A generic algorithm for finding restriction sites within DNA sequences

This paper describes a generic algorithm for finding restrictionsites within DNA sequences. The ‘genericity’ ofthe algorithm is made possible through the use of set theory.Basic elements of DNA sequences, i.e. nucleotides (bases), arerepresented in sets, and DNA sequences, whether specific, ambiguousor even protein-coding, are represented as sequences of thosesets. The set intersection operation demonstrates its abilityto perform pattern-matching correctly on various DNA sequences.The performance analysis showed that the degree of complexityof the pattern matching is reduced from exponential to linear.An example is given to show the actual and potential restrictionsites, derived by the generic algorithm, in the DNA sequencetemplate coding for a synthetic calmodulin. Received on October 2, 1990; accepted on December 18, 1990     

Conversion of 5′-Methylthioadenosine into S-adenosylmethionine by yeast cells

5′-Methylthio[U-¹⁴C]adenosine was used as a culture supplement for Candida utilitis. The resulting S-adenosylmethionine was hydrolyzed into its structural components. Virtually none of the label of the pentose was found in the carbohydrate part of the intracellular S-adenosylmethionine. Much of it was present in the four-carbon chain of the methionine part of the sulfonium compound. The U-¹⁴C)-labeled adenine of 5′-methylthio[U-¹⁴C]adenosine did not contribute to the labeling of the amino acid component of the sulfonium compound.     

The improper use of fossil nomenclature

Retention of obsolete genera and species, and premature acceptance of provisional genera and species unnecessarily inhibit meaningful communication between students of fossil man.     

Repeating structure of chick tropoelastin revealed by complementary DNA cloning

A cDNA library was constructed from chick aorta poly(adenylic acid)-containing RNA in the expression vector pEX1. Several clones were identified by screening the library with a polyclonal antiserum raised against chick tropoelastin and confirmed by DNA sequencing. Analysis of the deduced amino acid sequence, corresponding to the mature tropoelastin and most of the signal peptide, revealed that the molecule is composed of at least 8, and possibly 13, repeating units. The common features of each unit include an N-terminal region composed largely of alanines and lysines and ending with an aromatic amino acid, followed by a GAG span and then a C-terminal region consisting mostly of valines, prolines, and glycines often present in several copies of the sequence (VPGV). This structure is discussed in terms of the functional properties of the molecule.     

Static and dynamic assessment of the Biodex dynamometer

The validity and accuracy of the Biodex dynamometer was investigated under static and dynamic conditions. Static torque and angular position output correlated well with externally derived data (r = 0.998 and r greater than 0.999, respectively). Three subjects performed maximal voluntary knee extensions and flexions at angular velocities from 60 to 450 degrees.s-1. Using linear accelerometry, high speed filming and Biodex software, data were collected for lever arm angular velocity and linear accelerations, and subject generated torque. Analysis of synchronized angular position and velocity changes revealed the dynamometer controlled angular velocity of the lever arm to within 3.5% of the preset value. Small transient velocity overshoots were apparent on reaching the set velocity. High frequency torque artefacts were observed at all test velocities, but most noticeably at the faster speeds, and were associated with lever arm accelerations accompanying directional changes, application of resistive torques by the dynamometer, and limb instability. Isokinematic torques collected from ten subjects (240, 300 and 400 degrees.s-1) identified possible errors associated with reporting knee extension torques at 30 degrees of flexion. As a result of tissue and padding compliance, leg extension angular velocity exceeded lever arm angular velocity over most of the range of motion, while during flexion this compliance meant that knee and lever arm angles were not always identical, particularly at the start of motion. Nevertheless, the Biodex dynamometer was found to be both a valid and an accurate research tool; however, caution must be exercised when interpreting and ascribing torques and angular velocities to the limb producing motion.     

The LEC11 Chinese hamster ovary mutant synthesizes N-linked carbohydrates containing sialylated, fucosylated lactosamine units. Analysis by one- and two-dimensional 1H NMR spectroscopy

Glycoproteins synthesized by the Chinese hamster ovary cell mutants LEC11 and LEC12 carry the Lex determinant (Gal beta 1,4(Fuc alpha 1,3)GlcNAc), while those synthesized by LEC11 cells also carry the sialyl-Lex determinant (NeuAc alpha 2,3Gal beta 1,4(Fuc alpha 1,3)GlcNAc), and both mutants have been shown to possess a distinct alpha(1,3)-fucosyltransferase of the appropriate specificity to synthesize these determinants (Campbell, C., and Stanley, P. (1983) Cell 35, 303-309; Campbell, C., and Stanley, P. (1984), J. Biol. Chem. 259, 11208-11214; Howard, D. R., Fukuda, M., Fukuda, M. N., and Stanley, P. (1987) J. Biol. Chem. 262, 16830-16837). The LEC11 cells therefore provide a source of carbohydrates terminating in sialylated, fucosylated lactosamine, a relatively rare structure not previously characterized by 1H NMR spectroscopy when in association with an N-linked carbohydrate. In this paper we use a monoclonal antibody specific for Lex to show that the G glycoprotein of vesicular stomatitis virus (VSV) grown in LEC11 and LEC12 cells possesses the Lex determinant and that G from LEC11/VSV also possesses sialylated Lex. Biantennary carbohydrates purified from LEC11/VSV and LEC12/VSV were therefore used to examine the effects on the 1H NMR spectrum of the presence of alpha(1,3)-fucose residues on sialylated and unsialylated lactosamine units. Comparisons of one-dimensional spectra obtained at 500 MHz from LEC11/VSV and LEC12/VSV glycopeptides before and after neuraminidase treatment with spectra of biantennary carbohydrates lacking alpha(1,3)-fucose allowed the assignment of several new resonances. Resolution of certain signals and determinations of coupling constants were achieved by two-dimensional correlation spectroscopy (COSY) at 400 MHz and allowed the assignment of several more resonances in the one-dimensional spectrum.     

Castleman's disease, plasma-cell type. Diagnosis of central nervous system involvement by cerebrospinal fluid cytology

A case of Castleman's disease of the plasma-cell type is reported in which central nervous system (CNS) involvement was diagnosed by cerebrospinal fluid (CSF) cytology. The patient had multicentric disease with constitutional symptoms, immunologic abnormalities and peripheral blood cytopenias requiring cytotoxic agents and steroids for treatment. CNS symptoms and diagnostic cytologic findings in CSF occurred in the absence of morphologic lesions demonstrable by computed tomography or magnetic resonance imaging of the brain.     

Kinetic mechanisms of two NAD:arginine ADP-ribosyltransferases: the soluble, salt-stimulated transferase from turkey erythrocytes and choleragen, a toxin from Vibrio cholerae

A subunit of choleragen and an erythrocyte ADP-ribosyltransferase catalyze the transfer of ADP-ribose from NAD to proteins and low molecular weight guanidino compounds such as arginine. These enzymes also catalyze the hydrolysis of NAD to nicotinamide and ADP-ribose. The kinetic mechanism for both transferases was investigated in the presence and absence of the product inhibitor nicotinamide by using agmatine as the acceptor molecule. To obtain accurate estimates of kinetic parameters, the transferase and glycohydrolase reactions were monitored simultaneously by using [adenine-2,8-3H]NAD and [carbonyl-14C]NAD as tracer compounds. Under optimal conditions for the transferase assay, NAD hydrolysis occurred at less than 5% of the Vmax for ADP-ribosylation; at subsaturating agmatine concentrations, the ratio of NAD hydrolysis to ADP-ribosylation was significantly higher. Binding of either NAD or agmatine resulted in a greater than 70% decrease in affinity for the second substrate. All data were consistent with a rapid equilibrium random sequential mechanism for both enzymes.     

Quantitative defense theory and patterns of feeding by oak insects

Summary Patterns of herbivory over a two year period on Quercus emoryi (Fagaceae) were correlated with seasonal and yearly changes in tannin and protein content. Quantitative defense theory predicts that tannin and protein content in apparent plants should be negatively and positively correlated, respectively, with degree of herbivory. Most herbivory occurred early in the growing season, but the pattern varied between the two years. Tannin and protein content sometimes varied negatively and sometimes positively with degree of herbivory; they did not consistently covary with herbivory. Protein content was positively correlated with herbivory in 1981–1982 but not in 1982–1983. Condensed tannin content was negatively correlated with herbivory in 1981–1982 but not in 1982–1983. Hydrolysable tannin content was positively correlated with herbivory activity. Multiple regression analyses indicated these phytochemical variables explained either no significant variation in herbivory (1982–1983) or did so in a fashion opposite (1981–1982) to the predictions of the theory of quantitative defense.Feeding by oak insects was not solely a function of seasonal changes in quantitative defenses and nutrients. Obviously, population dynamics of the insects are sensitive to factors other than phytochemistry of the trees and I discuss other factors that can influence patterns of herbivory.