EnteriX 2003: Visualization tools for genome alignments of Enterobacteriaceae

We describe EnteriX, a suite of three web-based visualization tools for graphically portraying alignment information from comparisons among several fixed and user-supplied sequences from related enterobacterial species, anchored on a reference genome (http://bio.cse.psu.edu/). The first visualization, Enteric, displays stacked pairwise alignments between a reference genome and each of the related bacteria, represented schematically as PIPs (Percent Identity Plots). Encoded in the views are large-scale genomic rearrangement events and functional landmarks. The second visualization, Menteric, computes and displays 1 Kb views of nucleotide-level multiple alignments of the sequences, together with annotations of genes, regulatory sites and conserved regions. The third, a Java-based tool named Maj, displays alignment information in two formats, corresponding roughly to the Enteric and Menteric views, and adds zoom-in capabilities. The uses of such tools are diverse, from examining the multiple sequence alignment to infer conserved sites with potential regulatory roles, to scrutinizing the commonalities and differences between the genomes for pathogenicity or phylogenetic studies. The EnteriX suite currently includes >15 enterobacterial genomes, generates views centered on four different anchor genomes and provides support for including user sequences in the alignments.     

Using views of Systems Biology Cloud: application for model building

A large and growing network (“cloud”) of interlinked terms and records of items of Systems Biology knowledge is available from the web. These items include pathways, reactions, substances, literature references, organisms, and anatomy, all described in different data sets. Here, we discuss how the knowledge from the cloud can be molded into representations (views) useful for data visualization and modeling. We discuss methods to create and use various views relevant for visualization, modeling, and model annotations, while hiding irrelevant details without unacceptable loss or distortion. We show that views are compatible with understanding substances and processes as sets of microscopic compounds and events respectively, which allows the representation of specializations and generalizations as subsets and supersets respectively. We explain how these methods can be implemented based on the bridging ontology Systems Biological Pathway Exchange (SBPAX) in the Systems Biology Linker (SyBiL) we have developed.     

MetaSee: An Interactive and Extendable Visualization Toolbox for Metagenomic Sample Analysis and Comparison

The NGS (next generation sequencing)-based metagenomic data analysis is becoming the mainstream for the study of microbial communities. Faced with a large amount of data in metagenomic research, effective data visualization is important for scientists to effectively explore, interpret and manipulate such rich information. The visualization of the metagenomic data, especially multi-sample data, is one of the most critical challenges. The different data sample sources, sequencing approaches and heterogeneous data formats make robust and seamless data visualization difficult. Moreover, researchers have different focuses on metagenomic studies: taxonomical or functional, sample-centric or genome-centric, single sample or multiple samples, etc. However, current efforts in metagenomic data visualization cannot fulfill all of these needs, and it is extremely hard to organize all of these visualization effects in a systematic manner. An extendable, interactive visualization tool would be the method of choice to fulfill all of these visualization needs. In this paper, we have present MetaSee, an extendable toolbox that facilitates the interactive visualization of metagenomic samples of interests. The main components of MetaSee include: (I) a core visualization engine that is composed of different views for comparison of multiple samples: Global view, Phylogenetic view, Sample view and Taxa view, as well as link-out for more in-depth analysis; (II) front-end user interface with real metagenomic models that connect to the above core visualization engine and (III) open-source portal for the development of plug-ins for MetaSee. This integrative visualization tool not only provides the visualization effects, but also enables researchers to perform in-depth analysis of the metagenomic samples of interests. Moreover, its open-source portal allows for the design of plug-ins for MetaSee, which would facilitate the development of any additional visualization effects.     

Immunoelectron microscopic localization of glutamyl-/ prolyl-tRNA synthetase within the eukaryotic multisynthetase complex

A high molecular mass complex of aminoacyl-tRNA synthetases is readily isolated from a variety of eukaryotes. Although its composition is well characterized, knowledge of its structure and organization is still quite limited. This study uses antibodies directed against prolyl-tRNA synthetase for immunoelectron microscopic localization of the bifunctional glutamyl-/prolyl-tRNA synthetase. This is the first visualization of a specific site within the multisynthetase complex. Images of immunocomplexes are presented in the characteristic views of negatively stained multisynthetase complex from rabbit reticulocytes. As described in terms of a three domain working model of the structure, in "front" views of the particle and "intermediate" views, the primary antibody binding site is near the intersection between the "base" and one "arm." In "side" views, where the particle is rotated about its long axis, the binding site is near the midpoint. "Top" and "bottom" views, which appear as square projections, are also consistent with the central location of the binding site. These data place the glutamyl-/prolyl-tRNA synthetase polypeptide in a defined area of the particle, which encompasses portions of two domains, yet is consistent with the previous structural model.     

Population-ethnic group specific genome variation allele frequency data: a querying and visualization journey

National/ethnic mutation databases aim to document the genetic heterogeneity in various populations and ethnic groups worldwide. We have previously reported the development and upgrade of FINDbase (www.findbase.org), a database recording causative mutations and pharmacogenomic marker allele frequencies in various populations around the globe. Although this database has recently been upgraded, we continuously try to enhance its functionality by providing more advanced visualization tools that would further assist effective data querying and comparisons. We are currently experimenting in various visualization techniques on the existing FINDbase causative mutation data collection aiming to provide a dynamic research tool for the worldwide scientific community. We have developed an interactive web-based application for population-based mutation data retrieval. It supports sophisticated data exploration allowing users to apply advanced filtering criteria upon a set of multiple views of the underlying data collection and enables browsing the relationships between individual datasets in a novel and meaningful way.     

Imaging of all three coronary arteries by transthoracic echocardiography. an illustrated guide

Background

Improvements in ultrasound technology has enabled direct, transthoracic visualization of long portions of coronary arteries : the left anterior descending (LAD), circumflex (Cx) and right coronary artery (RCA). Transthoracic measurements of coronary flow velocity were proved to be highly reproducible and correlated with invasive measurements. While clinical applications of transthoracic echocardiography (TTE) of principal coronary arteries are still very limited they will likely grow. The echocardiographers may therefore be interested to know the ultrasonic views, technique of examination and be aware where to look for coronary arteries and how to optimize the images.

Methods

A step-by-step approach to direct, transthoracic visualization of the LAD, Cx and RCA is presented. The technique of examination is discussed, correlations with basic coronary angiography views and heart anatomy are shown and extensively illustrated with photographs and movie-pictures. Hints concerning optimization of ultrasound images are presented and artifacts of imaging are discussed.

Conclusions

Direct, transthoracic examination of the LAD, Cx and RCA in adults is possible and may become a useful adjunct to other methods of coronary artery examination but studies are needed to establish its role.     

MAVisto: a tool for the exploration of network motifs

SUMMARY: MAVisto is a tool for the exploration of motifs in biological networks. It provides a flexible motif search algorithm and different views for the analysis and visualization of network motifs. These views help to explore interesting motifs: the frequency of motif occurrences can be compared with randomized networks, a list of motifs along with information about structure and number of occurrences depending on the reuse of network elements shows potentially interesting motifs, a motif fingerprint reveals the overall distribution of motifs of a given size and the distribution of a particular motif in the network can be visualized using an advanced layout algorithm. AVAILABILITY: MAVisto is platform independent and available free of charge as a Java webstart application at http://mavisto.ipk-gatersleben.de/ CONTACT: schwoebb@ipk-gatersleben.de SUPPLEMENTARY INFORMATION: Can be found at http://mavisto.ipk-gatersleben.de/     

Characteristic views of prokaryotic 50S ribosomal subunits

Summary Multivariate statistical analysis and classification techniques are powerful tools in sorting noisy electron micrographs of single particles according to their principal features, enabling one to form average images with an enhanced signal-to-noise ratio and a better reproducible resolution. We apply this methodology here to determining the characteristic views of the large (50S) ribosomal subunits from the eubacteriumEscherichia coli and the archaebacteriaMethanococcus vannielii, Sulfolobus solfataricus, andHalobacterium marismortui. Average images were obtained of the subunit in the common crown and kidney projections, but views of the particle in orientations intermediate between these two extremes were also elucidated for all species. These averages show reproducible detail of up to 2.0 nm resolution, thus enabling the visualization and interspecies comparison of many structural features as a first step toward comparing the actual three-dimensional structures. Our results disprove evolutionary lineages recently postulated on the basis of electron microscopical images of ribosomal subunits.     

Organization of eukaryotic chromosomes: From Kol’tsov’s studies up to present day

N.K. Kol’tsov ideas and views on the organization of eukaryotic chromosomes, including the notion of a giant hereditary molecule (genoneme) and its structural functional organization, are considered. Different approaches to chromosome studies are discussed, ranging from the examination of a chromosome as a stained cell organelle and the visualization of individual chromosomes in a living cell to the identification of topological domains of human and murine chromosomes using 3C and 5C technologies. The prospects of studies of chromosome organization using up-to-date methods of cytology, molecular biology, and bioinformatics are discussed.     

Drawing Rooted Phylogenetic Networks

The evolutionary history of a collection of species is usually represented by a phylogenetic tree. Sometimes, phylogenetic networks are used as a means of representing reticulate evolution or of showing uncertainty and incompatibilities in evolutionary datasets. This is often done using unrooted phylogenetic networks such as split networks, due in part, to the availability of software (SplitsTree) for their computation and visualization. In this paper we discuss the problem of drawing rooted phylogenetic networks as cladograms or phylograms in a number of different views that are commonly used for rooted trees. Implementations of the algorithms are available in new releases of the Dendroscope and SplitsTree programs.     

IDR knowledge base for primary immunodeficiencies

Background

Structural information about epitopes, particularly the three-dimensional (3D) structures of antigens in complex with immune receptors, presents a valuable source of data for immunology. This information is available in the Protein Data Bank (PDB) and provided in curated form by the Immune Epitope Database and Analysis Resource (IEDB). With continued growth in these data and the importance in understanding molecular level interactions of immunological interest there is a need for new specialized molecular visualization and analysis tools.

Results

The EpitopeViewer is a platform-independent Java application for the visualization of the three-dimensional structure and sequence of epitopes and analyses of their interactions with antigen-specific receptors of the immune system (antibodies, T cell receptors and MHC molecules). The viewer renders both 3D views and two-dimensional plots of intermolecular interactions between the antigen and receptor(s) by reading curated data from the IEDB and/or calculated on-the-fly from atom coordinates from the PDB. The 3D views and associated interactions can be saved for future use and publication. The EpitopeViewer can be accessed from the IEDB Web site http://www.immuneepitope.org through the quick link 'Browse Records by 3D Structure.'

Conclusion

The EpitopeViewer is designed and been tested for use by immunologists with little or no training in molecular graphics. The EpitopeViewer can be launched from most popular Web browsers without user intervention. A Java Runtime Environment (RJE) 1.4.2 or higher is required.     

Development and validation of a graphic method for spatial interpretation and evaluation of biplanar coronary angiograms]

Visual evaluation and measurement of the lesion geometry is impaired by the foreshortening of the radiographically displayed target coronary segment. For this reason, we developed and validated a simple graphic procedure that facilitates the spatial interpretation and allows an objectifiable assessment of the view of the target coronary segment. The method computes a spatial axis of the coronary segment imaged in two planes and determines its inclination in the radiation path of each projection view. A triangle made up of the axis of the imaged segment, the unforeshortened axis of the imaged segment and the foreshortening height is displayed in each projection plane. The shape of the triangle indicates the degree of foreshortening while its position in the angiogram indicates the orientation of the spatial axis relative to the observer. The method was validated by comparing calculated and true foreshortening in the radiographic views of a centimetre grid obtained in the usual angiographic projections. The method has an accuracy and precision of 0.05 +/- 0.62%. It is applied clinically to evaluate biplane segmental visualization during coronary interventions and to select valid segmental views for measurements during quantitative biplane coronary angiography. This application may considerably facilitate the interpretation and assessment of biplane angiograms.     

HapScope: a software system for automated and visual analysis of functionally annotated haplotypes

We have developed a software analysis package, HapScope, which includes a comprehensive analysis pipeline and a sophisticated visualization tool for analyzing functionally annotated haplotypes. The HapScope analysis pipeline supports: (i) computational haplotype construction with an expectation-maximization or Bayesian statistical algorithm; (ii) SNP classification by protein coding change, homology to model organisms or putative regulatory regions; and (iii) minimum SNP subset selection by either a Brute Force Algorithm or a Greedy Partition Algorithm. The HapScope viewer displays genomic structure with haplotype information in an integrated environment, providing eight alternative views for assessing genetic and functional correlation. It has a user-friendly interface for: (i) haplotype block visualization; (ii) SNP subset selection; (iii) haplotype consolidation with subset SNP markers; (iv) incorporation of both experimentally determined haplotypes and computational results; and (v) data export for additional analysis. Comparison of haplotypes constructed by the statistical algorithms with those determined experimentally shows variation in haplotype prediction accuracies in genomic regions with different levels of nucleotide diversity. We have applied HapScope in analyzing haplotypes for candidate genes and genomic regions with extensive SNP and genotype data. We envision that the systematic approach of integrating functional genomic analysis with population haplotypes, supported by HapScope, will greatly facilitate current genetic disease research.     

Processing of natural language queries to a relational database

MOTIVATION: A new method is developed to query a relational database in natural language (NL). RESULTS: The method, based on a semantic approach, interprets grammatical and lexical units of a natural language into concepts of subject domain, which are given in a conceptual scheme. The conceptual scheme is mapped formally onto the logical scheme. We applied the method to query the FlyEx database in natural language. FlyEx contains information on the expression of segmentation genes in Drosophila melanogaster. The method allows formulation of queries in various natural languages simultaneously, and is adaptive to changes in the knowledge domain and user's views. It provides optimal transformation of queries from natural language to SQL, as well as visualization of information as a hyperscheme. The method does not require specification of all possible language constructions as well as a standard grammar accuracy in formulation of NL queries.     

Subunit structure of junctional feet in triads of skeletal muscle: a freeze-drying, rotary-shadowing study

Isolated heavy sarcoplasmic reticulum vesicles retain junctional specializations (feet) on their outer surface. We have obtained en face three-dimensional views of the feet by shadowing and replicating the surfaces of freeze-dried isolated vesicles. Feet are clearly visible as large structures located on raised platforms. New details of foot structure include a four subunit structure and the fact that adjacent feet do not abut directly corner to corner but are offset by half a subunit. Feet aligned within rows were observed to be rotated at a slight angle off the long axis of the row creating a center-to-center spacing (32.5 nm) slightly less than the average diagonal of the feet (35.3 nm). Comparison with previous information from thin sections and freeze-fracture showed that this approach to the study of membranes faithfully preserves structure and allows better visualization of surface details than either thin-sectioning or negative-staining.     

Freeze-fracture electron microscopy

The freeze-fracture technique consists of physically breaking apart (fracturing) a frozen biological sample; structural detail exposed by the fracture plane is then visualized by vacuum-deposition of platinum-carbon to make a replica for examination in the transmission electron microscope. The four key steps in making a freeze-fracture replica are (i) rapid freezing, (ii) fracturing, (iii) replication and (iv) replica cleaning. In routine protocols, a pretreatment step is carried out before freezing, typically comprising fixation in glutaraldehyde followed by cryoprotection with glycerol. An optional etching step, involving vacuum sublimation of ice, may be carried out after fracturing. Freeze fracture is unique among electron microscopic techniques in providing planar views of the internal organization of membranes. Deep etching of ultrarapidly frozen samples permits visualization of the surface structure of cells and their components. Images provided by freeze fracture and related techniques have profoundly shaped our understanding of the functional morphology of the cell.     

Interactive three-dimensional visualization and contextual analysis of protein interaction networks

To understand the biology of the interactome, the covisualization of protein interactions and other protein-related data is required. In this study, we have adapted a 3-D network visualization platform, GEOMI, to allow the coanalysis of protein-protein interaction networks with proteomic parameters such as protein localization, abundance, physicochemical parameters, post-translational modifications, and gene ontology classification. Working with Saccharomyces cerevisiae data, we show that rich and interactive visualizations, constructed from multidimensional orthogonal data, provide insights on the complexity of the interactome and its role in biological processes and the architecture of the cell. We present the first organelle-specific interaction networks, that provide subinteractomes of high biological interest. We further present some of the first views of the interactome built from a new combination of yeast two-hybrid data and stable protein complexes, which are likely to approximate the true workings of stable and transient aspects of the interactome. The GEOMI tool and all interactome data are freely available by contacting the authors.     

Blood vasculature of the lymph node in the dog: anatomical evidence for participation of extrahilar arterial vessels in the blood supply of the cortex.

The organization of the arterial vessels of dog lymph nodes (LN) was studied using methods of visualization of the vasculature by systemic injection of different tracers (colloidal carbon, Micropaque resin and methylmethacrylate) followed by observation of the samples by light microscopy (after clearing of the thick sections of LN) or scanning electron microscopy (corrosion casts). LN from all of the three groups of nodes studied (tracheobronchial, paratracheal and popliteal) showed an extensive network of arterial vessels encircling the capsule of the organ. We found that branches of these capsular arteries penetrated deeply into the cortical domain of LN. The capsule-originating vessels appeared to have a significant participation in the blood supply of the LN parenchyma at the cortical domains of the organs. Our findings are in contrast with current views on the angiology of the LN that consider that virtually all of the arterial capillaries of the LN parenchyma come from hilar arteries. We propose, therefore, that important segments of the LN cortex receive their blood supply from capsular arteries rather than from hilar vessels.     

Development of an Automated Imaging Pipeline for the Analysis of the Zebrafish Larval Kidney

The analysis of kidney malformation caused by environmental influences during nephrogenesis or by hereditary nephropathies requires animal models allowing the in vivo observation of developmental processes. The zebrafish has emerged as a useful model system for the analysis of vertebrate organ development and function, and it is suitable for the identification of organotoxic or disease-modulating compounds on a larger scale. However, to fully exploit its potential in high content screening applications, dedicated protocols are required allowing the consistent visualization of inner organs such as the embryonic kidney. To this end, we developed a high content screening compatible pipeline for the automated imaging of standardized views of the developing pronephros in zebrafish larvae. Using a custom designed tool, cavities were generated in agarose coated microtiter plates allowing for accurate positioning and orientation of zebrafish larvae. This enabled the subsequent automated acquisition of stable and consistent dorsal views of pronephric kidneys. The established pipeline was applied in a pilot screen for the analysis of the impact of potentially nephrotoxic drugs on zebrafish pronephros development in the Tg(wt1b:EGFP) transgenic line in which the developing pronephros is highlighted by GFP expression. The consistent image data that was acquired allowed for quantification of gross morphological pronephric phenotypes, revealing concentration dependent effects of several compounds on nephrogenesis. In addition, applicability of the imaging pipeline was further confirmed in a morpholino based model for cilia-associated human genetic disorders associated with different intraflagellar transport genes. The developed tools and pipeline can be used to study various aspects in zebrafish kidney research, and can be readily adapted for the analysis of other organ systems.