ISB News

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…

Xconomy Seattle 2035

Attend Xconomy’s Seattle 2035 on Oct. 30 at ISB’s event space (401 Terry Ave. N., Room 106). This conference, co-hosted by Northeastern University, highlights the next 20 years and beyond to explore long-term prospects of the local high-tech economy and what we can do to keep Seattle a city of the future. ISB President Dr. Lee Hood and ISB SVP and Director Dr. Nitin Baliga are featured speakers. The event…

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

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…

Bio-Fiction Recap

On May 7, ISB hosted the first-ever screening of BIO·FICTION in North America. More than 120 people attended the event, which took place as part of the South Lake Union Art Walk. BIO·FICTION explores the emerging field of synthetic biology from different disciplinary angles including science and engineering, social science, cultural studies, amateur biology, filmmaking, art and design. The original program had presentations, panel discussions, do-it-yourself biology demos, performances, art…

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…

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…

Washington Gov. Jay Inslee, center, chats with two of his staff members, left, and, at right, Dr. Nitin Baliga and Dr. Dana Riley Black, both of Institute for Systems Biology, Institute for Systems Biology/March 16, 2015

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…

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…

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…

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…

4 Minutes of Green Gold: Watch Algae Grow

There’s something calming about watching algae grow. What you see in the tubes are two types of algae: Thalassiosira pseudonana or “Thaps” is the brown diatom. Chlamydomonas reinhardtii or “Chlamy” is the green algae. We use Thaps to study ocean acidification and Chlamy is for studying biofuel production.

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…

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…

PROJECT BIOTECH Camp goers

PROJECT BIOTECH Summer Camp Report

Photo above: Students participating in PROJECT BIOTECH Summer Camp. Photo credit: Shoreline Community College By Dina Kovarik Project Manager, Baliga Lab The Shoreline Community College (SCC) Biotech Program and the Amgen Biotech Experience (ABE) program partnered with the Institute for Systems Biology (ISB) to develop a one‐week summer camp for high school students called PROJECT BIOTECH. The camp took place at SCC on July 7‐11, 2014. While the Puget Sound…

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…

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…

Decoding the Microbial Gene-Recycling Program: Researchers 'Unzip' Genetic Instruction Manuals

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…