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Researchers

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 seedsomething 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 grownot 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.”

Dr. Richard Amasino

Flowering Time Evolution

University of Wisconsin

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 floweringif 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 wheatour major grain cropsare 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.

PhylogenyAccording to Hugues, “You need a simpler monocot model that’s a diploid.”

Enter Brachypodium distachyonknown as Brachy for shortthe 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.

Alexander Betekhtin

Meiosis and Chromosome Painting

University of Silesia, Poland

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.