E(ek!) Coli Sampling for the Safety of Humans and the Environment
Guest blog post by Chelsea Silva, VISTA Member for the City Sustainability Department and the Friends of the Rio de Flag
Escherichia coli, more commonly known as E. coli, is a type of fecal coliform bacteria. Bacteria are single celled microorganisms that can either exist as independent organisms or depend on another organism to live. E. coli bacteria are found in the environment (soil and vegetation) and in the intestines and feces of all warm-blooded animals and humans. That’s right, fecal = relating to feces = poop!
Most coliform bacteria are not harmful, but their presence in drinking water indicates that disease-causing organisms (e.g. pathogens) could be in the water system. Only particular strains of E. coli cause serious illness, and people usually contact these strains (especially strain 0157:H7) through consuming undercooked meats such as hamburger. Disease symptoms include diarrhea, cramps, nausea, and sometimes jaundice, plus headache and fatigue.
Safeguarding against E. coli is part of the Arizona Department of Environmental Quality’s (ADEQ) mission to protect and enhance public health and the environment. The ADEQ conducts routine E. coli sampling throughout the state in order to reduce the risk of illness from disease causing organisms associated with sewage or animal wastes.
On June 28th, ADEQ staff trained staff and volunteers with Natural Channel Designs, Inc. and the Friends of the Rio de Flag on E. coli sampling. Trainees learned how to properly collect a water sample, how to process the sample using a handy “Processing Guide”, and how to record the data once processing is complete. Sampling in Flagstaff and the surrounding areas will provide the ADEQ with the data needed to protect our drinking water supplies.
Below show the initial and the final stage of processing the E. coli. After the sample incubates for 12 hours, you look at the large and small squares on the sample and count the ones that fluoresce under a black light.You then use a Most Probable Number (MPN) table to calculate the MPN of E. coli in the sample (you count the # large squares fluorescing in you sample and find this number on the X axis and do the same with the number of small squares fluorescing and find it on the Y axis to calculate the MPN of bacteria in the sample). The picture here shows that the sample contains bacteria, but not at a concerning level.
The Friends of the Rio de Flag is excited to partner with ADEQ and Natural Channel Designs, Inc. to engage citizen scientists in E. coli sampling. In the coming months, the Friends of the Rio will create a sampling plan with ADEQ to best fit the needs of our watershed. Afterwards, the Friends of the Rio will recruit volunteers to collect water samples throughout town. This will give us a better idea of water quality in our community.
Thank you to Meghan and Jake with the ADEQ for training us on E. coli sampling, and another thank you to Natural Channel Designs, Inc. for hosting the E. coli sample training day.
From L to R: Chris Tressler, Civil Engineer and Geomorphologist, Natural Channel Designs, Inc.; Mark Wirtanen, Biologist and Engineering Technician, Natural Channel Designs, Inc.; Oren Thomas, Conservation Projects Manager, Prescott Creeks; Jake Fleishman, Civil Engineering In-Training, Natural Channel Designs, Inc.; Chelsea Silva, STEM VISTA Member for Friends of the Rio de Flag and the City of Flagstaff Sustainability Division; Meghan Smart, Hydrologist, ADEQ; and Jake Breedlove, Grant & Watershed Coordinator, ADEQ
The dozen high school students in the iCREATE CTE Bioscience class toured two very different labs at NAU on Monday, April 24th. First, they ventured to the Geochronology Lab in the Science Lab Facility building where Lab Manager Katherine Whitacre described the process of amino acid racemization and how it is used to date small specimens including single microorganisms or bits of mollusk shells, egg shells, etc. Northern Arizona University has one of the few amino acid geochronology labs in the United States and has analyzed samples from all over the world for almost 20 years under the leadership of Lab Director and Regents Professor Darrell Kaufman. Below, graduate student Ethan Yackulic showed one of his sediment cores from Crater Lake in Colorado.
The lab has a large walk-in refrigerator with lake cores from all over the world, collected by NAU researchers and graduate students. The cores are kept cold so unwanted microorganisms don't grown on the surfaces. Ethan uses a Specim hyperspectral single core scanner designed for studying lake sediment core samples. By changing the range of wavelengths, he can detect locations of specific minerals or organic compounds, to help pinpoint where to collect his samples.
In the photos above: Katherine is dissolving mollusk shells with hydrochloric acid, an iCREATE student looks at shells under the microscope, and graduate student Kara Gibson uses a particle size analyzer on soil samples for her dissertation research.
Many of the research results from this lab focus on understanding paleoclimate change, which may then inform our understandings of, and models for, present climate change. You can learn more about this research here.
The next tour was to Nathan Nieto's lab in the Wettaw Biochemistry Building. Dr. Nieto has studied numerous animals in the past, but these days his lab is overwhelmed with ticks being mailed to him from all over the country. On an average day, the graduate students and undergraduate researchers in his lab will identify, grind, extract DNA and run real time PCR on 200-400 samples to determine whether the tick is host to pathogens such as Lyme disease and tick-borne relapsing fever. One week in May of 2016 he received over 2,000 ticks in the mail and it looks like he may exceed that this May. The tick study will identify what regions of the country have which species of ticks and what diseases they are carrying. This project will create a "heat map" of tick-borne diseases that can then be used by doctors and epidemiologists.
Photos above: Nate looks over where some of the many ticks are being mailed from, just a few of the mailboxes of ticks in his lab, and undergraduate Shienna Braga who is identifying the species of ticks at the microscope.
Photos above: Nate shows an iCREATE student the number of eggs one female tick laid, and graduate student Tanner Porter leads the lab tour for the students, including the refrigerator with thousands of samples from numerous animals including coyote tongues (possible reservoir for Rocky Mt. Spotted Fever), mice, squirrels, bats and more!
Nate's lab website explains what keeps him busy: "Our research focuses on the ecological maintenance and evolution of infectious diseases in wild animals and how this translates into transmission of disease to humans, domestic animals, and wildlife. We use a mixture of microbiology, molecular biology, phylogenetics and population ecology to investigate empirical infectious disease dynamics in wild animal populations.
Thank you Katherine, Nate, and generous students for sharing your time and knowledge with the iCREATE bioscience class!
Guest Blog Post contributed by Jake Burwell, STEM Capacity Development VISTA
The 5th grade teachers at Killip Elementary school designed a Problem-based Learning Unit that focused on the students reviewing FUSD's new Wellness Policy that restricts the food/drink items allowed in the classroom. This unit aligned standards for understanding "matter" while integrating real world relevance as the students learned some basic chemistry such as the three common states of matter, physical and chemical properties and changes. They learned what chemicals, including sugar, go into drinks and their final product was a recommendation to the FUSD governing board as to what additional drinks could be included in the policy as "acceptable."
Tracy Blahut, Katie Butterfield and Jillian Hernandez co-developed the unit, and STEM Coordinator Ted Komada helped find local experts to assist. On April 28th, Chemists Irina Barrow and Amy Sessions from W.L. Gore gave the students some basic background on matter and had the students do simple experiments on chemical and physical changes. Amy told the students that she struggled with chemistry in 10th grade, but persisted in her studies and now enjoys her work as a chemist at W.L. Gore! Students guessed from Irina's accent that she was born in Russia, and despite learning a complex career in a second language, is now a highly successful chemist at W.L. Gore.
After this introduction to chemistry, the students were given the following drinks to analyze: NOS, Rockstar, Monster, Sprite, Diet Coke, Coke, Capris Sun, Sunny D, and Propel water. They worked in teams to test their sugar content through a boiling process, taking notes on the results as they completed the experiment. The end results were shocking! With most of the drinks, a large amount of sludge remained after the water evaporated. Some drinks (i.e. energy drinks and Coke) contained over 14 g of solids out of an initial 100 g of liquid. They wrote up their results and created presentations for representatives from FUSD, with suggestions for the drinks that should, or should not, be included in the District's approved list, based on their sugar content.
A selected group of the 5th graders presented their findings to the Forest Highlands Foundation to demonstrate the relevant and educational value of this PBL unit. Thank you to the Forest Highlands Foundation for granting Killip Elementary the funds for the equipment for us to do this unit in the years to come!
Thank you to Irina Barrow and Amy Sessions for their great contributions to this unit!
Guest Blog Post by Larry Hendricks, PR and Publications Coordinator, Coconino Community College
CCC CAVIAT Students Focus on Health Professions
They’re taking college classes, but they’re still in high school. Not only that, but they’ve proved their mettle in problem solving in the health occupations, and they’re on their way to a statewide competition in April.
Twelve students in Coconino Community College’s Dual Enrollment/CAVIAT BIO 298 class took exams on Creative Problem Solving through Health Occupation Students of America (HOSA). This class is taught by CCC Science Faculty and Bridges to Baccalaureate Principal Investigator Dr. Aaron Tabor, NAU Graduate Students and CCC Instructors Christina Baze and Bobby Woodruff.
“Four of the students qualified to go to the state level,” Tabor said, adding that all of the students are equally intelligent and deserving of accolades. The team placed ninth overall.
The four students, all 10th graders, are Cate Cole and Ethan Perelstein from Flagstaff Arts and Leadership Academy; and Kaleb Herrelko and Jacqueline Slack from Coconino High School.
According to information from HOSA, its mission is to “promote career opportunities in the health care industry and to enhance the deliver of quality health care to all people.” The focus is on health science education and biomedical science programs to promote interest in pursuing careers in the health professions.
To prepare for the exams, Slack said that the team began by reading books on creative problem solving and by researching various health-related problems in the community. Cole added that the team tested one another with problems as well as timing the testing for solutions.
During testing, the team had 30 minutes to prepare and had 8 minutes to present their case in front of a panel to judge. They made the grade, and now they’re heading to Tucson for the statewide competition.
“I personally am excited to meet other students like us, who are science minded,” Perelstein said.
Herrelko added, “That could be fun.”
Slack said, “I’m very excited to compete.”
Cole said, “I’m really excited to see what we can come up with – real-world problems that affect millions across the globe.”
The team members are part of the iCREATE High School Bioscience program. The class offers six credit hours from CCC to apply to a college degree. The students meet five days a week at the Center for Teaching and Learning at Northern Arizona University for lectures and labs. The program is offered through the Coconino Association for Vocations, Industry and Technology.
“I love coming here and getting a taste of what college and medical school will offer,” Cole said.
Perelstein said, “For me, this class is challenging, it’s engaging, and that’s what I really love.”
Herrelko said, “I like the challenge and it requires more persistence.”
Slack said, “I’m excited that every day after school, I get to be around science-oriented, like-minded people.”
For Tabor, he said he thoroughly enjoys being the instructor for the class.
“Frankly, it’s the students,” he said. “I never in a thousand years anticipated teaching K-12 students at all, but this group of students is one of the best I’ve ever encountered.”
Tabor added that his job is to educate the students on the translational sciences and the epidemiology field, but he also is to assist them with their professional growth – creating curriculum vitaes, attending conferences, performing public speaking, seeking publication, and more.
As for the state competition in April, Tabor said the students can go to the national level in the event if they are rank high enough for it. So, the journey may not be over for one or several of them after the state competition.
And as for the future, all four team members have plans. Cole’s goal is to become a physician, an obstetrician. Perelstein is interested in mechanical engineering, particularly “biomimicry,” or solving problems through evolutionary processes. Herrelko is still exploring, but he knows he wants to be an engineer of some sort. Slack is dedicated to becoming a neurosurgeon.
“We challenge one another and work to put our best foot forward as a team,” Perelstein said.
The iCREATE HS Bioscience program is funded by a grant from the National Science Foundation. Community partners include CCC, CAVIAT, NAU, TGen North, North Country HealthCare, Coconino County Public Health Services District, and Flagstaff STEM City.
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!
The Girls on the Run season finale on November 11th at Coconino High School included a Hall of Heroes with many STEM professionals represented! Thank you so much to the following Wonder Women for participating in the 2016 Hall of Heroes!
Medical professionals, Dr. Kate Preston, Dr. Margaret Donnelly and Clinical Pharmacist Randee Fullenwider, all shared their experiences in the medical field with the girls.
Mechanical Engineer Beth Cooperrider, Lawyer Jennifer Mott, and Wildland Forest Fighter Maggie Knight shared their journeys and careers with the girls.
Lowell Observatory Astronomers Dr. Lisa Prato and Dr. Deidre Hunter shared starry wonders, and Lisa Lamberson, owner of Mountain Sports, described the joys and challenges of running a successful store in downtown Flagstaff.
Thank you all for your contributions to empowering our young women through the Girls on the Run Hall of Heroes!
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.
Guest Blog by Marney Babbitt, NAHEC Youth Program Coordinator, Girls on the Run of Northern Arizona Council Director, North Country HealthCare
In early June, 40 high school students from rural and underserved areas in Arizona attended the Future Health Leaders Summer Camp (FHL), including a Williams High School student from the iCREATE bioscience class. The camp was sponsored by the Northern Arizona, Eastern Arizona, Southern Arizona and Greater Valley Area Health Education Centers. This week long camp was hosted at the University of Arizona.
FHL has a number of objectives:
Highlights this year included:
Our 2017 camp for current high school students will be held at Northern Arizona University in June of 2017. Applications will be available in early 2017. Please contact Marney Babbitt (email@example.com) for more information.
Guest Blog by Marney Babbitt, NAHEC Youth Program Coordinator and Girls on the Run of Northern Arizona Council Director at North Country HealthCare
On Tuesday May 3rd, students from the AT Still University Community Campus at North Country HealthCare (NCHC) visited Curt Craig’s 6th grade science classes at Mount Elden Middle School (MEMS). The medical students shared their experiences in education and medical school through hands-on activities where MEMS students learned about heart and lung sounds, reflexes, and protecting ear drums.
This visit was an activity of the Greater Flagstaff Chamber of Commerce Skills for Workplace Success (S4WS) program. North Country HealthCare and Curt Craig’s 6th grade science classes at MEMS are paired in this program and met four times throughout the 2015-2016 school year. The MEMS students learn about careers in the health care field. Additional presentations introduced MEMS students to Public Health, Orthopedic Surgery, and Telemedicine.
Thank you North Country HealthCare and the Greater Flagstaff Chamber of Commerce!
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.
Flagstaff STEM Coordinator