24 research outputs found

    A draft physical map of a D-genome cotton species (Gossypium raimondii)

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    <p>Abstract</p> <p>Background</p> <p>Genetically anchored physical maps of large eukaryotic genomes have proven useful both for their intrinsic merit and as an adjunct to genome sequencing. Cultivated tetraploid cottons, <it>Gossypium hirsutum </it>and <it>G. barbadense</it>, share a common ancestor formed by a merger of the A and D genomes about 1-2 million years ago. Toward the long-term goal of characterizing the spectrum of diversity among cotton genomes, the worldwide cotton community has prioritized the D genome progenitor <it>Gossypium raimondii </it>for complete sequencing.</p> <p>Results</p> <p>A whole genome physical map of <it>G. raimondii</it>, the putative D genome ancestral species of tetraploid cottons was assembled, integrating genetically-anchored overgo hybridization probes, agarose based fingerprints and 'high information content fingerprinting' (HICF). A total of 13,662 BAC-end sequences and 2,828 DNA probes were used in genetically anchoring 1585 contigs to a cotton consensus genetic map, and 370 and 438 contigs, respectively to <it>Arabidopsis thaliana </it>(AT) and <it>Vitis vinifera </it>(VV) whole genome sequences.</p> <p>Conclusion</p> <p>Several lines of evidence suggest that the <it>G. raimondii </it>genome is comprised of two qualitatively different components. Much of the gene rich component is aligned to the <it>Arabidopsis </it>and <it>Vitis vinifera </it>genomes and shows promise for utilizing translational genomic approaches in understanding this important genome and its resident genes. The integrated genetic-physical map is of value both in assembling and validating a planned reference sequence.</p

    A physical map of Brassica oleracea shows complexity of chromosomal changes following recursive paleopolyploidizations

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    <p>Abstract</p> <p>Background</p> <p>Evolution of the Brassica species has been recursively affected by polyploidy events, and comparison to their relative, <it>Arabidopsis thaliana</it>, provides means to explore their genomic complexity.</p> <p>Results</p> <p>A genome-wide physical map of a rapid-cycling strain of <it>B. oleracea </it>was constructed by integrating high-information-content fingerprinting (HICF) of Bacterial Artificial Chromosome (BAC) clones with hybridization to sequence-tagged probes. Using 2907 contigs of two or more BACs, we performed several lines of comparative genomic analysis. Interspecific DNA synteny is much better preserved in euchromatin than heterochromatin, showing the qualitative difference in evolution of these respective genomic domains. About 67% of contigs can be aligned to the Arabidopsis genome, with 96.5% corresponding to euchromatic regions, and 3.5% (shown to contain repetitive sequences) to pericentromeric regions. Overgo probe hybridization data showed that contigs aligned to Arabidopsis euchromatin contain ~80% of low-copy-number genes, while genes with high copy number are much more frequently associated with pericentromeric regions. We identified 39 interchromosomal breakpoints during the diversification of <it>B. oleracea </it>and <it>Arabidopsis thaliana</it>, a relatively high level of genomic change since their divergence. Comparison of the <it>B. oleracea </it>physical map with Arabidopsis and other available eudicot genomes showed appreciable 'shadowing' produced by more ancient polyploidies, resulting in a web of relatedness among contigs which increased genomic complexity.</p> <p>Conclusions</p> <p>A high-resolution genetically-anchored physical map sheds light on Brassica genome organization and advances positional cloning of specific genes, and may help to validate genome sequence assembly and alignment to chromosomes.</p> <p>All the physical mapping data is freely shared at a WebFPC site (<url>http://lulu.pgml.uga.edu/fpc/WebAGCoL/brassica/WebFPC/</url>; Temporarily password-protected: account: pgml; password: 123qwe123.</p

    Molecular dynamics of adsorbed polymer thin films using NMR field cycling relaxometry

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    NMR Field cycling relaxometry was used to study polymer thin films formed on porous metal oxides surfaces. The thickness of the film was varied in the range from several monolayers to sub-monolayer nominally. In all cases, a slowing down of motion as reflected by lower relaxation times compared to bulk was observed, and a qualitative deviation from bulk occurred in cases of strong confinements. Two different polymers, poly(dimethylsiloxane) (PDMS) and polybutadiene (PB) were used. As confinements, porous alumina membranes (Anopore) and porous silica rods (Vycor) were used. The substrates differed in both size as well as surface interaction potential. The results from relaxation dispersions were analysed based on model theories available for melts and completely confined systems. The different polymer-substrate systems showed different effects. PB in Anopore showed a simple reduction in relaxation times with the underlying dynamics being similar to the bulk. As the layer thickness decreased, slowing down of motion was seen from the decreasing relaxation times. Poor wetting and weak interactions resulting in a bulk-like layer is discussed as the reason for this behaviour. PB in Vycor showed stronger motional restrictions. PB completely filling in Vycor pores showed a tendency to follow limit II of the reptation model, while partially filled samples showed a much weaker slope compared to the completely filled sample. Although it cannot be conclusively stated, the void space, the surface interactions and a change in characteristic times are discussed as some of the potential reasons. PDMS with differet molecular weights were studied in Anopore membranes. The mobility of all thin films of PDMS in Anopore were considerably reduced pending on the thickness. Relaxation dispersion of films below a certain thickness determined by the chain size showed deviation from bulk while thicker films only showed a reduction in relaxation times but followed bulk dynamics. The deviations occur due to a different weight of chain modes to the relaxation dispersion that can arrive from a change in the 3D topology as well as a change in chain conformations. The results are discussed on the basis of a model dividing the layer into two zones with different characteristics. The different effects arrive due to different contributions from the two zones and the dominance of one of them. Study on PDMS chain conformations were carried out using paramagnetic relaxation enhancement agents. The study clearly showed that a major part of the chain exists on the surface however did not conclusively give proof to flattened chain conformations at submonolayer coverages. Uneven distribution of the paramagnetic relaxation agent and the weak adsorption of the chain to the surface resulting in exchange dynamics are discussed as potential factors influencing the results

    Poly (dimethyl siloxane) films in porous media

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    Poly (Dimethyl siloxane) thin films were prepared by solvent evaporation method in porous alumina hosts. The thickness of these layers ranged from multilayer to sub-monolayer. Different NMR methods (FFC relaxometry, transverse relaxation, 1H Double quantum NMR) were applied to study the dynamics and order in these thin films. We found that dynamic restrictions and order increased with decreasing layer size. The increase of a short component of T2 from CPMG curves was attributed to the thawing of the adsorbed chains as seen in the decrease of the short component from Hahn echoes

    Recent Progress in Lanthanide-Doped Inorganic Perovskite Nanocrystals and Nanoheterostructures: A Future Vision of Bioimaging

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    All-inorganic lead halide perovskite nanocrystals have great potential in optoelectronics and photovoltaics. However, their biological applications have not been explored much owing to their poor stability and shallow penetration depth of ultraviolet (UV) excitation light into tissues. Interestingly, the combination of all-inorganic halide perovskite nanocrystals (IHP NCs) with nanoparticles consisting of lanthanide-doped matrix (Ln NPs, such as NaYF4:Yb,Er NPs) is stable, near-infrared (NIR) excitable and emission tuneable (up-shifting emission), all of them desirable properties for biological applications. In addition, luminescence in inorganic perovskite nanomaterials has recently been sensitized via lanthanide doping. In this review, we discuss the progress of various Ln-doped all-inorganic halide perovskites (LnIHP). The unique properties of nanoheterostructures based on the interaction between IHP NCs and Ln NPs as well as those of LnIHP NCs are also detailed. Moreover, a systematic discussion of basic principles and mechanisms as well as of the recent advancements in bio-imaging based on these materials are presented. Finally, the challenges and future perspectives of bio-imaging based on NIR-triggered sensitized luminescence of IHP NCs are discussed

    Data on synthesis and thermo-mechanical properties of stimuli-responsive rubber materials bearing pendant anthracene groups

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    The photo-reversible [4πs+4πs] cycloaddition reaction of pendant anthracene moieties represents a convenient strategy to impart wavelength dependent properties into hydrogenated carboxylated nitrile butadiene rubber (HXNBR) networks. The present article provides the 1H NMR data on the reaction kinetics of the side chain functionalization of HXNBR. 2-(Anthracene-9-yl)oxirane with reactive epoxy groups is covalently attached to the polymer side chain of HXNBR via ring opening reaction between the epoxy and the carboxylic groups. Along with the identification, 1H NMR data on the quantification of the attached functional groups are shown in dependence on reaction time and concentration of 2-(anthracene-9-yl)oxirane. Changes in the modification yield are reflected in the mechanical properties and DMA data of photo-responsive elastomers are illustrated in dependence on the number of attached anthracene groups. DMA curves over repeated cycles of UV induced crosslinking (λ>300 nm) and UV induced cleavage (λ=254 nm) are further depicted, demonstrating the photo-reversibility of the thermo-mechanical properties. Interpretation and discussion of the data are provided in “Design and application of photo-reversible elastomer networks by using the [4πs+4πs] cycloaddition reaction of pendant anthracene groups” (Manhart et al., 2016) [1]
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