Lake Lanier in Georgia is the primary water reservoir serving suburban and metropolitan Atlanta. When the lake’s water level drops below a certain point, calls go out for water conservation and news reports show images of the red mud shoreline. In some affected counties, water restrictions are imposed. The combination of usage restrictions and changes in precipitation eventually averts the crisis. But, when the crisis ends, water usage rebounds – until the next shortage.
Inspired by this example, researchers at the Georgia Institute of Technology have developed a theory to unite the study of behavior and its effect on the environment. In doing so, they combined theories of strategic behavior with those of resource depletion and restoration, leading to what they term an “oscillating tragedy of the commons.” The research was reported in November 8 in the journal Proceedings of the National Academy of Sciences.
The study of how behavior affects resource depletion has a long history. The originating example is that of small farmers who share a common pasture. Each farmer has to decide whether to graze some or all of his flock, while also considering what actions other farmers might take. To avoid losing out to a competitor, each farmer decides to attempt to maximize the benefit by grazing as many sheep as possible. Consequently, the sheep overgraze and damage the pasture. Paradoxically, the benefit to each farmer over the long run is less than if they had cooperated and each grazed fewer sheep.
That individuals acting out of their own self-interest can be worse off than had they coordinated is termed a “tragedy of the commons” – a concept introduced nearly 50 years ago by the ecologist Garrett Hardin. (The use of the term “tragedy” denotes its inevitability). However, the originating example does not include a mechanism by which incentives for cooperation change as the resource is depleted.
“Our actions can substantively change the environment and, in turn, the changing environment influences the incentives for future action,” said Joshua Weitz, who led the study and is a professor in Georgia Tech’s School of Biological Sciences and director of the Interdisciplinary Graduate Program in Quantitative Biosciences. “The theory in our paper proposes a unified approach for the co-evolution of actions and environment.”
Other authors on the study include postdoctoral fellow Ceyhun Eksin and graduate teaching assistant Keith Paarporn, both members of the Weitz group in the School of Electrical and Computer Engineering, as well as Professors Sam Brown and Will Ratcliff, both faculty in the School of Biological Sciences.
There are many other prominent examples of tragedies of the commons. One example is that of antibiotic resistance in microbes. The widespread use of antibiotics among humans and in agriculture selects for antibiotic resistance strains. Over time, the spread of resistance renders antibiotics ineffective for use in patients with otherwise curable infections. Hence, individuals trying to maximize their own benefit can unintentionally degrade the collective value of the antibiotics.
Another example stems from individual decisions about whether or not to vaccinate against childhood infectious diseases like measles, mumps and rubella. Crucially, a retracted study falsely linking autism to vaccination has inspired some parents not to vaccinate their children. Yet, when population levels of immunity drop, then these potentially lethal infectious diseases that had been prevented in the past will reappear in sporadic outbreaks or, dangerously, as large-scale epidemics.
“Individual agents acting in their own self-interest – trying to do what’s right for them alone – can end up in a worse state than if they coordinated,” Weitz said. “For example, the decision not to vaccinate increases the frequency of individuals having a dangerous, infectious disease. As people see the disease return, the incentives for vaccination change.”
The research proposes a new model of evolutionary games with a feedback loop in which changes to the resource – whether it be water supplies, pastureland, antibiotics, or vaccine use – change the incentives for people to take action in their own interests. The environment and the incentives co-evolve and are tied to one another, allowing the outcome to be predicted.
“Incentives to use a lot of water when water is in short supply are different than when water levels are replete,” Weitz said. “When things are bad and the commons is depleted, there may be greater incentives to cooperate than when the commons are in good condition.”
Unlike in the originating example of the tragedy of the commons, Weitz and colleagues report that tragedies can recur again and again. Formally, the researchers unite game theory with evolutionary models in which both the tendency to cooperate and the state of the environment coevolve.
The theoretical research also pointed the way to a testable principle to avert the tragedy of the commons in specific application domains. For example, in their analyses, Weitz and colleagues found that averting the tragedy of the commons was only possible when cooperation was incentivized even when the environment was depleted and others continued to act to degrade the resources.
“Another lesson is that idealism matters,” said Weitz, continuing, “A small group of cooperating individuals can, over time, change the social and environmental context for all and for the better.”
This work was supported by a grant W911NF-14-1-0402 from the Army Research Office. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the sponsor.
CITATION: Joshua S. Weitz, Ceyhun Eksin, Keith Paarporn, Sam P. Brown and William C. Ratcliff, "An oscillating tragedy of the commons in replicator dynamics with game-environment feedback," (Proceedings of the National Academy of Sciences, 2016). http://www.pnas.org/content/early/2016/11/02/1604096113.abstract
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In the fight against cancer, doctors dish out combination-blows of surgery, chemotherapy and other drugs to beat back a merciless foe. Now, scientists have taken early steps toward adding a stinging punch to clinicians’ repertoire.
With a novel targeted therapy researchers at the Georgia Institute of Technology have purged ovarian tumors in limited, in vivo tests in mice. “The dramatic effect we see is the massive reduction or complete eradication of the tumor, when the ‘nanohydrogel’ treatment is given in combination with existing chemotherapy,” said chief researcher John McDonald.
That nanohydrogel, a type of nanoparticle, is a minute gel pellet that honed in on malignant cells with a payload of an RNA strand. The RNA entered the cell, where it knocked down a protein gone awry that is involved in many forms of cancer.
In trials on mice, it put the brakes on ovarian cancer growth and broke down resistance to chemotherapy. That allowed a common chemotherapy drug, cisplatin, to drastically reduce or eliminate large carcinomas, with very similar speed and manner. The successful results treating four mice with the combination of siRNA and cisplatin showed little variance.
Chink in the armor
The therapeutic short interfering RNA (siRNA) developed by McDonald and Georgia Tech researchers Minati Satpathy and Roman Mezencev, thwarted cancer-causing overproduction of cell structures called epidermal growth factor receptors (EGFRs), which extend out of the wall of certain cell types. EGFR overproduction is associated with aggressive cancers.
The researchers from Georgia Tech’s School of Biological Sciences published their results on Monday, November 7, 2016, in the journal Scientific Reports. Research was funded by the National Institutes of Health’s IMAT Program, the Ovarian Cancer Institute, the Deborah Nash Endowment Fund, the Curci Foundation and the Markel Foundation.
The new treatment has not been tested on humans, and research would be required by science and by law to demonstrate consistent results – efficacy – among other things, before preliminary human trials could become possible.
The current in vivo success strengthens the idea that knocking out EGFR at the RNA level may be a worthy goal to explore in the fight against carcinomas in general. The same patented nanohydrogel packed with other types of therapeutic RNA is currently being tested for the treatment of other types cancers.
Helper turned killer
EGFRs are receptors found in epithelial cells, which line organs throughout the body: Lungs, mouth, throat, intestines and others. In women, it also lines reproductive organs: Ovaries, uterus and cervix.
They are long proteins that poke through the cell membrane, connecting the cell’s interior with the outside. They look like squiggly worms with tiny mouths on the outside that take up a messenger protein.
In a healthy cell, those messenger molecules cause EGFRs to trigger long chains of biochemical reactions that lead to the activation of genes involved in a variety of cellular functions. In carcinoma cells, the number of EGFRs present typically skyrockets.
“In many cancers, EGFR is overexpressed,” said McDonald, who heads Georgia Tech's Integrated Cancer Research Center. “The problem is that because of this overexpression, many cellular functions, including cell replication and resistance to certain chemotherapy drugs, are dramatically cranked up.”
The cell goes haywire, metabolizes too much sugar, divides too much, and resists chemotherapy. The cancer grows into a tumor and can spread through the body.
An overabundance of EGFRs found in a biopsy is usually a sign that cancer patient prognosis is poor. “In 70 percent of ovarian cancer patients, EGFR is overexpressed at very high levels,” McDonald said.
Cell suicide: apoptosis
EGFR overexpression also makes cancer cells resistant to chemotherapy by thwarting a natural defense mechanism.
“The platinum-based chemotherapies used to treat ovarian cancers cause DNA damage, which switches on apoptosis,” McDonald said. Apoptosis is cell suicide. When cells can’t repair DNA damage, they’re programmed to kill themselves to keep the damaged cells from spreading.
The primary chemotherapy used to treat ovarian cancer works by coaxing cancer cells to trigger the suicide program, but having too many epidermal growth factor receptors gets in the way.
“EGFR overexpression hinders apoptosis; they won’t die. By knocking down EGFR, we make the cell hypersensitive to the drug. Apoptosis is reactivated,” McDonald said.
Existing EGFR targeted drugs called tyrosine-kinase inhibitors disrupt an EGFR function, but their success in treating ovarian cancer has been limited. “Clinicians have tried EGFR inhibitors to treat ovarian cancers for some years, and they only get about 20% of patients responding to it,” McDonald said. “Apparently, the particular EGFR function inhibited by these drugs is not critical to ovarian cancer.”
Guided brass knuckles
The short interfering (si) RNA designed by the Georgia Tech researchers attacks the cancer much closer to its root.
To make the protein for EGFR, RNA has to transfer its genetic code from DNA. The researchers’ siRNA binds to the cell’s RNA and stops it from working.
“We’re knocking down EGFR at the RNA level,” he said. “Since EGFR is multi-functional, it’s not exactly clear which malfunctions contribute to ovarian cancer growth. By completely knocking out its production in ovarian cancer cells, all EGFR functions are blocked.”
The nanohydrogel that delivers the siRNA to the cancer cells is a colloid ball of a common, compact organic molecule and about 98 percent water. Another molecule is added to the surface of the nanohydrogel as a guide. It makes the pellets adhere to the cancer cells like sticky cluster bombs.
Cancerous tissue may also be aiding the nanohydrogel in targeting it. “When you get into a tumor, there are a lot of blood vessels, and many are broken,” McDonald said. “This may help the nanoparticles get passively trapped in the neighborhood of tumorous tissues.”
In the in vivo trials, the siRNA, which contained a fluorescent tag, allowed researchers to observe nanoparticles successfully honing in on the cancer cells.
“We originally selected to target the EGFR gene because its activity is easily measured, and we wanted to use it simply as an indicator that our nanoparticle siRNA delivery system was working,” McDonald said. “The fact that the EGFR knockdown so dramatically sensitized the cells to standard chemotherapy came as a bit of a surprise.”
At first, his team observed how the tumors responded to chemotherapy alone. Then they combined it with the nanoparticle treatment.
“When we gave the chemotherapy alone, the response was moderate, but with the addition of the nanoparticles, the tumor was either significantly reduced or completely gone,” McDonald said.
But he tempered enthusiasm with caution. “Further work will be required to see if the treatment completely destroyed every trace of cancer cells in the tumors that disappeared, or if future recurrence is possible.”
If the researchers’ continuing studies further prove to be consistent, the combination of the nanohydrogel with other therapeutic RNAs could represent a significant advancement in the treatment of a wide spectrum of cancers.
Georgia Tech’s Lijuan Wang and Dr. Benedict Benigno from Atlanta’s Northside Hospital coauthored the paper. Research was funded by the National Institutes of Health’s Program for Innovative Molecular Analysis Technologies Program (grant 1R21CA155479-01), the Ovarian Cancer Institute at Northside Hospital, the Deborah Nash Endowment Fund, the Curci Foundation, and the Markel Foundation. Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the sponsoring agencies.
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Luis Miguel Rodriguez-Rojas graduated with a Ph.D. in Bioinformatics with a minor in Biomedical Engineering. He came to Georgia Tech with an M.S. in Biological Sciences from Universidad de Los Andes, in Bogota, Colombia; an M.S. in Applied Informatics from Université Montpellier 2 (currently Université de Montpellier), in Montpellier, France; and B.S. in Biology from Universidad Nacional de Colombia, in Bogota. He is off to a postdoctoral position in Georgia Tech’s School of Civil and Environmental Engineering.
What attracted you to study in Georgia Tech? How did Georgia Tech meet your expectations?
The main reason was my advisor, Dr. Kostas Konstantinidis. I read some of his work while I was an undergraduate and was fascinated by his research. While studying for my master’s degree, I had the privilege of visiting his lab for two weeks. During this period, I became convinced that I wanted to work in microbial ecology, and he offered to receive me as a Ph.D. student. Once I started the program, I quickly realized that Georgia Tech exceeded my expectations, offering a far richer campus life than I had anticipated.
What is the most important thing you learned while at Georgia Tech?
Balancing work and academic life with other activities. I became involved in social dancing, a hobby I’ve cultivated and enjoyed for over three years now, learning salsa, bachata, zouk, and tango. I discovered in Georgia Tech the importance of this balance in carrying out a productive and happy academic life.
What surprised you the most at Georgia Tech? What disappointed you the most?
I was surprised by the variety of cultural activities. Having a stereotypical image of a technology institute in mind, I was pleasantly surprised by poetry recitals, concerts, dance and theater performances, and many more activities on campus. After the success of the BVN Youth Poetry Slam semifinals at Georgia Tech in summer 2015, it was a disappointment that Tech didn’t continue to build on promoting slam poetry.
Which professor(s) or class(es) made a big impact on you? Why?
Certainly my advisor, Dr. Konstantinidis. Not only did I learn about microbial ecology from him, but also his frequent encouragement to critically discuss ideas has prepared me for scholastic discussion outside of Tech.
What is your most vivid memory of your time at Georgia Tech?
I cherish with particular warmth my memories of the Salsa Club, first as a regular member and later as a board member and an instructor.
On the basis of your experience, what advice would you give to incoming new graduate students at Georgia Tech?
Learn to say no and value your free time.
Learning to say no is hard, but as graduate students we often get bombarded with options and our first instinct is to try and cover them all. Some diversity in research topics is highly desirable, but it’s important to find a balance in which, at the end, a consistent story can be told in the dissertation.
Another area in which balance is hard to find is time management. We tend to err on the side of too much academic involvement and little or no personal life. Hobbies are important, they keep us healthy, happy, and productive, and it’s our own job to cultivate them and devote some time to them.
What feedback would you give to Georgia Tech leaders, faculty, and/or staff to improve the Georgia Tech experience for future students?
I would encourage more curricular freedom for graduate students. I was fortunate enough to be in the Ph.D. in Bioinformatics, a program with great latitude on the courses I could (or should) take. And yet, even in this program, I was never presented with the possibility of attending classes outside of the main program areas, while most advisors explicitly discourage this. For example, Georgia Tech offers very interesting courses in the humanities that are never mentioned to graduate students in the sciences or engineering.
Where are you headed after graduation? How did your Georgia Tech education prepare you for this next step?
I’ll stay in Georgia Tech for a short-term postdoctoral position in the School of Civil and Environmental Engineering. I plan on continuing in an academic career, for which Georgia Tech has prepared me with valuable practical experience in research, collaborations with faculty and students from other laboratories, and proposals of novel research ideas and projects.
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Genetic mitochondrial disease is present in about 1 out of every 5,000 babies, who face insurmountable odds from the moment they are born. That’s because at present, there is no cure for these conditions. But a new assisted reproductive technology that prevents the transmission of mitochondrial disease from mother to child holds great promise.
Mitochondrial replacement (MR) therapy combines the nuclear DNA from the mother with healthy mitochondria from a donor egg to create a healthy new egg that can be fertilized with the father’s sperm, thereby yielding a “three-person baby.” Last year, the world’s first three-person baby resulting from this method was delivered by U.S. doctors in Mexico, where there are no laws prohibiting the procedure.
The healthy newborn got about 0.1 percent of his DNA from the donor, and the vast majority of his genetic code – specifying eye color, hair, etc. – from his mom and dad.
Mitochondrial DNA comprises just a small percentage of our total DNA, containing just 37 of the 20,000 to 25,000 protein-coding genes in our body. And while nuclear DNA comes from both parents, “our mitochondrial DNA comes directly from our mothers, so my mitochondrial genome will be exactly like my mother’s, yours will be like your mother’s, and so on,” says Lavanya Rishishwar, former grad student in the lab of Petit Institute researcher King Jordan and team lead for Applied Bioinformatics Laboratory (ABiL, a public-private partnership between Georgia Tech and IHRC Inc.).
While the method hasn’t been green lighted in the U.S. yet, the United Kingdom gave the go-ahead for MR therapy in December. This announcement came in the wake of concerns about the safety of MR therapy that were raised by evolutionary biologists, who argue that nuclear and mitochondrial genomes evolved concurrently, and therefore mitochondria from one person or population may not be compatible with nuclear material from another.
In support of the evolutionary biologists’ nuclear-mitochondrial mismatch hypothesis, a number of previous studies on model organisms have provided evidence for incompatibility between nuclear and mitochondrial genomes from divergent populations of the same species. But a recent study by Jordan and Rishishwar published in BMC Genomics lays those fears to rest.
“The alarm was raised based on work that was done on model systems,” says Jordan, associate professor in the School of Biological Sciences and director of the Bioinformatics Graduate Program. “They didn’t work with humans, they worked with fruit flies, with mice, and those experiments resulted in a host of different problems for the resulting offspring. The key is, those were artificial experiments. Meanwhile, there’s been an ongoing natural experiment that has been conducted over millennia in human populations.”
So Jordan and Rishishwar tested the nuclear-mitochondrial mismatch hypothesis for humans by observing the source: humanity. They used data from the 1,000 Genomes Project and the Human Genome Diversity Project, studying the incidents of nuclear- mitochondrial DNA mismatch seen in more than 3,500 people from about 60 populations on five continents.
“We’ve been working for some years on human population genomics and remain interested in admixed American populations,” Jordan says. “The trajectory of modern human evolution for the past 50,000 to 100,000 years starts with the journey out of Africa, followed by a long period when populations were geographically isolated for the most part. During that time, human populations genetically diverged since they were physically isolated.”
But over the past 500 years or so, since Columbus came to the new world from Europe, “that process of isolation and divergence got flipped upside down,” Jordan notes. “Over a very short evolutionary time, you had populations from the Americas, Europe, and shortly thereafter, Africa because of the transatlantic slave trade, that were all brought together.”
Hence, in the Americas we’ve seen the creation of genome sequences that are evolutionarily novel in the history of humanity, in that they contain combinations of variants that had never existed together before. Jordan and his team have been studying this for a while, and understood that healthy individuals can bear combinations of variants that had different ancestral sources within the same genomic background.
“We knew that at a very intuitive level because of our own research,” says Jordan, who stumbled on a paper in Nature expressing the grave concerns of evolutionary biologists and thought, “instead of relying on artificial experiment systems, why don’t we just try to read the results of this long, ongoing experiment of human evolution and see what it tells us.”
They found that even people with very similar nuclear DNA (nDNA) genomes can have highly divergent mitochondrial DNA (mtDNA) and vice versa. Ultimately, their results showed that mitochondrial and nuclear genomes from divergent human populations can co-exist in healthy individuals, indicating that mismatched nDNA-mtDNA combinations are basically harmless and not likely to jeopardize the safety of MR therapy.
“We tend to think that the story of our evolution is the story of migration, physical isolation, and genetic diversification,” Jordan says. “But all throughout that process, there was admixture along the way. It’s not like there was a linear, onward march. It confirms and underscores the fact that humans are a relatively evolutionarily young species, and from the genetic perspective, there is complete compatibility between human populations.”
Drexel University and Georgia Institute of Technology researchers have discovered how the Rad52 protein is a crucial player in RNA-dependent DNA repair. The results of their study, published June 8 in the journal Molecular Cell, uncover a surprising function of the homologous recombination protein Rad52. They also may help to identify new therapeutic targets for cancer treatment.
Radiation and chemotherapy can cause a DNA double-strand break, one of the most harmful types of DNA damage. The process of homologous recombination — which involves the exchange of genetic information between two DNA molecules — plays an important role in DNA repair, but certain gene mutations can destabilize a genome. For example, mutations in the tumor suppressor BRCA2, which is involved in DNA repair by homologous recombination, can cause the deadliest form of breast and ovarian cancer.
Alexander Mazin, a professor at Drexel University’s College of Medicine, and Francesca Storici, an associate professor at Georgia Tech’s School of Biological Sciences, have dedicated their research to studying mechanisms and proteins that promote DNA repair.
In 2014, Storici and Mazin made a major breakthrough when they discovered that RNA can serve as a template for the repair of a DNA double-strand break in budding yeast, and Rad52, a member of the homologous recombination pathway, is an important player in that process.
“We provided evidence that RNA can be used as a donor template to repair DNA and that the protein Rad52 is involved in the process,” said Mazin. “But we did not know exactly how the protein is involved.”
In their current study, the research team uncovered the unusual, important role of Rad52: It promotes “inverse strand exchange” between double-stranded DNA and RNA, meaning that the protein has a novel ability to bring together homologous DNA and RNA molecules. In this RNA-DNA hybrid, RNA can then be used as a template for accurate DNA repair.
It appeared that this ability of Rad52 is unique in eukaryotes, as otherwise similar proteins do not possess it.
“Strikingly, such inverse strand exchange activity of Rad52 with RNA does not require extensive processing of the broken DNA ends, suggesting that RNA-templated repair could be a relatively fast mechanism to seal breaks in DNA,” Storici said.
As a next step, the researchers hope to explore the role of Rad52 in human cells.
“DNA breaks play a role in many degenerative diseases of humans, including cancer,” Storici added. “We need to understand how cells keep their genomes stable. These findings help bring us closer to a detailed understanding of the complex DNA repair mechanisms.”
The research was supported by the National Institutes of Health, the National Science Foundation and the Howard Hughes Medical Institute.
These results offer a new perspective on the multifaceted relationship between RNA, DNA and genome stability. They also may help to identify new therapeutic targets for cancer treatment. It is known that active Rad52 is required for proliferation of BRCA-deficient breast cancer cells. Targeting this protein with small molecule inhibitors is a promising anticancer strategy. However, the critical activity of Rad52 required for cancer proliferation is currently unknown.
This new Rad52 activity in DNA repair, discovered by Mazin, Storici and their team, may represent this critical protein activity that can be targeted with inhibitors to develop more specific — and less toxic — anti-cancer drugs. Understanding of the mechanisms of RNA-directed DNA repair may also lead to development of new RNA-based mechanisms of genome engineering.
This research was supported by the National Institute of General Medical Sciences (NIGMS) of the NIH (grant GM115927), the National Science Foundation (grant 1615335), and the Howard Hughes Medical Institute Faculty Scholar Program (grant 55108574). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the sponsoring agencies.
Written by Drexel University.
CITATION: Olga M. Mazina, Havva Keskin, Kritika Hanamshet, Francesca Storici,
Alexander V. Mazin, “Rad52 Inverse Strand Exchange Drives RNA Templated
DNA Double-Strand Break Repair,” (Molecular Cell, 2017). http://dx.doi.org/10.1016/j.molcel.2017.05.019
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A group of researchers including Chong Shin, an assistant professor in the School of Biology and Christoph Fahrni, a professor in the School of Chemistry and Biochemistry at Georgia Tech conducted a study to visualize the distribution of transition metals in the zebrafish embryo by employing synchrotron X-ray fluorescence (SXRF) microtomography.
By combining the progressive lowering of temperature method (PLT) with femtosecond laser sectioning, a zebrafish embryo at 24 hours post fertilization was embedded, excised, and preserved in an X-ray compatible, transparent resin for tomographic elemental imaging. 3D distribution of zinc, iron, and copper was then reconstructed using the iterative maximum likelihood expectation maximization (MLEM) reconstruction algorithm based on a data set comprised of 60 projections, acquired with a step size of 2 μm during 100 hours of beam time. The volumetric elemental maps, which entail over 124 million individual voxels for each transition metal, demonstrated distinct elemental distributions correlated with characteristic anatomical features at this stage of embryonic development.
The study was published as an ‘inside front cover’ in the journal Metallomics (Bourassa et al., 2014 Sep;6(9):1648-55. doi: 10.1039/c4mt00121d). It has also been selected as one of the outstanding results by the management of the Advanced Photon Source (APS) sector where the work was done.
This project was supported by the National Science Foundation (CHE-1306943), the National Institutes of Health (K01DK081351), and the Vasser Woolley Foundation.
Plant scientists are working to improve important food crops such as rice, maize, and beans to meet the food needs of a growing world population. However, boosting crop output will require improving more than what can be seen of these plants above the ground. Root systems are essential to gathering water and nutrients, but understanding what’s happening in these unseen parts of the plants has until now depended mostly on lab studies and subjective field measurements.
To address that need, researchers from the Georgia Institute of Technology and Penn State University have developed an automated imaging technique for measuring and analyzing the root systems of mature plants. The technique, believed to be the first of its kind, uses advanced computer technology to analyze photographs taken of root systems in the field. The imaging and software are designed to give scientists the statistical information they need to evaluate crop improvement efforts.
“We’ve produced an imaging system to evaluate the root systems of plants in field conditions,” said Alexander Bucksch, a postdoctoral fellow in the Georgia Tech School of Biology and School of Interactive Computing. “We can measure entire root systems for thousands of plants to give geneticists the information they need to search for genes with the best characteristics.”
The research is supported by the National Science Foundation’s Plant Genome Research Program (PGRP) and Basic Research to Enable Agriculture Development (BREAD), the Howard Buffett Foundation, the Burroughs Wellcome Fund and the Center for Data Analytics at Georgia Tech. The research was reported as the cover story in the October issue of the journal Plant Physiology.
Beyond improving food crops, the technique could also help improve plants grown for energy production, materials, and other purposes.
Root systems are complicated and vary widely even among plants of the same species. Analyzing critical root properties in field-grown plants has depended on manual measurements, which vary with observer. In contrast, automated measurements have the potential to provide enhanced statistical information for plant improvement.
Imaging of root systems has, until now, largely been done in the laboratory, using seedlings grown in small pots and containers. Such studies provide information on the early stages of development, and do not directly quantify the effects of realistic growing conditions or field variations in water, soil, or nutrient levels.
The technique developed by Georgia Tech and Penn State researchers uses digital photography to provide a detailed image of roots from mature plants in the field. Individual plants to be studied are dug up and their root systems washed clean of soil. The roots are then photographed against a black background using a standard digital camera pointed down from a tripod. A white fabric tent surrounding the camera system provides consistent lighting.
The resulting images are then uploaded to a server running software that analyzes the root systems for more than 30 different parameters – including the diameter of tap roots, root density, the angles of brace roots, and detailed measures of lateral roots. Scientists working in the field can upload their images at the end of a day and have spreadsheets of results ready for study the next day.
“In the lab, you are just seeing part of the process of root growth,” said Bucksch, who works in the group of Associate Professor Joshua Weitz in the School of Biology and School of Physics at Georgia Tech. “We went out to the field to see the plants under realistic growing conditions.”
Developing the digital photography technique required iterative refinements to produce consistent images that could be analyzed using computer programs. To support the goal of making the system available worldwide, it had to be simple enough for field researchers to use consistently, able to be transported in backpacks to locations without electricity, and built on inexpensive components.
In collaboration with a research team led by Jonathan Lynch, a professor of plant sciences at Penn State, the system has been evaluated in South Africa with cowpea and maize plants.
With its ability to quickly gather data in the field, it was possible to evaluate a complete cowpea diversity panel. Penn State collaborator James Burridge compiled a novel cowpea reference data set that consists of approximately 1,500 excavated root systems. The data set was measured manually to validate and compare with the new computational approaches. In the future, the system could allow scientists to study crop roots over an entire growing season, potentially providing new life cycle data.
The research shows how quantitative measurement techniques from one discipline can be applied to other areas of science.
“Alexander has taken rigorous, computational principles and collaborated with leading plant root biologists from the Lynch group to study complex root structure under field conditions,” said Weitz. “In doing so, he has shown how automated methods can reveal new below-ground traits that could be targeted for breeding and improvement.”
Data generated by the new technique will be used in subsequent analyses to help understand how changes in genetics affect plant growth. For instance, certain genes may help plants survive in nitrogen-poor soils, or in areas where drought is a problem. The overall goal is to develop improved plants that can feed increasing numbers of people and provide sustainable sources of energy and materials.
“We have to feed an ever-growing population and we have to replace materials like oil-based fuels,” Bucksch said. “Integral to this change will be understanding plants and how they provide us with food and alternative materials. This imaging technique provides data needed to accomplish this.”
In addition to those already mentioned, the research team included Larry York and Eric Nord from Penn State and Abraham Das from Georgia Tech.
This research was supported by NSF Plant Genome Research Program Award 0820624, the NSF/BREAD Program Award 4184-UM-NSF-5380, the Howard G. Buffett Foundation, the Center for Data Analytics at Georgia Tech, and the Burroughs Wellcome Fund. Any opinions or conclusions are those of the authors and do not necessarily represent the official views of the funding agencies.
CITATION: Alexander Bucksch, et al, “Image-based high-throughput field phenotyping of crop roots,” (Plant Physiology 2014). http://dx.doi.org/10.1104/pp.114.243519
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By Hannah Ackermann
Georgia Tech scientists aren’t content with just making discoveries, they want to contribute to the community as well. That’s why this summer, Tonya Shearer, research scientist in the School of Biology, opened the Discover Science Center (DSC), a science enrichment lab serving the metro-Atlanta area.
“Teachers have a lot of topics to cover in class, and sometimes science gets left behind,” she said.
Shearer encourages the enthusiasm kids have for the sciences and hopes to educate the new generation in the arts and sciences with an engaging approach to learning.
“Kids are a lot smarter than we give them credit for,” said Shearer.
Rachel Whitmire, undergraduate student in the School of Biology and assistant at the DSC, said the kids are fascinated with the subject matter as the new facts they learn alter their perceptions of life around them.
“These kids bring such a wealth of knowledge. It is fun watching their opinions change,” said Whitmire.
The DSC also provides opportunities for teacher development, an important issue in Atlanta.
“Many teachers don’t even know how to use their classroom microscopes,” explained Shearer. “They can learn this skill and many more at the Discover Science Center.”
One important aspect of Shearer’s curriculum is the integration of art and science. For example, during Invertebrate Week the kids learned about how these organisms eat and reproduce. Then they made biology-inspired creative projects. They took what they learned about the adaptations and feeding mechanisms of invertebrates and created their own organism artifacts.
In the after-school programs, children learned about topics including fish, invertebrates, alien life, sea turtles, marine mammals and sharks. In the future, Shearer hopes to expand her programs to include other fields of science, such as physics and chemistry.
The DSC’s tanks house organisms including coral, anemones, crabs, sea stars, worms and live rocks. Shearer intends to enrich science education with marine biology. Because many of the topics in this field are globally relevant, it is easy to get the kids interested, said Whitmire. It also doesn’t hurt that kids love animals, she added.
Because it is outside of the school, the DSC has an informal learning environment. Kids not only learn about science, but also about the types of careers they can have in science. Whitmire is hopeful that these kids will want to get involved with research when they get older.
Shearer is in the process of training 14 teachers to teach this material to kids in classrooms all around Atlanta to expand the reach of the program. The DSC also offers home school classes and tutoring programs, as well as internships for high school and college students. These students will help to develop future programs for the kids, and cultivate a community lab for adult learning. The Discovery Science Center is a for-profit business located in Roswell, GA.
The sheer volume of cyanobacteria in the oceans makes them major players in the global carbon cycle and responsible for as much as a third of the carbon fixed. These photosynthetic microbes, which include Prochlorococcus and Synechococcus, are tiny – as many as 100 million cells can be found in a single liter of water – and yet they are not the most abundant entities on Earth. That distinction goes to viruses, up to 100 million of which can be found per 1 mL of seawater. However, researchers know very little about the viruses in the water, other than that there are three kinds of viruses, and that they are capable of drastically decreasing cyanobacterial populations, affecting the global regulation of biogeochemical cycles.
To help resolve this conspicuous lack of knowledge and learn more about viral diversity, a team led by Matt Sullivan, a professor at the University of Arizona and a collaborator with the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, conducted a population-scale survey using a game-changing new technique. Their results, he said, suggest that there is an ecology of viruses and it can be studied by harnessing more traditional approaches that have been applied to larger organisms. The work was published online July 13, 2014 in Nature.
“I often joke that viruses are only as interesting as their microbial hosts,” Sullivan said, “which makes cyanophages pretty important. Not only do they affect marine photosynthesis through mortality of cyanobacteria, but these viruses also encode photosynthesis genes – decade-old finding made in collaboration with JGI – that means cyanophages help drive global biogeochemical cycles that are crucial for running all kinds of energy conversions on the planet. The challenge for us, if we wanted to develop predictive capacity, was to develop a method that allowed us to simultaneously examine thousands (or more) of wild cyanobacterial viruses from the millions of non-cyanobacterial viruses in seawater – this would get us beyond learning about them one at a time.”
Sullivan’s team focused on the cyanophages isolated from a single sample of water collected in Monterey Bay, Calif. To resolve the challenge of figuring out “who infects whom” among marine viruses and cyanobacteria, they used a technique known as viral tagging, in which viruses and so-called “host bait” are stained with a fluorescent dye in order to find out with which hosts the phages associate. Sullivan credits the original idea for the project to study co-author Phil Hugenholtz, formerly a DOE JGI researcher and now Director of the Australian Centre for Ecogenomics at the University of Queensland.
“We subsequently found out that the basic idea of “labeling” bacteria with fluorescent viruses wasn’t novel, it had been proposed back in 1985, but the novelty of viral tagging lies in combining this with flow sorting and sequencing,” said Hugenholtz. “Viral tagging combined with flow sorting and sequencing provides an unbiased view of host-phage range.”
After screening for cyanophages that were tagged as being associated with a single Synechococcus strain (SynWH803), samples of the viral community metagenomes were sent to the DOE JGI for sequencing as part of a Community Science Program project proposed by Sullivan. The results indicated that there were “at least” 26 viral populations associated with the cyanobacterial strain, and many of them had been found and identified in culture. Additionally, the researchers wrote, “viral tagging also provided evidence… for 42 new uncultured viruses specific to SynWH7803…. [A]n unprecedented diversity of specific viruses were recovered for this single host despite two decades of isolation studies.”
The study also benefited from collaboration with Joshua Weitz, an Associate Professor and theoretical ecologist from the Georgia Institute of Technology, who was on sabbatical in the Sullivan Lab at UA. “This new method provides incredibly novel sequence data on viruses linked to a particular host,” Weitz explained. “The work is foundational for developing a means to count genome-based populations that serve as starting material for more rigorous predictive models of how viruses interact with their host microbes. Instead of counting ‘dots’ we can now map viral populations with their genomes, providing information about who they are and what they do.”
The team made several key findings, perhaps chief among them was that the fluorescently-tagged cyanophages sequenced existed in discrete populations when plotted in ‘genome sequence space’ (an abstract method the researchers used to visualize the relatedness of many viruses at once). This means that the conventional knowledge of viral genomes evolving by “rampant mosaicism” – i.e., recombining segments or modules from different cyanophages – might be wrong. Instead, these cyanophage genome “clusters” suggested that there was discrete population structure in the wild.
“The novel finding here isn’t the number of viruses, but rather the structured nature of the populations,” Sullivan said. “With these discrete populations in a complex natural community and the genome sequence information linked to each population, we are generating hypotheses on what might be driving particular population-host interactions and the abundances of particular populations – that’s viral ecology. And you can track how one population changes over time at a genetic level – that’s viral evolution,” he said. “The thinking before was that the viral genome sequence space would be one big blur, but this suggests there are units that we can count and study. That represents a whole new ballgame and opens up viral ecology to utilize decades of theory and practice from the study of more traditional study of larger organisms. Additionally, our method of viral tagging should be generalizable to many other virus-host studies so it should transform the way viruses in nature are studied moving forward.”
Matt Sullivan spoke about marine viruses at the 2012 DOE JGI Genomics of Energy & Environment Meeting. Watch the video at http://bit.ly/JGI7Sullivan. The Sullivan lab maintains publicly available protocols and informatics tools at http://eebweb.arizona.edu/Faculty/mbsulli/.
Since his arrival on campus in 2004, molecular biologist and Tech Professor John McDonald has been hard at work developing new solutions and strategies for targeting and treating cancer. Some of his latest research concerns the use of nanoparticles to seek out and deliver treatments to ovarian cancer cells without damaging the body’s healthy cells. Designing this technology has required collaboration between the McDonald Lab in the School of Biology and Andrew Lyon’s lab in the School of Chemistry.
Your lab is designing treatment methods that deliver medications through nanoparticles. What exactly is a nanoparticle?
Basically, they are synthetic particles that are smaller than viruses—there are all kinds of different nanoparticles. The kind we’re developing with the Lyon lab is a nano-hydrogel. They are 98 percent water, and I think of them sort of as microscopic sponges: When you put them in water they swell up and soak up the solution that’s around them. The therapeutic treatment we are using involves small regulatory RNAs [ribonucleic acid], and we use a technique called “breathing in,” because when the particles are exposed to the solution containing the therapeutic RNAs, they self-load the RNA into the particle.
How can a nanoparticle deliver medication to a cancer cell?
The next part of the design is functionalizing the particle. The particle has to be modified in such a way that it binds to the specific cells you want to target. The problem with chemotherapy is that it’s typically given systemically to all exposed cells, not just cancerous cells. In our case, we want to treat only the cancerous cells while leaving the healthy cells alone. This can be accomplished by identifying a surface feature that is unique to the cancer cell, and then engineering the nanoparticle to selectively attach to that feature.
How can a nanoparticle identify a cancer cell in the body?
Nanoparticles injected into the blood stream will circulate through the circulatory system looking for the targeted cancer cells. Once the nanoparticle encounters a cancer cell and attaches to the surface feature, the nanoparticle is taken up by the cell and the therapeutic treatment is slowly released. Nanoparticles have pores in them so that they will release the RNA payload at a controlled rate. In our pilot experiments, we have added a molecule to the nanoparticle that binds to a particular receptor protein that we know is highly expressed on the surface of ovarian cancer cells. In the future, nanoparticles will be designed to target other cell features unique to other types of cancer.
Your therapeutic treatment uses RNA instead of a drug. What is the difference between the two?
Think of the blueprint of the new Engineered Biosystems Building going up on campus. If you’re the guy building the foundation, you’re only interested in examining the section describing how to build the foundation. You don’t care how the roof is built. By analogy, DNA is carried in every cell in our body and is the blueprint of all cellular functions. But liver cells, for example, don’t care how to conduct brain cell functions so they transfer from the DNA blueprint the specific subset of information needed for liver cell function into a type of RNA called mRNA. This mRNA then serves as the template for synthesis of the proteins necessary for liver cell function. Take that concept and apply it to cancer. Cancer is a disease of misinformation. The cell is getting the wrong information—for example, it is being told to rapidly divide when it should remain quiescent. That misinformation could occur due to an error in the DNA blueprinting itself. We call such mistakes “mutations.” Alternatively, there could be a mistake in the flow of information from the DNA such that, for instance, mRNA is being produced when it should not be. The bottom line, in either case, is that abnormal kinds or levels of proteins are produced leading to formation of cancer cells. A new class of cancer drugs are currently being developed to target abnormal or abnormally expressed proteins in cancer cells. Many of these new targeted drugs show great promise but it is estimated that only 10 percent of proteins are “drugable” in this way. Thus, we are interested in developing therapies that can target abnormal or abnormally expressed genes on the mRNA rather than on the protein level. In theory all genes can be targeted on the mRNA level using small inhibitory RNAs. The problem is how do we deliver these inhibitory RNAs specifically to cancer cells? That leads us back to nanoparticles.
What problems are posed by traditional, systemic cancer treatments?
Ideally, we would prefer not to deliver inhibitory (or any) drug treatments systemically because of the unintended inhibitory effects they might have on normal healthy cells. In some cases these “negative side effects” can be quite severe or even lethal.
You’ve been working with Andrew Lyon of the School of Chemistry to develop the nanoparticles. How collaborative has this design process been?
Very collaborative. That’s the beauty of Georgia Tech: You have experts with the specialties you need right next door. I believe this kind of integrated approach will help Georgia Tech significantly contribute to cancer research in the future.
How involved were you with the nanoparticle’s design?
Dr. Lyon’s group had already developed the basic nanoparticle. A former post-doc in my lab, Erin Dickerson, a current research scientist, Roman Mezencev, and I discussed with Dr. Lyon various strategies to further engineer these particles to optimally deliver therapeutic RNAs to ovarian cancer cells. My lab provides the biological knowledge and Dr. Lyon’s lab provides the technical expertise to move the project forward.
What is the next step after designing the nanoparticle?
The next question one asks is, “Does it work?” We first tested the ability of the nanoparticles to deliver the therapeutic RNAs to cancer cells grown in culture. This worked very well which led us to the next level—testing delivery and efficiency in animal models.
Animal testing is currently underway. What obstacles stand in the way of making the treatment available to the public?
There are a number of things the FDA requires before approving any treatment like this for use in humans. We first have to show that these particles are non-toxic in their own right. We have recently demonstrated that this is the case. Now we have to demonstrate efficacy, that is, we have to show that treatment with these particles lowers or reduces the burden of cancer in experimental animals. Once that is validated, one can apply for FDA approval for Phase I experimental trials in humans.
Once the design for ovarian cancer treatment is released, what do you do? Start developing designs for other types of cancer?
At that point, the technology development would be done and the technology would move into the commercial sector. That’s not my area of expertise so I would leave that to someone more qualified. My job as a scientist would be to develop new types of RNAs that might be even more effective in treating different cancers, while using the same or maybe an improved class of delivery vehicles. We continue to work with other Georgia Tech researchers to develop even better delivery systems, as well as new and imaginative cancer diagnostics and therapeutics. It’s all about continued integration and collaboration. That’s one of the great things about being a scientist at Georgia Tech.