Gene expression data from isolated cortical cells after roots were treated with 140 mM NaCl for 1 hour Data quality was examined using the signal distribution of Affymetrix built-in controls (Spike-in and hybridization controls) using Expression Console software (Affymetrix) and AffyQCReport. GCRMA in R/Bioconductor was used for data normalization.

Gene expression data from isolated endodermal cells after roots were treated with 140 mM NaCl for 3 hour Data quality was examined using the signal distribution of Affymetrix built-in controls (Spike-in and hybridization controls) using Expression Console software (Affymetrix) and AffyQCReport. GCRMA in R/Bioconductor was used for data normalization.

Gene expression data from isolated stele cells after roots were treated with 140 mM NaCl for 20 hour Data quality was examined using the signal distribution of Affymetrix built-in controls (Spike-in and hybridization controls) using Expression Console software (Affymetrix) and AffyQCReport. GCRMA in R/Bioconductor was used for data normalization.

Plant environmental responses involve dynamic changes in growth and signaling, yet little is understood as to how progress through these events is regulated. Here, we explored the phenotypic and transcriptional events involved in the acclimation of the Arabidopsis thaliana seedling root to a rapid change in salinity. Using live-imaging analysis, we show that growth is dynamically regulated with a period of quiescence followed by recovery then homeostasis. Through the use of a new high-resolution spatio-temporal transcriptional map, we identify the key hormone signaling pathways that regulate specific transcriptional programs, predict their spatial domain of action, and link the activity of these pathways to the regulation of specific phases of growth. We use tissue-specific approaches to suppress the abscisic acid (ABA) signaling pathway and demonstrate that ABA likely acts in select tissue layers to regulate spatially localized transcriptional programs and promote growth recovery. Finally, we show that salt also regulates many tissue-specific and time point-specific transcriptional responses that are expected to modify water transport, Casparian strip formation, and protein translation. Together, our data reveal a sophisticated assortment of regulatory programs acting together to coordinate spatially patterned biological changes involved in the immediate and long-term response to a stressful shift in environment.

The development of the single cell layer skin or hypodermis of Caenorhabditis elegans is an excellent model for understanding cell fate specification and differentiation. Early in C. elegans embryogenesis, six rows of hypodermal cells adopt dorsal, lateral or ventral fates that go on to display distinct behaviors during larval life. Several transcription factors are known that function in specifying these major hypodermal cell fates, but our knowledge of the specification of these cell types is sparse, particularly in the case of the ventral hypodermal cells, which become Vulval Precursor Cells and form the vulval opening in response to extracellular signals. Previously, the gene pvl-4 was identified in a screen for mutants with defects in vulval development. We found by whole genome sequencing that pvl-4 is the Paired-box gene pax-3, which encodes the sole PAX-3 transcription factor homolog in C. elegans. pax-3 mutants show embryonic and larval lethality, and body morphology abnormalities indicative of hypodermal cell defects. We report that pax-3 is expressed in ventral P cells and their descendants during embryogenesis and early larval stages, and that in pax-3 reduction-of-function animals the ventral P cells undergo a cell fate transformation and express several markers of the lateral seam cell fate. Furthermore, forced expression of pax-3 in the lateral hypodermal cells causes them to lose expression of seam cell markers. We propose that pax-3 functions in the ventral hypodermal cells to prevent these cells from adopting the lateral seam cell fate. pax-3 represents the first gene required for specification solely of the ventral hypodermal fate in C elegans providing insights into cell type diversification. (C) 2016 Elsevier Inc. All rights reserved.

In contrast to ecological speciation, where reproductive isolation evolves as a consequence of divergent natural selection, speciation by parallel natural selection has been less thoroughly studied. To test whether parallel evolution drives speciation, we leveraged the repeated evolution of benthic and limnetic ecotypes of threespine stickleback fish and estimated fitness for pure crosses and within-ecotype hybrids in semi-natural ponds and in laboratory aquaria. In ponds, we detected hybrid breakdown in both ecotypes but this was counterbalanced by heterosis and the strength of post-zygotic isolation was nil. In aquaria, we detected heterosis in limnetic crosses and breakdown in benthic crosses, which is suggestive of process- and ecotype-specific environment-dependence. In ponds, heterosis and breakdown were three times greater in limnetic crosses than in benthic crosses, contrasting the prediction that the fitness consequences of hybridization should be greater in crosses among more derived ecotypes. Consistent with a primary role for stochastic processes, patterns differed among crosses between populations from different lakes. Yet, the observation of qualitatively similar patterns of heterosis and hybrid breakdown for both ecotypes when averaging the lake pairs indicates that the outcome of hybridization is repeatable in a general sense.

When divergent populations interbreed, their alleles are brought together in hybrids. In the initial F1 cross, most divergent loci are heterozygous. Therefore, F1 fitness can be influenced by dominance effects that could not have been selected to function well together. We present a systematic study of these F1 dominance effects by introducing variable phenotypic dominance into Fisher's geometric model. We show that dominance often reduces hybrid fitness, which can generate optimal outbreeding followed by a steady decline in F1 fitness, as is often observed. We also show that "lucky" beneficial effects sometimes arise by chance, which might be important when hybrids can access novel environments. We then show that dominance can lead to violations of Haldane's Rule (reduced fitness of the heterogametic F1) but strengthens Darwin's Corollary (F1 fitness differences between cross directions). Taken together, results show that the effects of dominance on hybrid fitness can be surprisingly difficult to isolate, because they often resemble the effects of uniparental inheritance or expression. Nevertheless, we identify a pattern of environment-dependent heterosis that only dominance can explain, and for which there is some suggestive evidence. Our results also show how existing data set upper bounds on the size of dominance effects. These bounds could explain why additive models often provide good predictions for later-generation recombinant hybrids, even when dominance qualitatively changes outcomes for the F1.

We present new constraints on the density profiles of dark matter (DM) halos in seven nearby dwarf galaxies from measurements of their integrated stellar light and gas kinematics. The gas kinematics of low-mass galaxies frequently suggest that they contain constant density DM cores, while N-body simulations instead predict a cuspy profile. We present a data set of high-resolution integral-field spectroscopy on seven galaxies and measure the stellar and gas kinematics simultaneously. Using Jeans modeling on our full sample, we examine whether gas kinematics in general produce shallower density profiles than are derived from the stars. Although two of the seven galaxies show some localized differences in their rotation curves between the two tracers, estimates of the central logarithmic slope of the DM density profile, gamma, are generally robust. The mean and standard deviation of the logarithmic slope for the population are gamma = 0.67 +/- 0.10 when measured in the stars and gamma = 0.58 +/- 0.24 when measured in the gas. We also find that the halos are not under-concentrated at the radii of half their maximum velocities. Finally, we search for correlations of the DM density profile with stellar velocity anisotropy and other baryonic properties. Two popular mechanisms to explain cored DM halos are an exotic DM component or feedback models that strongly couple the energy of supernovae into repeatedly driving out gas and dynamically heating the DM halos. While such models do not yet have falsifiable predictions that we can measure, we investigate correlations that may eventually be used to test models. We do not find a secondary parameter that strongly correlates with the central DM density slope, but we do find some weak correlations. The central DM density slope weakly correlates with the abundance of a elements in the stellar population, anti-correlates with Hi fraction, and anti-correlates with vertical orbital anisotropy. We expect, if anything, the opposite of these three trends for feedback models. Determining the importance of these correlations will require further model developments and larger observational samples.

Previous measurements of water in deformed quartzites using conventional Fourier transform infrared spectroscopy (FTIR) instruments have shown that water contents of larger grains vary from one grain to another. However, the non-equilibrium variations in water content between neighboring grains and within quartz grains cannot be interrogated further without greater measurement resolution, nor can water contents be measured in finely recrystallized grains without including absorption bands due to fluid inclusions, films, and secondary minerals at grain boundaries.