A 'Candidatus Liberibacter solanacearum' Haplotype B-Specific Family of Candidate Bacterial Effectors.

'Candidatus Liberibacter solanacearum' (Lso) is a phloem-limited pathogen associated with devastating diseases in members of the Solanaceae and Apiaceae and vectored by several psyllid species. Different Lso haplotypes have been identified, and LsoA and LsoB are responsible for diseases in Solanaceae crops. Our efforts are aimed at identifying pathogenicity factors used by this bacterium to thrive in different hosts. Bacterial secreted proteins can play a role in host colonization or the manipulation of the host immune responses; these proteins are called effectors. In this study, we identified six LsoB-specific proteins with a conserved secretion motif as well as a conserved N-terminal domain in the mature protein. These proteins had different expression and secretion patterns but a similar subcellular localization in Nicotiana benthamiana leaves, suggesting that they play different roles regardless of their conserved secretion motif. One of these proteins, CKC_04425, was expressed at high levels in the insect vector and the host plant, indicating that it could play a role in both the plant and insect hosts, whereas the others were mainly expressed in the plant. One protein, CKC_05701, was able to efficiently suppress programmed cell death and reactive oxygen species production, suggesting that it may have a virulence role in LsoB-specific pathogenesis.

CLIBASIA_00460 Disrupts Hypersensitive Response and Interacts with Citrus Rad23 Proteins.

'Candidatus Liberibacter asiaticus' (CLas) is a bacterium that causes Huanglongbing, also known as citrus greening, in citrus plants. 'Candidatus Liberibacter solanacearum' (Lso) is a close relative of CLas and in the US it infects solanaceous crops, causing zebra chip disease in potato. Previously, we have identified the Lso hypothetical protein effector 1 (Lso-HPE1). This protein uses a signal peptide for secretion; disrupts programmed cell death; and interacts with tomato RAD23c, d, and e proteins, but not with RAD23a. In this study, we evaluated whether CLIBASIA_00460, the CLas homolog of Lso-HPE1 interacted with citrus RAD23 proteins and disrupted their programmed cell death. Based on the yeast two-hybrid assay results, CLIBASIA_00460 interacted with citrus RAD23c and RAD23d, but not with citrus RAD23b. These results were confirmed using bimolecular fluorescence complementation assays, which showed that these interactions occurred in cell puncta, but not in the nucleus or cytoplasm. Additionally, CLIBASIA_00460 was able to disrupt the PrfD1416V-induced hypersensitive response. Therefore, based on the similar interactions between Lso-HPE1 and CLIBASIA_00460 with the host RAD23 proteins and their ability to inhibit cell death in plants, we propose that these effectors may have similar functions during plant infection.

Characteristics of sulfur atoms adsorbed on Ag(100), Ag(110), and Ag(111) as probed with scanning tunneling microscopy: experiment and theory.

In this paper, we report that S atoms on Ag(100) and Ag(110) exhibit a distinctive range of appearances in scanning tunneling microscopy (STM) images, depending on the sample bias voltage, VS. Progressing from negative to positive VS, the atomic shape can be described as a round protrusion surrounded by a dark halo (sombrero) in which the central protrusion shrinks, leaving only a round depression. This progression resembles that reported previously for S atoms on Cu(100). We test whether DFT can reproduce these shapes and the transition between them, using a modified version of the Lang-Tersoff-Hamann method to simulate STM images. The sombrero shape is easily reproduced, but the sombrero-depression transition appears only for relatively low tunneling current and correspondingly realistic tip-sample separation, dT, of 0.5-0.8 nm. Achieving these conditions in the calculations requires sufficiently large separation (vacuum) between slabs, together with high energy cutoff, to ensure appropriate exponential decay of electron density into vacuum. From DFT, we also predict that an analogous transition is not expected for S atoms on Ag(111) surfaces. The results are explained in terms of the through-surface conductance, which defines the background level in STM, and through-adsorbate conductance, which defines the apparent height at the point directly above the adsorbate. With increasing VS, for Ag(100) and Ag(110), we show that through-surface conductance increases much more rapidly than through-adsorbate conductance, so the apparent adsorbate height drops below background. In contrast, for Ag(111) the two contributions increase at more comparable rates, so the adsorbate level always remains above background and no transition is seen.

Lateral Hopping of CO on Ag(110) by Multiple Overtone Excitation.

A novel type of action spectrum representing multiple overtone excitations of the v(M-C) mode was observed for lateral hopping of a CO molecule on Ag(110) induced by inelastically tunneled electrons from the tip of a scanning tunneling microscope. The yield of CO hopping shows sharp increases at 261±4 mV, corresponding to the C-O internal stretching mode, and at 61±2, 90±2, and 148±7 mV, even in the absence of corresponding fundamental vibrational modes. The mechanism of lateral CO hopping on Ag(110) was explained by the multistep excitation of overtone modes of v(M-C) based on the numerical fitting of the action spectra, the nonlinear dependence of the hopping rate on the tunneling current, and the hopping barrier obtained from thermal diffusion experiments.

Formation of Two-Dimensional Copper Selenide on Cu(111) at Very Low Selenium Coverage.

Using scanning tunneling microscopy (STM), we observed that adsorption of Se on Cu(111) produced islands with a (√3×√3)R30° structure at Se coverages far below the structure's ideal coverage of 1/3 monolayer. On the basis of density functional theory (DFT), these islands cannot form due to attractive interactions between chemisorbed Se atoms. DFT showed that incorporating Cu atoms into the √3-Se lattice stabilizes the structure, which provided a plausible explanation for the experimental observations. STM revealed three types of √3 textures. We assigned two of these as two-dimensional layers of strained CuSe, analogous to dense planes of bulk klockmannite (CuSe). Klockmannite has a bulk lattice constant that is 11 % shorter than √3 times the surface lattice constant of Cu(111). This offers a rationale for the differences observed between these textures, for which strain limits the island size or distorts the √3 lattice. STM showed that existing step edges adsorb Se and facet toward ⟨12‾ 1⟩, which is consistent with DFT.

Identification of Au-S complexes on Au(100).

Using a combination of scanning tunneling microscopy and density functional theory (DFT) calculations, we have identified a set of related Au-S complexes that form on Au(100), when sulfur adsorbs and lifts the hexagonal surface reconstruction. The predominant complex is diamond-shaped with stoichiometry Au4S5. All of the complexes can be regarded as combinations of S-Au-S subunits. The complexes exist within, or at the edges of, p(2 × 2) sulfur islands that cover the unreconstructed Au regions, and are observed throughout the range of S coverage examined in this study, 0.009 to 0.12 monolayers. A qualitative model is developed which incorporates competitive formation of complexes, Au rafts, and p(2 × 2) sulfur islands, as Au atoms are released by the surface structure transformation.

Reconstruction of steps on the Cu(111) surface induced by sulfur.

A rich menagerie of structures is identified at 5 K following adsorption of low coverages (≤0.05 monolayers) of S on Cu(111) at room temperature. This paper emphasizes the reconstructions at the steps. The A-type close-packed step has 1 row of S atoms along its lower edge, where S atoms occupy alternating pseudo-fourfold-hollow (p4fh) sites. Additionally, there are 2 rows of S atoms of equal density on the upper edge, bridging a row of extra Cu atoms, together creating an extended chain. The B-type close-packed step exhibits an even more complex reconstruction, in which triangle-shaped groups of Cu atoms shift out of their original sites and form a base for S adsorption at (mostly) 4fh sites. We propose a mechanism by which these triangles could generate Cu-S complexes and short chains like those observed on the terraces.

Self-organization of S adatoms on Au(111): √3R30° rows at low coverage.

Using scanning tunneling microscopy, we observe an adlayer structure that is dominated by short rows of S atoms, on unreconstructed regions of a Au(111) surface. This structure forms upon adsorption of low S coverage (less than 0.1 monolayer) on a fully reconstructed clean surface at 300 K, then cooling to 5 K for observation. The rows adopt one of three orientations that are rotated by 30° from the close-packed directions of the Au(111) substrate, and adjacent S atoms in the rows are separated by √3 times the surface lattice constant, a. Monte Carlo simulations are performed on lattice-gas models, derived using a limited cluster expansion based on density functional theory energetics. Models which include long-range pairwise interactions (extending to 5a), plus selected trio interactions, successfully reproduce the linear rows of S atoms at reasonable temperatures.

Functionalization of graphene grown on metal substrate with atomic oxygen: enolate vs epoxide.

Graphene functionalization is of great importance in applying graphene as a component in functional devices or in activating it for use as a catalyst. Here we reveal that atomic oxidation of epitaxial graphene grown on a metal substrate results in the formation of enolate, i.e., adsorption of atomic oxygen at the on-top position, on the basal plane of a graphene, using periodic density functional theory calculations. This is striking because the enolate corresponds to the transition state between the epoxides on free-standing graphene and on graphite. Improved interfacial interaction between graphene and the metal substrate during atomic oxidation makes the graphene enolate a local minimum and further highly stabilizes it over the graphene epoxide. Our results provide not only a novel perspective for a chemical route to functionalizing graphene but also a new opportunity to utilize graphene enolate for graphene-based applications.

Treatment of Rapamycin and Evaluation of an Autophagic Response in the Gut of Bactericera cockerelli (Sulc).

Autophagy is a catabolic process that results in the autophagosomic-lysosomal degradation of bulk cytoplasmic content, abnormal protein aggregates, and excess of/or damaged organelles to promote cell survival. Autophagy is also a component of innate immunity in insects and is involved in the clearance of pathogens, including bacteria. The potato psyllid, Bactericera cockerelli, transmits the plant bacterial pathogen 'Candidatus Liberibacter solanacearum' (Lso) in the Americas and causes serious damage to solanaceous crops. Our previous studies showed that autophagy could be involved in the psyllid response to Lso and could affect pathogen acquisition. However, the tools to evaluate this response have not been validated in psyllids. To this end, the effect of rapamycin, a commonly used autophagy inducer, on potato psyllid survival and the expression of autophagy-related genes was evaluated. Further, the autophagic activity was assessed via microscopy and by measuring the autophagic flux. Artificial diet-feeding assays using rapamycin resulted in significant psyllid mortality, an increase in the autophagic flux, as well as an increase in the amount of autolysosomes. This study represents a stepping stone in determining the role of autophagy in psyllid immunity.

Accumulation and Transmission of 'Candidatus Liberibacter solanacearum' Haplotypes by the Nymphs of Two Psyllid Vectors.

'Candidatus Liberibacter solanacearum' (Lso) is a plant pathogenic bacterium transmitted by psyllids that causes significant agricultural damage. Several Lso haplotypes have been reported. Among them, LsoA and LsoB are transmitted by the potato psyllid Bactericera cockerelli and infect solanaceous crops, and LsoD is transmitted by the carrot psyllid B. trigonica and infects apiaceous crops. Several studies evaluated the transmission of these haplotypes by adult psyllids. However, fewer data are available on the transmission of different Lso haplotypes by psyllid nymphs. In this study, we investigated the transmission of these three haplotypes by psyllid nymphs to expand our basic understanding of Lso transmission. Specifically, the objective was to determine if the haplotypes differed in their transmission rates by nymphs and if LsoA and LsoB accumulated at different rates in the guts of nymphs as it occurs in adults. First, we quantified LsoA and LsoB titers in the guts of third- and fifth-instar potato psyllid nymphs. We found similar LsoA titers in the two nymphal stages, while LsoB titer was lower in the gut of the third-instar nymphs compared to fifth-instar nymphs. Second, we assessed the transmission efficiency of LsoA and LsoB by third-instar nymphs to tomato plants, revealing that LsoA was transmitted earlier and with higher efficiency than LsoB. Finally, we examined the transmission of LsoD by carrot psyllid nymphs to celery plants and demonstrated an age-related difference in the transmission rate. These findings provide valuable insights into the transmission dynamics of different Lso haplotypes by nymphal vectors, shedding light on their epidemiology and interactions with their psyllid vectors.

Angular intensity distribution of a molecular oxygen beam scattered from a graphite surface.

The scattering of the oxygen molecule from a graphite surface has been studied using a molecular beam scattering technique. The angular intensity distributions of scattered oxygen molecules were measured at incident energies from 291 to 614 meV with surface temperatures from 150 to 500 K. Every observed distribution has a single peak at a larger final angle than the specular angle of 45° which indicates that the normal component of the translation energy of the oxygen molecule is lost by the collision with the graphite surface. The amount of the energy loss by the collision has been roughly estimated as about 30-41% based on the assumption of the tangential momentum conservation during the collision. The distributions have also been analyzed with two theoretical models, the hard cubes model and the smooth surface model. These results indicate that the scattering is dominated by a single collision event of the particle with a flat surface having a large effective mass. The derived effective mass of the graphite surface for the incoming oxygen is 9-12 times heavier than that of a single carbon atom, suggesting a large cooperative motion of the carbon atoms in the topmost graphene layer.

Localized Graphitization on Diamond Surface as a Manifestation of Dopants.

Doped diamond electrodes have attracted significant attention for decades owing to their excellent physical and electrochemical properties. However, direct experimental observation of dopant effects on the diamond surface has not been available until now. Here, low-temperature scanning tunneling microscopy is utilized to investigate the atomic-scale morphology and electronic structures of (100)- and (111)-oriented boron-doped diamond (BDD) electrodes. Graphitized domains of a few nanometers are shown to manifest the effects of boron dopants on the BDD surface. Confirmed by first-principles calculations, local density of states measurements reveal that the electronic structure of these features is characterized by in-gap states induced by boron-related lattice deformation. The dopant-related graphitization is uniquely observed in BDD (111), which explains its electrochemical superiority over the (100) facet. These experimental observations provide atomic-scale information about the role of dopants in modulating the conductivity of diamond, as well as, possibly, other functional doped materials.

Identification of an AgS2 Complex on Ag(110).

Adsorbed sulfur has been investigated on the Ag(110) surface at two different coverages, 0.02 and 0.25 monolayers. At the lower coverage, only sulfur adatoms are present. At the higher coverage, there are additional bright features which we identify as linear, independent AgS2 complexes. This identification is based upon density functional theory (DFT) and its comparison with experimental observations including bias dependence and separation between complexes. DFT also predicts the absence of AgS2 complexes at low coverage, and the development of AgS2 complexes around a coverage of 0.25 monolayers of sulfur, as is experimentally observed. To our knowledge, this is the first example of an isolated linear sulfur-metal-sulfur complex.

Full-Length Infectious Clones of Two New Isolates of Tomato Mosaic Virus Induce Distinct Symptoms Associated with Two Differential Amino Acid Residues in 128-kDa Protein.

In 2017, two new tomato mosaic virus (ToMV) isolates were collected from greenhouses in Buyeo, Chungcheongnam-do, South Korea. Full-length cDNAs of the new ToMV isolates were cloned into dual cauliflower mosaic virus 35S and T7 promoter-driven vectors, sequenced and their pathogenicities investigated. The nucleotide sequences of isolates GW1 (MH507165) and GW2 (MH507166) were 99% identical, resulting in only two amino acid differences in nonconserved region II and the helicase domain, Ile668Thr and Val834Ile. The two isolates were most closely related to a ToMV isolate from Taiwan (KJ207374). Isolate GW1 (Ile668, Val834) induced a systemic hypersensitive response in Nicotiana benthamiana compared with the isolate GW2, which a single residue substitution showed was due to Val834.

Sulfur Atoms Adsorbed on Cu(100) at Low Coverage: Characterization and Stability against Complexation.

Using scanning tunneling microscopy, we characterize the size and bias-dependent shape of sulfur atoms on Cu(100) at low coverage (below 0.1 monolayers) and low temperature (quenched from 300 to 5 K). Sulfur atoms populate the Cu(100) terraces more heavily than steps at low coverage, but as coverage approaches 0.1 monolayers, close-packed step edges become fully populated, with sulfur atoms occupying sites on top of the step. Density functional theory (DFT) corroborates the preferential population of terraces at low coverage as well as the step adsorption site. In experiment, small regions with p(2 × 2)-like atomic arrangements emerge on the terraces as sulfur coverage approaches 0.1 monolayer. Using DFT, a lattice gas model has been developed, and Monte Carlo simulations based on this model have been compared with the observed terrace configurations. A model containing eight pairwise interaction energies, all repulsive, gives qualitative agreement. Experiment shows that atomic adsorbed sulfur is the only species on Cu(100) up to a coverage of 0.09 monolayers. There are no Cu-S complexes. In contrast, prior work has shown that a Cu2S3 complex forms on Cu(111) under comparable conditions. On the basis of DFT, this difference can be attributed mainly to stronger adsorption of sulfur on Cu(100) as compared with Cu(111).

Elucidation of Isomerization Pathways of a Single Azobenzene Derivative Using an STM.

The predominant pathway for the isomerization between cis- and trans-azobenzenes-either (i) inversion by the bending of an NNC bond or (ii) rotation by the torsion of two phenyl rings-continues to be a controversial topic. To elucidate each isomerization pathway, a strategically designed and synthesized azobenzene derivative was investigated on a Ag(111) surface. This was achieved by exciting the molecule with tunneling electrons from the tip of a scanning tunneling microscope (STM). Structural analyses of the molecularly resolved STM images reveal that both inversion and rotation pathways are available for isomerization on a metal surface and strongly depend on the initial adsorption structures of the molecule. On the basis of the potential energy diagrams for the isomerization, it is concluded that isomerization pathways on a metal surface are not simply related to the excited states.

Atomic-Scale Dynamics of Surface-Catalyzed Hydrogenation/Dehydrogenation: NH on Pt(111).

Low-temperature scanning tunneling microscopy (LT-STM) was used to move hydrogen atoms and dissociate NH molecules on a Pt(111) surface covered with an ordered array of nitrogen atoms in a (2 × 2) structure. The N-covered Pt(111) surface was prepared by ammonia oxydehydrogenation, which was achieved by annealing an ammonia-oxygen overlayer to 400 K. Exposing the N-covered surface to H2(g) forms H atoms and NH molecules. The NH molecules occupy face-centered cubic hollow sites, while the H atoms occupy atop sites. The STM tip was used to dissociate NH and to induce hopping of H atoms. Action spectra consisting of the reaction yield versus applied bias voltage were recorded for both processes, which revealed that they are vibrationally mediated. The threshold voltages for NH dissociation and H hopping were found to be 430 and 272 meV, corresponding to the excitation energy of the N-H stretching and the Pt-H stretching modes, respectively. Substituting H with D results in an isotopic shift of -110 and -84 meV for the threshold voltages for ND dissociation and D hopping, respectively. This further supports the conclusion that these processes are vibrationally mediated.

Thermally activated polymorphic transition from a 1D ribbon to a 2D carpet: squaric acid on Au(111).

Polymorphic transition from the 1D ribbon to the 2D carpet superstructure of squaric acid molecules on Au(111) was achieved through a thermally activated process. Our combined STM and DFT study revealed that the molecular arrangements in 1D and 2D superstructures are determined by the stability of their conformational isomers and assembled structures, respectively.

Scattering of O2 from a graphite surface.

Recently an extensive series of measurements has been presented for the angular distributions of oxygen molecules scattered from a graphite surface. Incident translational energies ranged from 291 to 614 meV with surface temperatures from 150 to 500 K. The measurements were taken with a fixed angle of 90° between the source beam and the detector and the angular distributions consisted of a single broad peak with the most probable intensity located at an angle slightly larger than the 45° specular position. Analysis with the hard cubes model for atom-surface scattering indicated that the scattering is primarily a single collision event with a surface having a collective effective mass much larger than a single carbon atom. Limited analysis with a classical diatomic molecular scattering theory was also presented. In this paper a more complete analysis using the classical diatomic molecular scattering theory is presented. The energy and temperature dependence of the observed angular distributions are well described as single collision events with a surface having an effective mass of 1.8 carbon graphite rings. In agreement with the earlier analysis and with other experiments, this suggests a large cooperative response of the carbon atoms in the outermost graphene layer.