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At least 883 records · Page 49Linked to original sources
PubMed2004

HrpA, a DEAH-box RNA helicase, is involved in mRNA processing of a fimbrial operon in Escherichia coli.

Endonucleolytic cleavage of mRNA in the daa operon of Escherichia coli is responsible for co-ordinate regulation of genes involved in F1845 fimbrial biogenesis. Cleavage occurs by an unidentified endoribonuclease, is translation dependent and involves a unique recognition mechanism. Here, we present the results of a genetic strategy used to identify factors involved in daa mRNA processing. We used a reporter construct consisting of the daa mRNA processing region fused to the gene encoding green fluorescent protein (GFP). A mutant defective in daa mRNA processing and expressing high levels of GFP was isolated by flow cytometry. To determine the location of mutations, two different genetic approaches, Hfr crosses and P1 transductions, were used. The mutation responsible for the processing defect was subsequently mapped to the 32 min region of the E. coli chromosome. A putative DEAH-box RNA helicase-encoding gene at this position, hrpA, was able to restore the ability of the mutant to cleave daa mRNA. Site-directed mutagenesis of the hrpA regions predicted to encode nucleotide triphosphate binding and hydrolysis functions abolished the ability of the gene to restore the processing defect in the mutant. We propose that HrpA is a novel enzyme involved in mRNA processing in E. coli.

Antigens, Bacterial↗
PubMed2006

Design and implementation of a tool for translating SBML into the biochemical stochastic pi-calculus.

MOTIVATION: SBML is becoming a standard 'de-facto' to represent and store biological models. Although SBML is very useful in defining ways of exchanging and storing biological information, it is not formal enough to allow direct translation into non ambiguous formal representation languages to perform analysis and simulation of models. We here suggest to map SBML models into process calculi representations. RESULTS: We implemented and validated a tool that translates SBML descriptions into stochastic pi-calculus specifications. AVAILABILITY: Source code is freely available for academic use by contacting the authors.

Algorithms↗
PubMed2004

Diffusion tensor magnetic resonance image regularization.

As multi-dimensional complex data become more common, new regularization schemes tailored to those data are needed. In this paper we present a scheme for regularising diffusion tensor magnetic resonance (DT-MR) data, and more generally multi-dimensional data defined by a direction map and one or several magnitude maps. The scheme is divided in two steps. First, a variational method is proposed to restore direction fields with preservation of discontinuities. Its theoretical aspects are presented, as well as its application to the direction field that defines the main orientation of the diffusion tensors. The second step makes use of an anisotropic diffusion process to regularize the magnitude maps. The main idea is that for a range of data it is possible to use the restored direction as a prior to drive the regularization process in a way that preserves discontinuities and respects the local coherence of the magnitude map. We show that anisotropic diffusion is a convenient framework to implement that idea, and define a regularization process for the magnitude maps from our DT-MR data. Both steps are illustated on synthetic and real diffusion tensor magnetic resonance data.

Algorithms↗
PubMed1990

Ultraviolet imaging densitometry of unstained gels for two-dimensional electrophoresis.

A system suitable for ultraviolet imaging densitometry of two-dimensional electrophoretic gels that are unstained is described, together with its applications. A flying-spot densitometer linked with a personal computer was used for data acquisition, generation of mapping data, and image processing. Randomly distributed zones of proteins on two-dimensional gels were detected at 280 nm without being stained by two-dimensional scanning, and the densitometric value of each pixel (0.2 x 0.2 mm) was memorized by the computer, which generated a mapping pattern with density contours. The amount and densitometric value of cytochrome c had a linear relationship in the range of 2-200 micrograms. Zone locations of bovine liver proteins separated on two-dimensional gels were indicated on a map expressed in X-Y coordinates, and the pIs and molecular weights could be calculated from the map by use of pI and molecular weight markers on the same gel.

Animals↗
PubMed1994

Antisense MAP-2 oligonucleotides induce changes in microtubule assembly and neuritic elongation in pre-existing neurites of rat cortical neurons.

Microtubule-associated protein 2 (MAP-2) is an abundant component of the cytoskeleton present in dendrites and cell bodies of neurons of the CNS. To examine the biological function of MAP-2, two MAP-2 antisense (AS) oligonucleotides complementary to the 5' region of the rat MAP-2 cDNA were added to rat primary embryonic day 17-18 (E17-18) cultured cortical neurons 24 h after plating and neurite outgrowth and morphology studied. The treatment of primary cortical cultures with either of the two MAP-2 AS oligonucleotides resulted in decreased MAP-2 and reduction in the number of neuritic processes relative to the control or MAP-2 sense-treated cultures. By immunostaining and light microscopy the AS-treated neurons appeared smaller, more rounded, and less intensely stained for MAP-2 than the untreated or the MAP-2 sense-treated cultures. By electron microscopy disorganized microtubules and a reduction in the number of microtubules within neurites of the AS-treated cultures were observed. We conclude that MAP-2 continues to be required for microtubule spacing and stability within neurites once they have formed.

Animals↗
PubMed2001

Axon collaterals of Meynert cells diverge over large portions of area V1 in the macaque monkey.

Patchy intrinsic connections, originating mainly from horizontal collaterals of pyramidal neurons, have been demonstrated in area V1 and many other cortical areas. In this article, we identify a network of intrinsic connections concentrated in layer 6 of area V1. These are visualized by extracellular injections of anterograde tracers in V1, which label small clusters of large terminal boutons in layer 6, in conjunction with thick axon segments. These segments can be traced back to infragranular Meynert cells (n = 10), which are retrogradely labeled from the injections. By using serial section analysis, we identified the following features of this distinctive system of Meynert cell collaterals: (1) terminal clusters are relatively small (<100 microm); (2) each cluster has a small number of rather large boutons (up to 3.0 microm); (3) there is typically a termination-free zone in the immediate vicinity (0.5-2.0 mm) of the cell body; (4) a single neuron has multiple branches that can extend up to 8.0 mm from the soma; and (5) the collaterals are concentrated in layer 6. These features are different from those of horizontal intrinsic connections in the supragranular layers of area V1. They are consistent with fast dynamics and a possible role in wide-field motion processing, such as has been associated with Meynert cells from other studies.

Animals↗
PubMed1993

MAP kinase becomes stably activated at metaphase and is associated with microtubule-organizing centers during meiotic maturation of mouse oocytes.

Using antisera generated against sequences conserved between the ERK1- and the ERK2-encoded species of mitogen-activated protein (MAP) kinases of the rat, species of approximate M(r) 42 and 44 kDa were identified in mouse oocytes. When oocytes underwent meiotic maturation, both species displayed a retarded electrophoretic mobility, consistent with modification by phosphorylation. The slow-migrating forms first appeared after the oocytes had entered metaphase, and their appearance was sensitive to inhibitors of protein synthesis or phosphorylation. These forms remained throughout maturation and in oocytes arrested at metaphase II. Following oocyte activation, which induces a transition to interphase, the slow-migrating forms were replaced by the fast-migrating forms observed in prophase oocytes. MAP kinase activity also increased after oocytes entered metaphase, and this increase required protein synthesis and phosphorylation. To investigate the intracellular distribution of the immunoreactive species, spindles were purified from metaphase II eggs. Both the 42- and the 44-kDa species were detected in immunoblots, and bright staining of the spindle poles was observed by immunofluorescence. When intact oocytes undergoing maturation were examined by immunofluorescence, foci of staining were initially detected on opposing sides of the condensing chromosomes and then became congregated at each pole of the first meiotic spindle. No localized staining was observed during the first meiotic division, but stained foci were present at the poles of the second meiotic spindle. In addition, several cytoplasmic foci of staining often could be seen. When oocytes were exposed to taxol, which permits nonspindle microtubule-organizing centers (MTOCs) present in the cytoplasm to nucleate microtubule assembly, the cytoplasmic foci labeled by the MAP kinase antibodies were found to contain tubulin. We conclude that mouse oocytes contain 42- and 44-kDa species of MAP kinase and that, after maturing oocytes enter metaphase, MAP kinase activity is stimulated by means of a process requiring protein synthesis and phosphorylation. MAP kinase is present in the spindle and is specifically associated with the MTOCs present at the spindle poles and in the cytoplasm. Evidence from cell-free systems suggests that the alterations in MTOC activity that normally occur at metaphase in oocytes may be regulated by MAP kinase. The association of MAP kinase with MTOCs provides a potential structural basis for this cell cycle-dependent change in MTOC activity.

Animals↗
PubMed2003

Elemental occurrence maps: a starting point for quantitative EELS spectrum image processing.

A mechanism for automatic detection, identification and compositional quantification of elements in an EELS spectrum image is described. The method is capable of locating elemental occurrences, discovering signal overlaps, correctly modeling and subtracting the background, or alternatively fitting reference spectra to each image pixel to convert image intensities at any point in a spectrum image to a concentration without almost any operator input, thus paving the way for a completely automated spectrum image analysis. We describe the steps involved in extracting the elemental content in a spectrum image and demonstrate how an image can be derived that clearly reveals the problem zones that prevent accurate results in a subsequent quantification. Such an automatically generated image can then serve as a binary mask, which allows performing selective calculations on certain specimen areas, when applied to the original data set. We demonstrate the feasibility of such an approach by displaying examples computed from ceramic as well as alloy and steel specimens.

Journal Article↗
PubMed2006

Cisplatin increases TNF-alpha mRNA stability in kidney proximal tubule cells.

Cisplatin induces acute renal injury in part by increasing the production of TNF-alpha. However, the mechanism by which cisplatin increases renal TNF-alpha expression is not known. The transcription, translation, and stability of TNF-alpha mRNA are sites of regulation of TNF-alpha production. This study investigated the effects of cisplatin on TNF-alpha mRNA stability and the role of MAP kinases in this process in cultured renal proximal tubule cells. Cisplatin increased the expression of TNF-alpha mRNA by proximal tubule cells in a time- and dose-dependent manner, as well as activated p42/44 ERK kinase, p38 MAP kinase, and JNK in a dose-dependent manner. The inhibition of these pathways reduced TNF-alpha expression significantly. Cisplatin also increased the stability of TNF-alpha mRNA, but this effect was not mediated by MAP kinases and did not require the synthesis of a new protein. The treatment of cells with cisplatin induced the formation of complexes of cytosolic proteins and the AU-rich region of the TNF-alpha 3'UTR. These results are consistent with the view that cisplatin increases TNF-alpha mRNA stability in a MAP kinase-independent manner. The stabilization of TNF-alpha mRNA by cisplatin may involve the binding of certain proteins to AU-rich regions in the 3'UTR.

Acute Kidney Injury↗
PubMed1977

Replication process of the parvovirus H-1. VIII. Partial denaturation mapping and localization of the replication origin of H-1 replicative-form DNA with electron microscopy.

Partial denaturation mapping, restriction endonuclease digestion, and electron microscopy were used to determine which end of the linear duplex replicative-form (RF) DNA molecule contains the origin of RF replication for the parvovirus H-1. This origin was localized within approximately 300 base pairs of the arbitrarily designated right end of the RF DNA, in the EcoRI or HaeII-A fragment. Based on denaturation behavior in formamide, the right end was also found to have a relatively high guanine plus cytosine content, whereas the region adjacent to the left terminus of the RF DNA molecule was adenine plus thymine rich.

DNA Replication↗
PubMed2002

In vivo role of p38 mitogen-activated protein kinase in mediating the anti-inflammatory effects of CpG oligodeoxynucleotide in murine asthma.

DNA containing unmethylated CpG motifs is intrinsically immunostimulatory, inducing the production of a variety of cytokines and chemokines by immune cells. The strong Th1 response triggered by CpG oligodeoxynucleotide (ODN) inhibits the development of Th2-mediated allergic asthma in mice. This work documents that CpG ODN-induced IL-12 production plays a critical role in this process, because intrapulmonary CpG ODN inhibits allergic inflammation in wild-type but not IL-12(-/-) mice. CpG ODN rapidly localized to alveolar macrophages (AM), thereby triggering the phosphorylation of p38 mitogen-activated protein kinase (MAP kinase). AM cultured with CpG but not control ODN up-regulated IL-12 p40 expression and release, and these effects were blocked by the highly specific p38 MAP kinase inhibitor SB202190. Intrapulmonary administration of this inhibitor blocked the ability of CpG ODN to produce IL-12 in the lungs and reversed the anti-inflammatory effects of CpG ODN on allergic lung inflammation. These findings indicate that IL-12 production by AM is stimulated by intrapulmonary CpG ODN administration through a p38 MAP kinase-dependent process, and IL-12 is a key cytokine that mediates CpG ODN-induced protection against allergic lung inflammation.

Adjuvants, Immunologic↗
PubMed1997

The mouse genes encoding the third pair of beta-type proteasome subunits regulated reciprocally by IFN-gamma: structural comparison, chromosomal localization, and analysis of the promoter.

Proteasomes are the multisubunit protease involved in the generation of peptides presented by MHC class I molecules. When cells are stimulated with IFN-gamma, two MHC-encoded subunits, low Mr polypeptide 2 (LMP2) and LMP7, are incorporated into the proteasomal complex by displacing the housekeeping subunits, designated Y and X, respectively. Recent evidence indicates that besides the LMP2/Y and LMP7/X subunits, there is another pair of structurally similar beta-type subunits, designated MECL1 and Z, whose expression is regulated reciprocally by IFN-y. In the present study we determined the genomic organizations of the mouse genes, Psmb10 and Psmb7, that encode the MECL1 and Z subunits, respectively. Although the two genes differ > 10-fold in size, they both have eight exons, with the exon-intron boundaries located precisely at the equivalent positions. The organization of the Psmb10 and Psmb7 genes differs from those of the genes encoding the other two pairs of IFN-gamma-regulated subunits. Thus, comparison of the gene structures supports the idea that Psmb10 and Psmb7 arose by duplication from an immediate common ancestor. The promoter region of the Psmb10 gene contains two IFN-stimulated response elements, the functionality of which was confirmed by in vitro mutagenesis. The mouse Psmb10 gene maps to chromosome 8, thus outside the MHC like its human counterpart. Besides the Psmb7 gene previously mapped to chromosome 2, a truncated processed pseudogene, designated Psmb7-ps, was identified and mapped to chromosome X.

Amino Acid Sequence↗
PubMed2001

A hierarchical dynamical map as a basic frame for cortical mapping and its application to priming.

A hierarchical dynamical map is proposed as the basic framework for sensory cortical mapping. To show how the hierarchical dynamical map works in cognitive processes, we applied it to a typical cognitive task known as priming, in which cognitive performance is facilitated as a consequence of prior experience. Prior to the priming task, the network memorizes a sensory scene containing multiple objects presented simultaneously using a hierarchical dynamical map. Each object is composed of different sensory features. The hierarchical dynamical map presented here is formed by random itinerancy among limit-cycle attractors into which these objects are encoded. Each limit-cycle attractor contains multiple point attractors into which elemental features belonging to the same object are encoded. When a feature stimulus is presented as a priming cue, the network state is changed from the itinerant state to a limit-cycle attractor relevant to the priming cue. After a short priming period, the network state reverts to the itinerant state. Under application of the test cue, consisting of some feature belonging to the object relevant to the priming cue and fragments of features belonging to others, the network state is changed to a limit-cycle attractor and finally to a point attractor relevant to the target feature. This process is considered as the identification of the target. The model consistently reproduces various observed results for priming processes such as the difference in identification time between cross-modality and within-modality priming tasks, the effect of interval between priming cue and test cue on identification time, the effect of priming duration on the time, and the effect of repetition of the same priming task on neural activity.

Brain Mapping↗
PubMed1991

Characterization and chromosomal mapping of a human steroid 5 alpha-reductase gene and pseudogene and mapping of the mouse homologue.

The enzyme steroid 5 alpha-reductase catalyzes the conversion of testosterone into the more powerful androgen, dihydrotestosterone. We previously described the cloning of rat and human cDNAs that encode steroid 5 alpha-reductase and their expression in oocytes and cultured cells. Here, we report the isolation, characterization, and chromosomal mapping of two human steroid 5 alpha-reductase genes. One gene (symbol SRD5A1) is functional, contains five exons separated by four introns, and maps to the distal short arm of chromosome 5. Two informative restriction fragment length polymorphisms are present in exons 1 and 2 of this gene. A second gene (symbol SRD5AP1) has all of the hallmarks of a processed pseudogene and was mapped to the q24-qter region of the X chromosome. In the mouse, a single steroid 5 alpha-reductase gene (Srd5 alpha-1) is linked to Xmv-13 on chromosome 13.

3-Oxo-5-alpha-Steroid 4-Dehydrogenase↗
PubMed2003

Biogeochemistry and isotope geochemistry of a landfill leachate plume.

The biogeochemical processes were identified which improved the leachate composition in the flow direction of a landfill leachate plume (Banisveld, The Netherlands). Groundwater observation wells were placed at specific locations after delineating the leachate plume using geophysical tests to map subsurface conductivity. Redox processes were determined using the distribution of solid and soluble redox species, hydrogen concentrations, concentration of dissolved gases (N(2), Ar, and CH(4)), and stable isotopes (delta15N-NO(3), delta34S-SO(4), delta13C-CH(4), delta2H-CH(4), and delta13C of dissolved organic and inorganic carbon (DOC and DIC, respectively)). The combined application of these techniques improved the redox interpretation considerably. Dissolved organic carbon (DOC) decreased downstream in association with increasing delta13C-DOC values confirming the occurrence of degradation. Degradation of DOC was coupled to iron reduction inside the plume, while denitrification could be an important redox process at the top fringe of the plume. Stable carbon and hydrogen isotope signatures of methane indicated that methane was formed inside the landfill and not in the plume. Total gas pressure exceeded hydrostatic pressure in the plume, and methane seems subject to degassing. Quantitative proof for DOC degradation under iron-reducing conditions could only be obtained if the geochemical processes cation exchange and precipitation of carbonate minerals (siderite and calcite) were considered and incorporated in an inverse geochemical model of the plume. Simulation of delta13C-DIC confirmed that precipitation of carbonate minerals happened.

Environmental Monitoring↗
PubMed2006

DHEA reduces NGF-mediated cell survival in serum-deprived PC12 cells.

Adrenocortical androgens, including dehydroepiandrosterone (DHEA), are produced in the inner zone of the adrenal cortex that is in direct contact with the neural crest-derived catecholamine-producing chromaffin cells. DHEA has recently been identified as a crucial regulator of neuronal stem cell proliferation. Thus, DHEA might play a hitherto unknown role in intra-adrenal tissue formation. In the present study, we examined the influence of DHEA on nerve growth factor (NGF)-mediated survival in serum-deprived PC12 cells and analyzed the influence of DHEA on NGF-induced ERK1/2 mitogen-activated protein (MAP) kinase activation by enzyme-linked immunosorbent assay (ELISA). Cell survival promoted by NGF in serum-deprived PC12 cells and neurite outgrowth was reduced by DHEA, pointing toward a role of DHEA in the differentiation process of chromaffin cells. Furthermore, NGF-induced ERK 1/2 activation was significantly inhibited by DHEA. Hence, we speculate that DHEA might influence NGF-mediated chromaffin differentiation processes using the ERK1/2 MAP kinase pathway during adrenal tissue development.

Animals↗