Introducing Our Authors - ACS Synthetic Biology (ACS Publications)

Introducing Our Authors pubs.acs.org/synthbio

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LITAL ALFONTA

Education. B.S. and M.S., Cell Biology, University of Osnabrück, Germany; Ph.D., Biology, University of Osnabrück, Germany and University of Oviedo, Spain. Advisors: Prof. Jürgen J. Heinisch and Prof. Rosaura Rodicio. Current Position. Postdoctoral fellow at the Institute of Pharmaceutical Biology and Biotechnology, Department of Pharmacy, Philipps-University Marburg, Germany. Advisor: Prof. Shu-Ming Li Nonscientific Interests. Hiking, traveling, movies. Beta-carboline derivatives are widely spread in nature and exhibit intriguing biological and pharmacological activities. In this paper, we employed Saccharomyces cerevisiae cultures for the production of novel prenylated beta-carboline derivatives. This was achieved by introduction of just one key gene encoding a fungal prenyltransferase. The yeast cultures provide all the necessary substrates as well as the required reaction conditions. The structural variety was increased by application of different prenyltransferases, which attach the prenyl moiety at different positions of the indole ring. Manipulation of precursor supply led to accumulation of 400 mg/L of the designed products. This work is an excellent example for the exploitation of yeast cultures in the synthetic biology of small molecules. (Read Backhaus’ article DOI: 10.1021/acssynbio.6b00387).

Michael Meijler

Education. B.Sc. Hebrew University of Jerusalem, Chemistry, Jerusalem, Israel; M.Sc. Hebrew University of Jerusalem, Jerusalem, Israel, Biochemistry and Chemistry, Advisors: Zvi Selinger and Chaim Gilon; Ph.D. Hebrew University of Jerusalem, Jerusalem, Israel, Bioelectrochemistry, Advisor: Itamar Willner. Postdoctoral Studies: Genetic code expansion, The Scripps Research Institute, La Jolla CA, Advisor: Peter G. Schultz. Current Position. Associate Professor, Department of Life Sciences, Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel. Nonscientific Interests. Tracking, hiking, camping, biking, movies. Lital Alfonta’s research group is interested in finding the limits and the governing factors of the translational machinery in prokaryotes throughout evolution using synthetic biology tools. In addition, studying the interface between microorganisms and enzymes to electrodes is one of the major directions the group has been taking in recent years with aiming toward understanding electron transfer processes, and engineering enzymes and microorganisms for improved electron transfer. (Read Alfonta’s article DOI: 10.1021/acssynbio.7b00019).

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ANKE BECKER

KATJA BACKHAUS Philipps-Universität Marburg/Reinhold Eckstein

Education. Dipl.Biol. (equivalent to M.Sc.), Biology, Bielefeld University; Ph.D., Bielefeld University, Advisor: Prof. Dr. Alfred Pühler. Current Position. Full Professor, LOEWE Center for Synthetic Microbiology and Department of Biology, Philipps-Universität Marburg. Nonscientific Interests. Sports. Research in my lab aims at a systems-level understanding of genome organization and regulatory networks in nitrogenfixing symbiotic alphaproteobacteria. We apply synthetic biology approaches to reorganize alpha-rhizobial genomes and to Received: May 31, 2017 Published: June 16, 2017

Katja Backhaus

© 2017 American Chemical Society

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DOI: 10.1021/acssynbio.7b00181 ACS Synth. Biol. 2017, 6, 915−920

ACS Synthetic Biology

Introducing Our Authors

Current Position. Postdoctoral researcher at the lab of Prof. Dr. Anke Becker, LOEWE Center for Synthetic Microbiology, Philipps Universität Marburg. Nonscientific Interests. Sports, Computer Hardware, Hiking. My research work focuses on developing genome editing and engineering tools on the one hand, and unraveling the genome biology of Sinorhizobium meliloti on the other hand. Regarding genome engineering, I established Cre/lox systems that enable megabase-scale genomic rearrangements, e.g., whole-genome fusions of the multipartite genome of S. meliloti. Comprehensive manipulations of the genome structure will help to identify fundamental design principles of a bacterial genome, thereby contributing to synthetic approaches, such as large-scale DNA assembly. For this purpose pABCs could constitute a solid basis. Cre/lox-mediated deletions, inversions and translocations of large genomic regions and the substitution of native oriVs with heterologous repABC regions will further facilitate analysis of the spatiotemporal regulation of DNA replication and segregation. (Read Döhlemann’s article DOI: 10.1021/acssynbio.6b00320).

reprogram natural or construct novel regulatory modules inthese bacteria, aiming at reconstruction of symbiotic traits. Another focus of our work is the development of tools and methods to support automated combinatorial experiments in synthetic biology. (Read Becker’s article DOI: 10.1021/acssynbio.6b00320).

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YONATAN CHEMLA

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Yonatan Chemla

Education. B.Sc. in Biotechnology Engineering, Ben-Gurion University of the Negev, Israel. B.A. in World History, Open University of Israel. M.Sc. in Life-Sciences, Ben-Gurion University of the Negev, Israel. Advisor: Prof. Lital Alfonta. Current Position. Ph.D. student, Department of Life Sciences, Ben-Gurion University of the Negev. Advisor: Prof. Lital Alfonta. Nonscientific Interests. Basketball, Football, Running, Board games, Computer games, Family life. My Ph.D. is focused on gaining a better understanding of the processes of bacterial transcription and translation. Specifically, I want to better understand the rudimentary principals that govern genetic code expansion. To do that, I explore and push to the limits the transcription/translation systems in bacteria such as E. coli and cyanobateria (S. elongatus). Under these conditions interesting phenomena appear and by understanding these I hope to infer new knowledge on the natural processes that occur in these bacteria. This work presents an interesting hypothesis regarding the spatial density of the transcription and translation processes in E. coli that needs to be further studied. (Read Chemla’s article DOI: 10.1021/acssynbio.7b00019).

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AKIHIRO FURUYA

Akihiro Furuya

Education. Bachelor’s degree, Department of Chemistry & Biotechnology, School of Engineering, the University of Tokyo, Tokyo, Japan, Advisor: Prof. Takashi Kato; Master’s degree, Department of General Systems Studies, Graduate School of Arts and Sciences, the University of Tokyo, Tokyo, Japan, Advisor: Assoc. prof. Moritoshi Sato. Current Position. Ph.D. candidate, Department of General Systems Studies, Graduate School of Arts and Sciences, the University of Tokyo, Tokyo, Japan, Advisor: Assoc. prof. Moritoshi Sato. Nonscientific Interests. Skateboarding, futsal, computer games, wine (grape or rice), and history of Japan and the world. My research interest involves using optogenetics to regulate cells throughout the body and in different species by using light in various ways. This will reveal mechanisms involved in neurons (memory) and cancer cells (cell migration), among others. In this study, we focused on improving a weak optogenetic tool. The strategy for enhancing the tool was to introduce the assembly domain to the cytosolic probe. The probe showed a high degree of spatiotemporality in photoregulation. Moreover, we fused the functional domain of Tiam1, DH/PH domain, to the enhanced tool described above and found that this new optogenetic tool induced large lamellipodia and vigorous ruffles on the plasma membrane. Additionally, we detected the dynamic morphologies of photoactivated apical ruffles by using 4D fluorescence microscopy. (Read Furuya’s article DOI: 10.1021/acssynbio.7b00022).

JOHANNES DÖ HLEMANN

Marcel Wagner

Education. B.Sc. and M.Sc. in Biology, TU Kaiserslautern; Ph.D. at the LOEWE Center for Synthetic Microbiology, Philipps Universität Marburg; Advisor: Prof. Dr. Anke Becker. 916



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ARAVIND NATARAJAN

Education. M.Eng. (Dipl.-Ing.) Technical University Berlin, Germany & Dongseo University Busan, Korea, Advisors: Prof. Vera Meyer and Dr. Marion Abraham. Current Position. Ph.D. student, Chair of Chemistry of Biogenic Resources, Technical University of Munich, Advisor: Prof. Volker Sieber. Nonscientific Interests. Traveling, cooking, swimming. My main research interest is in using biotechnology to create robust, efficient, and safe microorganisms that can produce valuable chemicals and therapeutics. My focus at present is on using the nonconventional yeast Pichia pastoris as a protein secretion platform. In this article, we develop a toolkit of parts to enable the efficient construction of biological circuits and protein secretion constructs for P. pastoris. We characterize the effectiveness of our toolkit by creating a large library of secretion constructs and observe interesting dependencies in many factors controlling gene expression and effective secretion. Looking forward, we are aiming to apply our toolkit to industrially relevant products to deepen our understanding of protein secretion. (Read Obst’s article DOI: 10.1021/acssynbio.6b00337).

Roger W. Theise

Education. B.Sc. in Biochemistry at Ramakrishna Mission Vivekananda College, University of Madras, India; M.Sc. in Genomics at Madurai Kamaraj University, India, Thesis Advisor: Professor Hussain Munavar. Current Position. Ph.D. candidate, Department of Microbiology, Cornell University, Advisor: Professor Matthew P. DeLisa. Nonscientific Interests. Working on diversity initiatives to foster an inclusive campus environment; Graduate Teaching Fellow, training teaching assistants in the College of Engineering, Cornell University in latest pedagogical techniques; softball; rowing. I am interested in (1) engineering bacteria for the affordable production of novel therapeutics and industrially relevant enzymes, and (2) unraveling fundamental processes in bacterial pathogenesis. In this study, we engineered a tunable survivalselection assay in Escherichia coli that links extracellular protein expression to antibiotic resistance, thereby generating a facile assay for understanding and engineering secretion phenotypes. Using this assay, we discovered a number of hypersecretory mutantssingle-gene knockouts that increased protein secretion up to 18-fold. This phenotype was extended to the secretion of diverse proteins including cellulolytic enzymes and glycosylated proteins. We anticipate that this generalizable survivalselection assay will enable the engineering of laboratory E. coli strains with greatly expanded secretomes comprised of both industrially and therapeutically relevant proteins. Further, this platform could be leveraged to probe the biology of pathogenesis-associated secretory systems and their substrate proteins. (Read Natarajan’s article DOI: 10.1021/acssynbio.6b00366).

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EDEN OZER

Eden Ozer

Education. B.Sc. Biotechnology Engineering, Ben-Gurion University of the Negev. Current Position. Ph.D. candidate, Department of Life Sciences, Ben-Gurion University of the Negev. Advisor: Prof. Lital Alfonta. Nonscientific Interests. Snowboarding, surfing and video games. The focus of my research is the employment of genetic code expansion to generate new biotechnological tools and systems, enriching the range of abilities of the scientific community. One of my current projects involves utilizing incorporation of unnatural amino acids for the creation of complex structures, eventually allowing the channeling of an electron transfer cascade in a biofuel cell. Another filed of interest of mine is the exploration of biofilms and their potential beneficial aspects. In time, I aspire to apply my knowledge at genetic code expansion on the subject of biofilms as well, and possibly create more efficient biofuel cells. (Read Ozer’s article DOI: 10.1021/ acssynbio.7b00019).

ULRIKE OBST

Lisa Steiner

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ORR SCHLESINGER

for the study of cell lineages. By creating an updateable record within an individual cell’s genome, we can enable the relationships between cells to be studied in unprecedented detail. This research has the potential to elucidate the complex mechanisms of cell differentiation and has implications for the study of processes within the body such as development and cancer. (Read Schmidt’s article DOI: 10.1021/acssynbio.6b00309).

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GAO-YI TAN

Vardit Schlesinger

Education. B.Sc. and M.Sc. in Biotechnology Engineering, Ben-Gurion University of the Negev. Advisor: Prof. Lital Alfonta. Current Position. Ph.D. candidate, Department of Life Sciences, Ben-Gurion University of the Negev. Advisor: Prof. Lital Alfonta. Nonscientific Interests. My hobbies include playing volleyball, hiking, cooking and spending time with my wife and son. My Ph.D. study is focused on using the technology of genetic code expansion to better understand bacterial transcription and translation kinetics and for protein engineering. In this work, we aim to improve the efficacy of biofuel cells by controlling electron pathways near the electrodes. We use noncanonical amino acids to control the orientation of immobilized redox enzymes toward the electrode surface in order to improve electron transfer efficiency. In this manuscript, we employ genetic code expansion, among other methods, to study and model the kinetics of the transcription and translation processes in E. coli, and present a hypothesis regarding a phenomenon that is greatly affecting the efficiency of protein synthesis. (Read Schlesinger’s article DOI: 10.1021/acssynbio.7b00019).

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Gao-Yi Tan

Education. Ph.D. in Microbiology, Shanghai Jiao Tong University, Advisor: Prof. Jian-Jiang Zhong & Prof. Linquan Bai; Postdoc in School of Pharmaceutical Sciences, Wuhan University, Advisor: Prof. Tiangang Liu. Current Position. Associate Professor, State Key Laboratory of Bioreactor Engineering, and East China University Science and Technology School of Biotechnology, Shanghai, China. Nonscientific Interests. Reading, movies and swimming. Due to the complicated transcriptional and metabolic regulation of natural product biosynthesis in Actinobacteria, especially in the cases of genome mining and heterologous expression, it is often difficult to rationally and systematically engineer synthetic pathways. To focus on this problem, Prof. Tiangang Liu and his group has developed the various strategies ranging from heterologous production of a natural product to subsequent application of omics guided synthetic modules optimization. Heterologous production of large type I PKS compound spinosad in Streptomyces albus has been demonstrated as an example of the application of these approaches. (Read Tan’s article DOI: 10.1021/acssynbio.6b00330).

STEPHANIE T. SCHMIDT

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MARCEL WAGNER

Stephanie T. Schmidt

Education. B.S., Bioengineering, Rice University, Advisor: Antonios Mikos; M.S., Bioengineering, Stanford University, Advisor: Stephen Quake. Current Position. Ph.D. Candidate, Quake Laboratory, Department of Bioengineering, Stanford University. Nonscientific Interests. Travel and photography. I am very excited about leveraging genome editing and high-throughput sequencing to engineer dynamic DNA barcodes

Johannes Döhlemann

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Education. B.Sc. in Biology and M.Sc. in Molecular and Cellular Biology at Philipps-Universität Marburg, Marburg, Germany. Current Position. Ph.D. Candidate, LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany. Advisor: Prof. Dr. Anke Becker. Nonscientific Interests. Outdoor activities like hiking, mountain biking, running and playing soccer. My scientific interests lie at elucidating the molecular principles underlying the spatial organization, replication and partitioning of bacterial multipartite genomes. The plantsymbiont Sinorhizobium meliloti possesses a tripartite genome composed of one main chromosome and the RepABC-type megaplasmids pSymA and pSymB. Partitioning of the replication origins follows a strict temporal order, commencing with the chromosome and followed by pSymA and then by pSymB. A comprehensive Cre/lox toolbox for genome reorganization as well as compatible repABC replication origins enable new experimental setups, which will facilitate analysis of the spatiotemporal regulation and partitioning of the chromosome and the two megaplasmids. Finally, applying biochemical approaches we further aim to find interaction partners and unravel the mechanistic basis of the process of megaplasmid segregation. (Read Wagner’s article DOI: 10.1021/acssynbio.6b00320).

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GUIHUA ZENG

Yongyi Wei

Education. B.S. in Applied Chemistry, Shantou University, China. Current Position. Ph.D. Candidate, Department of Chemistry and Chemical Biology, University of New Mexico, Advisor: Dr. Fu-Sen Liang. Nonscientific Interests. I enjoy gardening, reading and cooking, and love to play ping-pang and badminton. My academic concentration is focused on developing new chemical strategies to generate de novo signaling pathways that link signaling molecules to different downstream cellular events in mammalian cells. This approach integrates reactivity-based chemical sensors and chemically induced protein dimerization (CID). We chemically caged and inactivated the CID inducers with chemical probes. Only when exposed to specific signals, the caging groups can be removed and generate the free inducers to control downstream cellular events. We developed the strategy to induce the gene expression, protein translocation and cytoskeletal remolding, sensing to exogenous and endogenous H2O2 in previous work and sensing to Fe2+ in this paper, and designed signal circuitry incorporating “AND” and “OR” biologic gates that enables mammalian cells to translate different combinations of Fe2+ and H2O2 signals into predefined biological outputs. (Read Zeng’s article DOI: 10.1021/ acssynbio.6b00255).

YONGYI WEI

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Yongyi Wei

Education. M.S., Shanghai Normal University, Advisor: Hexing Li; Undergraduate, Chemistry, Nanjing University; Wuxi Pharmatech Ltd. Current Position. Ph.D. student, University of New Mexico Nonscientific Interests. Photography, travel, and hiking My research is focusing on the development of new small molecules for therapy and diagnosis application. On the basis of special recognition reactions, such as the ferric-hydroxylamine reaction, the drug or fluorophore can be released at targeted locations and applied for selective therapy. Our ferric-hydroxylamine system has been successfully applied for elucidating stroke mechanism in vitro, and drug targeting release for cancer therapy. We also developed a viscosity detector based on a fluorescent molecular rotor for stroke detection. Currently, we are developing a new photoresponding theranostic system. (Read Wei’s article DOI: 10.1021/acssynbio.6b00255).

JINGWEN ZHOU

Jingwen Zhou

Education. B.S. in Food Science and Engineering, Huazhong Agricultural University, China; M.S. in Microbiology, Huazhong Agricultural University, China; Ph.D in Fermentation Engineering, 919




Jiangnan University, China, Advisor: Prof. Jian Chen; Postdoc in Harvard University, Advisor: Prof. Eugene I. Shakhnovich. Current Position. Full Professor, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China. Nonscientific Interests. Travel, swimming, and cooking. Zhou’s research group focuses on the fine-tuning of complicated metabolic networks for efficient production of keto acids and flavonoids. During the design of metabolic engineering strategies to improve titer, yield and productivity of target products, tools for the fine-tuning of transcription or translation are vital. Escherichia coli is the most commonly used host for metabolic engineering. However, the available of gradient constitutive promoters significantly restricted the design of complicated metabolic networks in the bacterium. In this study, Zhou’s group obtained and validated a panel of cascade promoter-5′-UTR complexes with the ability to drive a wide range expression levels in E. coli. The panel of 5′-UTR complexes could be utilized for fine-tuning of even complicated metabolic networks and achieve more goals without the addition of inducers. (Read Zhou’s article DOI: 10.1021/acssynbio.7b00006).

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Introducing Our Authors - ACS Synthetic Biology (ACS Publications)

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