DIANA-EST: a statistical analysis.

MOTIVATION: Expressed Sequence Tags (ESTs) are next to cDNA sequences as the most direct way to locate in silico the genes of the genome and determine their structure. Currently ESTs make up more than 60% of all the database entries. The goal of this work is the development of a new program called DNA Intelligent Analysis for ESTs (DIANA-EST) based on a combination of Artificial Neural Networks (ANN) and statistics for the characterization of the coding regions within ESTs and the reconstruction of the encoded protein. RESULTS: 89.7% of the nucleotides from an independent test set with 127 ESTs were predicted correctly as to whether they are coding or non coding. AVAILABILITY: The program is available upon request from the author. CONTACT: Present address: Department of Genetics, University of Pennsylvania, School of Medicine, 475 Clinical Research Building, 415 Curie Boulevard, Philadelphia, PA 19104-6145, USA. artemis@pcbi.upenn.edu.     

Whole-genome analysis: annotations and updates.

The most important advances in the field of genome annotation over the past two years involve the use of cDNA sequences, protein structures and gene expression data to predict genes. These types of information not only improve gene identification, but they also give insights into variation in gene structure and function.     

Cholera vaccination: a decision analysis.

OBJECTIVE: To examine the clinical impact and financial cost of a vaccination program for the prevention of cholera in North Americans travelling to endemic and epidemic regions by means of the principles of decision analysis and a decision tree as well as to illustrate the effect of case attack rates on the cost per case prevented by vaccination. DESIGN: Review of the scientific literature to establish the probabilities of each significant outcome as well as a decision analysis and partial economic evaluation. OUTCOME MEASURES: Clinical impact (attack rates for cholera among vaccinated and nonvaccinated travellers), rates of death associated with cholera and vaccine-associated adverse events (VAAEs), and the number of VAAEs and the vaccine cost per case prevented. MAIN RESULTS: On the basis of our assumptions (including a rate of one case of cholera per 500,000 journeys to endemic regions), to prevent one case of cholera a vaccination program would cost $28.67 million and be associated with 105 VAAEs. CONCLUSION: Routine vaccination of travellers to endemic areas cannot be recommended; however, for people travelling to regions with a high transmission rate vaccination should be considered.     

Treponeme outer envelope: chemical analysis.

The chemical composition of the outer envelope (OE) of Treponema phagedenis biovar Kazan 5 was investigated. After cultivation in a lipid-defined medium, the OE was removed from the cells with 0.7 mM sodium dodecyl sulfate. The solubilized OE was reaggregated by dialysis against 20 mM MgCl2, washed, lyophilized, and subjected to chemical analysis. The average yield of OE was 14.6% of the whole cell (WC) dry weight. The magnesium content was 0.683 mug/mg OE. Peptidoglycan components such as muramic acid and ornithine were detected in the WC but not in the OE, and diaminopimelic acid was absent in both WC and OE. The OE contained protein (60-73%), carbohydrate (1-2%), and lipid (4-5%), primarily polar lipid. The major polar lipids were monogalactosyldiglyceride (43%) and phospholipid (57%), of which phosphatidylcholine was the main phospholipid component, with phosphatidylethanolamine present in lesser amounts.     

Discriminant analysis: methods and program.

Because of the disparity in the results obtained using different methods of discriminant analysis, we have written and used a unique program to test them. These methods can be divided into two groups corresponding to a classical probabilistic approach (i.e., Bayesian methods) or a topological approach (i.e., Sebestyen method).     

DIGICALC: a restriction fragment analysis program.

DIGICALC is a program designed to aid in the acquisition, storage, and analysis of nucleic acid restriction fragment data. The chief considerations during program design were (i) ease of use for people with varying degrees of computer experience, (ii) minimal hardware requirements (e.g. an IBM PC), (iii) portability and ease of modification, and (iv) improved functionality in sizing and comparing restriction fragments over manual methods. The program accepts manual or digitizer input of nucleic acid fragment mobility, calculates the fragments' sizes, and provides the means to search the fragment database and to produce charts of fragment sizes.     

Whole-genome expression analysis: challenges beyond clustering.

Measuring the expression of most or all of the genes in a biological system raises major analytic challenges. A wealth of recent reports uses microarray expression data to examine diverse biological phenomena - from basic processes in model organisms to complex aspects of human disease. After an initial flurry of methods for clustering the data on the basis of similarity, the field has recognized some longer-term challenges. Firstly, there are efforts to understand the sources of noise and variation in microarray experiments in order to increase the biological signal. Secondly, there are efforts to combine expression data with other sources of information to improve the range and quality of conclusions that can be drawn. Finally, techniques are now emerging to reconstruct networks of genetic interactions in order to create integrated and systematic models of biological systems.     

Fluorescence polarization: analysis of carbohydrate-protein interaction.

Fluorescence polarization has been widely used for the studies on the molecular motion in solution and has been applied to immunoassays for proteins, therapeutic drug monitoring in clinical pharmacy, and assays for environmentally toxic compounds. Because fluorescence polarization is most readily applicable to the kinetic analysis of the binding reaction between a substance having small molecular mass and a receptor molecule, this method is easily applied to the analysis of carbohydrate-lectin binding. In this tutorial Thematic Review, we briefly introduce the principles of fluorescence polarization and some applications of fluorescence polarization technique to glycobiology.     

Receptors for angiotensin: a critical analysis.

Angiotensin exerts numerous contractile and secretory effects by activating specific receptors. Recent pharmacological findings obtained with this peptide in various laboratories are analyzed, using the order of potency of agonists and the affinity of competitive antagonists as criteria for the classification of receptors for angiotensin in several systems. The analysis is restricted to experiments in which biological effects have been measured. Desensitization (the third criterion for classification of receptors) is discussed and a new protocol is proposed for its utilization. The analysis reveals that receptors for angiotensin in intestinal and vascular smooth muscles, in the heart, and in the vas deferens are all of the same type, while the receptors mediating the release of catecholamines from the adrenal medulla and those subserving the steroidogenic action on the adrenal cortex remain still unidentified. The recently proposed role of ATI as mediator of renin in the adrenal medulla is not substantiated by pharmacological findings with decapeptide antagonists. Moreover, the utilization of ATI as an agonist to determine the order of potency of angiotensins and the use of SQ 20881 as an inhibitor of the converting enzyme have shown serious limitations and should be reconsidered. The hypothetical role of ATIII as mediator of the renin-angiotensin system in the adrenal cortex, at least in other species than the rat, appears to be supported by the high affinity of heptapeptide antagonists for the adrenocortical receptor. However, these antagonists have generally been compared with [Sar1,Ala8]-ATII, A compound which is definitely inadequate for evaluating the affinities of octapeptides in the adrenal cortex. Therefore most of the data supporting the role of ATIII in this system have to be carefully reconsidered. Analogues of ATII are proposed for using as agonists and as antagonists instead of the natural angiotensins (for determining the order of potency of agonists) and instead of [Sar1,Ala8]-ATII (for measuring the affinities of competitive antagonists).     

Aeromonas hydrophila: analysis of 11 cases.

A retrospective analysis of 11 cases in which Aeromonas hydrophila was isolated indicated that the organsim caused local infection in 7 cases and asymptomatic colonization in 4. There were no cases of septicemia and none of the patients were known to have a malignant disease or immunosuppression. There were no deaths, although three of the patients required amputation of limbs because of myonecrosis. Chloramphenicol and aminoglycosides appeared to be appropriate therapeutic agents.     

LOGIT: a program for dose-response analysis.

We describe a FORTRAN computer program for fitting the logistic distribution function: (formula: see text) Where x represents dose or time, to dose-response data. The program determines both weighted least squares and maximum likelihood estimates for the parameters alpha and beta. It also calculates the standard errors of alpha and beta under both estimation methods, as well as the median lethal dose (LD50) and its standard error. Dose--response curves found by both fitting methods can be plotted as well as the 95% confidence bands for these lines.     

Aminolevulinate dehydratase (E.C. 4.2.1.24): Linkage analysis

Summary Linkage data on aminolevulinate dehydratase (ALADH, E.C. 4.2.1.24) and a series of other human genetic markers are presented. One hundred and two families (25 of them being informative) from southwestern Germany were tested. Close linkage (=0.05) between ALADH and the following markers could be excluded: Rh, PGM₁, Fy, ACP1, MNSs, HLA, Bf, GLO, PGM₃, Jk, Pi, PGP, K, GPT. There is some evidence of possible linkage with HPA.