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.

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.

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.

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.

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.

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.

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.

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.