Identification of Regulatory Elements in the Untranslated Regions of Streptolysin S Associated Gene A Messenger RNA from Group A Streptococcus

Streptococcus pyogenes, also known as group A Streptococcus (GAS), is a human pathogen associated with a variety of diseases such as strep throat, scarlet fever, toxic shock syndrome, and necrotizing fasciitis. One of the virulence factors released by GAS during an invasive infection is a cytotoxic peptide, streptolysin S (SLS), which inhibits the immune response to necrotizing fasciitis. The streptolysin S associated gene A product, SagA, is modified to produce SLS. Thesag operon includes sagA and the genes required for enzyme-mediated post-translational modifications of SagA and the export of SLS. The sagA gene is contained within the pleiotropic effect locus (pel), which produces a small RNA (sRNA) that regulates the expression of other virulence factors. Potential mRNA interactions with the Pel sRNA have been mapped to the 5\u27 and 3\u27 untranslated regions (UTRs) of sagA. Our studies aim to identify and characterize RNA structural motifs in Pel/sagA that regulate the expression of sagA and other virulence factors. Several RNA constructs of Pel/sagA were designed to include regions predicted to contain secondary structure. The corresponding sequences were isolated by PCR from genomic DNA to create templates for in vitro transcription. After purification, the RNA constructs were analyzed by gel electrophoresis to verify size, and by RNase T1 digestion to assay for secondary structure. Three-dimensional models were generated using the FARFAR algorithm in Rosetta in order to identify regions of Pel/sagA that may be involved in regulatory interactions. Differential scanning fluorimetry provided evidence that the 5\u27 and 3\u27 UTRs of Pel/sagA contain stable structural regions. It is expected that the identification of structural motifs necessary for the regulation of gene expression will aid in the design of therapeutic strategies to inhibit the production of streptolysin S and other virulence factors

Differentiation and fiber type-specific activity of a muscle creatine kinase intronic enhancer

Background: Hundreds of genes, including muscle creatine kinase (MCK), are differentially expressed in fast- and slow-twitch muscle fibers, but the fiber type-specific regulatory mechanisms are not well understood. Results: Modulatory region 1 (MR1) is a 1-kb regulatory region within MCK intron 1 that is highly active in terminally differentiating skeletal myocytes in vitro. A MCK small intronic enhancer (MCK-SIE) containing a paired E-box/myocyte enhancer factor 2 (MEF2) regulatory motif resides within MR1. The SIE's transcriptional activity equals that of the extensively characterized 206-bp MCK 5'-enhancer, but the MCK-SIE is flanked by regions that can repress its activity via the individual and combined effects of about 15 different but highly conserved 9- to 24-bp sequences. ChIP and ChIP-Seq analyses indicate that the SIE and the MCK 5'-enhancer are occupied by MyoD, myogenin and MEF2. Many other E-boxes located within or immediately adjacent to intron 1 are not occupied by MyoD or myogenin. Transgenic analysis of a 6.5-kb MCK genomic fragment containing the 5'-enhancer and proximal promoter plus the 3.2-kb intron 1, with and without MR1, indicates that MR1 is critical for MCK expression in slow- and intermediate-twitch muscle fibers (types I and IIa, respectively), but is not required for expression in fast-twitch muscle fibers (types IIb and IId). Conclusions: In this study, we discovered that MR1 is critical for MCK expression in slow- and intermediate-twitch muscle fibers and that MR1's positive transcriptional activity depends on a paired E-box MEF2 site motif within a SIE. This is the first study to delineate the DNA controls for MCK expression in different skeletal muscle fiber types

A Visual Data Mining Tool that Facilitates Reconstruction of Transcription Regulatory Networks

Background: Although the use of microarray technology has seen exponential growth, analysis of microarray data remains a challenge to many investigators. One difficulty lies in the interpretation of a list of differentially expressed genes, or in how to plan new experiments given that knowledge. Clustering methods can be used to identify groups of genes with similar expression patterns, and genes with unknown function can be provisionally annotated based on the concept of ‘‘guilt by association’’, where function is tentatively inferred from the known functions of genes with similar expression patterns. These methods frequently suffer from two limitations: (1) visualization usually only gives access to group membership, rather than specific information about nearest neighbors, and (2) the resolution or quality of the relationships are not easily inferred. Methodology/Principal Findings: We have addressed these issues by improving the precision of similarity detection over that of a single experiment and by creating a tool to visualize tractable association networks: we (1) performed metaanalysis computation of correlation coefficients for all gene pairs in a heterogeneous data set collected from 2,145 publicly available micorarray samples in mouse, (2) filtered the resulting distribution of over 130 million correlation coefficients to build new, more tractable distributions from the strongest correlations, and (3) designed and implemented a new Web based tool (StarNet

CD133 Positive Embryonal Rhabdomyosarcoma Stem-Like Cell Population Is Enriched in Rhabdospheres

Cancer stem cells (CSCs) have been identified in a number of solid tumors, but not yet in rhabdomyosarcoma (RMS), the most frequently occurring soft tissue tumor in childhood. Hence, the aim of this study was to identify and characterize a CSC population in RMS using a functional approach. We found that embryonal rhabdomyosarcoma (eRMS) cell lines can form rhabdomyosarcoma spheres (short rhabdospheres) in stem cell medium containing defined growth factors over several passages. Using an orthotopic xenograft model, we demonstrate that a 100 fold less sphere cells result in faster tumor growth compared to the adherent population suggesting that CSCs were enriched in the sphere population. Furthermore, stem cell genes such as oct4, nanog, c-myc, pax3 and sox2 are significantly upregulated in rhabdospheres which can be differentiated into multiple lineages such as adipocytes, myocytes and neuronal cells. Surprisingly, gene expression profiles indicate that rhabdospheres show more similarities with neuronal than with hematopoietic or mesenchymal stem cells. Analysis of these profiles identified the known CSC marker CD133 as one of the genes upregulated in rhabdospheres, both on RNA and protein levels. CD133+ sorted cells were subsequently shown to be more tumorigenic and more resistant to commonly used chemotherapeutics. Using a tissue microarray (TMA) of eRMS patients, we found that high expression of CD133 correlates with poor overall survival. Hence, CD133 could be a prognostic marker for eRMS. These experiments indicate that a CD133+ CSC population can be enriched from eRMS which might help to develop novel targeted therapies against this pediatric tumor

Aging Alters Functionally Human Dermal Papillary Fibroblasts but Not Reticular Fibroblasts: A New View of Skin Morphogenesis and Aging

Understanding the contribution of the dermis in skin aging is a key question, since this tissue is particularly important for skin integrity, and because its properties can affect the epidermis. Characteristics of matched pairs of dermal papillary and reticular fibroblasts (Fp and Fr) were investigated throughout aging, comparing morphology, secretion of cytokines, MMPs/TIMPs, growth potential, and interaction with epidermal keratinocytes. We observed that Fp populations were characterized by a higher proportion of small cells with low granularity and a higher growth potential than Fr populations. However, these differences became less marked with increasing age of donors. Aging was also associated with changes in the secretion activity of both Fp and Fr. Using a reconstructed skin model, we evidenced that Fp and Fr cells do not possess equivalent capacities to sustain keratinopoiesis. Comparing Fp and Fr from young donors, we noticed that dermal equivalents containing Fp were more potent to promote epidermal morphogenesis than those containing Fr. These data emphasize the complexity of dermal fibroblast biology and document the specific functional properties of Fp and Fr. Our results suggest a new model of skin aging in which marked alterations of Fp may affect the histological characteristics of skin

TEST PROTOCOLS FOR COMBUSTION TURBINE INLET COOLING FOGGERS

ABSTRACT This paper on test protocols for combustion turbine (CT) inlet cooling investigates the instrumentation and methodology options available for testing fogger systems for cooling CT inlet air. Test protocols are presented for the steady state water balance and heat balance measurements. Estimated test uncertainties are presented for the direct measurement of cooling, heat balance, and power curve test methods. In-situ hot wire instrumentation is considered for measuring the carryover. The benefits of computational fluid dynamics (CFD) analysis are illustrated for guidance in the location and in defining the requirements of the instrumentation. Supporting test data for in-situ, heat balance, and power curve tests are included in the report. Test procedures and a method to correct the test results to the guarantee condition are presented. This investigation supports the development of code tests being developed by the ASME PTC 51 Committee