In the planarian field, two techniques are mostly used for protein detection immunohistochemistry (IHC) and western blotting. While IHC is great for visualizing the spatial distribution of proteins in whole organisms, it has limitations in antibody availability and issues related to nonspecific expression. The use of western blotting can circumvent nonspecific expression, providing a dependable way to quantify proteins of interest. Here, we present a standardized, easily reproducible protocol with details on protein extractions of whole planarians and western blotting. For complete details on the use and execution of this protocol, please refer to Ziman et al. (2020a).The relative positioning of organelles underlies fundamental cellular processes, including signaling, polarization, and cellular growth. Here, we describe the usage of a light-dependent heterodimerization system, LOVpep-ePDZ, to alter organelle positioning locally and reversibly in order to study the functional consequences of organelle positioning. The protocol gives details on how to accomplish expression of fusion proteins encoding this system, describes the imaging parameters to achieve subcellular activation in C. elegans, and may be adapted for use in other model systems. For complete details on the use and execution of this protocol, please refer to De Henau et al. (2020).A FACS protocol is described that eliminates isolation and staining artifacts to allow accurate comparison between cell populations isolated from organs obtained from disparate mouse groups. This protocol was validated by characterizing the estrogen receptor positive cells within the mammary gland of transgenic mice with different genotypes at different stages of the estrous cycle. We include protocols necessary to batch stage animals within the cycle to proceed directly to FACS, which provides optimal RNA yields for RNA-seq. For complete details on the use and execution of this protocol, please refer to Ludwik et al. (2020).In this protocol, we took a "thermogenetics" approach to detect functional gap junction channels between cells in Drosophila egg chambers. We expressed the thermosensitive cation channel TrpA1-A in the germline using Gal4, and a fluorescent [Ca2+] sensor (GCaMP6), in all follicle cells using the LexA/LexAop system. If gap junctions connect germ cells and follicle cells, we expect a temperature-dependent TRPA1-A-dependent cation influx into the germline from the culture medium to result in a GCaMP signal in follicle cells. For complete details on the use and execution of this protocol, please refer to Miao et al. (2020).Synapses are crucial to brain function and frequent disease targets, but current analysis methods cannot report on individual synaptic components in situ or present barriers to widespread adoption. SEQUIN was developed to address this challenge. SEQUIN utilizes a widely available super-resolution platform in tandem with image processing and analysis to quantify synaptic loci over large regions of brain and characterize their molecular and nanostructural properties at the individual and population level. This protocol describes quantification of synaptic loci using SEQUIN. For additional details on the use and execution of this protocol, please refer to Sauerbeck et al. (2020).CD103+CD8+ tumor-resident memory T cells (TRM) are important components of anti-tumor immunity. However, their role in response to cancer immunotherapy is not fully understood. The protocol describes how to isolate CD8+ T cells and autologous tumor cells from human lung tumors to study the functional activities of CD8+ T cells. Tumors are heterogeneous in terms of the quantity and quality of immune cell types, so the yield of TRM cells depends on the features of the tumor. For complete details on the use and execution of this protocol, please refer to Corgnac et al. (2020).The patch-clamp recording technique is indispensable for studying ion channel functions of cells but is challenging to apply to the node of Ranvier, a key site where action potentials are conducted along myelinated nerves. We have developed a pressure-clamped patch-clamp recording method applying to the node of Ranvier of rat myelinated nerves. The step-by-step protocol described here allows researchers to apply this approach to study mechanisms underlying saltatory conduction and information processing in myelinated nerves of mammals. For complete information on the generation and use of this protocol, please refer to Kanda et al.  https://www.selleckchem.com/products/liraglutide.html  (2019).Alzheimer's disease is characterized by the deposition of extracellular amyloid-beta (Aβ) plaques. While microglial phagocytosis is a major mechanism through which Aβ is cleared, there is no method for quantitatively assessing Aβ phagocytic capacity of microglia in vivo. Here, we present a flow cytometry-based method for investigating the Aβ phagocytic capacity of microglia in vivo. This method enables the direct comparison of Aβ phagocytic capacity between different microglial subpopulations as well as the direct isolation of Aβ phagocytic microglia for downstream applications. For complete details on the use and execution of this protocol, please refer to Lau et al. (2020).In T cell-based cancer immunotherapy, tumor antigen (Ag)-specific CD8+ cytotoxic T lymphocytes (CTLs) can specifically target tumor Ags on malignant cells. This promising approach drove us to adopt this strategy of T cell transfer (ACT)-based immunotherapy for chronic viral infections. Here, we describe the generation of hepatitis B virus (HBV) Ag-specific CTLs from induced pluripotent stem cells (iPSCs), i.e., iPSC-CTLs. Ag-specific iPSC-CTLs can target HBV Ag+ cells and infiltrate into the liver to suppress HBV replication in a murine model. For complete details on the use and execution of this protocol, please refer to Haque et al. (2020).Targeted drug delivery to pancreatic islet β cells is an unmet clinical need. β cells possess a uniquely high Zn2+ concentration, and integrating Zn2+-binding activity into a small molecule can bias drug accumulation and activity toward β cells. This protocol can be used to evaluate a molecule's capacity to chelate islet Zn2+, accumulate in islets, and stimulate β cell-selective replication in mouse pancreas. One obstacle is establishing an LC-MS/MS-based method for compound measurement. Limitations include target compound ionizability and the time-sensitive nature of some experimental assay steps. For complete details on the use and execution of this protocol, please refer to Horton et al. (2019).