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At least 1,387 records · Page 77Linked to original sources
PubMed1982

The process for the activation of frog epidermis pro-tyrosinase.

1. Purified pro-tyrosinase from epidermis of the frog Rana esculenta ridibunda can be activated in vitro by several proteinases (trypsin, alpha-chymotrypsin, Pronase) and by light. 2. Both pro-tyrosinase and tyrosinase are composed of a single type of subunit having pI 7.2 and approximate molecular weights 68000 and 62000 respectively. A peptide of low molecular weight is released as a consequence of the proteolytic activation. Pro-tyrosinase and tyrosinase have different quaternary structures, the proenzyme being a dimer of Mr approx. 115000 and the enzyme a tetramer of Mr approx. 210 000. 3. The activation process was affected by several agents (L-3,4-dihydroxyphenylalanine, urea, formamide) that prevented, partially or totally, the activation of pro-tyrosinase. 4. The activation of pro-tyrosinase seems to be the result of a cleavage of the polypeptide chain that determines changes in tertiary or quaternary structure.

Animals↗
PubMed2002

Rapid and simultaneous HLA class I (-A, -B and -C loci) DNA typing using the microtitre plate-reverse hybridization assay (MRHA).

We have established a precise, rapid, simple and practical HLA class I DNA typing method using the microtitre plate-reverse hybridization assay (MRHA), which enables us to perform simultaneous DNA typing of the HLA-A, -B and -C loci using the same PCR parameters and hybridization conditions. PCR-amplified products for the HLA-A, -B and -C loci were hybridized, respectively, with sequence-specific oligonucleotide (SSO) probes, which were immobilized covalently onto a microtitre plate, in hybridization buffer containing formamide at 37 degrees C. After washing at room temperature, the bound PCR products were detected by peroxidase-conjugate streptavidine followed by colour development such as enzyme immunoassay (EIA). In addition to the simple thermoregulation for hybridization and postwashing, strong positive signals, low background and high reproducibility, this DNA typing method enabled simultaneous typing of the HLA-A, -B and -C loci using a single microtitre plate as in HLA serotyping. The assignment of the HLA genotype was easily achieved by automated colorimetric reading and computer software, based on the cut-off value (threshold) established for each probe. For routine HLA class I typing, it may be possible to replace serological typing with the HLA class I DNA typing system using our MRHA method.

DNA↗
PubMed2003

Labelling quality and chromosome morphology after low temperature FISH analysed by scanning far-field and near-field optical microscopy.

A non-enzymatic, low temperature fluorescence in situ hybridization (LTFISH) procedure was applied to metaphase spreads and interphase cell nuclei. In this context 'low temperature' means that the denaturation procedure of the chromosomal target DNA usually applied by heat treatment and chaotropic agents such as formamide was completely omitted so that the complete hybridization reaction took place at 37 degrees C. For LTFISH, the DNA probe had to be single-stranded, which was achieved by means of separate thermal denaturation of the DNA probe only. The DNA probe pUC1.77 was used for all LTFISH experiments. The labelling quality (number of binding sites, relative background intensity, relative intensity of major and minor binding sites) was analysed by confocal laser scanning microscopy (CLSM). An optimum in specificity and signal quality was obtained for 15 h hybridization time. For this hybridization condition of LTFISH, the chromosomal morphology was analysed by scanning near-field optical microscopy (SNOM). The results were compared with the morphology of chromosomes after (a) labelling of all centromeres using the same chemical treatment in the FISH procedure but with the application of target denaturation, and (b) labelling of all centromeres using a standard FISH protocol including thermal denaturation of the DNA probe and the chromosomal target. Depending on the FISH-procedure applied, SNOM images show substantial differences in the chromosome morphology. After LTFISH the chromosome morphology appeared to be much better preserved than after standard FISH. In contrast, the application of the LTFISH chemical treatment accompanied by heat denaturation had a very destructive influence on chromosomal morphology. The results indicate that, at least for certain DNA probes, specific chromosome labelling can be obtained without the usually applied heat and chemical denaturation of the DNA target, resulting in an apparently well preserved chromatin morphology as visualized by SNOM. LTFISH may be therefore a useful labelling technique whenever the chromosomal morphology had to be preserved after specific labelling of DNA regions. Binding mechanisms of single-stranded DNA probes to double-stranded DNA targets are discussed.

Cell Nucleus↗
PubMed2002

Biosynthesis of vitamin B2.

GTP cyclohydrolase II catalyzes the hydrolytic release of formate and pyrophosphate from GTP producing 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, the first committed intermediate in the biosynthesis of riboflavin. The enzyme was shown to contain one zinc ion per subunit. Replacement of cysteine residue 54, 65 or 67 with serine resulted in proteins devoid of bound zinc and unable to release formate from the imidazole ring of GTP or from the intermediate analog, 2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-triphosphate. However, the mutant proteins retained the capacity to release pyrophosphate from GTP and from the formamide-type intermediate analog. The data suggest that the enzyme catalyzes an ordered reaction in which the hydrolytic release of pyrophosphate precedes the hydrolytic attack of the imidazole ring. Ring opening and formate release are both dependent on a zinc ion acting as a Lewis acid, which activates the two water molecules involved in the sequential hydrolysis of two carbon-nitrogen bonds.

Amino Acid Sequence↗
PubMed1998

Characterisation of a binding-protein-dependent, active transport system for short-chain amides and urea in the methylotrophic bacterium Methylophilus methylotrophus.

Three genes (fmdCAB) encoding an outer-membrane porin for short-chain amides and urea, formamidase, and a putative regulatory protein in Methylophilus methylotrophus have previously been cloned and characterised. Three genes have now been identified downstream of fmdB, viz fmdD encoding a hydrophilic protein containing an N-terminal signal sequence, and fmdEF encoding hydrophobic transmembrane proteins. The derived amino acid sequence of mature FmdD (predicted molecular mass 41,870 Da) was similar to the cytoplasmic, amide-binding protein (AmiC) from Pseudomonas aeruginosa and to several periplasmic, solute-binding proteins from other bacteria. Mature FmdD was purified and shown to be a monomer (40-45 kDa) with the predicted N-terminal amino acid sequence (ADYPTA-). Equilibrium dialysis showed that the purified protein bound short-chain amides and urea with high affinity (Kd 7.2 microM for [14C]urea). SDS/PAGE and western blotting using antiserum to mature FmdD showed it was induced by short-chain amides and urea, and repressed by excess ammonia. The derived amino acid sequences of FmdE (32,822 Da) and FmdF (incomplete; >25,435 Da) were similar to the transmembrane proteins BraD/LivH and BraE/LivM, respectively, in various leucine/isoleucine/valine transport systems. Uptake of [14C]urea by washed cells was inhibited by the uncoupling agent carbonyl cyanide p-trifluoromethoxyphenylhydrazone and unlabelled formamide. It is concluded that FmdDEF comprise part of a high-affinity, binding-protein-dependent active-transport system for short-chain amides and urea in M. methylotrophus.

Amides↗
PubMed2002

A fluorimetric method for the estimation of G+C mol% content in microorganisms by thermal denaturation temperature.

G+C mol% content in microorganisms is one of the recommended characteristics for the standard description of bacterial species. In this study we present a novel fluorimetric method to estimate the G+C mol% content in microorganisms. Double-stranded DNA was specifically stained with SYBR Green I, and its thermal denaturalization was followed by measuring a decrease in fluorescence using a real-time PCR thermocycler. Unlike most previous determinations of G+C mol%, in this study only DNA from microorganisms with an available completely sequenced genome were used to prepare the calibration curves. Calibration curves showed a linear relationship between G+C mol% content and melting temperature and they were performed both in the absence and presence of 30% formamide. This protocol proves to be a rapid and inexpensive method to estimate DNA base ratios of novel microorganisms.

Base Composition↗
PubMed1999

The impact of vehicle on assessment of relative skin sensitization potency of 1,4-dihydroquinone in the local lymph node assay.

BACKGROUND: The murine local lymph node assay (LLNA) has been validated as an alternative method for the identification of skin sensitization hazards. Contact allergens are identified as a function of proliferative responses induced in draining lymph nodes. The quantitative nature of the LLNA data also provides the opportunity of assessing relative potency by reference to dose response analyses. OBJECTIVE: In the current investigations, the influence of vehicle on the skin sensitization potency of a known skin sensitizer (1,4-dihydroquinone) was assessed. METHODS: 1, 4-dihydroquinone was tested in the LLNA using 7 different vehicle systems in each of 2 independent laboratories. RESULTS: Results from the 2 laboratories were almost identical. LLNA dose response data were interpolated to derive the estimated concentration (EC) of 1, 4-dihydroquinone necessary to cause a three-fold stimulation of proliferation compared with controls, the EC3 value. The vehicles used and mean EC3 values obtained were: methyl ethyl ketone 0.07%, acetone 0.08%, acetone/olive oil (80/20 v/v) 0.15%, dimethyl formamide 0.22%, dimethyl sulfoxide 0.4%, and propylene glycol and acetone/saline (50/50 v/v) vehicles gave negative results. However, when tested at higher concentrations, positive results were obtained in these vehicles. CONCLUSION: These data reveal that the vehicle in which a chemical is encountered in the skin can have a significant impact on a quantitative measure of skin sensitization potency. The implication is that accurate assessment of risk to humans will require an understanding of the matrix in which skin exposure is likely to occur.

Animals↗
PubMed2001

A placebo controlled evaluation of the antifibrillatory effects of carvedilol.

This article evaluates the antifibrillatory effects of carvedilol 5 mg/kg and vehicle (dimethyl-formamide) over time. Sprague-Dawley rats were anesthetized and intubated. They underwent baseline ventricular fibrillation threshold (VFT) determination and then received 1 of the 2 treatments (n = 10/group) over 8 minutes. VFT and determinations were performed at 2, 7, 15, 30, 45, and 60 minutes postinfusion. Carvedilol significantly increased the VFT at 2, 7, 15, 30 minutes versus baseline and the vehicle control group. Carvedilol significantly reduced the heart rate and the mean arterial pressure at every evaluable time point versus baseline and vehicle control. Carvedilol showed significant antifibrillatory effects versus baseline and vehicle for the first 30 minutes but not thereafter, even though the heart rate and mean arterial pressure remain significantly reduced.

Adrenergic beta-Antagonists↗
PubMed1998

The effect of convection on a propagating front with a liquid product: Comparison of theory and experiments.

This work is devoted to the investigation of propagating polymerization fronts converting a liquid monomer into a liquid polymer. We consider a simplified mathematical model which consists of the heat equation and equation for the depth of conversion for one-step chemical reaction and of the Navier-Stokes equations under the Boussinesq approximation. We fulfill the linear stability analysis of the stationary propagating front and find conditions of convective and thermal instabilities. We show that convection can occur not only for ascending fronts but also for descending fronts. Though in the latter case the exothermic chemical reaction heats the cold monomer from above, the instability appears and can be explained by the interaction of chemical reaction with hydrodynamics. Hydrodynamics changes also conditions of the thermal instability. The front propagating upwards becomes less stable than without convection, the front propagating downwards more stable. The theoretical results are compared with experiments. The experimentally measured stability boundary for polymerization of benzyl acrylate in dimethyl formamide is well approximated by the theoretical stability boundary. (c) 1998 American Institute of Physics.

Journal Article↗
PubMed2006

Distributed polarizabilities obtained using a constrained density-fitting algorithm.

A computationally efficient method for obtaining distributed polarizabilities of arbitrary rank using a constrained density-fitting algorithm is demonstrated on the hydrogen, carbon dioxide, formamide, and N-methylpropanamide molecules. A description of the molecular polarization in terms of local polarizabilities without charge-flow terms is obtained when the nonlocal components of the polarizability tensor are transformed away using the localization method of Le Sueur and Stone [Mol. Phys. 83, 293 (1994)]. The resulting local polarizabilities are shown to be stable with respect to basis set used, exhibiting none of the artifacts of earlier basis-space partitioning methods. We also investigate the transferability of the resulting local polarizability models.

Journal Article↗
PubMed2006

Stability of the polar {111} NaCl crystal face.

We present a surface x-ray diffraction determination of the {111} NaCl-liquid interface structure. Using ultrathin water or formamide liquid layers we ascertained that the crystal surface is smooth at an atomic level and is not reconstructed. Our results reveal surprisingly small differences in surface structure between the two cases, which nevertheless lead to dramatic differences in crystal morphology. We determined that the rocksalt {111} surface is Na(+) terminated for both environmental conditions. A quarter to half a monolayer of laterally disordered Cl(-) ions is located on top of a fully ordered Na(+) crystal surface with occupancy 0.75-1.0. This means that the polar surface is stabilized through the formation of an electrochemical double layer.

Journal Article↗
PubMed2006

Generalization of the Gaussian electrostatic model: extension to arbitrary angular momentum, distributed multipoles, and speedup with reciprocal space methods.

The simulation of biological systems by means of current empirical force fields presents shortcomings due to their lack of accuracy, especially in the description of the nonbonded terms. We have previously introduced a force field based on density fitting termed the Gaussian electrostatic model-0 (GEM-0) J.-P. Piquemal et al. [J. Chem. Phys. 124, 104101 (2006)] that improves the description of the nonbonded interactions. GEM-0 relies on density fitting methodology to reproduce each contribution of the constrained space orbital variation (CSOV) energy decomposition scheme, by expanding the electronic density of the molecule in s-type Gaussian functions centered at specific sites. In the present contribution we extend the Coulomb and exchange components of the force field to auxiliary basis sets of arbitrary angular momentum. Since the basis functions with higher angular momentum have directionality, a reference molecular frame (local frame) formalism is employed for the rotation of the fitted expansion coefficients. In all cases the intermolecular interaction energies are calculated by means of Hermite Gaussian functions using the McMurchie-Davidson [J. Comput. Phys. 26, 218 (1978)] recursion to calculate all the required integrals. Furthermore, the use of Hermite Gaussian functions allows a point multipole decomposition determination at each expansion site. Additionally, the issue of computational speed is investigated by reciprocal space based formalisms which include the particle mesh Ewald (PME) and fast Fourier-Poisson (FFP) methods. Frozen-core (Coulomb and exchange-repulsion) intermolecular interaction results for ten stationary points on the water dimer potential-energy surface, as well as a one-dimensional surface scan for the canonical water dimer, formamide, stacked benzene, and benzene water dimers, are presented. All results show reasonable agreement with the corresponding CSOV calculated reference contributions, around 0.1 and 0.15 kcal/mol error for Coulomb and exchange, respectively. Timing results for single Coulomb energy-force calculations for (H(2)O)(n), n=64, 128, 256, 512, and 1024, in periodic boundary conditions with PME and FFP at two different rms force tolerances are also presented. For the small and intermediate auxiliaries, PME shows faster times than FFP at both accuracies and the advantage of PME widens at higher accuracy, while for the largest auxiliary, the opposite occurs.

Models, Chemical↗
PubMed1976

Studies on the apoproteins of the major lipoprotein of the yolk of hen's eggs II. The dimer-tetramer transition of apovitellenin I.

Further studies have been made of the physical properties of hen's apovitellenin I, the principal low-molecular-weight protein from the high-lipid low density lipoprotein of the yolk of hen's eggs. The methods used included chromatography, sedimentation, viscosity, optical rotation, and spin labelling; the solvents used were aqueous urea, and, for some experiments, aqueous formamide. It is concluded that a neutral pH the protein is present in these solvents as an aggregate of molecular weight 36000 corresponding to a tetramer. Below about pH 4-5 solutions of the tetramer increased greatly in viscosity; furthermore, a covalently bound spin label increased in mobility. These changes were reversible and were apparently the result of dissociation of the tetramer to a dimer. This disociation did not involve a change in the proportion of alpha-helix. In contrast to the results of previous experiments, it now seems probably that the apovitellenin I dimer is stabilized by an interchain disulphide bond.

Animals↗
PubMed1984

Ribosomal gene reiteration in a marsupial species with an X-linked nucleolar organizer.

The number of ribosomal cistrons in somatic cells of males and females of Macropus eugenii have been estimated using RNA/DNA hybridization in 70% (v/v) formamide. The male has one X-linked active nucleolar organizer and the female two and while the number of ribosomal cistrons is variable between the four males examined (31-65 copies), it is substantially less than the number present in the three females (94-103 copies). There is, therefore, no evidence of dosage compensation by amplification.

Animals↗
PubMed2004

Stereocontrolled total synthesis of (+)-vincristine.

An efficient total synthesis of (+)-vincristine has been accomplished through a stereoselective coupling of demethylvindoline and the eleven-membered carbomethoxyverbanamine presursor. Demethylvindoline was prepared by oxidation of 17-hydroxy-11-methoxytabersonine, followed by regioselective acetylation with mixed anhydride method. Although an initial attempt of coupling by using demethylvindoline formamide was not successful and resulted in recovery of the starting compounds, the reaction using demethylvindoline took place smoothly to furnish the desired bisindole product with the correct stereochemistry at C18'. After formation of the piperidine ring by sequential removal of the protective groups and intramolecular nucleophilic cyclization, the total synthesis of vincristine was completed by formylation of N1.

Antineoplastic Agents, Phytogenic↗
PubMed2003

Elucidation of crystal form diversity of the HIV protease inhibitor ritonavir by high-throughput crystallization.

Pharmaceutical compounds are molecular solids that frequently exhibit polymorphism of crystal form. One high profile case of polymorphism was ritonavir, a peptidomimetic drug used to treat HIV-1 infection and introduced in 1996. In 1998, a lower energy, more stable polymorph (form II) appeared, causing slowed dissolution of the marketed dosage form and compromising the oral bioavailability of the drug. This event forced the removal of the oral capsule formulation from the market. We have carried out high-throughput crystallization experiments to comprehensively explore ritonavir form diversity. A total of five forms were found: both known forms and three previously unknown forms. The novel forms include a metastable polymorph, a hydrate phase, and a formamide solvate. The solvate was converted to form I via the hydrate phase by using a simple washing procedure, providing an unusual route to prepare the form I "disappearing polymorph" [Dunitz, J. D. & Bernstein, J. (1995) Acc. Chem. Res. 28, 193-200]. Crystals of form I prepared by using this method retained the small needle morphology of the solvate and thus offer a potential strategy for particle size and morphology control.

Crystallography, X-Ray↗
PubMed1969

Comparative hybridization of mitochondrial and cytoplasmic aminoacyl transfer RNA with mitochondrial DNA from rat liver.

We have tested the specificity of hybridization of mitochondrial tRNA with mitochondrial DNA. Techniques are now available for performing RNA-DNA hybridization at low temperatures in the presence of 50 per cent formamide. With this technique, specific aminoacyl-tRNA-DNA hybridization can be followed in the presence of other species of RNA if the tRNA is acylated with radioactive amino acids. With this technique, mitochondrial leucyl-tRNA from rat liver has been found to anneal to mitochondrial DNA. Competitive hybridization between mitochondrial leucyl-tRNA and mitochondrial or cytoplasmic aminoacyl-tRNA shows that mitochondrial tRNA competes much more efficiently than cytoplasmic tRNA for sites of annealing to mitochondrial DNA. These results show that mitochondrial leucyl-tRNA differs from cytoplasmic leucyl-tRNA in its primary base sequence. They also imply that mitochondrial DNA may be the template from which mitochondrial tRNA is transcribed.

Amino Acids↗
PubMed1970

Conformations of the single-stranded DNA of bacteriophage M13.

At least two conformations of M13 single-stranded DNA have been demonstrated by measuring differences in sedimentation coefficient and by direct visualization in the electron microscope. Which form is obtained from infected cells and/or intact phage depends on the pH, ionic strength, and temperature. The slower-sedimenting form can be converted to the faster-sedimenting, single-stranded form by low ionic strength, alkali treatment, formamide, or formaldehyde, but not by exposure to 100 degrees C in 1.0 M NaCl. The ability to assume either conformation appears to be a function of the nucleic acid alone. Whether or not these different conformations are of biological significance is still unknown.

Centrifugation, Density Gradient↗