Determination of the (3x3)-Sn/Ge(111) structure by photoelectron diffraction

At a coverage of about 1/3 monolayer, Sn deposited on Ge(111) below 550 forms a metastable (sqrt3 x sqrt3)R30 phase. This phase continuously and reversibly transforms into a (3x3) one, upon cooling below 200 K. The photoemission spectra of the Sn 4d electrons from the (3x3)-Sn/Ge(111) surface present two components which are attributed to inequivalent Sn atoms in T4 bonding sites. This structure has been explored by photoelectron diffraction experiments performed at the ALOISA beamline of the Elettra storage ring in Trieste (Italy). The modulation of the intensities of the two Sn components, caused by the backscattering of the underneath Ge atoms, has been measured as a function of the emission angle at fixed kinetic energies and viceversa. The bond angle between Sn and its nearest neighbour atoms in the first Ge layer (Sn-Ge1) has been measured by taking polar scans along the main symmetry directions and it was found almost equivalent for the two components. The corresponding bond lengths are also quite similar, as obtained by studying the dependence on the photoelectron kinetic energy, while keeping the photon polarization and the collection direction parallel to the Sn-Ge1 bond orientation (bond emission). A clear difference between the two bonding sites is observed when studying the energy dependence at normal emission, where the sensitivity to the Sn height above the Ge atom in the second layer is enhanced. This vertical distance is found to be 0.3 Angstroms larger for one Sn atom out of the three contained in the lattice unit cell. The (3x3)-Sn/Ge(111) is thus characterized by a structure where the Sn atom and its three nearest neighbour Ge atoms form a rather rigid unit that presents a strong vertical distortion with respect to the underneath atom of the second Ge layer.Comment: 10 pages with 9 figures, added reference

Robustness encoded across essential and accessory replicons of the ecologically versatile bacterium <i>Sinorhizobium meliloti</i>

<div><p>Bacterial genome evolution is characterized by gains, losses, and rearrangements of functional genetic segments. The extent to which large-scale genomic alterations influence genotype-phenotype relationships has not been investigated in a high-throughput manner. In the symbiotic soil bacterium <i>Sinorhizobium meliloti</i>, the genome is composed of a chromosome and two large extrachromosomal replicons (pSymA and pSymB, which together constitute 45% of the genome). Massively parallel transposon insertion sequencing (Tn-seq) was employed to evaluate the contributions of chromosomal genes to growth fitness in both the presence and absence of these extrachromosomal replicons. Ten percent of chromosomal genes from diverse functional categories are shown to genetically interact with pSymA and pSymB. These results demonstrate the pervasive robustness provided by the extrachromosomal replicons, which is further supported by constraint-based metabolic modeling. A comprehensive picture of core <i>S</i>. <i>meliloti</i> metabolism was generated through a Tn-seq-guided <i>in silico</i> metabolic network reconstruction, producing a core network encompassing 726 genes. This integrated approach facilitated functional assignments for previously uncharacterized genes, while also revealing that Tn-seq alone missed over a quarter of wild-type metabolism. This work highlights the many functional dependencies and epistatic relationships that may arise between bacterial replicons and across a genome, while also demonstrating how Tn-seq and metabolic modeling can be used together to yield insights not obtainable by either method alone.</p></div

Visualization of the location of transposon insertion sites.

<p>An image of the <i>pst</i> locus of <i>S</i>. <i>meliloti</i> generated using the Integrative Genomics Viewer [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007357#pgen.1007357.ref078" target="_blank">78</a>]. Chromosomal nucleotide positions are indicated along the top of the image, and the location and relative abundance of transposon insertions are indicated by the red bars. Non-essential genes contain a high density of transposon insertions, whereas essential genes have few to no transposon insertions. Genes are color coded based on their fitness classification. The <i>pstS</i>, <i>pstC</i>, <i>pstA</i>, <i>pstB</i>, <i>phoU</i>, and <i>phoB</i> genes are co-transcribed as a single operon [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007357#pgen.1007357.ref092" target="_blank">92</a>], and previous work demonstrated that non-polar <i>phoU</i> mutations are lethal in <i>S</i>. <i>meliloti</i>, whereas polar mutations are not lethal [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007357#pgen.1007357.ref093" target="_blank">93</a>]. The lack of insertions within the <i>phoU</i> coding region is therefore consistent with the non-polar nature of the transposon.</p

<i>In silico</i> analysis of genetic redundancy in <i>S</i>. <i>meliloti</i>.

<p>The effects of single or double gene deletion mutants were predicted <i>in silico</i> with the genome-scale <i>S</i>. <i>meliloti</i> metabolic model. All data in this figure comes from <i>in silico</i> metabolic modeling. (<b>A</b>-<b>C</b>) The color of each hexagon is representative of the number of genes, gene pairs, or reaction pairs plotted at that location according to the density bar below each panel. The diagonal line serves as a reference line of a perfect correlation (i.e., where all data would fall if no effects were observed). The data underlying this figure and the corresponding gene/reaction names are provided in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007357#pgen.1007357.s035" target="_blank">S7 Dataset</a>. (<b>A</b>) A scatter plot comparing the grRatio (growth rate of mutant / growth rate of non-mutant) for gene deletion mutations in the presence (wild-type) versus absence (ΔpSymAB) of the pSymA/pSymB model genes. Genes whose deletion had either no effect or were lethal in both cases are not included in the plot. (<b>B</b>) A scatter plot comparing the grRatio for each double gene deletion pair (where one gene was on the chromosome and the other on pSymA or pSymB) observed <i>in silico</i> versus the predicted grRatio based on the grRatio of the single deletions (grRatio1 * grRatio2). Only gene pairs with an observed grRatio at least 10% less than the expected are shown. (<b>C</b>) A scatter plot comparing the grRatio for each double gene deletion pair (both genes on the chromosome) observed <i>in silico</i> versus the predicted grRatio. Only gene pairs with an observed grRatio at least 10% less than the expected are shown.</p

Sample genes showing strain specific phenotypes.

<p>The top ten genes from each of the indicated groupings, as determined based on the ratio of GEI (Gene Essentiality Index) scores of the two strains, are shown. GEI scores are shown first for the wild-type (WT) followed by the scores for the ΔpSymAB (dAB) strain.</p