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PubMed2005

Evolutionary genomics: codon volatility does not detect selection.

Plotkin et al. introduce a method to detect selection that is based on an index called codon volatility and that uses only the sequence of a single genome, claiming that this method is applicable to a large range of sequenced organisms. Volatility for a given codon is the ratio of non-synonymous codons to all sense codons accessible by one point mutation. The significance of each gene's volatility is assessed by comparison with a simulated distribution of 10(6) synonymous versions of each gene, with synonymous codons drawn randomly from average genome frequencies. Here we re-examine their method and data and find that codon volatility does not detect selection, and that, even if it did, the genomes of Mycobacterium tuberculosis and Plasmodium falciparum, as well as those of most sequenced organisms, do not meet the assumptions necessary for application of their method.

Animals↗
PubMed2003

The automated sample preparation system MixMaster for investigation of volatile organic compounds with mid-infrared evanescent wave spectroscopy.

For efficient development assessment, and calibration of new chemical analyzers a large number of independently prepared samples of target analytes is necessary. Whereas mixing units for gas analysis are readily available, there is a lack of instrumentation for accurate preparation of liquid samples containing volatile organic compounds (VOCs). Manual preparation of liquid samples containing VOCs at trace concentration levels is a particularly challenging and time consuming task. Furthermore, regularly scheduled calibration of sensors and analyzer systems demands for computer controlled automated sample preparation systems. In this paper we present a novel liquid mixing device enabling extensive measurement series with focus on volatile organic compounds, facilitating analysis of water polluted by traces of volatile hydrocarbons. After discussing the mixing system and control software, first results obtained by coupling with an FT-IR spectrometer are reported. Properties of the mixing system are assessed by mid-infrared attenuated total reflection (ATR) spectroscopy of methanol-acetone mixtures and by investigation of multicomponent samples containing volatile hydrocarbons such as 1,2,4-trichlorobenzene and tetrachloroethylene. Obtained ATR spectra are evaluated by principal component regression (PCR) algorithms. It is demonstrated that the presented sample mixing device provides reliable multicomponent mixtures with sufficient accuracy and reproducibility at trace concentration levels.

Electronic Data Processing↗
PubMed2000

Inactivation of Mycobacterium bovis in cattle slurry by five volatile chemicals.

This research was undertaken to evaluate volatile chemicals which retained mycobactericidal activity in cattle slurry. Mycobacterium bovis, suspended in sterilized cattle slurry, was treated with different concentrations of five volatile chemicals with mycobactericidal activity. Following treatment of the slurry for specified time intervals, the reaction mixture was lyophilized to remove the volatile chemicals, and samples of the reconstituted slurry were used to inoculate flasks of Lowenstein-Jensen medium to determine survival or inactivation of the mycobacteria. Acetone, at a concentration of 22.5%, inactivated M. bovis in less than 24 h. Ammonium hydroxide, at a concentration of 1%, was mycobactericidal after 36 h. Chloroform at a concentration of 0.5%, ethyl alcohol at a concentration of 17.5% and xylene at a concentration of 3% inactivated the mycobacteria within 48 h. Some of the volatile chemicals with mycobactericidal activity are potentially useful at farm level.

Acetone↗
PubMed2003

Volatile compounds produced by Lactobacillus fermentum, Saccharomyces cerevisiae and Candida krusei in single starter culture fermentations of Ghanaian maize dough.

AIMS: To identify and compare the volatile compounds associated with maize dough samples prepared by spontaneous fermentation and by the use of added starter cultures in Ghana. METHODS AND RESULTS: The starter cultures examined were Lactobacillus fermentum, Saccharomyces cerevisiae and Candida krusei. For identification of aroma volatiles, extracts by the Likens-Nickerson simultaneous distillation and extraction technique were analysed by gas chromatography-mass spectrometry (GC-MS) and using a trained panel of four judges by GC-Olfactometry (GC-sniffing). Compounds identified by GC-MS in maize dough samples after 72 h of fermentation included 20 alcohols, 22 carbonyls, 11 esters, seven acids, a furan and three phenolic compounds. Of the total 64 volatile compounds, 51 were detected by GC-sniffing as contributing to the aroma of the different fermented dough samples. Spontaneously fermented maize dough was characterized by higher levels of carbonyl compounds while fermentations with added L. fermentum recorded the highest concentration of acetic acid. S. cerevisiae produced higher amounts of fusel alcohols and increasing levels of esters with fermentation time and C. krusei showed similarity to L. fermentum with lower levels of most volatiles identified. CONCLUSION: The present study has given a detailed picture of the aroma compounds in fermented maize and demonstrated that the predominant micro-organisms in fermented maize dough can be used as starter cultures to modify the aroma of fermented maize dough. SIGNIFICANCE AND IMPACT OF THE STUDY: The study has documented the advantage of using starter cultures in African traditional food processing and provided a scientific background for introducing better controlled fermentations.

Alcohols↗
PubMed2006

The products of a single maize sesquiterpene synthase form a volatile defense signal that attracts natural enemies of maize herbivores.

Plants can defend themselves against herbivores by attracting natural enemies of the herbivores. The cues for attraction are often complex mixtures of herbivore-induced plant volatiles, making it difficult to demonstrate the role of specific compounds. After herbivory by lepidopteran larvae, maize releases a mixture of volatiles that is highly attractive to females of various parasitic wasp species. We identified the terpene synthase TPS10 that forms (E)-beta-farnesene, (E)-alpha-bergamotene, and other herbivory-induced sesquiterpene hydrocarbons from the substrate farnesyl diphosphate. The corresponding gene is expressed in response to herbivore attack and is regulated at the transcript level. Overexpression of tps10 in Arabidopsis thaliana resulted in plants emitting high quantities of TPS10 sesquiterpene products identical to those released by maize. Using these transgenic Arabidopsis plants as odor sources in olfactometer assays showed that females of the parasitoid Cotesia marginiventris learn to exploit the TPS10 sesquiterpenes to locate their lepidopteran hosts after prior exposure to these volatiles in association with hosts. This dissection of the herbivore-induced volatile blend demonstrates that a single gene such as tps10 can be sufficient to mediate the indirect defense of maize against herbivore attack.

Animals↗
PubMed2006

Tomato aromatic amino acid decarboxylases participate in synthesis of the flavor volatiles 2-phenylethanol and 2-phenylacetaldehyde.

An important phenylalanine-derived volatile compound produced by plants is 2-phenylethanol. It is a major contributor to flavor in many foods, including fresh fruits, such as tomato, and an insect-attracting scent in roses and many other flowers. Despite the centrality of 2-phenylethanol to flavor and fragrance, the plant genes responsible for its synthesis have not been identified. Here, we describe a biosynthetic pathway for 2-phenylethanol and other phenylalanine-derived volatiles in tomato fruits and a small family of decarboxylases (LeAADC1A, LeAADC1B, and LeAADC2) that can mediate that pathway's first step. These enzymes each catalyze conversion of phenylalanine to phenethylamine and tyrosine to tyramine. Although tyrosine is the preferred substrate in vitro, phenylalanine levels in tomato fruits far exceed those of tyrosine, indicating that phenylalanine is a physiological substrate. Consistent with this view, overexpression of either LeAADC1A or LeAADC2 in transgenic tomato plants resulted in fruits with up to 10-fold increased emissions of the products of the pathway, including 2-phenylacetaldehyde, 2-phenylethanol, and 1-nitro-2-phenylethane. Further, antisense reduction of LeAADC2 significantly reduced emissions of these volatiles. Besides establishing a biosynthetic route, these results show that it is possible to change phenylalanine-based flavor and aroma volatiles in plants by manipulating expression of a single gene.

Acetaldehyde↗
PubMed1998

Unc-1: a stomatin homologue controls sensitivity to volatile anesthetics in Caenorhabditis elegans.

To identify sites of action of volatile anesthetics, we are studying genes in a functional pathway that controls sensitivity to volatile anesthetics in the nematode Caenorhabditis elegans. The unc-1 gene occupies a central position in this pathway. Different alleles of unc-1 have unique effects on sensitivity to the different volatile anesthetics. UNC-1 shows extensive homology to human stomatin, an integral membrane protein thought to regulate an associated ion channel. We postulate that UNC-1 has a direct effect on anesthetic sensitivity in C. elegans and may represent a molecular target for volatile anesthetics.

Amino Acid Sequence↗
PubMed2001

Antagonism of inhalant and volatile anesthetic enhancement of glycine receptor function.

Recent studies suggest that alcohols, volatile anesthetics, and inhaled drugs of abuse, which enhance gamma-aminobutyric acid, type A, and glycine receptor-activated ion channel function, may share common or overlapping molecular sites of action on these receptors. To investigate this possibility, these compounds were applied singly and in combination to wild-type glycine alpha(1) receptors expressed in Xenopus laevis oocytes. Data obtained from concentration-response curves of the volatile anesthetic enflurane constructed in the presence and absence of ethanol, chloroform, or toluene were consistent with competition for a common binding pocket on these receptors. A mutant glycine receptor, insensitive to the enhancing effects of ethanol but not anesthetics or inhalants, demonstrated antagonism of anesthetic and inhalant effects on this receptor. Although ethanol (25-200 mm) had no effect on its own in this receptor, it was able to inhibit reversibly the enhancing effect of enflurane, toluene, and chloroform in a concentration-dependent manner. These data suggest the existence of overlapping molecular sites of action for ethanol, inhalants, and volatile anesthetics on glycine receptors and illustrate the feasibility of pharmacological antagonism of the effects of volatile anesthetics.

Anesthetics, Inhalation↗
PubMedDate not supplied

Recent chemical exposures and blood volatile organic compound levels in a large population-based sample.

Little is known about factors that influence blood levels of volatile organic compounds in nonoccupationally exposed populations. The authors examined the possible relationship between recent self-reported chemical exposures and elevated blood volatile organic compound levels among 982 adult participants in theThird National Health and Nutrition Examination Survey. A strong dose-response effect was indicated (p < .001) for increasing lifetime pack-years of cigarettes smoked for elevated levels of toluene, styrene, and benzene. A positive dose-response effect was indicated for daily alcohol consumption with respect to elevated blood levels of 2-butanone and acetone. For volatile organic compounds typically found in 10-75% of the population, the establishment of a link with specific environmental exposures is relatively easy because there is less effect of confounding in this group. Some volatile organic compounds, however, are seen in less than 10% of the general population; finding these compounds at any level may warrant a search for a particular exposure.

Adult↗
PubMedDate not supplied

Effect of adding non-volatile oil as a core material for the floating microspheres prepared by emulsion solvent diffusion method.

Eudragit microspheres, to float in the gastrointestinal tract, were prepared to prolong a gastrointestinal transit time. To enhance their buoyancy, non-volatile oil was added to the dispersed phase. When an oil component was not miscible with water, over 90% was entrapped within the microspheres and prolonged the floating time of the microspheres. Depending on the solvent ratio, the morphologies of the microspheres were different and the best result was obtained when the ratio of dichloromethane:ethanol:isopropanol was 5:6:4. As the isopropanol portion increased, the time to form microspheres was delayed and the amount of fibre-like substance produced was decreased, due to the slow diffusion rate of the solvent. Compared with microspheres prepared without non-volatile oil, the release rate of the drug from microspheres was faster in all cases tested, except the microspheres containing mineral oil. The solubility of the drug in the non-volatile oil affected the release profiles of the drugs. The non-volatile oil tends to decrease the glass transition temperature of prepared microspheres and change the release profile. The internal morphology of the microspheres was slightly different depending on the entrapped oil phase used. Tiny spherical objects were present at the inner surface of microspheres and the inside of the shell.

Acrylates↗
PubMed1986

Meat flavor volatiles: a review of the composition, techniques of analysis, and sensory evaluation.

Flavor is an important quality attribute which relates to the organoleptic characteristics of meat. Although perception of flavor is a complex phenomenon, odor is the most important single factor contributing to the overall characteristics of flavor. A large number of compounds have been identified in the volatile fraction of red meats and poultry. An overview of the chemical constituents present in the volatiles of beef, pork, mutton, and chicken is presented according to species and arranged by chemical class--hydrocarbons, alcohols, acids, aldehydes, ketones, sulfides, heterocyclic compounds, etc. The volatile components of cured and uncured pork are compared. The field of meat flavor is assessed in terms of what has been accomplished and the direction in which it may proceed. Techniques for analysis of these volatiles are briefly described.

Animals↗
PubMed1999

Responses of Xenopus laevis water nose to water-soluble and volatile odorants.

Using the whole-cell mode of the patch-clamp technique, we recorded action potentials, voltage-activated cationic currents, and inward currents in response to water-soluble and volatile odorants from receptor neurons in the lateral diverticulum (water nose) of the olfactory sensory epithelium of Xenopus laevis. The resting membrane potential was -46.5 +/- 1.2 mV (mean +/- SEM, n = 68), and a current injection of 1-3 pA induced overshooting action potentials. Under voltage-clamp conditions, a voltage-dependent Na+ inward current, a sustained outward K+ current, and a Ca2+-activated K+ current were identified. Application of an amino acid cocktail induced inward currents in 32 of 238 olfactory neurons in the lateral diverticulum under voltage-clamp conditions. Application of volatile odorant cocktails also induced current responses in 23 of 238 olfactory neurons. These results suggest that the olfactory neurons respond to both water-soluble and volatile odorants. The application of alanine or arginine induced inward currents in a dose-dependent manner. More than 50% of the single olfactory neurons responded to multiple types of amino acids, including acidic, neutral, and basic amino acids applied at 100 microM or 1 mM. These results suggest that olfactory neurons in the lateral diverticulum have receptors for amino acids and volatile odorants.

Action Potentials↗
PubMed1986

A static calibration method for the gas chromatographic determination of per cent concentrations of volatile anaesthetic agents.

A method is described for preparing static standards of per cent concentrations of volatile anaesthetic agents, that is designed to minimize adsorptive losses in the container used for the standards. The extent to which this aim has been realized was investigated for atmospheres of halothane, enflurane and isoflurane, both by monitoring the relative concentration within the container over a period of 30 min after the standard was prepared, and by measuring the absolute concentration of the volatile agents. Gas chromatography was used for both sets of measurements, with liquid standards being used for the absolute measurements. No discernible loss of volatile agent occurred over the 30-min period, and the measured concentrations agreed closely with the predicted values. The standard mixtures prepared by the method were suitable for calibrating a gas chromatograph, and allowed accurate determinations of volatile anaesthetics to be made. The relative standard error of the predicted concentration for a single standard mixture was less than 0.5%, and the calibration accuracy could be further improved by taking the mean chromatograph response to several standard mixtures prepared in succession.

Anesthetics↗
PubMed2004

Effects of volatile anaesthetic agents on enhanced airway tone in sensitized guinea pigs.

BACKGROUND: Although volatile anaesthetics afford protection against bronchospasm, their potential to reverse a sustained constriction of hyperreactive airways has not been characterized. Accordingly, we investigated the ability of halothane, isoflurane, sevoflurane and desflurane to reverse lung constriction induced by prolonged stimulation of the muscarinic receptors in guinea pigs sensitized to ovalbumin. METHODS: Pulmonary input impedance (ZL) was measured using forced oscillations in five groups of ovalbumin-sensitized, mechanically ventilated guinea pigs. ZL was measured under baseline conditions, during steady-state bronchoconstriction induced by an i.v. infusion of methacholine (MCh), and after administration of one of the volatile agents at 1 MAC after the induction of a steady-state bronchoconstriction. Airway resistance (Raw), and parenchymal tissue resistive and elastic coefficients were extracted from ZL by model fitting. RESULTS: All four volatile agents exhibited an initial relaxation of the MCh-induced airway constriction followed by gradual increases in Raw. The bronchodilatory effect of isoflurane was the most potent (-28.9 (SE 5.5)% at 2 min, P<0.05) and lasted longest (7 min); sevoflurane and halothane had shorter and more moderate effects (-21.1 (3.9)%, P<0.05, and -6.1 (1.7)%, P<0.05, respectively, at 1 min). Desflurane caused highly variable changes in Raw, with a tendency to enhance airway tone. CONCLUSIONS: Volatile agents can reverse sustained MCh-induced airway constriction only transiently in sensitized guinea pigs. Isoflurane proved most beneficial in temporally improving lung function in the presence of a severe constriction of allergic inflamed airways. Desflurane displayed potential to induce further airway constriction.

Airway Resistance↗
PubMed2005

Microflora species and their volatile compounds affecting development of an alcohol dehydrogenase homozygous strain (Adh-I) of Bactrocera (Dacus) oleae (Diptera: Tephritidae).

Microflora species and volatiles emitted from artificial diets were examined from the larvae of three homozygous alcohol dehydrogenase (Adh) strains of the olive fruit fly, Bactrocera (Dacus) oleae (Gmelin), reared under identical conditions. Differences in volatile composition were detected when Adh-I homozygous larvae developed in a diet lacking the preservative p-hydroxybenzoic acid methyl ester (nipagin). Larval development of the Adh-I strain in the preservative-free diet was reduced by 50%, whereas pupal emergence was completely inhibited. The larval development and pupal emergence of Adh-F and Adh-S strains were not affected. Unique microorganisms with characteristic volatile profiles were isolated from the preservative-free diet of the Adh-I strain that were different from those, isolated from Adh-S, Adh-F, laboratory colony, and wild insect populations. Our results indicated that the variations in volatile composition of the artificial diets, and the inhibition of larval development and pupal emergence in Adh-I strain were related to changes in the microflora that developed in the diets of the Adh-I strain.

Alcohol Dehydrogenase↗
PubMed1996

Effect of volatiles from neem and other natural products on gonotrophic cycle and oviposition of Anopheles stephensi and An. culicifacies (Diptera: Culicidae).

The gonotrophic cycle of female Anopheles was impaired by exposure to volatiles of neem, (Azadirachta indica), reetha, (Sapindus mukorossi), and garlic, (Allium sativum), but not to castor seeds and cotton seed oil. A brief exposure to contact or volatile extracts from neem suppressed rather than inhibited oviposition. Complete inhibition of oviposition was observed by exposure of mosquitoes to neem oil and 1 fraction containing volatile components. Vitellogenesis was impaired irreversably by long-term exposure to neem odor and some extracts. The effect of volatiles on oviposition seems to be regulated by absorption through the cuticle, although passage through the spiracles could not be excluded.

Animals↗
PubMed2006

Identification of loci affecting flavour volatile emissions in tomato fruits.

Fresh tomato fruit flavour is the sum of the interaction between sugars, acids, and a set of approximately 30 volatile compounds synthesized from a diverse set of precursors, including amino acids, lipids, and carotenoids. Some of these volatiles impart desirable qualities while others are negatively perceived. As a first step to identify the genes responsible for the synthesis of flavour-related chemicals, an attempt was made to identify loci that influence the chemical composition of ripe fruits. A genetically diverse but well-defined Solanum pennellii IL population was used. Because S. pennellii is a small green-fruited species, this population exhibits great biochemical diversity and is a rich source of genes affecting both fruit development and chemical composition. This population was used to identify multiple loci affecting the composition of chemicals related to flavour. Twenty-five loci were identified that are significantly altered in one or more of 23 different volatiles and four were altered in citric acid content. It was further shown that emissions of carotenoid-derived volatiles were directly correlated with the fruit carotenoid content. Linked molecular markers should be useful for breeding programmes aimed at improving fruit flavour. In the longer term, the genes responsible for controlling the levels of these chemicals will be important tools for understanding the complex interactions that ultimately integrate to provide the unique flavour of a tomato.

Carotenoids↗
PubMed2004

Codon volatility as an indicator of positive selection: data from eukaryotic genome comparisons.

It has been suggested that codon volatility (the proportion of the point-mutation neighbors of a codon that encode different amino acids) can be used as an index of past positive selection. We compared codon volatility with patterns of synonymous and nonsynonymous nucleotide substitution in genome-wide comparisons of orthologous genes between three pairs of related genomes: (1) the protists Plasmodium falciparum and P. yoelii, (2) the fungi Saccharomyces cerevisiae and S. paradoxus, and (3) the mammals mouse and rat. Codon volatility was not consistently associated with an elevated rate of nonsynonymous substitution, as would be expected under positive selection. Rather, the most consistent and powerful correlate of elevated codon volatility was nucleotide content at the second codon position, as expected, given the nature of the genetic code.

Animals↗