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.     

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.     

Why students do not turn on their video cameras during online classes and an equitable and inclusive plan to encourage them to do so

Enrollment in courses taught remotely in higher education has been on the rise, with a recent surge in response to a global pandemic. While adapting this form of teaching, instructors familiar with traditional face‐to‐face methods are now met with a new set of challenges, including students not turning on their cameras during synchronous class meetings held via videoconferencing. After transitioning to emergency remote instruction in response to the COVID‐19 pandemic, our introductory biology course shifted all in‐person laboratory sections into synchronous class meetings held via the Zoom videoconferencing program. Out of consideration for students, we established a policy that video camera use during class was optional, but encouraged. However, by the end of the semester, several of our instructors and students reported lower than desired camera use that diminished the educational experience. We surveyed students to better understand why they did not turn on their cameras. We confirmed several predicted reasons including the most frequently reported: being concerned about personal appearance. Other reasons included being concerned about other people and the physical location being seen in the background and having a weak internet connection, all of which our exploratory analyses suggest may disproportionately influence underrepresented minorities. Additionally, some students revealed to us that social norms also play a role in camera use. This information was used to develop strategies to encourage—without requiring—camera use while promoting equity and inclusion. Broadly, these strategies are to not require camera use, explicitly encourage usage while establishing norms, address potential distractions, engage students with active learning, and understand your students’ challenges through surveys. While the demographics and needs of students vary by course and institution, our recommendations will likely be directly helpful to many instructors and also serve as a model for gathering data to develop strategies more tailored for other student populations.     

Backyard evolutionary biology: Investigating local flowers brings learning to life

Inquiry‐based learning allows students to actively engage in and appreciate the process of science. As college courses transition to online instruction in response to COVID‐19, incorporating inquiry‐based learning is all the more essential for student engagement. However, with the cancelation of in‐person laboratory courses, implementing inquiry can prove challenging for instructors. Here, I describe a case that exemplifies a strategy for inquiry‐based learning and can be adapted for use in various course modalities, from traditional face‐to‐face laboratory courses to asynchronous and synchronous online courses. I detail an assignment where students explore the developmental basis of morphological evolution. Flowers offer an excellent example to address this concept and are easy for students to access and describe. Students research local flowering plants, collect and dissect flower specimens to determine their whorl patterns, and generate hypotheses to explain the developmental genetic basis of the patterns identified. This task allows students to apply their scientific thinking skills, conduct guided exploration in nature, and connect their understanding of the developmental basis of evolutionary change to everyday life. Incorporating inquiry using readily available, tangible, tractable real‐world examples represents a pragmatic and effective model that can be applied in a variety of disciplines during and beyond COVID‐19.     

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.     

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.     

Sudden challenges in teaching ecology and aligned disciplines during a global pandemic: Reflections on the rapid move online and perspectives on moving forward

The challenges facing higher education in response to COVID‐19 are significant and possibly none more so than in ecology and aligned disciplines. Not only did most ecology lecturers have to rush lectures and tutorials online, but also laboratory and field classes. We reflect on our experience of this move and also consider those of 30 other ecology‐aligned teaching academics to summarize the challenges faced in the move online early in 2020 and the developing plans for adapting ecology teaching and learning going into the 2020/21 academic year. The move online had the most significant impact on field classes, with more of these canceled than lectures or laboratory classes. Most respondents to an online poll also highlighted that many respondents (~45%) felt that ecology was more impacted by COVID‐19 that even other STEM disciplines. The availability of technological solutions is key to moving forward and will hopefully enhance the teaching and learning experience for many beyond the current crisis.     

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.     

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.     

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…

     

Dynamics of NK,CD8 and Tfh cell mediated the production of cytokines and antiviral antibodies in Chinese patients with moderate COVID‐19

Recent studies have demonstrated a marked decrease in peripheral lymphocyte levels in patients with coronavirus disease 2019 (COVID‐19) caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). Few studies have focused on the changes of NK, T‐ and B‐cell subsets, inflammatory cytokines and virus‐specific antibodies in patients with moderate COVID‐19. A total of 11 RT‐PCR‐confirmed convalescent patients with COVID‐19 and 11 patients with non‐SARS‐CoV‐2 pneumonia (control patients) were enrolled in this study. NK, CD8⁺ T, CD4⁺ T, Tfh‐like and B‐cell subsets were analysed using flow cytometry. Cytokines and SARS‐CoV‐2‐specific antibodies were analysed using an electrochemiluminescence immunoassay. NK cell counts were significantly higher in patients with COVID‐19 than in control patients (P = 0.017). Effector memory CD8⁺ T‐cell counts significantly increased in patients with COVID‐19 during a convalescent period of 1 week (P = 0.041). TIM‐3⁺ Tfh‐like cell and CD226⁺ Tfh‐like cell counts significantly increased (P = 0.027) and decreased (P = 0.022), respectively, during the same period. Moreover, ICOS⁺ Tfh‐like cell counts tended to decrease (P = 0.074). No abnormal increase in cytokine levels was observed. The high expression of NK cells is important in innate immune response against SARS‐CoV‐2. The increase in effector memory CD8⁺ T‐cell counts, the up‐regulation of inhibitory molecules and the down‐regulation of active molecules on CD4⁺ T cells and Tfh‐like cells in patients with COVID‐19 would benefit the maintenance of balanced cellular and humoural immune responses, may prevent the development of severe cases and contribute to the recovery of patients with COVID‐19.     

An at‐home laboratory in plant biology designed to engage students in the process of science

The COVID‐19 pandemic prompted a transition to remote delivery of courses that lack immersive hands‐on research experiences for undergraduate science students, resulting in a scientific research skills gap. In this report, we present an option for an inclusive and authentic, hands‐on research experience that all students can perform off‐campus. Biology students in a semester‐long (13 weeks) sophomore plant physiology course participated in an at‐home laboratory designed to study the impacts of nitrogen addition on growth rates and root nodulation by wild nitrogen‐fixing Rhizobia in Pisum sativum (Pea) plants. This undergraduate research experience, piloted in the fall semester of 2020 in a class with 90 students, was created to help participants learn and practice scientific research skills during the COVID‐19 pandemic. Specifically, the learning outcomes associated with this at‐home research experience were: (1) generate a testable hypothesis, (2) design an experiment to test the hypothesis, (3) explain the importance of biological replication, (4) perform meaningful statistical analyses using R, and (5) compose a research paper to effectively communicate findings to a general biology audience. Students were provided with an at‐home laboratory kit containing the required materials and reagents, which were chosen to be accessible and affordable in case students were unable to access our laboratory kit. Students were guided through all aspects of research, including hypothesis generation, data collection, and data analysis, with video tutorials and live virtual sessions. This at‐home laboratory provided students an opportunity to practice hands‐on research with the flexibility to collect and analyze their own data in a remote setting during the COVID‐19 pandemic. This, or similar laboratories, could also be used as part of distance learning biology courses.     

A close‐up view of dynamic biomarkers in the setting of COVID‐19: Striking focus on cardiovascular system

Based on the recent reports, cardiovascular events encompass a large portion of the mortality caused by the COVID‐19 pandemic, which drawn cardiologists into the management of the admitted ill patients. Given that common laboratory values may provide key insights into the illness caused by the life‐threatening SARS‐CoV‐2 virus, it would be more helpful for screening, clinical management and on‐time therapeutic strategies. Commensurate with these issues, this review article aimed to discuss the dynamic changes of the common laboratory parameters during COVID‐19 and their association with cardiovascular diseases. Besides, the values that changed in the early stage of the disease were considered and monitored during the recovery process. The time required for returning biomarkers to basal levels was also discussed. Finally, of particular interest, we tended to abridge the latest updates regarding the cardiovascular biomarkers as prognostic and diagnostic criteria to determine the severity of COVID‐19.     

QuoVidi: An open‐source web application for the organization of large‐scale biological treasure hunts

Learning biology, and in particular systematics, requires learning a substantial amount of specific vocabulary, both for botanical and zoological studies. While crucial, the precise identification of structures serving as evolutionary traits and systematic criteria is not per se a highly motivating task for students. Teaching this in a traditional teaching setting is quite challenging especially with a large crowd of students to be kept engaged. This is even more difficult if, as during the COVID‐19 crisis, students are not allowed to access laboratories for hands‐on observation on fresh specimens and sometimes restricted to short‐range movements outside their home. Here, we present QuoVidi, a new open‐source web platform for the organization of large‐scale treasure hunts. The platform works as follows: students, organized in teams, receive a list of quests that contain morphologic, ecologic, or systematic terms. They have to first understand the meaning of the quests, then go and find them in the environment. Once they find the organism corresponding to a quest, they upload a geotagged picture of their finding and submit this on the platform. The correctness of each submission is evaluated by the staff. During the COVID‐19 lockdown, previously validated pictures were also submitted for evaluation to students that were locked in low‐biodiversity areas. From a research perspective, the system enables the creation of large image databases by the students, similar to citizen science projects. Beside the enhanced motivation of students to learn the vocabulary and perform observations on self‐found specimens, this system allows instructors to remotely follow and assess the work performed by large numbers of students. The interface is freely available, open‐source and customizable. Unlike existing naturalist platforms, allows the educators to fully customize the quests of interest. This enables the creation of multiple teaching scenarios, without being bound to a fixed scope. QuoVidi can be used in other disciplines with adapted quests and we expect it to be of interest in many classroom settings.     

From a crisis to an opportunity: Eight insights for doing science in the COVID‐19 era and beyond

The COVID‐19 crisis has forced researchers in Ecology to change the way we work almost overnight. Nonetheless, the pandemic has provided us with several novel components for a new way of conducting science. In this perspective piece, we summarize eight central insights that are helping us, as early career researchers, navigate the uncertainties, fears, and challenges of advancing science during the COVID‐19 pandemic. We highlight how innovative, collaborative, and often Open Science‐driven developments that have arisen from this crisis can form a blueprint for a community reinvention in academia. Our insights include personal approaches to managing our new reality, maintaining capacity to focus and resilience in our projects, and a variety of tools that facilitate remote collaboration. We also highlight how, at a community level, we can take advantage of online communication platforms for gaining accessibility to conferences and meetings, and for maintaining research networks and community engagement while promoting a more diverse and inclusive community. Overall, we are confident that these practices can support a more inclusive and kinder scientific culture for the longer term.     

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.     

Increased risk for COVID‐19 breakthrough infection in fully vaccinated patients with substance use disorders in the United States between December 2020 and August 2021

Individuals with substance use disorders (SUDs) are at increased risk for COVID‐19 infection and for adverse outcomes of the infection. Though vaccines are highly effective against COVID‐19, their effectiveness in individuals with SUDs might be curtailed by compromised immune status and a greater likelihood of exposures, added to the waning vaccine immunity and the new SARS‐CoV‐2 variants. In a population‐based cohort study, we assessed the risk, time trends, outcomes and disparities of COVID‐19 breakthrough infection in fully vaccinated SUD patients starting 14 days after completion of vaccination. The study included 579,372 individuals (30,183 with a diagnosis of SUD and 549,189 without such a diagnosis) who were fully vaccinated between December 2020 and August 2021, and had not contracted COVID‐19 infection prior to vaccination. We used the TriNetX Analytics network platform to access de‐identified electronic health records from 63 health care organizations in the US. Among SUD patients, the risk for breakthrough infection ranged from 6.8% for tobacco use disorder to 7.8% for cannabis use disorder, all significantly higher than the 3.6% in non‐SUD population (p<0.001). Breakthrough infection risk remained significantly higher after controlling for demographics (age, gender, ethnicity) and vaccine types for all SUD subtypes, except for tobacco use disorder, and was highest for cocaine and cannabis use disorders (hazard ratio, HR=2.06, 95% CI: 1.30‐3.25 for cocaine; HR=1.92, 95% CI: 1.39‐2.66 for cannabis). When we matched SUD and non‐SUD individuals for lifetime comorbidities and adverse socioeconomic determinants of health, the risk for breakthrough infection no longer differed between these populations, except for patients with cannabis use disorder, who remained at increased risk (HR=1.55, 95% CI: 1.22‐1.99). The risk for breakthrough infection was higher in SUD patients who received the Pfizer than the Moderna vaccine (HR=1.49, 95% CI: 1.31‐1.69). In the vaccinated SUD population, the risk for hospitalization was 22.5% for the breakthrough cohort and 1.6% for the non‐breakthrough cohort (risk ratio, RR=14.4, 95% CI: 10.19‐20.42), while the risk for death was 1.7% and 0.5% respectively (RR=3.5, 95% CI: 1.74‐7.05). No significant age, gender and ethnic disparities for breakthrough infection were observed in vaccinated SUD patients. These data suggest that fully vaccinated SUD individuals are at higher risk for breakthrough COVID‐19 infection, and this is largely due to their higher prevalence of comorbidities and adverse socioeconomic determinants of health compared with non‐SUD individuals. The high frequency of comorbidities in SUD patients is also likely to contribute to their high rates of hospitalization and death following breakthrough infection.     

Heterogeneous expression of ACE2 and TMPRRS2 in mesenchymal stromal cells

The outbreak of COVID‐19 has become a serious public health emergency. The virus targets cells by binding the ACE2 receptor. After infection, the virus triggers in some humans an immune storm containing the release of proinflammatory cytokines and chemokines followed by multiple organ failure. Several vaccines are enrolled, but an effective treatment is still missing. Mesenchymal stem cells (MSCs) have shown to secrete immunomodulatory factors that suppress this cytokine storm. Therefore, MSCs have been suggested as a potential treatment option for COVID‐19. We report here that the ACE2 expression is minimal or nonexistent in MSC derived from three different human tissue sources (adipose tissue, umbilical cord Wharton`s jelly and bone marrow). In contrast, TMPRSS2 that is implicated in SARS‐CoV‐2 entry has been detected in all MSC samples. These results are of particular importance for future MSC‐based cell therapies to treat severe cases after COVID‐19 infection.     

Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data

Protein Data Bank Japan (PDBj), a founding member of the worldwide Protein Data Bank (wwPDB) has accepted, processed and distributed experimentally determined biological macromolecular structures for 20 years. During that time, we have continuously made major improvements to our query search interface of PDBj Mine 2, the BMRBj web interface, and EM Navigator for PDB/BMRB/EMDB entries. PDBj also serves PDB‐related secondary database data, original web‐based modeling services such as Homology modeling of complex structure (HOMCOS), visualization services and utility tools, which we have continuously enhanced and expanded throughout the years. In addition, we have recently developed several unique archives, BSM‐Arc for computational structure models, and XRDa for raw X‐ray diffraction images, both of which promote open science in the structural biology community. During the COVID‐19 pandemic, PDBj has also started to provide feature pages for COVID‐19 related entries across all available archives at PDBj from raw experimental data and PDB structural data to computationally predicted models, while also providing COVID‐19 outreach content for high school students and teachers.