National Centers for Coastal Ocean Science Coastal Ecosystem Assessment Program: a manual of methods

Environmental managers strive to preserve natural resources for future generations but have limited decision-making tools to define ecosystem health. Many programs offer relevant broad-scale, environmental policy information on regional ecosystem health. These programs provide evidence of environmental condition and change, but lack connections between local impacts and direct effects on living resources. To address this need, the National Oceanic and Atmospheric Administration/National Ocean Service (NOAA/NOS) Cooperative Oxford Laboratory (COL), in cooperation with federal, state, and academic partners, implemented an integrated biotic ecosystem assessment on a sub-watershed 14-digit Hydrologic Unit Code (HUD) scale in Chesapeake Bay. The goals of this effort were to 1) establish a suite of bioindicators that are sensitive to ecosystem change, 2) establish the effects of varying land-use patterns on water quality and the subsequent health of living resources, 3) communicate these findings to local decision-makers, and 4) evaluate the success of management decisions in these systems. To establish indicators, three sub-watersheds were chosen based on statistical analysis of land-use patterns to represent a gradient from developed to agricultural. The Magothy (developed), Corsica (agricultural), and Rhode (reference) Rivers were identified. A random stratified design was developed based on depth (2m contour) and river mile. Sampling approaches were coordinated within this structure to allow for robust system comparisons. The sampling approach was hierarchal, with metrics chosen to represent a range from community to cellular level responses across multiple organisms. This approach allowed for the identification of sub-lethal stressors, and assessment of their impact on the organism and subsequently the population. Fish, crabs, clams, oysters, benthic organisms, and bacteria were targeted, as each occupies a separate ecological niche and may respond dissimilarly to environmental stressors. Particular attention was focused on the use of pathobiology as a tool for assessing environmental condition. By integrating the biotic component with water quality, sediment indices, and land- use information, this holistic evaluation of ecosystem health will provide management entities with information needed to inform local decision-making processes and establish benchmarks for future restoration efforts.

魔芋葡甘聚糖结构及其应用研究

本文以葡甘聚糖为试材，运用分子模拟同仪器分析相结合的手段，预测了葡甘聚糖分子链的高级结构，分析了无机分子对其结构、性能的影响，探讨了葡甘聚糖与卡拉胶微观作用机理。 主要研究内容与结果如下： 1. 葡甘聚糖单链高级结构的预测 利用Hyperchem7.0、VM2.0分子结构计算软件采用分子动力学和分子力学的方法，以真空中葡甘聚糖单链为研究模型，研究了聚合度、取代基对动态构象的影响及影响链构象的作用力。首次提出了KGM链的动态模型，得到了以下结果：聚合度影响其链形态和稳定性，对于高聚合度的魔芋葡甘聚糖来说，其链呈现无规卷曲状态且稳定性下降，在整个动态运动过程中KGM链脱乙酰基前后都呈现无规卷曲状态，而且其伸展和卷曲的变化是周期性的，表现出了很好的柔性，说明乙酰基不是影响其链形态的主要因素，二面角能和静电作用是真空中影响单链构象的主要的键合作用力和非键合作用力，但是乙酰基对氢键作用的影响较大。 2. 无机分子对葡甘聚糖溶液体系结构性能影响的研究 利用Hyperchem7.0分子结构计算软件，采用分子动力学及红外光谱、核磁共振等技术，对无机分子对葡甘聚糖体系的影响进行分析，很好的解释了性能变化的结构原因，结合以往的研究及参考文献得出以下结论：KGM在碱性条件下由于化学作用乙酰基的脱除分子间氢键作用的加强提高了凝胶强度，分子间氢键的主要作用位点是葡萄糖 的O(6)与甘露糖的O(2)之间;硼与KGM形成的分子内和分子间配合作用及分子间作用力氢键的增强是KGM特性粘度和致密性提高的主要原因，分子间型配位反应发生在葡萄糖和甘露糖两个糖环之间的几率最大;加入尿素后，表现为宏观性能的下降，葡甘聚糖氢键网络被破坏，氢键的作用位点由甘露糖的O(2)、O（3）变为O(4)，葡萄糖的O（3）、O(6)变为O（1）、O（2）。 3. 葡甘聚糖与卡拉胶共混作用的研究 利用Hyperchem7.0分子结构计算软件运用分子动力学方法、DSC、红外光谱技术，研究了葡甘聚糖与卡拉胶的微观结构及作用过程，揭示了性能变化的结构原因和分子之间的作用位点。得出了以下结论：葡甘聚糖同卡拉胶共混后通过分子间氢键作用形成了强度高、弹性好的热可逆凝胶。其凝胶强度与单一胶相比较，凝胶特性得到了很大的改善。通过红外光谱可以发现形成复合溶胶后化学基团没有发生本质上的改变，但是氢键缔合作用增强;通过DSC分析可以发现仅出现1个吸热峰，两种生物大分子达到了相容的结果，经过分子动力学模拟表明，与单一体系比较，葡甘聚糖与卡拉胶共混时稳定性提高，分子间氢键作用力明显增强，主要的作用位点是葡甘聚糖的上甘露糖的O(2)、O(4)、O(6)、乙酰基位置及卡拉胶上糖环上的 O(6)、硫酸基。

Molecular dynamics research of G249 and S249 substitutions of p53 protein.

,The molecular dynamics research of the core domain of p53 protein crystal structure shows that besides the stability in biochemistry this domain also shows a high stability in molecular mechanics. Based on that work, the residue R249 was substituted with amino acids Gly and Ser respectively, and molecular dynamics researches were performed separately. The results show that these substitutions cause a relax tendency between loop2 and 3 domains, leading to an alteration of the whole conformation of p53 core domain and ruining its stability. The results visually explains the mechanism of p53 changes in immunological and biochemical reactions, which are caused by 249 residue substitutions from 3-D structure variations.

Novel cathelicidin-derived antimicrobial peptides from Equus asinus

In the present study, EA-CATH1 and EA-CATH2 were identified from a constructed lung cDNA library of donkey (Equus asinus) as members of cathelicidin-derived antimicrobial peptides, using a nested PCR-based cloning strategy. Composed of 25 and 26 residues, respectively, EA-CATH1 and EA-CATH2 are smaller than most other cathelicidins and have no sequence homology to other cathelicidins identified to date. Chemically synthesized EA-CATH1 exerted potent antimicrobial activity against most of the 32 strains of bacteria and fungi tested, especially the clinically isolated drug-resistant strains, and minimal inhibitory concentration values against Gram-positive bacteria were mostly in the range of 0.3-2.4 mu g center dot mL-1. EA-CATH1 showed an extraordinary serum stability and no haemolytic activity against human erythrocytes in a dose up to 20 mu g center dot mL-1. CD spectra showed that EA-CATH1 mainly adopts an alpha-helical conformation in a 50% trifluoroethanol/water solution, but a random coil in aqueous solution. Scanning electron microscope observations of Staphylococcus aureus (ATCC2592) treated with EA-CATH1 demonstrated that EA-CATH could cause rapid disruption of the bacterial membrane, and in turn lead to cell lysis. This might explain the much faster killing kinetics of EA-CATH1 than conventional antibiotics revealed by killing kinetics data. In the presence of CaCl2, EA-CATH1 exerted haemagglutination activity, which might potentiate an inhibition against the bacterial polyprotein interaction with the host erythrocyte surface, thereby possibly restricting bacterial colonization and spread.

Geometrical properties and turbulent flame speed measurements in stationary premixed V-flames using direct numerical simulation

Three dimensional, fully compressible direct numerical simulations (DNS) of premixed turbulent flames are carried out in a V-flame configuration. The governing equations and the numerical implementation are described in detail, including modifications made to the Navier-Stokes Characteristic Boundary Conditions (NSCBC) to accommodate the steep transverse velocity and composition gradients generated when the flame crosses the boundary. Three cases, at turbulence intensities, u′/sL, of 1, 2, and 6 are considered. The influence of the flame holder on downstream flame properties is assessed through the distributions of the surface-conditioned displacement speed, curvature and tangential strain rates, and compared to data from similarly processed planar flames. The distributions are found to be indistinguishable from planar flames for distances greater than about 17δth downstream of the flame holder, where δth is the laminar flame thermal thickness. Favre mean fields are constructed, and the growth of the mean flame brush is found to be well described by simple Taylor type diffusion. The turbulent flame speed, sT is evaluated from an expression describing the propagation speed of an isosurface of the mean reaction progress variable c̃ in terms of the imbalance between the mean reactive, diffusive, and turbulent fluxes within the flame brush. The results are compared to the consumption speed, sC, calculated from the integral of the mean reaction rate, and to the predictions of a recently developed flame speed model (Kolla et al., Combust Sci Technol 181(3):518-535, 2009). The model predictions are improved in all cases by including the effects of mean molecular diffusion, and the overall agreement is good for the higher turbulence intensity cases once the tangential convective flux of c̃ is taken into account. © 2010 Springer Science+Business Media B.V.

Statistics and modelling of turbulent kinetic energy transport in different regimes of premixed combustion

The statistical behaviour of turbulent kinetic energy transport in turbulent premixed flames is analysed using data from three-dimensional Direct Numerical Simulation (DNS) of freely propagating turbulent premixed flames under decaying turbulence. For flames within the corrugated flamelets regime, it is observed that turbulent kinetic energy is generated within the flame brush. By contrast, for flames within the thin reaction zones regime it has been found that the turbulent kinetic energy decays monotonically through the flame brush. Similar trends are observed also for the dissipation rate of turbulent kinetic energy. Within the corrugated flamelets regime, it is demonstrated that the effects of the mean pressure gradient and pressure dilatation within the flame are sufficient to overcome the effects of viscous dissipation and are responsible for the observed augmentation of turbulent kinetic energy in the flame brush. In the thin reaction zones regime, the effects of the mean pressure gradient and pressure dilatation terms are relatively much weaker than those of viscous dissipation, resulting in a monotonic decay of turbulent kinetic energy across the flame brush. The modelling of the various unclosed terms of the turbulent kinetic energy transport equation has been analysed in detail. The predictions of existing models are compared with corresponding quantities extracted from DNS data. Based on this a-priori DNS assessment, either appropriate models are identified or new models are proposed where necessary. It is shown that the turbulent flux of turbulent kinetic energy exhibits counter-gradient (gradient) transport wherever the turbulent scalar flux is counter-gradient (gradient) in nature. A new model has been proposed for the turbulent flux of turbulent kinetic energy, and is found to capture the qualitative and quantitative behaviour obtained from DNS data for both the corrugated flamelets and thin reaction zones regimes without the need to adjust any of the model constants. © 2010 Springer Science+Business Media B.V.

Guided growth of neurons and glia using microfabricated patterns of parylene-C on a SiO2 background.

This paper describes a simple technique for the patterning of glia and neurons. The integration of neuronal patterning to Multi-Electrode Arrays (MEAs), planar patch clamp and silicon based 'lab on a chip' technologies necessitates the development of a microfabrication-compatible method, which will be reliable and easy to implement. In this study a highly consistent, straightforward and cost effective cell patterning scheme has been developed. It is based on two common ingredients: the polymer parylene-C and horse serum. Parylene-C is deposited and photo-lithographically patterned on silicon oxide (SiO(2)) surfaces. Subsequently, the patterns are activated via immersion in horse serum. Compared to non-activated controls, cells on the treated samples exhibited a significantly higher conformity to underlying parylene stripes. The immersion time of the patterns was reduced from 24 to 3h without compromising the technique. X-ray photoelectron spectroscopy (XPS) analysis of parylene and SiO(2) surfaces before and after immersion in horse serum and gel based eluant analysis suggests that the quantity and conformation of proteins on the parylene and SiO(2) substrates might be responsible for inducing glial and neuronal patterning.

Effect of flow-geometry on turbulence-scalar interaction in premixed flames

Turbulent combustion of stoichiometric hydrogen-air mixture is simulated using direct numerical simulation methodology, employing complex chemical kinetics. Two flame configurations, freely propagating and V-flames stabilized behind a hot rod, are simulated. The results are analyzed to study the influence of flame configuration on the turbulence-scalar interaction, which is critical for the scalar gradient generation processes. The result suggests that this interaction process is not influenced by the flame configuration and the flame normal is found to align with the most extensive strain in the region of intense heat release. The combustion in the rod stabilized flame is found to be flamelet like in an average sense and the growth of flame-brush thickness with the downstream distance is represented well by Taylor theory of turbulent diffusion, when the flame-brushes are non-interacting. The thickness is observed to saturate when the flame-brushes interact, which is found to occur in the simulated rod stabilized flame with Taylor micro-scale Reynolds number of 97. © 2011 American Institute of Physics.

Design of carbon nanotube fiber microelectrode for glucose biosensing

BACKGROUND: Carbon nanotube (CNT) fiber directly spun from an aerogel has a unique, well-aligned nanostructure (nano-pore and nano-brush), and thus provides high electro-catalytic activity and strong interaction with glucose oxidase enzyme. It shows great potential as a microelectrode for electrochemical biosensors. RESULTS: Cyclic voltammogram results indicate that post-synthesis treatments have great influence on the electrocatalytic activity of CNT fibers. Raman spectroscopy and electrical conductivity tests suggest that fibers annealed at 250 °C remove most of the impurities without damaging the graphite-like structure. This leads to a nano-porous morphology on the surface and the highest conductivity value (1.1 × 10 5 S m -1). Two CNT fiber microelectrode designs were applied to enhance their electron transfer behaviour, and it was found that a design using a 30 nm gold coating is able to linearly cover human physiological glucose level between 2 and 30 mmol L -1. The design also leads to a low detection limit of 25 μmol L -1. CONCLUSIONS: The high performance of CNT fibers not only offers exceptional mechanical and electrical properties, but also provides a large surface area and electron transfer pathway. They consequently make excellent bioactive microelectrodes for glucose biosensing, especially for potential use in implantable devices. © 2011 Society of Chemical Industry.

Automatic object segmentation from calibrated images

This paper addresses the problem of automatically obtaining the object/background segmentation of a rigid 3D object observed in a set of images that have been calibrated for camera pose and intrinsics. Such segmentations can be used to obtain a shape representation of a potentially texture-less object by computing a visual hull. We propose an automatic approach where the object to be segmented is identified by the pose of the cameras instead of user input such as 2D bounding rectangles or brush-strokes. The key behind our method is a pairwise MRF framework that combines (a) foreground/background appearance models, (b) epipolar constraints and (c) weak stereo correspondence into a single segmentation cost function that can be efficiently solved by Graph-cuts. The segmentation thus obtained is further improved using silhouette coherency and then used to update the foreground/background appearance models which are fed into the next Graph-cut computation. These two steps are iterated until segmentation convergences. Our method can automatically provide a 3D surface representation even in texture-less scenes where MVS methods might fail. Furthermore, it confers improved performance in images where the object is not readily separable from the background in colour space, an area that previous segmentation approaches have found challenging. © 2011 IEEE.

The three dimensional structure and biological domains of the p53 C-terminus.

It was expected that there are a coil (289 similar to 325) and two a helix (alpha(1)368 similar to 373, alpha(2)381 similar to 388) structures in p53 protein C-terminal region based on its mRNA secondary structure template and Chou-Fasman's protein secondary structure principle of prediction. The result was conformed by the other four methods of protein secondary structure prediction that are based on the multiple sequence alignment (accuracy = 73.20%). Combine with the 31 amino acids crystal structure of the oligomerization, the three dimensional conformation of p53 C-terminal 108 residues was built using the SGI INDIGO(2) computer. This structure further expounds the relationship among those biological function domains of p53 C- terminus at three-dimensional level.

Stability and molecular modeling of triplex DNA inhibiting DNA binding protein binding to the core promoter of hepatitis B virus.

Two three-dimensional structure models of the 21nt oligodeoxyribonucleotides, CPI (G3TG-2TGT2G5TG2TGT) and CP3 (TGTG2TGST2GTG2TG3), were constructed by InsightII (MSI) software in IRIS Indigo2 (SGI) workstation using the crystal structure of TAT tripler formation as the template. The initial structures subsequently were minimized by molecular mechanics. The final structures were believed as the dominant conformation. The results showed that the energy of CP1 is lower than that of CP3, and the former is more stable than the latter. Moreover, the results further proved that the 21nt oligodeoxyribo-nucleotide CP1 stably combines with the core promoter (Cp) fragment of hepatitis B virus (HBV) to form a tripler DNA, and CP1 specifically inhibits a specific cellular factor (DNA binding protein) binding to Cp fragment. These results indicated that specific repression of gene transcription of HBV DNA might be possible by tripler-formation DNA.

Dynamics of RNA with A6 bulge loop

In order to understand the behavior of RNAs with large bulges In solution, molecular dynamics was performed on the RNA molecule in water with A6 bulge. The result of simulation showed that nonstacked conformation Is the main conformation in large bulges, and the backbone of large bulge is of great conformational flexibility, but bulges-induced bends are relatively rigid. The fluctuation in bulge has little influence on the bend angle of RNAs.

Structure-function relationship of three neurotoxins from the venom of Naja kaouthia: a comparison between the NMR-derived structure of NT2 with its homologues, NT1 and NT3

Three homologous short-chain neurotoxins, named NT1, NT2 and NT3, were purified from the venom of Naja kaouthia. NT1 has an identical amino acid sequence to cobrotoxin from Naja naja atra [Biochemistry 32 (1993) 2131]. NT3 shares the same sequence with cobrotoxin b [J. Biochem. (Tokyo) 122 (1997) 1252], whereas NT2 is a novel 6 1 -residue neurotoxin. Tests of their physiological functions indicate that NT1 shows a greater inhibition of muscle contraction induced by electrical stimulation of the nerve than do NT2 and NT3. Homonuclear proton two-dimensional NMR methods were utilized to study the solution tertiary structure of NT2. A homology model-building method was employed to predict the structure of NT3. Comparison of the structures of these three toxins shows that the surface conformation of NT1 facilitates the substituted base residues, Arg28, Arg30, and Arg36, to occupy the favorable spatial location in the central region of loop 11, and the cation groups of all three arginines face out of the molecular surface of NT1 This may contribute greatly to the higher binding of NT1 with AchR compared to NT2 and NT3. (C) 2002 Elsevier Science B,V. All rights reserved.

Molecular docking and 3D-QSAR study of pyranmycin derivatives against 16S rRNA A site

To understand pharmacophore properties of pyranmycin derivatives and to design novel inhibitors of 16S rRNA A site, comparative molecular field analysis (CoMFA) approach was applied to analyze three-dimensional quantitative structure-activity relationship (3D-QSAR) of 17 compounds. AutoDock 3.0.5 program was employed to locate the orientations and conformations of the inhibitors interacting with 16S rRNA A site. The interaction mode was demonstrated in the aspects of inhibitor conformation, hydrogen bonding and electrostatic interaction. Similar binding conformations of these inhibitors and good correlations between the calculated binding free energies and experimental biological activities suggest that the binding conformations of these inhibitors derived from docking procedure were reasonable. Robust and predictive 3D-QSAR model was obtained by CoMFA with q(2) values of 0.723 and 0.993 for cross-validated and noncross-validated, respectively. The 3D-QSAR model built here will provide clear guidelines for novel inhibitors design based on the Pyranmycin derivatives against 16S rRNA A site. (c) 2005 Elsevier B.V. All rights reserved.