LABBING TIPS from the bumbling biochemist! One of the great things about thesis committee meetings is they give you more experimental ideas to test – so the last few days have been experimenting with little rest – For the bumbling biochemist, this bench busy-bee-ness is nothing new – and from experience I’ve developed some tips I’d like to share with you! I spend a lot of time working in the lab – and when you do, you develop your own style – find what works best for you – these are just a few things that I have found helpful for myself so thought I’d share.
NOTES ON NOTE-TAKING
I keep hardbound & digital lab notebooks (I use OneNote for this) – the physical book is great for quickly jotting down experimental notes when your fingers are goopy (well not too goopy – at those times I write on a paper towel or something and then transfer it over once I’ve deglooped! But it’s hard to search through if you don’t know the date to look for (no command + F for paper). The digital version’s not always as detailed (but it is much neater…). A lot of it is bullet points of experiments I did, yields, etc. I include key terms so I can easily search & find the date I did something then cross-reference to physical book for more details.
I also take pictures of my written notes and save them to my computer – this is also great for when you’re too exhausted at the end of a long day to type everything up nicely – if you wrote down all the potentially forgettable things on paper and you have the pics you can type them up the next morning – and go get some sleep
I take pics of other things too (like when a protein you’re purifying turns a funny color or something) – and screenshots – Taking digital notes? Command + Control + Shift + 4 is your friend – it lets you take a screenshot of part of your screen and copies it to your clipboard. And, you know what they say, a screenshot says a thousand words!
When taking notes, think in terms of “future you.” At the time it’s easy to think “There’s no way I could forget this” – yes, yes, you can. Write it down. Future you will be grateful (Think of all the times current you has wished that past you wrote something down…) – Often I’ll go a few days/weeks working on 1 type of experiment (e.g. protein purification) then switch to a period working on a different type of experiment (e.g. activity assays). etc. Things that become 2nd-nature in 1 block may not stay that way…
As for what goes in those notes…
- it’s important to document *what* you do in an experiment – but it’s also super helpful to document *why* you did that experiment in the 1st place! What were you hoping to learn? Note down your goal & dates of anything you refer to (like when you tried it before etc.) If you’re using proteins you’ve purified, write down the date you purified it so you know what batch you took from – and even if you personally didn’t purify it, when you buy things like antibodies or enzymes they’ll have batch numbers and you want to write those down (thanks to IUBMB president-elect Alexandra Newton for this one!)
- it’s important to make note of anything that you did that was different from how you typically do it. It’s also important to include *why* you did it differently, so you don’t look back and think “Why in the world did I do that?!” Plus, you never know what minor details will make experiments go better or worse, so making note of any experimental deviations can help you notice trends and optimize!
- If you make a mistake, write it down! Even if it’s embarrassing, it’s important information (especially if your results turn out “interesting”!)
Keeping track of things
- When writing dates, always include the year. It may not seem like you need to, but the years do go by! Similarly, don’t label a box with something like “Bri’s box” – you will go through a lot of boxes, so organize from the get-go even if that means starting with a bunch of mostly empty boxes.
- Try to learn your labmates’ handwriting so if you find labeled tubes left in the centrifuge or somewhere else you know who they belong to
- I do a lot of protein making & purification, so I have lots of protein constructs to keep track of (different proteins or different versions of the same protein), all at various stages of prep/purification so I keep a spreadsheet w/each construct identified by numerical code & description & I update it w/the current status (i.e. 3L Sf9 expression 3/8/18 or 3mg frozen 3/7/18).
- I also number my electrophoresis gels (gel electrophoresis is a technique where you use charge to separate molecules like proteins & DNA by size by sending them through a gel mesh that slows bigger things down more). I run a lot of electrophoresis gels, so I number them (e.g. SDS-page #81, agarose #40). Just ran page #487! I use this number on the sample tubes & when staining then save the results image with the date & gel number as the file name (and of course include these numbers in my notebooks)
- These databases are only helpful if you keep them up to date – and save them! Save files early & often – and in a way that makes them findable. Don’t name folders/files “filename”_new… or you’ll end up with things “filename”_new5… I add “bad” to file names of experiments that didn’t work well so I can easily distinguish them when I’m trying to find them to work out what to change or avoid accidentally opening it when I want to show someone something – & not that!
- If you’re making big changes save as multiple file versions so you can go back & see what you took out. This is true for these spreadsheets as well as for report writing & is especially important if, like I do, you start out your writing process w/a kind of “word dump” to just try to get all your thoughts down.
- Speaking of report-writing, I’ve started making “paper-style” figure legends for my figures that are just for my notes (and potentially lab meeting) – I’ve found that it helps me when I look back on them later & it gets me excited about actually having legended-figures in a paper some day! Also – when it comes to making figures, work with vector graphics whenever possible – this way you can scale without losing quality (I use Adobe Illustrator, but there are free alternatives like GiMP & InkScape)
I like to periodically make a “to do list” of experimental plans. Instead of just a list of tasks, I specify *why* I want/need to do each thing – what am I hoping to learn and/or show? Sometimes, to do lists can stress me because I see there’s so much to be done – but the important thing is to remember it’s flexible and subject to change! Because ultimately you follow the experiments. So let’s talk a little more about those experiments…
When doing an experiment, you don’t need to know all the details, but make sure you at least know the purpose of each step in a protocol, especially if you’re working from a kit. In addition to just being important to “know what you’re doing,” this will help you troubleshoot and optimize. If you’re looking for info about commercial products (kits, etc.) you’re using, patents are often where the good stuff’s hidden! And despite the dry language they’re often surprisingly understandable because they have to make their stuff understandable to the law folks.
You can make tedious experiments more fun by thinking about what’s actually going on at each step and visualizing the molecules interacting. If you imagine what the molecules are doing as you do “boring” things like minipreps, it makes it a lot more fun. And it helps you really appreciate why you’re doing what & this is especially important when you’re working from a kit. if you aren’t sure if you are doing something right, ASK! It’s way easier to learn something the right way from the beginning than to try to re-learn it the right way once you’ve gotten used to doing it the wrong way
Sometimes the “hardest” experiments are those that are just repetitive enough your mind can wander but not repetitive enough you can let it! Or you can have the “opposite problem” – I often get really stressed running experiments, and that makes me brain-foggy too – so I try to do all thinking I’ll have to do before stress messes w/my head. I write out my experimental plan beforehand in a *super* specific way (almost to “open tube x” point) & double-check it before starting. Then I can focus fully on manual work. And remember that experimental plans typically seem less ambitious on paper then they really are…
To help me focus even better, I put on active noise-cancelling headphones without anything playing – I can still here if anyone’s talking to me, but the active noise cancelling reduces distracting background noises
I find I’m more prone to making calculation errors in the stress of an experiment, so I get all those down ahead of time whenever possible – speaking of calculating things – I write out the recipes for common formulas and solutions I need to make (buffers, etc.) on post-it notes and stick them on my shelves. I also keep “cheat sheets,” buffer recipes, details about protein construct sizes & pIs etc. (see yesterday’s post for more on pIs which tell you about a protein’s charge at various pH)
Some other random experimental advice…
- Parafilm is your friend.- from acting as a cylinder stopper for invention mixing (turn a tube up & down to mix it without everything spilling out) – to providing a nice hydrophobic surface drops of DNA will stay droppy on while you mix them with loading buffer before running an agarose gel – to preventing water from wandering out (evaporation) or dust & other cruddy stuff from wandering in – this “saran wrap on steroids” is one of my favorite things in the lab!
- Check to see if your cold room has a foot lever to help you open the door when your hands are full – it took me months before I realized ours does!
- Color code whenever possible
- If you don’t have a full gel-ful of samples, load your samples in the middle lanes for the straightest band-running
- When pouring from a beaker with a stir bar in it, I hold a second stir bar to the outside of the beaker to prevent the first stir bar from coming out
- Make sure that the centrifuge gets up to speed (or at least gets to a point where you’re sure it will) before walking away. If it’s not balanced, it won’t be able to get past an initial speed “hump” When timing things out, remember that the centrifuge will take a while to stop…
- From prep to prep, your yield will vary… (don’t get too discouraged – or too cocky!
- Take time to double check your data before you get deep into analyzing it. It can be tedious BUT it’s super important & can save you lots of pain later on! You want to make sure you can trust your analyses & if you find an error later on it’s MUCH harder to fix
When it comes to life in the lab, things don’t always go as planned. Be prepared to adapt and try not to be too discouraged. Scientific setbacks happen to everyone. That being said, there are some problems that can be avoided and I hope to help you avoid them!
LESSONS LEARNED THE HARD WAY:
- When working with solvents like ethanol, make sure you’re labeling with solvent-resistant marker!
- When doing minipreps or any other time when there’s a chance the cap of your Eppendorf tube might break off, make sure that you have also labeled the side of the tube! Similarly, for tubes with removable caps, make sure you label both the tube and the cap
- When labeling make sure you can distinguish between an upside-down “6” and a “9” a sidewise “4” & “5”
- When pipetting small volumes, look to make sure you actually took up liquid
- When pipetting the same volume multiple times, check periodically to make sure that the volume setting hasn’t drifted – this is especially apt to happen when you get a little too vigorous with your up-down-up-down mixing
- be careful going in and out of doors – I think the cold room door heard me say I hate the cold room – it decided to take a little of my skin yesterday…
- Make sure neither the outside of the bottle nor your gloves are wet before attempting to pick up that bottle of freshly-made buffer… And befriend the janitorial staff!
- Be careful not to pull the syringe plunger out too far…
Stuff somehow related to hot/cold-ness…
- Make sure the fridge/freezer door closed all the way. And if an eppendorf tube is literally frozen to the roof of your freezer, it might be in need of a defrost…
- When using a hot/stir plate, make sure the hot part’s not on if you just want it as a stir plate – actually put a piece of tape over my heating knob so I don’t accidentally bump it on (they should really have a “child lock” or something… And before wondering why your magnetic stir plate isn’t working, check to make sure you actually put in the your stir bar…
- When autoclaving, make sure the bottle lids are loose (but not too loose…), and don’t fully tighten them afterwards until they’ve cooled if you ever plan on opening them later!
- After dumping an ice bucket in the sink, always check to make sure there wasn’t a hidden Eppendorf tube!
- No matter how many hundreds of electrophoresis gels you’ve run in your lifetime, always check you put the electrodes in the right orientation to “run to red”!
- Blot off excess liquid before trying to image an agarose gel to thwart off its escape attempts
- When rolling out bubbles in a filter paper/gel/membrane sandwich before running blot, do so gently.. I had to present that squished gel pic in a presentation to the head of my first rotation lab. I was really embarrassed – but he made me feel much better by telling me a story about how his dissertation featured a gel that had torn into pieces and he’d had to puzzle back together! Which brings up another piece of advice – be open about being fallible – it helps your colleagues feel better when they do! And don’t believe colleagues if they claim they never mess up 😛
- Always sequence any cDNA plasmids you order (even if they say they’ve been verified – mistakes happen) Periodically sequence plasmid constructs you’ve made to check for mutations, especially if you’re having problems with expression, etc.
- Don’t rely fully on automation for image recognition. Check the images with your own eyes to confirm when possible.
- If something is making weird noises, investigate… (e.g. the sonicator should sound a bit screechy but not *that* screechy!)
Random experiment stuff
- When making buffers, master mixes, etc., always make more than you “should” need – On a related note, always take more pens than you think you’ll need
- When vacuum filtering solutions, start by pouring in just a small amount of liquid to make sure that the seal is tight before you pour it all in (so it doesn’t all leak out)
RANDOM OTHER STUFF
- Try to find ways to reuse/recycle packaging, etc. #reSCIcle
- If you have to work in a cold room, instant hand warmers in your shoes are toe-saver – and keep a “cold room survival kit” of micro-fleece leggings, hats, leg & arm warmers, etc. at your bench. If you get too cold, find a reason to be near an autoclave… Also – keep an extra set of socks at your desk (especially if you work where it snows!)
- When you make your own SDS-PAGE gels you don’t have to feel as guilty for running a 15-well gel for 2 samples!
- It’s easy to forget when you’re working in wet lab all day (sometimes just finding time to pee is something to cherish!), but remember to take water/snack breaks! And breathe! I have this really bad habit of holding my breath when I focus – not great for mind fogginess – turns out your brain needs that oxygen!
When I have a long to-do list and have a choice of order, I like to start with checking off the thing(s) causing me the most stress. Sometimes I prioritize tasks so that I can close out as many tabs/windows/programs as soon as I can… Makes things seem a bit less overwhelming. But sometimes things can feel overwhelming – like I love hearing all these ideas at my thesis committee meetings that I’m eager to try out but it also reminds me how much there is to do – and sometimes in your scientific journey you go through patches where nothing seems to work – so CELEBRATE THE SMALL SUCCESSES! Those #tinywins.
And, ABOVE ALL ELSE – Be a good person first, a good scientist second. We’re all in this together so let’s support one another! As the bumbling biochemist says – push electrons, not people!
This post is part of my weekly “broadcasts from the bench” for The International Union of Biochemistry and Molecular Biology. Be sure to follow the IUBMB if you’re interested in biochemistry! They’re a really great international organization for biochemistry.