A wheat/rye polymorphism affects seminal root length and yield across different irrigation regimes

The introgression of a small segment of wheat (Triticumaestivum L.) chromosome arm 1BS in the distal region of rye (Secalecereale L.) 1RS.1BL arm translocation in wheat (henceforth 1RSRW) was previously associated with reduced grain yield, carbon isotope discrimination and stomatal conductance, suggesting reduced access to soil moisture. Here we show that lines with the normal 1RS arm have longer roots than lines with the 1RSRW arm in both field and hydroponic experiments. In the 1RSRW lines, differences in seminal root length were associated with a developmentally regulated arrest of the root apical meristem (RAM). Approximately 10 days after germination, the seminal roots of the 1RSRW plants showed a gradual reduction in elongation rate, and stopped growing a week later. Seventeen days after germination, the roots of the 1RSRW plants showed altered gradients of reactive oxygen species and emergence of lateral roots close to the RAM, suggesting changes in the root meristem. The 1RSRW lines also showed reduced biomass (estimated by Normalized Differences Vegetation Index) and grain yield relative to the 1RS lines, with larger differences under reduced or excessive irrigation than under normal irrigation. These results suggest that this genetic variation could be useful to modulate root architecture.Fil: Howell, Tyson. University of California; Estados UnidosFil: Moriconi, Jorge Ignacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); ArgentinaFil: Zhao, Xueqiang. Chinese Academy of Sciences; República de ChinaFil: Joshua Hegarty. University of California; Estados UnidosFil: Fahima, Tzion. University of Haifa; IsraelFil: Santa Maria, Guillermo Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); Argentin

Galaxy-Galaxy Lensing by Non-Spherical Haloes I:Theoretical Considerations

We use Monte Carlo simulations to investigate the theory of galaxy-galaxy lensing by non-spherical dark matter haloes. The simulations include a careful accounting of the effects of multiple deflections. In a typical data set where the mean tangential shear of sources with redshifts zs ~ 0.6 is measured with respect to the observed symmetry axes of foreground galaxies with redshifts zl ~ 0.3, the signature of anisotropic galaxy-galaxy lensing differs substantially from the expectation that one would have in the absence of multiple deflections. The observed ratio of the mean tangential shears, g+/g-, is strongly suppressed compared to the function that one would measure if the intrinsic symmetry axes of the foreground galaxies were known. Depending upon the characteristic masses of the lenses, the observed ratio of the mean tangential shears may be consistent with an isotropic signal (despite the fact that the lenses are non-spherical), or it may even be reversed from the expected signal (i.e., the mean tangential shear for sources close to the observed minor axes of the lenses may exceed the mean tangential shear for sources close to the observed major axes of the lenses). These effects are caused primarily by the fact that the lens galaxies have, themselves, been lensed and therefore the observed symmetry axes of the lenses differ from their intrinsic symmetry axes. The effects of lensing of the foreground galaxies on the observed function g+/g- cannot be eliminated by the rejection of foreground galaxies with small image ellipticities, nor by focusing the analysis on sources that are located very close to the observed symmetry axes of the foreground galaxies. We conclude that any attempt to use a measurement of g+/g- to constrain the shapes of dark matter galaxy haloes must include Monte Carlo simulations that take multiple deflections properly into account.Comment: 15 pages, 17 figures, submitted to MNRAS, full manuscript with high-resolution version of Fig. 4 can be found at http://firedrake.bu.edu/preprints/preprints.htm

Characterizing and Propagating Modeling Uncertainties in Photometrically-Derived Redshift Distributions

The uncertainty in the redshift distributions of galaxies has a significant potential impact on the cosmological parameter values inferred from multi-band imaging surveys. The accuracy of the photometric redshifts measured in these surveys depends not only on the quality of the flux data, but also on a number of modeling assumptions that enter into both the training set and SED fitting methods of photometric redshift estimation. In this work we focus on the latter, considering two types of modeling uncertainties: uncertainties in the SED template set and uncertainties in the magnitude and type priors used in a Bayesian photometric redshift estimation method. We find that SED template selection effects dominate over magnitude prior errors. We introduce a method for parameterizing the resulting ignorance of the redshift distributions, and for propagating these uncertainties to uncertainties in cosmological parameters.Comment: 13 pages, 12 figures, version published in Ap

Structural rearrangements in wheat (1BS)–rye (1RS) recombinant chromosomes affect gene dosage and root length

Good understanding of the genes controlling root development is required to engineer root systems better adapted to different soil types. In wheat (Triticum aestivum L.), the 1RS.1BL wheat–rye (Secale cereale L.) translocation has been associated with improved drought tolerance and a large root system. However, an isogenic line carrying an interstitial segment from wheat chromosome arm 1BS in the distal region of the 1RS arm (1RSRW) showed reduced grain yield and shorter roots both in the field and in hydroponic cultures relative to isogenic lines with the complete 1RS arm. In this study, we used exome capture to characterize 1RSRW and its parental lines T-9 and 1B+40. We show that 1RSRW has a 7.0 Mb duplicated 1RS region and a 4.8 Mb 1BS insertion colinear with the 1RS duplication, resulting in triplicated genes. Lines homozygous for 1RSRW have short seminal roots, while lines heterozygous for this chromosome have roots of intermediate length. By contrast, near-isogenic lines carrying only the 1BS distal region or the 1RS-1BS duplication have long seminal roots similar to 1RS, suggesting a limited effect of the 1BS genes. These results suggest that the dosage of duplicated 1RS genes is critical for seminal root length. An induced deletion encompassing 38 orthologous wheat and rye duplicated genes restored root length and confirmed the importance of gene dosage in the short-root phenotype. We explored the expression profiles and functional annotation of these genes and discuss their potential as candidate genes for the regulation of seminal root length in wheat.Fil: Gabay, Gilad. University of California at Davis; Estados UnidosFil: Zhang, Junli. University of California at Davis; Estados UnidosFil: Burguener, German Federico. University of California at Davis; Estados UnidosFil: Howell, Tyson. University of California at Davis; Estados UnidosFil: Wang, Hanchao. University Of Haifa; IsraelFil: Fahima, Tzion. University of California at Davis; Estados UnidosFil: Lukaszewski, Adam. University of California at Davis; Estados UnidosFil: Moriconi, Jorge Ignacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); ArgentinaFil: Santa Maria, Guillermo Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); ArgentinaFil: Dubcovsky, Jorge. University of California at Davis; Estados Unido

Constraining dark matter halo properties using lensed SNLS supernovae

This paper exploits the gravitational magnification of SNe Ia to measure properties of dark matter haloes. The magnification of individual SNe Ia can be computed using observed properties of foreground galaxies and dark matter halo models. We model the dark matter haloes of the galaxies as truncated singular isothermal spheres with velocity dispersion and truncation radius obeying luminosity dependent scaling laws. A homogeneously selected sample of 175 SNe Ia from the first 3-years of the Supernova Legacy Survey (SNLS) in the redshift range 0.2 < z < 1 is used to constrain models of the dark matter haloes associated with foreground galaxies. The best-fitting velocity dispersion scaling law agrees well with galaxy-galaxy lensing measurements. We further find that the normalisation of the velocity dispersion of passive and star forming galaxies are consistent with empirical Faber-Jackson and Tully-Fisher relations, respectively. If we make no assumption on the normalisation of these relations, we find that the data prefer gravitational lensing at the 92 per cent confidence level. Using recent models of dust extinction we deduce that the impact of this effect on our results is very small. We also investigate the brightness scatter of SNe Ia due to gravitational lensing. The gravitational lensing scatter is approximately proportional to the SN Ia redshift. We find the constant of proportionality to be B = 0.055 +0.039 -0.041 mag (B < 0.12 mag at the 95 per cent confidence level). If this model is correct, the contribution from lensing to the intrinsic brightness scatter of SNe Ia is small for the SNLS sample.Comment: 11 pages, 7 figures, accepted for publication in MNRA

LIMD1 Is Induced by and Required for LMP1 Signaling, and Protects EBV-transformed Cells From DNA Damage-Induced Cell Death

LIMD1 (LIM domain-containing protein 1) is considered as a tumor suppressor, being deregulated in many cancers to include hematological malignancies; however, very little is known about the underlying mechanisms of its deregulation and its roles in carcinogenesis. Epstein-Barr Virus (EBV) is associated with a panel of malignancies of lymphocytic and epithelial origin. Using high throughput expression profiling, we have previously identified LIMD1 as a common marker associated with the oncogenic transcription factor IRF4 in EBV-related lymphomas and other hematological malignancies. In this study, we have identified potential conserved IRF4- and NFκB-binding motifs in the LIMD1 gene promoter, and both are demonstrated functional by promoter-reporter assays. We further show that LIMD1 is partially upregulated by EBV latent membrane protein 1 (LMP1) via IRF4 and NFκB in EBV latency. As to its role in the setting of EBV latent infection, we show that LIMD1 interacts with TRAF6, a crucial mediator of LMP1 signal transduction. Importantly, LIMD1 depletion impairs LMP1 signaling and functions, potentiates ionomycin-induced DNA damage and apoptosis, and inhibits p62-mediated selective autophagy. Taken together, these results show that LIMD1 is upregulated in EBV latency and plays an oncogenic role rather than that of a tumor suppressor. Our findings have identified LIMD1 as a novel player in EBV latency and oncogenesis, and open a novel research avenue, in which LIMD1 and p62 play crucial roles in linking DNA damage response (DDR), apoptosis, and autophagy and their potential interplay during viral oncogenesi

Functional correlates of clinical phenotype and severity in recurrent SCN2A variants

In SCN2A-related disorders, there is an urgent demand to establish efficient methods for determining the gain- (GoF) or loss-of-function (LoF) character of variants, to identify suitable candidates for precision therapies. Here we classify clinical phenotypes of 179 individuals with 38 recurrent SCN2A variants as early-infantile or later-onset epilepsy, or intellectual disability/autism spectrum disorder (ID/ASD) and assess the functional impact of 13 variants using dynamic action potential clamp (DAPC) and voltage clamp. Results show that 36/38 variants are associated with only one phenotypic group (30 early-infantile, 5 later-onset, 1 ID/ASD). Unexpectedly, we revealed major differences in outcome severity between individuals with the same variant for 40% of early-infantile variants studied. DAPC was superior to voltage clamp in predicting the impact of mutations on neuronal excitability and confirmed GoF produces early-infantile phenotypes and LoF later-onset phenotypes. For one early-infantile variant, the co-expression of the alpha(1) and beta(2) subunits of the Na(v)1.2 channel was needed to unveil functional impact, confirming the prediction of 3D molecular modeling. Neither DAPC nor voltage clamp reliably predicted phenotypic severity of early-infantile variants. Genotype, phenotypic group and DAPC are accurate predictors of the biophysical impact of SCN2A variants, but other approaches are needed to predict severity. A comprehensive biophysical analysis of disease-associated mutations in the voltage-gated sodium channel gene, SCN2A, suggests that dynamic action potential clamp may be a better predictor than voltage clamp of how these mutations alter neuronal excitability, though other approaches are needed to predict severity

Dosage differences in 12-OXOPHYTODIENOATE REDUCTASE genes modulate wheat root growth

Wheat, an essential crop for global food security, is well adapted to a wide variety of soils. However, the gene networks shaping different root architectures remain poorly understood. We report here that dosage differences in a cluster of monocot-specific 12-OXOPHYTODIENOATE REDUCTASE genes from subfamily III (OPRIII) modulate key differences in wheat root architecture, which are associated with grain yield under water-limited conditions. Wheat plants with loss-of-function mutations in OPRIII show longer seminal roots, whereas increased OPRIII dosage or transgenic over-expression result in reduced seminal root growth, precocious development of lateral roots and increased jasmonic acid (JA and JA-Ile). Pharmacological inhibition of JA-biosynthesis abolishes root length differences, consistent with a JA-mediated mechanism. Transcriptome analyses of transgenic and wild-type lines show significant enriched JA-biosynthetic and reactive oxygen species (ROS) pathways, which parallel changes in ROS distribution. OPRIII genes provide a useful entry point to engineer root architecture in wheat and other cereals.Fil: Gabay, Gilad. University of California at Davis; Estados UnidosFil: Wang, Hanchao. University of California at Davis; Estados Unidos. University Of Haifa; IsraelFil: Zhang, Junli. University of California at Davis; Estados UnidosFil: Moriconi, Jorge Ignacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; ArgentinaFil: Burguener, Germán Federico. University of California at Davis; Estados UnidosFil: Gualano, Leonardo David. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; ArgentinaFil: Howell, Tyson. University of California at Davis; Estados UnidosFil: Lukaszewski, Adam. University of California; Estados UnidosFil: Staskawicz, Brian. University of California; Estados UnidosFil: Cho, Myeong-Je. University of California; Estados UnidosFil: Tanaka, Jaclyn. University of California; Estados UnidosFil: Fahima, Tzion. University Of Haifa; IsraelFil: Ke, Haiyan. University of California; Estados UnidosFil: Dehesh, Katayoon. University of California; Estados UnidosFil: Zhang, Guo-Liang. Fudan University; ChinaFil: Gou, Jin Ying. Beijing Key Laboratory Of Crop Genetic Improvement; China. Fudan University; ChinaFil: Hamberg, Mats. Karolinska Huddinge Hospital. Karolinska Institutet; SueciaFil: Santa Maria, Guillermo Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; ArgentinaFil: Dubcovsky, Jorge. University of California at Davis; Estados Unidos. Howard Hughes Medical Institute; Estados Unido

Dosage differences in 12-OXOPHYTODIENOATE REDUCTASE genes modulate wheat root growth

Wheat, an essential crop for global food security, is well adapted to a wide variety of soils. However, the gene networks shaping different root architectures remain poorly understood. We report here that dosage differences in a cluster of monocot-specific 12-OXOPHYTODIENOATE REDUCTASE genes from subfamily III (OPRIII) modulate key differences in wheat root architecture, which are associated with grain yield under water-limited conditions. Wheat plants with loss-of-function mutations in OPRIII show longer seminal roots, whereas increased OPRIII dosage or transgenic over-expression result in reduced seminal root growth, precocious development of lateral roots and increased jasmonic acid (JA and JA-Ile). Pharmacological inhibition of JA-biosynthesis abolishes root length differences, consistent with a JA-mediated mechanism. Transcriptome analyses of transgenic and wild-type lines show significant enriched JA-biosynthetic and reactive oxygen species (ROS) pathways, which parallel changes in ROS distribution. OPRIII genes provide a useful entry point to engineer root architecture in wheat and other cereals.Fil: Gabay, Gilad. University of California at Davis; Estados UnidosFil: Wang, Hanchao. University of California at Davis; Estados Unidos. University Of Haifa; IsraelFil: Zhang, Junli. University of California at Davis; Estados UnidosFil: Moriconi, Jorge Ignacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; ArgentinaFil: Burguener, Germán Federico. University of California at Davis; Estados UnidosFil: Gualano, Leonardo David. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; ArgentinaFil: Howell, Tyson. University of California at Davis; Estados UnidosFil: Lukaszewski, Adam. University of California; Estados UnidosFil: Staskawicz, Brian. University of California; Estados UnidosFil: Cho, Myeong-Je. University of California; Estados UnidosFil: Tanaka, Jaclyn. University of California; Estados UnidosFil: Fahima, Tzion. University Of Haifa; IsraelFil: Ke, Haiyan. University of California; Estados UnidosFil: Dehesh, Katayoon. University of California; Estados UnidosFil: Zhang, Guo-Liang. Fudan University; ChinaFil: Gou, Jin Ying. Beijing Key Laboratory Of Crop Genetic Improvement; China. Fudan University; ChinaFil: Hamberg, Mats. Karolinska Huddinge Hospital. Karolinska Institutet; SueciaFil: Santa Maria, Guillermo Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; ArgentinaFil: Dubcovsky, Jorge. University of California at Davis; Estados Unidos. Howard Hughes Medical Institute; Estados Unido

Costs and benefits of thermal acclimation for codling moth, Cydia pomonella (Lepidoptera: Tortricidae): implications for pest control and the sterile insect release programme

Sterile insect release (SIR) is used to suppress insect pest populations in agro-ecosystems, but its success hinges on the performance of the released insects and prevailing environmental conditions. For example, low temperatures dramatically reduce SIR efficacy in cooler conditions. Here, we report on the costs and benefits of thermal acclimation for laboratory and field responses of codling moth, Cydia pomonella. Using a component of field fitness, we demonstrate that low temperature acclimated laboratory-reared moths are recaptured significantly more (∼2–4×) under cooler conditions in the wild relative to warm-acclimated or control moths. However, improvements in low temperature performance in cold-acclimated moths came at a cost to performance under warmer conditions. At high ambient temperatures, warm-acclimation improved field performance relative to control or cold-acclimated moths. Laboratory assessments of thermal activity and their limits matched the field results, indicating that these laboratory assays may be transferable to field performance. This study demonstrates clear costs and benefits of thermal acclimation on laboratory and field performance and the potential utility of thermal pretreatments for offsetting negative efficacy in SIR programmes under adverse thermal conditions. Consequently, the present work shows that evolutionary principles of phenotypic plasticity can be used to improve field performance and thus possibly enhance pest control programmes seeking increased efficacy