Plant Breeder's Rights: An Australian commentary December 2004

The aim of this manual is to provide a practical guide to the Plant Breeder's Rights Act 1994 (Cth). It is a resource of information about the legislation, its administration, and its operation. This commentary is intended to assist plant breeders, scientific researchers, and business managers who want to make a more effective use of the Plant Breeder's Rights Act 1994 (Cth) in the management and commercialisation of their intellectual property rights. It is also designed to enhance the understanding of the legislation among lawyers, patent attorneys, qualified persons, and policy-makers.

The new conquistadors: Patent law and expressed sequence tags

It's akin to the old Spanish, English and Portuguese explorers. They would take their boats until they found some edge of land, then they would go up and plant the flag of their king or queen. They didn't know what they'd discovered; how big it is, where it goes to - but they would claim it anyway. David Korn of the Association of American Medical Colleges This article analyses recent litigation over patent law and expressed sequence tags (ESTs). In the case of In re Fisher, the United States Court of Appeals for the Federal Circuit engaged in judicial consideration of the revised utility guidelines of the United States Patent and Trademark Office (USPTO). In this matter, the agricultural biotechnology company Monsanto sought to patent ESTs in maize plants. A patent examiner and the Board of Patent Appeals and Interferences had doubted whether the patent application was useful. Monsanto appealed against the rulings of the USPTO. A number of amicus curiae intervened in the matter in support of the USPTO - including Genentech, Affymetrix, Dow AgroSciences, Eli Lilly, the National Academy of Sciences, and the Association of American Medical Colleges. The majority of the Court of Appeals for the Federal Circuit supported the position of the USPTO, and rejected the patent application on the grounds of utility. The split decision highlighted institutional tensions over the appropriate thresholds for patent criteria - such as novelty, non-obviousness, and utility. The litigation raised larger questions about the definition of research tools, the incremental nature of scientific progress, and the role of patent law in innovation policy. The decision of In re Fisher will have significant ramifications for gene patents, in the wake of the human genome project. Arguably, the USPTO utility guidelines need to be reinforced by a tougher application of the standards of novelty and non-obviousness in respect of gene patents.

Owning omega-3: Monsanto and the invention of meat

In August of 2010, Anna Salleh of the Science Unit of the Australian Broadcasting Corporation broke a story about Monsanto seeking to patent the enhancement of meat, including omega-3 fatty acids: ‘Enhanced port is sparking debate over the ethics of placing patents on food. Patent applications covering the enhancement of meat, including pork with omega-3 fatty acids, are stimulating debate over the ethics and legalities of claiming intellectual property over food. Monsanto has filed patents that cover the feeding of animals soybeans, which have been genetically modified by the company to contain stearidonic acid (SDA), a plant-derived omega-3 fatty acid... Omega-3s have been linked to improved cardiovascular health and there are many companies engineering them into foodstuffs. But the new patent applications have touched a raw nerve among those who see them as an attempt by the company to exert control over the food chain.’ This article providers a critical evaluation of the controversy of Monsanto’s patent applications, and the larger issues over patenting food. It first considers the patent portfolio of Monsanto; the nature of the patent claims; and the examination of the claims by patent examiners. Second, it examines the withdrawal and revision of the patent claims by Monsanto in the wake of criticism by patent authorities and the public disquiet over the controversial application. Third, this article considers the larger policy issues raised by Monsanto’s patent applications – including the patenting of plants, animals, and foodstuffs. There is also a consideration of the impact of patents upon the administration of health-care, competition, and research.

General motor vehicle drivers' knowledge and practices regarding drink driving in Yinchuan and Guangzhou, China

Objective: Drink driving contributes to significant levels of injury and economic loss in China but is not well researched. This study examined knowledge, drink-driving practices, and alcohol misuse problems among general drivers in Yinchuan. The objectives were to gain a better understanding of drink driving in Yinchuan, identify areas that need to be addressed, and compare the results with a similar study in Guangzhou. Methods: This was a cross-sectional study with a survey designed to collect information on participants’ demographic characteristics and their knowledge and practices in relation to drinking and driving. The survey was composed of questions on knowledge and practices in relation to drink driving and was administered to a convenience sample of 406 drivers. Alcohol misuse problems were assessed by using the Alcohol Use Disorders Identification Test (AUDIT). Results: Males accounted for the main proportion of drivers sampled from the general population (“general drivers”). A majority of general drivers in both cities knew that drunk driving had become a criminal offense in 2011; however, knowledge of 2 legal blood alcohol concentration (BAC) limits was quite low. Fewer drivers in Yinchuan (22.6%) than in Guangzhou (27.9) reported having been stopped by police conducting breath alcohol testing at least once in the last 12 months. The mean AUDIT score in Yinchuan (M = 8.2) was higher than that in Guangzhou (M = 7.4), and the proportion of Yinchuan drivers with medium or higher alcohol misuse problems (31.2%) was correspondingly higher than in Guangzhou (23.1%). In Yinchuan, males had a significantly higher AUDIT score than females (t = 3.454, P < .001), similar to Guangzhou. Multiple regression analyses were conducted on potential predictors of the AUDIT score (age, gender, monthly income, education level, years licensed, and age started drinking). There were significant individual contributions of gender (beta = 0.173, P = .09) and age at which drinking started (beta = 0.141, P = .033), but the overall model for Yinchuan was not significant, unlike Guangzhou. Conclusions: The results show that there are shortfalls in knowledge of the legislation and how to comply with it and deficiencies in police enforcement. In addition, there was evidence of drink driving and drink riding at high levels in both cities. Recommendations are made to address these issues.

Characterization of epitopes for virus-neutralizing monoclonal antibodies to Ross River virus E2 using phage-displayed random peptide libraries

Ross River virus (RRV) is the predominant cause of epidemic polyarthritis in Australia, yet the antigenic determinants are not well defined. We aimed to characterize epitope(s) on RRV-E2 for a panel of monoclonal antibodies (MAbs) that recognize overlapping conformational epitopes on the E2 envelope protein of RRV and that neutralize virus infection of cells in vitro. Phage-displayed random peptide libraries were probed with the MAbs T1E7, NB3C4, and T10C9 using solution-phase and solid-phase biopanning methods. The peptides VSIFPPA and KTAISPT were selected 15 and 6 times, respectively, by all three of the MAbs using solution-phase biopanning. The peptide LRLPPAP was selected 8 times by NB3C4 using solid-phase biopanning; this peptide shares a trio of amino acids with the peptide VSIFPPA. Phage that expressed the peptides VSIFPPA and LRLPPAP were reactive with T1E7 and/or NB3C4, and phage that expressed the peptides VSIFPPA, LRLPPAP, and KTAISPT partially inhibited the reactivity of T1E7 with RRV. The selected peptides resemble regions of RRV-E2 adjacent to sites mutated in neutralization escape variants of RRV derived by culture in the presence of these MAbs (E2 210-219 and 238-245) and an additional region of E2 172-182. Together these sites represent a conformational epitope of E2 that is informative of cellular contact sites on RRV.

Combining transcriptome assemblies from multiple de novo assemblers in the allo-tetraploid plant Nicotiana benthamiana

Background Nicotiana benthamiana is an allo-tetraploid plant, which can be challenging for de novo transcriptome assemblies due to homeologous and duplicated gene copies. Transcripts generated from such genes can be distinct yet highly similar in sequence, with markedly differing expression levels. This can lead to unassembled, partially assembled or mis-assembled contigs. Due to the different properties of de novo assemblers, no one assembler with any one given parameter space can re-assemble all possible transcripts from a transcriptome. Results In an effort to maximise the diversity and completeness of de novo assembled transcripts, we utilised four de novo transcriptome assemblers, TransAbyss, Trinity, SOAPdenovo-Trans, and Oases, using a range of k-mer sizes and different input RNA-seq read counts. We complemented the parameter space biologically by using RNA from 10 plant tissues. We then combined the output of all assemblies into a large super-set of sequences. Using a method from the EvidentialGene pipeline, the combined assembly was reduced from 9.9 million de novo assembled transcripts to about 235,000 of which about 50,000 were classified as primary. Metrics such as average bit-scores, feature response curves and the ability to distinguish paralogous or homeologous transcripts, indicated that the EvidentialGene processed assembly was of high quality. Of 35 RNA silencing gene transcripts, 34 were identified as assembled to full length, whereas in a previous assembly using only one assembler, 9 of these were partially assembled. Conclusions To achieve a high quality transcriptome, it is advantageous to implement and combine the output from as many different de novo assemblers as possible. We have in essence taking the ‘best’ output from each assembler while minimising sequence redundancy. We have also shown that simultaneous assessment of a variety of metrics, not just focused on contig length, is necessary to gauge the quality of assemblies.

Multifractal analyses of daily rainfall time series in Pearl River basin of China

The multifractal properties of daily rainfall time series at the stations in Pearl River basin of China over periods of up to 45 years are examined using the universal multifractal approach based on the multiplicative cascade model and the multifractal detrended fluctuation analysis (MF-DFA). The results from these two kinds of multifractal analyses show that the daily rainfall time series in this basin have multifractal behavior in two different time scale ranges. It is found that the empirical multifractal moment function K(q)K(q) of the daily rainfall time series can be fitted very well by the universal multifractal model (UMM). The estimated values of the conservation parameter HH from UMM for these daily rainfall data are close to zero indicating that they correspond to conserved fields. After removing the seasonal trend in the rainfall data, the estimated values of the exponent h(2)h(2) from MF-DFA indicate that the daily rainfall time series in Pearl River basin exhibit no long-term correlations. It is also found that K(2)K(2) and elevation series are negatively correlated. It shows a relationship between topography and rainfall variability.

Temporal trend of pesticide concentrations in the Chikugo River (Japan) with changes in environmental regulation and field infrastructure

Contamination of pesticides, which are applied to rice paddy fields, in river water has been a major problem in Japan for decades. A prolonged water holding period after pesticide application in paddy fields is expected to reduce the concentration of rice pesticides in river water. Therefore, a long monitoring campaign was conducted from 2004 to 2010 to measure the concentrations of pesticides in water samples collected from several points along the Chikugo River (Japan) including tributaries and the main stream to see if there was any reduction in the level of pesticide contamination after the extension of the water holding period (from 3–4 days to 7 days) was introduced in 2007 by the new water management regulation. No significant difference (p > 0.05) was found in pesticide concentrations between the periods before and after 2007 in all monitoring points, except in one tributary where the pesticide concentrations after 2007 were even higher than that of the previous period. A detailed study in one of the tributaries also revealed that the renovated infrastructure did not reduce the pesticide concentrations in the drainage canals. Neither the introduction of the new regulation nor the improved infrastructure had any significant effect on reducing the contamination of pesticides in water of the Chikugo River. It is probably because most farmers did not properly implement the new requirement of holding paddy water within the field for 7 days after the application of pesticides. Only tightening the regulation would not be sufficient and more actions should be taken to enforce/provide extension support for the new water management regulation in order to reduce the level of residual pesticides in river water in Japan.

Do motor vehicle crashes arise from single or multiple unique risk processes? An inquiry into crash causes and modelling

Crashes at any particular transport network location consist of a chain of events arising from a multitude of potential causes and/or contributing factors whose nature is likely to reflect geometric characteristics of the road, spatial effects of the surrounding environment, and human behavioural factors. It is postulated that these potential contributing factors do not arise from the same underlying risk process, and thus should be explicitly modelled and understood. The state of the practice in road safety network management applies a safety performance function that represents a single risk process to explain crash variability across network sites. This study aims to elucidate the importance of differentiating among various underlying risk processes contributing to the observed crash count at any particular network location. To demonstrate the principle of this theoretical and corresponding methodological approach, the study explores engineering (e.g. segment length, speed limit) and unobserved spatial factors (e.g. climatic factors, presence of schools) as two explicit sources of crash contributing factors. A Bayesian Latent Class (BLC) analysis is used to explore these two sources and to incorporate prior information about their contribution to crash occurrence. The methodology is applied to the state controlled roads in Queensland, Australia and the results are compared with the traditional Negative Binomial (NB) model. A comparison of goodness of fit measures indicates that the model with a double risk process outperforms the single risk process NB model, and thus indicating the need for further research to capture all the three crash generation processes into the SPFs.

Development of multi-rotor localised surveillance using multi-spectral sensors for plant biosecurity

This report describes a proof of concept for multi-rotor localised surveillance using a multi-spectral sensor for plant biosecurity applications. A literature review was conducted on previous applications using airborne multispectral imaging for plant biosecurity purposes. A ready built platform was purchased and modified in order to fit and provide suitable clearance for a Tetracam Mini-MCA multispectral camera. The appropriate risk management documents were developed allowing the platform and the multi-spectral camera to be tested extensively. However, due to technical difficulties with the platform the Mini- MCA was not mounted to the platform. Once a suitable platform is developed, future extensions can be conducted into the suitability of the Mini-MCA for airborne surveillance of Australian crops.

Association between glaucoma and at–fault motor vehicle collision involvement among older drivers

Objective To examine the association between glaucoma and motor vehicle collision (MVC) involvement among older drivers, including the role of visual field impairment that may underlie any association found. Design A retrospective population-based study Participants A sample of 2,000 licensed drivers aged 70 years and older who reside in north central Alabama. Methods At-fault MVC involvement for five years prior to enrollment was obtained from state records. Three aspects of visual function were measured: habitual binocular distance visual acuity, binocular contrast sensitivity and the binocular driving visual field constructed from combining the monocular visual fields of each eye. Poisson regression was used to calculate crude and adjusted rate ratios (RR) and 95% confidence intervals (CI). Main Outcomes Measures At-fault MVC involvement for five years prior to enrollment. Results Drivers with glaucoma (n = 206) had a 1.65 (95% confidence interval [CI] 1.20-2.28, p = 0.002) times higher MVC rate compared to those without glaucoma after adjusting for age, gender and mental status. Among those with glaucoma, drivers with severe visual field loss had higher MVC rates (RR = 2.11, 95% CI 1.09-4.09, p = 0.027), whereas no significant association was found among those with impaired visual acuity and contrast sensitivity. When the visual field was sub-divided into six regions (upper, lower, left, and right visual fields; horizontal and vertical meridians), we found that impairment in the left, upper or lower visual field was associated with higher MVC rates, and an impaired left visual field showed the highest RR (RR = 3.16, p = 0.001) compared to other regions. However, no significant association was found in deficits in the right side or along the horizontal or vertical meridian. Conclusions A population-based study suggests that older drivers with glaucoma are more likely to have a history of at-fault MVC involvement than those without glaucoma. Impairment in the driving visual field in drivers with glaucoma appears to have an independent association with at-fault MVC involvement, whereas visual acuity and contrast sensitivity impairments do not.

Cytotoxic C20 diterpenoid alkaloids from the Australian endemic rainforest plant Anopterus macleayanus

In order to identify new anticancer compounds from nature, a prefractionated library derived from Australian endemic plants was generated and screened against the prostate cancer cell line LNCaP using a metabolic assay. Fractions from the seeds, leaves, and wood of Anopterus macleayanus showed cytotoxic activity and were subsequently investigated using a combination of bioassay-guided fractionation and mass-directed isolation. This led to the identification of four new diterpenoid alkaloids, 6α-acetoxyanopterine (1), 4′-hydroxy-6α-acetoxyanopterine (2), 4′-hydroxyanopterine (3), and 11α-benzoylanopterine (4), along with four known compounds, anopterine (5), 7β-hydroxyanopterine (6), 7β,4′-dihydroxyanopterine (7), and 7β-hydroxy-11α-benzoylanopterine (8); all compounds were purified as their trifluoroacetate salt. The chemical structures of 1–8 were elucidated after analysis of 1D/2D NMR and MS data. Compounds 1–8 were evaluated for cytotoxic activity against a panel of human prostate cancer cells (LNCaP, C4-2B, and DuCaP) and nonmalignant cell lines (BPH-1 and WPMY-1), using a live-cell imaging system and a metabolic assay. All compounds showed potent cytotoxicity with IC50 values of <400 nM; compound 1 was the most active natural product from this series, with an IC50 value of 3.1 nM toward the LNCaP cell line. The live-cell imaging assay on 1–8 showed a concentration- and time-dependent effect on the cell morphology and proliferation of LNCaP cells.

Fuzzy optimization model for water quality management of a river system - Closure

A fuzzy waste-load allocation model, FWLAM, is developed for water quality management of a river system using fuzzy multiple-objective optimization. An important feature of this model is its capability to incorporate the aspirations and conflicting objectives of the pollution control agency and dischargers. The vagueness associated with specifying the water quality criteria and fraction removal levels is modeled in a fuzzy framework. The goals related to the pollution control agency and dischargers are expressed as fuzzy sets. The membership functions of these fuzzy sets are considered to represent the variation of satisfaction levels of the pollution control agency and dischargers in attaining their respective goals. Two formulations—namely, the MAX-MIN and MAX-BIAS formulations—are proposed for FWLAM. The MAX-MIN formulation maximizes the minimum satisfaction level in the system. The MAX-BIAS formulation maximizes a bias measure, giving a solution that favors the dischargers. Maximization of the bias measure attempts to keep the satisfaction levels of the dischargers away from the minimum satisfaction level and that of the pollution control agency close to the minimum satisfaction level. Most of the conventional water quality management models use waste treatment cost curves that are uncertain and nonlinear. Unlike such models, FWLAM avoids the use of cost curves. Further, the model provides the flexibility for the pollution control agency and dischargers to specify their aspirations independently.

Gene patent practice across plant and human genomes

The uses of genetic sequences to inform, enable or create products or services for human biomedicine are substantially different from their uses in crop-based agriculture. Here, we explore what similarities and differences may emerge in patent use and strategies, and map patent-disclosed sequences onto three important plant genomes: maize (corn), rice and soybean. We focus on those referenced in the granted patent claims to compare their uses to the approach used in human gene patenting.

The ownership question of plant gene and genome intellectual properties

The restructuring of the crop agriculture industry over the past two decades has enabled patent holders to exclude, prevent and deter others from using certain research tools and delay or block further follow-on inventions