455 research outputs found
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Investigating the Genetic Control of Fusarium Root Rot Resistance in Snap Beans
Root rot diseases are a major constraint to bean (Phaseolus vulgaris L.)
production around the world. Both snap beans and dry beans are affected. Root rot diseases can be caused by a variety of pathogens; however, Fusarium solani is a common causal agent. Fusarium root rot is a primary yield limitation of snap bean production in Oregon. Cultural control methods are ineffective and the pathogen will be present at the end of one season of production on previously clean land, indicating the need for genetic resistance. In order to address this need, a diversity panel of 148 snap bean varieties (the BeanCAP Snap Bean Diversity Panel) was evaluated for resistance to Fusarium root rot in Oregon. Morphological traits potentially involved in root rot resistance were also evaluated. Genome-wide association studies were conducted to locate SNPs associated with Fusarium root rot resistance, aboveground biomass, adventitious roots, taproot diameter, basal root diameter, deepest root angle, shallowest root angle, root angle average, root angle difference, and root angle geometric mean. Significant associations were located for all traits evaluated, including associations with root rot resistance on Pv02, Pv08, Pv09, and Pv10. Genomic estimated breeding values based on BLUPs and BLUEs were generated for each variety and trait. In order to investigate the genetic
architecture of the diversity panel principal component analysis, a kinship heat map, and a neighbor-joining phylogenetic tree were generated. The first principal component axis separated varieties by center of domestication, while the second principal component axis separated European extra-fine beans from other Mesoamerican varieties. Kinship analysis demonstrated an average similarity coefficient between varieties of 0.67. The phylogenetic tree indicated two separate derivations of snap beans with extensive subsequent recombination. In this study we also converted previously published SNP markers associated with resistance to root rot diseases in snap bean into user-friendly INDEL and KASP markers to aid in the implementation of marker-assisted selection for resistance to root rot in snap bean
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A parallel/vector Monte Carlo MESFET model for shared memory machines
The parallelization and vectorization of Monte Carlo algorithms for modelling
charge transport in semiconductor devices are considered. The standard ensemble
Monte Carlo simulation of a three parabolic band model for GaAs is first
presented as partial verification of the simulation. The model includes scattering
due to acoustic, polar-optical and intervalley phonons. This ensemble simulation
is extended to a full device simulation by the addition of real-space positions, and
solution for the electrostatic potential from the charge density distribution using
Poisson's equation. Poisson's equation was solved using the cloud-in-cell scheme
for charge assignment, finite differences for spatial discretization, and simultaneous
over-relaxation for solution. The particle movement (acceleration and scattering)
and the solution of Poisson's are both separately parallelized. The parallelization
techniques used in both parts are based on the use of semaphores for the protection
of shared resources and processor synchronization. The speed increase results for
parallelization with and without vectorization on the Ardent Titan II are presented.
The results show saturation due to memory access limitations at a speed increase of
approximately 3.3 times the serial case when four processors are used. Vectorization
alone provides a speed increase of approximately 1.6 times when compared with the
nonvectorized serial case. It is concluded that the speed increase achieved with
the Titan II is limited by memory access considerations and that this limitation is
likely to plague shared memory machines for the forseeable future. For the program
presented here, vectorization is concluded to provide a better speed increase
per day of development time than parallelization. However, when vectorization is
used in conjunction with parallelization, the speed increase due to vectorization is
negligible
Bjerrum pairing correlations at charged interfaces
Electrostatic correlations play a fundamental role in aqueous solutions. In
this letter, we identify transverse and lateral correlations as two mutually
exclusive regimes. We show that the transverse regime leads to binding by
generalization of Bjerrum pair formation theory, yielding binding constants
from first-principle statistical-mechanical calculations. We compare our
theoretical predictions with experiments on charged membranes and Langmuir
monolayers and find good agreement. We contrast our approach with existing
theories in the strong-coupling limit and on charged modulated interfaces, and
discuss different scenarios that lead to charge reversal and equal-sign
attraction by macro-ions.Comment: 7 pages, 4 figure
Influence of the sterol aliphatic side chain on membrane properties: a molecular dynamics study
Following a recent experimental investigation of the effect of the length of the alkyl side chain in a series
of cholesterol analogues (Angew. Chem., Int. Ed., 2013, 52, 12848–12851), we report here an atomistic
molecular dynamics characterization of the behaviour of methyl-branched side chain sterols (iso series) in
POPC bilayers. The studied sterols included androstenol (i-C0-sterol) and cholesterol (i-C8-sterol), as well
as four other derivatives (i-C5, i-C10, i-C12 and i-C14-sterol). For each sterol, both subtle local effects and
more substantial differential alterations of membrane properties along the iso series were investigated. The
location and orientation of the tetracyclic ring system is almost identical in all compounds. Among all the
studied sterols, cholesterol is the sterol that presents the best matching with the hydrophobic length of
POPC acyl chains, whereas longer-chained sterols interdigitate into the opposing membrane leaflet. In
accordance with the experimental observations, a maximal ordering effect is observed for intermediate
sterol chain length (i-C5, cholesterol, i-C10). Only for these sterols a preferential interaction with the
saturated sn-1 chain of POPC (compared to the unsaturated sn-2 chain) was observed, but not for either
shorter or longer-chained derivatives. This work highlights the importance of the sterol alkyl chain in the
modulation of membrane properties and lateral organization in biological membranes
Probing the Influence of Single-Site Mutations in the Central Cross-β Region of Amyloid β (1–40) Peptides
Amyloid β (Aβ) is a peptide known to form amyloid fibrils in the brain of patients suffering from Alzheimer’s disease. A complete mechanistic understanding how Aβ peptides form neurotoxic assemblies and how they kill neurons has not yet been achieved. Previous analysis of various Aβ40 mutants could reveal the significant importance of the hydrophobic contact between the residues Phe19 and Leu34 for cell toxicity. For some mutations at Phe19, toxicity was completely abolished. In the current study, we assessed if perturbations introduced by mutations in the direct proximity of the Phe19/Leu34 contact would have similar relevance for the fibrillation kinetics, structure, dynamics and toxicity of the Aβ assemblies. To this end, we rationally modified positions Phe20 or Gly33. A small library of Aβ40 peptides with Phe20 mutated to Lys, Tyr or the non-proteinogenic cyclohexylalanine (Cha) or Gly33 mutated to Ala was synthesized. We used electron microscopy, circular dichroism, X-ray diffraction, solid-state NMR spectroscopy, ThT fluorescence and MTT cell toxicity assays to comprehensively investigate the physicochemical properties of the Aβ fibrils formed by the modified peptides as well as toxicity to a neuronal cell line. Single mutations of either Phe20 or Gly33 led to relatively drastic alterations in the Aβ fibrillation kinetics but left the global, as well as the local structure, of the fibrils largely unchanged. Furthermore, the introduced perturbations caused a severe decrease or loss of cell toxicity compared to wildtype Aβ40. We suggest that perturbations at position Phe20 and Gly33 affect the fibrillation pathway of Aβ40 and, thereby, influence the especially toxic oligomeric species manifesting so that the region around the Phe19/Leu34 hydrophobic contact provides a promising site for the design of small molecules interfering with the Aβ fibrillation pathway
Understanding the association between skin involvement and joint activity in patients with psoriatic arthritis: experience from the Corrona Registry.
Objective: To compare the characteristics of patients with psoriatic arthritis among patient groups stratified by degree of skin and joint involvement, and to evaluate the relationship between skin severity and joint activity.
Methods: Body surface area (BSA) and Clinical Disease Activity Index (CDAI) at enrolment were analysed. Patient characteristics were stratified by skin severity and joint activity. Baseline patient characteristics, clinical and disease characteristics and patient-reported outcomes were compared. The strength of the relationship of skin severity and joint activity was evaluated using methods for categorical variables (χ
Results: 1542 adult patients in the Corrona Psoriatic Arthritis/Spondyloarthritis Registry enrolled between 21 May 2013 and 20 September 2016 were analysed. Most patients in the BSA \u3e3%/CDAI moderate/high subgroup had worse clinical and patient-reported outcomes. A significant (p
Conclusion: Skin severity is modestly correlated with joint activity, and patients with higher skin severity are two times more likely to have increased joint involvement. Clinicians need to address both skin severity and joint activity in treatment decisions
Event-Related Potential Correlates of Performance-Monitoring in a Lateralized Time-Estimation Task
Performance-monitoring as a key function of cognitive control covers a wide range of diverse processes to enable goal directed behavior and to avoid maladjustments. Several event-related brain potentials (ERP) are associated with performance-monitoring, but their conceptual background differs. For example, the feedback-related negativity (FRN) is associated with unexpected performance feedback and might serve as a teaching signal for adaptational processes, whereas the error-related negativity (ERN) is associated with error commission and subsequent behavioral adaptation. The N2 is visible in the EEG when the participant successfully inhibits a response following a cue and thereby adapts to a given stop-signal. Here, we present an innovative paradigm to concurrently study these different performance-monitoring-related ERPs. In 24 participants a tactile time-estimation task interspersed with infrequent stop-signal trials reliably elicited all three ERPs. Sensory input and motor output were completely lateralized, in order to estimate any hemispheric processing preferences for the different aspects of performance monitoring associated with these ERPs. In accordance with the literature our data suggest augmented inhibitory capabilities in the right hemisphere given that stop-trial performance was significantly better with left- as compared to right-hand stop-signals. In line with this, the N2 scalp distribution was generally shifted to the right in addition to an ipsilateral shift in relation to the response hand. Other than that, task lateralization affected neither behavior related to error and feedback processing nor ERN or FRN. Comparing the ERP topographies using the Global Map Dissimilarity index, a large topographic overlap was found between all considered components.With an evenly distributed set of trials and a split-half reliability for all ERP components ≥.85 the task is well suited to efficiently study N2, ERN, and FRN concurrently which might prove useful for group comparisons, especially in clinical populations
Reduced Food Intake and Body Weight in Mice Deficient for the G Protein-Coupled Receptor GPR82
G protein-coupled receptors (GPCR) are involved in the regulation of numerous physiological functions. Therefore, GPCR variants may have conferred important selective advantages during periods of human evolution. Indeed, several genomic loci with signatures of recent selection in humans contain GPCR genes among them the X-chromosomally located gene for GPR82. This gene encodes a so-called orphan GPCR with unknown function. To address the functional relevance of GPR82 gene-deficient mice were characterized. GPR82-deficient mice were viable, reproduced normally, and showed no gross anatomical abnormalities. However, GPR82-deficient mice have a reduced body weight and body fat content associated with a lower food intake. Moreover, GPR82-deficient mice showed decreased serum triacylglyceride levels, increased insulin sensitivity and glucose tolerance, most pronounced under Western diet. Because there were no differences in respiratory and metabolic rates between wild-type and GPR82-deficient mice our data suggest that GPR82 function influences food intake and, therefore, energy and body weight balance. GPR82 may represent a thrifty gene most probably representing an advantage during human expansion into new environments
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