MnO2 superstructure cathode with boosted zinc ion intercalation for aqueous zinc ion batteries.

The simultaneous intercalation of protons and Zn2+ ions in aqueous electrolytes presents a significant obstacle to the widespread adoption of aqueous zinc ion batteries (AZIBs) for large-scale use, a challenge that has yet to be overcome. To address this, we have developed a MnO2/tetramethylammonium (TMA) superstructure with an enlarged interlayer spacing, designed specifically to control H+/Zn2+ co-intercalation in AZIBs. Within this superstructure, the pre-intercalated TMA+ ions work as spacers to stabilize the layered structure of MnO2 cathodes and expand the interlayer spacing substantially by 28 % to 0.92 nm. Evidence from in operando pH measurements, in operando synchrotron X-ray diffraction, and X-ray absorption spectroscopy shows that the enlarged interlayer spacing facilitates the diffusion and intercalation of Zn2+ ions (which have a large ionic radius) into the MnO2 cathodes. This spacing also helps suppress the competing H+ intercalation and the formation of detrimental Zn4(OH)6SO4·5H2O, thereby enhancing the structural stability of MnO2. As a result, enhanced Zn2+ storage properties, including excellent capacity and long cycle stability, are achieved.

Application of CRISPR/Cas12i.3 for targeted mutagenesis in broomcorn millet (Panicum miliaceum L.).

In the present study, we have successfully established a gene editing platform in broomcorn millet, one of the oldest crops originating from China, by using our CRISPR/Cas12i.3, and we also created new elite germplasm for this crop.

A pollen selection system links self and interspecific incompatibility in the Brassicaceae.

Self-incompatibility and recurrent transitions to self-compatibility have shaped the extant mating systems underlying the nonrandom mating critical for speciation in angiosperms. Linkage between self-incompatibility and speciation is illustrated by the shared pollen rejection pathway between self-incompatibility and interspecific unilateral incompatibility (UI) in the Brassicaceae. However, the pollen discrimination system that activates this shared pathway for heterospecific pollen rejection remains unknown. Here we show that Stigma UI3.1, the genetically identified stigma determinant of UI in Arabidopsis lyrata × Arabidopsis arenosa crosses, encodes the S-locus-related glycoprotein 1 (SLR1). Heterologous expression of A. lyrata or Capsella grandiflora SLR1 confers on some Arabidopsis thaliana accessions the ability to discriminate against heterospecific pollen. Acquisition of this ability also requires a functional S-locus receptor kinase (SRK), whose ligand-induced dimerization activates the self-pollen rejection pathway in the stigma. SLR1 interacts with SRK and interferes with SRK homomer formation. We propose a pollen discrimination system based on competition between basal or ligand-induced SLR1-SRK and SRK-SRK complex formation. The resulting SRK homomer levels would be sensed by the common pollen rejection pathway, allowing discrimination among conspecific self- and cross-pollen as well as heterospecific pollen. Our results establish a mechanistic link at the pollen recognition phase between self-incompatibility and interspecific incompatibility.

Genomic variation in weedy and cultivated broomcorn millet accessions uncovers the genetic architecture of agronomic traits.

Large-scale genomic variations are fundamental resources for crop genetics and breeding. Here we sequenced 1,904 genomes of broomcorn millet to an average of 40× sequencing depth and constructed a comprehensive variation map of weedy and cultivated accessions. Being one of the oldest cultivated crops, broomcorn millet has extremely low nucleotide diversity and remarkably rapid decay of linkage disequilibrium. Genome-wide association studies identified 186 loci for 12 agronomic traits. Many causative candidate genes, such as PmGW8 for grain size and PmLG1 for panicle shape, showed strong selection signatures during domestication. Weedy accessions contained many beneficial variations for the grain traits that are largely lost in cultivated accessions. Weedy and cultivated broomcorn millet have adopted different loci controlling flowering time for regional adaptation in parallel. Our study uncovers the unique population genomic features of broomcorn millet and provides an agronomically important resource for cereal crops.

Development and validation of a clinical-radiomics model for prediction of prostate cancer: a multicenter study.

PURPOSE: To develop an early diagnosis model of prostate cancer based on clinical-radiomics to improve the accuracy of imaging diagnosis of prostate cancer. METHODS: The multicenter study enrolled a total of 449 patients with prostate cancer from December 2017 to January 2022. We retrospectively collected information from 342 patients who underwent prostate biopsy at Minhang Hospital. We extracted T2WI images through 3D-Slice, and used mask tools to mark the prostate area manually. The radiomics features were extracted by Python using the "Pyradiomics" module. Least Absolute Shrinkage and Selection Operator (LASSO) regression was used for data dimensionality reduction and feature selection, and the radiomics score was calculated according to the correlation coefficients. Multivariate logistic regression analysis was used to develop predictive models. We incorporated the radiomics score, PI-RADS, and clinical features, and this was presented as a nomogram. The model was validated using a cohort of 107 patients from the Xuhui Hospital. RESULTS: In total, 110 effective radiomics features were extracted. Finally, 9 features were significantly associated with the diagnosis of prostate cancer, from which we calculated the radiomics score. The predictors contained in the individualized prediction nomogram included age, fPSA/tPSA, PI-RADS, and radiomics score. The clinical-radiomics model showed good discrimination in the validation cohort (C-index = 0.88). CONCLUSION: This study presents a clinical-radiomics model that incorporates age, fPSA/PSA, PI-RADS, and radiomics score, which can be conveniently used to facilitate individualized prediction of prostate cancer before prostate biopsy.

Ionic Layer Epitaxy Growth of Organic/Inorganic Composite Protective Layers for Large-Area Li and Zn Metal Anodes.

Li and Zn metal batteries using organic and aqueous electrolytes, respectively, are desirable next-generation energy storage systems to replace the traditional Li-ion batteries. However, their cycle life and safety performance are severely constrained by a series of issues that are attributed to dendrite growth. To solve these issues, a nanothick ZnO-oleic acid (ZnO-OA) composite protective layer is developed by a facile ionic layer epitaxy method. The ZnO-OA layer provides strong lithophilic and zincophilic properties, which can effectively induce uniform ion deposition. As a result, the ZnO-OA protected Li and Zn metal anodes can cycle stably for over 600 and 1000 h under a large current density of 10 mA cm-2. Employing the ZnO-OA protected anodes, the Li||LiFePO4 cell can maintain a capacity retention of 99.5% after 600 cycles at a 1 C rate and the Zn||MnO2 cell can operate stably for 1000 cycles at 1 A g-1 current density.

Dynamics of cis-regulatory sequences and transcriptional divergence of duplicated genes in soybean.

Transcriptional divergence of duplicated genes after whole genome duplication (WGD) has been described in many plant lineages and is often associated with subgenome dominance, a genome-wide mechanism. However, it is unknown what underlies the transcriptional divergence of duplicated genes in polyploid species that lack subgenome dominance. Soybean is a paleotetraploid with a WGD that occurred 5 to 13 Mya. Approximately 50% of the duplicated genes retained from this WGD exhibit transcriptional divergence. We developed accessible chromatin region (ACR) datasets from leaf, flower, and seed tissues using MNase-hypersensitivity sequencing. We validated enhancer function of several ACRs associated with known genes using CRISPR/Cas9-mediated genome editing. The ACR datasets were used to examine and correlate the transcriptional patterns of 17,111 pairs of duplicated genes in different tissues. We demonstrate that ACR dynamics are correlated with divergence of both expression level and tissue specificity of individual gene pairs. Gain or loss of flanking ACRs and mutation of cis-regulatory elements (CREs) within the ACRs can change the balance of the expression level and/or tissue specificity of the duplicated genes. Analysis of DNA sequences associated with ACRs revealed that the extensive sequence rearrangement after the WGD reshaped the CRE landscape, which appears to play a key role in the transcriptional divergence of duplicated genes in soybean. This may represent a general mechanism for transcriptional divergence of duplicated genes in polyploids that lack subgenome dominance.

A Multifunctional Organic Electrolyte Additive for Aqueous Zinc Ion Batteries Based on Polyaniline Cathode.

The practical applications of aqueous zinc ion batteries are hindered by the formation of dendrites on the anode, the narrow electrochemical window of electrolyte, and the instability of the cathode. To address all these challenges simultaneously, a multi-functional electrolyte additive of 1-phenylethylamine hydrochloride (PEA) is developed for aqueous zinc ion batteries based on polyaniline (PANI) cathode. Experiments and theoretical calculations confirm that the PEA additive can regulate the solvation sheath of Zn2+ and form a protective layer on the surface of the Zn metal anode. This broadens the electrochemical stability window of the aqueous electrolyte and enables uniform deposition of Zn. On the cathode side, the Cl- anions from PEA enter the PANI chain during charge and release fewer water molecules surrounding the oxidized PANI, thus suppressing harmful side reactions. When used in a Zn||PANI battery, this cathode/anode compatible electrolyte exhibits excellent rate performance and long cycle life, making it highly attractive for practical applications.

Physicochemical Synergistic Separator Coating Induces Uniform and Rapid Deposition of Li and Zn Ions.

Li and Zn metal batteries are the most promising candidates to replace conventional Li-ion batteries. However, a series of issues, especially dendrites caused by uneven deposition of cations during charge-discharge cycles, hinder their practical application. Here, we proposed a facile separator modification method which combines physical and chemical forces to regulate uniform and rapid deposition of both Li+ and Zn2+. Physically, the electronegativity of modified separators drives rapid transport of metal ions via a surface diffusion mode. Chemically, the polar surface functional groups on coated separators induce uniform deposition of metal ions so that the dendrite growth is effectively inhibited. As a result, the Li and Zn metal anodes employing modified separators can cycle stably for over 1000 h under a large current density of 10 mA cm-2.

Genome-Wide Identification of Open Chromatin in Plants Using MH-Seq.

Functional cis-regulatory elements (CREs) act as precise transcriptional switches for fine-tuning gene transcription. Identification of CREs is critical for understanding regulatory mechanisms of gene expression associated with various biological processes in eukaryotes. It is well known that CREs reside in open chromatin that exhibits hypersensitivity to enzyme cleavage and physical shearing. Currently, high-throughput methodologies, such as DNase-seq, ATAC-seq, and FAIRE-seq, have been widely applied in mapping open chromatin in various eukaryotic genomes. More recently, differential MNase (micrococcal nuclease) treatment has been successfully employed to map open chromatin in addition to profiling nucleosome landscape in both mammalian and plant species. We have developed a MNase hypersensitivity sequencing (MH-seq) technique in plants. The MH-seq procedure includes plant nuclei fixation and purification, differential treatments of purified nuclei with MNase, specific recovery of MNase-trimmed small DNA fragments within 20~100 bp in length, and MH-seq library construction followed by Illumina sequencing and data analysis. MH-seq has been successfully applied for global identification of open chromatin in both Arabidopsis thaliana and maize. It has been proven to be an attractive alternative for profiling open chromatin. Thus, MH-seq is expected to be valuable in probing chromatin accessibility on a genome-wide scale for other plants with sequenced genomes. Moreover, MHS data allow to implement footprinting assays to unveil binding sites of transcription factors.

Identification and functional validation of super-enhancers in Arabidopsis thaliana.

Super-enhancers (SEs) are exceptionally large enhancers and are recognized to play prominent roles in cell identity in mammalian species. We surveyed the genomic regions containing large clusters of accessible chromatin regions (ACRs) marked by deoxyribonuclease (DNase) I hypersensitivity in Arabidopsis thaliana. We identified a set of 749 putative SEs, which have a minimum length of 1.5 kilobases and represent the top 2.5% of the largest ACR clusters. We demonstrate that the genomic regions associating with these SEs were more sensitive to DNase I than other nonpromoter ACRs. The SEs were preferentially associated with topologically associating domains. Furthermore, the SEs and their predicted cognate genes were frequently associated with organ development and tissue identity in A. thaliana. Therefore, the A. thaliana SEs and their cognate genes mirror the functional characteristics of those reported in mammalian species. We developed CRISPR/Cas-mediated deletion lines of a 3,578-bp SE associated with the thalianol biosynthetic gene cluster (BGC). Small deletions (131-157 bp) within the SE resulted in distinct phenotypic changes and transcriptional repression of all five thalianol genes. In addition, T-DNA insertions in the SE region resulted in transcriptional alteration of all five thalianol genes. Thus, this SE appears to play a central role in coordinating the operon-like expression pattern of the thalianol BGC.

Temperature-Dependent Nucleation and Electrochemical Performance of Zn Metal Anodes.

A fundamental understanding of the nucleation and growth behaviors of Zn metal anodes over a wide range of temperatures is of great value for suppressing Zn dendrite growth. However, work focused on the early nucleation and growth behavior of Zn metal at various temperatures is still absent. Here, we study the effect of cycling temperature on Zn nuclei size and areal density and find that low temperature induces a smaller and dense nucleus, which prevents the formation of dendrites. Based on this finding, a cooling-treatment-based self-healing strategy is developed to in situ eliminate dendrites, which effectively prolongs the lifespan of the Zn anode by 520%. This novel self-healing strategy could be employed as a reliable strategy for restoring batteries in situ to reach a longer lifespan.

Inhibition of Rac1 attenuates radiation-induced lung injury while suppresses lung tumor in mice.

The lung is one of the most sensitive tissues to ionizing radiation, thus, radiation-induced lung injury (RILI) stays a key dose-limiting factor of thoracic radiotherapy. However, there is still little progress in the effective treatment of RILI. Ras-related C3 botulinum toxin substrate1, Rac1, is a small guanosine triphosphatases involved in oxidative stress and apoptosis. Thus, Rac1 may be an important molecule that mediates radiation damage, inhibition of which may produce a protective effect on RILI. By establishing a mouse model of radiation-induced lung injury and orthotopic lung tumor-bearing mouse model, we detected the role of Rac1 inhibition in the protection of RILI and suppression of lung tumor. The results showed that ionizing radiation induces the nuclear translocation of Rac1, the latter then promotes nuclear translocation of P53 and prolongs the residence time of p53 in the nucleus, thereby promoting the transcription of Trp53inp1 which mediates p53-dependent apoptosis. Inhibition of Rac1 significantly reduce the apoptosis of normal lung epithelial cells, thereby effectively alleviating RILI. On the other hand, inhibition of Rac1 could also significantly inhibit the growth of lung tumor, increase the radiation sensitivity of tumor cells. These differential effects of Rac1 inhibition were related to the mutation and overexpression of Rac1 in tumor cells.

A Rigid-Flexible Protecting Film with Surface Pits Structure for Dendrite-Free and High-Performance Lithium Metal Anode.

An artificial organic/inorganic composite protecting film for lithium metal anode with one-side surface pits structure was prepared by poly(vinylidene fluoride-co-hexafluoropropylene) and Al2O3+LiNO3 inorganic additives. Due to the unique surface structure, the composite film can not only serve as an artificial protective film, but also act as an additional lithium plating host, which synergistically enabled the lithium metal anode to adapt to high current densities meanwhile maintain dendrite-free during long-term cycling. As a result, the protected lithium metal anode can operate stably for 1000 h at a high current density of 10.0 mA cm-2. When paired with a LiFePO4 or sulfur cathode, the full cells with unflooded electrolyte showed significantly improved cycling performance, demonstrating great potential of this artificial protecting film in lithium metal batteries.

Magnesium Ion Storage Properties in a Layered (NH4)2V6O16·1.5H2O Nanobelt Cathode Material Activated by Lattice Water.

Magnesium ion batteries have attracted increasing attention as a promising energy storage device due to the high safety, high volumetric capacity, and low cost of Mg. However, the strong Coulombic interactions between Mg2+ ions and cathode materials seriously hinder the electrochemical performance of the batteries. To seek a promising cathode material for magnesium ion batteries, in this work, (NH4)2V6O16·1.5H2O and water-free (NH4)2V6O16 materials are synthesized by a one-step hydrothermal method. The effects of NH4+ and lattice water on the Mg2+ storage properties in these kinds of layered cathode materials are investigated by experiments and first-principles calculations. Lattice water is demonstrated to be of vital importance for Mg2+ storage, which not only stabilizes the layered structure of (NH4)2V6O16·1.5H2O but also promotes the transport kinetics of Mg2+. Electrochemical experiments of (NH4)2V6O16·1.5H2O show a specific capacity of 100 mA·h·g-1 with an average discharge voltage of 2.16 V vs Mg2+/Mg, highlighting the potential of (NH4)2V6O16·1.5H2O as a high-voltage cathode material for magnesium ion batteries.

Chorus2: design of genome-scale oligonucleotide-based probes for fluorescence in situ hybridization.

Oligonucleotide (oligo)-fluorescence in situ hybridization (FISH) has rapidly becoming the new generation of FISH technique in plant molecular cytogenetics research. Genome-scale identification of single-copy oligos is the foundation of successful oligo-FISH experiments. Here, we introduce Chorus2, a software that is developed specifically for oligo selection. We demonstrate that Chorus2 is highly effective to remove all repetitive elements in selection of single-copy oligos, which is critical for the development of successful FISH probes. Chorus2 is more effective than Chorus, the original version of the pipeline, and OligoMiner for repeat removal. Chorus2 allows to select oligos that are conserved among related species, which extends the usage of oligo-FISH probes among phylogenetically related plant species. We also implemented a new function in Chorus2 that allows development of FISH probes from plant species without an assembled genome. We anticipate that Chorus2 can be used in plants as well as in mammalian and other non-plant species. Chorus2 will broadly facilitate the design of FISH probes for various types of application in molecular cytogenetics research.

BAC- and oligo-FISH mapping reveals chromosome evolution among Vigna angularis, V. unguiculata, and Phaseolus vulgaris.

Cytogenomic resources have accelerated synteny and chromosome evolution studies in plant species, including legumes. Here, we established the first cytogenetic map of V. angularis (Va, subgenus Ceratotropis) and compared this new map with those of V. unguiculata (Vu, subgenus Vigna) and P. vulgaris (Pv) by BAC-FISH and oligopainting approaches. We mapped 19 Vu BACs and 35S rDNA probes to the 11 chromosome pairs of Va, Vu, and Pv. Vigna angularis shared a high degree of macrosynteny with Vu and Pv, with five conserved syntenic chromosomes. Additionally, we developed two oligo probes (Pv2 and Pv3) used to paint Vigna orthologous chromosomes. We confirmed two reciprocal translocations (chromosomes 2 and 3 and 1 and 8) that have occurred after the Vigna and Phaseolus divergence (~9.7 Mya). Besides, two inversions (2 and 4) and one translocation (1 and 5) have occurred after Vigna and Ceratotropis subgenera separation (~3.6 Mya). We also observed distinct oligopainting patterns for chromosomes 2 and 3 of Vigna species. Both Vigna species shared similar major rearrangements compared to Pv: one translocation (2 and 3) and one inversion (chromosome 3). The sequence synteny identified additional inversions and/or intrachromosomal translocations involving pericentromeric regions of both orthologous chromosomes. We propose chromosomes 2 and 3 as hotspots for chromosomal rearrangements and de novo centromere formation within and between Vigna and Phaseolus. Our BAC- and oligo-FISH mapping contributed to physically trace the chromosome evolution of Vigna and Phaseolus and its application in further studies of both genera.

Genomic editing of intronic enhancers unveils their role in fine-tuning tissue-specific gene expression in Arabidopsis thaliana.

Enhancers located in introns are abundant and play a major role in the regulation of gene expression in mammalian species. By contrast, the functions of intronic enhancers in plants have largely been unexplored and only a handful of plant intronic enhancers have been reported. We performed a genome-wide prediction of intronic enhancers in Arabidopsis thaliana using open chromatin signatures based on DNase I sequencing. We identified 941 candidate intronic enhancers associated with 806 genes in seedling tissue and 1,271 intronic enhancers associated with 1,069 genes in floral tissue. We validated the function of 15 of 21 (71%) of the predicted intronic enhancers in transgenic assays using a reporter gene. We also created deletion lines of three intronic enhancers associated with two different genes using CRISPR/Cas. Deletion of these enhancers, which span key transcription factor binding sites, did not abolish gene expression but caused varying levels of transcriptional repression of their cognate genes. Remarkably, the transcriptional repression of the deletion lines occurred at specific developmental stages and resulted in distinct phenotypic effects on plant morphology and development. Clearly, these three intronic enhancers are important in fine-tuning tissue- and development-specific expression of their cognate genes.

Enhancer-mediated reporter gene expression in Arabidopsis thaliana: a forward genetic screen.

Gene expression is controlled and regulated by interactions between cis-regulatory DNA elements (CREs) and regulatory proteins. Enhancers are one of the most important classes of CREs in eukaryotes. Eukaryotic genes, especially those related to development or responses to environmental cues, are often regulated by multiple enhancers in different tissues and/or at different developmental stages. Remarkably, little is known about the molecular mechanisms by which enhancers regulate gene expression in plants. We identified a distal enhancer, CREß, which regulates the expression of AtDGK7, which encodes a diacylglycerol kinase in Arabidopsis. We developed a transgenic line containing the luciferase reporter gene (LUC) driven by CREß fused with a minimal cauliflower mosaic virus (CaMV) 35S promoter. The CREß enhancer was shown to play a role in the response to osmotic pressure of the LUC reporter gene. A forward genetic screen pipeline based on the transgenic line was established to generate mutations associated with altered expression of the LUC reporter gene. We identified a suite of mutants with variable LUC expression levels as well as different segregation patterns of the mutations in populations. We demonstrate that this pipeline will allow us to identify trans-regulatory factors associated with CREß function as well as those acting in the regulation of the endogenous AtDGK7 gene.

Preferential meiotic chromosome pairing among homologous chromosomes with cryptic sequence variation in tetraploid maize.

Meiotic chromosome pairing between homoeologous chromosomes was reported in many nascent allopolyploids. Homoeologous pairing is gradually eliminated and replaced by exclusive homologous pairing in well-established allopolyploids, an evolutionary process referred to as the diploidization of allopolyploids. A fundamental question of the diploidization of allopolyploids is whether and to what extent the DNA sequence variation among homoeologous chromosomes contribute to the establishment of exclusive homologous chromosome pairing. We developed aneuploid tetraploid maize lines that contain three copies of chromosome 10 derived from inbred lines B73 and H99. We were able to identify the parental origin of each copy of chromosome 10 in the materials using oligonucleotide-based haplotype-specific chromosome painting. We demonstrate that the two identical copies of chromosome 10 from H99 pair preferentially over chromosome 10 from B73 in different stages of prophase I and metaphase I during meiosis. Thus, homologous chromosome pairing is favored to partners with the most similar DNA sequences and can be discriminated based on cryptic sequence variation. We propose that innate preference of homologous chromosome pairing exists in nascent allopolyploids and serves as the first layer that would eventually block all homoeologous chromosome pairing in allopolyploids.