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[LIVE] Writing DNA Code! | Learn Real Genetic Engineering - Part 2

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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...
Last episode: ru-vid.com...
Github repo of presentations: github.com/the...
Past genetic engineering streams/videos:
• [LIVE] Using HIV + Ma...
• I Grew Real Spider Sil...
Sebastian's work:
atinygreencell...
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.n...
parts.igem.org/...
www.jove.com/
www.researchga...
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Support the show and future projects:
Patreon: / thethoughtemporium
Ko-Fi: ko-fi.com/thou...
Become a member: / @thethoughtemporium
Store: teespring.com/...
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My Social Media Pages:
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Facebook: / thethoughtemporium
Twitter: / emporiumthought
Website: thethoughtempor...

Опубликовано:

19 авг 2024

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Комментарии : 178

@svg98 Год назад

Watching a stream on how to write DNA code. What a time to be alive!

@gustavprivat9464 Год назад

Dear fellow scholars, this is two minute papers with Dr. károly Zsolnai-Fehér.

@rikvermeer1325 Год назад

Imagine the possibilities, just two papers down the line! Incredible.

@cvspvr Год назад

@@gustavprivat9464 this video is sponsored by weights and biases

@jonathanjohnson9611 Год назад

Technology and social media truly are wonderful.

@pierrec3531 Год назад

Let's be honest here, we all heard this comment with his voice

@Slaketik Год назад

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 :)

@robstamm60 Год назад

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

@OfficialEpsilon Год назад

Imagine a compiler bug accidentally causing cancer

@namehidden8854 Год назад

Except genes form a library, not a syntax.

@thatJackBidenTalksAbout Год назад

1:00:39

@SourceCodeDeleted Год назад

Yes, this reminds me of assembly and code caving.

@SkyenNovaA Год назад

Bruh compiling high level language into DNA code would be so cool

@paxx4069 Год назад

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!!

@rikvermeer1325 Год назад

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.

@johnjohnson3681 Год назад

Amazing idea

@wasordx3245 Год назад

Ah yes, plague inc but with real viruses

@vivaankhabya Год назад

Thanks again please keep doing these! How can we help you to teach more?

@rieko7793 Год назад

Planning on watching the full vid soon but want to say you are amazing for sharing your knowledge!

@snowballeffect7812 Год назад

shoutout to scihub.

@petevenuti7355 Год назад

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

@minerharry Год назад

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

@linuxgirl_ 8 месяцев назад

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.

Год назад

I feel like the term "life hack" will get a totally new meaning in the next 10 years.

@SalMans838 Год назад

I woke up in the middle of the night watching this. What did I even stumble upon

@mh6276 3 месяца назад

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!

@phaZZi6461 5 месяцев назад

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

@Queekusme Год назад

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

@thethoughtemporium Год назад

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

@Queekusme Год назад

@@thethoughtemporium thanks, looking forward to future videos and streams in this series 😊

@housefull2432 6 месяцев назад

What u research on Kasper @@thethoughtemporium

@mh6276 3 месяца назад

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.

@Eagertail Год назад

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

@mh6276 3 месяца назад

Have you subscribed to him yet?

@neon_Nomad Год назад

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🐈🐶

@modakkagitplugga Год назад

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.

@jjs8426 Год назад

Expand your mind and your research

@thecrakp0t Год назад

Are you saying catdog can be real??

@greenjp779 Год назад

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?)

@subliminalfalllenangel2108 Год назад

@@greenjp779 these laws only apply to human embryos, which can be overturned anytime in the future.

@deleteyoursocialmedianow8183 Год назад

looking forward to your future book!

@koyosumi Год назад

youtube auto play goes CRAZY when you fall asleep i swear

@P3R_not 11 месяцев назад

Fr!

@mh6276 3 месяца назад

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.

@georgemichelakis1202 Год назад

Really appreciate your channel my friend. Please continue what you are doing. You have inspired me to plan for future physics projects.

@adicsbtw 7 месяцев назад

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

@halifakx Год назад

so good you are back in genetics!

@eduardschreder1623 Год назад

we need part 3 !

@mikee33oo Год назад

DNA & CODING is already complex. To WRITE it??? now that's something crazy

@Kram1032 Год назад

"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.

@Larsoff Год назад

As long as all living cells have to undergo oxidative stress then every living thing ages.

@Kram1032 Год назад

@@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.

@bobert3230 Год назад

There's like an immortal jellyfish or something

@blue..ridding..h00d 3 месяца назад

@@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 :)

@csbluechip Год назад

Absolutely fascinating. Thank you for sharing your knowledge.

@atomatopia1 8 месяцев назад

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?

@espanadorada7962 Год назад

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.

@espanadorada7962 Год назад

@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.

@espanadorada7962 Год назад

@Moonlight Gamers yes, but I’m still relatively inexperienced :)

@dannydyckgiesbrecht1343 Год назад

Thankyou I love learning new things

@TomsBackyardWorkshop Год назад

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.

@TheCanterlonian Год назад

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

@gregorymugeni9344 7 месяцев назад

Appreciate you guys ✊🏿such amazing content

@vikingskuld 7 месяцев назад

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.

@neon_Nomad Год назад

This and verilog are goals for when i have more time and money

@cronchulus5489 Год назад

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

@carlkenner4581 Год назад

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.

@janisialiardis543 Год назад

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?

@AmruMagdy 4 месяца назад

Thank you for sharing your knowledge

@hayes_creates 9 месяцев назад

if one was to put fuGFP in plants, does it still luminate after the host dies, i presume it doesn't?

@karahana Год назад

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?

@thethoughtemporium Год назад

300-500. Ish. Sometimes less, but anything bigger and more complex and the price shoots up

@ChaotikmindSrc Год назад

"if you're the right kind of crazy" i guess i fit in !

@petevenuti7355 Год назад

Don't forget to give us a heads up for the next episode, it sucks when you RU-vid notification when it's almost over or you don't see it till it's long over

@0xMN Год назад

Thanks!

@helping_others Год назад

Fantastic thanks x

@Brickkzz Год назад

"this is where I do DNA coding" 😂

@mh6276 3 месяца назад

What's so funny about it?

@peterschneider8080 Год назад

We need to go deeper...

@bugfighter5949 3 месяца назад

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 ?

@trejkaz Год назад

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.

@allahsz3232 Год назад

Do we know how to invent a new protein have desired characteristics and functions, instead of using an existing gene

@MStrong95 Год назад

So you say that genetic engineering is expensive? Maybe you can get Mr. Beast or some other science education RU-vid channel(s) to collaborate on a project together.

@Larsoff Год назад

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

@humblebeastkey4069 Год назад

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

@strat5520 Год назад

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.

@espanadorada7962 Год назад

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

@melody3741 Год назад

I was about to make a joke about evangelion but then you told me the basics of dna is called the central dogma 😩

@tempest7144 Год назад

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?

@thethoughtemporium Год назад

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.

@espanadorada7962 Год назад

@@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.

@jorgejimenez4325 5 месяцев назад

@@thethoughtemporiumEukaryotic RNA splicing is a huge field too. You could spend a livestream just talking about it.

@magicsasafras3414 6 дней назад

Could i get a culture to use the CYP19A1 gene? No reason...

@gregorysmith1134 Год назад

I like working with dangerous pathogens. When I get my nucleic acid synthesizer, the sky is going to be the limit.

@The_real_jamal Год назад

I don't know WTF I'm watching but i like it

@neon_Nomad Год назад

Dna pentesting will one day be a job.

@JQ3B94 Год назад

Virus design

@benruniko Год назад

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).

@shikanosuke8898 2 месяца назад

is there a link to the japanese study

@thomasgauthier5691 Год назад

48:00 they could want to break the cell to make it easier to collect the results...

@Ohykha Год назад

Its so ethicly wrong but so like what u doin. Mix it with AI and technology and u got my point

@grga621 Год назад

Bruw woke up to this no clue how i got to this

@mh6276 3 месяца назад

I HOPE YOU LIKE IT!!!!!!!!!🤣

@ramkitty 7 месяцев назад

Does the protien curl direction have to do with chirality or just convention

@FukU2222 Год назад

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.

@zezimadude13 Год назад

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.

@atomatopia1 8 месяцев назад

I like to think that fuGFP is pronounced F.U.GFP

@The_Arachnid Год назад

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.🤔

@HA-cy4vx Год назад

feels like writing code with 0 and 1

@hrig Год назад

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

@petevenuti7355 Год назад

Have you ever grown or even bred mushrooms?

@espanadorada7962 Год назад

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.

@2OXX Год назад

can you edit my genes to cure my erectile dysfunction??? my wife would be overjoyed. im 63

@neon_Nomad Год назад

🔹️

@mh6276 3 месяца назад

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.

@2OXX 3 месяца назад

@@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

@margodphd 11 месяцев назад

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 😂

@mlsh-azerty Год назад

nex step, growing geko finger cell 😄

@sebscripts 11 месяцев назад

chips: 26:34

@deyvismejia7529 Год назад

this video is really complicated, speaking as someone with a BA in biosci. i think less detail would have been better.. pka values lol

@mh6276 3 месяца назад

I think it is perfect and I have almost no experiance in biology at all but I have always been wanting to learn this.

@unanimatereactor5014 Год назад

K so i coded But i got a seg fault

Год назад

And I thought programming c++ was hard.

@roberttalada5196 Год назад

God is great. But he really do need to be commenting his code.

@yyhhttcccyyhhttccc6694 Год назад

im gonna make a meat creature that eats taco bell

@RandomNooby Год назад

Uplifting... (;

@kiedranFan2035 Год назад

Go on

@kobrapromotions Год назад

Was it you who engineered a virus to treat your lactose intolerance?

@mario110cc Год назад

Try to code in assembly xd

@aN0nyMas Год назад

Meko chan when 🐈‍⬛

@turking25 Год назад

Programming *in* python

@PetraKann Год назад

Forgive them Father for they know not what they do

@ChessMasterNate Год назад

So...then...I can make my poo glow?

@mh6276 3 месяца назад

In a hundred years. Clearly you are not interested and do not have the mental capacity to understand or you were not paying attention.

@TheScientist777 Год назад

Zymogen

@firetester280 11 месяцев назад

hellllllllllooooooooo

@galaxybrian8039 Год назад

the ads every 4 minutes make this borderline unwatchable

@namehidden8854 Год назад

I tried this and it killed me.

@shirtyLPminecraft Год назад

M Mnk

@jahirtec2210 Год назад

Lol

@N9TheNoob Год назад

😬

@FuckBitches831 9 месяцев назад

does the place on the total dna matter where a gene goes? and how do you control where a new gene is added?

@mete3254 Год назад

Hey, can you transform me to a butterfly?

@definitlynotbenlente7671 Год назад

I want to be a fox

@peaceenjoyer Год назад

i dont think this is allowed

@kiedranFan2035 Год назад

What about this is not allowed?

@JQ3B94 Год назад

It's perfectly legal

@LANSl0t Год назад

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?