Role of a Conserved Glutamate Residue in the \u3cem\u3eEscherichia coli\u3c/em\u3e SecA ATPase Mechanism

Escherichia coli SecA uses ATP to drive the transport of proteins across cell membranes. Glutamate 210 in the “DEVD” Walker B motif of the SecA ATP-binding site has been proposed as the catalytic base for ATP hydrolysis (Hunt, J. F., Weinkauf, S., Henry, L., Fak, J. J., McNicholas, P., Oliver, D. B., and Deisenhofer, J. (2002) Science 297, 2018–2026). Consistent with this hypothesis, we find that mutation of glutamate 210 to aspartate results in a 90-fold reduction of the ATP hydrolysis rate compared with wild type SecA, 0.3 s–1versus 27 s–1, respectively. SecA-E210D also releases ADP at a slower rate compared with wild type SecA, suggesting that in addition to serving as the catalytic base, glutamate 210 might aid turnover as well. Our results contradict an earlier report that proposed aspartate 133 as the catalytic base (Sato, K., Mori, H., Yoshida, M., and Mizushima, S. (1996) J. Biol. Chem. 271, 17439–17444). Re-evaluation of the SecA-D133N mutant used in that study confirms its loss of ATPase and membrane translocation activities, but surprisingly, the analogous SecA-D133A mutant retains full activity, revealing that this residue does not play a key role in catalysis

Fragmentation of foamed silicic melts: an experimental study

We present the first experimental investigation of the fragmentation behavior of two-phase (melt+gas) rhyolitic systems under rapid decompression. Two-phase samples have been generated by foaming water-oversaturated rhyolitic melts up to 900°C and up to 18 MPa prior to rapid decompression in a fragmentation bomb. The fragmented particles or experimental pyroclasts were recovered for analysis. Several features of naturally foamed pumices have been reproduced, including the generation of both isotropic and tube pumices. We focus here on the fragmentation behavior. Fragmentation occurred through a layer-by-layer process, in the brittle regime of melt response. We investigated the influence of the magnitude of the decompression (4 to 18 MPa), the porosity (0 to 85 vol%) and the pore morphology (tube versus isotropic) on the fragment size distribution. Less vesicular samples (porosity50 vol%) yield coarser fragments when decompressed below 15 MPa and finer fragments when decompressed above 15 MPa. Increasing decompression of the vesicular samples results in a decrease in fragment size of 0.2 Φ unit/MPa. The presence of tubes instead of isotropic pores in vesicular samples generates finer fragments under decompression. Implications for dome eruptions are discussed

Bromoform and dibromomethane measurements in the seacoast region of New Hampshire, 2002–2004

Atmospheric measurements of bromoform (CHBr3) and dibromomethane (CH2Br2) were conducted at two sites, Thompson Farm (TF) in Durham, New Hampshire (summer 2002–2004), and Appledore Island (AI), Maine (summer 2004). Elevated mixing ratios of CHBr3 were frequently observed at both sites, with maxima of 37.9 parts per trillion by volume (pptv) and 47.4 pptv for TF and AI, respectively. Average mixing ratios of CHBr3 and CH2Br2 at TF for all three summers ranged from 5.3–6.3 and 1.3–2.3 pptv, respectively. The average mixing ratios of both gases were higher at AI during 2004, consistent with AI\u27s proximity to sources of these bromocarbons. Strong negative vertical gradients in the atmosphere corroborated local sources of these gases at the surface. At AI, CHBr3 and CH2Br2 mixing ratios increased with wind speed via sea‐to‐air transfer from supersaturated coastal waters. Large enhancements of CHBr3 and CH2Br2 were observed at both sites from 10 to 14 August 2004, coinciding with the passage of Tropical Storm Bonnie. During this period, fluxes of CHBr3 and CH2Br2 were 52.4 ± 21.0 and 9.1 ± 3.1 nmol m−2 h−1, respectively. The average fluxes of CHBr3 and CH2Br2 during nonevent periods were 18.9 ± 12.3 and 2.6 ± 1.9 nmol m−2 h−1, respectively. Additionally, CHBr3 and CH2Br2 were used as marine tracers in case studies to (1) evaluate the impact of tropical storms on emissions and distributions of marine‐derived gases in the coastal region and (2) characterize the transport of air masses during pollution episodes in the northeastern United States

The Uniqueness Theorem for Entanglement Measures

We explore and develop the mathematics of the theory of entanglement measures. After a careful review and analysis of definitions, of preliminary results, and of connections between conditions on entanglement measures, we prove a sharpened version of a uniqueness theorem which gives necessary and sufficient conditions for an entanglement measure to coincide with the reduced von Neumann entropy on pure states. We also prove several versions of a theorem on extreme entanglement measures in the case of mixed states. We analyse properties of the asymptotic regularization of entanglement measures proving, for example, convexity for the entanglement cost and for the regularized relative entropy of entanglement.Comment: 22 pages, LaTeX, version accepted by J. Math. Phy

Hierarchical metabolomics demonstrates substantial compositional similarity between genetically-modified and conventional potato crops

There is current debate whether genetically modified (GM) plants might contain unexpected, potentially undesirable changes in overall metabolite composition. However, appropriate analytical technology and acceptable metrics of compositional similarity require development. We describe a comprehensive comparison of total metabolites in field-grown GM and conventional potato tubers using a hierarchical approach initiating with rapid metabolome “fingerprinting” to guide more detailed profiling of metabolites where significant differences are suspected. Central to this strategy are data analysis procedures able to generate validated, reproducible metrics of comparison from complex metabolome data. We show that, apart from targeted changes, these GM potatoes in this study appear substantially equivalent to traditional cultivars

Biodistributions, Myelosuppression and Toxicities in Mice Treated with an Anti-CD45 Antibody Labeled with the α-Emitting Radionuclides Bismuth-213 or Astatine-211

We previously investigated the potential of targeted radiotherapy using a bismuth-213- labeled anti-CD45 antibody to replace total body irradiation as conditioning for hematopoietic cell transplantation in a canine model. While this approach allowed sustained marrow engraftment, limited availability, high cost and short half-life of bismuth-213 induced us to investigate an alternative α-emitting radionuclide, astatine-211, for the same application. Biodistribution and toxicity studies were conducted with conjugates of the anti-murine CD45 antibody 30F11 with either bismuth-213 or astatine-211. Mice were injected with 2-50 μCi on 10 μg or 20 μCi on 2 or 40 μg 30F11 conjugate. Biodistribution studies showed that the spleen contained the highest concentration of radioactivity, ranging from 167±23 to 417±109 % injected dose/gram (%ID/g) after injection of the astatine-211 conjugate and 45±9 to 166±11 %ID/g after injection of the bismuth-213 conjugate. The higher concentrations observed for astatine-211- labeled 30F11 were due to its longer half-life, which permitted better localization of isotope to the spleen before decay. Astatine-211 was more effective at producing myelosuppression for the same quantity of injected radioactivity. All mice injected with 20 or 50 μCi astatine-211 but none with the same quantities of bismuth-213 had lethal myeloablation. Severe reversible acute hepatic toxicity occurred with 50 μCi bismuth-213, but not with lower doses of bismuth-213 or with any dose of astatine-211. No renal toxicity occurred with either radionuclide. The data suggest that smaller quantities of astatine-211-labeled anti-CD45 antibody are sufficient to achieve myelosuppression and myeloablation with less non-hematological toxicity compared with bismuth-213-labeled antibody

Production of 10-methyl branched fatty acids in yeast

Background: Despite the environmental value of biobased lubricants, they account for less than 2% of global lubricant use due to poor thermo-oxidative stability arising from the presence of unsaturated double bonds. Methyl branched fatty acids (BFAs), particularly those with branching near the acyl-chain mid-point, are a high-performance alternative to existing vegetable oils because of their low melting temperature and full saturation. Results: We cloned and characterized two pathways to produce 10-methyl BFAs isolated from actinomycetes and γ-proteobacteria. In the two-step bfa pathway of actinomycetes, BfaB methylates Δ9 unsaturated fatty acids to form 10-methylene BFAs, and subsequently, BfaA reduces the double bond to produce a fully saturated 10-methyl branched fatty acid. A BfaA-B fusion enzyme increased the conversion efficiency of 10-methyl BFAs. The ten-methyl palmitate production (tmp) pathway of γ-proteobacteria produces a 10-methylene intermediate, but the TmpA putative reductase was not active in E. coli or yeast. Comparison of BfaB and TmpB activities revealed a range of substrate specificities from C14-C20 fatty acids unsaturated at the Δ9, Δ10 or Δ11 position. We demonstrated efficient production of 10-methylene and 10-methyl BFAs in S. cerevisiae by secretion of free fatty acids and in Y. lipolytica as triacylglycerides, which accumulated to levels more than 35% of total cellular fatty acids. Conclusions: We report here the characterization of a set of enzymes that can produce position-specific methylene and methyl branched fatty acids. Yeast expression of bfa enzymes can provide a platform for the large-scale production of branched fatty acids suitable for industrial and consumer applications

Further developments towards a genome-scale metabolic model of yeast

BACKGROUND: To date, several genome-scale network reconstructions have been used to describe the metabolism of the yeast Saccharomyces cerevisiae, each differing in scope and content. The recent community-driven reconstruction, while rigorously evidenced and well annotated, under-represented metabolite transport, lipid metabolism and other pathways, and was not amenable to constraint-based analyses because of lack of pathway connectivity. RESULTS: We have expanded the yeast network reconstruction to incorporate many new reactions from the literature and represented these in a well-annotated and standards-compliant manner. The new reconstruction comprises 1102 unique metabolic reactions involving 924 unique metabolites - significantly larger in scope than any previous reconstruction. The representation of lipid metabolism in particular has improved, with 234 out of 268 enzymes linked to lipid metabolism now present in at least one reaction. Connectivity is emphatically improved, with more than 90% of metabolites now reachable from the growth medium constituents. The present updates allow constraint-based analyses to be performed; viability predictions of single knockouts are comparable to results from in vivo experiments and to those of previous reconstructions. CONCLUSIONS: We report the development of the most complete reconstruction of yeast metabolism to date that is based upon reliable literature evidence and richly annotated according to MIRIAM standards. The reconstruction is available in the Systems Biology Markup Language (SBML) and via a publicly accessible database http://www.comp-sys-bio.org/yeastnet/

Submillimeter Number Counts From Statistical Analysis of BLAST Maps

We describe the application of a statistical method to estimate submillimeter galaxy number counts from confusion limited observations by the Balloon-borne Large Aperture Submillimeter Telescope (BLAST). Our method is based on a maximum likelihood fit to the pixel histogram, sometimes called 'P(D)', an approach which has been used before to probe faint counts, the difference being that here we advocate its use even for sources with relatively high signal-to-noise ratios. This method has an advantage over standard techniques of source extraction in providing an unbiased estimate of the counts from the bright end down to flux densities well below the confusion limit. We specifically analyse BLAST observations of a roughly 10 sq. deg. map centered on the Great Observatories Origins Deep Survey South (GOODS-S) field. We provide estimates of number counts at the three BLAST wavelengths, 250, 350, and 500 microns; instead of counting sources in flux bins we estimate the counts at several flux density nodes connected with power-laws. We observe a generally very steep slope for the counts of about -3.7 at 250 microns and -4.5 at 350 and 500 microns, over the range ~0.02-0.5 Jy, breaking to a shallower slope below about 0.015 Jy at all three wavelengths. We also describe how to estimate the uncertainties and correlations in this method so that the results can be used for model-fitting. This method should be well-suited for analysis of data from the Herschel satellite.Comment: Accepted for publication in the Astrophysical Journal; see associated data and other papers at http://blastexperiment.info

Changing concentrations of CO, CH₄, C₅H₈, CH₃Br, CH₃I, and dimethyl sulfide during the Southern Ocean Iron Enrichment Experiments

Oceanic iron (Fe) fertilization experiments have advanced the understanding of how Fe regulates biological productivity and air–sea carbon dioxide (CO₂) exchange. However, little is known about the production and consumption of halocarbons and other gases as a result of Fe addition. Besides metabolizing inorganic carbon, marine microorganisms produce and consume many other trace gases. Several of these gases, which individually impact global climate, stratospheric ozone concentration, or local photochemistry, have not been previously quantified during an Fe-enrichment experiment. We describe results for selected dissolved trace gases including methane (CH₄), isoprene (C₅H₈), methyl bromide (CH₃Br), dimethyl sulfide, and oxygen (O₂), which increased subsequent to Fe fertilization, and the associated decreases in concentrations of carbon monoxide (CO), methyl iodide (CH₃I), and CO₂ observed during the Southern Ocean Iron Enrichment Experiments