Chemometric variance analysis of 1H NMR metabolomics data on the effects of oral rinse on saliva

Saliva is an easy to obtain bodily fluid that is specific to the oral environment. It can be used for metabolomic studies as it is representative of the overall wellbeing of an organism, as well as mouth health and bacterial flora. The metabolomic structure of saliva varies greatly depending on the bacteria present in the mouth as they produce a range of metabolites. In this study we have investigated the metabolomic profiles of human saliva that were obtained using ¹H NMR (nuclear magnetic resonance) analysis. 48 samples of saliva were collected from 16 healthy subjects over 3 days. Each sample was split in two and the first half treated with an oral rinse, while the second was left untreated as a control sample. The 96 ¹H NMR metabolomic profiles obtained in the dataset are affected by three factors, namely 16 subjects, 3 sampling days and 2 treatments. These three factors contribute to the total variation in the dataset. When analysing datasets from saliva using traditional methods such as PCA (principal component analysis), the overall variance is dominated by subjects’ contributions, and we cannot see trends that would highlight the effect of specific factors such as oral rinse. In order to identify these trends, we used methods such as MSCA (multilevel simultaneous component analysis) and ASCA (ANOVA simultaneous component analysis), that provide variance splits according to the experimental factors, so that we could look at the particular effect of treatment on saliva. The analysis of the treatment effect was enhanced, as it was isolated from the overall variance and assessed without confounding factors.

     

Comparison of human axillary odour profiles obtained by gas chromatography/mass spectrometry and skin microbial profiles obtained by denaturing gradient gel electrophoresis using multivariate pattern recognition

Several studies have shown that microbial action is responsible for many compounds responsible for human odour. In this paper, we compare the pattern of microbial profiles and that of chemical profiles of human axillary odour by using multivariate pattern matching techniques. Approximately 200 subjects from Carinthia, Austria, participated in the study. The microbial profiles were represented by denaturing gradient gel electrophoresis (DGGE) analysis and the axillary odour profiles were determined in the sweat samples collected by a stir-bar sampling device and analysed by gas chromatography/mass spectrometry (GC/MS). Both qualitative and quantitative distance metrics were used to construct dissimilarity matrices between samples which were then used to represent the patterns of these two types of profiles. The distance matrices were then compared by using the Mantel test and the Procrustean test. The results show that on the overall dataset there is no strong correlation between microbial and chemical profiles. When the data are split into family groups, correlations vary according to family with a range of estimated p values from 0.00 to 0.90 that the null hypothesis (no correlation) holds. When 32 subjects who followed four basic rules of behaviour were selected, the estimated p-values are 0.00 using qualitative and <0.01 using quantitative distance metrics, suggesting excellent evidence that there is a connection between the microbial and chemical signature.     

Adverse environmental conditions influence age-related innate immune responsiveness

Background-  

The innate immune system plays an important role in the recognition and induction of protective responses against infectious pathogens, whilst there is increasing evidence for a role in mediating chronic inflammatory diseases at older age. Despite indications that environmental conditions can influence the senescence process of the adaptive immune system, it is not known whether the same holds true for the innate immune system. Therefore we studied whether age-related innate immune responses are similar or differ between populations living under very diverse environmental conditions.     

Ecologists can enable communities to implement malaria vector control in Africa

Background

Malaria imposes significant costs on households and the poor are disproportionately affected. However, cost data are often from quantitative surveys with a fixed recall period. They do not capture costs that unfold slowly over time, or seasonal variations. Few studies investigate the different pathways through which malaria contributes towards poverty. In this paper, a framework indicating the complex links between malaria, poverty and vulnerability at the household level is developed and applied using data from rural Kenya.

Methods

Cross-sectional surveys in a wet and dry season provide data on treatment-seeking, cost-burdens and coping strategies (n = 294 and n = 285 households respectively). 15 case study households purposively selected from the survey and followed for one year provide in-depth qualitative information on the links between malaria, vulnerability and poverty.

Results

Mean direct cost burdens were 7.1% and 5.9% of total household expenditure in the wet and dry seasons respectively. Case study data revealed no clear relationship between cost burdens and vulnerability status at the end of the year. Most important was household vulnerability status at the outset. Households reporting major malaria episodes and other shocks prior to the study descended further into poverty over the year. Wealthier households were better able to cope.

Conclusion

The impacts of malaria on household economic status unfold slowly over time. Coping strategies adopted can have negative implications, influencing household ability to withstand malaria and other contingencies in future. To protect the poor and vulnerable, malaria control policies need to be integrated into development and poverty reduction programmes.     

Free brownian motion of individual lipid molecules in biomembranes

The mobility of phospolipids in free-standing and supported membranes was investigated on the level of individual molecules. For the analysis of trajectories a new statistical treatment was developed that permitted us to clearly distinguish different types of diffusional motion. A freely diffusing subfraction of lipids within supported membranes was identified. Its mobility was characterized by a mean lateral diffusion constant of D(supp) = 4.6 &mgr;m(2)/s. In comparison, the mobility of lipids embedded in "free-standing" planar membranes yielded an increase in the mean diffusion constant by a factor of 4.5, D(free) = 20.6 &mgr;m(2)/s. This increase is attributed to the ultrathin (</=1 nm) lubricating water layer between membranes and glass support.     

Site-directed mutagenesis of dimethyl sulfoxide reductase from Rhodobacter capsulatus: characterization of a Y114 --> F mutant

A system for expressing site-directed mutants of the molybdenum enzyme dimethyl sulfoxide reductase from Rhodobacter capsulatus in the natural host was constructed. This system was used to generate and express dimethyl sulfoxide reductase with a Y114F mutation. The Y114F mutant had an increased k(cat) and increased K(m) toward both dimethyl sulfoxide and trimethylamine N-oxide compared to the native enzyme, and the value of k(cat)/K(m) was lower for both substrates in the mutant enzyme. The Y114F mutant, as isolated, was able to oxidize dimethyl sulfide with phenazine ethosulfate as the electron acceptor but with a lower k(cat) than that of the native enzyme. The pH optimum of dimethyl sulfide:acceptor oxidoreductase activity in the Y114F mutant was shown to be shifted by +1 pH unit compared to the native enzyme. The Y114F mutant did not form a pink complex with dimethyl sulfide, which is characteristic of the native enzyme. The mutant enzyme showed a large increase in the K(d) for DMS. Direct electrochemistry showed that the Mo(V)/Mo(IV) couple was unaffected by the Y114F mutant, but the midpoint potential of the Mo(VI)/Mo(V) couple was raised by about 50 mV. These data confirm that the Y114 residue plays a critical role in oxidation-reduction processes at the molybdenum active site and in oxygen atom transfer associated with sulfoxide reduction.     

A solution NMR molecular model for the aspartate-ligated,cubane cluster containing ferredoxin from the hyperthermophilic archeaon Pyrococcus furiosus

A solution molecular model for the conformationally dynamically heterogeneous Pyrococcus furiosus ferredoxin with an intact disulfide bond has been constructed on the basis of reported (1)H NMR spectral parameters using distance geometry and simulated annealing protocols. Conventional long-mixing time NOESY and H-bonding constraints have been augmented by previously reported short-mixing time NOESY, steady-state NOE, and cluster paramagnetism-induced relaxation. The family of 15 structures with inconsequential violations exhibited low rms deviations for backbone atoms for the overwhelming majority of the residues, including the cluster ligating loop with the unprecedented ligated Asp14. Larger rms deviations were observed across the disulfide bond, but closer inspection revealed that the 15 structures can be factored into 10 substructures exhibiting an "S" or right-handed disulfide orientation and 5 exhibiting an "R" or left-handed disulfide orientation. The remainder of the structure is indistinguishable for the two disulfide orientations but confirms stabilizing extensions of secondary structural elements in the lengthening of the long helix and both the lengthening and incorporation of a third strand into the beta-sheet involving the termini, with these extensions interacting strongly in a modular fashion through the rings of Tyr46 and Trp2. These extensions of stabilizing interactions in Pyrococcus furiosus Fd, however, lead to strong destabilization of the disulfide bond and destabilization of the highly conserved first and last beta-turns in the sequence. It is concluded that the structural alternations in Pyrococcus Fd relative to other hyperthermostable Fds are not to increase thermostability but to place "stress" on the disulfide bond and render it more reducible. The possible physiological implications of this unique reducible disulfide bond are discussed.     

Phylogeny of the genus trichoderma based on sequence analysis of the internal transcribed spacer region 1 of the rDNA cluster

Sequences of the internal transcribed spacer region 1 (ITS1) of the ribosomal DNA were used to determine the phylogenetic relationships of species of Trichoderma sect. Pachybasium. To this end, 85 strains-including all the available ex-type strains-were analyzed. Parsimony analysis demonstrated that the section is nonmonophyletic, distributing the 85 strains among three main groups that were supported by bootstrap values. Group A comprises two clades (A1 and A2), with A1 including T. polysporum, T. piluliferum, and T. minutisporum, while A2 included T. hamatum, T. pubescens, and T. strigosum in addition to species previously included in sect. Trichoderma (i.e., T. viride, T. atroviride, and T. koningii). The ex-type strain of T. fasciculatum formed a separate branch basal to clade A. Clade B contained the sect. Pachybasium members T. harzianum, T. fertile, T. croceum, T. longipile, T. strictipile, T. tomentosum, T. oblongisporum, T. flavofuscum, T. spirale, and the anamorphs of Hypocrea semiorbis and H. cf. gelatinosa. Sequence differences among clades A1, A2, and B were in the same order of magnitude as between each of them and T. longibrachiatum, which was used as an outgroup in these analyses. Sequence differences within clades A1, A2, and B were considerably smaller: in some cases (i.e., T. virens and T. flavofuscum; T. strictipile and H. cf. gelatinosa), the ITS1-sequences were identical, suggesting conspecifity. In other cases (e.g., T. crassum and T. longipile; T. harzianum, T. inhamatum, T. croceum, T. fertile, and H. semiorbis; T. hamatum and T. pubescens; and T. viride, T. atroviride, and T. koningii) differences were in the range of 1-3 nt only, suggesting a very close phylogenetic relationship. The sequence of a previously described aggressive mushroom competitor group of T. harzianum strains (Th2) was strikingly different from that of the ex-type strain of T. harzianum and closely related species and is likely to be a separate species. Copyright 1998 Academic Press.     

Cost effectiveness of community leg ulcer clinics: randomised controlled trial

Objectives: To establish the relative cost effectiveness of community leg ulcer clinics that use four layer compression bandaging versus usual care provided by district nurses. Design: Randomised controlled trial with 1 year of follow up. Setting: Eight community based research clinics in four trusts in Trent. Subjects: 233 patients with venous leg ulcers allocated at random to intervention (120) or control (113) group. Interventions: Weekly treatment with four layer bandaging in a leg ulcer clinic (clinic group) or usual care at home by the district nursing service (control group). Main outcome measures: Time to complete ulcer healing, patient health status, and recurrence of ulcers. Satisfaction with care, use of services, and personal costs were also monitored. Results: The ulcers of patients in the clinic group tended to heal sooner than those in the control group over the whole 12 month follow up (log rank P=0.03). At 12 weeks, 34% of patients in the clinic group were healed compared with 24% in the control. The crude initial healing rate of ulcers in intervention compared with control patients was 1.45 (95% confidence interval 1.04 to 2.03). No significant differences were found between the groups in health status. Mean total NHS costs were £878.06 per year for the clinic group and £859.34 for the control (P=0.89). Conclusions: Community based leg ulcer clinics with trained nurses using four layer bandaging is more effective than traditional home based treatment. This benefit is achieved at a small additional cost and could be delivered at reduced cost if certain service configurations were used.

Key messages

• Leg ulcer clinics based in the community using four layer compression bandaging can be more clinically effective than usual care provided by the district nursing service
• Community based leg ulcer clinics could be provided more cost effectively than usual home based care for venous leg ulcers
• Recurrence of venous leg ulcers is an important variable that should be measured in future trials of venous leg ulcer care
• It is difficult to measure improvements in health related quality of life among people with venous leg ulcers