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  • 1
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: N15 is a bacteriophage of Escherichia coli that resembles λ, but, unlike λ, it lysogenizes as a linear plasmid. We show that stable maintenance of this unusual plasmid-prophage depends on the parA and parB genes, relatives of the partition genes of F and P1 plasmids. ParB of N15, like its F- and P1-encoded homologues, destabilizes plasmids carrying its target centromere, when present in excess. Within the genome of N15, we identified four unlinked, palindromic sequences that can promote the ParB-mediated destabilization of a moderate-copy vector in cis. They are distant from the parAB operon, unlike the centromeric sites of F and P1. Each of these palindromes could interact in vivo and in vitro with ParB. Each, when cloned separately, had properties characteristic of centromeric sites: exerted incompatibility against the N15 prophage and mini-N15 plasmids, and stabilized a mini-P1 plasmid depleted of its own partition genes when ParA and ParB of N15 were supplied. A pair of sites was more effective than a single site. Two of the centromeric sites are located in the proximity of promoters of phage genes, suggesting that, in addition to their function in partitioning of N15 prophage, they may control expression of N15 lytic functions.
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 1365-2486
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Energy, Environment Protection, Nuclear Power Engineering , Geography
    Notes: Based on review and original data, this synthesis investigates carbon pools and fluxes of Siberian and European forests (600 and 300 million ha, respectively). We examine the productivity of ecosystems, expressed as positive rate when the amount of carbon in the ecosystem increases, while (following micrometeorological convention) downward fluxes from the atmosphere to the vegetation (NEE = Net Ecosystem Exchange) are expressed as negative numbers. Productivity parameters are Net Primary Productivity (NPP=whole plant growth), Net Ecosystem Productivity (NEP = CO2 assimilation minus ecosystem respiration), and Net Biome Productivity (NBP = NEP minus carbon losses through disturbances bypassing respiration, e.g. by fire and logging). Based on chronosequence studies and national forestry statistics we estimate a low average NPP for boreal forests in Siberia: 123 gC m–2 y–1. This contrasts with a similar calculation for Europe which suggests a much higher average NPP of 460 gC m–2 y–1 for the forests there. Despite a smaller area, European forests have a higher total NPP than Siberia (1.2–1.6 vs. 0.6–0.9 × 1015 gC region–1 y–1). This arises as a consequence of differences in growing season length, climate and nutrition. For a chronosequence of Pinus sylvestris stands studied in central Siberia during summer, NEE was most negative in a 67-y old stand regenerating after fire (– 192 mmol m–2 d–1) which is close to NEE in a cultivated forest of Germany (– 210 mmol m–2 d–1). Considerable net ecosystem CO2-uptake was also measured in Siberia in 200- and 215-y old stands (NEE:174 and – 63 mmol m–2 d–1) while NEP of 7- and 13-y old logging areas were close to the ecosystem compensation point. Two Siberian bogs and a bog in European Russia were also significant carbon sinks (– 102 to – 104 mmol m–2 d–1). Integrated over a growing season (June to September) we measured a total growing season NEE of – 14 mol m–2 summer–1 (– 168 gC m–2 summer–1) in a 200-y Siberian pine stand and – 5 mol m–2 summer–1 (– 60 gC m–2 summer–1) in Siberian and European Russian bogs. By contrast, over the same period, a spruce forest in European Russia was a carbon source to the atmosphere of (NEE: + 7 mol m–2 summer–1 = + 84 gC m–2 summer–1). Two years after a windthrow in European Russia, with all trees being uplifted and few successional species, lost 16 mol C m–2 to the atmosphere over a 3-month in summer, compared to the cumulative NEE over a growing season in a German forest of – 15.5 mol m–2 summer–1 (– 186 gC m–2 summer–1; European flux network annual averaged – 205 gC m–2 y–1). Differences in CO2-exchange rates coincided with differences in the Bowen ratio, with logging areas partitioning most incoming radiation into sensible heat whereas bogs partitioned most into evaporation (latent heat). Effects of these different surface energy exchanges on local climate (convective storms and fires) and comparisons with the Canadian BOREAS experiment are discussed. Following a classification of disturbances and their effects on ecosystem carbon balances, fire and logging are discussed as the main processes causing carbon losses that bypass heterotrophic respiration in Siberia. Following two approaches, NBP was estimated to be only about 13–16 mmol m–2 y–1 for Siberia. It may reach 67 mmol m–2 y–1 in North America, and about 140–400 mmol m–2 y–1 in Scandinavia. We conclude that fire speeds up the carbon cycle, but that it results also in long-term carbon sequestration by charcoal formation. For at least 14 years after logging, regrowth forests remain net sources of CO2 to the atmosphere. This has important implications regarding the effects of Siberian forest management on atmospheric concentrations. For many years after logging has taken place, regrowth forests remain weaker sinks for atmospheric CO2 than are nearby old-growth forests.
    Type of Medium: Electronic Resource
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  • 3
    Publication Date: 2018-03-12
    Description: The basidiomycete yeast Rhodosporidium toruloides (a.k.a. Rhodotorula toruloides ) accumulates high concentrations of lipids and carotenoids from diverse carbon sources. It has great potential as a model for the cellular biology of lipid droplets and for sustainable chemical production. We developed a method for high-throughput genetics (RB-TDNAseq), using sequence-barcoded Agrobacterium tumefaciens T-DNA insertions. We identified 1337 putative essential genes with low T-DNA insertion rates. We functionally profiled genes required for fatty acid catabolism and lipid accumulation, validating results with 35 targeted deletion strains. We identified a high-confidence set of 150 genes affecting lipid accumulation, including genes with predicted function in signaling cascades, gene expression, protein modification and vesicular trafficking, autophagy, amino acid synthesis and tRNA modification, and genes of unknown function. These results greatly advance our understanding of lipid metabolism in this oleaginous species and demonstrate a general approach for barcoded mutagenesis that should enable functional genomics in diverse fungi.
    Electronic ISSN: 2050-084X
    Topics: Natural Sciences in General
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