Effects of Tetracaine on Voltage-activated Calcium Sparks in Frog Intact Skeletal Muscle Fibers

The properties of Ca2+ sparks in frog intact skeletal muscle fibers depolarized with 13 mM [K+] Ringer's are well described by a computational model with a Ca2+ source flux of amplitude 2.5 pA (units of current) and duration 4.6 ms (18 °C; Model 2 of Baylor et al., 2002). This result, in combination with the values of single-channel Ca2+ current reported for ryanodine receptors (RyRs) in bilayers under physiological ion conditions, 0.5 pA (Kettlun et al., 2003) to 2 pA (Tinker et al., 1993), suggests that 1–5 RyR Ca2+ release channels open during a voltage-activated Ca2+ spark in an intact fiber. To distinguish between one and greater than one channel per spark, sparks were measured in 8 mM [K+] Ringer's in the absence and presence of tetracaine, an inhibitor of RyR channel openings in bilayers. The most prominent effect of 75–100 μM tetracaine was an approximately sixfold reduction in spark frequency. The remaining sparks showed significant reductions in the mean values of peak amplitude, decay time constant, full duration at half maximum (FDHM), full width at half maximum (FWHM), and mass, but not in the mean value of rise time. Spark properties in tetracaine were simulated with an updated spark model that differed in minor ways from our previous model. The simulations show that (a) the properties of sparks in tetracaine are those expected if tetracaine reduces the number of active RyR Ca2+ channels per spark, and (b) the single-channel Ca2+ current of an RyR channel is ≤1.2 pA under physiological conditions. The results support the conclusion that some normal voltage-activated sparks (i.e., in the absence of tetracaine) are produced by two or more active RyR Ca2+ channels. The question of how the activation of multiple RyRs is coordinated is discussed

Intracellular calcium movements during relaxation and recovery of superfast muscle fibers of the toadfish swimbladder

© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Journal of General Physiology 143 (2014): 605-620, doi:10.1085/jgp.201411160.The mating call of the Atlantic toadfish is generated by bursts of high-frequency twitches of the superfast twitch fibers that surround the swimbladder. At 16°C, a calling period can last several hours, with individual 80–100-Hz calls lasting ∼500 ms interleaved with silent periods (intercall intervals) lasting ∼10 s. To understand the intracellular movements of Ca2+ during the intercall intervals, superfast fibers were microinjected with fluo-4, a high-affinity fluorescent Ca2+ indicator, and stimulated by trains of 40 action potentials at 83 Hz, which mimics fiber activity during calling. The fluo-4 fluorescence signal was measured during and after the stimulus trains; the signal was also simulated with a kinetic model of the underlying myoplasmic Ca2+ movements, including the binding and transport of Ca2+ by the sarcoplasmic reticulum (SR) Ca2+ pumps. The estimated total amount of Ca2+ released from the SR during a first stimulus train is ∼6.5 mM (concentration referred to the myoplasmic water volume). At 40 ms after cessation of stimulation, the myoplasmic free Ca2+ concentration ([Ca2+]) is below the threshold for force generation (∼3 µM), yet the estimated concentration of released Ca2+ remaining in the myoplasm (Δ[CaM]) is large, ∼5 mM, with ∼80% bound to parvalbumin. At 10 s after stimulation, [Ca2+] is ∼90 nM (three times the assumed resting level) and Δ[CaM] is ∼1.3 mM, with 97% bound to parvalbumin. Ca2+ movements during the intercall interval thus appear to be strongly influenced by (a) the accumulation of Ca2+ on parvalbumin and (b) the slow rate of Ca2+ pumping that ensues when parvalbumin lowers [Ca2+] near the resting level. With repetitive stimulus trains initiated at 10-s intervals, Ca2+ release and pumping come quickly into balance as a result of the stability (negative feedback) supplied by the increased rate of Ca2+ pumping at higher [Ca2+].This work was supported by a grant to S.M. Baylor from the National Institutes of Health (GM 086167) and a grant to L.C. Rome from the National Science Foundation (IOS-1145981)

Comparing ocean surface boundary vertical mixing schemes including langmuir turbulence

Six recent Langmuir turbulence parameterization schemes and five traditional schemes are implemented in a common single‐column modeling framework and consistently compared. These schemes are tested in scenarios versus matched large eddy simulations, across the globe with realistic forcing (JRA55‐do, WAVEWATCH‐III simulated waves) and initial conditions (Argo), and under realistic conditions as observed at ocean moorings. Traditional non‐Langmuir schemes systematically underpredict large eddy simulation vertical mixing under weak convective forcing, while Langmuir schemes vary in accuracy. Under global, realistic forcing Langmuir schemes produce 6% (−1% to 14% for 90% confidence) or 5.2 m (−0.2 m to 17.4 m for 90% confidence) deeper monthly mean mixed layer depths than their non‐Langmuir counterparts, with the greatest differences in extratropical regions, especially the Southern Ocean in austral summer. Discrepancies among Langmuir schemes are large (15% in mixed layer depth standard deviation over the mean): largest under wave‐driven turbulence with stabilizing buoyancy forcing, next largest under strongly wave‐driven conditions with weak buoyancy forcing, and agreeing during strong convective forcing. Non‐Langmuir schemes disagree with each other to a lesser extent, with a similar ordering. Langmuir discrepancies obscure a cross‐scheme estimate of the Langmuir effect magnitude under realistic forcing, highlighting limited understanding and numerical deficiencies. Maps of the regions and seasons where the greatest discrepancies occur are provided to guide further studies and observations

Impact of horizontal resolution on global ocean–sea ice model simulations based on the experimental protocols of the Ocean Model Intercomparison Project phase 2 (OMIP-2)

This paper presents global comparisons of fundamental global climate variables from a suite of four pairs of matched low- and high-resolution ocean and sea ice simulations that are obtained following the OMIP-2 protocol (Griffies et al., 2016) and integrated for one cycle (1958–2018) of the JRA55-do atmospheric state and runoff dataset (Tsujino et al., 2018). Our goal is to assess the robustness of climate-relevant improvements in ocean simulations (mean and variability) associated with moving from coarse (∼ 1∘) to eddy-resolving (∼ 0.1∘) horizontal resolutions. The models are diverse in their numerics and parameterizations, but each low-resolution and high-resolution pair of models is matched so as to isolate, to the extent possible, the effects of horizontal resolution. A variety of observational datasets are used to assess the fidelity of simulated temperature and salinity, sea surface height, kinetic energy, heat and volume transports, and sea ice distribution. This paper provides a crucial benchmark for future studies comparing and improving different schemes in any of the models used in this study or similar ones. The biases in the low-resolution simulations are familiar, and their gross features – position, strength, and variability of western boundary currents, equatorial currents, and the Antarctic Circumpolar Current – are significantly improved in the high-resolution models. However, despite the fact that the high-resolution models “resolve” most of these features, the improvements in temperature and salinity are inconsistent among the different model families, and some regions show increased bias over their low-resolution counterparts. Greatly enhanced horizontal resolution does not deliver unambiguous bias improvement in all regions for all models

Challenges and Prospects in Ocean Circulation Models

We revisit the challenges and prospects for ocean circulation models following Griffies et al. (2010). Over the past decade, ocean circulation models evolved through improved understanding, numerics, spatial discretization, grid configurations, parameterizations, data assimilation, environmental monitoring, and process-level observations and modeling. Important large scale applications over the last decade are simulations of the Southern Ocean, the Meridional Overturning Circulation and its variability, and regional sea level change. Submesoscale variability is now routinely resolved in process models and permitted in a few global models, and submesoscale effects are parameterized in most global models. The scales where nonhydrostatic effects become important are beginning to be resolved in regional and process models. Coupling to sea ice, ice shelves, and high-resolution atmospheric models has stimulated new ideas and driven improvements in numerics. Observations have provided insight into turbulence and mixing around the globe and its consequences are assessed through perturbed physics models. Relatedly, parameterizations of the mixing and overturning processes in boundary layers and the ocean interior have improved. New diagnostics being used for evaluating models alongside present and novel observations are briefly referenced. The overall goal is summarizing new developments in ocean modeling, including: how new and existing observations can be used, what modeling challenges remain, and how simulations can be used to support observations.Peer reviewe

A high-resolution map of human evolutionary constraint using 29 mammals.

The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering ∼4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for ∼60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease

Evaluation of global ocean–sea-ice model simulations based on the experimental protocols of the Ocean Model Intercomparison Project phase 2 (OMIP-2)

We present a new framework for global ocean- sea-ice model simulations based on phase 2 of the Ocean Model Intercomparison Project (OMIP-2), making use of the surface dataset based on the Japanese 55-year atmospheric reanalysis for driving ocean-sea-ice models (JRA55-do).We motivate the use of OMIP-2 over the framework for the first phase of OMIP (OMIP-1), previously referred to as the Coordinated Ocean-ice Reference Experiments (COREs), via the evaluation of OMIP-1 and OMIP-2 simulations from 11 state-of-the-science global ocean-sea-ice models. In the present evaluation, multi-model ensemble means and spreads are calculated separately for the OMIP-1 and OMIP-2 simulations and overall performance is assessed considering metrics commonly used by ocean modelers. Both OMIP-1 and OMIP-2 multi-model ensemble ranges capture observations in more than 80% of the time and region for most metrics, with the multi-model ensemble spread greatly exceeding the difference between the means of the two datasets. Many features, including some climatologically relevant ocean circulation indices, are very similar between OMIP-1 and OMIP- 2 simulations, and yet we could also identify key qualitative improvements in transitioning from OMIP-1 to OMIP- 2. For example, the sea surface temperatures of the OMIP- 2 simulations reproduce the observed global warming during the 1980s and 1990s, as well as the warming slowdown in the 2000s and the more recent accelerated warming, which were absent in OMIP-1, noting that the last feature is part of the design of OMIP-2 because OMIP-1 forcing stopped in 2009. A negative bias in the sea-ice concentration in summer of both hemispheres in OMIP-1 is significantly reduced in OMIP-2. The overall reproducibility of both seasonal and interannual variations in sea surface temperature and sea surface height (dynamic sea level) is improved in OMIP-2. These improvements represent a new capability of the OMIP-2 framework for evaluating processlevel responses using simulation results. Regarding the sensitivity of individual models to the change in forcing, the models show well-ordered responses for the metrics that are directly forced, while they show less organized responses for those that require complex model adjustments. Many of the remaining common model biases may be attributed either to errors in representing important processes in ocean-sea-ice models, some of which are expected to be reduced by using finer horizontal and/or vertical resolutions, or to shared biases and limitations in the atmospheric forcing. In particular, further efforts are warranted to resolve remaining issues in OMIP-2 such as the warm bias in the upper layer, the mismatch between the observed and simulated variability of heat content and thermosteric sea level before 1990s, and the erroneous representation of deep and bottom water formations and circulations. We suggest that such problems can be resolved through collaboration between those developing models (including parameterizations) and forcing datasets. Overall, the present assessment justifies our recommendation that future model development and analysis studies use the OMIP-2 framework

Evaluation of global ocean–sea-ice model simulations based on the experimental protocols of the Ocean Model Intercomparison Project phase 2 (OMIP-2)

We present a new framework for global ocean–sea-ice model simulations based on phase 2 of the Ocean Model Intercomparison Project (OMIP-2), making use of the surface dataset based on the Japanese 55-year atmospheric reanalysis for driving ocean–sea-ice models (JRA55-do). We motivate the use of OMIP-2 over the framework for the first phase of OMIP (OMIP-1), previously referred to as the Coordinated Ocean–ice Reference Experiments (COREs), via the evaluation of OMIP-1 and OMIP-2 simulations from 11 state-of-the-science global ocean–sea-ice models. In the present evaluation, multi-model ensemble means and spreads are calculated separately for the OMIP-1 and OMIP-2 simulations and overall performance is assessed considering metrics commonly used by ocean modelers. Both OMIP-1 and OMIP-2 multi-model ensemble ranges capture observations in more than 80 % of the time and region for most metrics, with the multi-model ensemble spread greatly exceeding the difference between the means of the two datasets. Many features, including some climatologically relevant ocean circulation indices, are very similar between OMIP-1 and OMIP-2 simulations, and yet we could also identify key qualitative improvements in transitioning from OMIP-1 to OMIP-2. For example, the sea surface temperatures of the OMIP-2 simulations reproduce the observed global warming during the 1980s and 1990s, as well as the warming slowdown in the 2000s and the more recent accelerated warming, which were absent in OMIP-1, noting that the last feature is part of the design of OMIP-2 because OMIP-1 forcing stopped in 2009. A negative bias in the sea-ice concentration in summer of both hemispheres in OMIP-1 is significantly reduced in OMIP-2. The overall reproducibility of both seasonal and interannual variations in sea surface temperature and sea surface height (dynamic sea level) is improved in OMIP-2. These improvements represent a new capability of the OMIP-2 framework for evaluating process-level responses using simulation results. Regarding the sensitivity of individual models to the change in forcing, the models show well-ordered responses for the metrics that are directly forced, while they show less organized responses for those that require complex model adjustments. Many of the remaining common model biases may be attributed either to errors in representing important processes in ocean–sea-ice models, some of which are expected to be reduced by using finer horizontal and/or vertical resolutions, or to shared biases and limitations in the atmospheric forcing. In particular, further efforts are warranted to resolve remaining issues in OMIP-2 such as the warm bias in the upper layer, the mismatch between the observed and simulated variability of heat content and thermosteric sea level before 1990s, and the erroneous representation of deep and bottom water formations and circulations. We suggest that such problems can be resolved through collaboration between those developing models (including parameterizations) and forcing datasets. Overall, the present assessment justifies our recommendation that future model development and analysis studies use the OMIP-2 framework.This research has been supported by the Integrated Research Program for Advancing Climate Models (TOUGOU) of the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan (grant nos. JPMXD0717935457 and JPMXD0717935561), the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) (grant no. 274762653), the Helmholtz Climate Initiative REKLIM (Regional Climate Change) and European Union's Horizon 2020 Research & Innovation program (grant nos. 727862 and 800154), the Research Council of Norway (EVA (grant no. 229771) and INES (grant no. 270061)), the US National Science Foundation (NSF) (grant no. 1852977), the National Natural Science Foundation of China (grant nos. 41931183 and 41976026), NOAA's Science Collaboration Program and administered by UCAR's Cooperative Programs for the Advancement of Earth System Science (CPAESS) (grant nos. NA16NWS4620043 and NA18NWS4620043B), and NOAA (grant no. NA18OAR4320123).Peer ReviewedPostprint (published version

Challenges and Prospects in Ocean Circulation Models

We revisit the challenges and prospects for ocean circulation models following Griffies et al. (2010). Over the past decade, ocean circulation models evolved through improved understanding, numerics, spatial discretization, grid configurations, parameterizations, data assimilation, environmental monitoring, and process-level observations and modeling. Important large scale applications over the last decade are simulations of the Southern Ocean, the Meridional Overturning Circulation and its variability, and regional sea level change. Submesoscale variability is now routinely resolved in process models and permitted in a few global models, and submesoscale effects are parameterized in most global models. The scales where nonhydrostatic effects become important are beginning to be resolved in regional and process models. Coupling to sea ice, ice shelves, and high-resolution atmospheric models has stimulated new ideas and driven improvements in numerics. Observations have provided insight into turbulence and mixing around the globe and its consequences are assessed through perturbed physics models. Relatedly, parameterizations of the mixing and overturning processes in boundary layers and the ocean interior have improved. New diagnostics being used for evaluating models alongside present and novel observations are briefly referenced. The overall goal is summarizing new developments in ocean modeling, including: how new and existing observations can be used, what modeling challenges remain, and how simulations can be used to support observations