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Demystifying Synthetic Biology II: Molecular Biology Advancements Enabling Synthetic Biology

Just joining us? Start with part one of our demystifying synthetic biology series.

Synthetic biology seems like a brand-new, precision scientific field – just bursting with potential – but is it really all that new? Biology is often seen as the unpredictable cousin of the math-based sciences chemistry and physics. But it’s exactly this inherent variation within biological systems that makes life uniquely adaptive and resilient – though it can also make these systems painfully difficult to understand. Only in the past century have researchers really understood the significance of DNA – the hard drive within all living cells that stores the information for life. Molecular biology research of the 20th Century has developed from crude tools into precision techniques which, when combined with new technologies in reading and writing DNA, has resulted in the field of synthetic biology.

We now have the ability to make accurate predictions on an organism’s physiology and metabolism just from looking at its genetic and product profiles, allowing us to manipulate or engineer those genes and pathways more rationally toward practical applications. Contrary to popular belief, synthetic biology is not a wholly new field. To paraphrase Sir Isaac Newton: if synthetic biology sees further, it is because we stand on the shoulders of molecular biology giants. This field stands atop the shoulders of technological titans in biology, chemistry, physics, engineering, and computer science. As part of our continuing blog series on demystifying synthetic biology, we will explore the basic approach to engineering an organism, the common research tools used in the field, and how they have advanced to enable synthetic biology.

Reading and Writing in the Language of Life

Cells are a lot like living factories, and at their core, the instructions are written in the universal language of life: DNA. DNA acts like a computer storing files for programs on a hard drive, but instead of 1s and 0s, DNA uses four nucleic acids – A, G, C, and T – which are arranged into genes that encode proteins. Collectively, all the genes from an organism make up its genome, and all the proteins make up the proteome. These proteins fill various roles, including forming the basic cellular functions like metabolic pathways.

Reading DNA – sequencing the precise AGCTs that make up a strand of DNA like a gene – is a critical element of synthetic biology. The original Sanger sequencing method took a day to read just 1,000 nucleic acid letters. Fortunately, next-generation sequencing (NGS) rapidly improved throughput, and with today’s methods, we can read whole genomes in a single day for a fraction of the cost. This development made genes (and genomes) of diverse organisms accessible to laboratories around the world, revealing new metabolic pathways creating compounds of interest across thousands of plants, animals, microbes, and viruses. It also meant that labs could more precisely make and validate DNA constructs, leading to the development of more accurate, high-throughput molecular biology techniques and paving the way for advanced genetic engineering tools like CRISPR.

Equally as critical as DNA sequencing is the ability to synthesize it, block by block. DNA synthesis has markedly improved accessibility to the diverse genomes revealed by the NGS sequencing mentioned above. On a practical level, this means researchers no longer have to grow an organism or its cells to obtain a genetic template. DNA synthesis also facilitates the rapid construction of metabolic pathways that can be assembled onto a single plasmid vector and introduced into an organism.

Since the development of improved sequencing technologies and the increasing accessibility of DNA synthesis, integrating genes and whole pathways into organisms has become commonplace in biological research. Together, these technological advancements have enabled precision molecular biology and, in doing so, ushered in the era of synthetic biology.

Biofactories in Nature

Going back to our factory analogy, proteins – specifically, enzymes – act as the factory workers in a cell. They use sugar, like glucose, or other compounds as raw materials to generate metabolic byproducts called metabolites. In a metabolic pathway, there may be several intermediate metabolites generated as different enzymes work together, similar to an assembly line. Enzyme A converts sugar into Compound 1, Enzyme B then turns Compound 1 into Compound 2, and so on until the final metabolite is reached. Humans have taken advantage of these natural processes industrially, such as in brewing beer. Beer brewing is a metabolic pathway in action. Yeast turns sugar into alcohol via a series of enzymes under the right growth conditions for fermentation.

The natural pathways of some plants and microbes generate intermediate metabolites that are precursors for other beneficial molecules. In synthetic biology, we take advantage of widely available data such as genome sequences and the metabolites those organisms produce. From there, we can determine which genes encode the enzymes for specific metabolic pathways. By adding genes from different organisms, we can redirect precursor molecules from the host organism into an entirely new pathway, producing novel and useful compounds. Through synthetic biology, making something entirely new becomes as straightforward as brewing beer. Of course, to achieve this, we must have tools that allow us to precisely harness the power of nature.

Harnessing the Power of Nature with Synthetic Biology

We complain that biology is often unpredictable but, until recently, the tools we used to study it have been clumsy and crude compared to the precision tools and techniques we employ in the field today. Not long ago, molecular biology was a messy science fraught with complications and potential error. For example, if you wanted a specific gene, you had to grow the organism first to extract its DNA. You would then use PCR (like a copy machine) to amplify a fragment and then use restriction enzymes (DNA cutters) to snip the ends of the DNA before pasting it into a target destination, like a plasmid vector for expression in a new host.

In synthetic biology today, many of these tools have improved markedly and are still in use, but are backed up by DNA synthesis, standardized genetic parts (genetic regulatory elements such as promoters and terminators), modular systems such as Golden Gate assembly, and gene editing systems like CRISPR. Genomic integration of DNA is now commonplace compared to 25 years ago. This is enabled by technologies such as CRISPR, a specific and targeted DNA-cutting molecular tool that allows precise genetic engineering of previously intractable host organisms. Ultimately, these tools have improved the speed, fidelity, and complexity of molecular biology, which has evolved to enable an engineering approach to biology and underpins the entire field of synthetic biology.

Biology is fundamentally about understanding how life, nature, and our ecosystem work. Mother Nature did pretty well before humans came along. If we can harness the power of nature through synthetic biology – specifically the precision editing of organisms to solve problems – we may be able to undo some of the damage mankind has caused during our time, while still enjoying the benefits that we created along the way.

Next time…

Now that we’ve seen how synthetic biology is simply the next generation of molecular biology tools developed in the 20th Century, we will explore how synthetic biology makes use of other 21st Century technology to scale R&D and allow rapid innovation of bio-based solutions. The greatest strength of this field is its ability to learn from data and iterate the R&D process in a rational, engineering-like approach.

In our next blog of this series, we will discuss how automation and software are applied in synthetic biology, how these technologies help scale the molecular biology tools underpinning the field, and where their values and limitations lie.

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Richard Sherwin

Head of Commercialization

Richard is an industry veteran with more than 30 years of experience in the KSM, API, and intermediate markets. He is responsible for leading the commercialization and revenue generation for Antheia’s robust pipeline of products. Richard brings an exceptional track record of leading international sales teams, driving revenue growth, building strategic partnerships, and delivering innovative products to market, including ANDA and NDA developments. Richard led commercial efforts at some of the leading global pharmaceutical companies and most recently, built his own consultancy business advising a range of clients, including $1B divisions of major multinationals.

Appropriate regulatory submissions will be prepared and submitted to support Antheia’s customers who need to reference and access necessary process-related information.

Yihui Zhu, PhD

Head of Fermentation

Yihui leads the fermentation team at Antheia. With over 25 years of hands-on experience in the field, he brings in-depth knowledge and expertise in microbial metabolism and fermentation process development. He is also skilled in developing comprehensive fermentation data collection, analysis, and visualization systems. Prior to joining Antheia, he served as a fermentation lead at Intrexon and Codexis where he successfully built fermentation labs and teams and led multiple biofuel and biochemical projects to reach stretch milestones and tech transfer. Yihui is passionate about the potential of fermentation and is dedicated to advancing the field through innovative research and development.

Yen-Hsiang Wang, PhD

Head of Strategy, Partnerships, and Finance

Yen-Hsiang leads strategy, partnerships and finance at Antheia. He completed his M.S. and Ph.D. in Bioengineering at Stanford, with extensive research experience in synthetic biology, metabolic engineering and computational modeling. Before joining Antheia, he worked at McKinsey and Tencent with a strong focus in corporate strategy and big data/advanced analytics. At Tencent, he served as Director of Strategy and Business Development for the AI Lab, leading corporate initiatives in healthcare AI/ML applications and commercialization. He also served in AI4H (Artificial Intelligence for Health), a collaboration between WHO and ITU, to establish global standards for AI in healthcare.

Audrey Wang

Head of Financial Planning and Analysis

Audrey leads financial planning and analysis at Antheia. With an MBA from Washington University in St. Louis, Audrey is passionate about leveraging financial analysis, digital technology, and data analytics to guide companies in making optimal investments and strategic business decisions. Audrey has a decade of experience in helping companies solve unique problems and creating long-term impact with unconventional approaches. Before joining Antheia, she was at Vir Biotechnology and Merck where she led various FP&A workstreams, including investment valuation, asset prioritization, and manufacturing sites operation finance support. Audrey completed CFA Level II and passed the U.S. CPA exam in 2011.

Antonij Tjahjadi, CPA

Head of Accounting

Antonij Tjahjadi leads accounting at Antheia and holds active CPA license. He joined Antheia with more than 20 years of experience in corporate accounting, bringing deep expertise in ramping up accounting operations for start-up companies, SEC reporting/technical accounting, and SOX implementation efforts. Before joining Antheia, he held various leading roles in both public and private company settings, including directing accounting functions at Ambys Medicines, where he successfully implemented Netsuite with Point Purchasing integration and set up various accounting policies and processes, and played a key role in the initial public offering of Nutanix, Inc.

Ken Takeoka

Head of Biology

Ken leads the Biology team at Antheia, which incorporates both strain and protein engineering functions. He has more than 16 years of experience in the synthetic biology field, working with leading companies, including Amyris and Novartis. One of his passions is molecular biology tool development and he previously worked to build the foundation for the automated strain engineering pipeline at Amyris. At Novartis, he modernized the molecular biology techniques and established a platform to model mechanisms of antibiotic resistance in a range of organisms.

Suzanne Sato

Head of Downstream Processing

Suzy leads downstream chemistry processes at Antheia. She has 19 years of experience in process development, including route development through synthetic chemistry and scale-up of small molecule APIs for GPCR targets under cGMP for Phase I-III trials. Before joining Antheia, Suzy led a full DSP team at Amyris where she successfully pivoted developments from biofuels hydrocarbon products to pharmaceutical intermediate, flavor, fragrance and nutraceutical products. She led a team that scaled 11 products and took five products to commercial manufacturing.

Farrah Pulce, PMP

Head of Project Management

Farrah leads program and project management at Antheia. She has over 20 years of experience leading program and project management, operations, and engineering for companies across the CPG, aerospace, and automotive industries. Prior to joining Antheia, Farrah implemented and led the sustaining program management team at Impossible Foods. She also led product operations, project management, and cost optimization at Blue Bottle Coffee and Tyson Foods to develop and commercialize new products. As a certified project management professional (PMP), Farrah has a proven record of successful project delivery, improving project management practices, and building collaborative teams.

Jordyn Lee

Head of Communications

Jordyn leads communications and external affairs at Antheia. She brings a decade of multidisciplinary communications experience in helping companies make complex science and technology accessible to broad audiences, all while maintaining technical accuracy and integrity. She has a passion for visionary storytelling and translating impact across the entire communications ecosystem – her work has spanned from public relations to corporate communications to marketing. Jordyn has served as an advisor to a number of different life sciences companies and most recently led corporate communications at Amyris.

Ben Kotopka, PhD

Head of Data Science

As Head of Data Science at Antheia, Ben manages in-house software development and external partnerships for storing and interpreting research data, executing bioinformatics analyses, and streamlining business processes. Prior to Antheia, Ben worked as an academic researcher at the intersection of machine learning, bioinformatics, and synthetic biology. Following this, as an entrepreneur and consultant, he developed and deployed data science solutions for biotechnology applications ranging from metabolomics-driven compound discovery to MRI segmentation.

Guerin Kob

Head of Supply Chain

Guerin is responsible for leading the design, development, management and improvement of Antheia’s end-to-end global supply chain. He has over 15 years of experience leading high-performing supply chain and procurement teams at leading biotechnology and specialty chemical companies, with extensive experience in process development and end-to-end supply chain optimization. Prior to joining Antheia, Guerin served as Senior Director of Global Supply Chain for Sumitomo Chemical’s biotechnology division with Valent Biosciences, where he led the end-to end supply chain including procurement, logistics and distribution, integrated business planning, materials management, customer service, and supply planning functions globally.

Pavel Aronov, PhD

Head of Bioanalytics

Pavel leads the Bioanalytics team at Antheia. He has 20 years of experience in analytical and clinical chemistry, mass spectrometry, chromatography, and metabolomics. Pavel built and led the original Chemistry and Analytics team at Impossible Foods enabling strain development, fermentation, DSP, regulatory, QC, and scale-up of leghemoglobin biomanufacturing. During his academic career at UC Davis and Stanford University Pavel developed a vitamin D assay used by all major clinical diagnostics laboratories and pioneered metabolomics studies to investigate kidney disease and microbiome.

Jesse Ahrendt

Head of Quality Assurance and Regulatory Affairs

Jesse has more than 25 years of experience in regulatory affairs, quality systems, manufacturing quality, and regulated industries, ranging from early- to late-stage pharmaceuticals, biomanufacturing, consumer care, and medical devices. He has supported global product launches and the underlying quality supply chain components in industries that require strict adherence to internationally accepted quality standards. Before Antheia, he led quality efforts at Zymergen and Sandoz, and supported many global pharmaceutical companies during his time in Biotech Consulting at NSF International, all to bring quality to the forefront in manufacturing, standardize global processes, and support customer regulatory requirements.

Heidi Pucel

Chief People Officer

Heidi is a results-driven human resources executive and HR business partner who leverages decades of experience in empowering, motivating, and inspiring to drive transformation within high-performing and rapidly-growing workforces. A certified executive coach and passionate advocate for people-oriented solutions, Pucel serves as a partner to executive teams to design programs that support employee development, engagement, and recruitment and retention. Pucel most recently served as Chief People Officer for Countsy, where she worked as an interim HR executive for clients in the biotechnology and software industries, such as Ceribell and Tune Therapeutics.

Zack McGahey

Chief Operating Officer

Zack is a leading executive in operations management, specializing in bioprocess engineering and manufacturing management. He has over 20 years of experience leading manufacturing functions for companies across the pharmaceutical, synthetic biology, diagnostics, and automotive industries. Before joining Antheia, Zack was VP of manufacturing and capex project management at Zymergen. He also gained experience managing commercial scale facilities operations for Tesla, where he was responsible for managing 10 million square feet of factory, lab and warehouse space during the Model 3 ramp.

Kristy Hawkins, PhD

Co-Founder & CSO

Kristy has over 20 years of experience in the field of synthetic biology, focusing on yeast metabolic engineering for the production of small molecules. She did the founding work on the benzylisoquinoline alkaloid pathway during her graduate studies and gained valuable industry experience at Amyris and Lygos. Kristy is an expert in tool development, high-throughput screening, and host strain and heterologous pathway engineering.

Christina Smolke, PhD

Co-Founder & CEO

Christina is a pioneer in synthetic biology and metabolic engineering, where she has over 20 years of experience. As Professor of Bioengineering and Chemical Engineering at Stanford University, her laboratory led the breakthrough research to engineer baker’s yeast to produce some of the most complex and valuable medicines known. Under her leadership, Antheia’s synthetic biology platform enables new possibilities for drug discovery and efficient, sustainable, transparent, and on-demand drug manufacturing at scale. Her vision and accomplishments have garnered numerous awards, including the Chan-Zuckerberg Biohub Investigator, NIH Director’s Pioneer Award, Nature’s 10, Novozymes Award for Excellence in Biochemical Engineering, and TR35 Award.

U.S. Secretary of State Antony J. Blinken visits Antheia to discuss biotechnology innovation

Appropriate regulatory submissions will be prepared and submitted to support Antheia’s customers who need to reference and access necessary process-related information.