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1. Instructional Innovations in College-Level Molecular Bioscience Labs during the Pandemic-Induced Shift to Online Learning

Author

Yu, Alder, Wisinski, Jaclyn, Osmundson, Todd, Sanderfoot, Anton, Cooper, Scott, and Klein, Jennifer

Abstract

The COVID-19 pandemic ushered in an unprecedented period of both crisis and innovation in higher education. The shift to an online learning environment was particularly problematic for courses in which students learn disciplinary practices. Scientific practice requires hands-on training and collaborative engagement with instructors and peers, dimensions of the learning environment that were challenging to recreate online. Here, we describe the resulting instructional innovations and challenges experienced in shifting multiple undergraduate- and graduate-level molecular bioscience labs, including Genetics, Cell Biology, Bioinformatics, and Advanced Microscopy, to an online learning environment. Instructors pursued novel approaches, techniques, and at-home lab tools with varying success. Many innovations were retained after the transition back to an in-person learning environment because they uniquely supported previously overlooked aspects of student learning. Consistent with other reports, we found that marginalized students pursuing science were disproportionately burdened by COVID-19 and the shift to an online learning environment. A description of what worked for online learning, what didn't, and what is worth holding onto in the future is valuable for constructing learning environments that effectively support learners in their disciplinary practice.

Published
2022

2. Sequence Information to Identify Motifs

Author

Cooper, Scott, Sanderfoot, Anton, Wells, Robert D., editor, Bond, Judith S., editor, Klinman, Judith, editor, Masters, Bettie Sue Siler, editor, Bell, Ellis, Managing Editor, and Kaguni, Laurie S., Book Editor

Published
2018
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3. Predictions from Sequence

Author

Cooper, Scott, Sanderfoot, Anton, Wells, Robert D., editor, Bond, Judith S., editor, Klinman, Judith, editor, Masters, Bettie Sue Siler, editor, Bell, Ellis, Managing Editor, and Kaguni, Laurie S., Book Editor

Published
2018
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5. Mass Spectrometry Approaches

Author

Cooper, Scott, Sanderfoot, Anton, Wells, Robert D., editor, Bond, Judith S., editor, Klinman, Judith, editor, Masters, Bettie Sue Siler, editor, Bell, Ellis, Managing Editor, and Kaguni, Laurie S., Book Editor

Published
2018
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7. Primary Structure

Author

Cooper, Scott, Sanderfoot, Anton, Wells, Robert D., editor, Bond, Judith S., editor, Klinman, Judith, editor, Masters, Bettie Sue Siler, editor, Bell, Ellis, Managing Editor, and Kaguni, Laurie S., Book Editor

Published
2018
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8. Sequence Determination, Classic Approaches to

Author

Cooper, Scott, Sanderfoot, Anton, Wells, Robert D., editor, Bond, Judith S., editor, Klinman, Judith, editor, Masters, Bettie Sue Siler, editor, Bell, Ellis, Managing Editor, and Kaguni, Laurie S., Book Editor

Published
2018
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10. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants

Author

Rensing, Stefan A., Lang, Daniel, Zimmer, Andreas D., Terry, Astrid, Salamov, Asaf, Shapiro, Harris, Nishiyama, Tomaoki, Perroud, Pierre-Francois, Lindquist, Erika A., Kamisugi, Yasuko, Tanahashi, Takako, Sakakibara, Keiko, Fujita, Tomomichi, Oishi, Kazuko, Shin, Tadasu, Kuroki, Yoko, Toyoda, Atsushi, Suzuki, Yutaka, Hashimoto, Shin-ichi, Yamaguchi, Kazuo, Sugano, Sumio, Kohara, Yuji, Fujiyama, Asao, Anterola, Aldwin, Aoki, Setsuyuki, Ashton, Neil, Barbazuk, W. Brad, Barker, Elizabeth, Bennetzen, Jeffrey L., Blankenship, Robert, Cho, Sung Hyun, Dutcher, Susan K., Estelle, Mark, Fawcett, Jeffrey A., Gundlach, Heidrum, Hanada, Kousuke, Melkozernov, Alexander, Murata, Takashi, Nelson, David R., Pils, Birgit, Prigge, Michael, Reiss, Bernd, Renner, Tanya, Rombauts, Stephane, Rushton, Paul J., Sanderfoot, Anton, Schween, Gabriele, Shiu, Shin-Han, Stueber, Kurt, Theodoulou, Frederica L., Tu, Hank, Peer, Yves Van de, Verrier, Paul J., Waters, Elizabeth, Wood, Andrew, Yang, Lixing, Cove, David, Cuming, Andrew C., Hasebe, Mitsayasu, Lucas, Susan, Mishler, Brent D., Reski, Ralf, Grigoriev, Igor V., Quatrano, Rakph S., and Boore, Jeffrey L.

Abstract

We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics.

Published
2007

11. The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions

Author

Merchant, Sabeeha S., Prochnik, Simon E., Vallon, Olivier, Harris, Elizabeth H., Karpowicz, Steven J., Witman, George B., Terry, Astrid, Salamov, Asaf, Fritz-Laylin, Lillian K., Maréchal-Drouard, Laurence, Marshal, Wallace F., Qu, Liang-Hu, Nelson, David R., Sanderfoot, Anton A., Spalding, Martin H., Kapitonov, Vladimir V., Ren, Qinghu, Ferris, Patrick, Lindquist, Erika, Shapiro, Harris, Lucas, Susan M., Grimwood, Jane, Schmutz, Jeremy, Cardol, Pierre, Cerutti, Heriberto, Chanfreau, Guillaume, Chen, Chun-Long, Cognat, Valérie, Croft, Martin T., Dent, Rachel, Dutcher, Susan, Fernández, Emilio, Fukuzawa, Hideya, González-Ballester, David, González-Halphen, Diego, Hallmann, Armin, Hanikenne, Marc, Hippler, Michael, Inwood, William, Jabbari, Kamel, Kalanon, Ming, Kuras, Richard, Lefebvre, Paul A., Lemaire, Stéphane D., Loba, Alexey V., Lohr, Martin, Manuell, Andrea, Meier, Iris, Mets, Laurens, Mittag, Maria, Mittelmeier, Telsa, Moroney, James V., Moseley, Jeffrey, Napoli, Carolyn, Nedelcu, Aurora M., Niyogi, Krishna, Novoselov, Sergey V., Paulsen, Ian T., Pazour, Greg, Purton, Saul, Ral, Jean-Philippe, Riano-Pachon, Diego Mauricio, Riekhof, Wayne, Rymarquis, Linda, Schroda, Michael, Stern, David, Umen, James, Willows, Robert, Wilson, Nedra, Zimmer, Sara Lana, Allmer, Jens, Balk, Janneke, Bisova, Katerina, Chen, Chong-Jian, Elias, Marek, Gendler, Karla, Hauser, Charles, Lamb, Mary Rose, Ledford, Heidi, Long, Joanne C., Minagawa, Jun, Page, M. Dudley, Pan, Junmin, Pootakham, Wirulda, Roje, Sanja, Rose, Annkatrin, Stahlberg, Eric, Terauchi, Aimee M., Yang, Pinfen, Ball, Steven, Bowler, Chris, Dieckmann, Carol L., Gladyshev, Vadim N., Green, Pamela, Jorgensen, Richard, Mayfield, Stephen, Mueller-Roeber, Bernd, Rajamani, Sathish, and Sayre, Richard T.

Abstract

Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.

Published
2007

19. Building the Impetus for Change: An Across-Curriculum Initiative in Biology

Author

Gerrish, Gretchen A., Sanderfoot, Anton, and King-Heiden, Tisha

Abstract

The authors wanted to improve student learning of evolutionary concepts by integrating content across the biology major. In this article they describe the process used to develop support among members of the department and administration to implement and measure the outcomes of curricular reforms.

Published
2015
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22. The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants

Author

Rensing, Stefan A., Lang, Daniel, Zimmer, Andreas D., Terry, Astrid, Salamov, Asaf, Shapiro, Harris, Nishiyama, Tomoaki, Perroud, Pierre-François, Lindquist, Erika A., Kamisugi, Yasuko, Tanahashi, Takako, Sakakibara, Keiko, Fujita, Tomomichi, Oishi, Kazuko, Shin-I, Tadasu, Kuroki, Yoko, Toyoda, Atsushi, Suzuki, Yutaka, Hashimoto, Shin-ichi, Yamaguchi, Kazuo, Sugano, Sumio, Kohara, Yuji, Fujiyama, Asao, Anterola, Aldwin, Aoki, Setsuyuki, Ashton, Neil, Barbazuk, W. Brad, Barker, Elizabeth, Bennetzen, Jeffrey L., Blankenship, Robert, Cho, Sung Hyun, Dutcher, Susan K., Estelle, Mark, Fawcett, Jeffrey A., Gundlach, Heidrun, Hanada, Kousuke, Heyl, Alexander, Hicks, Karen A., Hughes, Jon, Lohr, Martin, Mayer, Klaus, Melkozernov, Alexander, Murata, Takashi, Nelson, David R., Pils, Birgit, Prigge, Michael, Reiss, Bernd, Renner, Tanya, Rombauts, Stephane, Rushton, Paul J., Sanderfoot, Anton, Schween, Gabriele, Shiu, Shin-Han, Stueber, Kurt, Theodoulou, Frederica L., Tu, Hank, Van de Peer, Yves, Verrier, Paul J., Waters, Elizabeth, Wood, Andrew, Yang, Lixing, Cove, David, Cuming, Andrew C., Hasebe, Mitsuyasu, Lucas, Susan, Mishler, Brent D., Reski, Ralf, Grigoriev, Igor V., Quatrano, Ralph S., and Boore, Jeffrey L.

Published
2008
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34. The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions

Author

Mar&#233, Cognat, Val&#233, Fern&#225, Gonz&#225, Lemaire, St&#233, Merchant, Sabeeha S., Prochnik, Simon E., Vallon, Olivier, Harris, Elizabeth H., Karpowicz, Steven J., Witman, George B., Terry, Astrid, Salamov, Asaf, Fritz-Laylin, Lillian K., Marshal, Wallace F., Qu, Liang-Hu, Nelson, David R., Sanderfoot, Anton A., Spalding, Martin H., Kapitonov, Vladimir V., Ren, Qinghu, Ferris, Patrick, Lindquist, Erika, Shapiro, Harris, Lucas, Susan M., Grimwood, Jane, Schmutz, Jeremy, Cardol, Pierre, Cerutti, Heriberto, Chanfreau, Guillaume, Chen, Chun-Long, Croft, Martin T., Dent, Rachel, Dutcher, Susan, Fukuzawa, Hideya, Hallmann, Armin, Hanikenne, Marc, Hippler, Michael, Inwood, William, Jabbari, Kamel, Kalanon, Ming, Kuras, Richard, Lefebvre, Paul A., Loba, Alexey V., Lohr, Martin, Manuell, Andrea, Meier, Iris, Mets, Laurens, Mittag, Maria, Mittelmeier, Telsa, Moroney, James V., Moseley, Jeffrey, Napoli, Carolyn, Nedelcu, Aurora M., Niyogi, Krishna, Novoselov, Sergey V., Paulsen, Ian T., Pazour, Greg, Purton, Saul, Ral, Jean-Philippe, Riano-Pachon, Diego Mauricio, Riekhof, Wayne, Rymarquis, Linda, Schroda, Michael, Stern, David, Umen, James, Willows, Robert, Wilson, Nedra, Zimmer, Sara Lana, Allmer, Jens, Balk, Janneke, Bisova, Katerina, Chen, Chong-Jian, Elias, Marek, Gendler, Karla, Hauser, Charles, Lamb, Mary Rose, Ledford, Heidi, Long, Joanne C., Minagawa, Jun, Page, M. Dudley, Pan, Junmin, Pootakham, Wirulda, Roje, Sanja, Rose, Annkatrin, Stahlberg, Eric, Terauchi, Aimee M., Yang, Pinfen, Ball, Steven, Bowler, Chris, Dieckmann, Carol L., Gladyshev, Vadim N., Green, Pamela, Jorgensen, Richard, Mayfield, Stephen, Mueller-Roeber, Bernd, Rajamani, Sathish, Sayre, Richard T., Brokstein, Peter, Dubchak, Inna, Goodstein, David, Hornick, Leila, Huang, Wayne, Jhaveri, Jinal, Luo, Yigong, Martinez, Diego, Ngau, Wing Chi Abby, Otillar, Bobby, Poliakov, Alexander, Porter, Aaron, Szajkowski, Lukasz, Werner, Gregory, Zhou, Kemin, Grigoriev, Igor V., Rokhsar, Daniel S., and Grossman, Arthur R.

Subjects
food and beverages
Abstract

Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.

Published
2007

37. The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions

Author

Merchant, Sabeeha S., primary, Prochnik, Simon E., additional, Vallon, Olivier, additional, Harris, Elizabeth H., additional, Karpowicz, Steven J., additional, Witman, George B., additional, Terry, Astrid, additional, Salamov, Asaf, additional, Fritz-Laylin, Lillian K., additional, Maréchal-Drouard, Laurence, additional, Marshall, Wallace F., additional, Qu, Liang-Hu, additional, Nelson, David R., additional, Sanderfoot, Anton A., additional, Spalding, Martin H., additional, Kapitonov, Vladimir V., additional, Ren, Qinghu, additional, Ferris, Patrick, additional, Lindquist, Erika, additional, Shapiro, Harris, additional, Lucas, Susan M., additional, Grimwood, Jane, additional, Schmutz, Jeremy, additional, Cardol, Pierre, additional, Cerutti, Heriberto, additional, Chanfreau, Guillaume, additional, Chen, Chun-Long, additional, Cognat, Valérie, additional, Croft, Martin T., additional, Dent, Rachel, additional, Dutcher, Susan, additional, Fernández, Emilio, additional, Fukuzawa, Hideya, additional, González-Ballester, David, additional, González-Halphen, Diego, additional, Hallmann, Armin, additional, Hanikenne, Marc, additional, Hippler, Michael, additional, Inwood, William, additional, Jabbari, Kamel, additional, Kalanon, Ming, additional, Kuras, Richard, additional, Lefebvre, Paul A., additional, Lemaire, Stéphane D., additional, Lobanov, Alexey V., additional, Lohr, Martin, additional, Manuell, Andrea, additional, Meier, Iris, additional, Mets, Laurens, additional, Mittag, Maria, additional, Mittelmeier, Telsa, additional, Moroney, James V., additional, Moseley, Jeffrey, additional, Napoli, Carolyn, additional, Nedelcu, Aurora M., additional, Niyogi, Krishna, additional, Novoselov, Sergey V., additional, Paulsen, Ian T., additional, Pazour, Greg, additional, Purton, Saul, additional, Ral, Jean-Philippe, additional, Riaño-Pachón, Diego Mauricio, additional, Riekhof, Wayne, additional, Rymarquis, Linda, additional, Schroda, Michael, additional, Stern, David, additional, Umen, James, additional, Willows, Robert, additional, Wilson, Nedra, additional, Zimmer, Sara Lana, additional, Allmer, Jens, additional, Balk, Janneke, additional, Bisova, Katerina, additional, Chen, Chong-Jian, additional, Elias, Marek, additional, Gendler, Karla, additional, Hauser, Charles, additional, Lamb, Mary Rose, additional, Ledford, Heidi, additional, Long, Joanne C., additional, Minagawa, Jun, additional, Page, M. Dudley, additional, Pan, Junmin, additional, Pootakham, Wirulda, additional, Roje, Sanja, additional, Rose, Annkatrin, additional, Stahlberg, Eric, additional, Terauchi, Aimee M., additional, Yang, Pinfen, additional, Ball, Steven, additional, Bowler, Chris, additional, Dieckmann, Carol L., additional, Gladyshev, Vadim N., additional, Green, Pamela, additional, Jorgensen, Richard, additional, Mayfield, Stephen, additional, Mueller-Roeber, Bernd, additional, Rajamani, Sathish, additional, Sayre, Richard T., additional, Brokstein, Peter, additional, Dubchak, Inna, additional, Goodstein, David, additional, Hornick, Leila, additional, Huang, Y. Wayne, additional, Jhaveri, Jinal, additional, Luo, Yigong, additional, Martínez, Diego, additional, Ngau, Wing Chi Abby, additional, Otillar, Bobby, additional, Poliakov, Alexander, additional, Porter, Aaron, additional, Szajkowski, Lukasz, additional, Werner, Gregory, additional, Zhou, Kemin, additional, Grigoriev, Igor V., additional, Rokhsar, Daniel S., additional, and Grossman, Arthur R., additional

Published
2007
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38. Vesicle Traffic at Cytokinesis.

Author

Verma, Desh Pal S., Zonglie Hong, and Sanderfoot, Anton

Abstract

Cytokinesis, the mechanical process by which one cell becomes two, is essential to all life, be it single-celled bacteria or complex multicellular organisms like land plants or animals. It is now clear that new membrane must be added to the mother cell to accomplish the complete enclosure of the two daughters. In land plants, this is especially apparent because they accomplish cytokinesis with the cell plate, a structure newly assembled by addition of new membrane vesicles. This review will focus on what we know about the source of the vesicles that make up the cell plate membrane, the molecular machinery involved in assembling those vesicles, and just what those vesicles are carrying to the cell plate. [ABSTRACT FROM AUTHOR]

Published
2008
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39. Arabidopsis could shed light on human genome

Author

Sanderfoot, Anton A. and Raikhel, Natasha V.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Anton A. Sanderfoot [1]; Natasha V. Raikhel [1] Sir Although only recently published in Nature [1], the entire sequence of the model plant Arabidopsis thaliana has been in the [...]

Published
2001
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45. AtVPS45 Complex Formation at the trans-Golgi Network

Author

Bassham, Diane C., Sanderfoot, Anton A., Kovaleva, Valentina, Zheng, Haiyan, and Raikhel, Natasha V.

Abstract

The Sec1p family of proteins are thought to be involved in the regulation of vesicle fusion reactions through interaction with t-SNAREs (target soluble N-ethylmaleimide–sensitive factor attachment protein receptors) at the target membrane. AtVPS45 is a member of this family from Arabidopsis thalianathat we now demonstrate to be present on the trans-Golgi network (TGN), where it colocalizes with the vacuolar cargo receptor AtELP. Unlike yeast Vps45p, AtVPS45 does not interact with, or colocalize with, the prevacuolar t-SNARE AtPEP12. Instead, AtVPS45 interacts with two t-SNAREs, AtTLG2a and AtTLG2b, that show similarity to the yeast t-SNARE Tlg2p. AtTLG2a and -b each colocalize with AtVPS45 at the TGN; however, AtTLG2a is in a different region of the TGN than AtTLG2b by immunogold electron microscopy. Therefore, we propose that complexes containing AtVPS45 and either AtTLG2a or -b define functional subdomains of the TGN and may be required for different trafficking events. Among other ArabidopsisSNAREs, AtVPS45 antibodies preferentially coprecipitate AtVTI1b over the closely related isoform AtVTI1a, implying that AtVTI1a and AtVTI1b also have distinct functions within the cell. These data point to a functional complexity within the plant secretory pathway, where proteins encoded by gene families have specialized functions, rather than functional redundancy.

Published
2000
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