Techniques Flashcards
The Central Dogma
Replication, transcription, and translation
Next generation sequencing steps
Fragmentation into genes. Tagging to help sequence and help with amplification. Amplification to get many reads. And sequencing using fluorescent tags that bind to genes.
Why would we want to sequence RNA?
Measure gene expression
Bulk RNA-seq
Measures the average gene expression across a population of cells
Single-cell RNA-seq
Measures gene expression in individual cells
CRISPR
DNA sequences found in prokaryotic organisms — defense against viral infection
Cas
Enzyme that cleaves DNA
How can CRISPR be used
- Edit genes (insertion, deletion, knockout)
- Modify transcription
- Incorporate fluorescence to visualize structure of genom
scRNA Seq
Isolate single cells and tag the transcripts inside of them, involves conversion to cDNA
Guide RNA
- a crRNA contains a nucleotide sequence complementary to the target DNA called spacer
- a tracer RNA, a binding scaffhold for Cas nuclease
Intracellular electrode recording
A method in which a sharp
pipette is inserted into the cell to measure intracellular voltage relative to the “ground” outside the cell
Patch-clamp recording
A method that lets us measure the current flowing through a single ion channel or the entire cell. Variations of this method allow us to test the effect of different extracelular and intracelular conditions.
Extracellular electrode recording
A method in which an electrode inserted into living tissue measures electrical activity from neighboring neurons.
Multichannel extracellular recording
Measures electrical activity from a population of cells
Electrocorticography
Measures electrical activity from the cortical surface
Electroencephalography
(EEG)
A method that allows recording from the scalp surface
Computerized tomography (CT) or computerized axial tomography (CAT):
A technique that uses computers and X-rays to produce images inside the body
Positron emission tomography
Nuclear imaging technique that generates a 3d functional representation of the brain
Magnetic resonance imaging (MRI) and functional MRI (fMRI):
Use strong magnetic fields and radio waves to analyze structural and functional differences within the brain
Functional neuroimaging
Non-invasive techniques measure relative metabolic activity across different regions of the brain as a proxy for neuronal activity
Hemodynamic response
Active delivery of blood to active neurons
The blood oxygen leveldependent (BOLD) effect
oxygenated blood has a much stronger magnetic resonance signal than deoxygenated blood
- Diffusion spectrum imaging (DSI)
An MRI technique that measures the diffusion of water within neurons to identify neural pathways
Light microscopes
These microscopes use light to illuminate objects of interest. They have a resolution of 0.25 to 0.3 micrometers. They can observe live specimens and depict color.
Electron microscopes
These microscopes use electron beams to illuminate objects of interest. They have a resolution of 0.001 micrometers or 1 nanometer. This method cannot depict color and the specimen must be dead.
Correlated Light and Electron Microscopy (CLEM)
Light microscopes are used to observe synaptic activity in vivo. Then, electron microscopy elucidated these results with finer, structural details.
Expansion Microscopy (ExM)
A polymer system expands biological structures to aid in their identification
CLARITY
The transformation of intact tissue into a nanoporous hydrogel hybredized form which is structurally intact but macromolecule permeable. Lipids are removed, allowing for clearer imaging
