Sokurenko Lab research into a novel antibody with potential therapeutic uses against E. coli is featured here.
Congratulations to Joseph Mougous who has been named as one of 26 new HHMI Investigators. With this appointment, Joseph joins a very select group of highly innovative and productive scholars across the nation who are at the forefront of their respective fields. For more information about the announcement go to the HHMI web site.
The Microbiology Department welcomes our incoming graduate students:
Renae Cruz (University of California, Los Angeles)
Alex Pollock (University of California, Berkeley)
Brittany Ruhland (Tufts University)
Sofiya Shevchenko (University of Toronto)
Justin Ulrich-Lewis (University of Michigan)
Daniel Vogt (University of Wisconsin)
We are very proud of graduate students in the Microbiology Department who were recognized this month for excellence and outstanding effort. Mayumi Holly (Jason Smith lab) was awarded the Neal Groman Microbiology Graduate Student Award for Excellence in Teaching; Mayim Wiens (also from the Smith lab) received the Helen Riaboff Whiteley Fellowship Award; and Alevtina Gall (Molecular and Cellular Biology program, Nina Salama lab) was awarded the Stanley Falkow Microbiology Graduate Student Award. Congratulations to each of these awardees!
The University of Washington Microbiology Department was ranked #2 in "Best Global Universities for Microbiology" by U.S. News and World Report, up from #3 last year! More info here.
Postdoc John Whitney, part of a research team led by Joseph Mougous, UW Associate Professor of Microbiology and a Howard Hughes Medical Institute investigator, is featured in this UW Health Sciences NewsBeat article about the team's research into how Pseudomonas aeruginosa is able to deliver a deadly toxin to competitor bacteria.
Congratulations to Houra Merrikh, Ph.D., who was awarded the Vilcek Prize for Creative Promise in Biomedical Science. Read more about this prestigious award here and view a short video here about Dr. Merrikh's journey from Tehran to the University of Washington. Dr. Merrikh was recognized for her work in "uncovering hidden conflicts between the machinery that copies DNA in living cells and the one that transcribes its genetic code." The Vilcek Foundation raises awareness of immigrant contributions in America and fosters appreciation of the arts and sciences. Click here to find out more about the Vilcek Prizes.
Associate Professor Deb Fuller, Ph.D., collaborated with other UW researchers to develop a computationally designed protein that may have anti-viral and therapeutic benefits against flu viruses. Read more about their research here.
Molecular and Cellular Biology (MCB) graduate student Erica Sanchez was awarded the UW Graduate Student Medal, which is given to recognize Ph.D. candidates whose academic expertise and social awareness are integrated in a way that demonstrates an exemplary commitment to the University and its larger community. Find out more about the award here.
The Microbiology Department welcomes our newest faculty member, Jenny Hyde, Ph.D.
Dr. Hyde comes to us from the Washington University School of Medicine in St. Louis, Missouri, where she had her post-doctoral appointment. She completed her Ph.D. at the University of Queensland. Dr. Hyde's research focus is in virology.
Eleven undergraduate students were honored with various awards on June 2 during the department's annual celebration for graduating seniors and for current students demonstrating outstanding achievement. Undergraduate awardees, from left to right: Lydia Sweet, Research Award; Helen Warheit-Niemi, Research Award; Elaina Milton, Research Award; Bailey Marshall, Jacques Chiller Award; Vy Dang, Research Award; Claire Chisholm, Education Award; Matthew Hryniewicki, Charles A. and Allie Ann Evans Award; Michael Matwichuk, Research Award; Yashmira Naidoo, Don Bassett Award; Emily Anderson, Erling Ordal Award; and Elizabeth Thayer, David T. Kingsbury Award. Congratulations to all awardees and to all 89 graduating seniors!
Professor Carrie Harwood and colleagues have engineered a bacterium that can take carbon dioxide from the air and turn it into fuel in a single enzymatic step. The process draws on sunlight to produce methane and hydrogen inside the bacterium Rhodopseudomonas palustris, in essence reversing combustion. These engineered bacteria could guide scientists toward better carbon-neutral biofuels. Read more about the research here. The full paper is published in the September 22, 2016, edition of PNAS.
Microbiology Professor Evgeni Sokurenko's Seattle biotech startup, ID Genomics, is developing a solution to that conundrum: a system that tests the biological “fingerprint” of a bacteria and connects it to a huge database to determine what bacteria it is, and what the best treatment is. Click here to read the full article.
UW Micro has done well on yet another international ranking of Microbiology programs, with the Center for World University Rankings listing our department as the third best in the world behind Harvard and John Hopkins. See the list here.
A new study describes how head-on collisions between protein machines on chromosomes can disrupt DNA replication and boost the rate of gene mutations that help bacteria survive hostile environments, resist antibiotics, and blunt attacks by immune defenses.
The Department of Microbiology is proud to announce Brittany Ruhland (Reniere Lab) has been named the 2017 Neal Groman Award Winner, and Adelle McFarland (Woodward Lab) has been named the 2017 Helen Riaboff Whitely Fellowship Winner.
The UW Department of Microbiology is proud to announce that our own Dr. Houra Merrikh has been named a 2018 National Academy of Sciences Kavli Fellow for her leadership and contributions to her field. She will present her work at a symposium, February 15-17, 2018 at UC Irvine.
Eight University of Washington researchers are among the 396 new fellows of the American Association for the Advancement of Science, announced this week. Election as a fellow of AAAS is an honor bestowed upon members by their peers. Fellows are recognized for meritorious efforts to advance science or its applications.
Getting a flu shot every year can be a pain. One UW Medicine researcher is hoping to make the yearly poke a thing of the past with the development of a universal vaccine that would protect from all strains of influenza virus, even as the viruses genetically shape-shift from year to year.
Nitrogen-fixing bacteria are the chief means by which nitrogen gas in the air is changed into a form that plants and animals can use. Roughly 10 percent of these nitrogen-fixing microorganisms contain the genetic code for manufacturing a back-up enzyme, called iron iron-only nitrogenase, to do their job.
Recent research reveals that this enzyme allows these microorganisms to convert nitrogen gas to ammonia and carbon dioxide into methane at the same time. The ammonia is the main product; the methane is only a sideline.
This enzymatic pathway is a previously unknown route for the natural biological production of methane.
The findings are reported Jan. 15 in Nature Microbiology. The senior author is Caroline Harwood, the Gerald and Lyn Grinstein Endowed Professor of Microbiology at the University of Washington School of Medicine. The lead author is Yanning Zheng, a postdoctoral student in her lab.
A single scoop of sediment collected from the bottom of Lake Washington may not look like much to the untrained eye, but for UW researchers, the complex microbial communities living in the mud might hold the key to a cleaner world.
The UW medical school’s graduate program in microbiology tied for second in the nation!
Affiliate Associate Professor of Microbiology Jesse D. Bloom, Ph.D., of the Fred Hutchinson Cancer Research Center has been named a Howard Hughes Medical Institute (HHMI) Investigator for 2018, joining a select group of top scientists nationally. Read more here.
Jesse Bloom is fascinated by evolution.
Think how amazing it is, he says, that in nature, small, random genetic changes can add up to something new and wonderful – a stark contrast to the world of things. “If you make random mutations to your car with a baseball bat, you’re probably not going to improve the car very much,” he says. “So what is it about biology that allows living things to be so good at evolving?”
Bloom is tackling this question by helping to pioneer new approaches for studying evolution. He’s combining biology with computational wizardry. “Traditionally, evolutionary biology has been an observational science,” he explains. Researchers looked back on the creation of new species, like Darwin’s finches, or bold new innovations, like the ability to fly, then searched for the genetic steps that paved the way.
But thanks in part to Bloom, scientists don’t have to wait for nature to do its work. “Now we can do large-scale experiments in the lab that can help to explain evolution,” Bloom says. In his own lab, he’s making tens of thousands of mutations in flu viruses to see what effect they have. At the same time, he’s also charting genetic changes that appear in nature. Bloom’s goal is to discern patterns in evolution and use his mathematical modeling skills to predict what’s coming – offering a major public health advance.
His work is paying off. In one recent discovery, Bloom and his collaborators uncovered how the flu virus managed to develop resistance to the drug Tamiflu. One key mutation prevents the drug from attacking flu viruses. But that genetic change, by itself, is actually lethal to the virus because it causes the virus to break apart, Bloom discovered. Several other genetic alterations shore up the virus, letting it survive the drug-blocking mutation.
Another mystery has been the sequence of genetic steps that flu viruses take as they evolve from year to year. Bloom tackled this question by analyzing genetic changes in viruses in immunocompromised patients, whose flu infections often last for months. Not only do these viruses mutate rapidly, he found, but the changes surprisingly parallel what happens to viruses out in the world.
The similarity suggests that, with clever mathematical sleuthing, scientists can get better at guessing what new strains humanity will face in coming years. “I don’t think we will ever be able to completely forecast the future, but it will be interesting to see how good we can get,” says Bloom.
He is uniquely suited to the task. Growing up in Hamilton, Montana, Bloom loved all types of science, including biology, physics, chemistry, math, and computer programming. The problem was picking just one. Fortunately, at the time, biologists were beginning to explore the power of computers, so Bloom was able to combine his quantitative bent with his fascination for evolution.
After studying protein folding as a University of Chicago undergraduate, Bloom wanted to do something more mathematical, such as using his modeling expertise to predict proteins’ shapes from their sequence. That turned out to be fiendishly difficult, “so I thought maybe I can study how they evolved,” he says. That led him to the California Institute of Technology as a PhD student and postdoc, working to harness evolution to engineer new and useful enzymes. There, “I learned I was more of a curiosity-driven biologist than a problem-solving engineer,” he says.
Now, that curiosity – backed up by rigorous computation – may finally bring answers to some of the great questions of evolution.
NEW YORK – May 30, 2018 – The Blavatnik National Awards for Young Scientists today announced the 31 U.S. National Finalists who will compete for the world’s largest unrestricted prizes for early career scientists. Each year, three Blavatnik National Laureates in the categories of Life Sciences, Chemistry, and Physical Sciences & Engineering are awarded $250,000 each.
The Blavatnik National Finalists were selected from 286 outstanding faculty-rank researchers nominated by 146 institutions across 42 states (see list with brief summaries below). These institutions comprise the nation’s leading academic and research centers, and each is requested to name their single most promising candidate in one or all of the three categories.
Spearheaded by the Blavatnik Family Foundation and administered by the New York Academy of Sciences, the Blavatnik National Awards recognize both the past accomplishments and the future promise of the most talented scientific and engineering researchers aged 42 years and younger at America’s top academic and research institutions. The three 2018 National Laureates will be announced on June 27, 2018.
“We created the Blavatnik Awards to identify the brightest young minds in science early in their scientific careers,” said Len Blavatnik, Founder and Chairman of Access Industries, head of the Blavatnik Family Foundation and member of the President’s Council of the New York Academy of Sciences. “These 31 Finalists, through their creative, cutting-edge research, have demonstrated great promise for future discoveries of enormous scientific importance.”
Past Finalists have gone on to make discoveries that turn science fiction into reality, including creating plants that emit light or detect explosives, formulating new theories of time travel through black holes, bioengineering micro-robots that can swim through arteries and heart valves, gene-editing DNA and RNA sequences to treat previously incurable genetic diseases, and detecting infectious epidemic viruses through a cellphone. Blavatnik Scholars advance the progress of humanity through scientific discovery.
“The 31 National Finalists in the U.S. join the Blavatnik Awards community of scholars — a decade’s worth of Finalists and Laureates who are leading scientific research into the next century,” said Ellis Rubinstein, President and CEO of the New York Academy of Sciences and Chair of the Awards’ Scientific Advisory Council. “With continued support and recognition from the Blavatnik Awards, our goal is to launch these pioneering young scientists onto an even higher trajectory of scientific pursuit, giving them a visible platform to attract new collaborators, future grants, investors, and other key resources.”
The Blavatnik Awards, established by the Blavatnik Family Foundation in the United States in 2007, and administered by the New York Academy of Sciences, began by identifying outstanding scientific talent in New York, New Jersey, and Connecticut. The Blavatnik National Awards were inaugurated in 2014 and, in 2018, the Awards were expanded to include young scientists in the United Kingdom and Israel.
By the close of 2018, the Blavatnik Awards will have conferred prizes totaling $6.6 million, honoring 271 outstanding young scientists and engineers.
The 2018 Blavatnik National Laureates and Finalists will be honored at the Blavatnik National Awards on Monday, September 24, 2018, at the American Museum of Natural History in New York City.
About the Blavatnik Family Foundation
The Blavatnik Family Foundation is an active supporter of many leading educational, scientific, cultural, and charitable institutions in the United States, the United Kingdom, Israel, and throughout the world. Recipients of Foundation support include University of Oxford, Harvard University, Yale University, Tel Aviv University, Stanford University, New York University, the New York Academy of Sciences, Tate, the Victoria and Albert Museum, Carnegie Hall, the Royal Opera House, the Hermitage Museum, the Israel Museum, Lincoln Center, Jewish charitable organizations, and countless other philanthropic institutions. The Foundation is headed by Len Blavatnik, a major American and British entrepreneur and philanthropist. Len Blavatnik is the Founder and Chairman of Access Industries, a privately held U.S. industrial group with global strategic interests in natural resources and chemicals, media and telecommunications, venture capital, and real estate.
For more detailed information, please visit: www.accessindustries.com
About the New York Academy of Sciences
The New York Academy of Sciences is an independent, not-for-profit organization that since 1817 has been driving innovative solutions to society’s challenges by advancing scientific research, education, and policy. Throughout its history, the Academy's Membership has featured thinkers and innovators from all walks of life, including U.S. Presidents Jefferson and Monroe, Thomas Edison, Lord Kelvin, Charles Darwin, Margaret Mead, Louis Pasteur, and over 130 Nobel Laureates. Today, the Academy numbers over 20,000 Members in 100+ countries, with a President's Council that includes 36 Nobel Laureates and a distinguished Board of Governors comprised of leaders from business, academia, and philanthropy. It is also young and dynamic with nearly 10,000 post-doctoral, post-graduate, undergraduate, and gifted high school student Members. Through collective action, the Academy is partnering with the United Nations to address their Sustainable Development Goals, advising national leaders and organizing public-private partnerships to address the grand challenges of the planet.
THE 2018 BLAVATNIK NATIONAL AWARDS FINALISTS: A YEAR OF SCIENTIFIC POSSIBILITIES
2018 Blavatnik National Finalists in Life Sciences
The 2018 National Finalists in Life Sciences have addressed complex questions that reflect the next chapter in human health and development. The Finalists have expanded our understanding of the ways in which the human microbiome governs microbial infection and human health by studying the interactions between bacteria, pathogens and their host. They have developed extraordinary new technologies and discoveries, from harnessing cutting-edge CRISPR gene-editing technology to improve crop yields, editing RNA-based disease targets, identifying key metabolic and physical cues that control the growth and internal organization of cells, developing unique computational approaches to study cancer progression, and inventing technologies that advance our understanding of the brain and organ tissue development.
Janelle Ayres (Salk Institute for Biological Studies) – Working at the intersection of immunology and microbiology, Dr. Ayres’ pioneering research on host-pathogen interactions is re-defining our understanding of health. Dr. Ayres’ discovery that microbes have evolved mechanisms to promote the health of the host to support their own survival reveals a beneficial role for microbes in maintenance of host health. Promoting host “tolerance” of microbes may offer a novel therapeutic approach to treating infections that is not reliant on antibiotics.
Edward Boyden (Massachusetts Institute of Technology) – Dr. Boyden has invented multiple groundbreaking technologies that have advanced our understanding of the brain. Dr. Boyden revolutionized neuroscience research with the co-invention of optogenetics—using light to control cells in genetically modified living tissues. More recently, he developed expansion microscopy, a creative approach that involves physically expanding a specimen using swellable polymers to achieve high-resolution images instead of increasing the resolution of the microscope.
Clifford Brangwynne (Princeton University) – Dr. Brangwynne’s pioneering work at the interface of cell biology and soft matter physics focuses on membrane-less organelles within cells, and how their physical state plays a role in associated biological functions. Dr. Brangwynne’s seminal discovery that membrane-less organelles behave as liquids rather than solids has introduced a major paradigm shift in our understanding of intracellular organization and sheds light on the material physics underlying organelle processes.
Zachary Lippman (Cold Spring Harbor Laboratory) – Having identified several genes that determine flower production and crop productivity, geneticist Dr. Lippman is applying cutting-edge CRISPR gene-editing technologies to improve crop yield. Dr. Lippman has demonstrated that manipulating the genome of plants to fix undesirable combinations of mutations introduced by breeding or to introduce new gene mutations that improve the health or flowering capacity of the plant can improve yield. In doing so, Dr. Lippman’s work has the potential to help address one of our top public health concerns: global food supply shortage.
Franziska Michor (Dana-Farber Cancer Institute) – Dr. Michor’s work has led to the first clinical trials based on the evolutionary mathematical modeling of cancer. Dr. Michor investigates the evolutionary dynamics of cancer using mathematical modeling methodologies and a unique combination of approaches. She studies the process of cancer initiation and progression along with cancer stem cells, the evolution of drug resistance and the dynamics of metastasis formation focusing on lung, brain, breast and pancreatic cancers.
Joseph Mougous (University of Washington) – Dr. Mougous studies how bacteria interact with each other across a wide range of settings. Dr. Mougous’ discovery that bacteria use a specialized secretion system to deliver toxins to other bacteria during cell-to-cell contact has revolutionized our view of bacterial “communities”. Dr. Mougous has also shown that this ongoing battle between bacteria shapes the personalized combination of bacteria in an individual’s gut microbiome, opening the door to the development of innovative strategies for manipulating gut bacterial assemblages to promote human health.
Celeste Nelson (Princeton University) – Dr. Nelson’s biomedical engineering and biotechnology research focuses on how complex organs are formed during morphogenesis in branching tissues such as the lung, kidney and mammary gland. She is a pioneer in tissue engineering/microfabrication and smooth muscle development and seeks to understand the biomechanical and dynamic molecular mechanisms that influence tissue remodeling during development, wound repair and abnormal cell growth.
Bradley Pentelute (Massachusetts Institute of Technology) – Dr. Pentelute synthesizes new biomolecules for therapeutic compounds, focusing on peptides and proteins. He developed fast-flow peptide synthesis, a new technology that assembles polypeptides from smaller individual molecules at unprecedented speed. Dr. Pentelute’s group can form links between amino acids, the building blocks of proteins, in less than a minute, and generate complete peptide molecules containing up to 60 amino acids in less than an hour, a vast improvement from current technologies.
Benjamin Tu (UT Southwestern Medical Center) – Molecular and cellular biologist Dr. Tu studies metabolism and cellular processes using both yeast and mammalian systems. He has uncovered novel molecular mechanisms that govern cell growth and proliferation in response to metabolic and nutritional cues. Dr. Tu’s research focuses on the metabolic state of cells and responses to conditions that induce or halt cell proliferation to promote survival and homeostasis.
Gene Yeo (University of California, San Diego) – Dr. Yeo has created multiple novel technologies that have increased our understanding of RNA processing and RNA-binding proteins. Dr. Yeo was the first to target RNA (as opposed to DNA) using the CRISPR/Cas9 system in live cells and demonstrated reversal of key pathological features of microsatellite expansion diseases by destroying toxic RNA in patient cells. Dr. Yeo’s discoveries hint at the enormous possibilities of tapping the therapeutic potential of RNA manipulation in the treatment of human disease.
2018 Blavatnik National Finalists in Chemistry
The 2018 National Finalists in Chemistry are making significant advances in chemical research that have the potential to improve people’s lives. Their research efforts range from deciphering the chemistry of the human gut microbiome and its connection to disease to developing novel materials that will increase the efficiency of next-generation solar cells. They have designed novel ways of assessing the toxicology of nanoparticles in the environment, developed new tools for labeling biomolecules, pioneered new quantum dot–based technologies and created nano-sized sensors capable of making non-invasive measurements of brain activity.
Emily Balskus (Harvard University) – Dr. Balskus is a chemical biologist pioneering breakthrough advances at the interface of chemistry, enzymology and microbiology. Her research focuses on identifying the novel chemistry of the human gut microbiome and deciphering the role that gut microbial metabolism plays in human health and disease. One signature achievement is elucidating the mechanism by which bacterial toxins called Colibactins are biosynthesized and behave within the gut.
Luis Campos (Columbia University) – A creative polymer chemist focusing on molecular design of novel functional materials to address important problems in materials chemistry, Dr. Campos has spearheaded the synthesis and development of new chromophores—molecular modules that interact with light — that possess significantly advanced electronic properties and have the potential to increase the conversion efficiency of next-generation solar cells.
Bianxiao Cui (Stanford University) – Dr. Cui is a biophysical chemist making groundbreaking advances in the development of complex biophysical tools for observing how living cells interact with nano-scale materials and devices. Two of her signature innovations have been to identify membrane curvature as a key player at the cell-nanomaterial interface, and create nano-sized-pillar based electrical sensors that are capable of highly sensitive, non-invasive measurements of neuronal activity. Her work has immense implications on the fields of tissue engineering and regenerative medicine and will undoubtedly influence the design of implantable devices.
Mircea Dincă (Massachusetts Institute of Technology) – Dr. Dincă is a solid-state chemist pushing boundaries in the area of metal-organic frameworks (MOFs). MOFs were traditionally used for gas storage and separation and were usually electrical insulators. Dr. Dincă was the first to design new MOFs that function as conductors, with electrical conductivity comparable to that of the best conducting polymers used in organic solar cells. These materials open the door to a host of new applications in solar cells as well as new membranes for better lithium- and sodium-ion rechargeable batteries.
Neal Devaraj (University of California, San Diego) – Dr. Devaraj is a biochemist whose transformative work on the synthesis of artificial cells and membranes has created an exciting new field of research that aims to address one of the great challenges in synthetic biology. He has made several game-changing discoveries. Among his signature achievements is the development of new methods for labeling biological molecules, which are so widely used by researchers that reagent suppliers now include his probes in their catalogs.
Neil Garg (University of California, Los Angeles) – Dr. Garg is a synthetic organic chemist who is a world leader in the synthesis of complex molecules. Some of his creative work involves the development of reactions involving cyclic alkynes, which are a chemical species traditionally considered too reactive to be useful. His reactions are now employed by the pharmaceutical industry to synthesize new drug candidates. Dr. Garg is considered an innovator in chemical education and has made significant contributions to the field of catalysis — developing new reactions that allow chemists to break bonds that were once considered unbreakable.
Christy Haynes (University of Minnesota, Twin Cities) – Analytical chemist Dr. Haynes is a pioneer in the development of novel assays to assess the toxicology of nanoparticles in physiological and ecological systems. She has shown definitively that nanoparticles can alter cellular function and has been working to redesign nanoparticles so that they have maximal technological impact and minimal unintended consequences.
Bo Huang (University of California, San Francisco) – Dr. Huang, a chemical biologist, has innovatively repurposed CRISPR-Cas9 (a cutting-edge gene-editing tool) as a tool for visualizing the chromosomes in living cells, an advance that is reshaping how scientists approach the study of the function and alterations of the human genome. In addition, he has pioneered the development and application of endogenous labeling and super-resolution microscopy techniques to the study of various biological systems.
Joseph Subotnik (University of Pennsylvania) – Dr. Subotnik is a theoretical chemist who has made significant advances in the area of modeling electronic relaxation: the relaxation of electrons into their least energetic state. The work is significant because it provides one of the few practical and rigorous means of modeling catalytically active and photo-excited materials. Dr. Subotnik’s work has made great strides towards closing the gap between accurate theoretical chemistry models and experimentally obtained results.
Emily Weiss (Northwestern University) – Dr. Weiss is a physical chemist doing pioneering cross-disciplinary work using semiconductor quantum dots as model systems to study processes at interfaces between different materials. Quantum dots are excellent light absorbers and emitters over the entire visible and near-infrared spectrum, and have properties tunable by their size and chemical structure. As such, they find applications in solar energy conversion, photocatalysis of chemical reactions, and biological and chemical sensing.
2018 Blavatnik National Finalists in Physical Sciences & Engineering
From predicting and understanding the behavior and make-up of astronomical bodies with astonishing accuracy to using enormous data sets to understand more about the human condition, the 2018 National Finalists in Physical Sciences & Engineering are pushing the boundaries of human knowledge and understanding of the universe around us, both near and far. This year’s Finalists are also rapidly advancing our scientific understanding of unique physical phenomena that exist at the nano- and even atomic scale, helping to create technologies that will revolutionize the telecommunications, opto-electronics, and energy storage industries.
Andrea Alù (The Advanced Science Research Center at The Graduate Center of the City University of New York; formerly of University of Texas at Austin) – Electrical engineer and physicist Dr. Alù has made seminal contributions to the theory and engineering of metamaterials and introduced new concepts to create metamaterials that mold electromagnetic waves, light and sound in unusual ways. He has made pioneering discoveries in plasmonic cloaking and invisibility, optical nanocircuits and nanoantennas, and in generating nonlinear and nonreciprocal optical responses in metamaterials.
Alexandra Boltasseva (Purdue University) – A physicist and electrical engineer, Dr. Boltasseva’s research approach merges the field of optics with materials engineering and is making possible a new generation of nanophotonic technologies and all-optical devices for telecommunications, sensing, energy and information processing. Her research in plasmonics – where light is confined to the nanoscale enabling a range of new devices to be developed – has uncovered new tailorable ceramic plasmonic materials, which have improved performance over previously used materials.
Xiangfeng Duan (University of California, Los Angeles) – As a physical chemist, Dr. Duan focuses on the design and synthesis of highly complex nanostructures with controlled chemical composition, structural morphology and physical dimensions. He places particular emphasis on the integration of nanoscale structures with different chemical composition, structure or function, thereby creating a new generation of integrated nanosystems with unprecedented performance or unique functions to break the boundaries of traditional technologies.
Jonathan Fortney (University of California, Santa Cruz) – A planetary scientist, Dr. Fortney’s research challenges our current understanding of the formation, evolution and structure of distant exoplanets and planets in our very own solar system. For instance, his research investigating hot Jupiter-class exoplanet atmospheres has provided strong evidence for the existence of two unique classes of exoplanetary atmospheres on these planets and is shaping our understanding of planetary composition and formation.
Ryan Hayward (University of Massachusetts Amherst) – As a polymer scientist and chemical engineer, Dr. Hayward creates material systems with elastic buckling instabilities that transform their shape, surface morphology and material properties, on demand. He has developed microscale polymeric sheets that self-fold into origami structures and 3D shapes in response to external stimuli such as light and heat. His work also focuses on the assembly of nanoscale materials such as polymer nanowires and polymer-embedded nanoparticles to control macroscale properties.
Sergei V. Kalinin (Oak Ridge National Laboratory) – A materials scientist and nanoscientist, Dr. Kalinin creates novel technologies to study and control the functionality of nanomaterials by combining imaging, big data and materials theory. Dr. Kalinin and his collaborators recently challenged a 25-year paradigm by proposing and implementing the atomic forge — a new approach that uses the atomically-focused beam of a scanning transmission electron microscope to control and direct matter, manipulating single atoms to enable fundamental physical studies and also to develop quantum computing and single spin magnetoelectronic devices.
Jure Leskovec (Stanford University) – Dr. Leskovec is a computer scientist who has revolutionized our understanding of large social and information networks. Using experiments, analysis and modeling, he was first to validate the “six degrees of separation” hypothesis and demonstrated how influence and trust propagate through social networks and shape online communities, viral networking and media bias.
Ying Shirley Meng (University of California, San Diego) – Dr. Meng, a materials scientist and engineer, utilizes computational approaches and unique operando and in-situexperimental approaches to understand, develop and optimize the behavior and operation of electrolyte and electrode materials in batteries to drive better energy storage and conversion performance. She and her team recently developed a novel type of liquefied gas electrolyte material that allows battery operation at ultra-cold temperatures.
Brian Metzger (Columbia University) – As a theoretical astrophysicist, Dr. Metzger works on a broad range of topics related to the “transient” universe. In 2010, he predicted the visual flares — termed “kilonova” — that accompany the coalescence of binary neutron stars. In 2017, the LIGO/Virgo collaboration detected gravitational waves from merging neutron stars for the first time. The fading light seen following this event agreed remarkably well with Dr. Metzger’s predictions and revealed these mergers as factories of the heaviest elements — like gold — in the Universe.
Anastasia Volovich (Brown University) – Dr. Volovich is a theoretical physicist working in quantum field theory, general relativity and string theory. She has developed extremely efficient methods to evaluate scattering amplitudes, the key quantities that describe scattering of elementary particles, and discovered a remarkable connection between mathematical cluster algebras and scattering amplitudes, sparking an intense new interaction between physics and mathematics.
Gleb Yushin (Georgia Institute of Technology) – A materials scientist and nanoscientist, Dr. Yushin has made multiple transformative contributions to the synthesis of advanced materials for batteries and supercapacitors. Combining innovative nanoscale synthesis approaches with the development of novel analytical techniques, he develops nanostructured and nanocomposite materials with remarkable performance characteristics. He has recently discovered a fundamentally new synthesis mechanism to fabricate oxide nanowires from low-cost powders. His research has applications in next generation electric vehicles and electronic devices.
The lack of new antibiotics is among the most critical challenges facing medicine. Researchers have been on the hunt for new drugs to combat "superbugs" that cannot be penetrated by current antibiotics.
This side-view x-ray shows a pseudomonas infection at the top of the lung. It appers as a torn shroud with black cavities.
Rather than looking for drugs that forcibly penetrate bacteria, researchers tried a new approach: tricking bacteria into taking up a molecule that looks like food, but wreaks havoc once inside. A study of this approach shows initial success in mice and humans.
The work is described in the Sept. 26, 2018, issue of Science Translational Medicine. The two primary investigators, Pradeep Singh and Christopher Goss, are faculty members at the University of Washington School of Medicine.
Their study focused on one superbug, Pseudomonas aeruginosa, which causes infection in the lungs, urinary tract, wounds and elsewhere. It is a particular problem in patients whose ability to fight infection is impaired because of illnesses such as cystic fibrosis, cancer and AIDS.
The researchers studied gallium because it is a metal similar to iron, a critical nutrient for bacteria during infection.
"The body goes to great lengths to keep iron away from bacteria, and infecting organisms crank up special systems to import iron and steal it from the host," said Singh, the senior author and a UW professor of microbiology and medicine.
Goss, a UW professor of medicine and pediatrics and the paper's first author, described gallium as a Trojan horse. "Gallium not only fails to nourish bacteria as iron would, it actually harms them."
The researchers also discovered how gallium works. "Gallium disrupts machinery that bacteria use to make new DNA, and without this the bacteria can't multiply," said co-author Bradley Britigan, professor of internal medicine at the University of Nebraska Medical Center. "This and other essential processes require iron, and gallium is a monkey wrench that shuts the system down."
UW Medicine researchers Pradeep Singh and Christopher Goss
In lab studies, bacteria developed resistance to gallium at low rates, and gallium's potency was increased when used in combination with some existing antibiotics. These factors led the researchers to test gallium in mice and then in humans.
In mice, researchers found that a single dose cured lethal lung infections. They then studied gallium in 20 people with cystic fibrosis (CF) and difficult-to-treat lung infections caused by antibiotic-resistant Pseudomonas bacteria.
"Our preliminary study in a small group of people with CF suggests that gallium is safe and improves patients' lung function," Goss said. "These are exciting results, but we need to do more studies to determine if gallium can be developed into a routine, safe treatment."
The idea of disrupting bacterial nutrition as an antimicrobial strategy was raised in the 1800s by Louis Pasteur, but such treatments have been difficult to develop.
Crystals of gallium. Wikimedia Commons Photo
Could gallium-based therapies be the exception to that experience? "That's our hope, and we're encouraged by these results, but we've have to be cautious and do more work before we'll know," said Singh.
Researchers at the UW School of Pharmacy, Johns Hopkins University, University of Chicago, University of Iowa, and Osaka City University in Japan also contributed to this study.
The research was supported by the National Institutes of Health (UM1HL119073, R01HL085868, P30DK089507, and K24HL102246), Cystic Fibrosis Foundation, Arcadia Foundation, Burroughs Wellcome Fund, the U.S. Department of Veterans Affairs, and the University of Washington's Institute for Translational Health Sciences.
Can you provide a brief overview of your lab’s current research focus?
The research in the Greenberg laboratory focuses on the emerging field of sociomicrobiology – the group-behaviors of microbes. We are interested in the biochemistry and molecular biology of environmental sensing/response with a particular emphasis on a form of chemical communication between bacteria termed “quorum sensing”. In quorum sensing, bacteria synthesize chemical signals as cues to coordinate activities of individuals in groups. This signaling plays a critical role in the development of many bacterial infections.
What is the significance of the findings in this publication?
In many plant-associated bacteria, the quorum sensing receptor no longer senses its own quorum sensing signals – instead the system has evolved to recognize compounds present in the plant host. Although these plant-responsive receptors were described more than a decade ago, the factor(s) they sense were unknown until now. Our work describes the identification of an ethanolamine-derived molecule that serves as signal for a plant-responsive receptor in a Poplar tree endophyte, Pseudomonas sp GM79. Ethanolamine is a building block for plant membrane phospholipids and signaling molecules. This discovery connects at least one of the plant-responsive receptors to a growing understanding of ethanolamine chemistry and responses of bacterial cells to ethanolamine and its derivatives. These plant-responsive systems regulate virulence and symbiosis in plant-associated bacteria, so defining how they work and the plant molecules that control them could contribute to improved crop disease management and the resourceful use of biofertilizers.
What are the next steps for this research?
Our discovery leads to several questions regarding the biology and biochemistry of this interkingdom signaling system: do similar receptors in other plant-associated bacteria respond to the same, or related, ethanolamine-derived signal? What impact does the signal have on plant host-bacteria interactions? These are just some of the questions we are interested in answering in the near future.
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This work is part of a collaborative, multidisciplinary project with the Plant-Microbe Interfaces (PMI) Scientific Focus Area at Oak Ridge National Laboratory, funded by the Office of Biological and Environmental Research (BER) within the US Department of Energy (DOE) Office of Science. More information on the PMI research can be found at: https://pmiweb.ornl.gov/
Peter Greenberg, professor of microbiology at the University of Washington, Seattle, describing the phenomenon of quorum sensing, wherein microbes use chemical signals to determine the size of their group, and take action when it reaches an appropriately high number.
The University of Washington maintained its No. 10 spot on the U.S. News & World Report’s Best Global Universities rankings, released Tuesday. The UW is second among American public institutions. UW Microbiology is ranked #4!
With many disease-causing bacteria ratcheting up their shields against current drugs, new tactics are vital to protect people from treatment-resistant infections.
Lowering mutation rates in harmful bacteria might be an as yet untried way to hinder the emergence of antimicrobial-resistant pathogens. This proposed strategy comes from recent findings in infectious disease research at UW Medicine in Seattle.
The report on this work is published this week in Molecular Cell, one of the journals of Cell Press. The lead author is Mark N. Ragheb, an M.D./Ph.D. student at the University of Washington School of Medicine. The senior researcher is Houra Merrikh, associate professor of microbiology at the UW medical school.
For the second year, Microbiology Professor Joseph Mougous, PhD, has been selected as a finalist for the Blavatnik National Award for Young Scientists in Life Sciences. Congratulations to Dr. Mougous for this prestigious recognition and honor. Learn more about the Blavatnik National Awards and the recognition of Dr. Mougous' work here.
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.
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.
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.
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.