How to read charts like these?

[daftypatty]

Like, i have nil understanding, lol. What do the side bars mean?

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[EverStriving]

Looks like the patient was a heterozygous mutant for CCR5 before 'SCT', then became a homozygous mutant after. Hard to know what that means though without the accompanying text.

I'm pretty sure this is just testing your ability to understand mutation annotation. CCR5+/+ just means normal CCR5 status. CCR5+/delta32 I believe means that the CCR5 protein has a mutation at the 32nd amino acid, but only on one chromosome. CCR5 delta32/delta32 means homozygous mutated at AA 32. Match the bands in the patient before and after treatment to the reference bands (first 3 columns) to see what occurred in the patient.

 

[daftypatty]

Looks like the patient was a heterozygous mutant for CCR5 before 'SCT', then became a homozygous mutant after. Hard to know what that means though without the accompanying text.

I'm pretty sure this is just testing your ability to understand mutation annotation. CCR5+/+ just means normal CCR5 status. CCR5+/delta32 I believe means that the CCR5 protein has a mutation at the 32nd amino acid, but only on one chromosome. CCR5 delta32/delta32 means homozygous mutated at AA 32. Match the bands in the patient before and after treatment to the reference bands (first 3 columns) to see what occurred in the patient.

Ah okay, so the bands themselves dont necessarily mean anything other than to identify which patient matches which mutated/wild-type condition?

 

[El-Rami]

Isn't this a gel?

 

[remedy23]

Isn't this a gel?

That's what I was thinking too. It makes sense because the deleted regions means smaller DNA fragments = more distance travelled which is what I see.

 

[bearintraining]

View attachment 195532

Like, i have nil understanding, lol. What do the side bars mean?

It is a DNA gel. Look at it as follows:
Lane 1: Ladder. It is a size marker.. Smaller fragments are near the bottom, larger near the top
Lane 2: Empty for ease of visualization
Lane 3: You're given the genotype CCR5+/+ (homozygous wildtype) and single band. This tells you the expected size for what is likely a PCR product for the wildtype allele (copy) of CCR5 in this assay
Lane 4: You're given the genotype CCR5+/delta32 (heterozygous wildtype/deleted) and you see "two" bands near the size of the wildtype and one smaller one. Note that this really should be one band near the wildtype and one smaller. But this is what it means.
Lane 5: You're given CCRdelta32/delta32 (homozygous deleted) and you see one single smaller band. This gives you the size of CCR5 delta32 PCR product
Lane 6: Patient before SCT (stem cell transfer) is the same as Lane 4. Thus the patient was CCR5+/delta32 heterozygote
Lane 7: Patient after SCT day61 is the same as Lane 5. Now the patient is CCR5delta32/delta32 homozygous.

Background: stem cell transfer likely means bone marrow in this case. Thus, radioablation to destroy all bone marrow stem and entire immune system, and then infusion with donor bone marrow stem cells. What you're observing here is a patient's genotype based on a blood sample, and that's why it's changing after the SCT.

Bonus: CCR5 is the endogenous ligand on T-cells for HIV. So a question could ask you "Is this patient now resistant to HIV?" and the answer would be "Yes because they have the mutated/deleted CCR5 allele homozygously".

 

[jb94mg]

It is a DNA gel. Look at it as follows:
Lane 1: Ladder. It is a size marker.. Smaller fragments are near the bottom, larger near the top
Lane 2: Empty for ease of visualization
Lane 3: You're given the genotype CCR5+/+ (homozygous wildtype) and single band. This tells you the expected size for what is likely a PCR product for the wildtype allele (copy) of CCR5 in this assay
Lane 4: You're given the genotype CCR5+/delta32 (heterozygous wildtype/deleted) and you see "two" bands near the size of the wildtype and one smaller one. Note that this really should be one band near the wildtype and one smaller. But this is what it means.
Lane 5: You're given CCRdelta32/delta32 (homozygous deleted) and you see one single smaller band. This gives you the size of CCR5 delta32 PCR product
Lane 6: Patient before SCT (stem cell transfer) is the same as Lane 4. Thus the patient was CCR5+/delta32 heterozygote
Lane 7: Patient after SCT day61 is the same as Lane 5. Now the patient is CCR5delta32/delta32 homozygous.

Background: stem cell transfer likely means bone marrow in this case. Thus, radioablation to destroy all bone marrow stem and entire immune system, and then infusion with donor bone marrow stem cells. What you're observing here is a patient's genotype based on a blood sample, and that's why it's changing after the SCT.

Bonus: CCR5 is the endogenous ligand on T-cells for HIV. So a question could ask you "Is this patient now resistant to HIV?" and the answer would be "Yes because they have the mutated/deleted CCR5 allele homozygously".

Would taking classes like molecular biology and genetics help with knowing how to interpret this type of stuff??

 

[gothicfoxes]

Would taking classes like molecular biology and genetics help with knowing how to interpret this type of stuff??

Sure. When I studied genetics we did a bunch of crime case studies that required analysis of gels.

 

[bearintraining]

Would taking classes like molecular biology and genetics help with knowing how to interpret this type of stuff??

Absolutely. Especially population genetics. Which is awful btw, and I actually love genetics

 

[El-Rami]

Sure. When I studied genetics we did a bunch of crime case studies that required analysis of gels.

I did a lot of gels in undergrad, which are actually pretty fun to make!

 

[gothicfoxes]

I did a lot of gels in undergrad, which are actually pretty fun to make!

I agree. I loved gel lab days.