Archives for 2013

NWABR Bioethics, Day 6

 

 

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Stickleback Tanks at Fred Hutchinson Cancer Research Center

Today, we started early at Fred Hutchinson Cancer Research Center, being a part of a research laboratory meeting.  We had general conversations about the week at the start of the day, and learned about a really cool discovery that was discovered at Fred Hutchinson Cancer Research Center- tumor paint.  This paint glows when exposed to a particular light.  When paired with the correct binding materials, it will glow on a tumor.  Part of the worries around cancer surgery is that some can be missed during the initial surgery.  However, tumor paint changes this outcome.  Also impressive was the 27 high school students part of research at the center.

 

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Biological Specimens ready to be prepared for histology

Jesse Hubbard of the Torok-Storb Lab gave a talk about “Modeling MDS using iPSC.”  iPSC means induced pluripotent stem cells, which would be taken to a patient, reprogrammed, and put back into a patient.  Part of the great parts of stem cells is the fact that they are self-renewing.  Jesse talked specifically about the p53 tumor suppressor gene, as well as a 5q- deletion found in MDS patients.    They are hoping to move on to studying GATA 2 mutant and RUNX1 mutant iPSC models to further study the disease.

 

We then met with many different individuals who talked about their work- Dr. Beverly Torok- Staub, James Riddle, Brenda, including ethics and clinical trials, 3 spine sticklebacks and sex inheritance (they use a ZW system) and pathology and related histology jobs and the technology that is currently used to look at biological tissue.

We then went to the ISCRM which is made up of 50 research laboratories.  The ISCRM is a collaboration among the University of Washington, Fred Hutchinson Cancer Research Center, Seattle Children’s Hospital, Institute for Systems Biology, Benaroya Research Institute, and Paul Allen Institute for Brain Science.  The facility was beautiful and the 80,000 square foot facility was great for their purposes.

 

Dr. David Mack talked specifically about his research about myotubular myopathy.  His research was very promising, using a dog model and eventually looking towards using in human clinical trials.  Dr. Mack gave some bigger thoughts to think about, one of the most that was “Just because we can do something, should we?”

 

We then had a conversation with a couple of laboratory researchers about the ethics of using embryonic stem cells in research.  I was interested in finding out that they go through around 100 embryos to be able to make one successful stem cell line.  We went to the laboratory and looked at stem cells under the microscope.

 

We ended the day looking at Dr. Chuck Murry’s work with the heart.  He gave us a seminar about how heart attacks are the number one killer worldwide, blaming the culture shift from malnourished to an excess of food.  The heart has a stored ATP supply of about 1 minute.  It takes about 15 minutes before cell death happens in the heart, but many people do not come in during this time period- leading to a lot of cardiac damage.

 

Dr. Murry is looking at using stem cells as an intervention to stop the scarring that happens after a heart attack.  They use different growth factors to differentiate “beaters”- heart cells in a dish.  They’ve done experiments with 1000’s of rats, 100’s of mice, and 100’s of guinea pigs.  The issue with this therapy is the immune system recognizes the tissue as foreign, so a person would have to take immunosupressants…but that beats death. 

Heart Cells beating in a petri dish

NWABR Bioethics, Day 6

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Planaria using computer usb microscope

On Wednesday, we spent the entire day at Amgen in Seattle.  We started out the morning by debriefing our site visits.  I’m not going to type out the reviews of the places where I went, so if you’re interested, check out day 4 and day 5.

We were then lead in a discussion by Dr. Thomas McCormick, Professor Emeritus of the UW School of Medicine.  Dr. McCormick lead us in a discussion titled “Bioethics: Clinical Ethics at Work.”  We look at clinical ethics as a set of tools, in which we look at the history of the present illness, review the organ system, look at the psycho-social history, get a physical exam, run laboratory studies, and discuss diagnosis and care plan.  Clinical ethics is made of 2 views- one from a balloon- looking down at a situation big picture wise, and from a mountain bike on a mountain- looking ahead as situations can change very quickly.  We reviewed cases that Dr. McCormick had encountered, and how to reach an ethical outcome.  There were four major topics in clinical ethics: Medical Indications, Patient Preferences, Quality of Life, and Contextual features.  Dr. McCormick’s talk was really engaging, and had me think about a lot about clinical ethics.

In the afternoon, we each split up into different groups.  I was in the stem cell group, in which we looked at planaria and ran through the NWABR stem cell curriculum.  Planaria are really cool because they have neoblasts, which are totiptent.  The NWABR curriculum was really engaging with the use of playdoh in explaining the development of the germ layers.IMG_20130724_142236

3 germ layers in cell development

We ended the day by meeting with groups and discussing our action plans for how we will use this curriculum in our classrooms.  I am fully planning on adding ethics to my 9th grade curriculum, taking from the NIH curriculum on Bioethics, as well as the NWABR Bioethics 101 curriculum..  I also can’t wait to talk about morality in brain development, nuremberg, and human clinical trials during our holocaust unit, in which my coworkers do such a great job of explaining already.IMG_20130724_141335

Modeling development with playdoh

NWABR Bioethics, Day 5

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Benaroya Research Institute Laboratory

We spent the morning of the today talking about human subjects in research at Amgen.  Specifically, we focused in on the Belmont Report and how it related to four case studies, the most famous involving Henrietta Lacks and the HeLa cell line.  The conversation focused on principles related to benefits to families in research, ownership of genetic property, fair compensation for participants, the structure of informed consent,and  lack of education as it relates to research.  These are all principles that need to be rectified with the 3 facets of Ethics: Justice, Respect for Persons, and maximizing the benefits while minimizing the risk.  One of the most interesting facts that I learned was the fact that informed consent is meant to be written at the 8th grade level.

Dr. Kelly Edwards lead a discussion about Biobanking and how it relates to our current ethical understandings.  We talked about residual tissues leftover from a procedure and whether they can be used in research.  One of the biggest current topics in biology is the fact that many Universities are trying to build large biological sample collections.  We are trying to measure risk using risk models while respecting individuals privacy.  With the ease that genetic information may be amplified, it’s really hard to now guarantee that something is completely anonymous.  Kelly gave us two links- One to the People Matter Project and one for Reg 4 All.

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Machines at Benaroya Research Institute

Later, we went to Benaroya Research Institute, which is part of Virginia Mason here in Seattle.  I thought it was really interesting that their model was “BRIng it on,” (and they had really awesome t-shirts)because I think science is just a series of problems, and we need critical thinkers and people who live the adventure for trying to solve the problems.  We were greeted by Dr. Lynn Rose, who explained what Benaroya researches, and how there are 5 different departments- Immunology, Diabetes (type 1), Translational Research, Clinical Research, and Matrix Biology.

We were then given a talk about Matrix Biology and tissue engineering by Dr. Robert Vernon.  We talked about artificial tissues as a scaffold to cells, and how collagen from cattle can be used in humans as a therapeutic scaffold.  Lines placed in the collagen matrix can allow the cells to self-align.  Dr. Vernon spent a long time talking about bioengineered islet replacement using a delivery in a medical device with an alginate interior.  Ultimately, he’d like to be able to put a credit card sized device in a human to restore function to the pancreas with functional islets of langerhans.

We took a tour of Benaroya Research Institute laboratories, which was very interesting, up to date, and had a pleasant atmosphere.  It was really interesting to see how items that would be collected at the clinic are transported and prepared for analysis.

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Spun down cells seperated into different layers (of blood)

Next, we spoke with a panel of individuals that work at Benaroya Research institute.  I was amazed at how all 3 individuals did not plan to be where they are now, but are happy to have take STEM jobs and it worked out to where they are very happy with their jobs.  A lot of the thoughts I had need to be summarized on my personal blog.

We had two more guests at the end of the day.  The first of these guest was Dr. Jane Buckner, associate director of BRI.  She talked at length about what drives autoimmunity, but more towards what makes good science.  Her big thought involved how few people go into science clinical research.  We then met with Dr. Carla Greenbaum, who talked about clinical trials and how important they are.  So few people in the United States participate in clinical trials, which slows down progress for all.  Clinical trials are also super expensive, which is a problem (probably necessary) with FDA regulations.  Overall, it was a very interesting day, and so much of the topics we discussed will have a direct impact on how I teach my students about current research.  I am also planning on bringing in more scientists from the community, so that my students can see different STEM careers in action.

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A liquid nitrogen refrigerator at BRI

NWABR Bioethics, Day 4

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A rat from our “research” study

Today we started out at Amgen in Seattle, talking very specifically about NWABR’s research in animals topic.  This topic was specifically focused on the ethics of Animal Research.  We began with the thought “How can we talk about difficult issues in a civilized manner?”  We then learned about the different ways that animals are currently killed in the United States.  94% of animals are killed for food purposes.  4% of animals are roadkill.  .1% of animals are euthanized in shelters.  2% of animals are killed by hunting.  .3% of animals are used in laboratory research.

Most of the research being done uses mice- 90% of all animal research.  One of the fastest growing animal groups being used in research is zebra fish.  All of this information is very interesting, and will lead to great conversations in regards to animals in research.  I personally believe animals are an important aspect of research, as they server as models, leading to treatments for both humans and animals alike.  There are institutional boards for the care of animals and research, to minimize risks.

In the afternoon, we went to the Veteran’s Administration Puget Sound Health Care System Animal Research facility.  There, we met Dr. Cindy Pekow, one of the Veterinarians that deals with the well-being of the facility’s animals.  Cindy gave us an overview of her work, and lead us through the role of her job.  Many of the animals that the VA is interested in testing are related to diseases and conditions that primarily affect the VA population.  This population tends to be older, white males.

We were given a presentation by Dr. Jeanna Wheeler, with a focus of Alzheimer’s.  Jeanna works with both C. elegans and mice.  Jeanna’s research was very interesting, talking about the tau protein abnormalities, as well as the accumulation of beta-amyloid.

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Animal conditions in a testing facility

We then were able to tour the animal research facility.  We started by talking about the signs of healthy animals.  Healthy animals are essential for the tests, to control for fewer variables.  The veternarians and vet technicians check-in on each animal daily.  At present, that location only has mice and rats in their tests.  We were each given a rat, and told to check the animal’s health.  We were taught basic techniques of how you would ensure the well-being on the animals.  We were then shown how a simple experiment might look.

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Conducting our observation of the rat interaction with a substance (chocolate)

After touring the facility, we were given a presentation by Dr. J. Ernie Blevins about leptin and oxytocin in weight loss.  The results from this study seemed very interesting, although it was quite a bit above my head.  Basically, the talk was about the leptin pathway, and the role of oxytocin in weight regulation, specifically in weight management.  Parts of the hindbrain have oxytocin receptors, which seem to be amplified by the leptin response, to a certain extent.   We ended the day reflecting on the day’s material and how we would incorporate it into our classrooms.

NWABR Bioethics, Day 3

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Picture of Mount Rainier

Today started out with a delicious American breakfast of homefries, eggs, and sausage.  I hate to admit it, but the coffee here is absolutely amazing.  I might have slipped back into my old ways of drinking a lot of coffee, but when in Rome…

We started out the day by reviewing the gummy bear lab that we started yesterday.  Our results were very interesting- the control gummy bear increased by 10%, while the other gummy bears increased in size by 475%, 500%, and 550% respectively. 

The next activity we completed in class was very interesting- it was a “lab meeting,” in which each group explained their procedure, methods, and results.  This lead to some great talks about what was important in the study.

Furthermore, the following activity was to complete a new procedure for everyone in the lab to complete.  I can see this being a powerful way of showing students that science works in a process of groups of individuals working together, rather than “lone wolves” in the science field.

After lunch, we talked about using Socratic Seminars in our classrooms, in which you set the classroom up in a circle and have students discuss an article that they read.  It was amazing to see the thoughts that were generated through this process, and my understanding of the article increased ten-fold.  This is definitely an activity that I would use in my classroom to increase understandings of scientific articles.

We then drove back to Seattle, and had amazing views of Mount Rainier.  The drive was beautiful for a while, and then we were stuck in traffic, which is apparently very common in the Seattle-Tacoma area. I ended up finding the end of Interstate 90- of which I know well from the Massachusetts area.  It ends here in Seattle.  I made it to my dorm at the University of Washington- Seattle campus, and am getting ready to go to dinner with my dormmates.IMG_20130721_164504

I-90, which travels between Boston, MA and Seattle, WA

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Another beautiful picture of Mount Rainier

NWABR Bioethics in the Science Classroom, Day 2

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Giant Tree in Pack Forrest Woods

Today we started out by looking at a ton of resources that are useful for both Bioethics and general Biology topics.  The list is posted below:

 

Northwest Association for Biomedical Research

http://www.nwabr.org

Bioethics.net

 http://www.bioethics.net

Ethics Updates (University of San Diego)

http://ethics.sandiego.edu

Genetic Science Learning Center

http://learn.genetics.utah.edu

High School Bioethics Curriculum Project

http://highschoolbioethics.georgetown.edu

Genome Sciences- University of Washington

http://gsoutreach.gs.washington.edu

National center for Case Study Teaching in Science

http://sciencecases.lib.buffalo.edu/cs/

National Institute of Health- Exploring Bioethics

http://science.education.nih.gov/customers.nsf/HSBioethics.htm

Your Genes, Your Choices: Exploring the Issues Raised by Genetic Research

http://ehrweb.aaas.org/her/books/index.html

 

These topics were really awesome and you can request free resources from a lot of these resources.  I took a look at the National Institute of Health, which are very high quality, and ordered a lot of the free materials.  It is crucial to order these materials soon- as there is uncertainty due to budget constraints.  It appears that there is no funding going to the National Institute of Health in regards to educational outreach, basically getting rid of the office and all materials.

 

Next, we went through the basic curriculum of Bioethics 101 by NWABR.  We started by reviewing how many of the lead teachers integrate Bioethics into their current classes.  This was interesting, and I’m hoping to have a bioethical part of most of the units that I already cover.  Furthermore, when we cover Matt Killeen, our 9th grade World History teacher covers the Holocaust, I have some great resources on Ethics that came from the Nuremberg code as well as multiple articles that deal with morality.  I am very much interested in this collaboration to better teach our students.

 

We then reviewed the homework that we had to complete prior to the program.  I ended up reviewing most of the materials on the flight out here to Seattle.  Just the materials that we completed gave even greater understanding to the homework assignment, and I feel like I understand how to teach Ethics at a deeper level.

 

After lunch, we completed a case study called “Dennis’s Decision.”  This describes an ethical dilemma of treatment of a medical condition with a patient refusing treatment.  This was a very engaging case study, and the NWABR curriculum guides the process very thoroughly.  There’s just something extra when you have curriculum designed by teachers and created for teachers- everything just clicks better than from a textbook.

 

Finally, we ended the experience today by looking at the question “How much does the volume of a gummy bear increase after soaking in water?”  My group decided to check the gummy bears volume by water displacement.  We’ll look at our results tomorrow.

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Gummy Bear Experiment

Soon, it will be dinner time, and tonight at 7 pm we will be watching the movie “Rare.”

NWABR Bioethics, Day 1

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I made it out to Seattle around 8:30 pm last night, and was picked up at the airport by Jeanne Ting Chowning, who is the senior director of the NWABR Bioethics Program.  She pointed out some of the sights along the way, including the Cascades, the Olympic Mountains, and Mount Rainier.  The drive took a little less than two hours, and my dorm was already set up when I arrived at Pack Forest.

Today I started out having breakfast around 8, and chatting with other teachers that had arrived early.  More people kept arriving for the program, and we eventually made our way over to Scott hall for the welcome session and introduction to the program.  We talked about which sites we would be able to visit over the course of the week.

Lunch was delicious, it was chili, backed potatoes, and chicken Caesar salad.  We had a break time, and as always I tried to talk to as many different people as possible.  It seems that no matter which conferences I go to, it is always the same high-quality caliber people that attend.

In the afternoon, we talked about setting norms in the classroom, which I think is really important.  I try to do this at the beginning of the year which my students, and I had some good results this year.  The process we went through helped me think about how to improve this aspect of my teaching, and really get students invested in truly carrying out these norms.

We then went through a series of activities.  First, we compared science and ethics on a scale of 1 (being completely subjective) and 10 (being completely objective).  The class average was around an 8 for science and a 5 for ethics. 

Next, we completed an activity in which we looked at what makes an ethical questions.  I can’t wait to incorporate ethical questions into my classroom, because I think it will help students understandings and justifications for answers.  Furthermore, I am switching to an "Essential Question" based assessment for my class, where students have to make justifications using evidence to formulate a response to the unit essential question.

We ended the day by reviewing a "Pandemic Flu" activity, similar to the lifeboat "who would you save" activity.  There were 10 options, of which you could really only save 5, and you had to pick ethical reasoning for why you would save these individuals.  Themes included "Doing the most good," "Protect the Weakest," "Age, Experience & Knowledge," "Most life potential," and "All life is valuable."

Finally, we reflected on the day in our personal binders, and I’m now waiting until dinner time.  After dinner, we will be taking a hike to Mount Rainier.  I’m very much excited for the rest of the weekend and next week, as it seems like this is catered to Biology and will incorporate well into my classroom!

Cheung Lab, Day 9

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UMass College of Natural Sciences Research Greenhouse

Today started out by visiting the growth room on the 12th floor and selecting plants to collect seeds from.  We were collecting the T0 seeds from both arabidopsis wildtype and the feronia line.  The seed collection process uses newspaper and shaking the seed pods to release the seeds onto the newspaper.  Then you use a sifter, which allows the seeds through but keeps most of the debris from passing through.  In this way, you are able to get as many seeds as possible while minimizing the debris.

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Collected seeds in eppendorf tubes
One of the most important aspects of seed collection is the potential for contamination.  You must clean up your work bench, because if seeds from a previous line enter your tube for the new line, it can be catastrophic for results, and can cause a lot of confusion in regards to results.
After we collected seeds, Norice came into lab, and we started running a gel.  We used 15 microliters instead of 10, because we were having some slight issues seeing the results earlier in the week.  We left the gel running, and analyzed other gels.  We were able to tell which of the genes were homozygous and which of the genes were heterozygous.  I haven’t read a gel in years, so this was a great review for me.IMG_20130717_130343

Gel print-outs; can you tell which plants are homozygous vs heterozygous?

We then spent time in the greenhouse in the afternoon, collecting pollen from the tobacco plants.  The process was very straightfoward- remove the tobacco flowers with the most pollen on their anthers and lay them in a tray.  I worked collecting the wildtype pollen (wildtype means “normal”) and Norice collected the pollen from the transgenic plants.  We went back to the lab with these flowers, and started to empty the pollen into eppendorf tubes.

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Tobacco in research greenhouse

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Collected tobacco, ready for pollen extraction in the lab.

We then tried to analyze our gel, but there were no bands on the gel.  Something had gone wrong in the PCR process, and we were not sure what it was.  It ended up being time for me to leave, so I’m not sure what could have gone wrong in our PCR.

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Good example of a selection plate- the green plants are the transformed ones that survived the screening process due to antibiotic resistance.  The medium on these plates has antibiotics, which kills the other plants, which are more yellow in this picture.

Cheung Lab, Day 8

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Analyzing Gel results

Today started off with a lab meeting, so I was able to head in late after cleaning my house and starting to get ready for my trip to Seattle.  I started in the laboratory by reviewing the procedures for running gels (gel electrophoresis).  The lab meeting ran late, so I was able to review the other procedures and check on the GUS assay that we set up yesterday.  I can see that the rk10p:GUS now has blue roots as well, meaning that the gene is being expressed there.

When the lab meeting ended, I started work on running gels based on the work that we did yesterday.  The first step was preparing the gels.  We used 1x TBA to set up our gels, heating the medium in the microwave and then pouring it into the gel containers to cool.  We used plastic inserts to make sure that our gels had the appropriate wells.7164

Preparing gels for gel electrophoresis

While waiting for the gels to cool, we used dye to stain the DNA in each of the containers that had come from the PCR process.  This is essential, because you want the DNA to show up so that you can view it in your gel.

We then used a micropippette to drop a very small amount of DNA into each of the wells in the gel.  This will allow us to see which of the DNA samples is larger (moves slower through gel, will be nearest to well) and smaller (moves quicker through gel, will be further from well).  DNA is negatively charged, so you place the negative end closest to the DNA wells, and the positive end away from the wells.  It is crucial to keep all of the containers organized- so that you know which well corresponds with each sample.7161

Running a gel- notice wells (blue), negative lead (black) and positive lead (red)

While running the gels, we started preparing new samples for PCR.  We first made new labels and labeled all of the plants so that we would know which sample came from each plant leaf.  We then took these leaves off of the plants using forceps and placed them into different eppendorf tubes.

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Labeled plants, ready for leaf extraction

We followed the same procedure for preparing our samples for PCR that we used yesterday- the whole process takes around 3.5 hours from start to useable DNA.  In between preparing our new samples for PCR, we analyzed our earlier gels.

Cheung Lab, Day 7

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View from 11th floor, Lederle Graduate Research Center

Day 7 of working in Dr. Alice Cheung’s laboratory started with us setting up a GUS assay.  GUS is a gene that we put in to visualize where something is being expressed.  In our case, we were using the plates we set up on 7/2, put in the 4 degree Celsius refrigerator for 2 days, and left in a 22 degree growth chamber for a little over a week. 

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GUS assay, different genes (labeled)

To set up our GUS assay, we had to make a solution of x-glucose.  This will bind where GUS is being expressed, causing a blue color to happen.  The blue will continue to accumulate in the areas where the GUS gene is expressed until the reaction is stopped with ethanol. We started by making the solution, adding it to a Petri container, and vacuuming the air out.  Vacuuming the air out allowed more penetration of the solution containing the x-glucose, because air tends to accumulate on the edges of the plant.7154

Vacuuming out GUS assay for better infiltration

We then started learning the process for PCR- polymerase chain reaction.  PCR is used to amplify a gene that you are trying to study.  In our case, it has to do with the mutant lines of plants we are studying. First, you use a grinder to mash up the leaf and break open some of the cells.  Then, we added some extraction buffer to help extract some of the DNA.  We spun our tubes for 7 minutes, and then transferred the supernatant to a new tube.  We had to take care and not add any of the solids still left, as that would interfere with the results of the PCR.  We then added isopropanol, spun down the solution for 5 minutes, and were left with a supernatant to get rid of.  Our DNA was stuck to the bottom of our solution, so we washed whatever else was in there away with 70% ethanol.

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Eppendorf Tubes getting ready for PCR


We had to resuspend our DNA in EDTA, which is a chemical that helps our reaction.  Using the vortex, we resuspended the DNA, and put it in a new microfuge tube.  Finally, after We followed the directions and set up our PCR.  We had to wait 2.5 hours for the reaction to occur.  The PCR machine was full, so we wouldn’t be able to run the gels today.

Next, Norice and I started to think about the upcoming academic year, and how we could incorporate this into our classrooms.  I started to lay out a plan, and create a plants unit that teaches most of this plant anatomy.  It’s a real shame that both the Massachusetts Science and Technology Standards (2006, latest revision), and the Next Generation Science Standards (2013), do not focus enough on plants- the basis for all food on Earth. 

Finally, we were able to check our GUS assay, and see how it would be illuminated.  The roots in our of our samples RK8p:GUS were blue, which was very interesting to see.  We will have to check the rest of the samples tomorrow and see how they turn out.