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Results for “Poly(A) selection”

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PubMed2004

An Eu(III) sensor based on N,N-diethyl-N-(4-hydroxy-6-methylpyridin-2-yl)guanidine.

A highly selective poly(vinyl chloride)-based membrane sensor produced by using N,N-diethyl-N-(4-hydroxy-6-methylpyridin-2-yl)guanidine (GD) as active material is described. The electrode displays Nernstian behavior over the concentration range 7.0 x 10(-5) - 1.0 x 10(-1) M. The detection limit of the electrode is 5.0 x 10(-5) M. The best performance was obtained with the membrane containing 30% PVC, 55% benzyl acetate, 5% GD and 10% oleic acid. The response of the sensor is pH-independent in the range of 3.0 - 7.0. The sensor possesses satisfactory reproducibility, fast response time (< 20 s), and specially excellent discriminating ability for Eu(III) ion with respect to the alkali, alkaline earth, transition and heavy metal ions. The membrane sensor was used as an indicator electrode in potentiometric titration of Eu(III) ion with EDTA. It was also applied in determination of fluoride ions in mouth wash preparations.

Europium↗

PubMed2005

Elevated levels of the 64-kDa cleavage stimulatory factor (CstF-64) in lipopolysaccharide-stimulated macrophages influence gene expression and induce alternative poly(A) site selection.

Lipopolysaccharide (LPS) activation of murine RAW 264.7 macrophages influences the expression of multiple genes through transcriptional and post-transcriptional mechanisms. We observed a 5-fold increase in CstF-64 expression following LPS treatment of RAW macrophages. The increase in CstF-64 protein was specific in that several other factors involved in 3'-end processing were not affected by LPS stimulation. Activation of RAW macrophages with LPS caused an increase in proximal poly(A) site selection within a reporter mini-gene containing two linked poly(A) sites that occurred concomitant with the increase in CstF-64 expression. Furthermore, forced overexpression of the CstF-64 protein also induced alternative poly(A) site selection on the reporter minigene. Microarray analysis performed on CstF-64 overexpressing RAW macrophages revealed that elevated levels of CstF-64 altered the expression of 51 genes, 14 of which showed similar changes in gene expression with LPS stimulation. Sequence analysis of the 3'-untranslated regions of these 51 genes revealed that over 45% possess multiple putative poly(A) sites. Two of these 51 genes demonstrated alternative polyadenylation under both LPS-stimulating and CstF-64-overexpressing conditions. We concluded that the physiologically increased levels of CstF-64 observed in LPS-stimulated RAW macrophages contribute to the changes in expression and alternative polyadenylation of a number of genes, thus identifying another level of gene regulation that occurs in macrophages activated with LPS.

3' Untranslated Regions↗

PubMed2003

Selective labeling and detection of specific RNAs in an RNA mixture.

We report here a unique approach to selectively label and detect specific RNA in an RNA mixture (without separation or purification) using DNA polymerase, dNTP labels, and a short synthetic DNA template complementary to the 3(')-terminus of the RNA. The detection sensitivity is high, at attomole level (10-18 mole). The selective principle was demonstrated by individually labeling and detecting RNAs in a RNA mixture when different templates were provided. By taking advantage of the template-directed selectivity, poly(A) tail-containing mRNA in total RNA was detected and labeled at the 3(')-terminal on a poly(T) template. Nonradioactive labels, such as fluorophore and antigen labels, may also be used; this method can be applied in methodology for direct detection and quantification of viral RNAs.

DNA-Directed DNA Polymerase↗

PubMed2001

Separation of olanzapine, carbamazepine and their main metabolites by capillary electrophoresis with pseudo-stationary phases.

Conditions were worked out for the separation of carbamazepine, olanzapine, and their main metabolites carbamazepine 10,11-epoxide, 10-hydroxycarbamazepine, and desmethylolanzapine. The separation was based on electrokinetically driven methods in the capillary format. The main difficulty in separating these compounds is related to their different chemical classes. Whereas the carbamazepine members are amides, and are electrically neutral, the olanzapine members have aliphatic amino groups and are thus cationic under most experimental conditions. Different additives were applied as pseudo-stationary phases to implement selectivity. Poly(diallyldimethylammonium), PDADMA, is a polycationic replaceable and soluble polymer, that interacts mainly according to the polarisability of the analyte molecules. The MEKC principle was applied with the common SDS as micelle former. In both systems, only partial resolution of the analytes was obtained. The most favorable system consisted of a charged, oligomeric additive: full separation of all analytes within 4 min was achieved with heptakis-6-sulfato-beta-cyclodextrin (7 mM) in 30 mM borate buffer, pH 8.5.

Antipsychotic Agents↗

PubMed2006

Laser ablation inductively coupled plasma mass spectrometry assisted insight into ion-selective membranes.

Laser ablation inductively coupled plasma mass spectrometry was used to evaluate ion depth profiles across ion-selective membranes. Advantageously, this approach does not require incorporation of additional components (e.g., chromoionophore) in the membrane composition, as compared to that used in typical potentiometric applications. Moreover, comparison of the distribution of ions in differently pretreated membranes is possible. Concentration profiles of primary and interfering agent (Na+) ions were recorded, for example, of Pb2+-selective poly(vinyl chloride)-based membranes. It was found that the contents and the distribution of Pb(2+) and Na+ ions across the membrane is strongly dependent on the composition of the solutions to which both sides of the membrane are exposed during preconditioning and on the plasticizer included in the membrane formulation. Typical plasticizers, bis(2-ethylhexyl sebacate) (DOS) and the more polar 2-nitrophenyl octyl ether (o-NPOE), were used. It was found that faster ion transport occurs for o-NPOE, and the membrane saturation with Pb2+ ions was achieved within less than 20 h for a 400-microm-thick membrane. In the case of the less polar plasticizer DOS, due to slower rate of ion transport, even after 20 h, the Pb2+ concentration gradients were still visible within the membrane. On the basis of concentration profiles, primary ion diffusion coefficients in both membranes were calculated, and the value obtained for o-NPOE containing membrane was found to be approximately 2 times higher than for its DOS-plasticized counterpart.

Decanoic Acids↗

PubMedDate not supplied

Selective flocculation and precipitation for the improvement of virus-like particle recovery from yeast homogenate.

The purification of an intracellular product from a complex mixture of contaminants after cell disruption is a common problem in processes downstream of fermentation systems. This is particularly challenging for the recovery of particulate (80 nm in diameter) multimeric protein products, named virus-like particles (VLPs), from cell debris and other intracellular components. Selective flocculation for debris removal followed by selective precipitation of the target protein can be used as a preclarification step to aid purification. In this paper, selective borax flocculation of cell debris in yeast homogenate, followed by selective poly(ethylene glycol) precipitation of VLPs are defined with a view to demonstrating their potential in aiding the initial clarification stages of the purification sequence. The translation from laboratory scale to pilot scale operation is addressed, demonstrating the challenge of scale-up of solid-liquid separation stages for biological particle processing.

Borates↗

PubMed2005

Small-angle neutron scattering study of adsorbed pluronic tri-block copolymers on laponite.

The adsorption of selected poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) (PEO-PPO-PEO) tri-block copolymers on synthetic clay particles (laponite) has been investigated. The adsorbed amount and distribution of polymer was determined as a function of relative block composition and size, using the technique of contrast variation small-angle neutron scattering. The pluronic molecules appear to adsorb via a preferential segregation of hydrophobic PPO segments at the surface, with hydrophilic PEO segments dangling into solution. The effect of the PPO segments is substantial with large increases in adsorbed amount and layer thickness as the anchor fraction decreases/PEO chain length increases. This is in direct contrast to the behavior observed for PEO homopolymer adsorption (of much higher molecular weights) where the adsorbed amount and layer thickness are smaller and change little with molecular weight.

Journal Article↗

PubMed2002

Double-armed crown ethers: synergic pi-coordination effect on potentiometric sensing for Ag(I).

Three diaza-18-crown-6 derivatives having methyl (L1), methoxy (L2) and phenyl (L3) end-groups in para-substituted phenolic side-arms have been investigated as potentiometric sensing materials for silver(I)-selective poly(vinyl chloride) membrane electrodes. The aim of the present work is to establish whether a combination of macrocyclic coordination to Ag+ ion and Ag-pi interaction might produce synergic effect in Ag+ ion sensing. The electrode based on the aromatic end-groups, L3 was found to give remarkably better electrochemical performance than their aliphatic counterparts (L1 and L2). The sensing ability for Ag+ ion with the proposed electrode was enhanced noticeably due to the pi-coordination of Ag+ ion, which was elucidated by NMR. The present findings may serve as an alternative approach for designing advanced sensing materials.

Journal Article↗

PubMed1988

Cloning of cDNA to rat mammary-gland fatty acid synthase mRNA. Evidence for the expression of two mRNA species during lactation.

A cDNA library was constructed in the expression vector lambda gt11, by synthesizing cDNA from size-selected poly(A) RNA from lactating rat mammary gland, using random hexanucleotide primers. Using this library we identified two recombinants which, on addition of a lac z inducer, produced proteins recognized by affinity-purified anti-fatty-acid synthase antibody, and which, therefore, contained fatty acid synthase coding sequences. The inserts were subcloned, were shown to be between 500 and 600 base pairs in size, and to cross-hybridize. The cloned DNA was then used in Northern hybridizations with mRNA isolated at various stages throughout lactation. Two mRNA species were identified of approx. 9.7 and 10.4 kilobases, which increased and decreased in parallel during lactation, reaching a peak at 12-13 days. Both mRNA species disappeared rapidly if the pups were removed prematurely. This study provides evidence that, during hormonal induction in lactation, regulation of the level of fatty acid synthase protein can be accounted for by variation in the level of mRNA.

Animals↗

PubMed1982

Acute leukemia viruses E26 and avian myeloblastosis virus have related transformation-specific RNA sequences but different genetic structures, gene products, and oncogenic properties.

Replication-defective acute leukemia viruses E26 and myeloblastosis virus (AMV) cause distinct leukemias although they belong to the same subgroup of oncogenic avian tumor viruses based on shared transformation-specific (onc) RNA sequences. E26 causes predominantly erythroblastosis in chicken and in quail, whereas AMV induces a myeloid leukemia. However, upon cultivation in vitro for >1 month, a majority of surviving hemopoietic cells of E26-infected animals bear myeloid markers similar to those of AMV-transformed cells. We have analyzed the genetic structure and gene products of E26 virus for a comparison with those of AMV. An E26/helper virus complex was found to contain two RNA species: a 5.7-kilobase (kb) RNA that hybridizes with cloned AMV-specific proviral DNA and hence is probably the E26 genome; and an 8.5-kb RNA that is unrelated to AMV and represents helper virus RNA. Thus, E26 RNA is smaller than 7.5-kb AMV RNA. Hybridization of size-selected poly(A)-terminating E26 RNA fragments with AMV-specific DNA indicated that the shared specific sequences are located in the 5' half of the E26 genome as opposed to a 3' location in AMV RNA. In nonproducer cells transformed in vitro by E26, a gag-related nonstructural 135,000-dalton protein (p135) was found. No gag(Pr76) or gag-pol (Pr180) precursors of essential virion proteins, which are present in AMV nonproducer cells, were observed. p135 was also found in cultured E26 virus producing cells of several leukemic chickens, and its intracellular concentration relative to that of the essential virion proteins encoded by the helper virus correlates with the ratio of E26 to helper RNA in virions released by these cells. p135 is phosphorylated but not glycosylated; antigenically it is not related to the pol or env gene products. It appears to be coded for by a partial gag gene and by E26-specific RNA sequences, presumably including those shared with AMV. Hence, AMV and E26 appear to use different strategies for the expression of related onc sequences: AMV is thought to encode a transforming protein via a subgenomic mRNA, whereas E26 codes for a gag-related polyprotein via genomic RNA. It is speculated that differences in the oncogenic properties of E26 and AMV are due to differences in their genetic structures and gene products.

Animals↗

PubMed1986

Identification of the protein encoded by the human diffuse B-cell lymphoma (dbl) oncogene.

The dbl oncogene was initially isolated from a human diffuse B-cell lymphoma. Antisera from mice bearing tumors induced by this oncogene specifically detected a protein of about 66 kDa (p66) in dbl transformants. dbl cDNA-selected poly(A)+ RNA isolated from a transfectant clone expressing p66 directed the in vitro synthesis of this protein, establishing that it is encoded by dbl. Subcellular localization studies revealed that p66 is a cytoplasmic protein distributed between cytosol and crude membrane fractions. Moreover, p66 was shown to be a phosphoprotein, with phosphorylation specific to serine residues. Our characterization of the dbl-encoded protein appears to distinguish this transforming gene product from those of other known oncogenes.

B-Lymphocytes↗

PubMed2003

Properties of a new injectable type of root canal filling resin with adhesiveness to dentin.

The properties of a new, injectable type of root canal wall, adhesive filling resin, which we developed, were studied for its physical properties, adhesiveness to dentin and the root canal, and sealing ability. The new resin consisted of a powder composed of a specially selected poly(methyl methacrylate) and barium sulfate radiopacifier and liquid composed of methyl methacrylate monomer and tributylborane catalyst. A mixture of both components had a consistency suitable for injection. The physical properties, including radiopacity, were evaluated according to the ISO standard. The adhesiveness to dentin and the root canal was investigated by bond strength testing or by scanning electron microscopy. The apical sealing ability of the new resin was compared by a dye penetration test with that of gutta-percha/sealer. The findings of this study indicated that the new filling resin had physical properties satisfying all the ISO requirements for dental root canal sealing materials: a tensile bond strength to dentin of 7.3 MPa, a significantly better sealing ability compared with gutta-percha/sealer, the capability of forming resin tags in dentinal tubules, and removability.

Adhesiveness↗

PubMed1991

Immunology, biosynthesis and in vivo assembly of the branched-chain 2-oxoacid dehydrogenase complex from bovine kidney.

Specific, polyclonal antisera have been raised to the native branched-chain 2-oxoacid dehydrogenase complex (BCOADC) from bovine kidney and each of its three constituent enzymes: E1, the substrate-specific 2-oxoacid dehydrogenase; E2, the multimeric dihydrolipoamide acyltransferase 'core' enzyme and E3, dihydrolipoamide dehydrogenase. Purified BCOADC, isolated by selective poly(ethyleneglycol) precipitation and hydroxyapatite chromatography, contains only traces of endogenous E3 as detected by a requirement for this enzyme in assaying overall complex activity and by immunoblotting criteria. A weak antibody response was elicited by the E1 beta subunit relative to the E2 and E1 alpha polypeptides employing either purified E1 or BCOADC as antigens. Anti-BCOADC serum showed no cross-reaction with high levels of pig heart E3 indicating the absence of antibody directed against this component. However, immunoprecipitates of mature BCOADC from detergent extracts of NBL-1 (bovine kidney) or PK-15 (porcine kidney) cell lines incubated for 3-4 h in the presence of [35S]methionine contained an additional 55,000-Mr species which was identified as E3 on the basis of immunocompetition studies. Accumulation of newly synthesised [35S]methionine-labelled precursors for E2, E1 alpha and E3 was achieved by incubation of PK-15 cells for 4 h in the presence of uncouplers of oxidative phosphorylation. Pre-E2 exhibited an apparent Mr value of 56,500, pre-E1 alpha, 49,000 and pre-E3, 57,000 compared to subunit Mr values of 50,000, 46,000 and 55,000, respectively, for the mature polypeptides. Thus, like the equivalent lipoate acyltransferases of the mammalian pyruvate dehydrogenase (PDC) and 2-oxoglutarate dehydrogenase (OGDC) complexes, pre-E2 of BCOADC characteristically contains an extended presequence. In NBL-1 cells, pre-E2 was found to be unstable since no cytoplasmic pool of this precursor could be detected; moreover, processed E1 alpha was not assembled into intact BCOADC as evidenced by the absence of E2 or E3 in immunoprecipitates with anti-(BCOADC) serum after a 45-min 'chase' period in the absence of uncoupler. Dihydrolipoamide dehydrogenase (E3), in its precursor state, was not present in immune complexes with anti-(BCOADC) serum, indicating that its co-precipitation with mature complex is by virtue of its high affinity for assembled complex in vivo whereas no equivalent interaction of pre-E3 with its companion precursors occurs prior to mitochondrial import.

3-Methyl-2-Oxobutanoate Dehydrogenase (Lipoamide)↗

PubMed1988

Identification of the human pim-1 gene product as a 33-kilodalton cytoplasmic protein with tyrosine kinase activity.

The human pim-1 gene was recently identified as a new putative oncogene located on chromosome 6p21, a region showing karyotypic abnormalities in particular leukemias. In the present work we characterized the pim protein product. In vitro translation of positively selected poly(A)+ mRNA indicates that this gene encodes a 33-kilodalton protein. Anti-pim antibodies were raised against a fused TrpE-pim protein induced in a bacterial expression vector. This antibody immunoprecipitated a 33-kilodalton protein from in vivo [35S]methionine-labeled K562 and KCl myelogenous origin cell lines. This protein was localized to the cytoplasm, and in vivo labeling as well as in vitro kinase assay suggests that it is a phosphoprotein with tyrosine kinase activity. This was further confirmed by performing autophosphorylation directly on a p33pim-containing gel band cut out after sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The results imply that the tyrosine kinase activity of pim can be recovered after boiling the pim-1 protein in sample buffer: a feature not described yet for this class of protein. These results suggest that pim-1 is a new member of the subgroup of oncogenes encoding tyrosine kinases.

Cell Line↗

PubMed1989

Corticosterone-induced responses in rat brain RNA are also evoked in hippocampus by acute vibratory stress.

Corticosterone (CORT) induces responses in brain cells that are mediated by glucocorticoid receptors through regulation of gene activity. We previously found rapid increases in select poly(A)-containing RNAs in rat hippocampus following treatment with CORT that are mediated by low-affinity glucocorticoid receptors. To determine if these responses are hippocampal specific, we examined RNA responses to glucocorticoids in several brain regions, myocardium, and cultured astrocytes by two-dimensional gel electrophoretic resolution of 35S-methionine labelled, in vitro translation products. RNAs coding for similar 35-, 33-, and 20-kdalton polypeptides are induced after 3 days of CORT treatment (40 mg/kg/day) in hippocampus, hypothalamus, cortex, striatum, cerebellum, and myocardium. Primary astrocyte cultures (neonatal rat), however, showed increases after hydrocortisone (1 microgram/ml) in only the 20- and 33-kdalton translation products, while the 35-kdalton polypeptide was not detected. The hippocampal responses were maintained for up to 3 months during chronic daily CORT treatment. To determine if an increase in endogenous CORT levels would also evoke the RNA responses, we subjected rats to 2 h vibratory stress and analyzed the in vitro translation products. RNAs coding for the 35- and 20-kdalton polypeptides were increased 3- to 5-fold in the hippocampus after acute stress in intact rats, but not in stressed adrenalectomized rats. These results suggest a new class of molecular stress responses in brain cells that is glucocorticoid dependent under physiological conditions.

Animals↗

PubMed2003

Bioaugmentation of tar-contaminated soils under field conditions using Pleurotus ostreatus refuse from commercial mushroom production.

The influence of the white rot fungus Pleurotus ostreatus on the degradation of selected poly- and heterocyclic aromatic hydrocarbons (referred to as polycyclic aromatic hydrocarbons [PAHs]) in soil was investigated under field conditions representing the Northern temperate zone. Pleurotus ostreatus was added to two contaminated soils in the form of homogenized refuse from the commercial production of fungus. The soils were collected from a former shipyard (the B&W soil) and underneath a former coal tar storage at an old asphalt factory in Denmark (the Ringe soil). Treatments (control, soil mixed with autoclaved sawdust medium, and soil mixed with P. ostreatus refuse) were set up in triplicate in concrete cylinders (height, 50 cm; diameter, 60 cm). The activity of P. ostreatus was measured as laccase activity and phenanthrene (PHE)- and pyrene (PYR)-degrading bacteria were enumerated. Twenty-one different PAHs were quantified. After nine weeks the concentrations of the 3-, 4-, 5-, and 6-ring PAHs in the Ringe soil were reduced by 78, 41, and 4%, respectively. These reductions corresponded with high initial laccase activity, a decrease in pH caused by the fungus, and an increase in the number of PHE- and PYR-degrading bacteria. No significant PAH degradation was observed in the B&W soil. Reasons for the difference in performance of P. ostreatus in the two soils are discussed in terms of soil histories and bioavailability. The use of P. ostreatus refuse holds promising potential for bioremediation purposes.

Bacteria↗

PubMed2004

A comparison of RT-PCR-based assays for the detection of HAV from shellfish.

The hepatitis A virus (HAV) is the most common cause of viral infection linked to shellfish consumption. The lack of correlation between the fecal coliform indicators and the presence of enteric viruses in shellfish and their harvesting waters points to the need for molecular methods to detect viruses. We compared two RT-PCR based techniques currently available for the detection of the hepatitis A virus (HAV) in shellfish. Both approaches involve extraction of viral particles by glycine buffer and concentration of virus particles by one or two PEG precipitation steps. One procedure involves as RNA extraction method the use of oligo (dT) cellulose to select poly (A) RNA, and the other uses a system in which total RNA is bound on silica membrane. Comparison of the two RT-PCR based methods highlighted the efficiency of the first approach which is less time-consuming and technically demanding than the second.

Animals↗

PubMedDate not supplied

Properties of an HSV-1 regulatory protein that appears to impair host cell splicing.

The herpes simplex virus type 1 (HSV-1) immediate early (alpha) protein ICP27 is an essential regulatory protein that appears to be involved in a number of different processes during lytic viral infection. Viral mutants defective in ICP27 have a variety of phenotypes that include defects in the shutoff of host protein synthesis, overexpression of some immediate early and early genes, reduced levels of DNA replication, and severely reduced levels of late gene products. ICP27 has been shown to act posttranscriptionally in the performance of some of its regulatory roles. It affects mRNA processing at the level of both polyadenylation and splicing. During polyadenylation, ICP27 appears to stimulate 3' RNA processing at selected poly(A) sites. The opposite effect, occurs on host cell splicing, that is, during HSV-1 infection, an inhibition in host cell splicing was found that required ICP27 expression. This impairment of splicing contributes to the shutoff of host protein synthesis by decreasing levels of spliced cellular mRNAs available for translation. A redistribution of splicing factors regulated by ICP27 has also been seen. Mutational analysis has shown that the C-terminal repressor region of the protein is required for the effects seen on splicing, whereas the activator region, encompassing the C-terminal half of the protein is required for the effects on 3' processing and the induction of late gene expression during viral infection. A highly basic arginine-rich region in the N-terminal half of the protein is required for nuclear localization of ICP27. Details on the mechanisms by which ICP27 contributes to these regulatory processes have been poorly defined to date.

Herpesvirus 1, Human↗