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Ischemia/reperfusion is a key feature of acute ischemic stroke, which causes neuron dysfunction and death. Exosomes, small extracellular vesicles produced by most cell types, are implicated in the mediation of cellular interactions with their environment. Here, we investigated the contents and functions of exosomes from neurons under ischemic reperfusion injury. First, rat cortical primary neuronal cell cultures were placed in an oxygen- and glucose-deprived (OGD) medium, followed by reperfusion in a normoxic conditioned medium (OGD/R) to mimic ischemia/reperfusion in vitro. The neuron-derived exosomes were harvested from the conditioned medium under normoxia and OGD/R. Through next-generation sequencing, exosomal miRNA expression levels in normoxic and OGD/R condition were compared. Their functional activity in terms of neuron viability and quantitative analysis of neurite outgrowth were examined. The expression levels of 45 exosomal miRNAs were significantly different between normoxic and OGD/R conditions. Bioinformatics analysis of dysregulated exosomal miRNAs identified multiple pathways involved in cell survival and death processes and neuronal signaling. Moreover, treatment with exosomes from OGD/R to cultured cortical neurons significantly impaired neuronal cell viability and reduced neurite outgrowth in terms of the number of primary or total neurites as well as length of primary neurites, compared with exosomes from normoxic conditions. miRNA-packed exosomes released by neurons under OGD/R challenge may contribute to post ischemic neuronal injury and provide further understanding of the effect of stressed neurons on neighboring neuronal functions., (© 2021. The Author(s), under exclusive licence to Springer Science+Business Media, LLC part of Springer Nature.)

Extracellular vesicles (EVs), are membrane-bound nanoparticles of biological origin. These signature molecules of health and disease have raised remarkable attention of the biomedical arena due to its potential diagnostic and therapeutic applicability. Among the many different techniques available for EV isolation, size-exclusion chromatography (SEC) is widely accepted.In this chapter, we present a protocol of size-exclusion high-performance liquid chromatography (SE-HPLC) as a method of EV isolation. This method can be adapted as a low cost but a reliable and scalable method of EV isolation in those laboratories having access to the HPLC systems.

Repairing the damaged blood-CNS-barrier in amyotrophic lateral sclerosis (ALS) is necessary to prevent entry of detrimental blood-borne factors contributing to motor neuron dysfunction. Recently, we showed benefits of human bone marrow endothelial progenitor cell (hBM-EPC) transplantation into symptomatic ALS mice on barrier restoration by replacing damaged endothelial cells (ECs). Additionally, transplanted cells may endogenously repair ECs by secreting angiogenic factors as our subsequent in vitro study demonstrated. Based on these study results, hBM-EPCs may secrete extracellular vesicles, which may contain and transfer diverse vesicular biomolecules towards maintenance of EC functionality. The study aimed to characterize extracellular vesicles (EVs) derived from hBM-EPCs as potential cell-free therapeutics for endothelium repair in ALS. EVs were isolated from hBM-EPC media at different culture times and vesicle properties were evaluated. The protective effects of EVs on mouse brain endothelial cells (mBECs) exposed to ALS mouse plasma were investigated. Uptake and blockage of EVs from GFP-transfected hBM-EPCs in ECs were determined in vitro. Results showed that EVs isolated from hBM-EPCs as nanosized vesicles significantly reduced mBEC damage from the pathological environment and these EVs were taken up by cells. Blockage of β1 integrin on EVs prevented internalization of vesicles in mBECs. Together, these results provide evidence for potential of hBM-EPC-derived EVs as novel cell-free therapeutics for repair of endothelium in ALS. Although determining translational potential of hBM-EPC-derived EVs will require evaluation in vivo, this in vitro study represents a step towards an extracellular vesicle-based approach for repair of the damaged microvascular endothelium in ALS.

Cell surface proteolysis controls numerous biological processes including cell-cell attachment and the communication between cells. The membrane-tethered families of matrix metalloproteinases (MT-MMPs) and disintegrin metalloproteinases (ADAMs) are major enzymes involved in the cleavage of molecules at the cell surface, and their activity is finely regulated by their endogenous inhibitors, the tissue inhibitors of metalloproteinases (TIMPs). The biological function of a metalloproteinase closely depends on the subset of substrates that it cleaves. Similarly, molecular processes that are regulated by a specific TIMP strictly depend on its unique inhibitory profile.Herein, we describe a mass spectrometry-based method for the quantitative analysis of protein abundance in conditioned media of cultured cells that is particularly suited for substrate identification of membrane-tethered metalloproteinases and for the identification of membrane proteins whose cleavage is regulated by TIMPs. This unbiased proteomic method represents a valuable tool to investigate biological functions of metalloproteinases and TIMPs at the "omic" level.

Chemically induced cell fate conversion, including reprogramming to pluripotent stem cells and direct reprogramming to somatic cells, has been proved to be an alternative strategy with many advantages, in comparison with conventional transcription factors- or microRNAs-enabled cell reprogramming. Many functional and desirable cells have been generated via the chemically induced reprogramming. Neural stem cells (NSCs) hold great potential in basic research and clinical application. Here, we describe a detailed protocol for converting mouse fibroblasts into NSCs by a cocktail of chemical compounds.

Extracellular vesicles (EVs), including exosomes, are nano-sized membrane-bound particles which are released by cells. They have been found in all examined body fluids and can be isolated from conditioned cell culture media. These vesicles have gained increasing attention due to their importance in cellular cross talk, in both health and disease. For example, keratinocyte-derived EVs have been described to modulate melanin production in epidermis. Similar EVs were also shown to have an important role in skin immunology, by stimulating dendritic cells. In this chapter, we will describe how to isolate EVs from keratinocyte cultures and how to perform characterization by Western blot, nanoparticle tracking analysis, and transmission electron microscopy.

Here we describe the use of a decellularized ECM produced in vitro by BALB/c 3T3 fibroblasts for the identification of ADAMTS substrates. Seeding of ADAMTS protease-producing HEK cells on top of the cell-free ECM followed by analysis of the conditioned medium by liquid chromatography tandem mass spectrometry (LC-MS/MS), allows for screening of ADAMTS substrates without prior purification of full-length protease.

This chapter describes the methods for inducing, detecting, and purifying the Legionella pneumophila siderophore. The first protocol details the methods by which L. pneumophila is cultured to facilitate production of the siderophore, rhizoferrin. This chapter then describes how to purify siderophore from culture supernatants through sequential reversed-phase/weak-anion exchange chromatography and high-performance liquid chromatography. The next section describes assays which allow the detection of the iron-binding capability and the biological activity of the purified siderophore. Lastly, this chapter describes the growth of L. pneumophila in chemically defined liquid medium (CDM) containing various iron sources as a method to assess the iron requirements of L. pneumophila.

Exosomes are small vesicles of endosomal origin secreted by most cell types. Recent studies have identified exosomes as important mediators of intercellular communication and as important source materials for many clinical applications, including minimal invasive disease diagnosis. Exosomes have been purified from in vitro cell culture supernatants by many different methods; however the most simple and reliable method involves purification by ultracentrifugation. This chapter describes a detailed protocol for isolating exosomes from cell culture-conditioned medium using ultracentrifugation and their characterization based upon size, number, and protein expression by several complementary methods such as transmission electron microscopy, nanoparticle tracking analysis, western blotting, and flow cytometry.

Exosomes are nano-vesicles which can transport a range of molecules including but not limited to proteins and miRNA. This ability of exosomes renders them useful in cellular communication often resulting in biological changes. They have several functions in facilitating normal biological processes such as immune responses and an involvement in pregnancy. However, they have also been linked to pathological conditions including cancer and pregnancy complications such as preeclampsia. An understanding for the role of exosomes in preeclampsia is based on the ability to purify and characterize exosomes. There have been several techniques proposed for the enrichment of exosomes such as ultracentrifugation, density gradient separation, and ultrafiltration although there is no widely accepted optimized technique. Here we describe a workflow for isolating exosomes from cell-conditioned media and biological fluids using a combination of centrifugation, buoyant density, and ultrafiltration approaches.

Activity staining or zymography is a technique to detect enzymes based on their function/activity toward a specific substrate. Multiple enzyme-producing microbes secrete enzymes along with other proteins at varying time points during fermentation. The technique of zymography can be used to detect functionality of enzymes in complex protein/other enzyme mixtures. The protein bands corresponding to specific enzyme among other enzymes/proteins can be located by polyacrylamide gel electrophoresis (PAGE) followed by zymogram analysis. This can be employed to locate the secretion pattern of protein/enzyme from intracellular region to extracellular medium. Here we describe simple method for detection and cellular localization of esterases and protease secreted by single microbial strain in one PAGE gel.

Hypoxic microenvironment found in pancreatic ductal adenocarcinoma and other solid tumors is central to physiological and metabolic alterations of immune cells that significantly impact tumor growth dynamics. Hypoxic adaptations in the immune cells are primarily mediated by the stabilization of hypoxia-inducible factor-1 alpha (HIF-1α), which regulates cellular metabolism by modulating glycolysis and other interconnected metabolic pathways. HIF-1α plays distinct roles in M1 and M2 macrophage polarization, which, in turn, regulates tumor cell immune escape and growth. In this chapter, we describe a real-time PCR-based assay to monitor the transcript levels of Arg1 and Nos2 to assess the status of tumor-induced macrophage polarization under hypoxic conditions. This method can be effectively utilized to delineate the genes critical for M1/M2 polarization in the hypoxic tumor microenvironment and would provide opportunities to develop immunomodulating therapies to regulate the tumor growth, progression, and metastatic dissemination.

Scientific and clinical interest in extracellular vesicles (EVs) has increased rapidly as evidence mounts that they may constitute a new signaling paradigm. Recent studies have highlighted EVs carry preassembled complex biological information that elicit pleiotropic responses in target cells. It is well recognized that cells secrete essentially two EV subtypes that can be partially separated by differential centrifugation (DC): the larger size class (referred to as "microvesicles" or "shed microvesicles," sMVs) is heterogeneous (100-1500 nm), while the smaller size class (referred to as "exosomes") is relatively homogeneous in size (50-150 nm). A key issue hindering progress in understanding underlying mechanisms of EV subtype biogenesis and cargo selectivity has been the technical challenge of isolating homogeneous EV subpopulations suitable for molecular analysis. In this protocol we reveal a novel method for the isolation, purification, and characterization of distinct EV subtypes: exosomes and sMVs. This method, based on sequential centrifugal ultrafiltration (SCUF), affords unbiased isolation of EVs from conditioned medium from a human colon cancer cell model. For both EV subtypes, this protocol details extensive purification and characterization based on dynamic light scattering, cryoelectron microscopy, quantitation, immunoblotting, and comparative label-free proteome profiling. This analytical SCUF method developed is potentially scalable using tangential flow filtration and provides a solid foundation for future in-depth functional studies of EV subtypes from diverse cell types.

Cell lines propagating prions are an efficient and useful means for studying the cellular and molecular mechanisms implicated in prion disease. Utilization of cell-based models has led to the finding that PrP C and PrP Sc are released from cells in association with extracellular vesicles known as exosomes. Exosomes have been shown to act as vehicles for infectivity, transferring infectivity between cell lines and providing a mechanism for prion spread between tissues. Here, we describe the methods for generating a prion-propagating cell line with prion-infected brain homogenate, cell lysate, conditioned media, and exosomes and also detection of protease-resistant PrP with the prion-infected cell assay.

Exosomes were originally described 29 years ago as a mechanism for the removal of redundant molecules from reticulocytes, nothing but a process of removing cellular trash. It is now however, abundantly clear that exosomes have a more significant biological role. However, there is currently limited information pertaining to efficient isolation procedures that can be used to isolate exosomes from both cell culture media, and clinical samples such as plasma. Here, we present a reliable and efficient procedure that can be utilized for the isolation of exosomes from various starting materials.

Extracellular vesicles (EVs) have recently attracted substantial attention due to the potential diagnostic and therapeutic relevance. Although a variety of techniques have been used to isolate and analyze EVs, it is still far away from satisfaction. Size-exclusion chromatography (SEC), which separates subjects by size, has been widely applied in protein purification and analysis. The purpose of this chapter is to show the applications of size-exclusion high-performance liquid chromatography (HPLC) as methods for EV characterization of impurities or contaminants of small size, and thus for quality assay for the purity of the samples of EVs.

Cell microenvironment consists of various types of cells which communicate with each other by vast number of secreted proteins. An unbiased profiling of these secreted proteins on a global scale is often critical for understanding the intercellular signaling in an autocrine or paracrine manner. Mass spectrometry-based proteomics has become one of the most popular technology for characterization of the secreted proteins. In this chapter, we discuss the standard workflow for secreted proteins characterization, including harvesting secreted proteins from conditioned media, digesting the obtained proteins, liquid chromatography-mass spectrometry analysis, and downstream data analysis.

Quantification of cytokine production by CD4 and CD8 T cells after in vitro recall stimulation with the immunizing antigen is a powerful approach to characterize the cellular immune responses to immunization. Here we describe three complementary methods for such quantification including flow cytometric analysis of cytokine production by intracellular staining, ELISpot determination of the numbers of cytokine-producing cells, and generation of secreted cytokines and chemokines in culture supernatants for analysis by ELISA and/or cytometric bead arrays.

Human mesenchymal stem cells (hMSCs) have been proposed as possible therapeutic agents for central nervous system (CNS) disorders. Recently, it has been suggested that their effects are mostly mediated through their secretome, which contains a number of neuroregulatory molecules capable of increasing cell proliferation, differentiation, and survival in different physiological conditions. Here, we present an overview of the hMSC secretome as a possible candidate in the creation of new cell-free therapies, demonstrating the process of its collection and route of administration, focusing our attention on their effects in CNS regenerative medicine.

Antibodies are provided in a variety of formats that include antiserum, hybridoma culture supernatant, or ascites. They can all be used successfully in crude form for the detection of target antigens by immunoassay. However, it is advantageous to use purified antibody in defined quantity to facilitate assay reproducibility, economy, and reduced interference of nonspecific components as well as improved storage, stability, and bio-conjugation. Although not always necessary, the relative simplicity of antibody purification using commercially available protein-A, protein-G, or protein-L resins with basic chromatographic principles warrants purification when antibody source material is available in sufficient quantity. Here, we define three simple methods using immobilized (1) protein-A, (2) protein-G, and (3) protein-L agarose beads to yield highly purified antibody.

The sandwich immunoassay (sELISA) is an invaluable technique for concentrating, detecting, and quantifying target antigens. The two critical components required are a capture antibody and a detection antibody, each binding a different epitope on the target antigen. The specific antibodies incorporated into the test define most of the performance parameters of any subsequent immunoassay regardless of the assay format: traditional ELISA, lateral-flow immunoassay, various bead-based assays, antibody-based biosensors, or the reporting label. Here we describe an approach for identifying monoclonal antibodies (mAbs) suitable for use as capture antibodies and detector antibodies in a sELISA targeting bacterial protein toxins. The approach was designed for early identification of monoclonal antibodies (mAbs), in the initial hybridoma screen.

Proteins in living organisms have names that are usually derived from their function in the biochemical system their discoverer was investigating. Typical examples are acetylcholinesterase and agrin; however, for both of these, various other functions that are not related to the cholinergic system have been revealed. Our investigations have been focused on the alternative roles of acetylcholinesterase and agrin in the processes of muscle development and regeneration. Previously, we described a role for agrin in the development of excitability in muscle contraction. In this study, we report the effects of agrin on secretion of interleukin 6 in developing human muscle. At the myoblast stage, agrin increases interleukin 6 secretion. This effect seems to be general as it was observed in all of the cell models analysed (human, mouse, cell lines). After fusion of myoblasts into myotubes, the effects of agrin are no longer evident, although agrin has further effects at the innervation stage, at least in in vitro innervated human muscle. These effects of agrin are another demonstration of its non-synaptic roles that are apparently developmental-stage specific. Our data support the view that acetylcholinesterase and agrin participate in various processes during development of skeletal muscle.

Exosomes are membrane-bound 50-100 nm vesicles released from many cell types including normal and tumorous tissues. Exosomes transport mainly miRNAs, mRNAs, enzymes, cytokines, etc. from the cells of origin to the neighbor cells mediating the communication between them. The content of exosomes can be explored using RNA profiling after their isolation from medium conditioned by cultured cells or from other biofluids. This chapter includes detailed discussion on isolation, characterization, and miRNA profiling of exosomes. First, exosomes are isolated by filtration and ultracentrifugation, and then characterized using immunoblotting and transmission electron microscope. Finally, we used low density arrays to profile exosomal miRNA.

Circulating microRNAs (miRNAs) have been recently detected in extracellular body fluids and proved themselves as promising biomarkers for a broad spectrum of diseases. The techniques to isolate, detect, and characterize extracellular miRNAs vary significantly from report to report. In this chapter we describe a consistent, efficient and highly reproducible protocol for isolation and detection of microvesicles-free circulating miRNA from human blood plasma or cell culture media. Furthermore, since exosomes-free circulating miRNAs are associated with Argonaut proteins (the same proteins to which miRNAs are bound inside the cell), we provide a protocol for immunoprecipitation of AGO2 associated miRNAs.

MicroRNAs (miRNAs) are small, noncoding RNA molecules that negatively regulate gene expression and control a wide range of cellular processes. Extracellular forms of miRNA circulating in the bloodstream (circulating miRNA, c-miRNA) are of increasing interest for their potential as biomarkers and long-range physiological signaling molecules. Precise measurement of intracellular miRNA expression is possible but can be challenging, especially in the context of specialized tissue niches in vivo. The accurate measurement of extracellular miRNA presents other obstacles stemming from their low concentrations and confounding sources of intracellular miRNA that contaminate RNA extraction protocols. Here, we describe multiple methods to isolate extracellular miRNA from cell culture media, serum, and plasma in order to accurately measure their variable expression under different conditions. We additionally describe an in situ staining protocol designed to not only quantify but also localize miRNA in formalin-fixed paraffin-embedded tissue that may prove useful in describing the action of c-miRNA before they leave their tissue of origin and after they potentially arrive at their target destination.

In the past, various studies using different methods have been carried out to analyze proteins secreted by cells. There are several crucial steps that have to be followed to ensure successful secreted proteome detection and identification. Simultaneously with the optimization of the experimental conditions for various cell type culturing and subsequent cell conditioning to obtain conditioned medium with secreted proteins in vitro, the analytical separation methods for fractionation of complex protein mixture and mass spectrometry for protein identification are of high importance. The separation methods primarily used are either gel-based (e.g., 1-DE and 2-DE) or gel-free methods (e.g., liquid chromatography and capillary electrophoresis). Here we outline an optimized protocol for the preparation and analysis of conditioned medium containing proteins secreted by neonatal cardiac myocytes by using reversed-phase liquid chromatography (RPLC) followed by tandem mass spectrometry (LC-MS/MS). Although optimized for neonatal cardiac myocytes, the general steps described in the following chapter can be adapted to other cell types as well.

Mesenchymal stem cells (MSCs) derived from human embryonic stem cells (ESCs) have been shown to secrete exosomes that are cardioprotective against myocardial ischemia reperfusion injury in a mouse model. To elucidate this cardioprotective mechanism, we have characterized the protein, nucleic acid, and lipid composition of MSC exosomes. Here we describe the isolation and analysis of RNA in MSC exosome. We have previously reported that RNAs in MSC exosome are primarily small RNA molecules of <300 nt and they include many miRNAs. Many of these miRNAs are in the precursor form suggesting that pre-miRNAs, and not mature miRNAs are preferentially loaded into exosomes. The protocols described here include assays to ascertain the presence of pre-miRNAs, profiling of miRNA and pre-miRNA, and quantitative estimation of mature and pre-miRNA.

Currently, mammalian cells are the most commonly used hosts for the production of therapeutic monoclonal antibodies (mAbs). These hosts not only secrete mAbs with properly assembled two heavy and two light chains but also deliver mAbs with a glycosylation profile that is compatible with administration into humans. GlycoFi, a wholly owned subsidiary of Merck & Co., Inc., humanized the Pichia glycosylation pathway which allows it to express glycoproteins with a human-like glycan profile. This offers an alternative mAb production platform similar to mammalian hosts and in some cases it even provides more homogenous product and better efficacy, such as enhanced effector function. This chapter describes a protocol for using glycoengineered Pichia to produce full-length mAbs. It covers a broad spectrum of mAb expression technologies in yeast including expression vector construction, yeast transformation, high-throughput strain selection to fermentation, and antibody purification.

MicroRNA can be transferred across cells within extracellular vesicles such as exosomes. In order to analyze the biological effects of extracellular vesicle microRNA, it is necessary to isolate these vesicles and to extract their miRNA content.Here, we describe an approach to the isolation of cellular nanovesicles from liver cancer cell lines that can be used for the isolation of RNA and microRNA.

One of the major challenges in cardiovascular medicine is to identify candidate biomarker proteins. Between different proteomics studies, the secretome is a valuable tool in the search for biomarkers locally released by a studied tissue and remains particularly important while working with vascular tissues, since the secreted proteins would be probably shed to the blood. In this chapter, we described a method to validate the origin of secreted proteins in human aortic valves, demonstrating their synthesis and release by the tissue and ruling out blood origin.

Exosomes are extremely small (<100 nm) membrane vesicles, generated in the endocytic compartment that are released to the extracellular milieu by living cells. Although the biological function of exosomes in vivo remains unclear, they seem to function as mechanisms of cell-to-cell communication for horizontal transfer of proteins, antigens, prions, morphogens, mRNA, and noncoding regulatory RNAs, including microRNAs (miRNAs) (also known as exosome-shuttle miRNAs). Dendritic cells (DCs), the most potent professional antigen-presenting leukocytes of the immune system, release relatively high levels of exosomes and also interact with free exosomes present in the extracellular space. Therefore, DCs constitute a good model for the analysis of exosome-shuttle miRNAs and their horizontal propagation between cells. This chapter provides basic protocols for purification of exosomes released by mouse bone marrow-derived DCs, analysis of their miRNA content, and assessment of the function of exosome-shuttle miRNAs, once they are transferred to target/acceptor DCs.

Cellular senescence suppresses cancer by eliminating potentially oncogenic cells, participates in tissue repair, contributes to cancer therapy, and promotes organismal aging. Numerous activities of senescent cells depend on the aptitude of these cells to secrete myriads of bioactive molecules, a behavior termed the senescence-associated secretory phenotype (SASP). The SASP supports cell-autonomous functions like the senescence-associated growth arrest, and mediates paracrine interactions between senescent cells and their surrounding microenvironment. The biological functions and the regulation of the SASP are beginning to emerge, and current SASP assessment techniques include the analysis of SASP factors at the mRNA level, the direct measurement of factors inside or outside the cell (i.e., secreted), and the detection of SASP-provoked cellular responses. Here, we focus on a simple approach to collect SASP-conditioned media in order to directly measure secreted SASP factors using sandwich enzyme-linked immunosorbent assay. As an example, we discuss the assessment of the major SASP factor interleukin-6 in senescent human fibroblasts. Supplemental notes are provided to easily adapt this procedure to other SASP factors, change cell types, or scale the techniques for different volumes or high-throughput measurements. These techniques should facilitate the discovery of novel functions and regulators of the SASP.

The isolation and culture of both embryonic and extraembryonic stem cells provide an enormous opportunity to study the molecular processes that establish and maintain lineage-specific, monoallelic patterns of gene expression. This chapter describes the isolation an culture of trophectoderm stem cells from mouse blastocyst stage embryos. Using this powerful in vitro system, scientists can now begin to tease apart the epigenetic processes that result in placental patterns of imprinted gene expression and begin to better understand the role these genes play in development and disease.

In principle, the isolation of secondary metabolites from microbes does not differ from their isolation from other organisms. The extraction procedure may of course be quite different, especially if it is carried out in an industrial scale, but when an extract containing the metabolites of interest is at hand, it is the same palette of adsorbents and chromatographic techniques that provide the major tools for the fractionation and eventual isolation of the pure compounds. Compared to plants, in which one is sure to find secondary metabolites of certain types, e.g., flavonoids, microbes can be expected to produce virtually anything and it is important to go about the fractionation procedure with an open mind. This chapter presents an overview of preparation of extracts from microbial sources, and various methods and strategies involved in the isolation and characterization of microbial natural products.

Sequential cleavage of amyloid precursor protein (APP) by β- and γ-secretases and the formation of Aβ peptides are pivotal for Alzheimer's disease. Therefore, a large number of drugs has been developed targeting APP metabolism. However, many pharmacological compounds have been identified in vitro in immortalized APP overexpressing cell lines rather than in primary neurons. Here, we compared the effect of already characterized secretase inhibitors and modulators on Aβ formation in primary chicken telencephalic neurons and in a human neuroglioma cell line (H4) ectopically expressing human APP with the Swedish double mutation. Primary chicken neurons replicated the effects of a β-secretase inhibitor (β-secretase inhibitor IV), two γ-secretase inhibitors (DAPM, DAPT), two non-steroidal-anti-inflammatory drugs (sulindac sulfide, CW), and of the calpain inhibitor calpeptin. With the exception of the two γ-secretase inhibitors, all tested compounds were more efficacious in primary chicken telencephalic neurons than in the immortalized H4 cell line. Moreover, H4 cells failed to reproduce the effect of calpeptin. Hence, primary chicken telencephalic neurons represent a suitable cell culture model for testing drugs interfering with APP processing and are overall more sensitive to pharmacological interference than immortalized H4 cells ectopically expressing mutant human APP.

Recent data suggest that soluble, non-fibrillar assemblies of the amyloid β-protein (Aβ) may mediate the synaptic deficits that characterize the early stages of Alzheimer's disease. Consequently, much effort has been expended in isolating and studying a variety of different Aβ assemblies. Here, we describe the use of immunoprecipitation/western blotting and size exclusion chromatography/western blotting to characterize Aβ present in conditioned medium from cultured cells, human cerebrospinal fluid, and human cortex extracted with aqueous buffer, detergent, and formic acid.

Measles viruses have shown potent oncolytic activity as a therapeutic against a variety of human cancers in animal models and are currently being tested in clinical trials in patients. In contrast to using measles virus as a vaccine, oncolytic activity depends on high concentrations of infectious virus. For use in humans, the high-titer measles virus preparations must also be purified to remove significant levels of cellular proteins and nucleic acid resulting from the cytolytic products of measles virus replication and release. Pleomorphic measles virus must be treated as >1-μm particles that are extremely shear sensitive to maximize recoveries and retain infectivity. Therefore, to maximize the recovery of sterile, high titer infectious measles viruses, the entire production and purification process must be done using gentle conditions and aseptic processing. Here we describe a procedure applicable to the production of small (a few liters) to large (50-60 L) batches of measles virus amplified in Vero cells adapted to serum-free growth. Cell culture supernatant containing the measles virus is clarified by filtration to remove intact Vero cells and other debris, and then treated with Benzonase(®) in the presence of magnesium chloride to digest contaminating nucleic acid. The measles virus in the treated cell culture supernatant is then concentrated and purified using tangential flow filtration (TFF) and diafiltration. The concentrated and diafiltered measles virus is passed through a final clarifying filter prior to final vialing and storage at <-65°C. An infectivity assay to quantify infectious measles virus concentration based on the TCID(50) method is also described. This procedure can be readily adapted to the production and purification of measles viruses using good manufacturing practices (GMP).

Since the first report of derivation of human embryonic stem cell (hESC) lines in 1998, many progresses have been achieved to reliably and efficiently derive, maintain, and differentiate this therapeutically promising cell type. This chapter introduces some basic and widely recognized methods that we use in our hESC core laboratory. Specifically, it includes methods for (1) deriving hESC lines without using enzyme and antibody to isolate the inner cell mass; (2) sustaining hESC self-renewal under feeder-dependent, feeder-conditioned, and defined conditions as well as pluripotency validation and quality control assays; and (3) inducing hESC differentiation to trophoblast with BMP4.

Membranous vesicles are constitutively released by a multitude of cell types. Following fusion of multivesicular bodies with the plasma membrane, endocytic vesicles, 30-90 nm in size termed exosomes are released extracellularly. Whilst several groups have reported the presence of exosomes in cell-culture conditioned medium, their biological and physiological functions still remain unclear. In addition, exosomes have been detected in body fluids associated with disease, further demonstrating their potential as diagnostic biomarkers. This protocol employs size filtration followed by ultracentrifugation to isolate and purify exosomes from the colon carcinoma cell line LIM 1215. Morphological visualisation and characterisation is based on electron microscopy and western blotting, whilst protein identification is achieved using a combination of 1D SDS-PAGE and LC-MS/MS.

Two-dimensional electrophoresis (2DE) is a powerful method for separation of complex mixtures of proteins. The standard procedure is not, however, well suited to analysis of articular cartilage, which contains high concentrations of proteoglycans, the polyanionic glycosaminoglycan chains of which interfere with isoelectric focusing. We have developed a method for selective removal of proteoglycans by precipitation with cetylpyridinium chloride, after which the residual cartilage proteins are amenable to conventional 2DE analysis. Using this method, reproducible 2D-patterns can be obtained from proteins secreted by articular cartilage. The separated proteins may then be visualized by metabolic radiolabeling and silver staining, digested in gel with trypsin, and identified by tandem mass spectrometry.

The transport of catalysts (chemicals and enzymes) within plant biomass is believed to be a major bottleneck during thermochemical pretreatment and enzymatic conversion of lignocellulose. Subjecting biomass to size reduction and mechanical homogenization can reduce catalyst transport limitations; however, such processing adds complexity and cost to the overall process. Using high-resolution light microscopy, we have monitored the transport of an aqueous solution of Direct Blue-I (DB-I) dye through intact corn internodes under a variety of impregnation conditions. DB-I is a hydrophilic anionic dye with affinity for cellulose. This model system has enabled us to visualize likely barriers and mechanisms of catalyst transport in corn stems. Microscopic images were compared with calculated degrees of saturation (i.e., volume fraction of internode void space occupied by dye solution) to correlate impregnation strategies with dye distribution and transport mechanisms. Results show the waxy rind exterior and air trapped within individual cells to be the major barriers to dye transport, whereas the vascular bundles, apoplastic continuum (i.e., the intercellular void space at cell junctions), and fissures formed during the drying process provided the most utilized pathways for transport. Although representing only 20-30% of the internode volume, complete saturation of the apoplast and vascular bundles by fluid allowed dye contact with a majority of the cells in the internode interior.

We have developed a novel method to produce large numbers of neural stem cells and neurons directly from embryonic stem (ES) cells. The method is composed of three culture stages. In the first stage, floating ES cell colonies are cultured in astrocyte-conditioned medium to directly differentiate neural stem cells from ES cells, resulting in neural stem spheres. In the second stage, neural stem spheres are cultured as adhesive cells to produce neural stem cells by cell migration. In the third stage, neural stem cells are cultured as monolayers, which proliferate in the presence of fibroblast growth factor 2 and epidermal growth factor and differentiate into neurons in astrocyte-conditioned medium.

In this chapter, we present technical details for the generation of in vitro skin equivalents consisting of collagen gels with incorporated fibroblasts covered by proliferating and differentiating keratinocytes. Epithelial-mesenchymal interactions are clearly manifest in these skin equivalents. Therefore, they have proven to be suitable experimental tools for a broad range of applications, e.g., for studies on the the paracrine regulation of keratinocyte differentiation and proliferation. On the other hand, in vivo assays cannot be abandoned totally, in particular, when such properties as malignant growth potential, disturbed differentiation control in carcinogenesis, and impact on angiogenesis are concerned. For that reason, we additionally describe xenotransplantation techniques to graft human keratinocytes and skin equivalents, respectively, onto the dorsal muscle fascia of thymus-aplastic mice.

In living bodies, there are many cell-cell interactions, including epithelial-mesenchymal interactions, to control cell growth and differentiation, and disturbances to such systems are believed to be a critical reason for many diseases, including cancer. Recently, many growth factors mediating epithelial- mesenchymal interactions have been revealed by molecular biological research. These growth factors are critical tools for both basic research and medical applications. However, obtaining purified forms of such growth factor proteins is difficult. To conveniently analyze the biological effects of such factors on keratinocytes, in this protocol, we describe how to introduce ectopic genes of growth factors of interest (sonic hedgehog and wnt-3 genes as examples) into Swiss-3T3 cells, one of the most widely used feeder cells for epithelial cell culture, and how to coculture the keratinocytes with them.

This chapter deals with experimental protocols and considerations related to the culture of epithelial cells under anchorage-independent conditions in liquid media. This technique has proven to be a powerful tool in studying the effects of loss of extracellular matrix interaction on crucial aspects of epithelial cell biology. Specifically, examining cells in the absence of substrate attachment, as described in this chapter, will allow the investigator to study the effect of growth factors independently of cell adhesion. Several methods are discussed relating to the preparation of tissue culture plates for suspension cultures and to the choice of a suitable cell culture medium.

In vitro cell culture is a necessary prerequisite in acquiring a thorough understanding of the biology and behavior of the cells of interest and is a critical first step in developing cellular therapies. Somatic stem cell biology is concerned with stem cells of the adult and how they may be utilized in regenerating tissue and ameliorating disease. Moreover, the incidence of disease increases with age, hence the demand for therapeutics is greatest among mature individuals. Therefore, an ability to grow and manipulate primary adult epithelial keratinocytes in vitro is of paramount importance in gaining insights into the biology of skin that may have clinical implications. A methodology has been developed that will enable investigators to isolate and serially culture adult basal keratinocytes from the epidermis of the mouse in a supplemented culture medium that selects for epithelial lineages and enhances their proliferation while inhibiting differentiation through many passages.

Mouse epidermal keratinocytes have traditionally been difficult to grow in vitro. In this chapter, we present a method for isolating epidermal keratinocytes from a single, newborn mouse pup for long-term culture. The protocols we describe will be especially useful for the isolation and analysis of cells harvested from transgenic or knockout mice. We explain how to use a supplemented fibroblast-conditioned medium, along with mouse collagen IV-coated culture dishes, to establish and subculture these fastidious cells for multiple passages. We describe how to induce expression of markers of the late stages of epidermal differentiation in cultured cells and how to ship whole mouse skins for culture at a site removed from the mice, should it be required. This chapter also contains a method of cryopreservation that ensures high cell viability after periods of storage over liquid nitrogen. The techniques described here in detail should be of interest to investigators currently producing transgenic or null mice with epidermal defects.