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At least 793 records · Page 44Linked to original sources
PubMed2000

Histone H2A.Z has a conserved function that is distinct from that of the major H2A sequence variants.

Saccharomyces cerevisiae contains three genes that encode members of the histone H2A gene family. The last of these to be discovered, HTZ1 (also known as HTA3), encodes a member of the highly conserved H2A.Z class of histones. Little is known about how its in vivo function compares with that of the better studied genes (HTA1 and HTA2) encoding the two major H2As. We show here that, while the HTZ1 gene encoding H2A.Z is not essential in budding yeast, its disruption results in slow growth and formamide sensitivity. Using plasmid shuffle experiments, we show that the major H2A genes cannot provide the function of HTZ1 and the HTZ1 gene cannot provide the essential function of the genes encoding the major H2As. We also demonstrate for the first time that H2A.Z genes are functionally conserved by showing that the gene encoding the H2A.Z variant of the ciliated protozoan TETRAHYMENA: thermophila is able to rescue the phenotypes associated with disruption of the yeast HTZ1 gene. Thus, the functions of H2A.Z are distinct from those of the major H2As and are highly conserved.

Animals↗
PubMed1976

Studies on the low molecular weight RNA associated with 28S ribosomal RNA from Crotalus durissus terrificus liver.

A low molecular weight RNA was released from the purified rattlesnake 28 S RNA by brief heat treatment as well as by treatment with 80% dimethylsulfoxide or formamide. The sedimentation coeficient of this low molecular weight RNA was found to be 5.5 S, corresponding to a nucleotide number of 140 and a molecular weight of 46 000. It was also observed that 5.5S RNA is present in equimolar ratio to 5 S rRNA. Heat treatment of the purified 60 S ribosomal subunit also released the 5.5 S RNA. The possibility that this low molecular weight RNA is located on the surface of the large ribosomal subunit is discussed.

Animals↗
PubMed1981

Identification and suppression of secondary structures formed from deoxy-oligonucleotides during electrophoresis in denaturing polyacrylamide-gels.

Nature and stability of secondary structures formed from DNA-fragments during electrophoresis in urea containing polyacrylamide-gels were investigated. Duplices and especially hairpin loops were found to be surprisingly stable. Polyacrylamide-gels containing high concentrations of formamide effectively melt these structures. Such gels will improve nucleotide sequence analysis in regions of dyad symmetry that often cause 'band compressions' under standard electrophoresis conditions.

Electrophoresis, Polyacrylamide Gel↗
PubMed2003

Optimizing spotting solutions for increased reproducibility of cDNA microarrays.

The ability to extract meaningful information from transcriptome technologies such as cDNA microarrays relies on the precision, sensitivity and reproducibility of the measured values for a given gene across multiple samples. Given the lack of a 'gold standard' for the production of microarrays using current technologies, there is a high degree of variation in the quality of data derived from microarray experiments. Poor reproducibility not only adds to the cost of a given study but also leads to data sets that are difficult to interpret. For glass slide DNA microarrays, much of this variation is introduced systematically, during the spotting, or deposition, of the DNA onto the slide surface. In order to reduce this type of systematic variation we tested spotting solutions containing different detergent additives in the presence of one of two different denaturants and determined their effect on spot quality. We show that spotting cDNA in a solution consisting of the zwitterionic detergent 3-[(3-cholamidopropyl)dimethylammonio]-1-propane sulfonate (CHAPS) in the presence of formamide or dimethyl sulfoxide yields spots of superior quality in terms of morphology, size homogeneity and signal reproducibility, as well as overall intensity, when used with popular, commercially available slides.

Carbocyanines↗
PubMed1976

Enrichment of enzyme activity on deformylation of 1-NFK-lysozyme.

The formamide linkage of an inactive lysozyme derivative (1-NFK-lysozyme), formed by selective ozonization of tryptophan 62 in hen egg-white lysozyme [EC 3.2.1.17] was hydrolyzed with dilute acid faster in the frozen state at about --10 degrees than at 20 degrees. On hydrolysis of 1-NFK-lysozyme the low lytic activity increased to approximately 80% of that of native lysozyme. It is suggested that the binding ability associated with kynurenine 62 in the lysozyme derivative formed by this hydrolysis may be responsible for increase in enzymatic activity.

Binding Sites↗
PubMed1986

The structure of the rotavirus inner capsid studied by electron microscopy of chemically disrupted particles.

The inner capsid structure of the OSU strain of porcine rotavirus was studied by electron microscopy of freeze-dried preparations and of negatively stained chemically disrupted virus particles. The analysis of the particles by the freeze-drying technique revealed a T:13 l (laevo) symmetry for the organization of the inner capsid. Treatment of single-capsid rotavirus particles with 30% formamide or 5 M-urea resulted in their degradation, giving rise to very similar products, corresponding to isolated vertices, edges and faces of the virus icosahedron. An analysis of such structures confirmed the triangulation number and handedness of the rotavirus inner capsid, and provided evidence for the open-mesh model, in which the five- and six-coordinated axes are represented by 'holes' formed by smaller trimeric morphological subunits.

Animals↗
PubMed1976

Thermodynamic parameters of transfer of N-acetyl ethyl esters of different amino acids from organic solvents to water.

The distribution coefficients of N-acetyl ethyl esters of glycine, diglycine, beta-alanine, alanine, valine, norvaline, leucine and norleucine between water and different organic solvents have been measured at different temperatures. Similar distribution coefficients have been measured for simple amides, urea, formamide, acetamide and N-methyl acetamide. From the distribution measurements, deltaGtr, the free energy of transfer of the solutes from organic solvents to water has been calculated. The temperature dependence of the distribution coefficient values has been utilised to determine the enthalpy of transfer, deltaHtr, and entropy of transfer deltaStr for the above process. From these results similar thermodynamic parameters for the transfer of different nonpolar side chains and peptide groups have been determined and compared with the available data in the literature.

Acetamides↗
PubMed1978

The DNA . tyrocidine complex and its dissociation in the presence of gramicidin D.

The peptide antibiotic tyrocidine affects transcription in vitro by interfering with the initiation process. The complex formed between tyrocidine and native DNA is stable against nucleolytic enzymes. It is sensitive to variations in the salt concentration. Protection of DNA as a function of the tyrocidine concentration follows a curve suggesting cooperative binding of tyrocidine to DNA. The complex formation at low tyrocidine concentrations is accompanied by the presence of single stranded regions of unknown length. With single-stranded DNA, tyrocidine forms a complex which is relatively insensitive to high salt concentrations. Both native and single-stranded DNAs of the complexes become digestible in the presence of gramicidin D, another peptide antibiotic. Breakdown of the complex as a function of the gramicidin D concentration follows a curve which is the reverse of cooperative binding. Gramicidin D acts more effectively on single-stranded rather than on double-stranded DNA . tyrocidine complexes. The DNA . tyrocidine complex, which is broken down by formamide and dimethyl sulfoxide is stabilized by gramicidin D. The implications of these results are discussed with respect to a possible recognition of DNA sequences by tyrocidine and the interaction between DNA, tyrocidine and gramicidin D.

Bacillus↗
PubMed1986

The pterin (bactopterin) of carbon monoxide dehydrogenase from Pseudomonas carboxydoflava.

Radioactively labeled carbon monoxide (CO) dehydrogenase has been obtained in good yield and purity from Pseudomonas carboxydoflava grown in the presence of [32P]phosphate. One enzyme molecule contained an average of 8.32 molecules of phosphate. The entire phosphate content was confined to 2 molecules of FAD and 2 molecules of a pterin. These were noncovalently bound. Molybdoenzyme cofactors could be extracted into N-methyl formamide; pterins were isolated by thin-layer chromatography. CO dehydrogenase contained a novel pterin, different from molybdopterin, which was also resolved in other bacterial molybdoenzymes. Therefore, it was tentatively named bactopterin. The characteristic features of bactopterin were as follows. A relative molecular mass, Mr, of 730 which was much greater than that of molybdopterin (330) (Mr values refer to molybdenum-free forms of the cofactors; presumably, the latter were also devoid of the sulfhydryl groups contained in the native compounds). A content of 2 molecules of phosphate/molecule compared to only 1 phosphate in molybdopterin. Bactopterin was three times less susceptible to air oxidation than molybdopterin. Native bactopterin was cleaved by perchloric acid into two phosphorous-containing fragments with Mr of 330 and 420. The smaller one is believed to be very similar to molybdopterin, the larger one was not a pterin but probably contained an aromatic structure.

Aldehyde Oxidoreductases↗
PubMed1989

Catalytic activity and denaturation of enzymes in water/organic cosolvent mixtures. Alpha-chymotrypsin and laccase in mixed water/alcohol, water/glycol and water/formamide solvents.

The dependence of the catalytic activities of alpha-chymotrypsin and laccase on the concentration of organic cosolvents (alcohols, glycols and formamides) in mixed aqueous media has a pronounced threshold character: it does not change up to a critical concentration of the non-aqueous cosolvents added, yet further increase of the latter (by only a small percentage, by vol.) leads to an abrupt decrease in enzyme activity. Fluorescence studies indicate that the inactivation results from reversible conformational changes (denaturation) of the enzymes. There is a linear correlation between the critical concentration of residual water (at which the enzyme inactivation occurs in a threshold manner) and the hydrophobicity of the organic cosolvents added. A quantitative criterion is suggested for the selection of organic cosolvents to be used for enzymatic reactions in homogeneous water/organic solvent media.

Alcohols↗
PubMed1994

Correlation of high-temperature stability of alpha-chymotrypsin with 'salting-in' properties of solution.

A correlation between the stability of alpha-chymotrypsin against irreversible thermal inactivation at high temperatures (long-term stability) and the coefficient of Setchenov equation as a measure of salting-in/out efficiency of solutes in the Hofmeister series has been found. An increase in the concentration of salting-in solutes (KSCN, urea, guanidinium chloride, formamide) leads to a many-fold decrease of the inactivation rate of the enzyme. In contrast, addition of salting-out solutes has a small effect on the long-term stability of alpha-chymotrypsin at high temperatures. The effects of solutes are additive with respect to their salting-in/out capacities; the stabilizing action of the solutes is determined by the calculated Setchenov coefficient of solution. The correlation is explained by a solute-driven shift of the conformational equilibrium between the 'low-temperature' native and the 'high-temperature' denatured forms of the enzyme within the range of the kinetic scheme put forward in the preceding paper in this journal: irreversible inactivation of the high-temperature form proceeds much more slowly compared with the low-temperature form.

Chymotrypsin↗
PubMed1983

New inhibitors of alcohol dehydrogenase: studies in vivo and in vitro in the rat.

Two compounds bearing an amide group, p-butoxyphenol acetamide (BPA) and N-(p-butoxybenzyl)formamide (BBF) were studied as inhibitors of alcohol dehydrogenase (ADH) and their action compared with that of 4-methyl-pyrazole (4-MP), a known inhibitor of this enzyme. In vitro studies on pure horse liver ADH showed that BPA and BBF were noncompetitive inhibitors with respect to ethanol and that their Ki values were 22 and 0.14 micrometer, respectively. The apparent Ki values of BPA and BBF for rat liver ADH were found to be 90 and 2.3 micrometers, respectively (noncompetitive inhibition). Several in vivo experiments were carried out in the rat. Administration intraperitoneally of the substance (460 mumol/kg) 1 hr before intraperitoneal injection of alcohol (2 g/kg body weight) led to a significant decrease in ethanol catabolism. Injection of the substances at 460 mumol/kg brought about a decrease in rat liver ADH activity, but the activity of mitochondrial aldehyde dehydrogenase was only decreased in animals treated with BBF.

Acetamides↗
PubMed1975

The percutaneous absorption of phenolic compounds: the effect of vehicles on the penetration of phenol.

The effects of interactions between drug and skin, drug and vehicle, and vehicle and skin on the overall penetration rate of a drug through the skin may be evaluated by comparison of penetration rates through excised skin and an inert reference membrane such as polyethylene. Dimethyl sulphoxide, dimethyl formamide, ethanol and water increase the permeability of the skin but because of reduced thermodynamic activities in the vehicles low penetration rates are observed.

Animals↗
PubMed1983

Aequorin-calcium transients in frog twitch muscle fibres.

Intracellular Ca2+ transients, evoked either by action potentials or depolarizing clamp pulses, were studied in frog sartorius muscle fibres injected with aequorin. The time course of the Ca2+ transients became shorter as the temperature was increased. The half rise time and decay time constants showed straight lines between 3 and 30 degrees C in Arrhenius plots, with a Q10 of 2.5 and 2.3 respectively. The potential dependence of the Ca2+ transient was examined under voltage clamp. The peak light amplitude reached a plateau at around +50 mV, suggesting that Ca2+ release continues beyond the potential level at which contraction was saturated. During a prolonged depolarization, the Ca2+ transient gradually declined. The time course of decline became faster when long depolarizing pulses were repeated, or when the temperature was increased. The Q10 for half duration of the Ca2+ transient evoked by prolonged depolarization was 2.2. A Ca2+ transient could be evoked in Ca2+-free Ringer solution containing EGTA. Formamide, which is known to abolish excitation-contraction coupling, also abolished the Ca2+ transient. During maintained depolarization, the time integral of the Ca2+ transient was larger for larger depolarizations, suggesting that the total amount of Ca2+ released was greater for the more intense depolarization. The decline of the Ca2+ transient during maintained depolarization is probably due to inactivation of excitation-contraction coupling rather than the depletion of intracellular Ca2+ stores. These findings support the view that in frog skeletal muscle fibres the increase in intracellular Ca2+, caused by membrane depolarization, is produced by the release of Ca2+ from intracellular stores and that any influx of Ca2+ from the external medium does not contribute appreciably to the aequorin-Ca2+ transient.

Action Potentials↗
PubMed1997

Solvent-dependent rate-limiting steps in the conformational change of sodium channel gating in squid giant axon.

1. The time course of sodium currents (INa) in squid giant axon was analysed using viscous non-electrolyte solutions on both sides of the axolemma. It slowed reversibly as the non-electrolyte concentration increased. The activation, deactivation (closing) and inactivation processes were slowed in a similar manner. The gating current of the sodium channel was also slowed to the same extent as the activation time constant. 2. The voltage dependence observed in a time constant vs. voltage relationship and a chord conductance vs. voltage relationship (activation curve), did not change significantly. 3. The gating kinetics have a similar temperature dependence in non-electrolyte solutions, showing that the basic gating mechanism did not change in these solutions and only a slight increase in the activation free energy was one of the main causes of slowing. 4. Eight non-electrolytes, formamide, ethylene glycol, glycerol, erythritol, glucose, sorbitol, sucrose and polyethylene glycol (mean molecular weight 600) were used. The amount of slowing was correlated with the gram concentration (g l-1) of non-electrolytes, but not with molar concentration (M) and solution osmolarity (osmol l-1). 5. The percentage changes of the time constant were expressed as a function of the relative change in solution viscosity, eta/eta0. The proportionality constants alpha in the relationship alpha (eta/eta0), and gamma in the relationship 100 (eta/eta0)gamma, obtained using different non-electrolytes, were close to 100% and 1, respectively. The simplest model to explain the results assumes that a slowing of a global conformational change is a consequence of sequential viscosity-dependent movements of local structures (viscosity model). 6. Values of alpha and gamma deviated frequently from those in an ideal case, i.e. 100% for alpha and 1 for gamma, and they scattered, having a tendency to decrease as a function of molecular weight. 7. The slowing was also expressed as an exponential function of the solution osmolarity. A predicted solute-inaccessible volume Va ranged (in nm3 per molecule) between 0.09 and 1.45. The value of Va increased as a logarithmic function of the molecular weight of the non-electrolyte. 8. This solute-inaccessible volume should be distributed in all hydrophilic parts of the sodium channel protein, but is not located in the channel conducting pore itself. The slowing of gating could be explained by a model in which a rate-limiting step is a hydration process that occurs after local small structural changes have exposed new, unhydrated faces (transient hydrated-states model). 9. Considering the opposite dependencies of parameters alpha (or gamma) and beta on the molecular weight, sodium channel gating is likely to reflect a combination of these two models, which are coupled in microscopic segment movements. We emphasize with this combination of models that fluctuating hydrophilic structures play an important role in determining time constants in the gating process.

Animals↗
PubMed1970

Localization of 5S RNA genes on Drosophila chromosomes by RNA-DNA hybridization.

[(3)H]RNA with a high specific activity was prepared from larvae of Drosophila melanogaster grown 4 days in contact with [(3)H]uridine. Purified tritiated 5S RNA was annealed to the DNA of polytene chromosomes, which had been denatured in formamide. The 5S RNA genes are placed within the region 56E-F of the right arm of chromosome 2. This localization was determined from autoradiographs, where the radioactivity from hybrids of [(3)H]RNA and DNA was confined to the 56E-F segment.

Animals↗
PubMed2005

Emission characteristics of fluorescent labels with respect to temperature changes and subsequent effects on DNA microchip studies.

The effects of temperature, salt concentration, and formamide concentration on the emission characteristics of commonly used fluorescent labels were evaluated on DNA microchips. The emission intensities of different fluorophores without hybridization were observed to vary, each to a different extent, to mainly temperature changes. Rhodamine red, TAMRA (tetramethylrhodamine), and dyes from the carbocyanide group exhibited the largest variations, and Texas Red and Oregon Green exhibited the smallest variations. This temperature dependency was shown to affect results obtained during melting curve analysis in DNA microarray studies. To minimize the bias associated with the temperature-dependent emission of different fluorescent labels, a normalization step was proposed.

Fluorescein-5-isothiocyanate↗
PubMed1975

Chemical composition and immunological specificity of cell wall polysaccharide group antigens of streptococcal groups P and U.

The group antigens of streptococcal groups P and U were extracted with formamide and purified on diethylaminoethyl-Sephadex A-25 and Sephadex G-200. The antigens were shown to be polysaccharides located in the cell walls of the organisms. In a precipitin test, the P and U group antigens did not cross-react with homologous sera of each other, nor with specific antiserum of the group antigen of group E streptococci. The polysaccharide comprising the group P antigen contained rhamnose, glucose, galactose, glucosamine, and galactosamine; the group U antigen was similar in composition but lacked galactosamine and contained more galactose.

Bacterial Proteins↗