sj-pdf-1-apr-10.1177_1532673X211043445 – Supplemental material for Gasoline in the Voter’s Pocketbook: Driving Times to Work and the Electoral Implications of Gasoline Price Fluctuations

Supplemental material, sj-pdf-1-apr-10.1177_1532673X211043445 for Gasoline in the Voter’s Pocketbook: Driving Times to Work and the Electoral Implications of Gasoline Price Fluctuations by Sung Eun Kim and Joonseok Yang in American Politics Research</p

Two Opposing Effects of Monovalent Cations on the Stability of i‑Motif Structure

At acidic pH, cytosine-rich single-stranded DNA can be folded into a tetraplex structure called i-motif (iM). In recent studies, the effect of monovalent cations on the stability of iM structure has been addressed, but a consensus about the issue has not been reached yet. Thus, we investigated the effects of various factors on the stability of iM structure using fluorescence resonance energy transfer (FRET)-based analysis for three types of iM derived from human telomere sequences. We confirmed that the protonated cytosine-cytosine (C:C+) base pair is destabilized as the concentration of monovalent cations (Li+, Na+, K+) increases and that Li+ has the greatest tendency of destabilization. Intriguingly, monovalent cations would play an ambivalent role in iM formation by making single-stranded DNA flexible and pliant for an iM structure. In particular, we found that Li+ has a notably greater flexibilizing effect than Na+ and K+. All taken together, we conclude that the stability of iM structure is controlled by the subtle balance of the two counteractive effects of monovalent cations: electrostatic screening and disruption of cytosine base pairing

Location of temperature-dependent accessible residues.

<p>(A) Sequence alignment of pore domains of rat TRPV1 and mouse TRPV3. Predicted structural domains are indicated above. Residues with temperature-independent accessibility are highlighted in cyan and residues with temperature-dependent accessibility are in pink. (B) Homology models of pore domains. Same color coding was used as the above.</p

Cysteine scanning on TRPV1 and TRPV3 channels.

<p>(A) Schematic of MTSET labeling on a cysteine residue by covalent bond formation. (B–D) Chemical- and temperature- dose-response curves of cysteine-less TRPV1 after application of MTSET or buffer control (B), of cysteine-less TRPV3 after application of MTSET or buffer control (C), of cysteine-less and wild-type TRPV1 (D), and of cysteine-less and wild-type TRPV3 (E). For chemical dose-responses data are averages of five measurements (mean ± s.d.) and for temperature-responses averages of 16 wells (mean ±2× s.e.). (F) Reaction schemes of GSH with MTSET and GSH with OPA. (G) Fluorescence signal of obtained from competing reactions in (F) as a function of MTSET concentration at 4°C and 40°C. n>20 with from three independent experiments. Error bars are mean ± s.d.</p

Temperature-dependent labeling in TRPV3.

<p>(A) Temperature as a function of time during FLIPR temperature-activation assay. (B) Representative examples of fluorescence responses upon temperature stimulation of TRPV3 I652C. n>8 wells. Error bars are mean ±2x s.e. (C) Average basal fluorescence change of TRPV3 I652C after incubation of MTSET at 20°C and 40°C. For each experiment, the basal fluorescence is an average of fluorescence between 0 and 20 sec. Fluorescence change is the difference of MTSET incubation and buffer incubation basal fluorescence. Numbers of independent experiments are shown in the bar graph and n>8 wells per experiment. Error bars are mean ± s.e. Two-tailed t-test, ***p<0.0001. (D) Representative examples of fluorescence responses upon temperature stimulation of L655, n>8 wells, Error bars are mean ±2× s.e. (E) Average basal fluorescence change of TRPV3 L655C after incubation of MTSET at 20°C and 40°C. Number of experiments is shown in the bar graph and n>8 wells per experiment. Error bars are mean ± s.e. Two-tailed t-test, **p = 0.0062. (F) The basal fluorescence change of TRPV3 L655C after incubation of MTSET at 20°C and 40°C as a function of MTSET concentration. The incubation time was 10 min. n>5 wells. Error bars are mean ± s.d. Straight lines are exponential fits to the data.</p

Single Residues in the Outer Pore of TRPV1 and TRPV3 Have Temperature-Dependent Conformations

<div><p>Thermosensation is mediated by ion channels that are highly temperature-sensitive. Several members of the family of transient receptor potential (TRP) ion channels are activated by cold or hot temperatures and have been shown to function as temperature sensors in vivo. The molecular mechanism of temperature-sensitivity of these ion channels is not understood. A number of domains or even single amino acids that regulate temperature-sensitivity have been identified in several TRP channels. However, it is unclear what precise conformational changes occur upon temperature activation. Here, we used the cysteine accessibility method to probe temperature-dependent conformations of single amino acids in TRP channels. We screened over 50 amino acids in the predicted outer pore domains of the heat-activated ion channels TRPV1 and TRPV3. In both ion channels we found residues that have temperature-dependent accessibilities to the extracellular solvent. The identified residues are located within the second predicted extracellular pore loop. These residues are identical or proximal to residues that were shown to be specifically required for temperature-activation, but not chemical activation. Our data precisely locate conformational changes upon temperature-activation within the outer pore domain. Collectively, this suggests that these specific residues and the second predicted pore loop in general are crucial for the temperature-activation mechanism of these heat-activated thermoTRPs.</p> </div

Temperature-dependent labeling in TRPV1.

<p>(A) Temperature as a function of time during FLIPR temperature-activation assay. (B–D) Representative examples of fluorescence responses upon temperature stimulation of TRPV1 N652C (B), A657C (C) and Y53C (D) after incubation of MTSET at 20°C (blue) and 42°C (red). For both temperatures, buffer as a negative control is colored gray; n>8 wells. Error bars are 2× s.e. (E) Average basal fluorescence change of TRPV1 Y653C after incubation of MTSET at 20°C and 42°C. The basal fluorescence is averaged fluorescence level between 0 to 20 sec. For each experiment, the increase of basal fluorescence was obtained by subtracting buffer control from MTSET incubation. Five independent experiments were performed for 20°C and three for 40°C with n>5 wells per experiment. Two-tailed t-test, *p = 0.036. Error bars are mean ± s.e.</p

Electrophysiological characterization of temperature-dependent MTSET accessibility of TRPV1 Y653C.

<p>(A) Above: Temperature profile for a whole-cell voltage-step protocol. Middle: Voltage-step protocols were applied before (I) and after (II) MTSET application at 20°C or 40°C. Bottom: Example of current traces of Y653C before and after 2 mM MTSET at 20°C. (B) Average change of plateau current (+100 mV) upon application of MTSET at 20°C or 40°C. Data are averages from five patches. Two-tailed t-test, **p = 0.00034. (C) Current-voltage (IV) curves from whole-cell measurement. Error bars are mean ± s.e.</p

Deciphering Kinetic Information from Single-Molecule FRET Data That Show Slow Transitions

Single-molecule FRET is one of the most powerful and widely used biophysical techniques in biological sciences. It, however, often suffers from limitations such as weak signal and limited measurement time intrinsic to single-molecule fluorescence measurements. Despite several ameliorative measures taken to increase measurement time, it is nearly impossible to acquire meaningful kinetic information on a molecule if conformational transitions of the molecule are ultraslow such that transition times (⟨τ⟩_orig) are comparable to or longer than measurement times (<i>δt</i>) limited by the finite lifetime of fluorescent dye. Here, to extract a reliable and accurate mean transition time from a series of short time traces with ultraslow kinetics, we suggest a scheme called sHaRPer (serialized Handshaking Repeated Permutation with end removal) that concatenates multiple time traces. Because data acquisition frequency <i>f</i> and measurement time (<i>δt</i>) affect the estimation of mean transition time (⟨τ⟩), we provide mathematical criteria that <i>f</i>, <i>δt</i>, and ⟨τ⟩ should satisfy to make ⟨τ⟩ close enough to ⟨τ⟩_orig. Although application of the sHaRPer method has a potential risk of distorting the time constants of individual kinetic phases if the data are described with kinetic partitioning, we also provide criteria to avoid such distortion. Our sHaRPer method is a useful way to handle single-molecule data with slow transition kinetics. This study provides a practical guide to use sHaRPer

JED888252 Supplemental Material - Supplemental material for Environmental Degradation and Public Opinion: The Case of Air Pollution in Vietnam

Supplemental material, JED888252 Supplemental Material for Environmental Degradation and Public Opinion: The Case of Air Pollution in Vietnam by Sung Eun Kim, S. P. Harish, Ryan Kennedy, Xiaomeng Jin and Johannes Urpelainen in The Journal of Environment & Development: A Review of International Policy</p