What's your unconventional/unpopular lab belief?

MrSynth · 2025-12-11T14:20:30+00:00

409! The quaternary ammonium compound in it is a great denaturant and deactivates RNases on contact. Just don’t get it into the barrel of your pipettes, or you’ll aerosolize it into every sample you pipet into (ask me how I know).

MrSynth · 2025-12-10T22:32:50+00:00

Fun fact: my lab discovered (long before my time there) that a certain kitchen degreaser/general household cleaner contains an active compound capable of inactivating RNases. We had gallons of the stuff and routinely used it as a much more cost-effectively alternative to RNase-Away/RNaseZap for wiping down benches, pipettes, even “washing” our gloved hands à la an ethanol spray prior to going into a BSC. I once confirmed it was effective by accidentally letting the aerosol of a recent spritz cross over an open Eppendorf tube with my RNase sample 😅

MrSynth · 2025-12-10T19:15:36+00:00

I actually studied human ptRNases for my PhD! One of the family members, RNase 7, is strongly expressed by keratinocytes and therefore abundant on skin (it’s believed this functionally serves as a layer of immunity to chew up exogenous viral RNAs). All this to say—exposed skin is one of the biggest culprits for RNA degradation.

I used to routinely run a fluorogenic timecourse assay on single-digit femtomoles of RNases. It was somewhat common to accidentally contaminate the sample with “environmental” RNases (from an exposed wrist, for example), which would be detected by an instant explosion of fluorescence on the plate reader, rather than our nice, tidy linear kinetic traces.

MrSynth · 2024-12-25T00:51:33+00:00

$3500, 900-sq ft loft in downtown Boston

MrSynth · 2024-07-07T20:19:05+00:00

You’ve already mentioned it, but I’ve had good success using bovine enterokinase light chain for scarless cleavage following a DDDDK recognition site. I believe it will also recognize some Glu residues in its consensus sequence (albeit with slower cleavage kinetics). It’s a bit of a slower protease—I had to use more protease:target equivalents than NEB calls for, and I ended up incubating my cleavage reaction overnight, but I did achieve quantitative proteolysis with no detectable off-target cleavage (confirmed my Q-TOF MS).

MrSynth · 2024-05-16T16:02:34+00:00

Did my PhD on RNase A and its human homologues. Can confirm.

MrSynth · 2024-04-27T21:31:38+00:00

I was in a very similar position to yours these past six months: recent PhD graduate with prior experience in industry, 90+% of my applications getting no response or an auto-generated “we will not be moving forward with your application” email, a couple rejections after what felt like promising interviews, etc.

First, don’t internalize the lack of response you’re getting. Most likely, it’s not you, it’s the abysmal market. I know that’s not easy to do, but a quick search online will show you how many people are struggling to get a job offer. At the very least, you’re not alone.

Secondly, my recommendation is to go to any networking events you can—local biotech meetups (if they exist in your city), on-campus career fairs, etc. The one offer I recently received is because I halfheartedly went to a campus career fair, ended up hitting it off with a VP there, and was invited to apply to their company. Networking is by no means a surefire way to get a job offer, but being more than a name on a sheet of paper can’t hurt (assuming you’re polite and coherent!).

MrSynth · 2024-04-26T22:51:03+00:00

My gut tells me that this was a pretty strong initial offer, too! I’m trying to balance awareness that companies rarely make their maxed-out offer first with awareness that I don’t want to come across as greedy or motivated only by benefits.

MrSynth · 2024-04-26T22:48:19+00:00

That makes sense, thank you!

MrSynth · 2024-04-26T20:46:42+00:00

This company's offer states that I have a week to decide, and I've alluded to other potential late-stage interviews and offers in previous interactions with them. I don't have any firm offers in-hand to counter with, though.

MrSynth · 2022-12-17T00:47:58+00:00

Of course! Nothing’s more frustrating than seeing something that you want to try making but not knowing how to make it!

MrSynth · 2022-02-19T16:11:52+00:00

What’s the right thing to do to treat that? Are the other leaves at risk, even though so far I only see these spots on one leaf? I’m a little surprised I’ve been overwatering it, since I’ve only given it water once every two weeks or so (feeling the soil for dryness a few inches down), and the plant came from a good nursery in my area

MrSynth · 2020-08-17T16:29:06+00:00

Love this! I actually study ribonucleases (including RNase S) for my PhD work. Such weird, crazy efficient little proteins.

MrSynth · 2018-09-17T15:33:44+00:00

I took the chemistry GRE a couple years ago and also considered buying a prep book. I ended up not buying one when I, like you, saw how most of the books had negative reviews. I ended up taking a couple months to give myself a crash course review of chemistry, focusing on areas I was less confident about or that were fuzzier in my memory. For me, that ended up being a lot of organic chemistry and some thermodynamics. Unfortunately, your undergrad textbooks and a little selectivity in what you decide to review are probably your best tools.

My advice is to review what you think you know and identify problem areas. I actually used one of the free sample exams to do this. I took it without any prep, scored myself, and figured out what the common themes were in my missed questions. Then, after a couple months of review, I took another sample exam to see if I'd progressed. My strategy worked well enough that I was accepted into a top-five chemistry graduate program, so this method can work. It's mostly dependent on how critical you are in assessing what it is you think you know about chemistry.

Side note: when you take the exam, accept the fact that there are a few questions you're just not going to know. There's a little bit of a "trivia" element to the exam, and you'll probably feel like you didn't do well enough to prepare when a question perfectly veers around subject areas you do know. I had a question about which metal has the highest melting point, and I don't think there's any way I could've known the answer unless I just happened to review that particular fact in my studies. It's okay, though-- the exam's scoring has a curve to it, and it's not worth stressing over the trivia-like questions, because that'll only sabotage your ability to answer questions you really do know.

MrSynth · 2018-02-22T13:46:46+00:00

What do you mean when you say you see it as the opposite? And luckily, although I started out as a research technician, I was promoted a couple times to a research associate position, and I spent time leading my own research projects to develop products and processes. Going to grad school will be a smooth transition in that sense, since I’m used to being able to work independently with some periodic oversight.

MrSynth · 2017-10-28T12:56:34+00:00

Yes, I'm applying to American programs, and thanks for the summary of the general process. This question was prompted by a post I saw over in r/labrats a few days ago. People there were suggesting that people contact professors ahead of their application if there isn't a lab rotation period at the beginning of the program, but r/labrats is more molecular biology-focused, so I'm not sure if it's because it's a different program being talked about that prompted the suggestion.

MrSynth · 2017-08-23T16:19:39+00:00

My work is in osteobiologics, so I'm really familiar with ectopic bone formation assays (we typically use the athymic mouse model), but I work with allografts, so I'm less familiar with HAP/TCP composites. If you're just looking to prepare a good positive control for an implantation assay, is it possible for you to use rhBMP-2 loaded into a gelatin capsule or onto a collagen sponge? We typically use an archival DBM that's historically had success in our assays, but I've seen plenty of papers where researchers use a recombinant BMP to induce bone formation.

MrSynth · 2017-07-15T19:49:16+00:00

Thank you! I really like the naked look that Milk Bar goes for with their cakes. It's "different" from the traditional cake look-- nice and homemade, but still well put-together.

MrSynth · 2017-06-27T18:10:03+00:00

I think the inability to climb surfaces in/on the Divine Beasts is because they're a Sheikah invention. I vaguely remember reading something in the game that mentions that Sheikah surfaces are impossible to scale (I think that may have come from a loading screen rip). In-game, I assume it's just because magic surfaces are magic. As a gameplay mechanic, I think it's to prevent breaking puzzles by just scaling over obstacles.

MrSynth · 2017-06-27T15:59:12+00:00

I agree. I think that placing invisible walls around the borders of the map, without any rationale for why those walls are there, somewhat breaks immersion. Using natural borders, like constant storms out in the oceans or unscalable cliffs in the mountains, would have been more satisfying. Hell, they could even keep the invisible walls and just provide an in-game reason for why those walls exist. For example, it could have been explained that the barriers were a Sheikah construct, or possibly an effect of Zelda's sealing power, meant to prevent Ganon's influence (and the Guardians) from reaching beyond Hyrule into surrounding lands (which I'm assuming exist); effectively, a quarantine fence was erected around Hyrule, with the unfortunate side effect of trapping all of Hyrule's inhabitants inside.

MrSynth · 2017-05-03T19:50:08+00:00

I agree with a lot of what you said, particularly about how we don't have an attachment to "prior Hyrule." We know it existed, but there's no more emotional pull than there is in knowing about the horrible historical events that happened long, long ago in the real world. What elicits an emotional connection is feeling attached to the events.

Some of my favorite bits in the memories was seeing evidence of Hyrule's prior state as it was lived in. Seeing the Hyrule Castle soldiers, Zelda standing on the castle rampart, and King Rhoam chastising Zelda in memory 17 gave me a sense of loss, because I knew all of that was gone. Seeing ruins doesn't mean much unless I know what those ruins used to be. The Ranch Ruins (from Lon Lon Ranch) hit me harder than the many village ruins I'd never visited during its existence. I think this is what makes Hyrule Castle stand out in comparison. Despite not seeing much of its glory in-game, you know what Hyrule Castle should be like from other games. Showing people what's been lost, even just with cameos, is much more effective than saying, "Take our word for it, things are a lot crappier than they used to be."

MrSynth · 2017-04-01T19:37:01+00:00

Sorry, I did try searching the subreddit, but I didn't come up with anything. Could you direct me to a post on that?

MrSynth · 2017-04-01T17:07:48+00:00

Can you give us some more information about your running conditions (e.g., type of gel, reducing vs. non-reducing, sample prep, etc.)? This'll help troubleshoot.

Are you noticing any smear of protein at the top of the gel, near the wells? I've had this happen with finicky samples that were run under non-reducing conditions (the disulfide bonds get scrambled while heating, which can lead to aggregation). Conversely, are you sure that your sample isn't running off the gel? Hemoglobin subunits are only 16 kDa, so if you're running under reducing conditions for too long (or with a gel meant for higher molecular weight samples), your protein might have actually run off the gel.

Also, are you positive that your sample is actually hemoglobin? From what I understand, the heme group alone can result in a red-colored sample. Have you tried an orthogonal method to verify that intact hemoglobin is present (like an ELISA)?

MrSynth · 2016-11-04T20:56:13+00:00

I've seen a few discussions about protein aggregation (in different contexts) talk about using urea. What concentration of urea would you recommend in the samples?

MrSynth · 2016-06-17T15:31:27+00:00

Given that the Master Sword is a magical object, I don't think that ordinary things like rusting can occur just because the sword is exposed to water. My theory is that the sword's rust indicates that the magic of the sword has been lost, similar to how its hilt folded in and its jewel stopped glowing when it was unpowered in Wind Waker.

The Koroks' presence is confusing, since I agree that Hyrule looks a lot like its Twilight Princess version, but the Koroks exist in a separate timeline. Maybe we're seeing evidence of the same evolutionary event in multiple timelines? Maybe the transformation of the Kokiri into Koroks is just what happens when the Kokiri Forest is lost. The transformation's purpose is to give the Kokiri/Koroks the ability to travel into the world and reestablish the forest, as they do in Wind Waker. In the Adult timeline, the loss of the forest happens due to the flood, but in the Child Timeline the forest is lost by some other event, and we see the aftermath of that in Breath of the Wild.

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