Hexbyte Glen Cove Learning biology by playing with proteins thumbnail

Hexbyte Glen Cove Learning biology by playing with proteins

Hexbyte Glen Cove

Plastic models allow students to use building blocks to simulate DNA synthesis. Left: The models reflect both the form and function of DNA. Right, top: A protein in the cell membrane. Right, bottom: Protein synthesis taking place on a ribosome (green). Credit: Kathy Vandiver

It’s a cloudy July afternoon in Cambridge, Massachusetts, and MIT Edgerton Center Instructor Amanda Mayer is using brightly-colored plastic to build proteins. She takes a small yellow block and moves it to the end of a chain of blue and green ones, clicking it into place. “Congratulations,” she says to the four high school students guiding her hand over Zoom. “You’ve all become synthetic biologists.”

Together, the group has assembled a model of the complex molecules found in their food and bodies. “I used to think proteins were just one thing,” says a high school student named Fatima, who has the same blocks laid out before her at home. “Now I know that what I ate has lots and lots of in it.”

Mayer is one of two biologists who are crafting models and lesson plans that schoolteachers around the country—and the world: How cells use DNA to make proteins. Both she and Kathy Vandiver, MIT Edgerton Center advisor and director of the Community Outreach Education and Engagement Core at the MIT Center for Environmental Health Sciences, discovered their love for sharing biology with schoolchildren after completing their Ph.D.s.

Vandiver, who spent 16 years teaching middle school science before joining MIT in 2005, created classroom models throughout her career. In 2008, Mayer joined her at the Edgerton Center, helping her perfect the lessons and activity booklets that accompany the models. The duo uses their sets to teach students and schoolteachers, as well as nurses and biotechnologists. “This is about helping other people learn more about biology, and making it much more accessible,” Vandiver says.

Creating life: From blueprints to building blocks

In school, students learn that DNA determines the features they inherit from their parents, like the color of their eyes. This is because DNA contains the instructions for making proteins, which in turn make up our cells. Vandiver says that even though synthesis is the one lesson that every biology teacher has to teach, proteins don’t always get the attention they deserve. “DNA is the glamour molecule—it’s on T-shirts everywhere,” she says. “But DNA just stores the instructions for building proteins. They do all the work in the cell.”

Vandiver believes that if students are to grasp tricky processes like protein synthesis, they need more than just the labeled diagrams found frequently in science classrooms. Tactile decision-making is a much more engaging method of learning than looking at a diagram, or even watching a video, she says. “When you watch a cell do different things, you can still tune out. But here, you have to make a decision.”

Since students can learn by doing, they’re also not held back by the pressure to master vocabulary, a typical hurdle in the biology classroom. The models are useful for various levels: A sixth grader may use them simply as building blocks, while older students can use clever design details to learn higher-level concepts, such as directionality and bond strength.

Vandiver and Mayer are careful to put as much thought into the lessons that accompany the models. For a protein to do its job, its building blocks must be strung together in the right sequence. The standard classroom strategy for teaching protein synthesis is a chronological one, Vandiver says, in which the information stored in DNA is first transferred to another molecule called RNA, and then finally to proteins.

“But it’s so confusing for the students. They’re going through this multitude of steps, and they have no idea what they’re making,” she explains. Over the years, as Vandiver and Mayer taught thousands of students of different ages at the MIT Museum, they observed that students learned protein synthesis much better if they already knew what the end product looked like. So, in their lessons, students begin with a finished protein, containing a specific sequence of amino acids. Then they start from scratch, learning and following the body’s steps for putting those pieces together.

Working with teachers

Throughout the year, Mayer and Vandiver hold workshops for teachers in Massachusetts, Texas, and Arizona, training them how to use the kits. With the help of a grant, they’ve distributed sets to 30 of Boston’s public high schools for teachers to use in their classrooms.

Mayer says that after working with the kits, teachers understand the material much better—and feel more confident about teaching it. “Teaching teachers is fantastic,” she says. “Think of all the students they’ll teach in their lifetimes, and how many biologists they’re going to create by making students excited about doing this.”

The DNA kits are being used in other countries, as well: Vandiver has trained in Italy, India, China, Singapore, Cambodia, and Mexico. And when the center occasionally hosts students from abroad, Mayer and Vandiver hold workshops for them.

They also work with local students. For the past five summers, MIT’s biology department has partnered with the LEAH Knox Scholars program to host talented high-school students from communities underrepresented in science. Every year, the Edgerton Center kicks the program off by offering the students a crash course in molecular biology. “With the DNA kits, I actually felt like I was inside the cell in some way,” says Breetika Maharjan, a high-school senior who attended one of the . “It wasn’t like a boring high-school textbook with just words.”

Looking ahead

Mayer and Vandiver say they’ve still got a lot to do. Since 2014, they’ve been importing the parts for their kits from Singapore and assembling them in Cambridge with the help of volunteers; this allows them to offer the kits to educators at cost. They have a new set on chromosomes on the way, and they’re constantly designing lessons for new audiences such as nurses, who may soon be caring for patients with DNA-tailored treatment plans.

“The number one comment we get from people after they go through our lessons and play with this is, “Oh wow, if I had this, I would probably have liked biology. I might even have become a biology researcher,'” says Mayer.

Vandiver believes the kits are successful because they embody Doc Edgerton’s memorable motto about teaching: “The trick to education,” she quotes, “is to not let them know they’re learning anything until it’s too late.”

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Hexbyte Glen Cove 'Exciting biology' reveals central event of evolution of rhizobial endosymbiosis thumbnail

Hexbyte Glen Cove ‘Exciting biology’ reveals central event of evolution of rhizobial endosymbiosis

Hexbyte Glen Cove

Root nodules, each containing billions of Rhizobiaceae bacteria. Credit: Public Domain

Legumes, unlike most land plants, can form a root nodule symbiosis with nitrogen-fixing rhizobia. The anatomy of the nodule in legume plants was described in the 17th century, and nodule cells were found to host endosymbiotic rhizobia for nitrogen fixation in the 19th century.

The cortex is developmentally distinct from the cortex of non-legumes: It can de-differentiate in response to phytohormones or symbiotic signals from rhizobia, thereby enabling de novo organogenesis of nodules to accommodate nitrogen-fixing rhizobia. Nevertheless, why symbiotic is restricted to relatively few plant species, mainly in legumes, has remained unknown.

In a study published online in Nature, a research group led by Prof. Wang Ertao from CAS Center for Excellence in Molecular Plant Sciences of the Chinese Academy of Sciences found that the ancient SHORTROOT-SCARECROW (SHR-SCR) stem cell program in cortical cells of the legume Medicago truncatula specifies their distinct fate for novel nodule organogenesis.

To identify potential genetic pathway reprogramming events that underlie the cortical cell division response in legumes, the researchers generated EGFP-β-Glucuronidase reporters (promoter:EGFP-GUS) for M. truncatula and A. thaliana genes and found that the MtSCR reporter was highly expressed in M. truncatula endodermis, cortex and epidermis, which is in sharp contrast to A. thaliana AtSCR. Genetic data showed that nodule formations in scr and scr/scl23 mutants were greatly reduced and SCR expression in root cortex is required for cortical cell division during nodule initiation.

Besides, the researchers found that MtSHR1/2 mRNA expression is restricted to the stele, similar to the expression pattern of AtSHR in A. thaliana. Intriguingly, MtSHR-GUS fusion proteins accumulated GUS staining beyond the stele and endodermis, in the epidermis and cortex. Genetic data showed that cortical cell-specific accumulation of MtSHRs is required for cortical cell division during nodule initiation. Rhizobia spot inoculation and cytokinin treatment showed that cortical cell expressed MtSHR-MtSCR controls M. truncatula root cortical cells division ability.

Further studies revealed that rhizobial signals lead to the accumulation of MtSHR-MtSCR in cortical and nodule primordia. Ubiquitously overexpressed MtSHR in M. truncatula hairy roots promote cortical cell division and form pseudo-nodules without rhizobia inoculation. These data together demonstrate that the ancient SHR-SCR stem cell program specifies legume cortical cell fate for novel nodule organogenesis.

More information:
Wentao Dong et al. An SHR–SCR module specifies legume cortical cell fate to enable nodulation, Nature (2020). DOI: 10.1038/s41586-020-3016-z

‘Exciting biology’ reveals central event of evolution of rhizobial endosymbiosis (2020, December 10)
retrieved 11 December 2020
from https://phys.org/news/2020-12-biology-reveals-central-event-evolution.html

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