Lectures 16-27 (7 Questions)

Topics

o Electrodes

o Pressure measurements

o Flow measurements

o Respiratory measurements

o Chemical biosensors

o Lab instruments

explain and connect concepts together

draw diagrams
use equations (given on exam)

Lectures 29-39 (7 questions)

Topics

o Microscopy: understand the 5 contrasting techniques well, how they work,

characteristics

o Fluorescence Microscopy: how it works, characteristics, confocal

microscopy

o Non-OPT microscopy: understand transmission vs. scanning microscopy,

differences, how it works, characteristics

o Medical Imaging: X-ray, MRI, PEC/SPECT

o Ultrasound: how it works, characteristics,

o Neuroprosthesis: retinal, Dobelle Cortical Implant, neuroprothesis, target

innervation

o Neuromodulation: microstimulation, deep-brain stimulation, transcranial

magnetic stimulation, mangeto-thermal stimulation

o Gene Sequencing: know different types and approaches, especially the

well-known ones, how they work, characteristics, etc, Pacific Biosciences,
Sanger sequencing, Oxford Nanopore, Illumina
 Multiple choice

Short answer

Matching

Microscopy:
o Bright field
Pros:
Simplicity of setup
Living cells can be viewed
Stains can be seen well
Cons:
Very low contrast
Low apparent optical resolution

o Dark field: Exclude the unscattered beam, making the field around the
specimen dark
Pros:
Suited for live, unstained samples
Cons:
Low light levels seen in image. If light intensity is turned
up to resolve this it can damage the specimen.
o Phase Contrast: Converts phase shifts in light passing through a
transparent specimen to brightness changes in the image

Pros:
Reveals many cellular structures while specimen is still
alive
High contrast
Cons:
Not ideal for thick samples
Phase artifacts may occur (distortion around rim)
o Polarization contrast:

Pros:
Does not contain artifacts that phase contrast can create.
Can produce quasi 3D images
Cons:
Not suitable for thick samples
o Fluorescence Microscopy:

Pros:
High contrast staining
Immunofluorescence
Genetic modifying allows structures to be stained
Cons:
Not permanent staining.
Photobleaching
Treating cells with fluorescently stained molecules can
damage cells and produce artifacts.
o Confocal microscopy: Adding pinhole sized notch that only allows
images in the focal plain of the image to be viewed.

Pros
 Does not require slicing to take images along an axis.
Can be used with fluorescence microscopy
Images can be taken at multiple planes, stacked, and then
combined into a 3D image.
Can image live specimens.
Cons:
Fairly expensive
Prone to photo bleaching
Only removes out of focus light
o Transmission electron Microscopy: Electron beam is focused and
intersects sample. Transmission of beam is detected and analyzed.
Transmittance can also be analyzed to identify characteristics of
medium.

Pros:
Intracellular details can be visualized to a resolution of 0.2
nm.
Cons:
Conjugation of cells requires fixation and can damage the
sample causing artifacts.
Prep is lengthy
o SEM: Beam of electrons is sent and focused using electromagentics.
Scattered electrons (secondary electrons) hit detector. Second detector
collects backscattered electrons (come from surface and deeper
reflections).

Pros:
Good depth of field
Can be coupled with other techniques
Cons:
Need to be dehydrated, which can cause distortion and
artifacts. Thickness of material can obscure cellular
details.

Medical Imaging

X ray: Cathode and anode pair generate high energy X -rays that are filtered
so that only the correct wavelength is passed. Radiographic film is placed
below patient. Photons that pass through the patient and strike the sheet
cause a chemical reaction and darken the image. Therefore, bone and denser
tissues will appear lighter on the radiographic sheet due to the photon
attenuation.
 MRI: MRI is based upon the science of nuclear magnetic resonance (NMR).
Certain atomic nuclei can absorb and emit radio frequency energy when
placed in an external magnetic field. In clinical and research MRI, hydrogen
atoms are most-often used to generate a detectable radio-frequency signal
that is received by antennas in close proximity to the anatomy being
examined. Hydrogen atoms exist naturally in people and other biological
organisms in abundance, particularly in water and fat. For this reason, most
MRI scans essentially map the location of water and fat in the body. Pulses of
radio waves excite the nuclear spin energy transition, and magnetic field
gradients localize the signal in space. By varying the parameters of the pulse
sequence, different contrasts can be generated between tissues based on
the relaxation properties of the hydrogen atoms therein. Since its early
development in the 1970s and 1980s, MRI has proven to be a highly versatile
imaging technique. While MRI is most prominently used in diagnostic
medicine and biomedical research, it can also be used to form images of non-
living objects. MRI scans are capable of producing a variety
of chemical and physical data, in addition to detailed spatial images.
o MRI Video
o Pros:
Safe and painless
Does not use ionizing radiation
High FPS and getting faster.
3D images can be made.
o Cons:
No metal allowed
Patient must remain still for >30 mins
PET (Positron Emission Tomography): Radioactive molecules are injected
into body that conjugate to specific molecules according to what the doctor is
 looking for. Cancerous cells use a lot of sugar, and thus a fructose can be
radioactively labeled so that the cancerous cells uptake the sugar. The
particles produce positrons that interact with electrons and produce high
energy photons that are picked up by the PET machine.
o Though they cause radiation damage, the short half-lives of the
radioisotopes do not pose a large threat.
o Limited number of scans due to radiation damage
o Expensive
o Requires expensive fabrication of short lived radioisotopes.
Single Proton Emission Computer Tomography (SPECT): Nuclear
medicine that provides 3D images of the distribution of radioactive tracer
molecules that have been introduced into the patient.
o More widely used and cheaper than PET
o Longer half lives and thus longer imaging time. Also cheaper
radioisotopes
o Prone to artifacts and attenuation.
o Does not provide a quantitative measurement of blood flow unlike PET
Ultrasound: Piezoelectric crystals produce sound when electric current is
applied across it and produces current when vibrated by sound. Sound waves
are sent out, and if there is a difference in medium, then it is recognized and
the signal is transduced.

Neuroprosthesis:

Retinal Prosthesis: Located at the back of the eye.

o Epiretinal and subretinal implants
 o
Dobelle Cortical Implant:
o Electrode array is placed in the occipital lobe, and video information is
processed and sent to the array for innervations.
o Problems:
Kindling
Electrode and cabling problems
Targeted Reinnervation: A spare muscle of an amputated patient is de-
innervated then reinnervated with residual nerves of the amputated limb.
Resultant EMG signals of the targeted muscle now represent the motor
commands to the missing limb and are used to drive the prosthetic device.
o Pros:
No neural electrodes implanted in nerve, no foreign body
reactions.
Muscle as natural amplifier
Multiple EMG - multiple functions
 Intuitive control
Sensory feedback
o Cons:
Permanent paralysis of targeted muscle
Recurrence of phantom limb pain
Development of painful neuromas, a growth or tumor of nerve
tissue

Neuromodulation: Using electrical, magnetic, optical, ultrasound, and thermal

events to mdulate brain functions

Deep Brain Stimulation: Shows positive effects in movement disorders

(Parkinson's, Tremor, Dystonia, depression, OCD, Tourettes, Chronic pain,
cluster headaches)
o Four platinum electrodes are placed inside brain and 60 - 450
microsecond pulses are sent to the electrodes with voltage of 0-10.5V
and a few mA

o
Microstimulation: Very short 10-100 microsecond pulses using microscale
electrodes where each electrode affects a small group of neurons. Voltage up
to 100 V
o Drawbacks: Electrode corrosion, tissue damage, lesions
Transcranial Magnetic Stimulation: Noninvasive method in which a
pulsed AC magnetic waves generate current in the brain through inductive
coupling. There is no attenuation through skull.
 o Painless
o ~100 us pulses of 1T peaks
o

Magneto-thermal stimulation: Wireless magnetic pulses that use

nanoparticles??

Gene Sequencing:

Sanger Sequencing
 o
Illumina Sequencing
Pacific Biosciences Single Molecule Real Time Sequencing
Ion Torrent
Oxford Nanopore
o Very high error rate, but is predicted to improve and could be the
gold standard in the future.