Introducing our Authors - ACS Synthetic Biology (ACS Publications)

Introducing Our Authors pubs.acs.org/synthbio

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STIJN APER

Current Position. Professor, Department of Bioengineering, University of California, Berkeley; Interim Biosciences Area Science Deputy; E.O. Lawrence Berkeley National Laboratory; Director, Berkeley Synthetic Biology Institute; CEO/CSO, DOE Systems Biology Knowledgebase; PI and Co-Director, ENIGMA SFA. Education. 1998, Postdoc, Stanford University, Department of Developmental Biology, Advisors: Harley McAdams and Lucy Shapiro; 1995, Postdoc, Stanford University, Department of Chemistry, Advisor: John Ross; 1992 Ph.D., Massachusetts Institute of Technology, Physical Chemistry, Advisor: Douglas Youvan and Keith Nelson; 1988, B.A., Carleton College, Chemistry Nonscientific Interests. In the limited hours outside work I love spending time with my family especially finding bugs, fostering dogs and taking care of two peanut-crazed rats and a cat with my amazing daughter; reading any speculative fiction, especially that which requires changing perspectives radically to solve mysteries; and trying to walk every public staircase and large hill in San Francisco. I am interested in understanding and manipulating the genetic determinants of microbial fitness in changeable environments like the soil, water and animal environments. My laboratory develops new genetic and computational technologies to query and design gene function with the ultimate goal of providing enough information to enable prediction, control and design of microbial behavior in situ. Microbiomes composed of diverse and poorly understood bacteria, archaea, fungi and other single celled creatures have profound effects on environmental dynamics, on plant and animal health and productivity. I am excited to discover the mechanisms that lead to these complex ecologies among such a mysterious bunch of characters and use this information to improve health,agriculture and environmental stability. This paper demonstrates how to map and utilize the genetic mechanisms of microbial interactions effectively using controlled assembly, highthroughput genetics and metabolomics. A foundational step toward this goal. (Read Arkin’s article; DOI: 10.1021/acssynbio.5b00236).

Leola Metzemaekers

Current Position. Ph.D. Candidate, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology (TU/e), Eindhoven, The Netherlands. Advisor: Prof. Dr. Maarten Merkx. Education. B.S. and M.S. in Biomedical Engineering, TU/e. Advisor: Prof. Dr. Maarten Merkx. Nonscientific Interests. Tennis, race cycling, playing trumpet in brass band, reading. My research focuses on the engineering of protein switches that can be used for intracellular imaging, rewiring of cell signaling or integration in synthetic signaling circuits. The protein switches that we develop are designed following a modular, synthetic biology type of protein engineering. This paper represents an example of that generic approach, reengineering a previously developed FRET-based Zn2+ sensor into a lightresponsive Zn2+ binding protein based on light-induced dimerization of the Vivid protein (VividZn). VividZn enabled in vitro reversible optical control over Zn2+ binding, and Zn2+ affinities and releasing kinetics were shown to be highly tunable. Looking forward, I am particularly interested in applying either DNA- or protein-based synthetic biology strategies for performing industrial tasks or developing therapeutics. (Read Aper’s article; DOI: 10.1021/acssynbio.6b00027).

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IREM AVCILAR-KUCUKGOZE

ADAM PAUL ARKIN

Irem Avcilar-Kucukgoze

Received: June 28, 2016 Published: July 15, 2016

Peg Skorpinski

© 2016 American Chemical Society

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DOI: 10.1021/acssynbio.6b00181 ACS Synth. Biol. 2016, 5, 531−539

ACS Synthetic Biology

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Current Position. Ph.D. candidate, Department of Biochemistry, University of Potsdam, Germany. Advisor: Prof. Zoya Ignatova. Education. M.Sc. in Molecular Biology and Genetics and Biotechnology at Istanbul Technical University, Turkey. Advisor: Assoc. Prof. Gizem Dinler-Doganay. Nonscientific Interests. Travel, cooking and cycling. My research included the effect of cellular resources allocation on the dynamics of translation in Escherichia coli. The translation is a central process that is shaped by various parameters. Therefore, the prediction of behaviors of cellular functions upon heterologous gene expression is the heart of synthetic biology. In this study, we developed a model that enables us to estimate how the allocation of shared translational machineries influences the fundamental metabolic functions and expression of a foreign protein in E. coli. We experimentally verified the model predictions by reporter fluorescent gene with different expression levels and codon usage under ambient environmental stress. Furthermore, I am also interested in other cellular entities that are included in translational process, i.e., aminoacyl-tRNAs. (Read Avcilar-Kucukgoze’s article; DOI: 10.1021/acssynbio.6b00040).

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Introducing Our Authors

ROEL A. L. BOVENBERG

DSM

Current Position. Honorary Prof, Synthetic Biology and Cell Engineering, University of Groningen, NL; Corporate Science Fellow Biological Sciences, DSM, Delft, NL. Education. Ph.D. Molecular Biology, University of Utrecht, NL (1988), Advisor: Prof Henk Jansz; M.Sc. in Chemistry, University of Leiden (1983, cum laude), Advisor: Prof Pieter van de Putte. Nonscientific Interests. European history, culture and arts, outdoor sports. My scientific interests are focused on the engineering of enzymes and microbial cell factories for a wide range of industrial applications and the need to do this in a sustainable, more predictable, time and cost efficient manner. A special interest is to develop new cell engineering methods to accelerate the discovery of natural products foramong othersnew antibiotics. Also, the responsible, safe use and social acceptance of the genetic technologies developed is of utmost importance. This paper is part of a longterm program to facilitate cell engineering of filamentous fungi for these purposes. (Read Bovenberg’s article; DOI: 10.1021/ acssynbio.6b00082).

MARCELO C. BASSALO

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Marcelo C. Bassalo

Current Position. Ph.D. Candidate in Molecular, Cellular and Developmental Biology. University of Colorado Boulder, USA. Advisor: Ryan T. Gill. Education. M.S. in Genetics and Molecular Biology, University of Campinas (UNICAMP), Brazil. Advisor: Gonçalo A. G. Pereira; B.S. in Biological Sciences, University of Campinas (UNICAMP), Brazil. Nonscientific Interests. Listening to music, playing drums, snowboarding and running. I believe that rationally engineering bacterial genomes will open doors for a broad range of novel biotechnology applications, as well as help us better understand basic cellular functions. Therefore, I’m generally interested in developing new tools for synthetic biology to facilitate genome engineering in bacterial cells. The strategy described in this work is a first step toward rapidly testing novel metabolic pathways stably in the E. coli genome. In the near future, I believe that novel pathways could be synthesized de novo or imported from complex metagenomic samples to search for interesting biological functions, using the E. coli genome as a testing platform. Also, coupling this rapid testing strategy with multiplex editing technologies should further increase diversity and function and bring us a step closer to fully rationally engineered cells. (Read Bassalo’s article; DOI: 10.1021/acssynbio.5b00187).

ALEXANDER BROWN

Elora Orazio

Current Position. Postdoctoral researcher, Department of Bioengineering, University of Illinois at Urbana−Champaign. Advisor: Dr. Pablo Perez-Pinera. Education. Ph.D. Cell and Molecular Biology, University of Rhode Island (2014). Advisor: Dr. Gongqin Sun; B.S. Biological Sciences, B.S. Microbiology, University of Rhode Island (2006). 532



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Nonscientific Interests. Big fan of sports and travel; active biker, golfer and skier; comedy and science fiction enthusiast. I believe that time and resources are the only factors limiting scientific progress. Therefore, I am passionately engaged in engineering efficient new tools that both enhance the availability of scientific models for research and accelerate our understanding of biology. While engineered nucleases have recently made genome targeting enormously accessible, genome editing strategies are overly involved and still quite limited in scale. With these ideas in mind, the work presented here demonstrates the utility and great potential of a new genome editing platform, capable of eliminating a major bottleneck to the design and implementation of numerous high-value synthetic biology projects. In future work, I hope to expand upon these and other findings through constructing novel models of disease and exciting new research tools. (Read Brown’s article; DOI: 10.1021/acssynbio.6b00056).

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SEBASTIAN CASTILLO-HAIR

Sebastian Castillo-Hair

Current Position. Ph.D. Candidate, Bioengineering Department, Rice University. Advisors: Dr. Jeffrey Tabor, Dr. Oleg Igoshin. Education. B.Sc. In Mechatronic Engineering, Universidad Nacional de Ingenieria, Peru. Nonscientific Interests. Sports, singing. My research is focused on reverse-engineering natural gene networks involved in bacterial decision-making, with an emphasis on dynamics. For example, B. subtilis differentiate into metabolically inert spores upon starvation. The decision to differentiate is taken using intra- and extracellular information, which has been shown to be encoded in the temporal dynamics of gene expression and protein activity. Our lab previously published a method to control gene expression dynamics using light-sensing two-component systems. I use these systems to introduce timevarying perturbations to gene networks, study their response, and draw conclusions about their underlying design principles. My research has also resulted in the development of hardware for high-throughput optogenetics experiments, as well as software for gene expression analysis, particularly using flow cytometry. (Read Castillo-Hair’s article; DOI: 10.1021/acssynbio.5b00284).

PATRICIA CALERO

Patricia Calero

Current Position. Ph.D., Department of Bacterial Cell Factories at Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark Hørsholm, Denmark. Advisors: Prof. Alex T. Nielsen and Dr. Sheila I. Jensen. Education. M.Sc. in Industrial, Environmental and Food Biotechnology, University Pablo de Olavide, Seville. Advisor: Prof. Fernando Govantes. Nonscientific Interests. I have a great interest in graphic design, painting and music. I also enjoy traveling and practicing sports like yoga and pilates. My research is focused in finding solutions to the toxicity generated by the accumulation of chemicals in bacterial cell factories. For this purpose I work on the development of tools to increase the production of biochemicals in the soil bacteria Pseudomonas putida as well as on the identification of its natural mechanism of tolerance toward industrially relevant chemicals. P. putida strains possess a characteristic physiology that makes them able to tolerate a wide range of chemical compounds. By understanding and exploiting such characteristics we can use these strains for the production of very toxic chemical compounds. This will help to the improvement of the efficiency of cell factories, leading to a more sustainable chemical production industry. (Read Calero’s article; DOI: 10.1021/ acssynbio.6b00081).

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DANIEL A. CHARLEBOIS

Mariola Szenk

Current Position. Postdoctoral Institution/Advisor: Laufer Center for Physical and Quantitative Biology at Stony Brook University/Prof. Gábor Balázsi. Education. Graduate Institution/Degrees/Advisor: Ottawa Institute of Systems Biology at University of Ottawa/M.Sc. Physics and Ph.D. Physics/Prof. Mads Kærn; Undergraduate 533



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Institution/Degrees: University of Calgary/B.Sc. Biological Sciences and B.Sc. Physics with Applied Mathematics Minor. Nonscientific Interests. I enjoy working on American muscle car restoration and modification, playing acoustic guitar, and building salt water aquariums. My research focuses on developing mathematical models and population dynamics algorithms to study how nongenetic phenotypic variability enhances antimicrobial drug resistance. I also perform microbiology/evolution experiments in yeast to investigate gene network evolution in fluctuating drug environments. The present work is an example of how quantitative models and wet-lab experiments can be combined to provide new insights into the dynamics of biological systems. Namely, we were able to use modeling to predict how ABC efflux pumps affect synthetic gene circuit function, and generate a hypothesis for the counterintuitive finding that efflux pumps can increase dose−response sensitivity at low inducer concentrations. Looking forward, I plan to continue to use the tools of synthetic biology to study evolution, and investigate how the dynamics of synthetic gene circuits are affected by the extracellular environment. (Read Charlebois’ article; DOI: 10.1021/acssynbio.5b00154).

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ARNOLD J. M. DRIESSEN

Zernike Institute of Advanced Materials

Current Position. Full Professor in Molecular Microbiology, University of Groningen, University of Groningen. Education. Ph.D. at the University of Groningen, Department of Microbiology (Supervisor Prof. Dr. W.N. Konings) cum laude; Undergraduate studies Biology at the University of Groningen, The Netherlands. Nonscientific Interests. Traveling, nature photography and filming, outdoors, cooking. The introduction of the highly efficient CRISPR/Cas tool for filamentous fungi is a major step forward in the maturation of the genetic toolbox for these organisms. Filamentous fungi can be used as cell factories for the production of secondary metabolites and proteins. Now with CRISPR/Cas it will be possible to quickly tailor the genome in engineering projects, such as the introduction of genomic mutations, the deletion of complete genes and even the introduction of foreign genes while maintaining full control over selection markers or even avoiding such markers which unfortunately are still limited in filamentous fungi. By having a choice of plasmid or protein-delivery based methods for the introduction of Cas9, maximum versatily is realized. (Read Driessen’s article; DOI: 10.1021/acssynbio.6b00082).

JUNCHEN DIAO

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C. Spitzenberger

Current Position. Founder and CEO of JCBiomed LLC. Education. Ph.D. in Biostatistics, Bioinformatics and Systems Biology, Graduate School of Biomedical Sciences at MD Anderson Cancer Center/UTHealth, Advisor, Dr. Gabor Balazsi; B.S. in Biology, Wuhan University, China. Nonscientific Interests. Meditation, swimming, reading, connecting and inspiring people. Regulating gene expression noise with transcriptional gene circuits is has been on the minds of synthetic biologists. I became interested in regulating an active target gene (pump) which affects the regulatory elements in the gene circuits was the first attempt in yeast cells. With our collaborators, we predicted the pump gene expression pattern with stochastic simulations and verified them with biological experiments. This has many potential applications. First, our work provided an example of quantitatively understanding a pathway that regulates an active target gene. Such pathways are common in natural systems. Second, similar systems can be used in biomaterials productions, such as biofuels and drugs/vaccines. Production of such molecules can be toxic to the host cells and therefore reduce their fitness and production rate. A feedback-regulated pump that transports these molecules from cytoplasm out provides an alternative model with controllable efflux and toxicity. (Read Diao’s article; DOI: 10.1021/acssynbio.5b00154).

SHEILA I. JENSEN

Sheila I. Jensen

Current Position. Postdoc at the Novo Nordisk Foundation, Center for Biosustainability, Technical University of Denmark. Advisor: Prof. Alex T. Nielsen Education. M.Sc. in Biology from University of Copenhagen. Advisors: Prof. Michael Kühl and Prof. Anders Priemé. Ph.D. in Biology from University of Copenhagen. Advisors: Prof. Michael Kühl and Prof. Arthur R. Grossman. In my Ph.D. I further 534



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collaborated with and got valuable advice from Prof. Dave M. Ward, Prof. Donald A. Bryant, Prof. Frederick M. Cohan, and Prof. Emeritus Richard Castenholz. Nonscientific Interests. Climbing, kitesurfing, snowboarding, horseback riding, and playing music (djembe and classical guitar and piano). I also love to prepare and eat “gourmet” food and cakes together with my family and friends. I have a diverse research background. In my Master’s thesis, I studied the microbial diversity and microenvironmental conditions in the rhizosphere of seagrasses. My Ph.D. work focused on elucidating the ecophysiology of thermophilic cyanobacteria through in situ gene expression analysis and microsensor measurements in microbial biofilms in Yellowstone National Park. After my Ph.D., I shifted to biotechnology, where I have conceived and implemented ideas that improve the genetic toolboxes for P. putida and E. coli, and I have invented novel technologies that facilitate improved production of biochemicals. Looking forward, I would like to establish my own research group and focus on sustainable production of chemicals through interdisciplinary research efforts. If the opportunity arises I would also like to start up my own company. (Read Jensen’s article; DOI: 10.1021/acssynbio.6b00081).

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BRIAN LANDRY

Brian Landry

Current Position. Ph.D. Candidate in the Department of Bioengineering at Rice University. Member of Jeff Tabor’s lab. Education. Himadri Pakrasi, Undergraduate Advisor at Washington University in St. Louis. Nonscientific Interests. I run the Bactograph STEM outreach program, which seeks to educate high school students on synthetic biology. We have distributed experimental kits to over 1000 students which enable them to create bacterial photographs in their own classrooms. The artistic nature of bacterial photography is wonderful at demonstrating the principles of synthetic biology in a form other than a research paper. I am interested in creating technologies that empower researchers to transition synthetic biology from the lab to real world applications with ease. I am hopeful that the calibration of flow cytometry data conducted by the FlowCal package will help to speed up translation of data from the test tube to the production vat or human microbiome. I am currently using FlowCal to analyze protein engineering techniques to detect a wide range of concentrations of a metabolic product produced via a synthetic microbial consortium in a natural soil environment. (Read Landry’s article; DOI: 10.1021/acssynbio.5b00284).

NILESH KARALKAR

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Nilesh Karalkar

Current Position. Scientist, Foundation for Applied Molecular Evolution, Alachua, FL. Education. Ph.D., Organic and Bioorganic Chemistry, Mumbai University, 2000. Advisor: M. M. Salunkhe. Nonscientific Interests. Tennis, bicycling, swimming and snorkeling. My research is focused on the chemical synthesis of DNA base pairs that will recognize each other through hydrogen bonds in a manner similar to natural bases (A, C, G, T) but with altered hydrogen bonding patterns. Some of these unnatural nucleobases have minor tautomerism resulting in minor mutation during PCR. In this paper, we show how we have mitigated tautomerism in isoguanine by replacing the N-7 nitrogen of isoguanine by a CH unit. The results confirm our hypothesis that 7-deazaisoguanine shows a less undesired tautomer, resulting in higher fidelity during PCR. It has been shown by the Benner group that this expanded genetic alphabet technology can be implemented in a wide variety of applications, including mutation detection and multiplexed genetic analysis. (Read Karalkar’s article; DOI: 10.1021/acssynbio.5b00276).

NICOLE A. LEAL

Nicole A. Leal

Current Position. Senior Scientist at the Foundation for Applied Molecular Evolution and Firebird Biomolecular Sciences LLC. Education. Ph.D., Molecular Biology and Cell Science, University of Florida, 1999. Advisor: Dr. Thomas A. Bobik. 535



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Nonscientific Interests. Music, mountain biking, and tennis. My graduate work focused on using a bacterial system to identify an essential enzyme for human vitamin B12 metabolism. This gave me a background in biochemistry and molecular biology, with specific expertise in DNA, RNA, and peptide manipulations. I joined the Benner laboratory to apply those skills in the field of synthetic biology using unnatural nucleic acids; I have been involved in developing the manipulative and analytical technology needed to support the conversion of six-letter information encoded in DNA to give the corresponding information in encoding RNA as well as peptide synthesis in vitro. Further, I have been associated with Firebird Biomolecular Sciences, where I’ve overseen the production of enzymes in its catalog that deal with unnatural nucleic acids. (Read Leal’s article; DOI: 10.1021/ acssynbio.5b00276).

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ZHE LYU

Zhe Lyu

Current Position. Postdoctoral Research Associate, Department of Microbiology, University of Georgia. Advisor: Dr. William B. Whitman. Education. Ph.D. Biotechnology of Resources and Environment, China Agricultural University, China (2012). Advisor: Dr. Yahai Lu; B.S. Biotechnology, Shandong University, China (2006). Nonscientific Interests. Family, tennis, guitar, noodles, video games. I have been working on many aspects of methanogenic archaea, including their physiology and ecology, since my doctoral studies. Working with a group of talented and passionate iGEM students, I am currently focused on developing tools for genetic engineering of Methanococcus maripaludis, an excellent model organism for methanogenic archaea. Because of its uniquely autotrophic and methanogenic metabolism, we are constructing M. maripaludis as a platform species for making high value biochemicals with an ultrasmall carbon footprint. As a proof of concept, we have demonstrated in this paper that a recombinant M. maripaludis strain could produce geraniol using H2 and CO2 when a synthetic geraniol synthase gene was heterologously expressed. In parallel, the same set of genetic tools has also enabled us to explore some fundamental molecular mechanisms for methanogenesis. Another unique feature of M. maripaludis is that it shares many genes with human in the information processing system. Therefore, our platform could also promote development of an archaeal model for certain human diseases. (Read Lyu’s article; DOI: 10.1021/acssynbio.5b00267).

JIAZHANG LIAN

Jiazhang Lian

Current Position. Postdoc Research Associate, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana− Champaign. Advisor: Huimin Zhao. Education. Ph.D., Chemical Engineering, University of Illinois at Urbana−Champaign. Advisor: Huimin Zhao. B.S., Bioengineering, Zhejiang University, China. Advisor: Zhinan Xu. Nonscientific Interests. Pingpong, music, reading, and playing cards. My Ph.D. research was focused on the engineering of yeast cell factories for efficient production of fuels and chemicals via enhanced supply of precursor metabolites, especially acetylCoA. In this paper, we showed that the bacterial pyruvate dehydrogenase complex, one of the most efficient and energetic routes for acetyl-CoA generation in nature, could be functionally reconstituted in the cytosol of Saccharomyces cerevisiae. Through lipoylation machinery engineering, the requirement for the supplementation of expensive compounds such as lipoic acid was completely eliminated. Currently, I’m trying to develop CRISPR/Cas9 based genome-scale engineering methods to further improve the performance of the yeast cell factories, with the construction of an acetyl-CoA overproducing yeast strain as one of the goals. (Read Lian’s article; DOI: 10.1021/acssynbio.6b00019).

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MICHAEL MAGARACI

Michael Magaraci

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Current Position. Ph.D. Candidate, Department of Bioengineering, University of Pennsylvania. Advisor: Dr. Brian Chow. Education. B.SE. in Bioengineering from the School of Engineering and Applied Science and B.S. in Economics from the Wharton School at the University of Pennsylvania. Nonscientific Interests. Rock climbing, electronic music, Engineers without Borders, and my cat Lux (named after the luxR gene). I am broadly interested in engineering tools and applying them to elucidate the regulatory mechanisms of complex cellular processes. I am also passionate about growing the synthetic biology community through education and outreach initiatives. In this work, we created an educational toolbox to enable handson exploration of the modular regulation of gene expression via both experimentation and mathematical modeling. Through bacterial strain engineering and low-cost hardware development, we provide an infrastructure to ensure that the experiments scale in size from a few students to large classes, and intellectual scope from demo to multiweek modules. My current research seeks to build optogenetic tools for monitoring cellular physiology from the bottom up by combining de novo protein design with high throughput screening and directed evolution. (Read Magaraci’s article; DOI: 10.1021/acssynbio.6b00057).

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ALEX T. NIELSEN

Alex T. Nielsen

Current Position. Professor at The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark. Education. Ph.D. in Microbiology, Technical University of Denmark; M.Sc. in Chemical Engineering and Biotechnology, Technical University of Denmark. Nonscientific Interests. Photography, archeology, traveling and sailing. The main focus of my research is within the fields of metabolic engineering, systems and synthetic biology. I have a mixed industrial and academic background and focus on both applied and fundamental scientific questions. My laboratory currently works on developing novel tools and strategies for engineering microbial cell factories for the production of biochemicals and proteins. Several different bacterial hosts and novel production pathways are being pursued. Understanding and harnessing biological systems and circuits for solving relevant societal challenges is of key importance. I have published more than 30 papers and 18 patents/ patent applications that have been cited more than 2400 times. (Read Nielsen’s article; DOI: 10.1021/acssynbio.6b00081).

DMITRY NEVOZHAY

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YVONNE NYGÅRD

Ekaterina Berdnichenko

Current Position. Principal Scientist at Far Eastern Federal University, Vladivostok, Russia and Visiting Scientist at The University of Texas MD Anderson Cancer Center, Houston, TX. Education. M.D., Vladivostok State Medical University, Vladivostok, Russia; Ph.D., Experimental Oncology, Maria Sklodowska-Curie Memorial Cancer Center, Warsaw, Poland and Institute of Immunology and Experimental Therapy, Wroclaw, Poland. Advisors: Janusz Boratyński and Adam Opolski. Nonscientific Interests. I enjoy traveling. One of my passions is photographing cities and interesting landscapes around the world. My research interests are centered on using synthetic biology approach to study DNA damage repair pathways in eukaryotes, species bias in their functioning, and its relevance to genome modification and human cancers. These pathways, especially homologous recombination, play an important role in genome integrity maintenance. Deeper understanding of these pathways will benefit existing and emerging targeted genome editing technologies, in particular CRISPR/Cas9. I am also interested in studying factors affecting the degree of precision of gene expression in eukaryotes and using that knowledge to develop tunable systems for control of gene expression in eukaryotic cells. (Read Nevozhay’s article; DOI: 10.1021/acssynbio.5b00154).

Yvonne Nygård

Current Position. Postdoctoral fellow at DSM, Delft, The Netherlands. Education. Postdoctoral fellow, University of Groningen and DSM Biotechnology Center, The Netherlands (Advisors: Arnold Driessen and Roel Bovenberg); Ph.D., VTT Technical Research Centre of Finland (Advisor: Prof. Merja Penttilä); M.Sc., Biotechnology at the University of Helsinki, Finland (Advisor: Prof. Annele Hatakka). Nonscientific Interests. Outdoors and sports (skiing, biking, running), traveling, studying languages, reading and writing. 537




to deliver in higher eukaryotes the developed therapeutic tools, effectively and efficiently. Currently, I am the scientific advisor for clinical research at the Institute for Biomedical Investigation in Málaga, IBIMA. (Read Pimentel’s article; DOI: 10.1021/acssynbio.5b00096).

Filamentous fungi naturally produce many interesting compounds and contain a large number of secondary metabolite encoding genes that are not expressed under laboratory conditions. Thus, the production of novel secondary metabolites may need substantial genetic engineering efforts. Due to the complex physiology and limited genetic toolbox of filamentous fungi, the activation and discovery of novel secondary metabolites has thus far been very laborious and time-demanding. Therefore, CRISPR/Cas9 tools open up new exciting possibilities for exploitation of filamentous fungi such as Penicillium chrysogenum. On a broader perspective, I am interested in engineering biological systems that can be used for more predictable and efficient production of any type of compound. Synthetic biology for novel industrial biotechnology applications is crucial for the transition into a biobased economy. (Read Nygård’s article; DOI: 10.1021/acssynbio.6b00082).

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CARSTEN POHL

BELÉN PIMENTEL

Carsten Pohl

Current Position. Ph.D. Student in the Driessen lab, affiliated with the Marie-Skłodowska-Curie Initial Training Network “QuantFung”. Education. Diploma Thesis (DSM Biotechnology Center, Delft/ Department of Applied and Molecular Microbiology Technical University of Berlin; Supervisor Prof. Dr. Ing. V. Meyer); Engineer’s degree in Biotechnology, Technical University of Berlin. Nonscientific Interests. Mountain biking, hiking, snowboarding, DIY furniture, books of Phillipp Kerr. Supplying more tools to the engineer’s toolbox for filamentous fungi is my key motivation in this Ph.D. project. Apart from genome editing with targetable nucleases, I am interested in rewiring regulation of fungal secondary metabolite synthesis using synthetic biology approaches. Working for different teams during my internships, I quickly came to realize that well-characterized systems, documented methods and straightforward implementation of novel tools into existing pipelines are key elements to ensure acceptance by users. By harnessing the simple way of preparing ribonuclear particles for genome editing of filamentous fungi, we provide an interesting alternative for plasmid-based genomeediting. (Read Pohl’s article; DOI: 10.1021/acssynbio.6b00082).

Belén Pimentel

Current Position. Scientific advisor, Coordinator of the Methodology, Statistics and Scientific advisory Unit at Institute for Biomedicine Investigation in Málaga (IBIMA), Andalusian Public Foundation for Biomedicine and Health Investigation (FIMABIS), in Málaga, Spain. Education. Postdoctoral fellow, Department of Immunology and Oncology, National Centre for Biotechnology-CSIC, Madrid, Spain (Advisor: Dr. Ana Clara Carrera). European Marie Curie Fellow, Hutchison/MRC Cancer Cell Unit, Cambridge, UK (Advisors: Prof. Ron Laskey and Dr. G. De la Cueva-Méndez); Ph.D. Pharmacy, Department of Cell and Developmental, Biology, CIB-CSIC, Universidad Complutense de Madrid, Spain. (Advisors: Drs. Flora de Pablo and Enrique de la Rosa); B.Sc. in Pharmacy, M.Sc. In Biochemistry and Molecular Biology, Pharmaceutical Science, Universidad Complutense de Madrid, Spain. Nonscientific Interests. Traveling to new places and exploring new cultures, outdoor activities, nature, book reading and spending time with my family and friends. My scientific interest focuses on biomedical research. I have developed my scientific career performing both basic and translational research. Initially I studied the role that insulin and PI3Kase signaling have on the development of the central nervous system in various biological models. Later on I moved into translational research. During this stage, my research contributed to demonstrate the proof of principle of a new therapeutic strategy, designed following the Synthetic Biology principles and aiming to selectively kill eukaryotic target cells and to protect the nontarget ones. The last years of my career on the bench my research moved to the field of Nanotherapeutic Systems and focused on the development of Smart Therapeutic Systems aiming to vehicle, to target and

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MARK PRESTON

Mark Preston

Current Position. Life sciences consulting, KPMG, Manchester, UK. 538




Education. Ph.D., MRC Cancer Cell Unit/Department of Clinical Medicine, University of Cambridge. Supervisor: Dr. Guillermo de la Cueva-Méndez; M.A. Natural Sciences, University of Cambridge. Nonscientific Interests. Photography, technology, hiking, running and cycling My interests center on the use of synthetic biology to tackle medical problems. My research to date has aimed to develop potential solutions to one of the challenges facing cancer therapy: balancing the need to effectively eliminate tumor cells while at the same time protecting healthy tissue from off-target toxicity. To me, one of the most fascinating aspects of synthetic biology is the ability to use biological systems as modular tools, far from the context in which they evolved. Our approach to highly selective cell killing uses a toxin and its cognate antitoxin that originally evolved to function as a bacterial plasmid maintenance system. Excitingly, we find that this same system functions in human cells and, with appropriate regulation, can selectively eliminate oncogene-expressing cells. (Read Preston’s article; DOI: 10.1021/acssynbio.5b00096).

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JOHN T. SEXTON

John T. Sexton

Current Position. Ph.D. Candidate, Department of Bioengineering, Rice University, Houston, TX. Advisor: Dr. Jeffrey Tabor. Education. B.S. in Biomedical Engineering and Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA (2011). Nonscientific Interests. Soccer! (watching and playing) and volleyball. I use CRISPRi to build complex logic circuits in bacteria. Working toward this end, it became clear to me and my lab mates that we needed a better, more universal way to characterize our genetic circuits. FlowCal is the result of an endeavor to address this concern, and it has already transformed the way we characterize genetic circuits within our own lab. We’re hopeful that it will serve others as well as it has served us, and we’re actively working with other community members to extend this work to achieve a universal calibration workflow, which will allow researchers from different laboratories on different instruments to directly and quantitatively compare flow cytometry measurements. Achieving this goal will represent a major step forward for synthetic biology as an engineering discipline, and FlowCal is a very important first step toward this goal. (Read Sexton’s article; DOI: 10.1021/acssynbio.5b00284).

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Introducing our Authors - ACS Synthetic Biology (ACS Publications)

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