Protein A: nature's universal anti-antibody

Staphylococcal protein A specifically interacts with immunogobulins. This fact is being used in various disciplines of biology and some of the unique properties of protein A and their applications are summarized in this review.

Improvement of mango tree architecture

This paper discusses the role of mango canopy architecture in mango productivity and orchard management and considers potential increases on production of high density orchards through improved canopy architecture. Lower tree height, reduced vigour and smaller more open canopies are recognised as important aspects of high density orchards. However, vigour management, light relations, flowering and crop load of high density orchards needs to be better understood if we are to developed sustainable highly productive canopy training and pruning systems that are easy to maintain at high planting densities.

Identification of the sex pheromone of the tree infesting Cossid Moth Coryphodema tristis (Lepidoptera: Cossidae)

The cossid moth (Coryphodema tristis) has a broad range of native tree hosts in South Africa. The moth recently moved into non-native Eucalyptus plantations in South Africa, on which it now causes significant damage. Here we investigate the chemicals involved in pheromone communication between the sexes of this moth in order to better understand its ecology, and with a view to potentially develop management tools for it. In particular, we characterize female gland extracts and headspace samples through coupled gas chromatography electro-antennographic detection (GC-EAD) and two dimensional gas chromatography mass spectrometry (GCxGC-MS). Tentative identities of the potential pheromone compounds were confirmed by comparing both retention time and mass spectra with authentic standards. Two electrophysiologically active pheromone compounds, tetradecyl acetate (14:OAc) and Z9-tetradecenyl acetate (Z9-14:OAc) were identified from pheromone gland extracts, and an additional compound (Z9-14:OH) from headspace samples. We further determined dose response curves for the identified compounds and six other structurally similar compounds that are common to the order Cossidae. Male antennae showed superior sensitivity toward Z9-14:OAc, Z7-tetradecenyl acetate (Z7-14:OAc), E9-tetradecenyl acetate (E9-14:OAc), Z9-tetradecenol (Z9-14:OH) and Z9-tetradecenal (Z9-14:Ald) when compared to female antennae. While we could show electrophysiological responses to single pheromone compounds, behavioral attraction of males was dependent on the synergistic effect of at least two of these compounds. Signal specificity is shown to be gained through pheromone blends. A field trial showed that a significant number of males were caught only in traps baited with a combination of Z9-14:OAc (circa 95 of the ratio) and Z9-14:OH. Addition of 14:OAc to this mixture also improved the number of males caught, although not significantly. This study represents a major step towards developing a useful attractant to be used in management tools for C. tristis and contributes to the understanding of chemical communication and biology of this group of insects.

Activity recognition using binary tree SVM

This paper presents an effective classification method based on Support Vector Machines (SVM) in the context of activity recognition. Local features that capture both spatial and temporal information in activity videos have made significant progress recently. Efficient and effective features, feature representation and classification plays a crucial role in activity recognition. For classification, SVMs are popularly used because of their simplicity and efficiency; however the common multi-class SVM approaches applied suffer from limitations including having easily confused classes and been computationally inefficient. We propose using a binary tree SVM to address the shortcomings of multi-class SVMs in activity recognition. We proposed constructing a binary tree using Gaussian Mixture Models (GMM), where activities are repeatedly allocated to subnodes until every new created node contains only one activity. Then, for each internal node a separate SVM is learned to classify activities, which significantly reduces the training time and increases the speed of testing compared to popular the `one-against-the-rest' multi-class SVM classifier. Experiments carried out on the challenging and complex Hollywood dataset demonstrates comparable performance over the baseline bag-of-features method.

A universal equation to predict methane production of forage-fed cattle in Australia

The methods for estimating methane emissions from cattle as used in the Australian national inventory are based on older data that have now been superseded by a large amount of more recent data. Recent data suggested that the current inventory emissions estimates can be improved. To address this issue, a total of 1034 individual animal records of daily methane production (MP) was used to reassess the relationship between MP and each of dry matter intake (DMI) and gross energy intake (GEI). Data were restricted to trials conducted in the past 10 years using open-circuit respiration chambers, with cattle fed forage-based diets (forage >70%). Results from diets considered to inhibit methanogenesis were omitted from the dataset. Records were obtained from dairy cattle fed temperate forages (220 records), beef cattle fed temperate forages (680 records) and beef cattle fed tropical forages (133 records). Relationships were very similar for all three production categories and single relationships for MP on a DMI or GEI basis were proposed for national inventory purposes. These relationships were MP (g/day) = 20.7 (±0.28) × DMI (kg/day) (R2 = 0.92, P < 0.001) and MP (MJ/day) = 0.063 (±0.008) × GEI (MJ/day) (R2 = 0.93, P < 0.001). If the revised MP (g/day) approach is used to calculate Australia’s national inventory, it will reduce estimates of emissions of forage-fed cattle by 24%. Assuming a global warming potential of 25 for methane, this represents a 12.6 Mt CO2-e reduction in calculated annual emissions from Australian cattle.

Fine root dry matter relative to mango (Mangifera indica) tree scion size grafted on size-controlling rootstocks, is negatively related to scion growth rate

Knowledge of root dry matter (DM) allocation, in relation to differing vigour conferred by rootstock cultivars, is required to understand the structural relationships between rootstock and scion. We investigated the mass of roots (four size classes up to 23 mm diameter) by coring proximal to five polyembryonic mango rootstock cultivars known to differ in their effects on the vigour and productivity of scion cultivar ‘Kensington Pride’, in a field trial of 13-year-old trees. Significant differences in fine (<0.64 and 0.64–1.88 mm diameter) and small (1.88–7.50 mm) root DM contents were observed between rootstock cultivars. There was a complex relationship between the amount of feeder (fine and small size classes) roots and scion size (trunk cross sectional area, TCSA), with intermediate size trees on rootstock MYP having the most feeder roots, while the smallest trees, on the rootstock Vellaikulamban had the least of these roots. Across rootstock cultivars, tree vigour (TCSA growth rate) was negatively and significantly related to the ratio of fine root DM/scion TCSA, suggesting this may be a useful indicator of the vigour that different rootstocks confer on the scion. In contrast non-ratio root DM and scion TCSA results had no significant relationships. The significant rootstock effects on orchard root growth and tree size could not be predicted from earlier differences in nursery seedling vigour, nor did seedling vigour predict root DM allocation.

Lignin biosynthesis in Norway spruce: from a model system to the tree

Lignin is a hydrophobic polymer that is synthesised in the secondary cell walls of all vascular plants. It enables water conduction through the stem, supports the upright growth habit and protects against invading pathogens. In addition, lignin hinders the utilisation of the cellulosic cell walls of plants in pulp and paper industry and as forage. Lignin precursors are synthesised in the cytoplasm through the phenylpropanoid pathway, transported into the cell wall and oxidised by peroxidases or laccases to phenoxy radicals that couple to form the lignin polymer. This study was conducted to characterise the lignin biosynthetic pathway in Norway spruce (Picea abies (L.) Karst.). We focused on the less well-known polymerisation stage, to identify the enzymes and the regulatory mechanisms that are involved. Available data for lignin biosynthesis in gymnosperms is scarce and, for example, the latest improvements in precursor biosynthesis have only been verified in herbaceous plants. Therefore, we also wanted to study in detail the roles of individual gene family members during developmental and stress-induced lignification, using EST sequencing and real-time RT-PCR. We used, as a model, a Norway spruce tissue culture line that produces extracellular lignin into the culture medium, and showed that lignin polymerisation in the tissue culture depends on peroxidase activity. We identified in the culture medium a significant NADH oxidase activity that could generate H2O2 for peroxidases. Two basic culture medium peroxidases were shown to have high affinity to coniferyl alcohol. Conservation of the putative substrate-binding amino acids was observed when the spruce peroxidase sequences were compared with other peroxidases with high affinity to coniferyl alcohol. We also used different peroxidase fractions to produce synthetic in vitro lignins from coniferyl alcohol; however, the linkage pattern of the suspension culture lignin could not be reproduced in vitro with the purified peroxidases, nor with the full complement of culture medium proteins. This emphasised the importance of the precursor radical concentration in the reaction zone, which is controlled by the cells through the secretion of both the lignin precursors and the oxidative enzymes to the apoplast. In addition, we identified basic peroxidases that were reversibly bound to the lignin precipitate. They could be involved, for example, in the oxidation of polymeric lignin, which is required for polymer growth. The dibenzodioxocin substructure was used as a marker for polymer oxidation in the in vitro polymerisation studies, as it is a typical substructure in wood lignin and in the suspension culture lignin. Using immunolocalisation, we found the structure mainly in the S2+S3 layers of the secondary cell walls of Norway spruce tracheids. The structure was primarily formed during the late phases of lignification. Contrary to the earlier assumptions, it appears to be a terminal structure in the lignin macromolecule. Most lignin biosynthetic enzymes are encoded for by several genes, all of which may not participate in lignin biosynthesis. In order to identify the gene family members that are responsible for developmental lignification, ESTs were sequenced from the lignin-forming tissue culture and developing xylem of spruce. Expression of the identified lignin biosynthetic genes was studied using real-time RT-PCR. Candidate genes for developmental lignification were identified by a coordinated, high expression of certain genes within the gene families in all lignin-forming tissues. However, such coordinated expression was not found for peroxidase genes. We also studied stress-induced lignification either during compression wood formation by bending the stems or after Heterobasidion annosum infection. Based on gene expression profiles, stress-induced monolignol biosynthesis appeared similar to the developmental process, and only single PAL and C3H genes were specifically up-regulated by stress. On the contrary, the up-regulated peroxidase genes differed between developmental and stress-induced lignification, indicating specific responses.

The hydrogen bond: a molecular beam microwave spectroscopist's view with a universal appeal

In this manuscript, we propose a criterion for a weakly bound complex formed in a supersonic beam to be characterized as a `hydrogen bonded complex'. For a `hydrogen bonded complex', the zero point energy along any large amplitude vibrational coordinate that destroys the orientational preference for the hydrogen bond should be significantly below the barrier along that coordinate so that there is at least one bound level. These are vibrational modes that do not lead to the breakdown of the complex as a whole. If the zero point level is higher than the barrier, the `hydrogen bond' would not be able to stabilize the orientation which favors it and it is no longer sensible to characterize a complex as hydrogen bonded. Four complexes, Ar-2-H2O, Ar-2-H2S, C2H4-H2O and C2H4-H2S, were chosen for investigations. Zero point energies and barriers for large amplitude motions were calculated at a reasonable level of calculation, MP2(full)/aug-cc-pVTZ, for all these complexes. Atoms in molecules (AIM) theoretical analyses of these complexes were carried out as well. All these complexes would be considered hydrogen bonded according to the AIM theoretical criteria suggested by Koch and Popelier for C-H center dot center dot center dot O hydrogen bonds (U. Koch and P. L. A. Popelier, J. Phys. Chem., 1995, 99, 9747), which has been widely and, at times, incorrectly used for all types of contacts involving H. It is shown that, according to the criterion proposed here, the Ar-2-H2O/H2S complexes are not hydrogen bonded even at zero kelvin and C2H4-H2O/H2S complexes are. This analysis can naturally be extended to all temperatures. It can explain the recent experimental observations on crystal structures of H2S at various conditions and the crossed beam scattering studies on rare gases with H2O and H2S.