Measurement of the neutron radius of 208Pb through parity violation in electron scattering.

We report the first measurement of the parity-violating asymmetry A(PV) in the elastic scattering of polarized electrons from 208Pb. A(PV) is sensitive to the radius of the neutron distribution (R(n)). The result A(PV)=0.656±0.060(stat)±0.014(syst) ppm corresponds to a difference between the radii of the neutron and proton distributions R(n)-R(p)=0.33(-0.18)(+0.16) fm and provides the first electroweak observation of the neutron skin which is expected in a heavy, neutron-rich nucleus.

A comparison of approaches for association studies of polymorphisms and colorectal cancer risk.

AIM: Meta-analyses have been used to evaluate associations between polymorphisms and colorectal cancer risk, but the quality of individual studies used to inform them may vary substantially. Our aim was to apply well-established quality-control criteria to individual association studies and then compare the results of meta-analyses that included or excluded studies that did not meet these criteria. METHOD: We used meta-analyses of studies reporting a relationship between polymorphisms and colorectal cancer published between 1996 and 2008. Polymorphism-cancer associations were derived in separate meta-analyses including only those meeting the quality-control criteria. RESULTS: Relative ORs varied substantially between the open and restricted group meta-analyses for all variants except MTHFR 677 CT. However, the associations were modest and the direction of relative risk did not change after applying criteria. Publication bias was detected for all associations, except the restricted set of studies for GSTP1 GG. CONCLUSION: We observed variation in calculated relative risk and changes in tests for publication bias that were dependent on the inclusion criteria used for association studies of polymorphisms and colorectal cancer. Standardizing study inclusion criteria may reduce the variation in findings for meta-analyses of gene-association studies of common diseases such as colorectal cancer.

Recommended nomenclature for the vertebrate alcohol dehydrogenase gene family.

The alcohol dehydrogenase (ADH) gene family encodes enzymes that metabolize a wide variety of substrates, including ethanol, retinol, other aliphatic alcohols, hydroxysteroids, and lipid peroxidation products. Studies on 19 vertebrate animals have identified ADH orthologs across several species, and this has now led to questions of how best to name ADH proteins and genes. Seven distinct classes of vertebrate ADH encoded by non-orthologous genes have been defined based upon sequence homology as well as unique catalytic properties or gene expression patterns. Each class of vertebrate ADH shares <70% sequence identity with other classes of ADH in the same species. Classes may be further divided into multiple closely related isoenzymes sharing >80% sequence identity such as the case for class I ADH where humans have three class I ADH genes, horses have two, and mice have only one. Presented here is a nomenclature that uses the widely accepted vertebrate ADH class system as its basis. It follows the guidelines of human and mouse gene nomenclature committees, which recommend coordinating names across species boundaries and eliminating Roman numerals and Greek symbols. We recommend that enzyme subunits be referred to by the symbol "ADH" (alcohol dehydrogenase) followed by an Arabic number denoting the class; i.e. ADH1 for class I ADH. For genes we recommend the italicized root symbol "ADH" for human and "Adh" for mouse, followed by the appropriate Arabic number for the class; i.e. ADH1 or Adh1 for class I ADH genes. For organisms where multiple species-specific isoenzymes exist within a class, we recommend adding a capital letter after the Arabic number; i.e. ADH1A, ADH1B, and ADH1C for human alpha, beta, and gamma class I ADHs, respectively. This nomenclature will accommodate newly discovered members of the vertebrate ADH family, and will facilitate functional and evolutionary studies.

Evolution of class I alcohol dehydrogenase genes in catarrhine primates: gene conversion, substitution rates, and gene regulation.

The three class I alcohol dehydrogenases (ADHs) in humans comprise homo- and heterodimers of three subunits (alpha, beta, and gamma) with greater than 90% sequence identity. These are encoded by distinct genes (ADH1, ADH2, and ADH3, respectively) and are all expressed in the liver. In baboons, only the beta ADH subunit is expressed in liver. A second class I ADH is expressed in the kidney; we isolated, cloned, and sequenced the cDNA corresponding to this ADH and conclude that it is of the gamma ADH lineage. We also amplified and sequenced the 5' noncoding regions of all three class I baboon ADH genes and the rhesus monkey ADH1 gene and compared their nucleotide sequences with the corresponding human sequences. There is clear evidence that the evolution of these genes has been reticulate. At least three gene conversion events, affecting the coding and 3' noncoding regions of the genes, are inferred from compatibility and partition matrices and phylogenetic analysis of the sequences. Our estimation of the evolutionary history of these genes provides a framework for the investigation of relative substitution rates and functional variation among the sequences. Relative-rate tests, designed to account for the reticulate evolution of these genes, indicate no difference in substitution rate either between genes encoding different subunits or between human and Old World monkey lineages. The human and baboon gamma ADH sequences do not show clear differences at functionally important sites within the coding region, but they do differ at a number of sites in regions previously proposed to be regulatory sites for transcriptional control. This variation may explain the different patterns of gene expression in humans and baboons.

A genetic basis for corneal sensitivity to ultraviolet light among recombinant SWXJ inbred strains of mice.

PURPOSE: To examine a possible genetic basis for corneal sensitivity to UV-B light exposure. METHODS: To this end, adult male mice from the 14 SWXJ recombinant inbred albino strains (originating from SJL/J and SWR/J parental strains) were subjected to ultraviolet (UV) radiation exposure of 0.078 J/cm2 and photographed four days post-exposure, to assess corneal opacity and the possible correlation with corneal aldehyde dehydrogenase (ALDH) activity, alcohol dehydrogenase (ADH) activity and soluble protein content. RESULTS: Those recombinant strains that exhibited the SWR/J strain phenotype of having low levels of ALDH and decreased soluble protein levels also exhibited greater levels of corneal clouding after UV-exposure than the other strains, which exhibited "normal" levels of both ALDH activity and soluble protein in the cornea. CONCLUSIONS: These data support an hypothesis for a major role for ALDH in assisting the cornea to protect the eye against UV-induced tissue damage.

Alcohol dehydrogenases and aldehyde dehydrogenases among inbred strains of mice: multiplicity, development, genetic studies and metabolic roles.

Alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH) are the major enzymes responsible for the metabolism of alcohols and aldehydes in the body. Both exist as a family of isozymes in mammals, and have been extensively studied in animal models, particularly among inbred strains of mice. Mouse ADH exists as at least three major classes, which are predominantly localized in liver (classes I and III), and in stomach/cornea (class IV). Mouse ALDH exhibits extensive multiplicity, several forms of which have been characterized, including ALDH1 (liver cytoplasmic/class 1 isozyme); ALDH2 (liver mitochondrial/class 2.); ALDH3 (stomach cytosolic/class 3); ALDH4 (liver microsomal/class 3); and ALDH5 (testis cytosolic/class 3). Biochemical, genetic and molecular genetic analyses have been performed on several of these enzymes, including studies on variant forms of ADH and ALDH. Distinct metabolic roles are proposed, based upon their tissue and subcellular distribution characteristics and the biochemical properties for these enzymes.

Human stomach class IV alcohol dehydrogenase: molecular genetic analysis.

A partial human stomach alcohol dehydrogenase (ADH) encoding cDNA has been isolated, cloned, and sequenced, which contains 222 nucleotides encoding amino acid residues 227-299 of the ADH subunit. The amino acid sequence deduced from this cDNA was highly homologous with the rat stomach class IV ADH sequence recently reported (81.1% sequence identity). Homology with other human ADH classes was also observed: class I, 58.1% sequence identity; class II, 39.2% sequence identity; class III, 55.4% sequence identity; and class V, 50.0% sequence identity. These results support a proposal that the isolated cDNA encodes a partial sequence for human stomach class IV ADH. This sequence retains val294 for all other human ADH classes reported, as compared with an ala294 at this position reported for rat class IV ADH. This ala residue may contribute to the very high Km values with ethanol for the latter enzyme. In addition, three substitutions are reported for key residues in the coenzyme binding site: 251, gln/ser; 260, gly/asn; and 261, gly/asn, which may contribute to the weak coenzyme binding properties reported for human class IV ADH.

Alcohol dehydrogenases: a family of isozymes with differential functions.

Human alcohol dehydrogenases (ADHs) are encoded by at least 7 genes, and comprise at least 5 Classes. The isozymes are differentially distributed in tissues, with most Classes exhibiting highest activity in liver. Class IV (mu or sigma) ADH exhibits high activity in stomach and cornea. Class I ADHs have a wide range of physiological substrates, in addition to ethanol, involving metabolism of the following: bile compounds; testosterone; neurotransmitters; congeners; retinol; peroxidic aldehydes; and mevalonate. Class II (pi) ADH is involved in peroxidic aldehyde, norepinephrine, mevalonate and congener metabolism, but apparently plays a minor role in ethanol oxidation. Class III (chi) ADH is inactive with ethanol under physiological conditions, but functions in formaldehyde and omega-hydroxy fatty acid metabolism. Class IV (mu or sigma) is apparently involved in first-pass metabolism of gastric ethanol and other dietary alcohols, and in peroxidic aldehyde metabolism.

Differential corneal sensitivity to ultraviolet light among inbred strains of mice. Correlation of ultraviolet B sensitivity with aldehyde dehydrogenase deficiency.

Adult male mice from four inbred albino strains (SJL/J, NZW/BL, BALB/c HeA, and SWR/J) were subjected to ultraviolet radiation (UVR) exposure (302 nm peak wavelength, intensity 398 microW/cm2) for 3.25 min and photographed 4 days postexposure to assess corneal clouding. Corneal extracts from control (unexposed) mice from each strain, were also monitored for aldehyde dehydrogenase (ALDH) and alcohol dehydrogenase (ADH) activity and soluble protein content. The SWR/J strain exhibited more extensive corneal clouding after UV exposure than did the other strains, and control SWR/J mice exhibited a low activity variant phenotype for the major ocular ALDH AHD-4, and decreased levels of soluble protein in corneal extracts. These data support earlier proposals for a major role for ALDH in assisting the cornea in protecting the eye against UVR-induced tissue damage.

Human corneal aldehyde dehydrogenase: purification, kinetic characterisation and phenotypic variation.

Human corneal aldehyde dehydrogenase (designated ALDH3) was purified to homogeneity and characterised with respect to substrate specificity and inhibition by thiol reagents. The enzyme was present as a major soluble protein (5% of the total soluble protein) and was found to efficiently catalyse the oxidation of medium chain peroxidic aldehydes which may be found in the cornea. These findings are consistent with the proposal that ALDH3 plays a dual role in the absorption of UVR and in the oxidation of peroxidic aldehydes in the mammalian cornea. Disulfiram did not inhibit this enzyme under the conditions used in this study, however p-hydroxymercuribenzoate rapidly inactivated the enzyme. Analysis of the proteins of the cornea and surrounding tissue indicated that in both the cow and the human, changes in the nature and quantity of soluble proteins occurred. Phenotype variants of the ALDH3 were apparent in a small Australian population.

Purification and properties of murine corneal aldehyde dehydrogenase.

Murine corneal aldehyde dehydrogenase has been purified to homogeneity and characterized with a range of aldehyde substrates at pH 7.4. The enzyme was a dimer with a subunit molecular weight of 59 KDa. and appears to prefer aldehyde products of lipid peroxidation as substrates. The enzyme constituted approximately 5% of the total soluble protein of mouse cornea. A dual role has been proposed for corneal aldehyde dehydrogenase in providing the eye with protection against UV-B light: by oxidizing aldehydes generated through light-induced lipid peroxidation; and by the direct absorption of UV-B light by the enzyme.

Ultraviolet light-induced pathology in the eye: associated changes in ocular aldehyde dehydrogenase and alcohol dehydrogenase activities.

Adult male C57BL/6J inbred mice were subjected to ultraviolet radiation (UVR) exposure (302-nm peak wavelength; average intensity 282 microW/cm2) for 1 h and monitored for ocular aldehyde dehydrogenase (ALDH) and alcohol dehydrogenase (ADH) activity changes over a period of 25 days. Dramatic reductions in activities were observed by 4-6 days postexposure, resulting in enzyme levels of 15-16% of control animals. Major decreases in corneal enzyme levels were predominantly responsible for these changes. Ocular morphology was observed throughout using a photoslit-lamp biomicroscope, with maximum corneal clouding occurring at days 4-6. These data support earlier proposals for major roles for these corneal enzymes in assisting the cornea in protecting the eye against UVR-induced tissue damage.

Regional distribution of mammalian corneal aldehyde dehydrogenase and alcohol dehydrogenase.

The regional distribution of mouse aldehyde dehydrogenase (ALDH) and alcohol dehydrogenase activities in mouse ocular tissues was examined using spectrophotometric and agarose-isoelectric focusing techniques. The results established that these enzymes are predominantly localized in the cornea. Biochemical and histochemical analyses of the localization of these enzymes in the corneas of common domestic mammals (pigs, sheep, and cattle) and in baboons revealed species differences, with high levels being reported in corneal epithelium (pigs and baboons) and endothelium (sheep and cattle). The presence of these enzymes in the corneal epithelium is consistent with their proposed catalytic role in the detoxification of ultraviolet (UV)-induced peroxidic aldehydes, and with the proposed role for corneal ALDH in UVB absorption.

A gastric alcohol dehydrogenase in the baboon: purification and properties of a 'high-Km' enzyme, consistent with a role in 'first pass' alcohol metabolism.

The major isozyme of alcohol dehydrogenase in baboon stomach, ADH3, has been purified to homogeneity and characterized with a range of alcohol and aldehyde substrates. Using kcat/Km values as an indication of substrate efficacy, medium-chain length aliphatic alcohols and aldehydes were identified as the preferred substrates. ADH3 showed 'high-Km' properties with respect to ethanol, and is expected to significantly contribute to 'first-pass' metabolism of alcohol. The enzyme exhibited more than two orders of magnitude higher turnover of substrate than the baboon liver 'low-Km' ADH, and may play a role in the rapid metabolism of a wide range of ingested alcohols in the diet.

Biochemical genetics of alcohol dehydrogenase isozymes in the gray short-tailed opossum (Monodelphis domestica).

Polyacrylamide gel-isoelectric focusing (PAGE-IEF) methods were used to examine the multiplicity, tissue distribution, and biochemical genetics of alcohol dehydrogenase (ADH) isozymes among gray short-tailed opossums (Monodelphis domestica). Seven ADH isozymes were resolved and distinguished on the basis of their isoelectric points, tissue distributions, and substrate and inhibitor specificities. ADH1 and ADH2 exhibited Class I properties and were observed in liver (and intestine) extracts. ADH3, ADH4, and ADH5 showed "high-Km" (possibly Class IV) properties, with ADH3 and ADH4 exhibiting high activity in cornea, ear, stomach, and esophagus extracts. ADH6 and ADH7 exhibited Class III properties, including activities as formaldehyde dehydrogenases, with each showing different tissue distribution characteristics; ADH6 was widely distributed, and ADH7 was restricted to prostate extracts. An additional form of formaldehyde dehydrogenase (FDH) was observed, which was inactive with hexenol and ethanol as substrates. Isoelectric point variants were observed for ADH3 (three forms) and for ADH4 (two forms), and the inheritance of ADH3 was studied in 15 families of M. domestica. The data were consistent with codominant inheritance of two alleles (ADH3*A and ADH3*B) at a single autosomal locus (designated ADH3) and with a model involving a dimeric ADH isozyme: ADH3 (gamma 2 isozyme, forming three dimers designated gamma 1(2), gamma 1 gamma 2, and gamma 2(2) in heterozygous individuals).

Evidence for three genes encoding class-I alcohol dehydrogenase subunits in baboon and analysis of the 5' region of the gene encoding the ADH beta subunit.

Five alcohol dehydrogenases (ADH; alcohol: NAD+ oxidoreductase; EC 1.1.1.1) have been identified in the baboon. All are homodimers of five distinct ADH subunits, with the two class-I ADH subunits being differentially expressed in the liver (the beta-subunit) and kidney. We have hybridized restriction-enzyme-digested baboon DNA to a 30-bp probe or a 337-bp DNA fragment, to reveal the presence of three genes encoding class-I ADH subunits in the baboon genome. This result was confirmed by the amplification of three different baboon ADH (bADH) nucleotide (nt) sequences, corresponding to exon 5 in the human gene encoding ADH beta (hADHB) from baboon DNA. Two of these sequences are identical to previously isolated liver and kidney cDNA nt sequences. These results are consistent with a phylogenetic analysis of the nt sequences of class-I hADH and bADH genes. Then, using primers based on the nt sequence of hADHB, we amplified a 336-bp DNA fragment, from genomic DNA, encoding the 5' region of the bADHB gene. In a 49-bp region of overlap, the nt sequence of this DNA fragment was identical to the sequence of a cDNA fragment amplified from baboon liver mRNA, whereas there were seven differences between this DNA fragment and the sequence of a cDNA amplified from baboon kidney mRNA. We used primer extension analysis to identify three adjacent transcriptional start points (tsp) for bADHB mRNA. Initiation of transcription at the most 5' bp leaves a 72-bp untranslated region. Examination of the sequence upstream from the tsp reveals a number of conserved putative regulatory sequence elements.

Aldehyde dehydrogenase (ALDH) isozymes in the gray short-tailed opossum (Monodelphis domestica): tissue and subcellular distribution and biochemical genetics of ALDH3.

Polyacrylamide gel isoelectric focusing (PAGE-IEF), cellulose acetate electrophoresis, and histochemical techniques were used to examine the tissue and subcellular distribution, genetics and biochemical properties of aldehyde dehydrogenase (ALDH) isozymes in a didelphid marsupial, the gray short-tail opossum (Monodelphis domestica). At least 14 zones of activity were resolved by PAGE-IEF and divided into five isozyme groups and three ALDH classes, based upon comparisons with properties previously reported for human, baboon, rat, and mouse ALDHs. Opossum liver ALDHs were distributed among cytosol (ALDHs 1 and 5) and large granular (mitochondrial) fractions (ALDHs 2 and 5). Similarly, kidney ALDHs were distributed between the cytosol (ALDH5) and the mitochondrial fractions (ALDHs 2, 4, and 5), whereas a major isozyme (ALDH3), found in high activity in cornea, esophagus, ear pinna, tail, and stomach extracts, was localized predominantly in the cytosol fraction. Phenotypic variants of the latter enzyme were shown to be inherited in a normal Mendelian fashion, with two alleles at a single locus (ALDH3) showing codominant expression. The data provided evidence for genetic identity of corneal, ear pinna, tail, and stomach ALDH3 and supported biochemical evidence from other mammalian species that this enzyme has a dimeric subunit structure.