Human Practices

Who we are

The UBC iGEM team is composed of ten undergraduate students under the guidance of six graduate and two faculty advisors. We are pleased to be composed of students from over eight disciplines and multiple years of study. This year we are fortunate to be based out of the Murphy and Hallam Labs located in UBC’s Life Science Center to conduct our wet lab research. Our summer goal was to build off the findings of the Smit Lab (also located at UBC) to develop a new enzyme display system with the application for biomass decomposition.

Background

Petroleum-derived chemicals are used as building blocks to create a variety of products we take for granted in our day to day lives. And while these molecules have proven to be critical for modern society, their overuse has had significant negative environmental and societal impacts. As we push forward into a more responsible future, we must pivot towards sustainable solutions able to supersede petroleum-derived products with renewable alternatives.

One successfully implemented solution has been to use microbial biocatalysts to transform renewable biomass, from agricultural and forestry wastes, into bio-equivalent chemicals able to be directly used in established industrial processes. Companies such as BioAmber and Genomatica have championed this approach, creating important molecular building blocks such as succinic acid and 1,4-butanediol. While these early successes have highlighted the potential of these systems, renewable biomass as a whole remains underutilized.

A major roadblock to implementing successful industrial-scale bioprocesses is the high cost of processing raw biomass into a usable form. Comprising greater than 50 percent of total production costs, as estimated by the National Renewable Energy Lab, biomass processing creates a significant barrier that prevents all but the most mature technologies from utilizing renewable feedstocks.

Our project

What is it?

This year, our team aimed to make the processing and utilization of renewable biomass feedstocks cheaper and more efficient. Taking lessons from nature, we pursued a biomimicry approach, aiming to build a microbial community able to effectively transform biomass into useful products. To accomplish this task, we split our microbial community into two halves. One half responsible for transforming the biomass into usable growth substrates. While the other half focuses on using these growth substrates for the production of useful products.

Why are we doing it?

How are we doing it?

To display biomass transforming enzymes we utilized the robust surface expression system in the bacterium Caulobacter crescentus, mimicking the cellulosomes found on natural biomass degrading bacteria. Next we engineered Escherichia coli, a well-developed industrial workhorse, to produce astaxanthin. Astaxanthin is an expensive to fabricate natural keto-carotenoid with properties allowing for it to be easily detected and quantified, allowing for the validation of our approach. When combined, these two bacterial strains will work together to degrade and valorize biomass.

The Importance of Science Communication

How to Effectively Communicate Science

Common Mistakes in Science Communication

An Example: CRISPR Gene Editing Articles

On February 15th, 2013, an article was published in Science magazine about a new way of editing genes very precisely. We will compare and contrast the original article, with the press release following it, as well as articles aimed at the general public.

The original article (DOI 10.1126/science.1231143) contains many difficult words, such that only someone studying biology would understand the specifics. The main idea of the article can be understood from the abstract.

Functional elucidation of causal genetic variants and elements requires precise genome editing technologies. The type II prokaryotic CRISPR (clustered regularly interspaced short palindromic repeats)/Cas adaptive immune system has been shown to facilitate RNA-guided site-specific DNA cleavage. We engineered two different type II CRISPR/Cas systems and demonstrate that Cas9 nucleases can be directed by short RNAs to induce precise cleavage at endogenous genomic loci in human and mouse cells. Cas9 can also be converted into a nicking enzyme to facilitate homology-directed repair with minimal mutagenic activity. Lastly, multiple guide sequences can be encoded into a single CRISPR array to enable simultaneous editing of several sites within the mammalian genome, demonstrating easy programmability and wide applicability of the RNA-guided nuclease technology.

While a science student might know the meaning of causal, genome, or prokaryotic, they would have a harder time with functional elucidation, endogenous, or homology. Again, the main idea that the CRISPR system allows for precise editing of genes is clear.

The press release is more suitable for a general audience. Using simpler words, even colloquialisms such as home in, the press release explains more clearly the purpose of the CRISPR/Cas 9 system.

...the engineered CRISPR-Cas9 system can be programmed to target specific stretches of genetic code and to make cuts at precise locations. Over the past few years, those capabilities have been harnessed and used as genome editing tools, enabling researchers to permanently modify genes in mammalian cells. In the future, these tools may make it possible to correct mutations at precise locations in the three billion-letter sequence of the human genome to treat genetic causes of disease in patients.

Being meant for a general audience, the press release is a summary the key points of the article. Very little of the specifics of the CRISPR system are brought up, as the general public would be unable to understand anyways. Most importantly, the foggy main idea from above is clarified: "Researchers can now harness the engineered system to home in on specific nucleic acid sequences and cut the DNA at those precise targets."

Very rarely did the more "general audience" articles cite from just the original source. This nature article provides a good overview of recent developments in CRISPR, and explains the science in an accessible way. It cites 15 scholarly articles, and includes graphics to clearly illustrate the gene editing process. It is worth noting that, because the nature article covers so much, it is quite long. The writer offsets this by grouping the advancements into sections, to make the article easier to process.

More specialized websites such as Addgene referenced several articles about CRISPR as well. Like nature, the entry about CRISPR's history has diagrams illustrating the process. The short "reference" is a lot more technical in nature. Rather than mention the researchers, the webpage explains just the science and its strengths and limitations.

The McGovern Institute at MIT's article is similar in that it references more than just one scholarly article. Instead of illustrations, a video explains the process. The video is targeted to a very broad audience, even giving the definition of "a gene" in the introduction. The animations illustrate each step of the CRISPR/Cas9 process very clearly.