The life history of 21 breast cancers

Cancer evolves dynamically as clonal expansions supersede one another driven by shifting selective pressures, mutational processes, and disrupted cancer genes. These processes mark the genome, such that a cancer's life history is encrypted in the somatic mutations present. We developed algorithms to decipher this narrative and applied them to 21 breast cancers. Mutational processes evolve across a cancer's lifespan, with many emerging late but contributing extensive genetic variation. Subclonal diversification is prominent, and most mutations are found in just a fraction of tumor cells. Every tumor has a dominant subclonal lineage, representing more than 50% of tumor cells. Minimal expansion of these subclones occurs until many hundreds to thousands of mutations have accumulated, implying the existence of long-lived, quiescent cell lineages capable of substantial proliferation upon acquisition of enabling genomic changes. Expansion of the dominant subclone to an appreciable mass may therefore represent the final rate-limiting step in a breast cancer's development, triggering diagnosis.     

Galactoglucomannans increase cell population density and alter the protoxylem/metaxylem tracheary element ratio in xylogenic cultures of Zinnia

Xylogenic cultures of zinnia (Zinnia elegans) provide a unique opportunity to study signaling pathways of tracheary element (TE) differentiation. In vitro TEs differentiate into either protoxylem (PX)-like TEs characterized by annular/helical secondary wall thickening or metaxylem (MX)-like TEs with reticulate/scalariform/pitted thickening. The factors that determine these different cell fates are largely unknown. We show here that supplementing zinnia cultures with exogenous galactoglucomannan oligosaccharides (GGMOs) derived from spruce (Picea abies) xylem had two major effects: an increase in cell population density and a decrease in the ratio of PX to MX TEs. In an attempt to link these two effects, the consequence of the plane of cell division on PX-MX differentiation was assessed. Although GGMOs did not affect the plane of cell division per se, they significantly increased the proportion of longitudinally divided cells differentiating into MX. To test the biological significance of these findings, we have determined the presence of mannan-containing oligosaccharides in zinnia cultures in vitro. Immunoblot assays indicated that beta-1,4-mannosyl epitopes accumulate specifically in TE-inductive media. These epitopes were homogeneously distributed within the thickened secondary walls of TEs when the primary cell wall was weakly labeled. Using polysaccharide analysis carbohydrate gel electrophoresis, glucomannans were specifically detected in cell walls of differentiating zinnia cultures. Finally, zinnia macroarrays probed with cDNAs from cells cultured in the presence or absence of GGMOs indicated that significantly more genes were down-regulated rather than up-regulated by GGMOs. This study constitutes a major step in the elucidation of signaling mechanisms of PX- and MX-specific genetic programs in zinnia.     

High-performance liquid chromatographic determination of unreacted monomers and other residues contained in dental composites

HPLC method was developed for determination of bisphenol A diglycidyl methacrylate (bis-GMA), bisphenol A diglycidyl acrylate (bis-GA), bisphenol A dimethacrylate (bis-DMA), glycidylmethacrylate (GMA) and triethylenglycol dimethacrylate (TEGDMA). Separation was carried out on a reversed phase Omnisphere 5 C18 column with a gradient mobile phase of CH₃CN/H₂O. UV detection was set at 205 nm and 275 nm parallel. The limits of quantification were found. The method has been applied for quantification of unreacted monomers trapped in polymer network of fillings.     

Induction of the soxRS regulon of Escherichia coli by glycolaldehyde

The ability of short-chain sugars to cause oxidative stress has been examined using glycolaldehyde as the simplest sugar. Short-chain sugars autoxidize in air, producing superoxide and alpha,beta-dicarbonyls. In Escherichia coli the soxRS regulon mediates an oxidative stress response, which protects the cell against both superoxide-generating agents and nitric oxide. In superoxide dismutase-deficient E. coli mutants, glycolaldehyde induces fumarase C and nitroreductase A, which are regulated as members of the soxRS regulon. A mutational defect in soxRS eliminates that induction. This establishes that glycolaldehyde can cause induction of this defensive regulon. This effect of glycolaldehyde was oxygen-dependent, was not shown by glyoxal, and was not seen in the superoxide dismutase-replete parental strain, and it was abolished by a cell-permeable SOD mimetic. All of these suggest that superoxide radicals produced by the oxidation of glycolaldehyde played a key role in the induction.     

Role of rpoS in the regulation of glyoxalase III in Escherichia coli

Methylglyoxal is an endogenous electrophile produced in Escherichia coli by the enzyme methylglyoxal synthase to limit the accumulation of phosphorylated sugars. In enteric bacteria methylglyoxal is detoxified by the glutathione-dependent glyoxalase I/II system, by glyoxalase III, and by aldehyde reductase and alcohol dehydrogenase. Here we demonstrate that glyoxalase III is a stationary-phase enzyme. Its activity reached a maximum at the entry into the stationary phase and remained high for at least 20 h. An rpoS- mutant displayed normal glyoxalase I and II activities but was unable to induce glyoxalase III in stationary phase. It thus appears that glyoxalase III is regulated by rpoS and might be important for survival of non-growing E. coli cultures.     

Glycerol metabolism in superoxide dismutase-deficient Escherichia coli

Escherichia coli, which lacks cytoplasmic superoxide dismutases, exhibits various phenotypic deficits if grown aerobically. Here we report that sodAsodB E. coli cannot use glycerol under aerobic conditions. The reason is low activity of glycerol kinase (GK), the rate-limiting enzyme in glycerol metabolism. Superoxide does not inactivate GK, but makes it susceptible to inactivation by a heat-labile factor present in the cell-free extracts. This factor seems to be part of a proteolytic system, which recognizes and degrades oxidatively modified proteins.     

Aggregation of denatured membrane proteins--the initial stage of acid hemolysis]

Influence of some sulfhydryl reagents on kinetics of acid hemolysis has been investigated. The results obtained indicate that the mechanism of acid hemolysis includes aggregation of some denatured membrane integral proteins, following the intermolecular disulfide bond formation. A suggestion is made that in this hemolysis-inducing aggregation free SH-groups containing proteins only take place.     

Hemoglobin-catalyzed lipid peroxidation in the presence of mercuric chloride

In order to elucidate the possible mechanism of initiation of peroxidative processes in Hg2+-treated erythrocytes, the effect of HgCl2 on hemoglobin-catalyzed peroxidation of phospholipid liposomes was studied. It was demonstrated that HgCl2 significantly increases the rate of hemoglobin-catalyzed peroxidation. The addition of superoxide dismutase and catalase partially inhibits this effect. Furthermore, it was found that HgCl2 potentiates the hemoglobin oxidation. A suggestion was made that the acceleration of hemoglobin-catalyzed peroxidation by HgCl2 is associated at least in part with the increased production of superoxide anion radicals from hemoglobin.     

Initiation of peroxidation of liposome membrane lipids by activated polymorphonuclear leukocytes

The influence of active oxygen forms produced by zymosan-stimulated polymorphonuclear leukocytes (PMNL) on the initiation of liposome lipid peroxidation has been studied. It has been shown, by measuring the concentration of TBA-active products, that lipid peroxidation induced by PMNL stimulation occurs only in the presence of Fe-ADP. This fact demonstrates that OH'-radicals are responsible for the initiation of lipid peroxidation. Superoxide dismutase and catalase almost completely inhibited PMNL-stimulated peroxidation. The results obtained suggest that active oxygen forms that appear during PMNL stimulation can migrate at a considerable distance from the place of their origin, initiating peroxidation of cell membrane lipids and lipoproteins in the presence of Fe ions, which seems to underlie bacteriocidal and cytotoxic action of phagocytes.