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Advanced Research Methods > Exam > Flashcards

Exam Flashcards

1
Q

An antigen is a susbtance that triggers the production of

A

Immunoglobulins ( antibodies )

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2
Q

Different molecular sites on antigens are known as

A

Epitopes ( sites in antigens where specific antibodies attach )

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3
Q

When an antibody labeled with a chromogen is reacted with a tissue from a patient, the immunohistochemical technique is called

A

Direct labeling ( labeled antibody of known specificity is used to identify antigens in the patients tissue, biopsy)

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4
Q

How does the indirect immunohistochemical method work

A

The patients serum is added to tissue sections containing known antigens to test the patient for the presence of antibodies to those antigens.

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5
Q

What is a flurochrome

A

Dye that absorbs light and then emits it own light at a longer wavelenght

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6
Q

Tissue for immunofluorescence must be

A

Frozen and unfixed because antigenic reactivity is least impaired and fluorescent antibody satining is stronger

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7
Q

Which of the following link antibodies would most likely follow a monoclonal kappa primary antibody?
1. Rabbit anti-mouse
2 Rabbit anti-human
3. Rabbit anti-sheep
4. Rabbit anti-goat

A

Rabbit anti-mouse, because kappa antibodies are usually prepared in either mice or rabbits

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8
Q

What is specificity?

A

Competence of an antibody binding site to react with one epitope

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9
Q

What is cross reactivity?

A

Antibody capacity to bind to different antigens

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10
Q

How can we label antibodies?

A
  1. Fluorescence labeling
  2. Gold labeling
  3. Enzymatic reaction
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11
Q

What is flow cytometry?

A

Measurement of the characteristics of particles in a fluid stream

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12
Q

The x-axis on a 3-part diff shows the separation in

A

Cell size

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13
Q

The x-axis is size separation called?

A

Forward Scatter (FSC)

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14
Q

The y-axis show the separation in?

A

Complexity

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15
Q

The y-axis complexity separation called?

A

Side Scattering (SSC)

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16
Q

FSC and SSC refer to light?

A

Scattering

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17
Q

Immunophenotyping uses an antibody that is labeled with a?

A

Fluorescent compoud

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18
Q

Flow cytometry is a technology that takes simoultaneous measurements of multiple characteristics of a single cell or particle.

A

True

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19
Q

What cell or particle properties can be measured by a flow cytometer?

A
  1. Relative Size
  2. Internal Complexity
  3. Granulometry
  4. Fluorescence intensity
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20
Q

What physical properties contribute to forward scatter (FSC) and side scatter (SSC) light?

A
  1. Size
  2. Complexity
  3. Refractive index
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21
Q

Fluorescence intensity is proportional to the number of binding sites on a cell

A

True

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22
Q

Displays a single parameter against the number of events ( counts) to show intensity level

A

Histogram

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23
Q

Displays two parameters at a time and shows the distribution of events

A

Dot plot

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24
Q

This system converts optical signals to equivalent electronic signals, then into digitized date

A

Electronics

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25
Q

This systems carries samples to the inerrogation point

A

Fluidics

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26
Q

This subsystem provides excitation sources and collects light signals

A

Optics

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27
Q

This filter transmits light longer than or equal to a specific wavelength

A

Longpass

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28
Q

This filter transmits light within a narrow range of wavelenghts

A

Bandpass

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29
Q

This filter transmits light shorter than or equal to a specific wavelenght

A

Shortpass

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30
Q

The most sensitive type of photodetector is the

A

Photomultiplier tube (PMT)

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31
Q

What are cell sorters for

A

Separate populations of cells and quantitative information of properties

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32
Q

What should we take into account when selecting a fluorochrome?

A
  1. Excitation and emission wavelenghts
  2. Lasers and filters
  3. Avoid overlaps
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33
Q

What are the applications of flow cytometry?

A
  1. Immunophenotyping
  2. Apoptosis
  3. Cell cycle
  4. Cell proliferation
  5. Counting
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34
Q

What kind of data is collected from flow cytometry?

A

Forward Scatter

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35
Q

Advantages of fluorescence microscopy

A
  1. Live cell imaging
  2. High contrast and specificity
  3. Quantative
  4. When stored under proper conditions are detectable even after months
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36
Q

What is photobleaching?

A

Due to the high excitation light molecules aren’t able to emit light again

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37
Q

What are the applications of fluorescence microscopy?

A
  1. Multiple stain
  2. Co-localization
  3. In vivo analysis
  4. Quantification
38
Q

What are the epi-fluorescence microscopy advantages?

A
  1. Fast
  2. Simple
  3. Sensitive
39
Q

What are the epi-fluorescence disadvantages?

A
  1. Doesn’t do optical sectioning
  2. Best with thin samples
  3. Out of focus blur
40
Q

Where can epi-fluorescence by applied?

A

Live cell imaging

41
Q

What are the advantages of confocal microscopy?

A
  1. Shallow depth
  2. Blur elimination
  3. Optical sectioning
  4. Better resolution
42
Q

What are the disadvantages of confocal microscopy?

A
  1. Slow
  2. High phototoxicity
  3. Less signal
43
Q

Where can confocal microscopy be applied?

A

3D reconstruction

44
Q

What is the difference between confocal and epi in terms of light?

A

Confocal - lasers
Epi- LED

45
Q

What are the advantages of spinning disk microscopy?

A
  1. Fast acquisition
  2. Very low phototoxicity
  3. Optical sectioning
  4. Higher resolution in terms of 3D, less in terms of 2D
  5. The faster the disk goes the faster we get an image
46
Q

What are the disadvantages of spinning disk microscopy?

A
  1. Pinholes are optimized to one objective
  2. Lower resolution than confocal
  3. Low light transmission
47
Q

How must the samples be for lightsheet microscopy?

A

Transparent and can be big samples

48
Q

What is resolution?

A

Minimal distance between two points

49
Q

What are the different sample preparation methods for electron microscopy?

A
  1. Chemical fixation
  2. Cryofixation
  3. Mounting
  4. Dehydration
  5. Embedding
  6. Sectioning
  7. Staining
50
Q

If we want to see the outside of a tissue which electron microscopy technique do we use?

A

SEM ( 3D )

51
Q

If we want to see the inside of a tissue which electron microscopy technique do we use?

A

TEM ( 2D )

52
Q

What is sanger sequencing?

A

Ability to sequence nucleic acids

53
Q

What is epigenetics?

A

Study how our behaviours and the environment affect our genes function

54
Q

What is clustering?

A

Dividing the unlabeled data into different clusters

55
Q

What is a gene set?

A

Join certain biological pathways together under a certain condition

56
Q

What is dimension reduction?

A

Remove redundancy from correlated variables (signal-to-noise ratio)

57
Q

What do we use to measure gene expression and detect specific DNA sequences

A

Microarrays

58
Q

What are point mutations?

A
  1. Single nucleotide changes that result in silent amino acid substitutions ( missense mutations)
  2. Premature codon stops ( nonsense mutations )
  3. Splice site alterations
59
Q

What is proteomics?

A

Large scale characterization of the entire protein complement of a cell line, tissue or organism, and see where proteins are located

60
Q

What are the applications of mass spectometry based proteomics?

A
  1. Biomarker discovery
  2. Systems biology
  3. Personalised medicine and drug development
61
Q

What type of samples can we analyse with mass spectrometry?

A
  1. 2D cell cultures
  2. 3D cell cultures
  3. Biofluids
  4. Tissue
62
Q

What is mass spectrometry?

A

Measures the m/z ratio of ionised molecules, used for quantification and structural characterisation of molecules

63
Q

What is electrospray ionisation?

A

Technique used for the formation of iones, spectra with various peaks

64
Q

What are the 3 types of proteomics?

A
  1. Bottom-up
  2. Middle-down
  3. Top- down
65
Q

How can we confirm bottom-up proteomics results?

A
  1. Western blots
  2. Immunoprecipitation
66
Q

What are the applications of proteomics?

A
  1. Identifying expression profiles in different biological processes
  2. Diagnosing diseases
  3. Biomarkers
  4. Studying protein interaction
67
Q

What is an extracellular vesicle ( EV )?

A

Bilipid container secreted by most cells from the endosomal pathways

68
Q

How can we isolate extracellular vesicles?

A
  1. Ultracentrifugation
  2. Ultrafiltration
  3. SDS page
  4. Size exclusion chromatography
  5. Density gradient
  6. Immunoprecipitation
  7. Immunoaffinity
  8. Microfluidics
69
Q

Why should we use in vitro ( cell models) instead of in vivo ( animal models)?

A
  1. Low cost
  2. More rapid
  3. Less complex ( easier to obtain detail)
70
Q

Why are the eye and retina good for gene therapy?

A
  1. BRB
  2. Contained organ
  3. Monitored non invasively
  4. Small amount of therapy needed
  5. Variety of cell types
  6. Post mitotic cells
  7. All mutations are identified
71
Q

What are the advantages of using drosophila?

A
  1. Rapid life cycle
  2. Whole genome scale
  3. Less genetic redundancy
  4. Inexpensive
72
Q

What are the disadvantages of using drosophila?

A
  1. Biological processes only within vertebrate lineage
  2. Physiological differences
  3. When homologues are not found
73
Q

What are the advantages of using C. Elegans?

A
  1. Simple
  2. Small
  3. Easy and inexpensive to grow
  4. Non pathogenic
  5. Reproduce quickly
  6. Transparent
  7. Powerful genetics
  8. Described anatomy
  9. Sequenced genome
  10. Easy for RNAi and CRISPR
74
Q

How can we study C. Elegans function?

A
  1. Forward and reverse genetics
  2. PCR phenotyping
75
Q

What are the functions of post-translational modifications?

A
  1. Protein folding
  2. Protein stability
  3. Exocytosis and endocytosis
  4. Ligand biding
  5. Gene expression
  6. Cell division
  7. Apoptosis
76
Q

How can we purify proteins?

A
  1. SDS PAGE
  2. Purification optimization
  3. Cell disruption
  4. Fractionation
77
Q

What are the advantages of using zebrafish as a model?

A
  1. Vertebrate
  2. Short generation
  3. External development ( easy to follow drugs )
  4. Transparent
  5. Easy genetic manipulation
  6. Sequenced genome
  7. Close to humans
  8. Models diseases
  9. Regenerative capacity
78
Q

What are the disadvantages of zebrafish as a model?

A
  1. Non mammalian
  2. In vivo hard on adults
  3. Partial genome duplication
  4. Lack of antibodies for protein studies
79
Q

What are the applications of C. Elegans as a model?

A
  1. Genetic screens
  2. Gene knockdowns
  3. Transgenic models
  4. Gene editing
  5. Developmental biology
  6. Chemical and behavioural screens
  7. Cancer xenografts
80
Q

Why are miced more used than rats?

A
  1. Smaller
  2. Cheaper
  3. Easier to genetically modify
  4. Have to go less deeper

Rats are more used for behavioural tests

81
Q

What is pharmodynamics?

A

Study of drug mechanism that produce biochemical or physiological changes in the body

82
Q

What is pharmacokinetics?

A

The effect of the body on the drug, how they interact

83
Q

What does tracrRNA do?

A

Helps recruit the RNAse III and Cas9 enzymes, which together separate the individual crRNAs, serves as a guide forming sgRNA

84
Q

Cas9 can only bind when next to the sgRNA is a PAM sequence

A

True

85
Q

What are the applications of gene editing?

A
  1. knockout
  2. HDR
  3. Base editing without double strand breaks
  4. Prime editing
  5. CRISPRi
  6. CRISPRa
  7. RNA targeting
86
Q

What is a matrigel?

A
  1. Used to prepare human tumor xenografts in rodents for drug discovery
  2. Used for 2D and 3D cell cultures
  3. Resembles membrane composition
  4. Protein mixture secreted by EHS mouse sarcoma cells
87
Q

How can organoids be used?

A
  1. Recapitulating and maintaning histology
  2. Drug response predictability
  3. Improve drug development process
  4. Reduce the number of animals used
  5. hiPSC technology coupled with CRISPR technology to study pathologies
88
Q

What are the microphysiological systems applications?

A
  1. Study organ level responses
  2. Toxicological
  3. Drug discovery
  4. Disease modeling
  5. Understanding human biology
89
Q

What are examples of microphysiological systems?

A
  1. Organ-on-a-chip
    - better transition of compounds from preclinical to clinical phase
    - increase in predictivity
    - safer
    - faster
    - economical drug development
90
Q

What are the microphysiological systems advantages?

A
  1. Better mimic of human physiology
  2. Real time monitoring
91
Q

What are the disadvantages of microphysiological systems?

A
  1. Cost
  2. Limited complexity
  3. Limited sample size
  4. Time and labor

Advanced Research Methods (1 decks)

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