Somatically heritable switches in the DNA modification of Mu transposable elements monitored with a suppressible mutant in maize

Many transposable elements in maize alternate between active and inactive phases associated with the modification of their DNA. Elements in an inactive phase lose their ability to transpose, their ability to excise from reporter alleles and, in some cases, their ability to enhance or suppress mutant phenotypes caused by their insertion. The maize mutant hcf106 is a recessive pale green seedling lethal caused by the insertion of the transposable element Mu1. We show that the hcf106 mutant phenotype is suppressed in lines that have lost Mu activity. That is, homozygous hcf106 seedlings are dark green and viable when transposable elements belonging to the Robertson's Mutator family are modified in their terminal inverted repeats, a diagnostic feature of inactive lines. This property of the mutant phenotype has been used to follow clonal leaf sectors containing modified Mu elements that arise from single somatic cells during plant development. The distribution of these sectors indicates that epigenetic switches involving Mu DNA modification occur progressively as the meristem ages

Sequencing the maize genome

Sequencing of complex genomes can be accomplished by enriching shotgun libraries for genes. In maize, gene-enrichment by copy-number normalization (high C(0)t) and methylation filtration (MF) have been used to generate up to two-fold coverage of the gene-space with less than 1 million sequencing reads. Simulations using sequenced bacterial artificial chromosome (BAC) clones predict that 5x coverage of gene-rich regions, accompanied by less than 1x coverage of subclones from BAC contigs, will generate high-quality mapped sequence that meets the needs of geneticists while accommodating unusually high levels of structural polymorphism. By sequencing several inbred strains, we propose a strategy for capturing this polymorphism to investigate hybrid vigor or heterosis

Entangled-Photon Imaging of a Pure Phase Object

We demonstrate experimentally and theoretically that a coherent image of a pure phase object may be obtained by use of a spatially incoherent illumination beam. This is accomplished by employing a two-beam source of entangled photons generated by spontaneous parametric down-conversion. Though each of the beams is, in and of itself, spatially incoherent, the pair of beams exhibits higher-order inter-beam coherence. One of the beams probes the phase object while the other is scanned. The image is recorded by measuring the photon coincidence rate using a photon-counting detector in each beam. Using a reflection configuration, we successfully imaged a phase object implemented by a MEMS micro-mirror array. The experimental results are in accord with theoretical predictions.Comment: 11 pages, 3 figures, submittedto Phys. Rev. Let

Time interval distributions of atoms in atomic beams

We report on the experimental investigation of two-particle correlations between neutral atoms in a Hanbury Brown and Twiss experiment. Both an atom laser beam and a pseudo-thermal atomic beam are extracted from a Bose-Einstein condensate and the atom flux is measured with a single atom counter. We determine the conditional and the unconditional detection probabilities for the atoms in the beam and find good agreement with the theoretical predictions.Comment: 4 pages, 3 figure

Expressed sequence tag analysis in Cycas, the most primitive living seed plant

BACKGROUND: Cycads are ancient seed plants (living fossils) with origins in the Paleozoic. Cycads are sometimes considered a 'missing link' as they exhibit characteristics intermediate between vascular non-seed plants and the more derived seed plants. Cycads have also been implicated as the source of 'Guam's dementia', possibly due to the production of S(+)-beta-methyl-alpha, beta-diaminopropionic acid (BMAA), which is an agonist of animal glutamate receptors. RESULTS: A total of 4,200 expressed sequence tags (ESTs) were created from Cycas rumphii and clustered into 2,458 contigs, of which 1,764 had low-stringency BLAST similarity to other plant genes. Among those cycad contigs with similarity to plant genes, 1,718 cycad 'hits' are to angiosperms, 1,310 match genes in gymnosperms and 734 match lower (non-seed) plants. Forty-six contigs were found that matched only genes in lower plants and gymnosperms. Upon obtaining the complete sequence from the clones of 37/46 contigs, 14 still matched only gymnosperms. Among those cycad contigs common to higher plants, ESTs were discovered that correspond to those involved in development and signaling in present-day flowering plants. We purified a cycad EST for a glutamate receptor (GLR)-like gene, as well as ESTs potentially involved in the synthesis of the GLR agonist BMAA. CONCLUSIONS: Analysis of cycad ESTs has uncovered conserved and potentially novel genes. Furthermore, the presence of a glutamate receptor agonist, as well as a glutamate receptor-like gene in cycads, supports the hypothesis that such neuroactive plant products are not merely herbivore deterrents but may also serve a role in plant signaling

A diffusion model for the coordination of DNA replication in Schizosaccharomyces pombe

The locations of proteins and epigenetic marks on the chromosomal DNA sequence are believed to demarcate the eukaryotic genome into distinct structural and functional domains that contribute to gene regulation and genome organization. However, how these proteins and epigenetic marks are organized in three dimensions remains unknown. Recent advances in proximity-ligation methodologies and high resolution microscopy have begun to expand our understanding of these spatial relationships. Here we use polymer models to examine the spatial organization of epigenetic marks, euchromatin and heterochromatin, and origins of replication within the Schizosaccharomyces pombe genome. These models incorporate data from microscopy and proximity-ligation experiments that inform on the positions of certain elements and contacts within and between chromosomes. Our results show a striking degree of compartmentalization of epigenetic and genomic features and lead to the proposal of a diffusion based mechanism, centred on the spindle pole body, for the coordination of DNA replication in S. pombe

Sorghum Genome Sequencing by Methylation Filtration

Sorghum bicolor is a close relative of maize and is a staple crop in Africa and much of the developing world because of its superior tolerance of arid growth conditions. We have generated sequence from the hypomethylated portion of the sorghum genome by applying methylation filtration (MF) technology. The evidence suggests that 96% of the genes have been sequence tagged, with an average coverage of 65% across their length. Remarkably, this level of gene discovery was accomplished after generating a raw coverage of less than 300 megabases of the 735-megabase genome. MF preferentially captures exons and introns, promoters, microRNAs, and simple sequence repeats, and minimizes interspersed repeats, thus providing a robust view of the functional parts of the genome. The sorghum MF sequence set is beneficial to research on sorghum and is also a powerful resource for comparative genomics among the grasses and across the entire plant kingdom. Thousands of hypothetical gene predictions in rice and Arabidopsis are supported by the sorghum dataset, and genomic similarities highlight evolutionarily conserved regions that will lead to a better understanding of rice and Arabidopsis

Comprehensive DNA methylation profiling in a human cancer genome identifies novel epigenetic targets

Using a unique microarray platform for cytosine methylation profiling, the DNA methylation landscape of the human genome was monitored at more than 21,000 sites, including 79% of the annotated transcriptional start sites (TSS). Analysis of an oligodendroglioma derived cell line LN-18 revealed more than 4000 methylated TSS. The gene-centric analysis indicated a complex pattern of DNA methylation exists along each autosome, with a trend of increasing density approaching the telomeres. Remarkably, 2% of CpG islands (CGI) were densely methylated, and 17% had significant levels of 5 mC, whether or not they corresponded to a TSS. Substantial independent verification, obtained from 95 loci, suggested that this approach is capable of large scale detection of cytosine methylation with an accuracy approaching 90%. In addition, we detected large genomic domains that are also susceptible to DNA methylation reinforced inactivation, such as the HOX cluster on chromosome 7 (CH7). Extrapolation from the data suggests that more than 2000 genomic loci may be susceptible to methylation and associated inactivation, and most have yet to be identified. Finally, we report six new targets of epigenetic inactivation (IRX3, WNT10A, WNT6, RARalpha, BMP7 and ZGPAT). These targets displayed cell line and tumor specific differential methylation when compared with normal brain samples, suggesting they may have utility as biomarkers. Uniquely, hypermethylation of the CGI within an IRX3 exon was correlated with over-expression of IRX3 in tumor tissues and cell lines relative to normal brain samples

Performance and durability of broadband antireflection coatings for thin film CdTe solar cells

Light reflection from the glass surface of a photovoltaic (PV) module is a significant source of energy loss for all types of PV devices. The reflection at the glass and air interface accounts for 4% of the total energy. Single layer antireflection coatings with sufficiently low refractive index have been used, such as those using magnesium fluoride or porous silica, but these are only effective over a narrow range of wavelengths. In this paper, the authors report on the design, deposition, and testing of multilayer broadband antireflection coatings. These coatings reduce the weighted average reflection over the wavelength range used by thin film CdTe devices to just 1.22%, resulting in a 3.6% relative increase in device efficiency. The authors have used multilayer stacks consisting of silica and zirconia layers deposited using reactive magnetron sputtering. Details of the stack design, sputter deposition process parameters, and the optical and microstructural properties of the layers are provided. Antireflection coatings on glass exposed to the outdoors must not degrade over the lifetime of the module. A comprehensive set of accelerated environmental durability tests has been carried out in accordance with IEC 61646 PV qualification tests. The durability tests confirmed no damage to the coatings or performance drop as a result of thermal cycling or damp heat. All attempts to perform pull tests resulted in either adhesive or substrate failure, with no damage to the coating itself. The coatings also passed acid attack tests. Scratch resistance, abrasion resistance, and adhesion tests have also been conducted. The optical performance of the coatings was monitored during these tests, and the coatings were visually inspected for any sign of mechanical failure. These tests provide confidence that broadband antireflection coatings are highly durable and will maintain their performance over the lifetime of the solar module. All dielectric metal-oxide multilayer coatings have better optical performance and superior durability compared with alternative single layer porous sol–gel coatings. Thin film CdTe devices are particularly problematic because the antireflection coating is applied to one side of the glass, while device layers are deposited directly on to the opposite glass surface in the superstrate configuration. In thin film CdTe production, the glass is exposed to high temperature processes during the absorber deposition and the cadmium chloride activation treatment. If glass precoated with a broadband antireflection coating is to be used, then the coating must withstand temperatures of up to 550 C. Surprisingly, our studies have shown that multilayer silica/zirconia antireflection coatings on soda lime glass remain unaffected by temperatures reaching 600 C, at which point mild crazing is observed. This is an important observation, demonstrating that low cost glass, which is preprocessed with a broadband antireflection coating, is directly useable in thin film CdTe module production