High-throughput DNA sequencing technologies are leading to a revolution in how clinicians diagnose and treat cancer. The molecular profiles of individual tumors are beginning to be used in the design of chemotherapeutic programs optimized for the treatment of individual patients. The real revolution, however, is coming with the emerging capability to inexpensively and accurately sequence the entire genome of cancers, allowing for the identification of specific mutations responsible for the disease in individual patients.

There is only one downside. Those sequencing technologies provide massive amounts of data that are not easily processed and translated by scientists. That’s why Georgia Tech has created a new data analysis algorithm that quickly transforms complex RNA sequence data into usable content for biologists and clinicians. The RNA-Seq analysis pipeline (R-SAP) was developed by School of Biology Professor John McDonald and Ph.D. Bioinformatics candidate Vinay Mittal. Details of the pipeline are published in the journal Nucleic Acids Research.

“A major bottleneck in the realization of the dream of personalized medicine is no longer technological. It’s computational,” said McDonald, director of Georgia Tech’s newly created Integrated Cancer Research Center. “R-SAP follows a hierarchical decision-making procedure to accurately characterize various classes of gene transcripts in cancer samples.”

There are at least 23,000 pieces of RNA in the human genome that encode the sequence of proteins. Millions of other pieces help regulate the production of proteins. R-SAP is able to quickly determine every gene’s level of RNA expression and provide information about splice variants, biomarkers and chimeric RNAs. Biologists and clinicians will be able to more readily use this data to compare the RNA profiles or “transcriptomes” of normal cells with those of individual cancers and thereby be in a better position to develop optimized personal therapies.

Personalized approaches to cancer medicine are already in widespread use for a few “cancer biomarkers” including variants of the BRAC 1 gene that can be used to identify women with a high risk of developing breast and ovarian cancer.

“Our goal was to design a pipeline that is easily installable with parallel processing capabilities,” said Mittal. “R-SAP can make 100 million reads in just 90 minutes. Running the program simultaneously on multiple CPUs can further decrease that time.”

R-SAP is open source software, freely accessible at the McDonald Lab website.

“This is another example of Georgia Tech’s ability to merge computer technology with science to create an essential feature of next-generation bioinformatics tools,” said McDonald. “We hope that R-SAP will be a useful and user-friendly instrument for scientists and clinicians in the field of cancer biology.”

If we were able to resurrect a dinosaur in the laboratory today how could we be certain that the particular dinosaur actually existed in the distant past and does not simply represent some mutant frankensaurus?

Ongoing research at Georgia Tech aims to answer this question in an experimental approach by adding rigor to the methods and protocols used to resurrect components of ancient life.

Dr. Eric Gaucher, Associate Professor in the School of Biology, was recently awarded $700K from the National Science Foundation (NSF) to, for the first time, benchmark ancestral sequence reconstruction methods. Prof. Gaucher’s approach involves generating a known experimental phylogeny in the lab using fluorescent proteins cloned into bacteria. Generating such a “known” phylogeny with evolved sequences will, in turn, allow the group to test resurrection predictions since the true ancestral proteins are generated in the laboratory and are thus known.

An important component of the funding involves integrating evolutionary and molecular biology research into the greater Atlanta community. In collaboration with Dunwoody High school, Dr. Gaucher and Ryan Randall have developed a new Biotechnology curriculum whereby students are introduced to the connections between genotype and phenotype by evolving fluorescent proteins at the high school. In addition, The Gaucher Group annually hosts a team of Dekalb county high school students competing in the National Siemens Competition in Math, Science and Technology, that involves bioengineering of fluorescent proteins.

For his efforts, Prof. Gaucher is also a recent recipient of Georgia Tech’s Class of 1934 Teaching Award. This award is based on student evaluations and presented to faculty with the highest ratings in overall effectiveness in teaching.

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.

Research News & Publications Office
Georgia Institute of Technology
75 Fifth Street, N.W., Suite 314
Atlanta, Georgia 30308 USA

Media Relations Contacts: Abby Robinson (abby@innovate.gatech.edu; 404-385-3364) or John Toon (jtoon@gatech.edu; 404-894-6986)

Writer: Abby Robinson