Search

The magnitude and scale of current threats to ecosystems requires interdisciplinary approaches to both science and training. For example, urbanization has resulted in increased runoff from communities into coastal habitats, necessitating work across the marine-terrestrial interface. This runoff holds myriad pollutants which can impact vulnerable ecosystems, such as coastal rocky reefs. I evaluated two pollutants in domestic runoff, nitrogen-based nutrients and glyphosate-based herbicides, and their effects on rocky intertidal biodiversity and ecosystem health. Biweekly measurements were taken from runoff-affected tidepools, runoff-unaffected tidepools, drain sources, and the ocean to assess levels of both nutrients and glyphosate at our Southern California field site. Further, I experimentally added nutrients to tidepools and dosed the green seaweed "Ulva" sp. with glyphosate to determine the extent of effect these pollutants would exert on the ecosystem. In chapter 1, I showed that nitrate + nitrite concentrations varied over time, with runoff-affected tidepools exhibiting significantly higher concentrations than control tidepools. Internal nitrogen concentrations in "Ulva" correlated positively with nitrate + nitrite concentrations, and total grazer biomass increased with higher internal nitrogen in "Ulva." Experimental nitrogen additions enhanced "Ulva" cover compared to control pools. In chapter 2, I showed elevated glyphosate concentrations exceeding EPA safe drinking-water limits in the field, with substantial pH reductions observed at low glyphosate concentrations. These findings indicate that increased nutrients lead to bottom-up effects on nutrient cycling, and that reduction in pH associated with glyphosate has the potential for appreciable reduction in local pH. My findings underscore the need for regulatory consideration of these pollutants in coastal management, especially in protected areas, to mitigate risks to marine ecosystems and human health. However, environmental challenges, such as polluted freshwater runoff, are global in both scope and scale. Interdisciplinary and collaborative approaches to research can be used to better address these complex issues, and in chapter 3, I describe a graduate training program that centers these approaches. The Ridge 2 Reef National Science Foundation Research Traineeship Program was developed to provide transferable and cross-disciplinary training to graduate students of various academic backgrounds. The program was successful in improving the communication skills, career knowledge, and understanding of global perspectives in research of the trainees. The interdisciplinary and collaborative approaches to training were also successful in increasing trainee confidence and preparedness for environmental career paths. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com/en-US/products/dissertations/individuals.shtml.]

In an increasingly complex world, it is imperative that undergraduate science courses prepare students to make confident, informed decisions and predictions. The research presented in this thesis focuses on supporting students to engage in mechanistic reasoning (MR) about phenomena in chemistry and biology (that is, thinking about how and why these phenomena occur). Using a resources perspective of student knowledge construction, I investigated and characterized explanations for two phenomena: (1) preferential protein-ligand binding, leveraging ideas about electrostatic forces and interactions; and (2) ATP-driven coupled reactions, leveraging ideas about energy, reactivity, and favorability. We collected and analyzed over a thousand student responses for the protein-ligand binding task, a previously developed task that elicits productive student ideas and MR as a thinking strategy. Students across chemistry and biology courses engaged in MR to varying extents, but the responses that were fully mechanistic nearly always correlated with a correct prediction, suggesting the predictive power of this reasoning strategy. With a large selection of responses and access to demographic characteristics, I then calculated an ordinal regression model to determine if GPA, race/ethnicity, and/or binary gender predicted student engagement in MR. Binary gender identification did not contribute as a predictor; however, students with a higher GPA had significantly higher odds of engaging fully in MR, and being White (compared to Non-White), to a lesser extent than GPA, also resulted in higher odds of engaging fully in MR. In subsequent studies, I investigated student and instructor understandings of the role of ATP, an integral biological molecule that is directly related to energy, a core idea in both chemistry and biology, suggesting another opportunity for interdisciplinary learning. Due to the widespread misconception that breaking bonds releases energy, which is frequently associated with language about the "high-energy bond(s)" in ATP, we aimed to uncover a more coherent, mechanistic way of talking about ATP. To do this, we first interviewed a range of chemistry, biology, and biochemistry faculty to learn how they explain and teach the mechanism by which ATP provides energy. The findings from this study informed my final study, in which we designed a task that supports students' understanding of the mechanism by which ATP drives the unfavorable formation of glutamine from glutamate and ammonium. We focus specifically on the role of ATP in transferring a phosphoryl group to create a reactive intermediate, avoiding the common, yet irrelevant, ideas about ATP hydrolysis and bond energy. After working through this task, both molecular biology and organic chemistry students included more mechanistic resources in their final explanations about the role of ATP, suggesting the potential of formative tasks as learning opportunities for students to advance and refine their productive resources. The findings from these four studies point to the challenge, but importance, of incorporating MR into undergraduate science courses. Leveraging interdisciplinary thinking and MR are ways to support making informed decisions as citizens; for example, reasoning about how and why vaccines prevent the spread of infectious diseases, among other reasoning strategies (e.g., social and historical), can support one to make an informed choice. Further, many of the students we serve are pre-health majors, meaning they will pursue careers which often require deep reasoning and understanding about how or why symptoms occur, potential side effects of treatments, and how to appropriately address challenging decisions. MR is an important tool for certain contexts to ultimately help them do this. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com/en-US/products/dissertations/individuals.shtml.]

The central focus of my dissertation concerns the issue of representation. The issue of representation is important for science education research for two reasons: (1) the use of external representation in science teaching and learning, particularly in chemistry education, is ubiquitous as microscopic entities are not directly visible, and (2) the study of student learning relies on linguistic representation of student conceptions as thoughts are not directly visible. Therefore, the issue of representation is an issue of making the invisible visible, more specifically, an issue of making differences, whether differences among submicroscopic entities or differences among students, visible. If we take seriously Gombirch's (1980) notion that scientific images "do not, of course, aim to record what is visible, their purpose is to make visible" (p. 185), we must account for the practices of "making visible" and the underlying philosophical assumptions. With a focus on representation, my dissertation sets out to explore the implications of engaging with philosophical assumptions that may unsettle the normative worldview in science education research by working towards three goals: (1) to critically examine the implicit philosophical assumptions, namely representationalism, metaphysical individualism, and humanism, that underpin the current normative worldview in discipline-based science education, (2) to engage with the relational ontology of agential realism and develop agential variation theory as a framework for exploring the potential of conducting chemistry education research from post-humanist perspectives, and (3) to advance qualitative methodology for investigating representational practices in college chemistry education. The findings of my dissertation explore the analytical implications for the theoretical movement and methodological consideration. Starting with an analysis from the cognitive perspective of variation theory, my findings continuously weave in Marton's notion of critical features, Vygotsky's notion of semiotic mediation, and Barad's notion of intra-action to reconfigure the meaning of qualitative interview data. This weaving of multiple theories reconfigured these constructs to semiotic features, signifying practices, and participation of materiality. Coordination multiple theoretical constructs and onto-epistemological standpoints produced a multilayered reading that showed the fluid and situated evolution of external representations' meaning. Chemistry cultural practices such as structural-activity analysis is shown to both constitute and limit the possibility of external representations' meaning. In addition, the materiality of external representations is shown to play an active role in the production of meaning. These findings complement the interpretive perspective of the representational competence model of student learning with representations. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com/en-US/products/dissertations/individuals.shtml.]

The overarching goal of this dissertation is to examine institutional change initiatives in STEM and to understand the impact of engaging with a specific change strategy on a biochemistry educator's instructional practice. Institutional change initiatives involve executing an intentional strategy to influence teaching practices within a specific institution. This research investigates NSF-funded change initiatives at three public research universities that were focused on encouraging the adoption of evidenced-based instructional practices (EBIPs) by STEM faculty. As part of an effort to understand how the three institutions approached this task, framework analysis was performed using the initiative's annual reports to NSF. Further examination of the interaction between Community of Practice (CoP), a type of enacted change strategy, and how its impact's an instructor's use of EBIPs related to assessment. Instructors make assessment decisions based on their knowledge and experiences. Assessment practice is an essential element of instruction, and the outcomes of assessments have a broad impact on both students and instructors. Efforts to provide strengths-focused, relevant professional development support regarding assessment are enhanced by greater understanding of the complex nature of assessment practices. In this study, the Teacher Assessment Literacy in Practice (TALiP) framework was used along with framework analysis methodologies to guide our investigation of one biochemistry instructor's assessment literacy, relevant to her integration of a biochemistry threshold concept, the physical basis of interactions (PBI), into her course. Analysis revealed that community support and self-reflection influenced the instructor's enactment of specific assessments aligned with her instructional goals. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com/en-US/products/dissertations/individuals.shtml.]

Laboratory activities are a prevalent and essential part of chemistry learning because of their potential to help students develop problem solving abilities, visualize chemistry concepts learned in lecture, and gain practical skills. However, learning in the laboratory environment is not without its challenges. For example, cookbook-style chemistry laboratories can promote superficial learning, and cognitive overload can result from the study of new concepts and the use of new procedures in this environment. Multiple pedagogies and supports have been developed to address challenges such as these. The current research focuses upon external representations that are commonly used to support learning in the general chemistry laboratory. External representations are visual tools--such as graphs, pictures, charts, and equations--that are used to illustrate, model, and communicate ideas. These representations are often used in chemistry lecture and laboratory to illustrate concepts that are beyond the senses. Although external representations are used with the intent of supporting student learning, research indicates that students have difficulty interpreting and learning from them. Therefore, it is important to examine how students' learning from these figures, graphs, and symbols correlates with what their instructors intend for them to learn. External representations are commonly used in the chemistry laboratory environment; however, very few studies have examined what instructors intend for their students to learn from these external representations, what is possible for students to learn from these external representations, and what students actually learn from these representations. Specifically, I focus on external representations of acid-base titrations. I have chosen this subject because titrations are an important skill for practicing scientists; therefore, it is important that students master titrations during their training. Furthermore, external representations are commonly used (1) to illustrate how students should set up their laboratory equipment, (2) to demonstrate how to carry out a titration, and (3) to help students understand the chemical reactions that occur during a titration. This research utilizes variation theory to determine what instructors intend for their students to understand about acid-base titrations, what they can learn from the images we use to instruct, and what they ultimately do learn about acid-base titrations. In this dissertation, I first describe the 18 features which instructors deem as critical for their general chemistry students to understand about acid-base titrations. These include pH, chemical equations, and excess base, among others. The images the instructor participants then chose to share with the student participants included most of the critical features mentioned by the instructors, indicating that typical images used to teach students about acid-base titrations are consistent with the concepts that instructors want their students to understand about titrations. Students were interviewed about their understandings of acid-base titrations both before and after viewing the external representations selected by the instructors. Evidence suggests that students learned from the representations. In fact, the external representations used in the study facilitated learning. The external representations used in the study facilitated learning for many of the critical features; in some cases, they were essential for learning. Therefore, it is critical that external representations used to teach acid-base titrations are chosen with consideration to the critical features identified by instructors, the affordances that the representations can give for learning, and the features that students focus upon when learning about these important chemistry concepts. Based on the findings of the current study, recommendations are provided for the design, the selection, and the utilization of external representations used in teaching acid-base titrations. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com/en-US/products/dissertations/individuals.shtml.]

For centuries we have been using food for our well-being and health maintenance. As far back as Hippocrates (known as the father of medicine), food has been a center stone used as the good or suffering of humanity. The Bible references food and fasting, cleansing and revitalization to heal the spirit. Before the scientific discovery of synthetic pharmaceuticals, plants recovered the body and mind. Many cultures practice nutritional therapy to this day. The body recognizes food in the purest form, and food was created and grown to satisfy and nourish the body. Obesity and neurodevelopmental and mental health disorder diagnoses are astronomically more significant than prior years. Research has suggested that many underlying or chronic conditions can be attributed to inflammation in the body. Specifically, there is a greater prevalence of digestive diagnoses, gastrointestinal (GI) symptomology, and GI symptoms in children with autism spectrum disorder than their typically developing peers. The purpose of this qualitative study is to determine the practices, policies, and ideologies of nutritional therapy present in the special education (SE) preschool classroom from the perspective of SE preschool teachers. Early intervention and promotion of healthy eating through teaching and modeling could positively impact students' health and development. The lack of current research in nutritional therapies and their use specifically in preschool deserves advanced exploration. Recommendations for further research include (a) expanding the current research sampling to include more special education preschools, (b) exploring the phenomena of nutrition in special education preschools from the perspective of school administration, (c) further analyzing special education preschools food programs and the individualized education program process. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com/en-US/products/dissertations/individuals.shtml.]

Optimization is a component critical to method development. Mathematical modeling of physical phenomena enables an efficient search for the parameters and conditions that optimize methods and systems. Here, optimization of methods in sonoelectrochemistry, electrochemical separations, electrochemical education, and assessment of diabetic status are discussed. Sonochemistry is widely used in applications that include catalysis, synthesis, nanoparticle formation, analysis, and plating. In classical sonoelectrochemistry (CS), a high power transducer delivers ultrasound to a bulk fluid that contains the working electrode. The high frequency ultrasound deposits sufficient energy at the electrode to enhance kinetic rates and increase mass transport. These enhancements are at the cost of a disrupted diffusion layer that disallows quantitative assessment of electron transfer kinetics. An alternative is thin layer sonoelectrochemistry (TLS) where ultrasound from a low power transducer (e.g., quartz crystal oscillator) delivers ultrasound into a thin fluid layer with thickness on the order of the ultrasonic wavelength. TLS is designed to focus and transduce energy at the electrode|solution interface. Experience has shown the difficulties in construction of a reliable and reproducible setup for TLS. Here, mathematical modeling and optimization of TLS is presented. The results indicate that input sound, amplified through constructive interference and resonance, achieves energy delivery commensurate with CS. A stepwise checklist of provided to improve setup reliability and reproducibility. Electrochemical separation is used for the extraction and purification of metals used in important technological devices (e.g., batteries and motors). Reliance of modern society on technological devices, has sharply increased demand for high purity materials. Traditional electrochemical separation relies on differences in thermodynamic formal or standard potentials that restrict separations to systems where formal potentials differ by several hundred millivolts. This difference disallows many important separations. Here, a mathematical model for electrochemical separation in a monolayer is discussed. The monolayer contains two species with identical initial concentration and formal potential but different standard heterogeneous rate constants. Standard heterogeneous rate constants characterize the rate of electron transfer between the electrode and redox species immediately at the electrode surface. Inclusion of the kinetics of deposition opens access to many separations previously considered impossible. A general optimal waveform enables kinetically based separations. To more easily implement the separation with common electrochemical devices an approximation comprised of only ramps and steps is provided. Educational demonstrations of diffusion are often complicated and require expensive laboratory equipment. Here, a demonstration of diffusion based on physical therapy putty is provided to address the deficiency in simple and inexpensive demonstrations in the literature. Physical therapy putty is nontoxic and can be acquired online from many commercial sources. The expansion of physical therapy emulates a diffusional process where the radius is an analog for the diffusion length. The difference between radial and linear diffusion is discussed and the arial rates for physical therapy putty are calculated and used to demonstrate the diffusion coefficient. Discussion questions are provided that are designed to encourage students to form a hypothesis, design an experiment, analyze data, and discuss the results. Type 1 Diabetes (T1D) is a disease that limits the ability of an individual to regulate blood sugar. T1D affects nearly 34.2 million people in the US where 11.7 million people are diagnosed globally each year. Without sufficient assessment and regulation of blood sugar, fatal complications can result. At present, assessment of diabetic status involves often invasive and painful extraction of a blood sample for use with a personal glucose meter. Recently, alternative body fluids (e.g., sweat, tears, and saliva) have been investigated for biomarkers that indicate diabetic status (e.g., lactate and blood ketones). Here, the initial studies for a non-enzymatic sensor for [beta]-hydroxybutyrate, a blood ketone, are presented. The feasibility of the method in development of a sensor is discussed. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com/en-US/products/dissertations/individuals.shtml.]

Reducing risk associated with college student drinking is a major public health concern. The free-pour assessment has the potential to inform interventions aimed at reducing risks associated with college student drinking. Yet, few studies have assessed conditions that influence pouring abilities, and no identified studies have assessed pouring behavior under the influence of alcohol; further, no identified studies actual and perceived free-pouring behavior is subject to acute tolerance, which has been identified as an important factor in alcohol-related risk. It was hypothesized that ratings of subjective intoxication, free-pour accuracy, and ratings of free-pour accuracy would be subject to acute tolerance. Participants trained to pour a standard drink of beer received a dose of alcohol (n=7) or a placebo dose (n=6) and repeated free-pours and ratings of subjective impairment along the blood alcohol concentration (BAC) curve. Results suggested that participants were able to pour a standard drink of beer within the 10% training criterion range (12 oz) after a stimulus fading training procedure. Consistent with previous findings of acute tolerance, results supported the hypothesis that ratings of subjective intoxication were subject to acute tolerance. Inconsistent with hypotheses, free-poured ounces and subjective ratings of free-pour accuracy were not. These data suggest that free-pouring a standard drink of beer is a trainable skill that persists despite a moderate dose of alcohol. Future studies should examine if behavioral skills training of other protective skills in the context of elevated BAC reduces the risks associated with intoxication among college students. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com/en-US/products/dissertations/individuals.shtml.]

Freshmen and sophomores in college are historically at risk of disengaging with general and organic chemistry courses, performing poorly and not continuing in STEM. Utility value (UV) interventions, though, have increased the achievement and retention of low-performing students in psychology and introductory biology courses. In this study, a multi-semester UV intervention was implemented to increase curiosity, a predictor of increased learning and retention, of three student cohorts going through general and organic chemistry. Based on a preliminary analysis of Cohorts 1 and 2, students exposed to the multi-semester intervention perform a half letter grade better in introductory biochemistry after controlling for their ACT Composite and Math scores. Perhaps the most intriguing results from the FPIDC questionnaire is that the General Chemistry 2, Cohort 3 intervention resulted in a small positive effect on utility value of chemistry and moderate positive effect on interest in chemistry. These results contradict the earlier findings from the Epistemic Curiosity Scale results of General Chemistry 2, Cohort 2 which suggest that the PGX intervention had no effect on student curiosity and interest. The improved results in Cohort 3 are likely due to a major revision of the original General Chemistry 2 intervention. These results, therefore, support the notion that implementing new instructional methods in the classroom requires several iterations and revisions to be successful. In 2017, a grad-roots movement started within the Chemistry Department at University of Illinois Urbana-Champaign (UIUC) with the assistance of psychology PhD student from UIUC Department of Clinical Psychology. Data was collected with the permission of the Department Head of Chemistry at UIUC and administered by graduate students from the Department of Chemistry Graduate Student Advisory Committee (DCGSAC). The data collected using this survey was compiled into a concise report, the Department of Chemistry Graduate Student Wellness Report 2017 and posted throughout the halls of the UIUC chemistry department. In response to the publication of this report, the chemistry faculty organized, amongst other responses, a mandatory meeting to discuss the implications of this report. Graduate students in the chemistry department worked with the momentum that resulted from the Department of Chemistry Graduate Student Wellness Report 2017 to form a coalition of graduate student organizations in order to fund and organize the inaugural Summer Lecture Series directed at fostering a diverse and inclusive environment to support mental health and wellness within the Department of Chemistry at UIUC. This grad-roots movement toward mental health continues the arduous work of seeking expert guidance to promote mental health and wellness on campus and in graduate schools across the nation. The findings described in Chapter 4 suggest that depression and anxiety may, at least in part, be the result of insufficient or nonexistent management training for research advisors. The unique relationship between mentors and mentees in a research university consists of a steep power dynamic which may instill a sense of impotence over graduate student's job control and may exacerbate preexisting mental health conditions. This work heavily influenced the author's previous perspective on undergraduate education and the influence that instructors have on their students' classroom engagement and mental health. This current chapter presents the need for empathic communication training for instructors of undergraduate courses, including gateway courses, such as introductory chemistry. A research plan is proposed for the development of a text classification tool for measuring and analyzing empathic communication in written assignments. Currently, the data collection for training this text classifier is underway. The Kubler-Ross model (1969), which delineated the five stages of grief, and the SPIKES method (1992), which provided step-by-step instructions for recognizing and addressing the emotional states of patients, are two landmark publications that indicated the emerging need to prepare physicians to address the emotional states of patients. In 2015, the AAMC updated the MCAT to include a test section on social and behavioral sciences, reflecting the growing interest in preparing undergraduate pre-health students for the social and behavioral training in medical school. In previous research, an educational intervention in Organic Chemistry 1 and 2 required students to write journal entries reflecting a role-play exercise. This utility value intervention intended to increase the task value of organic chemistry by connecting students' academic tasks (studying organic chemistry) with their career aspirations (helping patients as practicing physicians). The goal of the research proposed herein is to analyze the text from these journal assignments to develop a proof of concept text classifier system able to recognize elements of empathy in text. Success of the text classifier will be assessed based on its agreement with human annotators of empathy in text. Further development of this text classifier will require data from medical school patient interview training and may lead to technology that will assist in consistently and objectively training future physicians to better address the emotional states of their patients. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com/en-US/products/dissertations/individuals.shtml.]

Recent calls in education have emphasized the critical need for curricula in the sciences to support student development of the general and disciplinary-specific practices that are relevant to modern scientific research and careers, as well as foundational scientific knowledge that reflects recent advances. In this regard, the life sciences, including biochemistry, have been under pressure to develop curricula that reflect current research knowledge and practices, and that develop student competence in areas such as experimentation and visualization. In contrast to these calls, biochemistry textbooks, and instruction based on them, seldom discuss how disciplinary knowledge is combined with experimental work or other disciplinary resources to investigate and communicate about biochemical phenomena. This is of great concern given that graduates entering life science careers must be able to reason with relevant disciplinary knowledge, utilize experimental research methods, and navigate data representations in order to solve research problems. It is therefore crucial for biochemistry instruction to expose students to the ways in which expert scientists navigate and reason with disciplinary resources in cutting-edge scientific research on topics such as protein folding and dynamics, the focus of this project. Thus, this dissertation aims to fill a gap in our understanding of how expert research scientists explain protein-folding and dynamics research, and how that research knowledge can be used to inform the development of instructional materials in this crucially important area of biochemistry. To address this goal, we explore three overarching research questions: How can we model experts' explanations of their research related to protein folding and dynamics? (RQ1); How do experts use representations to explain their protein-folding and dynamics research? (RQ2); and How can we use expert research to inform the design and implementation of instructional materials aimed at developing biochemistry students' understanding of protein-folding and dynamics? (RQ3). To address these research questions, we first collected and analyzed interview data from four experts to explore the nature of their research explanations. This data was used to develop a model (i.e. the MAtCH model) of how experts integrate theoretical knowledge with their research context, methods, and analogies when explaining how phenomena operate (RQ1). In doing so, we also established how the experts use and combine explanatory models depending on the phenomena discussed and their explanatory aims, as well as how they explain thermodynamic and kinetic concepts relevant to protein folding in ways that align with their experimental research methods. We then examined selected representations from the expert interviews to explore how experts use language and representations to create meaning when explaining their research (RQ2). In comparing these to representations from biochemistry textbooks, analysis of the data indicated that textbooks generally explain 'what is known' but seldom explain 'how it is known,' whereas the experts use a combination of language, multiple representations, and gestures to explain how experimental research methods can provide evidence for phenomena. From this analysis, suggestions were made regarding the design of instructional materials to support discussion of experimental research methods and student interpretation of representations in classroom activities. In the final study, these suggestions were used in combination with additional analysis of expert research to inform the development anticipated learning outcomes (ALOs) and the design of instructional materials aimed at developing biochemistry students' understanding of protein folding and dynamics (RQ3). The materials focus on the use of hydrogen-deuterium exchange mass spectrometry (HDX-MS) to study changes in protein structure due to denaturation and interactions with other molecules. The instructional materials were piloted in an undergraduate biochemistry course for the health sciences, and the nature of students' understandings were explored. Our findings suggest that research practice -- including research context, experimental methods, and representations -- influences reasoning and explanation, providing additional evidence of the importance of developing discursive literacy in science students. To that end, a major implication of this work is that student knowledge of experimentation and representation may be a critical component of developing functional scientific understanding. Each of the studies contained in this dissertation therefore suggests ways in which practitioners may use our findings to modify instruction and instructional materials so that they are more aligned with expert practices. In order to teach students how scientific research underpins factual knowledge in biochemistry, future research should continue to explore experts' use of disciplinary resources and ways of thinking in order to inform teaching and learning strategies and materials that can support the development of students' disciplinary literacy. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com/en-US/products/dissertations/individuals.shtml.]

Course-based Undergraduate Research Experiences (CUREs) have been described in a range of educational contexts. Although various learning objectives, termed anticipated learning outcomes (ALOs) in this project, have been proposed, processes for identifying them may not be rigorous or well-documented, which can lead to inappropriate assessment and speculation about what students actually learn from CUREs. Additionally, evaluation of CUREs has primarily relied on student and instructor perception data rather than more reliable measures of learning. This dissertation investigated a novel biochemistry laboratory curriculum for a Course-based Undergraduate Research Experience (CURE) known as the Biochemistry Authentic Scientific Inquiry Lab (BASIL). Students participating in this CURE use a combination of computational and biochemical wet-lab techniques to elucidate the function of proteins of known structure but unknown function. The goal of the project was to evaluate the efficacy of the BASIL CURE curriculum for developing students' research abilities across implementations. Towards achieving this goal, we addressed the following four research questions (RQs): RQ1) How can ALOs be rigorously identified for the BASIL CURE; RQ2) How can the identified ALOs be used to develop a matrix that characterizes the BASIL CURE; RQ3) What are students' perceptions of their knowledge, confidence and competence regarding their abilities to perform the top-rated ALOs for this CURE; RQ4) What are appropriate assessments for student achievement of the identified ALOs and what is the nature of student learning, and related difficulties, developed by students during the BASIL CURE? To address these RQs, this project focused on the development and use of qualitative and quantitative methods guided by constructivism and situated cognition theoretical frameworks. Data was collected using a range of instruments including, content analysis, Qualtrics surveys, open-ended questions and interviews, in order to identify ALOs and to determine student learning for the BASIL CURE. Analysis of the qualitative data was through inductive coding guided by the concept-reasoning-mode (CRM) model and the assessment triangle, while analysis of quantitative data was done by using standard statistical techniques (e.g. conducting a parried t-test and effect size). The results led to the development of a novel method for identifying ALOs, namely a process for identifying course-based undergraduate research abilities (PICURA; RQ1; Irby, Pelaez, & Anderson 2018b). Application of PICURA to the BASIL CURE resulted in the identification and rating by instructors of a wide range of ALOs, termed course-based undergraduate research abilities (CURAs), which were formulated into a matrix (RQs 2; Irby, Pelaez, & Anderson, 2018a,). The matrix was, in turn, used to characterize the BASIL CURE and to inform the design of student assessments aimed at evaluating student development of the identified CURAs (RQs 4; Irby, Pelaez, & Anderson, 2018a). Preliminary findings from implementation of the open-ended assessments in a small case study of students, revealed a range of student competencies for selected top-rated CURAs as well as evidence for student difficulties (RQ4). In this way we were able to confirm that students are developing some of the ALOs as actual learning outcomes which we term VLOs or verified learning outcomes. In addition, a participant perception indicator (PPI) survey was used to gauge students' perceptions of their gains in knowledge, experience, and confidence during the BASIL CURE and, therefore, to inform which CURAs should be specifically targeted for assessment in specific BASIL implementations (RQ3;). [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com/en-US/products/dissertations/individuals.shtml.]

In response to both nationwide calls for reform and a perception that the existing chemistry curriculum was not meeting the needs of life science students, faculty in the department of chemistry at Purdue created a redesigned chemistry course sequence specifically aimed at preparing biology majors. The new sequence, called the 1-2-1 curriculum, spans four semesters of instruction, including one semester of general chemistry, two semesters of organic chemistry, and one semester of biochemistry. The 1-2-1 curriculum was implemented in the 2013-2014 academic year, and students appeared to be progressing through successfully. However, there was a need for a more systematic evaluation of the impact of the new curriculum on student learning and achievement. The goals of the 1-2-1 curriculum include preparing students for success in future chemistry courses, building students' conceptual understanding of core chemistry topics relevant to biological systems, and having students apply their knowledge of chemistry to understanding biological systems at the molecular level. This study reports an evaluation of the 1-2-1 curriculum in three areas: students' performance in subsequent courses, their retention of knowledge over time, and their transfer of chemistry knowledge to solve problems in biologically relevant contexts. Three cohorts of students were tracked through the 1-2-1 sequence and their performance was measured by course grades and exam scores. We found that students in the 1-2-1 curriculum performed better or equally well when compared to their peers who had taken traditional chemistry courses in both organic chemistry and biochemistry. To assess students' retention of knowledge, a pre-test was administered at the beginning of biochemistry that included questions from the students' general and organic chemistry final exams that covered topics relevant to biochemistry. Students' responses to the pre-test were compared to their responses on final exams as a measure of retention. We found that students demonstrated higher retention for topics that were introduced in general chemistry and then revisited in different contexts in organic chemistry, including resonance, acid-base chemistry, intermolecular forces, and hybridization. Students demonstrated lower retention for topics that were introduced in general chemistry but not explicitly discussed in organic chemistry, including thermodynamics, kinetics, and buffers. Additionally, students generally demonstrated low retention when asked to draw mechanisms for reactions that they had been introduced to in organic chemistry. Transfer was assessed by asking students to propose mechanisms for reactions in both a traditional chemical context and a biochemical context. Students primarily constructed relations of similarity based on surface features of the starting materials, which often led them to propose incorrect mechanisms. Overall, these results demonstrate that the integration of topics throughout the 1-2-1 curriculum had a positive impact on students' understanding and retention of core chemistry concepts, however, more work is needed to fully integrate other topic areas in the curriculum. Future changes to the curriculum are suggested, as well as broader implications for teaching, research, and curriculum development. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com/en-US/products/dissertations/individuals.shtml.]

Research investigating faculty and instructors' perception of teaching in discipline-oriented fields such as biology, chemistry and physics suggest that faculty hold diverse conceptions about teaching and learning. This study extended this work to a discipline at the interface between traditional physical science and life science fields, upper-level biochemistry courses. It also compared instructors' perception, beliefs and actions when teaching biochemistry at research institutions with courses taught at primarily undergraduate institutions (PUI's). In a recently completed review of discipline-based educational research (DBER) in biochemistry, I noted the absence of research regarding the relationship between faculty beliefs and classroom practices in biochemistry and noted that different levels, associated with teaching and learning experiences, have not been studied in the context of the undergraduate chemistry curriculum. As a scientific field, biochemistry bridges chemistry and biology, which each have a consensus regarding the major concepts or ideas that should be taught within their disciplines. However, biochemistry, despite its increased relevance in recent years, has achieved hardly any consensus among those who teach this content material on what should be taught or how instructors should teach it. Biochemistry is also a rapidly growing field with increased relevance that is being taught as a unique discipline in more and more institutions. Another unique feature that distinguishes biochemistry from other scientific fields is that it is inherently interdisciplinary and taught in different departments, often for a versatile population of various majors and minors. Further research suggests that we overgeneralize conclusions on factors influencing teaching practices within classrooms, which could possible prevent the advancement of teaching methodologies used by instructors. To explore this research interest, classroom observations and semi-structured interviews were used. Within the scope of this study, I identified two main ways biochemistry instructors thought about their teaching of biochemistry: theory versus practice-oriented. The more theory-driven instructors reflected on their beliefs and perceptions, the more traditional their teaching practices were executed -- the contrary held true for instructors with a more practical conception of the teaching of biochemistry. Overall, I was able to portray a multitude of ways in which biochemistry is currently being taught at different institutions, identifying differences and communalities they shared. As well as the unique challenges instructors faced when implementing evidence-based teaching methodologies in their classrooms were identified and categorized. My research should improve the understanding of factors, barriers, and possible opportunities that various scientific disciplines face to inform the development of professional programs that can encourage the use and implementation of evidence-based instructional practices. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com/en-US/products/dissertations/individuals.shtml.]

The research presented in chapters 2, 3, and 4 in this dissertation uses a sociocultural and sociohistorical lens, particularly around power, authority of knowledge and identity formation, to investigate the complexity of engaging in, supporting, and evaluating high-quality argumentation within a college biochemistry inquiry-oriented classroom. Argumentation skills are essential to college and career (National Research Council, 2010) and for a democratic citizenry. It is central to science teaching and learning (Osborne et al., 2004a) and can deepen content knowledge (Jimenez-Aleixandre et al., 2000; Jimenez-Aleixandre & Pereiro-Munhoz, 2002). When students have opportunities to make claims and support it with evidence and reasoning they may also increase their problem-solving and critical thinking capacity (Case, 2005; Willingham, 2007). Overall, this has implications in supporting students to become increasingly literate in scientific ideas, language, and practices. However, supporting argumentation can be challenging for instructors, particularly in designing learning environments that facilitate and evaluate both the process and the product during student discussions (Duschl & Osborne, 2002). Fostering argumentation is complex and requires explicit modeling and multiple opportunities for dialogic interactions. This dissertation will examine how several facets influence argumentation in order to support instructors in implementing and improving argumentation in their inquiry-oriented classrooms. These facets include access to language and use of discursive moves, classroom design, curriculum and instructional activities, and interactional dynamics and power negotiation. The data set for this dissertation is a transcript generated from the audio- and video capture of a 7-minute student discussion around a mechanism in the TCA (TriCarboxylic Acid) cycle, as well as student writing, and course documents from student portfolios. This dissertation, organized using the manuscript style structure, will present three standalone chapters, each with a specific focus related to the central theme of supporting argumentation, which is the connecting thread. Chapter 2 will discuss how power is negotiated during the argumentation process and how interaction dynamics can support or inhibit the quality of argumentation. Chapter 3 will provide assessment and evaluation support to instructors who want to guide their students in meeting high quality levels in both the process and product of argumentation. Finally, chapter 4 will explore the influence of pedagogical, and instructional resources and tools on the quality of argumentation. This includes a discussion of the influence of classroom talk, particularly discursive moves and interactional dynamics, as well the curriculum and instructional activities, and the design features of the learning environment. Each chapter will conclude with instructional implications that provide practical guidance in the form of pedagogical activities to instructors. Partial funding for this dissertation was received from a PSC-CUNY Cycle 44 Research Award (66799-00 44). Findings suggest that the classroom design can support collaboration and the dialogic nature of argumentation, and the curriculum and activities can act as resources for students to share and negotiate multiple perspectives, but that instructors can also influence the process of argumentation by utilizing specific discursive moves, such as telling and revoicing, to promote or inhibit argumentation. The results, specifically from chapter 4, also propose that instructors model and share the expected criteria for high quality components of argumentation. The need for instructors to be aware of the criteria for high levels of quality for each of the argumentation components is a critical implication of this research. The criterion is presented in this dissertation and is derived from a review of multiple findings by researchers of argumentation, as well the scientific community at large. Creating structures and implementing targeted pedagogical strategies that support argumentation can lead students to use the process of argumentation as an empowerment tool to enact agency and negotiate power. This has the potential to sustain the success of science students, create a community of practice, and increase equity and access for all. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com/en-US/products/dissertations/individuals.shtml.]

Ubiquitin is essential for eukaryotic life and varies in only 3 amino acid positions between yeast and humans. However, recent deep sequencing studies indicate that ubiquitin is highly tolerant to single mutations. We hypothesized that this tolerance would be reduced by chemically induced physiologic perturbations. To test this hypothesis, a class of first year UCSF graduate students employed deep mutational scanning to determine the fitness landscape of all possible single residue mutations in the presence of seventeen different small molecule perturbations. These perturbations uncover "shared sensitized positions" localized to areas around the hydrophobic patch and the C-terminus. For the important residue Lys 63, we found sensitization in eight conditions and increased tolerance mutation in two conditions. In total, our experiments have uncovered a highly sensitizing condition for every position in ubiquitin except Ser57 and Gln62. Our data show how chemical stresses can reduce buffering effects in the ubiquitin proteasome system. Finally, this study demonstrates the potential of lab-based interdisciplinary graduate curriculum. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com/en-US/products/dissertations/individuals.shtml.]

The purpose of this study was to evaluate the chemistry collection of the College of Wooster's Chemistry Library. In particular, the extent to which the library supports the curriculum of the chemistry and biochemistry program by providing additional sources to supplement course textbooks was evaluated. Focus was on materials present in the collection on the College of Wooster campus, but the extent to which materials can be obtained through resource sharing was also considered. The study addressed: the extent of overlap of the College of Wooster's holdings with the materials cited in its required chemistry books; whether this overlap differs for the various subfields of chemistry and whether the overlap of monograph citations differs from that of journal citations; and whether this data indicates that the College of Wooster's chemistry collection is of high or low quality, gaps in its coverage, and suggestions that can be made for improvement. A total of eight undergraduate textbooks were examined for citations. (AEF)