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Recent developments in affordable depth imaging hardware and the use of 2D Convolutional Neural Networks (CNN) in object detection and segmentation have accelerated the adoption of machine vision in a range of applications, with mainstream models often out-performing previous application-specific architectures. The need for the release of training and test datasets with any work reporting model development is emphasized to enable the re-evaluation of published work. An additional reporting need is the documentation of the performance of the re-training of a given model, quantifying the impact of stochastic processes in training. Three mango orchard applications were considered: the (i) fruit count, (ii) fruit size and (iii) branch avoidance in automated harvesting. All training and test datasets used in this work are available publicly. The mAP 'coefficient of variation' (Standard Deviation, SD, divided by mean of predictions using models of repeated trainings × 100) was approximately 0.2% for the fruit detection model and 1 and 2% for the fruit and branch segmentation models, respectively. A YOLOv8m model achieved a mAP50 of 99.3%, outperforming the previous benchmark, the purpose-designed 'MangoYOLO', for the application of the real-time detection of mango fruit on images of tree canopies using an edge computing device as a viable use case. YOLOv8 and v9 models outperformed the benchmark MaskR-CNN model in terms of their accuracy and inference time, achieving up to a 98.8% mAP50 on fruit predictions and 66.2% on branches in a leafy canopy. For fruit sizing, the accuracy of YOLOv8m-seg was like that achieved using Mask R-CNN, but the inference time was much shorter, again an enabler for the field adoption of this technology. A branch avoidance algorithm was proposed, where the implementation of this algorithm in real-time on an edge computing device was enabled by the short inference time of a YOLOv8-seg model for branches and fruit. This capability contributes to the development of automated fruit harvesting.

Anthropogenically forced changes in global freshwater biodiversity demand more efficient monitoring approaches. Consequently, environmental DNA (eDNA) analysis is enabling ecosystem-scale biodiversity assessment, yet the appropriate spatio-temporal resolution of robust biodiversity assessment remains ambiguous. Here, using intensive, spatio-temporal eDNA sampling across space (five rivers in Europe and North America, with an upper range of 20-35 km between samples), time (19 timepoints between 2017 and 2018) and environmental conditions (river flow, pH, conductivity, temperature and rainfall), we characterise the resolution at which information on diversity across the animal kingdom can be gathered from rivers using eDNA. In space, beta diversity was mainly dictated by turnover, on a scale of tens of kilometres, highlighting that diversity measures are not confounded by eDNA from upstream. Fish communities showed nested assemblages along some rivers, coinciding with habitat use. Across time, seasonal life history events, including salmon and eel migration, were detected. Finally, effects of environmental conditions were taxon-specific, reflecting habitat filtering of communities rather than effects on DNA molecules. We conclude that riverine eDNA metabarcoding can measure biodiversity at spatio-temporal scales relevant to species and community ecology, demonstrating its utility in delivering insights into river community ecology during a time of environmental change., (© 2024. The Author(s).)

A global study on tap water samples has found that up to 83% of these contained microplastic fibres. These findings raise concerns about their potential health risks. Ingested microplastic particles have already been associated with harmful effects in animals, which raise concerns about similar outcomes in humans. Microplastics are ubiquitous in the environment, commonly found disposed in landfills and waste sites. Within indoor environments, the common sources are synthetic textiles, plastic bottles, and packaging. From the various point sources, they are globally distributed through air and water and can enter humans through various pathways. The finding of microplastics in fresh snow in the Antarctic highlights just how widely they are dispersed. The behaviour and health risks from microplastic particles are strongly influenced by their physicochemical properties, which is why their surfaces are important. Surface interactions are also important in pollutant transport via adsorption onto the microplastic particles. Our review covers the latest findings in microplastics research including the latest statistics in their abundance, their occurrence and fate in the environment, the methods of reducing microplastics exposure and their removal. We conclude by proposing future research directions into more effective remediation methods including new technologies and sustainable green remediation methods that need to be explored to achieve success in microplastics removal from waters at large scale., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier B.V.)

Bioprospecting native Australian plants offers the potential discovery of latent and novel bioactive compounds. The promising cytotoxic and antibacterial activity of methanolic extracts of Pittosporum angustifolium and Terminalia ferdinandiana led to further fractionation and isolation using our laboratory's bioassay-guided fractionation protocol. Hence, the aim of this study was to further evaluate the bioactivity of the fractions and subfractions and characterize bioactive compounds using liquid chromatography mass spectroscopy (LC-MS/MS) and gas chromatography MS (GC-MS). Compounds tentatively identified in P. angustifolium Fraction 1 using LC-ESI-QTOF-MS/MS were chlorogenic acid and/or neochlorogenic acid, bergapten, berberine, 8'-epitanegool and rosmarinic acid. GC-MS analysis data showed the presence of around 100 compounds, mainly comprising carboxylic acids, sugars, sugar alcohols, amino acids and monoalkylglycerols. Furthermore, the fractions obtained from T. ferdinandiana flesh extracts showed no cytotoxicity, except against HT29 cell lines, and only Fraction 2 exhibited some antibacterial activity. The reduced bioactivity observed in the T. ferdinandiana fractions could be attributed to the potential loss of synergy as compounds become separated within the fractions. As a result, the further fractionation and separation of compounds in these samples was not pursued. However, additional dose-dependent studies are warranted to validate the bioactivity of T. ferdinandiana flesh fractions, particularly since this is an understudied species. Moreover, LC-MS/GC-MS studies confirm the presence of bioactive compounds in P. angustifolium Fraction 1/subfractions, which helps to explain the significant acute anticancer activity of this plant. The screening process designed in this study has the potential to pave the way for developing scientifically validated phytochemical/bioactivity information on ethnomedicinal plants, thereby facilitating further bioprospecting efforts and supporting the discovery of novel drugs in modern medicine.

DNA metabarcoding has been performed on a large number of river phytobenthos samples collected from the UK, using rbcL primers optimised for diatoms. Within this dataset the composition of non-diatom sequence reads was studied and the effect of including these in models for evaluating the nutrient gradient was assessed. Whilst many non-diatom taxonomic groups were detected, few contained the full diversity expected in riverine environments. This may be due to the performance of the current primers in characterising the wider phytobenthic community and influenced by the sampling method employed, as both were developed specifically for diatoms. Nevertheless, the study identified considerable diversity in some groups, e.g. Eustigmatophyceae and a wider distribution than previously thought for freshwater Phaeophyceae. These results offer a strong case for the benefits of metabarcoding for expanding knowledge of aquatic biodiversity in the UK and elsewhere. Many of the ASVs associated with non-diatoms showed significant pressure responses; however, models that included non-diatoms had similar predictive strength to those based on diatoms alone. Whilst limitations of the primers for assessing non-diatoms may play a role in explaining these results, the diatoms provide a strong signal along the nutrient gradient and other algae, therefore, add little unique information. We recommend that future developments should use ASVs to calculate metrics, with links to reference databases made as a final step to generate lists of taxa to support interpretation. Any further exploration of the potential of non-diatoms would benefit from access to a well-curated reference database, similar to diat.barcode. Such a database does not yet exist, and we caution against the indiscriminate use of NCBI GenBank as a taxonomic resource as many rbcL sequences deposited have not been curated., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Forward estimates of harvest load require information on fruit size as well as number. The task of sizing fruit and vegetables has been automated in the packhouse, progressing from mechanical methods to machine vision over the last three decades. This shift is now occurring for size assessment of fruit on trees, i.e., in the orchard. This review focuses on: (i) allometric relationships between fruit weight and lineal dimensions; (ii) measurement of fruit lineal dimensions with traditional tools; (iii) measurement of fruit lineal dimensions with machine vision, with attention to the issues of depth measurement and recognition of occluded fruit; (iv) sampling strategies; and (v) forward prediction of fruit size (at harvest). Commercially available capability for in-orchard fruit sizing is summarized, and further developments of in-orchard fruit sizing by machine vision are anticipated.

Infrared spectroscopy (wavelengths ranging from 750-25,000 nm) offers a rapid means of assessing the chemical composition of a wide range of sample types, both for qualitative and quantitative analyses. Its use in the food industry has increased significantly over the past five decades and it is now an accepted analytical technique for the routine analysis of certain analytes. Furthermore, it is commonly used for routine screening and quality control purposes in numerous industry settings, albeit not typically for the analysis of bioactive compounds. Using the Scopus database, a systematic search of literature of the five years between 2016 and 2020 identified 45 studies using near-infrared and 17 studies using mid-infrared spectroscopy for the quantification of bioactive compounds in food products. The most common bioactive compounds assessed were polyphenols, anthocyanins, carotenoids and ascorbic acid. Numerous factors affect the accuracy of the developed model, including the analyte class and concentration, matrix type, instrument geometry, wavelength selection and spectral processing/pre-processing methods. Additionally, only a few studies were validated on independently sourced samples. Nevertheless, the results demonstrate some promise of infrared spectroscopy for the rapid estimation of a wide range of bioactive compounds in food matrices.

Early and accurate tomato disease detection using easily available leaf photos is essential for farmers and stakeholders as it help reduce yield loss due to possible disease epidemics. This paper aims to visually identify nine different infectious diseases (bacterial spot, early blight, Septoria leaf spot, late blight, leaf mold, two-spotted spider mite, mosaic virus, target spot, and yellow leaf curl virus) in tomato leaves in addition to healthy leaves. We implemented EfficientNetB5 with a tomato leaf disease (TLD) dataset without any segmentation, and the model achieved an average training accuracy of 99.84% ± 0.10%, average validation accuracy of 98.28% ± 0.20%, and average test accuracy of 99.07% ± 0.38% over 10 cross folds.The use of gradient-weighted class activation mapping (GradCAM) and local interpretable model-agnostic explanations are proposed to provide model interpretability, which is essential to predictive performance, helpful in building trust, and required for integration into agricultural practice.

A large variety of unique and distinct flora of Australia have developed exceptional survival methods and phytochemicals and hence may provide a significant avenue for new drug discovery. This study proposes a bioassay guided fractionation protocol that maybe robust and efficient in screening plants with potential bioactive properties and isolating lead novel compounds. Hence, five native Australian plants were selected for this screening process, namely Pittosporum angustifolium (Gumbi gumbi), Terminalia ferdinandiana (Kakadu plum, seeds (KPS), and flesh (KPF)), Cupaniopsis anacardioides (Tuckeroo, seeds (TKS) and flesh (TKF)), Podocarpus elatus (Illawarra plum, seeds (IPS) and flesh (IPF)) and Pleiogynium timoriense (Burdekin plum, seeds (BPS) and flesh (BPF)). The methanolic extracts of the plants samples were analysed for Total phenolic content (TPC) and antioxidant capacity measure by FRAP. The highest values were found in the KPF which were 12,442 ± 1355 mg GAE/ 100 g TPC and 16,670 ± 2275 mg TXE/100 g antioxidant capacity. Extracts of GGL was deemed to be most potent with complete cell inhibition in HeLa and HT29, and about 95% inhibition in HuH7 cells. Comparative activity was also seen for KPS extract, where more than 80% cell inhibition occurred in all tested cell lines. Dose-dependent studies showed higher SI values (0.72-1.02) in KPS extracts than GGL (0.5-0.73). Microbial assays of the crude extracts were also performed against five bacterial strains commonly associated with causing food poisoning diseases were selected (Gram positive- Staphylococcus aureus and Gram negative- Escherichia coli , Salmonella typhi and Pseudomonas aeruginosa bacteria). KPF extracts were effective in suppressing microbial growth of all tested bacterial strains except for P. aeruginosa , while TKS and TKF were only slightly effective against S. aureus. Due to the potential of the GGL crude extract to completely inhibit the cells compared to KPS, it was further fractionated and tested against the cell lines. HPLC phenolic profiling of the crude extracts were performed, and numerous peak overlaps were evident in the fruit extracts. The KPF extracts demonstrated the strongest peaks which was coherent with the fact that it had the highest TPC and antioxidant capacity values. A high occurrence of t-ferulic acid in the GGL extracts was found which may explain the cytotoxic activity of GGL extracts. Peaks in KPS and KPF extracts were tentatively identified as gallic acid, protocatechuic acid, 4-hydroxybenzoic acid and syringic acid and possibly ellagic acid. HPLC time-based fractionation of the GGL extract (F1-F5) was performed and Dose dependent cytotoxic effects were determined. It was construed that F1, having the highest SI value for HeLa, HT29 and HuH7 (1.60, 1.41 and 1.67, respectively) would be promising for further fractionation and isolation process.

Although Australia is the largest exporter of faba bean globally, there is limited information available on the levels of bioactive compounds found in current commercial faba bean varieties grown in this country. This study profiled the phenolic acid and flavonoid composition of 10 Australian faba bean varieties, grown at two different locations. Phenolic profiling by HPLC-DAD revealed the most abundant flavonoid to be catechin, followed by rutin. For the phenolic acids, syringic acid was found in high concentrations (72.4-122.5 mg/kg), while protocatechuic, vanillic, p -hydroxybenzoic, chlorogenic, p -coumaric, and trans-ferulic acid were all found in low concentrations. The content of most individual phenolics varied significantly with the variety, while some effect of the growing location was also observed. This information could be used by food processors and plant breeders to maximise the potential health benefits of Australian-grown faba bean.

Ethnopharmacological Relevance: Numerous common pharmaceuticals, including anti-cancer, antiviral and antidiabetic drugs, are derived from traditional plant-derived medicines. With approximately 25,000 species of flora occurring in Australia that are adapted to the harsh environment, there is a plethora of novel compounds awaiting research in the context of their medicinal properties. Anecdotal accounts of plant-based medicines used by the Australian Aboriginal and Torres Strait Islander peoples clearly illustrates high therapeutic activity., Aim: This review aims to demonstrate the medicinal potentials of selected native Australian plants based on scientific data. Furthermore, it is anticipated that work presented here will contribute towards enhancing our knowledge of native plants from Australia, particularly in the prevention and potential treatment of disease types such as cancer, microbial and viral infections, and diabetes. This is not meant to be a comprehensive study, rather it is meant as an overview to stimulate future research in this field., Methods: The EBSCOhost platform which included PubMed, SciFinder, Web of Knowledge, Scopus, and ScienceDirect databases were searched for papers using the keywords: medicinal plants, antioxidative, antimicrobial, antibacterial, anticancer, anti-tumor, antiviral or antidiabetic, as well as Australian, native, traditional and plants. The selection criteria for including studies were restricted to articles on plants used in traditional remedies which showed antioxidative potential and therapeutic properties such as anticancer, antimicrobial, antiviral and antidiabetic activity., Results: Some plants identified in this review which showed high Total Phenolic Content (TPC) and antioxidative capacity, and hence prominent bioactivity, included Tasmannia lanceolata (Poir.) A.C. Sm., Terminalia ferdinandiana Exell, Eucalyptus species, Syzygium species, Backhousia citriodora F.Muell., Petalostigma species, Acacia species, Melaleuca alternifolia (Maiden & Betche) Cheel, Eremophila species, Prostanthera rotundifolia R.Br., Scaevola spinescens R. Br. and Pittosporum angustifolium Lodd. The majority of studies found polar compounds such as caffeic acid, coumaric acid, chlorogenic acid, quercetin, anthocyanins, hesperidin, kaempferol, catechin, ellagic acid and saponins to be the active components responsible for the therapeutic effects. Additionally, mid to non-polar volatile organic compounds such as meroterpenes (serrulatanes and nerol cinnamates), monoterpenes (1,8-cineole and myodesert-1-ene), sesquiterpenes, diterpenes and triterpenes, that are known only in Australian plants, have also shown therapeutic properties related to traditional medicine., Conclusion: Australian plants express a diverse range of previously undescribed metabolites that have not been given full in vitro assessment for human health potential. This review has included a limited number of plant species of ethnomedicinal significance; hundreds of plants remain in need of exploration and detailed study. Future more elaborate studies are therefore required to screen out and purify lead bioactive compounds against numerous other disease types. This will not only improve our knowledge on the phytochemistry of Australian native flora, but also provide a platform to understand their health-promoting and bioactive effects for pharmaceutical interventions, nutraceuticals, cosmetics, and as functional foods. Finally, plant-derived natural compounds (phytochemicals), as well as plant-based traditional remedies, are significant sources for latent and novel drugs against diseases. Extensive investigation of native medicinal plants may well hold the key to novel drug discoveries., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Coronaviruses are responsible for a growing economic, social and mortality burden, as the causative agent of diseases such as severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), avian infectious bronchitis virus (IBV) and COVID-19. However, there is a lack of effective antiviral agents for many coronavirus strains. Naturally existing compounds provide a wealth of chemical diversity, including antiviral activity, and thus may have utility as therapeutic agents against coronaviral infections. The PubMed database was searched for papers including the keywords coronavirus, SARS or MERS, as well as traditional medicine, herbal, remedy or plants, with 55 primary research articles identified. The overwhelming majority of publications focussed on polar compounds. Compounds that show promise for the inhibition of coronavirus in humans include scutellarein, silvestrol, tryptanthrin, saikosaponin B 2 , quercetin, myricetin, caffeic acid, psoralidin, isobavachalcone, and lectins such as griffithsin. Other compounds such as lycorine may be suitable if a therapeutic level of antiviral activity can be achieved without exceeding toxic plasma concentrations. It was noted that the most promising small molecules identified as coronavirus inhibitors contained a conjugated fused ring structure with the majority being classified as being polyphenols., Competing Interests: Declaration of Competing Interest The authors declare that no conflict of interest exists., (Copyright © 2020 Elsevier B.V. All rights reserved.)

: Pre-harvest fruit yield estimation is useful to guide harvesting and marketing resourcing, but machine vision estimates based on a single view from each side of the tree ("dual-view") underestimates the fruit yield as fruit can be hidden from view. A method is proposed involving deep learning, Kalman filter, and Hungarian algorithm for on-tree mango fruit detection, tracking, and counting from 10 frame-per-second videos captured of trees from a platform moving along the inter row at 5 km/h. The deep learning based mango fruit detection algorithm, MangoYOLO, was used to detect fruit in each frame. The Hungarian algorithm was used to correlate fruit between neighbouring frames, with the improvement of enabling multiple-to-one assignment. The Kalman filter was used to predict the position of fruit in following frames, to avoid multiple counts of a single fruit that is obscured or otherwise not detected with a frame series. A "borrow" concept was added to the Kalman filter to predict fruit position when its precise prediction model was absent, by borrowing the horizontal and vertical speed from neighbouring fruit. By comparison with human count for a video with 110 frames and 192 (human count) fruit, the method produced 9.9% double counts and 7.3% missing count errors, resulting in around 2.6% over count. In another test, a video (of 1162 frames, with 42 images centred on the tree trunk) was acquired of both sides of a row of 21 trees, for which the harvest fruit count was 3286 (i.e., average of 156 fruit/tree). The trees had thick canopies, such that the proportion of fruit hidden from view from any given perspective was high. The proposed method recorded 2050 fruit (62% of harvest) with a bias corrected Root Mean Square Error (RMSE) = 18.0 fruit/tree while the dual-view image method (also using MangoYOLO) recorded 1322 fruit (40%) with a bias corrected RMSE = 21.7 fruit/tree. The video tracking system is recommended over the dual-view imaging system for mango orchard fruit count., Competing Interests: The authors declare no conflict of interest.

The impact of Stevia rebaudiana leaf on feeding preferences of an insect, a mite, and a mammal was investigated. The grasshopper, Valanga irregularis of the Acrididae family, avoided feeding on S. rebaudiana leaf, as evidenced by a decrease in animal weight. Increased mortality on S. rebaudiana feed was ascribed to feeding avoidance to the point of starvation. The extent of red spider mite ( Tetranychus urticae) damage was not proportional to leaf steviol glycoside (SG) concentration, a result ascribed to a feeding mechanism that avoids chlorenchyma cells that contain SGs. Guinea pigs ( Cavia porcellus) were presented with the choice between a control feed and feed amended to contain 5% sucrose or 0.02%, 4%, or 10% (dry weight) of S. rebaudiana leaf. Feed intake increased (39% above the control) for the diet involving high levels of SG amendment of feed (10% S. rebaudiana leaf). Encouragement of general mammalian herbivory may provide ecological fitness to S. rebaudiana if it is more tolerant of grazing pressure than other plants in its environment. Improvement in feed intake may have commercial implication for use of S. rebaudiana as an additive in stock feeds.

Increased global regulation and restrictions on the non-therapeutic use of antibiotics in the poultry industry means that there is a need to identify alternatives that prevent infection while still conveying the growth and performance benefits afforded by their use. Biochars are produced by the incomplete pyrolysis of organic materials, with reports of use as a feed supplement and activity against pathogenic bacteria. In the current study the dose-dependent effects of biochar dietary inclusion in layer diets at 1%, 2% and 4% w/w were investigated to determine a) the efficacy of biochar as an anti-pathogenic additive on the intestinal microbiota and b) the optimal inclusion level. Biochar inclusion for anti-pathogenic effects was found to be most beneficial at 2% w/w. Poultry pathogens such as Gallibacterium anatis and campylobacters, including Campylobacter hepaticus, were found to be significantly lower in biochar fed birds. A shift in microbiota was also associated with the incorporation of 2% w/w biochar in the feed in two large scale trials on two commercial layer farms. Biochar inclusion for anti-pathogenic effects was found to be most beneficial at 2% w/w. Differential effects of the timing of biochar administration (supplementation beginning at hatch or at point of lay) were also evident, with greater impact on community microbial structure at 48 weeks of age when birds were fed from hatch rather than supplemented at point of lay., Competing Interests: The authors have declared that no competing interests exist.

A novel dual excitation wavelength based bioaerosol sensor with multiple fluorescence bands called Spectral Intensity Bioaerosol Sensor (SIBS) has been assessed across five contrasting outdoor environments. The mean concentrations of total and fluorescent particles across the sites were highly variable being the highest at the agricultural farm (2.6 cm -3 and 0.48 cm -3 , respectively) and the composting site (2.32 cm -3 and 0.46 cm -3 , respectively) and the lowest at the dairy farm (1.03 cm -3 and 0.24 cm -3 , respectively) and the sewage treatment works (1.03 cm -3 and 0.25 cm -3 , respectively). In contrast, the number-weighted fluorescent fraction was lowest at the agricultural site (0.18) in comparison to the other sites indicating high variability in nature and magnitude of emissions from environmental sources. The fluorescence emissions data demonstrated that the spectra at different sites were multimodal with intensity differences largely at wavelengths located in secondary emission peaks for λex 280 and λex 370. This finding suggests differences in the molecular composition of emissions at these sites which can help to identify distinct fluorescence signature of different environmental sources. Overall this study demonstrated that SIBS provides additional spectral information compared to existing instruments and capability to resolve spectrally integrated signals from relevant biological fluorophores could improve selectivity and thus enhance discrimination and classification strategies for real-time characterisation of bioaerosols from environmental sources. However, detailed lab-based measurements in conjunction with real-world studies and improved numerical methods are required to optimise and validate these highly resolved spectral signatures with respect to the diverse atmospherically relevant biological fluorophores., (Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.)

Steviol glycosides (SG) (with stevioside and rebaudioside A predominating) are present in wild-type Stevia rebaudiana, at approximately 10% of dry weight (dw), prompting a consideration of the autoecological role played by these compounds in terms of energy (C) storage and/or osmoregulation. The leaf starch pool was observed to change diurnally with respect to the light cycle (from 3.29% to 0.73% of leaf dw between dusk and dawn) and also to increase under constant light treatment (from 1.53% to 6.25% of leaf dw), while SG pools were relatively constant (around 6% w/dw). A similar trend was observed during exposure to elevated CO 2 (800 ppm), with starch increasing (from 10% to 15% of leaf dw), while SG pool size was constant (around 12% w/dw). For plants subject to increasing water stress over several days, an increase in leaf sap osmolality was observed in the leaves of a severely stressed group (from -1 MPa to -3 MPa, after 2 days of treatment), while stevioside and rebaudioside A leaf concentration was relatively constant (around 16% w/dw). These results are not consistent with a role for SG as either a short-term C store or osmoregulator in S. rebaudiana.

In field (on tree) fruit sizing has value in assessing crop health and for yield estimation. As the mobile phone is a sensor and communication rich device carried by almost all farm staff, an Android application ("FruitSize") was developed for measurement of fruit size in field using the phone camera, with a typical assessment rate of 240 fruit per hour achieved. The application was based on imaging of fruit against a backboard with a scale using a mobile phone, with operational limits set on camera to object plane angle and camera to object distance. Image processing and object segmentation techniques available in the OpenCV library were used to segment the fruit from background in images to obtain fruit sizes. Phone camera parameters were accessed to allow calculation of fruit size, with camera to fruit perimeter distance obtained from fruit allometric relationships between fruit thickness and width. Phone geolocation data was also accessed, allowing for mapping fruits of data. Under controlled lighting, RMSEs of 3.4, 3.8, 2.4, and 2.0 mm were achieved in estimation of avocado, mandarin, navel orange, and apple fruit diameter, respectively. For mango fruit, RMSEs of 5.3 and 3.7 mm were achieved on length and width, benchmarked to manual caliper measurements, under controlled lighting, and RMSEs of 5.5 and 4.6 mm were obtained in-field under ambient lighting.

Feeding treatments were imposed in two feeding trials involving Cobb broiler and Bond Brown layer birds. Three feed additives (biochar, bentonite and zeolite) were supplied at four rates (0, 1, 2 and 4% w/w) in feed, as previously considered in the context of animal production, was considered in the context of Excreta chemical and water retention properties and granulation characteristics of decomposed excreta (manure) were characterised. At field capacity (- 0.01 MPa), manure produced from control and 4% bentonite diets contained significantly (p = 0.001) more water (at 1.93 and 2.44% v/v water, respectively) than zeolite and biochar treatments. Manure mesoporosity was significantly (p = 0.015) higher in 2 and 4% bentonite treatments than other feed additives. Fresh excreta from layer birds on the control diet contained 6% w/dw N and 35% C, which was decreased to 2.6% N and 28% C after decomposition, with C:N ratio changing from 5.9 to 12.1. Ammonia loss was higher from biochar and zeolite manures than control or bentonite, associated with higher pH in the biochar and zeolite manures. More N was unaccounted from bentonite manure than other treatments, presumably lost as N 2 O or N 2 , a result linked to its higher moisture content and its enhanced rate of denitrification. The highest proportion of granules in the size class desired for fertilizer spreading was achieved using decomposed manure from the 1 and 2% w/w biochar treatments of the broiler trial, and 1 and 2% zeolite and 4% biochar treatments of the layer trial. Thus the feed amendments improved poultry manure in specific ways., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

New applications of DNA and RNA sequencing are expanding the field of biodiversity discovery and ecological monitoring, yet questions remain regarding precision and efficiency. Due to primer bias, the ability of metabarcoding to accurately depict biomass of different taxa from bulk communities remains unclear, while PCR-free whole mitochondrial genome (mitogenome) sequencing may provide a more reliable alternative. Here, we used a set of documented mock communities comprising 13 species of freshwater macroinvertebrates of estimated individual biomass, to compare the detection efficiency of COI metabarcoding (three different amplicons) and shotgun mitogenome sequencing. Additionally, we used individual COI barcoding and de novo mitochondrial genome sequencing, to provide reference sequences for OTU assignment and metagenome mapping (mitogenome skimming), respectively. We found that, even though both methods occasionally failed to recover very low abundance species, metabarcoding was less consistent, by failing to recover some species with higher abundances, probably due to primer bias. Shotgun sequencing results provided highly significant correlations between read number and biomass in all but one species. Conversely, the read-biomass relationships obtained from metabarcoding varied across amplicons. Specifically, we found significant relationships for eight of 13 (amplicons B1FR-450 bp, FF130R-130 bp) or four of 13 (amplicon FFFR, 658 bp) species. Combining the results of all three COI amplicons (multiamplicon approach) improved the read-biomass correlations for some of the species. Overall, mitogenomic sequencing yielded more informative predictions of biomass content from bulk macroinvertebrate communities than metabarcoding. However, for large-scale ecological studies, metabarcoding currently remains the most commonly used approach for diversity assessment., (© 2018 John Wiley & Sons Ltd.)

In-field mango fruit sizing is useful for estimation of fruit maturation and size distribution, informing the decision to harvest, harvest resourcing (e.g., tray insert sizes), and marketing. In-field machine vision imaging has been used for fruit count, but assessment of fruit size from images also requires estimation of camera-to-fruit distance. Low cost examples of three technologies for assessment of camera to fruit distance were assessed: a RGB-D (depth) camera, a stereo vision camera and a Time of Flight (ToF) laser rangefinder. The RGB-D camera was recommended on cost and performance, although it functioned poorly in direct sunlight. The RGB-D camera was calibrated, and depth information matched to the RGB image. To detect fruit, a cascade detection with histogram of oriented gradients (HOG) feature was used, then Otsu's method, followed by color thresholding was applied in the CIE L*a*b* color space to remove background objects (leaves, branches etc.). A one-dimensional (1D) filter was developed to remove the fruit pedicles, and an ellipse fitting method employed to identify well-separated fruit. Finally, fruit lineal dimensions were calculated using the RGB-D depth information, fruit image size and the thin lens formula. A Root Mean Square Error (RMSE) = 4.9 and 4.3 mm was achieved for estimated fruit length and width, respectively, relative to manual measurement, for which repeated human measures were characterized by a standard deviation of 1.2 mm. In conclusion, the RGB-D method for rapid in-field mango fruit size estimation is practical in terms of cost and ease of use, but cannot be used in direct intense sunshine. We believe this work represents the first practical implementation of machine vision fruit sizing in field, with practicality gauged in terms of cost and simplicity of operation., Competing Interests: The authors declare no conflict of interest.

Microalgae are a varied group of organisms with considerable commercial potential as sources of various biochemicals, storage molecules and metabolites such as lipids, sugars, amino acids, pigments and toxins. Algal lipids can be processed to bio-oils and biodiesel. The conventional method to estimate algal lipids is based on extraction using solvents and quantification by gravimetry or chromatography. Such methods are time consuming, use hazardous chemicals and are labor intensive. For rapid screening of prospective algae or for management decisions (e.g. decision on timing of harvest), a rapid, high throughput, reliable, accurate, cost effective and preferably nondestructive analytical technique is desirable. This manuscript reviews the application of fluorescent lipid soluble dyes (Nile Red and BODIPY 505/515), nuclear magnetic resonance (NMR), Raman, Fourier transform infrared (FTIR) and near infrared (NIR) spectroscopy for the assessment of lipids in microalgae.

The use of environmental DNA (eDNA) in biodiversity assessments offers a step-change in sensitivity, throughput and simultaneous measures of ecosystem diversity and function. There remains, however, a need to examine eDNA persistence in the wild through simultaneous temporal measures of eDNA and biota. Here, we use metabarcoding of two markers of different lengths, derived from an annual time series of aqueous lake eDNA to examine temporal shifts in ecosystem biodiversity and in an ecologically important group of macroinvertebrates (Diptera: Chironomidae). The analyses allow different levels of detection and validation of taxon richness and community composition (β-diversity) through time, with shorter eDNA fragments dominating the eDNA community. Comparisons between eDNA, community DNA, taxonomy and UK species abundance data further show significant relationships between diversity estimates derived across the disparate methodologies. Our results reveal the temporal dynamics of eDNA and validate the utility of eDNA metabarcoding for tracking seasonal diversity at the ecosystem scale.

Bioaerosols are released in elevated quantities from composting facilities and are associated with negative health effects, although dose-response relationships are unclear. Exposure levels are difficult to quantify as established sampling methods are costly, time-consuming and current data provide limited temporal and spatial information. Confidence in dispersion model outputs in this context would be advantageous to provide a more detailed exposure assessment. We present the calibration and validation of a recognised atmospheric dispersion model (ADMS) for bioaerosol exposure assessments. The model was calibrated by a trial and error optimisation of observed Aspergillus fumigatus concentrations at different locations around a composting site. Validation was performed using a second dataset of measured concentrations for a different site. The best fit between modelled and measured data was achieved when emissions were represented as a single area source, with a temperature of 29°C. Predicted bioaerosol concentrations were within an order of magnitude of measured values (1000-10,000CFU/m 3 ) at the validation site, once minor adjustments were made to reflect local differences between the sites (r 2 >0.7 at 150, 300, 500 and 600m downwind of source). Results suggest that calibrated dispersion modelling can be applied to make reasonable predictions of bioaerosol exposures at multiple sites and may be used to inform site regulation and operational management., (Copyright © 2016 The Authors. Published by Elsevier GmbH.. All rights reserved.)

According to the World Health Organisation, antibiotics are rapidly losing potency in every country of the world. Poultry are currently perceived as a major source of pathogens and antimicrobial resistance. There is an urgent need for new and natural ways to control pathogens in poultry and humans alike. Porous, cation rich, aluminosilicate minerals, zeolites can be used as a feed additive in poultry rations, demonstrating multiple productivity benefits. Next generation sequencing of the 16S rRNA marker gene was used to phylogenetically characterize the fecal microbiota and thus investigate the ability and dose dependency of zeolite in terms of anti-pathogenic effects. A natural zeolite was used as a feed additive in laying hens at 1, 2, and 4% w/w for a 23 week period. At the end of this period cloacal swabs were collected to sample faecal microbial communities. A significant reduction in carriage of bacteria within the phylum Proteobacteria, especially in members of the pathogen-rich family Enterobacteriaceae, was noted across all three concentrations of zeolite. Zeolite supplementation of feed resulted in a reduction in the carriage of a number of poultry pathogens without disturbing beneficial bacteria. This effect was, in some phylotypes, correlated with the zeolite concentration. This result is relevant to zeolite feeding in other animal production systems, and for human pathogenesis., (Copyright © 2016 Elsevier GmbH. All rights reserved.)

Coal seam gas (CSG) is the extraction of methane gas that is desorbed from the coal seam and brought to the surface using a dewatering and depressurisation process within the saturated coalbed. The extracted water is often referred to as co-produced CSG water. In this study, co-produced water from the coal seam of the Bowen Basin (QLD, Australia) was characterised by high concentration levels of Na(+) (1156 mg/L), low concentrations of Ca(2+) (28.3 mg/L) and Mg(2+) (5.6 mg/L), high levels of salinity, which are expected to cause various environmental problems if released to land or waters. The potential treatment of co-produced water using locally sourced natural ion exchange (zeolite) material was assessed. The zeolite material was characterized for elemental composition and crystal structure. Natural, untreated zeolite demonstrated a capacity to adsorb Na(+) ions of 16.16 mEq/100 g, while a treated zeolite using NH4 (+) using a 1.0 M ammonium acetate (NH4C2H3O2) solution demonstrated an improved 136 % Na(+) capacity value of 38.28 mEq/100 g after 720 min of adsorption time. The theoretical exchange capacity of the natural zeolite was found to be 154 mEq/100 g. Reaction kinetics and diffusion models were used to determine the kinetic and diffusion parameters. Treated zeolite using a NH4 (+) pre-treatment represents an effective treatment to reduce Na(+) concentration in coal seam gas co-produced waters, supported by the measured and modelled kinetic rates and capacity.

A range of feed supplements, including antibiotics, have been commonly used in poultry production to improve health and productivity. Alternative methods are needed to suppress pathogen loads and maintain productivity. As an alternative to antibiotics use, we investigated the ability of biochar, bentonite and zeolite as separate 4% feed additives, to selectively remove pathogens without reducing microbial richness and diversity in the gut. Neither biochar, bentonite nor zeolite made any significant alterations to the overall richness and diversity of intestinal bacterial community. However, reduction of some bacterial species, including some potential pathogens was detected. The microbiota of bentonite fed animals were lacking all members of the order Campylobacterales. Specifically, the following operational taxonomic units (OTUs) were absent: an OTU 100% identical to Campylobacter jejuni; an OTU 99% identical to Helicobacter pullorum; multiple Gallibacterium anatis (>97%) related OTUs; Bacteroides dorei (99%) and Clostridium aldenense (95%) related OTUs. Biochar and zeolite treatments had similar but milder effects compared to bentonite. Zeolite amended feed was also associated with significant reduction in the phylum Proteobacteria. All three additives showed potential for the control of major poultry zoonotic pathogens.

Recent advances in embryology and related research offer considerable possibilities to accelerate genetic improvement in cattle breeding. Such progress includes optimization and standardization of laboratory embryo production (in vitro fertilization - IVF), introduction of a highly efficient method for cryopreservation (vitrification), and dramatic improvement in the efficiency of somatic cell nuclear transfer (cloning) in terms of required effort, cost, and overall outcome. Handmade cloning (HMC), a simplified version of somatic cell nuclear transfer, offers the potential for relatively easy and low-cost production of clones. A potentially modified method of vitrification used at a centrally located laboratory facility could result in cloned offspring that are economically competitive with elite animals produced by more traditional means. Apart from routine legal and intellectual property issues, the main obstacle that hampers rapid uptake of these technologies by the beef cattle industry is a lack of confidence from scientific and commercial sources. Once stakeholder support is increased, the combined application of these methods makes a rapid advance toward desirable traits (rapid growth, high-quality beef, optimized reproductive performance) a realistic goal. The potential impact of these technologies on genetic advancement in beef cattle herds in which improvement of stock is sought, such as in northern Australia, is hard to overestimate., (Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.)

Microbially enhanced compost extracts ('compost tea') are being used in commercial agriculture as a source of nutrients and for their perceived benefit to soil microbiology, including plant disease suppression. Rumen content material is a waste of cattle abattoirs, which can be value-added by conversion to compost and 'compost tea'. A system for compost extraction and microbial enhancement was characterised. Molasses amendment increased bacterial count 10-fold, while amendment based on molasses and 'fish and kelp hydrolysate' increased fungal count 10-fold. Compost extract incubated at 1:10 (w/v) dilution showed the highest microbial load, activity and humic/fulvic acid content compared to other dilutions. Aeration increased the extraction efficiency of soluble metabolites, and microbial growth rate, as did extraction of compost without the use of a constraining bag. A protocol of 1:10 dilution and aerated incubation with kelp and molasses amendments is recommended to optimise microbial load and fungal-to-bacterial ratio for this inoculum source., (Copyright © 2011 Elsevier Ltd. All rights reserved.)

A comparative study was performed on compost extracts prepared from cattle rumen content composted for three and nine months, nine month old compost inoculated with a Nutri-Life 4/20™ inoculum, and two commercial preparations (LivingSoil™ and Nutri-Life 4/20™), all incubated for 48h. Nutri-Life 4/20™ had the highest concentrations of NO(3)(-)-N and K(+)-K, while rumen compost extract had higher humic and fulvic acids concentration. The bacterial and fungal community level functional diversity of three month old compost extract and of LivingSoil™, assessed with Biolog™, were higher than that of nine month old rumen compost extract, with or without Nutri-Life 4/20™ inoculum, or Nutri-Life 4/20™. No difference in fungal diversity was observed between treatments, as indicated by Denaturing Gradient Gel Electrophoresis (DGGE) analysis, however, bacterial diversity was higher in all compost extracts and LivingSoil™ compared to the Nutri-Life 4/20™. Criteria for judging the quality of a microbially enhanced extract are discussed., (Copyright © 2011 Elsevier Ltd. All rights reserved.)

Physico-chemical and microbiological investigations were carried out on rumen content material composted for nine months, fresh vermicasts (obtained after passing the same compost through the guts of a mixture of three species of earthworms: Eisenia fetida, Lumbricus rubellus and Perionyx excavates) and microbially enhanced extracts derived from rumen compost, vermicast and vermicast leachate incubated for up to 48 h. Compared to composted rumen contents, vermicast was only improved in terms of microbial biomass C, while vermicast leached extract was significantly higher in NH(4)(+)-N,PO(4)(-)-P, humic acid, bacterial counts and total microbial activity compared to rumen compost extract. Although no difference between treatments was observed in genetic diversity as indicated by DGGE analysis, community level functional diversity of vermicast leached extract (Biolog™) was higher than that of composted rumen contents, vermicast and rumen compost extract indicating an enhancement of microbial activity rather than diversity due to liquid incubation., (Copyright © 2010 Elsevier Ltd. All rights reserved.)

Objective: This paper describes a scoping of adverse event categories and definitions in use across NHS Scotland and makes recommendations about the categories used., Methods: The design involved a network analysis making use of categories and subcategories supplied by 17 different Health Boards via their risk management/clinical governance functions. A total of 128 discrete categories and 1348 subcategories are used across 17 Health Boards (mean number of subcategories used: 164; SD 61; range 56-288)., Results: There is some redundancy with around half of all categories (65; 51%) used by one single board and a further 10 (8%) by just two boards. Many health boards use similar subcategories within different categories. This shows conceptual overlap between confounded categories. This overlap has implications for reliability and has been quantified via the network analysis., Conclusion: The eight most frequently used categories across the Health Boards have an average of 14.9 overlaps with other categories, suggesting some degree of variability in how adverse events are captured. This has implications for nationally collated data; however the formal links between categories identified in this work offer the opportunity of reliable data extraction at national level without substantial recoding by individual Health Boards.

Climate change is likely to affect the nature of pathogens/ chemicals in the environment and their fate and transport. We assess the implications of climate change for changes in human exposures to pathogens/chemicals in agricultural systems in the UK and discuss the effects on health impacts, using expert input and literature on climate change; health effects from exposure to pathogens/chemicals arising from agriculture; inputs of chemicals/pathogens to agricultural systems; and human exposure pathways for pathogens/chemicals in agricultural systems. We established the evidence base for health effects of chemicals/pathogens in the agricultural environment; determined the potential implications of climate change on chemical/pathogen inputs in agricultural systems; and explored the effects of climate change on environmental transport and fate of various contaminants. We merged data to assess the implications of climate change in terms of indirect human exposure to pathogens/chemicals in agricultural systems, and defined recommendations on future research and policy changes to manage adverse increases in risks.

Objective: Climate change is likely to affect the nature of pathogens and chemicals in the environment and their fate and transport. Future risks of pathogens and chemicals could therefore be very different from those of today. In this review, we assess the implications of climate change for changes in human exposures to pathogens and chemicals in agricultural systems in the United Kingdom and discuss the subsequent effects on health impacts., Data Sources: In this review, we used expert input and considered literature on climate change; health effects resulting from exposure to pathogens and chemicals arising from agriculture; inputs of chemicals and pathogens to agricultural systems; and human exposure pathways for pathogens and chemicals in agricultural systems., Data Synthesis: We established the current evidence base for health effects of chemicals and pathogens in the agricultural environment; determined the potential implications of climate change on chemical and pathogen inputs in agricultural systems; and explored the effects of climate change on environmental transport and fate of different contaminant types. We combined these data to assess the implications of climate change in terms of indirect human exposure to pathogens and chemicals in agricultural systems. We then developed recommendations on future research and policy changes to manage any adverse increases in risks., Conclusions: Overall, climate change is likely to increase human exposures to agricultural contaminants. The magnitude of the increases will be highly dependent on the contaminant type. Risks from many pathogens and particulate and particle-associated contaminants could increase significantly. These increases in exposure can, however, be managed for the most part through targeted research and policy changes.

Purpose: There are three main objectives of the research presented in this paper: to examine the challenges of using an electronic adverse incident recording and reporting system; to assess the method of using a prevention appraisal and failure model; and to identify the benefits of using quality costs in conjunction with incident reporting systems., Design/methodology/approach: Action diary, documentation and triangulation are used to obtain an understanding of the challenges and critical success factors in using quality costing within an adverse incident recording and reporting system., Findings: The paper provides healthcare professionals with the critical success factors for developing quality costing into an electronic adverse incident recording and reporting system. This approach would provide clinicians, managers and directors with information on patient safety issues following the effective use of data from an electronic adverse incident reporting and recording system., Originality/value: This paper makes an attempt of using a prevention, appraisal and failure model (PAF) within a quality-costing framework in relation to improving patient safety within an electronic adverse incident reporting and recording system.

Objective: The purpose of this study was to assess the effectiveness of a low-resource-intensive lifestyle modification program incorporating resistance training and to compare a gymnasium-based with a home-based resistance training program on diabetes diagnosis status and risk., Research Design and Methods: A quasi-experimental two-group study was undertaken with 122 participants with diabetes risk factors; 36.9% had impaired glucose tolerance (IGT) or impaired fasting glucose (IFG) at baseline. The intervention included a 6-week group self-management education program, a gymnasium-based or home-based 12-week resistance training program, and a 34-week maintenance program. Fasting plasma glucose (FPG) and 2-h plasma glucose, blood lipids, blood pressure, body composition, physical activity, and diet were assessed at baseline and week 52., Results: Mean 2-h plasma glucose and FPG fell by 0.34 mmol/l (95% CI -0.60 to -0.08) and 0.15 mmol/l (-0.23 to -0.07), respectively. The proportion of participants with IFG or IGT decreased from 36.9 to 23.0% (P = 0.006). Mean weight loss was 4.07 kg (-4.99 to -3.15). The only significant difference between resistance training groups was a greater reduction in systolic blood pressure for the gymnasium-based group (P = 0.008)., Conclusions: This intervention significantly improved diabetes diagnostic status and reduced diabetes risk to a degree comparable to that of other low-resource-intensive lifestyle modification programs and more intensive interventions applied to individuals with IGT. The effects of home-based and gymnasium-based resistance training did not differ significantly.

A nondestructive, chemical-free method is presented for the extraction of DNA from small insects. Blackflies were submerged in sterile, distilled water and sonicated for varying lengths of time to provide DNA which was assessed in terms of quantity, purity and amplification efficiency. A verified DNA barcode was produced from DNA extracted from blackfly larvae, pupae and adult specimens. A 60-second sonication period was found to release the highest quality and quantity of DNA although the amplification efficiency was found to be similar regardless of sonication time. Overall, a 66% amplification efficiency was observed. Examination of post-sonicated material confirmed retention of morphological characters. Sonication was found to be a reliable DNA extraction approach for barcoding, providing sufficient quality template for polymerase chain reaction amplification as well as retaining the voucher specimen for post-barcoding morphological evaluation., (© 2007 The Authors.)

Purpose: The purpose of this paper is to present the challenges and gaps in using an electronic adverse incident recording and reporting system from a commercial supplier to an acute health care setting., Design/methodology/approach: The paper used action diary, documentation and triangulation to obtain an understanding of the challenges and gaps., Findings: The paper provides health care with further understanding of the complexity, challenges and gaps of using an electronic adverse incident recording system to improve patient safety., Originality/value: This paper explains the important views of clinicians and managers in relation to improving patient safety by using an electronic adverse incident management system.

The hypothesis that hyperaccumulation of certain metals in plants may play a role in osmotic adjustment under water stress (drought) was tested in the context of nickel hyperaccumulator Stackhousia tryonii. Field-collected mature plants of S. tryonii, grown in native ultramafic soil, were pruned to soil level and the re-growth exposed to five levels of water stress (20, 40, 60, 80 and 100% field capacity; FC) for 20 weeks. Water stress had significant (P<0.05) influence on growth (biomass), water potential and shoot Ni concentrations, with progressively more impact as water stress was increased from 80 to 40% FC. Shoot Ni concentration increased significantly from 3,400 microg g(-1) dry weight (at 100% FC) to 9,400 microg g(-1) dry weight (at 20% FC). Assuming that Ni is uniformly distributed through the shoot tissue, the Ni concentration could account for 100% at the 80 and 60% FC conditions, and 50% at the 40 and 20% FC conditions of plant osmotic regulation. The results are consistent with a role of Ni in osmotic adjustment and protection of S. tryonii plants against drought.

Background and Aims: Stackhousia tryonii, a rare nickel hyperaccumulating herb, is endemic to ultramafic (serpentine) soils of central Queensland, Australia. The effects of eight dormancy-relieving treatments on germination of stored seeds of Stackhousia tryonii were investigated under controlled light and temperature conditions. *, Methods: The treatments were: untreated (control i), leached and dehydrated (primed control ii), treating with gibberellic acid (150 and 300 microM), smoke extract (5 and 10 %, v/v) and potassium cyanide (40 and 80 mM). *, Key Results: Freshly harvested seeds did not germinate. Germination percentage increased with time of storage for up to 18 months (38.3 %). Gibberellin, smoke extract and cyanide treatments did not significantly improve germination. Light did not affect seed germination and there was no interaction between dormancy-relieving treatments and light. A significant inhibition of germination occurred in seeds treated with 5 % (but not 10 %) aqueous smoke extract. Saturated fatty acids, predominantly tridecanoic (C13:0), constituted about 90 % of the total fatty acids in the oil of freshly harvested seeds. In contrast, there was increased accumulation (>75 %) of mono-unsaturated (oleic, c18:1) and poly-unsaturated (linoleic, c18:2; linolenic, c18:3) fatty acids in the oil of stored seeds. *, Conclusions: Seeds of S. tryonii require an after-ripening period for germination.

The physical path of sucrose unloading in the sugarcane stalk is described. About 50% of the vascular bundles in the internodes were located within 3 mm of the outside of the stalk. These bundles were inactive in long distance sucrose transport, as assessed by dye tracers of phloem flow. A sheath of fibres isolates the phloem apoplast from that of the storage parenchyma. In bundles associated with long distance transport (i.e. in the central region), the fibre sheath is narrowest to either side of the phloem fibre cap, and consists of living cells with plasmodesmata within pits in the secondary wall. Plasmodesmata were also arranged into pit fields between cells of the storage parenchyma. Since the vascular apoplast is isolated from the apoplast of the storage parenchyma, sucrose must move through the symplast of the fibre sheath. The calculated flux of sucrose through plasmodesmata of this cell layer was at the low end of reported values in the literature. Sucrose unloading within the storage parenchyma may also follow a symplastic route, with unloading into the apoplast of the storage parenchyma occurring as part of a turgor mechanism to increase sink strength.

Field-collected, young plants of Ni hyperaccumulator Stackhousia tryonii, grown in a glasshouse for 20 weeks, were exposed to low- (available Ni concentration in the native serpentine soil, i.e. 60 microg g(-1) dry soil) and high- (external application of 1000 ppm) Ni concentrations in the substrate. Nickel concentration in the freeze-dried leaf tissues increased from 3700 microg g(-1) to 13 700 microg g(-1) with soil Ni supplementation, of which >60% was extracted with dilute acid (0.025 M HCl). Nickel supplementation also elicited a 575%, 211%, and 37% increase in the final concentrations of oxalic, citric, and malic acids, respectively, in leaf tissues. Malic acid was the dominant organic acid, followed by citric and oxalic acids. The molar ratio of Ni to malic acid was 1.0, consistent with a role for malate as a ligand for Ni in hyperaccumulating plants, supporting detoxification/transport and storage of this heavy metal in S. tryonii. The total amino acid concentrations in the xylem sap did not change with Ni supplementation (21.7+/-3.7 mM and 17.9+/-5 mM, respectively, for low- and high-nickel-treated plants). Glutamine was the major amino acid in both the low- and high-Ni-treated plants. The concentration of glutamine decreased by >60%, with a corresponding increase in alanine, aspartic acid, and glutamic acid, on exposure to high Ni. A role of amino acids in Ni complexation and transport in S. tryonii is not immediately apparent.

Stackhousia tryonii Bailey is one of the three nickel hyperaccumulators reported from Australia. It is a rare, herbaceous plant that accumulates (Ni) both in leaf and stem tissues. Localisation of Ni in leaf and stem tissues of S. tryonii was studied using two micro-analytical techniques, energy dispersive X-ray spectrometry (EDXS) and micro-proton-induced X-ray emission spectrometry (micro-PIXE). Dimethylglyoxime complexation of Ni was also visualised by bright- and dark-field microscopy, but this technique was considered to create artefacts in the distribution of Ni. Energy dispersive X-ray spectrometric analysis indicated that guard cells possessed a lower Ni concentration than epidermal cells, and that epidermal cells and vascular tissue contained higher levels of Ni than mesophyll, as reported for other Ni hyperaccumulators. The highest Ni concentration was recorded (PIXE quantitative point analysis) in the epidermal cells and vascular tissue (5400 μg g -1 DW), approximately double that recorded in palisade cells (2500 μg g -1 DW). However, concentrations were variable within these tissues, explaining, in part, the similarity between average Ni concentrations of these tissues (as estimated by region selection mode). Stem tissues showed a similar distribution pattern as leaves, with relatively low Ni concentration in the pith (central) region. The majority of Ni (73-85% for leaves; 80-92% for stem) was extracted from freeze-dried sections by water extraction, suggesting that this metal is present in a highly soluble and mobile form in the leaf and stem tissues of S. tryonii.

•  Metal concentrations within reproductive tissues of metallophytes are rarely reported. Here, the spatial distribution of nickel (Ni) within the fruits (seeds) of the Ni hyperaccumulator Stackhousia tryonii was investigated. •  Two microanalytical techniques, energy dispersive x-ray spectrometry (EDXS) and nuclear microprobe (micro-proton-induced x-ray emission spectrometry; micro-PIXE) were employed for qualitative and quantitative assessment, respectively, of localized Ni, within the fruits of S. tryonii. The results were compared with quantitative analysis made using inductively coupled plasma-optical emission spectrometry (ICP-OES). •  Nickel analysis made using micro-PIXE was consistent with bulk (ICP-OES) analysis (at 1800 µg g -1 d. wt), however, a beam resolution of approx. 2 × 2 µm 2 allowed tissue localization. Nickel was partitioned to the fruit wall (pericarp) (4433 µg g -1 ), while endospermic and cotyledonary tissues possessed little Ni (309 and 182 µg g -1 d. wt, respectively). •  This distribution is consistent with the interpretation that principal pathway of Ni movement within the fruit is symplastic rather than apoplastic (as the filial generation lacks symplastic connection with the parent).

Anaerobic ammonium oxidation (anammox) is both a promising process in wastewater treatment and a long overlooked microbial physiology that can contribute significantly to biological nitrogen cycling in the world's oceans. Anammox is mediated by a monophyletic group of bacteria that branches deeply in the Planctomycetales. Here we describe a new genus and species of anaerobic ammonium oxidizing planctomycetes, discovered in a wastewater treatment plant (wwtp) treating landfill leachate in Pitsea, UK. The biomass from this wwtp showed high anammox activity (5.0 +/- 0.5 nmol/mg protein/min) and produced hydrazine from hydroxylamine, one of the unique features of anammox bacteria. Eight new planctomycete 16S rRNA gene sequences were present in the 16S rRNA gene clone library generated from the biomass. Four of these were affiliated to known anammox 16S rRNA gene sequences, but branched much closer to the root of the planctomycete line of descent. Fluorescence in situ hybridization (FISH) with oligonucleotide probes specific for these new sequences showed that two species (belonging to the same genus) together made up > 99% of the planctomycete population which constituted 20% of the total microbial community. The identification of these organisms as typical anammox bacteria was confirmed with electron microscopy and lipid analysis. The new species, provisionally named Candidatus "Scalindua brodae" and "Scalindua wagneri" considerably extend the biodiversity of the anammox lineage on the 16S rRNA gene level, but otherwise resemble known anammox bacteria. Simultaneously, another new species of the same genus, Candidatus "Scalindua sorokinii", was detected in the water column of the Black Sea, making this genus the most widespread of all anammox bacteria described so far.

Short-wavelength near-infrared (SW-NIR) (700-1100 nm) spectra of aqueous solutions of sucrose, D-glucose, and D-fructose were monitored with respect to change in temperature and sugar concentration. Sugar OH and CH related vibrations were identified by analysis of the spectra of sugar solutions in deuterium oxide (D2O), and of sucrose-d8 solutions in D2O. Absorption spectra were explained in terms of the second and third overtones of OH stretching vibrations and the third overtone of CH2 and CH stretchings. In deuterated solutions, CH and CH2 higher overtone vibration bands became apparent. The major spectral effect of decreased temperature or increased sugar concentration was a decrease in absorbance at 960 nm and an increase in absorbance at 984 nm, interpreted as an increase in the degree of H bonding. Partial least-squares (PLS) calibrations on sugar concentrations (with spectra collected at several sample temperatures) relied strongly on the 910 nm sugar CH related bands, whereas calibrations on temperature depended equally on all OH associated vibrations (750, 840, 960, and 985 nm).

Abstract There are many ecological diversity measures, but their suitability for use with highly diverse bacterial communities is unclear and seldom considered. We assessed a range of species richness and evenness/dominance indices, and the use of species abundance models using samples of bacteria from zinc-contaminated and control soils. Bacteria were assigned to operational taxonomic units (OTUs) using amplified ribosomal DNA restriction analysis of 236 clones from each soil. The reduced diversity apparent in the contaminated soil was reflected by the diversity indices to varying degrees. The number of clones analysed and the weighting given to rare vs. abundant OTUs are the most important considerations when selecting measures. Our preferences, arrived at using theory and practical experience, include: the log series index alpha; the Q statistic (but only if coverage is 50% or more); the Berger-Parker and Simpson's indices, although their ecological relevance may be limited; and, unexpectedly, the Shannon-Wiener and Shannon evenness indices, even though their meanings may not be clear and their values inaccurate when coverage is low. For extrapolation, the equation for the log series distribution seems the best for extrapolating from OTU accumulation curves while non-parametric methods, such as Chao 1, show promise for estimating total OTU richness. Due to a preponderance of single-occurrence OTUs, none of the five species abundance models fit the OTU abundance distribution of the control soil, but both the log and log normal models fit the less diverse contaminated soil. Species abundance models are useful, irrespective of coverage, because they address the whole distribution of a sample, aiding comparison by revealing overall trends as well as specific changes in particular abundance classes.

Bacteria associated with leachate from a constructed, surface-flow wetland effective at removing ammonium-N, were characterised using molecular methods which bypass the need for cultivation. DNA was extracted from the sample and bacterial 16S rDNA sequences amplified and cloned. Ninety-six individual clones were re-amplified and analysed by restriction digestion and targeted sequencing. A collector's curve was used to estimate the total number of bacterial groups (operational taxonomic units, OTUs) in the sample at 47. Thirty-six clones representing 28 OTUs were sequenced and characterised by aligning them against published sequences. Of these, 10 were confidently identified, whilst for the remaining 18, the closest match was obtained. The sequences in 64% of the OTUs were similar to those of the Proteobacteria but no classical nitrifying bacteria were identified. However, alkaliphilic Methylomicrobium sp. that oxidise ammonium and bacteria from the genus Alcaligenes, at least one species of which is capable of heterotrophic nitrification, were detected.