The meeting was held in Vancouver, Washington.

A new study provides a mechanistic explanation of how ribonucleotides embedded in genomic DNA are recognized and removed from cells. Two mechanisms, enzymes called ribonucleases (RNases) H and the DNA mismatch repair system, appear to interplay to root out the RNA components.

"We believe this is the first study to show that cells utilize independent repair pathways to remove mispaired ribonucleotides embedded in chromosomal DNA, which can be sources of genetic modification if not removed," said Francesca Storici, an assistant professor in the School of Biology at the Georgia Institute of Technology. "The results also highlight a novel case of genetic redundancy, where the mismatch repair system and RNase H mechanisms compete with each other to remove misincorporated ribonucleotides and restore DNA integrity."

The findings were reported Dec. 4, 2011 in the advance online publication of the journal Nature Structural & Molecular Biology. The research was supported by the Georgia Cancer Coalition, National Science Foundation and Georgia Tech Integrative BioSystems Institute.

Storici and Georgia Tech biology graduate students Ying Shen and Kyung Duk Koh conducted the study in collaboration with Bernard Weiss, a professor emeritus in the Department of Pathology and Laboratory Medicine at Emory University.

"We wanted to understand how cells of the bacterium Escherichia coli and the yeast Saccharomyces cerevisiae tolerate the presence of different ribonucleotides embedded in their genomic DNA. We found that the structure of a ribonucleotide tract embedded in DNA influenced its ability to cause genetic mutations more than the tract's length," said Storici.

With double-stranded DNA, when wrong bases are paired or one or few nucleotides are in excess or missing on one of the strands, a mismatch is generated. If mismatches are not corrected, they can lead to mutations.

The researchers found that single mismatched ribonucleotides in chromosomal DNA were removed by either the mismatch repair system or RNase H type 2. Mismatched ribonucleotides in the middle of at least four other ribonucleotides required RNase H type 1 for removal.

"We were excited to find that a DNA repair mechanism like mismatch repair was activated by RNA/DNA mismatches and could remove ribonucleotides embedded in chromosomal DNA," explained Storici. "In future studies, we plan to test whether other DNA repair mechanisms, such as nucleotide-excision repair and base-excision repair, can also locate and remove ribonucleotides in DNA."

Using gene correction assays driven by short nucleic acid polymers called oligonucleotides, the researchers showed that when ribonucleotides embedded in DNA were not removed, they served as templates for DNA synthesis and produced a mutation in the DNA. If both the mismatch repair system and RNase H repair mechanisms are disabled, ribonucleotide-driven gene modification increased by a factor of 47 in the yeast and 77,000 in the bacterium.

Defects in the mismatch repair system are known to predispose a person to certain types of cancer. Because the mismatch repair system is conserved from unicellular to multicellular organisms, such as humans, this study's findings open up the possibility that defects in the mismatch repair system could have consequences more critical than previously thought given the newly identified function of mismatch repair to target RNA/DNA mispairs.

The results also provide new information on the capacity of RNA to play an active role in DNA editing and remodeling, which could be the basis of an unexplored process of RNA-driven DNA evolution.

This project was supported by the National Science Foundation (NSF) (Award No. MCB-1021763). 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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Dr. Kacar will continue her research that combines paleogenetics (reconstructing ancestral states of genes based on phylogenetics) with experimental evolution (monitoring evolution in action) in bacteria. The NASA Astrobiology Program, element of the NASA Postdoctoral Program (NPP), provides opportunities for Ph.D. scientists and engineers of unusual promise and ability to perform research on problems largely of their own choosing, yet compatible with the research interests of the NASA Astrobiology Program. For more info: http://astrobiology.nasa.gov/nai/funding/nai-postdoctoral-fellowship-program/

As an amphibian taxonomist, he describes the sobering reality of "discovering" species new to science after they have already gone extinct-the discovery being made from the shelves of natural history museums, not in their former cloud forest habitats. These discoveries resemble paleontology, but they are so recent that the term does not fit. Mendelson suggests the term "Forensic Taxonomy" instead. Dr. Mendelson also is Curator of Herpetology at Zoo Atlanta and current President of the Society for the Study of Amphibians and Reptiles. He co-teaches Georgia Tech Biology undergraduates a research methods course at Zoo Atlanta.

Much of this research was conducted in the Parker H. Petit Institute for Bioengineering & Bioscience at Georgia Tech.

The research team lead by Georgia Tech Professor of BiologyJohn McDonald has verified that while the DNA sequence of genes between humansand chimpanzees is nearly identical, there are large genomic “gaps” in areas adjacentto genes that can affect the extent to which genes are “turned on” and “turnedoff.” The research shows that these genomic “gaps” between the two species are predominantlydue to the insertion or deletion (INDEL) of viral-like sequences calledretrotransposons that are known to comprise about half of the genomes of bothspecies. The findings are reported in the most recent issue of the online,open-access journal Mobile DNA.

“These genetic gaps have primarily been caused by theactivity of retroviral-like transposable element sequences,” said McDonald. “Transposableelements were once considered ‘junk DNA’ with little or no function. Now itappears that they may be one of the major reasons why we are so different fromchimpanzees.”

McDonald’s research team, comprised of graduate students NaliniPolavarapu, Gaurav Arora and Vinay Mittal, examined the genomic gaps in bothspecies and determined that they are significantly correlated with differencesin gene expression reported previously by researchers at the Max PlankInstitute for Evolutionary Anthropology in Germany.

“Our findings are generally consistent with the notion that themorphological and behavioral differences between humans and chimpanzees arepredominately due to differences in the regulation of genes rather than todifferences in the sequence of the genes themselves,” said McDonald.

The current analysis of the genetic differences betweenhumans and chimpanzees was motivated by the group’s previously publishedfindings (2009) that the higher propensity for cancer in humans vs. chimpanzeesmay have been a by-product of selection for increased brain size in humans.

He and his collaborators are using ecological interactions as leads to discover bioactive compounds in marine algae and invertebrates with potential as pharmaceuticals. On this trip Dr. Hay is writing a blog for the New York Times (http://scientistatwork.blogs.nytimes.com/2011/10/12/a-disappearing-underwater-world/), so you can follow along with him and his team as they explore the coral reefs of Fiji.

Theregenerative power of tissues and organs declines as we age. The modern daystem cell hypothesis of aging suggests that living organisms are as old as are itstissue specific or adult stem cells. Therefore, an understanding of themolecules and processes that enable human adult stem cells to initiateself-renewal and to divide, proliferate and then differentiate in order torejuvenate damaged tissue might be the key to regenerative medicine and an eventualcure for many age-related diseases. A research groupled by the Buck Institute for Research on Aging in collaboration with the Georgia Institute of Technology, conducted the study thatpinpoints what is going wrong with the biological clock underlying the limited division ofhuman adult stem cells as they age.

“Wedemonstrated that we were able to reverse the process of aging for human adultstem cells by intervening with the activity of non-protein coding RNAs originated fromgenomic regions once dismissed as non-functional  ‘genomic junk’,” said Victoria Lunyak, associate professor at the Buck Institutefor Research on Aging.

Adultstem cells are important because they help keep human tissues healthy byreplacing cells that have gotten old or damaged. They’re also multipotent,which means that an adult stem cell can grow and replace any number of bodycells in the tissue or organ they belong to. However, just as the cells inthe liver, or any otherorgan, can get damaged over time, adult stem cells undergo age-related damage. And when this happens, the bodycan’t replace damaged tissue as well as it once could, leading to a host of diseasesand conditions. But if scientists can find a way to keep these adult stem cellsyoung, they could possibly use these cells to repair damaged heart tissue aftera heart attack; heal wounds; correct metabolic syndromes; produce insulin forpatients with type 1 diabetes; cure arthritis and osteoporosis and regeneratebone.

Theteam began by hypothesizing that DNA damage in the genome of adult stem cells wouldlook very different from age-related damage occurring in regular body cells. They thoughtso because body cells are known to experience a shortening of the caps found atthe ends of chromosomes, known as telomeres. But adult stem cells are known tomaintain their telomeres. Much of the damage in aging is widely thought to be aresult of losing telomeres. So there must be different mechanismsat play that arekey to explaining how aging occurs in these adult stem cells, they thought.

Researchersused adult stem cells from humans and combined experimental techniques withcomputational approaches to study the changes in the genome associated withaging.  They compared freshly isolated human adult stem cells from young individuals, which canself-renew, to cellsfrom the same individuals that were subjected to prolonged passaging inculture. This accelerated model of adult stem cell aging exhausts the regenerativecapacity of the adult stem cells. Researchers looked at the changes in genomic sites that accumulateDNA damage in both groups.

“Wefound the majority of DNA damage and associated chromatin changes that occurredwith adult stem cell aging were due to parts of the genome known as retrotransposons,”said King Jordan, associate professor in the School of Biology at Georgia Tech.

“Retroransposonswere previously thought to be non-functional and were even labeled as ‘junk DNA’, but accumulating evidenceindicates these elements play an important role in genome regulation,” headded.

Whilethe young adult stem cells were able to suppress transcriptional activity ofthese genomic elements and deal with the damage to the DNA, older adult stem cells werenot able to scavenge this transcription. New discovery suggests that this event is deleteriousfor the regenerativeability of stem cells and triggers a process known as cellular senescence.

“Bysuppressing the accumulation of toxic transcripts from retrotransposons, wewere able to reverse the process of human adult stem cell aging in culture,”said Lunyak.

“Furthermore,by rewinding the cellular clock in this way, we were not only able torejuvenate ’aged’ human stem cells, but to our surprise we were able to resetthem to an earlier developmental stage, by up-regulating the “pluripotency factors” – the proteinsthat are critically involved in the self-renewal of undifferentiated embryonicstem cells.” she said.

Nextthe team plans to use further analysis to validate the extent to which therejuvenated stem cells may be suitable for clinical tissue regenerativeapplications.

Thestudy was conducted by a team with members from the Buck Institute for Researchon Aging, the Georgia Institute of Technology, the University of California,San Diego, Howard Hughes Medical Institute, Memorial Sloan-Kettering CancerCenter, International Computer Science Institute, Applied Biosystems andTel-Aviv University.

Citation:
Inhibitionof activated pericentromeric SINE/Alu repeat transcription in senescent human
adult stem cells reinstates self-renewal.  Cell Cycle, Volume 10, Issue 17, September 1, 2011

Written byDavid Terraso, Georgia Tech/Kris Rebillot, Buck Institute

Scientistshave studied a yeast protein called Lsb2 that can promote spontaneous prionformation. This unstable, short-lived protein is strongly induced by cellularstresses such as heat. Lsb2’s properties also illustrate how cells havedeveloped ways to control and regulate prion formation. The results arepublished in the July 22 issue of the journal Molecular Cell.

Thestudy was conducted by members of the Center for Nanobiology of the MacromolecularAssembly Disorders (NanoMAD) which is made up of scientists from the GeorgiaInstitute of Technology and Emory University. Scientists from the NationalInstitues of Health and the University of Illinois at Chicago also contributedto the study. The first author is senior associate Tatiana Chernova, PhD atEmory.

Theaggregated, or amyloid, forms of proteins connected with several otherneurodegenerative diseases such as Alzheimer’s, Parkinson’s and Huntington’scan, in some circumstances, act like prions. So the findings provide insightinto how the ways that cells deal with stress might lead to poisonous proteinaggregation in human diseases.

“Adirect human homolog of Lsb2 doesn’t exist, but there may be a protein thatperforms the same function,” said Keith Wilkinson, professor of biochemistry atEmory University School of Medicine. “The mechanism may say more about othertypes of protein aggregates than about classical prions in humans. Thismechanism of seeding and growth may be more important for aggregate formationin diseases such as Huntington’s.”

Lsb2does not appear to form stable prions by itself. Rather, it seems to bind toand encourage the aggregation of another protein, Sup35, which does formprions.

“Ourmodel is that stress induces high levels of Lsb2, which allows the accumulationof misfolded prion proteins,” Wilkinson said. “Lsb2 protects enough of thesenewborn prion particles from the quality control machinery for a few of them toget out.”

Incontinuation of previous research by Yury Chernoff, director of NanoMAD andprofessor in the School of Biology at Georgia Tech, the new data also show thatin addition to promoting new prions, Lsb2 strengthens existing prions duringstress.

"Littleis known about physiological and environmental conditions influencing amyloiddiseases in humans," said Chernoff. "Therefore, prophylacticmeasures, which could end up being more effective than therapies, areessentially non-existant. We hope that yeast model will help to fill thisgap."

Theresearch was supported by the National Institutes of Health.

Writtenby: Emory University and the Georgia Institute of Technology

A meta-analysis of the interactions shows that the infection patterns exhibit a nested structure, with hard-to-infect bacteria infected by generalist viruses and easy-to-infect bacteria attacked by both generalist and specialist viruses.

"Although it is well known that individual viruses do not infect all bacteria, this study provides an understanding of possibly universal patterns or principles governing the set of viruses able to infect a given bacteria and the set of bacteria that a given virus can infect," said Joshua Weitz, an assistant professor in the School of Biology at the Georgia Institute of Technology.

Discovering this general pattern of nested bacteria-virus infection could improve predictions of microbial population dynamics and community assembly, which affect human health and global ecosystem function. Knowing the patterns of which bacteria are susceptible to which viruses could also provide insights into strategies for viral-based antimicrobial therapies.

The results of the meta-analysis were published June 27, 2011 in the early edition of the journal Proceedings of the National Academy of Sciences. The work was sponsored by the James S. McDonnell Foundation, the Defense Advanced Projects Research Agency and the Burroughs Wellcome Fund.

Georgia Tech physics graduate student Cesar Flores, Michigan State University zoology graduate student Justin Meyer, Georgia Tech biology undergraduate student Lauren Farr, and postdoctoral researcher Sergi Valverde from the University Pompeu Fabra in Barcelona, Spain also contributed to this study.

The research team compiled 38 laboratory studies of interactions between bacteria and phages, the viruses that infect them. The studies represented approximately 12,000 distinct experimental infection assays across a broad spectrum of diversity, habitat and mode of selection. The studies covered a 20-year period and included hundreds of different host and phage strains.

The researchers converted each study into a matrix with rows containing bacterial types, columns containing phage strains, and cells with zeros or ones to indicate whether a given pair yielded an infection. Then they applied a rigorous network theory approach to examine whether the interaction networks exhibited a nonrandom structure, conformed to a characteristic shape, or behaved idiosyncratically -- making them hard to predict.

Of the 38 studies, the researchers found 27 that showed significant nestedness. Nestedness was measured by the extent to which phages that infected the most hosts tended to infect bacteria that were infected by the fewest phages. The researchers used statistical tests to rule out forms of bias. However, because the majority of the data consisted of closely related species, the researchers anticipate that more complex patterns of infection may form with species with more genetic diversity.

"Considering the large range of taxa, habitats and sampling techniques used to construct the matrices, the repeated sampling of a nested pattern of host-phage infections is salient, but the process driving the nestedness is not obvious. The pattern suggests a common mechanism or convergent set of mechanisms underlying microbial co-evolution and community assembly," explained Weitz.

The researchers examined three hypotheses to explain the nestedness pattern based on biochemical, ecological and evolutionary principles, but found that additional experiments will be required to determine why this pattern occurs so often.

This meta-analysis demonstrated the utility of network methods as a means for discovering novel interaction patterns. According to the researchers, viewing host-phage interaction networks through this type of unifying lens more often will likely unveil other hidden commonalities of microbial and viral communities that transcend species identity.

This research was supported in part by the Defense Advanced Research Projects Agency (DARPA) (Award No. HR0011-09-1-0055). The content is solely the responsibility of the principal investigator and does not necessarily represent the official views of DARPA.

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Led by PI Prof. Ian Akyildiz (ECE), with co-PI's Profs. Faramarz Fekri (ECE), Craig Forest (ME), Brian Hammer (Bio), and Raghupathy Sivakumar (ECE), the team will undertake a 4 year effort (2011-2015) to model, simulate, and experimentally validate with bacteria the fundamental limits and protocols for molecular communication. The grant was awarded through the Computer and Network Systems (CNS) program within the Directorate for Computer & Information Science and Engineering (CISE) at the National Science Foundation.

“We found that strategies thatprey use to defend themselves against predators can increase theirsusceptibility to infection by parasites,” said Meghan Duffy, assistantprofessor in Georgia Tech’s School of Biology.

Duffy,along with colleagues at the University of Illinois at Urbana-Champaign andIndiana University, took a look at a small aquatic crustacean, Daphnia dentifera, a water flea known tobe an important part of freshwater ecosystems. They exposed the crustacean tochemicals emitted by one of its predators, a phantom midge larva known as Chaoborus, known to feed on it. When theDaphnia detected those chemicals itgrew larger, making it harder for its predator to get its mouth around it.

“Unfortunatelyfor the Daphnia, this defense against predationmakes them more vulnerable to parasitism,” said Duffy.

That’sbecause while growing larger keeps Daphniasafe from Chaoborus, it actuallymakes it more susceptible to a virulent yeast parasite, known as Metschnikowia. When Daphnia senses a threat from its predator and grows larger, it ends up consuming more of these parasitic yeasts thanit does when normal size. When the yeast infects the crustacean, it kills it,causing the dead animal to release yeast spores as it decomposes. The largerthe host, the more spores it releases back into the water to prey on other Daphnia.

“Sincethey need to grow larger to defend themselves against the predator but theopposite to defend against the parasite, they're sort of stuck between a rockand a hard place,” she added.

Duffyreasons that this occurs because the predators are common year-round, while theparasites are more episodic in nature, with their populations expanding inepidemics only in the fall and not even yearly. This results in long periods ofpredation in the absence of the parasite, which probably explains why theyrespond so strongly to defend themselves against the predator even though itdecreases their defenses against the yeast, she added.

“Whilesome have argued for increasing predator densities to control disease, ourresults suggest that it is important to consider the indirect effects ofpredators, such as the one we found in which trying to avoid one enemyincreases the hosts vulnerability to another,” said Duffy.

This research wasfunded by the National Science Foundation.

By using RNA-containing oligos, the Storici's team (Assistant Professor, School of Biology) has found that RNA can function as a template for DNA synthesis without being reverse transcribed into cDNA, not only in yeast but also in Escherichia coli and in the human embryonic kidney (HEK-293) cells. These findings establish that a direct flow of genetic information from RNA to DNA can occur in organisms as diverse as bacteria and humans, and thus, it can be a significant source of genetic variation. The goal of future research is to understand the mechanisms by which RNA can directly transfer information to the DNA of cells and to reveal the circumstances in which RNA information can flow to DNA.
The study, which was published April 14 in the advance online edition of the journal Mutation Research, was conducted by a group of graduate and undergraduate students in the Storici's lab in the School of Biology at Georgia Tech in collaboration with Bernard Weiss from Emory University School of Medicine.

Fecal pollution of surface waters is measured by the concentration of E. coli bacteria in the water because E. coli is believed to live only in the intestines and waste of humans and other warm-blooded animals, and quickly dies outside its host. The presence of E. coli in water also serves as a marker for other potentially more harmful organisms that may accompany it. Positive E. coli tests may lead to the summertime closing of beaches and other recreational bodies of water.

In this new study, researchers report identifying and sequencing the genomes of nine strains of E. coli that have adapted to living in the environment independent of warm-blooded hosts. These strains are indistinguishable from typical E. coli based on traditional tests and yield a positive fecal coliform result though researchers say they may not represent a true environmental hazard.

"The basis for E. coli’s widespread use as a fecal pollution indicator is the traditional thinking that E. coli cannot survive for extended periods outside a host or waste, but this study indicates that's not true," said Kostas Konstantinidis, an assistant professor in the Georgia Tech School of Civil and Environmental Engineering. "These results suggest the need to develop a new culture-independent, genome-based coliform test so that the non-hazardous environmental types of E. coli are not counted as fecal contamination."

A paper describing the research was published April 11 in the early edition of the journal Proceedings of the National Academy of Sciences. The work was sponsored by the National Science Foundation and the National Institutes of Health.

Konstantinidis and Georgia Tech School of Biology graduate student Chengwei Luo compared the genomes of 25 different strains of E. coli and close relatives, which were sequenced by the Center for Microbial Ecology at Michigan State University, the Broad Institute in Massachusetts, or were publicly available in the National Center for Biotechnology Information database. Nine strains that were recovered primarily from environmental sources encoded all genes required for classification as E. coli.

"The orders-of-magnitude higher abundances of the group of organisms represented by these nine strains in environmental samples relative to those in human feces and the clinic indicate that they represent truly environmentally adapted organisms that are not associated primarily with mammal hosts," explained Konstantinidis, who also holds a joint appointment in the Georgia Tech School of Biology.

By comparing the full genomes of the samples, the Georgia Tech researchers identified 84 genes specific to or highly enriched in the genomes of the environmental E. coli and 120 genes specific to the strains commonly found in the gastrointestinal tract of healthy humans, which are called commensal E. coli. They also detected recent genetic exchange of core genes within the environmental E. coli and within the commensal strains, but not from commensal genomes to their environmental counterparts.

The environment-specific bacteria included genes important for resource acquisition and survival in the environment, such as the genes required to utilize energy sources and to break down dead cellular material. In contrast, the gastrointestinal E. coli included several genes involved in the transport and use of nutrients thought to be abundant in the gut.

"The genomic data suggest that the environmental E. coli are better at surviving in the external environment, but are less effective competitors in the gastrointestinal tract than commensal E. coli, which tells us that the environmental bacteria are highly unlikely to represent a risk to public health," explained Konstantinidis.

Collectively, this data also indicates that the environmental E. coli strains represent a distinct species from their commensal E. coli counterparts even though they are identified as E. coli based on the standard taxonomic methods. This work is consistent with a more stringent and ecologic definition for bacterial species than the current definition and suggests ways to start replacing traditional, culture-based approaches for defining diagnostic phenotypes of new species with genomic-based procedures.

The scientific, medical, regulatory and legal communities expect species to reasonably reflect the traits and habitat of an organism -- especially an organism like E. coli that has ramifications for diagnostic microbiology and for assessing fecal pollution of natural ecosystems. Efforts toward a more refined definition of this bacterial species are needed, according to Konstantinidis.

This study's findings provide a way to start redefining E. coli species and testing for fecal contamination with procedures based on genomics and ecology.

"We are now working to develop a molecular assay that uses the gastrointestinal-specific genes as robust biomarkers to count commensal E. coli cells in environmental samples more accurately than current methods," added Konstantinidis.

This project is supported by a National Science Foundation (NSF) award to Georgia Tech and Michigan State University (Award No. DEB0516252) and a National Institutes of Health (NIH/NIAID) award to the Broad Institute (Award No. HHSN2722009000018C). The content is solely the responsibility of the principal investigators and does not necessarily represent the official views of NSF or NIH.

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