Structure of the K6 capsular polysaccharide from Acinetobacter baumannii isolate RBH4

The structure of the capsular polysaccharide (CPS) from an Acinetobacter baumannii global clone 2 (GC2) clinical isolate RBH4 that carries the KL6 gene cluster was elucidated by means of chemical and spectroscopical methods. The repeating unit of K6 CPS is linear and contains N-acetyl-d-galactosamine (d-GalpNAc), two d-galactose (d-Galp) residues and 5,7-di-N-acetylpseudaminic acid (Pse5Ac7Ac). The synthesis of these sugars could be attributed to genes in the KL6 capsule biosynthesis gene cluster, and the formation of the linkages between the sugars were assigned to glycosyltransferases or the Wzy polymerase encoded in KL6.

Emerging Viruses: Coming in on a Wrinkled Wing and a Prayer

The role that bats have played in the emergence of several new infectious diseases has been under review. Bats have been identified as the reservoir hosts of newly emergent viruses such as Nipah virus, Hendra virus, and severe acute respiratory syndrome–like coronaviruses. This article expands on recent findings about bats and viruses and their relevance to human infections. It briefly reviews the history of chiropteran viruses and discusses their emergence in the context of geography, phylogeny, and ecology. The public health and trade impacts of several outbreaks are also discussed. Finally, we attempt to predict where, when, and why we may see the emergence of new chiropteran viruses.

The onset of warps in Spitzer observations of edge-on spiral galaxies

We analyse warps in the nearby edge-on spiral galaxies observed in the Spitzer/Infrared Array Camera (IRAC)4.5-mu m band. In our sample of 24 galaxies, we find evidence of warp in 14 galaxies. We estimate the observed onset radii for the warps in a subsample of 10 galaxies. The dark matter distribution in each of these galaxies are calculated using the mass distribution derived from the observed light distribution and the observed rotation curves. The theoretical predictions of the onset radii for the warps are then derived by applying a self-consistent linear response theory to the obtained mass models for six galaxies with rotation curves in the literature. By comparing the observed onset radii to the theoretical ones, we find that discs with constant thickness can not explain the observations; moderately flaring discs are needed. The required flaring is consistent with the observations. Our analysis shows that the onset of warp is not symmetric in our sample of galaxies. We define a new quantity called the onset-asymmetry index and study its dependence on galaxy properties. The onset asymmetries in warps tend to be larger in galaxies with smaller dis scalelengths. We also define and quantify the global asymmetry in the stellar light distribution, that we call the edge-on asymmetry in edge-on galaxies. It is shown that in most cases the onset asymmetry in warp is actually anticorrelated with the measured edge-on asymmetry in our sample of edge-on galaxies and this could plausibly indicate that the surrounding dark matter distribution is asymmetric.

Oidiopsis (Erysiphaceae) on Euphorbia spp. in Australia and Vanuatu

One specimen of powdery mildew on Euphorbia cyathophora from Vanuatu and 11 specimens on E. cyathophora, E. dentata, E. heterophylla and E. leucocephala from Australia were studied. All were shown to represent the Oidiopsis anamorph of Leveillula taurica, which is described. This is the first record of Oidiopsis in Vanuatu. E. leucocephala is a new host record for this powdery mildew.

Weed species richness, density and relative abundance on farms in the subtropical grain region of Australia

Weed management is one of the most important economic and agronomic issues facing farmers in Australia's grain regions. Weed species occurrence and abundance was monitored between 1997 and 2000 on 46 paddocks (sites) across 18 commercial farms located in the Northern Grain Region. The sites generally fell within 4 disjunct regions, from south to north: Liverpool Plains, Moree, Goondiwindi and Kingaroy. While high species richness was found (139 species or species groups), only 8 species occurred in all 4 regions and many (56 species) only occurred at 1 site or region. No species were observed at every site but 7 species (Sonchus spp., Avena spp., Conyza spp., Echinochloa spp., Convolvulus erubescens, Phalaris spp. and Lactuca serriola) were recorded on more than 70% of sites. The average number of species observed within crops after treatment and before harvest was less than 13. Species richness tended to be higher in winter pulse crops, cotton and in fallows, but overall was similar at the different sampling seasons (summer v. winter). Separate species assemblages associated with the Goondiwindi and Kingaroy regions were identified by correspondence analysis but these appeared to form no logical functional group. The species richness and density was generally low, demonstrating that farmers are managing weed populations effectively in both summer and winter cropping phases. Despite the apparent adoption of conservation tillage, an increase in opportunity cropping and the diversity of crops grown (13) there was no obvious effect of management practices on weed species richness or relative abundance. Avena spp. and Sonchus spp. were 2 of the most dominant weeds, particularly in central and southern latitudes of the region; Amaranthus spp. and Raphanus raphanistrum were the most abundant species in the northern part of the region. The ubiquity of these and other species shows that continued vigilance is required to suppress weeds as a management issue.

A new semi-dwarfing gene identified by molecular mapping of quantitative trait loci in barley.

Semi-dwarfing genes have been widely used in spring barley (Hordeum vulgare L.) breeding programs in many parts of the world, but the success in developing barley cultivars with semi-dwarfing genes has been limited in North America. Exploiting new semi-dwarfing genes may help in solving this dilemma. A recombinant inbred line population was developed by crossing ZAU 7, a semi-dwarf cultivar from China, to ND16092, a tall breeding line from North Dakota. To identify quantitative trait loci (QTL) controlling plant height, a linkage map comprised of 111 molecular markers was constructed. Simple interval mapping was performed for each of the eight environments. A consistent QTL for plant height was found on chromosome 7HL. This QTL is not associated with maturity and rachis internode length. We suggest the provisional name Qph-7H for this QTL. Qph-7H from ZAU 7 reduced plant height to about 3/4 of normal; thus, Qph-7H is considered a semi-dwarfing gene. Other QTLs for plant height were found, but their expression was variable across the eight environments tested.

Spatial subdivision among assemblages of Spanish mackerel, Scomberomorus commerson (Pisces: Scombridae) across northern Australia: implications for fisheries management

Aim: This study investigated the use of stable δ13C and δ18O isotopes in the sagittal otolith carbonate of narrow-barred Spanish mackerel, Scomberomorus commerson, as indicators of population structure across Australia. Location: Samples were collected from 25 locations extending from the lower west coast of Western Australia (30°), across northern Australian waters, and to the east coast of Australia (18°) covering a coastline length of approximately 9500 km, including samples from Indonesia. Methods: The stable δ13C and δ18O isotopes in the sagittal otolith carbonate of S. commerson were analysed using standard mass spectrometric techniques. The isotope ratios across northern Australian subregions were subjected to an agglomerative hierarchical cluster analysis to define subregions. Isotope ratios within each of the subregions were compared to assess population structure across Australia. Results: Cluster analysis separated samples into four subregions: central Western Australia, north Western Australia, northern Australia and the Gulf of Carpentaria and eastern Australia. Isotope signatures for fish from a number of sampling sites from across Australia and Indonesia were significantly different, indicating population separation. No significant differences were found in otolith isotope ratios between sampling times (no temporal variation). Main conclusions: Significant differences in the isotopic signatures of S. commerson demonstrate that there is unlikely to be any substantial movement of fish among these spatially discrete adult assemblages. The lack of temporal variation among otolith isotope ratios indicates that S. commerson populations do not undergo longshore spatial shifts in distribution during their life history. The temporal persistence of spatially explicit stable isotopic signatures indicates that, at these spatial scales, the population units sampled comprise functionally distinct management units or separate ‘stocks’ for many of the purposes of fisheries management. The spatial subdivision evident among populations of S. commerson across northern and western Australia indicates that it may be advantageous to consider S. commerson population dynamics and fisheries management from a metapopulation perspective (at least at the regional level).

Genome-wide meta-analysis identifies five new susceptibility loci for cutaneous malignant melanoma

Thirteen common susceptibility loci have been reproducibly associated with cutaneous malignant melanoma (CMM). We report the results of an international 2-stage meta-analysis of CMM genome-wide association studies (GWAS). This meta-analysis combines 11 GWAS (5 previously unpublished) and a further three stage 2 data sets, totaling 15,990 CMM cases and 26,409 controls. Five loci not previously associated with CMM risk reached genome-wide significance (P < 5 × 10−8), as did 2 previously reported but unreplicated loci and all 13 established loci. Newly associated SNPs fall within putative melanocyte regulatory elements, and bioinformatic and expression quantitative trait locus (eQTL) data highlight candidate genes in the associated regions, including one involved in telomere biology.

Theoretical investigations of the two-bond proton-carbon-13 coupling constants. Angular variations of the couplings involving carboxyl carbon

A formulation has been developed using perturbation theory to evaluate the π-contribution to the nuclear spin coupling constants involving nuclei at least one of which is an unsaturated center. This fromulation accounts for the π-contribution in terms of the core polarization and one-center exchange at the π-center. The formulation developed together with the Dirac vector model and Penney-Dirac bond-order formalisms was employed to calculate the geminal (two-bond) proton coupling constants of carboxyl carbons in α-disubstituted acetic acids. The calculated coupling constants were found to have an orientational dependence. The results of the calculation are in good agreement with the experimental values.

Serum uric acid and metabolic risk factors in three ethnic groups: Asian Indians and Creoles in Mauritius and Chinese in Qingdao, China

In humans with a loss of uricase the final oxidation product of purine catabolism is uric acid (UA). The prevalence of hyperuricemia has been increasing around the world accompanied by a rapid increase in obesity and diabetes. Since hyperuricemia was first described as being associated with hyperglycemia and hypertension by Kylin in 1923, there has been a growing interest in the association between elevated UA and other metabolic abnormalities of hyperglycemia, abdominal obesity, dyslipidemia, and hypertension. The direction of causality between hyperuricemia and metabolic disorders, however, is unceartain. The association of UA with metabolic abnormalities still needs to be delineated in population samples. Our overall aims were to study the prevalence of hyperuricemia and the metabolic factors clustering with hyperuricemia, to explore the dynamical changes in blood UA levels with the deterioration in glucose metabolism and to estimate the predictive capability of UA in the development of diabetes. Four population-based surveys for diabetes and other non-communicable diseases were conducted in 1987, 1992, and 1998 in Mauritius, and in 2001-2002 in Qingdao, China. The Qingdao study comprised 1 288 Chinese men and 2 344 women between 20-74, and the Mauritius study consisted of 3 784 Mauritian Indian and Mauritian Creole men and 4 442 women between 25-74. In Mauritius, re-exams were made in 1992 and/or 1998 for 1 941 men (1 409 Indians and 532 Creoles) and 2 318 non pregnant women (1 645 Indians and 673 Creoles), free of diabetes, cardiovascular diseases, and gout at baseline examinations in 1987 or 1992, using the same study protocol. The questionnaire was designed to collect demographic details, physical examinations and standard 75g oral glucose tolerance tests were performed in all cohorts. Fasting blood UA and lipid profiles were also determined. The age-standardized prevalence in Chinese living in Qingdao was 25.3% for hyperuricemia (defined as fasting serum UA > 420 μmol/l in men and > 360 μmol/l in women) and 0.36% for gout in adults between 20-74. Hyperuricemia was more prevalent in men than in women. One standard deviation increase in UA concentration was associated with the clustering of metabolic risk factors for both men and women in three ethnic groups. Waist circumference, body mass index, and serum triglycerides appeared to be independently associated with hyperuricemia in both sexes and in all ethnic groups except in Chinese women, in whom triglycerides, high-density lipoprotein cholesterol, and total cholesterol were associated with hyperuricemia. Serum UA increased with increasing fasting plasma glucose levels up to a value of 7.0 mmol/l, but significantly decreased thereafter in mainland Chinese. An inverse relationship occurred between 2-h plasma glucose and serum UA when 2-h plasma glucose higher than 8.0 mmol/l. In the prospective study in Mauritius, 337 (17.4%) men and 379 (16.4%) women developed diabetes during the follow-up. Elevated UA levels at baseline increased 1.14-fold in risk of incident diabetes in Indian men and 1.37-fold in Creole men, but no significant risk was observed in women. In conclusion, the prevalence of hyperuricemia was high in Chinese in Qingdao, blood UA was associated with the clustering of metabolic risk factors in Mauritian Indian, Mauritian Creole, and Chinese living in Qingdao, and a high baseline UA level independently predicted the development of diabetes in Mauritian men. The clinical use of UA as a marker of hyperglycemia and other metabolic disorders needs to be further studied. Keywords: Uric acid, Hyperuricemia, Risk factors, Type 2 Diabetes, Incidence, Mauritius, Chinese

Interaction of Alpha-tocopherol with diphenylpicryl hydrazyl a means to determine the polarity of the environment around Alpha-tocopherol and its binding with lipids

Alpha-Tocopherol is found to interact with the stable free radical DPPH orders of magnitude faster than ordinary phenols. It is suggested that the high reactivity arises from the coplanarity of the C-O-C framework with the aromatic ring. The rate constant of the reaction of Alpha-tocopherol with DPPH increases progressively with solvent polarity and can be quantitatively related to Kosower's Z parameter. Fatty acid derivatives slow down the reaction with DPPH due to binding with Alpha-tocopherol.

Spinorial relativistic rotator: The transformation from quasi-Newtonian to Minkowski coordinates

There exists a remarkably close relationship between the operator algebra of the Dirac equation and the corresponding operators of the spinorial relativistic rotator (an indecomposable object lying on a mass-spin Regge trajectory). The analog of the Foldy-Wouthuysen transformation (more generally, the transformation between quasi-Newtonian and Minkowski coordinates) is constructed and explicit results are discussed for the spin and position operators. Zitterbewegung is shown to exist for a system having only positive energies.

Hybridisation, paternal leakage and mitochondrial DNA linearization in three anomalous fish (Scombridae)

Using mitochondrial DNA for species identification and population studies assumes that the genome is maternally inherited, circular, located in the cytoplasm and lacks recombination. This study explores the mitochondrial genomes of three anomalous mackerel. Complete mitochondrial genome sequencing plus nuclear microsatellite genotyping of these fish identified them as Scomberomorus munroi (spotted mackerel). Unlike normal S. munroi, these three fish also contained different linear, mitochondrial genomes of Scomberomorus semifasciatus (grey mackerel). The results are best explained by hybridisation, paternal leakage and mitochondrial DNA linearization. This unusual observation may provide an explanation for mtDNA outliers in animal population studies. © 2013.

Digital elevation model error in terrain analysis

Digital elevation models (DEMs) have been an important topic in geography and surveying sciences for decades due to their geomorphological importance as the reference surface for gravita-tion-driven material flow, as well as the wide range of uses and applications. When DEM is used in terrain analysis, for example in automatic drainage basin delineation, errors of the model collect in the analysis results. Investigation of this phenomenon is known as error propagation analysis, which has a direct influence on the decision-making process based on interpretations and applications of terrain analysis. Additionally, it may have an indirect influence on data acquisition and the DEM generation. The focus of the thesis was on the fine toposcale DEMs, which are typically represented in a 5-50m grid and used in the application scale 1:10 000-1:50 000. The thesis presents a three-step framework for investigating error propagation in DEM-based terrain analysis. The framework includes methods for visualising the morphological gross errors of DEMs, exploring the statistical and spatial characteristics of the DEM error, making analytical and simulation-based error propagation analysis and interpreting the error propagation analysis results. The DEM error model was built using geostatistical methods. The results show that appropriate and exhaustive reporting of various aspects of fine toposcale DEM error is a complex task. This is due to the high number of outliers in the error distribution and morphological gross errors, which are detectable with presented visualisation methods. In ad-dition, the use of global characterisation of DEM error is a gross generalisation of reality due to the small extent of the areas in which the decision of stationarity is not violated. This was shown using exhaustive high-quality reference DEM based on airborne laser scanning and local semivariogram analysis. The error propagation analysis revealed that, as expected, an increase in the DEM vertical error will increase the error in surface derivatives. However, contrary to expectations, the spatial au-tocorrelation of the model appears to have varying effects on the error propagation analysis depend-ing on the application. The use of a spatially uncorrelated DEM error model has been considered as a 'worst-case scenario', but this opinion is now challenged because none of the DEM derivatives investigated in the study had maximum variation with spatially uncorrelated random error. Sig-nificant performance improvement was achieved in simulation-based error propagation analysis by applying process convolution in generating realisations of the DEM error model. In addition, typology of uncertainty in drainage basin delineations is presented.

Genome-wide association analysis and differential expression analysis of resistance to Sclerotinia stem rot in Brassica napus

Brassica napus is one of the most important oil crops in the world, and stem rot caused by the fungus Sclerotinia sclerotiorum results in major losses in yield and quality. To elucidate resistance genes and pathogenesis-related genes, genome-wide association analysis of 347 accessions was performed using the Illumina 60K Brassica SNP (single nucleotide polymorphism) array. In addition, the detached stem inoculation assay was used to select five highly resistant (R) and susceptible (S) B. napus lines, 48 h postinoculation with S. sclerotiorum for transcriptome sequencing. We identified 17 significant associations for stem resistance on chromosomes A8 and C6, five of which were on A8 and 12 on C6. The SNPs identified on A8 were located in a 409-kb haplotype block, and those on C6 were consistent with previous QTL mapping efforts. Transcriptome analysis suggested that S. sclerotiorum infection activates the immune system, sulphur metabolism, especially glutathione (GSH) and glucosinolates in both R and S genotypes. Genes found to be specific to the R genotype related to the jasmonic acid pathway, lignin biosynthesis, defence response, signal transduction and encoding transcription factors. Twenty-four genes were identified in both the SNP-trait association and transcriptome sequencing analyses, including a tau class glutathione S-transferase (GSTU) gene cluster. This study provides useful insight into the molecular mechanisms underlying the plant's response to S. sclerotiorum.