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[0] Suner S, Fellows MR, Vargas-Irwin C, Nakata GK, Donoghue JP, Reliability of signals from a chronically implanted, silicon-based electrode array in non-human primate primary motor cortex.IEEE Trans Neural Syst Rehabil Eng 13:4, 524-41 (2005 Dec)

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ref: -0 tags: GEVI review voltage sensor date: 03-18-2020 17:43 gmt revision:22 [21] [20] [19] [18] [17] [16] [head]

Various GEVIs invented and evolved:

Ace-FRET sensors

  • PMID-26586188 Ace-mNeonGreen, an opsin-FRET sensor, might still be better in terms of SNR, but it's green.
    • Negative ΔF/F\Delta F / F with depolarization.
    • Fast enough to resolve spikes.
    • Rational design; little or no screening.
    • Ace is about six times as fast as Mac, and mNeonGreen has a ~50% higher extinction coefficient than mCitrine and nearly threefold better photostability (12)

  • PMID-31685893 A High-speed, red fluorescent voltage sensor to detect neural activity
    • Fusion of Ace2N + short linker + mScarlet, a bright (if not the brightest; highest QY) monomeric red fluorescent protein.
    • Almost as good SNR as Ace2N-mNeonGreen.
    • Also a FRET sensor; negative delta F with depolarization.
    • Ace2N-mNeon is not sensitive under two-photon illumination; presumably this is true of all eFRET sensors?
    • Ace2N drives almost no photocurrent.
    • Sought to maximize SNR: dF/F_0 X sqrt(F_0); screened 'only' 18 linkers to see what worked the best. Yet - it's better than VARNAM.
    • ~ 14% dF/F per 100mV depolarization.

Arch and Mac rhodopsin sensors

  • PMID-22120467 Optical recording of action potentials in mammalian neurons using a microbial rhodopsin Arch 2011
    • Endogenous fluorescence of the retinal (+ environment) of microbial rhodopsin protein Archaerhodopsin 3 (Arch) from Halorubrum sodomense.
    • Proton pump without proton pumping capabilities also showed voltage dependence, but slower kinetics.
      • This required one mutation, D95N.
    • Requires fairly intense illumination, as the QY of the fluorophore is low (9 x 10-4). Still, photobleaching rate was relatively low.
    • Arch is mainly used for neuronal inhibition.

  • PMID-25222271 Archaerhodopsin Variants with Enhanced Voltage Sensitive Fluorescence in Mammalian and Caenorhabditis elegans Neurons Archer1 2014
    • Capable of voltage sensing under red light, and inhibition (via proton pumping) under green light.
    • Note The high laser power used to excite Arch (above) fluorescence causes significant autofluorescence in intact tissue and limits its accessibility for widespread use.
    • Archers have 3-5x the fluorescence of WT Arch -- so, QY of ~3.6e-3. Still very dim.
    • Archer1 dF/F_0 85%; Archer2 dF/F_0 60% @ 100mV depolarization (positive sense).
    • Screened the proton pump of Gloeobacter violaceus rhodopsin; found mutations were then transferred to Arch.
      • Maybe they were planning on using the Geobacter rhodopsin, but it didn't work for some reason, so they transferred to Arch..
    • TS and ER export domains for localization.

  • PMID-24755708 Imaging neural spiking in brain tissue using FRET-opsin protein voltage sensors MacQ-mOrange and MacQ-mCitrine.
    • L. maculans (Mac) rhodopsin (faster than Arch) + FP mCitrine, FRET sensor + ER/TS.
    • Four-fold faster kinetics and 2-4x brighter than ArcLight.
      • No directed evolution to optimize sensitivity or brightness. Just kept the linker short & trimmed residues based on crystal structure.
    • ~5% delta F/F, can resolve spikes up to 10Hz.
    • Spectroscopic studies of the proton pumping photocycle in bacteriorhodopsin and Archaerhodopsin (Arch) have revealed that proton translocation through the retinal Schiff base changes chromophore absorption [24-26]
    • Used rational design to abolish the proton current (D139N and D139Q aka MacQ) ; screens to adjust the voltage sensing kinetics.
    • Still has photocurrents.
    • Seems that slice / in vivo is consistently worse than cultured neurons... in purkinje neurons, dF/F 1.2%, even though in vitro response was ~ 15% to a 100mV depolarization.
    • Imaging intensity 30mw/mm^2. (3W/cm^2)

  • PMID-24952910 All-optical electrophysiology in mammalian neurons using engineered microbial rhodopsins QuasAr1 and QuasAr1 2014
    • Directed evolution approach to improve the brightness and speed of Arch D95N.
      • Improved the fluorescence QY by 19 and 10x. (1 and 2, respectively -- Quasar2 has higher sensitivity).
    • also developed a low-intensity channelrhodopsin, Cheriff, which can be activated by blue light (lambda max = 460 nm)dim enough to not affect QuasAr.
    • They call the two of them 'Optopatch 2'.
    • Incident light intensity 1kW / cm^2 (!)

  • PMID-29483642 A robotic multidimensional directed evolution approach applied to fluorescent voltage reporters. Archon1 2018
    • Started with QuasAr2 (above), which was evolved from Arch. Intrinsic fluorescence of retinal in rhodopsin.
    • Expressed in HEK293T cells; then FACS, robotic cell picking, whole genome amplification, PCR, cloning.
    • Also evolved miRFP, deep red fluorescent protein based on bacteriophytochrome.
    • delta F/F of 80 and 20% with a 100mV depolarization.
    • We investigated the contribution of specific point mutations to changes in localization, brightness, voltage sensitivity and kinetics and found the patterns that emerged to be complex (Supplementary Table 6), with a given mutation often improving one parameter but worsening another.
    • If the original QY of Arch was 9e-4, and Quasar2 improved this by 10, and Archon1 improved this by 2.3x, then the QY of Archon1 is 0.02. Given the molar extinction coefficient is ~ 50000 for retinal, this means the brightness of the fluorescent probe is low, 1. (good fluorescent proteins and synthetic dyes have a brightness of ~90).
    • Big paper, moderate improvement.
    • SomArchon1 and SomCheriff serve as the basis of Optopatch4, e.g. All-optical electrophysiology reveals excitation, inhibition, and neuromodulation in cortical layer 1
    • Slow photobleaching, consistent with other Arch based GEVIs.

VSD - FP sensors

  • PMID-28811673 Improving a genetically encoded voltage indicator by modifying the cytoplasmic charge composition Bongwoori 2017
    • ArcLight derivative.
    • Arginine (positive charge) scanning mutagenesis of the linker region improved the signal size of the GEVI, Bongwoori, yielding fluorescent signals as high as 20% ΔF/F during the firing of action potentials.
    • Used the mutagenesis to shift the threshold for fluorescence change more negative, ~ -30mV.
    • Like ArcLight, it's slow.
    • Strong baseline shift due to the acidification of the neuron during AP firing (!)

  • Attenuation of synaptic potentials in dentritic spines
    • Found that SNR / dF / F_0 is limited by intracellular localization of the sensor.
      • This is true even though ArcLight is supposed to be in a dark state in the lower pH of intracellular organelles.. a problem worth considering.
      • Makes negative-going GEVI's more practical, as those not in the membrane are dark.

  • Fast two-photon volumetric imaging of an improved voltage indicator reveals electrical activity in deeply located neurons in the awake brain ASAP3 2018
    • Opsin-based GEVIs have been used in vivo with 1p excitation to report electrical activity of superficial neurons, but their responsivity is attenuated for 2p excitation. (!)
    • Site-directed evolution in HEK cells.
    • Expressed linear PCR products directly in the HEK cells, with no assembly / ligation required! (Saves lots of time: normally need to amplify, assemble into a plasmid, transfect, culture, measure, purify the plasimd, digest, EP PCR, etc).
    • Screened in a motorized 384-well conductive plate, electroporation electrode sequentially activates each on an upright microscope.
    • 46% improvement over ASAP2 R414Q
    • Ace2N-4aa-mNeon is not responsive under 2p illum; nor is Archon1 or Quasar2/3
    • ULOVE = AOD based fast local scanning 2-p random access scope.

  • Bright and tunable far-red chemigenetic indicators
    • GgVSD (same as ASAP above) + cp HaloTag + Si-Rhodamine JF635
    • ~ 4% dF/F_0 during APs.
    • Found one mutation, R476G in the linker between cp Halotag and S4 of the VSD, which doubled the sensitivity of HASAP.
    • Also tested a ArcLight type structure, CiVSD fused to Halotag.
      • HarcLght had negative dF/F_0 and ~ 3% change in response to APs.
    • No voltage sensitivity when the synthetic dye was largely in the zwitterionic form, eg. tetramethylrodamine.

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ref: -0 tags: VARNUM GEVI genetically encoded voltage indicators FRET Ace date: 03-18-2020 17:12 gmt revision:5 [4] [3] [2] [1] [0] [head]

PMID-30420685 Fast in-vivo voltage imaging using a red fluorescent indicator

  • Kannan M, Vasan G, Huang C, Haziza S, Li JZ, Inan H, Schnitzer MJ, Pieribone VA.
  • Other genetically encoded voltage indicators (GEVI):
    • PMID-22958819 ArcLight (Peribone also last author) ; sign of ΔF/F\Delta F / F negative, but large, 35%! Slow tho? improvement in speed
    • ASAP3 ΔF/F\Delta F / F large, τ=3ms.\tau = 3 ms.
    • PMID-26586188 Ace-mNeon FRET based, Acetabularia opsin, fast kinetics + brightness of mNeonGreen.
    • Archon1 -- fast and sensitive, found (like VARNUM) using a robotic directed evolution or direct search strategy.
  • VARNAM is based on Acetabularia (Ace) + mRuby3, also FRET based, found via high-throughput voltage screen.
  • Archaerhodopsin require 1-12 W/mm^2 of illumination, vs. 50 mw/mm^2 for GFP based probes. Lots of light!
  • Systematic optimization of voltage sensor function: both the linker region (288 mutants), which affects FRET efficiency, as well as the opsin fluorophore region (768 mutants), which affects the wavelength of absorption / emission.
  • Some intracellular clumping (which will negatively affect sensitivity), but mostly localized to the membrane.
  • Sensitivity is still imperfect -- 4% in-vivo cortical neurons, though it’s fast enough to resolve 100 Hz spiking.
  • Can resolve post-synaptic EPSCs, but < 1 % ΔF/F\Delta F/F .
  • Tested all-optical ephys using VARNAM + blueshifted channelrhodopsin, CheRiff, both sparsely, and in PV targeted transgenetic model. Both work, but this is a technique paper; no real results.
  • Tested TEMPO fiber-optic recording in freely behaving mice (ish) -- induced ketamine waves, 0.5-4Hz.
  • And odor-induced activity in flies, using split-Gal4 expression tools. So many experiments.

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ref: Suner-2005.12 tags: Suner Utah probe electrophysiology reliability chronic electrode recording longevity histology MEA date: 01-31-2013 22:27 gmt revision:7 [6] [5] [4] [3] [2] [1] [head]

PMID-16425835Reliability of signals from a chronically implanted, silicon-based electrode array in non-human primate primary motor cortex

  • claim that they have done a logitudinal development series that included 39 array implants in 18 monkeys.
  • can get reliable recordings out to 3 months (only? probably the array was forced out of the brain?)
    • however, it seems that their recording quality did not decrease dramatically over those 3 months.
  • excellent methods section.
  • also {1027}


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ref: Suner-2005.12 tags: MEA Utah reliability longevity SNR date: 01-25-2013 02:03 gmt revision:7 [6] [5] [4] [3] [2] [1] [head]

PMID-16425835[0] Reliability of signals from a chronically implanted, silicon-based electrode array

  • see {597}
  • Percutaneous connector used pressure-fitted pogo pins, as Gary was thinking of.
  • Utah array coated in parylene for this exp.
    • After implantation, array and cortex was covered in gore-tex (to prevent dura adhesion) -- they do not highlight this fact.
  • polyester insulated 25um gold wires as leads.
  • Reasonable SNR over 82, 172, 154 days.
  • One monkey had an array to 569 days -- 76 electrodes still provided good or fair waveforms.
  • ancilary (?) measure of tuning of the neurons. most neurons were not tuned.
  • SNR calculated as peak-peak of waveform divided by 2x standard deviation of signal.
  • A total of 36 implants in 16 other monkeys, which were not systematically evaluated for reliability here, provided successful recordings for up to 1264 days. Most of these studies ended because of headcap failure.
    • They no longer use dental acrylic -- only titanium bone screws.
  • 50-800K impedance
  • Improvement of the signal quality and increased yield, for which there was no clear trend in the three animals, may result from recovery produced by variations in the initial insertion injury.
  • The cortical capillary bed is densely packed, with spacing on the order of 40um in primate cortical tissue [27] ( vasculature ) -- they suppose that variance may be due to this.


[0] Suner S, Fellows MR, Vargas-Irwin C, Nakata GK, Donoghue JP, Reliability of signals from a chronically implanted, silicon-based electrode array in non-human primate primary motor cortex.IEEE Trans Neural Syst Rehabil Eng 13:4, 524-41 (2005 Dec)

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ref: Rennaker-2005.03 tags: electrode recording longevity mechanical insertion Oklahoma MEA date: 01-25-2013 01:21 gmt revision:3 [2] [1] [0] [head]

PMID-15698656[0] A comparison of chronic multi-channel cortical implantation techniques: manual versus mechanical insertion.

  • Over 60% of the animals implanted with the mechanical insertion device had driven activity at week 6
    • whereas none of the animals with manually inserted arrays exhibited functional responses after 3 weeks.
      • Roughly identical responses immediately following surgery.
      • Could be that the manual inserter had horizontal movement / shear. (This is solveable with a stereotax).
      • Other research showed little difference in tissue response at 10um/s or 100um/s PMID-21896383[1]
  • Multi-wire electrodes.
  • Mechanical insertion device was capable of rapidly inserting the electrode without visible compression of the brain.
  • Response measured relative to auditory stimulus.
  • Their insertion device looks like a pen.


[0] Rennaker RL, Street S, Ruyle AM, Sloan AM, A comparison of chronic multi-channel cortical implantation techniques: manual versus mechanical insertion.J Neurosci Methods 142:2, 169-76 (2005 Mar 30)
[1] Welkenhuysen M, Andrei A, Ameye L, Eberle W, Nuttin B, Effect of insertion speed on tissue response and insertion mechanics of a chronically implanted silicon-based neural probe.IEEE Trans Biomed Eng 58:11, 3250-9 (2011 Nov)