Lecture 8

Question 1

C1C2 is ____ _____ produced from lab _____

Answer 1

Cl- channel ; rhodopsin

Question 2

The use of optogenetics shows that the locus coerulus controls __________ in the brain:

Answer 2

sleep-wake (arousal)

Question 3

Another name for qPCR is:

Answer 3

RealTime PCR

Question 4

Name the three things the opioid effect tells us about microglia and astrocytes (found with a cluster plot):

Answer 4

1. There are three astro types
2. Chronic exposure suppresses Astro gene exp.
3. Chronic exposure advances Microglia gene exp.

Question 5

T/F:

The IHC technique is not quantifiable.

Answer 5

FALSE

You can see with a microscope.

Question 6

Reverse transcriptase is a borrowed enzyme from RNA viruses, making a (DNA/RNA) copy from (DNA/RNA), and incorporates viral (DNA/RNA) copies into host (DNA/RNA)

Answer 6

DNA ; RNA ; RNA ; DNA

Question 7

The three steps in preparing RNA for comparison with qPCR is:

Answer 7

1. extract RNA
2. homogenize w qPCR rxn
3. purify RNA -> cDNA -> run qPCR w/ control

Question 8

Name the two mechanisms light-activated channels are expressed in neuronal cell membranes:

Answer 8

1. opsins
2. flow of specific ions

Question 9

Quantitative PCR (qPCR) in Bulk measures is a tool for _____ and ____ to be expressed.

Answer 9

proteins ; mRNAs

Question 10

In PCR, exponential amplification ____ the DNA with each cycle, allowing for 20 cycles to give ____-fold amplification

Answer 10

doubles ; twenty ; 1mil

Question 11

ELISA is competitive due to a more _______ and _______ process than what Western Blots use

Answer 11

sensitive ; quantitative

Question 12

In an experiment, qPCR benefits by (increasing/decreasing) present (DNA/mRNA) in the gene.

Answer 12

increases ; mRNA

Question 13

IHC is important due to it’s ______ ability

Answer 13

QUANTIFIABLE

Question 14

To use PCR on an RNA sample, the ____ must be converted to ____

Answer 14

RNA ; DNA

Question 15

Name the two methods we use to track molecular changes in the brain:

Answer 15

1. Bulk measures
2. Cellular level measures

Question 16

RNA-Seq is a (sc/high-throughput) measure

Answer 16

high-throughput

Question 17

The three steps in one PCR cycle are ______, _______, _______

Answer 17

1. denaturation
2. annealing
3. extension

Question 18

ChR2 stands for _______ ________

Answer 18

channel rhodopsin

Question 19

ISH analyzes (mRNA/Protein) expression

Answer 19

mRNA

Question 20

In PCR, cDNA is

Answer 20

copyDNA

(makes DNA copy from RNA in lab)

Question 21

Name how we can use florescence to monitor rhodopsin expression in light-gather channels:

Answer 21

Inject promoters into transgenic mice for us to track RHO gene expression, monitor stability and manipulation of affected cells

Question 22

Each PCR cycle causes a _______ of the PFC produce which results in DNA fragments being defined by two _____

Answer 22

doubling ; primers

Question 23

A _____ ____ reads _DNA on a computer

Answer 23

cluster plot ; cDNA

Question 24

In the cellular level measure method of gene expression, we measure _____

Answer 24

change

Question 25

List the four steps needed to make an antibody:

Answer 25

1. grow antibiotics 2. inject species with protein of dif. species 3. collect blood, harvest antibody 4. use to locate cultured protein

Question 26

T/F: PCR works for RNA

Answer 26

FALSE

Question 27

Name the two major advantages of light-activated gated channels:

Answer 27

1. selectivity 2. precision

Question 28

Name the four steps in the western blotting process:

Answer 28

1. prepare sample 2. use gel electrophoresis 3. ensure proteins move across membrane 4. stain protein to see movement

Question 29

In stimulating the locus coeruleus, no expression of the _____ channel causes an effect with light exposure:

Answer 29

ChR2 due to the fact that RHO, the excitatory gene in stimulating rod change, cannot be made nor expressed.

Question 30

In RealTime PCR, a right shift means the expression (increased/decreased) from before.

Answer 30

decreased

Question 31

In qPCR, the lowest fluorescence signal that is detectable means it's ____ _____

Answer 31

hit threshold

Question 32

Name the four steps of the ISH method:

Answer 32

1. R/DNA probe 2. synthesize probe 3. probe tissue 4. fluorescence microscope

Question 33

It's important to note that in RNA-seq reads, it _____ with gene expression

Answer 33

correlates

Question 34

NpHR is (excitatory/ inhibitory)

Answer 34

inhibitory (blocks, like the bouncer)

Question 35

Distance between clusters means there are gene ________

Answer 35

differences

Question 36

ISH can analyzes ___ RNA(s) per run.

Answer 36

ONE

Question 37

Methadone activates _____ ____ in microglia.

Answer 37

inflammatory genes

Question 38

ChR2 is (excitatory/ inhibitory)

Answer 38

EXCITATORY (lets things occur)

Question 39

PCR requires _____ to amplify DNA fragments

Answer 39

primers

Question 40

ELISA is associated with (bulk/cellular) measures

Answer 40

bulk

Question 41

Name one technique to measure each change of expression in bulk and cell level measures:

Answer 41

1. RNA-Seq (bulk) 2. single cell (sc) RNA-SEQ

Question 42

The first step to convert RNA to DNA in PCR is using _____ ______

Answer 42

reverse transcriptase

Question 43

Different rhodopsins are used for different ________ patterns

Answer 43

stimulation

Question 44

In cells using the bulk measure method of gene expression, (few/no) cellular resolution occurs.

Answer 44

No

Question 45

scRNA Seq is a ____ _____ analysis of change in single gene expression

Answer 45

high throughput

Question 46

Western Blotting is a (bulk/cellular) method to detect changes in expression of (many/single) proteins

Answer 46

bulk ; single

Question 47

Immunohistochemistry (IHC) analyzes (protein/mRNA) expression

Answer 47

protein

Question 48

A cluster plot program generates _____ gene expression (after treatment)

Answer 48

(all) altered control vs. treated to see variable gene expression after experiment

Question 49

the reads for RNA-Seq are (cDNA/mRNA) copies of (cDNA/mRNA) which align with corresponding genes exons

Answer 49

cDNA ; mRNA

Question 50

Name the three methods for measuring protein and RNA amount at the cellular level:

Answer 50

1. IHC (Immunohist) 2. ISH (in-situ) 3. scRNA Seq (single cell)

Question 51

In RealTime PCR, a left shift means the expression (increased/decreased) from before.

Answer 51

increased (hit threshold)

Question 52

Name the four steps in the IHC method:

Answer 52

1. fix brain 2. incubate w/ antibodies 3. let antibodies present 4. observe use of secondary antibody

Question 53

In RealTime PCR, ea. cycle means it _____ ______ in every cycle

Answer 53

doubles exponentially

Question 54

It takes _____ cycles of PCR for qPCR to detect threshold.

Answer 54

~20 doubles after that

Question 55

scRNA analyzes (RNA/Protein)

Answer 55

LOLLL NEITHER. Analyzes cells bruv.

Question 56

In sc RNA SEQ, RNAs are expressed in distinct subtypes of ____ and ____.

Answer 56

neurons ; glia

Question 57

NpHR stands for ___________

Answer 57

halorhodopsin

Question 58

IHC can analyze ___ protein(s) per trial

Answer 58

ONE

Question 59

Name the important exception to the Central Dogma (DNA -> RNA -> protein):

Answer 59

reverse transcriptase (makes RNA, copies DNA, makes DNA)

Question 60

scRNA Seq measures expression level of all genes in (one/many) cell(s).

Answer 60

ONE

Question 61

You can quantify RNA to cDNA (one/many) time(s) in qPCR.

Answer 61

ONE TIME. low-throughput

Question 62

IHC analyzes (RNA/ Proteins)

Answer 62

Proteins

Question 63

The four steps in RNA-seq method is as follows: 1. control (____) vs exp (___) 2. generate short ____ (reads) from tissue 3. # reads correlate w/ ____ _________ 4. ______, compare

Answer 63

1. control (bulk) vs exp (RNA) 2. generate short cDNA (reads) from tissue 3. # reads correlate w/ gene expression 4. quantify, compare

Question 64

In PCR, denaturation is the ____ point in (breaking/making) bonds.

Answer 64

boiling point ; breaking

Question 65

Western Blots use gel electrophoresis to separate (DNA/proteins) and an _____ to detect desired ones.

Answer 65

separate proteins; antibody

Question 66

A bulk method for mRNA would be _____

Answer 66

qPCR

Question 67

RNA Seq can read (one/many) mRNA sequences at a time.

Answer 67

MANY (bulk)

Question 68

With bulk approaches, you can tell if treatment is effective due to mRNA changes in expression. However, you can NOT look at ___-____ resolution.

Answer 68

cell-type

Question 69

IHC and ISH cell-type resolution methods are incredibly (high/low) throughput.

Answer 69

LOW

Question 70

scRNA-Seq is meant for (mRNA/proteins) and is (low/high) throughout AND cell-type _____.

Answer 70

mRNA ; high-throughout ; resolution

Question 71

IN scRNA-Seq, you can usually assess changes in gene expression types at one time for all ____ in those specific cells.

Answer 71

mRNA

Question 72

Each dot on a Seurat plot represents gene expression of (one/many) cells.

Answer 72

ONE.

Question 73

In a Seurat plot, the computer identifies all _____ _______ types with distinct clusters.

Answer 73

gene expression

Question 74

When you can't distinguish cell morphology in Seurat (cluster) plots, ____-___ is the only method to reveal cell subtypes.

Answer 74

scRNA-Seq

Question 75

In a Seurat (cluster) plot, the computer gives all gene expression which goes ___ or ____ after treatment

Answer 75

up or down

Question 76

Optogenetics can be done through cell _____, trans_____ and knock(in/out).

Answer 76

cell cultures, transgenics, knock-ins

Question 77

Optogenetics is meant to study the function of specific _____ types in a brain circuit while controlling animal ______.

Answer 77

specific cell types ; behavior

Question 78

The two channels involved with optogenetics are ___ and ____.

Answer 78

1. ChR2 (Light activated) 2. NpHR (dark activated)

Question 79

Due to it's inhibitory effects of light, NpHR assists in exiting _____ _____.

Answer 79

REM sleep.

Question 80

Viral vectors control where a desired protein is ______ by injecting virus into the brain.

Answer 80

desired protein is expressed

Question 81

Viral vectors are different from transgenics. The latter is expressed in (some/every) cell with the transgene where the viral is in (some/every cell) due to the injection.

Answer 81

EVERY ; SOME

Question 82

Viral vectors are meant to carry specific code to the desired (gene/protein).

Answer 82

protein