Software and methods for oligonucleotide and cDNA array data analysis.

Two HTML-based programs were developed to analyze and filter gene-expression data: 'Bullfrog' for Affymetrix oligonucleotide arrays and 'Spot' for custom cDNA arrays. The programs provide intuitive data-filtering tools through an easy-to-use interface. A background subtraction and normalization program for cDNA arrays was also built that provides an informative summary report with data-quality assessments. These programs are freeware to aid in the analysis of gene-expression results and facilitate the search for genes responsible for interesting biological processes and phenotypes

Overexpression of chloroplast-targeted ferrochelatase 1 results in a genomes uncoupled chloroplast-to-nucleus retrograde signalling phenotype.

Chloroplast development requires communication between the progenitor plastids and the nucleus, where most of the genes encoding chloroplast proteins reside. Retrograde signals from the chloroplast to the nucleus control the expression of many of these genes, but the signalling pathway is poorly understood. Tetrapyrroles have been strongly implicated as mediators of this signal with the current hypothesis being that haem produced by the activity of ferrochelatase 1 (FC1) is required to promote nuclear gene expression. We have tested this hypothesis by overexpressing FC1 and specifically targeting it to either chloroplasts or mitochondria, two possible locations for this enzyme. Our results show that targeting of FC1 to chloroplasts results in increased expression of the nuclear-encoded chloroplast genes GUN4, CA1, HEMA1, LHCB2.1, CHLH after treatment with Norflurazon (NF) and that this increase correlates to FC1 gene expression and haem production measured by feedback inhibition of protochlorophyllide synthesis. Targeting FC1 to mitochondria did not enhance the expression of nuclear-encoded chloroplast genes after NF treatment. The overexpression of FC1 also increased nuclear gene expression in the absence of NF treatment, demonstrating that this pathway is operational in the absence of a stress treatment. Our results therefore support the hypothesis that haem synthesis is a promotive chloroplast-to-nucleus retrograde signal. However, not all FC1 overexpression lines enhanced nuclear gene expression, suggesting there is still a lot we do not understand about the role of FC1 in this signalling pathway. This article is part of the theme issue 'Retrograde signalling from endosymbiotic organelles'.BBRS

Mapping The Interstellar Medium With Near-Infrared Diffuse Interstellar Bands

We map the distribution and properties of the Milky Way's interstellar medium as traced by diffuse interstellar bands (DIBs) detected in near-infrared stellar spectra from the SDSS-III/APOGEE survey. Focusing exclusively on the strongest DIB in the H band, at lambda similar to 1.527 mu m, we present a projected map of the DIB absorption field in the Galactic plane, using a set of about 60,000 sightlines that reach up to 15 kpc from the Sun and probe up to 30 mag of visual extinction. The strength of this DIB is linearly correlated with dust reddening over three orders of magnitude in both DIB equivalent width (Wpm) and extinction, with a power law index of 1.01 +/- 0.01, a mean relationship of W-DIB/A(v) = 0.1 angstrom mag(-1) and a dispersion of similar to 0.05 angstrom mag(-1) at extinctions characteristic of the Galactic midplane. These properties establish this DIB as a powerful, independent probe of dust extinction over a wide range of Av values. The subset of about 14,000 robustly detected DIB features have a W-DIB distribution that follows an exponential trend. We empirically determine the intrinsic rest wavelength of this transition to be lambda(0) = 15 272.42 angstrom and use it to calculate absolute radial velocities of the carrier, which display the kinematical signature of the rotating Galactic disk. We probe the DIB carrier distribution in three dimensions and show that it can be characterized by an exponential disk model with a scale height of about 100 pc and a scale length of about 5 kpc. Finally, we show that the DIB distribution also traces large-scale Galactic structures, including the Galactic long bar and the warp of the outer disk.NSF Astronomy & Astrophysics Postdoctoral Fellowship AST-1203017NSF AST-1109665Alfred P. Sloan FoundationNational Science FoundationU.S. Department of Energy Office of ScienceUniversity of ArizonaBrazilian Participation GroupBrookhaven National LaboratoryUniversity of CambridgeCarnegie Mellon UniversityUniversity of FloridaFrench Participation GroupGerman Participation GroupHarvard UniversityInstituto de Astrofisica de CanariasMichigan State/Notre Dame/JINA Participation GroupJohns Hopkins UniversityLawrence Berkeley National LaboratoryMax Planck Institute for AstrophysicsMax Planck Institute for Extraterrestrial PhysicsNew Mexico State UniversityNew York UniversityOhio State UniversityPennsylvania State UniversityUniversity of PortsmouthPrinceton UniversitySpanish Participation GroupUniversity of TokyoUniversity of UtahVanderbilt UniversityUniversity of VirginiaUniversity of WashingtonYale UniversitySpanish Ministry of Economy and Competitiveness AYA-2011-27754McDonald Observator

Deferiprone modulates in vitro responses by peripheral blood T cells from control and relapsing remitting multiple sclerosis subjects

T cells are important mediators of autoimmune inflammation in relapsing remitting multiple sclerosis (RRMS). Previous studies found that deferiprone, an iron chelator, suppressed disease activity in a mouse model of multiple sclerosis, and inhibition of T cell proliferation was implicated as a putative mechanism. The objective of the present study was to examine the effects of deferiprone on suppressing in vitro responses of T cells from control and RRMS subjects. Peripheral blood T cells were co-stimulated with anti-CD3 + anti-CD28 and cultured with or without interleukin 2 (IL-2). Proliferating CD4+ T cells from control and RRMS subjects, cultured with or without IL-2, decreased in response to 75 μM deferiprone, although the extent of decreased proliferation of CD4+ T cells from RRMS subjects was less than for control subjects. Proliferating CD8+ T cells from control subjects, cultured with or without IL-2, also decreased in response to 75 μM deferiprone, and this decrease was seen in proliferating CD8+ T cells from RRMS cultured with IL-2. CD4+CD25+ and CD8+CD25+ cells from control subjects, cultured with or without IL-2, declined in 75 M deferiprone, but the decrease was smaller than for the CD4+ and CD8+ proliferative responses. CD4+CD25+ and CD8+CD25+ cells from RRMS subjects showed more variability than for control subjects, but CD4+CD25+ cultured with IL-2 and CD8+CD25+ cells cultured without IL-2 significantly declined in 75 μM deferiprone. CD4+FoxP3+ and CD4+CD25+FoxP3+ cells tended to remain constant or increase. In summary, deferiprone induced declines in proliferative responses at a dosage that is within peak serum pharmacological concentrations

the SDSS-III APOGEE Spectral Line List for H-Band Spectroscopy

We present the H-band spectral line lists adopted by the Apache Point Observatory Galactic Evolution Experiment (APOGEE). The APOGEE line lists comprise astrophysical, theoretical, and laboratory sources from the literature, as well as newly evaluated astrophysical oscillator strengths and damping parameters. We discuss the construction of the APOGEE line list, which is one of the critical inputs for the APOGEE Stellar Parameters and Chemical Abundances Pipeline, and present three different versions that have been used at various stages of the project. The methodology for the newly calculated astrophysical line lists is reviewed. The largest of these three line lists contains 134,457 molecular and atomic transitions. In addition to the format adopted to store the data, the line lists are available in MOOG, Synspec, and Turbospectrum formats. The limitations of the line lists along with guidance for its use on different spectral types are discussed. We also present a list of H-band spectral features that are either poorly represented or completely missing in our line list. This list is based on the average of a large number of spectral fit residuals for APOGEE observations spanning a wide range of stellar parameters.Alfred P. Sloan FoundationNational Science FoundationU.S. Department of Energy Office of ScienceJanos Bolyai Research Scholarship of the Hungarian Academy of SciencesSpanish Ministry of Economy and Competitiveness AYA-2011-27754, AYA-2014-58082-PRSF 14-50-00043McDonald Observator

Examining the Influence of Ethnic/Racial Socialization on Aggressive Behaviors Among Juvenile Offenders

Risk assessment instruments are commonly used within the juvenile justice system to estimate a juvenile's likelihood of reoffending or engaging in aggressive or violent behavior. Although such instruments assess a broad range of factors, the influence of culture is often excluded. The current study examines the unique effect of ethnic/racial socialization on recent aggressive behaviors above and beyond three well-established risk and protective factors: delinquency history, moral disengagement, and social support. Participants were 95 juveniles who were either on probation or in detention centers in three Midwestern counties and who completed structured surveys related to personal experiences within and outside of the juvenile justice system. The findings provided partial support for our hypotheses: Consistent with previous findings, delinquency history and moral disengagement were significant predictors of recent aggressive behavior. Furthermore, when ethnic/racial socialization was added to the model, promotion of mistrust provided additional predictive validity for aggressive behavior above and beyond the other factors assessed. Based on these findings, the inclusion of education on culture may prove to be an important supplement to established intervention tools for juvenile offenders

Sustainable solvent selection for the manufacture of methylammonium lead triiodide (MAPbI3) perovskite solar cells

Perovskite solar cells have emerged as a promising and highly efficient solar technology. Despite efficiencies continuing to climb, the prospect of industrial manufacture is hampered by concerns regarding the safety and sustainability of the solvents used in lab scale manufacture. In this paper, we aim to present a methodology for green solvent selection informed by EHS considerations from the Chem-21 guide for succesful methylammonium lead triiodide (MAPbI3) precursor dissolution. Through the use of this methodology we present a N,N-dimethylformamide (DMF)-free alternative solvent system for deposition of MAPbI3 precursors (MAI and PbI2) consisting of dimethylsulfoxide (DMSO), dimethylpropyleneurea (DMPU), 2-methyltetrahydrofuran (2-MeTHF) and ethanol (EtOH). We have investigated 3 candidate solutions with slightly different compositions of these four solvents, all of which produce dense, uniform and pinhole-free perovskite films via spin coating. All three candidate solutions (A-C) match the average device efficiencies of the DMF/DMSO contol devices (12.4%) with Candidate A, which consists of 40% DMSO, 30 % DMPU, 20% 2-MeTHF and 10% EtOH (vol%), producing a champion PCE of 16.1% compared to 16.2% for DMF/DMSO (80/20 vol%). Perovskite films cast from the three candidate solutions show improved crystallinity, higher flourescence emission, and improved crystal size uniformity than those cast from DMF/DMSO. This work aims to: highlight the key solvent parameters which determine effective MAPbI3 precursor dissolution; provide a set of criteria for appropriate alternative solvent selection; and demonstrate the application of green chemistry principles to solvent selection for perovskite photovoltaic manufacturing

Supporting‐electrolyte‐free electrochemical methoxymethylation of alcohols using a 3D‐printed electrosynthesis continuous flow cell system

We describe the development of a novel low‐cost small‐footprint 3D‐printed electrosynthesis continuous flow cell system that was designed and adapted to fit a commercially available Electrasyn 2.0. The utility and effectiveness of the combined flow/electrochemistry system over the batch process was demonstrated in the development of an improved and supporting‐electrolyte‐free version of our anodic methoxymethylation of alcohols