Langleygotfredsen7526

Directed chemical manipulation provides an additional tool for deciphering the chemical biology of the gut microbiome and might advance microbiome-targeted therapeutics.New technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution and comprehensiveness. To help translate these methods to routine research and clinical practice, we developed a sequence-resolved benchmark set for identification of both false-negative and false-positive germline large insertions and deletions. To create this benchmark for a broadly consented son in a Personal Genome Project trio with broadly available cells and DNA, the Genome in a Bottle Consortium integrated 19 sequence-resolved variant calling methods from diverse technologies. The final benchmark set contains 12,745 isolated, sequence-resolved insertion (7,281) and deletion (5,464) calls ≥50 base pairs (bp). The Tier 1 benchmark regions, for which any extra calls are putative false positives, cover 2.51 Gbp and 5,262 insertions and 4,095 deletions supported by ≥1 diploid assembly. We demonstrate that the benchmark set reliably identifies false negatives and false positives in high-quality SV callsets from short-, linked- and long-read sequencing and optical mapping.In eukaryotes, genes are transcribed by RNA polymerase-II (Pol-II) and introns are removed by the spliceosome largely cotranscriptionally1-3; analysis using long-read sequencing revealed that splicing occurs immediately after Pol-II passes introns in yeast4,5. selleck inhibitor Here, we developed a Nanopore-based method to profile chromatin-bound RNA that enables the simultaneous detection of splicing status, Pol-II position and polyadenylation at the genome-wide scale in Arabidopsis. We found that more than half of the introns remain unspliced after Pol-II transcribes 1 kb past the 3' splice site, which is much slower than the rate of splicing reported in yeast4,5. Many of the full-length chromatin-bound RNA molecules are polyadenylated, yet still contain unspliced introns at specific positions. These introns are nearly absent in the cytoplasm and are resistant to nonsense-mediated decay, suggesting that they are post-transcriptionally spliced before the transcripts are released into the cytoplasm; we therefore termed these introns post-transcriptionally spliced introns (pts introns). Analysis of around 6,500 public RNA-sequencing libraries found that the splicing of pts introns requires the function of splicing-related proteins such as PRMT5 and SKIP, and is also influenced by various environmental signals. The majority of the intron retention events in Arabidopsis are at pts introns, suggesting that chromatin-tethered post-transcriptional splicing is a major contributor to the widespread intron retention that is observed in plants, and could be a mechanism to produce fully spliced functional mRNAs for rapid response.Understanding the gene regulation of plant pathogens is crucial for pest control and thus global food security. An integrated understanding of bacterial gene regulation in the host is dependent on multi-omic datasets, but these are largely lacking. Here, we simultaneously characterized the transcriptome and proteome of a bacterial pathogen in plants. We found a number of bacterial processes affected by plant immunity at the transcriptome and proteome levels. For instance, salicylic acid-mediated plant immunity suppressed the accumulation of proteins comprising the tip component of the bacterial type III secretion system. Interestingly, there were instances of concordant and discordant regulation of bacterial messenger RNAs and proteins. Gene co-expression analysis uncovered previously unknown gene regulatory modules underlying virulence. This study provides molecular insights into the multiple layers of gene regulation that contribute to bacterial growth in planta, and elucidates the role of plant immunity in affecting pathogen responses.Photosynthesis provides food, fibre and fuel that support our society; understanding the mechanisms controlling dynamic changes in this process helps identify new options to improve photosynthesis. Photosynthesis shows diel changes, which have been largely attributed to external light/dark conditions, as well as internal gene expression and the post-translational modification of critical enzymes. Here we report diel fluctuations of magnesium (Mg) in rice (Oryza sativa) chloroplasts, which may function as a rhythm regulator contributing to the post-translational regulation of photosynthetic CO2 assimilation in rice. We found that a chloroplast-localized Mg2+ transporter gene, OsMGT3, which is rhythmically expressed in leaf mesophyll cells, partly modulates Mg fluctuations in rice chloroplasts. Knockout of OsMGT3 substantially reduced Mg2+ uptake, as well as the amplitude of free Mg2+ fluctuations in chloroplasts, which was closely associated with a decrease in ribulose 1,5-bisphosphate carboxylase activity in vivo and a consequent decline in the photosynthetic rate. In addition, the mesophyll-specific overexpression of OsMGT3 remarkably improved photosynthetic efficiency and growth performance in rice. Taken together, these observations demonstrate that OsMGT3-dependent diel Mg fluctuations in chloroplasts may contribute to Mg-dependent enzyme activities for photosynthesis over the daily cycle. Enhancing Mg2+ input to chloroplasts could be a potential approach to improving photosynthetic efficiency in plants.Single-atom catalysts not only maximize metal atom efficiency, they also display properties that are considerably different to their more conventional nanoparticle equivalents, making them a promising family of materials to investigate. Herein we developed a general host-guest strategy to fabricate various metal single-atom catalysts on nitrogen-doped carbon (M1/CN, M = Pt, Ir, Pd, Ru, Mo, Ga, Cu, Ni, Mn). The iridium variant Ir1/CN electrocatalyses the formic acid oxidation reaction with a mass activity of 12.9 [Formula see text] whereas an Ir/C nanoparticle catalyst is almost inert (~4.8 × 10-3 [Formula see text]). The activity of Ir1/CN is also 16 and 19 times greater than those of Pd/C and Pt/C, respectively. Furthermore, Ir1/CN displays high tolerance to CO poisoning. First-principle density functional theory reveals that the properties of Ir1/CN stem from the spatial isolation of iridium sites and from the modified electronic structure of iridium with respect to a conventional nanoparticle catalyst.C-H activation reactions enable chemists to unveil new retrosynthetic disconnections and streamline conventional synthetic approaches. A long-standing challenge in C-H activation is the inability to distinguish electronically and sterically similar C-H bonds. Although numerous synergistic combinations of transition-metal complexes and chelating directing groups have been utilized to distinguish C-H bonds, undirected regioselective C-H functionalization strategies remain elusive. Here we report a regioselective C-H activation/amination reaction of various unsymmetrical dialkyl-substituted alkenes. The regioselectivity of C-H activation is correlated to the electronic properties of allylic C-H bonds indicated by the corresponding 1JCH coupling constants. A linear relationship between the difference in the 1JCH coupling constants of the two competing allylic C-H bonds (Δ1JCH) and the C-H activation barriers (ΔΔG‡) has also been determined.The use of nitrogen fertilizers has been estimated to have supported 27% of the world's population over the past century. Urea (CO(NH2)2) is conventionally synthesized through two consecutive industrial processes, N2 + H2 → NH3 followed by NH3 + CO2 → urea. Both reactions operate under harsh conditions and consume more than 2% of the world's energy. Urea synthesis consumes approximately 80% of the NH3 produced globally. Here we directly coupled N2 and CO2 in H2O to produce urea under ambient conditions. The process was carried out using an electrocatalyst consisting of PdCu alloy nanoparticles on TiO2 nanosheets. This coupling reaction occurs through the formation of C-N bonds via the thermodynamically spontaneous reaction between *N=N* and CO. Products were identified and quantified using isotope labelling and the mechanism investigated using isotope-labelled operando synchrotron-radiation Fourier transform infrared spectroscopy. A high rate of urea formation of 3.36 mmol g-1 h-1 and corresponding Faradic efficiency of 8.92% were measured at -0.4 V versus reversible hydrogen electrode.Quiescence is a hallmark of CD4+ T cells latently infected with human immunodeficiency virus 1 (HIV-1). While reversing this quiescence is an effective approach to reactivate latent HIV from T cells in culture, it can cause deleterious cytokine dysregulation in patients. As a key regulator of T-cell quiescence, FOXO1 promotes latency and suppresses productive HIV infection. We report that, in resting T cells, FOXO1 inhibition impaired autophagy and induced endoplasmic reticulum (ER) stress, thereby activating two associated transcription factors activating transcription factor 4 (ATF4) and nuclear factor of activated T cells (NFAT). Both factors associate with HIV chromatin and are necessary for HIV reactivation. Indeed, inhibition of protein kinase R-like ER kinase, an ER stress sensor that can mediate the induction of ATF4, and calcineurin, a calcium-dependent regulator of NFAT, synergistically suppressed HIV reactivation induced by FOXO1 inhibition. Thus, our studies uncover a link of FOXO1, ER stress and HIV infection that could be therapeutically exploited to selectively reverse T-cell quiescence and reduce the size of the latent viral reservoir.Cell-to-cell communication by exosomes controls normal and pathogenic processes1,2. Viruses can spread in exosomes and thereby avoid immune recognition3. While biogenesis, binding and uptake of exosomes are well characterized4,5, delivery of exosome cargo into the cytoplasm is poorly understood3. We report that the phosphatidylserine receptor HAVCR1 (refs. 6,7) and the cholesterol transporter NPC1 (ref. 8) participate in cargo delivery from exosomes of hepatitis A virus (HAV)-infected cells (exo-HAV) by clathrin-mediated endocytosis. Using CRISPR-Cas9 knockout technology, we show that these two lipid receptors, which interact in the late endosome9, are necessary for the membrane fusion and delivery of RNA from exo-HAV into the cytoplasm. The HAVCR1-NPC1 pathway, which Ebola virus exploits to infect cells9, mediates HAV infection by exo-HAV, which indicates that viral infection via this exosome mimicry mechanism does not require an envelope glycoprotein. The capsid-free viral RNA in the exosome lumen, but not the endosomal uncoating of HAV particles contained in the exosomes, is mainly responsible for exo-HAV infectivity as assessed by methylene blue inactivation of non-encapsidated RNA. In contrast to exo-HAV, infectivity of HAV particles is pH-independent and requires HAVCR1 or another as yet unidentified receptor(s) but not NPC1. Our findings show that envelope-glycoprotein-independent fusion mechanisms are shared by exosomes and viruses, and call for a reassessment of the role of envelope glycoproteins in infection.