People

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Principal Investigator

Lingchong You

Post-doctoral students

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Zhuojun Dai

Graduate Institution: The Chinese University of Hong Kong, China (PhD, Chemistry, 2015)

Research Description: Currently I am working on the generation of stimulus-sensitive microcapsules to encapsulate the bacterial. Ultimately we would like to build a general platform to achieve the efficient production and delivery of the effector.

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Tatyana (Tanya) Sysoeva

Graduate Institution: Pennsylvania State University (PhD, Biochemistry, Microbiology and Molecular Biology, 2011)

Research Description: My research interests focus on horizontal gene transfer in microbial communities. In particular, I aim to understand how the host-related stresses and human commensal microbiota affect HGT in bacterial pathogens. For example, I analyze how human uropathogens contribute to spreading of the antibiotic resistance genes in context of the urinary microbiome. In addition, I work to develop approaches for HGT detection and quantification using a combination of synthetic and molecular biology tools.

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Nan Luo

Graduate Institution: University of California, Riverside (PhD, Plant Biology, 2016)

Research Description: My research interests focus on system biology and mathematical modeling of biological systems. Currently I am working on developing new methodologies combining synthetic biology and modeling to rationally design and create patterns in petri dishes. Ultimately I wish to discover new design principles underlying pattern formation, and use the concepts to understand the development and patterning of higher organisms.

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Associates in Research

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Shangying Wang

Graduate Institution: Duke University (PhD, Physics, 2014)

Research Description: I am specialized in mathematical analysis and computational modeling. My current research interest is to use neural network to fast predict self-organized ring patterns in engineered bacteria. Although artificial intelligence is almost everywhere in our daily life, it is not been fully employed in biological research area. My work is to make biological lab more 'intelligent' in data generation, data analysis as well as data prediction.

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Graduate Students

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Will (Yangxiaolu) Cao

Undergraduate Institution: Tsinghua University, China (BS Mechanical Engineering, 2012)

Reseach Description: Currently I am engineering bacteria to fabricate inorganic materials. Ultimately, this projeect has energy applications.

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Carolyn Zhang

Undergraduate Institution: University of California, San Diego (BS Biochemistry and Cell Biology, Computer Science Minor 2014)

NSF Graduate Fellow

Reseach Description: The rise of antibiotic resistance has become a global health crisis as microbes develop numerous mechanisms to resist existing antibiotics. There are two major mechanisms by which bacteria become resistant, either through mutations in the genome or the acceptance of genes conferring resistance by horizontal gene transfer (HGT). Both have provided bacteria with varying levels in their capability to quickly evolve resistance in response to newly developed antimicrobial compounds. As a result, rapid and accurate diagnostic techniques are required for the strain and resistance identification of clinical samples. However, there exist numerous limitations with current methods. As a result, we intend to use the rich temporal dynamics of bacterial growth for both strain and antibiotic resistance identification.

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Feilun Wu

Undergraduate Institution: University of Virginia (BS Biomedical Engineering, 2014)

Research Description: Synthetic biology approaches serve as great tools for understanding our microbiome. A fundamental aspect of our microbiome is its microbial population dynamics. I am currently working on a synthetic gene circuit that emulates mutualistic relationship, which is one of the main symbiosis relationships that contribute to microbial population dynamics in microbiome and other microbial ecosystems. This mutualism circuit could draw novel insights into microbial ecology and evolution. Except for scientific implications, this circuit may also increase the robustness and stability of engineered multi-species microbial consortia and serve as a platform for division of labor of complex gene circuits. In addition, mutualism circuit may as well be implemented as a safeguard mechanism that eliminates engineered bacteria if they escape from controlled environments such as microbial swarmbots.

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Ryan Tsoi

Undergraduate Institution: University of California, Berkeley (BS Chemical Engineering, Bioengineering Minor 2014)

Integrative Bioinformatics for Investigating and Engineering Microbiomes (IBIEM) NSF Fellowship

Research Description: Microbial consortia are home to diverse members, some of which cooperate with one another to perform complex tasks via a division of labor (DOL). In DOL, different cells or populations each perform a different part of the overall function, which, depending on the application, can either increase or reduce the system’s performance relative to a homogenous population. As a result, I am currently investigating the conditions that favor DOL in microbial communities. This has implications in both improving our understanding of natural consortia and helping guide design of synthetic multi-population systems.

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Jonathan Bethke

Undergraduate Institution: University of Virginia (BS Biology, 2013)

Integrative Bioinformatics for Investigating and Engineering Microbiomes (IBIEM) NSF Fellowship

Research Description: My work is centered on horizontal gene transfer, specifically conjugation among antibiotic resistant pathogens in the Enterobacteriaceae family (e.g. E. coli, Salmonella, and Klebsiella). Through a merger of genotypic, phenotypic, and clinical data, I seek to understand the overarching characteristics of dominant pathogens and mobile elements. Once these are known, novel predictive and preventative strategies may be developed to curtail the spread of pathogens and resistance.

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Teng Wang

Undergraduate Institution: Peking University, China (BS Life Science, 2015)

Research Description: Currently I am working on modeling the plasmid dynamics of a population with multiple species. First, I established a mathematical model describing the distribution of plasmids across the community. Then, I am using this model to explore how the factors, like conjugation rates, the metabolic burden of the plasmids and the structure of the community, influence the plasmid distribution patterns.

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Helena Ma

Undergraduate Institution: Princeton University (BS Chemical Engineering, 2017)

Research Description: My research is focused on combating the growing problem of antibiotic resistance. Despite the threat it poses, the development of new antibiotics has not kept pace with the spread of resistance. Consequently, finding ways to reposition currently approved drugs, to which resistance may have already developed, can extend their useful life and increase the treatment options available to physicians. One way to reposition drugs is to use them in combination with resistance-inhibiting therapies. I am currently investigating ways to optimize such combination therapies to maximize efficacy and minimize antibiotic use and adverse side effects.

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Hye-in (Hailey) Son

Undergraduate Institution: University of California, Berkeley (BS Bioengineering Engineering, 2015)

Research Description: Microbial antibiotic resistance is a rising global health concern. I am interested in understanding the dynamics of antibiotic resistance spread among bacterial cells. This study may contribute to the development of a novel therapeutic method to reverse antibiotic resistance.

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Masters Students

Meidi Wang

Undergraduate Institution: Zhejiang University, China (BS Biomedical Engineering, 2016)

Research Description: I am currently working with Feilun to build a multiplexed antibiotic screening platform. I utilize micro-encapsulation to form single clones, barcode and next generation sequencing to quantify the different strains. This platform can reduce the cost while increase the efficiency of platform, which are the key limitations of current drug screening platforms.

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Xiao Peng

Undergraduate Institution: Beijing Institute of Technology, China (BS Electrical Engineering, 2017)

Research Description: I am currently working with Carolyn to establish a phage library for further clincal applications and other possible fields.

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Undergraduate Students

Joe Kreitz

Major: Biology Minors: Chemistry, Computational Biology & Bioinformatics

Howard Hughes Fellow

Dean's Fellow

Research Description: I am broadly interested in expanding the role of bacteriophage technology in clinical, industrial, as well as scientific settings. In addition to its usefulness for synthetic biologists as an effective method for controlling individual populations within synthetic microbial communities, this remarkable technology has also experienced increased interest recently due to its efficacy in the fight against antibiotic-resistant bacteria. Currently, I am developing and optimizing a library of novel phage-based therapeutics with the hopes of addressing multidrug-resistant pulmonary lung infections in cystic fibrosis (CF) patients. In what will ultimately become a collaboration with both the TAMU Center for Phage Technology and the UNC Marsico Lung Institute, I aim to provide a safe and effective alternative treatment option for patients suffering from particularly resistant or difficult-to-treat pulmonary infections. Previously, I worked with A.J. Lopatkin on her project to characterize the BaeRS stress response/efflux system as well as its role on post-antibiotic population recovery.

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Freddy Huang

Major: Biomedical Engineering Minor: Chemistry

Pratt Undergraduate Research Fellow

Research Description:Currently, I am exploring the capacity of TECAN robotic arms in hope to automate future experimental processes. In another word, I am coding the TECAN robot to automate repetitive, time-consuming experimental procedure such as pipetting and dilution. Thus far, my project has focused on creating a systematic program for long term cell culturing and cell strain characterization using input/output feedback. In the future, I plan to expand my project to study the dynamic system of bacterial growth.

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Youlim Kim

Major: Biology Minor: Chemistry

Research Description: I am currently involved in two different research projects that are both concerned with the prevalence of antibiotic resistance genes in bacteria. The first involves working with Dr. Tanya Sysoeva in determining the effect of bacterial cell physiological states on the efficiency of conjugation. The second project is a Bass Connections project focused on mapping the microbiome of Duke’s campus, and identifying hotspots of antibiotic resistant and/or enteric bacteria on campus.

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Adam Davidovich

Major: Biomedical Engineering Minor: Computer Science

Research Description: In my time at the You Lab, I have been a part of three projects. In my first project, I conducted innovative cancer therapy research with Dr. Igor Shats to deduce the time-dependent effects of the transcription factor E2F1 in mediating the cell-fate decisions of cancerous cell lines. Currently, I am an undergraduate coordinator of the Duke Resistome Project, attempting to map the distribution of antibiotic-resistant bacteria across Duke’s campus. In addition, I am helping with data analytics for Jon Bethke’s project attempting to further understand the characteristics of conjugation among antibiotic-resistant bacteria.

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Connor Pfeiffer

Major: Biology, Music Minor: Chemistry

Research Description: Horizontal gene transfer (HGT) is one mechanism by which bacteria develop antibiotic resistance. My work focuses on methods of reversing antibiotic resistance by utilizing compounds that limits conjugation efficiency between donor and recipient. These compounds may serve as an intervention strategy for disrupting the HGT mechanism of plasmid conjugation, and ultimately restore antibiotic susceptibility in clinical relevant pathogens. Other projects of mine include investigating how growth-state dependent regulation of conjugation affects plasmid maintenance.

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Won Suk Choi

Major: Biology Minor: Chemistry

Research Description: Previous research has shown that when E. coli cells were exposed to exposed to intermediate but lethal concentrations of β–lactams, time to lysis decreased as initial cell density increased, indicating a reverse inoculum effect (RIE). This RIE creates repeated cycles of negative feedback: when antibiotics are administered, a small portion of the entire cell population survive the treatment and repopulate the media, increasing chances of bacteria acquiring and preserving mutations that confer antibiotic resistance.I am currently working to find out the extent to which RIE holds under various experimental conditions. These include temperature, pH of media, different cell strains, and additional types of β–lactam antibiotics.

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