Expression of ATP6V1C1 during oral carcinogenesis

We investigated the gene and protein expressions of V-type ATPase protein subunit C1 (ATP6V1C1) in cases of oral squamous cell carcinoma (OSCC) and contralateral normal mucosa in smokers, nonsmokers and former smokers. Subjects were separated into five groups of 15: group 1, smokers with OSCC; group 2, normal contralateral mucosa of OSCC patients; group 3, chronic smokers; group 4, former smokers who had stopped smoking 1 year earlier; group 5, individuals who had never smoked. Exfoliative cytology specimens from oral mucosa of smokers, former smokers and nonsmokers showed normal gene and protein expression. We found significantly greater gene expression in the OSCC group than in the nonsmoker groups. No difference in gene expression was observed between normal contralateral mucosa and nonsmoker groups, smoker and nonsmoker groups or former smoker and nonsmoker groups. We observed intense immunostaining for ATP6V1C1 protein in all cases of OSCC and weak or no staining in smoker, former smoker and nonsmoker groups. Significantly greater expression of ATP6V1C1 protein was observed in the OSCC group compared to the other groups, which supports the role of ATP6V1C1 in effecting changes associated with oral cancer. Analysis of the mucosae of chronic smokers, former smokers and the normal contralateral mucosa of patients with OSCC showed unaltered ATP6V1C1 gene and protein expression. Early stages of carcinogenesis, represented by altered epithelium of chronic smokers, had neither gene nor protein alterations as seen in OSCC. Therefore, we infer that the changes in ATP6V1C1 occur during later stages of carcinogenesis. Our preliminary study provides a basis for future studies of using ATP6V1C1 levels for detecting early stage OSCC.     

Influence of Waist on Adiponectin and Insulin Sensitivity in Adolescence

It has been hypothesized that abdominal obesity leads to insulin resistance partly through decreased adiponectin. However, the cross‐sectional and longitudinal associations among waist, adiponectin, and insulin sensitivity have not been examined in older adolescents. Non‐Hispanic white and black children were recruited from the Minneapolis school district and underwent three examinations at mean ages 13, 15, and 19. Insulin sensitivity (measured using the gold‐standard euglycemic clamp) and waist circumference were measured at all exams. Adiponectin was measured at mean ages 15 and 19. Partial correlations were used to examine associations among waist, adiponectin, and insulin sensitivity at mean age 15 (n = 308) and mean age 19 (n = 218). Longitudinal correlations and a longitudinal regression model were used to predict adiponectin and insulin sensitivity measured at ages 15 and 19, from age 13 waist and change in waist. At age 15, waist and adiponectin were significantly correlated (r = ?0.32). At age 19, waist and adiponectin were significantly correlated (r = ?0.36), as were waist and insulin sensitivity (r = ?0.16). Both baseline waist and change in waist were significantly inversely associated with age 19 adiponectin but with age 19 insulin sensitivity only in men. In conclusion, in adolescents, the association between waist and adiponectin appears to develop several years before the association between waist and insulin sensitivity and there is a longitudinal association between waist and adiponectin. These results support the hypothesis that adiponectin may contribute to the association of waist and insulin sensitivity.     

Evidence from nuclear sequences that invariable sites should be considered when sequence divergence is calculated

It has long been known, from the distribution of multiple amino acid replacements, that not all amino acids of a sequence are replaceable. More recently, the phenomenon was observed at the nucleotide level in mitochondrial DNA even after allowing for different rates of transition and transversion substitutions. We have extended the search to globin gene sequences from various organisms, with the following results: (1) Nearly every data set showed evidence of invariable nucleotide positions. (2) In all data sets, substitution rates of transversions and transitions were never in the ratio of 2/1, and rarely was the ratio even constant. (3) Only rarely (e.g., the third codon position of beta hemoglobins) was it possible to fit the data set solely by making allowance for the number of invariable positions and for the relative rates of transversion and transition substitutions. (4) For one data set (the second codon position of beta hemoglobins) we were able to simulate the observed data by making the allowance in (3) and having the set of covariotides (concomitantly variable nucleotides) be small in number and be turned over in a stochastic manner with a probability that was appreciable. (5) The fit in the latter case suggests, if the assumptions are correct and at all common, that current procedures for estimating the total number of nucleotide substitutions in two genes since their divergence from their common ancestor could be low by as much as an order of magnitude. (6) The fact that only a small fraction of the nucleotide positions differ is no guarantee that one is not seriously underestimating the total amount of divergence (substitutions). (7) Most data sets are so heterogeneous in their number of transition and transversion differences that none of the current models of nucleotide substitution seem to fit them even after (a) segregation of coding from noncoding sequences and (b) splitting of the codon into three subsets by codon position. (8) These frequently occurring problems cannot be seen unless several reasonably divergent orthologous genes are examined together.      

Biochemical symptoms of stress in the mycorrhizal roots of Norway spruce (Picea abies)

Summary The mycorrhizal activity of spruce in a mixed-wood forest was monitored over 1 year by measuring biochemical characters in fine roots of six canopy trees and of a regrowth stand. The concentration of adenosine 5-triphosphate (ATP), a measure of living biomass, showed two peaks per year, one at bud break and one after main shoot growth. The concentration of storage polysaccharides in mycorrhizae showed the same cycles even more pronouncedly. It is proposed that these changes reflect growth and senescence of mycorrhizae and that the timing of the cycles is controlled by translocation of assimilates from the shoot. Differences between mycorrhizae collected from canopy trees and the regrowth stand were small and not significant. Characters known to be related to fungal activity of the mycorrhizal symbiosis (concentration of trehalose, glucose uptake, respiration) also varied little among the six canopy trees. Large differences among fine-root samples from different canopy trees, however, were detected in the concentrations of ATP and storage polysaccharides, measures which seemed to be physiologically integrated within trees. If low concentrations in roots precede losses of foliage from trees, these two symptoms could be used as early indicators of growth decline in individual spruce trees.     

Bayesian adaptive sequence alignment algorithms

The selection of a scoring matrix and gap penalty parameters continues to be an important problem in sequence alignment. We describe here an algorithm, the 'Bayes block aligner, which bypasses this requirement. Instead of requiring a fixed set of parameter settings, this algorithm returns the Bayesian posterior probability for the number of gaps and for the scoring matrices in any series of interest. Furthermore, instead of returning the single best alignment for the chosen parameter settings, this algorithm returns the posterior distribution of all alignments considering the full range of gapping and scoring matrices selected, weighing each in proportion to its probability based on the data. We compared the Bayes aligner with the popular Smith-Waterman algorithm with parameter settings from the literature which had been optimized for the identification of structural neighbors, and found that the Bayes aligner correctly identified more structural neighbors. In a detailed examination of the alignment of a pair of kinase and a pair of GTPase sequences, we illustrate the algorithm's potential to identify subsequences that are conserved to different degrees. In addition, this example shows that the Bayes aligner returns an alignment-free assessment of the distance between a pair of sequences.      

Expiratory flow limitation and intrinsic positive end-expiratory pressure in obesity

Breathing at very low lung volumes might beaffected by decreased expiratory airflow and air trapping. Our purposewas to detect expiratory flow limitation (EFL) and, as a consequence, intrinsic positive end-expiratory pressure(PEEP_i) in grossly obesesubjects (OS). Eight OS with a mean body mass index (BMI) of 44 ± 5 kg/m² and six age-matchednormal-weight control subjects (CS) were studied in different bodypositions. Negative expiratory pressure (NEP) was used to determineEFL. In contrast to CS, EFL was found in two of eight OS in the uprightposition and in seven of eight OS in the supine position. DynamicPEEP_i and mean transdiaphragmatic pressure (mean Pdi) were measured in all six CS and in six of eight OS.In OS, PEEP_i increased from 0.14 ± 0.06 (SD) kPa in the upright position to 0.41 ± 0.11 kPa inthe supine position (P < 0.05) anddecreased to 0.20 ± 0.08 kPa in the right lateral position(P < 0.05, compared with supine),whereas, in CS, PEEP_i wassignificantly smaller (<0.05 kPa) in each position. In OS, mean Pdiin each position was significantly larger compared with CS. Mean Pdiincreased from 1.02 ± 0.32 kPa in the upright position to 1.26 ± 0.17 kPa in the supine position (not significant) and decreasedto 1.06 ± 0.26 kPa in the right lateral position(P < 0.05, compared with supine),whereas there were no significant changes in CS. We conclude that in OS1) tidal breathing can be affectedby EFL and PEEP_i;2) EFL andPEEP_i are promoted by the supineposture; and 3) the increaseddiaphragmatic load in the supine position is, in part, related toPEEP_i.

     

Sensitivity and Specificity of Anthropometrics for the Prediction of Diabetes in a Biracial Cohort

Objective: To evaluate the ability of body mass index, waist circumference, waist‐to‐hip ratio, and combinations of these variables to discriminate individuals who will develop diabetes in adulthood. Research Methods and Procedures: Data were from 45‐ to 64‐year‐old men and women who were members of the Atherosclerosis Risk in Communities cohort. The analysis sample consisted of 12,814 African American and white participants who were free of diabetes at baseline. Body mass index, waist circumference, waist‐to‐hip ratio, and diabetes incidence (defined as one glucose measure ≥126 mg/dL after fasting for at least 8 hours, one nonfasting glucose measure ≥200 mg/dL, and self‐report of diabetes or report of taking medication for diabetes). Results: 1515 new cases of diabetes were identified over the 9‐year follow‐up. Areas under receiver operating characteristic curves ranged from 0.66 to 0.73 for single measures. The curves were smooth, with no indication of a threshold. Waist tended to have the highest receiver operating characteristic statistic in all groups, but differences were small. Discussion: The three anthropometric indices tested were approximately equivalent in their ability to predict diabetes. Sensitivity and specificities differed among ethnic and gender groups.