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Biocytin

Manufactured by Merck Group
Sourced in United States, Germany, United Kingdom

Biocytin is a biochemical compound that is commonly used as a labeling agent in neuroscience research. It is a conjugate of biotin and the amino acid lysine. Biocytin can be used to trace the connections and pathways between neurons in the nervous system.

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95 protocols using biocytin

1

Morphological Reconstruction of Patch-Clamped Neurons

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For morphological reconstruction of patch-clamped neurons, 0.2% biocytin (Sigma-Aldrich) was added to the internal solution. Cells were filled for at least 15 min after break-in. Pipettes were then retracted slowly, over 1–2 min, until the recorded membrane fully resealed. Following slice physiology procedures, slices were post-fixed in 4% PFA overnight at 4 °C and then washed with PBS X3 before being incubated with streptavidin-conjugated DyLight 549 or DyLight 405 (Vector Labs) at 1:1,000 dilution for 2 h at room temperature to label cells that were filled with biocytin (2%; Sigma-Aldrich) during patch clamp recordings. Slices were then mounted for microscopy on glass slides using Aquamount (Thermo Scientific) and imaged the next day on Leica TCS SP8 confocal microscope, using a ×40 1.3 NA, oil immersion objective, at ×0.9–1.0 zoom with an xy sampling frequency of approximately 7 pixels per micrometre. Z stacks at 1-μm intervals were serially obtained and z-stack tiling and Leica-based automated stitching were performed to cover the entire dendritic tree of each neuron. The neurons were subsequently semi-manually traced using the neuTube interface40 (link) and SWC files were generated. The files were next loaded into Fiji (ImageJ, version 2.1.0; NIH) plugin SimpleNeuriteTracer41 (link).
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2

In Vivo Electrophysiology and Histology

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For in vivo SCE, an Axoporator 800A (Molecular Devices USA) was used to deliver 500 μs pulses at 50 Hz for 0.3–2 s duration at various voltage amplitude (see text for details). About 9–15 penetrations were conducted per animal. At the termination of the experiment the craniotomy was covered with silicone (Kwik-cast) and mice were recovered from anesthesia and allowed to survive for 4–7 days before transcardial perfusion for histology. For in vivo whole-cell recording and biocytin filling (n=1 mouse), biocytin (0.3% w/v, Sigma-Aldrich) was included in the internal solution. Blind whole-cell recording was manually conducted as described previously. At the end of the filling, the pipette was slowly retracted to reseal the membrane of the cell patched.
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3

Morphological Analysis of Dentate Granule Cells

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Where indicated, dDGCs recorded from the outermost region of the dentate granule cell layer were backfilled with biocytin for morphological analysis using 0.5% of biocytin (Sigma) added to the internal pipet solution. The slices were then incubated in the recording chamber for 15–20 minutes to allow biocytin to fill distal processes, followed by fixation in 4% paraformaldehyde in 0.1M phosphate-buffered saline (PBS) overnight. Slices were washed with PBS for 30 minutes, permeabilized with 0.4% Triton-X100 in PBS for 30 minutes and incubated with Cy-3-conjugated Streptavidin (0.125 µg/ml in PBS containing 1% BSA) for 90 minutes. Slices were mounted on glass slides and coverslipped with Fluoromount-G™ (Electron Microscopy Sciences, Hatfield, PA).
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4

Whole-cell Patch-clamp Electrophysiology of Neurons and Astrocytes

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Whole-cell patch-clamp recordings were performed with thin-wall borosilicate glass pipettes (resistances of 5–8 MΩ for neurons and 7–12 MΩ for astrocytes), back-filled with intracellular solution (140 mM K+ gluconate, 6 mM NaCl, 1 mM EGTA, 10 mM HEPES, 4 mM MgATP, and 0.4 mM Na3GTP). For biocytin filling, 5 μg/mL biocytin (Sigma) was dissolved in the internal solution and left to disperse for at least 15 min. During recordings, the cultures were constantly perfused with external solution (140 mM NaCl, 5 mM KCl, 2 mM CaCl2, 10 mM HEPES, and 10 mM glucose) at a rate of 2 mL/min, heated to 33–35°C. Voltage-gated currents were elicited from cells clamped at −70 mV in voltage-clamp mode, using 10 mV voltage step protocols from −90 to +20 mV (neurons) or −140 to +30 mV (astrocytes). Action potentials were elicited in current-clamp mode by the injection of 200 ms square current pulses (5 or 10 pA steps), from a baseline Vm of −70 mV and were counted if their peak was greater than −10 mV. sEPSCs were recorded in voltage-clamp mode at the reversal potential of GABAA receptors (EGABA; −70 mV after +14mV junction potential correction). For further details of electrophysiological data analysis, see Supplemental Experimental Procedures.
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5

Optic Tectum Innervation Tracing

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(Re)innervation of the optic tectum was assessed in naive and injured fish using biocytin as an anterograde tracer (Beckers et al., 2019). In brief, fish were anesthetized, the optic nerve was transected between the eye and the crush site and a piece of gelfoam soaked in biocytin (MilliporeSigma) was placed on the nerve stump. After 3 hours, brains were dissected and biocytin (MilliporeSigma) was visualized on 50 µm-thick transverse vibratome sections using a Vectastain ABC kit (Vector Laboratories, Burlingame, CA, USA), using diaminobenzidine as chromogen. Histological photographs were acquired with a Zeiss imager Z1 with a 10x objective. Tectal (re)innervation was quantified via an in-house developed ImageJ script in the SO and SFGS of the optic tectum as previously described (Beckers et al., 2019). Per fish, tectal (re)innervation was analyzed on at least five sections containing the central optic tectum, and four to six animals were used per condition. The pia mater, the innermost layer of the meninges, was removed from the pictures to improve visualization of reinnervation in the optic tectum. In all experiments, tectal innervation of naive WT fish was set as a 100% reference value, and other values were put relative to this control.
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6

Neurobiotin/Biocytin Neuron Visualization

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After recordings, the brain slices containing the neurons filled with neurobiotin 350 (Vector Laboratories, Inc., Newark, CA, USA) or biocytin (Sigma-Aldrich, St. Louis, MO, USA) were fixed in paraformaldehyde (4%) and stored at 4 °C. Following extensive rinse in phosphate buffered saline (0.01 M PBS), slices with biocytin-filled neurons were incubated for 4 h in a solution containing PBS, AMCA Avidin D (1:200), and TritonX-100 (1%) at room temperature. Rinsed slices were mounted on glass slides and coverslipped with Vectashield mounting medium (Vector Laboratories, Inc., Newark, CA, USA). Images were taken with a confocal microscope (Nikon Ti2).
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7

Pharmacological modulation of glutamate signaling

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Reagents for ACSF and internal solutions, biocytin, NBQX, BaCl2, and picrotoxin were obtained from Sigma-Aldrich. CNQX, AP-5, DHK, DL-TBOA, TTX, ouabain, and D-serine were obtained from Tocris. L-glutamic acid from BioTrend and SR-101 from Invitrogen. NBQX, CNQX, and DL-TBOA were dissolved in DMSO. picrotoxin was dissolved in EtOH. AP-5, D-serine, TTX, ouabain, and DHK were dissolved in ddH2O.
In both patch-clamp and two-photon imaging experiments, following baseline recordings, drugs were applied in the external solution for at least 15 min prior to recordings. For the double pharmacology imaging experiments (Fig. 9) following baseline recordings, DHK (300 μM) was first applied and recordings were acquired 20 min later. Subsequently, DHK (300 μM) and DL-TBOA (68 μM) were applied for 20 min before recording. In a number of recordings in which we applied much higher doses of DL-TBOA (300 µM), we observed a change in baseline iGluSnFr fluorescence (similar to ref. 18 (link)), a reduced amplitude of the evoked responses and cellular swelling often accompanied by a lateral or Z drift. These experiments had to be excluded, which explains the low n value for this set of experiments (Supplementary Fig. 9).
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8

BLI Analysis of Clr4-SET Binding Kinetics

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BLI analyses were performed in black 96-well plates (greinerbio-one, Germany) on an OctetRED96 instrument (ForteBio, USA). Prior to use, biosensors were soaked in assay buffer (1X PBS, 0.01% NP-40, 0.5 mM DTT, and 0.2 ug/ml BSA) for 10 min. BLI assays consisted of six steps, all performed in the assay buffer: initial baseline (30 s), loading (120 s), and quenching (120 s), baseline (60 s), association (30 s), and dissociation (90 s). Each biotinylated peptide (3 μg/ml) was immobilized on the Streptavidin biosensor tip during the loading step. To quench free streptavidin, 4 μg/ml of biocytin (Sigma), a biotin analog, was used. During the association step, analyte (Clr4-SET WT or 3FA mutant) at various concentrations was diluted into the assay buffer. Biotinylated-peptide-loaded sensors itself was measured as a control to subtract from experimental values before data processing. Sensorgrams were fit using global/1:1 binding model by ForteBio Data analysis version 10.0.1.6, from which the equilibrium dissociation constant (Kd) and association (kon) and dissociation (koff) rate constants were calculated. To measure the interaction in the presence of SAM, the assay buffer in all steps was supplied with 10 μM SAM.
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9

Quantifying Purkinje Cell Dendritic Complexity

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Fresh mice cerebella were divided into right and left cerebellum. Sagittal brain slices were further sectioned at 300 μm. 1% biocytin (sigma B4261) in 2 M KCl was ionotophoretically injected into Purkinje cells by using 0.1–0.3 nA of depolarizing current for about 30 min at alternating intervals of 20 ms on and 20 ms off [29 (link)]. Brain slices were then fixed with 4% paraformaldehyde in 0.1 M PB at 4 °C for 16–18 h. Using a sliding microtome, serial frozen sections of 50 μm thickness were prepared and incubated in 0.5% H2O2 for 20 min to remove endogenous peroxidase. They were further blocked with blocking solution (3% Bovine serum albumin, 1% Triton X-100, 5% FBS) for 90 min at room temperature. Finally, slices were reacted with Avidin-biotinylated complex (ABC Kit, Vector) for 1 day, and developed with 3,3-diaminobenzidine. Focus was fine-tuned and all details of the cells were then depicted. Subsequently, the soma of the Purkinje cell was used as the center to quantify the maximal sagittal extension of their dendrites. Sholl analysis was applied to investigate the dendritic branches. Centered at the soma of the Purkinje cell, concentric circles with gradually increasing radii of 10 μm formed the grid. The numbers of ring-crossings of each branch (number of intersections) were counted and represented the complexity of dendritic branches [30 (link)].
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10

Dual Whole-Cell Voltage Recordings

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All experiments are performed at 32.0 ± 0.5°C. Single L5 pyramidal neurons are identified using infrared oblique illumination and a CCD camera (CoolSnap EZ; Roper Scientific). Slices are perfused with the same extracellular solution mentioned above. Recording pipettes are filled with intracellular solution containing the following (in mM): 130 K-gluconate, 5 KCl, 30 HEPES, 10 phosphocreatine, 4 MgATP, 0.3 GTP, pH 7.3. In addition, the somatic pipette contains the following: 10–50 μM Alexa 594 (Invitrogen) to visualize the dendritic arbor for dendritic patching, and 0.2% Biocytin (Sigma). Dual whole-cell voltage recordings are performed from the soma and dendrites (6–10 and 20–40 MΩ pipette resistances, respectively) using Axoclamp 2A (Molecular Devices) and Dagan BVC-700A amplifiers (Dagan Corporation). Access resistances for the dendritic recordings are 15–90 MΩ on break-through. Data is acquired with an ITC-18 board (Instrutech) and custom software written for the Igor environment (Wavemetrics).
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