New Study on How Microbes Learn to Predict the Future
July 28, 2017
In a study published in Genome Biology and Evolution, researchers at Institute for Systems Biology (ISB) designed an experiment to evolve novel adaptive prediction capability in yeast by repetitively exposing it to caffeine, followed by a toxin. Remarkably, the yeast cells learned the structure of this novel environmental pattern within as few as 50 generations to use caffeine as a cue for anticipating and mitigating lethal effects of the toxin.
3 Bullets:
- Like plants and animals, even microbes can anticipate and prepare in advance for future changes in their environment
- Similar to how Pavlov trained a dog to anticipate food when it heard a bell, ISB researchers trained yeast to anticipate a lethal toxin when it sensed caffeine
- The study revealed how in a very short period of time yeast can evolve to ‘learn’ and ‘predict’ new patterns in their environment
Related Articles
-
ISB develops stress test to predict how diatoms will react to ocean acidification
In a study published in Nature Communications and with implications for understanding effects of climate change, ISB researchers show microscopic phytoplankton are more resilient in an acidified environment.
Read More -
Dr. Sean Gibbons joins ISB faculty as WRF Distinguished Investigator
Dr. Sean Gibbons has joined ISB as our newest faculty member. Gibbons’ new position brings a number of changes, including relocating to the Pacific Northwest from the Northeast. Read on for a Q&A with Gibbons that sheds light on his research career to date, areas of study and even a hidden talent.
Read More -
ISB’s Dr. Eliza Peterson Earns TB Junior Investigator Award
Dr. Eliza Peterson, a senior research scientist who studies tuberculosis (TB) in the Institute for Systems Biology’s Baliga Lab, has been recognized by the University of Washington’s Tuberculosis Research and Training Center with a TB Junior Investigator Award.
Read More
-
The Other Malaria: Finding New Targets for a Vaccine Against Plasmodium vivax
A new report in PLOS Neglected Tropical Diseases describes the results of an international collaboration led by researchers at ISB and Seattle’s Center for Infectious Disease Research (CIDResearch). We used mass spectrometry-based proteomics to identify nearly 2,000 proteins present in Plasmodium vivax parasites, one of the Plasmodium species that cause the disease malaria in humans. The work was done on parasites dissected from mosquito salivary glands, parasites that were in…
Read More -
Institute for Systems Biology and Arivale “Pioneer 100 Study” Establishes Foundation for New Industry of Scientific Wellness
Institute for Systems Biology and Arivale “Pioneer 100 Study” Establishes Foundation for New Industry of Scientific Wellness. Personal, dense, dynamic data clouds enable novel insights into mechanisms of wellness and disease, new approaches to biomarker discovery, and the empowerment of individuals to enhance their own health.
Read More -
Spotlight: Ayodale Braimah, Undergraduate Intern
Congratulations to Ayodale Braimah, an undergraduate intern in the Baliga Lab, who has just been accepted into the medical school at the University of Kansas. Ayodale has been studying microbiology at the University of Washington and sought a position in the Baliga Lab in order to immerse himself in an authentic research experience in microbiology and molecular biology. He specifically wanted to better understand how organisms adapt to new environments….
Read More
-
Spotlight: Claudia Ludwig
Congratulations to Claudia Ludwig, Director, Systems Education Experiences (SEE), on being named the winner of the 2017 AWIS Award for Excellence in Science Outreach from the Seattle Chapter of Association for Women in Science (AWIS). Claudia, a former high school biology and chemistry teacher, is the Director of Systems Education Experiences at ISB, a program that she has been instrumental in building since she joined ISB in 2004. Because of…
Read More -
ISB Scientists Have Discovered When and Why a Microbial Community Might Collapse
Researchers in the Baliga Lab at Institute for Systems Biology have developed a framework for assessing the “health” of a microbial community through a stress test that enables them to ask when and why microbial communities collapse under different environmental conditions. The study, published on March 20, 2017, in the journal Molecular Systems Biology, determined that while microbes are equipped to respond to environmental changes, when pushed to the extreme…
Read More -
ISB High School Intern Gives TEDx Talk
Radhika Dalal, a student at Kamiak High School in Mukilteo, presented a talk at TEDxSnoIsleLibraries on Nov. 18. She also participated in a summer internship at ISB to learn how to become a student ambassador for Project Feed 1010, a Baliga Lab research initiative that aims to make scientific breakthroughs for scaling up sustainable agriculture as well as developing and implementing associated STEM curriculum in high schools across the United…
Read More
-
Project Feed 1010 High School Interns Launch Video
High school students Linnea Stavney and Ivan Esmeral produced this awesome documentary about their summer internship in our Baliga Lab, where they helped to oversee work related to Project Feed 1010.
Read More -
‘Invisible Forest’ Curriculum
By Claudia Ludwig Baliga Lab Education Program Manager The past nine days have been exciting for the Baliga Lab. Dr. Anne Thompson and I have been working with eight teachers to begin the process of translating Anne’s oceanography research on the Invisible Forest into curriculum that offers a hands-on, engaging experience for high school students. The group developed the framework and drafted lessons that will be field tested this year….
Read More -
New Baliga Lab Publication in Cell Systems
The Baliga Lab’s Dr. Christopher Plaisier was the lead author of the study “Causal Mechanistic Regulatory Network for Glioblastoma Deciphered Using Systems Genetics Network Analysis” which published online in Cell Systems on July 14. Dr. Plaisier wrote a summary of the research: 3 Bullets: Using data from TCGA and ENCODE, ISB researchers developed integrative database and analysis platforms that provide insight about the underpinnings of glioblastoma multiforme. Researchers developed a…
Read More
-
Project Feed 1010 Partners with Northeastern University to Advance Sustainable Agriculture
ISB’s Project Feed 1010 is building a global, crowd-sourced network of educators, students, researchers and farmers to optimize and scale-up sustainable agriculture practices and educate the future scientific workforce. To support this global network, we have partnered with Northeastern University to develop database, web and mobile infrastructures with functionalities for data tracking, monitoring, analytics and predictive modeling. For the next 10 weeks, more than 20 graduate-level computer science students will…
Read More -
Learning From Microalgae as ‘Biofactories’
In a newly published research, members of the Baliga and Price labs share discoveries from their studies of Chlamydomonas reinhardtii – Chlamy for short. Excerpt: To the casual observer, algae may appear to be a nuisance. But for researchers, photosynthetic microalgae and other microbes have the potential to become sustainable biofactories that can economically produce renewable biofuels and a wide variety of other valuable commodities. One such group of microalgae…
Read More -
ISB Q&A: Nina Arens and Pop-Up Science
Q: What is your role? A: I am a Research Associate for the Baliga Lab, where I perform genome-wide experiments that feed into the complex, predictive software tools that we create here. One project I work on investigates how microbial communities respond to stressful environmental changes over time. It is challenging research: my model organism—Desulfovibrio vulgaris—is hard to grow at the bench. Desulfovibrio is anaerobic; it likes to grow in…
Read More
-
Sustainable Agriculture: Project Feed 1010 Launches
ISB is crowdfunding for the first time. We are raising money to support high school science teachers and their students to become citizen scientists for Project Feed 1010, our new study that aims to optimize aquaponics and that will impact #STEM education. Watch our video: https://www.crowdrise.com/ProjectFeed101024forScience #24forScience
Read More -
Genetic Switch May Help Marine Microalgae Respond to Higher CO2 Levels
3 Bullets Rapid climate change, including ocean acidification caused by increasing carbon dioxide (CO2) levels, is predicted to affect the oceans, sea life, and the global carbon cycle. Marine microalgae, including diatoms, are responsible for converting CO2 into oxygen and biologically usable carbon through photosynthesis. How these organisms will respond over the short and long term to rising CO2 is unknown. Growth experiments and transcriptomic analyses performed by UW and…
Read More -
Monica Orellana Promoted to Principal Scientist
In her 11 years as a senior scientist in the Baliga lab at ISB, Monica has successfully developed a rigorous program on marine and oceanographic systems, and has been a pioneer in transcending traditional disciplinary boundaries and transferring systems methodology developed at ISB to explorecomplex oceanographic problems of global importance. Her highly collaborative and cross-disciplinary work involves laboratory and field studies that integrate physiological, molecular and physical-chemical approaches to understand…
Read More
-
ISB Q&A: On the Systems Biology Summer Course
From our inception, we at ISB have been committed to knowledge transfer. This profound sense of responsibility to share what we learn serves as the foundation for our signature professional course on systems biology. This year’s course, which takes place July 27-31 in ISB’s conference facility, will offer a few new features, including lightning talks about systems biology technologies and a mini symposium consisting of research vignettes from nine ISB…
Read More -
ISB Q&A: High School Science Teachers
From left to right: High school teachers Tami Caraballo and Jennifer Duncan-Taylor work with ISB’s Claudia Ludwig, Baliga Lab Education Program Manager, to learn about ocean acidification, cancer cells, and biofuel. Through the MJ Murdock Charitable Trust’s Partners in Science program, ISB has been able to host two high school science teachers in the Baliga Lab to participate in active research projects. The experience offers teachers valuable insight that textbooks…
Read More -
The Most Powerful Tool for Reconstructing a Gene Network
Scanning EM of bacteria being eaten by white blood cell Photo Credit: Adrian Ozinsky 3 Bullets: Nearly a decade ago, ISB’s Baliga Lab published a landmark paper describing cMonkey, an innovative method to accurately map gene networks within any organism from microbes to humans. Two new papers describe the benchmark results of cMonkey and also the release of cMonkey2, which performs with higher accuracy. Using this approach, genetic and molecular…
Read More
-
Baliga Lab: A Global Map To Fight Tuberculosis
3 Bullets: The disease progression of tuberculosis is extremely complex and it’s poorly understood. ISB and Seattle BioMed researchers have made an important step by developing a comprehensive map of gene regulation in tuberculosis. A resulting open-access web portal offers any scientist the ability to mine the collected data. By ISBUSA Tuberculosis (TB) remains a top global health threat due to its remarkable complexity in disease progression. To help understand…
Read More -
Gov. Inslee Hosts Round Table With College Students at ISB
Gov. Jay Inslee hosted a round table discussion today at Institute for Systems Biology with a group of invited college students, who were asked to share their thoughts on the affordability of education. We were honored to be able to provide the venue. ISB has had a long history of supporting systemic change at the K-12 school district level to improve the quality and access of STEM education. Now, our…
Read More -
Baliga Lab: ‘The Universe Under a Microscope’
This is an excerpt from Environmental Microbiology Reports, 2015, authored by Arjun Raman, a postdoc in the Baliga Lab here at Institute for Systems Biology. The beauty of a living thing is not the atoms that go into it, but the way those atoms are put together. Information distilled over four billion years of biological evolution. Incidentally, all the organisms on the Earth are made essentially of that stuff. An…
Read More
-
ISB Q&A: High School Intern Alex Kuo
Alex Kuo was a high school intern during summer 2014. She reflected on her ISB experience: Q: What were your first impressions of ISB? Alex: ISB is a pivotal force in Seattle’s scientific community, especially when it comes to collaboration across multiple disciplines. Given the magnitude and complexities of the research that’s done at ISB, it would seem unlikely that a high school student would be able to participate in…
Read More -
Tuberculosis Research: A ‘Molecular Road Map’ to Help Understand Gene Regulation
The journal “Trends in Microbiology” recently published a spotlight article on a tuberculosis research collaboration between scientists at Institute for Systems Biology and Seattle BioMed. The paper “The DNA-binding network of Mycobacterium tuberculosis” was published in the journal “Nature Communications” (Jan. 12, 2015): “MTB employs about 200 different molecular switches to sense and respond to the shifting, hostile landscape of the host. To identify and understand the intertwining gene regulatory…
Read More -
ISB’s Women in Oceanography
Photos above: (Left) Anne Thompson and (right) Mόnica Orellana as featured in “Women in Oceanography: A Decade Later.” BY ISBUSA Two of ISB’s senior research scientists are featured in the second edition of “Women in Oceanography.” Dr. Mόnica Orellana and Dr. Anne Thompson, both of the Baliga Lab, share their stories about what inspired their careers in oceanography and some of their thoughts about working in the field. The inaugural issue…
Read More
-
Pushing the Molecular Switches of Tuberculosis Into Overdrive to Map Interactions
3 Bullets: Mycobacterium tuberculosis (MTB) infects more than 1.5 billion people worldwide partly due to its ability to sense and adapt to the broad range of hostile environments that exist within hosts. To study how MTB controls its responses at a molecular level, ISB researchers and their collaborators at Seattle Biomed perturbed almost all MTB transcription factor regulators and identified the affected genes. This comprehensive map of molecular switches in…
Read More -
How One Family of Microbial Genes Rewires Itself for New Niches
3 Bullets: When an organism duplicates its genes, it increases its ability to adapt and colonize new environments. ISB researchers used the systems approach to study how one family of microbial genes evolved to bring functions that were adaptive to specific environments. This new understanding of how gene regulatory networks rewire themselves has many potential applications, including how to wire new functions into an organism for biofuel production, bio-remediation or…
Read More -
How Physics and Thermodynamics Help Assess DNA Defects in Cancer
3 Bullets: ‘Big data’ cancer research has revealed a new spectrum of genetic mutations across tumors that need understanding. Existing methods for analyzing DNA defects in cancer are blind to how those mutations actually behave. ISB scientists developed a new approach using physics- and structure-based modeling to systematically assess the spectrum of mutations that arise in several gene regulatory proteins in cancer. By Jake Valenzuela and Justin Ashworth A significant…
Read More
-
New Tool Uses 3-D Protein-DNA Structures to Predict Locations of Genetic ‘On-Off’ Switches
3 Bullets: Novel systems approach uses high-resolution structures of protein-DNA complexes to predict where transcription factors (genetic switches) bind and regulate the genome. This approach can help researchers better understand and predict binding sites for non-model organisms or ‘exotic’ species. Having such insight and predictive capabilities is critical for reverse- and forward-engineering organisms that could be pivotal for new green biotechnologies. By Jake Valenzuela and Justin Ashworth Researchers at the…
Read More -
Baliga Lab: Uncovering the Genetic Adaptability of Tuberculosis
3 Bullets: The Institute for Systems Biology and Seattle BioMed have collaborated to reconstruct the gene regulatory network of the human pathogen Mycobacterium tuberculosis. Finely tuned gene regulation has allowed Mycobacterium tuberculosis to survive unnoticed in an apparently healthy host for decades; understanding those subtleties is critical for advancing treatment. The identification of co-regulated sets of genes and their regulatory influences offers validated predictions that will help guide future research…
Read More -
New Structural Map Helps To Understand Aggressive Tumors
3 Bullets: Aggressive tumor growth is linked to high activity of a macromolecular assembly called RNA polymerase I. ISB and FHCRC researchers collaborate to map the architecture of the assembly using a powerful crosslinking-mass spectrometry (CXMS) technology. Structural maps provide important insights into therapeutic targets for cancer treatment. By Mark Gillespie Rapidly growing tumor cells require large amounts of protein for their survival. This increased protein synthesis, or translation, can…
Read More
-
New Open-Access Multiscale Model Captures Dynamic Molecular Processes in Unprecedented Detail
3 Bullets: Microbes are efficient because their streamlined genomes allow them to evolve and adapt rapidly to complex environmental changes. Decoding the highly-compressed information within a microbial genome requires sophisticated systems biology tools to map the genetic programs, and understand how they are executed. ISB researchers invented novel algorithms to unzip and decode microbial genomes into the EGRIN 2.0, an open-access multiscale model that captures instructions for executing the dynamic…
Read More -
LAB NOTEBOOK: Evolution Beyond Darwin
(Photo: Dr. Sui Huang presenting during an ISB systems biology discussion group on May 15, 2014.) LAB NOTEBOOK: At ISB, we hold systems biology discussion groups every Thursday during lunch. The topics vary from week to week, but the intention is to inspire exchanges amongst our staff. Today's discussion group was presented by Dr. Sui Huang – our resident theorist, who always poses just the right question to provoke thought…
Read More -
Tiniest Malfunctions in a Cell Can Cause Devastating Diseases
3 Bullets: ISB researchers are studying peroxisomes, which are cellular organelles that are linked to a rare syndrome that causes progressive organ complications and infant mortality. Peroxisomes have a role in metabolizing and breaking down cellular waste. Because peroxisomes easily change shape and function according to a cell’s needs, a systems approach is necessary to help decipher that complexity. By Dr. Thurston Herricks Dane Tolmie was a 19-month old boy…
Read More
-
Now Accepting ISB Internship Applications
ISB’s summer internships for high school and undergraduate students are highly competitive — who wouldn’t want to work leading experts in systems biology research? The application process is now open. If you or someone you know may be interested in applying, visit the following links: High School Internships Undergraduate Internships
Read More -
Science Education Impact
The educators who work at ISB continue to influence how science is taught in the State of Washington. Claudia Ludwig and Dina Kovarik, members of the Baliga Lab education team, recently helped the Highline School District apply for a $1,000 grant to use toward systems science materials and teacher training. Highline’s Arts and Academics Academy received the award, which will also provide students with “real-world” lab experience.
Read More -
Greater Good: Successful High School Interns
Every summer, ISB welcomes a group of high school interns, hosted through our Systems Education Experiences program. ISB is proud of its collaborative and cross-disciplinary culture and we work hard to nurture an environment that allows our staff to achieve at a high level. It was especially gratifying to get this comment from one of our interns, who had just completed her time here: “At ISB, I witnessed collaboration that…
Read More
-
Open Science: A Hack Your PhD Interview with Dr. Nitin Baliga
Célya Gruson-Daniel, the founder of HackYourPhD, has been traveling across the United States to make a documentary about open science. She stopped by ISB on Aug. 5, 2013, to interview Dr. Nitin Baliga, who is our senior vice president and director. The short interview is below. Learn more about the Hack Your PhD documentary at this site: http://hackyourphd.org/USA
Read More -
ISB in Antarctica
There have been many stories in the news about research projects in Antarctica. Most projects are related to the climate and environment, or to how organisms survive in such extreme conditions. On Feb. 6, for example, the New York Times published a report about the Wissard (Whillans Ice Stream Subglacial Access Research Drilling) project, which involves looking for a microbial community in the lake located half a mile under the…
Read More -
Science Luminaries
In June, Dr. Lee Hood, ISB’s president and co-founder, was one of the featured speakers at the Seattle Science Festival’s Science Luminaries event. His co-luminaries were world-renowned physicist Dr. Stephen Hawking and paleontologist Jack Horner. ISB also co-hosted the South Lake Union Science Trek for K-12 students.
Read More