MARIN ACADEMY RESEARCH COLLABORATIVE​

UPDATES

 

4/21/19

After two weeks of break, we got right back into it this week. Some of th e plates we were going to use for the lifespan froze so we had to make more. I also made up the bleach solution and will try to start the lifespan this week. After this week, I'll be spending all my time on this project and really grinding it out. I also did a little work on my manuscript, which is kind of coming together. 

 

3/22/19

We decided to postpone the lifespan because it should take around 3 weeks, and I will not be here three weeks from now. So that will happen after spring break. In the meantime, I’ve been looking at oxidative stress assays and also at feeding the worms liquid food. It seems somewhat reasonable that I could feed the bacteria the water and the worms would eat it, or that I could put a drop of water on top of the food and they would theoretically eat that, too. The oxidative stress assay seems slightly not possible given the amount of time we have left in the year and the complex procedure, but we’ll see. Next week is going to be more looking at food and oxidative stress assays

3/17/19

I spent this week making up an M9 solution and a hypochlorite solution so that I can hopefully start my lifespan as soon as I can next week. Those are now all ready, so that’s out of the way, which is good. I still need to plate worms so that they can newly starve, and I can start the lifespan mid to late next week. During that time, I hope I will also be able to figure out Oasis or SurvCurve.

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3/10/19

This week I have been setting up for a second lifespan that should hopefully begin in the next few weeks. I made new plates, this time without FUDR, and this should allow me to start soon. I’ve continued to do some research into nailing down the liquid media protocols, and I now have a few articles I think I can use to compile a solid SOP. Kristeen unfortunately doesn’t know a lot about liquid media, so I’m not sure who I will be able to run my SOP by, but I’m hopeful that I’ll be able to verify it somehow. I do need to figure out OASIS or SurvCurve before I start the lifespan, so I’ll try to get on that pretty quickly this week.

 

 

2/21/19

This week has been a little bit slow, but Thursday Kyra and I went to the Buck to pick up some new worms. We were concerned that because of contamination issues, the genotype was no longer pure, so it was good to get some that we know are the right strain. We also talked with Kristeen at the Buck about our projects, and she seemed to think that my plan is solid, so that is also nice. I do need to do some more research on liquid media (and potentially reach out to Kristeen to see what she knows about that) and on the oxidative stress assay. Kristeen seemed to think that I would be able to order some sort of kit, which would be fantastic, so I need to look into that as well. Also, I’ve decided to do my MARC project as my senior project, which extends my timeline by about a month, so it’s definitely nice to have that extra buffer for the project.

 

 

2/14/19

We reached out to the Kapahi Lab at the Buck Institute this week in order to get some further help from them, and they responded positively, which is fantastic! I was out sick on Monday, so I haven’t had as productive of a week as I would hope, but nonetheless, I made some progress on the graphs. I’ve also continued to do research on a liquid media lifespan, and I’m hoping to get more clarity on that when we meet with people at the Kapahi Lab (hopefully next week).

 

 

2/10/19

This past week has been a little bit of chaos. We have decided to do the baseline lifespan again, because the results from that were pretty off - the strains expected to live the shortest lived the longest. We also have some concerns about the WT strains due to issues with contamination, so we are thinking of ordering a new vial from the CGC (at the University of Minnesota). Additionally, the second lifespan will now likely be done in liquid media, so I need to figure out how that will work. I’m also beginning to research doing a oxidative stress assay with and without ERW. I’m thinking that if the lifespan does not work, I could maybe do this… I need to do a lot more research on it, though. Kyra and I started to talk about our projects with YiOu, and she was great and very helpful, so a big thank you to her! We hope to maybe start a lifespan by the end of the month, but that is dependent on whether or not we’re using a new batch of WT worms and how long they would take to come. Busy!!

 

 

2/3/19

We found water!! It has a pH of approximately 9.9, even once we pass it through a sterile filter, which is great! I also prepared some more plates without FUDR in preparation for the next lifespan. I am still working on figuring out the methods for that lifespan. I've been reading through a lot of papers, but nothing seems to look like what I need. I'm going to continue to work on those methods and further setup for the lifespan this week. 

 

1/27/19

I spent most of the last week working on things that were not related to the upcoming lifespan. While we did unfreeze the worms, they were mostly not viable. We did, however, find several live worms on the plates from two months ago, so we’ll see if that is more successful. Outside of that, you may notice a redesigned blog! It is easier for me to work on, and I think that it’s a more elegant and simple look. Additionally, I’ve started to process some of the data from our first lifespan, and I’ve been working on creating graphs of that data. I also received more feedback on my manuscript, so I should be able to put in some more work to that in the future. I need to do some more research about methods for administering the water, and I also have another brand of water to test in the next few days. We will also be making more plates. Busy week!

 

1/20/19

We unfroze the worms on Wednesday and are waiting for them to repopulate. We are also working on getting the water ordered and should have that done by the end of the month. I’ve started working with excel and analyzing the data from the last lifespan we did, working specifically towards a survival curve that should show the population change over time. That way, once the second lifespan is done, it should be easier to create a visual comparison to show the effects of the water. We’ve also been working on using excel for more functions and I’ve been figuring out where tables and figures fit in to my manuscript. Hopefully by next week, I should have some graphs and the water will be ordered. I’m also looking forward to getting some feedback on my manuscript next week, so I should be able to make some significant edits to that pretty soon.

 

 

1/13/19

This week was the first week back from break, so I’ve been preparing for another round of testing. I finished the baseline lifespan and am now setting up for the second lifespan. We did hit a bit of a roadblock in that the wild type worms all died over the break, so we will need to unfreeze some from our stock. This will take up some of the time I had set out to use for other things, but I’ll adjust accordingly. I have started doing more research into waters I may be able to use and how to administer them to the worms. We will order them and do some further testing to determine which is best. In the next few weeks, I hope to have set everything up for a second lifespan so that I can begin in early february. We are also learning about excel and I plan on using that in this lifespan. Additionally, I can refine the methods section of my manuscript, which I hope will be mostly complete by the end of february.

 

 

Semester One Update

This semester, I’ve started to work on my manuscript. My introduction and methodology are mostly complete, and I’ll continue to work on them through the rest of the year.

We are most of the way through the second lifespan, at about day 20. Most of the worms are already dead, which may be because we used FUDR this time, but if that’s not the explanation, then we really need to get to the bottom of what’s causing this.

We also began testing the pH of different H water on the market. I learned how to calibrate the pH machine in order to do this. We tested H Factor so far, which had a pH of about 7.5, which is nowhere near the 9.5 that we’re aiming for. It may be because there doesn’t seem to be any buffer in this water, which would mean that the H in the water just interacts with the environment and doesn’t remain in the bottle. We will test more types of water starting next semester.

Also next semester, we will determine the methodology of using the water in a lifespan, and then perform the lifespan.
 

12/13/18

I am currently on day 20 of my control lifespan experiment. Data collection is going pretty well, and the lifespan should be done in the next 10 days.

A few weeks ago, I learned how to calibrate the pH probe so that I would be able to accurately read the pH of different market ERW products and find one with the right pH. The first one I tested, H Factor, had a pH of 7.2, meaning that it is useless to my experiment. We now plan on testing the pH of several other brands of ERW. The main concern here is that none of these have a buffer, meaning that the extra H won't remain in the water.

Once the current lifespan is complete, I'll put more focus on the water, and then I'll run the second lifespan with whatever water is determined to be appropriate.

 

9/16/18

I am currently still working on setting up a bleaching to run in the coming weeks - doing one now is not super feasible because I'll be away for the next few weekends, so I will probably start that up in the first week of October. I am also still figuring out how to make ERW, which I will continue to do throughout the next semester until I run my second lifespan in the winter. So in the next few weeks, I will make new plates with FUDR to prepare for the lifespan and will prepare more for said lifespan.

 

 

8/16/18

Back to School! Over the summer, we froze the worms so we wouldn't have to come in. And when we thawed them out, they were alive and well and are currently repopulating like crazy! In the next few months, I will have to set up and run a bleaching and get right back in on another lifespan. The first was not successful (back in May) but I went over the procedure with my mentor a few weeks ago and it should run a bit more smoothly this time. I also still need to figure out how to make my ERW, which I will use in a second lifespan experiment which will run after the first is complete.

 

5/7/18

Posts have definitely not been quite weekly as of late, but it's been a busy few months. We got the C. elegans from Dr. Guha at the Buck Institute and have been slowly learning how to care for them and keep them alive. We have three strains right now: glod-4, wild type, and glod-4 OE GFP (you can find them here: https://wormbase.org/#01-23-6). Recently, we attempted to begin a lifespan assay using all three strains, but this attempt was unsuccessful and no eggs were found on the plates. In the next 2-3 weeks, we will be trying again and tweaking the procedure (similar to https://bio-protocol.org/bio101/e56) until it works. As we approach science symposium on May 18, Kyra and I will work together to create a poster and a writeup of our work so far.

 

3/11/18

So one month later and my project has completely changed again. I was looking through some articles and came across one about how water can affect diabetic mice. I first that that this was not possible, but there's a way to make water have more hydrogen molecules and particles of silver. This a type of function water called electrolyzed reduced water, or ERW. The properties of ERW are mostly unknown, but it has been shown that ERW has positive effects on oxidative diseases, of which diabetes is one. I also found that the effects of ERW in mice has conflicting results, and so my new plan is to induce Type One Diabetes in C. elegans using streptozotocin and administer ERW to these nematodes in different quanities using control groups that are both diabetic and non-diabetic. One thing that I am currently working on in how to obtain the C. elegans at a reasonabe price (possibly from the Buck Institute) and how to make my own ERW at a reasonable price, because the typical machines that are used for this are very expensive. Over the next 3 months, I will likely be figuring out precisely how to induce T1D in the worms and a method for creating ERW.

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Links to articles I've read:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3284969/

https://www.sciencedirect.com/science/article/pii/S0924224411002408

http://www.nihon-trim.co.jp/english/lab/about_ion.html

 

2/11/18

I'm in pretty much the same place as I was last week. I still want to look at the environmental determinants of T1D, but I'm not sure how to do that. I've been looking through articles and emailing doctors and professors, but I haven't really come up with anything helpful. Still looking for internships and people to talk to. This last week has been incredibly busy, so hopefully next week will be much more productive.

 

2/3/18

So TEDDY doesn't seem like a feasible option for a high schooler due to their rules for who they'll give the data to. Which means that I have to come up with something else to do for my project. I'm still interested in the environmental determinants of T1D, but there might be another way to look into that? Potentially through a closer examination of the beta cells, but again, I don't know how I'd get access to beta cells. Or what any of that would involve. So, that's what I'll be looking into for the next week. Well, that and summer internships/jobs.

 

1/28/18

So the research 101 thing this week was really interesting. It didn't help to clarify a whole lot, but they mentioned one thing that I'm looking into right now: TEDDY. TEDDY stands for The Environmental Determinants for Diabetes in the Young. It was a study from 2002-2017 in which scientists in 5 different countries tracked a whole bunch of aspects of almost 8 thousand children's lives. I'm trying to figure out if there's a way for me to access the data they collected and analyze it for my project to look for some environmental factors that may/may not contribute to T1D.

I'm also still looking for a summer internship. It's a process.

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1/21/18

This week, I've continued to finish my proposal. Additionally, I've begun looking for summer internships and jobs (if you know of any, please email me using the link above!).

I had my phone call with Dr. Frank, who described his research on hypoglycemia after T1D patients exercise, and suggested some innovative technology in T1D care right now. While this is not something I intend on pursuing, it was interesting.

I also got back in touch with Kathleen Fraser about internships and any other people she knows. She didn't have anyone to connect me with. I also reached out to someone who Dr. Frank introduced me to, but she has not responded regarding a phone call.

On Tuesday, I will go to a "Research 101" from JDRF, which will hopefully provide further clarity on what I can focus on for my project.

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1/10/18

After turning in my proposal last month, I am currently working on editing that for clarity, as well as adding to it as I gain further insight. Tomorrow, I will have a phone call with a fluid dynamics PhD who did his PhD in glucose-inslin dynamics. While I'm not too sure how this will be relevant to my work, I'm sure it will be informative in the very least. Additionally, I'm continuing to look for further articles and sources for background information and ideas to further narrow down my project, as well as more contacts to guide me in the process. In two weeks, I'll go to an informational session about T1D research, which should be helpful, as well.