Changes in ds/dn in the HIV-1 env gene.
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Computer Simulation↗
Biomedical subjects
R Nielsen
Publications and source records attributed to R Nielsen.
Docking phospholipase A2 on membranes using electrostatic potential-modulated spin relaxation magnetic resonance.
A method involving electron paramagnetic resonance spectroscopy of a site-selectively spin-labeled peripheral membrane protein in the presence and absence of membranes and of a water-soluble spin relaxant (chromium oxalate) has been developed to determine how bee venom phospholipase A2 sits on the membrane. Theory based on the Poisson-Boltzmann equation shows that the rate of spin relaxation of a protein-bound nitroxide by a membrane-impermeant spin relaxant depends on the distance (up to tens of angstroms) from the spin probe to the membrane. The measurements define the interfacial binding surface of this secreted phospholipase A2.
Bee Venoms↗
[Organization and results of ambulatory surgery for inguinal hernia].
The results of a reorganization of surgery for inguinal hernias within a department of surgical gastroenterology were assessed concerning staff simplifications, feasibility, patient satisfaction, safety, complications and resources. Five hundred consecutive, elective, open operations for unilateral reducible inguinal hernias were performed in 466 patients under local anaesthesia in an ambulatory setup. One hundred and fourteen of the operations were for a recurrent hernia. The median age was 60 years (44-74 years as 25% and 75% quartiles). Two of the operations were converted to general anaesthesia. The patients were discharged 85 min (median) post-operatively, but 12 patients were not discharged on the same day. Bleeding or wound infections in need of treatment were seen postoperatively in 1.6% and 1.6%, respectively. All patients were given a postoperative questionnaires with a response rate of 95%, 89% of the respondents were satisfied with the whole procedure, 11% were dissatisfied. A reorganization of surgery for inguinal hernias to a standardized ambulatory setup induced staff simplifications and saved resources with a preserved high patient satisfaction, safety and a low complication rate.
Adolescent↗
Maximum likelihood estimation of population divergence times and population phylogenies under the infinite sites model.
In this paper, a maximum likelihood estimator of population divergence time based on the infinite sites model is developed. It is demonstrated how this estimator may be applied to obtain maximum likelihood estimates of the topology of population phylogenies. This approach addresses several classical problems occurring in the inference of the phylogenetic relationship of populations, most notably the problem of shared ancestral polymorphisms. The method is applied to previously published data sets of human African populations and of Caribbean hawksbill turtles.
Animals↗
Synonymous and nonsynonymous rate variation in nuclear genes of mammals.
A maximum likelihood approach was used to estimate the synonymous and nonsynonymous substitution rates in 48 nuclear genes from primates, artiodactyls, and rodents. A codon-substitution model was assumed, which accounts for the genetic code structure, transition/transversion bias, and base frequency biases at codon positions. Likelihood ratio tests were applied to test the constancy of nonsynonymous to synonymous rate ratios among branches (evolutionary lineages). It is found that at 22 of the 48 nuclear loci examined, the nonsynonymous/synonymous rate ratio varies significantly across branches of the tree. The result provides strong evidence against a strictly neutral model of molecular evolution. Our likelihood estimates of synonymous and nonsynonymous rates differ considerably from previous results obtained from approximate pairwise sequence comparisons. The differences between the methods are explored by detailed analyses of data from several genes. Transition/transversion rate bias and codon frequency biases are found to have significant effects on the estimation of synonymous and nonsynonymous rates, and approximate methods do not adequately account for those factors. The likelihood approach is preferable, even for pairwise sequence comparison, because more realistic models about the mutation and substitution processes can be incorporated in the analysis.
Animals↗
Evaluation and application of ribotyping for epidemiological studies of Actinobacillus pleuropneumoniae in Denmark.
The aim of the present study was to evaluate ribotyping as an epidemiological tool for Actinobacillus pleuropneumoniae and apply the method in studies of A. pleuropneumoniae infections in Danish pig herds. The evaluation of ribotyping was based on the 13 international reference strains and 106 epidemiologically unrelated Danish field strains representing the nine serotypes of biotype 1 (1, 2, 5A/B, 6, 7, 8, 10, 12, and K2:O7) and one serotype 14 of biotype 2. Enzymes CfoI and HindIII were chosen for generation of ribotype patterns. Ribotyping of the reference strains resulted in 10 CfoI types and 11 HindIII types. Ribotyping of the Danish strains resulted in 17 different CfoI ribotypes and 24 different HindIII ribotypes. Combining HindIII- and CfoI-ribotyping divided the Danish strains into 26 different types. The stability, reproducibility and typability of ribotype patterns were good, and the discriminatory power was between 0.85-0.89. The relatively low discriminatory power was caused by four predominant types, containing 61% of the isolates. The typing system was applied in studies of routes of infection of specific pathogen-free (SPF) pig herds and included 112 strains of A. pleuropneumoniae. Airborne transmission from neighboring conventional pig farms was investigated in 12 cases of infected SPF herds. Transmission via vehicles transporting pigs between SPF herds was investigated in nine cases while transmission by trading of pigs between SPF herds was investigated in two cases. Serotype 2 was isolated from all SPF herds included in this study, except one, emphasizing the high prevalence of this serotype in Denmark. By ribotyping, airborne transmission was indicated in five of 12 cases, transmission via pig transporting vehicle was indicated in six of nine cases, and transmission via trading was indicated in one of two cases. In many cases findings of predominant ribotypes made interpretations of suspected routes of transmission difficult. The relationship of strains based on ribotypes was calculated using Dices coefficient and clustered by UPGMA. HindIII ribotypes of serotype 2 strains were closely related, though only showing 43% similarity to HindIII ribotypes of remaining serotypes.
Actinobacillus Infections↗
Binding of bee venom and human group IIa phospholipases A2 to membranes: a minor role for electrostatics.
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Animals↗
Pain after groin hernia repair.
BACKGROUND: The purpose of the study was to provide a detailed description of postoperative pain after elective day-case open inguinal hernia repair under local anaesthesia. METHODS: This was a prospective consecutive case series study. After 500 hernia operations in 466 unselected patients aged 18-90 years, pain was scored (none, light, moderate or severe) at rest, while coughing and during mobilization, daily for the first postoperative week and after 4 weeks. Pain scores were added together over the first postoperative week. RESULTS: On days 1, 6 and 28, 66, 33 and 11 per cent respectively had moderate or severe pain while coughing or mobilizing. Total pain scores were higher while coughing or mobilizing than at rest (P < 0.001). Younger patients had higher total pain scores than older patients while coughing or mobilizing (P0< 0.01), but not at rest. No significant differences were found between types of surgery or hernia. CONCLUSION: Pain remained a problem despite the pre-emptive use of opioids, non-steroidal anti-inflammatory drugs and local anaesthesia, irrespective of surgical technique.
Adolescent↗
Taxon sampling and the accuracy of large phylogenies.
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Models, Biological↗
Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene.
Several codon-based models for the evolution of protein-coding DNA sequences are developed that account for varying selection intensity among amino acid sites. The "neutral model" assumes two categories of sites at which amino acid replacements are either neutral or deleterious. The "positive-selection model" assumes an additional category of positively selected sites at which nonsynonymous substitutions occur at a higher rate than synonymous ones. This model is also used to identify target sites for positive selection. The models are applied to a data set of the V3 region of the HIV-1 envelope gene, sequenced at different years after the infection of one patient. The results provide strong support for variable selection intensity among amino acid sites The neutral model is rejected in favor of the positive-selection model, indicating the operation of positive selection in the region. Positively selected sites are found in both the V3 region and the flanking regions.
Amino Acids↗
Models of amino acid substitution and applications to mitochondrial protein evolution.
Models of amino acid substitution were developed and compared using maximum likelihood. Two kinds of models are considered. "Empirical" models do not explicitly consider factors that shape protein evolution, but attempt to summarize the substitution pattern from large quantities of real data. "Mechanistic" models are formulated at the codon level and separate mutational biases at the nucleotide level from selective constraints at the amino acid level. They account for features of sequence evolution, such as transition-transversion bias and base or codon frequency biases, and make use of physicochemical distances between amino acids to specify nonsynonymous substitution rates. A general approach is presented that transforms a Markov model of codon substitution into a model of amino acid replacement. Protein sequences from the entire mitochondrial genomes of 20 mammalian species were analyzed using different models. The mechanistic models were found to fit the data better than empirical models derived from large databases. Both the mutational distance between amino acids (determined by the genetic code and mutational biases such as the transition-transversion bias) and the physicochemical distance are found to have strong effects on amino acid substitution rates. A significant proportion of amino acid substitutions appeared to have involved more than one codon position, indicating that nucleotide substitutions at neighboring sites may be correlated. Rates of amino acid substitution were found to be highly variable among sites.
Amino Acid Substitution↗
Cryoanalgesia: effect on postherniorrhaphy pain.
UNLABELLED: Cryoanalgesia versus sham treatment was applied to the ilioinguinal and iliohypogastric nerves after mesh repair of an inguinal hernia under local anesthesia in 48 male patients in a prospective, randomized, and observer- and patient-blinded trial. Pain was scored daily during rest, while coughing, and during mobilization to the sitting position for 1 wk and weekly for 8 wk on a four-point verbal rank scale. Use of supplementary analgesics and sensory disturbances were recorded. Assessments were made for allodynia, hyperalgesia, and mechanical pain detection thresholds 8 wk postoperatively. Cumulative pain scores for the first postoperative week were equal in the two groups, as was the use of analgesics. Eight weeks postoperatively, three cases of hyperalgesia to pinprick were detected in the cryoanalgesia group, and 10 patients in the cryoanalgesia group versus 5 in the sham-treatment group reported disturbed sensibility. We conclude that cryoanalgesia of the iliohypogastrical and ilioinguinal nerve does not decrease postherniorrhaphy pain. IMPLICATIONS: Does freezing of sensory nerves in the groin reduce pain after hernia repair? Extreme cold (-60 degrees C) was applied in a double-blind, randomized study. No difference in pain scores was found. Sensory disturbances were seen in treatment and control patients. Freezing cannot be recommended for pain relief after hernia repair.
Aged↗
Characterization of a kidney proximal tubule cell line, LLC-PK1, expressing endocytotic active megalin.
Reabsorption and cellular handling of glomerular filtered vitamins, peptides, and hormones in the proximal tubule are essential, but thus far, poorly elucidated processes. The multiligand receptor megalin, initially described as a Heymann nephritis antigen and later identified as a member of the LDL receptor gene family, mediates reabsorption of several molecules, such as transcobalamin-vitamin B12 and albumin, in the proximal tubule. Consequently, a differentiated cell line of proximal tubular origin expressing megalin is an important requisite for examination of the above-mentioned processes. This study shows, using electron microscopy, that the cell line LLC-PK1, originating from the proximal tubule, maintained differentiated morphology and had a well developed endocytotic apparatus. Furthermore, by immunoblotting and immunohisto- and cytochemistry, megalin was identified in the endocytotic compartments of these cells. Megalin was situated mainly in the endosomes and in the dense apical tubules, but it was also identified in coated pits and in the brush border. The ability of megalin to mediate internalization and degradation of labeled receptor-associated protein (RAP) in a RAP-inhibitable manner was demonstrated. By autoradiography, the endocytosed, iodinated RAP was located in endosomes and lysosomes in the apical part of the cells. Moreover, the LLC-PK1 cells assembled in a monolayer with a hindrance toward diffusion of labeled mannitol, inulin, and dextran at a satisfactory level for the study of proximal tubule handling of smaller proteins. This study reveals a proximal tubule cell line expressing megalin in a functional manner well suited for binding, uptake, and transcellular transport studies.
Animals↗
Correlation between transepithelial Na+ transport and transepithelial water movement across isolated frog skin (Rana esculenta).
In the present work the coupling under short-circuited conditions between the net Na(+)-influx across isolated frog skin and the transepithelial transport of water was examined i.e., the short-circuit current (Isc) and the transepithelial water movement (TEWM) were measured simultaneously. It has been shown repeatedly that the Isc across isolated frog skin is equal to the net transepithelial Na+ transport. Furthermore the coupling between transepithelial uptake of NaCl under open-circuit conditions and TEWM was also measured. The addition of antidiuretic hormone (AVT) to skins incubated under short-circuited conditions resulted in an increase in the Isc and TEWM. Under control conditions Isc was 9.14 +/- 2.43 and in the presence of AVT 45.9 +/- 7.3 neq cm-2 min-1 (n = 9) and TEWM changed from 12.45 +/- 4.46 to 132.8 +/- 15.8 nL cm-2 min-1. The addition of the Na+ channel blocking agent amiloride resulted in a reduction both in Isc and TEWM, and a linear correlation between Isc and TEWM was found. The correlation corresponds to that 160 +/- 15 (n = 7) molecules of water follow each Na+ across the skin. In another series of experiments it was found that there was a linear correlation between Isc and the increase in apical osmolarity needed to stop the TEWM. The data presented indicate that the observed coupling between the net transepithelial Na+ transport and TEWM is caused by local osmosis.
Animals↗
Robustness of the estimator of the index of dispersion for DNA sequences.
If substitutions in DNA sequences follow a Poisson process, the ratio of the variance in the number of substitutions to the mean number of substitutions (the index of dispersion) should equal 1. In this paper, the robustness of the commonly applied estimator of the index of dispersion in replacement sites and silent sites to various assumptions regarding DNA evolution is explored using simulation methods. The estimate of the index of dispersion may be strongly biased if the assumptions of the model of substitution are violated. However, the results of this study support the conclusions of studies by Gillespie and Ohta that the process of substitution in replacement sites is overdispersed. This result contradicts those of a recent study and shows that the high index of dispersion for replacement sites is not an artifact caused by the method of estimation.
Computer Simulation↗
Serological characterization of Actinobacillus pleuropneumoniae biotype 2 strains isolated from pigs in two Danish herds.
Eight Actinobacillus pleuropneumoniae biotype 2 strains were isolated in pure culture from lungs of pigs originating from two Danish herds with growing and finishing pigs. The antigenic properties were studied by indirect haemagglutination (IHA) and immunodiffusion (ID) tests using soluble surface antigens and by enzyme-linked immunosorbent assays (ELISA) using capsular enriched fractions and LPS. In all tests the strains proved antigenically homogeneous and serologically distinct from the known biotype 1 and 2 serotypes. Thus, the strains represent a new serotype which is provisionally proposed as biotype 2 serotype 14.
Actinobacillus Infections↗
A likelihood approach to populations samples of microsatellite alleles.
This paper presents a likelihood approach to population samples of microsatellite alleles. A Markov chain recursion method previously published by GRIFFITHS and TAVARE is applied to estimate the likelihood function under different models of microsatellite evolution. The method presented can be applied to estimate a fundamental population genetics parameter theta as well as parameters of the mutational model. The new likelihood estimator provides a better estimator of theta in terms of the mean square error than previous approaches. Furthermore, it is demonstrated how the method may easily be applied to test models of microsatellite evolution. In particular it is shown how to compare a one-step model of microsatellite evolution to a multi-step model by a likelihood ratio test.
Alleles↗
Site-by-site estimation of the rate of substitution and the correlation of rates in mitochondrial DNA.
A maximum likelihood method for independently estimating the relative rate of substitution at different nucleotide sites is presented. With this method, the evolution of DNA sequences can be analyzed without assuming a specific distribution of rates among sites. To investigate the pattern of correlation of rates among sites, the method was applied to a data set consisting of the protein-coding regions of the mitochondrial genome from 10 vertebrate species. Rates appear to be strongly correlated at distances up to 40 codons apart. Furthermore, there appears to be some higher order correlation of sites approximately 75 codons apart. The method of site-by-site estimation of the rate of substitution may also be applied to examine other aspects of rate variation along a DNA sequence and to assess the difference in the support of a tree along the sequence.
Animals↗