coverage for each SLAF marker was 43-fold in the parents, and 9.8-fold in each F 8 individual. A linkage map was constructed that contained 913 SLAFs on 11 linkage groups (LGs) covering 1621.4 cM with an average density of 1.61 cM per locus. Among the 11 LGs, LG1 was the largest with 210 markers, a length of 406.34 cM, and an average distance of 1.93 cM between adjacent markers. LG11 was the smallest with only 25 markers, a length of 29.66 cM, and an average distance of 1.19 cM between adjacent markers. 'SNP_only' markers accounted for 85.54% and were the predominant markers on the map. QTL mapping based on the F 8 phenotypes detected 11 plant height QTLs including one major effect QTL across two cultivation locations, with each QTL accounting for 4.14-15.63% of the phenotypic variance. To our knowledge, the linkage map constructed here is the densest one available to date for white jute. This analysis also identified the first QTL in white jute. The results will provide an important platform for gene/QTL mapping, sequence assembly, genome comparisons, and marker-assisted selection breeding for white jute.

Ultrashort pulse high intensity laser illumination of a simple metal

NASA Astrophysics Data System (ADS)

Milchberg, H. M.; Freeman, R. R.; Davey, S. C.

1988-10-01

We have observed the self-reflection of intense, sub-picosecond 308 nm light pulse incident on a planar Al target and have inferred the electrical conductivity of solid density Al. The pulse lengths were sufficiently short that no significant expansion of the target occurred during the measurement.

Behavior Of A Simple Metal Under Ultrashort Pulse High Intensity Laser Illumination

NASA Astrophysics Data System (ADS)

Milchberg, H. M.; Freeman, R. R.; Davey, S. C.

1988-07-01

We have observed the self-reflection of intense, sub-picosecond 308 nm light pulse incident on a planar AI target and have inferred the electrical conductivity of solid density AI. The pulse lengths were sufficiently short that no significant expansion of the target occurred during the measurement.

Bricklaying an Academic Foundation

ERIC Educational Resources Information Center

Goldman, Jay P.

2005-01-01

A profile of R. Kirk Hamilton, superintendent of South-Western City Schools in Columbus, Ohio, is presented. Hamilton runs the Ohio school district featuring a full gamut of geography--from expansive cow pastures to high-density, urban housing complexes--yet he carries the same message to all corners that's grounded on a simple belief: All…

SC-CO2-assisted process for a high energy density aerogel supercapacitor: the effect of GO loading

NASA Astrophysics Data System (ADS)

Sarno, Maria; Baldino, Lucia; Scudieri, Carmela; Cardea, Stefano; Ciambelli, Paolo; Reverchon, Ernesto

2017-05-01

Energy density, safety, and simple and environmentally friendly preparation methods are very significant aspects in the realization of a compact supercapacitor. Herein we report the use of a supercritical CO2-assisted gel drying process (SC-CO2) for the preparation of porous electrodes containing dispersed graphene in a poly(vinylidene fluoride-co-hexafluoropropylene) (PVDF-HFP) binder membrane to sandwich in a new portable supercapacitor based on graphene oxide (GO). A GO loading of 60 wt.% was found to give the best combination of factors (porosity, wettability, mechanical and electrochemical properties). Cycling voltammetry and charge/discharge studies showed an excellent capacitance behaviour and stability in an ionic liquid electrolyte, suggesting SC-CO2 processing as a promising platform to produce highly bulky and porous films for supercapacitors. The supercapacitor device delivers a very high energy density of 79.2 Wh kg-1 at a power density of 0.23 KW kg-1 (current density 0.5 A g-1, specific capacitance 36.2 F g-1) while that of steel remains at 50.3 Wh kg-1 at a power density of 2.8 KW kg-1 (current density 6 A g-1, specific capacitance 23.5 F g-1).

SC-CO2-assisted process for a high energy density aerogel supercapacitor: the effect of GO loading.

PubMed

Sarno, Maria; Baldino, Lucia; Scudieri, Carmela; Cardea, Stefano; Ciambelli, Paolo; Reverchon, Ernesto

2017-05-19

Energy density, safety, and simple and environmentally friendly preparation methods are very significant aspects in the realization of a compact supercapacitor. Herein we report the use of a supercritical CO 2 -assisted gel drying process (SC-CO 2 ) for the preparation of porous electrodes containing dispersed graphene in a poly(vinylidene fluoride-co-hexafluoropropylene) (PVDF-HFP) binder membrane to sandwich in a new portable supercapacitor based on graphene oxide (GO). A GO loading of 60 wt.% was found to give the best combination of factors (porosity, wettability, mechanical and electrochemical properties). Cycling voltammetry and charge/discharge studies showed an excellent capacitance behaviour and stability in an ionic liquid electrolyte, suggesting SC-CO 2 processing as a promising platform to produce highly bulky and porous films for supercapacitors. The supercapacitor device delivers a very high energy density of 79.2 Wh kg -1 at a power density of 0.23 KW kg -1 (current density 0.5 A g -1 , specific capacitance 36.2 F g -1 ) while that of steel remains at 50.3 Wh kg -1 at a power density of 2.8 KW kg -1 (current density 6 A g -1 , specific capacitance 23.5 F g -1 ).

Consequences of splitting whole-genome sequencing effort over multiple breeds on imputation accuracy.

PubMed

Bouwman, Aniek C; Veerkamp, Roel F

2014-10-03

The aim of this study was to determine the consequences of splitting sequencing effort over multiple breeds for imputation accuracy from a high-density SNP chip towards whole-genome sequence. Such information would assist for instance numerical smaller cattle breeds, but also pig and chicken breeders, who have to choose wisely how to spend their sequencing efforts over all the breeds or lines they evaluate. Sequence data from cattle breeds was used, because there are currently relatively many individuals from several breeds sequenced within the 1,000 Bull Genomes project. The advantage of whole-genome sequence data is that it carries the causal mutations, but the question is whether it is possible to impute the causal variants accurately. This study therefore focussed on imputation accuracy of variants with low minor allele frequency and breed specific variants. Imputation accuracy was assessed for chromosome 1 and 29 as the correlation between observed and imputed genotypes. For chromosome 1, the average imputation accuracy was 0.70 with a reference population of 20 Holstein, and increased to 0.83 when the reference population was increased by including 3 other dairy breeds with 20 animals each. When the same amount of animals from the Holstein breed were added the accuracy improved to 0.88, while adding the 3 other breeds to the reference population of 80 Holstein improved the average imputation accuracy marginally to 0.89. For chromosome 29, the average imputation accuracy was lower. Some variants benefitted from the inclusion of other breeds in the reference population, initially determined by the MAF of the variant in each breed, but even Holstein specific variants did gain imputation accuracy from the multi-breed reference population. This study shows that splitting sequencing effort over multiple breeds and combining the reference populations is a good strategy for imputation from high-density SNP panels towards whole-genome sequence when reference populations are small and sequencing effort is limiting. When sequencing effort is limiting and interest lays in multiple breeds or lines this provides imputation of each breed.

Mathematical Modeling the Geometric Regularity in Proteus Mirabilis Colonies

NASA Astrophysics Data System (ADS)

Zhang, Bin; Jiang, Yi; Minsu Kim Collaboration

Proteus Mirabilis colony exhibits striking spatiotemporal regularity, with concentric ring patterns with alternative high and low bacteria density in space, and periodicity for repetition process of growth and swarm in time. We present a simple mathematical model to explain the spatiotemporal regularity of P. Mirabilis colonies. We study a one-dimensional system. Using a reaction-diffusion model with thresholds in cell density and nutrient concentration, we recreated periodic growth and spread patterns, suggesting that the nutrient constraint and cell density regulation might be sufficient to explain the spatiotemporal periodicity in P. Mirabilis colonies. We further verify this result using a cell based model.

SU-E-T-271: Direct Measurement of Tenth Value Layer Thicknesses for High Density Concretes with a Clinical Machine

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

Tanny, S; Parsai, E; Harrell, D

2015-06-15

Purpose: Use of high density concrete for radiation shielding is increasing, trading cost for space savings associated with the reduced tenth value layer (TVL). Precise information on the attenuation properties of high-density concretes is not readily present in the literature. A simple approximation is to scale the TVLs from NCRP 151 according relative increase in density. Here we present measured TVLs for heavy concretes of various densities using a built-in shielding test port. Methods: Concrete densities tested range from 2.35 g cc{sup −1} (147 pcf) to 5.6 g cc{sup −1} (350 pcf). Measurements were taken using 6MV, 6FFF, and 10FFFmore » on a Varian Truebeam linear accelerator. Field sizes of 4x4, 9x9 and 30x30 cm{sup 2} were measured. A PTW 31013 Farmer chamber with a buildup cap was positioned 5.5 m from isocenter along the beam CAX. Concrete thicknesses were incremented in 5 cm intervals. Comparison TVLs were determined by scaling the NCRP 151 TVLs by the density ratio between the sample and standard density. Results: The trend from the first to equilibrium TVL was an increase in thickness, compared with MC modeling, which predicted a decrease. Measured TVLs for 6 MV were reduced by as much as 8.9 cm for TVL{sub 1} and 3.4 cm for TVL{sub E} compared to values scaled from NCRP 151. There was 1–3 mm difference in TVL between measurements done at 4x4 versus 30x30 cm{sup 2}. TVL{sub 1} for 6FFF was 1.1 cm smaller than TVL{sub 1} for 6MV, but TVL{sub E} was consistent to within 4 mm. TVL{sub 1} and TVL{sub E} for 10FFF were reduced by 8.8 and 3.7 cm from scaled NCRP values, respectively. Conclusions: We have measured the TVL thicknesses for various concretes. Simple density scaling of the values in NCRP 151 is a conservatively safe approximation, but actual TVLs may be reduced enough to eliminate some of the expense of installation. Daniel Harrell and Jim Noller are employees of Shielding Construction Solutions, Inc, the shielding construction company that built the vault discussed in this abstract. Manjit Chopra is an employee of Universal Minerals International, Inc, the company that provided the aggregates for the high density concretes used in the vault construction.« less

A simple method for fabricating microwire tetrode with sufficient rigidity and integrity without a heat-fusing process.

PubMed

Liao, Yi-Fang; Tsai, Meng-Li; Yen, Chen-Tung; Cheng, Chiung-Hsiang

2011-02-15

Heat-fusing is a common process for fabricating microwire tetrodes. However, it is time-consuming, and the high-temperature treatment can easily cause the insulation of the microwire to overheat leading to short circuits. We herein provide a simple, fast method to fabricate microwire tetrodes without the heat-fusion process. By increasing the twisting density, we were able to fabricate tetrodes with good rigidity and integrity. This kind of tetrode showed good recording quality, penetrated the brain surface easily, and remained intact after chronic implantation. This method requires only general laboratory tools and is relatively simple even for inexperienced workers. © 2010 Elsevier B.V. All rights reserved.

Simple synthesis of amorphous NiWO4 nanostructure and its application as a novel cathode material for asymmetric supercapacitors.

PubMed

Niu, Lengyuan; Li, Zhangpeng; Xu, Ye; Sun, Jinfeng; Hong, Wei; Liu, Xiaohong; Wang, Jinqing; Yang, Shengrong

2013-08-28

This study reports a simple synthesis of amorphous nickel tungstate (NiWO4) nanostructure and its application as a novel cathode material for supercapacitors. The effect of reaction temperature on the electrochemical properties of the NiWO4 electrode was studied, and results demonstrate that the material synthesized at 70 °C (NiW-70) has shown the highest specific capacitance of 586.2 F g(-1) at 0.5 A g(-1) in a three-electrode system. To achieve a high energy density, a NiW-70//activated carbon asymmetric supercapacitor is successfully assembled by use of NiW-70 and activated carbon as the cathode and anode, respectively, and then, its electrochemical performance is characterized by cyclic voltammetry and galvanostatic charge-discharge measurements. The results show that the assembled asymmetric supercapacitor can be cycled reversibly between 0 and 1.6 V with a high specific capacitance of 71.1 F g(-1) at 0.25 A g(-1), which can deliver a maximum energy density of 25.3 Wh kg(-1) at a power density of 200 W kg(-1). Furthermore, this asymmetric supercapacitor also presented an excellent, long cycle life along with 91.4% specific capacitance being retained after 5000 consecutive times of cycling.

A common visual metric for approximate number and density

PubMed Central

Dakin, Steven C.; Tibber, Marc S.; Greenwood, John A.; Kingdom, Frederick A. A.; Morgan, Michael J.

2011-01-01

There is considerable interest in how humans estimate the number of objects in a scene in the context of an extensive literature on how we estimate the density (i.e., spacing) of objects. Here, we show that our sense of number and our sense of density are intertwined. Presented with two patches, observers found it more difficult to spot differences in either density or numerosity when those patches were mismatched in overall size, and their errors were consistent with larger patches appearing both denser and more numerous. We propose that density is estimated using the relative response of mechanisms tuned to low and high spatial frequencies (SFs), because energy at high SFs is largely determined by the number of objects, whereas low SF energy depends more on the area occupied by elements. This measure is biased by overall stimulus size in the same way as human observers, and by estimating number using the same measure scaled by relative stimulus size, we can explain all of our results. This model is a simple, biologically plausible common metric for perceptual number and density. PMID:22106276

The Three-part Structure of a Filament-unrelated Solar Coronal Mass Ejection

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

Song, H. Q.; Chen, Y.; Wang, B.

Coronal mass ejections (CMEs) often exhibit the typical three-part structure in the corona when observed with white-light coronagraphs, i.e., the bright leading front, dark cavity, and bright core, corresponding to a high-low-high density sequence. As CMEs result from eruptions of magnetic flux ropes (MFRs), which can possess either lower (e.g., coronal-cavity MFRs) or higher (e.g., hot-channel MFRs) density compared to their surroundings in the corona, the traditional opinion regards the three-part structure as the manifestations of coronal plasma pileup (high density), coronal-cavity MFR (low density), and filament (high density) contained in the trailing part of MFR, respectively. In this paper,more » we demonstrate that filament-unrelated CMEs can also exhibit the classical three-part structure. The observations were made from different perspectives through an event that occurred on 2011 October 4. The CME cavity corresponds to the low-density zone between the leading front and the high-density core, and it is obvious in the low corona and gradually becomes fuzzy when propagating outward. The bright core corresponds to a high-density structure that is suggested to be an erupting MFR. The MFR is recorded from both edge-on and face-on perspectives, exhibiting different morphologies that are due to projection effects. We stress that the zone (MFR) with lower (higher) density in comparison to the surroundings can appear as the dark cavity (bright core) when observed through white-light coronagraphs, which is not necessarily the coronal-cavity MFR (erupted filament).« less

Effects of the Absence of Apolipoprotein E on Lipoproteins, Neurocognitive Function, and Retinal Function

PubMed Central

Mak, Angel C. Y.; Pullinger, Clive R.; Tang, Ling Fung; Wong, Jinny S.; Deo, Rahul C.; Schwarz, Jean-Marc; Gugliucci, Alejandro; Movsesyan, Irina; Ishida, Brian Y.; Chu, Catherine; Poon, Annie; Kim, Phillip; Stock, Eveline O.; Schaefer, Ernst J.; Asztalos, Bela F.; Castellano, Joseph M.; Wyss-Coray, Tony; Duncan, Jacque L.; Miller, Bruce L.; Kane, John P.; Kwok, Pui-Yan; Malloy, Mary J.

2016-01-01

IMPORTANCE The identification of a patient with a rare form of severe dysbetalipoproteinemia allowed the study of the consequences of total absence of apolipoprotein E (apoE). OBJECTIVES To discover the molecular basis of this rare disorder and to determine the effects of complete absence of apoE on neurocognitive and visual function and on lipoprotein metabolism. DESIGN, SETTING, AND PARTICIPANTS Whole-exome sequencing was performed on the patient’s DNA. He underwent detailed neurological and visual function testing and lipoprotein analysis. Lipoprotein analysis was also performed in the Cardiovascular Research Institute, University of California, San Francisco, on blood samples from the proband’s mother, wife, 2 daughters, and normolipidemic control participants. MAIN OUTCOME MEASURES Whole-exome sequencing, lipoprotein analysis, and neurocognitive function. RESULTS The patient was homozygous for an ablative APOE frameshift mutation (c.291del, p.E97fs). No other mutations likely to contribute to the phenotype were discovered, with the possible exception of two, in ABCC2 (p.I670T) and LIPC (p.G137R). Despite complete absence of apoE, he had normal vision, exhibited normal cognitive, neurological, and retinal function, had normal findings on brain magnetic resonance imaging, and had normal cerebrospinal fluid levels of β-amyloid and tau proteins. He had no significant symptoms of cardiovascular disease except a suggestion of myocardial ischemia on treadmill testing and mild atherosclerosis noted on carotid ultrasonography. He had exceptionally high cholesterol content (760 mg/dL; to convert to millimoles per liter, multiply by 0.0259) and a high cholesterol to triglycerides ratio (1.52) in very low-density lipoproteins with elevated levels of small-diameter high-density lipoproteins, including high levels of prebeta-1 high-density lipoprotein. Intermediate-density lipoproteins, low-density lipoproteins, and very low-density lipoproteins contained elevated apoA-I and apoA-IV levels. The patient’s apoC-III and apoC-IV levels were decreased in very low-density lipoproteins. Electron microscopy revealed large lamellar particles having electron-opaque cores attached to electron-lucent zones in intermediate-density and low-density lipoproteins. Low-density lipoprotein particle diameters were distributed bimodally. CONCLUSIONS AND RELEVANCE Despite a profound effect on lipoprotein metabolism, detailed neurocognitive and retinal studies failed to demonstrate any defects. This suggests that functions of apoE in the brain and eye are not essential or that redundant mechanisms exist whereby its role can be fulfilled. Targeted knockdown of apoE in the central nervous system might be a therapeutic modality in neurodegenerative disorders. PMID:25111166

A Glance at Microsatellite Motifs from 454 Sequencing Reads of Watermelon Genomic DNA

USDA-ARS?s Scientific Manuscript database

A single 454 (Life Sciences Sequencing Technology) run of Charleston Gray watermelon (Citrullus lanatus var. lanatus) genomic DNA was performed and sequence data were assembled. A large scale identification of simple sequence repeat (SSR) was performed and SSR sequence data were used for the develo...

Functional renormalization group and Kohn-Sham scheme in density functional theory

NASA Astrophysics Data System (ADS)

Liang, Haozhao; Niu, Yifei; Hatsuda, Tetsuo

2018-04-01

Deriving accurate energy density functional is one of the central problems in condensed matter physics, nuclear physics, and quantum chemistry. We propose a novel method to deduce the energy density functional by combining the idea of the functional renormalization group and the Kohn-Sham scheme in density functional theory. The key idea is to solve the renormalization group flow for the effective action decomposed into the mean-field part and the correlation part. Also, we propose a simple practical method to quantify the uncertainty associated with the truncation of the correlation part. By taking the φ4 theory in zero dimension as a benchmark, we demonstrate that our method shows extremely fast convergence to the exact result even for the highly strong coupling regime.

Tracking of Indels by DEcomposition is a Simple and Effective Method to Assess Efficiency of Guide RNAs in Zebrafish.

PubMed

Etard, Christelle; Joshi, Swarnima; Stegmaier, Johannes; Mikut, Ralf; Strähle, Uwe

2017-12-01

A bottleneck in CRISPR/Cas9 genome editing is variable efficiencies of in silico-designed gRNAs. We evaluated the sensitivity of the TIDE method (Tracking of Indels by DEcomposition) introduced by Brinkman et al. in 2014 for assessing the cutting efficiencies of gRNAs in zebrafish. We show that this simple method, which involves bulk polymerase chain reaction amplification and Sanger sequencing, is highly effective in tracking well-performing gRNAs in pools of genomic DNA derived from injected embryos. The method is equally effective for tracing INDELs in heterozygotes.

Markers and mapping revisited: finding your gene.

PubMed

Jones, Neil; Ougham, Helen; Thomas, Howard; Pasakinskiene, Izolda

2009-01-01

This paper is an update of our earlier review (Jones et al., 1997, Markers and mapping: we are all geneticists now. New Phytologist 137: 165-177), which dealt with the genetics of mapping, in terms of recombination as the basis of the procedure, and covered some of the first generation of markers, including restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPDs), simple sequence repeats (SSRs) and quantitative trait loci (QTLs). In the intervening decade there have been numerous developments in marker science with many new systems becoming available, which are herein described: cleavage amplification polymorphism (CAP), sequence-specific amplification polymorphism (S-SAP), inter-simple sequence repeat (ISSR), sequence tagged site (STS), sequence characterized amplification region (SCAR), selective amplification of microsatellite polymorphic loci (SAMPL), single nucleotide polymorphism (SNP), expressed sequence tag (EST), sequence-related amplified polymorphism (SRAP), target region amplification polymorphism (TRAP), microarrays, diversity arrays technology (DArT), single-strand conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE) and methylation-sensitive PCR. In addition there has been an explosion of knowledge and databases in the area of genomics and bioinformatics. The number of flowering plant ESTs is c. 19 million and counting, with all the opportunity that this provides for gene-hunting, while the survey of bioinformatics and computer resources points to a rapid growth point for future activities in unravelling and applying the burst of new information on plant genomes. A case study is presented on tracking down a specific gene (stay-green (SGR), a post-transcriptional senescence regulator) using the full suite of mapping tools and comparative mapping resources. We end with a brief speculation on how genome analysis may progress into the future of this highly dynamic arena of plant science.

The novel primers for mammal species identification-based mitochondrial cytochrome b sequence: implication for reserved wild animals in Thailand and endangered mammal species in Southeast Asia.

PubMed

Muangkram, Yuttamol; Wajjwalku, Worawidh; Amano, Akira; Sukmak, Manakorn

2018-01-01

We presented the powerful techniques for species identification using the short amplicon of mitochondrial cytochrome b gene sequence. Two faecal samples and one single hair sample of the Asian tapir were tested using the new cytochrome b primers. The results showed a high sequence similarity with the mainland Asian tapir group. The comparative sequence analysis of the reserved wild mammals in Thailand and the other endangered mammal species from Southeast Asia comprehensibly verified the potential of our novel primers. The forward and reverse primers were 94.2 and 93.2%, respectively, by the average value of the sequence identity among 77 species sequences, and the overall mean distance was 35.9%. This development technique could provide rapid, simple, and reliable tools for species confirmation. Especially, it could recognize the problematic biological specimens contained less DNA material from illegal products and assist with wildlife crime investigation of threatened species and related forensic casework.

Merlon-type density waves in a compartmentalized conveyor system

NASA Astrophysics Data System (ADS)

Kanellopoulos, G.; van derWeele, K.

2016-09-01

Multi-particle flow through a cyclic array of K connected compartments with a preferential direction is known to be able to organize itself in the form of density waves [Kanellopoulos, Van der Meer, and Van der Weele, Phys. Rev. E 92, 022205 (2015)]. In this brief note we focus on the intriguing shape these waves take when K is even, in which case they travel through alternatingly dense and diluted compartments. We call them "merlon waves", since the sequence of high and low densities is reminiscent of the merlons and crenels on the battlements of medieval castles.

Use of microsatellite markers in management of conifer forest species

Treesearch

Craig S. Echt

1999-01-01

Within the past ten years a new class of genetic marker1 has risen to prominence as the tool of choice for many geneticists. Microsatellite DNAs, or simple sequence repeats (SSRs), were first characterized as highly informative genetic markers in humans (Weber and May, 1990; Litt and Luty, 1990), and have since been found in practically all...

A High Density Consensus Genetic Map of Tetraploid Cotton That Integrates Multiple Component Maps through Molecular Marker Redundancy Check

PubMed Central

Blenda, Anna; Fang, David D.; Rami, Jean-François; Garsmeur, Olivier; Luo, Feng; Lacape, Jean-Marc

2012-01-01

A consensus genetic map of tetraploid cotton was constructed using six high-density maps and after the integration of a sequence-based marker redundancy check. Public cotton SSR libraries (17,343 markers) were curated for sequence redundancy using 90% as a similarity cutoff. As a result, 20% of the markers (3,410) could be considered as redundant with some other markers. The marker redundancy information had been a crucial part of the map integration process, in which the six most informative interspecific Gossypium hirsutum×G. barbadense genetic maps were used for assembling a high density consensus (HDC) map for tetraploid cotton. With redundant markers being removed, the HDC map could be constructed thanks to the sufficient number of collinear non-redundant markers in common between the component maps. The HDC map consists of 8,254 loci, originating from 6,669 markers, and spans 4,070 cM, with an average of 2 loci per cM. The HDC map presents a high rate of locus duplications, as 1,292 markers among the 6,669 were mapped in more than one locus. Two thirds of the duplications are bridging homoeologous AT and DT chromosomes constitutive of allopolyploid cotton genome, with an average of 64 duplications per AT/DT chromosome pair. Sequences of 4,744 mapped markers were used for a mutual blast alignment (BBMH) with the 13 major scaffolds of the recently released Gossypium raimondii genome indicating high level of homology between the diploid D genome and the tetraploid cotton genetic map, with only a few minor possible structural rearrangements. Overall, the HDC map will serve as a valuable resource for trait QTL comparative mapping, map-based cloning of important genes, and better understanding of the genome structure and evolution of tetraploid cotton. PMID:23029214

Chemical characterization of the early evolutionary phases of high-mass star-forming regions

NASA Astrophysics Data System (ADS)

Gerner, Thomas

2014-10-01

The formation of high-mass stars is a very complex process and up to date no comprehensive theory about it exists. This thesis studies the early stages of high-mass star-forming regions and employs astrochemistry as a tool to probe their different physical conditions. We split the evolutionary sequence into four observationally motivated stages that are based on a classification proposed in the literature. The sequence is characterized by an increase of the temperatures and densities that strongly influences the chemistry in the different stages. We observed a sample of 59 high-mass star-forming regions that cover the whole sequence and statistically characterized the chemical compositions of the different stages. We determined average column densities of 18 different molecular species and found generally increasing abundances with stage. We fitted them for each stage with a 1D model, such that the result of the best fit to the previous stage was used as new input for the following. This is a unique approach and allowed us to infer physical properties like the temperature and density structure and yielded a typical chemical lifetime for the high-mass star-formation process of 1e5 years. The 18 analyzed molecular species also included four deuterated molecules whose chemistry is particularly sensitive to thermal history and thus is a promising tool to infer chemical ages. We found decreasing trends of the D/H ratios with evolutionary stage for 3 of the 4 molecular species and that the D/H ratio depends more on the fraction of warm and cold gas than on the total amount of gas. That indicates different chemical pathways for the different molecules and confirms the potential use of deuterated species as chemical age indicators. In addition, we mapped a low-mass star forming region in order to study the cosmic ray ionization rate, which is an important parameter in chemical models. While in chemical models it is commonly fixed, we found that it ! strongly varies with environment.

Fabrication of hierarchical hybrid structures using bio-enabled layer-by-layer self-assembly.

PubMed

Hnilova, Marketa; Karaca, Banu Taktak; Park, James; Jia, Carol; Wilson, Brandon R; Sarikaya, Mehmet; Tamerler, Candan

2012-05-01

Development of versatile and flexible assembly systems for fabrication of functional hybrid nanomaterials with well-defined hierarchical and spatial organization is of a significant importance in practical nanobiotechnology applications. Here we demonstrate a bio-enabled self-assembly technique for fabrication of multi-layered protein and nanometallic assemblies utilizing a modular gold-binding (AuBP1) fusion tag. To accomplish the bottom-up assembly we first genetically fused the AuBP1 peptide sequence to the C'-terminus of maltose-binding protein (MBP) using two different linkers to produce MBP-AuBP1 hetero-functional constructs. Using various spectroscopic techniques, surface plasmon resonance (SPR) and localized surface plasmon resonance (LSPR), we verified the exceptional binding and self-assembly characteristics of AuBP1 peptide. The AuBP1 peptide tag can direct the organization of recombinant MBP protein on various gold surfaces through an efficient control of the organic-inorganic interface at the molecular level. Furthermore using a combination of soft-lithography, self-assembly techniques and advanced AuBP1 peptide tag technology, we produced spatially and hierarchically controlled protein multi-layered assemblies on gold nanoparticle arrays with high molecular packing density and pattering efficiency in simple, reproducible steps. This model system offers layer-by-layer assembly capability based on specific AuBP1 peptide tag and constitutes novel biological routes for biofabrication of various protein arrays, plasmon-active nanometallic assemblies and devices with controlled organization, packing density and architecture. Copyright © 2011 Wiley Periodicals, Inc.

Compartmental analysis of [11C]flumazenil kinetics for the estimation of ligand transport rate and receptor distribution using positron emission tomography.

PubMed

Koeppe, R A; Holthoff, V A; Frey, K A; Kilbourn, M R; Kuhl, D E

1991-09-01

The in vivo kinetic behavior of [11C]flumazenil ([11C]FMZ), a non-subtype-specific central benzodiazepine antagonist, is characterized using compartmental analysis with the aim of producing an optimized data acquisition protocol and tracer kinetic model configuration for the assessment of [11C]FMZ binding to benzodiazepine receptors (BZRs) in human brain. The approach presented is simple, requiring only a single radioligand injection. Dynamic positron emission tomography data were acquired on 18 normal volunteers using a 60- to 90-min sequence of scans and were analyzed with model configurations that included a three-compartment, four-parameter model, a three-compartment, three-parameter model, with a fixed value for free plus nonspecific binding; and a two-compartment, two-parameter model. Statistical analysis indicated that a four-parameter model did not yield significantly better fits than a three-parameter model. Goodness of fit was improved for three- versus two-parameter configurations in regions with low receptor density, but not in regions with moderate to high receptor density. Thus, a two-compartment, two-parameter configuration was found to adequately describe the kinetic behavior of [11C]FMZ in human brain, with stable estimates of the model parameters obtainable from as little as 20-30 min of data. Pixel-by-pixel analysis yields functional images of transport rate (K1) and ligand distribution volume (DV"), and thus provides independent estimates of ligand delivery and BZR binding.

Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematics.

PubMed

Timmermans, M J T N; Dodsworth, S; Culverwell, C L; Bocak, L; Ahrens, D; Littlewood, D T J; Pons, J; Vogler, A P

2010-11-01

Mitochondrial genome sequences are important markers for phylogenetics but taxon sampling remains sporadic because of the great effort and cost required to acquire full-length sequences. Here, we demonstrate a simple, cost-effective way to sequence the full complement of protein coding mitochondrial genes from pooled samples using the 454/Roche platform. Multiplexing was achieved without the need for expensive indexing tags ('barcodes'). The method was trialled with a set of long-range polymerase chain reaction (PCR) fragments from 30 species of Coleoptera (beetles) sequenced in a 1/16th sector of a sequencing plate. Long contigs were produced from the pooled sequences with sequencing depths ranging from ∼10 to 100× per contig. Species identity of individual contigs was established via three 'bait' sequences matching disparate parts of the mitochondrial genome obtained by conventional PCR and Sanger sequencing. This proved that assembly of contigs from the sequencing pool was correct. Our study produced sequences for 21 nearly complete and seven partial sets of protein coding mitochondrial genes. Combined with existing sequences for 25 taxa, an improved estimate of basal relationships in Coleoptera was obtained. The procedure could be employed routinely for mitochondrial genome sequencing at the species level, to provide improved species 'barcodes' that currently use the cox1 gene only.

Normal and abnormal evolution of argon metastable density in high-density plasmas

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

Seo, B. H.; Kim, J. H., E-mail: jhkim86@kriss.re.kr; You, S. J., E-mail: sjyou@cnu.ac.kr

2015-05-15

A controversial problem on the evolution of Ar metastable density as a function of electron density (increasing trend versus decreasing trend) was resolved by discovering the anomalous evolution of the argon metastable density with increasing electron density (discharge power), including both trends of the metastable density [Daltrini et al., Appl. Phys. Lett. 92, 061504 (2008)]. Later, by virtue of an adequate physical explanation based on a simple global model, both evolutions of the metastable density were comprehensively understood as part of the abnormal evolution occurring at low- and high-density regimes, respectively, and thus the physics behind the metastable evolution hasmore » seemed to be clearly disclosed. In this study, however, a remarkable result for the metastable density behavior with increasing electron density was observed: even in the same electron density regime, there are both normal and abnormal evolutions of metastable-state density with electron density depending on the measurement position: The metastable density increases with increasing electron density at a position far from the inductively coupled plasma antenna but decreases at a position close to the antenna. The effect of electron temperature, which is spatially nonuniform in the plasma, on the electron population and depopulation processes of Argon metastable atoms with increasing electron density is a clue to understanding the results. The calculated results of the global model, including multistep ionization for the argon metastable state and measured electron temperature, are in a good agreement with the experimental results.« less

Dipeptide frequency/bias analysis identifies conserved sites of nonrandomness shared by cysteine-rich motifs.

PubMed

Campion, S R; Ameen, A S; Lai, L; King, J M; Munzenmaier, T N

2001-08-15

This report describes the application of a simple computational tool, AAPAIR.TAB, for the systematic analysis of the cysteine-rich EGF, Sushi, and Laminin motif/sequence families at the two-amino acid level. Automated dipeptide frequency/bias analysis detects preferences in the distribution of amino acids in established protein families, by determining which "ordered dipeptides" occur most frequently in comprehensive motif-specific sequence data sets. Graphic display of the dipeptide frequency/bias data revealed family-specific preferences for certain dipeptides, but more importantly detected a shared preference for employment of the ordered dipeptides Gly-Tyr (GY) and Gly-Phe (GF) in all three protein families. The dipeptide Asn-Gly (NG) also exhibited high-frequency and bias in the EGF and Sushi motif families, whereas Asn-Thr (NT) was distinguished in the Laminin family. Evaluation of the distribution of dipeptides identified by frequency/bias analysis subsequently revealed the highly restricted localization of the G(F/Y) and N(G/T) sequence elements at two separate sites of extreme conservation in the consensus sequence of all three sequence families. The similar employment of the high-frequency/bias dipeptides in three distinct protein sequence families was further correlated with the concurrence of these shared molecular determinants at similar positions within the distinctive scaffolds of three structurally divergent, but similarly employed, motif modules.

[Effect of FABP2 gene G54A polymorphism on lipid and glucose metabolism in simple obesity children].

PubMed

Xu, Yunpeng; Rao, Xiaojiao; Hao, Min; Hou, Lijuan; Zhu, Xiaobo; Chang, Xiaotong

2016-01-01

To explore the relationship between intestinal fatty acid binding protein (FABP2) gene G54A polymorphism and simple childhood obesity, the effect of mutant 54A FABP2 gene on serum lipids and glucose metabolism. The total of 83 subjects with overweight/obesity and 100 subjects with healthy/normal weight were involved in this study. The G54A FABP2 gene allele and genotype frequencies between control group and overweight/obesity group were detected using polymerase chain reaction (PCR) -restriction fragment length polymorphism (RFLP) technology, and DNA sequences were confirmed by DNA sequencing. The automatic biochemical analyzer was used to detect fasting blood glucose (FBG), triglyceride (TG), total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C) and low-density lipoprotein cholesterol (LDL-C) levels. Plasma insulin (Ins) was detected by radiation immune method, free fatty acids (FFA) was tested by ELISA method, insulin resistance index ( HOMA-IR ) was also calculated. The correlation between FABP2 G54A polymorphism and the development of children' obesity was analyzed. The relation between FABP2 G54A polymorphism and abnormal blood lipid and insulin resistance was assessed. The results of study on FABP2 gene polymorphism revealed as followed. In overweight/obese groups, the frequencies of GG, GA, AA genotypes was 33.7%, 49.4% and 16.9%, respectively. In control group, the frequencies of GG, GA, AA genotypes was 51. 0% , 40. 0% and 9. 0% , respectively. The differences between two groups was statistically significant (Χ2 = 6.27, P < 0.05). In overweight/obesity group, the frequencies of alleles were 58.4% for 54G and 41.6% for 54A. In control group, the frequencies of alleles were 71.0% for 54G and 29.0% for 54A. There was significant differences (Χ2 = 6.32, P < 0.05). The plasma biochemical variables results showed that compared with the normal control group, plasma TG (P < 0.01), Ins (P < 0.05), HOMA-IR (P < 0.05) were elevated in overweight/obesity group, the difference between two groups was statistically significant. At the same time, in overweight/obesity group, the carriers of AA homozygous genotypes had significantly higher plasma TG levels than those with GG wild genotypes (P < 0.05). A increased tendency of plasma Ins, FFA levels and HOMA-IR was found in the carriers with AA homozygous genotypes, but no differences compared with those with GG wild genotypes. Compared with those with GG wild genotypes, related plasma biochemical variables in the carriers with GA heterozygous genotypes had no differences (P > 0.05). The FABP2 gene G54A polymorphism is related to simple children obesity and lipid metabolism abnormality. The allele encoding in FABP2 gene may be a potential factor contributing to promoting lipid metabolism abnormality of and insulin resistance.

Recombination rate and the distribution of transposable elements in the Drosophila melanogaster genome.

PubMed

Rizzon, Carène; Marais, Gabriel; Gouy, Manolo; Biémont, Christian

2002-03-01

We analyzed the distribution of 54 families of transposable elements (TEs; transposons, LTR retrotransposons, and non-LTR retrotransposons) in the chromosomes of Drosophila melanogaster, using data from the sequenced genome. The density of LTR and non-LTR retrotransposons (RNA-based elements) was high in regions with low recombination rates, but there was no clear tendency to parallel the recombination rate. However, the density of transposons (DNA-based elements) was significantly negatively correlated with recombination rate. The accumulation of TEs in regions of reduced recombination rate is compatible with selection acting against TEs, as selection is expected to be weaker in regions with lower recombination. The differences in the relationship between recombination rate and TE density that exist between chromosome arms suggest that TE distribution depends on specific characteristics of the chromosomes (chromatin structure, distribution of other sequences), the TEs themselves (transposition mechanism), and the species (reproductive system, effective population size, etc.), that have differing influences on the effect of natural selection acting against the TE insertions.

High-pressure structural study of MnF 2

DOE PAGES

Stavrou, Elissaios; Yao, Yansun; Goncharov, Alexander F.; ...

2015-02-01

In this study, manganese fluoride (MnF 2) with the tetragonal rutile-type structure has been studied using a synchrotron angle-dispersive powder x-ray diffraction and Raman spectroscopy in a diamond anvil cell up to 60 GPa at room temperature combined with first-principles density functional calculations. The experimental data reveal two pressure-induced structural phase transitions with the following sequence: rutile → SrI 2 type (3 GPa)→ α–PbCl 2 type (13 GPa). Complete structural information, including interatomic distances, has been determined in the case of MnF 2 including the exact structure of the debated first high-pressure phase. First-principles density functional calculations confirm this phasemore » transition sequence, and the two calculated transition pressures are in excellent agreement with the experiment. Lattice dynamics calculations also reproduce the experimental Raman spectra measured for the ambient and high-pressure phases. The results are discussed in line with the possible practical use of rutile-type fluorides in general and specifically MnF 2 as a model compound to reveal the HP structural behavior of rutile-type SiO 2 (Stishovite).« less

Data encoding based on the shape of the ferroelectric domains produced by a scanning probe microscopy tip

DOE PAGES

Ievlev, Anton; Kalinin, Sergei V.

2015-05-28

Ferroelectric materials are broadly considered for information storage due to extremely high storage and information processing densities they enable. To date, ferroelectric based data storage has invariably relied on formation of cylindrical domains, allowing for binary information encoding. Here we demonstrate and explore the potential of high-density encoding based on domain morphology. We explore the domain morphogenesis during the tip-induced polarization switching by sequences of positive and negative pulses in a lithium niobate single-crystal and demonstrate the principal of information coding by shape and size of the domains. We applied cross-correlation and neural network approaches for recognition of the switchingmore » sequence by the shape of the resulting domains and establish optimal parameters for domain shape recognition. These studies both provide insight into the highly non-trivial mechanism of domain switching and potentially establish a new paradigm for multilevel information storage and content retrieval memories. Furthermore, this approach opens a pathway to exploration of domain switching mechanisms via shape analysis.« less

An Optimal Bahadur-Efficient Method in Detection of Sparse Signals with Applications to Pathway Analysis in Sequencing Association Studies.

PubMed

Dai, Hongying; Wu, Guodong; Wu, Michael; Zhi, Degui

2016-01-01

Next-generation sequencing data pose a severe curse of dimensionality, complicating traditional "single marker-single trait" analysis. We propose a two-stage combined p-value method for pathway analysis. The first stage is at the gene level, where we integrate effects within a gene using the Sequence Kernel Association Test (SKAT). The second stage is at the pathway level, where we perform a correlated Lancaster procedure to detect joint effects from multiple genes within a pathway. We show that the Lancaster procedure is optimal in Bahadur efficiency among all combined p-value methods. The Bahadur efficiency,[Formula: see text], compares sample sizes among different statistical tests when signals become sparse in sequencing data, i.e. ε →0. The optimal Bahadur efficiency ensures that the Lancaster procedure asymptotically requires a minimal sample size to detect sparse signals ([Formula: see text]). The Lancaster procedure can also be applied to meta-analysis. Extensive empirical assessments of exome sequencing data show that the proposed method outperforms Gene Set Enrichment Analysis (GSEA). We applied the competitive Lancaster procedure to meta-analysis data generated by the Global Lipids Genetics Consortium to identify pathways significantly associated with high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, triglycerides, and total cholesterol.

Genetic fidelity and variability of micropropagated cassava plants (Manihot esculenta Crantz) evaluated using ISSR markers.

PubMed

Vidal, Á M; Vieira, L J; Ferreira, C F; Souza, F V D; Souza, A S; Ledo, C A S

2015-07-14

Molecular markers are efficient for assessing the genetic fidelity of various species of plants after in vitro culture. In this study, we evaluated the genetic fidelity and variability of micropropagated cassava plants (Manihot esculenta Crantz) using inter-simple sequence repeat markers. Twenty-two cassava accessions from the Embrapa Cassava & Fruits Germplasm Bank were used. For each accession, DNA was extracted from a plant maintained in the field and from 3 plants grown in vitro. For DNA amplification, 27 inter-simple sequence repeat primers were used, of which 24 generated 175 bands; 100 of those bands were polymorphic and were used to study genetic variability among accessions of cassava plants maintained in the field. Based on the genetic distance matrix calculated using the arithmetic complement of the Jaccard's index, genotypes were clustered using the unweighted pair group method using arithmetic averages. The number of bands per primer was 2-13, with an average of 7.3. For most micropropagated accessions, the fidelity study showed no genetic variation between plants of the same accessions maintained in the field and those maintained in vitro, confirming the high genetic fidelity of the micropropagated plants. However, genetic variability was observed among different accessions grown in the field, and clustering based on the dissimilarity matrix revealed 7 groups. Inter-simple sequence repeat markers were efficient for detecting the genetic homogeneity of cassava plants derived from meristem culture, demonstrating the reliability of this propagation system.

An information maximization model of eye movements

NASA Technical Reports Server (NTRS)

Renninger, Laura Walker; Coughlan, James; Verghese, Preeti; Malik, Jitendra

2005-01-01

We propose a sequential information maximization model as a general strategy for programming eye movements. The model reconstructs high-resolution visual information from a sequence of fixations, taking into account the fall-off in resolution from the fovea to the periphery. From this framework we get a simple rule for predicting fixation sequences: after each fixation, fixate next at the location that minimizes uncertainty (maximizes information) about the stimulus. By comparing our model performance to human eye movement data and to predictions from a saliency and random model, we demonstrate that our model is best at predicting fixation locations. Modeling additional biological constraints will improve the prediction of fixation sequences. Our results suggest that information maximization is a useful principle for programming eye movements.

Nucleation of ordered solid phases of proteins via a disordered high-density state: Phenomenological approach

NASA Astrophysics Data System (ADS)

Pan, Weichun; Kolomeisky, Anatoly B.; Vekilov, Peter G.

2005-05-01

Nucleation of ordered solid phases of proteins triggers numerous phenomena in laboratory, industry, and in healthy and sick organisms. Recent simulations and experiments with protein crystals suggest that the formation of an ordered crystalline nucleus is preceded by a disordered high-density cluster, akin to a droplet of high-density liquid that has been observed with some proteins; this mechanism allowed a qualitative explanation of recorded complex nucleation kinetics curves. Here, we present a simple phenomenological theory that takes into account intermediate high-density metastable states in the nucleation process. Nucleation rate data at varying temperature and protein concentration are reproduced with high fidelity using literature values of the thermodynamic and kinetic parameters of the system. Our calculations show that the growth rate of the near-critical and supercritical ordered clusters within the dense intermediate is a major factor for the overall nucleation rate. This highlights the role of viscosity within the dense intermediate for the formation of the ordered nucleus. The model provides an understanding of the action of additives that delay or accelerate nucleation and presents a framework within which the nucleation of other ordered protein solid phases, e.g., the sickle cell hemoglobin polymers, can be analyzed.

Solvent evaporation induced graphene powder with high volumetric capacitance and outstanding rate capability for supercapacitors

NASA Astrophysics Data System (ADS)

Zhang, Xiaozhe; Raj, Devaraj Vasanth; Zhou, Xufeng; Liu, Zhaoping

2018-04-01

Graphene-based electrode materials for supercapacitors usually suffer from poor volumetric performance due to the low density. The enhancement of volumetric capacitance by densification of graphene materials, however, is usually accompanied by deterioration of rate capability, as the huge contraction of pore size hinders rapid diffusion of electrolytes. Thus, it is important to develop suitable pore size in graphene materials, which can sustain fast ion diffusion and avoid excessive voids to acquire high density simultaneously for supercapacitor applications. Accordingly, we propose a simple solvent evaporation method to control the pore size of graphene powders by adjusting the surface tension of solvents. Ethanol is used instead of water to reduce the shrinkage degree of graphene powder during solvent evaporation process, due to its lower surface tension comparing with water. Followed by the assistance of mechanical compression, graphene powder having high compaction density of 1.30 g cm-3 and a large proportion of mesopores in the pore size range of 2-30 nm is obtained, which delivers high volumetric capacitance of 162 F cm-3 and exhibits outstanding rate performance of 76% capacity retention at a high current density of 100 A g-1 simultaneously.

miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments.

PubMed

Hackenberg, Michael; Sturm, Martin; Langenberger, David; Falcón-Pérez, Juan Manuel; Aransay, Ana M

2009-07-01

Next-generation sequencing allows now the sequencing of small RNA molecules and the estimation of their expression levels. Consequently, there will be a high demand of bioinformatics tools to cope with the several gigabytes of sequence data generated in each single deep-sequencing experiment. Given this scene, we developed miRanalyzer, a web server tool for the analysis of deep-sequencing experiments for small RNAs. The web server tool requires a simple input file containing a list of unique reads and its copy numbers (expression levels). Using these data, miRanalyzer (i) detects all known microRNA sequences annotated in miRBase, (ii) finds all perfect matches against other libraries of transcribed sequences and (iii) predicts new microRNAs. The prediction of new microRNAs is an especially important point as there are many species with very few known microRNAs. Therefore, we implemented a highly accurate machine learning algorithm for the prediction of new microRNAs that reaches AUC values of 97.9% and recall values of up to 75% on unseen data. The web tool summarizes all the described steps in a single output page, which provides a comprehensive overview of the analysis, adding links to more detailed output pages for each analysis module. miRanalyzer is available at http://web.bioinformatics.cicbiogune.es/microRNA/.

Probing the solar corona with very long baseline interferometry.

PubMed

Soja, B; Heinkelmann, R; Schuh, H

2014-06-20

Understanding and monitoring the solar corona and solar wind is important for many applications like telecommunications or geomagnetic studies. Coronal electron density models have been derived by various techniques over the last 45 years, principally by analysing the effect of the corona on spacecraft tracking. Here we show that recent observational data from very long baseline interferometry (VLBI), a radio technique crucial for astrophysics and geodesy, could be used to develop electron density models of the Sun's corona. The VLBI results agree well with previous models from spacecraft measurements. They also show that the simple spherical electron density model is violated by regional density variations and that on average the electron density in active regions is about three times that of low-density regions. Unlike spacecraft tracking, a VLBI campaign would be possible on a regular basis and would provide highly resolved spatial-temporal samplings over a complete solar cycle.

Quantitative characterization of conformational-specific protein-DNA binding using a dual-spectral interferometric imaging biosensor

NASA Astrophysics Data System (ADS)

Zhang, Xirui; Daaboul, George G.; Spuhler, Philipp S.; Dröge, Peter; Ünlü, M. Selim

2016-03-01

DNA-binding proteins play crucial roles in the maintenance and functions of the genome and yet, their specific binding mechanisms are not fully understood. Recently, it was discovered that DNA-binding proteins recognize specific binding sites to carry out their functions through an indirect readout mechanism by recognizing and capturing DNA conformational flexibility and deformation. High-throughput DNA microarray-based methods that provide large-scale protein-DNA binding information have shown effective and comprehensive analysis of protein-DNA binding affinities, but do not provide information of DNA conformational changes in specific protein-DNA complexes. Building on the high-throughput capability of DNA microarrays, we demonstrate a quantitative approach that simultaneously measures the amount of protein binding to DNA and nanometer-scale DNA conformational change induced by protein binding in a microarray format. Both measurements rely on spectral interferometry on a layered substrate using a single optical instrument in two distinct modalities. In the first modality, we quantitate the amount of binding of protein to surface-immobilized DNA in each DNA spot using a label-free spectral reflectivity technique that accurately measures the surface densities of protein and DNA accumulated on the substrate. In the second modality, for each DNA spot, we simultaneously measure DNA conformational change using a fluorescence vertical sectioning technique that determines average axial height of fluorophores tagged to specific nucleotides of the surface-immobilized DNA. The approach presented in this paper, when combined with current high-throughput DNA microarray-based technologies, has the potential to serve as a rapid and simple method for quantitative and large-scale characterization of conformational specific protein-DNA interactions.DNA-binding proteins play crucial roles in the maintenance and functions of the genome and yet, their specific binding mechanisms are not fully understood. Recently, it was discovered that DNA-binding proteins recognize specific binding sites to carry out their functions through an indirect readout mechanism by recognizing and capturing DNA conformational flexibility and deformation. High-throughput DNA microarray-based methods that provide large-scale protein-DNA binding information have shown effective and comprehensive analysis of protein-DNA binding affinities, but do not provide information of DNA conformational changes in specific protein-DNA complexes. Building on the high-throughput capability of DNA microarrays, we demonstrate a quantitative approach that simultaneously measures the amount of protein binding to DNA and nanometer-scale DNA conformational change induced by protein binding in a microarray format. Both measurements rely on spectral interferometry on a layered substrate using a single optical instrument in two distinct modalities. In the first modality, we quantitate the amount of binding of protein to surface-immobilized DNA in each DNA spot using a label-free spectral reflectivity technique that accurately measures the surface densities of protein and DNA accumulated on the substrate. In the second modality, for each DNA spot, we simultaneously measure DNA conformational change using a fluorescence vertical sectioning technique that determines average axial height of fluorophores tagged to specific nucleotides of the surface-immobilized DNA. The approach presented in this paper, when combined with current high-throughput DNA microarray-based technologies, has the potential to serve as a rapid and simple method for quantitative and large-scale characterization of conformational specific protein-DNA interactions. Electronic supplementary information (ESI) available: DNA sequences and nomenclature (Table 1S); SDS-PAGE assay of IHF stock solution (Fig. 1S); determination of the concentration of IHF stock solution by Bradford assay (Fig. 2S); equilibrium binding isotherm fitting results of other DNA sequences (Table 2S); calculation of dissociation constants (Fig. 3S, 4S; Table 2S); geometric model for quantitation of DNA bending angle induced by specific IHF binding (Fig. 4S); customized flow cell assembly (Fig. 5S); real-time measurement of average fluorophore height change by SSFM (Fig. 6S); summary of binding parameters obtained from additive isotherm model fitting (Table 3S); average surface densities of 10 dsDNA spots and bound IHF at equilibrium (Table 4S); effects of surface densities on the binding and bending of dsDNA (Tables 5S, 6S and Fig. 7S-10S). See DOI: 10.1039/c5nr06785e

High-Density Amorphous Ice, the Frost on Interstellar Grains

NASA Technical Reports Server (NTRS)

Jenniskens, P.; Blake, D. F.; Wilson, M. A.; Pohorille, A.

1995-01-01

Most water ice in the universe is in a form which does not occur naturally on Earth and of which only minimal amounts have been made in the laboratory. We have encountered this 'high-density amorphous ice' in electron diffraction experiments of low-temperature (T less than 30 K) vapor-deposited water and have subsequently modeled its structure using molecular dynamics simulations. The characteristic feature of high-density amorphous ice is the presence of 'interstitial' oxygen pair distances between 3 and 4 A. However, we find that the structure is best described as a collapsed lattice of the more familiar low-density amorphous form. These distortions are frozen in at temperatures below 38 K because, we propose, it requires the breaking of one hydrogen bond, on average, per molecule to relieve the strain and to restructure the lattice to that of low-density amorphous ice. Several features of astrophysical ice analogs studied in laboratory experiments are readily explained by the structural transition from high-density amorphous ice into low-density amorphous ice. Changes in the shape of the 3.07 gm water band, trapping efficiency of CO, CO loss, changes in the CO band structure, and the recombination of radicals induced by low-temperature UV photolysis all covary with structural changes that occur in the ice during this amorphous to amorphous transition. While the 3.07 micrometers ice band in various astronomical environments can be modeled with spectra of simple mixtures of amorphous and crystalline forms, the contribution of the high-density amorphous form nearly always dominates.

High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis.

PubMed

Simonyan, Vahan; Mazumder, Raja

2014-09-30

The High-performance Integrated Virtual Environment (HIVE) is a high-throughput cloud-based infrastructure developed for the storage and analysis of genomic and associated biological data. HIVE consists of a web-accessible interface for authorized users to deposit, retrieve, share, annotate, compute and visualize Next-generation Sequencing (NGS) data in a scalable and highly efficient fashion. The platform contains a distributed storage library and a distributed computational powerhouse linked seamlessly. Resources available through the interface include algorithms, tools and applications developed exclusively for the HIVE platform, as well as commonly used external tools adapted to operate within the parallel architecture of the system. HIVE is composed of a flexible infrastructure, which allows for simple implementation of new algorithms and tools. Currently, available HIVE tools include sequence alignment and nucleotide variation profiling tools, metagenomic analyzers, phylogenetic tree-building tools using NGS data, clone discovery algorithms, and recombination analysis algorithms. In addition to tools, HIVE also provides knowledgebases that can be used in conjunction with the tools for NGS sequence and metadata analysis.

High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis

PubMed Central

Simonyan, Vahan; Mazumder, Raja

2014-01-01

The High-performance Integrated Virtual Environment (HIVE) is a high-throughput cloud-based infrastructure developed for the storage and analysis of genomic and associated biological data. HIVE consists of a web-accessible interface for authorized users to deposit, retrieve, share, annotate, compute and visualize Next-generation Sequencing (NGS) data in a scalable and highly efficient fashion. The platform contains a distributed storage library and a distributed computational powerhouse linked seamlessly. Resources available through the interface include algorithms, tools and applications developed exclusively for the HIVE platform, as well as commonly used external tools adapted to operate within the parallel architecture of the system. HIVE is composed of a flexible infrastructure, which allows for simple implementation of new algorithms and tools. Currently, available HIVE tools include sequence alignment and nucleotide variation profiling tools, metagenomic analyzers, phylogenetic tree-building tools using NGS data, clone discovery algorithms, and recombination analysis algorithms. In addition to tools, HIVE also provides knowledgebases that can be used in conjunction with the tools for NGS sequence and metadata analysis. PMID:25271953

Directly measuring of thermal pulse transfer in one-dimensional highly aligned carbon nanotubes

PubMed Central

Zhang, Guang; Liu, Changhong; Fan, Shoushan

2013-01-01

Using a simple and precise instrument system, we directly measured the thermo-physical properties of one-dimensional highly aligned carbon nanotubes (CNTs). A kind of CNT-based macroscopic materials named super aligned carbon nanotube (SACNT) buckypapers was measured in our experiment. We defined a new one-dimensional parameter, the “thermal transfer speed” to characterize the thermal damping mechanisms in the SACNT buckypapers. Our results indicated that the SACNT buckypapers with different densities have obviously different thermal transfer speeds. Furthermore, we found that the thermal transfer speed of high-density SACNT buckypapers may have an obvious damping factor along the CNTs aligned direction. The anisotropic thermal diffusivities of SACNT buckypapers could be calculated by the thermal transfer speeds. The thermal diffusivities obviously increase as the buckypaper-density increases. For parallel SACNT buckypapers, the thermal diffusivity could be as high as 562.2 ± 55.4 mm2/s. The thermal conductivities of these SACNT buckypapers were also calculated by the equation k = Cpαρ. PMID:23989589

Directly measuring of thermal pulse transfer in one-dimensional highly aligned carbon nanotubes.

PubMed

Zhang, Guang; Liu, Changhong; Fan, Shoushan

2013-01-01

Using a simple and precise instrument system, we directly measured the thermo-physical properties of one-dimensional highly aligned carbon nanotubes (CNTs). A kind of CNT-based macroscopic materials named super aligned carbon nanotube (SACNT) buckypapers was measured in our experiment. We defined a new one-dimensional parameter, the "thermal transfer speed" to characterize the thermal damping mechanisms in the SACNT buckypapers. Our results indicated that the SACNT buckypapers with different densities have obviously different thermal transfer speeds. Furthermore, we found that the thermal transfer speed of high-density SACNT buckypapers may have an obvious damping factor along the CNTs aligned direction. The anisotropic thermal diffusivities of SACNT buckypapers could be calculated by the thermal transfer speeds. The thermal diffusivities obviously increase as the buckypaper-density increases. For parallel SACNT buckypapers, the thermal diffusivity could be as high as 562.2 ± 55.4 mm(2)/s. The thermal conductivities of these SACNT buckypapers were also calculated by the equation k = Cpαρ.

Analysis of genetic diversity and population structure of oil palm (Elaeis guineensis) from China and Malaysia based on species-specific simple sequence repeat markers.

PubMed

Zhou, L X; Xiao, Y; Xia, W; Yang, Y D

2015-12-08

Genetic diversity and patterns of population structure of the 94 oil palm lines were investigated using species-specific simple sequence repeat (SSR) markers. We designed primers for 63 SSR loci based on their flanking sequences and conducted amplification in 94 oil palm DNA samples. The amplification result showed that a relatively high level of genetic diversity was observed between oil palm individuals according a set of 21 polymorphic microsatellite loci. The observed heterozygosity (Ho) was 0.3683 and 0.4035, with an average of 0.3859. The Ho value was a reliable determinant of the discriminatory power of the SSR primer combinations. The principal component analysis and unweighted pair-group method with arithmetic averaging cluster analysis showed the 94 oil palm lines were grouped into one cluster. These results demonstrated that the oil palm in Hainan Province of China and the germplasm introduced from Malaysia may be from the same source. The SSR protocol was effective and reliable for assessing the genetic diversity of oil palm. Knowledge of the genetic diversity and population structure will be crucial for establishing appropriate management stocks for this species.

Decoding DNA labels by melting curve analysis using real-time PCR.

PubMed

Balog, József A; Fehér, Liliána Z; Puskás, László G

2017-12-01

Synthetic DNA has been used as an authentication code for a diverse number of applications. However, existing decoding approaches are based on either DNA sequencing or the determination of DNA length variations. Here, we present a simple alternative protocol for labeling different objects using a small number of short DNA sequences that differ in their melting points. Code amplification and decoding can be done in two steps using quantitative PCR (qPCR). To obtain a DNA barcode with high complexity, we defined 8 template groups, each having 4 different DNA templates, yielding 158 (>2.5 billion) combinations of different individual melting temperature (Tm) values and corresponding ID codes. The reproducibility and specificity of the decoding was confirmed by using the most complex template mixture, which had 32 different products in 8 groups with different Tm values. The industrial applicability of our protocol was also demonstrated by labeling a drone with an oil-based paint containing a predefined DNA code, which was then successfully decoded. The method presented here consists of a simple code system based on a small number of synthetic DNA sequences and a cost-effective, rapid decoding protocol using a few qPCR reactions, enabling a wide range of authentication applications.

Free-standing porous manganese dioxide/graphene composite films for high performance supercapacitors.

PubMed

Guo, Wang-Huan; Liu, Teng-Jiao; Jiang, Peng; Zhang, Zhan-Jun

2015-01-01

A simple hard template method and hydrothermal process have been employed to fabricate a self-standing hierarchical porous MnO2/graphene film. Thus-constructed electrode materials for binder-free supercapacitors exhibit a high specific capacitance of 266.3 F g(-1) at the density of 0.2 A g(-1). Moreover, the two-electrode device demonstrates an excellent rate capability and cycling stability with capacitance retention of 85.1% after 2000 charge-discharge cycles at a current density of 1 A g(-1). The porous nanostructured design can effectively improve the specific surface areas and account for the shorter relaxation time for the electrodes, resulting in a high electrochemical performance. Copyright © 2014 Elsevier Inc. All rights reserved.

Human Mitochondrial DNA and Endogenous Bacterial Surrogates for Risk Assessment of Graywater Reuse

EPA Science Inventory

Previous graywater risk assessment studies have focused on fecal contamination, yet the low density of fecal indicators may not provide the most useful approach to assess pathogen removal during graywater treatment. In this study, we employed high throughput bacterial sequencing ...

High-Density Liquid-State Machine Circuitry for Time-Series Forecasting.

PubMed

Rosselló, Josep L; Alomar, Miquel L; Morro, Antoni; Oliver, Antoni; Canals, Vincent

2016-08-01

Spiking neural networks (SNN) are the last neural network generation that try to mimic the real behavior of biological neurons. Although most research in this area is done through software applications, it is in hardware implementations in which the intrinsic parallelism of these computing systems are more efficiently exploited. Liquid state machines (LSM) have arisen as a strategic technique to implement recurrent designs of SNN with a simple learning methodology. In this work, we show a new low-cost methodology to implement high-density LSM by using Boolean gates. The proposed method is based on the use of probabilistic computing concepts to reduce hardware requirements, thus considerably increasing the neuron count per chip. The result is a highly functional system that is applied to high-speed time series forecasting.

SU-E-T-404: Evaluation of the Effect of Spine Hardware for CyberKnife Spinal Stereotactic Radiosurgery

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

Yuan, J; Zhang, Y; Zheng, Y

2015-06-15

Purpose: Spine hardware made of high-Z materials such as titanium has the potential to affect the dose distribution around the metal rods in CyberKnife spinal stereotactic radiosurgery (SRS) treatments. The purpose of this work was to evaluate the magnitude of such effect retrospectively for clinical CyberKnife plans. Methods: The dose calculation was performed within the MultiPlan treatment planning system using the ray tracing (RT) and Monte Carlo (MC) method. A custom density model was created by extending the CT-to-Density table to titanium density of 4.5 g/cm3 with the CT number of 4095. To understand the dose perturbation caused by themore » titanium rod, a simple beam setup (7.5 mm IRIS collimator) was used to irradiate a mimic rod (5 mm) with overridden high density. Five patient spinal SRS cases were found chronologically from 2010 to 2015 in our institution. For each case, the hardware was contoured manually. The original plan was re-calculated using both RT and MC methods with and without rod density override without changing clinical beam parameters. Results: The simple beam irradiation shows that there is 10% dose increase at the interface because of electron backscattering and 7% decrease behind the rod because of photon attenuation. For actual clinical plans, the iso-dose lines and DVHs are almost identical (<2%) for calculations with and without density override for both RT and MC methods. However, there is a difference of more than 10% for D90 between RT and MC method. Conclusion: Although the dose perturbation around the metal rods can be as large as 10% for a single beam irradiation, for clinical treatments with complex beam composition the effect of spinal hardware to the PTV and spinal dose is minimal. As such, the MC dose algorithm without rod density override for CyberKnife spinal SRS is acceptable.« less

Correlations in the three-dimensional Lyman-alpha forest contaminated by high column density absorbers

NASA Astrophysics Data System (ADS)

Rogers, Keir K.; Bird, Simeon; Peiris, Hiranya V.; Pontzen, Andrew; Font-Ribera, Andreu; Leistedt, Boris

2018-05-01

Correlations measured in three dimensions in the Lyman-alpha forest are contaminated by the presence of the damping wings of high column density (HCD) absorbing systems of neutral hydrogen (H I; having column densities N(H I) > 1.6 × 10^{17} atoms cm^{-2}), which extend significantly beyond the redshift-space location of the absorber. We measure this effect as a function of the column density of the HCD absorbers and redshift by measuring three-dimensional (3D) flux power spectra in cosmological hydrodynamical simulations from the Illustris project. Survey pipelines exclude regions containing the largest damping wings. We find that, even after this procedure, there is a scale-dependent correction to the 3D Lyman-alpha forest flux power spectrum from residual contamination. We model this residual using a simple physical model of the HCD absorbers as linearly biased tracers of the matter density distribution, convolved with their Voigt profiles and integrated over the column density distribution function. We recommend the use of this model over existing models used in data analysis, which approximate the damping wings as top-hats and so miss shape information in the extended wings. The simple `linear Voigt model' is statistically consistent with our simulation results for a mock residual contamination up to small scales (|k| < 1 h Mpc^{-1}). It does not account for the effect of the highest column density absorbers on the smallest scales (e.g. |k| > 0.4 h Mpc^{-1} for small damped Lyman-alpha absorbers; HCD absorbers with N(H I) ˜ 10^{21} atoms cm^{-2}). However, these systems are in any case preferentially removed from survey data. Our model is appropriate for an accurate analysis of the baryon acoustic oscillations feature. It is additionally essential for reconstructing the full shape of the 3D flux power spectrum.

Toward CMOS image sensor based glucose monitoring.

PubMed

Devadhasan, Jasmine Pramila; Kim, Sanghyo

2012-09-07

Complementary metal oxide semiconductor (CMOS) image sensor is a powerful tool for biosensing applications. In this present study, CMOS image sensor has been exploited for detecting glucose levels by simple photon count variation with high sensitivity. Various concentrations of glucose (100 mg dL(-1) to 1000 mg dL(-1)) were added onto a simple poly-dimethylsiloxane (PDMS) chip and the oxidation of glucose was catalyzed with the aid of an enzymatic reaction. Oxidized glucose produces a brown color with the help of chromogen during enzymatic reaction and the color density varies with the glucose concentration. Photons pass through the PDMS chip with varying color density and hit the sensor surface. Photon count was recognized by CMOS image sensor depending on the color density with respect to the glucose concentration and it was converted into digital form. By correlating the obtained digital results with glucose concentration it is possible to measure a wide range of blood glucose levels with great linearity based on CMOS image sensor and therefore this technique will promote a convenient point-of-care diagnosis.

Simple Model of Macroscopic Instability in XeCl Discharge Pumped Lasers

NASA Astrophysics Data System (ADS)

Ahmed, Belasri; Zoheir, Harrache

2003-10-01

The aim of this work is to study the development of the macroscopic non uniformity of the electron density of high pressure discharge for excimer lasers and eventually its propagation because of the medium kinetics phenomena. This study is executed using a transverse mono-dimensional model, in which the plasma is represented by a set of resistance's in parallel. This model was employed using a numerical code including three strongly coupled parts: electric circuit equations, electron Boltzmann equation, and kinetics equations (chemical kinetics model). The time variations of the electron density in each plasma element are obtained by solving a set of ordinary differential equations describing the plasma kinetics and external circuit. The use of the present model allows a good comprehension of the halogen depletion phenomena, which is the principal cause of laser ending and allows a simple study of a large-scale non uniformity in preionization density and its effects on electrical and chemical plasma properties. The obtained results indicate clearly that about 50consumed at the end of the pulse. KEY WORDS Excimer laser, XeCl, Modeling, Cold plasma, Kinetic, Halogen depletion, Macroscopic instability.

Electrical enhancement of direct methanol fuel cells by metal-plasma ion implantation Pt-Ru/C multilayer catalysts.

PubMed

Weng, Ko-Wei; Chen, Yung-Lin; Chen, Ya-Chi; Lin, Tai-Nan

2009-02-01

Direct methanol fuel cells (DMFC) have been widely studied owing to their simple cell configuration, high volume energy density, short start-up time, high operational reliability and other favorable characteristics. However, major limitations include high production cost, poisoning of the catalyst and methanol crossover. This study adopts a simple technique for preparing Pt-Ru/C multilayer catalysts, including magnetron sputtering (MS) and metal-plasma ion implantation (MPII). The Pt catalysts were sputtered onto the gas diffusion layer (GDL), followed by the implantation of Ru catalysts using MPII (at an accelerating voltage of 20 kV and an implantation dose of 1 x 10(16) ions/cm2). Pt-Ru is repeatedly processed to prepare Pt-Ru/C multilayer catalysts. The catalyst film structure and microstructure were analyzed by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS) and scanning electronic microscopy (SEM), respectively. The cell performance was tested using a potential stat/galvano-stat. The results reveal that the membrane electrode assembly (MEA) of four multilayer structures enhances the cell performance of DMFC. The measured power density is 2.2 mW/cm2 at a methanol concentration of 2 M, with an OCV of 0.493 V.

A simple mass-conserved level set method for simulation of multiphase flows

NASA Astrophysics Data System (ADS)

Yuan, H.-Z.; Shu, C.; Wang, Y.; Shu, S.

2018-04-01

In this paper, a modified level set method is proposed for simulation of multiphase flows with large density ratio and high Reynolds number. The present method simply introduces a source or sink term into the level set equation to compensate the mass loss or offset the mass increase. The source or sink term is derived analytically by applying the mass conservation principle with the level set equation and the continuity equation of flow field. Since only a source term is introduced, the application of the present method is as simple as the original level set method, but it can guarantee the overall mass conservation. To validate the present method, the vortex flow problem is first considered. The simulation results are compared with those from the original level set method, which demonstrates that the modified level set method has the capability of accurately capturing the interface and keeping the mass conservation. Then, the proposed method is further validated by simulating the Laplace law, the merging of two bubbles, a bubble rising with high density ratio, and Rayleigh-Taylor instability with high Reynolds number. Numerical results show that the mass is a well-conserved by the present method.

Bayesian Analysis of Evolutionary Divergence with Genomic Data under Diverse Demographic Models.

PubMed

Chung, Yujin; Hey, Jody

2017-06-01

We present a new Bayesian method for estimating demographic and phylogenetic history using population genomic data. Several key innovations are introduced that allow the study of diverse models within an Isolation-with-Migration framework. The new method implements a 2-step analysis, with an initial Markov chain Monte Carlo (MCMC) phase that samples simple coalescent trees, followed by the calculation of the joint posterior density for the parameters of a demographic model. In step 1, the MCMC sampling phase, the method uses a reduced state space, consisting of coalescent trees without migration paths, and a simple importance sampling distribution without the demography of interest. Once obtained, a single sample of trees can be used in step 2 to calculate the joint posterior density for model parameters under multiple diverse demographic models, without having to repeat MCMC runs. Because migration paths are not included in the state space of the MCMC phase, but rather are handled by analytic integration in step 2 of the analysis, the method is scalable to a large number of loci with excellent MCMC mixing properties. With an implementation of the new method in the computer program MIST, we demonstrate the method's accuracy, scalability, and other advantages using simulated data and DNA sequences of two common chimpanzee subspecies: Pan troglodytes (P. t.) troglodytes and P. t. verus. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

A classical density functional theory of ionic liquids.

PubMed

Forsman, Jan; Woodward, Clifford E; Trulsson, Martin

2011-04-28

We present a simple, classical density functional approach to the study of simple models of room temperature ionic liquids. Dispersion attractions as well as ion correlation effects and excluded volume packing are taken into account. The oligomeric structure, common to many ionic liquid molecules, is handled by a polymer density functional treatment. The theory is evaluated by comparisons with simulations, with an emphasis on the differential capacitance, an experimentally measurable quantity of significant practical interest.

Optical properties and electronic transitions of DNA oligonucleotides as a function of composition and stacking sequence.

PubMed

Schimelman, Jacob B; Dryden, Daniel M; Poudel, Lokendra; Krawiec, Katherine E; Ma, Yingfang; Podgornik, Rudolf; Parsegian, V Adrian; Denoyer, Linda K; Ching, Wai-Yim; Steinmetz, Nicole F; French, Roger H

2015-02-14

The role of base pair composition and stacking sequence in the optical properties and electronic transitions of DNA is of fundamental interest. We present and compare the optical properties of DNA oligonucleotides (AT)10, (AT)5(GC)5, and (AT-GC)5 using both ab initio methods and UV-vis molar absorbance measurements. Our data indicate a strong dependence of both the position and intensity of UV absorbance features on oligonucleotide composition and stacking sequence. The partial densities of states for each oligonucleotide indicate that the valence band edge arises from a feature associated with the PO4(3-) complex anion, and the conduction band edge arises from anti-bonding states in DNA base pairs. The results show a strong correspondence between the ab initio and experimentally determined optical properties. These results highlight the benefit of full spectral analysis of DNA, as opposed to reductive methods that consider only the 260 nm absorbance (A260) or simple purity ratios, such as A260/A230 or A260/A280, and suggest that the slope of the absorption edge onset may provide a useful metric for the degree of base pair stacking in DNA. These insights may prove useful for applications in biology, bioelectronics, and mesoscale self-assembly.

Stokes-Einstein relation for pure simple fluids.

PubMed

Cappelezzo, M; Capellari, C A; Pezzin, S H; Coelho, L A F

2007-06-14

The authors employed the equilibrium molecular dynamics technique to calculate the self-diffusion coefficient and the shear viscosity for simple fluids that obey the Lennard-Jones 6-12 potential in order to investigate the validity of the Stokes-Einstein (SE) relation for pure simple fluids. They performed calculations in a broad range of density and temperature in order to test the SE relation. The main goal of this work is to exactly calculate the constant, here denominated by alpha, present in the SE relation. Also, a modified SE relation where a fluid density is raised to a power in the usual expression is compared to the classical expression. According to the authors' simulations slip boundary conditions (alpha=4) can be satisfied in some state points. An intermediate value of alpha=5 was found in some regions of the phase diagram confirming the mode coupling theory. In addition depending on the phase diagram point and the definition of hydrodynamics radius, stick boundary condition (alpha=6) can be reproduced. The authors investigated the role of the hydrodynamic radius in the SE relation using three different definitions. The authors also present calculations for alpha in a hard-sphere system showing that the slip boundary conditions hold at very high density. They discuss possible explanations for their results and the role of the hydrodynamic radius for different definitions in the SE relation.