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!
Joseph K. E. Ortega – Photograph of a stage IV sporangiophore of Phycomyces blakesleeanus with the micro-capillary tip of a pressure probe.
Algal, fungal, and plant cells interact with their environment by regulating their size and shape through expansive growth, an increase in cell volume due predominately to an increase in water uptake. This process presents a special challenge for algae, fungi, and plants because cells in these organisms have an exoskeleton-like cell wall that provides support, protection, and shape. When water enters these cells, turgor pressure builds up, which stretches (deforms) the cell wall; at the same time, new material is added to the cell wall to fill in the expanded regions and thereby control the size and shape of the enlarging cell. The interconnected processes of water uptake, wall deformation, and control of cell size and shape are crucial for algal, fungal, and plant survival.
Previous research has provided a good description of the molecular and mechanical changes accompanying expansive growth. Taking advantage of this foundation, Dr. Joseph K. E. Ortega, Professor of Mechanical Engineering at the University of Colorado, Denver, is bringing a new dimension to quantify cellular changes during expansive growth. He has developed a mathematical model of the interconnected processes, called the Augmented Growth Equations (AGE). As described in his new publication, the model organizes multiple equations to represent the relationships between variables and uses dimensional analysis to produce dimensionless coefficients. The dimensionless coefficients enable researchers to more easily quantify the biophysical processes and better predict how changes in water absorption and cell wall deformation regulate expansive growth. While the model does not address the shape of the cells, the mathematical framework provides insight as to how water uptake and wall deformation are regulated in algal, fungal, and plant cells to control expansive growth during normal conditions and in response to changes in the environment.
This work is partially funded by the Molecular Biophysics Cluster of the Division of Molecular and Cellular Biosciences, Awards #MCB-0948921.
Dr. Steven Van Doren – Example of how the TREND software can distinguish the patterns of a heart beating and lungs breathing from an MRI movie
Visual outputs, such as photographs or movies, contain important data from scientific experiments. For example, identifying biologically relevant signals over time (trends) can be challenging, as they may be subtle or mixed into background movements or noise. To identify trends, researchers scour the data looking for specific features, such as peaks, and either mark them by hand, which is time consuming and subjective, or set specific background thresholds in instrumentation, which can result in mistaking signal for noise. In a new publication, Dr. Steven Van Doren, Professor of Biochemistry at the University of Missouri, and his post-doctoral researcher, Dr. Jia Xu, describe a new software program called TREND (Tracking and Resolving Equilibrium and Nonequilibrium population shifts in Data). The software allows researchers to objectively extract information from two-dimensional images or videos, and in another recent publication, they describe extending the analysis to several different types of data.
TREND uses a statistical approach, called principal component analysis (PCA), on a series of individual measurements to compress and organize multivariate data so that researchers can select for and detect changes in a variety of factors over time. The factors can be anything: characteristics of a stream, grades in a class, or gene variants. When applied to movies, such as this sample video of a sunset, a trend in the data, such as the movement of the sun across the sky, can be plotted after removing background noise, such as motion from clouds. Another example is separating the pattern of a heart beating from lungs breathing using TREND (a photo of this video is shown above). TREND is available for licensing and download at http://biochem.missouri.edu/trend and https://nmrbox.org/.
This work is partially funded by the Molecular Biophysics Cluster of the Division of Molecular and Cellular Biosciences, Awards #MCB-1409898.
In April, the National Alliance for Broader Impacts (NABI) held its fifth annual Broader Impacts Summit at Skamania Lodge in Stevenson, WA. NABI is a network of more than 600 individuals working together to build institutional capacity, advance broader impacts, and demonstrate the societal benefits of research. NABI members come from educational institutions, museums, science centers, zoos, botanical gardens, professional societies, private industry, foundations, and other organizations. A list of member institutions is available on the NABI website and you can read about the objectives of NABI in a prior post on the MCB Blog. Established in part with funding provided by the Division of Molecular and Cellular Biosciences, NABI events and resources help researchers create and develop impactful broader impacts activities.
At the summit, Dr. Suzanne Iacono, Head of the Office of Integrative Activities (OIA) at the National Science Foundation, delivered a keynote address entitled Broader Impacts at NSF. She noted, across proposals, student education and broadening participation were two main focus areas. These areas were also a major point of discussion in several of the sessions at the meeting.
The theme of the three-day summit was the “Power of Partnerships.” Sessions focused on three strands: innovative BI approaches and activities, faculty and student development and training, and broader impacts infrastructure, skills, and tools. Research into the role of partnerships in empowering high-quality outreach, models for public engagement partnerships, and best practices in the assessment and evaluation of broader impacts were presented, which created a foundation for data-driven conversations about broader impacts for the 21st century and beyond. Presenters discussed how to construct strong science education and build outreach partnerships with a diverse array of partners such as citizen scientists, startup companies, museums, community partners, STEM graduate students, engineers, and faculty. Summit participants also learned how to use crowdfunding, cinema, social media, and Twitter as tools to facilitate outreach. Discussion also focused on how to reach non-traditional public audiences, minorities underrepresented in STEM fields, and the next generation of scientists. Panelists offered lessons learned while establishing outreach partnerships such as University of Wisconsin – Madison Science Alliance, which connect scientists with K-12 educators, parents, lifelong learners, students, and others. The Summit had a strong focus on the future of BI and NABI. Sessions engaged member feedback, discussed the creation of a peer-reviewed journal about broader impacts, and considered the role of the NSF CAREER Program in integrating intellectual merit and broader impacts. Slides for each presentation are available at https://broaderimpacts.net/2017-schedule/.
If you are interested in becoming a member of the National Alliance for Broader Impacts network, visit their website at https://broaderimpacts.net/join-nabi/ to join for free. Registration for the next summit, which will be held at the Providence Biltmore April 25-27, 2018 will become available on the NABI website at https://broaderimpacts.net/.
This work is partially funded by the Division of Molecular and Cellular Biosciences, Award #MCB – 1408736.
MCB congratulates Dr. Susan Gerbi on her 2017 George W. Beadle Award. Each year, the Genetics Society of America honors one investigator for “outstanding contributions to the community of genetics research” such as “creating and disseminating an invaluable technique or tool, assisting the community with the adoption of a model system, working to provide a voice for the community in public or political forums, and/or maintaining active leadership roles.” This distinguished honor was presented to Dr. Gerbi during the 58th Annual Drosophila Research Conference in California.
Dr. Gerbi is the George D. Eggleston Professor of Biochemistry and Professor of Biology at Brown University. In part with NSF support, she has made many notable scientific contributions in all of the areas described above. For example, together with Dr. Joseph Gall, Dr. Gerbi created in situ hybridization, an invaluable technique to locate genes on chromosomes. Additionally, she developed a novel Replication Initiation Point Mapping (RIP) technique that enabled researchers to pinpoint the start site for DNA replication in eukaryotes. Dr. Gerbi and her group also solved the first sequence of eukaryotic 28S ribosomal RNA (28S rRNA). By comparing it to its bacterial homologue (23S rRNA), Dr. Gerbi and her team identified both regions of variability (expansion segments), which aid researchers during phylogenetic analysis, and key regions of conservation (core secondary structure and domain specific conserved sequences) that are held constant among organisms to maintain rRNA function. Further, Dr. Gerbi was the first to identify an in vivo role for U3 small nucleolar RNA, which promotes ribosomal RNA folding and processing, and she was the first to develop a fluorescence-based method to track localization of small RNAs in vivo, which allowed for the identification of specific sequences that target the RNAs to the sites of ribosome assembly in the nucleolus.
Dr. Gerbi and her research team also developed Sciara coprophilia as a model organism, mapping the fly’s genome using a new, handheld DNA sequencing technology called the Oxford Nanopore MinION. (The MinION made a recent appearance in space when it was used by NASA Astronaut Kate Rubins to sequence DNA on the International Space Station.) With the genome, transcriptome, and methodology for genome editing now available, Dr. Gerbi is actively promoting the use of Sciara as a model organism to mine its unique biological features, including a monopolar spindle in meiosis, non-disjunction, chromosome imprinting, and elimination. Studies on Sciara offer new insights into the mechanisms of locus-specific DNA re-replication, which may serve as a paradigm for gene amplification in cancer. This work was partially funded by the Genetic Mechanisms cluster of the Division of Molecular and Cellular Biosciences, Award #MCB-1607411.
Dr. Gerbi has also served the scientific community in numerous leadership positions and science advocacy roles. For example, Dr. Gerbi was Founding Chair of the Department of Molecular Biology, Cell Biology, and Biochemistry at Brown University, serving in that role for 10 years. Just a few of the many broader impacts of her work that have focused on training the next generation of scientists include 33 years of service as principal investigator (PI) or co-PI on Brown University’s National Institutes of Health (NIH) predoctoral training grant. Dr. Gerbi has also served as President of the American Society for Cell Biology (ASCB), fellow of the American Association for the Advancement of Science (AAAS), chair of the Federation of American Societies for Experimental Biology (FASEB) Consensus Conference on Graduate Education, founding member and Chair of the Association of American Medical Colleges (AAMC) Graduate Research Education and Training (GREAT) group, and a member of the National Academy of Sciences Committee’s Study on the National Needs for Biomedical Research Personnel. She was also a member of the National Academy of Sciences committee on Bridges to Independence, which led to NIH’s Pathway to Independence K99 award that provides research funding opportunities to postdoctoral researchers who are transitioning to faculty positions.
For these and other efforts, Dr. Gerbi has contributed greatly to the genetics community through her dedication to scientific research, leadership, and advocacy. Please join us in congratulating Dr. Susan Gerbi!
Shutterstock.com images credited in order of appearance: ANDROMACHI; Mmaxer; NASA images; GarryKillian; Sergey Tarasov; Panimoni; Netta Arobas; Somchaij; Satenik Guzhanina. NSF INCLUDES available at https://www.nsf.gov/news/mmg/mmg_disp.jsp?med_id=132360.
Photo Credit: Adapted from Juliann/Shutterstock.com
NSF-Simons Research Centers for Mathematics of Complex Biological Systems hosted a webinar with Q & A on Thursday, June 15, 2017, and the slides presented can be viewed at: https://nsf.gov/attachments/242105/public/MathBioSys_Webinar_Presentation.pdf
Please read solicitation NSF 17-560 for more information.
What were you doing before you came to the NSF?
I was an associate professor in the Laboratory of Genome Integrity and Tumorigenesis at the Van Andel Research Institute in Michigan for 16 years, having joined the Institute at its founding in 2000. After moving to Boston for my wife’s Palliative Care Fellowship at Harvard Medical School, I closed down my lab and joined Phil Sharp’s lab at MIT as a visiting scientist.
What attracted you to work for the NSF?
I was funded by the NSF some years ago and saw the immense impact that it had on my ability to complete meaningful research. In my work as panelist, I came to know more about NSF and to appreciate its vital role for supporting basic science and education in the US. All my interactions with the staff and scientists here were very positive, so that led me to have an even higher opinion and appreciation for the mission of the NSF.
What was your first impression of the NSF? Has this impression changed since you began serving as a rotator?
While serving as a panelist, I saw NSF as an efficient and effective organization, and my first impressions after joining as a rotator confirmed these views. Although the steep learning curve of joining MCB in the middle of the grant review cycle was a bit overwhelming, my overall thoughts on NSF have not changed.
What personal goals would you like to accomplish while at the NSF?
I would like to support NSF’s mission, “to promote the progress of science; to advance the national health, prosperity, and welfare; to secure the national defense…”¸ by making funding decisions that have a positive impact on science in the MCB community, and hopefully positive effects throughout the country. I also want to learn more about the history of the NSF and the breadth of its activities to promote science and the public good.
What has surprised you most about working at the NSF?
What surprised me is that I could walk down to the 3rd floor with my laptop and someone would help me fix the problem immediately! The IT staff is great.
What are some of the challenges of serving as a rotator?
While BIO/MCB may seem relatively small, NSF is a mid-level federal agency with over a 1,000 employees, which means there are a wide range of projects in many different areas of science. One challenge has been learning about and keeping track of all the directorates, divisions, and wide range of opportunities at NSF.
What would you tell someone who is thinking about serving as a Program Director at the NSF?
Please consider it seriously. Serving as a Program Director allows researchers to gain more insight into the breadth of scientific research (even within your own field) and also how to write a better grant proposal.
When friends or colleagues find out that you work at the NSF, what do they say or ask?
They think my new role poses both unique challenges and opportunities and that it will be a great experience.
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