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Region Downstream (region + downstream)
Selected AbstractsMicrodeletion/duplication at the Xq28 IP locus causes a de novo IKBKG/NEMO/IKKgamma exon4_10 deletion in families with incontinentia pigmenti,HUMAN MUTATION, Issue 9 2009Fusco Francesca Abstract The Incontinentia Pigmenti (IP) locus contains the IKBKG/NEMO/IKKgamma gene and its truncated pseudogene copy, IKBKGP/deltaNEMO. The major genetic defect in IP is a heterozygous exon4_10 IKBKG deletion (IKBKGdel) caused by a recombination between two consecutive MER67B repeats. We analyzed 91 IP females carrying the IKBKGdel, 59 of whom carrying de novo mutations (65%). In eight parents, we found two recurrent nonpathological variants of IP locus, which were also present as rare polymorphism in control population: the IKBKGPdel, corresponding to the exon4_10 deletion in the pseudogene, and the MER67Bdup, that replicates the exon4_10 region downstream of the normal IKBKG gene. Using quantitative DNA analysis and microsatellite mapping, we established that both variants might promote the generation of the pathological IKBKGdel. Indeed, in family IP-516, the exon4_10 deletion was repositioned in the same allele from the pseudogene to the gene, whereas in family IP-688, the MER67Bdup generated the pathological IKBKGdel by recombination between two direct nonadjacent MER67Bs. Moreover, we found an instance of somatic recombination in a MER67Bdup variant, creating the IKBKGdel in an IP male. Our data suggest that the IP locus undergoes recombination producing recurrent variants that might be "at risk" of generating de novo IKBKGdel by NAHR during either meiotic or mitotic division. Hum Mutat 30:1,8, 2009. © 2009 Wiley-Liss, Inc. [source] Two-dimensional prediction of time dependent, turbulent flow around a square cylinder confined in a channelINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS, Issue 11 2010M. Raisee Abstract This paper presents two-dimensional and unsteady RANS computations of time dependent, periodic, turbulent flow around a square block. Two turbulence models are used: the Launder,Sharma low-Reynolds number k,, model and a non-linear extension sensitive to the anisotropy of turbulence. The Reynolds number based on the free stream velocity and obstacle side is Re=2.2×104. The present numerical results have been obtained using a finite volume code that solves the governing equations in a vertical plane, located at the lateral mid-point of the channel. The pressure field is obtained with the SIMPLE algorithm. A bounded version of the third-order QUICK scheme is used for the convective terms. Comparisons of the numerical results with the experimental data indicate that a preliminary steady solution of the governing equations using the linear k,, does not lead to correct flow field predictions in the wake region downstream of the square cylinder. Consequently, the time derivatives of dependent variables are included in the transport equations and are discretized using the second-order Crank,Nicolson scheme. The unsteady computations using the linear and non-linear k,, models significantly improve the velocity field predictions. However, the linear k,, shows a number of predictive deficiencies, even in unsteady flow computations, especially in the prediction of the turbulence field. The introduction of a non-linear k,, model brings the two-dimensional unsteady predictions of the time-averaged velocity and turbulence fields and also the predicted values of the global parameters such as the Strouhal number and the drag coefficient to close agreement with the data. Copyright © 2009 John Wiley & Sons, Ltd. [source] The identification of circular extrachromosomal DNA in the nuclear genome of Trypanosoma bruceiMOLECULAR MICROBIOLOGY, Issue 2 2003N. S. Alsford Summary Nuclear extrachromosomal DNA elements have been identified in several kinetoplastids such as Leishmania and Trypanosoma cruzi, but never in Trypanosoma brucei. They can occur naturally or arise spontaneously as the result of sublethal drug exposure of parasites. In most cases, they are represented as circular elements and are mitotically unstable. In this study we describe the presence of circular DNA in the nucleus of Trypanosoma brucei. This novel type of DNA was termed NR-element (NlaIII repeat element). In contrast to drug-induced episomes in other kinetoplastids, the T. brucei extrachromosomal NR-element is not generated by drug selection. Furthermore, the element is stable during mitosis over many generations. Restriction analysis of tagged NR-element DNA, unusual migration patterns during pulsed field gel electrophoresis (PFGE) and CsCl/ethidium bromide equilibrium centrifugation demonstrates that the NR-element represents circular DNA. Whereas it has been found in all field isolates of the parasites we analysed, it is not detectable in some laboratory strains notably the genome reference strain 927. The DNA sequence of this element is related to a 29 bp repeat present in the subtelomeric region of VSG-bearing chromosomes of T. brucei. It has been suggested that this subtelomeric region is part of a transition zone on chromosomes separating the relatively stable telomeric repeats from the recombinationaly active region downstream of VSG genes. Therefore, we discuss a functional connection between the occurrence of this circular DNA and subtelomeric recombination events in T. brucei. [source] Novel mode of transcription regulation by SdiA, an Escherichia coli homologue of the quorum-sensing regulatorMOLECULAR MICROBIOLOGY, Issue 5 2001Kaneyoshi Yamamoto SdiA, an Escherichia coli homologue of the quorum-sensing regulator, controls the expression of the ftsQAZ operon for cell division. Transcription of ftsQ is under the control of two promoters, upstream ftsQP2 and downstream ftsQP1, which are separated by 125 bp. SdiA activates transcription from ftsQP2 in vivo. Here, we demonstrate that SdiA facilitates the RNA polymerase binding to ftsQP2 and thereby stimulates transcription from P2. Gel shift and DNase I footprinting assays indicated that SdiA binds to the ftsQP2 promoter region between ,51 and ,25 with respect to the P2 promoter. Activation of ftsQP2 transcription by SdiA was observed with a mutant RNA polymerase containing a C-terminal domain (CTD)-deleted ,-subunit (,235) but not with RNA polymerase containing ,S or a CTD-deleted ,D (,D529). In good agreement with the transcription assay, no protection of P2 was observed with the RNA polymerase holoenzymes, E,S and E,D529. These observations together indicate that: (i) SdiA supports the RNA polymerase binding to ftsQP2; and (ii) this recruitment of RNA polymerase by SdiA depends on the presence of intact ,CTD. This is in contrast to the well-known mechanism of RNA polymerase recruitment by protein,protein contact between class I factors and ,CTD. In addition to the P2 activation, SdiA inhibited RNA polymerase binding to the ftsQP1 promoter and thereby repressed transcription from P1. Gel shift assays indicate weak binding of SdiA to the P1 promoter region downstream from ,13 (or +112 with respect to P2). Neither ,CTD nor ,CTD are required for this inhibition. Thus, the transcription repression of P1 by SdiA may result from its competition with the RNA polymerase in binding to this promoter. [source] The L49F mutation in alpha erythroid spectrin induces local disorder in the tetramer association region: Fluorescence and molecular dynamics studies of free and bound alpha spectrinPROTEIN SCIENCE, Issue 9 2009Yuanli Song Abstract The bundling of the N-terminal, partial domain helix (Helix C,) of human erythroid ,-spectrin (,I) with the C-terminal, partial domain helices (Helices A, and B,) of erythroid ,-spectrin (,I) to give a spectrin pseudo structural domain (triple helical bundle A,B,C,) has long been recognized as a crucial step in forming functional spectrin tetramers in erythrocytes. We have used apparent polarity and Stern,Volmer quenching constants of Helix C, of ,I bound to Helices A, and B, of ,I, along with previous NMR and EPR results, to propose a model for the triple helical bundle. This model was used as the input structure for molecular dynamics simulations for both wild type (WT) and ,I mutant L49F. The simulation output structures show a stable helical bundle for WT, but not for L49F. In WT, four critical interactions were identified: two hydrophobic clusters and two salt bridges. However, in L49F, the region downstream of Helix C, was unable to assume a helical conformation and one critical hydrophobic cluster was disrupted. Other molecular interactions critical to the WT helical bundle were also weakened in L49F, possibly leading to the lower tetramer levels observed in patients with this mutation-induced blood disorder. [source] Numerical Investigation of Turbulent Flow around a Rotating Stepped Cylinder for Corrosion StudyTHE CANADIAN JOURNAL OF CHEMICAL ENGINEERING, Issue 1 2003Kyung-Soo Yang Abstract Direct numerical simulation has been carried out for turbulent flow set up by a rotating cylinder with two backward-facing steps axisymmetrically mounted in the circumferential direction. This flow geometry creates a qualitatively similar flow pattern as observed near a sudden pipe expansion or a plane backward-facing step, characterized by flow separation and reattachment. A region of intense turbulence intensity and high wall-shear-stress fluctuations is formed in the recirculating region downstream of the step, where high mass-transfer capacity was also experimentally observed. Since corrosion is frequently mass-transfer controlled, our findings put forward this apparatus as a useful tool for future corrosion research. On a effectué une simulation numérique directe de l'écoulement turbulent créé par un cylindre rotatif ayant deux contractions axisymétriques dans la direction circonférentielle. Cette géométrie crée un profil d'écoulement qualitativement similaire à celui qu'on observe près d'une expansion de conduite soudaine ou d'une contraction planaire, caractérisés par la séparation et le ré-attachement de l'écoulement. Une région d'intense turbulence et de fortes fluctuations de contraintes de cisaillement pariétal se forment dans la région en recirculation en aval de la contraction, où une grande capacité de transfert de matière a également été observée expérimentalement. Étant donné que la corrosion dépend souvent du transfert de matière, nos résultats font la promotion de cet appareillage en tant qu'outil utile pour la recherche future sur la corrosion. [source] Identification of previously unrecognized predisposing factors for ankylosing spondylitis from analysis of HLA,B27 extended haplotypes in sardiniaARTHRITIS & RHEUMATISM, Issue 8 2007Isabella Cascino Objective To define the contribution of HLA genes other than HLA,B27 in conferring susceptibility to ankylosing spondylitis (AS), through analysis of HLA,B27 haplotypes in Sardinian subjects. Methods Ninety-eight patients with AS, 133 HLA,B27,positive controls (of whom 33 were positive for HLA,B*2709), and 190 randomly selected controls were genotyped for microsatellites and single-nucleotide polymorphisms (SNPs) spanning the HLA region. Results Haplotypes carrying either the B*2705 or the B*2709 allele were found to share a conserved region downstream of the HLA,B gene and a functional polymorphism in the HLA,E gene (R128G), while differing in all other markers. Notably, the presence of an A at SNP rs1264457, encoding for Arg-128, was significantly increased in the cohort of patients (P = 6 × 10,6, corrected P = 3 × 10,5) but not in B*2705- or B*2709-positive controls. Comparing the alleles co-occurring at each HLA marker, we identified a region differentiating patients with AS and B*2705-matched controls. In particular, there was a markedly increased prevalence of heterozygosity at rs1264457 among B27-positive controls (74%, versus 47% in patients and 54% in random controls), suggesting a protective role of G128 in AS. Moreover, other markers around the HLA,B gene were also differentially represented. Conclusion These results demonstrate a significant difference in the frequency of some HLA markers between AS patients and B*2705-positive controls, which could be attributed to the opposite chromosome. In particular, the differential distribution of a functional polymorphism in the HLA,E gene suggests a possible role of natural killer function in AS pathogenesis. [source] | |||||||||||||