Strength is in engagement: The rise of an online scientific community during the COVID‐19 pandemic

Many scientists, confined to home office by COVID‐19, have been gathering in online communities, which could become viable alternatives to physical meetings and conferences. Subject Categories: S&S: Careers & Training, Methods & Resources, S&S: Ethics

As COVID‐19 has brought work and travel to a grinding halt, scientists explored new ways to connect with each other. For the gene regulation community, this started with a Tweet that quickly expanded into the “Fragile Nucleosome” online forum, a popular seminar series, and many intimate discussions connecting scientists all over the world. More than 2,500 people from over 45 countries have attended our seminars so far and our forum currently has ~ 1,000 members who have kick‐started discussion groups and mentorship opportunities. Here we discuss our experience with setting up the Fragile Nucleosome seminars and online discussion forum, and present the tools to enable others to do the same.Too often, we forget the importance of social interactions in science. Indeed, many creative ideas originated from impromptu and fortuitous encounters with peers, in passing, over lunch, or during a conference coffee break. Now, the ongoing COVID‐19 crisis means prolonged isolation, odd working hours, and less social interactions for most scientists confined to home. This motivated us to create the “Fragile Nucleosome” virtual community for our colleagues in the chromatin and gene regulation field.

… the ongoing COVID‐19 crisis means prolonged isolation, odd working hours and less social interactions for most scientists confined to home.

While the need to address the void created by the COVID‐19 pandemic triggered our actions, a large part of the international community already has had limited access to research networks in our field. Our initiative offered new opportunities though, in particular for those who have not benefited from extensive networks, showing how virtual communities can address disparities in accessibility. This should not be a stop‐gap measure during the pandemic: Once we come out from our isolation, we still need to address the drawbacks of in‐person scientific conferences/seminars, such as economic disparities, travel inaccessibility, and overlapping family responsibilities (Sarabipour, 2020). Our virtual community offers some solutions to the standing challenges (Levine & Rathmell, 2020), and we hope our commentary can help start conversations about the advantages of virtual communities in a post‐pandemic world.

… once we come out from our isolation we still need to address the drawbacks of in‐person scientific conferences/seminars, such as economic disparities, travel inaccessibility and overlapping family responsibilities…

     

The role of fear in modern societies: Our ancient fear response to new situations is not always helpful in a civilised society

The COVID‐19 pandemic highlights how our ancient fear response can be exploited for nefarious purposes with social media lending a helping hand. Subject Categories: S&S: Economics & Business, Ecology, Microbiology, Virology & Host Pathogen Interaction

The COVID‐19 pandemic has underscored more than any previous crisis how fear can be exploited by multiple actors from outright conspiracy theorists with pernicious agendas to governments seeking to maximise public compliance with lockdowns and social distancing. The crisis has also given new urgency to the debate over how to handle fake news and its rapid propagation over social media, as well as the part science should play in leading and supporting governments'' decisions.At a fundamental level, the pandemic has highlighted the balance evolution has struck between fear and its aversion, between risk taking and risk avoidance. Indeed, for many animals, fear is necessary to avoid predation or accidental death, but it must be kept in check to avoid starvation by never setting out to search for food.

At a fundamental level, the pandemic has highlighted the balance evolution has struck between fear and its aversion, between risk taking and risk avoidance.

     

Bioinspiration as a method of problem‐based STEM education: A case study with a class structured around the COVID‐19 crisis

Bioinspiration is a promising lens for biology instruction as it allows the instructor to focus on current issues, such as the COVID‐19 pandemic. From social distancing to oxygen stress, organisms have been tackling pandemic‐related problems for millions of years. What can we learn from such diverse adaptations in our own applications? This review uses a seminar course on the COVID‐19 crisis to illustrate bioinspiration as an approach to teaching biology content. At the start of the class, students mind‐mapped the entire problem; this range of subproblems was used to structure the biology content throughout the entire class. Students came to individual classes with a brainstormed list of biological systems that could serve as inspiration for a particular problem (e.g., absorptive leaves in response to the problem of toilet paper shortages). After exploration of relevant biology content, discussion returned to the focal problem. Students dug deeper into the literature in a group project on mask design and biological systems relevant to filtration and transparency. This class structure was an engaging way for students to learn principles from ecology, evolution, behavior, and physiology. Challenges with this course design revolved around the interdisciplinary and creative nature of the structure; for instance, the knowledge of the participants was often stretched by engineering details. While the present class was focused on the COVID‐19 crisis, a course structured through a bioinspired approach can be applied to other focal problems, or subject areas, giving instructors a powerful method to deliver interdisciplinary content in an integrated and inquiry‐driven way.     

Taking practical learning in STEM education home: Examples from do‐it‐yourself experiments in plant biology

Practical teaching can give authentic learning experiences and teach valuable skills for undergraduate students in the STEM disciplines. One of the main ways of giving students such experiences, laboratory teaching, is met with many challenges such as budget cuts, increased use of virtual learning, and currently the university lockdowns due to the COVID‐19 pandemic. We highlight how at‐home do‐it‐yourself (DIY) experiments can be a good way to include physical interaction with your study organism, system, or technique to give the students a practical, authentic learning experience. We hope that by outlining the benefits of a practical, at‐home, DIY experiment we can inspire more people to design these teaching activities in the current remote teaching situation and beyond. By contributing two examples in the field of plant biology we enrich the database on experiments to draw inspiration from for these teaching methods.     

COVID19 Disease Map,a computational knowledge repository of virus–host interaction mechanisms

We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS‐CoV‐2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large‐scale community effort to build an open access, interoperable and computable repository of COVID‐19 molecular mechanisms. The COVID‐19 Disease Map (C19DMap) is a graphical, interactive representation of disease‐relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph‐based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS‐CoV‐2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID‐19 or similar pandemics in the long‐term perspective.     

Lessons learned through listening to biology students during a transition to online learning in the wake of the COVID‐19 pandemic

During the Spring Semester of 2020, an outbreak of a novel coronavirus (SARS‐CoV‐2) and the illnesses it caused (COVID‐19) led to widespread cancelling of on‐campus instruction at colleges and universities in the United States and other countries around the world. Response to the pandemic in university settings included a rapid and unexpected shift to online learning for faculty and students. The transition to teaching and learning online posed many challenges, and the experiences of students during this crisis may inform future planning for distance learning experiences during the ongoing pandemic and beyond. Herein, we discuss the experiences of first‐ and second‐year university students enrolled in a biology seminar course as their classes migrated to online environments. Drawing on reported student experiences and prior research and resources, we discuss the ways we will adjust our own teaching for future iterations of the course while offering recommendations for instructors tasked with teaching in online environments.     

How many animals are used for SARS‐CoV‐2 research?: An overview on animal experimentation in pre‐clinical and basic research

Non‐technical summaries of research projects allow tracking the numbers and purpose of animal experiments related to SARS‐CoV2 research so as to provide greater transparency on animal use. Subject Categories: Economics, Law & Politics, Pharmacology & Drug Discovery, Science Policy & Publishing

The COVID‐19 pandemic has accelerated biomedical research and drug development to an unprecedented pace. Governments worldwide released emergency funding for biomedical research that allowed scientists to focus on COVID‐19 and related drug and vaccine development. As a result, a flood of scientific articles on SARS‐CoV‐2 and COVID‐19 was published since early 2020. More importantly though, within less than 2 years, scientists in academia and industry developed vaccines against the virus from scratch: Several vaccines have now received regulatory approval and are being mass produced to immunize the human population worldwide.This colossal success of science rests in large part on the shoulders of animals that were used in basic and pre‐clinical research and regulatory testing. Notwithstanding, animal experimentation has remained a highly controversial and heated topic between advocates for research and animal rights activists. During the past decades, European policymakers responded to the debate by enacting stricter regulations, which inevitably has increased the bureaucratic hurdles for experimentation on animals. Scientists have for long spoken out against this additional burden, arguing that both basic and translational researches to improve human health crucially relies on animal experimentation—as the COVID‐19 pandemic aptly demonstrated (Genzel et al, 2020).     

Next‐generation field courses: Integrating Open Science and online learning

As Open Science practices become more commonplace, there is a need for the next generation of scientists to be well versed in these aspects of scientific research. Yet, many training opportunities for early career researchers (ECRs) could better emphasize or integrate Open Science elements. Field courses provide opportunities for ECRs to apply theoretical knowledge, practice new methodological approaches, and gain an appreciation for the challenges of real‐life research, and could provide an excellent platform for integrating training in Open Science practices. Our recent experience, as primarily ECRs engaged in a field course interrupted by COVID‐19, led us to reflect on the potential to enhance learning outcomes in field courses by integrating Open Science practices and online learning components. Specifically, we highlight the opportunity for field courses to align teaching activities with the recent developments and trends in how we conduct research, including training in: publishing registered reports, collecting data using standardized methods, adopting high‐quality data documentation, managing data through reproducible workflows, and sharing and publishing data through appropriate channels. We also discuss how field courses can use online tools to optimize time in the field, develop open access resources, and cultivate collaborations. By integrating these elements, we suggest that the next generation of field courses will offer excellent arenas for participants to adopt Open Science practices.     

Online but not remote: Adapting field‐based ecology laboratories for online learning

Teaching ecology effectively and experientially has become more challenging for at least two reasons today. Most experiences of our students are urban, and we now face the near immediate and continuing need to deliver courses (either partially or wholly) online because of COVID‐19. Therefore, providing a learning experience that connects students to their environment within an ecological framework remains crucial and perhaps therapeutic to mental health. Here, we describe how prior to the pandemic we adapted our field‐based laboratories to include data collection, analysis, and interpretation, along with the development of a citizen‐science approach for online delivery. This design is simple to implement, does not require extensive work, and maintains the veracity of original learning outcomes. Collaboration online following field data collection in ecology courses within the context of cities offers further options to adapt to student experience levels, resource availability, and accessibility, as well as bringing instructors and students together to build an open well‐curated data set that can be used in ecology courses where no laboratories are available. Finally, it promotes an open collaboration among ecology instructors that can drive lasting conversations about ecology curriculum.     

A comparative study between outcomes of an in‐person versus online introductory field course

The COVID‐19 pandemic has disrupted many standard approaches to STEM education. Particularly impacted were field courses, which rely on specific natural spaces often accessed through shared vehicles. As in‐person field courses have been found to be particularly impactful for undergraduate student success in the sciences, we aimed to compare and understand what factors may have been lost or gained during the conversion of an introductory field course to an online format. Using a mixed methods approach comparing data from online and in‐person field‐course offerings, we found that while community building was lost in the online format, online participants reported increased self‐efficacy in research and observation skills and connection to their local space. The online field course additionally provided positive mental health breaks for students who described the time outside as a much‐needed respite. We maintain that through intentional design, online field courses can provide participants with similar outcomes to in‐person field courses.     

Fostering equity,diversity, and inclusion in large,first‐year classes: Using reflective practice questions to promote universal design for learning in ecology and evolution lessons

Instructors can deliberately design for equity, diversity, and inclusion, including for large first‐year classes, and now instructors have added challenges given COVID‐19. Our paper explores the question: How do we integrate equity, diversity, and inclusion and universal design for learning (UDL) into first‐year, undergraduate ecology and evolution introductory lessons given the COVID‐19 pandemic? Given the large field exploring equity, diversity, and inclusion, we chose to focus on developing reflective practice question rubrics for before, during, and after lessons to encourage UDL for instructors, teaching assistants, and learners. We conducted a focus group within our team and discussed ideas related to online learning, including related pitfalls and solutions. Lastly, we created a figure to illustrate ideas and end with a general discussion. Our reflective practice questions for UDL rubrics, figure, focus group, and discussion aim to increase positive action for equity, diversity, and inclusion in the classroom and beyond.     

A virtual bird’s eye view: Live streaming nest boxes to continue outreach in the era of COVID‐19

COVID‐19 created a host of challenges for science education; in our case, the pandemic halted our in‐person elementary school outreach project on bird biology. This project was designed as a year‐long program to teach fifth‐grade students in Ithaca, New York, USA, about bird ecology and biodiversity using in‐person presentations, games, activities, and outdoor demonstrations. As a central part of this effort, we set up nest boxes on school property and planned to monitor them with students during bird breeding in the spring. Here, we describe our experiences transitioning this program online: we live streamed nest boxes to the students’ virtual classroom and used them as a focal point for virtual lessons on bird breeding and nestling development. In an era of social distancing and isolation, we propose that nest box live streaming and virtual lessons can support communities by providing access to the outdoors and unconventional science learning opportunities for all students. Instituting similar programs at local schools has the potential to increase equitable learning opportunities for students across geographic locations and with varying degrees of physical access to the outdoors and nature.     

The COVID‐19 pandemic: agile versus blundering communication during a worldwide crisis: Important lessons for efficient communication to maintain public trust and ensure public safety

Governments’ measures to control the COVID‐19 pandemic and public reaction hold important lessons for science and risk communication in times of crisis.

The world is in the grips of a global pandemic, the end of which is not yet in sight. Nations struggle to deal with the severe health, economic and social impacts of COVID‐19 with varying success. Their ability to handle this crisis depends on many factors, some of which, such as the availability of vaccines, are variable, while others – geographical location or population density – are determined. More importantly though, public health infrastructures, political will and action, and clear communication have so far proved to be the most successful levers for coping with the pandemic. This article examines how political will and communication in particular have helped to alleviate the impact of the virus in some countries.

… public health infrastructures, political will and action, and clear communication have so far proved to be the most successful levers for coping with the pandemic.

News that a new virus had emerged in Wuhan, China, was just of fleeting interest for most people in December 2019. This changed rapidly: by March 2020, large parts of the world had gone into lockdown to curtail the rapid spread of SARS‐CoV‐2. Many governments issued more or less harsh restrictions on private contacts, travel and other freedoms, followed by easing these regulations during the summer, which precipitated new outbreaks in the fall along with mutations of the virus that triggered new restrictions; it is likely that this pattern will continue until a sufficient number of people are vaccinated to achieve herd immunity.COVID‐19 came “out of the blue”, hit a largely unprepared human population and has therefore affected human civilisation in an unprecedented manner (Fig 1). People are not only concerned about their health: as the pandemic continues, citizens also worry about the social, economic and psychological impacts. Even though vaccination programmes are under way, only a few countries will be able to achieve herd immunity by the summer; in the meantime, public acceptance for the ongoing restrictions of freedom are waning as the negative social and economic effects become more urgent. Thus, political action and planning along with efficient communication in particular are crucially important to ensure the public’s understanding of the situation and maintain acceptance for restrictive measure until enough vaccines become available. The antipodes in communication strategies were a mixture of evidence‐based messages, transparency, building confidence and open discussion of scientific uncertainty to gain and maintain public trust versus the unfettered spread of alternative facts, targeted disinformation and omission of important information that eventually eroded said trust.Open in a separate windowFigure 1Fear in times of COVID‐19An elderly pedestrian wearing a face mask due to the COVID‐19 pandemic, walks past graffiti depicting the subjects within famous artworks, in Glasgow on 2 September 2020 after the Scottish government imposed fresh restrictions on the city after a rise in cases of the novel coronavirus (© Andy Buchanan/AFP via Getty Images)

… political action and planning along with efficient communication in particular are crucially important to ensure the public’s understanding of the situation and maintain acceptance for restrictive measure…

     

CyDisCo production of functional recombinant SARS‐CoV‐2 spike receptor binding domain

The COVID‐19 pandemic caused by SARS‐CoV‐2 has applied significant pressure on overtaxed healthcare around the world, underscoring the urgent need for rapid diagnosis and treatment. We have developed a bacterial strategy for the expression and purification of a SARS‐CoV‐2 spike protein receptor binding domain (RBD) that includes the SD1 domain. Bacterial cytoplasm is a reductive environment, which is problematic when the recombinant protein of interest requires complicated folding and/or processing. The use of the CyDisCo system (cytoplasmic disulfide bond formation in E. coli) bypasses this issue by pre‐expressing a sulfhydryl oxidase and a disulfide isomerase, allowing the recombinant protein to be correctly folded with disulfide bonds for protein integrity and functionality. We show that it is possible to quickly and inexpensively produce an active RBD in bacteria that is capable of recognizing and binding to the ACE2 (angiotensin‐converting enzyme) receptor as well as antibodies in COVID‐19 patient sera.     

Vitamin D and COVID‐19: A review on the role of vitamin D in preventing and reducing the severity of COVID‐19 infection

Severe Acute Respiratory Syndrome Coronavirus‐2 (SARS‐CoV‐2) is a pathogenic coronavirus causing COVID‐19 infection. The interaction between the SARS‐CoV‐2 spike protein and the human receptor angiotensin‐converting enzyme 2, both of which contain several cysteine residues, is impacted by the disulfide‐thiol balance in the host cell. The host cell redox status is affected by oxidative stress due to the imbalance between the reactive oxygen/nitrogen species and antioxidants. Recent studies have shown that Vitamin D supplementation could reduce oxidative stress. It has also been proposed that vitamin D at physiological concentration has preventive effects on many viral infections, including COVID‐19. However, the molecular‐level picture of the interplay of vitamin D deficiency, oxidative stress, and the severity of COVID‐19 has remained unclear. Herein, we present a thorough review focusing on the possible molecular mechanism by which vitamin D could alter host cell redox status and block viral entry, thereby preventing COVID‐19 infection or reducing the severity of the disease.     

Biology lessons in times of COVID: The pandemic has forced educators to teach and instruct online with varying success and challenges

Since COVID‐19 hit last year, lecturers and professors have been exploring digital and other tools to teach and instruct their students. Subject Categories: S&S: Careers & Training, Methods & Resources

As Director of the Digital Pedagogy Lab at the University of Colorado in Denver, USA, Michael Sean Morris’ work took on new significance as the COVID‐19 pandemic hit campuses around the world. “What happened with the pandemic was a lot of people who weren''t accustomed to teaching online, or dealing with distance learning, or remote learning in any way, shape, or form, really tried to create a live classroom situation on their screen, mostly using Zoom or other similar technologies”, Morris said. “With technology now, we can do things which make us feel closer. So, we can do a Zoom; there can be synchronous chat in technologies like Slack, or discussion forums or what‐have‐you to make you feel like you''re closer, to make you feel like you''re sort of together at the same time. But the majority of online learning actually has been asynchronous, it''s been everyone coming in when they can and doing their work when they can”.Educators have been divided over the use of online learning. But this changed when a deadly pandemic forced everyone from kindergarten to university into digital spaces. Luckily, many digital tools, such as Zoom, Slack, Blackboard Collaborate, or WhatsApp, were available to enable the migration. Nonetheless, teachers, lecturers, and professors struggle to educate their students with knowledge and the hands‐on training that is paramount for teaching biology.

… teachers, lecturers and professors struggle to educate their students with knowledge and the hands‐on training that is paramount for teaching biology.

     

Multiple sites on SARS‐CoV‐2 spike protein are susceptible to proteolysis by cathepsins B,K, L,S, and V

SARS‐CoV‐2 is the coronavirus responsible for the COVID‐19 pandemic. Proteases are central to the infection process of SARS‐CoV‐2. Cleavage of the spike protein on the virus''s capsid causes the conformational change that leads to membrane fusion and viral entry into the target cell. Since inhibition of one protease, even the dominant protease like TMPRSS2, may not be sufficient to block SARS‐CoV‐2 entry into cells, other proteases that may play an activating role and hydrolyze the spike protein must be identified. We identified amino acid sequences in all regions of spike protein, including the S1/S2 region critical for activation and viral entry, that are susceptible to cleavage by furin and cathepsins B, K, L, S, and V using PACMANS, a computational platform that identifies and ranks preferred sites of proteolytic cleavage on substrates, and verified with molecular docking analysis and immunoblotting to determine if binding of these proteases can occur on the spike protein that were identified as possible cleavage sites. Together, this study highlights cathepsins B, K, L, S, and V for consideration in SARS‐CoV‐2 infection and presents methodologies by which other proteases can be screened to determine a role in viral entry. This highlights additional proteases to be considered in COVID‐19 studies, particularly regarding exacerbated damage in inflammatory preconditions where these proteases are generally upregulated.