Computational analysis of interactomes: Current and future perspectives for bioinformatics approaches to model the host-pathogen interaction space

Bacterial and viral pathogens affect their eukaryotic host partly by interacting with proteins of the host cell. Hence, to investigate infection from a systems' perspective we need to construct complete and accurate host-pathogen protein-protein interaction networks. Because of the paucity of available data and the cost associated with experimental approaches, any construction and analysis of such a network in the near future has to rely on computational predictions. Specifically, this challenge consists of a number of sub-problems: First, prediction of possible pathogen interactors (e.g. effector proteins) is necessary for bacteria and protozoa. Second, the prospective host binding partners have to be determined and finally, the impact on the host cell analyzed. This review gives an overview of current bioinformatics approaches to obtain and understand host-pathogen interactions. As an application example of the methods covered, we predict host-pathogen interactions of Salmonella and discuss the value of these predictions as a prospective for further research.     

Current and future anatomical and functional imaging approaches to pheochromocytoma and paraganglioma

After establishing a biochemical diagnosis, pheochromocytomas and extra-adrenal paragangliomas (PPGLs) can be localized using different anatomical and functional imaging modalities. These include computed tomography, magnetic resonance imaging, single-photon emission computed tomography (SPECT) using 123I-metaiodobenzylguanidine or 111In-DTPA-pentetreotide, and positron emission tomography (PET) using 6-[18F]-fluorodopamine (18F-FDA), 6-[18F]-fluoro-l-3,4-dihydroxyphenylalanine (18F-DOPA), and 2-[18F]-fluoro-2-deoxy-d-glucose. We review the currently available data on the performance of anatomical imaging, SPECT, and PET for the detection of (metastatic) PPGL as well as parasympathetic head and neck paragangliomas. We show that there appears to be no 'gold-standard' imaging technique for all patients with (suspected) PPGL. A tailor-made approach is warranted, guided by clinical, biochemical, and genetic characteristics. In the current era of a growing number of PET tracers, PPGL imaging has moved beyond tumor localization towards functional characterization of tumors.     

Axillar compression syndrome: anatomical and clinical study

In order to evaluate the possibility of compression of axillar artery by medial and lateral fascicle of brachial plexus, authors performed 26 axillar dissections on cadavers. Second part included analysis of 24 selective angiograms of axillar artery of patients with diagnosis of TOS. Third part included the use of modified hyperabduction test for determination of vascular bruit as safe test for diagnosis of axillar compression. Macroscopic changes of axillar artery by compression of medial and lateral fascicle of brachial plexus were present in 11.5%. Specific angiographic horizontal spike-shaped stop of contrast behind the surgical neck of humerus was present in 12.5%. Use of modified hyperabduction test revealed vascular bruit 29.5%. Specific relation of axillar artery and medial and lateral fascicle of brachial plexus revealed another possible etiologic factor in hyperabduction syndrome as a part of TOS. Use of modified hyperabduction test revealed subclinical phase of possible syndrome.     

Electrophoretic approaches to the analysis of complex polysaccharides

Complex polysaccharides, glycosaminoglycans (GAGs), are a class of ubiquitous macromolecules exhibiting a wide range of biological functions. They are widely distributed as sidechains of proteoglycans (PGs) in the extracellular matrix and at cellular level. The recent emergence of enhanced analytical tools for their study has triggered a virtual explosion in the field of glycomics. Analytical electrophoretic separation techniques, including agarose-gel, capillary electrophoresis (HPCE) and fluorophore-assisted carbohydrate electrophoresis (FACE), of GAGs and GAG-derived oligosaccharides have been employed for the structural analysis and quantification of hyaluronic acid (HA), chondroitin sulfate (CS), dermatan sulfate (DS), keratan sulfate (KS), heparan sulfate (HS), heparin (Hep) and acidic bacterial polysaccharides. Furthermore, recent developments in the electrophoretic separation and detection of unsaturated disaccharides and oligosaccharides derived from GAGs by enzymatic or chemical degradation have made it possible to examine alterations of GAGs with respect to their amounts and fine structural features in various pathological conditions, thus becoming applicable for diagnosis. In this paper, the electromigration procedures developed to analyze and characterize complex polysaccharides are reviewed. Moreover, a critical evaluation of the biological relevance of the results obtained by these electrophoresis approaches is presented.     

Virulence signatures: microarray-based approaches to discovery and analysis

Rapid, accurate, and sensitive detection of biothreat agents requires a broad-spectrum assay capable of discriminating between closely related microbial or viral pathogens. Moreover, in cases where a biological agent release has been identified, forensic analysis demands detailed genetic signature data for accurate strain identification and attribution. To date, nucleic acid sequences have provided the most robust and phylogentically illuminating signature information. Nucleic acid signature sequences are not often linked to genomic or extrachromosomal determinants of virulence, a link that would further facilitate discrimination between pathogens and closely related species. Inextricably coupling genetic determinants of virulence with highly informative nucleic acid signatures would provide a robust means of identifying human, livestock, and agricultural pathogens. By means of example, we present here an overview of two general applications of microarray-based methods for: (1) the identification of candidate virulence factors; and (2) the analysis of genetic polymorphisms that are coupled to Bacillus anthracis virulence factors using an accurate, low cost solid-phase mini-sequencing assay. We show that microarray-based analysis of gene expression can identify potential virulence associated genes for use as candidate signature targets, and, further, that microarray-based single nucleotide polymorphism assays provide a robust platform for the detection and identification of signature sequences in a manner independent of the genetic background in which the signature is embedded. We discuss the strategy as a general approach or pipeline for the discovery of virulence-linked nucleic acid signatures for biothreat agents.     

Real-time PCR: A review of approaches to data analysis

The registration of the accumulation of polymerase chain reaction (PCR) products in the course of amplification (real-time PCR) requires specific equipment, i.e., detecting amplifiers capable of recording the level of fluorescence in the reaction tube during amplicon formation. When the time of the reaction is complete, researchers are able to obtain DNA accumulation graphs. This review discusses the most promising algorithms of the analysis of real-time PCR curves and possible errors, caused by the software used or by operators’ mistakes. The data included will assist researchers in understanding the features of a method to obtain more reliable results.     

2 parallel approaches to the analysis of plant cover

Two parallel approaches to the analysis of vegetation based on plant geography are being developed in modern science. In European countries, there is ecologo-morphological classification (EMC), in Russia--comparative floristics (CF). The development of CF in many theoretical aspects is similar to EMC. One of the reason of parallel development is late penetration of EMC ideas into Russia. The objective reason of this phenomenon is extremely low endemism of floras that were traditionally studied by Russian geobotanic schools, viz. steps and forests. The high level of endemism in central European floras (especially in Alps) allows to transform the principles of floristic division to vegetation classification. During last 20 years the Russian deviate of EMC demonstrates deviation with theoretical basement of EMC--conception of typical species, using non-differentiate block of diagnostic species. That does not provide any new content either to syntaxa and coenofloras that exist in European classifications or to the method of partial floras in CF.