MacMolecular: A program for visualization of molecular structures on the Macintosh

MacMolecular displays small- to medium-sized biomolecules, with particular emphasis on peptides. It has been developed to run on color Macintosh computers. The display can be stick, ball and stick, depth cued by thickness stick, or several types of space-filling representations. The program takes input from standard PDB files, simple Cartesian coordinate files, and, in addition, from Kinemage files in which atom information has been included. The program allows color changes of various types as well as the normal functions of translation, rotation, and zooming. In addition, animation files may be produced for subsequent display. Bonding of atoms is done by a distance algorithm (standard) or sequentially to properly display Cα traces and traces of peptides containing simplified representations of amino acids. Stereo viewing is available, and manipulated structures which were drawn from PDB files can be written out to new PDB files. In addition, PICT files of the drawing window can be generated.     

WinMGM: A fast CPK molecular graphics program for analyzing molecular structure

A molecular modeling program is presented which has been written for Microsoft windows 3.1 and Windows NT operating systems. The program permits interactive molecular manipulation and also provides analytical tools such as energy computations and solvent accessible surfaces. An extremely fast algorithm is used which generates realistic space-filling CPK images in addition to wire frame, ribbons, MIDAS, labels, and points. An important feature of this algorithm is a highly optimized Z-buffer, which is described.     

Photorealistic image generation of molecular structure on PC screen using the ray-tracing technique

A PC version of three-dimensional molecular graphics package has been developed to run under MS-DOS environment on IBM PC-compatible computers equipped with a VGA graphics board. The program consists of two parts: a menu-driven interactive system module in EGA mode, and a ray-tracing module in VGA mode. In the 256-color VGA mode, ray-tracing images are represented with a 4-color map, with 64 levels for each color: 32 levels of illuminance and 32 levels of saturation. Molecular structure can be analyzed along various directions with various light sources. Ray-tracing images are also represented in a 16-color EGA mode with the half-toning method, which can display 76 gray levels for each color. To obtain good photo-realistic images in an efficient way, we have used two light sources, with an intensity ratio of 7:3, which are located in front of the top right and bottom left corners of the screen.     

分子表面的计算机表示

提出了一种用于生成分子光滑表面的新算法.该算法从分布在一个包含整个分子表面的椭球上的三角网络开始,逐步收缩网络直到所有的三角形最佳贴近分子表面.所使用的收缩包络椭球的技术只要稍加修改就可用于蛋白质空腔的表示.     

Computer-aided construction of nucleic acid restriction maps using defined vectors

A new algorithm is described that will rapidly produce restrictionmaps of cloned DNA fragments. Information concerning the vectoris stored as a data file and used in constructing probable maps.As the program is based upon a permutation analysis it has twoprimary uses. First, preliminary restriction maps can be createdfrom fragment length data as a starting point for further analysis.Second, existing maps can be confirmed as being highly probable,and other probable maps examined to ensure certain combinationshave not been overlooked. Although primarily designed for linearvectors, the program can be used to calculate circular maps. Received on June 5, 1985; accepted on September 27, 1985     

Precise particle tracking against a complicated background: polynomial fitting with Gaussian weight

We present a new particle tracking software algorithm designed to accurately track the motion of low-contrast particles against a background with large variations in light levels. The method is based on a polynomial fit of the intensity around each feature point, weighted by a Gaussian function of the distance from the centre, and is especially suitable for tracking endogeneous particles in the cell, imaged with bright field, phase contrast or fluorescence optical microscopy. Furthermore, the method can simultaneously track particles of all different sizes, and allows significant freedom in their shape. The algorithm is evaluated using the quantitative measures of accuracy and precision of previous authors, using simulated images at variable signal-to-noise ratios. To these we add new tests: the error due to a non-uniform background, and the error due to two particles approaching each other. Finally the tracking of particles in real cell images is demonstrated. The method is made freely available for non-commercial use as a software package with a graphical user-interface, which can be run within the Matlab programming environment.     

SMILE-shaded molecular imaging on low-cost equipment

The SMILE program runs under MS-DOS on IBM PC AT-compatible computers equipped with the SM640 or the PG640 Matrox graphic board. The program allows real-time three-dimensional (3D) animation and modeling of several isolated molecules that can be built from scratch, manipulated interactively and compared by superimposition.SMILE enables users to compute atomic partial charges, molecular surface area, molecular volume, electrostatic and nonbonded potential energies. PLUTO, ORTEP, and MMP2 input files are set up automatically. The program also provides simple access to crystal packing by real-time animation of the unit cell contents, interactive inspection of the relevant stereochemical parameters and fragment manipulation within the unit cell. SMILE animates stereo views and produces beautiful shaded 3D images (8 colors, 32 shades each) of molecules in many different styles—stick, ball-and-stick, CPK (space filling), and transparent CPK with backbone.     

Ground monitoring the light–shadow windows of a tree canopy to yield canopy light interception and morphological traits

Monitoring the light–shadow windows of a tree via a grid system on the ground was performed on sunny summer days at high spatial resolution using a custom‐built, inexpensive scanner. The measurements were taken with two goals: (1) to quickly and remotely quantify the overall, short‐wave solar radiation (300–1100 nm) intercepted by the tree canopy, and (2) to yield such crown geometric traits as shape, size and the number of theoretical canopy leaf layers (leaf layer index, LLI) in relation to the section orthogonal to sunbeam direction (sun window). The ground readings at each measurement over the day were used to project a digitized shadow image. Image processing was applied and the intercepted radiation was calculated as the difference from the corresponding incoming radiation above the canopy. Tree‐crown size and shape were profiled via computer imaging by analysing the different shadow images acquired at the various solar positions during the day. It is notable that these combined images yielded the crown features without having to parameterize such canopy characteristics as foliage extension and spatial distribution.     

gerud1.0: a computer program for the reconstruction of parental genotypes from progeny arrays using multilocus DNA data

We have no standard computer algorithm for the reconstruction of parental genotypes from the data generated by molecular studies of progeny arrays. Here I present a computer program that uses the multilocus genotypes of parents and offspring to reconstruct the genotypes of unknown parents contributing gametes to a progeny array for which one parent is known a priori. A second program performs simulations to assess the reliability of the algorithm under various scenarios. These programs will aid scientists engaged in parentage analyses, particularly in species with large clutches.     

AGScan: a pluggable microarray image quantification software based on the ImageJ library

Many different programs are available to analyze microarray images. Most programs are commercial packages, some are free. In the latter group only few propose automatic grid alignment and batch mode. More often than not a program implements only one quantification algorithm. AGScan is an open source program that works on all major platforms. It is based on the ImageJ library [Rasband (1997-2006)] and offers a plug-in extension system to add new functions to manipulate images, align grid and quantify spots. It is appropriate for daily laboratory use and also as a framework for new algorithms. AVAILABILITY: The program is freely distributed under X11 Licence. The install instructions can be found in the user manual. The software can be downloaded from http://mulcyber.toulouse.inra.fr/projects/agscan/. The questions and plug-ins can be sent to the contact listed below.     

Automated image analysis for array hybridization experiments.

MOTIVATION: Image analysis is a major part of data evaluation for array hybridization experiments in molecular biology. The program presented here is designed to analyze automatically images from hybridization experiments with various arrangements: different kinds of probes (oligonucleotides or complex probes), different supports (nylon filters or glass slides), different labeling of probes (radioactively or fluorescently). The program is currently applied to oligonucleotide fingerprinting projects and complex hybridizations. The only precondition for the use of the program is that the targets are arrayed in a grid, which can be approximately transformed to an orthogonal equidistant grid by a projective mapping. RESULTS: We demonstrate that our program can cope with the following problems: global distortion of the grid, missing of grid nodes, local deviation of the spot from its specified grid position. This is checked by different quality measures. The image analysis of oligonucleotide fingerprint experiments on an entire genetic library is used, in clustering procedures, to group related clones together. The results show that the program yields automatically generated high quality input data for follow up analysis such as clustering procedures. AVAILABILITY: The executable files will be available upon request for academics.     

Image analysis in fluorescence microscopy: bacterial dynamics as a case study

Fluorescence microscopy is the primary tool for studying complex processes inside individual living cells. Technical advances in both molecular biology and microscopy have made it possible to image cells from many genetic and environmental backgrounds. These images contain a vast amount of information, which is often hidden behind various sources of noise, convoluted with other information and stochastic in nature. Accessing the desired biological information therefore requires new tools of computational image analysis and modeling. Here, we review some of the recent advances in computational analysis of images obtained from fluorescence microscopy, focusing on bacterial systems. We emphasize techniques that are readily available to molecular and cell biologists but also point out examples where problem-specific image analyses are necessary. Thus, image analysis is not only a toolkit to be applied to new images but also an integral part of the design and implementation of a microscopy experiment.     

Selection of cell‐type specific antibodies on tissue‐sections using phage display

With the advent of modern technologies enabling single cell analysis, it has become clear that small sub‐populations of cells or even single cells can drive the phenotypic appearance of tissue, both diseased and normal. Nucleic acid based technologies allowing single cell analysis has been faster to mature, while technologies aimed at analysing the proteome at a single cell level is still lacking behind, especially technologies which allow single cell analysis in tissue. Introducing methods, that allows such analysis, will pave the way for discovering new biomarkers with more clinical relevance, as these may be unique for microenvironments only present in tissue and will avoid artifacts introduced by in vitro studies. Here, we introduce a technology enabling biomarker identification on small sub‐populations of cells within a tissue section. Phage antibody libraries are applied to the tissue sections, followed by washing to remove non‐bound phage particles. To eliminate phage antibodies binding to antigens ubiquitously expressed and retrieve phage antibodies binding specifically to antigens expressed by the sub‐population of cells, the area of interest is protected by a ‘shadow stick’. The phage antibodies on the remaining areas on the slide are exposed to UV light, which introduces cross‐links in the phage genome, thus rendering them non‐replicable. In this work we applied the technology, guided by CD31 expressing endothelial cells, to isolate recombinant antibodies specifically binding biomarkers expressed either by the cell or in the microenvironment surrounding the endothelial cell.     

Flexibility in problem solving and tool use of kea and New Caledonian crows in a multi access box paradigm

Parrots and corvids show outstanding innovative and flexible behaviour. In particular, kea and New Caledonian crows are often singled out as being exceptionally sophisticated in physical cognition, so that comparing them in this respect is particularly interesting. However, comparing cognitive mechanisms among species requires consideration of non-cognitive behavioural propensities and morphological characteristics evolved from different ancestry and adapted to fit different ecological niches. We used a novel experimental approach based on a Multi-Access-Box (MAB). Food could be extracted by four different techniques, two of them involving tools. Initially all four options were available to the subjects. Once they reached criterion for mastering one option, this task was blocked, until the subjects became proficient in another solution. The exploratory behaviour differed considerably. Only one (of six) kea and one (of five) NCC mastered all four options, including a first report of innovative stick tool use in kea. The crows were more efficient in using the stick tool, the kea the ball tool. The kea were haptically more explorative than the NCC, discovered two or three solutions within the first ten trials (against a mean of 0.75 discoveries by the crows) and switched more quickly to new solutions when the previous one was blocked. Differences in exploration technique, neophobia and object manipulation are likely to explain differential performance across the set of tasks. Our study further underlines the need to use a diversity of tasks when comparing cognitive traits between members of different species. Extension of a similar method to other taxa could help developing a comparative cognition research program.     

Interactive program for visualization and modelling of proteins,nucleic acids and small molecules

The graphics package Insight for the DEC VAX and Evans and Sutherland PS300, created as part of a joint university-industry research project, provides a broad set of capabilities which allow the user to display molecular models in stick figure and surface representation. The Insight program allows the user to model and manipulate proteins, nucleic acids and small molecules. The software accepts coordinate input from several possible sources and provides both a command and menu interface for manipulation of the graphics objects. The command language and program structure make it easy for the biochemist or molecular biologist to use.     

Automated extraction of canopy shadow fraction using unmanned helicopter-based color vegetation indices

The canopy shadow fraction (CSF) is composed of the fractional area covered by shadowed tree crowns and shadowed backgrounds for a given illumination and view geometry. Since the CSF is related to the canopy biological and structural features, an accurate estimation of the CSF is expected for better understanding of the canopy characteristics. This study explores an algorithm for an automated extraction of the CSF using near-surface remote sensing method. The high-spatial resolution true-color images over different forested canopies were acquired using an unmanned helicopter. For each site, the images of the same target canopy from multiple view zenith angles (VZA) were taken at the principal plane. The digital images were processed to extract the CSF using the color vegetation indices (CVI) combined with an image threshold algorithm. The CSF was measured based on visual interpretation of the grayscale images. For an automated extraction of the CSF, different CVI related to CSF were assessed with Otsu threshold algorithm. A new CVI called the blue deficient index (BDI) was proposed as an indicator of the CSF exploiting the canopy spectral properties. The performance of each automated extraction method was evaluated with comparison to measured CSF. Among the methods assessed under the study, the CSF estimated by the BDI with the Otsu algorithm was found to be most closely related to the measured CSF. After a successful extraction of the CSF, the effect of VZA on CSF was analyzed. The substantial variation of the CSF with respect to the VZA in the principal plane was confirmed for a given solar position.     

Molecular chemistry imaging to reveal structural features of various plant feed tissues

Synchrotron Fourier transform infrared (FTIR) microspectroscopy as a rapid, direct, and non-destructive analytical technique can explore molecular chemical features of the micro-structure of biological samples. However, the application of this synchrotron technology to feed science and feed chemistry is extremely rare. This article reviews that with synchrotron FTIR microspectroscopy, the molecular chemistry of various feed tissues could be imaged. These images revealed spatial intensity and distribution of chemical functional groups in various feeds tissues within cellular dimensions. Such information can be used for plant breeding program for selecting superior variety of plant for targeted feed purposes and for prediction of feed quality and nutritive value. The final purpose of this article shows that Synchrotron FTIR microspectroscopy can be used for biological structure study.     

小麦高分子量麦谷蛋白亚基鉴定及其品质效应研究进展

高分子量谷蛋白亚基(HMW-GS,high molecular weight glutenin subunits)是小麦子粒贮藏蛋白的重要组成成分,其组成、搭配、表达水平及含量决定面团弹性和面包加工品质。本文主要介绍了小麦HMW-GS编码基因的克隆、分子特征、分子标记开发及其在小麦育种中的应用,并综述了不同HMW-GS与面粉加工品质之间的关系,以及HMW-GS基因遗传转化、微量配粉和突变体培育等方面的研究进展,分析了目前研究中存在的主要问题,认为通过分子标记辅助选择和转基因技术聚合优质亚基,培育优质面包小麦品种和明确各个HMW-GS基因的品质效应是今后的研究重点。     

Probing f-actin flow by tracking shape fluctuations of radial bundles in lamellipodia of motile cells

We examined the dynamics of radial actin bundles based on time-lapse movies of polarized light images of living neuronal growth cones. Using a highly sensitive computer vision algorithm for tracking, we analyzed the small shape fluctuations of radial actin bundles that otherwise remained stationary in their positions in the growth cone lamellipodium. Using the tracking software, we selected target points on radial bundles and measured both the local bundle orientations and the lateral displacements between consecutive movie frames. We found that the local orientation and the lateral displacement of a target point are correlated. The correlation can be explained using a simple geometric relationship between the lateral travel of tilted actin bundles and the retrograde flow of f-actin structures. Once this relationship has been established, we have turned the table and used the radial bundles as probes to measure the velocity field of f-actin flow. We have generated a detailed map of the complex retrograde flow pattern throughout the lamellipodium. Such two-dimensional flow maps will give new insights into the mechanisms responsible for f-actin-mediated cell motility and growth.