Over the years BTI’s education and outreach department has sponsored several programs linking schoolteachers with scientists at the institute. The programs have involved teacher training, curriculum development, and long-term experiments in the classrooms.
The BrachyBio! project is a past collaboration between the Boyce Thompson Institute (BTI), Cornell University, and high school and middle school students from across New York State and beyond. The purpose of this large-scale experiment is to understand gene function in plants, particularly crop plants. Students learn to grow, observe, and identify mutant Brachypodium plants. Scientists then use DNA sequencing technologies to determine the genes altered by mutations.
Scientists at BTI produce thousands of mutant Brachypodium seeds, and students grow and observe these plants over time. When students share their findings with scientists, the researchers hope to identify and catalog the genes in the Brachypodium plant. Students will play a key role by growing up and identifying the mutant Brachypodium plants, then submitting their data online.
This important research project could one day lead to better quality foods, improved crop yields, and the development of sustainable energy for the future. In addition, students are involved in a real scientific study and develop hands-on experience with the scientific method and the work of plant scientists.
Internships are funded by the National Science Foundation, Research Experiences for Undergraduates Award #1358843, the U.S. Department of Agriculture National Institute for Food and Agriculture Award #2011-67009-30055, individual faculty grants, and the generosity of local donors including the Ithaca Garden Club.
Brachypodium distachyon has many qualities that make it ideal as a model organism for genomic plant research:
Auricle: An ear-shaped appendage at the base of a leaf, leaflet, or corolla lobe.
Blade: The portion of the leaf, which is divided from the sheath by the collar and ligule. The lengths, width, type of tip, and roughness or smoothness are a few of the characteristics of various species.
Culm: The stem of a grass.
Inflorescence: The entire seed head.
Ligule: A protruding structure from the upper surface of the leaf where the blade and the sheath are joined. This structure may be membranous, a fringe of hairs, or a membrane with hairs. The ligule can vary in both shape and size, and may also be absent. This ligule is membranous.
Node: The point along a stem that gives rise to leaves, branches, or inflorescences.
Sheath: A tubular structure affected by the formation of leaf margins around the stem. The base of a grass leaf that runs from the node up to the blade.
Spikelet: One set of seeds in an inflorescence.
Kingdom Plantae – Plants
_Subkingdom Tracheobionta – Vascular plants
__Superdivision Spermatophyta – Seed plants
___Division Magnoliophyta – Flowering plants
____Class Liliopsida – Monocotyledons
_______Family Poaceae – Grass family
________Genus Brachypodium P. Beauv. – false brome
_________Species Brachypodium distachyon (L.) P. Beauv. – purple false brome
- Brachy is a model plant for studying cereal and biofuel crops.
- Brachy is very easy to grow and study in the lab.
- Brachy’s common name is purple false brome.
- Brachy is native to southern Europe, northern Africa, and southwestern Asia east to India.
- Brachy is closely related to the major cereal grain species including wheat, barley, oats, maize, and rice.
- Brachy’s entire genome—all 270 million base pairs—was first sequenced in 2010.
- Brachy grows from a seed to an adult plant that produces seeds in just six to eight weeks.
- Brachy is a species of small grass, that grows no taller than 20 cm (that’s the height of a #2 pencil!).
- Brachy is a monocot, more closely related to other grasses than broad-leafed plants like tomatoes and sunflowers, which are dicots.
- Brachy does not require pollinators to produce seeds—it can self-fertilize.
- Brachy seeds are much larger than the seeds of many other grasses.
- Understanding the genes and cell walls of Brachy will help scientists develop better biofuels.
Dr. Mary DeRome
Gene Function in Food and Fuel Crops
Dr. Mary DeRome is a cell biologist and senior scientist at Artificial Cell Technologies, Inc., a laboratory located in New Haven, Connecticut, that specializes in vaccine research.
Specifically, Dr. DeRome’s lab works with malaria as well as respiratory syncytial virus, or RSV, a virus that is similar to the common cold but can be very dangerous to young and elderly people. Currently, Dr. DeRome and her team are working on developing vaccines against these two diseases using nanotechnology to make artificial virus particles to create the vaccines.
Dr. DeRome became involved with the BrachyBio! project in late 2011.
As it turns out, she learned about the project because of Facebook. Noticing that a former colleague and friend had moved to the Midwest, she looked him up on the web to see what he was up to. She discovered that he was involved in the sequencing of the Brachypodium genome, and that he was one of the scientists who co-authored the Nature magazine paper where the complete Brachy genome sequence was first published.
Not long after, DeRome contacted her friend about his Brachypodium research, and he told her about the BrachyBio! project at BTI. Excited about the possibilities, she and her students joined a growing number of students participating in the project across the Northeast.
“It turned out to be a perfect fit,” she said.
“I was really intrigued that they were going to be using this plant as a model system to investigate the different functions of the genes and see how they could be important in the growth of food crops and also biofuel crops,” DeRome noted. Adding, “It immediately struck me that it would be perfect for my students who I mentor at the Science Fair every year.”
The science fair she is referring to is the New Haven Science Fair, a citywide annual event held in New Haven that includes more than two hundred projects by students ranging from kindergarten up through high school. Every year, DeRome mentors several students with their projects, and every year she has at least one student who is interested in the most “techy, up-to-date, kind of science.”
Currently, DeRome is working with two eleventh grade students from Wilbur Cross High School who are participating in the BrachyBio! project. So far, they have planted more than four hundred seeds representing twelve families; some of them mutant, and some wild type. By testing the plant growth under various conditions such as a control condition, drought, excessive moisture, and various soil conditions, the students hope to learn what effect these conditions will have on the growth of the plant and on the phenotype, and to see whether they can create a more vigorous plant containing a mutation that provides them with a growth advantage.
To elaborate, Dr. DeRome explains that Brachypodium can be used as a model for both biofuel plants and seed crops such as barley and wheat. If you’re looking for a growth advantage for a biofuel, for example, it would be strictly on the basis of size: The more plants you can grow, the more fuel you can produce. For a seed crop, it might be more interesting to have something that grows faster, or produces more seed—something that can grow under less ideal conditions so that it would improve the yield of the crop.
“So, the types of things that we’re looking for are related but slightly different,” she said. “We really don’t know what we’ll find, and it’s possible that we may not even find anything that will help these plants grow—not every mutation has something to do with growth.”
“Whether or not we’ll find something useful, I don’t know,” DeRome concludes. “We’ll just have to wait and find out.”
Meiosis and Chromosome Painting
Did you know that scientists as far away as Poland are learning from the BrachyBio! mutants?
Take Alexander Betekhtin, for example. Originally from Russia, Alex is currently a PhD candidate in the Department of Plant Anatomy and Cytology at the University of Silesia in Poland. Before moving to Poland, Alex was a master’s student at Kazan State University in Russia, where he worked with buckwheat, but when he moved to Poland he began working with Brachypodium, under the guidance of Professor Robert Hasterok.
Broadly speaking, Alex studies cytology, which is the study of cellular disease and the use of cellular changes for the diagnosis of disease. His graduate research is concerned with “comparative chromosome painting” through a process called Fish (Fluorescent In Situ Hybridization), which involves a fluorescent labeling of parts of the cell in order to identify the various cell components and to see how the parts interact.
Specifically, Alex is interested in analyzing the localization of centromeres and telomeres in the different stages of meiosis in Brachypodium distachyon, and especially in understanding mutations that cause disorders in the process of meiosis.
“I found information on the Internet about mutants,” Alex begins, “Through the BrachyBio! Project I found interesting mutants for my particular research, and I wanted to analyze some of the problems related to meiosis that can be found by looking at these mutants.”
Furthermore, as part of his dissertation research, Alex is interested in studying Brachy mutants that produce a white spike, because, he explains, it is indicative of a larger problem with photosynthesis in the plant, and as a result it also suggests a problem with the supply spike. This is especially interesting for Alex because these processes may ultimately provoke disorders in the process of meiosis.
“If I find any problems with meiosis by looking at the mutants, I will perform a Fish to examine them in greater detail,” he said.
He notes that he is waiting to return to Poland to grow the Brachy seeds because they do not perform Fish in Spain where he is currently spending five months at the University of Zaragoza studying new methods and phylogeny of grasses.
“If I happen to find any mutants who have some problems at different stages of meiosis, it will be very interesting for my research,” he said.
Meanwhile, if any students in the United States discover the mutant that controls the white spike, Alex is very interested in this data.
Dr. Richard Amasino
Flowering Time Evolution
Dr. Richard Amasino is the latest in a growing team of researchers to join forces with the BrachyBio! project. A biochemist at the University of Wisconsin, Dr. Amasino specializes in plant flowering, and specifically in a process known as vernalization, the process by which prolonged exposure to cold temperatures promotes flowering.
According to Dr. Amasino, there are two primary components to flowering:
1. When does a plant initiate the flowering process?
2. How do flowers develop?
A primary concern for Dr. Amasino is the issue of the timing of flowering: Namely, how do plants control their flowering timing?
It turns out that certain plants need to go through cold temperatures before they can flower. Going through winter enables these particular plants to flower in the spring. Dr. Amasino and his team of researchers are interested in studying this process, and they are interested in exploring it from a broad, evolutionary sense.
To elaborate, Dr. Amasino explains that the pathways and details of how these systems evolved is actually different in different groups of plants. For example, grasses have evolved independently of another plant that his lab studies, called Arabidopsis, a member of the cabbage family. While they have made some progress on the Arabidopsis, Dr. Amasino and his team are also interested in looking at other plants that have evolved independently to see how they were put together.
This is where BrachyBio! comes in.
Dr. Amasino notes that Brachypodium is a wonderful representative of the grasses to explore the process of how this aspect of flowering is controlled.
“I think Brachypodium is a great model system. It is actually an approachable system where we can understand the evolution of the regulation of flowering in grasses,” he said.
He adds that he is excited about looking at all the mutants that affect flowering compiled by students in the Brachybio! database.
“We’re excited about this project and the possibility that students might actually find some interesting mutants that reveal something new that wasn’t previously understood about flowering—if any students find mutants that affect flowering, we’re very interested in using that data.”
Dr. Amasino concludes by saying that his lab is available to answer questions about the flowering and vernalization processes, and to feel free to write to his lab for more information on that particular piece of biology.
“We’re excited that the Brachy model came along. It is a network that extends from people who have done all the genomics to people doing screens in classrooms. Brachy is a great system, if you’re going to study a different group of plants it is the way to go.”
Dr. Hugues Barbier
The Making of a Model
Dr. Hugues Barbier spends his days in the company of models … model plants that is.
To better understand the genetics and molecular biology of organisms that may be too difficult to grow or study directly, Hugues and fellow scientists work with other closely related organisms called genetic models. Model plant species tend to grow easily in the lab or greenhouse, and have small genomes that are easier to sequence and understand.
For the last twenty years, the top model plant was a small little weed from the mustard family called Arabidopsis thaliana. A close relative to radishes, Arabidopsis has only five chromosomes and 25,000 genes; in fact, its whole genome (all 250 million base pairs) was sequenced in 2000. It has a quick life cycle, growing from a seed to an adult plant that is producing seeds in just six weeks.
But as Hugues explained, “The problem is that Arabidopsis is not a close relative to crops. We grow plants for food. What we really need is a model plant that is a relative to a food crop.”
Unlike the dicotyledonous Arabidopsis, maize, rice, and wheat—our major grain crops—are all monocots [Phylogeny image, or Mandy’s Table]. Unfortunately, these crop plants are not quite model material. They can be difficult to work with in the field and lab. As anyone who’s walked or driven alongside a corn field in the late summer can attest, maize is a large plant that takes months to grow. Rice has a long life cycle and requires a great deal of water and special care to cultivate. And wheat is genetically complicated; durum wheat is tetraploid and bread wheat is hexaploid. That means wheat has four or six copies of every chromosome and four or six copies of every gene, with each gene copy acting in potentially different ways.
According to Hugues, “You need a simpler monocot model that’s a diploid.”
Enter Brachypodium distachyon—known as Brachy for short—the small grass that’s the star of the BrachyBio! project. Hugues began working on Brachy as a PhD student more than four years ago in France, his home country. During that time, Brachy emerged as an attractive, new model for studying food and biofuel crops. Although its genome is a bit bigger and more complex than Arabidopsis, it has one of the smallest of all of the grass species genomes sequenced to date, at 272 million base pairs [Spawns Phylogeny graphic]. Brachy is diploid, with just two copies of its five different chromosomes, and it grows rapidly in the greenhouse, requiring minimal care. Plants grow from seed to seed in just six to eight weeks.
Hugues is excited about Brachy’s potential to help scientists unlock some of the genes and pathways underlying important plant traits in grain and biofuel crops. “We know we have some features in Brachy that just aren’t present in Arabidopsis,” he said.
With a little help from the students participating in BrachyBio!, Hugues and Brachy scientists across the globe will be steps closer.
Students will identify mutant plants and share their data online at the Mutant Library
Scientists will utilize the mutant library as a source of information to help develop Brachypodium as a model system for C3 grasses, like rice, wheat, and barley. The mutant library is a valuable research site that not only links students to the scientific community, but also serves as a rich batch of shared data for important plant science research.
How to use the mutant library
Before planting and screening their plants, students can search through pictures of mutants to become visually acquainted with the wide range of phenotypes used to identify and classify Brachy. Once plants have been screened and classified, students can upload pictures to the library to share their data with other students and scientists. They may also be able to look for pictures of sibling mutants if another classroom planted Brachy seeds from the same line. Instructions for uploading pictures are provided in the “for teachers” section.
Go to the Data Central website.
The iPlant Data Central was developed to connect the profesional researcher with budding scientists at the junior and senior high school levels, enabling citizen science with classrooms around the world participating in large-scale experiments. This interactive portal provides a virtual meeting place for teachers, students, and researchers alike. With this site, iPlant hopes to increase a student’s understanding of gene function in plants. Currently being used for the BrachyBio! project from the Boyce Thompson Institute for Plant Research, “Data Central” can be quickly and easily modified to accommodate any type of phenotypic observation-based experiment.
For the BrachyBio! project…
Students or groups of students will plant the seed, watch the plant grow, and then observe any phenotypic changes over multiple observation points. Data from the observations can then be uploaded by the student/group by logging into “Data Central” and entering the information. Teachers will be able to monitor the student’s progress from within the portal and order more seeds to continue the experiment. Researchers will be able to view the observation data, order seeds from the same collection as the teachers, and connect with teachers and students to engage them in real research.
22 Hours of Light: Conditions for Optimal Growth
You will be given a light rack system developed here at BTI to use in the experiment. For the most part it simply bolts together and plugs in. Bulbs are NOT supplied in the kit and must be purchased by you. Bulbs are 48″ standard two-pin 34–40W Cool White fluorescent bulbs. You will need six of these bulbs. They can be purchased at any home center or hardware store and most discount stores such as WalMart. Cost should be ~ $2 per bulb. The light rack should be lowered using the supplied chain to a height of 35 cm from the lab table. This will generate a light intensity of ~ 6,300 lux or 80 umol/m2/sec.
Twelve Seeds per Family: Planting Brachypodium Seeds
You will receive from BTI several packets of seeds with each packet containing twelve seeds. This represents one family. The soil (Miracle Grow Potting Mix) you will be using must be purchased from a local home or garden center. A sixteen-quart bag should be enough to plant three full trays. Note how the far-right three-tray liner is removed to facilitate watering. Soil should be moist prior to planting. Each tray liner has three soil-filled containers. The twelve seeds you receive in each packet will be planted in these three areas with four seeds per container. Be sure to place the correct tag with the family number/date and teacher written on it into the soil liner as shown. The integrity of this experiment depends on getting the correct family number associated with the correct seeds. Seeds are pushed using a forceps gently just below the surface. Leaving a little of the awn (the long thread like stalk on top of the seed) exposed helps you see where you have planted them. Water the seeds thoroughly by adding water to the open area in the tray. Add water to just cover the BOTTOM of the tray (~ 200-300 ml of water). Keep adding water as needed to keep the soil moist. DO NOT OVERWATER! Make sure you account for weekends and holidays when you are develop your watering schedule. Brachypodium plants are tough and like most weeds require very little except sufficient water to grow.
Looking for Mutant Brachypodium Plants
Use the online mutant photo library to compare your plants with the mutants that we have identified. Visit http://www.bti.cornell.edu/brachymutants. When you find something interesting, share your data and images with us on the BrachyBio!website: http://www.bti.cornell.edu/brachybio.
Special Thanks to the Video Crew:
Tom Brutnell (email@example.com)
Tiffany Fleming (firstname.lastname@example.org)
The National Science Foundation
Special thanks go to Dave Parizek, Tom Brutnell, Tiffany Fleming, Camillo Rosero, Jill Yarmchuk, Nicole Hopkins, Nirav Merchant, and Mary Margaret Sprinkle.
Bioenergy & Bioproducts
The Bioenergy and Bioproducts Education Program (BBEP) was a multiinstitutional collaboration among educators and scientists at Boyce Thompson Institute (BTI) and Cornell University as well as historically black and land grant universities in the eastern United States. The program recently finished in its fifth year (2011–2015) and, over the last four years, BTI educators have engaged 445 teachers and nearly 7,000 students through BBEP-related activities. In addition to the summer institute, the BTI education team has presented BBEP classroom activities at regional workshops throughout New York State and elsewhere in the Northeast.
The Bioenergy and Bioproducts Education Program links teachers and their classrooms with scientists developing biofuel technology as well as plant-based renewable energy sources and products. The backbone of this program is teacher professional development: utilizing bioenergy and bioproduct systems as a platform to engage grades 7–12, community college, and preservice teachers in cross-cutting science, technology, engineering, and math (STEM) education. To do so, BTI educators and BBEP partners offer teacher institutes with hands-on and instructional activities that unify core principles in chemistry, environmental science, plant biology and biotechnology, and sustainable agriculture. Lesson plans and collaborative learning activities, including classroom materials, are provided to institute participants. These activities and materials are designed to deepen student competencies in an understanding of science and engineering practices fundamental to the production, distribution, and consumption (pipeline) of biofuels and bioproducts. Students are encouraged to have fun with “science inquiry,” think broadly (systems thinking), and apply their conceptual knowledge in biology, economics, and environmental and life sciences to agricultural and engineering challenges within emerging “green technologies.” To sustain participant engagement upon completion of the BBEP institute and beyond, teachers receive classroom support (e.g., activity or laboratory supplies/kits) and follow-up consultations with BTI-BBEP educators through social media and/or classroom visits.
Special thanks go to Dave Parizek, Tom Brutnell, Tiffany Fleming, Camillo Rosero, Jill Yarmchuk, Nicole Hopkins, Nirav Merchant, and Mary Margaret Sprinkle.
BBEP Summer Institute Highlights
BBEP Institute 2014. Middle school teacher Kenneth Huff (Left; Williamsville Central School, NY) and high school teacher Betsy Vinton (Right; The Harley School, NY) examine a new device developed by Dr. Arum Han’s laboratory at Texas A&M University to rapidly screen alga cells for growth and oil production. Dr. Han collaborates with Dr. David Stern’s laboratory (BTI) to demonstrate and advance this nanobiotechnology.
Conduct hands-on laboratories (wet labs) involving the culture of perennial biomass crops and algae, plant-pathogen interactions, anaerobic digestion of urban waste, conversion chemistry of biomass-to-liquid transportation fuels, and bioproducts.
Receive classroom materials for more than twenty laboratories and activities aimed at building student’s interest and science literacy in sustainable bioenergy systems.
Tours of biomass cropping systems (e.g., switchgrass and shrub willow) as well as research greenhouses and field sites.
Attend seminars and participate in open discussions with leading scientists in biomass production systems, liquid biofuels, renewable energy crops and resources, and environmental policy; providing a deep understanding of the “bioenergy pipeline” and the challenges ahead in developing “green technologies.”
Professional Development: Upon completion of the workshop…
- Each participant earns a program certificate and development credit hours.
- Current year participants remain in contact throughout the year through social media.
- Teachers collaborate with BTI educators to individualize and revise BBEP learning activities to fit their classroom, improving their application across diverse student audiences.
- As BBEP alumni, teachers have the opportunity to pilot and assist in the development of new BTI educational resources and classroom laboratories!
Testimonials: What part of the institute was most useful? Why?
- “Learning about sustainability and getting new insight into possible activities and projects that are appropriate for middle school students. Before the workshop, I had little knowledge about the ‘big picture’ of sustainability. I needed information and activities that would align with a STEM program.” – Sandra Clark (Sullivan County Schools, TN)
- “Completing the labs; because, it gave me the confidence to implement them in my own classroom.” – Heather Krieger (Heim Middle School/Williamsville Central School, NY)
- “Validated activities I already integrate into my program as well provided me with alternative means and ideas to expand my program.” – Dr. James Jacob (Tompkins Cortland Community College, NY)
- “Laboratory materials and activities, as they present me with tools I can immediately integrate into my curriculum.” – Kelly Mackey (Islip High School, NY)
The Bioenergy and Bioproducts Education Program (BBEP) is funded by the United States Department of Agriculture – National Institute for Food and Agriculture (award no. 2011-67009-30055) and the National Science Foundation.