Approximate Bayesian computation using indirect inference

We present a novel approach for developing summary statistics for use in approximate Bayesian computation (ABC) algorithms by using indirect inference. ABC methods are useful for posterior inference in the presence of an intractable likelihood function. In the indirect inference approach to ABC the parameters of an auxiliary model fitted to the data become the summary statistics. Although applicable to any ABC technique, we embed this approach within a sequential Monte Carlo algorithm that is completely adaptive and requires very little tuning. This methodological development was motivated by an application involving data on macroparasite population evolution modelled by a trivariate stochastic process for which there is no tractable likelihood function. The auxiliary model here is based on a beta–binomial distribution. The main objective of the analysis is to determine which parameters of the stochastic model are estimable from the observed data on mature parasite worms.

The relationship between self-reported animal fear and ERP modulation : Evidence for enhanced processing and fear of harmless invertebrates in snake- and spider-fearful individuals

The present study used ERPs to compare processing of fear-relevant (FR) animals (snakes and spiders) and non-fear-relevant (NFR) animals similar in appearance (worms and beetles). EEG was recorded from 18 undergraduate participants (10 females) as they completed two animal-viewing tasks that required simple categorization decisions. Participants were divided on a post hoc basis into low snake/spider fear and high snake/spider fear groups. Overall, FR animals were rated higher on fear and elicited a larger LPC. However, individual differences qualified these effects. Participants in the low fear group showed clear differentiation between FR and NFR animals on subjective ratings of fear and LPC modulation. In contrast, participants in the high fear group did not show such differentiation between FR and NFR animals. These findings suggest that the salience of feared-FR animals may generalize on both a behavioural and electro-cortical level to other animals of similar appearance but of a non-harmful nature.

Evaluation of Attacks and Countermeasures in Large Scale Networks

Computer worms represent a serious threat for modern communication infrastructures. These epidemics can cause great damage such as financial losses or interruption of critical services which support lives of citizens. These worms can spread with a speed which prevents instant human intervention. Therefore automatic detection and mitigation techniques need to be developed. However, if these techniques are not designed and intensively tested in realistic environments, they may cause even more harm as they heavily interfere with high volume communication flows. We present a simulation model which allows studies of worm spread and counter measures in large scale multi-AS topologies with millions of IP addresses.

Suppression of mRNAs encoding tegument tetraspanins from schistosoma mansoni results in impaired tegument turnover

Schistosomes express a family of integral membrane proteins, called tetraspanins (TSPs), in the outer surface membranes of the tegument. Two of these tetraspanins, Sm-TSP-1 and Sm-TSP-2, confer protection as vaccines in mice, and individuals who are naturally resistant to S. mansoni infection mount a strong IgG response to Sm-TSP-2. To determine their functions in the tegument of S. mansoni we used RNA interference to silence expression of Sm-tsp-1 and Sm-tsp-2 mRNAs. Soaking of parasites in Sm-tsp dsRNAs resulted in 61% (p = 0.009) and 74% (p = 0.009) reductions in Sm-tsp-1 and Sm-tsp-2 transcription levels, respectively, in adult worms, and 67%–75% (p = 0.011) and 69%–89% (p = 0.004) reductions in Sm-tsp-1 and Sm-tsp-2 transcription levels, respectively, in schistosomula compared to worms treated with irrelevant control (luciferase) dsRNA. Ultrastructural morphology of adult worms treated in vitro with Sm-tsp-2 dsRNA displayed a distinctly vacuolated and thinner tegument compared with controls. Schistosomula exposed in vitro to Sm-tsp-2 dsRNA had a significantly thinner and more vacuolated tegument, and morphology consistent with a failure of tegumentary invaginations to close. Injection of mice with schistosomula that had been electroporated with Sm-tsp-1 and Sm-tsp-2 dsRNAs resulted in 61% (p = 0.005) and 83% (p = 0.002) reductions in the numbers of parasites recovered from the mesenteries four weeks later when compared to dsRNA-treated controls. These results imply that tetraspanins play important structural roles impacting tegument development, maturation or stability.

Neuro-angiostrongylosis in wild Black and Grey-headed flying foxes (Pteropus spp)

Objective: To identify nematodes seen in histological sections of brains of flying foxes (fruit bats) and describe the associated clinical disease and pathology. Proceedures: Gross and histological examination of brains from 86 free-living flying foxes with neurological disease was done as part of an ongoing surveillance program for Australian bat lyssavirus. Worms were recovered, or if seen in histological sections, extracted by maceration of half the brain and identified by microscopic examination. Histological archives were also reviewed. Results: There was histological evidence of angiostrongylosis in 16 of 86 recently submitted flying foxes with neurological disease and in one archival case from 1992. In 10 flying foxes, worms were definitively identified as Angiostrongylus cantonensis fifth-stage larvae. A worm fragment and third stage larvae were identified as Angiostrongylus sp, presumably A cantonensis, in a further three cases. The clinical picture was dominated by paresis, particularly of the hindlimbs, and depression, with flying foxes surviving up to 22 days in the care of wildlife volunteers. Brains containing fifthstage larvae showed a moderate to severe eosinophilic and granulomatous meningoencephalitis (n = 14), whereas there was virtually no inflammation of the brains of bats which died when infected with only smaller, third-stage larvae (n = 3). There was no histological evidence of pulmonary involvement. Conclusion: This is the first report of the recovery and identification of A cantonensis from free-living Australian wildlife. While angiostrongylosis is a common cause of paresis in flying foxes, the initial clinical course cannot be differentiated from Australian bat lyssavirus infection, and wildlife carers should be urged not to attempt to rehabilitate flying foxes with neurological disease.

A detached leaf bioassay to screen Durian cultivars for susceptibility to Phytophthora palmivora

A detached-leaf bioassay was developed and used to screen five durian (Durio zibethinus) cultivars against Phytophthora palmivora isolates from a trunk canker, root and fruit. The fruit isolate was less aggressive than the canker and root isolates. The bioassay using the canker isolate was later used to determine the variation in resistance of D. macarantha and nineteen cultivars of D. zibethinus. The cultivars displayed a range of responses with Parung and Gob being most tolerant, with Gaan Yaow, Chanee and Penang 88 being susceptible. The remaining germplasm fell between Gaan Yaow and Penang 88 in susceptibility. The leaf bioassay was found to be a rapid and reliable method for assessing the susceptibility of durian cultivars.

Commercial application of polychaete sand filters for wastewater remediation and broodstock feeds

Summary Prototype sand-worm filtration beds were constructed at two prawn farms and one fish farm to assess and demonstrate their polychaete (marine worm) production and wastewater remediation capacities at semi-commercial scale. Wastewater treatment properties were monitored and worms produced were assessed and either sold for bait or used by the farms’ hatcheries as broodstock (prawn or fish breeder) feed. More than 34 megalitres of prawn- and fish-pond water was beneficially treated in the 116-319-d trial. The design of the polychaete-assisted sand filters (PASFs) constructed at each farm affected their water handling rates, which on average ranged from 315 to 1000 L m-2 d-1 at the three farms. A low profile design incorporating shallow bunded ponds made from polyethylene liner and timber stakes provided the easiest method of construction. This simple design applied at broad scale facilitated the highest quantities of treated water and the greatest worm production. Designs with higher sides increased the head pressure above the sand bed surface, thus increasing the amount of water that could be treated each day. Most water qualities were affected in a similar way to that demonstrated in the previous tank trials: dissolved oxygen, pH, total suspended solids and chlorophyll a levels were all consistently significantly lowered as pond water percolated through the sand bed, and dissolved forms of nitrogen and phosphorus were marginally increased on several occasions. However, unlike the previous smaller-scale tank trials, total nitrogen (TN) and total phosphorus (TP) levels were both significantly lowered by these larger-scale PASFs. The reasons for this are still unclear and require further research. Maximum TN and TP removals detected in the trial were 48.8% and 67.5%, respectively, and average removals (in unfed beds) at the three farms ranged from 20.0 to 27.7% for TN and from 22.8 to 40.8% for TP. Collectively, these results demonstrate the best suspended solids, chlorophyll and macronutrient removal capacities so far reported for any mariculture wastewater treatment methodology to date. Supplemental feeding of PASFs with fish meal was also investigated at one farm as a potential means of increasing their polychaete biomass production. Whilst fed beds produced higher biomass (152 ± 35 g m-2) compared with unfed beds (89 ± 17 g m-2) after 3.7 months of operation, the low number of replicates (2) prevented statistically significant differences from being demonstrated for either growth or survival. At harvest several months later, worm biomass production was estimated to be similar to, or in slight excess of, previously reported production levels (300-400 g m-2). Several qualities of filtered water appear to have been affected by supplemental feeding: it appeared to marginally lower dissolved oxygen and pH levels, and increased the TN and TP levels though not so much to eliminate significant beneficial water treatment effects. Periodic sampling during an artificial-tide demonstrated the tendency for treated-water quality changes during the first hour of filtration. Total nitrogen and ammonia peaked early in the tidal flow and then fell to more stable levels for the remainder of the filtration period. Other dissolved nutrients also showed signs of this sand-bed-flushing pattern, and dissolved oxygen tended to climb during the first hour and become more stable thereafter. These patterns suggest that the routine sampling of treated water undertaken at mid-inflow during the majority of the wider study would likely have overestimated the levels of TN and dissolved nutrients discharged from the beds, and hence underestimated the PASFs treatment efficacies in this regard. Analyses of polychaete biomass collected from each bed in the study revealed that the worms were free from contamination with the main prawn viruses that would create concerns for their feeding to commercial prawn broodstock in Australia. Their documented proximal and nutritional contents also provide a guide for hatchery operators when using live or frozen stock. Their dry matter content ranged from 18.3 to 22.3%, ash ranged from 10.2 to 14.0%, gross energy from 20.2 to 21.5 MJ kg-1, and fat from 5.0 to 9.2%. Their cholesterol levels ranged from 0.86 to 1.03% of dry matter, whilst total phospholipids range from 0.41 to 0.72%. Thirty-one different fatty acids were present at detectable (≥0.005% of dry matter) levels in the sampled worm biomass. Palmitic acid was by far the most prevalent fatty acid detected (1.21 ± 0.18%), followed by eicosapentaenoic (EPA) (0.48 ± 0.03%), stearic (0.46 ± 0.04%), vaccenic (0.38 ± 0.05%), adrenic (0.35 ± 0.02%), docosadienoic (0.28 ± 0.02%), arachidonic (AA) (0.22 ± 0.01%), palmitoleic (0.20 ± 0.04%) and 23 other fatty acids with average contents of less than 0.2% of dry matter. Supplemental feeding with fish meal at one farm appeared to increase the docosahexaenoic acid (DHA) content of the worms considerably, and modify the average AA : EPA : DHA from 1.0 : 2.7 : 0.3 to 1.0 : 2.0 : 1.1. Consistent with previous results, the three most heavily represented amino acids in the dry matter of sampled worms were glutamic acid (8.5 ± 0.2%), aspartic acid (5.5 ± 0.1%) and glycine (4.9 ± 0.5%). These biomass content results suggest that worms produced in PASF systems are well suited to feeding to prawn and fish broodstock, and provide further strong evidence of the potential to modify their contents for specific nutritional uses. The falling wild-fishery production of marine bloodworms in Queensland is typical of diminishing polychaete resources world-wide and demonstrates the need to develop sustainable production methods here and overseas. PASF systems offer the dual benefits of wastewater treatment for environmental management and increased productivity through a valuable secondary crop grown exclusively on waste nutrients.

Polychaete-assisted sand filters

The objective of this study was to investigate the productivity and functionality of sand filters stocked with marine worms for wastewater treatment at mariculture facilities. Medium bedding sand which is commonly available in coastal sedimentary deposits and nereidid polychaetes (Perinereis nuntia and P. helleri) from Moreton Bay in southeast Queensland were combined and studied in down-flow sand filtration beds. This combination appears to provide a new option for brackish wastewater treatment whereby the activities of the worms help to prevent sand filters from blocking with organic debris and their biomass offers a valuable by-product. Phytoplankton-rich pond waters percolating through sand-worm beds were reliably treated in several useful ways: suspended solids and chlorophyll a levels were consistently reduced by >50% by the process, and nutrients were converted into bio-available dissolved forms. Dissolved oxygen, redox and pH levels were also lowered significantly by the process. Water treatment rates of approx 1500 L m-2 d-1 were routinely achieved. P. nuntia appeared more suitable than P. helleri for stocking directly into sand filtration beds as nectochaetes, but generally exhibited slower growth. Survival and growth were influenced by stocking density. Sand-filter beds stocked with juvenile worms and fed only with eutrophic pond water demonstrated polychaete production capacities in the order of 300-400 g m-2 (eg. P. helleri: 328 g m-2 in 16 weeks). These results show how nereidid polychaetes can be reliably produced within simple, low-maintenance sand filters, and provide data necessary for the functional integration of this novel wastewater treatment system into contemporary seafood farming systems.

Polychaete-assisted sand filters – prawn farm wastewater remediation trial

Medium bedding sand which is commonly available in coastal sedimentary deposits, and a marine polychaete-worm species from Moreton Bay recently classified as Perinereis helleri (Nereididae), were deployed in a simple low-maintenance sand filter design that potentially has application at large scale. Previous work had shown that this physical and biological combination can provide a new option for saline wastewater treatment, since the worms help to prevent sand filter blocking with organic debris and offer a profitable by-product. To test the application of this new concept in a commercial environment, six 1.84 m2 Polychaete-assisted sand filters were experimentally tested for their ability to treat wastewater from a semi-intensive prawn culture pond. Polychaetes produced exclusively on the waste nutrients that collected in these gravity-driven sand filters were assessed for their production levels and nutritional contents. Water parameters studied included temperature, salinity, pH, dissolved oxygen (DO), oxidation/ reduction potential (redox), suspended solids, chlorophyll a, biological oxygen demand (BOD), and common forms of nitrogen and phosphorus. Pond water which had percolated through the sand bed had significantly lower pH, DO and redox levels compared with inflow water. Suspended solids and chlorophyll a levels were consistently more than halved by the process. Reductions in BOD appeared dependant on regular subsurface flows. Only marginal reductions in total nitrogen and phosphorus were documented, but their forms were altered in a potentially useful way: dissolved forms (ammonia and orthophosphate) were generated by the process, and this remineralisation also seemed to be accentuated by intermittent flow patterns. Flow rates of approximately 1,500 L m-2 d-1 were achieved suggesting that a 1 ha polychaete bed of this nature could similarly treat the discharge from a 10 ha semi-intensive prawn farm. Sixteen weeks after stocking sand beds with one-month-old P. helleri, over 3.6 kg of polychaete biomass (wet weight) was recovered from the trial. Production on a sand bed area basis was 328 g m-2. Similar (P>0.05) overall biomass production was found for the two stocking densities tested (2000 and 6000 m-2; n = 3), but survival was lower and more worms were graded as small (<0.6 g) when produced at the higher density (28.2 ± 1.5 % and approx. 88 %, respectively) compared with the lower density (46.8 ± 4.4 % and approx. 76 %, respectively). When considered on a weight for weight basis, about half of the worm biomass produced was generally suitable for use as bait. The nutritional contents of the worms harvested were analysed for different stocking densities and graded sizes. These factors did not significantly affect their percentages of dry matter (DM) (18.23 ± 0.57 %), ash (19.77 ± 0.80 % of DM) or gross energy 19.39 ± 0.29 MJ kg-1 DM) (n = 12). Although stocking density did not affect the worms’ nitrogen and phosphorus contents, small worms had a higher mean proportion of nitrogen and phosphorus (10.57 ± 0.17 % and 0.70 ± 0.01 % of DM, respectively) than large worms (9.99 ± 0.12 % and 0.65 ± 0.01 % of DM, respectively) (n = 6). More lipid was present in large worms grown at the medium density (11.20 ± 0.19 %) compared with the high density (9.50 ± 0.31 %) and less was generally found in small worms (7.1-7.6 % of DM). Mean cholesterol and total phospholipid levels were 5.24 ± 0.15 mg g-1 and 13.66 ± 2.15 mg g-1 DM, respectively (n = 12). Of the specific phospholipids tested, phosphatidyl-serine or sphingomyelin were below detection limits (<0.05 mg g-1), whilst mean levels of phosphatidyl-ethanolamine, phosphatidyl-inositol, phosphatidyl-choline and lysophosphatidyl-choline were 6.89 ± 1.09, 0.89 ± 0.26, 4.04 ± 1.17 and 1.84 ± 0.37 mg g-1, respectively (n = 12). Culture density generally had a more pronounced effect on phospholipid contents than did size of worms. By contrast, worm size had a more pronounced effect on total fatty acid contents, with large worms containing significantly higher (P<0.001) levels on a DM basis (46.88 ± 2.46 mg g-1) than smaller worms (27.76 ± 1.28 mg g-1). A very broad range of fatty acids were detected with palmitic acid being the most heavily represented class (up to 14.23 ± 0.49 mg g-1 DM or 27.28 ± 0.22 % of total fatty acids). Other heavily represented classes included stearic acid (7.4-8.8 %), vaccenic acid (6.8-7.8 %), arachidonic acid (3.5-4.4 %), eicosapentaenoic acid (9.9-13.8 %) and docosenoic acid (5.7-7.0 %). Stocking density did not affect (P>0.05) the levels of amino acids present in polychaete DM, but there was generally less of each amino acid tested on a weight per weight basis in large worms than in small worms. This difference was significant (P<0.05) for the most heavily represented classes being glutamic acid (73-77 mg g-1), aspartic acid (50-54 mg g-1), and glycine (46-53 mg g-1). These results demonstrate how this polychaete species can be planted and sorted at harvest according to various strategies aimed at providing biomass with specific physical and nutritional qualities for different uses.

CRC20093 Increasing Diagnostic Capacity in Thailand

Accurate identification of pests is essential for practically all aspects of agricultural development and is critical to the operations of biosecurity that safeguard agricultural integrity and facilitate trade. Diagnostic capability is at the forefront of and complementary to, activities such as border protection, incursion management, surveillance and pest and disease certification. The efficiency of a biosecurity system therefore depends largely on the feedback between these activities and diagnostics. Australian scientists will train Thai scientists in diagnostics and surveillance to provide the Thai DOA with skills that will aid in the development of a Thai Diagnostic Network. The skills will be taught using a range of pests, including some which have particular biosecurity importance for both Australia and Thailand such as citrus canker, potato viruses and fruit flies.

Stem cankers on sunflower (Helianthus annuus) in Australia reveal a complex of pathogenic Diaporthe (Phomopsis) species.

The identification of Diaporthe (anamorph Phomopsis) species associated with stem canker of sunflower (Helianthus annuus) in Australia was studied using morphology, DNA sequence analysis and pathology. Phylogenetic analysis revealed three clades that did not correspond with known taxa, and these are believed to represent novel species. Diaporthe gulyae sp. nov. is described for isolates that caused a severe stem canker, specifically pale brown to dark brown, irregularly shaped lesions centred at the stem nodes with pith deterioration and mid-stem lodging. This pathogenicity of D. gulyae was confirmed by satisfying Koch's Postulates. These symptoms are almost identical to those of sunflower stem canker caused by D. helianthi that can cause yield reductions of up to 40% in Europe and the USA, although it has not been found in Australia. We show that there has been broad misapplication of the name D. helianthi to many isolates of Diaporthe ( Phomopsis) found causing, or associated with, stem cankers on sunflower. In GenBank, a number of isolates had been identified as D. helianthi, which were accommodated in several clades by molecular phylogenetic analysis. Two less damaging species, D. kochmanii sp. nov. and D. kongii sp. nov., are also described from cankers on sunflower in Australia.

Effects of living crown reduction on needle element status of Scots pine

A wide range of biotic and abiotic factors, operating over different time perspectives and intensities, cause defoliation and a rapid decrease in the crown size of trees. Scleroderris canker disease [Gremmeniella abietina (Lagerb.) Morelet] has caused widespread crown reduction and tree mortality in Scots pine (Pinus sylvestris L) in forests in Scandinavia during the last three decades. In the 1980's, attempts were made to show, on the basis of the higher foliar N and S concentrations of affected pines in the diseased area, that sulphur and nitrogen deposition predispose trees to G. abietina. Unfortunately, in many studies on defoliated trees, exceptionally high or low needle mineral nutrient concentrations are still often interpreted as one of the causes of tree injury and not, conversely, as the result. In this thesis, three different field experiments, with foliar analysis as the main study method, were conducted in order to asses the possible long-term effects of living crown reduction on the needle nutrient concentrations of Scots pine trees in southern Finland. The crown ratio and length of the living crown were used to estimate the amount of defoliation in the reduced canopies. The material for the partial studies was collected and a total of 968 foliar samples were analysed individually (15-17 elements/sample) on a total of 488 sample trees (140 diseased, 116 pruned and 232 control trees) during the years 1987-1996 in 13 Scots pine stands. All the three experiments of this thesis provided significant evidence that severe, disease-induced defoliation or artificial pruning of the living branches can induce long-lasting nutritional changes in the foliage of the recovering trees under the typical growing conditions for Scots pine. The foliar concentrations of all the 17 mineral nutrients/elements analysed were affected, to a varying degree, by artificial pruning during the following three years. Although Scots pine, as an evergreen conifer, is considered to have low induced chemical responses to defoliation, this study proved experimentally under natural forest conditions that severe artificial pruning or disease-induced defoliation of Scots pine trees may induce biologically significant changes in the concentrations of most of the important macro- and micronutrients, as well as of carbon, in refoliated needles. Concerning the studies in this thesis, I find the results significant in providing new information about the long-term effects of rapid living crown reduction on the foliar nutrient and element status of Scots pine trees. Key words: Foliar analysis, defoliation, needle loss, pruning, nutrients, Pinus sylvestris, Gremmeniella abietina

Rhizoctonia solani as a potato pathogen : Variation of isolates in Finland and host response

Rhizoctonia solani is a soil inhabiting basidiomycetous fungus able to induce a wide range of symptoms in many plant species. This genetically complex species is divided to 13 anastomosis groups (AG), of which AG-3 is specialized to infect potato. However, also a few other AGs are able to infect or live in close contact with potato. On potato, R. solani infection causes two main types of diseases including stem canker observed as a dark brown lesions on developing stems and stolons, and black scurf that develops on new tubers close to the time of harvest. These disease symptoms are collectively called a ‘Rhizoctonia disease complex’. Between the growing seasons R. solani survives in soil and plant debri as sclerotia or as the sclerotia called black scurf on potato tubers which when used as seed offer the main route for dispersal of the fungus to new areas. The reasons for the dominance of AG-3 on potato seem to be attributable to its highly specialization to potato and its ability to infect and form sclerotia efficiently at low temperatures. In this study, a large nationwide survey of R. solani isolates was made in potato crops in Finland. Almost all characterized isolates belonged to AG-3. Additionally, three other AGs (AG-2-1, AG-4 and AG-5) were found associated with symptoms on potato plants but they were weaker pathogens on potato than AG-3 as less prone to form black scurf. According to phylogenetic analysis of the internal transcribed sequences (ITS) of the ribosomal RNA genes the Finnish AG-3 isolates are closely related to each other even though a wide variation of physiological features was observed between them. Detailed analysis of the ITS regions revealed single nucleotide polymorphism in 14 nucleotide positions of ITS-1 and ITS-2. Additionally, compensatory base changes on ITS-2 were detected which suggests that potato-infecting R. solani AG-3 could be considered as a separate species instead of an AG of R. solani. For the first time, molecular defence responses were studied and detected during the early phases of interaction between R. solani AG-3 and potato. Extensive systemic signalling for defence exploiting several known defence pathways was activated as soon as R. solani came into close contact with the base of a sprout. The defence response was strong enough to protect vulnerable sprout tips from new attacks by the pathogen. These results at least partly explain why potato emergence is eventually successful even under heavy infection pressure by R. solani.

The Oppenheimer Family

History of the Oppenheimer Family from Oppenheim and Worms; essay is built around 'seven remarkable Oppenheimers' since the year 1400.