News Listing

Dear Colleagues:

With great sadness, I write to inform you of the sudden passing of Dr. James Champoux, professor and former chair of the UW School of Medicine Department of Microbiology. He died on Monday [May 13, 2019], a week after being diagnosed with pancreatic cancer, at the age of 76.

Dr. Champoux was appointed department chair in October 2007, after serving twice before as interim chair, and he continued in that role until earlier this year. He was dedicated to his colleagues, truly generous in his service to the School of Medicine, and justifiably proud to lead one of the premier biological science departments in the country.

The Department of Microbiology has a national reputation for high-quality teaching and an international reputation for excellence in research. In the most recent U.S. News & World Report rankings, the department is No. 2 in the nation for best graduate programs in microbiology and No. 4 in the world among global universities.

A Seattle native, Dr. Champoux was part of the first group of students admitted to the University of Washington Honors Program when it was founded in 1961. After graduating with a major in chemistry, he completed his doctorate degree in biochemistry at Stanford University in 1970.

Dr. Champoux’s early career coincided with the biology revolution that began in the 1970s — a time when rapid advances in microbiology and the development of biotechnology were starting to increase our understanding of all living systems. He made his first contribution to this revolution during a postdoctoral fellowship at the Salk Institute in San Diego when he discovered an enzyme called DNA topoisomerase I while working with Nobel Prize recipient Renato Dulbecco.

When Dr. Champoux returned home to join the UW Department of Microbiology faculty in 1972, he embarked on an illustrious academic career that continued for the next 47 years. During this time, he made major contributions to our understanding of oncogenesis and viral infections through his research on enzymes and retroviruses.

Dr. Champoux published more than 125 papers, and he was recognized with numerous honors, including a Guggenheim Fellowship (1980-81) and the prestigious NIH Merit Award (1998). He was elected by his peers to be a fellow of the American Academy of Microbiology (2005) and a member of the Washington State Academy of Sciences (2010). More recently, he was named a fellow of the American Association for the Advancement of Science (2017).

As department chair, Dr. Champoux recruited six new faculty members and worked to increase diversity among our faculty and graduate students. He was committed to excellence in education and exemplified this important faculty role as a wonderful teacher of undergraduate and graduate students. In 1985, he won the UW Distinguished Teaching Award.

The news of Dr. Champoux’s unexpected passing has been received by all of his colleagues with shock and sadness. On their behalf, I want to extend our deepest sympathies to his wife, Sharon, and daughter, Katie, on their profound loss. We are very fortunate that Dr. Champoux chose to spend his faculty career in the Department of Microbiology. He will be greatly missed.

 

Sincerely,

Paul G. Ramsey, M.D. 
CEO, UW Medicine 
Executive Vice President for Medical Affairs and 
Dean of the School of Medicine, 
University of Washington

This article describes the recent FDA approval of the anti-TB agent pretomanid, and it’s use in a novel regimen that is saving lives of multiply-drug resistant (MDR) TB patients in South Africa. Department of Microbiology Professor and Chair David Sherman played a major role in the early stage development of pretomanid.

Fang Lab Members publish in Cell Host and Microbe:

 

Salmonella enterica serovar Typhi causes typhoid fever only in humans. Murine infection with S. Typhimurium is used as a typhoid model, but its relevance to human typhoid is limited. Non-obese diabetic-scid IL2rγnull mice engrafted with human hematopoietic stem cells (hu-SRC-SCID) are susceptible to lethal S. Typhi infection. In this study, we use a high-density S. Typhi transposon library in hu-SRC-SCID mice to identify virulence loci using transposon-directed insertion site sequencing (TraDIS). Vi capsule, lipopolysaccharide (LPS), and aromatic amino acid biosynthesis were essential for virulence, along with the siderophore salmochelin. However, in contrast to the murine S. Typhimurium model, neither the PhoPQ two-component system nor the SPI-2 pathogenicity island was required for lethal S. Typhi infection, nor was the CdtB typhoid toxin. These observations highlight major differences in the pathogenesis of typhoid and non-typhoidal Salmonellainfections and demonstrate the utility of humanized mice for understanding the pathogenesis of a human-specific pathogen.

Dr Rudy Urbano, a recent graduate of our program, has just been awarded a prestigious Hanna Gray Fellowship from the Howard Hughes Medical Institute. Dr Urbano was a member of Dr Ferric Fang's Lab and defended in Autumn 2017. 

As part of our long-term recruiting objectives, the Department of Microbiology at the University of Washington (https://microbiology.washington.edu ) has openings for three full-time positions at the rank of Assistant Professor tenure-track and one position at the rank of Associate Professor with tenure or Full Professor with tenure commensurate with experience. Successful candidates will perform research in any area of microbiology (bacteria, protisist or viruses), including but not limited to bacterial development or behavior, virus biology or pathogenesis, microbial evolution, structural microbiology, host-microbe interactions, or microbiome studies.
We offer the opportunity to join a vibrant and diverse group of researchers at the UW, its affiliated hospitals and the wider Seattle biomedical research community. The successful candidates will find highly interactive colleagues applying a wide range of approaches to fundamental microbiology, mechanisms of microbial-host interactions, and to the development of antimicrobial strategies.
The openings are 12-month service period positions in the School of Medicine with an anticipated start date of Fall 2020. In addition to research, our faculty teach outstanding trainees at the undergraduate, graduate and post-graduate levels, and engage widely in service activities.

Qualifications:
Candidates for this position must hold a PhD degree in microbiology or related discipline and/or MD, (or foreign equivalent), and have a strong record of graduate and postdoctoral experience and publication. In order to be eligible for University sponsorship for an H-1B visa, graduates of foreign (non U.S.) medical schools must show successful completion of all three steps of the U.S. Medical Licensing Exam (USMLE) or equivalent as determined by the Secretary of Health and Health and Human Services.
Application Instructions:
To apply, submit a cover letter, C.V. (including a full bibliography), a concise one-page summary of research accomplishments, and a two-page summary of future research interests through our web portal: http://apply.interfolio.com/68306. Applicants should also arrange for three letters of recommendation from reviewers who will receive separate instructions sent automatically by Interfolio.
Applications received by November 15 will receive a full review by the search committee. Short-listed candidates will be invited to visit the department early in 2020.

Prof. Daniel Wozniak, Prof Doriano Lamba and UW Microbiology's own Dr Matt Parsek were awarded the XXVII International
Prize "Saint Francis and Claire of Assisi" -  Science and Research section for our collaborative work on biofilm matrix proteins.

Dr. Michael Lagunoff was elected as a fellow of the American Association for the Advancement of Science (AAAS fellow).  The council elects members whose “efforts on behalf of the advancement of science or its applications are scientifically or socially distinguished”. Dr. Lagunoff was honored “for contributions to how viral infections cause cancer including demonstration that Kaposi’s Sarcoma herpesvirus activates oncogenic cell signaling pathways”.  He will receive his award in February as part of the Associations annual meeting.

All Microbiology classes will be taught online effective 3/9/20 through the end of Winter quarter. Please visit your class canvas page or contact your instructors for information on how to connect to online classrooms via Zoom. UW plans to resume normal class operations when the spring quarter begins March 30, pending public health guidance. UW provides daily updates and FAQs on COVID-19.

 

How the retired professor and department chair continues shaping the field — and UW Medicine.

It’s a Friday afternoon, but Eugene Nester, PhD, is still in the office. Although he’s retired, the professor emeritus of microbiology comes in regularly to review grant proposals and read up for his science discussion group — everything from math to oceanography. If he’s not in his office, you might find him volunteering at the Burke Museum, learning about dinosaurs or Native American basketry in order to answer visitors’ questions. Nester’s irrepressible curiosity has always led him to explore other disciplines, a habit that has served him well throughout a long and successful career.

A lifelong love of microbiology
Nester first became interested in microbiology in his teens, partly influenced by popular books like Arrowsmith and Microbe Hunters. “They influenced a lot of people who ended up going into microbiology by pointing out just how exciting a field it was,” says Nester.

After graduating with a bachelor’s degree in microbiology from Cornell, Nester was drafted into a biological warfare unit of the U.S. Army. Before his military service, he had planned to study food microbiology at graduate school in Wisconsin, but after his discharge, he decided to study genetics and biochemistry at Case Western Reserve University instead. It was there he met his wife Martha, a future elementary school science teacher.

By the time Nester finished his postdoctoral training at Stanford, they were ready for a change of scenery, and he accepted a position with the UW School of Medicine’s Department of Microbiology. “The future looked brightest here,” says Nester. “It was a relatively new medical school with an excellent microbiology department, and I felt that I could do good science here with the collegial support that the UW and the department offered.”

Throughout his career, Nester found a supportive and creative environment that welcomed interdisciplinary collaboration and his curiosity, both of which he nurtured during his years as a professor and department chair.

“Microbiology has a tremendous range of interests,” he says. “There are a lot of cross-disciplinary areas, so you have collaborations with people in biochemistry, genetics and computer science.”

A life-changing collaboration
One such partnership developed into his life’s work: the bacterium Agrobacterium.

It began when Nester’s curiosity turned to crown gall disease — specifically, how Agrobacterium caused the disease. Crown gall is caused by Agrobacterium infecting the plant, but killing the Agrobacterium doesn’t cure the disease.

“After a day or so, you could kill the Agrobacterium, but the disease would continue anyway,” says Nester. “So what is the mechanism by which it causes disease?”

Nester teamed up with biochemist Milt Gordon, PhD, and molecular geneticist Mary-Dell Chilton, PhD ’71. They discovered that Agrobacterium transferred and inserted its own DNA into the plant’s cell, becoming part of the plant’s genome. And, by adding DNA from other organisms to the transferred DNA, researchers could genetically modify the host plant.

It was the first step forward in the genetic engineering of plants. Their discovery would have an enormous impact on the ability to genetically modify plants for decades to come — both in scientific research and at the grocery store.

“The three of us combined had the expertise,” says Nester. “None of us singly could have done it, for sure. In addition, our research program was greatly enhanced by an amazing group of collegial undergraduate, graduate and post-doctoral trainees, most of whom have gone on to successful scientific careers.”

It’s that type of interdisciplinary cross-fertilization, agrees his wife, Martha, that they appreciated so much during his career and that they want to continue to encourage.

That’s why the Nesters decided to make a very special gift to the Department of Microbiology: an endowed professorship. They hope that their newly created endowment will help the department attract and retain top faculty with a commitment to cross-collaboration.

“It’s an outstanding department, and we wanted to help build on the quality that is already here,” says Nester. “Excellent faculty will attract outstanding grad students and postdocs.”

And, of course, excellent collaborations.

As of 3/16/2020, our office operations have moved online. Department Admin staff is available via email/phone and the student advisor (Andrea Pardo) is available via phone or zoom appointment. Please refer to the directory page if you would need a specific person's contact information. 

One concise place for all of your UW related Covid-19 questions including childcare, parking, and research efforts.

Spring quarter will begin with remote instruction on March 30, with fully remote instruction continuing through the end of spring quarter. There will be no in-person classes this spring.

 

Three undergraduate students at the University of Washington are among 396 around the country who have been named Goldwater Scholars for 2020.

The Goldwater Scholarship Program supports undergraduates who “show exceptional promise of becoming this nation’s next generation of research leaders” in science, technology, engineering and mathematics. The scholarships go toward tuition, room and board, fees and books up to $7,500 annually for one or two years.

The 2020 Goldwater Scholars from the UW are Keyan Gootkin, Parker Ruth and Karen Zhang.

Pictures of three students who received Goldwater Scholarships at the University of Washington.

 

Gootkin, Ruth and Zhang.University of Washington

  • Gootkin, who is majoring in astronomy and physics, studies how massive stars end their lives and volunteers with the Theodor Jacobsen Observatory, the League of Astronomers, and the UW’s campus and mobile planetariums.
  • Ruth is pursuing a double major in bioengineering and computer engineering, and studies computational tools to improve health care access. Ruth plans to pursue a doctoral degree in computer science.
  • Zhang, who is studying both microbiology and biochemistry, is interested in “the machineries of life at a molecular level and engineering them to perform novel tasks,” and after graduation would like to obtain a doctoral degree in either bioinformatics or synthetic biology.

The 2020 Goldwater Scholars were selected from a pool of more than 5,000 undergraduate students nominated by 461 academic institutions. A majority of this year’s awardees, 287, are studying the natural sciences, while 59 are majoring in engineering and 50 are majoring in mathematics or computer science. Most say that they intend to pursue a doctoral degree.

The Barry Goldwater Scholarship and Excellence in Education Program was established by Congress in 1986 to honor Barry Goldwater, a five-term senator from Arizona and Air Force Reserve major general. Since 1989, the program has provided 9,047 scholarships totaling more than $71 million dollars.

The University of Washington Population Health Initiative announced the award of approximately $350,000 in COVID-19 rapid response grants to 21 different faculty-led teams. These teams are composed of individuals representing 10 different schools and colleges. Funding was partially matched by additional school, college and departmental funds, bringing the total value of these awards to roughly $820,000.

“A challenge of this magnitude requires us to draw upon the breadth of the university’s expertise to respond, and the range of innovative, collaborative project ideas that were quickly developed for this funding call was both impressive and truly inspiring,” shared Ali H. Mokdad, the university’s chief strategy officer for population health and professor of health metrics sciences. “We believe the 21 projects selected for funding are all well positioned to rapidly accelerate our understanding of, or approach to mitigating, the impacts of this pandemic, which is touching every aspect of our lives.”

The Population Health Initiative COVID-19 rapid response research grants are intended to rapidly accelerate, or jumpstart, novel research designed to better understand or mitigate the impact of COVID-19 on multiple facets of life.

 

Investigators
James I Mullins, Professor, Department of Microbiology
Deborah H. Fuller, Professor, Department of Microbiology
Jesse Erasmus, Postdoctoral Scholar, Department of Microbiology
Jim Fuller, Research Scientist, Department of Microbiology

Project abstract
Nearly all SARS-CoV-2 vaccines efforts are aimed at directing neutralizing antibodies (NAb) towards the viral Spike protein, intended to block the virus from entering cells through its normal receptor. However, these same Spike-directed NAb also have the potential to facilitate viral entry into immune cells through a different receptor, which can lead to Antibody Dependent Enhancement (ADE) of infection and disease. Antibodies from SARS virus infected persons induce ADE in cell culture but it is unclear if this occurs in people. Furthermore, we do not know how much the Spike gene might evolve before possibly returning with new waves of infections. Hence, new Spike vaccines may need to be developed each year the virus returns, as is needed to fight influenza.

We therefore need to rapidly develop alternative vaccines to stop COVID-19 pandemics from current and mutated strains that might circulate in future years. To this end, we designed vaccines to Focus Immune Responses on the Structural inTegrity (FIRST) of SARS-CoV-2 viral proteins. FIRST vaccines are intended to drive T cell and antibody responses that avoid antigenic features of each protein most likely to result in ADE while targeting features unlikely to change rapidly. Here, we will determine the expression of FIRST immunogens in cells and immune responses elicited in mice following delivery as RNA. Subsequently, lead immunogens will be tested with alternative delivery platforms to enable greater stability, lower manufacturing costs and needle free vaccination and a lead formulation selected to take forward into non-human primates and clinical trials.

Monica Cesinger and Brittany Ruhland (both graduate students in the Reniere Lab) have first author papers accepted recently and will be published in the next few weeks. Brittany also had her painting accepted to be on the cover of the journal! According to Dr Reniere, "The watercolor painting by Brittany R. Ruhland represents the interaction between Spx (teal, left) and YjbH (pink, right). We found that the Listeria monocytogenes YjbH protein physically interacts with SpxA1. This watercolor will appear on the cover of the Journal of Bacteriology, vol. 202, no. 12."

Congratulations Monica and Brittany! To see the online publications of these articles, please follow the links below:

Brittany’s paper: https://jb.asm.org/content/early/2020/03/31/JB.00099-20

Monica’s paper: https://onlinelibrary.wiley.com/doi/10.1111/mmi.14508