Label-free quantitative mass spectrometry analysis of differential protein expression in the developing cochlear sensory epithelium.

Background: The sensory epithelium of the inner ear converts the mechanical energy of sound to electro-chemical energy recognized by the central nervous system. This process is mediated by receptor cells known as hair cells that express proteins in a timely fashion with the onset of hearing.

Methods: The proteomes of 3, 14, and 30 day-old mice cochlear sensory epithelia were revealed, using label-free quantitative mass spectrometry (LTQ-Orbitrap).

Ultrastructural Identification and Colocalization of Interacting Proteins in the Murine Cochlea by Post-Embedding Immunogold Transmission Electron Microscopy.

Verification of the presence and location of a protein within tissue can be accomplished by western blotting and immunohistochemistry, using either paraffin or frozen sections. Affinity purification by reciprocal coimmunoprecipitations using the tissue of interest can demonstrate the existence of an interacting pair of proteins. Ultimately, the ability to visualize the interaction at the cellular level is desired.

Protein Quantitation of the Developing Cochlea Using Mass Spectrometry.

Mass spectrometry-based proteomics allows for the measurement of hundreds to thousands of proteins in a biological system. Additionally, mass spectrometry can also be used to quantify proteins and peptides. However, observing quantitative differences between biological systems using mass spectrometry-based proteomics can be challenging because it is critical to have a method that is fast, reproducible, and accurate.

Bottom-up and shotgun proteomics to identify a comprehensive cochlear proteome.

Proteomics is a commonly used approach that can provide insights into complex biological systems. The cochlear sensory epithelium contains receptors that transduce the mechanical energy of sound into an electro-chemical energy processed by the peripheral and central nervous systems. Several proteomic techniques have been developed to study the cochlear inner ear, such as two-dimensional difference gel electrophoresis (2D-DIGE), antibody microarray, and mass spectrometry (MS).

In-depth proteomic analysis of mouse cochlear sensory epithelium by mass spectrometry.

Proteomic analysis of sensory organs such as the cochlea is challenging due to its small size and difficulties with membrane protein isolation. Mass spectrometry in conjunction with separation methods can provide a more comprehensive proteome, because of the ability to enrich protein samples, detect hydrophobic proteins, and identify low abundant proteins by reducing the proteome dynamic range. GELFrEE as well as different separation and digestion techniques were combined with FASP and nanoLC-MS/MS to obtain an in-depth proteome analysis of cochlear sensory epithelium from 30-day-old mice.

In vivo verification of protein interactions in the inner ear by coimmunoprecipitation.

Genomics has provided us with vast amounts of data and thus, the challenge to identify and characterize gene products. Proteomics analysis, using methods such as yeast two-hybrid screenings, isoelectric focusing, and mass spectroscopy, generate potentially useful information. To determine functional relationships between and among proteins, however, the initial data for putative protein interactions must first be validated.

The use of 2-D gels to identify novel protein-protein interactions in the cochlea.

Functional proteomics comprises a wide range of technologies for the identification of novel protein-protein interactions and biological markers. Studies of protein-protein interactions have gained from the development of techniques and technologies such as immunoprecipitation, preparative two-dimensional (2-D) gel electrophoresis for peptide mass fingerprinting (PMF), using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry, and liquid chromatography-tandem mass spectrometry (LC-MS/MS). These applications enabled the discovery of putative protein partners without a priori knowledge of which one(s) might be relevant.

Development and regeneration of hair cells share common functional features.

The structural phenotype of neural connections in the auditory brainstem is sculpted by spontaneous and stimulus-induced neural activities during development. However, functional and molecular mechanisms of spontaneous action potentials (SAPs) in the developing cochlea are unknown. Additionally, it is unclear how regenerating hair cells establish their neural ranking in the constellation of neurons in the brainstem.

Ion channel gene expression in the inner ear.

The ion channel genome is still being defined despite numerous publications on the subject. The ion channel transcriptome is even more difficult to assess. Using high-throughput computational tools, we surveyed all available inner ear cDNA libraries to identify genes coding for ion channels.

Survey of inward ionic currents acquired by the cochleovestibular ganglion of the early-aged embryonic chick.

The acquisition of ion channels is critical to the formation of neuronal pathways in the peripheral and central nervous systems. This study describes the different types of inward currents (Ii) recorded from the soma of isolated cochleovestibular ganglion (CVG) cells of the embryonic chicken, Gallus gallus. Cells were isolated for whole-cell tight-seal recording from embryonic day (ED) 3, an age when the CVG is a cell cluster, to ED 9, an age when the cochlear and vestibular ganglia (CG, VG) are distinct structures.

Identification and localization of an arachidonic acid-sensitive potassium channel in the cochlea.

Receptor cells of the auditory and vestibular end organs of vertebrates acquire various types of potassium channels during development. Their expression and kinetics can differ along the tonotopic axis as well as in different cell types of the sensory epithelium. These variations can play a crucial role in modulating sensory transduction and cochlear tuning.

Cloning and developmental expression of Shaker potassium channels in the cochlea of the chicken.

Signal coding by the receptor and neuronal cells of the auditory system involves various ion channels that modulate a sound stimulus. The genes that encode a number of these ion channels and their accessory subunits are presently unknown for channels found in the sensory epithelium and cochlear nerve. Among these genes are those that encode delayed rectifier and transient type potassium channels found in both the sensory cells and the ganglion.