Combining immunofluorescence with in situ proximity ligation assay: a novel imaging approach to monitor protein–protein interactions in relation to subcellular localization

The in situ Proximity Ligation Assay (PLA) is suited for visualizing protein–protein interactions and post-translational protein modifications in both tissue sections and in vitro cell cultures. Accurate identification and quantification of protein–protein interactions are critical for in vitro cell analysis, especially when studying the dynamic involvement of proteins in various processes, including cell proliferation, differentiation, and apoptosis. Here, we monitored the interactions between protein kinase-Cζ (PKCζ) and Bcl10 protein in untreated and etoposide (VP-16)-treated C4-I cells by means of a new combined morphological approach and validated it by taking stock of our previous proteomic and biochemical work (Chiarini et al. in J Proteome Res 11:3996–4012, 2012). We first analyzed the colocalization of PKCζ and Bcl10 proteins through classical immunofluorescent colocalization analysis. On the basis of these results, we developed a novel imaging approach combining immunofluorescence (IF) techniques with in situ PLA to identify the PKCζ·Bcl10 complexes at the level of a specific subcellular compartment, i.e., the nuclear envelope (NE). By this means, we could show that the amount of PKCζ·Bcl10 complexes localized at the NE of C4-I cells during proliferation or after treatment with VP-16 closely corresponded to our previous purely biochemical results. Hence, the present findings demonstrate that the combination of in situ PLA with classical IF detection is a novel powerful analytical tool allowing to morphologically demonstrate new specific protein–protein interactions at level of subcellular organelles, the complexes functions of which can next be clarified through proteomic/biochemical approaches.     

Exposure to strong static magnetic field slows the growth of human cancer cells in vitro

Proposals to enhance the amount of radiation dose delivered to small tumors with radioimmunotherapy by constraining emitted electrons with very strong homogeneous static magnetic fields has renewed interest in the cellular effects of prolonged exposures to such fields. Past investigations have not studied the effects on tumor cell growth of lengthy exposures to very high magnetic fields. Three malignant human cell lines, HTB 63 (melanoma), HTB 77 IP3 (ovarian carcinoma), and CCL 86 (lymphoma; Raji cells), were exposed to a 7 Tesla uniform static magnetic field for 64 hours. Following exposure, the number of viable cells in each group was determined. In addition, multicycle flow cytometry was performed on all cell lines, and pulsed-field electrophoresis was performed solely on Raji cells to investigate changes in cell cycle patterns and the possibility of DNA fragmentation induced by the magnetic field. A 64 h exposure to the magnetic field produced a reduction in viable cell number in each of the three cell lines. Reductions of 19.04 ± 7.32%, 22.06 ± 6.19%, and 40.68 ± 8.31% were measured for the melanoma, ovarian carcinoma, and lymphoma cell lines, respectively, vs. control groups not exposed to the magnetic field. Multicycle flow cytometry revealed that the cell cycle was largely unaltered. Pulsed-field electrophoresis analysis revealed no increase in DNA breaks related to magnetic field exposure. In conclusion, prolonged exposure to a very strong magnetic field appeared to inhibit the growth of three human tumor cell lines in vitro. The mechanism underlying this effect has not, as yet, been identified, although alteration of cell growth cycle and gross fragmentation of DNA have been excluded as possible contributory factors. Future investigations of this phenomenon may have a significant impact on the future understanding and treatment of cancer. © 1996 Wiley-Liss, Inc.     

A human source for ELF magnetic perturbations

ABSTRACT

Current models that frame consciousness in terms of electromagnetic field theory carry implications that have yet to be fully explored. Endogenous weak extremely low frequency (ELF) magnetic fields are generated by ionic charge flow in axons, dendrites and synaptic transmitters. Because neural tissues are transparent to such fields, these provide the basis for the globally unifying qualities required to properly describe consciousness as a field. At the same time, however, an electromagnetic approach predicts partial transmission of this 1–100 nT field, suggesting external interactions similar to the various ELF magnetic perturbations that are linked to homeostatic and endocrine-related physiological effects. It follows that humans may represent an additional, previously unrecognized source of weak (1–10 nT) ambient ELF magnetic fields.     

Biochemical approaches for discovering protein-protein interactions

Protein–protein interactions or protein complexes are integral in nearly all cellular processes, ranging from metabolism to structure. Elucidating both individual protein associations and complex protein interaction networks, while challenging, is an essential goal of functional genomics. For example, discovering interacting partners for a 'protein of unknown function' can provide insight into actual function far beyond what is possible with sequence-based predictions, and provide a platform for future research. Synthetic genetic approaches such as two-hybrid screening often reveal a perplexing array of potential interacting partners for any given target protein. It is now known, however, that this type of anonymous screening approach can yield high levels of false-positive results, and therefore putative interactors must be confirmed by independent methods. In vitro biochemical strategies for identifying interacting proteins are varied and time-honored, some being as old as the field of protein chemistry itself. Herein we discuss five biochemical approaches for isolating and characterizing protein–protein interactions in vitro : co-immunoprecipitation, blue native gel electrophoresis, in vitro binding assays, protein cross-linking, and rate-zonal centrifugation. A perspective is provided for each method, and where appropriate specific, trial-tested methods are included.     

In situ immunoassays for gene translation products in phage plaques and bacterial colonies

A series of simple, in situ immunoassays have been developed which can be used in screening for translation products of genes cloned in vitro recombination experiments with either phage or plasmid vectors. Antigen-antibody complex formation occurring within a vector-phage plaque can be used to detect the production of a specific protein from an amplified gene. Immunoassays of colonies lysed in situ either by λ prophage induction or by biochemical means afford a much higher level of sensitivity than the plaque assay probably adequate to detect the production of a few molecules of protein per cell.     

Carbohydrates as recognition determinants in phagocytosis and in lectin-mediated killing of target cells

Carbohydrate-lectin interactions serve as the basis of recognition by phagocytic cells of particles and of various target cells. Such interactions occur in the following systems: between sugars on the surface of the phagocytic cells and lectins on the surface of other cells—the best studied example is the binding of mannose-specific Escherichia coli and related organisms via their surface lectins to oligo-mannose residues on macrophages; between lectins on the surface of phagocytic cells and sugars on particles or other cells—phagocytosis of zymosan and of sialidase-treated erythrocytes, mediated respectively by mannose-specific and galactose-specific lectins on macrophages, belongs to this category; by extracellular lectins that form bridges between sugars on both types of cell—as shown by enhancement of phagocytosis of staphylococci by wheat germ agglutinin, and by lectin-dependent killing of target cells by macrophages. These interactions may play an important role in the activities of phagocytic cells in vivo. They may provide an initial host defense mechanism immediately after microbial infection, operate in tissues where phagocytic activity is poor, and participate in tumor rejection.     

Myosin Light Chain Modification Depending on Magnetic Fields: II. Experimental

Recent experiments have revealed that Ca²⁺ -calmodulin dependent myosin light chain phosphorylation in a cell-free preparation exhibits unexpectedly high sensitivity to weak magnetic fields. This enzyme system is a well-studied biochemical system, which appears to depend upon ion binding. A previous article in this journal discussed the theoretical background of myosin phosphorylation and the ion-dependent interactions of EMF with soft tissues. Because of the electromagnetic field (EMF) sensitivity of this cell-free system, experiments were designed to test the effect of a pulsed radio frequency (PRF) field, pulsating magnetic fields (TEMF), gradient magnetic fields (Magnabloc), and homogeneous static magnetic fields (in Helmholtz arrangement) designed for clinical application. It is concluded that these various magnetic fields affect this cell-free enzyme system by modulating ion–protein interactions.     

Creation of arrays of cell aggregates in defined patterns for developmental biology studies using dielectrophoresis

It is shown that dielectrophoresis—the movement of particles in non‐uniform electric fields—can be used to create engineered skin with artificial placodes of different sizes and shapes, in different spatial patterns. Modeling of the electric field distribution and image analysis of the cell aggregates produced showed that the aggregation is highly predictable. The cells in the aggregates remain viable, and reorganization and compaction of the cells in the aggregates occurs when the artificial skin is subsequently cultured. The system developed could be of considerable use for the in vitro study of developmental processes where local variations in cell density and direct cell–cell contacts are important. Biotechnol. Bioeng. 2010;105: 945–954. © 2009 Wiley Periodicals, Inc.     

In vitro systems in pneumocystis research

Most groups involved in Pneumocystis research need large quantities of well preserved, viable Pneumocystis organisms free of host cell contamination. Biological, biochemical, immunological, genetic or other studies on Pneumocystis usually involve the separation of Pneumocystis from lung tissue as well as elimination of host cell debris from parasite extracts. In other investigations, such as transmission, infectivity, life cycle, biochemical, in vitro culture or drug-screening studies, viable and infectious Pneumocystis organisms are urgently required. However, there is no generally accepted methodology for obtaining Pneumocystis from experimental hosts or from human clinical samples; methods are still far from reaching standardization, as discussed here by the members of the European Concerted Action (ECA) on Pneumocystis carinii, which is co-ordinated by Eduardo Dei-Cas and Jean-Charles Cailliez.     

蛋白激酶的生化活性检测方法研究进展

蛋白激酶在真核细胞信号转导中起重要作用,影响了生长、发育、迁移以及凋亡等各个细胞过程。其表达水平或活性异常时,就有可能导致癌症、心血管疾病以及其他各种疾病,因此蛋白激酶是治疗这些疾病很好的分子靶点。迄今为止,美国食品药品监督管理局已经批准了28个蛋白激酶的抑制剂作为上市药物,用于相应的临床治疗。目前存在着各种检测激酶活性的方法,激酶生化检测方法尤为众多,比较经典的有放射性同位素的方法,也有一些非均相非放射性同位素的方法,诸如酶联免疫法、反相高效液相色谱法、核磁共振分析法等等。而各种均相非放射性同位素的检测方法,由于其污染小、操作便捷,逐渐成为激酶抑制剂筛选的首选。本文综述了各种激酶生化检测方法及其发展历史,并介绍了一些新的趋势,如激酶酶谱筛选。     

The use of functionalized nanoparticles to treat Staphylococcus aureus-based surgical-site infections: a systematic review

Staphylococcus aureus-based surgical site infections have become the leading cause of failure for total joint arthroplasty operations and remain a major issue across surgical specialties. Moreover, S. aureus-based infections are becoming drastically more difficult to treat due to the development of antibiotic resistant strains and due to the bacteria's propensity to produce biofilms. The emergence of highly resistant S. aureus infections has created the need for a novel antimicrobial treatment. Functionalized nanoparticles have recently been suggested as being a viable option to fill this void due to their strong antimicrobial and antibiofilm properties. However, said research remains a novel and developing field. The presented systematic review aimed to synthesize the best and most recent evidence available to accurately direct new research towards a viable treatment mechanism. In doing so, the authors performed a comprehensive literature search as directed by the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The results showed that nanoparticles—particularly those including an iron-oxide component or acidic capping agent—are a viable treatment for S. aureus infections both in vivo and in vitro, and show even greater efficacy when combined with exposure to a magnetic field and irradiation.     

Advances in somatic cell genetics of higher plants — the protoplast approach in basic studies on mutagenesis and isolation of biochemical mutants

Summary Selection strategies developed in microbial genetics were successfully extrapolated to in vitro cell culture systems of higher plants and are having a major impact in the elucidation of regulatory mechanisms of basic cellular processes in eukaryotes. Although an increasing number and wide spectrum of biochemical variants have been isolated in such cell culture systems, their routine selection, characterization, and manipulation have not yet been achieved. Methodological limitations are considered to be one of the major reasons. Suspension or callus cultures, so extensively employed during the last decade in mutation-selection experiments and so useful in demonstrating the potentialities of in vitro screening techniques in obtaining various biochemical markers, have inherent drawbacks which limit in our opinion their further contribution in this field. Protoplast cultures represent an ideal tool for mutation and selection experiments. It is the purpose of this review to show how, due to recent methodological advances in the manipulation of some model protoplast culture systems, essential aspects of mutagenesis and selection of biochemical mutants can be reconsidered. These systems are simple and efficient, and lend themselves to statistical interpretation. Genetic analysis of selected variants should help us to understand and define better the new set of problems and concepts revealed by the somatic cell genetics of higher plants; combined with biochemical analyses it should elucidate the basic relationship between control of biological processes at cellular and whole organism level.     

A Novel Approach for In Vitro Studies Applying Electrical Fields to Cell Cultures by Transformer-Like Coupling

The purpose of this study was to develop a new apparatus for in vitro studies applying low frequency electrical fields to cells without interfering side effects like biochemical reactions or magnetic fields which occur in currently available systems. We developed a non-invasive method by means of the principle of transformer-like coupling where the magnetic field is concentrated in a toroid and, therefore, does not affect the cell culture. Next to an extensive characterization of the electrical field parameters, initial cell culture studies have focused on examining the response of bone marrow-derived human mesenchymal stem cells (MSCs) to pulsed electrical fields. While no significant differences in the proliferation of human MSCs could be detected, significant increases in ALP activity as well as in gene expression of other osteogenic markers were observed. The results indicate that transformer-like coupled electrical fields can be used to influence osteogenic differentiation of human MSCs in vitro and can pose a useful tool in understanding the influence of electrical fields on the cellular and molecular level.     

Nanopore sensing of γ-cyclodextrin induced host-guest interaction to reverse the binding of perfluorooctanoic acid to human serum albumin

Perfluorooctanoic acid (PFOA) has been one of the most common perfluorochemicals, which are globally pervasive contaminants that are persistent, bioaccumulative, toxic, and have adverse impacts on human health. The highest concentration of PFOA occurs in the blood, where it strongly binds to human serum albumins (HSA). Thus, a method to reverse the HSA-PFOA binding is critical to help facilitate the faster elimination of PFOA from the body to minimize its toxicological effects. Inspired by the remediation effect of cyclodextrin (CD) to PFOA through host-guest interactions, herein, by elucidating inter-molecular interactions using a nanopore sensor, we demonstrated in vitro reversal of the binding of PFOA to HSA using γ-cyclodextrin (γ-CD). The competition behavior for the complexation of PFOA between HSA and γ-CD was discussed in combination with in situ nanopore current recording and nuclear magnetic resonance (NMR) characterization. The present work not only demonstrates the potential therapeutic application of γ-CD for PFOA removal from human blood, but also provides an emerging method for investigating interactions between organic compounds and proteins.     

Mechanobiology of the relocation of proteins in advecting cells: in vitro experiments,multi-physics modeling,and simulations

Cell motility—a cellular behavior of paramount relevance in embryonic development, immunological response, metastasis, or angiogenesis—demands a mechanical deformation of the cell membrane and influences the surface motion of molecules and their biochemical interactions. In this work, we develop a fully coupled multi-physics model able to capture and predict the protein flow on endothelial advecting plasma membranes. The model has been validated against co-designed in vitro experiments. The complete picture of the receptor dynamics has been understood, and limiting factors have been identified together with the laws that regulate receptor polarization. This computational approach might be insightful in the prediction of endothelial cell behavior in different tumoral environments, circumventing the time-consuming and expensive empirical characterization of each tumor.

     

Selection of genomic target RNAs by iterative screening

A growing number of proteins are known to exert their regulatory or biological functions via RNA binding. In some cases genetic interactions allow us to infer candidate targets for RNA directed regulation, but in many other cases identification of potential regulatory targets is problematic. We have developed an in vitro biochemical screen, SETIS (SElection of Target RNAs by Iterative Screening) that allows screening of a major portion of the genome for identification of potential targets for RNA binding proteins.     

Effect of constitutively active Ras overexpression on cell growth in recombinant Chinese hamster ovary cells

Constitutively active Ras (CA-Ras) is known to enhance cell growth through the induction of various signaling cascades including the phosphoinositide 3-kinase (PI3K)/Akt and mitogen-activated protein kinase (MAPK)/ERK signaling pathways, although the cellular response is highly dependent on the cell type. To evaluate the effect of CA-Ras overexpression on cell growth in recombinant Chinese hamster ovary (rCHO) cells, an erythropoietin (EPO)-producing rCHO cell line with regulated CA-Ras overexpression (EPO-off-CA-Ras) was established using the Tet-off system. The CA-Ras expression level in EPO-off-CA-Ras cells was tightly regulated by doxycycline addition. Although CA-Ras overexpression slightly increased the viable cell concentration during the late exponential phase, it did not increase the maximum viable cell concentration or specific growth rate to a significant degree. Unexpectedly, CA-Ras overexpression in rCHO cells led only to the enhancement in the activation of the MAPK/ERK signaling pathway and not the PI3K/Akt signaling pathway. Taken together, CA-Ras overexpression in rCHO cells did not significantly affect cell growth; it also had no critical impact on viable cell concentration or EPO production, possibly due to a failure to activate the PI3K/Akt signaling pathway.     

Computer aided analysis for biosensing and screening

Biosensors with animal and microbial cells immobilized close to the tip of a membrane electrode have been developed for chemical and drug testing. Our experimental results show that biosensors can be used for drug screening and to provide useful information about various cell-chemical interactions. A computer aided analysis (CAA) software package is being developed here using the biosensor for various screening purposes. This software package enables us to use a computer to analyze the biosensor dynamic responses. Computer simulation and parameter estimation techniques are used to select the best model and to describe the biochemical and pharmacologic effects of various chemicals and drugs on different cell lines.     

Tubular Bridges for Bronchial Epithelial Cell Migration and Communication

Background

Biological processes from embryogenesis to tumorigenesis rely on the coordinated coalescence of cells and synchronized cell-to-cell communication. Intercellular signaling enables cell masses to communicate through endocrine pathways at a distance or by direct contact over shorter dimensions. Cellular bridges, the longest direct connections between cells, facilitate transfer of cellular signals and components over hundreds of microns in vitro and in vivo.

Methodology/Principal Findings

Using various cellular imaging techniques on human tissue cultures, we identified two types of tubular, bronchial epithelial (EP) connections, up to a millimeter in length, designated EP bridges. Structurally distinct from other cellular connections, the first type of EP bridge may mediate transport of cellular material between cells, while the second type of EP bridge is functionally distinct from all other cellular connections by mediating migration of epithelial cells between EP masses. Morphological and biochemical interactions with other cell types differentially regulated the nuclear factor-κB and cyclooxygenase inflammatory pathways, resulting in increased levels of inflammatory molecules that impeded EP bridge formation. Pharmacologic inhibition of these inflammatory pathways caused increased morphological and mobility changes stimulating the biogenesis of EP bridges, in part through the upregulation of reactive oxygen species pathways.

Conclusions/Significance

EP bridge formation appears to be a normal response of EP physiology in vitro, which is differentially inhibited by inflammatory cellular pathways depending upon the morphological and biochemical interactions between EP cells and other cell types. These tubular EP conduits may represent an ultra long-range form of direct intercellular communication and a completely new mechanism of tissue-mediated cell migration.     

Influence of near null magnetic field on in vitro growth of potato and wild Solanum species

The influence of near null magnetic field on in vitro growth of different cultures of potato and related Solanum species was investigated for various exposure times and dates. Potato (Solanum tuberosum L. cv. Désirée) in vitro cultures of shoot tips or nodal segments were used. Three different exposure periods revealed either stimulation or inhibition of root, stem, or leaf in vitro growth after 14 or 28 days of exposure. In one experiment the significant stimulation of leaf growth was also demonstrated at biochemical level, the quantity of chlorophyll a and b and carotenoids increasing more than two-fold. For the wild species Solanum chacoense, S. microdontum, and S. verrucosum, standardized in vitro cultures of nodal stem segments were used. Root and stem growth was either stimulated or slightly inhibited after 9 days exposure to near null magnetic field. Callus cultures obtained from potato dihaploid line 120/19 were maintained in near null magnetic field in 2 different months. For these experiments as well as for Solanum verrucosum, callus cultures recorded either slight inhibition or no effect on fresh weight. For all experiments significant growth variation was brought about only when geomagnetic activity (AP index) showed variations at the beginning of in vitro growth and when the explant had at least one meristematic tissue. Moreover longer maintenance in near null magnetic field, 28 days as compared to 14 days or the controls, can also make a difference in plant growth in response to geomagnetic field variations when static component was reduced to zero value. These results of in vitro plant growth stimulation by variable component of geomagnetic field also sustain the so-called seasonal "window" effect.