M1 L1 Flashcards
What does a correlated graph look like
What does an associated graph look like
What is association?
Variables seem to be related (have some relationship you can visualize)
What is correlation?
Variables are related in a linear and significant way. You can test it and confirm a relationship
What is the third variable?
A third variable may be secretly influencing both of the variables that appear to be related.
* something influences variables 1&2 and is actually responsible for
What is reverse causation?
The relationship could be reversed, meaning the variable that seems like the cause is the effect.
* 1 doesn’t cause 2 turns out 2 causes 1
What is coincidence
Two variables appear to be related by chance
Testing for causation: Loss of function
This is when you remove something such as a gene and see what happens
What’s an example of a loss of function?
Gene Knockouts where you break a gene and see what happens.
* ex they stop eating so the gene you knocked out was correlated with eating
Loss of function KO: Conventional KO
The target gene is knocked out in all tissues at all times
* protein is not found anywhere in the entire animal
Loss of function: conditional KO
You control where and when your target gene is knocked out
* not KO in entire animal, just a specific area
Example of a conventional knockout
It is a whole body knockout. So for example, Exon 3 gets entirely removed and the kb gets smaller.
Example of a conditional knockout
* what do u use to do it?
Cre recombinase in conjunction with loxP sites system.
Take 2 mice: 1 with the flexed allele (allele of interest). The other with Cre injected under a heart specific promoter (so only stopping exon in the heart).
Now produce an offspring from these 2 mice: It will have both floxed and Cre gene.
* Since Cre is only expressed in the heart, it excises exon 3 only in the heart, knocking out the gene only in that tissue.
* Other tissues don’t express Cre, so the gene remains intact and functional elsewhere.
What is Cre recombinase? Whats the point of it
An enzyme that cuts DNA at specific sites called loxP sites.
Cre cuts out the floxed exon only in tissues where it is expressed.
This allows tissue-specific gene knockouts—you can study what happens when a gene is lost only in a certain organ without affecting the rest of the organism.
Explain this picture
zoomed-in view of what Cre recombinase actually does at the DNA level when it acts on a floxed allele.
Originally have 3 parts (ABC). We see 2 LoxP sites (orange triangles) surround B so B is who we want to remove. Cre recombinase sees the LoxP sites and causes the DNA between them to loop out. Cre then cuts at the LoxP site and rejoins the ends, removing B. End up with AC as excised allele and B a throwaway fragment.
What is a gain of function manipulation?
Add more of something and see what happens - overexposes gene
Function of a promoter in gain of function manipulation?
promoter controls and enhances the expression of the introduced gene to express in all tissues
Explain the components of this experiment:
* STOP codon
* LoxP sites
* YFP
* Promotor
* Cre
- The STOP codon which stops Rosa26 from driving YFP expression.
- LoxP sites which let you just express in specific area
- YFP is the gene we are aiming to express
- Promoter Rosa26 to allow for widespread, consistent gene expression.
- Cre recombinase is an enzyme that cuts out the STOP codon only in the cells where you express it.
Explain whats happening in this experiment
Normally, the STOP codon blocks YFP from being expressed, even though Rosa26 is active.
You put loxP sites around the STOP codon (Lox-Stop-Lox or LSL).
If you add Cre, it removes the STOP, like cutting out a roadblock.
Now Rosa26 can drive expression of YFP, but only where Cre was added.
- “You use Lox to stop the stopper” and “Cre to make it only in one area.”
What are loxP sites used for in this experiment
They flank the STOP codon so Cre recombinase can cut it out.
Cre in the brain → STOP removed in the brain → YFP only shows up there.
A correlation is a specific type of association in which the relationship between two variables is:
linear
What is the best way to test if Variable 1 has a CAUSAL effect on Variable 2
change Variable 1 and measure Variable 2
A loss of function manipulation is when you BLANK gene or protein then determine the effects on another variable (physiology. behavior, etc.). An example of a loss of function manipulation is making a BLANK
1) remove
2) knockout mouse
A gain of function manipulation is when you BLANK and then determine the effects on another variable (physiology, behavior, etc.). An example of a gain-of-function manipulation to test the effect of a gene/protein on the amount of food that mice eat is BLANK
1) add more of a gene or protein
2) overexpress the protein and measure the amount of food that they eat
