Comment on ``Piecewise potential vorticity inversion: Elementary tests''

Egger (2008) constructs some idealised experiments to test the usefulness of piecewise potential vorticity inversion (PPVI) in the diagnosis of Rossby wave dynamics and baroclinic development. He concludes that, ``PPVI does not help us to understand the dynamics of linear Rossby waves. It provides local tendencies of the streamfunction which are unrelated to the true ones. The same way, the motion of baroclinic waves in shear flow cannot be understood by using PPVI. Moreover, the effect of boundary temperatures as determined by PPVI is unrelated to the flow evolution.'' He goes further in arguing that we should not consider velocities as ``induced'' by PV anomalies defined by carving up the global domain. However, these conclusions partly reflect the limitations of his idealised experiments and the manner in which the PV components were partitioned from one another.

Characterising the background errors for the boundary-layer capping inversion

The one-dimensional variational assimilation of vertical temperature information in the presence of a boundary-layer capping inversion is studied. For an optimal analysis of the vertical temperature profile, an accurate representation of the background error covariances is essential. The background error covariances are highly flow-dependent due to the variability in the presence, structure and height of the boundary-layer capping inversion. Flow-dependent estimates of the background error covariances are shown by studying the spread in an ensemble of forecasts. A forecast of the temperature profile (used as a background state) may have a significant error in the position of the capping inversion with respect to observations. It is shown that the assimilation of observations may weaken the inversion structure in the analysis if only magnitude errors are accounted for as is the case for traditional data assimilation methods used for operational weather prediction. The positional error is treated explicitly here in a new data assimilation scheme to reduce positional error, in addition to the traditional framework to reduce magnitude error. The distribution of the positional error of the background inversion is estimated for use with the new scheme.

Notations and conventions in molecular spectroscopy: part 3. Permutation and permutation-inversion symmetry notation

The field of Molecular Spectroscopy was surveyed in order to determine a set of conventions and symbols which are in common use in the spectroscopic literature. This document, which is Part 3 in a series, deals with symmetry notation referring to groups that involve nuclear permutations and the inversion operation. Further parts will follow, dealing inter alia with vibration-rotation spectroscopy and electronic spectroscopy.

Calculating the exclusion probability and paternity index for X-chromosomal loci in the presence of substructure

There has been recent interest in the use of X-chromosomal loci for forensic and relatedness testing casework, with many authors developing new X-linked short tandem repeat (STR) loci suitable for forensic use. Here we present formulae for two key quantities in paternity testing, the average probability of exclusion and the paternity index, which are suitable for Xchromosomal loci in the presence of population substructure.

The dynamics of a polar low assessed using potential vorticity inversion

The dynamics of a polar low are examined using a piecewise potential vorticity (PV) inversion method. In previous studies of this and other polar lows, structural evolution has been described in terms of regions of anomalous PV. In this study the relative importance of different PV anomalies and the interactions between them have been quantified using PV diagnostics. The intensification of the polar low occurred in three stages (in contrast to previous studies of polar lows that have only identified two stages). The dynamical characteristics of stages one and two are consistent with the proposed type C cyclogenesis mechanism. A diabatically-generated lower-tropospheric PV anomaly dominated intensification after initial triggering by a positive upper-level PV anomaly. A phase tilt between the upper and lower levels was maintained through retardation of the positive upper-level anomaly by the effects of latent heat release. Stage three was a period of growth dominated by wind-induced surface heat exchange (WISHE), which contributed at least 18% to the amplitude of the mature surface polar low.

A hierarchical Bayesian model for predicting the functional consequences of amino-acid polymorphisms

Genetic polymorphisms in deoxyribonucleic acid coding regions may have a phenotypic effect on the carrier, e.g. by influencing susceptibility to disease. Detection of deleterious mutations via association studies is hampered by the large number of candidate sites; therefore methods are needed to narrow down the search to the most promising sites. For this, a possible approach is to use structural and sequence-based information of the encoded protein to predict whether a mutation at a particular site is likely to disrupt the functionality of the protein itself. We propose a hierarchical Bayesian multivariate adaptive regression spline (BMARS) model for supervised learning in this context and assess its predictive performance by using data from mutagenesis experiments on lac repressor and lysozyme proteins. In these experiments, about 12 amino-acid substitutions were performed at each native amino-acid position and the effect on protein functionality was assessed. The training data thus consist of repeated observations at each position, which the hierarchical framework is needed to account for. The model is trained on the lac repressor data and tested on the lysozyme mutations and vice versa. In particular, we show that the hierarchical BMARS model, by allowing for the clustered nature of the data, yields lower out-of-sample misclassification rates compared with both a BMARS and a frequen-tist MARS model, a support vector machine classifier and an optimally pruned classification tree.

The tagged microarray marker (TAM) method for high-throughput detection of single nucleotide and indel polymorphisms

The tagged microarray marker (TAM) method allows high-throughput differentiation between predicted alternative PCR products. Typically, the method is used as a molecular marker approach to determining the allelic states of single nucleotide polymorphisms (SNPs) or insertion-deletion (indel) alleles at genomic loci in multiple individuals. Biotin-labeled PCR products are spotted, unpurified, onto a streptavidin-coated glass slide and the alternative products are differentiated by hybridization to fluorescent detector oligonucleotides that recognize corresponding allele-specific tags on the PCR primers. The main attractions of this method are its high throughput (thousands of PCRs are analyzed per slide), flexibility of scoring (any combination, from a single marker in thousands of samples to thousands of markers in a single sample, can be analyzed) and flexibility of scale (any experimental scale, from a small lab setting up to a large project). This protocol describes an experiment involving 3,072 PCRs scored on a slide. The whole process from the start of PCR setup to receiving the data spreadsheet takes 2 d.

Polymorphisms in the apolipoprotein L1 gene and their effects on blood lipid and glucose levels in middle age males

Apolipoprotein L1 in plasma is associated with high- density lipoprotein. Novel APOL1 polymorphisms are investigated along with the association of two common haplotypes (Lys166Glu, Ile244Met, Lys271Arg) with circulating lipid and glucose levels. Although the amino acid substitutions occur in the amphipathic alpha helices region involved in lipid binding, these substitutions were found not to independently account for variability in circulating lipid and glucose levels in 149 middle age males.

Chromosomal mapping of ANTP class homeobox genes in amphioxus: piecing together ancestral genomes

Homeobox genes encode DNA-binding proteins, many of which are implicated in the control of embryonic development. Evolutionarily, most homeobox genes fall into two related clades: the ANTP and the PRD classes. Some genes in ANTP class, notably Hox, ParaHox, and NK genes, have an intriguing arrangement into physical clusters. To investigate the evolutionary history of these gene clusters, we examined homeobox gene chromosomal locations in the cephalochordate amphioxus, Branchiostoma floridae. We deduce that 22 amphioxus ANTP class homeobox genes localize in just three chromosomes. One contains the Hox cluster plus AmphiEn, AmphiMnx, and AmphiDll. The ParaHox cluster resides in another chromosome, whereas a third chromosome contains the NK type homeobox genes, including AmphiMsx and ArnphiTlx. By comparative analysis we infer that clustering of ANTP class homeobox genes evolved just once, during a series of extensive cis-duplication events of genes early in animal evolution. A trans-duplication event occurred later to yield the Hox and ParaHox gene clusters on different chromosomes. The results obtained have implications for understanding the origin of homeobox gene clustering, the diversification of the ANTP class of homeobox genes, and the evolution of animal genomes.

The chromosomal assessment of salt tolerant substituted tritipyrum using genomic fluorescent in situ hybridiization (FISH)

Wheat, although moderately tolerant to salt, can not be cultivated in many areas. However, in the triticeae tribe, some of the wild wheat relatives are highly tolerant, e.g. Thinopyrum bessarabicum, which grows on the sea shore. Eight primary hexaploid tritipyrum lines, amphiploids between Triticum durum and Thinopyrum bessarabicum have been produced which can set seed in at least 250 mM NaCl. These tritipyrums (2n=6x=42, AABBEbEb) due to reasons such as brittle rachis, continuous production of tillers, late maturity, tall stature and meiotic instability will not fulfill the requirements of a successful commercial salt tolerant crop. To overcome such problems the substituted tritipyrum, in which selected Eb chromosomes are replaced by D genome chromosomes of 6x wheat, was produced from 6x tritipyrum x 6x wheat hybrids (F1: 2n=6x=42, AABBDEb) followed by selfing and backcrossing with 6x tritipyrum. The fertile plants among the above progenies were screened by the genomic fluorescent in situ hybridization technique to identify their Eb and D chromosome constitution. This study showed that producing tritiprum with variable numbers of Eb and D genome chromosomes is feasible and that FISH is a useful technique for determining the number of Eb chromosomes present.

Asymmetric aziridine synthesis by aza-Darzens reaction of N-diphenylphosphinylimines with chiral enolates. Part 2: inversion of diastereoselectivity

The aza-Darzens ('ADZ') reactions of N-diphenylphosphinyl ('N-Dpp') imines with chiral enolates derived from N-bromoacetyl 2S-2,10-camphorsultam proceed in generally good yield to give N-diphenylphosphinyl aziridinoyl sultams. However, the stereoselectivity of the reaction is dependent upon the structure of the imine substituent: when the chiral enolate was reacted with arylimines substituted in the ortho-position, mixtures of cis- and trans-2'R,3'R-aziridines were obtained, often with a complete selectivity in favour of the trans-isomer. (c) 2006 Elsevier Ltd. All rights reserved.

Evidence for associations between common polymorphisms of estrogen receptor beta gene with homocysteine and nitric oxide

Background Homocysteine and asymmetric dimethylarginine (ADMA) affect nitric oxide (NO) concentration, thereby contributing to cardiovascular disease (CVD). Both amino acids can be reduced in vivo by estrogen. Variation in the estrogen receptor (ER) may influence homocysteine and ADMA, yet no information is available on associations with single nucleotide polymorphisms in the estrogen receptor genes ER alpha (PvuII and XbaI) and ER beta (1730G -> A and cx+56 G -> A). Objective To find relationships between common polymorphisms associated with cardiovascular disease and cardiovascular risk factors homocysteine and ADMA. Methods In a cross-sectional study with healthy postmenopausal women (n = 89), homocysteine, ADMA, nitric oxide metabolites (NOx), plasma folate and ER alpha and beta polymorphisms ER alpha PvuII, ER alpha XbaI; ER beta 1730G -> A (AluI), ER beta cx+56 G -> A (Tsp5091) were analyzed. Results Women who are homozygotic for ER beta cx+56 G -> A A/A exhibited higher homocysteine (p = 0.012) and NOx (p = 0.056) levels than wildtype or heterozygotes. NOx concentration was also significantly affected by ER beta 1730 G -> A polymorphism (p = 0.025). The ER beta (p < 0.001) and ER alpha (p < 0.001) polymorphisms were in linkage disequilibrium. Conclusions Women who are homozygotic for ER beta cx+S6 G -> A A/A may be at increased risk for cardiovascular disease due to higher homocysteine levels.

Polymorphisms in the apolipoprotein L1 gene and their effects on blood lipid and glucose levels in middle age males

Apolipoprotein L1 in plasma is associated with high- density lipoprotein. Novel APOL1 polymorphisms are investigated along with the association of two common haplotypes (Lys166Glu, Ile244Met, Lys271Arg) with circulating lipid and glucose levels. Although the amino acid substitutions occur in the amphipathic alpha helices region involved in lipid binding, these substitutions were found not to independently account for variability in circulating lipid and glucose levels in 149 middle age males.