Teaching
2022
COURSE description
BIO129/229: Fundamentals and Frontiers in Plant Biology (3 Units)
Quarter/Year: Spring 2022 9:45-11:15 am Tues/Thurs
Location: STLC119 (SAPP Center first floor)
Highly recommended: Carnegie Seminar 4 – 5:30 Friday, 260 Panama Street
Optional: Prep session for Thursday presenters Wednesday at 5 (or TBA)
By arrangement: Individual meetings with the faculty to go over journal club papers
Faculty: Sue Rhee, Carnegie Institution for Science, [email protected]
Virginia Walbot, Department of Biology, [email protected]
Grading: Satisfactory/No Credit or Letter Grade: Based on attendance (required at all sessions for credit), participation in discussion, and turning in an acceptable critique for all 9 weekly assignments. The critique papers are due each Thursday.
Online, if required, through the Canvas Website and ZOOM: If Stanford designates spring quarter for online only classes, this course will be given via ZOOM, accessible to Stanford affiliates on Tuesday and registered students on Thursdays. If distance learning is required for an individual(s), the faculty will arrange either ZOOM class sessions or an individual discussion after a student has read the lecture presentation and assigned paper each week. Every effort will be made to make the course content and discussions available to all students.
Course Status as an Elective: This course can serve as an elective course for Biology Ph.D. candidates in the CMOB track for the following areas: Cell Biology, Genetic and Genomics, or the Biology of Molecules. This course can also serve as an upper division biology elective for undergraduates.
Audience: Graduate students at any level, co-term and upper-level undergraduate students with permission of instructor. Highly recommended for undergraduates doing research in plant biology.
Enrollment Cap: 20
Prerequisites: For graduate students, no prerequisites. For undergraduates, at least one of the following: Bio82 (Genetics), Bio86 (Cell Biology), Bio84 (Physiology), or ongoing research in a Stanford or Carnegie plant biology laboratory.
Class prep help: For all enrolled students, five types of support will be provided beyond the class
1) A pre-class zoom session to provide an overview and resources on how the Thurs journal club sessions will be structured, what a journal club is, and have students sign up for presentations. Recording available here Passcode: d6#HC8^v
2) A pre-journal club session by zoom on Wednesdays for the paper that will be discussed on the following day to go over the week’s paper and answer any questions: zoom link Password: 074620
3) One-on-one meetings by arrangement with students, especially undergraduates, who want help preparing their journal club presentations. Book here
4) We will be using the "Discussions" section of the Canvas site for people to pose questions or bring up things that they may not be familiar with. Please feel free to put up Qs as you read the papers or listen to the lectures. This will be mostly peer-based forum.
5) We will use a Google slide deck for people to upload their slides for their presentations
Auditing: Freshmen and Sophomores as well as TGR graduate students can audit lecture classes on Tuesdays. Other Stanford affiliates are invited to attend up to the room capacity seating.
Textbook (optional): The Botany Coloring Book – why not have fun learning the names of plant structures! About $22 at the bookstore or online.
Description and learning outcomes: This course will serve as a primer for all levels of graduate, co-term, and upper-level undergraduates interested in learning the fundamental principles of plant biology as well as the latest advances in tools, techniques, and theories that link basic science with translational science and applications for solving major societal challenges of today and tomorrow. Topics include plant evolution, genetics, breeding, plant-immune signaling, plant-environment interactions, tissue and organ development, metabolism, and systems and synthetic biology.
Overall learning goals: Students will learn major concepts and methods in plant biology and gain the tools and resources to research the literature more independently and deeply. In addition, students will learn fundamental ways that plants are different from animals and microbes. In each module, students will learn major concepts and skills from lectures and primary literature discussions. Students will also learn how to write a succinct critique of research papers and to analyze/present scientific papers to the class.
Class activities: There will be one lecture and one paper discussion class meeting each week. The discussion class is structured like a journal club, where individual students will lead discussions on specific sections of the paper. All students will write a 1-page critique of the paper and submit it before class (via Canvas online or as a printout at the start of Thursday discussions); faculty will provide feedback on composition and content. The Carnegie Spring Quarter Seminar Series will include speakers highly relevant to this class. Students are encouraged to attend, Fridays 4 – 5 pm at Carnegie Institution for Science (260 Panama St, Stanford) with a special session after each talk for students to interact with the speaker.
Topics:
Module 1 (Weeks 1-3): Plant Genetics, Genomics, and Evolution (Exposito-Alonso, Walbot)
Module 2 (Weeks 4-6): Plant Cell Signaling, Development, and Physiology (Mudgett, Dinneny, Bergmann)
Module 3 (Weeks 7-9): Plant Metabolism, Systems, and Synthetic Biology (Rhee, Brophy)
Date
Instructors (Teaching)
Topic/Papers/Learning Goals
*Stanford or Carnegie contribution
Mar 29 9:45-11:15am
Exposito-Alonso
Plant evolution: Introduction of plant macro- and micro- evolution from geological times to the Anthropocene. The complexity of plant genomes and its relationship to speciation, environmental adaptation, and contemporary rapid evolutionary processes.
Mar 31 9:45-11:15am
Exposito-Alonso
Classic paper: major contribution to the modern synthesis of evolution: *Clausen J, *Keck DD, *Hiesey WM. 1941. Regional differentiation in plant species. Am Nat. 75: 231–250. doi.org/10.1086/280955
Discussion paper: addressing global change problems using fundamental plant biological principles: Monroe JG, Powell T, Price N, Mullen JL, Howard A, Evans K, et al. Drought adaptation in Arabidopsis thaliana by extensive genetic loss-of-function. Elife. 2018;7: e41038.
doi.org/10.7554/eLife.41038
Apr 1
4-6 pm
Carnegie seminar
Speaker: Annie Schmidtt, UC Davis
https://plantgxe.ucdavis.edu/
“How natural variation in the seasonal germination niche shapes plant life histories and climate adaptation”
Apr 5
9:45-11:15am
Walbot
Plant genetics: Alternation of generations and practical applications of controlling reproduction: [1] genetics of sporophytic and gametophytic self-incompatibility, [2] gametophyte advantage genetics and the popcorn industry, [3] cytoplasmic male sterility and the risk of monoculture.
Apr 7
9:45-11:15am
Walbot
Classic paper: Specificity determinants and diversification of the Brassica self-incompatibility pollen ligand (2004) T. Chookajorn, A. Kachroo, D. R. Ripoll, A. G. Clark, and J. B. Nasrallah. PNAS 101: 911-917.
doi.org/10.1073/pnas.2637116100
Discussion paper: Y. *Lu et al. 2019. A pistil-expressed pectin methylesterase confers cross-incompatibility between strains of Zea mays. Nature Communications 10, 2304.doi.org/10.1038/s41467-019-10259-0
Apr 8
4-6pm
Carnegie seminar
Speaker: *Rachel Egger, Syngenta
https://www.linkedin.com/in/rachelegger/
“Novel Technologies for Haploid Genome Doubling in Corn”
Apr 12
9:45-11:15am
Walbot
Plant breeding: Historic plant breeding principles: line selection, hybrid vigor, mutation breeding, wide crosses, yield drag and time costs in historic improvement schemes. Modern solutions: transgenic introduction of specific alleles, haploid lines for instant homozygosity, quantitative and individual trait mapping, CRISPR-Cas9 targeted mutagenesis.
Apr 14
9:45-11:15am
Walbot
Classic paper: Donald N. Duvick. 2005. The contribution of breeding to yield advances in maize (Zea mays L.). Advances in Agronomy 86: 83-145. This review is long and comprehensive; suggest you search for a few specific traits (drought, planting density, herbicide resistance, etc.) to get a summary of the data on trait of interest.
doi.org/10.1016/S0065-2113(05)86002-X Discussion paper: *Kelliher, T. et al. 2019. One-step genome editing of elite crop germplasm during haploid induction. Nature Biotechnology 37: 287–292doi.org/10.1038/s41587-019-0038-x
Apr 15
4-6pm
Carnegie seminar
Speaker: Harry Klee, University of Florida
https://hos.ifas.ufl.edu/kleelab/
“What went wrong with the industrial tomato and how do we fix it?”
Apr 19
9:45-11:15am
Mudgett
Plant Immune Signaling: From genes to channels – A remarkable view into activation of immune signaling
Overview: We will discuss some of the most recent and exciting discoveries in plant innate immunity research. We will explore protein structural biology and biochemistry studies revealing the molecular mechanisms of host-pathogen recognition, defense signaling and homeostasis, and disease resistance execution. The focus will be on protein structure-based insights to intracellular immune receptor (NLR) activation and downstream signaling leading to a host response called effector-triggered immunity (ETI). The remarkable surprise uncovered in these studies points to a new mechanistic understanding of calcium signaling and homeostasis.
Apr 21
9:45-11:15am
Mudgett
Literature: A classic review on plant disease resistance proteins provides content for the discovery of the relevant genes and the ideas of researchers at the time for their putative function. The meeting review provides an overview of the most recent findings in this area. Two primary literature articles provide key functional data. Background information for ZAR1 and NRG1 can be found in the cited references.
Classic review: Staskawicz, B. J., Ausubel, F. M., Baker, B. J., Ellis, J. G., and Jones, J. D. G. 1995. Molecular genetics of plant disease resistance. Science 268, 661-667.
doi.org/10.1126/science.7732374
Discussion paper: Bi, G., Su, M., Li, N., Liang, Y., Dang, S., Xu, J., Hu, M., Wang, J., Zou, M., Deng, Y., Li, Q., Huang, S., Li, J., Chai, J., He, K., Chen, Y. H., and Zhou, J. M. 2021. The ZAR1 resistosome is a calcium-permeable channel triggering plant immune signaling. Cell 184:3528-3541.e12.
doi.org/10.1016/j.cell.2021.05.003
Optional reading:
Margets, Rima, Helm and Carter (2021) Molecular mechanisms and structure - Zooming in on plant immunity. MPMI 34, 12: 1346-1349.
doi.org/10.1094/MPMI-08-21-0208-MR
Jacob, P., Kim, N. H., Wu, F., El-Kasmi, F., Chi, Y., Walton, W. G., Furzer, O. J., Lietzan, A. D., Sunil, S., Kempthorn, K., Redinbo, M. R., Pei, Z. M., Wan, L., and Dangl, J. L. 2021. Plant “helper” immune receptors are Ca2+-permeable nonselective cation channels. Science 373:420-425.
doi.org/10.1126/science.abg7917
Apr 22
4-6pm
Carnegie seminar
Speaker: *Jazz Dickinson, UCSD
https://dickinsonlab.biology.ucsd.edu
“Discovering small molecule regulators of plant development”
Apr 26
9:45-11:15am
Dinneny
Plant-environment interactions: from the field to the Petri dish and back to the field
Apr 28
9:45-11:15am
Dinneny
Classic paper: Drew M.C. (1975) Comparison of the effects of a localised supply of phosphate, nitrate, ammonium and potassium on the growth of the seminal root system, and the shoot, in barley. The New Phytologist 75, 479–490.
doi.org/10.1111/j.1469-8137.1975.tb01409.x
Discussion paper: Pandey et al., (2021) Plant roots sense soil compaction through restricted ethylene diffusion. Science Jan 15;371(6526):276-280.
doi.org/10.1126/science.abf3013
Apr 29
4-6pm
Carnegie seminar
Speaker: Gitta Coaker - UC Davis
https://www.coakerlab.org
“The battle between bacterial pathogens and their hosts”
May 3
9:45-11:15am
Bergmann
Plant tissue and organ development: Plant bodies are diverse, but some design principles emerge from examination of how the above-ground portions of the plant are made and patterned.
May 5
9:45-11:15am
Bergmann
Classic paper:
Experiments on the cause of dorsiventrality in leaves.
Sussex IM. Nature. 1951 167:651-2. doi.org/10.1038/167651a0
Discussion paper:
Boundary formation through a direct threshold-based readout of mobile small RNA gradients. Skopelitis DS, Benkovics AH, Husbands AY, Timmermans MCP. Dev Cell. 2017
doi.org/10.1016/j.devcel.2017.10.003
Reviews and a modern classic paper (optional):
Role of PHABULOSA and PHAVOLUTA in determining radial patterning in shoots. McConnell…Barton MK. Nature. 2001 411:709-13.
doi.org/10.1038/35079635
Small RNAs Turn Over a New Leaf as Morphogens.
doi.org/10.1016/j.devcel.2017.10.025 [companion to Skopelitis paper]
The Sussex signal: insights into leaf dorsiventrality.
doi.org/10.1242/dev.131888 [a fun history]
Leaf adaxial-abaxial polarity specification and lamina outgrowth: evolution and development.
doi.org/10.1093/pcp/pcs074 [a wider view of leaves]
May 5
4-6pm
Carnegie seminar
Speaker: Aman Husbands, U. Penn
https://www.bio.upenn.edu/people/aman-husbands
“HD-ZIPIII transcription factors are controlled by deeply-conserved START domains”
May 10
9:45-11:15am
Rhee
Plant systems biology: Basic Concepts in Experimental Design and Quantitative Data Analysis
Overview of plant systems biology with topics including biological networks and modeling
May 12
9:45-11:15am
Rhee
Quantitative analysis papers:
Vaux DL, Fidler F, Cumming G. Replicates and repeats--what is the difference and is it significant? A brief discussion of statistics and experimental design. EMBO Rep. 13:291-296 (2012)
dx.doi.org/10.1038%2Fembor.2012.36
Streiner DL. Maintaining standards: differences between the standard deviation and standard error, and when to use each. Can J Psychiatry. 41(8):498-502 (1996)
doi.org/10.1177/070674379604100805
Sullivan GM, Feinn R. Using Effect Size-or Why the P Value Is Not Enough. J Grad Med Educ. 4(3):279-282 (2012)
dx.doi.org/10.4300%2FJGME-D-12-00156.1
Classic paper:
Milo, R. et al. Network motifs: simple building blocks of complex networks. Science 298, 824–827 (2002)
doi.org/10.1126/science.298.5594.824
Discussion paper:
Wei Liu, Ann Feke, Chun Chung Leung, Daniel A. Tarté, Wenxin Yuan, Morgan Vanderwall, Garrett Sager, Xing Wu, Ariela Schear, Damon A. Clark, Bryan C. Thines, *Joshua M. Gendron A metabolic daylength measurement system mediates winter photoperiodism in plants. Developmental Cell 56(17): 2501-2515.e5 (2021)
doi.org/10.1016/j.devcel.2021.07.016
May 13
4-6pm
Carnegie seminar
Speaker: *Joshua Gendron, Yale University
https://gendronlab.yale.edu
“Illuminating the plant calendar”
May 16
4-6pm
Stanford Bio Seminar
Speaker: Zach Lippman, Cold Spring Harbor Laboratory
http://lippmanlab.labsites.cshl.edu/
“Dynamic evolution of gene duplications and their interactions in shaping trait variation”
May 17
9:45-11:15am
Rhee
Plant metabolism: An overview of plant metabolism with a focus on photosynthesis
May 19
9:45-11:15am
Rhee
Classic paper:
Hatch MD, Slack CR. Photosynthesis by sugar-cane leaves. A new carboxylation reaction and the pathway of sugar formation. Biochem J. 101(1):103-111 (1966) doi.org/10.1042/bj1010103
Discussion paper:
*Nam, HI., Shahzad, Z., *Dorone, Y. et al. Interdependent iron and phosphorus availability controls photosynthesis through retrograde signaling. Nat Commun 12, 7211 (2021) doi.org/10.1038/s41467-021-27548-2
Reviews (optional):
Johnson MP. Photosynthesis. Essays Biochem. 60(3):255-273 (2016)
doi.org/10.1042/EBC20160016
Hiroshi A. Maeda and Alisdair R. Fernie Evolutionary History of Plant Metabolism Annual Review of Plant Biology 72(1):185-216 (2021)
doi.org/10.1146/annurev-arplant-080620-031054
May 20
4-6pm
Carnegie seminar
Speaker: *Hatem Rouached, Michigan State University
https://plantresilience.msu.edu/directory/faculty/hatem-rouached/
“Uncovering the molecular basis of photosynthesis regulation by nutrient signals”
May 24
9:45-11:15am
Brophy
Plant synthetic biology: Engineering features outside the reach of evolution: an overview of plant synthetic biology.
May 26
9:45-11:15am
Brophy
Classic paper: Construction of a genetic toggle switch in Escherichia coli. Gardner, T.S., Cantor, C.R., Collins, J.J. Nature (2000) 403, 339-342.
doi.org/10.1038/35002131
Discussion paper (technical):
Cary, T.J., Rylott, E.L., Zhang, L. et al. Field trial demonstrating phytoremediation of the military explosive RDX by XplA/XplB-expressing switchgrass. Nat Biotechnol 39, 1216–1219 (2021) doi.org/10.1038/s41587-021-00909-4
Discussion paper (opinion):
Wu, F., Wessler, J., Ziberman, D., Russell, r.m., Chen, C., Dubock, A.C. Opinion: Allow golden rice to save lives PNAS 118(51) e2120901118 (2021)
doi.org/10.1073/pnas.2120901118
May 27
4-6pm
Carnegie seminar
Speaker: Howard Salis, Penn State U.
https://salislab.net/
"Building an Engineering Discipline for Biology: Model-predictive Design of Genetic Systems for Reprogramming Cellular Functions"
June 3
4-6pm
Carnegie seminar
Speaker: Mark Urban, U. Connecticut
http://hydrodictyon.eeb.uconn.edu/people/urban/
“Improving the forecast for biodiversity in the global heat age”
Quarter/Year: Spring 2022 9:45-11:15 am Tues/Thurs
Location: STLC119 (SAPP Center first floor)
Highly recommended: Carnegie Seminar 4 – 5:30 Friday, 260 Panama Street
Optional: Prep session for Thursday presenters Wednesday at 5 (or TBA)
By arrangement: Individual meetings with the faculty to go over journal club papers
Faculty: Sue Rhee, Carnegie Institution for Science, [email protected]
Virginia Walbot, Department of Biology, [email protected]
Grading: Satisfactory/No Credit or Letter Grade: Based on attendance (required at all sessions for credit), participation in discussion, and turning in an acceptable critique for all 9 weekly assignments. The critique papers are due each Thursday.
Online, if required, through the Canvas Website and ZOOM: If Stanford designates spring quarter for online only classes, this course will be given via ZOOM, accessible to Stanford affiliates on Tuesday and registered students on Thursdays. If distance learning is required for an individual(s), the faculty will arrange either ZOOM class sessions or an individual discussion after a student has read the lecture presentation and assigned paper each week. Every effort will be made to make the course content and discussions available to all students.
Course Status as an Elective: This course can serve as an elective course for Biology Ph.D. candidates in the CMOB track for the following areas: Cell Biology, Genetic and Genomics, or the Biology of Molecules. This course can also serve as an upper division biology elective for undergraduates.
Audience: Graduate students at any level, co-term and upper-level undergraduate students with permission of instructor. Highly recommended for undergraduates doing research in plant biology.
Enrollment Cap: 20
Prerequisites: For graduate students, no prerequisites. For undergraduates, at least one of the following: Bio82 (Genetics), Bio86 (Cell Biology), Bio84 (Physiology), or ongoing research in a Stanford or Carnegie plant biology laboratory.
Class prep help: For all enrolled students, five types of support will be provided beyond the class
1) A pre-class zoom session to provide an overview and resources on how the Thurs journal club sessions will be structured, what a journal club is, and have students sign up for presentations. Recording available here Passcode: d6#HC8^v
2) A pre-journal club session by zoom on Wednesdays for the paper that will be discussed on the following day to go over the week’s paper and answer any questions: zoom link Password: 074620
3) One-on-one meetings by arrangement with students, especially undergraduates, who want help preparing their journal club presentations. Book here
4) We will be using the "Discussions" section of the Canvas site for people to pose questions or bring up things that they may not be familiar with. Please feel free to put up Qs as you read the papers or listen to the lectures. This will be mostly peer-based forum.
5) We will use a Google slide deck for people to upload their slides for their presentations
Auditing: Freshmen and Sophomores as well as TGR graduate students can audit lecture classes on Tuesdays. Other Stanford affiliates are invited to attend up to the room capacity seating.
Textbook (optional): The Botany Coloring Book – why not have fun learning the names of plant structures! About $22 at the bookstore or online.
Description and learning outcomes: This course will serve as a primer for all levels of graduate, co-term, and upper-level undergraduates interested in learning the fundamental principles of plant biology as well as the latest advances in tools, techniques, and theories that link basic science with translational science and applications for solving major societal challenges of today and tomorrow. Topics include plant evolution, genetics, breeding, plant-immune signaling, plant-environment interactions, tissue and organ development, metabolism, and systems and synthetic biology.
Overall learning goals: Students will learn major concepts and methods in plant biology and gain the tools and resources to research the literature more independently and deeply. In addition, students will learn fundamental ways that plants are different from animals and microbes. In each module, students will learn major concepts and skills from lectures and primary literature discussions. Students will also learn how to write a succinct critique of research papers and to analyze/present scientific papers to the class.
Class activities: There will be one lecture and one paper discussion class meeting each week. The discussion class is structured like a journal club, where individual students will lead discussions on specific sections of the paper. All students will write a 1-page critique of the paper and submit it before class (via Canvas online or as a printout at the start of Thursday discussions); faculty will provide feedback on composition and content. The Carnegie Spring Quarter Seminar Series will include speakers highly relevant to this class. Students are encouraged to attend, Fridays 4 – 5 pm at Carnegie Institution for Science (260 Panama St, Stanford) with a special session after each talk for students to interact with the speaker.
Topics:
Module 1 (Weeks 1-3): Plant Genetics, Genomics, and Evolution (Exposito-Alonso, Walbot)
Module 2 (Weeks 4-6): Plant Cell Signaling, Development, and Physiology (Mudgett, Dinneny, Bergmann)
Module 3 (Weeks 7-9): Plant Metabolism, Systems, and Synthetic Biology (Rhee, Brophy)
Date
Instructors (Teaching)
Topic/Papers/Learning Goals
*Stanford or Carnegie contribution
Mar 29 9:45-11:15am
Exposito-Alonso
Plant evolution: Introduction of plant macro- and micro- evolution from geological times to the Anthropocene. The complexity of plant genomes and its relationship to speciation, environmental adaptation, and contemporary rapid evolutionary processes.
Mar 31 9:45-11:15am
Exposito-Alonso
Classic paper: major contribution to the modern synthesis of evolution: *Clausen J, *Keck DD, *Hiesey WM. 1941. Regional differentiation in plant species. Am Nat. 75: 231–250. doi.org/10.1086/280955
Discussion paper: addressing global change problems using fundamental plant biological principles: Monroe JG, Powell T, Price N, Mullen JL, Howard A, Evans K, et al. Drought adaptation in Arabidopsis thaliana by extensive genetic loss-of-function. Elife. 2018;7: e41038.
doi.org/10.7554/eLife.41038
Apr 1
4-6 pm
Carnegie seminar
Speaker: Annie Schmidtt, UC Davis
https://plantgxe.ucdavis.edu/
“How natural variation in the seasonal germination niche shapes plant life histories and climate adaptation”
Apr 5
9:45-11:15am
Walbot
Plant genetics: Alternation of generations and practical applications of controlling reproduction: [1] genetics of sporophytic and gametophytic self-incompatibility, [2] gametophyte advantage genetics and the popcorn industry, [3] cytoplasmic male sterility and the risk of monoculture.
Apr 7
9:45-11:15am
Walbot
Classic paper: Specificity determinants and diversification of the Brassica self-incompatibility pollen ligand (2004) T. Chookajorn, A. Kachroo, D. R. Ripoll, A. G. Clark, and J. B. Nasrallah. PNAS 101: 911-917.
doi.org/10.1073/pnas.2637116100
Discussion paper: Y. *Lu et al. 2019. A pistil-expressed pectin methylesterase confers cross-incompatibility between strains of Zea mays. Nature Communications 10, 2304.doi.org/10.1038/s41467-019-10259-0
Apr 8
4-6pm
Carnegie seminar
Speaker: *Rachel Egger, Syngenta
https://www.linkedin.com/in/rachelegger/
“Novel Technologies for Haploid Genome Doubling in Corn”
Apr 12
9:45-11:15am
Walbot
Plant breeding: Historic plant breeding principles: line selection, hybrid vigor, mutation breeding, wide crosses, yield drag and time costs in historic improvement schemes. Modern solutions: transgenic introduction of specific alleles, haploid lines for instant homozygosity, quantitative and individual trait mapping, CRISPR-Cas9 targeted mutagenesis.
Apr 14
9:45-11:15am
Walbot
Classic paper: Donald N. Duvick. 2005. The contribution of breeding to yield advances in maize (Zea mays L.). Advances in Agronomy 86: 83-145. This review is long and comprehensive; suggest you search for a few specific traits (drought, planting density, herbicide resistance, etc.) to get a summary of the data on trait of interest.
doi.org/10.1016/S0065-2113(05)86002-X Discussion paper: *Kelliher, T. et al. 2019. One-step genome editing of elite crop germplasm during haploid induction. Nature Biotechnology 37: 287–292doi.org/10.1038/s41587-019-0038-x
Apr 15
4-6pm
Carnegie seminar
Speaker: Harry Klee, University of Florida
https://hos.ifas.ufl.edu/kleelab/
“What went wrong with the industrial tomato and how do we fix it?”
Apr 19
9:45-11:15am
Mudgett
Plant Immune Signaling: From genes to channels – A remarkable view into activation of immune signaling
Overview: We will discuss some of the most recent and exciting discoveries in plant innate immunity research. We will explore protein structural biology and biochemistry studies revealing the molecular mechanisms of host-pathogen recognition, defense signaling and homeostasis, and disease resistance execution. The focus will be on protein structure-based insights to intracellular immune receptor (NLR) activation and downstream signaling leading to a host response called effector-triggered immunity (ETI). The remarkable surprise uncovered in these studies points to a new mechanistic understanding of calcium signaling and homeostasis.
Apr 21
9:45-11:15am
Mudgett
Literature: A classic review on plant disease resistance proteins provides content for the discovery of the relevant genes and the ideas of researchers at the time for their putative function. The meeting review provides an overview of the most recent findings in this area. Two primary literature articles provide key functional data. Background information for ZAR1 and NRG1 can be found in the cited references.
Classic review: Staskawicz, B. J., Ausubel, F. M., Baker, B. J., Ellis, J. G., and Jones, J. D. G. 1995. Molecular genetics of plant disease resistance. Science 268, 661-667.
doi.org/10.1126/science.7732374
Discussion paper: Bi, G., Su, M., Li, N., Liang, Y., Dang, S., Xu, J., Hu, M., Wang, J., Zou, M., Deng, Y., Li, Q., Huang, S., Li, J., Chai, J., He, K., Chen, Y. H., and Zhou, J. M. 2021. The ZAR1 resistosome is a calcium-permeable channel triggering plant immune signaling. Cell 184:3528-3541.e12.
doi.org/10.1016/j.cell.2021.05.003
Optional reading:
Margets, Rima, Helm and Carter (2021) Molecular mechanisms and structure - Zooming in on plant immunity. MPMI 34, 12: 1346-1349.
doi.org/10.1094/MPMI-08-21-0208-MR
Jacob, P., Kim, N. H., Wu, F., El-Kasmi, F., Chi, Y., Walton, W. G., Furzer, O. J., Lietzan, A. D., Sunil, S., Kempthorn, K., Redinbo, M. R., Pei, Z. M., Wan, L., and Dangl, J. L. 2021. Plant “helper” immune receptors are Ca2+-permeable nonselective cation channels. Science 373:420-425.
doi.org/10.1126/science.abg7917
Apr 22
4-6pm
Carnegie seminar
Speaker: *Jazz Dickinson, UCSD
https://dickinsonlab.biology.ucsd.edu
“Discovering small molecule regulators of plant development”
Apr 26
9:45-11:15am
Dinneny
Plant-environment interactions: from the field to the Petri dish and back to the field
Apr 28
9:45-11:15am
Dinneny
Classic paper: Drew M.C. (1975) Comparison of the effects of a localised supply of phosphate, nitrate, ammonium and potassium on the growth of the seminal root system, and the shoot, in barley. The New Phytologist 75, 479–490.
doi.org/10.1111/j.1469-8137.1975.tb01409.x
Discussion paper: Pandey et al., (2021) Plant roots sense soil compaction through restricted ethylene diffusion. Science Jan 15;371(6526):276-280.
doi.org/10.1126/science.abf3013
Apr 29
4-6pm
Carnegie seminar
Speaker: Gitta Coaker - UC Davis
https://www.coakerlab.org
“The battle between bacterial pathogens and their hosts”
May 3
9:45-11:15am
Bergmann
Plant tissue and organ development: Plant bodies are diverse, but some design principles emerge from examination of how the above-ground portions of the plant are made and patterned.
May 5
9:45-11:15am
Bergmann
Classic paper:
Experiments on the cause of dorsiventrality in leaves.
Sussex IM. Nature. 1951 167:651-2. doi.org/10.1038/167651a0
Discussion paper:
Boundary formation through a direct threshold-based readout of mobile small RNA gradients. Skopelitis DS, Benkovics AH, Husbands AY, Timmermans MCP. Dev Cell. 2017
doi.org/10.1016/j.devcel.2017.10.003
Reviews and a modern classic paper (optional):
Role of PHABULOSA and PHAVOLUTA in determining radial patterning in shoots. McConnell…Barton MK. Nature. 2001 411:709-13.
doi.org/10.1038/35079635
Small RNAs Turn Over a New Leaf as Morphogens.
doi.org/10.1016/j.devcel.2017.10.025 [companion to Skopelitis paper]
The Sussex signal: insights into leaf dorsiventrality.
doi.org/10.1242/dev.131888 [a fun history]
Leaf adaxial-abaxial polarity specification and lamina outgrowth: evolution and development.
doi.org/10.1093/pcp/pcs074 [a wider view of leaves]
May 5
4-6pm
Carnegie seminar
Speaker: Aman Husbands, U. Penn
https://www.bio.upenn.edu/people/aman-husbands
“HD-ZIPIII transcription factors are controlled by deeply-conserved START domains”
May 10
9:45-11:15am
Rhee
Plant systems biology: Basic Concepts in Experimental Design and Quantitative Data Analysis
Overview of plant systems biology with topics including biological networks and modeling
May 12
9:45-11:15am
Rhee
Quantitative analysis papers:
Vaux DL, Fidler F, Cumming G. Replicates and repeats--what is the difference and is it significant? A brief discussion of statistics and experimental design. EMBO Rep. 13:291-296 (2012)
dx.doi.org/10.1038%2Fembor.2012.36
Streiner DL. Maintaining standards: differences between the standard deviation and standard error, and when to use each. Can J Psychiatry. 41(8):498-502 (1996)
doi.org/10.1177/070674379604100805
Sullivan GM, Feinn R. Using Effect Size-or Why the P Value Is Not Enough. J Grad Med Educ. 4(3):279-282 (2012)
dx.doi.org/10.4300%2FJGME-D-12-00156.1
Classic paper:
Milo, R. et al. Network motifs: simple building blocks of complex networks. Science 298, 824–827 (2002)
doi.org/10.1126/science.298.5594.824
Discussion paper:
Wei Liu, Ann Feke, Chun Chung Leung, Daniel A. Tarté, Wenxin Yuan, Morgan Vanderwall, Garrett Sager, Xing Wu, Ariela Schear, Damon A. Clark, Bryan C. Thines, *Joshua M. Gendron A metabolic daylength measurement system mediates winter photoperiodism in plants. Developmental Cell 56(17): 2501-2515.e5 (2021)
doi.org/10.1016/j.devcel.2021.07.016
May 13
4-6pm
Carnegie seminar
Speaker: *Joshua Gendron, Yale University
https://gendronlab.yale.edu
“Illuminating the plant calendar”
May 16
4-6pm
Stanford Bio Seminar
Speaker: Zach Lippman, Cold Spring Harbor Laboratory
http://lippmanlab.labsites.cshl.edu/
“Dynamic evolution of gene duplications and their interactions in shaping trait variation”
May 17
9:45-11:15am
Rhee
Plant metabolism: An overview of plant metabolism with a focus on photosynthesis
May 19
9:45-11:15am
Rhee
Classic paper:
Hatch MD, Slack CR. Photosynthesis by sugar-cane leaves. A new carboxylation reaction and the pathway of sugar formation. Biochem J. 101(1):103-111 (1966) doi.org/10.1042/bj1010103
Discussion paper:
*Nam, HI., Shahzad, Z., *Dorone, Y. et al. Interdependent iron and phosphorus availability controls photosynthesis through retrograde signaling. Nat Commun 12, 7211 (2021) doi.org/10.1038/s41467-021-27548-2
Reviews (optional):
Johnson MP. Photosynthesis. Essays Biochem. 60(3):255-273 (2016)
doi.org/10.1042/EBC20160016
Hiroshi A. Maeda and Alisdair R. Fernie Evolutionary History of Plant Metabolism Annual Review of Plant Biology 72(1):185-216 (2021)
doi.org/10.1146/annurev-arplant-080620-031054
May 20
4-6pm
Carnegie seminar
Speaker: *Hatem Rouached, Michigan State University
https://plantresilience.msu.edu/directory/faculty/hatem-rouached/
“Uncovering the molecular basis of photosynthesis regulation by nutrient signals”
May 24
9:45-11:15am
Brophy
Plant synthetic biology: Engineering features outside the reach of evolution: an overview of plant synthetic biology.
May 26
9:45-11:15am
Brophy
Classic paper: Construction of a genetic toggle switch in Escherichia coli. Gardner, T.S., Cantor, C.R., Collins, J.J. Nature (2000) 403, 339-342.
doi.org/10.1038/35002131
Discussion paper (technical):
Cary, T.J., Rylott, E.L., Zhang, L. et al. Field trial demonstrating phytoremediation of the military explosive RDX by XplA/XplB-expressing switchgrass. Nat Biotechnol 39, 1216–1219 (2021) doi.org/10.1038/s41587-021-00909-4
Discussion paper (opinion):
Wu, F., Wessler, J., Ziberman, D., Russell, r.m., Chen, C., Dubock, A.C. Opinion: Allow golden rice to save lives PNAS 118(51) e2120901118 (2021)
doi.org/10.1073/pnas.2120901118
May 27
4-6pm
Carnegie seminar
Speaker: Howard Salis, Penn State U.
https://salislab.net/
"Building an Engineering Discipline for Biology: Model-predictive Design of Genetic Systems for Reprogramming Cellular Functions"
June 3
4-6pm
Carnegie seminar
Speaker: Mark Urban, U. Connecticut
http://hydrodictyon.eeb.uconn.edu/people/urban/
“Improving the forecast for biodiversity in the global heat age”
2020
COURSE DESCRIPTION
BIO129/229: Fundamentals and Frontiers in Plant Biology
Quarter/Year: Winter 2020 Tues/Thurs 12-1:20 pm Grading: Satisfactory/No Credit
This course can serve as an elective course for Biology PhD candidates in the CMOB track for the following areas: Cell Biology, Genetic and Genomics, or the Biology of Molecules. This course can also serve as an upper division biology elective for undergraduates.
Location: STLC room 105 Number of Units: 3
Audience: Graduate students at any level, co-term and upper-level undergraduate students with permission of instructor.
Enrollment Cap: 20
Prerequisites: For graduate students, no prerequisites. For undergraduates, at least two of the following Bio82 (Genetics), Bio86 (Cell Biology), Bio84 (Physiology), and ongoing research in a Stanford or Carnegie plant biology laboratory.
Auditing: TGA graduate students can audit lecture classes on Tuesdays
Description and learning outcomes: This course will serve as a primer for all levels of graduate, co-term, and upper-level undergraduates interested in learning about the fundamental aspects of plant biology as well as the latest advances in tools, techniques, and theories that link basic science with translational science and applications for solving major societal challenges of today and tomorrow. Topics include plant evolution, genomics, genetics, biotic and abiotic interactions, cell and development, and systems and synthetic biology.
Overall learning goals: Students will learn major concepts and methods in plant biology and gain the tools and resources to research the literature more independently and deeply. In addition, students will learn fundamental ways that plants are different from animals and microbes. In each module, students will learn major concepts and skills from lectures and primary literature discussions. Students will also learn how to write a succinct critique of research papers.
Class activities: Each week will compose of one lecture and one paper discussion class. The discussion class is structured like a journal club, where teams of students will lead discussions on various sections of the paper. Students will write a 1 page critique of the paper and submit before class. Carnegie Winter Quarter Seminar Series will include speakers from the papers or topics of discussion and students will have an opportunity to meet with the speakers. There may be 1-2 field trips.
Grading: Based on attendance (required at all sessions for credit), participation in discussion, and turning in an acceptable critique for all 9 weekly assignments.
Topics (*Module Coordinator):
Module 1 (Weeks 1-3): Plant Genetics, Genomics, and Evolution (Walbot*, Evans, Exposito-Alonso)
Module 2 (Weeks 4-5): Plant Cell and Developmental Biology (Bergmann*, Ehrhardt)
Module 3 (Weeks 6-8): Biotic and Abiotic Interactions (Long*, Grossman, Wang)
Module 4 (Weeks 9-10): Plant Systems and Synthetic Biology (Rhee*, Bhaya)
Date
Module
Instructors (Teaching)
Topic/Papers/Learning Goals
Jan 7
12-1:20pm
Mod 1
Exposito-Alonso,
Walbot, Evans
Introduction of plant macro- and micro- evolution from geological times to the anthropocene. The complexity of plant genomes and its relationship to speciation, environmental adaptation, and contemporary rapid evolutionary processes.
Jan 9
12-1:20pm
Mod 1
Exposito-Alonso,
Walbot, Evans
Classic paper that contributed to the modern synthesis of evolution: Clausen J, Keck DD, Hiesey WM. Regional Differentiation in Plant Species. Am Nat. 1941;75: 231–250. Available: http://www.jstor.org/stable/2457513
Discussion paper addressing global change problems using fundamental plant biological principles: Monroe JG, Powell T, Price N, Mullen JL, Howard A, Evans K, et al. Drought adaptation in Arabidopsis thaliana by extensive genetic loss-of-function. Elife. 2018;7: e41038. https://doi.org/10.7554/eLife.41038
Jan 10
4-5 pm
Carnegie Seminar
Host: Moises Exposito-Alonso
Speaker: Dan Jacobson
Jan 14
12-1:20pm
Mod 1
Exposito-Alonso,
Walbot, Evans
Alternation of generations and practical applications of controlling reproduction: [1] genetics of sporophytic and gametophytic self-incompatibility, [2] gametophyte advantage genetics and the popcorn industry, [3] haploid induction and CRISPR editing via pollen in plant breeding.
Jan 16
12-1:20pm
Mod 1
Exposito-Alonso,
Walbot, Evans
Genetics of self-incompatibility:
Background paper: Specificity determinants and diversification of the Brassica self-incompatibility pollen ligand (2004) Thanat Chookajorn, Aardra Kachroo, Daniel R. Ripoll, Andrew G. Clark, and June B.Nasrallah. PNAS 101: 911-917. https://doi.org/10.1073/pnas.2637116100
Discussion paper: S-Locus F-Box proteins are solely responsible for S-RNase-based self-incompatibility of Petunia
Pollen (2018) Linhan Sun, Justin S. Williams, Shu Li, Lihua Wu, Wasi A. Khatri, Patrick G. Stone, Matthew D. Keebaugh, and Teh-hui Kao. The Plant Cell 30: 2959-2972. DOI:
https://doi.org/10.1105/tpc.18.00615
Jan 21
12-1:20pm
Mod 1
Exposito-Alonso,
Walbot, Evans
Epigenetic regulation of gene expression in the context of plant development and heritable gene silencing
Jan 23
12-1:20pm
Mod 1
Exposito-Alonso,
Walbot, Evans
One classic paper to read and one recent paper for discussion
Classic Paper: First demonstration of imprinting of an individual gene in any organism, showing that parent-of-origin, rather than gene dosage, is responsible for expression differences of R-r in maize endosperm.
J.L. Kermicle (1970) DEPENDENCE OF THE R-MOTTLED ALEURONE PHENOTYPE IN MAIZE ON MODE OF SEXUAL TRANSMISSION. Genetics 66:69-85.
https://www.genetics.org/content/66/1/69.long
Recent Papers: Movement of small RNAs from the vegetative cell to sperm cells in pollen for transposon silencing.
G. Martinez, K. Panda, C. Kohler, and R.K. Slotkin (2016) Silencing in sperm cells is directed by RNA movement from the surrounding nurse cell. Nature Plants 2:1-8. https://www.nature.com/articles/nplants201630
Demethylation in the endosperm is correlated with demethylation in the central cell.
Park et al. (2016) DNA demethylation is initiated in the central cells of Arabidopsis and rice. PNAS 113:15138-15143
https://www.pnas.org/content/113/52/15138
Jan 24 4-5 pm
Host: Ginny Walbot
Speaker: Tim Kelliher
Jan 28
12-1:20pm
Mod 2
Bergmann, Ehrhardt
The creation of plant bodies with an emphasis on defining features of plant development such as modularity, meristematic growth, and morphogenesis without cellular movement.
Jan 30
12-1:20pm
Mod 2
Bergmann, Ehrhardt
Several classic (short!) papers using microsurgery to define organ positions, https://www-nature-com.laneproxy.stanford.edu/articles/167651a0
https://www-nature-com.stanford.idm.oclc.org/articles/171224b0.pdf
A decades-later revisit of these surgeries
https://dev-biologists-org.stanford.idm.oclc.org/content/develop/132/1/15.full.pdf
and a recent paper identifying the molecules and mechanisms that are responsible for the positional information. https://elifesciences.org/articles/27421
Jan 31
4-5 pm
Carnegie seminar
Host: Dominique Bergmann
Speaker: Courtney Hollender
Feb 4
12-1:20pm
Mod 2
Bergmann, Ehrhardt
Principles of growth and morphogenesis in cells constrained by cell walls. Topics include biophysics of cells under high turgor pressure, organization of cell wall biosynthesis and yielding, establishment of asymmetries in cell growth.
Feb 6
12-1:20pm
Mod 2
Bergmann, Ehrhardt
Classic paper: Green P.B. (1962) Mechanism for plant cellular morphogenesis. Science 138: 1404-1405.
Recent Paper: Oda Y. Fukuda H. (2012) Initiation of cell wall pattern by a Rho- and microtubule-driven symmetry breaking. Science 337: 1333-1336.
Feb 11
12-1:20pm
Mod 3
Long, Grossman, Wang
Overview of plant-microbe interactions. Major topics: recognition, bacterial signals and plant responses; genes for symbiosis with bacteria and fungi; different levels of plant defense against pathogens.
Feb 13
12-1:20pm
Mod 3
Long, Grossman, Wang
Classic paper: Lerouge, P. et al (1990) Symbiotic host-specificity of Rhizobium meliloti is determined by a sulphated and acylated glucosamine oligosaccharide signal. Nature 344: 781-784.
https://www.nature.com/articles/344781a0.pdf
Recent paper: Feng F, Sun J, Radhakrishnan GV, Lee T, Bozsóki Z, Fort S, Gavrin A, Gysel K, Thygesen MB, Andersen KR, Radutoiu S, Stougaard J, Oldroyd GED. A combination of chitooligosaccharide and lipochitooligosaccharide recognition promotes arbuscular mycorrhizal associations in Medicago truncatula. Nat Commun. 2019 Nov 6;10(1):5047. doi: 10.1038/s41467-019-12999-5. PubMed PMID: 31695035; PubMed Central PMCID: PMC6834629.
Feb 14
4-5 pm
Carnegie seminar
Host suggestion: Sharon Long
Speaker suggestion: Ksenia Krasileva
Feb 18
12-1:20pm
Mod 3
Long, Grossman, Wang
Basic aspects of photosynthetic metabolism; from the fixation of inorganic carbon to the generation of reactive oxygen species.
Feb 20
12-1:20pm
Mod 3
Long, Grossman, Wang
Classic Papers:
Photosynthesis. (2016) Johnson MP. Essays Biochem. Oct 31;60(3):255-273. Review. PubMed PMID: 27784776; PubMed Central PMCID: PMC5264509.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5264509/pdf/bse0600255.pdf
Efficient photosynthesis in dynamic light environments: a chloroplast's perspective. (2019) Kaiser E, Correa Galvis V, Armbruster U. Biochem J. 2019 Oct 15;476(19):2725-2741. doi: 10.1042/BCJ20190134. PubMed PMID: 31654058.
https://portlandpress.com/biochemj/article-lookup/doi/10.1042/BCJ20190134
Recent paper: Improving photosynthesis and crop productivity by accelerating recovery from photoprotection. (2016) Kromdijk J, Głowacka K, Leonelli L, Gabilly ST, Iwai M, Niyogi KK, Long SP. Science Nov 18;354(6314):857-861. PubMed PMID: 27856901.
https://science.sciencemag.org/content/354/6314/857/tab-pdf
Feb 21 4-5 pm
Carnegie Seminar
Host suggestion: Arthur Grossman
Speaker suggestion: Kris Niyogi
Feb 25
12-1:20pm
Mod 3
Long, Grossman, Wang
Developmental plasticity and acclimation to the environment, the underlying cell signaling and regulatory systems, protein networks and proteomics.
Feb 27
12-1:20pm
Mod 3
Long, Grossman, Wang
Classic paper:
(1) Park et al., Abscisic acid inhibits type 2C protein phosphatases via the PYR/PYL family of START proteins. Science. 2009 May 22;324(5930):1068-71. PMID: 19407142
https://science.sciencemag.org/content/324/5930/1068/tab-pdf
(2) Pandey et al., Two novel GPCR-type G proteins are abscisic acid receptors in Arabidopsis. Cell. 2009 Jan 9;136(1):136-48. PMID: 19135895
https://www.ncbi.nlm.nih.gov/pubmed/19135895
Recent paper: Lin Z, Li Y, Zhang Z, Liu X, Hsu CC, Du Y, Sang T, Zhu C, Wang Y, Satheesh V, Pratibha P, Zhao Y, Song CP, Tao WA, Zhu JK, Wang P. A RAF-SnRK2 kinase cascade mediates early osmotic stress signaling in higher plants. Nat Commun. 2020 Jan 30;11(1):613. doi: 10.1038/s41467-020-14477-9. PubMed PMID: 32001690; PubMed Central PMCID: PMC6992735.
Mar 3
12-1:20pm
Mod 4
Rhee, Bhaya
Overview of plant systems biology with topics including biological networks, cell and tissue modeling, and comparison of traditional plant physiology with systems biology
Mar 5
12-1:20pm
Mod 4
Rhee, Bhaya
Classic papers:
Milo, R. et al. Network motifs: simple building blocks of complex networks. Science 298, 824–827 (2002).https://science.sciencemag.org/content/298/5594/824
Just-in-time transcription program in metabolic pathways. (2004) Zaslaver A, Mayo AE, Rosenberg R, Bashkin P, Sberro H, Tsalyuk M, Surette MG, Alon U. Nat Genet.May;36(5):486-91. Epub 2004 Apr 25. PubMed PMID: 15107854.
https://www.nature.com/articles/ng1348.pdf
Recent paper: Wang W, Li S, Li Z, Zhang J, Fan K, Tan G, Ai G, Lam SM, Shui G, Yang Z, Lu H, Jin P, Li Y, Chen X, Xia X, Liu X, Dannelly HK, Yang C, Yang Y, Zhang S, Alterovitz G, Xiang W, Zhang L. Harnessing the intracellular triacylglycerols for titer improvement of polyketides in Streptomyces. Nat Biotechnol. 2020 Jan;38(1):76-83. doi: 10.1038/s41587-019-0335-4. Epub 2019 Dec 9. Erratum in: Nat Biotechnol. 2019 Dec 18;:. PubMed PMID: 31819261.
Mar 10
12-1:20pm
Mod 4
Rhee, Bhaya
Principles of synthetic biology; a discussion of successes and challenges. How has synthetic biology been used in plant engineering?
Mar 12
12-1:20pm
Mod 4
Rhee, Bhaya
Classic paper: Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca. Temme K, Zhao D, Voigt CA.
Proc Natl Acad Sci U S A. 2012 May 1;109(18):7085-90. doi: 10.1073/pnas.1120788109. Epub 2012 Apr 16.
PMID: 22509035
Recent paper: Polyprotein strategy for stoichiometric assembly of nitrogen fixation components for synthetic biology. Proc Natl Acad Sci U S A. 2018 Sep 4E8509-E8517. doi: 10.1073/pnas.1804992115. Epub 2018 Jul 30.
Quarter/Year: Winter 2020 Tues/Thurs 12-1:20 pm Grading: Satisfactory/No Credit
This course can serve as an elective course for Biology PhD candidates in the CMOB track for the following areas: Cell Biology, Genetic and Genomics, or the Biology of Molecules. This course can also serve as an upper division biology elective for undergraduates.
Location: STLC room 105 Number of Units: 3
Audience: Graduate students at any level, co-term and upper-level undergraduate students with permission of instructor.
Enrollment Cap: 20
Prerequisites: For graduate students, no prerequisites. For undergraduates, at least two of the following Bio82 (Genetics), Bio86 (Cell Biology), Bio84 (Physiology), and ongoing research in a Stanford or Carnegie plant biology laboratory.
Auditing: TGA graduate students can audit lecture classes on Tuesdays
Description and learning outcomes: This course will serve as a primer for all levels of graduate, co-term, and upper-level undergraduates interested in learning about the fundamental aspects of plant biology as well as the latest advances in tools, techniques, and theories that link basic science with translational science and applications for solving major societal challenges of today and tomorrow. Topics include plant evolution, genomics, genetics, biotic and abiotic interactions, cell and development, and systems and synthetic biology.
Overall learning goals: Students will learn major concepts and methods in plant biology and gain the tools and resources to research the literature more independently and deeply. In addition, students will learn fundamental ways that plants are different from animals and microbes. In each module, students will learn major concepts and skills from lectures and primary literature discussions. Students will also learn how to write a succinct critique of research papers.
Class activities: Each week will compose of one lecture and one paper discussion class. The discussion class is structured like a journal club, where teams of students will lead discussions on various sections of the paper. Students will write a 1 page critique of the paper and submit before class. Carnegie Winter Quarter Seminar Series will include speakers from the papers or topics of discussion and students will have an opportunity to meet with the speakers. There may be 1-2 field trips.
Grading: Based on attendance (required at all sessions for credit), participation in discussion, and turning in an acceptable critique for all 9 weekly assignments.
Topics (*Module Coordinator):
Module 1 (Weeks 1-3): Plant Genetics, Genomics, and Evolution (Walbot*, Evans, Exposito-Alonso)
Module 2 (Weeks 4-5): Plant Cell and Developmental Biology (Bergmann*, Ehrhardt)
Module 3 (Weeks 6-8): Biotic and Abiotic Interactions (Long*, Grossman, Wang)
Module 4 (Weeks 9-10): Plant Systems and Synthetic Biology (Rhee*, Bhaya)
Date
Module
Instructors (Teaching)
Topic/Papers/Learning Goals
Jan 7
12-1:20pm
Mod 1
Exposito-Alonso,
Walbot, Evans
Introduction of plant macro- and micro- evolution from geological times to the anthropocene. The complexity of plant genomes and its relationship to speciation, environmental adaptation, and contemporary rapid evolutionary processes.
Jan 9
12-1:20pm
Mod 1
Exposito-Alonso,
Walbot, Evans
Classic paper that contributed to the modern synthesis of evolution: Clausen J, Keck DD, Hiesey WM. Regional Differentiation in Plant Species. Am Nat. 1941;75: 231–250. Available: http://www.jstor.org/stable/2457513
Discussion paper addressing global change problems using fundamental plant biological principles: Monroe JG, Powell T, Price N, Mullen JL, Howard A, Evans K, et al. Drought adaptation in Arabidopsis thaliana by extensive genetic loss-of-function. Elife. 2018;7: e41038. https://doi.org/10.7554/eLife.41038
Jan 10
4-5 pm
Carnegie Seminar
Host: Moises Exposito-Alonso
Speaker: Dan Jacobson
Jan 14
12-1:20pm
Mod 1
Exposito-Alonso,
Walbot, Evans
Alternation of generations and practical applications of controlling reproduction: [1] genetics of sporophytic and gametophytic self-incompatibility, [2] gametophyte advantage genetics and the popcorn industry, [3] haploid induction and CRISPR editing via pollen in plant breeding.
Jan 16
12-1:20pm
Mod 1
Exposito-Alonso,
Walbot, Evans
Genetics of self-incompatibility:
Background paper: Specificity determinants and diversification of the Brassica self-incompatibility pollen ligand (2004) Thanat Chookajorn, Aardra Kachroo, Daniel R. Ripoll, Andrew G. Clark, and June B.Nasrallah. PNAS 101: 911-917. https://doi.org/10.1073/pnas.2637116100
Discussion paper: S-Locus F-Box proteins are solely responsible for S-RNase-based self-incompatibility of Petunia
Pollen (2018) Linhan Sun, Justin S. Williams, Shu Li, Lihua Wu, Wasi A. Khatri, Patrick G. Stone, Matthew D. Keebaugh, and Teh-hui Kao. The Plant Cell 30: 2959-2972. DOI:
https://doi.org/10.1105/tpc.18.00615
Jan 21
12-1:20pm
Mod 1
Exposito-Alonso,
Walbot, Evans
Epigenetic regulation of gene expression in the context of plant development and heritable gene silencing
Jan 23
12-1:20pm
Mod 1
Exposito-Alonso,
Walbot, Evans
One classic paper to read and one recent paper for discussion
Classic Paper: First demonstration of imprinting of an individual gene in any organism, showing that parent-of-origin, rather than gene dosage, is responsible for expression differences of R-r in maize endosperm.
J.L. Kermicle (1970) DEPENDENCE OF THE R-MOTTLED ALEURONE PHENOTYPE IN MAIZE ON MODE OF SEXUAL TRANSMISSION. Genetics 66:69-85.
https://www.genetics.org/content/66/1/69.long
Recent Papers: Movement of small RNAs from the vegetative cell to sperm cells in pollen for transposon silencing.
G. Martinez, K. Panda, C. Kohler, and R.K. Slotkin (2016) Silencing in sperm cells is directed by RNA movement from the surrounding nurse cell. Nature Plants 2:1-8. https://www.nature.com/articles/nplants201630
Demethylation in the endosperm is correlated with demethylation in the central cell.
Park et al. (2016) DNA demethylation is initiated in the central cells of Arabidopsis and rice. PNAS 113:15138-15143
https://www.pnas.org/content/113/52/15138
Jan 24 4-5 pm
Host: Ginny Walbot
Speaker: Tim Kelliher
Jan 28
12-1:20pm
Mod 2
Bergmann, Ehrhardt
The creation of plant bodies with an emphasis on defining features of plant development such as modularity, meristematic growth, and morphogenesis without cellular movement.
Jan 30
12-1:20pm
Mod 2
Bergmann, Ehrhardt
Several classic (short!) papers using microsurgery to define organ positions, https://www-nature-com.laneproxy.stanford.edu/articles/167651a0
https://www-nature-com.stanford.idm.oclc.org/articles/171224b0.pdf
A decades-later revisit of these surgeries
https://dev-biologists-org.stanford.idm.oclc.org/content/develop/132/1/15.full.pdf
and a recent paper identifying the molecules and mechanisms that are responsible for the positional information. https://elifesciences.org/articles/27421
Jan 31
4-5 pm
Carnegie seminar
Host: Dominique Bergmann
Speaker: Courtney Hollender
Feb 4
12-1:20pm
Mod 2
Bergmann, Ehrhardt
Principles of growth and morphogenesis in cells constrained by cell walls. Topics include biophysics of cells under high turgor pressure, organization of cell wall biosynthesis and yielding, establishment of asymmetries in cell growth.
Feb 6
12-1:20pm
Mod 2
Bergmann, Ehrhardt
Classic paper: Green P.B. (1962) Mechanism for plant cellular morphogenesis. Science 138: 1404-1405.
Recent Paper: Oda Y. Fukuda H. (2012) Initiation of cell wall pattern by a Rho- and microtubule-driven symmetry breaking. Science 337: 1333-1336.
Feb 11
12-1:20pm
Mod 3
Long, Grossman, Wang
Overview of plant-microbe interactions. Major topics: recognition, bacterial signals and plant responses; genes for symbiosis with bacteria and fungi; different levels of plant defense against pathogens.
Feb 13
12-1:20pm
Mod 3
Long, Grossman, Wang
Classic paper: Lerouge, P. et al (1990) Symbiotic host-specificity of Rhizobium meliloti is determined by a sulphated and acylated glucosamine oligosaccharide signal. Nature 344: 781-784.
https://www.nature.com/articles/344781a0.pdf
Recent paper: Feng F, Sun J, Radhakrishnan GV, Lee T, Bozsóki Z, Fort S, Gavrin A, Gysel K, Thygesen MB, Andersen KR, Radutoiu S, Stougaard J, Oldroyd GED. A combination of chitooligosaccharide and lipochitooligosaccharide recognition promotes arbuscular mycorrhizal associations in Medicago truncatula. Nat Commun. 2019 Nov 6;10(1):5047. doi: 10.1038/s41467-019-12999-5. PubMed PMID: 31695035; PubMed Central PMCID: PMC6834629.
Feb 14
4-5 pm
Carnegie seminar
Host suggestion: Sharon Long
Speaker suggestion: Ksenia Krasileva
Feb 18
12-1:20pm
Mod 3
Long, Grossman, Wang
Basic aspects of photosynthetic metabolism; from the fixation of inorganic carbon to the generation of reactive oxygen species.
Feb 20
12-1:20pm
Mod 3
Long, Grossman, Wang
Classic Papers:
Photosynthesis. (2016) Johnson MP. Essays Biochem. Oct 31;60(3):255-273. Review. PubMed PMID: 27784776; PubMed Central PMCID: PMC5264509.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5264509/pdf/bse0600255.pdf
Efficient photosynthesis in dynamic light environments: a chloroplast's perspective. (2019) Kaiser E, Correa Galvis V, Armbruster U. Biochem J. 2019 Oct 15;476(19):2725-2741. doi: 10.1042/BCJ20190134. PubMed PMID: 31654058.
https://portlandpress.com/biochemj/article-lookup/doi/10.1042/BCJ20190134
Recent paper: Improving photosynthesis and crop productivity by accelerating recovery from photoprotection. (2016) Kromdijk J, Głowacka K, Leonelli L, Gabilly ST, Iwai M, Niyogi KK, Long SP. Science Nov 18;354(6314):857-861. PubMed PMID: 27856901.
https://science.sciencemag.org/content/354/6314/857/tab-pdf
Feb 21 4-5 pm
Carnegie Seminar
Host suggestion: Arthur Grossman
Speaker suggestion: Kris Niyogi
Feb 25
12-1:20pm
Mod 3
Long, Grossman, Wang
Developmental plasticity and acclimation to the environment, the underlying cell signaling and regulatory systems, protein networks and proteomics.
Feb 27
12-1:20pm
Mod 3
Long, Grossman, Wang
Classic paper:
(1) Park et al., Abscisic acid inhibits type 2C protein phosphatases via the PYR/PYL family of START proteins. Science. 2009 May 22;324(5930):1068-71. PMID: 19407142
https://science.sciencemag.org/content/324/5930/1068/tab-pdf
(2) Pandey et al., Two novel GPCR-type G proteins are abscisic acid receptors in Arabidopsis. Cell. 2009 Jan 9;136(1):136-48. PMID: 19135895
https://www.ncbi.nlm.nih.gov/pubmed/19135895
Recent paper: Lin Z, Li Y, Zhang Z, Liu X, Hsu CC, Du Y, Sang T, Zhu C, Wang Y, Satheesh V, Pratibha P, Zhao Y, Song CP, Tao WA, Zhu JK, Wang P. A RAF-SnRK2 kinase cascade mediates early osmotic stress signaling in higher plants. Nat Commun. 2020 Jan 30;11(1):613. doi: 10.1038/s41467-020-14477-9. PubMed PMID: 32001690; PubMed Central PMCID: PMC6992735.
Mar 3
12-1:20pm
Mod 4
Rhee, Bhaya
Overview of plant systems biology with topics including biological networks, cell and tissue modeling, and comparison of traditional plant physiology with systems biology
Mar 5
12-1:20pm
Mod 4
Rhee, Bhaya
Classic papers:
Milo, R. et al. Network motifs: simple building blocks of complex networks. Science 298, 824–827 (2002).https://science.sciencemag.org/content/298/5594/824
Just-in-time transcription program in metabolic pathways. (2004) Zaslaver A, Mayo AE, Rosenberg R, Bashkin P, Sberro H, Tsalyuk M, Surette MG, Alon U. Nat Genet.May;36(5):486-91. Epub 2004 Apr 25. PubMed PMID: 15107854.
https://www.nature.com/articles/ng1348.pdf
Recent paper: Wang W, Li S, Li Z, Zhang J, Fan K, Tan G, Ai G, Lam SM, Shui G, Yang Z, Lu H, Jin P, Li Y, Chen X, Xia X, Liu X, Dannelly HK, Yang C, Yang Y, Zhang S, Alterovitz G, Xiang W, Zhang L. Harnessing the intracellular triacylglycerols for titer improvement of polyketides in Streptomyces. Nat Biotechnol. 2020 Jan;38(1):76-83. doi: 10.1038/s41587-019-0335-4. Epub 2019 Dec 9. Erratum in: Nat Biotechnol. 2019 Dec 18;:. PubMed PMID: 31819261.
Mar 10
12-1:20pm
Mod 4
Rhee, Bhaya
Principles of synthetic biology; a discussion of successes and challenges. How has synthetic biology been used in plant engineering?
Mar 12
12-1:20pm
Mod 4
Rhee, Bhaya
Classic paper: Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca. Temme K, Zhao D, Voigt CA.
Proc Natl Acad Sci U S A. 2012 May 1;109(18):7085-90. doi: 10.1073/pnas.1120788109. Epub 2012 Apr 16.
PMID: 22509035
Recent paper: Polyprotein strategy for stoichiometric assembly of nitrogen fixation components for synthetic biology. Proc Natl Acad Sci U S A. 2018 Sep 4E8509-E8517. doi: 10.1073/pnas.1804992115. Epub 2018 Jul 30.
course description
BIO 380: Career Exploration and Planning
Dr. Sue Rhee ([email protected])
Senior Staff Scientist, Carnegie Institution for Science
Associate Professor by Courtesy, Biology Department, Stanford University
Format: Discussion
Enrollment Cap: 20
Quarter/Year: Spring 2020
Prerequisite: Grad students in Life Sciences PhD programs
Grading: Satisfactory/No Credit
Number of Units: 1
Meeting Time: Thursdays 4:30-6:20 pm Location: Carnegie Seminar Room
Course Assistants:
Benjamin Jin ([email protected])
Emily Fryer ([email protected])
Description
Thinking about and planning for life beyond graduate school is one of the most anxiety-provoking activities students face. In this course, students will share their personal stories and dilemmas about career decisions; have the opportunity to take various self-assessments for characterizing their personalities and identify fitting professions; discuss various career options with a life sciences PhD; and ultimately learn to design their own path. There will be three career panels with invited guests from various career tracks, including research, teaching, administration, business, law, journalism, policy, and more. Open to life sciences PhD students in year 3 or beyond. The class will meet at Carnegie Institution for Science's seminar room building 600, located at 260 Panama St, Stanford, CA 94305 (https://dpb.carnegiescience.edu/about/contact).
Requirements
Students are expected to attend all class meetings, actively contribute to group discussions, and give a short group presentation on the final class meeting.
Schedule
April 02 — Introductions and Class Logistics, myIDP Assessment
Introduction to the structure and context of the course: we will go over requirements and expectations, complete a preliminary survey, and engage in small groups to get to know each other and discuss career opportunities in the life sciences. What are our personal and professional dreams, how do we find an overlap between the two? We will conduct the myIDP assessment in class.
Homework: Take the Myers-Briggs Type Indicator Test, to be independently completed by Tuesday, April 7th, 5 pm PST.
April 09 — Discussion of Myers-Briggs Type Indicator Test Results (guest lecture by MJ Mangiarelli of Stanford BioSci Careers)
The Myers-Briggs Type Indicator (MBTI) personality inventory is widely acknowledged as one of the most accurate and respected personality tests in psychology. It can be utilized in considering future career decisions as a practical tool for investigating work styles and work settings that are most conducive to one’s personality. We will be discovering our personality types, and how to maximize our "gifts" (our personality preferences) in order to contribute to team success--while understanding how the many facets of our complex identities affect overall career satisfaction. Stanford’s BioSci Careers (https://med.stanford.edu/bioscicareers.html) will help with evaluating the results.
Homework: Take the CliftonStrengths test by Gallup, to be independently completed by Tuesday, April 14th, 5 pm PST.
April 16 — Discussion of CliftonStrengths Test Results (guest lecture by Marlene Scherer Stern of Stanford BioSci Careers)
The CliftonStrengths test is designed to highlight the user’s character strengths, which can be used to assess what roles would be best in both utilizing and developing such strengths. We will be discovering our individual strengths and how these can contribute to success in our future careers, while understanding how they are only a part of our unique personalities. Stanford’s BioSci Careers will help with evaluating the results.
April 23 — Self-Assessment Decompression and Career Planning Lecture
Post-MBTI/CliftonStrengths test discussion in small groups to put the results in the context of career choices. There will also be a lecture on career planning, regarding key concepts and tools that are useful in professional development, with small group discussions to follow. Final Presentation projects will be assigned and expectations will be discussed.
April 30 — Career Panel I: “Business”
Panelists will be briefly introduced, then the floor will be opened up for student questions. This panel, along with the panels to follow, will serve as the perfect opportunity for lively discussion, and give students unique insight regarding career options and expectations. Carnegie will provide a reception after the panel to continue discussions and networking.
Kirk Clark
Executive Director, Novartis Institutes for BioMedical Research
Pamela Marrone
CEO and Founder, Marrone Bio Innovations
Jayaranjan Anthonypillai
Founder/CEO, Berkeley BioLabs;
Co-Founder/Managing Partner, Focus Academy LLC
Mowgli Holms
Co-founder and CEO, Phylos Biosciences
May 7 — Career Panel II: “Academic Research”
Pleuni Pennings
Assistant Professor, San Francisco State University
Miriam Goodman
Professor, Molecular and Cellular Physiology, Stanford University
Jennifer Mortimer
Staff Scientist, Berkeley Lab;
Director of Plant Systems Biology, JBEI
Rebecca Albright
Assistant Curator, California Academy of Sciences
May 14 — Career Panel III: “Scientific Journalism, Administration, Law, Philanthropy”
Amy Adams
Director of Long Range Vision Communications, Stanford University
James Keddie
Senior Patent Agent, Bozicevic, Field & Francis LLP
Rieko Yajima
Director for Drug Discovery Innovation, SPARK Translational Research Program, Stanford University
Milan Karol
Senior Development Officer, Carnegie Institution for Science
May 21 — Career Panels Decompression and Preparation for Final Presentations
Group discussions to follow the career panels. Students will be encouraged to share their responses to the panel, their ideas about what careers in these fields may look like, as well as their likes and dislikes about panelist responses. We will also do some brainstorming exercises called 30 circles and mind-maps, and draft a personal mission statement. Small group discussions on the draft mission statements.
May 28 — Student Final Presentations
Students will give their final presentations, followed by extensive group discussions to wrap up all that we have discovered together about ourselves, and about the career options that are available to us. We will also discuss ways to follow up from this course and additional resources that are available on and off campus. Staff from BioSci Careers will be present to provide feedback.
Notices
Disability Access
Students with disabilities necessitating accommodation and/or services in class should notify the teaching assistants and initiate a request with the Office of Accessible Education (OAE). The OAE will evaluate the request with required documentation, recommend appropriate accommodations, and prepare a verification letter dated in the current academic term in which the request is being made. Please contact the OAE as soon as possible; timely notice is needed to arrange for appropriate accommodations. The OAE is located on the first floor of the Student Services Building, between the Munger Graduate Residences and the Haas Center for Public Service, at 563 Salvatierra Walk, Stanford, CA 94305 (office hours Monday - Friday, 9 am - 5 pm). You may contact them through their website (oae.stanford.edu), email ([email protected]), or phone (650-723-1066).
Honor Code
Please visit and read the honor code from Stanford’s community standards website: https://communitystandards.stanford.edu/policies-and-guidance/honor-code. The difference between utilizing information from or taking quotes and giving proper citation to external information sources versus plagiarism should be apparent by now. These standards will be strictly upheld throughout this class.
Career Panel Participants
Career Panel I (April 30th, 2020): Business
Kirk Clark
Executive Director, Novartis Institutes for BioMedical Research
Dr. Clark received his PhD in Biochemistry at Kansas State University. After training in protein crystallography as a postdoc at The Rockefeller University, he joined the Swiss pharmaceutical company Ciba-Geigy to establish in-house protein crystallography capabilities in New Jersey. Upon the Ciba-Giegy/Sandoz merger to form the Novartis Institutes for Biomedical Research, Dr. Clark has taken on increasing responsibilities locally and globally within the company, including heading their Protein Structure “home” in Cambridge, co-chairing the Drug Prototype project sub-portfolio, and participating in both the global Chemical Biology & Therapeutics and Protein Sciences global leadership teams. He currently serves as the Director of Novartis’ Protein Sciences group.
Pamela Marrone
CEO and Founder, Marrone Bio Innovations
Dr. Marrone received her PhD in Entomology from North Carolina State University. She has built her career towards the discovery and development of environmentally-responsible bio-based products for pest management and plant health. Originally working as the group leader of Monsanto’s Insect Biology group, she branched out and started her first company, Entotech, Inc., where she screened over 50,000 microorganisms for naturally-produced insecticidal products. Dr. Marrone subsequently started another company, AgraQuest, which developed a line of naturally-derived pest management products from similarly-robust screens of microorganisms. In 2006, she left AgraQuest to found her current company, Marrone Bio Innovations (MBI). MBI has produced award-winning bio-based products for use in many agricultural markets and is additionally marketing products for invasive zebra and quagga mussel control. Dr. Marrone also serves as a board member of a number of associations and companies, such as the Association for Women in Science, the Foundation for Food and Ag Research, and the startups Pheronym and AgShift. In addition, she is a Trustee of Cornell University.
Jayaranjan (J) Anthonypillai
Founder and CEO, Berkeley BioLabs; Co-Founder and Managing Partner, Focus Academy LLC
J is a scientist and entrepreneur devoted to facilitating healthy and productive biotech startup cultures. He has a background in developing, validating, and scaling technologies, and has worked in clinical, clean-tech, biotech, and agri-tech sectors. Leveraging his experience and background in biology and lipid chemistry, he has developed novel technologies for overcoming product development, process development, and engineering challenges. Through his creations, Berkeley Biolabs and Focus Academy, he has helped seed and grow over 50 companies in the biotech sector. Berkeley Biolabs is an incubator lab while Focus Academy serves as a ‘Soft Landing’ for international biotech startups in the Bay Area. As an entrepreneur and mentor for several startups, J’s emphasis is often on product/market fit as the main driver of R&D effort and strategy.
Mowgli Holmes
Co-founder and CEO, Phylos Biosciences
Dr. Holmes earned his PhD in Microbiology and Immunology from Columbia University, and works on applying biotechnological skills towards the development of the contemporary cannabis industry. His company, Phylos Biosciences, provides genetic and sex testing services for marijuana growers, and additionally maintains an evolutionary database of different cannabis strains from thousands of varieties from over eighty countries. They also work to provide discounted services to support small-scale local growers. Holmes is the founding board member of the Cannabis Safety Institute and the Open Cannabis Project, and serves as Chair of the Oregon State Cannabis Research Task Force.
Career Panel II (May 7th, 2020): Academia
Pleuni Pennings
Assistant Professor, San Francisco State University
Dr. Pennings received her PhD in Evolutionary Biology at the University of Munich in Germany. Throughout her time in academia, she has engaged in a plethora of projects across the scales of life, from work on ant population genetics, to her current work as an Assistant Professor at SFSU studying the evolution of Human Immunodeficiency Virus drug resistance. In addition to research, she has devoted herself to science education, starting her own consulting agency to promote science communication and education in Amsterdam, and coordinating the Munich Graduate Program for Evolution, Ecology, and Systematics.
Miriam Goodman
Professor, Molecular and Cellular Physiology, Stanford University
Dr. Goodman earned a PhD from the University of Chicago in Neurobiology. Her academic career has revolved around elucidating the biological mechanisms of sensation, from her dissertation research on the ion channels necessary for hearing, to the analysis of ion channel biophysics and touch sensing as a postdoctoral fellow at Columbia University. Currently, her work at the Stanford University School of Medicine includes using C. elegans as a model to better understand touch and pain sensation, and the mechanisms in which sensory neurons are protected from damage.
Jennifer Mortimer
Staff Scientist, Berkeley Lab and Director of Plant Systems Biology, JBEI
Dr. Mortimer received her PhD in Plant Science from the University of Cambridge, as well as a Masters of Research in Bioinformatics from the University of Exeter. After attaining her degrees, she worked as a Research Associate for several years, studying a number of topics regarding Arabidopsis physiology. Her research has focused on the synthesis, transport, and use of polysaccharides for plant cell wall formation and engineering. Currently she heads a lab that utilizes numerous different model plants to investigate these questions, and serves as Director of Plant Systems Biology at the Joint BioEnergy Institute (JBEI) at the Lawrence Berkeley National Lab, where she investigates how to make biofuels and biochemicals from plant biomass.
Rebecca Albright
Assistant Curator, California Academy of Sciences
Dr. Albright got her PhD from the University of Miami in Marine Biology and Fisheries. Her work has been devoted to in-depth research on the impacts of environmental changes upon coral reef ecosystem health. She has worked as a postdoc at both the Australian Institute of Marine Science and the Carnegie Institution for Science’s Global Ecology Department, studying coral reef biogeochemistry and carbonate chemistry, as well as the effects of ocean acidification upon these processes. Currently as a curator at the California Academy of Sciences in San Francisco, Dr. Albright works on creating a coral culturing facility.
Career Panel III (May 14th, 2020): Scientific Journalism, Administration, Law, Philanthropy
Amy Adams
Director of Long Range Vision Communications, Stanford University
Adams received her MS from Cornell University in genetics and development, as well as a certification from UC Santa Cruz in science communications. Her experiences with news and feature writing regarding a range of scientific topics include freelance writing and editing for a number of notable publications and websites, such as Science, Natural History, and CBSHealthWatch.com; science writing for the Stanford University School of Medicine; communications manager for the California Institute for Regenerative Medicine; and finally back to Stanford, where she has worked as the Director of Science Communications and currently serves as Director of Long Range Vision Communications.
James Keddie
Senior Patent Agent, Bozicevic, Field & Francis LLP
Dr. Keddie received his PhD in Plant Molecular Biology from the John Innes Institute in Norwich, UK. Though he began his post-doctoral career as a fellow in several plant biology labs, including the Carnegie Institution for Science’s Plant Biology Department, studying a range of topics from plant disease resistance to development to gene expression, he began work with intellectual property as a Senior Scientist and IP Manager at Mendel Biotechnology, Inc. Dr. Keddie currently serves as a Senior Patent Agent at Bozicevic, Field & Francis LLP, where his expertise in all aspects of patent prosecution are used to provide biotech-focused clients with patent drafting and prosecution services.
Rieko Yajima
Director for Drug Discovery Innovation, SPARK Translational Research Program, Stanford University
Dr. Yajima received her PhD in Chemical Biology from Penn State University. Her interests lie at the intersections of science, policy, and design. Dr. Yajima’s postdoctoral work as a Science & Design Research Scholar at Stanford University’s Center for Design Research investigated how design practices can catalyze scientific research and innovation; additionally, she has been an Associate Program Director at the American Association for the Advancement of Science in Washington, DC, and served as a science policy fellow at the National Academy of Sciences. She currently works on human-centered drug discovery research and translational medicine as a Director at Stanford’s SPARK Translational Research Program while also serving as a member of the Global Young Academy, an organization for young scientists to lead intersectional dialogue to diversify global decision-making.
Milan Karol
Senior Development Officer, Carnegie Institution for Science
Mr. Karol received an MS in Library and Information Science from the University of Illinois at Urbana-Champaign. Throughout his career, he has become an experienced development officer and fundraiser in various environments, from working as a Sales Representative for a company in the software industry, to working as a Development Officer at two liberal arts colleges, to raising philanthropic dollars for medical research at Johns Hopkins Medicine. Currently, he is the Senior Development Officer for the Carnegie Institution for Science, building relationships and working with donors and philanthropists to achieve institutional goals.
Dr. Sue Rhee ([email protected])
Senior Staff Scientist, Carnegie Institution for Science
Associate Professor by Courtesy, Biology Department, Stanford University
Format: Discussion
Enrollment Cap: 20
Quarter/Year: Spring 2020
Prerequisite: Grad students in Life Sciences PhD programs
Grading: Satisfactory/No Credit
Number of Units: 1
Meeting Time: Thursdays 4:30-6:20 pm Location: Carnegie Seminar Room
Course Assistants:
Benjamin Jin ([email protected])
Emily Fryer ([email protected])
Description
Thinking about and planning for life beyond graduate school is one of the most anxiety-provoking activities students face. In this course, students will share their personal stories and dilemmas about career decisions; have the opportunity to take various self-assessments for characterizing their personalities and identify fitting professions; discuss various career options with a life sciences PhD; and ultimately learn to design their own path. There will be three career panels with invited guests from various career tracks, including research, teaching, administration, business, law, journalism, policy, and more. Open to life sciences PhD students in year 3 or beyond. The class will meet at Carnegie Institution for Science's seminar room building 600, located at 260 Panama St, Stanford, CA 94305 (https://dpb.carnegiescience.edu/about/contact).
Requirements
Students are expected to attend all class meetings, actively contribute to group discussions, and give a short group presentation on the final class meeting.
Schedule
April 02 — Introductions and Class Logistics, myIDP Assessment
Introduction to the structure and context of the course: we will go over requirements and expectations, complete a preliminary survey, and engage in small groups to get to know each other and discuss career opportunities in the life sciences. What are our personal and professional dreams, how do we find an overlap between the two? We will conduct the myIDP assessment in class.
Homework: Take the Myers-Briggs Type Indicator Test, to be independently completed by Tuesday, April 7th, 5 pm PST.
April 09 — Discussion of Myers-Briggs Type Indicator Test Results (guest lecture by MJ Mangiarelli of Stanford BioSci Careers)
The Myers-Briggs Type Indicator (MBTI) personality inventory is widely acknowledged as one of the most accurate and respected personality tests in psychology. It can be utilized in considering future career decisions as a practical tool for investigating work styles and work settings that are most conducive to one’s personality. We will be discovering our personality types, and how to maximize our "gifts" (our personality preferences) in order to contribute to team success--while understanding how the many facets of our complex identities affect overall career satisfaction. Stanford’s BioSci Careers (https://med.stanford.edu/bioscicareers.html) will help with evaluating the results.
Homework: Take the CliftonStrengths test by Gallup, to be independently completed by Tuesday, April 14th, 5 pm PST.
April 16 — Discussion of CliftonStrengths Test Results (guest lecture by Marlene Scherer Stern of Stanford BioSci Careers)
The CliftonStrengths test is designed to highlight the user’s character strengths, which can be used to assess what roles would be best in both utilizing and developing such strengths. We will be discovering our individual strengths and how these can contribute to success in our future careers, while understanding how they are only a part of our unique personalities. Stanford’s BioSci Careers will help with evaluating the results.
April 23 — Self-Assessment Decompression and Career Planning Lecture
Post-MBTI/CliftonStrengths test discussion in small groups to put the results in the context of career choices. There will also be a lecture on career planning, regarding key concepts and tools that are useful in professional development, with small group discussions to follow. Final Presentation projects will be assigned and expectations will be discussed.
April 30 — Career Panel I: “Business”
Panelists will be briefly introduced, then the floor will be opened up for student questions. This panel, along with the panels to follow, will serve as the perfect opportunity for lively discussion, and give students unique insight regarding career options and expectations. Carnegie will provide a reception after the panel to continue discussions and networking.
Kirk Clark
Executive Director, Novartis Institutes for BioMedical Research
Pamela Marrone
CEO and Founder, Marrone Bio Innovations
Jayaranjan Anthonypillai
Founder/CEO, Berkeley BioLabs;
Co-Founder/Managing Partner, Focus Academy LLC
Mowgli Holms
Co-founder and CEO, Phylos Biosciences
May 7 — Career Panel II: “Academic Research”
Pleuni Pennings
Assistant Professor, San Francisco State University
Miriam Goodman
Professor, Molecular and Cellular Physiology, Stanford University
Jennifer Mortimer
Staff Scientist, Berkeley Lab;
Director of Plant Systems Biology, JBEI
Rebecca Albright
Assistant Curator, California Academy of Sciences
May 14 — Career Panel III: “Scientific Journalism, Administration, Law, Philanthropy”
Amy Adams
Director of Long Range Vision Communications, Stanford University
James Keddie
Senior Patent Agent, Bozicevic, Field & Francis LLP
Rieko Yajima
Director for Drug Discovery Innovation, SPARK Translational Research Program, Stanford University
Milan Karol
Senior Development Officer, Carnegie Institution for Science
May 21 — Career Panels Decompression and Preparation for Final Presentations
Group discussions to follow the career panels. Students will be encouraged to share their responses to the panel, their ideas about what careers in these fields may look like, as well as their likes and dislikes about panelist responses. We will also do some brainstorming exercises called 30 circles and mind-maps, and draft a personal mission statement. Small group discussions on the draft mission statements.
May 28 — Student Final Presentations
Students will give their final presentations, followed by extensive group discussions to wrap up all that we have discovered together about ourselves, and about the career options that are available to us. We will also discuss ways to follow up from this course and additional resources that are available on and off campus. Staff from BioSci Careers will be present to provide feedback.
Notices
Disability Access
Students with disabilities necessitating accommodation and/or services in class should notify the teaching assistants and initiate a request with the Office of Accessible Education (OAE). The OAE will evaluate the request with required documentation, recommend appropriate accommodations, and prepare a verification letter dated in the current academic term in which the request is being made. Please contact the OAE as soon as possible; timely notice is needed to arrange for appropriate accommodations. The OAE is located on the first floor of the Student Services Building, between the Munger Graduate Residences and the Haas Center for Public Service, at 563 Salvatierra Walk, Stanford, CA 94305 (office hours Monday - Friday, 9 am - 5 pm). You may contact them through their website (oae.stanford.edu), email ([email protected]), or phone (650-723-1066).
Honor Code
Please visit and read the honor code from Stanford’s community standards website: https://communitystandards.stanford.edu/policies-and-guidance/honor-code. The difference between utilizing information from or taking quotes and giving proper citation to external information sources versus plagiarism should be apparent by now. These standards will be strictly upheld throughout this class.
Career Panel Participants
Career Panel I (April 30th, 2020): Business
Kirk Clark
Executive Director, Novartis Institutes for BioMedical Research
Dr. Clark received his PhD in Biochemistry at Kansas State University. After training in protein crystallography as a postdoc at The Rockefeller University, he joined the Swiss pharmaceutical company Ciba-Geigy to establish in-house protein crystallography capabilities in New Jersey. Upon the Ciba-Giegy/Sandoz merger to form the Novartis Institutes for Biomedical Research, Dr. Clark has taken on increasing responsibilities locally and globally within the company, including heading their Protein Structure “home” in Cambridge, co-chairing the Drug Prototype project sub-portfolio, and participating in both the global Chemical Biology & Therapeutics and Protein Sciences global leadership teams. He currently serves as the Director of Novartis’ Protein Sciences group.
Pamela Marrone
CEO and Founder, Marrone Bio Innovations
Dr. Marrone received her PhD in Entomology from North Carolina State University. She has built her career towards the discovery and development of environmentally-responsible bio-based products for pest management and plant health. Originally working as the group leader of Monsanto’s Insect Biology group, she branched out and started her first company, Entotech, Inc., where she screened over 50,000 microorganisms for naturally-produced insecticidal products. Dr. Marrone subsequently started another company, AgraQuest, which developed a line of naturally-derived pest management products from similarly-robust screens of microorganisms. In 2006, she left AgraQuest to found her current company, Marrone Bio Innovations (MBI). MBI has produced award-winning bio-based products for use in many agricultural markets and is additionally marketing products for invasive zebra and quagga mussel control. Dr. Marrone also serves as a board member of a number of associations and companies, such as the Association for Women in Science, the Foundation for Food and Ag Research, and the startups Pheronym and AgShift. In addition, she is a Trustee of Cornell University.
Jayaranjan (J) Anthonypillai
Founder and CEO, Berkeley BioLabs; Co-Founder and Managing Partner, Focus Academy LLC
J is a scientist and entrepreneur devoted to facilitating healthy and productive biotech startup cultures. He has a background in developing, validating, and scaling technologies, and has worked in clinical, clean-tech, biotech, and agri-tech sectors. Leveraging his experience and background in biology and lipid chemistry, he has developed novel technologies for overcoming product development, process development, and engineering challenges. Through his creations, Berkeley Biolabs and Focus Academy, he has helped seed and grow over 50 companies in the biotech sector. Berkeley Biolabs is an incubator lab while Focus Academy serves as a ‘Soft Landing’ for international biotech startups in the Bay Area. As an entrepreneur and mentor for several startups, J’s emphasis is often on product/market fit as the main driver of R&D effort and strategy.
Mowgli Holmes
Co-founder and CEO, Phylos Biosciences
Dr. Holmes earned his PhD in Microbiology and Immunology from Columbia University, and works on applying biotechnological skills towards the development of the contemporary cannabis industry. His company, Phylos Biosciences, provides genetic and sex testing services for marijuana growers, and additionally maintains an evolutionary database of different cannabis strains from thousands of varieties from over eighty countries. They also work to provide discounted services to support small-scale local growers. Holmes is the founding board member of the Cannabis Safety Institute and the Open Cannabis Project, and serves as Chair of the Oregon State Cannabis Research Task Force.
Career Panel II (May 7th, 2020): Academia
Pleuni Pennings
Assistant Professor, San Francisco State University
Dr. Pennings received her PhD in Evolutionary Biology at the University of Munich in Germany. Throughout her time in academia, she has engaged in a plethora of projects across the scales of life, from work on ant population genetics, to her current work as an Assistant Professor at SFSU studying the evolution of Human Immunodeficiency Virus drug resistance. In addition to research, she has devoted herself to science education, starting her own consulting agency to promote science communication and education in Amsterdam, and coordinating the Munich Graduate Program for Evolution, Ecology, and Systematics.
Miriam Goodman
Professor, Molecular and Cellular Physiology, Stanford University
Dr. Goodman earned a PhD from the University of Chicago in Neurobiology. Her academic career has revolved around elucidating the biological mechanisms of sensation, from her dissertation research on the ion channels necessary for hearing, to the analysis of ion channel biophysics and touch sensing as a postdoctoral fellow at Columbia University. Currently, her work at the Stanford University School of Medicine includes using C. elegans as a model to better understand touch and pain sensation, and the mechanisms in which sensory neurons are protected from damage.
Jennifer Mortimer
Staff Scientist, Berkeley Lab and Director of Plant Systems Biology, JBEI
Dr. Mortimer received her PhD in Plant Science from the University of Cambridge, as well as a Masters of Research in Bioinformatics from the University of Exeter. After attaining her degrees, she worked as a Research Associate for several years, studying a number of topics regarding Arabidopsis physiology. Her research has focused on the synthesis, transport, and use of polysaccharides for plant cell wall formation and engineering. Currently she heads a lab that utilizes numerous different model plants to investigate these questions, and serves as Director of Plant Systems Biology at the Joint BioEnergy Institute (JBEI) at the Lawrence Berkeley National Lab, where she investigates how to make biofuels and biochemicals from plant biomass.
Rebecca Albright
Assistant Curator, California Academy of Sciences
Dr. Albright got her PhD from the University of Miami in Marine Biology and Fisheries. Her work has been devoted to in-depth research on the impacts of environmental changes upon coral reef ecosystem health. She has worked as a postdoc at both the Australian Institute of Marine Science and the Carnegie Institution for Science’s Global Ecology Department, studying coral reef biogeochemistry and carbonate chemistry, as well as the effects of ocean acidification upon these processes. Currently as a curator at the California Academy of Sciences in San Francisco, Dr. Albright works on creating a coral culturing facility.
Career Panel III (May 14th, 2020): Scientific Journalism, Administration, Law, Philanthropy
Amy Adams
Director of Long Range Vision Communications, Stanford University
Adams received her MS from Cornell University in genetics and development, as well as a certification from UC Santa Cruz in science communications. Her experiences with news and feature writing regarding a range of scientific topics include freelance writing and editing for a number of notable publications and websites, such as Science, Natural History, and CBSHealthWatch.com; science writing for the Stanford University School of Medicine; communications manager for the California Institute for Regenerative Medicine; and finally back to Stanford, where she has worked as the Director of Science Communications and currently serves as Director of Long Range Vision Communications.
James Keddie
Senior Patent Agent, Bozicevic, Field & Francis LLP
Dr. Keddie received his PhD in Plant Molecular Biology from the John Innes Institute in Norwich, UK. Though he began his post-doctoral career as a fellow in several plant biology labs, including the Carnegie Institution for Science’s Plant Biology Department, studying a range of topics from plant disease resistance to development to gene expression, he began work with intellectual property as a Senior Scientist and IP Manager at Mendel Biotechnology, Inc. Dr. Keddie currently serves as a Senior Patent Agent at Bozicevic, Field & Francis LLP, where his expertise in all aspects of patent prosecution are used to provide biotech-focused clients with patent drafting and prosecution services.
Rieko Yajima
Director for Drug Discovery Innovation, SPARK Translational Research Program, Stanford University
Dr. Yajima received her PhD in Chemical Biology from Penn State University. Her interests lie at the intersections of science, policy, and design. Dr. Yajima’s postdoctoral work as a Science & Design Research Scholar at Stanford University’s Center for Design Research investigated how design practices can catalyze scientific research and innovation; additionally, she has been an Associate Program Director at the American Association for the Advancement of Science in Washington, DC, and served as a science policy fellow at the National Academy of Sciences. She currently works on human-centered drug discovery research and translational medicine as a Director at Stanford’s SPARK Translational Research Program while also serving as a member of the Global Young Academy, an organization for young scientists to lead intersectional dialogue to diversify global decision-making.
Milan Karol
Senior Development Officer, Carnegie Institution for Science
Mr. Karol received an MS in Library and Information Science from the University of Illinois at Urbana-Champaign. Throughout his career, he has become an experienced development officer and fundraiser in various environments, from working as a Sales Representative for a company in the software industry, to working as a Development Officer at two liberal arts colleges, to raising philanthropic dollars for medical research at Johns Hopkins Medicine. Currently, he is the Senior Development Officer for the Carnegie Institution for Science, building relationships and working with donors and philanthropists to achieve institutional goals.
2019
course description
Description: Thinking about and planning for life beyond graduate school is one of the most anxiety-provoking activities students face. In this course, students will share their personal stories and dilemmas about career decisions, discuss various career options with a PhD in life sciences, and learn to design their own path. There will be three career panels with invited guests from various career tracks, including research, teaching, administration, business, law, journalism, policy, and more. Open to PhD students in Biosciences programs. The class will meet at Carnegie Institution for Science's seminar room building 600, located at 260 Panama St, Stanford, CA 94305.
Requirements: Students are expected to attend all class meetings, actively contribute to group discussions, and to give a short group presentation on the final class meeting.
Schedule
April 4 — Introductions
Introduction to the structure and context of the course, as well as an excellent opportunity for participants to get to know one another. We will go over requirements and expectations of the course, complete a preliminary survey, and engage in small group activities discussing career opportunities in the life sciences, personal/professional dreams, and how to find an overlap between the two.
April 11 — Myers-Briggs Type Indicator Test
The Myers-Briggs Type Indicator (MBTI) personality inventory is widely acknowledged as one of the most accurate and respected personality tests in psychology. It can be utilized in considering future career decisions as a practical tool for investigating work styles and work settings that are most conducive to one’s personality. We will be discovering our personality types, and how to maximize our "gifts" (our personality preferences) in order to contribute to team success--while understanding how the many facets of our complex identities affect overall career satisfaction. Staff from Stanford’s BioSci Careers (https://med.stanford.edu/bioscicareers.html) will help with evaluating the results.
April 18 — Career Panel I: “Policy, Administration, and Scientific Journalism”
Panelists will be briefly introduced, then the floor will be opened up for student questions. This panel, along with the panels to follow, will serve as the perfect opportunity for lively discussion, and give students unique insight regarding career options and expectations.
Policy: Mary Maxon, Ph.D. Associate Laboratory Director, Biosciences Labs at UC Berkeley
Govt Program Management: Devaki Bhaya, Ph.D. Adjunct Staff Scientist, Carnegie Institute for Science, Department of Plant Biology
Science Writing: Amy Adams, M.S. Director of Science Communications, Stanford University
Academic Administration: Rieko Yajima, Ph.D. Director for Drug Discovery Innovation, SPARK Translational Research Program, Stanford University
April 25 — Career Panel I Decompression
Group discussions to follow the “Policy, Administration, and Scientific Journalism” panel. Students will be encouraged to share their responses to the panel, their ideas about what careers in these fields may look like, as well as their likes and dislikes about panelist responses.
May 2 — Introduction to Final Presentations/Career Planning Lecture
Final Presentation projects will be assigned and expectations will be discussed. In addition, there will be a lecture on career planning to introduce students to key concepts and tools that are useful in professional development, with group discussions to follow.
May 9 — Career Panel II: “Business”
Venture Capital: James Zhang, Ph.D. Chief Strategy Officer, Centrillion Technologies Inc., and Partner, GRC Fund
Patent Law: James Keddie, Ph.D. Senior Patent Agent, Bozicevic, Field & Francis LLP
Industry: Lee Chae, Ph.D. Co-Founder and CTO, Brightseed
Entrepreneurship: Fred Hempel, Ph.D. Co-Owner of Baia Nicchia Farm and Artisan Seeds
Industry administration: Malavika Kannuswamy, M.S. Associate Director, Portfolio Planning and Program Management, Denali Therapeutics
May 16 — Career Panel III: “Research”
Academic Research: Ashby Morisson, Ph.D. Associate Professor of Biology, Stanford University
NGO Research: Rebecca Shaw, Ph.D. Senior Vice President and Chief Scientist, World Wildlife Fund
Government Research: John Vogel, Ph.D. Staff Scientist, Joint Genome Institute, and Adjunct Professor, UC Berkeley Department of Plant and Microbial Biology
Teaching: Jesse Miller, Ph.D. Lecturer, Stanford University
May 23 — Career Panels II & III Decompression
Group discussions to follow the “Business” and “Research” panels. Students will be encouraged to share their responses to the panel, their ideas about what careers in these fields may look like, as well as their likes and dislikes about panelist responses.
May 30 — Student Final Presentations
Students will give their final presentations, followed by extensive group discussions to wrap up all that we have discovered together about ourselves, and about the career options that are available to us. We will also discuss ways to follow up from this course and additional resources that are available on and off campus.
Notices
Disability Access: Students with disabilities necessitating accommodation and/or services in class should notify the teaching assistants and initiate a request with the Office of Accessible Education (OAE). The OAE will evaluate the request with required documentation, recommend appropriate accommodations, and prepare a verification letter dated in the current academic term in which the request is being made. Please contact the OAE as soon as possible; timely notice is needed to arrange for appropriate accommodations. The OAE is located on the first floor of the Student Services Building, between the Munger Graduate Residences and the Haas Center for Public Service, at 563 Salvatierra Walk, Stanford, CA 94305 (office hours Monday - Friday, 9 am - 5 pm). You may contact them through their website (oae.stanford.edu), email ([email protected]), or phone (650-723-1066).
Honor Code: Please visit and read the honor code from Stanford’s community standards website: https://communitystandards.stanford.edu/policies-and-guidance/honor-code. The difference between utilizing information from or taking quotes and giving proper citation to external information sources versus plagiarism should be apparent by now. These standards will be strictly upheld throughout this class.
Requirements: Students are expected to attend all class meetings, actively contribute to group discussions, and to give a short group presentation on the final class meeting.
Schedule
April 4 — Introductions
Introduction to the structure and context of the course, as well as an excellent opportunity for participants to get to know one another. We will go over requirements and expectations of the course, complete a preliminary survey, and engage in small group activities discussing career opportunities in the life sciences, personal/professional dreams, and how to find an overlap between the two.
April 11 — Myers-Briggs Type Indicator Test
The Myers-Briggs Type Indicator (MBTI) personality inventory is widely acknowledged as one of the most accurate and respected personality tests in psychology. It can be utilized in considering future career decisions as a practical tool for investigating work styles and work settings that are most conducive to one’s personality. We will be discovering our personality types, and how to maximize our "gifts" (our personality preferences) in order to contribute to team success--while understanding how the many facets of our complex identities affect overall career satisfaction. Staff from Stanford’s BioSci Careers (https://med.stanford.edu/bioscicareers.html) will help with evaluating the results.
April 18 — Career Panel I: “Policy, Administration, and Scientific Journalism”
Panelists will be briefly introduced, then the floor will be opened up for student questions. This panel, along with the panels to follow, will serve as the perfect opportunity for lively discussion, and give students unique insight regarding career options and expectations.
Policy: Mary Maxon, Ph.D. Associate Laboratory Director, Biosciences Labs at UC Berkeley
Govt Program Management: Devaki Bhaya, Ph.D. Adjunct Staff Scientist, Carnegie Institute for Science, Department of Plant Biology
Science Writing: Amy Adams, M.S. Director of Science Communications, Stanford University
Academic Administration: Rieko Yajima, Ph.D. Director for Drug Discovery Innovation, SPARK Translational Research Program, Stanford University
April 25 — Career Panel I Decompression
Group discussions to follow the “Policy, Administration, and Scientific Journalism” panel. Students will be encouraged to share their responses to the panel, their ideas about what careers in these fields may look like, as well as their likes and dislikes about panelist responses.
May 2 — Introduction to Final Presentations/Career Planning Lecture
Final Presentation projects will be assigned and expectations will be discussed. In addition, there will be a lecture on career planning to introduce students to key concepts and tools that are useful in professional development, with group discussions to follow.
May 9 — Career Panel II: “Business”
Venture Capital: James Zhang, Ph.D. Chief Strategy Officer, Centrillion Technologies Inc., and Partner, GRC Fund
Patent Law: James Keddie, Ph.D. Senior Patent Agent, Bozicevic, Field & Francis LLP
Industry: Lee Chae, Ph.D. Co-Founder and CTO, Brightseed
Entrepreneurship: Fred Hempel, Ph.D. Co-Owner of Baia Nicchia Farm and Artisan Seeds
Industry administration: Malavika Kannuswamy, M.S. Associate Director, Portfolio Planning and Program Management, Denali Therapeutics
May 16 — Career Panel III: “Research”
Academic Research: Ashby Morisson, Ph.D. Associate Professor of Biology, Stanford University
NGO Research: Rebecca Shaw, Ph.D. Senior Vice President and Chief Scientist, World Wildlife Fund
Government Research: John Vogel, Ph.D. Staff Scientist, Joint Genome Institute, and Adjunct Professor, UC Berkeley Department of Plant and Microbial Biology
Teaching: Jesse Miller, Ph.D. Lecturer, Stanford University
May 23 — Career Panels II & III Decompression
Group discussions to follow the “Business” and “Research” panels. Students will be encouraged to share their responses to the panel, their ideas about what careers in these fields may look like, as well as their likes and dislikes about panelist responses.
May 30 — Student Final Presentations
Students will give their final presentations, followed by extensive group discussions to wrap up all that we have discovered together about ourselves, and about the career options that are available to us. We will also discuss ways to follow up from this course and additional resources that are available on and off campus.
Notices
Disability Access: Students with disabilities necessitating accommodation and/or services in class should notify the teaching assistants and initiate a request with the Office of Accessible Education (OAE). The OAE will evaluate the request with required documentation, recommend appropriate accommodations, and prepare a verification letter dated in the current academic term in which the request is being made. Please contact the OAE as soon as possible; timely notice is needed to arrange for appropriate accommodations. The OAE is located on the first floor of the Student Services Building, between the Munger Graduate Residences and the Haas Center for Public Service, at 563 Salvatierra Walk, Stanford, CA 94305 (office hours Monday - Friday, 9 am - 5 pm). You may contact them through their website (oae.stanford.edu), email ([email protected]), or phone (650-723-1066).
Honor Code: Please visit and read the honor code from Stanford’s community standards website: https://communitystandards.stanford.edu/policies-and-guidance/honor-code. The difference between utilizing information from or taking quotes and giving proper citation to external information sources versus plagiarism should be apparent by now. These standards will be strictly upheld throughout this class.
Scientific Writing Workshop
Carnegie Institution for Science, Department of Plant Biology
Summer 2019
course description
Carnegie Scientific Writing Workshop Syllabus
Overview: To become a successful scientist, we must write well and effectively communicate our work to a broad audience. Nevertheless, many of us do not receive official training on the fundamentals of scientific writing, and as a result struggle to highlight the significance of our work. This summer, we are offering an intensive scientific writing workshop to help you set up a writing routine, improve your writing, and gain the tools and confidence you need to become a leader in your field. * In-class exercises and lessons will be adapted from Anne E.Greene’s book titled Writing Science in Plain English.
Schedule and Location: The Carnegie scientific writing workshop is a 10-week series starting June 28th, 2019. Meetings will be held in the Carnegie Institution for Science’s Plant Biology Department Seminar Room (260 Panama Street, Stanford, CA, Building 600) on Fridays from 3-5pm.
Topics:
Week 1 (6/28): Introduction to creating a compelling narrative
Week 2 (7/12): Workshop Scientific Storyboard
Week 3 (7/19): Workshop Background and Significance Sections
Week 5 (8/9) Workshop Results and Approach
Week 8 (8/30): Workshop Discussion and Impact sections
Week 9 (9/6): Workshop Abstract sections
Week 10 (9/13): Workshop three Cover letter sections/ Review a manuscript
Overview: To become a successful scientist, we must write well and effectively communicate our work to a broad audience. Nevertheless, many of us do not receive official training on the fundamentals of scientific writing, and as a result struggle to highlight the significance of our work. This summer, we are offering an intensive scientific writing workshop to help you set up a writing routine, improve your writing, and gain the tools and confidence you need to become a leader in your field. * In-class exercises and lessons will be adapted from Anne E.Greene’s book titled Writing Science in Plain English.
Schedule and Location: The Carnegie scientific writing workshop is a 10-week series starting June 28th, 2019. Meetings will be held in the Carnegie Institution for Science’s Plant Biology Department Seminar Room (260 Panama Street, Stanford, CA, Building 600) on Fridays from 3-5pm.
Topics:
Week 1 (6/28): Introduction to creating a compelling narrative
- Discuss the overview, goals and expectations of the writing workshop
- Form scientific writing groups based off of writing experience and document type
- Setup electronic folders for submitting writing material
- Discuss how to tell your scientific story
- Identifying your audience
- Informal vs. formal register
- Determining your tone
- Defining subjects and action verbs
- Using active vs. passive voice
- Benefits of short vs. long words
- Simplifying noun strings
- Defining technical terms
- Concise writing
- Using transition statements
- Affirmative vs. negative statements
- In-class writing exercises
Week 2 (7/12): Workshop Scientific Storyboard
- Present scientific storyboards in writing groups
- Discuss Background and Significance
- Identifying the scope and structure
- Incorporating new vs. old information
- Highlighting deficiencies in current knowledge and understanding
- Justifying your project
- Using parallel writing structures
- In-class exercises
Week 3 (7/19): Workshop Background and Significance Sections
- Review the Background and Significance section for two people in each writing group
- Discuss designing paragraphs
- Identifying the issue
- Development phase
- Conclusion sentences
- Coming to the point
- In-class exercises
- Review the Background and Significance section for remaining people in each writing group
- Discuss different ways to arrange paragraphs
- Chronological order
- Broad ideas to narrow ideas
- Least important to integral information
- Problem to solution
- Compare and contrast
- Transition statements associated with different paragraph styles
- In-class exercises
Week 5 (8/9) Workshop Results and Approach
- Review the results and approach section for two people in each writing group
- Discuss useful tips for making figures and figure legends
- Identify your message
- Writing strong captions
- Writing stand alone text
- Data visualization
- In-class exercise
- Discuss available authorship guidelines from journals and scientific societies
- Discuss the process of publishing and reviewing
- Review the results and approach section for remaining people in each writing group
- Discuss how to organize a discussion and impact
Week 8 (8/30): Workshop Discussion and Impact sections
- Review the discussion and impact section for all people in each writing group
- Discuss how to write an abstract
Week 9 (9/6): Workshop Abstract sections
- Review the abstract sections of all writing group members.
- Introduce how to write a cover letter
Week 10 (9/13): Workshop three Cover letter sections/ Review a manuscript
- Review the cover letters for all members in the writing group
- Discuss how to review a manuscript
