Impact of the invasive rust Puccinia psidii (myrtle rust) on native Myrtaceae in natural ecosystems in Australia

The invasive rust Puccinia psidii (myrtle rust) was detected in Australia in 2010 and is now established along the east coast from southern New South Wales to far north Queensland. Prior to reaching Australia, severe damage from P. psidii was mainly restricted to exotic eucalypt plantations in South America, guava plantations in Brazil, allspice plantations in Jamaica, and exotic Myrtaceous tree species in the USA; the only previous record of widespread damage in native environments is of endangered Eugenia koolauensis in Hawai’i. Using two rainforest tree species as indicators of the impact of P. psidii, we report for the first time severe damage to endemic Myrtaceae in native forests in Australia, after only 4 years’ exposure to P. psidii. A 3-year disease exclusion trial in a natural stand of Rhodamnia rubescens unequivocally showed that repeated, severe infection leads to gradual crown loss and ultimately tree mortality; trees were killed in less than 4 years. Significant (p < 0.001) correlations were found between both incidence (r = 0.36) and severity (r = 0.38) of P. psidii and subsequent crown loss (crown transparency). This provided supporting evidence to conclude a causal association between P. psidii and crown loss and tree mortality in our field assessments of R. rubescens and Rhodomyrtus psidioides across their native range. Assessments revealed high levels of damage by P. psidii to immature leaves, shoots and tree crowns—averaging 76 % (R. rubescens) and 95 % (R. psidioides) crown transparency—as well as tree mortality. For R. psidioides, we saw exceptionally high levels of tree mortality, with over half the trees surveyed dead and 40 % of stands with greater than 50 % tree mortality, including two stands where all trees were dead. Tree mortality was less prevalent for R. rubescens, with only 12 % of trees surveyed dead and two sites with greater than 50 % mortality. Any alternative causal agents for this tree mortality have been discounted. The ecological implications of this are unclear, but our work clearly illustrates the potential for P. psidii to negatively affect Australia’s biodiversity

Eddy correlation measurements of oxygen fluxes in permeable sediments exposed to varying current flow and light

Author Posting. © Association for the Sciences of Limnology and Oceanography, 2013. This article is posted here by permission of Association for the Sciences of Limnology and Oceanography for personal use, not for redistribution. The definitive version was published in Limnology and Oceanography 58 (2013): 1329–1343, doi:10.4319/lo.2013.58.4.1329.Based on noninvasive eddy correlation measurements at a marine and a freshwater site, this study documents the control that current flow and light have on sediment–water oxygen fluxes in permeable sediments. The marine sediment was exposed to tidal-driven current and light, and the oxygen flux varied from night to day between −29 and 78 mmol m−2 d−1. A fitting model, assuming a linear increase in oxygen respiration with current flow, and a photosynthesis–irradiance curve for light-controlled production reproduced measured fluxes well (R2 = 0.992) and revealed a 4-fold increase in oxygen uptake when current velocity increased from ∼ 0 to 20 cm s−1. Application of the model to a week-long measured record of current velocity and light showed that net ecosystem metabolism varied substantially among days, between −27 and 31 mmol m−2 d−1, due to variations in light and current flow. This variation is likely typical of many shallow-water systems and highlights the need for long-term flux integrations to determine system metabolism accurately. At the freshwater river site, the sediment–water oxygen flux ranged from −360 to 137 mmol m−2 d−1. A direct comparison during nighttime with concurrent benthic chamber incubations revealed a 4.1 times larger eddy flux than that obtained with chambers. The current velocity during this comparison was 31 cm s−1, and the large discrepancy was likely caused by poor imitation by the chambers of the natural pore-water flushing at this high current velocity. These results emphasize the need for more noninvasive oxygen flux measurements in permeable sediments to accurately assess their role in local and global carbon budgets.Support for this study was provided by the following National Science Foundation grants: OCE-0420575, OCE- 0536431, and OCE-1061364

Flux Discharge Cascades in Various Dimensions

We study the dynamics of electric flux discharge by charged particle pair or spherical string or membrane production in various dimensions. When electric flux wraps at least one compact cycle, we find that a single "pair" production event can initiate a cascading decay in real time that "shorts out" the flux and discharges many units of it. This process arises from local dynamics in the compact space, and so is invisible in the dimensionally-reduced truncation. It occurs in theories as simple as the Schwinger model on a circle, and has implications for any theory with compact dimensions and electric flux, including string theories and the string landscape.Comment: 19+8 pages, 3 figures, 3 appendice

A status report on the observability of cosmic bubble collisions

In the picture of eternal inflation as driven by a scalar potential with multiple minima, our observable universe resides inside one of many bubbles formed from transitions out of a false vacuum. These bubbles necessarily collide, upsetting the homogeneity and isotropy of our bubble interior, and possibly leading to detectable signatures in the observable portion of our bubble, potentially in the Cosmic Microwave Background or other precision cosmological probes. This constitutes a direct experimental test of eternal inflation and the landscape of string theory vacua. Assessing this possibility roughly splits into answering three questions: What happens in a generic bubble collision? What observational effects might be expected? How likely are we to observe a collision? In this review we report the current progress on each of these questions, improve upon a few of the existing results, and attempt to lay out directions for future work.Comment: Review article; comments very welcome. 24 pages + 4 appendices; 19 color figures. (Revised version adds two figures, minor edits.

Two-photon Lithography for 3D Magnetic Nanostructure Fabrication

Ferromagnetic materials have been utilised as recording media within data storage devices for many decades. Confinement of the material to a two dimensional plane is a significant bottleneck in achieving ultra-high recording densities and this has led to the proposition of three dimensional (3D) racetrack memories that utilise domain wall propagation along nanowires. However, the fabrication of 3D magnetic nanostructures of complex geometry is highly challenging and not easily achievable with standard lithography techniques. Here, by using a combination of two-photon lithography and electrochemical deposition, we show a new approach to construct 3D magnetic nanostructures of complex geometry. The magnetic properties are found to be intimately related to the 3D geometry of the structure and magnetic imaging experiments provide evidence of domain wall pinning at a 3D nanostructured junction

The interplay between the Rab27A effectors Slp4-a and MyRIP controls hormone-evoked Weibel-Palade body exocytosis.

Weibel-Palade body (WPB) exocytosis underlies hormone-evoked VWF secretion from endothelial cells (ECs). We identify new endogenous components of the WPB: Rab3B, Rab3D, and the Rab27A/Rab3 effector Slp4-a (granuphilin), and determine their role in WPB exocytosis. We show that Rab3B, Rab3D, and Rab27A contribute to Slp4-a localization to WPBs. siRNA knockdown of Slp4-a, MyRIP, Rab3B, Rab3D, Rab27A, or Rab3B/Rab27A, or overexpression of EGFP-Slp4-a or EGFP-MyRIP showed that Slp4-a is a positive and MyRIP a negative regulator of WPB exocytosis and that Rab27A alone mediates these effects. We found that ECs maintain a constant amount of cellular Rab27A irrespective of the WPB pool size and that Rab27A (and Rab3s) cycle between WPBs and a cytosolic pool. The dynamic redistribution of Rab proteins markedly decreased the Rab27A concentration on individual WPBs with increasing WPB number per cell. Despite this, the probability of WPB release was independent of WPB pool size showing that WPB exocytosis is not determined simply by the absolute amount of Rab27A and its effectors on WPBs. Instead, we propose that the probability of release is determined by the fractional occupancy of WPB-Rab27A by Slp4-a and MyRIP, with the balance favoring exocytosis

International lower limb collaborative (INTELLECT) study: a multicentre, international retrospective audit of lower extremity open fractures

Trauma remains a major cause of mortality and disability across the world1, with a higher burden in developing nations2. Open lower extremity injuries are devastating events from a physical3, mental health4, and socioeconomic5 standpoint. The potential sequelae, including risk of chronic infection and amputation, can lead to delayed recovery and major disability6. This international study aimed to describe global disparities, timely intervention, guideline-directed care, and economic aspects of open lower limb injuries

A framework for human microbiome research

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies

Structure, function and diversity of the healthy human microbiome

Author Posting. © The Authors, 2012. This article is posted here by permission of Nature Publishing Group. The definitive version was published in Nature 486 (2012): 207-214, doi:10.1038/nature11234.Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.This research was supported in part by National Institutes of Health grants U54HG004969 to B.W.B.; U54HG003273 to R.A.G.; U54HG004973 to R.A.G., S.K.H. and J.F.P.; U54HG003067 to E.S.Lander; U54AI084844 to K.E.N.; N01AI30071 to R.L.Strausberg; U54HG004968 to G.M.W.; U01HG004866 to O.R.W.; U54HG003079 to R.K.W.; R01HG005969 to C.H.; R01HG004872 to R.K.; R01HG004885 to M.P.; R01HG005975 to P.D.S.; R01HG004908 to Y.Y.; R01HG004900 to M.K.Cho and P. Sankar; R01HG005171 to D.E.H.; R01HG004853 to A.L.M.; R01HG004856 to R.R.; R01HG004877 to R.R.S. and R.F.; R01HG005172 to P. Spicer.; R01HG004857 to M.P.; R01HG004906 to T.M.S.; R21HG005811 to E.A.V.; M.J.B. was supported by UH2AR057506; G.A.B. was supported by UH2AI083263 and UH3AI083263 (G.A.B., C. N. Cornelissen, L. K. Eaves and J. F. Strauss); S.M.H. was supported by UH3DK083993 (V. B. Young, E. B. Chang, F. Meyer, T. M. S., M. L. Sogin, J. M. Tiedje); K.P.R. was supported by UH2DK083990 (J. V.); J.A.S. and H.H.K. were supported by UH2AR057504 and UH3AR057504 (J.A.S.); DP2OD001500 to K.M.A.; N01HG62088 to the Coriell Institute for Medical Research; U01DE016937 to F.E.D.; S.K.H. was supported by RC1DE0202098 and R01DE021574 (S.K.H. and H. Li); J.I. was supported by R21CA139193 (J.I. and D. S. Michaud); K.P.L. was supported by P30DE020751 (D. J. Smith); Army Research Office grant W911NF-11-1-0473 to C.H.; National Science Foundation grants NSF DBI-1053486 to C.H. and NSF IIS-0812111 to M.P.; The Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231 for P.S. C.; LANL Laboratory-Directed Research and Development grant 20100034DR and the US Defense Threat Reduction Agency grants B104153I and B084531I to P.S.C.; Research Foundation - Flanders (FWO) grant to K.F. and J.Raes; R.K. is an HHMI Early Career Scientist; Gordon&BettyMoore Foundation funding and institutional funding fromthe J. David Gladstone Institutes to K.S.P.; A.M.S. was supported by fellowships provided by the Rackham Graduate School and the NIH Molecular Mechanisms in Microbial Pathogenesis Training Grant T32AI007528; a Crohn’s and Colitis Foundation of Canada Grant in Aid of Research to E.A.V.; 2010 IBM Faculty Award to K.C.W.; analysis of the HMPdata was performed using National Energy Research Scientific Computing resources, the BluBioU Computational Resource at Rice University