Imaging spectrometry-derived estimates of regional ecosystem composition for the Sierra Nevada, California

The composition of the plant canopy is a key attribute of terrestrial ecosystems, influencing the fluxes of carbon, water, and energy between the land surface and the atmosphere. Terrestrial ecosystem and biosphere models, which are used to predict how ecosystems are expected to respond to changes in climate, atmospheric CO2, and land-use change, require accurate representations of plant canopy composition at large spatial scales. The ability to accurately specify plant canopy composition is important because it determines the physiological and ecological properties of plants (such as leaf photosynthetic capacity, patterns of plant carbon allocation and tissue turnover, and the resulting dynamics of plant demography) that govern the biophysical and biogeochemical functioning of ecosystems. Traditionally, plant canopy composition has been represented in a coarse-grained manner within terrestrial biosphere models, with ecosystems being comprised of a single plant functional type (PFT). However, models are increasingly seeking to represent fine-scale spatial variation in plant functional diversity. In this study, we show how imaging spectrometry measurements can provide spatially-comprehensive estimates of within-biome heterogeneity in PFT composition across a functionally diverse and topographically heterogeneous ~710 km2 area in the Southern Sierra Mountains of California. AVIRIS (Airborne Visible Infrared Imaging Spectrometer) data at 18 m resolution from the recent HyspIRI Preparatory Mission (Hyperspectral InfraRed Imager) were used to estimate the sub-pixel fractions of seven PFTs represented in the ED2 terrestrial biosphere model: Shrub, Oak, Western Hardwood, Western Pine, Cedar/Fir, and High-elevation Pine, plus a Grass/NPV (Non-Photosynthetic Vegetation) fraction using Multiple Endmember Spectral Mixture Analysis (MESMA). ED2 is an individual-based terrestrial biosphere model capable of representing fine-scale sub-pixel ecosystem heterogeneity. Our results show that this methodology captures important elevation-related shifts in canopy composition that occur within the study area that are not resolved by existing multi-spectral land-cover products. These estimates modestly improved when the putative PFT endmembers considered in the mixture analysis were constrained using available geospatial data about the presence and absence of the PFTs in particular areas: the average RMSEs (root-mean-square errors) with the geospatially-constrained versus conventional method were 11.3% and 11.9% respectively, with larger reductions in the bias (i.e. mean error) in the abundances of Oak, Cedar/Fir, and Western Hardwood PFTs (ranging from 2.0% to 7.8%). At the hectare scale around four flux towers in the Southern Sierra Mountains, the overall composition improved from an RMSE of 18.2% (5.0-24.2% for individual PFTs) to RMSE 9.5% (3.3-13.2% for individual PFTs). Downgrading AVIRIS to 30 m resolution resulted in a reduction in accuracy of the constrained method to an RMSE of 12.7% (0-23.7%) with < 1% change in bias for all tree and shrub PFTs. Our results demonstrate that imaging spectrometry measurements from planned satellite missions such as HyspIRI, EnMAP (Environmental Mapping and Analysis Program), and HISUI (Hyper-spectral Imager SUIte) can provide important and much-needed information about fine-scale heterogeneity in the composition of plant canopies for constraining and improving terrestrial ecosystem and biosphere model simulations of regional- and global-scale vegetation dynamics and function

An Ecosystem-Scale Model for the Spread of a Host-Specific Forest Pathogen in the Greater Yellowstone Ecosystem

The introduction of nonnative pathogens is altering the scale, magnitude, and persistence of forest disturbance regimes in the western United States. In the high-altitude whitebark pine (Pinus albicaulis) forests of the Greater Yellowstone Ecosystem (GYE), white pine blister rust (Cronartium ribicola) is an introduced fungal pathogen that is now the principal cause of tree mortality in many locations. Although blister rust eradication has failed in the past, there is nonetheless substantial interest in monitoring the disease and its rate of progression in order to predict the future impact of forest disturbances within this critical ecosystem. This study integrates data from five different field-monitoring campaigns from 1968 to 2008 to create a blister rust infection model for sites located throughout the GYE. Our model parameterizes the past rates of blister rust spread in order to project its future impact on high-altitude whitebark pine forests. Because the process of blister rust infection and mortality of individuals occurs over the time frame of many years, the model in this paper operates on a yearly time step and defines a series of whitebark pine infection classes: susceptible, slightly infected, moderately infected, and dead. In our analysis, we evaluate four different infection models that compare local vs. global density dependence on the dynamics of blister rust infection. We compare models in which blister rust infection is: (1) independent of the density of infected trees, (2) locally density-dependent, (3) locally density-dependent with a static global infection rate among all sites, and (4) both locally and globally density-dependent. Model evaluation through the predictive loss criterion for Bayesian analysis supports the model that is both locally and globally density-dependent. Using this best-fit model, we predicted the average residence times for the four stages of blister rust infection in our model, and we found that, on average, whitebark pine trees within the GYE remain susceptible for 6.7 years, take 10.9 years to transition from slightly infected to moderately infected, and take 9.4 years to transition from moderately infected to dead. Using our best-fit model, we project the future levels of blister rust infestation in the GYE at critical sites over the next 20 years

In situ oligonucleotide synthesis on poly(dimethylsiloxane): a flexible substrate for microarray fabrication

In this paper, we demonstrate in situ synthesis of oligonucleotide probes on poly(dimethylsiloxane) (PDMS) microchannels through use of conventional phosphoramidite chemistry. PDMS polymer was moulded into a series of microchannels using standard soft lithography (micro-moulding), with dimensions <100 μm. The surface of the PDMS was derivatized by exposure to ultraviolet/ozone followed by vapour phase deposition of glycidoxypropyltrimethoxysilane and reaction with poly(ethylene glycol) spacer, resulting in a reactive surface for oligonucleotide coupling. High, reproducible yields were achieved for both 6mer and 21mer probes as assessed by hybridization to fluorescent oligonucleotides. Oligonucleotide surface density was comparable with that obtained on glass substrates. These results suggest PDMS as a stable and flexible alternative to glass as a suitable substrate in the fabrication and synthesis of DNA microarrays

Differences in xylem and leaf hydraulic traits explain differences in drought tolerance among mature Amazon rainforest trees

Considerable uncertainty surrounds the impacts of anthropogenic climate change on the composition and structure of Amazon forests. Building upon results from two large-scale ecosystem drought experiments in the eastern Brazilian Amazon that observed increases in mortality rates among some tree species but not others, in this study we investigate the physiological traits underpinning these differential demographic responses. Xylem pressure at 50% conductivity (xylem-P50 ), leaf turgor loss point (TLP), cellular osmotic potential (πo ), and cellular bulk modulus of elasticity (ε), all traits mechanistically linked to drought tolerance, were measured on upper canopy branches and leaves of mature trees from selected species growing at the two drought experiment sites. Each species was placed a priori into one of four plant functional type (PFT) categories: drought-tolerant versus drought-intolerant based on observed mortality rates, and subdivided into early- versus late-successional based on wood density. We tested the hypotheses that the measured traits would be significantly different between the four PFTs and that they would be spatially conserved across the two experimental sites. Xylem-P50 , TLP, and πo , but not ε, occurred at significantly higher water potentials for the drought-intolerant PFT compared to the drought-tolerant PFT; however, there were no significant differences between the early- and late-successional PFTs. These results suggest that these three traits are important for determining drought tolerance, and are largely independent of wood density-a trait commonly associated with successional status. Differences in these physiological traits that occurred between the drought-tolerant and drought-intolerant PFTs were conserved between the two research sites, even though they had different soil types and dry-season lengths. This more detailed understanding of how xylem and leaf hydraulic traits vary between co-occuring drought-tolerant and drought-intolerant tropical tree species promises to facilitate a much-needed improvement in the representation of plant hydraulics within terrestrial ecosystem and biosphere models, which will enhance our ability to make robust predictions of how future changes in climate will affect tropical forests

How linear features alter predator movement and the functional response

In areas of oil and gas exploration, seismic lines have been reported to alter the movement patterns of wolves (Canis lupus). We developed a mechanistic first passage time model, based on an anisotropic elliptic partial differential equation, and used this to explore how wolf movement responses to seismic lines influence the encounter rate of the wolves with their prey. The model was parametrized using 5 min GPS location data. These data showed that wolves travelled faster on seismic lines and had a higher probability of staying on a seismic line once they were on it. We simulated wolf movement on a range of seismic line densities and drew implications for the rate of predator–prey interactions as described by the functional response. The functional response exhibited a more than linear increase with respect to prey density (type III) as well as interactions with seismic line density. Encounter rates were significantly higher in landscapes with high seismic line density and were most pronounced at low prey densities. This suggests that prey at low population densities are at higher risk in environments with a high seismic line density unless they learn to avoid them

Modelling climate change responses in tropical forests: similar productivity estimates across five models, but different mechanisms and responses

Accurately predicting the response of Amazonia to climate change is important for predicting climate change across the globe. Changes in multiple climatic factors simultaneously result in complex non-linear ecosystem responses, which are difficult to predict using vegetation models. Using leaf- and canopy-scale observations, this study evaluated the capability of five vegetation models (Community Land Model version 3.5 coupled to the Dynamic Global Vegetation model – CLM3.5–DGVM; Ecosystem Demography model version 2 – ED2; the Joint UK Land Environment Simulator version 2.1 – JULES; Simple Biosphere model version 3 – SiB3; and the soil–plant–atmosphere model – SPA) to simulate the responses of leaf- and canopy-scale productivity to changes in temperature and drought in an Amazonian forest. The models did not agree as to whether gross primary productivity (GPP) was more sensitive to changes in temperature or precipitation, but all the models were consistent with the prediction that GPP would be higher if tropical forests were 5 °C cooler than current ambient temperatures. There was greater model–data consistency in the response of net ecosystem exchange (NEE) to changes in temperature than in the response to temperature by net photosynthesis (An), stomatal conductance (gs) and leaf area index (LAI). Modelled canopy-scale fluxes are calculated by scaling leaf-scale fluxes using LAI. At the leaf-scale, the models did not agree on the temperature or magnitude of the optimum points of An, Vcmax or gs, and model variation in these parameters was compensated for by variations in the absolute magnitude of simulated LAI and how it altered with temperature. Across the models, there was, however, consistency in two leaf-scale responses: (1) change in An with temperature was more closely linked to stomatal behaviour than biochemical processes; and (2) intrinsic water use efficiency (IWUE) increased with temperature, especially when combined with drought. These results suggest that even up to fairly extreme temperature increases from ambient levels (+6 °C), simulated photosynthesis becomes increasingly sensitive to gs and remains less sensitive to biochemical changes. To improve the reliability of simulations of the response of Amazonian rainforest to climate change, the mechanistic underpinnings of vegetation models need to be validated at both leaf- and canopy-scales to improve accuracy and consistency in the quantification of processes within and across an ecosystem.This research was enabled by a grant from the Andes–Amazon Initiative of The Gordon and Betty Moore Foundation. L. Rowland gratefully acknowledges financial support from the Natural Environment Research Council (UK) for a NERC PhD studentship, and NERC grant NE/J011002/1; PM also acknowledges support from ARC FT110100457

Exploring High Aspect Ratio Gold Nanotubes as Cytosolic Agents: Structural Engineering and Uptake into Mesothelioma Cells.

The generation of effective and safe nanoagents for biological applications requires their physicochemical characteristics to be tunable, and their cellular interactions to be well characterized. Here, the controlled synthesis is developed for preparing high-aspect ratio gold nanotubes (AuNTs) with tailorable wall thickness, microstructure, composition, and optical characteristics. The modulation of optical properties generates AuNTs with strong near infrared absorption. Surface modification enhances dispersibility of AuNTs in aqueous media and results in low cytotoxicity. The uptake and trafficking of these AuNTs by primary mesothelioma cells demonstrate their accumulation in a perinuclear distribution where they are confined initially in membrane-bound vesicles from which they ultimately escape to the cytosol. This represents the first study of the cellular interactions of high-aspect ratio 1D metal nanomaterials and will facilitate the rational design of plasmonic nanoconstructs as cytosolic nanoagents for potential diagnosis and therapeutic applications.BLF-Papworth Fellowship from the British Lung Foundation and the Victor Dahdaleh Foundation

A neurophysiological study of semantic processing in Parkinson’s disease

Objectives: Cognitive-linguistic impairments in Parkinson's disease (PD) have been well documented; however, few studies have explored the neurophysiological underpinnings of semantic deficits in PD. This study investigated semantic function in PD using event-related potentials. Methods: Eighteen people with PD and 18 healthy controls performed a semantic judgement task on written word pairs that were either congruent or incongruent. Results: The mean amplitude of the N400 for new incongruent word pairs was similar for both groups, however the onset latency was delayed in the PD group. Further analysis of the data revealed that both groups demonstrated attenuation of the N400 for repeated incongruent trials, as well as attenuation of the P600 component for repeated congruent trials. Conclusions: The presence of N400 congruity and N400 repetition effects in the PD group suggests that semantic processing is generally intact, but with a slower time course as evidenced by the delayed N400. Additional research will be required to determine whether N400 and P600 repetition effects are sensitive to further cognitive decline in PD

Integrating evolution into ecological modelling: accommodating phenotypic changes in agent based models.

PMCID: PMC3733718This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Evolutionary change is a characteristic of living organisms and forms one of the ways in which species adapt to changed conditions. However, most ecological models do not incorporate this ubiquitous phenomenon. We have developed a model that takes a 'phenotypic gambit' approach and focuses on changes in the frequency of phenotypes (which differ in timing of breeding and fecundity) within a population, using, as an example, seasonal breeding. Fitness per phenotype calculated as the individual's contribution to population growth on an annual basis coincide with the population dynamics per phenotype. Simplified model variants were explored to examine whether the complexity included in the model is justified. Outputs from the spatially implicit model underestimated the number of individuals across all phenotypes. When no phenotype transitions are included (i.e. offspring always inherit their parent's phenotype) numbers of all individuals are always underestimated. We conclude that by using a phenotypic gambit approach evolutionary dynamics can be incorporated into individual based models, and that all that is required is an understanding of the probability of offspring inheriting the parental phenotype