Investigating bacteriophages targeting the opportunistic pathogen Acinetobacter baumannii

The multi-drug resistance of the opportunistic pathogen Acinetobacter baumannii is of growing concern, with many clinical isolates proving to be resistant to last resort as well as front line antibiotic treatments. The use of bacteriophages is an attractive alternative to controlling and treating this emerging nosocomial pathogen. In this study, we have investigated bacteriophages collected from hospital wastewater in Thailand and we have explored their activity against clinical isolates of A. baumannii. Bacteriophage vB_AbaM_PhT2 showed 28% host range against 150 multidrug resistant (MDR) isolates and whole genome sequencing did not detect any known virulence factors or antibiotic resistance genes. Purified vB_AbaM_PhT2 samples had endotoxin levels below those recommended for preclinical trials and were not shown to be directly cytotoxic to human cell lines in vitro. The treatment of human brain and bladder cell lines grown in the presence of A. baumannii with this bacteriophage released significantly less lactate dehydrogenase compared to samples with no bacteriophage treatment, indicating that vB_AbaM_PhT2 can protect from A. baumannii induced cellular damage. Our results have also indicated that there is synergy between this bacteriophage and the end line antibiotic colistin. We therefore propose bacteriophage vB_AbaM_PhT2 as a good candidate for future research and for its potential development into a surface antimicrobial for use in hospitals. View Full-Tex

An adaptable analysis workflow for characterization of platelet spreading and morphology

The assessment of platelet spreading through light microscopy, and the subsequent quantification of parameters such as surface area and circularity, is a key assay for many platelet biologists. Here we present an analysis workflow which robustly segments individual platelets to facilitate the analysis of large numbers of cells while minimizing user bias. Image segmentation is performed by interactive learning and touching platelets are separated with an efficient semi-automated protocol. We also use machine learning methods to robustly automate the classification of platelets into different subtypes. These adaptable and reproducible workflows are made freely available and are implemented using the open-source software KNIME and ilastik

Estimating hydrodynamic roughness in a wave-dominated environment with a high-resolution acoustic Doppler profiler

Author Posting. © American Geophysical Union, 2005. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 110 (2005): C06014, doi:10.1029/2003JC001814.Hydrodynamic roughness is a critical parameter for characterizing bottom drag in boundary layers, and it varies both spatially and temporally due to variation in grain size, bedforms, and saltating sediment. In this paper we investigate temporal variability in hydrodynamic roughness using velocity profiles in the bottom boundary layer measured with a high-resolution acoustic Doppler profiler (PCADP). The data were collected on the ebb-tidal delta off Grays Harbor, Washington, in a mean water depth of 9 m. Significant wave height ranged from 0.5 to 3 m. Bottom roughness has rarely been determined from hydrodynamic measurements under conditions such as these, where energetic waves and medium-to-fine sand produce small bedforms. Friction velocity due to current u *c and apparent bottom roughness z 0a were determined from the PCADP burst mean velocity profiles using the law of the wall. Bottom roughness k B was estimated by applying the Grant-Madsen model for wave-current interaction iteratively until the model u *c converged with values determined from the data. The resulting k B values ranged over 3 orders of magnitude (10−1 to 10−4 m) and varied inversely with wave orbital diameter. This range of k B influences predicted bottom shear stress considerably, suggesting that the use of time-varying bottom roughness could significantly improve the accuracy of sediment transport models. Bedform height was estimated from k B and is consistent with both ripple heights predicted by empirical models and bedforms in sonar images collected during the experiment

Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny

Scleractinian corals' microbial symbionts influence host health, yet how coral microbiomes assembled over evolution is not well understood. We survey bacterial and archaeal communities in phylogenetically diverse Australian corals representing more than 425 million years of diversification. We show that coral microbiomes are anatomically compartmentalized in both modern microbial ecology and evolutionary assembly. Coral mucus, tissue, and skeleton microbiomes differ in microbial community composition, richness, and response to host vs. environmental drivers. We also find evidence of coral-microbe phylosymbiosis, in which coral microbiome composition and richness reflect coral phylogeny. Surprisingly, the coral skeleton represents the most biodiverse coral microbiome, and also shows the strongest evidence of phylosymbiosis. Interactions between bacterial and coral phylogeny significantly influence the abundance of four groups of bacteria-including Endozoicomonas-like bacteria, which divide into host-generalist and host-specific subclades. Together these results trace microbial symbiosis across anatomy during the evolution of a basal animal lineage

Asphodelaceae : Alooideae. Gasteria croucheri subsp.Pondoensis, a new cremnophyte from Pondoland, South Africa

We describe a new subspecies of Gasteria croucheri (Hook.f.) Baker from northern Pondoland, Eastern Cape, an obligate cremnophyte belonging to Gasteria Duval sect. Longifl orae Haw. ser. Longifoliae Haw. The members of this series are all characterized by narrow, elliptical, comparatively dull-coloured fl owers in which the swelling in the upper half approximates the rather unpronounced basal gasteriform portion (Van Jaarsveld et al. 1994). Mature specimens of the new taxon produce both leaves (up to 1.5 m long) and fl owers (up to 50 mm long) that are exceptionally long in the genus. To date, plants have only been found in the Msikaba and Mtentu River systems adjacent to Mkambati Game Reserve (Figure 8), the topography of which is characterized by rugged plateaux of 100–500 m, dissected deeply by narrow river gorges. This distribution falls within the Pondoland Centre of Plant Endemism (Van Wyk & Smith 2001). Specimens grow on cliffs both fully exposed on southern aspects, as well as within the shaded margins of riverine forest. It is a clump-forming species with long, angular and often sickle-shaped leaves, most of which are pendulous in mature specimens (Figure 9).http://www.sanbi.or

Evaluation of the ECOSSE model for simulating soil organic carbon under Miscanthus and short rotation coppice-willow crops in Britain

Acknowledgements This work contributes to the ELUM (Ecosystem Land Use Modelling & Soil Carbon GHG Flux Trial) project, which was commissioned and funded by the Energy Technologies Institute (ETI). We acknowledge the E-OBS data set from the EU-FP6 project ENSEMBLES (http://ensembles-eu.metoffice.com) and the data providers in the ECA&D project (http://www.ecad.eu).Peer reviewedPublisher PD

Materiality in the future of history: things, practices, and politics

Frank Trentmann is professor of history at Birkbeck College, University of London. From 2002 to 2007, he was director of the £5 million Cultures of Consumption research program, cofunded by the Arts and Humanities Research Council and the Economic and Social Research Council (ESRC). He is working on a book for Penguin, The Consuming Passion: How Things Came to Seduce, Enrich, and Define Our Lives, from the Seventeenth Century to the Twenty‐First. This article is one of a pair seeking to facilitate greater exchange between history and the social sciences. Its twin—“Crossing Divides: Globalization and Consumption in History” (forthcoming in the Handbook of Globalization Studies, ed. Bryan Turner)—shows what social scientists (and contemporary historians) might learn from earlier histories. The piece here follows the flow in the other direction. Many thanks to the ESRC for grant number RES‐052‐27‐002 and, for their comments, to Heather Chappells, Steve Pincus, Elizabeth Shove, and the editor and the reviewer

A Miscanthus plantation can be carbon neutral without increasing soil carbon stocks

Acknowledgements The authors would like to thank the NERC Centre for Ecology & Hydrology and Shell for providing a joint PhD studentship grant award to Andy Robertson (CEH project number NEC04306). We are also grateful to Emily Clark, Simon Oakley and Rebecca Rowe at CEH Lancaster and Sean Case at the University of Copenhagen for help with fieldwork, laboratory work and manuscript comments.Peer reviewedPublisher PD