Earlier this month a team of undergraduates brought home a silver medal in the 2012 International Genetically Engineered Machine (iGEM) competition. iGEM is considered the premiere undergraduate synthetic biology competition where teams design, construct and analyze novel biological systems to perform new functions in living cells.

The competition, which featured 195 teams from around the globe, took place October 12-14 in Pittsburgh as part of iGEMs Americas East Regional Jamboree. Tech’s team consisted of five undergraduates: biology majors Natalie Chilcutt, Joseph Elsherbini and Jennifer Goff as well as Mitesh Agrawal and Jennifer Boothby from biomedical engineering.

The students began work on their project this past summer, engineering a synthetic biosensor system in bacteria, inspired by the cell-cell communication process called “quorum sensing” studied in the Hammer lab. The students used a technique called bimolecular fluorescence complementation (BiFC) to document a response to an extracellular chemical signal in the model bacterium E. coli. The bacteria were engineered to make two halves of a naturally green fluorescent protein (GFP) that are not fluorescent independently and only interact to form a complete fluorescent protein in the presence of a defined chemical signal. This novel system has the potential to be tailored to respond to different extracellular molecules, such as toxins, metabolites and pollutants,  and is designed to provide a more rapid response than traditional biosensor.

This year’s iGEM project (http://2012.igem.org/Team:Georgia_Tech) arose from a National Science Foundation-sponsored (NSF) collaborative synthetic biology project currently underway involving the Hammer lab and multiple engineering collaborators (http://www.ece.gatech.edu/research/labs/bwn/monaco/index.html). The team was supported by funding from the School of Biology, NSF as well as Georgia Tech’s President’s Undergraduate Research Awards and the Undergraduate Research Opportunities Program.

The team is advised by Brian Hammer, assistant professor in the School of Biology, and Mark Styczynski, assistant professor in the School of Chemical & Biomolecular Engineering. The team is mentored by postdoctoral fellow Patrick Bardill (biology) with assistance from Ph.D. students Samit Watve (biology) and Youssef Chahibi (electrical & computer engineering). The iGEM advisory board includes additional faculty, Joshua Weitz, Eric Gaucher and Harold Kim, who have served as past advisors.

Most of us gaze in wonder at how clouds of all different shapes and sizes form and vaporize across the beautiful October Atlanta sky. Few of us think about bacteria playing a role in this process. This is not the case for Natasha DeLeon-Rodriguez, a School of Biology graduate student in the lab of Kostas Konstantinidis (http://enve-omics.gatech.edu/).

Natasha aims to understand how bacteria affect cloud formation – a proposal that has earned her a NASA Earth and Space Science Fellowship (NASA-NESSF).  This competitive fellowship supports research at the intersection of microbiology, genomics and atmospheric science.

To accomplish her research, Natasha quantifies the number of bacterial cells collected from the mid-to-upper troposphere (five to six miles high in the atmosphere) onboard a NASA DC-3 aircraft. She is currently investigating the mechanism by which these bacterial cells serve as nuclei for cloud condensation and ice formation. The long-term goal of her project is to apply her discoveries to improve regional and global atmospheric models that are able to describe the cloud formation process.

This work is conducted in collaboration with the Nenes lab from the School of Earth and Atmospheric Sciences and Bruce Anderson of NASA Langley Research Center.

Yingying Zeng, a graduate student in the School of Biology, is the lead author on a new paper that describes the complete structure of satellite tobacco mosaic virus (STMV). This is the first model for the structure of any virus that specifies the position of every single atom. Zeng combined high-resolution data from x-ray crystallography, chemical data on the structure of the RNA genome, and knowledge-based molecular modeling methods to develop her model. STMV is a small virus that has served for many years as a model system for investigating the relationships between viral structure and function. The new model has implications for understanding the pathway of viral assembly. These methods can be extended to investigate the structures of human viral pathogens and, in the long run, to the design of novel drugs aimed at inhibiting viral assembly.

This was a collaborative effort headed by Steve Harvey (School of Biology), and it included contributions from Christine Heitsch (School of Mathematics) as well as Steven Larson and Alexander McPherson (University of California, Irvine). The paper appeared in the October issue of the Journal of Structural Biology.

Corals under attack by toxic seaweed do what anyone might do when threatened – they call for help. A study reported this week in the journal Science shows that threatened corals send signals to fish “bodyguards” that quickly respond to trim back the noxious alga – which can kill the coral if not promptly removed.

Scientists at the Georgia Institute of Technology have found evidence that these “mutualistic” fish respond to chemical signals from the coral like a 911 emergency call – in a matter of minutes. The inch-long fish – known as gobies – spend their entire lives in the crevices of specific corals, receiving protection from their own predators while removing threats to the corals.

This symbiotic relationship between the fish and the coral on which they live is the first known example of one species chemically signaling a consumer species to remove competitors. It is similar to the symbiotic relationship between Acacia trees and mutualist ants in which the ants receive food and shelter while protecting the trees from both competitors and consumers.

“This species of coral is recruiting inch-long bodyguards,” said Mark Hay, a professor in the School of Biology at Georgia Tech. “There is a careful and nuanced dance of the odors that makes all this happen. The fish have evolved to cue on the odor released into the water by the coral, and they very quickly take care of the problem.”

The research, supported the National Science Foundation, the National Institutes of Health and the Teasley Endowment at Georgia Tech, was reported November 8 in the journal Science. The research was done as part of a long-term study of chemical signaling on Fiji Island coral reefs aimed at understanding these threatened ecosystems and discovering chemicals that may be useful as pharmaceuticals.

Because they control the growth of seaweeds that damage coral, the importance of large herbivorous fish to maintaining the health of coral reefs has been known for some time. But Georgia Tech postdoctoral fellow Danielle Dixson suspected that the role of the gobies might be more complicated. To study that relationship, she and Hay set up a series of experiments to observe how the fish would respond when the coral that shelters them was threatened.

They studied Acropora nasuta, a species in a genus of coral important to reef ecosystems because it grows rapidly and provides much of the structure for reefs. To threaten the coral, the researchers moved filaments of Chlorodesmis fastigiata, a species of seaweed that is particularly chemically toxic to corals, into contact with the coral. Within a few minutes of the seaweed contacting the coral, two species of gobies – Gobidon histrio and Paragobidon enchinocephalus – moved toward the site of contact and began neatly trimming away the offending seaweed.

“These little fish would come out and mow the seaweed off so it didn’t touch the coral,” said Hay, who holds the Harry and Linda Teasley Chair in Environmental Biology at Georgia Tech. “This takes place very rapidly, which means it must be very important to both the coral and the fish. The coral releases a chemical and the fish respond right away.”

In corals occupied by the gobies, the amount of offending seaweed declined 30 percent over a three-day period, and the amount of damage to the coral declined by 70 to 80 percent. Control corals that had no gobies living with them had no change in the amount of toxic seaweed and were badly damaged by the seaweed.

To determine what was attracting the fish, Dixson and Hay collected samples of water from locations (1) near the seaweed by itself, (2) where the seaweed was contacting the coral, and (3) from coral that had been in contact with the seaweed – 20 minutes after the seaweed had been removed. They released the samples near other corals that hosted gobies, which were attracted to the samples taken from the seaweed-coral contact area and the damaged coral – but not the seaweed by itself.

“We demonstrated that the coral is emitting some signal or cue that attracts the fish to remove the encroaching seaweed,” Hay said. “The fish are not responding to the seaweed itself.”

Similar waters collected from a different species of coral placed in contact with the seaweed did not attract the fish, suggesting they were only interested in removing seaweed from their host coral.

Finally, the researchers obtained the chemical extract of the toxic seaweed and placed it onto nylon filaments designed to stimulate the mechanical effects of seaweed. They also created simulated seaweed samples without the toxic extract. When placed in contact with the coral, the fish were attracted to areas in which the chemical-containing mimic contacted the coral, but not to the area contacting the mimic without the chemical.  

By studying the contents of the fish digestive systems, the researchers learned that one species – Gobidon histrio – actually eats the noxious seaweed, while the other fish apparently bites it off without eating it. In the former, consuming the toxic seaweed makes the fish less attractive to predators.

The two species of fish also eat mucus from the coral, as well as algae from the coral base and zooplankton from the water column. By defending the corals, the gobies are thus defending the home in which they shelter and feed.

“The fish are getting protection in a safe place to live and food from the coral,” Hay noted. “The coral gets a bodyguard in exchange for a small amount of food. It’s kind of like paying taxes in exchange for police protection.”

As a next step, Hay and Dixson would like to determine if other species of coral and fish have similar symbiotic relationships. And they’d like to understand more about how the chemical signaling and symbiotic relationship came into being.

“These kinds of positive interactions needs to be better understood because they tell us something about the pressures that have gone on through time on these corals,” said Hay. “If they have evolved to signal these gobies when a competitor shows up, then competition has been important throughout evolutionary time.”

CITATION: Danielle L. Dixson and Mark E. Hay, Corals chemically signal mutualistic fishes to remove competing seaweeds, Science (2012).

This research has been supported by the National Science Foundation (NSF) under grant OCE-0929119 and by the National Institutes of Health under grant U01-TW007401. The content of this article is solely the responsibility of the authors and does not necessarily represent the official views of the NSF or the NIH.

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The National Institute of Allergy and Infectious Diseases, part of the National Institutes of Health, has awarded a five-year contract of up to $19.4 million, depending on contract options exercised, to establish the Malaria Host-Pathogen Interaction Center (MaHPIC).

The consortium includes researchers at Emory University, with partners at the Georgia Institute of Technology, University of Georgia (UGA) and the Centers for Disease Control and Prevention (CDC). The Yerkes National Primate Research Center of Emory University will administer the contract.

The MaHPIC team will use the comprehensive research approach of systems biology to study and catalog in molecular detail how malaria parasites interact with their human and animal hosts. This knowledge will be fundamental to developing and evaluating new diagnostic tools, antimalarial drugs and vaccines for different types of malaria. The project will integrate data generated by malaria research, functional genomics, proteomics, lipidomics and metabolomics cores via informatics and computational modeling cores.

MaHPIC combines Emory investigators’ interdisciplinary experience in malaria research, metabolomics, lipidomics and human and non-human primate immunology and pathogenesis with UGA’s expertise in pathogen bioinformatics and large database systems, and Georgia Tech’s experience in mathematical modeling and systems biology. The CDC will provide support in proteomics and malaria research, including nonhuman primate and vector/mosquito infections.

The principal investigator is Mary Galinski, PhD, professor of medicine, infectious diseases and global health at Emory University School of Medicine and director of Emory’s International Center for Malaria Research, Education & Development (ICMRED). She has been leading malaria research projects at the Emory Vaccine Center and Yerkes for 15 years.

“We are thankful to the National Institute of Allergy and Infectious Diseases for recognizing the enormous potential of taking a systems biology approach to studying malaria infections,” Galinski says.

“This project will help us better understand malaria as a disease in depth and pave the way for new preventive and therapeutic measures. We expect to provide a groundbreaking wealth of information that will address current challenges in fighting malaria. The Georgia team we have assembled is outstanding and we also look forward to working closely with prominent international partners from malaria endemic countries.”

A prestigious international Scientific Consultation Group is also involved, and met with the MaHPIC team at Emory recently, following the annual American Society of Tropical Medicine and Hygiene conference held in Atlanta.

The MaHPIC project involves studying both nonhuman primate infections and clinical samples from humans around the world. For the study of malaria, “systems biology” means first collecting comprehensive data on how a Plasmodium parasite infection produces changes in host and parasite genes, proteins, lipids, the immune response and metabolism.

Computational researchers will then design mathematical models to simulate and analyze what’s happening during an infection and to find patterns that predict the course of the disease and its severity. Together, the insights will help guide the development of new interventions. Co-infections and morbidities will also come into play, as well as different cultural and environmental backgrounds of the communities involved.

The team will use metabolomics techniques that will allow scientists to detect, analyze and make crucial associations with thousands of chemicals detectable in the blood via mass spectrometry. The techniques were developed at Emory by Dean Jones, PhD, professor and director of the Clinical Biomarkers Laboratory and MaHPIC’s metabolomics core leader.

“This is a wonderful opportunity to integrate multiple types of rich biological data into dynamic models that will help scientists around the world devise novel strategies to help control not just malaria but other infectious diseases,” says Greg Gibson, PhD, professor and director of the Center of Integrative Genomics at Georgia Tech.

“MaHPIC will generate experimental, clinical and molecular data associated with malaria infections in nonhuman primates on an unprecedented scale,” says Jessica Kissinger, PhD, who will direct the project’s informatics team. Kissinger is professor of genetics at UGA and director of UGA’s Institute of Bioinformatics.

“In addition to mining the massive quantities of integrated data for trends and patterns that may help us understand host and pathogen interaction biology, we may identify potential targets for early and species-specific diagnosis of malaria, which is critical for proper treatment,” Kissinger says.

The MaHPIC team will develop an informative public website and specialized web portal to share the project’s data and newly developed data analysis tools with the scientific community worldwide.

“The sheer amount of detailed, high-quality information amassed by the experimental groups will be unprecedented. With this project we have an incredible opportunity to integrate data with modern computational tools of dynamic modeling,” says Eberhard Voit, PhD, professor of biomedical engineering and cofounder of the Integrative BioSystems Institute at Georgia Tech. “This integration will allow us to analyze the complex networks of interactions between hosts and parasites in a manner never tried before. Systems biology will be the foundation for this integration.”

Georgia Tech's involvement:
Greg Gibson, PhD, professor and director of the Center of Integrative Genomics, will be the director of the functional genomics core. Eberhard Voit, PhD., professor and David D. Flanagan Chair in biological systems, Georgia Research Alliance Eminent Scholar, and cofounder of the Integrative BioSystems Institute, will be the director of the computational modeling core.  Mark Styczynski, an assistant professor in Chemical & Biomolecular Engineering, will serve as deputy director of the computational modeling core.

New research from Georgia Aquarium and Georgia Institute of Technology provides evidence that a suite of techniques called “metabolomics” can be used to determine the health status of whale sharks (Rhincodon typus), the world’s largest fish species. The study, led by Dr. Alistair Dove, director of Research & Conservation at Georgia Aquarium and an adjunct professor at Georgia Tech, found that the major difference between healthy and unhealthy sharks was the concentration of homarine in their in serum—indicating that homarine is a useful biomarker of health status for the species.

The paper, “Biomarkers of whale shark health: a metabolomic approach”, which is published in the journal PLOS ONE, is especially significant to the veterinary science community because the study documents the results of a rare opportunity to collect and analyze blood from whale sharks. The paper also comprises the only work yet carried out on biochemistry of the world’s largest fish.

“This research and its resulting findings are vitally important to ensuring Georgia Aquarium’s and the scientific community’s care, knowledge, and understanding of not only whale sharks, but similar species of sharks and rays,” said Dr. Greg Bossart, Senior Vice President of Animal Health, Research & Conservation and Chief Veterinary Officer at Georgia Aquarium. “The publishing of this clinical research provides a greater opportunity for scientists and Zoological professionals to understand the Animals in our care and can be used to help wild populations, which puts us ahead of the curve in the integrated understanding of animal biology.”

Previous research and observations showed that traditional veterinary blood chemistry tests were not as useful with whale sharks; most likely because such tests are designed for mammals and comparatively less is known about shark and ray blood. Dr. Dove and six colleagues from Georgia Tech set out to significantly increase knowledge of whale shark biochemistry by examining the metabolite composition of all six whale sharks which have been cared for at Georgia Aquarium. By using metabolomics, the researchers were able to determine which chemical compounds were present in the shark blood, without knowing ahead of time what they are.

“It is vitally important for us to continue to learn how to best support the whale sharks in our care,” said Dove, who, along with the GA Tech team, spent three years developing the research. “We began the study by asking ourselves, ‘What should we be looking for in whale shark serum?’ and ‘What compounds in serum might best indicate the health status of whale sharks?’”

Not only did the study determine that metabolic profiles of unhealthy whale sharks were markedly different than those of healthy sharks in general and particularly the different levels of homarine, but the research team also identified more than 25 other compounds that differed in concentration based on the health of the individual.

Findings detailed in “Biomarkers of whale shark health: a metabolomic approach” will help scientists and veterinarians to better understand the biology of whale sharks in their natural setting, and by homology, the biology of other shark and ray species that may be similar. Further, data compiled in the research will provide a reference library about whale shark biochemistry that can be consulted in future studies and importantly, adds new knowledge that will be useful to those who care for sharks and rays on a daily basis.

 “This sort of advanced research is only made possible through collaboration between aquarium scientists and experts at our partner universities,” said Dr. Dove.

The research team included, from Georgia Tech: Dr. Johannes Leisen, research scientist; Dr. Manshi Zhou, post-doctoral candidate; Dr. Jonathan Byrne, post-doctoral candidate; Krista Lim-Hing, student; Dr. Leslie Gelbaum, Dr. Mark Viant, Dr. Julia Kubanek, and Dr. Facundo Fernandez; and from Georgia Aquarium: Harry D. Webb, research technician. Additional support also came from Georgia Tech’s National Science Foundation (NSF) undergraduate research program in mathematical biology.

Written by Stephanie Johnson, senior public relations specialist at Georgia Aquarium.

If the 4.9 million barrels of oil that spilled into the Gulf of Mexico during the 2010 Deep Water Horizon spill was a ecological disaster, the two million gallons of dispersant used to clean it up apparently made it even worse – 52-times more toxic. That’s according to new research from the Georgia Institute of Technology and Universidad Autonoma de Aguascalientes (UAA), Mexico.

The study found that mixing the dispersant with oil increased toxicity of the mixture up to 52-fold over the oil alone. In toxicity tests in the lab, the mixture’s effects increased mortality of rotifers, a microscopic grazing animal at the base of the Gulf’s food web. The findings are published online by the journal Environmental Pollution and will appear in the February 2013 print edition.

Using oil from the Deep Water Horizon spill and Corexit, the dispersant required by the Environmental Protection Agency for clean up, the researchers tested toxicity of oil, dispersant and mixtures on five strains of rotifers. Rotifers have long been used by ecotoxicologists to assess toxicity in marine waters because of their fast response time, ease of use in tests and sensitivity to toxicants. In addition to causing mortality in adult rotifers, as little as 2.6 percent of the oil-dispersant mixture inhibited rotifer egg hatching by 50 percent.  Inhibition of rotifer egg hatching from the sediments is important because these eggs hatch into rotifers each spring, reproduce in the water column, and provide food for baby fish, shrimp and crabs in estuaries.

“Dispersants are preapproved to help clean up oil spills and are widely used during disasters,” said UAA’s Roberto-Rico Martinez, who led the study. “But we have a poor understanding of their toxicity. Our study indicates the increase in toxicity may have been greatly underestimated following the Macondo well explosion.”

Martinez performed the research while he was a Fulbright Fellow at Georgia Tech in the lab of School of Biology Professor Terry Snell. They hope that the study will encourage more scientists to investigate how oil and dispersants impact marine food webs and lead to improved management of future oil spills.

“What remains to be determined is whether the benefits of dispersing the oil by using Corexit are outweighed by the substantial increase in toxicity of the mixture,” said Snell, chair of the School of Biology. “Perhaps we should allow the oil to naturally disperse. It might take longer, but it would have less toxic impact on marine ecosystems.”

Researchers in the School of Biology at Georgia Tech have uncovered a novel mechanism of genome mutagenesis and remodeling that could help to explain abnormal DNA amplification in cancer and other degenerative disorders. Cancer and other degenerative disorders are commonly associated with abnormal DNA amplification (resulting in an increase in the number of copies of a DNA segment) in various locations throughout the genome. These mutations can facilitate the aggressiveness of cancer to the detriment of human health and are therefore of great scientific interest. Kuntal Mukherjee, former postdoctoral fellow in the lab of Francesca Storici, developed an approach to capture the events of DNA amplification driven by small pieces of DNA in yeast cells and provided initial characterization of the mechanism. The discovery, published this week in PLoS Genetics (http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003119), reveals that small pieces of DNA can be potent inducers of gene amplification and genomic rearrangement.

Small DNA fragments can form as byproducts of DNA metabolism, reverse transcription or DNA degradation. In addition after cells lyse, or undergo apoptosis, these fragments (or DNA debris) can be released into extracellular space and taken up by neighboring cells. Due to complementarity, the small DNA fragments can direct specific amplification events in homologous chromosomal regions, resulting in Small Fragment-driven DNA Amplification (SFDA). Mukherjee and Storici demonstrate that SFDA results in tandem chromosomal duplications or formation of extrachromosomal circles that mimic the DNA amplification structures commonly found in many cancer cells. Prominent examples of these mutations in cancer include the repeated units clustered at a single chromosomal locus (homogeneously staining regions) and the circular extrachromosomal elements replicating autonomously and lacking a centromere and telomeres (double minutes).

The implications of their discovery suggest that DNA debris could potentially spread chromosomal rearrangements from one cell to another like ‘infectious’ agents. Considering that DNA fragments are highly recombinogenic and also highly abundant in cells, the researchers propose that SFDA could be a common mechanism of DNA amplification-driven carcinogenesis, as well as a more general cause of DNA copy number variation in nature.

This project was supported by the Georgia Cancer Coalition grant (award R9028).

When you walk into Brian Hammer’s classroom, you might be greeted by the sounds of hip-hop artist Nicki Minaj or the Godfather of Soul James Brown. It all depends on the day’s lecture.

“Before class, I play a song that is related to what I’ll be discussing,” said Hammer, an assistant professor in the School of Biology. “For example, if we are talking about how genes are activated, I might play David Guetta and Nicki Minaj’s ‘Turn Me On,’ or if I’m talking about bacteria transferring DNA, I might play ‘Sex Machine’ by James Brown.”

Music is one of the ways that Hammer, who arrived at Georgia Tech in 2008, tries to  make often-complicated material understandable to students.

“My research focuses on concepts like cell-to-cell communication called ‘quorum sensing,’ which can be a challenge to wrap your brain around,” he said. “But I love the challenge of finding ways to explain my research to anyone — from my college students to my wife’s second graders.”

Read on to learn more about Hammer and his time at Tech.

How did you get to Tech?          
While doing my post-doctoral work at Princeton University, I realized that I wanted to work at an institution that was supportive of an interdisciplinary approach to research. At Georgia Tech, biologists are integrated with engineers and that appealed to me.

Tell us about your research.       
I study how bacteria use chemicals to communicate with their environments. For example, Vibrio cholerae, which causes the fatal disease cholera, lives in the ocean.  When it comes into contact with chitin from crab shells, the chitin acts as a signal that flips an “on” switch in the bacteria. The cholera bacteria then start to bring in DNA from their environment that can provide the microbes with new genetic material, allowing them to, for example, make new toxins or other disease-causing factors.

What is an average day like for you?    
I teach three days a week and then spend my remaining time doing office work, meeting with students and trying to inspire them, and presenting at meetings.  

Name a misconception that people have about your profession.
A seventh grade teacher who I collaborate with each summer told me that he thought all microbiologists used microscopes — but we don’t. Actually, most of our days are spent using pipettes to dispense fluid containing DNA into tiny tubes.  

What is the one piece of technology you couldn’t live without?
My iPhone.

What is the greatest challenge you’ve faced while teaching?
Coming to the realization that all of my students aren’t little clones of me, meaning that the way I learned things and did research might not work for them. I’m always reminding myself to think of students like I think of my successful colleagues. Just because the students’ approaches are different from mine doesn’t mean they can’t be just as effective.  

What do you think about the increasing popularity of massive open online courses?
I think we have to be open to them, because they are coming whether we like it or not. Personal interaction is important to me in my classes, and I think some of that will be lost in these courses. But I would be open to teaching one.

What is your favorite spot on campus?  
I like the biotech quad. The grassy area is a quiet place, and I love the fact that I’m also surrounded by science.

Where is your favorite place to have lunch?  
It would have to be Taqueria del Sol, and I’ll order enchiladas or fish tacos.

Tell us something unique about yourself.  
When I was an undergraduate at Boston College, I sang in the university chorale and had the opportunity to sing for Pope John Paul II in St. Peter’s Basilica.

What was the greatest risk you ever took — and did it pay off?  
While I was completing my master’s in ecology, it was difficult to admit that I didn’t know what I wanted to do with my life. It was a huge relief when I was able to admit this. I was finally able to figure out that microbiology was what I was interested in.

The rise of antibiotic-resistant bacteria has initiated a quest for alternatives to conventional antibiotics. One potential alternative is PlyC, a potent enzyme that kills the bacteria that causes strep throat and streptococcal toxic shock syndrome. PlyC operates by locking onto the surface of a bacteria cell and chewing a hole in the cell wall large enough for the bacteria’s inner membrane to protrude from the cell, ultimately causing the cell to burst and die.

Research has shown that alternative antimicrobials such as PlyC can effectively kill bacteria. However, fundamental questions remain about how bacteria respond to the holes that these therapeutics make in their cell wall and what size holes bacteria can withstand before breaking apart. Answering those questions could improve the effectiveness of current antibacterial drugs and initiate the development of new ones.

Researchers at the Georgia Institute of Technology and the University of Maryland recently conducted a study to try to answer those questions. The researchers created a biophysical model of the response of a Gram-positive bacterium to the formation of a hole in its cell wall. Then they used experimental measurements to validate the theory, which predicted that a hole in the bacteria cell wall larger than 15 to 24 nanometers in diameter would cause the cell to lyse, or burst. These small holes are approximately one-hundredth the diameter of a typical bacterial cell.  

“Our model correctly predicted that the membrane and cell contents of Gram-positive bacteria cells explode out of holes in cell walls that exceed a few dozen nanometers. This critical hole size, validated by experiments, is much larger than the holes Gram-positive bacteria use to transport molecules necessary for their survival, which have been estimated to be less than 7 nanometers in diameter,” said Joshua Weitz, an associate professor in the School of Biology at Georgia Tech. Weitz also holds an adjunct appointment in the School of Physics at Georgia Tech.

The study was published online on Jan. 9, 2013 in the Journal of the Royal Society Interface. The work was supported by the James S. McDonnell Foundation and the Burroughs Wellcome Fund.

Common Gram-positive bacteria that infect humans include Streptococcus, which causes strep throat; Staphylococcus, which causes impetigo; and Clostridium, which causes botulism and tetanus. Gram-negative bacteria include Escherichia, which causes urinary tract infections; Vibrio, which causes cholera; and Neisseria, which causes gonorrhea.

Gram-positive bacteria differ from Gram-negative bacteria in the structure of their cell walls. The cell wall constitutes the outer layer of Gram-positive bacteria, whereas the cell wall lies between the inner and outer membrane of Gram-negative bacteria and is therefore protected from direct exposure to the environment.

Georgia Tech biology graduate student Gabriel Mitchell, Georgia Tech physics professor Kurt Wiesenfeld and Weitz developed a biophysical theory of the response of a Gram-positive bacterium to the formation of a hole in its cell wall. The model detailed the effect of pressure, bending and stretching forces on the changing configuration of the cell membrane due to a hole. The force associated with bending and stretching pulls the membrane inward, while the pressure from the inside of the cell pushes the membrane outward through the hole.

“We found that bending forces act to keep the membrane together and push it back inside, but a sufficiently large hole enables the bending forces to be overpowered by the internal pressure forces and the membrane begins to escape out and the cell contents follow,” said Weitz.

The balance between the bending and pressure forces led to the model prediction that holes 15 to 24 nanometers in diameter or larger would cause a bacteria cell to burst. To test the theory, Daniel Nelson, an assistant professor at the University of Maryland, used transmission electron microscopy images to measure the size of holes created in lysed Streptococcus pyogenes bacteria cells following PlyC exposure.

Nelson found holes in the lysed bacteria cells that ranged in diameter from 22 to 180 nanometers, with a mean diameter of 68 nanometers. These experimental measurements agreed with the researchers’ theoretical prediction of critical hole sizes that cause bacterial cell death.

According to the researchers, their theoretical model is the first to consider the effects of cell wall thickness on lysis.

“Because lysis events occur most often at thinner points in the cell wall, cell wall thickness may play a role in suppressing lysis by serving as a buffer against the formation of large holes,” said Mitchell.

The combination of theory and experiments used in this study provided insights into the effect of defects on a cell’s viability and the mechanisms used by enzymes to disrupt homeostasis and cause bacteria cell death. To further understand the mechanisms behind enzyme-induced lysis, the researchers plan to measure membrane dynamics as a function of hole geometry in the future.

CITATION: Mitchell GJ, Wiesenfeld K, Nelson DC, Weitz JS, “Critical cell wall hole size for lysis in Gram-positive bacteria,” J R Soc Interface 20120892 (2013): http://dx.doi.org/10.1098/rsif.2012.0892.

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