In vivo outer hair cell length changes expose the active process in the cochlea

Background

Mammalian hearing is refined by amplification of the sound-evoked vibration of the cochlear partition. This amplification is at least partly due to forces produced by protein motors residing in the cylindrical body of the outer hair cell. To transmit power to the cochlear partition, it is required that the outer hair cells dynamically change their length, in addition to generating force. These length changes, which have not previously been measured in vivo, must be correctly timed with the acoustic stimulus to produce amplification.

Methodology/Principal Findings

Using in vivo optical coherence tomography, we demonstrate that outer hair cells in living guinea pigs have length changes with unexpected timing and magnitudes that depend on the stimulus level in the sensitive cochlea.

Conclusions/Significance

The level-dependent length change is a necessary condition for directly validating that power is expended by the active process presumed to underlie normal hearing.     

Modeling 3-D deformation of outer hair cells and their production of the active force in the cochlea

 We analyze the deformation of the outer hair cell and its production of active force under physiological conditions. The active force has two components. One results from the strain caused by loading in the organ of Corti in the cochlea and depends on the level of the acoustic signal; the other is related to the intrinsic active properties of the cell membrane. We demonstrate our approach by considering, as a basic model of an outer hair cell in the organ of Corti, a cylindrical shell that is filled with an incompressible fluid and located between two planes that move relative to each other. These planes represent the basilar membrane and tectorial membrane complexes. We show that the deformed state of the cell has a 3-D nature, including bending and twisting components. This is different from the experimental conditions in which the active force is usually measured. We estimate the active force as a function of the relative position of the planes, angle of the cell's inclination, and the cell length. Received: 25 October 2001 / Accepted: 30 May 2002 We thank Drs. Aleksander Popel and William Brownell for constructive discussions of the results. This work was supported by research grants DC02775 and DC00354 from NIDCD and AG014748 from NIA.     

A minimally parametrized branching process explaining plateau phase of qPCR amplification

Quantitative polymerase chain reaction (qPCR) is a commonly used molecular biology technique for measuring the concentration of a target nucleic acid sequence in a sample. The whole qPCR amplification process usually consists of an exponential, a linear and a plateau phase. In qPCR experiments, amplification curves of samples with different template concentrations often, even though not always, have the same plateau height. The biological theory for this phenomenon is that the plateau height is determined by reaction kinetics. Does it mean that the target concentration has no effect on the final plateau height? We proposed a branching process based on Michaelis–Menten kinetics. Our model can describe all phases of qPCR amplification despite its simplicity (it depends on only one parameter). We theoretically showed, through almost sure convergence, that amplification curves will eventually plateau at finite values in any experiment, under any condition. We conclude that the plateau height is largely determined by reaction kinetics but could also be affected by the template concentration. This is in accordance with the current biological theory.

     

Solid phase DNA amplification: characterisation of primer attachment and amplification mechanisms

Different chemical methods used to attach oligonucleotides by their 5′-end on a glass surface were tested in the framework of solid phase PCR where surface-bound instead of freely-diffusing primers are used to amplify DNA. Each method was first evaluated for its capacity to provide a high surface coverage of oligonucleotides essentially attached via a 5′-specific linkage that satisfyingly withstands PCR conditions and leaves the 3′-ends available for DNA polymerase activity. The best results were obtained with 5′-thiol-modified oligonucleotides attached to amino-silanised glass slides using a heterobifunctional cross-linker reagent. It was then demonstrated that the primers bound to the glass surface using the optimal chemistry can be involved in attaching and amplifying DNA molecules present in the reaction mix in the absence of freely-diffusing primers. Two distinct amplification processes called interfacial and surface amplification have been observed and characterised. The newly synthesised DNA can be detected and quantified by radioactive and fluorescent hybridisation assays. These new surface amplification processes are seen as an interesting approach for attachment of DNA molecules by their 5′-end on a solid support and can be used as an alternative route for producing DNA chips for genomic studies.     

Probabilistic secretion of quanta: spontaneous release at active zones of varicosities, boutons, and endplates.

The amplitude-frequency histogram of spontaneous miniature endplate potentials follows a Gaussian distribution at mature endplates. This distribution gives the mean and variance of the quantum of transmitter. According to the vesicle hypothesis, this quantum is due to exocytosis of the contents of a single synaptic vesicle. Multimodal amplitude-frequency histograms are observed in varying degrees at developing endplates and at peripheral and central synapses, each of which has a specific active zone structure. These multimodal histograms may be due to the near synchronous exocytosis of more than one vesicle. In the present work, a theoretical treatment is given of the rise of intraterminal calcium after the stochastic opening of a calcium channel within a particular active zone geometry. The stochastic interaction of this calcium with the vesicle-associated proteins involved in exocytosis is then used to calculate the probability of quantal secretions from one or several vesicles at each active zone type. It is shown that this procedure can account for multiquantal spontaneous release that may occur at varicosities and boutons, compared with that at the active zones of motor nerve terminals.     

Normal phase and reverse phase HPLC-UV-MS analysis of process impurities for rapamycin analog ABT-578: application to active pharmaceutical ingredient process development

ABT-578, an active pharmaceutical ingredient (API), is a semi-synthetic tetrazole derivative of the fermented polyene macrolide rapamycin. Reverse phase (RP)-HPLC-UV-MS and normal phase (NP)-HPLC-UV-MS methods employing an LC/MSD trap with electrospray ionization (ESI) have been developed to track and map all significant impurities from the synthetic process. Trace-level tracking of key impurities occurring at various process points was achieved using complimentary methodologies, including a stability indicating reverse phase HPLC method capable of separating at least 25 starting materials and process-related impurities from the API (YMC-Pack Phenyl column, UV-MS, 210 nm) and a targeted reverse phase HPLC method capable of separating very polar compounds from crude reaction mixtures (Phenomenex Synergi Polar RP column, UV, 265 nm). In addition, a normal phase HPLC method condition with post-column modifier infusion is described for the separation of epimeric impurities, and analysis of aqueous-sensitive reactive species (YMC-Pack SIL column, UV-MS, 278 nm). Process control strategies were established with these combinations of analytical technologies for impurities analyses to enable a rich understanding of the ABT-578 process.     

Interplay between traveling wave propagation and amplification at the apex of the mouse cochlea

Sounds entering the mammalian ear produce waves that travel from the base to the apex of the cochlea. An electromechanical active process amplifies traveling wave motions and enables sound processing over a broad range of frequencies and intensities. The cochlear amplifier requires combining the global traveling wave with the local cellular processes that change along the length of the cochlea given the gradual changes in hair cell and supporting cell anatomy and physiology. Thus, we measured basilar membrane (BM) traveling waves in vivo along the apical turn of the mouse cochlea using volumetric optical coherence tomography and vibrometry. We found that there was a gradual reduction in key features of the active process toward the apex. For example, the gain decreased from 23 to 19 dB and tuning sharpness decreased from 2.5 to 1.4. Furthermore, we measured the frequency and intensity dependence of traveling wave properties. The phase velocity was larger than the group velocity, and both quantities gradually decrease from the base to the apex denoting a strong dispersion characteristic near the helicotrema. Moreover, we found that the spatial wavelength along the BM was highly level dependent in vivo, such that increasing the sound intensity from 30 to 90 dB sound pressure level increased the wavelength from 504 to 874 μm, a factor of 1.73. We hypothesize that this wavelength variation with sound intensity gives rise to an increase of the fluid-loaded mass on the BM and tunes its local resonance frequency. Together, these data demonstrate a strong interplay between the traveling wave propagation and amplification along the length of the cochlea.     

Interlevel relations in neural memory: extrasynaptic reception of mediators, potentiation, and spontaneous activity

The firing of "spontaneous" spikes is regarded as a result of mediator propagation to extrasynaptic receptors. Receptor-receptor interaction unites them in dimer and dimer clusters, which accept three conformational states under agonist action. There are two cooperative and potential dependent transitions between the states, where cluster accumulates or releases energy. The released energy can trigger a mechanism of endogenous (spontaneous) neuron firing in potentiation condition. These accumulating and triggering properties are absent in third (passive) conformational state, where gating charges immobilization reduces conformational mobility. The features of ionotropic, metabotropic and combined mediator action are discussed for different level of slow potential. Conformational effect depends on conformity of pattern space-temporal structure to geometric and functional features of metabotropic mediator sources in cluster environment. Each cluster appears to be adjusted for recognizing a certain vast set of afferent patterns. Number, structure and dimensionality of the recognized patterns are given by: 1) threshold of conformational transition, 2) allocation of synaptic and extrasynaptic mediator ejecting points in gap-hole environment of the receptive cluster 3) combinatorial connections of presynaptic cells with inhibit and excite synapses and 4) signal delays in presynaptic ways and neuropil. Numerous receptive clusters of soma-dendrite membrane are capable to write down information, to keep and accumulate it and to recover. Engram stored as passive/active conformational receptive cluster states is recovered in inversion by "spontaneous" neuronal activity. The original information may be recovered by reading via inhibit synapses.     

The phase response of the cortical slow oscillation

Cortical slow oscillations occur in the mammalian brain during deep sleep and have been shown to contribute to memory consolidation, an effect that can be enhanced by electrical stimulation. As the precise underlying working mechanisms are not known it is desired to develop and analyze computational models of slow oscillations and to study the response to electrical stimuli. In this paper we employ the conductance based model of Compte et al. (J Neurophysiol 89:2707–2725, 2003) to study the effect of electrical stimulation. The population response to electrical stimulation depends on the timing of the stimulus with respect to the state of the slow oscillation. First, we reproduce the experimental results of electrical stimulation in ferret brain slices by Shu et al. (Nature 423:288–293, 2003) from the conductance based model. We then numerically obtain the phase response curve for the conductance based network model to quantify the network’s response to weak stimuli. Our results agree with experiments in vivo and in vitro that show that sensitivity to stimulation is weaker in the up than in the down state. However, we also find that within the up state stimulation leads to a shortening of the up state, or phase advance, whereas during the up–down transition a prolongation of up states is possible, resulting in a phase delay. Finally, we compute the phase response curve for the simple mean-field model by Ngo et al. (EPL Europhys Lett 89:68002, 2010) and find that the qualitative shape of the PRC is preserved, despite its different mechanism for the generation of slow oscillations.     

Genome reduplication: Redeployment of cyclin-CDK complexes and spontaneous oscillation of APC/C

Comment on: Ma HT, et al. Mol Cell Biol 2009; 29:6500-14.     

Finite element modelling of human auditory periphery including a feed-forward amplification of the cochlea

A three-dimensional finite element model is developed for the simulation of the sound transmission through the human auditory periphery consisting of the external ear canal, middle ear and cochlea. The cochlea is modelled as a straight duct divided into two fluid-filled scalae by the basilar membrane (BM) having an orthotropic material property with dimensional variation along its length. In particular, an active feed-forward mechanism is added into the passive cochlear model to represent the activity of the outer hair cells (OHCs). An iterative procedure is proposed for calculating the nonlinear response resulting from the active cochlea in the frequency domain. Results on the middle-ear transfer function, BM steady-state frequency response and intracochlear pressure are derived. A good match of the model predictions with experimental data from the literatures demonstrates the validity of the ear model for simulating sound pressure gain of middle ear, frequency to place map, cochlear sensitivity and compressive output for large intensity input. The current model featuring an active cochlea is able to correlate directly the sound stimulus in the ear canal with the vibration of BM and provides a tool to explore the mechanisms by which sound pressure in the ear canal is converted to a stimulus for the OHCs.     

Modeling the amplification dynamics of human Alu retrotransposons

Retrotransposons have had a considerable impact on the overall architecture of the human genome. Currently, there are three lineages of retrotransposons (Alu, L1, and SVA) that are believed to be actively replicating in humans. While estimates of their copy number, sequence diversity, and levels of insertion polymorphism can readily be obtained from existing genomic sequence data and population sampling, a detailed understanding of the temporal pattern of retrotransposon amplification remains elusive. Here we pose the question of whether, using genomic sequence and population frequency data from extant taxa, one can adequately reconstruct historical amplification patterns. To this end, we developed a computer simulation that incorporates several known aspects of primate Alu retrotransposon biology and accommodates sampling effects resulting from the methods by which mobile elements are typically discovered and characterized. By modeling a number of amplification scenarios and comparing simulation-generated expectations to empirical data gathered from existing Alu subfamilies, we were able to statistically reject a number of amplification scenarios for individual subfamilies, including that of a rapid expansion or explosion of Alu amplification at the time of human–chimpanzee divergence.     

Modeling of cardiac muscle thin films: pre-stretch, passive and active behavior

Recent progress in tissue engineering has made it possible to build contractile bio-hybrid materials that undergo conformational changes by growing a layer of cardiac muscle on elastic polymeric membranes. Further development of such muscular thin films for building actuators and powering devices requires exploring several design parameters, which include the alignment of the cardiac myocytes and the thickness/Young's modulus of elastomeric film. To more efficiently explore these design parameters, we propose a 3-D phenomenological constitutive model, which accounts for both the passive deformation including pre-stretch and the active behavior of the cardiomyocytes. The proposed 3-D constitutive model is implemented within a finite element framework, and can be used to improve the current design of bio-hybrid thin films and help developing bio-hybrid constructs capable of complex conformational changes.     

Modeling the oscillation dynamics of activated airway smooth muscle strips

When strips of activated airway smooth muscle are stretched cyclically, they exhibit force-length loops that vary substantially in both position and shape with the amplitude and frequency of the stretch. This behavior has recently been ascribed to a dynamic interaction between the imposed stretch and the number of actin-myosin interactions in the muscle. However, it is well known that the passive rheological properties of smooth muscle have a major influence on its mechanical properties. We therefore hypothesized that these rheological properties play a significant role in the force-length dynamics of activated smooth muscle. To test the plausibility of this hypothesis, we developed a model of the smooth muscle strip consisting of a force generator in series with an elastic component. Realistic steady-state force-length loops are predicted by the model when the force generator obeys a hyperbolic force-velocity relationship, the series elastic component is highly nonlinear, and both elastic stiffness and force generation are adjusted so that peak loop force equals isometric force. We conclude that the dynamic behavior of airway smooth muscle can be ascribed in large part to an interaction between connective tissue rheology and the force-velocity behavior of contractile proteins.     

Cardiogenic oscillation and phase III caused by pressure-volume heterogeneity: a model

The effect of heterogeneity of pressure-volume (PV) behavior of lung units and the effect of the pulsations of the heart on expired N2 following a single breath of O2 were studied mathematically in a model of the lung. The lung was pictured as consisting of three compartments, one of high compliance (HC) and another of low compliance (LC), both affected by cardiac pulsations, and a third, nonoscillatory compartment (NC). Three sigmoid PV curves were assigned to the three compartments, for both acini and airway (generation 10-23), so that total compliance summed up to 200 ml/cmH2O. Bifurcation of NC was at generation 5/6 and that of HC and LC at any chosen generation. A steepness constant, K, was defined to characterize the sharply descending portion of the sigmoid PV curve. For a ratio of the steepness constant for the oscillatory compartments, KHC/KLC = 1, a sloping alveolar plateau was produced. The plateau was concave for KHC/KLC greater than 1 and slightly convex for KHC/KLC less than 1. Cardiogenic oscillations (CO) of the expired N2 were produced by alternate flows from either NC or HC and LC. CO diminished in fast expiration, and a phase shift between the heart pulsation and the CO was seen; both agree with experimental findings.     

The significance of the "lung phase" in host-helminth relations.

Many helminth infections have a "lung phase" whose significance considering the host-parasite relations has not yet been clarified. In some nematode infections larvae must pass through the lungs, in others adult worms live in the respiratory tract, and some others cause tropical pulmonary eosinophilia. Some examples of these infections (Nippostrongylus brasiliensis, Schistosoma mansoni, Trichinella spiralis and Toxocara canis) are considered to clarify whether this phase of infection is a "pro-host" or a "pro-parasite" mechanism. Whereas in primary infections--in some cases--transit through the lungs may render the parasite more resistant to host defence mechanisms (e.g., Schistosoma and perhaps Trichinella infections) or enables completion of the cycle (Nippostrongylus and Toxocara infections), in secondary infections the lungs might be the site of parasite killing.     

Modeling the emergence of the 'hot zones': tuberculosis and the amplification dynamics of drug resistance

'Hot zones' are areas that have >5% prevalence (or incidence) of multidrug-resistant tuberculosis (MDRTB). We present a new mathematical model (the amplifier model) that tracks the emergence and evolution of multiple (pre-MDR, MDR and post-MDR) strains of drug-resistant Mycobacterium tuberculosis. We reconstruct possible evolutionary trajectories that generated hot zones over the past three decades, and identify the key causal factors. Results are consistent with recently reported World Health Organization (WHO) data. Our analyses yield three important insights. First, paradoxically we found that areas with programs that successfully reduced wild-type pansensitive strains often evolved into hot zones. Second, some hot zones emerged even when MDR strains were substantially less fit (and thus less transmissible) than wild-type pansensitive strains. Third, levels of MDR are driven by case-finding rates, cure rates and amplification probabilities. To effectively control MDRTB in the hot zones, it is essential that the WHO specify a goal for minimizing the amplification probability.     

Genotype assignment in Gaucher disease by selective amplification of the active glucocerebrosidase gene.

Genomic DNA prepared from human cells in culture was amplified by the polymerase chain-reaction technique using two primers specific for the active human glucocerebrosidase gene. The 1,036-bp amplified fragment derived from the active gene was tested for the existence of three mutations--designated "370," "NciI," and "HhaI"--by allele-specific oligonucleotide hybridization. The results obtained from the cell lines examined permitted a clear distinction between homozygous affected, heterozygous, and normal genotypes. However, 28% of the possible affected loci were normal with respect to the three mutations, indicating the presence of additional mutations that remain to be elucidated. While the NciI mutation could be found in both Ashkenazi Jewish and non-Jewish type 1 patients, the only homozygotes with this mutation had the neurological (type 2 or type 3) form of the disease. The 370 mutation, on the other hand, was only present in type 1 patients and was not identified among any of the patients with neurologic forms of the disease.