In humans, cholera is among the world’s most deadly diseases, killing as many as 140,000 persons a year, according to World Health Organization statistics. But in aquatic environments far away from humans, the same bacterium attacks neighboring microbes with a toxic spear – and often steals DNA from other microorganisms to expand its own capabilities.
A new study of more than 50 samples of Vibrio cholerae isolated from both patients and the environment demonstrates the diversity and resourcefulness of the organism. In the environment, the cholera bacterium is commonly found attached to chitin, a complex sugar used by aquatic creatures such as crabs and zooplankton to form protective shells. In the wild, most strains of cholera can degrade the shells for use as food, and the new study showed how the presence of chitin can signal the bacteria – which have receptors for the material – to produce behaviors very different from those seen in human disease.
Among the cholera strains studied, less than a quarter were able to take up DNA from other sources. Almost all of the samples taken from the environment were able to kill other bacteria – a phenomenon called “bacterial dueling” – but just 14 percent of the bacterial pathogen strains isolated from humans had that capability.
“It’s a dog-eat-dog world out there even for bacteria,” said Brian Hammer, an associate professor in the School of Biology at the Georgia Institute of Technology. “Bacteria such as Vibrio cholerae sense and respond to their surroundings, and they use that information to turn on and off the genes that benefit them in the specific environments in which they find themselves.”
The research, supported by the National Science Foundation and the Gordon and Betty Moore Foundation, provides information that could lead to development of better therapeutic agents against the disease, which is found in densely-populated areas with limited sanitation and clean water. The research was done with assistance from the Centers for Disease Control and Prevention (CDC), and was reported online March 4 in the journal Applied and Environmental Microbiology.
In humans, the cholera bacteria produce a diarrheal disease that can kill untreated patients in just a few hours. The deadly effects of the disease, however, are actually caused by a virus that infects the Vibrio cholerae strains found in humans. The toxin carried by the virus helps spread the disease among humans, but cholera strains quickly lose the virus and adapt other competitive mechanisms in the environment.
To study how cholera regulates these adaptations, Georgia Tech graduate student Eryn Bernardy obtained nearly 100 samples of cholera bacteria from a variety of sources globally, including one originally isolated from a 1910 Saudi Arabian outbreak of the disease. She then studied 53 of the samples for their ability to (1) degrade chitin, (2) take up DNA from the environment, and (3) kill other bacteria by poking them with a poisoned spear.
Colonies of each strain were grown in petri plates containing chitin material. The strains able to digest the material produced a clear ring showing that they had broken down the chitin in the agar growth medium. Only three of the cholera colonies failed to degrade the chitin.
To study their ability to take up DNA, bacterial cells were grown on crab shells, then exposed to raw DNA containing a gene for antibiotic resistance. The cells were scraped off the shells and placed onto agar plates containing an antibiotic that would normally kill the bacteria. Colonies that survived showed they had taken up the genetic material.
To study their ability to compete with other bacteria, each cholera strain was placed into contact with a billion or so E. coli cells on petri plates. After a few hours in contact, the researchers counted the number of E. coli remaining. Some cholera strains were able to kill nearly all of the E. coli cells, reducing their numbers to a few hundred thousand.
“We found a very sharp difference between the clinical isolates and the environmental isolates,” Hammer said. “For example, most of the isolates that came out of patients either couldn’t kill other bacteria, or were carefully controlling that behavior. Patient isolates have a very different way of competing inside the human body. They use the virus-encoded toxin to cause the diarrheal disease and remove their competitors from the intestine.”
With help from CDC scientists, the researchers correlated the behavior of each strain with their unique DNA sequences. They also examined the strains for the presence of the toxin used to cause disease.
To deduce the rules governing the bacterium’s behavior, Hammer and his lab have been studying cholera for the last 15 years, starting with a single strain first isolated in Peru in the early 1990s. When a cholera outbreak began in Haiti after the 2010 earthquake, his lab worked with the CDC to isolate these new strains. In further study, Hammer was surprised to find that the 2010 Haitian strains were less capable than the 1991 Peruvian variety.
“We were very surprised to find that most of the Haiti strains did not behave like the one we had been studying for years,” he said. “This was a reminder to us that we needed to embrace the diversity of the organisms we’ve been studying. We thought this would be an opportune time to start looking at how diverse Vibrio cholerae really is.”
Hammer compared the diversity of the cholera strains to the diversity of humans, who increasingly receive personalized health care.
“In humans, one size doesn’t fit all for patient care,” he said. “For cholera, the behavior is personalized for each strain. Understanding this will be useful in the development of future therapeutics, and we’re hopeful that knowing how these bacteria interact with other organisms in complex communities will lead us to things that can truly benefit humans.”
In addition to those already mentioned, the study included Maryann A. Turnsek and Cheryl L. Tarr from the CDC. Georgia Tech undergraduate Sarah K. Wilson from the Hammer lab, another author on the paper, is now a Ph.D. student at the University of Wisconsin-Madison.
This material is based upon work supported by the Gordon and Betty Moore Foundation and National Science Foundation Grant No. 1149925. 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 National Science Foundation or the Moore Foundation.
CITATION: Eryn E. Bernardy, et al., “Diversity of Clinical and Environmental Isolates of Vibrio cholerae in Natural Transformation and Contact-Dependent Bacterial Killing Indicative of Type VI Secretion System Activity,” (Applied and Environmental Microbiology, 2016). http://dx.doi.org/10.1128/AEM.00351-16.
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Effective on July 1, 2016, the Georgia Tech College of Sciences has a new unit focused on the life sciences – the School of Biological Sciences. Emerging from a reorganization of the former Schools of Applied Physiology and of Biology, the new unit reduces the number of College of Sciences academic schools to six: Biological Sciences, Chemistry and Biochemistry, Earth and Atmospheric Sciences, Mathematics, Physics, and Psychology.
For the period immediately following the transition, the current chair of the School of Biology, Professor Terry W. Snell, will serve as the chair of the School of Biological Sciences. From August 15, 2016, the school will be led by Professor J. Todd Streelman, who currently serves as Associate Chair for Graduate Studies in the School of Biology.
The reorganization was motivated by the College’s strategic goals to enhance the research ecosystem for the basic sciences and mathematics, enrich and diversify educational opportunities for science and mathematics majors, and strengthen the opportunities for creativity and innovation by the College.
“The life sciences are an exciting and fast moving field, and the issues it addresses are varied but interconnected. It is about the systems that make life possible,” said Rafael L. Bras, provost and executive vice president for Academic Affairs. “The new School of Biological Sciences brings together individuals that span the various aspects of living systems and their study. It will add synergies and create a resilient, flexible, and fast-responding academic unit in a fast-moving field.”
A single school focused on the life sciences offers many advantages:
- A unified voice to lead conversations about the life sciences within campus
- A focal point for interactions with life science groups, program, activities, and interests outside campus
- A broader base upon which to build research teams to address complex biomedical challenges
- A robust ability to advance new health-related majors in neuroscience, physiology, and human systems
- A unique opportunity to develop an undergraduate degree for pre-health students
The new school comprises 10 tenure-track faculty, three academic professionals, and four staff from Applied Physiology and 38 tenure-track faculty, six academic professionals, and 18 staff from Biology. The School of Biological Sciences will administer all the academic programs offered previously by the two schools it replaces.
“The life sciences, including neural systems, are destined to grow and become even more central as we define our research and education programs for the new millennium,” said Paul M. Goldbart, Dean of the College of Sciences. “I am grateful to the many members of our community who have stepped up to create a stronger, more coherent base from which to take on exciting challenges presented by the life sciences.”
College of Sciences Dean Paul M. Goldbart has appointed J. Todd Streelman to serve as the chair of the School of Biological Sciences, effective August 15, 2016. The School of Biological Sciences is a new unit within the College of Sciences, effective July 1, 2016.
A professor and associate chair for graduate studies in the School of Biology, Streelman joined Georgia Tech in 2004. Previously, he did research at the University of New Hampshire, where he was the recipient of an Alfred P. Sloan Foundation Postdoctoral Fellowship in Molecular Evolution. Since joining Georgia Tech, he has been honored as a Sloan Foundation Research Fellow in Computational and Evolutionary Molecular Biology and with a National Science Foundation CAREER Award.
Streelman’s research is focused on the relationship between genotype and phenotype in wild vertebrates, often via studies of cichlid fishes from Lake Malawi, in Africa. Major themes include aspects of the genomic and cellular circuitry of complex behavior, tooth and taste bud patterning and regeneration, and developmental diversification of the brain. Streelman served as associate editor for the journal Evolution and is a standing member of the National Institutes of Health Study Section on Skeletal Biology Development and Disease.
For the past four years, Streelman has played a pivotal role in defining the research themes for the Engineered Biosystems Building I, Georgia Tech’s inspiring new venture to catalyze interactions between life scientists and life engineers. He also co-chairs an Institute task force charged with developing Georgia Tech’s strengths in the field of neuroscience.
“My colleagues in the College of Sciences team and I are excited to be partnering with Todd and our colleagues in the School of Biological Sciences,” says College of Sciences Dean Paul M. Goldbart.
The new School of Biological Sciences combines the Schools of Applied Physiology and of Biology. The single entity is designed to capitalize on and add coherence to Georgia Tech’s broad strengths in the life sciences, both in research and in the suite of educational opportunities that the school will offer.
In taking on the role of chair, Streelman will be building on the outstanding leadership of Professors T. Richard Nichols and Terry W. Snell, says Dean Goldbart. “Richard and Terry have led their respective schools, Applied Physiology and Biology, with distinction, and they have guided the fusion of the schools with sensitivity and vision. I thank them for their critically important contributions.”
“I am thrilled to be named chair, on behalf of my colleagues in the School of Biological Sciences,” Streelman says. “I am excited to continue progress made under Richard and Terry, to both sustain and propel innovative research and teaching in the life sciences.”
Streelman’s appointment follows a national search conducted by Georgia Tech faculty members Linda E. Green, Brian K. Hammer, Julia Kubanek, Garrett B. Stanley, Joshua S. Weitz, Loren D. Williams, and Soojin Yi. Leading the search committee was Hang Lu, of Georgia Tech's School of Chemical and Biomolecular Engineering.
For elementary school children, an upcoming field trip is riveting, the one time they find themselves unable to sleep in anticipation. This year, fifth-grade students at Laurel Ridge Elementary School, in Decatur, were bound for a beach on Tybee Island, the easternmost point of the state of Georgia. But some couldn’t go. Thanks to School of Biology Professor Joel E. Kostka and his students, these fifth graders did not have to miss the excitement of a year-end activity.
“We were asked by the organizer of outreach opportunities – Tracy Hammer – to come, because half of the kids in the fifth-grade class could not make it to the beach,” Kostka said. “So we brought the beach to them.”
This clever solution had many positive outcomes. It advanced Hammer’s goal for science education at Laurel Ridge. It taught Georgia Tech researchers how to explain their work to school children. And it opened the eyes of elementary students to the excitement of scientific research.
Hammer is the science, technology, engineering, and mathematics (STEM) coordinator and teacher for gifted students at Laurel Ridge. She has dedicated her career to getting young children excited about mathematics and science. “Part of my mission at school is to expose all of the kids to science in as many ways as I can,” she said. “I refused to have our fifth graders staying behind, missing out on the hands-on experience the other kids were getting. So I decided to bring science to the school.”
Kostka came with graduate students Will A. Overholt, Boryoung Shin, and Xiaoxu Sun and undergraduate biology major Kyle Sexton. At Georgia Tech, one research focus in the Kostka lab is biodegradation of oil in the oceans, including oil spills in the Gulf of Mexico. Kostka and his students study how marine microbes break down oil, how fast the breakdown occurs, and what factors affect the process. Their goal is to learn enough to direct the management and cleanup of contaminated systems, such as the aftermath of the 2010 Deepwater Horizon oil spill in the Gulf of Mexico. The beach they brought to Laurel Ridge resembled those sullied by the environmental disaster.
One of Hammer’s goals is for Laurel Ridge to be STEM certified. The process requires the school to have community and industry partners. To fulfill this requirement, Hammer has been inviting researchers from Georgia Tech, including her husband, School of Biology’s Brian K. Hammer.
According to the Georgia Department of Education, STEM-certified schools offer an integrated curriculum in STEM “that is driven by problem solving, discovery, exploratory project/problem-based learning, and student-centered development of ideas and solutions.”
To doubters, who may think such a program would be too much for elementary-level students, Tracy Hammer would disagree. “I believe we underestimate elementary school children and their abilities and interest levels when it comes to science,” she said. “The more we offer, the more they want to learn, and the more questions they ask.”
The Georgia Tech researchers engaged the fifth-graders in activities they named “Oiled Beach,” designed by Beth Kostka, wife of Joel Kostka, and a teacher Renfroe Middle School, in Decatur. Working in small groups of six to eight members per group, the school children modeled oil spills, counted bacteria, discussed Gulf of Mexico ecosystems, and watched oil-eating bacteria at work.
“The children were really engaged, had fantastic questions,” Overholt said. “They seemed to really enjoy the two hours we spent with them.”
Seeing the students’ thirst for knowledge and ability to learn was an eye-opening experience for Overholt. “The kids were so excited about things that my peers and I take for granted,” he said. “It was very rewarding to see kids so curious about the world around them. I also think it is great practice to talk about our science at the fifth-grade level and still be able to communicate what we do.”
Through these activities led by research scientists, Tracy Hammer moves closer to her goal of getting Laurel Ridge STEM-certified. “When we expose our budding scientists to the world and the possibilities it holds,” she said, “then we can say we are truly doing our jobs as educators.”
She hopes Joel Kostka will return and that other Georgia Tech research groups would visit Laurel Ridge throughout the year.
“I will do it again,” said Joel Kostka. “The kids were very perceptive. I learned that kids as young as those in fifth grade can really understand the oceans and the implications of oil spills. Those kids have a lot to offer.”
Although the “beach” they had did not come with sun and ocean and waves, the children had a great time. “When the others returned from Tybee,” Tracy Hammer said, “the kids who stayed behind were the ones bragging about their experiences.”
Scott Smith
Student Assistant, College of Sciences
Effective July 1, the Georgia Tech College of Sciences has a new unit focused on the life sciences — the School of Biological Sciences.
The new school emerged from a reorganization of the former Schools of Applied Physiology and of Biology. The reorganization was motivated by the College’s strategic goals to enhance the research ecosystem for the basic sciences and mathematics, enrich and diversify educational opportunities for science and mathematics majors, and strengthen the opportunities for creativity and innovation by the College.
“The life sciences are an exciting and fast-moving field, and the issues it addresses are varied but interconnected,” said Rafael L. Bras, provost and executive vice president for Academic Affairs. “The new School of Biological Sciences brings together individuals that span the various aspects of living systems and their study. It will add synergies and create a resilient, flexible, and fast-responding academic unit in a fast-moving field.”
J. Todd Streelman, associate chair for Graduate Studies in the School of Biology, will serve as chair of the new School beginning August 15. Terry W. Snell, professor and chair for the School of Biology, will serve as chair in an interim role until then.
“I am thrilled to be named chair on behalf of my colleagues in the School of Biological Sciences,” Streelman said. “I am excited to continue progress made under Richard [Nichols] and Terry [Snell] to both sustain and propel innovative research and teaching in the life sciences.”
The new school comprises 10 tenure-track faculty, three academic professionals, and four staff members from Applied Physiology as well as 38 tenure-track faculty, six academic professionals, and 18 staff members from Biology. The School of Biological Sciences will administer all the academic programs offered previously by the two schools it replaces.
“The life sciences, including neural systems, are destined to grow and become even more central as we define our research and education programs for the new millennium,” said Paul M. Goldbart, dean of the College of Sciences. “I am grateful to the many members of our community who have stepped up to create a stronger, more coherent base from which to take on exciting challenges presented by the life sciences.”
The other academic schools in the College of Sciences include Chemistry and Biochemistry, Earth and Atmospheric Sciences, Mathematics, Physics, and Psychology.
In tough times, humans aren’t the only species that think twice about having children. Consider roundworm strain LSJ2.
Though it can’t think – much less think twice -- about anything, the laboratory worm underwent a surprising mutation that made it prioritize the survival of adults over creating abundant offspring. Researchers noticed the sweeping change in behavior, and the mutation, after LSJ2 had faced hardship for 50 years.
Such so-called life history trade-offs have been described in many living things from mice to elephants, but now, for the first known time, researchers at the Georgia Institute of Technology have pinned some to a specific mutation.
“This is a great hint at how life history trade-offs could be regulated genetically,” said lead researcher Patrick McGrath, an assistant professor in Georgia Tech’s School of Biological Sciences.
The researchers confirmed the link in LSJ2, a strain of the C. elegans species, by duplicating the mutation in another strain, which reproduced the mutation’s effects to a very high degree.
The researchers published their results in the journal PLOS Genetics on Thursday, July 28, 2016. Their work has been funded by the National Institutes of Health and the Ellison Medical Foundation.
Snowball to avalanche
The mutation in the LSJ2 strain amounted to a small deletion in its DNA. As a result, a large protein changed by a meager 10 of its roughly 3,000 amino acids.
But that triggered a huge behavioral overhaul that boosted lifespan and slowed down reproduction. The contrast between the minor genetic tweak and its transformative ramifications might compare well with a toddler knocking loose an avalanche with a snowball.
The new discovery also has a tangential connection to human genetics. The roundworm shares with us the NURF-1 gene, on which the mutation occurred. And an associated human protein is involved in, among other things, reproduction.
Evolve faster, please
All at once, LSJ2 did a lot of peculiar things, and that got the attention of McGrath and his team. And that’s what the lab roundworms are there for.
Since 1951, generations of scientists have been speeding up the evolution of lab-bound C. elegans by forcing the microscopic species of roundworms to adapt to new, mostly stressful, conditions. Then, when researchers have noticed changes, they’ve worked to trace them to the animals’ genes.
McGrath points to a thin, glass slide standing vertically under a light with tubules of fluid connected to it. Inside the slide, is a different lab strain of C. elegans.
“We’re raising those in fluid with gravity pulling them down to see if mutations will give them the ability to swim,” McGrath said.
50 years of bread and water
In the case of LSJ2, researchers came up with a different challenge to accelerate its evolution. They fed it bland food for 50 years.
“It’s a diet of watery soy extract with some beef liver extract,” said Wen Xu, a graduate student who researches with McGrath. Sounds yucky enough to humans, but to the roundworm, it's worse. It equates to a regimen of bread and water.
Mutations eventually took hold to promote LSJ2’s survival in the scanty broth, and they were head-turning.
Fewer kids, less sleep
“The stark thing that we noticed first was the propensity to no longer enter the state called dauer,” McGrath said. It’s a kind of hyper-hibernation. “Dauer is something most C. elegans do to extend their lives, but LSJ2 did not. And it lived longer in spite of it.”
Then the list of anomalies grew, and grew.
“We found that almost everything was affected – when they started reproducing, how many offspring they made, how long they lived,” McGrath said. Some even survived exposure to drugs and heavy metals.
“Eventually we realized that the worms were prioritizing individual survival over reproductive rate.”
Mutation sleuthing
In many species, sex dries up when food is scarce, resulting in fewer progeny to compete for it. In addition, many organisms are well-equipped to manage their energies to survive dearth.
But C. elegans LSJ2 had to mutate into those abilities, and so many mutation-based behavioral changes all at once is uncommon.
“What you usually find is mutations that play narrow, very specific roles,” McGrath said. “They only affect egg laying, or they only affect life span, or they only affect dauer formation."
McGrath and Xu went sleuthing for DNA alterations by mapping quantitative trait loci, which matches up changes in characteristics to genetic changes. They dug in for a long investigation, anticipating multiple suspects among LSJ2’s many mutations.
“There were hundreds of genetic differences between roundworm strain LSJ2 and the one we were comparing it to,” McGrath said.
‘Smoking gun’
The comparison laboratory strain is called N2, and it has led a pampered existence with a diet of E. coli -- optimal food for C. elegans. (Both the E. coli and the roundworms are strains that are not harmful to humans.)
So, N2 hadn’t been pushed to mutate so much. In addition, to avoid confusion in their research results, the researchers reset some of the mutations N2 did happen to undergo.
The comparison led to swift evidence in LSJ2. “Every single time, it pointed us to the same genetic region on the right arm of chromosome 2,” McGrath said. C. elegans has six chromosomes.
“There were only five genes that were candidates. One of the mutations was a smoking gun -- a 60-base-pair deletion just at the end of the NURF-1 gene.”
NURF-1 has the function of remodeling chromatin, which pairs DNA with proteins to wrap them into chromosomes. The resulting configurations strongly influence which genes are expressed. It appears the tiny mutation in the remodeling gene may have led to a massive change in the expression of other genes.
There are missing pieces needed to understand the pathway from the mutated gene to the massive real-life changes, and the researchers are working to fill them in.
Worm whoopy
To confirm the mutation as the trigger of the changes, Xu deployed a CRISPR Cas9 gene editor into N2 worms to make the deletion that LSJ2 had received via mutation, and the results left little doubt.
“It had a lot of the same effects – longer life, dauer formation,” Xu said. “The main difference was the reduction of reproduction rates. It was only about half as much in the comparison worm that got the gene editing.”
By the way, as sex goes, C. elegans are mostly hermaphrodites that produce eggs and their own sperm to fertilize them with. But there are also males that copulate with the hermaphrodites to add new sperm and with it genetic diversity.
Edward E. Large, Yuehui Zhao and Lijiang Long from Georgia Tech; Shannon Brady and Erik Andersen from Northwestern University, and Rebecca Butcher from the University of Florida coauthored the paper. Research was sponsored by grants from the National Institutes of Health (numbers R21AG050304 and R01GM114170) and by an Ellison Medical Foundation New Scholar in Aging grant.
In ocean expanses where oxygen has vanished, newly discovered bacteria are diminishing additional life molecules. They are helping make virtual dead zones even deader.
It’s natural for bacteria to deplete nitrogen in oxygen minimum zones (OMZs), ocean regions that have no detectable O2. But as climate change progresses, OMZs are ballooning, and that nitrogen depletion is also on the rise, drawing researchers to study it and possible ramifications for the global environment.
Now, a team led by the Georgia Institute of Technology has discovered members of a highly prolific bacteria group known as SAR11 living in the world’s largest oxygen minimum zone. The team has produced unambiguous evidence that the bacteria play a major role in denitrification.
7 questions, 7 answers
The new bacteria impact global nutrient supplies and greenhouse gas cycles. Below are questions and answers that illuminate the discovery and its significance.
The researchers published their findings in the journal Nature on Wednesday, August 3, 2016. They produced genomic and enzyme analyses that pave the way for further study of carbon and nitrogen cycles in oxygen minimum zones.
The research has been funded by the National Science Foundation, the NASA Exobiology Program, the Sloan Foundation and the U.S. Department of Energy.
1. Why does denitrification matter?
While melting ice caps and dying polar bears splash across headlines, climate change is stressing oceans in other ways, too – such as warming and acidifying waters. Loss of ocean oxygen and nitrogen are pieces of that bigger puzzle.
As to nitrogen: Anyone who has picked up a bag of fertilizer knows it as a building block of life.
“It’s an essential nutrient,” said Frank Stewart, an assistant professor at Georgia Tech’s School of Biological Sciences, who headed the team. “Nitrogen is used by all cells for proteins and DNA.”
Taking it away makes it harder for algae and other organisms to grow, or even live. But it doesn’t stop there. Algae absorb carbon dioxide, so, when algae are diminished, that leaves more of that greenhouse gas in the atmosphere.
But it’s not yet clear how heavily this particular loss of CO2 absorption weighs in the global balance.
2. How do these newly discovered bacteria deplete nitrogen?
In OMZs, with O2 gone, the newly discovered strains of SAR11 bacteria (and some other bacteria) respire NO3 (nitrate) instead, the Georgia Tech researchers found. They kick off a chemical chain that leads to nitrogen disappearing out of the ocean.
“They take nitrate, convert it into nitrite (NO2), and that can ultimately be used to produce gaseous nitrogen,” Stewart said. Plain nitrogen, N2, and nitrous oxide, N2O, would result. “Both of those gases have the potential to bubble out of the system and leave the ocean.”
That makes the oxygen-barren waters even less hospitable to life while putting more nitrogen into the air, as well as nitrous oxide, a key greenhouse gas.
The newly discovered members of the SAR11 bacteria clade – clade means a branch of living species -- appear to be the single largest contingent of bacteria in OMZs. That makes them a very significant player in nitrogen loss.
3. Ocean zones with no oxygen? Sounds wild. Did climate change do that?
No. Oxygen minimum zones are natural. The issue is that global warming is making them grow, just like it’s making ice caps shrink.
OMZs form mostly in the tropics, off coastlines where wind pushes surface waters out to sea, allowing deeper waters to rise up. These are full of nutrients and boost the growth of simple aquatic life like algae.
“Eventually, the algae die and sink slowly,” Stewart said. “Bacteria munch on it, and in the process, they breathe oxygen.” There’s so much algae that the bacteria consume oxygen at a dizzying rate, depleting the water of it.
Global warming is causing OMZs to spread because it makes seawater less able to hold oxygen. As OMZs expand, so does the potential for denitrification, tipping global balances of nitrogen, greenhouse gases, and nutrients.
4. I’ve heard of the disease SARS, but what is SAR11?
The two are unrelated.
SARS is caused by a virus and is potentially deadly. SAR11 bacteria are not only harmless to humans; hypothetically, we might starve without them. They’re at the base of an oceanic food chain, which is very important to the global food supply.
“After they eat dissolved organic carbon (dead stuff), then the bacteria are eaten by bigger cells, which are eaten by larger plankton, and so on up the food chain,” Stewart said.
Previously known SAR11 are so incredibly widespread in the ocean, it’s surprising they’re not a household name. They may even comprise the largest number of living organisms on Earth.
Under the microscope, SAR11 bacteria pretty much look the same. “They’re usually short little slightly bent rods,” Stewart said. Until now, SAR11 have been known to require oxygen to live, so finding SAR11 that respire nitrate is new and surprising.
5. Where did the team get these new nitrate breathing SAR11 strains?
Stewart and his team sailed for four days aboard a research vessel from San Diego, California, to an area off the Pacific coast of Mexico’s Calimo state. There, they dropped a carousel of tube-like bottles about four feet long down to the center of the world’s largest OMZ 1,000 feet below.
“The bottoms and tops of the bottles are open,” Stewart said. “When you get to the depth you want, you close them to get your sample.”
The new bacteria don’t have species names yet, but their genomes, which were sequenced in the study, indicate they’re members of the SAR11 bacteria clade.
6. Why is this discovery scientifically significant?
It upends quite justified scientific doubts.
Scientists thought SAR11 wouldn’t have strains that flourish in the harsh OMZ environment, because the SAR11 clade doesn’t have a reputation for being very adaptable. “When their genomes do change, they’re usually very subtle changes,” Stewart said.
Many other bacteria, by contrast, plunk in and out big chunks of their DNA, making them widely adaptable. Also, though researchers had already detected genetic signatures of SAR11 bacteria in OMZs, they didn’t think the bacteria were actually at home there.
These facts put Stewart and his team under a heavy burden of proof.
7. How did the scientists answer the doubts?
They flushed out the genomes of 15 individual new bacteria strains they had captured as intact single cells. Surprisingly, the researchers found the blueprints for an enzyme, nitrate reductase, which could allow the bacteria to breathe nitrate in place of oxygen.
Since the novel bacteria have not yet been grown in the lab, the researchers inserted their nitrate reduction gene sequences into E. coli bacteria to see if they would use the DNA to produce the enzyme and if the enzyme would then work.
It did.
“Not all studies that do this kind of genome-based analysis take that extra step,” Stewart said with a long exhale. But it nailed nagging doubts.
The thorough analyses produced a critical dataset for science to build upon. More research will be needed to find out what adaptations allow SAR11 bacteria to exist under such harsh conditions.
The following researchers coauthored the study: Despina Tsementzi, Jieying Wu, Luis M. Rodriguez-R, Andrew S. Burns, Piyush Ranjan, Cory C. Padilla, Neha Sarode, Jennifer B. Glass and Konstantinos T. Konstantinidis from Georgia Tech; Samuel Deutsch, Sangeeta Nath, Rex R. Malmstrom and Tanja Woyke from the U.S. Department of Energy; Benjamin K. Stone from Bowdoin College; Laura A. Bristow from the Max Planck Institute; Bo Thamdrup and Morten Larsen from the University of Southern Denmark.
The research was funded by the National Science Foundation (grants 1151698 and 1416673), the NASA Exobiology Program (grant NNX14AJ87G), the Sloan Foundation (RC944), and the U.S. Department of Energy’s Community Science Program. 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.
It’s called mental imbalance for a reason. Sanity hangs, in part, in the gentle balance of chemicals strung together within regions of the brain in an intricate matrix.
In schizophrenia, the matrix is sharply jarred, debilitating the mind and triggering hallucinations. Now, researchers at the Georgia Institute of Technology have created an interactive model of that matrix to fast-track research and treatment of the tormenting disorder.
Working memory disruptions paralyze the mental coherence of schizophrenia sufferers, yet there is a stark lack of medical treatment for it. Researchers Zhen Qi and Eberhard Voit hope their new, very accurate computational simulator built around this symptom will help change that to curb anquish for many patients.
Learn more about the simulator, which puts this brain dysfunction into a virtual setting.
For more than 10 years, the Center for GIS has been working with the Dian Fossey Gorilla Fund International on visualization, analysis, and management of their mountain gorilla ranging data. What started with a series of static maps has evolved into a fusion of cutting-edge, multidimensional interactive visualization and analytic tools available online and in-house at the DFGFI’s Karisoke Research Center in Musanze, Rwanda.
Recently, associate director of the Center for GIS, Tony Giarrusso, traveled to Karisoke to assemble and install the “Virtual Virungas” exhibit as part of a 50th anniversary retrospective of Dian Fossey, the pioneer of mountain gorilla field research in Rwanda. Funded by a Smithgall-Watts grant from the School of Biology, the “Virtual Virungas” is an immersive, four-dimensional visualization of mountain gorilla habit and ranging data, projected onto a bed of sand and operated through a variety of high-tech controls and input. Created by CGIS and IMAGINE Lab researchers, Matt Swarts, Noah Posner, and Giarrusso, the "Virtual Virungas" sandbox uses historic mountain gorilla ranging data plus satellite imagery, topographic maps, and other geo-referenced, spatio-temporal data to show how the gorilla groups have ranged during different periods of time. Visitors can even modify what is shown on the sand through their mobile phones or computers. Exhibit tours for local secondary school and university students, conservation officials and tourists are conducted during weekdays by Karisoke staff members.
Initial reviews of the exhibit have been outstanding. Karisoke Director of IT, Jules Abiyingoma, recently gave four tours to local high school students and said this about his and their experiences with the virtual sandbox: “This sand box technology is amazing! I had four demos yesterday for four different schools and it all went smoothly. Everyone loved it and the students did not want to leave that section. They asked so many questions about gorillas, the park and the technology itself. Ironically they were so quiet during the previous sections of the tour and when they reached the sand box, they came to life! And started asking even questions related to previous sections. It's as if the sandbox awakes them from a deep sleep!”
In addition to installing the virtual sandbox, Mr. Giarrusso held GIS training sessions for Karisoke staff members, which included an MS GIS student from the MS GIS program at the National University of Rwanda in Butare, Rwanda. Topics covered included geocoding animal observation data, analyzing animal movements, and basic computer practices.
Mr. Giarrusso was also fortunate enough to obtain a tourist permit to visit the mountain gorillas. He visited the group, Isabukuru, one of the DFGFI mountain gorilla research groups he has mapped, and was able to see more than 10 mountain gorillas in the wild, including a set of identical twins born in early 2016. It was an experience he said he will never forget and hopes to repeat again. He expects to return to Karisoke in 2017 to update the virtual sandbox and conduct a weeklong, more formal GIS training session for Karisoke staff.
Nine graduate students will make up the inaugural Fall 2016 class of the College of Sciences’ interdisciplinary Ph.D. program in Quantitative Biosciences (QBioS). QBioS was established in 2015 by more than 50 participating program faculty in the College of Sciences. It is directed by School of Biological Sciences Professor Joshua S. Weitz.
“QBioS faculty will train Ph.D. students to identify and solve foundational and applied problems in the biological sciences and prepare them for research challenges at scales spanning molecules to ecosystems,” Weitz says.
The QBioS program supports the College’s strategic goal to enhance the research ecosystem and provide new training opportunities. It is Georgia Tech’s third interdisciplinary Ph.D. focusing on life sciences, following the successful models for Bioengineering and Bioinformatics. As in these other programs, QBioS Ph.D. students can select a thesis advisor from the entire program faculty, irrespective of school. In this way, QBioS continues a tradition of fostering innovative, interdisciplinary research and education at Georgia Tech.
Of the nine new students, four are from overseas and one is a Georgia Tech alumnus; five will be based in the School of Biological Sciences, three in the School of Physics, and one in the School of Mathematics.
Shlomi Cohen earned a B.S. in Mechanical Engineering from the Technion-Israel Institute of Technology, in Haifa. Cohen followed his wife to Atlanta after she had been accepted to the Industrial and Systems Engineering Ph.D. program at Tech, and he soon applied for his own doctorate.
Cohen says QBioS is a natural choice for him, despite his engineering background. “I have been interested in biosciences for as long as I can remember,” Cohen says. In fact, he adds, he chose to study mechanical engineering at Technion because they offered a biosciences specialization.
“I look forward to obtaining knowledge and experience that will allow me to gain a set of professional tools to handle real scientific problems and achieve a better understanding of the amazing world around us.” Cohen will be based in the School of Physics during his time in the program.
Nolan Joseph English comes to QBioS with a B.S. in Chemical Engineering from Howard University, in Washington, D.C. English says he was drawn to Tech for its “incredibly strong focus on computer science and interdisciplinary studies that pervade both the culture and research.” That Tech is his father’s alma mater also played a role in his decision.
“The QBioS program allows one to experience many aspects of computational biology – such as systems biology, bioinformatics, and bioengineering – while building a strong core of computational capability and understanding,” English says. “This strong core is what I desire most and is something truly unique to Georgia Tech.”
What most excites English about QBioS is the prospect of learning “how to translate an in silico knowledge base into an in vivo actualization of concept.” For this reason, he says, “I am keenly interested in learning about modeling techniques at the transcriptome and genome levels.” English will be based in the School of Biological Sciences.
Elma Kajtaz earned her bachelor’s degree in behavioral sciences from the University of Sarajevo, in Bosnia-Herzegovina. No longer a stranger to Georgia Tech, Kajtaz had previously worked and studied in the former School of Applied Physiology, now the School of Biological Sciences, with Professor T. Richard Nichols. That research opportunity is what drew Kajtaz initially to Georgia Tech.
“The interdisciplinary and quantitative approach to behavior and physiology emphasized by the QBioS program is perfectly aligned with my research philosophy and interests,” Kajatz says. “I am looking forward to learning and working alongside faculty and researchers from different disciplines to contribute to our understanding of biological systems.” Kajtaz will be based in the School of Biological Sciences.
Alexander Bo-Ping Lee received his bachelor’s degree in mathematical biology at Harvey Mudd College, in Claremont, California. A paper on ant rafts by School of Biological Sciences Associate Professor David Hu intrigued Lee and sparked his interest in attending the QBioS program. Lee is most excited to be a teaching assistant during his time in the program and hopes to become a professor one day, in line with his love of teaching. Lee will be based in the School of Physics.
Joy Elizabeth Putney received her B.S. in Biology and Physics-Engineering from Washington and Lee University, in Lexington, Virginia. She was drawn to QBioS by her love of research that uses quantitative techniques to study biology.
“Life is full of examples of complex systems, from the molecular to the ecological scales, and most complex systems can be best understood using quantitative techniques,” Putney says. She’s excited to start research, taking advantage of the program’s rotation-based structure to gain experience in multiple labs. “This will give me the best opportunity to find a place where I can do research that aligns with my passions,” she says. Putney will be based in the School of Biological Sciences.
Putney may work government or industry after completing the program, but that is a long way in the future. “I hope that Georgia Tech will point me in the right direction,” she says, “even if it ends up being something completely different from what I thought or expected.”
Pedro Márquez-Zacarías has a bachelor’s degree in biomedical sciences from the School of Medicine at the National Autonomous University of Mexico, in Mexico City.
“Georgia Tech is a very prestigious university where science and technology are at the frontiers of knowledge” Márquez-Zacarías says. “I like how students and professors from different fields join efforts to tackle complex problems in the most diverse fields of science.”
Márquez-Zacarías is excited to be part of the diverse and collaborative groups of scientist in the QBioS program. “I can’t imagine a better program for my doctoral degree,” he says. He looks forward to collaborating with various research groups and learning cutting-edge techniques to study how nature works. Márquez-Zacarías will be based in the School of Biological Sciences.
Stephen Anthony Thomas is no stranger to Georgia Tech, where he earned bachelor’s and master’s degrees in electrical engineering. But it is mathematics where Thomas finds his passion.
The QBioS program offers “a great chance to apply a subject I love – mathematics – to areas that can make a real difference to society,” he says.
A potential research focus for Thomas is mathematical modeling for epidemiology. “It’s exciting to be able to work not only at Georgia Tech,” he says, “but also through partnerships with Emory University on critical problems, such as countering antibiotic resistance in bacterial infections.” Thomas will be based in the School of Mathematics.
Hector Augusto Velasco-Perez received his bachelor’s degree in physics from the Faculty of Sciences in the National Autonomous University of Mexico, also in Mexico City. “I was looking for a graduate program and a place that could combine theory and practice, physics and biology, pen and paper, and high-performance computing with GPUs [graphics-processing units],” he says. “I wanted my work to be something that someone can use, something that I can point at – big or small – and say, ‘Look, I did that!’.”
QBioS fits the bill, and Velasco-Perez looks forward to working in a diverse community. The QBioS program “is a perfect opportunity for new ideas to be created,” he says. Velasco-Perez will be based in the School of Physics.
Seyed Alireza Zamani-Dahaj received his master’s degree in physics from McMaster University, in Hamilton, Ontario, Canada. He was drawn to QBioS by the wide range of classes and the multiple labs doing interesting research. “Being among the first class of the QBioS Program is very exciting,” Zamani-Dehaj says. He will be based in the School of Biological Sciences.
“We warmly welcome our new graduate students in QBioS,” says College of Sciences Dean Paul M. Goldbart. “We look forward to their unique contributions to the College’s tradition of forging new paths of discovery.”
Scott Smith
Student Assistant
College of Sciences
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