Sharing MCB Science

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!

a closeup of a cell, it is shapes like a lollypop, a long thin stalk with a rounded top which is darker in color

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.

on the left is a still image from an MRI of a chest with the heart and lungs visible. On the right is a graph with the quick heartbead and slower respiration plotted as curves.

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.

Sharing MCB Science: Learning Much More about Spores

Like all living organisms, bacteria need nutrients in their environment to survive and grow. When the survival of bacteria like Bacillus subtilis is threatened by starvation they respond by going into a “hibernation” state by forming spores. The process for producing a spore, called sporulation, is highly complex and requires careful coordination with other cellular processes like DNA replication. To understand how cells are able to orchestrate this coordination, Dr. Oleg Igoshin, an Associate Professor at Rice University partnered with Associate Professor, Gurol Suel from the University of California San Diego to study sporulation of the soil bacterium Bacillus subtilis, a model organism for systems biology research.

Jatin Narula, Anna Kuchina, Dong-Yeon D. Lee, and Masaya Fujita compose the research team, led by Igoshin and Suel, interested in clarifying the genetic mechanism of spore formation or sporulation. By combining experimental methods from systems and synthetic biology with mathematical modeling, the researchers uncovered the coordination mechanism required for sporulation. The modeling predicted that the key to this coordination is the specific arrangement of two pivotal sporulation genes on the bacterial chromosome. This arrangement produces a temporary mismatch in the number of copies of these two genes during DNA replication. This mismatch is detected by the biochemical network controlling sporulation to ensure proper coordination and the completion of DNA replication. These predictions were confirmed when rearrangement of the two pivotal genes on the chromosome prevented cells from sporulating. The sporulation mechanism that Igoshin and his team elucidated is described in the video above and in a recent research article in Cell.

When asked about the broader impacts of this research for cell biology, Igoshin said “We found that the relative arrangement of the two sporulation genes on DNA were similar in more than 40 strains of spore-forming bacteria. This evidence suggests that this timing mechanism is highly conserved, and it is possible that other time-critical functions related to the cell cycle may be regulated in a similar way.”

In addition to the scientific impact of this research, the collaborative nature of the research provided interdisciplinary training for participating graduate students. Furthermore, the innovative approaches used by Igoshin and colleagues may be applicable to similar problems in other organisms and useful for teaching system-level concepts to students of various levels and backgrounds.

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.

Sharing MCB Science: The complex role of chromatin in transcriptional regulation

A central question in biology is how a single genome can give rise to the hundreds of distinct cell types that compose an organism. To achieve this task, the genome must be tightly and selectively regulated. Much of this regulation is thought to come from chromatin, a layer of proteins that cover and package our DNA or genomic code. In a recent report that was the cover article for Cell, Dr. Ahmad S. Khalil and his team of researchers at Boston University describe an experimental platform to engineer, design, and control this layer of regulation, which is distinct to eukaryotes. The team engineered molecular tools that could bind specific locations in the genomic code and alter the local structural and chemical properties of chromatin, thus affecting the expression of genes. This research introduces a new framework to engineer cells in organisms like yeast and mammalian cells. It also supports the use of synthetic biology approaches to control and harness this complex regulatory chromatin layer for future uses in disease intervention, biopharmaceutical production, and basic research.

This research study is the product of a collaborative effort between Dr. Ahmad Khalil and fellow Boston University colleague Dr. James Collins. It is supported by Khalil’s CAREER award from the Division of Molecular and Cellular Biosciences. The CAREER Award Program is a Foundation-wide activity that offers the National Science Foundation’s most prestigious awards in support of junior faculty who exemplify the role of teacher-scholars through outstanding research, excellent education and the integration of education and research within the context of the mission of their organizations. The Khalil group has a history of introducing undergraduate and high school students to synthetic biology through summer research, in addition to hosting regular outreach and education activities focused on molecular biology and microfluidics.

Sharing MCB Science: The Dynamic Transcriptional Response to Oxidative Stress

A common source of molecular damage in organisms is through oxidation, which can occur through natural processes, such as aerobic respiration, and from exposure to toxins such as ultraviolet radiation or pollution. Molecules that cause oxidation, known as reactive oxygen species (ROS), cause damage to proteins and DNA in cells and create a cell state of oxidative stress. In a recent study published in PLOS Genetics, MCB-funded investigator Dr. Amy Schmid and her team of researchers at Duke University describe the hierarchical dynamic response to oxidative stress in archaea, a single-cell model organism which has a gene regulation system similar to bacteria and eukaryotic cells.

This dynamic response controls the expression of over 100 genes whose RNA and protein products work to repair cellular damage caused by exposure to ROS. A key characteristic of this response is the presence of regulatory proteins which facilitate a sequential process to control damage repair. First, the proteins target genes to address cellular damage, then target genes to restore normal cellular function. Because the regulatory proteins involved in the response to stress are of a hybrid ancestry, these findings suggest that the evolution of gene networks may have been influenced by environmental forces, such as oxidative stress. When asked about the broader implications of her work, Dr. Schmid responded, “The results demonstrate that regulatory proteins of ancient evolutionary ancestry in archaea provide mechanistic links between various stress responses as well as between the regulatory network and its effects on cell physiology (e.g. transcriptional regulation, metabolic activity, growth rate, and cell morphology). These results have made significant progress in understanding gene network function, how it may be integrated with cell physiology, and how the network may evolve in response to stress throughout the tree of life”

The reported research was conducted by a team of varied experience and comprised graduate student Peter Tonner, research associates Adrianne Pittman and Kriti Sharma, and undergraduate researcher Jordan Gulli. As a result, trainees were integrated into research that addressed open questions in the fields of microbiology and mathematical modeling. In addition, the Schmid group hosts undergraduate students from Historically Black Colleges and Universities for summer research experiences and teaches a weeklong immersion course for high school students in collaboration with K-12 teachers. In this course, an interdisciplinary team of computational and experimental graduate students teaches high school students about mathematical modeling of microbial growth and response to oxidative stress.

Sharing MCB Science: Using Computational Models as a Tool to Study Plant growth
(Left) 2 color live cell imaging of the ARP2/3 complex (green) and microtubules (magenta) in a growing trichome branch undergoing tip refinment. (Right) Graphic of the growth distribution of the simulated cell using finite element modeling. Photo Credit: Dan Szymanski, Purdue University, Joe Turner, University of Nebraska-Lincoln

(Left) 2 color live cell imaging of the ARP2/3 complex (green) and microtubules (magenta) in a growing trichome branch undergoing tip refinment. (Right) Graphic of the growth distribution of the simulated cell using finite element modeling. Photo Credit: Dan Szymanski, Purdue University, Joe Turner, University of Nebraska-Lincoln

A major challenge in the area of plant growth control is to learn how protein assemblies inside the cell influence the mechanical properties and spatial patterns of the cell wall and its growth. Biologist Daniel B. Szymanski and Mechanical Engineer Joseph Turner joined forces to create a realistic computational model that reveals new insights into which cell wall mechanical properties are most important during cell growth. The research, which was recently reported in Nature Plants, also shows how protein assemblies allow these cell wall patterns to be generated and maintained during the growth process. Plants are sessile organisms; however, they grow rapidly over time to establish a body plan that enables efficient conversion of sunlight into biomass. Individual cells are the building blocks of the plant. As they grow, they collectively determine the size and shapes of important organs like leaves, stems, and roots. If researchers are able to discover the key control modules and growth mechanisms of plant cells, it would become possible to use modern genetic technologies to create new types of crop plants with customized architectures and chemical compositions.

In this paper, the team shows that an evolutionarily conserved module of signaling and cytoskeletal proteins generates a meshwork of actin cytoskeleton filaments near the cell apex. This apical actin meshwork organizes actin bundles that act as roadways which span the entire cell. The actin “roadways” transport the raw materials that are needed to support cell growth. Actin is known to influence growth indirectly by modulating the mechanical properties of the cell wall; however, the exact mechanism is unknown. By combining live cell imaging of dozens of cell growth parameters with a computational mechanical model of the cell wall, the team was able to learn how the apical actin patch influences cell wall thickness and mediates the normal shape change process in this cell type. These results not only will have a broad importance for the engineering of cell types like leaf trichomes and cotton fibers, but also provide a framework to understand how the actin and microtubule cytoskeletons cooperate to dictate plant cell growth mechanisms. The computational models created as part of this project will be used as a new type of tool to focus experimental work on biological processes that are important for plant productivity in both natural and agricultural settings.

This research project was conducted by Post-Doctoral Associates Makoto Yanagisawa and Anastasia Desyatova, with the assistance of graduate student Samuel A. Belteton and research technician Eileen L. Mallery. It created educational opportunities in which a diverse team of biologists and engineers at very different levels of experience attacked an important biological problem. This new collaboration accelerated the rate of discovery and provided new insights into plant growth that otherwise would not have been possible. As a result of this project, engineering students have been pulled toward biology, and biologists have a greater interest in using computational tools.

Want to have your research shared on the MCB blog? Submit your information here. 

Sharing MCB Science: Watching the STARs (Small Transcription Activating RNAs)

The editors are excited about the first of what we hope to be many blog posts featuring the science of MCB-funded investigators. We plan to share a broad sampling of this research and its outcomes on our blog. If you are a) an MCB-funded researcher and b) have recently published research that you would like to share, please fill out this form to be considered for a featured post.

RNA is an important molecule found in all living organisms. To use a computer analogy, RNA acts like a circuit board, controlling DNA, nature’s hard drive. RNA helps to read genetic information and enact the programs of life, through proteins and other important biologic materials. Dr. Julius Lucks, along with post-doctoral associate James Chappell and graduate student Melissa Takahashi, has capitalized on the ability of RNA to form different folded structures via complementary base pairing to create Small Transcription Activating RNAs or STARs. STARs are a molecular “on-switch”, whose shape controls the state (off or on) of the switch. In their recent paper in Nature Chemical Biology, the Lucks Lab researchers describe using STARs to activate the first steps in gene expression (the “printing out” of proteins) in bacteria. The researchers also provide data to support the idea of snapping STARs together to create advanced genetic programs within bacteria.  These examples demonstrate the potential application of STARS to allow bioengineers or synthetic biologists to write new genetic programs, which could engineer cells to address health and environmental challenges. Ongoing research in the lab is focused on using STARs for molecular diagnostics.

The research group is committed to broader impacts and they have recently created a summer course at Cold Spring Harbor Laboratories in Synthetic Biology, where they collaborate with other synthetic biology researchers to develop an ideal training ground for students interested in learning more about the field. Students range from first-year graduate students, to industry professionals, to senior Professors. The course, which has been held for the past 3 summers, is interactive, incorporating research, top-notch guest speakers, and hands-on activities.

To engage the broader community in synthetic biology, the Lucks Lab is closely collaborating with the Sciencenter in Ithaca, NY,as part of the NSF-funded “Multi-Site Public Engagement with Science – Synthetic Biology” project. The goal of the project is to create hands-on activities for children and their families. For example, the group is working on developing a card game that can teach adults and children about the basics of synthetic biology. The cards feature images and facts about engineered microbes, such as, how microbes help humans create important medicines.

Want to have your research shared on the MCB blog? Submit your information here. 

Share Your Science Via Our Blog

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. MCB invites you to submit your research to be featured on our blog in order to inform our stakeholders of the outstanding research we fund, and to better foster a sense of community among MCB principal investigators.

We hope to share a broad sampling of this research and its outcomes on our blog. If you are a) an MCB funded researcher and b) have recently published research that you would like to share, please fill out this form to have your research featured.

 This section of the blog will present highlights from the published research projects of MCB-funded principal investigators. By submitting this information, you acknowledge and agree that NSF MCB reserves the right to use and edit the submitted content in the preparation of an original blog post suitable for the MCB blog’s readership. MCB PIs who are interested in having their work considered for this section of the blog are invited to submit their information via this form with details of the publication on which a blog post would be based.  The Division continues to support a broad range of projects in the molecular and cellular biosciences, and highlighted projects should not be taken as examples of areas of special emphasis for support.