Biomedical subjects

David O'Hara

Publications and source records attributed to David O'Hara.

3 recordsLinked to original sources

PubMed2005

Structure of avian orthoreovirus virion by electron cryomicroscopy and image reconstruction.

Among members of the genus Orthoreovirus, family Reoviridae, a group of non-enveloped viruses with genomes comprising ten segments of double-stranded RNA, only the "non-fusogenic" mammalian orthoreoviruses (MRVs) have been studied to date by electron cryomicroscopy and three-dimensional image reconstruction. In addition to MRVs, this genus comprises other species that induce syncytium formation in cultured cells, a property shared with members of the related genus Aquareovirus. To augment studies of these "fusogenic" orthoreoviruses, we used electron cryomicroscopy and image reconstruction to analyze the virions of a fusogenic avian orthoreovirus (ARV). The structure of the ARV virion, determined from data at an effective resolution of 14.6 A, showed strong similarities to that of MRVs. Of particular note, the ARV virion has its pentameric lambda-class core turret protein in a closed conformation as in MRVs, not in a more open conformation as reported for aquareovirus. Similarly, the ARV virion contains 150 copies of its monomeric sigma-class core-nodule protein as in MRVs, not 120 copies as reported for aquareovirus. On the other hand, unlike that of MRVs, the ARV virion lacks "hub-and-spokes" complexes within the solvent channels at sites of local sixfold symmetry in the incomplete T=13l outer capsid. In MRVs, these complexes are formed by C-terminal sequences in the trimeric mu-class outer-capsid protein, sequences that are genetically missing from the homologous protein of ARVs. The channel structures and C-terminal sequences of the homologous outer-capsid protein are also genetically missing from aquareoviruses. Overall, the results place ARVs between MRVs and aquareoviruses with respect to the highlighted features.

Amino Acid Sequence↗

PubMed2005

Evaluation of capnography using a genetic algorithm to predict PaCO2.

INTRODUCTION: Noninvasive estimates of Paco(2) are usually done by measuring exhaled carbon dioxide at end-expiration (Petco(2)). While commonly used in studies involving healthy patients, it is less useful in sicker patients. Conditions that affect the terminal dead space and hence the accuracy of Petco(2) as a surrogate for Paco(2) may also affect other components of the capnogram. A genetic algorithm is a computer technique for discovering relationships between variables. The purpose of this study was to use a genetic algorithm to improve the precision of Paco(2) prediction in comparison to Petco(2). METHODS: Inspiratory and expiratory volumes were measured and analyzed by the computerized capnogram. Data were recorded for 2 min. Within 5 min of recording the capnograms, arterial blood gases were obtained. After excluding artifact and incomplete capnograms, five of the remaining breaths from each patient were selected. A genetic algorithm, constructed in postfix notation, consisted of 1,000 chromosomes with genes randomly selected from the 11 capnographic data fields and mathematical operators. The algorithm was constructed on 400 breaths from 83 randomly selected patients (construction group) and tested on 160 breaths from the remaining 32 patients (test group). RESULTS: For the construction group, the bias and precision between Petco(2) and Paco(2) were 4.3 +/- 4.9 mm Hg (mean +/- SD). For the 160 breaths in the test group, Petco(2) predicted Paco(2) with bias and precision of 2.9 +/- 4.2 mm Hg. The best chromosome found by the genetic algorithm was (10 x 5 + 5 x 5 x 5)/(10 x 10) x Petco(2) - (5 x 5 x 10 + 5 x 5)/(10 x 10) x int time + 2 x 2 x 2 x 2 + (2 x 2)/10, which reduces to 0.65 x Petco(2) - 2.75 x int time + 16.4. This produced a bias and precision of 0.9 +/- 4.1 mm Hg in the construction group and 0 +/- 3.7 mm Hg in the test group (p < 0.01). CONCLUSIONS: In this study of nonintubated emergency department patients, a genetic algorithm produced an improvement in bias and precision of Paco(2) prediction.

Adult↗

PubMed2002

Sequential partially overlapping gene arrangement in the tricistronic S1 genome segments of avian reovirus and Nelson Bay reovirus: implications for translation initiation.

Previous studies of the avian reovirus strain S1133 (ARV-S1133) S1 genome segment revealed that the open reading frame (ORF) encoding the final sigmaC viral cell attachment protein initiates over 600 nucleotides distal from the 5' end of the S1 mRNA and is preceded by two predicted small nonoverlapping ORFs. To more clearly define the translational properties of this unusual polycistronic RNA, we pursued a comparative analysis of the S1 genome segment of the related Nelson Bay reovirus (NBV). Sequence analysis indicated that the 3'-proximal ORF present on the NBV S1 genome segment also encodes a final sigmaC homolog, as evidenced by the presence of an extended N-terminal heptad repeat characteristic of the coiled-coil region common to the cell attachment proteins of reoviruses. Most importantly, the NBV S1 genome segment contains two conserved ORFs upstream of the final sigmaC coding region that are extended relative to the predicted ORFs of ARV-S1133 and are arranged in a sequential, partially overlapping fashion. Sequence analysis of the S1 genome segments of two additional strains of ARV indicated a similar overlapping tricistronic gene arrangement as predicted for the NBV S1 genome segment. Expression analysis of the ARV S1 genome segment indicated that all three ORFs are functional in vitro and in virus-infected cells. In addition to the previously described p10 and final sigmaC gene products, the S1 genome segment encodes from the central ORF a 17-kDa basic protein (p17) of no known function. Optimizing the translation start site of the ARV p10 ORF lead to an approximately 15-fold increase in p10 expression with little or no effect on translation of the downstream final sigmaC ORF. These results suggest that translation initiation complexes can bypass over 600 nucleotides and two functional overlapping upstream ORFs in order to access the distal final sigmaC start site.

Amino Acid Sequence↗