qualifying exam cram

Question 1

Can you pass this exam

Answer 1

Yes

Question 2

In the Wang et al paper about how Tip60 depletion protects against myocardial infarction, what mice did they use?

Answer 2

mice containing floxed Kat5 alleles, wherein exons 3–11 comprising two-thirds of the Tip60 coding sequence including the chromo and acetyltransferase domains are removed by Cre-recombinase. Mice were B6/SV129 background

Question 3

In the Wang et al paper about how Tip60 depletion protects against myocardial infarction, how old were the mice used, when was tam given and when was the MI given?

Answer 3

10-14 weeks, tam was given day “0” and MI was given 3 days later – they saw about 50% reduction in Tip60 in whole tissue

Question 4

In wang et al paper where did they get their tissue slices

Answer 4

IF staining was from 1mm below suture to apex; qpcr was from 1mm below suture to base

Question 5

2 ways to verify successful MI

Answer 5

cTnT/cTnI in serum (RIP)

Elevated ST segment in EKG being recorded during surgery (Tombstone, also RIP)

Question 6

which is the base and which is the apex of the heart

Answer 6

base is top, apex is bottom, because life is meaningless and scientists are annoying

Question 7

Left ventricular anteroposterior internal diameter (LVID)

Answer 7

You want this to be a certain range becauase you don’t want it to be too big (dilated ventricle) or too small (hypertrophied ventricle)

Question 8

posterior wall thickness (LVPW)

Answer 8

also indication of wall thickness - dilation vs hypertrophy

Question 9

left ventricular internal area (LVA)

Answer 9

area of LV cavity; at systole and diastole, this can be used to calculate fractional area change (FAC) which can give an idea of ventricular function

Question 10

Fractional Shortening

Answer 10

By using the formula: (LVEDD - LVESD / LVEDD) x 100 we get the percentage of size differences of the left ventricle as a parameter of how well the left ventricle is contracting itself and therefore reduces the size during systole. Values > 28% are considered to be normal.

Question 11

Ejection fraction

Answer 11

ejection fraction (EF %) = (end-diastolic volume – end-systolic volume)

Question 12

can you pass this exam

Answer 12

yes

Question 13

what does ionomycyin do

Answer 13

It’s a binder to Ca and Mg and acts as calcium activating - to the extent that it can fucking cause apoptosis

Question 14

are either acetylation sites on p62 in the consensus sequence you proposed for k464

Answer 14

of course not b/c life is hard

K420 and 435 on UBA domain (for noncovalent ub association)

Question 15

are either acetylation site on ulk1 in the consensus sequence you proposed for k464

Answer 15

yes kinda, K606 on ULK1 is RXXXK which is close to KXXXK and honestly i’ll take it at this point
Other is k162

Question 16

is the ryanodine receptor acetylated

Answer 16

thank the fucking lord no

Question 17

la place’s principal

Answer 17

T=deltaP*R/wall thickness

In other words, the thicker the wall, the less tension there is (good)

Question 18

did wang et al find anything about apoptosis with depleting tip60

Answer 18

Tip60 in the infarcted adult heart is associated with activation of the CM cell-cycle, concomitant with reduction of apoptosis and preservation of cardiac function

Question 19

Is K464 SERCA2A conserved in mammals

Answer 19

yes ma’am

Question 20

Does k464 exist in mice

Answer 20

yes ma’am thank god <3

Question 21

does serca k464 exist in rats

Answer 21

yes

Question 22

tau

Answer 22

exponential decay time constants of calcium

Question 23

bl10%, etc

Answer 23

Rise time of the calcium to x% of the peak

Question 24

what is the promoter the CRISPR and GCAMP vectors are behind

Answer 24

CAG prmoter – synthetic promoter that strongly drives expression in mammalian models

Question 25

mice used in gorski et al

Answer 25

Studies were conducted in male C57BL/6J mice aged 8 to 10 weeks (weight, 25–30 g) purchased from Jackson Laboratories – they used a tac model when looking at acetylation and serca in the live animals as well as general sirt1 knockdown -/-
this paper also looked at what happens if you induce sirt1 w/b-lap

Question 26

meraviglia et al paper showed saha has what effect on serca

Answer 26

no change of serca2a expression in adult rats- but increased serca activity in rat microsomes when given rat hearts 1-10uM Ca

Specifically, SAHA induced a 21% decrease in the time constant tau, as well as a significant reduction in the time to 10%, 50% and 90% of fluorescence signal decay (BL10, BL50, BL90; Figure 3c) (rat hearts).

Consistent with this finding, SAHA also affected CM mechanics during the re-lengthening phase, as documented by the significant increase in the maximal rate of re-lengthening (+dl/dtmax, approximately 16%) associated with a decrease in the time to 10%, 50% and 90% of re-lengthening (Figure 3b,d). Conversely, the average diastolic sarcomere length, the fraction of shortening and the maximal rate of shortening were comparable in CTR and CTR+SAHA cardiomyocytes (Figure 3d)

Question 27

What is another possible reason meraviglia et al proposed for the SERCA2A change

Answer 27

possible phospholamban binding site

Question 28

PTip60 by gsk3b

Answer 28

ser86

Question 29

Activated perk

Answer 29

p-perk is pSer980

Question 30

Tip60 role in apoptosis

Answer 30

activation of p53

Question 31

How did the Wang et al paper assess tip60 apoptosis

Answer 31

primarily through tunel staining but also via p21 expression (cell cycle inhibitor)