Sarah L. Morgan

Temporal and spatial changes in the microbial bioaerosol communities in green-waste composting.

In this study, the microbial community within compost, emitted into the airstream, downwind and upwind from a composting facility was characterized and compared through phospholipid fatty acid analysis and 16S rRNA gene analysis using denaturing gradient gel electrophoresis and bar-coded pyrosequencing techniques. All methods used suggested that green-waste composting had a significant impact upon bioaerosol community composition. Daily variations of the on-site airborne community showed how specific site parameters such as compost process activity and meteorological conditions affect bioaerosol communities, although more data are required to qualify and quantify the causes for these variations. A notable feature was the dominance of Pseudomonas in downwind samples, suggesting that this genus can disperse downwind in elevated abundances. Thirty-nine phylotypes were homologous to plant or human phylotypes containing pathogens and were found within compost, on-site and downwind microbial communities. Although the significance of this finding in terms of potential health impact was beyond the scope of this study, it clearly illustrated the potential of molecular techniques to improve our understanding of the impact that green-waste composting emissions may have on the human health.

Detection and imaging the expression of the trans-membrane protein CD44 in RT112 cells by use of enzyme-labeled antibodies and SECM.

The deposition of human RT112 cells in a patterned fashion onto glass substrates and subsequent imaging of the expression of the trans-membrane protein CD44 have been studied using scanning electrochemical microscopy (SECM). Patterns of RT112 cells derived from a transitional cell carcinoma of the bladder could be deposited on amino-modified glass substrates by cytospinning. These were then treated with horseradish peroxidase (HRP) labeled secondary antibodies to the trans-membrane protein CD44. Expression of CD44 protein by the cells directly leads to immobilisation of the labeled antibodies. The presence of the enzyme substrate (hydrogen peroxide) along with a hydroquinone mediator then allowed an enzymatic reaction to proceed, generating benzoquinone. Reduction of benzoquinone gave rise to positive feedback between the substrate and the SECM microelectrode tip. Control samples such as blank slides or slides not treated with HRP-labeled antibody showed negative feedback effects. Patterns of RT112 cells could be assembled and their expression of the target protein imaged whereas control samples showed minimal activity.

Polyphenol control of cell spreading on glycoprotein substrata

Cell–surface contacts are vital for many eukaryotic cells. The surface provides anchorage (facilitating spreading and proliferation), is involved in sensation, i.e., via mechano-, osmo- and chemoreceptors, and in addition nutrients may also be supplied via vessels adjacent to the basal lamina. Hence, the ability to manipulate the surface characteristics provides a mechanism for directly influencing cell behaviour. Applications such as medical implants and tissue engineering require biocompatible, stable surfaces for controlling cell behaviour. Mucin-coated surfaces inhibit cell spreading compared with poly(L-lysine) in vitro; here, we show that a composite layer assembled from mucin-EGCg aggregates counters the inhibition. Although the anti-spreading effects of the glycoprotein substratum on cell behaviour are similar to those observed for pure polysaccharide surfaces, the reversal of cell spreading inhibition by the admixture of polyphenol/glycoprotein substrata is remarkable and unexpected. Possible applications for a composite glycoprotein–polyphenol layer include medical devices, in particular for those operating at mucosal interfaces such as the oral, tracheal or gastrointestinal tract cavities, wound healing, cancer control and the controlled growth of therapeutic cell cultures.

Investigation and Development of Quantum Dot-Encoded Microsphere Bioconjugates for DNA Detection by Flow Cytometry

The development of screening assays continues to be an active area of research in molecular diagnostics. Fluorescent microspheres conjugated to biomarkers (nucleic acids, proteins, lipids, carbohydrates) and analyzed on flow cytometer instruments offered a new approach for multiplexed detection platform in a suspension format. Quantum dots encoded into synthetic microspheres have the potentials to improve current screening bioassays and specifically suspension array technology. In this paper, commercialized quantum dot-encoded microsphere were evaluated and optimized as fluorescent probes to address some of the limitations of suspension array technologies. A comprehensive study was undertaken to adapt the bioconjugation procedure to the quantum dot-encoded microsphere structural and optical properties. Both the leaching-out of quantum dots and microspheres degradation under bioconjugation experimental conditions were minimized. A rapid, efficient and reproducible conjugation method was developed for the detection of single-stranded DNA with the commercialized quantum dot-encoded microsphere. Approximately ten thousand microspheres were conjugated to short amino-modified DNA sequences in one hour with high efficiency. The bioconjugated microspheres acting as fluorescent probes successfully detected a DNA target in suspension with high specificity. Quantum dot-encoded microsphere commercial products are limited which strongly prevents reproducible and comparative studies between laboratories. The method developed here contributes to the understanding of quantum dot-encoded microsphere reactivity, and to the optimization of adapted experimental procedure. This step is essential in the development of this new fluorescent probe technology for multiplex genotyping assay and molecular diagnostic applications.

Application of multiple response optimization design to quantum dot-encoded microsphere bioconjugates hybridization assay.

The optimization of DNA hybridization for genotyping assays is a complex experimental problem that depends on multiple factors such as assay formats, fluorescent probes, target sequence, experimental conditions, and data analysis. Quantum dot-doped particle bioconjugates have been previously described as fluorescent probes to identify single nucleotide polymorphisms even though this advanced fluorescent material has shown structural instability in aqueous environments. To achieve the optimization of DNA hybridization to quantum dot-doped particle bioconjugates in suspension while maximizing the stability of the probe materials, a nonsequential optimization approach was evaluated. The design of experiment with response surface methodology and multiple optimization response was used to maximize the recovery of fluorescent probe at the end of the assay simultaneously with the optimization of target-probe binding. Hybridization efficiency was evaluated by the attachment of fluorescent oligonucleotides to the fluorescent probe through continuous flow cytometry detection. Optimal conditions were predicted with the model and tested for the identification of single nucleotide polymorphisms. The design of experiment has been shown to significantly improve biochemistry and biotechnology optimization processes. Here we demonstrate the potential of this statistical approach to facilitate the optimization of experimental protocol that involves material science and molecular biology.

Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee).

The Curriculum Task Force (CTF) of ISCB’s Education Committee seeks to define curricular guidelines for those who educate or train bioinformatics professionals at all career stages. A recent report of the CTF [1] presented a draft set of bioinformatics core competencies, derived from the results of surveys of (1) core facility directors, (2) career opportunities, and (3) existing curricula. Since the publication of its 2014 report, the CTF has focused on the application of the guidelines in varied contexts to identify areas where refinement is needed. As a first step, the task force held an open meeting at the ISMB conference in July 2014. The ideas discussed at the meeting spawned four working groups (WGs), which focus on (i) defining core competencies for specific types and levels of bioinformatics training, (ii) mapping the curriculum guidelines and competencies to existing materials in order to identify the need for development of new materials, and (iii) identifying where revision of the guidelines may be valuable. The CTF is engaging the ISCB community through open WG meetings at ISCB’s official conferences. Thus far, the WGs have convened at the ISCB Great Lakes Bioinformatics Conference (Purdue University, May 2015) and at the ISMB/ECCB Conference (Dublin, Ireland, July 2015). Additionally, the CTF held a workshop at the Annual General Meeting of the Global Organization of Bioinformatics Learning, Education and Training (Cape Town, South Africa, November 2015). Specifically, the draft competencies have been employed in a wide range of activities and contexts (see Table 1 and [2–11]), including the development of new curricula, the analysis of existing curricula, and the creation of new roles involving bioinformatics. These activities have resulted in the identification of several areas where refinement would be useful: Table 1 Summary of the activities of the ISCB Curriculum Task Force. Identify different levels or phases of competency. It would be helpful to define different phases of competency development, or different levels of competency appropriate for distinct roles. Define competency profiles for disciplines that don’t fit into our current silos. Bioengineering provides an illustrative example of a discipline that requires core competency in bioinformatics but does not fit into our current categories. There are almost certainly others. It would be helpful if we could provide some guidance on how to produce ‘hybrid’ competency profiles, perhaps borrowing some competencies from the TF’s core set and others from different disciplines. The LifeTrain initiative (www.lifetrain.eu) [2, 3] is collecting competency profiles for a range of disciplines of relevance to the biomedical sciences and may provide a useful resource kit for this. Broaden the scope of the competency profiles in response to cutting-edge and emerging research. Current areas requiring improvement include incorporating competencies that capture a fundamental understanding of the biological principles central to analyzing biomolecular data, and broadening the user WG to include applications beyond medicine. Provide guidance on the evidence required to assess whether someone has acquired each competency. For undergraduate, Master’s and PhD programs, learning outcomes for each competency, perhaps with examples of appropriate means of assessment, would be valuable. For established professionals who need to assimilate competencies into their working lives, a different approach may be required (such as keeping a portfolio to capture evidence of competency); the CTF should seek guidance from relevant professional bodies, especially in regulated professions such as healthcare. Provide indicative course content or examples of programs that map to the competency requirements. We do not wish to prescribe what course providers should teach or how they should teach it; however, if a course provider is designing a course to meet a specific competency requirement, it may be helpful to find examples of other programs that do this successfully. One way of achieving this is by mapping existing training content to the TF’s competencies. Another way might be to provide an indication, perhaps based on several courses, of the course content that would meet the competency requirements. This would give course providers the freedom to build their own course syllabi without having to reinvent the wheel. Initiatives to collect examples of Creative Commons (or otherwise reusable) course materials will provide an extremely valuable bank of training materials that could be mapped to the core competencies.

The development and application of bioinformatics core competencies to improve bioinformatics training and education

Bioinformatics is recognized as part of the essential knowledge base of numerous career paths in biomedical research and healthcare. However, there is little agreement in the field over what that knowledge entails or how best to provide it. These disagreements are compounded by the wide range of populations in need of bioinformatics training, with divergent prior backgrounds and intended application areas. The Curriculum Task Force of the International Society of Computational Biology (ISCB) Education Committee has sought to provide a framework for training needs and curricula in terms of a set of bioinformatics core competencies that cut across many user personas and training programs. The initial competencies developed based on surveys of employers and training programs have since been refined through a multiyear process of community engagement. This report describes the current status of the competencies and presents a series of use cases illustrating how they are being applied in diverse training contexts. These use cases are intended to demonstrate how others can make use of the competencies and engage in the process of their continuing refinement and application. The report concludes with a consideration of remaining challenges and future plans.

The application of project-based learning in bioinformatics training

As the rate of biological data generation continues to outstrip the rate at which life scientists are able to analyse and add meaning to these data, there is an increasing expectation for an ever more diverse group of life scientists to gain such analytical skills. Providing high-quality training in bioinformatics is more important than ever and, to this end, identifying learning practices and methods that contribute to training success is critical. We present here: the application of project-based learning in the context of a short (5-day) bioinformatics training course, an attempt to assess the impact upon participants of applying such an approach, and guidance to others who might wish to employ such a method in their courses. Effective bioinformatics training (as in other fields) is recognised as being engaging, promoting active thinking, and providing opportunities for interactivity and discussion. With a plethora of potential learning methods at trainers’ disposal, how do we know which methods are best? The consensus of opinion in the bioinformatics training literature is that diversity is key; by combining a range of approaches, we best meet the needs of a varied participant group [1–3]. Nonetheless, it is likely that some methods will be more effective than others, and thus, here, we explore the application of one such method, project-based learning, in the context of a 5-day training course: a bioinformatics summer school (http://www.ebi.ac.uk/training/ events/2014/joint-embl-ebiwellcome-trust-summer-school-bioinformatics-0) that took place in June 2014. The summer school is an established part of a broader training programme offered by EMBL-European Bioinformatics Institute (EMBL-EBI), which includes both faceto-face and elearning opportunities (www.ebi.ac.uk/training). Project-based learning has long been used in higher education as a method to educate students using realistic problem-based tasks [4,5]. These tasks typically require initiative and independence from the students; they take a considerable length of time to complete, result in the production of an end product (e.g., a report or presentation), and make use of educators in an advisory role [6–8]. Projects can often involve students working together in groups—an approach already adopted as good practice in bioinformatics training [9]—to foster collaboration and develop interpersonal competencies. While there are reports of group-based projects being used in university-level bioinformatics education [10–12] and there are a small number of training courses worldwide that take such an approach (e.g., Cold Spring Harbor’s “Programming for Biology” [13], SFU’s “Problem-based learning in bioinformatics” course for PhD & MSc students [9]), project-based learning is not yet embedded in mainstream bioinformatics

The ELIXIR-EXCELERATE Train-the-Trainer pilot programme: empower researchers to deliver high-quality training

One of the main goals of the ELIXIR-EXCELERATE project from the European Union’s Horizon 2020 programme is to support a pan-European training programme to increase bioinformatics capacity and competency across ELIXIR Nodes. To this end, a Train-the-Trainer (TtT) programme has been developed by the TtT subtask of EXCELERATE’s Training Platform, to try to expose bioinformatics instructors to aspects of pedagogy and evidence-based learning principles, to help them better design, develop and deliver high-quality training in future. As a first step towards such a programme, an ELIXIR-EXCELERATE TtT (EE-TtT) pilot was developed, drawing on existing ‘instructor training’ models, using input both from experienced instructors and from experts in bioinformatics, the cognitive sciences and educational psychology. This manuscript describes the process of defining the pilot programme, illustrates its goals, structure and contents, and discusses its outcomes. From Jan 2016 to Jan 2017, we carried out seven pilot EE-TtT courses (training more than sixty new instructors), collaboratively drafted the training materials, and started establishing a network of trainers and instructors within the ELIXIR community. The EE-TtT pilot represents an essential step towards the development of a sustainable and scalable ELIXIR TtT programme. Indeed, the lessons learned from the pilot, the experience gained, the materials developed, and the analysis of the feedback collected throughout the seven pilot courses have both positioned us to consolidate the programme in the coming years, and contributed to the development of an enthusiastic and expanding ELIXIR community of instructors and trainers.