Introducing our Authors - American Chemical Society

Introducing Our Authors pubs.acs.org/synthbio

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LEA DE MADDALENA

Stanford, CA (2016). Advisor: Dr. Matthew S. Munson. Ph.D. in Biomedical Engineering, University of Michigan, Ann Arbor, MI (2013). Advisor: Dr. Raoul Kopelman. B.S. in Bioengineering, UCLA, Los Angeles, CA (2008). Nonscientific Interests. Cycling through the Santa Cruz mountains, sports, traveling, cooking, guitar. I develop measurement methods for engineering biology at the Joint Initiative for Metrology in Biology in Stanford, CA. One of my projects is to develop an assay for inferring gene expression from engineered constructs in E. coli by competition with a reference construct for transcription and translation resources. My paper in this issue emerged from that project. We noticed a bias in measurements of optical density in E. coli that were engineered to express red fluorescent proteins. We showed that this bias can be avoided by measuring optical density at wavelengths that are not absorbed by fluorescent proteins. I am also working on measuring translation initiation from noncanonical start codons in both engineered and wild-type E. coli. In my graduate research I developed a protein assay based on the asynchronous magnetic rotation of aptamer-conjugated superparamagnetic microbes. (Read Hecht’s article; DOI: 10.1021/ acssynbio.6b00072).

Lea de Maddalena

Current Position. Master Student, Bioengineering with specialization in Regenerative Medicine, Swiss Federal Institute of Technology in Lausanne, Switzerland. Education. B.Sc. in Life Science, Swiss Federal Institute of Technology in Lausanne, Switzerland. Nonscientific Interests. Traveling, cooking, and swimming. Before I started to specialize into the direction of regenerative medicine, I did my bachelor thesis in synthetic biology and continued my research on the same project, which involved enhancing gene expression in a cell-free transcription-translation system. We enhanced the gene expression by adding two elongation factors that interact with the E. coli RNAP, which increases the transcription rate. Our work enabled the construction of endogenous bacterial networks in a well-defined system for the first time and therefore presents a new tool to study the underlying mechanism of life. (Read de Maddalena’s article; DOI: 10.1021/acssynbio.6b00017).

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KEITH HEYDE

ARIEL HECHT

Keith Heyde

Current Position. NSF Graduate Research Fellow at Virginia Polytechnic Institute and State University. Education. Masters in Engineering Science and Mechanics, Virginia Tech, Advisors: Dr. Mark Stremler and Dr. Warren Ruder. B.S. in Civil Engineering, Class of 2012, Columbia University. B.A. in Math and Physics, Class of 2011, Bowdoin College. Nonscientific Interests. Beyond the lab, I am interested in music, both as a listener and performer. In particular, I am a jazz enthusiast, and I play piano in both a small group and as a soloist. Also, I am an active, but washed-up triathlete, with my favorite distance being the half-ironman (70.3) length. I am drawn to the outdoors and I fancy myself an amateur, but impassioned, surfer, fisherman, climber, and trail runner. All said, I try to keep a

Sumit Kohli

Current Position. Bioengineer, National Institute of Standards and Technology − Joint Initiative for Metrology in Biology, Stanford, CA. Education. Postdoctoral Fellow, National Institute of Standards and Technology − Joint Initiative for Metrology in Biology, © 2016 American Chemical Society

Received: August 26, 2016 Published: September 16, 2016 915

DOI: 10.1021/acssynbio.6b00238 ACS Synth. Biol. 2016, 5, 915−919

ACS Synthetic Biology

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beginner’s mind about my life and interests, and I try to never let a fear of failure stop me from pursuing something new. My research career has been focused on developing novel ways to interface engineered cells with mechanical systems. My other projects have centered on developing an optical interface between synthetically engineered organisms, and mechatronic systems. In doing so, I’ve explored how engineered cells can control and optimize the behavior or mechanical systems, and in particular robots. In the context of our laboratory, this has allowed us to merge the technologies of synthetic biology with other disciplines, such as mechanical engineering and computer science. Similarly, the work in this paper represents a strategy for allowing engineered cells to interact with a material surface, effectively enabling cells to affect material assembly. I hope this work will lead to future applications in custom read-write drug manufacturing or evolvable nanoassembly strategies. (Read Heyde’s article; DOI: 10.1021/acssynbio.6b00037).

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Introducing Our Authors

SUNG-HO PAEK

Sung-Ho Paek

Current Position. ICTAS Doctoral Scholar at Virginia Polytechnic Institute and State University, Biological Systems Engineering. Education. M.S., Biomicrosystems Technology, Korea University, South Korea; Undergrad: Plant Biotechnology, Dongguk University, South Korea. Nonscientific Interests. Outside the lab, I enjoy all outdoor activities, some including tennis, soccer, hiking, cycling as well as snowboarding. I also always try to see and engage in new opportunities in life. I have been interested in approaches to cellular engineering that integrates engineering the nonliving (i.e., abiotic) environment with the direct engineering of living (i.e., biotic) cells with synthetic biology. As well as creating abiotic material surface that can interact with the biotin produced by living cells, I am also currently creating a method to probe biotic systems, specifically biofilms, by manipulating the ecosystem using the tools of microfabrication and microfluidics. (Read Paek’s article; DOI: 10.1021/acssynbio.6b00037).

ZHEN KANG

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Zhen Kang

Current Position. Associate Professor of School of Biotechnology, Jiangnan University, Wuxi (China). Education. B.SE. in Bioengineering (Laiyang Agricultural College); Ph.D. Microbiology (Shandong University); Visiting scholar studies: Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign. Nonscientific Interests. Kung fu, calligraphy, reading, cooking, outside activities. My research focuses on development of novel tools and strategies for rapidly engineering enzymes and optimizing synthetic pathways, which enables the industrial production of valuable enzymes and chemicals with high titer, productivity, and yield. This paper represents a scarless and sequence-independent DNA assembly method using thermal exonucleases (Taq and Pfu DNA polymerases) and Taq DNA ligase (DATEL). DATEL allows rapid assembly of 2−10 DNA fragments (1−2 h) with high accuracy (between 74 and 100%). Owing to the simple operation system with denaturation-annealing-cleavage-ligation temperature cycles in one tube, DATEL is expected to be a desirable choice for both manual and automated highthroughput assembly of DNA fragments, which will greatly facilitate the rapid progress of synthetic biology and metabolic engineering (Read Kang’s article; DOI: 10.1021/acssynbio.6b00078).

BENJAMIN PHILMUS

Benjamin Philmus

Current Position. Assistant Professor, College of Pharmacy, Oregon State University. Education. Postdoctoral research associate, Department of Chemistry, Texas A&M University, Mentor: Tadhg P. Begley; Ph.D., University of Hawai’I at Manoa, Department of Chemistry, Advisor: Thomas K. Hemscheidt; B.S., Marine Sciences/Biology, Southampton College, Long Island University. Nonscientific Interests. Hiking, ultimate frisbee, reading. My research group focuses on cyanobacterial natural products including biosynthesis, interesting enzymatic transformations and 916




production in heterologous hosts including Anabaena sp. strain PCC 7120. We are also interested in combinatorial biosynthesis to generate new, more efficacious analogues of cyanobacterial natural products and understanding their mechanism of action through our collaborations within the College of Pharmacy. (Read Philmus’ article; DOI: 10.1021/acssynbio.6b00038).

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Education. M.S. Biological Systems Engineering, Virginia Tech (2015). Advisor: Dr. Warren Ruder; B.S. Biology, Virginia Tech (2008). Nonscientific Interests. I enjoy listening to music and playing all types of instruments such as the saxophone, oboe, violin, guitar, and ukulele. Since I did not play sports growing up, I’ve enjoyed making up for lost time by trying out all different types. Recently, I’ve tried rock climbing, swimming, tennis, and golf. But what brings me most joy is simply dancing and singing with my husband and daughter in our living room. Generally, my research interests focus on using engineered cells to modify and manipulate biological systems. Specifically, this paper demonstrates that, by introducing specifically engineered bacterial cells to functionalized surfaces, surface chemistry is programmable through synthetic biology. In addition, I have focused on creating and characterizing a surface display system that allows the cell’s surface to be utilized as a tool for detecting genetic output spatially orthogonal to the cytosol. Alternatively, my other research projects are a good demonstration of the diversity in our lab, involving various techniques ranging from liposomal cell-free technologies to CRISPR Cas-9. Finally, my future research goals will shift toward using synthetic biology to controllably engineer hybrid materials. (Read Scott’s article; DOI: 10.1021/acssynbio.6b00037).

DAVID N. QUAN

David N. Quan

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Current Position. Postdoctoral associate, Institute of Bioscience and Biotechnology Research. Advisor: Dr. William Bentley. Education. Ph.D. Bioengineering, University of Maryland, College Park. Advisor: Dr. William Bentley. B.S. Bioengineering, University of California Berkeley. Nonscientific Interests. I enjoy a vigorous run, a good film noir, and a pinch of politics, ideally all before a very late breakfast. I am also curious about how embracing contradictions could ameliorate our civic life. Over the course of my Ph.D. I conducted computational studies to examine quorum sensing homologues in addition to some consequences of Lsr-based quorum sensing signaling topology. I am currently very interested in the dynamics of host-microbial commensal homeostases, the establishment of mutualism, and the effect of insults to these balances in the face of expected recalcitrance. This sort of interplay can be seen in ecologies as diverse and as similar as the gastrointestinal tract and plant roots. (Read Quan’s article; DOI: 10.1021/acssynbio.5b00261).

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SPENCER R. SCOTT

Garrett Graham

Current Position. Ph.D. Candidate in the Department of Bioengineering, UC San Diego. Advisor: Dr. Jeff Hasty. Education. B.S. in Bioengineering at UC Berkeley. Advisor: Dr. J. Christopher Anderson. Nonscientific Interests. I love traveling and photography, so give me a camera and a vehicle, and I’ll be a happy camper. Otherwise, conversing with good friends over a campfire is my ultimate aesthetic. Early in graduate school I became fixated on what was next for synthetic biology. I had this intuitive belief that engineered communities of bacteria could eventually out-perform any monoculture, leading me to focus on the emerging field of synthetic microbial consortia. Since there are currently very few tools for microbial consortia I focused on developing quorum sensing communication systems that could facilitate future efforts to engineer community interactions. I was able to create and characterize quorum sensing systems in E. coli that cover all the major communication paradigms possible with such constructs. As there is already evidence of engineered communities being capable of higher industrial yields, higher resistance to invasion, and higher resilience to environmental

FELICIA SCOTT

Michael Childress

Current Position. Ph.D. Candidate, Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia, USA. Advisor: Dr. Warren C. Ruder. 917




fluctuations, I’m excited to see how the field progresses and how interactions between and among members of the community are regulated. (Read Scott’s article; DOI: 10.1021/acssynbio.5b00286).

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Education. M.Sc. in Biochemistry, University of Turku, Finland. Nonscientific Interests. I play football in a superb team Kuuvuoren Laaki. When not in the field, I enjoy the nature by hiking, orienteering, fishing and picking mushrooms. My research is focused on the molecular mechanisms of transcription by the multisubunit RNA polymerase (RNAP). Although much of the gene regulation happens at the level of transcription initiation orchestrated by transcription factors and promoter elements, further regulation takes place during the elongation phase when RNAP is engaged in synthesizing RNA. For example, certain DNA sequences cause RNAP to pause and hinder gene expression. I study the mechanism of pausing and how RNAP activity is regulated by transcription elongation factors. In this paper we show that two elongation factors can significantly improve the gene expression by E. coli RNAP in a cell-free transcription-translation (TX-TL) system. Our work not only broadens the applicability of TX-TL systems but also demonstrates that transcription elongation should be considered when designing and studying genetic networks. (Read Turtola’s article; DOI: 10.1021/acssynbio.6b00017).

MIKI TASHIRO

Yohei Tashiro

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Current Position. Ph.D. candidate, Department of Applied Chemistry and Biotechnology, Chiba University. Education. Masters, Department of Applied Chemistry and Biotechnology, Chiba University (2014), Bachelor’s, Department of Applied Chemistry and Biotechnology, Chiba University (2012), Advisor, Prof. D. Umeno. Nonscientific Interests. Reading fiction (sci-fi and Japanese classics). I am interested in engineering pathways for the overproduction of valuable isoprenoids, especially by engineering the enzymes along the pathways. To this end, I am developing several different in vivo screening and selection methods for isoprenoid enzymes. In this paper, we describe high-throughput colorimetric screening system for cellular activities of monoterpene synthases. Using this system, we isolated a highly active mutant of pinene synthase in Escherichia coli and in cyanobacteria. Biochemical analysis revealed the altered metal dependency of the PS mutant, thereby adapting to the cytosolic environment of bacteria. I hope our approach enables to quickly improve the functions of various monoterpene synthases, hopefully by many different laboratories. (Read Tashiro’s article; DOI: 10.1021/acssynbio.6b00140).

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PAWEL L. URBAN

Yu-Chie Chen

Current Position. Leader of the research group for Biochemical Analysis, Associate Professor in Analytical Chemistry, Department of Applied Chemistry, National Chiao Tung University, Hsinchu, Taiwan. Education. 2008, Ph.D., Chemistry, Department of Chemistry, University of York, UK; Advisor: Prof. David Goodall; coadvisor: Prof. Neil Bruce. Nonscientific Interests. Watching documentaries and “007” movies; slow jogging; spending time in the mall. The work of my team builds on our expertise in analytical chemistry (optical and mass spectrometric methods) and biotechnology (biocatalysis). Our fascination with the concept of “time” led us to the development of a “biochemical timer”, which is presented in this article. Biochemical processes are programmed to occur in predefined temporal sequences. It was appealing to create a semiartificial system, in which the moment of light burst would depend on an initial conditionfor example, concentration of ATP. In the future, we shall anticipate more developments that mimic functions of daily life appliances (clocks, computers, motors), and incorporate biochemical building blocks. Such bioengineered systems can later be utilized when interfacing biology with electronic and mechanical devices. To achieve this ambitious goal, it is essential to provide multidisciplinary training to junior researchers. Hence, I encourage the

MATTI TURTOLA

Matti Turtola

Current Position. Ph.D. Candidate, Department of Biochemistry, University of Turku, Finland. Advisor: Dr. Georgiy A. Belogurov. 918




Education. Ph.D. Bioengineering, University of Maryland, College Park. Advisor: Dr. William Bentley. M.S. Chemical Engineering, University of Maryland, College Park. Advisor: Dr. Joseph Schork. B.S. Chemical Engineering, Georgia Institute of Technology. Nonscientific Interests. I enjoy any activities on the water: windsurfing, sailing, water-skiing, and kayaking. I recently moved to the Bay area so these opportunities are plentiful! In this paper, my coauthors and I create a genetically engineered bacterium with manipulated quorum sensing (QS) kinetics. These cells produce their own coordination molecules and then rapidly uptake these molecules, which subsequently trigger protein expression. Here, by enhancing the QS uptake, we increase coordination among the bacteria, resulting in increased protein expression. As induction molecules for protein expression are cost-prohibitive at industrial scale, we envision this kind of autonomous system will prove beneficial in metabolic engineering applications. Looking forward, I am interested in developing a platform to express “cryptic” biosynthetic gene clusters, particularly those elicited by two-component systems such as QS. (Read Zargar’s article; DOI: 10.1021/acssynbio.5b00261).

chemistry students in my lab to assimilate fundamentals of biology, electronics, and computer science, and to utilize the newly acquired knowledge in our projects. (Read Urban’s article; DOI: 10.1021/acssynbio.6b00116).

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PATRICK VIDEAU

Patrick Videau

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Current Position. Assistant Professor of Biology, College of Arts and Sciences, Dakota State University. Education. Postdoctoral Research in the Pharmaceutical Sciences, Oregon State University, Advisor: Benjamin Philmus; Ph.D. in Microbiology, University of Hawaii, Advisor: Sean Callahan; B.A. in the Biological Sciences, Goucher College. Nonscientific Interests. Theater, dance, trying new types of food, travel. My research program is based on understanding the many facets of Anabaena sp. strain PCC 7120 with respect to growth, cellular differentiation, genetic regulation, and compound production. Anabaena is an ideal system for heterologous expression because it is genetically tractable, easy and inexpensive to culture, and produces no known natural products of its own. The results presented show that Anabaena is an effective heterologous host for the production of lyngbyatoxin A, originally isolated from Moorea producens. The diversity of approaches used to modulate compound production in Anabaena show that this organism may be used as a general heterologous host for cyanobacterial natural products. (Read Videau’s article; DOI: 10.1021/ acssynbio.6b00038).

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RUIHUA ZHANG

Ruihua Zhang

Current Position. Ph.D. student, College of Engineering, University of Georgia. Advisor: Dr. Yajun Yan. Education. M.S. in Biological Systems Engineering, Virginia Tech. Advisor: Dr. Warren C. Ruder; B.S. in Biotechnology, Beijing Institute of Technology, China. Nonscientific Interests. Acoustic guitar; tennis; swimming; travel and photography. Synthetic biology is a powerful tool. It guides us to a deeper understanding of life and to reprogram organisms for desired molecular outputs. In this paper, we engineered bacteria to enable its communication with functionalized surfaces. I believe this interactive surface chemistry design has various potential applications in bioengineering and biomedical engineering. My current research focus is producing value-added chemicals via molecular and metabolic control. In the long run, I am interested in expanding the synthetic biology toolbox to establish new platforms and to overcome challenges for industrial biochemical production. (Read Zhang’s article; DOI: 10.1021/acssynbio.6b00037).

AMIN ZARGAR

Amin Zargar

Current Position. Postdoctoral fellow, Joint BioEnergy Institute. Advisor: Dr. Jay Keasling. 919


Introducing our Authors - American Chemical Society

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