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Description
Single cell analysis has become increasingly important in understanding disease onset, progression, treatment and prognosis, especially when applied to cancer where cellular responses are highly heterogeneous. Through the advent of single cell computerized tomography (Cell-CT), researchers and clinicians now have the ability to obtain high resolution three-dimensional (3D) reconstructions of single cells. Yet to date, no live-cell compatible version of the technology exists. In this thesis, a microfluidic chip with the ability to rotate live single cells in hydrodynamic microvortices about an axis parallel to the optical focal plane has been demonstrated. The chip utilizes a novel 3D microchamber design arranged beneath a main channel creating flow detachment into the chamber, producing recirculating flow conditions. Single cells are flowed through the main channel, held in the center of the microvortex by an optical trap, and rotated by the forces induced by the recirculating fluid flow. Computational fluid dynamics (CFD) was employed to optimize the geometry of the microchamber. Two methods for the fabrication of the 3D microchamber were devised: anisotropic etching of silicon and backside diffuser photolithography (BDPL). First, the optimization of the silicon etching conditions was demonstrated through design of experiment (DOE). In addition, a non-conventional method of soft-lithography was demonstrated which incorporates the use of two positive molds, one of the main channel and the other of the microchambers, compressed together during replication to produce a single ultra-thin (<200 µm) negative used for device assembly. Second, methods for using thick negative photoresists such as SU-8 with BDPL have been developed which include a new simple and effective method for promoting the adhesion of SU-8 to glass. An assembly method that bonds two individual ultra-thin (<100 µm) replications of the channel and the microfeatures has also been demonstrated. Finally, a pressure driven pumping system with nanoliter per minute flow rate regulation, sub-second response times, and < 3% flow variability has been designed and characterized. The fabrication and assembly of this device is inexpensive and utilizes simple variants of conventional microfluidic fabrication techniques, making it easily accessible to the single cell analysis community.
ContributorsMyers, Jakrey R (Author) / Meldrum, Deirdre (Thesis advisor) / Johnson, Roger (Committee member) / Frakes, David (Committee member) / Arizona State University (Publisher)
Created2012
Description
Students across the United States lack the necessary skills to be successful college students in Science, Technology and Math (STEM) majors and as a result post-secondary institutions are developing summer bridge programs to aid in their transition. As they develop these programs, effective theory and approach are critical to developing successful programs. Though there are a multitude of theories on successful student development, a focus on self-efficacy is critical. Summer Bridge programs across the country as well as the Bio Bridge summer program at Arizona State University were studied alone and through the lens of Cognitive Self-Efficacy Theory as mentioned in Albert Bandura's "Perceived Self-Efficacy in Cognitive Development and Functioning." Cognitive Self-Efficacy Theory provides a framework for self-efficacy development in academic settings. An analysis of fifteen bridge programs found that a large majority focused on developing academic capabilities and often overlooked development of community and social efficacy. An even larger number failed to focus on personal psychology in managing self-debilitating thought patterns based on published goals. Further, Arizona State University's Bio Bridge program could not be considered successful at developing cognitive self-efficacy or increasing retention as data was inconclusive. However, Bio Bridge was tremendously successful at developing social efficacy and community among participants and faculty. Further research and better evaluative techniques need to be developed to understand the program's effectiveness in cognitive self-efficacy development and retention.
ContributorsTummala, Sailesh Vardhan (Author) / Orchinik, Miles (Thesis director) / Brownell, Sara (Committee member) / Shortlidge, Erin (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
Collaborative learning has been found to enhance student learning experiences through interaction with peers and instructors in a way that typically does not occur in a traditional lecture course. However, more than half of all collaborative learning structures have failed to last very long after their initial introductions which makes understanding the factors of collaboration that make it successful very important. The purpose of this study was to evaluate collaborative learning in a blended learning course to gauge student perceptions and the factors of collaboration and student demographics that impact that perception. This was done by surveying a sample of students in BIO 282 about their experiences in the BIO 281 course they took previously which was a new introductory Biology course with a blended learning structure. It was found that students agree that collaboration is beneficial as it provides an opportunity to gain additional insight from peers and improve students' understanding of course content. Also, differences in student gender and first generation status have less of an effect on student perceptions of collaboration than differences in academic achievement (grade) bracket.
ContributorsVu, Bethany Thao-Vy (Author) / Stout, Valerie (Thesis director) / Brownell, Sara (Committee member) / Wright, Christian (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2014-05
Description
We, a team of students and faculty in the life sciences at Arizona State University (ASU), currently teach an Introduction to Biology course in a Level 5, or maximum-security unit with the support of the Arizona Department of Corrections and the Prison Education Program at ASU. This course aims to enhance current programs at the unit by offering inmates an opportunity to practice literacy and math skills, while also providing exposure to a new academic field (science, and specifically biology). Numerous studies, including a 2005 study from the Arizona Department of Corrections (ADC), have found that vocational programs, including prison education programs, reduce recidivism rates (ADC 2005, Esperian 2010, Jancic 1988, Steurer et al. 2001, Ubic 2002) and may provide additional benefits such as engagement with a world outside the justice system (Duguid 1992), the opportunity for inmates to revise personal patterns of rejecting education that they may regret, and the ability of inmate parents to deliberately set a good example for their children (Hall and Killacky 2008). Teaching in a maximum security prison unit poses special challenges, which include a prohibition on most outside materials (except paper), severe restrictions on student-teacher and student-student interactions, and the inability to perform any lab exercises except limited computer simulations. Lack of literature discussing theoretical and practical aspects of teaching science in such environment has prompted us to conduct an ongoing study to generate notes and recommendations from this class through the use of surveys, academic evaluation of students' work and ongoing feedback from both teachers and students to inform teaching practices in future science classes in high-security prison units.
ContributorsLarson, Anika Jade (Author) / Mor, Tsafrir (Thesis director) / Brownell, Sara (Committee member) / Lockard, Joe (Committee member) / Barrett, The Honors College (Contributor) / School of Politics and Global Studies (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
Background
Grading schemes for breast cancer diagnosis are predominantly based on pathologists' qualitative assessment of altered nuclear structure from 2D brightfield microscopy images. However, cells are three-dimensional (3D) objects with features that are inherently 3D and thus poorly characterized in 2D. Our goal is to quantitatively characterize nuclear structure in 3D, assess its variation with malignancy, and investigate whether such variation correlates with standard nuclear grading criteria.
Methodology
We applied micro-optical computed tomographic imaging and automated 3D nuclear morphometry to quantify and compare morphological variations between human cell lines derived from normal, benign fibrocystic or malignant breast epithelium. To reproduce the appearance and contrast in clinical cytopathology images, we stained cells with hematoxylin and eosin and obtained 3D images of 150 individual stained cells of each cell type at sub-micron, isotropic resolution. Applying volumetric image analyses, we computed 42 3D morphological and textural descriptors of cellular and nuclear structure.
Principal Findings
We observed four distinct nuclear shape categories, the predominant being a mushroom cap shape. Cell and nuclear volumes increased from normal to fibrocystic to metastatic type, but there was little difference in the volume ratio of nucleus to cytoplasm (N/C ratio) between the lines. Abnormal cell nuclei had more nucleoli, markedly higher density and clumpier chromatin organization compared to normal. Nuclei of non-tumorigenic, fibrocystic cells exhibited larger textural variations than metastatic cell nuclei. At p<0.0025 by ANOVA and Kruskal-Wallis tests, 90% of our computed descriptors statistically differentiated control from abnormal cell populations, but only 69% of these features statistically differentiated the fibrocystic from the metastatic cell populations.
Conclusions
Our results provide a new perspective on nuclear structure variations associated with malignancy and point to the value of automated quantitative 3D nuclear morphometry as an objective tool to enable development of sensitive and specific nuclear grade classification in breast cancer diagnosis.
Grading schemes for breast cancer diagnosis are predominantly based on pathologists' qualitative assessment of altered nuclear structure from 2D brightfield microscopy images. However, cells are three-dimensional (3D) objects with features that are inherently 3D and thus poorly characterized in 2D. Our goal is to quantitatively characterize nuclear structure in 3D, assess its variation with malignancy, and investigate whether such variation correlates with standard nuclear grading criteria.
Methodology
We applied micro-optical computed tomographic imaging and automated 3D nuclear morphometry to quantify and compare morphological variations between human cell lines derived from normal, benign fibrocystic or malignant breast epithelium. To reproduce the appearance and contrast in clinical cytopathology images, we stained cells with hematoxylin and eosin and obtained 3D images of 150 individual stained cells of each cell type at sub-micron, isotropic resolution. Applying volumetric image analyses, we computed 42 3D morphological and textural descriptors of cellular and nuclear structure.
Principal Findings
We observed four distinct nuclear shape categories, the predominant being a mushroom cap shape. Cell and nuclear volumes increased from normal to fibrocystic to metastatic type, but there was little difference in the volume ratio of nucleus to cytoplasm (N/C ratio) between the lines. Abnormal cell nuclei had more nucleoli, markedly higher density and clumpier chromatin organization compared to normal. Nuclei of non-tumorigenic, fibrocystic cells exhibited larger textural variations than metastatic cell nuclei. At p<0.0025 by ANOVA and Kruskal-Wallis tests, 90% of our computed descriptors statistically differentiated control from abnormal cell populations, but only 69% of these features statistically differentiated the fibrocystic from the metastatic cell populations.
Conclusions
Our results provide a new perspective on nuclear structure variations associated with malignancy and point to the value of automated quantitative 3D nuclear morphometry as an objective tool to enable development of sensitive and specific nuclear grade classification in breast cancer diagnosis.
ContributorsNandakumar, Vivek (Author) / Kelbauskas, Laimonas (Author) / Hernandez, Kathryn (Author) / Lintecum, Kelly (Author) / Senechal, Patti (Author) / Bussey, Kimberly (Author) / Davies, Paul (Author) / Johnson, Roger (Author) / Meldrum, Deirdre (Author) / Ira A. Fulton Schools of Engineering (Contributor) / School of Electrical, Computer and Energy Engineering (Contributor) / Biodesign Institute (Contributor) / Center for Biosignatures Discovery Automation (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor) / Department of Physics (Contributor)
Created2012-01-05
Description
This thesis contains three chapters, all of which involve using culturally inclusive education to explore the experiences of religious undergraduate biology students. The first chapter is an essay entitled "Toward Culturally Inclusive Undergraduate Biology Education," which describes a literature review performed with the aim of characterizing the landscape of cultural competence and related terms for biology educators and biology education researchers. This chapter highlights the use of 16 different terms related to cultural competence and presents these terms, their definitions, and highlights their similarities and differences. This chapter also identifies gaps in the cultural competence literature, and presents a set of recommendations to support better culturally inclusive interventions in undergraduate science education. The second chapter, entitled "Different Evolution Acceptance Instruments Lead to Different Research Findings," describes a study in which the source of 30 years of conflicting research on the relationship between evolution acceptance and evolution understanding was determined. The results of this study showed that different instruments used to measure evolution acceptance sometimes lead to different research results and conclusions. The final chapter, entitled "Believing That Evolution is Atheistic is Associated with Poor Evolution Education Outcomes Among Religious College Students," describes a study characterizing definitions of evolution that religious undergraduate biology students may hold, and examines the impact that those definitions of evolution have on multiple outcome variables. In this study, we found that among the most religious students, those who thought evolution is atheistic were less accepting of evolution, less comfortable learning evolution, and perceived greater conflict between their personal religious beliefs and evolution than those who thought evolution is agnostic.
ContributorsDunlop, Hayley Marie (Author) / Brownell, Sara (Thesis director) / Collins, James (Committee member) / Barnes, M. Elizabeth (Committee member) / School of Human Evolution & Social Change (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
In response to a national call within STEM to increase diversity within the sciences, there has been a growth in science education research aimed at increasing participation of underrepresented groups in science, such as women and ethnic/racial minorities. However, an underexplored underrepresented group in science are religious students. Though 82% of the United States population is religiously affiliated, only 52% of scientists are religious (Pew, 2009). Even further, only 32% of biologists are religious, with 25% identifying as Christian (Pew, 2009; Ecklund, 2007). One reason as to why Christian individuals are underrepresented in biology is because faculty may express biases that affect students' ability to persist in the field of biology. In this study, we explored how revealing a Christian student's religious identity on science graduate application would impact faculty's perception of the student during the biology graduate application process. We found that faculty were significantly more likely to perceive the student who revealed their religious identity to be less competent, hirable, likeable, and faculty would be less likely to mentor the student. Our study informs upon possible reasons as to why there is an underrepresentation of Christians in science. This further suggests that bias against Christians must be addressed in order to avoid real-world, negative treatment of Christians in science.
ContributorsTruong, Jasmine Maylee (Author) / Brownell, Sara (Thesis director) / Gaughan, Monica (Committee member) / Barnes, Liz (Committee member) / School of Life Sciences (Contributor) / W.P. Carey School of Business (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Learning student names has been promoted as an inclusive classroom practice, but it is unknown whether students value having their names known by an instructor. We explored this question in the context of a high-enrollment active-learning undergraduate biology course. Using surveys and semistructured interviews, we investigated whether students perceived that instructors know their names, the importance of instructors knowing their names, and how instructors learned their names. We found that, while only 20% of students perceived their names were known in previous high-enrollment biology classes, 78% of students perceived that an instructor of this course knew their names. However, instructors only knew 53% of names, indicating that instructors do not have to know student names in order for students to perceive that their names are known. Using grounded theory, we identified nine reasons why students feel that having their names known is important. When we asked students how they perceived instructors learned their names, the most common response was instructor use of name tents during in-class discussion. These findings suggest that students can benefit from perceiving that instructors know their names and name tents could be a relatively easy way for students to think that instructors know their names. Academic self-concept is one's perception of his or her ability in an academic domain compared to other students. As college biology classrooms transition from lecturing to active learning, students interact more with each other and are likely comparing themselves more to students in the class. Student characteristics, such as gender and race/ethnicity, can impact the level of academic self-concept, however this has been unexplored in the context of undergraduate biology. In this study, we explored whether student characteristics can affect academic self-concept in the context of a college physiology course. Using a survey, students self-reported how smart they perceived themselves in the context of physiology compared to the whole class and compared to the student they worked most closely with in class. Using logistic regression, we found that males and native English speakers had significantly higher academic self-concept compared to the whole class compared with females and non-native English speakers, respectively. We also found that males and non-transfer students had significantly higher academic self-concept compared to the student they worked most closely with in class compared with females and transfer students, respectively. Using grounded theory, we identified ten distinct factors that influenced how students determined whether they are more or less smart than their groupmate. Finally, we found that students were more likely to report participating less than their groupmate if they had a lower academic self-concept. These findings suggest that student characteristics can influence students' academic self-concept, which in turn may influence their participation in small group discussion.
ContributorsKrieg, Anna Florence (Author) / Brownell, Sara (Thesis director) / Stout, Valerie (Committee member) / Cooper, Katelyn (Committee member) / School of Life Sciences (Contributor) / School of Politics and Global Studies (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
Course-Based Undergraduate Research Experiences, or CUREs have become an increasingly popular way to integrate research opportunities into the undergraduate biology curriculum. Unlike traditional cookbook labs which provide students with a set experimental design and known outcome, CUREs offer students the opportunity to participate in novel and interesting research that is of interest to the greater biology community. While CUREs have been championed as a way to provide more students with the opportunity to experience, it is unclear whether students benefit differently from participating in different CURE with different structural elements. In this study we focused in on one proposed element of a CURE, collaboration, to determine whether student's perception of this concept change over the course of a CURE and whether it differs among students enrolled in different CUREs. We analyzed pre and post open-ended surveys asking the question "Why might collaboration be important in science?" in two CUREs with different structures of collaboration. We also compared CURE student responses to the responses of senior honors thesis students who had been conducting authentic research. Five themes emerged in response to students' conceptions of collaboration. Comparing two CURE courses, we found that students' conceptions of collaboration were varied within each individual CURE, as well as what students were leaving with compared to the other CURE course. Looking at how student responses compared between 5 different themes, including "Different Perspectives", "Validate/Verify Results", "Compare Results", "Requires Different Expertise", and "Compare results", students appeared to be thinking about collaboration in distinct different ways by lack of continuity in the amount of students discussing each of these among the classes. In addition, we found that student responses in each of the CURE courses were not significantly different for any of the themes except "Different Expertise" compared to the graduating seniors. However, due to the small (n) that the graduating seniors group had, 22, compared to each of the CURE classes composing of 155 and 98 students, this comparison must be taken in a preliminary manner. Overall, students thought differently about collaboration between different CUREs. Still, a gap filling what it means to "collaborate", and whether the structures of CUREs are effective to portray collaboration are still necessary to fully elaborate on this paper's findings.
ContributorsWassef, Cyril Alexander (Author) / Brownell, Sara (Thesis director) / Stout, Valerie (Committee member) / Cooper, Katelyn (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Evolution is a key feature of undergraduate biology education: the AmericanAssociation for the Advancement of Science (AAAS) has identified evolution as one of
the five core concepts of biology, and it is relevant to a wide array of biology-related
careers. If biology instructors want students to use evolution to address scientific
challenges post-graduation, students need to be able to apply evolutionary principles to
real-life situations, and accept that the theory of evolution is the best scientific
explanation for the unity and diversity of life on Earth. In order to help students progress
on both fronts, biology education researchers need surveys that measure evolution
acceptance and assessments that measure students’ ability to apply evolutionary concepts.
This dissertation improves the measurement of student understanding and acceptance of
evolution by (1) developing a novel Evolutionary Medicine Assessment that measures
students’ ability to apply the core principles of Evolutionary Medicine to a variety of
health-related scenarios, (2) reevaluating existing measures of student evolution
acceptance by using student interviews to assess response process validity, and (3)
correcting the validity issues identified on the most widely-used measure of evolution
acceptance - the Measure of Acceptance of the Theory of Evolution (MATE) - by
developing and validating a revised version of this survey: the MATE 2.0.
ContributorsMisheva, Anastasia Taya (Author) / Brownell, Sara (Thesis advisor) / Barnes, Elizabeth (Committee member) / Collins, James (Committee member) / Cooper, Katelyn (Committee member) / Sterner, Beckett (Committee member) / Arizona State University (Publisher)
Created2023