The sugar cane biofactory - building blocks for the future

The sugarcane plant, with its enormous genetic capacity to accumulate carbon and manufacture and store sucrose, also has the potential to accumulate carbon and metabolically create a wide range of new molecules for industrial and other commercial uses. The extent to which this change can be developed and realised commercially is a function of the technical competence of the industry's R&D capacity, the reality of the commercial drivers which support this global agenda, and the determination of the industry to achieve such goals. The outcomes of existing R&D work already strongly support the technical challenges of this opportunity in sugarcane. The current challenge remains the commercialisation of the technology in a global market in which the current business structures and systems for the manufacture and distribution of existing (competitive) products makes the development of new product lines a higher risk than might otherwise be the case. This is despite all the claims that global markets are expecting and (in some cases) legislating the creation of more sustainable production systems. The options and issues for the development of a sugarcane biofactory system are discussed.

First- and second-order stimulus length selectivity in New World monkey striate cortex

Motion is a powerful cue for figure-ground segregation, allowing the recognition of shapes even if the luminance and texture characteristics of the stimulus and background are matched. In order to investigate the neural processes underlying early stages of the cue-invariant processing of form, we compared the responses of neurons in the striate cortex (V1) of anaesthetized marmosets to two types of moving stimuli: bars defined by differences in luminance, and bars defined solely by the coherent motion of random patterns that matched the texture and temporal modulation of the background. A population of form-cue-invariant (FCI) neurons was identified, which demonstrated similar tuning to the length of contours defined by first- and second-order cues. FCI neurons were relatively common in the supragranular layers (where they corresponded to 28% of the recorded units), but were absent from layer 4. Most had complex receptive fields, which were significantly larger than those of other V1 neurons. The majority of FCI neurons demonstrated end-inhibition in response to long first- and second-order bars, and were strongly direction selective, Thus, even at the level of V1 there are cells whose variations in response level appear to be determined by the shape and motion of the entire second-order object, rather than by its parts (i.e. the individual textural components). These results are compatible with the existence of an output channel from V1 to the ventral stream of extrastriate areas, which already encodes the basic building blocks of the image in an invariant manner.

5,6-Dihydroxyindole-2-carboxylic acid: a first principles density functional study

We report first principles density functional calculations for 5,6-dihydroxyindole-2-carboxylic acid (DHICA) and several oxidised forms. DHICA and 5,6-dihydroxyindole (DHI) are believed to be the basic building blocks of the eumelanins. Our results show that carboxylation has a significant effect on the physical properties of the molecules. In particular, the relative stabilities and the highest occupied molecular orbital-lowest unoccupied molecular orbital gaps (calculated with the DeltaSCF method) of the various redox forms are strongly affected. We predict that, in contrast to DHI, the density of unpaired electrons, and hence the ESR signal, in DHICA is negligibly small. (C) 2004 Elsevier B.V. All rights reserved.

Quantitative fluorescence excitation spectra of synthetic eumelanin

Previously reported excitation spectra for eumelanin are sparse and inconsistent. Moreover, these studies have failed to account for probe beam attenuation and emission reabsorption within the samples, making them qualitative at best. We report for the first time quantitative excitation spectra for synthetic eumelanin, acquired for a range of solution concentrations and emission wavelengths. Our data indicate that probe beam attenuation and emission reabsorption significantly affect the spectra even in low-concentration eumelanin solutions and that previously published data do not reflect the true excitation profile. We apply a correction procedure (previously applied to emission spectra) to account for these effects. Application of this procedure reconstructs the expected relationship of signal intensity with concentration, and the normalized spectra show a similarity in form to the absorption profiles. These spectra reveal valuable information regarding the photophysics and photochemistry of eumelanin. Most notably, an excitation peak at 365 urn (3.40 eV), whose position is independent of emission wavelength, is possibly attributable to a 5,6-dihydroxyindole-2-carboxylic acid (DHICA) component singly linked to a polymeric structure.

Carbohydrate-based scaffolds in drug discovery

Carbohydrates have been proven as valuable scaffolds to display pharmocophores and the resulting molecules have demonstrated useful biological activity towards various targets including the somatostatin receptors (SSTR), integrins, HIV-1 protease, matrix metalloproteinases (MMP), multidrug resistance-associated protein (MRP), and as RNA binders. Carbohydrate-based compounds have also shown antibacterial and herbicidal activity.

Chemical and structural disorder in eumelanins: A possible explanation for broadband absorbance

We report the results of an experimental and theoretical study of the electronic and structural properties of a key eumelanin precursor-5,6,-dihydroxyindole-2-carboxylic acid ( DHICA) - and its dimeric forms. We have used optical spectroscopy to follow the oxidative polymerization of DHICA to eumelanin and observe red shifting and broadening of the absorption spectrum as the reaction proceeds. First principles density functional theory calculations indicate that DHICA oligomers ( possible reaction products of oxidative polymerization) have the gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital red-shifted gaps with respect to the monomer. Furthermore, different bonding configurations ( leading to oligomers with different structures) produce a range of gaps. These experimental and theoretical results lend support to the chemical disorder model where the broadband monotonic absorption characteristic of all melanins is a consequence of the superposition of a large number of nonhomogeneously broadened Gaussian transitions associated with each of the components of a melanin ensemble. These results suggest that the traditional model of eumelanin as an amorphous organic semiconductor is not required to explain its optical properties and should be thoroughly reexamined. These results have significant implications for our understanding of the physics, chemistry, and biological function of these important biological macromolecules. Indeed, one may speculate that the robust functionality of melanins in vitro is a direct consequence of its heterogeneity, i.e., chemical disorder is a "low cost" natural resource in these systems

Reversible active switching of the mechanical properties of a peptide film at a fluid-fluid interface

Designer peptides have recently been developed as building blocks for novel self-assembled materials with stimuli-responsive properties. To date, such materials have been based on self-assembly in bulk aqueous solution or at solid-fluid interfaces. We have designed a 21-residue peptide, AM1, as a stimuli-responsive surfactant that switches molecular architectures at a fluid-fluid interface in response to changes in bulk aqueous solution composition. In the presence of divalent zinc at neutral pH, the peptide forms a mechanically strong 'film state'. In the absence of metal ions or at acid pH, the peptide adsorbs to form a mobile 'detergent state'. The two interfacial states can be actively and reversibly switched. Switching between the two states by a change in pH or the addition of a chelating agent leads to rapid emulsion coalescence or foam collapse. This work introduces a new class of surfactants that offer an environmentally friendly approach to control the stability of interfaces in foams, emulsions and fluid-fluid interfaces more generally.

Radiative relaxation in synthetic pheomelanin

We report a detailed photoluminescence study of cysteinyldopa-melanin ( CDM), the synthetic analogue of pheomelanin. Emission spectra are shown to be a far more sensitive probe of CDM's spectroscopic behavior than are absorption spectra. Although CDM and dopa-melanin ( DM, the synthetic analogue of eumelanin) have very similar absorption spectra, we find that they have very different excitation and emission characteristics; CDM has two distinct photoluminescence peaks that do not shift with excitation wavelength. Additionally, our data suggest that the radiative quantum yield of CDM is excitation energy dependent, an unusual property among biomolecules that is indicative of a chemically disordered system. Finally, we find that the radiative quantum yield for CDM is similar to 0.2%, twice that of DM, although still extremely low. This means that 99.8% of the energy absorbed by CDM is dissipated via nonradiative pathways, consistent with its role as a pigmentary photoprotectant.

Dde as a protecting group for carbohydrate synthesis

Oligosaccharide synthesis using aminosugars requires the presence of a suitable amino protecting group. A number of protecting groups are currently used, and while many display favorable properties, most agents available still suffer from certain disadvantages. This report details the use of a hydrazine labile aminosugar protecting group, N -[1-(4,4-dimethyl-2,6-dioxocyclohex-1-ylidene)ethyl] (Dde), which can be introduced and removed in a facile and cost-effective manner.

Structural characteristics of GaSB / GaAs nanowire heterostructures grown by metal-organic chemical vapor deposition

Highly lattice mismatched (7.8%) GaAs/GaSb nanowire heterostructures were grown by metal-organic chemical vapor deposition and their detailed structural characteristics were determined by electron microscopy. The facts that (i) no defects have been found in GaSb and its interfaces with GaAs and (ii) the lattice mismatch between GaSb/GaAs was fully relaxed suggest that the growth of GaSb nanowires is purely governed by the thermodynamics. The authors believe that the low growth rate of GaSb nanowires leads to the equilibrium growth. (c) 2006 American Institute of Physics.

Parallel 3D Simulation of a Fault Gouge using the Lattice Solid Model

Despite the insight gained from 2-D particle models, and given that the dynamics of crustal faults occur in 3-D space, the question remains, how do the 3-D fault gouge dynamics differ from those in 2-D? Traditionally, 2-D modeling has been preferred over 3-D simulations because of the computational cost of solving 3-D problems. However, modern high performance computing architectures, combined with a parallel implementation of the Lattice Solid Model (LSM), provide the opportunity to explore 3-D fault micro-mechanics and to advance understanding of effective constitutive relations of fault gouge layers. In this paper, macroscopic friction values from 2-D and 3-D LSM simulations, performed on an SGI Altix 3700 super-cluster, are compared. Two rectangular elastic blocks of bonded particles, with a rough fault plane and separated by a region of randomly sized non-bonded gouge particles, are sheared in opposite directions by normally-loaded driving plates. The results demonstrate that the gouge particles in the 3-D models undergo significant out-of-plane motion during shear. The 3-D models also exhibit a higher mean macroscopic friction than the 2-D models for varying values of interparticle friction. 2-D LSM gouge models have previously been shown to exhibit accelerating energy release in simulated earthquake cycles, supporting the Critical Point hypothesis. The 3-D models are shown to also display accelerating energy release, and good fits of power law time-to-failure functions to the cumulative energy release are obtained.