The responses of single cortical neurons were measured as a function of the binocular disparity of dynamic random dot stereograms for a large sample of neurons (n = 787) from V1 of the awake macaque. From this sample, we selected 180 neurons whose tuning curves were strongly tuned for disparity, well sampled and well described by one-dimensional Gabor functions. The fitted parameters of the Gabor functions were used to resolve three outstanding issues in binocular stereopsis. First, we considered whether tuning curves can be meaningfully divided into discrete tuning types. Careful examination of the distributions of the Gabor parameters that determine tuning shape revealed no evidence for clustering. We conclude that a continuum of tuning types is present. Second, we investigated the mechanism of disparity encoding for V1 neurons. The shape of the disparity tuning function can be used to distinguish between position-encoding (in which disparity is encoded by an interocular shift in receptive field position) and phase-encoding (in which disparity is encoded by a difference in the receptive field profile in the 2 eyes). Both position and phase encoding were found to be common. This was confirmed by an independent assessment of disparity encoding based on the measurement of disparity sensitivity for sinusoidal luminance gratings of different spatial frequencies. The contributions of phase and position to disparity encoding were compared by estimating a population average of the rate of change in firing rate per degree of disparity. When this was calculated separately for the phase and position contributions, they were found to be closely similar. Third, we investigated the range of disparity tuning in V1 as a function of eccentricity in the parafoveal range. We find few cells which are selective for disparities greater than +/-1 degrees even at the largest eccentricity of approximately 5 degrees. The preferred disparity was correlated with the spatial scale of the tuning curve, and for most units lay within a +/-pi radians phase limit. Such a size-disparity correlation is potentially useful for the solution of the correspondence problem.

Inner ear hair cells detect sound through deflection of stereocilia, the microvilli-like projections that are arranged in rows of graded heights. Calcium and integrin-binding protein 2 is essential for hearing and localizes to stereocilia, but its exact function is unknown. Here, we have characterized two mutant mouse lines, one lacking calcium and integrin-binding protein 2 and one carrying a human deafness-related Cib2 mutation, and show that both are deaf and exhibit no mechanotransduction in auditory hair cells, despite the presence of tip links that gate the mechanotransducer channels. In addition, mechanotransducing shorter row stereocilia overgrow in hair cell bundles of both Cib2 mutants. Furthermore, we report that calcium and integrin-binding protein 2 binds to the components of the hair cell mechanotransduction complex, TMC1 and TMC2, and these interactions are disrupted by deafness-causing Cib2 mutations. We conclude that calcium and integrin-binding protein 2 is required for normal operation of the mechanotransducer channels and is involved in limiting the growth of transducing stereocilia.

Determining the genetic bases of age-related disease remains a major challenge requiring a spectrum of approaches from human and clinical genetics to the utilization of model organism studies. Here we report a large-scale genetic screen in mice employing a phenotype-driven discovery platform to identify mutations resulting in age-related disease, both late-onset and progressive. We have utilized N-ethyl-N-nitrosourea mutagenesis to generate pedigrees of mutagenized mice that were subject to recurrent screens for mutant phenotypes as the mice aged. In total, we identify 105 distinct mutant lines from 157 pedigrees analysed, out of which 27 are late-onset phenotypes across a range of physiological systems. Using whole-genome sequencing we uncover the underlying genes for 44 of these mutant phenotypes, including 12 late-onset phenotypes. These genes reveal a number of novel pathways involved with age-related disease. We illustrate our findings by the recovery and characterization of a novel mouse model of age-related hearing loss.

BackgroundNuclease-based technologies have been developed that enable targeting of specific DNA sequences directly in the zygote. These approaches provide an opportunity to modify the genomes of inbred mice, and allow the removal of strain-specific mutations that confound phenotypic assessment. One such mutation is the Cdh23ahl allele, present in several commonly used inbred mouse strains, which predisposes to age-related progressive hearing loss.ResultsWe have used targeted CRISPR/Cas9-mediated homology directed repair (HDR) to correct the Cdh23ahl allele directly in C57BL/6NTac zygotes. Employing offset-nicking Cas9 (D10A) nickase with paired RNA guides and a single-stranded oligonucleotide donor template we show that allele repair was successfully achieved. To investigate potential Cas9-mediated ‘off-target’ mutations in our corrected mouse, we undertook whole-genome sequencing and assessed the ‘off-target’ sites predicted for the guide RNAs (≤4 nucleotide mis-matches). No induced sequence changes were identified at any of these sites.Correction of the progressive hearing loss phenotype was demonstrated using auditory-evoked brainstem response testing of mice at 24 and 36 weeks of age, and rescue of the progressive loss of sensory hair cell stereocilia bundles was confirmed using scanning electron microscopy of dissected cochleae from 36-week-old mice.ConclusionsCRISPR/Cas9-mediated HDR has been successfully utilised to efficiently correct the Cdh23ahl allele in C57BL/6NTac mice, and rescue the associated auditory phenotype. The corrected mice described in this report will allow age-related auditory phenotyping studies to be undertaken using C57BL/6NTac-derived models, such as those generated by the International Mouse Phenotyping Consortium (IMPC) programme.Electronic supplementary materialThe online version of this article (doi:10.1186/s13073-016-0273-4) contains supplementary material, which is available to authorized users.

The sensory cells responsible for hearing include the cochlear inner hair cells (IHCs) and outer hair cells (OHCs), with OHCs being necessary for sound sensitivity and tuning. Both cell types are thought to arise from common progenitors, however our understanding of the factors that control IHC and OHC fate remains limited. Here we identify Ikzf2 /helios as an essential transcription factor required for OHC functional maturation and hearing. Ikzf2 /helios is expressed in postnatal mouse OHCs, and a mutation in Ikzf2 causes early-onset sensorineural hearing loss in the cello mouse model. Ikzf2 cello/cello OHCs have greatly reduced prestin-dependent electromotile activity, a hallmark of OHC functional maturation, and show reduced levels of critical OHC-expressed genes such as Slc26a5 /prestin and Ocm . Moreover, we show that ectopic expression of Ikzf2 /helios in IHCs induces expression of OHC-specific genes, reduces canonical IHC genes, and confers electromotility to IHCs, demonstrating that Ikzf2 /helios is capable of partially shifting the IHC transcriptome towards an OHC-like identity.

We describe a protocol for the production of mice carrying N-ethyl-N-nitrosourea (ENU) mutations and their screening for auditory and vestibular phenotypes. In comparison with the procedures describing individual phenotyping tests, this protocol integrates a set of tests for the comprehensive determination of the causes of hearing loss. It comprises a primary screen of relatively simple auditory and vestibular tests. A variety of secondary phenotyping protocols are also described for further investigating the deaf and vestibular mutants identified in the primary screen. The screen can be applied to potentially thousands of mutant mice, produced either by ENU or other mutagenesis approaches. Primary screening protocols take no longer than a few minutes, apart from ABR testing which takes upto 3.5 h per mouse. These protocols have been applied for the identification of mouse models of human deafness and are a key component for investigating the genes and genetic pathways involved in hereditary deafness.

Otitis media with effusion (OME) is the commonest cause of hearing loss in children, yet the underlying genetic pathways and mechanisms involved are incompletely understood. Ventilation of the middle ear with tympanostomy tubes is the commonest surgical procedure in children and the best treatment for chronic OME, but the mechanism by which they work remains uncertain. As hypoxia is a common feature of inflamed microenvironments, moderation of hypoxia may be a significant contributory mechanism. We have investigated the occurrence of hypoxia and hypoxia-inducible factor (HIF) mediated responses in Junbo and Jeff mouse mutant models, which develop spontaneous chronic otitis media. We found that Jeff and Junbo mice labeled in vivo with pimonidazole showed cellular hypoxia in inflammatory cells in the bulla lumen, and in Junbo the middle ear mucosa was also hypoxic. The bulla fluid inflammatory cell numbers were greater and the upregulation of inflammatory gene networks were more pronounced in Junbo than Jeff. Hif-1α gene expression was elevated in bulla fluid inflammatory cells, and there was upregulation of its target genes including Vegfa in Junbo and Jeff. We therefore investigated the effects in Junbo of small-molecule inhibitors of VEGFR signaling (PTK787, SU-11248, and BAY 43-9006) and destabilizing HIF by inhibiting its chaperone HSP90 with 17-DMAG. We found that both classes of inhibitor significantly reduced hearing loss and the occurrence of bulla fluid and that VEGFR inhibitors moderated angiogenesis and lymphangiogenesis in the inflamed middle ear mucosa. The effectiveness of HSP90 and VEGFR signaling inhibitors in suppressing OM in the Junbo model implicates HIF–mediated VEGF as playing a pivotal role in OM pathogenesis. Our analysis of the Junbo and Jeff mutants highlights the role of hypoxia and HIF–mediated pathways, and we conclude that targeting molecules in HIF–VEGF signaling pathways has therapeutic potential in the treatment of chronic OM.

Parkinson's disease (PD) is characterized in part by the presence of a-synuclein (a-syn) rich intracellular inclusions (Lewy bodies). Mutations and multiplication of the a-synuclein gene (SNCA) are associated with familial PD. Since Ca 2+ dyshomeostasis may play an important role in the pathogenesis of PD, we used fluorimetry in fura-2 loaded SH-SY5Y cells to monitor Ca 2+ homeostasis in cells stably transfected with either wild-type a-syn, the A53T mutant form, the S129D phosphomimetic mutant or with empty vector (which served as control homeostasis.