Optimization and clinical validation of a pathogen detection microarray

DNA microarrays used as 'genomic sensors' have great potential in clinical diagnostics. Biases inherent in random PCR-amplification, cross-hybridization effects, and inadequate microarray analysis, however, limit detection sensitivity and specificity. Here, we have studied the relationships between viral amplification efficiency, hybridization signal, and target-probe annealing specificity using a customized microarray platform. Novel features of this platform include the development of a robust algorithm that accurately predicts PCR bias during DNA amplification and can be used to improve PCR primer design, as well as a powerful statistical concept for inferring pathogen identity from probe recognition signatures. Compared to real-time PCR, the microarray platform identified pathogens with 94% accuracy (76% sensitivity and 100% specificity) in a panel of 36 patient specimens. Our findings show that microarrays can be used for the robust and accurate diagnosis of pathogens, and further substantiate the use of microarray technology in clinical diagnostics.     

Trophic level delineation and resource partitioning in a South African afromontane forest bird community using carbon and nitrogen stable isotopes

Southern African forests are naturally fragmented yet hold a disproportionately high number of bird species. Carbon and nitrogen stable isotopes were measured in feathers from birds captured at Woodbush (n = 27 species), a large afromontane forest in the eastern escarpment of Limpopo province, South Africa. The δ¹³C signatures of a range of forest plants were measured to categorise the food base. Most plants sampled, including two of five grass species, had δ¹³C signatures typical of a C₃ photosynthetic pathway (?29.5 ± 1.9‰). Three grass species had a C₄ signature (?12.0 ± 0.6‰). Most bird species had δ¹³C values representing a predominantly C₃‐based diet (?24.8‰ to ?20.7‰). δ¹⁵N values were as expected, with higher levels of enrichment associated with a greater proportion of dietary animal matter. The cohesive isotopic niche defining most species (n = 22), where the ranges for δ¹³C and δ¹⁵N were 2.4‰ and 3.4‰, respectively, highlight the difficulties in understanding diets of birds in a predominantly C₃‐based ecosystem using carbon and nitrogen stable isotopes. However, variation in isotopic values between and within species provides insight into possible niche width and the use of resources by different birds within a forest environment.     

Membrane diffusion- and capillary blood volume measurements are not useful as screening tools for pulmonary arterial hypertension in systemic sclerosis: a case control study

Background

Lung injury caused by both inhaled dusts and infectious agents depends on increased availability of iron and metal-catalyzed oxidative stress. Because inhaled particles, such as silica, and certain infections can cause secondary pulmonary alveolar proteinosis (PAP), we tested the hypothesis that idiopathic PAP is associated with an altered iron homeostasis in the human lung.

Methods

Healthy volunteers (n = 20) and patients with idiopathic PAP (n = 20) underwent bronchoalveolar lavage and measurements were made of total protein, iron, tranferrin, transferrin receptor, lactoferrin, and ferritin. Histochemical staining for iron and ferritin was done in the cell pellets from control subjects and PAP patients, and in lung specimens of patients without cardiopulmonary disease and with PAP. Lavage concentrations of urate, glutathione, and ascorbate were also measured as indices of oxidative stress.

Results

Lavage concentrations of iron, transferrin, transferrin receptor, lactoferrin, and ferritin were significantly elevated in PAP patients relative to healthy volunteers. The cells of PAP patients had accumulated significant iron and ferritin, as well as considerable amounts of extracellular ferritin. Immunohistochemistry for ferritin in lung tissue revealed comparable amounts of this metal-storage protein in the lower respiratory tract of PAP patients both intracellularly and extracellularly. Lavage concentrations of ascorbate, glutathione, and urate were significantly lower in the lavage fluid of the PAP patients.

Conclusion

Iron homeostasis is altered in the lungs of patients with idiopathic PAP, as large amounts of catalytically-active iron and low molecular weight anti-oxidant depletion are present. These findings suggest a metal-catalyzed oxidative stress in the maintenance of this disease.     

Resource partitioning of sympatric small mammals in an African forest‐grassland vegetation mosaic

It is often hypothesized that two species competing for the same resource cannot stably coexist unless they partition their resources in space and time. More recently stable isotope analyses have complemented traditional, observation‐based niche research by conceptualizing many of the characteristics of communities, for example, trophic niche width and the partitioning of resources. Here we quantify resource partitioning of sympatric small mammal species in an African ecosystem by analysing stable isotope ratios of hair collected from a South African forest‐grassland vegetation mosaic, and combine this with known spatial and temporal behavioural data to interpret community competition and resource partitioning. We observe niche separation to different degrees across the entire community, with different species displaying either unique isotopic dietary preferences, or partitioning resources in space and/or time. δ¹³C values were more enriched in species that inhabited afromontane grassland compared with those that inhabited afromontane forest, a reflection of the dominant vegetation in each habitat. Contrary to expectations, arboreal rodents occupied higher trophic positions than terrestrial rodents and approaching δ¹⁵N values similar to insectivorous shrews, suggesting that arboreal rodents feed on items such as arthropods enriched in ¹⁵N. While grassland species display phenotypic plasticity in terms of dietary preferences, small mammals that occurred in forests display narrow niche preferences, suggesting these species may be particularly sensitive to habitat modifications. Our results illustrate that the use of stable isotopes can be used in conjunction with spatial and temporal behavioural knowledge to elucidate resource partitioning in small African mammal communities.     

Design and Performance of Rechargeable Sodium Ion Batteries,and Symmetrical Li‐Ion Batteries with Supercapacitor‐Like Power Density Based upon Polyoxovanadates

The polyanion Li₇V₁₅O₃₆(CO₃) is a nanosized molecular cluster (≈1 nm in size), that has the potential to form an open host framework with a higher surface‐to‐bulk ratio than conventional transition metal oxide electrode materials. Herein, practical rechargeable Na‐ion batteries and symmetric Li‐ion batteries are demonstrated based on the polyoxovanadate Li₇V₁₅O₃₆(CO₃). The vanadium centers in {V₁₅O₃₆(CO₃)} do not all have the same V^IV/V redox potentials, which permits symmetric devices to be created from this material that exhibit battery‐like energy density and supercapacitor‐like power density. An ultrahigh specific power of 51.5 kW kg^?1 at 100 A g^?1 and a specific energy of 125 W h kg^?1 can be achieved, along with a long cycling life (>500 cycles). Moreover, electrochemical and theoretical studies reveal that {V₁₅O₃₆(CO₃)} also allows the transport of large cations, like Na⁺, and that it can serve as the cathode material for rechargeable Na‐ion batteries with a high specific capacity of 240 mA h g^?1 and a specific energy of 390 W h kg^?1 for the full Na‐ion battery. Finally, the polyoxometalate material from these electrochemical energy storage devices can be easily extracted from spent electrodes by simple treatment with water, providing a potential route to recycling of the redox active material.