Introducing Our Authors - ACS Synthetic Biology (ACS Publications)

Introducing Our Authors pubs.acs.org/synthbio

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MAX ADRIAN

Education. Ph.D. (Computer Science, expected in August 2017), Technical University of Denmark, Denmark, Advisor: Jan Madsen; Master of Engineering (Computer Engineering), Chosun University, South Korea, Advisor: Jeong-A Lee; Bachelor of Engineering (Electronic), NED University of Engineering and Technology, Pakistan. Current Position. Ph.D. Student, Department of Applied Mathematics and Computer Science, Technical University of Denmark. Nonscientific Interests. Traveling, cooking, and exercise. I am currently working on a future emerging technology in the domain of synthetic biology. One of the objectives of synthetic biology is to replace medical devices with the systems-on-cell, based on genetic circuits instead of electronic circuits. My contribution in this field is to develop methods, algorithms and tools for the analysis, verification and synthesis of genetic logic circuits. In this research, we proposed a methodology to analyze the timings and threshold values of genetic logic circuits. Similar to electronic circuits in which the circuit timing is a crucial design characteristic to ensure the correct functioning, we believe that the timing analysis of genetic circuits will also become an essential design characteristic for precise functionality. We proved through experimental simulations that the parameters, which effect the timings of genetic circuit, have an impact on the functionality of a circuit. (Read Hasan’s article DOI: 10.1021/ acssynbio.6b00296).

Max Adrian

Education. B.Sc., University College Utrecht, The Netherlands; M.Sc., Biomedical Sciences, Utrecht University, The Netherlands; Ph.D., Cell Biology, Utrecht University, The Netherlands, Advisor: Dr. Lukas Kapitein. Current Position. Postdoctoral Research Fellow, Hoogenraad lab, Neuroscience, Genentech Inc., San Francisco, USA. Nonscientific Interests. Hiking, paragliding, traveling, concerts, and skiing. I am fascinated by the ability of cells to create and maintain order. Many different biochemical reactions are efficiently distributed into cellular organelles and compartments to facilitate cellular functions. During my Ph.D., I studied different aspects of cellular transport mechanisms and developed novel techniques to manipulate protein and organelle positioning. We used the power of optogenetics to precisely control binding of cellular cargoes to selected motor proteins. This allows us to study the effect of enriching or depleting cargos at subcellular localizations over time. Here, we demonstrate the use of a red light-sensitive phytochromebased optogenetic system in these assays and show that we can now control two transport processes in parallel with higher patiotemporal precision. In my postdoctoral studies, I will further study cellular transport in the context of neurodegenerative diseases. (Read Max’s article DOI: 10.1021/acssynbio.6b00333).

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JULIO R. BANGA

HASAN BAIG

Julio R. Banga

Education. M.Sc. in Industrial Chemistry from the University of Santiago de Compostela (Spain) in 1988, and a Ph.D. in Chemical Engineering from the same University in 1991. Postdoc at UC Davis, 1992. Current Position. Research Professor at the BioProcess Engineering Group, located at the Institute of Marine Research, Vigo (Spain), which belongs to the Spanish Council for Scientific Research (C.S.I.C.). Received: June 28, 2017 Published: July 21, 2017

Hasan Baig

© 2017 American Chemical Society

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DOI: 10.1021/acssynbio.7b00232 ACS Synth. Biol. 2017, 6, 1235−1247

ACS Synthetic Biology

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Nonscientific Interests. Working out, rock music, reading, and robotics. I am interested in the application of mathematical modeling and optimization to biological processes and systems, with emphasis on problems from systems and synthetic biology. Current main topics include reverse engineering in systems biology, computer-aided design in synthetic biology, and the interplay between optimality and dynamics in biosystems. (Read Julio’s article DOI: 10.1021/acssynbio.6b00306).

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Introducing Our Authors

ILARIA BENEDETTI

ATTILA BECSKEI

Ilaria Benedetti

Education. B.S. in Biology, “Sapienza” University of Rome, Italy; M.S. in Microbiology, University Autónoma, Madrid, Spain; Ph.D. in Microbiology, University Autónoma, Madrid, ́ Spain, Advisor Prof. Victor de Lorenzo. Current Position. Postdoctoral at Centro Biologiá Molecular Severo Ochoa, department of Genome Dynamics and Function, advisors Dr. Margarita Salas and Dr Mario Mencia.́ Nonscientific Interests. Yoga, books, and music. I am interested in developing and improving molecular tools for bacteria. My most recent work was focused on the design of standardized genetic tools for the environmental bacterium Pseudomonas putida. The obtained constructs contributed to solve some issues regarding regulatory mechanisms and biotechnological potential of this strain. In this work we analyzed the Pm promoter activity of P. putida and its cognate regulator XylS by following the expression of Pm-gf p fusions in single cells. Experiments confirmed the predicted models describing how transcriptional noise depends on the intracellular physical distance between regulator source and target promoter. Currently I am working with the genome of phage ϕ29, which infects Bacillus subtilis and replicates with an efficient protein primed mechanism. The objective engineer an episome based on bacteriophage ϕ29; this replicon will provide an in vivo, stable system for storing sequence-defined genetic information isolated from cellular genome and able to replicate independently and therefore function as safe and effective tool for synthetic biology. (Read Ilaria’s article DOI: 10.1021/ acssynbio.6b00397).

A. Roulie

Education. M.D., University of Szeged, Szeged, Hungary; Ph.D. in Molecular Biology, European Molecular Biology Laboratory, Heidelberg, Germany, Advisor: Dr. Luis Serrano; Postdoc at Department of Physics, Massachusetts Institute of Technology, Cambridge, USA. Advisor: Dr. Alexander van Oudenaarden. Current Position. Associate Professor, Biozentrum, University of Basel, Basel Switzerland. Nonscientific Interests. Biking, traveling, gardening and philosophy. Becskei’s research group specializes in synthetic and systems biology of regulatory networks. His group combines mathematical and experimental approaches to study feedback regulation in genetic networks and to estimate parameters for systems biology. An important aim is to understand the stability and reversibility a cell fates, in particular, how they are influenced by stochastic gene expression and by the architecture of positive feedback loops in transcriptional and chromosomal epigenetic circuits. By developing methods to measure RNA and protein turnover rates and protein−protein binding constants, another aim of the research in his group is to predict network behavior. For example, weak protein dimerization in a feedback loop can stabilize a cell fate. While the main focus is on synthetic networks and yeast, the group also studies differentiation of embryonic stem cells. (Read Attila’s article DOI: 10.1021/ acssynbio.6b00282).

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SUN YOUNG CHOI

Akihiro Furuya

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Education. Ph.D., Korea University Green School, Advisor: Prof. Sang Jun Sim and Prof. Han Min Woo; B.S., M.S., Korea University, Advisor: Prof. Sehwan Baek. Current Position. Postdoctoral fellow, Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), Advisor: Prof. Han Min Woo. Nonscientific Interests. Swimming, movies, reading and traveling. I am interested in metabolically engineering approach and application to utilize cyanobacteria as cell factory, such as biobased chemical production for replace of petroleum-based chemicals and renewable concern for sustainable development. In this publication, the push-and-pull strategy for metabolic engineering was successfully demonstrated in Synechococcus elongatus PCC 7942 to produce squalene from CO2. Optimizing methylerythritol phosphate biosynthesis pathway and overexpressing the gene encoding a fusion squalene synthase allowed the success of the goal of the metabolic engineering. (Read Sun Young’s article DOI: 10.1021/acssynbio.7b00083).

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ONUR DAGLIYAN

Onur Dagliyan

Education. Ph.D., University of North Carolina at Chapel Hill, School of Medicine, NC, US, Advisors: Klaus M. Hahn and Nikolay V. Dokholyan; M.S. and B.S., Koç University, College of Engineering, Istanbul, Turkey. Current Position. Research Fellow, Harvard Medical School. Nonscientific Interests. Literature, music, cycling, cooking, art, and cinematography. My research focuses on the signaling of fast and dynamic biological processes such as cell motility, a field that demands new technologies to control protein activity in living cells and organisms. Traditional manipulation techniques such as knock out/in/down are often slow and ineffective if multiple protein isoforms are involved. Small molecule inhibitors are often not selective for the protein of interest. The PAK family is an example where these techniques fail to fully address the involvement of PAK in cell motility. In our paper, we designed PAK1 protein switches that can be selectively turned on in living cells using an inert small molecule. This approach allowed us to show how PAK1 affects breast cancer cell motility and dendritic protrusions in neurons. (Read Onur’s article DOI: 10.1021/ acssynbio.6b00359).

GEORGE M. CHURCH

Seth Kroll

Education. Gail Martin, University of California San Francisco (Post-Doctoral Fellowship, 1985−1986); Walter Gilbert, Harvard University (Ph.D., 1984); Sung-Hou Kim, Duke University (BA, 1974). Current Position. Professor of Genetics, and Health Sciences and Technology of Harvard and MIT (HST); Director of HMS NHGRI-Center of Excellence in Genomic Science; Broad Institute and Wyss Harvard Inst. of Biologically Inspired Engineering. Nonscientific Interests. Waterskiing, math, entomology (aquatic insects), mineralogy, choir, sailing, photography, tennis, skiing (snow), skating (ice and asphalt), medicine, biking, volunteer subject for human experiments, soaring, scuba, camping, technical rock climbing, aquaculture, home-robotics, ice swimming, and turtle breeding. George Church, professor at Harvard and MIT, coauthor of 425 papers, 95 patent publications and the book Regenesis, developed methods used for the first genome sequence (1994) and million-fold cost reductions since (via NGS and nanopores), plus barcoding, DNA assembly from chips, genome editing, writing and recoding. He co-initiated the BRAIN Initiative (2011) and Genome Projects (1984, 2005) to provide and interpret the world’s only open-access personal precision medicine data sets. (Read George’s article DOI: 10.1021/ acssynbio.6b00342).

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ROGER R. DRAHEIM

Christine Oswald

Education. Lecturer in Pharmacy, Durham University, U.K.; Junior Research Group Leader, Institute of Biochemistry (Biozentrum), Goethe University Frankfurt, Germany; NIH Kirschstein NRSA Fellow (Prof Gunnar von Heijne, Stockholm University, Sweden); Ph.D. Microbiology (Prof. Michael D. Manson, Texas A&M University, Texas, USA); B.S. Biochemistry 1237



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and Microbiology, B.S. Molecular and Cellular Biology, University of Maine, Orono, Maine, USA. Current Position. Senior Lecturer in Microbiology, University of Portsmouth, U.K. Nonscientific Interests. In my spare time, I enjoy cycling, traveling by backpack whenever possible, and mushroom hunting when the weather is good. Two-component signaling circuits (TCSs) possess vast untapped engineering potential. They govern the majority of environmental, pathogenic and industrial processes undertaken by bacteria. Therefore, controlling signal output from these circuits in a stimulus-independent manner is of central importance to synthetic microbiologists. Aromatic tuning, or repositioning the aromatic residues commonly found at the cytoplasmic end of the final transmembrane helix has been shown to modulate signal output from several TCSs. Here, we have developed a next-generation biological platform for highthroughput detection of compounds with novel antimicrobial activity by synergistically employing aromatic tuning and rational chimeric receptor design. We have begun to employ this platform by screening pre-existing small molecule libraries provided by an industrial partner. (Read Roger’s article DOI: 10.1021/ acssynbio.6b00288).

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MUMUN GENCOGLU

Mumun Gencoglu

Education. B.S. in Chemical Engineering, Koc University, Istanbul, Turkey; M.S. in Systems Biology, University of Zurich, Zurich, Switzerland, Ph.D. in Biozentrum, University of Basel, Basel Switzerland, Advisor: Dr. Attila Becskei. Current Position. Postdoc, Biozentrum, University of Basel, Basel Switzerland. Nonscientific Interests. Travel, movies and soccer. Combining experimental proteomic analysis with computational modeling and parameter fitting, my research has focused on the determination of in vivo binding constants in the yeast GAL network. We found that dimerization of a transcription factor is weak, which is utilized to amplify a signal. In a related paper, we have shown that weak dimerization also affects synthetic transcription factors, which helps to generate cellular memory. These findings indicate that the nonlinear effects of binding constants arise more commonly that generally assumed. The method we developed can be in principle applied to study the binding of any transcription factors to DNA and the binding of regulators to the transcription factors. (Read Mumun’s article DOI: 10.1021/acssynbio.6b00282).

Z. HUGH FAN

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JAN B. HEIDELBERGER

Z. Hugh Fan

Education. Postdoctoral Fellowship, Ames Lab, Iowa State University; Ph.D., University of Alberta (Canada); B.Sc. Yangzhou Teachers’ College (China). Current Position. Professor, Biomedical Engineering, University of Florida. Nonscientific Interests. Gym and travel. This is an excellent example of collaboration between platform developers and application specialists. Dr. Jun Li from Professor George Church’s lab approached me after reading our paper in Integrated Biology published in 2014. My former student, Dr. Kirsten Jackson, supplied a couple of devices to Dr. Li and the collaborative work was then initiated. In this paper, we significantly extended our previous effort and demonstrated the power of the platform by coexpressing 29 r-proteins in one pot. The high-throughput capability of the platform enables the optimization of various expression conditions. I hope this paper will be helpful to the community of synthesis biology. (Read Fan’s article DOI: 10.1021/acssynbio.6b00342).

Sofiá C. Lobato Gil

Education. Diploma in Biochemistry, Goethe University Frankfurt, Germany. Current Position. Ph.D. Candidate, Institute of Molecular Biology, Mainz, Germany, Advisor: Dr. Petra Beli. Nonscientific Interests. In my spare time, I go climbing with colleagues, play board games and perform historical dances. 1238



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After investigating in chimeric receptors and their use as a next-generation biological platform, I switched my research for posttranslational modifications within eukaryotic cells. First, I analyzed the crosstalk of different modifications on a transcription factor and their influence on the protein fate. My current research focuses on the modification of proteins by ubiquitin. Protein ubiquitylation is an essential posttranslational modification and can affect protein activity, localization, interactions or can lead to the degradation of the target protein by the proteasome. This regulated turnover of proteins by the ubiquitin-proteasome system is essential for cellular homeostasis. For a broad analysis, we are using quantitative proteomics approaches with stable isotope labeling by amino acids in cell culture (SILAC). (Read Jan’s article DOI: 10.1021/acssynbio.6b00288).

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HSIN-HO HUANG

Hsin-Ho Huang

Education. B.S. in Agriculture, M.S. in bioindustrial Chemistry, National Taiwan University, Taiwan. Advisor: Prof. Wen-Hsiung Liu; Ph.D. in Microbial Chemistry, Uppsala University, Sweden. Advisor: Prof. Peter Lindblad. Current Position. Postdoctoral Researcher, Department of Mechanical Engineering, Massachusetts Institute of Technology. Advisor: Prof. Domitilla Del Vecchio. Nonscientific Interests. Camping, hiking, kayaking, and travel. My research interests are in realizing prescribed behaviors of genetic circuits. Implementation of such circuits is a powerful tool not only to probe the underlying biological mechanisms in question, but also to introduce novel functionalities in a biological system for useful applications in human society and environment. This is not a trivial task when using a larger and more sophisticated genetic circuit. “Context dependence” is the key problem occurring at all scales of synthetic biology from parts, modules, cell types/strains, to cells’ living environment. In this paper, we focus on interconnected modules in a circuit and ask how competition for transcriptional/translational resources by different genes affects the circuit’s behavior. We use a model-guided design to accomplish the prescribed dose responses of activation cascades. (Read Hsin-Ho’s article DOI: 10.1021/acssynbio.6b00361).

MACIEJ B. HOLOWKO

Karolina Swiebodzinska

Education. M. Eng. in Industrial Biotechnology, Warsaw University of Technology, Poland; B. Eng. in Molecular Biotechnology, Gdansk University of Technology, Poland. Current Position. Research Associate, SynCTI, National University of Singapore Nonscientific Interests. Apart from the usualreading and sportsyou can often find me studying world history, enjoying a session of a strategy game or planning my next travel. My current research at National University of Singapore focuses on the Biofoundry technology development, whereas during my Ph.D. studies I have taken part in a project to design a sense and kill mechanism for Vibrio cholerae treatment. The work presented in this issue of ACS Synthetic Biology shows how our previously constructed Escherichia coli biosensor for detection of V. cholerae has been redesigned to become a sense and kill mechanism. Since our system was designed to be modular from the very beginning, we could quickly prototype the new module and incorporate it into the existing system. This system has now potential to become a viable option of V. cholerae treatment after further testing. (Read Maciej’s article DOI: 10.1021/acssynbio.7b00058).

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PREMKUMAR JAYARAMAN

Premkumar Jayaraman

Education. Ph.D. in Microbiology, Nanyang Technological University, Singapore; M.Sc. in Biomedical Engineering, Nanyang Technological University, Singapore; B.Tech. in Industrial Biotechnology, Anna University, India. Current Position. Research Fellow, SynCTI, National University of Singapore. 1239




Education. B.S./M.S. in School of Biological Sciences, Seoul National University, South Korea, Advisor: Dr. Kye Joon Lee. Current Position. Research Student, Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB). Ph.D. Candidate, Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Advisor: Dr. Seung-Goo Lee. Nonscientific Interests. I enjoy board games and movies. I am interested in developing a CRISPR interference system for reprogramming E. coli. In this work, we have characterized a Type V-A CRISPRi system for efficient gene repression, and compared its performance with a Type II CRISPRi system. We hope that these information will help you to repress genes of interest and construct genetic circuits to endow useful functions. Currently, I am working on expanding the Type V-A CRISPRi system to design and build a novel genetic circuit for enhanced production of recombinant proteins and biochemicals (Read Seong Keun’s article DOI: 10.1021/acssynbio.6b00368).

Nonscientific Interests. I love to do arts and read quintessentially about world history and crime novels. Avid cricket enthusiast as well. In this current work, we show that how using our previously engineered E. coli to sense V. cholerae pathogen, was repurposed into a sense and kill system. Apart from the detailed experimental setup, we present in this work the engineering challenges we faced in achieving our goal and how we managed to solve those challenges in a systematic approach. We believe this system has the potential to become a possible therapeutic option in the fight against cholera. (Read Premkumar’s article DOI: 10.1021/acssynbio.7b00058).

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RYUJI KAWANO

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Ryuji Kawano

Education. Ph.D. in Department of Chemistry and Biotechnology, Yokohama National University, Japan. Current Position. Associate Professor, Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology (TUAT), Japan. Nonscientific Interests. Trail running and climbing. The idea for this paper grew out of our experience developing “molecular robotics”, described in a previous publication. The molecular robot consists of sensors, actuators, and intelligence as well as a body to integrate these facilities. This type of robot is made with molecule systems, such as receptor proteins, DNA/ RNA computing, and liposome. In this paper, we developed a DNA/RNA logic gate operated in microdroplets. The output molecules were able to be detected by a biological nanopore and the information on the output molecules was converted to electrical signals. Our system contributes the parts of the molecular robot as the sensor combined with interagency. (Read Ryuji’s article DOI: 10.1021/acssynbio.7b00101).

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JASON R. KING

Jason R. King

Education. Ph.D., Chemistry, Duke University (2014); B.S., Chemistry, University of Alabama at Birmingham (2008). Current Position. Postdoctoral Associate, MIT Chemical Engineering. Nonscientific Interests. Hiking, running, tennis, history, and board games. In chemistry, there is a confidence that a molecule can be synthesized with known or yet discovered reactions. In metabolic engineering, there is a dogma that known reactions and enzymes must be leveraged together to rationally create metabolites. The value of this work is that we have shown that the same logic that chemists leverage to make any molecule in a flask can also be applied successfully in a cell. The trick we found was to look to enzymes high degrees of substrate plasticity. I am very excited to watch and see how this general idea is applied beyond atypical sugar biosynthesis with aldolases and kinases. (Read Jason’s article DOI: 10.1021/ acssynbio.7b00072).

SEONG KEUN KIM

Seong Keun Kim

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ERKIN KURU

Current Position. Senior Researcher, Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB). Nonscientific Interests. Listening to music, reading books, and sports (golf, tennis, swimming). My research has involved the development and application of synthetic biology tools for studying metabolic engineering of microbial cell factories. My early work focused on evolutionary engineering through adaptive laboratory evolution of bacterial cells. I then studied its exploration, harnessing genome, transcriptiome, and proteome. More recently my research has shifted to studies of dynamic sensing and regulation for developing smart cell factories through genetic circuits and CRISPR interference. This paper presents type V-A CRISPRCas endonuclease Cpf1-based CRISPR interference. We developed a programmable CRISPRi system with DNasedeactivated Cpf1 from Eubacterium eligens and compared its performance with catalytically deactivated Cas9 from Streptococcus pyogenes that has been widely used in CRISPR interference. Our findings will guide an efficient EedCpf1mediated CRISPRi genetic control. (Read Dae-Hee’s article DOI: 10.1021/acssynbio.6b00368).

Jason Sutherland

Education. Ph.D. in Chemical and Structural Biology, Indiana University Bloomington, Co-advisors: Michael VanNieuwenhze, Ph.D. and Yves Brun, Ph.D.; B.S. in Biological Sciences and Bioengineering, Sabanci University, Turkey. Current Position. Research Fellow, Department of Genetics, Harvard Medical School, Boston, MA, Advisor: George M. Church. Nonscientific Interests. I try to balance the repetitiveness of experimental biology with the pursuit of arts, in particular photography and music and by having a colorful social life. My current scientific interests include two main goals. First, following a childhood fascination, I am hoping to continue our efforts toward assembling a self-replicating system in vitro. We discussed our current progress in our paper in this issue. Second, by utilizing relatively new and efficient orthogonal protein translation systems, I am interested in developing new sitespecific and nonpervasive protein labeling technologies. Eventually, using these new technologies I hope to continue addressing fundamental questions in biology using bacteria or self-replicating systems as models. (Read Erkin’s article DOI: 10.1021/acssynbio.6b00342).

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DAE-HEE LEE

BENJAMIN A. E. LEHNER

Benjamin A. E. Lehner

Education. B.S. and M.S., University of Salzburg (partly TU Munich). Current Position. Ph.D. candidate, TU Delft Departments of Bionanoscience and Quantum Nanoscience, Advisors: Anne S. Meyer, Stan J.J. Brouns and Herre van der Zant. Nonscientific Interests. Tennis, martial arts, fitness, languages and self-improvement. Using bacteria to produce materials may reduce the need for toxic chemical precursors as well as the creation of toxic byproducts/waste during material synthesis. Therefore, they often lead to an improvement in sustainability and renewability of material production. Our research group is working on some promising technologies to develop and fabricate these materials in a reliable way. In this paper, we describe a straightforward approach to 3D print these bacteria to create a macroscopically structured product. The adaptability of the printing system to different organisms and the potential of synthetic biology to generate new materials on demand further improve the impact of this work. (Read Benjamin’s article DOI: 10.1021/acssynbio.6b00395).

Dae-Hee Lee

Education. Postdoc in Department of Bioengineering, University of California, San Diego, USA (2007−2010, Advisor: Dr. Bernhard Palsson); Ph.D. (2007, Advisor: Dr. Jin-Ho Seo), M.S. (2003, Advisor: Dr. Jin-Ho Seo), and B.S. (2000, Advisor: Dr. Kwan-Hwa Park) in Department of Food Science and Biotechnology, Seoul National University, South Korea. 1241



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CHRISTINA E. LEHNING

Current Position. Ph.D. Candidate, Département de biochimie, de microbiologie et de bioinformatique, Université Laval, Québec, Canada. Advisor: Prof. Sylvain Moineau. Nonscientific Interests. Zythology, gastronomy, sport and travel. I have always been amazed by phages (bacterial viruses). They are the most abundant and diverse biological entities on Earth and they play a significant role in maintaining the balance of ecosystems. Phages were, and still are, essential for the development of molecular biology and biotechnology. I aim to elucidate the function of uncharacterized phage proteins and advance the field of phage biology. I am currently working with the virulent lactococcal phage p2, a model for a predominant phage group in the dairy industry. In this paper, we describe how we developed a tool based on CRISPR-Cas9 to efficiently edit its genome. This tool allows us to generate gene knockouts and study protein function in vivo by investigating microbiological parameters associated with phage infection. (Read MarieLaurence’s article DOI: 10.1021/acssynbio.6b00388).

Christina E. Lehning

Education. Ph.D. in Genetic Engineering (Prof. Morten OA Sommer, NNF Center for Biosustainability, Denmarks Technical University, Denmark); Dipl. Biochem., Goethe University Frankfurt, Germany. Current Position. Freshly graduated Ph.D. and current traveler. Nonscientific Interests. You can always challenge me for a board game, but I am just as well interested in arts and crafts, especially when they meet science and technology. And my cats, of course! My scientific interest has focused on the implementation of genetic engineering and synthetic biology for the development of genetic biosensors. Genetic biosensors, adapted from transcription factors, two-component signaling circuits and riboswitches, possess a vast potential of implementations as well in fundamental research as applied biology. The rapidly advancing tools emerging from genetic engineering and synthetic biology, the steadily improving screening and selection technologies like fluorescent activated cell sorting (FACS) and microfluidics as well as the growing knowledge and experience of biosensor construction offer the possibilities of a biosensor development and refining that can keep up with the pace and needs of emerging research questions and demands of biotechnology. (Read Christina’s article DOI: 10.1021/acssynbio.6b00288).

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JUN LI

Sirui Zou

Education. Postdoctoral: Harvard Medical School, Advisor: Dr. George M. Church; Graduate: Harvard University, Advisor: Dr. George M. Church; Undergraduate: Tsinghua University, Advisor: Dr. Zihe Rao. Current Position. Postdoctoral research fellow in George Church lab, Harvard Medical School, Boston, MA. Advisor: George M. Church. Nonscientific Interests. Card games, singing, art/design, fishing, and travel. Under the great supervision of Dr. Church, I have been aiming for constructing a minimal self-replicating entity that represents the central dogma with the bottom-up approach. This paper demonstrates the feasibility of using PURE system as a starting platform to construct our proposed self-replicating entity. We are able to regenerate tens of ribosomal proteins in this platform with high efficiency with a series of optimizations. These regenerated 30S subunit ribosomal proteins can be reconstituted to active 30S subunits. Our progress is a great move on synthetic ribosome/self-replicating entity construction. It paves the road for future works in the minimal cell construction field. (Read Jun’s article DOI: 10.1021/acssynbio.6b00342).

MARIE-LAURENCE LEMAY

Jake Lavieille-Curran

Education. B.S. in microbiology, Université Laval, Québec, Canada. 1242



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SIERIN LIM

Electronic Engineering, Nanyang Technological University, Singapore (2001). Current Position. Associate Professor, Department of Biomedical Engineering, Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore. Nonscientific Interests. Watching movies, and leisure travel. My engineering biology research group @ NUS focuses on applying engineering principles to design and build microbes with useful capabilities for biomedical and industrial applications. We are also developing tools to accelerate the design and engineering of the microbes. My motivation is to make engineering of biology easier and more predictive, envisioning a day when we could design and build complex biological systems that work as desired the first time. We have been reprogramming microbes to fight infectious causing pathogen. Cholera remains a global health challenge, particularly in developing countries. This paper presents our recent effort in engineering E. coli to sense and kill pathogen Vibro cholerae, the causative agent of disease Cholera. It has potential to be further developed into a viable solution to fight Cholera. (Read Chueh Loo’s article DOI: 10.1021/acssynbio.7b00058).

Sierin Lim

Education. Postdoc in Chemical Engineering and Materials Sciences, University of California Irvine; Advisor: Szu-Wen Wang; Ph.D. in Biomedical Engineering and B.S. in Chemical Engineering with Bioengineering Option, University of California, Los Angeles (UCLA), USA; Advisors: Harold G. Monbouquette and Imke Schoeder. Current Position. Associate Professor, School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore Nonscientific Interests. Explore the world through hiking, camping, music, and food. Lim’s Bioengineered and Applied Nanomaterials Laboratory (BeANs Lab) at Nanyang Technological University (NTU) focuses on the design and engineering of hybrid nano/microscale devices from biological parts by utilizing protein engineering as a tool for applications in medicine, electronics, cosmetics, and food. The main platforms that the BeANs Lab has been studying are protein cages and bacterial cellulose. The studies range from understanding their self-assembly mechanisms to building hierarchical structures for various applications and engineering of microorganisms for production of bulk materials. The cholera biosensor developed in this paper is a fruitful collaboration with Poh’s Lab. The sense and kill mechanism for Vibrio cholerae engineered into E. coli has a potential to be developed as a probiotic treatment option. (Read Sierin’s article DOI: 10.1021/ acssynbio.7b00058).

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NATALIA I. MAJEWSKA

Natalia I. Majewska

Education. B.S. in Chemical and Biological Engineering, Northwestern University. Advisor: Michael C. Jewett. Current Position. Ph.D. Candidate, Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Advisor: Michael J. Betenbaugh. Nonscientific Interests. I love rock climbing, hiking and discovering new places. My research involves discovering new applications and gaining a better understanding of Chinese Hamster Ovary (CHO) cells. Our featured research deals with using synthetic biology to produce antibody drug candidates in a cell-free environment. This tool can speed up the screening process and be used to predict titers of monoclonal antibodies, lowering both time and cost for industrial development. Currently, I am working on optimizing growth conditions for CHO cells by characterizing their growth rates in different media formulations. I am also collaborating on a project to determine the epigenome and methylome of CHO cells. By understanding how genes of interest are inserted into the genome, and finding out insert locations and quantities, we can increase the production capabilities of CHO cells and understand the underlying factors that cause certain cells to be high producers and others to be low

CHUEH LOO POH

Chueh Loo Poh

Education. Ph.D. Bioengineering, Imperial College London, UK (2006), Advisor: Prof Richard Kitney; B.Eng. Electrical and 1243




University Medical Center Utrecht and Utrecht University. Advisor: Prof. Geert Kops. Current Position. Postdoctoral researcher in the lab of Dr. Lukas Kapitein at the division of Cell Biology, Biology Department, Faculty of Science, Utrecht University, The Netherlands. Nonscientific Interests. Camping, fishkeeping, movies, cooking, politics, and watching sports. My work focuses on exploring the relationship between intracellular architecture, in particular the specific positioning of organelles, and cellular function. These studies require acute and precise control of the directed transport and positioning of specific subsets of organelles. Here, we utilized the red/far-redlight sensitive photoswitch Phytochrome B to optogenetically control the recruitment of specific motor proteins to selected organelles. By irradiating the photoswitch with two separate wavelengths, this system enabled us to not only rapidly induce, but also actively reverse coupling of organelles and motor proteins. The ability to actively uncouple motor proteins from organelles, in combination with spatially patterned illumination, provided us with the acute and precise spatiotemporal control of organelle positioning that is needed to unravel the functional importance of specific organelle positioning. (Read Wilco’s article DOI: 10.1021/acssynbio.6b00333).

producers. (Read Natalia’s article DOI: 10.1021/acssynbio.7b00001).

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ANDREA MARTELLA

Andrea Martella

Education. Ph.D. in Cell Biology, Erasmus Medical Centre, Rotterdam, The Netherlands. Advisor: Prof. dr. Frank Grosveld; Master’s degree in Medical Genetics, Catholic University of the Sacred Heart, Rome, Italy. Advisor: Prof. Christina Brahe. B.S. in Biological Science, University of Salento, Italy. Current Position. Postdoctoral research associate, School of Biological Sciences, University of Edinburgh, Edinburgh, U.K. Advisor: Dr. Patrick Yizhi Cai. Nonscientific Interests. Art, sport, and traveling. My research interests are centered on applying synthetic biology to mammalian systems to accelerate the discovery process and process optimization in cell line generation for drug screening, cell therapy and production of therapeutic proteins. Specifically, in this paper I have been focusing on the development of EMMA, a high versatile and efficient DNA assembly toolkit specifically developed for mammalian systems. In EMMA we have standardized and simplified the designing and generation of expression vectors, making the entire process easier, cheaper, faster and suitable for automation. Moving forward, along with the building of a large library of parts, we are adapting EMMA to generate large-sized DNA constructs and mammalian artificial chromosomes, and developing new delivery methods. (Read Andrea’s article DOI: 10.1021/acssynbio.7b00016).

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IRENE OTERO-MURAS

Irene Otero-Muras

Education. Postdoc at ETH-Zürich (Computational Systems Biology Group, Department of BioSystems Science and Engineering) 2010−2013; Ph.D. in Applied Mathematics from the University of Vigo (Spain) in 2010; M.Sc. in Chemical Engineering from the University of Santiago de Compostela (Spain) in 2002. Current Position. Researcher at the BioProcess Engineering Group, located at the Institute of Marine Research, Vigo (Spain), which belongs to the Spanish Council for Scientific Research (C.S.I.C.). Nonscientific Interests. Hiking and enjoying nature, books, playing piano, and trial movies. Transcriptional regulatory networks controlling gene expression in living cells are highly complex. Network motifs have been defined as patterns of interconnections occurring in real transcription networks more often than in randomized ones. Why some motifs are more prominent in nature than others with the same behavior but different structure, or which are the evolutionary reasons behind nonintuitive topologies are questions which remain largely unanswered. In this paper we develop an approach to explore in a systematic manner design

WILCO NIJENHUIS

R. P. Tas

Education. B.Sc. and M.Sc. in Biomedical Sciences, Utrecht University, The Netherlands. Ph.D. in mitotic signal transduction, 1244




principles of transcriptional regulatory networks, searching for patterns in gene network structural and/or parametric features associated with predefined biological functions (like the capacity for biostability, adaptive responses or the formation of stripes). (Read Irene’s article DOI: 10.1021/acssynbio.6b00306).

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Education. Diploma in Biochemistry, Goethe-University Frankfurt, Germany. Current Position. Ph.D. candidate in Biochemistry, Saarland University, Homburg, Germany. Advisor: Prof. Dr. Robert Ernst. Nonscientific Interests. Hiking in the mountains, cycling everywhere, playing soccer and reading about philosophy of science. Our work elegantly shows how synthetic biology approaches can be used for technical applications and basic research. By making use of protein domain functionalities one can design signal outcomes and tinkering can let you find novel functionalities and study communication between domains. On the one hand, I’m convinced of the power of this rationale on the other hand I’m amazed at potential philosophical pitfalls. My research interest focuses on how membrane composition influences protein activities and cellular signaling. How are certain molecular or physical aspects of membranes sensed and how does the cell react upon this? It is exciting that aromatic tuning can alter the signal outcomes of our chimeras in such a drastic way and that all this happens at the lipid bilayer interface where a zoo of different lipid species is much more than just a structural matrix. (Read John’s article 10.1021/acssynbio.6b00288).

YILI QIAN

Hsin-Ho Huang

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Education. M.S. in Mechanical Engineering, Massachusetts Institute of Technology; B.S. in Mechanical Engineering, Purdue University, West Lafayette; B.S. in Mechanical Engineering, Shanghai Jiao Tong University, China. Current Position. Ph.D. Candidate, Department of Mechanical Engineering, Massachusetts Institute of Technology, Advisor: Prof. Domitilla Del Vecchio. Nonscientific Interests. Hiking, traveling, tennis, and music. A recurrent challenge in synthetic biology is our inability to build robust circuits and to predict design outcomes. This is often due to various forms of unintended interactions among the composing genes of a circuit. I am interested in developing predictive mathematical models that characterize such unintended interactions and then apply tools from control theory to mitigate their effects. In this paper, we performed a combined modeling and experimental study to demonstrate how competition for common cellular resources can dramatically affect a circuit’s behavior. In particular, the dose response of a genetic activation cascade can be inverted as a consequence of strong resource competition. We develop user-friendly algebraic and graphical models that can be used to make design choices to minimize resource competition effects. (Read Yili’s article DOI: 10.1021/acssynbio.6b00361).

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ALEXANDER SCHMIDT

Alexander Schmidt

Education. Diploma in Analytical Chemistry, University of Erlangen-Nuremberg, Germany; Ph.D. in Biochemistry, MaxPlanck Institute of Biochemistry, Munich, Germany, Advisor: Dr. Friedrich Lottspeich; Postdoc in Institute of Molecular Systems Biology, ETH Zurich, Switzerland, Advisor: Dr. Ruedi Aebersold. Current Position. Head of Proteomics Core Facility, Biozentrum, University of Basel, Switzerland. Nonscientific Interests. Outdoor activities (hiking, climbing, surfing, biking), squash, and table soccer. The focus of our group the development and application of new state-of-the art mass spectrometry (MS) approaches to quantify proteins and their modifications directly from cells and tissues. We are particular interest in novel targeted MS methods that allow monitoring of very low abundant proteins and their modification, like phosphorylation, within a complex cell lysate. The final aim is to make these approaches fast and precise enough to make them suitable for clinical research/diagnostics. On the other hand, we are also focusing on large-scale quantitative proteomics approaches to discover new markers for diseases or help to discover system-wide molecular difference of phenotypes. We are currently applying this strategy to investigate

JOHN REINHARD

Laura Layer

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Soon Lee, Prof. Jay Keasling; Forschungszentrum Jülich (Dr. rer. nat., Advisor: Prof. Michael Bott); Korea Advanced Institute of Science and Technology (M.S., Supervisor: Prof. Sang Yup Lee); Korea University (B.S.). Current Position. Assistant Professor, Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), Nonscientific Interests. Swimming and motor-racing. I am interested in designing microbial cell factories that produce industrially relevant biochemicals from renewable resources including CO2. Microbial genetics, metabolic engineering, synthetic biology, systems biology and automated biotechnology are my research fields. Currently, I am working with two model strains: Corynebacterium glutamicum ATCC13032 and Synechococcus elongatus PCC 7942. (Read Han Min’s article DOI: 10.1021/acssynbio.7b00083).

the precise molecular mechanism of antibiotic resistance in bacteria. This will eventually help to develop new antibiotic drugs that are, owing to the increasing existence of multidrug resistant bacteria, urgently needed. (Read Alexander’s article DOI: 10.1021/acssynbio.6b00282).

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GREGORY STEPHANOPOULOS

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BENJAMIN M. WOOLSTON

Gregory Stephanopoulos

Education. Ph.D., Chemical Engineering, University of Minnestoa (1978); M.S., Chemical Engineering, University of Florida (1975); B.S., Chemical Engineering, National Technical University of Athens, Greece (1973). Current Position. Willard Henry Dow Professor of Chemical Engineering, Massachusetts Institute of Technology. Nonscientific Interests. History, reading, and travel. Reflecting upon my days of tracking down my, then, infant son as he explored the wall fixtures and crevices of our home, I am reminded that science, like pure curiosity, is most exciting at the interfaces. Our lab has always strived to champion the application of chemical engineering principles to explore the interface of cellular biology and chemistry. In this work, we move to the exploration of non-native enzyme-catalyzed reactions to impart metabolic control for isoprenoid biosynthesis. This work is one example of multiple efforts in our group to provide new access to isoprenoids in living cells. Likewise, it offers new insight into the role of chemical exploration for the atypical use of enzyme promiscuity, rather than selectivity, to direct metabolism. (Read Gregory’s article DOI: 10.1021/acssynbio.7b00072).

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Benjamin M. Woolston

Education. Ph.D., Chemical Engineering, Massachusetts Institute of Technology (2017); B.S., Chemical Engineering, The Pennsylvania State University (2011). Current Position. Postdoctoral Associate, MIT Chemical Engineering, Advisor: Gregory Stephanopoulos. Nonscientific Interests. Cycling, tennis, triathlon, and outdoor activities. My research is focused on using alternative substrates in metabolic engineering, such as single carbon substrates like methanol and syngas, which are readily available and not used as food. In typical metabolic engineering hosts like E. coli, this requires significant rewiring of native metabolism. In this paper, we took advantage of the promiscuity of FSA to design a new route to the isoprenoid precursor DXP, bypassing the native DXS-dependent route. Activity of the rewired pathway was confirmed by 13C isotopic tracing, and enabled cell growth in the presence of a DXS inhibitor. The pathway also led to improved production of the isoprenoid lycopene compared to a strain overexpressing DXS. These results highlight the potential of promiscuous enzymes to divert significant flux outside the constraints of canonical metabolic pathways. (Read Benjamin’s article DOI: 10.1021/acssynbio.7b00072).

HAN MIN WOO

Han Min Woo

Education. Joint BioEnergy Institute, Post-Doctoral Fellowship, Lawrence Berkeley National Laboratory, Advisor: Dr. Taek 1246



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JING WUI YEOH

Jing Wui Yeoh

Education. Ph.D., Department of Biomedical Engineering, National University of Singapore; B.S., Faculty of Biomedical and Health Science Engineering, University of Technology Malaysia. Current Position. Postdoctoral Research Fellow, Department of Biomedical Engineering, National University of Singapore. Nonscientific Interests. I love to watch movies, especially scifiction movies. I also enjoy Chinese calligraphy and reading books for leisure. My research interest centers around the use of computational modeling to better understand the dynamics of biological systems, for the purpose of optimizing experimental design and process. In this work, we have employed an in silico mechanistic approach to characterize the killing behavior of a two-component system-based biosensor. We were able to support the hypothesis for the existence of a positive feedback killing mechanism. Additionally, the model also suggests the need for a more stable killing protein with low degradation rate to improve the system killing efficiency. In all, this modeling effort provided a means to study a hypothesis that would otherwise be difficult to prove experimentally. (Read Jing Wui’s article DOI: 10.1021/ acssynbio.7b00058).

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Introducing Our Authors - ACS Synthetic Biology (ACS Publications)

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