The Finale: Contamination galore!

Hello all,

This is my last post of the summer! I have really enjoyed my summer research experience here. Recently, I have had a bit of a hard time with my work. Most of my transformations are contaminated. I am not quite sure what has contaminated them–but it smells funky!

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Dog Days of Summer Research

Hello all!

I don’t have much to report in the realm of science research. It’s pretty been more of the same. My original transformations haven’t worked, so I spent about a week or so troubleshooting. I made new CloNat plates, grew up a whole new culture from the original colony strain, and boiled some fresh Carrier DNA. I did my last attempt at this transformation on Friday and am about to plate it as we speak. If it’s successful, I can continue with gene knock-outs on this particular gene. I can then also begin to transform other genes from this strain. I’ve begun work on that part and sent those genes off to be sequenced. Hopefully in the next day or so I will get those sequences back to begin analysis.

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A Summer Transformation: the SAC3 gene in S. cerevisiae

Hello, all! The past few weeks have been a bit more promising in the lab. I’ve begun preparations for my gene knock-out, which I will be performing on a previously sequenced gene, SAC3. I worked with this gene in the Spring semester. In order to prepare for my knock-out, I first had to transform the yeast to be able to take in this gene from the environment. Basically, I put the yeast under stress, which then allows for them to take up DNA from the environment.

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PCR and sequencing HMY7

Hello readers! (of which I am sure there are many)

Well, I have reached the end of the second week of summer research. So far, I have been working on the project that I have been on since the Spring semester. It isn’t my allantoin pathway work yet, but it will lead into that project, so I am excited to finish up this stuff so I can look into the allantoin research. I have been doing PCR, PCR, and some more PCR! I did PCR for all of the genes previously found to be significant to plastic adherence for the strain HMY7. In the Spring, I worked on the genes in the strain HMY355. PCR proved…difficult. Many of the genes in these two strains are particular to say the least. So, I ended up with a bunch more PCR hours under my belt, but only about 50% of them worked. But! That’s okay. I pushed on and did PCR clean-up for the genes and the corresponding segregants (high and low plastic adherence segregants) that did work. I then did a big push for sequencing and just submitted the samples. Hopefully the sequences will be back in a few days and I can begin analysis! What I will be looking for is a systematic difference (an SNP or change in allele) between the high and low segregants because this means that that difference is probably crucial to determining whether or not the segregant will have high or low adherence.

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The Role of the Allantoin Pathway in Plastic Adherence in Saccharomyces cerevisiae

The allantoin pathway is crucial for nitrogen degradation in Saccharomyces yeast. It has been discovered to be a fast-evolving pathway and has many applications for natural yeast strains. Allantoin is key for growth of yeast on different media, specifically natural substrate (Treu et al, 2014).  Allantoin utilization is encoded by a cluster (similar to an operon) of genes called the DAL genes. Previous research in the lab has indicated that the DAL genes are involved in plastic adherence in S. cerevisiae. Plastic adherence is a social phenotype in yeast, suggesting that it is evolutionary advantageous for yeast cells to form mats, floccs, and biofilms in order to fight against harsh environments and competitors (Deschaine et al, 2017). This connection implies that the the allantoin pathway, a typically biochemical degradation pathway, also has a role in social phenotypes. Globally available genomic data will be used to identify variation in the DAL cluster and its regulators. Gene-knockout analysis will be employed to determine the specific connection between allantoin, the DAL genes, and plastic adherence.

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