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Region I (region + i)
Selected AbstractsCommunication between E,54, promoter DNA and the conserved threonine residue in the GAFTGA motif of the PspF ,54 -dependent activator during transcription activationMOLECULAR MICROBIOLOGY, Issue 2 2004Patricia Bordes Summary Conversion of E,54 closed promoter complexes to open promoter complexes requires specialized activators which are members of the AAA (ATPases Associated with various cellular Activities) protein family. The ATP binding and hydrolysis activity of E,54 activators is used in an energy coupling reaction to remodel the E,54 closed promoter complex and to overcome the ,54 -imposed block on open complex formation. The remodelling target for the AAA activator within the E,54 closed complex includes a complex interface contributed to by Region I of ,54, core RNA polymerase and a promoter DNA fork junction structure, comprising the E,54 regulatory centre. One ,54 binding surface on E,54 activators is a conserved sequence known as the GAFTGA motif. Here, we present a detailed characterization of the interaction between Region I of ,54 and the Escherichia coli AAA ,54 activator Phage shock protein F. Using E,54 promoter complexes that mimic different conformations adopted by the DNA during open complex formation, we investigated the contribution of the conserved threonine residue in the GAFTGA motif to transcription activation. Our results suggest that the organization of the E,54 regulatory centre, and in particular the conformation adopted by the ,54 Region I and the DNA fork junction structure during open complex formation, is communicated to the AAA activator via the conserved T residue of the GAFTGA motif. [source] A model of corrosion fatigue crack growth in ship and offshore steelsFATIGUE & FRACTURE OF ENGINEERING MATERIALS AND STRUCTURES, Issue 8 2007M. JAKUBOWSKI ABSTRACT A model describing corrosion fatigue crack growth rate da/dN has been proposed. The crack growth rate is assumed to be proportional to current flowing through the electrolyte within the crack during a loading cycle. The Shoji formula for the crack tip strain rate has been assumed in the model. The obtained formula for the corrosion fatigue crack growth rate is formally similar to the author's empirical formulae established previously. The different effects of ,K and the fatigue loading frequency f on da/dN, in region I as compared to region II of the corrosion fatigue crack growth rate characteristics can be described by a change of one parameter only: the crack tip repassivation rate exponent. [source] Identification of a novel nuclear factor-kappaB sequence involved in expression of urokinase-type plasminogen activator receptorFEBS JOURNAL, Issue 11 2000Yao Wang We have previously defined the promoter of human urokinase-type plasminogen activator receptor (uPAR) gene in a 188-bp fragment between bases ,141 and +47 relative to the translation start site. Here, we report that a novel nuclear factor-kappaB (NF-,B)-like sequence (5,-GGGAGGAGTC-3,) at ,45 is located in the uPAR promoter and one of the two DNase I-protected regions, region I between bases ,51 and ,30. This NF-,B-like motif differs at positions 7,9 from the decameric consensus sequences of NF-,B (5,-GGGRNNYYCC-3, where R indicates A or G, Y indicates C or T, and N indicates any nucleotide) and at positions 1 and 7,9 from the ,B-like motifs (5,-HGGARNYYCC-3, where H indicates A, C, or T, R indicates A or G, Y indicates C or T, and N indicates any nucleotide). Nuclear extracts from HCT116 cells contain proteins that specifically bind to the NF-,B-like site at position ,45. Mutation of the NF-,B-like motif decreased the binding of transcription factor NF-,B and reduced the uPAR promoter activity in comparison with the wild-type sequences. Co-transfection with a dominant negative I-,B kinase-2 expression vector reduced uPAR promoter activity by 65,75%. These results demonstrate that a previously uncharacterized NF-,B motif is required for uPAR promoter activity. [source] Nanoscale uniformity of pore architecture in diatomaceous silica: a combined small and wide angle x-ray scattering studyJOURNAL OF PHYCOLOGY, Issue 1 2000Engel G. Vrieling Combined small and wide angle X-ray scattering (SAXS and WAXS) analysis was applied to purified biogenic silica of cultured diatom frustules and of natural populations sampled on marine tidal flats. The overall WAXS patterns did not reveal crystalline phases (WAXS domain between 0.07 to 0.5 nm) in this biogenic silica, which is in line with previous reports on the amorphous character of the SiO2 matrix of diatom frustules. One exception was the silica of the pennate species Cylindrotheca fusiformis Reimann et Lewin, which revealed wide peaks in the WAXS spectra. These peaks either indicate the presence of a yet unknown crystalline phase with a repetitive distance (d -value ,0.06 nm) or are caused by the ordering of the fibrous silica fragments; numerous girdle bands. The SAXS spectra revealed the size range of pores (diameter d between 3.0 and 65 nm), the presence of distinct pores (slope transitions), and structure factors (oscillation of the spectra). All slopes varied in the range of ,4.0 to ,2.5, with two clear common regions among species: d < 10 nm (slopes ,4, denoted as region I and also called the Porod region), and 10.0 < d < 40.0 nm (slopes ,2.9 to ,3.8, denoted as region II). The existence of these common regions suggests the presence of comparable form (region I) and structure (region II) factors, respectively the shape of the primary building units of the silica and the geometry of the pores. Contrast variation experiments using dibromomethane to fill pores in the SiO2 matrix showed that scattering was caused by pores rather than silica particles. Electron microscopic analysis confirmed the presence of circular, elliptical, and rectangular pores ranging in size from 3 to 65 nm, determining the structure factor. The fine architecture (length/width ratio of pore diameters) and distribution of the pores, however, seemed to be influenced by environmental factors, such as the salinity of and additions of AlCl3 to the growth medium. The results indicate that diatoms deposit silica with pores <50 nm in size and are highly homologous with respect to geometry. Consequently, it is suggested that in diatoms, whether pennate or centric, the formation of silica at a nanoscale level is a uniform process. [source] Population structure and history of southern African scrub hares, Lepus saxatilisJOURNAL OF ZOOLOGY, Issue 2 2004U. Kryger Abstract Genetic differentiation among populations of the South African scrub hare Lepus saxatilis was examined using hypervariable mitochondrial DNA control region I (CR-I) sequences. Neighbour-joining analysis revealed a pattern that did not correspond to the current subspecies delineations. The CR-I sequence data delimit scrub hares into three major maternal lineages. The three phylogenetic assemblages exhibited different geographical distributions. AMOVA analyses and exact tests for population differentiation confirmed this phylogeographic partitioning. One lineage (SW) was confined to the south-western Cape, the second lineage (N) was exclusively found in the northern part of South Africa and in the neighbouring countries, and the third lineage (C) was predominant in the central parts of South Africa. This spatial distribution did not coincide with the ranges of the 10 described subspecies covered by our sampling regime. The lineages C and N overlapped in an area including eastern parts of South Africa and southern Namibia. The presence of both lineages in that area of overlap was interpreted as the result of secondary contact due to recent range expansions after the two lineages had undergone a population restriction approximately 18 000 years ago. Analyses of contemporary gene flow disclosed an exchange of migrants between N and C, which was biased towards a movement from C to N. The SW group represents a very distinct evolutionary lineage that has been isolated for more than 45 000 years. It does not exchange female migrants with the other two groups. Mismatch distribution analyses indicated sudden population size expansions in the history of all three populations. [source] Conducting nanocomposites of polyacrylamide with acetylene black and polyanilinePOLYMER COMPOSITES, Issue 4 2009Pramod Kumar Verma A conducting nanocomposite of polyacrylamide (PAA) with acetylene black was prepared via Na2AsO3 -K2CrO4 redox initiated polymerization of acrylamide in water containing a suspension of acetylene black. FTIR analyses confirmed the presence of PAA in the nanocomposites. The composite possessed lower thermal stability than AB and exhibited three stages of decomposition upto 430°C. DSC thermogram revealed three endotherms due to minor thermal degradation (at ,100°C), melting and decomposition (at ,230°C) and major decomposition (at ,430°C). TEM analyses indicated the formation of globular composite particles with sizes in 30,70 nm range. In contrast to the very low conductivity of the base polymer the composite showed a dramatic increase in conductivity (0.19,6.0 S/cm) depending upon AB loading. Log (conductivity) ,1/T plot showed a change in slope at ,127°C indicating the manifestation of an intrinsic conductivity region and an impurity conductivity region. The activation energy for conduction as estimated from the slope of region I was 0.008 eV/mol. The C,V plot was linear showing a metallic behavior. For comparison in conductivity PAA-polyaniline composite was also prepared which however displayed much lower conductivity values. POLYM. COMPOS., 2009. © 2008 Society of Plastics Engineers [source] Mitochondrial DNA patterns in the Macaronesia islands: Variation within and among archipelagosAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 4 2010Cristina Santos Abstract Macaronesia covers four Atlantic archipelagos: the Azores, Madeira, the Canary Islands, and the Cape Verde islands. When discovered by Europeans in the 15th century, only the Canaries were inhabited. Historical reports highlight the impact of Iberians on settlement in Macaronesia. Although important differences in their settlement are documented, its influence on their genetic structures and relationships has yet to be ascertained. In this study, the hypervariable region I (HVRI) sequence and coding region polymorphisms of mitochondrial DNA (mtDNA) in 623 individuals from the Azores (120) and Canary Islands (503) were analyzed. Combined with published data, these give a total of 1,542 haplotypes from Macaronesia and 1,067 from the Iberian Peninsula. The results obtained indicate that Cape Verde is the most distinctive archipelago, with an mtDNA pool composed almost exclusively of African lineages. However, the other archipelagos present an mtDNA profile dominated by the presence of West-Eurasian mtDNA haplogroups with African lineages present in varying proportions. Moreover, no signs of integration of typical Canarian U6 lineages in the other archipelagos were detected. The four Macaronesia archipelagos currently have differentiated genetic profiles, and the Azores present the highest intra-archipelago differentiation and the lowest values of diversity. The analyses performed show that the present-day genetic profile of the Macaronesian archipelagos was mainly determined by the initial process of settlement and further microdifferentiation probably as a consequence of the small population size of some islands. Moreover, contacts between archipelagos seem to have had a low impact on the mtDNA genetic pool of each archipelago. Am J Phys Anthropol, 2010. © 2009 Wiley-Liss, Inc. [source] Mitochondrial DNA HVRI variation in Balearic populationsAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 1 2005A. Picornell Abstract The Balearic archipelago (Majorca, Minorca, and Ibiza islands and the Chuetas, a small and inbred community of descendants of Sephardic Jews) and Valencia were studied by means of the sequencing of a 404-bp segment of hypervariable region I (HVRI) mtDNA in 231 individuals. In total, 127 different haplotypes defined by 92 variable positions were identified. The incidence of unique haplotypes was very low, especially in Ibiza and the Chuetas. A remarkable observation in the Chueta community was the high frequency (23%) of preHV-1, a Middle Eastern lineage that is closely related, though not identical, to many others found at high frequencies in different Jewish populations. The presence of this haplogroup convincingly supported the Jewish origin of the Chueta community. The studied populations showed a reduced African contribution, and no individuals were detected with North African haplogroup U6, indicating a lack of maternal contribution from the Moslem settlement to these populations. Only Ibiza showed a lower diversity, indicating a possible genetic drift effect, also supported by the historical information known about this island. The variability in the sequence of mtDNA hypervariable region I correlated well with the existing information from the populations, with the exception of that of the Y-chromosome, which could indicate a differential contribution of the maternal and paternal lineages to the genetic pool of the Balearic Islands. The phylogenetic trees showed the intermediate position of the Chueta population between the Middle Eastern and Majorcan samples, confirming the Jewish origin of this population and their Spanish admixture. Am J Phys Anthropol 128:119-130, 2005. © 2005 Wiley-Liss, Inc. [source] | |||||||||||||