A comparative study of methods for surface area and three-dimensional shape measurement of coral skeletons

The three-dimensional morphology and surface area of organisms such as reef-building corals is central to their biology. Consequently, being able to detect and measure this aspect of corals is critical to understanding their interactions with the surrounding environment. This study explores six different methods of three-dimensional shape and surface area measurements using the range of morphology associated with the Scleractinian corals: Goniopora tenuidens, Acropora intermedia, and Porites cylindrica. Wax dipping; foil wrapping; multi-station convergent photogrammetry that used the naturally occurring optical texture for conjugate point matching; stereo photogrammetry that used projected light to provide optical texture; a handheld laser scanner that employed two cameras and a structured light source; and X-ray computer tomography (CT) scanning were applied to each coral skeleton to determine the spatial resolution of surface detection as well as the accuracy of surface area estimate of each method. Compared with X-ray CT wax dipping provided the best estimate of the surface area of coral skeletons that had external corallites, regardless of morphological complexity. Foil wrapping consistently showed a large degree of error on all coral morphologies. The photogrammetry and laser-scanning solutions were effective only on corals with simple morphologies. The two techniques that used projected lighting were both subject to skeletal light scattering, caused by both gross morphology and meso-coral architecture and which degraded signal triangulation, but otherwise provided solutions with good spatial resolution. X-ray CT scanning provided the highest resolution surface area estimates, detecting surface features smaller than 1000 mu m(2)

The production, purification and crystallization of a pocilloporin pigment from a reef-forming coral

Reef-building corals contain fluorescent pigments termed pocilloporins that function by regulating the light environment of coral and acting as a photoprotectant in excessive sunlight. These pocilloporins are related to the monomeric green fluorescent protein and the tetrameric DsRed fluorescent proteins, which have widespread use as biotechnological tools. An intensely blue-coloured pocilloporin, termed Rtms5, was expressed in Escherichia coli, purified and crystallized. Rtms5 was shown to be tetrameric, with deep blue crystals that diffract to 2.2 Angstrom resolution and belong to space group I4(1)22. The colour of this pocilloporin was observed to be sensitive to pH and a yellow (pH 3.5) and a red form (pH 4.5) of Rtms5 were also crystallized. These crystals belong to space group P4(2)22 and diffract to 2.4 Angstrom resolution or better

The Nondeterministic Waiting Time Algorithm: A Review

We present briefly the Nondeterministic Waiting Time algorithm. Our technique for the simulation of biochemical reaction networks has the ability to mimic the Gillespie Algorithm for some networks and solutions to ordinary differential equations for other networks, depending on the rules of the system, the kinetic rates and numbers of molecules. We provide a full description of the algorithm as well as specifics on its implementation. Some results for two well-known models are reported. We have used the algorithm to explore Fas-mediated apoptosis models in cancerous and HIV-1 infected T cells

One Year of Alendronate Treatment Lowers Microstructural Stresses Associated with Trabecular Microdamage Initiation

Alendronate, an anti-remodeling agent, is commonly used to treat patients suffering from osteoporosis by increasing bone mineral density. Though fracture risk is lowered, an increase in microdamage accumulation has been documented in patients receiving alendronate, leading to questions about the potentially detrimental effects of remodeling suppression on the local tissue (material) properties. In this study, trabecular bone cores from the distal femur of beagle dogs treated for one year with alendronate, at doses scaled by weight to approximate osteoporotic and Paget's disease treatment doses in humans, were subjected to uniaxial compression to induce microdamage. Tissue level von Mises stresses were computed for alendronate-treated and non-treated controls using finite element analysis and correlated to microdamage morphology. Using a modified version of the Moore and Gibson classification for damage morphology, we determined that the von Mises stress for trabeculae exhibiting severe and linear microcrack patterns was decreased by approximately 25% in samples treated with alendronate compared with non-treated controls (p<0.01), whereas there was no reduction in the von Mises stress state for diffuse microdamage formation. Furthermore, an examination of the architectural and structural characteristics of damaged trabeculae demonstrated that severely damaged trabeculae were thinner, more aligned with the loading axis, and less mineralized than undamaged trabeculae in alendronate-treated samples (p<0.01). Similar relationships with damage morphology were found only with trabecular orientation in vehicle-treated control dogs. These results indicate that changes in bone's architecture and matrix properties associated with one year of alendronate administration reduce trabecular bone's ability to resist the formation of loading-induced severe and linear microcracks, both of which dissipate less energy prior to fracture than does diffuse damage

Temperature change and Baltic sprat: from observations to ecological-economic modelling

Temperature effects on Baltic sprat are many and include both direct and indirect effects. Increasing temperature is thought to increase the survival of all early life stages, resulting in increased recruitment success. We quantified the spatially resolved temperature trend for major spawning grounds and depth layers being most relevant for sprat eggs and larvae, using a three-dimensional hydrodynamic model for 1979–2005. Results confirmed an underlying positive temperature trend. Next, we tested these time-series as new explanatory variables in an existing temperature-dependent recruitment function and applied these recruitment predictions in an agestructured ecological–economic optimization model, maximizing for profit. Economic optimal solutions depended upon variability in temperature trajectories. Under climate-change scenarios, mean optimal fishing mortality and related yields and profits increased. The extent of the increase was limited by the general shape of the stock–recruitment model and the assumption of density-dependence. This highlights the need to formulate better environmentally sensitive stock recruitment models. Under the current knowledge of Baltic sprat recruitment, the tested climate-change scenarios would result in a change in management targets. However, to serve as a quantitative management advice tool, models will have to address the above-mentioned concern

Biological Pathway Specificity in the Cell—Does Molecular Diversity Matter?

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/150499/1/bies201800244_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/150499/2/bies201800244.pd

Present Limits to Heat-Adaptability in Corals and Population-Level Responses to Climate Extremes

Climate change scenarios suggest an increase in tropical ocean temperature by 1–3°C by 2099, potentially killing many coral reefs. But Arabian/Persian Gulf corals already exist in this future thermal environment predicted for most tropical reefs and survived severe bleaching in 2010, one of the hottest years on record. Exposure to 33–35°C was on average twice as long as in non-bleaching years. Gulf corals bleached after exposure to temperatures above 34°C for a total of 8 weeks of which 3 weeks were above 35°C. This is more heat than any other corals can survive, providing an insight into the present limits of holobiont adaptation. We show that average temperatures as well as heat-waves in the Gulf have been increasing, that coral population levels will fluctuate strongly, and reef-building capability will be compromised. This, in combination with ocean acidification and significant local threats posed by rampant coastal development puts even these most heat-adapted corals at risk. WWF considers the Gulf ecoregion as “critically endangered”. We argue here that Gulf corals should be considered for assisted migration to the tropical Indo-Pacific. This would have the double benefit of avoiding local extinction of the world's most heat-adapted holobionts while at the same time introducing their genetic information to populations naïve to such extremes, potentially assisting their survival. Thus, the heat-adaptation acquired by Gulf corals over 6 k, could benefit tropical Indo-Pacific corals who have <100 y until they will experience a similarly harsh climate. Population models suggest that the heat-adapted corals could become dominant on tropical reefs within ∼20 years