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Biomedical subjects

A Bacher

Publications and source records attributed to A Bacher.

At least 19 recordsLinked to original sources
PubMed2006

High resolution dissociative electron attachment to gas phase adenine.

The dissociative electron attachment to the gas phase nucleobase adenine is studied using two different experiments. A double focusing sector field mass spectrometer is utilized for measurements requiring high mass resolution, high sensitivity, and relative ion yields for all the fragment anions and a hemispherical electron monochromator instrument for high electron energy resolution. The negative ion mass spectra are discussed at two different electron energies of 2 and 6 eV. In contrast to previous gas phase studies a number of new negative ions are discovered in the mass spectra. The ion efficiency curves for the negative ions of adenine are measured for the electron energy range from about 0 to 15 eV with an electron energy resolution of about 100 meV. The total anion yield derived via the summation of all measured fragment anions is compared with the total cross section for negative ion formation measured recently without mass spectrometry. For adenine the shape of the two cross section curves agrees well, taking into account the different electron energy resolutions; however, for thymine some peculiar differences are observed.

Adenine↗
PubMed2006

Cross sections and ion kinetic energy analysis for the electron impact ionization of acetylene.

Using a Nier-type electron impact ion source in combination with a double focusing two sector field mass spectrometer, partial cross sections for electron impact ionization of acetylene are measured for electron energies up to 1000 eV. Discrimination factors for ions are determined using the deflection field method in combination with a three-dimensional ion trajectory simulation of ions produced in the ion source. Analysis of the ion yield curves obtained by scanning the deflectors allows the assignment of ions with the same mass-to-charge ratio to specific production channels on the basis of their different kinetic energy distributions. This analysis also allows to determine, besides kinetic energy distributions of fragment ions, partial cross sections differential in kinetic energy. Moreover a charge separation reaction, the Coulomb explosion of the doubly charged parent ions C2H2++ into the fragment ions C2H+ and H+, is investigated and its mean kinetic energy release (KER=3.88 eV) is deduced.

Journal Article↗
PubMed2005

[A factorial trial of six interventions for the prevention of postoperative nausea and vomiting].

BACKGROUND: Untreated, one third of patients who undergo surgery will have postoperative nausea and vomiting. Although many trials have been conducted, the relative benefits of prophylactic antiemetic interventions given alone or in combination remain unknown. METHODS: In a randomized, controlled trial of factorial design, 5,199 patients at high risk for postoperative nausea and vomiting were randomly assigned to 1 of 64 possible combinations of 6 prophylactic interventions: 1) 4 mg of ondansetron or no ondansetron; 2) 4 mg of dexamethasone or no dexamethasone; 3) 1.25 mg of droperidol or no droperidol; 4) propofol or a volatile anesthetic; 5) nitrogen or nitrous oxide; 6) remifentanil or fentanyl. The primary aim parameter was nausea and vomiting within 24 h after surgery, which was evaluated blindly. RESULTS: Ondansetron, dexamethasone, and droperidol each reduced the risk of postoperative nausea and vomiting by about 26%, propofol reduced the risk by 19%, and nitrogen by 12%. The risk reduction with both of these agents (i.e., total intravenous anesthesia) was thus similar to that observed with each of the antiemetics alone. All the interventions acted independently of each other and independently of the patients' baseline risk. Consequently, the relative risks associated with the combined interventions could be estimated by multiplying the relative risks associated with each intervention. However, absolute risk reduction was a critical function of patients' baseline risk. CONCLUSIONS: Because antiemetic interventions are similarly effective and act independently, the safest or least expensive should be used first. Prophylaxis is rarely warranted in low-risk patients, moderate-risk patients may benefit from a single intervention, and multiple interventions should be reserved for high-risk patients.

Analgesics, Opioid↗
PubMed2005

Structures and reaction mechanisms of riboflavin synthases of eubacterial and archaeal origin.

The biosynthesis of one riboflavin molecule requires one molecule of GTP and two molecules of ribulose 5-phosphate as substrates. GTP is hydrolytically opened, converted into 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione by a sequence of deamination, side chain reduction and dephosphorylation. Condensation with 3,4-dihydroxy-2-butanone 4-phosphate obtained from ribulose 5-phosphate leads to 6,7-dimethyl-8-ribityllumazine. The dismutation of 6,7-dimethyl-8-ribityllumazine catalysed by riboflavin synthase produces riboflavin and 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. A pentacyclic adduct of two 6,7-dimethyl-8-ribityllumazines has been identified earlier as a catalytically competent reaction intermediate of the Escherichia coli enzyme. Acid quenching of reaction mixtures of riboflavin synthase of Methanococcus jannaschii, devoid of similarity to riboflavin synthases of eubacteria and eukaryotes, afforded a compound whose optical absorption and NMR spectra resemble that of the pentacyclic E. coli riboflavin synthase intermediate, whereas the CD spectra of the two compounds have similar envelopes but opposite signs. Each of the compounds could serve as a catalytically competent intermediate for the enzyme by which it was produced, but not vice versa. All available data indicate that the respective pentacyclic intermediates of the M. jannaschii and E. coli enzymes are diastereomers. Whereas the riboflavin synthase of M. jannaschii is devoid of similarity with those of eubacteria and eukaryotes, it has significant sequence similarity with 6,7-dimethyl-8-ribityllumazine synthases catalysing the penultimate step of riboflavin biosynthesis. 6,7-Dimethyl-8-ribityllumazine synthase and the archaeal riboflavin synthase appear to have diverged early in the evolution of Archaea from a common ancestor.

Archaea↗
PubMed2005

Isoprenoid biosynthetic pathways as anti-infective drug targets.

IPP (isopentenyl diphosphate) and DMAPP (dimethylallyl diphosphate) serve as the universal precursors for the biosynthesis of isoprenoids. Besides the well-known mevalonate pathway, the existence of a second biosynthetic pathway conducive to IPP and DMAPP formation through 1-deoxy-D-xylulose 5-phosphate and 2C-methyl-D-erythritol 4-phosphate was discovered approx. 10 years ago in plants and certain eubacteria. It is now known that this pathway is widely distributed in the bacterial kingdom including major human pathogens, such as Mycobacterium tuberculosis and Helicobacter pylori. The pathway is also essential in the malaria vector Plasmodium falciparum. During the last few years, the genes, enzymes, intermediates and mechanisms of the biosynthetic route have been elucidated by a combination of comparative genomics, enzymology, advanced NMR technology and crystallography. The results provide the basis for the development of novel anti-infective drugs.

Animals↗
PubMed2005

Pentoxifylline attenuates the increase in whole blood viscosity after transfusion.

BACKGROUND: Pentoxifylline improves tissue oxygenation and intestinal blood flow in models of haemorrhagic shock, and it has been used for the treatment of intermittent claudication due to its beneficial effects on haemorheology. We investigated the effects of pentoxifylline on whole blood viscosity during packed red-blood cell transfusion in critically ill adult patients. METHODS: Twenty critically ill patients were randomly assigned to one of two groups (pentoxifylline group: n = 11, placebo group: n = 9) and prospectively studied. Forty-five minutes before and during the packed red-blood cell transfusion (10 ml min(-1)) over a period of 80 min, 1.5 mg kg(-1) . h(-1) pentoxifylline or placebo were administered intravenously. Haematocrit, plasma fibrinogen concentration, total protein concentration, whole blood viscosity (at a shear rate of 10 s(-1), 50 s(-1), and 100 s(-1)) and plasma viscosity were measured. RESULTS: After the packed red-blood cell transfusion, haematocrit levels increased significantly in both groups (pentoxifylline group: from 26.1 +/- 2.8% to 33.0 +/- 3.2; placebo group: from 24.4 +/- 3.3% to 32.6 +/- 2.6%; means +/- standard deviation). Compared to baseline, whole blood viscosity increased in both groups at all shear rates after the transfusion, but the increase was significantly less in the pentoxifylline group (26 +/- 15% vs. 49 +/- 14%, 23 +/- 11% vs. 39 +/- 12%, and 22 +/- 11% vs. 35 +/- 12% for the pentoxifylline vs. placebo groups at shear rates of 10 s(-1), 50 s(-1), and 100 s(-1), respectively). Plasma viscosity, total protein concentration, and fibrinogen concentration remained unchanged and no significant differences among groups were observed. CONCLUSIONS: These results suggest that pentoxifylline is effective in attenuating the increase in whole blood viscosity after a transfusion of packed red-blood cells. Plasma viscosity is not influenced by pentoxifylline.

Adult↗
PubMed2004

Biosynthesis of isoprenoids via the non-mevalonate pathway.

The mevalonate pathway for the biosynthesis of the universal terpenoid precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), is known in considerable detail. Only recently, the existence of a second mevalonate-independent pathway for the biosynthesis of IPP and DMAPP was detected in plants and certain eubacteria. Experiments with 13C and/or 2H-labelled precursors were crucial in the elucidation of this novel route. The pathway is essential in plants, many eubacteria and apicomplexan parasites, but not in archaea and animals. The genes, enzymes and intermediates of this pathway were rapidly unravelled over the past few years. Detailed knowledge about the mechanisms of this novel route may benefit the development of novel antibiotics, antimalarials and herbicides.

Animals↗
PubMed2003

Evidence for a strong surface-plasmon resonance on ErAs nanoparticles in GaAs.

Room-temperature attenuation measurements are made between lambda=0.8 and 10.0 microm on three GaAs epitaxial samples containing layers of ErAs nanoparticles. An asymmetric attenuation peak is observed around 2.5 microm that increases in strength with ErAs density, and is modeled well by a Maxwell-Garnett formulation and semiclassical transport theory. The nanoparticles are assigned a distribution function of oblate spheroids having a minimum volume corresponding to a 1.0-nm sphere. This is consistent with the self-organizing tendency of ErAs in GaAs, and explains the sharp attenuation peak as a spherical-particle surface-plasmon (i.e., Fröhlich) resonance.

Journal Article↗
PubMed2001

Studies on the nonmevalonate pathway to terpenes: the role of the GcpE (IspG) protein.

Recombinant Escherichia coli cells engineered for the expression of the xylB gene in conjunction with genes of the nonmevalonate pathway were supplied with (13)C-labeled 1-deoxy-D-xylulose. Cell extracts were analyzed directly by NMR spectroscopy. (13)C-labeled 2C-methyl-D-erythritol 2,4-cyclodiphosphate was detected at high levels in cells expressing xylB, ispC, ispD, ispE, and ispF. The additional expression of the gcpE gene afforded 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate as an intermediate of the nonmevalonate pathway. Hypothetical mechanisms involving conserved cysteine residues are proposed for the enzymatic conversion of 2C-methyl-D-erythritol 2,4-cyclodiphosphate into 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate catalyzed by the GcpE protein.

Amino Acid Sequence↗
PubMed2001

Design, synthesis, and evaluation of 9-D-ribityl-1,3,7-trihydro-2,6,8-purinetrione, a potent inhibitor of riboflavin synthase and lumazine synthase.

Reduction of 5-nitro-6-D-ribitylaminouracil (9) afforded 5-amino-6-D-ribitylaminouracil (1), which reacted with ethyl chloroformate to yield 5-ethylcarbamoyl-6-D-ribitylaminouracil (12). The latter compound was cyclized to 9-D-ribityl-1,3,7-trihydropurine-2,6,8-trione (13), which was found to be a relatively potent inhibitor of both Escherichia coli riboflavin synthase (K(i) 0.61 microM) and Bacillus subtilis lumazine synthase (K(i) 46 microM). Molecular modeling of the lumazine synthase-inhibitor complex indicated the possibility for hydrogen bonding between the Lys135 epsilon-amino group of the enzyme and both the 8-keto group and the 4'-hydroxyl group of the ligand. A bisubstrate analogue of the riboflavin synthase-catalyzed reaction, 1,4-bis[1-(9-D-ribityl-1,3,7-trihydropurine-2,6,8-trionyl)]butane (18), was also synthesized using a similar route and was found to be inactive as an inhibitor of both riboflavin synthase and lumazine synthase.

Bacillus subtilis↗
PubMed2001

Biosynthesis of terpenoids: efficient multistep biotransformation procedures affording isotope-labeled 2C-methyl-D-erythritol 4-phosphate using recombinant 2C-methyl-D-erythritol 4-phosphate synthase.

This paper describes the recombinant expression of the ispC gene of Escherichia coli specifying 2C-methyl-D-erythritol 4-phosphate synthase in a modified form that can be purified efficiently by metal-chelating chromatography. The enzyme was used for the preparation of isotope-labeled 2C-methyl-D-erythritol 4-phosphate employing isotope-labeled glucose and pyruvate as starting materials. The simple one-pot methods described afford numerous isotopomers of 2C-methyl-D-erythritol 4-phosphate carrying (3)H, (13)C, or (14)C from commercially available precursors. The overall yield based on the respective isotope-labeled starting material is approximately 50%.

Aldose-Ketose Isomerases↗
PubMed2001

The NMR structure of the 47-kDa dimeric enzyme 3,4-dihydroxy-2-butanone-4-phosphate synthase and ligand binding studies reveal the location of the active site.

Recent developments in NMR have extended the size range of proteins amenable to structural and functional characterization to include many larger proteins involved in important cellular processes. By applying a combination of residue-specific isotope labeling and protein deuteration strategies tailored to yield specific information, we were able to determine the solution structure and study structure-activity relationships of 3,4-dihydroxy-2-butanone-4-phosphate synthase, a 47-kDa enzyme from the Escherichia coli riboflavin biosynthesis pathway and an attractive target for novel antibiotics. Our investigations of the enzyme's ligand binding by NMR and site-directed mutagenesis yields a conclusive picture of the location and identity of residues directly involved in substrate binding and catalysis. Our studies illustrate the power of state-of-the-art NMR techniques for the structural characterization and investigation of ligand binding in protein complexes approaching the 50-kDa range in solution.

Amino Acid Sequence↗
PubMed2001

An optomechanical transducer in the blue light receptor phototropin from Avena sativa.

The PHOT1 (NPH1) gene from Avena sativa specifies the blue light receptor for phototropism, phototropin, which comprises two FMN-binding LOV domains and a serine/threonine protein kinase domain. Light exposure is conducive to autophosphorylation of the protein kinase domain. We have reconstituted a recombinant LOV2 domain of A. sativa phototropin with various (13)C/(15)N-labeled isotopomers of the cofactor, FMN. The reconstituted protein samples were analyzed by NMR spectroscopy under dark and light conditions. Blue light irradiation is shown to result in the addition of a thiol group (cysteine 450) to the 4a position of the FMN chromophore. The adduct reverts spontaneously in the dark by elimination. The light-driven flavin adduct formation results in conformational modification, which was diagnosed by (1)H and (31)P NMR spectroscopy. This conformational change is proposed to initiate the transmission of the light signal via conformational modulation of the protein kinase domain conducive to autophosphorylation of NPH1.

Journal Article↗
PubMed2001

Crystal structure of rat GTP cyclohydrolase I feedback regulatory protein, GFRP.

Tetrahydrobiopterin, the cofactor required for hydroxylation of aromatic amino acids regulates its own synthesis in mammals through feedback inhibition of GTP cyclohydrolase I. This mechanism is mediated by a regulatory subunit called GTP cyclohydrolase I feedback regulatory protein (GFRP). The 2.6 A resolution crystal structure of rat GFRP shows that the protein forms a pentamer. This indicates a model for the interaction of mammalian GTP cyclohydrolase I with its regulator, GFRP. Kinetic investigations of human GTP cyclohydrolase I in complex with rat and human GFRP showed similar regulatory effects of both GFRP proteins.

Amino Acid Sequence↗
PubMed2001

Biosynthesis of riboflavin. Single turnover kinetic analysis of GTP cyclohydrolase II.

GTP cyclohydrolase II catalyzes the conversion of GTP into a mixture of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (Compound 2), formate, and pyrophosphate. Moreover, GMP was recently shown to be formed as a minor product. The major product (Compound 2) serves as the first committed intermediate in the biosynthesis of the vitamin, riboflavin. Numerous pathogenic microorganisms are absolutely dependent on endogenous synthesis of riboflavin. The enzymes of this pathway are therefore potential drug targets, and mechanistic studies appear relevant for development of bactericidal inhibitors. Pre-steady state quenched flow analysis of GTP cyclohydrolase II shows the rate-determining step to be located at the beginning of the reaction sequence catalyzed by the enzyme. Thus, GTP is consumed at a rate constant of 0.064 s(-1), and the reaction product, Compound 2, is formed at an apparent rate constant of 0.062 s(-1). Stopped flow experiments monitored by multiwavelength photometry are well in line with these data. 2-Amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone triphosphate can serve as substrate for GTP cyclohydrolase II but does not fulfill the criteria for a kinetically competent intermediate. A hypothetical reaction mechanism involves the slow formation of a phosphoguanosyl derivative of the enzyme under release of pyrophosphate. The covalently bound phosphoguanosyl moiety is proposed to undergo rapid hydrolytic release of formate from the imidazole ring and/or hydrolytic cleavage of the phosphodiester bond.

Chromatography, High Pressure Liquid↗
PubMed2001

Crystallization and preliminary crystallographic analysis of the recombinant N-terminal domain of riboflavin synthase.

Riboflavin synthase catalyzes the final step in the biosynthesis of riboflavin. Animals and humans lack this enzyme, whereas many bacteria and certain yeasts are absolutely dependent on endogenous riboflavin synthesis. Riboflavin synthase is therefore an attractive target for chemotherapy. The N-terminal domain of riboflavin synthase forms a dimer in solution and is capable of strongly binding riboflavin. It can serve as a model for the binding site of the native enzyme. Structural information obtained from this domain at high resolution will be helpful in the determination of the binding mode of riboflavin and thus for the development of antimicrobial drugs. Here, the crystallization and preliminary crystallographic analysis of the N-terminal domain of riboflavin synthase are reported. The crystals belong to the space group C222(1), with unit-cell parameters a = 50.3, b = 104.7, c = 85.3 A, alpha = beta = gamma = 90 degrees, and diffract to 2.6 A resolution.

Amino Acid Sequence↗
PubMed2001

Biosynthesis of pteridines. Stopped-flow kinetic analysis of GTP cyclohydrolase I.

GTP cyclohydrolase I catalyzes a mechanistically complex ring expansion affording dihydroneopterin triphosphate from GTP. The inherently slow enzyme reaction was studied under single turnover conditions monitored by multiwavelength ultraviolet spectroscopy. The spectroscopic data array was subjected to singular value decomposition and thereby shown to comprise six significant linearly independent optical processes. The data were fitted to a model of six consecutive unimolecular reaction steps where the first was considered to be reversible. The rate-limiting step was shown to occur rather late in the reaction sequence.

Catalysis↗