Interactive processing and visualization of image data for biomedical and life science applications

Background

Applications in biomedical science and life science produce large data sets using increasingly powerful imaging devices and computer simulations. It is becoming increasingly difficult for scientists to explore and analyze these data using traditional tools. Interactive data processing and visualization tools can support scientists to overcome these limitations.

Results

We show that new data processing tools and visualization systems can be used successfully in biomedical and life science applications. We present an adaptive high-resolution display system suitable for biomedical image data, algorithms for analyzing and visualization protein surfaces and retinal optical coherence tomography data, and visualization tools for 3D gene expression data.

Conclusion

We demonstrated that interactive processing and visualization methods and systems can support scientists in a variety of biomedical and life science application areas concerned with massive data analysis.

     

Nachweis geringer Mengen gewebsfixierten Silbers

Summary The visualization of very small amounts of tissue-bounded metallic silver is important in histochemistry. It is possible to show traces of silver by the method of physical developing which is known from photochemistry (precipitation of silver at the so called silver nuclei by catalysis). This method is also useful for evidence of tissue-bounded silver.     

DNATagger, colors for codons

DNATagger is a web-based tool for coloring and editing DNA, RNA and protein sequences and alignments. It is dedicated to the visualization of protein coding sequences and also protein sequence alignments to facilitate the comprehension of evolutionary processes in sequence analysis. The distinctive feature of DNATagger is the use of codons as informative units for coloring DNA and RNA sequences. The codons are colored according to their corresponding amino acids. It is the first program that colors codons in DNA sequences without being affected by "out-of-frame" gaps of alignments. It can handle single gaps and gaps inside the triplets. The program also provides the possibility to edit the alignments and change color patterns and translation tables. DNATagger is a JavaScript application, following the W3C guidelines, designed to work on standards-compliant web browsers. It therefore requires no installation and is platform independent. The web-based DNATagger is available as free and open source software at http://www.inf.ufrgs.br/~dmbasso/dnatagger/.     

Some introductory comments on silver staining

Silver staining has become a versatile method for the visualization of specific cell structures and products. The similarity of the impregnation "nuclei" of reduced silver staining to the silver "specks" or "nuclei" of the latent image in photography is noted. "Physical" development (reduction of ionic silver in solution) in silver staining as compared to "chemical" development (reduction of ionic silver remaining in a silver halide crystal) in photographic procedures is briefly discussed.     

Alcian blue staining of proteoglycans in polyacrylamide gels using the "critical electrolyte concentration" approach

A method is described here for Alcian blue staining of proteoglycans in polyacrylamide gels; this is illustrated using extracts obtained from bovine corneal stroma. Other available methods for visualization of proteoglycans can produce nonspecific staining and frequently a high background in the gel; with a "critical electrolyte concentration" approach, specific staining against a clear background can be obtained.     

Interactive visual exploration of overlapping similar structures for three-dimensional microscope images

Background

Recent advances in microscopy enable the acquisition of large numbers of tomographic images from living tissues. Three-dimensional microscope images are often displayed with volume rendering by adjusting the transfer functions. However, because the emissions from fluorescent materials and the optical properties based on point spread functions affect the imaging results, the intensity value can differ locally, even in the same structure. Further, images obtained from brain tissues contain a variety of neural structures such as dendrites and axons with complex crossings and overlapping linear structures. In these cases, the transfer functions previously used fail to optimize image generation, making it difficult to explore the connectivity of these tissues.

Results

This paper proposes an interactive visual exploration method by which the transfer functions are modified locally and interactively based on multidimensional features in the images. A direct editing interface is also provided to specify both the target region and structures with characteristic features, where all manual operations can be performed on the rendered image. This method is demonstrated using two-photon microscope images acquired from living mice, and is shown to be an effective method for interactive visual exploration of overlapping similar structures.

Conclusions

An interactive visualization method was introduced for local improvement of visualization by volume rendering in two-photon microscope images containing regions in which linear nerve structures crisscross in a complex manner. The proposed method is characterized by the localized multidimensional transfer function and interface where the parameters can be determined by the user to suit their particular visualization requirements.     

ggtreeExtra: Compact Visualization of Richly Annotated Phylogenetic Data

We present the ggtreeExtra package for visualizing heterogeneous data with a phylogenetic tree in a circular or rectangular layout (https://www.bioconductor.org/packages/ggtreeExtra). The package supports more data types and visualization methods than other tools. It supports using the grammar of graphics syntax to present data on a tree with richly annotated layers and allows evolutionary statistics inferred by commonly used software to be integrated and visualized with external data. GgtreeExtra is a universal tool for tree data visualization. It extends the applications of the phylogenetic tree in different disciplines by making more domain-specific data to be available to visualize and interpret in the evolutionary context.     

Visualization of freeze-dried and shadowed myosin molecules immobilized on electron microscopic films

The mica replication technique first described by Hall [5] has produced myosin molecules which were heterogeneous in appearance in terms of shadowing, decoration, contrast and background. Therefore, an alternative technique for the visualization of myosin molecules was developed: Myosin molecules are sprayed directly onto glow discharged or silicium-monoxide coated carbon filmed grids, omitting glycerol. After washing several times with distilled water, rapid freezing, and freeze-drying, the immobilized myosin molecules are visualized by shadow-casting at low temperature and at varying angles. After backing with carbon the "in situ" shadowed molecules are observed in the electron microscope. This technique has several advantages over the standard method in that it yields more reproducible results. It is potentially useful for investigating interactions of myosin binding proteins with myosin and for visualizing unshadowed myosin in the STEM.     

An improved immunofluorescence staining method for chloroplast proteins

Key message

An improved immunofluorescence staining method significantly facilitates the visualization of the subcellular localization of interested proteins in chloroplasts.

Abstract

As an important technical approach, immunofluorescence staining is widely used in the subcellular localization study of interested proteins. During the study of the functions of chloroplast division proteins, immunofluorescence staining was frequently adopted. Previously, a method has been developed to study the localization of a chloroplast division protein, FtsZ. However, it is laborious and time-consuming. In this study, we report a modified immunofluorescence staining method, in which protoplasts were isolated from leaf tissues, and then fixed for immunofluorescence staining. The time of the experiment was significantly reduced to several hours. Furthermore, we used correction pen in the fixation procedure and a new way to coat the slide, which greatly saved the cost of the experiment. With the chloroplast division protein ARC6 as an example, we can get a good fluorescence signal. Moreover, the localization of ARC6 in two chloroplast division mutants, arc3 and arc5, and three other plant species, such as cabbage, radish and pea, was also successfully analyzed with our new method. Overall, the immunofluorescence staining method we reported here is very practical, and it significantly facilitates the visualization of the subcellular localization of interested proteins in plant cells.

     

Coomassie blue-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for direct visualization of polypeptides during electrophoresis

A method for the direct visualization of Coomassie blue-stained polypeptide bands during electrophoresis with subsequent elution of polypeptides and removal of sodium dodecyl sulfate (SDS) and Coomassie blue is described. Primarily it is intended as a means for easy and--because there is no protein fixation step--nearly quantitative recovery of separated polypeptides for amino acid sequencing. It may also be used to obtain rapid information about the protein patterns during a run. Together with our new high resolution SDS-polyacrylamide gel electrophoresis system for small proteins and polypeptides (H. Sch?gger and G. Von Jagow (1987) Anal. Biochem. 166, 368-379) the method described allows the preparative separation of protein fragments as even protein fragments between 1 and 3.5 kDa are easily detected.     

Needle Aspiration Biopsy of Localized Pulmonary Lesions

Needle aspiration biopsy of localized pulmonary lesions is a direct, safe, relatively inexpensive method of diagnosis which is applicable for both in-patients and out-patients. It should be performed under direct visualization with image amplifier guidance. Proper application of this method can greatly increase diagnostic yield, diminish the diagnostic interval and expense and minimize the risks involved.     

FitDockApp：基于模板的分子对接PyMOL插件图形化计算软件

目的 分子对接在预测分子之间的结合模式和亲和力方面起着至关重要的作用,是计算结构生物学和计算机辅助药物设计研究的重要方法。本研究团队近期开发了一款基于模板的新型对接方法FitDock,当存在近似的蛋白质配体模板时,它在准确性和速度方面都超过了业界常用的分子对接方法。为了增强FitDock方法的可用性,使其在分子模拟领域得到更广泛的应用,很有必要发展图像化的软件工具。方法 基于Python图像化编程,本文开发了FitDockApp,这是分子可视化软件PyMOL的插件软件。结果 FitDockApp能够通过操作窗口界面,实现基于模板的分子对接和配体结构比对,实时显示预测三维结构,并提供将对接文件上传到实验室服务器获取最优模板的便利。此外,FitDockApp还具备批量对接功能。结论 FitDockApp通过用户友好的界面简化了对接过程,并提供丰富的功能,帮助研究人员获得精确的对接结果。FitDockApp是一款免费软件,兼容Windows和Linux系统,可在http://cao.labshare.cn/fitdock/下载。     

The chemical ionization mass spectrometric analysis of phenylthiohydantoin and 2-anilino-5-thiazolinone amino acids obtained from the Edman degradation of proteins and peptides

Using the ability of ammonia to form complexes with several compounds, we have developed a method for visualization and fixation of urease (EC 3.5.1.5) activity in polyacrylamide gels. In this method lead acetate was used alone or in combination with a pH-sensitive indicator to detect the enzyme activity. Results indicated a fairly linear relationship between the urease concentration (from 0.6 to 3.0 IU) and the amount of lead precipitate formed. Further, this method appears to be more sensitive than staining with pH indicator alone. It can also be effectively used to detect the enzyme activity in crude protein extracts. In addition, lead acetate-stained gels can be stored either wet or dry indefinitely with no visual loss in the activity profiles.     

Identification of proteins according to biological activity following separation by two-dimensional isoelectric focusing/sodium dodecyl sulfate gel electrophoresis: analysis of human exocrine pancreatic proteins

A novel procedure is described whereby proteins can be identified according to their biological activity after their separation in two dimensions using isoelectric focusing and polyacrylamide gel electrophoresis in sodium dodecyl sulfate (G. Scheele, 1975, J. Biol. Chem., 250, 5375–5385). This procedure includes an optimal staining method for the visualization of two-dimensional gel spots, which avoids the use of chemical fixatives, and a one-step method for elution and renaturation of proteins. Fifteen out of the twenty discrete proteins separated from human pancreatic juice by the two-dimensional gel method were successfully identified by this procedure.     

Cytochemical staining of a yeast polyphosphate fraction,localized outside the plasma membrane

Summary Primary aldehyde fixation in the presence of Ca²⁺ and Mg²⁺ followed by alkaline Pb²⁺ staining leads to electron microscopical visualization of lead precipitates in the yeastKluyveromyces marxianus. These lead precipitates are found in vacuoles, cytoplasm, and on the outside of the plasma membrane in the periplasmic and inner cell wall regions.X-ray microanalysis shows that the precipitates contain high amounts of Pb and P. The amount of precipitated material appeared to correlate with the cellular polyphosphate content. When Ca²⁺ and Mg²⁺ are omitted from the primary fixative no peripheral Pb/P deposits are observed. In a subsequent washing step a small amount of long chain polyphosphate is liberated. It is concluded that this method leads to visualization of cellular polyphosphate, including a fraction localized outside the plasma membrane ofKluyveromyces marxianus.     

A detection of allelic variants at microsatellite markers by using capillary and traditional electrophoresis

Microsatellite alleles are detected by PCR (polymerase chain reaction) that provides a manifold increase in the number of copies (amplification) of a given DNA fragment. The fragment visualization can be reached by two different methods. These are fragment analysis by capillary electrophoresis in denaturing gel and fragment separation in non-denaturing gel with subsequent gel staining. The first method is more accurate and automated, but expensive. The second method is much cheaper but less convenient. It requires manual processing and is presumably less accurate. In this study, we present the results of comparison of the allele typing at nine microsatellite loci using these two methods for one of the species of Pacific salmon, sockeye salmon Oncorhynchus nerka Walbaum. In most cases, both methods give identical fragment sizes or with a constant difference if the alleles are relatively small (not larger than 200–220 bp).