[LIVE] Writing DNA Code! | Learn Real Genetic Engineering - Part 2
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- čas přidán 4. 02. 2023
- Have you ever wanted to learn genetic engineering? Well today is your lucky day. This series will get into the nitty gritty of how it works, starting from the basics of DNA design, to assembly strategies, and even genetic logic. This episode is an overview of the basics, how one goes about planning and preparing for an experiment, and a lot of resources to help you learn.
Donations: streamlabs.com/thethoughtempo...
Last episode: czcams.com/users/liveE_TAHxPBqKY?...
Github repo of presentations: github.com/thethoughtemporium...
Past genetic engineering streams/videos:
• [LIVE] Using HIV + Ma...
• I Grew Real Spider Sil...
Sebastian's work:
atinygreencell.com/
Books:
Essential Cell Biology - Alberts, et al
Biobuilder - Natalie Kuldell et al
Synthetic Biology: A Primer - Baldwin et al
Concepts of Genetics - Klug et al.
Other channels:
/ @ibiology
/ @crashcourse
Tools:
benchling.com/
www.snapgene.com/
Other resources:
www.ncbi.nlm.nih.gov/
parts.igem.org/Catalog
www.jove.com/
www.researchgate.net/
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Support the show and future projects:
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Website: thethoughtemporium.com/ - Věda a technologie
Watching a stream on how to write DNA code. What a time to be alive!
Dear fellow scholars, this is two minute papers with Dr. károly Zsolnai-Fehér.
Imagine the possibilities, just two papers down the line! Incredible.
@@gustavprivat9464 this video is sponsored by weights and biases
Technology and social media truly are wonderful.
Let's be honest here, we all heard this comment with his voice
It's funny that a while ago I had no idea this existed, but it was so interesting to see how well it explains everything, that I saw the full video. Thank you, now I discovered something amazing and felt accompanied while doing my job :)
Thanks again please keep doing these! How can we help you to teach more?
This reminds me of the early stages of computer science - what you are doing here look pretty much exactly like directly writing machine code for a microcontroller. I wonder how long it takes until we get some decent compilers and linkers!, high level languages like c or even object oriented languages
Imagine a compiler bug accidentally causing cancer
Except genes form a library, not a syntax.
1:00:39
Yes, this reminds me of assembly and code caving.
Bruh compiling high level language into DNA code would be so cool
Planning on watching the full vid soon but want to say you are amazing for sharing your knowledge!
As a software engineer, playing with buffers and protocols, this looks really appealing. You always make it look so easy b.c. it seems a lot of it is done on the computer. Wouldn´t you agree that converting amino acid codes to codons is a transpiler, and therefor arguably a compiler? I think that the websites you showed could very well be combined into a simulation game, like SHENZEN I/O or Plague INC. Unencumbered by bio-protocol, scaling and balancing funds against complexity. I would love to play that, and understand DNA better.
Amazing idea
Ah yes, plague inc but with real viruses
Really appreciate your channel my friend. Please continue what you are doing. You have inspired me to plan for future physics projects.
Absolutely fascinating. Thank you for sharing your knowledge.
so good you are back in genetics!
48:05 Part of the rationale for inducible promoters for academic purposes is not just for precise timing in relation to stuff happening in the cell, but also so we can watch what happens when the gene triggers. For example our lab has a gene product that kills the cell in minutes, but the why the cell dies and the pathways that gets broken are not well understood, so they added an inducible component so the population could grow and then triggered it under a microscope to watch them die
We do similar things in my lab. Unfortunately, this creator just seems to be bitter and disdainful of academia in general, to no real purpose. This was easily the most self-congratulatory and least instructive science video I have ever seen.
Highschooler here! these livestreams have motivated me to learn more about genetic engeneering!! this is SO COOL OMG thank you for helping me see how insanely complicated and fascinating this is!!
shoutout to scihub.
looking forward to your future book!
Thankyou I love learning new things
Thank you for sharing your knowledge
With organisms that have a preference to specific codons, can you theoretically produce dna to make the tRNA for those codons, I’m not thinking whether it’s practical for a project more if you did it would it work to supplement the missing or lack of tRNA
Sure and that's one way you can improve protein production. If you can't avoid the rare codons, increase the pool of them. or if a normal codon is used a lot, boost it's level a bit
@@thethoughtemporium thanks, looking forward to future videos and streams in this series 😊
What u research on Kasper @@thethoughtemporium
Appreciate you guys ✊🏿such amazing content
Hey this is a great video thank you very very much. I rewlly appreciate you sharing this. It does such a great job explaining things out.
With the promoter that turns on only when the bacteria are at a specific growth stage, you could have that promoter lead into a gene that codes for the production of something that can be seen at a human scale, like for example you could have it make GFP and then use that as a sort of clock or timer that tells you when they have reached a specific growth stage.
1:52:27
It looks like it was saying that that restriction site didn't exist in the selected vector. If you had changed to pet28, I bet it would have shown up
I feel like the term "life hack" will get a totally new meaning in the next 10 years.
I woke up in the middle of the night watching this. What did I even stumble upon
I have heard so many of these comments and it is REALLY weird and funny how somehow the youtube algorithm is giving you this!🤣 It is also great!
As a child of the 70's, reading science magazine from the 60's, I used to visualize the ribosome, and other protein complexes, as Vectrix villains made of Tetris blocks
(Back before anyone decided if vector or bitmap was how a display should work)
After watching this, now the visual is more like giant chickens mud wrestling for worms..
& Only allowed to catch worms with their wet muddy wing elbows !
Fumbling the worm but at a rate of millions of times a second so progress gets made,
but the worm is eating mud off it's legs getting longer at the same speed until it eats something too slippery. Be
we need part 3 !
perhaps using inducible is like a safety measure "best practice". if what your growing escapes the lab, your mutation will probably stay off in the wild
In benching isn’t the bottom strand just the complement? Where as the reverse compliment takes the complement and then reverses it (the reversal being specifically what switches the direction of the arrows on the plasmid). Would there be any issues with taking just the reverse without taking the compliment?
Thanks for the video, very helpful!
I do have some questions, regarding plasmids construction.
- Is there a signal peptide needed for the secretion of a recombinant protein in E.coli?
- Why are there two different ORIs?
- Is it better to add the Histag (or other tags) at the N-terminal or C-terminal of the sequence?
- If you will be using a T7 promoter, is a T7 polymerase gene needed?
Fantastic thanks x
This and verilog are goals for when i have more time and money
I fell asleep to a videogame playthrough and woke up to this dazed and confused. I dont know how i got here but to be honest im too interested to ignore it now
Have you subscribed to him yet?
Thanks!
Could it be done to make an app for use of Benchling on mobile? I get it might sound silly but I think it could be practical for getting practice when your not actually committing to a real project
youtube auto play goes CRAZY when you fall asleep i swear
Fr!
This is amazing! have you subscribed to him yet? I hope you find this interesting, if you don't just don't say anything so I am not annoyed by the comment.
DNA & CODING is already complex. To WRITE it??? now that's something crazy
if one was to put fuGFP in plants, does it still luminate after the host dies, i presume it doesn't?
It would be interesting if you could say something about the pricing. You say its very expensive. But for an example the complete plasmid you designed here from genscript. What would that cost to order in a useable quantity?
300-500. Ish. Sometimes less, but anything bigger and more complex and the price shoots up
I think it’s worth mentioning at 1:03:39 that while yes, many organisms do have much more DNA than, for instance, humans, that does not make them more functionally complex. Obviously “simple” is still very vague and arguable, but amount of proteins including proteoforms is a much better measure of organismal complexity than are #of genes or genome size. As I’m sure a lot of people know, most of the genes in those standout organisms with tons of DNA are total junk, transposons etc. with little to no function. Protein variety equates much better with organism-level complexity.
@Moonlight Gamers of course non-coding DNA has many roles, most of which we don’t understand yet. My point was that # of unique proteins coded by genome correlates with organism complexity much better than total genome size or even # of genes.
@Moonlight Gamers yes, but I’m still relatively inexperienced :)
Don't forget to give us a heads up for the next episode, it sucks when you CZcams notification when it's almost over or you don't see it till it's long over
What role will AI have in genetic engineering? I feel like in the near future, a lot of genetic engineering work could be done better by computers and robots.
"if you're the right kind of crazy"
i guess i fit in !
I just came here to say it took me 20 years to figure out the letters on the raptor in the thumbnail were DNA sequences and that they came from a projector. That is all.
i thought they were from the lights in the ceiling coming through the grid of the drop ceiling but that doesn't make sense, no one puts lights behind the ceiling
I’ve always wanted to learn this type of stuff I’m not that smart and stuff tends to get very boring for me however I’m dedicated to at. Least learn if I can’t practice this science fully
We need to go deeper...
Does the protien curl direction have to do with chirality or just convention
Do we know how to invent a new protein have desired characteristics and functions, instead of using an existing gene
What would happen if you include two coding sections in one gene by separating them with stop codons and beginning the next with a RBS? Would this allow you to get multiple proteins from one gene?
That is possible, though an odd way to do it. Another way is to build a start codon into the stop codon, or 1-2 letters before it. It has to be slightly frame shifted to work properly, but it can lead to the ribosome skipping like a record and starting to make the next protein immediately. Some viral genes work like that.
@@thethoughtemporium does this result in the first protein product being cut off or are the two gene products stuck end to start? Why not keep the two genes in the same ORF, separated by a short protease site for post-translation cleavage? That’s what I’m more familiar with viruses doing.
@@thethoughtemporiumEukaryotic RNA splicing is a huge field too. You could spend a livestream just talking about it.
If you run out of tRNA won't the ribosome stay occupied ? How does it separate without reaching the stop codon ? Is the effect of tetracyclin the same as running out of tRNA in practice ?
"this is where I do DNA coding" 😂
What's so funny about it?
I have this feeling that "you cannot make a compiler" statement is going to be eaten eventually. Some key pieces will come together after diacoveries akin to CRISPR, and most likely AI will come to the rescue at the same time and a compiler will be made for at least certain things.
I still think a full-cell simulation is very very far away… like he said in the video it takes immense computational power to simulate all the energies of all those molecules as they change. Using QM/MM modeling is computationally expensive even for a motionless small molecule. It may happen (idk anything about quantum computing really) but my guess is a full, real-time model of a cell is decades and decades away at best
I have a genuine question;
Are there any processes inside cells that use only a specific isotope of an atom that isn’t the most common isotope? I ask because I have heard that there is no way to chemically separate and differentiate between isotopes of the same element; that takes physics (ex: uranium enrichment).
48:00 they could want to break the cell to make it easier to collect the results...
is there a link to the japanese study
"All liveforms age"
- I'm 99.9% confident that there is not a single thing in biology that doesn't have at least one exception. Biological laws are at best strongly preferred guidelines. Sometimes not even that strongly preferred.
As long as all living cells have to undergo oxidative stress then every living thing ages.
@@Larsoff he made a point in the video about how lobsters are functionally immortal.
The context was in terms of inevitably dying eventually as cells stop being able to split into new working cells. Which, apparently, isn't a problem lobsters ever run into.
There's like an immortal jellyfish or something
@@bobert3230the immortal jellyfish isn’t actually immortal it’s more of a new genesis of some of the old cells, it also does, like all jellyfish, age :)
I don't know WTF I'm watching but i like it
At around 1:09:00 and I think a lot of things are expensive if you want to really get into them. Cycling? Expensive. Photography? Expensive. Anime? Expensive.
People should just do what they wanna do.
SO you're like a general biologist with a number of specialist skills right? Is it a thing to maybe just specialize in something like, say, computer analysis of genomic data using open-source tools to get a cheap start and kind of learn enough from doing that to build up some kind of practical specialist skillset for lower cost that might actually apply to other things in biology down the road? (Like if/when one might actually be able to afford it.. maybe doing a few cheap CRISPR kits or ODIN things every couple of months to try something live) Or is even just doing any one thing kind completely dependent on every other other skillset and something that can't reallly be done or understood properly without this kind of constant and repeated physical experimentation that costs all this money for materials? I know this is kind of like the "could you make a compiler?" question but I know there are HUNDREDS of open source tools in linux repos if you just "apt search genomic" for sequencing and analytical stuff so it got me wondering.
Its so ethicly wrong but so like what u doin. Mix it with AI and technology and u got my point
I was about to make a joke about evangelion but then you told me the basics of dna is called the central dogma 😩
Fun fact in highschool i visited a college that was working on turning chicken embryos into raptors and creating glowing mice, one day well create chimeras, well technically we are, but in the more historical sense🐈🐶
That chicken experiment was a bust, I debunked it in a proto-doctoral thesis I accidentally wrote while at university.
None of those embryos were allowed to fully develop and the primary mutagen used to repress gene expression does nothing to enable other recessed genes to be expressed. The specific tampering done had already been well documented as causing facial bone deformities.
Those chicks weren't growing teeth and tails, they were developing malformed skeletons.
Expand your mind and your research
Are you saying catdog can be real??
Chimera projects are banned, aren't they? You're apparently not allowed to edit human DNA (which personally I think is whack and not an ethical concern, but I'm also just some commenter on yt. so what do I know?)
@@greenjp779 these laws only apply to human embryos, which can be overturned anytime in the future.
Wait have you heard of quantum computers? They are made to calculate things like every particle. I don’t think they can do that right now but they give me hope that it is possible. I don’t know for sure though so maybe you can correct me.🤔
Dna pentesting will one day be a job.
Virus design
I like working with dangerous pathogens. When I get my nucleic acid synthesizer, the sky is going to be the limit.
feels like writing code with 0 and 1
Bruw woke up to this no clue how i got to this
I HOPE YOU LIKE IT!!!!!!!!!🤣
Thank you for such a cool and concrete example. Is it too hard to show us the extra steps to actually insert a vector into a mammal? this would be a capital letter HELLO WORLD
Have you ever grown or even bred mushrooms?
Inserting naked vectors into mammalian cells doesn’t go well as far as I know… you need a viral vector because our cells destroy circularized DNA so readily.
nex step, growing geko finger cell 😄
Please read "The Revolutionary Phenotype: The amazing story of how life begins and how it ends" before continuing much further. This is not a threat - it's a warning. Consider your actions.
chips: 26:34
I like to think that fuGFP is pronounced F.U.GFP
So you say that genetic engineering is expensive? Maybe you can get Mr. Beast or some other science education CZcams channel(s) to collaborate on a project together.
Synthetic biology is insnely expensive, time consuming, sometimes luck dependant, and brain numbing to design at times but feels pretty rewarding when it works. Just don't get too attached to your project and make sure your PI isnt too narcisistic and you'll have a lot of fun
K so i coded
But i got a seg fault
this video is really complicated, speaking as someone with a BA in biosci. i think less detail would have been better.. pka values lol
I think it is perfect and I have almost no experiance in biology at all but I have always been wanting to learn this.
Programming *in* python
Meko chan when 🐈⬛
im gonna make a meat creature that eats taco bell
Biology. If masochism isn't doing it for you anymore.
And seriously. It's wild in Europe law wise but in some countries the enforcement is nonexistent and the people tasked with enforcing it don't have a clue. Trying to explain difference between e-coli and botulinum cultures to a cop is the kind of thought experiment one needs to be a chosen one to be able to undertake 😂
Uplifting... (;
Go on
Try to code in assembly xd
Forgive them Father for they know not what they do
And I thought programming c++ was hard.
Zymogen
God is great. But he really do need to be commenting his code.
M Mnk
hellllllllllooooooooo
can you edit my genes to cure my erectile dysfunction??? my wife would be overjoyed. im 63
🔹️
He can't but You might be able to work it out. Also stop polluting the comments with your problems. Take it to a doctor.
@@mh6276 im 64 now and have matured a lot since my first comment here. just because i cant get it up doesnt mean it isnt bigger than yours! i used to be in my 20s as well ya'know
Was it you who engineered a virus to treat your lactose intolerance?
So...then...I can make my poo glow?
In a hundred years. Clearly you are not interested and do not have the mental capacity to understand or you were not paying attention.
😬
Lol
does the place on the total dna matter where a gene goes? and how do you control where a new gene is added?
So there are some organisms that prefer certain codons. AUG is the typical start codon for methionine but are there some organisms that would benefit more from having a different kind of start codon? Would it make the ribosomes latch on easier?
I tried this and it killed me.
the ads every 4 minutes make this borderline unwatchable
Hey, can you transform me to a butterfly?
I want to be a fox
i dont think this is allowed
What about this is not allowed?
It's perfectly legal
I totally understand about 0% of this.
Thanks!