Engineering Success

For the 2022 iGEM Competition, Team SUNY_Oneonta aimed to create a ghost phagemid, modeled after a T7 cyanophage, that can be used as a method of gene delivery in cyanobacterial engineering. The process of designing and constructing this phagemid involved several redesign cycles where feedback from experts and scientific journals yielded new information where we had to re-evaluate aspects of our project. This engineering design cycle was also an important component of our educational outreach, where we developed a museum exhibit highlighting the functions of viruses using a bacteriophage as an example.

Phagemid Design

During the design of our phagemid, Team SUNY_Oneonta reached out to experts for feedback and insight into cyanophages.

• Dr. Andrew Millard, an expert in cyanophage genetics, suggested that we utilize HMMER for the determination of which genes we would use for creating our phagemid, when comparing Syn5 and S-TIP37 genomes. Thus, we began to use HMMER as our primary tool for sequence analysis.
• Dr. Stephan Klahn, an expert on Cyanobacterial engineering, provided us insight in the benefits our project may provide in Cyanobacterial engineering. Dr. Kiyoko Yokota shared her expertise in the biology of Cyanobacteria. Both explained the vast number species the term “Cyanobacteria” encompasses and the strain-specificity cyanophages possess. With this in mind we decided to design a generalist phagemid, which will be able to infect more than one strain of Synechoccocus.
• One challenge in the design process was determining the stoichiometry of the capsular components. For instance, more of the Capsid Proteins (scaffolding proteins) may be needed in comparison to Head-Tail Connector proteins. In response, we made our parts modular to be able to adjust protein stoichiometry. We selected a series of different promoter and RBS sequences of varying strength that can control the strength of protein expression for current and/or future use (Table 1).

Table 1: Promoter and RBS Parts Used in Phagmid Design

Collection	Name	Strength compared to consensus
T7 promoters	BBa_R0085	1
	BBa_R0180	0.72
	BBa_R0181	0.5
	BBa_R0182	0.3
	BBa_R0183	0.09
RBS	BBa_B0034	Reference
	BBa_B0032	Medium
	BBa_B0030	Strong
	BBa_B0033	Weak

Source: All parts were designed by the group Antiquity on iGEM’s Part Repository.

More information about our Phagemid Design can be found on our Design page.

Museum Exhibit

Our team designed an interactive museum exhibit on bacteriophage for a local science museum. We went through several design cycles for each exhibit component, consulting with experts in exhibit development, science museum operation, and 3D printing. A few of these are described below. We are also collecting feedback from users of a prototype of our exhibit and intend to incorporate their comments into our final round of refinement before deploying our exhibit at the AJ Read Science Discovery Center.

• Doug Reilly, the current Outreach Coordinator at SUNY Oneonta’s Science Discovery Center, provided insight into museum elements and how they can be used to target specific audiences. For instance, due to current day technology, young children are not building their fine motor skills and thus exhibits that have tactile parts are great for children. Thus, when constructing our Build-A-Phage portion of the exhibit, we wanted the assembly process to get the children to utilize those fine motor skills a variety of connection types.
• David Kenny provided additional insight our multiple iterations of the phage model. For example, to increase durability and ease of use, the t-socket that was initially designed for the attachment of the tail to the phage head piece was replaced with a ball-and-joint socket (see Figure below).
• Our first iteration of the phage head included a series of magnets to allow the top half of the capsid head to attach to the bottom. Our first test print revealed that the sizing of the holes made for the magnets needed to be altered.

More information about our museum exhibit development process can be found on our Education page.


The Design -> Prototype -> Test -> Refine cycle for the tail piece of the phage model.