As stated on their website: The Ancient DNA Lab provides support for researchers working with ancient, historical, forensic, or other sensitive (low DNA quantity/quality) genetic samples. Established by the School of Forestry’s Carol Chambers and Faith Walker in 2016, the Ancient DNA Lab is physically isolated from other genetics labs on campus and adheres to rigorous quality control measures to prevent contamination, both of which are internationally recognized standards for the early stages of ancient DNA handling and processing.
The Ancient DNA Lab is sterilized (left) and ready to use in 2018.
The 2017 iCREATE class (right) was able to go into the lab between cleanings.
Some of the projects the lab has been involved with include a 10,000 year old bat, research using both extant (living) bats and bat guano, the 8,500 year old bison (below), and work with extant wombats in Australia.
Undergraduate Research Assistant Sam Hershauer presented some basic information on how DNA is extracted, amplified and analyzed in the aDNA Lab. Sam is working on collaborative research project on DNA from organisms in Alaskan lake sediments going back thousands of years. This collaborative project is with the Arctic Lakes Project headed by Dr's. Nick McKay and Darrell Kaufman in the School of Earth Sciences and Sustainability.
Thank you to Faith, Colin and Sam for sharing your hidden treasure with the iCREATE students!
Guest Blog Post by Tad Theimer, NAU Professor of Biology
Flagstaff is a city of science. We are literally surrounded by science. Up on Mars Hill there lies Lowell Observatory, to the north the Museum of Northern Arizona, the offices of the USGS, to the east and west the laboratories of GORE, to the south Northern Arizona University, the Rocky Mountain Research Station, TGen, the Naval Observatory, to mention but a few.
So I stand here as a scientist in a city of scientists. How many of you out there are scientists? How many the family or friends of a scientist?
It’s been said that you know you are a scientist when you wake up on a Saturday morning and think, “I could walk the dog, I could read the paper, I could go for a run, but what I really want to do is analyze that new data set, or sneak off to the lab for one more quick experiment.” And all your friends and families of scientists have seen that, you’ve seen them sneak out the door late at night or early in the morning. So we here all know that inside the breast of every scientist beats a heart as passionate, as driven, as that of any artist, musician or poet. Scientists do what they do because they can’t help themselves. They are driven by an unquenchable thirst for knowledge, by an insatiable hunger to understand the world. That relentlessness, that dogged curiosity, is something folks who haven’t been around scientists may not realize, and as a result they may underestimate the power that stands here today. Because that same passion, that same resolution, that scientists bring to doing science, scientists will also bring to defending science. And that is why we stood here last year, and why we stand here today and why we will be here next year, and the year after that, and the year after that!
So we here in Flagstaff understand what science is, why it is important, and that we must help others understand the important role science plays in our lives. The speakers who went before me articulated that very well. But there is another point about science that we have to make folks understand. Scientists follow data to whatever truth they may lead, regardless of the implications that truth may have. And so scientists sometimes discover inconvenient truths, truths that make us have to question the way behave toward this earth, toward each other. Truths that are inconvenient because they come with costs. The cost of making sacrifices today so that our children and grandchildren can have a decent world to live in tomorrow. This is an important role scientists play, and
I have been trying to think of a simple analogy to help folks understand that important role of science, so let me try this out on you:
Let’s imagine that my inconvenient truth is that I only have $10 in my bank account. But because of this magical piece of plastic called a credit card, I can buy a car, I can buy fancy food and delicious drinks. And some of my friends will support me in ignoring my inconvenient truth because they like to ride in my car and drink my drinks and eat my food. But one or two of my friends will take me aside and say “Tad, what are you doing? You’re acting crazy! You only have ten bucks! If you keep this up you’re heading for financial ruin!” Now we all know which one of those friends is the most valuable. It’s the one with the courage to stand up and tell me the truth even though I didn’t want to hear it. And that’s what scientists do! They are the friends who stand up and tell us the truth even when we don’t want to hear it!!
We are passing through dark days for science. Honesty, reliability, consistency, responsible conduct. These are the cornerstones of science. These are also the foundations of a civil society. Yet every day these ideas are mocked, denigrated, cast aside! We live in a time when integrity has been replaced with irresponsibility, where falsehoods hold the same credence as facts. It is no wonder that we sometimes feel dazed, in a world turned upside down.
These are dark days, but we have seen darker. When I am most in despair for this world, I am reminded of Galileo, that great scientist who dared to follow his data to an inconvenient truth, that radical idea that the earth was not the center of the universe, fixed and immovable, but instead moved around the sun in its orbit. Today that seems like a ridiculously harmless fact, that the earth goes around the sun, but at the time, it was a very inconvenient truth, for it flew in the face of religious dogma. So at the age of 70, Galileo was dragged from his home, thrown in prison and eventually brought before the Inquisition in Rome, forced to kneel and to recant his life’s work, to state that the Earth was immobile and did not move in its orbit. But the story is told that as Galileo walked out of that room, he whispered under his breath, “and yet, it moves!” And so might we say to those who deny climate change today, “and yet, it changes!”
You can ignore the truth for a while. You can walk away from the Paris climate accords, you can tell your administrators to strike out all references to human-caused climate change. You can confuse the electorate by saying climate change is still debated, that there is no consensus. You can ignore the National Academy of Sciences and 17 other scientific societies that have stated that human-caused climate change is real and needs to be addressed. You can ignore all that and build yourself a beautiful house of cards. But eventually that house of cards will fall. Scientists know this. Scientists understand the meaning of that old Buddhist saying: “There are three things in this world that cannot long be hidden: the sun, the moon, and the truth”!
Make no mistake, the walls of ignorance are strong, especially when reinforced by girders of greed and self-interest. But history has shown us that that stone of ignorance will yield to the cold, hard steel of science-based fact. It is for us today to follow in the footsteps of all those scientists and believers in science that went before us, to pick up those hammers of steel and bring them down on that rock of ignorance, knowing all the while that those walls will not fall to one blow, or to a thousand, but the point is to keep on hammering, to keep those hammers ringing. So I say, make those hammers ring here in Flagstaff, but also make ring so that they can be heard down in the statehouse in Phoenix. Make those hammers ring here in Flagstaff, but also make them ring so that they echo in the halls of congress back in Washington. Make those hammers ring here in Flagstaff, but most importantly, make those hammers ring so that they rattle the very walls of the White House! Make those hammers ring!
The 12 CAVIAT students in the iCREATE high school bioscience class at NAU are learning some basic Geographic Information Systems (GIS) skills to help track patient health for their epidemiology projects. Corryn Smith patiently teaches the students the basics of GIS. Corryn has presented to the class twice this fall, and will certainly be helping them again as they prepare their group projects.
Corryn is an Instructor for the Geography, Planning, and Recreation department at NAU. She received her MS in Applied Geospatial Sciences with a Planning and Recreation Emphasis in May 2017. Her Master's thesis research looked at using geospatial technologies to locate travel networks (Forest Service roads and trails) in Flagstaff. Her interests include: geospatial technologies and recreation, geospatial technologies and sustainable land management, GIS in education, and Python Programming for Women and Minorities.
Thank you Corryn for your friendly and professional help!
Dr. Darlene Lee, an anatomical and clinical pathologist with Northern Arizona Healthcare, led a tour of Clinical and Pathology Laboratory at Flagstaff Medical Center to the high school iCREATE students. The iCREATE class is unique in the pronounced role of community members to the success of the class. Dr. Lee gave a tour last year, highlighted here, and it was one of the most memorable tours for the class. She made this one even more hands-on with additional partners from FMC.
Garn Bailey, Pathology Assistant, once again thoroughly engaged the students with a variety of human organs that he prepares for the pathologist to more critically analyze as needed. He dissected a gall bladder to show the gall stones, as well as a kidney that showed a cancerous area. He also went through the entire process of preparing thin sections from larger tissues and organs for analysis.
The surgeons in the hospital rely on the Clinical and Pathology Laboratory to rapidly prepare and assess samples while some patients are in surgery; to make sure they have removed all cancerous cells, or to determine the specific pathogen. When that occurs, tissues are quickly put on ice and are then sliced thinly in a cryostat, which keeps the tissues frozen. They are then rapidly stained and assessed by the pathologist. This entire process can occur in 20 minutes so the surgeon is able to receive the information during surgery to improve the patient's outcome.
The students then looked at blood samples with Dr. Lee. They were able to identify components of blood including white blood cells (leukocytes), red blood cells (erythrocytes), and platelets (thrombocytes). Platelets are tiny blood cells that help your body form clots to stop bleeding. She also showed them the image of the cancerous kidney tissue from the kidney Garn had shown them earlier.
Students observed the hospital's blood supply with Jordan Ippolito, a Medical Lab Scientist at FMC. She told the students that the shelf life of platelets is only 5 days, while frozen plasma is good for a year. Red blood cells are only functionally sound for 40 days because their ability to carry oxygen (their primary role) is impaired after that. The importance of donating blood cannot be overstated!
Two students volunteered to have their blood drawn so they could determine what blood type they are. Phlebotomist Troy Schafer cracked jokes with the students to put them at ease.
Jordan then had the remaining students look at blood sample directly through the microscope so they could put their earlier practice to use.
The final activity was to discuss what having blood types A,B, AB, or O really means, and then to complete the analysis of the blood types using the antigens that can cause blood to clot, depending on what the blood type is.
Thank you again for the fascinating and educational tour of the Clinical and Pathology Laboratory at FMC! Special thanks to Dr. Darlene Lee, Garn Bailey, Jordan Ippolito and Troy Schafer! You are living up to your mission and goal; you definitely wowed us!
Dr. Darlene Lee, an anatomical and clinical pathologist at Flagstaff Medical Center, led thirteen high school students in the iCREATE bioscience class on a fascinating tour of the Clinical and Pathology Laboratory at FMC on Monday, November 14th. Pathology is the study of disease, and a pathologist is a medical doctor (MD) who specializes in studying disease, including the source, extent, and cause of the disease in a patient. The students got to see many aspects of what this career entails.
The students began the tour by seeing some of the high-tech diagnostic tools available to test patient samples. These included urinalysis, PCR, flow cytometry and light microscopy. Jane Talisman, one of the laboratory lead technicians, even did a rapid test from Cate’s mucosal sample to determine if she had MRSA. Read to the end of the post to find out the result!
The students then watched Garn Bailey, the Pathologists’ Assistant, as he prepared to dissect an excised gall bladder. The students were able to touch the gall bladder to see what it felt like. The dissected gall bladder had several gallstones in it that were too large to exit the gall bladder on their own.
A frozen tissue sample from a patient came in, and the tour immediately switched over to observing the pathology team process this sample for the surgeon and patient waiting for it in the operating room. The pathology team can receive and process a sample, and return a diagnosis to a surgeon, within 20 minutes. This intraoperative pathology consultation helps guide the surgeon through the remainder of the procedure, so the patient has a better outcome.
Garn put the sample on the cryostat, a machine that keeps the sample frozen while shaving off very thin slices for placing on microscope slides. Audrey McMillon, a histotechnologist, then stained the samples with a specific stain to highlight what the surgeon needed to view. Histology is the study of the microscopic structure of tissues.
There are four pathologists at FMC and one at Verde Medical Center. In order to become a pathologist, you need a four-year college degree, then a four-year medical school degree, and then you need to complete your pathology residency for another four years! If you want to do a subspecialty fellowship, that takes another 1-2 years.
After the students completed the tour, Dr. Lee shared a presentation with three different case studies for the students to discuss. Just as Garn had previously, Dr. Lee reaffirmed that in order to recognize an abnormal pathology you need to know what the normal anatomy and histology looks like. During the cases, Dr. Lee asked the students what they thought, and what tests they would run to try and solve the case.
At the end of the presentation, Cate got the results from her diagnostic test. We were all thrilled she did not have Methicillin-resistant Staphylococcus aureus, commonly known as MRSA!
Note the sign above the door in the photo above. This important message reflects the commitment of the pathology team: Patients are our Purpose.
STEM City and the iCREATE collaborative thank Dr. Lee and the entire team in the Clinical and Pathology Lab for being such willing presenters, and for providing important and engaging information to the students. Thank you!
By Dave Engelthaler, Associate Professor at the Translational Genomics Research Institute and the Chair of the Northern Arizona Leadership Alliance. This column was adapted from the keynote speech, given by the author, at Science Foundation Arizona's "Giving a Voice to STEM" Conference at NAU on September 30, 2016.
I have often referred to Flagstaff as the Shining City on Arizona’s Hill. It is no accident that I borrow this phrase from the famous, precisely American, ideal of a “Shining City on a Hill”. The early pilgrims imagined that they could create such a community for themselves after escaping the historical norms of European controls on destiny.
Three hundred years later John F. Kennedy reminded of this founding ideal, stating that the world was watching our shining city and that we must live up to our promise; shortly there after, we embarked on one of the greatest journeys of all time and put a man’s foot on the moon (Flagstaff had something to do with that, more on that below).
Twenty years later, Ronald Reagan again reminded us of this American City on a Hill ideal; and while we may not often remember Reagan as a champion of science, he was convinced during his tenure to not only not cut the budget of the National Science Foundation, but rather double it, before he left office. But, as under Kennedy and Reagan and other presidents in before and after, no matter what our economic and cultural condition, we have always led the way in advancing humanity through the sciences.
It is this ideal that convinces me that in Flagstaff, we are a Shining STEM City on Arizona’s Hill.
In August of 2012, a group of Flagstaff Leaders, Businessmen, Educators, Scientists, and Concerned Citizens gathered in the woods on the base of the San Francisco Peaks. This group coalesced around the idea that Flagstaff is a STEM-rich City and that we as a community, businesses and schools, elected leaders and CEOs, teachers and families, needed to collectively band together to bring this rich surrounding to bear on the education of our children and enrich our communities.
There, up on our Hillside, we all mutually pledged our time, talent and resources towards making the STEM City ideals happen. In short – our goal was to have the most STEM literate graduates living and working in a thriving STEM-based economy.
We also had a unofficial motto for the day: “Dare Mighty Things”, which we borrowed from the Jet Propulsion Laboratory, who had, just the preceding night, coordinated the landing of the Curiosity Rover on Mars (and again, Flagstaff had something to do with this mission). And we both stole that from Teddy Roosevelt’s famous “Far better it is to dare mighty things” speech.
Historian, Fredrick Jackson Turner, just a few years before TR’s famous speech, gave us his “Frontier Thesis”, and proclaiming that with the end of the American Frontier, so might be the end the American spirit. While Jackson aptly, and controversially, linked Americanism and American spirit to the discovery and exploration of the American Frontier, I feel that he missed the mark in not understanding the new frontiers that we would identify and explore.
Our increased understanding and use of science and engineering opened up brand new frontiers, beyond land and sea.
One such Frontier, The Space Frontier, was no longer a pastoral landscape to watch from afar. Our STEM City has been at the forefront of the exploration of this new frontier, from the discovery of Pluto, to the training of Apollo astronauts in our backyard, to the camera control of the Mars Rover from our USGS facility, and now finally to the deep space explorations through our Discovery Channel telescope, providing insight into the beginnings of our universe and images of a frontier previously unseen.
Likewise, Flagstaff is home to TGen and the new Pathogen and Microbiome Institute at NAU, where some of the brightest minds are exploring another previously unseen universe – the microbiome. Every day, scientists in Flagstaff are embarking on the incredible journey into the human microbiome – the unseen ecosystem of bacteria and viruses and fungi that live on and in the human body. We are trying to understand how these microbes live, compete, collaborate and otherwise interact during our healthy and disease states. We, ourselves, our bodies, are the new frontier – and again that frontier exploration is here in our STEM City.
And we could go on about the new frontiers ventured by W.L.Gore engineers and SenesTech scientists and MNA paleontologists and Park Service geologists. The frontier is here in our STEM City and some of the greatest pioneers are the trainers of our next generation– the teachers and education professionals of our great public, charter and private schools. Most are ready, willing and able to interact with all of these resources; and some, like former STEM City Teacher of the Year Jillian Worssam, just kick down the door and say: “Let’s do this thing!”
Our STEM City is Worssam’s wildly successful Scientists in the Classroom. It is the Flagstaff Festival of Science (the longest running one in the country). We are the Coconuts; we are the Annual STEMMY'S Awards Ceremony; the STEM Art Competition; and the Super Bowl of STEM in the Dome event (where upwards of 8% of Flagstaff turns out!); we are the Space Station Science Experiment and the High Altitude Balloon Launches; and the superstar Killip Kindergarten Chess team that likes to challenge our Mayor. We are seventh-grade girls wearing lab coats inside a world-class research lab and we are a group of high schoolers rafting down our majestic Canyon to learn our geologic past. We are the Chamber Coding Camps. We are grad students teaching and learning in the K-12 classroom. We are parents, students and teachers on a hill having a star party. We are, in a phrase, America’s First STEM Community.
Arizona, and the rest of the country, is watching our shining STEM City
and we must live up to our promise.
The CAVIAT bioscience students from Williams High School toured TGen North on April 6th. Teacher Michael Lee brought the class to the Translational Genomics Research Institute in Flagstaff to learn about the research projects being done there and to tour the state-of-the-art research facilities.
TGen North and CAVIAT are key partners in a 3-year grant awarded to the Center for Science Teaching and Learning at NAU from the National Science Foundation. This project will test a model of community engagement in an innovative problem-based high school bioscience course. Other partners are North Country Health Care, the Northern Arizona Area Health Education Center, the Coconino County Health Department, and the Winslow Indian Care Center. You can read more about the iCREATE Project and how YOU can be a part of this initiative here.
NAU Undergraduate Erik Lemkuhl (below) describes his work to the students. Erik began at TGen in the prestigious Helios Scholars internship program last summer, and was so successful that TGen North hired him as a paid intern. Erik primarily works on Tuberculosis. Congratulations to Erik as he begins his doctoral work at the University of Arizona next semester.
Below, Mike explains the flow cell from the Illumina MiSeq sequencers. The flow cell contains the DNA libraries (samples) that TGen North is interested in sequencing. He also showed them the small USB-like sequencer called the Oxford Nanopore MinION. The technological advances since the Human Genome Project (1990-2003) are staggering, and the costs per sequence, time needed for each sequence, and sizes of the sequencers have all decreased dramatically.
Several of the students in the class are applying summer experiences, including a Health Camp. If you are in a health or bioscience profession and would be willing to have a student shadow you at your job or do an internship, please contact the STEM Coordinator.
The first CAVIAT bioscience class to participate in the iCREATE project is from Williams High School. CAVIAT instructor and science educator Michael Lee (center photo) brought his students to NAU to tour three different laboratories on February 26th.
The students met in NAU's Wettaw building and toured the Imaging and Histology Core Facility (IHCF) with the Lab's Assistant Director Aubrey Funke (bottom left photo). Insects coated with gold (top center photo) are visualized with the Scanning Electron Microscope (SEM) to see clear magnifications as small as 1/50th the width of a human hair! The students also saw the Transmission Electron Microscope (TEM) and were able to use the Keyence Digital Microscope (photos left center and bottom right).
Dr. Nathan Nieto (right side, second photo down) showed the students his lab and the equipment they use to study the ecology and evolution of infectious diseases in wild animals. They also study how this translates into transmission of disease to humans, domestic animals, and wildlife. They use a mixture of microbiology, molecular biology, phylogenetics and population ecology to investigate infectious disease dynamics in wild animal populations. Much of their work is conducted on reservoirs or the identification of reservoir hosts. You can learn more by linking to Dr. Nieto's lab page here.
Dr. Robert Kellar (upper right photo) runs the Tissue Engineering & Regenerative Medicine (TERM) Laboratory in the Center for Bioengineering Innovation at NAU. He is also the founder and president of Development Engineering Systems housed at the Northern Arizona Center for Entrepreneurship and Technology (NACET) in Flagstaff. (www.des-company.com). His undergraduate, Masters, PhD, and Post Doctoral team were all available to showcase different aspects of bioengineering science.
The three-hour tour was immensely engaging and educational. Thank you all!
The iCREATE partnerships include NAU, TGen North, Coconino County Health Department, North Country Health Care, Northern Arizona Healthcare, and more!
Note: iCREATE wants you! Read more about the project here and if you are interested in partnering to provide increased opportunities for our talented youth in any bioscience field, please contact the STEM Coordinator!
iCREATE is funded by a grant from the National Science Foundation.
Superbowl of STEM
The 3rd Annual Flagstaff Community STEM Celebration kicked off the week on Monday, March 7th at the NAU Skydome with almost every school, STEM business, government agency, and non-profit in Flagstaff! You can relive the excitement with Flg4TV's 2 minute video here!
High-Altitude Balloon Launch
On Wednesday, March 9th, Teacher Kaci Heins and 100 NPA 6th graders sent their payload to over 106,000 feet on a high-altitude balloon from the Flagstaff Airport. Community Leader Bruce Sidlinger and his Aeronautics Engineering class from Flag High, Airport Director Barney Helmick, the Coconino Amateur Radio Club, the Civil Air Patrol, and many other community partners were there to assist. You can see images and hear the story from KNAU's science and technology field reporter Melissa Sevigny here.
Women Executives in STEM Panel
NAU hosted the panel on Thursday, March 10th. All of the women had connections to NAU and facilitator Elizabeth Glass recommended that the many students in attendance use their alumni network as they search career opportunities.
AZ North Regional
The Skydome was brimming again on Friday and Saturday with the CocoNuts and 52 other teams, for NAU's inaugural FIRST Robotics Arizona North Regional contest, which pitted robots against each other to try to take down a castle. You can read Corina Vanek's article on the event here. Microchip sponsored pit tours by volunteers from many of the teams, as well as a VIP luncheon that was well-attended by Flagstaff's government, business, and education leaders. FIRST, which stands for --- , is a non-profit founded in 1989 by Dean Kamen, the inventor of the Segway. It encourages students to pursue STEM and also develops skills in teamwork, problem-solving, creativity, and gracious professionalism.
Congratulations to everyone on helping make STEM Week 2016 the best ever in Flagstaff STEM City!
Guest Blog by Dave Engelthaler, Originally published for the Northern Arizona Leadership Alliance in the Flagstaff Business News - November 10, 2015
As hopefully most readers know, Flagstaff declared itself as America’s first STEM Community in 2012. STEM (the ubiquitous acronym for Science, Technology, Engineering and Math) is commonly discussed in our schools, in academia and in workforce development as a goal for literacy in the 21st Century. In Flagstaff, we have a wealth of STEM resources in our businesses (e.g., Gore & Assoc., SenesTech, Machine Solutions, Northern Az Healthcare, etc.) and research institutions (e.g., Lowell Observatory, TGen North, Museum of Northern Arizona, etc.), let alone NAU and Coconino Community College. In the fall of 2012, Flagstaff Forty, now known as the Northern Arizona Leadership Alliance, initiated a community conversation and ensured a community commitment to using these resources to support and improve our local schools’ ability to achieve STEM literacy for all students.
Over past several years, our STEM City has grown in stature and success. We are continually held as a model for community leadership and collective action on STEM. The reasons are numerous but some of the highlights include: having a community board dedicated to advancing all STEM in the community; having the annual celebration of the STEM Teacher, Leader and Student of the Year; the Superbowl of STEM Event held annually in NAU’s Skydome, which brings out nearly 10% of the city’s population; Flagstaff’s Festival of Science, the longest running one of its kind in the nation; and most importantly the abundant activities and interactions between students, teachers and local scientists and engineers, which end in unparalleled STEM learning opportunities and radical inspiration of hundreds to thousands of our students.
Now, we are moving to the next level of community engagement – coordinated community impact. Rather than just one-on-one interfaces with STEM businesses and classrooms, we have now moved to a model of having multiple businesses work with academia and multiple schools on a coordinated program to educate and enrich both the students and the community. Through the leadership at NAU’s Center for Science Teaching and Learning, the National Science Foundation has recently awarded a three-year $840K grant to build a yearlong Bioscience course for Flagstaff high schoolers. NAU has brought together TGen North, North Country Healthcare, the County Public Health department, Flagstaff Unified Schools District, the Coconino Association for Vocations Industry and Technology (CAVIAT) and the STEM City Center to build a real-world problem solving bioscience course for CAVIAT students, 44% of which are Native American. The vision for this program encompasses outlying county schools as well. Where else would high school students get to work closely with doctors, nurses, epidemiologists, and genomic scientists on development of a tool to detect and track influenza-like illness in their schools and neighborhoods? Where else but our STEM City. The Northern Arizona Leadership Alliance strongly encourages all community members to join the movement towards a stronger, more sustainable 21st Century economy but supporting STEM literacy.
Find more information here!