Mike Scanlon

Research in the Scanlon lab focuses on mechanisms of plant development and evolution of plant morphology. Utilizing comparative developmental genetics and functional genomics, we are especially interested in the processes whereby meristems make leaves and embryos make meristems. Our lab exploits leaf and embryo mutants of maize, Arabidopsis, tomato, Selaginella, and the moss Physcomitrella as the foundation in comparative studies of these fundamental processes in plant development.

Selected Journal Publications

Google Scholar profile and publications.

• Leiboff, S., Strable, J., Johnston, R., Federici, S., Sylvester, A., Scanlon, M. J. 2020. Network Analyses Identify a Transcriptomic Proximodistal Pre-Pattern in the Maize Leaf Primordium.  https://doi.org/10.1111/nph.17132 .
• Satterlee, J.W., Strable, J., Scanlon, M. J. 2020. Plant stem cell organization and differentiation at single-cell resolution. P. N. A. S. 117:33689-33699. doi: 10.1073/pnas.2018788117.
• Conklin, P.A., Johnston, R., Conlon, B. R., Shimizu, R., Scanlon, M. J. 2020. Plant homeodomain proteins provide a mechanism for how leaves grow wide. Development 147: dev193623.doi: 10.1242/dev.193623.
• Pengfei Qiao, Richard Bourgault, Marc Mohammadi, Glenn Philippe, Susanne Matschi, Laurie G. Smith, Michael A. Gore, Isabel Molina, Michael J. Scanlon. 2020. Transcriptomic network analyses shed light on the regulation of cuticle development in maize leaves. P.N.A.S. 117: 12464-12471 DOI:10.1073/pnas.2004945117
• Cammarata, Joseph and Scanlon, Michael J. 2020. A Functionally Informed Evolutionary Framework for the Study of LRR-RLKs during Stem Cell Maintenance. J. Plant Research J. Plant Research. 133: 331-342.
• Satterlee, J.W, Scanlon, M. J. 2019. Coordination of Leaf Development Across Developmental Axes. Plants 8: 433.
• Joseph Cammarata, Adrienne H.K. Roeder, Michael J. Scanlon. 2019. Cytokinin and CLE signaling are highly intertwined developmental regulators across tissues and species. Curr Op Plant Biol 51: 96-104.
• Pengfei Qiao, Meng Lin, Miguel Vasquez, Susanne Matschi, James Chamness, Matheus Baseggio, Laurie G. Smith, Mert R. Sabuncu, Michael A. Gore and Michael J. Scanlon. 2019. Machine Learning Enables High-Throughput Phenotyping for Analyses of the Genetic Architecture of Bulliform Cell Patterning in Maize.  G3: GENES, GENOMES, GENETICS 9: 4235-4243.
• Conklin, P.A., Strable, J., Li, S., Scanlon, M. J. 2018. On the Mechanisms of Development in Monocot and Dicot Leaves (Tansley Review article). New Phytologist. 221, 706–724 doi: 10.1111/nph.15371
• Whitewoods, C.D., Cammarata, J., Venza, Z.N., Sang, S., Cook, A.D., Aoyama, T., Waller, M., Kamisugi, Y., Cuning, A.C., Szovenyi, P., Nimchuk, Z.L., Roeder, A.H.K., Scanlon, M.J., Harrison, C.J. 2018. CLAVATA was a genetic novelty for the morphological innovation of 3D growth in land plants. Current Biology 28: 2365–2376.

Outreach and Extension Focus

Scanlon is Pi on a new grant that will train Undergraduate students at Truman State University (TSU), a public liberal arts institution in rural Kirksville, MO, will perform morphological, expression and transcriptomic analyses of maize developmental mutants. Co-PI Timmermans’ lab will host a TSU undergraduate for 8-weeks during the summer of year 1 to perform LM-RNAseq on two maize developmental mutants and non-mutant siblings. Co-PI’s Janick-Buckner and Buckner will spend one week visiting the Timmermans’ lab to participate in data collection and to experience the many enriching opportunities available at CSHL. Co-PI Buckner will attend the CSHL workshop Statistical Analysis of Genomic Data in year 1, to facilitate the processing and analyses of the RNAseq data and to instruct TSU undergraduates in these techniques. TSU undergraduates will present their data annually at the Maize Genetics Conference, as well as at local and regional meetings. These activities will expose the TSU Co-PI’s and undergraduates to state-of-the art investigations in plant genomics. Co-PI Owens (Cornell) will mentor summer REU students (years 1-3) who will examine the photosynthetic physiology of maize lines exhibiting extremes in morphological aspects of shade avoidance. In addition, undergraduates in Owens’ Plant Physiology laboratory course will participate in the screening of photosynthetic variation using in vivo chlorophyll fluorescence monitoring.

Scanlon is PI on an NSF grant that provides the funding to create "Weed to Wonder", a multimedia public education initiative that is headed by collaborator DR. David Micklos of the Dolan DNA Learning Center (DDLC) in Cold Spring Harbor Laboratory. "Weed to Wonder" will present the continuity of research on corn - from native agriculturalists to agricultural breeders, corn geneticists, plant physiologists, and molecular biologists –that has culminated in the Maize Genome Sequencing Project. In parallel with this story of human impact on the evolution of the corn plant, "Weed to Wonder" also will tell the story of corn’s impact on human culture. Utilizing serialized podcasts in audio and video formats, "Weed to Wonder" will provide a case study of the interaction between science, technology, and society. Multimedia content will be integrated with online experiments and bioinformatics tools developed by the DDLC, and will be disseminated nationwide in conjunction with the NSF-funded initiative iPlant. A continuum of practical experiments will allow middle school, high school, and beginning college students to seamlessly progress from classical genetic analysis of kernel traits, through molecular genetic and bioinformatic analysis of mutations, to the examination of genome structure and evolution. The project is in its second year of development and is expected to be released early in 2011.

a. Goals.
The goals of outreach activities in the Scanlon laboratory are twofold: (1) To promote graduate and undergraduate education and research training in modern plant biology, and (2) to promote public education in modern plant biology.

b. Accomplishments / Outreach activities
Collaboration with Truman State University:
For the past seven years PI Scanlon has headed the Maize SAM Project, an NSF Plant Genome Research Program project that has incorporated a program of undergraduate hands-on training and education designed to disseminate an understanding and appreciation of plant science. During this time more than thirty different undergraduate students at Truman State University, a liberal arts institution in rural Kirksville, MO, have played pivotal roles in annotation of microarray data, creation and maintenance of the SAM database, and have been trained to perform genetic, histological, and molecular analyses of maize mutants generated during this project. Truman undergraduates participate in all project meetings and present their data annually at the International Maize Genetics Conference. Of these students, 12 have earned authorship on manuscripts, and over 20 have graduated from TSU and are enrolled in post-graduate degree programs.

Research Training Outreach Activities:
Scanlon has trained fifteen undergraduate students to perform lab work in molecular genetics during his tenure at UGA and Cornell. Scanlon taught a course "Gene Technology" for six years at UGA to graduate and undergraduate students. Two Biology undergraduates became interested in obtaining research experience in molecular biology and worked in Scanlon's lab after taking this course. Scanlon became co-advisor to a Geography Ph. D student enrolled in Gene Technology, and trained him to perform SSR analyses of an endangered plant species. All the molecular genetics in two papers published by this student (now an Assistant Professor at Florida Atlantic U.) was performed in Scanlon's laboratory at UGA. PI Scanlon, as part of NSF outreach activities, presented seminars at the AP Biology classroom of Cedar Shoals High School in Athens, GA; approximately 60% of the students enrolled at Cedar Shoals High School represent minority groups that are under-represented in science. One high school senior was recruited and worked part-time in the Scanlon laboratory. In summer 2006, PI Scanlon’s laboratory hosted Dr. Gokhan Hacisalihoglu for two weeks, where he was trained in qRT-PCR and laser-microdissection microarray technologies. Dr. Hacisalihoglu is a professor at Florida A &M, which is a historically black university in Tallahassee, FLA. Also during summer 2006 and 2007, Scanlon hosted and trained High School student Eric Kelsey, who was recruited from Kennebunkport, ME High School by Cornell’s PGRP REU outreach program. Kelsey worked on a project to analyze evolution of the narrow sheath duplicated genes in the genus Zea. Cornell undergraduate Devon Van Noble, an African-American student interested in public health and environmental law, worked as a laboratory assistant in the Scanlon laboratory for two years. During summer 2007, undergraduate student Doug Eudy (Truman State U) spent 10 weeks in the Scanlon lab studying reverse genetics and in summer 2008 undergraduate student Samantha Wronski (SUNY Canton) worked as an REU student learning reverse genetics and plant developmental biology. During summer 2009, NSF REU student Eric Schultz of Northern Illinois University worked with graduate student Margaret Frank on histological analyses of shoot branching in Selaginella and targeted mutagenesis of WOX genes in Physcomitrella. Currently, Cornell undergraduate biology students Molly Edwards and Neiman Tan are being trained for research work in the Scanlon laboratory. Scanlon currently serves as Co-PI on grant for the Cornell REU program funded by NSF.

Public Education Outreach Activities - Weed to Wonder:
Another outreach component that is funded by Scanlon’s NSF-PGRP SAM grant is a collaboration for public education headed by Dr. David Micklos - director of the Dolan DNA Learning Center (DDLC) - a non-profit public resource for genetics education located at Cold Spring Harbor. Micklos has developed a multimedia internet site entitled "Weed to Wonder", that presents the continuity of research on corn - from native agriculturalists to agricultural breeders, corn geneticists, plant physiologists, and molecular biologists –that has culminated in the Maize Genome Sequencing Project. In parallel with this story of human impact on the evolution of the corn plant, "Weed to Wonder" also tells the story of corn’s impact on human culture. Utilizing serialized podcasts in audio and video formats, "Weed to Wonder" provides a case study of the interaction between science, technology, and society. Anticipating the release of the corn genome sequence in November, 2009, a videography team from the DNALC went to Mexico to document the story behind the research and put the genome sequence into the context of the history of maize cultivation. This is presented in the podcast “Explosive Origins of Corn”. In addition, the "Sequencing the Maize Genome" link includes animations describing step-by-step the different DNA-sequencing approaches used by the American and Mexican teams, a video tour of the Genome Sequencing Center at Washington University in St. Louis, and commentary on the project by researchers involved. Another production for the Weed to Wonder site is an historical recreation of CSHL in 1909, with George Shull explaining his experiment on hybrid vigor that is the foundation of all hybrid corn grown today. In addition to the Shull video recreation, Development of Hybrid Maize features an animation of Shull’s experiment with hybrid maize, three of his original research papers, and an image gallery. Barbara McClintock’s World , on the life of the Nobel Prize winner, includes images of the scientist as well as artifacts from her lab at CSHL, where she discovered transposons (so-called “jumping genes”). Two animations explain her work with transposons, and a downloadable PDF timeline of McClintock’s life and work is also available.

Hands-on Experiments for Students includes two DNALC developed online lab notebooks. “Mendelian Inheritance” for middle-school students introduces Mendel’s Laws through exploration of inherited traits in humans and corn. “Detecting a Tranposon in Corn,” targeted at older students, investigates a bronze (bz) mutant of maize to analyze the molecular relationship between genotype and phenotype.

Weed to Wonder received 51,475 visits through March 31, 2010, which is significantly more than similar sites developed in collaboration with CSHL researchers (Greenomes, 10,461 visits and Dynamic Gene, 8,971 for the same time period). In the coming year, our collaborators will develop additional stories on the history of maize cultivation from footage shot in Mexico, and anticipate additional videography trips to capture other elements of the story of the development of maize as a staple crop and research model.

BIOPL1140 Foundations of Biology-course objectives. As an introductory level biology course for Life Science students who are not Biological Science majors, the objective of this newly designed course will be to provide a conceptual overview of the chemical and cellular emergent properties that have evolved in living organisms in response to extrinsic and intrinsic challenges. Emphasis will be placed on the shared, strategic concepts in physiology, genetics and developmental biology that define living things. As Life Science majors, another important objective is to enable students to communicate scientific concepts to a wide range of audiences, and to critically evaluate the design, execution, conclusions, and ramifications of biological experiments in adherence to the scientific method.

BIOPL2490 Hollywood Biology- course objectives. As a non-majors distribution course, the course is focused fundamental biological concepts that will enable students to read and understand biological issues raised in the Science Times section of The New York Times, the PBS program NOVA, or the popular science magazine Scientific American. This course will continue to examine biological concepts, methodologies, and theories and their cultural and ethical considerations as presented in the context of popular cinema. Currently, a number of flash-point biological questions are prominent in society, including stem cell research, personal genome data, animal cloning, GMOs, and evolution versus “Intelligent Design”. In the coming years, important legislative issues revolving around these and other biological concepts will be debated and decided. This course will provide students with real life examples of state-of-the-art science that will allow the non-scientist to make informed decisions and interpretations of biological issues as confronted in the media, in everyday life, and in society.

BIOPL6410 Laboratory in Plant Molecular Biology- course objectives. As an introductory laboratory techniques course designed to introduce incoming graduate students to standard and state-of-the-art techniques in modern plant molecular biology. I will continue to train the students in laser microdissection-mediated quantitative real time PCR analyses of gene expression in maize shoot meristems, while introducing them to the range of research applications to which laser-microdissection can be applied. An important part of my section of this course is the homework assignment, during which students are asked to creatively interpret the gene expression data they obtain in terms of shoot meristem structure and function.

Plant Developmental Genetics
Plant Molecular Biology
Undergraduate Biology for non-majors
Courses taught in past year:
1) BIOPL 2490 Hollywood Biology: biological science in cinema. Developed new undergraduate non-majors Biology course for Spring 2009. Currently ongoing in Spring 2010

2) BIOPL 4831 Concepts and Techniques in Plant Biology (50%). Revised course from previous years. team taught with two other instructors, Scanlon taught 50% of lectures in Fall 2008. In Fall 2009, expanded course to full semester.

3) BIOPL 6410 Laboratory in Plant Molecular Biology (1 of 7 instructors). Taught three lab sessions of this course in Fall 2006, 2007, 2008, and also in Fall 2009

Fall 2012 taught Lecture and prepared Discussion sections for BIOG 1140 Foundations in Biology . 189 students, 100%

Spring 2012 taught Lecture and Discussion sections for BIOPL 2490 Hollywood Biology , 40 students - 100%

• PLBIO 4220: Comparative Plant Development: Evo-Devo
• PLBIO 7430: Faculty Research in Plant Cell and Molecular Biology
• PLBIO 7490: Graduate Research in Botany
• PLSCI 4925: Plant Sciences Senior Portfolio
• PLSCI 4900: Reflection on Plant Sciences Experiential Learning