Topological analysis and interactive visualization of biological networks and protein structures

Computational analysis and interactive visualization of biological networks and protein structures are common tasks for gaining insight into biological processes. This protocol describes three workflows based on the NetworkAnalyzer and RINalyzer plug-ins for Cytoscape, a popular software platform for networks. NetworkAnalyzer has become a standard Cytoscape tool for comprehensive network topology analysis. In addition, RINalyzer provides methods for exploring residue interaction networks derived from protein structures. The first workflow uses NetworkAnalyzer to perform a topological analysis of biological networks. The second workflow applies RINalyzer to study protein structure and function and to compute network centrality measures. The third workflow combines NetworkAnalyzer and RINalyzer to compare residue networks. The full protocol can be completed in ～2 h.     

Magnetic stimulation for non-homogeneous biological structures

Background  

Magnetic stimulation has gained relatively wide application in studying nervous system structures. This technology has the advantage of reduced excitation of sensory nerve endings, and hence results in quasi-painless action. It has become clinically accepted modality for brain stimulation. However, theoretical and practical solutions for assessment of induced current distribution need more detailed and accurate consideration.     

A triaxial-measurement shear-test device for soft biological tissues

A novel shear-test device for soft biological tissue, capable of applying simple shear deformations simultaneously in two orthogonal directions while measuring the resulting forces generated in three axes, is described. We validated the device using a synthetic gel, the properties of which were ascertained from independent tensile and rotational shear tests. Material parameters for the gel were fitted using neo-Hookean analytical solutions to the independent test data, and these matched the results from the device. Preliminary results obtained with rat septal myocardium are also presented to demonstrate the feasibility of the apparatus in determining the shear characteristics of living tissue.     

Unconventional modes for STEM imaging of biological structures

In this paper recent developments are discussed in instrumentation and methodology associated with scanning transmission electron microscopes (STEM), which are of great potential interest for solving structural and chemical problems in biological specimens. After describing the main features of the instrument, an attempt is made to define which type of signal acquisition and processing is best suited to obtain a given type of information. Starting with a definition of cross sections of interest, a discussion follows of methods using angular selection, energy selection of the transmitted beam, and several ways of signal mixing. More specific attention is devoted to two main modes of processing signals: ratio contrast, which emphasizes slight changes in scattering factors, rather independent of thickness variations; and elemental mapping, which provides semi-quantitative information on the distribution of low Z elements of great significance in biological specimens. Data relevant to typical biological objects are presented and discussed; they allow for the definition of the capabilities and limitations of these methods. These unconventional imaging modes define a new attitude for improving the efficiency of this modern generation of electron microscopes.     

Mechanical analyses of morphological and topological transformation of liposomes

Liposomes are micro-compartments made of lipid bilayer membranes possessing the characteristics quite similar to those of biological membranes. To form artificial cell-like structures, we made liposomes that contained subunit proteins of cytoskeletons: tubulin or actin. Spherical liposomes were transformed into bipolar or cell-like shapes by mechanical forces generated by the polymerization of encapsulated subunits of microtubules. On the other hand, disk- or dumbbell-shaped liposomes were developed by the polymerization of encapsulated actin. Dynamic processes of morphological transformations of liposomes were visualized by high intensity dark-field light microscopy. Topological changes, such as fusion and division of membrane vesicles, play an essential role in cellular activities. To investigate the mechanism of these processes, we visualized the liposomes undergoing topological transformation in real time. A variety of novel topological transformations were found, including the opening-up of liposomes and the direct expulsion of inner vesicles.     

Modeling of biological tree structures

Biological tree-like structures, such as mammalian tracheobronchial airways, are complicated branching systems. One problem in modeling such systems is the reassignment of the number of segments at a given generation in the model being constructed. A hypothesis is proposed which has successfully been used in modeling mammalian lung airways. Research supported by the National Institute of Environmental Health Sciences through U.S. Department of Energy Contract Number EY-76-C-04-1013.     

ROC analysis: applications to the classification of biological sequences and 3D structures

ROC ('receiver operator characteristics') analysis is a visual as well as numerical method used for assessing the performance of classification algorithms, such as those used for predicting structures and functions from sequence data. This review summarizes the fundamental concepts of ROC analysis and the interpretation of results using examples of sequence and structure comparison. We overview the available programs and provide evaluation guidelines for genomic/proteomic data, with particular regard to applications to large and heterogeneous databases used in bioinformatics.     

Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis

Background

Chaos Game Representation (CGR) is an iterated function that bijectively maps discrete sequences into a continuous domain. As a result, discrete sequences can be object of statistical and topological analyses otherwise reserved to numerical systems. Characteristically, CGR coordinates of substrings sharing an L-long suffix will be located within 2 ^-L distance of each other. In the two decades since its original proposal, CGR has been generalized beyond its original focus on genomic sequences and has been successfully applied to a wide range of problems in bioinformatics. This report explores the possibility that it can be further extended to approach algorithms that rely on discrete, graph-based representations.

Results

The exploratory analysis described here consisted of selecting foundational string problems and refactoring them using CGR-based algorithms. We found that CGR can take the role of suffix trees and emulate sophisticated string algorithms, efficiently solving exact and approximate string matching problems such as finding all palindromes and tandem repeats, and matching with mismatches. The common feature of these problems is that they use longest common extension (LCE) queries as subtasks of their procedures, which we show to have a constant time solution with CGR. Additionally, we show that CGR can be used as a rolling hash function within the Rabin-Karp algorithm.

Conclusions

The analysis of biological sequences relies on algorithmic foundations facing mounting challenges, both logistic (performance) and analytical (lack of unifying mathematical framework). CGR is found to provide the latter and to promise the former: graph-based data structures for sequence analysis operations are entailed by numerical-based data structures produced by CGR maps, providing a unifying analytical framework for a diversity of pattern matching problems.     

Mechanical properties of soft biological tissues

Odd published data concerning the shear mechanical properties of some soft tissues in norm and pathology are reviewed.     

Unique floral structures and iterative evolutionary themes in Asparagales: Insights from a morphological cladistic analysis

A morphological cladistic analysis is presented of the lilioid order Asparagales, with emphasis on relationships within the “lower” asparagoids, in the context of recent new data on both floral and vegetative structures. The analysis retrieved a monophyletic “lower” asparagoid clade, in contrast to molecular analyses, in which lower asparagoids invariably form a grade. However, limited outgroup sampling in the current analysis is a significant factor in this “inside-out” topology; if the morphological tree is rerooted with Orchidaceae as the outgroup, the result is a topology broadly similar to the molecular one. The relatively low resolution of the “lower” asparagoid clade identified here is a result of high homoplasy in several characters, which could be regarded as iterative evolutionary themes within Asparagales, notably (among floral characters) epigyny and zygomorphy. Close relationships between some family pairs were inferred, including Orchidaceae and Hypoxidaceae, Boryaceae and Blandfordiaceae, Asphodelaceae and Hemerocallidaceae, and Iridaceae and Doryanthaceae. The small South African genusPauridia, which differs from other Hypoxidaceae in that it lacks the outer stamen whorl, was placed as sister to Orchidaceae rather than being embedded in Hypoxidaceae as in molecular analyses, because despite some significant similarities with other Hypoxidaceae (e.g., mucilage canals), it shares some characters with Orchidaceae, notably the presence of a gynostemium and pontoperculate pollen.Xanthorrhoea andLanaria were wild-card taxa in the context of this analysis, with characters in common with more than one different group.     

若干种天牛幼虫外部形态结构与危害特性的适应关系

本研究在观察比较隶属于鞘翅目天牛科3亚科16种天牛幼虫的外部形态特征的基础上,从结构与功能的角度,初步总结了天牛幼虫外部形态特征与危害特性的关系。结果表明:天牛亚科幼虫的上颚为圆凿型,沟胫天牛亚科和幽天牛亚科的幼虫上颚则为楔型。上颚圆凿型的天牛幼虫,外露上颚部分占头部面积比例值越小,上颚越发达;上颚楔型的天牛幼虫,外露上颚部分占头部面积比例值越大,上颚越发达。及时将粪屑排出蛀道外的幼虫之前胸背板、背腹部步泡突较发达,具有粗大的瘤突,气门相对面积比例较大;相反,不及时排出粪屑类的幼虫之前胸背板、背腹部泡突不发达,多具细皱纹,气门相对面积比例较小。