Deep Learning-based structure modelling illuminates structure and function in uncharted regions of ß-solenoid fold space.

Repeat proteins are common in all domains of life and exhibit a wide range of functions. One class of repeat protein contains solenoid folds where the repeating unit consists of ß-strands separated by tight turns. ß-solenoids have distinguishing structural features such as handedness, twist, oligomerisation state, coil shape and size which give rise to their diversity. Characterised ß-solenoid repeat proteins are known to form regions in bacterial and viral virulence factors, antifreeze proteins and functional amyloids. For many of these proteins, the experimental structure has not been solved, as they are difficult to crystallise or model. Here we use various deep learning-based structure-modelling methods to discover novel predicted ß-solenoids, perform structural database searches to mine further structural neighbours and relate their predicted structure to possible functions. We find both eukaryotic and prokaryotic adhesins, confirming a known functional linkage between adhesin function and the ß-solenoid fold. We further identify exceptionally long, flat ß-solenoid folds as possible structures of mucin tandem repeat regions and unprecedentedly small ß-solenoid structures. Additionally, we characterise a novel ß-solenoid coil shape, the FapC Greek key ß-solenoid as well as plausible complexes between it and other proteins involved in Pseudomonas functional amyloid fibres.

Reframing Educational Outcomes: Moving beyond Achievement Gaps.

The term "achievement gap" has a negative and racialized history, and using the term reinforces a deficit mindset that is ingrained in U.S. educational systems. In this essay, we review the literature that demonstrates why "achievement gap" reflects deficit thinking. We explain why biology education researchers should avoid using the phrase and also caution that changing vocabulary alone will not suffice. Instead, we suggest that researchers explicitly apply frameworks that are supportive, name racially systemic inequities and embrace student identity. We review four such frameworks-opportunity gaps, educational debt, community cultural wealth, and ethics of care-and reinterpret salient examples from biology education research as an example of each framework. Although not exhaustive, these descriptions form a starting place for biology education researchers to explicitly name systems-level and asset-based frameworks as they work to end educational inequities.

Pandemic-Related Instructor Talk: How New Instructors Supported Students at the Onset of the COVID-19 Pandemic.

At the same time that COVID-19 cases in the United States first began to increase, fellows in a mentored teaching apprenticeship for postdoctoral scientists began to teach undergraduate seminars. The fellows suddenly needed to support students emotionally and switch to online instruction. They were encouraged to acknowledge and address the pandemic during each class and decided to do so. In this case study, we examined the language fellows used in response to this encouragement, hypothesizing that they would engage in a variety of pandemic-related instructor talk, i.e., language that instructors use in the classroom that is not directly tied to educational content. We analyzed transcripts from 17 2-hour undergraduate biology seminar courses and found 167 instances of pandemic-related instructor talk. We used grounded theory to identify categories that emerged from these quotations: Positive coping mechanisms and self-care; Adjusting to online learning; Compassionate instruction; Personal impacts; COVID-19 and society; Dreaming; and Biology of COVID-19. Talk in these categories may help build relationships among instructors and students. The category about quickly Adjusting to online learning is unique, in that it is unlikely that there will be another time that will require simultaneous and rapid national movement to online instruction. In addition, four of the seven categories are direct consequences of COVID-19 specifically, and thus are unique to this time. Analyzing pandemic-related instructor talk has shed light on how new instructors navigated the trials of teaching in 2020.

Competing Discourses of Scientific Identity among Postdoctoral Scholars in the Biomedical Sciences.

The postdoctoral period is generally one of low pay, long hours, and uncertainty about future career options. To better understand how postdocs conceive of their present and future goals, we asked researchers about their scientific identities while they were in their postdoctoral appointments. We used discourse analysis to analyze interviews with 30 scholars from a research-intensive university or nearby research institutions to better understand how their scientific identities influenced their career goals. We identified two primary discourses: bench scientist and principal investigator (PI). The bench scientist discourse is characterized by implementing other people's scientific visions through work in the laboratory and expertise in experimental design and troubleshooting. The PI discourse is characterized by a focus on formulating scientific visions, obtaining funding, and disseminating results through publishing papers and at invited talks. Because these discourses represent beliefs, they can-and do-limit postdocs' understandings of what career opportunities exist and the transferability of skills to different careers. Understanding the bench scientist and PI discourses, and how they interact, is essential for developing and implementing better professional development programs for postdocs.

Development and Validation of the Homeostasis Concept Inventory.

We present the Homeostasis Concept Inventory (HCI), a 20-item multiple-choice instrument that assesses how well undergraduates understand this critical physiological concept. We used an iterative process to develop a set of questions based on elements in the Homeostasis Concept Framework. This process involved faculty experts and undergraduate students from associate's colleges, primarily undergraduate institutions, regional and research-intensive universities, and professional schools. Statistical results provided strong evidence for the validity and reliability of the HCI. We found that graduate students performed better than undergraduates, biology majors performed better than nonmajors, and students performed better after receiving instruction about homeostasis. We used differential item analysis to assess whether students from different genders, races/ethnicities, and English language status performed differently on individual items of the HCI. We found no evidence of differential item functioning, suggesting that the items do not incorporate cultural or gender biases that would impact students' performance on the test. Instructors can use the HCI to guide their teaching and student learning of homeostasis, a core concept of physiology.

Checking Equity: Why Differential Item Functioning Analysis Should Be a Routine Part of Developing Conceptual Assessments.

We provide a tutorial on differential item functioning (DIF) analysis, an analytic method useful for identifying potentially biased items in assessments. After explaining a number of methodological approaches, we test for gender bias in two scenarios that demonstrate why DIF analysis is crucial for developing assessments, particularly because simply comparing two groups' total scores can lead to incorrect conclusions about test fairness. First, a significant difference between groups on total scores can exist even when items are not biased, as we illustrate with data collected during the validation of the Homeostasis Concept Inventory. Second, item bias can exist even when the two groups have exactly the same distribution of total scores, as we illustrate with a simulated data set. We also present a brief overview of how DIF analysis has been used in the biology education literature to illustrate the way DIF items need to be reevaluated by content experts to determine whether they should be revised or removed from the assessment. Finally, we conclude by arguing that DIF analysis should be used routinely to evaluate items in developing conceptual assessments. These steps will ensure more equitable-and therefore more valid-scores from conceptual assessments.

The genetic drift inventory: a tool for measuring what advanced undergraduates have mastered about genetic drift.

Understanding genetic drift is crucial for a comprehensive understanding of biology, yet it is difficult to learn because it combines the conceptual challenges of both evolution and randomness. To help assess strategies for teaching genetic drift, we have developed and evaluated the Genetic Drift Inventory (GeDI), a concept inventory that measures upper-division students' understanding of this concept. We used an iterative approach that included extensive interviews and field tests involving 1723 students across five different undergraduate campuses. The GeDI consists of 22 agree-disagree statements that assess four key concepts and six misconceptions. Student scores ranged from 4/22 to 22/22. Statements ranged in mean difficulty from 0.29 to 0.80 and in discrimination from 0.09 to 0.46. The internal consistency, as measured with Cronbach's alpha, ranged from 0.58 to 0.88 across five iterations. Test-retest analysis resulted in a coefficient of stability of 0.82. The true-false format means that the GeDI can test how well students grasp key concepts central to understanding genetic drift, while simultaneously testing for the presence of misconceptions that indicate an incomplete understanding of genetic drift. The insights gained from this testing will, over time, allow us to improve instruction about this key component of evolution.

The Dominance Concept Inventory: A Tool for Assessing Undergraduate Student Alternative Conceptions about Dominance in Mendelian and Population Genetics.

Despite the impact of genetics on daily life, biology undergraduates understand some key genetics concepts poorly. One concept requiring attention is dominance, which many students understand as a fixed property of an allele or trait and regularly conflate with frequency in a population or selective advantage. We present the Dominance Concept Inventory (DCI), an instrument to gather data on selected alternative conceptions about dominance. During development of the 16-item test, we used expert surveys (n = 12), student interviews (n = 42), and field tests (n = 1763) from introductory and advanced biology undergraduates at public and private, majority- and minority-serving, 2- and 4-yr institutions in the United States. In the final field test across all subject populations (n = 709), item difficulty ranged from 0.08 to 0.84 (0.51 ± 0.049 SEM), while item discrimination ranged from 0.11 to 0.82 (0.50 ± 0.048 SEM). Internal reliability (Cronbach's alpha) was 0.77, while test-retest reliability values were 0.74 (product moment correlation) and 0.77 (intraclass correlation). The prevalence of alternative conceptions in the field tests shows that introductory and advanced students retain confusion about dominance after instruction. All measures support the DCI as a useful instrument for measuring undergraduate biology student understanding and alternative conceptions about dominance.

The EvoDevoCI: a concept inventory for gauging students' understanding of evolutionary developmental biology.

The American Association for the Advancement of Science 2011 report Vision and Change in Undergraduate Biology Education encourages the teaching of developmental biology as an important part of teaching evolution. Recently, however, we found that biology majors often lack the developmental knowledge needed to understand evolutionary developmental biology, or "evo-devo." To assist in efforts to improve evo-devo instruction among undergraduate biology majors, we designed a concept inventory (CI) for evolutionary developmental biology, the EvoDevoCI. The CI measures student understanding of six core evo-devo concepts using four scenarios and 11 multiple-choice items, all inspired by authentic scientific examples. Distracters were designed to represent the common conceptual difficulties students have with each evo-devo concept. The tool was validated by experts and administered at four institutions to 1191 students during preliminary (n = 652) and final (n = 539) field trials. We used student responses to evaluate the readability, difficulty, discriminability, validity, and reliability of the EvoDevoCI, which included items ranging in difficulty from 0.22-0.55 and in discriminability from 0.19-0.38. Such measures suggest the EvoDevoCI is an effective tool for assessing student understanding of evo-devo concepts and the prevalence of associated common conceptual difficulties among both novice and advanced undergraduate biology majors.

Getting to evo-devo: concepts and challenges for students learning evolutionary developmental biology.

To examine how well biology majors have achieved the necessary foundation in evolution, numerous studies have examined how students learn natural selection. However, no studies to date have examined how students learn developmental aspects of evolution (evo-devo). Although evo-devo plays an increasing role in undergraduate biology curricula, we find that instruction often addresses development cursorily, with most of the treatment embedded within instruction on evolution. Based on results of surveys and interviews with students, we suggest that teaching core concepts (CCs) within a framework that integrates supporting concepts (SCs) from both evolutionary and developmental biology can improve evo-devo instruction. We articulate CCs, SCs, and foundational concepts (FCs) that provide an integrative framework to help students master evo-devo concepts and to help educators address specific conceptual difficulties their students have with evo-devo. We then identify the difficulties that undergraduates have with these concepts. Most of these difficulties are of two types: those that are ubiquitous among students in all areas of biology and those that stem from an inadequate understanding of FCs from developmental, cell, and molecular biology.

Columellar muscle of neogastropods: muscle attachment and the function of columellar folds.

Malacologists often assume that ornamentation on snail shells is functional, and therefore adaptive. I conducted the first comprehensive test of the widely accepted hypothesis that columellar folds, a type of internal ornamentation, enhance the performance of the columellar muscle, which attaches the snail to its shell. Careful dissections of live, non-relaxed specimens reveal that the physical attachment between the columellar muscle and the columella is not restricted to a small, circular patch located deep within the shell. Instead, the attachment is long and narrow, extending approximately a full whorl along the length of the columella. I developed a novel technique for preparing three-dimensional reconstructions from photographs documenting the dissections. These reconstructions were then used to measure four parameters that describe the muscle: (1) the surface area of the physical attachment between the muscle and columella, (2) the total contact area between the muscle and the columella, (3) the depth of attachment, and (4) the length of attachment. None of these parameters differed significantly between species with and without folds. In light of the biomechanics of muscular hydrostats, values of the first parameter indicate that columellar folds probably do not guide the columellar muscle as the animal moves in and out of its shell. Values of the other parameters indicate that columellar folds neither increase an animal's ability to maneuver its shell nor facilitate deeper withdrawal. These results, and the fact that folds have evolved convergently several times, might indicate that folds are an easily evolvable solution to many functional problems, none of which are currently understood.

The impact of the pull of the recent on the history of marine diversity.

Up to 50% of the increase in marine animal biodiversity through the Cenozoic at the genus level has been attributed to a sampling bias termed "the Pull of the Recent," the extension of stratigraphic ranges of fossil taxa by the relatively complete sampling of the Recent biota. However, 906 of 958 living genera and subgenera of bivalve mollusks having a fossil record occur in the Pliocene or Pleistocene. The Pull of the Recent thus accounts for only 5% of the Cenozoic increase in bivalve diversity, a major component of the marine record, suggesting that the diversity increase is likely to be a genuine biological pattern.