Pub Date : 2023-08-01DOI: 10.35459/tbp.2022.000239
Jessica I. Kelz, Jose L. Uribe, M. Rasekh, Gemma R. Takahashi, Wyeth Gibson, Renée D. Link, K. McKnelly, Rachel W. Martin
Specifications grading is a student-centered assessment method that enables flexibility and opportunities for revision. Here, we describe the first known full implementation of specifications grading in an upper-division chemical biology course. Due to the rapid development of relevant knowledge in this discipline, the overarching goal of this class is to prepare students to interpret and communicate about current research. In the past, a conventional points-based assessment method made it challenging to ensure that satisfactory standards for student work were consistently met, particularly for comprehensive written assignments. Specifications grading was chosen because the core tenet requires students to demonstrate minimum learning objectives to achieve a passing grade and complete more content of increased cognitive complexity to achieve higher grades. This strict adherence to determining grades based on demonstrated skills is balanced by opportunities for revision or flexibility in assignment deadlines. These options are made manageable for the instructors through the use of a token economy with a limited number of tokens that students can choose to use when needed. Over the duration of the course, a validated survey on self-efficacy showed slight positive trends, student comprehension and demonstrated skills qualitatively improved, and final grade distributions were not negatively affected. Instructors noticed that discussions with students were more focused on course concepts and feedback, rather than grades, while overall grading time was reduced. Responses to university-administered student feedback surveys revealed some self-reported reduction in anxiety, as well as increased confidence in managing time and course material. Recommendations are provided on how to continue to improve the overall teaching and learning experience for both instructors and students.
{"title":"Implementation of Specifications Grading in an Upper-Division Chemical Biology Lecture Course","authors":"Jessica I. Kelz, Jose L. Uribe, M. Rasekh, Gemma R. Takahashi, Wyeth Gibson, Renée D. Link, K. McKnelly, Rachel W. Martin","doi":"10.35459/tbp.2022.000239","DOIUrl":"https://doi.org/10.35459/tbp.2022.000239","url":null,"abstract":"\u0000 Specifications grading is a student-centered assessment method that enables flexibility and opportunities for revision. Here, we describe the first known full implementation of specifications grading in an upper-division chemical biology course. Due to the rapid development of relevant knowledge in this discipline, the overarching goal of this class is to prepare students to interpret and communicate about current research. In the past, a conventional points-based assessment method made it challenging to ensure that satisfactory standards for student work were consistently met, particularly for comprehensive written assignments. Specifications grading was chosen because the core tenet requires students to demonstrate minimum learning objectives to achieve a passing grade and complete more content of increased cognitive complexity to achieve higher grades. This strict adherence to determining grades based on demonstrated skills is balanced by opportunities for revision or flexibility in assignment deadlines. These options are made manageable for the instructors through the use of a token economy with a limited number of tokens that students can choose to use when needed. Over the duration of the course, a validated survey on self-efficacy showed slight positive trends, student comprehension and demonstrated skills qualitatively improved, and final grade distributions were not negatively affected. Instructors noticed that discussions with students were more focused on course concepts and feedback, rather than grades, while overall grading time was reduced. Responses to university-administered student feedback surveys revealed some self-reported reduction in anxiety, as well as increased confidence in managing time and course material. Recommendations are provided on how to continue to improve the overall teaching and learning experience for both instructors and students.","PeriodicalId":72403,"journal":{"name":"Biophysicist (Rockville, Md.)","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45021314","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-08-01DOI: 10.35459/tbp.2022.000227
A. Tabatabai, Macquarrie Thomson, Reece Keller
There are many instances of collective behaviors in the natural world. For example, eukaryotic cells coordinate their motion to heal wounds; bacteria swarm during colony expansion; defects in alignment in growing bacterial populations lead to biofilm growth; and birds move within dynamic flocks. Although the details of how these groups behave vary across animals and species, they share the same qualitative feature: they exhibit collective behaviors that are not simple extensions of details associated with the motion of an individual. To learn more about these biological systems, we propose studying these systems through the lens of the foundational Vicsek model. Here, we present the process of building this computational model from scratch in a tutorial format that focuses on building the appropriate skills of an undergraduate student. In doing so, an undergraduate student should be able to work alongside this article, the corresponding tutorial, and the original manuscript of the Vicsek model to build their own model. We conclude by summarizing some of the current work involving computational modeling of flocking with Vicsek-type models.
{"title":"Undergraduate Tutorial for Simulating Flocking with the Vicsek Model","authors":"A. Tabatabai, Macquarrie Thomson, Reece Keller","doi":"10.35459/tbp.2022.000227","DOIUrl":"https://doi.org/10.35459/tbp.2022.000227","url":null,"abstract":"\u0000 There are many instances of collective behaviors in the natural world. For example, eukaryotic cells coordinate their motion to heal wounds; bacteria swarm during colony expansion; defects in alignment in growing bacterial populations lead to biofilm growth; and birds move within dynamic flocks. Although the details of how these groups behave vary across animals and species, they share the same qualitative feature: they exhibit collective behaviors that are not simple extensions of details associated with the motion of an individual. To learn more about these biological systems, we propose studying these systems through the lens of the foundational Vicsek model. Here, we present the process of building this computational model from scratch in a tutorial format that focuses on building the appropriate skills of an undergraduate student. In doing so, an undergraduate student should be able to work alongside this article, the corresponding tutorial, and the original manuscript of the Vicsek model to build their own model. We conclude by summarizing some of the current work involving computational modeling of flocking with Vicsek-type models.","PeriodicalId":72403,"journal":{"name":"Biophysicist (Rockville, Md.)","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48896499","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-08-01DOI: 10.35459/tbp.2022.000240
Thomas Zimmerman, R. Esquerra, Y. M. Chan, Anagha Kulkarni, N. Adelstein, Ashley Albright, Jiayu Luo, Ziah Dean, Salma Ahmed, Michelle Phillips, Simone Bianco, S. Capponi
Biophysics is an interdisciplinary pursuit requiring researchers with knowledge and skills in several areas. Optical instruments and computers are fundamental tools in biophysics research to collect and analyze data. We developed a 1-semester Optical Engineering Laboratory course to teach image processing, optical engineering, and research skills to undergraduate students majoring in biology and biochemistry. With the use of development systems on students' laptops and in the cloud, students learned image processing with Python and OpenCV. Each student constructed a microprocessor-based lensless holographic microscope, gaining hands-on experience with optical engineering. The class culminated in original, student-designed research projects. All lectures, hands-on labs, and student research projects were performed both in person and remotely, in response to the COVID-19 pandemic.
{"title":"Teaching Image Processing and Optical Engineering to University Biology Students","authors":"Thomas Zimmerman, R. Esquerra, Y. M. Chan, Anagha Kulkarni, N. Adelstein, Ashley Albright, Jiayu Luo, Ziah Dean, Salma Ahmed, Michelle Phillips, Simone Bianco, S. Capponi","doi":"10.35459/tbp.2022.000240","DOIUrl":"https://doi.org/10.35459/tbp.2022.000240","url":null,"abstract":"\u0000 Biophysics is an interdisciplinary pursuit requiring researchers with knowledge and skills in several areas. Optical instruments and computers are fundamental tools in biophysics research to collect and analyze data. We developed a 1-semester Optical Engineering Laboratory course to teach image processing, optical engineering, and research skills to undergraduate students majoring in biology and biochemistry. With the use of development systems on students' laptops and in the cloud, students learned image processing with Python and OpenCV. Each student constructed a microprocessor-based lensless holographic microscope, gaining hands-on experience with optical engineering. The class culminated in original, student-designed research projects. All lectures, hands-on labs, and student research projects were performed both in person and remotely, in response to the COVID-19 pandemic.","PeriodicalId":72403,"journal":{"name":"Biophysicist (Rockville, Md.)","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41889848","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-07-07DOI: 10.35459/tbp.2022.000232
Collette Higgins, Mason Ong, Alexander Sedley, Jacob Brothers, Callie J. Miller, N. Wright
{"title":"Bringing Biophysics Outreach to a Rural County Fair","authors":"Collette Higgins, Mason Ong, Alexander Sedley, Jacob Brothers, Callie J. Miller, N. Wright","doi":"10.35459/tbp.2022.000232","DOIUrl":"https://doi.org/10.35459/tbp.2022.000232","url":null,"abstract":"","PeriodicalId":72403,"journal":{"name":"Biophysicist (Rockville, Md.)","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44178407","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-04-11DOI: 10.35459/tbp.2022.000225
Caleigh M. Goodwin-Schoen, Rebecca E. Taylor
Dynamic and flexible nucleic acid models can provide current and future scientists with physical intuition for the structure of DNA and the ways that DNA and its synthetic mimics can be used to build self-assembling structures and advanced nanomachines. As more research labs and classrooms dive into the field of structural nucleic acid nanotechnology, students and researchers need access to interactive, dynamic, handheld models. Here, we present a 3D-printable kit for the construction of DNA and peptide nucleic acid (PNA). We have engineered a previous modular DNA kit to reduce costs while improving ease of assembly, flexibility, and robustness. We have also expanded the scope of available snap-together models by creating the first 3D-printable models of γPNA, an emerging material for nuclease- and protease-resistance nanotechnology. Building on previous research, representative nucleic acid duplexes were split into logical monomer segments, and atomic coordinates were used to create solid models for 3D printing. We used a human factors approach to customize 3 types of articulated snap-together connectors that allow for physically relevant motion characteristic of each interface in the model. Modules are easy to connect and separate manually but stay together when the model is manipulated. To greatly reduce cost, we bundled these segments for printing, and we created a miniaturized version that uses less than half the printing material to build. Our novel 3D-printed articulated snap-together models capture the flexibility and robustness of DNA and γPNA nanostructures. Resulting handheld helical models replicate the geometries in published structures and can now flex to form crossovers and allow biologically relevant zipping and unzipping to allow complex demonstrations of nanomachines undergoing strand displacement reactions. Finally, the same tools used to create these models can be readily applied to other types of backbones and nucleobases for endless research and education possibilities.
{"title":"Modular, Articulated Models of DNA and Peptide Nucleic Acids for Nanotechnology Education","authors":"Caleigh M. Goodwin-Schoen, Rebecca E. Taylor","doi":"10.35459/tbp.2022.000225","DOIUrl":"https://doi.org/10.35459/tbp.2022.000225","url":null,"abstract":"\u0000 Dynamic and flexible nucleic acid models can provide current and future scientists with physical intuition for the structure of DNA and the ways that DNA and its synthetic mimics can be used to build self-assembling structures and advanced nanomachines. As more research labs and classrooms dive into the field of structural nucleic acid nanotechnology, students and researchers need access to interactive, dynamic, handheld models. Here, we present a 3D-printable kit for the construction of DNA and peptide nucleic acid (PNA). We have engineered a previous modular DNA kit to reduce costs while improving ease of assembly, flexibility, and robustness. We have also expanded the scope of available snap-together models by creating the first 3D-printable models of γPNA, an emerging material for nuclease- and protease-resistance nanotechnology. Building on previous research, representative nucleic acid duplexes were split into logical monomer segments, and atomic coordinates were used to create solid models for 3D printing. We used a human factors approach to customize 3 types of articulated snap-together connectors that allow for physically relevant motion characteristic of each interface in the model. Modules are easy to connect and separate manually but stay together when the model is manipulated. To greatly reduce cost, we bundled these segments for printing, and we created a miniaturized version that uses less than half the printing material to build. Our novel 3D-printed articulated snap-together models capture the flexibility and robustness of DNA and γPNA nanostructures. Resulting handheld helical models replicate the geometries in published structures and can now flex to form crossovers and allow biologically relevant zipping and unzipping to allow complex demonstrations of nanomachines undergoing strand displacement reactions. Finally, the same tools used to create these models can be readily applied to other types of backbones and nucleobases for endless research and education possibilities.","PeriodicalId":72403,"journal":{"name":"Biophysicist (Rockville, Md.)","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44734290","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-03-23DOI: 10.35459/tbp.2022.000221
K. Skriver, Signe A. Sjørup, A. Langkilde, Evanthia Balouka, Caspar S. Christensen, Kathrine Carbel, Jens N. V. Decker, D. N. Essenbæk, Justus F. Gräf, Camilla H. Jessen, Peter Kristensen, Christoffer Merrild, Tobias S. Mortensen, Isabella F. Nalepa, Bjørn W. Nordsteen, Sophie K. Svoren, M. van Hall, Jan Weicher, Malene L. Wind, Danping Zhang, Daniel Saar, Helle Blæsild, M. Stahlhut, K. V. Andersen, R. Dagil, B. Vestergaard, Marie L. Ryberg, B. Kragelund
2,2,2-trifluoroethanol (TFE) as well as SAXS and 1-anilino-8-naphthalene sulphonate (ANS) binding supports a molten globule character. (b) The homology block 1 (HB1) domain of VAR2CSA (VAR2CSA 818–859 ) shows heterogeneity and oligomerization, as seen from the very few peaks in the NMR spectrum and the diversity of peaks originating from the single tryptophan (see figure insert). Addition of crowding agents as polyethylene glycol led to disappearance of the signals and fluorescence quenching, without visible precipitation. (c) A region of the intracellular domain of interleukin 22 receptor A1 (IL22RA1 L447–L532 ) was confirmed to be disordered by NMR and circular dichroism, with distinct cis - trans isomerism. (d) A lipidated, disordered C-terminal tail of KRAS form oligomers leading to broad peaks in the 1 H-NMR spectrum, that can be partly resolved by sodium dodecyl sulfate addition, but with an increasing SAXS Kratky plot indicating the presence of remaining disorder. (e) The N-terminal domain of galectin 3 is disordered as evidenced by the low dispersion in the 15N-HSQC and the increasing SAXS Kratky plot. NMR data indicate that it binds lactose and galactose very weakly at low pH. (f) The NMR signals of dehydrin Rab16c shows a low dispersion in the 15 N-HSQC spectrum, indicative of disorder, and elutes in two populations on a Sephadex S75 column, corresponding in sizes to the presence of a monomer–dimer equilibrium. The results presented in this figure are all preliminary data and would need repetition and validation.
{"title":"Intrinsically Disordered Proteins as an Instrument for Research-Integrating Teaching","authors":"K. Skriver, Signe A. Sjørup, A. Langkilde, Evanthia Balouka, Caspar S. Christensen, Kathrine Carbel, Jens N. V. Decker, D. N. Essenbæk, Justus F. Gräf, Camilla H. Jessen, Peter Kristensen, Christoffer Merrild, Tobias S. Mortensen, Isabella F. Nalepa, Bjørn W. Nordsteen, Sophie K. Svoren, M. van Hall, Jan Weicher, Malene L. Wind, Danping Zhang, Daniel Saar, Helle Blæsild, M. Stahlhut, K. V. Andersen, R. Dagil, B. Vestergaard, Marie L. Ryberg, B. Kragelund","doi":"10.35459/tbp.2022.000221","DOIUrl":"https://doi.org/10.35459/tbp.2022.000221","url":null,"abstract":"2,2,2-trifluoroethanol (TFE) as well as SAXS and 1-anilino-8-naphthalene sulphonate (ANS) binding supports a molten globule character. (b) The homology block 1 (HB1) domain of VAR2CSA (VAR2CSA 818–859 ) shows heterogeneity and oligomerization, as seen from the very few peaks in the NMR spectrum and the diversity of peaks originating from the single tryptophan (see figure insert). Addition of crowding agents as polyethylene glycol led to disappearance of the signals and fluorescence quenching, without visible precipitation. (c) A region of the intracellular domain of interleukin 22 receptor A1 (IL22RA1 L447–L532 ) was confirmed to be disordered by NMR and circular dichroism, with distinct cis - trans isomerism. (d) A lipidated, disordered C-terminal tail of KRAS form oligomers leading to broad peaks in the 1 H-NMR spectrum, that can be partly resolved by sodium dodecyl sulfate addition, but with an increasing SAXS Kratky plot indicating the presence of remaining disorder. (e) The N-terminal domain of galectin 3 is disordered as evidenced by the low dispersion in the 15N-HSQC and the increasing SAXS Kratky plot. NMR data indicate that it binds lactose and galactose very weakly at low pH. (f) The NMR signals of dehydrin Rab16c shows a low dispersion in the 15 N-HSQC spectrum, indicative of disorder, and elutes in two populations on a Sephadex S75 column, corresponding in sizes to the presence of a monomer–dimer equilibrium. The results presented in this figure are all preliminary data and would need repetition and validation.","PeriodicalId":72403,"journal":{"name":"Biophysicist (Rockville, Md.)","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47946602","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-02-15DOI: 10.35459/tbp.2022.000230
C. H. Crouch
{"title":"So Simple A Beginning: How Four Physical Principles Shape Our Living World by Raghuveer Parthasarathy","authors":"C. H. Crouch","doi":"10.35459/tbp.2022.000230","DOIUrl":"https://doi.org/10.35459/tbp.2022.000230","url":null,"abstract":"","PeriodicalId":72403,"journal":{"name":"Biophysicist (Rockville, Md.)","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48915849","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-02-06DOI: 10.35459/tbp.2022.000220
Hassler Stefan Macías-Sánchez, Irene Gómez-Oropeza, A. Rodríguez-Marín, María Fernanda Romero-Espinoza, Joseline Arroyo-Hernández, Jorge Alberto Guevara-Díaz
{"title":"Integrating CURE in Basic Medical Courses: The Perspective of Mexican Medical Students","authors":"Hassler Stefan Macías-Sánchez, Irene Gómez-Oropeza, A. Rodríguez-Marín, María Fernanda Romero-Espinoza, Joseline Arroyo-Hernández, Jorge Alberto Guevara-Díaz","doi":"10.35459/tbp.2022.000220","DOIUrl":"https://doi.org/10.35459/tbp.2022.000220","url":null,"abstract":"","PeriodicalId":72403,"journal":{"name":"Biophysicist (Rockville, Md.)","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42275876","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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