Analysis of pottery samples from Bourewa, the earliest known Lapita site in Fiji

We have carried out a thorough mineralogical analysis of 16 pottery samples from the Lapita site of Bourwera in Fiji, using micromorphological techniques with optical and polarising microscopes. While the overall mineralogy of all of the samples is similar the samples clearly divide into two groups, namely those with or without the mineral calcite. Our findings are backed up by chemical analysis using SEM–EDX and FTIR. SEM–EDX shows the clear presence of inclusions of calcite in some of the samples; FTIR shows bands arising from calcite in these samples. The study suggests that it is likely that more than one clay source was used for production of this pottery, but that most of the pottery comes from a single source. This finding is in line with previous studies which suggest some trading of pottery between the Fijian islands but a single source of clay for most of the pottery found at Bouwera. We found no evidence for the destruction of CaCO3 by heating upon production of the pottery in line with the known technology of the Lapita people who produced earthenware pottery but not high temperature ceramics.

Integrated cytokine and metabolic analysis of pathological responses to parasite exposure in rodents

Parasitic infections cause a myriad of responses in their mammalian hosts, on immune as well as on metabolic level. A multiplex panel of cytokines and metabolites derived from four parasite-rodent models, namely, Plasmodium berghei-mouse, Trypanosoma brucei brucei-mouse, Schistosoma mansoni-mouse, and Fasciola hepatica-rat were statistically coanalyzed. 1H NMR spectroscopy and multivariate statistical analysis were used to characterize the urine and plasma metabolite profiles in infected and noninfected animals. Each parasite generated a unique metabolic signature in the host. Plasma cytokine concentrations were obtained using the ‘Meso Scale Discovery’ multi cytokine assay platform. Multivariate data integration methods were subsequently used to elucidate the component of the metabolic signature which is associated with inflammation and to determine specific metabolic correlates with parasite-induced changes in plasma cytokine levels. For example, the relative levels of acetyl glycoproteins extracted from the plasma metabolite profile in the P. berghei-infected mice were statistically correlated with IFN-γ, whereas the same cytokine was anticorrelated with glucose levels. Both the metabolic and the cytokine data showed a similar spatial distribution in principal component analysis scores plots constructed for the combined murine data, with samples from all infected animals clustering according to the parasite species and whereby the protozoan infections (P. berghei and T. b. brucei) grouped separately from the helminth infection (S. mansoni). For S. mansoni, the main infection-responsive cytokines were IL-4 and IL-5, which covaried with lactate, choline, and D-3-hydroxybutyrate. This study demonstrates that the inherently differential immune response to single and multicellular parasites not only manifests in the cytokine expression, but also consequently imprints on the metabolic signature, and calls for in-depth analysis to further explore direct links between immune features and biochemical pathways.

Early detection of ovarian cancer in samples pre-diagnosis using CA125 and MALDI-MS peaks

Aim: A nested case-control discovery study was undertaken 10 test whether information within the serum peptidome can improve on the utility of CA125 for early ovarian cancer detection. Materials and Methods: High-throughput matrix-assisted laser desorption ionisation mass spectrometry (MALDI-MS) was used to profile 295 serum samples from women pre-dating their ovarian cancer diagnosis and from 585 matched control samples. Classification rules incorporating CA125 and MS peak intensities were tested for discriminating ability. Results: Two peaks were found which in combination with CA125 discriminated cases from controls up to 15 and 11 months before diagnosis, respectively, and earlier than using CA125 alone. One peak was identified as connective tissue-activating peptide III (CTAPIII), whilst the other was putatively identified as platelet factor 4 (PF4). ELISA data supported the down-regulation of PF4 in early cancer cases. Conclusion: Serum peptide information with CA125 improves lead time for early detection of ovarian cancer. The candidate markers are platelet-derived chemokines, suggesting a link between platelet function and tumour development.

Development and application of a method for the purification of free shigatoxigenic bacteriophage from environmental samples

Shiga toxin producing Escherichia coli (STEC) strains are foodborne pathogens whose ability to produce Shiga toxin (Stx) is due to the integration of Stx-encoding lambdoid bacteriophage (Stx phage). Circulating, infective Stx phages are very difficult to isolate, purify and propagate such that there is no information on their genetic composition and properties. Here we describe a novel approach that exploits the phage's ability to infect their host and form a lysogen, thus enabling purification of Stx phages by a series of sequential lysogen isolation and induction steps. A total of 15 Stx phages were rigorously purified from water samples in this way, classified by TEM and genotyped using a PCR-based multi-loci characterisation system. Each phage possessed only one variant of each target gene type, thus confirming its purity, with 9 of the 15 phages possessing a short tail-spike gene and identified by TEM as Podoviridae. The remaining 6 phages possessed long tails, four of which appeared to be contractile in nature (Myoviridae) and two of which were morphologically very similar to bacteriophage lambda (Siphoviridae).

A procedure for the simultaneous determination of total nitrogen and total phosphorus in freshwater samples using persulphate microwave digestion

In the absence of a suitable method for routine analysis of large numbers of natural river water samples for organic nitrogen and phosphorus fractions, a new simultaneous digestion technique was developed, based on a standard persulphate digestion procedure. This allows rapid analysis of river, lake and groundwater samples from a range of environments for total nitrogen and phosphorus. The method was evaluated using a range of organic nitrogen and phosphorus structures tested at low, mid and high range concentrations from 2 to 50 mg l-1 nitrogen and 0.2 to 10 mg l-1 phosphorus. Mean recoveries for nitrogen ranged from 94.5% (2 mg I-1) to 92.7% (50 mg I-1) and for phosphorus were 98.2% (0.2 mg l-1) to 100.2% (10 mg l-1). The method is precise in its ability m reproduce results from replicate digestions, and robust in its ability to handle a variety of natural water samples in the pH range 5-8.

Detection of Chlamydia psittaci DNA in avian clinical samples by polymerase chain reaction

A polymerase chain reaction (PCR) assay was developed to detect Chlamydia psittaci DNA in faeces and tissue samples from avian species. Primers were designed to amplify a 264 bp product derived from part of the 5' non-translated region and part of the coding region of the ompA gene which encodes the major outer membrane protein. Amplified sequences were confirmed by Southern hybridization using an internal probe. The sensitivity of the combined assay was found to be between 60 to 600 fg of chlamydial DNA (approximately 6 to 60 genome copies). The specificity of the assay was confirmed since PCR product was not obtained from samples containing several serotypes of C. trachomatis, strains of C. pneumoniae, the type strain of C. pecorum, nor from samples containing microorganisms commonly found in the avian gut flora. In this study, 404 avian faeces and 141 avian tissue samples received by the Central Veterinary Laboratory over a 6 month period were analysed by PCR, antigen detection ELISA and where possible, cell culture isolation. PCR performed favourably compared with ELISA and cell culture, or with ELISA alone. The PCR assay was especially suited to the detection of C. psittaci DNA in avian faeces samples. The test was also useful when applied to tissue samples from small contact birds associated with a case of human psittacosis where ELISA results were negative and chlamydial isolation was a less favourable method due to the need for rapid diagnosis.

Accurate analysis of noble gas concentrations in small water samples and its application to fluid inclusions in stalagmites

The concentrations of dissolved noble gases in water are widely used as a climate proxy to determine noble gas temperatures (NGTs); i.e., the temperature of the water when gas exchange last occurred. In this paper we make a step forward to apply this principle to fluid inclusions in stalagmites in order to reconstruct the cave temperature prevailing at the time when the inclusion was formed. We present an analytical protocol that allows us accurately to determine noble gas concentrations and isotope ratios in stalagmites, and which includes a precise manometrical determination of the mass of water liberated from fluid inclusions. Most important for NGT determination is to reduce the amount of noble gases liberated from air inclusions, as they mask the temperature-dependent noble gas signal from the water inclusions. We demonstrate that offline pre-crushing in air to subsequently extract noble gases and water from the samples by heating is appropriate to separate gases released from air and water inclusions. Although a large fraction of recent samples analysed by this technique yields NGTs close to present-day cave temperatures, the interpretation of measured noble gas concentrations in terms of NGTs is not yet feasible using the available least squares fitting models. This is because the noble gas concentrations in stalagmites are not only composed of the two components air and air saturated water (ASW), which these models are able to account for. The observed enrichments in heavy noble gases are interpreted as being due to adsorption during sample preparation in air, whereas the excess in He and Ne is interpreted as an additional noble gas component that is bound in voids in the crystallographic structure of the calcite crystals. As a consequence of our study's findings, NGTs will have to be determined in the future using the concentrations of Ar, Kr and Xe only. This needs to be achieved by further optimizing the sample preparation to minimize atmospheric contamination and to further reduce the amount of noble gases released from air inclusions.

Corynebacterium uterequi sp. nov., a non-lipophilic bacterium isolated from urogenital samples from horses

Three strains of a Gram-positive, catalase-positive, fermentative, non-lipophilic, previously unknown bacterium were isolated from urogenital samples taken from mares in Scotland (M401624/00/1) and Sweden (VM 2074 and VM 2298T). All were deposited with the CCUG with tentative identifications as Corynebacterium spp. The strains were characterized using a polyphasic taxonomic approach. Biochemically, the strains were very similar to each other, but phylogenetically distinct from Corynebacterium species with validly published names (≤95% sequence similarity). rpoB gene sequence data confirmed the strains belonged to the same species (>99% sequence similarity) and were distinct from species with validly published names (>13% sequence divergence). On the basis of phenotypic and sequence data, the strains represent a novel species within the genus Corynebacterium, for which the name Corynebacterium uterequi is proposed. The type strain is VM 2298T (=CCUG 61235T = DSM 45634T), isolated from equine uterus.

Using paint to investigate fires: an ATR-IR study of the degradation of paint samples upon heating

Fire investigation is a challenging area for the forensic investigator. The aim of this work was to use spectral changes to paint samples to estimate the temperatures to which a paint has been heated. Five paint samples (one clay paint, two car paints, one metallic paint, and one matt emulsion) have been fully characterized by a combination of attenuated total reflectance Fourier transform infrared (ATR-IR), Raman, X-ray fluorescence spectroscopy and powder X-ray diffraction. The thermal decomposition of these paints has been investigated by means of ATR-IR and thermal gravimetric analysis. Clear temperature markers are observed in the ATR-IR spectra namely: loss of m(C = O) band, >300°C; appearance of water bands on cooling, >500°C; alterations to m(Si–O) bands due to dehydration of silicate clays, >700°C; diminution of m(CO3) and d(CO3) modes of CaCO3, >950°C. We suggest the possible use of portable ATR-IR for nondestructive, in situ analysis of paints.

Optical dating of quartz from young samples and the effects of pre-heat temperature

The optically stimulated luminescence (OSL) signal within quartz may be enhanced by thermal transfer during pre-heating. This may occur via a thermally induced charge transfer from low temperature traps to the OSL traps. Thermal transfer may affect both natural and artificially irradiated samples. The effect, as empirically measured via recuperation tests, is typically observed to be negligible for old samples (<1% of natural signal). However, thermal transfer remains a major concern in the dating of young samples as thermal decay and transfers of geologically unstable traps (typically in the TL range 160–280°C) may be incomplete. Upon pre-heating such a sample might undergo thermal transfer to the dating trap and result in a De overestimate. As a result, there has been a tendency for workers to adopt less rigorous pre-heats for young samples. We have investigated the pre-heat dependence of 23 young quartz samples from various depositional environments using pre-heats between 170°C and 300°C, employing the single aliquot regeneration (SAR) protocol. SAR De's were also calculated for 25 additional young quartz samples of different depositional environments and compared with previous multiple aliquot additive dose (MAAD) data. Results demonstrate no significant De dependence upon pre-heat temperatures. A close correspondence between MAAD data and the current SAR data for the samples tested is also illustrated.

Potential of the slow component of quartz OSL for age determination of sedimentary samples

The slow component of quartz OSL exhibits a high thermal stability, and, in many of the samples studied, a high dose saturation level (several hundreds or, even thousands, of Grays). These properties suggest that the slow component has potential as a long-range dating tool. Initial attempts have been made to obtain equivalent doses for a number of sedimentary samples. Single- and multiple-aliquot techniques were modified for use with the slow component. The results indicate that there is a good potential for sediment dating, particularly for samples of significant age. Experiments concerning the optical resetting of the slow component suggest that, given its slow optical depletion rate, dating may be restricted to aeolian sediments.

An assessment of the prebiotic potential of single and blended substrates in anaerobic in vitro batch culture fermentations using canine faecal samples as inocula

Previously, using an in vitro static batch culture system, it was found that rice bran (RB), inulin, fibersol, mannanoligosaccharides (MOS), larch arabinogalactan and citrus pectin elicited prebiotic effects (in terms of increased numbers of bifidobacteria and lactic acid bacteria) on the faecal microbiota of a dog. The aim of the present study was to confirm the prebiotic potential of each individual substrate using multiple faecal donors, as well as assessing the prebiotic potential of 15 substrate blends made from them. Anaerobic static and stirred, pH-controlled batch culture systems inoculated with faecal samples from healthy dogs were used for this purpose. Fluorescence in situ hybridization (FISH) analysis using seven oligonucleotide probes targeting selected bacterial groups and DAPI (total bacteria) was used to monitor bacterial populations during fermentation runs. High-performance liquid chromatography was used to measure butyrate produced as a result of bacterial fermentation of the substrates. RB and a MOS/RB blend (1:1, w/w) were shown to elicit prebiotic and butyrogenic effects on the canine microbiota in static batch culture fermentations. Further testing of these substrates in stirred, pH-controlled batch culture fermentation systems confirmed the prebiotic and butyrogenic effects of MOS/RB, with no enhancement of Clostridium clusters I and II and Escherichia coli populations.