Students' Experiences and Perceptions of the Scientific Research Culture after Participating in Different Course-Based Undergraduate Research Experience Models

Undergraduate students interact with the culture of scientific research when they participate in direct mentorship experiences and laboratory courses such as course-based undergraduate research experiences (CUREs). Much work has been done to explore how CUREs impact the interest, motivation, and retention of undergraduate students in science. However, little work has been done exploring students' experiences and perceptions of the culture of scientific research in the CURE context, and how different CURE models representing different subfields of science impact these experiences and perceptions. This study explored which cultural aspects of scientific research students experienced after participating in a CURE and whether their perceptions of those cultural aspects differed based on students' participation in a bench-based or computer-based research project. Students discussed the Practices and Norms/Expectations of scientific research most frequently. Students in the bench-based and computer-based project areas mentioned different cultural aspects as important to their experiences. Bench-based and computational students also had different perceptions of some of the same cultural aspects, including Teamwork, Freedom & Independence, and Persistence & Resilience. These results suggest that different CURE models differentially impact students' experiences and perceptions of the culture of scientific research, which has implications for examining how students move into scientific research.

Improving Students' Understanding of Biological Variation in Experimental Design and Analysis through a Short Model-Based Curricular Intervention

When conducting biological investigations, experts constantly integrate their conceptual and quantitative understanding of variation with the design and analysis of the investigation. This process is difficult for students, because curricula often treat these concepts as separate components. This study describes the effect of a curricular intervention aimed at improving students' conceptual and quantitative understanding of variation in the context of experimental design and analysis. A model-based intervention curriculum consisting of five short modules was implemented in an introductory biology laboratory course. All students received the regular laboratory curriculum, and half of the students also received the Intervention curriculum. Students' understanding of variation was assessed using a published 16-question multiple-choice instrument designed and validated by the research team. Students were assessed before and after the intervention was implemented, and normalized gain scores were calculated. Students who received the intervention showed significantly higher normalized gains than students who did not receive the intervention. This effect was not influenced by students' gender or exposure to prior statistics courses and persisted into and through the following semester's laboratory course. These results provide support for the use of model-based approaches to improve students' understanding of biological variation in experimental design and analysis.

Development of a Framework for the Culture of Scientific Research

Scientific research has a culture that can be challenging to enter. Different aspects of this culture may act as barriers or entry points for different people. Recognition of these barriers and entry points requires identifying aspects of the culture of scientific research and synthesizing them into a single, descriptive framework. A systematic literature review encompassing a two-pronged search strategy, descriptive mapping of ideas, and consensus building, was performed to identify aspects of scientific research culture. This resulted in the Culture of Scientific Research (CSR) Framework, composed of 31 cultural aspects categorized as either Practices, Norms/Expectations, or Values/Beliefs. Additional evidence of validity was collected through a survey that asked biological researchers to indicate which aspects in the framework were relevant to their experiences of research. The majority of survey respondents (n = 161) perceived the 31 aspects in the CSR Framework as relevant to biological research. This framework provides a consistent structure for describing the experiences of people engaging with the culture of scientific research. The literature review included literature from multiple disciplines, so the CSR Framework should be broadly applicable. Future applications of the CSR Framework include identifying possible barriers and entry points experienced by groups currently underrepresented in scientific research.

Paired Multiple-Choice Questions Reveal Students' Incomplete Statistical Thinking about Variation during Data Analysis

Biologists consider variability during biological investigations. A robust quantitative understanding of variability is particularly important during data analysis, where statistics are used to quantify variation and draw conclusions about phenomena while accounting for variation. Many students struggle to correctly apply a quantitative understanding of variation to statistically analyze data. We present quantitative and qualitative analyses of introductory biology students' responses on two pairs of multiple-choice questions querying two concepts related to the quantitative analysis of variation. More students correctly identify a mathematical expression of variation than correctly interpret it. Many students correctly interpret a nonsignificant p-value in the context of a very small sample size, but fewer students do so in the context of a large sample size. These results imply that many students have an incomplete quantitative understanding of variation. These findings suggest that instruction focusing on conceptual understanding, not procedural problem solving, may elevate students' quantitative understanding of variation.

Development of the Biological Variation In Experimental Design And Analysis (BioVEDA) assessment

Variation is an important concept that underlies experimental design and data analysis. Incomplete understanding of variation can preclude students from designing experiments that adequately manage organismal and experimental variation, and from accurately conducting and interpreting statistical analyses of data. Because of the lack of assessment instruments that measure students' ideas about variation in the context of biological investigations, we developed the Biological Variation in Experimental Design and Analysis (BioVEDA) assessment. Psychometric analyses indicate that BioVEDA assessment scores are reliable/precise. We provide evidence that the BioVEDA instrument can be used to evaluate students' understanding of biological variation in the context of experimental design and analysis relative to other students and to their prior scores.

Exploring Students' Descriptions of Mutation from a Cognitive Perspective Suggests How to Modify Instructional Approaches

Prior studies have shown that students have difficulty understanding the role of mutation in evolution and genetics. However, little is known about unifying themes underlying students' difficulty with mutation. In this study, we examined students' written explanations about mutation from a cognitive science perspective. According to one cognitive perspective, scientific phenomena can be perceived as entities or processes, and the miscategorization of processes as entities can lead to noncanonical ideas about scientific phenomena that are difficult to change. Students' incorrect categorization of processes as entities is well documented in physics but has not been studied in biology. Unlike other scientific phenomena that have been studied, the word "mutation" refers to both the process causing a change in the DNA and the entity, the altered DNA, making mutation a relevant concept for exploration and extension of this theory. In this study, we show that, even after instruction on mutation, the majority of students provided entity-focused descriptions of mutation in response to a question that prompted for a process-focused description in a lizard or a bacterial population. Students' noncanonical ideas about mutation occurred in both entity- and process-focused descriptions. Implications for conceptual understanding and instruction are discussed.

Computer-Based and Bench-Based Undergraduate Research Experiences Produce Similar Attitudinal Outcomes

Course-based undergraduate research experiences (CUREs) have the potential to improve undergraduate biology education by involving large numbers of students in research. CUREs can take a variety of forms with different affordances and constraints, complicating the evaluation of design features that might contribute to successful outcomes. In this study, we compared students' responses to three different research experiences offered within the same course. One of the research experiences involved purely computational work, whereas the other two offerings were bench-based research experiences. We found that students who participated in computer-based research reported at least as much interest in their research projects, a higher sense of achievement, and a higher level of satisfaction with the course compared with students who did bench-based research projects. In open-ended comments, similar proportions of students in each research area expressed some sense of project ownership as contributing positively to their course experiences. Their comments also supported the finding that experiencing a sense of achievement was a predictor of course satisfaction. We conclude that both computer-based and bench-based CUREs can have positive impacts on students' attitudes. Development of more computer-based CUREs might allow larger numbers of students to benefit from participating in a research experience.

Evaluation of oxygen transfer efficiency under process conditions using the dynamic off-gas method

The off-gas method can be used to investigate standard oxygen transfer efficiencies under process conditions (alphaSOTE) over the operating life of an aeration system. A method to evaluate alphaSOTE is described in detail by US and German standards. The standards, however, do not describe how to evaluate dynamic changes in aSOTE over a day, which can be useful to uncover problems and unfavourable process conditions. Based on over three years experience gained in off-gas testing in Berlin wastewater treatment plants (WWTPs) under operating conditions, a method to evaluate and interpret the dynamic changes in oxygen transfer is presented. The application of the dynamic off-gas method brings important additional information, which can be used to increase operational efficiency of the aeration basin and to increase process reliability, with a relatively small increase in effort. This paper shows how to perform dynamic measurements under process conditions. Some results of such measurements under dynamic process conditions, performed in a Berlin WWTP, are discussed.

Evaluation of ceramic and membrane diffusers under operating conditions with the dynamic offgas method

The aeration systems of two full-scale, activated-sludge basins were compared during a period of three years, under the same operating conditions, using dynamic offgas testing. Only the material of the diffuser was different (membrane versus ceramic-tube diffusers). The investigation has shown that, although the membrane diffusers have higher initial standard-oxygen-transfer efficiency (alphaSOTE) and standard-aeration efficiency (alphaSAE), these decreased over time, while the alphaSAE of the ceramic diffusers started lower, but increased slightly over the whole period. A cost comparison makes clear how important it is to evaluate the aeration system under process conditions. The operating costs were the dominant factor (approximately 10x higher than capital costs), and operating costs were approximately 20% higher for membrane versus ceramic diffusers. The poor performance of the membrane-tube diffusers under process conditions could be explained on the basis of the actual alphaAE values in the basin, not the standardized values.

Potential of OUR and OTR measurements for identification of activated sludge removal processes in aerated basins

In order to develop a process control scheme to reduce energy costs for aeration in activated sludge systems with biological P removal, pre-denitrification and nitrification stages, the spatial distribution of carbon oxidation and nitrification was evaluated over a long full-scale plug flow aeration basin using an externally measured specific oxygen uptake rate (sOUR) and in basin measurement of the actual specific oxygen transfer rate (sOTR) with off-gas testing as well as with the calculated oxygen demand from NH4-N concentrations (sOTR(N)). Using a simple static model, a gas phase balance on oxygen and carbon dioxide, sOTR(N) values were also calculated from off-gas testing. Comparison of sOTR(N) to sOTR and sOUR for carbon oxidation (sOUR(C)) to nitrification (sOUR(N)) at different loading conditions allowed the oxidation processes to be followed over the three zones of the aeration basin. As expected, the distribution depended on the dissolved oxygen concentration (DO) in the basin. However, the major change was in the C-oxidation rate and not the nitrification rate. At a low DO, and when NH4-N was present in the zone, the amount of oxygen transferred for nitrification was nearly the same, but the overall sOTR was lower. The externally measured sOUR was only useful when it was differentiated into sOUR(N) and sOUR(C). sOUR(N) could be used to predict the nitrification rate in the basin. With further refinement, the gas phase balance model has potential to be used to monitor the degree of nitrification over the basin length. This can be integrated into a control scheme to reduce aeration costs by adjusting the DO setpoint according to loading conditions in the

A control strategy for reducing aeration costs during low loading periods

The efficiency of the aeration system in a full-scale activated sludge basin with 3 separately controlled aeration zones was improved for the low loading period in summer. The air flow rate to each aeration zone is currently regulated to hold a preset dissolved oxygen concentration (DO). Four different DO setpoint combinations were tested, each one for a one week period, using dynamic off-gas testing to measure the standardised oxygen transfer efficiency (alphaSOTE). As the DO setpoints were lowered, the total air flow rate to the basin decreased initially. A low DO in the first zones slowed biomass activity and pushed the load towards the end of the aeration basin. The relationship between alphaSOTE and the specific diffuser flow rate qD is different for each zone. In Zone 1 there was a strong decrease in alphaSOTE as qD increased, while Zones 2 and 3 were fairly independent of qD, Zone 2 at a higher level than Zone 3. Aeration costs were reduced by 15% for the most efficient combination. To achieve even more savings, a control strategy adjusting oxygen transfer rates over the aeration basin to the necessary oxygen transfer rates is suggested. It is based on changing the DO setpoints to reach the lowest total air flow rate while meeting the effluent requirements.

Distal ureter morphogenesis depends on epithelial cell remodeling mediated by vitamin A and Ret

Almost 1% of human infants are born with urogenital abnormalities, many of which are linked to irregular connections between the distal ureters and the bladder. During development, ureters migrate by an unknown mechanism from their initial integration site in the Wolffian ducts up to the base of the bladder in a process that we call ureter maturation. Rara(-/-) Rarb2(-/-) mice display impaired vitamin A signaling and develop syndromic urogenital malformations similar to those that occur in humans, including renal hypoplasia, hydronephrosis and mega-ureter, abnormalities also seen in mice with mutations in the proto-oncogene Ret. Here we show that ureter maturation depends on formation of the 'trigonal wedge', a newly identified epithelial outgrowth from the base of the Wolffian ducts, and that the distal ureter abnormalities seen in Rara(-/-) Rarb2(-/-) and Ret(-/-) mutant mice are probably caused by a failure of this process. Our studies indicate that formation of the trigonal wedge may be essential for correct insertion of the distal ureters into the bladder, and that these events are mediated by the vitamin A and Ret signaling pathways.

Comparison of the efficiency of large-scale ceramic and membrane aeration systems with the dynamic off-gas method

The aeration systems of two full-scale activated sludge basins were compared over 2.5 years under the same operating conditions using dynamic off-gas testing. Only the material of the diffuser was different, membrane vs. ceramic tube diffusers. The experimental design took the complexity and dynamics of the system into consideration. The investigation has shown that, although the membrane diffusers have higher initial standard oxygen transfer efficiency (SOTE) and standard aeration efficiency (SAE), these decreased over time, while the SAE of the ceramic diffusers started lower, but increased slightly over the whole period. Measurement of air distribution in the basins along with dissolved oxygen concentration profiles have provided important information on improving process control and reducing energy costs. The results show that dynamic off-gas testing can effectively be used for monitoring the aeration system and to check design assumptions under operating conditions. The information can be used to improve the design of new aeration systems or in retro-fitting existing basins.

BMPs as mediators of roof plate repulsion of commissural neurons

During spinal cord development, commissural (C) neurons, located near the dorsal midline, send axons ventrally and across the floor plate (FP). The trajectory of these axons toward the FP is guided in part by netrins. The mechanisms that guide the early phase of C axon extension, however, have not been resolved. We show that the roof plate (RP) expresses a diffusible activity that repels C axons and orients their growth within the dorsal spinal cord. Bone morphogenetic proteins (BMPs) appear to act as RP-derived chemorepellents that guide the early trajectory of the axons of C neurons in the developing spinal cord: BMP7 mimics the RP repellent activity for C axons in vitro, can act directly to collapse C growth cones, and appears to serve an essential function in RP repulsion of C axons.

RET proto-oncogene is important for the development of respiratory CO2 sensitivity

Brain stem muscarinic cholinergic pathways are important in respiratory carbon dioxide (CO2) chemosensitivity. Defects in the muscarinic system have been reported in children with congenital/developmental disorders of respiratory control such as sudden infant death syndrome (SIDS) and congenital central hypoventilation syndrome (CCHS). This early onset of disease suggests a possible genetic basis. The muscarinic system is part of the autonomic nervous system which develops from the neural crest. Ret proto-oncogene is important for this development. Thus, a potential role for ret in the development of respiratory CO2 chemosensitivity was considered. Using plethysmography, we assessed the ventilatory response to inhaled CO2 in the unanesthetized offsprings of ret +/- mice. Fractional increases in minute ventilation during hypercapnia relative to isocapnia were 5.1 +/- 3.2, 3.0 +/- 1.6 and 1.4 +/- 0.8 for the ret +/+, ret +/- and ret +/- mice, respectively. The ret knockout mice have a depressed ventilatory response to inhaled CO2. Therefore, the ret gene is an important factor in the pathway of neuronal development which allow respiratory CO2 chemosensitivity.

Increased expression of laminin-1 and collagen (IV) subunits in the aganglionic bowel of ls/ls, but not c-ret -/- mice

Extracellular matrix molecules, including laminin, affect the development of enteric neurons and accumulate in the aganglionic colon of ls/ls mice. Quantitative Northern analysis revealed that mRNAs encoding the beta 1 and gamma 1 subunits of laminin and collagens alpha 1(IV) and alpha 2(IV) are increased in the colons of ls/ls mice. Transcripts of laminin alpha 1 were evaluated quantitatively with reverse transcription and the competitive polymerase chain reaction (RT-cPCR). The abundance of laminin alpha 1 transcripts was developmentally regulated, but greater in the ls/ls than the wild-type colon at each age examined. In situ hybridization revealed that transcripts in the colon encoding laminin alpha 1 and beta 1 and collagen alpha 2(IV) were initially expressed in the endoderm, but by E15, expression shifted to cells of the colonic mesenchyme (ls/ls > wild type) where crest-derived cells migrate. The expression of laminin alpha 1 was examined in the totally aganglionic intestine of E15 and newborn c-ret -/- mice, to determine whether an increase occurs when neurogenesis fails independently of the ls/ls defect. RT-cPCR revealed no difference from control in mRNA encoding laminin alpha 1 in the c-ret -/- colon in either E15 or newborn animals. The accumulation of immunohistochemically demonstrable laminin that is prominent in the newborn ls/ls colon could not be detected in that of c-ret -/- animals. These observations suggest that transcripts encoding laminin-1 and collagen (IV) are increased in the colon and surrounding pelvic mesenchyme of ls/ls mice because of an intrinsic lesion, rather than a secondary consequence of aganglionosis. The data are compatible with the hypothesis that the increased expression of laminin-1 contributes to the failure of crest-derived cells to complete their colonization of the ls/ls colon.

Renal agenesis and hypodysplasia in ret-k- mutant mice result from defects in ureteric bud development

The c-ret gene encodes a receptor tyrosine kinase that is expressed in the Wolffian duct and ureteric bud of the developing excretory system. Newborn mice homozygous for a mutation in c-ret displayed renal agenesis or severe hypodysplasia, suggesting a critical role for this gene in metanephric kidney development. To investigate the embryological basis of these defects, we characterized the early development of the excretory system in mutant homozygotes, and observed a range of defects in the formation, growth and branching of the ureteric bud, which account for the spectrum of renal defects seen at birth. Co-culture of isolated ureteric buds and metanephric mesenchyme show that the primary defect is intrinsic to the ureteric bud. While the mutant bud failed to respond to induction by wild-type mesenchyme, mutant mesenchyme was competent to induce the growth and branching of the wild-type bud. Furthermore, the mutant metanephric mesenchyme displayed a normal capacity to differentiate into nephric tubules when co-cultured with embryonic spinal cord. These findings suggest a model in which c-ret encodes the receptor for a (yet to be identified) factor produced by the metanephric mesenchyme, which mediates the inductive effects of this tissue upon the ureteric bud. This factor appears to stimulate the initial evagination of the ureteric bud from the Wolffian duct, as well as its subsequent growth and branching.

Common origin and developmental dependence on c-ret of subsets of enteric and sympathetic neuroblasts

c-ret encodes a tyrosine kinase receptor that is necessary for normal development of the mammalian enteric nervous system. Germline mutations in c-ret lead to congenital megacolon in humans, while a loss-of-function allele (ret.k-) causes intestinal aganglionosis in mice. Here we examine in detail the function of c-ret during neurogenesis, as well as the lineage relationships among cell populations in the enteric nervous system and the sympathetic nervous system that are dependent on c-ret function. We report that, while the intestine of newborn ret.k- mice is devoid of enteric ganglia, the esophagus and stomach are only partially affected; furthermore, the superior cervical ganglion is absent, while more posterior sympathetic ganglia and the adrenal medulla are unaffected. Analysis of mutant embryos shows that the superior cervical ganglion anlage is present at E10.5, but absent by E12.5, suggesting that c-ret is required for the survival or proliferation of sympathetic neuroblasts. In situ hybridization studies, as well as direct labelling of cells with DiI, indicate that a common pool of neural crest cells derived from the postotic hindbrain normally gives rise to most of the enteric nervous system and the superior cervical ganglion, and is uniquely dependent on c-ret function for normal development. We term this the sympathoenteric lineage. In contrast, a distinct sympathoadrenal lineage derived from trunk neural crest forms the more posterior sympathetic ganglia, and also contributes to the foregut enteric nervous system. Overall, our studies reveal previously unknown complexities of cell lineage and genetic control mechanisms in the developing mammalian peripheral nervous system.

RET-deficient mice: an animal model for Hirschsprung's disease and renal agenesis

Receptor tyrosine kinases play a critical role in transducing signals involved in cell growth and differentiation. The c-ret proto-oncogene is a member of the receptor tyrosine kinase gene superfamily originally identified by its transforming ability. Somatic mutations of c-ret are responsible for a large proportion of thyroid papillary carcinomas, while germ-line mutations are responsible for multiple endocrine neoplasia types 2A and 2B, dominantly inherited cancer syndromes characterized by multiple tumours of neuroectodermal origin. In addition to its role in tumour formation. c-ret is thought to have a developmental role since mutations of the gene have been implicated in the aetiology of Hirschsprung's syndrome (congenital megacolon). A targeted mutation in the murine c-ret locus shows that the ret receptor is required for normal development of two lineally unrelated systems, the excretory system and the enteric nervous system.

Isolation and characterization of a chicken homolog of the c-ret proto-oncogene

The c-ret proto-oncogene encodes a receptor tyrosine kinase that plays important roles in human disease and in normal mammalian development. Mutations in the human RET gene are associated with multiple endocrine neoplasia syndromes and Hirschsprung's disease in humans, while targeted mutagenesis of murine c-ret resulted in severe developmental abnormalities affecting the excretory and peripheral nervous systems. To examine the evolutionary conservation of the ret protein sequence and its developmental expression pattern, we isolated and sequenced cDNA clones of chicken c-ret and examined its expression in chick embryos and adult tissues. The cytoplasmic domains of chicken and human ret were relatively well conserved (91% similar), but the extracellular domains were more divergent (68% similar), although the conservation of cysteine residues in this region suggests a conserved secondary structure. As in mouse and human, chicken c-ret encodes two protein isoforms. The number and sizes of the transcripts were similar to those in human and mouse cells, and during chick embryogenesis, c-ret mRNA was observed in many of the same sites as in the mouse, including the Wolffian duct and ureteric bud, the enteric, dorsal root, sympathetic and facioacoustic ganglia, and the ventral spinal cord. Evolutionary differences in expression were observed in the trigeminal ganglion, the ventral roots of the spinal cord, the mesenchymal cells of the branchial arches and the adult testes. The results are discussed with regard to the role of the ret receptor in normal development and disease.

Defects in the kidney and enteric nervous system of mice lacking the tyrosine kinase receptor Ret

Receptor tyrosine kinases (RTKs) are cell-surface molecules that transduce signals for cell growth and differentiation. The RTK encoded by the c-ret proto-oncogene is rearranged and constitutively activated in a large proportion of thyroid papillary carcinomas, and germ-line point mutations in c-ret seem to be responsible for the dominantly inherited cancer syndromes multiple endocrine neoplasia (MEN) types 2A and B. The gene is expressed in the developing central and peripheral nervous systems (sensory, autonomic and enteric ganglia) and the excretory system (Wolffian duct and ureteric bud epithelium) of mice, indicating that it may play a role in normal development. Here we show that mice homozygous for a targeted mutation in c-ret develop to term, but die soon after birth, showing renal agenesis or severe dysgenesis, and lacking enteric neurons throughout the digestive tract. Ret is thus an essential component of a signalling pathway required for renal organogenesis and enteric neurogenesis.