Genetic visualization of neurogenesis

Neurons are generated from stem or progenitor cells in discrete areas in the adult brain. The exact temporal and spatial distribution of adult neurogenesis has, however, been difficult to establish because of inherent limitations with the currently used techniques, and there are numerous controversies with regard to whether neurons are generated in specific regions or in response to insults. We describe here the generation of transgenic mice that express conditionally active Cre recombinase under the control of a nestin enhancer element. These mice allow the recombination of reporter alleles specifically in neural stem and progenitor cells and the visualization of their progeny in the adult brain. This offers a simple and efficient way to visualize live adult born neurons without the caveats of currently used techniques.     

Reliability-oriented bioinformatic networks visualization

SUMMARY: We present our protein-protein interaction (PPI) network visualization system RobinViz (reliability-oriented bioinformatic networks visualization). Clustering the PPI network based on gene ontology (GO) annotations or biclustered gene expression data, providing a clustered visualization model based on a central/peripheral duality, computing layouts with algorithms specialized for interaction reliabilities represented as weights, completely automated data acquisition, processing are notable features of the system. AVAILABILITY: RobinViz is a free, open-source software protected under GPL. It is written in C++ and Python, and consists of almost 30 000 lines of code, excluding the employed libraries. Source code, user manual and other Supplementary Material are available for download at http://code.google.com/p/robinviz/.     

Tumor blood vessel visualization

Significant advances have been made in understanding the role of tumor angiogenesis and its influence on tumor progression in cancer. Based on this knowledge, a series of inhibitors of angiogenesis have been developed and evaluated in preclinical and clinical trials. Since detailed information of tumor progression in response to therapy is important to assess the efficacy of anti-tumor treatment in vivo, noninvasive imaging techniques emerge more and more as important tools to monitor alterations in tumor growth and vessel recruitment, as well as metastatic spread over time. So far, remarkable efforts have been made to improve the technical capability of these imaging modalities based on better resolution, as well as to implement multimodal approaches combining molecular with anatomical information. Advanced imaging techniques not only allow the detection and monitoring of tumor development, but also facilitate a broad understanding of the cellular and molecular events that propagate tumor angiogenesis, as well as those occurring in response to therapy. This review provides an overview of different imaging techniques in preclinical settings of oncological research and discusses their potential impact on clinical translation. Imaging modalities will be presented that have been implemented to address key biological issues by exploring tumor angiogenic processes and evaluating antiangiogenic therapy.     

Histochemical visualization of oxidant stress

Free radicals induce oxidative modification in distinct components of the living matter (lipid, proteins, and DNA). For qualitative and quantitative determination of free radical-induced modifications, different, more or less sensitive biochemical methods are available. Because of the high reactivity and short life of free radicals, ongoing oxidative damage is generally analyzed by measurement of secondary products-such as H(2)O(2), oxidized proteins, peroxidized lipids, and their breakdown products, oxidized DNA-or by fluorographic analysis in combination with fluorescent dyes such as dichlorofluorescin (DCFH). In addition, the determination of free radical-related oxidation products is usually carried out in plasma, urine, or, less frequently, in bioptic material. Consequently, biochemical data seldom reflect the effects of free radical insults in situ. The histochemical visualization of selected molecular markers of oxidative damage can often provide more valuable information concerning the in vivo distribution of oxidative processes. This review summarizes the methods currently available for histochemical detection and indirect visualization of free radical-induced alterations in tissues and isolated cells.     

景观可视化及其应用

介绍了景观可视化的概念,回顾了景观可视化的发展历程,然后介绍了景观要素,包括地形、植被、水、人工构件(建筑物、基础设施等)、动物(包括人)、大气和光的可视化表达方法,阐述了景观可视化在景观规划、景观变化、气候变化、城市景观、景观视觉影响评价和森林管理等方面的应用,最后提出了景观可视化的未来发展趋势.     

GandrKB--ontological microarray annotation and visualization

SUMMARY: The Gandr (gene annotation data representation) knowledgebase is an ontological framework for laboratory-specific gene annotation. Gandr uses Protege 2000 for editing, querying and visualizing microarray data and annotations. Genes can be annotated with provided, newly created or imported ontological concepts. Annotated genes can inherit assigned concept properties and can be related to each other. The resulting knowledgebase can be visualized as interactive network of nodes and edges representing genes and their functional relationships. This allows for immediate and associative gene context exploration. Ontological query techniques allow for powerful data access.     

Single-molecule visualization in cell biology

Recent progress in single-molecule detection techniques has allowed us to visualize the dynamic behaviour and reaction kinetics of individual biological molecules inside living cells. Single-molecule visualization provides a direct way to quantify, with a high spatial and temporal resolution, biological events inside cells at the single-molecule level. In this article, we discuss how single-molecule visualization can be used in cell biology.     

Improved tree-ring visualization using autofluorescence

The great diversity of wood anatomical features found in trees worldwide results in a broad variety of growth-ring boundary types that are not always easy to recognize, especially in tropical woods. However, the presence of clearly visible limits between tree rings is essential for any tree-ring studies. Here, we propose the use of autofluorescence of wood in order to enhance tree-ring visualization. The multispectral light emitted from the fluorescence stereomicroscope can be filtered in specific wavelengths to improve the visualization of wood anatomical features. To evaluate the effectiveness of this technique, we compared visualization under natural light, GFP (green fluorescent protein) filter, RFP (red fluorescent protein) filter and UV filter. We tested this technique with a set of 38 tree species with different types of growth-ring boundaries. Although results are species-specific, fluorescence has been shown to improve the visualization of growth-ring boundaries by enhancing the contrast among cell types. It may highlight fibrous zones (e.g. Cavanillesia arborea, Aspidosperma polyneuron), different porosity patterns (e.g. Myracrodruon urundeuva), secretory canals (e.g. Copaifera langsdorffii), and parenchyma bands (e.g. Tipuana tipu). Fluorescence allows the visualization of growth-ring boundaries in species that were previously described as having indistinct growth rings under natural light. For species with clear tree-ring boundaries such as Cedrela fissilis and Hymenaea courbaril, this approach aids the identification of false rings. In addition to the visualization of growth-ring boundaries, autofluorescence may be useful for other qualitative and quantitative analyses of wood anatomy, such as wood identification and automated measurements of anatomical features. Scientists struggling with tree-ring counting and cross-dating due to difficult tree-ring visualization may find fluorescence useful. It may also aid to identify new species suitable for tree-ring studies.     

Ontological visualization of protein-protein interactions

Background  

Cellular processes require the interaction of many proteins across several cellular compartments. Determining the collective network of such interactions is an important aspect of understanding the role and regulation of individual proteins. The Gene Ontology (GO) is used by model organism databases and other bioinformatics resources to provide functional annotation of proteins. The annotation process provides a mechanism to document the binding of one protein with another. We have constructed protein interaction networks for mouse proteins utilizing the information encoded in the GO annotations. The work reported here presents a methodology for integrating and visualizing information on protein-protein interactions.     

Metabolic flux analysis and visualization

One of the ultimate goals of systems biology research is to obtain a comprehensive understanding of the control mechanisms of complex cellular metabolisms. Metabolic Flux Analysis (MFA) is a important method for the quantitative estimation of intracellular metabolic flows through metabolic pathways and the elucidation of cellular physiology. The primary challenge in the use of MFA is that many biological networks are underdetermined systems; it is therefore difficult to narrow down the solution space from the stoichiometric constraints alone. In this tutorial, we present an overview of Flux Balance Analysis (FBA) and (13)C-Metabolic Flux Analysis ((13)C-MFA), both of which are frequently used to solve such underdetermined systems, and we demonstrate FBA and (13)C-MFA using the genome-scale model and the central carbon metabolism model, respectively. Furthermore, because such comprehensive study of intracellular fluxes is inherently complex, we subsequently introduce various pathway mapping and visualization tools to facilitate understanding of these data in the context of the pathways. Specific visualization of MFA results using the BioCyc Omics Viewer and Pathway Projector are shown as illustrative examples.     

GECO--linear visualization for comparative genomics

In order to understand and interpret phylogenetic and functional relationships between multiple prokaryotic species, qualitative and quantitative data must be correlated and displayed. GECO allows linear visualization of multiple genomes using a client/server based approach by dynamically creating .png- or .pdf-formatted images. It is able to display ortholog relations calculated using BLASTCLUST by color coding ortholog representations. Irregularities on the genomic level can be identified by anomalous G/C composition. Thus, this software will enable researchers to detect horizontally transferred genes, pseudogenes and insertions/deletions in related microbial genomes. AVAILABILITY: http://bioinfo.mikrobio.med.uni-giessen.de/geco2/GecoMainServlet     

GPU-powered tools boost molecular visualization

Recent advances in experimental structure determination provide a wealth of structural data on huge macromolecular assemblies such as the ribosome or viral capsids, available in public databases. Further structural models arise from reconstructions using symmetry orders or fitting crystal structures into low-resolution maps obtained by electron-microscopy or small angle X-ray scattering experiments. Visual inspection of these huge structures remains an important way of unravelling some of their secrets. However, such visualization cannot conveniently be carried out using conventional rendering approaches, either due to performance limitations or due to lack of realism. Recent developments, in particular drawing benefit from the capabilities of Graphics Processing Units (GPUs), herald the next generation of molecular visualization solutions addressing these issues. In this article, we present advances in computer science and visualization that help biologists visualize, understand and manipulate large and complex molecular systems, introducing concepts that remain little-known in the bioinformatics field. Furthermore, we compile currently available software and methods enhancing the shape perception of such macromolecular assemblies, for example based on surface simplification or lighting ameliorations.