SynBioFromLeukipposInstitute

Traditional views of synthetic biology often treat the cell as an unstructured container in which biological reactions proceed uniformly. In reality, the organization of biological molecules has profound effects on cellular function: not only metabolic, but also physical and mechanical. Here, we discuss a variety of perturbations available to biologists in controlling protein, nucleotide, and membrane localization. These range from simple tags, fusions, and scaffolds to heterologous expression of compartments and other structures that confer unique physical properties to cells. Next, we relate these principles to those guiding the spatial environments outside of cells such as the extracellular matrix. Finally, we discuss new directions in building intercellular organizations to create novel symbioses.

Recently, synthetic biologists have developed the Synthetic Biology Open Language (SBOL), a data exchange standard for descriptions of genetic parts, devices, modules, and systems. The goals of this standard are to allow scientists to exchange designs of biological parts and systems, to facilitate the storage of genetic designs in repositories, and to facilitate the description of genetic designs in publications. In order to achieve these goals, the development of an infrastructure to store, retrieve, and exchange SBOL data is necessary. To address this problem, we have developed the SBOL Stack, a Resource Description Framework (RDF) database specifically designed for the storage, integration, and publication of SBOL data. This database allows users to define a library of synthetic parts and designs as a service, to share SBOL data with collaborators, and to store designs of biological systems locally. The database also allows external data sources to be integrated by mapping them to the SBOL data model. The SBOL Stack includes two Web interfaces: the SBOL Stack API and SynBioHub. While the former is designed for developers, the latter allows users to upload new SBOL biological designs, download SBOL documents, search by keyword, and visualize SBOL data. Since the SBOL Stack is based on semantic Web technology, the inherent distributed querying functionality of RDF databases can be used to allow different SBOL stack databases to be queried simultaneously, and therefore, data can be shared between different institutes, centers, or other users.

By feeding strings of human-written data into colonies of bacteria, scientists have discovered a way to turn tiny cells into living, squirming hard drives.

A team of Harvard scientists led by geneticist Seth Shipman has just developed a fascinating way to write chunks information into the genetic code of living, growing bacterial cells. It could be the code for a computer program or the lines of a poem. Either way, these living memory sticks can pass this data onto their descendants, and scientists can later read that data by genotyping the bacteria. As Shipman explains in a paper today in the journal Science, his method can upload roughly 100 bytes of data.

Bacterial Bytes

To be clear, scientists have already proven they can synthetically manufacture DNA in the lab and write into it pretty much whatever they want, including a full-length book on science. "But working within a living cell is an entirely different story and challenge," says Shipman. "Rather than synthesizing DNA and cutting it into a living cell, we wanted to know if we could use nature's own methods to write directly onto the genome of a bacterial cell, so it gets copied and pasted into every subsequent generation."

Before Shipman's experiment, the most information any scientist had ever permanently uploaded into a living cell was 11 bits of information. That's a mere 11 zeros and ones of binary data, and less information than your computer requires to code for two alphabetic letters. Shipman's technique expanded this record to roughly 100 bytes of data. For reference, it would take your computer precisely one hundred bytes to encode this very sentence.

Throughout biology, function is intimately linked with form. Across scales ranging from subcellular to multiorganismal, the identity and organization of a biological structure's subunits dictate its properties. The field of molecular morphogenesis has traditionally been concerned with describing these links, decoding the molecular mechanisms that give rise to the shape and structure of cells, tissues, organs, and organisms. Recent advances in synthetic biology promise unprecedented control over these molecular mechanisms; this opens the path to not just probing morphogenesis but directing it. This review explores several frontiers in the nascent field of synthetic morphogenesis, including programmable tissues and organs, synthetic biomaterials and programmable matter, and engineering complex morphogenic systems de novo. We will discuss each frontier's objectives, current approaches, constraints and challenges, and future potential.