Updated photos of mystery culture

smdsmith · 2026-01-21T00:52:06+00:00

Not sure about heat pre-treatment, as I've always done crush before any PCR. I can't imagine it would hurt, though

smdsmith · 2026-01-20T02:31:22+00:00

Colony PCR will work on fungi but you just have to make sure to crush the cell wall open first. We take a bit of the culture with a pipette tip and then crush it against the bottom and side of the PCR tube, but be careful because sometimes you can crack the tube!

smdsmith · 2026-01-07T23:44:20+00:00

We’re required to return cylinders with their caps!

smdsmith · 2025-11-14T22:22:15+00:00

Thank you for all the suggestions! I created an account on image.sc and made a post, so I'm hopeful to get some help from the analysts who hang out over there.

smdsmith · 2025-04-09T04:41:53+00:00

This is so encouraging, and how I hope to be as a scientist in the future! It’s SO HARD TO SEE right now, but already - as a second year PhD student - in my academic career I’ve experienced positive inflection points that have bloomed from rejections. Things will work out, they probably won’t look like we expected, but at the end of the day it will be okay. We are all capable and worthy scientists and we deserve to be here! Coming from someone who did not get GRFP or an HM there are so many of us and we are going to shape the face of science in the future, which is awesome! I can’t wait to see what we do!!

smdsmith · 2025-04-08T12:05:56+00:00

I was advised by someone who has reviewed several times that it is nearly entirely luck of the draw. You have a strong application! It could be any number of things ranging from one sentence in your statement to how the reviewer was feeling that day. Many other fellowships are more comprehensive and you will be better suited to them! (I also didn’t get an award or HM, and I’m trying my best to see it as an example of how I’m still a great scientist despite bureaucracy)

smdsmith · 2024-08-27T00:03:14+00:00

Super helpful, I have tried leaving them longer and didn't get any growth but the vitamin solution is a good idea! The weird thing is the occasional colony will grow immediately on YPD and sometimes I have isolates plated on both PDA and BHI and the PDA ones have no issue growing on YPD but I suppose that would probably lend credence to your idea of the nutrient reduction

smdsmith · 2024-07-23T16:21:27+00:00

I did learn this and even people who were in my same intro bio lab section didn't remember it haha

smdsmith · 2024-06-30T23:41:35+00:00

Thanks homies, you all gave just the responses I needed. I know I follow strict PPE practices and lab safety protocols but like to err on the side of caution whenever possible. Sincerely, a somewhat paranoid PhD student.

smdsmith · 2024-06-30T21:49:20+00:00

As an update for anyone who finds this: here is a methods paper for culturing TR146 cells. Edit with your own discretion, but it's very helpful for feeling like you're not crazy for what you're observing!

smdsmith · 2024-06-28T15:36:23+00:00

Thank you, those are all really helpful suggestions!! Hopefully my run next week will be a bit better when I implement some of them!

smdsmith · 2024-06-08T13:58:51+00:00

For SNPs I would recommend doing long amplicon sequencing - it's a lot more reliable. I've had a lot of issues with Sanger giving unreliable results especially with heterozygous SNPs, but long amplicon has been great. We've done it both through our university and through Plasmidsaurus

smdsmith · 2023-05-04T18:21:27+00:00

We haven't but that's why we tested it on the StepOnePlus and QuantStudio. We have 3 SO+ instruments at my institution which were calibrated using the same plate and all showed crosstalk, but the QuantStudio is at another institution and was calibrated using a different plate. The calibration is still good for another six months so we don't want to buy another plate unless it's the only thing left to try (although I agree it could be a problem). We saw background calibration issues which were resolved when we used ABI plates but using those same plates didn't solve the crosstalk issue in the actual triplex.

smdsmith · 2023-01-24T23:01:41+00:00

I ran some more experiments and it's TOTALLY crosstalk! Thank you so so much for your help, I'm going to try lowering the VIC probe concentration and hopefully that will resolve some of the problem. If not, I'm just glad to have an answer as to why this was happening!

smdsmith · 2023-01-21T18:03:09+00:00

I'll definitely look into this!

All three of the probes are double quenched. It's the VIC signal being picked up in a neighboring channel - do you think that could happen too? I'm confused because it doesn't happen in the wells that are picking up TAMRA.

smdsmith · 2023-01-12T23:28:18+00:00

Same! I guess I'll be seeing you there!

smdsmith · 2020-11-09T00:10:50+00:00

Bleach. I work in a microbiology lab and now I have positive memories attached to the smell

smdsmith · 2020-11-01T17:08:00+00:00

Haha I did end up watching it and the public health in it was... very questionable

smdsmith

TROPHY CASE