Synthesis of 2-chloro-2′-deoxyadenosine by microbiological transglycosylation using a recombinant <Emphasis Type="Italic">Escherichia coli</Emphasis> strain

Cladribine (2-chloro-2′-deoxyadenosine) was synthesized using intact cells of the recombinant Escherichia coli strain producing Geobacillus stearothermophilus B-2194 thermostable purine-nucleoside phosphorylase II (EC 2.4.2.1). Use of the cells containing this thermostable enzyme allowed the process to be conducted at a temperature of 70°C, which provided the maximal concentrations of sparingly soluble substrates. The best results were obtained with 2-chloroadenine as a modified base. The highest yield of the target 2-chloro-2′-deoxyadenosine (up to 95% in the case of deoxyguanosine) was reached when using 2′-deoxypurines as donors of deoxyribose. Use of thymidine for these purposes required its considerable molar excess over 2-chloroadenine (up to 6:1), which is connected with a nonoptimal amount of endogenous thymidine phosphorylase, necessary for synthesis of deoxyribose-1-phosphate, in the transglycosylation reaction.     

Sensitivity and positive predictive values of presurgical clinical diagnosis of excised benign and malignant skin tumors: a prospective study of 835 lesions in 778 patients.

This article reports on the sensitivity and positive predictive value of clinical diagnosis of benign and malignant skin tumors by expert plastic surgeons in an Israeli clinic. Most published reports have focused on the sensitivity of clinicians' diagnoses, a general measure of the physician's skill that does not predict the rate of accuracy of a physician's diagnoses. Our study of 835 lesions in 778 patients, one of the largest Israeli series, assesses the clinical diagnosis of malignant and benign skin tumors and is one of the few that provide information on the positive predictive value, the measure that is of interest to both physicians and patients. The majority of tumors were benign (56.8 percent), 31.6 percent were malignant, and 11.6 percent were premalignant. Among the 474 benign lesions, 46 percent were nevi. The most common nevi subclass was compound nevi (53 percent), 9 percent of the nevi were dysplastic, and 5 percent were blue nevi. The most common malignant tumor was basal cell carcinoma, accounting for 78 percent of malignant tumors.Although sensitivity for clinical diagnosis of malignancy was 91.3 percent, the positive predictive value for clinical diagnosis of malignancy was 71.3 percent. The sensitivity rate for clinically diagnosing premalignant tumors was 42.3 percent, whereas the positive predictive value for these diagnoses was higher (64.1 percent). The sensitivity rate for diagnosis of all benign lesions was 85.9 percent, and the positive predictive value was 94.2 percent. The sensitivity rate for diagnosis of all nevi was 87.6 percent, and the positive predictive value was 85.7 percent: i.e., only seven of the 218 pathologically proven diagnoses of nevi (3.2 percent) were falsely diagnosed as malignant lesions. Even more interestingly, five of the 223 clinical diagnoses of nevi (2.2 percent) were pathologically proven to be malignant melanomas, and seven were found to be premalignant lesions (3.1 percent). It was concluded that publications which report only on the sensitivity neglect to provide information of interest regarding the positive predictive value. Often, positive predictive value is qualitatively different from the sensitivity, and thus relying only on the sensitivity may lead to incorrect evaluation of a clinical judgment, which may result in erroneous surgical decisions.     

The study of the bacteriophage T5 deoxynucleoside monophosphate kinase active site by site-directed mutagenesis

The amino acid residues essential for the enzymatic activity of bacteriophage T5 deoxyribonucleoside monophosphate kinase were determined using a computer model of the enzyme active site. By site-directed mutagenesis, cloning, and gene expression in E. coli, a series of proteins were obtained with single substitutions of the conserved active site amino acid residues—S13A, D16N, T17N, T17S, R130K, K131E, Q134A, G137A, T138A, W150F, W150A, D170N, R172I, and E176Q. After purification by ion exchange and affine chromatography electrophoretically homogeneous preparations were obtained. The study of the enzymatic activity with natural acceptors of the phosphoryl group (dAMP, dCMP, dGMP, and dTMP) demonstrated that the substitutions of charged amino acid residues of the NMP binding domain (R130, R172, D170, and E176) caused nearly complete loss of enzymatic properties. It was found that the presence of the OH-group at position 17 was also important for the catalytic activity. On the basis of the analysis of specific activity variations we assumed that arginine residues at positions 130 and 172 were involved in the binding to the donor γ-phosphoryl and acceptor α-phosphoryl groups, as well as the aspartic acid residue at position 16 of the ATP-binding site (P-loop), in the binding to some acceptors, first of all dTMP. Disproportional changes in enzymatic activities of partially active mutants, G137A, T138A, T17N, Q134A, S13A, and D16N, toward different substrates may indicate that different amino acid residues participate in the binding to various substrates.     

In vivo oxidation of [9-14C] cyclic fatty acids derived from linolenic acid in the rat

Heating oils and fats may lead to cyclization of polyunsaturated fatty acids, as for example linolenic acid. Cyclohexenyl and cyclopentenyl fatty acids are subsequently present in some edible oils and these are suspected to induce metabolic disorders. In a previous experiment using [1-14C] labeled molecules, we published that these cyclic fatty acids are beta oxidized to the same extent as linolenic acid, at least for the first cycle of beta oxidation. However, it is possible that the presence of a ring could alter the ability of the organism to fully oxidize the molecule. In order to test this hypothesis, we assessed the oxidative metabolism of cyclic fatty acids carrying a 14C atom at the vicinity of the ring. For this purpose, rats were force-fed from 1.1 to 1.3 MBq of a representative fraction of dietary cyclohexenyl cyclic fatty acid monomers of [9-14C] 9-(6-propyl-cyclohex-3-enyl)-non-8-enoic acids and 14CO2 production was monitored for 24h. The animals were then necropsied and the radioactivity was determined in different tissues. No consistent radioactivity was recovered as 14CO2 24h after administration of the molecules. Sixty percent of the radioactivity was recovered in the urine and 30% in the gastrointestinal tract. By combining our previous data on the oxidation of [1-14C] cyclic fatty acids and the present results, we suggest that cyclohexenyl fatty acids are first beta oxidized in a similar way as linolenic acid and that the remaining molecule carrying the ring is detoxified and eliminated in the urine and feces.     

Data exploration in phylogenetic inference: scientific, heuristic, or neither

The methods of data exploration have become the centerpiece of phylogenetic inference, but without the scientific importance of those methods having been identified. We examine in some detail the procedures and justifications of Wheeler's sensitivity analysis and relative rate comparison (saturation analysis). In addition, we review methods designed to explore evidential decisiveness, clade stability, transformation series additivity, methodological concordance, sensitivity to prior probabilities (Bayesian analysis), skewness, computer‐intensive tests, long‐branch attraction, model assumptions (likelihood ratio test), sensitivity to amount of data, polymorphism, clade concordance index, character compatibility, partitioned analysis, spectral analysis, relative apparent synapomorphy analysis, and congruence with a “known” phylogeny. In our review, we consider a method to be scientific if it performs empirical tests, i.e., if it applies empirical data that could potentially refute the hypothesis of interest. Methods that do not perform tests, and therefore are not scientific, may nonetheless be heuristic in the scientific enterprise if they point to more weakly or ambiguously corroborated hypotheses, such propositions being more easily refuted than those that have been more severely tested and are more strongly corroborated. Based on common usage, data exploration in phylogenetics is accomplished by any method that performs sensitivity or quality analysis. Sensitivity analysis evaluates the responsiveness of results to variation or errors in parameter values and assumptions. Sensitivity analysis is generally interpreted as providing a measure of support, where conclusions that are insensitive (robust, stable) to perturbations are judged to be accurate, probable, or reliable. As an alternative to that verificationist concept, we define support objectively as the degree to which critical evidence refutes competing hypotheses. As such, degree of support is secondary to the scientific optimality criterion of maximizing explanatory power. Quality analyses purport to distinguish good, reliable, accurate data from bad, misleading, erroneous data, thereby assessing the ability of data to indicate the true phylogeny. Only the quality analysis of character compatibility can be judged scientific—and a weak test at that compared to character congruence. Methods judged to be heuristic include Bremer support, long‐branch extraction, and safe taxonomic reduction, and we underscore the great heuristic potential of a posteriori analysis of patterns of transformations on the total‐evidence cladogram. However, of the more than 20 kinds of data exploration methods evaluated, the vast majority is neither scientific nor heuristic. Given so little demonstrated cognitive worth, we conclude that undue emphasis has been placed on data exploration in phylogenetic inference, and we urge phylogeneticists to consider more carefully the relevance of the methods that they employ. [T]he cult of impressive technicalities or the cult of precision may get the better of us, and interfere with our search for clarity, simplicity, and truth [Popper, 1983, p. 60. Empirical papers chosen for publication are judged to be of interest to a broad systematics audience because they represent exemplary case studies involving some important contemporary issue or issues. These may be unusually thorough explorations of data, applications of new methodology, illustrations of fundamental principles, and/or investigations of interesting evolutionary questions. [Systematic Biology: Instructions for authors, 2002; italics added]     

Comparative assessment of toxic effects of surfactants using biotesting methods

This study assesses the comparative sensitivity and possibility of obtaining fast results of various methods of biotesting for several surfactants: Tween 85, sodium dodecyl sulfate (SDS), Fairy dishwashing gel, and Mif washing powder. The following test organisms are used for the study: luminescent bacteria Photobacterium phosphoreum (Beijerinck), preparation of Ecolum luminescent bacteria, unicellular algae Scenedesmus quadricauda (G.M. Smith), infusorian Paramecium caudatum (Ehrenberg), and crustacean Daphnia magna (Straus). It has been revealed that Fairy dishwashing gel possesses the strongest toxicity against the studied test objects. Daphnia and algae are most sensitive to the effects of Fairy and SDS, protozoan and luminescent bacteria are most sensitive to SDS, and Ecolum is most sensitive to Mif washing powder. The tested aquatic organisms and Ecolum are most tolerant to the effect of Tween 85.     

The effect of kringles K1-3, K4 and K5 on lysis of fibrin clots caused by the activation of Glu- and Lys-plasminogen by a tissue activator

Kringles K1-3, K4 and K5 are studied for their effect on tissue plasminogen activator-induced fibrin clot lysis in the presence of Glu- and Lys-plasminogen. It is established that kringles K4 and K5 inhibit fibrinolysis of Glu-plasminogen, and K1-3--that of Lys-plasminogen. The role of plasminogen molecule kringles in the plasminogen interaction with fibrin polymer is discussed.