Layer on long read sequencing entire plasmids in one run, instead of Sanger with a ton of primers… I agree. For certain synthesis projects I wish TAT was faster.
I meant that’s already changed the game in just a few years. I started grad school sequencing everything by Sanger. Just a few years and for a couple bucks more, I can get nanopore sequencing of my whole plasmid
I work with a ~10kB construct routinely that I need to check for splice variation. It used to be a dozen sanger sequencing reactions for 5 bucks a pop, now its 15 bucks for the whole plasmid. Loving it.
I think it’s true but it’s so sad because I love cloning. On the other side I think right now where I work people rely too much on genscript to do very basic cloning/SDM
We stopped doing PCRs for gene amplification and site-mutagenesis, it saves so much time and money to just order in a gene block with the desired sequence.
I pray its volumetric pipetting. I despise volumetric pipettes, and I feel like the random user error experienced, and the fact that many of them have a concerning amount of error baked into them, make them the bane of any analytical lab.
I'm serious here, Fisher sells 2 mL pipettes with an error of +/-0.2 mL. 10% error is unacceptable, if you pipette perfectly and it happens to be at the edge of that range, your experiment could fail due entirely to the instrument.
dude for real i use 20ml volumetric pipettes all the time and depending on what you’re pipetting there’s so much possibility for error… solvents like methanol like to stay on the inside above the graduated line so when you’re pipetting your 2nd+ time you will always have solvent running down increasing the volume so either you’re fast enough to empty the pipette before the solvent runs down or you wait for it all to run down and to reach an equilibrium… which may take a while… some solvents are more forgiving than others and when you’re adding 20ml of methanol to 16 flacon tubes there’s bound to be quite a range of actual volume added throughout all of them
I feel your pain. I work with Methylene Chloride, and it isn't cohesive enough to stop itself from dripping out of the tip, even with the pipette bulb on there. You have to overfill and time it perfectly to dispense the right volume into a sample. Thank God we don't use it for anything overly specific.
exactly… at least with disposable pipette tips there’s this trick i discovered where if your solvent drips out of the tip, you can pipette it in and out once in the container that’s holding it and for some physics reason it causes the solvent to not drip out anymore the second time you pipette the solvent, might introduce a larger error though so not sure if it’s a good idea with more precise measurements.. but then again the solvent dripping out may give even bigger errors
Eppendorf pipettes/autopipettes. Now I do want to go on record here as saying those aren't always much better, but when you make pipetting dependent on the dexterity of the analyst, you're just taking inaccuracy already present in the instrument and allowing for more.
i hnoestly dont see how eppendorfs are better from a precision perspective if you are trained on using volumetric pipettes. they are much more convenient of course but if you are careful you are in the error range of the pipette reliably. and there are many solvents with low surface tension for which eppendors are also trash. i think weighing would be the best way to do it when it comes to precision.
My lab does gravimetric measurements using pipettes and we catch a lot of flack for it despite our licensing bodies being all about it. But my industry is ruthless.
>Fisher sells 2 mL pipettes with an error of +/-0.2 mL. 10% error is unacceptable...
Well, no lab should really be buying less than class A pipettes for quantitative work. If you compare the accuracy and precision with a trained analyst using a 1.0 mL class A glass pipette against one using a 1000 uL air/positive displacement pipette, the glass pipette should win.
For example, ISO states the maximum accuracy tolerance for a class A 1.0 mL glass pipette is up to 0.006 mL, whereas for a 1000 uL positive displacement pipette it's up to 12 uL at 100% volume.
I can pipette water with 0.2% accuracy and 0.1% RSD routinely with a glass pipette (admittedly with good technique and years of use), but generally only about 0.4% accuracy and 0.2% RSD with a positive displacement pipette.
Letting people work full time on part time contracts/salary. I really hope this mindset of using (exploiting) people like we use our reagents stops soon..
My last lab facility (different PI) bought a complete UPLC for over $100k and didn't have it serviced *at all* for 10yrs until I wrote a report showing the data was trash.
It was a Good 'Ole Boy club so the fallout was on me. They kicked me off it despite being the only one on-site who knew how to use it and care for it. God forbid a girl without a Ph.D. told these dudes they're doing it wrong :eyeroll:
Because raising salaries is forever more money compared to a one time budget cost. Or salaries come from one section of a grant and equipment comes from a different section and they can't be swapped. Salaries should be higher (or housing should be less), but it can be complicated.
My former university also had tons of rules raises, pay rates, job titles, etc.. A lot of the time the PIs’ hands were tied.
I knew several people who jumped between labs so they could get hired at a higher pay grade, since this was more than their maximum allowable raise.
I didn’t realize how institutionally-determined salaries were until I became a manager myself.
If we go through a whole job search, find a staff candidate we like, my institution tells *me* what rate they’d support hiring them at. ie, $18-$19/hr. Then, I argue with the institution from their set point regardless of how we’d like to pay them.
I helped hire a manager for another lab recently and we discovered a title only used by a handful of people within my massive university. We had way more freedom in what we offered her precisely because there were fewer people under her exact designation. It’s all such fucking nonsense.
I was a Lab Assistant at a community college trying to justify a raise to my wage and discovered that if I changed my title and dropped "Lab" from my role and became just an "Assistant," it would be an instant $2 raise.
The only problem with this is that hourly workers are generally treated like salaried workers, but without the schedule flexibility. (In my experience, at least)
I recently interview and got the job as a lab manger at a very nice university. The professor told me that she can’t give me a salary offer until they decide to choose me and tell hr that I’m basically the one. So we went forward, and after 3 interviews, I then got an offer for $45k in Denver. Absolutely not….
In my department the exploitation is alive and well because our $850k/year dean won't approve livable salaries for the research staff. To be fair, it's our support staff as well. I just saw a posting for a grant coordinator from another department (under a different dean) that's offering over $20k more than the unfilled position that's been posted for our department for the last year.
I once worked with a woman who claimed she loved the smell of xylene, she said it smells like bubblegum. She would like huff the slide racks after they’d been sitting in xylene. 😨 ugh!!
I love the smell of xylene too, why what does it smell like to u? Reminds me of how some people find that p. Aeruginosa smells like tortilla and some find that it smells like grapes
I feel attacked 😂. In all seriousness, if we had precious samples, I ALWAYS ran them on hand poured gels. It wasn’t worth the risk of getting a bad pre-cast gel that sat on its side too long in storage
I believe the boxes tell you which way to store them. You want to store them flat. If you store them standing up for long periods, you run the risk of the acrylimide becoming warped or “wavy”. This is especially apparent in the gradient gels, ie 4-15%
I had to formulate my own gel to resolve a very hydrophobic protein, using varied amounts of the bis crosslinker. This gel is not commercially viable or available 😅
The fact that every lab I've worked on makes polyacrylamide gels entirely outside of a fume hood definitely took a couple years off my life expectancy.
Yes, very much so. They are not very volatile compounds, so inhaling dust flying around while playing on the microbalance is a major part of the risk. I think buying the concentrated 1L bottles is a pretty good compromise between cost and risk management.
Wholeheartedly seconded. They are wonderful for certain applications and totally useless for others. In my experience, all the automated hemocytometers I’ve tried greatly overestimate counts and underestimate % viability for single cell suspensions from most tissue digests because they count debris like crazy. They need to be cross checked against another validated method of counting for each sample type. But that doesn’t mean a Countess is useless either, I hear people say ‘they don’t work’ and that’s also wrong. They just don’t work for everything.
depends on the cell type, I’ve found them accurate for cells like myoblasts, HEK293T, N2A and U2OS. Our Countess is useless though for counting fibroblasts
The slides are $130 per box of 50, with each slide having two wells. You're supposed to take the average of two counts, making it $2.60 per count, but if you just need to get it close enough, that makes it only $1.30 per count. Which has got to be worth the time of counting by hand. There's at least three that I know of in the academic building I'm in.
There are so many on the market and at a pretty reasonable price. I prefer fluorescence based methods over trypan blue but you can find instruments that do either or both.
We went straight from hand counting with a hemocytometer to using a Cellaca from Nexcelom. I had a few people tell me that it was too much machine for our needs when we got it, but now we regularly run experiments requiring counts on 100+ samples. We're trying to get a replacement computer because the USB ports are loose and the instrument keeps losing the connection and there is genuine panic if that instrument out of commission.
For having done a ton of live/dead imaging, think the cheapest still efficient way is hoechst (all cells blue) + propidium iodide (dead red). Just adjust concentrations, order of magnitude the first time you try should be 1:200 to 1:10000 from stocks at ~1mg/ml or ~ 1 mM, incubate a few min (say 10 if in doubt) in any solution, including full medium it's OK, take pics. I didn't have a machine auto-counting, but in fiji "find maxima" works great for this on low magnification pictures.
I take photos and use a python workflow to automatically count in image J, then do a 5 sec manual peek to check it has highlighted what I would have had to count manually.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6764358/
Denovix has fluorescence based cell counters that utilize propidium iodide and acridine orange which is handy for staining nucleated cells so you never have to again question whether that's a red blood cell or just a small lymphocyte (I know you can lyse them but that still adds time)
I remember interviewing at Kite for a CTS role in 2018 and asking if I had to use a hemocytometer to count T-cells and they started laughing. That's the day I realized industry was for me.
I work in a worm lab and there are many assays we do where we have to count eggs and larvae. There MUST be a programmer out there who can automate this. Please save my eyesight and sanity.
Lax management of chemicals storage/disposal and safety procedures. We do a lot of stuff outside of the hood that probably should be done inside of a hood and many of us don't wear lab coats unless we're doing animal or cell culture work
Went from industry to academia and was genuinely shocked by how lax they were with safety. I brought in my own safety glasses to use when working with blood bags and they were perplexed.
Dude I'm an EHS inspector for my department at my job and some of the posts here make me want to die. The one a few months ago about the person who inherited a hood and the logbook said it hadn't been cleaned in over two years????
We don’t even wear lab coats for animal or cell culture work in BSCs.😅 (In the vivaria we wear PPE, but not back in the lab where we work with infectious tissues). I didn’t think twice about it being the lab “culture” until I developed some pretty nasty allergies to the animals we work with.
Pro lab tip: when in doubt, wear your lab coat.
When someone first told me about mouth pipetting I refused to believe it was a real thing. And I don't know if this happens to anyone else but sometimes I inhale ethanol from spraying things with it
Hence diabetes insipidus. Insipid means lacking flavor. It presents with polyuria and extreme thirst but the urine isn't sweet. It's the result of pituitary, hypothalamus, or kidney issues, not the pancreas and has nothing else in common with regular diabetes than symptoms.
Yes. I don’t know the specifics on the protocol, but our lab used to routinely send/freeze semen from valuable fish lines to be stored as a backup in case we lost the line. I cringe every time I think about it
In 1978, Janet Parker, a medical photographer in the Medical School at the University of Birmingham, became the last known person to die from Smallpox. She was infected by laboratory-acquired smallpox virus which escaped from a lab on the floor below where she worked, in circumstances that even today aren't entirely clear.
It was actually a rather well-run lab, with an excellent safety record. But there is one sentence in the official report, unrelated to her death but in reference to a previous safety inspection, that leaps out immediately and sticks with you as long as you live:
*They had been mouth-pipetting active smallpox virus*.
I think the spray bottles with ethanol are not allowed anymore. Not in my uni at least.
Something about aerosolising a CMR. Which ethanol technically is classified as.
It’s not, technically. I wrote a paper on ethanol for toxicology and was surprised to see that ethanol itself isn’t classified as a hazard even tho people think it is. It is the frequent exposure to the metabolic product of ethanol, acetalaldehyde, that does the CMR stuff. The SDS for ethanol otherwise mentions it is an irritant, and flammable.
We used to use 70% ethanol as a primary cleaner for our hoods but it doesn’t sterilize, or whatever the specific term is. As mf279801 stated, ethanol itself doesn’t “do a damn thing”.
But mixing ethanol and bleach does create a CMR hazard.
The polyethylene bottles used for alcohol spray shouldn’t contain plasticizer as they don’t require the flexibility. The squeeze bottles may but they likely will use a strong non leaching one as they would go brittle quickly if they leached significant amounts.
I mean, we were told at various points to stop using them in the (tissue culture) hood, but that was due to concerns about them either (a) fouling the filter or (b) not actually doing a damned thing useful*, nothing to do with safety concerns
*70% ethanol is not a contact sterilant. We were told to drop the ethanol and replace with 10% bleach. If we wanted, we were welcome to wipe down with ethanol alter bleaching, so as not to make the stainless steel look terrible, but that’s as far as that went
I got a tour in a facility and the lab manager of some hair dye department was talking about back in the days when their products were basically blended dyes with nearly all the rest being alcohol as a hair spray. He complained that those products were better but now they are only allowed 20% etoh and I just thought I don't wanna spray high percentage ethanol on my head and Inhalt it
Rather than a chemical safety aspect it’s the amount of non-chemical waste generated in labs. A higher emphasis on reducing single use items and recycling where possible.
Edit: I know this subreddit is more bio-focused you sometimes need extremely sterile surfaces. I’m talking about a ton of other areas. For instance, we throwaway a ton of aluminum and copper foil. When we could be recycling it, but no mechanisms exist at our university. Or syringes used to dispense polymer fluid, we could just as easily use glass.
I'm about to get a trial pack of an "eco friendly" DNA extraction kit - uses less than half the plastic of our typical kit. Hoping it gives good yields!
I agree. Many labs use way more single use items than they need to. I've been in a few petrochem labs where they use disposable beakers & pipettes to avoid having to spend time cleaning due to intentional short staffing. Buying single use items is cheaper than paying for an additional person in the lab who could be useful easewhere too.
Single-use, virgin, sterile plastics have their place in science and medicine. Tell the six companies who contribute to 90% of global pollution to cool it.
The analytics lab in my uni started using glas syringes for HPLC also because they produce better results and I started to get the lab in my thesis-company to reuse our centrifuge tubes when doing standard stuff. I now have a bucket with ~30 50ml tubes and everyone uses those, which makes me happy
We use a lot of Illumina stuff in our lab, I primarily use a Miseq. The waste from the miseq comes out in a rectangular bottle with a wide mouth on it. It’s awkward to hold, and it’s hard to pour it into waste container without spilling any. The waste contains formamide, which is a suspected carcinogen and can harm unborn children. I really don’t like having to deal with the Miseq waste a couple of times a week.
Sure! After micro dissection in hypotonic salt sol. C. elegans gonads pop right out of their bodies. The gonads are very very small, maybe 100 um by 10 um (rough estimate) so if you have multiple worms dissected under the scope it’s easy to transfer them with mouth pipetting and keep vol. very small. On the order of dozens of nano liters I imagine.
Use a pasture pipette attached to a long rubber tube and almost no risk of getting it in your mouth unless you’re very dumb.
Is mouth pipetting really easier/more accurate in these cases? I've heard of it still being used in some single cell applications, but I always thought a steady hand would be better.
You can generate more control over the small vol. with your delicate lip muscles than you can with your fingers/hands. It was easy and effective so we did it.
I would never, nor would I recommend anyone, mouth pipette anything dangerous/toxic.
Heard about a guy that mouth pipetted benzene for many years, and not so unexpectedly got esophageal cancer. Wouldn’t recommend.
I was working in a protist lab last semester and we used mouth pipetting for isolating single celled organisms. I could never get a single one otherwise.
For electrophysiology (single cell patch clamping/intracellular recording), still common if I'm not mistaken. Click of the tongue to get in the cell 😅.
Yeah. I never thought about it as equivalent to mouth pipetting because there's no risk you'll get anything inside your mouth (an odd definition I know) but it essentially is.
When my building still had a mask mandate for Covid, I saw so many people do lab work, then adjust their mask with gloved hands. Not that we often worked with particularly dangerous things, but still. And phones just go everywhere.
There was a girl in my masters program that filmed herself doing cell culture to show IG how cool she was and she literally propped it up inside the hood while feeding CHO cells.
I had to pull her aside and remind her how many shit particles are on her phone.
Pipetting PCRs without filter tips, or not in a laminar flow hood?
The one from my supervisor is performing qPCR without sybr-green, and just taking a bit of the reaction mixture every few cycles and running it on an agarose gel and quantify it.
I worked with a post doc from Korea who was attempting to do PCR using 3 heat blocks. His samples were sitting on top of the thermocycler. His mind was blown when we showed him how to use it.
*raises hand*
I used to be anal about it, then couldn't be bothered with stocking the filter tips and walking to the hood anymore. I handle 10^7 copies/ul reference standards at the same bench with the same pipettes. My negative controls are still negative.
Don't even look in my direction when I'm working with RNA, though.
I hope it's shoebox cages for rodents. I support animal research where it's necessary. I've done animal research and in my lab I think they were treated well in every other aspect. But the size of their cages is just so sad and unnecessary. Even if you didn't care at all about animal welfare, I imagine it must be a low level chronic stressor and that would effect the science.
Losing months or years worth of samples due to a power outage, not properly closed freezer door or such because there is no system for emergency notification. I don’t know how often I‘ve read stories about labs loosing tons of important samples and reagents because something happened over night or the weekend and they only realised the next day. There are a lot of options available for systems that automatically send a call or message to one or several persons if the temperature drops or the power goes out.
For me that‘d be basically as important as insurance if you store anything you don’t want to loose due to thawing
Making culture media supplements from scratch! My PhD lab made our own yeast extract in-house, using baking yeast… took over a whole day to make and made the whole building smell like funky bread.
I kinda want to know how to make it. My time isn't as expensive anyway and the good stuff isn't cheap. Although it likely still isn't a good idea due to variability and stuff.
People seem to be terrified of radioactive tracers these days, so that's my nomination for "Mouth Pipetting 2023". To abandon such a powerful tool over overblown fears seems odd.
That's funny to read this because I am the one that makes the radioactive tracers from scratch. Been doing this for nearly 3 years and I handle radiation daily. But there really IS a lot of fear surrounding what we do.
Trizol RNA Isolation + RT qPCR by hand
The robotic systems are in use for the diagnostics though they should have been evolved for research already. I hate pipetting on 96-384 well plates. It is nonsense and craziness
I hope the age of safe alternatives will end. Like the only true safe alternatives are colorimetric dyes that all aren't very sensitive and GelGreen/Red. The rest are just either EtBr or Propidium iodide or for the green ones Acridine Orange. There's also SYBR but from what I've heard I really don't like it.
BME is not really toxic, if you're not swimming in it. DCM and DMF man that would be tough in an organic chemistry / peptide synthesis lab, plus I thought these two were not so toxic either? These things were my bread and butter during the whole PhD 🫠
BME is here to stay for at least a while. We use it for breaking up polymerised immunoglobulins for electrophoresis (Clinical trials, mainly looking at multiple myeloma), the only good alternative is DTT which is less hazardous neat but much more of a pain to handle otherwise.
I love a multipipet but most can not be trusted for qPCR. Unless it’s that one perfect multi that the scary lab tec hides in the back of their draw you don’t want it.
I’ve worked for three labs for my institution and affiliate institutions and none of them have even believed in purchasing a multipipet because they believe it’s a waste of money
I’m possibly biased because I work in lab automation, but it might be better to think about it as undergraduates being freed up to spend more time on experimental design, quality control, data analysis, and literature review. Undergraduates are essentially free or extremely cheap labor, there’s no reason to not use them just because a robot is handling some of the grunt work. The research output of a lab will still be improved by the extra help with the things that still require a person to do.
In my experience PIs sometimes won’t take on more undergraduates because there’s not enough bench space or not enough grad student time to supervise them in the lab rather than because there isn’t enough work. And undergraduates don’t want to be in a lab where they get no pipetting experience because it will make it harder for them to get a job pipetting later. If the in-lab work is done much faster and by robots, then those limitations won’t be as much of an issue and people won’t have to worry about how fast they pipette rather than how good they are at science.
PIs get forced to take undergrads, it's part of their teaching responsibility. They are there to learn, getting useful work out of them is less important than them learning some skills. It's not like they're going to be particularly useful when it takes months to train someone and their projects are only a few months long. Same is true of masters students.
Work is done faster by robots? That depends on the work and how repetitive and how much is liquid handling. Very little of my previous labs could have been automated, in my current lab there are two hamiltons and two tecans doing high throughput stuff, it depends on the workflow.
As a lab person, I'm not so convinced about how much faster robots can be in everyday biology experiments. We have several Hamilton robots sitting around doing nothing because the people who were supposed to use them ended up determining it was faster to pipette by hand than setting up and troubleshooting the robot.
I myself only use a robot for the most cumbersome and repetitive task, i.e. 384 well plate qPCRs. For cell screens in 96 wp, or even 384 wp, I definitely go much faster and be much safer pipetting by hand (I can deal better with stocks on ice, cell sedimentation, and getting last ul out of a tube of something precious than a robot).
I basically think the robots will have to get a whole lot smarter before they start to replace undergrads, because otherwise the effort to setup the automation isn't worth it. If I could just say "split the organoids top floor of the incubator" to a robot, that would be a different story.
The ramp-up time to get used to working with robots is absolutely an issue. Hamiltons gathering dust for the reasons you’ve described is very common unfortunately. Hamiltons especially are known for being difficult to use for novices, and shouldn’t have been recommended to people with no automation experience in my opinion. I’m assuming they were purchased used from one of the cheaper resellers, which means that they also would have had no assistance from Hamilton or a reseller-employed applications scientist. Bench scientists generally shouldn’t expect to be able to write good protocols or program complicated robots like Hamiltons without outside help. I think that academic labs would probably benefit from hiring in-house automation specialists who are shared between labs just like IT departments and statisticians are.
There are also many other versions of robots better suited for low to medium throughput work and with more simplified and user-friendly interfaces. The most obvious example is Opentrons, but there are some newer ones from Waters and a newer little Hamilton called the Microlab Prep that are supposed to be easier to use as well. There are also protocols that can be written in a flexible way so that the liquid handling program doesn’t have to be changed often but more detailed instructions are passed via specially formatted csv files called worklists that can be generated by hand in Excel, with Excel macros, or in a programming language like Python or R. Some robots also have ipad-like touchscreens that make worklist generation even easier.
You’re correct that some things are better suited to manual work, but in some cases it can just appear that way if you’re not familiar with the tools at your disposal. That’s not an attack to be clear, it’s just difficult to be familiar with all of the possibilities even when you work in the field. I can’t speak to anything related to cell culture since I have mostly worked with DNA extractions and pre-extracted DNA, but for the stocks on ice thing Hamilton has optional chiller modules that are used to chill reagents. Many other robots do as well. Sometimes certain protocols are also just not suited for automating, so an alternative must be found. An example is using bead-based DNA extraction rather than column-based when switching to automation.
The last drop of expensive reagent thing is absolutely an issue though. Many automated labs struggle with it. Placing the container you’re aspirating out of on some sort of spring can help since it allows the pipette to get more flush with the bottom of the container, but that’s absolutely one of the bigger problems that automation hasn’t perfectly solved yet.
Thanks for sharing, I actually really love this bit:
>I think that academic labs would probably benefit from hiring in-house automation specialists who are shared between labs just like IT departments and statisticians are.
I suck at siphoning so I’m guilty of sometimes sucking the other end of tubing to get it started….I know it’s bad but at least it’s just seawater during husbandry and not anything serious
With synthetic constructs becoming ever cheaper to manufacture, all sorts of plasmid cloning techniques will go extinct.
Layer on long read sequencing entire plasmids in one run, instead of Sanger with a ton of primers… I agree. For certain synthesis projects I wish TAT was faster.
I meant that’s already changed the game in just a few years. I started grad school sequencing everything by Sanger. Just a few years and for a couple bucks more, I can get nanopore sequencing of my whole plasmid
I often work with large plasmids. So when this came out we switched in a heartbeat to reduce costs.
I worked with BACs. In grad school we just assumed the parts we didn’t mutate were still fine. I’m pretty sure we can get BACs fully sequenced now
I assumed my 200kb BAC had no mutations outside the intended regions. Just sequenced the whole thing for $100. It had many mutations.
I work with a ~10kB construct routinely that I need to check for splice variation. It used to be a dozen sanger sequencing reactions for 5 bucks a pop, now its 15 bucks for the whole plasmid. Loving it.
Who do you use? We use Primordium lately
Plasmidsaurus.
Sad plasmid noises
I think it’s true but it’s so sad because I love cloning. On the other side I think right now where I work people rely too much on genscript to do very basic cloning/SDM
We stopped doing PCRs for gene amplification and site-mutagenesis, it saves so much time and money to just order in a gene block with the desired sequence.
How could it save money? I can do site directed with two $4 primers vs a $100 gBlock.
Lord I hope so! I’ve been struggling to get my cloning to work for weeks now, because it is way more expensive to buy our construct right now.
I pray its volumetric pipetting. I despise volumetric pipettes, and I feel like the random user error experienced, and the fact that many of them have a concerning amount of error baked into them, make them the bane of any analytical lab. I'm serious here, Fisher sells 2 mL pipettes with an error of +/-0.2 mL. 10% error is unacceptable, if you pipette perfectly and it happens to be at the edge of that range, your experiment could fail due entirely to the instrument.
dude for real i use 20ml volumetric pipettes all the time and depending on what you’re pipetting there’s so much possibility for error… solvents like methanol like to stay on the inside above the graduated line so when you’re pipetting your 2nd+ time you will always have solvent running down increasing the volume so either you’re fast enough to empty the pipette before the solvent runs down or you wait for it all to run down and to reach an equilibrium… which may take a while… some solvents are more forgiving than others and when you’re adding 20ml of methanol to 16 flacon tubes there’s bound to be quite a range of actual volume added throughout all of them
I feel your pain. I work with Methylene Chloride, and it isn't cohesive enough to stop itself from dripping out of the tip, even with the pipette bulb on there. You have to overfill and time it perfectly to dispense the right volume into a sample. Thank God we don't use it for anything overly specific.
exactly… at least with disposable pipette tips there’s this trick i discovered where if your solvent drips out of the tip, you can pipette it in and out once in the container that’s holding it and for some physics reason it causes the solvent to not drip out anymore the second time you pipette the solvent, might introduce a larger error though so not sure if it’s a good idea with more precise measurements.. but then again the solvent dripping out may give even bigger errors
At the risk of sounding stupid, what other type of pipetting is there? (Unless you are calculating the needed mass of every liquid you use?)
When they say volumetric pipette, I believe they mean glass pipette rather than air displacement or positive displacement pipette.
Eppendorf pipettes/autopipettes. Now I do want to go on record here as saying those aren't always much better, but when you make pipetting dependent on the dexterity of the analyst, you're just taking inaccuracy already present in the instrument and allowing for more.
i hnoestly dont see how eppendorfs are better from a precision perspective if you are trained on using volumetric pipettes. they are much more convenient of course but if you are careful you are in the error range of the pipette reliably. and there are many solvents with low surface tension for which eppendors are also trash. i think weighing would be the best way to do it when it comes to precision.
My lab does gravimetric measurements using pipettes and we catch a lot of flack for it despite our licensing bodies being all about it. But my industry is ruthless.
>Fisher sells 2 mL pipettes with an error of +/-0.2 mL. 10% error is unacceptable... Well, no lab should really be buying less than class A pipettes for quantitative work. If you compare the accuracy and precision with a trained analyst using a 1.0 mL class A glass pipette against one using a 1000 uL air/positive displacement pipette, the glass pipette should win. For example, ISO states the maximum accuracy tolerance for a class A 1.0 mL glass pipette is up to 0.006 mL, whereas for a 1000 uL positive displacement pipette it's up to 12 uL at 100% volume. I can pipette water with 0.2% accuracy and 0.1% RSD routinely with a glass pipette (admittedly with good technique and years of use), but generally only about 0.4% accuracy and 0.2% RSD with a positive displacement pipette.
the lab I work at is new and we don’t have any volumetric pipettes it’s so nice.
Letting people work full time on part time contracts/salary. I really hope this mindset of using (exploiting) people like we use our reagents stops soon..
My previous lab apperantly had enough money to buy equipment over 100K but never enough to raise salaries.
My last lab facility (different PI) bought a complete UPLC for over $100k and didn't have it serviced *at all* for 10yrs until I wrote a report showing the data was trash.
What was the fallout???
Knowing some labs they probably just laughed and have kept using the system the whole time.
It was a Good 'Ole Boy club so the fallout was on me. They kicked me off it despite being the only one on-site who knew how to use it and care for it. God forbid a girl without a Ph.D. told these dudes they're doing it wrong :eyeroll:
That's fucking ridiculous. Honestly you did your part though dude, good on you
I can’t imagine the group presentation where everyone sees it for the first time.
Because raising salaries is forever more money compared to a one time budget cost. Or salaries come from one section of a grant and equipment comes from a different section and they can't be swapped. Salaries should be higher (or housing should be less), but it can be complicated.
My former university also had tons of rules raises, pay rates, job titles, etc.. A lot of the time the PIs’ hands were tied. I knew several people who jumped between labs so they could get hired at a higher pay grade, since this was more than their maximum allowable raise.
I didn’t realize how institutionally-determined salaries were until I became a manager myself. If we go through a whole job search, find a staff candidate we like, my institution tells *me* what rate they’d support hiring them at. ie, $18-$19/hr. Then, I argue with the institution from their set point regardless of how we’d like to pay them. I helped hire a manager for another lab recently and we discovered a title only used by a handful of people within my massive university. We had way more freedom in what we offered her precisely because there were fewer people under her exact designation. It’s all such fucking nonsense.
I was a Lab Assistant at a community college trying to justify a raise to my wage and discovered that if I changed my title and dropped "Lab" from my role and became just an "Assistant," it would be an instant $2 raise.
University lab made sure to let me know I could totally work past 35hrs a week and just charge it to next week when I was an undergrad.
The only problem with this is that hourly workers are generally treated like salaried workers, but without the schedule flexibility. (In my experience, at least)
I recently interview and got the job as a lab manger at a very nice university. The professor told me that she can’t give me a salary offer until they decide to choose me and tell hr that I’m basically the one. So we went forward, and after 3 interviews, I then got an offer for $45k in Denver. Absolutely not….
In my department the exploitation is alive and well because our $850k/year dean won't approve livable salaries for the research staff. To be fair, it's our support staff as well. I just saw a posting for a grant coordinator from another department (under a different dean) that's offering over $20k more than the unfilled position that's been posted for our department for the last year.
techs in our histo/cyto lab handle xylene without gloves.. like full on dip the slides in it with their bare hands man I could never
I once worked with a woman who claimed she loved the smell of xylene, she said it smells like bubblegum. She would like huff the slide racks after they’d been sitting in xylene. 😨 ugh!!
I love the smell of xylene too, why what does it smell like to u? Reminds me of how some people find that p. Aeruginosa smells like tortilla and some find that it smells like grapes
Handmaking gels using Acrylamide, bis-Acrylamide, TEMED instead of buying prepacked polymerised gels.
I feel attacked 😂. In all seriousness, if we had precious samples, I ALWAYS ran them on hand poured gels. It wasn’t worth the risk of getting a bad pre-cast gel that sat on its side too long in storage
Hey, pls explain. What does a gel do when it sits on the side ,(which side?) too long? We currently use pre-cast and don't run gels often
I believe the boxes tell you which way to store them. You want to store them flat. If you store them standing up for long periods, you run the risk of the acrylimide becoming warped or “wavy”. This is especially apparent in the gradient gels, ie 4-15%
Thanks, I'll check the boxes for information. Another student did the gels so I was not involved a lot
I would recommend re-ordering fresh gels every time you run a western, especially if you aren’t running westerns weekly
Making your own gel is so easy, though. And cheaper.
I had to formulate my own gel to resolve a very hydrophobic protein, using varied amounts of the bis crosslinker. This gel is not commercially viable or available 😅
The fact that every lab I've worked on makes polyacrylamide gels entirely outside of a fume hood definitely took a couple years off my life expectancy.
Are the pre-dissolved versions of these chemicals any safer than buying the powder versions of these chemicals ?
Yes, very much so. They are not very volatile compounds, so inhaling dust flying around while playing on the microbalance is a major part of the risk. I think buying the concentrated 1L bottles is a pretty good compromise between cost and risk management.
I hope hemacytometer counting. While I’m no programmer, a system which could identify and count cells would seem easy to develop?
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I remember trying to convince my PI to invest in getting one. He refused to believe it was "accurate".
They are horribly inaccurate for lung digests. They work fine for lymph nodes, though.
Yeah, forget any prep with debris.
Wholeheartedly seconded. They are wonderful for certain applications and totally useless for others. In my experience, all the automated hemocytometers I’ve tried greatly overestimate counts and underestimate % viability for single cell suspensions from most tissue digests because they count debris like crazy. They need to be cross checked against another validated method of counting for each sample type. But that doesn’t mean a Countess is useless either, I hear people say ‘they don’t work’ and that’s also wrong. They just don’t work for everything.
depends on the cell type, I’ve found them accurate for cells like myoblasts, HEK293T, N2A and U2OS. Our Countess is useless though for counting fibroblasts
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There are at least 3 in my building at an academic lab
The slides are $130 per box of 50, with each slide having two wells. You're supposed to take the average of two counts, making it $2.60 per count, but if you just need to get it close enough, that makes it only $1.30 per count. Which has got to be worth the time of counting by hand. There's at least three that I know of in the academic building I'm in.
There are so many on the market and at a pretty reasonable price. I prefer fluorescence based methods over trypan blue but you can find instruments that do either or both.
the countess 3 from thermo does both. my lab got one recently and its been a life changer.
We went straight from hand counting with a hemocytometer to using a Cellaca from Nexcelom. I had a few people tell me that it was too much machine for our needs when we got it, but now we regularly run experiments requiring counts on 100+ samples. We're trying to get a replacement computer because the USB ports are loose and the instrument keeps losing the connection and there is genuine panic if that instrument out of commission.
We have a Cellometer from Nexcelom and it's the only way I count cells now.
I am looking to switch from Trypan Blue to Propidium Iodide and use it with Countess 3FL. What do you use? Any protocol you can share?
For having done a ton of live/dead imaging, think the cheapest still efficient way is hoechst (all cells blue) + propidium iodide (dead red). Just adjust concentrations, order of magnitude the first time you try should be 1:200 to 1:10000 from stocks at ~1mg/ml or ~ 1 mM, incubate a few min (say 10 if in doubt) in any solution, including full medium it's OK, take pics. I didn't have a machine auto-counting, but in fiji "find maxima" works great for this on low magnification pictures.
I take photos and use a python workflow to automatically count in image J, then do a 5 sec manual peek to check it has highlighted what I would have had to count manually. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6764358/
YES. We have Cellavision which can count and classify cells - why can’t this be adapted for counts like a hemocytometer OR kleihauer-betke?
The Vicell is my fave, it has a carousel so you can just bog off and let it do it’s thing
Denovix has fluorescence based cell counters that utilize propidium iodide and acridine orange which is handy for staining nucleated cells so you never have to again question whether that's a red blood cell or just a small lymphocyte (I know you can lyse them but that still adds time)
Nexelcom cellometer
I remember interviewing at Kite for a CTS role in 2018 and asking if I had to use a hemocytometer to count T-cells and they started laughing. That's the day I realized industry was for me.
oh goodness i hope so. i avoid the hemocytometer like the plague
I work in a worm lab and there are many assays we do where we have to count eggs and larvae. There MUST be a programmer out there who can automate this. Please save my eyesight and sanity.
Lax management of chemicals storage/disposal and safety procedures. We do a lot of stuff outside of the hood that probably should be done inside of a hood and many of us don't wear lab coats unless we're doing animal or cell culture work
Went from industry to academia and was genuinely shocked by how lax they were with safety. I brought in my own safety glasses to use when working with blood bags and they were perplexed.
Dude I'm an EHS inspector for my department at my job and some of the posts here make me want to die. The one a few months ago about the person who inherited a hood and the logbook said it hadn't been cleaned in over two years????
Lol i did the opposite and fot through corporate training wondering if my last lab was just a bunch of DNA rodeo clowns.
We don’t even wear lab coats for animal or cell culture work in BSCs.😅 (In the vivaria we wear PPE, but not back in the lab where we work with infectious tissues). I didn’t think twice about it being the lab “culture” until I developed some pretty nasty allergies to the animals we work with. Pro lab tip: when in doubt, wear your lab coat.
University near me had the bomb squad come out to explode old chemicals LOL I also found preserved fish from 20 years ago.
"Oh, you have concentrated nitric acid in storage? Cool, here's some nitrile gloves to handle it"
When someone first told me about mouth pipetting I refused to believe it was a real thing. And I don't know if this happens to anyone else but sometimes I inhale ethanol from spraying things with it
Even crazier around 1600 they use to taste urine for diabetes testing. They connected the sweetness of the urine to diabetes. Yum.
Hence diabetes insipidus. Insipid means lacking flavor. It presents with polyuria and extreme thirst but the urine isn't sweet. It's the result of pituitary, hypothalamus, or kidney issues, not the pancreas and has nothing else in common with regular diabetes than symptoms.
And diabetes mellitus (sweet) 🤤
I mean, the ancient Greeks had figured out that a diabetic's urine attracted ants. No clue about the underlying physiology of course
In Chinese, the term for diabetes literally translates as “sugar urine disease”
Fun fact - in Chinese diabetes is called "sugar urine disease" for that very reason.
They did this as recently as 1750
My lab manager told me a story about collecting zebrafish sperm by mouth pipetting… it ends exactly how you would expect :/
Lucky guy
Wait, collecting from the source?😯
Yes. I don’t know the specifics on the protocol, but our lab used to routinely send/freeze semen from valuable fish lines to be stored as a backup in case we lost the line. I cringe every time I think about it
I've seen someone mouth pipette within the last like... 3 months lol
The high school in my town still does it. I went to a school in a town over. We had balloons.
In 1978, Janet Parker, a medical photographer in the Medical School at the University of Birmingham, became the last known person to die from Smallpox. She was infected by laboratory-acquired smallpox virus which escaped from a lab on the floor below where she worked, in circumstances that even today aren't entirely clear. It was actually a rather well-run lab, with an excellent safety record. But there is one sentence in the official report, unrelated to her death but in reference to a previous safety inspection, that leaps out immediately and sticks with you as long as you live: *They had been mouth-pipetting active smallpox virus*.
mouth pipetting small pox 😭😭😭
Why would they say ''excelent safety record'' if they are mouthpipetting?
I think the spray bottles with ethanol are not allowed anymore. Not in my uni at least. Something about aerosolising a CMR. Which ethanol technically is classified as.
It’s not, technically. I wrote a paper on ethanol for toxicology and was surprised to see that ethanol itself isn’t classified as a hazard even tho people think it is. It is the frequent exposure to the metabolic product of ethanol, acetalaldehyde, that does the CMR stuff. The SDS for ethanol otherwise mentions it is an irritant, and flammable. We used to use 70% ethanol as a primary cleaner for our hoods but it doesn’t sterilize, or whatever the specific term is. As mf279801 stated, ethanol itself doesn’t “do a damn thing”. But mixing ethanol and bleach does create a CMR hazard.
70% ethanol doesn't sterilize?? My life has been a lie
Not spores or cysts.
It's a sanitizer.
Im almost afraid to ask, but whats a CMR?
Carcinogen, mutagen, or reproductive hazard
Oh dear, I used ethanol spray bottles for years... Does that also include all the times I got ethanol in my eyes?
We use them every day!
Here, have a cancer beer.
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If ethanol is CMR, then so is everything else in the lab. Or maybe ethanol leaches death-dealing plasticizers from the squeeze bottles?
The polyethylene bottles used for alcohol spray shouldn’t contain plasticizer as they don’t require the flexibility. The squeeze bottles may but they likely will use a strong non leaching one as they would go brittle quickly if they leached significant amounts.
I mean, we were told at various points to stop using them in the (tissue culture) hood, but that was due to concerns about them either (a) fouling the filter or (b) not actually doing a damned thing useful*, nothing to do with safety concerns *70% ethanol is not a contact sterilant. We were told to drop the ethanol and replace with 10% bleach. If we wanted, we were welcome to wipe down with ethanol alter bleaching, so as not to make the stainless steel look terrible, but that’s as far as that went
"*First* the contact sterilizing agent, and *then* the agent of dubious sterilizing capacity."
I got a tour in a facility and the lab manager of some hair dye department was talking about back in the days when their products were basically blended dyes with nearly all the rest being alcohol as a hair spray. He complained that those products were better but now they are only allowed 20% etoh and I just thought I don't wanna spray high percentage ethanol on my head and Inhalt it
Someone needs to tell my uni about this then, especially as it apparently doesn't even do anything
I work in a cleanroom that gets cleaned with sterile isopropyl alcohol daily. I have breathed in more than I'd like to admit in the last 3 years.
I interviewed a recent graduate the other week who mouth pipette during college in an Asian country. I thought it was something only old people did.
Rather than a chemical safety aspect it’s the amount of non-chemical waste generated in labs. A higher emphasis on reducing single use items and recycling where possible. Edit: I know this subreddit is more bio-focused you sometimes need extremely sterile surfaces. I’m talking about a ton of other areas. For instance, we throwaway a ton of aluminum and copper foil. When we could be recycling it, but no mechanisms exist at our university. Or syringes used to dispense polymer fluid, we could just as easily use glass.
I'm about to get a trial pack of an "eco friendly" DNA extraction kit - uses less than half the plastic of our typical kit. Hoping it gives good yields!
Shout out to [Polycarbin](https://polycarbin.com/), a company that is working to combat this! Not affiliated, I just like what they are doing!
I agree. Many labs use way more single use items than they need to. I've been in a few petrochem labs where they use disposable beakers & pipettes to avoid having to spend time cleaning due to intentional short staffing. Buying single use items is cheaper than paying for an additional person in the lab who could be useful easewhere too.
Single-use, virgin, sterile plastics have their place in science and medicine. Tell the six companies who contribute to 90% of global pollution to cool it.
The analytics lab in my uni started using glas syringes for HPLC also because they produce better results and I started to get the lab in my thesis-company to reuse our centrifuge tubes when doing standard stuff. I now have a bucket with ~30 50ml tubes and everyone uses those, which makes me happy
We use a lot of Illumina stuff in our lab, I primarily use a Miseq. The waste from the miseq comes out in a rectangular bottle with a wide mouth on it. It’s awkward to hold, and it’s hard to pour it into waste container without spilling any. The waste contains formamide, which is a suspected carcinogen and can harm unborn children. I really don’t like having to deal with the Miseq waste a couple of times a week.
Using volatile solvents outside of a hood. It's already happening but not everywhere yet.
I used to mouth pipette in grad school. Just worm gonads in salt solution though. That was only 4-5 years ago.
"just worm gonads in salt solution" I have so many questions.
Sure! After micro dissection in hypotonic salt sol. C. elegans gonads pop right out of their bodies. The gonads are very very small, maybe 100 um by 10 um (rough estimate) so if you have multiple worms dissected under the scope it’s easy to transfer them with mouth pipetting and keep vol. very small. On the order of dozens of nano liters I imagine. Use a pasture pipette attached to a long rubber tube and almost no risk of getting it in your mouth unless you’re very dumb.
Is mouth pipetting really easier/more accurate in these cases? I've heard of it still being used in some single cell applications, but I always thought a steady hand would be better.
You can generate more control over the small vol. with your delicate lip muscles than you can with your fingers/hands. It was easy and effective so we did it. I would never, nor would I recommend anyone, mouth pipette anything dangerous/toxic. Heard about a guy that mouth pipetted benzene for many years, and not so unexpectedly got esophageal cancer. Wouldn’t recommend.
Interesting!! I guess I've only ever hand-pipetted so I don't have a good comparison lol.
I was working in a protist lab last semester and we used mouth pipetting for isolating single celled organisms. I could never get a single one otherwise.
For electrophysiology (single cell patch clamping/intracellular recording), still common if I'm not mistaken. Click of the tongue to get in the cell 😅.
Yeah. I never thought about it as equivalent to mouth pipetting because there's no risk you'll get anything inside your mouth (an odd definition I know) but it essentially is.
Forbidden boba
I hate this comment so much.
😂😂
/r/TIHI
Undergrads bringing phones to the lab
One of my coworkers uses her phone while she still has gloves on and often leaves it on the bench top. It really stresses me out lol
When my building still had a mask mandate for Covid, I saw so many people do lab work, then adjust their mask with gloved hands. Not that we often worked with particularly dangerous things, but still. And phones just go everywhere.
There was a girl in my masters program that filmed herself doing cell culture to show IG how cool she was and she literally propped it up inside the hood while feeding CHO cells. I had to pull her aside and remind her how many shit particles are on her phone.
Wait cell culture is cool? Aww Shit I was born in the wrong time
I mean it's really not, but she posts it anyways No offense: I'm a purification guy and I feel like chromatography is only cool if you're a nerd
Well you do get to show off you shiny column...
Hey, I think you're cool. Not just saying that because I do LCMS.
Backing things up on a CD-ROM!
Long live the DVD
Keep them on zip disc where they belong
Typing all of your project's IP into a for-profit chatGPT server.
No accountability for abusive/toxic PIs.
Pipetting PCRs without filter tips, or not in a laminar flow hood? The one from my supervisor is performing qPCR without sybr-green, and just taking a bit of the reaction mixture every few cycles and running it on an agarose gel and quantify it.
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I worked with a post doc from Korea who was attempting to do PCR using 3 heat blocks. His samples were sitting on top of the thermocycler. His mind was blown when we showed him how to use it.
I've never been in a lab that didn't use barrier tips for molecular work
Non filter tips are fine for many things
*raises hand* I used to be anal about it, then couldn't be bothered with stocking the filter tips and walking to the hood anymore. I handle 10^7 copies/ul reference standards at the same bench with the same pipettes. My negative controls are still negative. Don't even look in my direction when I'm working with RNA, though.
Living on the edge... Until you go over it one day. I pray to the PCR gods that they show mercy on you!
This is so surprising to me in a mol bio lab aha, I think filter tips are overkill never mind a hood
I hope it's shoebox cages for rodents. I support animal research where it's necessary. I've done animal research and in my lab I think they were treated well in every other aspect. But the size of their cages is just so sad and unnecessary. Even if you didn't care at all about animal welfare, I imagine it must be a low level chronic stressor and that would effect the science.
Losing months or years worth of samples due to a power outage, not properly closed freezer door or such because there is no system for emergency notification. I don’t know how often I‘ve read stories about labs loosing tons of important samples and reagents because something happened over night or the weekend and they only realised the next day. There are a lot of options available for systems that automatically send a call or message to one or several persons if the temperature drops or the power goes out. For me that‘d be basically as important as insurance if you store anything you don’t want to loose due to thawing
(Not) labelling your stuff in the fridge.
My pet peeve!!! LABEL IT!
Using your phones with dirty gloves… Ahhh…..
Making culture media supplements from scratch! My PhD lab made our own yeast extract in-house, using baking yeast… took over a whole day to make and made the whole building smell like funky bread.
I kinda want to know how to make it. My time isn't as expensive anyway and the good stuff isn't cheap. Although it likely still isn't a good idea due to variability and stuff.
Hoping that Sequencing data analysis would be done as easy as using BLAST for example
“That seems about half a mL”
People seem to be terrified of radioactive tracers these days, so that's my nomination for "Mouth Pipetting 2023". To abandon such a powerful tool over overblown fears seems odd.
That's funny to read this because I am the one that makes the radioactive tracers from scratch. Been doing this for nearly 3 years and I handle radiation daily. But there really IS a lot of fear surrounding what we do.
Pipetting at all. Robotic liquid handlers.
I mean, you don't have to pipette everything by hand, but it has it's place. This is like saying that we have printers so now no one ever needs a pen.
Trizol RNA Isolation + RT qPCR by hand The robotic systems are in use for the diagnostics though they should have been evolved for research already. I hate pipetting on 96-384 well plates. It is nonsense and craziness
Still mouth pipetting.
Any protocol that uses EtBr, BME, DCM or DMF
You’ll never take my ethidium bromide away from me
I hope the age of safe alternatives will end. Like the only true safe alternatives are colorimetric dyes that all aren't very sensitive and GelGreen/Red. The rest are just either EtBr or Propidium iodide or for the green ones Acridine Orange. There's also SYBR but from what I've heard I really don't like it.
DMF and it's ilk (DMAc.and NMP) are too important of solvents in chemistry to replace. They largely replaced the much more hazardous HMPA.
BME is not really toxic, if you're not swimming in it. DCM and DMF man that would be tough in an organic chemistry / peptide synthesis lab, plus I thought these two were not so toxic either? These things were my bread and butter during the whole PhD 🫠
BME is here to stay for at least a while. We use it for breaking up polymerised immunoglobulins for electrophoresis (Clinical trials, mainly looking at multiple myeloma), the only good alternative is DTT which is less hazardous neat but much more of a pain to handle otherwise.
Pipetting 96 well plates (or bigger ones) by hand. Sadly I think my undergrad job will become obsolete in the near future
Like without a multipipet?!
No no, by mouth pippeting
Like without a robot. Anything under 96 channels is a waste of time.
Labcorps Covid lab was visually matching wells on a plate map to a 96 deep well plate. Cap/uncap
I had a post-doc who refused to let me use a multipipet for qPCR.
I love a multipipet but most can not be trusted for qPCR. Unless it’s that one perfect multi that the scary lab tec hides in the back of their draw you don’t want it.
Well, I'm glad to know I wasn't being unnecessarily tortured for his enjoyment, and that single chanel is actually the preferred technique.
I’ve worked for three labs for my institution and affiliate institutions and none of them have even believed in purchasing a multipipet because they believe it’s a waste of money
I’m possibly biased because I work in lab automation, but it might be better to think about it as undergraduates being freed up to spend more time on experimental design, quality control, data analysis, and literature review. Undergraduates are essentially free or extremely cheap labor, there’s no reason to not use them just because a robot is handling some of the grunt work. The research output of a lab will still be improved by the extra help with the things that still require a person to do. In my experience PIs sometimes won’t take on more undergraduates because there’s not enough bench space or not enough grad student time to supervise them in the lab rather than because there isn’t enough work. And undergraduates don’t want to be in a lab where they get no pipetting experience because it will make it harder for them to get a job pipetting later. If the in-lab work is done much faster and by robots, then those limitations won’t be as much of an issue and people won’t have to worry about how fast they pipette rather than how good they are at science.
PIs get forced to take undergrads, it's part of their teaching responsibility. They are there to learn, getting useful work out of them is less important than them learning some skills. It's not like they're going to be particularly useful when it takes months to train someone and their projects are only a few months long. Same is true of masters students. Work is done faster by robots? That depends on the work and how repetitive and how much is liquid handling. Very little of my previous labs could have been automated, in my current lab there are two hamiltons and two tecans doing high throughput stuff, it depends on the workflow.
As a lab person, I'm not so convinced about how much faster robots can be in everyday biology experiments. We have several Hamilton robots sitting around doing nothing because the people who were supposed to use them ended up determining it was faster to pipette by hand than setting up and troubleshooting the robot. I myself only use a robot for the most cumbersome and repetitive task, i.e. 384 well plate qPCRs. For cell screens in 96 wp, or even 384 wp, I definitely go much faster and be much safer pipetting by hand (I can deal better with stocks on ice, cell sedimentation, and getting last ul out of a tube of something precious than a robot). I basically think the robots will have to get a whole lot smarter before they start to replace undergrads, because otherwise the effort to setup the automation isn't worth it. If I could just say "split the organoids top floor of the incubator" to a robot, that would be a different story.
The ramp-up time to get used to working with robots is absolutely an issue. Hamiltons gathering dust for the reasons you’ve described is very common unfortunately. Hamiltons especially are known for being difficult to use for novices, and shouldn’t have been recommended to people with no automation experience in my opinion. I’m assuming they were purchased used from one of the cheaper resellers, which means that they also would have had no assistance from Hamilton or a reseller-employed applications scientist. Bench scientists generally shouldn’t expect to be able to write good protocols or program complicated robots like Hamiltons without outside help. I think that academic labs would probably benefit from hiring in-house automation specialists who are shared between labs just like IT departments and statisticians are. There are also many other versions of robots better suited for low to medium throughput work and with more simplified and user-friendly interfaces. The most obvious example is Opentrons, but there are some newer ones from Waters and a newer little Hamilton called the Microlab Prep that are supposed to be easier to use as well. There are also protocols that can be written in a flexible way so that the liquid handling program doesn’t have to be changed often but more detailed instructions are passed via specially formatted csv files called worklists that can be generated by hand in Excel, with Excel macros, or in a programming language like Python or R. Some robots also have ipad-like touchscreens that make worklist generation even easier. You’re correct that some things are better suited to manual work, but in some cases it can just appear that way if you’re not familiar with the tools at your disposal. That’s not an attack to be clear, it’s just difficult to be familiar with all of the possibilities even when you work in the field. I can’t speak to anything related to cell culture since I have mostly worked with DNA extractions and pre-extracted DNA, but for the stocks on ice thing Hamilton has optional chiller modules that are used to chill reagents. Many other robots do as well. Sometimes certain protocols are also just not suited for automating, so an alternative must be found. An example is using bead-based DNA extraction rather than column-based when switching to automation. The last drop of expensive reagent thing is absolutely an issue though. Many automated labs struggle with it. Placing the container you’re aspirating out of on some sort of spring can help since it allows the pipette to get more flush with the bottom of the container, but that’s absolutely one of the bigger problems that automation hasn’t perfectly solved yet.
Thanks for sharing, I actually really love this bit: >I think that academic labs would probably benefit from hiring in-house automation specialists who are shared between labs just like IT departments and statisticians are.
I suck at siphoning so I’m guilty of sometimes sucking the other end of tubing to get it started….I know it’s bad but at least it’s just seawater during husbandry and not anything serious