Automatic step-detection algorithm for analysis of sarcomere dynamics

Motile systems exhibit a stepwise nature, seen most prominently in muscle contraction. A novel algorithm has been developed that detects steps automatically in sarcomere-length change data and computes their size. The method is based on a nonlinear filter and a step detection protocol that detects local slope values in comparison to a threshold. The algorithm was first evaluated using artificial data with various degrees of Gaussian noise. Steps were faithfully detected even with significant noise. With actual data, the algorithm detected 2.7 nm steps and integer multiples thereof. The results confirm a quantal 2.7 nm step-size reported earlier. As stepwise phenomena become increasingly evident, automatic step-detection algorithms become increasingly useful since the limiting factor is almost always noise. The algorithm presented here offers a versatile and accurate tool that should be useful not only within muscle contraction and motility fields, but in fields which quantal phenomena play a role.     

Uncovering chaotic structure in mechanomyography signals of fatigue biceps brachii muscle

The mechanomyography (MMG) signal reflects mechanical properties of limb muscles that undergo complex phenomena in different functional states. We undertook the study of the chaotic nature of MMG signals by referring to recent developments in the field of nonlinear dynamics. MMG signals were measured from the biceps brachii muscle of 5 subjects during fatigue of isometric contraction at 80% maximal voluntary contraction (MVC) level. Deterministic chaotic character was detected in all data by using the Volterra–Wiener–Korenberg model and noise titration approach. The noise limit, a power indicator of the chaos of fatigue MMG signals, was 22.20±8.73. Furthermore, we studied the nonlinear dynamic features of MMG signals by computing their correlation dimension D₂, which was 3.35±0.36 across subjects. These results indicate that MMG is a high-dimensional chaotic signal and support the use of the theory of nonlinear dynamics for analysis and modeling of fatigue MMG signals.     

Expression of Hsp27 correlated with rat detrusor contraction after acute urinary retention

Heat shock protein 27 (Hsp27) can regulate actin cytoskeleton dynamics and contractile protein activation. This study investigates whether Hsp27 expression is related to bladder contractile dysfunction after acute urinary retention (AUR). Female rats were randomized either to AUR by urethral ligation or to normal control group. Bladder and smooth muscle strip contraction at time points from 0 h to 7 days after AUR were estimated by cystometric and organ bath studies. Hsp27 expression in bladder tissue at each time point was detected with immunofluorescence, Western blots, and real-time PCR. Expression of the three phosphorylated forms of Hsp27 was detected by Western blots. Smooth muscle ultrastructure was observed by transmission electron microscopy. Data suggest that maximum detrusor pressure and both carbachol-induced and spontaneous detrusor strip contraction amplitude decreased gradually for the duration from 0 to 6 h, and then increased gradually to near-normal values at 24 h. Treatment of muscle strips with the p38MAK inhibitor, SB203580, inhibited carbachol-induced contractions. Smooth muscle ultrastructure damage was the highest at 6 h after AUR, and then lessened gradually during next 7 days, and ultrastructure was close to normal. Expressions of Hsp27 mRNA and protein and the proteins of the three phosphorylated forms were higher at 0 h, decreased to lower levels up to 6 h, and then gradually increased. Therefore, we conclude that rat bladder contractile function after AUR worsens during 0–6 h, and then gradually recovers. The findings of the current study suggest that Hsp27 modulates bladder smooth muscle contraction after AUR, and that phosphorylation of Hsp27 may be an important pathway modulating actin cytoskeleton dynamics in bladder smooth muscle contraction and reconstruction after injury.     

Stepwise length changes in single invertebrate thick filaments

Previous experiments on thick filaments of the anterior byssus retractor muscle of Mytilus and the telson-levator muscle of Limulus polyphemus have shown large, reversible length changes up to 23% and 66% of initial length, respectively, within the physiological tension range. Using nanofabricated cantilevers and newly developed high-resolution detection methods, we investigated the dynamics of isolated Mytilus anterior byssus retractor muscle thick filaments. Single thick filaments were suspended between the tips of two microbeams oriented perpendicular to the filament axis: a deflectable cantilever and a stationary beam. Axial stress was applied by translating the base of the deflectable nanolever away from the stationary beam, which bent the nanolever. Tips of flexible nanolevers and stationary beam were imaged onto a photodiode array to track their positions. Filament shortening and lengthening traces, obtained immediately after the motor had imposed stress on the filament, showed steps and pauses. Step sizes were 2.7 nm and integer multiples thereof. Steps of this same size paradigm have been seen both during contraction of single sarcomeres and during active interaction between single isolated actin and myosin filaments, raising the question whether all of these phenomena might be related.     

A mathematical model for sarcomere mechanics in cross-striated muscles taking into account the stretch and twist of actin filaments

A model of sarcomere mechanics, which takes into account the elongation of the actin and myosin filaments and twisting of the actin filaments during muscle contraction is suggested. The model accounts for the experimentally observed phenomena of the stretch and twist of actin filaments due to strong binding of myosin heads and pulling force. Some model parameters were estimated from published experimental data. The results of modelling suggest that the twist of actin filaments may play an essential role in mechanical responses of contracting muscle fibres to stepwise changes in their length.     

A model of muscle contraction based on the Langevin equation with actomyosin potentials

We propose a muscle contraction model that is essentially a model of the motion of myosin motors as described by a Langevin equation. This model involves one-dimensional numerical calculations wherein the total force is the sum of a viscous force proportional to the myosin head velocity, a white Gaussian noise produced by random forces and other potential forces originating from the actomyosin structure and intra-molecular charges. We calculate the velocity of a single myosin on an actin filament to be 4.9–49 μm/s, depending on the viscosity between the actomyosin molecules. A myosin filament with a hundred myosin heads is used to simulate the contractions of a half-sarcomere within the skeletal muscle. The force response due to a quick release in the isometric contraction is simulated using a process wherein crossbridges are changed forcibly from one state to another. In contrast, the force response to a quick stretch is simulated using purely mechanical characteristics. We simulate the force–velocity relation and energy efficiency in the isotonic contraction and adenosine triphosphate consumption. The simulation results are in good agreement with the experimental results. We show that the Langevin equation for the actomyosin potentials can be modified statistically to become an existing muscle model that uses Maxwell elements.     

Noise reduction from genotyping microarrays using probe level information

Genomic copy number change is one of the important phenomenon observed in cancer and other genetic disorders. Recently oligonucleotide microarrays have been used to analyze changes in the copy number. Although high density microarrays provide genome wide useful data on copy number, they are often associated with substantial amount of experimental noise that could affect the performance of the analyses. We used the high density oligonucleotide genotyping microarrays in our experiments that uses redundant probe tiling approach for individual SNPs. We found that the noise in the genotyping microarray data is associated with several experimental steps during target preparation and devised an algorithm that takes into account those experimental parameters. Additionally, defective probes that do not hybridize well to the target and therefore could not be modified inherently were detected and omitted automatically by using the algorithm. When we applied the algorithm to actual datasets, we could reduce the noise substantially without compressing the dynamic range. Additionally, combinatorial use of our noise reduction algorithm and conventional breakpoint detection algorithm successfully detected a microamplification of c-myc which was overlooked in the raw data. The algorithm described here is freely available with the software upon request to all non-profit researchers.     

The exocytotic fusion pore of small granules has a conductance similar to an ion channel

We measured capacitance changes in cell attached patches of human neutrophils using a high frequency lock-in method. With this technique the noise level is reduced to 0.025 fF such that capacitance steps of 0.1 fF are clearly detected corresponding to exo- and endocytosis of single 60 nm vesicles. It is thus possible to detect almost all known exocytotic and endocytotic processes including exocytosis of small neurotransmitter containing vesicles in most cell types as well as endocytosis of coated and uncoated pits. In neutrophils we demonstrate a stepwise capacitance decrease generated by 60-165 nm vesicles as expected for endocytosis of coated and non-coated pits. Following ionomycin stimulation a stepwise capacitance increase is observed consisting of 0.1-5 fF steps corresponding to the different granule types of human neutrophils from secretory vesicles to azurophil granules. The opening of individual fusion pores is resolved during exocytosis of 200 nm vesicles. The initial conductance has a mean value of 150 pS and can be as low as 35 pS which is similar to the conductance of many ion channels suggesting that the initial fusion pore is formed by a protein complex.     

Fully non-linear hyper-viscoelastic modeling of skeletal muscle in compression

Understanding the behavior of skeletal muscle is critical to implementing computational methods to study how the body responds to compressive loading. This work presents a novel approach to studying the fully nonlinear response of skeletal muscle in compression. Porcine muscle was compressed in both the longitudinal and transverse directions under five stress relaxation steps. Each step consisted of 5% engineering strain over 1 s followed by a relaxation period until equilibrium was reached at an observed change of 1 g/min. The resulting data were analyzed to identify the peak and equilibrium stresses as well as relaxation time for all samples. Additionally, a fully nonlinear strain energy density–based Prony series constitutive model was implemented and validated with independent constant rate compressive data. A nonlinear least squares optimization approach utilizing the Levenberg–Marquardt algorithm was implemented to fit model behavior to experimental data. The results suggested the time-dependent material response plays a key role in the anisotropy of skeletal muscle as increasing strain showed differences in peak stress and relaxation time (p < 0.05), but changes in equilibrium stress disappeared (p > 0.05). The optimizing procedure produced a single set of hyper-viscoelastic parameters which characterized compressive muscle behavior under stress relaxation conditions. The utilized constitutive model was the first orthotropic, fully nonlinear hyper-viscoelastic model of skeletal muscle in compression while maintaining agreement with constitutive physical boundaries. The model provided an excellent fit to experimental data and agreed well with the independent validation in the transverse direction.     

Oxygen uptake,heart rate and activities of locomotor muscles during a critical swimming speed protocol in the gilthead sea bream Sparus aurata

Oxygen uptake, heart rate and contraction frequencies of slow oxidative (SO) and fast glycolytic (FG) muscle were measured simultaneously in gilthead seabream Sparus aurata submitted to stepwise increases in current speed in a swimming respirometer. Variation in oxygen uptake was closely related to variation in heart rate, over initial steps these rose in concert with an increase in contraction frequency of SO muscle. There was an asymptote in oxygen uptake and heart rate at high speeds that reflected a transition from exclusive use of aerobic SO muscle to a combination of SO and anaerobic FG muscle, and which preceded fatigue.     

Torque-related changes in mechanomyographic intensity patterns for the superficial quadriceps femoris muscles

The purpose of this study was to investigate changes in mechanomyographic (MMG) intensity patterns for the vastus lateralis (VL), rectus femoris (RF) and vastus medialis (VM) during submaximal to maximal concentric isokinetic, eccentric isokinetic and isometric muscle actions of the leg extensors. Eleven men (mean ± SD age = 20.1 ± 1.1 years) performed concentric, eccentric and isometric muscle actions of the dominant leg extensors on 3 separate days. Surface MMG signals were detected from the VL, RF and VM, processed with a wavelet analysis and examined with a trend plot. The results indicated that the trend plot was capable of tracking systematic changes in MMG amplitude and frequency with an increase in torque. However, these changes were statistically significant in only 26% of the cases. There were also no consistent differences between muscles or contraction types for the significance of the trend plots.     

Effects of divergent resistance exercise contraction mode and dietary supplementation type on anabolic signalling,muscle protein synthesis and muscle hypertrophy

Greater force produced with eccentric (ECC) compared to concentric (CONC) contractions, may comprise a stronger driver of muscle growth, which may be further augmented by protein supplementation. We investigated the effect of differentiated contraction mode with either whey protein hydrolysate and carbohydrate (WPH + CHO) or isocaloric carbohydrate (CHO) supplementation on regulation of anabolic signalling, muscle protein synthesis (MPS) and muscle hypertrophy. Twenty-four human participants performed unilateral isolated maximal ECC versus CONC contractions during exercise habituation, single-bout exercise and 12 weeks of training combined with WPH + CHO or CHO supplements. In the exercise-habituated state, p-mTOR, p-p70S6K, p-rpS6 increased by approximately 42, 206 and 213 %, respectively, at 1 h post-exercise, with resistance exercise per se; whereas, the phosphorylation was exclusively maintained with ECC at 3 and 5 h post-exercise. This acute anabolic signalling response did not differ between the isocaloric supplement types, neither did protein fractional synthesis rate differ between interventions. Twelve weeks of ECC as well as CONC resistance training augmented hypertrophy with WPH + CHO group compared to the CHO group (7.3 ± 1.0 versus 3.4 ± 0.8 %), independently of exercise contraction type. Training did not produce major changes in basal levels of Akt-mTOR pathway components. In conclusion, maximal ECC contraction mode may constitute a superior driver of acute anabolic signalling that may not be mirrored in the muscle protein synthesis rate. Furthermore, with prolonged high-volume resistance training, contraction mode seems less influential on the magnitude of muscle hypertrophy, whereas protein and carbohydrate supplementation augments muscle hypertrophy as compared to isocaloric carbohydrate supplementation .     

Four-component power spectral density model of steady-state isometric force

The aim of this study was to develop and evaluate a model based upon four identified characteristics of the power spectral density associated with isometric force at a range of constant force levels (5–95% maximum voluntary contraction). The characteristics modeled were: (1) a low-frequency resonant peak located at about 1 Hz; (2) a region of 1/f-like fractional Gaussian noise (fGn); (3) the resonant peak in the 8–12 Hz region on the PSD; and (4) Gaussian white noise resulting from a combination of neural as well as equipment noise. When superimposed, these components were used in a direct fit to the isometric force data to generate a linear predictor that resulted in residual values on the order of the white noise present in the original force time series.     

Noise affects porpoise click detections – the magnitude of the effect depends on logger type and detection filter settings

Automatic click detectors and full-bandwidth sound recorders are widely used in passive acoustic monitoring of small cetaceans. Detection of these signals depends on a variety of factors, including signal to noise ratio. Passive acoustic monitoring is often used to study impact of underwater noise on small cetaceans, but as detection probability is affected by changes in signal to noise ratio, variable noise levels may affect conclusions drawn from these experiments. Therefore, we examine how different detectors and filters perform in varying ocean noise conditions. C-PODs and full-bandwidth recorders (Wildlife Acoustics, SM2M+) were deployed at two stations in an environment with fluctuating ambient noise for 42 days. Noise level and harbour porpoise (Phocoena phocoena) click trains simultaneously recorded on both loggers were compared. Overall, we found that porpoise click detections by the algorithm used to analyse full-band recorder data (Pamguard) paralleled detections by the C-POD. However, Pamguard detected significantly more clicks than the C-POD. A decrease in detections was seen for both loggers with increasing noise in the band 20 –160 kHz, in particular for levels above 100 dB re 1μPa rms. We also found that the Pamguard detection function changed the least over varying noise conditions when compared to the C-POD detectors. This study sheds light on the fact that inference of animal presence/absence or density that are based on echolocation cues (here, Porpoise Positive Minutes) shall account for the acoustic environments where probability of detecting signals may be affected by variability in ambient noise levels.     

A comparative study of the supramolecular structure of frog sartorius and dorsal semitendinosus muscle

This report describes a comparative X-ray diffraction study of the supramolecular structure of frog sartorius and semitendinosus muscles. For sarcomere lengths of 2.7 microns and below the X-ray diffraction diagrams of each muscle type are very similar; the only differences being that the diffraction diagram for semitendinosus muscles exhibit the presence of a broad diffraction band or a cluster of diffraction orders at a spacing of ca. 230.0 nm and, also, they lack a periodicity of ca. 102.0 nm. For sarcomere lengths greater than 2.7 microns disruption of the sarcomere from sartorius muscle occurs as seen by the loss of sampling in the diffraction diagram. The semitendinosus muscle can be stretched to much longer lengths (in excess of 3.0 microns) before a loss of sampling is detected. The data also shows that in the case of the semitendinosus muscle for long sarcomere lengths transverse bands of mass are able to move without retaining a defined distance to either the Z or the M lines. This is not observed in the case of the sartorius muscle. Thus, at resolutions between ca. 3.6 microns and 7.50 nm significant ultrastructural differences between these two muscles are apparent. The data suggest that the ability of these mass bands to move may be responsible for the differences in the development of passive tension exhibited by these two muscles.     

A Cross-Bridge Cycle with Two Tension-Generating Steps Simulates Skeletal Muscle Mechanics

We examined whether cross-bridge cycle models with one or two tension-generating steps can account for the force-velocity relation of and tension response to length steps of frog skeletal muscle. Transition-state theory defined the strain dependence of the rate constants. The filament stiffness was non-Hookean. Models were refined against experimental data by simulated annealing and downhill simplex runs. Models with one tension-generating step were rejected, as they had a low efficiency and fitted the experimental data relatively poorly. The best model with two tension-generating steps (stroke distances 5.6 and 4.6 nm) and a cross-bridge stiffness of 1.7 pN/nm gave a good account of the experimental data. The two tensing steps allow an efficiency of up to 38% during shortening. In an isometric contraction, 54.7% of the attached heads were in a pre-tension-generating state, 44.5% of the attached heads had undergone the first tension-generating step, and only 0.8% had undergone both tension-generating steps; they bore 34%, 64%, and 2%, respectively, of the isometric tension. During slow shortening, the second tensing step made a greater contribution. During lengthening, up to 93% of the attached heads were in a pre-tension-generating state yet bore elevated tension by being dragged to high strains before detaching.     

Fabrication and Optical Properties of Au-Coated Polystyrene Nanosphere Arrays with Controlled Gaps

Large area monolayer of self-assembled polystyrene sphere (PS) arrays were formed by an interface self-assembly method and the gap of PS was adjusted by O₂ plasma treatment (OPT). After different duration of OPT, the spacing between the PSs varied from 5 to 88 nm. Then, 20 nm Au film was deposited on the PS arrays by electron beam deposition. The absorption peaks of Au-coated PS array red-shifted obviously by changing the gap of PS. The new absorption peaks emerged when the gap of the PS decreased to about 20 nm. The surface plasmon resonance (SPR) was employed to explain the absorption proportion of this Au-PS structure. These micro-nano structures exhibit tunable SPR bands, which may be useful to the applications in some research fields, such as biosensing, single molecule detection, and novel optoelectronic devices.     

A Cross-Bridge Cycle with Two Tension-Generating Steps Simulates Skeletal Muscle Mechanics

We examined whether cross-bridge cycle models with one or two tension-generating steps can account for the force-velocity relation of and tension response to length steps of frog skeletal muscle. Transition-state theory defined the strain dependence of the rate constants. The filament stiffness was non-Hookean. Models were refined against experimental data by simulated annealing and downhill simplex runs. Models with one tension-generating step were rejected, as they had a low efficiency and fitted the experimental data relatively poorly. The best model with two tension-generating steps (stroke distances 5.6 and 4.6 nm) and a cross-bridge stiffness of 1.7 pN/nm gave a good account of the experimental data. The two tensing steps allow an efficiency of up to 38% during shortening. In an isometric contraction, 54.7% of the attached heads were in a pre-tension-generating state, 44.5% of the attached heads had undergone the first tension-generating step, and only 0.8% had undergone both tension-generating steps; they bore 34%, 64%, and 2%, respectively, of the isometric tension. During slow shortening, the second tensing step made a greater contribution. During lengthening, up to 93% of the attached heads were in a pre-tension-generating state yet bore elevated tension by being dragged to high strains before detaching.     

Thr649Ala-AS160 knock-in mutation does not impair contraction/AICAR-induced glucose transport in mouse muscle

AS160 and its closely related protein TBC1D1 have emerged as key mediators for both insulin- and contraction-stimulated muscle glucose uptake through regulating GLUT4 trafficking. Insulin increases AS160 phosphorylation at multiple Akt/PKB consensus sites, including Thr(649), and promotes its binding to 14-3-3 proteins through phospho-Thr(649). We recently provided genetic evidence that AS160-Thr(649) phosphorylation/14-3-3 binding plays a key role in mediating insulin-stimulated glucose uptake in muscle. Contraction has also been proposed to increase phosphorylation of AS160 and TBC1D1 via AMPK, which could be detected by a generic phospho-Akt substrate (PAS) antibody. Here, analysis of AS160 immunoprecipitates from muscle extracts with site-specific phospho-antibodies revealed that contraction and AICAR caused no increase but rather a slight decrease in phosphorylation of the major PAS recognition site AS160-Thr(649). In line with this, contraction failed to enhance 14-3-3 binding to AS160. Consistent with previous reports, we also observed that in situ contraction stimulated the signal intensity of PAS antibody immunoreactive protein of ～150-160 kDa in muscle extracts. Using a TBC1D1 deletion mutant mouse, we showed that TBC1D1 protein accounted for the majority of the PAS antibody immunoreactive signals of ～150-160 kDa in extracts of contracted muscles. Consistent with the proposed role of AS160-Thr(649) phosphorylation/14-3-3 binding in mediating glucose uptake, AS160-Thr(649)Ala knock-in mice displayed normal glucose uptake upon contraction and AICAR in isolated muscles. We conclude that the previously reported PAS antibody immunoreactive band ～150-160 kDa, which were increased upon contraction, does not represent AS160 but TBC1D1, and that AS160-Thr(649)Ala substitution impairs insulin- but neither contraction- nor AICAR-stimulated glucose uptake in mouse skeletal muscle.