Electrophoretic mobility shift assays for the analysis of DNA-protein interactions.

Electromobility shift assay is a simple, efficient, and rapid method for the study of specific DNA-protein interactions. It relies on the reduction in the electrophoretic mobility conferred to a DNA fragment by an interacting protein. The technique is suitable to qualitative, quantitative, and kinetic analyses. It can also be used to analyze conformational changes.

Control of integrin genes expression in the eye.

The ending race for sequencing the human genome has left the scientists faced with new challenges. Indeed, now that almost every human gene has been sequenced and precisely positioned on the human chromosomes, one of the next, most burning task consist in understanding how transcription of these genes is ensured in any given cell. The integrins encoding genes are no exception. Integrins bridge the cell to the many components from the extracellular matrix (ECM), such as laminins (LM) and collagens, and thereby transduce intracellular signals that will alter many of the cell's properties such as adhesion, migration, proliferation and survival. As a much clearer picture of the many proteins that belong to this family has emerged over the last few years, tremendous efforts have been dedicated to the identification of the regulatory sequences that modulate their expression. This review provides an overview of the current state of knowledge about the organization of the regulatory elements and the transcription factors (TF) they bind that are used by the cell in order to ensure transcription of each of the integrins gene. A particular attention has been given to those reported to be expressed in the eye. It also explores how components from the ECM might participate in the control of integrins gene expression and establishes links to wound healing of the corneal epithelium, a process that transiently alter the composition of the basement membrane on which the epithelial cells lie.

Influence of remedial professional development programs for poorly performing physicians.

INTRODUCTION: The Collège des Médecins du Québec (CMQ) offers an individualized remedial professional development program to help physicians overcome selected clinical shortcomings. To measure the influence of the remedial professional development program, physicians who completed the program between 1993 and 2004 and who were assessed by peer review during a 2-year period preceding or following the remedial activities were tracked. METHODS: For each physician, 30 to 50 patient records were selected randomly for review. Ratings were assigned for the quality of record keeping and for 3 elements pertaining to the quality of care: the clinical investigation plan, diagnostic accuracy, and patient treatment and follow-up. The impact of the program was measured by comparing the proportion of physicians with satisfactory ratings assigned by peer review before and after the remedial professional development program. RESULTS: Statistically significant improvements (p < .05) were observed for a proportion of physicians (n = 51) with satisfactory ratings with regard to record keeping (20% before and 54% after remediation), the clinical investigation plan (13% before and 59% after remediation), diagnostic accuracy (32% before and 61% after remediation), and patient treatment and follow-up (31% before and 67% after remediation). DISCUSSION: Participation in a CMQ remedial professional development program can result in improved clinical performance, as assessed through peer review.

Expression of the gene encoding poly(ADP-ribose) polymerase-1 is modulated by fibronectin during corneal wound healing.

PURPOSE: Poly(ADP-ribose) polymerase (PARP)-1 is a nuclear enzyme essential in several cellular functions such as DNA repair, DNA transcription, carcinogenesis, and apoptosis. Expression of the PARP-1 gene is mainly dictated by the transcription factor Sp1. Fibronectin (FN), a component from the extracellular matrix transiently expressed at high levels during wound healing of the corneal epithelium, was reported to exert a positive influence on expression of the alpha5 integrin subunit gene promoter by altering the state of Sp1 phosphorylation, a process that depended on the activation of the ERK signaling pathway. The present study was undertaken to investigate whether PARP-1 gene expression might be similarly regulated by FN through the same signaling pathways and attempted to link expression of this gene to corneal wound healing in vitro. METHODS: Expression of PARP-1, Sp1/Sp3, ERK1/2, phospho-ERK1/2, P38 and phospho-P38 was monitored by Western blot in cultures of rabbit corneal epithelial cells (RCECs) grown on FN in the presence of inhibitors of the MAPK, PI3K, and P38 signaling pathways. Electrophoretic mobility shift assays (EMSAs) were conducted to assess the binding of Sp1 and Sp3 in nuclear extracts from RCECs grown on FN in the presence of inhibitors. Plasmids bearing the PARP-1 promoter fused to the CAT reporter gene were also transfected into RCECs grown under similar culture conditions to assess the influence of these inhibitors on PARP-1 promoter activity. RESULTS: Expression of PARP-1, Sp1, and Sp3 increased considerably in RCECs grown on FN and translated into increased binding of Sp1 and Sp3 to their DNA target sites. In addition, FN increased PARP-1 promoter activity in a cell-density-dependent manner. Inhibition of both the MAPK and the PI3K pathways entirely abolished these properties. CONCLUSIONS: PARP-1 gene expression was strongly activated by FN through alterations in the phosphorylation state of Sp1 and Sp3 that resulted from the activation of the MAPK and PI3K signaling pathways, thereby suggesting that PARP-1 may play a critical function during the highly proliferative phase that characterizes wound healing of the corneal epithelium.

Functional Impact of Collagens on the Activity Directed by the Promoter of the α5 Integrin Subunit Gene in Corneal Epithelial Cells.

PURPOSE: The early step of corneal wound healing is characterized by the massive production of fibronectin (FN), whose secretion is progressively replaced by collagens from the basal membrane as wound healing proceeds. Here, we examined whether expression of the gene encoding the α5 subunit from the FN-binding integrin α5ß1 changes as corneal epithelial cells (CECs) are cultured in the presence of collagen type I (CI) or type IV (CIV). METHODS: Responsiveness of the α5 gene toward collagen was determined by transfection of α5 promoter/chloramphenicol acetyltransferase (CAT) plasmids into rabbit and human CECs cultured on BSA or collagens. Electrophoretic mobility shift assays and Western blots were used to monitor the transcription factors required for basal α5 gene transcription in the presence of collagens. Gene profiling on microarrays was used to determine the impact of collagens on the patterns of genes expressed by CECs. RESULTS: All collagen types repressed the full-length α5/CAT promoter activity in confluent CECs. A moderate increase was observed in subconfluent rabbit CECs grown on CIV but not on CI. These collagen-dependent regulatory influences also correlated with alterations in the transcription factors Sp1/Sp3, NFI, and AP-1 that ensure α5 gene basal transcription. Microarray analyses revealed that CI more profoundly altered the pattern of genes expressed by human CECs than CIV. CONCLUSIONS: Collagens considerably suppressed α5 gene expression in CECs, suggesting that during wound healing, they may interfere with the influence FN exerts on CECs by altering their adhesive and migratory properties through a mechanism involving a reduction in α5 gene expression.

Regulation of the integrin subunit alpha5 gene promoter by the transcription factors Sp1/Sp3 is influenced by the cell density in rabbit corneal epithelial cells.

PURPOSE: Expression of the alpha5beta1 fibronectin (Fn) integrin is well recognized in the corneal epithelium and has been postulated to increase during wound healing. In the present study, the regulatory influence of the positive transcription factors Sp1/Sp3 on the activity directed by the promoter of the alpha5 gene was examined in rabbit corneal epithelial cells (RCECs) primary cultured at various cell densities. METHODS: Expression of the alpha5 subunit was assessed at the transcriptional level by semiquantitative RT-PCR analyses. The regulatory elements necessary to direct expression of the alpha5 gene were identified by transfecting RCECs with recombinant plasmids bearing various lengths from the alpha5 gene promoter fused to the CAT reporter gene. Binding of Sp1/Sp3 to the alpha5 promoter was assessed by both electrophoretic mobility shift assays (EMSAs) and DNaseI footprinting. Endogenous levels of Sp1/Sp3 were determined by Western blot and supershift analyses. The regulatory influence exerted by Sp1/Sp3 on the alpha5 promoter was evaluated both by site-directed mutagenesis and cotransfection in Sp1-deficient Drosophila SL-2 Schneider cells. RESULTS: Subconfluent RCECs expressed nearly five times more alpha5 transcript than 48-hour postconfluent RCECs. The activity directed by the alpha5 promoter was found to be affected by cell density. Strong promoter activity was observed in subconfluent RCECs, whereas a dramatic repression was measured in postconfluent cells. EMSA and DNaseI footprinting provided evidence for the binding of Sp1 to both a proximal site located within the previously reported alpha5 fibronectin responsive element (FRE), and a distal site located between positions -117 and -101. Cotransfection experiments in Schneider cells, as well as transfection of RCECs with recombinant constructs bearing mutations into the distal Sp1 site, confirmed the positive regulatory influence of Sp1 on both the -42/-92 and -92/-132 alpha5 promoter segments. Most of all, EMSA and Western blot analyses demonstrated the expression of substantial amounts of Sp1/Sp3 in subconfluent but not postconfluent RCECs. CONCLUSIONS: These results provide support to the hypothesis that the strong reduction in the activity of the alpha5 promoter when RCECs reach a high cell density is the consequence of a reduced expression of Sp1/Sp3 under such cell culture conditions.

Development and validation of a rapid liquid chromatography isotope dilution tandem mass spectrometry (LC-IDMS/MS) method for serum creatinine.

OBJECTIVES: To develop an isotope dilution liquid chromatography tandem mass spectrometry (LC-IDMS/MS) method for the standardization of serum creatinine. DESIGN AND METHODS: Supernatants obtained by protein precipitation were injected into a LC-MS/MS. Chromatography was performed on a cation exchanger pre-column in normal phase isocratic mode. Creatinine and creatinine-D(3) were quantified using ion transitions of m/z 114-->44 and 117-->47, respectively. RESULTS: The method was calibrated with the NIST Standard Reference Material 914a and was found to be exact in analyzing the certified reference material SRM 967 from NIST (97.1+/-0.9% and 102.1+/-0.9% of target value for levels 1 and 2, respectively) and by calculating recuperation of spiked creatinine in 10 different patient samples (103.6+/-4.1%). Intra-assay imprecision was 0.9% at both 64.6 and 354 micromol/L creatinine, while inter-assay imprecisions were 1.9% and 1.8%. Absence of ion suppression was confirmed by spiking experiments. The method was shown to be free of carryover. A good correlation was obtained between the LC-MS/MS method and a Jaffe method run on an automated analyzer (r=0.999). CONCLUSIONS: We have developed a fast and simple method for the quantification of serum creatinine by isotope dilution tandem mass spectrometry (IDMS/MS) and we propose that this method can be used as a reference method by laboratories that wish to validate their serum creatinine automated assay.

Differential binding of the transcription factors Sp1, AP-1, and NFI to the promoter of the human alpha5 integrin gene dictates its transcriptional activity.

PURPOSE: Damage to the corneal epithelium results in the massive secretion of fibronectin (FN) shortly after injury and induces the expression of its integrin receptor alpha5beta1. The authors reported previously that FN induces alpha5 expression in human corneal epithelial cells and rabbit corneal epithelial cells by altering the binding of the transcription factor (TF) Sp1 to a regulatory element from the alpha5 promoter that it is also flanked by binding sites for the TFs NFI and AP-1. Here, they assessed the function of NFI and AP-1 on alpha5 gene expression and evaluated the contribution of FN to their overall regulatory influence. METHODS: TF binding to the alpha5 promoter was evaluated in vitro by electrophoretic mobility shift assays and in vivo by ligation-mediated PCR or chromatin immunoprecipitation. TFs expression was monitored by Western blot, whereas their influence was assessed by transfection and RNAi analyses. RESULTS: Coexpression of Sp1, NFI, and AP-1 was demonstrated in all cell types, and each TF was shown to bind efficiently to the alpha5 promoter. Whereas both AP-1 and Sp1 activated expression directed by the alpha5 promoter, NFI functioned as a potent repressor of that gene. Interestingly, FN could either promote or repress alpha5 promoter activity in a cell density-dependent manner by differentially altering the ratio of these TFs. CONCLUSIONS: These results suggest that alpha5 gene expression is likely dictated by subtle alterations in the nuclear ratio of TFs that either repress (NFI) or activate (Sp1 and AP-1) alpha5 transcription in corneal epithelial cells.

Transcriptional regulation of the human alpha6 integrin gene by the transcription factor NFI during corneal wound healing.

PURPOSE: Wound healing of the corneal epithelium is highly influenced by regulation of integrin gene expression. A recent study demonstrated that laminin (LM), a major constituent of the extracellular matrix (ECM), reduces expression of the human alpha6 integrin subunit gene by altering the properties of the transcription factor (TF) Sp1. In this work, a target site was identified for the TF nuclear factor I (NFI) on the human alpha6 gene, and its regulatory influence was characterized in corneal epithelial cells. METHODS: Plasmids bearing the alpha6 promoter fused to the CAT gene were transfected into human (HCECs) and rabbit (RCECs) corneal epithelial cells grown on LM. The DNA-binding site for NFI in the alpha6 promoter was identified by DNase I footprinting. Expression and DNA binding of NFI was monitored by Western blot, RT-PCR, and electrophoretic mobility shift assays (EMSAs), and its function was investigated through RNAi and NFI overexpression assays. RESULTS: All NFI isoforms were found to be expressed in HCECs and RCECs. Transfection analyses revealed that NFI is a repressor of alpha6 expression in both types of cells. LM increases expression of NFI, whereas inhibition of each NFI isoform increases promoter activity suggesting that NFI is a key repressor of alpha6 transcription. In addition, the negative influence of NFI appears to be potentiated by the degradation of Sp1 when cells are grown on LM. CONCLUSIONS: Repression of alpha6 expression therefore contributes to the final steps of corneal wound healing by both reducing proliferation and allowing attachment of the epithelium to the basal membrane.