Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis

The dynamic nature of gene regulatory networks allows cells to rapidly respond to environmental change. However, the underlying temporal connections are missed, even in kinetic studies, as transcription factor (TF) binding within at least one time point is required to identify primary targets. The TF-regulated but unbound genes are dismissed as secondary targets. Instead, we report that these genes comprise transient TF-target interactions most relevant to rapid signal transduction. We temporally perturbed a master TF (Basic Leucine Zipper 1, bZIP1) and the nitrogen (N) signal it transduces and integrated TF regulation and binding data from the same cell samples. Our enabling approach could identify primary TF targets based solely on gene regulation, in the absence of TF binding. We uncovered three classes of primary TF targets: (i) poised (TF-bound but not TF-regulated), (ii) stable (TF-bound and TF-regulated), and (iii) transient (TF-regulated but not TF-bound), the largest class. Unexpectedly, the transient bZIP1 targets are uniquely relevant to rapid N signaling in planta, enriched in dynamic N-responsive genes, and regulated by TF and N signal interactions. These transient targets include early N responders nitrate transporter 2.1 and NIN-like protein 3, bound by bZIP1 at 1-5 min, but not at later time points following TF perturbation. Moreover, promoters of these transient targets are uniquely enriched with cis-regulatory motifs coinherited with bZIP1 binding sites, suggesting a recruitment role for bZIP1. This transient mode of TF action supports a classic, but forgotten, "hit-and-run" transcription model, which enables a "catalyst TF" to activate a large set of targets within minutes of signal perturbation

Palladium nanoparticles supported on fluorine-doped tin oxide as an efficient heterogeneous catalyst for Suzuki coupling and 4-nitrophenol reduction

Immobilization of palladium nanoparticles onto the fluorine-doped tin oxide (FTO) as support Pd/FTO, resulted in a highly active heterogeneous catalyst for Suzuki-Miyaura cross-coupling reactions and 4-nitrophenol reduction. The Pd/FTO catalyst has been synthesized by immobilization of palladium nanoparticles onto FTO via a simple impregnation method. ICP-MS analysis confirmed that there is 0.11 mmol/g of palladium was loaded successfully on FTO support. The crystallinity, morphologies, compositions and surface properties of Pd/FTO were fully characterized by various techniques. It was further examined for its catalytic activity and robustness in Suzuki coupling reaction with different aryl halides and solvents. The yields obtained from Suzuki coupling reactions were basically over 80%. The prepared catalyst was also tested on mild reaction such as reduction of 4-nitrophenol (4-NP) to 4-aminophenol (4-AP). Pd/FTO catalyst exhibited high catalytic activity towards 4-NP reduction with a rate constant of 1.776 min(-1) and turnover frequency (TOF) value of 29.1 hr(-1). The findings revealed that Pd/FTO also maintained its high stability for five consecutive runs in Suzuki reactions and 4-NP reductions. The catalyst showed excellent catalytic activities by using a small amount of Pd/FTO for the Suzuki coupling reaction and 4-NP reduction

Rapid Genotyping of Soybean Cultivars Using High Throughput Sequencing

Soybean (Glycine max) breeding involves improving commercially grown varieties by introgressing important agronomic traits from poor yielding accessions and/or wild relatives of soybean while minimizing the associated yield drag. Molecular markers associated with these traits are instrumental in increasing the efficiency of producing such crosses and Single Nucleotide Polymorphisms (SNPs) are particularly well suited for this task, owing to high density in the non-genic regions and thus increased likelihood of finding a tightly linked marker to a given trait. A rapid method to develop SNP markers that can differentiate specific loci between any two parents in soybean is thus highly desirable. In this study we investigate such a protocol for developing SNP markers between multiple soybean accessions and the reference Williams 82 genome. To restrict sampling frequency reduced representation libraries (RRLs) of genomic DNA were generated by restriction digestion followed by library construction. We chose to sequence four accessions Dowling (PI 548663), Dwight (PI 597386), Komata (PI200492) and PI 594538A for their agronomic importance as well as Williams 82 as a control

The transcriptional landscape of Arabidopsis thaliana pattern-triggered immunity

Plants tailor their metabolism to environmental conditions, in part through the recognition of a wide array of self and non-self molecules. In particular, the perception of microbial or plant-derived molecular patterns by cell-surface-localized pattern recognition receptors (PRRs) induces pattern-triggered immunity, which includes massive transcriptional reprogramming1. An increasing number of plant PRRs and corresponding ligands are known, but whether plants tune their immune outputs to patterns of different biological origins or of different biochemical natures remains mostly unclear. Here, we performed a detailed transcriptomic analysis in an early time series focused to study rapid-signalling transcriptional outputs induced by well-characterized patterns in the model plant Arabidopsis thaliana. This revealed that the transcriptional responses to diverse patterns (independent of their origin, biochemical nature or type of PRR) are remarkably congruent. Moreover, many of the genes most rapidly and commonly upregulated by patterns are also induced by abiotic stresses, suggesting that the early transcriptional response to patterns is part of the plant general stress response (GSR). As such, plant cells' response is in the first instance mostly to danger. Notably, the genetic impairment of the GSR reduces pattern-induced antibacterial immunity, confirming the biological relevance of this initial danger response. Importantly, the definition of a small subset of 'core immunity response' genes common and specific to pattern response revealed the function of previously uncharacterized GLUTAMATE RECEPTOR-LIKE (GLR) calcium-permeable channels in immunity. This study thus illustrates general and unique properties of early immune transcriptional reprogramming and uncovers important components of plant immunity

A Practical and Efficient Synthesis of Thalidomide via Na/Liquid NH₃ Methodology¹

A facile, efficient, concise, cost-effective, and scalable synthesis of thalidomide in high overall yield (55%) is presented. Treatment of Boc-protected l-glutamic acid diester via Na/liquid (liq.) NH3 (−33 °C) mediated cyclization methodology produces a corresponding glutarimide ring which was subsequently condensed with phthalic anhydride in the presence of glacial acetic acid to afford thalidomide