525 research outputs found
Bias dependence of spin transfer torque in Co<sub>2</sub>MnSi Heusler alloy based magnetic tunnel junctions
Heusler compounds are of interest as electrode materials for use in magnetic tunnel junctions (MTJs) due to their half metallic character, which leads to 100% spin polarization and high tunneling magnetoresistance. Most work to date has focused on the improvements to tunneling magnetoresistance that can stem from the use of Heusler electrodes, while there is much less work investigating the influence of Heusler electrodes on the spin transfer torque properties of MTJs. Here, we investigate the bias dependence of the anti-damping like and field-like spin transfer torque components in both symmetric (Co2MnSi/MgO/Co2MnSi) and asymmetric (Co2MnSi/MgO/CoFe) structure Heusler based MTJs using spin transfer torque ferromagnetic resonance. We find that while the damping like torque is linear with respect to bias for both MTJ structures, the asymmetric MTJ structure has an additional linear component to the ordinarily quadratic field like torque bias dependence and that these results can be accounted for by a free electron tunneling model. Furthermore, our results suggest that the low damping and low saturation magnetization properties of Heusler alloys are more likely to lead significant improvements to spin torque switching efficiency rather than their half metallic character
CURTAIN – A unique web-based tool for exploration and sharing of MS-based proteomics data
To facilitate analysis and sharing of mass spectrometry (MS)-based proteomics data, we created online tools called CURTAIN (https://curtain.proteo.info) and CURTAIN-PTM (https://curtainptm.proteo.info) with an accompanying series of video tutorials (https://www.youtube.com/@CURTAIN-me6hl). These are designed to enable non-MS experts to interactively peruse volcano plots and deconvolute primary experimental data so that replicates can be visualized in bar charts or violin plots and exported in publication-ready format. They also allow assessment of overall experimental quality by correlation matrix and profile plot analysis. After making a selection of protein "hits", the user can analyze known domain structure, AlphaFold predicted structure, reported interactors, relative expression as well as disease links. CURTAIN-PTM permits analysis of all identified PTM sites on protein(s) of interest with selected databases. CURTAIN-PTM also links with the Kinase Library to predict upstream kinases that may phosphorylate sites of interest. We provide examples of the utility of CURTAIN and CURTAIN-PTM in analyzing how targeted degradation of the PPM1H Rab phosphatase that counteracts the Parkinson's LRRK2 kinase impacts cellular protein levels and phosphorylation sites. We also reanalyzed a ubiquitylation dataset, characterizing the PINK1-Parkin pathway activation in primary neurons, revealing data of interest not highlighted previously. CURTAIN and CURTAIN-PTM are free to use and open source, enabling researchers to share and maximize the impact of their proteomics data. We advocate that MS data published in volcano plot format be reported containing a shareable CURTAIN weblink, thereby allowing readers to better analyze and exploit the data.</p
The Molecular Mechanisms of OPA1-Mediated Optic Atrophy in Drosophila Model and Prospects for Antioxidant Treatment
Mutations in optic atrophy 1 (OPA1), a nuclear gene encoding a mitochondrial protein, is the most common cause for autosomal dominant optic atrophy (DOA). The condition is characterized by gradual loss of vision, color vision defects, and temporal optic pallor. To understand the molecular mechanism by which OPA1 mutations cause optic atrophy and to facilitate the development of an effective therapeutic agent for optic atrophies, we analyzed phenotypes in the developing and adult Drosophila eyes produced by mutant dOpa1 (CG8479), a Drosophila ortholog of human OPA1. Heterozygous mutation of dOpa1 by a P-element or transposon insertions causes no discernable eye phenotype, whereas the homozygous mutation results in embryonic lethality. Using powerful Drosophila genetic techniques, we created eye-specific somatic clones. The somatic homozygous mutation of dOpa1 in the eyes caused rough (mispatterning) and glossy (decreased lens and pigment deposition) eye phenotypes in adult flies; this phenotype was reversible by precise excision of the inserted P-element. Furthermore, we show the rough eye phenotype is caused by the loss of hexagonal lattice cells in developing eyes, suggesting an increase in lattice cell apoptosis. In adult flies, the dOpa1 mutation caused an increase in reactive oxygen species (ROS) production as well as mitochondrial fragmentation associated with loss and damage of the cone and pigment cells. We show that superoxide dismutase 1 (SOD1), Vitamin E, and genetically overexpressed human SOD1 (hSOD1) is able to reverse the glossy eye phenotype of dOPA1 mutant large clones, further suggesting that ROS play an important role in cone and pigment cell death. Our results show dOpa1 mutations cause cell loss by two distinct pathogenic pathways. This study provides novel insights into the pathogenesis of optic atrophy and demonstrates the promise of antioxidants as therapeutic agents for this condition
Influence of Hydrodynamic Interactions on Mechanical Unfolding of Proteins
We incorporate hydrodynamic interactions in a structure-based model of
ubiquitin and demonstrate that the hydrodynamic coupling may reduce the peak
force when stretching the protein at constant speed, especially at larger
speeds. Hydrodynamic interactions are also shown to facilitate unfolding at
constant force and inhibit stretching by fluid flows.Comment: to be published in Journal of Physics: Condensed Matte
Genome-wide association mapping for root traits in a panel of rice accessions from Vietnam
Background: Despite recent sequencing efforts, local genetic resources remain underexploited, even though they carry alleles that can bring agronomic benefits. Taking advantage of the recent genotyping with 22,000 single-nucleotide polymorphism markers of a core collection of 180 Vietnamese rice varieties originating from provinces from North to South Vietnam and from different agrosystems characterized by contrasted water regimes, we have performed a genome-wide association study for different root parameters. Roots contribute to water stress avoidance and are a still underexploited target for breeding purpose due to the difficulty to observe them. Results: The panel of 180 rice varieties was phenotyped under greenhouse conditions for several root traits in an experimental design with 3 replicates. The phenotyping system consisted of long plastic bags that were filled with sand and supplemented with fertilizer. Root length, root mass in different layers, root thickness, and the number of crown roots, as well as several derived root parameters and shoot traits, were recorded. The results were submitted to association mapping using a mixed model involving structure and kinship to enable the identification of significant associations. The analyses were conducted successively on the whole panel and on its indica (115 accessions) and japonica (64 accessions) subcomponents. The two associations with the highest significance were for root thickness on chromosome 2 and for crown root number on chromosome 11. No common associations were detected between the indica and japonica subpanels, probably because of the polymorphism repartition between the subspecies. Based on orthology with Arabidopsis, the possible candidate genes underlying the quantitative trait loci are reviewed. Conclusions: Some of the major quantitative trait loci we detected through this genome-wide association study contain promising candidate genes encoding regulatory elements of known key regulators of root formation and development
Risk factors for exacerbations and pneumonia in patients with chronic obstructive pulmonary disease: a pooled analysis.
BACKGROUND: Patients with chronic obstructive pulmonary disease (COPD) are at risk of exacerbations and pneumonia; how the risk factors interact is unclear. METHODS: This post-hoc, pooled analysis included studies of COPD patients treated with inhaled corticosteroid (ICS)/long-acting β2 agonist (LABA) combinations and comparator arms of ICS, LABA, and/or placebo. Backward elimination via Cox's proportional hazards regression modelling evaluated which combination of risk factors best predicts time to first (a) pneumonia, and (b) moderate/severe COPD exacerbation. RESULTS: Five studies contributed: NCT01009463, NCT01017952, NCT00144911, NCT00115492, and NCT00268216. Low body mass index (BMI), exacerbation history, worsening lung function (Global Initiative for Chronic Obstructive Lung Disease [GOLD] stage), and ICS treatment were identified as factors increasing pneumonia risk. BMI was the only pneumonia risk factor influenced by ICS treatment, with ICS further increasing risk for those with BMI <25 kg/m2. The modelled probability of pneumonia varied between 3 and 12% during the first year. Higher exacerbation risk was associated with a history of exacerbations, poorer lung function (GOLD stage), female sex and absence of ICS treatment. The influence of the other exacerbation risk factors was not modified by ICS treatment. Modelled probabilities of an exacerbation varied between 31 and 82% during the first year. CONCLUSIONS: The probability of an exacerbation was considerably higher than for pneumonia. ICS reduced exacerbations but did not influence the effect of risks associated with prior exacerbation history, GOLD stage, or female sex. The only identified risk factor for ICS-induced pneumonia was BMI <25 kg/m2. Analyses of this type may help the development of COPD risk equations
Hydrodynamic interactions in colloidal ferrofluids: A lattice Boltzmann study
We use lattice Boltzmann simulations, in conjunction with Ewald summation
methods, to investigate the role of hydrodynamic interactions in colloidal
suspensions of dipolar particles, such as ferrofluids. Our work addresses
volume fractions of up to 0.20 and dimensionless dipolar interaction
parameters of up to 8. We compare quantitatively with Brownian
dynamics simulations, in which many-body hydrodynamic interactions are absent.
Monte Carlo data are also used to check the accuracy of static properties
measured with the lattice Boltzmann technique. At equilibrium, hydrodynamic
interactions slow down both the long-time and the short-time decays of the
intermediate scattering function , for wavevectors close to the peak of
the static structure factor , by a factor of roughly two. The long-time
slowing is diminished at high interaction strengths whereas the short-time
slowing (quantified via the hydrodynamic factor ) is less affected by the
dipolar interactions, despite their strong effect on the pair distribution
function arising from cluster formation. Cluster formation is also studied in
transient data following a quench from ; hydrodynamic interactions
slow the formation rate, again by a factor of roughly two
Nonlinear rheology of colloidal dispersions
Colloidal dispersions are commonly encountered in everyday life and represent
an important class of complex fluid. Of particular significance for many
commercial products and industrial processes is the ability to control and
manipulate the macroscopic flow response of a dispersion by tuning the
microscopic interactions between the constituents. An important step towards
attaining this goal is the development of robust theoretical methods for
predicting from first-principles the rheology and nonequilibrium microstructure
of well defined model systems subject to external flow. In this review we give
an overview of some promising theoretical approaches and the phenomena they
seek to describe, focusing, for simplicity, on systems for which the colloidal
particles interact via strongly repulsive, spherically symmetric interactions.
In presenting the various theories, we will consider first low volume fraction
systems, for which a number of exact results may be derived, before moving on
to consider the intermediate and high volume fraction states which present both
the most interesting physics and the most demanding technical challenges. In
the high volume fraction regime particular emphasis will be given to the
rheology of dynamically arrested states.Comment: Review articl
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