Pulmonary aspiration in preschool children with cystic fibrosis

Pulmonary aspiration of gastric refluxate (PAGR) has been demonstrated in association with pulmonary inflammation in school aged children with Cystic Fibrosis (CF). We sought to determine if similar findings were present in preschool children. Pepsin was measured in Broncho-alveolar lavage (BAL) fluid collected from clinically stable preschool children with CF and controls. Elevated pepsin levels were found in a subgroup of children with CF, but this was not found to be associated with pulmonary infection, pulmonary inflammation or respiratory or gastrointestinal symptoms.     

Tropical rainforest canopies and climate change

Abstract There is less certainty about the impact of climate change on tropical rainforests than on temperate forests because of the comparative lack of background data and because few large scale experiments have been, and are being, carried out in tropical rainforests. Many of the factors critical to the future of tropical rainforests concern canopies, the key processes that take place there, and the roles and interactions of canopy biodiversity. In particular there are almost no data on how forest canopies and processes are changing with increased carbon dioxide levels. The implications of elevated carbon dioxide, climatic stress and related changes in water‐use efficiency, nutrient availability and other such changes are discussed particularly with references to Australia's tropical rainforests.     

Value of long‐term ecological studies

Long‐term ecological studies are critical for providing key insights in ecology, environmental change, natural resource management and biodiversity conservation. In this paper, we briefly discuss five key values of such studies. These are: (1) quantifying ecological responses to drivers of ecosystem change; (2) understanding complex ecosystem processes that occur over prolonged periods; (3) providing core ecological data that may be used to develop theoretical ecological models and to parameterize and validate simulation models; (4) acting as platforms for collaborative studies, thus promoting multidisciplinary research; and (5) providing data and understanding at scales relevant to management, and hence critically supporting evidence‐based policy, decision making and the management of ecosystems. We suggest that the ecological research community needs to put higher priority on communicating the benefits of long‐term ecological studies to resource managers, policy makers and the general public. Long‐term research will be especially important for tackling large‐scale emerging problems confronting humanity such as resource management for a rapidly increasing human population, mass species extinction, and climate change detection, mitigation and adaptation. While some ecologically relevant, long‐term data sets are now becoming more generally available, these are exceptions. This deficiency occurs because ecological studies can be difficult to maintain for long periods as they exceed the length of government administrations and funding cycles. We argue that the ecological research community will need to coordinate ongoing efforts in an open and collaborative way, to ensure that discoverable long‐term ecological studies do not become a long‐term deficiency. It is important to maintain publishing outlets for empirical field‐based ecology, while simultaneously developing new systems of recognition that reward ecologists for the use and collaborative sharing of their long‐term data sets. Funding schemes must be re‐crafted to emphasize collaborative partnerships between field‐based ecologists, theoreticians and modellers, and to provide financial support that is committed over commensurate time frames.     

Dynamic palaeoredox and exceptional preservation in the Cambrian Spence Shale of Utah

Garson, D.E., Gaines, R.R., Droser, M.L., Liddell, W.D. & Sappenfield, A. 2011: Dynamic palaeoredox and exceptional preservation in the Cambrian Spence Shale of Utah. Lethaia, Vol. 45, pp. 164–177. Burgess Shale‐type faunas provide a unique glimpse into the diversification of metazoan life during the Cambrian. Although anoxia has long been thought to be a pre‐requisite for this particular type of soft‐bodied preservation, the palaeoenvironmental conditions that regulated extraordinary preservation have not been fully constrained. In particular, the necessity of bottom water anoxia, long considered a pre‐requisite, has been the subject of recent debate. In this study, we apply a micro‐stratigraphical, ichnological approach to determine bottom water oxygen conditions under, which Burgess Shale‐type biotas were preserved in the Middle Cambrian Spence Shale of Utah. Mudstones of the Spence Shale are characterized by fine scale (mm‐cm) alternation between laminated and bioturbated intervals, suggesting high‐frequency fluctuations in bottom water oxygenation. Whilst background oxygen levels were not high enough to support continuous infaunal activity, brief intervals of improved bottom water oxygen conditions punctuate the succession. A diverse skeletonized benthic fauna, including various polymerid trilobites, hyolithids, brachiopods and ctenocystoids suggests that complex dysoxic benthic community was established during times when bottom water oxygen conditions were permissive. Burgess Shale‐type preservation within the Spence Shale is largely confined to non‐bioturbated horizons, suggesting that benthic anoxia prevailed in intervals, where these fossils were preserved. However, some soft‐bodied fossils are found within weakly to moderately bioturbated intervals (Ichnofabric Index 2 and 3). This suggests that Burgess Shale‐type preservation is strongly favoured by bottom water anoxia, but may not require it in all cases. □Anoxia, Burgess Shale, Burgess Shale type‐preservation, Langston Formation, Spence Shale Member, Utah.     

Marine metagenomics: strategies for the discovery of novel enzymes with biotechnological applications from marine environments

Metagenomic based strategies have previously been successfully employed as powerful tools to isolate and identify enzymes with novel biocatalytic activities from the unculturable component of microbial communities from various terrestrial environmental niches. Both sequence based and function based screening approaches have been employed to identify genes encoding novel biocatalytic activities and metabolic pathways from metagenomic libraries. While much of the focus to date has centred on terrestrial based microbial ecosystems, it is clear that the marine environment has enormous microbial biodiversity that remains largely unstudied. Marine microbes are both extremely abundant and diverse; the environments they occupy likewise consist of very diverse niches. As culture-dependent methods have thus far resulted in the isolation of only a tiny percentage of the marine microbiota the application of metagenomic strategies holds great potential to study and exploit the enormous microbial biodiversity which is present within these marine environments.     

Strain persistence of invasive Candida albicans in chronic hyperplastic candidosis that underwent malignant change

Objectives: The aim of this study was to assess persistence and tissue invasion of Candida albicans strains isolated from a 65 year‐old patient with chronic hyperplastic candidosis (CHC), that subsequently developed into squamous cell carcinoma (SCC). Materials and Methods: C. albicans (n=7) were recovered from the oral cavity of the patient over seven years. Confirmation of CHC and SCC in this patient was achieved by histopathological examination of incisional biopsy tissue. DNA fingerprinting was performed on the seven isolates from the CHC patient together with a further eight isolates from patients with normal oral mucosa (n=2), chronic atrophic candidosis (n=1), SCC (n=1) and CHC (n=4). Genotyping involved the use of inter‐repeat PCR using the eukaryotic repeat primer 1251. Characterisation of the tissue invasive abilities of the isolates was achieved by infecting a commercially available reconstituted human oral epithelium (RHE; SkinEthic, Nice, France). After 24 h. C. albicans tissue invasion was assessed by histopathological examination. Results: DNA fingerprinting demonstrated strain persistence of C. albicans in the CHC patient over a seven year period despite provision of systemic antifungal therapy. The strain of C. albicans isolated from this patient was categorised as a high invader within the RHE compared to other isolates. Conclusions: Candidal strain persistence was evident in a patient with CHC over seven years. This persistence may be due to incomplete eradication from the oral cavity following antifungal therapy or subsequent recolonisation from other body sites or separate exogenous sources. The demonstration of enhanced in vitro tissue invasion by this particular strain may, in part, explain the progression to carcinoma.     

Methods and strategies for detecting Solanum tuberosum dihaploids in interspecific crosses with S. phureja

The frequency of dihaploid production following the interspecific pollination of Solanum tuberosum clones with Solanum phureja has been investigated. Seventeen hybrid combinations were tested and the crosses differed significantly in the number of seed produced, the proportions that were viable and the proportions that were dihaploid. The overall frequency of dihaploid production was 62%. The dominant embryo spot marker of the pollinator (IVP 48) in conjunction with seed diameter was used to classify the seed samples. Number of days taken to germinate was also recorded. It was therefore possible to examine retrospectively the effect of selecting sub-sets of the seed based on the presence or absence of the embryo spot, seed size and germination time. A seed selection system based on the absence of the embryo spot in conjunction with seed greater than 1.25 mm in diameter resulted in 93.6% of the potential dihaploids being identified.     

Polarized Growth of Fungal Hyphae Is Defined by an Alkaline pH Gradient

Robson, G. D., Prebble, E., Rickers, A., Hosking, S., Denning, D. W., Trinci, A. P. J., and Robertson, W. 1996. Polarized growth of fungal hyphae is defined by an alkaline pH gradient. Fungal Genetics and Biology 20, 289-298. Polarized cell growth is exhibited by a diverse range of eukaryotic and prokaryotic cells. The events which are responsible for this growth are poorly understood. However, the existence of ion gradients may play an important role in establishing and driving cell polarity. Using a pH-sensitive, ratiometric fluorescent dye to monitor intracellular pH in growing fungal hyphae, we report a gradient at the extending hyphal tip that is up to 1.4 pH units more alkaline than more distal regions. Both the magnitude and the length of the pH gradient were strongly correlated with the rate of hyphal extension and eradication of the gradient-arrested growth. These results suggest that alkaline pH gradients may be integral to hyphal extension in fungi.