A pan-grass transcriptome reveals patterns of cellular divergence in crops.

Different plant species within the grasses were parallel targets of domestication, giving rise to crops with distinct evolutionary histories and traits1. Key traits that distinguish these species are mediated by specialized cell types2. Here we compare the transcriptomes of root cells in three grass species-Zea mays, Sorghum bicolor and Setaria viridis. We show that single-cell and single-nucleus RNA sequencing provide complementary readouts of cell identity in dicots and monocots, warranting a combined analysis. Cell types were mapped across species to identify robust, orthologous marker genes. The comparative cellular analysis shows that the transcriptomes of some cell types diverged more rapidly than those of others-driven, in part, by recruitment of gene modules from other cell types. The data also show that a recent whole-genome duplication provides a rich source of new, highly localized gene expression domains that favour fast-evolving cell types. Together, the cell-by-cell comparative analysis shows how fine-scale cellular profiling can extract conserved modules from a pan transcriptome and provide insight on the evolution of cells that mediate key functions in crops.

Isobavachalcone inhibits RANKL-induced osteoclastogenesis via miR-193-3p/NF-κB/NFATc1 signaling pathway in BMMs cells.

Inhibition of extensive osteoclastogenesis and bone resorption is considered a potential therapeutic target for the treatment of osteoporosis. Isobavachalcone (IBC) is derived from the traditional Chinese herb Psoralea corylifolia Linn. We showed that IBC dose-dependently suppressed receptor activator of nuclear factor kappa B ligand (RANKL)-induced osteoclastogenesis in bone marrow monocyte/macrophage (BMMs) and osteoclastic bone-resorption function without cytotoxicity at a dose of no more than 8 µmin vitro. Mechanistically, the results of western blot and quantitative real-time polymerase chain reaction (qRT-PCR) indicated that IBC inhibited the RANKL-induced degradation of IκBα and phosphorylation of nuclear factor kappa B (NF-κB) in BMMs, and subsequently downregulated the expression of osteoclastic-specific genes and osteoclastogenesis-related proteins. TRAP staining and qRT-PCR showed that IBC can inhibit osteoclast differentiation by down-regulating the expression of miR-193-3p on osteoclast differentiation. Overall, our findings suggest that IBC may serve as a promising compound for the treatment of osteoporosis and other metabolic bone diseases.

General Design Concepts for CAPodes as Ionologic Devices.

Capacitive analogues of semiconductor diodes (CAPodes) present a new avenue for energy-efficient and nature-inspired next-generation computing devices. Here, we disclose the generalized concept for bias-direction-adjustable n- and p-CAPodes based on selective ion sieving. Controllable-unidirectional ion flux is realized by blocking electrolyte ions from entering sub-nanometer pores. The resulting CAPodes exhibit charge-storage characteristics with a high rectification ratio (96.29 %). The enhancement of capacitance is attributed to the high surface area and porosity of an omnisorbing carbon as counter electrode. Furthermore, we demonstrate the use of an integrated device in a logic gate circuit architecture to implement logic operations ('OR', 'AND'). This work demonstrates CAPodes as a generalized concept to achieve p-n and n-p analogue junctions based on selective ion electrosorption, provides a comprehensive understanding and highlights applications of ion-based diodes in ionologic architectures.

A COP1-PIF-HEC regulatory module fine-tunes photomorphogenesis in Arabidopsis.

Light responses mediated by the photoreceptors play crucial roles in regulating different aspects of plant growth and development. An E3 ubiquitin ligase complex CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1)1/SUPPRESSOR OF PHYA (SPA), one of the central repressors of photomorphogenesis, is critical for maintaining skotomorphogenesis. It targets several positive regulators of photomorphogenesis for degradation in darkness. Recently, we revealed that basic helix-loop-helix factors, HECATEs (HECs), function as positive regulators of photomorphogenesis by directly interacting and antagonizing the activity of another group of repressors called PHYTOCHROME-INTERACTING FACTORs (PIFs). It was also shown that HECs are partially degraded in the dark through the ubiquitin/26S proteasome pathway. However, the underlying mechanism of HEC degradation in the dark is still unclear. Here, we show that HECs also interact with both COP1 and SPA proteins in darkness, and that HEC2 is directly targeted by COP1 for degradation via the ubiquitin/26S proteasome pathway. Moreover, COP1-mediated polyubiquitylation and degradation of HEC2 are enhanced by PIF1. Therefore, the ubiquitylation and subsequent degradation of HECs are significantly reduced in both cop1 and pif mutants. Consistent with this, the hec mutants partially suppress photomorphogenic phenotypes of both cop1 and pifQ mutants. Collectively, our work reveals that the COP1/SPA-mediated ubiquitylation and degradation of HECs contributes to the coordination of skoto/photomorphogenic development in plants.

Molecular bases for the constitutive photomorphogenic phenotypes in Arabidopsis.

The transition from skotomorphogenesis to photomorphogenesis is regulated in part by the COP1/SPA complex and phytochrome-interacting factors (PIFs) in Arabidopsis The constitutive photomorphogenic (cop) phenotypes of cop1 and spaQ mutants have been shown to result from a high abundance of positively acting transcription factors. Here, we show that the four major PIF proteins are unstable in cop1 mutants and that overexpression of PIF1, PIF3, PIF4 and PIF5 suppresses cop1 phenotypes in the dark. A comparison of the transcriptome data among cop1, spaQ and pifQ reveals remarkably overlapping gene expression profiles with preferential regulation of PIF direct target genes. Additionally, HFR1 strongly inhibits the in vivo binding and transcriptional activation activity of PIF1 in the dark. Taken together, these data suggest that the cop phenotypes of the cop1 and spaQ mutants are due to a combination of the reduced level of PIFs, increased levels of positively acting transcription factors (e.g. HY5/HFR1) and the HFR1-mediated inhibition of PIF-targeted gene expression in the dark. This article has an associated 'The people behind the papers' interview.

On the Optimal Lawful Intercept Access Points Placement Problem in Hybrid Software-Defined Networks.

For the law enforcement agencies, lawful interception is still one of the main means to intercept a suspect or address most illegal actions. Due to its centralized management, however, it is easy to implement in traditional networks, but the cost is high. In view of this restriction, this paper aims to exploit software-defined network (SDN) technology to contribute to the next generation of intelligent lawful interception technology, i.e., to optimize the deployment of intercept access points (IAPs) in hybrid software-defined networks where both SDN nodes and non-SDN nodes exist simultaneously. In order to deploy IAPs, this paper puts forward an improved equal-cost multi-path shortest path algorithm and accordingly proposes three SDN interception models: T interception model, ECMP-T interception model and Fermat-point interception model. Considering the location relevance of all intercepted targets and the operation and maintenance cost of operators from the global perspective, by the way, we further propose a restrictive minimum vertex cover algorithm (RMVCA) in hybrid SDN. Implementing different SDN interception algorithms based RMVCA in real-world topologies, we can reasonably deploy the best intercept access point and intercept the whole hybrid SDN with the least SDN nodes, as well as significantly optimize the deployment efficiency of IAPs and improve the intercept link coverage in hybrid SDN, contributing to the implementation of lawful interception.

Reciprocal proteasome-mediated degradation of PIFs and HFR1 underlies photomorphogenic development in Arabidopsis.

The phytochrome-mediated regulation of photomorphogenesis under red and far-red light conditions involves both positively and negatively acting factors. The positively acting factors (e.g. HY5/HFR1/LAF1 and others) are degraded in the dark to prevent photomorphogenesis. By contrast, the negatively acting factors (e.g. phytochrome-interacting factors or PIFs) are degraded in response to light to promote photomorphogenesis. Here, we show that the negatively acting factor PIF1 is also degraded in the dark by direct heterodimerization with the positively acting factor HFR1. Conversely, PIF1 also promotes the degradation of HFR1 in darkness. PIF1 enhances the poly-ubiquitylation of HFR1 by COP1 in vivo and in vitro In addition, the reciprocal co-degradation of PIF1 and HFR1 is dependent on the 26S proteasome pathway in vivo Genetic evidence shows that the hfr1 mutant partially suppresses the constitutive photomorphogenic phenotypes of cop1-6 pif1 and of the quadruple mutant pifq both in the dark and in far-red light conditions. Taken together, these data uncover a co-degradation mechanism between PIFs and HFR1 that underlies photomorphogenic development in Arabidopsis thaliana.

Ultrastable Surface-Dominated Pseudocapacitive Potassium Storage Enabled by Edge-Enriched N-Doped Porous Carbon Nanosheets.

The development of ultrastable carbon materials for potassium storage poses key limitations caused by the huge volume variation and sluggish kinetics. Nitrogen-enriched porous carbons have recently emerged as promising candidates for this application; however, rational control over nitrogen doping is needed to further suppress the long-term capacity fading. Here we propose a strategy based on pyrolysis-etching of a pyridine-coordinated polymer for deliberate manipulation of edge-nitrogen doping and specific spatial distribution in amorphous high-surface-area carbons; the obtained material shows an edge-nitrogen content of up to 9.34 at %, richer N distribution inside the material, and high surface area of 616 m2 g-1 under a cost-effective low-temperature carbonization. The optimized carbon delivers unprecedented K-storage stability over 6000 cycles with negligible capacity decay (252 mA h g-1 after 4 months at 1 A g-1 ), rarely reported for potassium storage.

Unraveling the Correlation between Structures of Carbon Nanospheres Derived from Polymeric Spheres and Their Electrochemical Performance to Achieve High-Rate Supercapacitors.

Understanding correlation between the nanostructure of porous carbons and their ion transport behavior is critical for achieving high-performance supercapacitors. Herein, the relationship between size and shell thickness of carbon nanospheres (CNSs) and capacitive electrochemical performance is clarified. Structural uniform CNSs with controlled diameters, prepared via template-free interfacial copolymerization, are emerging as an ideal platform for investigating the ion transport behavior. It is found that ionic transport is significantly enhanced while the introduction of hollow cores with thinner shell, by virtue of the hollow nanopore-accelerated mass transport to reduce ion diffusion length. The proof-of-concept supercapacitors, constituted of carbons with diameter and shell thickness of 91 and 28 nm, respectively, can maintain highest capacitance retention ratio of 86% at a high sweep rate of 300 mVs-1 , also far outperforming the commercial activated carbon in terms of capacitance, rate capability, and surface efficiency, promising a brilliant application.

PHYTOCHROME INTERACTING FACTOR1 Enhances the E3 Ligase Activity of CONSTITUTIVE PHOTOMORPHOGENIC1 to Synergistically Repress Photomorphogenesis in Arabidopsis.

CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1) is a RING/WD40 repeat-containing ubiquitin E3 ligase that is conserved from plants to humans. COP1 forms complexes with SUPPRESSOR OF PHYTOCHROME A (SPA) proteins, and these complexes degrade positively acting transcription factors in the dark to repress photomorphogenesis. Phytochrome-interacting basic helix-loop-helix transcription factors (PIFs) also repress photomorphogenesis in the dark. In response to light, the phytochrome family of sensory photoreceptors simultaneously inactivates COP1-SPA complexes and induces the rapid degradation of PIFs to promote photomorphogenesis. However, the functional relationship between PIFs and COP1-SPA complexes is still unknown. Here, we present genetic evidence that the pif and cop1/spa Arabidopsis thaliana mutants synergistically promote photomorphogenesis in the dark. LONG HYPOCOTYL5 (HY5) is stabilized in the cop1 pif1, spa123 pif1, and pif double, triple, and quadruple mutants in the dark. Moreover, the hy5 mutant suppresses the constitutive photomorphogenic phenotypes of the pifq mutant in the dark. PIF1 forms complexes with COP1, HY5, and SPA1 and enhances the substrate recruitment and autoubiquitylation and transubiquitylation activities of COP1. These data uncover a novel function of PIFs as the potential cofactors of COP1 and provide a genetic and biochemical model of how PIFs and COP1-SPA complexes synergistically repress photomorphogenesis in the dark.

Large-scale single-cell profiling of stem cells uncovers redundant regulators of shoot development and yield trait variation.

Stem cells in plant shoots are a rare population of cells that produce leaves, fruits and seeds, vital sources for food and bioethanol. Uncovering regulators expressed in these stem cells will inform crop engineering to boost productivity. Single-cell analysis is a powerful tool for identifying regulators expressed in specific groups of cells. However, accessing plant shoot stem cells is challenging. Recent single-cell analyses of plant shoots have not captured these cells, and failed to detect stem cell regulators like CLAVATA3 and WUSCHEL . In this study, we finely dissected stem cell-enriched shoot tissues from both maize and arabidopsis for single-cell RNA-seq profiling. We optimized protocols to efficiently recover thousands of CLAVATA3 and WUSCHEL expressed cells. A cross-species comparison identified conserved stem cell regulators between maize and arabidopsis. We also performed single-cell RNA-seq on maize stem cell overproliferation mutants to find additional candidate regulators. Expression of candidate stem cell genes was validated using spatial transcriptomics, and we functionally confirmed roles in shoot development. These candidates include a family of ribosome-associated RNA-binding proteins, and two families of sugar kinase genes related to hypoxia signaling and cytokinin hormone homeostasis. These large-scale single-cell profiling of stem cells provide a resource for mining stem cell regulators, which show significant association with yield traits. Overall, our discoveries advance the understanding of shoot development and open avenues for manipulating diverse crops to enhance food and energy security.

Single-cell analysis opens a goldmine for plant functional studies.

Functional studies in biology require the identification of genes, regulatory elements, and networks, followed by a deep understanding of how they orchestrate to specify cell types, mediate signaling, and respond to internal and external cues over evolutionary timescales. Advances in single-cell analysis have enabled biologists to tackle these questions at the resolution of the individual cell. Here, we highlight recent studies in plants that have embraced single-cell analyses to facilitate functional studies. This review will provide guidance and perspectives for incorporating these advanced approaches in plant research for the coming decades.

Fluorinated porous frameworks enable robust anode-less sodium metal batteries.

Sodium metal batteries hold great promise for energy-dense and low-cost energy storage technology but are severely impeded by catastrophic dendrite issue. State-of-the-art strategies including sodiophilic seeding/hosting interphase design manifest great success on dendrite suppression, while neglecting unavoidable interphase-depleted Na+ before plating, which poses excessive Na use, sacrificed output voltage and ultimately reduced energy density. We here demonstrate that elaborate-designed fluorinated porous framework could simultaneously realize superior sodiophilicity yet negligible interphase-consumed Na+ for dendrite-free and durable Na batteries. As elucidated by physicochemical and theoretical characterizations, well-defined fluorinated edges on porous channels are responsible for both high affinities ensuring uniform deposition and low reactivity rendering superior Na+ utilization for plating. Accordingly, synergistic performance enhancement is achieved with stable 400 cycles and superior plateau to sloping capacity ratio in anode-free batteries. Proof-of-concept pouch cells deliver an energy density of 325 Watt-hours per kilogram and robust 300 cycles under anode-less condition, opening an avenue with great extendibility for the practical deployment of metal batteries.

Trafficking and localization of KNOTTED1 related mRNAs in shoot meristems.

Multicellular organisms use transcripts and proteins as signaling molecules for cell-to-cell communication. Maize KNOTTED1 (KN1) was the first homeodomain transcription factor identified in plants, and functions in maintaining shoot stem cells. KN1 acts non-cell autonomously, and both its messenger RNA (mRNA) and protein traffic between cells through intercellular nanochannels called plasmodesmata. KN1 protein and mRNA trafficking are regulated by a chaperonin subunit and a catalytic subunit of the RNA exosome, respectively. These studies suggest that the function of KN1 in stem cell regulation requires the cell-to-cell transport of both its protein and mRNA. However, in situ hybridization experiments published 25 years ago suggested that KN1 mRNA was missing from the epidermal (L1) layer of shoot meristems, suggesting that only the KN1 protein could traffic. Here, we show evidence that KN1 mRNA is present at a low level in L1 cells of maize meristems, supporting an idea that both KN1 protein and mRNA traffic to the L1 layer. We also summarize mRNA expression patterns of KN1 homologs in diverse angiosperm species, and discuss KN1 trafficking mechanisms.

Laser-Derived Interfacial Confinement Enables Planar Growth of 2D SnS2 on Graphene for High-Flux Electron/Ion Bridging in Sodium Storage.

Establishing covalent heterointerfaces with face-to-face contact is promising for advanced energy storage, while challenge remains on how to inhibit the anisotropic growth of nucleated crystals on the matrix. Herein, face-to-face covalent bridging in-between the 2D-nanosheets/graphene heterostructure is constructed by intentionally prebonding of laser-manufactured amorphous and metastable nanoparticles on graphene, where the amorphous nanoparticles were designed via the competitive oxidation of Sn-O and Sn-S bonds, and metastable feature was employed to facilitate the formation of the C-S-Sn covalent bonding in-between the heterostructure. The face-to-face bridging of ultrathin SnS2 nanosheets on graphene enables the heterostructure huge covalent coupling area and high loading and thus renders unimpeded electron/ion transfer pathways and indestructible electrode structure, and impressive reversible capacity and rate capability for sodium-ion batteries, which rank among the top in records of the SnS2-based anodes. Present work thus provides an alternative of constructing heterostructures with planar interfaces for electrochemical energy storage and even beyond.

Atomic Sn-enabled high-utilization, large-capacity, and long-life Na anode.

Constructing robust nucleation sites with an ultrafine size in a confined environment is essential toward simultaneously achieving superior utilization, high capacity, and long-term durability in Na metal-based energy storage, yet remains largely unexplored. Here, we report a previously unexplored design of spatially confined atomic Sn in hollow carbon spheres for homogeneous nucleation and dendrite-free growth. The designed architecture maximizes Sn utilization, prevents agglomeration, mitigates volume variation, and allows complete alloying-dealloying with high-affinity Sn as persistent nucleation sites, contrary to conventional spatially exposed large-size ones without dealloying. Thus, conformal deposition is achieved, rendering an exceptional capacity of 16 mAh cm-2 in half-cells and long cycling over 7000 hours in symmetric cells. Moreover, the well-known paradox is surmounted, delivering record-high Na utilization (e.g., 85%) and large capacity (e.g., 8 mAh cm-2) while maintaining extraordinary durability over 5000 hours, representing an important breakthrough for stabilizing Na anode.

Ground tissue circuitry regulates organ complexity in maize and Setaria.

Most plant roots have multiple cortex layers that make up the bulk of the organ and play key roles in physiology, such as flood tolerance and symbiosis. However, little is known about the formation of cortical layers outside of the highly reduced anatomy of Arabidopsis. Here, we used single-cell RNA sequencing to rapidly generate a cell-resolution map of the maize root, revealing an alternative configuration of the tissue formative transcription factor SHORT-ROOT (SHR) adjacent to an expanded cortex. We show that maize SHR protein is hypermobile, moving at least eight cell layers into the cortex. Higher-order SHR mutants in both maize and Setaria have reduced numbers of cortical layers, showing that the SHR pathway controls expansion of cortical tissue to elaborate anatomical complexity.

Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery.

Crop productivity depends on activity of meristems that produce optimized plant architectures, including that of the maize ear. A comprehensive understanding of development requires insight into the full diversity of cell types and developmental domains and the gene networks required to specify them. Until now, these were identified primarily by morphology and insights from classical genetics, which are limited by genetic redundancy and pleiotropy. Here, we investigated the transcriptional profiles of 12,525 single cells from developing maize ears. The resulting developmental atlas provides a single-cell RNA sequencing (scRNA-seq) map of an inflorescence. We validated our results by mRNA in situ hybridization and by fluorescence-activated cell sorting (FACS) RNA-seq, and we show how these data may facilitate genetic studies by predicting genetic redundancy, integrating transcriptional networks, and identifying candidate genes associated with crop yield traits.

Porous Functionalized Covalent-Triazine Frameworks for Enhanced Adsorption Toward Polysulfides in Li-S Batteries and Organic Dyes.

The incorporation of functional building blocks to construct functionalized and highly porous covalent triazine frameworks (CTFs) is essential to the emerging adsorptive-involved field. Herein, a series of amide functionalized CTFs (CTF-PO71) have been synthesized using a bottom-up strategy in which pigment PO71 with an amide group is employed as a monomer under ionothermal conditions with ZnCl2 as the solvent and catalyst. The pore structure can be controlled by the amount of ZnCl2 to monomer ratio. Benefitting from the highly porous structure and amide functionalities, CTF-PO71, as a sulfur cathode host, simultaneously demonstrates physical confinement and chemical anchoring of sulfur species, thus leading to superior capacity, cycling stability, and rate capability in comparison to unfunctionalized CTF. Meanwhile, as an adsorbent of organic dye molecules, CTF-PO71 was demonstrated to exhibit strong chemical interactions with dye molecules, facilitating adsorption kinetics and thereby promoting the adsorption rate and capacity. Furthermore, the dynamic adsorption experiments of organic dyes from solutions showed selectivity/priority of CTF-PO71s for specific dye molecules.

Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud.

MaizeCODE is a project aimed at identifying and analyzing functional elements in the maize genome. In its initial phase, MaizeCODE assayed up to five tissues from four maize strains (B73, NC350, W22, TIL11) by RNA-Seq, Chip-Seq, RAMPAGE, and small RNA sequencing. To facilitate reproducible science and provide both human and machine access to the MaizeCODE data, we enhanced SciApps, a cloud-based portal, for analysis and distribution of both raw data and analysis results. Based on the SciApps workflow platform, we generated new components to support the complete cycle of MaizeCODE data management. These include publicly accessible scientific workflows for the reproducible and shareable analysis of various functional data, a RESTful API for batch processing and distribution of data and metadata, a searchable data page that lists each MaizeCODE experiment as a reproducible workflow, and integrated JBrowse genome browser tracks linked with workflows and metadata. The SciApps portal is a flexible platform that allows the integration of new analysis tools, workflows, and genomic data from multiple projects. Through metadata and a ready-to-compute cloud-based platform, the portal experience improves access to the MaizeCODE data and facilitates its analysis.