2,393 research outputs found

    Gene Family Encoding Hordeum vulgare Translation Elongation Factor 1 alpha (EF-1a): Assignment Based on Bioinformatic Analysis of cDNA Sequences

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    Search of international DNA database, Genbank, produced eight barley cDNA EFlα sequences with unique accession numbers. The length of these sequences varied from an incomplete 502 bp to a full length 1646 bp encoding a 447 amino acid protein. The knowledge that there are four EF-lα gene family members in barley led us to query whether all four genes were represented in the group of eight database submitted sequences. Also of great importance was the correct assignment of gene family member to its mRNA and protein expression profiles. Before we could begin to address the expression studies, we undertook the task of ascribing to the published cDNA sequences its grouping in the gene family. Bioinformatic tools were used to identify the 5\u27 and 3\u27 UTRs of the cDNA sequences. The 5\u27 & 3\u27 UTR comparisons revealed that sequences with accession numbers LI 1740 & Z23130 were identical. Thus these were designated as derived from the EF-lαA gene. Sequences BQ294517, BQ739965, & Z50789 represented the same gene family member designated EF-lα B. BQ740018 was derived from a third gene designated EF-lα C. BQ740062 also differed enough to be classified as derived from the fourth member of the gene family herein designated EF-lα D. Absence of 5\u27 and 3\u27 UTRs, for BQ739951 prevented designation with respect to gene family. Thus it is placed in the family group U (unknown)

    Stability of self-consistent solutions for the Hubbard model at intermediate and strong coupling

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    We present a general framework how to investigate stability of solutions within a single self-consistent renormalization scheme being a parquet-type extension of the Baym-Kadanoff construction of conserving approximations. To obtain a consistent description of one- and two-particle quantities, needed for the stability analysis, we impose equations of motion on the one- as well on the two-particle Green functions simultaneously and introduce approximations in their input, the completely irreducible two-particle vertex. Thereby we do not loose singularities caused by multiple two-particle scatterings. We find a complete set of stability criteria and show that each instability, singularity in a two-particle function, is connected with a symmetry-breaking order parameter, either of density type or anomalous. We explicitly study the Hubbard model at intermediate coupling and demonstrate that approximations with static vertices get unstable before a long-range order or a metal-insulator transition can be reached. We use the parquet approximation and turn it to a workable scheme with dynamical vertex corrections. We derive a qualitatively new theory with two-particle self-consistence, the complexity of which is comparable with FLEX-type approximations. We show that it is the simplest consistent and stable theory being able to describe qualitatively correctly quantum critical points and the transition from weak to strong coupling in correlated electron systems.Comment: REVTeX, 26 pages, 12 PS figure

    Complex patterns of local adaptation in teosinte

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    Populations of widely distributed species often encounter and adapt to specific environmental conditions. However, comprehensive characterization of the genetic basis of adaptation is demanding, requiring genome-wide genotype data, multiple sampled populations, and a good understanding of population structure. We have used environmental and high-density genotype data to describe the genetic basis of local adaptation in 21 populations of teosinte, the wild ancestor of maize. We found that altitude, dispersal events and admixture among subspecies formed a complex hierarchical genetic structure within teosinte. Patterns of linkage disequilibrium revealed four mega-base scale inversions that segregated among populations and had altitudinal clines. Based on patterns of differentiation and correlation with environmental variation, inversions and nongenic regions play an important role in local adaptation of teosinte. Further, we note that strongly differentiated individual populations can bias the identification of adaptive loci. The role of inversions in local adaptation has been predicted by theory and requires attention as genome-wide data become available for additional plant species. These results also suggest a potentially important role for noncoding variation, especially in large plant genomes in which the gene space represents a fraction of the entire genome

    Cryotomography of budding influenza a virus reveals filaments with diverse morphologies that mostly do not bear a genome at their distal end

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    Influenza viruses exhibit striking variations in particle morphology between strains. Clinical isolates of influenza A virus have been shown to produce long filamentous particles while laboratory-adapted strains are predominantly spherical. However, the role of the filamentous phenotype in the influenza virus infectious cycle remains undetermined. We used cryo-electron tomography to conduct the first three-dimensional study of filamentous virus ultrastructure in particles budding from infected cells. Filaments were often longer than 10 microns and sometimes had bulbous heads at their leading ends, some of which contained tubules we attribute to M1 while none had recognisable ribonucleoprotein (RNP) and hence genome segments. Long filaments that did not have bulbs were infrequently seen to bear an ordered complement of RNPs at their distal ends. Imaging of purified virus also revealed diverse filament morphologies; short rods (bacilliform virions) and longer filaments. Bacilliform virions contained an ordered complement of RNPs while longer filamentous particles were narrower and mostly appeared to lack this feature, but often contained fibrillar material along their entire length. The important ultrastructural differences between these diverse classes of particles raise the possibility of distinct morphogenetic pathways and functions during the infectious process

    Naturally occurring circadian rhythm and sleep duration are related to executive functions in early adulthood

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    Experimental sleep deprivation studies suggest that insufficient sleep and circadian misalignment associates with poorer executive function. It is not known whether this association translates to naturally occurring sleep patterns. A total of 512 of full-term-born members of the Arvo Ylppö Longitudinal Study [mean age = 25.3, standard deviation (SD) = 0.65] (44.3% men) wore actigraphs to define sleep duration, its irregularity and circadian rhythm (sleep mid-point) during a 1-week period (mean 6.9 nights, SD = 1.7). Performance-based executive function was assessed with the Trail-Making Test, Conners’ Continuous Performance Test and Stroop. The self-rated adult version of Behavior Rating Inventory of Executive Function was used to assess trait-like executive function. We found that performance-based and self-reported trait-like executive function correlated only modestly (all correlations ≤0.17). Shorter sleep duration associated with more commission errors. Later circadian rhythm associated with poorer trait-like executive function, as indicated by the Brief Metacognitive Index and the Behavior Regulation Index. Those belonging to the group with the most irregular sleep duration performed slower than others in the Trail-Making Test Part A. All associations were adjusted for sex, age, socioeconomic status and body mass index. In conclusion, naturally occurring insufficient sleep and later circadian rhythm showed modest associations with poorer executive function. Shorter habitual sleep duration was associated with lower scores of performance-based tests of executive function, and later circadian rhythm was associated mainly with poorer trait-like executive function characteristics. Our findings suggest additionally that sleep duration and circadian rhythm associate with different domains of executive function, and there are no additive effects between the two

    MWCNTs of different physicochemical properties cause similar inflammatory responses, but differences in transcriptional and histological markers of fibrosis in mouse lungs

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    Multi-walled carbon nanotubes (MWCNTs) are extensively produced and used in composite materials and electronic applications, thus increasing risk of worker and consumer exposure. MWCNTs are an inhomogeneous group of nanomaterials that come in various lengths, shapes and with different metal contaminations, which makes hazard evaluation difficult. However, several studies suggest that length plays an important role in the toxicity induced by MWCNTs. How the length influences toxicity at the molecular level is yet to be characterized. Female C57BL/6 mice were exposed by single intratracheal instillation to 18, 54 or 162 µg/mouse of a short MWCNT (NRCWE-026, 847±102 nm in length) or long MWCNT (NM-401, 4048±366 nm in length). The two MWCNTs were extensively characterized. Lung tissues were harvested 24 h, 3 d and 28 d after exposure. We employed DNA microarrays, bronchoalveolar lavage fluid analysis, comet assay and dichlorodihydrofluorescein assay in order to profile the pulmonary responses. Bioinformatics tools were then applied to compare and contrast the expression profiles and to build a length dependent property-response matrix for gene-by-gene comparison. The toxicogenomic analysis of the global mRNA changes after exposure to the short, entangled NRCWE-026 or the longer, stiffer NM-401 showed high degree of similarities. The toxicity of both MWCNTs was driven by strong inflammatory and acute phase responses, which peaked at day 3 and was observed both in bronchoalveolar lavage cell influx and in gene expression profiles. The inflammatory response was sustained at post-exposure day 28. Also, at the sub-chronic level, we identified a sub-set of 14 fibrosis related genes that were uniquely differentially regulated after exposure to NM-401. Acellular ROS production occurred almost exclusively with NRCWE-026, however the longer NM-401 induced in vivo DNA strand breaks and differential regulation of genes involved in free radical scavenging more readily than NRCWE-026. Our results indicate that the global mRNA response after exposure to MWCNTs is length independent at the acute time points, but that fibrosis may be length dependent sub-chronic end point.JRC.H.6-Digital Earth and Reference Dat

    Exploiting the Achilles' heel of membrane trafficking in trypanosomes

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    Pathogenic protozoa are evolutionarily highly divergent from their metazoan hosts, reflected in many aspects of their biology. One particularly important parasite taxon is the trypanosomatids. Multiple transmission modes, distinct life cycles and exploitation of many host species attests to great prowess as parasites, and adaptability for efficient, chronic infection. Genome sequencing has begun uncovering how trypanosomatids are well suited to parasitism, and recent genetic screening and cell biology are revealing new aspects of how to control these organisms and prevent disease. Importantly, several lines of evidence suggest that membrane transport processes are central for the sensitivity towards several frontline drugs

    Early-stage rifting of the northern Tyrrhenian Sea Basin: Results from a combined wide-angle and multichannel seismic study

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    Extension of the continental lithosphere leads to the formation of rift basins and ultimately may create passive continental margins. The mechanisms that operate during the early stage of crustal extension are still intensely debated. We present the results from coincident multichannel seismic and wide-angle seismic profiles that transect across the northern Tyrrhenian Sea Basin. The profiles cross the Corsica Basin (France) to the Latium Margin (Italy) where the early-rift stage of the basin is well preserved. We found two domains, each with a distinct tectonic style, heat flow and crustal thickness. One domain is the Corsica Basin in the west that formed before the main rift phase of the northern Tyrrhenian Sea opening (∼8–4 Ma). The second domain is rifted continental crust characterized by tilted blocks and half-graben structures in the central region and at the Latium Margin. These two domains are separated by a deep (∼10 km) sedimentary complex of the eastern portion of the Corsica Basin. Travel-time tomography of wide-angle seismic data reveals the crustal architecture and a subhorizontal 15–17 ± 1 km deep Moho discontinuity under the basin. To estimate the amount of horizontal extension we have identified the pre-, syn-, and post-tectonic sedimentary units and calculated the relative displacement of faults. We found that major faults initiated at angles of 45°–50° and that the rifted domain is horizontally stretched by a factor of β ∼ 1.3 (∼8–10 mm/a). The crust has been thinned from ∼24 to ∼17 km indicating a similar amount of extension (∼30%). The transect represents one of the best imaged early rifts and implies that the formation of crustal-scale detachments, or long-lived low-angle normal faults, is not a general feature that controls the rift initiation of continental crust. Other young rift basins, like the Gulf of Corinth, the Suez Rift or Lake Baikal, display features resembling the northern Tyrrhenian Basin, suggesting that half-graben formations and distributed homogeneous crustal thinning are a common feature during rift initiation
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