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

The Hydrogen Atom in Combined Electric and Magnetic Fields with Arbitrary Mutual Orientations

For the hydrogen atom in combined magnetic and electric fields we investigate the dependence of the quantum spectra, classical dynamics, and statistical distributions of energy levels on the mutual orientation of the two external fields. Resonance energies and oscillator strengths are obtained by exact diagonalization of the Hamiltonian in a complete basis set, even far above the ionization threshold. At high excitation energies around the Stark saddle point the eigenenergies exhibit strong level repulsions when the angle between the fields is varied. The large avoided crossings occur between states with the same approximately conserved principal quantum number, n, and this intramanifold mixing of states cannot be explained, not even qualitatively, by conventional perturbation theory. However, it is well reproduced by an extended perturbation theory which takes into account all couplings between the angular momentum and Runge-Lenz vector. The large avoided crossings are interpreted as a quantum manifestation of classical intramanifold chaos. This interpretation is supported by both classical Poincar\'e surfaces of section, which reveal a mixed regular-chaotic intramanifold dynamics, and the statistical analysis of nearest-neighbor-spacingComment: two-column version, 10 pages, REVTeX, 10 figures, uuencoded, submitted to Rhys. Rev.

Bringing metabolic networks to life: convenience rate law and thermodynamic constraints

BACKGROUND: Translating a known metabolic network into a dynamic model requires rate laws for all chemical reactions. The mathematical expressions depend on the underlying enzymatic mechanism; they can become quite involved and may contain a large number of parameters. Rate laws and enzyme parameters are still unknown for most enzymes. RESULTS: We introduce a simple and general rate law called "convenience kinetics". It can be derived from a simple random-order enzyme mechanism. Thermodynamic laws can impose dependencies on the kinetic parameters. Hence, to facilitate model fitting and parameter optimisation for large networks, we introduce thermodynamically independent system parameters: their values can be varied independently, without violating thermodynamical constraints. We achieve this by expressing the equilibrium constants either by Gibbs free energies of formation or by a set of independent equilibrium constants. The remaining system parameters are mean turnover rates, generalised Michaelis-Menten constants, and constants for inhibition and activation. All parameters correspond to molecular energies, for instance, binding energies between reactants and enzyme. CONCLUSION: Convenience kinetics can be used to translate a biochemical network – manually or automatically - into a dynamical model with plausible biological properties. It implements enzyme saturation and regulation by activators and inhibitors, covers all possible reaction stoichiometries, and can be specified by a small number of parameters. Its mathematical form makes it especially suitable for parameter estimation and optimisation. Parameter estimates can be easily computed from a least-squares fit to Michaelis-Menten values, turnover rates, equilibrium constants, and other quantities that are routinely measured in enzyme assays and stored in kinetic databases

Biological sequences as pictures – a generic two dimensional solution for iterated maps

<p>Abstract</p> <p>Background</p> <p>Representing symbolic sequences graphically using iterated maps has enjoyed an enduring popularity since it was first proposed in Jeffrey 1990 as chaos game representation (CGR). The usefulness of this representation goes beyond the convenience of a scale independent representation. It provides a variable memory length representation of transition. This includes the representation of succession with non-integer order, which comes with the promise of generalizing Markovian formalisms. The original proposal targeted genomic sequences only but since then several generalizations have been proposed, many specifically designed to handle protein data.</p> <p>Results</p> <p>The challenge of a general solution is that of deriving a bijective transformation of symbolic sequences into bi-dimensional planes. More specifically, it requires the regular fractal nesting of polygons. A first attempt at a general solution was proposed by Fiser 1994 by using non-overlapping circles that contain the polygons. This was used as a starting point to identify a more efficient solution where the encapsulating circles can overlap without the same happening for the sequence maps which are circumscribed to fractal polygon domains.</p> <p>Conclusion</p> <p>We identified the optimal inscribed packing solution for iterated maps of any Biological sequence, indeed of any symbolic sequence. The new solution maintains the prized bijective mapping property and includes the Sierpinski triangle and the CGR square as particular solutions of the more encompassing formulation.</p

Skin Lesions on Common Bottlenose Dolphins (Tursiops truncatus) from Three Sites in the Northwest Atlantic, USA

Skin disease occurs frequently in many cetacean species across the globe; methods to categorize lesions have relied on photo-identification (photo-id), stranding, and by-catch data. The current study used photo-id data from four sampling months during 2009 to estimate skin lesion prevalence and type occurring on bottlenose dolphins (Tursiops truncatus) from three sites along the southeast United States coast [Sarasota Bay, FL (SSB); near Brunswick and Sapelo Island, GA (BSG); and near Charleston, SC (CHS)]. The prevalence of lesions was highest among BSG dolphins (P = 0.587) and lowest in SSB (P = 0.380), and the overall prevalence was significantly different among all sites (p<0.0167). Logistic regression modeling revealed a significant reduction in the odds of lesion occurrence for increasing water temperatures (OR = 0.92; 95%CI:0.906–0.938) and a significantly increased odds of lesion occurrence for BSG dolphins (OR = 1.39; 95%CI:1.203–1.614). Approximately one-third of the lesioned dolphins from each site presented with multiple types, and population differences in lesion type occurrence were observed (p<0.05). Lesions on stranded dolphins were sampled to determine the etiology of different lesion types, which included three visually distinct samples positive for herpesvirus. Although generally considered non-fatal, skin disease may be indicative of animal health or exposure to anthropogenic or environmental threats, and photo-id data provide an efficient and cost-effective approach to document the occurrence of skin lesions in free-ranging populations

Ion homeostasis in the Chloroplast

peer reviewedThe chloroplast is an organelle of high demand for macro- and micro-nutrient ions, which are required for the maintenance of the photosynthetic process. To avoid deficiency while preventing excess, homeostasis mechanisms must be tightly regulated. Here, we describe the needs for nutrient ions in the chloroplast and briefly highlight their functions in the chloroplastidial metabolism. We further discuss the impact of nutrient deficiency on chloroplasts and the acclimation mechanisms that evolved to preserve the photosynthetic apparatus. We finally present what is known about import and export mechanisms for these ions. Whenever possible, a comparison between cyanobacteria, algae and plants is provided to add an evolutionary perspective to the description of ion homeostasis mechanisms in photosynthesis