Guidance Receptors Find Their Places in the Axonal Order

In this issue of Neuron, Katsuki and colleagues show that cell-autonomous mechanisms divide Drosophila axons into proximal and distal compartments. Axon guidance receptors selectively localize to one compartment. A diffusion barrier exists near the compartment boundary, suggesting that it may have properties like those of the axon initial segment in mammalian neurons

Live Dissection of Drosophila Embryos: Streamlined Methods for Screening Mutant Collections by Antibody Staining

Drosophila embryos between stages 14 and 17 of embryonic development can be readily dissected to generate "fillet" preparations. In these preparations, the central nervous system runs down the middle, and is flanked by the body walls. Many different phenotypes have been examined using such preparations. In most cases, the fillets were generated by dissection of antibody-stained fixed whole-mount embryos. These "fixed dissections" have some disadvantages, however. They are time-consuming to execute, and it is difficult to sort mutant (GFP-negative) embryos from stocks in which mutations are maintained over GFP balancer chromosomes. Since 2002, our group has been conducting deficiency and ectopic expression screens to identify ligands for orphan receptors. In order to do this, we developed streamlined protocols for live embryo dissection and antibody staining of collections containing hundreds of balanced lines. We have concluded that it is considerably more efficient to examine phenotypes in large collections of stocks by live dissection than by fixed dissection. Using the protocol described here, a single trained individual can screen up to 10 lines per day for phenotypes, examining 4-7 mutant embryos from each line under a compound microscope. This allows the identification of mutations conferring subtle, low-penetrance phenotypes, since up to 70 hemisegments per line are scored at high magnification with a 40X water-immersion lens

Transferability of Insights from Fundamental Investigations into Practical Applications of Prechamber Combustion Systems

Efforts to reduce CO2 emissions from spark ignition engines have driven engine development to lean-burn or high-dilution operation, which results in high combustion variability as well as increased unburned hydrocarbon emissions. A widely used technology to reduce these issues are prechamber ignition systems, in which the external ignition source is located in a separate small volume, connected to the main chamber via small orifices. This setup allows for design of favourable ignition conditions near the ignition source, which results in fast and repeatable early flame propagation. The pressure increase resulting from combustion taking place inside the prechamber leads to the ejection of jets containing hot combustion products and possibly active radicals into the main chamber, which ignite the lean or diluted mixture; this process is often dubbed turbulent jet ignition or TJI. The use of TJI systems in engines allows the combustion of very lean/diluted mixtures, resulting in higher efficiencies and lower NOx emissions. In this work we shed light into the importance of quenching for practical applications involving turbulent jet ignition. This is achieved through optical investigations in a generic, constant volume test-rig, combined with zero-dimensional (0-D) model calculations. The 0-D model is applied to the generic setup and in real engine applications under varying operating conditions, in order to highlight the relative importance of quenching under the various thermochemical conditions encountered. The results indicate that thermal quenching in the nozzle should not be expected due to the small flame thickness under high pressure encountered in internal combustion engines. Nevertheless, under the jet mixing conditions expected in engines, hydrodynamic quenching due to mixing of burned products with unburned (cold) main chamber mixture can be expected. In most engine conditions, the re-ignition process of the initially quenched jet after their exit from the prechamber is expected to be so fast, that quenching will not be apparent in most measurements

Investigating brain connectivity heritability in a twin study using diffusion imaging data

Heritability of brain anatomical connectivity has been studied with diffusion-weighted imaging (DWI) mainly by modeling each voxel's diffusion pattern as a tensor (e.g., to compute fractional anisotropy), but this method cannot accurately represent the many crossing connections present in the brain. We hypothesized that different brain networks (i.e., their component fibers) might have different heritability and we investigated brain connectivity using High Angular Resolution Diffusion Imaging (HARDI) in a cohort of twins comprising 328 subjects that included 70 pairs of monozygotic and 91 pairs of dizygotic twins. Water diffusion was modeled in each voxel with a Fiber Orientation Distribution (FOD) function to study heritability for multiple fiber orientations in each voxel. Precision was estimated in a test-retest experiment on a sub-cohort of 39 subjects. This was taken into account when computing heritability of FOD peaks using an ACE model on the monozygotic and dizygotic twins. Our results confirmed the overall heritability of the major white matter tracts but also identified differences in heritability between connectivity networks. Inter-hemispheric connections tended to be more heritable than intra-hemispheric and cortico-spinal connections. The highly heritable tracts were found to connect particular cortical regions, such as medial frontal cortices, postcentral, paracentral gyri, and the right hippocampus

PTArcade

This is a lightweight manual for PTArcade, a wrapper of ENTERPRISE and ceffyl that allows for easy implementation of new-physics searches in PTA data. In this manual, we describe how to get PTArcade installed (either on your local machine or an HPC cluster). We discuss how to define a stochastic or deterministic signal and how PTArcade implements these signals in PTA-analysis pipelines. Finally, we show how to handle and analyze the PTArcade output using a series of utility functions that come together with PTArcade.Comment: 26 pages, 2 figures, 2 table

A powerful and flexible approach to the analysis of RNA sequence count data

Motivation: A number of penalization and shrinkage approaches have been proposed for the analysis of microarray gene expression data. Similar techniques are now routinely applied to RNA sequence transcriptional count data, although the value of such shrinkage has not been conclusively established. If penalization is desired, the explicit modeling of mean–variance relationships provides a flexible testing regimen that ‘borrows’ information across genes, while easily incorporating design effects and additional covariates

The Solar--Stellar Connection

Stars have proven to be surprisingly prolific radio sources and the added sensitivity of the Square Kilometer Array will lead to advances in many directions. This chapter discusses prospects for studying the physics of stellar atmospheres and stellar winds across the HR diagram.Comment: to appear in "Science with the Square Kilometer Array," eds. C. Carilli and S. Rawlings, New Astronomy Reviews (Elsevier: Amsterdam

The Infrared Imaging Spectrograph (IRIS) for TMT: Instrument Overview

We present an overview of the design of IRIS, an infrared (0.84 - 2.4 micron) integral field spectrograph and imaging camera for the Thirty Meter Telescope (TMT). With extremely low wavefront error (<30 nm) and on-board wavefront sensors, IRIS will take advantage of the high angular resolution of the narrow field infrared adaptive optics system (NFIRAOS) to dissect the sky at the diffraction limit of the 30-meter aperture. With a primary spectral resolution of 4000 and spatial sampling starting at 4 milliarcseconds, the instrument will create an unparalleled ability to explore high redshift galaxies, the Galactic center, star forming regions and virtually any astrophysical object. This paper summarizes the entire design and basic capabilities. Among the design innovations is the combination of lenslet and slicer integral field units, new 4Kx4k detectors, extremely precise atmospheric dispersion correction, infrared wavefront sensors, and a very large vacuum cryogenic system.Comment: Proceedings of the SPIE, 9147-76 (2014

Reduced Efficacy of Natural Selection on Codon Usage Bias in Selfing Arabidopsis and Capsella Species

Population genetic theory predicts that the efficacy of natural selection in a self-fertilizing species should be lower than its outcrossing relatives because of the reduction in the effective population size (Ne) in the former brought about by inbreeding. However, previous analyses comparing Arabidopsis thaliana (selfer) with A. lyrata (outcrosser) have not found conclusive support for this prediction. In this study, we addressed this issue by examining silent site polymorphisms (synonymous and intronic), which are expected to be informative about changes in Ne. Two comparisons were made: A. thaliana versus A. lyrata and Capsella rubella (selfer) versus C. grandiflora (outcrosser). Extensive polymorphism data sets were obtained by compiling published data from the literature and by sequencing 354 exon loci in C. rubella and 89 additional loci in C. grandiflora. To extract information from the data effectively for studying these questions, we extended two recently developed models in order to investigate detailed selective differences between synonymous codons, mutational biases, and biased gene conversion (BGC), taking into account the effects of recent changes in population size. We found evidence that selection on synonymous codons is significantly weaker in the selfers compared with the outcrossers and that this difference cannot be fully accounted for by mutational biases or BGC