Methods Flashcards
positive control (2)
- group that receives treatment with a known results
- indicate that the procedure is optimized and working correctly
negative control (2)
- group that is treated the same as all other groups, but is expected to show no change during the treatment
- indicate whether the procedure is creating false positives
gain of function (2)
- genetically altering an organism to have some enhanced function
- used to test if something is sufficient to trigger a phenotype
it is thought that virus A is infecting humans because it binds to surface receptor A, how could we test our hypothesis with a gain of function approach?
- alter mice cells to express surface receptor A and see if virus A is able to infect the mouse
loss of function (2)
- genetically alter organism to lack a function that the wild-type normally has
- used to test if something is necessary for a phenotype to occur
it is thought that virus A is infecting humans because it binds to surface receptor A, how could we test our hypothesis with a loss of function approach?
- alter human cells to lose expression of surface receptor A and see if virus A is still able to infect these cells
full-body knockout mice (3)
- completely deficient for targeted gene
- genes have may roles, so it is difficult to observe the cause of the resulting phenotype
- knockouts can be embryologically lethal
full-body knockout mice nomenclature
- geneX^-/-
Cre-loxP system steps (2)
- gene to be targeted out is flanked with palindromic loxP sequences
- cre recombinase activity will remove sequences flanked by loxP
Cre-loxP nomenclature
- geneX^fl/fl or gene-promoter^Cre GeneX^fl/fl
how can Cre-loxP be used to make knockouts specific to certain cell types (2)
- insert Cre into genomes downstream of a specific cell marker promoter
- only cells that express that specific marker will also express Cre in their cells
how can Cre-loxP be used to induce specific expression of other genes
- insert floxed stop codon downstream of a promoter, but upstream of the coding sequence so that the gene will only be expressed when Cre activity remove the stop codon
- Cre reporter strain used to assess specificity of Cre activity
Cre-ER system (3)
- temporal control of gene knockouts
- attachment of a modified estrogen receptor (ER) to Cre allows use to use drug to induce Cre activity
- Cre-ER is localized in the cytoplasm and can’t access loxP sites
DTR system
- diptheria toxin receptor system is used to knockout specific cell types
DTR
- diptheria toxin is a potent toxin which requires DTR on cell surfaces to work
how does the DTR system work in mice (2)
- wildtype mice do not express DTR, so DT has no effect on them
- we can introduce the DTR gene in specific cell types ad then knock these cell types out by administering DT
in vitro
- the study of microorganisms, cellular responses, and other molecules outside of their normal biological context
which common techniques are done in vitro (8)
- reporter gene assays
- IF microscopy
- ELISA
- SDS-PAGE
- Western Blot
- Immunoprecipitation
- FACS
- scRNA-Seq
reporter genes (2)
- reveal when a gene is being expressed
- reporter gene sequences can be inserted downstream of the gene you want to measure expression of
reporter gene: GFP
- can be physically linked to proteins of interest to track their cellular location
small interfering (si)RNA transfection
- what it is
- process (3)
- siRNA reflects a LOF approach; mRNA is transcribed from the DNA, but it cannot be translated into a protein
- siRNA is a dsRNA complementary to a target mRNA
- dicer protein complex processes siRNA into a ssRNA guide, which is then bound by RISC (RNA induced silencing complex)
- recognition of complementary mRNA by guide RNA results in RISC cleavage of mRNA, preventing translation of targeted mRNA
characteristics of siRNA transfection (4)
- fast and simple to accomplish
- extremely specific knockdown of target
- not a total knockout, but useful for examining dose effects
- very difficult to do in vivo
how is the magnitude of siRNA transfection measured
- must use western blot or ELISA
siRNA transfection: postitive control (2)
- un-transfected cells should be used to see if transfection influences cell behaviour
- siRNAs known to achieve high levels of knockdown, typically for a constitutively expressed protein