Mix'n'Match: an improved multiple sequence alignment procedure for distantly related proteins using secondary structure predictions, designed to be independent of the choice of gap penalty and scoring matrix.

A new multiple sequence alignment procedure is presented. Several different multiple alignments are made using differing criteria. Having divided the sequences into strongly conserved regions (SCRs) and loosely conserved regions (LCRs), the 'best' alignment for each LCR is chosen, independently of the other LCRs, from a selection of possibilities in the multiple alignments. To help make this choice for each LCR, the secondary structure is predicted and shown alongside each different possible alignment. One advantage of this method over automatic, non-interactive methods, is that the final alignment is not dependent on the choice of a single set of scoring parameters. Another is that, by allowing interactive choice and by taking account of secondary structural information, the final alignment is based more on biological rather than mathematical factors. This method can produce better alignments than any of the initial automatic multiple alignment methods used.

Pyrrolidine ring puckering in cis and trans-proline residues in proteins and polypeptides. Different puckers are favoured in certain situations.

In a set of proteins studied at high resolution by X-ray crystallography over a half of all cis and trans-proline residues could be unambiguously assigned to one of the two forms of pyrrolidine ring puckering, called UP and DOWN. Of these, 89% of the cis-proline residues exhibit the DOWN pucker, while the trans-proline residues, on average, are about evenly distributed between the two forms. Of trans-proline residues found in alpha-helices, 79% have the UP ring pucker. trans-proline residues occurring in other situations are more equally distributed between the two forms of pucker, although further generalizations may be possible. Proline residues in a set of crystal structures of short polypeptides were also examined. As in the protein sample, a tendency for the cis-proline residues to have the DOWN pucker was observed, but the effect was less pronounced.

The prehospital use of albuterol inhalation treatments.

The use of bronch odilators in the prehospital EMS setting is common. This study examined the safety of the administration of 2.5 mg albuterol using a hand-held nebulizer for the treatment of such patients. A total of 55 patients were included. Following treatment, peak expiratory flow rates (PEFR) increased a mean of 27 L/min, ventilatory rate decreased four breaths/min, heart rate decreased slightly, and systolic blood pressure increased 10 mmHg. Five of the 53 patients in whom cardiac rhythm was monitored, had premature ventricular complexes prior to treatment; only one did following therapy. Breath sounds improved in 61% and were unchanged in 39%. Breathing was reported by the patient as improved in 51 of the 53 (93%) and only one felt worse. Adverse reactions were reported in 15%, but none were severe. This study shows that albuterol (2.5 mg) administration by hand-held nebulizer is both safe and efficacious in the prehospital setting.