Hypotheses
Midterm Practice 1:
TRUE OR FALSE: The following Alternative Hypothesis regarding the effect of Compound X is CLEAR, TESTABLE and DIRECTION-SPECIFIC.
"Administration of Compound-X will reduce AB plaque load and cognitive decline in 5XFAD mice."
False
How can you make this hypothesis better?
Midterm Practice 1:
What type of variable is the mice's time to complete a maze test?
Dependent variable, health/functional outcome
Midterm Practice 1:
What type of variable is a Wild Type mouse who receives a daily dose of the vehicle alone?
Negative control for disease model
Midterm Practice 1:
Which of the three R's of animal research?
Using a power analysis to determine group size.
Reduce
Midterm Practice 1:
Baseline for disease model; demonstrates what outcomes are expected as normal.
Wild-type mice
Midterm Practice 1:
Required components of a clear, testable, direction-specific alternative hypothesis regarding the effects of Compound X. (based on goals of study)
- inclusion of timing of administering Compound X
- predicted effects on AB plaque formation w/ treatment
- predicted effects on cognitive function w/ treatment
- explicit comparison to control
Midterm Practice 1:
What proponents should dependent variables measure
- Measure of pathology: amount of AB plaques
- Health/functional outcome: performance on some cognitive test
- Verification of pathology and molecular MECHANISM: microglial activation in brain (referring to context and bg)
Midterm Practice 1:
Negative control for use of the drug
vehicle-treated AD mouse model
Midterm Practice 1:
Prevented by blinding who conducts the measurements of the dependent variables to the treatment the mice receive.
researcher bias
Midterm Practice 1:
Quantification of AB plaques in brain
- immunohistochemistry
- ELISA on tissue lysates
Fill in the blanks: Early administration of Drug SHrinK will ___ the prespecified primary disease outcome in ____ - mutant ____ compared with vehicle treatment.
reduce; YIKES
List all potential dependent variables (and their outcome types) needed to study the effects of Drug SHrinK
mRNA abundance and protein abundance (molecular); teratoma incidence/skin-lesion severity (functional), body growth (physiological)
YIKES-mutant mice
What is the negative control for Drug SHrinK?
Drug SHrinK finally enters human clinical trials. To verify the effectiveness of the drug, you ask each patient for their DNA sequences. What are some potential consequences/breach of ethics of not handling patient data correctly?
To the patient: breach of confidentiality, secondary use of data without consent, de-identification of genomic data (VERY BAD), genetic discrimination, psychological stress
To researcher: fired without a doubt, loss of credibility, loss of reputation, legality issues
What technique could be used to quantify mRNA/protein abundance?
If mRNA - RT-qPCR
If protein - Western blot
Testable, specific/clear, defines variables, builds upon preexisting knowledge, simple, and relevant
What makes a good hypothesis?
What are the independent variables of the study on Drug SHrinK?
receiving Drug SHrinK/vehicle, timing of administration
Drug YEESH is a current therapeutic on the market for reducing effects of the OMG disease.
What is a potential positive control?
How many replicates should you do to ensure reproducibility and rigor in the experiment? How many mice per treatment group should you do?
3 replicates.
10 per group = remember the 3 R's
Besides this mice model system for testing Drug SHrinK, what other model systems can you think of that could test out the research question and why?
Zebrafish - can test for YIKES gene function and disease mechanism
Rats - can reproduce aspects of disease thanks to similar physiological functions
Human tissue organoids - same cells, reduces animal usage
Experimental Design Exercise
TRUE or FALSE, the following is a clear, testable, and direction-specific null hypothesis:
"Early administration of mAb-101 at 6 hours following LPS treatment will significantly increase the 48-hour survival rate, reduce serum IL-6 levels, and reduce organ injury compared to LPS-only control."
FALSE
this is an applicable alt hypothesis
provide a good null hypothesis
Experimental Design Exercise
What aspect of the dependent variables does obtaining serum concentration of IL-6 at early time point fulfill?
mechanism
Experimental Design Exercise
How to control for the disease model?
LPS + Vehicle
Experimental Design Exercise
Which key component of scientific rigor?
Random assignment to different treatment groups
Consideration of biological variables: allows us to control for pre-existing biological differences between the mice
Experimental Design Exercise
Techniques to evaluate inflammation
(specify which aspect of inflammation)
- enzyme-linked immunosorbent assays (ELISA)
- multiplex cytokine arrays
- flow cytometry