Meditation and vacation effects have an impact on disease-associated molecular phenotypes.

Meditation is becoming increasingly practiced, especially for stress-related medical conditions. Meditation may improve cellular health; however, studies have not separated out effects of meditation from vacation-like effects in a residential randomized controlled trial. We recruited healthy women non-meditators to live at a resort for 6 days and randomized to either meditation retreat or relaxing on-site, with both groups compared with 'regular meditators' already enrolled in the retreat. Blood drawn at baseline and post intervention was assessed for transcriptome-wide expression patterns and aging-related biomarkers. Highly significant gene expression changes were detected across all groups (the 'vacation effect') that could accurately predict (96% accuracy) between baseline and post-intervention states and were characterized by improved regulation of stress response, immune function and amyloid beta (Aß) metabolism. Although a smaller set of genes was affected, regular meditators showed post-intervention differences in a gene network characterized by lower regulation of protein synthesis and viral genome activity. Changes in well-being were assessed post intervention relative to baseline, as well as 1 and 10 months later. All groups showed equivalently large immediate post-intervention improvements in well-being, but novice meditators showed greater maintenance of lower distress over time compared with those in the vacation arm. Regular meditators showed a trend toward increased telomerase activity compared with randomized women, who showed increased plasma Aß42/Aß40 ratios and tumor necrosis factor alpha (TNF-α) levels. This highly controlled residential study showed large salutary changes in gene expression networks due to the vacation effect, common to all groups. For those already trained in the practice of meditation, a retreat appears to provide additional benefits to cellular health beyond the vacation effect.

Extracting insights from the shape of complex data using topology.

This paper applies topological methods to study complex high dimensional data sets by extracting shapes (patterns) and obtaining insights about them. Our method combines the best features of existing standard methodologies such as principal component and cluster analyses to provide a geometric representation of complex data sets. Through this hybrid method, we often find subgroups in data sets that traditional methodologies fail to find. Our method also permits the analysis of individual data sets as well as the analysis of relationships between related data sets. We illustrate the use of our method by applying it to three very different kinds of data, namely gene expression from breast tumors, voting data from the United States House of Representatives and player performance data from the NBA, in each case finding stratifications of the data which are more refined than those produced by standard methods.

An integrative genomics approach to the reconstruction of gene networks in segregating populations.

The reconstruction of genetic networks in mammalian systems is one of the primary goals in biological research, especially as such reconstructions relate to elucidating not only common, polygenic human diseases, but living systems more generally. Here we propose a novel gene network reconstruction algorithm, derived from classic Bayesian network methods, that utilizes naturally occurring genetic variations as a source of perturbations to elucidate the network. This algorithm incorporates relative transcript abundance and genotypic data from segregating populations by employing a generalized scoring function of maximum likelihood commonly used in Bayesian network reconstruction problems. The utility of this novel algorithm is demonstrated via application to liver gene expression data from a segregating mouse population. We demonstrate that the network derived from these data using our novel network reconstruction algorithm is able to capture causal associations between genes that result in increased predictive power, compared to more classically reconstructed networks derived from the same data.

Molecular requirements of the human nucleoside transporters hCNT1, hCNT2, and hENT1.

Concentrative nucleoside transporters (CNTs) and equilibrative nucleoside transporters (ENTs) are important in physiological and pharmacological activity and disposition of nucleosides and nucleoside drugs. A better understanding of the structural requirements of inhibitors for these transporters will aid in designing therapeutic agents. To define the relative and unified structural requirements of nucleoside analogs for interaction with hCNT1, hCNT2, and hENT1, we applied an array of structure-activity techniques. Unique pharmacophore models for each respective nucleoside transporter were generated. These models reveal that hCNT2 affinity is dominated by hydrogen bonding features, whereas hCNT1 and hENT1 displayed mainly electrostatic and steric features. Hydrogen bond formation over 3'-OH is essential for all nucleoside transporters. Inhibition of nucleoside transporters by a series of uridine and adenosine analogs and a variety of drugs was analyzed by comparative molecular field analysis. Cross-validated r2 (q2) values were 0.65, 0.52, and 0.74 for hCNT1, hCNT2, and hENT1, respectively. The predictive quality of the models was further validated by successful prediction of the inhibition of a set of test compounds. Addition of a hydroxyl group around the 2-position of purine (or 3-position of pyrimidine) may increase inhibition to hCNT2 transporter; addition of hydroxyl group around the 2,7-position of purine (or the 3,5-position of pyrimidine) would increase the inhibition to hENT1 transporter. Utilization of these models should assist the design of high-affinity nucleoside transporter inhibitors and substrates for both anticancer and antiviral therapy.

Clustering of hepatotoxins based on mechanism of toxicity using gene expression profiles.

Microarray technology, which allows one to quantitate the expression of thousands of genes simultaneously, has begun to have a major impact on many different areas of drug discovery and development. The question remains of whether microarray analysis and gene expression signature profiles can be applied to the field of toxicology. To date, there are very few published studies showing the use of microarrays in toxicology and important questions remain regarding the predictability and accuracy of applying gene expression profiles to toxicology. To begin to address these questions, we have treated rats with 15 different known hepatotoxins, including allyl alcohol, amiodarone, Aroclor 1254, arsenic, carbamazepine, carbon tetrachloride, diethylnitrosamine, dimethylformamide, diquat, etoposide, indomethacin, methapyrilene, methotrexate, monocrotaline, and 3-methylcholanthrene. These agents cause a variety of hepatocellular injuries including necrosis, DNA damage, cirrhosis, hypertrophy, and hepatic carcinoma. Gene expression analysis was done on RNA from the livers of treated rats and was compared against vehicle-treated controls. The gene expression results were clustered and compared to the histopathology findings and clinical chemistry values. Our results show strong correlation between the histopathology, clinical chemistry, and gene expression profiles induced by the agents. In addition, genes were identified whose regulation correlated strongly with effects on clinical chemistry parameters. Overall, the results suggest that microarray assays may prove to be a highly sensitive technique for safety screening of drug candidates and for the classification of environmental toxins.

Experimental annotation of the human genome using microarray technology.

The most important product of the sequencing of a genome is a complete, accurate catalogue of genes and their products, primarily messenger RNA transcripts and their cognate proteins. Such a catalogue cannot be constructed by computational annotation alone; it requires experimental validation on a genome scale. Using 'exon' and 'tiling' arrays fabricated by ink-jet oligonucleotide synthesis, we devised an experimental approach to validate and refine computational gene predictions and define full-length transcripts on the basis of co-regulated expression of their exons. These methods can provide more accurate gene numbers and allow the detection of mRNA splice variants and identification of the tissue- and disease-specific conditions under which genes are expressed. We apply our technique to chromosome 22q under 69 experimental condition pairs, and to the entire human genome under two experimental conditions. We discuss implications for more comprehensive, consistent and reliable genome annotation, more efficient, full-length complementary DNA cloning strategies and application to complex diseases.

Functional discovery via a compendium of expression profiles.

Ascertaining the impact of uncharacterized perturbations on the cell is a fundamental problem in biology. Here, we describe how a single assay can be used to monitor hundreds of different cellular functions simultaneously. We constructed a reference database or "compendium" of expression profiles corresponding to 300 diverse mutations and chemical treatments in S. cerevisiae, and we show that the cellular pathways affected can be determined by pattern matching, even among very subtle profiles. The utility of this approach is validated by examining profiles caused by deletions of uncharacterized genes: we identify and experimentally confirm that eight uncharacterized open reading frames encode proteins required for sterol metabolism, cell wall function, mitochondrial respiration, or protein synthesis. We also show that the compendium can be used to characterize pharmacological perturbations by identifying a novel target of the commonly used drug dyclonine.

Human intestinal es nucleoside transporter: molecular characterization and nucleoside inhibitory profiles.

PURPOSE: To clone and sequence the equilibrative nitrobenzylthioinosine (NBMPR)-sensitive nucleoside transporter (es) from the human small intestine and to examine the capacities of nucleosides and nucleoside analogs to inhibit the uptake of uridine by this transporter. METHODS: Using PCR, es was cloned from a cDNA library of the human small intestine. The uptake of 3H-uridine (10 microM) by the recombinant es, expressed in Xenopus oocytes, was measured in the presence (2 mM) and absence of nucleosides and nucleoside analogs. RESULTS: The amino acid sequence of this es transporter was identical to that of the human placental es transporter. Uptake of 3H-uridine by this es transporter was inhibitable by 1 microM NBMPR. Removal of the oxygen from the 3' position or from both the 2' and 3' positions, but not from 2' or 5' position, resulted in a partial or total loss of the capacity of the nucleosides to inhibit 3H-uridine uptake. No modifications of the adenosine base or of the uridine base (except for 3 and 6 positions on uracil) affected nucleoside inhibitory capacity. CONCLUSION: The es transporters of the human intestine and placenta are identical in their amino acid sequences. Moreover, the inhibitory profiles of various nucleoside analogs in inhibiting the uptake of uridine by the intestinal es transporter are similar to those obtained with the as-yet-uncloned human erythrocyte es transporter. Collectively, these findings suggest that the es transporter does not appear to be functionally variant in the human placenta, small intestine or erythrocytes.

Molecular, functional and evolutionary characterization of the gene encoding HMG-CoA reductase in the fission yeast, Schizosaccharomyces pombe.

The synthesis of mevalonate, a molecule required for both sterol and isoprene biosynthesis in eukaryotes, is catalysed by 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase. Using a gene dosage approach, we have isolated the gene encoding HMG-CoA reductase hmgl+, from the fission yeast Schizosaccharomyces pombe (Accession Number L76979). Specifically, hmgl+ was isolated on the basis of its ability to confer resistance to lovastatin, a competitive inhibitor of HMG-CoA reductase. Gene disruption analysis showed that hmgl+ was an essential gene. This result provided evidence that, unlike Saccharomyces cerevisiae, S. pombe contained only a single functional HMG-CoA reductase gene. The presence of a single HMG-CoA reductase gene was confirmed by genomic hybridization analysis. As observed for the S. cerevisiae HMGlp, the hmgl+ protein induced membrane proliferations known as karmellae. A previously undescribed 'feed-forward' regulation was observed in which elevated levels of HMG-CoA synthase, the enzyme catalysing the synthesis of the HMG-CoA reductase substrate, induced elevated levels of hmgl+ protein in the cell and conferred partial resistance to lovastatin. The amino acid sequences of yeast and human HMG-CoA reductase were highly divergent in the membrane domains, but were extensively conserved in the catalytic domains. We tested whether the gene duplication that produced the two functional genes in S. cerevisiae occurred before or after S. pombe and S. cerevisiae diverged by comparing the log likelihoods of trees specified by these hypotheses. We found that the tree specifying post-divergence duplication had significantly higher likelihood. Moreover, phylogenetic analyses of available HMG-CoA reductase sequences also suggested that the lineages of S. pombe and S. cerevisiae diverged approximately 420 million years ago but that the duplication event that produced two HMG-CoA reductase genes in the budding yeast occurred only approximately 56 million years ago. To date, S. pombe is the only unicellular eukaryote that has been found to contain a single HMG-CoA reductase gene. Consequently, S. pombe may provide important opportunities to study aspects of the regulation of sterol biosynthesis that have been difficult to address in other organisms and serve as a test organism to identify novel therapies for modulating cholesterol synthesis.

Degradation of HMG-CoA reductase-induced membranes in the fission yeast, Schizosaccharomyces pombe.

Elevated levels of certain membrane proteins, including the sterol biosynthetic enzyme HMG-CoA reductase, induce proliferation of the endoplasmic reticulum. When the amounts of these proteins return to basal levels, the proliferated membranes are degraded, but the molecular details of this degradation remain unknown. We have examined the degradation of HMG-CoA reductase-induced membranes in the fission yeast, Schizosaccharomyces pombe. In this yeast, increased levels of the Saccharomyces cerevisiae HMG-CoA reductase isozyme encoded by HMG1 induced several types of membranes, including karmellae, which formed a cap of stacked membranes that partially surrounded the nucleus. When expression of HMG1 was repressed, the karmellae detached from the nucleus and formed concentric, multilayered membrane whorls that were then degraded. During the degradation process, CDCFDA-stained compartments distinct from preexisting vacuoles formed within the interior of the whorls. In addition to these compartments, particles that contained neutral lipids also formed within the whorl. As the thickness of the whorl decreased, the lipid particle became larger. When degradation was complete, only the lipid particle remained. Cycloheximide treatment did not prevent the formation of whorls. Thus, new protein synthesis was not needed for the initial stages of karmellae degradation. On the contrary, cycloheximide promoted the detachment of karmellae to form whorls, suggesting that a short lived protein may be involved in maintaining karmellae integrity. Taken together, these results demonstrate that karmellae membranes differentiated into self-degradative organelles. This process may be a common pathway by which ER membranes are turned over in cells.

DiOC6 staining reveals organelle structure and dynamics in living yeast cells.

When present at low concentrations, the fluorescent lipophilic dye, DiOC6, stains mitochondria in living yeast cells [Pringle et al.: Methods in Cell Biol. 31:357-435, 1989; Weisman et al.: Proc. Natl. Acad. Sci. U.S.A. 87:1076-1080, 1990]. However, we found that the nuclear envelope and endoplasmic reticulum were specifically stained if the dye concentration was increased or if certain respiratory-deficient yeast strains were examined. The quality of nuclear envelope staining with DiOC6 was sufficiently sensitive to reveal alterations in the nuclear envelope known as karmellae. These membranes were previously apparent only by electron microscopy. At the high dye concentrations required to stain the nuclear envelope, wild-type cells could no longer grow on non-fermentable carbon sources. In spite of this effect on mitochondrial function, the presence of high dye concentration did not adversely affect cell viability or general growth characteristics when strains were grown under standard conditions on glucose. Consequently, time-lapse confocal microscopy was used to examine organelle dynamics in living yeast cells stained with DiOC6. These in vivo observations correlated very well with previous electron microscopic studies, including analyses of mitochondria, karmellae, and mitosis. For example, cycles of mitochondrial fusion and division, as well as the changes in nuclear shape and position that occur during mitosis, were readily imaged in time-lapse studies of living DiOC6-stained cells. This technique also revealed new aspects of nuclear disposition and interactions with other organelles. For example, the nucleus and vacuole appeared to form a structurally coupled unit that could undergo coordinated movements. Furthermore, unlike the general view that nuclear movements occur only in association with division, the nucleus/vacuole underwent dramatic migrations around the cell periphery as cells exited from stationary phase. In addition to the large migrations or rotations of the nucleus/vacuole, DiOC6 staining also revealed more subtle dynamics, including the forces of the spindle on the nuclear envelope during mitosis. This technique should have broad application in analyses of yeast cell structure and function.

Primary role of adipokinetic hormone in the formation of low density lipophorin in locusts.

It was demonstrated that the primary action of adipokinetic hormone (AKH) is to stimulate calcium ion uptake into the fat body cell, subsequently causing the formation of diacylglycerol from triacylglycerol. Furthermore, it was also shown that AKH is not directly responsible for increased diacylglycerol uptake by lipophorin from the fat body. The diacylglycerol level of the fat body was found to increase by an average of 2.4-fold after 90 min of incubation in the presence of AKH. Calcium ion was also found to be essential in the action of AKH on the fat body. Supporting this is the observation that calcium ionophore mimics the AKH action in vivo and in vitro; injection of calcium ionophore into adult locusts as well as incubation of hemolymph with fat body and ionophore caused the transformation of high density lipophorin to low density lipophorin. When the fat body, preincubated with or without AKH, was reincubated with hemolymph, diacylglycerol uptake by lipophorin occurred for both incubations. In some sets of experiments, low density lipophorin particles were formed even in the hemolymph that was incubated with fat body preincubated without AKH, indicating that AKH is not directly responsible for its formation. Calcium ion was found not to be necessary for the diacylglycerol uptake process to occur.

Trehalose, the insect blood sugar, inhibits loading of diacylglycerol by lipophorin from the fat body in locusts.

Trehalose, the insect blood sugar, was found to inhibit diacylglycerol uptake by lipophorin from the fat body in vitro. Trehalose inhibited diacylglycerol uptake by about 40%-50% at various physiological concentrations. This suggests that trehalose may play a dual role in the hemolymph, i.e. serving as the insect's fuel and as a regulator in lipid transport.

Induction of cytochrome P-448 activity as exemplified by the O-deethylation of ethoxyresorufin. Effects of dose, sex, tissue and animal species.

The effects of tissue, sex, animal species and dose on the induction of cytochrome P-448 activity by various inducing agents were investigated using O-ethoxyresorufin as a model substrate. The liver was by far more effective in catalysing the O-deethylation of ethoxyresorufin (EROD) than the lung and kidney. The extent of induction was also highest in the liver, with the exception of benzo(a)pyrene and 3-methylcholanthrene where inducibility was more pronounced in the kidney. The benzo(a)pyrene-induced hepatic EROD activity in the rat decayed to reach control levels four days after a single administration. Rat hepatic EROD activity was induced in both sexes but tended to be higher in the male. Marked species differences in the inducibility of hepatic EROD activity by various chemicals was observed, the rat being always more responsive when compared to the hamster or mouse. The induction of rat hepatic EROD activity by benzo(a)pyrene, 2-acetylaminofluorene and safrole was dose-dependent, maximum induction being achieved with single doses of 5, 2 and 5 mg/kg, respectively.

Alkoxyresorufin O-dealkylases: association with the murine Ah locus.

The hepatic microsomal dealkylation of a series of alkoxyresorufins and the oxidation of phenoxazone to resorufin were investigated in C57BL/6 and DBA/2 mice of both sexes. In both strains of mice and in both sexes the dealkylation rate decreased with increasing length of the alkyl chain. With all alkoxyresorufins the dealkylation rates were higher in the C57BL mice than the DBA mice, whereas the rate of phenoxazone hydroxylation was higher in the latter. In the C57BL mice, and to a lesser extent in the DBA mice, females were more efficient in dealkylating the resorufin ethers. Treatment with 3-methylcholanthrene (3MC) enhanced the rates of dealkylation of all alkoxyresorufins in the C57BL mice but not in the DBA mice, the extent of stimulation being highest for the propoxy- and butoxyresorufins and least for pentoxy-, heptoxy- and benzyloxyresorufins. The same treatment had no effect on the oxidation of phenoxazone in either strain of mice. It is concluded that the dealkylation of alkoxyresorufins, not the oxidation of phenoxazone, is associated with the murine Ah locus.

Foetal and neonatal development of cytochrome P-450 and cytochrome P-448 catalysed mixed function oxidases in the rat: induction by 3-methylcholanthrene.

Benzphetamine N-demethylase (cytochrome P-450) and ethoxyresorufin O-deethylase activities (cytochrome P-448) were determined in the growing neonate and foetus of control and 3-methylcholanthrene-pretreated rats. Ethoxyresorufin O-deethylase activity was highest in the 1-2-week-old animals and then decreased with age. The inducibility of this activity by 3-methylcholanthrene was low in the young animals, but increased with age. In contrast, benzphetamine N-demethylase activity in the control animals was low at birth and increased with age, and was not induced by 3-methylcholanthrene. In the foetal liver, ethoxyresorufin O-deethylase was the only activity present at higher levels than in the maternal liver. Transplacental administration of 3-methylcholanthrene failed to induce the foetal activities while the maternal liver showed the expected response. These observations demonstrate that cytochrome P-448 may be a predominant hepatic form in the foetus and neonate but cytochrome P-450 becomes a major form as the animal grows. The implications of these findings in chemical toxicity are discussed.

Determination of cytochrome P-448 activity in biological tissues.

Three enzymes used for the determination of cytochrome P-448 activity, namely aryl hydrocarbon hydroxylase, biphenyl 2-hydroxylase and ethoxyresorufin O-de-ethylase, were evaluated with respect to their specificity, sensitivity and inducibility. Purified cytochrome P-448 (LM4), but not cytochrome P-450 (LM2), catalysed the O-de-ethylation of ethoxyresorufin in a reaction that was markedly inhibited by 9-hydroxyellipticine. After the administration of 3-methylcholanthrene to rats all three activities were induced, the extent of induction being highest for ethoxyresorufin O-de-ethylase. Administration of very small doses of benzo[a]pyrene (50 micrograms/kg) to rats to induce cytochrome P-448 specifically increased only the O-de-ethylation of ethoxyresorufin. 3-Hydroxybenzo[a]pyrene, the major metabolite determined by the aryl hydrocarbon hydroxylase assay, undergoes further NADPH-dependent oxygenation leading to loss of fluorescence. On the basis of these observations and those by other workers, we conclude that ethoxyresorufin O-de-ethylase provides the most specific, sensitive and reproducible means of determining cytochrome P-448 activity.

Cytochrome P-448 and the activation of toxic chemicals and carcinogens.

The metabolic activation of carcinogens and some toxic chemicals appears to involve oxygenation in conformationally hindered positions in the chemical molecules. Oxygenation of xenobiotics in hindered positions is effected by cytochrome P-448 (LM4) but not by cytochrome P-450 (LM2). Substrate-interaction spectra show that cytochrome P-448 has an active site with a conformation different from that of cytochrome P-450. Induction of cytochrome P-448, as specifically measured by ethoxyresorufin O-deethylase activity, occurs in rat liver, kidney and lung after administration of the carcinogens, 3-methylcholanthrene, Aroclor 1254, 2-anthramine, safrole, 7,12-dimethylbenz[a]anthracene, MNNG and 2-acetamidofluorene. The doubtful carcinogens, saccharin, DDT and aldrin, resulted in no significant induction. The drugs paracetamol, antipyrine, imipramine and rifampicin resulted in diminished enzyme activity, indicating the absence of any induction of cytochrome P-448. In studies with the matched pairs of carcinogens and non-carcinogens, benzo[a]pyrene and benzo[e]pyrene, and 1,2,5,6-dibenzanthracene and anthracene, only the carcinogenic analogue resulted in induction of cytochrome P-448. With alpha- and beta-naphthylamine, both resulted in marked induction of cytochrome P-448 in liver, kidney and lung, indicating that both isomers might be carcinogenic.