DEVELOPMENTAL DYNAMICS, Issue 4 2005
Tomoko Ishibashi
Abstract Oligonucleotide-based microarray analyses were carried out to identify retinoic acid target genes in embryos of the ascidian Ciona intestinalis. Of 21,938 spots, 50 (corresponding to 43 genes) showed over twofold up-regulation in retinoic acid-treated tail bud embryos. In situ hybridization verified retinoic acid-induced up-regulation of 23 genes. Many of them were expressed in the anterior tail region, where a retinaldehyde dehydrogenase homolog is expressed. Homologs of vertebrate genes involved in neurogenesis and/or neuronal functions (e.g., COUP-TF, Ci-Hox1, and SCO-spondin) were expressed in the central nervous system of Ciona embryos, and activated by retinoic acid. Genes encoding transcription factors (e.g., Ci-lmx1.2, vitamin D receptor, and Hox proteins) and apoptosis-related proteins (e.g., transglutaminase and an apoptosis-inducing factor homolog) were also activated by retinoic acid. Simultaneous treatment of embryos with retinoic acid and puromycin revealed a few direct targets, including genes encoding Ci-Hox1, Ci-Cyp26, and an Rnf126-like ring finger protein. Developmental Dynamics 233:1571,1578, 2005. © 2005 Wiley-Liss, Inc. [source]

Inhibition of Proinflammatory Cytokine Expression by NF-,B (p65) Antisense Oligonucleotide in Helicobacter pylori -Infected Mice

HELICOBACTER, Issue 6 2005
Sang Gyun Kim
ABSTRACT Background.,Helicobacter pylori induces the expression of proinflammatory cytokines in vitro by activating nuclear factor-,B, a transcriptional regulator. However, it has not been clarified whether H. pylori -induced proinflammatory cytokines are also mediated through nuclear factor-,B in vivo. The aim of this study was to evaluate the role of nuclear factor-,B on the expressions of proinflammatory cytokines in H. pylori -infected mice. Materials and Methods., We evaluated nuclear factor-,B (p65) activation in the H. pylori -infected gastric mucosa of mice by immunofluorescent staining using antip65 polyclonal antibody, and the expressions of proinflammatory cytokines with inhibition of nuclear factor-,B pathway by using phosphorothioate antisense and sense oligonucleotide against the nuclear factor-,B (p65). Results., In the H. pylori -infected gastric mucosa of mice, immunofluorescent staining using antip65 polyclonal antibody showed nuclear factor-,B (p65) activation, which was particularly localized to epithelial cells. Tumor necrosis factor-, and interleukin-1, concentrations in gastric mucosa by enzyme-linked immunosorbent assay (ELISA) were elevated in the infected group versus the uninfected group. Pretreatment with nuclear factor-,B (p65) antisense oligonucleotide inhibited the activation of nuclear factor-,B and the expressions of tumor necrosis factor-, and interleukin-1, in H. pylori -infected gastric mucosa. Sense oligonucleotide did not influence on the expression of proinflammatory cytokines. Conclusions.,H. pylori infection was found to activate the expressions of proinflammatory cytokines via nuclear factor-,B in vivo, and this may play an important role in the initiation of H. pylori- induced gastric inflammation. [source]

Stability of Hoogsteen -Type Triplexes , Electrostatic Attraction between Duplex Backbone and Triplex-Forming Oligonucleotide (TFO) Using an Intercalating Conjugate

HELVETICA CHIMICA ACTA, Issue 5 2008
Daniel Globisch
Abstract Syntheses are described for two novel twisted intercalating nucleic acid (TINA) monomers where the intercalator comprises a benzene ring linked to a naphthalimide moiety via an ethynediyl bridge. The intercalators Y and Z have a 2-(dimethylamino)ethyl and a methyl residue on the naphthalimide moiety, respectively. When used as triplex-forming oligonucleotides (TFOs), the novel naphthalimide TINAs show extraordinary high thermal stability in Hoogsteen -type triplexes and duplexes with high discrimination of mismatch strands. DNA Strands containing the intercalator Y show higher thermal triplex stability than DNA strands containing the intercalator Z. This observation can be explained by the ionic interaction of the protonated dimethylamino group under physiological conditions, targeting the negatively charged phosphate backbone of the duplex. This interaction leads to an extra binding mode between the TFO and the duplex, in agreement with molecular-modeling studies. We believe that this is the first example of an intercalator linking the TFO to the phosphate backbone of the duplex by an ionic interaction, which is a promising tool to achieve a higher triplex stability. [source]

Lancefield group C Streptococcus dysgalactiae infection responsible for fish mortalities in Japan

JOURNAL OF FISH DISEASES, Issue 12 2004
R Nomoto
Abstract A Lancefield serological group C Streptococcus sp. was isolated from cultured amberjack, Seriola dumerili Risso, and yellowtail, Seriola quinqueradiata Temminck and Schlegel, immunized with Lactococcus garvieae commercial vaccines in Japan. The isolated bacteria were Gram-positive cocci, auto-aggregating in saline, morphologically long chains in growth medium, catalase negative and , -haemolytic on blood agar. An almost complete gene sequence of the 16S rDNA of two isolates was determined and compared with that of bacterial strains in the database. The isolates were identified as Streptococcus dysgalactiae based on the results of the 16S rDNA sequence, the bacteriological properties and the Lancefield serological grouping. Oligonucleotide primers specifically designed for the 16S,23S rDNA intergenic spacer region of S. dysgalactiae amplified a gene from all the fish isolates, as well as the type strains , -haemolytic S. dysgalactiae subsp. dysgalactiae ATCC430738 and , -haemolytic S. dysgalactiae subsp. equisimilis ATCC35666, but not those of S. equi ATCC33398, Lactococcus garvieae ATCC43921 and L. garvieae KG9408. The severe necrotic lesions of the caudal peduncle seen in experimentally infected fish were similar to those seen in naturally infected fish. [source]

Untersuchung von Quadruplex-Konformationen der humanen Telomerensequenz mit Puls-EPR,

ANGEWANDTE CHEMIE, Issue 51 2009
Vijay Singh Dr.
Unter physiologischen Bedingungen nehmen Telomersequenzen unterschiedliche Quadruplexkonformationen ein, deren genaue Strukturen jedoch noch nicht zweifelsfrei bekannt sind. Doppelt spinmarkierte Oligonucleotide, die aus G-reichen Telomerabschnitten bestehen, wurden synthetisiert und mithilfe von Puls-EPR charakterisiert. In K+ -haltiger Lösung liegen die Propeller- und die Korbform als 1:1-Mischung nebeneinander vor. [source]

Oligonucleotide , Minor Groove Binder 1:2 Conjugates: Side by Side Parallel Minor Groove Binder Motif in Stabilization of DNA Duplex

CHEMINFORM, Issue 6 2005
Vladimir A. Ryabinin
Abstract For Abstract see ChemInform Abstract in Full Text. [source]

An Oligonucleotide-based Fluorescence Sensor for Mercury(II) in Aqueous Solutions

CHINESE JOURNAL OF CHEMISTRY, Issue 8 2009
Huiwang WU
Abstract A highly selective fluorescence sensor was developed for Hg(II) ion detection in aqueous solutions based on the selective binding of Hg(II) ions with a pair of thymine-thymine mismatch. The sensor consists of two DNA probes functionalized with a fluorophore (fluorescein, F) and a quencher (tetramethyl rhodamine, Q) moiety separately. This pair of DNA probes contains two pairs of thymine-thymine mismatches used to detect Hg(II) ions. In the presence of Hg(II) ions, thymine-Hg2+ -thymine was formed between thymine residues of probes. From that, the interaction of the two DNA probes increased. Thus, the DNA probes formed a double-stranded structure. Both the fluorophore and quencher were brought close to each other leading to the fluorescence resonance energy transfer (FRET) between F and Q. Under the optimum conditions, the sensor was used to detect the Hg(II) ions from 50 to 1000 nmol·L,1 with a regression equation y=5281.13,1650.56 lg[Hg2+] (R2=0.985). The linear range covers 100 to 500 nmol·L,1, and the limit of detection (LOD) is 79 nmol·L,1. The disturbance of some co-existing metal ions was explored, and no significant fluorescence quenching in the presence of 1.0 ,mol·L,1 other metal ions was observed. The fluorescence sensor has good sensitivity and selectivity for Hg(II) ions providing a rapid, simple and low cost method for the detection of mercury(II) ions in aqueous solutions. [source]

Neuronal leucine-rich repeat 6 (XlNLRR-6) is required for late lens and retina development in Xenopus laevis

DEVELOPMENTAL DYNAMICS, Issue 4 2006
Adam D. Wolfe
Abstract Leucine-rich repeat proteins expressed in the developing vertebrate nervous system comprise a complex, multifamily group, and little is known of their developmental function in vivo. We have identified a novel member of this group in Xenopus laevis, XlNLRR-6, and through sequence and phylogenetic analysis, have placed it within a defined family of vertebrate neuronal leucine-rich repeat proteins (NLRR). XlNLRR-6 is expressed in the developing nervous system and tissues of the eye beginning at the neural plate stage, and expression continues throughout embryonic and larval development. Using antisense morpholino oligonucleotide (MO) -mediated knockdown of XlNLRR-6, we demonstrate that this protein is critical for development of the lens, retina, and cornea. Reciprocal transplantation of presumptive lens ectoderm between MO-treated and untreated embryos demonstrate that XlNLRR-6 plays autonomous roles in the development of both the lens and retina. These findings represent the first in vivo functional analysis of an NLRR family protein and establish a role for this protein during late differentiation of tissues in the developing eye. Developmental Dynamics 235:1027,1041, 2006. © 2006 Wiley-Liss, Inc. [source]

Genomic profiling of Mixer and Sox17, targets during Xenopus endoderm development

DEVELOPMENTAL DYNAMICS, Issue 2 2006
Kari Dickinson
Abstract The transcription factors Mixer and Sox17, have well-characterized roles in endoderm specification during Xenopus embryogenesis. In order to more thoroughly understand the mechanisms by which these endodermal regulators act, we expressed Mixer and Sox17, in naïve ectodermal tissue and, using oligonucleotide-based microarrays, compared their genomic transcriptional profile to that of unaffected tissue. Using this approach, we identified 71 transcripts that are upregulated by Mixer or Sox17,, 63 of which have previously uncharacterized roles in endoderm development. Furthermore, an in situ hybridization screen using antisense probes for several of these clones identified six targets of Mixer and/or Sox17, that are expressed in the endoderm during gastrula stages, providing new and regional markers of the endoderm. Our results contribute further insight into the functions of Mixer and Sox17, and bring us closer to understanding at the molecular level the pathways that regulate endoderm development. Developmental Dynamics 235:368,381, 2006. © 2005 Wiley-Liss, Inc. [source]

Zebrafish IRX1b in the embryonic cardiac ventricle,

DEVELOPMENTAL DYNAMICS, Issue 4 2004
Elaine M. Joseph
Abstract The synchronous contraction of the vertebrate heart requires a conduction system. While coordinated contraction of the cardiac chambers is observed in zebrafish larvae, no histological evidence yet has been found for the existence of a cardiac conduction system in this tractable teleost. The homeodomain transcription factor gene IRX1 has been shown in the mouse embryo to be a marker of cells that give rise to the distinctive cardiac ventricular conduction system. Here, I demonstrate that zebrafish IRX1b is expressed in a restricted subset of ventricular myocytes within the embryonic zebrafish heart. IRX1b expression occurs as the electrical maturation of the heart is taking place, in a location analogous to the initial expression domain of mouse IRX1. The gene expression pattern of IRX1b is altered in silent heart genetic mutant embryos and in embryos treated with the endothelin receptor antagonist bosentan. Furthermore, injection of a morpholino oligonucleotide targeted to block IRX1b translation slows the heart rate. Developmental Dynamics 231:720,726, 2004. © 2004 Wiley-Liss, Inc. [source]

Preparation of Nanogapped Gold Nanoparticle Array for DNA Detection

ELECTROANALYSIS, Issue 4 2008
Shiho Tokonami
Abstract A novel DNA detection technique using a gold nanoparticle array film electrode has been reported here. The gold nanoparticles molecularly linked with binder molecule (1,10-decanedithiol) were separated 1.3,nm from each other, and the DNA conductivity change from single to double strand was measured by monitoring a voltage drop across the particles, between which a probe of a 12-mer oligonucleotide was immobilized. In adding a complementary oligonucleotide on the nanoparticle film chip, an immediate decrease in the film resistance (ca. 1.4 ,) due to a hybridization event occurred in a reproducible manner with this simple setup. In the paper, we have an interest in the primary sensing properties; effect of the film resistance on the sensor response, dependence of the resistance change on the DNA concentration, and the performance of the system for DNA detection including single nucleotide polymorphisms were described. [source]

Electrochemical Biosensor for the Detection of Interaction Between Arsenic Trioxide and DNA Based on Guanine Signal

ELECTROANALYSIS, Issue 7 2003
Mehmet Ozsoz
Abstract The interaction of arsenic trioxide (As2O3) with calf thymus double-stranded DNA (dsDNA), calf thymus single-stranded DNA (ssDNA) and also 17-mer short oligonucleotide (Probe,A) was studied electrochemically by using differential pulse voltammetry (DPV) with carbon paste electrode (CPE) at the surface and also in solution. Potentiometric stripping analysis (PSA) was employed to monitor the interaction of As2O3 with dsDNA in solution phase by using a renewable pencil graphite electrode (PGE). The changes in the experimental parameters such as the concentration of As2O3, and the accumulation time of As2O3 were studied by using DPV; in addition, the reproducibility data for the interaction between DNA and As2O3 was determined by using both electrochemical techniques. After the interaction of As2O3 with dsDNA, the DPV signal of guanine was found to be decreasing when the accumulation time and the concentration of As2O3 were increased. Similar DPV results were also found with ssDNA and oligonucleotide. PSA results observed at a low DNA concentration such as 1,ppm and a different working electrode such as PGE showed that there could be damage to guanine bases. The partition coefficients of As2O3 after interaction with dsDNA and ssDNA in solution by using CPE were calculated. Similarly, the partition coefficients (PC) of As2O3 after interaction with dsDNA in solution was also calculated by PSA at PGE. The features of this proposed method for the detection of DNA damage by As2O3 are discussed and compared with those methods previously reported for the other type of DNA targeted agents in the literature. [source]

Two-Surface Strategy in Electrochemical DNA Hybridization Assays: Detection of Osmium-Labeled Target DNA at Carbon Electrodes

ELECTROANALYSIS, Issue 5-6 2003
Miroslav Fojta
Abstract Target DNAs, including a 71-mer oligonucleotide, a PCR product and a plasmid DNA, all containing oligo(A) stretches, were hybridized at magnetic Dynabeads oligo(dT)25 (DBT). The hybridization events were detected using a technique based on chemical modification of the target DNA with a complex of osmium tetroxide with 2,2,-bipyridine (Os,,bipy) and voltammetric detection at carbon electrodes. DNA was modified with Os,,bipy prior to capture at DBT, at the beads, or after release from the beads. In the latter case, DNA-Os,,bipy was detected in the reaction mixture using adsorptive transfer stripping voltammetry involving extraction of unreacted Os,,bipy from the electrode by organic solvents. Pre-labeling of the target plasmid DNA and the PCR product with Os,,bipy significantly increased the yield of DNA captured at the beads. Tens of femtomoles of both short (the 71-mer oligonucleotide) and long (the 3-kilobase plasmid) target DNAs in a 20-microliter hybridization sample can be easily detected by means of these techniques. Various carbon electrode materials, including pyrolytic graphite (PGE), highly oriented pyrolytic graphite (HOPGE), carbon paste (CPE), glassy carbon and pencil graphite, were tested regarding their suitability for the detection of osmium-labeled DNA. Among them, PGE and HOPGE appeared usable in the measurements of both purified DNA-Os,,bipy and its mixtures with unreacted Os,,bipy while CPE was suitable for the detection purified osmium-labeled DNA. [source]

A novel approach for analysis of oligonucleotide,cisplatin interactions by continuous elution gel electrophoresis coupled to isotope dilution inductively coupled plasma mass spectrometry and matrix-assisted laser desorption/ionization mass spectrometry

ELECTROPHORESIS, Issue 7 2008
Wolfram Brüchert
Abstract In this work we present a novel approach for in vitro studies of cisplatin interactions with 8-mer oligonucleotides. The approach is based on the recently developed coupling of continuous elution gel electrophoresis (GE) to an inductively coupled plasma-sector field mass spectrometer (ICP-SFMS) with the aim of monitoring the interaction process between this cytostatic drug and the nucleotides. In contrast to existing methods, the electrophoretic separation conditions used here allow both the determination of the reaction kinetics in more detail as well as the observation of dominant intermediates. Two different nucleotides sequences have been investigated for comparison purposes, one containing two adjacent guanines (5,-TCCGGTCC-3,) and one with a combination of thymine and guanine (5,-TCCTGTCC-3,), respectively. In order to gain further structural information, MALDI-TOF MS measurements have been performed after fraction collection. This allows for identification of the intermediates and the final products and confirms the stepwise coordination of cisplatin via monoadduct to bisadduct formation. Furthermore, the ICP-MS results were quantitatively evaluated in order to calculate the kinetics of the entire process. [source]

Detection and separation of nucleoside-5'-monophosphates of DNA by conjugation with the fluorescent dye BODIPY and capillary electrophoresis with laser-induced fluorescence detection

ELECTROPHORESIS, Issue 13 2005
Michael Cornelius
Abstract We investigated the separation and detection of the 5'-monophosphates of 2'-deoxynucleosides selectively conjugated with 4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza- s -indacene-3-propionyl ethylene diamine hydrochloride (BODIPY FL EDA) at the 5'-phosphate group using capillary electrophoresis with laser-induced fluorescence detection (CE-LIF). BODIPY conjugates of the four common deoxynucleoside-5'-monophosphates (2'-deoxyguanosine-5'-monophosphate, 2'-deoxyadenosine-5'-monophosphate, 2'-deoxycytidine-5'-monophosphate, and thymidine-5'-monophosphate) were prepared and subjected to CE-LIF to serve as standard compounds for peak assignment and to develop separation conditions for the analysis of DNA. BODIPY conjugates were detected and resolved by CE-LIF after digestion of DNA or an oligonucleotide to 5'-monophosphates by nuclease P1 (NP 1) and fluorescence labeling without further purification step. Comparative analyses of calf-thymus DNA digested either with micrococcal nuclease/spleen phosphodiesterase to 3'-monophosphates or with NP 1 to 5'-monophosphates showed that both versions of the fluorescence postlabeling assay were equally efficient and sensitive. Moreover, using the same assay, 2'-deoxyuridine and 2'-deoxy-5methylcytidine were identified in bisulfite treated DNA after NP 1 digestion indicating that fluorescence postlabeling of 2'-deoxyribonucleoside-5'-monophosphates with BODIPY FL EDA and detection by CE-LIF has the potential to determine DNA damage and genomic DNA methylation. [source]

Capillary electrophoresis as a probe of enantiospecific interactions between photoactive transition metal complexes and DNA

ELECTROPHORESIS, Issue 15 2003
James P. Schaeper
Abstract Recently, we have demonstrated the capacity to separate chiral transition metal (TM) complexes of the type [M(diimine)3]n+ using CE buffers containing chiral tartrate salts. In separate work, several chromium(III)- tris -diimine complexes in particular have been shown to bind enantioselectively with calf-thymus (CT) DNA, and a qualitative assessment of the relative strength and enantiospecificity of this interaction is of significant interest in the characterization of these complexes as potential DNA photocleavage agents. Here, we describe two convenient approaches to investigate such binding behavior using chiral CE. For complexes with lower DNA affinities exhibiting primarily surface binding, DNA itself is used as the chiral resolving agent in the electrophoretic buffer. In this approach, resolution of the TM complexes into their , and , isomers is achieved with the isomer eluting later exhibiting superior binding affinity toward DNA. For more strongly bound TM complexes containing ligands known to intercalate with DNA, the [Cr(diimine)3]3+ complexes are preincubated with oligonucleotide and subsequently enantiomerically resolved in a dibenzoyl- L -tartrate buffer system that facilitates analysis of the unbound TM species only. Differences in isomer binding affinity are distinguished by the relative peak areas of the ,- and ,-isomers, and relative binding strengths of different complexes can be inferred from comparison of the total amount of unbound complex at equivalent DNA/TM ratios. [source]

Transcription factor binding study by capillary zone electrophoretic mobility shift assay

ELECTROPHORESIS, Issue 1-2 2003
Zsolt Ronai
Abstract Regulation of gene expression through interaction of proteins with specific DNA sequences is a central issue in functional genomics. Capillary electrophoretic mobility shift assay is an efficient novel method for the investigation of sequence specific protein-DNA interactions, allowing rapid and sensitive quantification of the complex formation. In this paper, we present a pilot study on capillary zone electrophoretic mobility shift assay (CZEMSA) to investigate the interaction between the transcription factors of HeLa nuclear extract and Sp1-specific fluorescein-labeled oligonucleotide, using the unlabeled probe as competitor. The mobility shift assay was accomplished by CZE in coated capillaries without polymeric buffer additives. Specificity of the DNA protein complex formation was verified by competition experiments, as well as by supershift assay with an anti-Sp1 antibody. The applied electric field strength did not affect the stability of DNA-protein complex during the electrophoretic analysis, allowing rapid identification and quantification of the protein DNA interaction. A practical application to study the interaction between Oryza sativa MADS-box transcription factor 4 (OsMADS4) and its consensus sequence is also reported. [source]

Development of specific oligonucleotide probes for the identification and in situ detection of hydrocarbon-degrading Alcanivorax strains

ENVIRONMENTAL MICROBIOLOGY, Issue 6 2001
Kazuaki Syutsubo
The genus Alcanivorax comprises diverse hydrocarbon-degrading marine bacteria. Novel 16S rRNA-targeted oligonucleotide DNA probes (ALV735 and ALV735-b) were developed to quantify two subgroups of the Alcanivorax/Fundibacter group by fluorescence in situ hybridization (FISH), and the conditions for the single-mismatch discrimination of the probes were optimized. The specificity of the probes was improved further using a singly mismatched oligonucleotide as a competitor. The growth of Alcanivorax cells in crude oil-contaminated sea water under the biostimulation condition was investigated by FISH with the probe ALV735, which targeted the main cluster of the Alcanivorax/Fundibacter group. The size of the Alcanivorax population increased with increasing incubation time and accounted for 91% of the 4,,6-diamidino-2-phenylindole (DAPI) count after incubation for 2 weeks. The probes developed in this study are useful for detecting Alcanivorax populations in petroleum hydrocarbon-degrading microbial consortia. [source]

Development of a daphnia magna DNA microarray for evaluating the toxicity of environmental chemicals

ENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 4 2007
Hajime Watanabe
Abstract Toxic chemical contaminants have a variety of detrimental effects on various species, and the impact of pollutants on ecosystems has become an urgent issue. However, the majority of studies regarding the effects of chemical contaminants have focused on vertebrates. Among aquatic organisms, Daphnia magna has been used extensively to evaluate organism- and populationlevel responses of invertebrates to pollutants in acute toxicity or reproductive toxicity tests. Although these types of tests can provide information concerning hazardous concentrations of chemicals, they provide no information about their mode of action. Recent advances in molecular genetic techniques have provided tools to better understand the responses of aquatic organisms to pollutants. In the present study, we adapted some of the techniques of molecular genetics to develop new tools, which form the basis for an ecotoxicogenomic assessment of D. magna. Based on a Daphnia expressed sequence tag database, we developed an oligonucleotide-based DNA microarray with high reproducibility. The DNA microarray was used to evaluate gene expression profiles of neonatal daphnids exposed to several different chemicals: Copper sulfate, hydrogen peroxide, pentachlorophenol, or ,-naphthoflavone. Exposure to these chemicals resulted in characteristic patterns of gene expression that were chemical-specific, indicating that the Daphnia DNA microarray can be used for classification of toxic chemicals and for development of a mechanistic understanding of chemical toxicity on a common freshwater organism. [source]

Region-specific changes in gene expression in rat brain after chronic treatment with levetiracetam or phenytoin

EPILEPSIA, Issue 9 2010
Bjørnar Hassel
Summary Purpose:, It is commonly assumed that antiepileptic drugs (AEDs) act similarly in the various parts of the brain as long as their molecular targets are present. A few experimental studies on metabolic effects of vigabatrin, levetiracetam, valproate, and lamotrigine have shown that these drugs may act differently in different brain regions. We examined effects of chronic treatment with levetiracetam or phenytoin on mRNA levels to detect regional drug effects in a broad, nonbiased manner. Methods:, mRNA levels were monitored in three brain regions with oligonucleotide-based microarrays. Results:, Levetiracetam (150 mg/kg for 90 days) changed the expression of 65 genes in pons/medulla oblongata, two in hippocampus, and one in frontal cortex. Phenytoin (75 mg/kg), in contrast, changed the expression of only three genes in pons/medulla oblongata, but 64 genes in hippocampus, and 327 genes in frontal cortex. Very little overlap between regions or drug treatments was observed with respect to effects on gene expression. Discussion:, We conclude that chronic treatment with levetiracetam or phenytoin causes region-specific and highly differential effects on gene expression in the brain. Regional effects on gene expression could reflect regional differences in molecular targets of AEDs, and they could influence the clinical profiles of AEDs. [source]

TLR9 stimulation drives naïve B cells to proliferate and to attain enhanced antigen presenting function

EUROPEAN JOURNAL OF IMMUNOLOGY, Issue 8 2007
Wei Jiang
Abstract Mechanisms that regulate naïve B cell proliferation and function are incompletely defined. In this study, we test the hypothesis that naïve B cell expansion, survival and ability to present antigen to T,lymphocytes can be directly modulated by Toll-like receptor (TLR) agonists. In the absence of B cell receptor stimulation, CpG oligonucleotide, a TLR9 agonist, was particularly efficient in inducing naïve B cell proliferation and survival. Although the expanded naïve B cells did not mature into CD27+ or IgG+ memory B cells, these cells did differentiate into IgM-secreting cells with increased surface expression of HLA-DR, CD40 and CD80. This was associated with an increased potential for these B cells to activate allogeneic T cells. We propose that the activation and expansion of naïve B cells induced by TLR9 agonists could enhance the potential of these cells to interact with cognate antigens and facilitate cell-mediated immune responses. [source]

Oligonucleotide Duplexes with Tethered Photoreactive Ruthenium(II) Complexes: Influence of the Ligands and Their Linker on the Photoinduced Electron Transfer and Crosslinking Processes of the Two Strands

EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 4 2009
Stéphanie Deroo
Abstract The photoreactivity of new RuII -oligonucleotide conjugates is investigated in the presence of their complementary strands. The goal is to determine the origins of different effects of parameters that control the photocrosslinking process of the two strands. Therefore, two RuII compounds, either [Ru(tap)3]2+or [Ru(tap)2phen]2+ (tap = 1,4,5,8-tetraazaphenanthrene, phen = 1,10-phenanthroline) with different oxidation powers, were tethered with different linkers to either the 5,- or 3,-phosphate end of the probe strand before hybridization with the complementary strand. These systems were studied by time-resolved emission spectroscopy, UV/Vis absorption experiments, PAGE and MS (ESI) analyses. The best yields of photocrosslinking (45,%) obtained with [Ru(tap)3]2+ tethered to the 3,-position are due to (i) a higher oxidation power of the complex and (ii) its attachment at the 3,-position. Indeed, this tethering favours the interaction of the Ru compound with the duplex and, therefore, inhibits its photodechelation. This work allows better design of sequence-specific DNA photodamaging agents prior to biological applications.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009) [source]

Inhibition of tyrosine kinase receptor type B synthesis blocks axogenic effect of estradiol on rat hypothalamic neurones in vitro

EUROPEAN JOURNAL OF NEUROSCIENCE, Issue 2 2004
V. I. Brito
Abstract 17-,-estradiol (E2) increases axonal growth and tyrosine kinase receptor (Trk)B levels of male-derived hypothalamic neurones in vitro. To investigate whether the axogenic response depends on the upregulation of TrkB, we analysed neuritic growth and neuronal polarization in cultures treated with an antisense oligonucleotide against TrkB mRNA. In cultures without E2, treatment with 7.5 or 10 µm antisense reduced TrkB levels and the percentage of neurones showing an identifiable axon; the number and length of minor processes were increased. In cultures treated with 5 µm antisense, morphometric parameters were normal although total TrkB levels were reduced. The same dose prevented the E2-dependent increase of TrkB levels and suppressed the axogenic effect of E2. These results indicate that TrkB is necessary for normal neuronal growth and maturation and further suggest that an increase in TrkB is necessary for E2 to exert its axogenic effect in male-derived neurones. [source]

Overexpression of spermidine/spermine N1 -acetyltransferase in transgenic mice protects the animals from kainate-induced toxicity

EUROPEAN JOURNAL OF NEUROSCIENCE, Issue 2 2000
Kyllikki Kaasinen
Abstract We recently generated a transgenic mouse line with activated polyamine catabolism through overexpression of spermidine/spermine N1 -acetyltransferase (SSAT). A detailed analysis of brain polyamine concentrations indicated that all brain regions of these animals showed distinct signs of activated polyamine catabolism, e.g. overaccumulation of putrescine (three- to 17-fold), appearance of N1 -acetylspermidine and decreases in spermidine concentrations. In situ hybridization analyses revealed a marked overexpression of SSAT-specific mRNA all over the brain tissue of the transgenic animals. The transgenic animals appeared to tolerate subcutaneous injections of high-dose kainate substantially better as their overall mortality was less than 50% of that of their syngenic littermates. We used the expression of glial fibrillary acidic protein (GFAP) as a marker of brain injury in response to kainate. In situ hybridization analysis with GFAP oligonucleotide up to 7 days after the administration of sublethal kainate doses showed reduced GFAP expression in transgenic animals in comparison with their non-transgenic littermates. This difference was especially striking in the cerebral cortex of the transgenic mice where the exposure to kainate hardly induced GFAP expression. The treatment with kainate likewise resulted in loss of the hippocampal (CA3) neurons in non-transgenic but not transgenic animals. These results support our earlier findings indicating that elevated concentrations of brain putrescine, irrespective whether derived from an overexpression of ornithine decarboxylase, or as shown here, from an overexpression of SSAT, play in all likelihood a neuroprotective role in brain injury. [source]

Visible-Light Photoresponsivity of a 4-(Dimethylamino)azobenzene Unit Incorporated into Single-Stranded DNA: Demonstration of a Large Spectral Change Accompanying Isomerization in DMSO and Detection of Rapid (Z)-to-(E) Isomerization in Aqueous Solution

EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 11 2007
Takashi Kamei
Abstract We demonstrate significant visible-light photoresponsivity in a synthesized oligonucleotide containing a built-in pseudo-nucleotide possessing a 4-(dimethylamino)azobenzene (4-DMAzo) side chain. In dry DMSO as solvent, two clearly distinguishable spectra corresponding to the (E) and (Z) forms of the 4-DMAzo moiety tethered to the oligonucleotide were recorded with a conventional spectrophotometer before and after irradiation with 420 nm wavelength light, which induced (E)-to-(Z) isomerization. In addition, (Z)-to-(E) isomerization was accelerated by irradiation with either visible (, = 550 nm) or UV (, = 350 nm) light, demonstrating reversible photoresponsivity of the pseudo-oligonucleotide. In aqueous solutions the (Z)-to-(E) thermal isomerization of the photoresponsive pseudo-oligonucleotide was very rapid and was only detectable by laser flash photolysis.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source]

Aptamer-Conjugated Nanoparticles Efficiently Control the Activity of Thrombin

ADVANCED FUNCTIONAL MATERIALS, Issue 18 2010
Yen-Chun Shiang
Abstract Thrombin-binding aptamer-conjugated gold nanoparticles (TBA-Au NPs) for highly effective control of thrombin activity towards fibrinogen are demonstrated. While a 29-base long oligonucleotide (TBA29) has known no enzymatic inhibitory functions for thrombin-mediated coagulation, the ultrahigh anticoagulant potency of TBA29 -Au NPs can be demonstrated via the steric blocking effect, at two orders of magnitude higher than that of free TBA29. The surface aptamer density on the Au NPs is important in determining their enzymatic inhibition of thrombin and their stability in the presence of nuclease. The practicality of 100TBA29 -Au NPs (100 TBA29 molecules per Au NP) for controlling thrombin-mediated coagulation in plasma is found, and the 100TBA29 -Au NPs has an ultra binding affinity towards thrombin (Kd = 2.7 × 10,11M) due to their high ligand density. The anticoagulant activity of TBA29 -Au NPs is found to be suppressed by TBA29 complementary sequence (cTBA29) modified Au NPs (cTBA29 -Au NPs), with a suppression rate 4.6-fold higher than that of cTBA29. The easily prepared and low-cost TBA29 -Au NPs and cTBA29 -Au NPs show their potential in biomedical applications for treating various diseases related to blood clotting disorders. In principle, this study opens the possibility of regulation of molecule binding, protein recognizing, and enzyme activity by using aptamer-functionalized nanomaterials. [source]

The role of ADAM10 and ADAM17 in the ectodomain shedding of angiotensin converting enzyme and the amyloid precursor protein

FEBS JOURNAL, Issue 12 2004
Tobias M. J. Allinson
Numerous transmembrane proteins, including the blood pressure regulating angiotensin converting enzyme (ACE) and the Alzheimer's disease amyloid precursor protein (APP), are proteolytically shed from the plasma membrane by metalloproteases. We have used an antisense oligonucleotide (ASO) approach to delineate the role of ADAM10 and tumour necrosis factor-, converting enzyme (TACE; ADAM17) in the ectodomain shedding of ACE and APP from human SH-SY5Y cells. Although the ADAM10 ASO and TACE ASO significantly reduced (> 81%) their respective mRNA levels and reduced the ,-secretase shedding of APP by 60% and 30%, respectively, neither ASO reduced the shedding of ACE. The mercurial compound 4-aminophenylmercuric acetate (APMA) stimulated the shedding of ACE but not of APP. The APMA-stimulated secretase cleaved ACE at the same Arg-Ser bond in the juxtamembrane stalk as the constitutive secretase but was more sensitive to inhibition by a hydroxamate-based compound. The APMA-activated shedding of ACE was not reduced by the ADAM10 or TACE ASOs. These results indicate that neither ADAM10 nor TACE are involved in the shedding of ACE and that APMA, which activates a distinct ACE secretase, is the first pharmacological agent to distinguish between the shedding of ACE and APP. [source]

Specific inhibition of transforming growth factor-,2 expression in human osteoblast cells by antisense phosphorothioate oligonucleotides

FEBS JOURNAL, Issue 8 2001
Zhong-Jian Shen
To elucidate the role of endogenous transforming growth factor (TGF)-,2 on human osteoblast cell, antisense phosphorothioate oligonucleotides (S-ODNs) complementary to regions in mRNA of TGF-,2 were synthesized and examined their effects on TGF-,2 production and cell proliferation in a human osteoblast cell line ROS 17/2. Antisense S-ODNs were designated for three different target regions in the mRNA of TGF-,2. Among several antisense S-ODN analyzed, an oligonucleotide (AS-11) complementary to the translation initiation site of mRNA of TGF-,2 demonstrated a selective and strong inhibitory effect on TGF-,2 production in osteoblast cells. Other antisense S-ODNs which were designated for other regions in mRNA of TGF-,2 and one- or three-base mismatched analogs of AS-11 showed little or much less antisense activities than AS-11. Therefore, the most effective target site in mRNA of TGF-,2 is at the initiation codon region. The antisense effects of AS-11 were observed without reduction of levels of mRNA of TGF-,2. Furthermore, the inhibition of TGF-,2 expression by antisense S-ODN appeared to enhance cell proliferation, demonstrating the growth inhibitory effect of autocrine TGF-,2 in osteoblast cells. [source]

Effect of cadmium on the relationship between replicative and repair DNA synthesis in synchronized CHO cells

FEBS JOURNAL, Issue 22 2000
Gaspar Banfalvi
Repair and replicative DNA synthesis were measured at different stages of the cell cycle in control and cadmium-treated Chinese hamster ovary (CHO-K1) cells. Cells were synchronized by counterflow centrifugal elutriation. Elutriation resulted in five repair and four replication subphases. On Cd treatment, repair synthesis was elevated in certain subphases. Replicative subphases were suppressed by Cd treatment, with some of the peaks almost invisible. The number of spontaneous strand breaks measured by random oligonucleotide primed synthesis assay showed a cell-cycle-dependent fluctuation in control cells and was greatly increased after Cd treatment throughout the S phase. Elevated levels of the oxidative DNA damage product, 8-oxodeoxyguanosine, were observed after Cd treatment, with the highest level in early S phase, which gradually declined as damaged cells progressed through the cell cycle. [source]

Delivery of Nucleic Acids through the Controlled Disassembly of Multifunctional Nanocomplexes

ADVANCED FUNCTIONAL MATERIALS, Issue 24 2009
Mahmoud Elsabahy
Abstract In this study, novel pH-responsive polyion complex micelles (PICMs) were developed for the efficient delivery of nucleic acid drugs, such as antisense oligonucleotide (AON) and short interfering RNA (siRNA). The PICMs consisted of a poly(amidoamine) (PAMAM) dendrimer,nucleic acid core and a detachable poly(ethylene glycol)- block -poly(propyl methacrylate- co -methacrylic acid) (PEG- b -P(PrMA- co -MAA)) shell. The micelles displayed a mean hydrodynamic diameter ranging from 50 to 70,nm, a narrow size distribution, and a nearly neutral surface charge. They could be lyophilized without any additives and stored in dried form. Upon redispersion in water, no change in complexation efficiency or colloidal properties was observed. Entry of the micelles into cancers cells was mediated by a monoclonal antibody fragment positioned at the extremity of the PEG segment via a disulfide linkage. Upon cellular uptake and protonation of the MAA units in the acidic endosomal environment, the micelles lost their corona, thereby exposing their positively charged endosomolytic PAMAM/nucleic acid core. When these pH-responsive targeted PICMs were loaded with AON or siRNAs that targeted the oncoprotein Bcl-2, they exhibited a greater transfection activity than nontargeted PICMs or commercial PAMAM dendrimers. Moreover, their nonspecific cytotoxicity was lower than that of PAMAM. The pH-responsive PICMs reported here appear as promising carriers for the delivery of nucleic acids. [source]