Structural distance and evolutionary relationship of networks

Exploring common features and universal qualities shared by a particular class of networks in biological and other domains is one of the important aspects of evolutionary study. In an evolving system, evolutionary mechanism can cause functional changes that forces the system to adapt to new configurations of interaction pattern between the components of that system (e.g. gene duplication and mutation play a vital role for changing the connectivity structure in many biological networks. The evolutionary relation between two systems can be retraced by their structural differences). The eigenvalues of the normalized graph Laplacian not only capture the global properties of a network, but also local structures that are produced by graph evolutions (like motif duplication or joining). The spectrum of this operator carries many qualitative aspects of a graph. Given two networks of different sizes, we propose a method to quantify the topological distance between them based on the contrasting spectrum of normalized graph Laplacian. We find that network architectures are more similar within the same class compared to between classes. We also show that the evolutionary relationships can be retraced by the structural differences using our method. We analyze 43 metabolic networks from different species and mark the prominent separation of three groups: Bacteria, Archaea and Eukarya. This phenomenon is well captured in our findings that support the other cladistic results based on gene content and ribosomal RNA sequences. Our measure to quantify the structural distance between two networks is useful to elucidate evolutionary relationships.     

Novel self-associative and multiphasic nanostructured soft carriers based on amphiphilic hyaluronic acid derivatives

The purpose of the present study was to investigate the physicochemical properties in aqueous media of amphiphilic hyaluronic acid (HA) derivatives obtained by reaction of HA's hydroxyl groups with octenyl succinic anhydride (OSA). The self-associative properties of the resulting octenyl succinic anhydride-modified hyaluronic acid (OSA-HA) derivatives were studied by fluorescence spectroscopy using Nile Red as fluorophore. The morphology, size and surface charge of the OSA-HA assemblies were determined by transmission electron microscopy, dynamic light scattering and by measuring their electrophoretic mobility, respectively. OSA-HA was shown to spontaneously self-associate in aqueous media into negatively charged spherical and multiphasic nanostructures with a hydrodynamic diameter between 170 and 230 nm and to solubilize hydrophobic compounds such as Nile Red. This was a good indication that OSA-HA could be used as building block for the formulation of soft nanocarriers towards the encapsulation and controlled delivery of hydrophobic active ingredients or drugs.     

Affinity-purification coupled to mass spectrometry: basic principles and strategies

Identifying the interactions established by a protein of interest can be a critical step in understanding its function. This is especially true when an unknown protein of interest is demonstrated to physically interact with proteins of known function. While many techniques have been developed to characterize protein-protein interactions, one strategy that has gained considerable momentum over the past decade for identification and quantification of protein-protein interactions, is affinity-purification followed by mass spectrometry (AP-MS). Here, we briefly review the basic principles used in affinity-purification coupled to mass spectrometry, with an emphasis on tools (both biochemical and computational), which enable the discovery and reporting of high quality protein-protein interactions.     

Paired Nanoinjection and Electrophysiology Assay to Screen for Bioactivity of Compounds using the Drosophila melanogaster Giant Fiber System

Screening compounds for in vivo activity can be used as a first step to identify candidates that may be developed into pharmacological agents^1,2. We developed a novel nanoinjection/electrophysiology assay that allows the detection of bioactive modulatory effects of compounds on the function of a neuronal circuit that mediates the escape response in Drosophila melanogaster^3,4. Our in vivo assay, which uses the Drosophila Giant Fiber System (GFS, Figure 1) allows screening of different types of compounds, such as small molecules or peptides, and requires only minimal quantities to elicit an effect. In addition, the Drosophila GFS offers a large variety of potential molecular targets on neurons or muscles. The Giant Fibers (GFs) synapse electrically (Gap Junctions) as well as chemically (cholinergic) onto a Peripheral Synapsing Interneuron (PSI) and the Tergo Trochanteral Muscle neuron (TTMn)⁵. The PSI to DLMn (Dorsal Longitudinal Muscle neuron) connection is dependent on Dα7 nicotinic acetylcholine receptors (nAChRs)⁶. Finally, the neuromuscular junctions (NMJ) of the TTMn and the DLMn with the jump (TTM) and flight muscles (DLM) are glutamatergic^7-12. Here, we demonstrate how to inject nanoliter quantities of a compound, while obtaining electrophysiological intracellular recordings from the Giant Fiber System¹³ and how to monitor the effects of the compound on the function of this circuit. We show specificity of the assay with methyllycaconitine citrate (MLA), a nAChR antagonist, which disrupts the PSI to DLMn connection but not the GF to TTMn connection or the function of the NMJ at the jump or flight muscles.Before beginning this video it is critical that you carefully watch and become familiar with the JoVE video titled "Electrophysiological Recordings from the Giant Fiber Pathway of D. melanogaster " from Augustin et al⁷, as the video presented here is intended as an expansion to this existing technique. Here we use the electrophysiological recordings method and focus in detail only on the addition of the paired nanoinjections and monitoring technique.     

The Absorption and Fluorescence Spectra of the Cyanobacterial Phycobionts of Cryptoendolithic Lichens in the High-Polar Regions of Antarctica

The algologically pure cultures of the green–brown cyanobacterium Chroococcidiopsissp. and three cyanobacteria of the genus Gloeocapsa, the blue–green Gloeocapsa sp.₁, the brown Gloeocapsa sp.₂, and the red–orange Gloeocapsa sp.₃, were isolated from sandstones and rock fissures in the high-polar regions of Antarctica. These cyanobacteria are the most widespread phycobionts of cryptoendolithic lichens in these regions. The comparative analysis of the absorption and the second-derivative absorption spectra of the cyanobacteria revealed considerable differences in the content of chlorophyll a and in the content and composition of carotenoids and phycobiliproteins. In addition to phycocyanin, allophycocyanin, and allophycocyanin B, which were present in all of the cyanobacteria studied, Gloeocapsa sp.₂ also contained phycoerythrocyanin and Gloeocapsa sp.₃ phycoerythrocyanin and C-phycoerythrin (the latter pigment is typical of nitrogen-fixing cyanobacteria). The fluorescence spectra of Gloeocapsa sp.₂ and Gloeocapsa sp.₃ considerably differed from the fluorescence spectra of the other cyanobacteria as well. The data obtained suggest that various zones of the lichens may be dominated either by photoheterotrophic or photoautotrophic cyanobacterial phycobionts, which differ in the content and composition of photosynthetic pigments.     

Structural and mode of action studies on bio-active molecules

The technique of nuclear Overhauser effect difference spectroscopy allows the determination, from¹H nuclear magnetic resonance spectra, of those protons in a structure which are near in space to a selected, irradiated proton. The experiment is extremely powerful in the determination of structure in solution, and is sufficiently precise often to give stereochemical detail. The method was used in determination of the structures of the antibiotics of the teicoplanin complex (members of the vancomycin group), and the principles are briefly illustrated. Additionally, nuclear magnetic resonance pulse sequences can be used to edit¹³C spectra (separate the spectrum into four spectra, containing C, CH, CH₂, and CH₃ carbons), and this technique also aided the structure elucidation of the teicoplanin complex. Finally, it is emphasised that nuclear Overhauser effect difference spectroscopy can be used to determine the molecular details of drug binding sites, and an example is given.     

Chalcones of the root bark of Derris sericea

In addition to two chalcones and one flavanone previously isolated from the root bark of Derris sericea, a third chalcone, derricidin, has been found and its structure determined (III). Cyclization of this, and of the already known derricin (II), to the corresponding flavanones was accomplished. The almost, but not completely, identical fragmentation of such chalcone-flavanone pairs in the mass spectrometer is discussed and interpreted. NMR data, which contribute decisively to structure elucidation, are also presented.     

Linking vein properties to leaf biomechanics across 58 woody species from a subtropical forest

• Leaf venations have elements with relatively lower elasticity than other leaf tissue components, which are thought to contribute to leaf biomechanics. A better mechanistic understanding of relationships between vein traits and leaf mechanical properties is essential for ecologically relevant interpretation of leaf structural variations.
• We investigated 13 major (first to third order) and minor (>third order) vein traits, six leaf mechanical properties and other structural traits across 58 woody species from a subtropical forest to elucidate how vein traits contribute to leaf biomechanics.
• Across species, vein dry mass density (ρ_v), total vein dry mass per leaf area (VMA) and minor vein diameter (VD_min), but not the lower‐order vein density (VLA_1?2), were positively correlated with leaf force to punch (F_p) and force to tear (F_t). Structural equation models showed that ρ_v and VD_min not only contribute to leaf mechanical properties directly (direct pathway), but also had impacts on leaf biomechanics by influencing leaf thickness and leaf dry mass per area (indirect pathway).
• Our study demonstrated that vein dry mass density and minor vein diameter are the key vein properties for leaf biomechanics. We also suggest that the mechanical characteristics of venations are potential factors influencing leaf mechanical resistance, structure and leaf economics spectrum.

     

Species accumulation within land use and tree diameter categories in Burkina Faso,Mali, Niger and Senegal

Although farmers have managed west African parkland savanna systems for 1,000 of years, concerns have been raised about the sustainability of these agro-ecosystems due to human population growth, shortening of fallow periods, droughts, desertification and new orientations towards cash generation away from subsistence farming. We conducted a tree diversity survey in 16 villages from Burkina Faso, Mali, Niger and Senegal, recording total species composition for 300 quadrats (mainly 50 × 20 m²) that were randomly sampled from the main landuse categories of parklands of village fields (VF), bush fields (BF), sylvopastoral zone (SP) and forest reserves (FR). About 110 tree species were encountered, including 100 indigenous species. The results from balanced species accumulation curves (based on randomized subsampling of the same number of quadrats from each village) showed that the accumulated number of species was smallest in VF, largest in FR and almost equal in BF and SP, whereas classical (unbalanced) species accumulation curves yielded different results. Although there was a significant within-village reduction in species richness with increasing diameter class [averaging 8.5–13.1 more species in the smallest (<5 cm) compared to the largest diameter class (>80 cm)] for the different landuse categories, new species were also encountered in larger diameter classes (2.7–7.2 species). The evidence for tree regeneration problems (including problems in FR) suggest that farmer-managed tree regeneration should be further explored and that advances in domestication and marketing of indigenous tree species may be crucial to tree conservation in parkland systems.