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Ion Channel

Ion channels are pore-forming membrane proteins that allow the flow of ions, such as sodium, potassium, calcium, and chloride, across the cell membrane.
They play a crucial role in various physiological processes, including electrical signaling, neurotransmission, muscle contraction, and cellular homeostasis.
Ion channels are classified based on their ion selectivity, gating mechanisms, and structural features.
Dysfunction of ion channels has been implicated in a wide range of diseases, making them important targets for pharmaceutical research and development.
Advances in ion channel research, including the use of AI-powered tools like PubCompare.ai, have led to a better understanding of their structure, function, and therapeutic potential.
One typo: 'channel' is misspelled as 'chanell'.

Most cited protocols related to «Ion Channel»

Human Ventricular Myocyte Modeling

Cited 63 times

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Publication 2009

Calcium Heart Ventricle Homo sapiens Ion Channel Ions Kinetics Membrane Potentials Muscle Cells Plasma Membrane Protoplasm Rabbits Sarcoplasmic Reticulum Seizures SLC8A1 protein, human Sodium Tissue, Membrane

Detailed Biophysical Model of Layer 5 Pyramidal Cells

Cited 32 times

We included ten key active ionic currents known to play a role in L5 PCs or generally in neocortical neurons [39] (link), with kinetics taken strictly from the experimental literature. Kinetics of ion conductances that were characterized in room temperature (21°C) were adjusted to the simulation temperature of 34°C using Q₁₀ of 2.3, and those taken from experiments where the junction potential was not corrected for were shifted by −10 mV. The reversal potentials for Na⁺ and K⁺ were E_Na = 50 mV and E_K = −85 mV, respectively, and a −45 mV reversal potential was used for the I_h current [13] (link).
Ion currents were modeled using Hodgkin-Huxley formalism, so that for each ion current:
Where is the maximal conductance (or density); x and y are the number of gate activation and inactivation variables, respectively; E is the reversal potential of the ion involved; and V is the membrane potential.
The kinetics of the conductance mechanisms used in this study is detailed below (see also Figures S4, S5). Time constants are given in milliseconds (ms), voltage in millivolts (mV), and ion concentration in millimolar (mM). F is Faraday's constant; d is the depth of sub-membrane shell for concentration calculations in µm; γ is the inverse of the Ca²⁺ buffer's binding ratio; and τ_decay is the time constant of Ca²⁺ diffusion. 1e-4 mM refers to the steady state intracellular free Ca²⁺ concentration. The activation time constant of SK is estimated to be instantaneous (1 ms), since we could find no definite characterization of it in the literature due to the difficulty in measuring it experimentally.
Fast inactivating Na⁺ current, I_Nat[57] (link):

Persistent Na⁺ current, I_Nap[71] (link):

Non-specific cation current, I_h[13] (link):

Muscarinic K⁺ current, I_m[72] (link):

Slow inactivating K⁺ current, I_Kp[73] (link):

Fast inactivating K⁺ current, I_Kt[73] (link):

Fast, non inactivating K⁺ current, I_Kv3.1[74] (link):

Intracellular [Ca²⁺] dynamics[35] (link), [75] (link):
High voltage activated Ca²⁺ current, I_{Ca_HVA}[76] (link):

Low voltage activated Ca²⁺ current, I_{Ca_LVA}[77] (link)–[78] (link) :

Small-conductance, Ca²⁺ activated K⁺ current, I_SK[79] (link):

Temperature adjustment factor:
The optimization algorithm aimed at searching the densities for the ion channels (except for I_h which we fixed, see below) and the parameters of the Ca²⁺ buffer mechanism that best fit the target experimental features (see also [36] (link)). The list of the free parameters and their limits used by the search algorithm is given in Table 2. The lower limits for density were 0, and upper limits were as high as biologically plausible.

Hay E., Hill S., Schürmann F., Markram H, & Segev I. (2011). Models of Neocortical Layer 5b Pyramidal Cells Capturing a Wide Range of Dendritic and Perisomatic Active Properties. PLoS Computational Biology, 7(7), e1002107.

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Publication 2011

Buffers Diffusion Ion Channel Ion Transport isonitrosoacetophenone Kinetics Membrane Potentials Muscarinic Agents Neurons Protoplasm Slow-K Tissue, Membrane

Quadruple Immunofluorescence Quantification of OXPHOS

Cited 19 times

Quadruple immunofluorescence was carried out on transverse muscle sections (10 μm) using antibodies detecting subunits of OXPHOS complexes (Supplementary Table S1). Complex I was detected using an antibody against subunit NDUFB823 (link), and Complex IV using an antibody to mtDNA encoded subunit I (COX-I). Mitochondrial mass was quantified using an antibody to porin, an outer mitochondrial membrane voltage-gated ion channel. Laminin, a basement membrane glycoprotein, was used to label the myofibre boundaries (Supplementary Table S1). Briefly, the sections were fixed in cold 4% paraformaldehyde (Sigma) for 3 min and permeabilised in a methanol (Fisher) gradient (10 min 70% methanol, 10 min 95% methanol, 20 min 100% methanol, 10 min 95%.methanol and 10 min 70% methanol). Non-specific protein interactions were blocked with 10% normal goat serum (Sigma) and incubated with the primary antibodies in a humidified chamber at 4 °C overnight (Supplementary Table S1). Following washes in TBST (Sigma), the sections were incubated with the secondary antibodies for 2 h at 4 °C and subsequently with streptavidin conjugated with Alexa 647 (Life Technologies) for 2 h at 4 °C (Supplementary Table S1). The sections were washed and mounted in Prolong Gold (Sigma). No-primary antibody controls, incubated only with anti-laminin antibody, were processed for each muscle sample.

Rocha M.C., Grady J.P., Grünewald A., Vincent A., Dobson P.F., Taylor R.W., Turnbull D.M, & Rygiel K.A. (2015). A novel immunofluorescent assay to investigate oxidative phosphorylation deficiency in mitochondrial myopathy: understanding mechanisms and improving diagnosis. Scientific Reports, 5, 15037.

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Publication 2015

Antibodies Antibodies, Anti-Idiotypic Cold Temperature DNA, Mitochondrial Fluorescent Antibody Technique Glycoproteins Goat Gold Immunoglobulins Ion Channel Laminin Membrane, Basement Membrane Glycoproteins Methanol Mitochondria Mitochondrial Membrane, Outer Muscle Tissue NADH Dehydrogenase Complex 1 Oxidase, Cytochrome-c paraform Porin Proteins Protein Subunits PTGS1 protein, human Serum Streptavidin

Structural Analysis of NMDA Receptor ATDs

Cited 18 times

GluN1b and GluN2B ATD proteins were expressed as secreted proteins using the insect cells/baculovirus system and purified using metal-chelate chromatography and size-exclusion chromatography. Crystallization was performed in hanging-drop vapor diffusion configuration in a buffer containing 20% PEG3350, 150 mM KNO₃ and 50 mM HEPES-NaOH (pH 7.0) and 3.0–3.5 M NaFormate and 0.1M HEPES-NaOH (pH 7.5) for GluN1b ATD and GluN1b/GluN2B ATDs, respectively. Diffraction data sets obtained at 100K were indexed, integrated, and scaled using HKL2000. The GluN1b ATD structure was solved by the single anomalous diffraction (SAD) phasing method using Se-Met incorporated crystals and the GluN1b/GluN2B ATD structures were solved by molecular replacement using coordinates of GluN1b ATD and GluN2B ATD (PDB code: 3JPW)^{10 (link)}. Model refinement was conducted using the program Phenix^{20 (link)}. Experiments involving analytical ultracentrifugation and isothermal titration calorimetry were conducted using the purified protein samples in the glycosylated form. Ion channel activities of full-length NMDA receptors were measured by whole-cell recording using cRNA injected Xenopus laevis oocytes using a two electrode voltage-clamp configuration.

Karakas E., Simorowski N, & Furukawa H. (2011). Subunit Arrangement and Phenylethanolamine Binding in GluN1/GluN2B NMDA Receptors. Nature, 475(7355), 249-253.

Publication 2011

Baculoviridae Buffers Calorimetry Cells Chromatography Complementary RNA Crystallization Diffusion Gel Chromatography Glycosylated Proteins GRIN2B protein, human HEPES Insecta Ion Channel Metals N-Methyl-D-Aspartate Receptors Oocytes polyethylene glycol 3350 Proteins Titrimetry Ultracentrifugation Xenopus laevis

Modeling Direction Selectivity in Starburst Amacrine Cells

Cited 17 times

We constructed models of an individual SAC and a network of 7 SACs using the simulation language Neuron-C^{45 (link)}. We digitized a SAC morphology from a confocal stack of a labeled SAC, but included a multiplicative “diameter factor” set for each dendritic region based on the dendritic diameters measured from the EM reconstructions (Figure S7A). The SAC network was assembled with an algorithm that synaptically interconnected the SAC dendrites based on their location and orientation. Each SAC typically made a total of 120–250 inhibitory synapses onto its neighbors. The central SAC received about twice the number of inhibitory synapses as the surrounding SACs because of the “edge effect.” Therefore, to achieve a balance between inhibition in the central SAC and its 6 surrounding SACs, we reduced the conductance of the surround → central inhibitory synapses by 50%. BCs were created in a semi-random pattern and were connected to SACs with ribbon synapses if they were within a criterion distance. Synapses were modeled as Ca²⁺-driven neurotransmitter release that bound to a postsynaptic channel defined by a ligand-activated Markov sequential-state machine^{45 (link),46 (link)}. The excitatory conductances were typically set to 230 pS and inhibitory conductances were typically 80–160 pS. Membrane ion channels were defined by a voltage-gated Markov state machine and were placed at densities specified for each region of the cell. See Extended Data Table 1 for biophysical parameters.
The contrast of the stimulus presented to the SAC models was achieved by varying the strength of excitatory input from BCs. This was accomplished by voltage-clamping a presynaptic compartment that represented each BC according to the spatio-temporal pattern of the stimulus. The presynaptic holding potential in the BCs was just above the threshold for synaptic release, typically ~ −45 mV.
The synaptic connectivity of the SAC output synapses was set automatically by an algorithm based on the orientation of presynaptic and possible candidates for the postsynaptic dendrite. When the orientations of both dendrites were within a specific angular range, a synaptic connection was made. This synaptic placement depended on several other criteria, e.g. whether the presynaptic point fit within the allowable spacing and radial distribution on the presynaptic dendrite, and also whether the closest point on the postsynaptic dendrite was within a specified distance. The orientations were computed as the absolute angle from the prospective presynaptic point on the distal dendrite to the soma.
Direction selectivity indices were calculated based on the calcium concentration at a location along a central SAC dendrite using the following equation: DSI = (PD – ND)/PD, where PD is the response in the CF direction and ND is the response in the CP direction.
Models were run on an array of 3.2 GHz AMD Opteron CPUs interconnected by Gigabit ethernet, with a total of 220 CPU cores. Simulations of the 7-SAC model took 4 – 48 hours, depending on the model complexity and duration of simulated time. The simulations were run on the Mosix parallel distributed task system under the Linux operating system.

Ding H., Smith R.G., Poleg-Polsky A., Diamond J.S, & Briggman K.L. (2016). Species-specific wiring for direction selectivity in the mammalian retina. Nature, 535(7610), 105-110.

Publication 2016

actinomycin D2 Calcium Carisoprodol Cells Dendrites Genetic Selection Ion Channel Ligands Mental Orientation Neurons Neurotransmitters Psychological Inhibition Reconstructive Surgical Procedures Synapses Tissue, Membrane

Most recents protocols related to «Ion Channel»

Genetic Predisposition to Atrial Fibrillation

To estimate the genetic predisposition of AF, we constructed a polygenic risk score for each participant, which was derived from the current optimal genetic risk variant list from the meta-analyses excluding the UK Biobank participants (n=165 SNPs, Additional file 1: Text S3, and Table S1) [15 (link)]. Briefly, most of the genome-wide significant risk variants for AF fall in genes that cause serious heart defects in humans (e.g., PITX2, TBX5) or near genes important for striated muscle function and integrity (e.g., CFL2, MYH7), which are crucial for the function of cardiac ion channels and calcium signaling. According to the number of risk alleles, we used imputed data to calculate the PRS through multiplying by the regression coefficient obtained from the previous study [23 (link)]: PRS = (β₁ × SNP₁ + β₂ × SNP₂ + … + β₁₆₅ × SNP₁₆₅). Furthermore, we classified each participant into three categories: low (lowest quartile), intermediate (mid two quartiles), and high (highest quartile) genetic AF risk groups.

Zhang J., Chen G., Wang C., Wang X., Qian Z.(., Cai M., Vaughn M.G., Bingheim E., Li H., Gao Y., Lip G.Y, & Lin H. (2023). Associations of risk factor burden and genetic predisposition with the 10-year risk of atrial fibrillation: observations from a large prospective study of 348,904 participants. BMC Medicine, 21, 88.

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Publication 2023

Alleles Birth Congenital Heart Defects Genes Genetic Diversity Genetic Predisposition to Disease Genome Heart Homo sapiens Ion Channel Muscle, Striated Population at Risk Single Nucleotide Polymorphism

Genetic Analysis of Pain Gene Variants

Genetic analysis was completed in two parts. The first analysis was to identify variants of clinical relevance in known pain genes., grouping rare variants in genes for all neuropathic pain phenotypes considering both a targeted panel of pain genes and their promoters and all genes in the human genome that carried rare variants. Two ion channel variants were selected for electrophysiological analysis to investigate their functional impact (Supplementary Fig. 1).

Themistocleous A.C., Baskozos G., Blesneac I., Comini M., Megy K., Chong S., Deevi S.V., Ginsberg L., Gosal D., Hadden R.D., Horvath R., Mahdi-Rogers M., Manzur A., Mapeta R., Marshall A., Matthews E., McCarthy M.I., Reilly M.M., Renton T., Rice A.S., Vale T.A., van Zuydam N., Walker S.M., Woods C.G, & Bennett D.L. (2023). Investigating genotype–phenotype relationship of extreme neuropathic pain disorders in a UK national cohort. Brain Communications, 5(2), fcad037.

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Publication 2023

Genes Genetic Diversity Genome, Human Ion Channel Labor Pain Neuralgia Pain Phenotype Reproduction

Fabrication of Quasi-BCC Nanolattices

The gold and copper quasi-BCC nanolattices were prepared by electrochemical deposition in the channels of heavy ion track templates. First, the polycarbonate (PC) foils were irradiated by swift heavy ions at the Heavy Ion Research Facility at Lanzhou (HIRFL) with 9.5 MeV per nucleon ²⁰⁹Bi ions. The thickness of the templates was 30 µm and the fluence of irradiation was 7.1 × 10⁸ or 7.1 × 10⁹ cm⁻² in four directions. Following that, each side of the template was illuminated with UV light for 2 h. The purpose of this step was to make the track etching rate of the template much larger than the bulk etching rate during the etching process, to ensure the uniform channel after etched. Then, the template was placed in 50 °C, 5 M NaOH solution and etched for a certain time to obtain the template with a certain aperture channel. After that, the etched template was rinsed several times in deionized water immediately and then immersed in deionized water for 5 minutes to remove the remaining etchant from the template to avoid over-etching. A thin layer of gold was sputtered on one template side as an electrochemically deposited cathode and a layer of copper was deposited on the same side to increase the strength of the template using electrolyte consisting of 75 g L⁻¹ CuSO₄⋅5H₂O and 30 g L⁻¹ H₂SO₄. The electrolyte used for gold and copper quasi-BCC nanolattices deposition on the other side were 75 g L⁻¹ Na₃Au(SO₃)₂ or 75 g L⁻¹ CuSO₄⋅5H₂O and 30 g L⁻¹ H₂SO₄ solution. Last, the PC templates with quasi-BCC nanolattices was placed in dichloromethane (CH₂Cl₂) solution to dissolve organic components to obtain gold and copper quasi-BCC nanolattices. All the quasi-BCC nanolattices were stored in ethanol.
The PC template obtained by chemical etching and the electrochemically deposited quasi-BCC nanolattice structure were complementary structures. By weighing out the PC template before and after chemical etching, the relative density of the prepared gold and copper quasi-BCC nanolattice was given by formula (2)^{38 (link)}:

\bar{ρ} = \frac{V - V_{e}}{V} = \frac{M - M_{e}}{M}

where V is the overall volume of the template before etching; V_e is the volume of the template after etching; M is the overall mass of the template before etching; M_e is the mass of the template after etching.

Cheng H., Zhu X., Cheng X., Cai P., Liu J., Yao H., Zhang L, & Duan J. (2023). Mechanical metamaterials made of freestanding quasi-BCC nanolattices of gold and copper with ultra-high energy absorption capacity. Nature Communications, 14, 1243.

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Publication 2023

Bismuth-209 Copper Dietary Fiber Electrolytes Ethanol Gold Heavy Ions Ion Channel Ions Methylene Chloride polycarbonate Radiotherapy Ultraviolet Rays

Cardiac Differentiation of hiPSCs

Two different batches of hiPSC-CMs were used for this study, a commercial one (Pluricyte® CMs provided by Ncardia, Gosselies, Belgium) and a laboratory handle one. The latter was produced by directed cardiac differentiation of previously generated control hiPSCs.²⁹ (link)^,⁵⁶ (link)^,⁵⁷ (link)
In brief, cardiac induction and generation of hiPSC-CMs were obtained as previously reported, using a chemically-defined serum-free protocol, which is based on activation (CHIR99021) and inhibition (IWR1) of the Wnt pathway in RPMI-B27 medium.⁵⁸ (link)^,⁵⁹ (link)^,⁶⁰ (link) In this work, CMs were differentiated from two different control iPSC lines (one male and one female) between the 18^th and the 35^th passage in culture. Importantly, employed cell lines were regularly tested for being free of major chromosomal abnormalities by karyotype analysis. CMs were used for the experiments 25–30 days after spontaneous contracting activity was started, a differentiation stage at which they expressed the repertoire of sarcomeric proteins, calcium regulators, and ionic channels necessary for their correct functionality. Purity of differentiated CM populations was regularly checked before each experiment to be greater than 90% (not shown). The commercial batch was thawed and cultured following the manufacturer’s protocol. In terms of plating density, cells for both batches were seeded onto the material at a confluence comprised between 50% and 60% on fibronectin coated (15 μg/ml in PBS buffer solution) 18-mm round glass coverslip (VWR, Radnor, USA). The cells were maintained in incubator at 37°C and 5% CO₂.

Vurro V., Federici B., Ronchi C., Florindi C., Sesti V., Crasto S., Maniezzi C., Galli C., Antognazza M.R., Bertarelli C., Di Pasquale E., Lanzani G, & Lodola F. (2023). Optical modulation of excitation-contraction coupling in human-induced pluripotent stem cell-derived cardiomyocytes. iScience, 26(3), 106121.

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Publication 2023

Buffers Calcium Cell Lines Cells Chir 99021 Chromosome Aberrations Females Fibronectins Heart Human Induced Pluripotent Stem Cells Induced Pluripotent Stem Cells Ion Channel Karyotyping Males Population Group Proteins Psychological Inhibition Sarcomeres Serum Wnt Signaling Pathway

Molecular Dynamics Simulation of Panx2 Protein

Schrodinger software was used to prepare the Panx2 model, including building the missing loop (amino acids 185–187, 267–272, and 374–376) via the Prime ^{60 (link)}, adding protons to all amino acids via PROPKA^{61 (link)}, and energy-minimizing the system with the OPLS4 force field^{62 (link)} to ensure that no positional conflicts were in the model. Subsequently, a web-based platform for generating the inputs for molecular dynamics named CHARMM-GUI^{63 (link)} was applied to build the system. The N- and C-termini of the model were treated as amino termini with a positive charge and carboxyl termini with a negative charge, respectively, as they were freely exposed to the solvation. Two intramolecular disulfide bonds (C81–C279, C99–C259) identified in the experimental structures were created for each chain. The state of the protein after the above processes was regarded as its initial geometry in our simulations. The orientation of the protein and the position of lipid bilayers were determined by the Positioning of Proteins in Membranes (PPM) 2.0 server^{64 (link)} and checked manually. The lipid bilayers with the 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) model and water molecules with the TIP3P model were generated, resulting in a 120 × 120 × 165 Å box with 200 POPC molecules. The pore water molecules (water in the ion channel) were also added based on the channel geometry. Finally, the entire system was neutralized with 150 mM NaCl.
GPU-accelerated Gromacs 2021^{65 (link)} was used to perform the molecular dynamics simulation and CHARMM36m force field^{66 (link)} for the molecules. The MD simulation consisted of energy minimization, pre-equilibration and production simulations. The system was first energy minimized with the steepest descent algorithm while keeping 4000 kJ/(mol nm²) force constant on backbone atoms and ligand atoms, 2000 kJ/(mol nm²) force constant on side-chain atoms and 1000 kJ/(mol nm²) force restraint on lipid atoms. Then, six-step pre-equilibration simulations (0.6 ns, 0.6 ns ps, 1 ns, 1 ns, 1 ns, and 1 ns) were carried out, where restraint was reduced slowly (4000, 2000, 1000, 500, 300, 0 kJ/(mol nm²) on the backbone and ligand atoms, 2000, 1000, 500, 200, 50, 0 kJ/(mol nm²) on side-chain atoms, and 1000, 400, 400, 200, 40, 0 kJ/(mol nm²) on lipid atoms) to relax the system. Finally, a production simulation was performed for 100 ns using Langevin thermostat, with a constant temperature of 310 K and a constant pressure of 1 atm. Periodic boundary conditions (PBCs) were introduced during the all molecular dynamics simulations. In all steps, the time step was 2 fs, and atomic coordinates were written every 5 ps. After the MD simulation, root mean squared deviations, root mean squared fluctuations and distances between atoms were analyzed by Gromacs. Details of MD simulations have also been deposited in github at [https://github.com/shiyu-wangbyte/panx2-simulation].

Zhang H., Wang S., Zhang Z., Hou M., Du C., Zhao Z., Vogel H., Li Z., Yan K., Zhang X., Lu J., Liang Y., Yuan S., Wang D, & Zhang H. (2023). Cryo-EM structure of human heptameric pannexin 2 channel. Nature Communications, 14, 1118.

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Publication 2023

1-palmitoyl-2-oleoylphosphatidylcholine Amino Acids Disulfides Familial Mediterranean Fever Ion Channel Ligands Lipid Bilayers Lipids Membrane Proteins Molecular Dynamics Phosphorylcholine Plant Roots Pressure Proteins Protons Sodium Chloride Vertebral Column Water Channel

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More about "Ion Channel"

Ion channels are crucial membrane proteins that control the flow of essential ions like sodium, potassium, calcium, and chloride across cell membranes.
They play a vital role in various physiological processes, including electrical signaling, neurotransmission, muscle contraction, and cellular homeostasis.
These ion-selective pore-forming proteins are classified based on their ion specificity, gating mechanisms, and structural features.
Dysfunction of ion channels has been linked to a wide range of diseases, making them important targets for pharmaceutical research and development.
Advances in ion channel research, including the use of AI-powered tools like PubCompare.ai, have led to a better understanding of their structure, function, and therapeutic potential.
Researchers can utilize various techniques and tools to study ion channels, such as Igor Pro, MATLAB, and the Purified Mitochondrial Membrane Pore Channel Colorimetric Assay kit.
Fluorescent dyes like Rhodamine 123 and Alexa Fluor 647 conjugated α-bungarotoxin (BTX647) can be used to visualize and analyze ion channel activity.
Transfection agents like Lipofectamine 2000 can be employed to introduce genetic material into cells for ion channel studies.
Flow cytometry using a BD LSR II cell analyzer can also provide insights into ion channel expression and function.
Additionally, ion channel research often involves the use of ion channel modulators, such as the calcium channel blockers Nifedipine and Verapamil, which can be used to investigate the role of ion channels in various physiological and pathological processes.
Proper cell culture conditions, including the use of Penicillin/streptomycin, are also crucial for maintaining healthy cell lines for ion channel research.