- Видео 856
- Просмотров 1 232 629
the bumbling biochemist
Добавлен 8 сен 2012
New biochemistry professor (full-time, visiting professor) at St. Mary's College of California trying to make biochemistry fun and accessible for all. I aim for lots of detail without lots of jargon (or at least with jargon explained). Much more on my blog
Quick note from the Bibel lab update #8: O-CAS assay for siderophore production detection
The O-CAS (overalay CAS) assay tests for the production of siderophores, which are small organic molecules that some bacteria secrete to chelate (bind to) metals. Either to take them in to use (such as in low iron situations) or to remove them (such as removing toxic heavy metals, which is good for them and plants!)
You plate bacteria on media that has been deferrated (had iron removed, in our case by pre-treating the media with Chelex-100 resin, which binds to cations like iron). This iron starvation promotes the formation of siderophores by siderophore-producing strains. You let them grow on the plates for 3 days, then overlay the plates with a detection reagent that will change color in...
You plate bacteria on media that has been deferrated (had iron removed, in our case by pre-treating the media with Chelex-100 resin, which binds to cations like iron). This iron starvation promotes the formation of siderophores by siderophore-producing strains. You let them grow on the plates for 3 days, then overlay the plates with a detection reagent that will change color in...
Просмотров: 324
Видео
Some of the most important lab math to know (in my opinion)
Просмотров 44712 часов назад
Downloadable version with figures & live links to more resources: bit.ly/importantlabmath * Metric conversions * Get really comfortable moving decimal places to convert between μ, m, etc. (esp. μL, mL & L) * Converting between molecular weight (MW) or formula weight (FW)*, molarity, and weight/volume * MW (or FW) = g/mol * Molarity (M) = mol/L * g/L =(MW)(molarity) * M = (g/L) / (MW or FW) * al...
Salvaging mis-measured solutions. Adjusting mass &/or volume to still get the desired concentration
Просмотров 23214 часов назад
You can probably salvage that solution! How to adjust mass and/or volume to match what you have to still get the concentration you want. Too much mass? Calculate volume Measured mass/X = desired concentration X = measured mass/desired concentration Needed additional volume = X - current volume Too much volume? Calculate mass X/current volume = desired concentration X = desired concentration x c...
Tip: with small masses, adjust volume rather than mass when making a solution
Просмотров 52619 часов назад
When you have a small amount to weigh out, don’t worry about being exact. Instead, it’s easier to change the volume to match what you weigh to get your desired concentration. If you start with a desired weight/volume concentration, divide your actual measured weight by that desired concentration. Taking any unit conversions into account, the weights cancel out, leaving you with volume If you st...
Displaying sidechains in PyMol? (Or other stick & cartoon combo?) Turn cartoon sidechain helper on!
Просмотров 153День назад
Common PyMol problems to avoid when mixing sticks & cartoons... If you want to show sticks in the context of cartoon, you typically just want to show the side chain as sticks, so turn on cartoon sidechain helper (under settings → cartoon) in the upper toolbar. Then, if you select show → sticks, it will just show the sidechain as sticks, connected to a cartoon backbone. You can set this in comma...
PyMol tips to not lose orientations & styling: save views, scenes, & selections
Просмотров 247День назад
A few tips so you don't lose your hard work styling things and getting a view that you like If you want to save representation style, coloring, & orientation etc. (“everything”): save as scene In command line: scene auto, store (or replace auto with the name you want) pymolwiki.org/index.php/Scene If you just want to just use the orientation: use get_view & set_view get_view - provides code blo...
Tips for Bradford assays (or other microplate assays) without bubbles
Просмотров 56514 дней назад
Bubbly Bradfords? (Or other microplate assays?) Those bubbles can mess up the plate readings, so the best thing is to avoid forming them in the first place by: * Making sure your pipet doesn’t come out of the liquid when you’re mixing to avoid introducing air * Setting the pipet to a lower volume to mix and/or only sucking up partway when mixing * Pipetting slow But, if they do form, all hope’s...
Quick note from the Bibel lab 7 - His-tag purification & “too much protein”?
Просмотров 57714 дней назад
Much more on all of this in past posts and videos! bit.ly/proteinpurificationtech & bit.ly/proteincleaning ; RUclips: ruclips.net/video/uK78bBIhzMA/видео.html more about all sorts of things: #365DaysOfScience All (with topics listed) 👉 bit.ly/2OllAB0 or search blog: thebumblingbiochemist.com
Quick note from the Bibel lab 6 - after a freeze thaw, our MDH’s still got it!
Просмотров 43814 дней назад
Quick note from the Bibel lab 6 - after a freeze thaw, our MDH enzyme’s still got it! More excitement today as Nicholas and I discovered that the malate dehydrogenase he purified is still super active after a freeze thaw. So active we have to dilute it 150-fold to use in these MDH activity assays. The below is copy/pasted from my update last Friday for context… *Basically it shines light throug...
Skills for aspiring scientists (such as people wanting to go to grad school) to develop early on
Просмотров 53214 дней назад
So you think you want to be a scientist? Maybe you're an undergrad or postbac hoping to go to grad school? Here are some skills to try to develop as early as possible (at least in my opinion & in an ideal world) A lot of this can be found here: bit.ly/bumblingbiochemisttoolbox thebumblingbiochemist.com/uncategorized/skills-for-aspiring-scientists-such-as-people-wanting-to-go-to-grad-school-to-d...
Lab hacks: tips for drying cuvettes
Просмотров 74221 день назад
Lab hacks for drying cuvettes - use a pipet tip attached to vacuum tubing (gently) to suction out liquid, then stick the cuvette inverted over a hold in a membrane in a vacuum filter. Thanks Dr. Sigman! ruclips.net/video/SVslLNniKnw/видео.html More on all sorts of practical lab tips: bit.ly/lab_tricks_page & ruclips.net/p/PLUWsCDtjESrFEAWZCRKJL7sMc6a_KgfLU more on UV-Vis measurement: bit.ly/try...
Quick note from the Bibel Lab 6: protein purifying finale
Просмотров 49521 день назад
And Nicholas claims he's never purified protein before... 🤨 Much more on all of this in past posts and videos! bit.ly/proteinpurificationtech & bit.ly/proteincleaning ; RUclips: ruclips.net/video/uK78bBIhzMA/видео.html & ruclips.net/p/PLUWsCDtjESrEtqQkEXsQpTyRfMhywBVQ7 More updates from the Bibel lab: ruclips.net/p/PLUWsCDtjESrF-KFUDoxwfjB7S2mPmHVx7
Quick note from the Bibel Lab 5: protein purifying
Просмотров 70321 день назад
So many grad school flashbacks today! I'm so grateful for my training at CSHL in the Leemor Joshua-Tor lab! Especially grateful to the postdoc who taught me, Elad Elkayam! Much more on all of this in past posts and videos! bit.ly/proteinpurificationtech & bit.ly/proteincleaning ; RUclips: ruclips.net/video/uK78bBIhzMA/видео.html & ruclips.net/p/PLUWsCDtjESrEtqQkEXsQpTyRfMhywBVQ7 More updates fr...
Quick note from the Bibel lab 4 - our selection strategy has hope
Просмотров 37421 день назад
Usually, we're sad when we don't see any colonies (clumps of bacteria) on our plates. But today we were super stoked by the absence of growth because it meant that the wild-type (unaltered) bacteria we want to genetically manipulate are susceptible to the antibiotic kanamycin (which was present in the plates). This was exciting because it means that we can use kanamycin as a "selection marker."...
Quick note from the Bibel lab 3 - PVKA phosphate solubilization assay
Просмотров 36228 дней назад
Yep - these agar plates are teal!!!! And I finally broke in my lab coat with proof my scienceing is real! The teal color isn’t mold, instead it’s a dye called bromocresol green. And although it looks cool, it’s actually not the coolest part of this media. Instead, the really cool part, the super special part is the calcium phosphate. Basically it’s an inorganic form of phosphate. Phosphorus is ...
Quick note from the Bibel lab 2 - autoinduction pt. 2
Просмотров 24028 дней назад
Quick note from the Bibel lab 2 - autoinduction pt. 2
Quick note from the Bibel lab 1 - autoinduction pt. 1
Просмотров 54728 дней назад
Quick note from the Bibel lab 1 - autoinduction pt. 1
Worked fatty acid catabolism problems: Energy yields for breakdown of palmitate & 17:0 fatty acids
Просмотров 2982 месяца назад
Worked fatty acid catabolism problems: Energy yields for breakdown of palmitate & 17:0 fatty acids
Informal peer review - get in the habit early on!
Просмотров 5202 месяца назад
Informal peer review - get in the habit early on!
Integrated lipid metabolism - overview/review
Просмотров 3112 месяца назад
Integrated lipid metabolism - overview/review
Key things to know about Lipid Metabolism
Просмотров 2402 месяца назад
Key things to know about Lipid Metabolism
Breaking down lipid catabolism, with emphasis on β-oxidation & coordinated regulation
Просмотров 2452 месяца назад
Breaking down lipid catabolism, with emphasis on β-oxidation & coordinated regulation
Lipid synthesis (focusing on fatty acid synthesis)
Просмотров 2072 месяца назад
Lipid synthesis (focusing on fatty acid synthesis)
Glucose metabolic tracking - modeling radiolabeled glucose to track flow through TCA, PDH, & PPP
Просмотров 2872 месяца назад
Glucose metabolic tracking - modeling radiolabeled glucose to track flow through TCA, PDH, & PPP
Tips for studying metabolism- things to focus on (e.g. logic, cofactors, reaction types, etc.)
Просмотров 3542 месяца назад
Tips for studying metabolism- things to focus on (e.g. logic, cofactors, reaction types, etc.)
Intuitive thinking about regulation of the TCA (citric acid cycle/Krebs) & adjacent rxns (e.g. PDH)
Просмотров 3242 месяца назад
Intuitive thinking about regulation of the TCA (citric acid cycle/Krebs) & adjacent rxns (e.g. PDH)
β- vs. α-keto acids & their decarboxylations: When things do and don't need to get *complex*
Просмотров 2372 месяца назад
β- vs. α-keto acids & their decarboxylations: When things do and don't need to get *complex*
Walk/talk-through the chemistry of the TCA (tricarboxylic acid) cycle (aka citric acid, Krebs cycle)
Просмотров 2442 месяца назад
Walk/talk-through the chemistry of the TCA (tricarboxylic acid) cycle (aka citric acid, Krebs cycle)
Wow Beautiful , from korea
Thank you! Best wishes from the US!
Hello Why do we quantify the concentration of the protein before putting it on the western blot? I tried searching this up and sources say to standardize how much protein we add to each well but if we standarize it wont it become that all of our bands will be equal and we cannot compare expression between bands? Thanks
Good question. The key thing to remember is that you're standardizing the amount of *total* protein, not the amount of each band. This way, the bands correspond more to the fraction of the sample, rather than absolute quantities. Does that make sense?
ahhhh your content is sooooo so good, thank you so frkn much.
You're so welcome!
Thank you for this video! I needed these for the my class lab report <3
Glad it was helpful! Good luck with class!
Worth subscribing ❤
Thanks!
Great lesson! I'd recommend some of the scientific calculators that exist online for folks to take advantage of for the sake of speed. EndMemo, Graphpad QuickCalcs, and WolframAlpha are a few that come to mind immediately.
I noticed that I never commented to any of the videos, however I would like you to know that your laboratory experience contribute me substantially as a potential MSc Molecular Biology graduate. Thank you for your efforts.
Thank you! I'm so happy to hear I've been able to help
Hi, Do you know how can we remove paralogs using bioinformatics?
I don't, sorry!
Is O-CAS just qualitative or is there a way to look at absorbance or something to get some numbers for siderophore production? BTW I've learned to never try to quickly cool a glass bottle after autoclaving bc same thing happened to one of my buffers where the bottom broke off and I got imidazole buffer all over my PI 😂😭 I'm sticking to good 'ol newtonian cooling on the bench
The O-CAS is just qualitative, but there are quantitative liquid-based CAS assays. That review article I link to has some more info. Sorry to hear about your bottle breakage! I put them in there all the time. Normally it works fine and is really useful for cooling things evenly (so the bottom doesn't solidify) and keeping things from over-cooling and instead having them ready to pour whenever you are!
You've given me the inspiration I need to get back to studying! Thanks!
You can do it!
Do you know if EZvision will work for ssDNA? Currently trying to visualize an ssDNA synthesis and I'm not getting any signal in the ssDNA lanes.
I don't know sorry!
You are a life saver. I've watched many of your videos are really appreciate you sharing your years of experience with noobs like me who are trying to get into plasmid cloning and recombinant protein expression! 🙏
I'm so happy I could help! There's definitely a lot to learn but it gets easier. Good luck!
Amazing content! :D
Thanks! Glad you found it helpful!
Thank you ❤
Hi... I have a doubt.. how to thaw Protein sample from -20 ? Any suggestions?
It's best to let it thaw slowly on ice, but I'm typically impatient and let it thaw sitting above the ice and then stick it in the ice once thawed
@@thebumblingbiochemist thank you
❤
this is great! i have a presentation on this in biochem and i cant express how much this help, also great visuals hahaha
So happy it was helpful. Good luck!
Thank you ❤
This was so useful and well explained!
Thanks! So glad you found it helpful. The more I work with students the more I realize there are these little things you get so used to over time but people don't often take time to explain.
Why would you need/want a filler protein like BSA?
It can help provide molecular crowding and prevent sticking to the walls of the tubes, etc.
my favorite scientist on the internet, youre so good at explaining the really practical matters, so much thanks :D
Thanks so much! I'm so happy I can help!
Unit canceling calculation reminds me of Chemistry AP exam haha
Hi, I have a plasmid sample with the size of around 2.5kb and I am doing restriction digest on the sample where the RE is very near to each other, and will cut out around 6-10bp. Since I have not been getting results in my ligation procedure. I am suspecting if there could be anything wrong with my digestion. Therefore, I would like to verify if my digestion is actually successful or has failed. And to differentiate between my uncut and uncut plasmid samples, with only 6-10bp difference, I might want to try to run the samples with polyacrylamide gel. However, after trying 4% and 6% gel, the bands showing are at the same position, and here, I am not sure if the digestion failed or the difference still cannot be differentiated. Then, my senior suggested to use 20% gel and I did, but nothing showed up on my gel. I no longer know what to do now. If you can maybe help give some suggestions, I would greatly appreciate them. Thank you.
I don't know sorry. Good luck!
this is so good thank you
Thanks! Glad it helped!
This helps! Thanks!
Glad to hear it!
I often get a white residue/little ‘filaments’ when i spray my gloves with 70% ethanol. Have you had that happen? and if so, do you know why? I’m assuming it’s due to coating or residue on the glove itself, but I’ve been wondering if maybe it’s a sign that our di tap isn’t working properly
That happens to me as well, not sure why but it does. Sorry!
I have my entrance tests in 3 days and I wish I found your channel earlier. Love the content❤❤Thank you for the clear and concise explanations
So happy I could help. Good luck!!!!
When using the same syringe between different wells how can we avoid contamination? If it’s just used to pop the bubbles is that okay? Does contamination even matter for the Bradford assay? Apologies for so many questions, great video once again! 💖
Thanks! I don't worry about it for this. Any contamination would me miniscule.
@@thebumblingbiochemist Thank you!
Hello from iran! This is so cool! Thank you for sharing it on youtube!
My pleasure! Thanks!
guys this is the org chem tutor in practice
Resuspending pellets from a 1L culture is a pain still...even with vortexing+titruation...
Unfortunately, yes... I feel your pain!
ChimeraX is just as good as Pymol now. And ChimeraX is free.
I'm still much more comfortable with PyMol, so that's what I personally prefer to use. There are free versions of PyMol as well and we get it free for educational use. But I do highly support ChimeraX as well
This video is great (The diagrams, narration, show+tell) - it's more detailed and actionable than the videos and written guides provided by Addgene itself!
Thanks! Glad it was helpful!
But doesn't 70% ethanol mean there are 7 parts ethanol and 3 parts water in a volume of 10 parts meaning if u do it that way u would and up adding too much water?
70% means 70 parts of the total
Such a pain in the A** for mixing in pcr tubes specially !
Hey! Great videos! I am a master student from Germany and following you. Does splicing or alternative splicing have a relationship with enzyme variation (like in CYP enzymes)? I know that it is about aminoacid changes in certain positions, but how about splicing? How it affects drug metabolism (biotransformation)? Why different isoforms give different response to same drug? Does it have a relationship with e.g. recombinant proteins produced in bacteria sometimes missing some sugar motifs and this proteins shows different activity and to compansate this, sometimes these motifs are added synthetically. Maybe this is a different way to think but I wanted find a connection between different topics
Thanks! Alternative splicing can definitely affect enzyme activities. I'm not sure about CYPs. I'm not really sure what you mean about the recombinant protein stuff, sorry!
Hi, thanks very much for the video, it helps me understand a lot. I'm not very clear what do you mean at 3:05. WB only tells the presence of one type of protein, so do SDS and what at the same time?
Happy it helped! You can do coomassie to see purity
hey , really greatful for what you're doing with us you have an amazing talent , actualy i'm a cancer researcher and I'm preparing my final Master's project , i want to ask u some questions so may i email u please thanks an advance
Thanks so much! Best of luck with the project!
So cool!
This video is perfect! I'm learning how to grow bacteria to express proteins, and this demystified the options available; have each variant jotted down a notes document now.
Glad it was helpful!
Hey I have a question, so basically I want to look up the science behind things I want to look up. Like I want to know the stages of testosterone being increased . I don’t want to know the general answer like increasing testosterone is by sleep and muscles it says in google , I want to know the stages behind testosterone being increased.
try including + science or + mechanism or something. Good luck!
Amazing video!
Great explanation! Loved it, thank you!
Glad it was helpful!
OMG WooooooooooooW🎉🎉🎉hope one day I can be like you 😢
You're too kind. Thanks!
Amazing, 15 mLs sounds like a lot! How many liters was your E. coli growth? What is the concentration of your undiluted stock? I'd like to compare it to my yields 😂
This was just from 400 mL! ~1.8 mg/mL undiluted
@thebumblingbiochemist Wow! You actually got nearly 5X as much as i do. You aren't using a bioreactor, are you? Lol
@@thebumblingbiochemist 👀
It really depends on the protein!!!!
Been slowly discovering your videos and just wanted to say thank you so much for the content you make 😭🙏 it’s been a blessing in just a few days in aiding me in understanding the things and process in lab as a rising sophomore undergrad; my only regret is to not have found these videos sooner 🙇♂️
So happy I could help! You are at a great point to discover them, as you still have the bulk of your training as a scientist yet to come!
Is there any real prospect for someone with a mere bachelor's degree in bioengineering (somehow the syllabus barely contained any real wet lab skills aside from my interning/final year project) and not going for post-grad studies, and aiming to get into research, perhaps as a research assistant? I have heard that it is a dead-end job...
Research assistant is definitely not a dead-end job!! In fact, that's often how people build research experience before going to grad school. And for people who decide to not go the grad school route, there are different levels of research assistant that you can work your way up. Bes tof luck!
@@thebumblingbiochemist Interesting, thanks.
I thought I wanted to do something else with my life then when I really thought about it, there aren’t other careers that interest me enough to devote most of my waking hours to. So now I am 27 and considering STARTING grad school, feeling like a fool.
Don't feel like a fool! You are definitely not too late! Your best bet is probably to start by getting a research tech or similar job to build some lab experience if you don't have it already, then apply. Best of luck!!!
thank u internet mom
I really, really appreciate your videos and the resources you put in your descriptions. Thank you so much.
So nice of you - I'm so glad they're helpful!!!