Two polypeptide changes associated with butyric acid resistance and the neoplastic state of Syrian hamster cells.

Seven differences in the polypeptide species of parental Syrian hamster embryo cells and cells of the highly tumorigenic derivative cell line BP6T were identified previously by employing the technique of two-dimensional polyacrylamide gel electrophoresis (Leavitt, J. and Moyzis, R. (1978) J. Biol. Chem. 253, 2497-2500). To determine which of these polypeptide changes are correlated with expression of the neoplastic state this work was extended to the comparative examination of nine established neoplastic cell lines which resulted from independent transformation events catalyzed by chemical carcinogen treatment, virus infection, or an unknown spontaneous event. Although no perfect correlation with a specific polypeptide change was found, two polypeptide changes, occurring independently or simultaneously, appear to be consistently associated with expression of neoplasticity. One polypeptide species, designated tau, having an isoelectric point of 4.6 and a molecular weight of 60 000 was lost or physically altered in all but one of these transformed cell lines; a second polypeptide species designated nu having an isoelectric point 5.5 and a molecular weight of 42 000 appeared in highly tumorigenic chemically transformed cell lines and in two virally transformed cell lines. A butyric acid supplement, used as a selective agent for butyric acid resistant cells, was employed to identify and isolate in a single step nascent neoplastic clonal lines transformed by ethylmethanesulfonate. These cell lines exhibited alterations either in tau or nu. The changes observed in tau are consistent with those expected to result from a somatic mutation event in the structural gene coding for tau; however, the alterations in tau could also be governed by a post-translational process. These findings suggest that alterations in expression of at least two major polypeptide species, tau and nu, are closely associated with primary steps in the neoplastic transformation process of Syrian hamster cells irrespective of the nature of the transforming agent.     

DETECTION AND DEMONSTRATION OF INHIBITORY ACTIVITIES OF BACTERIOCINS BY ISOELECTRIC FOCUSING

A technique utilizing isoelectric focusing (IEF) was developed and compared with a modified Bhunia's sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) method for directly detecting antimicrobial activities of inhibitory peptides or proteins (bacteriocins). In IEF, the gel containing separated peptide or protein bands was directly overlaid with indicator bacteria without any fixation or rinsing as done in the SDS-PAGE method. The IEF gave clear zones of inhibition surrounding inhibitory bands. Bhunia's method was modified to reduce the time for fixation and rinsing, and a 15-min fixation followed by 2-h rinsing with dd H₂O was determined to be necessary for a detection similar to the IEF. In addition, results of this study showed that denaturation of bacteriocins and, subsequently, failure to detect the presence of a bacteriocin could occur in the SDS-PAGE analysis while little denaturation was observed in the IEF assay. Therefore, the IEF assay developed in this study was more rapid and less destructive as compared with the SDS-PAGE method.     

A simple method using β-globin polymerase chain reaction for the species identification of animal cell lines—A progress report

Continuous cell lines are widely used in cell biology and serve as model systems in basic and applied research. Fundamental requirements for the use of cell lines are a well-identified origin and the exclusion of cross-contamination by prokaryotic or eukaryotic cells. Because the cross-contamination of one cell line with another cell line may occur in a concealed manner, special emphasis must be taken to (1) prevent such an "accident" and (2) monitor regularly the identity of the cell line(s) in use. Apart from human cell lines, mouse-, rat-, and hamster-derived cell lines are used in basic cell culture and biotechnology. We established a polymerase chain reaction (PCR) assay to detect and confirm the species origin for these species and to detect interspecies cross-contamination. Our PCR method is based on oligonucleotide primers annealing to specific sequences in the beta-globin gene, which were designed to amplify one deoxyribonucleic acid (DNA) segment only per analyzed sample. We confirmed the species identity of 82 cell lines as human, mouse, rat, and Syrian hamster by beta-globin PCR. The DNAs from eight additional cell lines of less frequently used species were not amplified with the primers chosen. Cross-contamination of 5-10% of either mouse or rat DNA was detectable. One species-specific primer pair was sufficient for confirmation of the expected species, and for identification of an unknown cell line the combination of two or more primer pairs is suggested. Our PCR assay represents a powerful, fast, easy, robust, and inexpensive method for speciation and does not need any elaborate sequencing or computer-based analysis system.     

The polymorphism of the vitamin D-binding protein (Gc); Isoelectric focusing in 3 M urea as additional method for identification of genetic variants

Since the last report numerous new DBP (Gc) variants have been observed; at present a total of 84 different mutants can be distinguished. Several of them have similar electrophoretic mobilities and/or isoelectric points of conventional isoelectric focusing (IEF). IEF in polyacrylamide gels in the presence of 3 M urea is a convenient and efficient method for the detection of hidden variation.     

A proteomics approach to identifying fish cell lines

Fish cell lines are relatively easy to culture and most have simple growth requirements that make cross contamination a potential problem. Cell line contamination is not an uncommon incident in laboratories handling more than one cell line and many reports have been made on cross contamination of mammalian cell lines. Although problems of misidentification and cross-contamination of fish cell lines have rarely been reported, these are issues of concern for cell culturists that can make scientific results and their reproducibility unreliable. Proper identification of cell lines is thus crucial and protocols for routine and rapid screening are preferred. Cytogenetic evaluation, DNA fingerprinting, microsatellite analysis and PCR methods have been published for inter-species identification of many cell lines, but discerning intra-species contamination has been challenging. More complex DNA fingerprinting and hybridization techniques coupled with isoenzyme analysis have been developed to discriminate intra-species contamination, however, these require complex and time consuming procedures to enable cell identification thus are difficult to apply for routine use. A simple proteomic approach has been made to identify several fish cell lines derived from tissues of the same or differing species. Protein expression signatures (PES) of the evaluated fish cell lines have been developed using 2-DE and image analysis. A higher degree of concordance was seen among cell lines derived from rainbow trout, than from other fish species. Similar concordance was seen in cells derived from the same tissues than from other tissues within the same species. These profiles have been saved in an electronic databank and could be made available to be used for discerning the origins of the various cell lines evaluated. This proteomic approach could thus serve as an additional, valuable and reliable technique for the identification of fish cell lines.     

On the possibility of applying noncovalent dyes for protein labeling in isoelectric focusing

Noncovalent fluorescent dyes are widely used for protein quantification and postcolumn detection in electrophoretic separations and recently some attempts to separate the precolumn labeled proteins using isoelectric focusing (IEF) have been made. In the present study, the possibility of applying the technique of protein labeling with noncovalent dyes for IEF is investigated. We found that fluorescent signal emitted by NanoOrange dye increases essentially in presence of carrier ampholyte (CA) components, which makes problematic a reliable protein detection in CA environment. Since in an isoelectric focusing mode the CA species are present in much greater concentration than the concentrations of fractionated proteins, the method of protein labeling with NanoOrange is not suitable for precolumn labeling and cannot be used for CA-IEF, at least without more detailed study of the dye-protein interaction mechanism.     

Apolipoprotein E genotyping using the polymerase chain reaction and allele-specific oligonucleotide primers

A method for apolipoprotein (apo) E genotyping was developed using the polymerase chain reaction (PCR) with allele-specific oligonucleotide primers (ASP). Synthetic oligonucleotides with base-pair mismatches at the 3' terminus were used as primers to amplify the apoE gene in subjects previously phenotyped using isoelectric focusing (IEF). Complementary primer-allele combinations were specifically amplified by PCR, together with a control pair of primers specific to the human prothrombin gene. Identification of genotype by PCR using ASP was consistent with the phenotypes that were determined by IEF for 14 healthy normolipidemic subjects. These results were achieved using DNA isolated from buccal epithelial cells obtained from a mouthwash or DNA extracted from leukocytes. Genotype identification required analysis of the PCR products on an ethidium-stained agarose gel, yielding results 3 h after DNA extraction. In comparison with other current methods, PCR using ASP is suggested as a rapid and simple noninvasive technique for determining population apoE allelic distribution.     

A procedure for the immunoblotting of proteins separated on isoelectric focusing gels

A method has been devised for performing Western blot assays on proteins resolved by isoelectric focusing. Electrophoretic transfer of proteins directly from isoelectric focusing (IEF) tube gels to nitrocellulose sheets allowed their immunoassay without conventional second dimension SDS gel electrophoresis. The same method can also be used for IEF slab gels. For the immunostaining of nonmuscle actin isoforms in extracts of cultured cells, the resolution of this technique was much improved over that of Western blots of two-dimensional gels.     

Rapid detection of mycoplasma contamination in cell cultures using sybr green-based real-time polymerase chain reaction

Summary We have developed a simple method for rapid detection of mycoplasma contamination in cell cultures using SYBR Green-based real-time polymerase chain reaction (PCR). To detect eight common contaminant mollicutes, including Mycoplasma (M. arginini, M. fermentans, M. orale, M. hyorhinis, M. hominis, M. salivarium, M. pirum) and Acholeplasma laidlawii, four primers were prepared based on the 23S rRNA regions. Using these primers and a minimum of 100 fg of mycoplasma genomic DNA, the 23S rRNA regions of these eight mycoplasma species were consistently amplified by real-time PCR. In contrast, no specific specific amplification product was observed using DNA templates prepared from various mammalian cell lines. Frozen and cultured samples of several cell lines were tested for mycoplasma contamination to evaluated the utility of this method. Of 25 samples that tested positive for mycoplasma by Hoechst staining, which requires two passages of cell cultures started from frozen samples, mycoplasma was detected by real-time PCR in 24 samples of cell extracts prepared directly from frozen samples. When cultured samples were used for this assay, the accuracy of the diagnoses was further improved. Thus, this technique, which is simple, rapid, and sensitive enough for practical application, in suitable for handling many samples and for routine screening for mycoplasma contamination of cell cultures.     

Short tandem repeat profiling: part of an overall strategy for reducing the frequency of cell misidentification

The role of cell authentication in biomedical science has received considerable attention, especially within the past decade. This quality control attribute is now beginning to be given the emphasis it deserves by granting agencies and by scientific journals. Short tandem repeat (STR) profiling, one of a few DNA profiling technologies now available, is being proposed for routine identification (authentication) of human cell lines, stem cells, and tissues. The advantage of this technique over methods such as isoenzyme analysis, karyotyping, human leukocyte antigen typing, etc., is that STR profiling can establish identity to the individual level, provided that the appropriate number and types of loci are evaluated. To best employ this technology, a standardized protocol and a data-driven, quality-controlled, and publically searchable database will be necessary. This public STR database (currently under development) will enable investigators to rapidly authenticate human-based cultures to the individual from whom the cells were sourced. Use of similar approaches for non-human animal cells will require developing other suitable loci sets. While implementing STR analysis on a more routine basis should significantly reduce the frequency of cell misidentification, additional technologies may be needed as part of an overall authentication paradigm. For instance, isoenzyme analysis, PCR-based DNA amplification, and sequence-based barcoding methods enable rapid confirmation of a cell line’s species of origin while screening against cross-contaminations, especially when the cells present are not recognized by the species-specific STR method. Karyotyping may also be needed as a supporting tool during establishment of an STR database. Finally, good cell culture practices must always remain a major component of any effort to reduce the frequency of cell misidentification.     

Separation of bacterial cells by isoelectric focusing, a new method for analysis of complex microbial communities.

A simple isoelectric focusing (IEF) method for whole bacterial cells was developed. In a pH gradient of 2 to 10 and an electric field of 11.5 V cm-1, mixtures of cells from the three different bacterial strains Chlorobium limicola 6230, Pseudomonas stutzeri DSM 50227, and Micrococcus luteus DSM 20030 could be separated. A density gradient of Ficoll prevented convective currents in the system. The method was tested with a concentrated mixture of bacteria from a shallow eutrophic lake and yielded up to 10 different bands. Species composition in each IEF band was analyzed by PCR plus denaturing gradient gel electrophoresis (DGGE). Each IEF band exhibited a different species composition. After the separation of cells by IEF three times more 16S ribosomal DNA signals could be detected by DGGE than in the unfractionated natural bacterial community. It is concluded that the resolution of these molecular biological methods is significantly enhanced if cells are first separated by IEF. At the same time, the IEF fractions are enriched for certain species, which can be used in subsequent cultivation experiments.     

Genetic analysis of Triticeae shikimate dehydrogenase

Starch gel electrophoresis and polyacrylamide gel isoelectric focusing (IEF) were used to investigate the genetic control of Triticeae shikimate dehydrogenase-1 (SKDH-1). Studies of wheat-alien species chromosome addition lines established thatSkdh-1 ofHordeum vulgare cv. Betzes is located in chromosome 5H,Skdh-V1 ofDasypyrum villosum in 5V,Skdh-R1 ofSecale cereale cvs. Dakold and King II in 5R, andSkdh-S ¹1 ofTriticum longissimum in 5S¹S. Also, the chromosomal locations of the genes that encode SKDH-1 inT. aestivum cv. Chinese Spring,T. umbellulatum, andS. cereale cv. Imperial, determined earlier using zone electrophoresis, were reconfirmed using IEF. Zone electrophoresis and IEF do not differ markedly in their ability to detect the expression of alienSkdh-1 genes in wheat-alien species chromosome addition lines. However, IEF may be superior to zone electrophoresis as a technique for detecting and analyzing SKDH-1 genetic variants within Triticeae species; among the species studied, IEF generally resolved two or more isozymes perSkdh-1 allele present, while zone electrophoresis resolved only one.Technical article No. 22791 of the Texas Agricultural Experiment Station. This paper is based upon research supported in part by the U.S. Department of Agriculture under Agreement No. 83-CRCR-1-1322.     

An analysis of class I antigens of man and other species by one-dimensional IEF and immunoblotting

A procedure for the molecular identification of MHC class I products based on 1-D IEF and subsequent immunoblotting is described. Optimal conditions for 1-D IEF, the electrophoretic transfer of proteins out of denaturing, nonionic detergent-containing gels to nitrocellulose, and the requisite antibodies, both polyclonal and monoclonal, for the visualization of class I heavy chains have been established. Cross-reactivity of antibodies has enabled the biochemical analysis of class I heavy chains in the dog. The procedure reported here requires modest amounts of cells and allows a rapid molecular characterization of class I heavy chain polymorphisms in man and other species without the need for radiochemical methods.Abbreviations used in this paper FCS fetal calf serum - MHC major histocompatibility complex - NP-40 Nonidet P-40 - PBL peripheral blood lymphocytes - PHA phytohemagglutinin - RaHC rabbit anti-heavy chain serum - TX-114 Triton X-114 - 1-D IEF one-dimensional isoelectric focusing     

Rapid detection of low‐level HeLa cell contamination in cell culture using nested PCR

HeLa cells are a commonly used cell line in many biological research areas. They are not picky for culture medium and proliferate rapidly. HeLa cells are a notorious source of cell cross‐contamination and have been found to be able to contaminate a wide range of cell lines in cell culture. In this study, we reported a simple and efficient method for detecting the presence of HeLa cell contamination in cell culture. HPV‐18 was used as a biomarker. The cell culture supernatant was used directly as the template for nested PCR without extracting nucleic acid. By PCR amplification of the cell culture supernatant with the designed primers, we were able to detect the presence of HeLa cells in the culture. The sensitivity of this method can reach 1%, which is 10‐fold higher than Short tandem repeat sequence (STR) profiling. This simple, rapid, and “noninvasive” quality checking method should find applications in routine cell culture practice.     

Applications of MALDI-TOF mass spectrometry in clinical diagnostic microbiology

Until recently, microbial identification in clinical diagnostic laboratories has mainly relied on conventional phenotypic and gene sequencing identification techniques. The development of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) devices has revolutionized the routine identification of microorganisms in clinical microbiology laboratories by introducing an easy, rapid, high throughput, low-cost, and efficient identification technique. This technology has been adapted to the constraint of clinical diagnostic laboratories and has the potential to replace and/or complement conventional identification techniques for both bacterial and fungal strains. Using standardized procedures, the resolution of MALDI-TOF MS allows accurate identification at the species level of most Gram-positive and Gram-negative bacterial strains with the exception of a few difficult strains that require more attention and further development of the method. Similarly, the routine identification by MALDI-TOF MS of yeast isolates is reliable and much quicker than conventional techniques. Recent studies have shown that MALDI-TOF MS has also the potential to accurately identify filamentous fungi and dermatophytes, providing that specific standardized procedures are established for these microorganisms. Moreover, MALDI-TOF MS has been used successfully for microbial typing and identification at the subspecies level, demonstrating that this technology is a potential efficient tool for epidemiological studies and for taxonomical classification.     

High-sensitivity isoelectric focusing of biotinylated peptides: a new method

A novel technique to selectively analyze prelabeled peptides by isoelectric focusing (IEF) is presented. The conditions are described for biotinylation of peptides, their separation in polyacrylamide gels by IEF, and their fixation to the gel matrix with glutaraldehyde. The gels are developed by a color reaction catalyzed by an avidin-coupled enzyme. The technique is suitable for peptides with at least one free amino group or guanidino group after N-terminal biotinylation. The presence of other peptides or proteins does not interfere with the detection. The sensitivity is below 10 pmol, representing a 1000-fold improvement over existing techniques for analyzing low molecular weight peptides by IEF.     

One and two dimensional isoelectric focusing of lactate dehydrogenase from the tissues of Ovis aries

• 1.1. Lactate dehydrogenase in ovine tissues was separated by electrophoresis, one dimensional isoelectric focusing (IEF) and a two dimensional technique.
• 2.2. Tissues showed five zones of enzyme activity consisting of multiple bands after IEF.
• 3.3. The IEF zymograms were unique for each tissue and differed from those of other species.
• 4.4. Two dimensional separation revealed that the five zones of activity observed on IEF corresponded to the five isoenzymes separable by conventional electrophoresis.

     

State-of-the-art two-dimensional gel electrophoresis: a key tool of proteomics research

Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) is the most popular and versatile method of protein separation among a rapidly growing array of proteomics technologies. Based on two distinct procedures, it combines isoelectric focusing (IEF), which separates proteins according to their isoelectric point (pI), and SDS-PAGE, which separates them further according to their molecular mass. At present, 2D-PAGE is capable of simultaneously detecting and quantifying up to several thousand protein spots in the same gel image. Here we provide comprehensive step-by-step instructions for the application of a standardized 2D-PAGE protocol to a sample of human plasma or cerebrospinal fluid (CSF). The method can be easily adapted to any type of sample. This four-day protocol provides detailed information on how to apply complex biological fluids to an immobilized dry strip gel, cast home-made gradient acrylamide gels, run the gels, and perform standard staining methods. A troubleshooting guide is also included.     

Isoelectric focusing and crossed immunoelectrophoresis of heme proteins in the Escherichia coli cytoplasmic membrane.

Isoelectric focusing (IEF), agarose electrophoresis, and crossed immunoelectrophoresis (CIE) were used to resolve the heme-containing proteins of the Escherichia coli cytoplasmic membrane after solubilization by Triton X-100. Two bands in IEF stained for heme with pI values of 4.7 and 5.3. One of the bands, with an isoelectric point of pH 5.3, was present only when the cells were grown to late log or stationary phase and possessed N,N,N,'N'-tetramethyl-p-phenylene-diamine (TMPD) oxidase activity. The pI 4.7 band was present in cells harvested in both mid-log and stationary phases. Agarose electrophoresis, using larger samples, revealed the same two components apparent by IEF, and, in addition, a third component. The heme-containing fractions were extracted after agarose electrophoresis and subjected to further study. The component which was present in cells grown to stationary phase contained hemes b, a1, and d. The other two fractions contained only b heme. One of these corresponded to the component with pI 4.7 in IEF and had catalase activity. Antisera were raised against Triton X-100-solubilized cytoplasmic membranes and against the focused TMPD oxidase complex. With these anti-sera, CIE in the presence of Triton X-100 revealed four precipitin complexes containing heme. Three of these corresponded to the components identified by IEF and agarose electrophoresis. We demonstrate that the combined use of IEF and CIE is valuable for analysis of membrane proteins. In particular, this work represents a substantial initial step toward a structural elucidation of the E. coli aerobic respiratory chain.     

Levels of synthesis of primate-specific nuclear proteins differ between growth-arrested and proliferating cells

A monoclonal antibody that reacts specifically with the proliferation-sensitive nuclear proteins, isoelectric focusing (IEF) 8Z30 and 8Z31 (molecular weight (MW), 76,000 charge variants, HeLa protein catalogue number) has been characterized. As determined by indirect immunofluorescence, the antibody stains the nucleolus and nucleoplasm of interphase-cultured cells of primate origin, but does not react with cells of other species. Proteins having similar MWs and isoelectric points as the human or monkey (primates) proteins were not observed in cultured cells of the following species: aves, bat, dog, dolphin, goat, hamster, mink, mouse, pisces, potoroo, rabbit and rat. Quantitative two-dimensional (2D) gel electrophoretic analysis of [35S]methionine-labeled proteins synthesized by normal (quiescent, proliferating) and SV40-transformed human MRC-5 fibroblasts revealed significant differences in the levels of synthesis of both IEF 8Z30 and 8Z31. In quiescent cells the main labelled product corresponded to IEF 8Z31 (ratio IEF 8Z31/8Z30, 2.3), while in the transformed cells the major product was IEF 8Z30 (ratio, 0.62). Normal proliferating fibroblasts exhibited similar levels of both proteins (ratio, 1.21). Combined levels of synthesis of both proteins were 1.50 and 1.20 times as high in the transformed cells as in the quiescent and proliferating cells, respectively. Similar results were observed in other pairs of normal and transformed human cells, such as WI38/WI38 SV40 and amnion/AMA. Modulation of the levels of synthesis of these proteins may play a role in cell proliferation.