The effect of initial spacing and thinning on wood quality and graded sawn recovery of mature Caribbean pine grown in Queensland.

A mature Caribbean pine (Pinus caribaea var. hondurensis) silviculture experiment provided initial square spacing treatments of 1.8 m2, 2.4 m2, 3.0 m2 and 3.6 m2 (equal to 3088, 1737, 1111 and 772 stems/ha) that were thinned at age 10 years to 600, 400 and 200 stems/ha, retaining an unthinned control for each initial spacing. The trial was destructively sampled at age of 28 years and discs taken along 8 various stem heights were analysed for variation in basic density and SilviScan wood properties. In addition, the logs from ten stocking × thinning treatments were processed in a sawing study. Results indicate thinning effects were generally more pronounced than initial spacing effects. Fast growing trees produced wood with significantly higher average wood densities and higher average stiffness values. Detailed SilviScan densitometry results obtained radially and at various stem heights enabled construction of tree maps for wood properties, providing insights into the variation in juvenile to mature wood proportion across the initial and post-thinning stocking treatments studied. Dried dressed recovery was strongly related to tree size, and log value decreased consistently from butt to top logs across all treatments. The estimated value per hectare was highest in unthinned plots due to values being multiplied by high stem numbers per hectare. However, a complete economic analysis considering all cost structures is required to investigate the optimal silviculture to maximise economic returns to growers and processors. Improved understanding of the relationship between initial spacing, post-thinning stocking and wood and end-product quality should help to customize future forest management strategies required to produce better quality wood and wood products.

Prediction of protein-protein interactions in dengue virus coat proteins guided by low resolution cryoEM structures

Background: Dengue virus along with the other members of the flaviviridae family has reemerged as deadly human pathogens. Understanding the mechanistic details of these infections can be highly rewarding in developing effective antivirals. During maturation of the virus inside the host cell, the coat proteins E and M undergo conformational changes, altering the morphology of the viral coat. However, due to low resolution nature of the available 3-D structures of viral assemblies, the atomic details of these changes are still elusive. Results: In the present analysis, starting from C alpha positions of low resolution cryo electron microscopic structures the residue level details of protein-protein interaction interfaces of dengue virus coat proteins have been predicted. By comparing the preexisting structures of virus in different phases of life cycle, the changes taking place in these predicted protein-protein interaction interfaces were followed as a function of maturation process of the virus. Besides changing the current notion about the presence of only homodimers in the mature viral coat, the present analysis indicated presence of a proline-rich motif at the protein-protein interaction interface of the coat protein. Investigating the conservation status of these seemingly functionally crucial residues across other members of flaviviridae family enabled dissecting common mechanisms used for infections by these viruses. Conclusions: Thus, using computational approach the present analysis has provided better insights into the preexisting low resolution structures of virus assemblies, the findings of which can be made use of in designing effective antivirals against these deadly human pathogens.

Network approach for capturing ligand-induced subtle global changes in protein structures

Ligand-induced conformational changes in proteins are of immense functional relevance. It is a major challenge to elucidate the network of amino acids that are responsible for the percolation of ligand-induced conformational changes to distal regions in the protein from a global perspective. Functionally important subtle conformational changes (at the level of side-chain noncovalent interactions) upon ligand binding or as a result of environmental variations are also elusive in conventional studies such as those using root-mean-square deviations (r.m.s.d.s). In this article, the network representation of protein structures and their analyses provides an efficient tool to capture these variations (both drastic and subtle) in atomistic detail in a global milieu. A generalized graph theoretical metric, using network parameters such as cliques and/or communities, is used to determine similarities or differences between structures in a rigorous manner. The ligand-induced global rewiring in the protein structures is also quantified in terms of network parameters. Thus, a judicious use of graph theory in the context of protein structures can provide meaningful insights into global structural reorganizations upon perturbation and can also be helpful for rigorous structural comparison. Data sets for the present study include high-resolution crystal structures of serine proteases from the S1A family and are probed to quantify the ligand-induced subtle structural variations.

Synthesis and Characterization of Carbon Nanotube-Polymer Multilayer Structures

We develop lightweight, multilayer materials composed of alternating layers of poly dimethyl siloxane (PDMS) polymer and vertically aligned carbon nanotube (CNT) arrays, and characterize their mechanical response in compression. The CNT arrays used In the assembly are synthesized with graded mechanical properties along their thickness, and their use enables the creation of multilayer structures with low density (0.12-0.28 g/cm(3)). We test the mechanical response of structures composed of different numbers of CNT layers partially embedded in PDMS polymer, under quasi-static and dynamic loading. The resulting materials exhibit a hierarchical, fibrous structure with unique mechanical properties: They can sustain large compressive deformations (up to similar to 0.8 strain) with a nearly complete recovery and present strain localization in selected sections of the materials. Energy absorption, as determined by the hysteresis observed In stress-strain curves, is found to be at least 3 orders of magnitude larger than that of natural and synthetic cellular materials of comparable density. Conductive bucky paper Is Included within the polymer interlayers. This allows the measurement of resistance variation as a function of applied stress, showing strong correlation with the observed strain localization In compression.

Graded IR Filters: Distinguishing Between Single and Multipoint NO2 center dot center dot center dot I Halogen Bonded Supramolecular Synthons (P, Q, and R Synthons)

The NO2 center dot center dot center dot I supramolecular synthon is a halogen bonded recognition pattern that is present in the crystal structures of many compounds that contain these functional groups. These synthons have been previously distinguished as P, Q, and R types using topological and geometrical criteria. A five step IR spectroscopic sequence is proposed here to distinguish between these synthon types in solid samples. Sets of known compounds that contain the P, Q, and R synthons are first taken to develop IR spectroscopic identifiers for them. The identifiers are then used to create graded IR filters that sieve the synthons. These filters contain signatures of the individual NO2 center dot center dot center dot I synthons and may be applied to distinguish between P, Q, and R synthon varieties. They are also useful to identify synthons that are of a borderline character, synthons in disordered structures wherein the crystal structure in itself is not sufficient to distinguish synthon types, and in the identification of the NO2 center dot center dot center dot I synthons in compounds with unknown crystal structures. This study establishes clear differences for the three different geometries P, Q, and Rand in the chemical differences in the intermolecular interactions contained in the synthons. Our IR method can be conveniently employed when single crystals are not readily available also in high throughput analysis. It is possible that such identification may also be adopted as an input for crystal structure prediction analysis of compounds with unknown crystal structures.

Adhesive behavior of two-dimensional power-law graded materials

In this paper, we investigate the adhesive contact between a rigid cylinder of radius R and a graded elastic half-space with a Young's modulus varying with depth according to a power-law, E = E-0(y/c(0))(k) (0 < k < 1), while the Poisson's ratio v remains constant. The results show that, for a given value of ratio R/C-0, a critical value of k exists at which the pull-off force attains a maximum; for a fixed value of k, the larger the ratio R/c(0), the larger the pull-off force is. For Gibson materials (i.e., k = 1 and v = 0.5), closed-form analytical solutions can be obtained for the critical contact half-width at pull-off and pull-off force. We further discuss the perfect stick case with both externally normal and tangential loads.

Distinct intron DNA structures in simian virus 40 T-antigen and adenovirus 2 E1A genes

Distinct structures delineating the introns of Simian Virus 40 T-antigen and Adenovirus 2 E1A genes have been discovered. The structures, which are centered around the branch points of the genes inserted in supercoiled double-stranded plasmids, are specifically targeted through photoactivated strand cleavage by the metal complex tris(4,7-diphenyl-1,10-phenanthroline)rhodium(III). The DNA sites that are recognized lack sequence homology but are similar in demarcating functionally important sites on the RNA level. The single-stranded DNA fragments corresponding to the coding strands of the genes were also found to fold into a structure apparently identical to that in the supercoiled genes based on the recognition by the metal complex. Further investigation of different single-stranded DNA fragments with other structural probes, such as another metal complex bis(1,10-phenanthroline)(phenanthrenequinone diimine)rhodium(III), AMT (4'aminomethyl-4,5',8 trimethylpsoralen), restriction enzyme Mse I, and mung bean nuclease, showed that the structures require the sequ ences at both ends of the intron plus the flanking sequences but not the middle of the intron. The two ends form independent helices which interact with each other to form the global tertiary structures. Both of the intron structures share similarities to the structure of the Holliday junction, which is also known to be specifically targeted by the former metal complex. These structures may have arisen from early RNA intron structures and may have been used to facilitate the evolution of genes through exon shuffling by acting as target sites for recombinase enzymes.

Deep centers in AlGaAs/GaAs GRIN-SCH SQW laser structures grown by MBE and MOCVD

The deep centers in AlGaAs/GaAs graded index-separate confinement heterostructure single quantum well (GRIN-SCHSQW) laser structures grown by MBE and MOCVD have been investigated using deep level transient spectroscopy (DLTS) technique, The majority and minority carrier DLTS spectra show that the deep (hole and electron) traps (Hi and E3), having large capture cross sections and concentrations, are observed in the graded n-AlxGa1-xAs layer of laser structures in addition to the well-known DX centers. For laser structures grown by MBE, the deep hole trap H1 and the deep electron trap E3 may be spatially localized in the interface regions of discontinuous variation Al mole fraction of the n-AlxGa1-xAs layer with x = 0.20-0.43. For laser structures grown by MOCVD, the deep electron trap E3 may be spatially localized in the n-AlxGa1-xAs layer with x = 0.18-0.30, and the DX center may be spatially localized in the interface regions of discontinuous variation Al mole fraction of the AlxGa1-xAs layer with x = 0.22-0.30.

Dielectric response of composites with graded cylindrical particles

Effective dielectric responses of graded cylindrical composites are investigated when an external uniform field is applied to the composites. Considering linear random composites of cylindrical particles with a specific dielectric function, which varies along the radial direction of the particles, we have studied three cases of dielectric profiles: exponential function, linear and power-law profiles. For each case, the effective dielectric response of graded composites is given on the basis of exact solutions of the local potentials of composites in the dilute limit. For a larger volume fraction, we have proposed an effective medium approximation to estimate the effective dielectric response.

Engineering N-linked protein glycosylation with diverse O antigen lipopolysaccharide structures in Escherichia coli

Campylobacter jejuni has a general N-linked protein glycosylation system that can be functionally transferred to Escherichia coli. In this study, we engineered E. coli cells in a way that two different pathways, protein N-glycosylation and lipopolysaccharide (LPS) biosynthesis, converge at the step in which PglB, the key enzyme of the C. jejuni N-glycosylation system, transfers O polysaccharide from a lipid carrier (undecaprenyl pyrophosphate) to an acceptor protein. PglB was the only protein of the bacterial N-glycosylation machinery both necessary and sufficient for the transfer. The relaxed specificity of the PglB oligosaccharyltransferase toward the glycan structure was exploited to create novel N-glycan structures containing two distinct E. coli or Pseudomonas aeruginosa O antigens. PglB-mediated transfer of polysaccharides might be valuable for in vivo production of O polysaccharides-protein conjugates for use as antibacterial vaccines.

On Quillen's calculation of graded K-theory

We adapt Quillen’s calculation of graded K-groups of Z-graded rings with support in N to graded K-theory, allowing gradings in a product Z×G with G an arbitrary group. This in turn allows us to use induction and calculate graded K-theory of Z -multigraded rings.

Cupins: the most functionally diverse protein superfamily?

The cupin superfamily of proteins, named on the basis of a conserved β-barrel fold (‘cupa’ is the Latin term for a small barrel), was originally discovered using a conserved motif found within germin and germin-like proteins from higher plants. Previous analysis of cupins had identified some 18 different functional classes that range from single-domain bacterial enzymes such as isomerases and epimerases involved in the modification of cell wall carbohydrates, through to two-domain bicupins such as the desiccation-tolerant seed storage globulins, and multidomain transcription factors including one linked to the nodulation response in legumes. Recent advances in comparative genomics, and the resolution of many more 3-D structures have now revealed that the largest subset of the cupin superfamily is the 2-oxyglutarate-Fe2+ dependent dioxygenases. The substrates for this subclass of enzyme are many and varied and in total amount to probably 50–100 different biochemical reactions, including several involved in plant growth and development. Although the majority of enzymatic cupins contain iron as an active site metal, other members contain either copper, zinc, cobalt, nickel or manganese ions as a cofactor, with each cofactor allowing a different type of chemistry to occur within the conserved tertiary structure. This review discusses the range of structures and functions found in this most diverse of superfamilies.