Pub Date : 2024-07-25DOI: 10.35459/tbp.2024.000266
Y. M. Chan, Michelle Phillips, Katherine Nielsen, Diana S. Chu
A framework for a 2-wk summer research course is presented, with a mindset of discovery and self-advocacy that is interdisciplinary and inclusive. The foundations of the course are built upon 2 pillars: (a) a well-defined educational plan focused on cellular engineering, with a goal to instill an engineering mindset into the cell biology field; and (b) a tailored Dimensions of Mentoring policy, which uses a structured feedback system to define and strengthen mentor attributes and provide multiple opportunities for mentorship and mentorship training. Undergraduate and master’s student participants work with PhD students or postdoctoral/professor team leaders in small teams in discovery-based research projects. Multiple teams work in parallel during the 2-wk period and convene in course-wide meetings to share findings and give feedback. Working in small teams with multiple levels of peer and team lead mentoring, students experience advancement in research and technical skills. Participants also experience gains in their understanding of the overarching educational goals in cellular engineering and science communication skills through course-wide activities. The principles from the Dimensions of Mentoring were also effective, with mentors at different levels building strong inclusive teams, coaching practical skills, and promoting individual advocacy. Meeting basic needs, providing relatable role models, and prioritizing enjoyable team-building activities were found to be critical factors in providing inclusive and productive environments. Overall, participants report high satisfaction with a discovery-based interdisciplinary research experience because of a supported environment. This creation of a strong community benefits individual career development and contributes to sustainable research productivity.
{"title":"Building Interdisciplinary Skills and Mentorship Opportunities in a 2-Week Research Experience","authors":"Y. M. Chan, Michelle Phillips, Katherine Nielsen, Diana S. Chu","doi":"10.35459/tbp.2024.000266","DOIUrl":"https://doi.org/10.35459/tbp.2024.000266","url":null,"abstract":"\u0000 A framework for a 2-wk summer research course is presented, with a mindset of discovery and self-advocacy that is interdisciplinary and inclusive. The foundations of the course are built upon 2 pillars: (a) a well-defined educational plan focused on cellular engineering, with a goal to instill an engineering mindset into the cell biology field; and (b) a tailored Dimensions of Mentoring policy, which uses a structured feedback system to define and strengthen mentor attributes and provide multiple opportunities for mentorship and mentorship training. Undergraduate and master’s student participants work with PhD students or postdoctoral/professor team leaders in small teams in discovery-based research projects. Multiple teams work in parallel during the 2-wk period and convene in course-wide meetings to share findings and give feedback. Working in small teams with multiple levels of peer and team lead mentoring, students experience advancement in research and technical skills. Participants also experience gains in their understanding of the overarching educational goals in cellular engineering and science communication skills through course-wide activities. The principles from the Dimensions of Mentoring were also effective, with mentors at different levels building strong inclusive teams, coaching practical skills, and promoting individual advocacy. Meeting basic needs, providing relatable role models, and prioritizing enjoyable team-building activities were found to be critical factors in providing inclusive and productive environments. Overall, participants report high satisfaction with a discovery-based interdisciplinary research experience because of a supported environment. This creation of a strong community benefits individual career development and contributes to sustainable research productivity.","PeriodicalId":137456,"journal":{"name":"The Biophysicist","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141805826","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 : 2024-07-25DOI: 10.35459/tbp.2022.000237
Timothy E. Saunders, Robert A. Cross, Andrew J. Bowman
With the arrival of new technologies, the biological sciences have become significantly more quantitative over the past 30 years. These new approaches have drawn in researchers from a broad range of disciplines; for example, trained physicists are now commonplace among biology department faculty. Yet, education in the biological sciences often does not reflect this large shift. Here, we outline a new program developed and taught at the University of Warwick to tackle the challenge of bringing quantitative, interdisciplinary education to the biosciences. We provide an overview of the course and the rationale for its structure. We then discuss lessons learned to aid others planning to implement interdisciplinary undergraduate courses based on teaching from research.
{"title":"Designing and Delivering an Interdisciplinary Undergraduate Degree in Quantitative Biology","authors":"Timothy E. Saunders, Robert A. Cross, Andrew J. Bowman","doi":"10.35459/tbp.2022.000237","DOIUrl":"https://doi.org/10.35459/tbp.2022.000237","url":null,"abstract":"\u0000 With the arrival of new technologies, the biological sciences have become significantly more quantitative over the past 30 years. These new approaches have drawn in researchers from a broad range of disciplines; for example, trained physicists are now commonplace among biology department faculty. Yet, education in the biological sciences often does not reflect this large shift. Here, we outline a new program developed and taught at the University of Warwick to tackle the challenge of bringing quantitative, interdisciplinary education to the biosciences. We provide an overview of the course and the rationale for its structure. We then discuss lessons learned to aid others planning to implement interdisciplinary undergraduate courses based on teaching from research.","PeriodicalId":137456,"journal":{"name":"The Biophysicist","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141805785","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 : 2024-07-04DOI: 10.35459/tbp.2024.000261
Raghuveer Parthasarathy
Microscopy is crucial to much of biophysics. The variety of approaches to imaging exemplified by contemporary microscopes is remarkable, yet this breadth is generally unknown to students, limiting perceptions of biology, physics, and related fields and of potential career paths. We therefore created and implemented an outreach activity as part of a day camp that especially targeted low-income high school students. The students engaged with 3 very different microscopes: a simple transmitted light microscope; a light sheet fluorescence microscope; and a newly invented multicamera array microscope. With these instruments, we examined subjects such as transgenic zebrafish larvae with fluorescent immune cells, contrasting the various instruments’ capabilities, including resolution and field of view. Pre- and postactivity questions showed that the activity succeeded in expanding students’ understanding and appreciation of the varied aims and abilities of modern microscopes and moreover led to discussions of model organisms, biophysics, and science funding. Additional activities briefly illustrated the nature of digital images and mathematic manipulation. I describe here the activities and goals, as well as ways they can be generalized and implemented at other institutions with access to different sorts of imaging tools.
{"title":"A Microscope Medley for High School Students","authors":"Raghuveer Parthasarathy","doi":"10.35459/tbp.2024.000261","DOIUrl":"https://doi.org/10.35459/tbp.2024.000261","url":null,"abstract":"\u0000 Microscopy is crucial to much of biophysics. The variety of approaches to imaging exemplified by contemporary microscopes is remarkable, yet this breadth is generally unknown to students, limiting perceptions of biology, physics, and related fields and of potential career paths. We therefore created and implemented an outreach activity as part of a day camp that especially targeted low-income high school students. The students engaged with 3 very different microscopes: a simple transmitted light microscope; a light sheet fluorescence microscope; and a newly invented multicamera array microscope. With these instruments, we examined subjects such as transgenic zebrafish larvae with fluorescent immune cells, contrasting the various instruments’ capabilities, including resolution and field of view. Pre- and postactivity questions showed that the activity succeeded in expanding students’ understanding and appreciation of the varied aims and abilities of modern microscopes and moreover led to discussions of model organisms, biophysics, and science funding. Additional activities briefly illustrated the nature of digital images and mathematic manipulation. I describe here the activities and goals, as well as ways they can be generalized and implemented at other institutions with access to different sorts of imaging tools.","PeriodicalId":137456,"journal":{"name":"The Biophysicist","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141677942","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 : 2024-07-02DOI: 10.35459/tbp.2024.000246
Paulo F. Almeida, A. Pokorny, Elizabeth G. Shingleton, Koby P. Higgs
Students beginning the study of biochemistry or biophysics at the undergraduate or even early graduate level are often overwhelmed by the complexity of the systems and the nomenclature. By comparison, chemical systems appear simple, as students can more easily relate to introductory chemistry courses, where the molecules are smaller and bind yet smaller ions. This allows students to write the structure of the entire molecule on a piece of paper and see exactly to which functional groups an ion, such as a proton (H+) in the simplest case, binds. Yet, concepts that are fundamental in biochemical macromolecules, namely proteins, can perfectly well be taught at the undergraduate or beginning graduate level, and probably be more easily understood, by using simpler, familiar chemical examples. The concept of interacting binding sites, which is at the root of cooperativity in protein binding reactions and conformational changes, is already present in simple molecules, such as ethylenediaminetetraacetic acid (EDTA). In this article, we show how to teach these topics by using the idea of the partition function, rather than a formal algebraic approach, to treat the binding of protons to EDTA. Profound concepts, such as that of interacting sites, appear naturally in a small molecule, where the origin can be easily ascribed, in this case, mainly to electrostatic interactions. Equipped with this understanding and this approach, students will be able to tackle more complicated biochemical systems, in which the molecules are larger, but the concepts are the same.
{"title":"Understanding Microscopic Interactions in Binding Reactions: The pH Titration of EDTA","authors":"Paulo F. Almeida, A. Pokorny, Elizabeth G. Shingleton, Koby P. Higgs","doi":"10.35459/tbp.2024.000246","DOIUrl":"https://doi.org/10.35459/tbp.2024.000246","url":null,"abstract":"\u0000 Students beginning the study of biochemistry or biophysics at the undergraduate or even early graduate level are often overwhelmed by the complexity of the systems and the nomenclature. By comparison, chemical systems appear simple, as students can more easily relate to introductory chemistry courses, where the molecules are smaller and bind yet smaller ions. This allows students to write the structure of the entire molecule on a piece of paper and see exactly to which functional groups an ion, such as a proton (H+) in the simplest case, binds. Yet, concepts that are fundamental in biochemical macromolecules, namely proteins, can perfectly well be taught at the undergraduate or beginning graduate level, and probably be more easily understood, by using simpler, familiar chemical examples. The concept of interacting binding sites, which is at the root of cooperativity in protein binding reactions and conformational changes, is already present in simple molecules, such as ethylenediaminetetraacetic acid (EDTA). In this article, we show how to teach these topics by using the idea of the partition function, rather than a formal algebraic approach, to treat the binding of protons to EDTA. Profound concepts, such as that of interacting sites, appear naturally in a small molecule, where the origin can be easily ascribed, in this case, mainly to electrostatic interactions. Equipped with this understanding and this approach, students will be able to tackle more complicated biochemical systems, in which the molecules are larger, but the concepts are the same.","PeriodicalId":137456,"journal":{"name":"The Biophysicist","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141687847","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 : 2024-06-10DOI: 10.35459/tbp.2023.000259
Alba Alfonso-Garcia, Katjana Ehrlich, G. Ariño-Estrada, Hannah J. O’Toole, Abigail L. Humphries, Megan G. Villasenor, Sharon Aviran, Eleonora Grandi
The underrepresentation of women in science, technology, engineering, and mathematics (STEM) fields, including biomedical engineering, remains a persistent challenge and emphasizes the need for initiatives that attract and retain more women in the field. Such initiatives should address this gender imbalance and aim to harness the diverse perspectives and talents of all genders. Women in engineering face unique challenges due to the field’s male-dominated nature. Gender bias, stereotypes, and family-unfriendly expectations can significantly affect women’s experiences, hindering their opportunities for recognition and career advancement. A 2021 survey of the Biomedical Engineering Department and Graduate Group at the University of California Davis revealed that women and marginalized individuals experience a different sense of belonging compared with their white male counterparts, frequently encounter challenges related to implicit bias, microaggressions, and a lack of adequate support, mentorship, and opportunities for professional development. Here, we describe and reflect on the efforts by the Biomedical Engineering Health, Equity, and Wellness Committee to begin to address these challenges. We launched the Women+ in Biomedical Engineering Lunch Series, which provides a platform for women, marginalized individuals, and their allies to come together, connect, and share experiences. The lunch series aims to facilitate open dialogue, mentorship, and support and promote networking opportunities to bridge the gender gap in the field. The initial meetings in the Spring quarter of 2023 focused on key topics such as mentoring, mental health and stress management, and the effect of legislation on women’s professional lives. By providing a safe space for discussion, sharing experiences, and addressing these topics, the lunch series aims to break down barriers and build networks, foster a supportive environment, and empower women to thrive in biomedical engineering.
{"title":"Empowering Women in Biomedical Engineering: A Departmental Pathway to Inclusion and Support","authors":"Alba Alfonso-Garcia, Katjana Ehrlich, G. Ariño-Estrada, Hannah J. O’Toole, Abigail L. Humphries, Megan G. Villasenor, Sharon Aviran, Eleonora Grandi","doi":"10.35459/tbp.2023.000259","DOIUrl":"https://doi.org/10.35459/tbp.2023.000259","url":null,"abstract":"\u0000 The underrepresentation of women in science, technology, engineering, and mathematics (STEM) fields, including biomedical engineering, remains a persistent challenge and emphasizes the need for initiatives that attract and retain more women in the field. Such initiatives should address this gender imbalance and aim to harness the diverse perspectives and talents of all genders. Women in engineering face unique challenges due to the field’s male-dominated nature. Gender bias, stereotypes, and family-unfriendly expectations can significantly affect women’s experiences, hindering their opportunities for recognition and career advancement. A 2021 survey of the Biomedical Engineering Department and Graduate Group at the University of California Davis revealed that women and marginalized individuals experience a different sense of belonging compared with their white male counterparts, frequently encounter challenges related to implicit bias, microaggressions, and a lack of adequate support, mentorship, and opportunities for professional development. Here, we describe and reflect on the efforts by the Biomedical Engineering Health, Equity, and Wellness Committee to begin to address these challenges. We launched the Women+ in Biomedical Engineering Lunch Series, which provides a platform for women, marginalized individuals, and their allies to come together, connect, and share experiences. The lunch series aims to facilitate open dialogue, mentorship, and support and promote networking opportunities to bridge the gender gap in the field. The initial meetings in the Spring quarter of 2023 focused on key topics such as mentoring, mental health and stress management, and the effect of legislation on women’s professional lives. By providing a safe space for discussion, sharing experiences, and addressing these topics, the lunch series aims to break down barriers and build networks, foster a supportive environment, and empower women to thrive in biomedical engineering.","PeriodicalId":137456,"journal":{"name":"The Biophysicist","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141362975","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 : 2024-01-12DOI: 10.35459/tbp.2022.000238
Khovesh A. Ramdin, M. Hackl, S. Chundawat
The analysis of particles bound to surfaces by tethers can facilitate understanding of biophysical phenomena (e.g., DNA–protein or protein–ligand interactions and DNA extensibility). Modeling such systems theoretically aids in understanding experimentally observed motions, and the limitations of such models can provide insight into modeling complex systems. The simulation of tethered particle motion (TPM) allows for analysis of complex behaviors exhibited by such systems; however, this type of experiment is rarely taught in undergraduate science classes. We have developed a MATLAB simulation package intended to be used in academic contexts to concisely model and graphically represent the behavior of different tether–particle systems. We show how analysis of the simulation results can be used in biophysical research using single-molecule force spectroscopy (SMFS). Students in physics, engineering, and chemistry will be able to make connections with principles embedded in the field of study and understand how those principles can be used to create meaningful conclusions in a multidisciplinary context. The simulation package can model any given tether–particle system and allows the user to generate a parameter space with static and dynamic model components. Our simulation was successfully able to recreate generally observed experimental trends by using acoustic force spectroscopy (AFS). Further, the simulation was validated through consideration of the conservation of energy of the tether–bead system, trend analyses, and comparison of particle positional data from actual TPM in silico experiments conducted to simulate data with a parameter space similar to the AFS experimental setup. Overall, our TPM simulator and graphical user interface is primarily for demonstrating behaviors characteristic to TPM in a classroom setting but can serve as a template for researchers to set up TPM simulations to mimic a specific SMFS experimental setup.
对通过系链结合到表面的粒子进行分析有助于理解生物物理现象（如 DNA 与蛋白质或蛋白质与配体之间的相互作用以及 DNA 的延伸性）。对这类系统进行理论建模有助于理解实验观察到的运动，而这类模型的局限性也能为复杂系统的建模提供启示。通过模拟系留粒子运动（TPM），可以分析此类系统表现出的复杂行为；然而，这种类型的实验很少在本科科学课上讲授。我们开发了一个 MATLAB 仿真软件包，用于在学术环境中对不同系留粒子系统的行为进行简明建模和图形表示。我们展示了如何利用单分子力谱（SMFS）将模拟结果分析用于生物物理研究。物理学、工程学和化学专业的学生将能够与研究领域中的原理建立联系，并了解如何利用这些原理在多学科背景下得出有意义的结论。该模拟软件包可以模拟任何给定的系绳-粒子系统，并允许用户生成一个包含静态和动态模型组件的参数空间。我们的模拟利用声学力谱（AFS）成功地再现了普遍观察到的实验趋势。此外，我们还考虑了系留珠系统的能量守恒、趋势分析，并与实际 TPM 硅学实验中的粒子位置数据进行了比较，以模拟参数空间与 AFS 实验装置相似的数据，从而验证了模拟的有效性。总之，我们的 TPM 模拟器和图形用户界面主要用于在课堂上演示 TPM 的特征行为，但也可作为研究人员设置 TPM 模拟的模板，以模仿特定的 SMFS 实验装置。
{"title":"Visualization of Tethered Particle Motion with a Multidimensional Simulation","authors":"Khovesh A. Ramdin, M. Hackl, S. Chundawat","doi":"10.35459/tbp.2022.000238","DOIUrl":"https://doi.org/10.35459/tbp.2022.000238","url":null,"abstract":"\u0000 The analysis of particles bound to surfaces by tethers can facilitate understanding of biophysical phenomena (e.g., DNA–protein or protein–ligand interactions and DNA extensibility). Modeling such systems theoretically aids in understanding experimentally observed motions, and the limitations of such models can provide insight into modeling complex systems. The simulation of tethered particle motion (TPM) allows for analysis of complex behaviors exhibited by such systems; however, this type of experiment is rarely taught in undergraduate science classes. We have developed a MATLAB simulation package intended to be used in academic contexts to concisely model and graphically represent the behavior of different tether–particle systems. We show how analysis of the simulation results can be used in biophysical research using single-molecule force spectroscopy (SMFS). Students in physics, engineering, and chemistry will be able to make connections with principles embedded in the field of study and understand how those principles can be used to create meaningful conclusions in a multidisciplinary context. The simulation package can model any given tether–particle system and allows the user to generate a parameter space with static and dynamic model components. Our simulation was successfully able to recreate generally observed experimental trends by using acoustic force spectroscopy (AFS). Further, the simulation was validated through consideration of the conservation of energy of the tether–bead system, trend analyses, and comparison of particle positional data from actual TPM in silico experiments conducted to simulate data with a parameter space similar to the AFS experimental setup. Overall, our TPM simulator and graphical user interface is primarily for demonstrating behaviors characteristic to TPM in a classroom setting but can serve as a template for researchers to set up TPM simulations to mimic a specific SMFS experimental setup.","PeriodicalId":137456,"journal":{"name":"The Biophysicist","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139532008","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 : 2023-12-07DOI: 10.35459/tbp.2023.000248
T. Sedighi, T. Radu, Q. F. Ashraf, B. Kumar, E. J. Quilates, R. Rahmatullah, J. N. Milstein
We developed the Interdisciplinary Science Program in Research and Entrepreneurship (INSPIRE) to address the changing career landscape that students with an interest in Biophysics, Physical Chemistry, and Biochemistry face. Third and fourth-year undergraduate Chemistry and Physics students participated in a 4-week, hands-on program that introduced applications of biophysical and biochemical techniques to drug discovery, while simultaneously engaging in a crash course on entrepreneurship and pharma. The principal objective of this inaugural, pilot program was to introduce undergraduate students interested in pursuing a PhD to the interdisciplinary nature of Chemistry and Physics research in the Life Sciences, while simultaneously introducing the idea of translating their future graduate work into a career in biotechnology.
{"title":"INSPIRE: Development of an Interdisciplinary Science Program in Research and Entrepreneurship","authors":"T. Sedighi, T. Radu, Q. F. Ashraf, B. Kumar, E. J. Quilates, R. Rahmatullah, J. N. Milstein","doi":"10.35459/tbp.2023.000248","DOIUrl":"https://doi.org/10.35459/tbp.2023.000248","url":null,"abstract":"\u0000 We developed the Interdisciplinary Science Program in Research and Entrepreneurship (INSPIRE) to address the changing career landscape that students with an interest in Biophysics, Physical Chemistry, and Biochemistry face. Third and fourth-year undergraduate Chemistry and Physics students participated in a 4-week, hands-on program that introduced applications of biophysical and biochemical techniques to drug discovery, while simultaneously engaging in a crash course on entrepreneurship and pharma. The principal objective of this inaugural, pilot program was to introduce undergraduate students interested in pursuing a PhD to the interdisciplinary nature of Chemistry and Physics research in the Life Sciences, while simultaneously introducing the idea of translating their future graduate work into a career in biotechnology.","PeriodicalId":137456,"journal":{"name":"The Biophysicist","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138592758","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 : 2023-12-07DOI: 10.35459/tbp.2023.000253
Alexandra Bermudez, Samanta Negrete Muñoz, Rita Blaik, Amy C. Rowat, Jimmy Hu, Neil Y.C. Lin
Epithelial mechanics and mechanobiology have become 2 important research fields in life sciences and bioengineering. These fields investigate how physical factors induced by cell adhesion and collective behaviors can directly regulate biologic processes, such as organ development and disease progression. Cell mechanics and mechanobiology thus make exciting biophysics education topics to illustrate how fundamental physics principles play a role in regulating cell biology. However, the field currently lacks hands-on activities that engage students in learning science and outreach programs in these topics. One such area is the development of robust hands-on modules that allow students to observe features of cell shape and mechanics and connect them to fundamental physics principles. Here, we demonstrate a workflow that engages students in studying epithelial cell mechanics by using commercial histology slides of frog skin. We show that by using recently developed artificial intelligence–based image-segmentation tools, students can easily quantify different cell morphologic features in a high-throughput manner. Using our workflow, students can reproduce 2 essential findings in cell mechanics: the common gamma distribution of normalized cell aspect ratio in jammed epithelia and the constant ratio between the nuclear and cellular area. Importantly, because the only required instrument for this active learning module is a readily available light microscope and a computer, our module is relatively low cost, as well as portable. These features make the module scalable for students at various education levels and outreach programs. This highly accessible education module provides a fun and engaging way to introduce students to the world of epithelial tissue mechanics.
{"title":"Using Histologic Image Analysis to Understand Biophysical Regulations of Epithelial Cell Morphology","authors":"Alexandra Bermudez, Samanta Negrete Muñoz, Rita Blaik, Amy C. Rowat, Jimmy Hu, Neil Y.C. Lin","doi":"10.35459/tbp.2023.000253","DOIUrl":"https://doi.org/10.35459/tbp.2023.000253","url":null,"abstract":"\u0000 Epithelial mechanics and mechanobiology have become 2 important research fields in life sciences and bioengineering. These fields investigate how physical factors induced by cell adhesion and collective behaviors can directly regulate biologic processes, such as organ development and disease progression. Cell mechanics and mechanobiology thus make exciting biophysics education topics to illustrate how fundamental physics principles play a role in regulating cell biology. However, the field currently lacks hands-on activities that engage students in learning science and outreach programs in these topics. One such area is the development of robust hands-on modules that allow students to observe features of cell shape and mechanics and connect them to fundamental physics principles. Here, we demonstrate a workflow that engages students in studying epithelial cell mechanics by using commercial histology slides of frog skin. We show that by using recently developed artificial intelligence–based image-segmentation tools, students can easily quantify different cell morphologic features in a high-throughput manner. Using our workflow, students can reproduce 2 essential findings in cell mechanics: the common gamma distribution of normalized cell aspect ratio in jammed epithelia and the constant ratio between the nuclear and cellular area. Importantly, because the only required instrument for this active learning module is a readily available light microscope and a computer, our module is relatively low cost, as well as portable. These features make the module scalable for students at various education levels and outreach programs. This highly accessible education module provides a fun and engaging way to introduce students to the world of epithelial tissue mechanics.","PeriodicalId":137456,"journal":{"name":"The Biophysicist","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138594455","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 : 2023-05-09DOI: 10.35459/tbp.2022.000228
Peter E. Beshay, Anjelica Kucinic, Nicholas Wile, Patrick Halley, Lilly Des Rosiers, Amjad Chowdhury, Julia L. Hall, Carlos E. Castro, Michael W. Hudoba
ABSTRACT DNA origami is a rapidly emerging nanotechnology that enables researchers to create nanostructures with unprecedented geometric precision that have tremendous potential to advance a variety of fields, including molecular sensing, robotics, and nanomedicine. Hence, many students could benefit from exposure to basic knowledge of DNA origami nanotechnology. However, due to the complexity of design, cost of materials, and cost of equipment, experiments with DNA origami have been limited mainly to research institutions in graduate-level laboratories with significant prior expertise and well-equipped laboratories. This work focuses on overcoming critical barriers to translating DNA origami methods to educational laboratory settings. In particular, we present a streamlined protocol for fabrication and analysis of DNA origami nanostructures that can be carried out within a 2-h laboratory course using low-cost equipment, much of which is readily available in educational laboratories and science classrooms. We focus this educational experiment module on a DNA origami nanorod structure that was previously developed for drug delivery applications. In addition to fabricating nanostructures, we demonstrate a protocol for students to analyze structures via gel electrophoresis using classroom-ready gel equipment. These results establish a basis to expose students to DNA origami nanotechnology and can enable or reinforce valuable learning milestones in fields such as biomaterials, biological engineering, and nanomedicine. Furthermore, introducing students to DNA nanotechnology and related fields can also have the potential to increase interest and future involvement by young students.
{"title":"Translating DNA Origami Nanotechnology to Middle School, High School, and Undergraduate Laboratories","authors":"Peter E. Beshay, Anjelica Kucinic, Nicholas Wile, Patrick Halley, Lilly Des Rosiers, Amjad Chowdhury, Julia L. Hall, Carlos E. Castro, Michael W. Hudoba","doi":"10.35459/tbp.2022.000228","DOIUrl":"https://doi.org/10.35459/tbp.2022.000228","url":null,"abstract":"ABSTRACT DNA origami is a rapidly emerging nanotechnology that enables researchers to create nanostructures with unprecedented geometric precision that have tremendous potential to advance a variety of fields, including molecular sensing, robotics, and nanomedicine. Hence, many students could benefit from exposure to basic knowledge of DNA origami nanotechnology. However, due to the complexity of design, cost of materials, and cost of equipment, experiments with DNA origami have been limited mainly to research institutions in graduate-level laboratories with significant prior expertise and well-equipped laboratories. This work focuses on overcoming critical barriers to translating DNA origami methods to educational laboratory settings. In particular, we present a streamlined protocol for fabrication and analysis of DNA origami nanostructures that can be carried out within a 2-h laboratory course using low-cost equipment, much of which is readily available in educational laboratories and science classrooms. We focus this educational experiment module on a DNA origami nanorod structure that was previously developed for drug delivery applications. In addition to fabricating nanostructures, we demonstrate a protocol for students to analyze structures via gel electrophoresis using classroom-ready gel equipment. These results establish a basis to expose students to DNA origami nanotechnology and can enable or reinforce valuable learning milestones in fields such as biomaterials, biological engineering, and nanomedicine. Furthermore, introducing students to DNA nanotechnology and related fields can also have the potential to increase interest and future involvement by young students.","PeriodicalId":137456,"journal":{"name":"The Biophysicist","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135711517","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 : 2020-06-01DOI: 10.35459/tbp.2019.000113
J. Madrid-Wolff, Manu Forero-Shelton
Transmitted light imaging is an important tool in biophysics for applications that include sample analysis, recording samples whose viability is compromised by high levels of illumination (e.g., live cell tracking), and finding regions of interest in a sample. Koehler transillumination is a powerful illumination method used in commercial microscopes; yet commercial Koehler condensers are expensive, are difficult to integrate into tabletop systems, and make learning the concepts of Koehler illumination difficult because of their closed-box nature. Here, we show a protocol to build a simple 4f Koehler illumination system that offers advantages with respect to commercial condensers in terms of simplicity, cost, and compatibility with tabletop systems, such as open-source light sheet fluorescence microscopes. We include step-by-step instructions that can be followed by advanced undergraduate or graduate students without experience in optics on how to align and assemble the illuminator, along with a list of the necessary parts for assembly. We also include supplemental material that describes 4 supporting educational activities students can conduct with the apparatus and helps in the understanding of key concepts relevant to Koehler illumination and optics. The performance of the system is comparable to that of commercial condensers and significantly better, in terms of illumination homogeneity and depth of field (optical sections are possible), than that of LED flashlights, such as those found in low-cost diagnostic devices and tabletop systems.
{"title":"4f Koehler Transmitted Illumination Condenser for Teaching and Low-Cost Microscopic Imaging","authors":"J. Madrid-Wolff, Manu Forero-Shelton","doi":"10.35459/tbp.2019.000113","DOIUrl":"https://doi.org/10.35459/tbp.2019.000113","url":null,"abstract":"\u0000 Transmitted light imaging is an important tool in biophysics for applications that include sample analysis, recording samples whose viability is compromised by high levels of illumination (e.g., live cell tracking), and finding regions of interest in a sample. Koehler transillumination is a powerful illumination method used in commercial microscopes; yet commercial Koehler condensers are expensive, are difficult to integrate into tabletop systems, and make learning the concepts of Koehler illumination difficult because of their closed-box nature. Here, we show a protocol to build a simple 4f Koehler illumination system that offers advantages with respect to commercial condensers in terms of simplicity, cost, and compatibility with tabletop systems, such as open-source light sheet fluorescence microscopes. We include step-by-step instructions that can be followed by advanced undergraduate or graduate students without experience in optics on how to align and assemble the illuminator, along with a list of the necessary parts for assembly. We also include supplemental material that describes 4 supporting educational activities students can conduct with the apparatus and helps in the understanding of key concepts relevant to Koehler illumination and optics. The performance of the system is comparable to that of commercial condensers and significantly better, in terms of illumination homogeneity and depth of field (optical sections are possible), than that of LED flashlights, such as those found in low-cost diagnostic devices and tabletop systems.","PeriodicalId":137456,"journal":{"name":"The Biophysicist","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127557594","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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