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Selected AbstractsA Phenomenological Probe Model of Fast Ion Measurement Using a Hybrid Directional ProbeCONTRIBUTIONS TO PLASMA PHYSICS, Issue 5-7 2008K. Nagaoka Abstract A phenomenological probe model was developed for quantitative fast-ion-measurement using a hybrid directional probe (HDP), which is a directional probe to measure ion current and heat flux at the same position. The secondary electrons due to fast-ion-injection onto the probe surface enhances the ion-saturation-current, thus a thermal probe method was required for quantitative measurement of fast ions. The model gives a simple expression of the secondary electron yield as a function of ion currents and heat fluxes measured by the HDP, and can determine the net fast-ion-current without the calibrations of the thermal probe method. The model was applied to the experimental results of fast-ion-measurements using a HDP in CHS, and the secondary electron yield obtained by the model agrees with the calibration results of the HDP. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] The fidelity of the cortical retinotopic map in human amblyopiaEUROPEAN JOURNAL OF NEUROSCIENCE, Issue 5 2007Xingfeng Li Abstract To delineate the fidelity of the functional cortical organization in humans with amblyopia, we undertook an investigation into how spatial information is mapped across the visual cortex in amblyopic observers. We assessed whether the boundaries of the visual areas controlled by the amblyopic and fellow fixing eye are in the same position, the fidelity of the retinotopic map within different cortical areas and the average receptive field size in different visual areas. The functional organization of the visual cortex was reconstructed using a fMRI phase-encoded retinotopic mapping analysis. This method sequentially stimulates each point in the visual field along the axes of a polar-coordinate system, thereby reconstructing the representation of the visual field on the cortex. We found that the cortical areas were very similar in normals and amblyopes, with only small differences in boundary positions of different visual areas between fixing and fellow amblyopic eye activation. Within these corresponding visual areas, we did find anomalies in retinotopy in some but not all amblyopes that were not simply a consequence of the poorer functional responses and affected central and peripheral field regions. Only a small increase in the average (or collective) receptive field size was found for full-field representation in amblyopes and none at all for central field representation. The former may simply be a consequence of the poorer functional responses. [source] The role of the medial caudate nucleus, but not the hippocampus, in a matching-to sample task for a motor responseEUROPEAN JOURNAL OF NEUROSCIENCE, Issue 7 2006Raymond P. Kesner Abstract A delayed-match-to-sample task was used to assess memory for motor responses in rats with control, hippocampus, or medial caudate nucleus (MCN) lesions. All testing was conducted on a cheeseboard maze in complete darkness using an infrared camera. A start box was positioned in the centre of the maze facing a randomly determined direction on each trial. On the sample phase, a phosphorescent object was randomly positioned to cover a baited food well in one of five equally spaced positions around the circumference of the maze forming a 180-degree arc 60 cm from the box. The rat had to displace the object to receive food and return to the start box. The box was then rotated to face a different direction. An identical baited phosphorescent object was placed in the same position relative to the start box. A second identical object was positioned to cover a different unbaited well. On the choice phase, the rat must remember the motor response made on the sample phase and make the same motor response on the choice phase to receive a reward. Hippocampus lesioned and control rats improved as a function of increased angle separation used to separate the correct object from the foil (45, 90, 135, and 180 degrees) and matched the performance of controls. However, rats with MCN lesions were impaired across all separations. Results suggest that the MCN, but not the hippocampus, supports working memory and/or a process aimed at reducing interference for motor response selection based on vector angle information. [source] In the Search of Glycogen Phosphorylase Inhibitors: Synthesis of C- D -Glycopyranosylbenzo(hydro)quinones , Inhibition of and Binding to Glycogen Phosphorylase in the Crystal,EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 4 2007Li He Abstract Penta- O -acetyl-,- D -glycopyranoses and 1,4-dimethoxybenzene led selectively by electrophilic substitution to C-,- D -glycopyranosyl-1,4-dimethoxybenzenes which were converted by simple and efficient reactions (oxidation, reduction and deacetylation) to the corresponding C-glycosylhydro- and C-glycosylbenzoquinones, with either an acetylated or deprotected sugar moiety. C-,- D -Glucosylbenzoquinone 19 and C-,- D -Glucosylhydroquinone 23 were found to be competitive inhibitors of rabbit muscle glycogen phosphorylase b (GPb), with respect to the substrate ,- D -glucose-1-phosphate, with Ki values of 1.3 and 0.9 mM, respectively, whereas C-,- D -glucosylhydroquinone 17 was not effective up to a concentration of 8 mM. In order to elucidate the structural basis of inhibition, we determined the crystal structures of 19 and 23 in complex with GPb at a 2.03,2.05 Å resolution. The complex structures reveal that the inhibitors can be accommodated at the catalytic site at approximately the same position as ,- D -glucose and stabilise the transition state conformation of the 280s loop by making several favourable contacts to Asp283 and Asn284 of this loop. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source] Expression of a homologue of the fushi tarazu (ftz) gene in a cirripede crustaceanEVOLUTION AND DEVELOPMENT, Issue 2 2002Emmanuèle Mouchel-Vielh SUMMARY In Metazoa, Hox genes control the identity of the body parts along the anteroposterior axis. In addition to this homeotic function, these genes are characterized by two conserved features: They are clustered in the genome, and they contain a particular sequence, the homeobox, encoding a DNA-binding domain. Analysis of Hox homeobox sequences suggests that the Hox cluster emerged early in Metazoa and then underwent gene duplication events. In arthropods, the Hox cluster contains eight genes with a homeotic function and two other Hox -like genes, zerknullt (zen)/Hox3 and fushi tarazu (ftz). In insects, these two genes have lost their homeotic function but have acquired new functions in embryogenesis. In contrast, in chelicerates, these genes are expressed in a Hox -like pattern, which suggests that they have conserved their ancestral homeotic function. We describe here the characterization of Diva, the homologue of ftz in the cirripede crustacean Sacculina carcini. Diva is located in the Hox cluster, in the same position as the ftz genes of insects, and is not expressed in a Hox -like pattern. Instead, it is expressed exclusively in the central nervous system. Such a neurogenic expression of ftz has been also described in insects. This study, which provides the first information about the Hox cluster in Crustacea, reveals that it may not be much smaller than the insect cluster. Study of the Diva expression pattern suggests that the arthropod ftz gene has lost its ancestral homeotic function after the divergence of the Crustacea/Hexapoda clade from other arthropod clades. In contrast, the function of ftz during neurogenesis is well conserved in insects and crustaceans. [source] Crystal structure of human Rad GTPase of the RGK-familyGENES TO CELLS, Issue 8 2006Arry Yanuar Rad (Ras associated with diabetes) is an RGK-family small GTPase that is over-expressed in the skeletal muscle of humans with type II diabetes. Unlike other small GTPases, RGK family members including Rad lack several conserved residues in the GTPase domain. Here, we report the crystal structure of the GTPase domain of human Rad in the GDP-bound form at 1.8 Å resolution. The structure revealed unexpected disordered structures of both switches I and II. We showed that the conformational flexibility of both switches is caused by non-conservative substitutions in the G2 and G3 motifs forming the switch cores together with other substitutions in the structural elements interacting with the switches. Glycine-rich sequences of the switches would also contribute to the flexibility. Switch I lacks the conserved phenylalanine that makes non-polar interactions with the guanine base in H-Ras. Instead, water-mediated hydrogen bonding interactions were observed in Rad. The GDP molecule is located at the same position as in H-Ras and adopts a similar conformation as that bound in H-Ras. This similarity seems to be endowed by the conserved hydrogen bonding interactions with the guanine base-recognition loops and the magnesium ion that has a typical octahedral coordination shell identical to that in H-Ras. [source] Structural Changes in the BODIPY Dye PM567 Enhancing the Laser Action in Liquid and Solid Media,ADVANCED FUNCTIONAL MATERIALS, Issue 16 2007I. García-Moreno Abstract In the search for more efficient and photostable solid-state dye lasers, newly synthesized analogs of the borondipyrromethene (BODIPY) dye PM567, bearing the polymerizable methacryloyloxypropyl group at position 2 (PMoMA) or at positions 2 and 6 (PDiMA), have been studied in the form of solid copolymers with methyl methacrylate (MMA). The parent dye PM567, as well as the model analogs bearing the acetoxypropyl group in the same positions, PMoAc and PDiAc, respectively, have been also studied both in liquid solvents and in solid poly(MMA) (PMMA) solution. Although in liquid solution PMoAc and PDiAc have the same photophysical properties as PM567, PDiAc exhibited a photostability up to 10 times higher than that of PM567 in ethanol under 310,nm-irradiation. The possible stabilization factors of PDiAc have been analyzed and discussed on the basis of the redox potentials, the ability for singlet molecular oxygen [O2(1,g)] generation, the reactivity with O2(1,g), and quantum mechanical calculations. Both PMoAc and PDiAc, pumped transversally at 532,nm, lased in liquid solution with a high (up to 58,%), near solvent-independent efficiency. This enhanced photostabilization has been also observed in solid polymeric and copolymeric media. While the solid solution of the model dye PDiAc in PMMA showed a lasing efficiency of 33,%, with a decrease in the laser output of ca.,50,% after 60,000 pump pulses (10,Hz repetition rate) in the same position of the sample, the solid copolymer with the double bonded chromophore, COP(PDiMA-MMA), showed lasing efficiencies of up to 37,%, and no sign of degradation in the laser output after 100,000 similar pump pulses. Even under the more demanding repetition rate of 30,Hz, the laser emission from this material remained at 67,% of its initial laser output after 400,000 pump pulses, which is the highest laser photostability achieved to date for solid-state lasers based on organic polymeric materials doped with laser dyes. This result indicates that the double covalent linkage of the BODIPY chromophore to a PMMA polymeric matrix is even more efficient than the simple linkage, for its photostabilization under laser operation. [source] Fine mapping of a quantitative trait locus on chromosome 9 affecting non-return rate in Swedish dairy cattleJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 5 2007M. Holmberg Summary We previously mapped a quantitative trait locus (QTL) affecting the trait non-return rate at 56 days in heifers to bovine chromosome 9. The purpose of this study was to confirm and refine the position of the QTL by using a denser marker map and fine mapping methods. Five families that previously showed segregation for the QTL were included in the study. The mapping population consisted of 139 bulls in a granddaughter design. All bulls were genotyped for 25 microsatellite markers surrounding the QTL on chromosome 9. We also analysed the correlated trait number of inseminations per service period in heifers. Both traits describe the heifer's ability to become pregnant after insemination. Linkage analysis, linkage disequilibrium and combined linkage and linkage disequilibrium analysis were used to analyse the data. Analysis of the families jointly by linkage analysis resulted in a significant but broad QTL peak for non-return rate. Results from the combined analysis gave a sharp QTL peak with a well-defined maximum in between markers BMS1724 and BM7209, at the same position as where the highest peak from the linkage disequilibrium analysis was found. One of the sire families segregated clearly at this position and the difference in effects between the two sire haplotypes was 2.9 percentage units in non-return rate. No significant results were found for the number of inseminations in the combined analysis. [source] Synthesis and in-vitro antitumour activity of new naphthyridine derivatives on human pancreatic cancer cellsJOURNAL OF PHARMACY AND PHARMACOLOGY: AN INTERNATI ONAL JOURNAL OF PHARMACEUTICAL SCIENCE, Issue 8 2009Irene Banti Abstract Objectives The aim of the study was to evaluate the antitumour effect in vitro of newly synthesized 7-substituted 2,3-dihydro-1,8-naphthyridines. Methods Characterization tools included cell viability assay, caspase 3/7 induction, DNA fragmentation, fibroblast growth factor type 1 receptor kinase inhibition, and in-vitro antiangiogenic analysis. Key findings Treatment of MIA PaCa-2 human pancreatic cancer cells with test compounds showed time- and concentration-dependent cytotoxicity with IC50 values in the micromolar range. Compounds with an aminoalkyl or a diaminoalkyl side chain at the 7-position exhibited remarkable cytotoxicity, whereas the presence of a methyl group or a cyclic amine in the same position led to a significant decrease in their biological activity. Cytotoxicity screening demonstrated that the most active was compound 11 (mean 50% inhibition of cell proliferation (IC50) 11 ,M). This compound had an in-vitro antitumour efficacy superior to 5-fluorouracil (the lowest cell viability value after treatment (Emax) 0.2% and 19%, respectively) and proved to be less toxic than 5-fluorouracil against non-cancerous human oral epithelial cells. In addition, compound 11 induced apoptosis in MIA PaCa-2 cells and it was able to promote antiangiogenic effects in vitro. Finally, its cytotoxicity was enhanced in pancreatic cancer cells stimulated with fibroblast growth factor, while no substantial effect was observed on human bronchial smooth muscle cells stimulated with the same growth factor. Conclusions These findings suggest that 1,8-naphthyridine derivatives are a promising class of compounds in cancer research. In particular, the antitumour activity of compound 11 is worth further investigation. [source] Natural selection for salt tolerance quantitative trait loci (QTLs) in wild sunflower hybrids: Implications for the origin of Helianthus paradoxus, a diploid hybrid speciesMOLECULAR ECOLOGY, Issue 5 2003C. Lexer Abstract For a new diploid or homoploid hybrid species to become established, it must diverge ecologically from parental genotypes. Otherwise the hybrid neospecies will be overcome by gene flow or competition. We initiated a series of experiments designed to understand how the homoploid hybrid species, Helianthus paradoxus, was able to colonize salt marsh habitats, when both of its parental species (H. annuus×H. petiolaris) are salt sensitive. Here, we report on the results of a quantitative trait locus (QTL) analysis of mineral ion uptake traits and survivorship in 172 BC2 hybrids between H. annuus and H. petiolaris that were planted in H. paradoxus salt marsh habitat in New Mexico. A total of 14 QTLs were detected for mineral ion uptake traits and three for survivorship. Several mineral ion QTLs mapped to the same position as the survivorship QTLs, confirming previous studies, which indicated that salt tolerance in Helianthus is achieved through increased Ca uptake, coupled with greater exclusion of Na and related mineral ions. Of greater general significance was the observation that QTLs with effects in opposing directions were found for survivorship and for all mineral ion uptake traits with more than one detected QTL. This genetic architecture provides an ideal substrate for rapid ecological divergence in hybrid neospecies and offers a simple explanation for the colonization of salt marsh habitats by H. paradoxus. Finally, selection coefficients of +0.126, ,0.084 and ,0.094 for the three survivorship QTLs, respectively, are sufficiently large to account for establishment of new, homoploid hybrid species. [source] Comparison of the sequences of the Aspergillus nidulans hxB and Drosophila melanogaster ma-l genes with nifS from Azotobacter vinelandii suggests a mechanism for the insertion of the terminal sulphur atom in the molybdopterin cofactorMOLECULAR MICROBIOLOGY, Issue 1 2000Laïla Amrani The molybdopterin cofactor (MoCF) is required for the activity of a variety of oxidoreductases. The xanthine oxidase class of molybdoenzymes requires the MoCF to have a terminal, cyanolysable sulphur ligand. In the sulphite oxidase/nitrate reductase class, an oxygen is present in the same position. Mutations in both the ma-l gene of Drosophila melanogaster and the hxB gene of Aspergillus nidulans result in loss of activities of all molybdoenzymes that necessitate a cyanolysable sulphur in the active centre. The ma-l and hxB genes encode highly similar proteins containing domains common to pyridoxal phosphate-dependent cysteine transulphurases, including the cofactor binding site and a conserved cysteine, which is the putative sulphur donor. Key similarities were found with NifS, the enzyme involved in the generation of the iron,sulphur centres in nitrogenase. These similarities suggest an analogous mechanism for the generation of the terminal molybdenum-bound sulphur ligand. We have identified putative homologues of these genes in a variety of organisms, including humans. The human homologue is located in chromosome 18.q12. [source] Stage-specific regulatory element of mouse Sry gene,MOLECULAR REPRODUCTION & DEVELOPMENT, Issue 4 2003Kou Yokouchi Abstract Sry expression is essential for initiating male sex differentiation, and the expression occurs only during a restricted period in the developing gonad. It is thought that Sry is part of a pathway of genes that regulate sex determination. Although the interactions of several genes with Sry expression have been suggested, the exact cascade of gene expression regulating Sry transcription is entirely obscure because there is no available cell line expressing Sry and reflecting an in vivo condition. The present study was carried out to investigate the cis -acting element of the mouse Sry that responds stage specifically to its expression, in part, using transgenic mice expressing GFP on the Y chromosome. Ten DNA fragments were generated by digesting the 5, upstream region (positions 5491,8039; 2,549 bp) of mouse Sry with appropriate restriction enzymes. In an electrophoretic mobility assay with these fragments, the region from position 5491 to position 5799 (309 bp) was identified as forming specific protein,DNA complexes with nuclear extracts from 11.5 days post coitus (dpc) gonads, but not from 12.5 and 13.5-dpc gonads. This region also formed specific protein,DNA complexes with the nuclear extracts from adult testicular germ cells that generate only a circular form from Sry. This stage-specific responsive region was narrowed down to positions 5559,5616 by DNase I footprinting analysis. The assay of DNase I hypersensitive (HS) using the nuclear lysates from the 11.5-dpc urogenital ridges demonstrated that the novel HS site was located in the proximity of position 5600. This region DNase I HS was also detected at the same position when the lysates from adult testicular germ cells were applied. The results indicate that the present HS site may be involved in the transcriptional regulation of the linear and/or circular molecule transcripts from mouse Sry gene. Mol. Reprod. Dev. 64: 389,396, 2003. © 2003 Wiley-Liss, Inc. [source] Novel mutation in the ceruloplasmin gene causing a cognitive and movement disorder with diabetes mellitusMOVEMENT DISORDERS, Issue 12 2006Hui-Fang Shang MD Abstract In a Chinese woman who had diabetes mellitus, undetectable ceruloplasmin, hand tremor, neck dystonia, and cognitive disturbances, genetic analyses revealed a novel homozygous mutation (848G>C or W283S) in exon 5 in the ceruloplasmin gene. Another member with a milder phenotype was also affected by this mutation. The healthy sister was heterozygous at the same position. Aceruloplasminemia has not yet been reported in China. This case suggests that increased awareness should be paid to this disorder in the presence of the typical symptoms. © 2006 Movement Disorder Society [source] The Crystal Structure of the L1 Intermediate of Halorhodopsin at 1.9 Å Resolution,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 2 2007Walter Gmelin The mutant T203V of the light driven chloride pump halorhodopsin from Halobacterium salinarum was crystallized and the X-ray structure was solved at 1.6 Å resolution. The T203V structure turned out to be nearly identical to the wild type protein with a root mean square deviation of 0.43 Å for the carbon , atoms of the protein backbone. Two chloride binding (CB) sites were demonstrated by a substitution of chloride with bromide and an analysis of anomalous difference Fourier maps. The CB1 site was found at the same position as in the wild type structure. In addition, a second chloride binding site CB2 was identified around Q105 due to higher resolution in the mutant crystal. As T203V showed a 10 times slower decay of its photocycle intermediate L, this intermediate could be trapped with an occupancy of 60% upon illumination at room temperature and subsequent cooling to 120°K. Fourier transform infrared spectroscopy clearly identified the crystal to be trapped in the L1 intermediate state and the X-ray structure was solved to 1.9 Å resolution. In this intermediate, the chloride moved by 0.3 Å within binding site CB1 as indicated by peaks in difference Fourier density maps. The chloride in the second binding site CB2 remained unchanged. Thus, intraproteinous chloride translocation from the extracellular to the cytoplasmic part of the protein must occur in reaction steps following the L1 intermediate in the catalytic cycle of halorhodopsin. [source] Global phosphoproteome analysis on human HepG2 hepatocytes using reversed-phase diagonal LCPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 14 2005Kris Gevaert Professor Abstract We present a phosphoproteomics approach using diagonal RP chromatography as the basic isolation principle. Phosphopeptides present in a tryptic digest of total cellular lysates were first enriched by Fe3+ -immobilized metal ion affinity chromatography. Further sorting of the phosphopeptides took place in three steps. First, the resulting peptide mixture was fractionated over reversed-phase chromatography. Second, peptides present in each fraction were treated with phosphatases. Third, the dephosphorylated peptides were then more hydrophobic and shifted towards a later elution interval from the contaminating non-phosphopeptides eluting at the same position as during the primary run. Since the phosphopeptides are isolated as their dephosphorylated form, additional proof for their original phosphorylation state was obtained by split-differential 16O ,18O labeling. The method was validated with alpha-casein phosphopeptides and consecutively applied on HepG2 cells. We identified 190,phosphorylated peptides from 152,different proteins. This dataset includes 38,novel protein phosphorylation sites. [source] CT-Soft Tissue Window of the Cranial Abdomen in Clinically Normal Dogs: An Anatomical description using Macroscopic Cross-Sections with Vascular InjectionANATOMIA, HISTOLOGIA, EMBRYOLOGIA, Issue 1 2009M. A. Rivero Summary The aim of this study was to provide a detailed anatomic atlas of the cranial abdomen by means of computed tomography (CT). Three mature dogs, all mixed breed males, were used. The dogs were sedated, anaesthetized and positioned in sternal recumbency. CT scans from the eighth thoracic vertebra to the fourth lumbar vertebra were performed using a third-generation equipment (TOSHIBA 600HQ scanner) with 1 cm slice thickness. CT-images of the cranial abdomen were taken with soft-tissue window (WL: ,14, WW: 658) settings. Dogs were killed and vascular-injection technique was performed: red and blue latex filled the vascular system. Injected dogs were frozen in the same position as used for CT examination and sectioned with an electric bandsaw at 1-cm-thick intervals. The cuts matched as closely as possible to the CT-images. The anatomic sections were compared and studied with the corresponding CT-images, and clinically relevant abdominal anatomic structures were identified and labelled on the corresponding CT-images. The results of our study could be used as a reference for evaluating CT-images of the canine cranial abdomen with abdominal diseases. [source] Age-dependent quantitative trait loci affecting growth traits in Scottish Blackface sheepANIMAL GENETICS, Issue 2 2009G. Hadjipavlou Summary To dissect age-dependent quantitative trait loci (QTL) associated with growth and to examine changes in QTL effects over time, the Gompertz growth model was fitted to longitudinal live weight data on 788 Scottish Blackface lambs from nine half-sib families. QTL were mapped for model parameters and weekly live weights and growth rates using microsatellite markers on chromosomes 1, 2, 3, 5, 14, 18, 20 and 21. QTL significance (using , = 0.05 chromosome-wide significance thresholds, unless otherwise stated) varied with age, and those for growth rate occurred earlier than equivalent QTL for live weight. A chromosome 20 QTL for growth rate was significant from 4 to 9 weeks (maximum significance at 6 weeks) and for maximum growth rate. For live weight, this QTL was significant from 8 to 16 weeks (maximum significance at 12 weeks). A nominally significant chromosome 14 QTL was detected for growth rates from birth to week 2 in the same families and location as an 8-week weight QTL. In addition, at the same position on chromosome 14, a QTL was significant for growth rate for 17,28 weeks (maximum significance at 24 weeks). A chromosome 3 QTL was significant for weights at early ages (birth to week 4) and a growth rate QTL on chromosome 18 was significant from 8 to 12 weeks. Fitting growth curves allowed the combination of information from multiple measurements into a few biologically meaningful variables, and the detection of growth QTL that were not observed from analyses of raw weight data. These QTL describe distinct parts of an animal's growth curve trajectory, possibly enabling manipulation of this trajectory. [source] Characterization of the porcine melanocortin 2 receptor gene (MC2R,)ANIMAL GENETICS, Issue 6 2002K. Jacobs A porcine bacterial artificial chromosome (BAC) clone, containing the melanocortin 2 receptor gene (MC2R) was isolated. The complete coding sequence of the MC2R gene, contained in 1 exon, was determined. Polymerase chain reaction-single stranded conformational polymorphism (PCR-SSCP) was performed on a 241-bp coding fragment. An AluI polymorphism, detecting a silent mutation, was found and typed on unrelated animals of five different pig breeds. The Meishan, Piétrain and Large White breeds differ significantly in allele frequencies from the Landrace and Czech Meat Pig breeds. The melanocortin 5 receptor gene (MC5R) was detected by PCR in the same BAC clone, as could be expected from the human and porcine mapping data. PCR-SSCP was performed on a 200-bp coding of MC5R, but no polymorphisms were detected. The BAC clone was mapped to Sscr6q27 by fluorescent in situ hybridization (FISH). A (CA)n microsatellite (SGU0002), isolated from the BAC, was localized on chromosome 6 by RH mapping near marker SW1473 and by linkage mapping on the MARC reference family at the same position as the marker SW2173 (97 cM). Allele frequencies, heterozygosity and polymorphism information contents (PIC) values were calculated for the five different pig breeds examined. The transcription of both genes in porcine liver, heart, kidney, fat, brain, pancreas, stomach, bladder, ovaries, lung, spleen, skin, adrenal gland and muscle tissues was examined by reverse transcriptase-polymerase chain reaction. Transcription was detected in skin and adrenal gland tissues for MC2R, while a positive signal was detected for MC5R in kidney, fat, pancreas, skin, adrenal gland and spleen tissues. [source] CARD15 mutations in familial granulomatosis syndromes: A study of the original Blau syndrome kindred and other families with large-vessel arteritis and cranial neuropathyARTHRITIS & RHEUMATISM, Issue 11 2002Xiaoju Wang Objective To analyze the CARD15 gene in families with heritable multi-organ granulomatoses, including the original Blau syndrome kindred as well as other families with related granulomatous conditions. Methods Linkage mapping was performed in 10 families. Observed recombination events were used to exclude regions centromeric or telomeric to 16q12.1, and the Blau gene critical region was refined to <3 cM, corresponding to a physical distance of 3.5 megabasepairs. Based on its known biochemical function, CARD15 was analyzed as a positional candidate for the Blau syndrome susceptibility gene, by direct DNA sequencing. Results These studies resulted in the identification, in 5 of the families, of 2 sequence variants at position 334 of the gene product (R334W and R334Q). Affected family members from the original Blau syndrome kindred were heterozygous for the R334W missense mutation; mutations at the same position were also observed in several unrelated Blau syndrome families, some of whose phenotypes included large-vessel arteritis and cranial neuropathy. The missense mutations segregated with the disease phenotype in the families, and were not seen in 208 control alleles. Conclusion These findings demonstrate that CARD15 is an important susceptibility gene for Blau syndrome and for other familial granulomatoses that display phenotypic traits beyond those of classic Blau syndrome. [source] Critical catalytic functional groups in the mechanism of aspartate-,-semialdehyde dehydrogenaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 10 2004Julio Blanco Aspartate-,-semialdehyde dehydrogenase (ASADH) catalyzes the reductive dephosphorylation of ,-aspartyl phosphate to l -aspartate-,-semialdehyde in the aspartate biosynthetic pathway. This pathway is not found in humans or other eukaryotic organisms, yet is required for the production of threonine, isoleucine, methionine and lysine in most microorganisms. The mechanism of this enzyme has been examined through the structures of two active-site mutants of ASADH from Haemophilus influenzae. Replacement of the enzyme active-site cysteine with serine (C136S) leads to a dramatic loss of catalytic activity caused by the expected decrease in nucleophilicity, but also by a change in the orientation of the serine hydroxyl group relative to the cysteine thiolate. In contrast, in the H277N active-site mutant the introduced amide is oriented in virtually the same position as that of the histidine imidazole ring. However, a shift in the position of the bound reaction intermediate to accommodate this shorter asparagine side chain, coupled with the inability of this introduced amide to serve as a proton acceptor, results in a 100-fold decrease in the catalytic efficiency of H277N relative to the native enzyme. These mutant enzymes have the same overall fold and high structural identity to native ASADH. However, small perturbations in the positioning of essential catalytic groups or reactive intermediates have dramatic effects on catalytic efficiency. [source] Crystallization and preliminary X-ray analysis of a DNA dodecamer containing 2,-deoxy-5-formyluridine; what is the role of magnesium cation in crystallization of Dickerson-type DNA dodecamers?ACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2001Masaru Tsunoda To investigate the role of divalent cations in crystal packing, four different crystals of a Dickerson-type dodecamer with the sequence d(CGCGAATXCGCG), containing 2,-deoxy-5-formyluridine at X, were obtained under several conditions with and without divalent cations. The crystal structures are all isomorphous. The octahedrally hydrated magnesium cations found in the major groove cement the two neighbouring duplexes along the b axis. In the Mg2+ -free crystals, a five-membered ring of water molecules occupies the same position as the magnesium site and connects the two duplexes similarly to the hydrated Mg2+ ion. It has been concluded that water molecules can take the place of the hydrated magnesium cation in crystallization, but the magnesium cation is more effective and gives X-ray diffraction at slightly higher resolution. In all four crystals, the 5-formyluracil residues form the canonical Watson,Crick pair with adenine residues. [source] X-ray analysis of bilirubin oxidase from Myrothecium verrucaria at 2.3,Å resolution using a twinned crystalACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 7 2010Kimihiko Mizutani Bilirubin oxidase (BOD), a multicopper oxidase found in Myrothecium verrucaria, catalyzes the oxidation of bilirubin to biliverdin. Oxygen is the electron acceptor and is reduced to water. BOD is used for diagnostic analysis of bilirubin in serum and has attracted considerable attention as an enzymatic catalyst for the cathode of biofuel cells that work under neutral conditions. Here, the crystal structure of BOD is reported for the first time. Blue bipyramid-shaped crystals of BOD obtained in 2-methyl-2,4-pentanediol (MPD) and ammonium sulfate solution were merohedrally twinned in space group P63. Structure determination was achieved by the single anomalous diffraction (SAD) method using the anomalous diffraction of Cu atoms and synchrotron radiation and twin refinement was performed in the resolution range 33,2.3,Å. The overall organization of BOD is almost the same as that of other multicopper oxidases: the protein is folded into three domains and a total of four copper-binding sites are found in domains 1 and 3. Although the four copper-binding sites were almost identical to those of other multicopper oxidases, the hydrophilic Asn residue (at the same position as a hydrophobic residue such as Leu in other multicopper oxidases) very close to the type I copper might contribute to the characteristically high redox potential of BOD. [source] Structure of the ligand-binding domain of rat VDR in complex with the nonsecosteroidal vitamin D3 analogue YR301ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 11 2008Shinji Kakuda Vitamin D receptor (VDR) is a ligand-inducible hormone receptor that mediates 1,,25(OH)2D3 action, regulating calcium and phosphate metabolism, induces potent cell differentiation activity and has immunosuppressive effects. Analogues of 1,,25(OH)2D3 have been used clinically for some years. However, the risk of potential side effects limits the use of these substances. LG190178 is a novel nonsecosteroidal ligand for VDR. (2S)-3-[4-(3-{4-[(2R)-2-hydroxy-3,3-dimethylbutoxy]-3-methylphenyl}pentan-3-yl)-2-methylphenoxy] propane-1,2-diol (YR301) is the only one of the four evaluated stereoisomers of LG190178 to have strong activity. To understand the strong activity of YR301, the crystal structure of YR301 complexed with the rat VDR ligand-binding domain (VDR LBD) was solved at 2.0,Å resolution and compared with the structure of the VDR LBD,1,,25(OH)2D3 complex. YR301 and 1,,25(OH)2D3 share the same position and the diethylmethyl group occupies a similar space to the C and D rings of 1,,25(OH)2D3. YR301 has two characteristic hydroxyl groups which contribute to its potent activity. The first is 2,-OH, which forms hydrogen bonds to the NE2 atoms of both His301 and His393. The other is 2-OH, which interacts with Ser233,OG and Arg270,NH1. These two hydroxyl groups of YR301 correspond exactly to 25-OH and 1-OH, respectively, of 1,,25(OH)2D3. The terminal hydroxyl group (3-OH) of YR301 is directly hydrogen bonded to Arg270 and also interacts indirectly with Tyr232,OH and the backbone NH of Asp144 via water molecules. Additional derivatization of the terminal hydroxyl group using the positions of the water molecules might be useful for the design of more potent compounds. [source] The D4Mit12 locus on mouse chromosome 4 provides susceptibility to both ,-ray-induced and N-methyl-N-nitrosourea-induced thymic lymphomasCANCER SCIENCE, Issue 8 2003Hiroki Sato Low-penetrance genes control different susceptibilities to ,-ray-induced thymic lymphomas in mouse strains. Our previous genetic analyses with backcross mice between BALB/c and MSM strains and congenic lines localized one such gene near the D4Mit12 locus on chromosome 4. N-Methyl-N-nitrosourea (MNU) is a guanine base-alkylating agent and differs from ,-radiation in its mechanism of mutagenic action. Accordingly, in this study, we examined whether or not the locus also provides susceptibility to MNU-induced thymic lymphomas using 84 offsprings derived from congenic mice for D4Mit12. Association analysis provided a suggestive linkage at D4Mit12 (P=0.0075) and the linkage was sustained by the peak of likelihood ratio statistical values being at the same position as that for the ,-ray-induced lymphomas. The results strongly suggest that the BALB/c allele near D4Mit12 is associated with susceptibility to lymphomas induced by two carcinogenic agents having different mechanisms of mutagenic action. [source] A nonsense mutation in exon 8 of the APC gene (Arg283Ter) causes clinically variable FAP in a Malaysian Chinese familyCANCER SCIENCE, Issue 8 2003Zulqarnain Mohamed The present study was carried out to characterize the causative genetic mutation in a medium-sized Malaysian Chinese pedigree of three generations affected with familial adenomatous polyposis (FAP). Clinical data and genetic studies revealed considerable phenotypic variability in affected individuals in this family. Blood was obtained from members of the FAP-01 family and genomic DNA was extracted. Mutation screening of the adenomatous polyposis coli (APC) gene was carried out using the single strand conformation polymorphism (SSCP) technique. The possibility of exon skipping was predicted by splicing motif recognition software (ESEfinder release2.0). SSCP results showed mobility shifts in exon 8 of the APC gene which segregated with affected members of the family. Sequence analysis revealed that the affected individuals are heterozygous for a C847T transition, whilst all the unaffected family members and control individuals are homozygous C at the same position. This nucleotide substitution generates a stop codon at amino acid position 283, in place of the usual arginine (Arg283Ter). We conclude that an Arg283Ter mutation in the APC gene is causative of the FAP phenotype in this family, although there is considerable variation in the presentation of this disease among affected individuals. Computational analysis predicts that this mutation occurs within sequences that may function as splicing signals, so that the sequence change may affect normal splicing. [source] Pre-/post-otic rhombomeric interactions control the emergence of a fetal-like respiratory rhythm in the mouse embryoDEVELOPMENTAL NEUROBIOLOGY, Issue 12 2006C. Borday Abstract How regional patterning of the neural tube in vertebrate embryos may influence the emergence and the function of neural networks remains elusive. We have begun to address this issue in the embryonic mouse hindbrain by studying rhythmogenic properties of different neural tube segments. We have isolated pre- and post-otic hindbrain segments and spinal segments of the mouse neural tube, when they form at embryonic day (E) 9, and grafted them into the same positions in stage-matched chick hosts. Three days after grafting, in vitro recordings of the activity in the cranial nerves exiting the grafts indicate that a high frequency (HF) rhythm (order: 10 bursts/min) is generated in post-otic segments while more anterior pre-otic and more posterior spinal territories generate a low frequency (LF) rhythm (order: 1 burst/min). Comparison with homo-specific grafting of corresponding chick segments points to conservation in mouse and chick of the link between the patterning of activities and the axial origin of the hindbrain segment. This HF rhythm is reminiscent of the respiratory rhythm known to appear at E15 in mice. We also report on pre-/post-otic interactions. The pre-otic rhombomere 5 prevents the emergence of the HF rhythm at E12. Although the nature of the interaction with r5 remains obscure, we propose that ontogeny of fetal-like respiratory circuits relies on: (i) a selective developmental program enforcing HF rhythm generation, already set at E9 in post-otic segments, and (ii) trans-segmental interactions with pre-otic territories that may control the time when this rhythm appears. © 2006 Wiley Periodicals, Inc. J Neurobiol, 2006 [source] The structural comparison of the bacterial PepX and human DPP-IV reveals sites for the design of inhibitors of PepX activityFEBS JOURNAL, Issue 8 2005Pascal Rigolet X-prolyl dipeptidyl aminopeptidases (X-PDAP) are enzymes catalysing the release of dipeptides from the amino termini of polypeptides containing a proline or an alanine at the penultimate position. Involved in various mammalian regulation processes, as well as in chronic human diseases, they have been proposed to play a role in pathogenicity for Streptococci. We compared the structure of X-PDAP from Lactococcus lactis (PepX) with its human counterpart DPP-IV. Despite very different overall folds, the residues most implicated for X-PDAP activity are conserved in the same positions and orientations in both enzymes, thus defining a structural signature for the X-PDAP specificity that crosses the species frontiers of evolution. Starting from this observation, we tested some inhibitors of DPP-IV on PepX activity, for which no specific inhibitor is known. We thus found that PepX was highly sensitive to valine-pyrrolidide with a KI of 9.3 µm, close to that reported in DPP-IV inhibition. We finally used the structure of PepX from L. lactis as a template for computer-based homology modeling of PepX from the pathogenic Streptococcus gordonii. Docking simulations of valine-pyrrolidide into the active site of PepX led to the identification of key residues for a rational drug design against PepX from Streptococci. These results could have applications in human health giving new perspectives to the struggle against pathogens. [source] Structural Changes in the BODIPY Dye PM567 Enhancing the Laser Action in Liquid and Solid Media,ADVANCED FUNCTIONAL MATERIALS, Issue 16 2007I. García-Moreno Abstract In the search for more efficient and photostable solid-state dye lasers, newly synthesized analogs of the borondipyrromethene (BODIPY) dye PM567, bearing the polymerizable methacryloyloxypropyl group at position 2 (PMoMA) or at positions 2 and 6 (PDiMA), have been studied in the form of solid copolymers with methyl methacrylate (MMA). The parent dye PM567, as well as the model analogs bearing the acetoxypropyl group in the same positions, PMoAc and PDiAc, respectively, have been also studied both in liquid solvents and in solid poly(MMA) (PMMA) solution. Although in liquid solution PMoAc and PDiAc have the same photophysical properties as PM567, PDiAc exhibited a photostability up to 10 times higher than that of PM567 in ethanol under 310,nm-irradiation. The possible stabilization factors of PDiAc have been analyzed and discussed on the basis of the redox potentials, the ability for singlet molecular oxygen [O2(1,g)] generation, the reactivity with O2(1,g), and quantum mechanical calculations. Both PMoAc and PDiAc, pumped transversally at 532,nm, lased in liquid solution with a high (up to 58,%), near solvent-independent efficiency. This enhanced photostabilization has been also observed in solid polymeric and copolymeric media. While the solid solution of the model dye PDiAc in PMMA showed a lasing efficiency of 33,%, with a decrease in the laser output of ca.,50,% after 60,000 pump pulses (10,Hz repetition rate) in the same position of the sample, the solid copolymer with the double bonded chromophore, COP(PDiMA-MMA), showed lasing efficiencies of up to 37,%, and no sign of degradation in the laser output after 100,000 similar pump pulses. Even under the more demanding repetition rate of 30,Hz, the laser emission from this material remained at 67,% of its initial laser output after 400,000 pump pulses, which is the highest laser photostability achieved to date for solid-state lasers based on organic polymeric materials doped with laser dyes. This result indicates that the double covalent linkage of the BODIPY chromophore to a PMMA polymeric matrix is even more efficient than the simple linkage, for its photostabilization under laser operation. [source] Soil water content and yield variability in vineyards of Mediterranean northeastern Spain affected by mechanization and climate variabilityHYDROLOGICAL PROCESSES, Issue 11 2006M. C. Ramos Abstract The objective of this paper was to analyse the combined influence of the Mediterranean climate variability (particularly the irregular rainfall distribution throughout the year) and the land transformations carried out in vineyards of northeastern Spain on soil water content evolution and its influence on grape production. The study was carried out in a commercial vineyard located in the Anoia,Alt Penedès region (Barcelona province, northeastern Spain), which was prepared for mechanization with important land transformations. Two plots were selected for the study: one with low degree of transformation of the soil profile, representing a non-disturbed situation, and the second one in which more than 3 m were cut in the upper part of the plot and filled in the lower part, representing the disturbed situation. Soil water content was evaluated at three positions along the slope in each plot and at three depths (0,20, 20,40, 40,60 cm) during the period 1999,2001, years with different rainfall characteristics, including extreme events and long dry periods. Rainfall was recorded in the experimental field using a pluviometer linked to a data-logger. Runoff rates and yield were evaluated at the same positions. For the same annual rainfall, the season of the year in which rainfall is recorded and its intensity are critical for water availability for crops. Soil water content varies within the plot and is related to the soil characteristics existing at the different positions of the landscape. The differences in soil depth created by soil movements in the field mechanization give rise to significant yield reductions (up to 50%) between deeper and shallow areas. In addition, for the same annual rainfall, water availability for crops depends on its distribution over the year, particularly in soils with low water-storage capacity. The yield was strongly affected in years with dry or very dry winters. Copyright © 2005 John Wiley & Sons, Ltd. [source] The role of controlled drainage under drought conditions in an irrigated area in NWFP, Pakistan,IRRIGATION AND DRAINAGE, Issue 2 2003Gul Daraz Khan sécheresse; drainage commandé; eaux souterraines; efficacité d'utilisation de l'eau et rendement Abstract The River Swat is the source of irrigation for the entire irrigation system of Mardan, Nowshera and Charsadda districts. Reductions of water and overdrainage have influenced the yield of major crops. The impact of reduced supply at the inlet from the source, drought conditions and overdrainage from the area have lowered the groundwater to a disastrous level. Thus the present groundwater level cannot contribute to the crops. A subsurface collector at its exit in drainage unit 106 was controlled to raise the watertable. The study area was divided into 10 zones. Each zone was separately assessed to analyze the groundwater impact in response to the controlled technique adopted for mitigating drought in different strategies of the canal operation. The interaction of groundwater level with irrigation depth, crop yield, water use efficiency and water saving were also studied. During the rotational period of the canal, irrigations applied in section II raised the water level by nearly 1 m. The upslope area of section III also needed a large irrigation depth. The groundwater level on the downslopes of the lateral drains in sections I and V was at the design depth of 1.1 m during the rotational strategy, while it decreased only slightly on the upslopes of the lateral drains for the same positions. Because of effective control by the collector, the watertable on the downslopes of the laterals in sections II and III was affected less while in the respective upslope area of section III it dropped more than 2 m. The water levels in section IV (both in the upslope and downslope areas along the laterals) remained very close to the design level. A significant contribution of seepage in the upslope of the collector drain considerably reduced the irrigation depths. During the canal closure period, the watertables in the study area dropped to the limit from 2.3 to 3.25 m. After the reopening of the canal, the watertables in sections II, III and IV were raised from 2.55 to 0.70 m. During this period the water levels near the canal reached the design level. The maximum yield of 6.5 tons ha,1 on the downslopes of the lateral drains in section II was obtained, resulting in maximum water use efficiency of 0.93 kg m,3. However, the minimum yield of 3.5 tons ha,1 on the upslopes of the lateral drains in section I was obtained, resulting in the lowest water use efficiency of 0.35 kg m,3 near the deep surface drain (5 m). The impact of controlled subsurface drainage in zones 2, 3 and 7 resulted in the best maintenance of optimum groundwater level and moisture content. Therefore large amounts of extra irrigation water applied (ranging from 23 to 129% of that actually required) in different zones of the controlled area can be saved for drought conditions. Copyright © 2003 John Wiley & Sons, Ltd. RÉSUMÉ Le fleuve Swat est la source d'irrigation pour les systèmes d'irrigation entiers des zones de Mardan, de Nowshera et de Charsadda. Les réductions de drainage de l'eau et d'excédent ont influencé le rendement de récoltes principales. L'impact de l'approvisionnement réduit à l'admission de la source, des conditions de sécheresse et du drainage d'excédent du secteur ont laissé tomber les eaux souterraines à un niveau désastreux. Ainsi le niveau actuel d'eaux souterraines ne peut pas contribuer aux récoltes. Un collecteur à fleur de terre à sa sortie dans l'unité 106 de drainage a été commandé pour soulever le niveau hydrostatique. Le secteur d'étude a été divisé en dix zones. Chaque zone a été séparément évaluée pour analyser l'impact d'eaux souterraines en réponse à la technique commandée adoptée pour atténuer la sécheresse dans différentes stratégies de l'opération de canal. L'interaction du niveau d'eaux souterraines sur la profondeur d'irrigation, le rendement de récolte, l'efficacité d'utilisation de l'eau et l'économie de l'eau ont été également étudié. Pendant la période de rotation du canal, les irrigations appliquées dans la section II ont élevé le niveau d'eau de presque un mètre. Le secteur demontée de la section III avait besoin d'une grande profondeur d'irrigation. Le niveau d'eaux souterraines des déscentes de la vidange latérale dans les sections I et V était à la profondeur de conception de 1.1 m pendant la stratégie de rotation, tandis qu'il diminuait seulement légèrement aux montée des drains latéraux pour les mêmes positions. En raison de la commande efficace du collecteur, le niveau hydrostatique des déscentes des parties latérales dans les sections II et III a été affecté moins, tandis que dans le secteur respectif demontée de la section III il descentait à plus de deux mètres. Les niveaux d'eau dans la section IV (tous les deux dans les secteurs demontée etde déscentes le long des parties latérales) ont demeuré très près de la conception. La contribution significative de l'infiltration dans lamontee du drain de collecteur a considérablement réduit les profondeurs d'irrigation. Pendant la période de fermeture du canal, les niveaux hydrostatiques dans le secteur d'étude sont descendus la limite de 2.3 à 3.25 m. A la réouverture du canal, les niveaux hydrostatiques dans les sections II, III et IV augmenté de 2.55 à 0.70 m. Pendant cette période les niveaux d'eau près du canal ont atteint celui de la concept. Le rendement maximum de 6.5 tons ha,1 aux déscentes des drains latéraux dans la section II a été obtenu, ayant pour résultat l'efficacité maximum d'utilisation de l'eau de 0.93 kg m,3.Cependant le rendement minimum de 3.5 tons ha,1 aux montées des drains latéraux dans la section a été obtenu, ayant pour résultat la plus basse efficacité d'utilisation de l'eau de 0.35 kg m,3 près du drain extérieur profond (5 m). L'impact du drainage à fleur de terre commandé dans les zones 2, 3 et 7 a maintenu le meillear niveau d'eaux souterraines et le contenu d'humidité optimum. Par conséquent la grande quantité de l'eau supplémentaire d'irrigation celle appliquée (s'étendant de 23 à 129% deréellement requise) dans différentes zones de la zone de contrôle peut être sauvée pour les conditions de sécheresse. Copyright © 2003 John Wiley & Sons, Ltd. [source] | ||||||||||||||||||||||||||||||||||