Sarah Prehim, Ph.D.
Department of Environmental Health & Engineering
Johns Hopkins University

Abstract
Pollution from agricultural and urban areas fuels excessive algae and cyanobacteria growth, resulting in low oxygen dead-zones during decomposition. These microbial processes deteriorate water quality, reduce the habitat of many economically important aquatic animals and drive biogeochemical processes that alter nutrient cycling and generate potent greenhouse gases. Since population growth and climate change are expected to exacerbate these problems, understanding the dynamic chemical and microbial changes that impact aquatic dead-zones will aid modeling efforts that guide remediation strategies. I will present work to 1.) improve our understanding of the relationship between genes, populations and biogeochemical processes to improve predictive biogeochemical models and 2.) identify viral infections that contribute to cyanobacteria mortality with a novel high-throughput, culture-independent method, epicPCR. To investigate the relationship between microbial genes, populations and the biogeochemical processes they mediate, we used genome reconstruction from metagenomic data and a previously developed biogeochemical model to identify microbial populations implicated in major biogeochemical transformations in a model lake ecosystem. By reconstructing microbial genomes from complex assemblages of microorganisms, we gained insight into microbial processes in the lake and identified additional biogeochemical processes previously omitted from the model that could significantly alter the predicted biogeochemistry of the lake if active. We are also investigating the relationship between microbes, their genes and model predictions in a more complex ecosystem, the Chesapeake Bay. Viral infections will also be identified in the Chesapeake Bay through epicPCR. Identifying populations under the most viral pressure in the environment can improve models of biogeochemical cycling, providing a holistic picture of viruses in the trophic structure of marine environments. Yet, these efforts are stalled because the specific host a virus infects remains largely unknown for a majority of observed viruses. We hope to identify infections that contribute to ecological shifts and alter biogeochemical processes with our to high-throughput, culture-independent approach. Although this method is currently under development, preliminary data suggests the approach can identify specific infections in the environment and reveal the complex network of viral infections in natural microbial communities.

About the Preheim Lab
Research in the Preheim lab focuses on the ecology of microorganisms and microbial processes impacting water quality. Pathogens, low oxygen and harmful algal blooms (HABs) are the most common factors that impair in-land and coastal water bodies. Since population growth and climate change are expected to exacerbate these problems, understanding and modeling the interactions of microbial communities with the chemical, physical and biotic environment will improve of efforts to reduce the impact microbial processes have on water quality.

While traditional microbiology focuses on understanding microorganisms as they function in isolation, environmental microbiology focuses on the complex interactions they experience in most natural settings and the challenges of studying them within environmental systems. To achieve this, we observe microorganisms in various aquatic ecosystems using their genetic information as a proxy for their presence and distribution. We use high-throughput sequencing techniques to capture as much genetic signal from the microbial community as possible, coupled with bioinformatics and computational modeling to understand why microbial populations are present where and when they are. Eventually, the knowledge we gather from observing the structure and function of natural microbial communities will translate into the informed design of synthetic microbial communities or ecological management techniques.

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Leucine Zipper and the Zinc Fingers, the world's first genetically modified rock band, have been a staple of the Atlanta Science Festival. This summer they went into a studio and recorded their first album, Atomic Anarchy. The band celebrates the recording with a live performance.

Band leader Leucine Zipper is the clone of College of Science' Jennifer Leavey. The Zinc Fingers are clones of amphibian ecologist Joe Mendelson, chemist Michael Evans, and biologist Ben Prosser. 

This event is free; all ages welcome!

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Owen Beck, Ph. D.
Departments of Mechanical Engineering
School of Biological Sciences
Georgia Institute of
 Techology

Abstract
Athletes with transtibial amputations use running-specific prostheses to run. Running-specific prostheses are passive-elastic carbon-fiber devices that attach in-series to residual limbs. These devices are available across many different models, stiffness categories, and heights. Typically, prosthetic stiffness and height are set based on the respective manufacturer’s recommendation. This talk presents evidence that current prosthetic model, stiffness, and height recommendations do not optimize running biomechanics or economy for athletes with unilateral or bilateral transtibial amputations. Therefore, the distance-running performance of athletes with transtibial amputations can be further enhanced by updating prosthetic configuration recommendations.

About the Speaker
Owen Beck is a postdoc in Dr. Greg Sawicki’s Physiology of Wearable Robotics Lab. He has a B.S. in Kinesiology from Humboldt State University and a Ph.D. in Integrative Physiology from the University of Colorado Boulder. For his doctorate, Owen investigated how prosthetic configuration affects distance-running and sprinting performance for athletes with unilateral and bilateral transtibial amputations. At Georgia Tech, Owen’s research focuses on tuning assistive devices to biological leg characteristics, with the goal of augmenting locomotion performance.

Physiology Brownbag Seminars
The Physiology Group in the School of Biological Sciences hosts Brownbag Lunchtime Seminars twice a month on Wednesdays at noon in room 1253 of the Applied Physiology Building located at 555 14th Street NW, Atlanta, GA 30318. You are welcome to bring a lunch and join us as we ruminate with us on topics in Physiology! A full listing of seminars can be found at http://pwp.gatech.edu/bmmc/physiology-brownbag-seminars-fall-2018/.

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Peter Freddolino, Ph.D.
Department of Biological Chemistry
Department of Computational Medicine and Bioinformatics
University of Michigan

Abstract
Recent advances in high-throughput sequencing technology have yielded a huge increase in our knowledge of genomic sequences, but DNA sequence information remains meaningless without corresponding functional insight. It is only through a synthesis of computational approaches and high-throughput experiments that any meaningful headway can be made in the task of moving from genome sequence information to functional information at the scales of modern biology.We have recently launched two such initiatives, aimed at completely mapping the transcriptional regulatory logic and functional proteome of Escherichia coli. Using a broadly applicable non-specific method for mapping genome-wide protein occupancy, we have begun to identify the binding motifs, functions, and condition-dependent behavior of many cryptic E. coli transcription factors. In the process, we have also identified the presence of heterochromatin-like silenced regions on bacterial chromosomes, which we have found play a key role in regulating stress-response and virulence genes across several bacterial species. To address the problem of assigning functions to poorly annotated proteins without suitably close homologs for sequence-based annotation methods to be effective, we have recently developed a hybrid pipeline combining structural prediction/alignment, sequence alignment, and protein-protein interaction information to obtain combined structure predictions and functional annotations for entire proteomes. We find that our inclusion of structural information makes our workflow unusually strong in performance on difficult targets with limited sequence identity to annotated proteins. Application of our methods at the scale of entire proteomes yields a rich new source of information to seed detailed investigation of the functions of many previously mysterious protein-coding genes.

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Irene Chiolo, Ph.D.
Department of Biological Sciences
University of Southern California

ABSTRACT
Advancing our knowledge of heterochromatin repair is a high impact investment for improving human health: heterochromatin is a poorly characterized region that comprises nearly a third of the human genome; double-strand break (DSB) repair failures in this region affect not just specific genes but also genome-wide stability; and failures here are a high risk because of the abundance of repeated sequences that characterizes this domain. Our studies in Drosophila cells revealed that ‘safe’ DSB repair by homologous recombination relies on the relocalization of repair sites to the nuclear periphery before strand invasion. The mechanisms responsible for this movement were unknown. Our recent studies revealed that relocalization occurs by directed motion along striking nuclear actin filaments, which are assembled at repair sites by the Arp2/3 complex. Relocalization also requires nuclear myosins associated with the heterochromatin repair complex Smc5/6. This remarkable pathway is conserved in mammalian cells and its defects result in impaired heterochromatin repair, chromosome rearrangements and widespread genome instability. These findings identify de novo nuclear actin filaments and myosins as effectors of chromatin dynamics for heterochromatin repair and stability in multicellular eukaryotes.

About the Chiolo Lab

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Kaixiong Ye, Ph.D.
Department of Genetics
University of Georgia

ABSTRACT
Diet plays important roles in human evolution. Genetic adaptation to local diet assisted the global expansion of modern humans and contributed to geographically varying patterns of genetic variations. Identifying genetic variants adaptive to diet not only unravels the history of human evolution but also elucidates the genetic basis of current individual differences in dietary responses and metabolic disease risks. In this talk, I will present a research paradigm that integrates evolutionary genomics, functional genomics, genotype-phenotype association studies, and human clinical studies to identify nutritionally relevant genetic variants. I will present a novel case of genetic adaptation to diet: the recurrent dietary adaptation of FADS (Fatty Acid Desaturases) genes in multiple human populations by modulating the biosynthesis of omega-6 and omega-3 fatty acids. I will elaborate on the geographically and temporally varying adaptive patterns of FADS genes with genomic data from global populations and ancient samples (i.e., ancient DNA). I will further demonstrate the effects of these adaptive genetic variants on gene expression, fatty acid biosynthesis, and cardiovascular and inflammatory diseases. My research aims to assist the development of genome-informed Personalized Nutrition, which holds the promise of addressing the current public health burden of metabolic diseases by fulfilling individual nutritional needs. 

About the Ye Lab

Host: Patrick McGrath

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Libusha Kelly, Ph.D.
Department of Systems & Computational Biology
Department of Microbiology & Immunology
Albert Einstein College of Medicine

ABSTRACT
The microbiome is unique in individuals, associated with numerous diseases, and rapidly changeable by diet. Despite many studies profiling the microbiome in health and disease and insights into how our microbiomes can influence our physiology, to date the only condition for which we use the microbiome as a treatment is recurrent infection with the bacterium Clostridium difficile. I will discuss the promise and current limitations of using the microbiome as a clinical diagnostic and treatment tool. I will argue that we still need discovery-based basic research, particularly when it comes to the viruses that stalk the microbial allies and enemies in our bodies. We recently reported a novel family of tailless viruses that are major unrecognized killers of marine viruses with the Polz lab at MIT. With this work as a foundation, my lab discovered and is characterizing related, broadly distributed, viruses in the human microbiome. In the clinic, we aim to provide patients and their doctors with actionable information about their microbiomes to improve health and treatment plans. We recently reported that the microbiomes of different individuals have different capacities to activate irinotecan, an anti-cancer drug. We linked this differential metabolism to specific microbial carbohydrate active enzymes. We hypothesize that the life-threatening diarrhea that afflicts metastatic colorectal cancer patients who take this drug might also be caused by microbial turnover. We are working with oncologists to analyze the fecal microbiomes and metabolomes of patients receiving irinotecan. Our goal is to provide patients with early warnings that they are likely high irinotecan metabolizers, enabling prophylactic diarrheal treatment and closer monitoring. More broadly, we are constructing a chemical landscape of the gut to identify new microbe/drug/food interactions that influence drug efficacy and toxicity and suggest unrecognized off-target effects driven by microbial activity.

About the Kelly Lab

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Nick Willett, Ph. D.
Department of Orthopedics
School of Medicine
Emory University

Abstract
The field of tissue engineering and regenerative medicine has long integrated fundamental principles of stem cell biology, biomaterials and mechanical engineering to better design new tissues. As regenerative technologies become more prevalent in the clinic, however, it is becoming increasingly apparent that the rehabilitation regimen and management of the intervention after the delivery/implantation is just as critical to the success of the implant as the fundamental technology itself. The research of the Willett lab focuses on a systems integration approach to musculoskeletal disease and regenerative engineering by applying novel imaging and engineering techniques to clinical motivated challenges. The lab’s current work has three main thrusts: (i) cell and biologic therapies for the healing of large bone and muscle defects, (ii) multi-scale mechanical regulation of bone regeneration, and (iii) intra-articular therapeutic delivery for post-traumatic osteoarthritis. This seminar will discuss fundamental principles to Regenerative Rehabilitation and show how we utilize these rehabilitation principles to enhance the therapeutic efficacy of regenerative and tissue engineering therapies.

About the Speaker
Nick Willett is an Assistant Professor in the Department of Orthopaedics at Emory University and runs a research lab with a focus on engineering strategies for musculoskeletal regeneration and rehabilitation. Nick has a secondary appointment in the joint Biomedical Engineering Department between Emory University and Georgia Institute of Technology as well as an appointment in the Research Division at the Atlanta VA Medical Center. Nick performed his postdoctoral training at the Georgia Institute of Technology working with Prof. Robert Guldberg in Mechanical Engineering. He received his Ph.D. (2010) in Biomedical Engineering from the joint program between Georgia Institute of Technology and Emory University. Prior to his graduate work he received his B.S. (2005) in Mechanical Engineering from the University of Colorado at Boulder. Nick has been an active member of TERMIS since 2011 and is a member of the TERMIS thematic group on Regenerative Rehabilitation. He is the Emory Representative for the International Consortium on Regenerative Rehabilitation and was on the scientific organizing committee for the 2016 Alliance for Regenerative Rehabilitation Research and Training, Regenerative Rehabilitation Symposium. He has received numerous awards and honors including the Gandy Diaz Teaching Fellowship from Georgia Tech, the Young Investigator Award from the American Society for Bone and Mineral Research, and the Ruth L. Kirschstein National Research Service Award Postdoctoral Fellowship from the NIH. Nick has published 24 peer reviewed manuscripts—including multiple in Tissue Engineering—and 4 book chapters. He has served as a reviewer for grant proposals for the Arthritis Foundation and applications for the Petit Scholars program at Georgia Tech. He currently reviews for numerous journals including Tissue Engineering, Biomaterials, and Acta Biomaterialia, among numerous others. The research of the Willett lab focuses on a systems integration approach to musculoskeletal disease and regenerative engineering by applying novel imaging and engineering techniques to clinical motivated challenges. The lab’s current work has three main thrusts: (i) cell and biologic therapies for the healing of large bone and muscle defects, (ii) multi-scale mechanical regulation of bone regeneration, and (iii) intra-articular therapeutic delivery for post-traumatic osteoarthritis. The Willett lab sits at the interface between the engineering and clinical disciplines and is composed of engineering students, medical students, residents, and fellows.

Physiology Brownbag Seminars
The Physiology Group in the School of Biological Sciences hosts Brownbag Lunchtime Seminars twice a month on Wednesdays at noon in room 1253 of the Applied Physiology Building located at 555 14th Street NW, Atlanta, GA 30318. You are welcome to bring a lunch and join us as we ruminate with us on topics in Physiology! A full listing of seminars can be found at http://pwp.gatech.edu/bmmc/physiology-brownbag-seminars-fall-2018/.

Host: Young C. Jang, Ph.D.

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Erol Akçay, Ph.D.
Department of Biology
University of Pennsylvania

Abstract
Evolution of social behaviors is one of the most fascinating and active fields of evolutionary biology. During the past half century, social evolution theory developed into a mature field with powerful tools to understand the dynamics of social traits such as cooperation under a wide range of conditions. But when these conditions themselves evolve remains a largely open question, which I argue represents the next step in the development of social evolution theory. In this talk, I will present a few examples of such co-evolutionary dynamics leading to unexpected results. In particular I will talk about two models where social network structure co-evolves with (i) a social trait such as cooperation, and (ii) with cumulative culture, and a third model where the strategies individuals play in a game co-evolves with the resource environment that determines with game is being played.

About the Akçay Lab

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THIS SEMINAR WAS CANCELED DUE TO WEATHER.

Michael Hecht, Ph.D.
Department of Chemistry
Princeton University

ABSTRACT
A key goal of synthetic biology is to design novel proteins that fold and function in vivo.  A particularly challenging objective would be to produce non-natural proteins that don’t merely generate interesting phenotypes, but which actually provide essential functions necessary for the growth of living cells. Successful design of such life-sustaining proteins would represent a step toward constructing “artificial proteomes” of non-natural sequences.  In initial work toward this goal, we designed large libraries of novel proteins encoded by millions of synthetic genes.  Many of these new proteins fold into stable 3-dimensional structures; and many bind biologically relevant metals, metabolites, and cofactors.  Several of the novel proteins function in vivo providing essential activities necessary to sustain the growth of E. coli cells. In some cases, these novel proteins rewire gene regulation and alter the expression of endogenous genes.  In other cases, the novel protein sustains cell growth by functioning as bona fide enzyme that catalyzes an essential biochemical reaction. These results suggest that (i) the molecular toolkit of life need not be limited to sequences that already exist in nature, and  (ii) artificial genomes and proteomes might be built from non-natural sequences.

About the Hecht Lab

Host: Frank Rosenzweig

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