Methods

Published by Elsevier
Online ISSN: 1095-9130
Publications
Article
The chemical nucleases 1,10-phenanthroline-Cu(II) and EDTA-Fe(II), have proven to be valuable tools for structural analysis of nucleic acids. Both have found applications in footprinting and directed proximity studies of DNA and RNA. Derivatives of each that provide for tethering to nucleic acid or protein are commercially available, allowing their widespread use for structural analysis of macromolecules. Although their applications are somewhat overlapping, differences in their cleavage mechanisms and chemical properties allow them to provide distinct and complementary structural information. The purpose of this study is to compare directly the cleavage patterns of tethered 1,10-phenanthroline-Cu(II) and EDTA-Fe(II) complexes within a similar experimental system. Here, the region surrounding nucleotide 1400 of 16S rRNA from Escherichia coli serves as a substrate for chemical cleavage directed by a derivatized complementary oligonucleotide. This region of rRNA is known to be involved in the decoding of mRNA during translation. The results of this study provide evidence in support of the mechanistic differences previously established for EDTA-Fe(II) and 1,10-phenathroline-Cu(II). The delocalized cleavage envelope produced by EDTA-Fe(II) cleavage suggests the involvement of a diffusible reactive species. On the other hand, rRNA cleavage induced by the tethered 1,10-phenanthroline-Cu(II) complex appears localized to the proximity of the chemical nuclease under normal conditions, although the production of an unknown diffusible species appears to occur during long reaction times.
 
Article
Inositol 1,4,5-trisphosphate receptors (InsP3R) are a family of ubiquitously expressed intracellular Ca2+ channels. Isoform-specific properties of the three family members may play a prominent role in defining the rich diversity of the spatial and temporal characteristics of intracellular Ca2+ signals. Studying the properties of the particular family members is complicated because individual receptor isoforms are typically never expressed in isolation. In this article, we discuss strategies for studying Ca2+ release through individual InsP3R family members with particular reference to methods applicable following expression of recombinant InsP3R and mutant constructs in the DT40-3KO cell line, an unambiguously null InsP3R expression system.
 
Article
Experimental lesions of the peripheral nerve system can be visualized in vivo by magnetic resonance imaging (MRI). Many studies of the rat peripheral nervous systems were performed on dedicated animal MR scanners with a high magnetic field strength for good spatial resolution. Here, we present an MR protocol to study experimental lesions of the rat nervous system with clinical 1.5-T MR scanners and commercially available coils. Using a three-sequence approach (T1-weighted imaging, fat-saturated T2-weighted imaging and fat-saturated T1-weighted imaging with Gd-DTPA in the same plane), the relevant signal changes of the lesioned nerve can be visualized and separated from other structures, e.g., blood vessels. Furthermore, we give an overview on different types of contrast agents used for peripheral nerve MR imaging and MR findings in selected experimental models of rat peripheral nerve injury.
 
Article
Because of superior soft-tissue contrast compared to other imaging techniques, non-invasive abdominal magnetic resonance imaging (MRI) is ideal for monitoring organ regeneration, tissue repair, cancer stage, and treatment effects in a wide variety of experimental animal models. Currently, sophisticated MR protocols, including technically demanding procedures for motion artefact compensation, achieve an MRI resolution limit of < 100 microm under ideal conditions. However, such a high spatial resolution is not required for most experimental rodent studies. This article describes both a detailed imaging protocol for MR data acquisition in a ubiquitously and commercially available 1.5 T MR unit and 3-dimensional volumetry of organs, tissue components, or tumors. Future developments in MR technology will allow in vivo investigation of physiological and pathological processes at the cellular and even the molecular levels. Experimental MRI is crucial for non-invasive monitoring of a broad range of biological processes and will further our general understanding of physiology and disease.
 
Article
Cardiac magnetic resonance (CMR) imaging can provide noninvasive, high resolution images of heart anatomy, viability, perfusion, and function. However, the adoption of clinical CMR imaging protocols for small rodents has been limited due to the small heart size and rapid heart rates. Therefore, most CMR studies in small rodents have been performed on non-clinical, high-field MR magnets. Because such high-field systems are not readily available at most institutions, the technical aspects that are needed to perform CMR on clinical 1.5 T and 3.0 T MR scanners are presented in this paper. Equipment requirements are presented, and a comprehensive description of the methods needed to complete a CMR exam including the animal preparation, imaging, and image analysis are discussed. In addition, the advanced applications of myocardial tagging and delayed-contrast-enhanced imaging are reviewed for the assessment of regional contractile function and myocardial viability, respectively.
 
Article
Signal-to-noise ratio improvement is of major importance to achieve microscopic spatial resolution in magnetic resonance experiments. Magnetic resonance imaging of small animals is particularly concerned since it typically requires voxels of less than (100 microm)(3) to observe the small anatomical structures having size reduction by a factor of more than 10 as compared to human being. The signal-to-noise ratio can be increased by working at high static magnetic field strengths, but the biomedical interest of such high-field systems may be limited due to field-dependent contrast mechanisms and severe technological difficulties. An alternative approach that allows working in clinical imaging system is to improve the sensitivity of the radio-frequency receiver coil. This can be done using small cryogenically operated coils made either of copper or high-temperature superconducting material. We report the technological development of cryo-cooled superconducting coils for high-resolution imaging in a whole-body magnetic resonance scanner operating at 1.5 T. The technological background supporting this development is first addressed, including HTS coil design, simulation tools, cryogenic mean description and electrical characterization procedure. To illustrate the performances of superconducting coils for magnetic resonance imaging at intermediate field strength, in-vivo mouse images of various anatomic sites acquired with a 12 mm diameter cryo-cooled superconducting coil are presented.
 
Article
It is frequently useful to determine the methylation state of samples containing limited amounts of DNA such as from embryos, or from fixed tissue samples in which DNA is degraded or difficult to isolate. By modification of the standard protocols for DNA preparation and bisulfite treatment, it is possible to obtain DNA methylation sequence data for such samples. We present methods for bisulfite treatment of embryos, fixed sections, and samples obtained by laser capture microdissection, and discuss the additional experimental considerations required when working with small numbers of cells or degraded DNA samples.
 
Article
The three-dimensional culture of MCF-10A mammary epithelial cells on a reconstituted basement membrane results in formation of polarized, growth-arrested acini-like spheroids that recapitulate several aspects of glandular architecture in vivo. Oncogenes introduced into MCF-10A cells disrupt this morphogenetic process, and elicit distinct morphological phenotypes. Recent studies analyzing the mechanistic basis for phenotypic heterogeneity observed among different oncogenes (e.g., ErbB2, cyclin D1) have illustrated the utility of this three-dimensional culture system in modeling the biological activities of cancer genes, particularly with regard to their ability to disrupt epithelial architecture during the early aspects of carcinoma formation. Here we provide a collection of protocols to culture MCF-10A cells, to establish stable pools expressing a gene of interest via retroviral infection, as well as to grow and analyze MCF-10A cells in three-dimensional basement membrane culture.
 
Article
The burgeoning of phosphoinositide-binding domains and proteins in cellular signaling and trafficking has drawn laboratories from a wide variety of fields into the study of lipid interactions with peripheral membrane proteins. Many different approaches have been developed to assess phosphoinositide binding, some of which are more problematic than others, and some of which can be quantitated more readily than others. With a focus on the methods used in our laboratory, we describe here the considerations that need to be taken into account when establishing-and quantitating-the specific binding of a protein or domain to phosphoinositides in membranes. We also discuss briefly a few examples in which no clear consensus has yet been reached as to the specificity of a given domain or protein because of discrepancies between different commonly used approaches.
 
Article
Classically, experiments aimed at studying changes in protein expression have always followed a small set of proteins. This focused approach was necessary since tools to efficiently analyze large numbers of proteins were simply not available. Large-scale quantitative proteomics promises to produce reams of data that previously would have taken decades to measure with classical methods. Mass spectrometry is already a well-established protein identification tool and recent methodological developments indicate that it can also be successfully applied to extract quantitative data of protein abundance. From the first reports 4 years ago, numerous schemes to take advantage of stable isotope nuclei incorporation in proteins and peptides have been developed. Here we review the benefits and pitfalls of some of the most commonly used protocols, focusing on a procedure now being used extensively in our laboratory, stable isotope labeling with amino acids in cell culture (SILAC). The basic theory, application, and data analysis of a SILAC experiment are discussed. The emerging nature of these techniques and the rapid pace of technological development make forecasting the directions of the field difficult but we speculate that SILAC will soon be a key tool of quantitative proteomics.
 
Article
We analyzed the production and the roles of IL-6, IL-10, and IL-13 in B-lymphoid malignancies and in specific diseases with B-lymphocyte hyperactivity. Both IL-13 and IL-10 genes are expressed in B-cell lymphomas. However, their contribution to tumor progression is unclear. In certain lymphoproliferative disorders that develop in transplanted patients, IL-6 is produced by malignant cells and is a major factor of their proliferation. In other lymphomas, the IL-6 gene is expressed only in malignancies where differentiated malignant cells are present. In these lymphomas, IL-6 is produced by stromal cells, and the malignant cells express the IL-6 receptor. In patients with HIV infection, the level of production of IL-6, IL-10, and IL-13 is not higher than those of other conditions with immune activation. However, IL-6 contributes to increased production of IgG and IgA in vivo. In Castleman's disease, IL-6 is produced in the lymph node germinal centers, partly originating from follicular dendritic cells, which may explain some of the pathogenesis of this disease. In systemic lupus erythematosus, the critical cytokine is IL-10, which is produced in large amounts by B lymphocytes and monocytes and is responsible for autoantibody production. Taken together, these data emphasize the roles of IL-6 and IL-10, usually produced by nonlymphoid cells, on B lymphocytes, either malignant or hyperactivated.
 
Article
Metaiodobenzylguanidine (MIBG) is a tracer that selectively targets neuroendocrine cells. On this basis, radiolabeled iodinated-MIBG (I-131-MIBG) has been introduced as a molecular nuclear therapy in the management of neuroendocrine tumors, including neuroblastoma, pheochromocytoma, paraganglioma, neuroendocrine carcinomas, and other rare neuroendocrine tumors. Extensive work has been addressed to develop I-131-MIBG therapy: doses, therapeutic schemes, and efficiency. In this paper, we present an overview on I-131-MIBG therapy, with main focus on different aspects how to perform this treatment.
 
Article
The incidence of hepatocellular carcinoma (HCC) is worldwide sharply on the rise and patients with advanced disease carry a poor prognosis. HCC is the sixth most common cancer and the third leading cause of cancer associated deaths in the world. Intra-arterially administered (131)I-Lipiodol is selectively retained by hepatocellular carcinomas, and has been used as a vehicle for delivery of therapeutic agents to these tumours. In this review we focus on the therapeutic indications, usefulness and methods of treatment with 131-Iodine Lipiodol. The effectiveness of (131)I-Lipiodol treatment is proven both in the treatment of HCC with portal thrombosis and also as an adjuvant to surgery after the resection of HCCs. It is at least as effective as chemoembolization and is tolerated much better. Severe liver dysfunction represents theoretic contraindication for radioembolization as well as for TACE. In such cases (131)I-Lipiodol is an alternative therapy option especially in tumours smaller than 6cm.
 
Article
Spurred by the growing demand for panels of validated disease biomarkers, increasing efforts have focused on advancing qualitative and quantitative tools for more highly multiplexed and sensitive analyses of a multitude of analytes in various human biofluids. In quantitative proteomics, evolving strategies involve the use of the targeted multiple reaction monitoring (MRM) mode of mass spectrometry (MS) with stable isotope-labeled standards (SIS) used for internal normalization. Using that preferred approach with non-invasive urine samples, we have systematically advanced and rigorously assessed the methodology toward the precise quantitation of the largest, multiplexed panel of candidate protein biomarkers in human urine to date. The concentrations of the 136 proteins span >5 orders of magnitude (from 8.6 μg/mL to 25 pg/mL), with average CVs of 8.6% over process triplicate. Detailed here is our quantitative method, the analysis strategy, a feasibility application to prostate cancer samples, and a discussion of the utility of this method in translational studies. Copyright © 2015. Published by Elsevier Inc.
 
Article
Lipases and esterases constitute a large category of enzymes. They are ubiquitous in nature, found in bacteria, fungi, and animals. The family members address a wide variety of structurally diverse substrates. Appropriately, a large number of assays have been developed to analyze their activity in vitro. Here, we present an overview of these enzymes, along with protocols for common assays performed in solution. An emphasis is placed on assays for enzymes that can hydrolyze triacylglycerols. (c) 2005 Elsevier Inc. All rights reserved.
 
Article
We have evaluated UVR-induced erythema in previously unexposed buttock skin of volunteers of skin types I, II, III, and IV. Studies were done with solar-simulated radiation (SSR), UVB, and UVAI and we determined the just perceptible minimal erythema dose (MED) and, in some cases, quantified erythema with a reflectance device. The results show that there is a trend for increased SSR MED with skin type, with the MED of skin type IV being approximately twice that of skin type I, a smaller difference than one might have expected. However, there is a very considerable overlap of MED between skin types which shows that MED is a very poor indictor of skin type. Quantitative dose-response and time course studies with SSR and UVAI showed broadly similar responses when comparable MED-based exposures were given. We used our data to test the new concept of the standard erythema dose (SED) with two different erythema action spectra, and confirmed that the SED approach works with the different UVR sources that we studied.
 
Article
Cytosine methylation is the quintessential epigenetic mark. Two well-established methods, bisulfite sequencing and methyl-DNA immunoprecipitation (MeDIP) lend themselves to the genome-wide analysis of DNA methylation by high throughput sequencing. Here we provide an overview and brief review of these methods. We summarize our experience with MeDIP followed by high throughput Illumina/Solexa sequencing, exemplified by the analysis of the methylated fraction of the Neurospora crassa genome ("methylome"). We provide detailed methods for DNA isolation, processing and the generation of in vitro libraries for Illumina/Solexa sequencing. We discuss potential problems in the generation of sequencing libraries. Finally, we provide an overview of software that is appropriate for the analysis of high throughput sequencing data generated by Illumina/Solexa-type sequencing by synthesis, with a special emphasis on approaches and applications that can generate more accurate depictions of sequence reads that fall in repeated regions of a chosen reference genome.
 
Article
The stochastic nature of generating eukaryotic transcripts challenges conventional methods for obtaining and analyzing single-cell gene expression data. In order to address the inherent noise, detailed methods are described on how to collect data on multiple genes in a large number of single cells using microfluidic arrays. As part of a study exploring the effect of genotype on Wnt pathway activation, data were collected for 96 qPCR assays on 1440 lymphoblastoid cells. The description of methods includes preliminary data processing steps. The methods used in the collection and analysis of single-cell qPCR data are contrasted with those used in conventional qPCR.
 
Article
Quantitative real-time PCR (qPCR) is a frequently used, sensitive and accurate method to study gene expression profiles. However, its throughput was so far limited for routine laboratories to 384 reactions per run based on the limitations of the available instruments. Recently, the LightCycler 1536 Instrument was launched providing a high-throughput solution for qPCR with the analysis of 1536 reactions in approximately 45 min. We assessed the accuracy and sensitivity of this novel technology for the analysis of gene expression profiles in combination with the Innovadyne Nanodrop Express pipetting robot. We compared expression profiles obtained for 42 genes in 71 samples between the Universal ProbeLibrary and the LightCycler 1536 Instrument and SYBR Green I and the ABI PRISM 7900HT system. We found that the results were highly reproducible between both systems. Beside the higher throughput, the advantage of the LightCycler 1536 Instrument was the reduced consumption of reagents and sample material.
 
Article
Intrinsic affinity tags are useful tools for the study of macromolecular targets. Although polypeptide affinity tags are routinely used in purification and detection of protein complexes, there has been a relative lack of powerful RNA affinity tags that can be embedded within RNA sequences. Here, the preparation and use of two RNA affinity tags against Sephadex or streptavidin are described. The two tags have different strengths that make them appropriate for slightly different uses. One is a high-affinity ligand for streptavidin that can be specifically eluted by competition with biotin under otherwise native binding conditions. The other tag binds selectively to Sephadex beads, and can be eluted by competition with the soluble dextran that composes Sephadex. When properly placed within another RNA molecule, the tags can be used to effect dramatic purification of RNA or ribonucleoprotein complexes from complex mixtures of cellular RNA.
 
Schematic of the general procedure for 15 N metabolic labeling One culture of WT Tetrahymena cells was 15 N metabolically labeled as a global standard, while WT and HMT KO cell were normally grown in the SPP medium. Histones were acid extracted and separated by reversed-phase HPLC. The light forms were equally mixed with 15 N-histones before propionylation and trypsinization. The digests were analyzed by nano-LC-MS/MS. PTMs were identified by CID tandem mass spetra and quantified by AUC of light vs heavy forms. A final ratio was calculated from the individual ratios of light vs heavy forms.
HPLC and SDS-PAGE separation of core histones
H/L ratios of 3 tryptic peptides from histone H3 Histones typically are labeled with high efficiency using 15 N as indicated by tryptic peptides.
Down-regulation of H3K27Me2 in the HMT mutant
Article
Mass spectrometry has made major contributions to recent discoveries in the field of epigenetics, particularly in the characterization of the myriad post-translational modifications (PTMs) of histones which are technically challenging to analyze. These new developments have further aroused great interest in development of robust, new mass spectrometric methods to quantitatively study the dynamics of histone modifications. This review covers quantitative analysis of histone PTMs and discuss an 15N metabolic labeling procedure for quantifying histone PTMs applied to the analysis of methyltransferase knockouts in the model organism, Tetrahymena thermophila.
 
Article
The [(18)F]fluorodeoxyglucose (FDG) method to measure glucose metabolism quantitatively in humans is reviewed. The assumptions and the mathematical formulation of the underlying autoradiographic Sokoloff model and its adaptation to positron emission tomography (PET) are described. Various implementations to estimate glucose consumption from measured tissue activity with PET are presented. The dependence on the "lumped constant" and on the accuracy of the input function is discussed. Recommendations for the practical application of different procedures for performing FDG studies are given.
 
Article
Interleukin (IL)-18 is a newly discovered cytokine, structurally similar to IL-1, with profound effects on T-cell activation. This short review summarizes the present knowledge on IL-18, to give an insight into the future perspectives for its possible use as vaccine adjuvant. Formerly called interferon (IFN) gamma inducing factor (IGIF), IL-18 is the new name of a novel cytokine that plays an important role in the T-cell-helper type 1 (Th1) response, primarily by its ability to induce IFNgamma production in T cells and natural killer (NK) cells. Mice deficient in IL-18 have suppressed IFNgamma production despite the presence of IL-12 IL-18 is related to the IL-1 family in terms of structure, receptor family, and function. In terms of structure, IL-18 and IL-1beta share primary amino acid sequences of the so-called "signature sequence" motif and are similarly folded as all-beta pleated sheet molecules. Also similar to IL-1beta, IL-18 is synthesized as a biologically inactive precursor molecule lacking a signal peptide which requires cleavage into an active, mature molecule by the intracellular cysteine protease called IL-1beta-converting enzyme (ICE, also called caspase-1). The activity of mature IL-18 is closely related to that of IL-1. IL-18 induces gene expression and synthesis of tumor necrosis factor (TNF), IL-1, Fas ligand, and several chemokines. The activity of IL-18 is via an IL-18 receptor (IL-18R) complex. This IL-18R complex is made up of a binding chain termed IL-18Ralpha, a member of the IL-1 receptor family previously identified as the IL-1 receptor-related protein (IL-1Rrp), and a signaling chain, also a member of the IL-1R family. The IL-18R complex recruits the IL-1R-activating kinase (IRAK) and TNFR-associated factor-6 (TRAF-6) which phosphorylates nuclear factor kappaB (NFkappaB)-inducing kinase (NIK) with subsequent activation of NFkappaB. Thus on the basis of primary structure, three-dimensional structure, receptor family, signal transduction pathways and biological effects, IL-18 appears to be a new member of the IL-1 family. Similar to IL-1, IL-18 participates in both innate and acquired immunity.
 
Article
Deregulated cell cycle progression is a hallmark of cancer. Accordingly, a major part of therapeutic drugs has been designed to inhibit cell proliferation and tumor growth. Metabolic imaging with positron emission tomography (PET) and the glucose analog 2'-[(18)F]fluoro-2'-deoxyglucose (FDG) has been demonstrated to sensitively detect malignant tumors and to identify responding tumors early in the course of anticancer treatment. However, tumoral uptake of FDG reflects proliferation only in part and is associated with false positive findings due to unspecific tracer retention in inflammatory processes. Most recent advances in cancer treatment have come from the development of disease specific, molecular agents, many of which induce cell cycle arrest (cytostatic effect) instead of tumor cell death (cytotoxic effect). Thus, evaluating alterations in DNA metabolism may reflect response to treatment better than alterations in glucose utilization. PET with the thymidine analog 3'-deoxy-3'-[(18)F]fluorothymidine (FLT) enables non-invasive imaging and quantification of the proliferation fraction of tumors. Furthermore, FLT has been suggested as surrogate marker for assessment of response to treatment, especially when targeted drugs are utilized. This article reports on metabolic pathways of radionucleosides in proliferating cells. Methods for in vivo assessment of the proliferative activity in preclinical and clinical studies are described with a focus on early monitoring response to therapy.
 
Article
RNA interference (RNAi) is a highly conserved gene silencing mechanism that uses double-stranded RNA (dsRNA) as a signal to trigger the degradation of homologous mRNA. The mediators of sequence-specific mRNA degradation are 21- to 23-nt small interfering RNAs (siRNAs) generated by ribonuclease III cleavage from longer dsRNAs. Twenty-one-nucleotide siRNA duplexes trigger specific gene silencing in mammalian somatic cells without activation of the unspecific interferon response. Here we provide a collection of protocols for siRNA-mediated knockdown of mammalian gene expression. Because of the robustness of the siRNA knockdown technology, genomewide analysis of human gene function in cultured cells has now become possible.
 
Article
In vivo(1)H magnetic resonance spectroscopy (MRS) can be used to directly monitor brain ethanol. Previously, studies of human subjects have lead to the suggestion that the ethanol methyl (1)H MRS signal intensity relates to tolerance to ethanol's intoxicating effects. More recently, the ethanol (1)H MRS signal intensity has been recognized to vary between brain gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF) due to differences in T(2) within these environments. The methods presented here extend ethanol MRS techniques to non-human primate subjects. Twelve monkeys were administered ethanol while sedated and positioned within a 3T MRI system. Chemical shift imaging (CSI) measurements were performed following intravenous infusion of 1g/kg ethanol. Magnetic resonance imaging (MRI) data were also recorded for each monkey to provide volume fractions of GM, WM, and CSF for each CSI spectrum. To estimate co-variance of ethanol MRS intensity with GM, WM, and CSF volume fractions, the relative contribution of each tissue subtype was determined following corrections for radiofrequency pulse profile non-uniformity, chemical shift artifacts, and differences between the point spread function in the CSI data and the imaging data. The ethanol MRS intensity per unit blood ethanol concentration was found to differ between GM, WM, and CSF. Individual differences in MRS intensity were larger in GM than WM. This methodology demonstrates the feasibility of ethanol MRS experiments and analysis in non-human primate subjects, and suggests GM may be a site of significant variation in ethanol MRS intensity between individuals.
 
Article
The advent of high-throughput sequencing has led to an explosion of studies into the diversity, expression, processing, and lifespan of RNAs. Recently, three different high-throughput sequencing-based methods have been developed to specifically study RNAs that are in the process of being degraded. All three methods-genome-wide mapping of uncapped and cleaved transcripts (GMUCT), parallel analysis of RNA ends (PARE), and degradome sequencing-take advantage of the fact that Illumina sequencing libraries use T4 RNA ligase 1 to ligate an adapter to the 5' end of RNAs that have a free 5'-monophosphate. This condition for T4 RNA ligase 1 substrates means that mature mRNAs are not substrates of the enzyme because they have a 5'-cap moiety. As a result, these sequencing libraries are specifically made up of clones of decapped or degrading mRNAs resulting from 5'-to-3' decay or nonsense-mediated decay (NMD) and the 3' fragment of cleaved microRNA (miRNA) and small interfering RNA (siRNA) target RNAs. Here, we present a massively streamlined protocol for GMUCT that takes 2 - 3 days, can be initiated with as little as 5 μg of starting total RNA, and involves only one gel size-selection step. We show that the resulting datasets are similar to those produced using the previous GMUCT and PARE protocols. In total, our results suggest that this method will be the preferable approach for future studies of RNA degradation intermediates and small RNA-mediated cleavage in eukaryotic transcriptomes.
 
Article
Several contradictory papers concerning the effects of microwaves on living organisms and on in vitro cell suspensions have been published through the years. These papers are difficult to interpret, because temperature measurement data are often lacking. Reliable temperature measurements are important, because they enable one to determine whether the observed microwave effects are thermal or nonthermal. Therefore, a method was developed to investigate microwave effects on cellular processes, in which the temperature was precisely monitored during microwave treatment using a fiberoptic thermometer. This method involved the processes required for in vitro production of monoclonal antibodies. Monoclonal antibodies are vital ingredients in (microwave-stimulated) immunostaining techniques and ELISAs, which have become important techniques in neuroscience. The effects of 2.45-GHz microwaves on mouse myeloma and (neural) hybridoma cell replication rates and on antibody production were investigated. In addition, the effects on the cell fusion abilities of spleen lymphocytes and myeloma cells and on in vitro immunization were studied. The results of this study show no effects of microwaves on either of the processes mentioned using exposure times up to 5 h a day at a physiologically normal temperature of 37 degrees C. It was concluded that the effects of 2.45-GHz microwaves detected at higher temperatures are thermal effects and that no indications for nonthermal 2.45-GHz microwave effects exist under the exposure conditions used in the present study.
 
Article
Lipofectamine 2000 is a cationic liposome based reagent that provides high transfection efficiency and high levels of transgene expression in a range of mammalian cell types in vitro using a simple protocol. Optimum transfection efficiency and subsequent cell viability depend on a number of experimental variables such as cell density, liposome and DNA concentrations, liposome-DNA complexing time, and the presence or absence of media components such as antibiotics and serum. The importance of these factors in Lipofectamine 2000 mediated transfection will be discussed together with some specific applications: transfection of primary neurons, high throughput transfection, and delivery of small interfering RNAs.
 
Article
DNA vaccine strategies can differ greatly, with significant effects on the outcome of immunization. In this article, we discuss plasmid design strategies and vaccine regimens. Effectiveness against a pathogen can be affected by the choice of antigen and inclusion of multiple antigens. Gene expression and the resulting immune response can be improved by gene modification and choice of promoters. In designing vaccine regimens, one must consider further dose, timing of doses, adjuvants, and routes of vaccination. Many vaccines are enhanced by combining DNA with other vaccines in "prime-boost" regimens, in which the second vaccine is often a recombinant viral vector or purified protein subunit. Prime-boost vaccines including DNA can elicit immune responses that differ in magnitude, quality, and balance of cellular and humoral responses from those elicited by single components and thus provide further enhancement for DNA immunizations.
 
Article
The application of in vivo microdialysis to the study of acetylcholine (ACh) release has contributed greatly to our understanding of cholinergic brain systems. This article reviews standard experimental procedures for dialysis probe selection and implantation, perfusion parameters, neurochemical detection, and data analysis as they relate to microdialysis assessments of cholinergic function. Particular attention is focused on the unique methodological considerations that arise when in vivo microdialysis is dedicated expressly to the recovery and measurement of ACh as opposed to other neurotransmitters. Limitations of the microdialysis technique are discussed, as well as methodological adaptations that may prove useful in overcoming these limitations. This is followed by an overview of recent studies in which the application of in vivo microdialysis has been used to characterize the basic pharmacology and physiology of cholinergic neurons. Finally, the usefulness of the microdialysis approach for testing hypotheses regarding the cholinergic systems' involvement in cognitive processes is examined. It can be concluded that, in addition to being a versatile and practical method for studying the neurochemistry of cholinergic brain systems, in vivo microdialysis represents a valuable tool in our efforts to better comprehend ACh's underlying role in a variety of behavioral processes.
 
Article
The nanoparticle gadolinium endohedral metallofullerenol [Gd@C82(OH)22]n is a new candidate for cancer treatment with low toxicity. However, its anti-cancer mechanisms remain mostly unknown. In this study, we took a systems biology view of the gene expression profiles of human breast cancer cells (MCF-7) and human umbilical vein endothelial cells (ECV304) treated with and without [Gd@C82(OH)22]n, respectively, measured by the Agilent Gene Chip G4112F. To properly analyze these data, we modified a suit of statistical methods we developed. For the first time we applied the sub-sub normalization to Agilent two-color microarrays. Instead of a simple linear regression, we proposed to use an one-knot SPLINE model in the sub-sub normalization to account for nonlinear spatial effects. The parameters estimated by least trimmed squares- and S-estimators show similar normalization results. We made several kinds of inferences by integrating the expression profiles with the bioinformatic knowledge in KEGG pathways, Gene Ontology, JASPAR, and TRANSFAC. In the transcriptional inference, we proposed the BASE2.0 method to infer a transcription factor's up-regulation and down-regulation activities separately. Overall, [Gd@C82(OH)22]n induces more differentiation in MCF-7 cells than in ECV304 cells, particularly in the reduction of protein processing such as protein glucosylation, folding, targeting, exporting, and transporting. Among the KEGG pathways, the ErbB signaling pathway is up-regulated, whereas protein processing in endoplasmic reticulum (ER) is down-regulated. CHOP, a key pro- apoptotic gene downstream of the ER stress pathway, increases to nine folds in MCF-7 cells after treatment. These findings indicate that ER stress may be one important factor that induces apoptosis in MCF-7 cells after [Gd@C82(OH)22]n treatment. The expression profiles of genes associated with ER stress and apoptosis are statistically consistent with other profiles reported in the literature, such as those of HEK293T and MCF-7 cells induced by the miR-23a∼27a∼24-2 cluster. Furthermore, one of the inferred regulatory mechanisms comprises the apoptosis network centered around TP53, whose effective regulation of apoptosis is somehow reestablished after [Gd@C82(OH)22]n treatment. These results elucidate the application and development of [Gd@C82(OH)22]n and other fullerene derivates.
 
Article
The normal human breast comprises an inner layer of luminal epithelial cells and an outer layer of myoepithelial cells separated from the connective tissue stroma by an intact basement membrane. In breast cancer, tumor cells are in direct contact with the surrounding highly activated collagenous stroma, with little or no discernible myoepithelial fence from the original double-layered structure. To understand the evolution of these two scenarios, we took advantage of a three-dimensional hydrated collagen gel approach. The contribution of myoepithelial cells to normal morphogenesis was studied by ablation and rescue experiments, and genes regulated on tumor cell-fibroblast interaction were identified in a tumor environment assay. In normal breast morphogenesis, the ability to correctly polarize sialomucin to the luminal membrane of emerging acini was used as a criterion for apical polarity and functional differentiation. In the assay of breast neoplasia, the consequence of reciprocal tumor cell-fibroblast interaction was addressed morphologically as well as by a differential display approach. Normal breast epithelial cells were purified immunomagnetically and an established cell line, MCF-7, was used as a surrogate tumor cell. With regard to the importance of myoepithelial cells in normal breast epithelial morphogenesis, the collagen gel assay elucidated the following subtleties: In contrast to culturing in basement membrane gels, luminal epithelial cells when cultured alone made structures that were all inversely polarized. This aberrant polarity could be rescued by co-culture with myoepithelial cells. The molecular activity of myoepithelial cells responsible for correct morphogenesis was narrowed down to the laminin-1 component of the basement membrane. As for the consequence of interaction of tumor cells with connective tissue fibroblasts, the assay allowed us to identify a hitherto undescribed gene referred to as EPSTI1. The relevance of the assay-based identification of regulated genes was confirmed in a series of breast carcinomas in which EPSTI1 was highly upregulated compared with normal breast. Few if any of these observations would have been possible on two-dimensional tissue culture plastic.
 
Article
We present a rapid flow cytometric and non-radioactive functional assay developed for the determination of the cytotoxic activity of T lymphocytes, natural killer cells, and lymphokine-activated killer cells. In contrast to indirect evaluation of cytotoxicity using radioactive assays, this assay is based on the quantitative and qualitative flow cytometric analysis of cell damage on a single cell level. Target cells are stained with PKH-26, a lipophilic dye that stably integrates into the cell membrane, without disturbing its surface marker expression. It, thus, permits the distinction between target and effector cells. After short term in vitro incubation (1.5-3h), AnnexinV-FITC (ann-FITC) staining allows to discriminate between apoptotic and non-apoptotic target cells. Data analysis is performed first by gating on PKH-26 positive target cells, followed by the analysis of the ann-FITC positive subpopulation. The percentage of cytotoxicity in the PKH-26 gated cell population is calculated by subtracting unspecific ann-FITC positive target cells, measured in appropriate controls without effector cells. Using in vitro generated antigen-specific cytotoxic T lymphocytes, we demonstrate that this flow cytometric assay is sensitive, correlates well with the standard 51Cr release assay, and is easy to handle.
 
Article
With the development of genome-wide RNAi libraries, it is now possible to screen for novel components of mitogen-activated protein kinase (MAPK) pathways in cell culture. Although genetic dissection in model organisms and biochemical approaches in mammalian cells have been successful in identifying the core signaling cassettes of these pathways, high-throughput assays can yield unbiased, functional genomic insight into pathway regulation. We describe general high-throughput approaches to assaying MAPK signaling and the receptor tyrosine kinase (RTK)/extracellular signal-regulated kinase (ERK) pathway in particular using a phospho-specific antibody-based readout of pathway activity. We also provide examples of secondary validation screens and methods for managing large datasets for future in vivo functional characterization.
 
Article
Ultraviolet (UV) radiation present in sunlight plays a critical role in the initiation and promotion of nonmelanoma skin carcinogenesis and immune suppression. The immune suppressive effects of UV have been identified as a risk factor for skin cancer induction. For these reasons, scientists have focused on elucidating the mechanisms of UV-induced immune suppression to better understand the pathogenesis of skin cancer induction. A hallmark of UV-induced immune suppression is the generation of antigen-specific suppressor T cells. These suppressor cells have been shown to suppress antitumor immunity as well as other cell-mediated responses such as delayed-type hypersensitivity (DTH) reactions. Due to the excessive cost and time involved in traditional UV carcinogenic experiments, scientists have opted to use UV-induced suppression of DTH reactions as a surrogate model. DTH has been, and continues to be, a widely used assay system to measure in vivo immune function. Although somewhat unsophisticated by today's standards, this assay has great advantages because it presents a fast, inexpensive, and reliable model system to help dissect the mechanisms involved in UV-induced immune suppression. Furthermore, the murine model of DTH enables scientists to perform additional procedures, such as adoptive transfer studies with suppressor T cells, which are currently unavailable with human subjects.
 
Article
It is often an immense challenge to overexpress human membrane proteins at levels sufficient for structural studies. The use of Human Embryonic Kidney 293 (HEK 293) cells to express full-length human membrane proteins is becoming increasingly common, since these cells provide a near-native protein folding and lipid environment. Nevertheless, the labor intensiveness and low yields of HEK 293 cells and other mammalian cell expression systems necessitate the screening for suitable expression as early as possible. Here we present our methodology used to generate constructs of human membrane proteins and to rapidly assess their suitability for overexpression using transiently transfected, glycosylation-deficient GnT I-HEK 293 cells (HEK 293S). Constructs, in the presence or absence of a C-terminal enhanced green fluorescence protein (EGFP) molecule, are made in a modular manner, allowing for the rapid generation of several combinations of fusion tags and gene paralogues/orthologues. Solubilization of HEK 293S cells, using a range of detergents, followed by Western blotting is performed to assess relative expression levels and to detect possible degradation products. Fluorescence-detection size exclusion chromatography (FSEC) is employed to assess expression levels and overall homogeneity of the membrane proteins, to rank different constructs for further downstream expression trials. Constructs identified as having high expression are instantly suitable for further downstream large scale transient expression trials and stable cell line generation. The method described is accessible to all laboratory scales and can be completed in approximately 3 weeks.
 
Article
MicroRNAs (miRNAs) are small (approximately 22 nt) RNAs that play important roles in gene regulatory networks by binding to and repressing the activity of specific target mRNAs. Recent studies have indicated that miRNAs circulate in a stable, cell-free form in the bloodstream and that the abundance of specific miRNAs in plasma or serum can serve as biomarkers of cancer and other diseases. Measurement of circulating miRNAs as biomarkers is associated with some special challenges, including those related to pre-analytic variation and data normalization. We describe here our procedure for qRT-PCR analysis of circulating miRNAs as biomarkers, and discuss relevant issues of sample preparation, experimental design and data analysis.
 
Article
We describe a methodology for studying protein kinetics using a rapid-scan technology for collecting 2D IR spectra. In conjunction with isotope labeling, 2D IR spectroscopy is able to probe the secondary structure and environment of individual residues in polypeptides and proteins. It is particularly useful for membrane and aggregate proteins. Our rapid-scan technology relies on a mid-IR pulse shaper that computer generates the pulse shapes, much like in an NMR spectrometer. With this device, data collection is faster, easier, and more accurate. We describe our 2D IR spectrometer, as well as protocols for (13)C(18)O isotope labeling, and then illustrate the technique with an application to the aggregation of the human islet amyloid polypeptide implicated in type 2 diabetes.
 
Article
Multidimensional liquid chromatography techniques have been coupled to tandem mass spectrometry to provide a robust method to identify proteins in complex mixtures. Data acquisition is interfaced directly with search algorithms for identification through cross-correlation with databases. This review describes the most recent advances in methodologies for protein identification by mass spectrometry and describes the limitations of the application of the technologies. (c) 2004 Elsevier Inc. All rights reserved.
 
Article
In biological membranes many proteins are organized in complexes. The method of choice for the global analysis of the subunits of these complexes is two-dimensional blue native (2D BN)/SDS-PAGE. In the 1st dimension complexes are separated by BN-PAGE, and in the 2nd dimension their subunits are resolved by SDS-PAGE. In the currently available protocols the 1st dimension BN gel lanes get distorted during their transfer to the 2nd dimension separation gels. This leads to low reproducibility and high variation of 2D BN/SDS-gels, rendering them unsuitable for comparative analysis. We have developed a 2D BN/SDS-PAGE protocol where the 1st dimension BN gel is cast on a GelBond PAG film. Immobilization prevents distortion of BN gel lanes, which lowers variation and greatly improves reproducibility of 2D BN/SDS-gels. 2D BN/SDS-PAGE with an immobilized 1st dimension was used for the comparative analysis of the cytoplasmic membrane proteomes of Escherichia coli cells overexpressing a membrane protein and to create a 2D BN/SDS-PAGE reference map of the E. coli cytoplasmic membrane proteome with 143 identified proteins from 165 different protein spots.
 
Article
Two-dimensional (2D) agarose gel electrophoresis is one of the most powerful methods to analyze the mass and shape of replication intermediates. It is often use to map replication origins but it is also useful to characterize termination of replication, replication fork barriers and even replication fork reversal. Here, we present protocols, figures and movies with a thorough description of different modes of replication for linear DNA fragments and the corresponding patterns they generate in 2D gels.
 
Article
Mitochondria are crucial for many aspects of cellular homeostasis and a sufficiently negative membrane potential (Deltapsi) across the mitochondrial inner membrane (MIM) is required to sustain most mitochondrial functions including ATP generation, MIM fusion, and calcium uptake and release. Here, we present a microscopy approach for automated quantification of Deltapsi and mitochondrial position, shape and calcium handling in individual living cells. In the base protocol, cells are stained with tetramethyl rhodamine methyl ester (TMRM), a fluorescent cation that accumulates in the mitochondrial matrix according to Deltapsi, and visualized using video-microscopy. Next, the acquired images are processed to generate a mitochondria-specific binary image (mask) allowing simultaneous quantification of mitochondrial TMRM fluorescence intensity, shape and position. In a more advanced version of this protocol a mitochondria-targeted variant of green fluorescent protein (mitoAcGFP1) is expressed to allow mask making in TMRM-stained cells. The latter approach allows quantification of Deltapsi in cells with a substantially depolarized Deltapsi. For automated quantification of mitochondrial calcium handling in space and time mitoAcGFP1-expressing cells are stained with rhod-2, a fluorescent calcium indicator that accumulates in the mitochondrial matrix. In this paper, a detailed step-by-step description of the above approaches and its pitfalls is provided.
 
Article
Stable isotope mass spectrometry has become a widespread tool in quantitative biology. Pulse-chase monitored by quantitative mass spectrometry (PC/QMS) is a recently developed stable isotope approach that provides a powerful means of studying the in vitro self-assembly kinetics of macromolecular complexes. This method has been applied to the Escherichia coli 30S ribosomal subunit, but could be applied to any stable self-assembling complex that can be reconstituted from its component parts and purified from a mixture of components and complex. The binding rates of 18 out of the 20 ribosomal proteins have been measured at several temperatures using PC/QMS. Here, PC/QMS experiments on 30S ribosomal subunit assembly are described, and the potential application of the method to other complexes is discussed. A variation on the PC/QMS experiment is introduced that enables measurement of kinetic cooperativity between proteins. In addition, several related approaches to stable isotope labeling and quantitative mass spectrometry data analysis are compared and contrasted.
 
Top-cited authors
Johannes Schindelin
Sebastian Bednarek
  • University of Wisconsin–Madison
Emmanuel Laplantine
  • Institut Pasteur
Gregory D Reynolds
  • University of Wisconsin–Madison
Kevin Eliceiri
  • University of Wisconsin–Madison