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1.  Genome Resilience and Prevalence of Segmental Duplications Following Fast Neutron Irradiation of Soybean 
Genetics  2014;198(3):967-981.
Fast neutron radiation has been used as a mutagen to develop extensive mutant collections. However, the genome-wide structural consequences of fast neutron radiation are not well understood. Here, we examine the genome-wide structural variants observed among 264 soybean [Glycine max (L.) Merrill] plants sampled from a large fast neutron-mutagenized population. While deletion rates were similar to previous reports, surprisingly high rates of segmental duplication were also found throughout the genome. Duplication coverage extended across entire chromosomes and often prevailed at chromosome ends. High-throughput resequencing analysis of selected mutants resolved specific chromosomal events, including the rearrangement junctions for a large deletion, a tandem duplication, and a translocation. Genetic mapping associated a large deletion on chromosome 10 with a quantitative change in seed composition for one mutant. A tandem duplication event, located on chromosome 17 in a second mutant, was found to cosegregate with a short petiole mutant phenotype, and thus may serve as an example of a morphological change attributable to a DNA copy number gain. Overall, this study provides insight into the resilience of the soybean genome, the patterns of structural variation resulting from fast neutron mutagenesis, and the utility of fast neutron-irradiated mutants as a source of novel genetic losses and gains.
doi:10.1534/genetics.114.170340
PMCID: PMC4224183  PMID: 25213171
soybean; fast neutron; structural variation; deletion; duplication
2.  Magnesium Coated Bioresorbable Phosphate Glass Fibres: Investigation of the Interface between Fibre and Polyester Matrices 
BioMed Research International  2013;2013:735981.
Bioresorbable phosphate glass fibre reinforced polyester composites have been investigated as replacement for some traditional metallic orthopaedic implants, such as bone fracture fixation plates. However, composites tested revealed loss of the interfacial integrity after immersion within aqueous media which resulted in rapid loss of mechanical properties. Physical modification of fibres to change fibre surface morphology has been shown to be an effective method to improve fibre and matrix adhesion in composites. In this study, biodegradable magnesium which would gradually degrade to Mg2+ in the human body was deposited via magnetron sputtering onto bioresorbable phosphate glass fibres to obtain roughened fibre surfaces. Fibre surface morphology after coating was observed using scanning electron microscope (SEM). The roughness profile and crystalline texture of the coatings were determined via atomic force microscope (AFM) and X-ray diffraction (XRD) analysis, respectively. The roughness of the coatings was seen to increase from 40 ± 1 nm to 80 ± 1 nm. The mechanical properties (tensile strength and modulus) of fibre with coatings decreased with increased magnesium coating thickness.
doi:10.1155/2013/735981
PMCID: PMC3771308  PMID: 24066297
3.  Mobilizing the Genome of Lepidoptera through Novel Sequence Gains and End Creation by Non-autonomous Lep1 Helitrons 
Transposable elements (TEs) can affect the structure of genomes through their acquisition and transposition of novel DNA sequences. The 134-bp repetitive elements, Lep1, are conserved non-autonomous Helitrons in lepidopteran genomes that have characteristic 5′-CT and 3′-CTAY nucleotide termini, a 3′-terminal hairpin structure, a 5′- and 3′-subterminal inverted repeat (SIR), and integrations that occur between AT or TT nucleotides. Lep1 Helitrons have acquired and propagated sequences downstream of their 3′-CTAY termini that are 57–344-bp in length and have termini composed of a 3′-CTRR preceded by a 3′-hairpin structure and a region complementary to the 5′-SIR (3′-SIRb). Features of both the Lep1 Helitron and multiple acquired sequences indicate that secondary structures at the 3′-terminus may have a role in rolling circle replication or genome integration mechanisms, and are a prerequisite for novel end creation by Helitron-like TEs. The preferential integration of Lep1 Helitrons in proximity to gene-coding regions results in the creation of genetic novelty that is shown to impact gene structure and function through the introduction of novel exon sequence (exon shuffling). These findings are important in understanding the structural requirements of genomic DNA sequences that are acquired and transposed by Helitron-like TEs.
doi:10.1093/dnares/dsr038
PMCID: PMC3276263  PMID: 22086996
Helitron; sequence gain; genome rearrangement
4.  Applying Small-Scale DNA Signatures as an Aid in Assembling Soybean Chromosome Sequences 
Advances in Bioinformatics  2010;2010:976792.
Previous work has established a genomic signature based on relative counts of the 16 possible dinucleotides. Until now, it has been generally accepted that the dinucleotide signature is characteristic of a genome and is relatively homogeneous across a genome. However, we found some local regions of the soybean genome with a signature differing widely from that of the rest of the genome. Those regions were mostly centromeric and pericentromeric, and enriched for repetitive sequences. We found that DNA binding energy also presented large-scale patterns across soybean chromosomes. These two patterns were helpful during assembly and quality control of soybean whole genome shotgun scaffold sequences into chromosome pseudomolecules.
doi:10.1155/2010/976792
PMCID: PMC2933861  PMID: 20827309
5.  Pursuing structure in microcrystalline solids with independent molecules in the unit cell using 1H–13C correlation data 
The 1H–13C solid-state NMR heteronuclear correlation (HETCOR) experiment is demonstrated to provide shift assignments in certain powders that have two or more structurally independent molecules in the unit cell (i.e. multiple molecules per asymmetric unit). Although this class of solids is often difficult to characterize using other methods, HETCOR provides both the conventional assignment of shifts to molecular positions and associates many resonances with specific molecules in the asymmetric unit. Such assignments facilitate conformational characterization of the individual molecules of the asymmetric unit and the first such characterization solely from solid-state NMR data is described. HETCOR offers advantages in sensitivity over prior methods that assign resonances in the asymmetric unit by 13C–13C correlations and therefore allows shorter average analysis times in natural abundance materials. The 1H–13C analysis is demonstrated first on materials with known shift assignments from INADEQUATE data (santonin and Ca(OAc)2 phase I) to verify the technique and subsequently is extended to a pair of unknown solids: (+)-catechin and Ca(OAc)2 phase II. Sufficient sensitivity and resolution is achieved in the spectra to provide assignments to one of the specific molecules of the asymmetric unit at over 54% of the sites.
doi:10.1016/j.jmr.2007.06.017
PMCID: PMC2819409  PMID: 17869558
Heteronuclear correlation; Powders; Asymmetric unit
6.  Redetermination of 1,4-dimethoxy­benzene 
The structure of the centrosymmetric title compound, C8H10O2, originally determined by Goodwin et al. [Acta Cryst.(1950), 3, 279–284], has been redetermined to modern standards of precision to aid in its use as a model compound for 13C chemical-shift tensor measurements in single-crystal NMR studies. In the crystal structure, a C—H⋯O inter­action helps to establish the packing.
doi:10.1107/S1600536808044231
PMCID: PMC2968136  PMID: 21581867

Results 1-6 (6)