Courses Based on iGEM/BIOMOD Competitions Are the Ideal Format for Research-Based Learning of Xenobiology.

Synthetic biology and especially xenobiology, as emerging new fields of science, have reached an intellectual and experimental maturity that makes them suitable for integration into the university curricula of chemical and biological disciplines. Novel scientific fields that include laboratory work are perfect playgrounds for developing highly motivating research-based teaching modules. We believe that research-based learning enriched by digital tools is the best approach for teaching new emerging essentials of academic education. This is especially true when the scientific field as such is still not canonized with text books and best-practice examples. Our experience shows that iGEM/BIOMOD competitions represent an excellent basis for designing research-based courses in xenobiology. Therefore, we present a report on "iGEM-Synthetic Biology" offered at the Technische Universität Berlin as an example.

Advancing undergraduate synthetic biology education: insights from a Canadian iGEM student perspective.

The last two decades have seen vigorous activity in synthetic biology research and the ever-increasing applications of these technologies. However, pedagogical research pertaining to teaching synthetic biology is scarce, especially when compared to other science and engineering disciplines. Within Canada, there are only three universities that offer synthetic biology programs, two of which are at the undergraduate level. Rather than taking place in formal academic settings, many Canadian undergraduate students are introduced to synthetic biology through participation in the annual International Genetically Engineered Machine (iGEM) competition. Although the iGEM competition has had a transformative impact on synthetic biology training in other nations, its impact in Canada has been relatively modest. Consequently, the iGEM competition remains a major setting for synthetic biology education in Canada. To promote further development of synthetic biology education, we surveyed undergraduate students from the Canadian iGEM design teams of 2019. We extracted insights from these data using qualitative analysis to provide recommendations for best teaching practices in synthetic biology undergraduate education, which we describe through our proposed Framework for Transdisciplinary Synthetic Biology Education (FTSBE).

Developing synthetic biology in Argentina: the Latin American TECNOx community as an alternative way for growth of the field.

Synthetic biology emerged in the USA and Europe twenty years ago and quickly developed innovative research and technology as a result of continued funding. Synthetic biology is also growing in many developing countries of Africa, Asia and Latin America, where it could have a large economic impact by helping its use of genetic biodiversity in order to boost existing industries. Starting in 2011, Argentine synthetic biology developed along an idiosyncratic path. In 2011-2012, the main focus was not exclusively research but also on community building through teaching and participation in iGEM, following the template of the early "MIT school" of synthetic biology. In 2013-2015, activities diversified and included society-centered projects, social science studies on synthetic biology and bioart. Standard research outputs such as articles and industrial applications helped consolidate several academic working groups. Since 2016, the lack of a critical mass of researchers and a funding crisis were partially compensated by establishing links with Latin American synthetic biologists and with other socially oriented open technology collectives. The TECNOx community is a central node in this growing research and technology network. The first four annual TECNOx meetings brought together synthetic biologists with other open science and engineering platforms and explored the relationship of Latin American technologies with entrepreneurship, open hardware, ethics and human rights. In sum, the socioeconomic context encouraged Latin American synthetic biology to develop in a meandering and diversifying manner. This revealed alternative ways for growth of the field that may be relevant to other developing countries.

Muscular performance analysis in "cross" modalities: comparison between "AMRAP," "EMOM" and "RFT" configurations.

Introduction: In recent years, a surge of interest in high-intensity training methods, associated with "cross" modalities has emerged as a promising approach for improving performance and overall health. Therefore, the main aim of this study was to compare the acute effects on heart rate, mean propulsive velocity and intra and inter-set velocity loss in "Cross" modalities. Materials and methods: Twelve athletes, 10 men's and 2 women's (age: 31.5 ± 6.74 years; height: 174.17 ± 6.05 cm; weight: 75.34 ± 7.16 kg) with at least 1 year of experience in "cross" training. The participants performed three different "cross" modalities, Rounds for Time (RFT), Every Minute on the Minute (EMOM) and As Many Rounds As Possible (AMRAP) across three separate days. In each modality participants carried out 10 repetitions of squat, pull-ups, and shoulder press with difference rates of work-rest. Mean propulsive velocity (MPV) and heart rate (HR) were recorded and analysed for each athlete. Repeated measures one-way ANOVA and repeated measures two-way ANOVA were performed to analyse the differences between modalities and subjects. Besides, a Bonferroni post hoc analysis was carried out to assess the differences between modalities in each subject. Results: Significant differences in MPV were observed among the modalities. The comparisons between RFT and AMRAP, as well as EMOM and AMRAP, revealed lower MPV in the AMRAP modality (p < 0.01). RFT exhibited the greatest intra-set velocity loss, while EMOM showed the least, with significant distinctions (p < 0.01) between them. Furthermore, significant differences in the HR results were noted among all modalities (p < 0.05). Conclusion: Findings consistently identify the AMRAP modality as having the lowest MPV values due to its prolonged duration, promoting self-regulated tempo for optimal performance and technique, while the RFT modality exhibits higher fatigue and intra-set MPV losses. These insights into propulsive velocity, intensity, fatigue, and pacing across various "Cross" modalities provide valuable guidance for athletes and trainers seeking to enhance their exercise programs.

[Developing a curriculum cluster in "Synthetic Biology" to cultivate inter-disciplinary and innovative talents for biomanufacturing].

Synthetic Biology, as an emerging discipline, has gained widespread attention and is developing rapidly, profoundly impacting the fields of life sciences and biotechnology. Concurrently, as emerging engineering education programs take shape, accelerated cultivation of multifaceted innovative talents represents a new mission and imperative for higher education in China. In the context of the flourishing development of Synthetic Biology, East China University of Science and Technology has established a curriculum cluster in Synthetic Biology, focusing on microbiological drug discovery and biomanufacturing. The teaching team initially reviewed the curriculum system related to Synthetic Biology and its upstream and downstream courses. Subsequently, they expanded the core courses in Synthetic Biology, creating a curriculum cluster that encompasses not only the theoretical foundations and cutting-edge technologies but also integrates with related disciplines. Moreover, the curriculum cluster leverages lectures from renowned domestic and international professors in the State Key Laboratory of Bioreactor Engineering, and harnesses the rich resources of the Program of Introducing Talents of Discipline to Universities (the "111 plan"), aiming to enhance students' innovation capabilities. With the support of this curriculum cluster and teaching team, undergraduate students actively participate in international Synthetic Biology competitions like international genetic engineering machine competition (iGEM), consistently achieving gold awards. Furthermore, many students have applied for patents and made contributions to research paper publications. This work stands as a valuable exemplar for cultivating multifaceted talents with exceptional innovative capabilities.

A Modular Cloning Toolkit for the production of recombinant proteins in Leishmania tarentolae.

Modular Cloning (MoClo) is based on libraries of standardized genetic parts that can be directionally assembled via Golden Gate cloning in one-pot reactions into transcription units and multigene constructs. Here, a team of bachelor students established a MoClo toolkit for the protist Leishmania tarentolae in the frame of the international Genetically Engineered Machine (iGEM) competition. Our modular toolkit is based on a domesticated version of a commercial LEXSY expression vector and comprises 34 genetic parts encoding various affinity tags, targeting signals as well as fluorescent and luminescent proteins. We demonstrated the utility of our kit by the successful production of 16 different tagged versions of the receptor binding domain (RBD) of the SARS-CoV-2 spike protein in L. tarentolae liquid cultures. While highest yields of secreted recombinant RBD were obtained for GST-tagged fusion proteins 48 h post induction, C-terminal peptide tags were often degraded and resulted in lower yields of secreted RBD. Fusing secreted RBD to a synthetic O-glycosylation SP20 module resulted in an apparent molecular mass shift around 10 kDa. No disadvantage regarding the production of RBD was detected when the three antibiotics of the LEXSY system were omitted during the 48-h induction phase. Furthermore, the successful purification of secreted RBD from the supernatant of L. tarentolae liquid cultures was demonstrated in pilot experiments. In summary, we established a MoClo toolkit and exemplified its application for the production of recombinant proteins in L. tarentolae.

Measuring the burden of hundreds of BioBricks defines an evolutionary limit on constructability in synthetic biology.

Engineered DNA will slow the growth of a host cell if it redirects limiting resources or otherwise interferes with homeostasis. Populations of engineered cells can rapidly become dominated by "escape mutants" that evolve to alleviate this burden by inactivating the intended function. Synthetic biologists working with bacteria rely on genetic parts and devices encoded on plasmids, but the burden of different engineered DNA sequences is rarely characterized. We measured how 301 BioBricks on high-copy plasmids affected the growth rate of Escherichia coli. Of these, 59 (19.6%) negatively impacted growth. The burden imposed by engineered DNA is commonly associated with diverting ribosomes or other gene expression factors away from producing endogenous genes that are essential for cellular replication. In line with this expectation, BioBricks exhibiting burden were more likely to contain highly active constitutive promoters and strong ribosome binding sites. By monitoring how much each BioBrick reduced expression of a chromosomal GFP reporter, we found that the burden of most, but not all, BioBricks could be wholly explained by diversion of gene expression resources. Overall, no BioBricks reduced the growth rate of E. coli by >45%, which agreed with a population genetic model that predicts such plasmids should be "unclonable" because escape mutants will take over during growth of a bacterial colony or small laboratory culture from a transformed cell. We made this model available as an interactive web tool for synthetic biology education and added our burden measurements to the iGEM Registry descriptions of each BioBrick.

Unigems: plasmids and parts to facilitate teaching on assembly, gene expression control and logic in E. coli.

Synthetic biology enables the creative combination of engineering and molecular biology for exploration of fundamental aspects of biological phenomena. However, there are limited resources available for such applications in the educational context, where straightforward setup, easily measurable phenotypes and extensibility are of particular importance. We developed unigems, a set of ten plasmids that enable classroom-based investigation of gene-expression control and biological logic gates to facilitate teaching synthetic biology and genetic engineering. It is built on a high-copy plasmid backbone and is easily extensible thanks to a common primer set that facilitates Gibson assembly of PCR-generated or synthesized DNA parts into the target vector. It includes two reporter genes with either two constitutive (high- or low-level) or two inducible (lactose- or arabinose-) promoters, as well as a single-plasmid implementation of an AND logic gate. The set can readily be employed in undergraduate teaching settings, during outreach events and for training of iGEM teams. All plasmids have been deposited in Addgene.

[Design and implementation of the course on Synthetic Biology based on the concept of general education].

As an emerging branch of biology, Synthetic Biology has seen rapid development with great potential in theoretical research and application. With a lot of brand-new concepts and research methods, it brings challenges to university teachers, and little experience is available in China on the teaching of Synthetic Biology. In this study, we discussed the general education-based development and application of the course on Synthetic Biology (a discipline in "liberal arts" in Zhejiang University) from the background, design, implementation, outcome, and problems of the course, hoping to provide a reference for the optimization of the course and the design of similar courses in other universities in China.

Engineering and characterization of dehalogenase enzymes from Delftia acidovorans in bioremediation of perfluorinated compounds.

Per- and Polyfluorinated alkyl substances (PFAS) are a broad class of synthetic compounds that have fluorine substituted for hydrogen in several or all locations and are globally categorized as PFCs (perfluorochemicals; commonly called fluorinated chemicals). These compounds have unique chemical and physical properties that enable their use in non-stick surfaces, fire-fighting efforts, and as slick coatings. However, recent concerns over the health effects of such compounds, specifically perfluorooctanoic acid and perfluorooctane sulfonic acid (PFOA, PFOS; PFOA/S), have led to increased attention and research by the global community into degradation methods. In this study, soil samples from PFAS-contamination sites were cultured and screened for microbes with PFOA/S degradation potential, which led to the identification of Delftia acidovorans. It was found that D. acidovorans isolated from PFAS-contaminated soils was capable of growth in minimal media with PFOA as a sole carbon resource, and an observable fluoride concentration increase was observed when cells were exposed to PFOA. This suggests potential activity of a dehalogenase enzyme that may be of use in PFOA or PFAS microbial remediation efforts. Several associated haloacid dehalogenases have been identified in the D. acidovorans genome and have been engineered for expression in Escherichia coli for rapid production and purification. These enzymes have shown potential for enzymatic defluorination, a significant step in biological degradation and removal of PFOA/S from the environment. We hypothesize that bioremediation of PFAS using naturally occurring microbial degradation pathways may represent a novel approach to remove PFAS contamination.

[Cultivation of college students' innovative and entrepreneurial thinking and ability based on Synthetic Biology and iGEM].

Synthetic Biology is one of the most promising fields of modern Biology and a frontier interdisciplinary subject in the 21st century. With the rapid development of synthetic biology, the International Genetically Engineered Machine (iGEM) competition has emerged. The iGEM competition, based on the subject foundation of Synthetic Biology, intends to solve the biological problems in our daily life by applying modern biological technology. In recent years, with the continuous increase of participating teams, the iGEM competition has received extensive attention and achieved great progress. On the basis of the development of Synthetic Biology, we analyzed the 2018-2020 award-winning projects of the iGEM competition and illustrated the role and significance of the iGEM competition in cultivating college students' innovative thinking and ability with the participation experience of the iGEM team of Southwest Jiaotong University as an example.

[Development of the iGEM high school track].

The international genetically engineered machine (iGEM) competition is a global top college academic competition in synthetic biology. The iGEM competition has exhibited extensive international influence and attracted teams from more than 40 countries and regions around the world to participate in. The annual iGEM outputs have attracted the attention of top academic journals or international media such as Science, Nature, Scientific American, The Economist, British Broadcasting Corporation (BBC), etc. High school teams participated in iGEM since 2011, and the number of high school teams has increased year by year. High school participants are increasingly becoming one of the most important forces to promote the development of iGEM and synthetic biology. IGEM competition has also become an important platform to foster the core literacy of high school students. This paper summarized the track rules, topic selection tendency and awards of high school teams based on data of 2017 to 2021 iGEM competition. In addition, we analyzed the significance of iGEM competition on fostering of high school students' core literacy and discussed the development trend of global high school teams, with the aim to provide a reference for high school team building in the future.

iGEM and Gene Drives: A Case Study for Governance.

Gene drives have already challenged governance systems. In this case study, we explore the International Genetically Engineered Machine (iGEM) competition's experiences in gene drive-related research and lessons in developing, revising, and implementing a governance system. iGEM's experiences and lessons are distilled into 6 key insights for future gene drive policy development in the United States: (1) gene drives deserve special attention because of their potential for widescale impact and remaining uncertainty about how to evaluate intergenerational and transboundary risks; (2) an adaptive risk management approach is logical for gene drives because of the rapidly changing technical environment; (3) review by individual technical experts is limited and may fail to incorporate other forms of expertise and, therefore, must be complemented with a range of alternative governance methods; (4) current laboratory biosafety and biosecurity review processes may not capture gene drive research or its components in practice even if they are covered theoretically; (5) risk management for research and development must incorporate discussions of values and broader implications of the work; and (6) a regular technology horizon scanning capacity is needed for the early identification of advances that could pose governance system challenges.

Curation Principles Derived from the Analysis of the SBOL iGEM Data Set.

As an engineering endeavor, synthetic biology requires effective sharing of genetic design information that can be reused in the construction of new designs. While there are a number of large community repositories of design information, curation of this information has been limited. This in turn limits the ways in which design information can be put to use. The aim of this work was to improve this situation by creating a curated library of parts from the International Genetically Engineered Machines (iGEM) registry data set. To this end, an analysis of the Synthetic Biology Open Language (SBOL) version of the iGEM registry was carried out using four different approaches-simple statistics, SnapGene autoannotation, SYNBICT autoannotation, and expert analysis-the results of which are presented herein. Key challenges encountered include the use of free text, insufficient part provenance, part duplication, lack of part removal, and insufficient continuous curation. On the basis of these analyses, the focus has shifted from the creation of a curated iGEM part library to instead the extraction of a set of lessons, which are presented here. These lessons can be exploited to facilitate the creation and curation of other part libraries using a simpler and less labor intensive process.

BioMaster: An Integrated Database and Analytic Platform to Provide Comprehensive Information About BioBrick Parts.

Synthetic biology seeks to create new biological parts, devices, and systems, and to reconfigure existing natural biological systems for custom-designed purposes. The standardized BioBrick parts are the foundation of synthetic biology. The incomplete and flawed metadata of BioBrick parts, however, are a major obstacle for designing genetic circuit easily, quickly, and accurately. Here, a database termed BioMaster http://www.biomaster-uestc.cn was developed to extensively complement information about BioBrick parts, which includes 47,934 items of BioBrick parts from the international Genetically Engineered Machine (iGEM) Registry with more comprehensive information integrated from 10 databases, providing corresponding information about functions, activities, interactions, and related literature. Moreover, BioMaster is also a user-friendly platform for retrieval and analyses of relevant information on BioBrick parts.

Implementing adaptive risk management for synthetic biology: Lessons from iGEM's safety and security programme.

Synthetic biology offers exciting possibilities to deal with local and global challenges over the coming decades. As we make greater use of biological engineering, it will be increasingly important to balance potential risks and benefits. The rate, scale, and diffusion of relevant capabilities will make this challenging. There will be a growing need for flexible risk management approaches, which can be rapidly adapted as technology and societal needs change. This study details efforts by the International Genetically Engineered Machine (iGEM) competition in creating and implementing an adaptive risk management approach. It concludes with key lessons and challenges: working with hazardous materials, such as dangerous pathogens, toxins and chemicals; managing risks to plants, animals and the environment; use of samples from people, animals, and the environment; improving the hazards identified; variations in risk perception and tolerance; variation in terminology that complicates interpretation of risk management plans; and connections with broader societal or ethical questions, such as animal use, gender and sexuality, or benefit sharing.

Bioengineering bacterial encapsulin nanocompartments as targeted drug delivery system.

The development of Drug Delivery Systems (DDS) has led to increasingly efficient therapies for the treatment and detection of various diseases. DDS use a range of nanoscale delivery platforms produced from polymeric of inorganic materials, such as micelles, and metal and polymeric nanoparticles, but their variant chemical composition make alterations to their size, shape, or structures inherently complex. Genetically encoded protein nanocages are highly promising DDS candidates because of their modular composition, ease of recombinant production in a range of hosts, control over assembly and loading of cargo molecules and biodegradability. One example of naturally occurring nanocompartments are encapsulins, recently discovered bacterial organelles that have been shown to be reprogrammable as nanobioreactors and vaccine candidates. Here we report the design and application of a targeted DDS platform based on the Thermotoga maritima encapsulin reprogrammed to display an antibody mimic protein called Designed Ankyrin repeat protein (DARPin) on the outer surface and to encapsulate a cytotoxic payload. The DARPin9.29 chosen in this study specifically binds to human epidermal growth factor receptor 2 (HER2) on breast cancer cells, as demonstrated in an in vitro cell culture model. The encapsulin-based DDS is assembled in one step in vivo by co-expressing the encapsulin-DARPin9.29 fusion protein with an engineered flavin-binding protein mini-singlet oxygen generator (MiniSOG), from a single plasmid in Escherichia coli. Purified encapsulin-DARPin_miniSOG nanocompartments bind specifically to HER2 positive breast cancer cells and trigger apoptosis, indicating that the system is functional and specific. The DDS is modular and has the potential to form the basis of a multi-receptor targeted system by utilising the DARPin screening libraries, allowing use of new DARPins of known specificities, and through the proven flexibility of the encapsulin cargo loading mechanism, allowing selection of cargo proteins of choice.

iGEM and the Biotechnology Workforce of the Future.

An important factor in growing the US bioeconomy is recruiting and training its future workforce. Other science, technology, engineering, and math (STEM) fields have relied on diverse educational opportunities for recruitment, including prestigious high school and collegiate competitions. For genetic engineering and synthetic biology, there are very few competitions; they include the Biodesign Competition and the much larger and scientifically focused International Genetically Engineered Machine (iGEM) competition. iGEM, run by an independent nonprofit organization, is often cited as a measure of progress in developing the synthetic biology workforce. Starting in 2021, iGEM will move its main competitive event, the "Giant Jamboree," from its long-standing home in Boston to Paris, which is likely to negatively affect participation by the US team. In this article, we describe the value of iGEM to the bioeconomy and its upcoming challenges through a review of available literature, observation of the iGEM Jamboree, and interviews with 10 US-based iGEM team coaches. The coaches expressed positive views about the iGEM process for their students in providing a hands-on biotechnology experience, but they were concerned about the funding US students received to participate in iGEM compared with teams from other countries. They were also concerned that the relocation to Paris would negatively affect or preclude their participation. Possible options to continue the benefits of experiential learning in synthetic biology are discussed, including alternative funding for iGEM teams through a grant process and the need for additional biology competitions.

Developing a Comprehensive, Adaptive, and International Biosafety and Biosecurity Program for Advanced Biotechnology: The iGEM Experience.

Introduction: The international synthetic biology competition iGEM (formally known as the international Genetically Engineered Machines competition) has a dedicated biosafety and biosecurity program. Method: A review of specific elements of the program and a series of concrete examples illustrate how experiences in implementing the program have helped improved policy, including an increasing diversity of sources for genetic parts and organisms, keeping pace with technical developments, considering pathways toward future environmental release, addressing antimicrobial resistance, and testing the efficacy of current biosecurity arrangements. Results: iGEM's program is forward-leaning, in that it addresses both traditional (pathogen-based) and emerging risks both in terms of new technologies and new risks. It is integrated into the technical work of the competition-with clearly described roles and responsibilities for all members of the community. It operates throughout the life cycle of projects-from project design to future application. It makes use of specific tools to gather and review biosafety and biosecurity information, making it easier for those planning and conducting science and engineering to recognize potential risks and match them with appropriate risk management approaches, as well as for specialists to review this information to identify gaps and strengthen plans. Discussion: Integrating an increasingly adaptive risk management approach has allowed iGEM's biosafety and biosecurity program to become comprehensive, be cross-cutting, and cover the competition's life cycle.

YouTube resources for synthetic biology education.

Online video resources have increasingly become a common way to effectively share scientific research ideas and engage viewers at many levels of interest or expertise. While synthetic biology is a comparatively young field, it has accumulated online videos across a spectrum of content and technical depth. Such video content can be used to introduce viewers to synthetic biology, supplement college course content, teach new lab skills and entertain. Here, we compile online videos concerning synthetic biology into public YouTube playlists tailored for six different, though potentially overlapping, audiences: those wanting an introduction to synthetic biology, those wanting to get quick overviews of specific topics within synthetic biology, those wanting teaching or public lectures, those wanting more technical research lectures, those wanting to learn lab protocols and those interested in the International Genetically Engineered Machine competition.