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Proceedings of the National Academy of... Jun 2017Sensing is fundamental to the control of movement: From grasping objects to speech production, sensing guides action. So far, most of our knowledge about sensorimotor...
Sensing is fundamental to the control of movement: From grasping objects to speech production, sensing guides action. So far, most of our knowledge about sensorimotor integration comes from visually guided reaching and oculomotor integration, in which the time course and trajectories of movements can be measured at a high temporal resolution. By contrast, production of vocalizations by humans and animals involves complex and variable actions, and each syllable often lasts a few hundreds of milliseconds, making it difficult to infer underlying neural processes. Here, we measured and modeled the transfer of sensory information into motor commands for vocal amplitude control in response to background noise, also known as the Lombard effect. We exploited the brief vocalizations of echolocating bats to trace the time course of the Lombard effect on a millisecond time scale. Empirical studies revealed that the Lombard effect features a response latency of a mere 30 ms and provided the foundation for the quantitative audiomotor model of the Lombard effect. We show that the Lombard effect operates by continuously integrating the sound pressure level of background noise through temporal summation to guide the extremely rapid vocal-motor adjustments. These findings can now be extended to models and measures of audiomotor integration in other animals, including humans.
Topics: Acoustic Stimulation; Animals; Chiroptera; Echolocation; Female; Male; Nervous System Physiological Phenomena; Noise; Sensorimotor Cortex; Sound Spectrography; Vocalization, Animal
PubMed: 28584095
DOI: 10.1073/pnas.1702671114 -
IUCrJ Jul 2017Crystal structure determination of biological macromolecules using the novel technique of serial femtosecond crystallography (SFX) is severely limited by the scarcity of...
Crystal structure determination of biological macromolecules using the novel technique of serial femtosecond crystallography (SFX) is severely limited by the scarcity of X-ray free-electron laser (XFEL) sources. However, recent and future upgrades render microfocus beamlines at synchrotron-radiation sources suitable for room-temperature serial crystallography data collection also. Owing to the longer exposure times that are needed at synchrotrons, serial data collection is termed serial millisecond crystallography (SMX). As a result, the number of SMX experiments is growing rapidly, with a dozen experiments reported so far. Here, the first high-viscosity injector-based SMX experiments carried out at a US synchrotron source, the Advanced Photon Source (APS), are reported. Microcrystals (5-20 µm) of a wide variety of proteins, including lysozyme, thaumatin, phycocyanin, the human A adenosine receptor (AAR), the soluble fragment of the membrane lipoprotein Flpp3 and proteinase K, were screened. Crystals suspended in lipidic cubic phase (LCP) or a high-molecular-weight poly(ethylene oxide) (PEO; molecular weight 8 000 000) were delivered to the beam using a high-viscosity injector. In-house data-reduction (hit-finding) software developed at APS as well as the SFX data-reduction and analysis software suites and enabled efficient on-site SMX data monitoring, reduction and processing. Complete data sets were collected for AAR, phycocyanin, Flpp3, proteinase K and lysozyme, and the structures of AAR, phycocyanin, proteinase K and lysozyme were determined at 3.2, 3.1, 2.65 and 2.05 Å resolution, respectively. The data demonstrate the feasibility of serial millisecond crystallography from 5-20 µm crystals using a high-viscosity injector at APS. The resolution of the crystal structures obtained in this study was dictated by the current flux density and crystal size, but upcoming developments in beamline optics and the planned APS-U upgrade will increase the intensity by two orders of magnitude. These developments will enable structure determination from smaller and/or weakly diffracting microcrystals.
PubMed: 28875031
DOI: 10.1107/S205225251700570X -
Science Advances Aug 2016Phytochromes are light sensor proteins found in plants, bacteria, and fungi. They function by converting a photon absorption event into a conformational signal that...
Phytochromes are light sensor proteins found in plants, bacteria, and fungi. They function by converting a photon absorption event into a conformational signal that propagates from the chromophore through the entire protein. However, the structure of the photoactivated state and the conformational changes that lead to it are not known. We report time-resolved x-ray scattering of the full-length phytochrome from Deinococcus radiodurans on micro- and millisecond time scales. We identify a twist of the histidine kinase output domains with respect to the chromophore-binding domains as the dominant change between the photoactivated and resting states. The time-resolved data further show that the structural changes up to the microsecond time scales are small and localized in the chromophore-binding domains. The global structural change occurs within a few milliseconds, coinciding with the formation of the spectroscopic meta-Rc state. Our findings establish key elements of the signaling mechanism of full-length bacterial phytochromes.
Topics: Bacterial Proteins; Kinetics; Models, Molecular; Photoreceptors, Microbial; Phytochrome; Protein Conformation; Structure-Activity Relationship
PubMed: 27536728
DOI: 10.1126/sciadv.1600920 -
International Journal of Molecular... Aug 2020Serial crystallography (SX) using X-ray free electron laser or synchrotron X-ray allows for the determination of structures, at room temperature, with reduced radiation...
Serial crystallography (SX) using X-ray free electron laser or synchrotron X-ray allows for the determination of structures, at room temperature, with reduced radiation damage. Moreover, it allows for the study of structural dynamics of macromolecules using a time-resolved pump-probe, as well as mix-and-inject experiments. Delivering a crystal sample using a viscous medium decreases sample consumption by lowering the flow rate while being extruded from the injector or syringe as compared to a liquid jet injector. Since the environment of crystal samples varies, continuous development of the delivery medium is important for extended SX applications. Herein, I report the preparation and characterization of a lard-based sample delivery medium for SX. This material was obtained using heat treatment, and then the soluble impurities were removed through phase separation. The lard injection medium was highly stable and could be injected via a syringe needle extruded at room temperature with a flow rate < 200 nL/min. Serial millisecond crystallography experiments were performed using lard, and the room temperature structures of lysozyme and glucose isomerase embedded in lard at 1.75 and 1.80 Å, respectively, were determined. The lard medium showed X-ray background scattering similar or relatively lower than shortenings and lipidic cubic phase; therefore, it can be used as sample delivery medium in SX experiments.
Topics: Crystallography, X-Ray; Lipids; Viscosity
PubMed: 32825186
DOI: 10.3390/ijms21175977 -
Proceedings of the National Academy of... Jun 2019Biological systems are subjected to continuous environmental fluctuations, and therefore, flexibility in the structure and function of their protein building blocks is...
Biological systems are subjected to continuous environmental fluctuations, and therefore, flexibility in the structure and function of their protein building blocks is essential for survival. Protein dynamics are often local conformational changes, which allows multiple dynamical processes to occur simultaneously and rapidly in individual proteins. Experiments often average over these dynamics and their multiplicity, preventing identification of the molecular origin and impact on biological function. Green plants survive under high light by quenching excess energy, and Light-Harvesting Complex Stress Related 1 (LHCSR1) is the protein responsible for quenching in moss. Here, we expand an analysis of the correlation function of the fluorescence lifetime by improving the estimation of the lifetime states and by developing a multicomponent model correlation function, and we apply this analysis at the single-molecule level. Through these advances, we resolve previously hidden rapid dynamics, including multiple parallel processes. By applying this technique to LHCSR1, we identify and quantitate parallel dynamics on hundreds of microseconds and tens of milliseconds timescales, likely at two quenching sites within the protein. These sites are individually controlled in response to fluctuations in sunlight, which provides robust regulation of the light-harvesting machinery. Considering our results in combination with previous structural, spectroscopic, and computational data, we propose specific pigments that serve as the quenching sites. These findings, therefore, provide a mechanistic basis for quenching, illustrating the ability of this method to uncover protein function.
Topics: Fluorescence; Light; Light-Harvesting Protein Complexes; Photosynthesis; Single Molecule Imaging
PubMed: 31101718
DOI: 10.1073/pnas.1821207116 -
Biology Letters Aug 2019Recent work suggests that the circadian pacemaker responds optimally to millisecond flashes of light, not continuous light exposure as has been historically believed. It...
Recent work suggests that the circadian pacemaker responds optimally to millisecond flashes of light, not continuous light exposure as has been historically believed. It is unclear whether these responses are influenced by the physical characteristics of the pulsing. In the present study, Drosophila (n = 2199) were stimulated with 8, 16 or 120 ms flashes. For each duration, the energy content of the exposure was systematically varied by changing the pulse irradiance and the number of stimuli delivered over a fixed 15 min administration window (64 protocols surveyed in all). Results showed that per microjoule invested, 8 ms flashes were more effective at resetting the circadian activity rhythm than 16- and 120 ms flashes (i.e. left shift of the dose-response curve, as well as a higher estimated maximal response). These data suggest that the circadian pacemaker's photosensitivity declines within milliseconds of light contact. Further introduction of light beyond a floor of (at least) 8 ms leads to diminishing returns on phase-shifting.
Topics: Animals; Circadian Rhythm; Drosophila
PubMed: 31387472
DOI: 10.1098/rsbl.2019.0371 -
JTCVS Open Jun 2021Atrial extrasystoles are usually benign; however, they can also trigger atrial fibrillation. It is most likely that if atrial extrasystoles provoke a larger amount of...
OBJECTIVES
Atrial extrasystoles are usually benign; however, they can also trigger atrial fibrillation. It is most likely that if atrial extrasystoles provoke a larger amount of conduction disorders and a greater degree of endo-epicardial asynchrony, the risk of postoperative atrial fibrillation increases. To test this hypothesis, we investigated the effect of programmed atrial extrasystoles on endo-epicardial conduction and postoperative atrial fibrillation.
METHODS
Twelve patients (58% male, age 68 ± 7 years) underwent simultaneous endo-epicardial mapping (256 electrodes) of the right atrium during sinus rhythm and programmed atrial extrasystoles provoked from the right atrial free wall. Areas of conduction block were defined as conduction delays of ≥12 milliseconds and endo-epicardial asynchrony as activation time differences of exact opposite electrodes of ≥15 milliseconds.
RESULTS
Endo-epicardial mapping data of all programmed atrial extrasystoles were analyzed and compared with sinus rhythm (median preceding cycle length = 531 milliseconds [345-787] and median sinus rhythm cycle length = 843 milliseconds [701-992]). All programmed atrial extrasystoles were aberrant (severe, moderate, and mildly aberrant, respectively, n = 6, 3, and 3) and had a mean prematurity index of 50.1 ± 11.9%. The amount of endo-epicardial asynchrony (1% [1-2] vs 6.7 [2.7-16.9], = .006) and conduction block (1.4% [0.6-2.6] vs 8.5% [4.2-10.4], = .005) both increased during programmed atrial extrasystoles. Interestingly, conduction block during programmed atrial extrasystoles was more severe in patients (n = 4, 33.3%) who developed postoperative atrial fibrillation (5.1% [2.9-8.8] vs 11.3% [10.1-12.1], = .004).
CONCLUSIONS
Atrial conduction disorders and endo-epicardial asynchrony, which play an important role in arrhythmogenesis, are enhanced during programmed atrial extrasystoles compared with sinus rhythm. The findings of this pilot study provide a possible explanation for enhanced vulnerability for postoperative atrial extrasystoles to induce postoperative atrial fibrillation in patients after cardiac surgery.
PubMed: 36003566
DOI: 10.1016/j.xjon.2021.01.014 -
PloS One 2020Optimizing stimulation protocol is essential for clinical application of retinal prosthesis. Elongating stimulation pulse width (~25ms /phase) has been proposed as an...
BACKGROUND
Optimizing stimulation protocol is essential for clinical application of retinal prosthesis. Elongating stimulation pulse width (~25ms /phase) has been proposed as an effective method to improve spatial resolution of epi-retinal implants. However, it is unknown whether longer stimulus pulse width will increase the risk of damaging the retina. In addition, with the advent of next generation retinal prosthesis featuring high-density microelectrode array, it is tempting to optimizing a single set of parameters for all electrodes instead of optimizing parameters of each electrode, but this approach raised biosafety concern. We sought to study the effect of stimulus pulse width on the response of retinal ganglion cells to electrical stimulation, and evaluate if the single parameter set approach was valid based on biosafety measures.
METHODS
We stimulated mouse retina using biphasic pulse waveform generated by chosen electrodes (single or a 3x3 assembly) from multiple microelectrode arrays, recorded their action potentials and performed spike sorting. We tested various stimulus intensity with two fixed pulse width: a short one for 1 millisecond per phase, and a long one for 25 milliseconds per phase. All these assays were performed on two mouse models: the wildtype C57BL/6J mice and the photoreceptor degenerated rd10 mice. The action-potential-frequency vs stimulus amplitude profiles were plotted, and three parameters were extracted: the threshold (the lowest stimulus amplitude activating RGC units), safety-limit (stimulus amplitude that attenuated the firing rate to half of the maximum response), and the stimulation amplitude range (the difference between threshold and safety limit parameters).
RESULTS
In single-electrode stimulation experiment, we found that on average 85% of the recorded units showed attenuated response to extreme stimulation; among those units, an average of 51% stopped responding during stimulation ramping and failed to recover after one-hour post-stimulation, indicating extreme stimulation can damage RGC units. Twenty-five-millisecond pulse stimulation significantly reduced safety-limit and stimulation-amplitude-range parameters of recorded RGC units compared to 1ms pulse stimulation. During stimulus amplitude ramping, the maximum proportion of responsive healthy RGC units was 51% on average in 25ms pulse condition, and 76% on average in 1ms pulse condition, indicating long pulse may inflict more strain on RGCs, and a significant amount of inappropriately stimulated RGCs always exist. The contrast of these proportions could be explained by the tight correlation between the threshold and safety-limit parameter in 25ms pulse condition. These results were corroborated by those from 3x3 array stimulation experiments.
CONCLUSION
Base on a biosafety measure (RGCs' evoked firing rate in response to electrical stimulation), we proposed that longer stimulation pulse width could lead to reduced retinal response and thus highlighted the importance of carefully setting the stimulation amplitude in this case. Our results also suggested that optimizing a single set of parameters for all electrodes without individual tweaking always generated a significant amount of inappropriately stimulated RGCs, especially in the long pulse stimulation condition.
Topics: Action Potentials; Animals; Containment of Biohazards; Electric Stimulation; Humans; Mice; Microelectrodes; Retinal Degeneration; Retinal Ganglion Cells; Time Factors; Visual Prosthesis
PubMed: 32697792
DOI: 10.1371/journal.pone.0236176 -
JMIR Cardio Jan 2023Drug-induced prolongation of the corrected QT interval (QTc) increases the risk for Torsades de Pointes (TdP) and sudden cardiac death. Medication effects on the QTc...
BACKGROUND
Drug-induced prolongation of the corrected QT interval (QTc) increases the risk for Torsades de Pointes (TdP) and sudden cardiac death. Medication effects on the QTc have been studied in controlled settings but may not be well evaluated in real-world settings where medication effects may be modulated by patient demographics and comorbidities as well as the usage of other concomitant medications.
OBJECTIVE
We demonstrate a new, high-throughput method leveraging electronic health records (EHRs) and the Surescripts pharmacy database to monitor real-world QTc-prolonging medication and potential interacting effects from demographics and comorbidities.
METHODS
We included all outpatient electrocardiograms (ECGs) from September 2008 to December 2019 at a large academic medical system, which were in sinus rhythm with a heart rate of 40-100 beats per minute, QRS duration of <120 milliseconds, and QTc of 300-700 milliseconds, determined using the Bazett formula. We used prescription information from the Surescripts pharmacy database and EHR medication lists to classify whether a patient was on a medication during an ECG. Negative control ECGs were obtained from patients not currently on the medication but who had been or would be on that medication within 1 year. We calculated the difference in mean QTc between ECGs of patients who are on and those who are off a medication and made comparisons to known medication TdP risks per the CredibleMeds.org database. Using linear regression analysis, we studied the interaction of patient-level demographics or comorbidities on medication-related QTc prolongation.
RESULTS
We analyzed the effects of 272 medications on 310,335 ECGs from 159,397 individuals. Medications associated with the greatest QTc prolongation were dofetilide (mean QTc difference 21.52, 95% CI 10.58-32.70 milliseconds), mexiletine (mean QTc difference 18.56, 95% CI 7.70-29.27 milliseconds), amiodarone (mean QTc difference 14.96, 95% CI 13.52-16.33 milliseconds), rifaximin (mean QTc difference 14.50, 95% CI 12.12-17.13 milliseconds), and sotalol (mean QTc difference 10.73, 95% CI 7.09-14.37 milliseconds). Several top QT prolonging medications such as rifaximin, lactulose, cinacalcet, and lenalidomide were not previously known but have plausible mechanistic explanations. Significant interactions were observed between demographics or comorbidities and QTc prolongation with many medications, such as coronary disease and amiodarone.
CONCLUSIONS
We demonstrate a new, high-throughput technique for monitoring real-world effects of QTc-prolonging medications from readily accessible clinical data. Using this approach, we confirmed known medications for QTc prolongation and identified potential new associations and demographic or comorbidity interactions that could supplement findings in curated databases. Our single-center results would benefit from additional verification in future multisite studies that incorporate larger numbers of patients and ECGs along with more precise medication adherence and comorbidity data.
PubMed: 36662566
DOI: 10.2196/41055 -
Normal Values of Magnetic Relaxation Parameters of Spine Components with the Synthetic MRI Sequence.AJNR. American Journal of Neuroradiology Apr 2018SyMRI is a technique developed to perform quantitative MR imaging. Our aim was to analyze its potential use for measuring relaxation times of normal components of the...
BACKGROUND AND PURPOSE
SyMRI is a technique developed to perform quantitative MR imaging. Our aim was to analyze its potential use for measuring relaxation times of normal components of the spine and to compare them with values found in the literature using relaxometry and other techniques.
MATERIALS AND METHODS
Thirty-two spine MR imaging studies (10 cervical, 5 dorsal, 17 lumbosacral) were included. A modified multiple-dynamic multiple-echo sequence was added and processed to obtain quantitative T1 (millisecond), T2 (millisecond), and proton density (percentage units [pu]) maps for each patient. An ROI was placed on representative areas for CSF, spinal cord, intervertebral discs, and vertebral bodies, to measure their relaxation.
RESULTS
Relaxation time means are reported for CSF (T1 = 4273.4 ms; T2 = 1577.6 ms; proton density = 107.5 pu), spinal cord (T1 = 780.2 ms; T2 = 101.6 ms; proton density = 58.7 pu), normal disc (T1 = 1164.9 ms; T2 = 101.9 ms; proton density = 78.9 pu), intermediately hydrated disc (T1 = 723 ms; T2 = 66.8 ms; proton density = 60.8 pu), desiccated disc (T1 = 554.4 ms; T2 = 55.6 ms; proton density = 47.6 ms), and vertebral body (T1 = 515.3 ms; T2 = 100.8 ms; proton density = 91.1 pu). Comparisons among the mean T1, T2, and proton density values showed significant differences between different spinal levels (cervical, dorsal, lumbar, and sacral) for CSF (proton density), spinal cord (T2 and proton density), normal disc (T1, T2, and proton density), and vertebral bodies (T1 and proton density). Significant differences were found among mean T1, T2, and proton density values of normal, intermediately hydrated, and desiccated discs.
CONCLUSIONS
Measurements can be easily obtained on SyMRI and correlated with previously published values obtained using conventional relaxometry techniques.
Topics: Cerebrospinal Fluid; Female; Humans; Intervertebral Disc; Magnetic Resonance Imaging; Male; Reference Values; Spinal Cord; Spine
PubMed: 29496723
DOI: 10.3174/ajnr.A5566