Hybridization Properties of RNA Containing 8-Methoxyguanosine and 8-Benzyloxyguanosine.

Directory of Open Access Journals (Sweden)

Daniel Sylwester Baranowski

Full Text Available Modified nucleobase analogues can serve as powerful tools for changing physicochemical and biological properties of DNA or RNA. Guanosine derivatives containing bulky substituents at 8 position are known to adopt syn conformation of N-glycoside bond. On the contrary, in RNA the anti conformation is predominant in Watson-Crick base pairing. In this paper two 8-substituted guanosine derivatives, 8-methoxyguanosine and 8-benzyloxyguanosine, were synthesized and incorporated into oligoribonucleotides to investigate their influence on the thermodynamic stability of RNA duplexes. The methoxy and benzyloxy substituents are electron-donating groups, decreasing the rate of depurination in the monomers, as confirmed by N-glycoside bond stability assessments. Thermodynamic stability studies indicated that substitution of guanosine by 8-methoxy- or 8-benzyloxyguanosine significantly decreased the thermodynamic stability of RNA duplexes. Moreover, the presence of 8-substituted guanosine derivatives decreased mismatch discrimination. Circular dichroism spectra of modified RNA duplexes exhibited patterns typical for A-RNA geometry.

Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps

Energy Technology Data Exchange (ETDEWEB)

Chojnowski, Grzegorz, E-mail: gchojnowski@genesilico.pl [International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw (Poland); Waleń, Tomasz [International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw (Poland); University of Warsaw, Banacha 2, 02-097 Warsaw (Poland); Piątkowski, Paweł; Potrzebowski, Wojciech [International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw (Poland); Bujnicki, Janusz M. [International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw (Poland); Adam Mickiewicz University, Umultowska 89, 61-614 Poznan (Poland)

2015-03-01

A computer program that builds crystal structure models of nucleic acid molecules is presented. Brickworx is a computer program that builds crystal structure models of nucleic acid molecules using recurrent motifs including double-stranded helices. In a first step, the program searches for electron-density peaks that may correspond to phosphate groups; it may also take into account phosphate-group positions provided by the user. Subsequently, comparing the three-dimensional patterns of the P atoms with a database of nucleic acid fragments, it finds the matching positions of the double-stranded helical motifs (A-RNA or B-DNA) in the unit cell. If the target structure is RNA, the helical fragments are further extended with recurrent RNA motifs from a fragment library that contains single-stranded segments. Finally, the matched motifs are merged and refined in real space to find the most likely conformations, including a fit of the sequence to the electron-density map. The Brickworx program is available for download and as a web server at http://iimcb.genesilico.pl/brickworx.

Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps

International Nuclear Information System (INIS)

Chojnowski, Grzegorz; Waleń, Tomasz; Piątkowski, Paweł; Potrzebowski, Wojciech; Bujnicki, Janusz M.

2015-01-01

A computer program that builds crystal structure models of nucleic acid molecules is presented. Brickworx is a computer program that builds crystal structure models of nucleic acid molecules using recurrent motifs including double-stranded helices. In a first step, the program searches for electron-density peaks that may correspond to phosphate groups; it may also take into account phosphate-group positions provided by the user. Subsequently, comparing the three-dimensional patterns of the P atoms with a database of nucleic acid fragments, it finds the matching positions of the double-stranded helical motifs (A-RNA or B-DNA) in the unit cell. If the target structure is RNA, the helical fragments are further extended with recurrent RNA motifs from a fragment library that contains single-stranded segments. Finally, the matched motifs are merged and refined in real space to find the most likely conformations, including a fit of the sequence to the electron-density map. The Brickworx program is available for download and as a web server at http://iimcb.genesilico.pl/brickworx

Expression microarray reproducibility is improved by optimising purification steps in RNA amplification and labelling

Directory of Open Access Journals (Sweden)

Brenton James D

2004-01-01

Full Text Available Abstract Background Expression microarrays have evolved into a powerful tool with great potential for clinical application and therefore reliability of data is essential. RNA amplification is used when the amount of starting material is scarce, as is frequently the case with clinical samples. Purification steps are critical in RNA amplification and labelling protocols, and there is a lack of sufficient data to validate and optimise the process. Results Here the purification steps involved in the protocol for indirect labelling of amplified RNA are evaluated and the experimentally determined best method for each step with respect to yield, purity, size distribution of the transcripts, and dye coupling is used to generate targets tested in replicate hybridisations. DNase treatment of diluted total RNA samples followed by phenol extraction is the optimal way to remove genomic DNA contamination. Purification of double-stranded cDNA is best achieved by phenol extraction followed by isopropanol precipitation at room temperature. Extraction with guanidinium-phenol and Lithium Chloride precipitation are the optimal methods for purification of amplified RNA and labelled aRNA respectively. Conclusion This protocol provides targets that generate highly reproducible microarray data with good representation of transcripts across the size spectrum and a coefficient of repeatability significantly better than that reported previously.

Role of Electrostatics in Protein-RNA Binding: The Global vs the Local Energy Landscape.

Science.gov (United States)

Ghaemi, Zhaleh; Guzman, Irisbel; Gnutt, David; Luthey-Schulten, Zaida; Gruebele, Martin

2017-09-14

U1A protein-stem loop 2 RNA association is a basic step in the assembly of the spliceosomal U1 small nuclear ribonucleoprotein. Long-range electrostatic interactions due to the positive charge of U1A are thought to provide high binding affinity for the negatively charged RNA. Short range interactions, such as hydrogen bonds and contacts between RNA bases and protein side chains, favor a specific binding site. Here, we propose that electrostatic interactions are as important as local contacts in biasing the protein-RNA energy landscape toward a specific binding site. We show by using molecular dynamics simulations that deletion of two long-range electrostatic interactions (K22Q and K50Q) leads to mutant-specific alternative RNA bound states. One of these states preserves short-range interactions with aromatic residues in the original binding site, while the other one does not. We test the computational prediction with experimental temperature-jump kinetics using a tryptophan probe in the U1A-RNA binding site. The two mutants show the distinct predicted kinetic behaviors. Thus, the stem loop 2 RNA has multiple binding sites on a rough RNA-protein binding landscape. We speculate that the rough protein-RNA binding landscape, when biased to different local minima by electrostatics, could be one way that protein-RNA interactions evolve toward new binding sites and novel function.

Profil Sensori dan Nilai Gizi Beberapa Jenis Ikan Patin dan Hibrid Nasutus

Directory of Open Access Journals (Sweden)

Theresia Dwi Suryaningrum

2010-11-01

Full Text Available Penelitian mengenai profil sensori dan nilai gizi filet patin Siam (Pangasius hypopthalmus, Jambal (Pangasius djambal Bleeker, Pasupati, Nasutus serta hasil silangan Siam dan Nasutus (hibrid Nasutus telah dilakukan. Analisis sensori dilakukan dengan uji pembeda menyeluruh, uji pembeda atribut, uji kesukaan, dan uji rangking. Pengamatan lainnya dilakukan terhadap edible portion dan nilai gizi (proksimat dan profil asam amino. Hasil penelitian menunjukkan bahwa filet patin hibrid Nasutus lebih memiliki kesamaan warna dengan filet patin Nasutus daripada filet patin Siam. W arna daging filet patin hibrid Nasutus berbeda nyata dengan induknya yaitu patin Nasutus dan patin Siam. Panelis lebih menyukai warna filet patin hibrid Nasutus dibandingkan dengan patin Pasupati. Patin hibrid Nasutus mempunyai tekstur yang berbeda nyata dengan Nasutus dan Jambal yang kompak dan padat, tetapi mempunyai kesamaan dengan patin Siam dan Pasupati yang agak kompak dan agak padat. Berdasarkan intensitas warna, hasil uji pembeda atribut dan uji kesukaan, maka secara berturut-turut panelis menyukai filet patin Jambal, Nasutus, hibrid Nasutus, Pasupati, dan Siam. Hibrid Nasutus mempunyai edible portionpaling tinggi (49% dibandingkan dengan patin lainnya tetapi mempunyai kadar air, kadar lemak, dan kadar protein yang lebih rendah dan berbeda nyata dengan induknya (patin Siam dan Nasutus. Patin Siam mengandung asam amino esensial paling tinggi di antara berbagai jenis patin yang diteliti. Profil asam amino patin hibrid Nasutus, Jambal, Pasupati, dan Nasutus hampir sama, kecuali pada patin Siam yang mengandung glisin, leusin, isoleusin, histidin, serin, treonin, dan prolin yang lebih tinggi dibandingkan dengan patin lainnya

Inclusion of methoxy groups inverts the thermodynamic stabilities of DNA-RNA hybrid duplexes: A molecular dynamics simulation study.

Science.gov (United States)

Suresh, Gorle; Priyakumar, U Deva

2015-09-01

Modified nucleic acids have found profound applications in nucleic acid based technologies such as antisense and antiviral therapies. Previous studies on chemically modified nucleic acids have suggested that modifications incorporated in furanose sugar especially at 2'-position attribute special properties to nucleic acids when compared to other modifications. 2'-O-methyl modification to deoxyribose sugars of DNA-RNA hybrids is one such modification that increases nucleic acid stability and has become an attractive class of compounds for potential antisense applications. It has been reported that modification of DNA strands with 2'-O-methyl group reverses the thermodynamic stability of DNA-RNA hybrid duplexes. Molecular dynamics simulations have been performed on two hybrid duplexes (DR and RD) which differ from each other and 2'-O-methyl modified counterparts to investigate the effect of 2'-O-methyl modification on their duplex stability. The results obtained suggest that the modification drives the conformations of both the hybrid duplexes towards A-RNA like conformation. The modified hybrid duplexes exhibit significantly contrasting dynamics and hydration patterns compared to respective parent duplexes. In line with the experimental results, the relative binding free energies suggest that the introduced modifications stabilize the less stable DR hybrid, but destabilize the more stable RD duplex. Binding free energy calculations suggest that the increased hydrophobicity is primarily responsible for the reversal of thermodynamic stability of hybrid duplexes. Free energy component analysis further provides insights into the stability of modified duplexes. Copyright © 2015 Elsevier Inc. All rights reserved.

Bioinformatics of cardiovascular miRNA biology.

Science.gov (United States)

Kunz, Meik; Xiao, Ke; Liang, Chunguang; Viereck, Janika; Pachel, Christina; Frantz, Stefan; Thum, Thomas; Dandekar, Thomas

2015-12-01

MicroRNAs (miRNAs) are small ~22 nucleotide non-coding RNAs and are highly conserved among species. Moreover, miRNAs regulate gene expression of a large number of genes associated with important biological functions and signaling pathways. Recently, several miRNAs have been found to be associated with cardiovascular diseases. Thus, investigating the complex regulatory effect of miRNAs may lead to a better understanding of their functional role in the heart. To achieve this, bioinformatics approaches have to be coupled with validation and screening experiments to understand the complex interactions of miRNAs with the genome. This will boost the subsequent development of diagnostic markers and our understanding of the physiological and therapeutic role of miRNAs in cardiac remodeling. In this review, we focus on and explain different bioinformatics strategies and algorithms for the identification and analysis of miRNAs and their regulatory elements to better understand cardiac miRNA biology. Starting with the biogenesis of miRNAs, we present approaches such as LocARNA and miRBase for combining sequence and structure analysis including phylogenetic comparisons as well as detailed analysis of RNA folding patterns, functional target prediction, signaling pathway as well as functional analysis. We also show how far bioinformatics helps to tackle the unprecedented level of complexity and systemic effects by miRNA, underlining the strong therapeutic potential of miRNA and miRNA target structures in cardiovascular disease. In addition, we discuss drawbacks and limitations of bioinformatics algorithms and the necessity of experimental approaches for miRNA target identification. This article is part of a Special Issue entitled 'Non-coding RNAs'. Copyright © 2014 Elsevier Ltd. All rights reserved.

Triplet-Based Codon Organization Optimizes the Impact of Synonymous Mutation on Nucleic Acid Molecular Dynamics.

Science.gov (United States)

Babbitt, Gregory A; Coppola, Erin E; Mortensen, Jamie S; Ekeren, Patrick X; Viola, Cosmo; Goldblatt, Dallan; Hudson, André O

2018-02-01

Since the elucidation of the genetic code almost 50 years ago, many nonrandom aspects of its codon organization remain only partly resolved. Here, we investigate the recent hypothesis of 'dual-use' codons which proposes that in addition to allowing adjustment of codon optimization to tRNA abundance, the degeneracy in the triplet-based genetic code also multiplexes information regarding DNA's helical shape and protein-binding dynamics while avoiding interference with other protein-level characteristics determined by amino acid properties. How such structural optimization of the code within eukaryotic chromatin could have arisen from an RNA world is a mystery, but would imply some preadaptation in an RNA context. We analyzed synonymous (protein-silent) and nonsynonymous (protein-altering) mutational impacts on molecular dynamics in 13823 identically degenerate alternative codon reorganizations, defined by codon transitions in 7680 GPU-accelerated molecular dynamic simulations of implicitly and explicitly solvated double-stranded aRNA and bDNA structures. When compared to all possible alternative codon assignments, the standard genetic code minimized the impact of synonymous mutations on the random atomic fluctuations and correlations of carbon backbone vector trajectories while facilitating the specific movements that contribute to DNA polymer flexibility. This trend was notably stronger in the context of RNA supporting the idea that dual-use codon optimization and informational multiplexing in DNA resulted from the preadaptation of the RNA duplex to resist changes to thermostability. The nonrandom and divergent molecular dynamics of synonymous mutations also imply that the triplet-based code may have resulted from adaptive functional expansion enabling a primordial doublet code to multiplex gene regulatory information via the shape and charge of the minor groove.

Serratia marcescens arn, a PhoP-Regulated Locus Necessary for Polymyxin B Resistance

Science.gov (United States)

Lin, Quei Yen; Tsai, Yi-Lin; Liu, Ming-Che; Lin, Wei-Cheng; Hsueh, Po-Ren

2014-01-01

Polymyxins, which are increasingly being used to treat infections caused by multidrug-resistant bacteria, perform poorly against Serratia marcescens. To investigate the underlying mechanisms, Tn5 mutagenesis was performed and two mutants exhibiting increased polymyxin B (PB) susceptibility were isolated. The mutants were found to have Tn5 inserted into the arnB and arnC genes. In other bacteria, arnB and arnC belong to the seven-gene arn operon, which is involved in lipopolysaccharide (LPS) modification. LPSs of arn mutants had greater PB-binding abilities than that of wild-type LPS. Further, we identified PhoP, a bacterial two-component response regulator, as a regulator of PB susceptibility in S. marcescens. By the reporter assay, we found PB- and low-Mg2+-induced expression of phoP and arn in the wild-type strain but not in the phoP mutant. Complementation of the phoP mutant with the full-length phoP gene restored the PB MIC and induction by PB and low Mg2+ levels, as in the wild type. An electrophoretic mobility shift assay (EMSA) further demonstrated that PhoP bound directly to the arn promoter. The PB challenge test confirmed that pretreatment with PB and low Mg2+ levels protected S. marcescens from a PB challenge in the wild-type strain but not in the phoP mutant. Real-time reverse transcriptase-PCR also indicated that PB serves as a signal to regulate expression of ugd, a gene required for LPS modification, in S. marcescens through a PhoP-dependent pathway. Finally, we found that PB-resistant clinical isolates displayed greater expression of arnA upon exposure to PB than did susceptible isolates. This is the first report to describe the role of S. marcescens arn in PB resistance and its modulation by PB and Mg2+ through the PhoP protein. PMID:24957827

Gene expression profiling of two distinct neuronal populations in the rodent spinal cord.

Directory of Open Access Journals (Sweden)

Jesper Ryge

Full Text Available BACKGROUND: In the field of neuroscience microarray gene expression profiles on anatomically defined brain structures are being used increasingly to study both normal brain functions as well as pathological states. Fluorescent tracing techniques in brain tissue that identifies distinct neuronal populations can in combination with global gene expression profiling potentially increase the resolution and specificity of such studies to shed new light on neuronal functions at the cellular level. METHODOLOGY/PRINCIPAL FINDINGS: We examine the microarray gene expression profiles of two distinct neuronal populations in the spinal cord of the neonatal rat, the principal motor neurons and specific interneurons involved in motor control. The gene expression profiles of the respective cell populations were obtained from amplified mRNA originating from 50-250 fluorescently identified and laser microdissected cells. In the data analysis we combine a new microarray normalization procedure with a conglomerate measure of significant differential gene expression. Using our methodology we find 32 genes to be more expressed in the interneurons compared to the motor neurons that all except one have not previously been associated with this neuronal population. As a validation of our method we find 17 genes to be more expressed in the motor neurons than in the interneurons and of these only one had not previously been described in this population. CONCLUSIONS/SIGNIFICANCE: We provide an optimized experimental protocol that allows isolation of gene transcripts from fluorescent retrogradely labeled cell populations in fresh tissue, which can be used to generate amplified aRNA for microarray hybridization from as few as 50 laser microdissected cells. Using this optimized experimental protocol in combination with our microarray analysis methodology we find 49 differentially expressed genes between the motor neurons and the interneurons that reflect the functional

Transcriptome Profile of the Response of Paracoccidioides spp. to a Camphene Thiosemicarbazide Derivative.

Directory of Open Access Journals (Sweden)

Lívia do Carmo Silva

Full Text Available Paracoccidioidomycosis (PCM is a systemic granulomatous human mycosis caused by fungi of the genus Paracoccidioides, which is geographically restricted to Latin America. Inhalation of spores, the infectious particles of the fungus, is a common route of infection. The PCM treatment of choice is azoles such as itraconazole, but sulfonamides and amphotericin B are used in some cases despite their toxicity to mammalian cells. The current availability of treatments highlights the need to identify and characterize novel targets for antifungal treatment of PCM as well as the need to search for new antifungal compounds obtained from natural sources or by chemical synthesis. To this end, we evaluated the antifungal activity of a camphene thiosemicarbazide derivative (TSC-C compound on Paracoccidioides yeast. To determine the response of Paracoccidioides spp. to TSC-C, we analyzed the transcriptional profile of the fungus after 8 h of contact with the compound. The results demonstrate that Paracoccidioides lutzii induced the expression of genes related to metabolism; cell cycle and DNA processing; biogenesis of cellular components; cell transduction/signal; cell rescue, defense and virulence; cellular transport, transport facilities and transport routes; energy; protein synthesis; protein fate; transcription; and other proteins without classification. Additionally, we observed intensely inhibited genes related to protein synthesis. Analysis by fluorescence microscopy and flow cytometry revealed that the compound induced the production of reactive oxygen species. Using an isolate with down-regulated SOD1 gene expression (SOD1-aRNA, we sought to determine the function of this gene in the defense of Paracoccidioides yeast cells against the compound. Mutant cells were more susceptible to TSC-C, demonstrating the importance of this gene in response to the compound. The results presented herein suggest that TSC-C is a promising candidate for PCM treatment.

DNAzyme-mediated recovery of small recombinant RNAs from a 5S rRNA-derived chimera expressed in Escherichia coli

Directory of Open Access Journals (Sweden)

Willson Richard C

2010-12-01

Full Text Available Abstract Background Manufacturing large quantities of recombinant RNAs by overexpression in a bacterial host is hampered by their instability in intracellular environment. To overcome this problem, an RNA of interest can be fused into a stable bacterial RNA for the resulting chimeric construct to accumulate in the cytoplasm to a sufficiently high level. Being supplemented with cost-effective procedures for isolation of the chimera from cells and recovery of the recombinant RNA from stabilizing scaffold, this strategy might become a viable alternative to the existing methods of chemical or enzymatic RNA synthesis. Results Sequence encoding a 71-nucleotide recombinant RNA was inserted into a plasmid-borne deletion mutant of the Vibrio proteolyticus 5S rRNA gene in place of helix III - loop C segment of the original 5S rRNA. After transformation into Escherichia coli, the chimeric RNA (3×pen aRNA was expressed constitutively from E. coli rrnB P1 and P2 promoters. The RNA chimera accumulated to levels that exceeded those of the host's 5S rRNA. A novel method relying on liquid-solid partitioning of cellular constituents was developed for isolation of total RNA from bacterial cells. This protocol avoids toxic chemicals, and is therefore more suitable for large scale RNA purification than traditional methods. A pair of biotinylated 8-17 DNAzymes was used to bring about the quantitative excision of the 71-nt recombinant RNA from the chimera. The recombinant RNA was isolated by sequence-specific capture on beads with immobilized complementary deoxyoligonucleotide, while DNAzymes were recovered by biotin affinity chromatography for reuse. Conclusions The feasibility of a fermentation-based approach for manufacturing large quantities of small RNAs in vivo using a "5S rRNA scaffold" strategy is demonstrated. The approach provides a route towards an economical method for the large-scale production of small RNAs including shRNAs, siRNAs and aptamers for use

Escherichia coli under Ionic Silver Stress: An Integrative Approach to Explore Transcriptional, Physiological and Biochemical Responses.

Directory of Open Access Journals (Sweden)

Claire Saulou-Bérion

Full Text Available For a better understanding of the systemic effect of sub-lethal micromolar concentrations of ionic silver on Escherichia coli, we performed a multi-level characterization of cells under Ag+-mediated stress using an integrative biology approach combining physiological, biochemical and transcriptomic data. Physiological parameters, namely bacterial growth and survival after Ag+ exposure, were first quantified and related to the accumulation of intracellular silver, probed for the first time by nano secondary ion mass spectroscopy at sub-micrometer lateral resolution. Modifications in E. coli biochemical composition were evaluated under Ag+-mediated stress by in situ synchrotron Fourier-transform infrared microspectroscopy and a comprehensive transcriptome response was also determined. Using multivariate statistics, correlations between the physiological parameters, the extracellular concentration of AgNO3 and the intracellular silver content, gene expression profiles and micro-spectroscopic data were investigated. We identified Ag+-dependent regulation of gene expression required for growth (e.g. transporter genes, transcriptional regulators, ribosomal proteins, for ionic silver transport and detoxification (e.g. copA, cueO, mgtA, nhaR and for coping with various types of stress (dnaK, pspA, metA,R, oxidoreductase genes. The silver-induced shortening of the acyl chain of fatty acids, mostly encountered in cell membrane, was highlighted by microspectroscopy and correlated with the down-regulated expression of genes involved in fatty acid transport (fadL and synthesis/modification of lipid A (lpxA and arnA. The increase in the disordered secondary structure of proteins in the presence of Ag+ was assessed through the conformational shift shown for amides I and II, and further correlated with the up-regulated expression of peptidase (hfq and chaperone (dnaJ, and regulation of transpeptidase expression (ycfS and ycbB. Interestingly, as these

Cognitive impairment and stroke in elderly patients

Directory of Open Access Journals (Sweden)

Lo Coco D

2016-03-01

Full Text Available Daniele Lo Coco,1 Gianluca Lopez,1 Salvatore Corrao,2,31Neurology and Stroke Unit, 2Department of Internal Medicine, National Relevance and High Specialization Hospital Trust ARNAS Civico, Di Cristina, Benfratelli, Palermo, 3Centre of Research for Effectiveness and Appropriateness in Medicine (C.R.E.A.M., Di.Bi.M.I.S., University of Palermo, Palermo, Italy Abstract: We reviewed current knowledge about the interaction between stroke and vascular risk factors and the development of cognitive impairment and dementia. Stroke is increasingly recognized as an important cause of cognitive problems and has been implicated in the development of both Alzheimer's disease and vascular dementia. The prevalence of cognitive impairment after stroke is high, and their combined effects significantly increase the cost of care and health resource utilization, with reflections on hospital readmissions and increased mortality rates. There is also substantial evidence that vascular risk factors (such as hypertension, diabetes, obesity, dyslipidemia, and tobacco smoking are independently associated with an increased risk of cognitive decline and dementia. Thus, a successful management of these factors, as well as optimal acute stroke management, might have a great impact on the development of cognitive impairment. Notwithstanding, the pathological link between cognitive impairment, stroke, and vascular risk factors is complex and still partially unclear so that further studies are needed to better elucidate the boundaries of this relationship. Many specific pharmacological treatments, including anticholinergic drugs and antihypertensive medications, and nonpharmacological approaches, such as diet, cognitive rehabilitation, and physical activity, have been studied for patients with vascular cognitive impairment, but the optimal care is still far away. Meanwhile, according to the most recent knowledge, optimal stroke care should also include cognitive assessment in the

Ulipristal acetate: a novel pharmacological approach for the treatment of uterine fibroids

Directory of Open Access Journals (Sweden)

Biglia N

2014-02-01

Full Text Available Nicoletta Biglia,1 Silvestro Carinelli,2 Antonio Maiorana,3 Marta D'Alonzo,1 Giuseppe Lo Monte,4 Roberto Marci4 1Department of Obstetrics and Gynaecology, Mauriziano "Umberto I" Hospital, University of Turin, Turin, 2Department of Pathology, European Institute of Oncology, Milan, 3Department of Obstetrics and Gynecology, ARNAS Civico Hospital, Palermo, 4Department of Morphology, Surgery and Experimental Medicine, Section of Obstetrics and Gynecology, Infertility Unit, University of Ferrara, Ferrara, Italy Abstract: Uterine fibroids are the most common benign tumors of the female genital tract. The management of symptomatic fibroids has traditionally been surgical; however, alternative pharmacological approaches have been proposed to control symptoms. To date, gonadotropin-releasing hormone analogs are the only available drugs for the preoperative treatment of fibroids. However, the US Food and Drug Administration recently authorized ulipristal acetate (UPA, an oral selective progesterone-receptor modulator, for the same indication. UPA is a new, effective, and well-tolerated option for the preoperative treatment of moderate and severe symptoms of uterine fibroids in women of reproductive age. According to clinical data, UPA shows several advantages: it is faster than leuprolide in reducing the fibroid-associated bleeding, it significantly improves hemoglobin and hematocrit levels in anemic patients, and it grants a significant reduction in the size of fibroids, which lasts for at least 6 months after the end of the treatment. Furthermore, UPA displays a better tolerability profile when compared to leuprolide; in fact, it keeps estradiol levels at mid follicular phase range, thereby reducing the incidence of hot flushes and exerting no impact on bone turnover. On the grounds of this evidence, the administration of 5 mg/day ulipristal acetate for 3 months is suggested for different patient categories and allows for planning a treatment strategy

Proteomic View of Interactions of Shiga Toxin-Producing Escherichia coli with the Intestinal Environment in Gnotobiotic Piglets.

Directory of Open Access Journals (Sweden)

Rembert Pieper

Full Text Available Shiga toxin (Stx-producing Escherichia coli cause severe intestinal infections involving colonization of epithelial Peyer's patches and formation of attachment/effacement (A/E lesions. These lesions trigger leukocyte infiltration followed by inflammation and intestinal hemorrhage. Systems biology, which explores the crosstalk of Stx-producing Escherichia coli with the in vivo host environment, may elucidate novel molecular pathogenesis aspects.Enterohemorrhagic E. coli strain 86-24 produces Shiga toxin-2 and belongs to the serotype O157:H7. Bacterial cells were scrapped from stationary phase cultures (the in vitro condition and used to infect gnotobiotic piglets via intestinal lavage. Bacterial cells isolated from the piglets' guts constituted the in vivo condition. Cell lysates were subjected to quantitative 2D gel and shotgun proteomic analyses, revealing metabolic shifts towards anaerobic energy generation, changes in carbon utilization, phosphate and ammonia starvation, and high activity of a glutamate decarboxylase acid resistance system in vivo. Increased abundance of pyridine nucleotide transhydrogenase (PntA and PntB suggested in vivo shortage of intracellular NADPH. Abundance changes of proteins implicated in lipopolysaccharide biosynthesis (LpxC, ArnA, the predicted acyltransferase L7029 and outer membrane (OM assembly (LptD, MlaA, MlaC suggested bacterial cell surface modulation in response to activated host defenses. Indeed, there was evidence for interactions of innate immunity-associated proteins secreted into the intestines (GP340, REG3-γ, resistin, lithostathine, and trefoil factor 3 with the bacterial cell envelope.Proteomic analysis afforded insights into system-wide adaptations of strain 86-24 to a hostile intestinal milieu, including responses to limited nutrients and cofactor supplies, intracellular acidification, and reactive nitrogen and oxygen species-mediated stress. Protein and lipopolysaccharide compositions of the OM

Accurate distance determination of nucleic acids via Förster resonance energy transfer: implications of dye linker length and rigidity.

Science.gov (United States)

Sindbert, Simon; Kalinin, Stanislav; Nguyen, Hien; Kienzler, Andrea; Clima, Lilia; Bannwarth, Willi; Appel, Bettina; Müller, Sabine; Seidel, Claus A M

2011-03-02

In Förster resonance energy transfer (FRET) experiments, the donor (D) and acceptor (A) fluorophores are usually attached to the macromolecule of interest via long flexible linkers of up to 15 Å in length. This causes significant uncertainties in quantitative distance measurements and prevents experiments with short distances between the attachment points of the dyes due to possible dye-dye interactions. We present two approaches to overcome the above problems as demonstrated by FRET measurements for a series of dsDNA and dsRNA internally labeled with Alexa488 and Cy5 as D and A dye, respectively. First, we characterize the influence of linker length and flexibility on FRET for different dye linker types (long, intermediate, short) by analyzing fluorescence lifetime and anisotropy decays. For long linkers, we describe a straightforward procedure that allows for very high accuracy of FRET-based structure determination through proper consideration of the position distribution of the dye and of linker dynamics. The position distribution can be quickly calculated with geometric accessible volume (AV) simulations, provided that the local structure of RNA or DNA in the proximity of the dye is known and that the dye diffuses freely in the sterically allowed space. The AV approach provides results similar to molecular dynamics simulations (MD) and is fully consistent with experimental FRET data. In a benchmark study for ds A-RNA, an rmsd value of 1.3 Å is achieved. Considering the case of undefined dye environments or very short DA distances, we introduce short linkers with a propargyl or alkenyl unit for internal labeling of nucleic acids to minimize position uncertainties. Studies by ensemble time correlated single photon counting and single-molecule detection show that the nature of the linker strongly affects the radius of the dye's accessible volume (6-16 Å). For short propargyl linkers, heterogeneous dye environments are observed on the millisecond time scale. A

Phenolic indeno[1,2-b]indoles as ABCG2-selective potent and non-toxic inhibitors stimulating basal ATPase activity

Directory of Open Access Journals (Sweden)

Gozzi GJ

2015-07-01

Full Text Available Gustavo Jabor Gozzi,1,2 Zouhair Bouaziz,3 Evelyn Winter,1,4 Nathalia Daflon-Yunes,1 Mylène Honorat,1 Nathalie Guragossian,3 Christelle Marminon,3 Glaucio Valdameri,1,2 Andre Bollacke,5 Jean Guillon,6 Noël Pinaud,7 Mathieu Marchivie,8 Silvia M Cadena,2 Joachim Jose,5 Marc Le Borgne,3 Attilio Di Pietro11Equipe Labellisée Ligue 2014, BMSSI UMR5086 CNRS/Lyon I University, IBCP, Lyon, France; 2Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, Paraná, Brazil; 3Faculty of Pharmacy – ISPB, EA 4446 Biomolecules, Cancer and Chemoresistance, Health SFR of East Lyon CNRS UMS3453 - INSERM US7, University of Lyon, Lyon I University, Lyon Cedex 8, France; 4Department of Pharmaceutical Sciences, PGFAR, Federal University of Santa Catarina, Florianopolis, Santa Catarina, Brazil; 5Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, Münster, Germany; 6ARNA Laboratory, Pharmaceutical Sciences UFR, INSERM U869, University of Bordeaux, Bordeaux Cedex, France; 7ISM – CNRS UMR 5255, University of Bordeaux Cedex, France; 8ICMCB CNRS-UPR 9048, University of Bordeaux, Pessac Cedex, FranceAbstract: Ketonic indeno[1,2-b]indole-9,10-dione derivatives, initially designed as human casein kinase II (CK2 inhibitors, were recently shown to be converted into efficient inhibitors of drug efflux by the breast cancer resistance protein ABCG2 upon suited substitutions including a N5-phenethyl on C-ring and hydrophobic groups on D-ring. A series of ten phenolic and seven p-quinonic derivatives were synthesized and screened for inhibition of both CK2 and ABCG2 activities. The best phenolic inhibitors were about threefold more potent against ABCG2 than the corresponding ketonic derivatives, and showed low cytotoxicity. They were selective for ABCG2 over both P-glycoprotein and MRP1 (multidrug resistance protein 1, whereas the ketonic derivatives also interacted with MRP1, and they additionally displayed a lower

Changes in the AIDS epidemiologic situation in Puerto Rico following health care reform and the introduction of HAART Cambios en la situación epidemiológica del sida en Puerto Rico tras la reforma sanitaria y la introducción de la TARGA

Directory of Open Access Journals (Sweden)

Doris V. Báez-Feliciano

2005-02-01

Full Text Available OBJECTIVES: To compare the occurrence of AIDS as well as the sociodemographic and clinical profiles of AIDS patients in Puerto Rico before and after the introduction of highly active antiretroviral therapy (HAART and the privatization of the island’s public health care system. METHODS: We compared the incident AIDS cases for two three-year periods, 1992-1994 and 1998-2000, in four populations: (1 entire United States, (2 Puerto Rico, (3 Bayamón Health Region (located in north-central Puerto Rico, it includes 11 of the island’s 78 municipalities, and (4 an HIV cohort enrolled at the Universidad Central del Caribe (UCC School of Medicine. The UCC is located in Bayamón, Puerto Rico, within an academic medical complex that houses the teaching hospital (Ramón Ruíz Arnaú University Hospital, the ambulatory health care facilities (Immunology Clinics for patients with HIV, and administrative buildings. This represents the major government-sponsored health care infrastructure within the Bayamón Health Region. RESULTS: Incident AIDS declined substantially between the two periods in each of the four populations studied. The 48.1% decline in Puerto Rico exceeded the 40.9% decline in the United States. The decline in Puerto Rico likely resulted from increased availability and implementation of HAART and the delivery of health care to HIV/AIDS patients in an integrated fashion within each regional ambulatory clinic. In spite of this improvement, the absolute number of patients with AIDS on the island remains high. Substantial resources for treatment and prevention are required. The proportion of new AIDS cases was lower among women, persons 40 years of age or older, the less educated, and those living alone. Injection drug use remains the predominant mode of transmission in Puerto Rico. CONCLUSIONS: Further gains in Puerto Rico’s fight against AIDS will depend on the island’s ability to reduce the transmission that occurs through injection drug

Palenie papierosów w ciąży = Cigarette smoking in pregnancy

Directory of Open Access Journals (Sweden)

Agnieszka Konstancja Pawłowska-Muc

2016-01-01

4 Doctoral Candidate at the Department and Clinic of Gynaecology and Gynaecological Endocrinology, School of Health Studies, Medical University of Lublin, Al. Racławickie 23   Adres do korespondencji: mgr piel. Agnieszka Konstancja Pawłowska-Muc Ośrodek Kształcenia Podyplomowego Pielęgniarek i Położnych Radomski Szpital Specjalistyczny im. dr Tytusa Chałubińskiego w Radomiu, ul. Lekarska 4 tel. 48  3615616; fax: 48 3615437 e-mail: agmich@vp.pl   Streszczenie Wprowadzenie. Palenie papierosów jest dużym problemem zdrowotnym i społeczno – ekonomicznym. Stanowi zagrożenie dla rozrodu, przebiegu ciąży i zdrowia dziecka. Cel pracy. Ukazanie problemu palenia papierosów przez kobiety ciężarne na podstawie przeglądu piśmiennictwa.             Skrócony opis stanu wiedzy. W opracowaniu przedstawiono epidemiologię i skalę problemu oraz konsekwencje palenia w okresie ciąży, z uwzględnieniem podziału na przebieg ciąży i zdrowie dziecka. Omówiono też świadomość kobiet odnośnie negatywnych skutków takich zachowań. Podsumowanie. Z przeglądu piśmiennictwa wynika, że palenie papierosów przez kobiety ciężarne nie należy do rzadkości. Skala problemu nie jest łatwa do oceny, gdyż wiele z nich po prostu nie przyznaje się do tego. Negatywne konsekwencje palenia w ciąży są dość liczne i dotyczą zarówno jej przebiegu, jak i stanu noworodka oraz zdrowia dziecka w późniejszym okresie życia. Istnieje potrzeba kształtowania postaw antynikotynowych, zwłaszcza wśród dziewcząt i kobiet w wieku rozrodczym.   Słowa kluczowe: kobieta ciężarna, palenie papierosów w ciąży.                                                                   Summary Introduction. Smoking cigarettes is a major health and social-economical problem. It poses a threat to reproduction, parturition and the health of the baby. Aim. Illustrating the problem of smoking cigarettes by

Używki w ciąży – kofeina = Stimulants in pregnancy – caffeine

Directory of Open Access Journals (Sweden)

Agnieszka Konstancja Pawłowska-Muc

2015-06-01

3 Independent Obstetric Skills Workshop, Medical University of Lublin, ul. Staszica 4/6   Adres do korespondencji: mgr piel. Agnieszka Konstancja Pawłowska-Muc Ośrodek Kształcenia Podyplomowego Pielęgniarek i Położnych Radomski Szpital Specjalistyczny im. dr Tytusa Chałubińskiego w Radomiu, ul. Lekarska 4 tel. 48  3615616; fax: 48 3615437 e-mail: agmich@vp.pl   Używki w ciąży - kofeina Streszczenie Wprowadzenie. Kofeina należy do substancji psychoaktywnych, ogólnodostępnych i najbardziej rozpowszechnionych na całym świecie. Jej wpływ na zdrowie kobiet, przebieg ciąży i rozwój płodu jest od lat przedmiotem wielu dyskusji, sporów i dociekań naukowych. Cel pracy. Przegląd piśmiennictwa na temat wpływu działania kofeiny na organizm kobiety oraz skutków jej spożywania w okresie ciąży i laktacji. Skrócony opis stanu wiedzy. Działanie kofeiny na organizm kobiety oraz jej wpływ na przebieg ciąży i zdrowie dziecka nie zostały dotychczas w pełni poznane. Znajduje się ona w wielu produktach, a to sprawia, że jej całkowite, dzienne spożycie jest trudne do oceny.             Podsumowanie. Z przeglądu piśmiennictwa wynika, że duży odsetek kobiet ciężarnych ma zwyczaj codziennego picia herbaty i/lub kawy z kofeiną. Zakres embriotoksycznego działania tej substancji zależy od jej dawki, częstości spożywania oraz stanu zdrowia kobiety ciężarnej. Stanowiska  autorów, co do stosowania napojów zawierających kofeinę w tym czasie, a także ich skutków, są podzielone. Większość jednak podziela pogląd, iż w ciąży i w okresie laktacji należy ograniczyć, a najlepiej zaniechać, spożywanie takich napojów. Zasadne jest zatem, aby działania promujące i wspierające zdrowy styl życia kobiet w wieku rozrodczym dotyczyły, między innymi, tej kwestii. Słowa kluczowe: kofeina, ciężarna, zdrowie, ciąża, płód.   Stimulants in pregnancy - caffeine Summary Introduction. Caffeine belongs to the group of