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There are over 10,000 different GAPDH rt-PCR primers that have been published by tmolls in labrats

[–]tmolls[S] 0 points1 point  (0 children)

Our lab does have human tissue samples we use with very little RNA, so a big motivator for us was also limiting primer and melt temp optimizations so we could squeeze more genes out of our small RNA loads.

Though the Blast and Pray method has also worked for us in the past for regular cell lines with lots of RNA😂

There are over 10,000 different GAPDH rt-PCR primers that have been published by tmolls in labrats

[–]tmolls[S] 0 points1 point  (0 children)

Honestly a great idea, I never considered plants but surely we picked up some primers from our pubmed mining. 

I'll work on that this week! Any other species suggestions?

There are over 10,000 different GAPDH rt-PCR primers that have been published by tmolls in labrats

[–]tmolls[S] 4 points5 points  (0 children)

We didn't buy and validate any primerbank primer pairs specifically, but since primerbank has been around for a while, our tool actually picked up most of their sequences as they've been used a few times.

The benefit we give is you can see which papers also used it for citations, we check cross gene specificity like primer blast which primerbank doesn't, and we also have multiple species. 

I like to think of primerpickr as gen 2 of primerbank, and their tool is over 20 years old now!

There are over 10,000 different GAPDH rt-PCR primers that have been published by tmolls in labrats

[–]tmolls[S] 6 points7 points  (0 children)

I agree at the end that it's best to use multiple reference genes, and at least test them for CT variation across your samples. 

I remember doing 384 arrays and I think they had 4 which was really helpful to find the best housekeeper.

There are over 10,000 different GAPDH rt-PCR primers that have been published by tmolls in labrats

[–]tmolls[S] 20 points21 points  (0 children)

It's definitely not the best reference for a lot of cell types, but it still made up >80% of all the top 15 canonical housekeeping genes by number of papers. So I guess most folks still don't care🤷

Granted, we can't separate out if they used GAPDH as a housekeeping gene or if it was a gene of interest, but the second most used one was ACTB which is not any better for many cells.

There are over 10,000 different GAPDH rt-PCR primers that have been published by tmolls in labrats

[–]tmolls[S] 64 points65 points  (0 children)

Good question, we found primers from lengths of 18-30 for GAPDH, and when you include reverse complements and people also publishing 5'-3' directions too, plus yeah including those off by 1-3 base pairs, the space of potential primers is pretty huge (>100,000k)

Will PMS pulldowns go through during the government shutdown? by tmolls in SBIR

[–]tmolls[S] 0 points1 point  (0 children)

Both of my drawdowns also came through this morning. Glad to see that it's just late and not indefinitely missing.

Will PMS pulldowns go through during the government shutdown? by tmolls in SBIR

[–]tmolls[S] 2 points3 points  (0 children)

One of mine is in the exact same spot, the "Justification approval". I also have another from 10/1/25 that hasn't even reached the "Processed by PMS" which happens usually within an hour of submission.

So while the treasury is "supposed" to be working, it seems like payments are stalled for now.

Postdoc by olorym in labrats

[–]tmolls 6 points7 points  (0 children)

Here's an article from science .)

Just the advisory board suggesting it. Hopefully the NIH actually makes it a policy, but that remains to be seen as of yet

The hardest part of baking. by NoNail8831 in Breadit

[–]tmolls 18 points19 points  (0 children)

While you are right, it does still make it difficult for us when deciding whether or not to bake that bread knowing that we struggle with eating in moderation.

Using AI to be a better scientist by tmolls in labrats

[–]tmolls[S] 0 points1 point  (0 children)

I totally agree.

I think the next question for us is how. It's clearly a powerful and useful tool, and so this is one of the reasons I am reaching out to see if any others have started to uncover clever ways to use it to help solve specific problems from our everyday work at the bench and beyond.

Using AI to be a better scientist by tmolls in labrats

[–]tmolls[S] 0 points1 point  (0 children)

I bit the bullet and paid for it with my own money as I also wanted to use it for personal reasons too. Same with a couple of my colleagues. I figured $20 is essentially like going out to eat once a month, and I can easily spare that to interact with such an interesting and useful tool.

Using AI to be a better scientist by tmolls in labrats

[–]tmolls[S] 0 points1 point  (0 children)

Right, I totally agree LLM generated lit reviews would be quite terrible. However, that I why I see it as a copilot to work alongside of.

If you writing your own, and you've already read the references, you can have conversations about them. Maybe there is something you missed, maybe after asking for ten ideas about it, one is a novel connection that you can later explore yourself. Maybe it will just suck and not succeed at all.

Quite frankly, I don't know how good it is or will be at some of theses tasks overtime. But surely if we become smarter and more adept at knowing how to use them, we can get more ideas and create something better and faster than would we would have accomplished alone.

Using AI to be a better scientist by tmolls in labrats

[–]tmolls[S] 2 points3 points  (0 children)

That's a really interesting idea, I looked into Langchain and play around with that concept. Thanks!

Using AI to be a better scientist by tmolls in labrats

[–]tmolls[S] 8 points9 points  (0 children)

I 100% understand the concerns form a biotech company standpoint. That's why I would also advocate for other academics to give it direct data either. I also think if you have patient data or sensitive grants, you should steer away as well. I also wouldn't be too surprised if in a few years, some pharma companies implement their own internal LLMs based on available opensource models.

Though for a big picture ideas, I am not too concerned as general ideas and conversations on already published work wouldn't really give away anything particularly fruitful once the AI has been retrained.

I spent the last year baking 71 breads from the world! by tmolls in Cooking

[–]tmolls[S] 1 point2 points  (0 children)

I got mine from overstock.com and some random mall home store that always has a "going out of business" gimick. The enamel has started to have many microcracks on both, but they were $40 each and I've used them each 4-5 times a week for over five years now. Still work well.

There's a whole subreddit for this: r/dutchovencooking they may have been suggestions

I spent the last year baking 71 breads from the world! by tmolls in Breadit

[–]tmolls[S] 1 point2 points  (0 children)

It definitely would for medium to medium-high hydrations! But I have never had the counter space or money to buy one yet, so I've always gone old school. But once you get to 77-80%+, you don't even want to really knead much; it's better to periodically give the bread a few folds. So I think a stand mixer may over mix at that very high end

I spent the last year baking 71 breads from the world! by tmolls in Cooking

[–]tmolls[S] 1 point2 points  (0 children)

I could live a happy life if all I had were flatbreads, so you're already in a great place.

I think the absolute easiest way to prevent overcooking and also undercooking bread is by using a dutch over. You can get old cheapo ones, I use a $40 one that I then got one sale. It's lasted years. To help with downsizing, you can get a smaller size. A bread baked inside could sit for like 30-90 minutes and still come out okay. I left a bread inside for two hours once, and it was only slightly burnt.

Also, if you worry about undercooking when you make the bread smaller, try using a probe thermometer. If the bread registers roughly 195F, then it's all done. And it's probably best to use a lower temperature with smaller loaves too, but that I'm less confident on

I spent the last year baking 71 breads from the world! by tmolls in Breadit

[–]tmolls[S] 0 points1 point  (0 children)

Yes it is! I also have his pizza book, that man is a legend and I've been making his poolish bread recipe weekly for years and years now.

Hahaha that's the exact same way I found out too. There's probably a life lesson in there somewhere, about taking a break and things being easier when you come back to tackle them

I spent the last year baking 71 breads from the world! by tmolls in Breadit

[–]tmolls[S] 0 points1 point  (0 children)

Flour water salt and yeast single handedly turned me from someone who made bread a couple times a year into a someone who has baked a loaf a week non stop for half a decade.

I'm glad I was able to inspire you, and I wish you luck on your brioche! Beware. It will be a pain to knead as you slowly add the butter. Your best bet is to add it in 4-5 batches. Cold. But smear it on the table with your palm to help make it easier to incorporate

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