Project Update - Current Progress, Continuing Work, Future Plans
Hello everyone,
So seeing as I've been updating my project mainly on smaller details or sub-projects, I figured I'd do a update on this study as a whole, recapping what's already been done, what's coming up in the near future, and longer term ideas as well.
So what's the project looking like currently?
I've been working on this large project since around September of last year, when I first collected some of the algae which I am now culturing and studying regularly. However, it was only after my project was fully funded on this site in June that I really began to work heavily on its major experimental phases. Over the summer, I preoccupied myself with amplifying and sequencing the DNA of six genes from around 30 strains of cultured or wild-collected algae, which was completed in late August. This first round has been reasonably successful, yielding several dozen usable DNA sequences, but I realized after about that point that the project would likely be extended beyond the deadline that I had originally set for myself.
What's the new timeline?
I'll work on updating the milestones section of my research page here, but the new rough timeline looks something like this: finish a second round of PCR by the end of the year, pound out most of the DNA sequence editing and analysis in early 2018, and come up with stronger phylogenetic justifications (or refutations) for my current, preliminary conclusions on what, exactly, constitutes a "good" barcode for assisting the identification of green algae. The summer of 2018 turns out to be a very good time for me to communicate more professionally about this project, as there are a couple of conferences I may want to present at and lots of time for me to work on getting a more polished write-up prepared. Some of this sequence data and analysis I expect I will continue to work on in college, where it could help me transition into other areas of potential interest for me, such as bioinformatics or more in vivo genetics and molecular biology.
What's the cool stuff that's been done so far?
Although not all of the sequence data has been worked up yet, some of what I've been able to find has been pretty interesting and a few sequences, as I've explained previously in my lab notes, are completely new to the scientific community. I've detailed the three new gene sequences I've published to GenBank, never before sequenced or specifically sequenced for their respective genera of algae, which are a part of my filamentous algae sub-project. In addition, there's some other cool stuff which I haven't been able to share as individual pieces so far, which I may perhaps work on writing up here as well: one of these new areas of interest surrounds my strains JIAC13 and JIAC14, which DNA evidence is telling me may be strains of normally endosymbiotic algae (zoochlorellae), which are normally found in protozoa like Paramecium bursaria, Stentor, and even some amoebae!
Talking about these algae, how are they doing?
Since this project started over a year ago, I have been continuously culturing algae and adding new strains to my main collection. Occasionally I lose some, add a few more, or work with DNA extracted from algae that are only collected from the wild and never grown in the lab. So here's a look at how things are doing in my collection now:
There's been a little bit of a fungal outbreak, and bacteria have returned to many cultures, but by and large the algae are doing well and they should get through this current unsightly phase without long-term problems. Some of these algae I may start streaking with aseptic loop technique and growing separately - I haven't needed to do this before, but I figure I may want to keep some strains axenic for future projects (explained more below), and as I have bought a can of refill butane for my creme-brulee torch I use as a mini Bunsen burner, I have the ability to.
So for additional clarity, my surviving strains are listed as follows: JIACs 1, 2, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 19, 20, 23, 25, 26, 27, 28, 13i, 29, 30, 31, 32, 33, 34, 35, and 36. I realize some of these haven't been introduced before, so I'll work on writing about them soon.
So what's the immediate plan of attack?
As I mentioned above, I plan to get a second round of sequencing completed by the end of this year, and technically that's all the budget I have left. In my eagerness to complete my first round of sequencing, I somehow forgot that high-throughput sequencing is not charged per reaction but per 96-well plate...and I sent in a plate only about a quarter-full, which sucked a good amount out of the budget that I could've saved on if I had waited to fill up the rest of the plate with additional PCR products to purify and sequence. Oh well. By my calculations, I do have enough funds left after routine costs (e.g. new pipette tips, algal media, petri dishes, etc.) to run two more plates' worth of sequencing reactions, so I will make these ones count. I'm running my final PCRs for strains JIAC32-36 this weekend, and I will confirm the success of those reactions probably in a couple of weeks (as next week will be insanely busy for me). Then, by the end of November, I will have two full plates ready to send out for sequencing, and accounting for processing times, I should get my data before 2018. That's how things are looking for this main project.
How about the filamentous algal sub-project?
Although I consider it to be a practice run and an opportunity for me to exercise my skills in phylogenetic analysis and scientific writing, this sub-project is pretty important to me because a) it will be my first official communication of results from this research and b) it's for a very important school project as well. I plan to share the write-up of this sub-project sometime in December, after it's turned in for school, to avoid there being some unpleasant conflicts of sharing my work before it gets submitted for review and evaluation.
And what about these "future projects"?
This is where things get fun, and I'll probably actually detail all of my potential ideas in a future post. Although I will continue this research for probably at least another year, finishing it sometime next summer or fall with the current amount of funding, I have a good several ideas I want to explore, including: the investigation into other aspects of algal biochemistry or molecular biology with some of the species I have; specializing in the phylogeny of certain common groups of algae; and applying my knowledge of basic DNA analysis techniques to a wider variety of organisms. In which direction I'll head, I really don't know yet; when I start planning out this next area of research and what exactly it involves will depend heavily on whether I can fund it, whether I have or can access the right algae and materials, and where I pursue my undergradute studies.
So this is a pretty big update and a lot of information at once. In future lab notes, I'll go back to explaining most of the day-to-day work in the lab, including some new methods, discoveries, or updates on experimental and analytical progress. Stay tuned.
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