Spontaneous formation of highly ordered nanostructures: thermal instability and mode selection in surface-capped polymer films.

We demonstrate a controllable formation process of wave-like patterns in thermally unstable surface-capped polymer films on a rigid substrate. Self-ordered wave-like structures over a large area can be created by applying a small lateral tension to the film, whereupon it becomes unstable. A clear mode selection process which includes creation, decay and interference between coexisting waves at different annealing conditions has been observed, which makes it possible to restrain the patterns which are formed finally. Our results provide a clear and new evidence of spinodal behaviour in such a film due to thermal instability. Furthermore, we show that the well-controlled patterns generated in such a process can be used to fabricate nanostructures for various applications.

A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series.

Understanding the regulatory mechanisms that are responsible for an organism's response to environmental change is an important issue in molecular biology. A first and important step towards this goal is to detect genes whose expression levels are affected by altered external conditions. A range of methods to test for differential gene expression, both in static as well as in time-course experiments, have been proposed. While these tests answer the question whether a gene is differentially expressed, they do not explicitly address the question when a gene is differentially expressed, although this information may provide insights into the course and causal structure of regulatory programs. In this article, we propose a two-sample test for identifying intervals of differential gene expression in microarray time series. Our approach is based on Gaussian process regression, can deal with arbitrary numbers of replicates, and is robust with respect to outliers. We apply our algorithm to study the response of Arabidopsis thaliana genes to an infection by a fungal pathogen using a microarray time series dataset covering 30,336 gene probes at 24 observed time points. In classification experiments, our test compares favorably with existing methods and provides additional insights into time-dependent differential expression.

A surveillance strategy for invasive species of concern in deepwater habitats of the Northwestern Hawaiian Islands

This report describes a surveillance strategy to detect deepwater invasive species in the Northwestern Hawaiian Islands. A need for this strategy was identified in the Papahānaumokuākea Marine National Monument Management Plan and the Monument’s Draft Natural Resources Science Plan. This strategy focuses on detecting two species of concern, the octocoral Carijoa riisei and the red alga Hypnea musciformis. Most research on invasive species in the Hawaiian archipelago has focused on shallow water habitats within the limits of conventional SCUBA (0-30 m). Deeper habitats such as mesophotic reefs are much more difficult to access and consequently little is known about the distribution of deepwater invasive species or their impacts. Recent deepwater (>30 m) sightings of H. musciformis and C. riisei, in and near NWHI, respectively, have prompted a call for further research and surveillance of invasive species in deepwater habitats. This report compiles the most up to date information about these two species of concern in deepwater habitats. A literature search and conversations with subject matter experts was used to identify their current distribution, preferred habitat types, optimal detection methods and ways to efficiently sample the vast extent of NWHI. The proposed sampling strategy prioritizes survey effort where C. riisei and H. musciformis are most likely to be found. At coarse spatial scales (tens to hundreds of kilometers), opportunistic observations and distance from the Main Hawaiian Islands, a principal propagule source, are used to identify high-risk islands and banks. At fine spatial scales (meters to tens of kilometers) a habitat suitability model was developed to identify high-risk habitats. The habitat suitability model focused on habitat preferences of C. riisei, since the species is well studied and adequate data exists to map habitats. There was insufficient information to identify suitable habitat for H. muscifomis. Habitat preferences for the algae are poorly understood and there is a lack of data at relevant spatial scales to map those preferences which are known. The principal habitats identified by the habitat suitability model were ledges and the edges of rugose coral reefs, where the shade loving octocoral would likely be found. Habitat suitability maps were developed for seven atolls and banks to aid in survey site selection. The protocol relied on technical divers to conduct visual surveys of benthic habitats. It was developed to increase the efficiency of surveys, maximize the probability of detection, identify important information relevant to future surveys and standardize results. The strategy, model and protocol were tested during a field mission in 2009 at several atolls and islands in NWHI. The field mission did not detect any invasive species among deepwater habitats and much was learned to improve future surveys. Data gaps and improvements are discussed.

Field applications of the second-generation Environmental Sample Processor (ESP) for remote detection of harmful algae: 2006-2007

We assess the application of the second-generation Environmental Sample Processor (ESP) for the detection of harmful algal bloom (HAB) species in field and laboratory settings using two molecular probe techniques: a sandwich hybridization assay (SHA) and fluorescent in situ hybridization (FISH). During spring 2006, the first time this new instrument was deployed, the ESP successfully automated application of DNA probe arrays for various HAB species and other planktonic taxa, but non-specific background binding on the SHA probe array support made results interpretation problematic. Following 2006, the DNA array support membrane that we were using was replaced with a different membrane, and the SHA chemistry was adjusted. The sensitivity and dynamic range of these modifications were assessed using 96-well plate and ESP array SHA formats for several HAB species found commonly in Monterey Bay over a range of concentrations; responses were significantly correlated (p < 0.01). Modified arrays were deployed in 2007. Compared to 2006, probe arrays showed improved signal:noise, and remote detection of various HAB species was demonstrated. We confirmed that the ESP and affiliated assays can detect HAB populations at levels below those posing human health concerns, and results can be related to prevailing environmental conditions in near real-time.