Bringing Standards to Life: Synthetic Biology Standards and Intellectual Property

In aspiring to become a true engineering discipline for the biological sciences, the field of synthetic biology has a unique opportunity to create and encourage the widespread adoption of standards to enhance innovation and social impact in the field. This article presents a study of the standards setting efforts by the institutions, firms, governments, and individuals within the field of synthetic biology. Numerous standards have been proposed in synthetic biology, including those relevant to structure, function, description, measurement, data, information exchange, software, biosafety and biosecurity, and even law. At the present time, the adoption of technical standards has been relatively modest and no one technical standard appears to have dominated the field. Standards covering policies in biosecurity, by comparison, are more firmly established and biosecurity practices governing commercial orders for synthetic DNA have been widely adopted. Among standards-setting groups within the synthetic biology community, most have expressed a preference that standards remain open and accessible to the community as a whole. Recent developments, including the U.S. Supreme Court's decision in AMP v. Myriad and the Leahy-Smith America's Invents Act, could help give greater clarity to the scope of patent rights covering innovations and standards in synthetic biology. Copyright and trademark may provide alternatives mechanisms for conferring rights in synthetic biology inventions, setting and reinforcing standards, or promoting open innovation. Whether formal policies requiring the disclosure and licensing of property rights covering technical standards could be made mandatory or would ultimately be beneficial to the field of synthetic biology remain open questions. What is certain is that the synthetic biology community is unusually attuned to debates surrounding intellectual property and standards setting, and views its engagement in these debates as vital to ensure the continued success of synthetic biology

A survey of enabling technologies in synthetic biology

BACKGROUND: Realizing constructive applications of synthetic biology requires continued development of enabling technologies as well as policies and practices to ensure these technologies remain accessible for research. Broadly defined, enabling technologies for synthetic biology include any reagent or method that, alone or in combination with associated technologies, provides the means to generate any new research tool or application. Because applications of synthetic biology likely will embody multiple patented inventions, it will be important to create structures for managing intellectual property rights that best promote continued innovation. Monitoring the enabling technologies of synthetic biology will facilitate the systematic investigation of property rights coupled to these technologies and help shape policies and practices that impact the use, regulation, patenting, and licensing of these technologies. RESULTS: We conducted a survey among a self-identifying community of practitioners engaged in synthetic biology research to obtain their opinions and experiences with technologies that support the engineering of biological systems. Technologies widely used and considered enabling by survey participants included public and private registries of biological parts, standard methods for physical assembly of DNA constructs, genomic databases, software tools for search, alignment, analysis, and editing of DNA sequences, and commercial services for DNA synthesis and sequencing. Standards and methods supporting measurement, functional composition, and data exchange were less widely used though still considered enabling by a subset of survey participants. CONCLUSIONS: The set of enabling technologies compiled from this survey provide insight into the many and varied technologies that support innovation in synthetic biology. Many of these technologies are widely accessible for use, either by virtue of being in the public domain or through legal tools such as non-exclusive licensing. Access to some patent protected technologies is less clear and use of these technologies may be subject to restrictions imposed by material transfer agreements or other contract terms. We expect the technologies considered enabling for synthetic biology to change as the field advances. By monitoring the enabling technologies of synthetic biology and addressing the policies and practices that impact their development and use, our hope is that the field will be better able to realize its full potential

BBF RFC 107: Copyright and Licensing of BBF RFCs

In this BioBricks Foundation Request for Comments (BBF RFC), we update and clarify the copyright and licensing notice of BBF RFC documents

Metabolic biomarkers assessed with PET/CT predict sex-specific longitudinal outcomes in patients with diffuse large B-cell lymphoma

In many cancers, including lymphoma, males have higher incidence and mortality than females. Emerging evidence demonstrates that one mechanism underlying this phenomenon is sex differences in metabolism, both with respect to tumor nutrient consumption and systemic alterations in metabolism, i.e., obesity. We wanted to determine if visceral fat and tumor glucose uptake with fluorodeoxyglucose-positron emission tomography/computed tomography (FDG-PET/CT) could predict sex-dependent outcomes in patients with diffuse large B-cell lymphoma (DLBCL). We conducted a retrospective analysis of 160 patients (84 males; 76 females) with DLBCL who had imaging at initial staging and after completion of therapy. CT-based relative visceral fat area (rVFA), PET-based SUVmax normalized to lean body mass (SULmax), and end-of-treatment FDG-PET 5PS score were calculated. Increased rVFA at initial staging was an independent predictor of poor OS only in females. At the end of therapy, increase in visceral fat was a significant predictor of poor survival only in females. Combining the change in rVFA and 5PS scores identified a subgroup of females with visceral fat gain and high 5PS with exceptionally poor outcomes. These data suggest that visceral fat and tumor FDG uptake can predict outcomes in DLBCL patients in a sex-specific fashion

An open toolkit for tracking open science partnership implementation and impact.

Serious concerns about the way research is organized collectively are increasingly being raised. They include the escalating costs of research and lower research productivity, low public trust in researchers to report the truth, lack of diversity, poor community engagement, ethical concerns over research practices, and irreproducibility. Open science (OS) collaborations comprise of a set of practices including open access publication, open data sharing and the absence of restrictive intellectual property rights with which institutions, firms, governments and communities are experimenting in order to overcome these concerns. We gathered two groups of international representatives from a large variety of stakeholders to construct a toolkit to guide and facilitate data collection about OS and non-OS collaborations. Ultimately, the toolkit will be used to assess and study the impact of OS collaborations on research and innovation. The toolkit contains the following four elements: 1) an annual report form of quantitative data to be completed by OS partnership administrators; 2) a series of semi-structured interview guides of stakeholders; 3) a survey form of participants in OS collaborations; and 4) a set of other quantitative measures best collected by other organizations, such as research foundations and governmental or intergovernmental agencies. We opened our toolkit to community comment and input. We present the resulting toolkit for use by government and philanthropic grantors, institutions, researchers and community organizations with the aim of measuring the implementation and impact of OS partnership across these organizations. We invite these and other stakeholders to not only measure, but to share the resulting data so that social scientists and policy makers can analyse the data across projects

Opening options for material transfer.

UNLABELLED: The Open Material Transfer Agreement is a material-transfer agreement that enables broader sharing and use of biological materials by biotechnology practitioners working within the practical realities of technology transfer. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nbt.4263) contains supplementary material, which is available to authorized users

Draft OpenMTA 11 June 2017, for comment

The Open Material Transfer Agreement (OpenMTA) is designed to allow researchers to share materials on an open basis while working within the practical realities of technology transfer. Our goal it to help reduce transaction costs, support collaboration among researchers across institutional and international boundaries, promote access to materials for researchers in less privileged institutions and world regions, and provide an avenue for researchers and their institutions to be credited for materials made openly available. The OpenMTA was developed as a collaborative effort led by the BioBricks Foundation and OpenPlant Synthetic Biology Research Centre, with input from researchers, technology transfer professionals, legal experts, social scientists and other stakeholders. Design goals for the OpenMTA include access, attribution, reuse, redistribution, and nondiscrimination, in line with open access and open data principles. A proposed draft of the OpenMTA Master Agreement is herewith made available for public review and comment. Please send comments to Linda Kahl via [email protected]

Loss of the keratin cytoskeleton is not sufficient to induce epithelial mesenchymal transition in a novel KRAS driven sporadic lung cancer mouse model.

Epithelial-to-mesenchymal transition (EMT), the phenotypical change of cells from an epithelial to a mesenchymal type, is thought to be a key event in invasion and metastasis of adenocarcinomas. These changes involve loss of keratin expression as well as loss of cell polarity and adhesion. We here aimed to determine whether the loss of keratin expression itself drives increased invasion and metastasis in adenocarcinomas and whether keratin loss leads to the phenotypic changes associated with EMT. Therefore, we employed a recently described murine model in which conditional deletion of the Keratin cluster II by Cre-recombinase leads to the loss of the entire keratinmultiprotein family. These mice were crossed into a newly generated Cre-recombinase inducible KRAS-driven murine lung cancer model to examine the effect of keratin loss on morphology, invasion and metastasis as well as expression of EMT related genes in the resulting tumors. We here clearly show that loss of a functional keratin cytoskeleton did not significantly alter tumor morphology or biology in terms of invasion, metastasis, proliferation or tumor burden and did not lead to induction of EMT. Further, tumor cells did not induce synchronously expression of vimentin, which is often seen in EMT, to compensate for keratin loss. In summary, our data suggest that changes in cell shape and migration that underlie EMT are dependent on changes in signaling pathways that cause secondary changes in keratin expression and organization. Thus, we conclude that loss of the keratin cytoskeleton per se is not sufficient to causally drive EMT in this tumor model