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1. Expression-Based Cell Lineage Analysis inDrosophilaThrough a Course-Based Research Experience for Early Undergraduates

Author

Daniel Chang, Earl Yoon, David Loppato, Justin N. Maghen, Silverio D. Alvarez, Kristy Ou, Katherine E. Peterson, Manjeet Bhamra, Helen H.-L. Chan, Lilit Gevorgyan, Clifton Lee, Peter Trinh, David M. Li, Elizabeth Kim, Garrick Iwamoto, Yue Zhao, Victor W. Yee, Kimberly Gon, Lisa M. Scully, Akram V. Uraizee, Sangita Datta, Sae Ho Song, Lisa Han, Andrew C. J. Huang, PhuongThao Tran, George K. Yeh, John M. Olson, Shawn J. Kim, Lili Sadri, Hannah G. Ahn, Grace E. Lee, Cindy L. Trang, Arezou Babaesfahani, Stephanie Wang, Saif Ansari, Hanwool Kim, Rakesh Bhatia, Brandon Lung, Victoria Ragland, Noemi E. Lee, Casey Shapiro, Van Thanh Mai, Sean H. K. Lee, Holly Dickinson, Joseph Park, Rona Law, Carrou Lee, Cameron M. Rice, Kirandeep Sumra, Alexandra L. Pourzia, Raj Dhaliwal, Vijay A. Patel, Michael Guillermo Daniel, Elaine L. Hsia, Hiu Wai Lam, Yujin Park, Jason H. Melehani, Annie Tigranyan, Xin Zheng, Nasser Heyrani, Jennifer Chang, Neda Asem, Joseph Duy Nguyen, Hanh H. Nguyen, Ted T. Uotani, Harnek Singh, Riley Guerin, Han-Ching H. Tseng, Kevin K. T. Vu, Max Mittelman, Gregory E. Tong, Cynthia Yeh, Jonathan Tran, Steven V. Pham, Bryan Lau, Kenny Lee, Tulika Ghosh, Roger K. Lau, An Huynh Pham, Christopher M. From, Elizabeth B. Johnson, Bobby Asem, Abhik Banerjee, Utpal Banerjee, Derek J. Cheung, Kambria Nguyen, Zainab Saifee, Carmel M. Moazez, Hung G. Trinh, Hannah Kim, Sonja Darwish, Lu Chen, Sondra L. Snyder, Pei-Yun Kao, Kevin Chen, Youngho Cho, Joseph Hargan Calvopina, Neil D. Poria, Vanessa Shih, Danica D. Wiredja, Shuo Wang, Zunera Ghaznavi, Jenny Dinh, Andrew J. Kim, Simran Kahlon, Awais M. Khan, Yuyu Chen, Julie Ko, Elise M. Calonico, Joseph N. Dickan, Huy D. Le, Leslie Jaworski, Xingfu Liang, Brooke Scruggs, Marc Levis-Fitzgerald, Susie Moon, Sara K. Taylor, An An Jiang, Nicholas Bumacod, Siddharth Sukumar, Matthew G. Keehn, Aleksandar Kitich, Cheng-An Tony Chien, Alexander N. Patananan, Jesse J. Cheung, Ragini Bhargava, Michael J. Jang, Alana M. Chin, Nikki Villarasa, Carman Chan, Ami Patel, Stacy Hu, Chiaen Chang, Solomon Rojhani, Michelle J. Kim, Shivani K. Thaker, Daisuke Furukawa, Arunit Singh Chugh, Volker Hartenstein, Hao Li, Akash Bhakta, Khoa T. Truong-N, Mark Sy, Daniel Rothberg, Melinda Feng, Kristine Kim, Nicole A. Azarian, David J. Groves, Sravya Mallam, Man Ting Chou, Katelyn F. Sobotka, Kathy T. Ngo, Justin Hsueh, Jasmine Y. Chen, Jessica Chew, Ira E. Clark, Zhong Ye, Mark R. Cubberly, Komal Wadhwani, Sumedha Singh, Jonathan J. Caine, Tamir Sholklapper, Jane Kuon, Nicholas G. Kouzelos, Emmylou Dowling, Francie Diep, Carolyn Chu, Kalkidan K. Gurara, Isabella Niu, Yaelim A. Park, Yong Jun Lee, Ali R. Haghighi, Nauman Charania, Nitish Mittal, Chee Jia Chin, Ben Sprung-Keyser, Naseem Moridzadeh, Donald N. Allen, Virginia Chu, Cory J. Evans, Luke Berry, Ahmad Bahrami, Justin J. Houman, Jesse M. Zaretsky, Kimberly A. Passmore, Chris Iwuchukwu, Rebecca S. Wang, Christina Lee, David Roh, Hee Jong Kim, Szuyao Lee, Rameen S. Moridzadeh, Randi K. Oyama, Amy A. Patel, Regina Lee, Serena S. Luong, Manpreet Kaur, Dhruv Patel, Xi Xue, Johnny He, Seo-Kyung Oh, Sabrena M. Ahmadi, Angela W. Nieh, Anke Ziegenbalg, Thien Nguyen, Jacinda N. Tran, John Y. Yu, Brian S. Kim, Eric Lin, Omair Khan, Ross G. Kelley, Sung Kyu Lee, Jessica S. Ma, Tanya Hioe, Nicole B. Chew, Kayla G. H. Gurley, Mark R Murata, Jiwon Lee, Hande Tan, Andrew L. Wong, Michael Koenig, Sung-Ling D. Lee, In Young Choi, Daniel Sitz, Paluk K. Walia, Maggie K. Chu, Ke-Huan K. Chow, Jessica R. Ong, Michelle J. Lee, Jenny Huynh, Rachael Le, Riki D. Ranat, Griselda Yanez, Yung-Hsuan Yang, Molly Howland, Ross A. Kornberg, Agafe Saguros, Peter Lin, Jessie C. Wu, Rahul Kumar Ghosh, Anand D. Gandhi, Jaskaran Gill, Edward Kuoy, Tulsi Thakore, Ritika Dutta, Himaja Gaddipati, Truc Ta, Melissa E. Phuphanich, Stacey Lu, Suji Kim, Letty Liang, Megan J. Leong, Derrick M. Chu, Michelle M. Lin, Alejandro LaRiviere, Alexandra L. Havard, Subir Bhatia, Minh-Tu Do, Sarah Kang, Jon Alkali, Kent K. T. Vu, Brian A. Shin, Samira J. Akhave, Kirim Hong, Thomas A. Caldwell, Jonathan Hofman, Vivi Tran, Katherine Chuang, Paul D. Picard, Jay Wang, Nicole A. Calica, Tiffany Y. Lin, Ryan C. Miller, Ida Azizkhanian, Manjot Sandhu, Dhaval Dixit, Kaley Ngo, Daniel Wu, Halley C. Sullivan, Jasmine C. Huynh, Tirth Patel, Vivian Yip, Manish M. Padhiar, Li Ma, Ryen Castillo, Shivtaj Mann, Tuan D. Tran, Albert J. Chang, and Kunal Thaker

Subjects
Lineage (genetic), QH426-470, Biology, 03 medical and health sciences, Gene expression, Genetics, stem, Molecular Biology, Drosophila, Genetics (clinical), 030304 developmental biology, education, 0303 health sciences, g-trace, 4. Education, 05 social sciences, 050301 education, biology.organism_classification, cure, Imaginal disc, Haematopoiesis, Undergraduate research, Expression (architecture), Evolutionary biology, gene expression, 0503 education, Functional genomics
Abstract

A variety of genetic techniques have been devised to determine cell lineage relationships during tissue development. Some of these systems monitor cell lineages spatially and/or temporally without regard to gene expression by the cells, whereas others correlate gene expression with the lineage under study. The GAL4 Technique for Real-time and Clonal Expression (G-TRACE) system allows for rapid, fluorescent protein-based visualization of both current and past GAL4 expression patterns and is therefore amenable to genome-wide expression-based lineage screens. Here we describe the results from such a screen, performed by undergraduate students of the University of California, Los Angeles (UCLA) Undergraduate Research Consortium for Functional Genomics (URCFG) and high school summer scholars as part of a discovery-based education program. The results of the screen, which reveal novel expression-based lineage patterns within the brain, the imaginal disc epithelia, and the hematopoietic lymph gland, have been compiled into the G-TRACE Expression Database (GED), an online resource for use by the Drosophila research community. The impact of this discovery-based research experience on student learning gains was assessed independently and shown to be greater than that of similar programs conducted elsewhere. Furthermore, students participating in the URCFG showed considerably higher STEM retention rates than UCLA STEM students that did not participate in the URCFG, as well as STEM students nationwide.

Published
2019
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2. Belantamab mafodotin associated corneal microcyst-like epithelial changes

Author

Katherine Chuang, Roberto Pineda, and Shaohui Liu

Subjects
Cornea, Ophthalmology, genetic structures, Belantamab mafodotin, Drug adverse effects, sense organs, RE1-994, eye diseases
Abstract

Purpose: To report a case of bilateral corneal microcyst-like epithelial changes associated with belantamab mafodotin (belamaf) therapy. Observations: A 70-year-old man with refractory multiple myeloma was placed on belamaf, a recently FDA-approved treatment for relapsed or refractory multiple myeloma. He developed decreased visual acuity and bilateral corneal microcyst-like peripheral epithelial changes. Belamaf was withheld.Anterior segment OCT showed intra-epithelial opacities at various depths. After resolution of corneal changes and recovery of vision, belamaf was restarted. The patient underwent two additional treatments, each time with recurrence of diffuse microcyst-like corneal epithelial changes. It took a total of 8, 11.5 and 17 weeks after each respective infusion for the microcyst-like epithelial changes to resolve. This suggested a longer recovery time after each subsequent infusion. Conclusions and importance: The care for patients on belamaf requires the collaboration of eye care providers and hematologists-oncologists to assess for ocular adverse effects and adjust treatment as necessary. Further study is needed to illustrate the mechanism of corneal microcyst-like epithelial changes and its effects on limbal stem cells.

Published
2021

3. Author response for 'Identification of Retinal Ganglion Cell Types and Brain Nuclei expressing the transcription factor Brn3c/Pou4f3 using a Cre recombinase knock‐in allele'

Author

Katherine Chuang, Tudor C. Badea, Sophia Rose Wienbar, Lijin Dong, Eileen Nguyen, Nadia Parmhans, David Swygart, Anne Drury Fuller, Zbynek Kozmik, Gregory W. Schwartz, and Tyger Lin

Subjects
medicine.anatomical_structure, Retinal ganglion cell, Gene knockin, medicine, Cre recombinase, Identification (biology), Biology, Allele, Transcription factor, Cell biology
Published
2020
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4. Expression-Based Cell Lineage Analysis in

Author

John M, Olson, Cory J, Evans, Kathy T, Ngo, Hee Jong, Kim, Joseph Duy, Nguyen, Kayla G H, Gurley, Truc, Ta, Vijay, Patel, Lisa, Han, Khoa T, Truong-N, Letty, Liang, Maggie K, Chu, Hiu, Lam, Hannah G, Ahn, Abhik Kumar, Banerjee, In Young, Choi, Ross G, Kelley, Naseem, Moridzadeh, Awais M, Khan, Omair, Khan, Szuyao, Lee, Elizabeth B, Johnson, Annie, Tigranyan, Jay, Wang, Anand D, Gandhi, Manish M, Padhiar, Joseph Hargan, Calvopina, Kirandeep, Sumra, Kristy, Ou, Jessie C, Wu, Joseph N, Dickan, Sabrena M, Ahmadi, Donald N, Allen, Van Thanh, Mai, Saif, Ansari, George, Yeh, Earl, Yoon, Kimberly, Gon, John Y, Yu, Johnny, He, Jesse M, Zaretsky, Noemi E, Lee, Edward, Kuoy, Alexander N, Patananan, Daniel, Sitz, PhuongThao, Tran, Minh-Tu, Do, Samira J, Akhave, Silverio D, Alvarez, Bobby, Asem, Neda, Asem, Nicole A, Azarian, Arezou, Babaesfahani, Ahmad, Bahrami, Manjeet, Bhamra, Ragini, Bhargava, Rakesh, Bhatia, Subir, Bhatia, Nicholas, Bumacod, Jonathan J, Caine, Thomas A, Caldwell, Nicole A, Calica, Elise M, Calonico, Carman, Chan, Helen H-L, Chan, Albert, Chang, Chiaen, Chang, Daniel, Chang, Jennifer S, Chang, Nauman, Charania, Jasmine Y, Chen, Kevin, Chen, Lu, Chen, Yuyu, Chen, Derek J, Cheung, Jesse J, Cheung, Jessica J, Chew, Nicole B, Chew, Cheng-An Tony, Chien, Alana M, Chin, Chee Jia, Chin, Youngho, Cho, Man Ting, Chou, Ke-Huan K, Chow, Carolyn, Chu, Derrick M, Chu, Virginia, Chu, Katherine, Chuang, Arunit Singh, Chugh, Mark R, Cubberly, Michael Guillermo, Daniel, Sangita, Datta, Raj, Dhaliwal, Jenny, Dinh, Dhaval, Dixit, Emmylou, Dowling, Melinda, Feng, Christopher M, From, Daisuke, Furukawa, Himaja, Gaddipati, Lilit, Gevorgyan, Zunera, Ghaznavi, Tulika, Ghosh, Jaskaran, Gill, David J, Groves, Kalkidan K, Gurara, Ali R, Haghighi, Alexandra L, Havard, Nasser, Heyrani, Tanya, Hioe, Kirim, Hong, Justin J, Houman, Molly, Howland, Elaine L, Hsia, Justin, Hsueh, Stacy, Hu, Andrew J, Huang, Jasmine C, Huynh, Jenny, Huynh, Chris, Iwuchukwu, Michael J, Jang, An An, Jiang, Simran, Kahlon, Pei-Yun, Kao, Manpreet, Kaur, Matthew G, Keehn, Elizabeth J, Kim, Hannah, Kim, Michelle J, Kim, Shawn J, Kim, Aleksandar, Kitich, Ross A, Kornberg, Nicholas G, Kouzelos, Jane, Kuon, Bryan, Lau, Roger K, Lau, Rona, Law, Huy D, Le, Rachael, Le, Carrou, Lee, Christina, Lee, Grace E, Lee, Kenny, Lee, Michelle J, Lee, Regina V, Lee, Sean H K, Lee, Sung Kyu, Lee, Sung-Ling D, Lee, Yong Jun, Lee, Megan J, Leong, David M, Li, Hao, Li, Xingfu, Liang, Eric, Lin, Michelle M, Lin, Peter, Lin, Tiffany, Lin, Stacey, Lu, Serena S, Luong, Jessica S, Ma, Li, Ma, Justin N, Maghen, Sravya, Mallam, Shivtaj, Mann, Jason H, Melehani, Ryan C, Miller, Nitish, Mittal, Carmel M, Moazez, Susie, Moon, Rameen, Moridzadeh, Kaley, Ngo, Hanh H, Nguyen, Kambria, Nguyen, Thien H, Nguyen, Angela W, Nieh, Isabella, Niu, Seo-Kyung, Oh, Jessica R, Ong, Randi K, Oyama, Joseph, Park, Yaelim A, Park, Kimberly A, Passmore, Ami, Patel, Amy A, Patel, Dhruv, Patel, Tirth, Patel, Katherine E, Peterson, An Huynh, Pham, Steven V, Pham, Melissa E, Phuphanich, Neil D, Poria, Alexandra, Pourzia, Victoria, Ragland, Riki D, Ranat, Cameron M, Rice, David, Roh, Solomon, Rojhani, Lili, Sadri, Agafe, Saguros, Zainab, Saifee, Manjot, Sandhu, Brooke, Scruggs, Lisa M, Scully, Vanessa, Shih, Brian A, Shin, Tamir, Sholklapper, Harnek, Singh, Sumedha, Singh, Sondra L, Snyder, Katelyn F, Sobotka, Sae Ho, Song, Siddharth, Sukumar, Halley C, Sullivan, Mark, Sy, Hande, Tan, Sara K, Taylor, Shivani K, Thaker, Tulsi, Thakore, Gregory E, Tong, Jacinda N, Tran, Jonathan, Tran, Tuan D, Tran, Vivi, Tran, Cindy L, Trang, Hung G, Trinh, Peter, Trinh, Han-Ching H, Tseng, Ted T, Uotani, Akram V, Uraizee, Kent K T, Vu, Kevin K T, Vu, Komal, Wadhwani, Paluk K, Walia, Rebecca S, Wang, Shuo, Wang, Stephanie J, Wang, Danica D, Wiredja, Andrew L, Wong, Daniel, Wu, Xi, Xue, Griselda, Yanez, Yung-Hsuan, Yang, Zhong, Ye, Victor W, Yee, Cynthia, Yeh, Yue, Zhao, Xin, Zheng, Anke, Ziegenbalg, Jon, Alkali, Ida, Azizkhanian, Akash, Bhakta, Luke, Berry, Ryen, Castillo, Sonja, Darwish, Holly, Dickinson, Ritika, Dutta, Rahul Kumar, Ghosh, Riley, Guerin, Jonathan, Hofman, Garrick, Iwamoto, Sarah, Kang, Andrew, Kim, Brian, Kim, Hanwool, Kim, Kristine, Kim, Suji, Kim, Julie, Ko, Michael, Koenig, Alejandro, LaRiviere, Clifton, Lee, Jiwon, Lee, Brandon, Lung, Max, Mittelman, Mark, Murata, Yujin, Park, Daniel, Rothberg, Ben, Sprung-Keyser, Kunal, Thaker, Vivian, Yip, Paul, Picard, Francie, Diep, Nikki, Villarasa, Volker, Hartenstein, Casey, Shapiro, Marc, Levis-Fitzgerald, Leslie, Jaworski, David, Loppato, Ira E, Clark, and Utpal, Banerjee

Subjects
education, Universities, Research, Brain, Gene Expression, G-TRACE, Investigations, STEM, Eye, Lymphatic System, Animals, Wings, Animal, Cell Lineage, Drosophila, Students, CURE
Abstract

A variety of genetic techniques have been devised to determine cell lineage relationships during tissue development. Some of these systems monitor cell lineages spatially and/or temporally without regard to gene expression by the cells, whereas others correlate gene expression with the lineage under study. The GAL4 Technique for Real-time and Clonal Expression (G-TRACE) system allows for rapid, fluorescent protein-based visualization of both current and past GAL4 expression patterns and is therefore amenable to genome-wide expression-based lineage screens. Here we describe the results from such a screen, performed by undergraduate students of the University of California, Los Angeles (UCLA) Undergraduate Research Consortium for Functional Genomics (URCFG) and high school summer scholars as part of a discovery-based education program. The results of the screen, which reveal novel expression-based lineage patterns within the brain, the imaginal disc epithelia, and the hematopoietic lymph gland, have been compiled into the G-TRACE Expression Database (GED), an online resource for use by the Drosophila research community. The impact of this discovery-based research experience on student learning gains was assessed independently and shown to be greater than that of similar programs conducted elsewhere. Furthermore, students participating in the URCFG showed considerably higher STEM retention rates than UCLA STEM students that did not participate in the URCFG, as well as STEM students nationwide.

Published
2019

5. Conjunctival Fungal Ball Mimicking Melanoma

Author

Alexander O. Vortmeyer, Katherine Chuang, and Shaohui Liu

Subjects
Pathology, medicine.medical_specialty, business.industry, Melanoma, Conjunctival Neoplasms, Periodic Acid-Schiff Reaction, Eye infection, medicine.disease, Conjunctival Diseases, Diagnosis, Differential, Ophthalmology, Mycoses, medicine, Humans, Female, business, Cladosporium, Eye Infections, Fungal, Melanoma diagnosis, Aged
Published
2020
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6. Molecular codes for cell type specification in Brn3 retinal ganglion cells

Author

Octavian Popescu, Katherine Chuang, Tudor C. Badea, Miruna Georgiana Ghinia, Friedrich Kretschmer, Matthew Brooks, Szilard Sajgo, Zhijian Wu, and Suja Hiriyanna

Subjects
Male, Retinal Ganglion Cells, 0301 basic medicine, Cell type, genetic structures, Upstream and downstream (transduction), Synaptogenesis, Dendrite, Cell Communication, Biology, Retinal ganglion, Transcriptome, Mice, 03 medical and health sciences, medicine, Animals, Transcription factor, Multidisciplinary, Gene Expression Profiling, Brain, High-Throughput Nucleotide Sequencing, Membrane Proteins, eye diseases, Axon Guidance, Transcription Factor Brn-3, 030104 developmental biology, medicine.anatomical_structure, PNAS Plus, Female, Axon guidance, sense organs, Neuroscience
Abstract

Visual information is conveyed from the eye to the brain by distinct types of retinal ganglion cells (RGCs). It is largely unknown how RGCs acquire their defining morphological and physiological features and connect to upstream and downstream synaptic partners. The three Brn3/Pou4f transcription factors (TFs) participate in a combinatorial code for RGC type specification, but their exact molecular roles are still unclear. We use deep sequencing to define (i) transcriptomes of Brn3a- and/or Brn3b-positive RGCs, (ii) Brn3a- and/or Brn3b-dependent RGC transcripts, and (iii) transcriptomes of retinorecipient areas of the brain at developmental stages relevant for axon guidance, dendrite formation, and synaptogenesis. We reveal a combinatorial code of TFs, cell surface molecules, and determinants of neuronal morphology that is differentially expressed in specific RGC populations and selectively regulated by Brn3a and/or Brn3b. This comprehensive molecular code provides a basis for understanding neuronal cell type specification in RGCs.

Published
2017
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7. Novel heterotypic rox sites for combinatorial dre recombination strategies

Author

Katherine Chuang, Yuri V. Sergeev, Eileen Nguyen, and Tudor C. Badea

Subjects
0301 basic medicine, Genetic Vectors, Mutagenesis (molecular biology technique), Cre recombinase, Investigations, Biology, Cre recombination, QH426-470, Cell Line, gene targeting, Recombinases, 03 medical and health sciences, 0302 clinical medicine, Gene Order, Recombinase, Genetics, Humans, Genomic library, site specific recombination, Site-specific recombination, Homologous Recombination, Molecular Biology, Genetics (clinical), Floxing, Gene Library, Dre recombinase, Integrases, Escherichia coli Proteins, Gene targeting, 030104 developmental biology, Mutagenesis, DNA Nucleotidyltransferases, Mutation, Homologous recombination, 030217 neurology & neurosurgery
Abstract

Site-specific recombinases (SSRs) such as Cre are widely used in gene targeting and genetic approaches for cell labeling and manipulation. They mediate DNA strand exchange between two DNA molecules at dedicated recognition sites. Precise understanding of the Cre recombination mechanism, including the role of individual base pairs in its loxP target site, guided the generation of mutant lox sites that specifically recombine with themselves but not with the wild type loxP. This has led to the development of a variety of combinatorial Cre-dependent genetic strategies, such as multicolor reporters, irreversible inversions, or recombination-mediated cassette exchange. Dre, a Cre-related phage integrase that recognizes roxP sites, does not cross-react with the Cre-loxP system, but has similar recombination efficiency. We have previously described intersectional genetic strategies combining Dre and Cre. We now report a mutagenesis screen aimed at identifying roxP base pairs critical for self-recognition. We describe several rox variant sites that are incompatible with roxP, but are able to efficiently recombine with themselves in either purified systems or bacterial and eukaryotic tissue culture systems. These newly identified rox sites are not recognized by Cre, thus enabling potential combinatorial strategies involving Cre, Dre, and target loci including multiple loxP and roxP variants.

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