44 research outputs found

    A bacterial genome in transition - an exceptional enrichment of IS elements but lack of evidence for recent transposition in the symbiont Amoebophilus asiaticus

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    <p>Abstract</p> <p>Background</p> <p>Insertion sequence (IS) elements are important mediators of genome plasticity and are widespread among bacterial and archaeal genomes. The 1.88 Mbp genome of the obligate intracellular amoeba symbiont <it>Amoebophilus asiaticus </it>contains an unusually large number of transposase genes (n = 354; 23% of all genes).</p> <p>Results</p> <p>The transposase genes in the <it>A. asiaticus </it>genome can be assigned to 16 different IS elements termed ISCaa1 to ISCaa16, which are represented by 2 to 24 full-length copies, respectively. Despite this high IS element load, the <it>A. asiaticus </it>genome displays a GC skew pattern typical for most bacterial genomes, indicating that no major rearrangements have occurred recently. Additionally, the high sequence divergence of some IS elements, the high number of truncated IS element copies (n = 143), as well as the absence of direct repeats in most IS elements suggest that the IS elements of <it>A. asiaticus </it>are transpositionally inactive. Although we could show transcription of 13 IS elements, we did not find experimental evidence for transpositional activity, corroborating our results from sequence analyses. However, we detected contiguous transcripts between IS elements and their downstream genes at nine loci in the <it>A. asiaticus </it>genome, indicating that some IS elements influence the transcription of downstream genes, some of which might be important for host cell interaction.</p> <p>Conclusions</p> <p>Taken together, the IS elements in the <it>A. asiaticus </it>genome are currently in the process of degradation and largely represent reflections of the evolutionary past of <it>A. asiaticus </it>in which its genome was shaped by their activity.</p

    Estimating the blue water footprint of in-field crop losses: A case study of U.S. potato cultivation

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    Given the high proportion of water consumption for agriculture, as well as the relatively common occurrence of crop losses in the field, we estimate the amount of water embedded in crops left on the farm. We are particularly interested in understanding losses associated with fruits and vegetables, having a higher level of harvesting selectivity and perishability (and thus, losses) than grain crops. We further refined the study to focus on potatoes, as they represent the largest acreage under cultivation of all fruit and vegetable crops in the U.S. We attempt to get the most complete understanding of pre-harvest and harvest loss data for potatoes by leveraging three centralized data sets collected and managed by the United States Department of Agriculture (USDA). By integrating these three distinct data sets for the five-year period 2012-2016, we are able to estimate water consumption for potato cultivation for total in-field losses by production stage and driver of loss for seven major potato-producing states (representing 77% of total U.S. potato production). Our results suggest that 3.6%-17.9% of potatoes are lost in the field with a total estimated blue water footprint of approximately 84.6 million cubic meters. We also find that the leading driver for crop loss for in-field potato production is harvest sorting and grading, accounting for 84% of total lost production at the farm. We conclude with a discussion of opportunities for improved national level data collection to provide a better understanding of in-field crop losses over time and the resource footprints of these losses

    The estimated impact of California's urban water conservation mandate on electricity consumption and greenhouse gas emissions

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    In April 2015, the Governor of California mandated a 25% statewide reduction in water consumption (relative to 2013 levels) by urban water suppliers. The more than 400 public water agencies affected by the regulation were also required to report monthly progress towards the conservation goal to the State Water Resources Control Board. This paper uses the reported data to assess how the water utilities have responded to this mandate and to estimate the electricity savings and greenhouse gas (GHG) emissions reductions associated with reduced operation of urban water infrastructure systems. The results show that California succeeded in saving 524 000 million gallons (MG) of water (a 24.5% decrease relative to the 2013 baseline) over the mandate period, which translates into 1830 GWh total electricity savings, and a GHG emissions reduction of 521 000 metric tonnes of carbon dioxide equivalents (MT CO2e). For comparison, the total electricity savings linked to water conservation are approximately 11% greater than the savings achieved by the investor-owned electricity utilities' efficiency programs for roughly the same time period, and the GHG savings represent the equivalent of taking about 111 000 cars off the road for a year. These indirect, large-scale electricity and GHG savings were achieved at costs that were competitive with existing programs that target electricity and GHG savings directly and independently. Finally, given the breadth of the results produced, we built a companion website, called 'H2Open' (https://cwee.shinyapps.io/greengov/), to this research effort that allows users to view and explore the data and results across scales, from individual water utilities to the statewide summary
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