A frameshift error detection algorithm for DNA sequencing projects.

During the determination of DNA sequences, frameshift errors are not the most frequent but they are the most bothersome as they corrupt the amino acid sequence over several residues. Detection of such errors by sequence alignment is only possible when related sequences are found in the databases. To avoid this limitation, we have developed a new tool based on the distribution of non-overlapping 3-tuples or 6-tuples in the three frames of an ORF. The method relies upon the result of a correspondence analysis. It has been extensively tested on Bacillus subtilis and Saccharomyces cerevisiae sequences and has also been examined with human sequences. The results indicate that it can detect frameshift errors affecting as few as 20 bp with a low rate of false positives (no more than 1.0/1000 bp scanned). The proposed algorithm can be used to scan a large collection of data, but it is mainly intended for laboratory practice as a tool for checking the quality of the sequences produced during a sequencing project.     

Effects of tumour necrosis factor-alpha on BrdU incorporation in cultured human enterocytes

Bromodeoxyuridine incorporation is a useful method for studying the pattern of DNA synthesis in proliferating cells. The distribution pattern of incorporated BrdU in villus enterocytes of duodenal explants was analysed after exposure to TNFalpha in organ culture. TNFalpha caused a consistent, low level uptake of BrdU in the portion of the nucleus close to the nuclear membrane, this pattern was absent from the control cultures. As these epithelial cells are terminally arrested in G(0), the BrdU incorporation was thought not to be due to S phase DNA synthesis, but rather a response to the cytotoxic influence of TNFalpha. Microtitre plate proliferation assays of cell density and DNA synthesis were devised to study the effects of TNFalpha on confluent monolayers of the human foetal jejunal cell line I407 and the mouse fibrosarcoma cell line L929. Both cell lines showed a similar response to TNFalpha. Exposure to TNFalpha alone did not reduce cell numbers but did cause a significant increase in DNA synthesis (p < 0.05). When cycloheximtde was added in tandem with TNFalpha there was a significant reduction in cell number (p < 0.001) and level of DNA synthesis (p < 0.01) indicative of cell death. The DNA of cells exposed to TNFalpha and cycloheximide was fragmented when viewed on an electrophoresis gel. The results show that BrdU incorporation might be a good indicator of damage to the DNA of cells after cytotoxic insult. TNFalpha may be responsible for villus enterocyte damage in enteropathies such as coeliac disease and GVHR of the small bowel.     

Effect of Mating Structure on Variation in Linkage Disequilibrium

Measurement of linkage disequilibrium involves two sampling processes. First, there is the sampling of gametes in the population to form successive generations, and this generates disequilibrium dependent on the effective population size (N_e) and the mating structure. Second, there is sampling of a finite number (n) of individuals to estimate the population disequilibrium.——Two-locus descent measures are used to describe the mating system and are transformed to disequilibrium moments at the final sampling. Approximate eigenvectors for the transition matrix of descent measures are used to obtain formulae for the variance of the observed disequilibria as a function of N_e, mating structure, n, and linkage or recombination parameter.——The variance of disequilibrium is the same for monoecious populations with or without random selfing and for dioecious populations with random pairing for each progeny. With monogamy, the variance is slightly higher, the proportional difference being greater for unlinked loci.     

Stimulation of gastrin secretion from the perfused rat stomach by somatostatin antiserum

The effect of a high capacity somatostatin antiserum on antral gastrin secretion was examined in an isolated vascularly perfused rat stomach preparation. Infusion of somatostatin antiserum diluted 1:1 and 1:9 with Krebs buffer solution produced significant increases in gastrin secretion throughout the period of infusion. Neither infusion of somatostatin antiserum diluted 1:99 nor infusion of control rabbit serum had any effect on gastrin secretion. The data indicate that antral somatostatin excercises a continous restraint on gastrin secretion in the basal state.     

The biological activity of catfish pancreatic somatostatin

Catfish pancreatic somatostatin, which contains eight additional amino acids on the amino terminus of a tetradecapeptide with considerable homology to tetradecapeptide somatostatin (SRIF), is a naturally occurring homology of the hypothalamic peptide. The purpose of these studies was to determibe the biological activity of this somatostatin homolog. Inhibition of ¹²⁵I-labelled tyr¹-SRIF binding to bovine pituitart plasma membranes by catfish pancreatic somatostatin was approximately 33% that of SRIF. Pancreatic somatostatin has full biological activity measured by inhibition of growth hormone release from isolated rat pituitary cells, but 0.01–0.1% the potency of SRIF. Pancreatic somatostatin at 100 ng/ml produced a 50–60% inhibition of insulin and glucagon secretion from perfused rat pancreas, while SRIF produced comparable inhibition at 10 ng/ml. This report demonstrates that a larger molecular form and natural homolog of SRIF, isolated from fish pancreas, has the same (but reduced) biological activities in rat assay systems as somatostatin originally isolated from sheep hypothalamus.     

Two-locus inbreeding measures for recurrent selection

Summary For a population undergoing recurrent selection, a method is presented for determining the average inbreeding coefficients at the end of each breeding cycle. The coefficients are derived in terms of probability measures that genes are identical by descent. For the one-locus case, two digametic measures are defined and employed in the derivation of a recurrence formula for the inbreeding coefficient. Two further classes of measures, trigametic and quadrigametic, are required for transition from one cycle to the previous one to allow the calculation of the inbreeding function for the two-locus case. Numerical values of the average probability of double identity by descent for populations with various imposed assumptions are listed to illustrate the effects of linkage and population size on the accrual of inbreeding and hence of homozygosity.Paper number 5018 of the Journal Series of the North Carolina Agricultural Experiment Station, Raleigh, North Carolina. This investigation was supported in part by NIH research grant number GM 11546 from the National Institute of General Medical Sciences.     

Myocardial Revascularization in Patients 70 Years of Age and Older

Myocardial revascularization has been carried out by us in 67 patients 70 years of age or older. Advanced coronary artery disease was found at angiography in more than two thirds of the patients. The postoperative morbidity and mortality compare very favorably with those in younger patients. The early and late mortality in the 67 patients was 4.5 percent and 6.0 percent, respectively. Fifty-seven survivors have been followed an average of 21 months; for most patients there has been a pronounced improvement in clinical classification. Properly selected, patients of advanced age can undergo successful revascularization surgical procedures. The adequacy of function of the left ventricle, proper timing of the surgical operation and an aggressive yet realistic approach seem to be major determinants for a good result.     

Independence of Vntr Alleles Defined as Fixed Bins

An analysis is presented of data collected by the Federal Bureau of Investigation at six unlinked variable number of tandem repeats (VNTR) loci for the United States population. Databases have been constructed of VNTR profiles of Caucasians, Blacks and Hispanics from Florida, Texas and California. There was very little evidence for correlations between lengths for pairs of VNTR fragments, within or between loci. When the fragment lengths were amalgamated into discrete bins, there was also little evidence for disequilibrium over all genotypes, within or between loci, for the Caucasian database, although some disequilibrium was found for the Black and Hispanic databases. No disequilibrium was found for the Caucasian or Black databases when tests were confined to heterozygous individuals. In cases of global disequilibrium, local tests can be applied to specific genotypes. The results suggest that, at the bin level, frequencies of VNTR profiles can generally be estimated as the products of the frequencies of the constituent elements. This overcomes the problem of estimating population frequencies when any particular profile does not exist in the database. There is some evidence for different frequencies, at the individual bin level, between geographic samples within each of the Caucasian, Black and Hispanic databases, and considerable evidence for differences between the three databases. These differences are less evident for the frequencies of four-locus profiles.     

Uptake of 36Cl and 22Na by the Brain-Cerebrospinal Fluid System: Comparison of the Permeability of the Blood-Brain and Blood-Cerebrospinal Fluid Barriers

Abstract: Transport and permeability properties of the blood-brain and blood-CSF barriers were determined by kinetic analysis of radioisotope uptake from the plasma into the CNS of the adult rat. Cerebral cortex and cerebellum uptake curves for ³⁶Cl and ²²Na were resolved into two components. The fast component (t_½ 0.02–0.05 h, fractional volume 0.04–0.08) is comprised of the vascular compartment and a small perivascular space whereas the slow component (t_½ 1.06–1.69 h, fractional volume 0.92–0.96) represents isotope movement across the blood-brain barrier into the brain extracellular and cellular compartments. Uptake curves of both ³⁶Cl and ²²Na into the CSF were also resolved into two components, a fast component (t_½ 0.18 h, fractional volume 0.24) and a slow component (t_½ 1.2 h, fractional volume 0.76). Evidence suggests that the fast component represents isotope movement across the blood-CSF barrier, i.e., the choroid plexuses, whereas the CSF slow component probably reflects isotope penetration primarily from the brain extracellular fluid into the CSF. The extracellular fluid volume of the cerebral cortex and cerebellum was estimated as ?13% from the initial slope of the curve of brain space versus CSF space curve for both ³⁶Cl and ²²Na. Like the choroid plexuses, the glial cell compartment of the brain appears to accumulate Cl from 2 to 6 times that predicted for passive distribution. The relative permeability of the blood-CSF and blood-brain barriers to ³⁶Cl, ²²Na, and [³H]mannitol was determined by calculating permeability surface-area products (PA). Analysis of the PA values for all three isotopes indicates that the effective permeability of the choroidal epithelium (blood/CSF barrier) is significantly greater than that of the capillary endothelium in the cerebral cortex and cerebellum (blood-brain barrier).