Assessing movements of three buoy line types using DSTmilli Loggers: Implications for entanglements of bottlenose dolphins in the crab pot fishery

A study was conducted in October 2006 in the Charleston, South Carolina area to test the movements of three different buoy line types to determine which produced a preferred profile that could reduce the risk of dolphin entanglement. Tests on diamond-braided nylon commonly used in the crab pot fishery were compared with stiffened line of Esterpro and calf types in both shallow and deep water environments using DSTmilli data loggers. Loggers were placed at intervals along the lines to record depth, and thus movements, over a 24 hour period. Three observers viewed video animations and charts created for each of the six trial days from the collected logger data and provided their opinions on the most desirable line type that fit set criteria. A quantitative analysis (ANCOVA) of the data was conducted taking into consideration daily tidal fluctuations and logger movements. Loggers tracking the tides had an r2 value approaching 1.00 and produced little movement other than with the tides. Conversely, r2 values approaching 0.00 were less affected by tidal movement and influenced by currents that cause more erratic movement. Results from this study showed that stiffened line, in particular the medium lay Esterpro type, produced the more desirable profiles that could reduce risk of dolphin entanglement. Combining the observer’s results with the ANCOVA results, Esterpro was chosen nearly 60% of the time as opposed to the nylon line which was only chosen 10% of the time. ANCOVA results showed that the stiffened lines performed better in both the shallow and deep water environments, while the nylon line only performed better during one trial in a deep water set, most probably due to the increased current velocities experienced that day. (58pp.)(PDF contains 68 pages

Depth alone is an inappropriate proxy for physiological change in the mesophotic coral Agaricia lamarcki

The physiology of mesophotic Scleractinia varies with depth in response to environmental change. Previous research has documented trends in heterotrophy and photosynthesis with depth, but has not addressed between-site variation for a single species. Environmental differences between sites at a local scale and heterogeneous microhabitats, because of irradiance and food availability, are likely important factors when explaining the occurrence and physiology of Scleractinia. Here, 108 colonies of Agaricia lamarcki were sampled from two locations off the coast of Utila, Honduras, distributed evenly down the observed 50 m depth range of the species. We found that depth alone was not sufficient to fully explain physiological variation. Pulse Amplitude-Modulation fluorometry and stable isotope analyses revealed that trends in photochemical and heterotrophic activity with depth varied markedly between sites. Our isotope analyses do not support an obligate link between photosynthetic activity and heterotrophic subsidy with increasing depth. We found that A. lamarcki colonies at the bottom of the species depth range can be physiologically similar to those nearer the surface. As a potential explanation, we hypothesize sites with high topographical complexity, and therefore varied microhabitats, may provide more physiological niches distributed across a larger depth range. Varied microhabitats with depth may reduce the dominance of depth as a physiological determinant. Thus, A. lamarcki may ‘avoid’ changes in environment with depth, by instead existing in a subset of favourable niches. Our observations correlate with site-specific depth ranges, advocating for linking physiology and abiotic profiles when defining the distribution of mesophotic taxa

The structural properties of the multi-layer graphene/4H-SiC(000-1) system as determined by Surface X-ray Diffraction

We present a structural analysis of the multi-layer graphene-4HSiC(000-1}) system using Surface X-Ray Reflectivity. We show for the first time that graphene films grown on the C-terminated (000-1}) surface have a graphene-substrate bond length that is very short (0.162nm). The measured distance rules out a weak Van der Waals interaction to the substrate and instead indicates a strong bond between the first graphene layer and the bulk as predicted by ab-initio calculations. The measurements also indicate that multi-layer graphene grows in a near turbostratic mode on this surface. This result may explain the lack of a broken graphene symmetry inferred from conduction measurements on this system [C. Berger et al., Science 312, 1191 (2006)].Comment: 9 pages with 6 figure

Photophysiological Responses of Canopy-Forming Kelp Species to Short-Term Acute Warming

The frequency of short-term oceanic warming events [“marine heatwaves” (MHWs) or heat spikes] has increased over the past century and is projected to further increase because of anthropogenic climate change. Given that marine organisms are strongly influenced by temperature, an increased occurrence of warming events could alter the structure of populations, communities, and ecosystems. The distribution and ecophysiological performance of kelp species – globally important foundation species that play significant roles in nutrient cycling and habitat creation in temperate coastal systems – is particularly constrained by temperature. However, their photophysiological responses to warming events remains unclear, which hinders attempts to understand, and predict the effects of ocean warming on kelp populations and the ecosystems they underpin. Here, we experimentally simulated a heat spike (+2 ◦C and +4 ◦C in magnitude, 3 days in duration, and compared with ambient controls) and examined the photophysiological responses of two canopy-forming kelp species widely distributed across the northeast Atlantic – Laminaria digitata and Laminaria hyperborea. Both species were resilient to the realistic warming treatments in terms of their photosynthetic characteristics. However, we found that L. digitata individuals, which were collected from populations found toward the upper limit of this species’ thermal range, exhibited increased oxygen production at higher temperatures, particularly after multiple days of exposure to the warming event. L. digitata also exhibited a greater poise for dissipating excess energy through non-photochemical pathways. In contrast, L. hyperborea, which extends further south into warmer waters and tends to occupy deeper reefs that are almost constantly submerged, appeared to be photo-physiologically insensitive to the heat spike. This study enhances our mechanistic understanding of the photophysiological and photoprotective responses of kelps to short-term acute warming events – features which are likely to emerge as important drivers of ecological change in coming decades

MageComet—web application for harmonizing existing large-scale experiment descriptions

Motivation: Meta-analysis of large gene expression datasets obtained from public repositories requires consistently annotated data. Curation of such experiments, however, is an expert activity which involves repetitive manipulation of text. Existing tools for automated curation are few, which bottleneck the analysis pipeline

The cellular microscopy phenotype ontology

BACKGROUND: Phenotypic data derived from high content screening is currently annotated using free-text, thus preventing the integration of independent datasets, including those generated in different biological domains, such as cell lines, mouse and human tissues. DESCRIPTION: We present the Cellular Microscopy Phenotype Ontology (CMPO), a species neutral ontology for describing phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations. CMPO is compatible with related ontology efforts, allowing for future cross-species integration of phenotypic data. CMPO was developed following a curator-driven approach where phenotype data were annotated by expert biologists following the Entity-Quality (EQ) pattern. These EQs were subsequently transformed into new CMPO terms following an established post composition process. CONCLUSION: CMPO is currently being utilized to annotate phenotypes associated with high content screening datasets stored in several image repositories including the Image Data Repository (IDR), MitoSys project database and the Cellular Phenotype Database to facilitate data browsing and discoverability

Nature of bonding and electronic structure in MgB2, a boron intercalation superconductor

Chemical bonding and electronic structure of MgB2, a boron-based newly discovered superconductor, is studied using self-consistent band structure techniques. Analysis of the transformation of the band structure for the hypothetical series of graphite - primitive graphite - primitive graphite-like boron - intercalated boron, shows that the band structure of MgB2 is graphite-like, with pi-bands falling deeper than in ordinary graphite. These bands possess a typically delocalized and metallic, as opposed to covalent, character. The in-plane sigma-bands retain their 2D covalent character, but exhibit a metallic hole-type conductivity. The coexistence of 2D covalent in-plane and 3D metallic-type interlayer conducting bands is a peculiar feature of MgB2. We analyze the 2D and 3D features of the band structure of MgB2 and related compounds, and their contributions to conductivity.Comment: 4 pages in revtex, 3 figures in 4 separate EPS file

Larval supply, settlement, and recruitment of American lobster, Homarus americanus

This thesis contains three studies on the American lobster, Homarus americanus. Two took place in Bonne Bay, Newfoundland and a third used a long-term young-of-year (YoY) recruitment index from New England, USA. In the first study, planktonic larval and benthic suction sampling along the Bonne Bay estuary indicated larval concentrations were consistently highest at the mouth of the bay, with a more dramatic drop in density from early to late stages than reported elsewhere. The second study evaluated the spatial scale of correlations between YoY recruitment and older juvenile densities at some 70 sampling sites in New England. Strong correlations at even the finest scale (metre's), along with behavioural experiments, suggest postlarvae preferentially settle among resident conspecifics. The third study compared fishers' local knowledge of lobster hatching and nursery locations in Bonne Bay against ground-truth data collected by fishery-dependent and -independent surveys. Fishers accurately identified hatching but not nursery locations in the bay. -- Keywords: Homarus americanus; larvae; advection; juvenile; recruitment; mortality; Local Environmental Knowledge