An international consensus on effective, inclusive, and career-spanning short-format training in the life sciences and beyond.

Science, technology, engineering, mathematics, and medicine (STEMM) fields change rapidly and are increasingly interdisciplinary. Commonly, STEMM practitioners use short-format training (SFT) such as workshops and short courses for upskilling and reskilling, but unaddressed challenges limit SFT's effectiveness and inclusiveness. Education researchers, students in SFT courses, and organizations have called for research and strategies that can strengthen SFT in terms of effectiveness, inclusiveness, and accessibility across multiple dimensions. This paper describes the project that resulted in a consensus set of 14 actionable recommendations to systematically strengthen SFT. A diverse international group of 30 experts in education, accessibility, and life sciences came together from 10 countries to develop recommendations that can help strengthen SFT globally. Participants, including representation from some of the largest life science training programs globally, assembled findings in the educational sciences and encompassed the experiences of several of the largest life science SFT programs. The 14 recommendations were derived through a Delphi method, where consensus was achieved in real time as the group completed a series of meetings and tasks designed to elicit specific recommendations. Recommendations cover the breadth of SFT contexts and stakeholder groups and include actions for instructors (e.g., make equity and inclusion an ethical obligation), programs (e.g., centralize infrastructure for assessment and evaluation), as well as organizations and funders (e.g., professionalize training SFT instructors; deploy SFT to counter inequity). Recommendations are aligned with a purpose-built framework-"The Bicycle Principles"-that prioritizes evidenced-based teaching, inclusiveness, and equity, as well as the ability to scale, share, and sustain SFT. We also describe how the Bicycle Principles and recommendations are consistent with educational change theories and can overcome systemic barriers to delivering consistently effective, inclusive, and career-spanning SFT.

Preprint Peer Review Enhances Undergraduate Biology Students' Disciplinary Literacy and Sense of Belonging in STEM.

Education about scientific publishing and manuscript peer review is not universally provided in undergraduate science courses. Since peer review is integral to the scientific process and central to the identity of a scientist, we envision a paradigm shift where teaching peer review becomes integral to undergraduate science education. We hypothesize that teaching undergraduates how to peer review scientific manuscripts may facilitate their development of scientific literacy and identity formation. To this end, we developed a constructivist, service-learning curriculum for biology undergraduates to learn about the mechanisms of peer review using preprints and then to write and publish their own peer reviews of preprints as a way to authentically join the scientific community of practice. The curriculum was implemented as a semester-long intervention in one class and, in another class, as an embedded module intervention. Students' scientific literacy and peer review ability were assessed using quantitative methods. Student's perceptions of their scientific literacy and identity were assessed using thematic analysis of students' reflective writing. Here, we present data on the improvement in the peer review ability of undergraduates in both classes and data on the curriculum's interrelated impact on students' development of scientific literacy, identity, and belonging in peer and professional discourse spaces. These data suggest that undergraduates can and should be trained in peer review to foster the interrelated development of their scientific literacy, scientific identity, and sense of belonging in science.

Recommendations for empowering early career researchers to improve research culture and practice.

Early career researchers (ECRs) are important stakeholders leading efforts to catalyze systemic change in research culture and practice. Here, we summarize the outputs from a virtual unconventional conference (unconference), which brought together 54 invited experts from 20 countries with extensive experience in ECR initiatives designed to improve the culture and practice of science. Together, we drafted 2 sets of recommendations for (1) ECRs directly involved in initiatives or activities to change research culture and practice; and (2) stakeholders who wish to support ECRs in these efforts. Importantly, these points apply to ECRs working to promote change on a systemic level, not only those improving aspects of their own work. In both sets of recommendations, we underline the importance of incentivizing and providing time and resources for systems-level science improvement activities, including ECRs in organizational decision-making processes, and working to dismantle structural barriers to participation for marginalized groups. We further highlight obstacles that ECRs face when working to promote reform, as well as proposed solutions and examples of current best practices. The abstract and recommendations for stakeholders are available in Dutch, German, Greek (abstract only), Italian, Japanese, Polish, Portuguese, Spanish, and Serbian.

How to bring peer review ghostwriters out of the dark.

Early career researchers are frequent and valuable contributors to peer review. Systemic changes that acknowledge this fact would result in ethical co-reviewing, peer reviews of greater quality, and a reduction in peer reviewer burden.

Peer review and preprint policies are unclear at most major journals.

Clear and findable publishing policies are important for authors to choose appropriate journals for publication. We investigated the clarity of policies of 171 major academic journals across disciplines regarding peer review and preprinting. 31.6% of journals surveyed do not provide information on the type of peer review they use. Information on whether preprints can be posted or not is unclear in 39.2% of journals. 58.5% of journals offer no clear information on whether reviewer identities are revealed to authors. Around 75% of journals have no clear policy on co-reviewing, citation of preprints, and publication of reviewer identities. Information regarding practices of open peer review is even more scarce, with <20% of journals providing clear information. Having found a lack of clear information, we conclude by examining the implications this has for researchers (especially early career) and the spread of open research practices.

Insights from the Inclusive Environments and Metrics in Biology Education and Research Network: Our Experience Organizing Inclusive Biology Education Research Events.

In contrast to efforts focusing on improving inclusion in STEM classrooms from kindergarten through undergraduate (K-16), efforts to improve inclusion in scientific meetings and conferences, important hubs of STEM culture, are more recent. Markers of inclusion that are sometimes overlooked at these events can include the composition of panels, how workshops are run, the affordability of conferences, and various other mechanisms that maintain pre-existing hierarchies and norms that limit the participation of early-career researchers and individuals of minoritized cultural, linguistic, and economic backgrounds. The Inclusive Environments and Metrics in Biology Education and Research (iEMBER) network coordinates efforts of researchers from many fields interested in diversity and inclusion in biology education. Given the concerns regarding inclusion at professional meetings, iEMBER has developed and implemented several practices in planning and executing our meetings to make them more inclusive. In this report, we share our experiences developing inclusive meetings on biology education research and discuss the outcomes of such efforts. Specifically, we present our approach to planning and executing the iEMBER 2019 conference and the National Association of Biology Teachers iEMBER 2019 workshop. This report adds to the growing body of resources on inclusive meetings, provides readers with an account of how such an attempt at implementation might unfold, and complements existing theories and work relating to the importance and functioning of such meetings in terms of representation in STEM.

Co-reviewing and ghostwriting by early-career researchers in the peer review of manuscripts.

Many early-career researchers are involved in the peer review of manuscripts for scientific journals, typically under the guidance of or jointly with their advisor, but most of the evidence about this activity is anecdotal. Here we report the results of a literature review and a survey of researchers, with an emphasis on co-reviewing and 'ghostwriting'. The literature review identified 36 articles that addressed the involvement of early-career researchers in peer review, most of them about early-career researchers and their advisors co-reviewing manuscripts for the purposes of training: none of them addressed the topic of ghostwriting in detail. About three quarters of the respondents to the survey had co-reviewed a manuscript. Most respondents believe co-reviewing to be a beneficial (95%) and ethical (73%) form of training in peer review. About half of the respondents have ghostwritten a peer review report, despite 81% responding that ghostwriting is unethical and 82% agreeing that identifying co-reviewers to the journal is valuable. Peer review would benefit from changes in both journal policies and lab practices that encourage mentored co-review and discourage ghostwriting.

Formation of the Inclusive Environments and Metrics in Biology Education and Research (iEMBER) Network: Building a Culture of Diversity, Equity, and Inclusion.

The Inclusive Environments and Metrics in Biology Education and Research (iEMBER) network is a newly forming national community of practice that engages diversity, equity, and inclusion stakeholders in interdisciplinary collaborative projects. iEMBER was initiated with incubator funding from the National Science Foundation program for Research Coordination Networks in Undergraduate Biology Education. In June 2017, biology education researchers, social scientists, biologists, and program and policy administrators, all with interests in diversity, equity, and inclusion, met to lay the foundation for the iEMBER network. iEMBER provides a distinct forum to coordinate efforts through networking, professional development, and the initiation of collaborative research. iEMBER advances science, technology, engineering, and mathematics reform focused on diversity, equity, and inclusion through the initiation of research teams at the iEMBER biennial conference and outreach efforts at discipline-specific meetings and conferences. The focus of iEMBER is on understanding how to create inclusive, supportive, and engaging environments to foster the success of all biology students and trainees. This report focuses on the structure of the iEMBER network, two takeaways that emerged from the 2017 conference (interdisciplinary networking/collaboration and intradisciplinary broadening participation strategies), and ways for prospective members to engage in ongoing dialogue and future events. Learn more at http://iember.org .

Assessing Ubiquitylation of Individual Proteins Using Xenopus Extract Systems.

Xenopus extract systems have been used to study ubiquitylation of proteins, and to uncover some of the fundamental processes of the ubiquitylation pathway itself. They provide a simple, quick, and robust method for studying ubiquitylation. In this protocol, methods are provided for studying protein ubiquitylation using Xenopus egg or embryo extracts and in vitro radiolabeled proteins. These methods also enable examination of whether proteins undergo noncanonical ubiquitylation, through modification of the protein by covalent linkage to ubiquitin through residues other than lysine, such as cysteine, serine, and threonine.

Calculating the Degradation Rate of Individual Proteins Using Xenopus Extract Systems.

The Xenopus extract system has been used extensively as a simple, quick, and robust method for assessing the stability of proteins against proteasomal degradation. In this protocol, methods are provided for assessing the half-life of in vitro translated radiolabeled proteins using Xenopus egg or embryo extracts.

Changing the Culture of Science Communication Training for Junior Scientists.

Being successful in an academic environment places many demands on junior scientists. Science communication currently may not be adequately valued and rewarded, and yet communication to multiple audiences is critical for ensuring that it remains a priority in today's society. Due to the potential for science communication to produce better scientists, facilitate scientific progress, and influence decision-making at multiple levels, training junior scientists in both effective and ethical science communication practices is imperative, and can benefit scientists regardless of their chosen career path. However, many challenges exist in addressing specific aspects of this training. Principally, science communication training and resources should be made readily available to junior scientists at institutions, and there is a need to scale up existing science communication training programs and standardize core aspects of these programs across universities, while also allowing for experimentation with training. We propose a comprehensive core training program be adopted by universities, utilizing a centralized online resource with science communication information from multiple stakeholders. In addition, the culture of science must shift toward greater acceptance of science communication as an essential part of training. For this purpose, the science communication field itself needs to be developed, researched and better understood at multiple levels. Ultimately, this may result in a larger cultural change toward acceptance of professional development activities as valuable for training scientists.

What's in a name?

Numerous concerns have been raised about the sustainability of the biomedical research enterprise in the United States. Improving the postdoctoral training experience is seen as a priority in addressing these concerns, but even identifying who the postdocs are is made difficult by the multitude of different job titles they can carry. Here, we summarize the detrimental effects that current employment structures have on training, compensation and benefits for postdocs, and argue that academic research institutions should standardize the categorization and treatment of postdocs. We also present brief case studies of two institutions that have addressed these challenges and can provide models for other institutions attempting to enhance their postdoctoral workforces and improve the sustainability of the biomedical research enterprise.

From cytoskeletal dynamics to organ asymmetry: a nonlinear, regulative pathway underlies left-right patterning.

Consistent left-right (LR) asymmetry is a fundamental aspect of the bodyplan across phyla, and errors of laterality form an important class of human birth defects. Its molecular underpinning was first discovered as a sequential pathway of left- and right-sided gene expression that controlled positioning of the heart and visceral organs. Recent data have revised this picture in two important ways. First, the physical origin of chirality has been identified; cytoskeletal dynamics underlie the asymmetry of single-cell behaviour and patterning of the LR axis. Second, the pathway is not linear: early disruptions that alter the normal sidedness of upstream asymmetric genes do not necessarily induce defects in the laterality of the downstream genes or in organ situs Thus, the LR pathway is a unique example of two fascinating aspects of biology: the interplay of physics and genetics in establishing large-scale anatomy, and regulative (shape-homeostatic) pathways that correct molecular and anatomical errors over time. Here, we review aspects of asymmetry from its intracellular, cytoplasmic origins to the recently uncovered ability of the LR control circuitry to achieve correct gene expression and morphology despite reversals of key 'determinant' genes. We provide novel functional data, in Xenopus laevis, on conserved elements of the cytoskeleton that drive asymmetry, and comparatively analyse it together with previously published results in the field. Our new observations and meta-analysis demonstrate that despite aberrant expression of upstream regulatory genes, embryos can progressively normalize transcriptional cascades and anatomical outcomes. LR patterning can thus serve as a paradigm of how subcellular physics and gene expression cooperate to achieve developmental robustness of a body axis.This article is part of the themed issue 'Provocative questions in left-right asymmetry'.

Ubiquitin-mediated proteolysis in Xenopus extract.

The small protein modifier, ubiquitin, can be covalently attached to proteins in the process of ubiquitylation, resulting in a variety of functional outcomes. In particular, the most commonly-associated and well-studied fate for proteins modified with ubiquitin is their ultimate destruction: degradation by the 26S proteasome via the ubiquitin-proteasome system, or digestion in lysosomes by proteolytic enzymes. From the earliest days of ubiquitylation research, a reliable and versatile "cell-in-a-test-tube" system has been employed in the form of cytoplasmic extracts from the eggs and embryos of the frog Xenopus laevis. Biochemical studies of ubiquitin and protein degradation using this system have led to significant advances particularly in the study of ubiquitin-mediated proteolysis, while the versatility of Xenopus as a developmental model has allowed investigation of the in vivo consequences of ubiquitylation. Here we describe the use and history of Xenopus extract in the study of ubiquitin-mediated protein degradation, and highlight the versatility of this system that has been exploited to uncover mechanisms and consequences of ubiquitylation and proteolysis.

Conserved roles for cytoskeletal components in determining laterality.

Consistently-biased left-right (LR) patterning is required for the proper placement of organs including the heart and viscera. The LR axis is especially fascinating as an example of multi-scale pattern formation, since here chiral events at the subcellular level are integrated and amplified into asymmetric transcriptional cascades and ultimately into the anatomical patterning of the entire body. In contrast to the other two body axes, there is considerable controversy about the earliest mechanisms of embryonic laterality. Many molecular components of asymmetry have not been widely tested among phyla with diverse bodyplans, and it is unknown whether parallel (redundant) pathways may exist that could reverse abnormal asymmetry states at specific checkpoints in development. To address conservation of the early steps of LR patterning, we used the Xenopus laevis (frog) embryo to functionally test a number of protein targets known to direct asymmetry in plants, fruit fly, and rodent. Using the same reagents that randomize asymmetry in Arabidopsis, Drosophila, and mouse embryos, we show that manipulation of the microtubule and actin cytoskeleton immediately post-fertilization, but not later, results in laterality defects in Xenopus embryos. Moreover, we observed organ-specific randomization effects and a striking dissociation of organ situs from effects on the expression of left side control genes, which parallel data from Drosophila and mouse. Remarkably, some early manipulations that disrupt laterality of transcriptional asymmetry determinants can be subsequently "rescued" by the embryo, resulting in normal organ situs. These data reveal the existence of novel corrective mechanisms, demonstrate that asymmetric expression of Nodal is not a definitive marker of laterality, and suggest the existence of amplification pathways that connect early cytoskeletal processes to control of organ situs bypassing Nodal. Counter to alternative models of symmetry breaking during neurulation (via ciliary structures absent in many phyla), our data suggest a widely-conserved role for the cytoskeleton in regulating left-right axis formation immediately after fertilization of the egg. The novel mechanisms that rescue organ situs, even after incorrect expression of genes previously considered to be left-side master regulators, suggest LR patterning as a new context in which to explore multi-scale redundancy and integration of patterning from the subcellular structure to the entire bodyplan.