During chronic viral infection, virus-specific CD8(+) T cells become exhausted, exhibit poor effector function and lose memory potential. However, exhausted CD8(+) T cells can still contain viral replication in chronic infections, although the mechanism of this containment is largely unknown. Here we show that a subset of exhausted CD8(+) T cells expressing the chemokine receptor CXCR5 has a critical role in the control of viral replication in mice that were chronically infected with lymphocytic choriomeningitis virus (LCMV). These CXCR5(+) CD8(+) T cells were able to migrate into B-cell follicles, expressed lower levels of inhibitory receptors and exhibited more potent cytotoxicity than the CXCR5(-) [corrected] subset. Furthermore, we identified the Id2-E2A signalling axis as an important regulator of the generation of this subset. In patients with HIV, we also identified a virus-specific CXCR5(+) CD8(+) T-cell subset, and its number was inversely correlated with viral load. The CXCR5(+) subset showed greater therapeutic potential than the CXCR5(-) [corrected] subset when adoptively transferred to chronically infected mice, and exhibited synergistic reduction of viral load when combined with anti-PD-L1 treatment. This study defines a unique subset of exhausted CD8(+) T cells that has a pivotal role in the control of viral replication during chronic viral infection.

Allotetraploid cotton species (Gossypium hirsutum and Gossypium barbadense) have long been cultivated worldwide for natural renewable textile fibers. The draft genome sequences of both species are available but they are highly fragmented and incomplete 1-4. Here we report referencegrade genome assemblies and annotations for G. hirsutum accession Texas Marker-1 (TM-1) and G. barbadense accession 3-79 by integrating single-molecule real-time sequencing, BioNano optical mapping and high-throughput chromosome conformation capture techniques. Compared with previous assembled draft genomes 1,3 , these genome sequences show considerable improvements in contiguity and completeness for regions with high content of repeats such as centromeres. Comparative genomics analyses identify extensive structural variations that probably occurred after polyploidization, highlighted by large paracentric/pericentric inversions in 14 chromosomes. We constructed an introgression line population to introduce favorable chromosome segments from G. barbadense to G. hirsutum, allowing us to identify 13 quantitative trait loci associated with superior fiber quality. These resources will accelerate evolutionary and functional genomic studies in cotton and inform future breeding programs for fiber improvement. Cotton represents the largest source of natural textile fibers in the world. Over 90% of annual fiber production comes from allotetraploid cotton (G. hirsutum and G. barbadense), which originated from an allopolyplodization event approximately 1-2 million year ago, followed by millennia of asymmetric subgenome selection 5,6. G. hirsutum is cultivated all over the world because of its high yield and G. barbadense is prized for its superior fiber quality. To cultivate G. hirsutum that produces longer, finer and stronger fibers, one approach is to introduce the superior fiber traits from G. barbadense into G. hirsutum. A genomics-enabled breeding strategy requires a detailed and robust understanding of genomic organization. Genomic feature G. hirsutum G. barbadense

We isolated two T-DNA insertion mutants of Arabidopsis thaliana GLUTATHIONE PEROXIDASE3 (ATGPX3) that exhibited a higher rate of water loss under drought stress, higher sensitivity to H 2 O 2 treatment during seed germination and seedling development, and enhanced production of H 2 O 2 in guard cells. By contrast, lines engineered to overexpress ATGPX3 were less sensitive to drought stress than the wild type and displayed less transpirational water loss, which resulted in higher leaf surface temperature. The atgpx3 mutation also disrupted abscisic acid (ABA) activation of calcium channels and the expression of ABA-and stress-responsive genes. ATGPX3 physically interacted with the 2C-type protein phosphatase ABA INSENSITIVE2 (ABI2) and, to a lesser extent, with ABI1. In addition, the redox states of both ATGPX3 and ABI2 were found to be regulated by H 2 O 2 . The phosphatase activity of ABI2, measured in vitro, was reduced approximately fivefold by the addition of oxidized ATGPX3. The reduced form of ABI2 was converted to the oxidized form by the addition of oxidized ATGPX3 in vitro, which might mediate ABA and oxidative signaling. These results suggest that ATGPX3 might play dual and distinctive roles in H 2 O 2 homeostasis, acting as a general scavenger and specifically relaying the H 2 O 2 signal as an oxidative signal transducer in ABA and drought stress signaling.

As sessile organisms, plants must adapt to variations in the environment. Environmental stress triggers various responses, including growth inhibition, mediated by the plant hormone abscisic acid (ABA). The mechanisms that integrate stress responses with growth are poorly understood. Here, we discovered that the Target of Rapamycin (TOR) kinase phosphorylates PYL ABA receptors at a conserved serine residue to prevent activation of the stress response in unstressed plants. This phosphorylation disrupts PYL association with ABA and with PP2C phosphatase effectors, leading to inactivation of SnRK2 kinases. Under stress, ABA-activated SnRK2s phosphorylate Raptor, a component of the TOR complex, triggering TOR complex dissociation and inhibition. Thus, TOR signaling represses ABA signaling and stress responses in unstressed conditions, whereas ABA signaling represses TOR signaling and growth during times of stress. Plants utilize this conserved phospho-regulatory feedback mechanism to optimize the balance of growth and stress responses.

Publisher's copyright statement:Additional information: Use policyThe full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-pro t purposes provided that:• a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders.Please consult the full DRO policy for further details. Dt, 0.56 × 10 -3 ) ( Fig. 1d and Supplementary Fig. 3). This shows that a large amount is associated with the development of the long fiber trait in cultivated cotton (Fig. 3b). 217Domestication has led to the transformation of cotton fiber from brown to white. 218To understand this phenomenon, we examined two homoeologous gene pairs only 219 subjected to domestication selection in the Dt, 4-COUMARATE:COA LIGASE (4CL) 220 and CHALCONE SYNTHASE (CHS), which encode enzymes involved in the 221 phenylpropanoid metabolic pathway ( Fig. 3c and Supplementary Fig. 6 Fig. 3c). These SNPs display reductions in nucleotide diversity that occurred 225 during domestication (Fig. 3c). Interestingly, we found that the two SNPs in the Fig. 8) 42 . We identified a total of 188,360 DNase I-hypersensitive 248 sites (DHSs) in cotton leaves and fibers, of which ca. 47% are common to both tissues 249 (Fig. 4a). DHSs were preferentially identified in chromosomal arms and 250 approximately half were detected in promoter and intergenic regions ( Fig. 4b and 251 Supplementary Fig. 9). We found DHSs are hypo-methylated, consistent with 252 previous studies 42 (Fig. 4c) H3K4me1 and inactive H3K9me2 (Fig. 4d). Intergenic DHSs were also found to 255 exhibit an enrichment of H3K4me3 and H3K27me3, but depletion of H3K9me2 and 256 no enrichment of H3K4me1 (Fig. 4e). As predicted, the patterns of chromatin 257 modification marks in cotton are different between genic and TE regions 258 ( Supplementary Fig. 10). In addition, genes with promoter DHSs are generally 259 expressed at a higher level in both tissues than those without promoter DHSs (Fig. 4f), 260 and tissue-specific promoter DHSs corresponded to higher levels of gene expression 261 ( Fig. 4g) Hi-C analysis was carried out using the TM-1 accession to characterize global 296 chromatin interactions. We generated 1.1 billion Hi-C paired-end reads, of which ca. possible Hi-C bias, HindIII fragments of less than 2 kb were merged to obtain 299 305,682 chromosomal anchor regions (Fig. 5a). On the basis of a high-quality 300 genome assembly of TM-1 (Supplementary Fig. 11), we used the Hi-C data to 301 characterize the cotton chromatin interactome (Supplementary Fig. 12) and ( Fig. 5b), but many topologically associated domain-like (TAD-like) regions were 305 identified (Fig. 5c, Supplementary Fig. 13 and Supplementary are less frequent at regions marked by H3K9me2 (Fig. 5d). (Fig. 5g). 320We...

Singly or doubly bonded polynitrogen compounds can decompose to dinitrogen (N) with an extremely large energy release. This makes them attractive as potential explosives or propellants, but also challenging to produce in a stable form. Polynitrogen materials containing nitrogen as the only element exist in the form of high-pressure polymeric phases, but under ambient conditions even metastability is realized only in the presence of other elements that provide stabilization. An early example is the molecule phenylpentazole, with a five-membered all-nitrogen ring, which was first reported in the 1900s and characterized in the 1950s. Salts containing the azide anion (N) or pentazenium cation (N) are also known, with compounds containing the pentazole anion, cyclo-N, a more recent addition. Very recently, a bulk material containing this species was reported and then used to prepare the first example of a solid-state metal-N complex. Here we report the synthesis and characterization of five metal pentazolate hydrate complexes [Na(HO)(N)]·2HO, [M(HO)(N)]·4HO (M = Mn, Fe and Co) and [Mg(HO)(N)]·4HO that, with the exception of the Co complex, exhibit good thermal stability with onset decomposition temperatures greater than 100 °C. For this series we find that the N ion can coordinate to the metal cation through either ionic or covalent interactions, and is stabilized through hydrogen-bonding interactions with water. Given their energetic properties and stability, pentazole-metal complexes might potentially serve as a new class of high-energy density materials or enable the development of such materials containing only nitrogen. We also anticipate that the adaptability of the N ion in terms of its bonding interactions will enable the exploration of inorganic nitrogen analogues of metallocenes and other unusual polynitrogen complexes.

DNA methylation is an important epigenetic modification. Ten-eleven translocation (TET) proteins are involved in DNA demethylation through iteratively oxidizing 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). Here we show that human TET1 and TET2 are more active on 5mC-DNA than 5hmC/5fC-DNA substrates. We determine the crystal structures of TET2-5hmC-DNA and TET2-5fC-DNA complexes at 1.80 Å and 1.97 Å resolution, respectively. The cytosine portion of 5hmC/5fC is specifically recognized by TET2 in a manner similar to that of 5mC in the TET2-5mC-DNA structure, and the pyrimidine base of 5mC/5hmC/5fC adopts an almost identical conformation within the catalytic cavity. However, the hydroxyl group of 5hmC and carbonyl group of 5fC face towards the opposite direction because the hydroxymethyl group of 5hmC and formyl group of 5fC adopt restrained conformations through forming hydrogen bonds with the 1-carboxylate of NOG and N4 exocyclic nitrogen of cytosine, respectively. Biochemical analyses indicate that the substrate preference of TET2 results from the different efficiencies of hydrogen abstraction in TET2-mediated oxidation. The restrained conformation of 5hmC and 5fC within the catalytic cavity may prevent their abstractable hydrogen(s) adopting a favourable orientation for hydrogen abstraction and thus result in low catalytic efficiency. Our studies demonstrate that the substrate preference of TET2 results from the intrinsic value of its substrates at their 5mC derivative groups and suggest that 5hmC is relatively stable and less prone to further oxidation by TET proteins. Therefore, TET proteins are evolutionarily tuned to be less reactive towards 5hmC and facilitate the generation of 5hmC as a potentially stable mark for regulatory functions.

SUMMARY Mitogen-activated protein kinase cascades are important signaling modules that convert environmental stimuli into cellular responses. We show that MPK3, MPK4, and MPK6 are rapidly activated after cold treatment. The mpk3 and mpk6 mutants display increased expression of CBF genes and enhanced freezing tolerance, whereas constitutive activation of the MKK4/5-MPK3/6 cascade in plants causes reduced expression of CBF genes and hypersensitivity to freezing, suggesting that the MKK4/5-MPK3/6 cascade negatively regulates the cold response. MPK3 and MPK6 can phosphorylate ICE1, a bHLH transcription factor that regulates the expression of CBF genes, and the phosphorylation promotes the degradation of ICE1. Interestingly, the MEKK1-MKK2-MPK4 pathway constitutively suppresses MPK3 and MPK6 activities, and has a positive role in the cold response. Furthermore, the MAPKKK YDA, and two calcium/calmodulin-regulated receptor-like kinases, CRLK1 and CRLK2, negatively modulate the cold-activation of MPK3/6. Our results uncover important roles of MAPK cascades in the regulation of plant cold response.