Conformational Electroresistance and Hysteresis in Nanoclusters

The existence of multiple thermodynamically stable isomer states is one of the most fundamental properties of small clusters. This work shows that the conformational dependence of the Coulomb charging energy of a nanocluster leads to a giant electroresistance, where charging induced conformational distortion changes the blockade voltage. The intricate interplay between charging and conformation change is demonstrated in a nanocluster Zn3O4 by combining a first-principles calculation with a temperature-dependent transport model. The predicted hysteretic Coulomb blockade staircase in the current–voltage curve adds another dimension to the rich phenomena of tunneling electroresistance. The new mechanism provides a better controlled and repeatable platform to study conformational electroresistance

Evolutionary history of ExoR is congruent with speciation history of Rhizobiales.

<p>ML and Bayesian phylogenetic patterns support the existence of an ExoR ancestor that arose prior to diversification among the <i>Rhizobiales</i> and five <i>Rhodobacterales</i> species identified in our genomic searches. The ExoR gene was maintained among these species, giving rise to the ortholog set. Phylogenetic reconstruction of ExoR orthologs agrees with currently accepted speciation patterns.</p

ExoR, ExoS, and ChvI proteins interact to create the RSI Invasion Switch in <i>S</i>. <i>meliloti</i>.

<p>ExoR is composed of Sel1 repeats, is secreted to the periplasm as ExoR_m (lacking the signal peptide), and is cleaved to release its suppression of ExoS. The domain architectures of ExoS and ChvI, along with phosphorylation sites, are illustrated here. Signal transmission is achieved via a phosphorylation cascade and ChvI completes the “switch” by binding to DNA to alter gene expression [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135655#pone.0135655.ref096" target="_blank">96</a>]. Our current model suggests that the levels of ExoR_m in the periplasm are maintained through the combination of biosynthesis and proteolysis. Proteolysis is possibly sensitive to host signals or to changes in environmental conditions. These mechanisms allow for (1) ExoR_m levels to be dramatically reduced in the presence of host signals, (2) the turning “ON” of the RSI invasion switch, (3) the activation of host-invading genes, and (4) the suppression of free-living genes.</p

RSI Synteny analysis within Rhizobiales and ancestral Alphaproteobacteria.

<p>Clusters of orthologous gene (COG) groups for representative Proteobacteria are presented for comparison to the prototype, the loci of Rm1021. Each COG, as defined in the IMG database, is represented by an arrow of different color. For the <i>exoR-exoS-chvI</i> genes, a lack of homologs or orthologs is presented as an ORF with a solid or dotted slash, respectively. The sizes and positions of the ORFs are approximate, representing relative expansions/deletions. The ExoR ortholog found in <i>Azorhizobium caulinodans</i>, although annotated as an exopolysaccharide regulator, is predicted to encode transmembrane helices and is a structural outlier as compared to ExoR-like molecules found in other Rhizobiales. Lifestyles and host type are given by A (animal pathogen), P (plant pathogen), or S (symbionts). Gene loss/gain is indicated with-/+, respectively. COG# color key (L to R): Dark yellow, 0499; green, 1925; light blue, 2893; dark violet, 1493; blue (exoS/chvG), 0642; orange (chvI), 0745; light violet, 1866; pale green, 1186; grey, 1652; white, 3145; red (exoR), 0790; purple, 0708; magenta, 1502; bright yellow, 0232; turquoise (sporulation-domain encoding). In Rm1021 RSI loci are <i>exoS</i> (bp49252–51039), <i>chvI</i> (51419–52141), and <i>exoR</i> (1637310–1638116) on the SMc chromosome.</p

The identification of ExoR orthologs.

<p>The identification of ExoR orthologs.</p

Conserved sequence evolution of ChvI in Rhizobiales and selected Rhodobacterales.

<p>As a cognate TCS pair, ChvI and ExoS sequences are expected to diversify at similar rates. However, the ChvI phylogeny suggests that it is under strong purifying selection with the lowest amino-acid substitution rate among the three components. It is possible that the functional role of ChvI orthologs (i.e., DNA binding) limits diversification.</p

Phylogenetic Co-Occurrence of ExoR, ExoS, and ChvI, Components of the RSI Bacterial Invasion Switch, Suggests a Key Adaptive Mechanism Regulating the Transition between Free-Living and Host-Invading Phases in Rhizobiales

<div><p>Both bacterial symbionts and pathogens rely on their host-sensing mechanisms to activate the biosynthetic pathways necessary for their invasion into host cells. The Gram-negative bacterium <i>Sinorhizobium meliloti</i> relies on its RSI (ExoR-ExoS-ChvI) Invasion Switch to turn on the production of succinoglycan, an exopolysaccharide required for its host invasion. Recent whole-genome sequencing efforts have uncovered putative components of RSI-like invasion switches in many other symbiotic and pathogenic bacteria. To explore the possibility of the existence of a common invasion switch, we have conducted a phylogenomic survey of orthologous ExoR, ExoS, and ChvI tripartite sets in more than ninety proteobacterial genomes. Our analyses suggest that functional orthologs of the RSI invasion switch co-exist in Rhizobiales, an order characterized by numerous invasive species, but not in the order’s close relatives. Phylogenomic analyses and reconstruction of orthologous sets of the three proteins in Alphaproteobacteria confirm Rhizobiales-specific gene synteny and congruent RSI evolutionary histories. Evolutionary analyses further revealed site-specific substitutions correlated specifically to either animal-bacteria or plant-bacteria associations. Lineage restricted conservation of any one specialized gene is in itself an indication of species adaptation. However, the orthologous phylogenetic co-occurrence of all interacting partners within this single signaling pathway strongly suggests that the development of the RSI switch was a key adaptive mechanism. The RSI invasion switch, originally found in <i>S</i>. <i>meliloti</i>, is a characteristic of the Rhizobiales, and potentially a conserved crucial activation step that may be targeted to control host invasion by pathogenic bacterial species.</p></div

Site-specific evolutionary rates of ExoR (A) and ExoS (B).

<p>Substitution rates (y-axis) at amino-acid positions (x-axis, numbers based on (A) the periplasmic region of <i>S</i>. <i>meliloti</i> ExoS and (B) full-length ExoR) were obtained using Rate4Site [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135655#pone.0135655.ref094" target="_blank">94</a>]. While variable and conserved residues are evenly dispersed in ExoR (B), two variable residues are notable and specific to two regions in ExoS (A). We hypothesize, subject to experimental verification, that these two variable regions form binding domains to ExoR and are the molecular basis of host-specific responses among Rhizobiales species.</p

Two host-associated radical amino-acid substitutions in ExoS.

<p>Sequences within the two hypervariable regions (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135655#pone.0135655.g006" target="_blank">Fig 6</a>) of ExoS are displayed according to a phylogeny of ExoS sequences. Based on parsimony reasoning, an asparagine residue (N131of the ExoS periplasmic region) is an evolutionarily derived state that is conserved among plant- or dinoflagellate-associated taxa. A tryptophan residue (W61of the ExoS periplasmic region) is derived from a leucine ancestor and conserved among animal-infecting species with the exception of <i>Rhizobium leguminosarum</i> (a plant pathogen).</p

Clar’s Goblet on Graphene: Field-Modulated Charge Transfer in a Hydrocarbon Heterostructure

In certain configurations, the aromatic properties of benzene ring structured molecules allow for unpaired, reactive valence electrons (known as radicals). Clar’s goblets are such molecules. With an even number of unpaired radicals, these nanographenes are topologically frustrated hydrocarbons in which π-bonding network and topology of edges give rise to the magnetism. Clar’s goblets are therefore valued as prospective qubits provided they can be modulated between magnetic states. Using first-principles DFT, we demonstrate the effects of adsorption on both molecule and substrate in a graphene–Clar’s goblet heterostructure. We look at the energy difference bewteen FM and AFM states of the system and discuss underlying physical and chemical mechanisms in reference to the highest occupied molecular orbital (HOMO) and second HOMO (HOMO–1). We find that the HOMO of the molecule in the FM state is right at the Fermi surface, which leads to the hybridization between molecular state and the graphene state near the Dirac point. Furthermore, we investigate qualitative changes in charge realignment and magnetic state under a variable electric field. Transitions from FM to AFM and back to FM states are observed