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Neuroscience Lab > Exam 1 Review Compilation > Flashcards

Exam 1 Review Compilation Flashcards

1
Q

How do you recognize pseudoscience?

A
  • Lack of credible references
  • Illogical leaps
  • Draws on “ancient wisdom”
  • Cites awards/training of the author
  • A pitch to sell you something
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2
Q

What is a pilot study?

A

A small scale, preliminary study run before a larger scale study to determine overall feasability of the larger study, design parameters, possible adverse events so that time and money are not wasted

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3
Q

What is a falsifiable hypothesis?

A

You should be able to show that the hypothesis is false

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4
Q

What is an operationalized hypothesis?

A

Written in terms of the operations and procedures used to test

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5
Q

What is the internal validity of a research project?

A

How reliable and replicable the results are, and ifyou can determine the causal relationship between variables.

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6
Q

What is external validity?

A

How well the research generalizes to other populations or settings

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7
Q

What is period (per) mRNA?

A

mRNA that encodes for an element of the molecular clock that controls circadian rhythms.

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8
Q

What is the suprachiasmatic nucleus (SCN)?

A

Master pacemaker in the hypothalamus of the mammalian brain.

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9
Q

What are confounding variables?

A

Variables that influence both the independent and dependent variables

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10
Q

What is a positive control?

A

Checks the procedure is working by using a known sample that should produce a result

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11
Q

What is a negtive control?

A

Checks your procedure is not giving you false positive results by using a known sample that should not produce a result.

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12
Q

What is a vehicle control?

A

Using the solvent for the drug without the drug in order to control fo all other variables associated with drug administration

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13
Q

What is sham surgery?

A

Sham-surgery is the appropriate control for an experiment involving surgery in order to mimic the procedure without introducing an indp vairable

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14
Q

What are the important aspects of randominatizaion in a study design?

A
  • Random assignment: randomly assign subjects to experimental groups or control
  • Randomization of treatment: Order of treatment should be randomized
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15
Q

What is a within subject design?

A

Each subject experiences all the experimental conditions

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16
Q

What is a matched sample design?

A

Subjects are matched for that variable between groups

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17
Q

What is attrtion?

A

The loss of subjects before the end of the experiment

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18
Q

What is a quasi-experiment?

A

When your independent variable is a subject characteristic

Ex: you are comparing healthy controls to people with a particular disease

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19
Q

What is a placebo?

A

Inert substance (not the vehicle) sometimes used as a control in drug administration studies in people

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20
Q

What is a single-blind study?

A

The experimenter knows which group the subject is in, but the subject does not

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21
Q

What is a double-blind experiment?

A

Neither the experimenter nor the subject knows which group the subject is in

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22
Q

What is a time-series design?

A

A within subjects design where the dependent variable is measured at multiple times for the control and experimental conditions

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23
Q

What is a blocked design?

A

Experimental conditions are alternated, sometimes with a rest period in between

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24
Q

What is an event-related design?

A

Present test stimuli for a very short period of time, with longer time in between for control condition

25
Q

How do you deem something as necessary?

A

If effect y doesn’t happen when x is removed, then x is necessary for y

26
Q

How do you deem something suffcient?

A

If y happens when x is added, then x is sufficient for y

27
Q

What is a null hypothesis?

A

There is no difference between samples (groups)

28
Q

What is a Type I error?

A

You reject the null hypothesis and conclude that the groups differ, when they do not

29
Q

What is a Type II error?

A

You accept the null hypothesis, but it is false

30
Q

How does a spectrophotometer measure protein concentration?

A

Light will be absorbed by the solution. More light is absorbed as the concentration of protein increases. Any light not absorbed is detected and measured.

31
Q

Describe the Tuskegee Syphilis Study.

A

Tuskegee Syphilis study was an example of unethical research involving black man who were not told they had Syphilis or gave consent for the study and did not recieve the standard of care.

32
Q

What is the common rule policy?

A

Came into effect in 1991 and regulates human research studies under many general agencies.

33
Q

What is an Insitutional Review Board?

A

An IRB is a committe with at least 5 members that reviews all research on human participants at that instiution.

34
Q

What are the 3 major principles that were outline in the Belmont report for ethical guidelines?

A
  1. Respect for persons/ informed consent
  2. Beneficience: particpant is protected from harm and has confidentiality
  3. Justice: study population that would benefit the most
35
Q

What is the animal welfare act?

A

First legislation to set standards for the use of animals in research

36
Q

What are the protocols for Institutional Animal Care and Use Committee?

A
  1. Rational for the use of animals
  2. Specfic Experimental Procedures, including housing conditions
  3. Educational or research benefit
  4. Description of pain and distress experienced by the animal
37
Q

How can personal beliefs affect data collection?

A

Our personal beliefs can bias data collection & analysis, either consciously or unconsciously

38
Q

What breaks down RNA?

A

Ribonuclease (RNase) enzymes that are present in tissues

39
Q

What was in the lysis buffer and why did we add these?

A
  1. Guanidine thiocyanate
  2. 1-Thioglycerol
    - both inactivate RNases present in tissue sample and on our skin
40
Q

Why did we amplify cDNA in order to measure per mRNA levels?

A

Levels of per mRNA are too low to measure directly, so we need to amplify them. We can’t amplify RNA, but we can amplify DNA using PCR.

41
Q

Using the cDNA synthesis method, how many copies of cDNA are made per mRNA molecule?

A

1:1 ratio of mRNA: cDNA

42
Q

What primer did we use for cDNA synthesis?

What mRNA does it bind too?

A

oligo(dT) primer; will bind to polyA tails so it will bind to all mRNA

43
Q

What is qPCR?

A

Quantitative PCR is used to both amplify and detect in real-time, a specific sequence of DNA

44
Q

What is the first step of qPCR?

A

A relatively long heating step occurs only once at the start, and is included to “hot start” Taq polymerase and denature the hy

45
Q

What is the Cq value?

A

At some point, the amount of SYBR green bound to the double-stranded DNA reaches the threshold at which the fluorescence can be detected above background and is on the linear/exponential part of the curve.

46
Q

Why is qPCR a quantitative procedure?

A

qPCR is a quantitative procedure because measurements are taken in the exponential phase.

47
Q

What is a melt curve?

How many peaks should there be?

A

After the qPCR, the temperature is raised gradually and this melts dsDNA & causes an abrupt change in fluorescence. Only one peak should be present, if more than one peak occurs, it indicates more than one product was made.

48
Q

What is a no template control?

Should it give a Cq value, what does that indicate?

A

Contains only master mix (no DNA template). Should not give a Cq value, if it does there is extranous DNA contamination.

49
Q

What is a no reverse transcriptase?

Should it give a Cq value, what does that indicate?

A

Contains Master Mix + RNA. Should not give a Cq value, If it does, and NTC does not give a Cq value suggests genomic DNA contamination.

50
Q

What was the positive control in the cockroach experiment?

Should it give a Cq value, what does that indicate?

A

cDNA that contains the qPCR target sequence. Should give a Cq value, if it does not then qPCR was not set up correctly.

51
Q

What was the negative control in the cockroack experiment?

Should it give a Cq value, what does that indicate?

A

cDNA that does not contain the qPCR target sequence. Should not give a Cq value, if it does then the primers bind to non-target DNA.

52
Q

Why did we use a reference gene?

A

To determine if we started with the same amount of cDNA in each reaction because differences in Cq values generated in a qPCR for B-actin reflect differences in total amoutn of cDNA added and not changes in mRNA levels.

53
Q

What do we assume about our reference gene?

A

We assume our independent variable doesn’t change mRNA levels of the reference gene.

54
Q

What does it mean if sample A generates a Cq value of 20 while sample B generates a Cq value of 21?

A

It took sample B 1 more cycle to reach threshold, therefore it had half as much starting cDNA

55
Q

What were the “ingredients” that we used for our cDNA synthesis and what function does each preform?

A
  • oligo(dT) primers: binds to all mRNA
  • reverse transcriptase: takes mRNA to DNA
  • RNA template
  • buffer (DTT+ RNase inhibitor): maintain pH
  • dNTP: building blocks for DNA
  • water: adds volume
56
Q

What were the “indredients” that we used for qPCR and what function did each preform?

A
  • Taq polymerase: amplifies the DNA
  • SYBR green: a fluroscent marker that binds to the minor groove of double stranded DNA
  • primers: bind to specific target sequences
  • MgCl2: cofactor for enzyme
  • dNTP: nucleotides for extension
  • buffer: maintain pH
  • cDNA template
  • water
57
Q

What are the components of the buffer used in RNA extraction?

What are the roles of each?

A
  1. Guanodine Thiocyanate: Lyses cells
  2. 1-Thioglycerol: inhibts RNase
58
Q

What are examples of chemical disruption vs mechanical disruption?

A

Chemical disruption: chemical lyses by buffer
Mechanical disruption: Homogonizer

59
Q

Describe the methods for RNA extraction.

What are the pros and cons?

A
  1. Spin column method: faster, but causes blockages
  2. Organic method: requires fume hood, slower

Neuroscience Lab (3 decks)

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