Ion channel gene expression in the inner ear

Potassium Ion Channels in Malignant Central Nervous System Cancers

Malignant central nervous system (CNS) cancers are among the most difficult to treat, with low rates of survival and a high likelihood of recurrence. This is primarily due to their location within the CNS, hindering adequate drug delivery and tumour access via surgery. Furthermore, CNS cancer cells are highly plastic, an adaptive property that enables them to bypass targeted treatment strategies and develop drug resistance. Potassium ion channels have long been implicated in the progression of many cancers due to their integral role in several hallmarks of the disease. Here, we will explore this relationship further, with a focus on malignant CNS cancers, including high-grade glioma (HGG). HGG is the most lethal form of primary brain tumour in adults, with the majority of patient mortality attributed to drug-resistant secondary tumours. Hence, targeting proteins that are integral to cellular plasticity could reduce tumour recurrence, improving survival. This review summarises the role of potassium ion channels in malignant CNS cancers, specifically how they contribute to proliferation, invasion, metastasis, angiogenesis, and plasticity. We will also explore how specific modulation of these proteins may provide a novel way to overcome drug resistance and improve patient outcomes.

Generative Models of Brain Dynamics

This review article gives a high-level overview of the approaches across different scales of organization and levels of abstraction. The studies covered in this paper include fundamental models in computational neuroscience, nonlinear dynamics, data-driven methods, as well as emergent practices. While not all of these models span the intersection of neuroscience, AI, and system dynamics, all of them do or can work in tandem as generative models, which, as we argue, provide superior properties for the analysis of neuroscientific data. We discuss the limitations and unique dynamical traits of brain data and the complementary need for hypothesis- and data-driven modeling. By way of conclusion, we present several hybrid generative models from recent literature in scientific machine learning, which can be efficiently deployed to yield interpretable models of neural dynamics.

Creating a Novel Mathematical Model of the Kv10.1 Ion Channel and Controlling Channel Activity with Nanoelectromechanical Systems

The use of nanoelectromechanical systems or nanorobots offers a new concept for sensing and controlling subcellular structures, such as ion channels. We present here a novel method for mathematical modeling of ion channels based on control system theory and system identification. We investigated the use of nanoelectromechanical devices to control the activity of ion channels, particularly the activity of the voltage-gated ion channel Kv10.1, an important channel in cancer development and progression. A mathematical model of the dynamic behavior of the selected ion channel Kv10.1 in the Laplace (s) domain was developed, which is given in the representation of a transfer function. In addition, we addressed the possibilities of controlling ion channel activity by nanoelectromechanical devices and nanorobots and finally presented a control algorithm for the Kv10.1 as a control object. A use case demonstrates the potential of a Kv10.1 controlled nanorobot for cancer treatment at a single-cell level.

iCDI-W2vCom: Identifying the Ion Channel-Drug Interaction in Cellular Networking Based on word2vec and node2vec

Ion channels are the second largest drug target family. Ion channel dysfunction may lead to a number of diseases such as Alzheimer's disease, epilepsy, cephalagra, and type II diabetes. In the research work for predicting ion channel-drug, computational approaches are effective and efficient compared with the costly, labor-intensive, and time-consuming experimental methods. Most of the existing methods can only be used to deal with the ion channels of knowing 3D structures; however, the 3D structures of most ion channels are still unknown. Many predictors based on protein sequence were developed to address the challenge, while most of their results need to be improved, or predicting web servers are missing. In this paper, a sequence-based classifier, called "iCDI-W2vCom," was developed to identify the interactions between ion channels and drugs. In the predictor, the drug compound was formulated by SMILES-word2vec, FP2-word2vec, SMILES-node2vec, and ECFPs via a 1184D vector, ion channel was represented by the word2vec via a 64D vector, and the prediction engine was operated by the LightGBM classifier. The accuracy and AUC achieved by iCDI-W2vCom via the fivefold cross validation were 91.95% and 0.9703, which outperformed other existing predictors in this area. A user-friendly web server for iCDI-W2vCom was established at http://www.jci-bioinfo.cn/icdiw2v. The proposed method may also be a potential method for predicting target-drug interaction.

Kcnb1 plays a role in development of the inner ear

The function of the inner ear depends on the maintenance of high concentrations of K⁺ ions. The slow-inactivating delayed rectifier Kv2.1/KCNB1 channel works in the inner ear in mammals. The kcnb1 gene is expressed in the otic vesicle of developing zebrafish, suggesting its role in development of the inner ear. In the present study, we found that a Kcnb1 loss-of-function mutation affected development of the inner ear at multiple levels, including otic vesicle expansion, otolith formation, and the proliferation and differentiation of mechanosensory cells. This resulted in defects of kinocilia and stereocilia and abnormal function of the inner ear detected by behavioral assays. The quantitative transcriptional analysis of 75 genes demonstrated that the kcnb1 mutation affected the transcription of genes that are involved in K⁺ metabolism, cell proliferation, cilia development, and intracellular protein trafficking. These results demonstrate a role for Kv2.1/Kcnb1 channels in development of the inner ear in zebrafish.

GWAS and gene networks for milk-related traits from test-day multiple lactations in Portuguese Holstein cattle

This study focused on the identification of QTL regions, candidate genes, and network related genes based on the first 3 lactations (LAC3) of milk, fat, and protein yields, and somatic cell score (SCS) in Portuguese Holstein cattle. Additionally, the results were compared with those from only first lactation (LAC1) data. The analyses were performed using the weighted single-step GWAS under an autoregressive test-day (TD) multiple lactations model. A total of 11,434,294 and 4,725,673 TD records from LAC3 and LAC1, respectively, including 38,323 autosomal SNPs and 1338 genotyped animals were used in GWAS analyses. A total of 51 (milk), 5 (fat), 24 (protein), and 4 (SCS) genes were associated to previously annotated relevant QTL regions for LAC3. The CACNA2D1 at BTA4 explained the highest proportion of genetic variance respectively for milk, fat, and protein yields. For SCS, the TRNAG-CCC at BTA14, MAPK10, and PTPN3 genes, both at BTA6 were considered important candidate genes. The accessed network refined the importance of the reported genes. CACNA2D1 regulates calcium density and activation/inactivation kinetics of calcium transport in the mammary gland; whereas TRNAG-CCC, MAPK10, and PTPN3 are directly involved with inflammatory processes widely derived from mastitis. In conclusion, potential candidate genes (TRNAG-CCC, MAPK10, and PTPN3) associated with somatic cell were highlighted, which further validation studies are needed to clarify its mechanism action in response to mastitis. Moreover, most of the candidate genes identified were present in both (LAC3 and LAC1) for milk, fat and protein yields, except for SCS, in which no candidate genes were shared between LAC3 and LAC1. The larger phenotypic information provided by LAC3 dataset was more effective to identify relevant genes, providing a better understanding of the genetic architecture of these traits over all lactations simultaneously.

Prediction of Ion Channels and their Types from Protein Sequences: Comprehensive Review and Comparative Assessment

BACKGROUND

Ion channels are a large and growing protein family. Many of them are associated with diseases, and consequently, they are targets for over 700 drugs. Discovery of new ion channels is facilitated with computational methods that predict ion channels and their types from protein sequences. However, these methods were never comprehensively compared and evaluated.

OBJECTIVE

We offer first-of-its-kind comprehensive survey of the sequence-based predictors of ion channels. We describe eight predictors that include five methods that predict ion channels, their types, and four classes of the voltage-gated channels. We also develop and use a new benchmark dataset to perform comparative empirical analysis of the three currently available predictors.

RESULTS

While several methods that rely on different designs were published, only a few of them are currently available and offer a broad scope of predictions. Support and availability after publication should be required when new methods are considered for publication. Empirical analysis shows strong performance for the prediction of ion channels and modest performance for the prediction of ion channel types and voltage-gated channel classes. We identify a substantial weakness of current methods that cannot accurately predict ion channels that are categorized into multiple classes/types.

CONCLUSION

Several predictors of ion channels are available to the end users. They offer practical levels of predictive quality. Methods that rely on a larger and more diverse set of predictive inputs (such as PSIONplus) are more accurate. New tools that address multi-label prediction of ion channels should be developed.

Transcriptomic Analyses of Inner Ear Sensory Epithelia in Zebrafish

Analysis of gene expression has the potential to assist in the understanding of multiple cellular processes including proliferation, cell-fate specification, senesence, and activity in both healthy and disease states. Zebrafish model has been increasingly used to understand the process of hearing and the development of the vertebrate auditory system. Within the zebrafish inner ear, there are three otolith organs, each containing a sensory macula of hair cells. The saccular macula is primarily involved in hearing, the utricular macula is primarily involved in balance and the function of the lagenar macula is not completely understood. The goal of this study is to understand the transcriptional differences in the sensory macula associated with different otolith organs with the intention of understanding the genetic mechanisms responsible for the distinct role each organ plays in sensory perception. The sensory maculae of the saccule, utricle, and lagena were dissected out of adult Et(krt4:GFP)^sqet4 zebrafish expressing green fluorescent protein in hair cells for transcriptional analysis. The total RNAs of the maculae were isolated and analyzed by RNA GeneChip microarray. Several of the differentially expressed genes are known to be involved in deafness, otolith development and balance. Gene expression among these otolith organs was very well conserved with less than 10% of genes showing differential expression. Data from this study will help to elucidate which genes are involved in hearing and balance. Furthermore, the findings of this study will assist in the development of the zebrafish model for human hearing and balance disorders. Anat Rec, 303:527-543, 2020. © 2019 American Association for Anatomy.

Predicting Ion Channels Genes and Their Types With Machine Learning Techniques

Motivation: The number of ion channels is increasing rapidly. As many of them are associated with diseases, they are the targets of more than 700 drugs. The discovery of new ion channels is facilitated by computational methods that predict ion channels and their types from protein sequences. Methods: We used the SVMProt and the k-skip-n-gram methods to extract the feature vectors of ion channels, and obtained 188- and 400-dimensional features, respectively. The 188- and 400-dimensional features were combined to obtain 588-dimensional features. We then employed the maximum-relevance-maximum-distance method to reduce the dimensions of the 588-dimensional features. Finally, the support vector machine and random forest methods were used to build the prediction models to evaluate the classification effect. Results: Different methods were employed to extract various feature vectors, and after effective dimensionality reduction, different classifiers were used to classify the ion channels. We extracted the ion channel data from the Universal Protein Resource (UniProt, http://www.uniprot.org/) and Ligand-Gated Ion Channel databases (http://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php), and then verified the performance of the classifiers after screening. The findings of this study could inform the research and development of drugs.

Developmental Synaptic Changes at the Transient Olivocochlear-Inner Hair Cell Synapse

In the mature mammalian cochlea, inner hair cells (IHCs) are mainly innervated by afferent fibers that convey sound information to the CNS. During postnatal development, however, medial olivocochlear (MOC) efferent fibers transiently innervate the IHCs. The MOC-IHC synapse, functional from postnatal day 0 (P0) to hearing onset (P12), undergoes dramatic changes in the sensitivity to acetylcholine (ACh) and in the expression of key postsynaptic proteins. To evaluate whether there are associated changes in the properties of ACh release during this period, we used a cochlear preparation from mice of either sex at P4, P6-P7, and P9-P11 and monitored transmitter release from MOC terminals in voltage-clamped IHCs in the whole-cell configuration. The quantum content increased 5.6× from P4 to P9-P11 due to increases in the size and replenishment rate of the readily releasable pool of synaptic vesicles without changes in their probability of release or quantum size. This strengthening in transmission was accompanied by changes in short-term plasticity properties, which switched from facilitation at P4 to depression at P9-P11. We have previously shown that at P9-P11, ACh release is supported by P/Q- and N-type voltage-gated calcium channels (VGCCs) and negatively regulated by BK potassium channels activated by Ca2+ influx through L-type VGCCs. We now show that at P4 and P6-P7, release is mediated by P/Q-, R- and L-type VGCCs. Interestingly, L-type VGCCs have a dual role: they both support release and fuel BK channels, suggesting that at immature stages presynaptic proteins involved in release are less compartmentalized.SIGNIFICANCE STATEMENT During postnatal development before the onset of hearing, cochlear inner hair cells (IHCs) present spontaneous Ca2+ action potentials that release glutamate at the first auditory synapse in the absence of sound stimulation. The IHC Ca2+ action potential frequency pattern, which is crucial for the correct establishment and function of the auditory system, is regulated by the efferent medial olivocochlear (MOC) system that transiently innervates IHCs during this period. We show here that developmental changes in synaptic strength and synaptic plasticity properties at the MOC-IHC synapse upon MOC fiber activation at different frequencies might be crucial for tightly shaping the pattern of afferent activity during this critical period.

Genome-wide DNA methylation analysis of human peripheral blood reveals susceptibility loci of diabetes-related hearing loss

Diabetes-related hearing loss (DRHL) is a complication of diabetes mellitus that is drawing more attention currently. DNA methylation has a critical role in the pathogenesis of type 2 diabetes mellitus (T2DM) and its complications. Therefore, we investigated the genome-wide DNA methylation of peripheral blood of T2DM patients with/without hearing loss in order to explore the susceptibility loci of DRHL. Between DRHL group and control group, 113 gene sites were identified to be differentially methylated regions (DMRs). Among 38 DMRs with whole samples, the classification accuracy is up to 90%. With alignment to T2DM susceptibility genes and deafness genes published, KCNJ11 was found to be the only overlapped gene. The DNA methylation level of KCNJ11 was associated with stroke (t = 2.595, p < 0.05), but not with diabetic nephropathy and diabetic retinopathy. The detective rate of distortion product otoacoustic emissions (DPOAE) from low to high frequencies (0.7-6 kHz) on the right ear was significantly correlated with the methylation level of KCNJ11. The auditory brainstem response (ABR) threshold on the right ear was also correlated (r = 0.678, p < 0.05). This DNA methylation profile indicates the susceptibility loci of DRHL. The potassium metabolism may have a critical role in the hearing loss caused by hyperglycemia.

Nanotechnology for Neuroscience: Promising Approaches for Diagnostics, Therapeutics and Brain Activity Mapping

Unlocking the secrets of the brain is a task fraught with complexity and challenge - not least due to the intricacy of the circuits involved. With advancements in the scale and precision of scientific technologies, we are increasingly equipped to explore how these components interact to produce a vast range of outputs that constitute function and disease. Here, an insight is offered into key areas in which the marriage of neuroscience and nanotechnology has revolutionized the industry. The evolution of ever more sophisticated nanomaterials culminates in network-operant functionalized agents. In turn, these materials contribute to novel diagnostic and therapeutic strategies, including drug delivery, neuroprotection, neural regeneration, neuroimaging and neurosurgery. Further, the entrance of nanotechnology into future research arenas including optogenetics, molecular/ion sensing and monitoring, and piezoelectric effects is discussed. Finally, considerations in nanoneurotoxicity, the main barrier to clinical translation, are reviewed, and direction for future perspectives is provided.

IonchanPred 2.0: A Tool to Predict Ion Channels and Their Types

Ion channels (IC) are ion-permeable protein pores located in the lipid membranes of all cells. Different ion channels have unique functions in different biological processes. Due to the rapid development of high-throughput mass spectrometry, proteomic data are rapidly accumulating and provide us an opportunity to systematically investigate and predict ion channels and their types. In this paper, we constructed a support vector machine (SVM)-based model to quickly predict ion channels and their types. By considering the residue sequence information and their physicochemical properties, a novel feature-extracted method which combined dipeptide composition with the physicochemical correlation between two residues was employed. A feature selection strategy was used to improve the performance of the model. Comparison results of in jackknife cross-validation demonstrated that our method was superior to other methods for predicting ion channels and their types. Based on the model, we built a web server called IonchanPred which can be freely accessed from http://lin.uestc.edu.cn/server/IonchanPredv2.0.

RNA Extraction from Xenopus Auditory and Vestibular Organs for Molecular Cloning and Expression Profiling with RNA-Seq and Microarrays

The amphibian Xenopus offers a unique model system for uncovering the genetic basis of auditory and vestibular function in an organism that is well-suited for experimental manipulation during animal development. However, many procedures for analyzing gene expression in the peripheral auditory and vestibular systems mandate the ability to isolate intact RNA from inner ear tissue. Methods presented here facilitate preparation of high-quality inner ear RNA from larval and post-metamorphic Xenopus specimens that can be used for a variety of purposes. We demonstrate that RNA isolated with these protocols is suitable for microarray analysis and Illumina-Solexa sequencing (RNA-Seq) of inner ear organs, and for cloning of large transcripts, such as those for ion channels. Genetic sequences cloned with these procedures can be used for transient transfection of Xenopus kidney cell lines with fluorescent protein fusion constructs.

PSIONplus: Accurate Sequence-Based Predictor of Ion Channels and Their Types

Ion channels are a class of membrane proteins that attracts a significant amount of basic research, also being potential drug targets. High-throughput identification of these channels is hampered by the low levels of availability of their structures and an observation that use of sequence similarity offers limited predictive quality. Consequently, several machine learning predictors of ion channels from protein sequences that do not rely on high sequence similarity were developed. However, only one of these methods offers a wide scope by predicting ion channels, their types and four major subtypes of the voltage-gated channels. Moreover, this and other existing predictors utilize relatively simple predictive models that limit their accuracy. We propose a novel and accurate predictor of ion channels, their types and the four subtypes of the voltage-gated channels called PSIONplus. Our method combines a support vector machine model and a sequence similarity search with BLAST. The originality of PSIONplus stems from the use of a more sophisticated machine learning model that for the first time in this area utilizes evolutionary profiles and predicted secondary structure, solvent accessibility and intrinsic disorder. We empirically demonstrate that the evolutionary profiles provide the strongest predictive input among new and previously used input types. We also show that all new types of inputs contribute to the prediction. Results on an independent test dataset reveal that PSIONplus obtains relatively good predictive performance and outperforms existing methods. It secures accuracies of 85.4% and 68.3% for the prediction of ion channels and their types, respectively, and the average accuracy of 96.4% for the discrimination of the four ion channel subtypes. Standalone version of PSIONplus is freely available from https://sourceforge.net/projects/psion/

Analysis of molecular structures and mechanisms for toxins derived from venomous animals

As predominant component in the venom of many dangerous animal species, toxins have been thoroughly investigated for drug design or as pharmacologic tools. The present study demonstrated the use of size and hydrophobicity of amino acid residues for the purposes of quantifying the valuable sequence-structure relationship and performing further analysis of interactional mechanisms in secondary structure elements (SSEs) for toxin native conformations. First, we showed that the presence of large and hydrophobic residues varying in availability in the primary sequences correspondingly affects the amount of these residues being used in the SSEs in accordance with linear behavioral patterns from empirical assessments of experimentally derived toxins and non-toxins. Subsequent derivation of prediction rules was established with the aim of analyzing molecular structures and mechanisms by means of 114 residue compositions for venom toxins. The obtained results concerning the linear behavioral patterns demonstrated the nature of the information transfer occurring from the primary to secondary structures. A dual action mechanism was established, taking into account steric and hydrophobic interactions. Finally, a new residue composition prediction method for SSEs of toxins was suggested.

KCNK5 channels mostly expressed in cochlear outer sulcus cells are indispensable for hearing

In the cochlea, K(+) is essential for mechano-electrical transduction. Here, we explore cochlear structure and function in mice lacking K(+) channels of the two-pore domain family. A profound deafness associated with a decrease in endocochlear potential is found in adult Kcnk5(-/-) mice. Hearing occurs around postnatal day 19 (P19), and completely disappears 2 days later. At P19, Kcnk5(-/-) mice have a normal endolymphatic [K(+)] but a partly lowered endocochlear potential. Using Lac-Z as a gene reporter, KCNK5 is mainly found in outer sulcus Claudius', Boettcher's and root cells. Low levels of expression are also seen in the spiral ganglion, Reissner's membrane and stria vascularis. Essential channels (KCNJ10 and KCNQ1) contributing to K(+) secretion in stria vascularis have normal expression in Kcnk5(-/-) mice. Thus, KCNK5 channels are indispensable for the maintenance of hearing. Among several plausible mechanisms, we emphasize their role in K(+) recycling along the outer sulcus lateral route.

RNA-Seq Analysis of Human Trigeminal and Dorsal Root Ganglia with a Focus on Chemoreceptors

The chemosensory capacity of the somatosensory system relies on the appropriate expression of chemoreceptors, which detect chemical stimuli and transduce sensory information into cellular signals. Knowledge of the complete repertoire of the chemoreceptors expressed in human sensory ganglia is lacking. This study employed the next-generation sequencing technique (RNA-Seq) to conduct the first expression analysis of human trigeminal ganglia (TG) and dorsal root ganglia (DRG). We analyzed the data with a focus on G-protein coupled receptors (GPCRs) and ion channels, which are (potentially) involved in chemosensation by somatosensory neurons in the human TG and DRG. For years, transient receptor potential (TRP) channels have been considered the main group of receptors for chemosensation in the trigeminal system. Interestingly, we could show that sensory ganglia also express a panel of different olfactory receptors (ORs) with putative chemosensory function. To characterize OR expression in more detail, we performed microarray, semi-quantitative RT-PCR experiments, and immunohistochemical staining. Additionally, we analyzed the expression data to identify further known or putative classes of chemoreceptors in the human TG and DRG. Our results give an overview of the major classes of chemoreceptors expressed in the human TG and DRG and provide the basis for a broader understanding of the reception of chemical cues.

Briefing in application of machine learning methods in ion channel prediction

In cells, ion channels are one of the most important classes of membrane proteins which allow inorganic ions to move across the membrane. A wide range of biological processes are involved and regulated by the opening and closing of ion channels. Ion channels can be classified into numerous classes and different types of ion channels exhibit different functions. Thus, the correct identification of ion channels and their types using computational methods will provide in-depth insights into their function in various biological processes. In this review, we will briefly introduce and discuss the recent progress in ion channel prediction using machine learning methods.

Sudden sensorineural hearing loss and polymorphisms in iron homeostasis genes: new insights from a case-control study

Background. Even if various pathophysiological events have been proposed as explanations, the putative cause of sudden hearing loss remains unclear. Objectives. To investigate and to reveal associations (if any) between the main iron-related gene variants and idiopathic sudden sensorineural hearing loss. Study Design. Case-control study. Materials and Methods. A total of 200 sudden sensorineural hearing loss patients (median age 63.65 years; range 10-92) were compared with 400 healthy control subjects. The following genetic variants were investigated: the polymorphism c.-8CG in the promoter of the ferroportin gene (FPN1; SLC40A1), the two isoforms C1 and C2 (p.P570S) of the transferrin protein (TF), the amino acidic substitutions p.H63D and p.C282Y in the hereditary hemochromatosis protein (HFE), and the polymorphism c.-582AG in the promoter of the HEPC gene, which encodes the protein hepcidin (HAMP). Results. The homozygous genotype c.-8GG of the SLC40A1 gene revealed an OR for ISSNHL risk of 4.27 (CI 95%, 2.65-6.89; P = 0.001), being overrepresented among cases. Conclusions. Our study indicates that the homozygous genotype FPN1 -8GG was significantly associated with increased risk of developing sudden hearing loss. These findings suggest new research should be conducted in the field of iron homeostasis in the inner ear.

Short-term plasticity and modulation of synaptic transmission at mammalian inhibitory cholinergic olivocochlear synapses

The organ of Corti, the mammalian sensory epithelium of the inner ear, has two types of mechanoreceptor cells, inner hair cells (IHCs) and outer hair cells (OHCs). In this sensory epithelium, vibrations produced by sound waves are transformed into electrical signals. When depolarized by incoming sounds, IHCs release glutamate and activate auditory nerve fibers innervating them and OHCs, by virtue of their electromotile property, increase the amplification and fine tuning of sound signals. The medial olivocochlear (MOC) system, an efferent feedback system, inhibits OHC activity and thereby reduces the sensitivity and sharp tuning of cochlear afferent fibers. During neonatal development, IHCs fire Ca²⁺ action potentials which evoke glutamate release promoting activity in the immature auditory system in the absence of sensory stimuli. During this period, MOC fibers also innervate IHCs and are thought to modulate their firing rate. Both the MOC-OHC and the MOC-IHC synapses are cholinergic, fast and inhibitory and mediated by the α9α10 nicotinic cholinergic receptor (nAChR) coupled to the activation of calcium-activated potassium channels that hyperpolarize the hair cells. In this review we discuss the biophysical, functional and molecular data which demonstrate that at the synapses between MOC efferent fibers and cochlear hair cells, modulation of transmitter release as well as short term synaptic plasticity mechanisms, operating both at the presynaptic terminal and at the postsynaptic hair-cell, determine the efficacy of these synapses and shape the hair cell response pattern.

iCTX-type: a sequence-based predictor for identifying the types of conotoxins in targeting ion channels

Conotoxins are small disulfide-rich neurotoxic peptides, which can bind to ion channels with very high specificity and modulate their activities. Over the last few decades, conotoxins have been the drug candidates for treating chronic pain, epilepsy, spasticity, and cardiovascular diseases. According to their functions and targets, conotoxins are generally categorized into three types: potassium-channel type, sodium-channel type, and calcium-channel types. With the avalanche of peptide sequences generated in the postgenomic age, it is urgent and challenging to develop an automated method for rapidly and accurately identifying the types of conotoxins based on their sequence information alone. To address this challenge, a new predictor, called iCTX-Type, was developed by incorporating the dipeptide occurrence frequencies of a conotoxin sequence into a 400-D (dimensional) general pseudoamino acid composition, followed by the feature optimization procedure to reduce the sample representation from 400-D to 50-D vector. The overall success rate achieved by iCTX-Type via a rigorous cross-validation was over 91%, outperforming its counterpart (RBF network). Besides, iCTX-Type is so far the only predictor in this area with its web-server available, and hence is particularly useful for most experimental scientists to get their desired results without the need to follow the complicated mathematics involved.

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). MS is the most comprehensive and versatile tool in proteomics and in conjunction with separation methods can provide an in-depth proteome of biological samples. Separation methods combined with MS has the ability to enrich protein samples, detect low molecular weight and hydrophobic proteins, and identify low abundant proteins by reducing the proteome dynamic range. Different digestion strategies can be applied to whole lysate or to fractionated protein lysate to enhance peptide and protein sequence coverage. Utilization of different separation techniques, including strong cation exchange (SCX), reversed-phase (RP), and gel-eluted liquid fraction entrapment electrophoresis (GELFrEE) can be applied to reduce sample complexity prior to MS analysis for protein identification.

TRPs in hearing

Hearing is a particularly sensitive form of mechanosensation that relies on dedicated ion channels transducing sound-induced vibrations that hardly exceed Brownian motion. Attempts to molecularly identify these auditory transduction channels have put the focus on TRPs in ears. In Drosophila, hearing has been shown to involve TRPA, TRPC, TRPN, and TRPV subfamily members, with candidate auditory transduction channels including NOMPC (=TRPN1) and the TRPVs Nan and Iav. In vertebrates, TRPs are unlikely to form auditory transduction channels, yet most TRPs are expressed in inner ear tissues, and mutations in TRPN1, TRPVA1, TRPML3, TRPV4, and TRPC3/TRPC6 have been implicated in inner ear function. Starting with a brief introduction of fly and vertebrate auditory anatomies and transduction mechanisms, this review summarizes our current understanding of the auditory roles of TRPs.

TRPM3

Like most other members of the TRP family, the Trpm3 gene encodes proteins that form cation-permeable ion channels on the plasma membrane. However, TRPM3 proteins have several unique features that set them apart from the other members of this diverse family. The Trpm3 gene encodes for a surprisingly large number of isoforms generated mainly by alternative splicing. Only for two of the (at least) eight sites at which sequence diversity is generated the functional consequences have been elucidated, one leading to nonfunctional channels, the other one profoundly affecting the ionic selectivity. In the Trpm3 gene an intronic microRNA (miR-204) is co-transcribed with Trpm3. By regulating the expression of a multitude of genes, miR-204 increases the functional complexity of the Trpm3 locus. Over the past years, important progress has been made in discovering pharmacological tools to manipulate TRPM3 channel activity. These substances have facilitated the identification of endogenously expressed functional TRPM3 channels in nociceptive neurons, pancreatic beta cells, and vascular smooth muscle cells, among others. TRPM3 channels, which themselves are temperature sensitive, thus have been implicated in sensing noxious heat, in modulating insulin release, and in secretion of inflammatory cytokines. However, in many tissues where TRPM3 proteins are known to be expressed, no functional role has been identified for these channels so far. Because of the availability of adequate pharmacological and genetic tools, it is expected that future investigations on TRPM3 channels will unravel important new aspects and functions of these channels.

iCDI-PseFpt: identify the channel-drug interaction in cellular networking with PseAAC and molecular fingerprints

Many crucial functions in life, such as heartbeat, sensory transduction and central nervous system response, are controlled by cell signalings via various ion channels. Therefore, ion channels have become an excellent drug target, and study of ion channel-drug interaction networks is an important topic for drug development. However, it is both time-consuming and costly to determine whether a drug and a protein ion channel are interacting with each other in a cellular network by means of experimental techniques. Although some computational methods were developed in this regard based on the knowledge of the 3D (three-dimensional) structure of protein, unfortunately their usage is quite limited because the 3D structures for most protein ion channels are still unknown. With the avalanche of protein sequences generated in the post-genomic age, it is highly desirable to develop the sequence-based computational method to address this problem. To take up the challenge, we developed a new predictor called iCDI-PseFpt, in which the protein ion-channel sample is formulated by the PseAAC (pseudo amino acid composition) generated with the gray model theory, the drug compound by the 2D molecular fingerprint, and the operation engine is the fuzzy K-nearest neighbor algorithm. The overall success rate achieved by iCDI-PseFpt via the jackknife cross-validation was 87.27%, which is remarkably higher than that by any of the existing predictors in this area. As a user-friendly web-server, iCDI-PseFpt is freely accessible to the public at the website http://www.jci-bioinfo.cn/iCDI-PseFpt/. Furthermore, for the convenience of most experimental scientists, a step-by-step guide is provided on how to use the web-server to get the desired results without the need to follow the complicated math equations presented in the paper just for its integrity. It has not escaped our notice that the current approach can also be used to study other drug-target interaction networks.

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. Digestion with LysC/trypsin followed by SCX fractionation and multiple nanoLC-MS/MS analyses identified 3773 proteins with a 1% FDR. Of these, 694 protein IDs were in the plasmalemma. Protein IDs obtained by combining outcomes from GELFrEE/LysC/trypsin with GELFrEE/trypsin/trypsin generated 2779 proteins, of which 606 additional proteins were identified using the GELFrEE/LysC/trypsin approach. Combining results from the different techniques resulted in a total of 4620 IDs, including a number of previously unreported proteins. GO analyses showed high expression of binding and catalytic proteins as well as proteins associated with metabolism. The results show that the application of multiple techniques is needed to provide an exhaustive proteome of the cochlear sensory epithelium that includes many membrane proteins. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD000231.

Lipid nanobilayers to host biological nanopores for DNA translocations

We characterize a recently introduced novel nanobilayer technique [Gornall, J. L., Mahendran, K. R., Pambos, O. J., Steinbock, L. J., Otto, O., Chimerel, C., Winterhalter, M., and Keyser, U. F. Simple reconstitution of protein pores in nano lipid bilayers. Nano Lett. 2011, 11 (8), 3334-3340] and its practical aspects for incorporating the biological nanopore α-hemolysin from Staphylococcus aureus and subsequent studies on the translocation of biomolecules under various conditions. This technique provides advantages over classical bilayer methods, especially the quick formation and extended stability of a bilayer. We have also developed a methodology to prepare a uniform quality of giant unilamellar vesicles (GUVs) in a reproducible way for producing nanobilayers. The process and the characteristics of the reconstitution of α-hemolysin in nanobilayers were examined by exploiting various important parameters, including pH, applied voltage, salt concentration, and number of nanopores. Protonation of α-hemolysin residues in the low pH region affects the translocation durations, which, in turn, changes the statistics of event types as a result of electrostatics and potentially the structural changes in DNA. When the pH and applied voltage were varied, it was possible to investigate and partly control the capture rates and type of translocation events through α-hemolysin nanopores. This study could be helpful to use the nanobilayer technique for further explorations, particularly owing to its advantages and technical ease compared to existing bilayer methods.

Site-directed mutagenesis to study the structure-function relationships of ion channels

Ion channels mediate a wide variety of physiological processes by forming small pores across the membranes that allow regulated flow of ions into or out of the cell. The primary linear sequences of ion channel proteins, like any proteins, are composed by 20 different amino acids, each of which is determined by specific triplet codon in their genes. Site-directed mutagenesis is a widely used molecular biology method to change the triplet in the coding sequence and thereby the amino acid residue in the protein sequence. Functional characterization of the ion channels carrying point mutations allows us to interrogate the structure-function relationships of the ion channels. Here, we will describe the site-directed mutagenesis procedures, in which the wide-type cDNA or plasmid is used as a template to synthesize the complementary mutation-containing DNAs from two mutagenic primers in the polymerase chain reaction.

Probing the Xenopus laevis inner ear transcriptome for biological function

Background

The senses of hearing and balance depend upon mechanoreception, a process that originates in the inner ear and shares features across species. Amphibians have been widely used for physiological studies of mechanotransduction by sensory hair cells. In contrast, much less is known of the genetic basis of auditory and vestibular function in this class of animals. Among amphibians, the genus Xenopus is a well-characterized genetic and developmental model that offers unique opportunities for inner ear research because of the amphibian capacity for tissue and organ regeneration. For these reasons, we implemented a functional genomics approach as a means to undertake a large-scale analysis of the Xenopus laevis inner ear transcriptome through microarray analysis.

Results

Microarray analysis uncovered genes within the X. laevis inner ear transcriptome associated with inner ear function and impairment in other organisms, thereby supporting the inclusion of Xenopus in cross-species genetic studies of the inner ear. The use of gene categories (inner ear tissue; deafness; ion channels; ion transporters; transcription factors) facilitated the assignment of functional significance to probe set identifiers. We enhanced the biological relevance of our microarray data by using a variety of curation approaches to increase the annotation of the Affymetrix GeneChip® Xenopus laevis Genome array. In addition, annotation analysis revealed the prevalence of inner ear transcripts represented by probe set identifiers that lack functional characterization.

Conclusions

We identified an abundance of targets for genetic analysis of auditory and vestibular function. The orthologues to human genes with known inner ear function and the highly expressed transcripts that lack annotation are particularly interesting candidates for future analyses. We used informatics approaches to impart biologically relevant information to the Xenopus inner ear transcriptome, thereby addressing the impediment imposed by insufficient gene annotation. These findings heighten the relevance of Xenopus as a model organism for genetic investigations of inner ear organogenesis, morphogenesis, and regeneration.

Second-order Poisson Nernst-Planck solver for ion channel transport

The Poisson Nernst-Planck (PNP) theory is a simplified continuum model for a wide variety of chemical, physical and biological applications. Its ability of providing quantitative explanation and increasingly qualitative predictions of experimental measurements has earned itself much recognition in the research community. Numerous computational algorithms have been constructed for the solution of the PNP equations. However, in the realistic ion-channel context, no second order convergent PNP algorithm has ever been reported in the literature, due to many numerical obstacles, including discontinuous coefficients, singular charges, geometric singularities, and nonlinear couplings. The present work introduces a number of numerical algorithms to overcome the abovementioned numerical challenges and constructs the first second-order convergent PNP solver in the ion-channel context. First, a Dirichlet to Neumann mapping (DNM) algorithm is designed to alleviate the charge singularity due to the protein structure. Additionally, the matched interface and boundary (MIB) method is reformulated for solving the PNP equations. The MIB method systematically enforces the interface jump conditions and achieves the second order accuracy in the presence of complex geometry and geometric singularities of molecular surfaces. Moreover, two iterative schemes are utilized to deal with the coupled nonlinear equations. Furthermore, extensive and rigorous numerical validations are carried out over a number of geometries, including a sphere, two proteins and an ion channel, to examine the numerical accuracy and convergence order of the present numerical algorithms. Finally, application is considered to a real transmembrane protein, the Gramicidin A channel protein. The performance of the proposed numerical techniques is tested against a number of factors, including mesh sizes, diffusion coefficient profiles, iterative schemes, ion concentrations, and applied voltages. Numerical predictions are compared with experimental measurements.

Strategies for enhanced annotation of a microarray probe set

We aim to determine the biological relevance of genes identified through microarray-mediated transcriptional profiling of Xenopus sensory organs and brain. Difficulties with genetic data analysis arise because of limitations in probe set annotation and the lack of a universal gene nomenclature. To overcome these impediments, we used sequence based and semantic linking methods in combination with computational approaches to augment probe set annotation on a commercially available microarray. Our curation efforts enabled linkage of probe sets and expression data to public databases, increased the biological significance of our microarray data, and assisted with the tentative identification of unidentified probe sets.

Advances in Auditory and Vestibular Medicine

Auditory and Vestibular medicine is becoming more accepted as a specialty of its own, Medical NeurOtology. Recent advances in the field have been instrumental in the understanding of the scientific foundations, pathophysiology, clinical approach and management of patients with hearing and vestibular disorders. This paper will review these advances.

A quantitative analysis of the spatiotemporal pattern of transient receptor potential gene expression in the developing mouse cochlea

TRP genes encode a diverse family of ion channels which have been implicated in many sensory functions. Because several TRP channels have similar properties to the elusive hair cell transduction channel, recent attention has focused on TRP gene expression in the inner ear. At least four TRP genes are known to be expressed in hair cells: TRPC3, TRPV4, TRPA1, and TRPML3. However, there is little evidence supporting any of these as a component of the transduction complex. Other less well-characterized TRP channels are expressed in the inner ear, in particular, within the organ of Corti. Because of their potential role in sensory function, we investigated the developmental expression of RNA that encodes all 33 TRP subunits as well as several splice variants. We designed a quantitative PCR screen using cochlear samples acquired before, during, and after the time when mechanotransduction is acquired in sensory hair cells (embryonic day 17 to postnatal day 8). Cochleas, which included the organ of Corti, stria vascularis, and Reissner's membrane, were subdivided into four equal quadrants which allowed for regional comparison during development. Expression of RNA transcripts that encoded 33 TRP subunits plus several splice forms and beta-actin were quantified in 28 samples for a total of 1,092 individual measurements, each done in triplicate. We detected RNA that encoded all TRP channels except two: TRPC7 and TRPM8. The largest changes in RNA expression were for TRPA1 (>100-fold), TRPP3 (>50-fold), and TRPC5.2 (>20-fold) which suggested that these subunits may contribute to normal cochlear function. Furthermore, the screen revealed TRPP3 and PKD1L3 RNA expression patterns that were correlated with the acquisition of sensory transduction in outer hair cells (Lelli et al., J Neurophysiol. 101:2961-2973, 2009). Numerous spatiotemporal expression gradients were identified many of which may contribute to the normal functional development of the mouse cochlea.

A protein interaction network for the large conductance Ca(2+)-activated K(+) channel in the mouse cochlea

The large conductance Ca(2+)-activated K(+) or BK channel has a role in sensory/neuronal excitation, intracellular signaling, and metabolism. In the non-mammalian cochlea, the onset of BK during development correlates with increased hearing sensitivity and underlies frequency tuning in non-mammals, whereas its role is less clear in mammalian hearing. To gain insights into BK function in mammals, coimmunoprecipitation and two-dimensional PAGE, combined with mass spectrometry, were used to reveal 174 putative BKAPs from cytoplasmic and membrane/cytoskeletal fractions of mouse cochlea. Eleven BKAPs were verified using reciprocal coimmunoprecipitation, including annexin, apolipoprotein, calmodulin, hippocalcin, and myelin P0, among others. These proteins were immunocolocalized with BK in sensory and neuronal cells. A bioinformatics approach was used to mine databases to reveal binary partners and the resultant protein network, as well as to determine previous ion channel affiliations, subcellular localization, and cellular processes. The search for binary partners using the IntAct molecular interaction database produced a putative global network of 160 nodes connected with 188 edges that contained 12 major hubs. Additional mining of databases revealed that more than 50% of primary BKAPs had prior affiliations with K(+) and Ca(2+) channels. Although a majority of BKAPs are found in either the cytoplasm or membrane and contribute to cellular processes that primarily involve metabolism (30.5%) and trafficking/scaffolding (23.6%), at least 20% are mitochondrial-related. Among the BKAPs are chaperonins such as calreticulin, GRP78, and HSP60 that, when reduced with siRNAs, alter BKalpha expression in CHO cells. Studies of BKalpha in mitochondria revealed compartmentalization in sensory cells, whereas heterologous expression of a BK-DEC splice variant cloned from cochlea revealed a BK mitochondrial candidate. The studies described herein provide insights into BK-related functions that include not only cell excitation, but also cell signaling and apoptosis, and involve proteins concerned with Ca(2+) regulation, structure, and hearing loss.

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. Here, we report the methods by which membrane proteins are isolated from cochlear tissues and prepared for identification by mass spectrometry techniques.

Issues, indications, and controversies regarding intratympanic steroid perfusion

PURPOSE OF REVIEW

Office-based intratympanic inner ear steroid perfusion (ITPs) treatment for Ménière's disease, autoimmune inner ear disease, and sudden sensorineural hearing loss has been expanding over the past 10-15 years, yet remains controversial. The purpose of this review is to examine the current literature of basic science and human studies of ITPs treatment.

RECENT FINDINGS

Animal studies exist regarding the delivery, distribution, biochemical, and microbiological changes in the inner ear post ITPs. However, few clinical studies exist on ITPs treatment in sudden sensorineural hearing loss and even less in treating Ménière's disease. There are no consistent studies regarding drug delivery methods, type, and concentration of steroids. Moreover, there are no studies comparing ITPs results to the natural history of Ménière's disease.

SUMMARY

ITPs has impacted otology and neurotology practice due to increased utilization. A sound understanding of the basic science and clinical studies is needed to establish long-term efficacy of ITPs in controlling hearing loss in Ménière's disease by comparison to its natural history, as well as, potential application to other disorders.

RNA isolation from Xenopus inner ear sensory endorgans for transcriptional profiling and molecular cloning

The amphibian Xenopus offers a unique model system for uncovering the genetic basis of auditory and vestibular function in an organism that is well-suited for experimental manipulation during animal development. However, many procedures for analyzing gene expression in the peripheral auditory and vestibular systems mandate the ability to isolate intact RNA from inner ear tissue. Methods presented here facilitate preparation of high quality inner ear RNA from larval and post-metamorphic Xenopus specimens that can be used for a variety of purposes. We demonstrate that RNA isolated with these protocols is suitable for microarray analysis of inner ear organs, and for cloning of large transcripts, such as those for ion channels. Genetic sequences cloned with these procedures can be used for transient transfection of Xenopus kidney cell lines with GFP fusion constructs.