2D and 3D cubic monocrystalline and polycrystalline materials: their stability and mechanical properties

We consider 2- and 3-dimensional cubic monocrystalline and polycrystalline materials. Expressions for Young's and shear moduli and Poisson's ratio are expressed in terms of eigenvalues of the stiffness tensor. Such a form is well suited for studying properties of these mechanical characteristics on sides of the stability triangles. For crystalline high-symmetry directions lines of vanishing Poisson's ratio are found. These lines demarcate regions of the stability triangle into areas of various auxeticity properties. The simplest model of polycrystalline 2D and 3D cubic materials is considered. In polycrystalline phases the region of complete auxetics is larger than for monocrystalline materials.Comment: 9 pages, 3 figures, in proceedings of the Tenth International School on Theoretical Physics, Symmetry and Structural Properties of Condensed Matter, Myczkowce 200

Elastic properties of cubic crystals: Every's versus Blackman's diagram

Blackman's diagram of two dimensionless ratios of elastic constants is frequently used to correlate elastic properties of cubic crystals with interatomic bondings. Every's diagram of a different set of two dimensionless variables was used by us for classification of various properties of such crystals. We compare these two ways of characterization of elastic properties of cubic materials and consider the description of various groups of materials, e.g. simple metals, oxides, and alkali halides. With exception of intermediate valent compounds, the correlation coefficients for Every's diagrams of various groups of materials are greater than for Blackaman's diagrams, revealing the existence of a linear relationship between two dimensionless Every's variables. Alignment of elements and compounds along lines of constant Poisson's ratio $\nu(,\textbf{m})$, ($\textbf{m}$ arbitrary perpendicular to ) is observed. Division of the stability region in Blackman's diagram into region of complete auxetics, auxetics and non-auxetics is introduced. Correlations of a scaling and an acoustic anisotropy parameter are considered.Comment: 8 pages, 9 figures, presented on The Ninth International School on Theoretical Physics "Symmetry and Structural Properties of Condensed Matter", 5 - 12 September 2007, Myczkowce, Polan

Gene loss and lineage specific restriction-modification systems associated with niche differentiation in the Campylobacter jejuni Sequence Type 403 clonal complex

Campylobacter jejuni is a highly diverse species of bacteria commonly associated with infectious intestinal disease of humans and zoonotic carriage in poultry, cattle, pigs, and other animals. The species contains a large number of distinct clonal complexes that vary from host generalist lineages commonly found in poultry, livestock, and human disease cases to host-adapted specialized lineages primarily associated with livestock or poultry. Here, we present novel data on the ST403 clonal complex of C. jejuni, a lineage that has not been reported in avian hosts. Our data show that the lineage exhibits a distinctive pattern of intralineage recombination that is accompanied by the presence of lineage-specific restriction-modification systems. Furthermore, we show that the ST403 complex has undergone gene decay at a number of loci. Our data provide a putative link between the lack of association with avian hosts of C. jejuni ST403 and both gene gain and gene loss through nonsense mutations in coding sequences of genes, resulting in pseudogene formation

Heat capacity and phonon mean free path of wurtzite GaN

We report on lattice specific heat of bulk hexagonal GaN measured by the heat flow method in the temperature range 20-300 K and by the adiabatic method in the range 5-70 K. We fit the experimental data using two temperatures model. The best fit with the accuracy of 3 % was obtained for the temperature independent Debye's temperature $\theta_{\rm D}=365$ {\rm K} and Einstein's temperature $\theta_{\rm E}=880$ {\rm K}. We relate these temperatures to the function of density of states. Using our results for heat conduction coefficient, we established in temperature range 10-100 K the explicit dependence of the phonon mean free path on temperature $\it{l}_{\rm ph}\propto T^{-2}$. Above 100 K, there is the evidence of contribution of the Umklapp processes which limit phonon free path at high temepratures. For phonons with energy $k_{\rm B}\times 300$ {\rm K} the mean free path is of the order 100 {\rm nm}Comment: 5 pages, 4 figure

Correction: Studholme et al., Draft Genome Sequences of Xanthomonas sacchari and Two Banana-Associated Xanthomonads Reveal Insights into the Xanthomonas Group 1 clade. Genes 2011, 2, 1050-1065

Published ErratumThis is the final version of the article. Available from MDPI via the DOI in this record.NOTE: the original article is in ORE at http://hdl.handle.net/10036/3880Following publication of our article [1], we found errors in analyses performed by the corresponding author (DJS) related to the phylogenetic relationship between Xylella species and the other xanthomonads. These errors do not make any difference to the main findings and conclusions reported in our paper. For example, the phylogenetic positions of NCPPB1131, NCPPB1132 and NCPPB4393 within the Group 1 Xanthomonas species are unaffected. However, we wish to apologize to the authors of a previous work [2] for creating any negative impression on the quality of their phylogenetic analyses and to take this opportunity to rectify the errors. [...]

Local adsorption structure and bonding of porphine on Cu(111) before and after self-metalation

We have experimentally determined the lateral registry and geometric structure of free-base porphine (2H-P) and copper-metalated porphine (Cu-P) adsorbed on Cu(111), by means of energy-scanned photoelectron diffraction (PhD), and compared the experimental results to density functional theory (DFT) calculations that included van der Waals corrections within the Tkatchenko-Scheffler approach. Both 2H-P and Cu-P adsorb with their center above a surface bridge site. Consistency is obtained between the experimental and DFT-predicted structural models, with a characteristic change in the corrugation of the four N atoms of the molecule's macrocycle following metalation. Interestingly, comparison with previously published data for cobalt porphine adsorbed on the same surface evidences a distinct increase in the average height of the N atoms above the surface through the series 2H-P, Cu-P, cobalt porphine. Such an increase strikingly anti-correlates the DFT-predicted adsorption strength, with 2H-P having the smallest adsorption height despite the weakest calculated adsorption energy. In addition, our findings suggest that for these macrocyclic compounds, substrate-to-molecule charge transfer and adsorption strength may not be univocally correlated

Draft genome sequences of xanthomonas sacchari and two banana-associated xanthomonads reveal insights into the xanthomonas group 1 clade

Original article plus subsequent corrections as described below: Following publication of our article [1], we found errors in analyses performed by the corresponding author (DJS) related to the phylogenetic relationship between Xylella species and the other xanthomonads. These errors do not make any difference to the main findings and conclusions reported in our paper. For example, the phylogenetic positions of NCPPB1131, NCPPB1132 and NCPPB4393 within the Group 1 Xanthomonas species are unaffected. However, we wish to apologize to the authors of a previous work [2] for creating any negative impression on the quality of their phylogenetic analyses and to take this opportunity to rectify the errors. The details of the errors are listed.Freely available on Open AccessNOTE: the published correction is in ORE at http://hdl.handle.net/10871/25734We present draft genome sequences for three strains of Xanthomonas species, each of which was associated with banana plants (Musa species) but is not closely related to the previously sequenced banana-pathogen Xanthomonas campestris pathovar musacearum. Strain NCPPB4393 had been deposited as Xanthomonas campestris pathovar musacearum but in fact falls within the species Xanthomonas sacchari. Strain NCPPB1132 is more distantly related to Xanthomonas sacchari whilst strain NCPPB 1131 grouped in a distinct species-level clade related to X. sacchari, along with strains from ginger, rice, cotton and sugarcane. These three newly sequenced strains share many genomic features with the previously sequenced Xanthomonas albilineans, for example possessing an unsual metE allele and lacking the Hrp type III secretion system. However, they are distinct from Xanthomonas albilineans in many respects, for example showing little evidence of genome reduction. They also lack the SPI-1 type III secretion system found in OPEN ACCESSGenes 2011, 2 1051 Xanthomonas albilineans. Unlike X. albilineans, all three strains possess a gum gene cluster. The data reported here provide the first genome-wide survey of non-Hrp Xanthomonas species other than Xanthomonas albilineans, which is an atypical member of this group. We hope that the availability of complete sequence data for this group of organisms is the first step towards understanding their interactions with plants and identifying potential virulence factors

Common Host Responses in Murine Aerosol Models of Infection Caused by Highly Virulent Gram-Negative Bacteria from the Genera Burkholderia, Francisella and Yersinia

This is the final version. Available on open access from MDPI via the DOI in this recordContent includes material subject to © Crown copyright (2019), Dstl. This material is licensed under the terms of the Open Government Licence except where otherwise stated. To view this licence, visit: http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3 or write to the Information Policy Team, The National Archives, Kew, London TW9 4DU, or email: [email protected] virulent bacterial pathogens cause acute infections which are exceptionally difficult to treat with conventional antibiotic therapies alone. Understanding the chain of events that are triggered during an infection of a host has the potential to lead to new therapeutic strategies. For the first time, the transcriptomic responses within the lungs of Balb/C mice have been compared during an acute infection with the intracellular pathogens Burkholderia pseudomallei, Francisella tularensis and Yersinia pestis. Temporal changes were determined using RNAseq and a bioinformatics pipeline; expression of protein was also studied from the same sample. Collectively it was found that early transcriptomic responses within the infected host were associated with the (a) slowing down of critical cellular functions, (b) production of circulatory system components, (c) lung tissue integrity, and (d) intracellular regulatory processes. One common molecule was identified, Errfi1 (ErbB receptor feedback inhibitor 1); upregulated in response to all three pathogens and a potential novel marker of acute infection. Based upon the pro-inflammatory responses observed, we sought to synchronise each infection and report that 24 h p.i. of B. pseudomallei infection closely aligned with 48 h p.i. of infection with F. tularensis and Y. pestis. Post-transcriptional modulation of RANTES expression occurred across all pathogens, suggesting that these infections directly or indirectly modulate cell trafficking through chemokine expression/detection. Collectively, this unbiased NGS approach has provided an in-depth characterisation of the host transcriptome following infection with these highly virulent pathogens ultimately aiding in the development of host-directed therapies as adjuncts or alternatives to antibiotic treatment

Genome Sequencing of Xanthomonas vasicola Pathovar vasculorum Reveals Variation in Plasmids and Genes Encoding Lipopolysaccharide Synthesis, Type-IV Pilus and Type-III Secretion Effectors

This is the final version. Available on open access from MDPI via the DOI in this recordXanthomonas vasicola pathovar vasculorum (Xvv) is the bacterial agent causing gumming disease in sugarcane. Here, we compare complete genome sequences for five isolates of Xvv originating from sugarcane and one from maize. This identified two distinct types of lipopolysaccharide synthesis gene clusters among Xvv isolates: one is similar to that of Xanthomonas axonopodis pathovar citri (Xac) and is probably the ancestral type, while the other is similar to those of the sugarcane-inhabiting species, Xanthomonas sacchari. Four of six Xvv isolates harboured sequences similar to the Xac plasmid, pXAC47, and showed a distinct Type-IV pilus (T4P) sequence type, whereas the T4P locus of the other two isolates resembled that of the closely related banana pathogen, Xanthomonas campestris pathovar musacearum (Xcm). The Xvv isolate from maize has lost a gene encoding a homologue of the virulence effector, xopAF, which was present in all five of the sugarcane isolates, while xopL contained a premature stop codon in four out of six isolates. These findings shed new light on evolutionary events since the divergence of Xvv and Xcm, as well as further elucidating the relationships between the two closely related pathogens.This study was supported in part by the National Agriculture Research Organisation, Uganda, under the MSI/World Bank grant 2009

Draft genome sequence of Pseudomonas fuscovaginae, a broad-host-range pathogen of plants.

addresses: International Centre for Genetic Engineering & Biotechnology, Trieste, Italy.notes: PMCID: PMC3347198types: Journal Article; Research Support, Non-U.S. Gov'tFreely available on Open AccessPseudomonas fuscovaginae was first reported as a pathogen of rice causing sheath rot in plants grown at high altitudes. P. fuscovaginae is now considered a broad-host-range plant pathogen causing disease in several economically important plants. We report what is, to our knowledge, the first draft genome sequence of a P. fuscovaginae strain