Department of Microbiology – UW News /news Thu, 19 Jun 2025 03:43:17 +0000 en-US hourly 1 https://wordpress.org/?v=6.9.4 UW is the No. 8 university in the world, according to new US News & World Report rankings /news/2025/06/18/uw-is-the-no-8-university-in-the-world-according-to-new-us-news-world-report-rankings/ Wed, 18 Jun 2025 22:24:55 +0000 /news/?p=88435
The UW is No. 8 on the 2025-26 U.S. News & World Report鈥檚 Best Global Universities rankings. Photo: 天美影视传媒

The 天美影视传媒 is No. 8 on the 2025-26 U.S. News & World Report鈥檚 Best Global Universities rankings, 聽on Tuesday. The UW maintained its No. 2 ranking among U.S. public institutions.

The UW also placed in the top 10 in eight subject areas ranked by U.S. News.

Harvard University, Massachusetts Institute of Technology and Stanford University topped the list in that order. The University of Oxford is No. 4, followed by University of Cambridge, the University of California, Berkeley, University College London and the UW. Yale University and Columbia University rounded out the top 10.

鈥淯nquestionably, the UW is advancing discovery that saves and improves lives, promotes prosperity, makes our nation stronger and expands human knowledge for the good of all,鈥 said UW President Ana Mari Cauce. 鈥淚鈥檓 very proud to see this extraordinary impact recognized through this latest ranking.鈥

The U.S. News ranking聽聽鈥斅燽ased on data and metrics provided by Clarivate 鈥 weighs factors that measure a university鈥檚 global and regional research reputation and academic research performance. For the overall rankings, this includes bibliometric indicators such as the number of publications, citations and international collaboration.

The overall Best Global Universities ranking encompasses 2,250 institutions spread across 105 countries, according to U.S. News.

Here are the UW fields of study that are in the top 10 in U.S. News鈥 subject rankings:

Molecular biology and genetics 鈥 No. 6

Clinical medicine 鈥 No. 6

Public, environmental and occupational health 鈥 No. 6

Microbiology 鈥 No. 7

Biology and biochemistry 鈥 No. 8 (up from 9)

Infectious diseases 鈥 No. 9

Marine and freshwater biology 鈥 No. 9

Social sciences and public health 鈥 No. 9

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ArtSci Roundup: June 2025 /news/2025/05/23/artsci-roundup-june-2025/ Fri, 23 May 2025 21:35:36 +0000 /news/?p=88071

From campus to wherever you call home, we welcome you to learn from and connect with the College of Arts & Sciences community through public events spanning the arts, humanities, natural sciences, and social sciences. We hope to see you this June.


ArtSci on the Go

Looking for more ways to get more out of Arts & Sciences? Check out these resources to take ArtSci wherever you go!

Zev J. Handel, “Chinese Characters Across Asia: How the Chinese Script Came to Write Japanese, Korean, and Vietnamese”聽()

Black Composers Project engages the School of Music faculty and students ()

Ladino Day Interview with Leigh Bardugo & MELC Professor Canan Bolel ()

Back to School Podcast 聽with Liz Copland ()


Featured Podcast: “Ways of Knowing” (College of Arts & Sciences)

This podcast highlights how studies of the humanities can reflect everyday life. Through a partnership between and the 天美影视传媒, each episode features a faculty member from the UW College of Arts & Sciences, who discusses the work that inspires them and suggests resources to learn more about the topic.

Episode 1: Digital Humanities with assistant professor of English and data science, Anna Preus.

Episode 2: Paratext with associate professor of French, Richard Watts.

Episode 3: Ge’ez with聽associate professor of Middle Eastern languages and cultures, Hamza Zafer.


Closing Exhibits

: Christine Sun Kim: Ghost(ed) Notes at the Henry Art Gallery

Week of June 2

Prof. Daniel Bessner

Monday, June 2, 5:00 – 6:20 pm | ONLINE ONLY: (Jackson School)

Join the Jackson School for Trump in the World 2.0, a series of talks and discussions on the international impact of the second Trump presidency.

This week: Daniel Bessner; Anne H.H. and Kenneth B. Pyle Associate Professor in American Foreign Policy at the Henry M. Jackson School of International Studies.


Monday, June 2, 5:00 – 7:00 pm | (Jackson School)

Mediha Sorma, Ph.D

This talk discusses the unconventional forms of care that emerge out of Kurdish resistance in Turkey, where mothering becomes a powerful response against necropolitical state violence. By centering the stories of two Kurdish mothers who had to care for their dead children and mother beyond life under the violent state of emergency regime declared in 2015; the talk examines how Kurdish mothers 鈥渞escue the dead鈥 (Antoon, 2021) from the necropolitical state and create their necropolitical power through a radical embrace of death and decoupling of mothering from the corporeal link between the mother and the child.


Monday, June 2, 3:30 – 5:00 pm | (The Ellison Center for Russian, East European and Central Asian Studies)

Prof. Masaaki Higashijima

Why do some protests in autocracies attract popular participation while others do not? Masaaki Higashijima’s, University of Tokyo, paper argues that when opposition elites and the masses have divergent motivations for protesting, anti-regime mobilization struggles to gain momentum. Moreover, this weak elite-mass linkage is further exacerbated when autocrats selectively repress protests led by opposition elites while making concessions to those organized by ordinary citizens.

 


Tuesday, June 3, 5:00 – 6:30 pm | (Communications)

Mary Gates Hall

A conversation with local public media leaders about current challenges–including federal funding cuts–and pathways forward for sustaining public service journalism.

Speakers include:

Rob Dunlop, President and CEO, Cascade PBS
David Fischer, President and General Manager, KNKX
Tina Pamintuan, incoming President and CEO, KUOW
Matthew Powers, Professor and Co-Director, Center for Journalism, Media and Democracy


Wednesday, June 4, 3:30 – 4:30 pm | (Psychology)

Prof. Hadas Okon-Singer

Cognitive biases 鈥 such as attentional biases toward aversive cues, distorted expectations of negative events, and biased interpretations of ambiguity 鈥 are central features of many forms of psychopathology. Gaining a deeper understanding of the neurocognitive mechanisms underlying these biases is crucial for advancing theoretical models and clinical interventions.

In this talk, Prof. Hadas Okon-Singer will present a series of studies exploring emotional biases in both healthy individuals and participants diagnosed with social anxiety, major depressive disorder, and generalized anxiety disorder.


Wednesday, June 4, 12:30 – 1:30 pm | (Center for Statistics & Social Sciences)

Prof. Tyler McCormick

Many statistical analyses, in both observational data and randomized control trials, ask: how does the outcome of interest vary with combinations of observable covariates? How do various drug combinations affect health outcomes, or how does technology adoption depend on incentives and demographics? Tyler McCormick’s, Professor, Statistics & Sociology, 天美影视传媒, goal is to partition this factorial space into “pools” of covariate combinations where the outcome differs across the pools (but not within a pool).


Friday, June 6, 7:30 pm | (School of Music)

David Alexander Rahbee leads the UW Symphony in a program of concerto excerpts by York Bowen, Keiko Abe, and Camille Saint-Sa毛ns, performed with winners of the 2024-25 School of Music Concerto Competitions: Flora Cummings, viola; Kaisho Barnhill, marimba; and Sandy Huang, piano. Also on the program, works by Mikhail Glinka, Richard Wagner, and Giuseppe Verdi.


Saturday, June 7 & Sunday, June 8, 10:00 am – 5:00 pm | (Burke Museum)

Artist Stewart Wong

Stewart Wong will share knowledge and personal experiences about working with Broussonetia Papyrifera. He will talk about the history, uses, and cultivation of the paper mulberry plant. In addition, Stewart plans on dyeing, drawing on, and printing kapa. Stewart will have printed information and material samples to supplement the talk.


Saturday, June 7, 11:00 am – 12:00 pm | On Our Terms with Wakulima USA (Burke Museum)

Join the Burke Museum for a short screening from “,” plus a conversation with co-producer Aaron McCanna and Wakulima USA’s David Bulindah and Maura Kizito about food sovereignty and community building.


Additional Events

June 2 | (Music)

June 2 | (Asian Languages & Literature)

June 2 – June 6 | (Astronomy)

June 3 | (Music)

June 4 | (Music)

June 4 | (Psychology)

June 5 | (Music)

June 5 | (Speech & Hearing)

June 5 | (Labor Studies)

June 5 | (Art + Art History + Design)

June 6 | (Dance)

June 6 | (Geography)

June 7 | (Music)


Week of June 9

Wednesday, June 11 to Friday, June 27 | (Jacob Lawrence Gallery)

At the end of the spring quarter, the academic year culminates in comprehensive exhibitions of design work created by graduating students. The UW Design Show 2025, showcasing the capstone projects of graduating BDes students, will be held from June 11 to June 27 in the Jacob Lawrence Gallery.


Additional Events

June 11 | (Henry Art Gallery)

June 11 | (Art + Art History + Design)

June 12 & June 13 | (DXARTS)

June 13 | (Art + Art History + Design)


Events for the week of June 23

June 24 | (Information Sessions)

June 25 | (Information Sessions)

June 26 | (Information Sessions)

June 27 | (Information Sessions)


Commencement

June marks the end of many College of Arts & Sciences students’ undergraduate experience. Interested in attending a graduation ceremony? Click here to find information on ceremonies across campus.


Have an event that you would like to see featured in the ArtSci Roundup? Connect with Kathrine Braseth (kbraseth@uw.edu).

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Five UW researchers named AAAS Fellows /news/2025/03/27/five-uw-researchers-named-aaas-fellows/ Thu, 27 Mar 2025 14:14:58 +0000 /news/?p=87837 Five portraits surround the text "AAAS Fellows"
Five 天美影视传媒 researchers have been named AAAS Fellows. They are, beginning upper left and across, Celeste A. Berg; Sharon Lafferty Doty; Matthew R. Parsek; Donald L. Chi; and Xiaosong Li.

Five 天美影视传媒 researchers have been named AAAS Fellows, according to a . They are among 471 newly elected fellows from around the world, who are recognized for their 鈥渟cientifically and socially distinguished achievements鈥 in science and engineering. A tradition dating back to 1874, election as an AAAS Fellow is a lifetime honor. All fellows are expected to meet the commonly held standards of professional ethics and scientific integrity.

This year鈥檚 UW AAAS fellows are:

, professor of genome sciences in UW Medicine, was recognized for her distinguished contributions to the field of the evolution of tissue development by signaling pathways and to the training of junior scientists. She studies developmental biology, and her work focuses on the patterns and shapes that appear as an organism forms into a living creature composed of a variety of cell types and organs. Her laboratory models are fruit flies, and her investigations begin in the egg chamber and the laid egg. Among her research interests are cell signals and cell migration critical to development, and the evolution of these processes. In addition, new genomic technologies are enabling her research team to manipulate the timing and location of gene activity within developing fly cells. Berg and her team also have designed a system to obtain live imaging of some of the developmental events that take place. Among Berg鈥檚 overarching goals is to better understand the genetic and molecular dysfunctions that lead to prenatal malformations and other disorders. The hope, Berg says, is that basic research, over the long term, might lead to clinical diagnostics for risk factors and to evaluation of potential treatments. Berg鈥檚 course topics are wide-ranging, and include introductory biology, biomedical ethics and forensic genetics at crime scenes.

, the David R. M. Scott Endowed Professor in Forest Resources and professor of plant microbiology in the UW School of Environmental and Forest Sciences, was recognized for distinguished contributions to unraveling mechanisms by which microbes colonize plants, increase plant growth and yields in nutrient-limited conditions, increase water use efficiency and drought tolerance, and improve plant health. Her research is on the importance of the plant microbiome as a resource for nature-based solutions to environmental challenges including pollution, climate change and colonizing the moon. A UW faculty member since 2003, she has received several awards and honors including the Lockwood Endowed Professorship (2013-2021), Director鈥檚 Faculty Award for 鈥渆xemplary contributions to student mentoring鈥 and the Faculty Member of the Year award (2014). She serves on the executive teams of the International Poplar Commission (Co-Vice Chair, Environmental and Ecosystem Services) and the International Symbiosis Society (VP, Education). She holds an adjunct faculty appointment in the Department of Microbiology.

, professor of microbiology in UW Medicine, was recognized for his distinguished contributions to the field of microbial interactions, particularly with regard to unraveling mechanisms responsible for the formation of surface-attached communities called biofilms. Parsek explores the social biology of bacterial communities. One of his areas of investigation is quorum-sensing 鈥 how bacteria use signaling molecules to sense the presence of others of the same species. This communication system allows them to coordinate their behavior as a group. Another of his related fields of interest is biofilms. These are bacteria that produce an extracellular matrix to bind themselves together. The matrix protects the community and plays a role, for example, in resistance to antimicrobials and antibiotics and in the persistence of chronic infection. Parsek鈥檚 lab studies the composition of this matrix and how it is assembled. They are especially interested in Pseudomonas aeruginosa, which lives in several different environmental niches, but is notorious for infecting the lungs of cystic fibrosis patients and for colonizing burn wounds and growing on implanted biomaterials. In recent work his lab looked at how these bacteria can sense surfaces. A UW faculty member since 2011, Parsek is a member of the American Academy of Microbiology and was named a Kavli fellow by the National Academy of Sciences.

, the Lloyd and Kay Chapman Endowed Chair for Oral Health in the UW School of Dentistry, was recognized for translating knowledge from the behavioral and social sciences to address the causes of children鈥檚 oral health inequities. In recent years Chi has studied why some parents reject fluoride for their children and worked with Yup鈥檌k communities to improve the oral health of Alaska Native children. In 2018 he was named Pediatric Dentist of the Year by the American Academy of Pediatric Dentistry, and in 2025 he received the Presidential Early Career Award for Scientists and Engineers (PECASE) from President Joe Biden. A member of the UW faculty since 2010, Chi is also the associate dean for research in the School of Dentistry and a professor of health systems and population health in the UW School of Public Health. He is editor-in-chief the International Journal of Paediatric Dentistry and treats patients at the Odessa Brown Children鈥檚 Clinic in Seattle.

, the Larry R. Dalton Endowed Chair in Chemistry and associate dean for research in the College of Arts & Sciences, is honored for his contributions to the development and application of time-dependent quantum theory and relativistic electronic structure theory, and for advancing educational pathways and diversity in STEM. Li conducts research at the intersection of physics, chemistry, materials science, mathematics and scientific computing, and he has developed widely used computational software. A UW faculty member since 2005, Li’s honors include a Sloan Research Fellowship, the NSF CAREER Award, the American Chemical Society Jack Simons Award in Theoretical Physical Chemistry and the UW Distinguished Teaching Award. He is a fellow of the American Physical Society (APS) and the Royal Society of Chemistry (RSC), a Lab Fellow at Pacific Northwest National Laboratory and an elected member of the Washington State Academy of Sciences.

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UW鈥檚 Daniel Chen, 鈥22, named prestigious Marshall Scholar /news/2022/12/12/uws-daniel-chen-22-named-prestigious-marshall-scholar/ Mon, 12 Dec 2022 15:00:33 +0000 /news/?p=80232 profile image
Daniel Chen, class of 2022, was selected as a Marshall Scholar. Photo: 天美影视传媒

天美影视传媒 alumnus Daniel Guorui Chen, Class of 2022, has been named a, one of the highest honors available to college graduates in the U.S. Chen plans to attend the University of Cambridge.

鈥淚 was so surprised when I learned I was awarded. This is such an honor,鈥 Chen, 19, said. 鈥淭he Marshall Scholarship is a great example of taking U.S. and U.K. perspectives and putting them together to work and discover and push for better health, not just for these two countries, but for the world at large.鈥

Founded by an act of the British Parliament in 1953, the awards pay all expenses for up to three years of study at a British university of the student鈥檚 choice. Marshall scholarships finance young Americans of high ability to study for a degree in the United Kingdom. This year, 40 scholars were selected to pursue graduate study in any field at a UK institution.

Chen, a Sammamish, Wash., native, graduated with majors in informatics (data science) and microbiology. He plans to pursue a Master of Philosophy degree at Cambridge, delving deeper into biological sciences and genomic medicine. Eventually, Chen hopes to earn an M.D. and a Ph.D., to become a physician-scientist and professor conducting research while practicing in clinic.

profile shot
Daniel Chen Photo: 天美影视传媒

Chen is the first UW student to achieve this honor since Havana McElvaine was selected in 2018. Prior to that, UW鈥檚 Jeffrey Eaton was selected in 2008. This year, 951 students from across the United States applied for the scholarship. Only four candidates from the San Francisco region, which includes Washington, Alaska, Idaho, Montana, Northern California and most of Nevada, were selected.

鈥淒aniel鈥檚 rigorous undergraduate scholarship on topical and complex medical issues is exemplary,鈥 said Ed Taylor, vice provost and dean of Undergraduate Academic Affairs. 鈥淭his recognition will provide a wonderful opportunity for Daniel, who is already dedicated to the medical sciences, to deepen and extend his scholarship.鈥

 

Read more about Chen here.

 

Chen arrived at the UW when he was 14, through the Early Entrance Program. During his undergraduate career, he conducted research at UW and at some of the most prestigious research labs in the Puget Sound region, including聽 the, Institute for Systems Biology and the. Chen鈥檚 research examines how and why some people contract long COVID and what鈥檚 happening at the cellular level. He also conducted single-cell research on pancreatic cancer and COVID-19 patients, and gained experience in bacterial cloning and genetic engineering while working in a medical microbiology lab.

鈥淒aniel is an amazing young scientist,鈥 said James R. Heath, president of the ISB and one of Chen鈥檚 mentors. Chen was the second author out of more than 50 on a research paper, 鈥,鈥 published in 2020 in Cell.

 

For media: B-roll and soundbites of Chen available .

 

Greg Hay, an assistant teaching professor in the Information School, asked Chen to be a teaching assistant after he exceled during an introductory class. Later, Hay tapped Chen to lead a project supervising both undergraduate and graduate students.

鈥淒aniel has a superpower processor,鈥 Hay said. 鈥淗is mind is always active, engaged and blasting forward at double-speed. He is fearless, focused and curious.鈥

While in Britain, Chen plans to study with of the to acquire an understanding of the computational biology toolkit. He said he鈥檚 looking forward to immersing himself in British culture and learning from people who are different from him. He believes that a diversity of thought is what 鈥渄rives knowledge forward.鈥

鈥淲hen we come from different backgrounds and perspectives, we can work together to chip away at the truth,鈥 Chen said. 鈥淭ogether we can figure out rich solutions.鈥

Chen was the recipient of the Goldwater Scholarship, Mary Gates Research Scholarship, Microbiology Undergraduate Research Award and Levinson Emerging Scholar Award. He received the Microbiology Erling J. Ordal Award for best senior thesis, a Washington Research Foundation Fellowship and a Microbiology Summer Interdisciplinary Research Fellowship. In 2022, he was named to the Husky 100. Chen, who identifies as LGBTQIA+, also co-founded , a student group that promotes visibility and acceptance of neurodiversity at the UW and beyond.

For more information, contact Jackson Holtz at jjholtz@uw.edu.

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Four UW researchers elected to the National Academy of Sciences for 2022 /news/2022/05/06/nas-2022/ Fri, 06 May 2022 17:27:22 +0000 /news/?p=78384
Another lovely day at the 天美影视传媒’s Seattle campus. Photo: Pamela Dore/天美影视传媒

Four faculty members at the 天美影视传媒 have been elected to the National Academy of Sciences. The new members from the UW are:

  • , professor and chair of physiology and biophysics
  • , professor of microbiology
  • Dr. , professor of genome sciences
  • James Truman, professor emeritus of biology

They are among 120 new members and 30 international members to the National Academy of Sciences this year. Election 鈥渞ecognizes achievement in science by election to membership, and 鈥 with the National Academy of Engineering and the National Academy of Medicine 鈥 provides science, engineering, and health policy advice to the federal government and other organizations,鈥 according to an May 3 by the academy.

is noted for her research on the neural mechanisms behind learning and remembering. She studies how a system of structures in the brain, including the hippocampus and its surrounding cortical regions, set up new memories and how this system functions during memory retrieval. These structures are the first to be affected in Alzheimer鈥檚 disease. Lesions within these structures are associated with profound memory deficits. Her work may help improve the understanding of what foreshadows the onset Alzheimer鈥檚 and other dementias. She has a particular interest in how the brain maps surroundings, because getting lost in familiar locations is a common early symptom of Alzheimer鈥檚. Buffalo earned her doctoral degree at the University of California, San Diego and did postdoctoral training in neuropsychology at the National Institute of Mental Health. She received the 2011 Troland Research Award for her innovative studies from the National Academy of Sciences.

is known for his research on how bacteria interact with each other in the environment and in our bodies. Much of his work focuses on the battles that occur within communities of bacteria. He examines the arsenals they deploy to attack each other and defend themselves. Among his areas of study are antibacterial toxins that disable target cells in a variety of ways, secretion systems that mediate antagonism between bacteria, and the toxins that virulent bacteria secrete to overcome host defense strategies. His laboratory also studies the densely populated mammalian gut microbiome, where conflict rages among microbes as bacteria compete for resources and struggle to survive. His lab is hoping to harness the antimicrobial tactics of bacteria to develop new therapies for infections and other purposes. Mougous earned his doctoral degree from the University of California, Berkeley. He is a Howard Hughes Medical Institute investigator and a researcher at the UW Medicine Institute for Stem Cell and Regenerative Medicine. In 2021, he received the National Institute of Sciences Award in Molecular Biology for his pioneering studies in microbiology.

Dr. 鈥檚 research group has pioneered a variety of genome sequencing and analysis methods, including exome sequencing and its earliest applications to gene discovery for Mendelian disorders and autism; cell-free DNA diagnostics for cancer and reproductive medicine; massively parallel reporter assays; saturation genome editing; whole organism lineage tracing; and massively parallel molecular profiling of single cells. He has received numerous awards, including the 2012 Curt Stern Award from the American Society of Human Genetics, a 2013 National Institutes of Health Director’s Pioneer Award and the 2019 Richard Lounsbery Award from the National Academy of Sciences. Dr. Shendure has been an advisor to the NIH Director, the U.S. Precision Medicine Initiative, the National Human Genome Research Institute, the Chan-Zuckerberg Initiative and the Allen Institutes for Cell Science and Immunology. He received his M.D. and Ph.D. degrees in 2007 from Harvard Medical School, where he trained with geneticist and molecular biologist George Church on advancing DNA sequencing techniques. He is currently an investigator with the Howard Hughes Medical Institute, director of the Allen Discovery Center for Cell Lineage Tracing and scientific director of the Brotman Baty Institute for Precision Medicine.

Truman鈥檚 studies have focused on the genes, hormones and neural architecture underlying insect development and evolution. Early in his career, he identified the key hormone in moths that induces molting, as well as the brain-based circadian rhythms that exert overall control over this process. He later studied regulation of molting in the fruit fly and genes that control metamorphosis in moths. Truman earned a doctoral degree from Harvard University in 1970, where he continued as a Harvard Junior Fellow until joining the UW faculty in 1973. He became a full professor in 1978. He retired from the UW in 2007 and became a Group Leader at the Howard Hughes Medical Institute鈥檚 Janelia Research Campus, where he studied nervous system metamorphosis in fruit flies. In 2016, Truman returned to the UW as a professor emeritus, and today continues to study the evolution and development of insects and crustaceans at the UW鈥檚 Friday Harbor Laboratories. In 1970, he received the American Association for the Advancement of Science鈥檚 Newcomb Cleveland Research Prize and was a Guggenheim Fellow in 1986. Truman was elected to the American Academy of Arts and Sciences in 2009.

With this year鈥檚 addition, the National Academy of Sciences now has 2,512 active members and 517 nonvoting international members, who hold citizenship outside of the U.S.

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O-pH, a new UW dental tool prototype, can spot the acidic conditions that lead to cavities /news/2022/03/08/o-ph-a-new-uw-dental-tool-prototype-can-spot-the-acidic-conditions-that-lead-to-cavities/ Tue, 08 Mar 2022 17:10:39 +0000 /news/?p=77559
A new 天美影视传媒 dental tool prototype uses a low-power light system to monitor reactions with a florescent dye solution to find where teeth enamel is most at risk from the acidity of plaque. Photo: 天美影视传媒 and IEEE Xplore/Creative Commons

You and your dentist have a lot of tools and techniques for stopping cavities, but detecting the specific chemical conditions that can lead to cavities and then preventing them from ever getting started is much harder. Now, in a new , 天美影视传媒 researchers have shown that a dental tool they created can measure the acidity built up by the bacteria in plaque that leads to cavities.

The O-pH system is a prototype optical device that emits an LED light and measures the reactions of that light, the fluorescence, with an FDA-approved chemical dye applied to teeth. The O-pH then produces a numerical reading of the pH, or acidity, of the plaque covering those teeth. Knowing how acidic the plaque is can tell dentists and patients what area of a tooth is most at risk of developing a cavity.

鈥淧laque has a lot of bacteria that produce acid when they interact with the sugar in our food,鈥 said , lead author and a doctoral student in the UW Department of Electrical & Computer Engineering. 鈥淭his acid is what causes the corrosion of the tooth surface and eventually cavities. So, if we can capture information about the acidic activity, we can get an idea of how bacteria are growing in the dental biofilm, or plaque.鈥

The UW optical O-pH prototype can non-invasively measure the acidity of oral biofilm. Photo: 天美影视传媒 and IEEE Xplore/Creative Commons

Sharma explained that not all bacteria in that biofilm are bad or will lead to cavities, so measuring the acidity of the environment can tell a dentist what they need to know about the threat of developing problems. That can limit the need to test for specific harmful bacteria, of which there can be a multitude.

To test their device, the researchers recruited 30 patients between the ages of 10 and 18, with a median age of 15, in the UW School of Dentistry鈥檚 . The researchers chose kids for their study in large part because the enamel on kids鈥 teeth is much thinner than that of adults, so getting early warning of acid erosion is even more important. To perform the measurements with the O-pH device, the researchers also recruited second- and third-year students in the dentistry school, who were supervised by a faculty member.

The test is non-invasive. While the dye is applied to the teeth, at the end of a length of cord is the probe that transmits and collects light while hovering over the surface of a tooth (see photos). The collected light travels back to a central box that provides a pH reading. The conditions on the patients鈥 teeth were read several times before and after sugar rinses and other condition changes, such as pre- and post-professional dental cleaning.

, senior author and research professor of mechanical engineering in the UW College of Engineering, said the idea for adding the acidity test as a new clinical procedure came from envisioning that when a patient first sits in the dental chair, before their teeth get cleaned, 鈥渁 dentist would rinse them with the tasteless fluorescent dye solution and then get their teeth optically scanned to look for high acid production areas where the enamel is getting demineralized.鈥

The was published in February in IEEE Transactions on Biomedical Engineering. The research team reported that one limitation to their study was being unable to consistently measure the same location on each tooth during each phase of testing. To address this limitation, in particular, the researchers are evolving their device to a version that produces images for dentists that instantly show the exact location of high acidity, where the next cavity may occur.

鈥淲e do need more results to show how effective it is for diagnosis, but it can definitely help us understand some of your oral health quantitatively,鈥 said Sharma. 鈥淚t can also help educate patients about the effects of sugar on the chemistry of plaque. We can show them, live, what happens, and that is an experience they鈥檒l remember and say, OK, fine, I need to cut down on sugar!鈥

Co-authors include Lauren Lee, UW Department of Microbiology; Matthew Carson, UW Human Photonics Laboratory; David Park, Se An, Micah Bovenkamp, Jess Cayetano, Ian Berude, Zheng Xu, Alireza Sadr, UW School of Dentistry; and Shwetak Patel, UW Electrical & Computer Engineering and the Paul G. Allen School of Computer Science & Engineering. This research was funded by the National Science Foundation, Oral Health Monitor, Institute of Translational Health Sciences; and the National Center for Advancing Translational Sciences of the National Institutes of Health.

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For more information, contact Seibel at eseibel@uw.edu.

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Three UW students selected as 2020 Goldwater Scholars /news/2020/03/30/2020-goldwater-scholars/ Mon, 30 Mar 2020 18:11:11 +0000 /news/?p=67123 Three undergraduate students at the 天美影视传媒 are among 396 around the country who have been named .

The Goldwater Scholarship Program supports undergraduates who 鈥渟how exceptional promise of becoming this nation鈥檚 next generation of research leaders鈥 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.

Gootkin, Ruth and Zhang. Photo: 天美影视传媒
  • 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鈥檚 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 鈥渢he machineries of life at a molecular level and engineering them to perform novel tasks,鈥 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鈥檚 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.

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Six UW faculty members named AAAS fellows /news/2019/11/26/six-uw-faculty-members-named-aaas-fellows/ Tue, 26 Nov 2019 20:24:59 +0000 /news/?p=64924 The American Association for the Advancement of Science has named six faculty members from the 天美影视传媒 as AAAS Fellows, according to a Nov. 26 . They are part of a cohort of 443 new fellows for 2019, all chosen by their peers for 鈥渟cientifically or socially distinguished efforts to advance science or its applications.鈥

The six UW faculty members who have been named as fellows are:

Karl Banse

, professor emeritus in the School of Oceanography, is honored for his continuing work on the ecology of the plankton, the very small algae and animals that float with the currents. His career has focused on how plankton interact with light, temperature, oxygen, bound nitrogen, iron and other nutrients. At sea, Banse worked in the Baltic, the North Sea and Puget Sound, but especially the Arabian Sea. In other work, using an early color global satellite, he investigated the offshore seasonality of phytoplankton chlorophyll. With former students he also studied bottom-living polychaetous annelid worms and published identification keys for the nearly 500 species of these worms found between Oregon and southeast Alaska, between the shore and about 200 meters depth. Banse joined the UW faculty in 1960. The 90-year-old researcher became emeritus in 1995 and remains scientifically active.

Simon Hay

, a professor of health metrics sciences and director of the at the Institute for Health Metrics and Evaluation, was selected for his research resolving infectious diseases in space and time in order to expose inequalities in health metrics and improve intervention strategies. He currently leads an international collaboration of researchers from a wide variety of academic disciplines to create even better maps of infectious disease. He has published over 400 peer-reviewed articles and other contributions, including two major, in-depth research papers published independently. His published works are cited more than 18,000 times each year, leading to more than 82,000 lifetime citations. With the support of the Bill & Melinda Gates Foundation, Hay has embarked on a project to expand this research to a much wider range of diseases to ultimately harmonize this mapping with the Global Burden of Disease Study, IHME’s signature project.

Michael Lagunoff

, a professor of microbiology, studies Kaposi鈥檚 Sarcoma Herpesvirus, a virus that alters the cells lining blood and lymphatic vessels. Those changes can cause Kaposi鈥檚 Sarcoma, a form of cancer that commonly affects AIDS patients worldwide and people in parts of central Africa. Lagunoff鈥檚 lab has studied how the Kaposi鈥檚 Sarcoma Herpesvirus interferes with endothelial cell signaling, gene expression and metabolism to promote the formation of tumors containing numerous blood vessels. His lab used RNA-sequencing, metabolomics, proteomics and other techniques to determine global changes in host-cell gene expression and signaling. This information has helped to identify key cellular pathways induced by the virus. His team is studying how the virus alters the host cell metabolism to mimic cancer cell metabolism, and is searching for novel therapeutic targets for Kaposi鈥檚 Sarcoma.

Raymond Monnat, Jr.

, a professor of pathology and genome sciences and an investigator at the , studies DNA damage and repair mechanisms, genome instability, and its role in cancer and other conditions. He is noted for his work on Werner, Bloom and Rothman-Thomson syndromes. These inherited disorders cause distinctive physical characteristics, such as premature aging in Werner鈥檚, and predispose to cancer. Monnat鈥檚 team explores how the loss of key proteins important to DNA metabolism may underlie these rare syndromes. Aberrant expression of those proteins may be common in some adult cancers and affect response to chemotherapy. Monnat and his group use certain genome engineering techniques to try to correct disease-causing mutations in patient-derived stem cells. His lab has also identified 鈥渟afe-harbor sites鈥 in the human genome where new genetic elements might be inserted without disrupting the expression of nearby genes.

Julia Parrish

, professor in the School of Aquatic and Fishery Sciences and the Department of Biology, is elected for her work in marine ecology. Her research focuses on seabird ecology, marine conservation and public science. A committed advocate of citizen science, she founded and directs the , which for two decades has enlisted coastal residents from California to Alaska to monitor West Coast beaches for dead birds and marine debris. Parrish spoke at the White House in 2013 about public engagement in science and scientific literacy. She holds the Lowell A. and Frankie L. Wakefield endowed professorship, and is associate dean for academic affairs in the UW College of the Environment.

Eric Steig

, a professor of Earth and space sciences, is honored for his work in glaciology and climate science. Steig uses ice cores and other records to study climate variability over thousands of years. He works on the climate history and dynamics of polar ice sheets and mountain glaciers, and develops new tools to extract the chemical clues in samples of ice and other material. Steig was among the leaders of a project to drill the first deep ice core at South Pole, and was on the team that drilled a 2-mile-deep ice core in West Antarctica. His recent research has focused on the links between large-scale climate conditions and changes in West Antarctica, where glaciers are rapidly retreating. In addition to his research and teaching, he is committed to fostering greater public understanding of climate change, and is a founding contributor to RealClimate.org.

In addition, , an investigator at the Fred Hutchinson Cancer Research Center and an affiliate professor of genome sciences at the UW, was selected for his research on genetic conflict.

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5 UW professors among HHMI’s inaugural class of Faculty Scholars /news/2016/09/22/five-uw-professors-among-hhmis-inaugural-class-of-faculty-scholars/ Thu, 22 Sep 2016 17:35:25 +0000 /news/?p=49708 Photo by Katherine Turner.
Photo by Katherine Turner. Photo: 天美影视传媒

Amid a decline in funding for scientific research, is partnering with the Bill & Melinda Gates Foundation and the Simons Foundation to launch a new Faculty Scholars program. by HHMI, the of early career scientists includes five faculty members from the 天美影视传媒.

The Faculty Scholars program, which is distinct from the HHMI , is intended to support scientists in their initial years as research faculty. With dwindling grant opportunities, early and mid-career research scientists may feel more pressure to shelve innovative yet risky projects in favor of “safe,” more conventional alternatives. According to its , HHMI intends for this support to provide faculty members freedom and flexibility to pursue more innovative or risky projects 鈥 endeavors which have greater potential for scientific advancements but also less certainty for success.

The 84 scholars will share $84 million in funds over five years, broken down into $600,000 to $1.8 million for each recipient. Scholars are based at 43 institutions across the United States.

Three HHMI Faculty Scholars have primary appointments at the UW or the College of Arts & Sciences.

Maitreya Dunham

: associate professor of genome sciences

Dunham uses comparative genomics and experimental evolution techniques to investigate how yeast genomes evolve over spans of a few weeks to millions of years. Her research informs therapies that counter the evolution of drug resistance in fungal and bacterial pathogens, viruses and cancer.

Jennifer Nemhauser

: professor of biology

Nemhauser studies plant signaling pathways to learn how multicellular organisms develop and respond to their environment. She gleans information about molecular networks in natural systems and then synthetically programs these core functions into yeast cells to measure the effect of evolved and engineered changes. Her ultimate aim is to develop technologies that support farmers and foster global health.

Daniel Stetson

: associate professor of immunology

Stetson studies how our cells detect infection by a virus. Sensors of foreign DNA and RNA are essential for activating immune responses to viruses, but they can also cause autoimmune disease if not properly regulated. Stetson鈥檚 lab explores this dichotomy of protective immunity and autoimmunity activated by the same antiviral sensors.

In addition, two scholars based at the Fred Hutchinson Cancer Research Center have joint appointments as UW faculty members.

Jesse Bloom

: assistant member at the Fred Hutchinson Cancer Research Center and UW affiliate associate professor of genome sciences and microbiology

Bloom studies the evolution of proteins and viruses. He develops experimental and computational techniques to understand the forces that shape evolution at the molecular level. This work provides insight into how viruses such as influenza can rapidly change to evade immune system defenses.

Frederick “Erick” Matsen

: associate member at the Fred Hutchinson Cancer Research Center and UW affiliate associate professor of statistics

Matsen is developing computational algorithms to analyze large sets of genetic data from an evolutionary perspective. He also is working to improve the accuracy of analyses used by biologists to infer evolutionary relationships between species or individual organisms.

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Portions of this post were adapted from provided by HHMI.

For more information, contact James Urton in the UW Office of News & Information at 206-543-2580 or jurton@uw.edu.

 

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TB bacteria mask their identity to intrude into deeper regions of lungs /news/2013/12/19/tb-bacteria-mask-their-identity-to-intrude-into-deeper-regions-of-lungs-2/ Thu, 19 Dec 2013 19:31:36 +0000 /news/?p=29805 TB-causing bacteria appear to mask their identity to avoid recognition by infection-killing cells in the upper airways. The bacteria call up more permissive white blood cells in the deeper regions of the lungs and hitch a ride inside them to get into the host’s body.

TB in lower lungs
Flying under the radar: tuberculosis-causing mycobacteria initiate infection in the lower lung to evade pathogen-killing cells. Photo: Ramakrishnan lab

These findings are reported Dec. 16 in the advanced online edition of the journal Nature. The research was a collaboration between the 天美影视传媒 and the Seattle Biomedical Research Institute.

Dr. Lalita Ramakrishan, who studies how TB evades the body’s immune system and manipulates the body’s defenses for its own ends, is the senior author. She is a UW professor of microbiology, medicine and immunology. The lead author is C.J. Cambier of the UW Department of Immunology.

Ramakrishnan noted that the recent study suggests an explanation for the longstanding observation that tuberculosis infections begin in the comparatively sterile lower lungs. In the upper respiratory tract, resident microbes and inhaled microbes of a variety of species signal their presence.

These tip-offs alert and attract many infection-fighting cells to the upper airways. The presence of other microbes in the upper airway may thereby help to keep TB infections at bay by creating a hostile environment.

Their presence may explain why TB is less contagious than diseases caused by several other respiratory pathogens.

To produce an illness, TB bacteria must sneak through this well-patrolled area and head for parts of the lungs where fewer microbiocidal cells are policing.

Like most other bacteria, TB pathogens have telltale molecular patterns that should activate an immune response. However, TB pathogens have evolved mechanisms to circumvent tripping the alarm. Almost like home intruders wearing a stocking over their faces, the TB pathogens produce particular types of fatty substances, or lipids, on their cell surfaces.

These lipids, abbreviated as PDIM, are already known to be associated with bacterial virulence. The researchers showed that PDIM lipids function by masking the underlying molecular patterns that would reveal their dangerous nature to infection-fighting cells.

At the same time, a related lipid – called PGL – on the bacterium’s cell surface promotes the recruitment of clean-up cells that engulf but don’t kill the TB pathogens. Instead, they take them across the lung lining, deep into the lung tissue where the bacteria can establish an infection.

The TB pathogens then use the other lipid molecule, PGL, to co-opt a host chemical pathway that triggers the recruitment of the permissive macrophages.

The present study expands on earlier work in the Ramakrishan and collaborative labs, which helped describe the strategies by which TB pathogens manipulate host pathways for their own purposes after they enter certain host cells.

These include the secretion of proteins that expand the niche for TB by recruiting macrophages to the early lung tubercles characteristic of the disease. The present study describes earlier stages in infection, when the pathogens first come in contact with their potential host at the surface of the lung lining.

“The current study suggests the manner in which the TB pathogens manipulate recruitment of the first responding macrophages to gain access to their preferred niche,” the researchers noted.

“The choreographed entry involves two related TB cell lipids acting in concert to avoid one host pathway while inducing another,” they wrote. The findings link the previously known, absolutely essential virulence factor on the surface of TB cells, PDIM, to the evasion of immune cell detection. On the other hand, PGL is not required on the surface of TB cells for them to infect the body.

Ramakrishnan noted that globally, a lot of samples of TB taken from infected patients do not have PGL. “However,” she and her research team noted, “the importance of PGL in mediating TB virulence or transmission is underscored by its presence in many of the W-Beijing strains” of TB which are starting to appear in more patient samples, and which have predominated in outbreaks in North America.

Ramakrishnan explains that their findings suggest how PGL may be important in increasing TB’s infectivity.

“The presence of PGL in ancestral strains of TB suggest it played an integral role in the evolution of TB infectivity,” the researchers noted. “TB is an ancient disease and the enhanced infectivity conferred by PGL may have been essential for most of its history before human crowding, with its increased opportunity for transmission, made it dispensable.”

The study findings, and previous work on TB, might also explain why smaller droplets of TB are more infectious than larger ones. Only the smaller droplets can make their way down into the lower airways. All it takes is 3 or fewer TB mycobacteria with PGL-producing ability to enter the lower lungs and start an infection.

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The other researchers on the study, in addition to Cambier and Ramkrishnan, were Kevin K. Takaki, David M. Tobin, and Christina L. Cosma, all of the UW Department of Microbiology; Ryan Larson and Kevin N. Urdahl of the of the UW Department of Immunology and the Seattle Biomedical Research Institute. Urdahl also is from the UW Department of Pediatrics.

The research was supported by training and research grants from the National Science Foundation, American Lung Association, National Institutes of Health, and American Cancer Society. Tobin is an NIH New Innovator and Ramakrishnan is an NIH Pioneer.

 

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