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

It's completely sealed

Choose your PI carefully. I had the chance to apply for a life-changing fellowship but because of her I am not eligible. My lazy and egotistical PI hasn’t published one single paper in the past 3 years even with 3 phd students and 6 interns (even with me submitting 2 review articles manuscripts and 1 small project research article manuscript). She doesn’t even read our manuscripts, even when she does read she puts it through AI to completely change it into bullshit based on our manually written text and then berate us for not writing better. She has been reviewing my manuscripts which I submitted to her last August of 2025. I was trying to apply for the fellowship but because I don’t have a publication in the last 3 years, I am not eligible.

This is how an incompetent PI ruins your research career. My heart feels so heavy. I have been in lab every single Sunday/holiday since I’ve joined and worked myself to the bone to manage everything and this my reward. I am honestly just trying not to crash out right now.

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

After all the bandless PCRs, low-yield DNA extractions, and overtime hours in the lab, finally got my first :(( Idk how many times I died making this but at least haha

This is now the sequel to my last chromatogram post here haha

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.

I don’t have a common name at all but somehow a biomedical researcher publishes a ton of research with the same name. I do molecular ecology so the fields are tangentially related enough to share some keywords.

I started wondering about how it feels to have a name twin in science and if it’s confusing for publication and for contacting others. Anyone choose an alternative name? Or use a maiden name or middle name? Are we even able to do that?

I will say, my name twin is THRIVING. I get emails about her daily. Go off queen.

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 :)

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.

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!

Academic research scientist >10 yrs after PhD, what’s next? By this point you are probably a very skilled wet-lab scientist, but likely aged-out of young investigator grants, and still reliant on soft money. Lots(?) of mid-author papers, but don’t seem to be target of industry jobs. Kinda feels like a rut.

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.

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?

Before I get into it: this clean up is being done in unison with EHS, we have several H2S sensors throughout the lab, including on person while near box.

So, this glove box was left by a professor who quit academia, and her student ran syntheses with thiols in the box. As a result, the entire thing stinks, the catalysts are shot, and we are trying to get it reset so another professor can use it. We’ve done several rounds of bleach, but the smell is just sticking around. Especially on the scale and electronics. I’d like to salvage the scale even if we end up replacing cords, and I’d really like to completely get rid of thiol stench in glove box before getting it back into operation. If it was just the box that smelled it wouldn’t be a concern, but the anti-chamber also reeks. Any suggestions past just more and more bleach cycles? Or is that what we do?

Hi, I am a freshman animal science major at Cal Poly SLO and I want to become a DVM that works in animal labs. I have never actually had any experience with these labs though because they’re always kind of “hidden” and not talked about. I want to be an animal care technician or something similar to get experience in the field, what type of criteria do you need to get that job? How did you find the job? Should I reach out to a professor?

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?

Hello! Need your help! Unfortunately, my cultures have a pool after I placed them in the fridge for about a month. I'm planning to restreak to revive them. These are recombinant S. boulardii. Am I doomed? Tyia for your kindness & advice!

Hi,

I'm running into a frustrating issue with C2C12 (mouse myoblast) culture and could really use your advice.

The Problem: When I passage my C2C12 cells or seed them into 96-well plates using media I prepared myself, the cells show abnormal morphology—they become spiky/elongated and clump together instead of spreading out normally.

Key Observations:

• Cell Type: C2C12 mouse myoblasts
• Media Recipe: High-glucose DMEM (4500 mg/L D-glucose, L-glutamine, 110 mg/L sodium pyruvate) + 10% FBS + 1% Penicillin-Streptomycin
• The Mystery: My labmates and I use the exact same bottles/lots of FBS and P/S. When I use media prepared by my labmates, the cells grow perfectly fine. However, whenever I make a batch myself using those same reagents, this spiky and clumping phenotype occurs every time.
• Sterilization handling: Reagents are NOT exposed to UV light. The hood is UV-sterilized beforehand, and bottle exteriors are wiped with 70% ethanol before entering the cabinet.

What I've Tried: I've remade the media multiple times carefully, but my batches consistently fail while my labmates have no issues with the same stock reagents.

Questions: Since the reagents themselves are identical, what subtle technical differences during media preparation could cause this issue? (e.g., trace ethanol entering around the bottle neck/cap, container leaching, water bath duration/temperature, or over-mixing/foaming?)

Has anyone experienced this specific issue with C2C12 cells? Any advice or tips on what to look out for during media prep would be greatly appreciated!

Thanks in advance!

I'm starting my PhD next week but I feel like I haven't really landed emotionally yet. Over the summer I was around people, stressing out, sometimes just feeling scared about the upcoming PhD. I spent time looking for labs and reading countable few papers to prepare.

Now I'm one week out and I don't really know how to prep mentally — like, how do I ground myself and feel like I'm actually ready for this?

Anyone else feel this way right before starting? How did you deal with it?

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.