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At least 235 records · Page 13Linked to original sources
PubMed1986

Transient correction of excision repair defects in fibroblasts of 9 xeroderma pigmentosum complementation groups by microinjection of crude human cell extracts.

Crude extracts from human cells were microinjected into the cytoplasm of cultured fibroblasts from 9 excision-deficient xeroderma pigmentosum (XP) complementation groups. The level of UV-induced unscheduled DNA synthesis (UDS) was measured to determine the effect of the extract on the repair capacity of the injected cells. With a sensitive UDS assay procedure a (transient) increase in UV-induced UDS level was found in fibroblasts from all complementation groups after injection of extracts from repair-proficient (HeLa) or complementing XP cells (except in the case of XP-G), but not after introduction of extracts from cells belonging to the same complementation group. This indicates that the phenotypic correction is exerted by complementation-group-specific factors in the extract, a conclusion that is in agreement with the observation that different levels of correction are found for different complementation groups. The XP-G-correcting factor was shown to be sensitive to proteolytic degradation, suggesting that it is a protein like the XP-A factor.

Cell Fusion↗
PubMed1999

Abnormal, error-prone bypass of photoproducts by xeroderma pigmentosum variant cell extracts results in extreme strand bias for the kinds of mutations induced by UV light.

Xeroderma pigmentosum (XP) is a rare genetic disease characterized by a greatly increased susceptibility to sunlight-induced skin cancer. Cells from the majority of patients are defective in nucleotide excision repair. However, cells from one set of patients, XP variants, exhibit normal repair but are abnormally slow in replicating DNA containing UV photoproducts. The frequency of UV radiation-induced mutations in the XP variant cells is significantly higher than that in normal human cells. Furthermore, the kinds of UV-induced mutations differ very significantly from normal. Instead of transitions, mainly C-->T, 30% of the base substitutions consist of C-->A transversions, all arising from photoproducts located in one strand. Mutations involving cytosine in the other strand are almost all C-->T transitions. Forty-five percent of the substitutions involve thymine, and the majority are transversions. To test the hypothesis that the UV hypermutability and the abnormal spectrum of mutations result from abnormal bypass of photoproducts in DNA, we compared extracts from XP variant cells with those from HeLa cells and a fibroblast cell strain, MSU-1.2, for the ability to replicate a UV-irradiated form I M13 phage. The M13 template contains a simian virus 40 origin of replication located directly to the left or to the right of the target gene, lacZalpha, so that the template for the leading and lagging strands of DNA replication is defined. Reduction of replication to approximately 37% of the control value required only 1 photoproduct per template for XP variant cell extracts, but approximately 2.2 photoproducts for HeLa or MSU-1.2 cell extracts. The frequency of mutants induced was four times higher with XP variant cell extracts than with HeLa or MSU-1.2 cell extracts. With XP variant cell extracts, the proportion of C-->A transversions reached as high as 43% with either M13 template and arose from photoproducts located in the template for leading-strand synthesis; with HeLa or MSU-1.2 cell extracts, this value was only 5%, and these arose from photoproducts in either strand. With the XP variant extracts, 26% of the substitutions involved thymine, and virtually all were T-->A transversions. Sequence analysis of the coding region of the catalytic subunit of DNA polymerase delta in XP variant cell lines revealed two polymorphisms, but these do not account for the reduced bypass fidelity. Our data indicate that the UV hypermutability of XP variant cells results from reduced bypass fidelity and that unlike for normal cells, bypass of photoproducts involving cytosine in the template for the leading strand differs significantly from that of photoproducts in the lagging strand.

Cell Extracts↗
PubMed1990

Accurate initiation by RNA polymerase II in a whole cell extract from Saccharomyces cerevisiae.

We have developed a simple procedure for isolating a transcriptional extract from whole yeast cells which obviates the requirement for nuclear isolation. Detection of accurate mRNA initiation by RNA polymerase II in the extract requires the use of a sensitive assay, recently described by Kornberg and co-workers (Lue, N. F., Flanagan, P. M., Sugimoto, K., and Kornberg, R. D. (1989) Science 246, 661-664) that involves activation by a GAL4-VP16 fusion protein and a template lacking guanosine residues in the coding strand. The extract is prepared from fresh or frozen yeast cells by disruption with glass beads and fractionation of proteins by ammonium sulfate precipitation. The alpha-amanitin-sensitive transcripts synthesized in the assay were identical to those produced in a parallel assay using a yeast nuclear extract. The activity of the whole cell extract is lower per mg of protein than a nuclear extract but proportional to the volume of the nucleus relative to the whole cell. The optimal ranges for several reaction components including template, mono- and divalent cations, and nucleotide substrate concentration were determined. Under optimal conditions the whole cell extract produced a maximum of approximately 1 X 10(-2) transcripts/template molecule in 30 min.

Amanitins↗
PubMed2005

DNA repair fidelity of base excision repair pathways in human cell extracts.

Base excision repair (BER), responsible for the removal of altered DNA bases, is accomplished via two pathways that involve different subsets of repair enzymes and result in removal and replacement of one (short-patch BER) or several (long-patch BER) nucleotides. In this study, we constructed single-lesion containing DNA substrates that are predominantly repaired via one of the two pathways and investigated the fidelity of pathway specific repair in human whole cell extracts. We find that a single nucleotide deletion generated during addition of the first nucleotide into the repair gap is the major mutation characteristic for both pathways. This data suggest that for both BER pathways, mutations generated during repair in human whole cell extracts are principally the result of a slippage of DNA polymerase during initiation of repair synthesis.

Base Sequence↗
PubMed1999

Replication protein A stimulates proliferating cell nuclear antigen-dependent repair of abasic sites in DNA by human cell extracts.

Base excision repair (BER) pathway is the major cellular process for removal of endogenous base lesions and apurinic/apyrimidinic (AP) sites in DNA. There are two base excision repair subpathways in mammalian cells, characterized by the number of nucleotides synthesized into the excision patch. They are the "single-nucleotide" (one nucleotide incorporated) and the "long-patch" (several nucleotides incorporated) BER pathways. Proliferating cell nuclear antigen (PCNA) is known to be an essential factor in long-patch base excision repair. We have studied the role of replication protein A (RPA) in PCNA-dependent, long-patch BER of AP sites in human cell extracts. PCNA and RPA were separated from the other BER proteins by fractionation of human whole-cell extract on a phosphocellulose column. The protein fraction PC-FII (phosphocellulose fraction II), which does not contain RPA and PCNA but otherwise contains all core BER proteins required for PCNA-dependent BER (AP endonuclease, DNA polymerases delta, beta and DNA ligase, and FEN1 endonuclease), had reduced ability to repair plasmid DNA containing AP sites. Purified PCNA or RPA, when added separately, could only partially restore the PC-FII repair activity of AP sites. However, additions of both proteins together greatly stimulated AP site repair by PC-FII. These results demonstrate a role for RPA in PCNA-dependent BER of AP sites.

Base Sequence↗
PubMed1985

Site-directed cleavage of immunoglobulin gene segments by lymphoid cell extracts.

To study the enzyme(s) involved in the site-specific recombination of immunoglobulin (Ig) gene segments, we designed an assay to detect V-J joining in vitro. The DNA from a hybrid phage (lambda VJCK) containing the VK41 gene segment separated by a 6-kilobase spacer region from the entire J-CK sequence was incubated with lymphoid cell extracts and packaged in vitro. Phages carrying genomic deletions were selected by screening for ethylenediaminetetraacetic acid resistance. Although no site-specific V-J fusion events were detected, the packaging efficiency of lambda VJCK DNA was 10(2)- to 10(3)-fold lower than that of lambda DNA. This suggested the presence in the cell extracts of an endonucleolytic activity with a specificity for the mouse DNA sequences. To detect the endonuclease cleavage products, plasmids containing VK or JK gene segments were used as a DNA substrate and the products of the in vitro reaction were visualized by autoradiography in Southern blots. Double-stranded cleavages were observed to occur near the 5' end of each one of the five JK gene segments and near the 3' end of a VK gene segment. A plasmid containing the mouse I-A beta gene was found to be resistant to cleavage, thus confirming the specificity of the endonucleolytic activity for sequences associated with the mouse Ig gene segments.

Animals↗
PubMed1997

Peptide substrates suitable for assaying glycogen synthase kinase-3 in crude cell extracts.

In this study we describe the characterization and use of new peptide substrates for assaying glycogen synthase kinase-3 (GSK-3) which are based on the sequence around the single GSK-3 phosphorylation site in the translation factor eIF2B. The new peptides offer important advantages over previous substrates, which were based on the sequence around the multiple GSK-3 phosphorylation sites in glycogen synthase (GS), for the assay of GSK-3 in cell extracts. In particular, decreases in GSK-3 activity following, e.g., insulin treatment, are partially or completely masked when the GS-based peptides are used but are readily measured using the new, eIF2B-based, peptides. The new peptides, unlike those based on GS, are therefore suitable for the assay of changes in GSK-3 activity in cell extracts without the need for prior immunoprecipitation or ion-exchange chromatography.

3T3 Cells↗
PubMed1999

Generation of carboxy-terminally deleted forms of STAT5 during preparation of cell extracts.

Carboxy-terminally deleted forms of STAT5 have been described to be generated in vivo either by proteolytic processing or by differential splicing mechanisms. By comparing two different cell extraction procedures, we can show that in the mammary gland carboxy-terminally deleted forms are produced in vitro and are not detectable in extracts prepared by SDS lysis.

Alternative Splicing↗
PubMed2002

Quantitative analysis of c-myc-tagged protein in crude cell extracts using fluorescence polarization.

A fluorescence polarization (FP) assay was developed to determine the concentration of a c-myc-tagged recombinant protein in a crude cell extract. The basis of the assay was a competition between a c-myc-tagged protein and a fluorescein-labeled c-myc peptide for a c-myc antibody Fab. Fluorescein-labeled c-myc peptide produced a high-fluorescence polarization signal upon binding to the c-myc antibody, which can be inhibited in the presence of a c-myc-tagged protein. Quantitation of a c-myc-tagged protein was realized by measuring the decrease in fluorescence polarization. The observed IC(50) values in the competition FP assay were similar among all monomeric c-myc-tagged proteins tested, indicating that the interaction of the c-myc tag with the antibody was independent of the fusion protein sequence. The c-myc-tagged protein concentrations measured by FP were found to correlate well with values derived from a spike experiment and with values obtained by quantitative immunoblot. This assay was not perturbed by the presence of crude cell lysate, dithiothreitol or detergents, and worked with both native and denatured samples from several expression systems, including Escherichia coli, Pichia, insect cells, and mammalian cells. The assay under the current condition can detect as low as 0.05% expression level of c-myc-tagged protein with regards to total proteins, depending on the expression system. This assay is both quantitative and rapid (less than 15min) and is therefore suitable for the optimization of recombinant protein expression conditions as well as for the monitoring of protein purification procedures.

Binding, Competitive↗
PubMed2002

High-efficiency solid-phase capture using glass beads bonded to microcentrifuge tubes: immunoprecipitation of proteins from cell extracts and assessment of ras activation.

We have bonded glass microbeads (425-600 microm diameter) to the inner walls of polypropylene microcentrifuge tubes. In addition to increasing the surface area of the tubes manyfold, the beads provide surface Si groups which can be reacted with a silane compound such as aminopropyltriethoxysilane, yielding a free amino group. The amino group is reacted with another cross-linking reagent, for example, the homobifunctional compound dimethyl suberimidate, which can form a covalent bond with amine groups of proteins. After binding protein A or G to the dimethyl suberimidate, the beads were used to immunoprecipitate proteins from cell extracts; we show that the protein A/G-coated glass beads yield similar amounts of immunoprecipitated proteins as a standard method using protein A- or G-agarose beads, but with fewer contaminating proteins. In addition, we show that when immunoprecipitating Ras from cell extracts and measuring the amounts of Ras-bound GTP and GDP, the new method yielded higher guanine nucleotide levels than protein G-agarose beads, suggesting that it caused less denaturation of Ras. Because the glass beads are bonded to the walls of the tubes, the immunoprecipitates can be washed rapidly and efficiently, and we show that 20-30 tubes can be washed in 1/10 the time required to wash immunoprecipitates on protein A- or G-agarose beads.

3T3 Cells↗
PubMed1994

Suppressing effects of human fetal cell extract on micronuclei induced by cyclophosphamide in mice.

The genotoxicity of human fetal cell extract (HFCE) and its effect on the frequency of micronucleated polychromatic erythrocytes (PCE-MNF) in mice induced by cyclophosphamide (CP) were studied. Statistically significant differences were not found between the control group and each group treated with HFCE (0.3, 3, 30 mg/kg bw). CP (200 mg/kg bw) induced a marked increase in MNF (P < 0.01). Administered together with CP, HFCE suppressed the increase of MNF induced by CP. The reduction effect is dependent on the dose of HFCE. At doses of 3 and 30 mg/kg bw HFCE, MNF decreased markedly (P < 0.05 and < 0.01, respectively). It showed that HFCE did not induce micronucleus formation, while it could suppress the micronucleus formation induced by CP in mice. The results suggested that HFCE might be antimutagenic and have potential value in clinical application.

Animals↗
PubMed1981

Cofactor requiremets for 7 alpha-dehydroxylation of cholic and chenodeoxycholic acid in cell extracts of the intestinal anaerobic bacterium, Eubacterium species V.P.I. 13708.

The characteristics of 7 alpha-dehydroxylase, a bile acid-biotransforming enzyme, were determined using dialyzed cell extracts of Eubacterium sp. V.P.I. 12708. 7 alpha-Dehydroxylase was induced by cholic acid in this organism. Induction by cholic acid resulted in the differential synthesis of at least five new polypeptides with molecular weights of 77,000, two at 56,000, 27,000 and 23,500, as determined by both one and two-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis. The relative molecular weight of 7 alphs-dehydroxylase activity was estimated by anaerobic Bio-Gel A 1.5 M gel filtration chromatography to be 114,000. NAD+ was the only cofactor to consistently stimulate 7 alpha-dehydroxylase activity in dialyzed cell extracts. The specific activity increased 4- to 6-fold with either cholic or chenodeoxycholic acid as a substrate in the presence of NAD+. NAD+ was also required for the reduction of the delta 6-intermediate to deoxycholic acid. Other pyridine or flavin nucleotides were ineffective cofactors when added alone. Saturation kinetics for NAD+ with cholic or chenodeoxycholic acid as substrates were hyperbolic, and Lineweaver-Burk plots yielded apparent Km values of 0.13 mM and 0.006 mM, respectively. Similar kinetics were obtained with cholic acid giving an apparent Km of 25 microM. The substrate saturation curve for chenodeoxycholic acid 7 alpha-dehydroxylation indicated substrate inhibition at high concentrations of chenodeoxycholic acid (greater than 50 microM). These studies show that 7 alpha-dehydroxylase is an inducible enzyme and requires NAD+ as a cofactor in this bacterium.

Bile Acids and Salts↗
PubMed2002

Repair of damaged DNA by Arabidopsis cell extract.

All living organisms have to protect the integrity of their genomes from a wide range of genotoxic stresses to which they are inevitably exposed. However, understanding of DNA repair in plants lags far behind such knowledge in bacteria, yeast, and mammals, partially as a result of the absence of efficient in vitro systems. Here, we report the experimental setup for an Arabidopsis in vitro repair synthesis assay. The repair of plasmid DNA treated with three different DNA-damaging agents, UV light, cisplatin, and methylene blue, after incubation with whole-cell extract was monitored. To validate the reliability of our assay, we analyzed the repair proficiency of plants depleted in AtRAD1 activity. The reduced repair of UV light- and cisplatin-damaged DNA confirmed the deficiency of these plants in nucleotide excision repair. Decreased repair of methylene blue-induced oxidative lesions, which are believed to be processed by the base excision repair machinery in mammalian cells, may indicate a possible involvement of AtRAD1 in the repair of oxidative damage. Differences in sensitivity to DNA polymerase inhibitors (aphidicolin and dideoxy TTP) between plant and human cell extracts were observed with this assay.

Aphidicolin↗
PubMed2003

[Component analysis of bone matrix via cell extraction].

OBJECTIVE: To investigate the preparation of bone acellular extra-cell matrix(AECM) and to analyze its component. METHODS: With low-osmosis theory and method of cell extraction by detergent, bone acellular extra-cell matrix was prepared. We observed morphologic changes with HE, Mallory-Heidenhain rapid one-step dyeing and Alcian blue dyeing and examined fibronectin(FN) and laminin(LN) with immunohistochemistry. RESULTS: Light microscope showed that the collagen fibers arranged regularly in AECM with blankness of bone lacunas by HE, Mallory-Heidenhain rapid one-step dyeing and that the region around bone lacunas was stained different degrees of blue-green by Alcian blue dyeing. The result of immunohistochemistry showed there are positive markers of FN and LN in ECM. CONCLUSION: This method for preparation of bone acellular extra-cell matrix is effective, and it can keep natural structure of collagen fibers and maintain components of ECM, such as proteoglycan, FN and LN.

Bone and Bones↗
PubMed1987

Phenotypic and functional analysis of T cells extracted from chronically inflamed human periodontal tissues.

T-cell subsets extracted from chronically inflamed periodontal tissues were identified using monoclonal antibodies, and their functional activity was analysed using the autologous mixed lymphocyte reaction (AMLR). Tissue was obtained from a total of 33 adult periodontitis (AP) patients and 6 normal/marginal gingivitis (N/MG) patients. All AP patients had received repeated oral hygiene instruction and root planing prior to the surgery, and the majority (30 out of 33) had at least one site with greater than 6 mm loss of attachment from the cementoenamel junction within the surgical field. The N/MG patients had no loss of attachment, and probing depths were less than 3 mm. Single cell suspensions were obtained following collagenase digestion (90 minutes at 37 degrees C) and mechanical disruption of the tissue. T-cell subsets were identified using an indirect immunofluorescence assay on cells obtained from 19 AP patients and the 6 N/MG patients. The mean (+/- standard error) helper:suppressor (T4:T8) ratio for the AP patients was found to be 0.94 +/- 0.48 compared with 1.65 +/- 0.16 for the N/MG group and 1.51 +/- 0.12 for peripheral blood controls. HLA-DR positive macrophages were identified and were found to include both acid phosphatase (AcP) positive and adenosine triphosphatase (ATPase) positive populations. Functional analysis was carried out using cells extracted from the remaining 14 AP patients. Cells from six of these 14 patients were found to be capable of spontaneous proliferation. Co-culture experiments using autologous T and non-T populations revealed that cells from only four patients were able to respond in an AMLR while those from only one of the 14 patients were able to stimulate the AMLR.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗
PubMed1994

Functional analysis of human bronchial mucosal T cells extracted with interleukin-2.

Functional analysis of T cells from the bronchial mucosa has been limited by difficulties in extracting T cells from this tissue. Because interleukin-2 (IL-2) is chemotactic for T cells, we determined whether this cytokine could be used to extract T cells from human bronchial wall (BW). Fresh tissue was obtained from 21 patients undergoing surgery for malignancy. Within the BW, 95% of T cells stained for the memory/activation marker CD45RO. When BW sections were incubated with IL-2 for 24 h, 88 to 91% of T cells emigrated into the culture medium. Compared with autologous blood T cells (also exposed to IL-2), these BW T cells expressed CD2 at a greater intensity and showed a fourfold reduction in cloning efficiency in response to phytohemagglutinin, and T-cell clones derived from the BW population displayed a tendency for higher interferon-gamma production. Furthermore, we were also able to extract and clone T cells from bronchoscopic biopsies in four subjects, suggesting that this method will provide a new avenue for examining T-cell function in airway inflammatory diseases.

Aged↗
PubMed1995

An ion-pairing high-performance liquid chromatographic method for the direct simultaneous determination of nucleotides, deoxynucleotides, nicotinic coenzymes, oxypurines, nucleosides, and bases in perchloric acid cell extracts.

An ion-pairing high-performance liquid chromatographic method for the direct and simultaneous determination of nucleotides, deoxynucleotides, cAMP, nicotinic coenzymes, oxypurines, nucleosides, and bases in perchloric acid cell extracts is presented. By using an Alltima C-18, 250 x 4.6-mm, 5-microns particle size column, a high resolution of 38 acid-soluble compounds, including ATP, GTP, dTTP, CTP, UTP, ADP, GDP, dTDP, CDP, UDP, dATP, dGTP, dCTP, dUTP, dADP, dGDP, dCDP, dUDP, and cAMP, is obtained. Elution is performed with a step gradient from buffer A (consisting of 10 mM tetrabutylammonium hydroxide, 10 mM KH2PO4, 0.25% methanol, pH 7.00) to buffer B (consisting of 2.8 mM tetrabutylammonium hydroxide, 100 mM KH2PO4, 30% methanol, pH 5.50). Perchloric acid extracts of resting and phytohemagglutinin-stimulated human lymphocytes were analyzed. Data indicate that this chromatographic method offers, for the first time to the best of our knowledge, the possibility of simultaneously determining di- and triphosphate nucleosides and their corresponding deoxynucleosides without any chemical manipulation of samples except for perchloric acid deproteinization. Hence, the present HPLC assay minimizes the risks of modification or loss of metabolite concentration and allows one to obtain, with a single chromatographic run, the complete pattern of those metabolites which are known to be involved in energy metabolism and in DNA and RNA synthesis, resulting therefore of great advantage in cell biology studies.

Cell Extracts↗