Rapid lab-on-a-chip profiling of human gut bacteria

The human gut microbiota has a substantial impact on human health. Different factors such as disease, diet and drug use can have significant impacts on the gut microbiota. Therefore, it is of interest to have simple, rapid methods for analysis of the composition of the gut microbiota for clinical diagnostic purposes. Since only a minor fraction of the gastrointestinal bacterial community is presently possible to cultivate, molecular approaches are currently the best suited to investigate its composition. However, most of these molecular approaches require technical expertise and expensive equipment to run and they are not routinely available. Ideally, the analyses should be point-of-care options that can be run on a chip. In this study, an existing lab-on-chip (LOC) system for sizing/quantifying DNA was combined with length heterogeneity PCR (LH-PCR), a PCR-based profiling method targeting bacterial 16S rRNA gene sequences, to develop a fast, straightforward, reproducible, and economical method for profiling bacterial communities. The LOC LH-PCR method was first evaluated using a standardized gut cocktail containing genomic DNA from eight different bacterial species representing different genera of relevance for human health. The method was also tested on DNA that was directly extracted from human faecal samples and it was consistently capable of detecting alterations in the bacterial samples before and after antibiotic treatment. Although the resolution of the method needs improvement, this study represents the first step towards development of a diagnostic LOC for profiling gut bacterial communities.     

Preliminary results in the immunodiagnosis of tuberculosis in children based on T cell responses to ESAT-6 and PPD antigens

The aim of this work was to study the difference in interferon gamma (IFN-gamma) production by T lymphocytes after early secretory antigen target 6 (ESAT-6) or purified protein derivate (PPD) stimulation in whole blood culture supernatants from children with suspected tuberculosis (TB) disease (n = 21), latent TB infection (n = 16) and negative controls (NC) (n = 22) from an endemic area in Brazil. The concentration of IFN-gamma (pg/ml) was measured by enzyme linked immunosorbent assay and the differences in the IFN-gamma levels for each group were compared and evaluated using an unpaired Student's t-test; p values < 0.05 were considered significant. Measurement of IFN-gamma levels after ESAT-6 stimulation raised the possibility of early diagnosis in the latent TB group (p = 0.0030). Nevertheless, the same group showed similar responses to the NC group (p > 0.05) after PPD stimulation. The IFN-gamma assay using ESAT-6 as an antigenic stimulus has the potential to be used as a tool for the immunodiagnosis of early TB in children.     

Cellular Uptake of α-Synuclein Oligomer-Selective Antibodies is Enhanced by the Extracellular Presence of α-Synuclein and Mediated via Fcγ Receptors

Immunotherapy targeting aggregated α-synuclein has emerged as a potential treatment strategy against Parkinson’s disease and other α-synucleinopathies. We have developed α-synuclein oligomer/protofibril selective antibodies that reduce toxic α-synuclein in a human cell line and, upon intraperitoneal administration, in spinal cord of transgenic mice. Here, we investigated under which conditions and by which mechanisms such antibodies can be internalized by cells. For this purpose, human neuroglioma H4 cells were treated with either monoclonal oligomer/protofibril selective α-synuclein antibodies, linear epitope monoclonal α-synuclein antibodies, or with a control antibody. The oligomer/protofibril selective antibody mAb47 displayed the highest cellular uptake and was therefore chosen for additional analyses. Next, α-synuclein overexpressing cells were incubated with mAb47, which resulted in increased antibody internalization as compared to non-transfected cells. Similarly, regular cells exposed to mAb47 together with media containing α-synuclein displayed a higher uptake as compared to cells incubated with regular media. Finally, different Fcγ receptors were targeted and we then found that blockage of FcγRI and FcγRIIB/C resulted in reduced antibody internalization. Our data thus indicate that the robust uptake of the oligomer/protofibril selective antibody mAb47 by human CNS-derived cells is enhanced by extracellular α-synuclein and mediated via Fcγ receptors. Altogether, our finding lend further support to the belief that α-synuclein pathology can be modified by monoclonal antibodies and that these can target toxic α-synuclein species in the extracellular milieu. In the context of immunotherapy, antibody binding of α-synuclein would then not only block further aggregation but also mediate internalization and subsequent degradation of antigen–antibody complexes.     

Bacterial resistance to arsenic protects against protist killing

Protists kill their bacterial prey using toxic metals such as copper. Here we hypothesize that the metalloid arsenic has a similar role. To test this hypothesis, we examined intracellular survival of Escherichia coli (E. coli) in the amoeba Dictyostelium discoideum (D. discoideum). Deletion of the E. coli ars operon led to significantly lower intracellular survival compared to wild type E. coli. This suggests that protists use arsenic to poison bacterial cells in the phagosome, similar to their use of copper. In response to copper and arsenic poisoning by protists, there is selection for acquisition of arsenic and copper resistance genes in the bacterial prey to avoid killing. In agreement with this hypothesis, both copper and arsenic resistance determinants are widespread in many bacterial taxa and environments, and they are often found together on plasmids. A role for heavy metals and arsenic in the ancient predator–prey relationship between protists and bacteria could explain the widespread presence of metal resistance determinants in pristine environments.     

Assessing acid stress in Swedish boreal and alpine streams using benthic macroinvertebrates

Sixty streams in northern Sweden were sampled for benthic macroinvertebrates in spring and autumn of 2000 as part of the European Union project AQEM (the Development and Testing of an Integrated Assessment System for the Ecological Quality of Streams and Rivers throughout Europe using Benthic Macroinvertebrates). Samples were taken using a harmonised multi-habitat sampling procedure and a large number of parameters describing the streams and their catchments were recorded for all sampling sites. From the stream water chemistry characteristics unbiased measures of acid stress were derived, based on the Swedish Ecological Quality Criteria (EQC) for acidity status. These criteria do not, however, assess the degree of human influence to a stream. Therefore, in the following analysis of classification, the Swedish EQC status criteria are applied as if they were a measure of human influence. Three new multimetric acid indices using benthic macroinvertebrates were developed for the AQEM project. These, together with a large number of other benthic macroinvertebrate indices including a number of indices aimed at detecting acid stress, were evaluated for their ability to detect acid stress, using both spring/early summer and autumn sampling. Surprisingly, the acid index that is in general use in northern Sweden worked well in spring/early summer, but because of a (probable) re-colonisation of more acid sensitive taxa, the index values changed from classifying streams as affected in spring/early summer to classify streams as non-affected by acid stress in autumn. Another Swedish acid index (included in the Swedish Environmental Quality Criteria developed by the Swedish EPA) and developed for southern Sweden was strongly correlated between spring/early summer and autumn and could thus be sampled in the autumn and indicate acid stress from spring flood declines in pH. This is of great importance since the local County boards of northern Sweden generally argue that sampling has to be done in the spring to see the effects of acid stress, when sampling is difficult for logistic reasons. Whether or not the three indices developed for the AQEM project (and extensively based on the south Swedish acid index) were truly better than the south-Swedish acid index to assess acid stress in northern Sweden could not be clearly determined in the present study.     

Genotyping by apyrase-mediated allele-specific extension

This report describes a single-step extension approach suitable for high-throughput single-nucleotide polymorphism typing applications. The method relies on extension of paired allele-specific primers and we demonstrate that the reaction kinetics were slower for mismatched configurations compared with matched configurations. In our approach we employ apyrase, a nucleotide degrading enzyme, to allow accurate discrimination between matched and mismatched primer-template configurations. This apyrase-mediated allele-specific extension (AMASE) protocol allows incorporation of nucleotides when the reaction kinetics are fast (matched 3′-end primer) but degrades the nucleotides before extension when the reaction kinetics are slow (mismatched 3′-end primer). Thus, AMASE circumvents the major limitation of previous allele-specific extension assays in which slow reaction kinetics will still give rise to extension products from mismatched 3′-end primers, hindering proper discrimination. It thus represents a significant improvement of the allele-extension method. AMASE was evaluated by a bioluminometric assay in which successful incorporation of unmodified nucleotides is monitored in real-time using an enzymatic cascade.     

Simian Immunodeficiency Virus (SIV) Envelope-Specific Fabs with High-Level Homologous Neutralizing Activity: Recovery from a Long-Term-Nonprogressor SIV-Infected Macaque

An antibody phage display library was constructed from RNA extracted from lymph node cells of a simian immunodeficiency virus (SIV)-infected long-term-nonprogressor macaque. Seven gp120-reactive Fabs were obtained by selection of the library against SIV monomeric gp120. Although each of the Fabs was unique in sequence, there were two distinct groups based on epitope recognition, neutralizing activity in vitro, and molecular analysis. Group 1 Fabs did not neutralize SIV and bound to a linear epitope in the V3 loop of the SIV envelope. In contrast, two of the group 2 Fabs neutralized homologous, neutralization-sensitive SIVsm isolates with high efficiency but failed to neutralize heterologous SIVmac isolates. Based on competition enzyme-linked immunosorbent assays with mouse monoclonal antibodies of known specificity, these Fabs reacted with a conformational epitope that includes domains V3 and V4 of the SIV envelope. These neutralizing and nonneutralizing Fabs provide valuable standardized and renewable reagents for studying the role of antibody in preventing or modifying SIV infection in vivo.     

Plant sex and hare feeding preferences

Summary To evaluate the general extent to which sex-related differences in palatability occur in boreal dioecious woody plants, males and females of five dioecious woody plant species were presented to free-ranging mountain hares (Lepus timidus) during winter. Hares strongly preferred branches from male plants when feeding on Populus tremula and Salix caprea and weakly preferred male S. pentandra. However, they did not show any sex-related preference when feeding on the other two species studied (Myrica gale and Juniperus communis). Nitrogen concentration and, to some degree, digestibility showed strong relationships with hare food preferences. By contrast, the concentration of phenolics was only weakly related to feeding preference. Phenolics could, nevertheless, still be important if only one or a few specific compounds deter hare feeding. These results indicate that sex-related differences in plant palatability in the boreal forest might be more widespread than previously believed, particularly for species of the family Salicaceae. Thus, herbivores might be responsible for the female-biased sex ratios found in willow populations in northern Scandinavia (e.g. Elmqvist et al. 1988).     

Investigation of a tartaric acid-based linear polyamide and dimer as chiral selectors in liquid chromatography

A twin selector for enantioselective liquid chromatography based on O,O'-bis(dimethyl)benzoyl tartaric diamide was synthesized and compared to commercially available Kromasil CHI-DMB (O,O'-bis(dimethyl)benzoyl tartaric diamide). A linear polyamide based on the same tartaric acid derivative was also synthesized, immobilized on silica, and evaluated as stationary phase. The twin selector was immobilized as a brush-type phase, with similar bonding chemistry as in Kromasil CHI-DMB. It was shown to exhibit lower resolution power than Kromasil CHI-DMB. However, retention and separation factors obtained on the respective sorbents were shown to exhibit interdependence. CD spectra of the twin selector give no indication that the respective branches interact in the solvent mixtures employed for chromatography. The linear polyamide showed lower enantioselectivity and higher retention than Kromasil CHI-DMB.