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Biomedical subjects

D Walther

Publications and source records attributed to D Walther.

At least 19 recordsLinked to original sources
PubMed2001

Reversible fixation of carbon dioxide at nickel(0) centers: a route for large organometallic rings, dimers, and tetramers.

The reaction between bis(cycloocta-1,5-diene)nickel(0), carbon dioxide and benzaldehyde-N-furfurylideneimine (A) in 1,4-dioxane or THF results in the formation of the 24-membered organometallic macrocycles of the type [(A)Ni(-CH(R1)-N(R2)-COO-)]6(solv)n (R1: phenyl, R2: furfurylidene, solv: 1,4-dioxane in 1a, THF in 1b). According to the X-ray analyses, six monomeric nickelacyclic units are connected through six Ni-mu2-OCO-Ni bridges in these macrocycles. The cavities of the metallomacrocycles (diameter: 9.410(1) A in 1a, 9.250(1) A in 1b) each contain one solvent molecule. Reaction of 1b with Me3P results in the displacement of the peripheral ligands A by the phosphine to form the 24-membered organometallic macrocycle 1c. Both 1a and 1b isomerize in benzene to form the dimeric complex [(A)Ni(-CH(R1)-N(R2)-COO-)]2(solv)n (2). The X-ray crystal structure reveals that 2 consists of the same monomeric units as found in 1a and 1b. However two Ni-mu2-O-Ni bonds link the carboxylato groups. The solvent-dependent isomerization of 1b yielding 2 is a reversible reaction. Furthermore, the macrocycle 1b partially eliminates carbon dioxide above 20 degrees C, followed by elimination of half of the monodentately coordinated Schiff base ligands to form the planar tetrameric complex 6. This is also a reversible process.

Carbon Dioxide↗
PubMed2001

Polysubstance abuse-vulnerability genes: genome scans for association, using 1,004 subjects and 1,494 single-nucleotide polymorphisms.

Strong genetic contributions to drug abuse vulnerability are well documented, but few chromosomal locations for human drug-abuse vulnerability alleles have been confirmed. We now identify chromosomal markers whose alleles distinguish drug abusers from control individuals in each of two samples, on the basis of pooled-sample microarray and association analyses. Reproducibly positive chromosomal regions defined by these markers in conjunction with previous results were especially unlikely to have been identified by chance. Positive markers identify the alcohol dehydrogenase (ADH) locus, flank the brain-derived neurotropic factor (BDNF) locus, and mark seven other regions previously linked to vulnerability to nicotine or alcohol abuse. These data support polygenic contributions of common allelic variants to polysubstance abuse vulnerability.

Adult↗
PubMed2001

Dopaminergic mRNA expression in the intact substantia nigra of unilaterally 6-OHDA-lesioned and grafted rats: an in situ hybridization study.

The present study was performed to investigate the influence of intrastriatal fetal mesencephalic grafts on dopaminergic mRNA expression in the non-lesioned substantia nigra pars compacta of unilaterally 6-hydroxydopamine-lesioned rats. The expression of dopamine transporter mRNA, synaptic vesicular monoamine transporter mRNA and tyrosine hydroxylase mRNA was assessed in adjacent cryostat sections using in situ hybridization. Rotational behavior induced by apomorphine and amphetamine as well as hybridization of striatal sections cut at the grafting coordinates were used to prove the functional recovery and the presence of grafted cells, respectively. After grafting, the number of rotations was decreased and hybridization signals overlying cells in the grafted striatum were detected. Mean grain densities overlying labeled neurons in the substantia nigra pars compacta of grafted rats were compared to those of shamgrafted rats and revealed differential expression of dopamine transporter mRNA, whereas synaptic vesicular monoamine transporter mRNA and tyrosine hydroxylase mRNA expression showed no difference. The results will be discussed in relation to previous in vitro and in vivo studies suggesting a reduction of functional dopamine transporter molecules in the contralateral striatum.

Animals↗
PubMed2001

Basecalling with LifeTrace.

A pivotal step in electrophoresis sequencing is the conversion of the raw, continuous chromatogram data into the actual sequence of discrete nucleotides, a process referred to as basecalling. We describe a novel algorithm for basecalling implemented in the program LifeTrace. Like Phred, currently the most widely used basecalling software program, LifeTrace takes processed trace data as input. It was designed to be tolerant to variable peak spacing by means of an improved peak-detection algorithm that emphasizes local chromatogram information over global properties. LifeTrace is shown to generate high-quality basecalls and reliable quality scores. It proved particularly effective when applied to MegaBACE capillary sequencing machines. In a benchmark test of 8372 dye-primer MegaBACE chromatograms, LifeTrace generated 17% fewer substitution errors, 16% fewer insertion/deletion errors, and 2.4% more aligned bases to the finished sequence than did Phred. For two sets totaling 6624 dye-terminator chromatograms, the performance improvement was 15% fewer substitution errors, 10% fewer insertion/deletion errors, and 2.1% more aligned bases. The processing time required by LifeTrace is comparable to that of Phred. The predicted quality scores were in line with observed quality scores, permitting direct use for quality clipping and in silico single nucleotide polymorphism (SNP) detection. Furthermore, we introduce a new type of quality score associated with every basecall: the gap-quality. It estimates the probability of a deletion error between the current and the following basecall. This additional quality score improves detection of single basepair deletions when used for locating potential basecalling errors during the alignment. We also describe a new protocol for benchmarking that we believe better discerns basecaller performance differences than methods previously published.

Algorithms↗
PubMed2000

Solution structural studies and low-resolution model of the Schizosaccharomyces pombe sap1 protein.

Sap1 is a DNA-binding protein involved in controlling the mating type switch in fission yeast Schizosaccharomyces pombe. In the absence of any significant sequence similarity with any structurally known protein, a variety of biophysical techniques has been used to probe the solution low-resolution structure of the sap1 protein. First, sap1 is demonstrated to be an unusually elongated dimer in solution by measuring the translational diffusion coefficient with two independent techniques: dynamic light-scattering and ultracentrifugation. Second, sequence analysis revealed the existence of a long coiled-coil region, which is responsible for dimerization. The length of the predicted coiled-coil matches estimates drawn from the hydrodynamic experimental behaviour of the molecule. In addition, the same measurements done on a shorter construct with a coiled-coil region shortened by roughly one-half confirmed the localization of the long coiled-coil region. A crude T-shape model incorporating all these information was built. Third, small-angle X-ray scattering (SAXS) of the free molecule provided additional evidence for the model. In particular, the P(r) curve strikingly demonstrates the existence of long intramolecular distances. Using a novel 3D reconstruction algorithm, a low resolution 3D model of the protein has been independently constructed that matches the SAXS experimental data. It also fits the translation diffusion coefficients measurements and agrees with the first T-shaped model. This low-resolution model has clearly biologically relevant new functional implications, suggesting that sap1 is a bifunctional protein, with the two active sites being separated by as much as 120 A; a tetrapeptide repeated four times at the C terminus of the molecule is postulated to be of utmost functional importance.

Algorithms↗
PubMed2000

Co-evolution of proteins with their interaction partners.

The divergent evolution of proteins in cellular signaling pathways requires ligands and their receptors to co-evolve, creating new pathways when a new receptor is activated by a new ligand. However, information about the evolution of binding specificity in ligand-receptor systems is difficult to glean from sequences alone. We have used phosphoglycerate kinase (PGK), an enzyme that forms its active site between its two domains, to develop a standard for measuring the co-evolution of interacting proteins. The N-terminal and C-terminal domains of PGK form the active site at their interface and are covalently linked. Therefore, they must have co-evolved to preserve enzyme function. By building two phylogenetic trees from multiple sequence alignments of each of the two domains of PGK, we have calculated a correlation coefficient for the two trees that quantifies the co-evolution of the two domains. The correlation coefficient for the trees of the two domains of PGK is 0. 79, which establishes an upper bound for the co-evolution of a protein domain with its binding partner. The analysis is extended to ligands and their receptors, using the chemokines as a model. We show that the correlation between the chemokine ligand and receptor trees' distances is 0.57. The chemokine family of protein ligands and their G-protein coupled receptors have co-evolved so that each subgroup of chemokine ligands has a matching subgroup of chemokine receptors. The matching subfamilies of ligands and their receptors create a framework within which the ligands of orphan chemokine receptors can be more easily determined. This approach can be applied to a variety of ligand and receptor systems.

Chemokines↗
PubMed2000

Detection of C-type natriuretic peptide in fetal circulation.

C-type natriuretic peptide (CNP) belongs to the natriuretic peptide family that plays an important role in the control of blood pressure, renal function and volume homeostasis. In contrast to the atrial natriuretic peptide and brain natriuretic peptide, CNP acts in an autocrine/paracrine fashion and is considered to be the endothelial component of the natriuretic peptide system. CNP has a high expression and tissue-specific regulation in reproductive organs. Using a radio-immunoassy for CNP-22 we measured for the first time CNP in fetal blood. Samples were taken by cordocentesis in a group of fetuses with rhesus isoimmunisation (10.74 +/- 2.81 pg/ml), fetuses with rhesus isoimmunisation after intravascular transfusion (10.03 +/- 4.01 pg/ml) and a group with structural anomalies (12.9 +/- 5.67 pg/ml). A group of healthy fetuses was used as controls (11.64 +/- 4.32 pg/ml). In contrast to ANP, the fetal CNP-plasma concentrations remain stable in the investigated fetal diseases and after volume load during intravascular transfusion. Moreover, fetal CNP-plasma levels are higher than previously measured maternal concentrations in normal pregnancies. Therefore, the fetus expresses CNP independently of the maternal circulation.

Blood Transfusion, Intrauterine↗
PubMed1999

A molecular scanner to automate proteomic research and to display proteome images.

Identification and characterization of all proteins expressed by a genome in biological samples represent major challenges in proteomics. Today's commonly used high-throughput approaches combine two-dimensional electrophoresis (2-DE) with peptide mass fingerprinting (PMF) analysis. Although automation is often possible, a number of limitations still adversely affect the rate of protein identification and annotation in 2-DE databases: the sequential excision process of pieces of gel containing protein; the enzymatic digestion step; the interpretation of mass spectra (reliability of identifications); and the manual updating of 2-DE databases. We present a highly automated method that generates a fully annoated 2-DE map. Using a parallel process, all proteins of a 2-DE are first simultaneously digested proteolytically and electro-transferred onto a poly(vinylidene difluoride) membrane. The membrane is then directly scanned by MALDI-TOF MS. After automated protein identification from the obtained peptide mass fingerprints using PeptIdent software (http://www.expasy.ch/tools/peptident.html + ++), a fully annotated 2-D map is created on-line. It is a multidimensional representation of a proteome that contains interpreted PMF data in addition to protein identification results. This "MS-imaging" method represents a major step toward the development of a clinical molecular scanner.

Automation↗
PubMed1999

An endocytic pathway essential for renal uptake and activation of the steroid 25-(OH) vitamin D3.

Steroid hormones may enter cells by diffusion through the plasma membrane. However, we demonstrate here that some steroid hormones are taken up by receptor-mediated endocytosis of steroid-carrier complexes. We show that 25-(OH) vitamin D3 in complex with its plasma carrier, the vitamin D-binding protein, is filtered through the glomerulus and reabsorbed in the proximal tubules by the endocytic receptor megalin. Endocytosis is required to preserve 25-(OH) vitamin D3 and to deliver to the cells the precursor for generation of 1,25-(OH)2 vitamin D3, a regulator of the calcium metabolism. Megalin-/- mice are unable to retrieve the steroid from the glomerular filtrate and develop vitamin D deficiency and bone disease.

Animals↗
PubMed1999

Two-dimensional electrophoresis resources available from ExPASy.

This paper describes the set of two-dimensional electrophoresis (2-DE) resources currently available from the ExPASy proteomics Web server. These resources include the SWISS-2DPAGE database, 2-DE software packages, 2-DE technical and educational services, as well as indexes and search engines for 2-DE related sites over the Internet.

Databases, Factual↗
PubMed1999

C-type natriuretic peptide levels in women with gestational hypertension and preeclampsia.

OBJECTIVE: To measure plasma levels of C-type natriuretic peptide in women with normal pregnancies and those complicated by gestational hypertension and preeclampsia. METHODS: We collected venous plasma samples from 20 women with normal pregnancies, 15 with gestational hypertension, and nine with preeclampsia. Gestational ages ranged from 26-39 weeks. We measured C-type natriuretic peptide concentrations by radioimmunoassay. Statistical comparisons were made by one-way analysis of variance and Tukey test. RESULTS: The mean plasma concentration of C-type natriuretic peptide in the women with normal pregnancy was 7.1 +/-2.5 pg/mL, in those with gestational hypertension 9.6+/-4.2 pg/mL, and in those with preeclampsia 8.1+/-2.4 pg/mL. There were no statistically significant differences between groups. The statistical power to detect a difference of 3 pg/mL at the 5% significance level was 78% for the group with gestational hypertension and 64% for the preeclamptic group. CONCLUSION: Our results suggest that C-type natriuretic peptide plasma levels are not significantly different in normal pregnancies and those complicated by gestational hypertension or preeclampsia. In hypertensive pregnancy disorders, C-type natriuretic peptide showed a distinct course compared with atrial natriuretic peptide and brain natriuretic peptide.

Adult↗
PubMed1999

Conformational attractors on the Ramachandran map.

Frequency distributions of protein backbone dihedral angles phi and psi have been analyzed systematically for their apparent correlation with various crystallographic parameters, including the resolution at which the protein structures had been determined, the R factor and the free R factor, and the results have been displayed in novel differential Ramachandran maps. With improved sensitivity compared with conventionally derived heuristic Ramachandran maps, such differential maps automatically reveal conformational 'attractors' to which phi/psi distributions converge as the crystallographic resolution improves, as well as conformations tied specifically to low-resolution structures. In particular, backbone angular combinations associated with residues in alpha--helical conformation show a pronounced consolidation with substantially narrowed phi/psi distributions at higher (better) resolution. Convergence to distinct conformational attractors was also observed for all other secondary-structural types and random-coil conformations. Similar resolution-dependent phi/psi evolutions were obtained for different crystallographic refinement packages, documenting the absence of any significant artificial biases in the refinement programs investigated here. A comparison of differential Ramachandran maps derived for the R factor and the free R factor as independent parameters proved the better suitability of the free R factor for structure-quality assessment. The resolution-based differential Ramachandran map is available as a reference for comparison with actual protein structural data under WebMol, a Java-based structure viewing and analysis program (http://www. cmpharm.ucsf.edu/cgi-bin/webmol.pl).

Crystallography↗
PubMed1998

Helix-helix packing angle preferences for finite helix axes.

Recently, James Bowie addressed the question of how to normalize correctly the distribution of observed helix-helix packing angles in proteins (Bowie, Nature Struct. Biol. 4:915-917, 1997). A hitherto unrealized yet significant bias toward crossed packing angles was revealed. However, the derived random reference distribution of packing angles requires that helices have to be assumed as infinite in length. Here, we complement Bowie's analysis by consideration of the more realistic case where helices are of finite length. As a result, the statistical bias toward near perpendicular packings appears to be even stronger.

Models, Molecular↗
PubMed1998

Absence of phospholipase A2 activity in genital Mycoplasma hominis.

The clinical relevance of vaginal colonization with Mycoplasma hominis (M hominis) as a cause of prematurity is doubtful. One of the possible pathways which could explain the role of M hominis in the induction of preterm labour is an increased synthesis of prostaglandins by a phospholipase A2 activity. The aim of this study was to prove whether M hominis secrets proteins with a PLA2 activity and to test whether there are strain differences in the enzyme activity between M hominis isolated from women with normal pregnancy and those with preterm labour. Using specific radio-immunoassay we could not measure any PLA2 activity in the supernatant of all investigated M hominis strains. We exclude the mechanism of induction of preterm labour by M hominis via an increased prostaglandin synthesis. Our findings make a relation between vaginal colonization with M hominis and prematurity unlikely.

Female↗
PubMed1998

Detection of C-type natriuretic peptide in normal pregnancy.

C-type natriuretic peptide (CNP) is a recently identified member of the family of natriuretic peptides that plays an important role in the regulation of blood pressure, renal function and volume homeostasis. Its effects are mainly hypotensive and natriuretic. CNP is also considered to be an autocrine/paracrine regulator of the endothelium as well as a neuropeptide. Little is known about its role as a circulating substance. There are only few data of CNP plasma levels and changes in disease. Using a highly specific radioimmunoassay we established for the first time CNP plasma levels of normal pregnancies 5.9 +/- 1.5-8.6 +/- 2.1 pg/ml) and a non-pregnant control group (8.1 +/- 1.7 pg/ml). In contrast to atrial natriuretic peptide and brain natriuretic peptide we have not found significant differences of the plasma levels during normal pregnancy and no difference to the non-pregnant control group.

Atrial Natriuretic Factor↗
PubMed1997

Identification of a prion protein epitope modulating transmission of bovine spongiform encephalopathy prions to transgenic mice.

There is considerable concern that bovine prions from cattle with bovine spongiform encephalopathy (BSE) may have been passed to humans (Hu), resulting in a new form of Creutzfeldt-Jakob disease (CJD). We report here the transmission of bovine (Bo) prions to transgenic (Tg) mice expressing BoPrP; one Tg line exhibited incubation times of approximately 200 days. Like most cattle with BSE, vacuolation and astrocytic gliosis were confined in the brainstems of these Tg mice. Unexpectedly, mice expressing a chimeric Bo/Mo PrP transgene were resistant to BSE prions whereas mice expressing Hu or Hu/Mo PrP transgenes were susceptible to Hu prions. A comparison of differences in Mo, Bo, and Hu residues within the C terminus of PrP defines an epitope that modulates conversion of PrPC into PrPSc and, as such, controls prion transmission across species. Development of susceptible Tg(BoPrP) mice provides a means of measuring bovine prions that may prove critical in minimizing future human exposure.

Animals↗
PubMed1997

Solution structure of the spectrin repeat: a left-handed antiparallel triple-helical coiled-coil.

Cytoskeletal proteins belonging to the spectrin family have an elongated structure composed of repetitive units. The three-dimensional solution structure of the 16th repeat from chicken brain alpha-spectrin (R16) has been determined by NMR spectroscopy and distance geometry-simulated annealing calculations. We used a total of 1035 distance restraints, which included 719 NOE-based values obtained by applying the ambiguous restraints for iterative assignment (ARIA) method. In addition, we performed a direct refinement against 1H-chemical shifts. The final ensemble of 20 structures shows an average RMSD of 1.52 A from the mean for the backbone atoms, excluding loops and N and C termini. R16 is made up of three antiparallel alpha-helices separated by two loops, and folds into a left-handed coiled-coil. The basic unit of spectrin is an antiparallel heterodimer composed of two homologous chains, beta and alpha. These assemble a tetramer via a mechanism that relies on the completion of a single repeat by association of the partial repeats located at the C terminus of the beta-chain (two helices) and at the N terminus of the alpha-chain (one helix). This tetramer is the assemblage able to cross-link actin filaments. Model building by homology of the "tetramerization" repeat from human erythrocyte spectrin illuminates the possible role of point mutations which cause hemolytic anemias.

Amino Acid Sequence↗