Lots of people have commented about ethidium bromide not actually being toxic. OK then. It'll take a while, but I'll plan a mutation test and see which of the stains is actually the most mutagenic. Don't expect the video soon though. Will take a while to source everything and I'm busy with other projects. But I'll try and get to it when I can
lol, so I know my homie's housemate is this cute biochem major, so when she came over I had this on right as you were getting into the part about ethidium bromide. oh yeah...got dat cred, tho I got to admit the hardcore parts of electrophoresis still had me shook! keep up the awesomeness!
As a private sector, and disabled (and therefore independent) neurobiologist and psychopharmacologist, and somebody that started an organization solely devoted to independently and privately investigate and vet discoveries in this (and related) field(s), my team and I absolutely f*cking LOVE this channel! 😎👍 As can be expected, my team and I operate on an almost nonexistent budget (and often donated materials). Our only objective is to fund our own research and to offer free educational workshops to schools, colleges, and universities (at least as often as possible) to spread the scientific pursuit of curiosity to the next generation in whatever humble way we can... based upon equipment and supply donations. Hopefully, we will soon be able to share information with the many other independent researchers out there, including this channel! Right now, we are attempting to either acquire and/or build several new analytical instruments (primarily spectrometric and spectrographic instruments) to allow us to better analyze (primarily small-molecule) psychoactive compounds - such as SSRIs, endogenous phenetylamines, and isolated plant alkaloids, etc. May I ask, what is the white/orange instrument pictured at 4:00 is..? A colleague sent me a schematic recently for a similar instrument. Is this a spectrometer, microplate reader, etc..? Something about it looks very familiar, but I just can't place it... Any information that anybody can provide would be most appreciated!
As a physicist this is something I'm not really familiar with at all and I'm not sure I understand much of it, but it's a great way of broadening my horizon
As another physicist (with enough chemistry to be a teacher of both) I second that. I have always been intrigued by these biochem streaky chromatographic-ish separations and always wondered why and how. Super interesting, right?
Information presentation is the biggest factor for me when learning because I technically know all this stuff, but because of the way you presented it as if its no big deal, I feel more confident in it.
Love that you made your own equipment again! If you do eventually expand this with blotting, I'd like to see something about isoelectric focussing too.
Got 3-4 more diy equipment builds coming up. Already finished one, starting on the next two soon. I've been looking at 2d gels and isoelectric focusing is the first step. Been wanting to try it
For me who will probably watch this video several times. The speed is just right. The volt/mm is more than enough value in the learning vs time spent watching for me. And there is slower videos with less parts on other channels. (Mostly the companies who sell the stuff)
you can use 50%-60% glycerol instead of a colored loading dye if your DNA content is low. some dyes can leave a shadow and when the exposure times are high the shadow can ruin the picture.
This was wonderful. We had this topic in our biology class just very recently and I requested our teacher to do a demonstration. To her knowledge our school owns a kit that does not work, I will ask for it on Monday and see what's wrong as this seems like a very simple concept. In our textbook we had the example of cutting up DNA using enzymes that cut at specific base sequences into shorter strangs. And uses gel to confirm the results. What kind of simple demonstration do you suggest that shows results easily? We don't had access to a PCR machine.
I mean the very simplest demo is to load a mixture of dyes. But for DNA you'll need some more reagents. A plasmid with known cut sites and the corresponding restriction enzymes works, which is what you were taught about.
I still use EtBr... it’s pretty common. And there is actually no evidence of any mutagenic behavior. And I mean 0 evidence. People just guessed it would be because it intercalates dna. And why did you mix the amplified dna and loading dye on a piece if para-film? It’s so much easier to just add it to your master-mix. But anyways cool series! It’s great to get people into molecular bio!!!
I'd still be more concerned about the vast amount of metabolites that are unknown. Even then this requires relatively high amounts of exposure for an average sized human .
Awesome video, I have an elecrophoresis power supply sitting around, it's great to see such a detailed but concise video explaining the concept. I had a rough idea of what it was for but this is fantastic. It has quite a range of voltages up to several hundred volts, would that be to help samples separate faster, or would it be more for larger sections of gel for longer ladders/higher "resolution" for lack of a better term?
@@thethoughtemporiumCool to know. I can't recall the specifics, too lazy to dig around through my videos but I think the one I have goes up to 600v or something along that range. The output is relatively unstable, but I suppose it doesn't need to be dead solid for this sort of application. (or maybe it's defective, not sure if a 20v fluctuation is acceptable). Might be fun to try and use it for it's proper use sometime.
You can even make your own power supply with some basic electronics skills. Get the cheapest ATX power supply on amazon and add a boost converter and a DC voltage panel readout meter to the 12v rail with a variable PWM switch input. Use an Arduino to take a potentiometer input and generate the fast variable PWM output for the boost circuit at 40khz or higher and a PID control loop to stabilize it. That will be much more than enough power for what you have built and could run many gels in parallel if designed to use 80 percent of the output power of the ATX PSU. You can even keep the Arduino hooked up to the computer and use serial terminal at max speed for the interface to keep the cost below $50-$80 and the engineering time short. ~one electrical engineer
@@thethoughtemporium Yes, that is exactly what I am talking about making, and with mine, you have more adjustment and power. Its also a good educational experience in basic electronics and control systems. Using a program called LTSpice, you can do easy and efficient circuit modelling. Though this takes self education to get into and many don't have the time, it pays for any BMEs watching to have knowledge of how the electronics they use work. Control systems is also a useful field of study with applications to artificial repair of biological systems by means of establishing a control loop. Take diabetes for example. The long term health effects of type 1 diabetes can be completely eliminated through creation of an artificial pancreas. The amount of glucose in the blood can be monitored and controlled in real time for a more stable blood glucose level. Low and High sugar levels will happen only as they do to a normal human. Lyunapov stability of blood sugar by means of manual injection is a poor standard of care and involves excessive need to innovate in the design of more and more expensive insulin products rather than a suitable system for dispensing them for a superior outcome. The Math and Science: www.ncbi.nlm.nih.gov/pmc/articles/PMC4455398/ www.physiology.org/doi/full/10.1152/jappl.1998.85.3.935 en.wikipedia.org/wiki/State-space_representation The Engineered Outcome: www.bloomberg.com/news/features/2018-08-08/the-250-biohack-that-s-revolutionizing-life-with-diabetes
@@notamouse5630 OR, you could not because its a massive waste of time. What you're describing is called "learning electrical engineering". If I wanted to study control systems, I would do that. I just want my gel box to work. If I have to take a week to design and test my circuit, order all the parts, wait for it to all arrive, and then build and test a thing, I've monumentally wasted my time if my goal is to just do biology. But the premade thing, wait 2 days for it to arrive, adjust it to your gel box, then connect it up and never think about it again. I only build my own tools when I need to, and if I need control systems, I use them and at that point extra effort is worth it. But a gel box needs nothing more than an upconverter and a light switch.
@@ashimahmed2193 no, this isn't even my real name, I was obsessed with the musical Hamilton when I made this account, so my name here is a pun on Aaron Burr
Ethidium bromide is not something you want to use to flavour your coffee, naturally, but it is not the boogeyman people make it out to be. For the application of staining gels, with a modicum of sensible procedures, it is perfectly safe to work with. Please don't take my word for it though, and look into the literature yourself. But If you were to ask me, I think the people seemingly sounding off the loudest are those with supposedly 'safer' alternatives on offer.
I have been reading on it, for a home lab would it still be considered safe? I was also wondering how you would dispose of it in a home lab if it is safe?
No you reaaaaally should. Our results at 30v sucked. Use the proper voltage for the length of gel. The minione runs at 42v and the gel is 42mm. That one is close enough that you could get away with 30V. But a 60mm gel needs more voltage.
Making a tank of spider silk, spinning it into fabric, and using it to build super lightweight airplanes without needing furnaces to make carbon fiber, or smelters to prepare aluminum. Producing drugs in vats. Bioremediation. ETC ETC ETC. Biology is the most versatile technology on earth and allows you to manipulate matter in ways nanoscientists and chemists can only dream of. PCR specifically can be used to tell if you've got mutations that will wreck your life like huntingtons disease, or any of 10000 other uses. Its ubiquitous for a reason. Also this same basic principle is how a massive variety of techniques work.
@@thethoughtemporium thank you, those are some excellent points and illustrations. I think hearing and reading that kind of information when viewing these great videos gives proper CONTEXT for inspiration and getting your own ideas. Thanks!
@@FedericoAOlivieri Ahh as i suspected, well might be good to invest in the proper materials then and use agar agar for less sensitive applications. thank you for the answer. :)
Luckily you can pause, relisten if you mean the entire video. Or if you mean specific areas, he might already have expanded it in other videos or will in future ones.
@@thethoughtemporium Try to use a flourscent substance instead of water in your sample. The easiest one to get is Chlorophyll. It's pretty easy to isolate it from any green plant. All what you need is ethanol to lower the concentration of Chlorophyll. Chlorophyll is green and it "shifts" the UV light to the red color range. Hope you succeed ❤️
@@thethoughtemporium by the way, you didn't fail. Actually, you have built a real flourscent microscope, but it is an old one. the old flourscent microscopes were just like what you have built. Open the page of the "University of Toronto" on Wikipedia. You will see down under the section of "research" a real photo of stem cell which was captured back in the 80s. It's just the same as what you have done
Not. That's the myth of biology. Chances of you successfully making the thing are way lower than getting yourself killed in the process. That's a biosafety level 4 kind of thing which I'm sooooo not set up for. My lab is for working with bacteria and yeast that are non pathogenic.
Lots of people have commented about ethidium bromide not actually being toxic. OK then. It'll take a while, but I'll plan a mutation test and see which of the stains is actually the most mutagenic. Don't expect the video soon though. Will take a while to source everything and I'm busy with other projects. But I'll try and get to it when I can
lol, so I know my homie's housemate is this cute biochem major, so when she came over I had this on right as you were getting into the part about ethidium bromide. oh yeah...got dat cred, tho I got to admit the hardcore parts of electrophoresis still had me shook! keep up the awesomeness!
man, that's cool!
This still on the agenda? I think this kinda video would be veryy interesting. Cheers mate
As a private sector, and disabled (and therefore independent) neurobiologist and psychopharmacologist, and somebody that started an organization solely devoted to independently and privately investigate and vet discoveries in this (and related) field(s), my team and I absolutely f*cking LOVE this channel! 😎👍 As can be expected, my team and I operate on an almost nonexistent budget (and often donated materials). Our only objective is to fund our own research and to offer free educational workshops to schools, colleges, and universities (at least as often as possible) to spread the scientific pursuit of curiosity to the next generation in whatever humble way we can... based upon equipment and supply donations. Hopefully, we will soon be able to share information with the many other independent researchers out there, including this channel!
Right now, we are attempting to either acquire and/or build several new analytical instruments (primarily spectrometric and spectrographic instruments) to allow us to better analyze (primarily small-molecule) psychoactive compounds - such as SSRIs, endogenous phenetylamines, and isolated plant alkaloids, etc. May I ask, what is the white/orange instrument pictured at 4:00 is..? A colleague sent me a schematic recently for a similar instrument. Is this a spectrometer, microplate reader, etc..? Something about it looks very familiar, but I just can't place it... Any information that anybody can provide would be most appreciated!
It's called a bentolab, though this one was a prototype. It's a PCR, centrifuge and gel box all in one.
As a physicist this is something I'm not really familiar with at all and I'm not sure I understand much of it, but it's a great way of broadening my horizon
As another physicist (with enough chemistry to be a teacher of both) I second that. I have always been intrigued by these biochem streaky chromatographic-ish separations and always wondered why and how. Super interesting, right?
*Invents a working tardis*
Thought Emporium: "It's just a box"
I literally learned about and how to use Gel Electrophoresis for DNA this morning.
So interesting.
It was so tense and nerve wracking though.
Information presentation is the biggest factor for me when learning because I technically know all this stuff, but because of the way you presented it as if its no big deal, I feel more confident in it.
I remember doing this in my 3rd and 4th year of my university, though bacterial transformation is my favorite. Thank you for providing instructions!!
Love that you made your own equipment again!
If you do eventually expand this with blotting, I'd like to see something about isoelectric focussing too.
Got 3-4 more diy equipment builds coming up. Already finished one, starting on the next two soon.
I've been looking at 2d gels and isoelectric focusing is the first step. Been wanting to try it
So much data in pitch perfect speed.ty 😊
I'd say it's a bit too fast here and there. Great video though.
For me who will probably watch this video several times. The speed is just right. The volt/mm is more than enough value in the learning vs time spent watching for me. And there is slower videos with less parts on other channels. (Mostly the companies who sell the stuff)
Got a Thermo Fisher gel electrophoresis ad lol
hey, at least it's not a google ad
and it actually relates
Got the Same add but it’s quite funny
Ad
wrightcj01 Same
You do tend to get "a higher class" of ads on Thought Emporium videos.
you can use 50%-60% glycerol instead of a colored loading dye if your DNA content is low. some dyes can leave a shadow and when the exposure times are high the shadow can ruin the picture.
My lab also uses ethidium bromide to stain gels. According to the PI, it's not cell permeable and therefore not a major carcinogen.
Good idea to make your own gel dock!
Also, southern blots are cool!
Love your videos they're really informative!!
Gel boxes and what they're good for demystified - Thought Emporium, keep up the amazing work!
I recently used this in my Bio class, and it was pretty interesting
Keep up the good work!
**watches one thought emporium video** I'M SO POWERFUL, MY MIND UGHHH IT EVEN AMAZES ME SOMETIMES.
Those ladders look sick yo!
This was wonderful. We had this topic in our biology class just very recently and I requested our teacher to do a demonstration.
To her knowledge our school owns a kit that does not work, I will ask for it on Monday and see what's wrong as this seems like a very simple concept.
In our textbook we had the example of cutting up DNA using enzymes that cut at specific base sequences into shorter strangs. And uses gel to confirm the results.
What kind of simple demonstration do you suggest that shows results easily? We don't had access to a PCR machine.
I mean the very simplest demo is to load a mixture of dyes. But for DNA you'll need some more reagents. A plasmid with known cut sites and the corresponding restriction enzymes works, which is what you were taught about.
I still use EtBr... it’s pretty common. And there is actually no evidence of any mutagenic behavior. And I mean 0 evidence. People just guessed it would be because it intercalates dna.
And why did you mix the amplified dna and loading dye on a piece if para-film? It’s so much easier to just add it to your master-mix.
But anyways cool series! It’s great to get people into molecular bio!!!
I'd still be more concerned about the vast amount of metabolites that are unknown. Even then this requires relatively high amounts of exposure for an average sized human .
Bok well, obviously don’t drink it haha. But it isn’t any more dangerous than any of the other dyes
Yea of course. Even then a few uL won't do much lol.
EtBr is used as an antiparasitic in cattle in comparatively high doses and there are still no known metabolites recognized to be harmful.
How should you dispose of it if many people think its safer than what it is said to be?
Awesome video, I have an elecrophoresis power supply sitting around, it's great to see such a detailed but concise video explaining the concept. I had a rough idea of what it was for but this is fantastic. It has quite a range of voltages up to several hundred volts, would that be to help samples separate faster, or would it be more for larger sections of gel for longer ladders/higher "resolution" for lack of a better term?
Mostly gel size. My friend runs gels that are almost a foot long from time to time so it needs a ton of voltage.
@@thethoughtemporiumCool to know. I can't recall the specifics, too lazy to dig around through my videos but I think the one I have goes up to 600v or something along that range. The output is relatively unstable, but I suppose it doesn't need to be dead solid for this sort of application. (or maybe it's defective, not sure if a 20v fluctuation is acceptable).
Might be fun to try and use it for it's proper use sometime.
Could you provide a link where you bought the agarose?
You can even make your own power supply with some basic electronics skills. Get the cheapest ATX power supply on amazon and add a boost converter and a DC voltage panel readout meter to the 12v rail with a variable PWM switch input. Use an Arduino to take a potentiometer input and generate the fast variable PWM output for the boost circuit at 40khz or higher and a PID control loop to stabilize it. That will be much more than enough power for what you have built and could run many gels in parallel if designed to use 80 percent of the output power of the ATX PSU. You can even keep the Arduino hooked up to the computer and use serial terminal at max speed for the interface to keep the cost below $50-$80 and the engineering time short. ~one electrical engineer
Or you buy a DC to DC up-converter for 10 dollars which is what I'll be using.
@@thethoughtemporium Yes, that is exactly what I am talking about making, and with mine, you have more adjustment and power. Its also a good educational experience in basic electronics and control systems. Using a program called LTSpice, you can do easy and efficient circuit modelling. Though this takes self education to get into and many don't have the time, it pays for any BMEs watching to have knowledge of how the electronics they use work.
Control systems is also a useful field of study with applications to artificial repair of biological systems by means of establishing a control loop. Take diabetes for example. The long term health effects of type 1 diabetes can be completely eliminated through creation of an artificial pancreas. The amount of glucose in the blood can be monitored and controlled in real time for a more stable blood glucose level. Low and High sugar levels will happen only as they do to a normal human. Lyunapov stability of blood sugar by means of manual injection is a poor standard of care and involves excessive need to innovate in the design of more and more expensive insulin products rather than a suitable system for dispensing them for a superior outcome.
The Math and Science:
www.ncbi.nlm.nih.gov/pmc/articles/PMC4455398/
www.physiology.org/doi/full/10.1152/jappl.1998.85.3.935
en.wikipedia.org/wiki/State-space_representation
The Engineered Outcome:
www.bloomberg.com/news/features/2018-08-08/the-250-biohack-that-s-revolutionizing-life-with-diabetes
@@notamouse5630 OR, you could not because its a massive waste of time. What you're describing is called "learning electrical engineering". If I wanted to study control systems, I would do that. I just want my gel box to work. If I have to take a week to design and test my circuit, order all the parts, wait for it to all arrive, and then build and test a thing, I've monumentally wasted my time if my goal is to just do biology. But the premade thing, wait 2 days for it to arrive, adjust it to your gel box, then connect it up and never think about it again. I only build my own tools when I need to, and if I need control systems, I use them and at that point extra effort is worth it. But a gel box needs nothing more than an upconverter and a light switch.
Thanks for this, I finally understand it!
Are you perhaps some way related to bill burr?
@@ashimahmed2193 no, this isn't even my real name, I was obsessed with the musical Hamilton when I made this account, so my name here is a pun on Aaron Burr
...We're kinda also covered in lots of microbes like S. aureus and sometimes eggs for multicellular parasites...
What organism produces DNAase?
S. aureus that you mentioned can produce DNase.
you do not want to cover yourself with DNase
@@Nagytika yes.... I know that man...
+Anthony M my bad, i jumped to a concluson too fast. sorry man.
Ethidium bromide is not something you want to use to flavour your coffee, naturally, but it is not the boogeyman people make it out to be. For the application of staining gels, with a modicum of sensible procedures, it is perfectly safe to work with. Please don't take my word for it though, and look into the literature yourself. But If you were to ask me, I think the people seemingly sounding off the loudest are those with supposedly 'safer' alternatives on offer.
As is often the case! Thanks for the info.
I have been reading on it, for a home lab would it still be considered safe? I was also wondering how you would dispose of it in a home lab if it is safe?
What about copper-clad graphite?
Could you please let me know how to remove the loading dye from gel
nice as always
Pls more video... I love you
The gel electrophoresis box is just a box!? :O
Next you'll tell me that the PCR machine is just a glorified kettle!
Every video convinces me more that you would be a great backwards-time-traveler
I have put an fair amount of thought into that particular fantasy XD I don't think you're wrong
@@thethoughtemporium my number 1 item to take back would be a roll of aluminum foil...so much value and use in the past
I learned this in biology
if dna is negatically chatrged couldnt a strong enoghth electro static field seperate the negatically charged dna
All DNA is negatively charged. That's why the electric field makes it move.
@@FedericoAOlivieri dont you mean current
So you don't need to step up the voltage from 30V?
No you reaaaaally should. Our results at 30v sucked. Use the proper voltage for the length of gel. The minione runs at 42v and the gel is 42mm. That one is close enough that you could get away with 30V. But a 60mm gel needs more voltage.
@@thethoughtemporium Thank you. I wanted to build one and this has been the main question
Damn, we still use EtBr in our lab/ (._. )
Though we're all informed about its toxicity and take all precautions that we can think of.
Rip caveman eyeballs. Time to genetically modify my eyes.
Let's make our eyes like the witcher or shiringans and rinnegans from Naruto
Do you ever plan on publishing independently?
So, really curious, while these are fantastic videos, can you please give us a rundown of your ultimate - or any hypothetical - use cases for this?
Making a tank of spider silk, spinning it into fabric, and using it to build super lightweight airplanes without needing furnaces to make carbon fiber, or smelters to prepare aluminum. Producing drugs in vats. Bioremediation. ETC ETC ETC. Biology is the most versatile technology on earth and allows you to manipulate matter in ways nanoscientists and chemists can only dream of. PCR specifically can be used to tell if you've got mutations that will wreck your life like huntingtons disease, or any of 10000 other uses. Its ubiquitous for a reason. Also this same basic principle is how a massive variety of techniques work.
@@thethoughtemporium thank you, those are some excellent points and illustrations. I think hearing and reading that kind of information when viewing these great videos gives proper CONTEXT for inspiration and getting your own ideas. Thanks!
Have a quick question, Can you use agar agar powder for this? or is it better with pure Agarose? mainly asking due to the price difference.
You can use agar powder, but the result won't be as good.
@@FedericoAOlivieri Ahh as i suspected, well might be good to invest in the proper materials then and use agar agar for less sensitive applications. thank you for the answer. :)
i have that exact same power supply!
2:35 not gonna pay 300$ for a box but has this machine that cost so much more
You have 1 hater, you're famous now
Madlad!!!!
is your lactose intolerance still cured?
please peel off that plastic foil from the mini one for me
And what about electroporation devices? hehe
"Just make sure the whole room is dark and it makes seeing things a lot easier" Well...
I wonder what unsophisticated barbarian disliked this.
cool as all hell
Is this sped up or am I just being slow right now?
I feel the same, haha. I think it's a bit too fast in certain places.
Maybe you should reduce your shrooms consumption? ;p dude sure is fast-paced!
Luckily you can pause, relisten if you mean the entire video. Or if you mean specific areas, he might already have expanded it in other videos or will in future ones.
@@jimmiununger2767 It's less that it's too fast to follow, it just _sounds_ sped up somehow. As if all the sounds are cut short a bit.
What are your thoughts on the man who genetically modified babies
i miss biotech lab.
👍👍👍
What happened with your fluorescent microscope? Have you succeeded?
Got busy and further attempts didn't really work. Will keep tinkering with it
@@thethoughtemporium
Try to use a flourscent substance instead of water in your sample. The easiest one to get is Chlorophyll. It's pretty easy to isolate it from any green plant. All what you need is ethanol to lower the concentration of Chlorophyll. Chlorophyll is green and it "shifts" the UV light to the red color range. Hope you succeed ❤️
@@thethoughtemporium by the way, you didn't fail. Actually, you have built a real flourscent microscope, but it is an old one. the old flourscent microscopes were just like what you have built. Open the page of the "University of Toronto" on Wikipedia. You will see down under the section of "research" a real photo of stem cell which was captured back in the 80s. It's just the same as what you have done
Hopefully you don't get duped again and get water😂
How easy is to create a super virus with the equipment you have right now?
Not. That's the myth of biology. Chances of you successfully making the thing are way lower than getting yourself killed in the process. That's a biosafety level 4 kind of thing which I'm sooooo not set up for. My lab is for working with bacteria and yeast that are non pathogenic.
i did not understand shite, but still it was interesting to watch.
1 CRISPR modified baby voted down this video.