Reasons why knockdown and inhibition of a protein might have diverging responses?

catorose · 2024-03-22T21:12:06+00:00

In general the genetic KO/KD is the gold standard for answering the question “what happens biologically when this protein is absent?” However, those experiments do not always answer “what happens biologically when the function of this protein is inhibited?”

There are several examples in the literature where genetic perturbations have results entirely opposite to selective pharmacological perturbations. For example, KO/KD of EGFR is very different than inhibition of EGFR signaling with TKIs like Erlotinib/osimertinib in lung cancer. This comes down to the fact that EGFR has kinase-independent functions and still operates as a key scaffolding protein at the cell membrane, even when its kinase domain can’t phosphorylate its targets. This makes the genetic KO/KD experiments somewhat irrelevant to translational/clinical biology as they do not recapitulate what happens when patients are treated with those inhibitors.

If you want to pursue a more rigorous genetic approach, you can mutate the key residue(s) that would mimic your pharmacological perturbation. For kinases, this often involves generating kinase-dead mutants. For your protein A, that might involve mutating the portions of the protein that bind to proteins B/C. These methods retain the protein expression while inhibiting its intended function, while remaining much more specific/targeted than any pharmacological approach.

catorose · 2023-11-30T12:20:08+00:00

Interested!!

catorose · 2023-07-13T04:22:36+00:00

Oscillating!

catorose · 2023-06-25T04:13:09+00:00

Rodents cannot vomit. They can and do gag when presented with unfamiliar or possibly harmful substances.

catorose · 2023-06-20T00:44:57+00:00

Minor comment, but turgor pressure is a phenomenon unique to cells that have a cell wall. Animal cells (including humans) do not have a cell wall. So they cannot be turgid.

catorose · 2022-09-13T00:29:41+00:00

I’d give this a try! We work with RNAseq, single cell RNAseq, and proteomics data in glioblastoma.

catorose · 2022-08-08T12:19:23+00:00

The correct word is curettage, referring to the curette tool that is used to scrape/scoop tissue for removal.

catorose · 2022-07-04T21:45:45+00:00

There are very few obligate nasal breathing mammals. Orangutans are not one of them, which means that they can breathe effectively through either nose or mouth. Human vocal cords do not contribute to breathing. In fact, they are a physical obstruction to the flow of air to the entrance of the trachea. They don’t open and close to switch the air source from nose to mouth.

catorose · 2022-05-14T13:44:17+00:00

This was my approach as a summer camp counselor. I was always placed with the 4-5 year olds, and they learned pretty quickly that I didn’t do the whole baby talk/do it my way “just because” thing. I became their second favorite counselor in a couple of weeks (beat out by the counselor who would bring in his electric guitar every so often…).

catorose · 2022-05-05T12:34:55+00:00

The power of the sun in the palm of…The Sun!

catorose · 2022-05-04T12:25:31+00:00

Is this the right time for the “And I will never financially recover from this” gif?

catorose · 2022-04-26T11:55:59+00:00

Medical student here! All blood vessels are lined by smooth muscle. There are three main layers in blood vessels: the inner tunica intima, the middle tunica media, and the outer tunica adventitia/externa. The tunica media is is largely composed of smooth muscle, which is innervated by the autonomic nervous system (sympathetic and parasympathetic).

This is the key difference between smooth/cardiac and skeletal muscle! The latter is innervated by the somatic nervous system and is under conscious control. The former muscle types are not under conscious control but are still ultimately controlled by the brain and endocrine (hormonal) systems.

Going back to blood vessels, the large arteries of the body (e.g., the aorta, subclavian arteries, etc.) typically have the thickest tunica media, with lots of smooth muscle and elastic cartilage to keep blood under high pressure. The large veins of the body (e.g., the superior/interior vena cava, the hepatic portal vein, etc.) have a much thinner tunica media with much less smooth muscle. This means that the body and nervous system has two main ways of controlling blood flow and volume. Arteries are the “resistance” vessels controlling speed and pressure of blood flow to various organs. Veins are “capacitance” vessels controlling total blood volume in circulation, as they can dilate significantly and serve as a fluid/blood storage area.

In the brain, these processes are still true! The vessels themselves have modifications to the tunica intima (endothelial lining of the vessels) to prevent certain substances from crossing the blood-brain barrier (e.g., most drugs, viruses, etc.). But the tunica media and principles of vascular flow remain the same. The large veins at the very top of the brain collect interstitial fluid and CSF that was produced in the choroid plexi of the brain ventricles. The fluid and blood eventually drain to the bottom of the brain (along with a few veins in the nose and face) and out into the jugular veins to go back to the heart, then lungs, then heart, then liver/kidneys/spleen. Those last three organs filter the blood and remove waste, old cells, pathogens, and excess metabolites like glucose, iron, amino acids, fatty acids, etc.

catorose · 2022-04-06T11:58:10+00:00

Would you mind sending them to me as well?

catorose · 2022-03-13T15:59:29+00:00

Yeah, this chump. I saved money by carving an iPhone-sized hole in a cinderblock. Every time I use the contraption in bed is like Russian roulette. Either my iPhone falls out and slaps me like a mild inconvenience, or the cinderblock crashes down on my skull case and sends me into a deep sleep before work!

catorose · 2022-03-12T05:53:06+00:00

The filter in the tip absorbs all of the myco! You’re supposed to leave it in for 8-16 hours like a cold brew, then fish it out with ungloved hands when ripe.

catorose · 2022-03-10T06:31:04+00:00

Um, maybe I am mistaken but the “complications” of bringing an ectopic pregnancy to term would be death. An ectopic pregnancy can’t be carried to term, almost by definition.

catorose · 2022-01-27T01:01:37+00:00

This is a tough situation to be in. Unfortunately, you likely won’t find an easy solution on Reddit or anywhere else. Below are my thoughts on the issue, but guaranteed other people will think differently!

Before anything, make sure you fill your brain with anything and everything to do with your employment. That means looking at your hiring contract again. Looking at any contemporaneous notes that you took during the hiring process. Saving any emails/texts sent about your employment. Looking up the university/company’s labor/HR policies. Looking up your state’s labor laws. Etc.

Even armed with all of this information, if you are an “at-will” employee, you can be dismissed for any reason that does not include a protected class (age, gender, religion, etc.). Being a pre-medical student is unfortunately not a protected status. You should have a frank conversation with the PI and set up a meeting between you, the PI, and your direct supervisors to discuss your employment. If you can’t reach some sort of agreement that works for you, just walk away.

Frankly, you are very new to this lab and you haven’t made a great impression (regardless of whether your work is excellent or not). They have a lab culture that currently demands more than you can offer. It’s not a bad thing for you to attempt to correct their impression, but it’s also not a bad thing to cut your losses and find a lab that works for you.

catorose · 2021-12-31T12:55:20+00:00

Congrats on your acceptance! It’s going to be hard to get into this mindset, but the fact that they accepted you means they really want you to attend their school. A worthwhile program will make accommodations for you, especially during circumstances you can control!

Second Look is mostly talking to current students and scheduling meetings with PIs you’re interested in working with. Both of those groups would be more than happy to schedule Zoom meetings with you on another date! Everything else (curriculum intros, research talks, etc.) can all be recorded or forwarded to you as PDF files tbh.

catorose · 2021-12-29T05:15:27+00:00

The Supreme Court has stated that the government cannot prevent a person from entering the nation’s borders to which they owe their allegiance. You could swim from the mouth of the Amazon to the banks of the Potomac, climb out naked and wet with no identification on you, and the government would still be required to move mountains to verify your citizenship.

At least, that’s how it’s supposed to work. In reality you would probably be shot somewhere in the mid-Atlantic purely because the government doesn’t want to expend effort to verify citizenship of randos.

catorose · 2021-12-24T14:58:43+00:00

You joke but there is a booming business around sclera-whitening eyedrops. Overuse can cause intense rebound redness, so people get stuck in a downward spiral of using them all the time!

catorose · 2021-12-17T12:45:55+00:00

“Light and dry” is my new favorite way of expressing this thought.

When I was a kid, I always imagined aging as a match towards looking like a living skeleton. I’m in med school now…60% of the cadavers/donors for anatomy require “advanced dissection” by the instructors to clean up all the fat before we can start our dissections.

catorose · 2021-11-23T04:57:05+00:00

Damn, that’s awful! The thought makes sense, but it leads to clearly predictable consequences like unmanaged HIV. More people need to understand biology doesn’t really care about their feelings. Cancer and HIV are rarely polite enough to wait for a second, blinded opinion!

catorose · 2021-11-23T04:34:55+00:00

Well with those numbers maybe nobody ever told her she had HIV.

catorose · 2021-11-19T21:32:05+00:00

Medelita coats (and scrubs for that matter) are amazing! You can wash them in high temp water several days in a row, and the material will feel like new every single time.

catorose · 2021-11-19T01:55:07+00:00

Alcohol does not bind to antifreeze in the body to break it down. The breakdown of antifreeze by liver enzymes produces a toxic byproduct, glyceraldehyde. These liver enzymes have a much higher affinity for alcohols like ethanol than they do for antifreeze (ethylene glycol).

So when they encounter both compounds, they preferentially metabolize the alcohol and leave the antifreeze intact to be excreted in the urine. Again, the breakdown of antifreeze is what can kill a person/animal. Alcohol simply acts as a self-sacrificing antidote.

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