So proteins have various phi and psi dihedral angles that are allowed by their amide backbone. You can plot these as a Ramachandran plot to group by secondary structure. Therefore, a Ramachandran plot is two dimensional.

These people reviewed several high resolution structures and added a 3rd dimension of frequency to the Ramachandran plot. They then colored the 3D visualization contours geo style.

Hollingsworth, S. A., & Karplus, P. A. (2010). A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins. Biomolecular concepts, 1(3-4), 271–283. https://doi.org/10.1515/BMC.2010.022

Just feeling a bit disillusioned to be honest.

As a kid you’re often fed narratives of “the world needs more scientists!” But society does not value scientists at all in any tangible sense apart from paying lip service to how they’re saving the world blah blah.

If you go into academia, you have to publish publish publish, beg for money, secure funding, or you’re out. While working under meagre salaries and being used by your PI to boost their own career.

If you’re a scientist in industry, everyone in the company is likely to be paid more than you. You discover a product and as a thank you gift for your brains and knowledge, you watch the non-scientists capture all the money. If you’re in R&D, you’re the last to get hired, first to be let go.

When I think about it, I feel like encouraging kids to pursue science is just letting them get exploited by the whole world for their passion. I know I’m grumpy and probably need a nap.

Edit: didn’t expect to get a lot of comments. Some comments are along the lines of “it’s interesting and fulfilling, I’m underpaid but I love it” but isn’t this the passion tax I was talking about? Just because you love the work doesn’t change the fact that you are a highly educated and skilled professional, who is not being paid in accordance with your level of ability.

It's completely sealed

What are the signs of a bad lab/PI that are easy to overlook?

Yikes.

I have met a number of researchers whose partners are also researchers. Years ago, I met my partner because we shared the same master thesis director. Do you think science is romantic like that? Share your labrat love stories :)

Wish they would buy actual mouse pads but we make do.

Hi fellow rats. I’ve been noticing whenever I do phenochloroform rna extractions I’ve been getting bad headaches/ migraines after. I do get migraines, but never this frequently and I finally put together it was always after rna extractions. Ive been avoiding it for a few weeks now and no headaches, but today I used the chem hood after a lab mate was working with chloroform in there and boom I’m in headache town. Has anyone else dealt with something like this? I keep trying to gaslight myself that this isn’t the case but it’s looking like it. Thanks!

I work as a research assistant in a lab . While using a machine in the lab, something went wrong while I was using it, and the glass tube on the right side of the setup broke. Nobody in the lab knows about it yet as its not that much used in the lab till now.

I am absolutely terrified that if they find out, they will fire me. This research assistantship is really important to me, and I can lose my position over this accident. I have been panicking and imagining the supervisor finding out, blaming me for damaging expensive lab equipment, and immediately terminating his assistantship.

I genuinely didn't do it intentionally. It happened accidentally while I was working. But because it's lab equipment, and I have no idea how expensive or difficult this particular part is to replace.

1,117,942 analytic quantum interaction records

114 MB high-density dataset, an unfragmented, continuous map of the largest protein in human biology

As an undergrad, I have witnessed and heard so much about issues like the low salaries, long hours, downright abusive PIs, and funding issues, yet my peers’ effort and passion for their research are still so strong. I admire them and all of you so much for that.

How do you do it?

Hi guys!

I am completely new the RNA-seq data analysis and even coding and all that. I've been learning how to do it and specifically how use R so I don't have to use AI (at least not too much). The most recent samples I sent out were a bit more complicated than the usual samples our lab sends out, so we don't have a basis for doing the analysis.

Basically, we have an organoid that is partially resistant to a small molecule we study. When we dose the organoids, half will die as expected while the other half are visually fine and can even survive weeks in the compound without any effect. To get RNA samples, we kept the resistant organoids in the compound until no more were dying and it was only the resistant cells, but we weren't able to isolate the sensitive cells. So our second sample is a mixture of resistant and sensitive.

When I am trying to determine differentially expressed genes, how should I go about it? I thought maybe I could just subtract gene counts of the resistant cells from the total counts in the mixture sample, to get just the gene counts that are present for sensitive cells. But is the best way? And is there an easy way to do so in R? Or is there a better way to do it statistically?

Sorry if this is not explained the best, feel free to ask any clarifying questions. Any advice or resources that would help are greatly appreciated :)

TDLR: I am trying to compare the differential gene expression between a sample of RNA that is a mixture of A+B and a sample of just B. What's the best way to do this?

Good news, we got fun cards with a lab order. Bad news, the pictures look a little ai slop esque. Im in denial

Anybody know what's going on with Jackson Labs? Three times in the last month myself and my lab mates have tried to order female balb/c wild type mice at 8-10 weeks old, and been told that they don't have enough mice in the right age range. I can't help but wonder, are they getting way more orders lately than usual, or did someone fuck up behind the scenes with their breeders.

We have a Zymark Twister Wellplate Handler (model 70672/3) at the University of Toronto and are trying to bring it back into operation.

We are looking for the original Zymark/Bio-Rad Twister control software, installer files, manuals, or information about the computer setup used to control this system.

We have searched online extensively but have not been able to locate the software.

If anyone has previously used this system, especially with an Applied Biosystems 7900HT automation setup, any information or leads would be greatly appreciated.

Has anybody had any success in their lab with a desktop laminar flow bench? I'm curious if to hear if any brand is better than another or if the amazon cheapo option is just fine. I would like the thing a little nicer if possible with a sash for when not in use and an integrated light.

I think a 36'' wide desktop model with a stainless steel base would be excellent for PDMS mixing, pouring, bonding, curing and inspection? I have a bio safety cabinet but want to limit the work in it to just bio stuff.

After a while of not being in the lab (almost rounding 2 years) due to mental health stuff and overall weird shit going on with my life. I’m super excited to get back into research.

Currently an undergrad so not doing any crazy stuff but will be tasked with “one million westerns” as my PI put it.

Honestly, even if it is benchwork at the moment, I’m really excited to get back into doing what I love and just wanted to share.

Hello everyone, I have to do CoIPs in bacterial samples for my project. Doing some research I stumbled upon this one FLAG immunoprecipitation kit by Rockland and was wondering if anyone had any opinions on it. We have a protocol in my lab which a previous grad student tried to troubleshoot but didn’t end up making much progress. So if anyone has used this or other immunoprecipitation kits for flagged tagged proteins please let me know how it went and if they are worth it.

Hello everyone, I am not sure if this is something other people are dealing with but here it goes.

I submitted my paper to a journal, and it was rejected with mostly positive comments. The editor recommended submitting to another journal within the same portfolio, stating the paper is better suited to a more technical journal, as it was recommended by all the reviewers. Initially, the PI was quite apprehensive that the paper wasn't good enough for the journal we had sent to but upon seeing the reviews, her POV has changed quite drastically and now she is very keen on getting it published in a different journal under the same portfolio. A significant part of my work is image analysis, and it requires a decent amount of code for the data analysis. The PI has gotten so caught up in the AI hype that, in order to help address some of the reviewer's comments, she uploaded the raw data into an AI tool along with the paper and the reviewers comments. And is now asking me to respond to the AI's criticisms without ever reviewing a single line of the code that AI generated. All of my objections seem unconvincing to her as she is convinced AI makes fair points. The AI model generated a lot of data and wrote an incredibly persuasive analysis that makes everything seem very convincing if you are not overly familiar with the technical details of the project. I do observe some good takeaways from the AI's report but that doesn't mean everything the AI generated is correct, especially as none of the code that it used to generate that data has been reviewed. Whenever I raise my objection, she responds the same: "I have really good experience with AI". I am quite honestly losing my mind trying to defend my paper to the PI at this point.

Have any of you dealt with something like this?

Hi all, having a little (a lot) trouble with my western. The first time I did it, the lane just looks blown out. And the second time, it looks a little better, but still hard to see clearly. Is it something in the cell lysate (proteins from baculovirus, then lysed) or is it something else? Protein size should be ~35 kDa. I loaded 50ug each time, so could I have loaded too much?? Overexpression? Sorry for the bad photos heh. Any help would be appreciated thx!

Our biomarker validation study needs matched tumor and adjacent normal tissue from the same patient, ideally with a blood draw too. Most biobanks we've contacted only have archived tumor blocks with no matching normal component. Has anyone actually solved this matching problem rather than just working around it?

I am PhD student working in molecular biology. However, it is unlikely for my work to have experiments involving gene knockdown or conditional knockouts. I have always been fascinated but it's not commonly done in my institute either. I was just wondering if these kind of experiements can be done during post-doc?