Variation in dynamic elastic shear modulus of sandstone upon fluid saturation and substitution

Experimental acoustic measurements on sandstone rocks at both sonic and ultrasonic frequencies show that fluid saturation can cause a noticeable change in both the dynamic bulk and shear elastic moduli of sandstones. We observed that the change in dynamic shear modulus upon fluid saturation is highly dependent on the type of saturant, its viscosity, rock microstructure, and applied pressures. Frequency dispersion has some influence on dynamic elastic moduli too, but its effect is limited to the ultrasonic frequency ranges and above. We propose that viscous coupling, reduction in free surface energy, and, to a limited extent, frequency dispersion due to both local and global flow are the main mechanisms responsible for the change in dynamic shear elastic modulus upon fluid saturation and substitution, and we quantify influences.

Nitrous acid: vibrational frequency shifts due to 15N substitution, and the harmonic force field

Vibration rotation spectra of HO15 NO and DO15 NO have been measured at a resolution of 0•04 cm-1 to determine the isotopic shifts in the vibrational band origins. These have been used together with recently determined data on the vibrational band origins, Coriolis constants, and centrifugal distorition constants, to determine the harmonic force field of both cis and trans nitrous acid in least squares refinement calculations. The results are discussed in relation to recent ab initio calculations, the inertia defects, and the torsional potential function.

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.

Degradation pathway of bisphenol A: Does ipso substitution apply to phenols containing a quaternary alpha-carbon structure in the para position?

The degradation of bisphenol A and nonylphenol involves the unusual rearrangement of stable carboncarbon bonds. Some nonylphenol isomers and bisphenol A possess a quaternary alpha-carbon atom as a common structural feature. The degradation of nonylphenol in Sphingomonas sp. strain TTNP3 occurs via a type II ipso substitution with the presence of a quaternary alpha-carbon as a prerequisite. We report here a new degradation pathway of bisphenol A. Consequent to the hydroxylation at position C-4, according to a type 11 ipso substitution mechanism, the C-C bond between the phenolic moiety and the isopropyl group of bisphenol A is broken. Besides the formation of hydroquinone and 4-(2-hydroxypropan-2-yl) phenol as the main metabolites, further compounds resulting from molecular rearrangements consistent with a carbocationic intermediate were identified. Assays with resting cells or cell extracts of Sphingomonas sp. strain TTNP3 under an 18 02 atmosphere were performed. One atom of 180, was present in hydroquinone, resulting from the monooxygenation of bisphenol A and nonylphenol. The monooxygenase activity was dependent on both NADPH and flavin adenine dinucleotide. Various cytochrome P450 inhibitors had identical inhibition effects on the conversion of both xenobiotics. Using a mutant of Sphingomonas sp. strain TTNP3, which is defective for growth on nonylphenol, we demonstrated that the reaction is catalyzed by the same enzymatic system. In conclusion, the degradation of bisphenol A and nonylphenol is initiated by the same monooxygenase, which may also lead to ipso substitution in other xenobiotics containing phenol with a quaternary a-carbon.

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.

Insights into the effects on metal binding of the systematic substitution of five key glutamate ligands in the ferritin of Escherichia coli

Ferritins are nearly ubiquitous iron storage proteins playing a fundamental role in iron metabolism. They are composed of 24 subunits forming a spherical protein shell encompassing a central iron storage cavity. The iron storage mechanism involves the initial binding and subsequent O-2-dependent oxidation of two Fe2+ ions located at sites A and B within the highly conserved dinuclear "ferroxidase center" in individual subunits. Unlike animal ferritins and the heme-containing bacterioferritins, the Escherichia coli ferritin possesses an additional iron-binding site (site C) located on the inner surface of the protein shell close to the ferroxidase center. We report the structures of five E. coli ferritin variants and their Fe3+ and Zn2+ (a redox-stable alternative for Fe2+) derivatives. Single carboxyl ligand replacements in sites A, B, and C gave unique effects on metal binding, which explain the observed changes in Fe2+ oxidation rates. Binding of Fe2+ at both A and B sites is clearly essential for rapid Fe2+ oxidation, and the linking of Fe-B(2+) to Fe-C(2+) enables the oxidation of three Fe2+ ions. The transient binding of Fe2+ at one of three newly observed Zn2+ sites may allow the oxidation of four Fe2+ by one dioxygen molecule.

Effect of chymosin reduction and salt substitution on the properties of white salted cheese

A whey salts mixture was used as a partial substitute for sodium chloride to provide a modified Na:K ratio (1:3.4) in the manufacture of white salted cheese using ultrafiltration. Reduction of chymosin addition from 20 to 8 mu L kg(-1) of cheese was also investigated. Variation of salt and chymosin levels did not result in any significant differences in composition and physicochemical properties. The rates of proteolysis in terms of water-soluble nitrogen (WSN) and nitrogen soluble in 12% trichloroacetic acid (TCA-SN) were affected by chymosin levels but not by salt treatment. Urea-PAGE electrophoretic analysis of caseins from the cheeses manufactured using three levels of chymosin and two salt types showed that the hydrolysis of alpha(s1)-casein was higher than for beta-caseins but the differences between the cheeses were not significant (P > 0.05). The chymosin level did not have a significant effect (P > 0.05) on hardness and fracturability, suggesting that any variation in hardness due to the initial hydrolysis was being confounded by other variables. Cheeses including the whey salts product were harder and more fracturable (P < 0.01) than the cheese treated with NaCl only. Both hardness and fracturability values decreased (P < 0.05) over the maturation period. The scores for bitterness were low; neither the effects of salt nor chymosin levels were significant (P > 0.05). (c) 2005 Elsevier Ltd. All rights reserved.

Probing the effect of allylic substitution on cyclic ammonium ylid rearrangements

The [2,3]-sigmatropic rearrangement of tetrahydropyridine-derived ammonium ylids is a valuable method for the preparation of substituted pyrrolidine carboxylates. The presence of an allylic substituent does not intrinsically reduce the yield of rearrangements, and the diastereoselectivity of rearrangement is related to the structure of the diazo reactant. The method represents a very rapid means of accessing complex pyrrolidines, as shown by preparation of a precursor to the core of lactacystin.

Substitution of dietary monounsaturated fatty acids for saturated fatty acids in a free-living population: a feasibility study

The fatty acid composition of the diet of seven free-living subjects (five men and two women) aged 41–56 years was altered for 1 month. The aim was to increase the intake of monounsaturated fatty acids (MUFAs) from subjects current habitual levels of 12% dietary energy to a target intake of 18% dietary energy, and to decrease saturated fatty acid (SFA) from habitual levels of 16% dietary energy to target levels of 10% dietary energy. The change in fatty acid intake was achieved by supplying volunteers with foods prepared using MUFA-containing spreads or olive oil (ready meals, sweet biscuits and cakes) and also by supplying spreads, cooking oil and MUFA-enriched milk for domestic use. Body weight and plasma total cholesterol measurements were made at baseline and at 2 and 4 weeks on the diet as an aid to maintaining subject compliance. MUFA consumption was significantly increased from 12% dietary energy to 16% dietary energy (P<0.01), and SFA intake was reduced from 16% dietary energy to 6% dietary energy (P<0.01) during the 4-week intervention. The diet failed to achieve the target increase in MUFA but exceeded the target reduction in SFA. This was due to the fact that subjects reduced their total fat intake from a mean habitual level of 38% dietary energy to a mean level of 30% dietary energy. During the dietary period, mean plasma cholesterol levels were lower at 2 weeks (P<0.01) and at 4 weeks (P<0.01) than the baseline, with a mean reduction of 20% over the dietary period. This study demonstrates the difficulty of achieving increased MUFA intakes (by SFA substitution) in free-living populations when only a limited range of fatty-acid modified food products are provided to volunteers.

Patterns of nucleotide substitution in angiosperm cpDNA trnL (UAA)-trnF (GAA) regions

Patterns of substitution in chloroplast encoded trnL_F regions were compared between species of Actaea (Ranunculales), Digitalis (Scrophulariales), Drosera (Caryophyllales), Panicoideae (Poales), the small chromosome species clade of Pelargonium (Geraniales), each representing a different order of flowering plants, and Huperzia (Lycopodiales). In total, the study included 265 taxa, each with > 900-bp sequences, totaling 0.24 Mb. Both pairwise and phylogeny-based comparisons were used to assess nucleotide substitution patterns. In all six groups, we found that transition/transversion ratios, as estimated by maximum likelihood on most-parsimonious trees, ranged between 0.8 and 1.0 for ingroups. These values occurred both at low sequence divergences, where substitutional saturation, i.e., multiple substitutions having occurred at the same (homologous) nucleotide position, was not expected, and at higher levels of divergence. This suggests that the angiosperm trnL-F regions evolve in a pattern different from that generally observed for nuclear and animal mtDNA (transitional/transversion ratio > or = 2). Transition/transversion ratios in the intron and the spacer region differed in all alignments compared, yet base compositions between the regions were highly similar in all six groups. A>-C transversions were significantly less frequent than the other four substitution types. This correlates with results from studies on fidelity mechanisms in DNA replication that predict A<->T and G<->C transversions to be least likely to occur. It therefore strengthens confidence in the link between mutation bias at the polymerase level and the actual fixation of substitutions as recorded on evolutionary trees, and concomitantly, in the neutrality of nucleotide substitutions as phylogenetic markers.

Complex history of a chromosomal paralogy region: insights from amphioxus aromatic amino acid hydroxylase genes and insulin-related genes

Aromatic amino acid hydroxylase (AAAH) genes and insulin-like genes form part of an extensive paralogy region shared by human chromosomes 11 and 12, thought to have arisen by tetraploidy in early vertebrate evolution. Cloning of a complementary DNA (cDNA) for an amphioxus (Branchiostoma floridae) hydroxylase gene (AmphiPAH) allowed us to investigate the ancestry of the human chromosome 11/12 paralogy region. Molecular phylogenetic evidence reveals that AmphiPAH is orthologous to vertebrate phenylalanine (PAH) genes; the implication is that all three vertebrate AAAH genes arose early in metazoan evolution, predating vertebrates. In contrast, our phylogenetic analysis of amphioxus and vertebrate insulin-related gene sequences is consistent with duplication of these genes during early chordate ancestry. The conclusion is that two tightly linked gene families on human chromosomes 11 and 12 were not duplicated coincidentally. We rationalize this paradox by invoking gene loss in the AAAH gene family and conclude that paralogous genes shared by paralogous chromosomes need not have identical evolutionary histories.