Automatic lattice determination for two-dimensional crystal images

Electron crystallography determines the structure of membrane proteins and other periodic samples by recording either images or diffraction patterns. Computer processing of recorded images requires the determination of the reciprocal lattice parameters in the Fourier transform of the image. We have developed a set of three programs 2dx_peaksearch, 2dx_findlat and 2dx_getlat, which can determine the reciprocal lattice from a Fourier transformation of a 2D crystal image automatically. 2dx_peaksearch determines a list of Fourier peak coordinates from a processed calculated diffraction pattern. These coordinates are evaluated by 2dx_findlat to determine one or more lattices, using a-priori knowledge of the real-space crystal unit cell dimensions, and the sample tilt geometry. If these are unknown, then the program 2dx_getlat can be used to obtain a guess for the unit cell dimensions. These programs are available as part of the 2dx software package for the image processing of 2D crystal images at http://2dx.org.     

Single particle 3D reconstruction for 2D crystal images of membrane proteins

In cases where ultra-flat cryo-preparations of well-ordered two-dimensional (2D) crystals are available, electron crystallography is a powerful method for the determination of the high-resolution structures of membrane and soluble proteins. However, crystal unbending and Fourier-filtering methods in electron crystallography three-dimensional (3D) image processing are generally limited in their performance for 2D crystals that are badly ordered or non-flat. Here we present a single particle image processing approach, which is implemented as an extension of the 2D crystallographic pipeline realized in the 2dx software package, for the determination of high-resolution 3D structures of membrane proteins. The algorithm presented, addresses the low single-to-noise ratio (SNR) of 2D crystal images by exploiting neighborhood correlation between adjacent proteins in the 2D crystal. Compared with conventional single particle processing for randomly oriented particles, the computational costs are greatly reduced due to the crystal-induced limited search space, which allows a much finer search space compared to classical single particle processing. To reduce the considerable computational costs, our software features a hybrid parallelization scheme for multi-CPU clusters and computer with high-end graphic processing units (GPUs). We successfully apply the new refinement method to the structure of the potassium channel MloK1. The calculated 3D reconstruction shows more structural details and contains less noise than the map obtained by conventional Fourier-filtering based processing of the same 2D crystal images.     

AcrB contamination in 2-D crystallization of membrane proteins: lessons from a sodium channel and a putative monovalent cation/proton antiporter

Contamination with the multidrug transporter AcrB represents a potential pitfall in the structural analysis of recombinant membrane proteins expressed in Escherichia coli, especially when high-throughput approaches are adopted. This can be a particular problem in two-dimensional (2-D) crystallization for electron cryomicroscopy since individual crystals are too small for compositional analysis. Using a broad ‘sparse matrix’ of buffer conditions typically used in 2-D crystallization, we have identified at least eight unique crystal forms of AcrB. Reference to images and projection maps of these different forms can greatly facilitate the early identification of false leads in 2-D crystallization trials of other membrane proteins of interest. We illustrate the usefulness of such data by highlighting two studies of membrane proteins in our laboratories. We show in one case (a bacterial sodium channel, NaChBac) how early crystallization ‘hits’ could be attributed to contaminating AcrB by comparison against our AcrB crystal image database. In a second case, involving a member of the monovalent cation/proton antiporter-1 family (MPSIL0171), a comparison with the observed AcrB crystal forms allowed easy identification of reconstituted AcrB particles, greatly facilitating the eventual purification and crystallization of the correct protein in pure form as ordered helical arrays. Our database of AcrB crystal images will be of general use in assisting future 2-D crystallization studies of other membrane proteins.     

Computer vision-assisted photogrammetry and one-image 3D modeling in marine mammals

Image processing using traditional photogrammetric methods is a labor-intensive process. The collection of photogrammetry images during aerial surveys is expanding rapidly, creating new challenges to analyze images promptly and efficiently, while reducing human error during processing. Computer vision-assisted photogrammetry, a field of artificial intelligence (AI), can automate image processing, greatly enhancing the efficiency of photogrammetry. Here, we present a practical and efficient program capable of automatically extracting the fine-scale photogrammetry of East Asian finless porpoises (Neophocaena asiaeorientalis sunameri). Our results indicated that computer vision-assisted photogrammetry could achieve the same accuracy as traditional photogrammetry, and the results of the comparisons were validated against the direct measurements. Three-dimensional (3D) models using computer vision-assisted photogrammetric morphometrics generated trustworthy body volume estimates. We also explored the one image-based 3D modeling technique, which is less accurate, but still useful when only one image of the animal is available. Although several limitations exist in the current program, improvements could be made to narrow the virtual-reality gap when more images are available for machine learning and training. We recommend this program for analyzing images of marine mammals possessing a similar morphological contour.     

A new H-2.1-PositiveD region allele,D dx,controlling two molecules,H-2Ddx and H-2Ldx

The inbred strains GRS/A and LIS/A carry the haplotypeH-2 ^dx , which had earlier been shown to have theK ^d ,I ^f ,S ^f , andG ^f alleles and a previously unknownD region allele,D ^dx . We show here that theD ^dx allele determines a new private specificity, H-2.63, is H-2.28 negative, and determines at least one public specificity of the H-2.1 family. It is thus a second example (afterD ^k ) of a H-2.1-positive H-2.28-negativeD region allele. Capping experiments show that the D^dx product comprises two molecules: H-2D^dx bearing the private specificity H-2.63, and H-2L^dx, which is H-2.63-negative but reacts with sera against the H-2.1 family of specificities. SDS gel electrophoresis of detergent-solubilized immunoprecipitated D^dx products shows that the H-2L^dx antigen has a molecular weight of approximately 45,000 daltons and is associated with a smaller polypeptide (mol. wt. 12,000).     

A maximum likelihood approach to two-dimensional crystals

Maximum likelihood (ML) processing of transmission electron microscopy images of protein particles can produce reconstructions of superior resolution due to a reduced reference bias. We have investigated a ML processing approach to images centered on the unit cells of two-dimensional (2D) crystal images. The implemented software makes use of the predictive lattice node tracking in the MRC software, which is used to window particle stacks. These are then noise-whitened and subjected to ML processing. Resulting ML maps are translated into amplitudes and phases for further processing within the 2dx software package. Compared with ML processing for randomly oriented single particles, the required computational costs are greatly reduced as the 2D crystals restrict the parameter search space. The software was applied to images of negatively stained or frozen hydrated 2D crystals of different crystal order. We find that the ML algorithm is not free from reference bias, even though its sensitivity to noise correlation is lower than for pure cross-correlation alignment. Compared with crystallographic processing, the newly developed software yields better resolution for 2D crystal images of lower crystal quality, and it performs equally well for well-ordered crystal images.     

Fast processing of microscopic images using object-based extended depth of field

Background

Microscopic analysis requires that foreground objects of interest, e.g. cells, are in focus. In a typical microscopic specimen, the foreground objects may lie on different depths of field necessitating capture of multiple images taken at different focal planes. The extended depth of field (EDoF) technique is a computational method for merging images from different depths of field into a composite image with all foreground objects in focus. Composite images generated by EDoF can be applied in automated image processing and pattern recognition systems. However, current algorithms for EDoF are computationally intensive and impractical, especially for applications such as medical diagnosis where rapid sample turnaround is important. Since foreground objects typically constitute a minor part of an image, the EDoF technique could be made to work much faster if only foreground regions are processed to make the composite image. We propose a novel algorithm called object-based extended depths of field (OEDoF) to address this issue.

Methods

The OEDoF algorithm consists of four major modules: 1) color conversion, 2) object region identification, 3) good contrast pixel identification and 4) detail merging. First, the algorithm employs color conversion to enhance contrast followed by identification of foreground pixels. A composite image is constructed using only these foreground pixels, which dramatically reduces the computational time.

Results

We used 250 images obtained from 45 specimens of confirmed malaria infections to test our proposed algorithm. The resulting composite images with all in-focus objects were produced using the proposed OEDoF algorithm. We measured the performance of OEDoF in terms of image clarity (quality) and processing time. The features of interest selected by the OEDoF algorithm are comparable in quality with equivalent regions in images processed by the state-of-the-art complex wavelet EDoF algorithm; however, OEDoF required four times less processing time.

Conclusions

This work presents a modification of the extended depth of field approach for efficiently enhancing microscopic images. This selective object processing scheme used in OEDoF can significantly reduce the overall processing time while maintaining the clarity of important image features. The empirical results from parasite-infected red cell images revealed that our proposed method efficiently and effectively produced in-focus composite images. With the speed improvement of OEDoF, this proposed algorithm is suitable for processing large numbers of microscope images, e.g., as required for medical diagnosis.

     

Streptavidin crystals as nanostructured supports and image-calibration references for cryo-EM data collection

For cryo-EM structural studies, we seek to image membrane proteins as single particles embedded in proteoliposomes. One technical difficulty has been the low density of liposomes that can be trapped in the approximately 100nm ice layer that spans holes in the perforated carbon support film of EM grids. Inspired by the use of two-dimensional (2D) streptavidin crystals as an affinity surface for biotinylated DNA (Crucifix et al., 2004), we propose to use the crystals to tether liposomes doped with biotinylated lipids. The 2D crystal image also serves as a calibration of the image formation process, providing an absolute conversion from electrostatic potentials in the specimen to the EM image intensity, and serving as a quality control of acquired cryo-EM images. We were able to grow streptavidin crystals covering more than 90% of the holes in an EM grid, and which remained stable even under negative stain. The liposome density in the resulting cryo-EM sample was uniform and high due to the high-affinity binding of biotin to streptavidin. Using computational methods, the 2D crystal background can be removed from images without noticeable effect on image properties.     

Interactive, computer-assisted tracking of speckle trajectories in fluorescence microscopy: application to actin polymerization and membrane fusion

Analysis of particle trajectories in images obtained by fluorescence microscopy reveals biophysical properties such as diffusion coefficient or rates of association and dissociation. Particle tracking and lifetime measurement is often limited by noise, large mobilities, image inhomogeneities, and path crossings. We present Speckle TrackerJ, a tool that addresses some of these challenges using computer-assisted techniques for finding positions and tracking particles in different situations. A dynamic user interface assists in the creation, editing, and refining of particle tracks. The following are results from application of this program: 1), Tracking single molecule diffusion in simulated images. The shape of the diffusing marker on the image changes from speckle to cloud, depending on the relationship of the diffusion coefficient to the camera exposure time. We use these images to illustrate the range of diffusion coefficients that can be measured. 2), We used the program to measure the diffusion coefficient of capping proteins in the lamellipodium. We found values ∼0.5 μm²/s, suggesting capping protein association with protein complexes or the membrane. 3), We demonstrate efficient measuring of appearance and disappearance of EGFP-actin speckles within the lamellipodium of motile cells that indicate actin monomer incorporation into the actin filament network. 4), We marked appearance and disappearance events of fluorescently labeled vesicles to supported lipid bilayers and tracked single lipids from the fused vesicle on the bilayer. This is the first time, to our knowledge, that vesicle fusion has been detected with single molecule sensitivity and the program allowed us to perform a quantitative analysis. 5), By discriminating between undocking and fusion events, dwell times for vesicle fusion after vesicle docking to membranes can be measured.     

膜蛋白晶体的生长及其进展

生物膜中与脂双层结合的蛋白质称为膜蛋白.由于它们具有很大的疏水表面以及既亲水又疏水的两性特点致使其纯化与结晶都十分困难.在膜蛋白晶体生长系统中引入小分子去污剂与小的两性分子获得突破性进展.迄今为止,结晶出来的膜蛋白为数不多.其中只有光合细菌绿色红假单胞菌及球型红假单胞菌的反应中心得到3分辨率的晶体结构与解析.一系列膜蛋白形成二维晶体,可用电子显微镜与像重构技术获得三维结构信息.     

A high-throughput strategy to screen 2D crystallization trials of membrane proteins

Electron microscopy of two-dimensional (2D) crystals has demonstrated potential for structure determination of membrane proteins. Technical limitations in large-scale crystallization screens have, however, prevented a major breakthrough in the routine application of this technology. Dialysis is generally used for detergent removal and reconstitution of the protein into a lipid bilayer, and devices for testing numerous conditions in parallel are not readily available. Furthermore, the small size of resulting 2D crystals requires electron microscopy to evaluate the results and automation of the necessary steps is essential to achieve a reasonable throughput. We have designed a crystallization block, using standard microplate dimensions, by which 96 unique samples can be dialyzed simultaneously against 96 different buffers and have demonstrated that the rate of detergent dialysis is comparable to those obtained with conventional dialysis devices. A liquid-handling robot was employed to set up 2D crystallization trials with the membrane proteins CopA from Archaeoglobus fulgidus and light-harvesting complex II (LH2) from Rhodobacter sphaeroides. For CopA, 1 week of dialysis yielded tubular crystals and, for LH2, large and well-ordered vesicular 2D crystals were obtained after 24 h, illustrating the feasibility of this approach. Combined with a high-throughput procedure for preparation of EM-grids and automation of the subsequent negative staining step, the crystallization block offers a novel pipeline that promises to speed up large-scale screening of 2D crystallization and to increase the likelihood of producing well-ordered crystals for analysis by electron crystallography.     

Projection maps of three members of the KdgM outer membrane protein family

We present the projection structures of the three outer membrane porins KdgM and KdgN from Erwinia chrysanthemi and NanC from Escherichia coli, based on 2D electron crystallography. A wide screening of 2D crystallization conditions yielded tubular crystals of a suitable size and quality to perform high-resolution electron microscopy. Data processing of untilted samples allowed us to separate the information of the two crystalline layers and resulted in projection maps to a resolution of up to 7 Å. All three proteins exhibit a similar putative β-barrel structure and the three crystal forms have the same symmetry. However, there are differences in the packing arrangements of the monomers as well as the densities of the projections. To interpret these projections, secondary structure prediction was performed using β-barrel specific prediction algorithms. The predicted transmembrane β-barrels have a high similarity in the arrangement of the putative β-strands and the loops, but do not match those of OmpG, a related protein porin whose structure was solved.     

Erratum to: Proteome Analysis of <Emphasis Type="Italic">Aspergillus fumigatus</Emphasis> Total Membrane Proteins Identifies Proteins Associated with the Glycoconjugates and Cell Wall Biosynthesis Using 2D LC-MS/MS

We attempted to identify membrane proteins associated with the glycoconjugates and cell wall biosynthesis in the total membrane preparations of Aspergillus fumigatus. The total membrane preparations were first run on 1D gels, and then the stained gels were cut and submitted to in-gel digestion followed by 2D LC-MS/MS and database search. A total of 530 proteins were identified with at least two peptides detected with MS/MS spectra. Seventeen integral membrane proteins were involved in N-, O-glycosylation or GPI anchor biosynthesis. Nine membrane proteins were involved in cell wall biosynthesis. Eight proteins were identified as enzymes involved in sphingolipid synthesis. In addition, the proteins involved in cell wall and ergosterol biosynthesis can potentially be used as antifungal drug targets. Our method, for the first time, clearly provided a global view of the membrane proteins associated with glycoconjugates and cell wall biosynthesis in the total membrane proteome of A. fumigatus.     

Preprocessing of 2-Dimensional Gel Electrophoresis Images Applied to Proteomic Analysis: A Review

Various methods and specialized software programs are available for processing twodimensional gel electrophoresis(2-DGE)images.However,due to the anomalies present in these images,a reliable,automated,and highly reproducible system for 2-DGE image analysis has still not been achieved.The most common anomalies found in 2-DGE images include vertical and horizontal streaking,fuzzy spots,and background noise,which greatly complicate computational analysis.In this paper,we review the preprocessing techniques applied to 2-DGE images for noise reduction,intensity normalization,and background correction.We also present a quantitative comparison of non-linear?ltering techniques applied to synthetic gel images,through analyzing the performance of the?lters under speci?c conditions.Synthetic proteins were modeled into a two-dimensional Gaussian distribution with adjustable parameters for changing the size,intensity,and degradation.Three types of noise were added to the images:Gaussian,Rayleigh,and exponential,with signal-to-noise ratios(SNRs)ranging 8–20 decibels(d B).We compared the performanceof wavelet,contourlet,total variation(TV),and wavelet-total variation(WTTV)techniques using parameters SNR and spot ef?ciency.In terms of spot ef?ciency,contourlet and TV were more sensitive to noise than wavelet and WTTV.Wavelet worked the best for images with SNR ranging 10–20 d B,whereas WTTV performed better with high noise levels.Wavelet also presented the best performance with any level of Gaussian noise and low levels(20–14 d B)of Rayleigh and exponential noise in terms of SNR.Finally,the performance of the non-linear?ltering techniques was evaluated using a real 2-DGE image with previously identi?ed proteins marked.Wavelet achieved the best detection rate for the real image.     

Structural analysis of theridiid spider's testicular cyst using 3D reconstruction rendering

A three dimensional reconstruction technique was used for the analysis of a theridiid spider's (Achaearanea tepidariorum) testicular cyst. Although microscopic techniques have greatly improved, most of the information gathered is still based on two‐dimensional images. Particularly in spiders, it is very difficult to count the exact number of sperm in a single cyst, since their spermatogenetic processes takes place within the spherical cysts through the flagellar coiling process. Since morphological features of spider sperm provide detailed information on the whole spermatogenetic processes, we analyzed the exact number of germ cells per cyst in A. tepidariorum through a three‐dimensional image reconstruction technique. For image processing, serially sectioned histological images were scanned using a light microscope and 3D rendering images were reconstructed from these sections. Based on the three dimensional image analysis of the testicular cyst, the number of secondary spermatocytes per cyst was calculated to be 32 (2⁵). Therefore the total number of sperm produced from a single cyst can be calculated as 64 (2⁶), which indicates that a single spermatogonium undergoes four mitotic divisions and an additional two meiotic divisions to produce mature spermatozoa.     

Reconstruction of low-resolution molecular structures from simulated atomic force microscopy images

BackgroundAtomic Force Microscopy (AFM) is an experimental technique to study structure-function relationship of biomolecules. AFM provides images of biomolecules at nanometer resolution. High-speed AFM experiments produce a series of images following dynamics of biomolecules. To further understand biomolecular functions, information on three-dimensional (3D) structures is beneficial.MethodWe aim to recover 3D information from an AFM image by computational modeling. The AFM image includes only low-resolution representation of a molecule; therefore we represent the structures by a coarse grained model (Gaussian mixture model). Using Monte-Carlo sampling, candidate models are generated to increase similarity between AFM images simulated from the models and target AFM image.ResultsThe algorithm was tested on two proteins to model their conformational transitions. Using a simulated AFM image as reference, the algorithm can produce a low-resolution 3D model of the target molecule. Effect of molecular orientations captured in AFM images on the 3D modeling performance was also examined and it is shown that similar accuracy can be obtained for many orientations.ConclusionsThe proposed algorithm can generate 3D low-resolution protein models, from which conformational transitions observed in AFM images can be interpreted in more detail.General significanceHigh-speed AFM experiments allow us to directly observe biomolecules in action, which provides insights on biomolecular function through dynamics. However, as only partial structural information can be obtained from AFM data, this new AFM based hybrid modeling method would be useful to retrieve 3D information of the entire biomolecule.     

Automated Confocal Laser Scanning Microscopy and Semiautomated Image Processing for Analysis of Biofilms

The purpose of this study was to develop and apply a quantitative optical method suitable for routine measurements of biofilm structures under in situ conditions. A computer program was designed to perform automated investigations of biofilms by using image acquisition and image analysis techniques. To obtain a representative profile of a growing biofilm, a nondestructive procedure was created to study and quantify undisturbed microbial populations within the physical environment of a glass flow cell. Key components of the computer-controlled processing described in this paper are the on-line collection of confocal two-dimensional (2D) cross-sectional images from a preset 3D domain of interest followed by the off-line analysis of these 2D images. With the quantitative extraction of information contained in each image, a three-dimensional reconstruction of the principal biological events can be achieved. The program is convenient to handle and was generated to determine biovolumes and thus facilitate the examination of dynamic processes within biofilms. In the present study, Pseudomonas fluorescens or a green fluorescent protein-expressing Escherichia coli strain, EC12, was inoculated into glass flow cells and the respective monoculture biofilms were analyzed in three dimensions. In this paper we describe a method for the routine measurements of biofilms by using automated image acquisition and semiautomated image analysis.