We present extensive early photometric (ultraviolet through near-infrared) and spectroscopic (optical and near-infrared) data on supernova (SN) 2008D as well as X-ray data analysis on the associated Swift X-ray transient (XRT) 080109. Our data span a time range of 5 hours before the detection of the X-ray transient to 150 days after its detection, and detailed analysis allowed us to derive constraints on the nature of the SN and its progenitor; throughout we draw comparisons with results presented in the literature and find several key aspects that differ. We show that the X-ray spectrum of XRT 080109 can be fit equally well by an absorbed power law or a superposition of about equal parts of both power law and blackbody. Our data first established that SN 2008D is a spectroscopically normal SN Ib (i.e., showing conspicuous He lines), and show that SN 2008D had a relatively long rise time of 18 days and a modest optical peak luminosity. The early-time light curves of the SN are dominated by a cooling stellar envelope (for ∆t ≈ 0.1 − 4 day, most pronounced in the blue bands) followed by 56 Ni decay. We construct a reliable measurement of the bolometric output for this stripped-envelope SN, and, combined with estimates of E K and M ej from the literature, estimate the stellar radius R ⋆ of its probable Wolf-Rayet progenitor. According to the model of Waxman et al. and of Chevalier & Fransson, we derive R W07 ⋆ = 1.2 ± 0.7 R ⊙ and R CF08 ⋆ = 12 ± 7 R ⊙ , respectively; the latter being more in line with typical WN stars. Spectra obtained at 3 and 4 months after maximum light show double-peaked oxygen lines that we associate with departures from spherical symmetry, as has been suggested for the inner ejecta of a number of SN Ib cores.
Iron (Fe) is an essential mineral nutrient which severely affects the growth, yield and nutritional quality of plants if not supplied in sufficient quantities. We here report that a short C-terminal amino acid sequence consensus motif (IRON MAN; IMA) conserved across numerous, highly diverse peptides in angiosperms, is essential for Fe uptake in plants.
Phosphate (P i ) deficiency impairs plant growth and productivity in many agricultural ecosystems, causing severe reductions in crop yield. To uncover novel aspects in acclimation to P i starvation, we investigated the correlation between P i deficiency-induced changes in transcriptome and proteome profiles in Arabidopsis roots. Using exhaustive tandem mass spectrometry-based shotgun proteomics and whole-genome RNA sequencing to generate a nearly complete catalog of expressed mRNAs and proteins, we reliably identified 13,298 proteins and 24,591 transcripts, subsets of 356 proteins and 3106 mRNAs were differentially expressed during P i deficiency. Most dramatic changes were noticed for genes involved in P i acquisition and in processes that either liberate P i or bypass P i /ATP-consuming metabolic steps, for example during membrane lipid remodeling and glycolytic carbon flux. The concordance between the abundance of mRNA and its encoded protein was generally high for highly up-regulated genes, but the analysis also revealed numerous discordant changes in mRNA/protein pairs, indicative of divergent regulation of transcription and post-transcriptional processes. In particular, a decreased abundance of proteins upon P i deficiency was not closely correlated with changes in the corresponding mRNAs. In several cases, up-regulation of gene activity was observed solely at the protein level, adding novel aspects to key processes in the adaptation to P i deficiency. We conclude that integrated measurement and interpretation of changes in protein and transcript abundance are mandatory for generating a complete inventory of the compo-
Due to its ease to donate or accept electrons, iron (Fe) plays a crucial role in respiration and metabolism, including tetrapyrrole synthesis, in virtually all organisms. In plants, Fe is a component of the photosystems and thus essential for photosynthesis. Fe deficiency compromises chlorophyll (Chl) synthesis, leading to interveinal chlorosis in developing leaves and decreased photosynthetic activity. To gain insights into the responses of photosynthetically active cells to Fe deficiency, we conducted transcriptional profiling experiments on leaves from Fe-sufficient and Fe-deficient plants using the RNA-seq technology. As anticipated, genes associated with photosynthesis and tetrapyrrole metabolism were dramatically down-regulated by Fe deficiency. A sophisticated response comprising the down-regulation of HEMA1 and NYC1, which catalyze the first committed step in tetrapyrrole biosynthesis and the conversion of Chl b to Chl a at the commencement of Chl breakdown, respectively, and the up-regulation of CGLD27, which is conserved in plastid-containing organisms and putatively involved in xanthophyll biosynthesis, indicates a carefully orchestrated balance of potentially toxic tetrapyrrole intermediates and functional end products to avoid photo-oxidative damage. Comparing the responses to Fe deficiency in leaves to that in roots confirmed subgroup 1b bHLH transcription factors and POPEYE/BRUTUS as important regulators of Fe homeostasis in both leaf and root cells, and indicated six novel players with putative roles in Fe homeostasis that were highly expressed in leaves and roots and greatly induced by Fe deficiency. The data further revealed down-regulation of organ-specific subsets of genes encoding ribosomal proteins, which may be indicative of a change in ribosomal composition that could bias translation. It is concluded that Fe deficiency causes a massive reorganization of plastid activity, which is adjusting leaf function to the availability of Fe.
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