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Behavior Assays

Behavior assays quantitatively measure the behavior of a subject. These are commonly done to assess the effect or presence of a mutation.

behavior assay

A behavior maze in action (Ricci Lab).

Behavior Assay Nicolson Lab

Dorsal light reflex in adult zebrafish. The fish on the right have a mutation in Cadherin 23 and do not sense gravity. Mutations in this gene cause deafness in fish, mice and humans (Nicolson Lab)

Tracking the vestibulospinal reflex in zebrafish larvae (Nicolson Lab)

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Biochemistry is the study of chemical interactions occurring within living organisms. Biochemistry allows researchers to study in vitro biological molecules like proteins like testing their capacity to bind other proteins or lipids.

molecule structure
molecule structure
molecule structure

Structure of a protein domain carrying a deafness mutation (Grillet Lab).

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Data is king in the 21st century, and there is no better example of this than the rapidly growing field of bioinformatics. Bioinformatics involves figuring out ways to collect, process and analyze large amounts of complex biological data.

gif of celltrails software

CellTrails, a bioinformatics package to identify spatial and temporal transitions among related cell groups. Shown here is a CellTrails map in 3D, which represents the expression level of the ATOH1 gene among progenitor cells that differentiate into new hair cells; the red line is the “trail”. The peak of ATOH1 gene activation is visible and shown as a topological map (Heller Lab).

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Biophysics applies theoretical physics laws and formulae to the microscopic biological processes occurring within living organisms.

Single channel measurements reveal lipid regulation of mechanotransduction (Ricci Lab)
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Computing includes the development of computer algorithms to analyze and visualize large quantities of data. Computational modeling is also crucial for understanding experimental observations and for driving new experimental directions.

Computational simulations explain why sounds emitted from the ear (red) shift in frequency and amplitude when the ambient pressure is increased (green) (Ó Maoiléidigh Lab).

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Drug Discovery

Drug discovery is a process combining research-based hypotheses with trial and error, with a goal of discovering a drug that can enact desired change within a biological system.

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Electronic Microscopy

Electronic microscopy (EM) uses electrons instead of photons for light and fluorescence microscopy. This technique provides higher resolution but is not compatible with live-imaging. In Transmission EM (TEM), a thin-section of a tissue fixed and stained with heavy metals to give contrast by preventing the electron beam from going across the section. In Scanning EM (SEM), the sample is dehydrated and coated with a layer of metal. The electron beam interacts with the metal atoms on the samples, and the emitted secondary electrons are detected by the microscope, giving information about the surface of the sample.

transmission electron microscopy
hair bundles

Transmission EM (Grillet Lab).

Transmission EM (Grillet Lab).

TEM image nicolson
SEM Image Nicolson Lab

Ribbon synapse in a zebrafish inner ear hair cell (Nicolson Lab).

SEM image of a cluster of zebrafish hair cells at the surface of the skin (Nicolson Lab).
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Electrophysiology is the study of how electric currents and potentials affect the physiology of natural models. Electricity across cell membranes is often studied in biological systems.

Nicolson Lab TEM

Hearing cells turn mechanical motion into nerve potentials at the synaptic boutons, where nerves meet the bottom of the hearing cell. Ions are released through vesicles that create an electrical signal, and this signal can be measured (Ricci Lab)

Recording extracellular potentials of inner ear hair cells in a zebrafish larva (Nicolson Lab)

shefin project schematic and data

Moving hair cells using patch-clamping. Pushing the hair cells creates an electric current (Ricci Lab)

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Fish Genetics

Genetics is the study of DNA, genes, and inherited attributes. Genetics plays a large role in the era of Precision Medicine, where medical treatments and scientific research are tailored to the genetic code. The genes required for hearing and balance are highly conserved from humans to fish. Currently, SICHL researchers are using genetic methods in zebrafish to study hearing loss.

zebrafish genetics

A dramatization of fish genetics (Nicolson Lab).

Live cell imaging of transgenic fish expressing GFP-tagged tip link protein Pcdh15 in hair bundles (Nicolson Lab).

Live cell imaging of transgenic fish expressing GFP-tagged Actin protein in hair bundles (Nicolson Lab).

Live cell imaging of transgenic fish expressing RFP in hair cells and GFP in dopaminergic efferent fibers (Nicolson Lab).

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Immunochemistry is the use of antibodies to specifically detect proteins. These antibodies are detected by secondary antibodies carrying fluorophores which are detected by fluorescence microscopy.

hair cell stain
hair bundles immunostain

Tympanic perforation. Blue (Dapi). Green (EGFR reporter) (Santa Maria Lab).

Cochlear hair cells and their hair bundles (Grillet Lab).

shefin project schematic and data

FLIM and FRAP are special uses of immunocytochemistry that look at immunolabel staining over time (Ricci Lab)

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Live imaging of neurons in the brain of zebrafish larva. (Red, MAGUK, a postsynaptic marker; Green, Vglut3, synaptic vesicle protein; Blue, NSF, component of the membrane fusion machinery) (Nicolson Lab)

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Live-Cell Imaging

Live-cell imaging is different from most microscope imaging techniques because the cell is not fixed, and still alive. This imaging can be useful to view biological processes happening in real-time, such as the flow of calcium across a membrane.

Here, alive hearing cells are stimulated, and their electrical response is visualized via fluorescence (Ricci Lab)

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Live cell imaging of actin filaments in hair bundles in a larval inner ear and corresponding surface rendering images (Nicolson Lab)

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Mathematical techniques are used to analyze experimental data and to understand computational modeling. Mathematical models also help to explain experimental observations and make predictions to be tested by additional experiments.


The ear may use self-oscillating elements to detect sound signals. External signals skew the probability distribution of a self-oscillating system (Ó Maoiléidigh Lab).

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Modeling Biological Systems

Mathematical and computational models are built to help explain how a biological system behaves. Systems of equations describe the properties and interactions between the components of a biological system. These models are guided by experimental observations and their predictions are tested by additional experiments.

Modeling predictions describing the behavior of the ear’s sensory cell were subsequently verified by experimental observations (Ó Maoiléidigh Lab).

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Molecular Biology

Molecular biology studies the smallest building blocks of life – molecules. Understanding structure and function of common molecules such as DNA and proteins help scientists determine their effect on cells. Molecular biology is a toolbox for researchers enabling for example to edit in vitro the genetic code of genes or to detect the expression of a gene within a tissue (In situ hybridization).

cochlea stain
cochlea stain

Gene expression can be detected by in situ hybridization at the cellular level. Here a gene is expressed in the mouse cochlea and their hair cells (Grillet Lab).

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Mouse Genetics

The genome of mice can be modified from embryonic stem cells or zygotes. The modification allows researchers to model human mutation responsible for hearing loss to study them, or when done randomly, it enables the discovery of novel genes causing this condition. We use homologous recombination and CRISPR/Ca9 editing technologies.

cochlea stain immunochemistry

Mouse Cochlear Hair Cells are genetically fluorescently labeled (Math1-CR; Ai9 flox) (Grillet Lab).

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Single-Cell Transcriptomics

Single-cell transcriptomics looks at gene expression levels in a cell. It does this by breaking up the cell and measuring messenger RNA (mRNA) levels. Depending on the mRNA messages found, the “active” genes can be deduced.

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Surgical Approaches

Surgery is essential to many SICHL research endeavors. Finding the optimal procedures and routes to tissue access is an area of constant refinement and improvement.

surgical approach
surgical technique

Upper image: Shown is a small opening of ~1mm in diameter to expose one of the chicken’s vestibular canals.
Lower image: injection of drugs into the chicken inner ear via the vestibular canal (Heller Lab).

Transcervical Eustachian tube occlusion (Santa Maria Lab).

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Theoretical Physics

Theoretical physics uses mathematical and computational models to describe nature. Because biological systems obey the laws of physics, it is often useful to employ physical principles to construct models of these systems. The behavior of biological systems is better understood by taking their physics into account.

The physics of a sensory cell embedded in the inner ear is described by a simplified model (Ó Maoiléidigh Lab).

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Tissue Culture

Tissue culture is the science of keeping tissue alive outside of the model organism. Tissue can also be cultured to replicate and grow outside of the donor. To test hypotheses, the auditory and vestibular sensory epithelia can be dissected out of the inner ear and cultured in vitro with different conditions or drugs.

Cochlea culture (Grillet Lab).

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Viral Transduction

Viral transduction refers to the use of a virus as a vector to affect genetic change. A virus is made to carry genetic information (DNA, RNA), that is inserted into a cell and changes the intrinsic DNA. This technique is often used to induce and study genetic mutations.

A viral vector carrying a fluorescent-tagged protein was injected into the posterior semi-circular canal. Five weeks later, fluorescence has appeared within the cochlea (Ricci Lab).

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Virtual Reality

You might associate virtual reality with video games, but it can also be used to teach surgical techniques and analyze anatomy. SICHL researchers also use virtual reality to analyze data.

Visualizing data in 3D (Heller Lab).

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Whole Animal Physiology

Whole Animal Physiology is the study of a particular function of an organism. To study the auditory or vestibular function, we record electric potentials non invasively in the back of the brain, which reflects the sequence of neurons activated by sound or head movements. The amplitude of these responses at different intensities of stimulation provides a threshold of hearing or head motion detection.

an abr trace from the ricci lab

Waveforms of the auditory waveform response (Ricci Lab).