Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites

Detection of positive Darwinian selection has become ever more important with the rapid growth of genomic data sets. Recent branch-site models of codon substitution account for variation of selective pressure over branches on the tree and across sites in the sequence and provide a means to detect short episodes of molecular adaptation affecting just a few sites. In likelihood ratio tests based on such models, the branches to be tested for positive selection have to be specified a priori. In the absence of a biological hypothesis to designate so-called foreground branches, one may test many branches, but a correction for multiple testing becomes necessary. In this paper, we employ computer simulation to evaluate the performance of 6 multiple test correction procedures when the branch-site models are used to test every branch on the phylogeny for positive selection. Four of the methods control the familywise error rates (FWERs), whereas the other 2 control the false discovery rate (FDR). We found that all correction procedures achieved acceptable FWER except for extremely divergent sequences and serious model violations, when the test may become unreliable. The power of the test to detect positive selection is influenced by the strength of selection and the sequence divergence, with the highest power observed at intermediate divergences. The 4 correction procedures that control the FWER had similar power. We recommend Rom's procedure for its slightly higher power, but the simple Bonferroni correction is useable as well. The 2 correction procedures that control the FDR had slightly more power and also higher FWER. We demonstrate the multiple test procedures by analyzing gene sequences from the extracellular domain of the cluster of differentiation 2 (CD2) gene from 10 mammalian species. Both our simulation and real data analysis suggest that the multiple test procedures are useful when multiple branches have to be tested on the same data set.     

Bacterial mutagenicity of two cyclopentafused isomers of benzpyrene

Two novel cyclopentafused polycyclic aromatic hydrocarbons, naphtho(1,2,3-mno)acephenanthrylene (cyclopenta benzo[e]pyrene) and naphtho(2,1,8-hij)acephenanthrylene (cyclopenta(ij)benzo[a]pyrene) were evaluated for mutagenic activity in the Ames Salmonella typhimurium plate incorporation assay. Both compounds required S9 metabolic activation, and showed optimal activity at low S9 concentrations (below 0.6 mg/plate). Both compounds induced frameshift and base-pair substitution mutations, being active in strains TA98, TA100, TA1537, TA1538 and TA104, but not in strain TA1535. Cyclopenta(ij)benzo[a]pyrene was more active than cyclopentabenzo[e]pyrene, and both were more potent than their parent ring systems, benzo[a]pyrene and benzo[e]pyrene, respectively. Cyclopenta(ij)benzo[a]pyrene was more active in strain TA104 than in TA100 or TA98 (250-470, 340 and 80-100 rev/nmole) as was benzo[a]pyrene (120, 70 and 40 rev/nmole respectively); cyclopentabenzo[e]pyrene was more active in TA100 than TA104 or TA98 (70 versus 50 and 40 rev/nmole), and benzo[e]pyrene showed a similar pattern (4, 3.5 and 0.6 rev/nmole). The relative potencies of the four compounds are in accord with predictions based on perturbational molecular orbital calculations. The peak of activity at low S9 concentrations is consistent with epoxidation at the cyclopentafused ring being the major route of metabolic activation for both these cyclopentafused compounds.     

Incorporation of mammalian metabolism into mutagenicity testing

In the 1950's and 1960's it became obvious that many chemicals in daily use were mutagenic or carcinogenic, but there seemed to be little relation between the two activities. As scientists were debating the cause of this discrepancy, it was hypothesized that mammalian metabolism could form highly reactive intermediates from rather innocuous chemicals and that these intermediates could react with DNA and were mutagenic. This commentary presents the historical development of metabolic activation in mutagenicity tests, beginning with Udenfriend's hydroxylation system, which mimics aspects of mammalian metabolism in a purely chemical mixture, and extending through procedures that moved closer and closer to incorporating actual mammalian metabolism into the test systems. The stages include microsomal activation systems, host-mediated assays, incorporation of human P450 genes into the target cells or organisms, and detecting mutations in single cells in vivo. A recent development in this progression is the insertion of recoverable vectors containing mutational targets into the mammalian genome. Since the target genes of transgenic assays are in the genome, they are not only exposed to active metabolites, but they also undergo the same repair processes as endogenous genes of the mammalian genome.     

Bacterial mutagenicity of the tranquilizing constituents of Valerianaceae roots

The valepotriates valtrate/isovaltrate and dihydrovaltrate are considered to be the main tranquilizing constituents of drugs derived from the roots of several Valerianaceae. The decomposition products of valtrate and isovaltrate include the metabolites baldrinal and homobaldrinal, respectively, whereas the decomposition products of dihydrovaltrate do not include baldrinal-like metabolites. Purified valtrate/isovaltrate, dihydrovaltrate, baldrinal and homobaldrinal were investigated for their genotoxic activity in the Salmonella/microsome test and the SOS-chromotest. The valepotriates developed mutagenic activity in these test systems only in the presence of S9 mix, whereas both baldrinals showed mutagenic effects in both tests with and without metabolic activation.     

Effect of bacterial growth-inhibiting ingredients on the Ames mutagenicity of medicinal herbs

A solvent fractionation method was introduced to screen for mutagenicity in 10 medicinal herbs being consumed in Korea. The Ames mutagenicity test result of Scutellariae and Rhei was significantly increased by eliminating growth-inhibiting substances through solvent fractionation of the crude extract. It is suggested that a physicochemical pretreatment should reduce the false-negative results which are caused by the presence of growth-inhibiting substances in complex mixtures.     

Bacterial mutagenicity and carcinogenic potential of some azapyrene derivatives

The mutagenic and carcinogenic activities of 5 azapyrenes, which are suspected of being environmental pollutants, were assessed using the Salmonella assay and the anchorage-independent survival assay. The compounds tested were: 1-azapyrene, 2-azapyrene, 4-azapyrene, 1-aza-2-hydroxypyrene, and 2-aza-1-hydroxypyrene. The compounds were mutagenic and some were also carcinogenic.     

Accurate cancer classification using expressions of very few genes

We aim at finding the smallest set of genes that can ensure highly accurate classification of cancers from microarray data by using supervised machine learning algorithms. The significance of finding the minimum gene subsets is three-fold: 1) it greatly reduces the computational burden and "noise" arising from irrelevant genes. In the examples studied in this paper, finding the minimum gene subsets even allows for extraction of simple diagnostic rules which lead to accurate diagnosis without the need for any classifiers, 2) it simplifies gene expression tests to include only a very small number of genes rather than thousands of genes, which can bring down the cost for cancer testing significantly, 3) it calls for further investigation into the possible biological relationship between these small numbers of genes and cancer development and treatment. Our simple yet very effective method involves two steps. In the first step, we choose some important genes using a feature importance ranking scheme. In the second step, we test the classification capability of all simple combinations of those important genes by using a good classifier. For three "small" and "simple" data sets with two, three, and four cancer (sub)types, our approach obtained very high accuracy with only two or three genes. For a "large" and "complex" data set with 14 cancer types, we divided the whole problem into a group of binary classification problems and applied the 2-step approach to each of these binary classification problems. Through this "divide-and-conquer" approach, we obtained accuracy comparable to previously reported results but with only 28 genes rather than 16,063 genes. In general, our method can significantly reduce the number of genes required for highly reliable diagnosis     

Legislative and technical aspects of mutagenicity testing.

A brief account is given of the history of the legislative acts that give responsibility to the U.S. Food and Drug Administration (FDA) for ensuring the safety of foods, drugs, and cosmetics. Within the present legislative framework the FDA has the authority to impose regulations which are designed to ensure the safety of all foods, drugs, and cosmetics. The existing legislative authority is adequate for this purpose; however, the difficulty lies instead with technology and the inadequacy of scientific perspective in the emerging area of mutagenicity testing. Earlier efforts in development of mutagenicity screening systems culminated only a few years ago in the proposal to use the host-mediated assay, somatic cell cytogenetics, and dominant lethal tests collectively. Subsequent research efforts indicated that there were serious practical and scientific deficiencies in using this approach. More recently a new proposal, the tier system, has been suggested as an alternative measure. The proposed tier system at FDA consists of three testing levels of increasing complexity. The first tier is an initial screening effort using techniques having maximum sensitivity that are also useful for large-scale, rapid testing. The second tier is designed to identify and confirm that the presumptive mutagens detected in the first tier are truly mutagenic for higher organisms, most especially, for mammals. The third tier would be devoted to explicit genetic tests in mammals designed to ascertain the imposed risk to man by the introduction of a mutagen in our environment. The FDA is currently involved in a number of research activities in the area of mutagenicity safety screening which will explore the adequacies and possible deficiencies of the tier system approach. These efforts are described for our in-house activities, our contract activities, and our cooperative and collaborative activities with other government agencies and institutions.     

Bacterial,SCFA and gas profiles of a range of food ingredients following in vitro fermentation by human colonic microbiota

It is now apparent that there is a strong link between health and nutrition and this can be seen clearly when we talk of obesity. The food industry is trying to capitalise on this by adapting high sugar/fat foods to become healthier alternatives. In confectionery food ingredients can be used for a range of purposes including sucrose replacement. Many of these ingredients may also evade digestion in the upper gut and be fermented by the gut microbiota upon entering the colon. This study was designed to screen a range of ingredients and their activities on the gut microbiota. In this study we screened a range of these ingredients in triplicate batch culture fermentations with known prebiotics as controls. Changes in bacteriology were monitored using FISH. SCFA were measured by GC and gas production was assessed during anaerobic batch fermentations. Bacterial enumeration showed significant increases (P ≤ 0.05) in bifidobacteria and lactobacilli with polydextrose and most polyols with no significant increases in Clostridium histolyticum/perfringens. SCFA and gas formation indicated that the substrates added to the fermenters were being utilised by the gut microbiota. It therefore appears these ingredients exert some prebiotic activity in vitro. Further studies, particularly in human volunteers, are necessary.     

Evaluation of azo food dyes for mutagenicity and inhibition of mutagenicity by methods using Salmonella typhimurium

The mutagenicity of 4 azo dyes (FD&C Yellow No. 5, FD&C Yellow No. 6, FD&C Red No. 40 and amaranth) that are widely used to color food has been evaluated. 4 different methods were used: (1) the standard Ames plate-incorporation assay performed directly on the dyes in the absence of S9 and in the presence of rat- or hamster-liver S9; (2) application of the standard plate assay to ether extracts of aqueous solutions of the dyes; (3) a variant of the standard assay, using hamster liver S9, preincubation, flavin mononucleotide (FMN) and other modifications designed to facilitate azo reduction; and (4) reduction of the dyes with sodium dithionite, followed by ether extraction and the standard plate assay. Assays that include chemical reduction (methods 3 and 4) were included because azo compounds ingested orally are reduced in the intestine with the release of free aromatic amines. No mutagenic activity was seen for any of the azo dyes tested by using the standard Ames plate assay (method 1). Ether extracts of some samples of FD&C Yellow No. 6, FD&C Red No. 40 and amaranth were active (method 2), but only at high doses, generally 250 mg-equivalents or more per plate. These results indicate the presence of low levels of ether-extractable mutagenic impurities. The FMN preincubation assay (method 3) gave negative results for all dye samples tested. Most batches of FD&C Red No. 40 tested had mutagenic activity that was detectable when the ether extract of less than 1 mg of dithionite-reduced dye was plated in the presence of S9 (method 4). This finding implies that an impurity in these samples of FD&C Red No. 40 can be reduced to yield an ether-extractable mutagen. Dithionite-reduced samples of FD&C Yellow No. 6 and amaranth showed ether-extractable mutagenic activity only at much higher doses than those at which activity was seen with most dithionite-reduced samples of FD&C Red No. 40 (method 4). FD&C Yellow No. 5 showed no mutagenic activity with this method. Mutagenic activity was not detected when FD&C Red No. 40 was tested by using the azo reduction preincubation assay with FMN (method 3).(ABSTRACT TRUNCATED AT 400 WORDS)     

Biostatistical assessment of mutagenicity studies by including the positive control

Statistical analysis plays a fundamental part in the evaluation of mutagenicity experiments. However, a statistically significant or non-significant test result without incorporating the biological relevance cannot be a valid scientific criterion for concluding a positive or negative effect of the underlying compound (Hauschke et al., 1997). The classification of an experiment as being negative or positive should be based also on the magnitude of the responses in the positive control. We address the problem of determining the maximum safe dose by incorporating a biologically meaningful threshold value, which is expressed as a fraction of the difference between positive and vehicle control.     

Bacterial mutagenicity of some tobacco aromatic nitrogen bases and their mixtures

The first aim was to compare the genotoxicities of two tobacco-specific nitrosamines (TSNA), 4-(methylnitrosamino)-(3-pyridyl)-1-butanone (NNK) and N'-nitrosonornicotine (NNN) in two types of tests, the Salmonella reverse mutation assay (250-2000 microg per plate) and the Mutatox test (up to 1000 microg/ml) using dark mutant M-169 of Vibrio fischeri. The second aim was to assess the effects of single other tobacco chemicals and metabolites (nicotine (NIC), cotinine (COT), trans-3-hydroxycotinine (3HC), cotinine-N-oxide (CNO) and nicotine-N-oxide (NNO)) on the mutagenic responses at relative concentrations observed physiologically. The Salmonella strains were TA100, TA7004, TA7005, and TA7006, all showing missense backmutations that are characteristic of the TSNA. NNN was a direct mutagen to strains TA100, TA7004, and in the Mutatox test, and was not mutagenic in the presence of rat or hamster S9. NNK was mutagenic only in strain TA7004 with rat and hamster S9, but not in TA100, but was directly mutagenic in the Mutatox test. While all the other tobacco chemicals were not mutagenic alone to strains TA100 and TA7004 in the presence and absence of rat or hamster S9, the Mutatox test produced direct mutagenicity for COT, 3HC, and NNO, but not CNO. The latter was mutagenic in the Mutatox test with rat or hamster S9, but only rat S9 was effective for COT, NNO and 3HC. Inhibitory potentiations of NNN by NIC and COT were observed on strain TA7004, and by NIC on strain TA100. There were no interactions on NNK in the presence of S9 for strain TA7004 or TA100. In contrast, a complex inhibition and enhancement behavior occurred in the Mutatox test for each interaction, but no effects were observed for CNO on NNK without S9, and few for NIC on NNK with hamster S9. Compounds which showed no activity alone modulated the genotoxicity of two potent TSNAs in both types of tests.     

Distribution of thermophilic aerobic sporeforming bacteria in food ingredients

Samples of sugar, starch, spices, and miscellaneous products were tested for thermophilic sporeformers of Bacillus to determine the dominant species present. Surface colonies selected at random were identified. Six species of Bacillus were isolated: B. stearothermophilus, B. coagulans, B. licheniformis, B. subtilis, B. circulans, and B. pumilus. Samples of starch and pepper were tested for thermophilic sporeformers of Bacillus to determine the distribution of rough and smooth variants. Colonies were classified as rough or smooth variants by colonial characteristics. The distribution of variant forms in these two products was significantly different. Starch samples showed predominantly rough variants; pepper samples showed predominantly smooth variants.     

Microbial production of antioxidant food ingredients via metabolic engineering

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