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  • 1
    Publication Date: 2013-11-09
    Description: The genome of potato, a major global food crop, was recently sequenced. The work presented here details the integration of the potato reference genome (DM) with a new sequence-tagged site marker–based linkage map and other physical and genetic maps of potato and the closely related species tomato. Primary anchoring of the DM genome assembly was accomplished by the use of a diploid segregating population, which was genotyped with several types of molecular genetic markers to construct a new ~936 cM linkage map comprising 2469 marker loci. In silico anchoring approaches used genetic and physical maps from the diploid potato genotype RH89-039-16 (RH) and tomato. This combined approach has allowed 951 superscaffolds to be ordered into pseudomolecules corresponding to the 12 potato chromosomes. These pseudomolecules represent 674 Mb (~93%) of the 723 Mb genome assembly and 37,482 (~96%) of the 39,031 predicted genes. The superscaffold order and orientation within the pseudomolecules are closely collinear with independently constructed high density linkage maps. Comparisons between marker distribution and physical location reveal regions of greater and lesser recombination, as well as regions exhibiting significant segregation distortion. The work presented here has led to a greatly improved ordering of the potato reference genome superscaffolds into chromosomal "pseudomolecules".
    Electronic ISSN: 2160-1836
    Topics: Biology
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  • 2
    Electronic Resource
    Electronic Resource
    Chichester [u.a.] : Wiley-Blackwell
    International Journal for Numerical Methods in Engineering 9 (1975), S. 477-483 
    ISSN: 0029-5981
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics , Technology
    Notes: The paper considers the question of reduction of loads on a pipe network, which may be necessary as a result of failure in supply or interruption of a pipe. The non-linear relationship between pressure loss and flow along a pipe makes the problem of minimizing the reduction of loads also non-linear. An iterative linear approximation technique is therefore adopted. When the question is formulated as a problem in linear programming, the constraints include nodal pressures as well as loads. It is shown how the number of these constraints may be reduced.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    Chichester [u.a.] : Wiley-Blackwell
    International Journal for Numerical Methods in Engineering 11 (1977), S. 963-973 
    ISSN: 0029-5981
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics , Technology
    Notes: A measure of the severity of a pipeline failure is the minimum reduction in load in the network necessary to ensure that no node falls below its minimum pressure. The expected loss of sales is calculated as the product of the minimum reduction in load and the expected duration of the period during which the pipeline will be in the inoperable state, and thus reflects both the severity and the frequency of the failure. Consequently, this index, whose evaluation involves network theory, optimization and probability theory, serves as a measure of the insecurity of the gas network.The security index can be evaluated for all points within a system, providing a basis of comparison between the relative vulnerability of different parts. The relative level of security of different design proposals can also be assessed using this index.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 1045-4861
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine , Technology
    Notes: Hydroxyapatite induction by a synthesized pure silica hydrogel was examined in various simulated body fluids (SBFs) having different magnesium, calcium, and phosphate ion concentrations as well as pH values. The silica hydrogel generated biologically active apatite on its surface by taking up calcium and phosphorous ionic groups from a surrounding SBF that was prepared to emulate the human plasma in inorganic composition. The induction period for apatite nucleation on the surface of the silica was largely decreased with the addition of a small amount of the calcium or phosphate ions to the SBF and with an increase in pH, but increased with the addition of magnesium ion. Bioactivity of bioactive materials like Bioglass® and glass-ceramic A-W was well interpreted in terms of the rate of apatite formation reflected in these results. Moreover, the results provide the basic knowledge for designing new bioactive materials. © 1993 John Wiley & Sons, Inc.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Hoboken, NJ : Wiley-Blackwell
    Journal of Biomedical Materials Research 34 (1997), S. 79-86 
    ISSN: 0021-9304
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine , Technology
    Notes: The bone-bonding polymer known as Polyactive® is a block copolymer composed of a polyethylene oxide (PEO) soft segment and a polybutylene terephthalate (PBT) hard segment. This study focuses on the in vitro induction of hydroxyapatite by Polyactive®. Our results show that Polyactive® is capable of inducing hydroxycarbonate apatite (HCAp) formation from a metastable calcium phosphate solution analogous to a physiological solution. In a 4-day incubation, the HCAp formation extended approximately 100 μm deep from the surface. A great number of globules about 1 μm large were found in the calcified Polyactive®. These globules were composed of HCAp crystals embedded in the polymer matrix. There were so many globules in the surface that they connected with each other and formed a calcified layer. Next to the calcified layer was a zone where the globules were scattered. The calcified surface may have acted to promote HCAp growth from the solution, bringing about the formation of a HCAp layer on top of the calcified layer. The transition of solid Polyactive® into a Polyactive® hydro-gel in calcium phosphate solution permitted HCAp formation within the polymer. It is proposed that the COOH groups produced during hydrolysis of Polyactive® play an important role in nucleating hydroxyapatite. A remarkable affinity of the PEO segment of the polymer for calcium ions may facilitate moving calcium and phosphate from the solution into the polymer for the growth of HCAp. © 1997 John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
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  • 6
    Publication Date: 2016-06-02
    Description: Cotton seed trichomes are the most important source of natural fibers globally. The major fiber thickness properties influence the price of the raw material, and the quality of the finished product. The recessive immature fiber ( im ) gene reduces the degree of fiber cell wall thickening by a process that was previously shown to involve mitochondrial function in allotetraploid Gossypium hirsutum . Here, we present the fine genetic mapping of the im locus, gene expression analysis of annotated proteins near the locus, and association analysis of the linked markers. Mapping-by-sequencing identified a 22-bp deletion in a pentatricopeptide repeat (PPR) gene that is completely linked to the immature fiber phenotype in 2837 F 2 plants, and is absent from all 163 cultivated varieties tested, although other closely linked marker polymorphisms are prevalent in the diversity panel. This frame-shift mutation results in a transcript with two long open reading frames: one containing the N-terminal transit peptide that targets mitochondria, the other containing only the RNA-binding PPR domains, suggesting that a functional PPR protein cannot be targeted to mitochondria in the im mutant. Taken together, these results suggest that PPR gene Gh_A03G0489 is involved in the cotton fiber wall thickening process, and is a promising candidate gene at the im locus. Our findings expand our understanding of the molecular mechanisms that modulate cotton fiber fineness and maturity, and may facilitate the development of cotton varieties with superior fiber attributes.
    Electronic ISSN: 2160-1836
    Topics: Biology
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  • 7
    Publication Date: 2015-10-06
    Description: Physical appearance traits, such as feather-crested head, comb size and type, beard, wattles size, and feathered feet, are used to distinguish between breeds of chicken and also may be associated with economic traits. In this study, a genome-wide linkage analysis was used to identify candidate regions and genes for physical appearance traits and to potentially provide further knowledge of the molecular mechanisms that underlie these traits. The linkage analysis was conducted with an F2 population derived from Beijing-You chickens and a commercial broiler line. Single-nucleotide polymorphisms were analyzed using the Illumina 60K Chicken SNP Beadchip. The data were used to map quantitative trait loci and genes for six physical appearance traits. A 10-cM/0.51-Mb region (0.0–10.0 cM/0.00–0.51 Mb) with 1% genome-wide significant level on LGE22C19W28_E50C23 linkage group (LGE22) for crest trait was identified, which is likely very closely linked to the HOXC8 . A QTL with 5% chromosome-wide significant level for comb weight, which partly overlaps with a region identified in a previous study, was identified at 74 cM/25.55 Mb on chicken ( Gallus gallus ; GG) chromosome 3 ( i.e. , GGA3). For beard and wattles traits, an identical region 11 cM/2.23 Mb (0.0–11.0 cM/0.00–2.23 Mb) including WNT3 and GH genes on GGA27 was identified. Two QTL with 1% genome-wide significant level for feathered feet trait, one 9-cM/2.80-Mb (48.0-57.0/13.40-16.20 Mb) region on GGA13, and another 12-cM/1.45-Mb (41.0–53.0 cM/11.37–12.82 Mb) region on GGA15 were identified. These candidate regions and genes provide important genetic information for the physical appearance traits in chicken.
    Electronic ISSN: 2160-1836
    Topics: Biology
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  • 8
    Publication Date: 2014-01-11
    Description: Tandem repeats (TRs) extensively exist in the genomes of prokaryotes and eukaryotes. Based on the sequenced genomes and gene annotations of 31 plant and algal species in Phytozome version 8.0 ( http://www.phytozome.net/ ), we examined TRs in a genome-wide scale, characterized their distributions and motif features, and explored their putative biological functions. Among the 31 species, no significant correlation was detected between the TR density and genome size. Interestingly, green alga Chlamydomonas reinhardtii (42,059 bp/Mbp) and castor bean Ricinus communis (55,454 bp/Mbp) showed much higher TR densities than all other species (13,209 bp/Mbp on average). In the 29 land plants, including 22 dicots, 5 monocots, and 2 bryophytes, 5'-UTR and upstream intergenic 200-nt (UI200) regions had the first and second highest TR densities, whereas in the two green algae ( C. reinhardtii and Volvox carteri ) the first and second highest densities were found in intron and coding sequence (CDS) regions, respectively. In CDS regions, trinucleotide and hexanucleotide motifs were those most frequently represented in all species. In intron regions, especially in the two green algae, significantly more TRs were detected near the intron–exon junctions. Within intergenic regions in dicots and monocots, more TRs were found near both the 5' and 3' ends of genes. GO annotation in two green algae revealed that the genes with TRs in introns are significantly involved in transcriptional and translational processing. As the first systematic examination of TRs in plant and green algal genomes, our study showed that TRs displayed nonrandom distribution for both intragenic and intergenic regions, suggesting that they have potential roles in transcriptional or translational regulation in plants and green algae.
    Electronic ISSN: 2160-1836
    Topics: Biology
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  • 9
    Publication Date: 2012-10-10
    Description: Construction of high-density genetic linkage maps is crucially important for quantitative trait loci (QTL) studies, and they are more useful when integrated with physical maps. Such integrated maps are valuable genome resources for fine mapping of QTL, comparative genomics, and accurate and efficient whole-genome assembly. Previously, we established both linkage maps and a physical map for channel catfish, Ictalurus punctatus , the dominant aquaculture species in the United States. Here we added 2030 BAC end sequence (BES)-derived microsatellites from 1481 physical map contigs, as well as markers from singleton BES, ESTs, anonymous microsatellites, and SNPs, to construct a second-generation linkage map. Average marker density across the 29 linkage groups reached 1.4 cM/marker. The increased marker density highlighted variations in recombination rates within and among catfish chromosomes. This work effectively anchored 44.8% of the catfish BAC physical map contigs, covering ~52.8% of the genome. The genome size was estimated to be 2546 cM on the linkage map, and the calculated physical distance per centimorgan was 393 Kb. This integrated map should enable comparative studies with teleost model species as well as provide a framework for ordering and assembling whole-genome scaffolds.
    Electronic ISSN: 2160-1836
    Topics: Biology
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  • 10
    Publication Date: 2016-04-08
    Description: In recent years, genome engineering technology has provided unprecedented opportunities for site-specific modification of biological genomes. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) 9 is one such means that can target a specific genome locus. It has been applied in human cells and many other organisms. Meanwhile, to efficiently enrich targeted cells, several surrogate systems have also been developed. However, very limited information exists on the application of CRISPR/Cas9 in chickens. In this study, we employed the CRISPR/Cas9 system to induce mutations in the peroxisome proliferator-activated receptor- ( PPAR -), ATP synthase epsilon subunit ( ATP5E ), and ovalbumin ( OVA ) genes in chicken DF-1 cells. The results of T7E1 assays showed that the mutation rate at the three different loci was 0.75%, 0.5%, and 3.0%, respectively. In order to improve the mutation efficiency, we used the Puro R gene for efficient enrichment of genetically modified cells with the surrogate reporter system. The mutation rate, as assessed via the T7E1 assay, increased to 60.7%, 61.3%, and 47.3%, and subsequent sequence analysis showed that the mutation efficiency increased to 94.7%, 95%, and 95%, respectively. In addition, there were no detectable off-target mutations in three potential off-target sites using the T7E1 assay. As noted above, the CRISPR/Cas9 system is a robust tool for chicken genome editing.
    Electronic ISSN: 2160-1836
    Topics: Biology
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