The genetics and structure of the O-specific polysaccharide of Yersinia pseudotuberculosis serotype O:10 and its relationship with Escherichia coli O111 and Salmonella enterica O35

The O-specific polysaccharide (OPS) is a variable constituent of the lipopolysaccharide of Gram-negative bacteria. The polymorphic nature of OPSs within a species is usually first defined serologically, and the current serotyping scheme for Yersinia pseudotuberculosis consists of 21 O serotypes of which 15 have been characterized genetically and structurally. Here, we present the structure and DNA sequence of Y. pseudotuberculosis O:10 OPS. The O unit consists of one residue each of d-galactopyranose, N-acetyl-d-galactosamine (2-amino-2-deoxy-d-galactopyranose) and d-glucopyranose in the backbone, with two colitose (3,6-dideoxy-l-xylo-hexopyranose) side-branch residues. This structure is very similar to that shared by Escherichia coli O111 and Salmonella enterica O35. The gene cluster sequences of these serotypes, however, have only low levels of similarity to that of Y. pseudotuberculosis O:10, although there is significant conservation of gene order. Within Y. pseudotuberculosis, the O10 structure is most closely related to the O:6 and O:7 structures.

The O-specific polysaccharide structure and gene cluster of serotype O:12 of the Yersinia pseudotuberculosis complex, and the identification of a novel L-quinovose biosynthesis gene

A major virulence factor for Yersinia pseudotuberculosis is lipopolysaccharide, including O-polysaccharide (OPS). Currently, the OPS based serotyping scheme for Y. pseudotuberculosis includes 21 known O-serotypes, with genetic and structural data available for 17 of them. The completion of the OPS structures and genetics of this species will enable the visualization of relationships between O-serotypes and allow for analysis of the evolutionary processes within the species that give rise to new serotypes. Here we present the OPS structure and gene cluster of serotype O:12, thus adding one more to the set of completed serotypes, and show that this serotype is present in both Y. pseudotuberculosis and the newly identified Y. similis species. The O:12 structure is shown to include two rare sugars: 4-C[(R)-1-hydroxyethyl]-3,6-dideoxy-d-xylo-hexose (d-yersiniose) and 6-deoxy-l-glucopyranose (l-quinovose). We have identified a novel putative guanine diphosphate (GDP)-l-fucose 4-epimerase gene and propose a pathway for the synthesis of GDP-l-quinovose, which extends the known GDP-l-fucose pathway.

Structure of the K2 capsule associated with the KL2 gene cluster of Acinetobacter baumannii

The repeat unit structure of the K2 capsule from an extensively antibiotic-resistant Acinetobacter baumannii global clone 2 (GC2) strain was determined. The oligosaccharide contains three simple sugars, d-glucopyranose, d-galatopyranose and N-acetyl-d-galactosamine, and the complex sugar, 5,7-diacetamido-3,5,7,9-tetradeoxy-l-glycero-l-manno-non-2-ulosonic acid (Pse5Ac7Ac or pseudaminic acid), which has not previously been reported in any A. baumannii capsule. The strain was found to carry all the genes required for the synthesis of the sugars and construction of the K2 structure. The linkages catalyzed by the initiating transferase, three glycosyltransferases and the Wzy polymerase were also predicted. Examination of publicly available A. baumannii genome sequences revealed that the same gene cluster, KL2, often occurs in extensively antibiotic-resistant GC2 isolates and in further strain types. The gene module responsible for the synthesis of pseudaminic acid was also detected in four other K loci. A related module including genes for an acylated relative of pseudaminic acid was also found in two new KL types. A polymerase chain reaction scheme was developed to detect all modules containing genes for sugars based on pseudaminic acid and to specifically detect KL2.

Raman and infrared spectroscopic studies of phurcalite from Red Canyon, Utah, USA – Implications for the molecular structure

Raman and infrared spectra of the uranyl mineral phurcalite, Ca2(UO2)3O2(PO4)2⋅7H2O, from Red Canyon, Utah, USA, were studied and tentatively interpreted. Observed bands were assigned to the stretching and bending vibrations of (UO2)2+ and (PO4)3− units and to the stretching and bending vibrations and libration modes of water molecules. Approximate lengths of U–O in (UO2)2+ and O–H⋯O hydrogen bond lengths were inferred from observed stretching vibrations. The presence of structurally nonequivalent U6+ and P5+ was inferred from the number of corresponding stretching bands of (UO2)2+ and (PO4)3− units observed in the Raman and infrared spectra..

A vibrational spectroscopic study of the borate mineral ezcurrite Na4B10O17·7H2O – Implications for the molecular structure

We have studied the boron containing mineral ezcurrite Na4B10O17·7H2O using electron microscopy and vibrational spectroscopy. Both tetrahedral and trigonal boron units are observed. The nominal resolution of the Raman spectrometer is of the order of 2 cm−1 and as such is sufficient enough to identify separate bands for the stretching bands of the two boron isotopes. The Raman band at 1037 cm−1 is assigned to BO stretching vibration. Raman bands at 1129, 1163, 1193 cm−1 are attributed to BO stretching vibration of the tetrahedral units. The Raman band at 947 cm−1 is attributed to the antisymmetric stretching modes of tetrahedral boron. The sharp Raman peak at 1037 cm−1 is from the 11-B component such a mode, then it should have a smaller 10-B satellite near (1.03) × (1037) = 1048 cm−1, and indeed a small peak at 1048 is observed. The broad Raman bands at 3186, 3329, 3431, 3509, 3547 and 3576 cm−1 are assigned to water stretching vibrations. Broad infrared bands at 3170, 3322, 3419, 3450, 3493, 3542, 3577 and 3597 cm−1 are also assigned to water stretching vibrations. Infrared bands at 1330, 1352, 1389, 1407, 1421 and 1457 cm−1 are assigned to the antisymmetric stretching vibrations of trigonal boron. The observation of so many bands suggests that there is considerable variation in the structure of ezcurrite. Infrared bands at 1634, 1646 and 1681 cm−1 are assigned to water bending modes. The number of water bending modes is in harmony with the number of water stretching vibrations.

Quantification of the total neuronal structure of the fear conditioning circuit of the lateral amygdala of the rat

During Pavlovian auditory fear conditioning a previously neutral auditory stimulus (CS) gains emotional significance through pairing with a noxious unconditioned stimulus (US). These associations are believed to be formed by way of plasticity at auditory input synapses on principal neurons in the lateral nucleus of the amygdala (LA). In order to begin to understand how fear memories are stored and processed by synaptic changes in the LA, we have quantified both the entire neural number and the sub-cellular structure of LA principal neurons.We first used stereological cell counting methods on Gimsa or GABA immunostained rat brain. We identified 60,322+/-1408 neurons in the LA unilaterally (n=7). Of these 16,917+/-471 were GABA positive. The intercalated nuclei were excluded from the counts and thus GABA cells are believed to represent GABAergic interneurons. The sub-nuclei of the LA were also independently counted. We then quantified the morphometric properties of in vitro electrophysiologically identified principal neurons of the LA, corrected for shrinkage in xyz planes. The total dendritic length was 9.97+/-2.57mm, with 21+/-4 nodes (n=6). Dendritic spine density was 0.19+/-0.03 spines/um (n=6). Intra-LA axon collaterals had a bouton density of 0.1+/-0.02 boutons/um (n=5). These data begin to reveal the finite cellular and sub-cellular processing capacity of the lateral amygdala, and should facilitate efforts to understand mechanisms of plasticity in LA.

Vibrational spectroscopic characterization of the arsenate mineral barahonaite: Implications for the molecular structure

The mineral barahonaite is in all probability a member of the smolianinovite group. The mineral is an arsenate mineral formed as a secondary mineral in the oxidized zone of sulphide deposits. We have studied the barahonaite mineral using a combination of Raman and infrared spectroscopy. The mineral is characterized by a series of Raman bands at 863 cm−1 with low wavenumber shoulders at 802 and 828 cm−1. These bands are assigned to the arsenate and hydrogen arsenate stretching vibrations. The infrared spectrum shows a broad spectral profile. Two Raman bands at 506 and 529 cm−1 are assigned to the triply degenerate arsenate bending vibration (F 2, ν4), and the Raman bands at 325, 360, and 399 cm−1 are attributed to the arsenate ν2 bending vibration. Raman and infrared bands in the 2500–3800 cm−1 spectral range are assigned to water and hydroxyl stretching vibrations. The application of Raman spectroscopy to study the structure of barahonaite is better than infrared spectroscopy, probably because of the much higher spatial resolution.

Tailoring surface properties and structure of layered double hydroxides using silanes with different number of functional groups

Four silanes, trimethylchlorosilane (TMCS), dimethyldiethoxylsilane (DMDES), 3-aminopropyltriethoxysilane (APTES) and tetraethoxysilane (TEOS), were adopted to graft layered double hydroxides (LDH) via an induced hydrolysis silylation method (IHS). Fourier transform infrared spectra (FTIR) and 29Si MAS nuclear magnetic resonance spectra (29Si MAS NMR) indicated that APTES and TEOS can be grafted onto LDH surfaces via condensation with hydroxyl groups of LDH, while TMCS and DMDES could only be adsorbed on the LDH surface with a small quantity. A combination of X-ray diffraction patterns (XRD) and 29Si MAS NMR spectra showed that silanes were exclusively present in the external surface and had little influence on the long range order of LDH. The surfactant intercalation experiment indicated that the adsorbed and/or grafted silane could not fix the interlamellar spacing of the LDH. However, they will form crosslink between the particles and affect the further surfactant intercalation in the silylated samples. The replacement of water by ethanol in the tactoids and/or aggregations and the polysiloxane oligomers formed during silylation procedure can dramatically increase the value of BET surface area (SBET) and total pore volumes (Vp) of the products.

BPMN Miner: Automated Discovery of BPMN Process Models with Hierarchical Structure

Existing techniques for automated discovery of process models from event logs gen- erally produce flat process models. Thus, they fail to exploit the notion of subprocess as well as error handling and repetition constructs provided by contemporary process modeling notations, such as the Business Process Model and Notation (BPMN). This paper presents a technique for automated discovery of hierarchical BPMN models con- taining interrupting and non-interrupting boundary events and activity markers. The technique employs functional and inclusion dependency discovery techniques in order to elicit a process-subprocess hierarchy from the event log. Given this hierarchy and the projected logs associated to each node in the hierarchy, parent process and subprocess models are then discovered using existing techniques for flat process model discovery. Finally, the resulting models and logs are heuristically analyzed in order to identify boundary events and markers. By employing approximate dependency discovery tech- niques, it is possible to filter out noise in the event log arising for example from data entry errors or missing events. A validation with one synthetic and two real-life logs shows that process models derived by the proposed technique are more accurate and less complex than those derived with flat process discovery techniques. Meanwhile, a validation on a family of synthetically generated logs shows that the technique is resilient to varying levels of noise.

Quantitative characterization of kaolinite dispersibility in styrene–butadiene rubber composites by fractal dimension

A fractal method was introduced to quantitatively characterize the dispersibility of modified kaolinite (MK) and precipitated silica (PS) in styrene–butadiene rubber (SBR) matrix based on the lower magnification transmission electron microscopic images. The fractal dimension (FD) is greater, and the dispersion is worse. The fractal results showed that the dispersibility of MK in the latex blending sample is better than that in the mill blending samples. With the increase of kaolinite content, the FD increases from 1.713 to 1.800, and the dispersibility of kaolinite gradually decreases. There is a negative correlation between the dispersibility and loading content. With the decrease of MK and increase of PS, the FD significantly decreases from 1.735 to 1.496 and the dipersibility of kaolinite remarkably increases. The hybridization can improve the dispersibility of fillers in polymer matrix. The FD can be used to quantitatively characterize the aggregation and dispersion of kaolinite sheets in rubber matrix.

Structure evolution characterization of Anyang anthracites via H2O2 oxidization and HF acidification

The structural characteristics of the raw coal (AY), the H2O2 oxidized coals (AY–H2O2) and the HF acidized AY–H2O2 (AY–H2O2–HF) were investigated by SEM, X-ray diffraction, Raman and FTIR spectroscopy. The results indicate that the derivative coals show an obvious increase in the aromaticity, crystalline carbon content and hydroxyl content, especially the AY–H2O2–HF. The stacking layer number of crystalline carbon decreases and the aspect ratio (La/Lc) remarkably increases for AY–H2O2 and AY–H2O2–HF. The crystalline layers become much thinner. The particle size of AY–H2O2–HF in width significantly decreases from 1 μm to less than 100 nm. The combination of H2O2 oxidization and HF acidification is effective to reduce the size of the aromatic layers and to increase the reactivity of derivative coals. The process can help us obtain the superfine crystalline carbon materials like graphite structure.

Leaf and inflorescence structure and phylogenetics of Tripogon and affiliated genera (Poaceae: Chloridoideae)

This thesis provides new knowledge on an understudied group of grasses, some of which are resurrection grasses (i.e. able to withstand extreme drought). The sole Australian species (Tripogon loliiformis) is morphologically diverse and could be more than one species. This study sought to determine how many species of Tripogon occur in Australia, their relationships to other species in the genus and to two other genera of resurrection grasses (Eragrostiella and Oropetium). Results of the research indicate there is not enough evidence, from DNA sequence data, to warrant splitting up T. loliiformis into multiple species. The extensive morphological diversity seems to be influenced by environmental conditions. The three genera are so closely related that they could be grouped into a single genus. This new knowledge opens up pathways for future investigations, including studying genes responsible for desiccation tolerance and the conservation of native grasses that occur in rocky habitats.

SEM, EDX and vibrational spectroscopic study of the phosphate mineral ushkovite MgFe3+2(PO4)2(OH)2·8H2O: Implications of the molecular structure

The mineral ushkovite has been analyzed using a combination of electron microscopy with EDX and vibrational spectroscopy. Chemical analysis shows the mineral contains P, Mg with very minor Fe. Thus, the formula of the studied ushkovite is Mg32+(PO4)2·8H2O. The Raman spectrum shows an intense band at 953 cm−1 assigned to the ν1 symmetric stretching mode. In the infrared spectra complexity exists with multiple antisymmetric stretching vibrations observed, due to the reduced tetrahedral symmetry. This loss of degeneracy is also reflected in the bending modes. Strong infrared bands around 827 cm−1 are attributed to water librational modes. The Raman spectra of the hydroxyl-stretching region are complex with overlapping broad bands. Hydroxyl stretching vibrations are identified at 2881, 2998, 3107, 3203, 3284 and 3457 cm−1. The wavenumber band at 3457 cm−1 is attributed to the presence of FeOH groups. This complexity is reflected in the water HOH bending modes where a strong infrared band centered around 1653 cm−1 is found. Such a band reflects the strong hydrogen bonding of the water molecules to the phosphate anions in adjacent layers. Spectra show three distinct OH bending bands from strongly hydrogen-bonded, weakly hydrogen bonded water and non-hydrogen bonded water. Vibrational spectroscopy enhances our knowledge of the molecular structure of ushkovite.

Spectroscopic characterization and solubility investigation on the effects of As(V) on mineral structure tooeleite (Fe6(AsO3)4SO4(OH)4·H2O)

Tooeleite is an unique ferric arsenite sulfate mineral, which has the potential significance of directly fixing As(III) as mineral trap. The tooeleite and various precipitates were hydrothermally synthesized under the different of initial As(III)/As(V) molar ratios and characterized by XRD, FTIR, XPS and SEM. The crystallinity of tooeleite decreases with the amount of As(V). The precipitate is free of any crystalline tooeleite at the level of that XRD could detect when the ratio of As(III)/As(V) of 7:3 and more. The characteristic bands of tooeleite are observed in 772, 340, 696 and 304 cm−1, which are assigned to the ν1, ν2, ν3 and ν4 vibrations of AsO33−. These intensities of bands gradually decreases with the presence of As(V) and its increasing. An obviously wide band is observed in 830 cm−1, which is the ν1 vibration of AsO4. The result of XPS reveals that the binding energies of As3d increase from 44.0 eV to 45.5 eV, which indicates that the amount of As(V) in the precipitates increases. The concentrations of arsenic released of these precipitates are 350–650 mg/L. The stability of tooeleite decreases by comparison when the presence of coexisting As(V) ions.

The molecular structure of the borate mineral szaibelyite MgBO2(OH): A vibrational spectroscopic study

We have studied the borate mineral szaibelyite MgBO2(OH) using electron microscopy and vibrational spectroscopy. EDS spectra show a phase composed of Mg with minor amounts of Fe. Both tetrahedral and trigonal boron units are observed. The nominal resolution of the Raman spectrometer is of the order of 2 cm−1 and as such is sufficient enough to identify separate bands for the stretching bands of the two boron isotopes. The Raman band at 1099 cm−1 with a shoulder band at 1093 cm−1 is assigned to BO stretching vibration. Raman bands at 1144, 1157, 1229, 1318 cm−1 are attributed to the BOH in-plane bending modes. Raman bands at 836 and 988 cm−1 are attributed to the antisymmetric stretching modes of tetrahedral boron. The infrared bands at 3559 and 3547 cm−1 are assigned to hydroxyl stretching vibrations. Broad infrared bands at 3269 and 3398 cm−1 are assigned to water stretching vibrations. Infrared bands at 1306, 1352, 1391, 1437 cm−1 are assigned to the antisymmetric stretching vibrations of trigonal boron. Vibrational spectroscopy enables aspects of the molecular structure of the borate mineral szaibelyite to be assessed.