March 29, 2012 | Atlanta, GA

When battling an epidemic of a deadly parasite, less resistance can sometimes be better than more, a new study suggests. 

A freshwater zooplankton species known as Daphnia dentifera endures periodic epidemics of a virulent yeast parasite that can infect more than 60 percent of the Daphnia population. During these epidemics, the Daphnia population evolves quickly, balancing infection resistance and reproduction.

A new study led by Georgia Institute of Technology researchers reveals that the number of vertebrate predators in the water and the amount of food available for Daphnia to eat influence the size of the epidemics and how these “water fleas” evolve during epidemics to survive.

The study shows that lakes with high nutrient concentrations and lower predation levels exhibit large epidemics and Daphnia that become more resistant to infection by the yeast Metschnikowia bicuspidata. However, in lakes with fewer resources and high predation, epidemics remain small and Daphnia evolve increased susceptibility to the parasite.

“It’s counterintuitive to think that hosts would ever evolve greater susceptibility to virulent parasites during an epidemic, but we found that ecological factors determine whether it is better for them to evolve enhanced resistance or susceptibility to infection,” said the study’s lead author Meghan Duffy, an assistant professor in the School of Biology at Georgia Tech. “There is a trade-off between resistance and reproduction because any resources an animal devotes to defense are not available for reproduction. When ecological factors favor small epidemics, it is better for hosts to invest in reproduction rather than defense.”

This study was published in the March 30, 2012 issue of the journal Science. The research was supported by the National Science Foundation and the James S. McDonnell Foundation.

In addition to Duffy, also contributing to this study were Indiana University Department of Biology associate professor Spencer Hall and graduate student David Civitello; Christopher Klausmeier, an associate professor in the Department of Plant Biology and W.K. Kellogg Biological Station at Michigan State University; and Georgia Tech research technician Jessica Housley Ochs and graduate student Rachel Penczykowski.

For the study, the researchers monitored the levels of nutritional resources, predation and parasitic infection in seven Indiana lakes on a weekly basis for a period of four months. They calculated infection prevalence visually on live hosts using established survey methods, estimated resources by measuring the levels of phosphorus and nitrogen in the water, and assessed predation by measuring the size of uninfected adult Daphnia.

The researchers also conducted infection assays in the laboratory on Daphnia collected from each of the seven lake populations at two time points: in late July before epidemics began and in mid-November as epidemics waned. The assays measured the zooplankton’s uptake of Metschnikowia bicuspidata and infectivity of the yeast once consumed.

The infection assays showed a significant evolutionary response of Daphnia to epidemics in six of the seven lake populations. The Daphnia population became significantly more resistant to infection in three lakes and significantly more susceptible to infection in three other lakes. The hosts in the seventh lake did not show a significant change in susceptibility, but trended toward increased resistance. In the six lake populations that showed a significant evolutionary response, epidemics were larger when lakes had lower predation and higher levels of total nitrogen.

Daphnia became more susceptible to the yeast in lakes with fewer resources and higher vertebrate predation, but evolved toward increased resistance in lakes with increased resources and lower predation,” noted Duffy.

The study’s combination of observations, experiments and mathematical modeling support the researchers’ theoretical prediction that when hosts face a resistance-reproduction tradeoff, they evolve increased resistance to infection during larger epidemics and increased susceptibility during smaller ones. Ultimately, ecological gradients, through their effects on epidemic size, influence evolutionary outcomes of hosts during epidemics.

“While the occurrence and magnitude of disease outbreaks can strongly influence host evolution, this study suggests that altering predation pressure on hosts and productivity of ecosystems may also influence this evolution,” added Duffy.

The team plans to repeat the study this summer in the same Indiana lakes to examine whether the relationships between ecological factors, epidemic size and host evolution they found in this study can be corroborated.

This work was supported in part by the National Science Foundation (NSF) (Award Nos. DEB-0841679, DEB-0841817, DEB-0845825 and OCE-171 0928819). The content is solely the responsibility of the principal investigators and does not necessarily represent the official views of the NSF.

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April 12, 2012 | Atlanta, GA

Rachel Penczykowski, a Biology PhD student in Meghan Duffy’s lab, has been chosen as a winner of a PEO Scholar Award. This $15,000 award is given by the International Chapter of the PEO Sisterhood, which is a philanthropic group that promotes educational opportunities for women. The PEO Scholar Awards were established in 1991, and provide substantial merit-based support for women pursuing doctoral degrees.

This award will help support Rachel in her doctoral research, which focuses on interactions between infectious diseases and aquatic ecosystems. Rachel is particularly interested in feedbacks between nutrients such as nitrogen and phosphorus and infectious diseases in freshwater systems.

Congratulations, Rachel!

April 19, 2012 | Atlanta, GA

Dr. Michael Cortez, a postdoctoral researcher in Dr. Joshua Weitz's Lab in the School of Biology, has received a Mathematical Sciences Postdoctoral Research Fellowship (MSPRF) from the National Science Foundation (NSF).  This fellowship is an award of $150,000 over two years that supports Dr. Cortez's research in the fields of mathematics and theoretical biology.   Postdoctoral research fellowships are prestigious awards that according to the NSF, "provide increased flexibility for fellows in choosing postdoctoral environments that have maximal impact on their future scientific development." Dr. Cortez's proposed research focuses on developing theory to understand the population dynamics that arise in predator-prey systems where both the predator and the prey populations are evolving.

In addition, Dr. Cortez recently received the 2011 prize for an outstanding paper in ecology theory from the Theoretical Section of the Ecological Society of America (ESA) for his paper "Comparing the qualitatively different effects of rapidly evolving and rapidly induced defences have on predator-prey interactions" published in the journal Ecology Letters.  That work focused on understanding how defence evolution and defence induction in response to predation have different effects on the population dynamics of predator-prey systems.

May 10, 2012 | Atlanta, GA

New research findings show that embryonic stem cells unable to fully compact the DNA inside them cannot complete their primary task: differentiation into specific cell types that give rise to the various types of tissues and structures in the body.

Researchers from the Georgia Institute of Technology and Emory University found that chromatin compaction is required for proper embryonic stem cell differentiation to occur. Chromatin, which is composed of histone proteins and DNA, packages DNA into a smaller volume so that it fits inside a cell. 

A study published on May 10, 2012 in the journal PLoS Genetics found that embryonic stem cells lacking several histone H1 subtypes and exhibiting reduced chromatin compaction suffered from impaired differentiation under multiple scenarios and demonstrated inefficiency in silencing genes that must be suppressed to induce differentiation.

“While researchers have observed that embryonic stem cells exhibit a relaxed, open chromatin structure and differentiated cells exhibit a compact chromatin structure, our study is the first to show that this compaction is not a mere consequence of the differentiation process but is instead a necessity for differentiation to proceed normally,” said Yuhong Fan, an assistant professor in the Georgia Tech School of Biology.

Fan and Todd McDevitt, an associate professor in the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University, led the study with assistance from Georgia Tech graduate students Yunzhe Zhang and Kaixiang Cao, research technician Marissa Cooke, and postdoctoral fellow Shiraj Panjwani.

The work was supported by the National Institutes of Health’s National Institute of General Medical Sciences (NIGMS), the National Science Foundation, a Georgia Cancer Coalition Distinguished Scholar Award, and a Johnson & Johnson/Georgia Tech Healthcare Innovation Award.

To investigate the impact of linker histones and chromatin folding on stem cell differentiation, the researchers used embryonic stem cells that lacked three subtypes of linker histone H1 -- H1c, H1d and H1e -- which is the structural protein that facilitates the folding of chromatin into a higher-order structure. They found that the expression levels of these H1 subtypes increased during embryonic stem cell differentiation, and embryonic stem cells lacking these H1s resisted spontaneous differentiation for a prolonged time, showed impairment during embryoid body differentiation and were unsuccessful in forming a high-quality network of neural cells.

“This study has uncovered a new, regulatory function for histone H1, a protein known mostly for its role as a structural component of chromosomes,” said Anthony Carter, who oversees epigenetics grants at NIGMS.  “By showing that H1 plays a part in controlling genes that direct embryonic stem cell differentiation, the study expands our understanding of H1’s function and offers valuable new insights into the cellular processes that induce stem cells to change into specific cell types.”

During spontaneous differentiation, the majority of the H1 triple-knockout embryonic stem cells studied by the researchers retained a tightly packed colony structure typical of undifferentiated cells and expressed high levels of Oct4 for a prolonged time. Oct4 is a pluripotency gene that maintains an embryonic stem cell’s ability to self-renew and must be suppressed to induce differentiation.

“H1 depletion impaired the suppression of the Oct4 and Nanog pluripotency genes, suggesting a novel mechanistic link by which H1 and chromatin compaction may mediate pluripotent stem cell differentiation by contributing to the epigenetic silencing of pluripotency genes,” explained Fan. “While a significant reduction in H1 levels does not interfere with embryonic stem cell self-renewal, it appears to impair differentiation.”

The researchers also used a rotary suspension culture method developed by McDevitt to produce with high efficiency homogonous 3D clumps of embryonic stem cells called embryoid bodies. Embryoid bodies typically contain cell types from all three germ layers -- the ectoderm, mesoderm and endoderm -- that give rise to the various types of tissues and structures in the body. However, the majority of the H1 triple-knockout embryoid bodies formed in rotary suspension culture lacked differentiated structures and displayed gene expression signatures characteristic of undifferentiated stem cells.

“H1 triple-knockout embryoid bodies displayed a reduced level of activation of many developmental genes and markers in rotary culture, suggesting that differentiation to all three germ layers was affected.” noted McDevitt.  

The embryoid bodies also lacked the epigentic changes at the pluripotency genes necessary for differentiation, according to Fan.

“When we added one of the deleted H1 subtypes to the embryoid bodies, Oct4 was suppressed normally and embryoid body differentiation continued,” explained Fan. “The epigenetic regulation of Oct4 expression by H1 was also evident in mouse embryos.”

In another experiment, the researchers provided an environment that would encourage embryonic stem cells to differentiate into neural cells. However, the H1 triple-knockout cells were defective in forming neuronal and glial cells and a neural network, which is essential for nervous system development. Only 10 percent of the H1 triple-knockout embryoid bodies formed neurites and they produced on average eight neurites each. In contrast, half of the normal embryoid bodies produced, on average, 18 neurites.

In future work, the researchers plan to investigate whether controlling H1 histone levels can be used to influence the reprogramming of adult cells to obtain induced pluripotent stem cells, which are capable of differentiating into tissues in a way similar to embryonic stem cells.

Research reported in this publication was supported by the National Institute of General Medical Sciences of the National Institutes of Health (NIH) under award number GM085261 and the National Science Foundation under award number CBET-0939511. The content is solely the responsibility of the principal investigators and does not necessarily represent the official views of the NIH or NSF.

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May 23, 2012 | Atlanta, GA

A marine ecologist known for his work on community ecology and chemical ecology has been selected to receive the 2012 Robert L. and Bettie P. Cody Award in Ocean Sciences from Scripps Institution of Oceanography at UC San Diego. Mark Hay, Teasley Professor of Environmental Biology and co-director of the Center for Aquatic Chemical Ecology at Georgia Tech, will be awarded the prestigious prize during a private ceremony on June 14.

As part of the award, Hay will present a public lecture on June 15 at 11 a.m. in the Robert Paine Scripps Forum for Science, Society and the Environment (Scripps Seaside Forum), 8610 Kennel Way, just north of El Paseo Grande on the Scripps campus in La Jolla. The lecture, "The Language of the Sea: How Chemically-mediated Interactions Structure Marine Populations, Communities, and Ecosystems," is designed for a lay audience. On June 14 at 3 p.m. he will present a technical lecture, also in the Scripps Seaside Forum. "The Biotic Death Spiral of Coral Reefs: Can Local Intervention Reverse the Global Decline?" is intended for a scientific audience. Both talks are free and open to the public (street parking only).
The biennial Cody Award, which consists of a gold medal and a $10,000 prize, recognizes outstanding scientific achievement in oceanography, marine biology and Earth science.

The award, part of the Scripps Distinguished Lecture Series, was established by an endowment from the late Robert Cody and his wife Bettie, and a substantial contribution from Capital Research & Management Company, in recognition of Mr. Cody's service to the Los Angeles-based firm. Robert Cody's affiliation with Scripps Oceanography dates back to his youth and his association with William E. Ritter, his great uncle and founder and first director of Scripps.

Hay is an experimental field ecologist who investigates the processes and mechanisms affecting the structure and function of marine communities, with most of his research focusing on consumer-prey interactions, and on the cascading effects of these interactions on the ecology and evolution of marine communities. His research has transformed and deepened our understanding of plant-herbivore interactions in the sea (the base upon which marine food webs are built), and he helped found the modern field of marine chemical ecology.

His fundamental research has provided key insights on critical aspects of the conservation and restoration of coral reefs and challenged how scientists view ecological and evolutionary processes affecting the establishment and impact of invasive species. Hay has commonly worked with media outlets to assure that his basic findings are made accessible and understandable to the general public.

Hay's field research has focused on tropical coral reefs throughout the Caribbean and South Pacific. He has participated in many ship-based expeditions but more commonly works for extended periods in remote field stations to conduct longer-term experiments. Coral reefs have been his primary focus, although insights from that focus system are often applied to temperate rocky reefs, open ocean plankton communities, inland freshwaters and occasionally to desert and other terrestrial systems.

Hay's research has been pivotal in structuring science's understanding of the critical role that consumers play in affecting community structure and function in marine systems. By conducting tests in unrelated systems he is often able to demonstrate that discoveries from marine investigations constitute robust, fundamental concepts that transcend particular species and ecosystems.

Hay completed B.A. degree requirements in Zoology and Philosophy at the University of Kentucky in 1974, and a Ph.D. in Ecology and Evolutionary Biology from the University of California, Irvine, in 1980. He was a pre-doctoral fellow at the Smithsonian Tropical Research Institute in Panama and a post-doctoral fellow in paleobiology at the Smithsonian National Museum of Natural History. From 1982-1999 he was on the faculty at the University of North Carolina at Chapel Hill's Institute of Marine Sciences.

In 1999, he moved to Georgia Tech as recipient of the Teasley Chair. He has conducted more than 5,000 scuba dives, and has led three saturation diving missions (using both Hydrolab and Aquarius) - where scientists live and work at depth on a coral reef for periods of 10 days.

May 31, 2012 | Atlanta, GA

On the periodic table of the elements, iron and magnesium are far apart. But new evidence suggests that 3 billion years ago, iron did the chemical work now done by magnesium in helping RNA fold and function properly.

There is considerable evidence that the evolution of life passed through an early stage when RNA played a more central role before DNA and coded proteins appeared. During that time, more than 3 billion years ago, the environment lacked oxygen but had an abundance of soluble iron.

In a new study, researchers from the Georgia Institute of Technology used experiments and numerical calculations to show that iron, in the absence of oxygen, can substitute for magnesium in RNA binding, folding and catalysis. The researchers found that RNA’s shape and folding structure remained the same and its functional activity increased when magnesium was replaced by iron in an oxygen-free environment.

“The primary motivation of this work was to understand RNA in plausible early earth conditions and we found that iron could support an array of RNA structures and catalytic functions more diverse than RNA with magnesium,” said Loren Williams, a professor in the School of Chemistry and Biochemistry at Georgia Tech.

The results of the study were published online on May 31, 2012 in the journal PLoS ONE. The study was supported by the NASA Astrobiology Institute.

In addition to Williams, Georgia Tech School of Biology postdoctoral fellow Shreyas Athavale, research scientist Anton Petrov, and professors Roger Wartell and Stephen Harvey, and Georgia Tech School of Chemistry and Biochemistry postdoctoral fellow Chiaolong Hsiao and professor Nicholas Hud also contributed to this work.

Free oxygen gas was almost nonexistent more than 3 billion years ago in the early earth’s atmosphere. When oxygen began entering the environment as a product of photosynthesis, it turned the earth’s iron to rust, forming massive banded iron formations that are still mined today. The free oxygen produced by advanced organisms caused iron to be toxic, even though it was -- and still is -- a requirement for life.

This environmental transition triggered by the introduction of free oxygen into the atmosphere would have caused a slow, but dramatic, shift in biology that required transformations in biochemical mechanisms and metabolic pathways. The current study provides evidence that this transition may have caused a shift from iron to magnesium for RNA binding, folding and catalysis processes.

The researchers used quantum mechanical calculations, chemical footprinting and two ribozyme assays to determine that in an oxygen-free environment, iron, Fe2+, can be substituted for magnesium, Mg2+, in RNA folding and catalysis.

Quantum mechanical calculations showed that the structure of RNA was nearly identical when it included iron or magnesium. When large RNAs fold into native, stable structures, negatively charged phosphate groups are brought into close proximity. The researchers calculated one small difference between the activity of iron and magnesium structures: more charge was transferred from phosphate to iron than from phosphate to magnesium.

Chemical probing under anaerobic conditions showed that iron could replace magnesium in compacting and folding large RNA structures, thus providing evidence that iron and magnesium could be nearly interchangeable in their interactions with RNA.

Under identical anaerobic conditions, the activity of two enzymes was enhanced in the presence of iron, compared to their activity in the presence of magnesium. The initial activity of the L1 ribozyme ligase, an enzyme that glues together pieces of RNA, was 25 times higher in the presence of iron. Activity of the hammerhead ribozyme, an enzyme that cuts RNA, was three times higher in the presence of iron compared to magnesium.

“The results suggest that iron is a superior substitute for magnesium in these catalytic roles,” said Williams, who is also director of the Center for Ribosomal Origins and Evolution at Georgia Tech. “Our hypothesis is that RNA evolved in the presence of iron and is optimized to work with iron.”

In future studies, the researchers plan to investigate what unique functions RNA can possess with iron that are not possible with magnesium.

This work was supported by NASA (Award No. NNA09DA78A). The content is solely the responsibility of the principal investigators and does not necessarily represent the official views of NASA.

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June 6, 2012 | Atlanta, GA

New research into the cell-damaging effects of Huntington’s disease suggests a new approach for identifying possible therapeutic targets for treating the nerve-destroying disorder.

Huntington’s disease causes the progressive breakdown of nerve cells in the brain and affects an individual’s movement, cognition and mental state. Genetically, the disease is associated with a mutation in the Huntingtin gene that causes the huntingtin protein to be produced with an extended region containing the amino acid glutamine.

The mechanisms that control the severity and onset of the disease are poorly understood, as individuals with the same amount of expansion in their huntingtin proteins experience differences in toxicity and onset of the disease.  

A new study led by Georgia Institute of Technology researchers suggests that the toxic effects of the huntingtin protein on cells may not be driven exclusively by the length of the protein’s expansion, but also by which other proteins are present in the cell.

The researchers placed human huntingtin protein with an expanded region, called a polyglutamine tract, into yeast cells and found toxicity differences that were based on the other protein aggregates -- called prions -- present in the cells.

“This study clarifies genetic and epigenetic mechanisms that modulate polyglutamine’s toxicity on cells and establishes a new approach for identifying potential therapeutic targets through characterization of pre-existing proteins in the cell,” said Yury Chernoff, a professor in the School of Biology at Georgia Tech. “While this study was conducted in yeast, it is possible that there are differences in aggregated proteins present in human cells as well, which are causing variation in huntingtin toxicity among individuals.”

The results of the study were published in the April 2012 issue of the journal PLoS Genetics. This work was supported by the National Institutes of Health and the Hereditary Disease Foundation.

Also contributing to this research were former Georgia Tech graduate student He Gong and postdoctoral fellow Nina Romanova, University of North Carolina at Chapel Hill School of Medicine research assistant professor Piotr Mieczkowski, and Boston University School of Medicine professor Michael Sherman.

Expanded huntingtin forms clumps in human cells that are typically transported and stored in an internal compartment called an aggresome until they can be removed from the body. While the compartment is thought to protect the contents of the cell from the toxic contents inside the aggresome, the current study shows that huntingtin molecules inside an aggresome can still be toxic to the cell.

In the study, aggresome formation in the cells containing the prion form of the Rnq1 protein reduced the toxicity of the huntingtin protein in Saccharomyces cerevisiae yeast cells, whereas the huntingtin protein’s toxicity remained in the presence of the prion form of translation release factor Sup35.

“It remains uncertain whether the toxicity was primarily driven by sequestration of Sup35 into the aggresome or by its sequestration into the smaller huntingtin protein aggregates that remained in the cytoplasm,” explained Chernoff, who is also director of the Center for Nanobiology of the Macromolecular Assembly Disorders (NanoMAD). “While Sup35 was detected in the aggresome, we don’t know if the functional fraction of Sup35 was sequestered there.”

In a follow-on experiment, the researchers increased the level of another release factor, Sup45, in the presence of Sup35 and found that this combination counteracted the toxicity.

“While the Rnq1 and Sup35 prions did not cause significant toxicity on their own, the results show that prion composition in the cell drove toxicity,” noted Chernoff. “Prions modulated which proteins were sequestered by the aggresome, as proteins associated with the pre-existing prions were more likely to be sequestered, such as Sup45 because of its association with Sup35.”

It remains unknown if polyglutamines can sequester the human versions of the Sup35 and Sup45 release factors, but this study shows the possibility that organisms may differ by the protein composition in their cells, and this in turn may influence their susceptibility to polyglutamine disorders such as Huntington’s disease.

Research reported in this publication was supported by the National Institute of General Medical Sciences of the National Institutes of Health (NIH) under award numbers GM058763, GM093294 and GM086890. The content is solely the responsibility of the principal investigators and does not necessarily represent the official views of the NIH.

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July 9, 2012 | Atlanta, GA

By Josh Fischman

The ecological effects of the 2010 Deepwater Horizon oil spill are still largely unknown. Senior writer Josh Fischman is on the research vessel Endeavor in the Gulf of Mexico with a team of university scientists seeking answers. He is filing reports from the ship.

One hundred and twenty miles south of the Mississippi Delta—The Endeavor is moving at 1 knot through a thin but wide slick of oil. The sheen glints in the water for a hundred yards or more around the ship. “It’s a little disturbing when you see fish swimming underneath it,” says Nigel D’Souza, a postdoctoral researcher at Lamont-Doherty Earth Observatory, part of Columbia University. “I was on deck earlier collecting some of the oil with a bucket, and some mahi-mahi swam by. It makes you wonder how much of this stuff is in the food chain, and in what form.”

When I pointed out that he was on the ship to help answer that question, he said, “Yes, well, this makes it seem more urgent.”

Urgency is never lacking on the Endeavor, where science is a mixture of precision and controlled frenzy. Ship time is staggeringly expensive, so the 17 scientists and technicians on board have crammed round-the-clock experiments and sample-collecting into fewer than 10 days at sea. On July 5 they are off the ship because other researchers are waiting to use it.

But the rush to get everything done doesn’t negate the need to get it right. Sampling bottles are sent 1,200 meters down to the bottom of the gulf, and temperature, oxygen levels, and the pigment chlorophyll (derived from phytoplankton) are measured every moment. The bottles are opened remotely at very specific depths. Back on the surface, in the ship’s main lab, recovered water is filtered for gases like methane and the chemicals that reveal the presence of microorganisms. A highly specialized instrument called a flow cytometer can count the number of single-celled creatures in a droplet of water. All of this, and more, is done over and over again, to compare different locations at different depths at different times of day.

“We have to push pretty hard,” says Chief Scientist Joseph Montoya, a biogeochemist from the Georgia Institute of Technology. Every day, Montoya figures out how many nets, drift traps, sampling bottles, and bottom-sediment cores can be taken from each site, and posts a plan that has scientists and crew members lowering equipment over the side and recovering it at all hours of the day and night. He and I share a cabin, and I’m sure he slept for five hours at a stretch—once. “If you snap a picture of Joe cat-napping,” says one of his students in the science contingent, “you win a prize.”

Everyone was awake as last Monday night ticked into Tuesday morning and the Endeavor arrived at the Deepwater Horizon site. The ruined wellhead that blew apart in April 2010 was some 1,600 meters below us. From the starboard side of the boat, as Captain John Wilder held the 185-foot ship steady in the currents and wind, scientists paid out a wire that held a cluster of sampling bottles called a CTD. Then Montoya and Patrick Quigley, the botswain, headed for the fantail, at the back of the ship, crowded with so much scientific equipment it was hard to walk. As Quigley attached shackles and lines and directed hydraulic hoists and heavy-powered winches, two sediment traps went over the side and down to the bottom, where they will collect samples for a year, anchored by big iron train wheels. An underwater camera went over next, followed by a “robotic” CTD that dives and samples free of the ship; we will collect it—if its radio beacon works—on our way back to port.

“Look at all this room!” called Quigley, standing in the middle of the now-empty fantail.

The Endeavor then turned southwest and farther into the Gulf, toward the site the scientists called GC 600, where oil and methane seep from the ocean bottom naturally—a good comparison with the unnatural Deepwater Horizon. The ship arrived at 10:30 Tuesday evening and the routine began again.

Well, it was the routine plus, which meant minus more sleep. Melitza Crespo-Medina, a microbiologist, postdoctoral researcher, and leader of what has been dubbed “the mud people” from the University of Georgia, had to find active gas or oil plumes on the sea floor, so Montoya and the other scientists would know where to focus their sampling. That meant a fine-grained sonar survey starting at 4 in the morning; the sound waves can reveal streams of bubbles from mud that’s more than 1,000 meters below the ship. That evening, Crespo-Medina sent a device to the bottom to bring back tubes of mud and sediment. These meter-long cores need to be extracted from the machine, cut into sections, and looked at for hydrocarbon content and signs of bacterial activity. Crespo-Medina was up for 24 hours straight, slept for three hours, then went at it again.

Thursday began with a problem. The sonar survey hadn’t homed in on a plume, and then Joy Battles, a graduate student who works with Crespo-Medina, announced that levels of methane in the water were on the low side. Seeps flow irregularly, and we seem to have caught this one napping. Bad news for a project aimed at measuring the effects of natural seeps. Montoya is worried that further experiments where we’ve been working are a waste of time.

And we’ve been working that area, around the edges of GC 600, because the middle—which had been bubbling nicely on previous visits—is now in a “no go” zone, a box on the map indicating we can’t sample there. Another scientist has a package of instruments at the bottom, and is afraid our coring might disturb it.

The solution is, of course, more work and less sleep. Getting permission to edge into the “no go” box, the scientists begin redoing surveys done yesterday. Crespo-Medina does another painstaking sonar pass over the bottom, and Battles combs new water samples for signs of gas. Another cost of doing this extra work is the team gives up a planned trip to a nearby site that could hold a new seep. But better the devil you know is the consensus aboard ship.

The gamble pays off. Just after midnight Thursday, as the ship was completing another 1,200-meter surface-to-bottom probe, Battles bursts into the main lab to announce methane levels at the new target shot way up. They were, in fact, about 15 times higher than the levels we were seeing yesterday. And oil slicks began drifting by. Montoya put down his laptop and clapped.

This was not a medical miracle, no cure for cancer, but it meant the central premise of the project, comparing the natural to the unnatural, would work. A delicately placed core even returned some oil-impregnated mud from the bottom, droplets that winked back at Crespo-Medina as she illuminated them with a flashlight.

“I found the methane,” she sang softly and repeatedly, as she worked on deck drawing water from the sample bottles her colleagues had sent into the deep.

For More Information Contact

Josh Fischman

Josh Fischman is a senior writer with The Chronicle of Higher Education, focused on the biological and physical sciences.

Jerry Pullman and Undergraduate Students Help to Save Endangered Plant Species in the Southeast

July 31, 2012 | Atlanta, GA

IPST faculty member Jerry Pullman, Ph.D., a Georgia Tech Biology professor, has partnered with the Atlanta Botanical Garden to help save some of the South’s rarest plants. Jerry uses the knowledge and skills he has gained over decades of developing cloning technology for high-value pines and Douglas fir to help multiply and preserve Georgia’s rare and critically endangered species. In the process, he has created some life-changing experiences for his students.

Over one-fifth of the world’s plants are becoming rare and endangered due to loss of habitat, over-collection, diseases, competition from exotic and invasive species, and global warming. Jerry strives to help save these species for the future by preserving them in seed banks, at safekeeping sites like botanical gardens, and by multiplying the rarest plants using plant tissue culture techniques.

One of his projects involves an ancient evergreen tree—Torreya taxifolia—of which fewer than 1,000 are known to remain. Jerry and his staff have worked out methods of somatic  embryogenesis to keep natural multiplication processes going in culture, resulting in multiple plant copies. The multiplying embryos can often be stored for the long term at ultra-low temperatures in liquid nitrogen (cryogenic storage) and retrieved when needed.

Several years ago, during a construction project at the Atlanta Botanical Garden, Conservatory Director Ron Determann arranged to store some rare seeds at normal freezer temperatures in a federal government installation at Fort Collins, CO. When the seeds were retrieved about six years later, 98% of them were no longer viable. Jerry’s work with the Atlanta Botanical Garden and his students at Georgia Tech has developed improved, species-specific methods of propagation and long-term storage to address this problem.

In vitro germination and micropropagation experiments with the threatened Georgia aster (Symphyotrichum georgianum) produced methods to store and retrieve seeds after cryopreservation and 300 viable plants that were recently installed at the Chattahoochee River National Recreation Area. With ongoing interest in Georgia’s natural heritage, there is talk of the threatened aster replacing the Cherokee rose as the Georgia state flower.

This work captures the imagination of many undergraduate students. One student, who wanted to culture a seaweed, explored a Fijian Sea alga with cancer-fighting properties. Another student, who was interested in shark biology, was put to work cloning the carnivorous pitcher plant (Sarracenia oreophila) and returning the plants to the field. Some of the students come back after graduating to help complete the research. Several students have wound up as authors on publications. One student even continued her education in forest policy and is now employed by the US Fish and Wildlife Service.

Georgia Tech and members of the botanical community have created a stronger bond through these research projects saving plants. Those interested in supporting the work can contact Jerry at References to some recent papers on the work are found at this link

“I am proud to work with undergraduate students teaching them how to conduct research while at the same time helping to save endangered plants,” says Jerry. “And this is my way of making the world a little better place.”

Hammer receives NSF CAREER Award

August 7, 2012 | Atlanta, GA

Dr. Brian Hammer (Assistant Professor, School of Biology), was recently honored with an award from the Faculty Career Development (CAREER) Program at the National Science Foundation.   The CAREER award supports junior faculty who exemplify the role of teacher-scholars through effective integration of outstanding research and excellent education.  Hammer was chosen for this highly competitive award from among the very best young scientists in the United States. The award provides $900,000 over five years to support his research project in molecular microbiology. 

The overall goal of Dr. Hammer's research project is to understand the contribution of extracellular chemical signaling in the exchange of genetic material that accelerates bacterial adaptation. The process of natural transformation is one mechanism that bacteria use for such horizontal gene transfer. The bacterium Vibrio cholerae, a common marine inhabitant and causative agent of the fatal cholera disease, induces the uptake of extracellular DNA in response to two signaling pathways, a chitin utilization system and a bacterial cell-cell communication (or "quorum sensing") system. The project will identify novel genes, proteins, and regulatory connections of the natural transformation network in Vibrio cholerae to dissect the role that both habitat and genetics play in the evolution of this bacterial pathogen.

A major component of Dr. Hammer’s CAREER project includes activities that promote integration of academic community members with the broader society in the process of modern scientific discovery. Dr. Hammer hosts seventh grade science teacher, Mr. David Taube, and an undergraduate student to work in his lab each summer.  During the academic year this team engages ethnically diverse urban K-12 students in stimulating hands-on scientific activities, which will be shared with local educators that teach under-represented minority students in the metro-Atlanta area.


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