Invasive Tephritid fruit flies rank among the most destructive agricultural and horticultural pests worldwide. Heat treatment is commonly employed as a post-harvest method to exterminate fruit flies in fruits or vegetables. These pest species exhibit distinct tolerance to heat treatments, suggesting that the molecular pathways affected by heat may differ among species. In this study, the Queensland fruit fly (Qfly), Bactrocera tryoni, was utilised as a model investigate its molecular response to heat stress through heat bioassays. RNA samples from flies before and after heat treatment were extracted and sequenced to identify genes with significant changes in expression. These findings were compared to another serious Tephritid fruit fly species, the Mediterranean fruit fly (Medfly), Ceratitis capitata, under similar heat treatment conditions. The analysis reveals only three common genes: heat shock protein 70 (HSP70), HSP68, and 14-3-3 zeta protein. However, despite these shared genes, their expression patterns differ between Qfly and Medfly. This suggests that these genes might play different roles in the heat responses of each species and could be regulated differently. This study presents the first evidence of differing molecular responses to heat between Qfly and Medfly, potentially linked to their varied origins, habitats, and genetic backgrounds. These findings offer new insights into Tephritid fruit fly responses to heat at the molecular level, which may help refine post-harvest strategies to control these pests in the future.

As urban communities continue to grow, demand for recreational access (including swimming) in drinking water sources have increased, yet relatively little is understood about the public health implications this poses for drinking water consumers. Preventative risk-based approaches to catchment management, informed by quantitative microbial risk assessment (QMRA), requires accurate input data to effectively model risks. A sound understanding of the knowledge gaps is also important to comprehend levels of uncertainty and help prioritise research needs. Cryptosporidium is one of the most important causes of waterborne outbreaks of gastroenteritis globally due to its resistance to chlorine. This review was undertaken by Water Research Australia to provide the most up-to-date information on current Cryptosporidium epidemiological data and underlying assumptions for exposure assessment, dose response and risk assessment for generic components of QMRA for Cryptosporidium and highlights priorities for common research. Key interim recommendations and guidelines for numerical values for relatively simple screening level QMRA modelling are provided to help support prospective studies of risks to drinking water consumers from Cryptosporidium due to body-contact recreation in source water. The review does not cover site-specific considerations, such as the levels of activity in the source water, the influence of dilution and inactivation in reservoirs, or water treatment. Although the focus is Australia, the recommendations and numerical values developed in this review, and the highlighted research priorities, are broadly applicable across all drinking source water sources that allow recreational activities.

Invasive Tephritid fruit flies are a global threat to both agriculture and horticulture industries. Biosecurity has played a critical role in reducing their damage but becomes more and more challenging after several key chemical pesticides were banned or withdrawn for health or environmental reasons. This has led to non-chemical approaches including heat and cold treatments being broadly utilized to get rid of fruit fly infestation. However, the molecular mechanisms to kill the flies underlying these stressors are not clear yet. This knowledge will certainly help refine current post-harvest treatment strategies and develop more efficient, cost-effective and environmentally friendly approaches for fruit fly management. Previously, the molecular response of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann) to heat was examined thoroughly, in which 31 key genes were identified with significant changes in expression levels and their high-resolution expression timeline was constructed across 11 timepoints. However, whether these candidate genes respond to cold in the same way was unknown. Here, a temperature bioassay was conducted and the expression profiles of these genes were investigated across the same 11 timepoints using cold treatment. The results showed that most of candidate genes exhibited divergent expression profiles compared to heat treatment, suggesting that the fly molecular response to cold may be different from those to heat. This study provides new knowledge of Tephritid fruit fly response to cold at a molecular level, which could aid in improving current fruit fly management and facilitate the development of new strategies to control this serious horticultural insect pest.

Computational chemistry techniques are used along with spectroscopy to characterize acetaminophen synthesized in an undergraduate chemistry laboratory experiment. The inclusion of electronic structure calculations to provide infrared and Raman spectra in the synthesis and characterization of acetaminophen connects over-the-counter medications with which students are familiar to the experience of producing and characterizing a compound, and the growing role of computational chemistry in the chemical enterprise. The visualization of molecular motions associate with the absorption frequencies enhanced the understanding of the spectroscopic techniques.

Invasive Tephritid fruit flies are a global threat to both agriculture and horticulture industries. Biosecurity has played a critical role in reducing their damage but becomes more and more challenging after several key chemical pesticides were banned or withdrawn for health or environmental reasons. This has led to non-chemical approaches including heat and cold treatments being broadly utilized to get rid of fruit fly infestation. However, the molecular mechanisms to kill the flies underlying these stressors are not clear yet. This knowledge will certainly help refine current post-harvest treatment strategies and develop more efficient, cost-effective and environmentally friendly approaches for fruit fly management. Previously, the molecular response of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann) to heat was examined thoroughly, in which 31 key genes were identified with significant changes in expression levels and their high-resolution expression timeline was constructed across 11 timepoints. However, whether these candidate genes respond to cold in the same way was unknown. Here, a temperature bioassay was conducted and the expression profiles of these genes were investigated across the same 11 timepoints using cold treatment. The results showed that most of candidate genes exhibited divergent expression profiles compared to heat treatment, suggesting that the fly molecular response to cold may be different from those to heat. This study provides new knowledge of Tephritid fruit fly response to cold at a molecular level, which could aid in improving current fruit fly management and facilitate the development of new strategies to control this serious horticultural insect pest.

Wastewater monitoring (WM) of SARS-CoV-2 from sewers was applied throughout the world early in the COVID-19 pandemic. Sharing of protocols and experiences in WM of SARS-CoV-2 by national and international researchers and practitioners has been vital to ensuring the sensitivity and specificity of the methods. WM has been a valuable adjunct to human clinical testing, and when positive results occur in sewage, community testing has been increased. WM findings allow public health officials to track and respond to the impacts of loosening lockdown restrictions, demonstrating when return to normal social activities might occur without a resurgence of rapid community transmission, and they are particularly useful in areas with low human case numbers and/or low clinical testing rates. New research is required to address several practical knowledge gaps, for example, sampling protocols, prediction of case prevalence from viral numbers by modelling, and determination of detection limits. Communication to the Australian public of WM of SARS-CoV-2 has been via interactive, visual dashboards. Once SARS-CoV-2 vaccinations are introduced, WM could help track the underlying circulation of the virus in the population, the spread of known variants and its future evolution.

The shedding of pathogens by infected humans enables the use of sewage monitoring to conduct wastewater-based epidemiology (WBE). Although most WBE studies use data from large sewage treatment plants, timely data from smaller catchments are needed for targeted public health action. Traditional sampling methods, like autosamplers or grab sampling, are not conducive to quick ad hoc deployments and high-resolution monitoring at these smaller scales. This study develops and validates a cheap and easily deployable passive sampler unit, made from readily available consumables, with relevance to the COVID-19 pandemic but with broader use for WBE. We provide the first evidence that passive samplers can be used to detect SARS-CoV-2 in wastewater from populations with low prevalence of active COVID-19 infections (0.034 to 0.34 per 10,000), demonstrating their ability for early detection of infections at three different scales (lot, suburb, and city). A side by side evaluation of passive samplers (n = 245) and traditionally collected wastewater samples (n = 183) verified that the passive samplers were sensitive at detecting SARS-CoV-2 in wastewater. On all 33 days where we directly compared traditional and passive sampling techniques, at least one passive sampler was positive when the average SARS-CoV-2 concentration in the wastewater equaled or exceeded the quantification limit of 1.8 gene copies per mL (n = 7). Moreover, on 13 occasions where wastewater SARS-CoV-2 concentrations were less than 1.8 gene copies per mL, one or more passive samplers were positive. Finally, there was a statistically significant (p < 0.001) positive relationship between the concentrations of SARS-CoV-2 in wastewater and the levels found on the passive samplers, indicating that with further evaluation, these devices could yield semi-quantitative results in the future. Passive samplers have the potential for wide use in WBE with attractive feasibility attributes of cost, ease of deployment at small-scale locations, and continuous sampling of the wastewater. Further research will focus on the optimization of laboratory methods including elution and extraction and continued parallel deployment and evaluations in a variety of settings to inform optimal use in wastewater surveillance.

The presence of SARS-CoV-2 RNA in wastewater was first reported in March 2020. Over the subsequent months, the potential for wastewater surveillance to contribute to COVID-19 mitigation programmes has been the focus of intense national and international research activities, gaining the attention of policy makers and the public. As a new application of an established methodology, focused collaboration between public health practitioners and wastewater researchers is essential to developing a common understanding on how, when and where the outputs of this non-invasive community-level approach can deliver actionable outcomes for public health authorities. Within this context, the NORMAN SCORE "SARS-CoV-2 in sewage" database provides a platform for rapid, open access data sharing, validated by the uploading of 276 data sets from nine countries to-date. Through offering direct access to underpinning meta-data sets (and describing its use in data interpretation), the NORMAN SCORE database is a resource for the development of recommendations on minimum data requirements for wastewater pathogen surveillance. It is also a tool to engage public health practitioners in discussions on use of the approach, providing an opportunity to build mutual understanding of the demand and supply for data and facilitate the translation of this promising research application into public health practice.

It is timely to assess where we are in the current SARS Coronavirus-2 pandemic.This edition of Microbiology Australia has national, and international, authorities authoring a series of papers on SARS Coronavirus 2 and related subjects.We are extremely fortunate to have papers on the overarching issues of zoonotic spread (Gartner, Selleck) and how this relates to the practicalities of our responses via public health (Bennett), vaccination (Macintyre), antivirals (De Clercq), and immunotherapies (Kelleher).Diagnosis and transmission control have been at the centre of public health responses (Blackall, Speers), as has been research informing our understanding of the virus (Dhakal, Zaunders, Eden).A focus on basic research, translated into outcomes in real time, has been a very successful feature of the COVID-19 pandemic.We are privileged to be able to feature some of this research, in these papers, although this is only part of the extensive and excellent Australian work in reducing the impact of SARS CoV2 infection, and COVID-19 disease.It is salient to reflect on where we are now, but also the background to the current pandemic.In early 2003, following outbreaks in the Hong Kong Special Administrative Region (SAR), and Guangdong province in China, the WHO issued a 'global alert about cases of atypical pneumonia' (WHO press release, 12 March 2003).This led to a global response with identification of the causative organism, and postulates about transmission from bats via civet cats in 'wet markets'.More recent research has suggested this may be an oversimplification, and some of the complexities are explored in this edition of Microbiology Australia.Reviews of different approaches previously to SARS control are interesting to read, in the context of the current outbreak.Particularly thought provoking

We demonstrate quantitative polymerase chain reaction (qPCR) using an all-fibre all-optical device. Through direct optical measurement of the sample refractive index, we show the potential of the system to operate as a label-free qPCR system.

Tephritid fruit flies are highly successful invaders and some-such as the Mediterranean fruit fly, Ceratitis capitata (Wiedemann)-are able to adapt to a large range of crops. Biosecurity controls require that shipments of produce are ensured to be pest-free, which is increasingly difficult due to the ban of key pesticides. Instead, stress-based strategies including controlled atmosphere, temperature, and irradiation can be used to eradicate flies inside products. However, unlike pesticide science, we do not yet have a robust scientific approach to measure cost-effectively whether a sufficiently lethal stress has been delivered and understand what this stress does to the biology of the pest. The latter is crucial as it would enable a combination of stresses targeting multiple molecular pathways and thus allow for lower doses of each to achieve higher lethality and reduce the development of resistance. Using heat as an example, this is the first study investigating the molecular stress response to heat in Tephritidae. Using a novel setup delivering measured doses of heat on C. capitata larvae and a high-density 11 timepoint gene expression experiment, we identified key components of lethal heat-stress response. While unraveling the complete molecular mechanism of fruit fly response to lethal stress would be a long-term project, this work curates and develops 31 potential biomarkers to assess whether sufficient lethal stress has been delivered. Further, as these protocols are straightforward and less expensive than other-omic approaches, our studies and approach will assist other researchers working on stress response.

Quantitative polymerase chain reaction (qPCR), the real-time amplification and measurement of a targeted DNA molecule, has revolutionized the biological sciences and is routinely applied in areas such as medical diagnostics, forensics, and agriculture. Despite widescale use of qPCR technology in the lab, the availability of low-cost and high-speed portable systems remains one of the barriers to routine in-field implementation. Here we propose and demonstrate a potential solution using a photonics-based qPCR system. By using an all-optical approach, we achieve ultra-fast temperature response with real-time temperature feedback using nanoliter scale reaction volumes. The system uses a microcavity to act as a nanoliter scale reaction vessel with a laser-driven and optically monitored temperature cycling system for ultrafast thermal cycling and incorporates an all-fiber fluorescence excitation/detection system to achieve real-time, high sensitivity fluorescence monitoring of the qPCR process. Further, we demonstrate the potential of the system to operate as a label-free qPCR system through direct optical measurement of the sample refractive index. Due to advantages in portability and fabrication simplicity, we anticipate that this platform technology will offer a new strategy for fundamental techniques in biochemistry applications, such as point-of-care and remote diagnostics.

Wastewater surveillance of pathogens may be a useful tool to help determine whether clinical surveillance of disease is effective or inadequate due to under-reporting and under-detection. In addition, tracking of pathogen concentrations over time could potentially provide a measure of the effectiveness of public health control measures and the impact of the gradual relaxation of these controls. Analysis of wastewater using quantitative molecular methods offers a real-time measure of infections in the community, and thus is expected to provide a more sensitive and rapid indication of changes in infection rates before such effects become detectable by clinical health surveillance. Models may help to back-calculate wastewater prevalence to population prevalence or to correct pathogen counts for wastewater catchment-specific and temporal effects. They may also help to design the wastewater sampling strategy. This article provides a brief summary of the history of pathogen wastewater surveillance to help set the context for the SARS-CoV-2 wastewater-based epidemiology (WBE) programmes currently being undertaken globally.

We demonstrate an all-fiber, all-optical, real-time quantitative polymerase chain reaction system with ultra-fast temperature response, real-time temperature feedback, picoliter scale reaction volume and high fluorescence sensitivity.

A number of bee RNA viruses, including Deformed wing virus (DWV), are so far unreported from Australia. These viruses can be introduced together with imported live honey bees (Apis mellifera) and their products, with other bee species, and bee parasites. Given that bee viruses have a profound impact on bee health, it is surprising that since the introduction of bumble bees (Bombus terrestris) onto Tasmania in 1992 from New Zealand, no work has been done to investigate which RNA viruses are associated with these bees. Consequently, we investigate the current prevalence of RNA viruses in B. terrestris and A. mellifera collected in south-eastern Tasmania. We did not find DWV in either A. mellifera and B. terrestris. However, both bee species shared Kashmir bee virus (KBV) and Sacbrood virus (SBV), but Black queen cell virus (BQCV) was detected only in A. mellifera. This reinforces the importance of ongoing strong regulation of the anthropogenic movement of live bees and their products.

Invasive pest species pose a major threat to agricultural production around the world. Until recently, the Russian wheat aphid, Diuraphis noxia Kurdjumov, a major pest of wheat and barley crops worldwide, was considered a high-priority exotic pest threat to the Australian grains industry. Here, we document the initial detection and establishment of D. noxia in Australia in 2016. These are the first records for this genus from South Australia, Victoria and New South Wales. Morphological and molecular information is presented for confirmed diagnosis of the species based on voucher specimens. Known distribution data are provided, along with a list of Poaceae hosts on which D. noxia has been recorded, and a brief description of the typical damage symptoms caused by these aphids. The potential impact of this aphid on Australian cereal production is discussed, and we identify research areas required to underpin future management of this new threat to the Australian cereal industry.

This paper investigates the sediment retention behaviour of laboratory-based permeable pavements using mono-sized sediments that were representative of the sizes typically found in urban stormwater. The sediments were applied in two cycles, namely in order of increasing and decreasing size. The results indicated that most of the sediment accumulation could be attributed to the depth of the pavement and the material used in the joint and bedding aggregates. Most of the sediment was retained in the bedding and surface layers, and little difference to the retention was made by the incorporation of a basecourse layer. When the mono-sized sediments were added in decreasing size order with the coarsest sediments applied first, the overall rate of retention increased.

Bee pollination is critical for improving productivity of one third of all plants or plant products consumed by humans. The health of honey bees is in decline in many countries worldwide, and RNA viruses together with other biological, environmental and anthropogenic factors have been identified as the main causes. The rapid genetic variation of viruses represents a challenge for diagnosis. Thus, application of deep sequencing methods for detection and analysis of viruses has increased over the last years. In this study, we leverage from the innate Dicer-2 mediated antiviral response against viruses to reconstruct complete viral genomes using virus-derived small interfering RNAs (vsiRNAs). Symptomatic A. mellifera larvae collected from hives free of Colony Collapse Disorder (CCD) and the parasitic Varroa mite (Varroa destructor) were used to generate more than 107 million small RNA reads. We show that de novo assembly of insect viral sequences is less fragmented using only 22 nt long vsiRNAs rather than a combination of 21-22 nt small RNAs. Our results show that A. mellifera larvae activate the RNAi immune response in the presence of Sacbrood virus (SBV). We assembled three SBV genomes from three individual larvae from different hives in a single apiary, with 1-2% nucleotide sequence variability among them. We found 3-4% variability between SBV genomes generated in this study and earlier published Australian variants suggesting the presence of different SBV quasispecies within the country.

Alstroemeria (Liliales: Alstroemeriaceae) is a plant genus native to South America with many interspecific hybrids cultivated as ornamentals worldwide. Several yellow larvae of an undescribed gall midge (Diptera: Cecidomyiidae) were found feeding inside flower buds of Alstroemeria plants grown in production greenhouses in South Australia in 2013; Queensland, Australia, in 2015 and the Netherlands in 2016. Infested buds became malformed, did not produce flowers and turned necrotic later. In Queensland and the Netherlands, the necrotised buds became additionally infected by a saprophytic fungus Cladosporium sp. With up to 80% of flower buds infested, the new gall midge decreased the value of plants aimed for the cut flower market and reduced seed of reproduction plants. The new species, named Contarinia jongi Kolesik sp. nov., is described, and a segment of its Cytochrome Oxidase unit I mitochondrial gene is sequenced. This is the first gall midge known to feed on a host plant from the family Alstroemeriaceae. Previously, Alstroemeria cut flowers imported from Australia and New Zealand to Japan were found to contain viable larvae of the new species, demonstrating that the new species can spread with the flower trade. It is possible that Contarinia jongi is native to South America, the homeland of its host plant.

This paper was to investigate the removal behaviour of asphalt in pore-space on dissolved zinc from road runoff based on laboratory experiments. Asphalt films were soaked with different initial concentrations of Zn2+ solutions over 720 h. The surface chemical state of asphalt films before and after experiment were examined by X-ray photoelectron spectroscopy(XPS), while solution samples were analysed for Zn2+ concentrations by an inductively coupled plasma atomic emission spectrometer(ICP-AES). Experimental data were further analysed using both kinetics and adsorption isotherms. It confirmed that Zn2+ in solution had been adsorbed to the asphalt film. The initial stage of adsorption matched both the first-order equation and the parabolic diffusion equation; whereas the entire adsorption process was found fit the second-order equation. Moreover, the adsorptive behaviour satisfied the Freundlich model. These provide evidence to support the adsorption ability of asphalt on the pore-walls in porous asphalt with regard to Zn2+ in road runoff.