Activity 2: Nucleic Acid Extraction

Question 1

matsches genomic data with transcriptomics

Answer 1

expression profiling

Question 2

higly dependent on quantity and quality of extracted nucleic acids

Answer 2

downstream application

Question 3

DNA hybridization procedure

Answer 3

southern blot

Question 4

RNA hybridization procedure

Answer 4

northern blot

Question 5

protein hybridization

Answer 5

western blot

Question 6

short sequences are (amplified/hybridized)

Answer 6

amplify

Question 7

for unculturable sources of DNA

Answer 7

amplify withou reproduction

Question 8

for long sequences

Answer 8

hybridization

Question 9

gold standard of amplicon characterization

Answer 9

sequence analysis

Question 10

Specimen type: MERS-COV

Answer 10

upper RT
NP swab
OP swab
etc

Question 11

Specimen type: Influenza virus

Answer 11

Upper RT
NP swab
OP swab
sputum

Question 12

Specimen type: Ebola virus

Answer 12

blood borne
serum yellow top

Question 13

Specimen type: Zika virus

Answer 13

nervous system

serum yellow top
CSF
urine
amniotic fluid
salive

Question 14

Specimen type: malaria

Answer 14

blood borne
EDTA whole jlood
dried blood spot

Question 15

Specimen type: varicella voster

Answer 15

chicken pox (cutaneous lymphatic)
tissues
vesicular fluid
crust from lesions
shingles (nervous system)
CSF

Question 16

Specimen type: CMV

Answer 16

blood borne
blood
congenital
saliva
urine (confirmation)

Question 17

Specimen type: EBV

Answer 17

bloodborne
blood
CSF

Question 18

HOV, HCV HBV

Answer 18

whole blood EDTA

Question 19

N. gonorrhoea
C. trachomatis

Answer 19

urine
endocervical swab
urethral swab
oral/ pharyngeal swab
rectal swab

Question 20

main consideration in specimen handling and processing

Answer 20

contamination

Question 21

contamination of jucleic acids reasult into

Answer 21

FP

Question 22

contamination of nucleases cause

Answer 22

FN

Question 23

when to collect sample

Answer 23

within 3-5 of onset of symptoms

Question 24

likelihood ofbdiscovering viruses and bacteria diminishes in

Answer 24

> 72 hrs after onset

Question 25

collection should be done no later than

Answer 25

7 days after onset

Question 26

breaking open cellsnto release contents of cells with homogenizers or strong acids and bases

Answer 26

crude lysis

Question 27

separates hydrophilic nucleic acids from hydrophobic lipids and proteins

Answer 27

liquid phase organic extraction

Question 28

uses guanidium salts or isothiocyanate salt to precipitate out proteins

Answer 28

liquid phase inorganic extraction

Question 29

postively charged silica membrane adsorbs negatively charged DNA under high salt conditions

Answer 29

solid phase extraction

Question 30

cell lysed with chaotropic reagent

Answer 30

lysis

Question 31

examples of chaotropic reagents

Answer 31

SDS
SLS

Question 32

nucleic acids bind to membrane

Answer 32

binding

Question 33

unwanted molecules filtered out while nucleic acids remain bound

Answer 33

washing

Question 34

nucleic acid released from silica membrane to new container

Answer 34

elution

Question 35

4 general steps in nucleic acid extraction

Answer 35

lysis
binding
washing
eluting

Question 36

criteria for good nucleic acid protocol

Answer 36

efficient extraction
sufficient downstream application
remove contaminanthighy pure nucleic acid

Question 37

enumerate bacterial DNA extraction protocol

Answer 37

1. 1 min 13000 g 1 mL bacterial suspension
2. 100 uL EL buffer, mix, 20 mins 37°
3. 100 uL RS buffer, 10 uL PK, 20 mins 56°
4. 200 GA buffer, mix, 1 min 13000 g
5. 400 BA, mix, 1 min 13000 g
6. 500 Gbinding 10,000 g
7. 500 washing buffer 10,000 g x 2
8. spin dry 1 min 10,000 g
9. 100 uL elution buffer
10. RT 1 min 10,000 g