Abstract: Immunoblotting (western blotting) is used to identify specific antigens recognized by polyclonal or monoclonal antibodies. This unit provides protocols for all steps, starting with solubilization of the protein samples, usually by means of SDS and reducing agents. Following solubilization, the material is separated by SDS-PAGE and the antigens are electrophoretically transferred to a membrane, a process that can be monitored by reversible staining with Ponceau S. The transferred proteins are bound to the surface of the membrane, providing access to immunodetection reagents. After nonspecific binding sites are blocked, the membrane is probed with the primary antibody and washed. The antibody-antigen complexes are tagged with fluorophores, horseradish peroxidase, or alkaline phosphatase coupled to a secondary anti-IgG antibody, and detected using appropriate fluorescent imaging technologies or with chromogenic or luminescent substrates. Finally, membranes may be stripped and reprobed. © 2017 by John Wiley & Sons, Inc.

Abstract: Animal tests of anxiety are used to screen novel compounds for anxiolytic or anxiogenic activity, to investigate the neurobiology of anxiety, and to assess the impact of other occurrences such as exposure to predator odors or early rearing experiences. This unit presents protocols for the most commonly used animal tests of anxiety. The Geller-Seifter conflict test, the social interaction test, light/dark exploration, the elevated plus-maze, defensive burying, and the thirsty rat conflict. The protocols are described in terms of drug screening tests, but can be modified easily for other purposes.

Abstract: This overview provides an illustrated, comprehensive survey of some commonly observed protein-fold families and structural motifs, chosen for their functional significance It opens with descriptions and definitions of the various elements of protein structure and associated terminology Following is an introduction into web-based structural bioinformatics that includes surveys of interactive web servers for protein fold or domain annotation, protein-structure databases, protein-structure-classification databases, structural alignments of proteins, and molecular graphics programs available for personal computers The rest of the overview describes selected families of protein folds in terms of their secondary, tertiary, and quaternary structural arrangements, including ribbon-diagram examples, tables of representative structures with references, and brief explanations pointing out their respective biological and functional significance

Abstract: A basic protocol is described for extracting protein from plants. Suggestions are included for overcoming some of the common obstacles encountered (e.g., acidity, phenolics, cell walls). Keywords: Plant protein extracts; proteinases; phenols; oxidizing agents; acids

Abstract: In culture, hippocampal cells can develop to express neuronal antigens and acquire mature neuronal morphologies, including axons, complex dendritic trees, and synapses that are electrophysiologically active. This system is suitable for studying neuronal differentiation and other events, such as synaptogenesis. It is also a valuable model for investigating synaptic plasticity and exploring the mechanisms of neuronal degeneration. This unit provides a protocol for culturing neurons prepared from embryonic (E-18) rat or mouse hippocampus, but could also be used to grow neurons from embryonic cortex, olfactory bulb, striatum, or spinal cord. A second method is included for preparing neuronal cultures from embryos with different genotypes, such as those from transgenic mice. Also described is the preparation of polyornithine- and fibronectin-coated coverslips, which are highly adhesive and promote neurite outgrowth, for use in the culture protocols.

Abstract: For the safety of the handler and the animal, proper methods for handling and restraining laboratory animals should be followed. Improper handling can result in increased stress and injury to the animal. In addition, the handler risks injury from bite wounds or scratches inflicted when the animal becomes fearful or anxious. By using sure, direct movements with a determined attitude, the animal can be easily handled and restrained. Animals can be restrained either manually or in a plastic restrainer. The protocols in this unit describe handling and manual restraint of mice, rats, hamsters, and rabbits. Alternate protocols describe restraint using the plastic restrainer.

Abstract: Traumatic brain injury is a leading cause of death and disability, particularly among young adults. During closed head trauma, the injury process is initiated by the impact of the brain against the inner table of the calvarium. Subsequently, there is prompt initiation of a complex biochemical, cellular, and physiological injury cascade that may take days to complete. From a functional standpoint, this culminates in neurologic dysfunction and, if severe, death. This unit describes an impact-induced brain trauma model in rats which replicates nonpenetrating head injury. It does not model either penetrating or ischemic brain injuries.

Abstract: Proper identification of animals is crucial in research, whether the animals are being used as experimental subjects, for breeding purposes, or as a source for tissues, cells, or fluids. This unit provides specific protocols for the ear punch (notch) and ear tag methods for mouse, rat and hamster; tattoos for mouse, rat and rabbit; and the correct use of a subcutaneous transponder system for all of the above species. Keywords: identification; mouse; rat; hamster; rabbit; tag; transponder; tattoo; notch

Abstract: S-nitrosylation is the binding of an NO group to a cysteine or other thiol. Like phosphorylation, S-nitrosylation is a precisely targeted and rapidly reversible post-translational modification that serves as an on/off switch for protein function during cell signaling. However, unlike phosphorylation, S-nitrosylation of proteins occurs nonenzymatically and is mediated, at least in part, by redox-regulated chemical reactions in cells. Alterations in pH, pO(2), cellular reductants, transition metals, and UV light lead to the loss and/or gain of S-NO bonds. Due to the redox-sensitive nature of the modification, analysis of protein S-nitrosylation is technically difficult, since the S-NO bond is easily disrupted during sample preparation. In addition, the level of S-nitrosylated proteins in cells approaches the limit of detection of currently available technology. Despite these technical challenges, several useful methods have been developed recently to measure protein S-nitrosylation in biological samples, and these are described in this unit.

Abstract: The formation of disulfide bonds in proteins is an important post-translational modification that is critical for stabilizing the native structures of proteins. The disulfide linkages in a protein cannot be predicted from its amino acid sequence; therefore, determination of disulfide bond linkages in the protein will provide insights into its three-dimensional structure and contribute to the understanding of its structural-functional relationship. This unit details a series of protocols that have been applied successfully to locate disulfide bonds in proteins. The general strategy involves chemical or proteolytic cleavage of the protein followed by chromatographic separation of the resultant peptides. Disulfide-containing peptides are identified by the alteration of mobility as a consequence of disulfide bond reduction, and are further characterized by mass spectrometry and/or N-terminal sequencing. A partial reduction and alkylation strategy for mapping disulfide linkages in peptides with multiple disulfide bonds is also presented.

Abstract: The Schneider-2 (S2) Drosophila cell line is well suited for the stable overexpression of recombinant proteins using plasmid-based protein expression vectors. Following drug selection, a polyclonal S2 cell line can be induced to express on the order of 2 to 100 pmol/mg membrane protein for G-coupled protein receptors, 4000 to 100,000 sites/cell for other membrane receptors and 3 to 35 mg/liter for soluble and secreted proteins.

Abstract: Many physiological studies require microscopic examination of the recorded neuron for identification. This unit describes how intracellular and extracellular recording can be combined with single-neuron staining to enable sequential physiological and morphological studies.

Abstract: Patch clamping refers to a wide range of electrophysiological measurements, all of which have in common the use of patch pipets and the formation of gigaohm seals. The purpose of this unit is to describe the fabrication of patch pipets. The aspects of the pipet geometry that are important to different applications and the different procedures that have been found to most reliably and simply achieve these results are described. Parameters for glass selection are detailed in the beginning of the unit. Pulling patch and whole-cell pipets, elastomer coating, fire polishing, pipet filling, and pipet testing in an experimental setup are highlighted. Additional support protocols describe alternative ways to optimize pipet geometry and cleaning the glass before pulling. Considerations for noise and dynamic performance are emphasized as these two requirements for single-channel and whole-cell current measurements dictate how the pipets must be fabricated.

Abstract: Stereological methods allow for the determination of cell numbers, terminal densities, and, subsequently, the estimation of terminal arbor size within a given brain nucleus. This unit provides an explanation for determining the terminal arbor size of dopaminergic neurons of the nigrostriatal pathway in rodents. In contrast to previously used single-axon reconstructions, these stereological methods allow for quick and easy determination of terminal arbor size.

Abstract: Recent genome sequencing projects have identified new peptidases in multiple organisms, many with unknown functions, suggesting the need for new tools to study these enzymes. This unit outlines selection and use of small-molecule and protein-based probes to covalently modify peptidases in complex cellular environments. These activity-based probes (ABPs) have been designed based on well characterized peptidase inhibitor scaffolds, but make use of new techniques to greatly enhance their utility for studying families of related peptidases. In particular, ABPs can be used to track activity of peptidases in crude cell extracts, intact cells, and in vivo, allowing rapid purification and identification of labeled targets. They can be used with libraries of small molecules to rapidly assess potency and selectivity of compounds in complex, physiologically relevant samples. Probe selection, probe tagging using reporters, labeling of recombinant targets, crude protein extracts, and peptidase targets in cell culture systems, affinity purification of targets, and inhibitor screening using affinity probes are outlined. Keywords: affinity labels; activity based probes; cysteine peptidases; serine peptidases; DUBs; affinity purification; inhibitor competition; inhibitor selectivity

Abstract: Gel electrophoresis has become a ubiquitous method in molecular biology for separating biomolecules. This prominence is the result of several factors, including the robustness, speed, and potentially high throughput of the technique. The results of this method are traditionally documented using silver halide-based photography followed by manual interpretation. While this remains an excellent method for qualitative documentation of single-gel results, digital capture offers a number of significant advantages when documentation requires quantitation and sophisticated analysis. Digital images of gel electropherograms can be obtained rapidly using an image-capture device, and the images can be easily manipulated using image analysis software. This overview presents reasons for digital documentation and analysis, defines some important key terms for imaging, explains the capture process and reviews the devices used for image capture, and provides an introduction to the software and methods used for one- and two-dimensional digital image analysis. Keywords: electrophoresis; imaging; software; digital analysis; quantitation

Abstract: Pyramidal neurons of the central nervous system have extensively arborized apical dendrites that contribute importantly to the signaling properties of the neuron. Recent advances in electrophysiological techniques have allowed recording from neuronal dendrites. These techniques depend on using infrared optics to visualize dendritic processes in the unstained brain slice preparation, on pipet positioning with high resolution micromanipulators, and on stringent techniques for brain slice preparation that preserved healthy dendritic processes, even in tissue from mature animals. The procedures underlying these techniques are described in this unit. Keywords: dendrites; patch-clamp recording; brain slice; hippocampus; IR-DIC microscopy

Abstract: Investigation of synaptic vesicle membrane proteins using multidisciplinary approaches, particularly to characterize synaptic vesicle proteins in synapses, can greatly advance our knowledge of the molecular mechanisms involved in synaptic vesicle exocytosis and neurotransmission. Three approaches are presented in this unit to identify and characterize synaptic vesicle proteins. The first is a subcellular fractionation method used to isolate synaptic vesicles from rat brain synaptosomal preparations, which can then be used in a variety of biochemical studies on synaptic vesicle proteins. The second is a detailed procedure for pre-embedding immunogold staining and electron microscopic observation, techniques that permit the morphological identification of synaptic vesicle proteins in individual vesicles at the intact synapse. Finally, a protocol for immunocytochemical staining of cultured hippocampal neurons for light microscopic examination is provided, which allows one to stain multisynaptic vesicle proteins and determine their localization in relation to other proteins or subcellular structures in synapses. Keywords: Synaptosomes; hippocampal neurons; synapses; light-microscopy; electron-microscopy; immunocytochemistry; immunoblotting

Abstract: Hydroxyl-radical protein footprinting is a straightforward and direct method to map protein sites involved in macromolecular interactions. The first step is to radioactively end-label the protein. Using hydroxyl radicals as a peptide backbone cleavage reagent, the protein is then cleaved in the absence and presence of ligand. Cleavage products are separated by high resolution gel electrophoresis. The digital image of the footprinting gel can be subjected to quantitative analysis to identify changes in the sensitivity of the protein to hydroxyl-radical cleavage. Molecular weight markers are electrophoresed on the same gel and hydroxyl-radical cleavage sites assigned by interpolation between the known cleavage sites of the markers. The results are presented in the form of a difference plot that shows regions of the protein that change their susceptibility to cleavage while bound to a ligand.

Abstract: This unit describes basic protocols for efficient and reproducible protein solubilization from a variety of biological samples, including cultured animal cells and tissues, plant cells and tissues, bacteria, nuclei, other subcellular organelles, plasma, serum, and other biological fluids. The optimized extraction process is strongly sample-dependent and cannot be described for every type of sample. Instead, typical protocols are provided as general guidelines and illustrate good starting points for sample-preparation optimization. These solubilization procedures take into account the constraints brought by two-dimensional electrophoresis and are thus well suited for proteomic approaches. Keywords: proteomics; protein extraction; sample preparation; two-dimensional electrophoresis; protein solubilization

Abstract: Expression of genes is manifested by the production of RNA transcripts within cells. Hybridization histochemistry (or in situ hybridization) permits localization of these transcripts with cellular resolution or better. Furthermore, the relative amounts of transcripts detected in different tissues or in the same tissues in different states (e.g., physiological or developmental) may be quantified. This unit describes hybridization histochemical techniques using either oligodeoxynucleotide probes (see Basic Protocols 1 and 2, Alternate Protocol 1) or RNA probes (riboprobes; see Basic Protocols 3 and 5). These methods include a more recent approach using commercially available sets of oligodeoxynucleotide pairs for colorimetric and fluorescent detection (see Basic Protocol 2), as well as a method for detection of the Y chromosome using either mouse or human riboprobes (see Basic Protocol 5). Additional methods include colorimetric detection (see Basic Protocol 4) and tyramide signal amplification (TSA) of digoxigenin-labeled probes (see Alternate Protocol 2), and autoradiographic detection of radiolabeled probes (see Basic Protocol 6). Finally, methods are provided for labeling oligodeoxynucleotide (see Support Protocol 1) and RNA (see Support Protocol 2) probes, and verifying the probes by northern analysis (see Support Protocol 3). © 2016 by John Wiley & Sons, Inc.

Abstract: X-ray crystallography has evolved into a very powerful tool to determine the three-dimensional structure of macromolecules and macromolecular complexes. The major bottleneck in structure determination by X-ray crystallography is the preparation of suitable crystalline samples. This unit outlines steps for the crystallization of a macromolecule, starting with a purified, homogeneous sample. The first protocols describe preparation of the macromolecular sample (i.e., proteins, nucleic acids, and macromolecular complexes). The preparation and assessment of crystallization trials is then described, along with a protocol for confirming whether the crystals obtained are composed of macromolecule as opposed to a crystallization reagent. Next, the optimization of crystallization conditions is presented. Finally, protocols that facilitate the growth of larger crystals through seeding are described. Curr. Protoc. Protein Sci. 66:17.4.1-17.4.26. © 2011 by John Wiley & Sons, Inc. Keywords: macromolecular crystallography; crystal screening; crystal optimization

Abstract: Protein databases have become a crucial part of modern biology. Huge amounts of data for protein structures, functions, and particularly sequences are being generated. Searching databases is often the first step in the study of a new protein. Comparison between proteins and between protein families in databases provides information about the relationship between proteins within a genome or across different species, and hence offers much more information than can be obtained by studying only an isolated protein. In addition, secondary databases derived from experimental databases are also widely available. These databases reorganize and annotate the data or provide predictions. The use of multiple databases often helps researchers understand the structure and function of proteins. Although some protein databases are widely known, they are far from being fully utilized in the protein science community. This unit provides a starting point for readers to explore the potential of protein databases on the Internet.

Abstract: The goal of neurogenetics is an understanding of the genetic basis of brain structure and function Neurogenetics deals with multiple areas of investigation, including the genetic basis of neural induction, patterning, cell fate specification, neuron maturation, axonal and dendritic organization, synapse function, neural information processing, and learning and behavior This appendix provides links to databases and other Web sites used by neurobiologists for discovery of information about genes and cellular networks involved in neural development and neuron function Special care has been taken to curate sites involving model organisms, since great strides have been made using Drosophila and C elegans for understanding neural development and function Published 2019 US Government

Abstract: S-nitrosylation is the binding of an NO group to a cysteine or other thiol. Like phosphorylation, S-nitrosylation is a precisely targeted and rapidly reversible post-translational modification that serves as an on/off switch for protein function during cell signaling. However, unlike phosphorylation, S-nitrosylation of proteins occurs nonenzymatically and is mediated, at least in part, by redox-regulated chemical reactions in cells. Alterations in pH, pO2, cellular reductants, transition metals, and UV light lead to the loss and/or gain of S-NO bonds. Due to the redox-sensitive nature of the modification, analysis of protein S-nitrosylation is technically difficult, since the S-NO bond is easily disrupted during sample preparation. In addition, the level of S-nitrosylated proteins in cells approaches the limit of detection of currently available technology. Despite these technical challenges, several useful methods have been developed recently to measure protein S-nitrosylation in biological samples, and these are described in this unit. Keywords: nitric oxide; S-nitrosylation; Saville assay; chemical reduction/chemiluminescence; DAN assay; DAF-2 assay; DAF gel assay; biotin switch assay; anti-SNO immunofluorescence

Abstract: The social transmission of food preference (STFP) is an ethologically relevant test of olfactory memory that can be used in mice. In this test, "observer" mice interact with a "demonstrator" mouse that has recently eaten a novel food. When observer mice are presented with a choice between the food eaten by the demonstrator and some other novel food, observer mice prefer the food eaten by the demonstrator. This phenomenon depends on the observer mice detecting olfactory cues on the breath of the demonstrator mouse during their interaction. The subsequent food preference serves as a measure of memory for those olfactory cues. This unit describes a method for performing STFP in mutant mice. The method explains how to address potential confounding factors and avoid possible pitfalls.

Abstract: Painful peripheral neuropathy is a common secondary complication of diabetes. The streptozotocin (STZ)-induced diabetic rat is the most commonly employed animal model used to study mechanisms of painful diabetic neuropathy and to evaluate potential therapies. A low dose STZ protocol is described for inducing experimental diabetes in the rat. Several behavioral assays are described, which are routinely used to assess different aspects of neuropathic pain in this animal model of diabetes mellitus, including mechanical allodynia and heat hyperalgesia.

Abstract: Addition of an affinity tag is a useful method for differentiating recombinant proteins expressed in bacterial and eukaryotic expression systems from the background of total cellular proteins, as well as for detecting protein-protein interactions. This overview describes the historical basis for the development of affinity tags, affinity tags that are commonly used today, how to choose an appropriate affinity tag for a particular purpose, and several recently developed affinity tag technologies that may prove useful in the near future.

Abstract: Immunoblotting (western blotting) is used to identify specific antigens recognized by polyclonal or monoclonal antibodies. This unit provides numerous protocols for all steps starting with solubilization of the protein samples, usually with SDS and reducing agents. Following solubilization, the material is separated by SDS-PAGE and the antigens are then electrophoretically transferred to a membrane, a process that can be monitored by reversible staining or Ponceau S staining. The transferred proteins are bound to the surface of the membrane, providing access to immunodetection reagents. Any remaining binding sites are blocked by immersing the membrane in a blocking solution. After probing with the primary antibody, the membrane is washed and the antibody-antigen complexes are identified with horseradish peroxidase (HRPO) or alkaline phosphatase enzymes coupled to the secondary anti-IgG antibody (e.g., goat anti-rabbit IgG) and appropriate chromogenic or luminescent substrates. Finally, membranes may be stripped and reprobed. Keywords: immunoblot; western blot; horseradish peroxidase; alkaline phosphatase; antibodies