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.
In the latest issue of the journal Science, Will Ratcliff, assistant professor in Georgia Tech Biology, has a piece on a new theory he and Eric Libby, from the Santa Fe Institute, are positing that explains the rules governing how life may have evolved from single-celled organisms into multi-cellular productions.
How multicellular complexity arises in evolution is a central problem in biology, but we know little about how early groups evolved into the complex multicellular organisms we see today. The first steps in this process are often a big hurdle, because the fitness interests of cells and groups of cells can conflict. In this short piece, we propose a new idea for how early life in multicellular groups can be stabilized. Ratcheting is the idea that once cells in groups evolve traits that costly to single cells, the path back to unicellularity is cut off.
Apoptosis is a great example of this. At the single cell level, it causes the death of the organism, but in a multi-cellular organism it can be a good thing because it allows for things like the death of damaged cells, disease prevention as well as helping organisms regulate the number and size of offspring they produce.
You can imagine that there are many other examples that allow groups to get more complex and at the same time makes it harder for them to get off the multicellular train. We’re testing a few of these experimentally right now.
Full Paper: http://www.sciencemag.org/content/346/6208/426.full
Dr. Joshua Weitz, Associate Professor of Biology, was named a Simons Foundation Investigator in Ocean Processes and Ecology and awarded a three-year grant from the Simons Foundation. Dr. Weitz will examine physical and ecological principles governing the interplay between viruses and zooplankton in the North Pacific Ocean. Dr. Weitz joins a new initiative, SCOPE -- the Simons Collaboration on Ocean Processes and Ecology -- co-directed by Edward DeLong and David Karl at the University of Hawai'i, Manoa. The purpose of the collaboration is to advance understanding of the biology, ecology, and biogeochemistry of microbial processes that dominate Earth's largest biome: the global ocean. The collaborative effort will measure, model and conduct experiments at a model ecosystem site located 100 km north of Oahu. The Simons Foundation's mission is to advance the frontiers of research in mathematics and the basic sciences. The Foundation sponsors a range of programs that aim to promote a deeper understanding of our world.
In the past year, more than 21,000 individuals have been infected with Ebola virus disease in West Africa and more than 8,000 are reported to have died. The outbreak response is one of the largest and most complex that the CDC and global health community have conducted. Although the outbreak seems to be turning around, there is an ongoing need for intervention and monitoring to reduce the new case count to zero.
This past week the Georgia Institute of Technology hosted a two-day workshop, "Modeling the Spread and Control of Ebola in West Africa," with more than 180 participants to discuss the use of dynamical models to support, interpret and enhance public health practices to help stop the spread of the disease.
"There is a growing coalition of modelers working at different scales - from how the disease is transmitted at the community level, to how the virus is evolving - who can contribute to support the response effort on the ground," said Joshua Weitz, chair of the organizing committee and associate professor in Georgia Tech's School of Biology.
The lectures and discussions focused on four major questions: How much confidence should we have in forecasts of the epidemic? How do we evaluate control strategies? What are the challenges in implementing these strategies? How do we communicate models to each other, public health scientists and to the broader community?
Participants in the workshop came from universities in the United States, Canada and England, as well as from the Centers for Disease Control and Prevention (CDC), the White House Office of Science Technology and Policy, the Biomedical Advanced Research and Development Authority, the Red Cross, Intel, IBM and the United States national laboratories. Speakers and panelists represented a wide array of professions and backgrounds.
Ebola is particularly tricky to model, said one speaker, because "this Ebola outbreak has not developed in the way that past outbreaks have evolved, that means we've not been able to rely on past experiences to map out our response this time around."
Epidemiological modeling, including forecasting and evaluating control strategies, is vital to the success of the response. Initially, models of Ebola spread had high degrees of uncertainty regarding the potential scope of the outbreak. This uncertainty stemmed, in part, from the lack of detailed case data and chains of transmission. Models were also poorly informed with respect to the relative importance of urban and rural transmission. Models did not have accurate estimates of the extent and speed at which safe burials would become widespread and Ebola treatment units would be built. Changes in behavior and widespread interventions are necessary to avert worst-case scenarios.
The challenge in linking models to case data are many. Much of the data needed is gathered by public health professionals and doctors, many of whom are responding to patients and working to slow the spread of the disease. Multiple panelists pointed out the need to identify data collection protocols that could serve to inform predictive models while balancing the need to respond to those they are sent to aid.
There were many other challenges to modeling the effectiveness of control efforts. Logistical challenges included traveling along roads in Africa, the transmission of Ebola from animals to humans, as well as the complications of dealing with a number of governments and scientists with different ideas of how to respond and what data to share. Communication was considered essential to move from model predictions to policies that could support an effective response.
The final panel addressed this issue by considering communication of models amongst three sectors: government, academia and the media. Experts in modeling are not usually trained to communicate with policy makers. This can lead to miscommunication, or a lack of communication. Translating scientists' results to the public and to policy makers is key. For example, communicating the need for safe burials helped to reduce the transmission of Ebola during burial ceremonies. Informing policy makers of the risks of inaction helped to galvanize support for a much larger response effort in Fall 2014.
Despite the challenges, there is some room for optimism. New cases of Ebola virus disease have dropped in the past month, particularly in Liberia. The reasons are many, including changes in behavior and the impact of interventions. Individuals with Ebola are not infectious until symptomatic, which facilitates contact tracing and leads many to believe that a successful public health response is possible. New Ebola vaccines have also been developed to be utilized in Phase II trials planned by the CDC for testing in West Africa in the coming months. Vaccine trial design was the topic of an extended breakout discussion and panel talk.
"The modeling community has work to do," remarked Weitz at the close of the meeting. "This workshop has helped to identify many scientific and engineering challenges necessary to understand how the virus spread to so many people (unlike past Ebola outbreaks), how to enact a more effective response to the ongoing epidemic and how to prevent future epidemics."
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Biology faculty member Dr. Danielle Dixson is among 126 scientists in North America who have been awarded a 2015 Sloan Research Fellowship, a two-year grant given to early career scholars to support their pursuit of scientific knowledge.
Dixson, an assistant professor in the School of Biology, investigates the influence sensory cues have on the behavior of coral reef organisms. Her recent work, featured on the cover of the journal Science, found that coral larvae and juvenile fishes can smell the difference between a reef that is unhealthy and one that is a suitable home. She has also published recent work showing that acidic oceans make sharks less interested in their food.
Dixson conducts research around the globe on coral reef ecology, and the Sloan Research Fellowship will allow her to continue conducting the fieldwork vital to her research.
“I am very honored and excited to have been selected as a Sloan Fellow,” Dixson said. “These funds will allow my lab to conduct research in Belize investigating how larval fishes and corals use chemical cues in settlement site selection and predator evasion.”
Dr. Frank Stewart was awarded $540,000 in March 2015 by the Simons Foundation to investigate the microbiomes of reef fish. The Simons Foundation has made ocean processes and ecology one of their priority areas for investigation. They have initiated a Collaboration on Ocean Processes and Ecology (SCOPE) that will measure, model and experimentally manipulate a complex system representative of a broad swath of the North Pacific Ocean. This collaboration aims to advance our understanding of the biology, ecology and biogeochemistry of microbial processes that dominate the global ocean. A central premise of SCOPE is that we must study the ocean ecosystem in situ, at a variety of levels of biological organization (e.g., genetic, biochemical, physiological, biogeochemical and ecological), and at highly resolved, nested scales of space and time in order to fully describe and model it.
By investigating fish microbiomes, Dr. Stewart hopes to better understand how bacteria interact with their hosts in the ocean. Symbiosis between microorganisms and higher eukaryotes is among the most pervasive evolutionary and ecological strategies in nature, impacting fundamental processes including speciation, ecosystem structuring, primary production, nutrient cycling, and disease. A surge of studies exploring the commensal microbiome of the human body has identified complex networks of factors shaping microbiome acquisition, composition, and function, as well as a range of host developmental and immunological outcomes affected by microbiome activity. For most animal lineages, excluding humans, the ecology and evolution of host-associated microbiomes are almost completely unexplored. This is true for the largest and most diverse of the vertebrate groups, the teleost fishes. In many ocean regions, notably in productive coastal zones and reefs, teleosts play vital roles in material and energy transport and ecosystem structuring. Teleosts on coral reefs represent over 2500 fish species and engage in a complex network of ecological interactions including nutrient recycling, herbivory, corallivory, and symbiosis. Fish also serve cryptic roles as habitats for microorganisms. Given the phylogenetic and ecological breadth of reef teleosts and the potential for host species-specificity in vertebrate microbiomes, reef fish microbiomes are hypothesized to harbor a wide diversity of uncharacterized bacterial lineages. Such lineages may play important roles as mediators of fish nutrition and disease prevention and as inocula for free-living or coral microbiome populations.
Dr. Stewart will execute an integrated research plan over three years to sample deeply across this spectrum, combining 1) 16S rRNA gene sequencing, multivariate, and indicator analyses to identify determinants of fish gut and mucus microbiome composition, 2) quantitative metagenomic and single-amplified genome (SAG) sequencing of indicator microbes to identify shared (core) and peripheral (host-specific) functional properties, and to enable comparisons to pathways in microbiomes of other major vertebrate groups, and 3) targeted experiments to quantify acquisition and transmission dynamics of fish microbiomes. The proposed work will help to quantify connectivity between host-associated and external microbial niches, as well as identify host benefits of microbial-association, potentially including unrecognized contributions to immunity, digestion, and chemical signaling between host individuals.
Dr. Joel Kostka’s research group has a paper soon to be published in the International Society for Microbial Ecology journal entitled “Metabolic potential of fatty acid oxidation and anaerobic respiration by abundant members of Thaumarchaeota and Thermoplasmata in deep anoxic peat”. It is an important contribution because archaea are thought to play a key role in the microbial carbon cycle of peatlands, which store close to one-third of all soil carbon. One reviewer commented, "The value of this communication is immense for the understanding of bioactive carbon sequestration as the representatives of both phyla account for the vast majority of the microbial community in peat bogs."
They studied archaea that are very abundant in global soils as well as those of peatlands. In spite of their abundance on a global scale, the metabolism of archaea is not understand nor is their role in the carbon cycle because none of these organisms has been cultivated. This paper uses a metagenomic approach to determine the metabolic potential of these archaea which could play a key role in the response of peat microbial communities to climate change. Samples were collected at the Marcell Experimental Forest in northern Minnesota, where the DOE is carrying out a large scale climate manipulation study. SPRUCE site.
Researchers have developed a new informatics technology that analyzes existing data repositories of protein modifications and 3D protein structures to help scientists identify and target research on “hotspots” most likely to be important for biological function.
Known as SAPH-ire (Structural Analysis of PTM Hotspots), the tool could accelerate the search for potential new drug targets on protein structures, and lead to a better understanding of how proteins communicate with one another inside cells. SAPH-ire has been tested on a well studied class of proteins involved in cellular communication, where it correctly predicted a previously-unknown regulatory element.
“SAPH-ire predicts positions on proteins that are likely to be important for biological function based on how many times those parts of the proteins have been found in a chemically-modified state when they are taken out of a cell,” explained Matthew Torres, an assistant professor in the School of Biology at the Georgia Institute of Technology. “SAPH-ire is a tool for discovery, and we think it will lead to a new understanding of how proteins are connected in cells.”
The tool and its proof-of-concept testing were reported June 12 in the journal Molecular and Cellular Proteomics. The research was supported by the National Institutes of Health’s National Institute of General Medical Sciences (NIGMS) and Georgia Tech.
Through modern mass spectrometry proteomics techniques, scientists have identified more than 300,000 post-translational modifications (PTMs) in different families of proteins across numerous species. These PTMs come in many forms, resulting from the action of different enzymes, and are often indicators of how and where proteins contact one another to bring about different cell behaviors. The number of PTMs detected by mass spectrometry has grown so rapidly that researchers experimentally investigating the function of the modifications have been unable to keep up.
“Mass spectrometry is so effective that it has created an exponential curve in the knowledge of how proteins are modified,” said Torres. “The rate at which we can detect new PTMs has now far surpassed the rate at which we can understand what they do, from a classical biochemical approach. You have so much information that you don’t know where to begin.”
But that’s exactly where SAPH-ire begins. Aimed at bridging the gap between PTM detection and analysis of function, SAPH-ire collects non-redundant and experimentally verified PTM data across all known members of a protein family. Since members of a protein family share the same or similar protein structures, PTMs found within the family can be related to one another in three-dimensional space to produce a set of observed PTM frequencies, termed “hotspots.”
The PTM hotspots are projected onto 3D protein structures available in the Protein Data Bank (PDB), which allows the entire set of family-specific PTMs to be visualized on any protein structure that is representative for the family. Once projected there, SAPH-ire integrates multiple quantitative features from each hotspot to create a PTM “Functional Potential Score.” Each PTM hotspot can then be ranked in order of highest to lowest potential for having significant biological function.
“We have gone through all of what might be considered the meta-data that exists in the public domain, collected all the PTMs and all the structures, then organized them into their specific protein families,” Torres explained. “We are looking at PTMs through time, in a sense, because we have information from organisms that are evolutionarily distant from each other, though their proteins are related as members of a protein family.”
To prioritize research with the most significant potential impact, scientists might examine PTM hotspots that SAPH-ire identifies as having high function potential, but no known function.
Torres’ lab has been investigating unique families of “G” proteins, some of which cooperate with cell surface receptors that control the binding of hormones and neurotransmitters, as well as a majority of pharmaceutical drugs. Because of their importance to therapeutics, these proteins have been extensively studied over a period of 50 years or so. Using SAPH-ire, the researchers discovered something surprising about this group of protein families.
“We discovered a new regulatory element within a specific G protein family that has been largely ignored because it’s pretty unimpressive from a purely structural viewpoint,” Torres said. “SAPH-ire predicted that this element was going to be important from a modification point of view, and we confirmed experimentally that it was.”
SAPH-ire was conceived by Torres and developed by him and graduate student Henry Dewhurst, while experimental validation of the tool was accomplished by graduate student Shilpa Choudhury. Their next step is to develop collaborations with scientists who will try it out on the protein families they study. The Georgia Tech researchers are also creating a database that other protein scientists can query to help them identify and prioritize PTM hotspots, and they expect to see their program become part of informatics systems used to analyze large volumes of proteomics data emerging from labs around the world.
“SAPH-ire will help bring meaning and context to all the data that is being produced about PTMs,” Torres said. “Connecting SAPH-ire to other programs that convert mass spec data into actual PTM data could provide immediate biological relevance and prioritization for biochemists and others. It is likely to expose many new and unsuspected relationships between protein modification, protein structure and function.”
This research was supported by the National Institutes of Health, National Institute of General Medical Sciences (NIGMS), under grant number 5R00 GM094533-05. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
CITATION: Henry M. Dewhurst, Shilpa Choudhury and Matthew P. Torres, “Structural Analysis of PTM Hotspots (SAPH-ire) – a Quantitative Informatics Method Enabling the Discovery of Novel Regulatory Elements in Protein Families,” (Molecular and Cellular Proteomics, 2015). http://dx.doi.org/10.1074/mcp.M115.051177
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