ALBERT

Description: Background: DNA methylation is an epigenetic mark that balances plasticity with stability. While DNA methylation exhibits tissue specificity, it can also vary with age and potentially environmental exposures. In studies of DNA methylation, samples from specific tissues, especially brain, are frequently limited and so surrogate tissues are often used. As yet, we do not fully understand how DNA methylation profiles of these surrogate tissues relate to the profiles of the central tissue of interest. Results: We have adapted principal component analysis to analyze data from the Illumina 450K Human Methylation array using a set of 17 individuals with 3 brain regions and whole blood. All of the top five principal components in our analysis were associated with a variable of interest: principal component 1 (PC1) differentiated brain from blood, PCs 2 and 3 were representative of tissue composition within brain and blood, respectively, and PCs 4 and 5 were associated with age of the individual (PC4 in brain and PC5 in both brain and blood). We validated our age-related PCs in four independent sample sets, including additional brain and blood samples and liver and buccal cells. Gene ontology analysis of all five PCs showed enrichment for processes that inform on the functions of each PC. Conclusions: Principal component analysis (PCA) allows simultaneous and independent analysis of tissue composition and other phenotypes of interest. We discovered an epigenetic signature of age that is not associated with cell type composition and required no correction for cellular heterogeneity.

Description: Limitation of plant productivity by the low partial pressure of atmospheric CO 2 ( C a ) experienced during the last glacial period is hypothesised to have been an important constraint on the origins of agriculture. In support of this hypothesis, previous work has shown that glacial C a limits vegetative growth in the wild progenitors of both C 3 and C 4 founder crops. Here we present data showing that glacial C a also reduces grain yield in both crop types. We grew four wild progenitors of C 3 (einkorn wheat and barley) and C 4 crops (foxtail and broomcorn millets) at glacial and post-glacial C a , measuring grain yield, and the morphological and physiological components contributing to these yield changes. The C 3 species showed a significant increase in unthreshed grain yield of ~50% with the increase in C a , which matched the stimulation of photosynthesis, suggesting that increases in photosynthesis are directly translated into yield at sub-ambient levels of C a . Increased yield was controlled by a higher rate of tillering, leading to a larger number of tillers bearing fertile spikes, and increases in seed number and size. The C 4 species showed smaller, but significant, increases in grain yield of 10-15%, arising from larger seed numbers and sizes. Photosynthesis was enhanced by C a in only one C 4 species and the effect diminished during development, suggesting that an indirect mechanism mediated by plant water relations could also be playing a role in the yield increase. Interestingly, the C 4 species at glacial C a showed some evidence that photosynthetic capacity was upregulated to enhance carbon capture. Development under glacial C a also impacted negatively on the subsequent germination and viability of seeds. These results suggest that the grain production of both C 3 and C 4 crop progenitors was limited by the atmospheric conditions of the last glacial period, with important implications for the origins of agriculture. This article is protected by copyright. All rights reserved.

Description: When possible, many species will shift in elevation or latitude in response to rising temperatures. However, before such shifts occur, individuals will first tolerate environmental change and then modify their behavior to maintain heat balance. Behavioral thermoregulation allows animals a range of climatic tolerances and makes predicting geographic responses under future warming scenarios challenging. Because behavioral modification may reduce an individual's fecundity by, for example, limiting foraging time and thus caloric intake, we must consider the range of behavioral options available for thermoregulation to accurately predict climate change impacts on individual species. To date, few studies have identified mechanistic links between an organism's daily activities and the need to thermoregulate. We used a biophysical model, Niche Mapper, to mechanistically model microclimate conditions and thermoregulatory behavior for a temperature-sensitive mammal, the American pika ( Ochotona princeps ). Niche Mapper accurately simulated microclimate conditions, as well as empirical metabolic chamber data for a range of fur properties, animal sizes, and environmental parameters. Niche Mapper predicted pikas would be behaviorally constrained because of the need to thermoregulate during the hottest times of the day. We also showed that pikas at low elevations could receive energetic benefits by being smaller in size and maintaining summer pelage during longer stretches of the active season under a future warming scenario. We observed pika behavior for 288 h in Glacier National Park, Montana, and thermally characterized their rocky, montane environment. We found that pikas were most active when temperatures were cooler, and at sites characterized by high elevations and north-facing slopes. Pikas became significantly less active across a suite of behaviors in the field when temperatures surpassed 20°C, which supported a metabolic threshold predicted by Niche Mapper. In general, mechanistic predictions and empirical observations were congruent. This research is unique in providing both an empirical and mechanistic description of the effects of temperature on a mammalian sentinel of climate change, the American pika. Our results suggest that previously underinvestigated characteristics, specifically fur properties and body size, may play critical roles in pika populations' response to climate change. We also demonstrate the potential importance of considering behavioral thermoregulation and microclimate variability when predicting animal responses to climate change. We built a mechanistic model, focusing on thermoregulation, for a climate change sentinel, the American pika, and tested it against 288 h of field observations. We observed and the model predicted heat stress when ambient temperatures at animal height were above 20°C. We predict that future climate warming may place enhanced selective pressure on factors important for pika thermoregulation, specifically body size and molt-timing.

Description: Field observations and numerical circulation modeling revealed the spatial variability of the tidally driven dynamics in the topographically complex, continuously stratified, macrotidal environment of the Browse Basin on the Australian North West Shelf. Internal wave generation occurred at a number of discrete topographic features, and the resultant interaction of multiple waves led to a spatially variable internal wave climate. The generation of baroclinic energy was most intense in regions where the barotropic tide was aligned with steep topography. Generation of low-mode internal waves occurred at the inner-shelf break, where the ratio of tidal excursion distance to topographic length scale was large. In contrast, generation of high-mode beam-like internal waves occurred at the outer-shelf break, where the ratio of tidal excursion distance to topographic length scale was very small. The most efficient conversion from barotropic to baroclinic energy occurred at the outer-shelf break. The internal waves generated at the inner- and outer-shelf breaks interacted to produce a partly standing internal wave, resulting in a large along-shelf energy flux, and discrete locations with small ratios of horizontal kinetic energy to available potential energy. This phenomenon is likely to occur in other regions with semienclosed topography and multiple generation sites.

Description: Shallow coastal regions are among the fastest evolving landscapes, but are notoriously difficult to measure with high spatio-temporal resolution. Using Uninhabited Aerial Vehicle Synthetic Aperture Radar (UAVSAR) data, we demonstrate that high signal-to-noise L-band synthetic aperture radar (SAR) can reveal subaqueous channel networks at the distal ends of river deltas. Using 27 UAVSAR images collected between 2009 and 2015 from the Wax Lake Delta in coastal Louisiana, USA, we show that under normal tidal conditions, planform geometry of the distributary channel network is frequently resolved in the UAVSAR images, including ~700 m of seaward network extension over five years for one channel. UAVSAR also reveals regions of subaerial and subaqueous vegetation, streaklines of biogenic surfactants, and what appear to be small distributary channels aliased by the survey grid, all illustrating the value of fine resolution, low noise, L-band SAR for mapping the nearshore subaqueous delta channel network.

Description: Coral reefs across the world have been seriously degraded and have a bleak future in response to predicted global warming and ocean acidification (OA). However, this is not the first time that biocalcifying organisms, including corals, have faced the threat of extinction. The end-Triassic mass extinction (200 million years ago) was the most severe biotic crisis experienced by modern marine invertebrates, which selected against biocalcifiers; this was followed by the proliferation of another invertebrate group, sponges. The duration of this sponge-dominated period far surpasses that of alternative stable-ecosystem or phase-shift states reported on modern day coral reefs and, as such, a shift to sponge-dominated reefs warrants serious consideration as one future trajectory of coral reefs. We hypothesise that some coral reefs of today may become sponge reefs in the future, as sponges and corals respond differently to changing ocean chemistry and environmental conditions. To support this hypothesis, we discuss: 1) the presence of sponge reefs in the geological record; 2) reported shifts from coral- to sponge-dominated systems; and 3) direct and indirect responses of the sponge holobiont and its constituent parts (host and symbionts) to changes in temperature and pH. Based on this evidence, we propose that sponges may be one group to benefit from projected climate change and ocean acidification scenarios, and that increased sponge abundance represents a possible future trajectory for some coral reefs, which would have important implications for overall reef functioning. © 2013 Blackwell Publishing Ltd

Description: Miscanthus is a rhizomatous C4 grass of great interest as a biofuel crop because it has the potential to produce high yields over a wide geographical area with low agricultural inputs on marginal land less suitable for food production. At the moment a clonal interspecific hybrid Miscanthus x giganteus is the most widely cultivated and studied in Europe and the US but breeding programs are developing newer more productive varieties. Here we quantified the physiological processes relating to whole season yield in a replicated plot trial in Wales, UK. Light capture and conversion efficiency were parameterised for four carefully selected genotypes ( M. sinensis , M. sacchariflorus and Miscanthus x giganteus ). Differences in the canopy architecture in mature stands as measured by the extinction coefficient (k) were small (0.55-0.65). Sensitivity analysis on a mathematical model of Miscanthus were performed to quantify the accumulative intercepted photosynthetically active radiation (iPAR) in the growing season using 1) k, 2) variation in the thermal responses of leaf expansion rate, 3) base temperature for degree days and 4) date start of canopy expansion. A 10% increase in k or leaf area per degree day both had a minimal effect on iPAR (3%). Decreasing base temperature from 10°C to 9°C gave an 8% increase in iPAR. If the starting date for canopy expansion was the same as shoot emergence date, then the iPAR increases by 12.5%. In M. x giganteus the whole season above ground and total (including below ground) radiation use efficiency (RUE) ranged from 45% to 37% higher than the non-interspecific hybrid genotypes. The greater yields in the interspecific hybrid M. x giganteus are explained by the higher RUE and not by differences in iPAR or partitioning effects. Studying the mechanisms underlying this complex trait could have wide benefits for both fuel and food production. This article is protected by copyright. All rights reserved.