Expansion of the Gene Ontology knowledgebase and resources

The Gene Ontology (GO) is a comprehensive resource of computable knowledge regarding the functions of genes and gene products. As such, it is extensively used by the biomedical research community for the analysis of -omics and related data. Our continued focus is on improving the quality and utility of the GO resources, and we welcome and encourage input from researchers in all areas of biology. In this update, we summarize the current contents of the GO knowledgebase, and present several new features and improvements that have been made to the ontology, the annotations and the tools. Among the highlights are 1) developments that facilitate access to, and application of, the GO knowledgebase, and 2) extensions to the resource as well as increasing support for descriptions of causal models of biological systems and network biology. To learn more, visit http://geneontology.org/.National Institutes of Health/National Human Genome Research Institute [HG002273] awarded to the PI group formed by (alphabetically) Judith A. Blake, J. Michael Cherry, Suzanna E. Lewis, Paul W. Sternberg and Paul D. Thomas, as well as additional funding awarded to each participating institution. For more details please visit: http://geneontology.org/page/go-consortium-contributors-list. Funding for open access charge: National Institutes of Health/National Human Genome Research Institute [HG002273]

μSR studies of magnetic order and dynamics of the n = 2 Ruddlesden-Popper phases Sr₂RMn₂O₇ (R = Pr, Nd, Sm, Eu, Gd, Tb, Dy, and Ho)

Zero field muon spin relaxation (μSR) has been used to study the magnetic properties of n=2 Ruddlesden-Popper phases Sr2RMn2O7, where R = Pr, Nd, Sm, Eu, Gd, Tb, Dy, and Ho. The results show that the size of the lanthanide ion is crucial in determining the magnetic state and dynamics of the system. Because muons are implanted throughout the bulk of the sample, impurity phases contribute only according to their volume fraction. Hence in the case of biphasic samples the data are dominated by the majority phase. Although none of our samples has a ferromagnetic ground state, colossal magnetoresistance (CMR) is observed over a wide temperature range, 4 K<T<150 K, for both the Pr and Nd compounds. The μSR results show that the magnetic transition in both these samples is broad. Ordered, but fluctuating, regions form at ∼150 K, the reported onset of CMR, with the fluctuation rates gradually decreasing with temperature. Even at 5 K, fluctuations are still observed. The ferromagnetic double exchange between Mn ions becomes weaker as the size of the lanthanide ion decreases. Sr2SmMn2O7 shows weak clustering at a much reduced temperature of 30 K whereas Sr2EuMn2O7 shows spin-glass-like behavior. For all lanthanide ions smaller than Eu no long range magnetic ordering of the spins is observed and the observed relaxation rates follow an activated dependence. The technique allows us to extract the effective activation energy associated with the magnetic fluctuations of the lanthanide moments in samples with R = Sm, Eu, Gd, Tb, Dy, and Ho. CMR is only observed where μSR measurements show a broad magnetic transition associated with fluctuations. We therefore believe that these fluctuating ordered regions are responsible for the extended temperature regime in which CMR has been observed in these nonferromagnetic n=2 Ruddlesden-Popper phases. ©1999 The American Physical Society

&mu;SR studies of magnetic order in La_2-xSr_xNiO₄

We report muon-spin-relaxation measurements on a series of compounds with composition La2-xSrxNiO4+δ where the net hole concentration x+2δ is greater than 0.4. A magnetic transition is found in all the samples studied which occurs at a composition-dependent temperature TM. Below TM clear precession signals are observed in zero applied magnetic field, indicating the existence of at least short-range magnetic order on a time scale greater than 10-8 s. Above TM the correlation times decrease by several orders of magnitude. The measurements of TM as a function of the net hole concentration extend the determination of Néel temperatures by previous neutron diffraction measurements to higher doping levels

Probing magnetic order in heavily doped La_{2-x}Sr_{x}NiO_{4+delta}

We report mu SR measurements on a series of compounds with composition La2-xSrxNiO4+delta where the net hole concentration x + 2 delta is greater than 0.4. A magnetic transition is found in all the samples studied which occurs at a composition-dependent temperature T-M. Below T-M, clear precession signals are observed in zero applied magnetic field. The possible muon sites are discussed within the context of dipole-field calculations

Material properties of perovskites in the quasi-ternary system LaFeO3-LaCoO3-LaNiO3

An overview is presented on the variation of electrical conductivity, oxygen permeation, and thermal expansion coefficient as a function of the composition of perovskites in the quasi-ternary system LaFeO3-LaCoO3-LaNiO3. Powders of thirteen nominal perovskite compositions were synthesized under identical conditions by the Pechini method. The powder X-ray diffraction data of two series, namely La(Ni0.5Fe0.5)1-xCoxO3 and LaNi0.5-xFexCo0.5O3, are presented after the powders had been sintered at 1100 °C for 6 h in air. The measurements revealed a rhombohedral structure for all compositions except LaNi0.5Fe0.5O3 for which 60% rhombohedral and 40% orthorhombic phase was found. The maximum DC electrical conductivity value of the perovskites at 800 °C was 1229 S cm-1 for the composition LaCoO3 and the minimum was 91 S cm-1 for the composition LaCo0.5Fe0.5O3. The oxygen permeation of samples with promising conductivities at 800 °C was one order of magnitude lower than that of La0.6Sr0.4Co0.8Fe0.2O3 (LSCF). The highest value of 0.017 ml cm-2 min-1 at 950 °C was obtained with LaNi0.5Co0.5O3. The coefficients of thermal expansion varied in the range of 13.2×10-6 K-1 and 21.9×10-6 K-1 for LaNi0.5Fe0.5O3 and LaCoO3, respectively. 57Fe Mössbauer spectroscopy was used as probe for the oxidation states, local environment and magnetic properties of iron ions as a function of chemical composition. The substitution had a great influence on the chemical properties of the materials. © 2016 Elsevier Inc. All rights reserved

Analysis of the Drosophila Compound Eye with Light and Electron Microscopy.

The Drosophila compound eye is composed of about 750 units, called ommatidia, which are arranged in a highly regular pattern. Eye development proceeds in a stereotypical fashion, where epithelial cells of the eye imaginal discs are specified, recruited, and differentiated in a sequential order that leads to the highly precise structure of an adult eye. Even small perturbations, for example in signaling pathways that control proliferation, cell death, or differentiation, can impair the regular structure of the eye, which can be easily detected and analyzed. In addition, the Drosophila eye has proven to be an ideal model for studying the genetic control of neurodegeneration, since the eye is not essential for viability. Several human neurodegeneration diseases have been modeled in the fly, leading to a better understanding of the function/misfunction of the respective gene. In many cases, the genes involved and their functions are conserved between flies and human. More strikingly, when ectopically expressed in the fly eye some human genes, even those without a Drosophila counterpart, can induce neurodegeneration, detectable by aberrant phototaxis, impaired electrophysiology, or defects in eye morphology and retinal histology. These defects are often rather subtle alteration in shape, size, or arrangement of the cells, and can be easily scored at the ultrastructural level. This chapter aims to provide an overview regarding the analysis of the retina by light and electron microscopy