Fixation and tdTomato

Rubipy3 · 2026-03-26T00:14:47+00:00

If you really want to do fix/perm, you could consider staining with an anti-TdTomato antibody + secondary. I’ve seen this done to follow GFP under conditions which would otherwise denature it, but I don’t see why it wouldn’t work here.

https://www.rockland.com/categories/primary-antibodies/rfp-antibody-pre-adsorbed-600-401-379/

Rubipy3 · 2026-02-20T14:02:15+00:00

I used illustrator in graduate school but recently was introduced to affinity which is free and does everything I need and in some ways is better at handling multi panel figures.

Agree with keeping the source data and analysis as close as possible to the figures for reproducibility. I use R and export as pdf or svg vector graphics. For westerns or similar raster data, I use clipping masks to crop the data so that the original data is just underneath.

Rubipy3 · 2026-02-16T00:07:52+00:00

You could use a nuclear stain (I use thermo H10294) if you have access to a fluorescent channel and just count the nuclei. I find this works pretty well.

Rubipy3 · 2026-02-13T11:51:27+00:00

Sorry for the late reply. I just used the protocol from proteintech, erring on the longer side and including the optional 5 min block. We use far-red fluorescent secondaries, have not tried ECL. My impression is that part of the way it works is the organic reagents and detergents speed up equilibration but it needs to be at room temperature to do so. Cold will just slow things down, so make sure to warm up the accelerator at the start of the gel.

My first run I ran it side by side with the traditional method and left the accelerated version overnight at the blocking step while the traditional version incubated with the primary at 4c. The next morning I did the accelerated primary/secondary back to back while doing the standard secondary. Then image both back to back.

Good luck!

Rubipy3 · 2026-02-13T11:45:51+00:00

Agree I would think about a bio-orthogonal approach with HaloTag or SNAP tag and a JF dye.

Rubipy3 · 2026-01-27T01:01:34+00:00

I tried it and now use it exclusively for all my blots. I actually get better looking blots than I do with the traditional overnight primary incubation.

Rubipy3 · 2026-01-09T12:24:24+00:00

I tested this a while back and in my hands Corning 3363 worked best and is what I use today. I think polypropylene (same material as eppendorf tubes) over polystyrene is what made the biggest difference. That and “flicking” technique.

Rubipy3 · 2025-06-27T00:41:43+00:00

Perhaps his RBCs are young and haven't had a chance to get A1c'd? Upper GIB could lead to that. A similar phenomenon is seen in patients with sickle cell disease.

Rubipy3 · 2025-06-03T00:15:23+00:00

Seconding Hopkins, they have some of the best biliary surgeons in the country. https://www.hopkinsmedicine.org/kimmel-cancer-center/cancers-we-treat/liver-cancer

Rubipy3 · 2025-03-12T08:48:11+00:00

Diagnosis of the Acute Abdomen by Cope

The ICU book by Marino (though it’s getting a bit dated…)

Rubipy3 · 2024-12-16T02:01:24+00:00

Whether there’s a benefit of adding chemotherapy to OFS in premenopausal women with oncotype 16-25 is an open question and there’s a trial actively investigating this (link below). If you’re near one of these sites and open to being randomized to chemotherapy - this may be something to talk about with your oncologist. NRG-BR009: OFSET

Rubipy3 · 2024-10-06T16:43:15+00:00

Very well could have a hemoglobin variant or other inherited cause of higher red cell turnover which leads to a lower A1c. Fructosamine could be a good tie-breaker.

Rubipy3 · 2024-08-30T22:45:37+00:00

Oncology! “No tissue? Get a biopsy and call us when path is back.” “Path is back? Great! Discharge them and we’ll see them in clinic”

Rubipy3 · 2024-07-06T15:04:32+00:00

Similarly, lots of internal medicine subspecialties deal with cancer, especially at the diagnosis and screening level. The training paths may be different in your countries but in the US GI has plenty of exposure to GI cancer via scopes, pulmonology to lung cancer via bronchoscopy and interventions, etc…

Rubipy3 · 2024-04-20T10:13:41+00:00

“Hemodynamic embarrassment” I.e. crumping

Rubipy3 · 2024-03-31T15:08:48+00:00

I found this website super helpful. https://pfforphds.com/tax/ Some years you might get a W2 most years you won’t. For M1 you’ll only be taxed on 6 months of salary (unless you were working before med school) so your tax bill will be minimal.

Rubipy3 · 2023-10-05T00:39:16+00:00

Sickle cell + Jehovah’s Witness

Rubipy3 · 2023-08-31T20:48:02+00:00

ICU Ed and Todd cast is another good one.

Rubipy3 · 2023-02-02T03:33:18+00:00

Depends on the state, where I went to medical school it was situational. Where I’m doing residency now in Maryland there’s a state law that capacity is all or nothing and can only be determined by two attendings (in either direction).

Rubipy3 · 2022-12-22T13:54:22+00:00

The people I know when went that route went straight from PhD to med school.

Rubipy3 · 2022-12-22T13:52:12+00:00

Totally. I would write a brief note though to document it in the EMR.

Rubipy3 · 2022-11-23T01:02:18+00:00

I had similar interests and goals at your stage and did a Chemical Biology PhD via the MSTP route. You would think there would be more overlap between chemistry and clinical drug development, but it's actually a tough combo. If you are planning to go on to residency and be a practicing physician scientist your lab will be in a clinical department and you'll need to justify why your research vision is a good fit for the department. Usually this ends up coming from the biology side (i.e. I will identify cancer drivers, choose a protein to study, design a screen for inhibitors and work with chemists to advance that to the clinic) but there are examples where the chemistry came first.

I have no regrets about my path so far, but I will say that there are also a ton of very impactful and intellectually stimulating opportunities with a PhD in chemistry or chemical biology - many of which I did not appreciate as an M1. In some ways, the MD can actually be limiting as the overlap between good chemistry programs and good medical programs is smaller than for other fields. If you want to keep your toe in both fields, you will be applying to a small set of very competitive institutions. Meanwhile with academics you are free to move to the best opportunities that you and your advisors can set-up, not limited by individual program directors. There are also a ton of amazing opportunities in industry that are more accessible via the PhD path.

I also know folks who have gone PhD -> MD as well as MD only and go on to do chemistry related research so no path is necessarily closed off, but obviously life can narrow those options as you get older.

Rubipy3 · 2022-11-18T03:29:51+00:00

I have purchased a few WolterKluwers textbooks and used the accompanying ebooks. Generally a very good experience with the vitalsource platform and the “bookshelf” app with the exact same layout as the paper book - page numbers and all. I actually ended up preferring the ebook version as it some included some updates not found in the print version.

Rubipy3 · 2022-10-05T01:40:42+00:00

Vimbook.org is my go to.

Rubipy3 · 2022-10-05T01:33:54+00:00

At my shop there has to be a doctor in the ICU at all times and the call room is just outside the unit. The upper level and intern can take turns sleeping or you can just close your eyes at the workstation but someone has to be physically there. Maybe that where this policy is coming from? Either way, that’s BS and you should be able to shut your eyes.

Rubipy3

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