The Kellogg Lab
Our Research
Welcome to the Kellogg Lab at the Donald Danforth Plant Science Center. As you can see in the descriptions of projects below, the lab is a small business supported by grant funding, much of which represents federal tax dollars brought home to Missouri. Like the other labs in the Center, we are an employer, a small business that keeps the economic engine of the city running. This is one part of the Center’s mission to “enhance the St. Louis region as a world center for plant science.”
“Feed the hungry and improve human health”
This is the central mission of the Center. We believe that food security is a human right, and that plant scientists have an obligation to contribute to feeding the growing global population. Cereal crops in the grass family - including rice, maize (corn), wheat, sorghum, barley, and oats - have fed civilizations for millennia, and are the center of our research. These crops were selected by humans from an entire ecosystem of wild grasses, which dominate more than 25% of the land area of the earth. In our lab, we study how these wild plants grow, make seeds, and adapt to drought and floods. Another mission of the Center is to “preserve and renew the environment.” By studying cereal crops and their relatives in the grass family, we can then predict how wild species may adapt to a warmer, drier climate.
Our research in the Kellogg Lab, along with that of the Center’s many talented scientists, contributes to a bigger picture: increase our understanding of the underlying mechanisms of plants, so we can make more resilient crops, and protect and enhance one of Earth’s most precious resources – food.
NSF-IOS 1938086
COLLABORATIVE RESEARCH: Evolution of genetic networks in grass abscission zones
Agriculture depends on plants that hold on to their seeds until harvest, yet wild plants need to drop their seeds in a process known as shattering or abscission. People have selected for spontaneous mutant plants that do not shatter, leading to domesticated crops such as wheat, rice, and corn. In a world facing rapid population growth and changing climates, we need to understand how shattering occurs to domesticate and improve new wild or less domesticated cereal crops, thereby diversifying food choices and improving agriculture in marginal environments. This project examines the shattering process, which is controlled by a specialized set of cells known as an abscission zone (AZ). Cell development and cell wall structure of the AZ is compared in foxtail millet, pearl millet, tef and fonio and their wild relatives. We have identified two genes that are required for a functional AZ in most species. We have mutated these genes in four species to determine exactly how they cause morphological differences in the AZ. We have involved high school students, undergraduates and secondary school teachers in conducting the research, and the secondary school teachers have used their experiences to develop new lesson plans, and further impact next generation education in science.
This project is a collaboration with the lab of Andrew Doust at Oklahoma State University (https://www.doustlab.com/).
RESEARCH-PGR: PANAND: Harnessing convergence and constraint to predict adaptations to abiotic stress for maize and sorghum
Increases in crop productivity will be crucial if we are to feed a growing world population and expanding adaptation of crops to a diverse range of environments would help immensely. However, to design crops to be adapted to a wider range of environments will require more knowledge on the genetic variation that produces phenotypic variation and adaptation. This project proposes to use nearly a thousand species, collectively representing over a billion years of evolutionary history, to understand the rules of convergence and constraint in the genomes with an aim to model fitness under drought and temperature stress. The sampling will focus on Andropogoneae, a tribe of grass that are among the most productive and water efficient plants, but for which breeding has taken advantage of variation in only a few species such as maize, sorghum, and sugarcane. By combining genomics, population genetics, and computational biology, DNA variants, genes, mechanisms, and pathways critical for performance and tolerance to heat and drought will be identified.
Integration and modularity in grass diversification
This project will incorporate the treasure trove of data the PANAND project will produce, and relate it to morphological studies of the Andropogoneae.
People
Yunqing Yu
Postdoctoral Associate
B.A. in biology, Nankai University, China
Ph.D. in Plant Biology, Penn State, University, USA
"My PhD dissertation studied the functions of heterotrimeric G proteins in salinity tolerance and guard cell responses, using Arabidopsis as a model species. My current project focuses on abscission zone development in grasses. I am fascinated by the vast diversity of plants, and am interested in understanding the molecular mechanisms underlying plant developmental programs using comparative approaches."
Taylor AuBuchon-Elder
Senior Lab Technician
B.A. Biology, Minor Sustainability, Webster University, USA
Taylor has been researching the Andropogoneae grass clade as Dr. Kellogg’s technician for the past 4 years. She takes care of the live plant collections in their greenhouse as well as running experiments within the lab. Currently, she is managing field collections and germplasm care for the PANAND local adaptation project (NSF: IOS-PGRP, 2018-2022). Her interests include field botany, conservation science, restoration ecology, ethnobotany, and project management. She enjoys working collaboratively and providing mentorship to visiting undergraduate and high school students.
David Huss
Lab technician
B.S. Biology, Truman State University
David has worked on research projects in numerous fields including neuroscience, otolaryngology and nutritional science. Most recently, David helped develop novel transgenic quail lines as model systems for studying early embryonic development. His microscopy experience will help Toby and Kurt gather morphometric data on Andropogoneae grass spikelets. His other interests include the Missouri outdoors, especially prairie and wetland habitats
Recent Publications
2021
Welker, C. A. D., M. S. Vorontsova, and E. A. Kellogg. 2020. A new combination in the genus Tripidium (Poaceae: Andropogoneae). Phytotaxa 471: 297-300. doi: 10.11646/phytotaxa.471.3.12
Goad, D., I. Baxter, E. Kellogg, K. Olsen. 2021. Hybridization, polyploidy and clonality in the model halophyte seashore paspalum (Paspalum vaginatum). Molecular Ecology 30: 148-161. doi: 10.1111/mec.15715
Zhu, C., L. Liu, H. Zhao, O. Crowell, T. P. Brutnell, D. Jackson, and E. A. Kellogg. 2021. The CLV3 homolog in Setaria viridis selectively controls inflorescence meristem size. Frontiers in Plant Science 12:636749. Doi: 10.3389/fpls.2021.636749.
Kaggwa, R. J., H. Jiang, R. Ryan, J. P. Zahller, E. Kellogg, and K. Callis-Duehl. 2021. Exploring grass morphology and mutant phenotypes using Setaria viridis. American Biology Teacher 83: 311-319. Doi.org/10.1525/abt.2021.83.5.311
Arthan, W., L. T. Dunning, G. Besnard, E. A. Kellogg, J. Hackel, C. E. R. Lehmann, J. Mitchley, and M. S. Vorontsova. 2021. Complex evolutionary history of two pantropical grass genera, Themeda and Heteropogon (Poaceae: Panicoideae). Botanical Journal of the Linnaean Society 196: 437-455.
Welker, C. A. D., J. Prado, E. A. Kellogg, and K. N. Gandhi. 2021. Clarifying the type of the polyphyletic genus Schizachyrium Nees (Poaceae: Andropogoneae). Kew Bulletin 76: 327-331.
Fuentes-Soriano, S., and E. A. Kellogg. 2021. Molecular systematics of the tribe Physarieae (Brassicaceae) Based on the Nuclear ITS, LUMINIDEPENDENS, and Chloroplast ndhF. Systematic Botany 46: 611-627.
Song, B., E. S. Buckler, H. Wang, Y. Wu, E. Rees, E. A. Kellogg, D. J. Gates, M. Khaipho-Burch, P. J. Bradbury, J. Ross-Ibarra, M. B. Hufford, and M. C. Romay. Constrained non-coding sequences provide insights into regulatory sequence and loss of gene expression in maize. Genome Research: doi: 10.1101/gr.266528.120
Goad, D. M., E. A. Kellogg, K. M. Olsen, and I. Baxter. 2021. Intraspecific variation in elemental accumulation and its association with salt tolerance in Paspalum vaginatum. G3: Genes, genetics and genomics 11: jkab275. https://doi.org/10.1093/g3journal/jkab275
Seetharam, A., Y. Yu, S. Belanger, L. G. Clark, B. C. Meyers, E. A. Kellogg and M. B. Hufford. 2021. The Streptochaeta genome and the evolution of the grasses. Frontiers in Plant Science 12: 710383 https://doi.org/10.3389/fpls.2021.710383.
2020
Ramachandran, D., M. McKain, E. Kellogg, J. Hawkins. 2020. Evolutionary dynamics of transposable elements following a shared polyploidization event in the tribe Andropogoneae. G3: Genes, genomes, genetics 10: 4387-4398. Doi: 10.1534/g3.120.401596.
Taylor AuBuchon-Elder, Viktoriya Coneva, David M. Goad, Lauren M. Jenkins, Yunqing Yu, Doug K.
Allen, Elizabeth A. Kellogg, Sterile Spikelets Contribute to Yield in Sorghum and Related Grasses, The
Plant Cell, Volume 32, Issue 11, November 2020, Pages 3500–3518, https://doi.org/10.1105/tpc.20.00424
Yu, Y., H. Hu, A. N. Doust, and E. A. Kellogg. 2020. Divergent gene expression networks underlie morphological diversity of abscission zone development in grasses (Poaceae). New Phytologist 225: 1799-1815. doi.org/10.1111/nph.16087.
Bianconi, M. E., J. Hackel, M. S. Vorontsova, A. Alberti, W. Arthan, S. V. Burke, M. R. Duvall, E. A. Kellogg, S. Lavergne, M. R. McKain, A. Meunier, C. P. Osborne, P. Traiperm, P.-A. Christin, and G. Besnard. 2020. Continued adaptation of C4 photosynthesis after an initial burst of changes in the Andropogoneae grasses. Systematic Biology 69: 445-461.
Yu, Y., P. Leyva, R. Tavares, and E. A. Kellogg. 2020. The anatomy of abscission zones in Poaceae changes rapidly in evolutionary time. American Journal of Botany 107: 549-561. doi.org/10.1002/ajb2.1454
Kellogg, E. A., J. R. Abbott, K. S. Bawa, K. N. Gandhi, B. R. Kailash, U. Babu Shrestha, and P. Raven. 2020. Checklist of the grasses of India. Phytokeys: in press.
Li, M., M.-R. Shao, D. Zeng, T. Ju, E. A. Kellogg, and C. N. Topp. 2020. Comprehensive digital 3D phenotyping reveals continuous morphological
variation across genetically diverse sorghum inflorescences. New Phytologist: in press.
Yu, Y. (2020). Commentary: LACCASE2 negatively regulates lignin deposition of Arabidopsis roots. Plant Physiology 182 (3), 1190-1191
Yu, Y. (2020). Commentary: Paving the way for C4 evolution: study of C3-C4 intermediate species in grasses. Plant Physiology 182 (1), 453
2019
One Thousand Plant Transcriptomes Initiative. 2019. One thousand plant transcriptomes and the phylogenomics of green plants. Nature 574: 679-685.
Teisher, J. K., M. R. McKain, and B. A. Schaal, and E. A. Kellogg. 2019. Evolution of C4 photosynthesis in subfamily Micrairoideae (Poaceae). Systematic Botany 44: 32-40. doi: 10.1600/036364419X697877
Kumar, D., and E. A. Kellogg. 2019. Tansley Insight: Getting closer: vein density in C4 leaves. New Phytologist 221: 1260-1267.
Welker, C. A. D., M. R. McKain, M. S. Vorontsova, M. C. Peichoto, and E. A. Kellogg. 2019. Plastome phylogenomics of sugarcane and relatives confirms the segregation of the genus Tripidium (Poaceae-Andropogoneae). Taxon 68: 246-267. doi.org/10.1002/tax.12030
Yu, Y., H. Hu, A. N. Doust, and E. A. Kellogg. 2019. Divergent gene expression networks underlie morphological diversity of abscission zone development in grasses (Poaceae). New Phytologist: early view. doi.org/10.1111/nph.16087
Kellogg, E. A. 2019. Different ways to be redundant. Nature Genetics 51: 770-771. Doi: 10.1038/s41588-019-0406-y
Submitted: Huang, P., S. Mamidi, A. Healey, J. Grimwood, J. Jenkins, K. Barry, A. Sreedasyam, S. Shu, M. Feldman, J. Wu, Y. Yu, C. Chen, J. Johnson, H. Sakakibara, T. Kiba, T. Sakurai, D. Rokhsar, I. Baxter, J. Schmutz, T. P. Brutnell, E. A. Kellogg. The Setaria viridis genome and diversity panel enables discovery of a novel domestication gene. Submitted to Nature Biotechnology. Preprint at: https://www.biorxiv.org/content/10.1101/744557v1
2018
Yu, Y., and E. A. Kellogg. 2018. Inflorescence abscission zones in grasses: diversity and genetic regulation. Annual Plant Reviews 1: 1-35. doi: 10.1002/9781119312994.apr0619.
Zhu, C., J. Yang, M. C. Box, E. A. Kellogg, and A. L. Eveland. A dynamic co-expression map of early inflorescence development in Setaria viridis provides a resource for gene discovery and comparative genomics. Frontiers in Plant Science 9: 1309. doi: 10.3389/fpls.2018.01309.
McAllister, C., M. R. McKain, M. Li, B. Bookout, and E. A. Kellogg. Specimen-based analysis of morphology and the environment in ecologically dominant grasses: the power of the herbarium. Philosophical Transactions of the Royal Society, Series B 374: 20170403.
Teisher, J. K., M. R. McKain, and E A. Kellogg. Evolution of C4 photosynthesis in the Micrairoideae (Poaceae). Systematic Botany 44: 32-40. doi: 10.1600/036364419X697877.
Welker, C. A. D., M. R. McKain, M. S. Vorontsova, M. C. Peichoto, and E. A. Kellogg. Plastome phylogenomics of sugarcane and relatives confirms the segregation of the genus Tripidium (Poaceae-Andropogoneae). Taxon 68: 246-267. doi.org/10.1002/tax.12030.
Kumar, D., and E. A. Kellogg. Tansley Insight: Getting closer: vein density in C4 leaves.. New Phytologist 221: 1260-1267.
2017
Zhong, J., J. C. Preston, L. Hileman, and E. A. Kellogg. Parallel losses of corolla bilateral symmetry correlate with distinct developmental genetic changes in the Lamiales. Annals of Botany: in press
Huang, P. H. Jiang, K. Barry, J. Jenkins, J. Schmutz, M. S. Box, C. Zhu, E. A. Kellogg, and T. P. Brutnell. 2017. The sparse panicle1 gene of Setaria viridis and maize is required for inflorescence branch development and root agravitropism. Nature Plants: 3: 17054. DOI: 10.1038/nplants.2017.54 | www.nature.com/natureplants
Welker, C. A. D., T. T. de Souza-Chies, M. C. Peichoto, R. P. Oliveira, L. C. Carvalho, V. B. S. Mucillo, E. A. Kellogg, E. Kaitchuk-Santos. A new allopolyploid species of Saccharum (Poaceae - Andropogoneae) from South America, with notes on its cytogenetics. Systematic Botany: 42: 507-515. Doi.org/10.1600/036364417X696005
J. K. Teisher, M. R. McKain, B. A. Schaal and E. A. Kellogg.. Polyphyly of Arundinoideae (Poaceae) and evolution of the twisted geniculate lemma awn. Annals of Botany: in press. Doi.org/10.1093/aob/mcx058
Arthan, W., M. R. McKain, P. Traiperm, C. A. D. Welker, J. K. Teisher, and E. A. Kellogg. Relationships of Southeast Asian Andropogoneae (Poaceae). Systematic Botany: 42: 418-431. Doi.org/10.1600/036364417X696023
Saeidi, S., M. R. McKain, and E. A. Kellogg. High throughput DNA isolation and Illumina sequencing library construction for grasses from herbarium
specimens. JOVE (Journal of Visualized Experiments): in press.
Gehan, M. A., and E. A. Kellogg. 2017. High-throughput phenotyping. American Journal of Botany doi:10.3732/ajb.1700044
2016
Kellogg, E. A. 2016. Has the connection between polyploidy and diversification actually been tested? Current Opinion in Plant Biology 30: 25-32. doi: 10.1016/j.pbi.2016.01.002
Kellogg, E. A. 2016. Evolution of Setaria. In A. Doust and X. Diao, eds. Genetics and genomics of Setaria. Springer. In press.
S. Schröder, D. M. Eudy, D. Layton, E. A. Kellogg, B. A. Bahri, and K. M. Devos. 2016. Genetic diversity and origin of North American green foxtail [Setaria viridis (L.) Beauv.] accessions. Genetic Resources and Crop Evolution. doi: 10.1007/s10722-016-0363-6
Welker, C. A. D., T. T. de Souza-Chies, H. M. Longhi-Wagner, M. C. Peichoto, M. R. McKain, E. A. Kellogg. 2016. Phylogeny of Eriochrysis P. Beauv. (Poaceae – Andropogoneae) based on low-copy nuclear genes and complete plastome sequences: taxonomic implications and evidence of interspecific hybridization. Molecular Phylogenetics and Evolution 99: 155-167.
Hodge, J. G., and E. A. Kellogg. 2016. Morphology and characterization of abscission zone development and domestication in Setaria viridis and Setaria italica. American Journal of of Botany. 103: 998-1005. doi: 10.3732/ajb.1500499
Huang, P., A. J. Studer, J. Schnable, E. A. Kellogg, and T. P. Brutnell. 2016. Cross species selection scans identify components of C4 photosynthesis in the grasses. Journal of Experimental Botany. doi:10.1093/jxb/erw256
Hackenberg, D., M. McKain, S. G. Lee, T. McCann, S. Schrier, J. M. Jez, E. Kellogg, and S. Pandey. 2016. Gα:RGS protein pairs maintain functional compatibility and conserved interaction interfaces throughout evolution despite frequent loss of RGS proteins in plants. New Phytologist: doi: 10.1111/nph.14180.
McKain, M. R., R. Hartsock, M. Wohl, and E. A. Kellogg. 2016. Verdant: Automated annotation, alignment, and phylogenetic analysis for whole chloroplast sequences. Bioinformatics 33: 130-132. doi: 10.1093/bioinformatics/btw583
Studer, A. J., J. C. Schnable, S. Weissmann, A. R. Kolbe, M. R. McKain, Y. Shao, A. B. Cousins, E. A. Kellogg, T. P. Brutnell. 2016. The draft genome of Dichanthelium oligosanthes: A C3 panicoid grass species. Genome Biology 17: 223. doi: 10.1186/s13059-016-1080-3.
Goad, D., C. Zhu, and E. A. Kellogg. 2016. Comprehensive identification and clustering of CLV3/ESR-related (CLE) genes in plants finds groups with potentially shared function. New Phytologist: doi: 10.1111/nph.14348.
2015
Grotewold, E., J. Chappell, and E. Kellogg. 2015. Plant Genes, Genomes and Genetics. Wiley-Blackwell
ISBN: 978-1-119-99888-4.
Kellogg, E. A. 2015. Poaceae. In K. Kubtizki, ed., The Families and Genera of Vascular Plants. Springer. In press.
Zhong, J., and E. A. Kellogg. 2015. Duplication and expression of CYC2-like genes in the origin and maintenance of floral symmetry in Lamiales. New Phytologist 205: 852-868. doi 10.1111/nph.13104.
Welker, C. A. D., T. Teixeira de Souza-Chies, H. M. Longhi-Wagner, M. C. Peichoto, M. R. McKain, E. A. Kellogg. 2015. Phylogenetic analysis of Saccharum s.l. (Poaceae-Andropogoneae), with emphasis on the South American species. American Journal of Botany 102: 248-263. doi:10.3732/ajb.1400397
Zhong, J., and E. A. Kellogg. 2015. Stepwise evolution of the expression pattern of corolla symmetry patterning genes CYC2-like and RAD-like in Lamiales. American Journal of Botany 102: 1260-1267. doi: 10.3732/ajb.1500191
Welker, C. A. D., T. T. de Souza-Chies, H. M. Longhi-Wagner, M. C. Peichoto, M. R. McKain, E. A. Kellogg. 2016. Phylogeny of Eriochrysis P. Beauv. (Poaceae – Andropogoneae) based on low-copy nuclear genes and complete plastome sequences: taxonomic implications and evidence of interspecific hybridization. Molecular Phylogenetics and Evolution. In press.
Kellogg, E. A. 2015. Poaceae. In K. Kubtizki, ed., The Families and Genera of Vascular Plants. Springer.
Grotewold, E., E. A. Kellogg, and J. Chappell,. 2015. Plant genes, genomes and genetics. Wiley.
Judd, W. S., C. S. Campbell, E. A. Kellogg, P. F. Stevens, and M. J. Donoghue. 2015. Plant Systematics: A phylogenetic approach. 4th edition. Sinauer Associates: Sunderland, MA.
Kellogg, E. A. 2015. Brachypodium distachyon as a genetic model system. Annual Review of Genetics 49: 1-20.
Miller, A. J., A. Novy, J. Glover, J. E. Maul, P. Raven, and P. Wyse Jackson. 2015. Plants, agriculture and the future of food: expanding the role of botanical gardens. Nature Plants 1: 15078.
Kellogg, E. A. 2015. Genome sequencing: Long reads for a short plant. Nature Plants 1: 15169. DOI: 10.1038/nplants.2015.169.
Outreach & Honors
2021
Elizabeth "Toby" Kellogg, PhD, Member and Robert E. King Distinguished Investigator, Donald Danforth Plant Science Center recently received the 2021 Asa Gray Award from The American Society of Plant Taxonomists (ASPT). The prestigious award is named after the most influential North American Botanist of the 19th century and recognizes a lifetime of achievements in plant systematics. The Asa Gray Award ASPT's top honor recognizes plant systematists who have cultivated a career that has contributed significant research to systematic botany, while making lasting contributions to their community, profession, and students
2020
Toby was elected as a member of the National Academy of Sciences!
Toby spoke at Corteva Plant Breeding Symposium, Ithaca, NY, April 2020 (virtual) and at the Departmental seminar, University of Pennsylvania, Philadelphia, PA
Yunqing and Taylor judge science projects for Academy of Science St. Louis Science Fair
Taylor was selected for the Botanical Society of America Public Policy Award to attend Congressional Visits Day with the AIBS
We welcome our new postdoc, Kurt, to the Kellogg Lab!
2019
The St. Louis Post-Dispatch published a story on David’s Paspalum project, https://www.stltoday.com/business/local/missouri-researchers-study-golf-course-grass-to-address-agricultural-challenges/article_1ff3b7af-5f02-5b73-8461-0bb491273007.html
Toby participated in the Women in STEM panel, Washington University
Toby presented on the tallgrasses of the Missouri prairie, Webster Groves Nature Study Society
UMSL Daily, article on mentoring featured Toby, https://blogs.umsl.edu/news/2018/12/03/crowell-nuraini/
Yunqing gave an oral presentation on her research " Diversity of abscission zone development and underlying transcriptomic regulation in grasses” at the pre-meeting of the 61st Annual
Maize Genetics Conference. March
Yunqing volunteered for STEM day teaching “grocery store botany” at Meadows Elementary School, St. Louis. March
Yunqing volunteered at the MO Middle School Science Bowl Competition. March
A high school student Molly Li from STARs program and a REU Patricia Leyva joined the lab for their summer internship. They studied the genetic control and abscission zone diversity in grasses.
Patricia Leyva presented a poster at the ASPB meeting on her REU project "Abscission Zone Anatomy of Grasses Changes Rapidly Through Evolutionary Time”
2018
Two high school students in the STARS (Students and Teachers as Research Scientists) program joined the lab for the summer mentored by Taylor, Rachel, and Mei. They studied meristem regulator genes and screened for mutants in Setaria viridis. They then presented their work at UMSL after 6 weeks of hard work!
Yunqing Yu joined the team of Associate Features Editors at Plant Physiology and published a commentary on ring chromosomes (doi.org/10.1104/pp.18.00083). March 2018
Yunqing Yu volunteered as a poster judge for the Missouri Tri-County Regional Science and Engineering Fair. March 2018
Yunqing Yu volunteered for the Raspberry Pi Jam event held at Donald Danforth Plant Science Center. January 2018
We are pleased to welcome our former intern and newest lab technician, Rachel Foister! She will be assisting Yunqing and Dhinesh in their research and gain experience for graduate school. This is another reason Danforth Center internships are so valuable; you may return as a future employee! If you'd like to learn more about the Center's undergraduate internship program, visit www.danforthcenter.org/education-outreach/research-internships
2017
Chuanmei Zhu was invited to talk at the Local Auxin Meeting in Tyson Research Center, MO on "Understanding the function of auxin influx carrier genes in grasses using Setaria as a model"
Chuanmei Zhu gave a talk at the Second International Setaria Genetics Conference and wrote a meeting report for this conference. Zhu C., Yang J., and Shyu C. (2017). "Setaria comes of age: meeting report on the second International Setaria Genetics Conference. Frontiers in Plant Science. 28.
E. A. Kellogg and Peter Stevens participated in STEM day at Jury Elementary School, Florissant, MO, March
E. A. Kellogg presented a seminar at the Max Planck Institute for Plant Breeding, Cologne, Germany, April
Olivia Crowell is joining the lab for summer as a STARS student; and Rachel Foister will be our REU intern
E. A. Kellogg and Michael McKain were featured in the Roots & Shoots Blog by the Donald Danforth Plant Science Center https://www.danforthcenter.org/news-media/roots-shoots-blog/blog-item/preserving-and-renewing-the-environment
E. A. Kellogg, Taylor AuBuchon, and Tina Zudock participated in the Girl Scouts of Eastern Missouri's and the Danforth Center's "Girls STEAM Ahead" program, which inspires girls in grades 2-12 to get involved in science, technology, engineering, art and math (STEAM).
E. A. Kellogg presented seminars at the University of Nebraska-Lincoln, Arnold Arboretum of Harvard University, the Boyce Thompson Institute in Ithaca, New York, and Washington University in St. Louis, Missouri
E. A. Kellogg gave a Science Day presentation to 2nd and 3rd graders, Jury Elementary School, Hazelwood, Missouri
Paper and poster contributions: St. Louis area Evolution, Ecology and Conservation Retreat, St. Louis University, 1 poster; Botanical Society of America, Forth Worth, Texas, 1 poster; Maize Genetics Meeting, St. Louis, Missouri, 4 posters;
2016
E. A. Kellogg taught at the Cereal Genomics Workshop, Cold Spring Harbor Laboratory
E. A. Kellogg taught a workshop on grasses for high school teachers, Purdue University, IN
(June) Our REU summer interns and STARS students have arrived! Welcome Tina from WashU, Abigail from UMSL, Callista and Alex!
Chuanmei Zhu has joined the Kellogg Lab. Welcome!
Michael McKain was invited to talk in a seminar series at Michigan State University, Lansing, MI, on "Modern Consequences of Ancient Polyploidy: Comparative Phylogenomics of Maize Subgenomes," and at Kennesaw State University, Kennesaw, GA, on "Phylogenomics and Evolution of Ecologically Dominant Grasses."
E. A. Kellogg was selected by the American Association for the Advancement of Science (AAAS) to serve as chair-elect for the Biological Sciences Section
Tools
Verdant
Verdant provides an easy-to-use environment for visualization, annotation, manipulation, alignment, and phylogenomic analysis of whole chloroplast genomes. Verdant is hosted by CyVerse and is built on a growing database of chloroplast genomes.
Includes a user friendly step-by-step tutorial
Visit this link to get started
Fast-Plast
Fast-Plast is a pipeline that leverages existing and novel programs to quickly assemble, orient, and verify whole chloroplast genome sequences. For most datasets with sufficient data, Fast-Plast is able to produce a full-length de novo chloroplast genome assembly in approximately 30 minutes with no user mediation.
Currently, Fast-Plast is written to accomodate Illumina data, though most data types could be used with a few changes.
Fast-Plast uses a de novo assembly approach by combining the de bruijn graph-based method of SPAdes with an iterative seed-based assembly implemented in afin to close gaps of contigs with low coverage. The pipeline then identifies regions from the quadripartite structure of the chloroplast genome, assigns identity, and orders them according to standard convention. A coverage analysis is then conducted to assess the quality of the final assembly.
Primaclade
Primaclade is a web-based application that accepts a multiple species nucleotide alignment file as input and identifies a set of PCR primers that will bind across the alignment. The Primaclade program iteratively runs the Primer3 application for each alignment sequence and collates the results. The user may adjust a number of parameters to improve and refine the results. These options include: 1) the maximum number of degenerate base pairs allowed, 2) the number of gapped lines in the alignment to ignore, 3) a region of the alignment to exclude for primer discovery, 4) the primer melting temperature and 5) the approximate GC content of the primer. Primaclade creates an HTML results page that recaps the original alignment, provides a consensus sequence and lists primers for each alignment area. In addition, the generated primers are color-coded to reflect the level of degeneracy in the primer.
Click here to go to the Primaclade website
Please note that the server that hosts Primaclade has no back-up power, so whenever the electricity flickers the server goes down. If you are unable to access the site, please contact Elizabeth Kellogg, ekellogg@danforthcenter.org
Gallery
Life in the Kellogg Lab
2017 Kellogg Lab
Meeting with Andrew Doust and Hao Hu
Sorghum panicle collecting at Bradford Research Center, Columbia, Missouri
Field work with STARS students
Field work with STARS students
Summers with undergraduate REU interns
2016 Lab and summer interns
Shaw Nature Reserve Field Trip
High school STARS students presenting their summer research at UMSL
High school STARS students presenting their summer research at UMSL
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