Surface modeling of craniofacial form in human embryos with a limited graphics terminal

Three-dimensional morphology of the human embryo typically is visualized through computerized modeling techniques utilizing planar contours as the data base. Through this approach, tissue outlines are digitized, and contour lines are superimposed, providing a depth perspective. However, these techniques represent embryonic tissues as discontinuous surfaces and therefore ignore morphological information between sections. The purpose of this study was to develop a computerized routine for the three-dimensional surface modeling of craniofacial morphology in human embryos. Tissue outlines are digitized, thus converting contour information into x,y,z coordinate data. The three-dimensional reconstruction program BCSURF opens the data file and plots each tissue polygon. A center is determined for each contour, and this value is used to divide each polygon into four segments. Surface patches are generated by mapping each segment onto the corresponding segment of subsequent sections. A face table is constructed representing the surface patches and plane normals are generated for each patch. The normal and depth values are appended to the face table, and these measures determine the color intensity for each patch. Finally, patches are plotted providing a polygon mesh model, and each patch is filled with a dither pattern according to shading values. Three-dimensional reconstructions of the craniofacial region in Carnegie embryos (stages 15-17) are generated, and major morphological features are observed. Although bilevel shading capabilities cause discontinuous shading textures, this simple and inexpensive system can be easily upgraded for high-resolution graphics.     

Effects of environment,habitat configuration and forest continuity on the distribution of forest plant species

In present day European landscapes many forest plant species are restricted to isolated remnants of a formerly more or less continuous forest cover. The two major objectives of this study were (1) to determine the relative importance of habitat quality (mainly in terms of soil parameters), habitat configuration (patch size and isolation) and habitat continuity for the distribution of herbaceous forest plant species in a highly fragmented landscape and (2) to examine if groups of species with different habitat requirements are affected differently. Deciduous forest patches in northwestern Germany were surveyed for the presence of a large set of forest species. For each patch, habitat quality, configuration and continuity were determined. Data were analysed by Redundancy Analysis with variation partitioning for effects on total species composition and multivariate logistic regression for effects on individual species, for two different data sets (base‐rich and base‐poor forest patches). Overall, we found strong effects of habitat quality (particularly of soil pH, water content and topographic heterogeneity in the base‐rich forest patches; and of calcium content and disturbance in the base‐poor patches), but only relatively weak effects of habitat configuration and habitat continuity. However, a number of species were positively affected by patch area and negatively affected by patch isolation. Furthermore, the relative importance of habitat configuration tended to be higher for species predominantly growing in closed forests compared to species occurring both in the forest and in the open landscape.     

A method for detecting hydrophobic patches on protein surfaces

A method for the detection of hydrophobic patches on the surfaces of protein tertiary structures is presented. It delineates explicit contiguous pieces of surface of arbitrary size and shape that consist solely of carbon and sulphur atoms using a dot representation of the solvent-accessible surface. The technique is also useful in detecting surface segments with other characteristics, such as polar patches. Its potential as a tool in the study of protein-protein interactions and substrate recognition is demonstrated by applying the method to myoglobin, Leu/Ile/Val-binding protein, lipase, lysozyme, azurin, triose phosphate isomerase, carbonic anhydrase, and phosphoglycerate kinase. Only the largest patches, having sizes exceeding random expectation, are deemed meaningful. In addition to well-known hydrophobic patches on these proteins, a number of other patches are found, and their significance is discussed. The method is simple, fast, and robust. The program text is obtainable by anonymous ftp. © 1996 Wiley-Liss, Inc.     

Grid map analysis and its application for detecting vegetation changes in Japan

Abstract. Grid maps are used as a basic vegetation data base in Japan; they are simplified from vector-based vegetation maps. We estimated the frequency error or lack of information corresponding to reduced resolution and examined the reliable limits of this data base. We produced 10 grid maps on five different scales from 50 m to 1000 m using two different methods using both the whole cell (W-method) and only the central circle (C-method) from a vegetation map at scale 1: 25 000. We found that patches larger than the area of a cell on a vector-based map could be kept almost certainly on any map, but many patches of less than the cell size were lost. The number of missing patches with the C-method is fewer at every scale than those with the W-method. Though the value of Morisita's Cλ (p) index showed that the similarity with the original map was high - from the 50-m to the 200-m resolution - it was increasingly lower on the 400-m and 1000-m grid maps. The values of the Shannon index on the original map, 50-m and 100-m grid maps were not different, but they decreased from the 200-m to 1000-m grid maps. Because the vegetation data base of the Japanese Environment Agency used a 1000-m C-method grid map, we found that much information on patches less than 100 ha had disappeared. Information about dominant vegetation or large patches is almost accurate in this data base.     

Hydrophobic patches on the surfaces of protein structures

A survey of hydrophobic patches on the surface of 112 soluble, monomeric proteins is presented. The largest patch on each individual protein averages around 400 Ų but can range from 200 to 1,200 Ų. These areas are not correlated to the sizes of the proteins and only weakly to their apolar surface fraction. Ala, Lys, and Pro have dominating contributions to the apolar surface for smaller patches, while those of the hydrophobic amino acids become more important as the patch size Increases. The hydrophilic amino acids expose an approximately constant fraction of their apolar area independent of patch size; the hydrophobic residue types reach similar exposure only in the larger patches. Though the mobility of residues on the surface is generally higher, it decreases for hydrophilic residues with Increasing patch size. Several characteristics of hydrophobic patches catalogued here should prove useful in the design and engineering of proteins. © 1996 Wiley-Liss, Inc.     

异质养分环境中一年生分蘖草本黍根系的生长特征

为揭示黍（Panicum miliaceum L.)根系对异质养分环境的生长反应,作研究了黍根系从起始斑块向目标斑块水平生长时,时始斑块和目标斑块养分水平根生长的影响,就低养分起始珏块而言,粗根生物量,粗根长度,粗根表面积和细极长度在高养分目标斑块中的分配比例均小于其在低养分目标斑块中的分配比例,而细根长度及其密度,细根表面积指及其密度的变化恰好相反,就高养分起始斑块而言,高养分目标斑块的细根长度,细根长度密度,细根表面积指数和细根表面积密均不于低养分目标斑块,而粗根对目标斑块中养分状的反应不明显。当黍根系从桢的起始斑块进入不同的目标斑块后,目标斑块的养分状况对细根生物量及其分配无影响,而显影响细根长度和表现积,这指示细根是通过长度和表面积可塑性而不是生物量变化响应目标斑块中的养分差异。     

Vesicle trafficking and cell surface membrane patchiness.

Membrane proteins and lipids often appear to be distributed in patches on the cell surface. These patches are often assumed to be membrane domains, arising from specific molecular associations. However, a computer simulation (Gheber and Edidin, 1999) shows that membrane patchiness may result from a combination of vesicle trafficking and dynamic barriers to lateral mobility. The simulation predicts that the steady-state patches of proteins and lipids seen on the cell surface will decay if vesicle trafficking is inhibited. To test this prediction, we compared the apparent sizes and intensities of patches of class I HLA molecules, integral membrane proteins, before and after inhibiting endocytic vesicle traffic from the cell surface, either by incubation in hypertonic medium or by expression of a dominant-negative mutant dynamin. As predicted by the simulation, the apparent sizes of HLA patches increased, whereas their intensities decreased after endocytosis and vesicle trafficking were inhibited.     

Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins

A method to detect DNA-binding sites on the surface of a protein structure is important for functional annotation. This work describes the analysis of residue patches on the surface of DNA-binding proteins and the development of a method of predicting DNA-binding sites using a single feature of these surface patches. Surface patches and the DNA-binding sites were initially analysed for accessibility, electrostatic potential, residue propensity, hydrophobicity and residue conservation. From this, it was observed that the DNA-binding sites were, in general, amongst the top 10% of patches with the largest positive electrostatic scores. This knowledge led to the development of a prediction method in which patches of surface residues were selected such that they excluded residues with negative electrostatic scores. This method was used to make predictions for a data set of 56 non-homologous DNA-binding proteins. Correct predictions made for 68% of the data set.     

Root Growth of the Annual Tillering Grass Panicum miliaceum in Heterogeneous Nutrient Environments (in English)

To study growth responses of the roots of Panicum miliaceum L. to heterogeneous supply of nutrients. The authors analyzed the effects of the nutrient levels in both original patches (O) and destination patches (D) on the root growth of P. miliaceum when its roots were allowed to extend from original patch into destination patch. When the nutrient levels in the original patches were low, coarse root biomass ratio (coarse root biomass in the D/total coarse root biomass), coarse root length ratio (coarse root length in the D/total coarse root length), coarse root surface area ratio (coarse root surface area in the D/total coarse root surface area) and fine root length ratio (fine root length in the D/total fine root length) were greater in the destination patches with lower nutrient levels than in the destination patches with higher nutrient levels, while fine root length, fine root length density, fine root surface index, and fine root surface area density were smaller in the former than in the latter. When the nutrient levels in the original patches were high, fine root length, fine root length density, fine root surface area index and fine root surface density were greater in the destination patches with lower nutrient levels than in the destination patches with higher nutrient levels, coarse roots did not respond to the nutrient levels in the destination patches significantly. When the roots extended from the original patches with the same nutrient level into the destination patches with contrasting nutrient levels, fine root biomass and its percentage allocation did not respond to the nutrient levels in the destination patches significantly, whereas both root length and root surface area did. This indicates that the fine roots of P. miliaceum responded to difference in nutrient supply by plasticity in their length and surface area, rather than in their root biomass.     

Patch and soil characteristics of pastures with water‐spreading banks and woody encroachment in semi‐arid Australia

Water‐spreading banks are used in semi‐arid areas such as the Cobar pediplain in western New South Wales, Australia to encourage pasture growth, often after removal of woody encroachment. We studied the arrangement of bare inter‐patches and vegetated patches, and associated surface soil variables, in three pastures following installation of water‐spreading banks (2, 15, 38 years ago) and in an area of woody encroachment near Cobar. The aims of the study were as follows: (i) to determine the number and percent area of inter‐patches and vegetated patches, and associated surface soil variables at the three pasture sites and at the woody encroachment site and (ii) by inference, explore effects of establishing water‐spreading banks and pasture following removal of woody encroachment on these factors, to understand the role of water‐spreading banks as a management tool. The percent area of inter‐patches in pasture with 38‐year‐old water‐spreading banks was much lower, and the percent area of medium‐vegetated patches (but not of well‐vegetated patches) was substantially higher, than in the woody encroachment. Differences in soil carbon and nitrogen between the sites were related to their percent areas of inter‐patches and vegetated patches. The results suggest that the mosaic of bare inter‐patches and vegetated patches changes over time after clearing of woody encroachment and establishment of pasture with water‐spreading banks, from many large inter‐patches to a few small inter‐patches, and from small to large medium‐vegetated patches. Water‐spreading banks are a useful management tool in these landscapes because of their benefits for landscape function, that is, bare areas become less connected, the percent area of moderately vegetated patches increases, and soil carbon builds up with time following their installation.     

A landscape perspective of surface–subsurface hydrological exchanges in river corridors

1. River corridors can be visualised as a three‐dimensional mosaic of surface–subsurface exchange patches over multiple spatial scales. Along major flow paths, surface water downwells into the sediment, travels for some distance beneath or along the stream, eventually mixes with ground water, and then returns to the stream. 2. Spatial variations in bed topography and sediment permeability result in a mosaic of patch types (e.g. gravel versus sandy patches) that differ in their hydrological exchange rate with the surface stream. Biogeochemical processes and invertebrate assemblages vary among patch types as a function of the flux of advected channel water that determines the supply of organic matter and terminal electron acceptors. 3. The overall effect of surface–subsurface hydrological exchanges on nutrient cycling and biodiversity in streams not only depends on the proportion of the different patch types, but also on the frequency distribution of patch size and shape. 4. Because nutrients are essentially produced or depleted at the downwelling end of hyporheic flow paths, reach‐scale processing rates of nutrients should be greater in stretches with many small patches (e.g. short compact gravel bars) than in stretches with only a few large patches (e.g. large gravel bars). 5. Based on data from the Rhône River, we predict that a reach with many small bars should offer more hyporheic refugia for epigean fauna than a reach containing only a few large gravel bars because benthic organisms accumulate preferentially in sediments located at the upstream and downwelling edge of bars during floods. However, large bars are more stable and may provide the only refugia during severe flood events. 6. In river floodplain systems exhibiting pronounced expansion/contraction cycles, hyporheic assemblages within newly created patches not only depend on the intrinsic characteristics of these patches but also on their life span, hydrological connection with neighbouring patches, and movement patterns of organisms. 7. Empirical and theoretical evidence illustrate how the spatial arrangement of surface–subsurface exchange patches affects heterogeneity in stream nutrient concentration, surface water temperature, and colonisation of dry reaches by invertebrates. 8. Interactions between fluvial action and geomorphic features, resulting from seasonal and episodic flow pulses, alter surface–subsurface exchange pathways and repeatedly modify the configuration of the mosaic, thereby altering the contribution of the hyporheic zone to nutrient transformation and biodiversity in river corridors.     

Distinct spatiotemporal patterns and PARP dependence of XRCC1 recruitment to single-strand break and base excision repair

Single-strand break repair (SSBR) and base excision repair (BER) of modified bases and abasic sites share several players. Among them is XRCC1, an essential scaffold protein with no enzymatic activity, required for the coordination of both pathways. XRCC1 is recruited to SSBR by PARP-1, responsible for the initial recognition of the break. The recruitment of XRCC1 to BER is still poorly understood. Here we show by using both local and global induction of oxidative DNA base damage that XRCC1 participation in BER complexes can be distinguished from that in SSBR by several criteria. We show first that XRCC1 recruitment to BER is independent of PARP. Second, unlike SSBR complexes that are assembled within minutes after global damage induction, XRCC1 is detected later in BER patches, with kinetics consistent with the repair of oxidized bases. Third, while XRCC1-containing foci associated with SSBR are formed both in eu- and heterochromatin domains, BER complexes are assembled in patches that are essentially excluded from heterochromatin and where the oxidized bases are detected.     

Computational protein design with explicit consideration of surface hydrophobic patches

De novo protein design requires the identification of amino-acid sequences that favor the target-folded conformation and are soluble in water. One strategy for promoting solubility is to disallow hydrophobic residues on the protein surface during design. However, naturally occurring proteins often have hydrophobic amino acids on their surface that contribute to protein stability via the partial burial of hydrophobic surface area or play a key role in the formation of protein-protein interactions. A less restrictive approach for surface design that is used by the modeling program Rosetta is to parameterize the energy function so that the number of hydrophobic amino acids designed on the protein surface is similar to what is observed in naturally occurring monomeric proteins. Previous studies with Rosetta have shown that this limits surface hydrophobics to the naturally occurring frequency (～28%), but that it does not prevent the formation of hydrophobic patches that are considerably larger than those observed in naturally occurring proteins. Here, we describe a new score term that explicitly detects and penalizes the formation of hydrophobic patches during computational protein design. With the new term, we are able to design protein surfaces that include hydrophobic amino acids at naturally occurring frequencies, but do not have large hydrophobic patches. By adjusting the strength of the new score term, the emphasis of surface redesigns can be switched between maintaining solubility and maximizing folding free energy.     

Dibucaine effects on structural and elastic properties of lipid bilayers

In this work we report the interaction effects of the local anesthetic dibucaine (DBC) with lipid patches in model membranes by Atomic Force Microscopy (AFM). Supported lipid bilayers (egg phosphatidylcholine, EPC and dimyristoylphosphatidylcholine, DMPC) were prepared by fusion of unilamellar vesicles on mica and imaged in aqueous media. The AFM images show irregularly distributed and sized EPC patches on mica. On the other hand DMPC formation presents extensive bilayer regions on top of which multibilayer patches are formed. In the presence of DBC we observed a progressive disruption of these patches, but for DMPC bilayers this process occurred more slowly than for EPC. In both cases, phase images show the formation of small structures on the bilayer surface suggesting an effect on the elastic properties of the bilayers when DBC is present. Dynamic surface tension and dilatational surface elasticity measurements of EPC and DMPC monolayers in the presence of DBC by the pendant drop technique were also performed, in order to elucidate these results. The curve of lipid monolayer elasticity versus DBC concentration, for both EPC and DMPC cases, shows a maximum for the surface elasticity modulus at the same concentration where we observed the disruption of the bilayer by AFM. Our results suggest that changes in the local curvature of the bilayer induced by DBC could explain the anesthetic action in membranes.     

DNA-tethered membranes formed by giant vesicle rupture

We have developed a strategy for preparing tethered lipid bilayer membrane patches on solid surfaces by DNA hybridization. In this way, the tethered membrane patch is held at a controllable distance from the surface by varying the length of the DNA used. Two basic strategies are described. In the first, single-stranded DNA strands are immobilized by click chemistry to a silica surface, whose remaining surface is passivated to prevent direct assembly of a solid supported bilayer. Then giant unilamellar vesicles (GUVs) displaying the antisense strand, using a DNA–lipid conjugate developed in earlier work [Chan, Y.-H.M., van Lengerich, B., et al., 2008. Lipid-anchored DNA mediates vesicle fusion as observed by lipid and content mixing. Biointerphases 3 (2), FA17–FA21], are allowed to tether, spread and rupture to form tethered bilayer patches. In the second, a supported lipid bilayer displaying DNA using the DNA–lipid conjugate is first assembled on the surface. Then GUVs displaying the antisense strand are allowed to tether, spread and rupture to form tethered bilayer patches. The essential difference between these methods is that the tethering hybrid DNA is immobile in the first, while it is mobile in the second. Both strategies are successful; however, with mobile DNA hybrids as tethers, the patches are unstable, while in the first strategy stable patches can be formed. In the case of mobile tethers, if different length DNA hybrids are present, lateral segregation by length occurs and can be visualized by fluorescence interference contrast microscopy making this an interesting model for interactions that occur in cell junctions. In both cases, lipid mobility is high and there is a negligible immobile fraction. Thus, these architectures offer a flexible platform for the assembly of lipid bilayers at a well-defined distance from a solid support.     

Joint surface modeling with thin-plate splines.

Mathematical joint surface models based on experimentally determined data points can be used to investigate joint characteristics such as curvature, congruency, cartilage thickness, joint contact areas, as well as to provide geometric information well suited for finite element analysis. Commonly, surface modeling methods are based on B-splines, which involve tensor products. These methods have had success; however, they are limited due to the complex organizational aspect of working with surface patches, and modeling unordered, scattered experimental data points. An alternative method for mathematical joint surface modeling is presented based on the thin-plate spline (TPS). It has the advantage that it does not involve surface patches, and can model scattered data points without experimental data preparation. An analytical surface was developed and modeled with the TPS to quantify its interpolating and smoothing characteristics. Some limitations of the TPS include discontinuity of curvature at exactly the experimental surface data points, and numerical problems dealing with data sets in excess of 2000 points. However, suggestions for overcoming these limitations are presented. Testing the TPS with real experimental data, the patellofemoral joint of a cat was measured with multistation digital photogrammetry and modeled using the TPS to determine cartilage thicknesses and surface curvature. The cartilage thickness distribution ranged between 100 to 550 microns on the patella, and 100 to 300 microns on the femur. It was found that the TPS was an effective tool for modeling joint surfaces because no preparation of the experimental data points was necessary, and the resulting unique function representing the entire surface does not involve surface patches. A detailed algorithm is presented for implementation of the TPS.     

Prediction of protein-protein interactions based on surface patch comparison

A method to predict if two proteins interact, based on their three-dimensional structures, is presented. It consists of five steps: (i) the surface of each protein, represented by the solvent accessible atoms, is divided into small patches; (ii) the shape of each patch is described by the atom distributions along its principal axes; (iii) the shape complementarity between two patches is estimated by comparing, through contingency table analysis, their atom distributions along their principal axes; (iv) given protein A, with nA surface patches, and protein B, with nB surface patches, nA x nB shape complementarity values are obtained; and (v) the distribution of the latter allows one to discriminate pairs of interacting and of noninteracting proteins. Only a few seconds are necessary to predict if two proteins interact, with accuracy close to 80%, sensitivity over 70% and specificity close to 50%.     

哈尼梯田景观格局对地表水δ18O海拔效应的影响

本研究以哈尼梯田文化景观遗产核心区的全福庄河小流域为对象,对在2015年5月—2016年4月间逐月采集的森林景观类型和梯田景观类型下12个样点的地表水样品进行氢氧稳定同位素组成和效应分析。结果表明: 1)在地表水氢氧稳定同位素组成上,森林斑块δ¹⁸O平均值小于梯田斑块,森林斑块δ¹⁸O随时间的变化幅度也小于梯田斑块;2)研究区地表水δ¹⁸O除8月和3月外,均具有显著的海拔效应,其一元线性回归方程为:δ¹⁸O=-0.012H+13.84(r=-0.83, n=12);3)地表水δ¹⁸O海拔梯度为-1.2‰·(100 m)^-1,但并不是受降水影响的“真”海拔梯度,而是森林斑块和梯田斑块间地表水δ¹⁸O景观梯度影响下的海拔梯度;4)在森林-梯田的景观格局组合下,森林斑块与梯田斑块间的地表水δ¹⁸O值差异增强了海拔效应。因此,当流域景观格局异质性强时,地表水稳定同位素效应会被强化或者出现完全相反的同位素效应。