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Biomedical subjects

R Gilmour

Publications and source records attributed to R Gilmour.

At least 19 recordsLinked to original sources

The association of respiratory viruses, temperature, and other climatic parameters with the incidence of invasive pneumococcal disease in Sydney, Australia.

BACKGROUND: Increases in incidence of invasive pneumococcal disease (IPD) during the colder months of the year in temperate regions are well recognized, but few detailed studies of possible interactions are available. We examined the relationship between virus activity, climatic parameters, and IPD during a winter in which there were separate peak incidences of influenza and respiratory syncytial virus (RSV) infection. METHODS: We performed an ecological study that correlated population-based data on IPD and respiratory virus activity in the year 2000 in metropolitan New South Wales, Australia, with climatic parameters, including weekly mean maximum and minimum temperature, relative humidity, rainfall, and wind speed. RESULTS: In children, RSV activity was significantly positively correlated with IPD activity (r = 0.578; P = .002) but not with influenza virus activity. There was a weak inverse relationship between parainfluenza virus activity and IPD activity (r = -0.401; P = .043) and a stronger inverse relationship between weekly mean maximum temperature (r = -0.458; P = .001), weekly mean minimum temperature (r = -0.437; P = .001), and IPD activity. In adults, there was no significant correlation between RSV or influenza virus activity alone and IPD, but the combination of RSV and influenza was significantly correlated with IPD (r = 0.481; P = .013). CONCLUSIONS: This study suggests that RSV infection and influenza contribute to IPD incidence peaks differently for children than for adults. Data from other geographic areas and more rigorous study designs are required to confirm these findings.

Adult↗

A population based study of the impact of corticosteroid therapy and delayed diagnosis on the outcome of childhood pneumococcal meningitis.

BACKGROUND: Despite an extensive literature, the impact of both adjunctive steroid therapy and delayed diagnosis on the outcome of childhood pneumococcal meningitis is controversial. AIM: To determine the independent contribution of corticosteroid therapy and delayed diagnosis on the outcome of childhood pneumococcal meningitis in a representative population with good access to medical services. METHODS: Data were obtained from laboratories and hospital records to assemble a population register in Sydney, Australia, 1994-99. Follow up questionnaires were completed by attending physicians. RESULTS: A total of 122 cases of pneumococcal meningitis aged 0-14 years were identified. Almost 50% of 120 children with available records either died (n = 15) or had permanent neurological impairment (n = 39). Early use (before or with parenteral antibiotics) of corticosteroids protected against death or severe morbidity (adjusted OR 0.21, 95% CI 0.05 to 0.77). Delayed diagnosis was associated with increased morbidity in survivors (OR 3.4, 95% CI 1.03 to 11.4) but not with increased mortality. CONCLUSION: In a population with good access to health care and after adjusting for other known prognostic variables, early recognition of pneumococcal meningitis and treatment with adjunctive dexamethasone significantly improves outcomes. These data add to those from randomised controlled trials. Implementation requires development of protocols and guidelines for use in emergency departments.

Administration, Oral↗

The emergence of resistant pneumococcal meningitis--implications for empiric therapy.

BACKGROUND: Following the emergence of penicillin and cephalosporin resistant pneumococcal meningitis in the United States, inclusion of vancomycin in empiric therapy for all suspected bacterial meningitis was recommended by the American Academy of Pediatrics. Few data are available to evaluate this policy. AIMS: To examine the management and clinical course in relation to antibiotic therapy of a large unselected cohort of children with pneumococcal meningitis in a geographic area where antibiotic resistance has recently increased. METHODS: Retrospective review of all cases of pneumococcal meningitis in a defined population (Sydney, Australia), 1994-99. RESULTS: A total of 104 cases without predisposing illnesses were identified; timing of lumbar puncture (LP) was known in 103. Resistance to penicillin increased from 0 to 20% over the study period. Only 57 (55%) had an early LP (prior to parenteral antibiotics); 55 (96%) had organisms on Gram stain. Severe disease (intensive care admission or death) increased significantly from 57 cases with early LP (28%) to 33 with delayed LP (42%) to 13 with no LP (62%). Evidence of pneumococcal infection was available within 24 hours in 85% of those with delayed or no LP. Outcome was not related to empiric vancomycin use, which increased from 5% prior to 1998 to 48% in 1999. CONCLUSION: LP is frequently delayed in pneumococcal meningitis. Based on disease severity, empiric vancomycin is most justified when LP is deferred. If an early LP is done, vancomycin can be withheld if Gram positive diplococci are not seen.

Adolescent↗

15-deoxy-delta12,14-prostaglandin J2-induced apoptosis in amnion-like WISH cells.

Apoptosis at the site of rupture has been proposed to play a role in premature rupture of the fetal membranes, a condition associated with increased risk of neonatal sepsis and preterm birth. We investigated the ability of peroxisome proliferator-activated receptor (PPAR)-gamma ligands 15-deoxy-delta12,14PGJ2 (15d-PGJ2), delta12PGJ2, ciglitizone and rosiglitazone to induce apoptosis in the amnion-like WISH cell line. 15d-PGJ2 (10 microM) induced morphological characteristics of apoptosis within 2 h, with biochemical indices (caspase activation and substrate cleavage) following shortly after; maximum cell death (approximately 60%) was observed by 16 h, with an EC50) of approximately 7 microM 15d-PGJ2. Delta12-PGJ2 also induced apoptosis but was less potent and acted at a much slower rate. While ciglitizone also induced apoptosis, rosiglitazone had no effect on cell viability. The mechanism of induction of apoptosis by 15d-PGJ2 and delta12PGJ2, which may be independent of PPAR-gamma activation, requires further elucidation.

Amino Acid Chloromethyl Ketones↗

Cultural values and happiness: an East-West dialogue.

Happiness as a state of mind may be universal, but its meaning is complex and ambiguous. The authors directly examined the relationships between cultural values and experiences of happiness in 2 samples, by using a measurement of values derived from Chinese culture and a measurement of subjective well-being balanced for sources of happiness salient in both the East and the West. The participants were university students-439 from an Eastern culture (Taiwan) and 344 from a Western culture (the United Kingdom). Although general patterns were similar in the 2 samples, the relationships between values and happiness were stronger in the Taiwanese sample than in the British sample. The values social integration and human-heartedness had culture-dependent effects on happiness, whereas the value Confucian work dynamism had a culture-general effect on happiness.

Adolescent↗

Absolute pitch, early musical instruction, and spatial abilities.

The results of the study show that AP possessors performed better in the Hidden Figure Test than did NMs and musicians with RP and that age at which music instruction is initiated affects performance in specific spatial tasks. Individuals who begin extensive musical instruction at a very early age may have an advantage when completing selected spatial tests over those with no formal musical training. However, characteristics other than starting age of musical instruction are associated with AP and seem to affect musicians' performance in the Hidden Figure Test. The differences found between the performance of AP possessors and RP possessors in this nonmusical task suggest further research.

Aging↗

Genome of the bacterium Streptococcus pneumoniae strain R6.

Streptococcus pneumoniae is among the most significant causes of bacterial disease in humans. Here we report the 2,038,615-bp genomic sequence of the gram-positive bacterium S. pneumoniae R6. Because the R6 strain is avirulent and, more importantly, because it is readily transformed with DNA from homologous species and many heterologous species, it is the principal platform for investigation of the biology of this important pathogen. It is also used as a primary vehicle for genomics-based development of antibiotics for gram-positive bacteria. In our analysis of the genome, we identified a large number of new uncharacterized genes predicted to encode proteins that either reside on the surface of the cell or are secreted. Among those proteins there may be new targets for vaccine and antibiotic development.

Bacterial Proteins↗

Taxonomic markup language: applying XML to systematic data.

SUMMARY: An XML document type definition (DTD) is provided for the description of taxonomic relationships between organisms. Two XSL style-sheets for the graphical presentation of simple taxonomic trees are also provided. AVAILABILITY: The DTD and stylesheets along with sample files are available at http://www.albany.edu/gilmr/pubxml/.

Classification↗

Two-dimensional gel electrophoresis analyses of pH-dependent protein expression in facultatively alkaliphilic Bacillus pseudofirmus OF4 lead to characterization of an S-layer protein with a role in alkaliphily.

The large majority of proteins of alkaliphilic Bacillus pseudofirmus OF4 grown at pH 7.5 and 10.5, as studied by two-dimensional gel electrophoresis analyses, did not exhibit significant pH-dependent variation. A new surface layer protein (SlpA) was identified in these studies. Although the prominence of some apparent breakdown products of SlpA in gels from pH 10.5-grown cells led to discovery of the alkaliphile S-layer, the largest and major SlpA forms were present in large amounts in gels from pH 7.5-grown cells as well. slpA RNA abundance was, moreover, unchanged by growth pH. SlpA was similar in size to homologues from nonalkaliphiles but contained fewer Arg and Lys residues. An slpA mutant strain (RG21) lacked an exterior S-layer that was identified in the wild type by electron microscopy. Electrophoretic analysis of whole-cell extracts further indicated the absence of a 90-kDa band in the mutant. This band was prominent in wild-type extracts from both pH 7.5- and 10.5-grown cells. The wild type grew with a shorter lag phase than RG21 at either pH 10.5 or 11 and under either Na(+)-replete or suboptimal Na(+) concentrations. The extent of the adaptation deficit increased with pH elevation and suboptimal Na(+). By contrast, the mutant grew with a shorter lag and faster growth rate than the wild type at pH 7. 5 under Na(+)-replete and suboptimal Na(+) conditions, respectively. Logarithmically growing cells of the two strains exhibited no significant differences in growth rate, cytoplasmic pH regulation, starch utilization, motility, Na(+)-dependent transport of alpha-aminoisobutyric acid, or H(+)-dependent synthesis of ATP. However, the capacity for Na(+)-dependent pH homeostasis was diminished in RG21 upon a sudden upward shift of external pH from 8. 5 to 10.5. The energy cost of retaining the SlpA layer at near-neutral pH is apparently adverse, but the constitutive presence of SlpA enhances the capacity of the extremophile to adjust to high pH.

Alkalies↗

The surface-charge asymmetry and dimerisation of cytochrome c550 from Paracoccus denitrificans--implications for the interaction with cytochrome c peroxidase.

The implications of the dimeric state of cytochrome c550 for its binding to Paracoccus cytochrome c peroxidase and its delivery of the two electrons required to restore the active enzyme during catalysis have been investigated. The amino acid sequence of cytochrome c550 of Paracoccus denitrificans strain LMD 52.44 was determined and showed 21 differences from that of strain LMD 22.21. Based on the X-ray structure of the latter, a structure for the cytochrome c550 monomer from strain 52.44 is proposed and a dipole moment of 945 debye was calculated with an orientation close to the exposed haem edge. The behaviour of the cytochrome on molecular-exclusion chromatography is indicative of an ionic strength-dependent monomer (15 kDa)/dimer (30 kDa) equilibrium that can also be detected by 1H-NMR spectroscopy. The apparent mass of 50 kDa observed at very low ionic strength was consistent with the presence of a strongly asymmetric dimer. This was confirmed by cross-linking studies, which showed that a cross-linked species of mass 30 kDa on SDS behaved with an apparent mass of 50 kDa on molecular-exclusion chromatography. A programme which carried out and evaluated molecular docking of two monomers to give a dimer generated a most probable dimer in which the monomer dipoles lay almost antiparallel to each other. The resultant dipole moment of the dimer is therefore small. Although this finding calls into question the possibility of preorientation of a strongly asymmetrically charged cytochrome as it collides with a redox partner, the stoichiometry of complex formation with cytochrome c peroxidase as studied by 1H-NMR spectroscopy shows that it is the monomer that binds.

Amino Acid Sequence↗

pH homeostasis and ATP synthesis: studies of two processes that necessitate inward proton translocation in extremely alkaliphilic Bacillus species.

Alkaliphilic Bacillus species that are isolated from nonmarine, moderate salt, and moderate temperature environments offer the opportunity to explore strategies that have developed for solving the energetic challenges of aerobic growth at pH values between 10 and 11. Such bacteria share many structural, metabolic, genomic, and regulatory features with nonextremophilic species such as Bacillus subtilis. Comparative studies can therefore illuminate the specific features of gene organization and special features of gene products that are homologs of those found in non-extremophiles, and potentially identify novel gene products of importance in alkaliphily. We have focused our studies on the facultative alkaliphile Bacillus firmus OF4, which is routinely grown on malate-containing medium at either pH 7.5 or 10.5. Current work is directed toward clarification of the characteristics and energetics of membrane-associated proteins that must catalyze inward proton movements. One group of such proteins are the Na+/H+ antiporters that enable cells to adapt to a sudden upward shift in pH and to maintain a cytoplasmic pH that is 2-2.3 units below the external pH in the most alkaline range of pH for growth. Another is the proton-translocating ATP synthase that catalyzes robust production of ATP under conditions in which the external proton concentration and the bulk chemiosmotic driving force are low. Three gene loci that are candidates for Na+/H+ antiporter encoding genes with roles in Na(+)-dependent pH homeostasis have been identified. All of them have homologs in B. subtilis, in which pH homeostasis can be carried out with either K+ or Na+. The physiological importance of one of the B. firmus OF4 loci, nhaC, has been studied by targeted gene disruption, and the same approach is being extended to the others. The atp genes that encode the alkaliphile's F1F0-ATP synthase are found to have interesting motifs in areas of putative importance for proton translocation. As an initial step in studies that will probe the importance and possible roles of these motifs, the entire atp operon from B. firmus OF4 has been cloned and functionally expressed in an Escherichia coli mutant that has a full deletion of its atp genes. The transformant does not exhibit growth on succinate, but shows reproducible, modest increases in the aerobic growth yields on glucose as well as membrane ATPase activity that exhibits characteristics of the alkaliphile enzyme.

Adenosine Triphosphate↗

Energetics of alkaliphilic Bacillus species: physiology and molecules.

The challenge of maintaining a cytoplasmic pH that is much lower than the external pH is central to the adaptation of extremely alkaliphilic Bacillus species to growth at pH values above 10. The success with which this challenge is met may set the upper limit of pH for growth in these bacteria, all of which also exhibit a low content of basic amino acids in proteins or protein segments that are exposed to the outside bulk phase liquid. The requirement for an active Na(+)-dependent cycle and possible roles of acidic cell wall components in alkaliphile pH homeostasis are reviewed. The gene loci that encode Na+/H+ antiporters that function in the active cycle are described and compared with the less Na(+)-specific homologues thus far found in non-alkaliphilic Gram-positive prokaryotes. Alkaliphilic Bacillus species carry out oxidative phosphorylation using an exclusively H(+)-coupled ATPase (synthase). Nonetheless, ATP synthesis is more rapid and reaches a higher phosphorylation potential at highly alkaline pH than at near-neutral pH even though the bulk electrochemical proton gradient across the coupling membrane is lower at highly alkaline pH. It is possible that some of the protons extruded by the respiratory chain are conveyed to the ATP synthase without first equilibrating with the external bulk phase. Mechanisms that might apply to oxidative phosphorylation in this type of extensively studied alkaliphile are reviewed, and note is made of the possibility of different kinds of solutions to the problem that may be found in new alkaliphilic bacteria that are yet to be isolated or characterized.

Bacillus↗

Mechanisms of cytoplasmic pH regulation in alkaliphilic strains of Bacillus.

The central challenge for extremely alkaliphilic Bacillus species is the need to establish and sustain a cytoplasmic pH that is over two units lower than the highly alkaline medium. Its centrality is suggested by the strong correlation between the growth rate in the upper range of pH for growth, i.e., at values above pH 10.5, and the cytoplasmic pH. The diminishing growth rate at extremely high pH values correlates better with the rise in cytoplasmic pH than with other energetic parameters. There are also general adaptations of alkaliphiles that are crucial prerequisites for pH homeostasis as well as other cell functions, i.e., the reduced basic amino acid content of proteins or segments thereof that are exposed to the medium, and there are other challenges of alkaliphily that emerge from solution of the cytoplasmic pH problem, i.e., reduction of the chemiosmotic driving force. For cells growing on glucose, strong evidence exists for the importance of acidic cell wall components, teichuronic acid and teichuronopeptides, in alkaliphily. These wall macromolecules may provide a passive barrier to ion flux. For cells growing on fermentable carbon sources, this and other passive mechanisms may have a particularly substantial role, but for cells growing on both fermentable and nonfermentable substrates, an active Na+-dependent cycle is apparently required for alkaliphily and the alkaliphile's remarkable capacity for pH homeostasis. The active cycle involves primary establishment of an electrochemical gradient via proton extrusion, a secondary electrogenic Na+/H+ antiport to achieve net acidification of the cytoplasm relative to the outside pH, and mechanisms for Na+ re-entry. Recent work in several laboratories on the critical antiporters involved in this cycle has begun to clarify the number and characteristics of the porters that support active mechanisms of pH homeostasis.

Bacillus↗

Construction and characterization of a mutant of alkaliphilic Bacillus firmus OF4 with a disrupted cta operon and purification of a novel cytochrome bd.

The caa3-type terminal oxidase of Bacillus firmus OF4 has been proposed to play an important role in the growth and bioenergetics of this alkaliphile (A. A. Guffanti and T. A. Krulwich, J. Biol. Chem. 267:9580-9588, 1992). A mutant strain was generated in which the cta operon encoding the oxidase was disrupted by insertion of a spectinomycin resistance cassette. The mutant was unable to oxidize ascorbate in the presence of N,N,N',N'-tetramethyl-p-phenylenediamine (TMPD). Absorption spectra of membranes confirmed the loss of the enzyme and indicated the presence of a cytochrome bd-type terminal oxidase. The mutant could grow on glucose but was unable to grow on malate or other nonfermentative carbon sources, despite the presence of the cytochrome bd. The cytochrome bd was purified from the mutant. The enzyme consisted of two subunits and, with menadiol as substrate, consumed oxygen with a specific activity of 12 micromol of O2 x min(-1) x mg(-1). In contrast to both cytochromes bd of Escherichia coli, the enzyme did not utilize TMPD as an electron source. A number of additional features, including subunit size and spectral properties, distinguish this cytochrome bd from its counterparts in E. coli and Azotobacter vinelandii.

Alkalies↗

Purification and characterization of the succinate dehydrogenase complex and CO-reactive b-type cytochromes from the facultative alkaliphile Bacillus firmus OF4.

The presence of a cytochrome bo-type terminal oxidase in Bacillus firmus OF4 had been suggested from the effects of CO on the spectra of reduced membrane cytochromes (Hicks, D.B., Plass, R.J. and Quirk, P.G. (1991) J. Bacteriol. 173, 5010-5016). In that study the CO-binding b-type cytochrome was partially purified by anion exchange chromatography. No further purification was attempted but later HPLC analysis indicated the absence of significant heme O in the B. firmus OF4 membranes. The current work shows that the partially purified cytochrome b is actually composed of three different b-type cytochromes which can be separated and purified by a combination of ion-exchange, hydroxyapatite and gel filtration chromatographies. Two of the cytochromes were CO-reactive but lacked the characteristic multisubunit composition of known terminal oxidases. Neither purified cytochrome catalyzed quinol or ferrocytochrome c oxidation. The more abundant CO-reactive b-type cytochrome (cytochrome b560) had an apparent molecular mass of 10 kDa, whereas the other, more minor component (cytochrome b558), was partially purified and showed two bands of 23 and 17 kDa on SDS-PAGE. The functions of the cytochromes b560 and b558 remain unknown but together they account for the spectrum originally attributed to cytochrome bo. The third, non-CO reactive, cytochrome b was associated with substantial succinate dehydrogenase activity and was purified as a three subunit succinate dehydrogenase complex with high specific activity (17.7 mumol/min/mg). Limited N-terminal sequence of each subunit demonstrated marked similarity to the complex from Bacillus subtilis. The cytochrome b of the alkaliphile enzyme was reduced about 50% by succinate compared to the level of reduction achieved by dithionite. The enzyme reacted with both napthoquinones and benzoquinones. The results presented indicate that Bacillus firmus OF4 contains a succinate dehydrogenase complex with very similar properties to the enzyme from Bacillus subtilis, but does not contain a cytochrome o-type terminal oxidase under the growth conditions studied.

Amino Acid Sequence↗

Energetic problems of extremely alkaliphilic aerobes.

Over a decade of work on extremely alkaliphilic Bacillus species has clarified the extraordinary capacity that these bacteria have for regulating their cytoplasmic pH during growth at pH values well over 10. However, a variety of interesting energetic problems related to their Na(+)-dependent pH homeostatic mechanism are yet to be solved. They include: (1) the clarification of how cell surface layers play a role in a category of alkaliphiles for which this is the case; (2) identification of the putative, electrogenic Na+/H+ antiporter(s) that, in at least some alkaliphiles, may completely account for a cytoplasmic pH that is over 2 pH units lower than the external pH; (3) the determination of whether specific modules or accessory proteins are essential for the efficacy of such antiporters; (4) the mechanistic basis for the increase in the transmembrane electrical potential at the high external pH values at which the potential-consuming antiporter(s) must be most active; and (5) an explanation for the Na(+)-specificity of pH homeostasis in the extremely alkaliphilic bacilli as opposed to the almost equivalent efficacy of K+ for pH homeostasis in at least some non-alkaliphilic aerobes. The current status of such studies and future strategies will be outlined for this central area of alkaliphile energetics. Also considered, will be strategies to elucidate the basis for robust H(+)-coupled oxidative phosphorylation by alkaliphiles at pH values over 10. The maintenance of a cytoplasmic pH over 2 units below the high external pH results in a low bulk electrochemical proton gradient (delta p). To bypass this low delta p, Na(+)-coupling is used for solute uptake even by alkaliphiles that are mesophiles from environments that are not especially Na(+)-rich. This indicates that these bacteria indeed experience a low delta p, to which such coupling is an adaptation. Possible reasons and mechanisms for using a H(+)-coupled rather than a Na(+)-coupled ATP synthase under such circumstances will be discussed.

Bacillus↗

The affinity and specificity of Ca(2+)-binding sites of cytochrome-c peroxidase from Paracoccus denitrificans.

The binding of Ca2+ to the dihaem cytochrome-c peroxidase from Paracoccus denitrificans was analysed by following perturbations in the visible and 1H-NMR spectra of both haem groups. The enzyme contains at least two types of Ca(2+)-binding site. Site I is occupied in the isolated enzyme, binds Ca2+ with a redox-state-independent Kd of 1.2 microM and accommodates neither Mg2+ nor Mn2+. Site II is unoccupied in dilute solutions of the isolated oxidised enzyme and binds Ca2+ cooperatively with a Kd of 0.52 mM. In the mixed valence form, the binding affinity increases to resemble that of site I. The cooperativity was shown by -Ca2+ binding to site II, the titration of haem methyl 1H-NMR resonances, and a half-of-sites effect observed for modification of an essential histidine with diethylpyrocarbonate. These are all consistent with site II being situated at the interface between two monomers of a dimeric enzyme. Thus the equilibrium of binding to site II is a reflection of the equilibrium for dimerisation and conditions which shift that equilibrium towards the dimer, such as increased ionic strength or high protein concentration, also increase Ca2+ affinity. Binding of Ca2+ to site II is required for formation of the active high spin state at the peroxidatic haem.

Ascorbic Acid↗

Mössbauer characterization of Paracoccus denitrificans cytochrome c peroxidase. Further evidence for redox and calcium binding-induced heme-heme interaction.

Mössbauer and electron paramagnetic resonance (EPR) spectroscopies were used to characterize the diheme cytochrome c peroxidase from Paracoccus denitrificans (L.M.D. 52.44). The spectra of the oxidized enzyme show two distinct spectral components characteristic of low spin ferric hemes (S = 1/2), revealing different heme environments for the two heme groups. The Paracoccus peroxidase can be non-physiologically reduced by ascorbate. Mössbauer investigation of the ascorbate-reduced peroxidase shows that only one heme (the high potential heme) is reduced and that the reduced heme is diamagnetic (S = 0). The other heme (the low potential heme) remains oxidized, indicating that the enzyme is in a mixed valence, half-reduced state. The EPR spectrum of the half-reduced peroxidase, however, shows two low spin ferric species with gmax = 2.89 (species I) and gmax = 2.78 (species II). This EPR observation, together with the Mössbauer result, suggests that both species are arising from the low potential heme. More interestingly, the spectroscopic properties of these two species are distinct from that of the low potential heme in the oxidized enzyme, providing evidence for heme-heme interaction induced by the reduction of the high potential heme. Addition of calcium ions to the half-reduced enzyme converts species II to species I. Since calcium has been found to promote peroxidase activity, species I may represent the active form of the peroxidatic heme.

Animals↗