Integrating Research into the Undergraduate Curriculum: 2. Scaffolding Research Skills and Transitioning toward Independent Research

Undergraduate research experiences are widely regarded as high-impact practices that foster meaningful mentoring relationships, enhance retention and graduation, and stimulate postbaccalaureate enrollment in STEM graduate and professional programs. Through immersion in a mentored original research project, student develop and apply their skills in critical thinking, problem solving, intellectual independence, communication, collaboration, project ownership, innovation, and leadership. These skills are readily transferable to a wide array of future careers in and beyond STEM that are well-served by evidence-based approaches. The 2019 Society for Neuroscience meeting included a well-attended workshop on integrating research into the curriculum at primarily undergraduate institutions (PUIs). This article is the second of three articles that summarize, analyze, and expand the workshop discussions. In this second article, we specifically describe approaches to transitional research courses that prepare students for independent research experiences such as undergraduate research theses. Educators can intentionally scaffold research experience and skills across the curriculum, to foster participation in scientific research and enhance diversity, equity, and inclusivity in research training. This article provides an overview of important goals and considerations for intermediate undergraduate research experiences, specific examples from several institutions of transitional courses that scaffold research preparation using different structures, and a summary of lessons learned from these experiences.

Integrating Research into the Undergraduate Curriculum: 1. Early Research Experiences and Training

Undergraduate research experiences have emerged as some of the most beneficial high-impact practices in education, providing clear benefits to students that include improved critical thinking and scientific reasoning, increased academic performance, and enhanced retention both within STEM majors and in college overall. These benefits extend to faculty members as well. Several disciplines, including neuroscience, have implemented research as part of their curriculum, yet many research opportunities target late stage undergraduates, despite evidence that early engagement can maximize the beneficial nature of such work. A 2019 Society for Neuroscience professional development workshop provided multiple examples of integrating research into an undergraduate curriculum, including early engagement (Fernandes, 2020). This article is the first in a series of three that expands upon the information presented in those workshop discussions, focusing on ways to promote early research opportunities. The benefits and challenges associated with early research engagement suggest thoughtful consideration of the best mechanisms for implementation are warranted; some options might include apprenticeship models or course-based approaches. Regardless of mechanism, early research can serve to initiate more prolonged, progressive, scaffolded experiences that span the academic undergraduate career.

Integrating Research into the Undergraduate Curriculum: 3. Research Training in the Upper-level Neuroscience Curriculum

The benefits of undergraduate training in research are significant. Integration of such training into the undergraduate experience, however, can be challenging at institutions without extensive research programs, and may inadvertently exclude some populations of students. Therefore, inclusion of research into the academic curriculum ensures all students can access this important training. The 2019 annual meeting of the Society for Neuroscience included a workshop on integrating research into the curriculum at primarily undergraduate institutions (PUIs). In this last article of a three-part series, we describe models for integrating research into advanced stages of the undergraduate curriculum, specifically for juniors and seniors. First, we describe multiple models of faculty-mentored group-based research. Second, we detail a peer-mentored research system, in which seniors mentor groups of first through third year students. Third, we describe multiple examples of integrating research into "capstone" courses for seniors. Fourth, we describe models in which a senior thesis is a graduation requirement for all students. Lastly, we describe several models of implementing an optional honors thesis for students. Although similarities exist across these programs, their differences allow for specific secondary objectives to be met, which are often unique to institutions and/or departments. Therefore, for each of these examples, we describe the context, specific design, and required student assessments. We conclude by discussing some of the key successes and challenges of developing programs that facilitate undergraduate research by upper-level students, and suggest a number of concepts that should be considered by individuals developing and assessing new programs.

Effectiveness of a Low-Cost, Graduate Student-Led Intervention on Study Habits and Performance in Introductory Biology

Institutions have developed diverse approaches that vary in effectiveness and cost to improve student performance in introductory science, technology, engineering, and mathematics courses. We developed a low-cost, graduate student-led, metacognition-based study skills course taught in conjunction with the introductory biology series at Miami University. Our approach aimed to improve performance for underachieving students by combining an existing framework for the process of learning (the study cycle) with concrete tools (outlines and concept maps) that have been shown to encourage deep understanding. To assess the effectiveness of our efforts, we asked 1) how effective our voluntary recruitment model was at enrolling the target cohort, 2) how the course impacted performance on lecture exams, 3) how the course impacted study habits and techniques, and 4) whether there are particular study habits or techniques that are associated with large improvements on exam scores. Voluntary recruitment attracted only 11-17% of our target cohort. While focal students improved on lecture exams relative to their peers who did not enroll, gains were relatively modest, and not all students improved. Further, although students across both semesters of our study reported improved study habits (based on pre and post surveys) and on outlines and concept maps (based on retrospectively scored assignments), gains were more dramatic in the Fall semester. Multivariate models revealed that, while changes in study habits and in the quality of outlines and concept maps were weakly associated with change in performance on lecture exams, relationships were only significant in the Fall semester and were sometimes counterintuitive. Although benefits of the course were offset somewhat by the inefficiency of voluntary recruitment, we demonstrate the effectiveness our course, which is inexpensive to implement and has advantage of providing pedagogical experience to future educators.

Substitution of critical isoleucines in the KH domains of Drosophila fragile X protein results in partial loss-of-function phenotypes

Fragile X mental retardation proteins (FMRP) are RNA-binding proteins that interact with a subset of cellular RNAs. Several RNA-binding domains have been identified in FMRP, but the contribution of these individual domains to FMRP function in an animal model is not well understood. In this study, we have generated flies with point mutations in the KH domains of the Drosophila melanogaster fragile X gene (dfmr1) in the context of a genomic rescue fragment. The substitutions of conserved isoleucine residues within the KH domains with asparagine are thought to impair binding of RNA substrates and perhaps the ability of FMRP to assemble into mRNP complexes. The mutants were analyzed for defects in development and behavior that are associated with deletion null alleles of dfmr1. We find that these KH domain mutations result in partial loss of function or no significant loss of function for the phenotypes assayed. The phenotypes resulting from these KH domain mutants imply that the capacities of the mutant proteins to bind RNA and form functional mRNP complexes are not wholly disrupted and are consistent with biochemical models suggesting that RNA-binding domains of FMRP can function independently.

The adult abdominal neuromuscular junction of Drosophila: a model for synaptic plasticity

During its life cycle, Drosophila makes two sets of neuromuscular junctions (NMJs), embryonic/larval and adult, which serve distinct stage-specific functions. During metamorphosis, the larval NMJs are restructured to give rise to their adult counterparts, a process that is integrated into the overall remodeling of the nervous system. The NMJs of the prothoracic muscles and the mesothoracic dorsal longitudinal (flight) muscles have been previously described. Given the diversity and complexity of adult muscle groups, we set out to examine the less complex abdominal muscles. The large bouton sizes of these NMJs are particularly advantageous for easy visualization. Specifically, we have characterized morphological attributes of the ventral abdominal NMJ and show that an embryonic motor neuron identity gene, dHb9, is expressed at these adult junctions. We quantified bouton numbers and size and examined the localization of synaptic markers. We have also examined the formation of boutons during metamorphosis and examined the localization of presynaptic markers at these stages. To test the usefulness of the ventral abdominal NMJs as a model system, we characterized the effects of altering electrical activity and the levels of the cell adhesion molecule, FasciclinII (FasII). We show that both manipulations affect NMJ formation and that the effects are specific as they can be rescued genetically. Our results indicate that both activity and FasII affect development at the adult abdominal NMJ in ways that are distinct from their larval and adult thoracic counterparts

A dominant negative form of Rac1 affects myogenesis of adult thoracic muscles in Drosophila

Blocking Rac1 function in precursors of the indirect flight muscle of Drosophila severely disrupts muscle formation. The DLM fibers that develop using larval scaffolds are reduced in number and fiber size, while the DVMs, which develop using founder cells, are mostly absent. These adult muscle phenotypes are in part due to a reduced myoblast pool present at the third larval instar. BrDU labeling studies indicated that this is primarily due to a reduction in proliferation. In addition, DVM myoblasts display altered morphology and are unable to segregate into primordia. This defect precedes the evident block in fusion. We also show that the recently described DVM founder cells can be labeled with 22C10 and beta-3 tubulin, and that they are present under conditions of dominant negative Rac1(N17) expression. Despite the presence of founder cells, DVM fiber formation is rarely observed. Although DLM myoblasts are able to segregate around their larval scaffolds, the pace of fusion is reduced and consequently there is a delay in DLM fiber formation. Thus, in addition to its well-established role in fusion, Rac1 is also involved in the regulation of myoblast proliferation and segregation during adult myogenesis. These are two new roles for Rac1 in Drosophila.

A role for Fas II in the stabilization of motor neuron branches during pruning in Drosophila

During insect metamorphosis, the nervous system is extensively remodeled resulting in the development of new circuits that will execute adult-specific behaviors. The peripheral remodeling seen during development of innervation to the Dorsal Longitudinal (flight) Muscle (DLM) in Drosophila involves an initial retraction of larval neuromuscular junctions followed by adult-specific branch outgrowth. Subsequently, a phase of pruning occurs during which motor neuron branches are pruned back to reveal the stereotypic pattern of multiple contact points (or arbors) along the length of each DLM fiber. In this study, we show that the cell adhesion molecule, Fasciclin II (Fas II), is important for generating the stereotypic pattern. In Fas II hypomorphs, the number of contact points is increased, and the phenotype is rescued by targeted expression of Fas II in either synaptic partner. Arbor development has three distinct phases: outgrowth and elaboration, pruning and stabilization, and expansion of stabilized arbors. Fas II is expressed during the first two phases. A subset of branches is labeled during the elaboration phase, which is likely to initiate a stabilization pathway allowing branches to survive the pruning phase. However, since not all Fas II positive branches are retained, we propose that it primes branches for stabilization. Our data suggest that Fas II functions to restrict branch length and arbor expanse.

Motoneurons regulate myoblast proliferation and patterning in Drosophila

Motoneurons directly influence the differentiation of muscle fibers, regulating features such as muscle fiber type and receptor development. Less well understood is whether motoneurons direct earlier events, such as the patterning of the musculature. In Drosophila, the denervation of indirect flight muscles results in a diminished myoblast population and smaller or missing muscle fibers. We have examined whether the neuron-dependent control of myoblast number is due to regulation of cell division, motoneuron-dependent apoptosis, or nerve-dependent localization and migration of myoblasts. We found that denervation resulted in a reduced rate of cell division, as revealed by BrDU incorporation. There was no change in the frequency of apoptotic myoblasts following denervation. Using time lapse imaging of GFP-expressing myoblasts in vivo in pupae, we observed that despite denervation, the migration and localization of myoblasts remained unchanged. In addition to reducing myoblast proliferation, denervation also altered the segregation of myoblasts into the de novo arising dorso-ventral muscles (DVMs). To address this effect on muscle patterning, we examined the expression of the founder-cell marker Dumbfounded/Kirre (Duf) in imaginal pioneer cells. We show that there is a strong correspondence between cells that express Dumbfounded/Kirre and the number of DVM fibers, consistent with a role for these cells in establishing adult muscles. In the absence of innervation the Duf-positive cells are no longer detected, and muscle patterning is severely disrupted. Our results support a model where specialized founder cells prefigure the adult muscle fibers under the control of the nervous system.

Pruning of motor neuron branches establishes the DLM innervation pattern in Drosophila

During the Drosophila life-cycle two sets of neuromuscular junctions are generated: the embryonic/larval NMJs develop during the first half, followed by the period of metamorphosis during which the adult counterpart is generated. Development of the adult innervation pattern is preceded by a withdrawal of larval NMJs, which occurs at the onset of metamorphosis, and is followed by adult-specific motor neuron outgrowth to innervate the newly developing adult fibers. Establishment of the adult innervation pattern occurs in the context of a broader restructuring of the nervous system, which results in the development of neural circuits that are necessary to carry out behaviors specific to the adult. In this article, we follow development of the dorsal longitudinal muscle (DLM) innervation pattern through metamorphosis. We find that the initial period of motor neuron elaboration is followed by a phase of extensive pruning resulting in a threefold reduction of neuromuscular contacts. This event establishes the adult pattern of second order branching. Subsequent higher order branching from the second order "contact" points generates the characteristic multiterminal innervation pattern of the DLMs. Boutons begin to appear after the pruning phase, and are much smaller than their larval counterparts. Additionally, we demonstrate that the DLM innervation is altered in the hyperexcitable double mutant, ether a go-go Shaker, and that the phenotype is suppressed by the hypoexcitable mutant, nap(ts1). Our results demonstrate that electrical activity regulates the patterning of DLM innervation during metamorphosis.

Distribution and genetic diversity of tomato-infecting begomoviruses in Brazil

Tomato-infecting begomoviruses have been reported throughout Brazil since the introduction of the B biotype of Bemisia tabaci. Here, we report a large scale survey on the distribution and genetic diversity of tomato-infecting begomoviruses. Tomato samples with typical begomovirus symptoms were collected in seven different states, comprising the major tomato growing areas of the country. Viruses were detected by polymerase chain reaction (PCR) using universal primers for the genus Begomovirus. PCR-amplified fragments were cloned and sequenced. Based on sequence comparisons and phylogenetic analyses, at least seven previously undescribed species of begomoviruses were found. Four of the new viruses were found exclusively in the Southeastern states, two exclusively in the Northeastern states, and one was found in both regions. Sequence comparisons reveal strong evidence of recombination among the Brazilian begomoviruses. Together, the results indicate the existence of a high degree of pre-existing genetic diversity among tomato-infecting begomoviruses in Brazil and suggest that these viruses have emerged after being transferred from natural hosts to tomatoes, due to the introduction into Brazil of a novel polyfagous biotype of the whitefly vector.

Widespread Occurrence of Tomato Geminiviruses in Brazil, Associated with the New Biotype of the Whitefly Vector

Although tomato golden mosaic virus (TGMV) was reported in Brazil more than 20 years ago (3), tomato-infecting geminiviruses have not been of economic significance in the country until recently. However, a sharp increase in the incidence of geminivirus-like symptoms in tomatoes has been reported in several areas of Brazil since 1994. This has coincided with the appearance of the B biotype of Bemisia tabaci, which, as opposed to the A biotype, readily colonizes solanaceous plants (2). We have isolated geminiviruses from symptomatic tomato plants in the Federal District, in two different areas of the state of Minas Gerais, and in the state of Pernambuco. Tomato plants in these areas showed a variety of symptoms, including yellow mosaic, severe leaf distortion, down-cupping, and epinasty. Whitefly infestation was high in all fields sampled, and in some fields, particularly in Pernambuco, incidence of virus-like symptoms was close to 100%, and no tomatoes of commercial value were harvested (1). Using primer pairs PAL1v1978/PAR1c496 and PCRc1/PBL1v2040 (4), DNA-A and -B fragments were polymerase chain reaction (PCR)-amplified from total DNA extracted from diseased plants, cloned, and sequenced. Sequence comparisons of the PCR fragments indicated the existence of at least six different geminiviruses. The nucleotide sequence homologies for DNA-A fragments ranged from 67 to 80% for the 5' end of the cp gene, and from 44 to 80% for the 5' end of the rep gene. Data base comparisons indicated the viruses are most closely related to TGMV, bean golden mosaic virus from Brazil (BGMV-Br), and tomato yellow vein streak virus (ToYVSV), although homologies were less than 80% for the fragments compared. A similar lack of a close relationship with each other and other geminiviruses was obtained with two DNA-B component PCR products compared, corresponding to the 5' end of the BC1 open reading frame. Infectious, full-length genomic clones from the tomato viruses are being generated for biological and molecular characterization. References: (1) I. C. Bezerra et al. Fitopatol. Bras. 22:331, 1997. (2) F. H. França et al., Ann. Soc. Entomol. Bras. 25:369, 1996. (3) J. C. Matyis et al. Summa Phytopathol. 1:267, 1975. (4) M. R. Rojas et al. Plant Dis. 77:340, 1993.

Nerve-muscle interactions during flight muscle development in Drosophila

During Drosophila pupal metamorphosis, the motoneurons and muscles differentiate synchronously, providing an opportunity for extensive intercellular regulation during synapse formation. We examined the existence of such interactions by developmentally delaying or permanently eliminating synaptic partners during the formation of indirect flight muscles. When we experimentally delayed muscle development, we found that although adult-specific primary motoneuron branching still occurred, the higher order (synaptic) branching was suspended until the delayed muscle fibers reached a favourable developmental state. In reciprocal experiments we found that denervation caused a decrease in the myoblast pool. Furthermore, the formation of certain muscle fibers (dorsoventral muscles) was specifically blocked. Exceptions were the adult muscles that use larval muscle fibers as myoblast fusion targets (dorsal longitudinal muscles). However, when these muscles were experimentally compelled to develop without their larval precursors, they showed an absolute dependence on the motoneurons for their formation. These data show that the size of the myoblast pool and early events in fiber formation depend on the presence of the nerve, and that, conversely, peripheral arbor development and synaptogenesis is closely synchronized with the developmental state of the muscle.

Patterning the dorsal longitudinal flight muscles (DLM) of Drosophila: insights from the ablation of larval scaffolds

The six Dorsal Longitudinal flight Muscles (DLMs) of Drosophila develop from three larval muscles that persist into metamorphosis and serve as scaffolds for the formation of the adult fibers. We have examined the effect of muscle scaffold ablation on the development of DLMs during metamorphosis. Using markers that are specific to muscle and myoblasts we show that in response to the ablation, myoblasts which would normally fuse with the larval muscle, fuse with each other instead, to generate the adult fibers in the appropriate regions of the thorax. The development of these de novo DLMs is delayed and is reflected in the delayed expression of erect wing, a transcription factor thought to control differentiation events associated with myoblast fusion. The newly arising muscles express the appropriate adult-specific Actin isoform (88F), indicating that they have the correct muscle identity. However, there are frequent errors in the number of muscle fibers generated. Ablation of the larval scaffolds for the DLMs has revealed an underlying potential of the DLM myoblasts to initiate de novo myogenesis in a manner that resembles the mode of formation of the Dorso-Ventral Muscles, DVMs, which are the other group of indirect flight muscles. Therefore, it appears that the use of larval scaffolds is a superimposition on a commonly used mechanism of myogenesis in Drosophila. Our results show that the role of the persistent larval muscles in muscle patterning involves the partitioning of DLM myoblasts, and in doing so, they regulate formation of the correct number of DLM fibers.

Development of the indirect flight muscle attachment sites in Drosophila: role of the PS integrins and the stripe gene

Using markers that are expressed at muscle attachment sites, we have examined the early pupal development (first 36 hr) of Indirect Flight Muscle (IFM) attachments in the fruit fly Drosophila melanogaster. Expression of the Drosophila homologs of vertebrate integrins, the Position-Specific (PS) antigens, is known to differentially mark epidermal (PS1alpha) and muscle (PS2alpha) components of the developing IFM attachment sites. During myogenesis, PS2alpha is detected transiently in imaginal myoblasts that fuse with persistent larval muscles to give rise to the Dorsal Longitudinal Muscles (DLMs), but not in myoblasts that fuse de novo to give rise to the Dorso Ventral Muscles. The integrins are not expressed at attachment sites when the muscle fibers first make their appearance (12-20 hr). Following muscle-epidermal contact, PS1 and PS2 are detected at muscle attachment sites. PS1 expression is at the muscle ends and also in the long epidermal processes that connect the developing muscle fibers to their sites of attachment in the epidermis, while PS2 expression is restricted to the muscle ends. Epidermal cells that will contribute to the adult attachment sites are defined as early as the third larval instar. Both anterior and posterior sites of attachment of the IFMs are marked by the expression of reporter beta-galactosidase activity in a P-element line B14.0, which is an insertion at the stripe locus. B14.0 (stripe) is seen in distinct domains in the wing and leg imaginal discs which give rise to the thoracic cuticle. The expression is maintained during pupal development. The B14.0 (stripe) expressing epidermal cells contact the developing muscle fibers, leading to the formation of the myotendon junction. We show that the dorsal and ventral attachment sites of one group of IFMs, the DVMs arise from two different imaginal discs (wing and leg, respectively), which may explain the differential effect of mutations such as bendless on these muscles. Attachment sites for the other group of IFMs, the DLMs, on the other hand, arise from one imaginal disc (wing). B14.0 (stripe) expression defines epidermal cells of the adult attachment sites and is likely to function during early events leading to the formation of muscle-epithelial contacts. The PS integrins are detected at later stages, suggesting a role in the stabilization and maturation of the muscle-epidermal contacts into myotendon junctions.

Hepatitis testing update

During a 25-year period, four types of hepatitis-causing virus have been identified and can now be evaluated serologically. This final article in this clinical laboratory medicine series reviews routes of virus transmission and persistence and the availability of tests.

Therapeutic drug monitoring: lithium levels

Lithium has been used in the treatment of mania since 1949. Although its effectiveness is well recognized, the mechanism by which it stabilizes manic behavior is not well understood. In addition, it has some serious toxic properties combined with a narrow therapeutic range. For this reason, monitoring of serum lithium levels is mandatory. Suggested mechanisms of action and protocols for monitoring of serum levels are presented.

DNA technology

Scientific developments in molecular biology enable clinical laboratory testing to directly examine genetic information coded in biologic specimens. These efforts, accomplished by the use of DNA probe technology in the in situ hybridization and other tests will allow for the specific identification of pathogens; recognition of genetic diseases; and the critical evaluation of the genetic basis of cancer. The authors discuss the concepts and uses of DNA testing.

Human immunodeficiency virus testing: update

Human immunodeficiency virus (HIV) types 1 and 2 have been associated with the acquired immunodeficiency syndrome (AIDS). The detection of HIV infections is based on the screening of serum samples for the presence of antibodies to HIV proteins. Serum samples that test positive on screening must be assayed by a confirmatory test to provide a definitive report on the presence of HIV infection. This article reviews the currently available screening and confirmatory testing procedures and their limitations.

Group A Streptococcus detection: office versus reference laboratory

Clinical differentiation between a virus and beta-hemolytic streptococci as a cause of pharyngitis remains difficult. In the physician's laboratory, more rapid procedures using immunologic methods have replaced culture methods, traditionally requiring 2 to 3 days for identification of beta-hemolytic streptococci. Attention to the diagnostic sensitivity and specificity of these procedures will guide appropriate use.

Realistic expectations of laboratory testing

The ordering, reviewing, and interpreting of laboratory tests require recognition and familiarity with the concepts of normal values, sensitivity, specificity, predictive values, and prevalence. The significance of these test properties in clinical decision-making is explained.

Laboratory instruments for the physician's office laboratory: technology and cost-benefits

During the past two decades, medicine has witnessed the decentralization of laboratory testing from the hospital into the physician's office. This article focuses on the technical aspects of the instruments now available for laboratory testing in the physician's office. Consideration is given to specific instruments, methods, and cost-benefit.

Blood ethanol testing

The justification for blood ethanol testing springs from the ubiquitous abuse of alcoholic beverages. Those dealing with patients who abuse alcohol must understand the correlations between dose, time, blood level, and behavior. Enumerated here are the strengths of various testing methods and the requisites for legally defensible testing. The challenge remains to determine blood ethanol levels in such a manner that the results are scientifically valid and legally defensible.

Metastasis of prostate gland adenocarcinoma to penile and scrotal cutaneous tissues

The metastatic sites of adenocarcinoma of the prostate are well documented. Bone metastasis is the most frequently encountered site. Skin metastasis is rarely reported. Its presence, however, is associated with a poor prognosis. The possible cause of cutaneous spread is discussed in the case report. The possible role that external-beam radiotherapy may play in this setting is also analyzed.