Data management and analysis for gene expression arrays.

Microarray technology makes it possible to simultaneously study the expression of thousands of genes during a single experiment. We have developed an information system, ArrayDB, to manage and analyse large-scale expression data. The underlying relational database was designed to allow flexibility in the nature and structure of data input and also in the generation of standard or customized reports through a web-browser interface. ArrayDB provides varied options for data retrieval and analysis tools that should facilitate the interpretation of complex hybridization results. A sampling of ArrayDB storage, retrieval and analysis capabilities is available (www.nhgri.nih.gov/DIR/LCG/15K/HTML/ ), along with information on a set of approximately 15,000 genes used to fabricate several widely used microarrays. Information stored in ArrayDB is used to provide integrated gene expression reports by linking array target sequences with NCBI's Entrez retrieval system, UniGene and KEGG pathway views. The integration of external information resources is essential in interpreting intrinsic patterns and relationships in large-scale gene expression data.

Understanding Ras: 'it ain't over 'til it's over'.

Since 1982, Ras has been the subject of intense research scrutiny, focused on determining the role of aberrant Ras function in human cancers and defining the mechanism by which Ras mediates its actions in normal and neoplastic cells. The long-term goal has been to develop antagonists of Ras as novel approaches for cancer treatment. Although impressive strides have been made in these endeavours, and our knowledge of Ras is quite extensive, it appears that we are at the beginning, rather than at the end, of fully understanding Ras function. This review highlights new issues that have further complicated our efforts to understand Ras.

Editing of pre-mRNAs can occur before cis- and trans-splicing in Petunia mitochondria.

Plant mitochondrial mRNAs have recently been shown to undergo editing, involving cytidine-to-uridine changes relative to the DNA sequence. We have examined the temporal relationship of editing and intron removal in coxII mRNAs in Petunia mitochondria. By using differential hybridization to probes specific for edited and unedited RNA and by sequencing of individual unspliced coxII pre-mRNA cDNAs, we found that RNA editing at any editing site can precede the splicing event. Similar results were obtained from examinations of pre-mRNA cDNAs of nad1, a gene composed of multiple exons that are both cis and trans spliced. Thus, intron removal is not required before editing can occur. The existence of editing intermediates indicates that the editing process is not strictly coincident with transcription.

RefSeq and LocusLink: NCBI gene-centered resources.

Thousands of genes have been painstakingly identified and characterized a few genes at a time. Many thousands more are being predicted by large scale cDNA and genomic sequencing projects, with levels of evidence ranging from supporting mRNA sequence and comparative genomics to computing ab initio models. This, coupled with the burgeoning scientific literature, makes it critical to have a comprehensive directory for genes and reference sequences for key genomes. The NCBI provides two resources, LocusLink and RefSeq, to meet these needs. LocusLink organizes information around genes to generate a central hub for accessing gene-specific information for fruit fly, human, mouse, rat and zebrafish. RefSeq provides reference sequence standards for genomes, transcripts and proteins; human, mouse and rat mRNA RefSeqs, and their corresponding proteins, are discussed here. Together, RefSeq and LocusLink provide a non-redundant view of genes and other loci to support research on genes and gene families, variation, gene expression and genome annotation. Additional information about LocusLink and RefSeq is available at http://www.ncbi.nlm.nih.gov/LocusLink/.

Molecular and Cellular Changes During Cancer Progression Resulting From Genetic and Epigenetic Alterations.

Tumorigenesis is a complex process that involves a persistent dismantling of cellular safeguards and checkpoints. These molecular and cellular changes that accumulate over months or decades lead to a change in the fundamental identity of a cell as it transitions from normal to malignant. In this chapter, we will examine some of the molecular changes in the evolving relationship between the genome and epigenome and highlight some of the key changes that occur as normal cells progress to tumor cells. For many years tumorigenesis was almost exclusively attributed to mutations in protein-coding genes. This notion that mutations in protein-coding genes were a fundamental driver of tumorigenesis enabled the development of several novel therapeutics that targeted the mutant protein or overactive pathway responsible for driving a significant portion of the tumor growth. However, because many therapeutic challenges remained in the face of these advances, it was clear that other pieces to the puzzle had yet to be discovered. Advances in molecular and genomics techniques continued and the study of epigenetics began to expand and helped reshape the view that drivers of tumorigenesis extended beyond mutations in protein-coding genes. Studies in the field of epigenetics began to identify aberrant epigenetic marks which created altered chromatin structures and enabled protein expression in tissues that defied rules governing tissue-specificity. Not only were epigenetic alterations found to enable overexpression of proto-oncogenes, they also led to the silencing of tumor suppressor genes. With these discoveries, it became clear that tumor growth could be stimulated by much more than mutations in protein-coding genes. In fact, it became increasingly clear that much of the human genome, while transcribed, did not lead to proteins. This discovery further led to studies that began to uncover the role of noncoding RNAs in regulating chromatin structure, gene transcription, and tumor biology. In this chapter, some of the key alterations in the genome and epigenome will be explored, and some of the cancer therapies that were developed as a result of these discoveries will be discussed.

Kinetics of hypothiocyanite production during peroxidase-catalyzed oxidation of thiocyanate.

We report here a kinetic study of the generation of hypothiocyanite (OSCN-), a product of lactoperoxidase-catalyzed oxidation of thiocyanate ion. Previous studies have measured OSCN- by reactions involving the oxidation of sulfhydryl compounds. Our results show that a more suitable kinetic analysis of OSCN- can be based on absorbance changes measured at 235 nm. About 90% of the oxidation products of SCN- observed at 235 nm were reactive with sulfhydryls and could be reduced with 2-mercaptoethanol. Both thiocyanate and peroxide were rate-limiting and the formation of OSCN- was proportional to the initial concentration of H2O2 until an equimolar concentration of H2O2 and SCN- was reached. This equimolar concentration gave the maximum generation of OSCN-. High concentrations (greater than 100 micrograms/ml) of lactoperoxidase decreased OSCN- generation, but only if the SCN- was added to the enzyme prior to addition of H2O2. With lactoperoxidase concentrations exceeding 1 microgram/ml, the reaction velocity was rapid, but the decay of OSCN- was slow. Free H2O2 in the reaction mixture always resulted in rapid decay of OSCN-. Addition of varying concentrations of peroxide to solutions containing 1 microgram/ml of enzyme and [SCN-] = 5 mM gave a family of hyperbolic A235 vs. time curves. Both the initial slopes and the plateaus of these curves increased linearly with increasing initial peroxide concentrations up to [H2O2] = 0.4 mM, remained relatively constant in the range [H2O2] = 0.4 to 0.8 mM, and decreased rapidly above [H2O2] = 0.8 mM. These results are consistent with the following kinetic model: Hydrogen peroxide reacts rapidly with lactoperoxidase to produce compound I. This compound I oxidizes SCN- to OSCN- and also oxidizes OSCN- to O2SCN-. The OSCN- also reacts with SCN-. The formation of OSCN- is associated with the appearance of an absorbance peak at 225-235 nm. The oxidation of OSCN- by excess peroxide or its decomposition at high concentrations is associated with a decrease in A235 and the appearance of a peak at 245-255 nm. The extinction coefficient for OSCN- was determined to be 1.29 x 10(3) M-1 . cm-1. The second-order rate constant for the oxidation of thiocyanate by compound I was estimated to be 2 x 10(5) M-1 . s-1.

Lactoperoxidase-catalyzed inactivation of hexokinase.

The enzymatic activity of hexokinase (ATP : D-hexose 6-phosphotransferase, EC 2.7.1.1) decreased rapidly when the enzyme was exposed to the lactoperoxidase antimicrobial system (consisting of lactoperoxidase, H2O2 and SCN-). Inactivation did not begin until the reaction of one sulfhydryl group per hexokinase monomer was completed. Loss of enzyme activity accompanied the reaction of at least one additional sulfhydryl group per monomer. Covalent incorporation of 14C-labeled SCN- into hexokinase increased as the inactivation reaction progressed. The rate of the hexokinase activity loss dependent on temperature, pH and the presence of glucose and phosphate ion. When H2O2 and SCN- were applied to a Sepharose column bearing covalently attached lactoperoxidase, the column eluate inactivated hexokinase. This demonstrated that the lactoperoxidase molecule itself need not be in contact with hexokinase in order to catalyze hexokinase inactivation. The sulfhydryl-reactive oxidation product of SCN- which is generated by the column is sufficient. The results are consistent with a two-stage reaction in which the exposed, non-essential sulfhydryl groups on the hexokinase molecule react first to produce an enzymatically active but unstable form of hexokinase. This modified form of hexokinase then undergoes a spontaneous, temperature-dependent structural change, which allows reaction of previously shielded, essential sulfhydryl groups. The phenomenon described here suggests a possible mechanism for the antimicrobial effects of the lactoperoxidase system.

Human milk peroxidase is derived from milk leukocytes.

Peroxidase enzymes present in human colostrum, saliva, polymorphonuclear leukocytes, and bovine milk were compared with respect to their molecular exclusion chromatographic behavior and immunological cross-reactivity. Human milk peroxidase gave an elution profile similar to myeloperoxidase derived from blood polymorphonuclear leukocytes. Human salivary peroxidase reacted with an antibody directed against bovine lactoperoxidase, but with the same antibody preparation no reaction was detected either with human milk peroxidase or leukocyte myeloperoxidase. We conclude that the peroxidase enzyme in human milk is different from the human salivary and the bovine enzymes and is probably derived from milk leukocytes.

Products of thiocyanate peroxidation: properties and reaction mechanisms.

The lactoperoxidase-catalyzed oxidation of thiocyanate (SCN-) was studied in the pH range 3-8. The ultraviolet spectra of the oxidation products, the hypothiocyanite ion, OSCN- (at pH 8) and hypothiocyanous acid, HOSCN (at pH 3), were recorded. The absorbance maxima for OSCN- and HOSCN were observed at 220 and 240 nm, respectively. The extinction coefficients for OSCN- and HOSCN were determined to be 3870 (at 220 nM) and 95 M-1 X cm-1 (at 240 nM), respectively. Pure solutions of OSCN- (at pH 8) and HOSCN (at pH 3) were stable, but the mixtures of these two species at intermediate pH values were unstable. The decomposition could be divided into two periods, an initial period of rapid increase in oxidizing equivalents and a second period of decomposition. Decomposition during the second period followed first-order kinetics, and the pH-dependence of the apparent first-order rate constant was consistent with a decomposition mechanism which involved HOSCN. The first-order rate constant for this step was estimated to be 6 X 10(-3) s-1 at 37 degrees C.

Is thiocyanate peroxidation at equilibrium in vivo?

The peroxidase-catalyzed oxidation of SCN- by H2O2 is an important in vivo reaction because it limits the accumulation of toxic H2O2 and provides significant concentrations of the antimicrobial agents, HOSCN and OSCN-. Data presented in this report suggest that the reaction: (Formula: see text) is in a state of dynamic equilibrium in vivo. Since OSCN- can form the weak acid HOSCN (pKa = 5.3), the equilibrium constant expression (Kox) for thiocyanate peroxidation is dependent on the concentration of hydrogen ions as well as the concentrations of H2O2, SCN-, HOSCN, OSCN- and water, and on the HOSCN ionization constant, Ka: (Formula: see text). The concentration of water is assumed to be constant and unaffected by the other components and is omitted from the Kox equation. The value of Kox was estimated from in vitro data to be 3.7 X 10(3) M-1 (S.D. = 0.8 X 10(3) M-1, n = 8). Using this value for Kox and observations of salivary concentrations of SCN- and HOSCN + OSCN- from several previous reports, the equilibrium concentrations of H2O2 in whole saliva were calculated to range from 8 to 13 microM. This range is consistent with reported estimates of 10 microM as the hydrogen peroxide tolerance limit for human cells.

5-Fluoroindole resistance identifies tryptophan synthase beta subunit mutants in Arabidopsis thaliana.

A study of the biochemical genetics of the Arabidopsis thaliana tryptophan synthase beta subunit was initiated by characterization of mutants resistant to the inhibitor 5-fluoroindole. Thirteen recessive mutations were recovered that are allelic to trp2-1, a mutation in the more highly expressed of duplicate tryptophan synthase beta subunit genes (TSB1). Ten of these mutations (trp2-2 through trp2-11) cause a tryptophan requirement (auxotrophs), whereas three (trp2-100 through trp2-102) remain tryptophan prototrophs. The mutations cause a variety of changes in tryptophan synthase beta expression. For example, two mutations (trp2-5 and trp2-8) cause dramatically reduced accumulation of TSB mRNA and immunologically detectable protein, whereas trp2-10 is associated with increased mRNA and protein. A correlation exists between the quantity of mutant beta and wild-type alpha subunit levels in the trp2 mutant plants, suggesting that the synthesis of these proteins is coordinated or that the quantity or structure of the beta subunit influences the stability of the alpha protein. The level of immunologically detectable anthranilate synthase alpha subunit protein is increased in the trp2 mutants, suggesting the possibility of regulation of anthranilate synthase levels in response to tryptophan limitation.

The sirtuins promote Dishevelled-1 scaffolding of TIAM1, Rac activation and cell migration.

Rac1-GTPases serve as intermediary cellular switches, which conduct transient and constitutive signals from upstream cues, including those from Ras oncoproteins. Although the sirtuin1 (SIRT1) deacetylase is overexpressed in several human cancers and has recently been linked to cancer cell motility as a context-dependent regulator of multiple pathways, its role in Rac1 activation has not been reported. Similarly, SIRT2 has been demonstrated to be upregulated in some cancers; however, studies have also reported its role in tumor suppression. Here, we demonstrate that SIRT1 and SIRT2 positively regulate the levels of Rac1-GTP and the activity of T-cell lymphoma invasion and metastasis 1 (TIAM1), a Rac guanine nucleotide exchange factor (GEF). Transient inhibition of SIRT1 and SIRT2 resulted in increased acetylation of TIAM1, whereas chronic SIRT2 knockdown resulted in enhanced acetylation of TIAM1. SIRT1 regulates Dishevelled (DVL) protein levels in cancer cells, and DVL along with TIAM1 are known to augment Rac activation; however, SIRT1 or 2 has not been previously linked with TIAM1. We found that diminished sirtuin activity led to the disruption of the DVL1-TIAM1 interaction. We hence propose a model for Rac activation where SIRT1/2 positively modulates the DVL/TIAM1/Rac axis and promotes sustained pathway activation.

Ras and Rho regulation of the cell cycle and oncogenesis.

The important contribution of aberrant Ras activation in oncogenesis is well established. Our knowledge of the signaling pathways that are regulated by Ras is considerable. However, the number of downstream effectors of Ras continues to increase and our understanding of the role of these effector signaling pathways in mediating oncogenesis is far from complete and continues to evolve. Similarly, our understanding of the components that control mitogen-stimulated cell cycle progression is also very advanced. Where our understanding has lagged has been the delineation of the mechanism by which Ras causes a deregulation of cell cycle progression to promote the uncontrolled proliferation of the cancer cell. In this review, we summarize our current knowledge of how deregulated Ras activation alters the function of cyclin D1, p21(Cip1), and p27(Kip1). The two themes that we have emphasized are the involvement of Rho small GTPases in cell cycle regulation and the cell-type differences in how Ras signaling interfaces with the cell cycle machinery.

Comparison of the effects of linear and cyclic phosphates on the adsorption of proteins by human enamel.

Treatment of human enamel powder with cyclic trimetaphosphate or linear tripolyphosphate changes subsequent adsorption of amylase, lysozyme, and salivary protein from aqueous solutions. Treated enamel samples adsorb more lysozyme, less amylase, and more salivary protein (at concentrations exceeding 12 mug/ml) than controls treated with distilled water.

Peroxidase antimicrobial system of human saliva: hypothiocyanite levels in resting and stimulated saliva.

The antimicrobial oxidizing agent hypothiocyanite ion (OSCN-) was measured in resting (drooling) and stimulated (expectorated) whole saliva. Stimulation of the saliva flow rate resulted in a rapid decrease in OSCN- concentration, whereas the thiocyanate ion (SCN-) concentration and peroxidase activity were increased. The decrease in OSCN- levels was greater than could be accounted for by dilution of the whole saliva volume. Assuming that the antimicrobial activity of the salivary peroxidase system is proportional to OSCN- concentration, this system may be more effective in resting saliva than in stimulated saliva.

Effects of variations in pH and hypothiocyanite concentrations on S. mutans glucose metabolism.

Hypothiocyanous acid (HOSCN) and hypothiocyanite (OSCN-) were generated by the antibody-independent salivary peroxidase (SP) system. The metabolism of Streptococcus mutans NCTC 10449 was examined by uniformly labeled glucose incorporation studies. We found that the SP-system causes a pH-dependent inhibition of 14C-labeled glucose uptake, and that the effects of HOSCN/OSCN- are bacteriostatic. The results also showed that, at low pH, bacteria required more time to recover fully from HOSCN/OSCN- inhibition. When control experiments were performed in the absence of HOSCN/OSCN-, but the pH was varied, we found a positive correlation between pH and the rate of 14C-glucose incorporation. The results also showed that pH did not affect the maximum incorporation of 14C-glucose, demonstrating that S. mutans can adapt to pH changes in the environment. Based on the data obtained, we postulate that the antibody-independent SP system plays an important role in the regulation of the metabolism of oral streptococci.

A mouthrinse which optimizes in vivo generation of hypothiocyanite.

We report here the properties of a mouthrinse which enhances one of the natural defense factors in human saliva, the salivary peroxidase system. Concentrations of the antimicrobial agent, the hypothiocyanite (OSCN-) ion, can be increased in vivo to bacteriostatic levels by use of a mouthrinse which is 4 mM (0.014%) in hydrogen peroxide and 1 mM (0.0097%) in potassium thiocyanate at pH 5.5. The volume of the rinse, the H2O2 concentrations, and the pH were shown to be determinants of the concentration of OSCN- generated by the rinse.

The effects of human saliva on the hemolytic activity of complement.

Human saliva was tested for the presence of factors that affect the complement system. Parotid saliva and salivary fractions were incubated at 37 C with human serum as a source of complement. Samples removed from the mixtures within the first 15 minutes had higher levels of whole hemolytic complement activity than did appropriate controls. The final ionic strength of the saliva-serum mixtures was critical to the hemolytic activity of complement. After 60 minutes all serum-saliva mixtures had lower levels of hemolytic activity than did serum-buffer controls. With regard to whole saliva, the salivary sediment was found to be strongly complement-reactive.

Drug-biomolecule interactions: interactions of mononucleotides and polybasic amino acids.

Histones and ribosomal proteins are basic proteins that participate in gene regulation and protein synthesis, respectively. How these proteins interact with nucleic acids is not yet clear, although specificities in these interactions have been observed. Study of the interaction of mononucleotides with basic polyamino acids is one approach to understanding such interactions. The results of studies with the mononucleotides can help elucidate the normal molecular processes in biological systems and also shed light on some effects of drugs, such as puromycin and tubericidin, that are nucleotide derivatives. A review of studies on the interaction of mononucleotides and basic polyamino acids such as polylysine and polyarginine is presented. In addition, a short review of the self-associative properties of mononucleotides is given. Studies of the mononucleotide-polyamino acid interaction have involved a wide variety of techniques including equilibrium dialysis, NMR, optical rotatory dispersion, circular dichroism, and precipitate analysis.

Detection of the hypothiocyanite (OSCN-) ion in human parotid saliva and the effect of pH on OSCN- generation in the salivary peroxidase antimicrobial system.

Human whole saliva contains the hypothiocyanite ion (OSCN-) which is the principal antimicrobial product of the salivary peroxidase system. The peroxidase system requires a source of peroxide in order to produce OSCN- and in the human mouth this source has been assumed to be primarily the peroxidogenic oral bacteria. However, we report here studies which show that samples of stimulated human parotid saliva collected directly from Stenson's duct have concentrations of OSCN- which are similar to those found in human whole saliva. Thus, the peroxidogenic bacteria are not an absolute requirement for the generation of significant levels of OSCN- in the human mouth. Supplementation of human whole saliva with components [thiocyanite (SCN-), hydrogen peroxide (H2O2)] of the peroxidase system produces a 10-fold or greater increase in OSCN- concentration. However, the magnitude of this increase is critically dependent upon pH and upon the relative and absolute concentrations of SCN- and H2O2. The pH dependence of OSCN- generation is similar for human whole saliva and for the lactoperoxidase/SCN-/H2O2 system. The optimum is in the range 6.5-7.0. Samples of parotid saliva adjusted to pH 6.5 and supplemented with appropriate amounts of SCN- and H2O2 show increases in OSCN- concentrations which are similar to those observed with whole saliva. The results show that there is a significant source of H2O2 within the parotid gland, that the OSCN- generating potential of parotid saliva is similar to that of whole saliva and that the enhancement of OSCN- levels in saliva by addition of SCN- and H2O2 is critically dependent upon pH and upon the relative and absolute concentrations of H2O2 and SCN-.