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Bestrophin-1 (BEST1) is a calcium-activated chloride channel (CaCC) predominantly expressed at the basolateral membrane of the retinal pigment epithelium (RPE). Over 250 mutations in the BEST1 gene have been documented to cause at least five retinal degenerative disorders, commonly termed bestrophinopathies, to which no treatment is currently available. Therefore, understanding the influences of BEST1 disease-causing mutations on the physiological function of BEST1 in RPE is critical for deciphering the pathology of bestrophinopathies and developing therapeutic strategies for patients. However, this task has been impeded by the rarity of BEST1 mutations and limited accessibility to native human RPE cells. Here, we describe a pluripotent stem cell (PSC)-based pipeline for reproducibly generating RPE cells expressing endogenous or exogenous mutant BEST1, which provides us with a powerful "disease-in-a-dish" approach for studying BEST1 mutations in physiological environments.Alternative splicing of RNA transcripts allows a single gene to generate multiple products and is a key means of generating functionally diverse voltage-gated ion channels. Splicing can be regulated according to cell type, cell state, and stage of development to produce a bespoke complement of protein isoforms. Characterizing the identities of full-length transcript isoforms is essential in order to fully understand a gene's expression and function. However, the repertoire of transcript isoforms is not well characterized for most genes. Long read nanopore sequencing allows full-length isoforms to be sequenced, therefore identifying full-length transcripts. Using this approach, we recently discovered that the human CACNA1C gene gives rise to a far greater repertoire of splice isoforms than previously appreciated. Here we provide a detailed overview of the technical approach we used to achieve this. The method described in this chapter combines long read nanopore sequencing with PCR targeting to selectively sequence transcripts of a specific gene of interest.Melanocytes are specialized cells that produce melanin pigments responsible for skin, hair, and eye pigmentation. The synthesis and storage of melanin occurs in unique lysosome-related organelles called melanosomes, which regulate melanin production via complex regulatory mechanisms. Maintenance of the melanosome luminal ionic environment and pH is crucial for proper function of the main melanogenic enzymes. Defects in genes encoding pH-regulating melanosomal proteins result in oculocutaneous albinism, which is characterized by hypopigmentation, impaired vision, and increased susceptibility to skin and eye cancers. We recently uncovered several ion channels and transporters that modulate melanin synthesis by acidifying or neutralizing the luminal pH of melanosomes. However, our understanding of how melanosomes and other related organelles maintain their luminal pH is far from complete. The study of melanosome pH regulation requires robust imaging and quantification tools. Despite recent advances in the development of such methods, many limitations remain, particularly for quantitative analysis of individual organelle pH. In this chapter, we will provide an overview of the available methods used for melanosome pH determination, including their advantages, limitations, and challenges. To address the critical, unmet need for reliable melanosome pH quantification tools, we engineered a novel genetically encoded, ratiometric pH sensor for melanosomes that we named RpHiMEL. Here, we describe the design and optimization of RpHiMEL, and provide a pH quantification method for individual melanosomes in live cells. We demonstrate that RpHiMEL is a highly versatile tool with the potential to advance our understanding of pH regulation in melanosomes and related organelles.As an increasing number of protein structures are resolved at atomic and near-atomic resolution, conventional amino acid mutagenesis may be insufficient to test many mechanistic hypotheses. As a result, the development of new tRNA/aminoacyl-tRNA synthetase (aaRS) pairs has become an important tool for determining intricate molecular interactions and understanding protein structures. This chapter describes in detail the directed evolution of new tRNA/aaRS pairs in Escherichia coli for the incorporation of non-canonical amino acids (ncAA). Section 1 describes the selection of new tRNA/aaRS pairs in E. coli. Section 2 details the use of a synthetase to incorporate an ncAA into a mammalian cell line, and Sections 1 and 2 both include methods on the determination of synthetase efficacy and fidelity.The choroid plexus (CP) is an epithelial tissue primarily responsible for the secretion of the cerebrospinal fluid (CSF). Choroid plexuses are found in each of the four brain ventricles two laterals, third and fourth. learn more They ensure continuous production of CSF to provide nutrients, remove waste products and provide a mechanical buffer to protect the brain. Tight junctions in the CP epithelium form a barrier between the blood plasma and the CSF, which allow channels and transporters in the CP to establish a highly regulated concentration gradient of ions between the two fluids, thereby controlling the composition of CSF. CP plays an important part in healthy brain homeostasis, as its failure to maintain adequate CSF perfusion is implicated in Alzheimer's disease and traumatic brain injury. And yet, the physiology of CP and the mechanism of its age-related functional decline is one of the most understudied areas of neurobiology. Here, we describe a protocol to isolate and identify individual choroid plexus epithelial cells (CPEC) from murine brain for whole-cell patch-clamp recordings and ion channel identification. Using the recording from the inwardly rectifying potassium channel Kir7.1 and TRPM3 that are abundant in CP, we demonstrate a technique to study the regulators of ion channels in the choroid plexus.Connexin hemichannels are permeable to both atomic ions and small molecules. Yet, they have different selectivity for ions and signaling molecules critical for biological functions. Activity of connexin hemichannels in living cells is commonly evaluated by methods that include electrophysiology and fluorescence-based approaches. Although less common, luminescence and radioactivity-based uptake/release assays have been also successfully used to determine selectivity and permeability to different molecules. The current methods, however, have important technical and quantitative limitations that make them unsuitable for simultaneously evaluating ionic and molecular permeability using different stimuli that control channel gating (e.g., voltage or extracellular Ca2+). To address this, we have recently designed a novel methodology that combines two-electrode voltage clamp (TEVC) and dye uptake assays in translucent Xenopus oocytes. This method allows for the evaluation of molecular transport kinetics in connexin hemichannels, and its utility can also be extended to other large pore channels, such as those formed by pannexin and CALHM.