Systems and Synthetic Biology Cluster

Spotlight on MCB-funded Science

 

A spotlight illuminates the words 'Spotlight on MCB-funded Science.'

Photo Credit: Matusciac Alexandru/Shutterstock.com

Sharing MCB Science is one of our six blog themes where you can learn about exciting MCB-funded research submitted by our investigators (via this webform). We greatly appreciate the overwhelmingly positive response of the MCB scientific community and have received many more submissions than can be featured in long form on the blog. Enjoy this shorter spotlight of submissions we have received!

Ever wonder how a cell makes a tough decision? When food is scarce, Bacillus subtilis (a common soil bacteria) faces a difficult choice of when to shut down cellular processes and become dormant via sporulation (spore formation). Timing is key: wait too long and die from starvation; sporulate too early and die from crowding by rapidly dividing neighboring bacteria. What serves as the trigger – a specific biochemical signal or a more general physiological response – to enable starvation sensing and sporulation was unknown. As part of a collaborative project, Dr. Oleg Igoshin, an Associate Professor in the Department of Bioengineering at Rice University, Dr. Masaya Fujita, an Associate Professor in the Department of Biology and Biochemistry at the University of Houston, and their research teams applied computational and mathematical tools to this biological question. As described in this publication, they discovered the rate at which the cell grows may serve as a signal of starvation, triggering spore formation. This work could lessen food spoilage and control food-borne pathogens by offering new ways to inhibit sporulation in close relatives of B. subtilis that live on food.

This work is partially funded by the Systems and Synthetic Biology Cluster of the Division of Molecular and Cellular Biosciences, Awards #MCB – 1244135 and #MCB – 1244423.

Diatoms (a unicellular photosynthetic microalgae) are an important part of food webs, especially in areas of the ocean with an abundance of fish frequented by the fishing industry. Because conditions and availability of environmental resources change, diatoms regulate physiological functions (such as the carbon-concentrating mechanisms (CCMs) and photorespiration previously described) at the level of gene expression. Instead of focusing on one environmental condition or type of diatom, Dr. Justin Ashworth (Post-doctoral Fellow),  Dr. Monica Orellana (Principal Scientist) and Dr. Nitin Baliga (Senior Vice President and Director) of the Institute for Systems Biology integrated all publicly available microarray data (displaying gene expression levels) from multiple conditions for the model diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum to look for trends. As described in this publication and in the resulting integrative analysis available online at the Diatom Portal, the research team uncovered common patterns of gene expression and function. They also identified potential cis-regulatory DNA sequence motifs and distinct regions induced in response to changes in ocean pH levels and the availability of nitrate, silicic acid, and carbon. A greater understanding of this fundamental level of regulation enables scientists to better support diatoms in their role as biogeochemical nutrient recyclers.

This work is partially funded by the Cellular Dynamics and Function Cluster of the Division of Molecular and Cellular Biosciences, Award #MCB – 1316206.

As we previously described on the MCB Blog, the laboratory of Dr. Alexander Mankin and Dr. Nora Vázquez-Laslop at the Center for Biomolecular Sciences, University of Illinois – Chicago, studies fundamental mechanisms in protein synthesis. Ribosomes inside the cell read three mRNA nucleotides at a time (a reading frame) during protein synthesis (translation). Sometimes, the ribosome slips one or two nucleotides on the mRNA to a different reading frame (frameshift). Recent work on the E. coli bacterial copper transporter gene (copA) by Drs. Mankin, Vázquez-Laslop, and their research team uncovered a slippery sequence in the mRNA that led to “programmed frameshifts.” Depending on whether or not the ribosome slipped, two different proteins were made – a previously unidentified copper chaperon protein or a copper transporter protein. Together, the copper chaperon and transporter proteins help protect the bacterial cell from internalizing too much copper. This work provides new insight into how bacteria change gene expression in different environmental conditions and offers training for student researchers such as lead author Sezen Meydan, who was highlighted in the ‘Meet the Author’ section of Molecular Cell.

This work is partially funded by the Genetic Mechanisms Cluster of the Division of Molecular and Cellular Biosciences, Awards #MCB – 1244455 and #MCB – 1615851.

CONGRATULATIONS TO 2017 PRESIDENTIAL EARLY CAREER AWARDEE, DR. AHMAD KHALIL!

Dr. Ahmad Khalil is smiling, arms crossed, standing in front of his lab bench while wearing a blue and white checked shirt and glasses.

MCB would like to congratulate Dr. Ahmad (Mo) Khalil, recipient of the 2017 Presidential Early Career Award for Scientists and Engineers (PECASE). The PECASE award is the most prestigious honor a scientist or engineer can receive from the U.S. government early in their independent research career.

PECASE selection is a highly competitive process. As we previously noted on the MCB Blog, awardees must first receive a Faculty Early Career Development (CAREER) award. Dr. Khalil received his CAREER award from the Systems and Synthetic Biology Cluster in the Division of MCB. The National Science Foundation annually nominates up to twenty CAREER awardees for the PECASE award, and the White House Office of Science and Technology Policy makes the final selection of PECASE awardees.

Dr. Khalil was selected to receive a PECASE award because his work is an outstanding example of innovative research at the frontiers of science and technology and because of his strong commitment to service, scientific leadership, education, and outreach. His research uses synthetic biology to engineer cellular networks; the specific focus of his CAREER award is to develop synthetic tools to study the function of prions in yeast cells and populations. You can read more about his research at Boston University on his lab’s website or in a post we featured via the Share MCB Science blog theme.

Please join us in congratulating Dr. Khalil!

This work is partially funded by the Systems and Synthetic Biology Cluster of the Division of Molecular and Cellular Biosciences, CAREER Award #MCB-1350949.

MCB WELCOMES DR. DEVAKI BHAYA, PROGRAM DIRECTOR FOR THE SYSTEMS AND SYNTHETIC BIOLOGY CLUSTER

This is a headshot style photograph of Dr. Devaki Bhaya smiling at the camera with glasses on her head. Wearing silver jewelry and a black shirt, she is standing in front of forest covered mountains.

What were you doing before you came to the NSF?

I am a staff scientist at the Carnegie Institution for Science, Department of Plant Biology, which is a full-time research position, and I have a courtesy appointment as a Professor in the Department of Biology at Stanford University. I mentor both graduate and undergraduate students, collaborate with several faculty, and teach a range of courses.

What attracted you to work for the NSF?

Well, a number of things. I have been funded for most of my career by the NSF. NSF support allowed me to get back into research (after several years in India) and to develop several interdisciplinary projects. I felt this was a good time in my career to use my experience to help identify the most innovative science. Being a rotator allows me to explore the complex funding landscape, which may help me better develop future research projects. I also think strong interactions between scientists and funding agencies can bring in new ideas.

What was your first impression of the NSF? Has this impression changed since you began serving as a rotator?

I came in the day before the start of a panel, which was a bit overwhelming, but prepared me for what lies ahead. I was struck by the collegiality among the Program Directors and the professionalism of the staff. If anything, I am now even more impressed because I realize that everyone is trying to do their best, under sometimes challenging circumstances.

What personal goals would you like to accomplish while at the NSF?

I am deeply immersed in my own research, but I have become more curious about how all the pieces of the foundation fit together and how policies and directions are decided.  That’s hard to see from the “outside”, and I have already been able to get a better sense by attending seminars, retreats, and meeting people. I also felt this experience would allow me to decide whether or not I could make a difference and be happy in a longer term position at the NSF or one of the other funding agencies in the latter part of my career.

What has surprised you most about working at the NSF?

What surprised me most are the various opportunities that exist at the NSF if you can take time out of a busy schedule. I’ve been able to meet academics and Program Directors from different fields, talk to young scientists about their career goals, and attend several talks – all in the first few months! I have also been surprised at how much organizational flux there is with new people joining and others leaving; yet all the programs still run efficiently.

What are some of the challenges of serving as a rotator?

So far, the challenge has been learning the ropes (software, processes, etc.). In the future, I see the bigger challenge to make the best funding decisions. But in both cases, the fact that there are several experienced Program Directors who are always willing to answer questions and discuss issues is a huge help. This role is very different from being an established academic where one is familiar with the territory.

What would you tell someone who is thinking about serving as a Program Director at the NSF?

Serving as a Program Director is a unique opportunity to witness firsthand how much thought, complexity, and effort lies behind funding decisions. I would recommend early or mid-career scientists serve if they can afford to take the time. I’d especially encourage those who like challenges, are curious, and like to cross both social and scientific boundaries. To use an analogy – doing one’s own research is like focusing on a single star; at the NSF, you realize there are whole galaxies out there and enjoy the “big picture.”

When friends or colleagues find out that you work at the NSF, what do they say or ask?

For most of my scientist friends, working at the NSF represents the daunting challenge of using scarce resources to promote excellence in basic science and build diversity. There are some who say I must be a risk-taker who likes a challenge, but others who think I have a great opportunity to contribute to and strengthen the science community. Frankly, I think it’s a bit of both and I am eager to see how my perspectives change over the next few months.

MCB AT YOUR MEETING: OUTREACH AT THE UNIVERSITY OF PUERTO RICO AT CAROLINA

Image of Dr. Jose Garcia (Investigator at UPRC), Dr. Karilys González Nieves (Investigator at UPRC), Dr. Luis Cubano (Co-Project Director, UPRC Title V), Dr. Reyda González-Nieves (MCB Acting Operations Manager), Dr. Larry Halverson (SSB Program Director), Ms. Raquel Marti (Project Director, UPRC Title V), Dr. Linda Hyman (MCB Division Director), Dr. Wilson Francisco (MB Program Director), Dr. Jose Alvarez (Faculty Development, UPRC Title V), Dr. Moisés Orengo Avilés (UPRC Chancellor), Dr. Awilda Nueñez (Academic Dean at UPRC), and Dr. Jose Santiago (Investigator at UPRC)

Workshop Coordinators and Presenters (from left): Dr. Jose Garcia (Investigator at UPRC), Dr. Karilys González Nieves (Investigator at UPRC), Dr. Luis Cubano (Co-Project Director, UPRC Title V), Dr. Reyda González-Nieves (MCB Acting Operations Manager), Dr. Larry Halverson (SSB Program Director), Ms. Raquel Marti (Project Director, UPRC Title V), Dr. Linda Hyman (MCB Division Director), Dr. Wilson Francisco (MB Program Director), Dr. Jose Alvarez (Faculty Development, UPRC Title V), Dr. Moisés Orengo Avilés (UPRC Chancellor), Dr. Awilda Nueñez (Academic Dean at UPRC), and Dr. Jose Santiago (Investigator at UPRC)

MCB Program Directors and Division leadership regularly attend scientific meetings and workshops to garner input from the scientific community, spread the word about funding opportunities, recruit panelists, and otherwise provide information to encourage the submission of grant proposals. In September, Dr. Linda Hyman (MCB Division Director), Dr. Wilson Francisco (MCB Program Director for Molecular Biophysics (MB)), Dr. Larry Halverson (MCB Program Director for Systems and Synthetic Biology (SSB)), and Dr. Reyda González-Nieves (MCB Acting Operations Manager) traveled to Puerto Rico to support the “How to Write an Excellent Proposal” workshop hosted by the University of Puerto Rico at Carolina (UPRC).

This workshop provided an overview of the National Science Foundation (NSF) and MCB, discussed best practices in NSF grant writing and submission, and highlighted funding opportunities in MCB and across NSF. Prior to the start of the workshop, Drs. Hyman, Francisco, and Halverson met with workshop coordinators at the University of Puerto Rico at Carolina to strategize how best to conduct personalized outreach during the workshop given the larger than expected number of registrants. The workshop was attended by over 60 participants from eight different institutions throughout the island of Puerto Rico. During the morning session of the workshop, MCB representatives gave three presentations: “Overview of NSF and the Directorate for Biological Sciences,” “Cluster Overviews and Opportunities between MCB and other Divisions/Directorates,” and “How to Write an Excellent Proposal.”

Image of MCB Workshop Presenters: (top) Dr. Linda Hyman; (bottom left) Dr. Wilson Francisco; and (bottom right) Dr. Larry Halverson

MCB Workshop Presenters: (top) Dr. Linda Hyman; (bottom left) Dr. Wilson Francisco; and (bottom right) Dr. Larry Halverson

These presentations were followed by individual meetings between MCB representatives and PIs, faculty, and graduate students from the University of Puerto Rico at Carolina to discuss project ideas and their fit for funding opportunities within MCB and NSF. These personalized sessions provided attendees the opportunity to have their questions answered by MCB experts, and to get to know MCB Division Leadership, Program Directors, and staff. In post-workshop feedback, attendees rated their experience “excellent.”

Drs. Hyman, Francisco, Halverson, and González-Nieves felt this workshop was a unique opportunity to encourage new collaborations, cultivate new ideas, discuss funding opportunities, and keep inspiring new and undiscovered talent in the scientific community. The Division of MCB would like to thank the University of Puerto Rico at Carolina for hosting MCB at Your Meeting. To find out about our future travel plans, visit the “MCB at Your Meeting” page on the MCB Blog.

Welcome to MCB Kelly Ann Parshall!

Hear from Program Specialist Kelly Ann Parshall

What is your educational background?

I majored in English writing with a concentration in African Studies. My objective was to work in development in sub-Saharan Africa. However, when I received my Peace Corps invitation, it was to the South Pacific. Despite the surprise, I had a great experience working in health and environmental initiatives in the small island nation of Vanuatu. This fall I will start attending American University part-time to pursue a masters in Global Environmental Policy.

What is your position? When did you start working in MCB?

As a Program Specialist, I support the Genetic Mechanisms cluster as well as the Systems and Synthetic Biology cluster. I started working in MCB in April 2016.

What attracted you to work for NSF?

When my Peace Corps service concluded, I knew I wanted to work for the government or at a nonprofit. I particularly loved my third year assignment working for the German government on climate change, conservation and natural resource management initiatives. In the biology community in Vanuatu, I saw extraordinary technology-facilitated advances like drones zapping invasive crown of thorns starfish to save reefs. While the projects MCB funds are a bit different, I am happy to support such a wonderful mission.

What have you learned so far from your position?

As someone who has worked in aid, I have spent a significant amount of time applying to grants, assembling funding leads and liaising with donors. It’s nice to be on the other side! NSF operates on a significantly larger scale than any organization I’ve ever been a part of before. It’s amazing to see the thoroughness and transparency with which grantees are selected. I’m looking forward to supporting the entire proposal process as the year progresses.

Dr. Theresa Good Honored by the American Institute of Chemical Engineers

Dr. Theresa Good, Deputy Division Director of the Division of Molecular and Cellular Biosciences at NSF was recognized by the American Institute of Chemical Engineers as the 2015 recipient of their prestigious Food, Pharmaceutical and Bioengineering Division Distinguished Service Award in Chemical Engineering. Recipients of this award have made an exceptional contribution to the profession of food engineering, pharmaceutical engineering, and/or bioengineering in general.

Dr. Good completed her doctoral degree in Chemical Engineering at the University of Wisconsin-Madison. She began her career as an Assistant Professor in Chemical Engineering at Texas A&M University where she was tenured. She then worked as a Professor of Chemical and Biochemical Engineering at the University of Maryland, Baltimore County. Her research focus was understanding the role of protein aggregation in neurotoxicity associated with Alzheimer’s disease.

From 2010 to 2012, Dr. Good worked in the Engineering Directorate at the NSF, and from 2013 to present she has been part of the Molecular and Cellular Biosciences Division as a Program Director in the Systems and Synthetic Biology Cluster, and most recently as the Deputy Division Director.

Dr. Good’s work on problems at the interface of biological sciences and engineering and her tireless efforts in service to the profession and science community were rewarded with this distinguished award. Dr. Good was recognized for “her sustained service in bioengineering leadership, programming, mentoring, and for personal investment in the success of other faculty and students.” Join us in congratulating Dr. Good as the Division celebrates this outstanding recognition.

MCB AT YOUR MEETING: COMPUTATIONAL ADVANCES IN MICROBIOME RESEARCH WORKSHOP

Program Directors in MCB regularly attend scientific meetings and workshops in an effort to garner input from the community, spread the word about funding opportunities, recruit panelists, and encourage submissions to our division. Last July, Dr. Pamela Morris and Dr. Susanne von Bodman, Program Directors for Systems and Synthetic Biology (SSB) cluster traveled to Knoxville, Tennessee for the Computational Advances in Microbiome Research (CAMR) Workshop hosted by the National Institute for Mathematical and Biological Synthesis (NIMBioS). NIMBioS is an NSF-supported institute that seeks to strengthen interdisciplinary efforts across mathematics and biology fields.

The CAMR workshop focused on identifying state-of-the-art computational approaches and integrating novel bioinformatics techniques from numerous areas of microbiome research. Attendees represented research in the human, soil, plant, and marine microbiomes (just to name a few!). The workshop was co-chaired by Drs. Curtis Huttenhower (Harvard University) and Jill Banfield (University of California-Berkeley) and brought together top leaders in the microbiome community and computational fields to discuss the present state of the science, current techniques across fields, current gaps in capability, and future directions. Dr. Morris was the Program Director managing the NIMBioS supplement that funded the CAMR workshop. The workshop was well attended, with various federal agencies (NIFA/USDA, NIH) and national laboratories (Joint Genome Institute/Lawrence Berkeley National Laboratory, Pacific Northwest National Laboratory), participating either in-person or virtually.

Dr. Morris and Dr. von Bodman felt this workshop was a unique opportunity to showcase research/training opportunities in MCB with the goal of inspiring scientists to integrate strong and novel computational approaches into their research. They both interacted with prospective PIs, University of Tennessee faculty, postdocs, and graduate students about opportunities at NSF. The eight presentations at the workshop have been archived and can be viewed online. After the workshop concluded, Dr. Matthew D. Kane, Program Director for the Ecosystem Science Cluster in the Division of Environmental Biology gave a talk on the breadth of opportunities at NSF available to researchers. Events like this provides a perfect setting to encourage new collaborations, cultivate new ideas, and move the exciting field of microbiome science forward.

Sharing MCB Science: The Genetic Response of Diatoms to Ocean Acidification

The ocean is a vast ecosystem, the health of which depends on balanced interactions between the chemical composition of the water and the organisms that inhabit it. One major threat to this balance is ocean acidification. Ocean acidification is the result of the rapid increase in atmospheric carbon dioxide (CO2) in the past 200 years. Carbon dioxide in the atmosphere is absorbed by the ocean, triggering a chemical reaction that lowers the pH of the water, making it acidic. This chemical change in the water may negatively impact vital organisms in this ecosystem. Diatoms, a type of algae, are of particular interest because they form the base of food webs in nutrient-rich coastal systems. These systems support fisheries, which are important to the human food supply. In addition, diatoms play a central role in nutrient and carbon cycling within their ecosystem, and account for 40% of total marine primary production. Despite the importance of diatoms, their response to ocean acidification is not well-understood.

To address this gap in knowledge, Dr. Monica Orellana, a principal scientist at the Institute for Systems Biology and the Polar Science Center at the University of Washington (pictured above on the right), and Dr. Nitin Baliga professor at the Institute for Systems Biology (pictured above on the left), partnered with Dr. Virginia Armbrust, Director of the School of Oceanography at the University of Washington. Together, these researchers and their teams developed experiments to mimic ocean acidification in the laboratory, and observe the DNA transcription response in the model diatom cell, T. pseudonana, to forecast diatoms’ response to projected environmental scenarios for the 21st century.

In a recent article published in Nature Climate Change, the research team reports that the diatom cell responds to increasing CO2 levels (i.e., increasingly acidic water) by decreasing the products of groups of genes involved in carbon-concentrating mechanisms (CCMs) and photorespiration, which are regulated by the same transcription factor. This response may allow diatoms to save energy when exposed to the increased CO2 levels predicted for the end of the century. This acclimation process also suggests one may see a shift in the species composition and primary productivity of marine microbial ecosystems at higher CO2 levels.

As a broader impact of this research, an inquiry-based curriculum module for high school science courses was developed to teach the process of systems science in the context of ocean acidification. This module engages and motivates students to be involved in the learning process and helps develop critical thinking skills necessary to solve a global problem. The students act as interdisciplinary scientists and delegates to investigate how increasing atmospheric carbon is affecting the oceans’ chemistry and biology, as well as integral populations of organisms. The students are trained to think on a systems level to critically assess information, predict effects of high CO2, and design and conduct collaborative, multivariable experiments to explore the consequences of high CO2 in seawater. In the concluding activity, the students discuss the system consequences of ocean acidification and they make recommendations for further research, policy-making, and lifestyle changes.

This is MCB! Hear from Dr. Susanne von Bodman

The Division of Molecular and Cellular Biosciences (MCB) supports fundamental research and related activities designed to promote understanding of complex living systems at the molecular, sub-cellular, and cellular levels. Behind our mission stands a group of individuals whose efforts and great work make this Division outstanding; we are proud to showcase their hard work via this blog.

Dr. Susanne von Bodman completed her doctoral degree at the University of Illinois at Urbana-Champaign. She currently works as a Program Director and Cluster Leader for the Systems and Synthetic Biology Cluster. Dr. von Bodman started working in MCB in September of 2010. As a cluster leader, Dr. von Bodman is involved in Program Management, outreach activities, and community development activities. She also provides advice to investigators, participates on strategic working groups, represents NSF in international funding activities in the area of Systems and Synthetic Biology. She coordinates the funding decision process, maintains cluster budgets, develops post-panel reports, and coordinates cross-directorate activities including multi-disciplinary panels.

Dr. von Bodman area of expertise is in Microbial cell-cell communication, Biofilms, Biotechnology, and Genetic Engineering. Prior to joining the National Science Foundation, she spent 12 years as a professor at the University of Connecticut, Storrs Campus. In her spare time, she greatly enjoys playing golf, and appreciates all the diverse activities the DC and Northern Virginia areas have to offer.

This is MCB! Hear from Uebonda Denise McGee

The Division of Molecular and Cellular Biosciences (MCB) supports fundamental research and related activities designed to promote understanding of complex living systems at the molecular, sub-cellular, and cellular levels. Behind our mission stands a group of individuals whose efforts and great work make this Division outstanding; we are proud to showcase their hard work via this blog.

Uebonda Denise McGee attended the University of Phoenix and began providing administrative support to MCB in March of 2008. Ms. McGee greatly enjoys working with the Genetic Mechanisms and System and Synthetic Biology clusters. As Program Assistant, Ms. McGee provides customer service, travel, and panel support to the division and the scientific community. In her spare time, she enjoys listening to music, reading books, and shopping.