Combined DNA and protein alignment.
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Algorithms↗
Biomedical subjects
J Hein
Publications and source records attributed to J Hein.
A maximum-likelihood approach to analyzing nonoverlapping and overlapping reading frames.
A model is presented for sequence evolution on the basis of which one can analyze combinations of noncoding, singly coding, and multiply coding regions of aligned homologous DNA sequences. It is a generalization of Kimura's (J. Mol. Evol. 16:111-120, 1980) and Li et al.'s (J. Mol. Evol. 36:96-99, 1985) transition-transversion models with selection on replacement substitutions. Based on a hierarchy of hypotheses, one will be able to estimate selection factors and transition and transversion distances for different combinations of regions ranging from many regions, each with their private set of parameters, to one set of parameters for all regions. The method is demonstrated on two aligned HIV1 retroviruses.
Amino Acid Sequence↗
Low resolution DNA typing of the HLA-B5 cross-reactive group by nested PCR-SSP.
We have established a DNA typing system for the HLA-B5 serologically cross-reactive group (CREG) by means of a two-step PCR amplification with nested sequence-specific primers (nPCR-SSP). The present study provides a low resolution definition of the HLA-B5 CREG, i.e. identifying polymorphism equivalent to serology. Two different primer combinations allow group-specific amplification of all HLA-B5 CREG alleles and other related HLA class I alleles from genomic DNA. The amplified DNA is subjected to a second amplification step using eleven nested primer pairs. This assay permits the detection of the HLA-B5 CREG specificities B35, B51, B52, B53, and B7801 in all homozygous and heterozygous combinations. Sensitivity and specificity as judged by a blind quality control study investigating a reference panel (n = 50) is 100%. Extension of this approach should allow rapid DNA typing of all serologically defined HLA-B specificities by nPCR-SSP.
Alleles↗
An algorithm combining DNA and protein alignment.
An algorithm is presented that aligns two DNA sequences minimizing the overall amount of evolution that the associated proteins have experienced. It is generalized to minimizing a weighted average of protein and DNA evolution.
Algorithms↗
Antibody response of rabbits and cystic fibrosis patients to an alginate-specific outer membrane protein of a mucoid strain of Pseudomonas aeruginosa.
The aim of this work was to study the immunogenicity of an outer membrane (OM) protein (AlgE; 54 kDa) which is produced solely by mucoid, i.e. alginate-producing strains of P. aeruginosa. The source of AlgE used for our study was the mucoid strain CF3/M1 originally isolated from sputum of a cystic fibrosis (CF) patient. The purified non-denatured protein served as antigen to raise polyclonal monospecific anti-AlgE antibodies in rabbits and to assay sera from 41 cystic fibrosis (CF) patients for anti-AlgE antibodies. According to clinical protocols the sputa of 22 CF patients were positive for P. aeruginosa, 18 were negative and one case was unknown. Our ELISA studies showed that high titers of anti-AlgE antibodies (IgG) corresponded well with the infection status of the CF patients. None of 23 control sera derived from healthy volunteers contained significant levels of anti-AlgE antibodies. Thus the ELISA should be considered as a sensitive diagnostic tool for the early detection of mucoid P. aeruginosa infections in CF patients. Furthermore, we suggest to include AlgE in a multicomponent experimental vaccine for potential protection of non-colonized CF patients from colonization with mucoid P. aeruginosa.
Animals↗
Genomic alignment.
As sequencing techniques become increasingly efficient, the average length of a sequence is bound to grow. Traditional sequence-comparison algorithms can either compare DNA or protein, but not a mixture, which is actually a common situation. Most obtained DNA sequences contain coding regions, and it is more reliable to compare the coding regions as protein than just as DNA. A heuristic algorithm is presented that can compare DNA with both coding and noncoding regions, but that also can compare multiple reading frames and determine which exons are homologous. A program, GenA1 (Genomic Alignment), was developed that implements the algorithm. Its use is demonstrated on two retroviruses.
Algorithms↗
[Superselective embolization of the facial branches of the external carotid artery].
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Angiography, Digital Subtraction↗
[Long-term treatment of mucoviscidosis. Results with a microencapsulated pancreatic enzyme preparation].
METHODS: In 30 children suffering from cystic fibrosis, the long-term effect (2 years) of treatment with an acid-protected micro-encapsulated pancreatin preparation was investigated in comparison with prior enzyme replacement with a conventional pancreatin preparation given over a period of years. Assessment criteria was the development of body length and body weight, lung function (vital capacity, FEF1) and the Shwachman-Kulczycki score. RESULTS: The therapeutic efficacy of the acid-protected micro-encapsulated preparation is considered to be higher than that of conventional preparations, since the same effect was achieved with only one-quarter to one-third of the pancreatin dose of the conventional preparation (average: 6.5 +/- 2.9 g pancreatin/d, as compared with 1.6 +/- 0.6 g pancreatin in the case of the acid-protected micro-encapsulated preparation). However, none of the clinical parameters investigated revealed any significant changes during the course of the observation period. The results indicate that, if the general state of health and nutritional status of patients with cystic fibrosis is to be improved further, in addition to a special diet, attempts must be made to achieve further optimization of the intraluminal digestion.
Adolescent↗
Prevalence of cystic fibrosis mutations in the East German population.
A representative multicenter cystic fibrosis (CF) mutation analysis on about half of all known cystic fibrosis patients of the 5 East German Länder is reported. Analyses for 17 mutations, among them Delta F508, R553X, G542X, S549R,N,I, G551D, S1255X, R347P,H, and Y122X, were performed. As expected, the delta F508 mutation in exon 10 of the CFTR gene is the major gene alteration causing CF in our patients. However, in comparison to studies from Western Germany, a significantly lower percentage of just over 60% is found in our patients, resembling data obtained from slavonic populations. The severe phenotype of cystic fibrosis is most frequently associated with homozygosity for the delta F508 mutation. No particular allele association could be found with the intermediate and mild phenotypes of this disease. The next most frequent of the investigated mutations is R553X (13.3% of non-delta F chromosomes) followed by R347P (9.2%) and G542X (4.4%).
Cystic Fibrosis↗
Effect of inhaled methanol on pituitary and testicular hormones in chamber acclimated and non-acclimated rats.
Two experiments were conducted in which the acute effects of inhaled methanol on serum hormones associated with reproductive function in the male rat were evaluated. In the first experiment, rats exposed to methanol (0, 200, 5000 and 10,000 ppm) for 6 h were killed at the end of the exposure period (6 h) or the following morning (24 h). Also, because the process of exposure itself could modify neuroendocrine function, the effect of the handling associated with placing the rat in the exposure chamber was evaluated further by dividing the exposed animals into acclimated (2 weeks of prior handling) and non-acclimated groups. At 6 h, an effect of prior handling was noted in the sham-exposed rats, with serum luteinizing hormone (LH) of the non-acclimated group being greater than that of the acclimated group. Serum LH concentrations were altered by methanol exposure, but the direction of change and the exposure level at which an effect was noted differed between the acclimated and non-acclimated rats. Methanol (5000 ppm) reduced serum LH in the non-acclimated animals, while 10,000 ppm increased LH in the acclimated rats. Follicle stimulating hormone (FSH) and testosterone were unchanged by methanol in rats killed at 6 h. Thus, this experiment did not confirm earlier reports that exposure to 200 ppm for 6 h reduced serum testosterone. At 24 h, an effect of prior handling was still present in the hormonal measures, with serum and interstitial fluid testosterone concentrations being greater in the non-acclimated rats. Also, there was a dose x handling interaction with methanol exposure inducing an increase in serum testosterone in the non-acclimated rats (up to 5000 ppm) and a decrease in the acclimated rats (up to 10,000 ppm). In the second experiment, groups of acclimated and non-acclimated rats were exposed to 0 or 5000 ppm methanol for 1, 2 and 6 h and killed immediately after removal from the chamber. Serum LH, testosterone and FSH values were not different in sham- vs methanol-exposed rats at any time point. As in experiment 1, an effect of prior handling was noted. In general, the concentrations of these hormones and serum prolactin in the non-acclimated rats were greater than those observed for acclimated rats. Methanol exposure resulted in increased prolactin concentrations under both handling conditions.(ABSTRACT TRUNCATED AT 400 WORDS)
Acclimatization↗
[Bronchoalveolar lavage--a diagnostic method in chronic nonspecific bronchopulmonary diseases in childhood? 2. Studies of cellular and humoral parameters in BAL irrigation fluid].
With a view of the pathogenesis of chronic bronchopulmonary diseases the interrelations between infections and evolving defense system are of interest, they are perhaps detectable by means of diagnostic bronchoalveolar lavage. We carried out cytodifferentiation, investigated adenosine deaminase activities and interleukin 1 formation of macrophages, determined immunoglobulin concentrations (secretory IgA), lysozyme, alpha 2-macroglobulin, alpha 1-antitrypsin, albumin. Because the cytodifferentiation yields insight into topical inflammatory reactions, shows diagnostic useful informations in single cases and because it is simple to carry out we can recommend it for each bronchological examination. There were no results specific for any disease group for parameters mentioned above.
Adenosine Deaminase↗
[Thiocyanate--a pathogenetic factor in cystic fibrosis (mucoviscidosis)?].
Thiocyanate (SCN-) concentrations in serum samples of 32 cystic fibrosis (CF) patients, 30 controls as well as 23 heterozygotes (parents of CF patients) were investigated, because SCN- influenced viscosity of secretions, membrane functions as well as nonspecific and specific defense processes. CF patients showed little smaller SCN- serum levels, but the differences were not statistically significant. There were remarkable smaller values for CF patients with most serious clinical conditions due to severe pulmonary changes.
Adolescent↗
First analysis of the F508 deletion in cystic fibrosis patients from the GDR.
Cystic fibrosis (CF) patients (n = 157) from the GDR were analysed for the occurrence of the recently discovered 3bp deletion causing CF. About 50% of all investigated patients were homozygotes and about 30% heterozygotes for this deletion. Of the analysed CF chromosomes from these patients, 62% carry the deletion, which is in strong linkage disequilibrium with the KM19 restriction fragment length polymorphism allele 2 and the 1/2 XV2c/KM19 haplotype.
Chromosome Deletion↗
Reconstructing evolution of sequences subject to recombination using parsimony.
The parsimony principle states that a history of a set of sequences that minimizes the amount of evolution is a good approximation to the real evolutionary history of the sequences. This principle is applied to the reconstruction of the evolution of homologous sequences where recombinations or horizontal transfer can occur. First it is demonstrated that the appropriate structure to represent the evolution of sequences with recombinations is a family of trees each describing the evolution of a segment of the sequence. Two trees for neighboring segments will differ by exactly the transfer of a subtree within the whole tree. This leads to a metric between trees based on the smallest number of such operations needed to convert one tree into the other. An algorithm is presented that calculates this metric. This metric is used to formulate a dynamic programming algorithm that finds the most parsimonious history that fits a given set of sequences. The algorithm is potentially very practical, since many groups of sequences defy analysis by methods that ignore recombinations. These methods give ambiguous or contradictory results because the sequence history cannot be described by one phylogeny, but only a family of phylogenies that each describe the history of a segment of the sequences. The generalization of the algorithm to reconstruct gene conversions and the possibility for heuristic versions of the algorithm for larger data sets are discussed.
Algorithms↗
Unified approach to alignment and phylogenies.
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Algorithms↗
Secretory immunoglobulin A in serum of CF patients.
Increased sIgA values were found in CF patients in about 70 per cent (3 studies with 23, 43, 45 CF patients). With higher severity of CF disease (Shwachman score) we could observe higher sIgA levels. Postmortem histological findings and sIgA concentrations correlated well in 13 cases. Determinations of sIgA in serum could serve as parameter for hepatobiliary involvement in CF. Secretory immunoglobulin A (sIgA) is the predominant immunoglobulin of exocrine secretions. In serum large and frequent elevations of sIgA could be found in patients with chronic liver disease characterized by biliary obstruction (3). Slight and irregular elevations were observed in patients with disorders of gastrointestinal tract and of respiratory tract as well as in lactating women (3). Manifestations of the hepatobiliary system in CF will become more important with advancing age and progressively higher life expectancy of CF patients. A simple reliable test for detection of hepatobiliary involvement in CF would be useful.
Biliary Tract Diseases↗
Bacterial spectrum of the germs in the respiratory tract of patients with CF at smaller centres.
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Adolescent↗