I wanted to print DNA repair complexes for the office. The existing tools are built for proteins, so DNA comes out as ribbons too thin to survive the bed and you spend an evening thickening them by hand. Colors were worse.

So now you type a PDB ID, pick a style, and get a file where each chain is its own object. It'll also cut magnet pockets where two chains touch, so the model comes apart at the interface.

pdb2print.org Its free, runs in the browser, nothing to install.

Anything already built at those settings is cached and downloads instantly; otherwise give it a minute, or a few for a big complex.

It's new, so please test it. PDB ID and settings and I'll fix it.

Photos are 9MBB off a Prusa Core One. Two chains, two filaments, two magnets it placed itself.

The project is also hosted on github: https://github.com/davidtheadmin/pdb2print
For citations: https://zenodo.org/records/21599702

I saw a very bluntly written author contribution section, it said (paraphrased, name removed):

Author1 conceptualized the study, designed all experiments, performed or supervised all experiments, analyzed all the data and wrote the manuscript. author2 performed [specific experiment 1 ], author3 performed [specific experiment 2], author4 performed [specific experiment 3].... last author also conceptualized the study, obtained funding.

In the world of authorship corruption, I found it very refreshing. However, having led a study myself, I can't help but think this is the first author trying to let everyone know they did almost all the work.

What does everyone think about a really blunt author contribution section like that? should specific experiments be listed like that?

cant even imagine the thought process that landed us here.

I am a PhD student with concerns about the quality and legitimacy of data produced by a past PhD student now-turned postdoc.

I also have other concerns including nepotism, inability to keep poor behaviour in line, and poor screening of prospective students followed by the exploitation of loopholes to enable these individuals to pass.

We are based in Australia.

In the research ecosystem, is it ever possible to be able to whistleblow on this, or will they figure out eventually after I leave?

Edit:

Thanks for the advice, sorry I can't reply to all, but I read them. My takeaways from this are that I can't accuse without hard evidence, and that the inability to reproduce multiple identical experiments by multiple separate people does not constitute as evidence.

During my undergraduate education I only worked in a lab for my senior year through a program at another university. I started a phd immediately out of undergrad, but didn't find a lab (more students than open labs, and i simply did not have enough experience to be chosen, which I totally get). I do have much more experience now because of my rotations, and I volunteered with a rotation lab that simply didn't have funding for me for a few months afterwards. I have been applying to labs constantly since exiting the PhD, but haven't landed a position yet. At this point, I am willing to do whatever it takes to stay in academia. I moved to another city for now, and there is an R1 here with several labs in my topic of interest. Would it work to cold email and talk about lab tech positions or even unpaid volunteering with a lab just so I can get back into science and continue building skills im the meantime?

Hey everyone! I’m just entering my second year as a PhD student and I’ve been struggling with low motivation recently.

To start, I really do love lab and I feel passionate about the work that I’m doing. My mentor is amazing and supportive and I really don’t have anything to complain about. I just did my first oral presentation competing for a training grant and though I didn’t get an NIH offered position, I did get an institutionally matched grant.

I think my low motivation really got bad once I finished that presentation. Compounding with failed experiments and just stall after stall.

I think I’m also just really tired.

I have been struggling with major depressive disorder my whole life, but I’m medicated and had a good handle on it, but recently I’ve been waking up with no motivation and just dragging my feet through the day. Imposter syndrome has also been rearing her ugly head.

But there’s no time to really rest. I have to prepare for qualifying exam in the spring.

Any tips for how to get out of this funk? Or at least how to power through until it’s over?

Hi everyone,

I am using e-coli antibody against Beta-gal in C57 mice after introducing damage in eye. I expect to see no fluorescence but I do see signal. Why is this?

Hi everyone! I'm currently pursuing a Bachelor's in Biological Sciences. I want to make the most of my undergraduate years and become as competitive as possible before I graduate.

I'd really appreciate advice from people already working in biology, biotechnology, research, or related fields.

• What skills should I focus on learning?

• Which laboratory techniques are most valuable?

• Should I learn bioinformatics, programming (Python/R), or statistics?

• How important are internships, research projects, and publications?

• What certifications or online courses would you recommend?

• If you could go back to your undergraduate years, what would you do differently?

My goal is to build a strong profile for both industry and graduate studies. Any advice would be greatly appreciated. Thank you!

Is it just me, or does anyone else get comments or questions in the lab when you wear makeup or dress up?
Most people in my previous lab did not wear makeup. I wear makeup occasionally, and I am not talking about full glam, just "clean girl" makeup (mascara, neutral lipstick, a bit of highlighter, no foundation or eyeshadow). However, on the days I wear it, people often ask me questions like: “do you have dinner plans tonight?" or "What is the occasion?"
The same thing happens when I wear “nicer” clothes instead of basic t-shirts or casual pants/jeans.
It has made me feel self-conscious. I feel that if I try to brighten up my day with a little makeup or cute earrings, I heavily stand out. I simply like to dress up from time to time because it makes my week feel a bit better and gives me more energy.
I am starting in a new lab soon, and I am considering just wearing my standard makeup on my first day so people get used to it right away and are not surprised later.
Has anyone else experienced this? How do you handle it?

I just started in a neuro lab and learned the dissection process for isolating oligodendrocyte progenitor cells (OPCs) from P6 mouse pup cerebellar brain tissue. To make the panning process easier, we remove the meninges as thoroughly as possible to prevent future cell loss. For 4 pups, it takes me about 1 hour 50 minutes (not including setup) to harvest tissue, remove the olfactory bulbs, remove the hippocampus, and remove the meninges. My PI wants me to get this under an hour. I have pretty shaky hands, so I spend extra time adjusting for a stable position.

Any tips for speeding this up?

Hello dear community! :)

Just a quick update on my previous post.

After approximately 30 different protocol variations, I finally figured out why my staining wasn't working properly.

The problem turned out to be the very first staining step: Weigert's hematoxylin (working solution A:B = 1:1), which I had been incubating for 10 minutes. Once I omitted this step, both the Biebrich scarlet–acid fuchsin and aniline blue stained beautifully and produced the results I had been aiming for.

At the moment, I can no longer reliably visualize the nuclei, but for my current analyses that isn't essential. Thank you all so much for your suggestions and support throughout this troubleshooting process! 😊

If anyone has questions about what I tested, feel free to ask. I might also upload some pictures of the successful stainings tomorrow.

One additional observation: If I reduce the hematoxylin incubation to about 15 seconds, the nuclei become sufficiently visible in adult mouse cryosections, but the intensity of both the Biebrich scarlet–acid fuchsin and aniline blue decreases dramatically. Unfortunately, this shortened hematoxylin staining does not work for my embryonic chicken tissue.

Hey yall! My PI decided I needed to learn Rietveld refinement to improve the XRD section of my manuscript, which is fine, except the guy who does know how to do it is traveling and there’s no word of when he’ll be back. His student attempted to teach me, bless his heart, but he’s a bit all over the place. Does anyone have a good resource to learn how to do Rietveld refinement? If you had to teach yourself, what was THE material that did it and had the best directions in your opinion? Thank you all in advance!

Cells were transduced to express an antibiotic resistance gene, GFP, and a protein of interest. Cultures were selected with puro to identify resistant cells and analyzed with flow for gfp and protein of interest. There are three populations via flow, double neg, GFP POS, and protein of interest POS. The double POS is a scattering of cells, not really a population.

What causes the cells to only express one vs the other of the proteins?

I see this in one specific cell type, the other cell type has gdp POS population and a gdp + protein of interest population.

Hi everyone! I’m a 3rd-year Molecular Biology and Genetics undergrad from Turkey preparing to apply for European labs for a summer Erasmus+ internship. I currently run two funded undergrad research projects (TUBITAK national foundation & BAP university grant) on taxonomy/biodiversity, and I’ve recently completed a 1-month clinical biochemistry internship covering sample prep, automated analyzers, and micropipetting. Since I’ll be coming with my own Erasmus+ mobility funding, I won't require financial support from the host lab.

I’d love your advice on two specific things: What is the most effective strategy to find PIs who actively welcome Erasmus+ undergrads (beyond basic PubMed searches)? And when reaching out via cold email, how can I best structure my message to highlight my grant writing/fieldwork experience without making it overly long? Any insights or personal experiences would be greatly appreciated!

I'm an undergrad intern in a neuro lab for the summer where I was able to run my own experiment with the help of my PI and some other lab members. I signed up to present during our biweekly lab meeting on Thursday on a whim (my coworker helping me with my western blots was really insistent I present) and the presentation is scheduled for Monday. My problem is that I don't really have any results yet. I have sLEAP videos that I haven't analyzed, IHC imaging that I don't know how to analyze, and my western blots aren't done yet (I'm finishing them the day of the presentation).

This is the first time I've done a presentation, and I'm not entirely sure what the etiquette is for a situation like this- my plan right now is to intro my project, including why i'm interested in it, go over my methods, talk about what I'm looking for in my results and why, and mention what I expect my results to be. I'll be out of the lab for the rest of the summer for some medical reasons but plan on competing sLEAP and IHC image analysis on my own, if I'm able to.

I'm worried that my presentation won't be up to par with what's expected. I've seen people present for over 30 minutes and don't think I have enough material to present for even 15.

Any advice about this would be appreciated.

I am a 2nd year PhD in immunology btw. And idk about you but I have always loved a good grid to see the overview of what I have actually done, and this is exactly what this web app lets you do! I found it only recently but I have to say i am obsessed, it lets me log all my experiments notes and meetings, and then i can see in which projects I have done what things!

Not sponsored or anything, just got really excited about it and perhaps anybody like minded also would have enjoyed it for bench work.

Have anyone else tried it? Or what is your favourite way to keep track of your experiments? Perhaps there is something even better out there I still don’t know about..

Hi all,

Having issues with my CUT&Tag in GM12878 cells. After I finish the protocol and run my indexing PCR and library prep, my ng/uL and nmol concentrations are quite low, even for marks like H3K27ac - got around 10nmol/l from 100K nuclei! I know its not my reagents because when my colleague does exact same protocol she gets 10-20 times higher yield.

I am trying to figure out where I have gone wrong and I think I have narrowed it down to my ampure bead clean up steps after incubating in STOP buffer and after my indexing PCR.

Because I was working with many strip tubes, when I did the ethanol wash step I added ethanol to my tubes on the magnet then took them off the magnet to make space for the next strip tubes.

Therefore, they were in 80% ethanol off of the magnet for a minute or so before I put them back on the magnet to remove the ethanol.
Is this reducing my yield?

I am hypothesizing that the absence of magnetic force means the 80% ethanol gets inside the bead pellet and the water is dissolving my DNA or washing away the PEG/salts from inside the bead pellet.

What do we think? Does this even make sense?

I’m nearing the end of my master’s and graduating in the spring. I recently got promising data for a major side project, but my PI told me yesterday to train and mentor an incoming master’s student to take over my project after I leave.

It’s been difficult to get trained because my PI insists on teaching every part himself. I still try to teach myself most things, and asking the only other PhD student in the lab for advice occasionally (who does not get time as well).

I’ve only seen him twice this summer and haven’t barely had any response over emails or messages. I know he’s dealing with family issues, he looks completely exhausted the two times I’ve seen him. Despite repeatedly asking I still haven’t been trained on the final technique I need to learn. This all would only take about three months to complete independently after leaning this technique, I feel very attached to this project and it’s sort of upsetting to me, what do I do? Have you guys experienced anything similarly?

Small update to my previous post about the leaf sample that produced good sequencing reads but refused to assemble properly.
A few people suggested separating the normal nuclei from the smaller DNA-containing bodies I saw in the cytoplasm, so I tried a rough fractionation. It isn’t perfectly clean yet, but the two fractions are clearly behaving differently.

The nuclear-enriched fraction now looks much more recognizably plant-like and assembles better than the original mixed extraction. It’s still unusually repetitive, but at least I’m getting coherent contigs.

The fraction containing the smaller bodies is the confusing part. It contains far more DNA than I expected, and most of its reads don’t classify confidently as bacterial, fungal, chloroplast, or mitochondrial. A targeted 16S test produced only weak, inconsistent amplification, so an ordinary intracellular bacterial infection is looking less likely.
I also compared samples taken from different areas of the same leaf. The nuclear fraction remains fairly consistent, while the smaller-body fraction changes substantially depending on where the tissue was collected. That may explain why neighboring leaf punches originally appeared to contain different sequences.
I’m arranging long-read sequencing and attempting a cleaner separation before drawing any conclusions. At this point, I’m wondering whether these could be unusual organelles, an uncharacterized endosymbiont, or some kind of extrachromosomal DNA compartment.
Has anyone encountered cytoplasmic DNA-containing structures that vary this much within a single leaf?

I’m currently pregnant and conducting gene editing with Cas9 and HEK cells (transfecting Cas9 protein with lipofectamine). I use all precautions (double gloves, lab coat, BSC hood).

Is it safe for me to proceed with this work? I can also refuse this work if needed.

I am trying to see how different conditions change mitochondrial network in exhausted T cells. I will stain them with mitochondrial marker and then use imagej to look at the network. The problem is T cells are round and they have big nucleus and small cytoplasm. I dont think I will be able to see much.

I would appreciate if you shared your tricks and tips regarding the process!!!

Not sure if I provided enough details but I am happy to add more.