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A large body of literature has established the benefits of undergraduate research experiences via the traditional apprenticeship model. More recently, several studies have shown that many of these benefits can be recapitulated in course-based undergraduate research experiences (CUREs) that are more scalable and easier for students to participate in, compared to the apprenticeship-based research experiences. Many Biology curricula also incorporate more traditional laboratory courses, where students learn to use common laboratory techniques through guided exercises with known outcomes. Indeed, many programs across the nation provide such programs or courses for students early in their careers, with a view toward increasing student interest and engagement in Biology. While there is general consensus that all lab experiences have some benefits for students, very few studies have examined whether either research experiences or learning biological techniques in more traditional lab courses directly impacts student performance in lecture courses. Here, we show that prior familiarity with laboratory techniques does not improve student performance in a lecture course, even if these techniques are directly related to content being taught in the course. However, having prior research experience improves performance in the course, irrespective of whether the research experience included the use of course-related laboratory techniques.

Having students work in small groups has been shown to promote better student outcomes, even in large lecture classes. On an institutional scale, the creation of learning communities that span multiple classes has also been proven to improve student outcomes. Research has shown that both interventions can help narrow the performance gaps that are often observed for students from certain demographic backgrounds. However, both have their drawbacks. When used solely for discussions in class, students in small groups rarely continue working together outside lecture in an intentional manner. Grading based on group performance leads to the perception of unfairness due to "weak" or "poor" members or disproportionate workloads. Learning communities, on the other hand, require a fair amount of administrative support to implement. Here, we describe a novel course and incentive structure that allows individual instructors to create sustainable learning communities in their classes. This course structure is relatively easy to implement, requiring very few changes to existing courses, and is adaptable to a variety of contexts, including remote teaching. Finally, we show that such learning communities provide additional learning gains for students and demonstrate that these class-based learning communities help narrow performance gaps for minoritized students.

The tragic murder of Mr. George Floyd brought to the head long-standing issues of racial justice and equity in the United States and beyond. This prompted many institutions of higher education, including professional organizations and societies, to engage in long-overdue conversations about the role of scientific institutions in perpetuating racism. Similar to many professional societies and organizations, the Society for the Advancement of Biology Education Research (SABER), a leading international professional organization for discipline-based biology education researchers, has long struggled with a lack of representation of People of Color (POC) at all levels within the organization. The events surrounding Mr. Floyd’s death prompted the members of SABER to engage in conversations to promote self-reflection and discussion on how the society could become more antiracist and inclusive. These, in turn, resulted in several initiatives that led to concrete actions to support POC, increase their representation, and amplify their voices within SABER. These initiatives included: a self-study of SABER to determine challenges and identify ways to address them, a year-long seminar series focused on issues of social justice and inclusion, a special interest group to provide networking opportunities for POC and to center their voices, and an increase in the diversity of keynote speakers and seminar topics at SABER conferences. In this article, we chronicle the journey of SABER in its efforts to become more inclusive and antiracist. We are interested in increasing POC representation within our community and seek to bring our resources and scholarship to reimagine professional societies as catalyst agents towards an equitable antiracist experience. Specifically, we describe the 12 concrete actions that SABER enacted over a period of a year and the results from these actions so far. In addition, we discuss remaining challenges and future steps to continue to build a more welcoming, inclusive, and equitable space for all biology education researchers, especially our POC members. Ultimately, we hope that the steps undertaken by SABER will enable many more professional societies to embark on their reflection journeys to further broaden scientific communities.

Universities use prerequisites to regulate the path of students through a program or major. However, the impact of prerequisites on follow-up courses in anatomy and physiology is not well understood. If success in follow-up courses depends on completion of prerequisite courses, then students should earn higher grades on exam questions that assess prerequisite knowledge. To test this hypothesis, we investigated the potential impact of a required prerequisite human physiology lecture course on a followup human physiology laboratory course and a follow-up molecular pharmacology course. We also investigated the potential impact of a recommended prerequisite human physiology laboratory course on a follow-up human anatomy course. We assessed student exam performance in the follow-up courses based on their familiarity with the material from the required prerequisite course or the recommended prerequisite course. Our results were mixed and demonstrated limited performance gains in the follow-up courses despite overlap of material among the courses. These results suggest that prerequisite courses may not have a significant impact on the outcome of future related courses and that individual academic programs should evaluate the effectiveness of prerequisite courses in a local context.

Studies have demonstrated that utilizing spacing (spreading out study sessions at regular intervals) and self-testing strategies are optimal for learning. While some applied work has examined the relationship between these strategies on general academic achievement, there is still a need to explore how both spacing and self-testing are related to course-level learning outcomes. The goal of this study was to examine whether utilizing spacing and self-testing strategies was related to final course grade. Participants were asked to report the study strategies they utilized during the course. We found no relationship between using spacing strategies and final course grade. However, self-testing was significantly related to higher final course grades. The relationship between self-testing and final course grade remained significant even after accounting for demographic differences and prior academic achievement. Our results suggest that self-testing strategies can enhance learning even in a highly structured course.

Quantitative data analysis skills are basic competencies students in a STEM field should master. In this article, we describe a classroom activity using isolated figures from papers as a simple exercise to practice data analysis skills. We call this approach Just Figures. With this technique, instructors find figures from primary papers that address key concepts related to several of their course learning objectives. These figures are assigned as homework prior to class discussion. In class, instructors teach the lesson and include a 10- to 20-minute discussion of the figures assigned. Frequent and repeated discussion of paper figures during class increased students' confidence in reading and analyzing data. The Just Figures approach also increased student accuracy when interpreting data. After six weeks of Just Figures practice, students scored, on average, three points higher on a 20-point data analysis assessment instrument than they had done before the Just Figures exercises. In addition, a course in which students consistently practiced Just Figures performed just as well on the data analysis assessment instrument and on a class exam dedicated to paper reading compared with courses where students practiced reading three entire papers. The Just Figures method is easy to implement and can effectively improve student data analysis skills in microbiology classrooms.

Repetitive elements, including LINE-1 (L1), comprise approximately half of the human genome. These elements can potentially destabilize the genome by initiating their own replication and reintegration into new sites (retrotransposition). In somatic cells, transcription of L1 elements is repressed by distinct molecular mechanisms, including DNA methylation and histone modifications, to repress transcription. Under conditions of hypomethylation (e.g. in tumor cells), a window of opportunity for L1 derepression arises, and additional restriction mechanisms become crucial. We recently demonstrated that the microRNA miR-128 represses L1 activity by directly binding to L1 ORF2 RNA. In this study, we tested whether miR-128 can also control L1 activity by repressing cellular proteins important for L1 retrotransposition. We found that miR-128 targets the 3' UTR of nuclear import factor transportin 1 (TNPO1) mRNA. Manipulation of miR-128 and TNPO1 levels demonstrated that induction or depletion of TNPO1 affects L1 retrotransposition and nuclear import of an L1-ribonucleoprotein complex (using L1-encoded ORF1p as a proxy for L1-ribonucleoprotein complexes). Moreover, TNPO1 overexpression partially reversed the repressive effect of miR-128 on L1 retrotransposition. Our study represents the first description of a protein factor involved in nuclear import of the L1 element and demonstrates that miR-128 controls L1 activity in somatic cells through two independent mechanisms: direct binding to L1 RNA and regulation of a cellular factor necessary for L1 nuclear import and retrotransposition.

Prerequisites are embedded in most STEM curricula. However, the assumption that the content presented in these courses will improve learning in later courses has not been verified. Because a direct comparison of performance between students with and without required prerequisites is logistically difficult to arrange in a randomized fashion, we developed a novel familiarity scale, and used this to determine whether concepts introduced in a prerequisite course improved student learning in a later course (in two biology disciplines). Exam questions in the latter courses were classified into three categories, based on the degree to which the tested concept had been taught in the prerequisite course. If content familiarity mattered, it would be expected that exam scores on topics covered in the prerequisite would be higher than scores on novel topics. We found this to be partially true for "Very Familiar" questions (concepts covered in depth in the prerequisite). However, scores for concepts only briefly discussed in the prerequisite ("Familiar") were indistinguishable from performance on topics that were "Not Familiar" (concepts only taught in the later course). These results imply that merely "covering" topics in a prerequisite course does not result in improved future performance, and that some topics may be able to removed from a course thereby freeing up class time. Our results may therefore support the implementation of student-centered teaching methods such as active learning, as the time-intensive nature of active learning has been cited as a barrier to its adoption. In addition, we propose that our familiarity system could be broadly utilized to aid in the assessment of the effectiveness of prerequisites.

Undergraduate biology education is often viewed as being focused on memorization rather than development of students' critical-thinking abilities. We speculated that open-note testing would be an easily implemented change that would emphasize higher-order thinking. As open-note testing is not commonly used in the biological sciences and the literature on its effects in biology education is sparse, we performed a comprehensive analysis of this intervention on a primary literature-based exam across three large-enrollment laboratory courses. Although students believed open-note testing would impact exam scores, we found no effect on performance, either overall or on questions of nearly all Bloom's levels. Open-note testing also produced no advantage when examined under a variety of parameters, including research experience, grade point average, course grade, prior exposure to primary literature-focused laboratory courses, or gender. Interestingly, we did observe small differences in open- and closed-note exam performance and perception for students who experienced open-note exams for an entire quarter. This implies that student preparation or in-test behavior can be altered by exposure to open-note testing conditions in a single course and that -increased experience may be necessary to truly understand the impact of this intervention.

Primary literature is essential for scientific communication and is commonly utilized in undergraduate biology education. Despite this, there is often little time spent training our students how to critically analyze a paper. To address this, we introduced a primary literature module in multiple upper-division laboratory courses. In this module, instructors conduct classroom discussions that dissect a paper as researchers do. While previous work has identified classroom interventions that improve primary literature comprehension within a single course, our goal was to determine whether including a scientific paper module in our classes could produce long-term benefits. On the basis of performance in an assessment exam, we found that our module resulted in longitudinal gains, including increased comprehension and critical-thinking abilities in subsequent lab courses. These learning gains were specific to courses utilizing our module, as no longitudinal gains were seen in students who had taken other upper-division labs that lacked extensive primary literature discussion. In addition, we assessed whether performance on our assessment correlated with a variety of factors, including grade point average, course performance, research background, and self-reported confidence in understanding of the article. Furthermore, all of the study conclusions are independent of biology disciplines, as we observe similar trends within each course.

Reversible phosphoinositide phosphorylation provides a dynamic membrane code that balances opposing cell functions. However, in vivo regulatory relationships between specific kinases, phosphatases, and phosphoinositide subpools are not clear. We identified myotubularin (mtm), a Drosophila melanogaster MTM1/MTMR2 phosphoinositide phosphatase, as necessary and sufficient for immune cell protrusion formation and recruitment to wounds. Mtm-mediated turnover of endosomal phosphatidylinositol 3-phosphate (PI(3)P) pools generated by both class II and III phosphatidylinositol 3-kinases (Pi3K68D and Vps34, respectively) is needed to down-regulate membrane influx, promote efflux, and maintain endolysosomal homeostasis. Endocytosis, but not endolysosomal size, contributes to cortical remodeling by mtm function. We propose that Mtm-dependent regulation of an endosomal PI(3)P pool has separable consequences for endolysosomal homeostasis and cortical remodeling. Pi3K68D depletion (but not Vps34) rescues protrusion and distribution defects in mtm-deficient immune cells and restores functions in other tissues essential for viability. The broad interactions between mtm and class II Pi3K68D suggest a novel strategy for rebalancing PI(3)P-mediated cell functions in MTM-related human disease.

BackgroundGenetic deletions or deficiencies have been used for gene mapping and discovery in various organisms, ranging from the nematode Caenorhabditis elegans all the way to humans. One problem with large deletions is the determination of the location of their breakpoints. This is exacerbated in the case of complex deficiencies that delete a region of the genome, while retaining some of the intervening sequence. Previous methods, using genetic complementation or cytology were hampered by low marker density and were consequently not very precise at positioning the breakpoints of complex deficiencies. The identification of increasing numbers of Single Nucleotide Polymorphisms (SNPs) has resulted in the use of these as genetic markers, and consequently in their utilization for defining the breakpoints of deletions using molecular biology methods.ResultsHere, we show that SNPs can be used to help position the breakpoints of a complex deficiency in C. elegans. The technique uses a combination of genetic crosses and molecular biology to generate robust and highly reproducible results with strong internal controls when trying to determine the breakpoints of deficiencies. The combined use of this technique and standard genetic mapping allowed us to rapidly narrow down the region of interest in our attempts to clone a gene.ConclusionUnlike previous methods used to locate deficiency breakpoints, our technique has the advantage of not being limited by the amount of starting material. It also incorporates internal controls to eliminate false positives and negatives. The technique can also easily be adapted for use in other organisms in which both genetic deficiencies and SNPs are available, thereby aiding gene discovery in these other models.

BackgroundCaenorhabditis elegans hermaphrodites are capable of producing hundreds of progeny. However, genetic and environmental factors can keep many animals from attaining their full reproductive potential. In these situations, efficient use of any functional gametes becomes more important for reproductive success. To learn about this aspect of C. elegans reproductive biology, we examined oocyte production and sperm utilization patterns in a unique collection of semi-fertile sperm function mutants.ResultsIn the mutants examined here, broods can be very small but sperm induced high levels of ovulation. Ovulation rates reach maximum levels between the first and second day of adulthood. Ovulations rates remain high during the reproductive period and gradually decline with age. These results further demonstrate a decoupling of the ability of sperm to fertilize oocytes and induce ovulation. We also observe that in our semi-fertile mutants the peak of successful fertilization events precedes the bulk of oocyte production. Mixing populations of functional and nonfunctional sperm under conditions without sperm competition also shows that functional sperm are utilized efficiently. Although overall brood size can be similar for different mutant strains, slight differences in the pattern of sperm utilization in these strains can lead to significant differences in resource utilization and population growth.ConclusionsThis study represents the first detailed description of oocyte and progeny production patterns over the entire reproductive period for wild-type and fertility impaired strains of C. elegans. The phenotype of our mutants provide an ideal system for studying sperm utilization patterns since they only affect one major process, the ability to fertilize oocytes. In semi-fertile mutants, the nature of the reproductive process and/or specific molecular mechanisms ensures that any functional sperm are utilized quickly. Only a fraction of the sperm produced by our semi-sterile mutants are functional as opposed to every sperm having a low but equal chance of fertilizing an oocyte. In addition to the number of progeny produced, the pattern of progeny production can have an important influence on the dynamics of population growth.

Undergraduate biology education is often viewed as being focused on memorization rather than development of students' critical-thinking abilities. We speculated that open-note testing would be an easily implemented change that would emphasize higher-order thinking. As open-note testing is not commonly used in the biological sciences and the literature on its effects in biology education is sparse, we performed a comprehensive analysis of this intervention on a primary literature--based exam across three large-enrollment laboratory courses. Although students believed open-note testing would impact exam scores, we found no effect on performance, either overall or on questions of nearly all Bloom's levels. Open-note testing also produced no advantage when examined under a variety of parameters, including research experience, grade point average, course grade, prior exposure to primary literature--focused laboratory courses, or gender. Interestingly, we did observe small differences in open-and closed-note exam performance and perception for students who experienced open-note exams for an entire quarter. This implies that student preparation or in-test behavior can be altered by exposure to open-note testing conditions in a single course and that increased experience may be necessary to truly understand the impact of this intervention.

Primary literature is essential for scientific communication and is commonly utilized in undergraduate biology education. Despite this, there is often little time spent "training" our students how to critically analyze a paper. To address this, we introduced a primary literature module in multiple upper-division laboratory courses. In this module, instructors conduct classroom discussions that dissect a paper as researchers do. While previous work has identified classroom interventions that improve primary literature comprehension within a single course, our goal was to determine whether including a scientific paper module in our classes could produce long-term benefits. On the basis of performance in an assessment exam, we found that our module resulted in longitudinal gains, including increased comprehension and critical-thinking abilities in subsequent lab courses. These learning gains were specific to courses utilizing our module, as no longitudinal gains were seen in students who had taken other upper-division labs that lacked extensive primary literature discussion. In addition, we assessed whether performance on our assessment correlated with a variety of factors, including grade point average, course performance, research background, and self-reported confidence in understanding of the article. Furthermore, all of the study conclusions are independent of biology disciplines, as we observe similar trends within each course.

Dynamic regulation of cell shape underlies many developmental and immune functions. Cortical remodeling is achieved under the central control of Rho GTPase pathways that modulate an exquisite balance in the dynamic assembly and disassembly of the cytoskeleton and focal adhesions. Macroautophagy (autophagy), associated with bulk cytoplasmic remodeling through lysosomal degradation, has clearly defined roles in cell survival and death. Moreover, it is becoming apparent that proteins, organelles, and pathogens can be targeted for autophagic clearance by selective mechanisms, although the extent and roles of such degradation are unclear. Here we report a conserved role for autophagy specifically in the cortical remodeling of Drosophila blood cells (hemocytes) and mouse macrophages. Continuous autophagy was required for integrin-mediated hemocyte spreading and Rho1-induced cell protrusions. Consequently, hemocytes disrupted for autophagy were impaired in their recruitment to epidermal wounds. Cell spreading required ref(2)P, the Drosophila p62 multiadaptor, implicating selective autophagy as a novel mechanism for modulating cortical dynamics. These results illuminate a specific and conserved role for autophagy as a regulatory mechanism for cortical remodeling, with implications for immune cell function.

Microinjection is a commonly used technique for DNA transformation in Caenorhabditis elegans. It is a powerful tool that links genetic and molecular analysis to phenotypic analysis. In this chapter we shall provide an overview of microinjection for germline transformation in worms. Our discussion will emphasize C. elegans reproductive biology, applications and protocols for carrying out microinjection in order to successfully obtain transgenic worms.

Fertilization triggers egg activation and converts the egg into a developing embryo. The events of this egg-to-embryo transition typically include the resumption of meiosis, the reorganization of the cortical actin cytoskeleton, and the remodeling of the oocyte surface. The factors that regulate sperm-dependent egg-activation events are not well understood. Caenorhabditis elegans EGG-3, a member of the protein tyrosine phosphatase-like (PTPL) family, is essential for regulating cell-surface and cortex rearrangements during egg activation in response to sperm entry. Although fertilization occurred normally in egg-3 mutants, the polarized dispersal of F-actin is altered, a chitin eggshell is not formed, and no polar bodies are produced. EGG-3 is associated with the oocyte plasma membrane in a pattern that is similar to CHS-1 and MBK-2. CHS-1 is required for eggshell deposition, whereas MBK-2 is required for the degradation of maternal proteins during the egg-to-embryo transition. The localization of CHS-1 and EGG-3 are interdependent and both genes were required for the proper localization of MBK-2 in oocytes. Therefore, EGG-3 plays a central role in egg activation by influencing polarized F-actin dynamics and the localization or activity of molecules that are directly involved in executing the egg-to-embryo transition.

Major sperm protein, a cytoskeletal molecule required for the amoeboid motility of sperm in Caenorhabditis elegans, also functions as a signaling molecule that regulates the rates of meiotic maturation and ovulation. Recent work has begun to uncover new genes required for the response to this signal in both somatic and germ line cells.

The molecular machinery that mediates sperm-egg interactions at fertilization is largely unknown. We identify two partially redundant egg surface LDL receptor repeat-containing proteins (EGG-1 and EGG-2) that are required for Caenorhabditis elegans fertility in hermaphrodites, but not males. Wild-type sperm cannot enter the morphologically normal oocytes produced by hermaphrodites that lack egg-1 and egg-2 function despite direct gamete contact. Furthermore, we find that levels of meiotic maturation/ovulation and sperm migratory behavior are altered in egg-1 mutants. These observations suggest an unexpected regulatory link between fertilization and other events necessary for reproductive success. egg-1 and egg-2 are the result of a gene duplication in the nematode lineage leading to C. elegans. The two closely related species C. briggsae and C. remanei encode only a single egg-1/egg-2 homolog that is required for hermaphrodite/female fertility. In addition to being the first identified egg components of the nematode fertilization machinery, the egg-1 and egg-2 gene duplication could be vital with regards to maximizing C. elegans fecundity and understanding the evolutionary differentiation of molecular function and speciation.