Assessing precollege science education outreach initiatives: a funder's perspective

We describe an assessment of the collective impact of 35 grants that the Howard Hughes Medical Institute (HHMI) made to biomedical research institutions in 1999 to support precollege science education outreach programs. Data collected from funded institutions were compared with data from a control group of institutions that had advanced to the last stage of review but had not been funded. The survey instrument and the results reveal outcomes and impacts that HHMI considers relevant for these programs. The following attributes are considered: ability to secure additional, non-HHMI funding; institution buy-in as measured by gains in dedicated space and staff; enhancement of the program director's career; number and adoption of educational products developed; number of related publications and awards; percentage of programs for which teachers received course credit; increase in science content knowledge; and increase in student motivation to study science.     

Model-driven user interfaces for bioinformatics data resources: regenerating the wheel as an alternative to reinventing it

Background  

The proliferation of data repositories in bioinformatics has resulted in the development of numerous interfaces that allow scientists to browse, search and analyse the data that they contain. Interfaces typically support repository access by means of web pages, but other means are also used, such as desktop applications and command line tools. Interfaces often duplicate functionality amongst each other, and this implies that associated development activities are repeated in different laboratories. Interfaces developed by public laboratories are often created with limited developer resources. In such environments, reducing the time spent on creating user interfaces allows for a better deployment of resources for specialised tasks, such as data integration or analysis. Laboratories maintaining data resources are challenged to reconcile requirements for software that is reliable, functional and flexible with limitations on software development resources.     

Global health: a successful context for precollege training and advocacy

Despite a flourishing biomedical and global health industry too few of Washington state's precollege students are aware of this growing sector and emerging ideas on bacteria, fungi, parasites and viruses. Against the backdrop of numerous reports regarding declining precollege student interest in science, a precollege program was envisioned at Seattle Biomedical Research Institute (as of 2010, Seattle BioMed) to increase youth engagement in biomedical research and global health, increase community interest in infectious diseases and mobilize a future biomedical workforce. Since 2005, 169 rising high school juniors have participated in the BioQuest Academy precollege immersion program at Seattle BioMed. Assembling in groups of 12, students conduct laboratory experiments (e.g., anopheline mosquito dissection, gene expression informed tuberculosis drug design and optimizing HIV immunization strategies) related to global health alongside practicing scientific mentors, all within the footprint the institute. Laudable short-term impacts of the program include positive influences on student interest in global health (as seen in the students' subsequent school projects and their participation in Seattle BioMed community events), biomedical careers and graduate school (e.g., 16.9% of teens departing 2008-2009 Academy report revised goals of attaining a doctorate rather than a baccalaureate diploma). Long-term, 97% of alumni (2005-2008) are attending postsecondary schools throughout North America; eight graduates have already published scientific articles in peer-reviewed journals and/or presented their scientific data at national and international meetings, and 26 have been retained by Seattle BioMed researchers as compensated technicians and interns. Providing precollege students with structured access to practicing scientists and authentic research environments within the context of advancing global health has been a robust means of both building a future pool of talented leaders and engaged citizenry and increasing the visibility of health disparities within the community.     

Strategies for the reduction of live animal use in microsurgical training and education

Education and training in microsurgical techniques have historically relied on the use of live animal models. Due to an increase in the numbers of microsurgical operations in recent times, the number of trainees in this highly-specialised surgical field has continued to grow. However, strict legislation, greater public awareness, and an increasing sensitivity toward the ethical aspects of scientific research and medical education, emphatically demand a significant reduction in the numbers of animals used in surgical and academic education. Hence, a growing number of articles are reporting on the use of alternatives to live animals in microsurgical education and training. In this review, we report on the current trends in the development and use of microsurgical training models, and on their potential to reduce the number of live animals used for this purpose. We also share our experiences in this field, resulting from our performance of numerous microsurgical courses each year, over more than ten years. The porcine heart, in microvascular surgery training, and the fresh chicken leg, in microneurosurgical and microvascular surgery training, are excellent models for the teaching of basic techniques to the microsurgical novice. Depending on the selected level of expertise of the trainee, these alternative models are capable of reducing the numbers of live animals used by 80-100%. For an even more enhanced, "closer-to-real-life" scenario, these non-animated vessels can be perfused by a pulsatile pump. Thus, it is currently possible to provide excellent and in-depth training in microsurgical techniques, even when the number of live animals used is reduced to a minimum. With these new and innovative techniques, trainees are able to learn and prepare themselves for the clinical situation, with the sacrifice of considerably fewer laboratory animals than would have occurred previously.     

Innovations in human genetics education. Genetic applications for health professionals: an outreach continuing-education model program

A system for extending continuing education in genetics to nurses and other practicing health professionals was developed in an eight-state area. Coordinators from state agencies received special training at the University of Colorado to administer the course in local communities. A combination of classroom instruction, independent study, computer-assisted instruction, and case-study methods for course delivery was included. More than 300 health professionals have completed the course, and 14 coordinators from seven states have been prepared to administer future courses. The model has demonstrated high potential for replication in other regions.     

Sorghum root length density and the potential for avoiding striga parasitism

Striga hermonthica is a serious root parasite of sorghum in the semiarid tropics. Successful parasitism is dependent on interactions of Striga seeds and host roots. Several sorghum cultivars have been found which resist parasitism. The basis of resistance is not well known. One possible method for reducing the chances of parasitism is by restricted host root development. This research was conducted to evaluate this hypothesis in sorghum known to possess resistance to parasitism by Striga.Root length density of 21-day-old pot-grown resistant cultivars, Framida, N-13, IS-9830, Tetron and P-967083, were compared to that of the susceptible check, Dabar, using the line intercept method of measuring root length. There was no significant difference between resistant cultivars and the susceptible cultivar Dabar. The RLD of resistant P-967083 however was significantly less than Framida, another resistant cultivar.The RLD of Dabar was compared to that of Framida and P-967083 in USA and Niger field trials. Root length density was determined on soil cores taken at flowering with a Giddings Soil Sampler. Each core was divided into 10-cm fractions for estimating RLD by the line intercept method. In the USA Dabar had significantly greater RLD than the two resistant cultivars in the upper 10-cm portion of the soil profile, but only significantly greater than P-967083 in the 10–20-cm portion. Significant differences in RLD between susceptible and resistant cultivars were not found at depths between 20–60 cm. In field trials in Niger, RLD of Dabar was significantly greater than either resistant cultivar in the (0 to 30 cm) portion of the soil core. These results suggest that part of the Striga resistance of P-967083 and perhaps Framida may be a result of avoiding interactions between parasitic seeds and host roots.     

Mammalian organogenesis in deep time: tools for teaching and outreach

Mammals constitute a rich subject of study on evolution and development and provide model organisms for experimental investigations. They can serve to illustrate how ontogeny and phylogeny can be studied together and how the reconstruction of ancestors of our own evolutionary lineage can be approached. Likewise, mammals can be used to promote 'tree thinking' and can provide an organismal appreciation of evolutionary changes. This subject is suitable for the classroom and to the public at large given the interest and familiarity of people with mammals and their closest relatives. We present a simple exercise in which embryonic development is presented as a transformative process that can be observed, compared, and analyzed. In addition, we provide and discuss a freely available animation on organogenesis and life history evolution in mammals. An evolutionary tree can be the best tool to order and understand those transformations for different species. A simple exercise introduces the subject of changes in developmental timing or heterochrony and its importance in evolution. The developmental perspective is relevant in teaching and outreach efforts for the understanding of evolutionary theory today.     

Statistical strategies for avoiding false discoveries in metabolomics and related experiments

Many metabolomics, and other high-content or high-throughput, experiments are set up such that the primary aim is the discovery of biomarker metabolites that can discriminate, with a certain level of certainty, between nominally matched ‘case’ and ‘control’ samples. However, it is unfortunately very easy to find markers that are apparently persuasive but that are in fact entirely spurious, and there are well-known examples in the proteomics literature. The main types of danger are not entirely independent of each other, but include bias, inadequate sample size (especially relative to the number of metabolite variables and to the required statistical power to prove that a biomarker is discriminant), excessive false discovery rate due to multiple hypothesis testing, inappropriate choice of particular numerical methods, and overfitting (generally caused by the failure to perform adequate validation and cross-validation). Many studies fail to take these into account, and thereby fail to discover anything of true significance (despite their claims). We summarise these problems, and provide pointers to a substantial existing literature that should assist in the improved design and evaluation of metabolomics experiments, thereby allowing robust scientific conclusions to be drawn from the available data. We provide a list of some of the simpler checks that might improve one’s confidence that a candidate biomarker is not simply a statistical artefact, and suggest a series of preferred tests and visualisation tools that can assist readers and authors in assessing papers. These tools can be applied to individual metabolites by using multiple univariate tests performed in parallel across all metabolite peaks. They may also be applied to the validation of multivariate models. We stress in particular that classical p-values such as “p < 0.05”, that are often used in biomedicine, are far too optimistic when multiple tests are done simultaneously (as in metabolomics). Ultimately it is desirable that all data and metadata are available electronically, as this allows the entire community to assess conclusions drawn from them. These analyses apply to all high-dimensional ‘omics’ datasets.     

Revealing and avoiding bias in semantic similarity scores for protein pairs

Background  

Semantic similarity scores for protein pairs are widely applied in functional genomic researches for finding functional clusters of proteins, predicting protein functions and protein-protein interactions, and for identifying putative disease genes. However, because some proteins, such as those related to diseases, tend to be studied more intensively, annotations are likely to be biased, which may affect applications based on semantic similarity measures. Thus, it is necessary to evaluate the effects of the bias on semantic similarity scores between proteins and then find a method to avoid them.     

An integrated biochemistry and genetics outreach program designed for elementary school students

Exposure to genetic and biochemical experiments typically occurs late in one's academic career. By the time students have the opportunity to select specialized courses in these areas, many have already developed negative attitudes toward the sciences. Given little or no direct experience with the fields of genetics and biochemistry, it is likely that many young people rule these out as potential areas of study or career path. To address this problem, we developed a 7-week (~1 hr/week) hands-on course to introduce fifth grade students to basic concepts in genetics and biochemistry. These young students performed a series of investigations (ranging from examining phenotypic variation, in vitro enzymatic assays, and yeast genetic experiments) to explore scientific reasoning through direct experimentation. Despite the challenging material, the vast majority of students successfully completed each experiment, and most students reported that the experience increased their interest in science. Additionally, the experiments within the 7-week program are easily performed by instructors with basic skills in biological sciences. As such, this program can be implemented by others motivated to achieve a broader impact by increasing the accessibility of their university and communicating to a young audience a positive impression of the sciences and the potential for science as a career.     

Plants as bioreactors for protein production: avoiding the problem of transgene silencing

Plants are particularly attractive as large-scale production systems for proteins intended for therapeutical or industrial applications: they can be grown easily and inexpensively in large quantities that can be harvested and processed with the available agronomic infrastructures. The effective use of plants as bioreactors depends on the possibility of obtaining high protein accumulation levels that are stable during the life cycle of the transgenic plant and in subsequent generations. Silencing of the introduced transgenes has frequently been observed in plants, constituting a major commercial risk and hampering the general economic exploitation of plants as protein factories. Until now, the most efficient strategy to avoid transgene silencing involves careful design of the transgene construct and thorough analysis of transformants at the molecular level. Here, we focus on different aspects of the generation of transgenic plants intended for protein production and on their influence on the stability of heterologous gene expression.These authors contributed equally to this work