Predicting food production potential of urban vacant lots through soil quality

Post-industrial cities such as Cleveland have accumulated substantial number of vacant lots due to home foreclosures and urban sprawl over the past two decades. Interest in this land has escalated recently due to increased demand for food security in disadvantaged urban neighborhoods. We measured soil physical, chemical, and biological parameters in vacant lots in the Hough neighborhood in Cleveland to assess their suitability for food production. Each lot was divided into three approximately equal sections and nine soil cores were collected from each section. The results revealed huge spatial variability in soil properties within vacant lots. Soil pH ranged from 6.24-7.46 and moisture from 1.5-20.5%. Soil clay content ranged from 4-33%, sand 40-92%, and silt 0-50%. Soil NH4-N ranged from 1.7-21.0 ppm, NO3-N from 2.3-35.3 ppm, microbial biomass from 40.2-245.7 ppm (N), soil organic matter from 2.0-7.0%, and soil active carbon from 413.3-694.8 mg/kg. Thirty-four nematode genera were identified, and nematode abundance ranged from 34 to 988 per sample. Soil active carbon, a rapid soil quality indicator, significantly correlated with other measures of ecosystem condition including NH4-N, microbial biomass, soil organic matter, nematode abundance, maturity index, and combined maturity index. Principle Component Analysis revealed that vacant lots had less structured soil food webs than turfgrass lawns, but not from community gardens and vegetable farms. There were also no differences in nematode abundance, genus diversity, and enrichment index among vacant lots, turfgrass lawns, community gardens and vegetable farms. Our results indicate high potential for food production in urban vacant lots.Urban Landscape Ecology Program, The Ohio State UniversityCenter for Urban Environment and Economic Development, The Ohio State UniversityOARDC Research Internships Program, The Ohio State Universit

Phase retrieval by hyperplanes

We show that a scalable frame does phase retrieval if and only if the hyperplanes of its orthogonal complements do phase retrieval. We then show this result fails in general by giving an example of a frame for $\mathbb R^3$ which does phase retrieval but its induced hyperplanes fail phase retrieval. Moreover, we show that such frames always exist in $\mathbb R^d$ for any dimension $d$. We also give an example of a frame in $\mathbb R^3$ which fails phase retrieval but its perps do phase retrieval. We will also see that a family of hyperplanes doing phase retrieval in $\mathbb R^d$ must contain at least $2d-2$ hyperplanes. Finally, we provide an example of six hyperplanes in $\mathbb R^4$ which do phase retrieval

DNA transposons have colonized the genome of the giant virus Pandoravirus salinus

BACKGROUND: Transposable elements are mobile DNA sequences that are widely distributed in prokaryotic and eukaryotic genomes, where they represent a major force in genome evolution. However, transposable elements have rarely been documented in viruses, and their contribution to viral genome evolution remains largely unexplored. Pandoraviruses are recently described DNA viruses with genome sizes that exceed those of some prokaryotes, rivaling parasitic eukaryotes. These large genomes appear to include substantial noncoding intergenic spaces, which provide potential locations for transposable element insertions. However, no mobile genetic elements have yet been reported in pandoravirus genomes. RESULTS: Here, we report a family of miniature inverted-repeat transposable elements (MITEs) in the Pandoravirus salinus genome, representing the first description of a virus populated with a canonical transposable element family that proliferated by transposition within the viral genome. The MITE family, which we name Submariner, includes 30 copies with all the hallmarks of MITEs: short length, terminal inverted repeats, TA target site duplication, and no coding capacity. Submariner elements show signs of transposition and are undetectable in the genome of Pandoravirus dulcis, the closest known relative Pandoravirus salinus. We identified a DNA transposon related to Submariner in the genome of Acanthamoeba castellanii, a species thought to host pandoraviruses, which contains remnants of coding sequence for a Tc1/mariner transposase. These observations suggest that the Submariner MITEs of P. salinus belong to the widespread Tc1/mariner superfamily and may have been mobilized by an amoebozoan host. Ten of the 30 MITEs in the P. salinus genome are located within coding regions of predicted genes, while others are close to genes, suggesting that these transposons may have contributed to viral genetic novelty. CONCLUSIONS: Our discovery highlights the remarkable ability of DNA transposons to colonize and shape genomes from all domains of life, as well as giant viruses. Our findings continue to blur the division between viral and cellular genomes, adhering to the emerging view that the content, dynamics, and evolution of the genomes of giant viruses do not substantially differ from those of cellular organisms. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12915-015-0145-1) contains supplementary material, which is available to authorized users