PHAMCL biosynthesis systems in Pseudomonas aeruginosa and Pseudomonas putida strains show differences on monomer specificities

The production of PHA from plant oils by Pseudomonas species soil isolated from a sugarcane crop was evaluated. Out of 22 bacterial strains three were able to use efficiently plant oils to grow and to accumulate PHA. Pseudomonas putida and Pseudomonas aeruginosa strains produced PHA presenting differences on monomer composition compatible with variability on monomer specificity of their PHA biosynthesis system. The molar fraction of 3-hydroxydodecanoate detected in the PHA was linearly correlated to the oleic acid supplied. A non-linear relationship between the molar fractions of 3-hydroxy-6-dodecenoate (3HDdΔ₆) detected in PHA and the linoleic acid supplied was observed, compatible with saturation in the biosynthesis system capability to channel intermediate of β-oxidation to PHA synthesis. Although P. putida showed a higher 3HDdΔ₆ yield from linoleic acid when compared to P. aeruginosa, in both species it was less than 10% of the maximum theoretical value. These results contribute to the knowledge about the biosynthesis of PHA with a controlled composition from plant oils allowing in the future establishing the production of these polyesters as tailor-made polymers.     

Towards predicting Ca2+‐binding sites with different coordination numbers in proteins with atomic resolution

Ca²⁺‐binding sites in proteins exhibit a wide range of polygonal geometries that directly relate to an equally‐diverse set of biological functions. Although the highly‐conserved EF‐Hand motif has been studied extensively, non‐EF‐Hand sites exhibit much more structural diversity which has inhibited efforts to determine the precise location of Ca²⁺‐binding sites, especially for sites with few coordinating ligands. Previously, we established an algorithm capable of predicting Ca²⁺‐binding sites using graph theory to identify oxygen clusters comprised of four atoms lying on a sphere of specified radius, the center of which was the predicted calcium position. Here we describe a new algorithm, MUG (MUltiple Geometries), which predicts Ca²⁺‐binding sites in proteins with atomic resolution. After first identifying all the possible oxygen clusters by finding maximal cliques, a calcium center (CC) for each cluster, corresponding to the potential Ca²⁺ position, is located to maximally regularize the structure of the (cluster, CC) pair. The structure is then inspected by geometric filters. An unqualified (cluster, CC) pair is further handled by recursively removing oxygen atoms and relocating the CC until its structure is either qualified or contains fewer than four ligand atoms. Ligand coordination is then determined for qualified structures. This algorithm, which predicts both Ca²⁺ positions and ligand groups, has been shown to successfully predict over 90% of the documented Ca²⁺‐binding sites in three datasets of highly‐diversified protein structures with 0.22 to 0.49 Å accuracy. All multiple‐binding sites (i.e. sites with a single ligand atom associated with multiple calcium ions) were predicted, as were half of the low‐coordination sites (i.e. sites with less than four protein ligand atoms) and 14/16 cofactor‐coordinating sites. Additionally, this algorithm has the flexibility to incorporate surface water molecules and protein cofactors to further improve the prediction for low‐coordination and cofactor‐coordinating Ca²⁺‐binding sites. Proteins 2009. © 2008 Wiley‐Liss, Inc.     

Development of molecularly imprinted polymers for the binding of nitrofurantoin

Novel molecularly imprinted polymers (MIPs) for the recognition of nitrofurantoin (NFT) were prepared by photoinitiated polymerisation in polar solvent using 2,6-bis(methacrylamido) pyridine (BMP) as the functional monomer and carboxyphenyl aminohydantoin (CPAH) as the analogue of the template. The binding constants of the complex between BMP and nitrofurantoin or CPAH in DMSO were determined with 1H NMR titration to be 630 ± 104 and 830 ± 146 M⁻¹, respectively. To study the influence of the functional monomer, two polymer compositions were prepared containing the template, the functional monomer and the crosslinker in the molar ratio 1:1:12 for MIP1 and 1:4:20 for MIP2, respectively. The imprinting factor at saturation concentration of nitrofurantoin, which is the ratio of the amount bound to the MIP and the non-imprinted control polymer (NIP), was determined to be 2.47 for MIP1 and 2.49 for MIP2. The cross reactivity of the imprinted polymers seems to be determined by the ability to form hydrogen bonds to the functional monomer while the shape of the molecule has no real influence.     

Management on the basis of the best scientific data or integration of ecological research within management? Lessons learned from the Northern spotted owl saga on the connection between research and management in conservation biology

The case of the Northern spotted owl (Strix occidentalis caurina) has now become a classic case study in conservation biology, characterized by a harsh social battle but also by the quantity and quality of the research performed. Based on this example, I study the way the research-management interface was organized. The main lessons I have learned were: 1. laws that involve science in management are crucial but should be more precise; 2. scientific ad-hoc groups are useful reviewers of management plans and interpreters of the best scientific data available, even if more transparent scientific argumentation is needed on some points; 3. in such applied cases, even science that has not been strongly integrated with management can produce results that are useful for management; 4. stronger links between science and management appear necessary, but difficult to implement. This last point makes me wonder whether environmental laws should not more frequently target the incorporation of science into the management process itself rather than “only” basing management on the best scientific data available. On a more ecological level, perhaps the habitat issue has been underrated during the last few years compared to other emerging threats such as the invasion of the spotted owl range by barred owls.     

Extrusion of transmitter, water and ions generates forces to close fusion pore

During exocytosis the fusion pore opens rapidly, then dilates gradually, and may subsequently close completely, but what controls its dynamics is not well understood. In this study we focus our attention on forces acting on the pore wall, and which are generated solely by the passage of transmitter, ions and water through the open fusion pore. The transport through the charged cylindrical nano-size pore is simulated using a coupled system of Poisson-Nernst-Planck and Navier-Stokes equations and the forces that act radially on the wall of the fusion pore are then estimated. Four forces are considered: a) inertial force, b) pressure, c) viscotic force, and d) electrostatic force. The inertial and viscotic forces are small, but the electrostatic force and the pressure are typically significant. High vesicular pressure tends to open the fusion pore, but the pressure induced by the transport of charged particles (glutamate, ions), which is predominant when the pore wall charge density is high tends to close the pore. The electrostatic force, which also depends on the charge density on the pore wall, is weakly repulsive before the pore dilates, but becomes attractive and pronounced as the pore dilates. Given that the vesicular concentration of free transmitter can change rapidly due to the release, or owing to the dissociation from the gel matrix, we evaluated how much and how rapidly a change of the vesicular K⁺-glutamate⁻ concentration affects the concentration of glutamate⁻ and ions in the pore and how such changes alter the radial force on the wall of the fusion pore. A step-like rise of the vesicular K⁺-glutamate⁻ concentration leads to a chain of events. Pore concentration (and efflux) of both K⁺ and glutamate⁻ rise reaching their new steady-state values in less than 100 ns. Interestingly within a similar time interval the pore concentration of Na⁺ also rises, whereas that of Cl⁻ diminishes, although their extra-cellular concentration does not change. Finally such changes affect also the water movement. Water efflux changes bi-phasically, first increasing before decreasing to a new, but lower steady-state value. Nevertheless, even under such conditions an overall approximate neutrality of the pore is maintained remarkably well, and the electrostatic, but also inertial, viscotic and pressure forces acting on the pore wall remain constant. In conclusion the extrusion of the vesicular content generates forces, primarily the force due to the electro-kinetically induced pressure and electrostatic force (both influenced by the pore radius and even more by the charge density on the pore wall), which tend to close the fusion pore.     

Conservation of Silk Genes in Trichoptera and Lepidoptera

Larvae of the sister orders Trichoptera and Lepidoptera are characterized by silk secretion from a pair of labial glands. In both orders the silk filament consists of heavy (H)- and light (L)-chain fibroins and in Lepidoptera it also includes a P25 glycoprotein. The L-fibroin and H-fibroin genes of Rhyacophila obliterata and Hydropsyche angustipennis caddisflies have exon/intron structuring (seven exons in L-fibroin and two in H-fibroin) similar to that in their counterparts in Lepidoptera. Fibroin cDNAs are also known in Limnephilus decipiens, representing the third caddisfly suborder. Amino acid sequences of deduced L-fibroin proteins and of the terminal H-fibroin regions are about 50% identical among the three caddisfly species but their similarity to lepidopteran fibroins is <25%. Positions of some residues are conserved, including cysteines that were shown to link the L-fibroin and H-fibroin by a disulfide bridge in Lepidoptera. The long internal part of H-fibroins is composed of short motifs arranged in species-specific repeats. They are extremely uniform in R. obliterata. Motifs (SX)_n, GGX, and GPGXX occur in both Trichoptera and Lepidoptera. The trichopteran H-fibroins further contain charged amphiphilic motifs but lack the strings of alanines or alanine-glycine dipeptides that are typical lepidopteran motifs. On the other hand, sequences composed of a motif similar to ERIVAPTVITR surrounded by the (SX)_4-6 strings and modifications of the GRRGWGRRG motif occur in Trichoptera and not in Lepidoptera.

An extended biphasic model for charged hydrated tissues with application to the intervertebral disc

Finite element models for hydrated soft biological tissue are numerous but often exhibit certain essential deficiencies concerning the reproduction of relevant mechanical and electro-chemical responses. As a matter of fact, singlephasic models can never predict the interstitial fluid flow or related effects like osmosis. Quite a few models have more than one constituent, but are often restricted to the small-strain domain, are not capable of capturing the intrinsic viscoelasticity of the solid skeleton, or do not account for a collagen fibre reinforcement. It is the goal of this contribution to overcome these drawbacks and to present a thermodynamically consistent model, which is formulated in a very general way in order to reproduce the behaviour of almost any charged hydrated tissue. Herein, the Theory of Porous Media (TPM) is applied in combination with polyconvex Ogden-type material laws describing the anisotropic and intrinsically viscoelastic behaviour of the solid matrix on the basis of a generalised Maxwell model. Moreover, other features like the deformation-dependent permeability, the possibility to include inhomogeneities like varying fibre alignment and behaviour, or osmotic effects based on the simplifying assumption of Lanir are also included. Finally, the human intervertebral disc is chosen as a representative for complex soft biological tissue behaviour. In this regard, two numerical examples will be presented with focus on the viscoelastic and osmotic capacity of the model.     

The Design of Silk Fiber Composition in Moths Has Been Conserved for More Than 150 Million Years

The silk of caterpillars is secreted in the labial glands, stored as a gel in their lumen, and converted into a solid filament during spinning. Heavy chain fibroin (H-fibroin), light chain fibroin (L-fibroin), and P25 protein constitute the filament core in a few species that have been analyzed. Identification of these proteins in Yponomeuta evonymella, a moth from a family which diverged from the rest of Lepidoptera about 150 million years ago, reveals that the mode of filament construction is highly conserved. It is proposed that association of the three proteins is suited for long storage of hydrated silk dope and its rapid conversion to filament. Interactions underlying these processes depend on conserved spacing of critical amino acid residues that are dispersed through the L-fibroin and P25 and assembled in the short ends of the H-fibroin molecule. Strength, elasticity, and other physical properties of the filament are determined by simple amino acid motifs arranged in repetitive modules that build up most of the H-fibroin. H-Fibroin synergy with L-fibroin and P25 does not interfere with motif diversification by which the filament acquires new properties. Several types of motifs in complex repeats occur in the silks used for larval cobwebs and pupal cocoons. Restriction of silk use to cocoon construction in some lepidopteran families has been accompanied by simplification of H-fibroin repeats. An extreme deviation of the silk structure occurs in the Saturniidae silkmoths, which possess modified H-fibroin and lack L-fibroin and P25. [Reviewing Editor: Dr. David Pollok]     

A new method to model change in cutaneous blood flow due to mechanical skin irritation part II: parameter identification procedure

Mechanical skin irritation, for example a light scratch with a needle, induces histamine and neuropeptide release on the line of stroke and in the surrounding tissue. Both histamine and neuropeptides are vasodilators. They cause vasodilation by changing the contraction state of the vascular smooth muscles and hence vessel compliance. Smooth muscle contraction state is very difficult to measure in vivo. For that reason we propose in this article an identification procedure to establish an irritation law. The law gives change in vessel compliance as a function of space, time and the intensity of the stroke. We have showed that vessel compliance increases immediately after the stroke not only on the line of stroke, but also in the surrounding tissue. Then, after a short delay, vessel compliance starts decreasing in the surrounding tissue, whereas vessel compliance on the line of stroke keeps increasing. Hence, blood is transported from the surrounding tissue to the line of stroke. In this way, higher blood volume on the line of stroke can be obtained than by only changing vessel compliance locally.     

Nano-channels in the spider fang for the transport of Zn ions to cross-link His-rich proteins pre-deposited in the cuticle matrix

We identify the presence of multiple vascular channels within the spider fang. These channels seem to serve the transport of zinc to the tip of the fang to cross-link the protein matrix by binding to histidine residues. According to amino acid and elemental analysis of fangs extracted shortly after ecdysis, His-rich proteins are deposited before Zn is incorporated into the cuticle. Microscopic and spectroscopic investigations in the electron microscope and synchrotron radiation experiments suggest that Zn ions are transported through these channels in a liable (yet unidentified) form, and then form stable complexes upon His binding. The resulting cross-linking through the Zn–His complexes is conferring hardness to the fang. Our observations of nano-channels serving the Zn-transport within the His-rich protein matrix of the fibre reinforced spider fang may also support recent bio-inspired attempts to design artificial polymeric vascular materials for self-healing and in-situ curing.