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1. Expression-Based Cell Lineage Analysis in Drosophila Through a Course-Based Research Experience for Early Undergraduates

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
g-trace, gene expression, education, stem, cure, Genetics, QH426-470
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
Full Text
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2. 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
Full Text
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3. Cultivation and characterization of thermophilicNitrospiraspecies from geothermal springs in the US Great Basin, China, and Armenia

Author

Tara A. Edwards, Brian P. Hedlund, Weiguo Hou, Liuqin Huang, Namritha Manoharan, Hovik Panosyan, Dolores A. Huang, Nicole A. Calica, and Hailiang Dong

Subjects
China, Biology, Applied Microbiology and Biotechnology, Microbiology, Enrichment culture, Hot Springs, chemistry.chemical_compound, Nitrate, RNA, Ribosomal, 16S, Nitrite, Nitrogen cycle, Nitrites, Bacteria, Ecology, Nitrospira moscoviensis, Thermophile, Armenia, biology.organism_classification, Nitrification, chemistry, Environmental chemistry, Oxidation-Reduction, Nitrospira, Nevada
Abstract

Despite its importance in the nitrogen cycle, little is known about nitrite oxidation at high temperatures. To bridge this gap, enrichment cultures were inoculated with sediment slurries from a variety of geothermal springs. While nitrite-oxidizing bacteria (NOB) were successfully enriched from seven hot springs located in US Great Basin, south-western China, and Armenia at ≤ 57.9 °C, all attempts to enrich NOB from10 hot springs at ≥ 61 °C failed. The stoichiometric conversion of nitrite to nitrate, chlorate sensitivity, and sensitivity to autoclaving all confirmed biological nitrite oxidation. Regardless of origin, all successful enrichments contained organisms with high 16S rRNA gene sequence identity (≥ 97%) with Nitrospira calida. In addition, Armenian enrichments also contained close relatives of Nitrospira moscoviensis. Physiological properties of all enrichments were similar, with a temperature optimum of 45-50 °C, yielding nitrite oxidation rates of 7.53 ± 1.20 to 23.0 ± 2.73 fmoles cell(-1) h(-1), and an upper temperature limit between 60 and 65 °C. The highest rates of NOB activity occurred with initial NO2 - concentrations of 0.5-0.75 mM; however, lower initial nitrite concentrations resulted in shorter lag times. The results presented here suggest a possible upper temperature limit of 60-65 °C for Nitrospira and demonstrate the wide geographic range of Nitrospira species in geothermal environments.

Published
2013
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