Identification of vaccine candidate antigens from a genomic analysis of Porphyomonas gingivalis

Porphyromonas gingivalis is a key periodontal pathogen which has been implicated in the etiology of chronic adult periodontitis. Our aim was to develop a protein based vaccine for the prevention and or treatment of this disease. We used a whole genome sequencing approach to identify potential vaccine candidates. From a genomic sequence, we selected 120 genes using a series of bioinformatics methods. The selected genes were cloned for expression in Escherichia coli and screened with P. gingivalis antisera before purification and testing in an animal model. Two of these recombinant proteins (PG32 and PG33) demonstrated significant protection in the animal model, while a number were reactive with various antisera. This process allows the rapid identification of vaccine candidates from genomic data. (C) 2001 Elsevier Science Ltd. All rights reserved.

Multiple genotypes of Chlamydia pneumoniae identified in human carotid plaque

Chlamydia pneumoniae is an obligate intracellular respiratory pathogen that causes 10% of community-acquired pneumonia and has been associated with cardiovascular disease. Both whole-genome sequencing and specific gene typing suggest that there is relatively little genetic variation in human isolates of C. pneumoniae. To date, there has been little genomic analysis of strains from human cardiovascular sites. The genotypes of C. pneumoniae present in human atherosclerotic carotid plaque were analysed and several polymorphisms in the variable domain 4 (VD4) region of the outer-membrane protein-A (ompA) gene and the intergenic region between the ygeD and uridine kinase (ygeD-urk) genes were found. While one genotype was identified that was the same as one reported previously in humans (respiratory and cardiovascular), another genotype was found that was identical to a genotype from non-human sources (frog/koala).

Evaluation and comparison of mammalian subcellular localization prediction methods

Background: Determination of the subcellular location of a protein is essential to understanding its biochemical function. This information can provide insight into the function of hypothetical or novel proteins. These data are difficult to obtain experimentally but have become especially important since many whole genome sequencing projects have been finished and many resulting protein sequences are still lacking detailed functional information. In order to address this paucity of data, many computational prediction methods have been developed. However, these methods have varying levels of accuracy and perform differently based on the sequences that are presented to the underlying algorithm. It is therefore useful to compare these methods and monitor their performance. Results: In order to perform a comprehensive survey of prediction methods, we selected only methods that accepted large batches of protein sequences, were publicly available, and were able to predict localization to at least nine of the major subcellular locations (nucleus, cytosol, mitochondrion, extracellular region, plasma membrane, Golgi apparatus, endoplasmic reticulum (ER), peroxisome, and lysosome). The selected methods were CELLO, MultiLoc, Proteome Analyst, pTarget and WoLF PSORT. These methods were evaluated using 3763 mouse proteins from SwissProt that represent the source of the training sets used in development of the individual methods. In addition, an independent evaluation set of 2145 mouse proteins from LOCATE with a bias towards the subcellular localization underrepresented in SwissProt was used. The sensitivity and specificity were calculated for each method and compared to a theoretical value based on what might be observed by random chance. Conclusion: No individual method had a sufficient level of sensitivity across both evaluation sets that would enable reliable application to hypothetical proteins. All methods showed lower performance on the LOCATE dataset and variable performance on individual subcellular localizations was observed. Proteins localized to the secretory pathway were the most difficult to predict, while nuclear and extracellular proteins were predicted with the highest sensitivity.

Spontaneous transitions in the coordination of a whole body task

This paper describes an example of spontaneous transitions between qualitatively different coordination patterns during a cyclic lifting and lowering task. Eleven participants performed 12 trials of repetitive lifting and lowering in a ramp protocol in which the height of the lower shelf was raised or lowered 1 cm per cycle between 10 and 50 cm. Two distinct patterns of coordination were evident: a squat technique in which moderate range of hip, knee and ankle movement was utilised and ankle plantar-flexion occurred simultaneously with knee and hip extension; and a stoop technique in which the range of knee movement was reduced and knee and hip extension was accompanied by simultaneous ankle dorsi-flexion. Abrupt transitions from stoop to squat techniques were observed during descending trials, and from squat to stoop during ascending trials. Indications of hysteresis was observed in that transitions were more frequently observed during descending trials, and the average shelf height at the transition was 5 cm higher during ascending trials. The transitions may be a consequence of a trade-off between the biomechanical advantages of each technique and the influence of the lift height on this trade-off.

Biomolecular interaction analysis of IFN gamma-induced signaling events in whole-cell lysates: Prevalence of latent STAT1 in high-molecular weight complexes

The basic framework for the JAK/STAT pathway is well documented. Recruitment of latent cytoplasmic STAT transcription factors to tyrosine phosphorylated docking sites on cytokine receptors and their JAK-mediated phosphorylation instigates their translocation to the nucleus and their ability to bind DNA, The biochemical processes underlying recruitment and activation of this pathway have commonly been studied in reconstituted in vitro systems using previously defined recombinant signaling components. We have dissected the Interferon gamma (IFN gamma) signal transduction pathway in crude extracts from wild-type and STAT1-negative mutant cell Lines by real-time BIAcore analysis, size-exclusion (SE) chromatography and immune-detection. The data indicate that in detergent-free cell extracts: (1) the phospho-tyrosine (Y440P)-containing peptide motif of the IFN gamma-receptor ct-chain interacts directly with STAT1, or STAT1 complexes, and no other protein; (2) nonactivated STAT 1 is present in a higher molecular weight complex(es) and, at least for IFN gamma-primed cells, is available for recruitment to the activated IFN gamma-receptor from only a subset of such complexes; (3) activated STAT1 is released from the receptor as a monomer.

Whole-body pre-cooling and heat storage during self-paced cycling performance in warm humid conditions

The aim of this study was to establish the effect that pre-cooling the skin without a concomitant reduction in core temperature has on subsequent self-paced cycling performance under warm humid (31 degrees C and 60% relative humidity) conditions. Seven moderately trained males performed a 30 min self-paced cycling trial on two separate occasions. The conditions were counterbalanced as control or whole-body pre-cooling by water immersion so that resting skin temperature was reduced by approximate to 5-6 degrees C. After pre-cooling, mean skin temperature was lower throughout exercise and rectal temperature was lower (P < 0.05) between 15 and 25 min of exercise. Consequently, heat storage increased (P < 0.003) from 84.0 +/- 8.8 W . m(-2) to 153 +/- 13.1 W . m(-2) (mean +/- s((x) over bar)) after pre-cooling, while total body sweat fell from 1.7 +/- 0.1 1 . h(-1) to 1.2 +/- 0.1 1 . h(-1) (P < 0.05). The distance cycled increased from 14.9 +/- 0.8 to 15.8 +/- 0.7 km (P < 0.05) after pre-cooling. The results indicate that skin pre-cooling in the absence of a reduced rectal temperature is effective in reducing thermal strain and increasing the distance cycled in 30 min under warm humid conditions.

Assessment of intracellular water by whole body bioelectrical impedance and total body potassium in HIV-positive patients

.:Abstract-Objective: Bioelectrical impedance analysis (BIA) is widely used as bedside assessment of body composition. Body cell mass (BCM) and intracellular water (ICW) are clinically important body compartments. Estimates of ICW obtained from BIA by different calculation approaches were compared to a reference method in male HIV-infected patients. Patients: Representative subsample of clinically stable HIV-infected outpatients, consisting of 42 men with a body mass index of 22.4 +/- 3.8 kg/m(2) (range, 13-31 kg/m(2)). Methods: Total body potassium was assessed in a whole body counter, and compared to 50 kHz mono-frequency BIA and multifrequency bioelectrical impedance spectroscopy. Six different prediction equations for ICW from BIA data were applied. Methods were compared by the Bland-Altman method. Results: BIA-derived ICW estimates explained 58% to 73% of the observed variance in ICW (TBK), but limits of confidence were wide (-16.6 to +18.2% for the best method). BIA overestimated low ICW (TBK) and underestimated high ICW (TBK) when normalized for weight or height. Mono- and multifrequency BIA were not different in precision but population-specific equations tended to narrower confidence limits. Conclusion: BIA is an unreliable method to estimate ICW in this population, in contrast to the better established estimation of total body water and extracellular water. Potassium depletion in severe malnutrition may contribute to this finding but a major part of the residual between methods remains unexplained. (C) 2000 Harcourt Publishers Ltd.

An economic evaluation of plasma production via erythroplasmapheresis and whole blood collection

This paper presents cost-effectiveness analyses (CEAs) of plasma collection via two alternative methods: whole blood collection (WBC) and erythroplasmapheresis collection (EPC). The objective of the study is to provide an answer to the question 'What is the least-cost method of plasma production'. This question is answered, both from the viewpoint of the blood collection agency (using financial CEA) and from that of 'society' as a whole (using economic CEA). We employ detailed financial data and economic survey data for collections made by a blood collection agency and to WBC and EPC donors in Brisbane, Australia. The results indicate that, despite the superior yield provided by EPC, WBC is actually more cost-effective. This result is robust to thorough sensitivity analysis and arises regardless of whether an economic or financial perspective is taken. We conclude that, ceteris paribus, the cost of recruiting new plasma donors would need to be quite substantial for marginal investments in EPC to be considered cost-effective. Crown Copyright (C) 2002 Published by Elsevier Science Ltd. All rights reserved.

A medial to lateral shift in premovement cortical activity in hemi-Parkinson's disease: Studies of event-related potentials and whole-scalp magneto encephalography

Cortical activity associated with voluntary movement is shifted from medial to lateral premotor areas in Parkinson's disease. This occurs bilaterally, even for unilateral movements. We have used both EEG and MEG to further investigate medial and lateral premotor activity in patients with hemi-Parkinson's disease, in whom basal ganglia impairment is most pronounced in one hemisphere. The CNV, recorded from 21 scalp positions in a Go/NoGo task, was maximal over central medial regions in control subjects. For hemi-Parkinson's disease subjects, activity was shifted more frontally, reduced in the midline and lateralised towards the side of greatest basal ganglia impairment. With 143 channel whole-scalp magneto encephalography (MEG) we are further examining asymmetries in supplementary motor/premotor cortical activity prior to self-paced voluntary movement. In preliminary results, one hemi-Parkinson's disease patient with predominantly left-side symptoms showed strong medial activity consistent with a dominant source in the left supplementary motor area (SMA). Three patients showed little medial activity, but early bilateral sources within lateral premotor cortex. Results suggest greater involvement of lateral premotor rather than the SMA prior to movement in Parkinson's disease and provide evidence for asymmetric function of the SMA in hemi- Parkinson's disease, with reduced activity on the side of greatest basal ganglia deficit.

Mineral chemistry, whole-rock compositions, and petrogenesis of leg 176 gabbros: Data and discussion

We report mineral chemistry, whole-rock major element compositions, and trace element analyses on Hole 735B samples drilled and selected during Leg 176. We discuss these data, together with Leg 176 shipboard data and Leg 118 sample data from the literature, in terms of primary igneous petrogenesis. Despite mineral compositional variation in a given sample, major constituent minerals in Hole 735B gabbroic rocks display good chemical equilibrium as shown by significant correlations among Mg# (= Mg/[Mg+Fe2+]) of olivine, clinopyroxene, and orthopyroxene and An (=Ca/[Ca+Na]) of plagioclase. This indicates that the mineral assemblages olivine + plagioclase in troctolite, plagioclase + clinopyroxene in gabbro, plagioclases + clinopyroxene + olivine in olivine gabbro, and plagioclase + clinopyroxene + olivine + orthopyroxene in gabbronorite, and so on, have all coprecipitated from their respective parental melts. Fe-Ti oxides (ilmenite and titanomagnetite), which are ubiquitous in most of these rocks, are not in chemical equilibrium with olivine, clinopyroxene, and plagioclase, but precipitated later at lower temperatures. Disseminated oxides in some samples may have precipitated from trapped Fe-Ti–rich melts. Oxides that concentrate along shear bands/zones may mark zones of melt coalescence/transport expelled from the cumulate sequence as a result of compaction or filter pressing. Bulk Hole 735B is of cumulate composition. The most primitive olivine, with Fo = 0.842, in Hole 735B suggests that the most primitive melt parental to Hole 735B lithologies must have Mg# ≤ 0.637, which is significantly less than Mg# = 0.714 of bulk Hole 735B.

Spoilage patterns of skim and whole milks

The reason for the reported difference in spoilage behaviour of skim and whole pasteurised milks was investigated The rates of growth of psychrotrophic bacteria were not significantly different in the two milks and the bacterial types. till pseudomonad, present at spoilage were also similar. However. when representative spoilage organisms were cultured into freshly pasteurised skim and whole milks, skim milks exhibited predominantly bitter flavours while whole milk showed mostly sour flavours. The different spoilage, behaviours can be largely explained by greater proteolysis in skim milk than in whole milk. caused by, higher production of protease and greater susceptibility of the protein to protease attack. In addition, lipolysis in whole milk, caused by the substantial quantities of lipase produced by spoilage pseudomonads in this milk. also contributes to the different flavours produced during cold storage of these milk types.