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PubMed2001

Variable site of oropharyngeal narrowing and regional variations of oropharyngeal collapsibility among snoring patients during wakefulness and sleep.

The oropharynx shows rhythmic caliber changes in accordance with the respiratory cycle. Dynamic imaging of the oropharynx is required to evaluate airway changes associated with snoring and obstructive sleep apnea. The purpose of this study was to determine the sites of narrowing/obstruction and to measure the regional collapsibility of the oropharynx during respiration during the sleep and awake cycles in snoring patients. Seven snoring patients were included for this study. Electron Beam Tomograms of the oropharynx were taken while the patient was awake and asleep, and dynamic views were reconstructed. The site of narrowing or obstruction varied widely among patients and differed from awake to asleep. The mean of smallest minimum cross-sectional area of the oropharynx was 60.38+/-42.97 mm2 in the awake state and 16.90+/-20.43 mm2 in the asleep state. Although the collapsibility of the oropharynx showed considerable regional variations, it increased during sleep at the overall oropharynx. The low retropalatal region showed the smallest minimum cross-sectional area and the highest collapsibility; however, the most prominent changes in the minimum cross-sectional area and collapsibility during sleep were observed in the high retroglossal region.

Adult↗
PubMed1997

Site-to-site variability of drug concentrations in skeletal muscle.

The homogeneity of drug concentrations in skeletal muscle was assessed in eight fatal overdoses. Ten to 30 random samples were taken from leg muscle weighing 1,650 to 7,985 g. For cases involving paracetamol the mean muscle-to-blood ratio ranged from 0.1 to 1.1 (n = 4) for amitriptyline 1.1 to 3.6 (n = 3), and for dothiepin 0.8 to 2.1 (n = 2). The coefficient of variance was large for all drugs, ranging from 10.5 (carbamazepine) to 50 (thioridazine). Skeletal muscle is not homogeneous with respect to drug concentrations in fatal overdose cases. Of 16 instances of drug detection in blood 2 (nortriptyline and promethazine) were not detected in muscle. Muscle-to-blood drug ratios varied significantly among cases, possibly influenced by survival time after drug ingestion. Quantitative interpretations of muscle drug levels present significant difficulties. However, skeletal muscle can be used for qualitative corroboration of blood analyses and is a suitable specimen for drug detection where none other is available.

Acetaminophen↗
PubMed1986

Variable site of airway narrowing among obstructive sleep apnea patients.

The purpose of this was to determine whether the site of physiological narrowing within the upper airway was uniform or differed among patients with obstructive sleep apnea. Inspiratory pressures were measured with an esophageal balloon catheter and three catheters located at different sites along the upper airway: supralaryngeal airway, oropharynx, and nasopharynx. Peak inspiratory pressure differences between catheters allowed assessment of pressure gradients across three airway segments: lungs-larynx-retroepiglottal airway (esophageal-supralaryngeal pressure), hypopharynx (supralaryngeal-oropharynx pressure), and transpalatal airway (oropharynx-nasopharynx pressure). In five patients, hypopharyngeal obstruction was present, and in four patients no hypopharyngeal obstruction existed. In these four patients the site of obstruction was located at the level of the palate. In a given subject, the site of obstruction was the same during repeated measurements. The presence or absence of hypopharyngeal narrowing during sleep was not predictable from gradients measured across different segments of the upper airway during wakefulness. We conclude that the site of physiological upper airway obstruction varies among patients with obstructive sleep apnea and is not predictable from pressure measured during wakefulness. We speculate that uvulopalatopharyngoplasty may not relieve obstructive apneas in patients with hypopharyngeal obstruction.

Adult↗
PubMed1999

Examination of the Montastraea annularis Species Complex (Cnidaria: Scleractinia) Using ITS and COI Sequences.

: The Caribbean coral Montastraea annularis has recently been proposed to be a complex of at least three sibling species. To test the validity of this proposal, we sequenced the ITS region of the nuclear ribosomal RNA gene family (ITS-1, 5.8S, and ITS-2), and a portion of the mitochondrial DNA gene cytochrome c oxidase subunit I (COI) from the three proposed species (M. annularis, M. faveolata, and M. franksi) from Florida reefs. The ITS fragment was 665 nucleotides long and had 19 variable sites, of which 6 were parsimony-informative sites. None of these sites was fixed within the proposed species. The COI fragment was 658 nucleotides long with only two sites variable in one individual. Thus, under both the biological species concept and the phylogenetic species concept, the molecular evidence gathered in this study indicates the Montastraea annularis species complex to be a single evolutionary entity as opposed to three distinct species. The three proposed Montastraea species can interbreed, ruling out prezygotic barriers to gene flow (biological species concept), and the criterion of monophyly is not satisfied if hybridization is occurring among taxa (phylogenetic species concept).

Journal Article↗
PubMed2006

Study on tandem repeat sequence variation in sheep mtDNA D-loop region.

The 75-nt-long tandem repeat sequence in the control region of mtDNA of 77 individuals, of which 69 were from different indigenous sheep breeds in China and 8 were from imported breeds, was sequenced and analyzed to investigate the origin and differentiation of Chinese indigenous sheep breeds and also the genetic diversities and relationships among them. A total of 28 variable sites were detected within 309 repeated sequences, among which 7 sites were singleton variable sites with two variants, 1 site was a singleton variable site with three variants, and 20 sites were parsimony informative sites with two variants. A total of 63 haplotypes were sorted from 28 polymorphic sites, among which two main and basic haplotypes, namely, Hap 1 and Hap 3 were present at a much higher proportion, at 12.94% and 30.42%, respectively. It could be inferred that Chinese indigenous sheep breeds originated from two maternal ancestors because of the maternal inheritance characteristics of the mtDNA. Altay sheep and Kazakstan sheep are closely related and do not differentiate significantly. Mongolian sheep and Ujumuqin sheep also share a close relationship. Tibetan sheep, Mongolian sheep, and Ujumuqin sheep have lower genetic diversity than Altay sheep and Kazakstan sheep.

Animals↗
PubMed1990

Assessment of relationships between site-specific variables.

The assessment of relationships between site-specific variables has been a matter of controversy because of the claim that periodontal sites within individuals can be used as independent observations in statistical models. One problem with this approach is the unreliability of the calculated Type I and Type II error rates. Another problem is that such inappropriate analysis may prohibit a correct assessment of causal relationships between site-specific variables. The host-factor can act as an effect modifier and modulate the magnitude of the site-specific effects and/or the host-factor can act as a confounder by superimposing a patient-effect on the studied site-specific effects leading to bias. As a result, site-specific biological mechanisms of disease progression may be misinterpreted. Sites can be used as the experimental unit of analysis, but the sampling design from which the site-specific data originated should not be ignored.

Causality↗
PubMed1980

Immunoglobulin V/J recombination is accompanied by deletion of joining site and variable region segments.

A site-specific recombination event is responsible for the somatic activation of immunoglobulin genes and for generating a major share of immunoglobulin gene diversity. Although several possible mechanisms can be proposed to account for this process, recombinatio accompanied by deletion is a particularly attractive mechanism because it might utilize inverted repeat sequences noted on the 3' side of all variable regions and on the 5' side of all joining site segments thus far studied. Testing this model is complicated by the fact that antibody cells are at least diploid and gene segments on the inactive chromosome can obscure deletions occurring within the active gene. Accordingly, we have screened several immunoglobulin-producing plasmacytoma lines to select those in which both chromosomes are rearranged. By using appropriate cell lines and variable and joining region probes in in situ hybridization experiments, we show that recombination is accompanied by the deletion of both variable and joining region genes. These experiments also allow us to map the site of V/J recombination of several active immunoglobulin genes and suggest an order and orientation for variable, joining, and constant region sequences.

Animals↗
PubMed1985

Molecular organization of ribosomal RNA genes clustered at variable chromosomal sites in Triturus vulgaris meridionalis (Amphibia, Urodela).

The ribosomal RNA genes of Triturus vulgaris meridionalis (Amphibia, Urodela) show the peculiar feature of being clustered not only at the nucleolar organizer, present in the species at a definite chromosome location, but also at "additional ribosomal sites" which are highly variable in number and chromosomal distribution among individuals. The additional ribosomal sites are most often found at specific chromosome regions, such as telomeres, C-bands and centromeres, in virtually all the chromosomes. With increasing numbers of additional clusters, the genomic dosages of ribosomal RNA genes are found to increase over a tenfold range, though not linearly. At a molecular level, the ribosomal DNA repeats differ in size because of discrete variations in the length of the non-transcribed spacers. However, the resulting length heterogeneity of the gene family is rather limited within a single genome as well as within the species. Many of the ribosomal loci appear to be internally homogeneous with respect to the repeat length. Moreover, separate clusters from distant genomic regions can share the same size class of ribosomal repeats even in the same specimen. The nucleolar organizer is mostly endowed with "shorter" ribosomal repeating units, ranging in size from 13.7 X 10(3) to 15.2 X 10(3) base-pairs. The additional ribosomal sites are characterized by the occurrence of "longer" repeats, ranging in size from 16.2 X 10(3) to 19.7 X 10(3) base-pairs. The "shorter" class of ribosomal repeats is always detected in the amplified ribosomal DNA, suggesting that the nucleolar organizer locus is involved in the amplification process in most oocytes. "Longer" ribosomal repeats are also detectable in the amplified ribosomal DNA of a few females.

Animals↗
PubMed2005

Relative contribution of patient-, tooth-, and site-associated variability on the clinical outcomes of subgingival debridement. I. Probing depths.

BACKGROUND: The objective of this clinical trial was to assess the relative contribution of patient-, tooth-, and site-associated variables on changes in probing depths (PD) following delivery of a standard non-surgical phase of periodontal therapy. METHODS: Ninety-four (94) systemically healthy subjects with severe generalized periodontitis were included in this 6-month prospective longitudinal study. Medical, periodontal, and microbiological parameters were collected at baseline and 2 and 6 months after completion of oral hygiene instructions, motivation, and subgingival debridement using a piezoelectric instrument. The relative contribution of patient-, tooth-, and site-associated variables was evaluated with a hierarchical multilevel analysis. RESULTS: Eighty percent (80%) of variability in PD reductions was attributed to site level parameters, while 12% was at the tooth level and 8% at the patient level. The multilevel analysis associated PD reductions with patient factors (cigarette smoking status and carriage of the rare allele of a specific polymorphism for the interleukin-6 [IL-6] gene), tooth factors (tooth mobility and tooth type), and site factors (mesial and distal location). Cigarette smoking and carriage of the rare allele of the IL- 6-174 G/C polymorphism were associated with less PD reduction. Incisors and canines responded better than premolars and molars. A dose-dependent effect of mobility was observed: teeth with higher baseline mobility resulted in significantly greater decreases in PD. At the site level, greater reductions were observed at interdental sites (compared to facial or oral), and at deeper sites (1.2 mm for 4 to 5 mm pockets and 2.4 mm for pockets > or =6 mm). CONCLUSION: These data provided an estimation of the relative contribution of site-, tooth-, and patient-associated variables in terms of PD reductions following a standard course of machine-driven subgingival debridement.

Cytosine↗
PubMed2000

Recombinational and mutational hotspots within the human lipoprotein lipase gene.

Here an analysis is presented of the roles of recombination and mutation in shaping previously determined haplotype variation in 9.7 kb of genomic DNA sequence from the human lipoprotein lipase gene (LPL), scored in 71 individuals from three populations: 24 African Americans, 24 Finns, and 23 non-Hispanic whites. Recombination and gene-conversion events inferred from data on 88 haplotypes that were defined by 69 variable sites were tested. The analysis revealed 29 statistically significant recombination events and one gene-conversion event. The recombination events were concentrated in a 1.9-kb region, near the middle of the segment, that contains a microsatellite and a pair of tandem and complementary mononucleotide runs; both the microsatellite and the runs show length variation. An analysis of site variation revealed that 9.6% of the nucleotides at CpG sites were variable, as were 3% of the nucleotides found in mononucleotide runs of >/=5 nucleotides, 3% of the nucleotides found </=3 bp from certain putative polymerase alpha-arrest sites, and 0. 5% of the remaining nucleotides. This nonhomogeneous distribution of variation suggests that multiple mutational hits at certain sites are common, an observation that challenges the fundamental assumption of the infinite-sites-mutation model. The nonrandom patterns of recombination and mutation suggest that randomly chosen single-nucleotide polymorphisms may not be optimal for disequilibrium mapping of this gene. Overall, these results indicate that both recombinational and mutational hotspots have played significant roles in shaping the haplotype variation at the LPL locus.

Black People↗
PubMed2005

Genetic variation within exon 2 of the MHC B-LB // gene in Tibetan chicken.

Genetic variation within exon 2 of chicken major histocompatibility complex B-LB // genes was investigated by PCR amplification, cloning and sequencing of a 374 bp fragment of the indigenous Tibetan chicken genomic DNA. Fifteen novel B-LB // alleles were found. Alignment and comparison of 18 allelic sequences from the individuals sampled revealed a total of 62 variable sites (total of 80 mutations) in exon 2, of which 41 were parsimony informative sites. The nucleotide diversity (pi) within the sequence of exon 2 was calculated to be 0.0718. Analysis of nucleotide variation confirmed a lower level of divergence (0.056 +/- 0.008) as estimated by average pairwise distance within the Tibetan chicken population than the five exotic breeds detected. The relative frequencies of synonymous and non-synonymous nucleotide substitutions within the region were 3.25 +/- 0.94% and 15.61 +/- 2.69% , respectively. These results indicated that the genetic variation within exon 2 seemed to have arisen largely by gene recombination and balancing selection. Alignment of the deduced amino acid sequences of beta1 domain coded by exon 2 revealed 11 synonymous mutations and 27 non-synonymous substitutions at the 38 separate sites. Fifty percent (12/24) of the proposed peptide-binding sites were variable within beta1 domain of chicken MHC B-LB // molecules, of which 11 were unique non-synonymous amino acid substitutions. These particular non-synonymous substitutions are considered to be associated with immunological specificity of MHC B-LB // molecule in Tibetan chicken, and they can provide a molecular biological basis for the study of disease resistance in chicken.

Animals↗
PubMed1996

Variants within the 5'-flanking region and the intron I of the bovine growth hormone gene.

In order to identify DNA variants potentially involved in the regulation of the expression of the bovine growth hormone gene, the 5'-flanking, the 5'-untranslated and the signal peptide coding regions of 15 cows (four German Friesian, two German Simmental, two Jersey, two Galloway, two Scottish Highland, two Charolais and one Ceylon Dwarf Zebu) were analysed. For each animal a region of about 1.2 kb was amplified by polymerase chain reaction (PCR) and sequenced. Six sites of variable nucleotides were identified in the 5'-flanking region of the gene and one in the intron I. Some of these variable sites are also potential binding sites for trans-acting factors (CAAT/enhancer binding protein (C/EBP), polyoma virus enhancer A binding protein 3 (PEA3), thyroid hormone response element (TRE)) and therefore possibly involved in the expression of the growth hormone gene. PCR amplification of specific alleles (PASA) tests for two of the sites (G2, G3) were established and the genotypes for these variants were analysed in 190 cows. The frequencies of the C alleles of the sites G2 and G3 were 0.63 and 0.76, respectively.

Animals↗
PubMed2002

Polymorphisms in control region of mtDNA relates to individual differences in endurance capacity or trainability.

The purpose of this study was to investigate whether the polymorphisms in the control region of mitochondrial DNA (mtDNA) related to individual difference in the endurance capacity or trainability. Fifty-five sedentary males participated in this study and were submitted to an 8-week endurance training program. The VO(2 max) was determined before and after training. Total DNA was extracted from the blood, and the sequence of the mtDNA control region was determined. The polymorphism in the mtDNA control region was decided based on the "Cambridge sequence." In 29 of the 55 subjects, vastus lateralis muscle biopsy samples were taken at rest before and after the training program. MtDNA content and CS (citrate synthase) activity in skeletal muscle was measured as the phenotype of the polymorphisms in the mtDNA control region. The VO(2 max) increased to 48.2 +/- 6.3 ml/min/kg from 42.1 +/- 6.0 as a result of the 8-week training (p < 0.05). The numbers of polymorphisms in determined 1,122 bp were 11.1 +/- 2.9 variable sites per person, and the total numbers of polymorphisms were 125 variable sites. The subjects were classified into two groups at each variable site, the Cambridge sequence (Cam) group and the non-Cambridge sequence (non-Cam) group. There were significant differences in pre-VO(2 max) between the two groups at each mtDNA nucleotide positions 16298, 16325, and 199, and in % Delta VO(2 max) at 16223 and 16362. Twenty-nine subjects who underwent the biopsy revealed significant differences in pre-CS activity at 194 and pre-mtDNA content at 514. Also, significant differences were found in the change rate of VO(2 max )and CS activity as a result of training between the two groups at 16519. In conclusion, it suggested that mtDNA polymorphisms in the control region might result in individual differences in endurance capacity or trainability.

Adult↗
PubMed2006

SNAP: Combine and Map modules for multilocus population genetic analysis.

We have added two software tools to our Suite of Nucleotide Analysis Programs (SNAP) for working with DNA sequences sampled from populations. SNAP Map collapses DNA sequence data into unique haplotypes, extracts variable sites and manipulates output into multiple formats for input into existing software packages for evolutionary analyses. Map collapses DNA sequence data into unique haplotypes, extracts variable sites and manipulates output into multiple formats for input into existing software packages for evolutionary analyses. Map includes novel features such as recoding insertions or deletions, including or excluding variable sites that violate an infinite-sites model and the option of collapsing sequences with corresponding phenotypic information, important in testing for significant haplotype-phenotype associations. SNAP Combine merges multiple DNA sequence alignments into a single multiple alignment file. The resulting file can be the union or intersection of the input files. SNAP Combine currently reads from and writes to several sequence alignment file formats including both sequential and interleaved formats. Combine also keeps track of the start and end positions of each separate alignment file allowing the user to exclude variable sites or taxa, important in creating input files for multilocus analyses.

Algorithms↗
PubMed1992

Estimating the fraction of invariable codons with a capture-recapture method.

A codon-based approach to estimating the number of variable sites in a protein is presented. When first and second positions of codons are assumed to be replacement positions, a capture-recapture model can be used to estimate the number of variable codons from every pair of homologous and aligned sequences. The capture-recapture estimate is compared to a maximum likelihood estimate of the number of variable codons and to previous approaches that estimate the number of variable sites (not codons) in a sequence. Computer simulations are presented that show under which circumstances the capture-recapture estimate can be used to correct biases in distance matrices. Analysis of published sequences of two genes, calmodulin and serum albumin, shows that distance corrections that employ a capture-recapture estimate of the number of variable sites may be considerably different from corrections that assume that the number of variable sites is equal to the total number of positions in the sequence.

Biological Evolution↗
PubMed1987

Radiotherapy and hyperthermia. Analysis of clinical results and identification of prognostic variables.

Site- and tumor-specific data obtained from two groups of patients with head and neck and melanoma lesions, respectively, showed that both immediate response and response duration were enhanced by the addition of heat. Two important variables, however, such as tumor volume and "isoeffect thermal dose" appeared to influence local tumor control. The volume effect was less pronounced in the lesions treated with radiotherapy plus heat than in those treated with radiotherapy alone, suggesting that the addition of heat was more damaging to the large than to the small lesions. Furthermore, a striking isoeffect thermal dose-response relationship was shown in head and neck lesions. Those data were collected and used to design a mathematical model relating the probability of local control to clinical and treatment variables. The analysis shows that, by using the same radiation parameters, the probability of local tumor control is a function of both "isoeffect thermal dose" and tumor volume.

Carcinoma, Squamous Cell↗
PubMed2006

Signatures of ecological resource availability in the animal and plant proteomes.

Although substantial and ecologically significant differences in elemental composition are well documented for whole organisms, little is known about whether such differences extend to lower levels of biological organization, such as the elemental composition of major molecules. In a proteome-scale investigation of 9 plant genomes and 9 animal genomes, we find that the nitrogen (N) content of plant proteins is lower than that in animal proteins. Furthermore, protein N content declines with the intensity of gene expression for plants, whereas the N content of animal proteins shows no consistent pattern with expression. Additional analyses indicate that the differences in N content between plant and animal proteomes and in plant proteins as a function of gene expression cannot be attributed to protein size, GC content, gene function, or amino acid properties. These patterns suggest that ecophysiological selection has operated to conserve N in plants via decreased reliance on N-rich amino acids. This inference was supported by an analysis of conserved and variable sites indicating that the N content of plant amino acids coded by variable sites is similar to that of the sites conserved between plant and animal genomes and shows no association with expression level. In contrast, in animals, the N content of amino acids coded by variable sites is significantly higher than that for conserved sites, suggesting relaxation of selective constraints for N usage in the animal lineage. This constitutes the first evidence for an influence of environmental resource availability on proteomes of multicellular organisms.

Amino Acids↗
PubMed2006

VOMBAT: prediction of transcription factor binding sites using variable order Bayesian trees.

Variable order Markov models and variable order Bayesian trees have been proposed for the recognition of transcription factor binding sites, and it could be demonstrated that they outperform traditional models, such as position weight matrices, Markov models and Bayesian trees. We develop a web server for the recognition of DNA binding sites based on variable order Markov models and variable order Bayesian trees offering the following functionality: (i) given datasets with annotated binding sites and genomic background sequences, variable order Markov models and variable order Bayesian trees can be trained; (ii) given a set of trained models, putative DNA binding sites can be predicted in a given set of genomic sequences and (iii) given a dataset with annotated binding sites and a dataset with genomic background sequences, cross-validation experiments for different model combinations with different parameter settings can be performed. Several of the offered services are computationally demanding, such as genome-wide predictions of DNA binding sites in mammalian genomes or sets of 10(4)-fold cross-validation experiments for different model combinations based on problem-specific data sets. In order to execute these jobs, and in order to serve multiple users at the same time, the web server is attached to a Linux cluster with 150 processors. VOMBAT is available at http://pdw-24.ipk-gatersleben.de:8080/VOMBAT/.

Algorithms↗