A fixed-point alignment technique for detection of recurrent and common sequence motifs associated with biological features

A fixed-point alignment analysis technique is presented whichis designed to locate common sequence motifs in collectionsof proteins or nucleic acids. Initially a program aligns a collectionof sequences by a common sequence pattern or known biologicalfeature. The common pattern or feature (fixed-point) may bea user-specified sequence string or a known sequence positionlike mRNA start site, which may be taken directly from the annotatedfeature table of GenBank. Once all alignment markers are located,the sequences are scanned for occurrences of given oligomerswithin a specified span both upstream and downstream of thefixed-point. The occurrences may then be plotted as a functionof the position relative to the fixed-point, displayed as anactual sequence alignment or selectively summarized via variousprogram options. Applications of the technique are discussed. Received on August 17, 1987; accepted on November 17, 1987     

Effect of hyperinflation on inspiratory function of the diaphragm.

The inspiratory efficiency of the diaphragm during unilateral and bilateral phrenic stimulation (UEPS and BEPS) with constant stimulus was studied in seven dogs from FRC to 120% TLC. Alveolar pressures (PAl) were recorded during relaxation, BEPS and UEPS at each lung volume in the closed respiratory system. From the PAl-lung volume curves, tidal volume (VT), and pressure developed by the diaphragm (Pmus) were derived. Results are summarized below. a) Hyperinflation impaired the inspiratory efficiency of the diaphragm which behaved as an expiratory muscle beyond the lung volume of 103.7% TLC (Vinef). b) The diaphragm during UEPS became expiratory at the same Vinef as during (BEPS. C) The VT-lung volume relationship was linear during BEPS, allowing simple quantitation of VT loss with hyperinflation and prediction of Vinef. d) With only one phrenic nerve stimulated, the functional loss is less pronounced in VT than in Pmus, as compared to BEPS, indicating that the respiratory system was more compliant during UEPS than BEPS. This compliance difference from UEPS to BEPS diminished with severe hyperinflation.     

Scanning mutagenesis of regions in the Galpha protein Gpa1 that are predicted to interact with yeast mating pheromone receptors.

The mechanism by which receptors activate heterotrimeric G proteins was examined by scanning mutagenesis of the Saccharomyces cerevisiae pheromone-responsive Galpha protein (Gpa1). The juxtaposition of high-resolution structures for rhodopsin and its cognate G protein transducin predicted that at least six regions of Galpha are in close proximity to the receptor. Mutagenesis was targeted to residues in these domains in Gpa1, which included four loop regions (beta2-beta3, alpha2-beta4, alpha3-beta5, and alpha4-beta6) as well as the N and C termini. The mutants displayed a range of phenotypes from nonsignaling to constitutive activation of the pheromone pathway. The constitutive activity of some mutants could be explained by decreased production of Gpa1, which permits unregulated signaling by Gbetagamma. However, the constitutive activity caused by the F344C and E335C mutations in the alpha2-beta4 loop and F378C in the alpha3-beta5 loop was not due to decreased protein levels, and was apparently due to defects in sequestering Gbetagamma. The strongest loss of the function mutant, which was not detectably induced by a pheromone, was caused by a K314C substitution in the beta2-beta3 loop. Several other mutations caused weak signaling phenotypes. Altogether, these results suggest that residues in different interface regions of Galpha contribute to activation of signaling.     

S. cerevisiae alpha pheromone receptors activate a novel signal transduction pathway for mating partner discrimination.

Wild-type S. cerevisiae cells of both mating types prefer partners producing high levels of pheromone and mate very infrequently to cells producing no pheromone. However, some mutants that are supersensitive to pheromone lack this ability to discriminate. In this study, we provide evidence for a novel role of alpha pheromone receptors in mating partner discrimination that is independent of the known G protein-mediated signal transduction pathway. Furthermore, in response to pheromone, receptors become localized to the emerging region of morphogenesis that is positioned adjacent to the nucleus, suggesting that receptor localization may be involved in mating partner discrimination. Actin, myosin 2, and clathrin heavy chain are involved in mating partner discrimination, since strains carrying mutations in the genes encoding these proteins result in a small but significant defect in mating partner discrimination.     

Low-dose PGI2 prevents monocrotaline-induced thromboxane production and lung injury

In animals, monocrotaline induces an acute lung injury secondary to capillary endothelial damage. To date, no reports have appeared dealing with the role of prostaglandins in monocrotaline-induced injury. Our studies, in dogs, revealed that monocrotaline (30 mg/kg iv) caused an acute and persistent thrombocytopenia, lung platelet deposition, pulmonary hypertension, and increased extravascular lung water (EVLW). The pulmonary hypertensive response was biphasic. Thromboxane B2 levels were similarly biphasic, peaking at 5 min and 2 h. The levels of 6-keto-PGF1 alpha peaked at 30 min and returned to base line at 3 h. Pulmonary vascular resistance paralleled thromboxane levels. Infusion of prostacyclin (PGI2) at 50 ng X kg-1 X min-1 effectively prevented the thrombocytopenia, lung platelet deposition, pulmonary hypertension, and increased EVLW; and it decreased excess thromboxane production by 79%. These results suggest that platelet activation and lung sequestration play a role in acute lung injury due to monocrotaline, and that the resultant thromboxane production may contribute to the pulmonary hypertension. PGI2 ameliorates monocrotaline-induced injury, perhaps by preventing platelet activation.     

Anaerobic degradation of chloroacetanilide herbicides

Anaerobic microbial transformations of chloroacetanilide herbicides (alachlor, metolachlor, and propachlor) and aniline were investigated. Modest microbial transformations (in most cases 30–60% losses) of chloroacetanilide herbicides were found in agricultural soils incubated under anaerobic conditions for 30 days. Greater anaerobic losses were observed in anaerobic digestor sludge or rumen fluid. Anilines were not substantially transformed in any system within 30 days. The highest anaerobic activities metabolizing alachlor or propachlor occurred in anaerobic sludge. However, this biological activity could only be transferred if autoclaved sludge digestor material was added to the transfer medium, which suggests that the activities involved co-metabolism of the substrates.     

Physiological Changes Within a Metalimnetic Layer of Oscillatoria rubescens

Different depths within a metalimnetic layer of Oscillatoria rubescens were sampled, and changes in biochemical composition and photosynthetic rate were analyzed. Although differences in pigment and protein content were found, the photosynthetic rates of the samples were not significantly different.