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Domain I (domain + i)
Selected AbstractsIsolation and characterization of a novel copper-inducible metallothionein gene of a ciliate, Tetrahymena tropicalis lahorensisJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 3 2010Raheela Chaudhry Abstract The two isoforms of copper metallothionein (CuMT) gene of a copper resistant ciliate, Tetrahymena tropicalis lahorensis (Ttl), have been isolated and characterized. The molecular cloning and nucleotide sequencing of cDNAs coding for the two CuMT isoforms revealed that TtlCuMT1 gene has 300, while TtlCuMT2 has 327 nucleotides, both with ATG as the initiation codon and TGA as the translational termination codon. TAG codes for glutamine in TtlCuMT2 gene which is peculiar to Tetrahymena. The deduced or translated TtlCuMT1 and TtlCuMT2 peptide sequences contain 100 and 108 amino acid residues including 28 and 32 cysteine residues, respectively. The amino acid sequences of TtlCuMT1 and TtlCuMT2 have special features of two and three CXCXXCXCXXCXC intragenic tandem repeats with a conserved structural pattern of cysteine, respectively. The predicted tertiary structures of these two isoforms indicate two domains. Domain I and the initial part of domain II showed >98% homology with other Tetrahymena CuMT. On the basis of the differences in the domain II, the metallothionein subfamily 7b can be divided into two groups, one (TtlCuMT1) comprising >100 amino acids and the other (TtlCuMT2) comprising <100 amino acids. This is a novel finding of the present study as no such report on this type of classification exists at the moment. TtlCuMT1 has 95%, while TtlCuMT2 has 97% resemblance with the previously reported CuMT genes of Tetrahymena spp. SDS-PAGE analysis using fluorescent probe as well as coomassie brilliant blue staining also confirmed the presence of metallothionein. J. Cell. Biochem. 110: 630,644, 2010. © 2010 Wiley-Liss, Inc. [source] Transitions of serum albumin in patients with glomerulosclerosis ,in vivo' characterization by electrophoretic titration curvesELECTROPHORESIS, Issue 14 2006Maurizio Bruschi Abstract HSA functions as a physiological transporter of solutes and small molecules that induce structural transitions ,in vitro'. Analysis of these transitions requires prior purification of HSA that could introduce bias due to conformational changes. We utilized electrophoretic titration curves to describe a neutral to acid (N,A) transition of HSA directly in sera of seven patients with active focal segmental glomerulosclerosis (FSGS). The divergent electrophoretic profile of HSA was characterized by a shift in the range of pHs between 4.5 and 7.5 with an average variation of free electrophoretic mobility corresponding to loss of 1 positive charge in the pKa protonation range of histidyl residues and should involve domain I of HSA. ,In-gel' determination by maleimide-PEO2-biotin of free SH 34 of domain I showed inaccessibility of the dye at this site in pathological HSA and alkylation with the same complex induced N,A transition in normal HSA. Potential binders of free imidazoles such as Ca++ and/or of SH 34 such as NO were excluded on the basis of direct titration and studies on binding stimulation. This is the first report describing a transition of HSA directly ,in vivo', and the utilization of electrophoretic titration curves was critical to this purpose. This transition appears to be specific to FSGS and is unrelated to the nephrotic syndrome, Ca++ and NO binding. Spectroscopic analysis will elucidate the structural implication. [source] Chimeric receptor analyses of the interactions of the ectodomains of ErbB-1 with epidermal growth factor and of those of ErbB-4 with neuregulinFEBS JOURNAL, Issue 9 2002Jae-Hoon Kim A series of chimeric receptors was generated between the epidermal growth factor (EGF) receptor, ErbB-1, and its homologue, ErbB-4, to investigate the roles of the extracellular domains (I,IV) in the ligand specificities. As compared with ErbB-1 and the chimeras with both domains I and III of ErbB-1, the chimeras with only one of these domains exhibited reduced binding of 125I-labeled EGF. Particularly, the contribution of domain III was appreciably larger than that of domain I of ErbB-1 in 125I-labeled EGF binding. Nevertheless, the chimeras with domain III of ErbB-1 and domain I of ErbB-4 were prevented from binding to 125I-labeled EGF competitively by the ErbB-4 ligand, neuregulin (NRG). On the other hand, NRG did not compete with 125I-labeled EGF for binding to the chimeras with the ErbB-1 domain I and the ErbB-4 domain III. Therefore, NRG binding to ErbB-4 depends much more on domain I than on domain III. With respect to autophosphorylation and subsequent ERK activation, EGF activated the chimeras with either domain I or III of ErbB-1. In contrast, NRG activated the chimeras with the ErbB-4 domain I and the ErbB-1 domain III, but not those with the ErbB-1 domain,I and the ErbB-4 domain III. Therefore, the relative contributions between domains I and III of ErbB-4 in the NRG signaling are different from those of ErbB-1 in the EGF signaling. [source] Cryptic differentiation and geographic variation in genetic diversity of Hall's Babbler Pomatostomus halliJOURNAL OF AVIAN BIOLOGY, Issue 2 2001Grant I. Miura Sequence variation was examined in domain I of the mitochondrial control region in three Queensland populations of Hall's Babbler Pomatostomus halli, a geographically restricted, monotypic songbird in eastern Australia. Surprisingly, we found that domain I sequences were strongly differentiated into two major clades differing by 3.29%. These two clades exhibited nearly complete geographic concordance with northern and southern populations, except for two haplotypes which were sampled in the north of the range but were phylogenetically allied to the southern clade. We also found a seven-fold higher level of genetic diversity in the northern than in the southern populations. Neutrality and molecular clock tests suggested that selection or differences in substitution rates were not responsible for this difference in diversity. However, a maximum likelihood analysis of gene flow between the north and south suggested that the difference in diversity could be due to both greater population size in the north and asymmetric gene flow dominated by south to north dispersal events. A likelihood ratio test rejected a model in which population sizes were equal and rates of gene flow symmetric, and came close to rejecting a model in which only population sizes were constrained to be equal. These results suggest that different population sizes and asymmetric gene flow could be a major source of differences in genetic variation between populations of Hall's Babbler, although ecological and biogeographic causes for these differences are obscure. [source] Involvement of HAb18G/CD147 in T cell activation and immunological synapse formationJOURNAL OF CELLULAR AND MOLECULAR MEDICINE, Issue 8 2010Jinsong Hu Abstract HAb18G/CD147, a glycoprotein of the immunoglobulin super-family (IgSF), is a T cell activation-associated molecule. In this report, we demonstrated that HAb18G/CD147 expression on both activated CD4+ and CD8+ T cells was up-regulated. In vitro cross-linking of T cells with an anti-HAb18G/CD147 monoclonal antibody (mAb) 5A12 inhibited T cells proliferation upon T cell receptor stimulation. Such co-stimulation inhibited T cell proliferation by down-regulating the expression of CD25 and interleukin-2 (IL-2), decreased production of IL-4 but not interferon-,. Laser confocal imaging analysis indicated that HAb18G/CD147 was recruited to the immunological synapse (IS) during T cell activation; triggering HAb18G/CD147 on activated T cells by anti-HAb18G/CD147 mAb 5A12 strongly dispersed the formation of the IS. Further functional studies showed that the ligation of HAb18G/CD147 with mAb 5A12 decreased the tyrosine phosphorylation and intracellular calcium mobilization levels of T cells. Through docking antibody,antigen interactions, we demonstrated that the function of mAb 5A12 is tightly dependent on its specificity of binding to N-terminal domain I, which plays pivotal role in the oligomerization of HAb18G/CD147. Taken together, we provide evidence that HAb18G/CD147 could act as a co-stimulatory receptor to negatively regulate T cell activation and is functionally linked to the formation of the IS. [source] In vivo inhibition of antiphospholipid antibody-induced pathogenicity utilizing the antigenic target peptide domain I of ,2 -glycoprotein I: proof of conceptJOURNAL OF THROMBOSIS AND HAEMOSTASIS, Issue 5 2009Y. IOANNOU Summary.,Objectives:,In the antiphospholipid syndrome (APS), the immunodominant epitope for the majority of circulating pathogenic antiphospholipid antibodies (aPLs) is the N-terminal domain I (DI) of ,2 -glycoprotein I. We have previously shown that recombinant DI inhibits the binding of aPLs in fluid phase to immobilized native antigen, and that this inhibition is greater with the DI(D8S/D9G) mutant and absent with the DI(R39S) mutant. Hence, we hypothesized that DI and DI(D8S/D9G) would inhibit aPL-induced pathogenicity in vivo. Methods:,C57BL/6 mice (n = 5, each group) were injected with purified IgG derived from APS patients (IgG-APS, 500 ,g) or IgG from normal healthy serum (IgG-NHS) and either recombinant DI, DI(R39S), DI(D8S/D9G), or an irrelevant control peptide (at 10,40 ,g). Outcome variables measured were femoral vein thrombus dynamics in treated and control groups following standardized vessel injury, expression of vascular cell adhesion molecule-1 (VCAM-1) on the aortic endothelial surface, and tissue factor (TF) activity in murine macrophages. Results:,IgG-APS significantly increased thrombus size as compared with IgG-NHS. The IgG-APS thrombus enhancement effect was abolished in mice pretreated with recombinant DI (P , 0.0001) and DI(D8S/D9G) (P , 0.0001), but not in those treated with DI(R39S) or control peptide. This inhibitory effect by DI was dose-dependent, and at lower doses DI(D8S/D9G) was a more potent inhibitor of thrombosis than wild-type DI (P , 0.01). DI also inhibited IgG-APS induction of VCAM-1 on the aortic endothelial surface and TF production by murine macrophages. Conclusion:,Our findings in this proof-of-concept study support the development of recombinant DI or the novel variant DI(D8S/D9G) as a potential future therapeutic agent for APS. [source] On the complexity of finding paths in a two-dimensional domain I: Shortest pathsMLQ- MATHEMATICAL LOGIC QUARTERLY, Issue 6 2004Arthur W. Chou Abstract The computational complexity of finding a shortest path in a two-dimensional domain is studied in the Turing machine-based computational model and in the discrete complexity theory. This problem is studied with respect to two formulations of polynomial-time computable two-dimensional domains: (A) domains with polynomialtime computable boundaries, and (B) polynomial-time recognizable domains with polynomial-time computable distance functions. It is proved that the shortest path problem has the polynomial-space upper bound for domains of both type (A) and type (B); and it has a polynomial-space lower bound for the domains of type (B), and has a #P lower bound for the domains of type (A). (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Genetic divergence and migration patterns in a North American passerine bird: implications for evolution and conservationMOLECULAR ECOLOGY, Issue 8 2006LESLIE A. DAVIS Abstract Like many other migratory birds, the black-throated blue warbler (Dendroica caerulescens) shows pronounced differences in migratory behaviour and other traits between populations: birds in the southern part of the breeding range have darker plumage and migrate to the eastern Caribbean during the winter, whereas those in the north have lighter plumage and migrate to the western Caribbean. We examined the phylogeography of this species, using samples collected from northern and southern populations, to determine whether differentiation between these populations dates to the Pleistocene or earlier, or whether differences in plumage and migratory behaviour have arisen more recently. We analysed variation at 369 bp of the mitochondrial control region domain I and also at seven nuclear microsatellites. Analyses revealed considerable genetic variation, but the vast majority of this variation was found within rather than between populations, and there was little differentiation between northern and southern populations. Phylogeographic analyses revealed a very shallow phylogenetic tree, a star-like haplotype network, and a unimodal mismatch distribution, all indicative of a recent range expansion from a single refugium. Coalescent modelling approaches also indicated a recent common ancestor for the entire group of birds analysed, no split between northern and southern populations, and high levels of gene flow. These results show that Pleistocene or earlier events have played little role in creating differences between northern and southern populations, suggesting that migratory and other differences between populations have arisen very recently. The implications of these results for the evolution of migration and defining taxonomic groups for conservation efforts are discussed. [source] Prognostic significance of urokinase plasminogen activator receptor and its cleaved forms in blood from patients with non-small cell lung cancerAPMIS, Issue 10 2009CHARLOTTE ELBERLING ALMASI Urokinase plasminogen activator (uPA) cleaves its three-domain cell surface receptor, uPAR, liberating domain I [uPAR(I)] and leaving the cleaved uPAR(II-III) on the cell surface. Both intact and cleaved uPAR can be shed from the cell surface. uPAR(I) was previously shown to be a prognostic factor in lung tumour extracts. Here we analyse uPAR forms in blood from patients with non-small cell lung cancer (NSCLC). Preoperatively sampled plasma/serum from 32 patients with NSCLC was analysed. Three time-resolved fluoroimmunoassays (TR-FIAs) measuring intact uPAR(I-III) (TR-FIA 1), uPAR(I-III) + uPAR(II-III) (TR-FIA 2) and uPAR(I) (TR-FIA 3) were applied. The Spearman rank correlations between plasma and serum levels of uPAR(I-III), uPAR(I-III) + uPAR(II-III), and uPAR(I) were 0.89, 0.94 and 0.68 respectively. Survival analysis demonstrated that high levels of all uPAR forms were associated with shorter survival. Adjusted for histological subtype high plasma uPAR(I-III) and uPAR(I) levels as well as serum uPAR(I) levels were significantly associated with shorter OS (hazards ratios = 4.3, 2.8 and 3.8 respectively). High blood levels of intact uPAR and its cleaved forms are associated with poor prognosis in NSCLC. [source] Structure of the diaminopimelate epimerase DapF from Mycobacterium tuberculosisACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2009Veeraraghavan Usha The meso (or d,l) isomer of diaminopimelic acid (DAP), a precursor of l -lysine, is a key component of the pentapeptide linker in bacterial peptidoglycan. While the peptidoglycan incorporated in the highly complex cell wall of the pathogen Mycobacterium tuberculosis structurally resembles that of Escherichia coli, it is unique in that it can contain penicillin-resistant meso -DAP,meso -DAP linkages. The interconversion of l,l -DAP and meso -DAP is catalysed by the DAP epimerase DapF, a gene product that is essential in M. tuberculosis. Here, the crystal structure of the ligand-free form of M. tuberculosis DapF (MtDapF) refined to a resolution of 2.6,Å is reported. MtDapF shows small if distinct deviations in secondary structure from the two-domain ,/,-fold of the known structures of Haemophilus influenzae DapF and Bacillus anthracis DapF, which are in line with its low sequence identity (,27%) to the former. Modelling the present structure onto that of l,l -aziridino-DAP-bound H. influenzae DapF illustrates that a rigid-body movement of domain II and a rearrangement of the B4,A2 loop (residues 80,90) of domain I are likely to accompany the transition from the present inactive form to a catalytically competent enzyme. Despite a highly conserved active-site architecture, the model indicates that stabilization of the DAP backbone occurs in MtDapF through a tyrosine residue that is specific to mycobacterial DAP epimerases. [source] Association between particular polymorphic residues on apical membrane antigen 1 (AMA-1) and platelet levels in patients with vivax malariaCLINICAL MICROBIOLOGY AND INFECTION, Issue 11 2007P. Grynberg Abstract Apical membrane antigen 1 (AMA-1) is an immunogenic type 1 integral membrane protein, present in all Plasmodium spp., that probably has a role in the initiation of the invasion process of the erythrocyte. The DNA sequence of variable domain I of the Plasmodium vivax ama1 gene was sequenced in Brazilian isolates obtained from thrombocytopenic patients (n = 32) and patients with normal platelet counts (n = 22). There was a significant negative correlation between parasite density and platelet counts. It was concluded that there is an additional effect of sequence on platelet counts. The presence of amino-acid residues Y193 and S210 was associated significantly with normal platelet counts in P. vivax malaria, independent of the level of parasitaemia (p <0.0001). These data have implications for AMA-1-based vaccine design and suggest the possible use of this molecule as a marker of morbidity. [source] Distribution and functional characterization of human Nav1.3 splice variantsEUROPEAN JOURNAL OF NEUROSCIENCE, Issue 1 2005R. Thimmapaya Abstract The focus of the present study is the molecular and functional characterization of four splice variants of the human Nav1.3 , subunit. These subtypes arise due to the use of alternative splice donor sites of exon 12, which encodes a region of the , subunit that resides in the intracellular loop between domains I and II. This region contains several important phosphorylation sites that modulate Na+ channel kinetics in related sodium channels, i.e. Nav1.2. While three of the four Nav1.3 isoforms, 12v1, 12v3 and 12v4 have been previously identified in human, 12v2 has only been reported in rat. Herein, we evaluate the distribution of these splice variants in human tissues and the functional characterization of each of these subtypes. We demonstrate by reverse transcriptase-polymerase chain reaction (RT-PCR) that each subtype is expressed in the spinal cord, thalamus, amygdala, cerebellum, adult and fetal whole brain and heart. To investigate the functional properties of these different splice variants, each , subunit isoform was cloned by RT-PCR from human fetal brain and expressed in Xenopus oocytes. Each isoform exhibited functional voltage-dependent Na+ channels with similar sensitivities to tetrodotoxin (TTX) and comparable current amplitudes. Subtle shifts in the V1/2 of activation and inactivation (2,3 mV) were observed among the four isoforms, although the functional significance of these differences remains unclear. This study has demonstrated that all four human splice variants of the Nav1.3 channel , subunit are widely expressed and generate functional TTX-sensitive Na+ channels that likely modulate cellular excitability. [source] Chimeric receptor analyses of the interactions of the ectodomains of ErbB-1 with epidermal growth factor and of those of ErbB-4 with neuregulinFEBS JOURNAL, Issue 9 2002Jae-Hoon Kim A series of chimeric receptors was generated between the epidermal growth factor (EGF) receptor, ErbB-1, and its homologue, ErbB-4, to investigate the roles of the extracellular domains (I,IV) in the ligand specificities. As compared with ErbB-1 and the chimeras with both domains I and III of ErbB-1, the chimeras with only one of these domains exhibited reduced binding of 125I-labeled EGF. Particularly, the contribution of domain III was appreciably larger than that of domain I of ErbB-1 in 125I-labeled EGF binding. Nevertheless, the chimeras with domain III of ErbB-1 and domain I of ErbB-4 were prevented from binding to 125I-labeled EGF competitively by the ErbB-4 ligand, neuregulin (NRG). On the other hand, NRG did not compete with 125I-labeled EGF for binding to the chimeras with the ErbB-1 domain I and the ErbB-4 domain III. Therefore, NRG binding to ErbB-4 depends much more on domain I than on domain III. With respect to autophosphorylation and subsequent ERK activation, EGF activated the chimeras with either domain I or III of ErbB-1. In contrast, NRG activated the chimeras with the ErbB-4 domain I and the ErbB-1 domain III, but not those with the ErbB-1 domain,I and the ErbB-4 domain III. Therefore, the relative contributions between domains I and III of ErbB-4 in the NRG signaling are different from those of ErbB-1 in the EGF signaling. [source] Comparative analysis of mt LSU rRNA secondary structures of Odonates: structural variability and phylogenetic signalINSECT MOLECULAR BIOLOGY, Issue 6 2003B. Misof Abstract Secondary structures of the most conserved part of the mt 16S rRNA gene, domains IV and V, have been recently analysed in a comparative study. However, full secondary structures of the mt LSU rRNA molecule are published for only a few insect species. The present study presents full secondary structures of domains I, II, IV and V of Odonates and one representative of mayflies, Ephemera sp. The reconstructions are based on a comparative approach and minimal consensus structures derived from sequence alignments. The inferred structures exhibit remarkable similarities to the published Drosophila melanogaster model, which increases confidence in these structures. Structural variance within Odonates is homoplastic, and neighbour-joining trees based on tree edit distances do not correspond to any of the phylogenetically expected patterns. However, despite homoplastic quantitative structural variation, many similarities between Odonates and Ephemera sp. suggest promising character sets for higher order insect systematics that merit further investigations. [source] Mitochondrial DNA control region diversity in the endangered blue chaffinch, Fringilla teydeaMOLECULAR ECOLOGY, Issue 9 2000J. Pestano Abstract The blue chaffinch (Fringilla teydea) is found only on the two central Canary Islands of Gran Canaria and Tenerife, where it is restricted to pine forest habitat. It is reasonably abundant on the latter island but endangered on the former. Here, sequence variation was studied in a fragment spanning domains I and II of the mitochondrial DNA (mtDNA) control region. Phylogenetic analysis of all haplotypes with a F. coelebs outgroup indicated the two island populations were reciprocally monophyletic, supporting their individual conservation. Unlike in other species, most within-island haplotype diversity was due to mutations in the domain II region. Surprisingly, genetic diversity was greater in the smaller Gran Canarian population. We suggest that this is unlikely to be maintained under current population sizes although it may be mitigated by incorporating genetic information into the captive breeding programme. [source] The Comparative Analysis of Osmotins and Osmotin-Like PR-5 ProteinsPLANT BIOLOGY, Issue 2 2003S. An, lovar Abstract: One of the ways that plants respond to biotic and/or abiotic stress factors is the accumulation of pathogenesis-related proteins of class 5 (PR-5), which are evolutionary conserved in the plant kingdom. Within the PR-5 family, a distinct subgroup of osmotin and closely related proteins has been characterized. In contrast to the extracellular forms of PR-5 proteins, osmotins presumably accumulate in the vacuole of the cell. They contain a C-terminal propeptide that is considered to be a determinant for vacuolar targeting. The comparison of the three-dimensional structure of tobacco PR-5 d with the sequences of some osmotins showed that the proteins consist of three conserved domains, with the acidic cleft between domains I and II. Besides the constitutive species and tissue-specific presence, the osmotins are also induced by several abiotic and biotic stresses. Among them, fungal infections can elicit osmotin gene expression, and most known proteins from the family have antifungal activity in in vitro assays. In agreement with the osmotin structure and data on the activity of similar proteins, a two-step mechanism, which involves reaction of osmotins with the fungal wall and the permeabilization of fungal membranes, is discussed. [source] | ||||||||||||||||