Promoter Usage and Dynamics in Vascular Smooth Muscle Cells Exposed to Fibroblast Growth Factor-2 or Interleukin-1β.

Smooth muscle cells (SMC) in blood vessels are normally growth quiescent and transcriptionally inactive. Our objective was to understand promoter usage and dynamics in SMC acutely exposed to a prototypic growth factor or pro-inflammatory cytokine. Using cap analysis gene expression (FANTOM5 project) we report differences in promoter dynamics for immediate-early genes (IEG) and other genes when SMC are exposed to fibroblast growth factor-2 or interleukin-1β.

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.

Although it is generally accepted that cellular differentiation requires changes to transcriptional networks, dynamic regulation of promoters and enhancers at specific sets of genes has not been previously studied en masse. Exploiting the fact that active promoters and enhancers are transcribed, we simultaneously measured their activity in 19 human and 14 mouse time courses covering a wide range of cell types and biological stimuli. Enhancer RNAs, then messenger RNAs encoding transcription factors, dominated the earliest responses.

A promoter-level mammalian expression atlas.

Regulated transcription controls the diversity, developmental pathways and spatial organization of the hundreds of cell types that make up a mammal. Using single-molecule cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body. We find that few genes are truly 'housekeeping', whereas many mammalian promoters are composite entities composed of several closely separated TSSs, with independent cell-type-specific expression profiles.

DNAzyme targeting c-jun suppresses skin cancer growth.

Worldwide, one in three cancers is skin-related, with increasing incidence in many populations. Here, we demonstrate the capacity of a DNAzyme-targeting c-jun mRNA, Dz13, to inhibit growth of two common skin cancer types-basal cell and squamous cell carcinomas-in a therapeutic setting with established tumors. Dz13 inhibited tumor growth in both immunodeficient and immunocompetent syngeneic mice and reduced lung nodule formation in a model of metastasis.

A rapid genetic screening system for identifying gene-specific suppression constructs for use in human cells.

We describe a rapid cell-based genetic screen using fission yeast for identifying efficient gene suppression constructs (GSCs) from large libraries (10(5)) for any target sequence for use in human cells. In this system, target sequences are fused to the 5' end of the lacZ reporter gene and expressed in yeast. Random fragment expression libraries derived from the target sequence are screened in the fusion gene-expressing strain using the lacZ gene-encoded colony color phenotype.

Comparative analysis of artificial antisense RNA regulation in fission yeast and human cells.

The fission yeast Schizosaccharomyces pombe has recently been established as an experimental model for the study of antisense RNA-mediated gene suppression. To validate the use of S. pombe as a host for identifying antisense genes for use in human cells, it was important to determine if sequences identified in yeast were as equally effective in a human cell line.

Comparison of three 3' non-coding regions in Schizosaccharomyces pombe expression vectors: efficiencies of transcription termination and mRNA 3'-end formation.

Analysis of an established Schizosaccharomyces pombe episomal shuttle vector suggested that inefficient transcription termination was deleterious to plasmid function. We undertook a study to determine if transcription in the presence and absence of 3'-processing within a vector could affect the ability of the plasmid to transform, transcribe and translate the RNA produced. This report provides an analysis of the effects that three S.

Gene regulation by antisense RNA in the fission yeast Schizosaccharomyces pombe.

This report describes experiments designed to demonstrate the suitability of the fission yeast Schizosaccharomyces pombe as a host for antisense RNA regulation. A lacZ gene-expressing yeast strain was constructed and used as a host for the expression of a series of antisense RNAs complementary to various regions of the target lacZ mRNA. All lacZ antisense genes were placed under control of the thiamine-repressible nmt1 promoter of S.

Degradative enzymes of oral streptococci.

Members of the Streptococcus sanguis group (SSG) and Streptococcus milleri group (SMG) were screened for their ability to produce glycosidase, arylamidase (peptidase), protease, dextranase and glycosyltransferase activities. Species within each group produced unique patterns of activity. The most commonly produced glycosidases were beta-D-glucosidase, beta-D-galactosidase, N-acetyl-beta-D-glucosaminidase and N-acetyl-beta-D-galactosaminidase and the least commonly produced glycosidase activity was beta-fucosidase with Streptococcus intermedius (SMG) being the only species capable of producing the activity.

The ade6 gene of the fission yeast as a target for antisense and ribozyme RNA-mediated suppression.

A genetic system for the analysis of antisense and ribozyme mechanisms is a much needed experimental tool, and yeast represent a favorable organism on which to base such a system. We have shown previously that the fission yeast Schizosaccharomyces pombe has potential to satisfy the requirements of such a system. This report describes experiments designed to determine if antisense and ribozyme RNA-mediated gene suppression will be generally applicable to other genes in S.

Pathogenic potential of lactobacilli.

Lactobacilli are often considered to be commensal or beneficial participants in human microbial ecology and considerable research is being carried out into the effects of the use of lactobacilli as additives in both human and animal diets. However, lactobacilli also cause some human diseases (e.g.

Lancefield group C Streptococcus milleri group strains aggregate human platelets.

Lancefield group C Streptococcus milleri group (SMG) strains are the only SMG types that are able to aggregate human platelets. Complete aggregation occurred within 10 min of mixing bacterial cells and platelets together in the ratio 8:1. Substances which (i) chelated cations; (ii) inhibited the cycloxygenase pathway in platelets; (iii) reduced the availability of ADP and disrupted platelet membrane stability; (iv) reduced bacterial aggregation of platelets.

The aggregation of human platelets by Lactobacillus species.

The ability to aggregate human platelets was examined for five Lactobacillus rhamnosus strains and five Lactobacillus paracasei subsp. paracasei strains isolated from patients with infective endocarditis (IE), 25 laboratory isolates from the same two species, and 14 strains from five other oral species, namely Lactobacillus acidophilus, Lactobacillus fermentum, Lactobacillus oris, Lactobacillus plantarum and Lactobacillus salivarius. Amongst the L.

Coaggregation of oral lactobacilli with streptococci from the oral cavity.

The ability of oral lactobacilli to coaggregate with streptococci and actinomycetes was investigated. Of the 7 species of lactobacilli studied, only two were capable of coaggregation and the coaggregation was restricted to streptococci. Lactobacillus salivarius strains (2/4) coaggregated with Streptococcus salivarius, Streptococcus gordonii, Streptococcus crista and tufted Streptococcus sanguis II strains.

Albumin-binding proteins on the surface of the Streptococcus milleri group and characterization of the albumin receptor of Streptococcus intermedius C5.

Members of the Streptococcus milleri group (SMG) that react with Lancefield group C antisera were shown to bind large amounts of albumin although there was no direct relation between these two properties as polyclonal antisera to Lancefield group C antigen did not prevent the binding of albumin. There was a specificity for albumin binding, with albumin from man, monkeys, cat, dog and mouse being bound to a greater degree than albumin from cow, horse, goat or rabbit. Gold-labelled albumin was shown to be located close to the surface of strains by transmission electron microscopy.

Biochemical properties of Streptococcus sobrinus reisolates from the gastrointestinal tract of a gnotobiotic rat.

Streptococcus sobrinus strain 6715-13-201 was inoculated into the oral cavity of a gnotobiotic rat and then reisolated from different portions of the gastrointestinal tract. Fourteen isolates, selected on the basis of their colonial morphology, were then screened for their ability to adhere to saliva-coated hydroxyapatite (SHA) in vitro, and their ability to produce extracellular polysaccharide from sucrose, and low pH in glucose broth. Certain isolates were also tested for their cariogenic potential as monoinfectants in gnotobiotic rats.