Paleoenvironmental controls on the abundances of magnetofossils in Southwestern Iberian margin

The file is the dataset for the manuscript entitled 'Paleoenvironmental controls on the abundances of magnetofossils in Southwestern Iberian margin' by He et al., including paleointensity, geochemical, gain size, rock magnetic and diversity of magnetofossils data shown in the manuscript. </p

Paleoenvironmental controls on the abundances of magnetofossils in Southwestern Iberian margin

The file is the dataset for the manuscript entitled 'Paleoenvironmental controls on the abundances of magnetofossils in Southwestern Iberian margin' by He et al., including paleointensity, geochemical, gain size, rock magnetic and diversity of magnetofossils data shown in the manuscript.</p

Inflating Graphene with Atomic Scale Blisters

Using 80 kV electron beam irradiation we have created graphene blister defects of additional carbon atoms incorporated into a graphene lattice. These structures are the antithesis of the vacancy defect with blister defects observed to contain up to six additional carbon atoms. We present aberration-corrected transmission electron microscopy data demonstrating the formation of a blister from an existing divacancy, together with further examples that undergo reconfiguration and annihilation under the electron beam. The relative stability of the observed variations of blister are discussed and considered in the context of previous calculations. It is shown that the blister defect is seldom found in isolation and is more commonly coupled with dislocations where it can act as an intermediate state, permitting dislocation core climb without the atom ejection from the graphene lattice required for nonconservative motion

Intermolecular phosphoryl transfer events assayed among CheS₃, CheA₃, and CheY₃.

<p>2–5 µM CheS₃, CheA₃, or their REC mutant forms were autophosphorylated in 200 µM ATP for 30 min before 1/10 volumes of 65 mM CheY₃ or REC domain truncations were added. (A, B) Neither CheA₃∼P nor CheA₃:D663A∼P are able to phosphorylate CheY₃ in Buffer 9 containing K⁺ and 6 mM Ca²⁺. (C, D) CheS₃∼P and CheS₃:D54A∼P phosphorylates CheY₃ within 15 sec of CheY₃ addition in Buffer 5 containing Na⁺, 3 mM Ca²⁺, and 3 mM Mg²⁺. (E) Intermolecular phosphoryl transfer analyses of CheA₃ and CheS₃. (A) CheA₃:D663A∼P phosphorylates CheS₃-REC1 in Buffer 15 containing K⁺ and 18 mM Mg²⁺. (F) CheS₃ is unable to phosphorylate CheA₃-REC in Buffer 15.</p

Metal ion dependent phosphorylation of CheA₃ and CheS₃.

<p>(A) Four possible phosphorylation states of phosphorylated hybrid histidine kinases (HHKs). (B) Metal cation dependencies of phosphorylation of isolated HHKs CheS₃ and CheA₃ and their receiver domain mutants.</p

Phosphate Flow between Hybrid Histidine Kinases CheA₃ and CheS₃ Controls <i>Rhodospirillum centenum</i> Cyst Formation

<div><p>Genomic and genetic analyses have demonstrated that many species contain multiple chemotaxis-like signal transduction cascades that likely control processes other than chemotaxis. The Che₃ signal transduction cascade from <i>Rhodospirillum centenum</i> is one such example that regulates development of dormant cysts. This Che-like cascade contains two hybrid response regulator-histidine kinases, CheA₃ and CheS₃, and a single-domain response regulator CheY₃. We demonstrate that <i>cheS₃</i> is epistatic to <i>cheA₃</i> and that only CheS₃∼P can phosphorylate CheY₃. We further show that CheA₃ derepresses cyst formation by phosphorylating a CheS₃ receiver domain. These results demonstrate that the flow of phosphate as defined by the paradigm <i>E. coli</i> chemotaxis cascade does not necessarily hold true for non-chemotactic Che-like signal transduction cascades.</p></div

Half-lives of phospho-HHKs.

<p>Standard deviations were calculated from two replicate experiments for each protein.</p

Characterization of <i>cheS₃</i>, <i>cheA₃</i> and <i>cheY₃</i> mutants.

<p>The encystment phenotypes of 11 strains including wild type and single, double, and point mutants of <i>cheS₃</i>, <i>cheA₃</i> and <i>cheY₃</i> were measured qualitatively by phase contrast microscopy and quantitatively by flow cytometry. (A) Growth on nutrient-rich CENS medium reveals hyper-cyst strains that overproduce cysts relative to wild type. (B) Growth on nutrient-limiting CENBA medium identifies hypo-cyst strains that under-produce cyst cells relative to wild type. Error bars in the bar graphs represent standard deviation obtained from two biological replicates. * (p<0.05), ** (p<0.01) when compared to the wild type (wt) strain in an unpaired <i>t</i>-test.</p

Identification of intramolecular phosphoryl transfer within CheA₃ and CheS₃.

<p>(A) CheA₃∼P is acid- and alkaline-labile, whereas the REC mutant CheA₃:D663A∼P is acid-labile and base-resistant. (B) Both CheS₃∼P and its REC mutant CheS₃:D54A are acid-labile and alkaline-stable. (C) CheA₃:D663A∼P phosphorylates CheA₃-REC truncation protein in Buffer 15 containing K⁺ and 18 mM Mg²⁺. (D) Phosphoryl transfer from CheS₃:D54A∼P to CheS₃-REC1 truncation protein was not observed in Buffer 15.</p

Gene arrangement of the <i>R. centenum che₃</i> cluster and domain organizations of CheA₃, CheS₃, and CheY₃.

<p>Arrow length is proportional to gene length. Abbreviations: REC, receiver domain; PAS, <u>P</u>er, <u>A</u>rnt, <u>S</u>im domains; HWE_HK, HWE superfamily of histidine kinases; Hpt, histidine phosphotransfer domain; CA, catalytic and ATP-binding domain. Conserved histidine and aspartate residues as putative phosphorylation sites are denoted for each protein. The start and end amino acid positions of the receiver domains as well as those of the full proteins are also labeled according to the prediction by SMART <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004002#pgen.1004002-Schultz1" target="_blank">[48]</a>.</p