Morphological and molecular diversity of Colletotrichum spp. causing pepper spot and anthracnose of lychee (Litchi chinensis) in Australia

Since the 1980s a new disease has been affecting Australian lychee. Pepper spot appears as small, black superficial lesions on fruit, leaves, petioles and pedicels and is caused by Colletotrichum gloeosporioides, the same fungus that causes postharvest anthracnose of lychee fruit. The aim of this study was to determine if a new genotype of C.gloeosporioides is responsible for the pepper spot symptom. Morphological assessments, arbitrarily-primed PCR (ap-PCR) and DNA sequencing studies did not differentiate isolates of C.gloeosporioides from anthracnose and pepper spot lesions. The ap-PCR identified 21 different genotypes of C.gloeosporioides, three of which were predominant. A specific genotype identified using ap-PCR was associated with the production of the teleomorph in culture. Analysis of sequence data of ITS and -tubulin regions of representative isolates did not group the lychee isolates into a monophyletic clade; however, given the majority of the isolates were from one of three genotypes found using ap-PCR, the possibility of a lychee specific group of C.gloeosporioides is discussed.

Pleistocene isolation, secondary introgression and restricted contemporary gene flow in the pig-eye shark, Carcharhinus amboinensis across northern Australia

We examine the structure and phylogeography of the pig-eye shark (Carcharhinus amboinensis) common in shallow coastal environments in northern Australia using two types of genetic markers, two mitochondrial (control region and NADH hydrogenase 4) and two nuclear (microsatellite and Rag 1) DNA. Two populations were defined within northern Australia on the basis of mitochondrial DNA evidence, but this result was not supported by nuclear microsatellite or Rag 1 markers. One possibility for this structure might be sex-specific behaviours such as female philopatry, although we argue it is doubtful that sufficient time has elapsed for any potential signatures from this behaviour to be expressed in nuclear markers. It is more likely that the observed pattern represents ancient populations repeatedly isolated and connected during episodic sea level changes during the Pleistocene epoch, until current day with restricted contemporary gene flow maintaining population genetic structure. Our results show the need for an understanding of both the history and ecology of a species in order to interpret patterns in genetic structure.

Evaluation of ELISA coupled with Western blot as a surveillance tool for Trichinella infection in wild boar (Sus scrofa)

Trichinella surveillance in wildlife relies on muscle digestion of large samples which are logistically difficult to store and transport in remote and tropical regions as well as labour-intensive to process. Serological methods such as enzyme-linked immunosorbent assays (ELISAs) offer rapid, cost-effective alternatives for surveillance but should be paired with additional tests because of the high false-positive rates encountered in wildlife. We investigated the utility of ELISAs coupled with Western blot (WB) in providing evidence of Trichinella exposure or infection in wild boar. Serum samples were collected from 673 wild boar from a high- and low-risk region for Trichinella introduction within mainland Australia, which is considered Trichinella-free. Sera were examined using both an 'in-house' and a commercially available indirect-ELISA that used excretory secretory (E/S) antigens. Cut-off values for positive results were determined using sera from the low-risk population. All wild boar from the high-risk region (352) and 139/321 (43.3%) of the wild boar from the low-risk region were tested by artificial digestion. Testing by Western blot using E/S antigens, and a Trichinella-specific real-time PCR was also carried out on all ELISA-positive samples. The two ELISAs correctly classified all positive controls as well as one naturally infected wild boar from Gabba Island in the Torres Strait. In both the high- and low-risk populations, the ELISA results showed substantial agreement (k-value = 0.66) that increased to very good (k-value = 0.82) when WB-positive only samples were compared. The results of testing sera collected from the Australian mainland showed the Trichinella seroprevalence was 3.5% (95% C.I. 0.0-8.0) and 2.3% (95% C.I. 0.0-5.6) using the in-house and commercial ELISA coupled with WB respectively. These estimates were significantly higher (P < 0.05) than the artificial digestion estimate of 0.0% (95% C.I. 0.0-1.1). Real-time PCR testing of muscle from seropositive animals did not detect Trichinella DNA in any mainland animals, but did reveal the presence of a second larvae-positive wild boar on Gabba Island, supporting its utility as an alternative, highly sensitive method in muscle examination. The serology results suggest Australian wildlife may have been exposed to Trichinella parasites. However, because of the possibility of non-specific reactions with other parasitic infections, more work using well-defined cohorts of positive and negative samples is required. Even if the specificity of the ELISAs is proven to be low, their ability to correctly classify the small number of true positive sera in this study indicates utility in screening wild boar populations for reactive sera which can be followed up with additional testing. (C) 2013 Elsevier B.V. All rights reserved.

A Bayesian hurdle model for analysis of an insect resistance monitoring database

Motivated by the analysis of the Australian Grain Insect Resistance Database (AGIRD), we develop a Bayesian hurdle modelling approach to assess trends in strong resistance of stored grain insects to phosphine over time. The binary response variable from AGIRD indicating presence or absence of strong resistance is characterized by a majority of absence observations and the hurdle model is a two step approach that is useful when analyzing such a binary response dataset. The proposed hurdle model utilizes Bayesian classification trees to firstly identify covariates and covariate levels pertaining to possible presence or absence of strong resistance. Secondly, generalized additive models (GAMs) with spike and slab priors for variable selection are fitted to the subset of the dataset identified from the Bayesian classification tree indicating possibility of presence of strong resistance. From the GAM we assess trends, biosecurity issues and site specific variables influencing the presence of strong resistance using a variable selection approach. The proposed Bayesian hurdle model is compared to its frequentist counterpart, and also to a naive Bayesian approach which fits a GAM to the entire dataset. The Bayesian hurdle model has the benefit of providing a set of good trees for use in the first step and appears to provide enough flexibility to represent the influence of variables on strong resistance compared to the frequentist model, but also captures the subtle changes in the trend that are missed by the frequentist and naive Bayesian models. © 2014 Springer Science+Business Media New York.

Herbicide resistance modelling: Past, present and future

Computer simulation modelling is an essential aid in building an integrated understanding of how different factors interact to affect the evolutionary and population dynamics of herbicide resistance, and thus in helping to predict and manage how agricultural systems will be affected. In this review, we first discuss why computer simulation modelling is such an important tool and framework for dealing with herbicide resistance. We then explain what questions related to herbicide resistance have been addressed to date using simulation modelling, and discuss the modelling approaches that have been used, focusing first on the earlier, more general approaches, and then on some newer, more innovative approaches. We then consider how these approaches could be further developed in the future, by drawing on modelling techniques that are already employed in other areas, such as individual-based and spatially explicit modelling approaches, as well as the possibility of better representing genetics, competition and economics, and finally the questions and issues of importance to herbicide resistance research and management that could be addressed using these new approaches are discussed. We conclude that it is necessary to proceed with caution when increasing the complexity of models by adding new details, but, with appropriate care, more detailed models will make it possible to integrate more current knowledge in order better to understand, predict and ultimately manage the evolution of herbicide resistance. © 2014 Society of Chemical Industry.

Polarized immune responses modulated by layered double hydroxides nanoparticle conjugated with CpG

Modulation of the immune response is an important step in the induction of protective humoral and cellular immunity against pathogens. In this study, we investigated the possibility of using a nanomaterial conjugated with the toll-like receptor (TLR) ligand CpG to modulate the immune response towards the preferred polarity. MgAl-layered double hydroxide (LDH) nanomaterial has a very similar chemical composition to Alum, an FDA approved adjuvant for human vaccination. We used a model antigen, ovalbumin (OVA) to demonstrate that MgAl-LDH had comparable adjuvant activity to Alum, but much weaker inflammation. Conjugation of TLR9 ligand CpG to LDH nanoparticles significantly enhanced the antibody response and promoted a switch from Th2 toward Th1 response, demonstrated by a change in the IgG2a:IgG1 ratio. Moreover, immunization of mice with CpG-OVA-conjugated LDH before challenge with OVA-expressing B16/F10 tumor cells retarded tumor growth. Together, these data indicate that LDH nanomaterial can be used as an immune adjuvant to promote Th1 or Th2 dominant immune responses suitable for vaccination purposes.

Bioactive Properties of Mushroom (Agaricus bisporus) Stipe Extracts

The antibacterial activity and total phenolic (TP) content of Agaricus bisporus stipes were assessed using solvent and water extracts to determine its bioactivity. Extraction methods included accelerated solvent extraction (ASE) and hot water followed by membrane concentration. Water extract from ASE had the highest TP of 1.08 gallic acid equivalents (GAE)/g dry weight (DW) followed by ethanol at 0.61 mg GAE/g DW and 0.11 mg GAE/g DW for acetone. Acetone extracts inhibited Escherichia coli and Staphylococcus aureus at less than 50%; ethanol inhibited E. coli at 61.9% and S. aureus at 56.6%; and ASE water inhibited E. coli at 78.6% and S. aureus at 65.4%. The TP content of membrane concentrated extract of mushroom was 17 mg GAE in 100 mL. Membrane concentrated water extracts had a higher percentage inhibition on S. aureus than E. coli. Overall, the results were promising for further application of mushroom stipe extracts as a functional food additive. Practical Applications Mushrooms are known for their health benefits and have been identified as a good source of nutrients. The highly perishable nature of mushrooms warrants further processing and preservation to minimize losses along the supply chain. This study explores the possibility of adding value to mushroom stipes, a by-product of the fresh mushroom industry. The extracts assessed indicate the antibacterial activity and phenolic content, and the potential of using these extracts as functional ingredients in the food industry. This study provides valuable information to the scientific community and to the industries developing novel ingredients to meet the market demand for natural food additives.

Prevalence and potential fitness cost of weak phosphine resistance in Tribolium castaneum (Herbst) in eastern Australia

The prevalence of resistance to phosphine in the rust-red flour beetle, Tribolium castaneum, from eastern Australia was investigated, as well as the potential fitness cost of this type of resistance. Discriminating dose tests on 115 population samples collected from farms from 2006 to 2010 showed that populations containing insects with the weakly resistant phenotype are common in eastern Australia (65.2 of samples), although the frequency of resistant phenotypes within samples was typically low (median of 2.3). The population cage approach was used to investigate the possibility that carrying the alleles for weak resistance incurs a fitness cost. Hybridized populations were initiated using a resistant strain and either of two different susceptible strains. There was no evidence of a fitness cost based on the frequency of susceptible phenotypes in hybridized populations that were reared for seven generations without exposure to phosphine. This suggests that resistant alleles will tend to persist in field populations that have undergone selection even if selection pressure is removed. The prevalence of resistance is a warning that this species has been subject to considerable selection pressure and that effective resistance management practices are needed to address this problem. The resistance prevalence data also provide a basis against which to measure management success.

Commercial-scale Alternaria brown spot resistance screening as the first step in breeding new mandarins for Australia

Rapid screening tests and an appreciation of the simple genetic control of Alternaria brown spot (ABS) susceptibility have existed for many years, and yet the application of this knowledge to commercial-scale breeding programs has been limited. Detached leaf assays were first demonstrated more than 40 years ago and reliable data suggesting a single gene determining susceptibility has been emerging for at least 20 years. However it is only recently that the requirement for genetic resistance in new hybrids has become a priority, following increased disease prevalence in Australian mandarin production areas previously considered too dry for the pathogen. Almost all of the high-fruit-quality parents developed so far by the Queensland-based breeding program are susceptible to ABS necessitating the screening of their progeny to avoid commercialisation of susceptible hybrids. This is done effectively and efficiently by spraying 3-6 month old hybrid seedlings with a spore suspension derived from a toxin-producing field isolate of Alternaria alternate, then incubating these seedlings in a cool room at 25°C and high humidity for 5 days. Susceptible seedlings show clear disease symptoms and are discarded. Analysis of observed and expected segregation ratios loosely support the hypothesis for a single dominant gene for susceptibility, but do not rule out the possibility of alternative genetic models. After implementing the routine screening for ABS resistance for three seasons we now have more than 20,000 hybrids growing in field progeny blocks that have been screened for resistance to the ABS disease.

Bioactive Properties of Mushroom (Agaricus bisporus) Stipe Extracts

The antibacterial activity and total phenolic (TP) content of Agaricus bisporus stipes were assessed using solvent and water extracts to determine its bioactivity. Extraction methods included accelerated solvent extraction (ASE) and hot water followed by membrane concentration. Water extract from ASE had the highest TP of 1.08 gallic acid equivalents (GAE)/g dry weight (DW) followed by ethanol at 0.61 mg GAE/g DW and 0.11 mg GAE/g DW for acetone. Acetone extracts inhibited Escherichia coli and Staphylococcus aureus at less than 50%; ethanol inhibited E. coli at 61.9% and S. aureus at 56.6%; and ASE water inhibited E. coli at 78.6% and S. aureus at 65.4%. The TP content of membrane concentrated extract of mushroom was 17 mg GAE in 100 mL. Membrane concentrated water extracts had a higher percentage inhibition on S. aureus than E. coli. Overall, the results were promising for further application of mushroom stipe extracts as a functional food additive. Practical Applications Mushrooms are known for their health benefits and have been identified as a good source of nutrients. The highly perishable nature of mushrooms warrants further processing and preservation to minimize losses along the supply chain. This study explores the possibility of adding value to mushroom stipes, a by-product of the fresh mushroom industry. The extracts assessed indicate the antibacterial activity and phenolic content, and the potential of using these extracts as functional ingredients in the food industry. This study provides valuable information to the scientific community and to the industries developing novel ingredients to meet the market demand for natural food additives.