Computer modelling and estimation of recruitment patterns of non-branching coral colonies at three sites in Wakatobi Marine Park, S.E. Sulawesi, Indonesia; implications for coral reef conservation

We have studied growth and estimated recruitment of massive coral colonies at three sites, Kaledupa, Hoga and Sampela, separated by about 1.5 km in the Wakatobi Marine National Park, S.E. Sulawesi, Indonesia. There was significantly higher species richness (P<0.05), coral cover (P<0.05) and rugosity (P<0.01) at Kaledupa than at Sampela. A model for coral reef growth has been developed based on a rational polynomial function, where dx/dt is an index of coral growth with time; W is the variable (for example, coral weight, coral length or coral area), up to the power of n in the numerator and m in the denominator; a1……an and b1…bm are constants. The values for n and m represent the degree of the polynomial, and can relate to the morphology of the coral. The model was used to simulate typical coral growth curves, and tested using published data obtained by weighing coral colonies underwater in reefs on the south-west coast of Curaçao [‘Neth. J. Sea Res. 10 (1976) 285’]. The model proved an accurate fit to the data, and parameters were obtained for a number of coral species. Surface area data was obtained on over 1200 massive corals at three different sites in the Wakatobi Marine National Park, S.E. Sulawesi, Indonesia. The year of an individual's recruitment was calculated from knowledge of the growth rate modified by application of the rational polynomial model. The estimated pattern of recruitment was variable, with little numbers of massive corals settling and growing before 1950 at the heavily used site, Sampela, relative to the reef site with little or no human use, Kaledupa, and the intermediate site, Hoga. There was a significantly greater sedimentation rate at Sampela than at either Kaledupa (P<0.0001) or Hoga (P<0.0005). The relative mean abundance of fish families present at the reef crests at the three sites, determined using digital video photography, did not correlate with sedimentation rates, underwater visibility or lack of large non-branching coral colonies. Radial growth rates of three genera of non-branching corals were significantly lower at Sampela than at Kaledupa or at Hoga, and there was a high correlation (r=0.89) between radial growth rates and underwater visibility. Porites spp. was the most abundant coral over all the sites and at all depths followed by Favites (P<0.04) and Favia spp. (P<0.03). Colony ages of Porites corals were significantly lower at the 5 m reef flat on the Sampela reef than at the same depth on both other reefs (P<0.005). At Sampela, only 2.8% of corals on the 5 m reef crest are of a size to have survived from before 1950. The Scleractinian coral community of Sampela is severely impacted by depositing sediments which can lead to the suffocation of corals, whilst also decreasing light penetration resulting in decreased growth and calcification rates. The net loss of material from Sampela, if not checked, could result in the loss of this protective barrier which would be to the detriment of the sublittoral sand flats and hence the Sampela village.

Analysis of chain and blood group type and branching pattern of sialylated oligosaccharides by negative ion electrospray tandem mass spectrometry

We previously reported sequence determination of neutral oligosaccharides by negative ion electrospray tandem mass spectrometry on a quadrupole-orthogonal time-of-flight instrument with high sensitivity and without the need of derivatization. In the present report, we extend our strategies to sialylated oligosaccharides for analysis of chain and blood group types together with branching patterns. A main feature in the negative ion mass spectrometry approach is the unique double glycosidic cleavage induced by 3-glycosidic substitution, producing characteristic D-type fragments which can be used to distinguish the type 1 and type 2 chains, the blood group related Lewis determinants, 3,6-disubstituted core branching patterns, and to assign the structural details of each of the branches. Twenty mono- and disialylated linear and branched oligosaccharides were used for the investigation, and the sensitivity achieved is in the femtomole range. To demonstrate the efficacy of the strategy, we have determined a novel complex disialylated and monofucosylated tridecasaccharide that is based on the lacto-N-decaose core. The structure and sequence assignment was corroborated by :methylation analysis and H-1 NMR spectroscopy.

Effect of molecule branching and glycosidic linkage on the degradation of polydextrose by gut microbiota.

Polydextrose is a randomly linked complex glucose oligomer that is widely used as a sugar replacer, bulking agent, dietary fiber and prebiotic. Polydextrose is poorly utilized by the host and, during gastrointestinal transit, it is slowly degraded by intestinal microbes, although it is not known which parts of the complex molecule are preferred by the microbes. The microbial degradation of polydextrose was assessed by using a simulated model of colonic fermentation. The degradation products and their glycosidic linkages were measured by combined gas chromatography and mass spectrometry, and compared to those of intact polydextrose. Fermentation resulted in an increase in the relative abundance of non-branched molecules with a concomitant decrease in single-branched glucose molecules and a reduced total number of branching points. A detailed analysis showed a preponderance of 1,6 pyranose linkages. The results of this study demonstrate how intestinal microbes selectively degrade polydextrose, and provide an insight into the preferences of gut microbiota in the presence of different glycosidic linkages.

Perspex machine X: software development

The Perspex Machine arose from the unification of computation with geometry. We now report significant redevelopment of both a partial C compiler that generates perspex programs and of a Graphical User Interface (GUI). The compiler is constructed with standard compiler-generator tools and produces both an explicit parse tree for C and an Abstract Syntax Tree (AST) that is better suited to code generation. The GUI uses a hash table and a simpler software architecture to achieve an order of magnitude speed up in processing and, consequently, an order of magnitude increase in the number of perspexes that can be manipulated in real time (now 6,000). Two perspex-machine simulators are provided, one using trans-floating-point arithmetic and the other using transrational arithmetic. All of the software described here is available on the world wide web. The compiler generates code in the neural model of the perspex. At each branch point it uses a jumper to return control to the main fibre. This has the effect of pruning out an exponentially increasing number of branching fibres, thereby greatly increasing the efficiency of perspex programs as measured by the number of neurons required to implement an algorithm. The jumpers are placed at unit distance from the main fibre and form a geometrical structure analogous to a myelin sheath in a biological neuron. Both the perspex jumper-sheath and the biological myelin-sheath share the computational function of preventing cross-over of signals to neurons that lie close to an axon. This is an example of convergence driven by similar geometrical and computational constraints in perspex and biological neurons.

A study of the ethene-ozone reaction with photoelectron spectroscopy: measurement of product branching ratios and atmospheric implications

The ozone-ethene reaction has been investigated at low pressure in a flow-tube interfaced to a u.v. photoelectron spectrometer. Photoelectron spectra recorded as a function of reaction time have been used to estimate partial pressures of the reagents and products, using photoionization cross-sections for selected photoelectron bands of the reagents and products, which have been measured separately. Product yields compare favourably with results of other studies, and the production of oxygen and acetaldehyde have been measured as a function of time for the first time. A reaction scheme developed for the ozone-ethene reaction has been used to simulate the reagents and products as a function of time. The results obtained are in good agreement with the experimental measurements. For each of the observed products, the simulations allow the main reaction (or reactions) for production of that product to be established. The product yields have been used in a global model to estimate their global annual emissions in the atmosphere. Of particular interest are the calculated global annual emissions of formaldehyde (0.96 ± 0.10 Tg) and formic acid, (0.05 ± 0.01 Tg) which are estimated as 0.04% and 0.7% of the total annual emission respectively.

First observation of the Cabibbo-suppressed decays Xi(+)(c)->Sigma(+)pi(-)pi(+) and Xi(+)(c)->Sigma(-)pi(+)pi(+) and measurement of their branching ratios

We report the first observation of two Cabibbo-suppressed ecay modes, Xi(+)(c) -> Sigma(+)pi(-)pi(+) and Xi c+ -> Sigma(-)pi(+)pi(+). We observe 59 +/- 14 over a background of 87, and 22 +/- 8 over a background of 13 events, respectively, for the signals. The data were accumulated using the SELEX spectrometer during the 1996-1997 fixed target run at Fermilab, chiefly from a 600 Gev/c Sigma(-) beam. The branching ratios of the decays relative to the Cabibbo-favored Xi c+ -> Xi(-)pi(+)pi(+) are measured to be B(Xi(+)(c) -> Sigma(+)pi(-)pi(+))/B(Xi(+)(c) -> Xi(-)pi(+)pi(+)) = 0.48 +/- 0.20, and B(Xi(+)(c) -> Sigma(-)pi(+)pi(+))/B(Xi(+)(c) -> Sigma(-)pi(+)pi(+)) = 0.18 +/- 0.09, respectively. We also report branching ratios for the same decay modes of the Delta(+)(c) relative to Delta(+)(c) -> pK(-)pi(+.) (C) 2008 Elsevier B.V. All rights reserved.

Influence of fixed electric charges on potential profile across the squid axon membrane

The potential profile for a model of squid axon membrane has been determined for two physiological states: resting and action states. The non-linear Poisson-Boltzmann equation has been solved by considering the volumetric charge densities due to charges dissolved in an electrolytic solution and fixed on both glycocalyx and cytoplasmatic proteins. Results showing the features of the potential profile along the outer electrolytic region are similar for both resting and action states. However, the potential fall along glycocalyx at action state is lower than at resting. A small variation in the Na+ concentration drastically affects the surface membrane potentials and vice versa. We conclude that effects on the potential profile due to surface lipidic bilayer charge and contiguous electric double layers are more relevant than those provoked by fixed charges distributed along the cell cytoplasm. (c) 2007 Elsevier B.V. All rights reserved.

Epidemics in networks of spatially correlated three-dimensional root-branching structures

Using digitized images of the three-dimensional, branching structures for root systems of bean seedlings, together with analytical and numerical methods that map a common susceptible-infected- recovered (`SIR`) epidemiological model onto the bond percolation problem, we show how the spatially correlated branching structures of plant roots affect transmission efficiencies, and hence the invasion criterion, for a soil-borne pathogen as it spreads through ensembles of morphologically complex hosts. We conclude that the inherent heterogeneities in transmissibilities arising from correlations in the degrees of overlap between neighbouring plants render a population of root systems less susceptible to epidemic invasion than a corresponding homogeneous system. Several components of morphological complexity are analysed that contribute to disorder and heterogeneities in the transmissibility of infection. Anisotropy in root shape is shown to increase resilience to epidemic invasion, while increasing the degree of branching enhances the spread of epidemics in the population of roots. Some extension of the methods for other epidemiological systems are discussed.

Undersampled Critical Branching Processes on Small-World and Random Networks Fail to Reproduce the Statistics of Spike Avalanches

The power-law size distributions obtained experimentally for neuronal avalanches are an important evidence of criticality in the brain. This evidence is supported by the fact that a critical branching process exhibits the same exponent t~3=2. Models at criticality have been employed to mimic avalanche propagation and explain the statistics observed experimentally. However, a crucial aspect of neuronal recordings has been almost completely neglected in the models: undersampling. While in a typical multielectrode array hundreds of neurons are recorded, in the same area of neuronal tissue tens of thousands of neurons can be found. Here we investigate the consequences of undersampling in models with three different topologies (two-dimensional, small-world and random network) and three different dynamical regimes (subcritical, critical and supercritical). We found that undersampling modifies avalanche size distributions, extinguishing the power laws observed in critical systems. Distributions from subcritical systems are also modified, but the shape of the undersampled distributions is more similar to that of a fully sampled system. Undersampled supercritical systems can recover the general characteristics of the fully sampled version, provided that enough neurons are measured. Undersampling in two-dimensional and small-world networks leads to similar effects, while the random network is insensitive to sampling density due to the lack of a well-defined neighborhood. We conjecture that neuronal avalanches recorded from local field potentials avoid undersampling effects due to the nature of this signal, but the same does not hold for spike avalanches. We conclude that undersampled branching-process-like models in these topologies fail to reproduce the statistics of spike avalanches.

Canine spinal cord neuron and axon myelin sheath morphometry

This inedited morphometric study has been developed from healthy canine spinal cord neuron cytoplasm and nucleus, and white matter axonal myelin sheath, from cervical, thoracic and lumbar regions. For the morphometric study, the parameters were area, perimeter, maximum and minimum diameters and roundness for neurons and myelin thickness for axon. For each parameter, 300 neurons were analysed. The results revealed that lumbar neurons had the highest mean values for the analysed parameters, indicating the presence of large neurons in this region, with large axons as a result of myelin thickness, which is proportional to axon calibre. We conclude that these morphometric results can contribute for the establishment of normal patterns, for canine spinal cord cervical, thoracic and lumbar segments.

The X-ray crystallographic structure of Escherichia coli branching enzyme

Branching enzyme catalyzes the formation of alpha-1,6 branch points in either glycogen or starch. We report the 2.3-Angstrom crystal structure of glycogen branching enzyme from Escherichia coli. The enzyme consists of three major domains, an NH2-terminal seven-stranded beta-sandwich domain, a COOH-terminal domain, and a central alpha/beta-barrel domain containing the enzyme active site. While the central domain is similar to that of all the other amylase family enzymes, branching enzyme shares the structure of all three domains only with isoamylase. Oligosaccharide binding was modeled or branching enzyme using the enzyme-oligosaccharide complex structures of various alpha-amylases and cyclodextrin glucanotransferase and residues were implicated in oligosaccharide binding. While most of the oligosaccharides modeled well in the branching enzyme structure, an approximate 50degrees rotation between two of the glucose units was required to avoid steric clashes with Trp(298) of branching enzyme. A similar rotation was observed in the mammalian alpha-amylase structure caused by an equivalent tryptophan residue in this structure. It appears that there are two binding modes for oligosaccharides in these structures depending on the identity and location of this aromatic residue.