Statistical Design of Experiments for Synthetic Biology.

The design and optimization of biological systems is an inherently complex undertaking that requires careful balancing of myriad synergistic and antagonistic variables. However, despite this complexity, much synthetic biology research is predicated on One Factor at A Time (OFAT) experimentation; the genetic and environmental variables affecting the activity of a system of interest are sequentially altered while all other variables are held constant. Beyond being time and resource intensive, OFAT experimentation crucially ignores the effect of interactions between factors. Given the ubiquity of interacting genetic and environmental factors in biology this failure to account for interaction effects in OFAT experimentation can result in the development of suboptimal systems. To address these limitations, an increasing number of studies have turned to Design of Experiments (DoE), a suite of methods that enable efficient, systematic exploration and exploitation of complex design spaces. This review provides an overview of DoE for synthetic biologists. Key concepts and commonly used experimental designs are introduced, and we discuss the advantages of DoE as compared to OFAT experimentation. We dissect the applicability of DoE in the context of synthetic biology and review studies which have successfully employed these methods, illustrating the potential of statistical experimental design to guide the design, characterization, and optimization of biological protocols, pathways, and processes.

Using a Design of Experiments Approach to Inform the Design of Hybrid Synthetic Yeast Promoters.

Hybrid promoter engineering takes advantage of the modular nature of eukaryotic promoters by combining discrete promoter motifs to confer novel regulatory function. By combinatorially screening sequence libraries for trans-acting transcriptional operators, activators, repressors and core promoter sequences, it is possible to derive constitutive or inducible promoter collections covering a broad range of expression strengths. However, combinatorial approaches to promoter design can result in highly complex, multidimensional design spaces, which can be experimentally costly to thoroughly explore in vivo. Here, we describe an in silico pipeline for the design of hybrid promoter libraries that employs a Design of Experiments (DoE) approach to reduce experimental burden and efficiently explore the promoter fitness landscape. We also describe a software pipeline to ensure that the designed promoter sequences are compatible with the YTK assembly standard.

Optimally Designed Model Selection for Synthetic Biology.

Modeling parts and circuits represents a significant roadblock to automating the Design-Build-Test-Learn cycle in synthetic biology. Once models are developed, discriminating among them requires informative data, computational resources, and skills that might not be readily available. The high cost entailed in model discrimination frequently leads to subjective choices on the selected structures and, in turn, to suboptimal models. Here, we outline frequentist and Bayesian approaches to model discrimination. We ranked three candidate models of a genetic toggle switch, which was adopted as a test case, according to the support from in vivo data. We show that, in each framework, efficient model discrimination can be achieved via optimally designed experiments. We offer a dynamical-systems interpretation of our optimization results and investigate their sensitivity to key parameters in the characterization of synthetic circuits. Our approach suggests that optimal experimental design is an effective strategy to discriminate between competing models of a gene regulatory network. Independent of the adopted framework, optimally designed perturbations exploit regions in the input space that maximally distinguish predictions from the competing models.

A design of experiments approach for the rapid formulation of a chemically defined medium for metabolic profiling of industrially important microbes.

Geobacillus thermoglucosidans DSM2542 is an industrially important microbe, however the complex nutritional requirements of Geobacilli confound metabolic engineering efforts. Previous studies have utilised semi-defined media recipes that contain complex, undefined, biologically derived nutrients which have unknown ingredients that cannot be quantified during metabolic profiling. This study used design of experiments to investigate how individual nutrients and interactions between these nutrients contribute to growth. A mathematically derived defined medium has been formulated that has been shown to robustly support growth of G. thermoglucosidans in two different environmental conditions (96-well plate and shake flask) and with a variety of lignocellulose-based carbohydrates. This enabled the catabolism of industrially relevant carbohydrates to be investigated.

Rapid, Heuristic Discovery and Design of Promoter Collections in Non-Model Microbes for Industrial Applications.

Well-characterized promoter collections for synthetic biology applications are not always available in industrially relevant hosts. We developed a broadly applicable method for promoter identification in atypical microbial hosts that requires no a priori understanding of cis-regulatory element structure. This novel approach combines bioinformatic filtering with rapid empirical characterization to expand the promoter toolkit and uses machine learning to improve the understanding of the relationship between DNA sequence and function. Here, we apply the method in Geobacillus thermoglucosidasius, a thermophilic organism with high potential as a synthetic biology chassis for industrial applications. Bioinformatic screening of G. kaustophilus, G. stearothermophilus, G. thermodenitrificans, and G. thermoglucosidasius resulted in the identification of 636 100 bp putative promoters, encompassing the genome-wide design space and lacking known transcription factor binding sites. Eighty of these sequences were characterized in vivo, and activities covered a 2-log range of predictable expression levels. Seven sequences were shown to function consistently regardless of the downstream coding sequence. Partition modeling identified sequence positions upstream of the canonical -35 and -10 consensus motifs that were predicted to strongly influence regulatory activity in Geobacillus, and artificial neural network and partial least squares regression models were derived to assess if there were a simple, forward, quantitative method for in silico prediction of promoter function. However, the models were insufficiently general to predict pre hoc promoter activity in vivo, most probably as a result of the relatively small size of the training data set compared to the size of the modeled design space.

A Hybrid Sequencing Approach Completes the Genome Sequence of Thermoanaerobacter ethanolicus JW 200.

Thermoanaerobacter ethanolicus JW 200 has been identified as a potential sustainable biofuel producer due to its ability to readily ferment carbohydrates to ethanol. A hybrid sequencing approach, combining Oxford Nanopore and Illumina DNA sequence reads, was applied to produce a single contiguous genome sequence of 2,911,280 bp.

The Brief Military Career of Dr. William H. Welch.

INTRODUCTION: The purpose of this article is to examine the Army service of Dr. William H. Welch during World War I. MATERIALS AND METHODS: Archival research utilizing prime source documents in the William H. Welch Collection of the Alan M. Chesney Medical Archives for the Johns Hopkins Medical Institutions. RESULTS: Welch joined the Army at the age of 67 after serving as one of the principal transformational forces for reforming medical education in the United States and founding the first academic institution for educating public health professionals in the United States, the Johns Hopkins School of Public Health and Hygiene. His longstanding relationship with Army Surgeon General William Gorgas served as the backdrop for Welch's service. Welch served as both a staff officer and as a traveling medical inspector general, assessing the medical care of troops preparing for overseas duty. He did not adapt particularly well to military dress and decorum but his status as one of the icons of American medicine rendered these shortcomings insignificant. Welch was joined in Army service by a number of American medical luminaries-both Mayo brothers, George Crile, and Harvey Cushing among them. Although Welch remained on active duty for only 13 months, he maintained a nominal relationship with Army medicine through appointment to the Medical Officer Reserve Corps until the time of his death. CONCLUSION: 2016 marks the centennial of the establishment of the first independent academic institution in America dedicated to education and training of professionals focused on public health and hygiene issues. 2017 marks the centennial of U.S. entry into World War I. Dr. William H. Welch played an important role in both of these historic events and, although his active service was brief, the impact of his example was substantial. Analysis of his military career in its full historical context provides insight into the relationship between academic medicine and military medicine during periods of armed conflict.

Synthetic promoter design for new microbial chassis.

The judicious choice of promoter to drive gene expression remains one of the most important considerations for synthetic biology applications. Constitutive promoter sequences isolated from nature are often used in laboratory settings or small-scale commercial production streams, but unconventional microbial chassis for new synthetic biology applications require well-characterized, robust and orthogonal promoters. This review provides an overview of the opportunities and challenges for synthetic promoter discovery and design, including molecular methodologies, such as saturation mutagenesis of flanking regions and mutagenesis by error-prone PCR, as well as the less familiar use of computational and statistical analyses for de novo promoter design.

A model of federal interagency cooperation: the National Interagency Confederation for Biological Research.

The terrorist attacks of September 11 and the anthrax mailings a month later prompted a sweeping response by the federal government to improve the preparedness of the US to meet the potential threat posed by a terrorist using a biological agent. This response transcended traditional interagency boundaries, creating new opportunities while producing unique fiscal and leadership challenges. The National Interagency Confederation for Biological Research has made significant progress over the past 12 years because of its ability to adapt to the need for interagency cooperation and overcome many of these challenges. As construction of the National Interagency Biodefense Campus at Fort Detrick nears completion, the US has the capability to pursue a unique whole-of-government approach to the development of medical measures to counter the threat of bioterrorism. In addition to the high-level support of many in the federal government, the key success factors for this effort have been (1) a critical mass of leaders with the right leadership characteristics, (2) development of a compelling vision and accompanying narrative understood and articulated by all partnering organizations, and (3) recognition of the need for a partnership office to do the important communication and collaboration work in the organization to synchronize the information available to all the partners. The major barrier to interagency cooperative efforts of this kind is the inability to comingle funds from different appropriations.

Three cases of large retinal capillary hemangiomas treated with verteporfin and photodynamic therapy.

OBJECTIVE: To investigate the efficacy of verteporfin and photodynamic therapy in the treatment of large retinal capillary hemangiomas. METHODS: Case reports of 3 patients with large retinal capillary hemangiomas treated with photodynamic therapy using verteporfin. Standard verteporfin dosages (6 mg/m(2) of body surface area) were given. Both standard and modified photodynamic protocols were followed. Modified protocols included shorter verteporfin infusion times and longer light exposure times. RESULTS: Pretreatment best-corrected Snellen visual acuity of the 3 affected eyes were 20/100, 20/50, and 2/200, respectively. All cases had associated exudative retinal detachments involving the macula. Cases 1 and 2 were classic endophytic retinal capillary hemangiomas. Case 3 was a reactive retinal capillary hemangioma. Case 1 had 2 photodynamic therapy treatments, and after 8 months, visual acuity improved to 20/40. Two years after initiating photodynamic therapy, the visual acuity was 20/30 and there was no reperfusion of the hemangioma. Case 2 had 3 photodynamic therapy treatments. The hemangioma was fibrotic, and 20 months after initiating photodynamic therapy visual acuity improved to 20/30. Case 3 had 1 treatment, 11 weeks later and visual acuity improved to 20/400. Four months after treatment, visual acuity returned to counting fingers because of tractional elevation of the macula as the capillary hemangioma fibrosed. Vitrectomy surgery was performed, and choroidal and retinal neovascularization was discovered. Three months after vitrectomy visual acuity was 20/400. In cases 1 and 2, the capillary hemangioma ultimately regressed, and the exudative detachment resolved. CONCLUSIONS: Verteporfin and photodynamic therapy were effective in achieving closure of large retinal capillary hemangiomas. In all cases, the hemangioma underwent fibrosis with consequent macular puckering due to retinal traction. In all cases, the visual acuity improved.