Differential display and gene arrays to examine auditory plasticity

A combined genome-wide association and molecular study of age-related hearing loss in H. sapiens

BACKGROUND

Sensorineural hearing loss is one of the most common sensory deficiencies. However, the molecular contribution to age-related hearing loss is not fully elucidated.

METHODS

We performed genome-wide association studies (GWAS) for hearing loss-related traits in the UK Biobank (N = 362,396) and selected a high confidence set of ten hearing-associated gene products for staining in human cochlear samples: EYA4, LMX1A, PTK2/FAK, UBE3B, MMP2, SYNJ2, GRM5, TRIOBP, LMO-7, and NOX4.

RESULTS

All proteins were found to be expressed in human cochlear structures. Our findings illustrate cochlear structures that mediate mechano-electric transduction of auditory stimuli, neuronal conductance, and neuronal plasticity to be involved in age-related hearing loss.

CONCLUSIONS

Our results suggest common genetic variation to influence structural resilience to damage as well as cochlear recovery after trauma, which protect against accumulated damage to cochlear structures and the development of hearing loss over time.

DNA Microarrays in Otolaryngology-Head and Neck Surgery

OBJECTIVES: Our goal was to review the technologies underlying DNA microarrays and to explore their use in otolaryngology-head and neck surgery.

STUDY DESIGN: The current literature relating to microarray technology and methodology is reviewed, specifically the use of DNA microarrays to characterize gene expression. Bioinformatics involves computational and statistical methods to extract, organize, and analyze the huge amounts of data produced by microarray experiments. The means by which these techniques are being applied to otolaryngology-head and neck surgery are outlined.

RESULTS: Microarray technologies are having a substantial impact on biomedical research, including many areas relevant to otolaryngology-head and neck surgery.

CONCLUSIONS: DNA microarrays allow for the simultaneous investigationof thousands of individual genes in a single experiment. In the coming years, the application of these technologies to clinical medicine should allow for unprecedented methods ofdiagnosis and treatment.

SIGNIFICANCE: These highly parallel experimental techniques promise to revolutionize gene discovery, disease characterization, and drug development.

Proteomic identification of hair cell repair proteins in the model sea anemone Nematostella vectensis

Sea anemones have an extraordinary capability to repair damaged hair bundles, even after severe trauma. A group of secreted proteins, named repair proteins (RPs), found in mucus covering sea anemones significantly assists the repair of damaged hair bundle mechanoreceptors both in the sea anemone Haliplanella luciae and the blind cavefish Astyanax hubbsi. The polypeptide constituents of RPs must be identified in order to gain insight into the molecular mechanisms by which repair of hair bundles is accomplished. In this study, several polypeptides of RPs were isolated from mucus using blue native PAGE and then sequenced using LC-MS/MS. Thirty-seven known polypeptides were identified, including Hsp70s, as well as many polypeptide subunits of the 20S proteasome. Other identified polypeptides included those involved in cellular stress responses, protein folding, and protein degradation. Specific inhibitors of Hsp70s and the 20S proteasome were employed in experiments to test their involvement in hair bundle repair. The results of those experiments suggested that repair requires biologically active Hsp70s and 20S proteasomes. A model is proposed that considers the function of extracellular Hsp70s and 20S proteasomes in the repair of damaged hair cells.

In frame exon skipping in UBE3B is associated with developmental disorders and increased mortality in cattle

Background

Inherited developmental diseases can cause severe animal welfare and economic problems in dairy cattle. The use of a small number of bulls for artificial insemination (AI) carries a risk that recessive defects rapidly enrich in the population. In recent years, an increasing number of Finnish Ayrshire calves have been identified with signs of ptosis, intellectual disability, retarded growth and mortality, which constitute an inherited disorder classified as PIRM syndrome.

Results

We established a cohort of nine PIRM-affected calves and 38 unaffected half-siblings and performed a genome-wide association study (GWAS) to map the disease to a 700-kb region on bovine chromosome 17 (p = 1.55 × 10^-9). Whole genome re-sequencing of an unaffected carrier, its affected progeny and 43 other unaffected animals from another breed identified a G > A substitution mutation at the last nucleotide of exon 23 in the ubiquitin protein ligase E3B encoding gene (UBE3B). UBE3B transcript analysis revealed in-frame exon skipping in the affected animals resulting in an altered protein lacking 40 amino acids, of which 20 are located in the conserved HECT-domain, the catalytic site of the UBE3B protein. Mutation screening in 129 Ayrshire AI bulls currently used in Finland indicated a high carrier frequency (17.1%). We also found that PIRM syndrome might be connected to the recently identified AH1 haplotype, which has a frequency of 26.1% in the United States Ayrshire population.

Conclusion

We describe PIRM syndrome in cattle, which is associated with the mutated UBE3B gene. The bovine phenotype resembles human Kaufman oculocerebrofacial syndrome, which is also caused by mutations in UBE3B. PIRM syndrome might be connected with the recently identified AH1 haplotype, which is associated with reduced fertility in the US Ayrshire population. This study enables the development of a genetic test to efficiently reduce the high frequency of mutant UBE3B in Ayrshires, significantly improving animal health and reducing economic loss.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-890) contains supplementary material, which is available to authorized users.

Identification of a gene set to evaluate the potential effects of loud sounds from seismic surveys on the ears of fishes: a study with Salmo salar

Functional genomic studies were carried out on the inner ear of Atlantic salmon Salmo salar following exposure to a seismic airgun. Microarray analyses revealed 79 unique transcripts (passing background threshold), with 42 reproducibly up-regulated and 37 reproducibly down-regulated in exposed v. control fish. Regarding the potential effects on cellular energetics and cellular respiration, altered transcripts included those with roles in oxygen transport, the glycolytic pathway, the Krebs cycle and the electron transport chain. Of these, a number of transcripts encoding haemoglobins that are important in oxygen transport were up-regulated and among the most highly expressed. Up-regulation of transcripts encoding nicotinamide riboside kinase 2, which is also important in energy production and linked to nerve cell damage, points to evidence of neuronal damage in the ear following noise exposure. Transcripts related to protein modification or degradation also indicated potential damaging effects of sound on ear tissues. Notable in this regard were transcripts associated with the proteasome-ubiquitin pathway, which is involved in protein degradation, with the transcript encoding ubiquitin family domain-containing protein 1 displaying the highest response to exposure. The differential expression of transcripts observed for some immune responses could potentially be linked to the rupture of cell membranes. Meanwhile, the altered expression of transcripts for cytoskeletal proteins that contribute to the structural integrity of the inner ear could point to repair or regeneration of ear tissues including auditory hair cells. Regarding potential effects on hormones and vitamins, the protein carrier for thyroxine and retinol (vitamin A), namely transthyretin, was altered at the transcript expression level and it has been suggested from studies in mammalian systems that retinoic acid may play a role in the regeneration of damaged hair cells. The microarray experiment identified the transcript encoding growth hormone I as up-regulated by loud sound, supporting previous evidence linking growth hormone to hair cell regeneration in fishes. Quantitative (q) reverse transcription (RT) polymerase chain reaction (qRT-PCR) analyses confirmed dysregulation of some microarray-identified transcripts and in some cases revealed a high level of biological variability in the exposed group. These results support the potential utility of molecular biomarkers to evaluate the effect of seismic surveys on fishes with studies on the ears being placed in a priority category for development of exposure-response relationships. Knowledge of such relationships is necessary for addressing the question of potential size of injury zones.

WDR1 expression in normal and noise-damaged Sprague-Dawley rat cochleae

WD40 repeat protein 1 (WDR1) has been suggested as a protective mechanism or a sign of regeneration in avian cochlea. However, its role in mammalian cochlea has yet to be determined. Hence, we investigated WDR1 expression in sound-overstimulated Sprague-Dawley rats. Rats were divided into three groups (the permanent and temporary threshold shift [PTS and TTS] groups and the control group) according to the extent of noise exposure and euthanized immediately, 3, or 7 days after noise exposure for cochlear harvest. Immunocytochemistry localized WDR1 to outer hair cells, Deiter's cells, outer sulcus cells, and Reissner's membrane in the control group, and the PTS and TTS groups exhibited stronger WDR1 expression in the same cochlear regions than the controls. Moreover, WDR1 expression in these noise-exposed groups was extended to inner hair cells and basal cells of the stria vascularis. The expression of WDR1 in the PTS and TTS groups showed differences in intensity and shifts of localization, based on exposure length and recovery duration. Contrary to the avian cochlea, hair cell regeneration does not naturally occur in the acoustically damaged mammalian cochlea. Therefore, elevated WDR1 expression after acoustic overstimulation in the current experiments may provide a mechanism for protection against noise exposure.

Identification of new altered genes in rat cochleae with noise-induced hearing loss

Because genes that are highly expressed in the cochlea after noise stress may have crucial regulatory roles in hearing, the identification of these genes may be useful for restoring normal auditory function. This study assessed altered gene expression at 1h following the cessation of noise exposure by using microarrays and real-time polymerase chain reaction (qPCR) in rats. In addition, the auditory threshold shifts and morphological changes of hair cells were observed. This study indicated that applied noise induced outer hair cell loss and a 40-50 dB hearing loss. Totally 239 altered genes were involved in the immune system process, response to stress, or response to stimulus. The expression of five up-regulated genes (Reg3b, Lcn2, Serpina3n, Nob1 and Hamp) was confirmed by qPCR. Future experiments will focus on several of these new candidate genes and may provide insight into the underlying auditory pathophysiology.

Functional genomics in chickens: development of integrated-systems microarrays for transcriptional profiling and discovery of regulatory pathways

The genetic networks that govern the differentiation and growth of major tissues of economic importance in the chicken are largely unknown. Under a functional genomics project, our consortium has generated 30 609 expressed sequence tags (ESTs) and developed several chicken DNA microarrays, which represent the Chicken Metabolic/Somatic (10 K) and Neuroendocrine/Reproductive (8 K) Systems (http://udgenome.ags.udel.edu/cogburn/). One of the major challenges facing functional genomics is the development of mathematical models to reconstruct functional gene networks and regulatory pathways from vast volumes of microarray data. In initial studies with liver-specific microarrays (3.1 K), we have examined gene expression profiles in liver during the peri-hatch transition and during a strong metabolic perturbation—fasting and re-feeding—in divergently selected broiler chickens (fast vs. slow-growth lines). The expression of many genes controlling metabolic pathways is dramatically altered by these perturbations. Our analysis has revealed a large number of clusters of functionally related genes (mainly metabolic enzymes and transcription factors) that control major metabolic pathways. Currently, we are conducting transcriptional profiling studies of multiple tissues during development of two sets of divergently selected broiler chickens (fast vs. slow growing and fat vs. lean lines). Transcriptional profiling across multiple tissues should permit construction of a detailed genetic blueprint that illustrates the developmental events and hierarchy of genes that govern growth and development of chickens. This review will briefly describe the recent acquisition of chicken genomic resources (ESTs and microarrays) and our consortium's efforts to help launch the new era of functional genomics in the chicken.

Differential gene expression during compensatory sprouting of dendrites in the auditory system of the cricket Gryllus bimaculatus

Neurones that lose their presynaptic partners because of injury usually retract or die. However, when the auditory interneurones of the cricket Gryllus bimaculatus are denervated, dendrites respond by growing across the midline and forming novel synapses with the opposite auditory afferents. Suppression subtractive hybridization was used to detect transcriptional changes 3 days after denervation. This is a stage at which we demonstrate robust compensatory dendritic sprouting. Whereas 49 unique candidates were down-regulated, no sufficiently up-regulated candidates were identified at this time point. Several candidates identified in this study are known to influence the translation and degradation of proteins in other systems. The potential role of these factors in the compensatory sprouting of cricket auditory interneurones in response to denervation is discussed.

Birdsong "transcriptomics": neurochemical specializations of the oscine song system

Background

Vocal learning is a rare and complex behavioral trait that serves as a basis for the acquisition of human spoken language. In songbirds, vocal learning and production depend on a set of specialized brain nuclei known as the song system.

Methodology/Principal Findings

Using high-throughput functional genomics we have identified ∼200 novel molecular markers of adult zebra finch HVC, a key node of the song system. These markers clearly differentiate HVC from the general pallial region to which HVC belongs, and thus represent molecular specializations of this song nucleus. Bioinformatics analysis reveals that several major neuronal cell functions and specific biochemical pathways are the targets of transcriptional regulation in HVC, including: 1) cell-cell and cell-substrate interactions (e.g., cadherin/catenin-mediated adherens junctions, collagen-mediated focal adhesions, and semaphorin-neuropilin/plexin axon guidance pathways); 2) cell excitability (e.g., potassium channel subfamilies, cholinergic and serotonergic receptors, neuropeptides and neuropeptide receptors); 3) signal transduction (e.g., calcium regulatory proteins, regulators of G-protein-related signaling); 4) cell proliferation/death, migration and differentiation (e.g., TGF-beta/BMP and p53 pathways); and 5) regulation of gene expression (candidate retinoid and steroid targets, modulators of chromatin/nucleolar organization). The overall direction of regulation suggest that processes related to cell stability are enhanced, whereas proliferation, growth and plasticity are largely suppressed in adult HVC, consistent with the observation that song in this songbird species is mostly stable in adulthood.

Conclusions/Significance

Our study represents one of the most comprehensive molecular genetic characterizations of a brain nucleus involved in a complex learned behavior in a vertebrate. The data indicate numerous targets for pharmacological and genetic manipulations of the song system, and provide novel insights into mechanisms that might play a role in the regulation of song behavior and/or vocal learning.

Pitch strength decreases as F0 and harmonic resolution increase in complex tones composed exclusively of high harmonics

A melodic pitch experiment was performed to demonstrate the importance of time-interval resolution for pitch strength. The experiments show that notes with a low fundamental (75 Hz) and relatively few resolved harmonics support better performance than comparable notes with a higher fundamental (300 Hz) and more resolved harmonics. Two four note melodies were presented to listeners and one note in the second melody was changed by one or two semitones. Listeners were required to identify the note that changed. There were three orthogonal stimulus dimensions: F0 (75 and 300 Hz); lowest frequency component (3, 7, 11, or 15); and number of harmonics (4 or 8). Performance decreased as the frequency of the lowest component increased for both F0's, but performance was better for the lower F0. The spectral and temporal information in the stimuli were compared using a time-domain model of auditory perception. It is argued that the distribution of time intervals in the auditory nerve can explain the decrease in performance as F0, and spectral resolution increase. Excitation patterns based on the same time-interval information do not contain sufficient resolution to explain listener's performance on the melody task.

WDR1 presence in the songbird basilar papilla

WD40 repeat 1 protein (WDR1) was first reported in the acoustically injured chicken inner ear, and bioinformatics revealed that WDR1 has numerous WD40 repeats, important for protein-protein interactions. It has significant homology to actin interacting protein 1 (Aip1) in several lower species such as yeast, roundworm, fruitfly and frog. Several studies have shown that Aip1 binds cofilin/actin depolymerizing factor, and that these interactions are pivotal for actin disassembly via actin filament severing and actin monomer capping. However, the role of WDR1 in auditory function has yet to be determined. WDR1 is typically restricted to hair cells of the normal avian basilar papilla, but is redistributed towards supporting cells after acoustic overstimulation, suggesting that WDR1 may be involved in inner ear response to noise stress. One aim of the present study was to resolve the question as to whether stress factors, other than intense sound, could induce changes in WDR1 presence in the affected avian inner ear. Several techniques were used to assess WDR1 presence in the inner ears of songbird strains, including Belgian Waterslager (BW) canary, an avian strain with degenerative hearing loss thought to have a genetic basis. Reverse transcription, followed by polymerase chain reactions with WDR1-specific primers, confirmed WDR1 presence in the basilar papillae of adult BW, non-BW canaries, and zebra finches. Confocal microscopy examinations, following immunocytochemistry with anti-WDR1 antibody, localized WDR1 to the hair cell cytoplasm along the avian sensory epithelium. In addition, little, if any, staining by anti-WDR1 antibody was observed among supporting cells in the chicken or songbird ear. The present observations confirm and extend the early findings of WDR1 localization in hair cells, but not in supporting cells, in the normal avian basilar papilla. However, unlike supporting cells in the acoustically damaged chicken basilar papilla, the inner ear of the BW canary showed little, if any, WDR1 up-regulation in supporting cells. This may be due to the fact that the BW canary already has established hearing loss and/or to the possibility that the mechanism(s) involved in BW hearing loss may not be related to WDR1.

Pitch cue learning in chinchillas: the role of spectral region in the training stimulus

Chinchillas were trained to discriminate a cosine-phase harmonic tone complex (COS) from wideband noise (WBN) and tested in a stimulus generalization paradigm with tone complexes in which phase differed between frequency regions. In this split-phase condition, responses to complexes made of random-phase low frequencies, cosine-phase high frequencies were similar to responses to the COS-training stimulus. However, responses to complexes made of cosine-phase low frequencies, random-phase high frequencies were generally lower than their responses to the COS-training stimulus. When tested with sine-phase (SIN) and random-phase (RND) tone complexes, responses were large for SIN, but were small for RND. Chinchillas were then trained to discriminate infinitely-iterated rippled noise (IIRN) from WBN and tested with noises in which the spectral ripple differed between frequency regions. In this split-spectrum condition, responses were large to noises made of rippled-spectrum low frequencies, flat-spectrum high frequencies, whereas responses were generally lower to noises made of flat-spectrum low frequencies, rippled-spectrum high frequencies. The results suggest that chinchillas listen across all frequencies, but attend to high frequencies when discriminating COS from WBN and attend to low frequencies when discriminating IIRN from WBN.

Differential gene expression in the rat cochlea after exposure to impulse noise

Understanding the molecular biology of noise trauma is vital to developing effective and timely interventions. In a model of explosion-mediated impulse noise injury, differential gene expression was studied in whole rat cochlea preparations at 3 and 24 h following the exposure. We developed a technique using mRNA from a single cochlea on each oligonucleotide microarray to avoid pooling of mRNA samples. Application of a conservative statistical analysis approach resulted in the identification of 61 differentially expressed genes. Within 3 h after the exposure, there was an up-regulation of immediate early genes, mainly transcription factors and genes involved in the tissue's response to oxidative stress. No genes were found to be significantly down-regulated. At 24 h following the exposure, up-regulated genes included members of inflammatory and antioxidant pathways and one gene involved in glutathione metabolism was down-regulated. A subset of genes was confirmed by real-time reverse transcriptase-polymerase chain reaction (RT-PCR). The present study demonstrates the power of the microarray technique in providing a global view of the gene regulation following noise exposure, and in identifying genes that may be mechanistically important in hearing loss, and thereby serve as a basis for the development of therapeutic interventions.

A perceptual learning investigation of the pitch elicited by amplitude-modulated noise

Noise that is amplitude modulated at rates ranging from 40 to 850 Hz can elicit a sensation of pitch. Here, the processing of this temporally based pitch was investigated using a perceptual-learning paradigm. Nine listeners were trained (1 hour per day for 6-8 days) to discriminate a standard rate of sinusoidal amplitude modulation (SAM) from a faster rate in a single condition (150 Hz SAM rate, 5 kHz low-pass carrier). All trained listeners improved significantly on that condition. These trained listeners subsequently showed no more improvement than nine untrained controls on pure-tone and rippled-noise discrimination with the same pitch, and on SAM-rate discrimination with a 30 Hz rate, although they did show some improvement with a 300 Hz rate. In addition, most trained, but not control, listeners were worse at detecting SAM at 150 Hz after, compared to before training. These results indicate that listeners can learn to improve their ability to discriminate SAM rate with multiple-hour training and that the mechanism that is modified by learning encodes (1) the pitch of SAM noise but not that of pure tones and rippled noise, (2) different SAM rates separately, and (3) differences in SAM rate more effectively than cues for SAM detection.

Keynote review: The auditory system, hearing loss and potential targets for drug development

There is a huge potential market for the treatment of hearing loss. Drugs are already available to ameliorate predictable, damaging effects of excessive noise and ototoxic drugs. The biggest challenge now is to develop drug-based treatments for regeneration of sensory cells following noise-induced and age-related hearing loss. This requires careful consideration of the physiological mechanisms of hearing loss and identification of key cellular and molecular targets. There are many molecular cues for the discovery of suitable drug targets and a full range of experimental resources are available for initial screening through to functional analysis in vivo. There is now an unparalleled opportunity for translational research.

Listening experience with iterated rippled noise alters the perception of 'pitch' strength of complex sounds in the chinchilla

Behavioral responses obtained from chinchillas trained to discriminate a cosine-phase harmonic tone complex from wideband noise indicate that the perception of 'pitch' strength in chinchillas is largely influenced by periodicity information in the stimulus envelope. The perception of 'pitch' strength was examined in chinchillas in a stimulus generalization paradigm after animals had been retrained to discriminate infinitely iterated rippled noise from wideband noise. Retrained chinchillas gave larger behavioral responses to test stimuli having strong fine structure periodicity, but weak envelope periodicity. That is, chinchillas learn to use the information in the fine structure and consequently, their perception of 'pitch' strength is altered. Behavioral responses to rippled noises having similar periodicity strengths, but large spectral differences were also tested. Responses to these rippled noises were similar, suggesting a temporal analysis can be used to account for the behavior. Animals were then retested using the cosine-phase harmonic tone complex as the expected signal stimulus. Generalization gradients returned to those obtained originally in the naïve condition, suggesting that chinchillas do not remain "fine structure listeners," but rather revert back to being "envelope listeners" when the periodicity strength in the envelope of the expected stimulus is high.

Down-regulation of otospiralin mRNA in response to acoustic stress in guinea pig

Noise over-stimulation will induce or influence molecular pathways in the cochlea; one approach to the identification of the components of these pathways in the cochlea is to examine genes and proteins that change following different types and levels of stress. Quantitative reverse transcription polymerase chain reaction provides a method to look at differential expression of genes in the acoustic stress response. By using this technique we have revealed a down-regulation of the level of otospiralin mRNA in the cochlea of guinea pigs after white noise over-stimulation for 2 h at 108 dB SPL. Otospiralin represents an inner ear specific protein found in fibrocytes of spiral limbus and spiral ligament in the cochlea, and some regions of the vestibule as the stroma underlying the utricle and crista sensory epithelia and the subepithelial layer of the walls of semicircular canals and maculae. It has been recently reported that transient down-regulation of otospiralin in guinea pigs causes vestibular syndrome and deafness. Our results suggest a possible role of this gene in response to acoustical stress, although the exact mechanism remains to be resolved.

Differential expression of genes within the cochlea as defined by a custom mouse inner ear microarray

Microarray analyses have contributed greatly to the rapid understanding of functional genomics through the identification of gene networks as well as gene discovery. To facilitate functional genomics of the inner ear, we have developed a mouse inner-ear-pertinent custom microarray chip (CMA-IE1). Nonredundant cDNA clones were obtained from two cDNA library resources: the RIKEN subtracted inner ear set and the NIH organ of Corti library. At least 2000 cDNAs unique to the inner ear were present on the chip. Comparisons were performed to examine the relative expression levels of these unique cDNAs within the organ of Corti, lateral wall, and spiral ganglion. Total RNA samples were obtained from the three cochlear-dissected fractions from adult CF-1 mice. The total RNA was linearly amplified, and a dendrimer-based system was utilized to enhance the hybridization signal. Differentially expressed genes were verified by comparison to known gene expression patterns in the cochlea or by correlation with genes and gene families deduced to be present in the three tissue types. Approximately 22-25% of the genes on the array had significant levels of expression. A number of differentially expressed genes were detected in each tissue fraction. These included genes with known functional roles, hypothetical genes, and various unknown or uncharacterized genes. Four of the differentially expressed genes found in the organ of Corti are linked to deafness loci. None of these are hypothetical or unknown genes.

Identification of markers of the midface

Currently, much remains unknown of the genes that mediate the biological events during growth and fusion of the midfacial region, and the possible pathways through which these genes function. We took advantage of high-throughput microarray analysis to search for genes that may play a critical role in the growth and fusion of the midfacial region to become the primary palate. We identified several genes that were potentially expressed at different levels between tail somite (TS) 6-8 (pre-fusion) and TS 12-14 (fusion) in the 3 midfacial processes. Expression of 4 of these genes (Tbx14/15, Dickkopf-1, Fibroblast Growth Factor 8, and Keratin-18) was further verified by reverse-transcription/quantitative PCR and in situ hybridization at the 2 stages of midfacial development. With the identification of these genes, and possibly others, functional analyses can be conducted to improve our understanding of the mechanisms and pathways by which the midface forms.

Mouse homolog of KIAA0143 protein: hearing deficit induces specific changes of expression in auditory brainstem neurons

Hearing deficit induced by mechanical cochlear damage, intense noise or ototoxic drugs produces a variety of structural and functional changes in the inner ear and the auditory brainstem. In the present study, we identified a novel gene that has activity dependent plasticity in the superior olivary complex by using suppression subtractive hybridization. We cloned a gene that encodes mouse homolog of KIAA0143 protein, one derived from a series of unidentified human genes. This gene termed mKIAA0143 shows differential expression of mRNA in the lateral superior olive between mice with hearing deficit and those with normal hearing ability. The mRNA thus obtained encodes a unique membrane-bound protein that consists of 819 amino acids. The gene locus was mapped using genomic DNA databases to the mouse chromosome 15D1. Green fluorescent protein-tagged mKIAA0143 was expressed in COS-1 cells. It was amply seen in the cellular plasma membrane.

Characterization of the human UBE3B gene: structure, expression, evolution, and alternative splicing

E3 ubiquitin ligases target proteins for degradation by adding ubiquitin residues. We characterized full-length cDNAs for human and mouse UBE3B, a novel HECT-domain E3 ligase, and analyzed the structure of human UBE3B on chromosome 12q24.1. Alternative splicing of exon 20 of UBE3B generated two major transcripts. The 5.7-kb mRNA lacked exon 20 and encoded a full-length protein ligase, variant 1 (UBE3B_v1). A second transcript contained a 97-bp insertion encoded by exon 20 that introduced an in-frame stop codon. The predicted protein (UBE3B_v2) would lack the HECT domain and would be nonfunctional, since the HECT domain constitutes the active site for ubiquitin transfer. No alternative splicing was observed in this region of mouse UBE3B. Elimination of the HECT domain by alternative splicing has not been reported in any genes encoding HECT domain ligases and may represent a novel mechanism in regulating intracellular levels of functional HECT-domain ligases.

Application of microarray technology in environmental and comparative physiology

DNA microarray technology is revolutionizing many aspects of biological research, allowing the expression of many thousands of gene transcripts to be monitored simultaneously. This provides powerful tools for the genome-wide correlation of gene transcript levels with physiological responses and alterations in physiological states. To date, microarray analyses have been applied almost exclusively to a few model species for which the abundant gene sequence data permit the fabrication of whole-genome microarrays. However, many interesting physiological traits and responses are poorly expressed or absent in model species and may be better illustrated in nonmodel organisms. Comparative approaches to understanding function traditionally focus on species that by virtue of their unusual adaptations, lifestyles, and phylogeny are particularly suited to address a specific biological process or problem. In this review, we show that microarray technology can be successfully applied to these nonmodel species and used to generate new insights of comparative and evolutionary significance into animal function.

cDNA microarray analysis of gene expression in anxious PVG and SD rats after cat-freezing test

To identify genes involved in the development of anxiety or fear, we analyzed the gene expression profiles of the cortex of anxious hooded PVG and Sprague-Dawley (SD) rats after exposure to the cat-freezing test apparatus. These two rat strains showed a marked difference in the extent of anxious behavior on the cat-freezing test; the hooded PVG rats showed highly anxious behavior while a low anxiety state was observed in SD rats. A cDNA microarray consisting of 5,931 genes was employed to investigate the global mRNA expression profiles of anxiety-related genes. According to the assumption that an abundance ratio of > or =1.5 is indicative of a change in gene expression, we detected 16 upregulated and 38 downregulated genes in PVG hooded and SD rats. Some of these genes have not yet been associated with anxiety (e.g. FGF), while other genes were recently found to be expressed in an anxious state (e.g., rat nerve growth factor-induced gene, NGFI-A). Our study also focused on the expression of some neurotransmitter receptors that have already been proven to be relevant to anxiety or fear, e.g., gamma-aminobutyric acid (GABA), cholecystokinin (CCK) and 5-HT(3) receptors. To further confirm the microarray data, the mRNA expressions of three genes: rat activity-regulated cytoskeleton-associated gene (Arc), rat NGFI-A gene and rat 5-HT(3) receptor (5-HT(3)R) mRNA, were studied by reverse transcription-polymerase chain reaction (RT-PCR). The results of RT-PCR were basically consistent with those from cDNA microarray. Our study therefore demonstrated that the microarray technique is an efficient tool for analyzing global expression profiles of anxiety-related genes, which may also provide further insight into the molecular mechanisms underlying the states of anxiety and fear.

Hair cell regeneration: winging our way towards a sound future

The discovery of hair cell regeneration in the inner ear of birds provides new optimism that there may be a treatment for hearing and balance disorders. In this review we describe the process of hair cell regeneration in birds; including restoration of function, recovery of perception and what is currently known about molecular events, such as growth factors and signalling systems. We examine some of the key recent findings in both birds and mammals.

Identification of gene expression profiles in rat ears with cDNA microarrays

The physiological processes of hearing implicate thousands of molecules acting in harmony; however, their identities are only partially understood. We used cDNA microarrays containing 1,176 genes to identify >150 genes expressed in rat middle and inner ear tissue. Expressed genes covered several gene families and biological pathways, many of which have previously not been described. Transcription factor genes that were expressed included inhibitors of DNA binding protein (Id). These were localized to the spiral ganglion, organ of Corti and stria vascularis, and they are possibly involved in neurogenesis and angiogenesis. Transcriptional factors that were highly expressed included Gax (homeobox) and I-kappaB, which inhibit cellular proliferation. Their presence suggests that inhibitory programs for cell proliferation are enforced in the ear. Ion channel genes that were expressed included voltage-dependent L-type calcium channels (LTCC) and proton-gated cation channels (PGCC). Genes involved in neurotransmitter production and release included glutamic acid decarboxylase (GAD1). Genes involved in postsynaptic inhibition included neuropeptide Y5 receptors (NPY5) and GAD1. Due to the existence of receptors and/or enzymes involved in their biochemical synthesis, neurotransmitters associated with these might include serotonin, glutamide, acetylcholine, gamma-aminobutyric acid (GABA), neurotensin, and dopamine.

Changes in mRNA expression in mouse postnatal cochlea by differential display method

We compared mRNA expression by mRNA differential display method in postnatal day 11 (P11), P13 and adult C3H/HeJ mouse cochlea. Forty-seven bands were differentially displayed on polyacrylamide gel when 27 patterns of PCR primer sets were used, and 24 of them showed a remarkable increase within only two days (P11 and P13). DNA sequences of the bands were analyzed for homology to known genes using the BLAST search. Most of the clones were identical to sequences of functions unknown. However, one of the clones showing an increase of mRNA expression between P11 and P13 was identified as mouse TIS7 which is known to markedly increase during differentiation of PC-12 cells to neurons by NGF-treatment. TIS7 expression may be involved in differentiation of neuronal progenitor cells to spiral ganglion cells by the initial sound input. The comparison among P11, P13 and adult mouse cochlear mRNA expressions investigated the genes involved in the various growing stages of the postnatal cochlea.

Approaches to the analysis of gene expression using mRNA: a technical overview

Messenger RNA is the blueprint for all proteins expressed within living systems. Therefore, the study of mRNA expression within normal and diseased tissues is central to our understanding of biological systems. However, blueprints, in themselves, perform no function unless they are used to produce the material for which they code. Spurious results may frequently result from poorly designed or inappropriate studies. This review seeks to highlight both the pitfalls and the promise of various approaches to the analysis of mRNA in different systems and to place these studies in the wider context of research approaches aimed at understanding the function of living systems. The various techniques for the analysis of mRNA are discussed, with particular reference to their potential uses and problems and relevant examples are cited from the literature. It is hoped that this overview of the uses of analytical approaches will allow both the novice researcher and the more experienced scientist to better structure research approaches.

From gene identification to gene therapy

Inner ear disease due to hair cell loss is common, and no restorative treatments for the balance and hearing impairment are currently available. To develop clinical means for enhancing protection and regeneration in the inner ear, it is necessary to understand the molecular basis for hereditary and acquired deafness and vestibular disorders. One approach is to identify and characterize genes that regulate protection or repair in other systems. For that purpose, we have used the differential display assay and compared gene expression between normal and acoustically traumatized inner ears of chicks. Several chick cDNAs that were identified are considered as candidates for roles in the reparative process that follows trauma in the basilar papilla. The mammalian vestibular epithelium has a limited regenerative capability. To identify genes that may participate in the regenerative response, we have used gene arrays profiling, comparing normal to drug-traumatized vestibular epithelia. We identified several genes that are differentially expressed in traumatized vestibular epithelium, including several insulin-like growth factor-I binding proteins. To use this molecular knowledge for enhancing protection and repair in the organ of Corti, it is necessary to overexpress the genes of choice in the inner ear. Using viral-mediated gene transfer, we overexpressed transgenic glial cell line-derived neurotrophic factor and demonstrated a robust protective effect against acoustic and ototoxic inner ear trauma. Future identification of the genes that are important for protection and regeneration, along with improved gene transfer technology, will allow the use of gene therapy for treating hereditary and environmental inner ear disease.

Application of new biological approaches to stimulate sensory repair and protection

The inner ear governs hearing and balance via six sense organs, each composed of a few thousand mechanosensory hair cells. Most inner ear disorders involve irreversible loss of hair cells and their associated nerves. They are a function of age, genetic abnormalities and environmental factors such as noise and the use of ototoxic drugs. The genetics and cell biology of the inner ear have revealed some key molecular mechanisms of development and sensory degeneration that raise hopes for new therapeutic approaches to the regeneration of sensory function. This review highlights these advances and the approaches that might be taken to effect protection and repair. It concludes with the suggestion that we can expect tangible, practical progress towards the clinic over the next 5-10 years and that, to provide the training and skills required to take full advantage of emerging technologies, we should forge much closer links between specialist clinicians and basic scientists.

Gene expression profiling of acute spinal cord injury reveals spreading inflammatory signals and neuron loss

We have completed the first large-scale gene expression study of acute spinal cord injury (SCI) in rat. Oligonucleotide microarrays containing 1,200 gene-specific probes were used to quantify mRNA levels, relative to uninjured controls, in spinal cords injured using a standard contusion model. Our results revealed a marked loss of neuron-specific mRNAs at the injury site. The surviving cells showed a characteristic inflammatory response that started at the injury site and spread to the distal cord. Changes in several mRNA levels were associated with putative regenerative responses in the spinal cord. Notably, phosphodiesterase 4, nestin, glia-derived neurite promoting factor, and GAP-43 mRNAs increased significantly. Other mRNAs clustered temporally and spatially with these regeneration-associated genes. Thus we have described global patterns of gene expression following acute SCI, and we have identified targets for future study and possible therapeutic intervention.

DFNA25, a novel locus for dominant nonsyndromic hereditary hearing impairment, maps to 12q21-24

Using linkage analysis, we identified a novel dominant locus, DFNA25, for delayed-onset, progressive, high-frequency, nonsyndromic sensorineural hearing loss in a large, multigenerational United States family of Czech descent. On the basis of recombinations in affected individuals, we determined that DFNA25 is located in a 20-cM region of chromosome 12q21-24 between D12S327 (centromeric) and D12S84 (telomeric), with a maximum two-point LOD score of 6.82, at recombination fraction.041, for D12S1030. Candidate genes in this region include ATP2A2, ATP2B1, UBE3B, and VR-OAC. DFNA25 may be the human ortholog of bronx waltzer (bv).