Project update, future research ideas + more
Hello everyone,
So it's been a pretty productive several weeks for me in the lab. Thanks to a one-week break with no school, I was able to finish my final rounds of PCR, set up my sample and primer plates for sequencing, make up large amounts of algal media, test run some interesting qualitative assays for potential new projects, and isolate at least a half-dozen new strains of algae! Oh, and something about turkey. Yes.
All jokes aside, I do want to take the time and thank all of you (yes, you too, reading this now) for helping to support my project and research. Working with these little buggers and sequencing DNA and photographing them...it really is an obsession of mine. I'm probably going to continue aspects of algal-related research in college (more on that below), and I'm certainly going to take my microscope with me and survey all of the lakes and ponds in the nearby vicinity of wherever that happens to be. Research and culturing stuff is awesome. But you, the audience, and Experiment, the website, is more than that. It's meaningful. It's the outlet for my work, and it allows me to not only record for myself my progress on this project but also share it, give all of you a window into my science as it's happening. Eventually, when I publish my work (be it this project or another), it will have its own form of impact in the scientific world, but this right here is the reason I do it. To not only assume that the polished and professional science will someday make its way to contributing to the real world, but also to show the real world how it happens, in all its raw, sometimes imperfect, sometimes even boring, but always honest, way. So thank you, for taking the time to look at my research notes and follow along. That support means everything to me.
Now, back to the juicy stuff:
Project Update
As I said above, my sequencing is about ready to go; I just need to finish my communications with the organization providing me the service, and this seems likely to happen around January to February of next year. Currently, I'm about to use up my first round of funding that this Experiment page was originally created for - the last of it will pay for the sequencing service and the final few consumables to keep the lab running low until next summer (by which time I plan on moving to a new lab!). After sequencing is done, this project will go entirely onto the computer, and I'll finally get around to the one thing I've been putting off this whole time: sequence editing (groans). I'll go through, manually base-call, trim and assemble the gene reads for each strain of algae, and then I'll start the official process of identifying my algae, describing them (as best I can), and performing the real-deal phylogenetic analyses. This process will run through the spring of 2018, and hopefully I'll communicate it in the professional sphere for the first time in the summer of next year. I may have mentioned it before, but there are a couple of conferences where I'd really like to give a talk on this project. And (I hate to keep dragging on this project, but I think it would be very helpful) as I go into college, I will probably take this research with me, find a professor willing to assist me with it, and hopefully get some final advice as I work on writing it up before I seek publication for it and finally close the deal on this project. Some time before then, I'll retire this page and hopefully start a new one.
As for my algae, they're doing pretty well. I still have 29 strains from this study which I am actively culturing, and I've managed to clear fungal contamination from most of them (the secret is to transfer them quickly; the algae tend to outgrow the fungus and the fungus is usually localized, so it doesn't cover all of the algae). One strain, however, JIAC33 (a new, pure culture of Dictyosphaerium that I very much like) is still infested with a mold of some kind; I tried an experimental wash with nystatin but that just killed most of the algae and the mold survived fine. I'll eventually figure it out, maybe get my hands on some carbendazim, and I'll clear up that culture. In the long term, I'll plan to give many of my strains away to a culture collection, as I simply won't be able to maintain all of them in college; I'll try speaking with a couple of algal collections and see if they can use my postings on Experiment and relevant DNA data as suitable descriptions of their identities, and they will take them.
Future Research Ideas
Honestly, this is just really for my own edification, as I anticipate the end of lab work for this current project and I want to think about ideas for research at uni. It's really hard to present all of my ideas in a very orderly fashion (nor can I give away a great many details about my intended projects!), so I guess I'll work by species groups, as most of my projects involve certain species of algae.
JIAC2/8/9/10/19/20/25/29/31/34/35/36 (Scenedesmus/Desmodesmus sp.): As I have a lot of Scenedesmus cultures, and these algae are decently well studied, I figured it would be interesting to use them for a variety of studies. One thing I've wanted to do for a while is generate starchless mutants of algae, which have lost the ability to produce starch. As cells normally accumulate both starches as a metabolic reservoir, I want to investigate how the production of starch (or the ability to produce starch) correlates with the cell's capacity to fix carbon for other purposes. Studies have already been done to investigate the link between starch production and intrinsic lipid production; however, I plan on continuing to investigate this link with my own strains, and I am particularly curious if any of mine demonstrate greater promise than the currently studied strains. The lab work I'd preoccupy myself with along this line of research includes UV mutagenesis and screening colonies for the lack of starch production; I recently bought myself some iodine crystals for this purpose, and I will be continuing to experiment with a colorimetric, qualitative assay using these, as I alluded to at the beginning of my lab note. Another major project of interest is to sequence and map the chloroplast genomes of a few strains of these algae - I believe it's been done before with other Scenedesmus, but I definitely am excited by the possibilities of doing it again with some new strains.
JIAC13/14/27/13i (Symbiotic Chlorella): Two major areas of study. First of all concerns the actual process of endosymbiosis. I want to investigate which organisms can take up and successfully partner with my strains of what I presume to be Chlorella variabilis; DNA data says that JIACs 13, 14, and 13i are most closely related to algae symbiotic with a variety of testate amoebae, but I'm curious if other protozoa like Paramecium bursaria can form a stable partnership as well. (Update: I'm officially thinking of becoming an algae-ciliate human Tinder.) And along that line of research, I'm also curious if I can engineer related (or even non-related) species of algae to the point where they are capable of stably integrating into a host organism, when their wild-type forms previously could not. I have a variety of ideas of how I might go about doing both. My second area of interest concerning this group of algae involves studying more closely the viruses that specifically affect them. Although I currently know next to nothing about virology, it's been fascinating to read the pioneering, now twenty-year-old research on these relatively understudied green algal viruses, and joining it with the benefit of modern technology may help uncover new secrets into algal biology and engineering.
ML strains (Chlamydomonas reinhardtii): These are some strains I haven't yet introduced on this site, and I'm still thinking about whether or not I want to do that here or on another site (more on that below). But basically, as I think I mentioned in a previous lab note, Chlamydomonas reinhardtii is a veritable paragon of algal research model organisms, so there is no shortage of research I can follow with these little ones. I'll probably elect to keep strains of these and some strains of Scenedesmus as I go to college, as they're the most versatile algae I have and I can probably pursue studies in all sorts of areas with them. As of yet, I don't have any particular individual ideas for this species yet, but I will probably look to connect them with other relevant research happening at my school.
and finally...
A new blog: Algal Ramblings
So this blog comes from my realization that I've been writing a lot about algae and miscellaneous non-related lab work on this project page, which I wish to dedicate more to my progress on this project in particular. Seeing as I do want to talk about both, I created a new site for me to discuss my pond water finds, algal science in general, and slightly more personal goings-on. This new site can be found at http://www.algalramblings.wordpress.com - if you like what you see here, please go check it out! And if you don't like what you see here, still go check it out. It already has a few posts on some algae as well as other aquatic microorganisms, as well as lots of (what I hope are) high-quality and interesting pictures and videos. As I mentioned above, I don't expect to get any new DNA sequenced for about a month or two, so this site will mostly go dormant (perhaps I'll post something on my PCR protocols during this down time); thus most of my online activity will occur on Algal Ramblings. It's loaded up at the current moment - practically daily posts - but by the time 2018 rolls around I should be updating both the blog and this site about once every one to two weeks with regular news and project updates.
So that's a wrap for now - another new look at this project's progress (the lab work is slowing down, but I'll jumpstart it with new data analysis next year); some interesting avenues for future algal research; and a new site for the more personal me, so that I can devote my Experiment site to my computer work come a few months. A belated thanks again to you all. Stay tuned.
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