Genomic Analysis of Drosophila Neuronal Remodeling: A Role for the RNA-Binding Protein Boule as a Negative Regulator of Axon Pruning

Drosophila mushroom body (MB) {gamma} neurons undergo axon pruning during metamorphosis through a process of localized degeneration of specific axon branches. Developmental axon degeneration is initiated by the steroid hormone ecdysone, acting through a nuclear receptor complex composed of USP (ultraspiracle) and EcRB1 (ecdysone receptor B1) to regulate gene expression in MB {gamma} neurons. To identify ecdysone-dependent gene expression changes in MB {gamma} neurons at the onset of axon pruning, we use laser capture microdissection to isolate wild-type and mutant MB neurons in which EcR (ecdysone receptor) activity is genetically blocked, and analyze expression changes by microarray. We identify several molecular pathways that are regulated in MB neurons by ecdysone. The most striking observation is the upregulation of genes involved in the UPS (ubiquitin–proteasome system), which is cell autonomously required for {gamma} neuron pruning. In addition, we characterize the function of Boule, an evolutionarily conserved RNA-binding protein previously implicated in spermatogenesis in flies and vertebrates. boule expression is downregulated by ecdysone in MB neurons at the onset of pruning, and forced expression of Boule in MB {gamma} neurons is sufficient to inhibit axon pruning. This activity is dependent on the RNA-binding domain of Boule and a conserved DAZ (deleted in azoospermia) domain implicated in interactions with other RNA-binding proteins. However, loss of Boule does not result in obvious defects in axon pruning or morphogenesis of MB neurons, suggesting that it acts redundantly with other ecdyonse-regulated genes. We propose a novel function for Boule in the CNS as a negative regulator of developmental axon pruning

Subcellular Localization of the Leucine Biosynthetic Enzymes in Yeast

When baker's yeast spheroplasts were lysed by mild osmotic shock, practically all of the isopropylmalate isomerase and the β-isopropylmalate dehydrogenase was released into the 30,000 × g supernatant fraction, as was the cytosol marker enzyme, glucose-6-phosphate dehydrogenase. α-Isopropylmalate synthase, however, was not detected in the initial supernatant, but could be progressively solubilized by homogenization, appearing more slowly than citrate synthase but faster than cytochrome oxidase. Of the total glutamate-α-ketoisocaproate transaminase activity, approximately 20% was in the initial soluble fraction, whereas solubilization of the remainder again required homogenization of the spheroplast lysate. Results from sucrose density gradient centrifugation of a cell-free particulate fraction and comparison with marker enzymes suggested that α-isopropylmalate synthase was located in the mitochondria. It thus appears that, in yeast, the first specific enzyme in the leucine biosynthetic pathway (α-isopropylmalate synthase) is particulate, whereas the next two enzymes in the pathway (isopropylmalate isomerase and β-isopropylmalate dehydrogenase) are “soluble,” with glutamate-α-ketoisocaproate transaminase activity being located in both the cytosol and particulate cell fractions

A note on reducing spurious pressure oscillations in fully conservative discontinuous Galerkin simulations of multicomponent flows

A well-known issue associated with the use of fully conservative schemes in multicomponent-flow simulations is the generation of spurious pressure oscillations at contact interfaces. These oscillations can rapidly lead to solver divergence even in the presence of smooth interfaces that are not fully resolved. In this note, we compare various strategies for reducing such oscillations that do not (a) introduce conservation error, (b) rely on artificial viscosity or limiting, or (c) degrade order of accuracy in smooth regions of the flow. The considered test case is one-dimensional advection of a high-pressure nitrogen/n-dodecane thermal bubble using the thermally perfect gas model. Several results are presented that contradict those corresponding to the more conventional hydrogen/oxygen thermal-bubble case

Detection of electronic nematicity using scanning tunneling microscopy

Electronic nematic phases have been proposed to occur in various correlated electron systems and were recently claimed to have been detected in scanning tunneling microscopy (STM) conductance maps of the pseudogap states of the cuprate high-temperature superconductor Bi2Sr2CaCu2O8+x (Bi-2212). We investigate the influence of anisotropic STM tip structures on such measurements and establish, with a model calculation, the presence of a tunneling interference effect within an STM junction that induces energy-dependent symmetry-breaking features in the conductance maps. We experimentally confirm this phenomenon on different correlated electron systems, including measurements in the pseudogap state of Bi-2212, showing that the apparent nematic behavior of the imaged crystal lattice is likely not due to nematic order but is related to how a realistic STM tip probes the band structure of a material. We further establish that this interference effect can be used as a sensitive probe of changes in the momentum structure of the sample's quasiparticles as a function of energy.Comment: Accepted for publication (PRB - Rapid Communications). Main text (5 pages, 4 figures) + Supplemental Material (4 pages, 4 figures

TurbuStat: Turbulence Statistics in Python

We present TurbuStat (v1.0): a Python package for computing turbulence statistics in spectral-line data cubes. TurbuStat includes implementations of fourteen methods for recovering turbulent properties from observational data. Additional features of the software include: distance metrics for comparing two data sets; a segmented linear model for fitting lines with a break-point; a two-dimensional elliptical power-law model; multi-core fast-fourier-transform support; a suite for producing simulated observations of fractional Brownian Motion fields, including two-dimensional images and optically-thin HI data cubes; and functions for creating realistic world coordinate system information for synthetic observations. This paper summarizes the TurbuStat package and provides representative examples using several different methods. TurbuStat is an open-source package and we welcome community feedback and contributions.Comment: Accepted in AJ. 21 pages, 8 figure