A scientific approach to agent selection

The prioritisation of potential agents on the basis of likely efficacy is an important step in biological control because it can increase the probability of a successful biocontrol program, and reduce risks and costs. In this introductory paper we define success in biological control, review how agent selection has been approached historically, and outline the approach to agent selection that underpins the structure of this special issue on agent selection. Developing criteria by which to judge the success of a biocontrol agent (or program) provides the basis for agent selection decisions. Criteria will depend on the weed, on the ecological and management context in which that weed occurs, and on the negative impacts that biocontrol is seeking to redress. Predicting which potential agents are most likely to be successful poses enormous scientific challenges. 'Rules of thumb', 'scoring systems' and various conceptual and quantitative modelling approaches have been proposed to aid agent selection. However, most attempts have met with limited success due to the diversity and complexity of the systems in question. This special issue presents a series of papers that deconstruct the question of agent choice with the aim of progressively improving the success rate of biological control. Specifically they ask: (i) what potential agents are available and what should we know about them? (ii) what type, timing and degree of damage is required to achieve success? and (iii) which potential agent will reach the necessary density, at the right time, to exert the required damage in the target environment?

Seasonal changes in pasture quality and diet selection and their relationship with liveweight gain of steers grazing tropical grass and grass-legume pastures in northern Australia.

The variation in liveweight gain in grazing beef cattle as influenced by pasture type, season and year effects has important economic implications for mixed crop-livestock systems and the ability to better predict such variation would benefit beef producers by providing a guide for decision making. To identify key determinants of liveweight change of Brahman-cross steers grazing subtropical pastures, measurements of pasture quality and quantity, and diet quality in parallel with liveweight were made over two consecutive grazing seasons (48 and 46 weeks, respectively), on mixed Clitoria ternatea/grass, Stylosanthes seabrana/grass and grass swards (grass being a mixture of Bothriochloa insculpta cv. Bisset, Dichanthium sericeum and Panicum maximum var. trichoglume cv. Petrie). Steers grazing the legume-based pastures had the highest growth rate and gained between 64 and 142 kg more than those grazing the grass pastures in under 12 months. Using an exponential model, green leaf mass, green leaf %, adjusted green leaf % (adjusted for inedible woody legume stems), faecal near infrared reflectance spectroscopy predictions of diet crude protein and diet dry matter digestibility, accounted for 77, 74, 80, 63 and 60%, respectively, of the variation in daily weight gain when data were pooled across pasture types and grazing seasons. The standard error of the regressions indicated that 95% prediction intervals were large (+/- 0.42-0.64 kg/head.day) suggesting that derived regression relationships have limited practical application for accurately estimating growth rate. In this study, animal factors, especially compensatory growth effects, appeared to have a major influence on growth rate in relation to pasture and diet attributes. It was concluded that predictions of growth rate based only on pasture or diet attributes are unlikely to be accurate or reliable. Nevertheless, key pasture attributes such as green leaf mass and green leaf% provide a robust indication of what proportion of the potential growth rate of the grazing animals can be achieved.

Estimation of peak ground acceleration and spectral acceleration for South India with local site effects: probabilistic approach

In this work an attempt has been made to evaluate the seismic hazard of South India (8.0 degrees N-20 degrees N; 72 degrees E-88 degrees E) based on the probabilistic seismic hazard analysis (PSHA). The earthquake data obtained from different sources were declustered to remove the dependent events. A total of 598 earthquakes of moment magnitude 4 and above were obtained from the study area after declustering, and were considered for further hazard analysis. The seismotectonic map of the study area was prepared by considering the faults, lineaments and the shear zones in the study area which are associated with earthquakes of magnitude 4 and above. For assessing theseismic hazard, the study area was divided into small grids of size 0.1 degrees x0.1 degrees, and the hazard parameters were calculated at the centre of each of these grid cells by considering all the seismic sources with in a radius of 300 km. Rock level peak horizontal acceleration (PHA) and spectral acceleration (SA) values at 1 corresponding to 10% and 2% probability of exceedance in 50 years have been calculated for all the grid points. The contour maps showing the spatial variation of these values are presented here. Uniform hazard response spectrum (UHRS) at rock level for 5% damping and 10% and 2% probability of exceedance in 50 years were also developed for all the grid points. The peak ground acceleration (PGA) at surface level was calculated for the entire South India for four different site classes. These values can be used to find the PGA values at any site in South India based on site class at that location. Thus, this method can be viewed as a simplified method to evaluate the PGA values at any site in the study area.

How Good is the Assumption About Visible Surface Reflectance in MODIS Aerosol Retrieval Over Land? A Comparison With Aircraft Measurements Over an Urban Site in India

In this paper, we discuss the measurements of spectral surface reflectance (rho(s)(lambda)) in the wavelength range 350-2500 nm measured using a spectroradiometer onboard a low-flying aircraft over Bangalore (12.95 degrees N, 77.65 degrees E), an urban site in southern India. The large discrepancies in the retrieval of aerosol propertiesover land by the Moderate-Resolution Imaging Spectroradiometer (MODIS), which could be attributed to the inaccurate estimation of surface reflectance at many sites in India and elsewhere, provided motivation for this paper. The aim of this paper was to verify the surface reflectance relationships assumed by the MODIS aerosol algorithm for the estimation of surface reflectance in the visible channels (470 and 660 nm) from the surface reflectance at 2100 nm for aerosol retrieval over land. The variety of surfaces observed in this paper includes green and dry vegetations, bare land, and urban surfaces. The measuredreflectance data were first corrected for the radiative effects of atmosphere lying between the ground and aircraft using the Second Simulation of Satellite Signal in the Solar Spectrum (6S) radiative transfer code. The corrected surface reflectance in the MODIS's blue (rho(s)(470)), red (rho(s)(660)), and shortwave-infrared (SWIR) channel (rho(s)(2100)) was linearly correlated. We found that the slope of reflectance relationship between 660 and 2100 nm derived from the forward scattering data was 0.53 with an intercept of 0.07, whereas the slope for the relationship between the reflectance at 470 and 660 nm was 0.85. These values are much higher than the slope (similar to 0.49) for either wavelengths assumed by the MODIS aerosol algorithm over this region. The reflectance relationship for the backward scattering data has a slope of 0.39, with an intercept of 0.08 for 660 nm, and 0.65, with an intercept of 0.08 for 470 nm. The large values of the intercept (which is very small in the MODIS reflectance relationships) result in larger values of absolute surface reflectance in the visible channels. The discrepancy between the measured and assumed surface reflectances could lead to error in the aerosol retrieval. The reflectance ratio (rho(s)(660)/rho(s)(2100)) showed a clear dependence on the N D V I-SWIR where the ratio increased from 0.5 to 1 with an increase in N V I-SWIR from 0 to 0.5. The high correlation between the reflectance at SWIR wavelengths (2100, 1640, and 1240 nm) indicated an opportunity to derive the surface reflectance and, possibly, aerosol properties at these wavelengths. We need more experiments to characterize the surface reflectance and associated inhomogeneity of land surfaces, which play a critical role in the remote sensing of aerosols over land.

High resolution satellite imagery and GPS collars can help assist in the assessment of patch selection by grazing cattle in semi-arid savannas.

The selection of different patch types for grazing by cattle in tropical savannas is well documented. Advances in high resolution satellite imagery and computing power now allow us to identify patch types over an entire paddock, combined with GPS collars as a non instrusive method of capturing positional data, an accurate and comprehensive picture of landscape use by cattle can be quantified.

Patch selection by cattle can be quantified using satellite imagery and GPS in extensive, semi-arid savannas.

Patch selection by grazing animals is difficult to quantify, particularly in large, extensive paddocks like those in northern Australia. However, advances in high resolution satellite imagery now allow identification of patch types over an entire paddock which combined with GPS collars to capture positional data, can give an accurate and comprehensive picture of landscape use by cattle.

Optimising between and within family selection for harvest weight in prawns with restricted harvest size.

Manual grading of prawns restricts the number that can be harvested. A restricted harvest size places a limit on the opposing within family and between family sources of selection pressure. A simulation study with inbreeding constrained at 0.5% per generation, a harvest size of 2000, heritability of 0.3, common family environmental effect of 0.1, indicates that maximum response to selection could be achieved with as few as 40 families. Increasing the number of families above 80 may reduce total selection response. It is important to be aware that increasing the number of families may not always yield a greater genetic response.

Refining the process of agent selection through understanding plant demography and plant response to herbivory

Understanding plant demography and plant response to herbivory is critical to the selection of effective weed biological control agents. We adopt the metaphor of 'filters' to suggest how agent prioritisation may be improved to narrow our choices down to those likely to be most effective in achieving the desired weed management outcome. Models can serve to capture our level of knowledge (or ignorance) about our study system and we illustrate how one type of modelling approach (matrix models) may be useful in identifying the weak link in a plant life cycle by using a hypothetical and an actual weed example (Parkinsonia aculeata). Once the vulnerable stage has been identified we propose that studying plant response to herbivory (simulated and/or actual) can help identify the guilds of herbivores to which a plant is most likely to succumb. Taking only potentially effective agents through the filter of host specificity may improve the chances of releasing safe and effective agents. The methods we outline may not always lead us definitively to the successful agent(s), but such an empirical, data-driven approach will make the basis for agent selection explicit and serve as testable hypotheses once agents are released.

Quantitative and molecular genetics of juvenile wood traits in radiata and slash/Caribbean pines.

The Juvenile Wood Initiative (JWI) project has been running successfully since July 2003 under a Research Agreement with FWPA and Letters of Association with the consortium partners STBA (Southern Tree Breeding Association), ArborGen and FPQ (Forestry Plantations Queensland). Over the last five and half years, JWI scientists in CSIRO, FPQ, and STBA have completed all 12 major milestones and 28 component milestones according to the project schedule. We have made benchmark progress in understanding the genetic control of wood formation and interrelationships among wood traits. The project has made 15 primary scientific findings and several results have been adopted by industry as summarized below. This progress was detailed in 10 technical reports to funding organizations and industry clients. Team scientists produced 16 scientific manuscripts (8 published, 1 in press, 2 submitted, and several others in the process of submission) and 15 conference papers or presentations. Primary Scientific Findings. The 15 major scientific findings related to wood science, inheritance and the genetic basis of juvenile wood traits are: 1. An optimal method to predict stiffness of standing trees in slash/Caribbean pine is to combine gravimetric basic density from 12 mm increment cores with a standing tree prediction of MoE using a time of flight acoustic tool. This was the most accurate and cheapest way to rank trees for breeding selection for slash/Caribbean hybrid pine. This method was also recommended for radiata pine. 2. Wood density breeding values were predicted for the first time in the STBA breeding population using a large sample of 7,078 trees (increment cores) and it was estimated that selection of the best 250 trees for deployment will produce wood density gains of 12.4%. 3. Large genetic variation for a suite of wood quality traits including density, MFA, spiral grain, shrinkage, acoustic and non-acoustic stiffness (MoE) for clear wood and standing trees were observed. Genetic gains of between 8 and 49% were predicted for these wood quality traits with selection intensity between 1 to 10% for radiata pine. 4. Site had a major effect on juvenile-mature wood transition age and the effect of selective breeding for a shorter juvenile wood formation phase was only moderate (about 10% genetic gain with 10% selection intensity, equivalent to about 2 years reduction of juvenile wood). 5. The study found no usable site by genotype interactions for the wood quality traits of density, MFA and MoE for both radiata and slash/Caribbean pines, suggesting that assessment of wood properties on one or two sites will provide reliable estimates of the genetic worth of individuals for use in future breeding. 6. There were significant and sizable genotype by environment interactions between the mainland and Tasmanian regions and within Tasmania for DBH and branch size. 7. Strong genetic correlations between rings for density, MFA and MoE for both radiata and slash/Caribbean pines were observed. This suggests that selection for improved wood properties in the innermost rings would also result in improvement of wood properties in the subsequent rings, as well as improved average performance of the entire core. 8. Strong genetic correlations between pure species and hybrid performance for each of the wood quality traits were observed in the hybrid pines. Parental performance can be used to identify the hybrid families which are most likely to have superior juvenile wood properties of the slash/Caribbean F1 hybrid in southeast Queensland. 9. Large unfavourable genetic correlations between growth and wood quality traits were a prominent feature in radiata pine, indicating that overcoming this unfavourable genetic correlation will be a major technical issue in progressing radiata pine breeding. 10. The project created the first radiata pine 18 k cDNA microarray and generated 5,952 radiata pine xylogenesis expressed sequence tags (ESTs) which assembled into 3,304 unigenes. 11. A total of 348 genes were identified as preferentially expressed genes in earlywood or latewood while a total of 168 genes were identified as preferentially expressed genes in either juvenile or mature wood. 12. Juvenile earlywood has a distinct transcriptome relative to other stages of wood development. 13. Discovered rapid decay of linkage disequilibrium (LD) in radiata pine with LD decaying to approximately 50% within 1,700 base pairs (within a typical gene). A total of 913 SNPS from sequencing 177,380 base pairs were identified for association genetic studies. 14. 149 SNPs from 44 genes and 255 SNPs from a further 51 genes (total 95 genes) were selected for association analysis with 62 wood traits, and 30 SNPs were shortlisted for their significant association with variation of wood quality traits (density, MFA and MoE) with individual significant SNPs accounting for between 1.9 and 9.7% of the total genetic variation in traits. 15. Index selection using breeding objectives was the most profitable selection method for radiata pine, but in the long term it may not be the most effective in dealing with negative genetic correlations between wood volume and quality traits. A combination of economic and biological approaches may be needed to deal with the strong adverse correlation.

Characterization of the mitochondrial active-site serine protein LACTB: filaments in the mitochondrial intermembrane space

Mitochondria have evolved from endosymbiotic alpha-proteobacteria. During the endosymbiotic process early eukaryotes dumped the major component of the bacterial cell wall, the peptidoglycan layer. Peptidoglycan is synthesized and maintained by active-site serine enzymes belonging to the penicillin-binding protein and the β-lactamase superfamily. Mammals harbor a protein named LACTB that shares sequence similarity with bacterial penicillin-binding proteins and β-lactamases. Since eukaryotes lack the synthesis machinery for peptidoglycan, the physiological role of LACTB is intriguing. Recently, LACTB has been validated in vivo to be causative for obesity, suggesting that LACTB is implicated in metabolic processes. The aim of this study was to investigate the phylogeny, structure, biochemistry and cell biology of LACTB in order to elucidate its physiological function. Phylogenetic analysis revealed that LACTB has evolved from penicillin binding-proteins present in the bacterial periplasmic space. A structural model of LACTB indicates that LACTB shares characteristic features common to all penicillin-binding proteins and β-lactamases. Recombinat LACTB protein expressed in E. coli was recovered in significant quantities. Biochemical and cell biology studies showed that LACTB is a soluble protein localized in the mitochondrial intermembrane space. Further analysis showed that LACTB preprotein underwent proteolytic processing disclosing an N-terminal tetrapeptide motif also found in a set of cell death-inducing proteins. Electron microscopy structural studies revealed that LACTB can polymerize to form stable filaments with lengths ranging from twenty to several hundred nanometers. These data suggest that LACTB filaments define a distinct microdomain in the intermembrane space. A possible role of LACTB filaments is proposed in the intramitochondrial membrane organization and microcompartmentation. The implications of these findings offer novel insight into the evolution of mitochondria. Further studies of the LACTB function might provide a tool to treat mitochondria-related metabolic diseases.

Temporal genetic structure patterns in tropical maize populations under reciprocal recurrent selection.

In order to investigate the effect of long term recurrent selection on the pattern of gene diversity, thirty randomly-selected individuals from the progenitors (p) and four selection cycles (C0, C3, C6 and C11) were sampled for DNA analysis from the tropical maize (Zea mays L.) breeding populations, Atherton 1 (AT1) and Atherton 2 (AT2). Fifteen polymorphic Simple Sequence Repeat markers amplified a total of 284 and 257 alleles in AT1 and AT2 populations, respectively. Reductions in the number of alleles were observed at advanced selection cycles. About 11 and 12% of the alleles in AT1 and AT2 populations respectively, were near to fixation. However, a higher number of alleles (37% in AT1 and 33% in AT2) were close to extinction. Fisher's exact test and analysis of molecular variance (AMOVA) showed significant population differentiations. Gene diversity estimates and AMOVA revealed increased genetic differentiations at the expense of loss of heterozygosity. Population differentiations were mainly due to fixation of complementary alleles at a locus in the two breeding populations. The estimates of effective population at an advanced selection cycle were close to the population size predicted by the breeding method.

Management Guidelines for New Warm-Season Grasses in Australia

After more than 30 years in which ‘Tifgreen’ and ‘Tifdwarf’ were the only greens-quality varieties available, the choice for golf courses and bowls clubs in northern Australia has been expanded to include six new Cynodon hybrids [Cynodon dactylon (L.) Pers x Cynodon transvaalensis Burtt-Davy]. Five of these – ‘Champion Dwarf’ (Texas), ‘MS-Supreme’ (Mississippi), FloraDwarf™ (Florida), ‘TifEagle’ (Georgia), MiniVerde™ (Arizona) - are from US breeding programs, while the sixth, ‘TL2’ (marketed as Novotek™) was selected in north Queensland. The finer, denser and lower growing habit of the “ultradwarf” cultivars allows very low mowing heights (e.g. 2.5 mm) to be imposed, resulting in denser and smoother putting and bowls surfaces. In addition to the Cynodon hybrids, four new greens quality seashore paspalum (Paspalum vaginatum O. Swartz) cultivars including ‘Sea Isle 2000’, Sea Isle Supreme™, Velvetene™ and Sea Dwarf™ (where tolerance of salty water is required) expands the range of choices for greens in difficult environments. The project was developed to determine (a) the appropriate choice of cultivar for different environments and budgets, and (b) best management practices for the new cultivars which differ from the Cynodon hybrid industry standards ‘Tifgreen’ and ‘Tifdwarf’. Management practices, particularly fertilising, mowing heights and frequency, and thatch control were investigated to determine optimum management inputs and provide high quality playing surfaces with the new grasses. To enable effective trialling of these new and old cultivars it was essential to have a number of regional sites participating in the study. Drought and financial hardship of many clubs presented an initial setback with numerous clubs wanting to be involved in the study but were unable to commit due to their financial position at the time. The study was fortunate to have seven regional sites from Queensland, New South Wales, Victoria and South Australia volunteer to be involved in the study which would add to the results being collected at the centralised test facility being constructed at DEEDI’s Redlands Research Station. The major research findings acquired from the eight trial sites included: • All of the new second generation “ultradwarf” couchgrasses tend to produce a large amount of thatch with MiniVerde™ being the greatest thatch producer, particularly compared to ‘Tifdwarf’ and ‘Tifgreen’. The maintenance of the new Cynodon hybrids will require a program of regular dethatching/grooming as well as regular light dustings of sand. Thatch prevention should begin 3 to 4 weeks after planting a new “ultradwarf” couchgrass green, with an emphasis on prevention rather than control. • The “ultradwarfs” produced faster green speeds than the current industry standards ‘Tifgreen’ and ‘Tifdwarf’. However, all Cynodon hybrids were considerably faster than the seashore paspalums (e.g. comparable to the speed diference of Bentgrass and couchgrass) under trial conditions. Green speed was fastest being cut at 3.5 mm and rolled (compared to 3.5 mm cut, no roll and 2.7 mm cut, no roll). • All trial sites reported the occurrence of disease in the Cynodon hybrids with the main incidence of disease occurring during the dormancy period (autumn and winter). The main disease issue reported was “patch diseases” which includes both Gaumannomyces and Rhizoctonia species. There was differences in the severity of the disease between cultivars, however, the severity of the disease was not consistent between cultivars and is largely attributed to an environment (location) effect. In terms of managing the occurrence of disease, the incidence of disease is less severe where there is a higher fertility rate (about 3 kgN/100m2/year) or a preventitatve fungicide program is adopted. • Cynodon hybrid and seashore paspalum cultivars maintained an acceptable to ideal surface being cut between 2.7 mm and 5.0 mm. “Ultradwarf” cultivars can tolerate mowing heights as low as 2.5 mm for short periods but places the plant under high levels of stress. Greens being maintained at a continually lower cutting height (e.g. 2.7 mm) of both species is achievable, but would need to be cut daily for best results. Seashore paspalums performed best when cut at a height of between 2.7 mm and 3.0 mm. If a lower cutting height is adopted, regular and repeated mowings are required to reduce scalping and produce a smooth surface. • At this point in time the optimum rate of nitrogen (N) for the Cynodon hybrids is 3 kg/100m2/year and while the seashore paspalums is 2 to 3 kg/100m2/year. • Dormancy occurred for all Cynodon and seashore paspalum culitvars from north in Brisbane (QLD) to south in Mornington Peninsula (VIC) and west to Novar Gardens (SA). Cynodon and Paspalum growth in both Victoria and South Australia was less favourable as a result of the cooler climates. • After combining the data collected from all eight sites, the results indicated that there can be variation (e.g. turfgrass quality, colour, disease resistance, performace) depending on the site and climatic conditions. Such evidence highlights the need to undertake genotype by environment (G x E) studies on new and old cultivars prior to conversion or establishment. • For a club looking to select either a Cynodon hybrid or seashore paspalum cultivar for use at their club they need to: - Review the research data. - Look at trial plots. - Inspect greens in play that have the new grasses. - Select 2 to 3 cultivars that are considered to be the better types. - Establish them in large (large enough to putt on) plots/nursery/practice putter. Ideally the area should be subjected to wear. - Maintain them exactly as they would be on the golf course/lawn bowls green. This is a critical aspect. Regular mowing, fertilising etc. is essential. - Assess them over at least 2 to 3 years. - Make a selection and establish it in a playing green so that it is subjected to typical wear.

Wood properties and processing outcomes for plantation grown African mahogany (Khaya senegalensis) trees from Clare, Queensland (18 and 20 year-old trees) and Katherine, Northern Territory (14 year-old trees).

Khaya senegalensis, African mahogany, a high-value hardwood, was introduced in the Northern Territory (NT) in the 1950s; included in various trials there and at Weipa, Q in the 1960s-1970s; planted on ex mine sites at Weipa (160 ha) until 1985; revived in farm plantings in Queensland and in trials in the NT in the 1990s; adopted for large-scale, annual planting in the Douglas-Daly region, NT from 2006 and is to have the planted area in the NT extended to at least 20,000 ha. The recent serious interest from plantation growers, including Forest Enterprises Australia Ltd (FEA), has seen the establishment of some large scale commercial plantations. FEA initiated the current study to process relatively young plantation stands from both Northern Territory and Queensland plantations to investigate the sawn wood and veneer recovery and quality from trees ranging from 14 years (NT – 36 trees) to 18-20 years (North Queensland – 31 trees). Field measures of tree size and straightness were complemented with log end splitting assessment and cross-sectional disc sample collection for laboratory wood properties measurements including colour and shrinkage. End-splitting scores assessed on sawn logs were relatively low compared to fast grown plantation eucalypts and did not impact processing negatively. Heartwood proportion in individual trees ranged from 50% up to 92 % of butt cross-sectional disc area for the visually-assessed dark coloured central heartwood and lighter coloured transition wood combined. Dark central heartwood proportion was positively related to tree size (R2 = 0.57). Chemical tests failed to assist in determining heartwood – sapwood boundary. Mean basic density of whole disc samples was 658 kg/m3 and ranged among trees from 603 to 712 kg/m3. When freshly sawn, the heartwood of African mahogany was orange-red to red. Transition wood appeared to be pinkish and the sapwood was a pale yellow colour. Once air dried the heartwood colour generally darkens to pinkish-brown or orange-brown and the effect of prolonged time and sun exposure is to darken and change the heartwood to a red-brown colour. A portable colour measurement spectrophotometer was used to objectively assess colour variation in CIE L*, a* and b* values over time with drying and exposure to sunlight. Capacity to predict standard colour values accurately after varying periods of direct sunlight exposure using results obtained on initial air-dried surfaces decreased with increasing time to sun exposure. The predictions are more accurate for L* values which represent brightness than for variation in the a* values (red spectrum). Selection of superior breeding trees for colour is likely to be based on dried samples exposed to sunlight to reliably highlight wood colour differences. A generally low ratio between tangential and radial shrinkages was found, which was reflected in a low incidence of board distortion (particularly cupping) during drying. A preliminary experiment was carried out to investigate the quality of NIR models to predict shrinkage and density. NIR spectra correlated reasonably well with radial shrinkage and air dried density. When calibration models were applied to their validation sets, radial shrinkage was predicted to an accuracy of 76% with Standard Error of Prediction of 0.21%. There was also a strong predictive power for wood density. These are encouraging results suggesting that NIR spectroscopy has good potential to be used as a non-destructive method to predict shrinkage and wood density using 12mm diameter increment core samples. Average green off saw recovery was 49.5% (range 40 to 69%) for Burdekin Agricultural College (BAC) logs and 41.9% (range 20 to 61%) for Katherine (NT) logs. These figures are about 10% higher than compared to 30-year-old Khaya study by Armstrong et al. (2007) however they are inflated as the green boards were not docked to remove wane prior to being tallied. Of the recovered sawn, dried and dressed volume from the BAC logs, based on the cambial face of boards, 27% could potentially be used for select grade, 40% for medium feature grade and 26% for high feature grades. The heart faces had a slightly higher recovery of select (30%) and medium feature (43%) grade boards with a reduction in the volume of high feature (22%) and reject (6%) grade boards. Distribution of board grades for the NT site aged 14 years followed very similar trends to those of the BAC site boards with an average (between facial and cambial face) 27% could potentially be used for select grade, 42% for medium feature grade, 26% for high feature grade and 5% reject. Relatively to some other subtropical eucalypts, there was a low incidence of borer attack. The major grade limiting defects for both medium and high feature grade boards recovered from the BAC site were knots and wane. The presence of large knots may reflect both management practices and the nature of the genetic material at the site. This stand was not managed for timber production with a very late pruning implemented at about age 12 years. The large amount of wane affected boards is indicative of logs with a large taper and the presence of significant sweep. Wane, knots and skip were the major grade limiting defects for the NT site reflecting considerable amounts of sweep with large taper as might be expected in younger trees. The green veneer recovered from billets of seven Khaya trees rotary peeled on a spindleless lathe produced a recovery of 83% of green billet volume. Dried veneer recovery ranged from 40 to 74 % per billet with an average of 64%. All of the recovered grades were suitable for use in structural ply in accordance to AS/NZ 2269: 2008. The majority of veneer sheets recovered from all billets was C grade (27%) with 20% making D grade and 13% B grade. Total dry sliced veneer recovery from the logs of the two largest logs from each location was estimated to be 41.1%. Very positive results have been recorded in this small scale study. The amount of colour development observed and the very reasonable recoveries of both sawn and veneer products, with a good representation of higher grades in the product distribution, is encouraging. The prospects for significant improvement in these results from well managed and productive stands grown for high quality timber should be high. Additionally, the study has shown the utility of non-destructive evaluation techniques for use in tree improvement programs to improve the quality of future plantations. A few trees combined several of the traits desired of individuals for a first breeding population. Fortunately, the two most promising trees (32, 19) had already been selected for breeding on external traits, and grafts of them are established in the seed orchard.

Eliciting and encoding expert knowledge on variable selection into classical or Bayesian species distribution models

The quality of species distribution models (SDMs) relies to a large degree on the quality of the input data, from bioclimatic indices to environmental and habitat descriptors (Austin, 2002). Recent reviews of SDM techniques, have sought to optimize predictive performance e.g. Elith et al., 2006. In general SDMs employ one of three approaches to variable selection. The simplest approach relies on the expert to select the variables, as in environmental niche models Nix, 1986 or a generalized linear model without variable selection (Miller and Franklin, 2002). A second approach explicitly incorporates variable selection into model fitting, which allows examination of particular combinations of variables. Examples include generalized linear or additive models with variable selection (Hastie et al. 2002); or classification trees with complexity or model based pruning (Breiman et al., 1984, Zeileis, 2008). A third approach uses model averaging, to summarize the overall contribution of a variable, without considering particular combinations. Examples include neural networks, boosted or bagged regression trees and Maximum Entropy as compared in Elith et al. 2006. Typically, users of SDMs will either consider a small number of variable sets, via the first approach, or else supply all of the candidate variables (often numbering more than a hundred) to the second or third approaches. Bayesian SDMs exist, with several methods for eliciting and encoding priors on model parameters (see review in Low Choy et al. 2010). However few methods have been published for informative variable selection; one example is Bayesian trees (O’Leary 2008). Here we report an elicitation protocol that helps makes explicit a priori expert judgements on the quality of candidate variables. This protocol can be flexibly applied to any of the three approaches to variable selection, described above, Bayesian or otherwise. We demonstrate how this information can be obtained then used to guide variable selection in classical or machine learning SDMs, or to define priors within Bayesian SDMs.

Biochemical and structural characterization of residue 96 mutants of Plasmodium falciparum triosephosphate isomerase: active-site loop conformation, hydration and identification of a dimer-interface ligand-binding site

Plasmodium falciparum TIM (PfTIM) is unique in possessing a Phe residue at position 96 in place of the conserved Ser that is found in TIMs from the majority of other organisms. In order to probe the role of residue 96, three PfTIM mutants, F96S, F96H and F96W, have been biochemically and structurally characterized. The three mutants exhibited reduced catalytic efficiency and a decrease in substrate-binding affinity, with the most pronounced effects being observed for F96S and F96H. The k(cat) values and K-m values are (2.54 +/- 0.19) x 10(5) min(-1) and 0.39 +/- 0.049 mM, respectively, for the wild type; (3.72 +/- 0.28) x 10(3) min(-1) and 2.18 +/- 0.028 mM, respectively, for the F96S mutant;(1.11 +/- 0.03) x 10(4) min(-1) and 2.62 +/- 0.042 mM, respectively, for the F96H mutant; and (1.48 +/- 0.05) x 10(5) min(-1) and 1.20 +/- 0.056 mM, respectively, for the F96W mutant. Unliganded and 3-phosphoglycerate (3PG) complexed structures are reported for the wild-type enzyme and the mutants. The ligand binds to the active sites of the wild-type enzyme (wtPfTIM) and the F96W mutant, with a loop-open state in the former and both open and closed states in the latter. In contrast, no density for the ligand could be detected at the active sites of the F96S and F96H mutants under identical conditions. The decrease in ligand affinity could be a consequence of differences in the water network connecting residue 96 to Ser73 in the vicinity of the active site. Soaking of crystals of wtPfTIM and the F96S and F96H mutants resulted in the binding of 3PG at a dimer-interface site. In addition, loop closure at the liganded active site was observed for wtPfTIM. The dimer-interface site in PfTIM shows strong electrostatic anchoring of the phosphate group involving the Arg98 and Lys112 residues of PfTIM.