Implementation of a Collaborative Series of Classroom-Based Undergraduate Research Experiences Spanning Chemical Biology, Biochemistry, and Neurobiology

Kowalski, Jennifer R.; Johnson, R. Jeremy

doi:10.1187/cbe.16-02-0089

Cited by 44 publications

(34 citation statements)

References 56 publications

(163 reference statements)

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“…The enzymatic activity of ybfF, Rv0045c, and their variants was measured against the fluorogenic SAR library (Fig. 1) using a 96-well microplate assay (31,35,77). Fluorogenic substrates were prepared as stock solutions in DMSO (10 mM) and were diluted into PBS containing acetylated BSA (PBS-BSA; 0.1 mg/ml) to a starting concentration of 100 M. Acetylated BSA was added to reduce nonspecific adsorption to the plasticware common in microplate analysis (29).…”

Section: Kinetic Measurements With Fluorogenic Sar Librarymentioning

confidence: 99%

Fluorogenic structure activity library pinpoints molecular variations in substrate specificity of structurally homologous esterases

White

Koelper

Russell

et al. 2018

Journal of Biological Chemistry

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Cellular esterases catalyze many essential biological functions by performing hydrolysis reactions on diverse substrates. The promiscuity of esterases complicates assignment of their substrate preferences and biological functions. To identify universal factors controlling esterase substrate recognition, we designed a 32-member structure-activity relationship (SAR) library of fluorogenic ester substrates and used this library to systematically interrogate esterase preference for chain length, branching patterns, and polarity to differentiate common classes of esterase substrates. Two structurally homologous bacterial esterases were screened against this library, refining their previously broad overlapping substrate specificity. esterase ybfF displayed a preference for γ-position thioethers and ethers, whereas Rv0045c from displayed a preference for branched substrates with and without thioethers. We determined that this substrate differentiation was partially controlled by individual substrate selectivity residues Tyr-119 in ybfF and His-187 in Rv0045c; reciprocal substitution of these residues shifted each esterase's substrate preference. This work demonstrates that the selectivity of esterases is tuned based on transition state stabilization, identifies thioethers as an underutilized functional group for esterase substrates, and provides a rapid method for differentiating structural isozymes. This SAR library could have multifaceted future applications, including imaging, biocatalyst screening, molecular fingerprinting, and inhibitor design.

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Section: Kinetic Measurements With Fluorogenic Sar Librarymentioning

confidence: 99%

Fluorogenic structure activity library pinpoints molecular variations in substrate specificity of structurally homologous esterases

White

Koelper

Russell

et al. 2018

Journal of Biological Chemistry

Self Cite

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“…Many of the items on the survey focused on learning specific subject matter, and we did not expect students to have learned many facts, but rather we expected that gains would be apparent in specifically those items addressing working in groups, on working on problems without clear solutions, on data collection/organization and interpretation, and on using this technology and related data to describe the complexity of human movement. The capacity of the RISC survey or its components to measure students increasing dexterity with these research skills has been demonstrated repeatedly in inquiry-driven science classrooms (Burnette & Wessler, 2013;Call et al, 2007;Clark et al, 2009;Jordan et al, 2014;Kowalski, Hoops & Johnson, 2016;Lopatto et al, 2008;Mader et al, 2017;Makarevitch, Frechette & Wiatros, 2015;Miller et al, 2013;Reed & Richardson, 2013;Staub et al, 2016;Sarmah et al, 2016). We hoped to identify whether there were post-course gains that might exceed the average of all students responding to the RISC that semester.…”

Section: The Risc Surveymentioning

confidence: 98%

Teaching movement science with full-body motion-capture in an undergraduate liberal-arts psychology class

Yao¹,

Queathem²,

Neville³

et al. 2018

Preprint

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Movement science is a field that is quickly growing in its scope, leaning heavily on psychological expertise for research design with human participants but requiring computational and engineering ability. Undergraduate psychology curricula are in a unique position to train some of its future scholars. This report reviews an attempt to pilot a class on motion-capture for undergraduate psychology students. Recent developments in motion-capture technology have opened up the opportunity for giving hands-on experience with high-quality motion capture for students at liberal-arts colleges with lean research budgets. Post-course responses to the Research on Integrated Science Curriculum (RISC) survey demonstrated that our students made significantly large gains in their ability to organize an empirical approach to studying a complex problem with no clear solution, and to collect and analyze data to produce a coherent insight about that problem. Students may benefit from incorporating motion-capture into their undergraduate psychology curriculum.

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“…Many of the items on the survey focused on learning specific subject matter, and we did not expect students to have learnt many facts; rather we expected that gains would be apparent in specifically those items addressing working in groups, working on problems without clear solutions, on data collection/organisation and interpretation, and on using this technology and related data to describe the complexity of human movement. The capacity of the RISC survey or its components to measure students' increasing dexterity with these research skills has been demonstrated repeatedly in inquiry-driven science classrooms (Burnette and Wessler 2013;Call et al 2007;Clark et al 2009;Jordan et al 2014;Kowalski, Hoops and Johnson 2016;Lopatto et al 2008;Mader et al 2017;Makarevitch, Frechette and Wiatros 2015;Miller et al 2013;Reed and Richardson 2013;Sarmah et al 2016;Staub et al 2016). We aimed to identify whether there were post-course gains that might exceed the average of all students responding to the RISC of that semester.…”

Section: The Risc Surveymentioning

confidence: 99%

Teaching movement science with full-body motion capture in an undergraduate liberal arts psychology class

Yao

Queathem

Neville

et al. 2018

Research in Learning Technology

View full text Add to dashboard Cite

Movement science is a field that is quickly growing in its scope, leaning heavily on psychological expertise for research design with human participants but requiring computational and engineering ability. Undergraduate psychology curricula are in a unique position to train some of its future scholars. This report reviews an attempt to pilot a class on motion capture for undergraduate psychology students. Recent developments in motion-capture technology have opened up the opportunity for giving hands-on experience with high-quality motion capture for students at liberal-arts colleges with leaner research budgets. Post-course responses to the Research on Integrated Science Curriculum (RISC) survey demonstrated that our students made significantly large gains in their ability to organise an empirical approach to study a complex problem with no clear solution, and to collect and analyse data to produce a coherent insight about that problem. Students may benefit from incorporating motion capture into their undergraduate psychology curriculum.

show abstract

Implementation of a Collaborative Series of Classroom-Based Undergraduate Research Experiences Spanning Chemical Biology, Biochemistry, and Neurobiology

Cited by 44 publications

References 56 publications

Fluorogenic structure activity library pinpoints molecular variations in substrate specificity of structurally homologous esterases

Fluorogenic structure activity library pinpoints molecular variations in substrate specificity of structurally homologous esterases

Teaching movement science with full-body motion-capture in an undergraduate liberal-arts psychology class

Teaching movement science with full-body motion capture in an undergraduate liberal arts psychology class

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