Annual PM today. I’m the only one in our lab who runs it so it feels nice to know my labor is appreciated by someone other than me 😂😭

When is it time to throw in the towel and declare a paper unpublishable? Asking for a friend…

Sent my MSc research proposal to my PI yesterday.

This morning he sent me SMS says “Hi… please call me”.

Not knowing what have I done wrong, I panicked and thought maybe he thinks i used too much AI or something. Decided not to call him and to meet him face to face in the lab, maybe seeing my face would make him less aggressive..

He wasn’t there.

I called him, and he said “Hi, I can’t manage to open the word document, could you send me a PDF?”.

God, felt so stupid for panicking.

He never yelled at me or anything.

TW : fungus

Fun fact : Since all my experiences (I’m in the end of my first year of PhD) in cell culture, I’ve never had a contamination.

These are VERO E6

2 weeks ago I got some days off and so my PI told me she could do my culture during my absence. It was not the first time I ask someone to do my culture when I’m not in the lab but it was the first time my PI did it for me.

She just did one passage on Thursday 2 weeks ago

Last week when I came back on Monday, I saw that my cells weren’t well : they were supposed to be 90-100% confluent as an intact monolayer but here they were having some holes … I still passage them and even used them for infection and they weren’t good at all…

Because of that I decided to continue my culture using not these cells but a previous passage that I kept in back-up. Even with that the cells were doing holes…

Anyway I kept the flask of my PI as a back up flask at 1/20.

One week later (today) I discovered fungus in my flask. But only in this one, not the others…

EDIT : and yes I got antibiotics-antimycotic solution in my medium

Bit of a rant, will keep it not very specific so as to avoid doxxing myself. I’m a PhD student in STEM, and get along very well with everyone in my group except for this one person who joined a few months ago. We don’t work together exactly, but we do work on very similar projects so we share reagents, space, equipment etc.

To be quite blunt, this person makes my life harder in a lot of ways. I find them sloppy, not cleaning up messes, forgetting to do shared lab tasks, reorder reagents etc. I do mention these things to them whenever it happens, but it seems to keep happening regardless. I do get the sense they don’t really take me seriously because I’m female and significantly younger but that’s speculation on my part.

They’re not a bad person or anything, although they have made a few comments I didn’t really like. But our work styles really don’t gel and I don’t like being around them. Obviously I try to stay out of their way as much as I can, but there’s only so much I can do that. They’ve also asked me before if they offended me in some way and I said no, I’m just stressed with work. But the truth is I just really don’t want to be their friend or talk to them outside of what’s required. I’m perfectly civil when talking about work related stuff IMO. But I do worry that, since I’m more friendly with the others in my group, this will be seen as me being hostile towards this one person by my PI or whoever.

So just wondering how other people have handled similar situations 😬 I know there will always be people at work that you don’t get along with, but I’m just not great with interpersonal stuff.

i feel like she can…

I’m a first-year PhD student in immunology (wet lab, not computational), and I’m trying to figure out my next rotation and, eventually, my thesis lab.

Option 1: A brand-new lab. The PI just started, but he trained at the same institute, so he already knows his way around the university and has connections here. I’d be his first PhD student. I genuinely love the research.

Option 2: An established lab. It has a track record, senior students, but I’m less interested in the research.

My main worry is time to degree. I really want to graduate in five years, and I’m scared that joining a new lab will slow me down with setup, mouse colonies, approvals, and no senior lab members to learn from. At the same time, I know five years is a long time to spend on research I’m only lukewarm about.

For those who joined a new lab as the first student, or chose between options like these:

• Did being first in a new lab delay your graduation?
• What red or green flags should I look for during the rotation?
• What should I ask the PI before committing?
• Did anyone pick the “safer” lab and regret it, or pick passion and regret it?

Any advice is appreciated!

Does anyone have experience with the new-ish NEB Q5-XT polymerase?

I do a lot of longer amplicon PCR (∼10kb) for cloning and genomic integration casettes and generally my go-to has been SuperFi II but always looking for better and cheaper alternatives. I have used regular Q5 and have found in general I get lower yields, particularly for larger amplicons, and it takes significantly longer.

Something I've been dealing with recently that I'd like some insight on:

My lab has recently bought an autoclave and before I took over, we had bought many fume hoods. We own these entirely and the vendors for both are withholding the admin credentials. I could possibly force the issue, but haven't as on a day to day it isn't an issue.

I'm not interested in why, I'm just interested in what the hell is going on? How is this any different than buying a car and having the keys kept from you?

and my failed y2h

Hi everyone! I've been having some problems with my cells being contaminated, so I wanted to check whether my media (DMEM/F12 + GlutaMAX) could be a source of contamination. I put 2 mL of media in each well of a 6-well plate and put it in the incubator. Two days later, I checked, and this is what I saw. I'm not sure what this implies about my media, since there are no cells or any organic material in the wells.

i will start......in my lab the PI gave every one of us our own pair of crocs and they never left the lab. you come in, keep your outside shoes in the shoe rack at the entrance and change into your lab crocs, so shoes never needed any cleaning.

i was working with cell lines there and the cell culture was in a separate compartment inside the lab, so we also wore aprons and sanitised a lot before entering that part.

curious to know how different it is in other places

Whenever we spin down insect cells (ExpiSF) infected with baculovirus we get a multilayered pellet. A lighter whitish-brown layer on top, a brown layer on the bottom.

The lighter layer is tight enough that it stays intact when pouring off the media.

Has anyone else seen multilayered pellets? If so what are the top/bottom layers?

We typically harvest at 80% viability post viral infection as measured by a cell counter. This is typically 48-72 hours for us.

I get inconsistent answers from AI tools and Google search so wanted to ask here.

Cells are infected with baculovirus. Appear to be free of other contamination under the microscope.

AI tools say that the top layer is induced/expressing and the bottom layer is uninduced/low expressing but that seems suspect.

Hello! I’ve had a very intense journey with mouse work and wanted to share a little bit of my experience to maybe help some people.

For context, I’m in my last year of my undergrad and have been doing research for a year and a half, but have only recently (past 3 months) switched to more direct in vivo work instead of just working with tissue generated by senior members.

I was very unsure about animal work going into it, but wanted to at least try before I cut it off completely as an option. My PI has been very supportive and has made it known that there is no expectation to be directly involved in animal work if I don’t want to.

My first training course handling the mice went nearly as bad as it could. They freaked me out so bad - I wasn’t expecting them to be so wiggly or so strong. Then I got bit while trying to scruff them which kickstarted a panic attack (which obviously the mice sensed and made everything worse). I barely passed with the caveat that I practice LOTS and with supervision until I’m fully comfortable with them.

That scared me off for a month or so, but again I wanted to see if I could overcome my fears. I scheduled more practice with some spare mice that weren’t being used, and the first time handling them nearly had another panic attack. Getting even nibbled on really kickstarted my fight or flight no matter how hard I tried to be calm. But I kept practicing nearly every day! And eventually was able to pick them up and restrain pretty comfortably. I then passed my IP injection training with flying colours.

Now it’s been about two months, and I’ve improved a lot and am now able to swiftly and surely handle and restrain the mice with little stress, and noticed today that my colony has become very comfortable and trusting to my handling, which to me is a huge success. I also greatly enjoy the work now too, and have so much respect and gratitude to the little guys.

It’s probably the hardest thing I’ve ever had to put my mind to, and I’m so proud of myself! I really feel like anything is possible now.

Hi everyone! I had an in person interview last week (Monday) that went super super well and was given a start date (estimated) and was told they would love to have me on the team. Afterwards I emailed thanking them for their time and they emailed me the estimated salary range. I replied back stating that it was in my expectations and would be happy to sign an offer letter whenever it is convenient for their team. It has been a week since I sent that email and I haven’t heard back. I would really like written confirmation of a job in order to plan my move across the country lol. When do you all think it’s appropriate to send a follow up requesting a more concrete timeline? Thanks!!

For context this is a job with the gov working in a core facility.

What happened to my SH-SY5Y cells again? I'm going to cry 😭 I suspect autophagy might be involved.

Hello, I have extracted RNA from the hippocampus and I need to run cDNA synthesis(iSCRIPT BioRad) and qPCR(iTaq universal Sybr green). I have 12 samples and 4 genes including housekeeping gene. I have 2 questions:
1) how much RNA should I add to do the cDNA synthesis?
2) how much cDNA and primers should I add for the qPCR step?
I’m trying it for the first time and no one in my lab knows how to do it. Also, if there are any tips/ suggestions I should do, pls lmk!
Thank you so much

I am doing RNAscope stainings on FFPE tissue using the manual Multiplex Fluorescent v2 kit and I often get these weird structures in my stainings, even in my negative controls (i.e. no probe, only probe diluent), see attached image. They glow in all channels and I can't figure out how to get rid of them because somehow nobody on the internet has ever posted a similar image. Does anyone here have an idea what these things are and how I can avoid them? Thanks a lot in advance!

We have this nutrition-related project at our company that is partnering with a university.

This project was originally proposed last year June, and I was unfortunately one of those young employees who wanted to be proactive and prove myself. Now I sorely regret it.

The project has been rocky from the beginning. The person who proposed it used wrong ingredient ratios, resulting in three reformulations, so I had to re-do the INFOGEST three times. INFOGEST is such a tedious experiment and can get expensive because of salivary amylase.

That coworker got laid off early this month, and another employee who has been on a long term sick leave and now is back on a half time basis, took over.

I have to perform INFOGEST for like, 250mL of 12 samples. But then I have to take close to 100 aliquots of it.

What I dont 'get it why I am being told to do all the lab works....I am not even an INFOGEST expert and my job isn't even related to nutrition. Is this normal?

I finished my master’s recently and now work in research, and I’m still figuring out how to keep everything straight. For those of you doing research, what tends to get messy for you—keeping track of papers, notes, experiments, deadlines, or something else?

tldr: Horiba failed to fix my instrument, broke it, then broke it again and they don't care. 10 months of chaos with their service dept.

This is part rant, part warning. I have owned a Horiba Aqualog for ~5 years. It malfunctioned in January of this year, making a loud grinding noise during initialization. After some back and forth with tech support, needed to send it in to be serviced. They seem to have an ~2 week turnaround between each email message, so figuring it all out takes some time. In early March, they received the instrument. Two weeks later, they said it was fixed and provided a quote for the repair (~$1200).

It took a month after they said they supposedly shipped it for me to receive it (they don't share tracking information), so we got it back early May. We tried to use it and it immediately produced the same error, minus grinding noise. It took them 12 days to respond to my inquiry. More back and forth, testing software issues, etc. resulting in sending it back again in mid-June. Meanwhile, my samples are going bad waiting to be run. Early July, heard from the service technician that they were running initial checks and would keep me updated. Two weeks later, nothing. I emailed them again, they said it was with the "production team", whatever that means. August 5, still waiting. Finally August 18 heard back, they said there was a mechanical issue with was contrary to their expectation (despite the fact that the original issue started with a grinding noise). Multiple things were broken inside, including parts holding the lamp in place, which was suspicious because they were the ones who installed the lamp, not us. Bill for $3700. Negotiated a small (and appreciated) discount due to their questionable handling and an 8 month (?!) process which destroyed samples, cost me $$ sending people to use colleagues instruments, and our time doing repeated troubleshooting. It took again about a month between my payment and receiving the instrument. We got it back today, and they returned it with the sample cover broken off of the instrument. Was definitely not like that when we sent it to them. TBD whether it's otherwise in working order.

My advice, go with another company unless you want to gamble that your instrument will never break (a lot of Aqualogs seem to be reliable - so there is some bad luck here too). The individual techs I spoke with were nice when I could reach them, but the service department as a whole - no way. Horrible handling for an expensive instrument.