4,218 research outputs found

    AIP1 is a novel Agenet/Tudor domain protein from Arabidopsis that interacts with regulators of DNA replication, transcription and chromatin remodeling

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    Background: DNA replication and transcription are dynamic processes regulating plant development that are dependent on the chromatin accessibility. Proteins belonging to the Agenet/Tudor domain family are known as histone modification "readers" and classified as chromatin remodeling proteins. Histone modifications and chromatin remodeling have profound effects on gene expression as well as on DNA replication, but how these processes are integrated has not been completely elucidated. It is clear that members of the Agenet/Tudor family are important regulators of development playing roles not well known in plants. Methods: Bioinformatics and phylogenetic analyses of the Agenet/Tudor Family domain in the plant kingdom were carried out with sequences from available complete genomes databases. 3D structure predictions of Agenet/Tudor domains were calculated by I-TASSER server. Protein interactions were tested in two-hybrid, GST pulldown, semi-in vivo pulldown and Tandem Affinity Purification assays. Gene function was studied in a T-DNA insertion GABI-line. Results: In the present work we analyzed the family of Agenet/Tudor domain proteins in the plant kingdom and we mapped the organization of this family throughout plant evolution. Furthermore, we characterized a member from Arabidopsis thaliana named AIP1 that harbors Agenet/Tudor and DUF724 domains. AIP1 interacts with ABAP1, a plant regulator of DNA replication licensing and gene transcription, with a plant histone modification "reader" (LHP1) and with non modified histones. AIP1 is expressed in reproductive tissues and its down-regulation delays flower development timing. Also, expression of ABAP1 and LHP1 target genes were repressed in flower buds of plants with reduced levels of AIP1. Conclusions: AIP1 is a novel Agenet/Tudor domain protein in plants that could act as a link between DNA replication, transcription and chromatin remodeling during flower development

    On the 'centre of gravity' method for measuring the composition of magnetite/maghemite mixtures, or the stoichiometry of magnetite-maghemite solid solutions, via Fe-57 Mossbauer spectroscopy

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    We evaluate the application of 57Fe Mössbauer spectroscopy to the determination of the composition of magnetite (Fe3O4)/maghemite (Îł-Fe2O3) mixtures and the stoichiometry of magnetite-maghemite solid solutions. In particular, we consider a recently proposed model-independent method which does not rely on a priori assumptions regarding the nature of the sample, other than that it is free of other Fe-containing phases. In it a single parameter, ÎŽRT—the ‘centre of gravity’, or area weighted mean isomer shift at room temperature, T = 295 ± 5 K—is extracted by curve-fitting a sample’s Mössbauer spectrum, and is correlated to the sample’s composition or stoichiometry. We present data on highpurity magnetite and maghemite powders, and mixtures thereof, as well as comparison literature data from nanoparticulate mixtures and solid solutions, to show that a linear correlation exists between ÎŽRT and the numerical proportion of Fe atoms in the magnetite environment: α = Femagnetite/Fetotal = − ( ) ÎŽ ÎŽ RT o /m, where ÎŽo = 0.3206 ± 0.0022mm s−1 and m = 0.2135 ± 0.0076mm s−1 . We also present equations to relate α to the weight percentage w of magnetite in mixed phases, and the magnetite stoichiometry x = Fe2+/Fe3+ in solid solutions. The analytical method is generally applicable, but is most accurate when the absorption profiles are sharp; in some samples this may require spectra to be recorded at reduced temperatures. We consider such cases and provide equations to relate ÎŽ ( ) T to the corresponding α value

    Evaluating Acquisition Time of rfMRI in the Human Connectome Project for Early Psychosis. How Much Is Enough?

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    Resting-state functional MRI (rfMRI) correlates activity across brain regions to identify functional connectivity networks. The Human Connectome Project (HCP) for Early Psychosis has adopted the protocol of the HCP Lifespan Project, which collects 20 min of rfMRI data. However, because it is difficult for psychotic patients to remain in the scanner for long durations, we investigate here the reliability of collecting less than 20 min of rfMRI data. Varying durations of data were taken from the full datasets of 11 subjects. Correlation matrices derived from varying amounts of data were compared using the Bhattacharyya distance, and the reliability of functional network ranks was assessed using the Friedman test. We found that correlation matrix reliability improves steeply with longer windows of data up to 11–12 min, and ≄14 min of data produces correlation matrices within the variability of those produced by 18 min of data. The reliability of network connectivity rank increases with increasing durations of data, and qualitatively similar connectivity ranks for ≄10 min of data indicates that 10 min of data can still capture robust information about network connectivities

    Chemical Evolution of CoCrMo Wear Particles: An in Situ Characterization Study

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    The unexpected high failure rates of CoCrMo hip implants are associated with the release of a large number of inflammatory wear particles. CoCrMo is nominally a stable material; however, previous chemical speciation studies on CoCrMo wear particles obtained from periprosthetic tissue revealed only trace amounts of Co remaining despite Co being the major component of the alloy. The unexpected high levels of Co dissolution in vivo raised significant clinical concerns particularly related to the Cr speciation in the dissolution process. At high electrochemical potentials, the alloy's Cr-rich passive film breaks down (transpassive polarization), facilitating alloy dissolution. The potential release of the carcinogenic Cr(VI) species in vivo has been a subject of debate. While the large-scale Co dissolution observed on in vivo produced particles could indicate a highly oxidizing in vivo environment, Cr(VI) species were not previously detected in periprosthetic tissue samples (except in the specific case of post-mortem tissue of diabetic patients). However, Cr(VI) is likely to be an unstable (transient) species in biological environments, and studies on periprosthetic tissue do not provide information about intermediate reaction products or the exposure history of the wear particles. Here, an in situ spectromicroscopy approach was developed, utilizing the high chemical resolution of synchrotron radiation, to study CoCrMo reactivity as a function of time and oxidizing conditions. The results reveal limited Co dissolution from CoCrMo particles, which increases dramatically at a critical electrochemical potential. Furthermore, in situ XAS detected only Cr(III) dissolution, even at potentials where Cr(VI) is known to be produced, suggesting that Cr(VI) species are extremely transient in simulated biological environments where the oxidation zone is small

    Housekeeping genes for quantitative expression studies in the three-spined stickleback Gasterosteus aculeatus

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    Background During the last years the quantification of immune response under immunological challenges, e.g. parasitation, has been a major focus of research. In this context, the expression of immune response genes in teleost fish has been surveyed for scientific and commercial purposes. Despite the fact that it was shown in teleostei and other taxa that the gene for beta-actin is not the most stably expressed housekeeping gene (HKG), depending on the tissue and experimental treatment, the gene has been us Results To establish a reliable method for the measurement of immune gene expression in Gasterosteus aculeatus, sequences from the now available genome database and an EST library of the same species were used to select oligonucleotide primers for HKG, in order to perform quantitative reverse-transcription (RT) PCR. The expression stability of ten candidate reference genes was evaluated in three different tissues, and in five parasite treatment groups, using the three algorithms BestKeeper, geNorm and N Conclusion As they were the most stably expressed genes in all tissues examined, we suggest using the genes for the L13a ribosomal binding protein and ubiquitin as alternative or additional reference genes in expression analysis in Gasterosteus aculeatus.

    Spin readout of a CMOS quantum dot by gate reflectometry and spin-dependent tunnelling

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    Silicon spin qubits are promising candidates for realising large scale quantum processors, benefitting from a magnetically quiet host material and the prospects of leveraging the mature silicon device fabrication industry. We report the measurement of an electron spin in a singly-occupied gate-defined quantum dot, fabricated using CMOS compatible processes at the 300 mm wafer scale. For readout, we employ spin-dependent tunneling combined with a low-footprint single-lead quantum dot charge sensor, measured using radiofrequency gate reflectometry. We demonstrate spin readout in two devices using this technique, obtaining valley splittings in the range 0.5-0.7 meV using excited state spectroscopy, and measure a maximum electron spin relaxation time (T1T_1) of 9±39 \pm 3 s at 1 Tesla. These long lifetimes indicate the silicon nanowire geometry and fabrication processes employed here show a great deal of promise for qubit devices, while the spin-readout method demonstrated here is well-suited to a variety of scalable architectures

    Chronic heart failure with diabetes mellitus is characterized by a severe skeletal muscle pathology

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    Background Patients with coexistent chronic heart failure (CHF) and diabetes mellitus (DM) demonstrate greater exercise limitation and worse prognosis compared with CHF patients without DM, even when corrected for cardiac dysfunction. Understanding the origins of symptoms in this subgroup may facilitate development of targeted treatments. We therefore characterized the skeletal muscle phenotype and its relationship to exercise limitation in patients with diabetic heart failure (D‐HF). Methods In one of the largest muscle sampling studies in a CHF population, pectoralis major biopsies were taken from age‐matched controls (n = 25), DM (n = 10), CHF (n = 52), and D‐HF (n = 28) patients. In situ mitochondrial function and reactive oxygen species, fibre morphology, capillarity, and gene expression analyses were performed and correlated to whole‐body exercise capacity. Results Mitochondrial respiration, content, coupling efficiency, and intrinsic function were lower in D‐HF patients compared with other groups (P < 0.05). A unique mitochondrial complex I dysfunction was present in D‐HF patients only (P < 0.05), which strongly correlated to exercise capacity (R2 = 0.64; P < 0.001). Mitochondrial impairments in D‐HF corresponded to higher levels of mitochondrial reactive oxygen species (P < 0.05) and lower gene expression of anti‐oxidative enzyme superoxide dismutase 2 (P < 0.05) and complex I subunit NDUFS1 (P < 0.05). D‐HF was also associated with severe fibre atrophy (P < 0.05) and reduced local fibre capillarity (P < 0.05). Conclusions Patients with D‐HF develop a specific skeletal muscle pathology, characterized by mitochondrial impairments, fibre atrophy, and derangements in the capillary network that are linked to exercise intolerance. These novel preliminary data support skeletal muscle as a potential therapeutic target for treating patients with D‐HF

    Primary thermometry of a single reservoir using cyclic electron tunneling to a quantum dot

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    At the nanoscale, local and accurate measurements of temperature are of particular relevance when testing quantum thermodynamical concepts or investigating novel thermal nanoelectronic devices. Here, we present a primary electron thermometer that allows probing the local temperature of a single-electron reservoir in single-electron devices. The thermometer is based on cyclic electron tunneling between a system with discrete energy levels and the reservoir. When driven at a finite rate, close to a charge degeneracy point, the system behaves like a variable capacitor whose full width at half maximum depends linearly with temperature. We demonstrate this type of thermometer using a quantum dot in a silicon nanowire transistor. We drive cyclic electron tunneling by embedding the device in a radio-frequency resonator which in turn allows reading the thermometer dispersively. Overall, the thermometer shows potential for local probing of fast heat dynamics in nanoelectronic devices and for seamless integration with silicon-based quantum circuits
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