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.     

Double pot and double compartment: Integrating two approaches to study nutrient uptake by arbuscular mycorrhizal fungi

Plant and Soil - The double compartment technique has been commonly used in studies on nutrient uptake by mycorrhizas whereas the double pot technique has been used to assess the nutritional stress...     

Technical note: Forearm pronation efficiency analysis in skeletal remains

This work presents an original methodology for analyzing forearm‐pronation efficiency from skeletal remains and its variation with regard to changes in the elbow position. The methodology is based on a biomechanical model that defines rotational efficiency as a mathematical function expressing a geometrical relationship between the origin and insertion of the pronator teres. The methodology uses humeral distal epiphysis photography, from which the geometrical parameters for the efficiency calculus can be obtained. Rotational efficiency is analyzed in a human specimen and in a living nonhuman hominoid (Symphalangus syndactylus) for a full elbow extension (180°) and an intermediate elbow position (90°). In both specimens, the results show that this rotational‐efficiency parameter varies throughout the entire rotational range and show a dependency on the elbow joint position. The rotational efficiency of the siamang's pronator teres is less affected by flexion of the forearm than that of the human. The fact that forearm‐pronation efficiency can be inferred, even quantified, allows us to interpret more precisely the functional and evolutionary significance of upper‐limb skeletal design in extant and fossil primate taxa. Am J Phys Anthropol 2009. © 2009 Wiley‐Liss, Inc.     

Landscape approaches to the analysis of aquatic ecosystems

1. In the mid-1970s, Hynes (1975) wrote eloquently about the complex interactions between aquatic and terrestrial systems. Central theories in stream ecology developed thereafter have dealt with the longitudinal flow of energy, materials and organisms in streams, and, with the exception of the flood pulse concept (Junk, Bayley & Sparks, 1989), have largely ignored areas outside the riparian zone. The structure of the upland and activities occurring there play a more important part than previously recognized in regulating community structure and ecosystem processes in streams.
2. These new perspectives are made possible by developments in hierarchy theory, patch dynamics, and the refinement of tools used to quantify spatial and temporal heterogeneity.
3. Geographical information systems (GIS), image processing technology and spatial statistical techniques allow quantitative assessment of lateral, longitudinal and vertical components of the landscape that interact at several spatial and temporal scales to influence streams. When GIS is used in concert with geostatistics, multivariate statistics, or landscape models, complex relationships can be elucidated and predicted.
4. To a certain extent, the tools discussed above have only automated functions that were previously performed manually. This suite of tools has improved the ability of aquatic ecologists to examine relationships and test theories over larger, more heterogeneous regions than were previously possible.
5. At the local, state and federal level, management and regulatory frameworks are currently being re-evaluated to incorporate this new perspective in resource management and policy decision making.
6. We will discuss current and future trends in technologies and tools used for aquatic ecosystem research, and the use of techniques as they are applied in these regional assessments are also discussed.     

Molecular approaches to the analysis of nitrate assimilation

Abstract. The application of molecular approaches such as mutant analysis and recombinant DNA technology, in conjunction with immunology, are set to revolutionize our understanding of the nitrate assimilation pathway. Mutant analysis has already led to the identification of genetic loci encoding a functional nitrate reduction step and is expected to lead ultimately to the identification of genes encoding nitrate uptake and nitrite reduction. Of particular significance would be identification of genes whose products contribute to regulatory networks controlling nitrogen metabolism. Recombinant DNA techniques are particularly powerful and have already allowed the molecular cloning of the genes encoding the apoprotein of nitrate reductase and nitrite reductase. These successes allow for the first lime the possibility to study directly the role of environmental factors such as type of nitrogen source (NO₃⁻ or NH₄⁺) available to the plant, light, temperature water potential and CO₂ and O₂ tensions on nitrate assimilation gene expression and its regulation at the molecular level. This is an important advance since our current understanding of the regulation of nitrate assimilation is based largely on changes of activity of the component steps. The availability of mutants, cloned genes, and gene transfer systems will permit attempts to manipulate the nitrate assimilation pathway.     

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.