The Carlisle Mosquito Online

Friday, December 18, 2009

Hooked on Science: Gene sequencing and robots come to CCHS

Extracting Science: Students work at extracting DNA from Lemongrass plants as part of the Biotechnology Seminar. Pictured (L to R) are Sonia Boor, Tommy Veitch, Katie Mills, Kerry Nix, Carolyn Zuk and Catherine Harris.

Last spring, the Concord Education Fund made a large investment at the Concord-Carlisle High School (CCHS) to give students more opportunities in science and engineering. Their funding transformed an old industrial arts area into a high-end scientific laboratory and today, students are using that space to build robots and to perform biotechnology experiments in two seminars being offered as part of the new Hooked on Science program.

Gene sequencing

CCHS Biology teacher Jennifer Benson is teaching a Biotechnology seminar from November to February which is allowing students to do real research. The objective of the seminar is to have the students isolate, clone and characterize a gene of a plant species which codes for an important enzyme for cellular metabolism. Students will publish their gene sequence in an online databank called GeneBank. “The fact that it’s authentic with a real goal makes the kids very enthusiastic,” said Benson. Junior Sonia Boor likes the thought that their data could be used by other researchers.

The seminar is given on Saturday afternoons. “Through a series of experiments, students are learning a range of important biotechnology techniques,” said Benson. Techniques include use of: micropipettor, sterile bacterial culturing, DNA extraction, nested Polymerase Chain Reaction (PCR) thermocycler machine, gel electrophoresis, ligation, transformation and restriction digestion. Benson explains, “Ligation means to bind the DNA fragment we are studying to a circular piece of bacterial DNA called a plasmid. Transformation means putting this now recombinant (recombined - our plant DNA and plasmid bound together) plasmid into bacteria to let the organisms grow, divide and make many copies. A restriction digestion is mixing DNA with restriction enzymes, which cuts the DNA at specific places, letting a researcher analyze the DNA.”

New equipment in the lab, such as an ultra-violet light box, a high-speed centrifuge, a shaking-water box and an autoclave will make these experiments possible. “The lab they built at the high school is amazing,” commented senior Katie Mills. Junior Tommy Veitch said, “It is fascinating technology we are getting to use.”

Benson explained that the prepared DNA will then be brought to a research lab to be sequenced, which will reveal the exact sequence of DNA bases that make up the gene the students cloned. Students are exposed to further aspects of research when they do gene analysis using bioinformatics, which is a set of software tools. Students will use a search engine called BLAST, a Basic Local Alignment Search Tool, which is an algorithm for comparing primary biological sequence information. They will be able to identify certain DNA regions and they will become acquainted with different bioinformatics databases.

In addition to the research project, the seminar students are participating in a number of field trips to local pharmaceutical companies and academic research labs. They will have the opportunity to listen to and ask questions of a variety of guest speakers in order to explore the diversity of biotechnology-related fields and learn about potential career opportunities.

Benson explained, “The students visited Biogen Idec in Cambridge, Massachusetts and while there, performed an ELISA immunoassay experiment in their Community Labs.” A tour of Merck Research Laboratories in Boston is also part of the seminar. Next week Abbey Scott, a researcher with the Forensic Biology Unit for the Massachusetts State Police will be talking to the seminar students about the use of biotechnology in forensics. In January, Gina LaCorcia, Genzyme researcher and CCHS alumna (’94), will speak about her research.

A lot is packed into each weekend seminar. Benson described the most recent class. “This past weekend we extracted DNA out of the lemongrass plant and did a PCR reaction to amplify a region of the genome that has the GAPDH gene in it. Next week we will run some of the PCR out on a gel to visualize the DNA, and if it works, we will go forward with a second ‘nested’ PCR reaction. If it doesn’t work, we will re-do the first PCR.” She noted that the students will be the first to provide the GAPDH gene sequence of lemongrass to GeneBank.

Benson noted, “The students taking the biotechnology seminar are doing so during their own free time, outside of school hours, which shows their high level of interest and dedication to learning about this exciting field.” Students are able to see that the individual techniques they learn each weekend are steps in a longer investigatory process.

Benson spread the word about the seminar via the CCHS student news and by speaking to many upper-level science classes. Twenty-eight students submitted the application and required essay to compete for 15 spots in the seminar. A panel of science teachers read through the applications and selected the students. There will be no record of students taking the seminar on their transcript; however, the expectation is that this seminar will become a semester-long course next fall. Benson hopes that students who did not get into the seminar will be able to take the course next year.

Robotics competition

Another new initiative for Hooked on Science is a robotics class in which students are preparing for the national “First Robotics Competition” in February. The first round will take place at Worcester Polytechnic Institute, the first college in the country to offer a degree in robotics. Aspects of mechanical and electrical engineering and software programming are needed in building a robot.

CCHS Science Department Chair Mike Vela explained that to get students ready for the competition, the group divided into two teams for an internal competition culminating this month. Freshman Daniel Beckwith said that building a robot is all about teamwork. Senior Marcus Kulik explained. “We have to design robots using the VEX kits we have.” These kits include building materials for a robot such as tank treads, sprockets and chains and cables, a microprocessor, a transmitter and receiver, other motors, gears and additional hardware.

For the December competition, robots need to maneuver up a ramp and use a light sensor to stop under an awning on that ramp. Kulik has been working on getting tilt sensors to work so the robot will go up the ramp correctly.

Designing robots takes time. Students work on hardware design at least two days a week and work on programming two other days a week. Vela said students have been asking him to get into the lab during lunch and free blocks.

Participants are enthusiastic. Senior Bennett Hartnett said, “The program is really great for getting people involved. ” Kulik of Carlisle said, “It’s a lot of fun.”

Students have received mentoring from six engineers who have been volunteering their time teaching students some basics of electronics and mechanics. Except for Carlisle resident Paul Anagnostopoulos, all the other adults are from outside Concord or Carlisle. Vela is exceedingly grateful they stepped forward, because he does not have expertise in these areas. Also, co-advisor and CCHS physics teacher Michael Hamblin has been a resource for training in electronics.

Anagnostopoulos has been teaching students the programming language C++ which is used to program the robot. The students must learn to write software code, download it into the onboard computer in the robot and test that it can properly control the robot. Anagnostopoulos said, “There is way too little programming being done at the high school.” As a result of last spring’s budget cuts, CCHS lost a faculty member who had been teaching programming. Beckwith had some programming background, but not in C++.

Competition heats up in January

The real competition starts in early January when “First” sends out kits for the 2010 competition. Kulik said, “We’ll get professional parts and we’ll need to put the robot together from scratch.” As defined at, “First” is a Manchester, New Hampshire not-for-profit company founded in 1989 to encourage youth interest in science and technology. Students will have six weeks to come up with a robot that meets the objective and criteria for competition.

Vela explains the competition is quite sophisticated. He shows two videos on YouTube that demonstrate the point: and In the videos, robots are manipulating very large balls and shooting balls at baskets.

Vela said, “There is nothing like this at the high school. We have a goal, something we need to achieve.” Like Benson, Vela went to many science classes in all four grades to get students interested. No application was necessary. There are ten students in the program. “Come January, they will be meeting five days a week.” Vela explains that students in the program have to forego participation in winter sports or the spring musical due to the time commitment needed for the robotic program.

Vela praised the Concord Education Fund for their support. “They have funded everything, the VEX robots, the tools.” There was also a $5,500 entrance fee for the First Robotics Competition, which includes the building materials for the competition. Anagnostopoulos is hoping interest in the program will grow after students see the competition this year. Vela noted that Bedford started this program three years ago and now has almost 10% of its school participating.

Spring offering

In the spring, CCHS earth science teacher Ray Pavlik will be giving an earth science seminar called “Geologic Mapping and Structural Geology.” Students will study structural and bedrock geology in the classroom and in the field, as well as meet with professional geologists. The course will include an overnight field trip to explore the coastal geology of Maine. In addition, students will be given an introduction to the GIS software program ArcView. Students will learn to collect data within one meter of accuracy, transfer their data into ArcView and create their own maps. ∆

© 2009 The Carlisle Mosquito