After collecting seagrass in San Diego during the MJ Murdock Partners in Science Conference, it was identified by reference, and affirmed by correspondence with James Cook University, as Zostera marina. This is a common species in undersea meadows from the warm California waters I visited all the way north past Puget Sound. The samples were wrapped in a sea-soaked USA Today and flown back to New York in my checked luggage. It is important to store seagrasses pulled out of the water in moist, cool conditions to prevent them either from drying out or suffering freeze damage. Some of the plants even survived well enough to end up (for now) in the aquarium in my classroom!
Once in the school, we separated herbarium specimens to serve as the intact ‘voucher’ of what we found in the wild, should anyone ever wish to verify that the sample indeed came from the species we claimed it to be. Next, I extracted DNA from the samples using the Epoch mini genomic plant DNA kit. Although this task was finished by Wednesday the 20th, it was only a week later that we were able to check the results of the effort by gel electrophoresis. In the crush of a school week full of state exams, portfolio sessions, and a reorganization of classrooms for the new semester, it’s tough to spare even an hour for even an innocuous biotech task.
The result of our work at last proved successful. We were able to retrieve DNA from our plants and image it on our new Fotodyne gel imaging apparatus. I did a much better job adjusting the settings for a clear image, and even took the opportunity to tinker with the loading of samples, one with only DNA and dye, another with DNA and an additional dose of fluorescent marker. We also verified that the reference ‘ladder’ used as a size standard for measuring the size of a DNA worked better than the prior one we received. Though the effort was not without small hiccups (crossed wires ran the DNA backwards briefly before it was noted and corrected) it was another step forward in the development of a full-fledged biotech lab capability in our school.
This task concludes our initial efforts with seagrass, and leaves us (pun intended) looking ahead to working with tree DNA in the spring. . Being able to grow this program for the kids in our building, and provide a chance to do authentic research is deeply fulfilling. It would not be possible without the continued support of benefactors giving to DonorsChoose, the indulgence of our school administration, the DNALC’s gifts of reagents, the jumpstart the Waycott lab provided, or the inspiration of our students. It’s a web of critical elements that come together to make this happen, and I’m pleased to have the opportunity to play near that junction.
On January 15th through the 17th, I had an opportunity to present for a third year at the M.J. Murdock Charitable Trust Partners in Science Conference in San Diego. Proving out my theory that I’m better at things I do iteratively, it seemed like the third time was charmed. I got in on Thursday evening after having taught all day and got checked into my room. Looking through the packet, I confirmed my scheduled speaking time at 10 am the following morning, immediately following the opening plenary session.
I reviewed my powerpoint slides, redacting excess, clarifying a few points, and of course, making sure to include the Trust’s artwork in my acknowledgement slide, which has become something of a conference ritual to me. If I’m not up until the wee hours on the day before the presentation, something just isn’t right! I was extremely time conscious and a bit nervous through the early morning and opening talks. A pen from the hotel leaked all over my hand. I was having a difficult time calling home. I didn’t see as many familiar faces, since prior years’ cohorts I knew better had cycled through. I met with the room facilitator, reviewed my intro, and after seeing a standing room only group in the room (about sixty people all told) it was time to begin. I started up my discussion.
The stress from such events comes from the fact that one is talking quite publicly about something into which one has invested considerable personal care and attention. The audience of other teachers who have participated in similar such research immersions is a select one. They have experienced the same journey between the two worlds of secondary education and advanced scientific research. The people in the room are in a unique position to comment on how well you have done at this task – atypical of both the school and lab contexts, and so in some ways it feels like a true jury of one’s peers. Thankfully, I had spent a lot of time keeping the project alive in my science club, and so when it came time to talk about it, it felt quite natural. The questions and details were present in my thinking, and there was an immediacy to being able to refer to something ongoing, rather than archived as of the summer before.
The reaction I received following the talk and throughout the rest of my time at the conference was universally positive. I think people responded to the fact that this work was something I was able to translate into a classroom experience. I had a lot of thought-provoking discussions with teachers and lab hosts from across the West, and it gave me a lot to think about, especially with regards to identifying vehicle for sharing the student work that comes from such research projects.
But on a practical level, the location of the conference in San Diego afforded me access to Mission Bay and San Diego Bay, two sites with known seagrasses. I searched whenever and wherever I reasonably could at intertidal sites around the conference center, as well as among the boats of the marina. I was able to collect (and confirm the identification with my advisor at James Cook University in Australia) one species new to me (Zostera marina) and fragments of a pair of others. These samples were wrapped in sea-soaked newsprint, folded into Ziploc bags and stored in the minibar refrigerator before the long trip home to New York. With luck, I will be able to replicate the success we had with the Tampa samples (including keeping some alive in the aquarium) on these new San Diego samples. Whatever comes of this latest piece of work, the trip was an exceedingly productive one. Veni vidi vici!
After receiving a pair of lovely donations – including a Fotodyne UV Gel Illuminator camera setup (Thanks, Donorschoose!) as well as the gel green needed to visualize DNA (thanks, Cold Spring Harbor!) we were able to check our results from last week’s extraction of Tampa seagrass samples.
The results are thrilling to say the least! Though our reference ‘ladder’ in lane one curiously didn’t show up (second time this has happened) we have a strong positive result for DNA from sample 0058-0060. Within a week, we will package and ship the materials off to James Cook University in Townsville for future processing. It’s a HUGE step forward for our program and a strong indication that we’re making progress to doing novel science in a NYC public high school for immigrant youth. This proof of concept will now lead to an attempt to replicate our results (and then some) using the trees around the school. Go FIHS!
After a flight back to New York as checked luggage, inspection by the TSA, a ride on the Airtrain to the E to the 6 to the W45 bus…..a stint in my fridge in New Rochelle…..then rides back on the W45 to meet the QBX1, the second batch of Tampa GIBS samples made their way to the FIHS science challenge club meeting for processing. After saving voucher specimens in a plant press, we began the process of extracting DNA. Using the same Qiagen materials and protocol as JCU and a fresh set of mortars, we ground, span, bonded and eluted the specimens collected. The leftover samples were added to the saltwater aquarium, where they are possibly the only seagrass living through our chilly yankee winter!
We are shortly expecting to receive GelGreen from Cold Spring Harbor, and now have a Fotodyne gel imaging system via DonorsChoose (see my links!) So this time next week, we hope to have documented our work, and shipped samples off to Townsville! Fingers crossed!
After successfully collecting seagrass on my last visit to Florida in September, I broke away from the normal round of family responsibilities on the last day of the year to try to add a few more samples to the GIBS project. This is part of an international effort to identify differences among specific genes that might help us learn about the history and relationships of these marine plants.
Since it was winter time during my visit, the water was fairly cold and conditions were difficult. I managed (again) to find samples of Halodule beaudettei growing pretty close to shore. But the next one I had hoped to find, Thalassia testudinum, eluded me. All I found were a few floating scraps, which let me know it was in the right area, but the plant was certainly NOT where I was searching. Field guides online indicate that Thalassia is a deeper water species, which will require me to get more than the 20 or 30 meters I was able to get away from the shoreline. In the Summer, when I next return, I will need to come ready to snorkel….and looking for a few ‘tips’ along the way of likely places to look wouldn’t hurt, either!
Later this morning, I fly back to New York with my samples, which will remain cool (but not frozen) until Tuesday, when science club members will help to extract the DNA using the same protocol effectively used in my summer lab immersion as well as in our prior extraction activity in October. Stay tuned to this channel for updates!
After sitting in the FIHS lab freezer for a few months, we were finally able to get the Tampa seagrass DNA gels run out using SYBR green, and visualized with UV light. This process yields a much better picture of DNA than the ‘blue’ staining we had previously attempted.
The results confirm that we were able to extract DNA from H. beaudetteii back in September from Tampa. We ran two extractions from each individual plant, but the best results consistently came from those done by the students on the first selection of material, despite the inefficiency of the plant grinding tools we had on hand at that time. The next steps will first be to attempt a second collection while visiting Florida on break for the winter holidays, and next to get the positive samples to JCU for eventual sequencing.
I have some concern that my RNAse got warm in transit to the school, that any plants I collect in Tampa this time will degrade in the time it takes to get it to a lab for extraction, and that we’re still using warm water as our elution medium. But all that said – we have a system that has worked, if at a less than optimal level. Anyhow – no one else I’m aware of is doing this, so in a sense, we’re world class, anyway!
In the past few weeks, the CBOL has finalized their recommendation for a 2-loci plant barcode, which means that the administrative hold that was placed on our project is now resolved. rbcL and matK are the winning genes, so in theory, we can proceed with ordering primers to amplify these regions and sequence the resulting product! I’ll share updates as I have them….
http://barcoding.si.edu/PDF/PlantWG/CBOL%20Decision%20-%20Plant%20Barcode%20Regions.pdf
A special thanks to Dr. Rios at the Harlem DNA Learning Center for her help in processing our images!
This semester, we have included a for-credit astronomy course at FIHS. It meets (usually) during ‘team’ periods on Mondays and Fridays and attempts to take a hands-on approach to learning about the heavens. Given my biological training, it’s been a learning experience for both me and the kids, and each week, I feel like we do work together that will eventually lead to a very robust program.
Thanks to our generous benefactors at DonorsChoose (see their link on this page!) we were recently provided a solarscope, which is a small reflecting telescope useful for safely looking at the sun. It was utterly perfect timing since the instrument arrived JUST as we were beginning to work on the ’stellar’ portion of our curriculum. Having the opportunity to do direct, observational astronomy in the middle of the day is a huge advance for our program, since we are often limited to early morning observations of the moon, or night-time work when the building is already open for other purposes. The logistics of such events are daunting, given the necessary translation and approval of permission slips, provision of security and administrative staff, and of course, the vagaries of kids and weather. Having something we can casually run outside to use on an as-permitted basis is wonderful.
On our first attempt, we cross-referenced inclinometer readings of the sun’s position versus one we took at the same time of day back in October, which illustrated the seasonal change in the sun’s arc. Next, we used the spotter to look directly at the sun. Though we didn’t observe any sun spots, we were able to see its steady westward movement, as well as the shimmering of sunlight caused by atmospheric conditions.
We then double-checked our observations versus those current for NASA’s orbiting Solar and Heliospheric Observatory, nicknamed SOHO. The results above compare our image to theirs. Needless to say, we were encouraged to get a comparable result for a miniscule fraction of a space agency’s budget! To be sure – their tool has instrumentation ours doesn’t, but it was pretty neat to be able to independently observe what practicing astrophysicists are.
Thanks again to our wonderful donors. As the tax write-off window begins to close for 2009, why not consider making a tax-deductible donation to a teacher’s proposal? We have two up for UV transilluminators, in case you’re wondering! Clear skies, everyone!
In the meantime, check out the rest of the SOHO mission webpage at:
http://sohowww.nascom.nasa.gov/
For students seeking extra credit using the ‘blue’ listening sheets, go to one of the two pages linked below. Listen to the audio article posted there, then use the information in the piece to reflect on what you heard. These are due by 12/23/09. Happy listening!
Option 1 – On how an animal’s size is related to its heartbeat:
http://www.npr.org/templates/story/story.php?storyId=12877984
Option 2 – On how we can survive heat that would make blood boil:
http://www.npr.org/templates/story/story.php?storyId=106880000
After attempting to extract DNA, it’s necessary to run a ‘check’ gel to verify that any product has survived the crushing, spinning, filtering and chemically washing of the plant sample. In a research lab, this involves the use of chemistry a little more carcinogenic than is usually accomodated in public schools. The chemicals used are mutagenic, and the visualization utilizes the kind of UV light that burns the skin if one works around it unprotected. Instead, we used a safe but inexact tool to look at the samples proceed a week prior. tinting is added to the sample and soaked to resolve if any DNA has been found. the initail results were not at all promising
But after a night in the ink, and a rinse in deionized water, I can say with some confidence that we indeed managed to get a DNA sample from the grasses brought from Tampa. Though another verification step away from school will be needed to stand up to the level of inquiry the project demands to move forward, we have passed another milestone in doing authentic research in a high school classroom.
At school on Tuesday, we had many, but not all of the components we needed to run the DNA extraction as I had done at james Cook University. Instead of ethanol, we had access to the less drink-able ethanol. There was no TBE to elute the DNA, so we had to use warm distilled water. The mortars we had were waaay too big for 100mg of plant tissue. But improvising like a chef in a mobile home kitchenette, we crushed the cells directly in the Eppendorf, and made do the best we could. The kids did a great job handling the many steps, and eventually, we were done for the day. What I projected to complete in an hour had taken two with all the improvisations and make-do needed, but whether we had succeeded or not, we had attempted the first ever extraction of genomic seagrass DNA in a NYC public school…..I think I can say that without fear of contradiction!
