PMI in the news
Dr. David Engelthaler, Dr Paul Keim and Dr. Michael Worobey, Cracking COVID-19 Accordion Closed
Genomics researchers at Northern Arizona University, University of Arizona and the Translational Genomics Research Institute (TGen) have formed the Arizona COVID-19 Genomics Union to track the coronavirus’ origins and impacts.
The collaboration offers unique advantages in studying such a stealthy pathogen.
“You start to get this picture of how these viruses are moving, spreading, starting local epidemics, how often new things are jumping to a new area and taking off, how often you just have a sort of one-off dead end,” said Michael Worobey, who heads UA’s Ecology and Evolutionary Biology department.
Genomics experts study the structure, function and evolution of an organism’s complete set of genes, or genome.
Tools that allow researchers to sequence large quantities of DNA or RNA at once have transformed genomics over the past 15 years into an epidemiological powerhouse. From its time in the wings studying rare conditions, the field has moved to center stage, offering better estimates of heritability and environmental risk factors.
Indeed, genomic epidemiology was instrumental in tracking the family tree and transmission paths of the severe acute respiratory syndrome virus (SARS), and researchers have applied related methods to bird flu and human influenza.
Dr. Paul Keim provides an update on COVID-19 Accordion Closed
Arizona scientists have joined forces to study the coronavirus disease in a new institute called the Arizona COVID-19 Genomics Union. The group’s co-founder is Dr. Paul Keim, an infectious disease expert with Northern Arizona University and the nonprofit institute TGen North. He spoke with KNAU’s Melissa Sevigny in the first installment of a regular weekly update about the science of COVID-19.
So we know the coronavirus disease is a new disease to humans, so how did that happen?
Coronaviruses do exist in humans. This is the seventh recognized coronavirus…. This particular one follows the same pattern we saw with SARS and MERS, in that it existed in an animal reservoir, quite likely bats. We don’t know a lot about that, but the idea is it’s tolerated, maybe causes mild disease, in bats, and then it undergoes natural evolutionary processes. For example, one of the differences that we know exists between this virus and the bat viruses is in the region of the spike protein. Everybody’s seen these picture of the coronavirus, it’s a round little ball and it has these spikes coming out. Artists like to color those spikes red, they’re not really red, but that makes for an attractive looking virus on the TV screen. Those spike proteins are really important for the virus when it infects humans. The virus comes into our respiratory tract and binds to cells in our respiratory tract via the tips of those spikes…. So the mutations that occurred to allow that virus to jump from animals to humans, definitely one of the most important mutations that occurred is right at the tip of those spikes.
Breezy Brock and another NAU Undergraduate are selected as national Goldwater Scholars Accordion Closed
Two Northern Arizona University students have been named national Goldwater Scholars, making this the fourth year in a row NAU has been represented and the third year with multiple scholarship winners. This prestigious award provides scholarships to undergraduates who intend to pursue research in their chosen field of natural sciences, mathematics or engineering.
Third-year student Beau Prince, studying mathematics, physics and astronomy, and sophomore Breezy Brock, studying microbiology, were selected from 1,343 students nationwide who were nominated. Only 396 are selected.
Dr. Paul Keim on COVID-19 and why ‘good behavior’ matters Accordion Closed
There are now tens of thousands of confirmed cases of the coronavirus disease in the United States. The Centers for the Disease Control and other health experts have asked people to avoid large groups, stay at least six feet away from one other, and self-quarantine when sick. KNAU’s Melissa Sevigny spoke with infectious disease expert Paul Keim about why these measures matter. He’s a professor at Northern Arizona University and the nonprofit research institute TGen.
Paul Keim: I actually think of the world as a series of probabilities. When you’re six feet away from somebody else who has this disease and they cough, a lot of those particles are going to go flying out of their mouth and then they’re going to fall to the ground, or fall to the surface around them, and the hope is, by being six feet away you’ve lowered your probability of encountering one of those to a very small number. We don’t know what that number is. Six feet is just a guideline. But the further you are away from somebody, the better. Now, one thing that isn’t fully appreciated is there’s another component to this probability of getting infected, and that’s time. I was in a grocery store in Flagstaff and I had to go up the cashier and pay for the food, and I was only about two feet away from her. But I tried to make sure I was only two feet away from her for about a minute. And then I got further away.
Dr. Paul Keim explains how labs test for COVID-19 Accordion Closed
Coconino County’s next positive case of the COVID-19 disease is treated the same as its hundreds of negative tests, starting as a nasal swab and confirmed in a biosecurity lab a few days later.
As of Saturday night, the county reported 60 confirmed cases with 21 cases in Flagstaff and 14 in Page. The county is currently reporting positive cases at a rate of 11.5%, meaning about 60 of 520 total samples, including pending tests, taken from people who are symptomatic test positive for COVID-19.
Recipient of 2020 Viola Legacy Award, Dr. Paul Keim Accordion Closed
Paul Keim is a critical participant in the development of vaccines and has made Flagstaff an international leader in genomic research. He actively works to bridge the gap between Northern Arizona University and the community. And, his work exemplifies science exploration and research that is not as well known to the broader public in Flagstaff.
NAU, community partners share updates on latest coronavirus information Accordion Closed
As coronavirus (COVID-19) diagnoses become more widespread, Northern Arizona University is focused on protecting its campus communities against the disease and concerns surrounding health and safety.
This week, President Rita Cheng gathered a panel of experts from NAU and local health organizations to share the most current information regarding the disease, discuss protocols and address questions.
Three PMI Employees honored at 2020 NAU Years of Service ceremony Accordion Closed
The 2020 Years of Service ceremony celebrated career milestones for nearly 150 Northern Arizona University staff and faculty on Jan. 9. These individuals have given 15-40 years of service to NAU.
Those recognized from PMI:
NAU breaks into top 200 for nationwide ranking of all elite research universities Accordion Closed
For the first time in its 120-year history, Northern Arizona University broke through the country’s top 200 research universities, reaching No. 196 in the National Science Foundation’s (NSF) national research rankings.
According to just-released NSF rankings, which take into account research expenditures, NAU also rose to No. 93 for universities without a medical school and No. 75 in the nation for public institutions without a medical school.
The NSF’s Higher Education Research and Development (HERD) annual survey ranks more than 900 colleges and universities and is the primary source of information on research and development expenditures.
NAU’s climb is attributed to a 15 percent increase in research expenditures from 2017 to nearly $53 million in 2018.
Breaking into these elite ranks has been an important goal for President Rita Cheng since arriving at NAU in 2014. She says it represents the university’s commitment to and investment in research that is vital to students, faculty and the state.
“These rankings reflect the achievements of NAU’s world-class faculty, dedicated research and support staff and talented graduate and undergraduate students,” Cheng said. “These rankings also are attributed to the vision and determination of academic and research leadership throughout the NAU campus.
“I would like to congratulate our expert faculty on this national recognition. They are at the peak of their disciplines and I’m proud of the impact of their work. We are dedicated to teaching students to thrive in this new knowledge and technology-driven economy. Our faculty serve as mentors and role models to our students, a critical component of the graduate and undergraduate learning experience.”
Paul Keim, NAU Regents’ Professor and executive director of the Pathogen and Microbiome Institute and a world-renowned expert on genomic analysis, says he is proud of NAU expanding its boundaries of knowledge in recent years.
“NAU’s research programs have been increasing steadily and consistently over the last few years,” Keim said. “Breaking into the top 100 is the result of hard work and perseverance by the entire NAU research community. Our advances are sustainable and will continue well into the future.”
PMI Associate Director, Dr. Faith Walker; Forestry Professor, Dr. Carol Chambers; and the BEGL team expand the answers we can get from bat guano through new research Accordion Closed
Here’s the thing about bats: They can fly. And they do that in the dark.
Those two factors make bats, which make up 20 percent of the mammal species, extremely difficult to study.
Geneticist Faith Walker and wildlife ecologist Carol Chambers wanted a better look at the 1,406 known species of bats, so after years of trying to meet the bats where they were, the two Northern Arizona University researchers instead turned to what the bats left behind: feces. Research into bat guano led to the creation of the Species from Feces assay, which can test DNA from bat guano and tell the researchers which species of bats live in a particular area.
“Poop doesn’t fly around in the dark and it’s easy to collect,” said Walker, who along with Chambers is co-director of the Bat Ecology and Genetics Lab at NAU. “You can walk around in the day with a collection kit in one hand and a cup of coffee in the other and sample in 10 leisurely minutes, instead of the tour de force required by mist netting (when we net bats we often have four cars, eight people and are out until midnight eating Oreos to stay awake). Hence, the fecal method is friendlier to bats and us, and it gives a broader timeframe for the bat species that were using a roost.”
PMI Director, Dr. Greg Caporaso and his team awarded Chan Zuckerberg grant Accordion Closed
Even as NAU associate professor Greg Caporaso and his team were putting the final touches on their QIIME 2™ paper, published earlier this year, he was already planning several major enhancements to this open source and free bioinformatics software that enables scientists to perform microbiome analysis from increasingly large amounts of DNA sequencing and other data.
Caporaso submitted a proposal to the Chan Zuckerberg Initiative’s (CZI) new Essential Open Source Software for Science funding program, which, according to its website, was launched “to provide one-year grants to support software maintenance, growth, development and community engagement for critical open source tools.”
Today, Caporaso was awarded a $150,000 grant by CZI for the one-year project, with an opportunity to reapply for renewal for a second year.
“This project is directly aimed at building a more diverse community of users and developers by making it easier for microbiome scientists and software developers around the world to learn and contribute to QIIME 2,” Caporaso said. “We’re very excited about the new functionality that this grant will enable, and honored to be selected for funding in the first round of this new program.”
NAU Associate Professor of Biological Sciences and PMI Assistant Director, Jeff Foster, collaborates on major genetic study of white-nose syndrome in bats Accordion Closed
Often maligned and largely misunderstood throughout history, bats have more recently been recognized for the important role they play in ecosystems all over the world, pollinating flowers, dispersing seeds and controlling pests by eating insects.
But many North American species are now threatened by white-nose syndrome (WNS), a deadly fungal disease affecting millions of bats, primarily in the eastern US. The Ecology and Evolution of Infectious Diseases program of the National Science Foundation (NSF) is funding two major research projects investigating the disease in hopes of preventing the potential extinction of some species in the region.
One such project, led by infectious disease ecologists Kate Langwig and Joseph Hoyt from Virginia Tech, is funded through a $2.9 million joint award from the NSF and the National Natural Science Foundation of China to understand the long-term host and pathogen dynamics of WNS in bats.
Northern Arizona University wildlife disease ecologist Jeff Foster received a $563,000 subaward to collaborate with Langwig, Hoyt and several other scientists on the five-year project. Other collaborators are Beth Shapiro and A. Marm Kilpatrick from the University of California Santa Cruz and Jiang Feng and Keping Sun from Northeast Normal University in China. At NAU, Foster’s team includes lab manager Katy Parise and a graduate student Foster will be hiring to assist on the project.
On April 5th, 2019, the Keim Genetics Lab celebrated 30 years of cutting edge research. Check out the Inside NAU video about this big event Accordion Closed
NAU maintaining lab safety Accordion Closed
Ever since the lab of world-renowned pathogen geneticist Paul Keim was temporarily closed in 2010, Northern Arizona University’s biosafety and security practices have been as airtight as the suits worn by researchers entering this research space, the highest security lab on campus.
Chris Keefe, a PMI Undergraduate Researcher in Dr. Greg Caporaso’s lab, talks about using bioinformatics to find connections between gut microbiome and Alzheimer’s Accordion Closed
Chris Keefe is blending his passions for biology and computer science to help tackle the sixth leading cause of death in the United States—Alzheimer’s disease. To do that, he is using microbiome bioinformatics and computer software development to investigate the connections between the disease’s symptoms and the bacteria that live in the intestines of mice.
“We know that there are pretty strong connections between the gut microbial communities in mammals and the central nervous system’s behavior and health,” Keefe said. “And based on that, we’re essentially exploring whether the critters in our gut—or in the case of this specific study, in mouse models—are causing Alzheimer’s disease or exacerbating symptoms.”
Mosquito smoothie on the menu? Mentors inspire undergraduate researcher to focus on mosquito-borne viruses Accordion Closed
Despite the fact that Daryn Erickson’s research regularly involves making what she refers to as “mosquito smoothies”—preparing mosquito samples in the blender for testing–she loves her work. She has been working at NAU’s Pathogen and Microbiome Institute (PMI) for two years testing mosquitoes for the viruses that cause West Nile, Zika and dengue fever.
Erickson, who is majoring in microbiology and minoring in chemistry, will graduate in December. When she began her research, she worked with assistant professor Crystal Hepp to test Culex mosquitoes to identify the different strains of West Nile circulating in the Southwest.
Crystal Hepp and her team find two samples of West Nile in Coconino County came from different sources Accordion Closed
After sequencing more than 400 different genomes of the West Nile Virus, an NAU scientist discovered the two reports of West Nile Virus in Coconino County came from two different places. One migrated north from the Phoenix area. The other is a bit more of a mystery.
It started with samples from throughout the western United States arriving at the lab of evolutionary biologist Crystal Hepp, who works with both the School of Informatics, Computing, and Cyber Systems and the Pathogen and Microbiome Institute at Northern Arizona University. She collaborates with a dozen different public health departments throughout the West. They send her West Nile (WNV) samples found in their areas, and her team sequences the viral genomes and analyzes the data to reconstruct each sample’s family tree, which allows her to determine how the virus is moving over time and throughout the region.
NAU researchers receive grants to study threatened, endangered species in American Southwest Accordion Closed
Three Northern Arizona University professors received grants through the Arizona Game and Fish Department to research ways to help threatened animal species in Arizona survive.
The grants—$67,000 to Joe Mihaljevic’s lab and $71,000 to Carol Chambers‘ and Faith Walker’s lab—are both part of the Identification, Inventory, Acquisition, Protection and Management of Sensitive Habitat sub-category. Competitive Heritage Fund grants go toward conservation efforts to protect endangered or threatened species.
The grants also provide opportunities for graduate and undergraduate students to conduct lab and field work, gaining hands-on experience while contributing to creating healthy ecosystems throughout the state.
QIIME 2: PMI Director, Dr. Greg Caporaso and his team reengineer bioinformatic software for next generation of microbiome science Accordion Closed
In the last 20 years, rapid advances in DNA sequencing and bioinformatics technologies have significantly improved scientists’ understanding of the microbial world. Examples include increased knowledge about the vast diversity of microorganisms; how microbiota and microbiomes impact disease and medical treatment; how microorganisms impact the health of our planet; and the potential for applications of microbiome biotechnology in the medical, forensic, environmental and agricultural fields.
In 2009, Northern Arizona University associate professor Greg Caporaso of the Center for Applied Microbiome Science, part of the Pathogen and Microbiome Institute—who was at that time working as a postdoctoral scholar in Rob Knight’s laboratory, then at the University of Colorado at Boulder—led the development of the first open-source QIIME (Quantitative Insights Into Microbial Ecology) bioinformatics software platform under Knight’s guidance. An announcement of the software launch was published in Nature Methods in 2010. The software enables scientists to perform microbiome analysis from increasingly large amounts of DNA sequencing data, and was designed to take users from raw sequencing data through publication-quality graphics and statistics.
PMI’s Executive Director Dr. Paul Keim shares his experience in forensics on the Science History Podcast. Accordion Closed
Keim, a Regents professor of biology and director of the Pathogen and Microbiome Institute at Northern Arizona University, shared his experience in forensics with fellow biology professor Frank von Hippel, an ecotoxicologist who hosts the monthly Science History Podcast.
PMI Executive Director Paul Keim traveled to South Korea to speak about the growing dangers of Botox production. Accordion Closed
Professor of biological sciences and PMI Executive Director Paul Keim traveled to South Korea to meet with Wonjong Jang, head of the Korean Biological Safety Association and professor at Konkuk University, and to speak about the growing dangers of Botox production in South Korea. Keim was highlighted in Pulse, the country’s major business publication.
Crystal Hepp, assistant professor in SICCS and PMI Affiliate Researcher, published Accordion Closed
Crystal Hepp, assistant professor in the School of Informatics, Computing, and Cyber Systems, published “Phylogenetic analysis of West Nile Virus in Maricopa County, Arizona: Evidence for dynamic behavior of strains in two major lineages in the American Southwest” in the peer-reviewed journal PLOS ONE. The paper examines whether cases of West Nile Virus in Maricopa County are endemic or imported each year.
Greg Caporaso of the Pathogen and Microbiome Institute was included on the Highly Cited Researchers of 2018 list Accordion Closed
Greg Caporaso of the Pathogen and Microbiome Institute was included on the Highly Cited Researchers of 2018 list released by Clarivate Analytics. The list, drawn from the top 1 percent of scientific citations over the last decade, offers a benchmark of researchers’ influence within and across 21 scientific fields. Caporaso was recognized for his publications in microbiology.
PMI researchers Dr. Jeffrey Foster and Katy Parise found previously unknown connections can spread diseases between species Accordion Closed
Researchers have long known how diseases are spread, most of which involve contracting germs through air, feces, mucus membranes, blood or other bodily fluids. But because germs are naked to the human eye, seeing the process in which these pathogens move has remained a mystery. Until now.
A team of biologists from several institutions throughout the United States, including Northern Arizona University researchers Jeffrey Foster and Katy Parise, looked at disease transmission in bats. What they found revealed previously unknown connections can spread diseases between species and lead to large-scale outbreaks, like white-nose syndrome—responsible for killing millions of North American bats since 2006.
PMI’s Dr. David Wagner receives $2.25 million grant to study potential biological warfare agent Accordion Closed
Francisella tularensis is one of the most infectious pathogenic bacteria known to science—so virulent, in fact, that it is considered a serious potential bioterrorist threat. Humans can contract respiratory tularemia—a rare and deadly disease—by inhaling as few as 10 airborne organisms.
Northern Arizona University professor David Wagner, director of the Pathogen and Microbiome Institute’s (PMI) Biodefense and Disease Ecology Center, was recently awarded a $2.25 million grant by the U.S. Defense Threat Reduction Agency (DTRA) for a three-year project to better understand the life cycle and behavior of F. tularensis.
Wagner, who has been performing advanced DNA “fingerprinting” of this pathogen for almost 15 years, said that because some countries have developed biological warfare agents based on F. tularensis, it is imperative that the U.S. government develop the tools and knowledge to protect Americans from this potential threat.
“This project is critical to the science of countering weapons of mass destruction because F. tularensis is a potential biological warfare agent and its natural life cycle is poorly understood,” Wagner said.
Hyenas, hippos and lions joined PMI’s Dr. Faith Walker’s inaugural study abroad class in Zambia Accordion Closed
For most of us, seeing lions on an African safari would rank as the highlight of the trip, if not the year.
Seeing them defecate? Not so much. But that is the first moment Northern Arizona University wildlife geneticist Faith Walker recollects when she talks about her trip to Zambia in June.
Oh, and seeing a pride of lions take down a puku later that night was pretty cool, too. Two safari jeeps filled with NAU faculty and students sat quietly and watched the circle of life.
It wasn’t the typical study abroad or research experience, perhaps, but it was the trip of a lifetime.
PMI’s Dr. Faith Walker, along with School of Forestry professor Carol Chambers, led a group of students—four undergraduates and grad student Dan Sanchez—halfway around the world to experience what only Africa has to offer. They spent a week at Zikomo Safari Lodge near Mfuwe, outside South Luangwa National Park, exploring the park, doing non-invasive research on the wildlife and learning about Africa’s conservation history and challenges. Thanks to an NAU grant, they also got to donate school supplies to local schoolchildren and help with an unusual two-pronged economic development program in the village.
PMI’s Dr. Jason Ladner on international study reporting first known case of virus transmission from female Ebola survivor Accordion Closed
According to the Centers for Disease Control and Prevention (CDC), the 2014-2015 outbreak of Ebola virus disease in Western Africa was unprecedented, with 28,000 cases killing more than 11,000 people in Liberia, Guinea and Sierra Leone.
While Ebola virus is typically spread through the bodily fluids of symptomatic individuals, the virus can persist in some compartments of the body, such as the male reproductive system. In several cases, sexual transmission from these persistent infections has resulted in the renewed spread of Ebola virus disease in Western Africa.
A new study recently published in The Lancet Infectious Diseases, however, reports on the first known case of Ebola virus transmission from a female Ebola survivor. Northern Arizona University geneticist Jason Ladner, assistant director of The Pathogen and Microbiome Institute, is a joint first author of the study, along with colleagues on an international team of scientists from organizations including the CDC, the National Institutes of Health, the World Health Organization, the U.S. Army Medical Research Institute of Infectious Diseases and the International Rescue Committee.
“This investigation underscores the need for focused prevention efforts among survivors, as well as sustained capacity to rapidly detect new cases, in order to prevent further spread of the virus following an outbreak,” Ladner said.
NAU makes history with three students chosen as Goldwater Scholars, two from PMI Accordion Closed
For the first time in the school’s history, three Northern Arizona University students have been selected as Goldwater Scholars.
The prestigious award, given to undergraduate students studying natural sciences, mathematics or engineering, provides one- or two-year full-ride scholarships to each of the recipients.
This year, 1,280 STEM students were nominated by campus representatives from more than 2,000 colleges and universities nationwide. Among the 211 selected to receive scholarships for the 2018-19 academic year were NAU biology students Austin Dikeman and Shelby Hutton and mechanical engineering student Dan Rivera. An additional 281 nominees were named as honorable mentions.
“This says a lot about the caliber of students at NAU,” NAU President Rita Cheng said. “I could not be prouder of these Lumberjacks for I know they will continue to accomplish nothing but great things. Hurrah for NAU!”
PMI’s Dr. Emily Cope uses microbial sequencing to understand and treat respiratory diseases Accordion Closed
According to the Centers for Disease Control and Prevention, more than 16 percent of adults in the United States have been diagnosed with chronic rhinosinusitis, or CRS—commonly defined as a sinus infection and inflammation that lasts more than 12 weeks. Not only do CRS patients report a significantly worse quality of life than those with asthma, congestive heart failure and chronic back pain, but the disease results in $65 billion per year in health care costs. Yet, despite the substantial socioeconomic impact of sinonasal inflammation, its underlying cause is not well understood.
Emily Cope, an assistant professor of microbiology and assistant director of the Pathogen and Microbiome Institute at Northern Arizona University, is out to change that with her research.
“The goals of my lab are to first understand the biology of the airway and the microbiome in the context of human health and disease and then to use that knowledge to develop new therapeutics, such as microbial therapies—prebiotics or probiotics—to help treat CRS and asthma,” Cope said.