Submitted by [deleted] t3_xvjjwl in askscience
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[deleted] OP t1_ir1iv1f wrote
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CrateDane t1_ir1k7n7 wrote
> > > > > Now assume you find a gene that seems highly conserved amongst a vast amount of species. But you have zero clue what it does. And you want to know. Usually, first step is to just delete it in a model and see what happens. Nothing happens? Okay, over express it. Nothing happens? Okay, try to see what the produced protein (theoretically or experimentally known) is similar to in sequence and structure (domains). That might give you a vague hint at what it might be involved it. If you have that hint, perhaps now you can delete it and challenge your cells or animal model with a stressor relevant to that hint. For example, perhaps you find the protein is similar to those involved in tight junctions, so now you can try to challenge your model with different deficiencies in whatever ions or other things to see if the mutated group is more severely affected.
Or you could screen for synthetic lethality / synthetic phenotypic alteration. It's not uncommon for there to be other genes that can compensate for the loss of your gene of interest; but then a double or triple mutant will usually have the relevant altered phenotype.
NakoL1 t1_ir2iznu wrote
a common approach nowadays is called "genome-wide associations"
if for a set of individuals you have both:
- measurements for a trait of interest, and
- genotypes at all genes in the genome,
then you can assess the correlation between the genetic variation and the trait variation. Typically, you might expect that most genes will have little to no correlation with your trait, but that one of a few genes will have strong correlations with that trait
that said, correlation isn't causality, so in principle you still have to figure out exactly what this or that gene does at the molecular level, what are the consequences of its interactions with other genes, and how this ultimately impacts the trait
Adorable-Breakfast t1_ir3wdrm wrote
To add to that, it's been found that rather than depending strongly on a few genes, a lot of characteristics (e.g. personality traits, mental health conditions, etc.) depend weakly on many genes, as many as several thousand. Any single gene on its own may account for only a fraction of a percent of the total variance, which would've been undetectable until large enough data sets became available in recent years.
regular_modern_girl t1_ir2u0pa wrote
Generally-speaking in recent times, it has been done by taking animal models (usually mice, as they reproduce fast and actually share the vast majority of their genome with us), and creating “knockout” forms of them where one or more stretches of DNA that code for a protein (which is actually all that a gene is) are “switched off”, and then seeing how this effects the animal.
I actually once got to meet Mario Capecchi, the researcher who pioneered “knockout mice”, and won a Nobel Prize for it.
Prior to this innovation (which I believe only came in the 2000s, although maybe it’s a bit older), biologists were mostly in the dark about which genes related to which traits, and it was really mostly guesswork. Genetics used to focus more on Mendelian heredity (which if you ever learned any biology in school you were likely introduced to), which connects observably inherited traits with a sort of theoretical entity called an “allele” (which don’t necessarily correlate to genes), and then attempts to sort of reverse engineer the rules for how that trait is passed on (whether it is recessive or dominant, etc.). Since most traits actually have more than one gene involved (since literally all a gene does is act as a molecular blueprint for a single protein, that’s it), sometimes in fairly complex ways, this way of looking at genetics is obviously very imprecise and rudimentary, and it’s mind-boggling how much genetics has advanced just in the past twenty years (it really is almost like going from abacuses to electronic supercomputers in just a couple decades). Thirty years ago we hadn’t even sequenced a whole human genome, now we can pin down certain traits to particular stretches of DNA, and then even selectively alter that DNA if we want (or put it in other organisms, etc.).
EDIT: There are other methods as well, but they tend to be more indirect and imprecise. Like mutant forms of some simpler organisms like C. elegans roundworms and E. coli bacteria have been studied and selectively bred for a while to try to disentangle which stretches of their DNA the mutations might lay in (as with bacteria especially there’s generally less DNA to look at, so this is more feasible than with organisms that have huge genomes like us, or surprisingly like a lot of plants; seriously, plants are so much more genetically-complex than you might expect, in part because a lot of them require a ton of different enzymes for complex biosynthetic pathways of various organic chemicals, and enzymes are proteins, and therefore each is tied to a particular gene).
foul_dwimmerlaik t1_ir3g11k wrote
Drosophila melanogaster, the common fruit fly, is another commonly used model organism for genetics, and several Drosophila geneticists have won a Nobel for their efforts.
_What_How_Why t1_ir4mcu4 wrote
Nice.
How do scientists switch off a specific gene?
mordinvan t1_ir4o270 wrote
A few genetic tools exist, but a fairly common method when I was studying it was to use a retro-virus containing failed copy of the gene, and insert it into very young, often single cell embryos, so it would infect all the cells in the target animal, and damage the target gene, either by removing the stretch of DNA it was on, or by changing the portion of the DNA strand which tells the body there is a protein to build here, which I believe is called the promoter.
CrateDane t1_ir6uxa4 wrote
Nowadays CRISPR-Cas is a very popular tool, but it can also be delivered by viral vectors (lenti or AAV mainly). Or by viral-like particles for that matter.
mordinvan t1_ir7k7k7 wrote
CRISPR is the new and much more efficient way yes. It just wasn't around when I got my degree.
CrateDane t1_ir6tx4r wrote
Nowadays, CRISPR-Cas is one of the easiest tools to use to knock out a gene. You deliver Cas9 (or Cas12a etc) plus sgRNA to cells, which causes a break to be made in a very specific spot. Then the cell tries to repair the break, usually via a messy pathway called NHEJ which often leaves the gene functionally inactive.
If you can live with just partially shutting off the gene, RNA interference is also very popular and can be very quick and easy to do.
newappeal t1_irb4i7b wrote
Before CRISPR/Cas9, it was actually quite hard to disable a specific gene at will. There are some proteins that can bind to and cut specific DNA sequences, causing function-disrupting mutations, but these are not very accurate and only available for a relatively small subset of sequences.
It's much easier to induce random mutations and then find a gene that got knocked out, resulting in a noticeable phenotypic change in the organism. Random mutations can be introduced with chemical treatments, radiation, particle bombardment (e.g. gold nanoparticles, which can also introduce foreign DNA), or biological systems (e.g. viral vectors in animals, Agrobacterium tumefaciens in plants). Nowadays, many model organisms (e.g. Drosophila, mice, Arabidopsis) have mutant libraries available, which contain specimens (seeds for plants, frozen embryos for animals or at least for mice) which each have a knockout in one gene, and you can order these for your research. A "saturated" library has at least one knockout line available for every single putative gene - putative because some genes are predicted from sequences but have not yet been confirmed to actually be functional genes.
aragorn1780 t1_ir4vepr wrote
100+ years of collective accumulated research by a global community of geneticists who freely share their research with each other coupled with modern genetic simulation technologies
But, a lot of it is deductive reasoning, by sequencing genomes of literally millions of individual organisms, they can pay attention to shared traits and find individual genetic sequences that are shared by multiple individuals with those similar physiological traits; for example, by sequencing the genomes of multiple down syndrome patients they'll eventually notice all of them carry an extra chromosome and the same one at that,
before the days of modern database technology this process was exhaustive and required hundreds of people working together just to sequence one genome, now it can be done quicker but it's still quite exhaustive
In short: clinical research and statistics
TomatoOverall1679 t1_irbu5st wrote
By splicing the dna of mice and observing what happends to them. Since 95% of mice dna is identical to humans it gives biologist a good idea on what will happen to humans with the same mutation.
Surveys and statistical analysis of human dna is also used to identify if certain genes are responsible for certain traits. 23 and me Is a company that does this.
[deleted] OP t1_irj09y4 wrote
How do we know how accurate the sites are and which one is more accurate than another?. If they all use different methods to gather their data?. Also assuming that the statement "mice's DNA are 95% similar to humans" is true, what does the other 5% account for and are missing anything by not having that extra 5%?.
TomatoOverall1679 t1_irnitcb wrote
There is no way of knowing how accurate the research is at those sites or any other site. one can only hope, wish and pray that the scientist/ceo's are honest....
That said, a meta study was conducted back in 2015 and found that over 60% of all biomedical research could not be repeated any ways. Some argue this is because of fraud on the part of the researcher , or just the inability to geting the equipment to repeat the study. Regardless its not good for science . its arguably not science if no one can repeat the study. Its just becomes statistical noise and makes research that more difficult.
Regarding mice dna similarity to human dna. Some recent research indicates that percentage could be as low as 70% . just depends on who you ask and what criteria was used to get the numbers. But as more research is done it seems the percentage is going down.
The other 5- 30% of dna that is not identical to human is unknown or not understood. But im sure its important for the mouse to have:)
[deleted] OP t1_ir1kk4j wrote
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[deleted] OP t1_ir1w4m4 wrote
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[deleted] OP t1_ir22wdv wrote
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[deleted] OP t1_ir2epgx wrote
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[deleted] OP t1_ir2icid wrote
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[deleted] OP t1_ir2sqmw wrote
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[deleted] OP t1_ir3vznb wrote
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[deleted] OP t1_ir4ntsn wrote
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Sibaron t1_ir1i6ke wrote
Often it is done by knocking down or knocking out the genes and seeing the effects. So simply seeing what happens if the gene isn't their to produce a protein or RNA species. Sometimes you can also look at what other genes or gene products they interact with and seeing the effects of these interactions.sometimes you can also run predictive algorithms using machine learning using previous known protein and functions to predict a new gene/gene product function.