Dr. Frank Stewart, an assistant professor in the School of Biology, has received a Faculty Early Career Development (CAREER) Award from the National Science Foundation (NSF).  This award provides $1.2 million over five years in support of research and educational activities in Dr. Stewart’s field of marine microbiology.  According to NSF, the CAREER Program “offers the National Science Foundation's most prestigious awards in support of junior faculty who exemplify the role of teacher-scholars through outstanding research, excellent education and the integration of education and research within the context of the mission of their organizations.”

Dr. Stewart’s CAREER research will investigate the microorganisms responsible for key steps of the biological sulfur cycle in marine oxygen minimum zones (OMZs).  OMZs and other low-oxygen regions (e.g., dead zones) are likely to expand in response to future climate change.  The microbial communities that dominate these unique environments are ecologically diverse and are known to be critical mediators of global cycles, notably the nitrogen cycle.  New evidence, including work from Dr. Stewart and his collaborators, has indicated that OMZ microbes (mostly bacteria) are also actively involved in moving sulfur through the marine ecosystem, with potentially links to both the nitrogen and carbon cycles.  However, the biogeography, genomic diversity, and metabolic activity of the organisms responsible for these processes remain largely uncharacterized.  Dr. Stewart’s research will use a combination of high throughput molecular methods, microbial culturing, and shipboard experiments to shed new light on this important group of marine microorganisms.  This research will involve four oceanographic research cruises in both the Pacific Ocean and the Gulf of Mexico.

Dr. Stewart’s CAREER project is also devoted to enhancing science education across multiple academic levels.  Through a partnership with local K-12 educators and teacher-development experts at Georgia Tech, Dr. Stewart and his lab will implement A Summer Workshop in Marine Science (SWIMS), designed to help train local teachers to merge key topics in marine science with new national standards in science education.  Additional science education activities will involve internship opportunities through partnerships with other Atlanta area colleges.

Chong Shin (Assistant professor, School of Biology) has received a pilot grant from the Georgia Tech & Emory Center for Regenerative Medicine (GTEC). The objective of the project is to unveil mechanisms to program/reprogram hepatocytes/insulin secreting beta cells in zebrafish. Zebrafish not only has homologous liver and pancreas structure with mammals but also has significant capacity for regeneration. The knowledge from this study can be applied to stimulate endogenous generation/regeneration mechanisms in the human body.

Two PhD students of the School of Biology, Mustafa Burak Boz and Jin Xu, received $1,500 travel grants for their posters at the recent Georgia Tech Research and Innovation Conference (GTRIC 2012).

The title of Burak's poster is "Assembly of an icosahedral single stranded RNA virus" advised by Dr. Steve Harvey (Professor and Georgia Research Alliance Eminent Scholar in Structural Biology, School of Biology).
The title of Jin's poster is "Unraveling a new regulator in liver and endocrine pancreas fate decision and regeneration " advised by Dr. Chong Shin (Assistant Professor, School of Biology).
A total of five 5K fellowships and 30 travel grants were awarded of the approximate 300 posters in the competition.

The Georgia Tech School of Biology is pleased to announce that three of our faculty won campus-wide teaching awards this year.  Dr. Jennifer Leavey is the recipient of the 2012 Class of 1940 W. Roane Beard Outstanding Teacher award.  This award recognizes extraordinary efforts in teaching, inspiration transmitted to students, direct impact and involvement with students, intellectual integrity and scholarship, and impact on post-graduate success of students. Dr. Linda Green is the recipient of the CETL Undergraduate Educator Award. This award recognizes teaching excellence in large classes, impact on multiple diverse student populations, educational innovations, educational outreach beyond the classroom and a passion for teaching and learning. Dr. Cara Gormally will be receiving the 2012 Innovation in Co-Curricular Education Award.  This award is given to faculty who increase student learning outside the traditional curriculum and help Georgia Tech achieve its strategic goal of graduating global citizens who can contribute to all sectors of society.  Dr. Cara Gormally was nominated in particular to recognize her collaborations with the Atlanta Botanical Gardens and the Piedmont Park Conservancy in her Honors Biological Principles and Honors Organismal Biology laboratory courses.  Congratulations!

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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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!

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.

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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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.

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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