Prioritising targets for biological control of weeds - a decision support tool for policy makers

This report outlines a framework of the overall process of prioritising targets for biological control and includes a decision support tool that enables policy makers to determine whether biological control is a suitable option for a proposed target species.Introduction Establishing effective biological control agents in Australia is costly in both resources and time, yet it is often a valuable component of weed control. It has been estimated that biological control of weeds in Australia has provided around $10 billion worth of agricultural protection over the past century. To date significant investment has been made in the selection process of biocontrol agents and the identification of priority weeds for biocontrol. However there is no nationally agreed system that facilitates prioritisation of weed targets for biological control. The Department of Agriculture commissioned ABARES to develop:• a framework that outlines the overall process of prioritising targets for biological control and• a decision support tool that enables policy makers to determine whether biological control is a suitable option for the proposed target species.A recent work related to the selection and prioritisation of weeds for biological control targets was published by Paynter et al 2009 (hereafter \u27Paynter\u27). Paynter was used as a basis for discussion about how to assist policy makers in assessing whether biocontrol is an appropriate option for weed control.The proposal for a decision support tool for policy makers was discussed at a workshop fully recognising that such a system would need to have a science basis that is both transparent and repeatable to be rigorous. The participants were experts in biocontrol or other weed science, state representatives and other relevant stakeholders. The proposal was outlined in a background/discussion paper and provided to participants prior to the workshop. The purpose of the paper was to provide participants with relevant background information and a proposed approach for a decision support tool for policy makers to be debated and progressed at the workshop.Aim of the workshop and background/discussion paper The workshop was held in Canberra on 4 April 2013. The objectives of the workshop were to:• discuss whether the approach based on Paynter is suitable as a decision support tool at the policy level to prioritise targets for biological control• reach a consensus amongst workshop participants on key principles that need to be considered in the prioritisation process of biological control targetsSuggestions made at the workshop are addressed in this report. Many of the concerns raised at the workshop corresponded with the common \u27core\u27 issues recorded in Paynter. These include concerns about lack of data, the tendency of the framework to overlook weeds outside the Weeds of National Significance, concerns that weightings are arbitrary, and a need for the framework to be able to anticipate emergent weeds and potential future problems. Here, those issues that are relevant to policy have been considered with the acknowledgement that remaining \u27core\u27 issues need to be addressed elsewhere

Prevention of obesity : weighing ethical arguments

Taxes on unhealthy food, limits to commercial advertising, a ban on chocolate drink at schools, or compulsory physical exercise for obese employees: efforts to counter the rise in overweight and obesity sometimes rais

The MCGA (multiple cubic gradient approximation) method for the analysis of Raman spectra

An easily accessible interactive method for the analysis of Raman spectra consisting of many overlapping peaks is presented. A combination of a three- or four-dimensional grid and gradient searching is applied. The method can handle spectra with up to about 50 lines, based on a broad background. Analytical and user-defined or tabulated basic functions can be included. The merits of the method are discussed with both artificial and real spectra

The aspartic proteinase family of three Phytophthora species

Background - Phytophthora species are oomycete plant pathogens with such major social and economic impact that genome sequences have been determined for Phytophthora infestans, P. sojae and P. ramorum. Pepsin-like aspartic proteinases (APs) are produced in a wide variety of species (from bacteria to humans) and contain conserved motifs and landmark residues. APs fulfil critical roles in infectious organisms and their host cells. Annotation of Phytophthora APs would provide invaluable information for studies into their roles in the physiology of Phytophthora species and interactions with their hosts. Results - Genomes of Phytophthora infestans, P. sojae and P. ramorum contain 11-12 genes encoding APs. Nine of the original gene models in the P. infestans database and several in P. sojae and P. ramorum (three and four, respectively) were erroneous. Gene models were corrected on the basis of EST data, consistent positioning of introns between orthologues and conservation of hallmark motifs. Phylogenetic analysis resolved the Phytophthora APs into 5 clades. Of the 12 sub-families, several contained an unconventional architecture, as they either lacked a signal peptide or a propart region. Remarkably, almost all APs are predicted to be membrane-bound. Conclusions - One of the twelve Phytophthora APs is an unprecedented fusion protein with a putative G-protein coupled receptor as the C-terminal partner. The others appear to be related to well-documented enzymes from other species, including a vacuolar enzyme that is encoded in every fungal genome sequenced to date. Unexpectedly, however, the oomycetes were found to have both active and probably-inactive forms of an AP similar to vertebrate BACE, the enzyme responsible for initiating the processing cascade that generates the Aß peptide central to Alzheimer's Disease. The oomycetes also encode enzymes similar to plasmepsin V, a membrane-bound AP that cleaves effector proteins of the malaria parasite Plasmodium falciparum during their translocation into the host red blood cell. Since the translocation of Phytophthora effector proteins is currently a topic of intense research activity, the identification in Phytophthora of potential functional homologues of plasmepsin V would appear worthy of investigation. Indeed, elucidation of the physiological roles of the APs identified here offers areas for future study. The significant revision of gene models and detailed annotation presented here should significantly facilitate experimental design

HMMER cut-off threshold tool (HMMERCTTER): Supervised classification of superfamily protein sequences with a reliable cut-off threshold

Background: Protein superfamilies can be divided into subfamilies of proteins with different functional characteristics. Their sequences can be classified hierarchically, which is part of sequence function assignation. Typically, there are no clear subfamily hallmarks that would allow pattern-based function assignation by which this task is mostly achieved based on the similarity principle. This is hampered by the lack of a score cut-off that is both sensitive and specific. Results: HMMER Cut-off Threshold Tool (HMMERCTTER) adds a reliable cut-off threshold to the popular HMMER. Using a high quality superfamily phylogeny, it clusters a set of training sequences such that the cluster-specific HMMER profiles show cluster or subfamily member detection with 100% precision and recall (P&R), thereby generating a specific threshold as inclusion cut-off. Profiles and thresholds are then used as classifiers to screen a target dataset. Iterative inclusion of novel sequences to groups and the corresponding HMMER profiles results in high sensitivity while specificity is maintained by imposing 100% P&R self detection. In three presented case studies of protein superfamilies, classification of large datasets with 100% precision was achieved with over 95% recall. Limits and caveats are presented and explained. Conclusions: HMMERCTTER is a promising protein superfamily sequence classifier provided high quality training datasets are used. It provides a decision support system that aids in the difficult task of sequence function assignation in the twilight zone of sequence similarity. All relevant data and source codes are available from the Github repository at the following.Fil: Pagnuco, Inti Anabela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Científicas y Tecnológicas en Electrónica. Universidad Nacional de Mar del Plata. Facultad de Ingeniería. Instituto de Investigaciones Científicas y Tecnológicas en Electrónica; ArgentinaFil: Revuelta, María Victoria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Biológicas. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Biológicas; ArgentinaFil: Bondino, Hernán Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Biológicas. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Biológicas; ArgentinaFil: Brun, Marcel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Científicas y Tecnológicas en Electrónica. Universidad Nacional de Mar del Plata. Facultad de Ingeniería. Instituto de Investigaciones Científicas y Tecnológicas en Electrónica; ArgentinaFil: Ten Have, Arjen. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Biológicas. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Biológicas; Argentin

Should family doctors counsel patients on genetic testing and screening?

Family Doctors are in an ideal situation to counsel patients on most medical technologies and new developments. In this sense they are in the best position to guide and counsel patients on genetic testing and screening. Indeed most often it is the patient who seeks counsel from the Family Doctor (General Practitioner). The special nature of genetic tests and the potential to exploit people's money with dubious testing puts the doctor in a special situation. Whilst it is argued that the Family Doctor maintains a strategic position to impart information to the patient, it is also argued that the new nature of genetic tests and the way the family may be affected, (including the multitude of ethical dilemmas these tests may pose), favours the position that Family Doctors should be the health professionals who should impart generic genetic counselling. Specialised genetic counsellors may then continue to dedicate their time to special cases. Tests should not be made available over-the-counter. It is the onus of the Family Doctor to refer patients for further counseling should this be necessary. Colleges and Academies of Family Physicians are in the ideal place to outpace industry especially in second and third world countries.peer-reviewe

Quantitative profiling of the human substantia nigra proteome from laser-capture microdissected FFPE tissue

Laser-capture microdissection (LCM) allows the visualization and isolation of morphologically distinct subpopulations of cells from heterogeneous tissue specimens. In combination with formalin-fixed and paraffin-embedded (FFPE) tissue it provides a powerful tool for retrospective and clinically relevant studies of tissue proteins in a healthy and diseased context. We first optimized the protocol for efficient LCM analysis of FFPE tissue specimens. The use of SDS containing extraction buffer in combination with the single-pot solid-phase-enhanced sample preparation (SP3) digest method gave the best results regarding protein yield and protein/peptide identifications. Microdissected FFPE human substantia nigra tissue samples (~3,000 cells) were then analyzed, using tandem mass tag (TMT) labeling and LC-MS/MS, resulting in the quantification of &gt;5,600 protein groups. Nigral proteins were classified and analyzed by abundance, showing an enrichment of extracellular exosome and neuron-specific gene ontology (GO) terms among the higher abundance proteins. Comparison of microdissected samples with intact tissue sections, using a label-free shotgun approach, revealed an enrichment of neuronal cell type markers, such as tyrosine hydroxylase and alpha-synuclein, as well as proteins annotated with neuron-specific GO terms. Overall, this study provides a detailed protocol for laser-capture proteomics using FFPE tissue and demonstrates the efficiency of LCM analysis of distinct cell subpopulations for proteomic analysis using low sample amounts.</p

Adult participation in children’s word searches: on the use of prompting, hinting, and supplying a model

Although word searching in children is very common, very little is known about how adults support children in the turns following the child’s search behaviours, an important topic because of the social, educational and clinical implications. This study characterises, in detail, teachers’ use of prompting, hinting and supplying a model. From a classroom dataset of 53 instances, several distinctive patterns emerged. A prompted completion sequence is initiated by a ‘word retrieval elicitor’ (‘fishing’) and is interpreted as a request to complete the phrase. Non-verbal prompting is accomplished through a combination of gaze and gesture and, also, as a series of prompts. Hinting supplies a verbal clue, typically via a wh-question, or by specifying the nature of the repairable. In contrast, the strategies that supply a linguistic model include both embedded and exposed corrections and offers of candidates. A sequential relationship was found between prompting, hinting and supplying a model which has implications for how clinicians and teachers can foster self-repair