Biomedical subjects

Andreas Ziegler

Publications and source records attributed to Andreas Ziegler.

At least 55 records · Page 3Linked to original sources

PubMed2005

Haplotypes and haplotype-tagging single-nucleotide polymorphism: presentation Group 8 of Genetic Analysis Workshop 14.

Moderately dense maps of single-nucleotide polymorphism (SNP) markers across the human genome for both the simulated data set and data from the Collaborative Study of the Genetics of Alcoholism were available at Genetic Analysis Workshop 14 for the first time. This allowed examination of various novel and existing methods for haplotype analyses. Three contributors applied Mantel statistics in different ways for both linkage and association analysis by using the shared length between two haplotypes at a marker locus as a measure of genetic similarity. The results indicate that haplotype-sharing based on Mantel statistics can be a powerful approach and needs further methodological evaluation. Four contributors investigated haplotype-tagging SNP (htSNP) selection procedures, two contributors examined the use of multilocus haplotypes compared to single loci in association tests, and two contributors compared the accuracy of various methods for reconstructing haplotypes and estimating haplotype frequencies for both pedigree data and data from unrelated individuals. For all three different tasks, software packages and procedures gave similar results in regions of high linkage disequilibrium (LD). However, they were not as consistent in regions of moderate to low LD. One coalescence-based approach for estimating haplotype frequencies, coupled with a Markov chain Monte Carlo technique, outperformed the other haplotype frequency estimation methods in regions of low LD. In conclusion, regardless of the task, results were similar in chromosomal regions of high LD. However, based on the differing results observed here, methodological improvements are required for chromosomal regions of low to moderate LD.

Alcoholism↗

PubMed2005

Female choice and the MHC.

In animals, it is the female that typically selects a mating partner. This decision can occur before, during and after copulation. Here, recent evidence for the involvement of genes within the MHC in female choice is reviewed and the roles of MHC I and II antigens, various types of chemoreceptors, as well as MHC-encoded transcription factors, in securing an optimal genetic constitution of the offspring are discussed. Some particularly interesting and as yet unanswered questions are raised and some experiments that could provide deeper insight into the molecular mechanisms underlying female choice are suggested.

Animals↗

PubMed2005

Architecture of the organic matrix in the sternal CaCO3 deposits of Porcellio scaber (Crustacea, Isopoda).

Before the molt terrestrial isopods resorb calcium from the posterior cuticle and store it in large deposits within the first four anterior sternites. In Porcellio scaber the deposits consist of three structurally distinct layers consisting of amorphous CaCO3 (ACC) and an organic matrix that consists of concentric and radial elements. It is thought that the organic matrix plays a role in the structural organization of deposits and in the stabilization of ACC, which is unstable in vitro. In this paper, we present a thorough analysis of the ultrastructure of the organic matrix in the CaCO3 deposits using high-resolution field-emission scanning electron microscopy. The spherules and the homogeneous layer contain an elaborate organic matrix with similar structural organization consisting of concentric reticules and radial strands. The decalcification experiments reveal an inhomogeneous solubility of ACC within the spherules probably caused by variations in the stabilizing properties of matrix components. The transition between the three layers can be explained by changes in the number of spherule nucleation sites.

Animals↗

PubMed2005

Microscopical and functional aspects of calcium-transport and deposition in terrestrial isopods.

Terrestrial isopods (Crustacea) are excellent model organisms to study epithelial calcium-transport and the regulation of biomineralization processes. They molt frequently and resorb cuticular CaCO(3) before the molt to prevent excessive loss of Ca(2+) ions when the old cuticle is shed. The resorbed mineral is stored in CaCO(3) deposits within the ecdysial gap of the first four anterior sternites. After the molt, the deposits are quickly resorbed to mineralise the posterior part of the new cuticle. The deposits contain numerous small spherules composed of an organic matrix and amorphous CaCO(3), which has a high solubility and, therefore, facilitates quick mobilization of Ca(2+) and HCO(3)(-) ions. During the formation and resorption of the deposits large amounts of Ca(2+), HCO(3)(-) and H(+) are transported across the anterior sternal epithelial cells. Within the last years, various light and electron microscopical techniques have been used to characterize the CaCO(3) deposits and the cellular mechanisms involved in biomineralization. The work on the CaCO(3) deposits includes studies on the ultrastructure of the deposits, the sequence of events during deposit formation and dissolution, and the mineral composition of the sternal deposits. The differentiation of the anterior sternal epithelial cells and the mechanisms of epithelial ion transport required for the mineralization and demineralisation of the deposits was studied using various analytical light and electron microscopical techniques including polarized light microscopy, immunocytochemistry, electron microprobe analysis, electron energy loss spectroscopy and electron spectroscopic imaging. Comparative analysis of deposit morphology and the differentiation of the sternal epithelia provide information on the evolution of CaCO(3) deposit formation in relation to the degree of adaptation to terrestrial environments.

Animals↗

PubMed2005

No association between three xeroderma pigmentosum group C and one group G gene polymorphisms and risk of cutaneous melanoma.

Xeroderma pigmentosum (XP) patients exhibit a 1000-fold increased risk for developing skin cancers including malignant melanoma. We investigated the role of three variant alleles of the DNA repair gene XPC and one variant allele of the XPG gene in a hospital-based case-control study of 294 Caucasian patients from Germany with malignant melanoma and 375 healthy control individuals from the same area matched by sex. The polymorphisms G1580A (XPC exon 8; Arg492His), T1601C (XPC exon 8; Val499Ala), G2166A (XPC exon 10; Arg687Arg), and C3507G (XPG exon 15; Asp1104His) were not in linkage disequilibrium. The allele frequencies (cases: controls) were for 1580A 6.29%: 5.63%, for 1601C 79.08%: 78.28%, for 2166A 26.19%: 28.13%, and for 3507G 79.86%: 78.61%. We found no association of the homozygous 1580A, 1601C, 2166A, and 3507G genotypes with increased risks of melanoma: OR 1.254 (95% CI: 0.486-3.217), OR 1.108 (95% CI: 0.629-1.960), OR 0.817 (95% CI: 0.490-1.358), and OR 1.168 (95% CI: 0.670-2.044), respectively. Exploratory analyses of subgroups of melanoma patients compared to all controls indicated no association of these genotypes with increased risks for development of multiple primary melanomas (n = 28), a negative family history for melanoma (n = 277), melanomas in individuals with a low number of nevi (n = 273), melanomas in individuals older than 55 years (n = 142), and melanomas thicker than 1 mm (n = 126).

Amino Acid Substitution↗

PubMed2005

Specific amplification of cDNA ends (SPACE): a new tool for the analysis of rare transcripts and its application for the promoter analysis of killer cell receptor genes.

The expression control of activating and inhibitory killer cell Ig-like receptors (KIR) on natural killer (NK) cells is highly relevant for the initiation of NK cell mediated cytolysis and cytokine secretion. Transcription start points of nine human KIR genes from two Caucasian donors and the NK cell line NK3.3 were investigated. To overcome sensitivity problems due to the low abundance of the respective transcripts, a novel protocol, specific amplification of cDNA ends (SPACE) with superior specificity and sensitivity was applied. A total of 235 individual SPACE clones resulting from different KIR genes were analysed and revealed a series of transcription start sites tightly clustered between 10 and 60 bp upstream of the start codon. The comparison of the adjacent putative promoter region of the human, chimpanzee and macaque KIR genes revealed a very high conservation for almost all of the KIR family members. An inter-gene and inter-species comparative approach revealed transcription factor binding sites at regions of maximal homology for all primate KIR genes analysed.

5' Untranslated Regions↗

PubMed2004

Allele-dependent similarity between viral and self-peptide presentation by HLA-B27 subtypes.

Molecular mimicry is discussed as a possible mechanism that may contribute to the development of autoimmune diseases. It could also be involved in the differential association of the human major histocompatibility subtypes HLA-B(*)2705 and HLA-B(*)2709 with ankylosing spondylitis. These two subtypes differ only in residue 116 of the heavy chain (Asp in B(*)2705 and His in B(*)2709), but the reason for the differential disease association is not understood. Using x-ray crystallography, we show here that the viral peptide pLMP2 (RRRWRRLTV, derived from latent membrane protein 2 (residues 236-244) of Epstein-Barr virus) is presented by the B(*)2705 and B(*)2709 molecules in two drastically deviating conformations. Extensive structural similarity between pLMP2 and the self-peptide pVIPR (RRKWRRWHL, derived from vasoactive intestinal peptide type 1 receptor (residues 400-408)) is observed only when the peptides are presented by B(*)2705 because of a salt bridge between Arg(5) of both peptides and the subtype-specific heavy chain residue Asp(116). Combined with functional studies using pLMP2/pVIPR-cross-reactive cytotoxic T cell lines and clones, together with target cells presenting these peptides or a modified peptide analogue, our results reveal that a pathogen-derived peptide can exhibit major histocompatibility complex class I subtype-dependent, drastically distinct binding modes. Furthermore, the results demonstrate that molecular mimicry between pLMP2 and pVIPR in the HLA-B27 context is an allele-dependent property.

Alleles↗

PubMed2004

A major histocompatibility complex-peptide-restricted antibody and t cell receptor molecules recognize their target by distinct binding modes: crystal structure of human leukocyte antigen (HLA)-A1-MAGE-A1 in complex with FAB-HYB3.

Antibodies with T cell receptor-like specificity possess a considerable diagnostic and therapeutic potential, but the structural basis of the interaction between an antibody and an histocompatibility antigen has so far not been determined. We present here the crystal structure (at 2.15 A resolution) of the recombinant, affinity-matured human antibody fragment Fab-Hyb3 bound to the tumor-associated human leukocyte antigen (HLA)/peptide complex HLA-A1.MAGE-A1. Fab-Hyb3 employs a diagonal docking mode resembling that of T cell receptors. However, other than these natural ligands, the antibody uses only four of its six complementarity-determining regions for direct interactions with the target. It recognizes the C-terminal half of the MAGE-A1 peptide, the HLA-A1 alpha1-helix, and N-terminal residues of the alpha2-helix, accompanied by a large tilting angle between the two types of molecules within the complex. Interestingly, only a single hydrogen bond between a peptide side chain and Fab-Hyb3 contributes to the interaction, but large buried surface areas with pronounced shape complementarity assure high affinity and specificity for MAGE-A1. The HLA-A1.MAGE-A1.antibody structure is discussed in comparison with those of natural ligands recognizing HLA.peptide complexes.

Amino Acid Sequence↗

PubMed2004

Prevalence of familial pancreatic cancer in Germany.

Based on several case-control studies, it has been estimated that familial aggregation and genetic susceptibility play a role in up to 10% of patients with pancreatic cancer, although conclusive epidemiologic data are still lacking. Therefore, we evaluated the prevalence of familial pancreatic cancer and differences to its sporadic form in a prospective multicenter trial. A total of 479 consecutive patients with newly diagnosed, histologically confirmed adenocarcinoma of the pancreas were prospectively evaluated regarding medical and family history, treatment and pathology of the tumour. A family history for pancreatic cancer was confirmed whenever possible by reviewing the tumour specimens and medical reports. Statistical analysis was performed by calculating odds ratios, regression analysis with a logit-model and the Kaplan-Meier method. Twenty-three of 479 (prevalence 4.8%, 95% CI 3.1-7.1) patients reported at least 1 first-degree relative with pancreatic cancer. The familial aggregation could be confirmed by histology in 5 of 23 patients (1.1%, 95% CI 0.3-2.4), by medical records in 9 of 23 patients (1.9%, 95% CI 0.9-3.5) and by standardized interviews of first-degree relatives in 17 of 23 patients (3.5%, 95% CI 2.1-5.6), respectively. There were no statistical significant differences between familial and sporadic pancreatic cancer cases regarding sex ratio, age of onset, presence of diabetes mellitus and pancreatitis, tumour histology and stage, prognosis after palliative or curative treatment as well as associated tumours in index patients and families, respectively. The prevalence of familial pancreatic cancer in Germany is at most 3.5% (range 1.1-3.5%) depending on the mode of confirmation of the pancreatic carcinoma in relatives. This prevalence is lower than so far postulated in the literature. There were no significant clinical differences between the familial and sporadic form of pancreatic cancer.

Adult↗

PubMed2004

Reduction of vascular noradrenaline sensitivity by AT1 antagonists depends on functional sympathetic innervation.

Blockade of angiotensin II type-1 (AT1) receptors has been shown to reduce the magnitude of the blood pressure response to noradrenaline in pithed rats via an unidentified mechanism. Dose-response curves were established for the noradrenaline-induced (10(-12) to 10(-7) mol/kg) increase of diastolic blood pressure in pithed rats treated with tubocurarine, propranolol, and atropine. Candesartan (1 mg/kg) increased the ED50 of the noradrenaline response (1.3+/-0.1 nmol/kg) up to 20-fold. Vasopressor responsiveness to noradrenaline was attenuated specifically, whereas the vasopressin-induced increase in diastolic blood pressure was maintained. Specific involvement of AT1 receptors was confirmed by equivalent actions of losartan. Blockade of norepinephrine transporter or alpha2-adrenoceptors using desipramine or rauwolscine reduced the losartan-induced shifts in the ED50 values of noradrenaline by 63% and 21%, respectively. Combined blockade of norepinephrine transporter and alpha2-adrenoceptors eliminated the influence of losartan on noradrenaline sensitivity (ED50 5.5+/-1.3 versus 5.6+/-1.2 nmol/kg), a result also observed after sympathetic denervation by reserpine (ED50 7.1+/-0.8 versus 7.8+/-0.8 nmol/kg). Our experiments show that the reduction of vascular noradrenaline sensitivity by AT1 blockade is dependent on the intact functioning of both neuronal noradrenaline uptake via norepinephrine transporter and presynaptic alpha2-mediated autoinhibition, exclusively provided by the sympathetic innervation. These newly identified mechanisms may contribute to the antihypertensive and protective actions of AT1 blockers.

Adrenergic alpha-Antagonists↗

PubMed2004

Extended single nucleotide polymorphism and haplotype analysis of the elastin gene in Caucasians with intracranial aneurysms provides evidence for racially/ethnically based differences.

BACKGROUND: There is growing evidence that genetic variants have an impact on the pathogenesis of intracranial aneurysm (IA). Recently, the genetic locus around the elastin gene (7q11) has been identified as linked to IA in a Japanese population. Our aim was to confirm these results in Caucasian populations. METHODS: We conducted a case-control study in 120 Caucasian patients with IA and 172 controls to investigate 8 single nucleotide polymorphisms (SNPs) and various haplotypes within the elastin gene, which were frequently found and associated with the phenotype in the Japanese populations. Real-time PCR and melting curve analysis were used for the detection of genotypes. RESULTS: Allele frequencies and genotypes were equally distributed between Caucasian cases and controls. We failed to identify haplotypes that are associated with the phenotype in our population, which is in contrast to the Japanese study. However, allele frequencies in control populations differ between Caucasians and Japanese. CONCLUSIONS: We found no association between SNPs and haplotypes of the elastin gene and the occurrence of IA in our Caucasian populations. However, our data provide strong evidence for racial/ethnic differences in the association of SNP and specific haplotypes of the elastin gene with the phenotype. There might be other genetic variants of the elastin gene associated with IA in Caucasians.

Adult↗

PubMed2004

GEE approaches to marginal regression models for medical diagnostic tests.

The evaluation of a new medical diagnostic test may focus on two different scientific questions: (1). The new test may replace an existing one because of lower cost or higher validity. A related question would be the selection of the 'best' test(s) from a bundle of new or established measurements. (2). The new test may be used supplementary to other new or established procedures. In a recent publication, Leisenring and co-workers (Stat Med 1997; 16:1263-1281) developed a general marginal regression model for comparisons of diagnostic tests focussing on question (1). i.e. on the selection of the 'best' procedure. They applied the GEE approach of Liang and Zeger (Biometrika 1987; 73:13-22) to adjust for the correlation of data as a nuisance parameter. Using the general framework provided by Leisenring et al., we extend their approach and apply the GEE methodology to question (2). i.e. to the investigation of which of several diagnostic tests should be used supplementary to each other. We analyse data from a longitudinal study concerning pathogenesis, diagnosis and long-term course of the eye disease glaucoma. We find a dependence of the correlation structure of several diagnostic measurements on the severity of the disease. This result may be useful in clinical applications as regards the selection of subsets of diagnostic measurements in individual diagnostic processes but also in investigations concerning the relationship of the pathogenic process and the rationales of the different diagnostic procedures.

Biometry↗

PubMed2004

Differential peptide dynamics is linked to major histocompatibility complex polymorphism.

Peptide presentation by major histocompatibility complex (MHC) molecules is of central importance for immune responses, which are triggered through recognition of peptide-loaded MHC molecules (pMHC) by cellular ligands such as T-cell receptors (TCR). However, a unifying link between structural features of pMHC and cellular responses has not been established. Instead, pMHC/TCR binding studies suggest conformational and/or flexibility changes of the binding partners as a possible cause of differential T-cell stimulation, but information on real-time dynamics is lacking. We therefore probed the real-time dynamics of a MHC-bound nonapeptide (m9), by combining time-resolved fluorescence depolarization and molecular dynamics simulations. Here we show that the nanosecond dynamics of this peptide presented by two human MHC class I subtypes (HLA-B*2705 and HLA-B*2709) with differential autoimmune disease association varies dramatically, despite virtually identical crystal structures. The peptide dynamics is linked to the single, buried polymorphic residue 116 in the peptide binding groove. Pronounced peptide flexibility is seen only for the non-disease-associated subtype HLA-B*2709, suggesting an entropic control of peptide recognition. Thermodynamic data obtained for two additional peptides support this hypothesis.

Entropy↗

PubMed2004

Water-soluble terpolymer-mediated calcium carbonate crystal modification.

The structure of the polymeric substrate plays an important role in the nucleation of calcium carbonate crystals. In this study a synthetic water-soluble poly(acrylamide-co-2-acrylamido-2-methyl-1-propane sodium sufonate-co-n-vinyl pyrrolidone) was found to be a substrate favoring the nucleation of polymorphs of calcium carbonate crystals under specific experimental conditions. Morphological characterization of the polymorphs was done using atomic force microscopy, scanning electron microscopy, energy dispersive spectroscopy, FTIR analysis, and X-ray diffraction. If calcium carbonate is precipitated in the presence of terpolymer, a remarkable increase in nucleation density (number of crystals per unit area) was observed. Stacked crystals of rhombohedral morphology that formed may be due to the presence of sodium sulfonate groups on the terpolymer. However, in the presence of poly-L-aspartic acid, almost all crystals are hollow and have needlelike or plate like morphology was formed. This change in calcium carbonate morphology can be explained by the variation of the polymer conformation, if poly- L-aspartic acid is present.

Journal Article↗

PubMed2004

Variations in the genes encoding the peroxisome proliferator-activated receptors alpha and gamma in psoriasis.

The three peroxisome proliferator-activated receptor (PPAR) subtypes alpha, delta (beta), and gamma belong to the group of nuclear receptors that act as ligand-activated transcription factors. Recently, expression of PPAR alpha and gamma in keratinocytes has been demonstrated, and ligands of PPAR alpha and gamma have been found to enhance epidermal maturation and protect against cutaneous inflammation. There is evidence for a possible role of PPARs in psoriasis, as the expression of PPAR alpha and gamma is decreased in lesional skin and treatment with PPAR gamma agonists improves psoriatic keratinocyte pathology in vitro and in vivo. We performed a case-control study to search for possible associations between variations in the genes encoding PPAR alpha and gamma and psoriasis. Seven variations in these genes were analyzed in 192 patients with chronic plaque-type psoriasis and 330 healthy controls by PCR-based methods. No association between any of the investigated PPAR variants and psoriasis was found. Our findings argue against a significant contribution of the investigated PPAR variations to the genetic basis of psoriasis.

Adult↗

PubMed2004

Dual, HLA-B27 subtype-dependent conformation of a self-peptide.

The products of the human leukocyte antigen subtypes HLA-B*2705 and HLA-B*2709 differ only in residue 116 (Asp vs. His) within the peptide binding groove but are differentially associated with the autoimmune disease ankylosing spondylitis (AS); HLA-B*2705 occurs in AS-patients, whereas HLA-B*2709 does not. The subtypes also generate differential T cell repertoires as exemplified by distinct T cell responses against the self-peptide pVIPR (RRKWRRWHL). The crystal structures described here show that pVIPR binds in an unprecedented dual conformation only to HLA-B*2705 molecules. In one binding mode, peptide pArg5 forms a salt bridge to Asp116, connected with drastically different interactions between peptide and heavy chain, contrasting with the second, conventional conformation, which is exclusively found in the case of B*2709. These subtype-dependent differences in pVIPR binding link the emergence of dissimilar T cell repertoires in individuals with HLA-B*2705 or HLA-B*2709 to the buried Asp116/His116 polymorphism and provide novel insights into peptide presentation by major histocompatibility antigens.

Amino Acid Sequence↗

PubMed2004

Analysis of SNPs in pooled DNA: a decision theoretic model.

Systematic analysis of the genetic background of complex diseases using single nucleotide polymorphisms (SNPs) affords a tremendous amount of genotypings. To reduce the amount of genotypings necessary and hence the overall cost of a case-control study with SNPs, the genotyping is often performed in two stages. In the first, the DNA of all cases and all controls are mixed into two pools and genotyped for each SNP. The frequency of both alleles is determined in both pooled DNA samples. If different frequencies are observed in the pools of cases and controls, genotyping is performed individually in the second stage and analyzed conventionally. However, so far no well-founded algorithm is available to guide the decision on whether to genotype a SNP individually. In this report, an approach is introduced for the decision on individual genotyping based on the results from pooled DNA. The analysis is modeled as a decision process with the specific goal to decide on whether to genotype a specific SNP individually. For a given situation, the resulting decision criteria are aimed to be optimal for those conducting the study. Different loss functions and decision rules are presented. Using Monte-Carlo simulations, we show that for a given situation, the genotyping rates and hence the costs can be reduced remarkably while maintaining acceptable overall error rates.

Case-Control Studies↗

PubMed2004

Gene map of the extended human MHC.

The major histocompatibility complex (MHC) is the most important region in the vertebrate genome with respect to infection and autoimmunity, and is crucial in adaptive and innate immunity. Decades of biomedical research have revealed many MHC genes that are duplicated, polymorphic and associated with more diseases than any other region of the human genome. The recent completion of several large-scale studies offers the opportunity to assimilate the latest data into an integrated gene map of the extended human MHC. Here, we present this map and review its content in relation to paralogy, polymorphism, immune function and disease.

Autoimmune Diseases↗