ELEC473-2019-midterm2

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ELEC 473, 2019, midterm 2 pg. 1/11 THE UNIVERSITY OF BRITISH COLUMBIA Department of Electrical and Computer Engineering ELEC 473 – Bio-MicroElectroMechanical Systems – Midterm Exam 2 Time: 80 minutes. This examination consists of 11 pages. Please check that you have a complete copy. You may use both sides of each sheet if needed, but make a note on the front if you use the back. Question # MAX GRADE 1 16 2 20 3 10 4 10 5 14 6 10 TOTAL 80 IMPORTANT NOTE: The announcement “stop writing” will be made at the end of the examination. Anyone writing after this announcement will receive a score of 0. No exceptions, no excuses. Students are permitted to have a two-sided sheet of hand-written notes as well as a calculator. 1. Each examination candidate must be prepared to produce, upon the request of the invigilator or examiner , his or her UBCcard for identification. 2. Examination candidates are not permitted to ask questions of the examiners or invigilators , except in cases of supposed errors or ambiguities in examination questions, illegible or missing material, or the like. 3. No examination candidate shall be permitted to enter the examination room after the expiration of one-half hour from the scheduled starting time, or to leave during the first half hour of the examination . Should the examination run forty-five (45) minutes or less, no examination candidate shall be permitted to enter the examination room once the examination has begun. 4. Examination candidates must conduct themselves honestly and in accordance with established rules for a given examination, which will be articulated by the examiner or invigilator prior to the examination commencing. Should dishonest behaviour be observed by the examiner(s) or invigilator(s) , pleas of accident or forgetfulness shall not be received. 5. Examination candidates suspected of any of the following, or any other similar practices, may be immediately dismissed from the examination by the examiner/invigilator, and may be subject to disciplinary action: i. speaking or communicating with other examination candidates , unless otherwise authorized; ii. purposely exposing written papers to the view of other examination candidates or imaging devices; iii. purposely viewing the written papers of other examination candidates ; iv. using or having visible at the place of writing any books, papers or other memory aid devices other than those authorized by the examiner(s); and, v. using or operating electronic devices including but not limited to telephones, calculators, computers, or similar devices other than those authorized by the examiner(s) —(electronic devices other than those authorized by the examiner(s) must be completely powered down if present at the place of writing). 6. Examination candidates must not destroy or damage any examination material, must hand in all examination papers, and must not take any examination material from the examination room without permission of the examiner or invigilator. 7. Notwithstanding the above, for any mode of examination that does not fall into the traditional, paper-based method, examination candidates shall adhere to any special rules for conduct as established and articulated by the examiner . 8. Examination candidates must follow any additional examination rules or directions communicated by the examiner(s) or invigilator(s). Surname First name Student Number

Name: ELEC 473, 2019, midterm 2 pg. 2/11 1. (16 Points) Match the words and descriptions which best fit. ( Not all descriptions are used. ) _____ A b sorbance A Compound of carbon and hydrogen that has only single covalent bonds. _____ A d sorption B Adhesion of a chemical species (atoms, ions, or molecules) onto a surface through non-specific interactions. _____ Conformation C A process usually consisting of 20 to 35 thermal cycles for making multiple copies of DNA. _____ Denaturation D A process for making multiple copies of DNA which does not require thermocycling. _____ Dissociation Constant E For components A and B and the binding equilibrium A + B ⇌ AB, it is given by [A][B]/[AB] _____ Enzyme F For components A and B and a binding equilibrium A + B ⇌ AB, it is given by [AB]/[A][B] _____ Fluorescence G A short linear or branched chain of covalently linked sugars. _____ Integrin H A linear polymer of amino acids linked together by peptide bonds in a specific sequence. _____ Ion Channel I Fluid elements follow streamlines parallel to the main direction of the flow. _____ Isoelectric point J Flow is dominated by inertial forces and is characterized by random eddies. _____ Laminar flow K The spatial arrangement of atoms in three dimensions in a macromolecule such as a protein or nucleic acid. _____ Ligand L A protein that catalyzes a specific chemical reaction (e.g., DNA polymerase) _____ Pe M An optical method for measuring the refractive index of very thin layers of material adsorbed on a metal. _____ Polymerase chain reaction N An optical method where the transmission of light through a sample is measured. _____ Polypeptide O An optical method where the number of photons emitted is measured. _____ Surface Plasmon Resonance P Transmembrane protein involved in the adhesion of cells to the extracellular matrix. Q Transmembrane protein that forms a channel across the lipid bilayer through which specific ions can diffuse down their electrochemical gradients. R Dramatic change in conformation of a protein or nucleic acid caused by heating or by exposure to chemicals and usually resulting in the loss of biological function. S The process by which proteins or complementary strands of nucleic acids re-form their native conformations. T The pH at which a charged molecule in solution has no net electric charge. U The pH at which an acid is half dissociated. W Dimensionless number: ratio of convective effects to diffusion effects. X Dimensionless number: ratio of convective effects to viscous effects. Y Dimensionless number: ratio of momentum diffusivity to thermal diffusivity. Z Dimensionless number: ratio of gravity to surface tension effects. Ω Any molecule that binds to a specific site on a protein or other molecule.

Name: ELEC 473, 2019, midterm 2 pg. 3/11 2. (20 Points) Multiple choice: circle all that apply . 1. 2D-PAGE is an example of a multidimensional separation. (a) The two separation methods in 2D PAGE comprise isoelectric focusing and electrophoresis. (b) 2D PAGE separates molecules based on size and refractive index. (c) SDS is often introduced as a denaturing agent in the gel electrophoresis. In this case, the two separation methods in 2D PAGE resolve proteins according to isoelectric point and size. (d) Electrophoresis separates proteins on the basis of charge-to-mass differences (electrophoretic mobility). (e) IEF-focused protein bands continue migrating after the bands have reached their respective isoelectric points. 2. Nanoparticles have been used to deliver drugs because: (a) the nanoparticles are retained in tumors due to the enhanced permeability and retention effect. (b) poorly soluble drugs can be loaded into the liposomal core to improve the encapsulation efficiency. (c) liposomes can mask the taste of a bitter drug by shielding it from the taste buds. (d) all liposomal formulations of hydrophobic drugs always give improvement in pharmacokinetics compared to the free drug. (e) liposomal encapsulation can reduce toxicity of the drug. 3. Microbiota include bacteria, viruses, and fungi. (a) The microenvironment (pH, O 2 level) is constant along the entire length of the gut. Thus, there is no need to study the microbiota within its spatial context. (b) Changes our microbiota can be caused by diet or antibiotics, and this can lead to disease. (c) In the gut, mucus thickness decreases with low fiber diet; this can be observed by imaging the host-microbiota interface. (d) Microfluidic systems cannot be used to study single bacteria, because it is difficult to create micron-sized microfluidic chambers. (e) Microfluidic systems can be used to study single bacteria, because partitioning a sample can lead to enrichment effects and reduction of interfering compounds. 4. This figure shows two ways to image the gut microbiota. (a) Immunostaining can involve the use of fluorescently labelled antibodies. (b) Fluorescence in situ hybridization is based on the differences in the exponential decay rate of the fluorescence from a fluorescent sample. (c) Fluorescence in situ hybridization involves fluorescent probes that bind only to a complementary a nucleic acid sequence. (d) It would always be better to use fluorescent proteins such as GFP, because all bacterial species in the gut have been genetically modified and cultured. (e) It would be better to use fluorescent proteins such as GFP to see microbiota throughout the entire gut.

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Name: ELEC 473, 2019, midterm 2 pg. 4/11 5. This is an example of a paper-based microfluidic assay. (a) An assay is a procedure to quantitatively measure the presence or amount of an analyte. (b) The hydrophobic photoresist serves to confine the flow of the sample as it moves. (c) The photoresist can be patterned using standard photolithography techniques. (d) A fluid sample moves through the hydrophilic paper by gravity. (e) This assay would require two separate samples in order to determine both the glucose level and the protein level. 6. This image shows rat cortical neurons growing on a grid pattern. (a) Dissociated cortical neurons from rat embryos were seeded onto the patterned substrates. (b) The brain tissue was sliced, the slice was laid down onto the substrate, and these cortical neurons were the ones that migrated out and adhered to the substrate. (c) The grid pattern was created by using microcontact printing to stamp PEG onto the lines and nodes. (d) The grid pattern was created by using microcontact printing to stamp a mixture of extracellular matrix proteins onto the lines and nodes. (e) PEG-coated surfaces are cell-repellent. 7. This image shows patch clamp recording from a patterned network of rat cortical neurons. Neuron C1 was stimulated experimentally to fire an action potential. (a) Presynaptic signals are recorded in neuron C2 and C3 – you can tell because of the amplitudes of the signals. (b) Postsynaptic signals are recorded in neuron C2 and neuron C3 – you can tell because of the characteristic time delay of several milliseconds. (c) If you applied a sodium channel blocker, you would likely measure no activity in neurons C2 and C3. (d) If you applied a sodium channel blocker, you would likely measure increased activity in neurons C2 and C3. (e) Signal can be transmitted from one cell to the next by the release of neurotransmitter into the synaptic cleft between them.

Name: ELEC 473, 2019, midterm 2 pg. 5/11 8. Stimulation from excitatory synaptic activities generates electrical signals within the neuron. (a) At position A in the figure, neurotransmitters diffuse through the synapse and open ligand-gated ion channels in the dendrite of the post-synaptic neuron. (b) Position B in the figure shows local depolarization of the membrane, and thus an excitatory signal. (c) Position B in the figure shows local hyperpolarization of the membrane, and thus an inhibitory signal. (d) Action potentials are initiated at position C because the threshold is low at that position. (e) Position D shows an action potential: the membrane potential becomes positive within about a millisecond before turning negative again. 9. You are using a bare glass capillary to separate a mixture of molecules. Capillary electrophoresis of histones (pI = 8.5, r = 3.5 nm) and myoglobin (pI = 5.5, r = 1.52 nm) under physiological conditions (pH = 7.0) results in: (a) electrophoretic velocity v EP, histone > 0 (b) electrophoretic velocity v EP, myoglobin > 0 (c) both proteins migrate to the anode (+). (d) both proteins migrate to the cathode (-). (e) fast separation because flow through the capillary is driven by pressure. 10. Capacitive Micromachined Ultrasonic Transducer (CMUT) arrays: (a) feature piezoelectric transducers as a key component. (b) have tiny membranes actuated by electrical forces to vibrate and emit acoustic waves. (c) have been made from conventional microfabrication materials including silicon, silicon nitride, and silicon dioxide. (d) can be fabricated using maskless lithography and photosensitive polymers. (e) can be used in conformal ultrasound imaging wherein CMUT arrays are fabricated on flexible substrates.

Name: ELEC 473, 2019, midterm 2 pg. 6/11 3. (10 Points) Protein secretion monitoring. This figure shows integration of a high-density antibody barcode array chip and a sub-nanoliter microchamber array chip for high-throughput multiplexed protein secretion assay at the single cell level. When the PDMS microchambers are sealed against the glass slide, the antibody barcodes are perpendicular to the length of the microchambers. i) (1 point) The high-density antibody barcode array is fabricated using a microchannel-guided flow patterning technique: individual antibody solutions were injected into microchannels and flowed through the microfluidic channels. How do the antibodies attach to the glass surface? ii) (2 points) Single cells are trapped in the microwell array and the assembly is allowed to incubate for 24 hours to allow for cell secretion. The antibody barcode glass slide is then removed. Biotinylated detection antibodies are pipetted onto the glass slide and incubated; fluorescent dye- labeled streptavidin is added. Biotin and streptavidin have a dissociation constant K d = 10 -14 M. Does this represent a strong binding interaction or a weak binding interaction? Why? iii) (2 points) These curves were generated for 18 of the proteins assayed in these single cell microchips. Why would these curves have different shapes for the different proteins?

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Name: ELEC 473, 2019, midterm 2 pg. 7/11 iv) (2 points) Each chamber has a volume of approximately 0.5 nL. This platform has the sensitivity to detect proteins secreted from a single cell (typical copy number ∼ 10 2 to 10 5 ). Why? v) (2 points) During the flow patterning of antibody barcodes, FITC-BSA is always flowed in channel 1 to form a continuous line of fluorescence signal. What is the purpose of this step? vi) (1 point) And, why is it possible to use only one fluorescent dye for protein quantification, when the goal is to examine secretion of ~ 20 different proteins?

Name: ELEC 473, 2019, midterm 2 pg. 8/11 4. (10 Points) ELISA. For an ELISA enzymatic reaction occuring for 100 seconds, the surface enzyme concentration is 1 fmol/cm 2 and the enzyme turnover rate is 1000 substrate molecules per second. The substrate is converted to a fluorescent molecule. vii) (4 points) calculate the product concentration in the following two cases: • a standard microwell (surface area = 1 cm 2 , volume = 100 μL) • a microchannel (surface area = 0.050 cm 2 , volume = 50 nL) viii) (2 points) In question (i) above, would the standard microwell or the microchannel give higher sensitivity, and why ? ix) (4 points) Sandwich ELISA assay. Put the following steps in order from 2 to 5. Next to each step, describe briefly why steps 2 to 5 are needed . 1 Immobilization of capture antibody (1 st antibody). Binding of detection antibody (2 nd antibody). Blocking buffer. Signal generation: production of colorimetric or fluorescent product. Target binding.

Name: ELEC 473, 2019, midterm 2 pg. 9/11 5. (14 points) Planar microelectrode array (MEA). i) (2 points) When cultured on planar MEAs to form neural networks, some neurons exhibit spontaneous action potentials. Why would adding tetrodotoxin, a sodium channel blocker, suppress spontaneous activity? Consider the patch of membrane described by this model: ii) (4 points) If the resting transmembrane potential is V rest = -64 mV, what is the sodium Nernst potential? iii) (4 points) Imagine that the cell is spherical with a diameter of 10 µm. What is the steady-state transmembrane potential when a current I inj = 14 pA is injected into the intracellular space?

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Name: ELEC 473, 2019, midterm 2 pg. 10/11 iv) (4 points) Your lab mate wants to improve the recording quality from the MEA. Why would you recommend your lab mate use something similar to this peptide-terminated molecule illustrated here? How would it work?

Name: ELEC 473, 2019, midterm 2 pg. 11/11 6) (10 points) Herringbone structures A. Circulating tumor cells are suspended in a solution, and captured in this microfluidic chip as the solution is flowed through. B. This device presents a method for mixing streams of pressure-driven flows. i) (2 points) In Figure A above, the herringbone channels are coated with antibodies against Epithelial Cell Adhesion Molecule (EpCAM). In this scenario ( circle all that apply ): a) In order to capture tumor cells, the tumor cells should express EpCAM intracellularly. b) In order to capture tumor cells, the tumor cells should express EpCAM on their cell surfaces. c) By creating the micro vortices, the herringbone structures increase the number of cell-surface interactions in the antibody-coated device compared to a flat-walled device. d) By creating the micro vortices, the herringbone structures should decrease the tumor cell capture efficiency compared to a flat-walled device. ii) (2 points) In Figure B above ( circle all that apply ): a) The herringbones change the diffusion coefficient and thus improve mixing between the fluids. b) The herringbones stretch and fold volumes of fluid over the cross section of the channel, thus improving mixing by viscous effects. c) The herringbones stretch and fold volumes of fluid over the cross section of the channel, thus improving mixing by diffusion. d) This device requires variable-frequency off-chip pumps to alternately push the fluids to achieve mixing in the chip. iii) (4 points) In the herringbone chamber, distance along the channel that is required for mixing to occur grows logarithmically with the Peclet number (i.e. L ~ ln( Pe ) ). In the flat chamber, how does the distance along the channel that is required for mixing to occur depend on Pe? iv) (2 points) How could you create the herringbone microfluidic channel through soft lithography, if you were limited to making only 1 mold master?

ELEC473-2019-midterm2

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