Lil Bub's Genome | Science News 1.1
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- čas přidán 10. 02. 2020
- We're trying something new! This is the first of two videos. Here, I’ve summarized a recent genetics news story, and I want to know what your questions are about it. What didn’t you get, what do you want to learn more about, where do you want to go with this? You can leave your questions in the comments down below and then this Friday at 10am PST, I’ll come back and do a livestream to dive deeper and answer those questions, and have a discussion about it with anyone who’s interested.
Part two: • LilBUBome Q&A Livestre...
You might know Lil Bub as one of the internet’s favorite cats. A perma-kitten who suffered from a form of feline dwarfism, her tiny stature and adorable protruding tongue made her truly loved by all. While she sadly passed away in 2019, she made some important contributions to the scientific world by having her genome sequenced.
Further Reading:
Summary News Articles:
phys.org/news/2019-03-reveals...
www.smithsonianmag.com/smart-...
Scientific Paper:
www.biorxiv.org/content/biorx...
Another giant thank you to my Patreon supporters, including my amazing ribosomes:
Marcel Ward
Russell Determan
Ben Krasnow
Palle Helenius
Tim Rhodes
Peter Cook
Brad
Jerry
Diane & George Dainis
Don Burlone
Tim McNally
Brandon C.
William Pilkington
Twitter: @AlexDainis
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Patreon: / alexdainis
Music by Bad Snacks
Space Photo: Photo by Jeremy Thomas on Unsplash
Images of LilBub from www.biorxiv.org/content/10.11...
Video produced by Helicase Media LLC (my new science production company!) www.helicasemedia.com - Věda a technologie
Also, please help me brainstorm a better series title than "Science News." I'm exceptionally bad at naming things.
1. The goop scoop (goop is the DNA)
2. Dainis bulletin (not sure if you’d want to have your name in it)
3. Science forum/sciforum (love the forum aspect but not how close it sounds to scishow)
4. Brains on Broadcast
Science Today?
Scientific tea party! At least it looks like comfortable format for the livestream :)
@@andreytimashov1123 +1
“The Dainis minute” “Genetics with Dainis” “Science with Dainis”
Once the genome is sequenced, how would a cure be made?
What makes certain diseases rarer than others? Is there even a known factor? Or just the nature of the disease itself?
Science and Magic.
RIP Lil Bub.
Lil bub was pure magic from another Galaxy. I miss her
Shouldn't the bones being dense make them less prone to fractures? Whats the mechanism there?
density /= durability
this is also why cast iron swords don't work (and bulletproof armour does)
in order that a structure may endure shocks it needs to redistribute the shockwave (ideally) over the entire surface of the structure.
actually it's better to build a shock absorber that has an over all larger area of shock absorbtion (springs, or in this case fat, muscle, and bonemarrow tissues increase the area of shock absorbtion )
the same is true for gold (the purer the gold, the more liquid'y it get's)
for more info. see japanese 'earthquake proof' buildings
Great starting off point! I'm an engineer, and my education on genomics ended in 10th grade biology.
How do scientists determine exactly where the mutation is? Is it just a comparison with the 'average' genetic sequence of an 'average' cat? If someone gave you Lil Bub's sequence without saying what the mutation resulted in, would you be able to resolve the impact of the different sequences?
Fantastic format, really great idea. Looking forward to more of the same.
Iff you have the time after the other great questions, could you touch on what the paper refers to as "cytokine-replacement therapy"?
I love that we can use Lil Bub to discuss this. I believe that her treatments worked very well. Lil Bub's symptoms were obvious mobility problems so her treatment was very practical. Do you know from her genome whether she had problems that were not readily apparent? I mean do we have the knowledge now to say, "I see her SSH gene is mutated, therefore she will have extra toes and.... maybe her life span will be shortened. Or are scientists at the stage where they are still matching gene mutations with diseases? You spoke of funding, could a person have gotten the intensive testing, the analysis of the results, and the follow through that then developed, tested, and administered her treatments? And would a doctor know to suggest this type of testing for a patient? Or is LilBub's case a look into the future of gene science?
What are the main breakthroughs that made genome sequencing faster and cheaper? Is this trend expected to continue in the future? Are there any new promising technologies?
Hahaha I have my department's journal club tomorrow and I actually read the paper this time (tap tap on my own back xD). I think this two-part video on a certain topic is a great idea. Questions: Any specific reason for the name Sonic the Hedgehog besides a scientists's sense of humor? Are there genes homologous to these in humans?
I think it would be cool to see the software they use to see mutations in a genome. Like what does the user interface look like
Don't they have like... Copyright for using game character names for naming mutations in the gene sequence? 😂
Hahaha, I actually don't know if the scientists had to ask permission! I'll see if I can find out by Friday :)
You mentined the question of whether the cat had only one mutation or different, unrelated ones. This made me wonder if there could ever be such a thing as to train an AI with enough cat pictures and their genomes and let the AI give us cool unexpected real predictions. Like, predicting mutations' interactions(?); how would cats be like if they had certain mutations the AI had never seen before.
Could it be that the two mutations somehow correlate with each other, i.e. that they influence the same signalling pathway, but only specifically at different points in time or in different tissues, so that the different phenotype occurs and the general phenotype might even be weaker (osteopetrosis less pronounced, for example) if only one of the mutations were present?
Hi, this is a great idea ! So my question is a beginner one: how would you identify a mutation like these ? how would you know that it is different from usually normal genes (of a cat !) ? Is that done by comparing to other cats genome (like compared to stored different ideal configurations) ? And by the way, thank you for your videos, that's also great to see you presenting science "at us" (like you said) don't worry. You're a great (and beautiful) Science promoter/advocate 😉
Are there genes, that are known to cause specific conditions in humans, that do have the same or nearly the same effect in animals we have studied?
Like the dwarfism in the cat and dwarfism in humans, are those linked?
It is amazing that the cat ever lived with a mutation in SHH. @3:25 deep cut Dr. Dainis, made me chuckle. How is SSH different from say HOX box genes?
How clear cut is the distinction between genetic diseases and epigenetic diseases? How do epigenetic factors control the expression of a genetic disease or determine a persons ability to cope with a particular condition?
Also, how does the Sonic the Hedgehog pathway control cell differentiation in healthy organisms and how does it fail in diseased ones?
It would be interesting if we could determine whether L'il Bub inherited both genetic mutations - that is, if the condition is recessive or the condition had occurred in her lineage before - or occurred independently at the same generation, or one was inherited and the other was a mutation that occurred first with her. How often do such gene copying errors occur?
Can you cure the 1 disease without effecting anything else in the body? Like let’s say they cured bubs ostioperosis but would that cure effect her fur color or something random like that?
I always have noticed that science communication will discuss "a mutation in this gene caused such and such disease", but it rarely (if ever) goes deeper into how that mutation actually caused it. I've always wanted to know more about the technical details of how a mutated gene behaves, at what points in the organism's life it matters, and what other mutations to the same gene can do. Is it from a misfolded protein? Something else? I've always just felt like there's never enough detail into how something actually works.
This is an awesome question! Will absolutely talk about this Friday.
While you were discussing the mutations and their "common names", I was wondering whether they were somewhat specific to cats/felines or if there are similar mutations in humans, perhaps by other names?
I am so glad you asked :) Very excited to chat about this on Friday.
How do we know those two mutations are responsible?
Would it be possible that one of the mutation without the other wouldn't trigger a different phenotype?
How long is a typical gene and how many mutations different mutations could it have? How often do mutations occur? How often is the mutation recessive? Do these numbers match up with the number of rare diseases that we know of? Or do most go unnoticed?
First of all, I can't participate (fathers birthday dinner), but second of all I have questions anyway :).
Could you go more into the specifics how the project worked and the science communication was shaped + how the reactions and interactions were? Maybe which illness were communicated, what was learned, how the organizitional side of all things went down (as a project)? As some others I would be interested in the mechanism of genom sequinzing: Which molecules (?) are involved, how precise is it and which apperatuses are used (maybe interwined with some lab experiences of your own)?
Last but not least some questions concerning the chemistry and biology of things:
How reilable are the methods? How do you connect gens to their expressions, here genetic illnesses?
I think that's it for the moment. Pick would you like and wanna talk about it.
(+ Whisky in the background (y))
I will try and pass some of these questions on to the scientists to see if they can give more insight into the project/communication points!
1:29 Biomedical Research
What about Bub's dwarfism? Didn't that show up in her genome?
I am surprised about myself: I always thought my interest for science and technology included all sciences, but I find myself less and less intrigued by biological sciences, since the other sciences are more closer to "what makes the world". Anyhow, your videos are good and I urge you to keep making them, even if I may not watch every single one of them any more.
Sounds like a fun Friday - but you’re right I probably won’t have time to read before the journal club, just like our IRL ones, LOL.
As an astronomer I’m very curious about how you sequence genomes! How much sample from LilBub does one need? What does the actual data look like? (An image, a big csv file?) I remember when headlines raved about the modern glory of finally sequencing the human genome, but is this now a “simple”, commercially available process?
These are all awesome questions! I'll try and tackle them all Friday :)
It is commercially available, cost around 1K USD for a human genome. The results of that project should be in Genbank. A cat genome (www.ncbi.nlm.nih.gov/assembly/GCA_000003115.1#/def) click on a chromosome. clinking on FASTA will give you the sequence.
In fairness, polydactyli isn't *that* rate in cats. So Li'l Bub had one rare condition, and one semi-rare condition.
A very good point!
You ready for some nanopore tech??
But, do you think Lil' Bub's genome will be helpful for more than just her specific conditions?
What was the likelihood she inherited these mutations? Where they on the same chromosome? Where they both point mutations?
These are great questions! I'll try and address them Friday!
How did this poor cat wind up with two unrelated mutations? Bad luck, or something else?
Speaking of DNA errors. Alex, can there be situation when two mutations harmful on their own cancel each other out?
Maybe call it something like byte sci-zed instead of Science News?