Agrobacterium-Mediated Gene Transfer to Cereal Crop Plants: Current Protocols for Barley, Wheat, Triticale, and Maize

The development of powerful “omics” technologies has enabled researchers to identify many genes of interest for which comprehensive functional analyses are highly desirable. However, the production of lines which ectopically express recombinant genes, or those in which endogenous genes are knocked down via stable transformation, remains a major bottleneck for the association between genetics and gene function in monocotyledonous crops. Methods of effective DNA transfer into regenerable cells of immature embryos from cereals by means of Agrobacterium tumefaciens have been modified in a stepwise manner. The effect of particular improvement measures has often not been significantly evident, whereas their combined implementation has resulted in meaningful advances. Here, we provide updated protocols for the Agrobacterium-mediated generation of stably transgenic barley, wheat, triticale and maize. Based upon these methods, several hundred independent transgenic lines have been delivered, with efficiencies of inoculated embryos leading to stably transgenic plants reaching 86% in barley, 10% in wheat, 4% in triticale, and 24% in maize

Evaluation of a clinical decision support tool for osteoporosis disease management: protocol for an interrupted time series design

<p>Abstract</p> <p>Background</p> <p>Osteoporosis affects over 200 million people worldwide at a high cost to healthcare systems. Although guidelines on assessing and managing osteoporosis are available, many patients are not receiving appropriate diagnostic testing or treatment. Findings from a systematic review of osteoporosis interventions, a series of mixed-methods studies, and advice from experts in osteoporosis and human-factors engineering were used collectively to develop a multicomponent tool (targeted to family physicians and patients at risk for osteoporosis) that may support clinical decision making in osteoporosis disease management at the point of care.</p> <p>Methods</p> <p>A three-phased approach will be used to evaluate the osteoporosis tool. In phase 1, the tool will be implemented in three family practices. It will involve ensuring optimal functioning of the tool while minimizing disruption to usual practice. In phase 2, the tool will be pilot tested in a quasi-experimental interrupted time series (ITS) design to determine if it can improve osteoporosis disease management at the point of care. Phase 3 will involve conducting a qualitative postintervention follow-up study to better understand participants' experiences and perceived utility of the tool and readiness to adopt the tool at the point of care.</p> <p>Discussion</p> <p>The osteoporosis tool has the potential to make several contributions to the development and evaluation of complex, chronic disease interventions, such as the inclusion of an implementation strategy prior to conducting an evaluation study. Anticipated benefits of the tool may be to increase awareness for patients about osteoporosis and its associated risks and provide an opportunity to discuss a management plan with their physician, which may all facilitate patient self-management.</p

Usability evaluation of a clinical decision support tool for osteoporosis disease management

<p>Abstract</p> <p>Background</p> <p>Osteoporosis affects over 200 million people worldwide at a high cost to healthcare systems. Although guidelines are available, patients are not receiving appropriate diagnostic testing or treatment. Findings from a systematic review of osteoporosis interventions and a series of focus groups were used to develop a functional multifaceted tool that can support clinical decision-making in osteoporosis disease management at the point of care. The objective of our study was to assess how well the prototype met functional goals and usability needs.</p> <p>Methods</p> <p>We conducted a usability study for each component of the tool--the Best Practice Recommendation Prompt (BestPROMPT), the Risk Assessment Questionnaire (RAQ), and the Customised Osteoporosis Education (COPE) sheet--using the framework described by Kushniruk and Patel. All studies consisted of one-on-one sessions with a moderator using a standardised worksheet. Sessions were audio- and video-taped and transcribed verbatim. Data analysis consisted of a combination of qualitative and quantitative analyses.</p> <p>Results</p> <p>In study 1, physicians liked that the BestPROMPT can provide customised recommendations based on risk factors identified from the RAQ. Barriers included lack of time to use the tool, the need to alter clinic workflow to enable point-of-care use, and that the tool may disrupt the real reason for the visit. In study 2, patients completed the RAQ in a mean of 6 minutes, 35 seconds. Of the 42 critical incidents, 60% were navigational and most occurred when the first nine participants were using the stylus pen; no critical incidents were observed with the last six participants that used the touch screen. Patients thought that the RAQ questions were easy to read and understand, but they found it difficult to initiate the questionnaire. Suggestions for improvement included improving aspects of the interface and navigation. The results of study 3 showed that most patients were able to understand and describe sections of the COPE sheet, and all considered discussing the information with their physicians. Suggestions for improvement included simplifying the language and improving the layout.</p> <p>Conclusions</p> <p>Findings from the three studies informed changes to the tool and confirmed the importance of usability testing on all end users to reduce errors, and as an important step in the development process of knowledge translation interventions.</p

An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes

Two collections of oligonucleotides have been designed for preparing pangenomic human and mouse microarrays. A total of 148 993 and 121 703 oligonucleotides were designed against human and mouse transcripts. Quality scores were created in order to select 25 342 human and 24 109 mouse oligonucleotides. They correspond to: (i) a BLAST-specificity score; (ii) the number of expressed sequence tags matching each probe; (iii) the distance to the 3′ end of the target mRNA. Scores were also used to compare in silico the two microarrays with commercial microarrays. The sets described here, called RNG/MRC collections, appear at least as specific and sensitive as those from the commercial platforms. The RNG/MRC collections have now been used by an Anglo-French consortium to distribute more than 3500 microarrays to the academic community. Ad hoc identification of tissue-specific transcripts and a ∼80% correlation with hybridizations performed on Affymetrix GeneChip™ suggest that the RNG/MRC microarrays perform well. This work provides a comprehensive open resource for investigators working on human and mouse transcriptomes, as well as a generic method to generate new microarray collections in other organisms. All information related to these probes, as well as additional information about commercial microarrays have been stored in a freely-accessible database called MEDIANTE

Development of a prototype clinical decision support tool for osteoporosis disease management: a qualitative study of focus groups

<p>Abstract</p> <p>Background</p> <p>Osteoporosis affects over 200 million people worldwide, and represents a significant cost burden. Although guidelines are available for best practice in osteoporosis, evidence indicates that patients are not receiving appropriate diagnostic testing or treatment according to guidelines. The use of clinical decision support systems (CDSSs) may be one solution because they can facilitate knowledge translation by providing high-quality evidence at the point of care. Findings from a systematic review of osteoporosis interventions and consultation with clinical and human factors engineering experts were used to develop a conceptual model of an osteoporosis tool. We conducted a qualitative study of focus groups to better understand physicians' perceptions of CDSSs and to transform the conceptual osteoporosis tool into a functional prototype that can support clinical decision making in osteoporosis disease management at the point of care.</p> <p>Methods</p> <p>The conceptual design of the osteoporosis tool was tested in 4 progressive focus groups with family physicians and general internists. An iterative strategy was used to qualitatively explore the experiences of physicians with CDSSs; and to find out what features, functions, and evidence should be included in a working prototype. Focus groups were conducted using a semi-structured interview guide using an iterative process where results of the first focus group informed changes to the questions for subsequent focus groups and to the conceptual tool design. Transcripts were transcribed verbatim and analyzed using grounded theory methodology.</p> <p>Results</p> <p>Of the 3 broad categories of themes that were identified, major barriers related to the accuracy and feasibility of extracting bone mineral density test results and medications from the risk assessment questionnaire; using an electronic input device such as a Tablet PC in the waiting room; and the importance of including well-balanced information in the patient education component of the osteoporosis tool. Suggestions for modifying the tool included the addition of a percentile graph showing patients' 10-year risk for osteoporosis or fractures, and ensuring that the tool takes no more than 5 minutes to complete.</p> <p>Conclusions</p> <p>Focus group data revealed the facilitators and barriers to using the osteoporosis tool at the point of care so that it can be optimized to aid physicians in their clinical decision making.</p

Mapping and analysing cropland use intensity from a NPP perspective

Meeting expected surges in global biomass demand while protecting pristine ecosystems likely requires intensification of current croplands. Yet many uncertainties relate to the potentials for cropland intensification, mainly because conceptualizing and measuring land use intensity is intricate, particularly at the global scale. We present a spatially explicit analysis of global cropland use intensity, following an ecological energy flow perspective. We analyze (a) changes of net primary production (NPP) from the potential system (i.e. assuming undisturbed vegetation) to croplands around 2000 and relate these changes to (b) inputs of (N) fertilizer and irrigation and (c) to biomass outputs, allowing for a three dimensional focus on intensification. Globally the actual NPP of croplands, expressed as per cent of their potential NPP (NPP _act% ), amounts to 77%. A mix of socio-economic and natural factors explains the high spatial variation which ranges from 22.6% to 416.0% within the inner 95 percentiles. NPP _act% is well below NPP _pot in many developing, (Sub-) Tropical regions, while it massively surpasses NPP _pot on irrigated drylands and in many industrialized temperate regions. The interrelations of NPP losses (i.e. the difference between NPP _act and NPP _pot ), agricultural inputs and biomass harvest differ substantially between biogeographical regions. Maintaining NPP _pot was particularly N-intensive in forest biomes, as compared to cropland in natural grassland biomes. However, much higher levels of biomass harvest occur in forest biomes. We show that fertilization loads correlate with NPP _act% linearly, but the relation gets increasingly blurred beyond a level of 125 kgN ha ^−1 . Thus, large potentials exist to improve N-efficiency at the global scale, as only 10% of global croplands are above this level. Reallocating surplus N could substantially reduce NPP losses by up to 80% below current levels and at the same time increase biomass harvest by almost 30%. However, we also show that eradicating NPP losses globally might not be feasible due to the high input costs and associated sustainability implications. Our analysis emphasizes the necessity to avoid mono-dimensional perspectives with respect to research on sustainable intensification pathways and the potential of integrated socio-ecological approaches for consistently contrasting environmental trade-offs and societal benefits of land use intensification