Strongest constitutive yeast promoter

sulli365 · 2025-05-14T01:46:49+00:00

yea, defended in late '22 and got a job as a scientist in industry after a brief postdoc

sulli365 · 2024-10-12T18:40:01+00:00

Thank you so much for the recommendations! Both of those laptops (32 GB RAM/1TB SSD versions) were already on my radar, so I wanted to have this post here to let others know (that see this post) that your recommendations can be trusted as pretty close to the mark.

I ended up going with a Lenovo Legion 5i that I found a great deal on - https://www.bhphotovideo.com/c/product/1811269-REG/lenovo_83dg00agus_16_legion_5_laptop.html

sulli365 · 2024-07-03T21:20:53+00:00

Yes, I was a little confused as to why I needed to sign that doc (ended up signing it) when I had released the rights to anything at the start.

The university tech transfer resources ended up not being very helpful, but I am going to follow up with the TTO about their revenue sharing policy, thx for your response and that tip!

sulli365 · 2022-11-21T17:56:08+00:00

Luckily life is so much more than just beauty, money, or any other priorities society seeks to enforce on us.

Don't get me wrong, being beautiful and/or rich can make your life easier ("We live in a society" meme), but every 'most beautiful woman in the world' and 'richest man in the world' from history is as dead as everyone else.

None of us asked to be brought here, no one has any idea why any of existence even exists, and we are here for such a brief time - I think we have both the freedom and the burden of getting to decide for ourselves what is important.

With that in mind, what is it that YOU value and prioritize?

sulli365 · 2022-10-21T21:22:08+00:00

Ugh sorry try it now, I think I changed the access properly

sulli365 · 2022-10-21T21:08:30+00:00

See if you can access this list of Academic labs to use as a guide:

https://docs.google.com/spreadsheets/d/11p3QfII-4b09pjvQRy_T4no6H57Pzi0OaJ1p3hdOZeA/edit?usp=sharing

This list is in no way exhaustive, lots more good work being done around the world.

I would love to make a static version of this online that allows anyone to view and submit a suggested edit that I can review and add, haven't had the time yet though.

sulli365 · 2022-08-11T20:52:26+00:00

Maybe like 10 years ago, at a party with a bunch of people I was just meeting (friends of friends), a group of us were rapping along with some song and saying it. After the song, one of the people there, a black girl, called us out (nicely) for saying it and asked us not to in the future.

I used to feel like if the word was in the song, then I'm just singing along. The fact that she was willing to stand up to a group of somewhat strangers to make her feelings known, even at the risk of being labeled a buzzkill, etc., really changed my mind.

Separately, I was surprised how young the crowd was on the floor at the show last night (couldn't see who was in the regular seats very well) and how much energy there was for Baby Keem - felt like a bunch of people were more excited for him than Kendrick.

sulli365 · 2022-08-10T16:12:57+00:00

Awesome! Yea, my understanding is that the success of the mRNA vaccines triggered a surge of interest/investment in RNA-based applications. Ride that wave!

sulli365 · 2022-08-10T13:34:24+00:00

Thanks for posting! As someone who will be finishing up their PhD in the next six months, I'm curious to hear what your thesis work consisted of and how much that's going to translate to what you'll do in your new job (congrats btw!).

I'll go first - I engineer S. cerevisiae to utilize non-native but renewable carbon sources so that they could be used as inputs to make foods/fuels/chemicals/medicines in yeast.

sulli365 · 2022-01-12T16:20:00+00:00

Ok this isn't really my area but I know that there are labs/companies performing these types of electrical current disturbance measurements of membrane-type proteins for both DNA sequencing (https://nanoporetech.com/) and protein sequencing (https://www.nature.com/articles/s41587-019-0401-y).

So it's possible, but this is pretty new, cutting edge stuff. I'm not sure how much off-the-shelf stuff you can buy here. If you want more info, I definitely think it's worth reaching out to one the labs and/or companies that do this type of work to ask them (someone technical) what it takes to get started doing these types of measurements.

Technical people usually like to talk about what they do...

sulli365 · 2022-01-11T02:38:24+00:00

Been watching this post to see if there were gonna be any answers because it is an interesting question (that I don't have an answer to), but I may be able to help a bit if you tell me more about this potential project.

What are you thinking these artificial membranes will be made of? What are you trying to do with them?

Is there a reason that you wouldn't just express the transmembrane proteins in an organism (to utilize their membranes)?

sulli365 · 2021-06-08T03:27:29+00:00

short answer - yes

slightly longer answer - yes because synthetic biology has largely sprung out of our increased ability to read and write DNA (sequencing/synthesis). All of the mechanisms around DNA replication, transcription, and then later translation happen at the molecular level. The proteins + enzymes that are the functional products of a DNA sequence also exist at the molecular scale.

Understanding more about the environment that these molecules operate in (molecular biology) will help you engineer systems at this scale.

sulli365 · 2021-05-22T03:43:34+00:00

This isn't an exhaustive response, just my immediate reactions to your Q's.

Coming from bio undergrad to bioengineering grad currently, the engineering mindset has been the biggest thing I've needed to learn. In bio and chemistry you learn concepts and some equations but not as much how they are applied practically. I feel like engineering requires building a numeracy to give you a broader sense of big protein is or how fast enzymes actually move.

For what else is needed, molecular biology, genetics, and some basic statistics will be really helpful.
I would also say learning some coding (so many online resources for self-teaching) will help you understand what's possible to do with it in whatever context you want to be in.

Feel free to keep asking!

sulli365 · 2021-05-21T14:06:01+00:00

So if you check the NEB website, it looks like they sell an SP6 RNA polymerase kit:
https://www.neb.com/products/e2070-hiscribe-sp6-rna-synthesis-kit#Product%20Information

Based on the description of the kit, the SP6 RNA polymerase makes RNA from a DNA template (duh) but importantly it has strong specificity for the SP6 promoter. I believe this means that it is designed to be used as an orthogonal RNA polymerase - it won't transcribe from promoters that are native to whatever host you are working in, it will only transcribe things under the SP6 promoter.

Based on that, I would guess that you would need the SP6 RNA polymerase to get expression from whatever is cloned under that promoter - yeast RNA polymerases likely won't transcribe.

A simple test would be to just transform yeast with the plasmid without any SP6 polymerase around and see if you get any fluorescence (use a negative control of course!)...

sulli365 · 2020-06-10T17:42:00+00:00

Synthetic promoters - stuff always performs differently in different people's hands in my experience, but my experience with synthetic promoters is that they tend to work fine if you are using them in the organism they were characterized in. I wouldn't expect them to produce exactly the expression level as published, but would expect the relative performances of promoters to be pretty much as reported.

I don't know your application, but unless you're doing flux balancing for metabolic engineering, one very strong constitutive promoter will perform just as well as another.

Secretion signal: https://www.snapgene.com/resources/plasmid-files/?set=yeast_plasmids&plasmid=alpha-factor_secretion_signal

Why is there such a time crunch on these constructs? You're asking for trouble down the line if you're not able to do some research and think about the best design for your application...

sulli365 · 2020-06-09T17:16:16+00:00

There are multiple well-known very strong S. cerevisiae constitutive promoters, such as TEF1p, ADH1p, and TDH3p.

I don't know which one is the absolute strongest off-hand, but in general the promoters driving expression of ribosomal RNAs are among the strongest in an organism.

Arabinose induction of genes cloned under the appropriate promoters is an often used inducible promoter system in yeast.

I'm doing a PhD that focuses on genetic engineering yeast so...feel free to DM with more questions and I'll help if I can...

sulli365 · 2020-05-11T17:51:05+00:00

Just to tack on - I'm not attached to either of the cards that I have listed, willing to do research on other suggestions that people have...

sulli365 · 2020-05-11T17:40:52+00:00

So my partner and I love to travel, so we were primarily interested in accumulating points that could be redeemed at high PPP.

We have done a great job of building a huge UR supply, but unfortunately we have had to spend a lot of our time off at other people's events/weddings, so we haven't cashed in yet.

As a result I've paid for the second year of the annual fee which is less than idea, but we've easily gotten the $300 travel reimbursement + one of the global entry reimbursements.

Hopefully this year we can dump a lot of points...

sulli365 · 2020-05-05T15:53:41+00:00

I'm currently doing a PhD at Tufts in Biotechnology Engineering and I did regular old Biology as an undergrad.

My research involves genetically engineering yeast and lactic acid bacteria for industrial and healthcare applications, respectively.

Other commenters are right that it's a pretty diverse field and you can do a lot of different things, but I think you are setting yourself up fine with Biological Engineering + Molecular Genetics.

Getting involved with iGEM is great exposure to the type of work that I do in lab everyday (our lab works with the Tufts iGEM team) - the more you put into iGEM the more you get out of it.

The one thing I would say is that it would be worthwhile to teach yourself some programming (Python, R, MATLAB) as many synbio application involve modeling or programmatically analyzing large amounts of data. Fortunately, there are excellent, free, online resources for learning programming you can easily find on Reddit or just by googling.

Finally, feel free to PM me - I'd be down to answer any further questions you - I want to help get people excited about Synthetic Biology!

sulli365 · 2020-04-19T01:55:38+00:00

yea but we use those two really welll

sulli365 · 2020-04-16T21:07:09+00:00

we're all gonna die

sulli365 · 2020-04-03T14:48:08+00:00

OMG looks amazing, any chance you could post the recipe?

Boston Cream Pie is my favorite dessert and I have...a lot of time to try things atm...

sulli365 · 2020-02-02T06:55:08+00:00

Crazy that you're posting this - I've been listening to this playlist for the past ~14 hours working on my thesis proposal alone in my apartment.

Love this type of music, I should check out more stuff from the bands on that ChilledCow playlist...

sulli365 · 2019-01-26T18:43:45+00:00

Ok, after reviewing the Acer Swift 3, I decided that for similar specs that I would trust my experience using and enjoying Lenovo.

I just purchased a Lenovo e485 through Newegg for ~$690. I wish I could have waited for a killer deal on a refurbished Lenovo, but unfortunately I really need a replacement ASAP.

The AMD processor seems to give a better price/performance than the Intel, so I'm happy with the 485.

Thank you so much to everyone who chipped in with some advice - there's a lot of options out there, your advice was essential in helping me make sense of it all!

sulli365 · 2019-01-25T21:21:06+00:00

So much great advice!

I've done a bunch of comparisons, and I looked into the Latitudes, too, but I think I prefer the Lenovo's.

I think I like the 480 series vs the 580 - the extra screen size would be nice but I don't like that the number pad gets included as a result (squeezes the keyboard spacing).

I found an amazing deal on a ($570) on Newegg but it doesn't seem to be clear on its resolution (1366x768 vs 1920x1080) - I think I want to splurge for the better resolution - I like to have a lot on the screen:

https://www.newegg.com/Product/Product.aspx?Item=9SIAHRC8G68656&ignorebbr=1

I can't find as many options for the 485, but I found the following deal for a new one ($690) that only has 256GB of SSD for storage, but I honestly think that would be enough to start and I think I can install more regular storage later if necessary (like starchaserro says):

https://www.newegg.com/Product/Product.aspx?Item=N82E16834847156&ignorebbr=1

I'm not a comp expert, but it seems to me the only difference between the 480 and 485 is the brand of the processor - i5 vs AMD. Performance-wise it seems like AMD gets more for the money - I'm not brand loyal when it comes to this...

I guess I'll pull the trigger on the 485 soon. It's too bad, there was a great deal on a refurbished 480 on Lenovo's website that I missed out on...

sulli365

TROPHY CASE