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Cambridge Synthetic Biology Meetup

Cafe Synthetique: engineering algae for energy

Monday, Sep 19, 2016, 6:00 PM

Panton Arms
43 Panton Street CB2 1HL Cambridge, GB

9 Members Attending

Café Synthetique is the monthly meetup for the Cambridge synthetic biology community with informal talks, discussion and pub snacks. Algae are exciting organisms for synthetic biology: easy to grow and manufacturing an abundance of useful compounds, they are used in research on biofuels, medicines and carbon capture among many other applications. M...

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Café Synthetique is the monthly meetup for the Cambridge synthetic biology community with informal talks, discussion and pub snacks.
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Programmed DNA destruction by miniature CRISPR-Cas14 enzymes

CRISPR-Cas9 systems have been causing a revolution in biology. Harrington et al. describe the discovery and technological implementation of an additional type of CRISPR system based on an extracompact effector protein, Cas14. Metagenomics data, particularly from uncultivated samples, uncovered the CRISPR-Cas14 systems containing all the components necessary for adaptive immunity in prokaryotes. At half the size of class 2 CRISPR effectors, Cas14 appears to target single-stranded DNA without class 2 sequence restrictions. By leveraging this activity, a fast and high-fidelity nucleic acid detection system enabled detection of single-nucleotide polymorphisms.
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A Genetic Circuit Compiler: Generating Combinatorial Genetic Circuits with Web Semantics and Inference 

A Genetic Circuit Compiler: Generating Combinatorial Genetic Circuits with Web Semantics and Inference  | SynBioFromLeukipposInstitute | Scoop.it
A central strategy of synthetic biology is to understand the basic processes of living creatures through engineering organisms using the same building blocks. Biological machines described in terms of parts can be studied by computer simulation in any of several languages or robotically assembled in vitro. In this paper we present a language, the Genetic Circuit Description Language (GCDL) and a compiler, the Genetic Circuit Compiler (GCC). This language describes genetic circuits at a level of granularity appropriate both for automated assembly in the laboratory and deriving simulation code. The GCDL follows Semantic Web practice and the compiler makes novel use of the logical inference facilities that are therefore available. We present the GCDL and compiler structure as a study of a tool for generating κ-language simulations from semantic descriptions of genetic circuits.
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Focus on the benefits of building life’s systems from scratch

Focus on the benefits of building life’s systems from scratch | SynBioFromLeukipposInstitute | Scoop.it
Evolution has famously never produced a wheel. Humans famously did — and have spent much of the time since urging each other not to reinvent it. This example illustrates a clear difference between two approaches to problem solving. Nature works with what it has from the bottom up, and eventually finds a solution through an inefficient process of trial and error. Nature has never explicitly asked itself: how can I move this bulk from here to there as quickly and easily as possible? Hence, no wheeled animals, although plenty of legs, wings and other ways of getting about. Humans tend to take the opposite approach: reduce, simplify and break down a complex problem to find the most efficient solution.
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Which biological systems should be engineered?

Which biological systems should be engineered? | SynBioFromLeukipposInstitute | Scoop.it
The difference between tweaking and engineering is subtle but important. Scientists have been tweaking cells at the molecular scale for decades. In 1974, two researchers loaded DNA from a frog into a bacterium, prompting the microbe to produce a foreign RNA1. Twenty years later, scientists used a fluorescent protein from jellyfish to track gene expression in nematode worms, and to tag selected molecules in fruit flies2,3. The fluorescent components lit up under a microscope — kicking off a new era of watching cell biology in action.
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Metabolic Engineering and Synthetic Biology

Metabolic Engineering and Synthetic Biology | SynBioFromLeukipposInstitute | Scoop.it
In the modern era of next-generation genomics and Fourth Industrial Revolution, there is a growing demand for translational research that brings about not only impactful research but also potential commercialisation of R- and D-based products. Advancement of metabolic engineering and synthetic biology has put forward a viable and innovative biotechnological platform for bioproduct development especially using microbial chassis. In this chapter, readers will be introduced on the concepts of metabolic engineering, synthetic biology and microbial chassis and the applications of these biological engineering (BioE) components in the advancement of industrial and agricultural biotechnology. Main strategies in employing BioE platform are discussed especially for waste bioconversion and value-added product development. More importantly, this chapter will also discuss current endeavours in integrating systems and synthetic biology for microbial production of natural products by introducing flavonoid biosynthesis genes of Polygonum minus, a medicinally important tropical plant in engineered yeast.
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The Future Is Synthetic Biology

Increasingly, synthetic biological systems and molecules are being used to drive biological applications and discovery. At the 2018 Fall Meeting of the American Chemical Society, Cell’s Andrew Rennekamp met up with John Glass, Jim Collins, and Floyd Romesberg to discuss synthetic biology as a discipline and to get their take on where it’s headed. Annotated excerpts from this conversation are presented below, and the full conversation is available with the article online.
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Pre-existing CRISPR immunity found in 96% of humans in study

Pre-existing CRISPR immunity found in 96% of humans in study | SynBioFromLeukipposInstitute | Scoop.it
The happier and healthier future promised by CRISPR-Cas9, the gene-snipping technology that has been heralded as a potential way to treat cancer and other genetic diseases, may take a little longer to achieve. Researchers in Germany found that 96% of the people in their study had a pre-existing immunity to CRISPR.

For the new study, published in the peer-reviewed journal Nature Medicine, researchers took blood samples from 48 healthy volunteers and exposed them to Cas9, the DNA-cutting enzyme derived from Streptococcus pyogenes, which is one of the most commonly used in CRISPR research. As Xconomy first reported, the researchers found that 96% of the people were immune to Cas9, and 85% had antibodies against it.

While being immune to CRISPR sounds bad, CRISPR’s gene editing is typically built on the use of the bacterial protein Cas9. Scientists get the Cas9 from either Staphylococcus aureus, which is either harmless or the cause of staph infections, or from Streptococcus pyogenes, which causes strep throat and can lead to so-called flesh-eating bacteria if it spreads to other parts of the body. So it’s good that your body is immune, even it makes CRISPR’s seeming miracle slightly harder to achieve. For now, scientists are developing work-arounds for those of us with an immunity to CRISPR proteins, including potentially using other enzymes to cut and paste DNA.

This isn’t the first time that scientists have warned about this issue. Back in January, Stanford researchers posted a paper, before it was peer reviewed, noting that the human immune system may be the wrench in the CRISPR works. The research caused the price of CRISPR stocks to tumble, just like when another study was released showing that the DNA editing technique could result in unintended genomic consequences.
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Frontiers | Programming Bacteria with Light - Sensors and Applications in Synthetic Biology 

Photo-receptors are widely present in both prokaryotic and eukaryotic cells, which serves as the foundation of tuning cell behaviors with light. While practices in eukaryotic cells have been relatively established, trials in bacterial cells have only been emerging in the past few years. A number of light sensors have been engineered in bacteria cells and most of them fall into the categories of two-component and one-component systems. Such a sensor toolbox has enabled practices in controlling synthetic circuits at the level of transcription and protein activity which is a major topic in synthetic biology according to the central dogma. Additionally, engineered light sensors and practices of tuning synthetic circuits have served as a foundation for achieving light based real-time feedback control. Here we review programming bacteria cells with light, introducing engineered light sensors in bacteria and their applications, including tuning synthetic circuits and achieving feedback controls over microbial cell culture.
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Programming dynamic control of bacterial gene expression with the chimeric ligand and light-based promoter system

To control cells in a dynamic manner, synthetic biologists require precise control over the threshold levels and timing of gene expression. However, in practice modulating gene expression is widely carried out using prototypical ligand-inducible promoters which have limited tunability and spatiotemporal resolution. Here, we built two dual-input hybrid promoters, each retaining the function of the ligand-inducible promoter while being enhanced with a blue light-switchable tuning knob. Using the new promoters, we show that both ligand and light inputs can be synchronously modulated to achieve desired amplitude or independently regulated to generate desired frequency at a specific amplitude. We exploit the versatile programmability and orthogonality of the two promoters to build the first reprogrammable logic gene circuit, capable of reconfiguring into OR/N-IMPLY logic on the fly in both space and time without the need to modify the circuit. Overall, we demonstrate concentration and time-based combinatorial regulation in live bacterial cells with potential applications in biotechnology and synthetic biology.
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Gene synthesis allows biologists to source genes from farther away in the tree of life

Gene synthesis allows biologists to source genes from farther away in the tree of life | SynBioFromLeukipposInstitute | Scoop.it
Gene synthesis enables creation and modification of genetic sequences at an unprecedented pace, offering enormous potential for new biological functionality but also increasing the need for biosurveillance. In this paper, we introduce a bioinformatics technique for determining whether a gene is natural or synthetic based solely on nucleotide sequence. This technique, grounded in codon theory and machine learning, can correctly classify genes with 97.7% accuracy on a novel data set. We then classify ∼19,000 unique genes from the Addgene non-profit plasmid repository to investigate whether natural and synthetic genes have differential use in heterologous expression. Phylogenetic analysis of distance between source and expression organisms reveals that researchers are using synthesis to source genes from more genetically-distant organisms, particularly for longer genes. We provide empirical evidence that gene synthesis is leading biologists to sample more broadly across the diversity of life, and we provide a foundational tool for the biosurveillance community.
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New CRISPR tool opens up more of the genome for editing: Enzyme can target almost half of the genome's 'zipcodes' and could enable editing of many more disease-specific mutations

New CRISPR tool opens up more of the genome for editing: Enzyme can target almost half of the genome's 'zipcodes' and could enable editing of many more disease-specific mutations | SynBioFromLeukipposInstitute | Scoop.it
The genome editing system CRISPR has become a hugely important tool in medical research, and could ultimately have a significant impact in fields such as agriculture, bioenergy, and food security.

The targeting system can travel to different points on the genome, guided by a short sequence of RNA, where a DNA-cutting enzyme known as Cas9 then makes the desired edits.

However, despite the gene-editing tool's considerable success, CRISPR-Cas9 remains limited in the number of locations it can visit on the genome.

That is because CRISPR needs a specific sequence flanking the target location on the genome, known as a protospacer adjacent motif, or PAM, to allow it to recognize the site.

For example, the most widely used Cas9 enzyme, Streptococcus pyogenes Cas9 (SpCas9), requires two G nucleotides as its PAM sequence, significantly restricting the number of locations it can target, to around 9.9 percent of sites on the genome.

As yet, there are only a handful of CRISPR enzymes with minimal PAM requirements, meaning they are able to target a wider range of locations.

Now researchers at the MIT Media Lab, led by Joseph Jacobson, a professor of media arts and sciences and head of the Molecular Machines research group, have discovered a Cas9 enzyme that can target almost half of the locations on the genome, significantly widening its potential use. They report their findings in the Science Advances.

"CRISPR is like a very accurate and efficient postal system, that can reach anywhere you want to go very precisely, but only if the ZIP code ends in a zero," Jacobson says. "So it is very accurate and specific, but it limits you greatly in the number of locations you can go to."

To develop a more general CRISPR system, the researchers implemented computational algorithms to conduct a bioinformatics search of bacterial sequences, to determine if there were any similar enzymes with less restrictive PAM requirements.

To carry out the search, the researchers developed a data analysis software tool, which they called SPAMALOT (Search for PAMs by Alignment of Targets).

This revealed a number of interesting possible enzymes, but no clear winner. So the team then built synthetic versions of the CRISPRs in the laboratory, to evaluate their performance.

They found that the most successful enzyme, a Cas9 from Streptococcus canis (ScCas9), was strikingly similar to the Cas9 enzyme already widely used, according to co-lead author Pranam Chatterjee, a graduate student in the Media Lab, who carried out the research alongside fellow graduate student Noah Jakimo.

"The enzyme looks almost identical to the one that was originally discovered ... but it is able to target DNA sequences that the commonly used enzyme cannot," Chatterjee says.

Rather than two G nucleotides as its PAM sequence, the new enzyme needs just one G, opening up far more locations on the genome.

This should allow CRISPR to target many disease-specific mutations that have previously been out of reach of the system.

For example, a typical gene is around 1,000 bases in length, giving researchers a number of different locations to target if their aim is to simply knock out the entire gene, Jacobson says.

However, many diseases, such as sickle cell anemia, are caused by the mutation of a single base, making them much more difficult to target.

"Base editing is not just a matter of hitting that gene anywhere over the 1,000 bases and knocking it out; it is a matter of going in and correcting, in a very precise way, that one base that you want to change," Jacobson says.

"You need to be able to go to that very exact location, put your piece of CRISPR machinery right next to it, and then with a base editor -- another protein that's attached to the CRISPR -- go in and repair or change the base," he says.

The new CRISPR tool could be particularly helpful in such applications.

"We are excited to get ScCas9 into the hands of the genome editing community and receive their feedback for future development," Chatterjee says.

The researchers are now hoping to use their technique to find other enzymes that could expand the targeting range of the CRISPR system even further, without reducing its accuracy, according to Jacobson.

"We feel confident of being able to go after every address on the genome," he says.

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CRISPR heals genetic liver disorder in mice

CRISPR heals genetic liver disorder in mice | SynBioFromLeukipposInstitute | Scoop.it
Researchers healed mice with a genetic metabolic disorder that also affects humans by using a new editing tool to target and correct genetic mutations.
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Transcriptional recording by CRISPR spacer acquisition from RNA

Transcriptional recording by CRISPR spacer acquisition from RNA | SynBioFromLeukipposInstitute | Scoop.it
The ability to record transcriptional events within a cell over time would help to elucidate how molecular events give rise to complex cellular behaviours and states. However, current molecular recording technologies capture only a small set of defined stimuli. Here we use CRISPR spacer acquisition to capture and convert intracellular RNAs into DNA, enabling DNA-based storage of transcriptional information. In Escherichia coli, we show that defined stimuli, such as an RNA virus or arbitrary sequences, as well as complex stimuli, such as oxidative stress, result in quantifiable transcriptional records that are stored within a population of cells. We demonstrate that the transcriptional records enable us to classify and describe complex cellular behaviours and to identify the precise genes that orchestrate differential cellular responses. In the future, CRISPR spacer acquisition-mediated recording of RNA followed by deep sequencing (Record–seq) could be used to reconstruct transcriptional histories that describe complex cell behaviours or pathological states.
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A biomimetic receptor for glucose

A biomimetic receptor for glucose | SynBioFromLeukipposInstitute | Scoop.it
Specific molecular recognition is routine for biology, but has proved difficult to achieve in synthetic systems. Carbohydrate substrates are especially challenging, because of their diversity and similarity to water, the biological solvent. Here we report a synthetic receptor for glucose, which is biomimetic in both design and capabilities. The core structure is simple and symmetrical, yet provides a cavity which almost perfectly complements the all-equatorial β-pyranoside substrate. The receptor’s affinity for glucose, at Ka ~ 18,000 M−1, compares well with natural receptor systems. Selectivities also reach biological levels. Most other saccharides are bound approximately 100 times more weakly, while non-carbohydrate substrates are ignored. Glucose-binding molecules are required for initiatives in diabetes treatment, such as continuous glucose monitoring and glucose-responsive insulin. The performance and tunability of this system augur well for such applications.
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SBOL on the Web: Bringing the Synthetic Biology Open Language to the Web browser 

SBOL on the Web: Bringing the Synthetic Biology Open Language to the Web browser  | SynBioFromLeukipposInstitute | Scoop.it
The Synthetic Biology Open Language (SBOL) is a data standard for the in silico representation of biological designs, such as engineered genetic circuits and their constituent DNA and protein components. The SBOL specification is implemented in the form of software libraries, which can then be used to add SBOL support to both new and existing software tools. Examples of existing SBOL libraries include libSBOLj for Java, libSBOL for C, and pySBOL for Python. These libraries can be used to develop software that runs on a server or is installed locally on a computer. However, currently there are no libraries that can be used to develop SBOL software that runs directly in a Web browser. This omission is notable considering the increasing dominance of JavaScript and the Web as a platform for modern applications. This paper presents sboljs, a JavaScript software library for SBOL that is capable of being used both on the server and in the Web browser.
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How biologists are creating life-like cells from scratch

How biologists are creating life-like cells from scratch | SynBioFromLeukipposInstitute | Scoop.it
Built from the bottom up, synthetic cells and other creations are starting to come together and could soon test the boundaries of life.
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Cell-free transcription–translation: engineering biology from the nanometer to the millimeter scale 

Cell-free transcription–translation (TXTL) has become a highly versatile technology to construct, characterize and interrogate genetically programmed biomolecular systems implemented outside living organisms. By recapitulating gene expression in vitro, TXTL offers unparalleled flexibility to take apart, engineer and analyze quantitatively the effects of chemical, physical and genetic contexts on the function of biochemical systems, from simple regulatory elements to millimeter-scale pattern formation. Here, we review the capabilities of the current cell-free platforms for executing DNA programs in vitro. We describe the recent advances in programming using cell-free expression, a multidisciplinary playground that has enabled a myriad of novel applications in synthetic biology, biotechnology, and biological physics. Finally, we discuss the challenges and perspectives in the research area of TXTL-based constructive biology.
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Programming Morphogenesis through Systems and Synthetic Biology

Programming Morphogenesis through Systems and Synthetic Biology | SynBioFromLeukipposInstitute | Scoop.it
Mammalian tissue development is an intricate, spatiotemporal process of self-organization that emerges from gene regulatory networks of differentiating stem cells. A major goal in stem cell biology is to gain a sufficient understanding of gene regulatory networks and cell–cell interactions to enable the reliable and robust engineering of morphogenesis. Here, we review advances in synthetic biology, single cell genomics, and multiscale modeling, which, when synthesized, provide a framework to achieve the ambitious goal of programming morphogenesis in complex tissues and organoids.
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High prevalence of Streptococcus pyogenes Cas9-reactive T cells within the adult human population

High prevalence of Streptococcus pyogenes Cas9-reactive T cells within the adult human population | SynBioFromLeukipposInstitute | Scoop.it
The discovery of the highly efficient site-specific nuclease system CRISPR–Cas9 from Streptococcus pyogenes has galvanized the field of gene therapy1,2. The immunogenicity of Cas9 nuclease has been demonstrated in mice3,4. Preexisting immunity against therapeutic gene vectors or their cargo can decrease the efficacy of a potentially curative treatment and may pose significant safety issues3,4,5,6. S. pyogenes is a common cause for infectious diseases in humans, but it remains unclear whether it induces a T cell memory against the Cas9 nuclease7,8. Here, we show the presence of a preexisting ubiquitous effector T cell response directed toward the most widely used Cas9 homolog from S. pyogenes (SpCas9) within healthy humans. We characterize SpCas9-reactive T cells within the CD4/CD8 compartments for multi-effector potency, cytotoxicity, and lineage determination. In-depth analysis of SpCas9-reactive T cells reveals a high frequency of SpCas9-reactive regulatory T cells that can mitigate SpCas9-reactive effector T cell proliferation and function in vitro. Our results shed light on T cell–mediated immunity toward CRISPR-associated nucleases and offer a possible solution to overcome the problem of preexisting immunity.
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Engineering with Biomolecular Motors

Biomolecular motors, such as the motor protein kinesin, can be used as off-the-shelf components to power hybrid nanosystems. These hybrid systems combine elements from the biological and synthetic toolbox of the nanoengineer and can be used to explore the applications and design principles of active nanosystems. Efforts to advance nanoscale engineering benefit greatly from biological and biophysical research into the operating principles of motor proteins and their biological roles. In return, the process of creating in vitro systems outside of the context of biology can lead to an improved understanding of the physical constraints creating the fitness landscape explored by evolution. However, our main focus is a holistic understanding of the engineering principles applying to systems integrating molecular motors in general. To advance this goal, we and other researchers have designed biomolecular motor-powered nanodevices, which sense, compute, and actuate. In addition to demonstrating that biological solutions can be mimicked in vitro, these devices often demonstrate new paradigms without parallels in current technology. Long-term trends in technology toward the deployment of ever smaller and more numerous motors and computers give us confidence that our work will become increasingly relevant. Here, our discussion aims to step back and look at the big picture. From our perspective, energy efficiency is a key and underappreciated metric in the design of synthetic motors. On the basis of an analogy to ecological principles, we submit that practical molecular motors have to have energy conversion efficiencies of more than 10%, a threshold only exceeded by motor proteins. We also believe that motor and system lifetime is a critical metric and an important topic of investigation. Related questions are if future molecular motors, by necessity, will resemble biomolecular motors in their softness and fragility and have to conform to the "universal performance characteristics of motors", linking the maximum force and mass of any motor, identified by Marden and Allen. The utilization of molecular motors for computing devices emphasizes the interesting relationship among the conversion of energy, extraction of work, and production of information. Our recent work touches upon these topics and discusses molecular clocks as well as a Landauer limit for robotics. What is on the horizon? Just as photovoltaics took advantage of progress in semiconductor fabrication to become commercially viable over a century, one can envision that engineers working with biomolecular motors leverage progress in biotechnology and drug development to create the engines of the future. However, the future source of energy is going to be electricity rather than fossil or biological fuels, a fact that has to be accounted for in our future efforts. In summary, we are convinced that past, ongoing, and future efforts to engineer with biomolecular motors are providing exciting demonstrations and fundamental insights as well as opportunities to wander freely across the borders of engineering, biology, and chemistry.
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Synthetic biology for fundamental biochemical discovery

Synthetic biology for fundamental biochemical discovery | SynBioFromLeukipposInstitute | Scoop.it
Synthetic biologists have developed sophisticated molecular and genetic tools in order to engineer new biochemical functions in cells. Applications for these tools have focused on important problems in energy and medicine, but they can also be applied to address basic science topics that are not easily accessible by classical approaches. We focus on recent work that has utilized synthetic biology approaches – ranging from promoter engineering to the de novo synthesis of cellular parts – to investigate a wide-range of biochemical and cellular questions. Insights obtained by these efforts include how fatty acid composition mediates cellular metabolism, how transcriptional circuits act to stabilize multicellular networks, and fitness trade-offs involved in the selection of genetic regulatory elements. We also highlight common themes about how ‘discovery by synthesis’ approaches can aid fundamental research. For example, re-wiring of native metabolism through metabolic engineering is a powerful tool for investigating biological molecules whose exact composition and abundance is key for function. Meanwhile, endeavors to synthesize cells and their components allow scientists to address evolutionary questions that are otherwise constrained by extant laboratory models.
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Ginkgo Bioworks Is Turning Human Cells Into On-Demand Factories

Ginkgo Bioworks Is Turning Human Cells Into On-Demand Factories | SynBioFromLeukipposInstitute | Scoop.it
The synthetic biology company has opened a new foundry to churn out mammal cells, first for drug development, and later to build potentially anything at all.
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Identifying synthetic genes and understanding their use in bioengineering

Identifying synthetic genes and understanding their use in bioengineering | SynBioFromLeukipposInstitute | Scoop.it
How do new tools influence innovation in research? Neil Thompson’s group at the MIT Sloan School of Management was interested in this question and considered the field of synthetic biology as a testbed for studying the influence of new tools. In the summer of 2014, they reached out to MIT labs participating in the Synthetic Biology Engineering Research Consortium (Synberc, now EBRC) in search of a tutor who could provide subject matter expertise. I was intrigued by what lessons synthetic biologists could potentially draw from innovation across other fields and expressed interest in that tutoring role. Our collaboration began as I covered topics ranging from the basics of the central dogma to genome editing tools such as CRISPR-Cas9. The influence of CRISPR on research innovation was interesting but perhaps too new, so we continued discussing other tools until we reached DNA synthesis and DNA sequencing.

DNA synthesis is considered the key enabling technology for the field of synthetic biology. Its cost has decreased by orders of magnitude during the last two decades, and as a result it has become a routine service used by academic labs across the world. While this has fostered the development of academic and commercial technologies across numerous industrial sectors, some communities are concerned about the reduced barriers to engineering organisms.

Neil observed that the clear decrease in cost during the last two decades could make for a rich economics-oriented manuscript on how this trend has affected innovation in synthetic biology. The ability to identify synthetic DNA sequences would be essential to conduct this kind of study. Yet, to our knowledge the technical literature in synthetic biology contained no strategy for identification of synthetic sequences. Moreover, the need to identify synthetic sequences and the engineered organisms that harbor them had never been greater. These realizations became the genesis of a related but separate line of inquiry that was better suited for a scientific publication.

In “Gene synthesis allows biologists to source genes from farther away in the tree of life”, we present a bird’s eye view on a trend enabled by affordable gene synthesis within the academic biological research community. First, we developed a robust classifier for natural or synthetic genes based on sequence alone. We had a sense that sequences from nature would be contained in a publicly available database and that synthetic sequences would need to be different, but we did not know in what ways and by how much. We used a combination of theory, simulation, and machine learning to arrive at a threshold of sequence percentage identity arising from use of the nucleotide basic local alignment search tool (BLASTn) against the RefSeq reference genomic collection. Philipp Pfingstag’s development and implementation of this simple classifier on a test set of 173 sequences compiled by me resulted a remarkable 97.7% accuracy. Encouraged by this result and outside interest in applying our method to biosurveillance, we applied the strategy to a larger sequence database to investigate whether synthetic sequences were being used differently than their natural counterparts.

We could not have performed this study without tremendous assistance from the Addgene plasmid repository, which provided us with a database that contained over 19,000 unique sequences. Equipped with this rich dataset, Philipp examined one of my pet hypotheses about whether gene synthesis was being used disproportionately for expressing heterologous genes in model organisms. As a metabolic engineer, I view evolutionarily distant genome and metagenome collections as rich treasure troves of biosynthetic clusters, genetic parts, and orthogonal tools. From my own experience I knew that amplification of these natural genes for subsequent expression in the model organism Escherichia coli presents the risk of failed expression due to codon usage and that genomic DNA templates could take a long time to obtain. While in graduate school, I switched over to ordering synthetic codon-optimized DNA sequences to address both concerns and because affordable and synthetic linear DNA fragments became commercially available. But what about the community at large?

It was exciting to observe that the average genetic distance between organisms that we defined as the “source” and “expression” organisms for individual gene sequences was significantly greater for synthetic genes than for natural genes. This underscores one of the effects that DNA synthesis is having on synthetic biology innovation while also highlighting why synthetic sequences are strong indicators of engineered organisms that efficiently exhibit non-native traits. We hope our classification strategy will be part of a suite of tools used to identify such organisms as DNA synthesis technology continues to be democratized.
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Synthetic biology for fundamental biochemical discovery

Synthetic biology for fundamental biochemical discovery | SynBioFromLeukipposInstitute | Scoop.it
Synthetic biologists have developed sophisticated molecular and genetic tools in order to engineer new biochemical functions in cells. Applications for these tools have focused on important problems in energy and medicine, but they can also be applied to address basic science topics that are not easily accessible by classical approaches. We focus on recent work that has utilized synthetic biology approaches – ranging from promoter engineering to the de novo synthesis of cellular parts – to investigate a wide-range of biochemical and cellular questions. Insights obtained by these efforts include how fatty acid composition mediates cellular metabolism, how transcriptional circuits act to stabilize multicellular networks, and fitness trade-offs involved in the selection of genetic regulatory elements. We also highlight common themes about how ‘discovery by synthesis’ approaches can aid fundamental research. For example, re-wiring of native metabolism through metabolic engineering is a powerful tool for investigating biological molecules whose exact composition and abundance is key for function. Meanwhile, endeavors to synthesize cells and their components allow scientists to address evolutionary questions that are otherwise constrained by extant laboratory models.
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A Systems and Synthetic Biology Framework for Regulatory Systems Unitn-eprints.PhD - University of Trento

Biological regulatory systems are complex due to their role in living organisms in modulating precise responses to changes in internal and external conditions. In this respect, mathematical models have become essential tools to address their complexity for a better understanding of their mechanisms. The vision here, based on integrating experimental and theoretical techniques, provides a systematic means to quantitatively study the characteristics of the interactions that occur in living organisms. The outcome of such an endeavour should provide insights in terms of predictions and quantifications for further investigations in systems and synthetic biology. In this thesis, we establish an integrated modelling framework that can ensure the interaction of experimental biology with the development of quantitative mathematical descriptions of biological systems. To this end, we develop a framework to simulate and analyse biological regulatory systems by integrating different layers of regulatory information. The work herein presents a biological model development workflow in terms of a step by step approach, highlighting challenges and “real life” problems associated with each stage of model development. In the first part, we have focused on applying systems and synthetic biology modelling tools to the phosphate system at the cellular and genetic levels in Escheria coli. Then, we have analysed the interaction mechanisms and the dynamic behaviour of the phosphate starvation response deactivation and evaluated the role of phosphatase activity. We have investigated how the properties of these signalling systems depend on the network structure. Moreover, we have constructed detailed transcriptional regulatory network models and models for promoter design. In the second part, we have designed a multi-level dynamical set up by providing a novel closed loop whole body model of glucose homeostasis coupled with molecular signalling. We have then developed a system embracing the intracellular metabolic level, the cellular level involving the dynamics of the cells, the organ level, and the processes within the whole body. The output of each model directly has been fed with the variables and the parameters of the next aggregated model. This allowed us to observe the metabolic changes that occur at all levels and monitor inter-level communications for Type 2 Diabetes disease.
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