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Photogrammetry is an emerging tool that allows scientists to measure important habitat characteristics of coral reefs at multiple spatial scales. However, the ecological benefits of using photogrammetry to measure reef habitat have rarely been assessed through direct comparison to traditional methods, especially in settings where manual measurements are more feasible and affordable. Here, we applied multiple methods to measure coral colonies (Pocillopora spp.) and asked whether photogrammetric or manual observations better describe short-term colony growth and links between colony size and the biodiversity of coral-dwelling fishes and invertebrates. Using photogrammetry, we measured patterns in changes in coral volume that were otherwise obscured by high variation from manual measurements. Additionally, we found that photogrammetry-based estimates of colony skeletal volume best predicted the abundance and richness of animals living within the coral. This study highlights that photogrammetry can improve descriptions of coral colony size, growth, and associated biodiversity compared to manual measurements. 

IntroductionChanges in temperature can fundamentally transform how species interact, causing wholesale shifts in ecosystem dynamics and stability. Yet we still have a limited understanding of how temperature-dependence in physiology drives temperature-dependence in species-interactions. For predator-prey interactions, theory predicts that increases in temperature drive increases in metabolism and that animals respond to this increased energy expenditure by ramping up their food consumption to meet their metabolic demand. However, if consumption does not increase as rapidly with temperature as metabolism, increases in temperature can ultimately cause a reduction in consumer fitness and biomass via starvation. MethodsHere we test the hypothesis that increases in temperature cause more rapid increases in metabolism than increases in consumption using the California spiny lobster (Panulirus interruptus) as a model system. We acclimated individual lobsters to temperatures they experience sacross their biogeographic range (11, 16, 21, or 26°C), then measured whether lobster consumption rates are able to meet the increased metabolic demands of rising temperatures. Results and discussionWe show positive effects of temperature on metabolism and predation, but in contrast to our hypothesis, rising temperature caused lobster consumption rates to increase at a faster rate than increases in metabolic demand, suggesting that for the mid-range of temperatures, lobsters are capable of ramping up consumption rates to increase their caloric demand. However, at the extreme ends of the simulated temperatures, lobster biology broke down. At the coldest temperature, lobsters had almost no metabolic activity and at the highest temperature, 33% of lobsters died. Our results suggest that temperature plays a key role in driving the geographic range of spiny lobsters and that spatial and temporal shifts in temperature can play a critical role in driving the strength of species interactions for a key predator in temperate reef ecosystems. 

Proteins and nucleic acids participate in essentially every biochemical process in living organisms, and the elucidation of their structure and motions is essential for our understanding how these molecular machines perform their function. Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful versatile technique that provides critical information on the molecular structure and dynamics. Spin-relaxation data are used to determine the overall rotational diffusion and local motions of biological macromolecules, while residual dipolar couplings (RDCs) reveal local and long-range structural architecture of these molecules and their complexes. This information allows researchers to refine structures of proteins and nucleic acids and provides restraints for molecular docking. Several software packages have been developed by NMR researchers in order to tackle the complicated experimental data analysis and structure modeling. However, many of them are offline packages or command-line applications that require users to set up the run time environment and also to possess certain programming skills, which inevitably limits accessibility of this software to a broad scientific community. Here we present new science gateways designed for NMR/structural biology community that address these current limitations in NMR data analysis. Using the GenApp technology for scientific gateways (https://genapp.rocks), we successfully transformed ROTDIF and ALTENS, two offline packages for bio-NMR data analysis, into science gateways that provide advanced computational functionalities, cloud-based data management, and interactive 2D and 3D plotting and visualizations. Furthermore, these gateways are integrated with molecular structure visualization tools (Jmol) and with gateways/engines (SASSIE-web) capable of generating huge computer-simulated structural ensembles of proteins and nucleic acids. This enables researchers to seamlessly incorporate conformational ensembles into the analysis in order to adequately take into account structural heterogeneity and dynamic nature of biological macromolecules. ROTDIF-web offers a versatile set of integrated modules/tools for determining and predicting molecular rotational diffusion tensors and model-free characterization of bond dynamics in biomacromolecules and for docking of molecular complexes driven by the information extracted from NMR relaxation data. ALTENS allows characterization of the molecular alignment under anisotropic conditions, which enables researchers to obtain accurate local and long-range bond-vector restraints for refining 3-D structures of macromolecules and their complexes. We will describe our experience bringing our programs into GenApp and illustrate the use of these gateways for specific examples of protein systems of high biological significance. We expect these gateways to be useful to structural biologists and biophysicists as well as NMR community and to stimulate other researchers to share their scientific software in a similar way. 

The scattering of neutrons can be used to provide information on the structure and dynamics of biological systems on multiple length and time scales. Pursuant to a National Science Foundation-funded workshop in February 2018, recent developments in this field are reviewed here, as well as future prospects that can be expected given recent advances in sources, instrumentation and computational power and methods. Crystallography, solution scattering, dynamics, membranes, labeling and imaging are examined. For the extraction of maximum information, the incorporation of judicious specific deuterium labeling, the integration of several types of experiment, and interpretation using high-performance computer simulation models are often found to be particularly powerful.