The conservation of allelic DNA methylation and its relationship with imprinting in maize.

Genomic imprinting refers to allele-specific expression of genes depending on parental origin, and it is regulated by epigenetic modifications. Intraspecific allelic variation for imprinting has been detected; however, the intraspecific genome-wide allelic epigenetic variation in maize and its correlation with imprinting variants remain unclear. Here, three reciprocal hybrids were generated by crossing Zea mays inbred lines CAU5, B73, and Mo17 in order to examine the intraspecific conservation of the imprinted genes in the kernel. The majority of imprinted genes exhibited intraspecific conservation, and these genes also exhibited interspecific conservation (rice, sorghum, and Arabidopsis) and were enriched in some specific pathways. By comparing intraspecific allelic DNA methylation in the endosperm, we found that nearly 15% of DNA methylation existed as allelic variants. The intraspecific whole-genome correlation between DNA methylation and imprinted genes indicated that DNA methylation variants play an important role in imprinting variants. Disruption of two conserved imprinted genes using CRISPR/Cas9 editing resulted in a smaller kernel phenotype. Our results shed light on the intraspecific correlation of DNA methylation variants and variation for imprinting in maize, and show that imprinted genes play an important role in kernel development.

Characterization of Genes That Exhibit Genotype-Dependent Allele-Specific Expression and Its Implications for the Development of Maize Kernel.

Heterosis or hybrid vigor refers to the superior phenotypic traits of hybrids relative to their parental inbred lines. An imbalance between the expression levels of two parental alleles in the F1 hybrid has been suggested as a mechanism of heterosis. Here, based on genome-wide allele-specific expression analysis using RNA sequencing technology, 1689 genes exhibiting genotype-dependent allele-specific expression (genotype-dependent ASEGs) were identified in the embryos, and 1390 genotype-dependent ASEGs in the endosperm, of three maize F1 hybrids. Of these ASEGs, most were consistent in different tissues from one hybrid cross, but nearly 50% showed allele-specific expression from some genotypes but not others. These genotype-dependent ASEGs were mostly enriched in metabolic pathways of substances and energy, including the tricarboxylic acid cycle, aerobic respiration, and energy derivation by oxidation of organic compounds and ADP binding. Mutation and overexpression of one ASEG affected kernel size, which indicates that these genotype-dependent ASEGs may make important contributions to kernel development. Finally, the allele-specific methylation pattern on genotype-dependent ASEGs indicated that DNA methylation plays a potential role in the regulation of allelic expression for some ASEGs. In this study, a detailed analysis of genotype-dependent ASEGs in the embryo and endosperm of three different maize F1 hybrids will provide an index of genes for future research on the genetic and molecular mechanism of heterosis.

Conservation Study of Imprinted Genes in Maize Triparental Heterozygotic Kernels.

Genomic imprinting is a classic epigenetic phenomenon related to the uniparental expression of genes. Imprinting variability exists in seeds and can contribute to observed parent-of-origin effects on seed development. Here, we conducted allelic expression of the embryo and endosperm from four crosses at 11 days after pollination (DAP). First, the F1 progeny of B73(♀) × Mo17(♂) and the inducer line CAU5 were used as parents to obtain reciprocal crosses of BM-C/C-BM. Additionally, the F1 progeny of Mo17(♀) × B73(♂) and CAU5 were used as parents to obtain reciprocal crosses of MB-C/C-MB. In total, 192 and 181 imprinted genes were identified in the BM-C/C-BM and MB-C/C-MB crosses, respectively. Then, by comparing the allelic expression of these imprinted genes in the reciprocal crosses of B73 and CAU5 (BC/CB), fifty-one Mo17-added non-conserved genes were identified as exhibiting imprinting variability. Fifty-one B73-added non-conserved genes were also identified by comparing the allelic expression of imprinted genes identified in BM-C/C-BM, MB-C/C-MB and MC/CM crosses. Specific Gene Ontology (GO) terms were not enriched in B73-added/Mo17-added non-conserved genes. Interestingly, the imprinting status of these genes was less conserved across other species. The cis-element distribution, tissue expression and subcellular location were similar between the B73-added/Mo17-added conserved and B73-added/Mo17-added non-conserved imprinted genes. Finally, genotypic and phenotypic analysis of one non-conserved gene showed that the mutation and overexpression of this gene may affect embryo and kernel size, which indicates that these non-conserved genes may also play an important role in kernel development. The findings of this study will be helpful for elucidating the imprinting mechanism of genes involved in maize kernel development.

Solvent-Driven Chirality Switching of a Pillar[4]arene[1]quinone Having a Chiral Amine-Substituted Quinone Subunit.

Several new chiral pillar[4]arene[1]quinone derivatives were synthesized by reacting pillar[4]arene[1]quinone (EtP4Q1), containing four 1,4-diethoxybenzene units and one benzoquinone unit, with various chiral amines via Michael addition. Due to the direct introduction of chiral substituents on the rim of pillar[n]arene and the close location of the chiral center to the rim of EtP4Q1, the newly prepared compounds showed unique chiroptical properties without complicated chiral resolution processes, and unprecedented high anisotropy factor of up to -0.018 at the charge transfer absorption band was observed. Intriguingly, the benzene sidearm attached pillar[4]arene[1]quinone derivative 1a showed solvent- and complexation-driven chirality inversion. This work provides a promising potential for absolute asymmetric synthesis of pillararene-based derivatives.

Pressure-driven, solvation-directed planar chirality switching of cyclophano-pillar[5]arenes (molecular universal joints).

Planar chiral cyclophanopillar[5]arenes with a fused oligo(oxyethylene) or polymethylene subring (MUJs), existing as an equilibrium mixture of subring-included (in) and -excluded (out) conformers, respond to hydrostatic pressure to exhibit dynamic chiroptical property changes, leading to an unprecedented pressure-driven chirality inversion and the largest ever-reported leap of anisotropy (g) factor for the MUJ with a dodecamethylene subring. The pressure susceptivity of MUJs, assessed by the change in g per unit pressure, is a critical function of the size and nature of the subring incorporated and the solvent employed. Mechanistic elucidations reveal that the in-out equilibrium, as the origin of the MUJ's chiroptical property changes, is on a delicate balance of the competitive inclusion of subrings versus solvent molecules as well as the solvation of the excluded subring. The present results further encourage our use of pressure as a unique tool for dynamically manipulating various supramolecular devices/machines.

Overtemperature-protection intelligent molecular chiroptical photoswitches.

Stimuli-responsive intelligent molecular machines/devices are of current research interest due to their potential application in minimized devices. Constructing molecular machines/devices capable of accomplishing complex missions is challenging, demanding coalescence of various functions into one molecule. Here we report the construction of intelligent molecular chiroptical photoswitches based on azobenzene-fused bicyclic pillar[n]arene derivatives, which we defined as molecular universal joints (MUJs). The Z/E photoisomerization of the azobenzene moiety of MUJs induces rolling in/out conformational switching of the azobenzene-bearing side-ring and consequently leads to planar chirality switching of MUJs. Meanwhile, temperature variation was demonstrated to also cause conformational/chiroptical inversion due to the significant entropy change during the ring-flipping. As a result, photo-induced chiroptical switching could be prohibited when the temperature exceeded an upper limit, demonstrating an intelligent molecular photoswitch having over-temperature protection function, which is in stark contrast to the low-temperature-gating effect commonly encountered.

Electrochemiluminescent Chiral Discrimination with a Pillar[5]arene Molecular Universal Joint-Coordinated Ruthenium Complex.

A bicyclic pillar[5]arene derivative fused with a bipyridine side ring, a so-called molecular universal joint (MUJ), was synthesized, and the pair of enantiomers was resolved by high-performance liquid chromatography enantioresolution. The electrochemiluminescent detection based on the ruthenium complex of the enantiopure MUJ showed excellent chiral discrimination toward certain amino acids.

Supramolecular spectral/visual detection of urinary polyamines through synergetic/competitive complexation with γ-CD and CB[7].

A supramolecular strategy for detecting the concentration of polyamines has been established through competitive/synergetic complexation among polyamines, CB[7], γ-CD, and pyrene derivatives, which allows for convenient, rapid, and high throughput spectral/visual detection of the concentration of urinary polyamines based on the switching on/off of the pyrene excimer fluorescence.

Guest-Binding-Induced Interhetero Hosts Charge Transfer Crystallization: Selective Coloration of Commonly Used Organic Solvents.

Unprecedented interheteromacrocyclic hosts charge transfer (CT) crystals were generated by cooling organic solutions containing p-dimethoxybenzene-constituted pillar[5]arene (P5A) and p-benzoquinone-constituted pillar[5]quinone (P5Q). Despite the weak CT interaction known between p-dimethoxybenzene and p-benzoquinone and the lack of formation of CT complexes between P5A and P5Q in the solution phase, CT cocrystals between P5A and P5Q were formed with solvent molecules included into the hosts' cavities. Such a cocrystallization arises from an elegant synergy between the CT interaction and solvent-binding-promoted crystallization. The interhetero hosts CT crystals were studied by optical and electron microscopic techniques, X-ray powder diffraction, solid-state NMR, UV-vis, IR spectroscopic studies, and X-ray single-crystal studies. The solvent complexation was critical for formation of the supramolecular CT microcrystals. The CT absorption bands faded upon removing the solvent molecules under vacuum, but they could be recovered by reuptake of the solvent molecules. Intriguingly, the CT absorption bands and uptake kinetics are distinguishably different for various organic solvents, thus providing a unique way to distinguish between different commonly used chemicals.

pH-Controlled Chirality Inversion in Enantiodifferentiating Photocyclodimerization of 2-Antharacenecarboxylic Acid Mediated by γ-Cyclodextrin Derivatives.

Several γ-cyclodextrin (γ-CDx) derivatives were used as chiral hosts for the photocyclodimerization of 2-anthracenecarboxylic acid (AC). The effect of pH on photoreactivity and stereochemical outcome of photoproducts was investigated. Upon changing the solution pH, the stereochemical outcome of HH cyclodimer 3 was inverted from 25.2% to -64.4% and 41.2% to -76.2%, respectively, in the photocyclodimerization of AC mediated by bis-quinoline-modified γ-CDx 7 and its N-methylated derivative 8.

A Quinoline-Appended Cyclodextrin Derivative as a Highly Selective Receptor and Colorimetric Probe for Nucleotides.

The design and development of specific recognition and sensing systems for biologically important anionic species has received growing attention in recent years, as they play significant roles in biology, pharmacy, and environmental sciences. Herein, a new supramolecular sensing probe L1 was developed for highly selective differentiation of nucleotides. L1 displayed extremely marked absorption and emission differentiation upon binding with nucleotide homologs of AMP, ADP, and ATP, due to the divergent spatial orientations of guests upon binding, which allowed for a naked-eye colorimetric differentiation for nucleotides. A differentiating mechanism was unambiguously rationalized by using various spectroscopic studies and theoretical calculations. Furthermore, we successfully demonstrated that L1 can be applied to the real-time monitoring of the enzyme-catalyzed phosphorylation/dephosphorylation processes and thus demonstrated an unprecedented visualizable strategy for selectively differentiating the structurally similar nucleotides and real-time monitoring of biological processes via fluorescent and colorimetric changes.

Fulleropillar[4]arene: The Synthesis and Complexation Properties.

A multihydroquinone ether dialdehyde derivative 2 was incidentally obtained through an unexpected ring opening of pillar[4]arene[1]quinone 1. And the Prato reaction of 2 with [60]fullerene led to [60]fullerene bisadducts, from which trans-4 cyclic regioisomer 3 was isolated and characterized. The fulleropillar[4]arene 3 showed a larger cavity and can accommodate a viologen derivative C12V2+ with a much stronger affinity than permethyl pillar[5]arene (MP5) and pillar[4]arene[1]quinone 1.

Effect of anolytic nitrite concentration on electricity generation and electron transfer in a dual-chamber microbial fuel cell.

This study reports the effect of anolytic nitrite concentration on electricity generation and electron transfer in microbial fuel cells (MFCs). Anolytic nitrite enhanced the electricity generation capability of the MFCs at relatively low concentrations (< 60 mg·L-1) but inhibited the activity of anodic electrogenic bacteria at high concentrations. In the anode chamber of the MFC, nitrite was converted to nitrate-releasing electrons before being quickly removed through denitrification. Nitrite alone (in the absence of organic matters) could not perform as an electricity production matrix but promoted electricity production as a co-matrix in the MFC. At an influent nitrite concentration of 60 mg·L-1, the coulombic efficiency of the MFC was minimized at approximately 5.4%, and the charge transfer resistance was also lowest, while the concentrations of extracellular polymeric substances (EPS) and cytochrome c were both maximized. Higher anolytic nitrite concentrations (> 60 mg·L-1) inhibited the production of cytochrome c and EPS and increased the charge transfer resistance, thereby reducing the efficiency of electron transfer in the anodic biofilm. The results provide valuable guidelines for MFC applications in wastewater treatment processes with nitrite-containing influents.

Precise Manipulation of Temperature-Driven Chirality Switching of Molecular Universal Joints through Solvent Mixing.

Three chiral bicyclic pillar[5]arene derivatives termed as molecular universal joints (MUJs), were synthesized and separated enantiomerically. These MUJs showed temperature-driven chirality switching in certain solvents. Herein, it is demonstrated that temperature-driven chirality switching could also be realized by mixing two miscible organic solvents, in each of which chirality inversion is not accomplishable. Additionally, solvent mixing drastically varied the inversion temperature of the MUJs, for example, from far below zero to room temperature. Moreover, the temperature-driven Sp /Rp to Rp /Sp chirality switching direction could be reversed by the solvent mixing and it was critically controlled by the mixing ratios of the two solvents. These observations allowed precise manipulation of the chirality switching behavior of the MUJs. Such a chirality switching was ascribed to the influences of solvent and temperature on the in-out equilibrium of the side rings, which is delicately controlled by several processes, including the solvation/desolvation and the inclusion/exclusion of the side rings and solvent molecules. Crucially, the solvent mixing introduced new supramolecular processes, in particular the desolvation of solvent molecules from the mixed solvent system and the solvation of the side ring by the mixed solvent, which significantly disturbed the original in-out equilibrium of MUJs and drastically switched the entropy and enthalpy changes of conformational interconversion.

Temperature-Driven Planar Chirality Switching of a Pillar[5]arene-Based Molecular Universal Joint.

The study of an enantiopure bicyclic pillar[5]arene-based molecular universal joint (MUJ) by single-crystal X-ray diffraction allowed for the first time the unequivocal assignment of the absolute configuration of a planar chiral pillar[5]arene by circular dichroism spectroscopy. Crucially, the absolute configuration of the MUJ was switched reversibly by temperature, with an accompanying sign inversion of the anisotropy factor that varied by as much as 0.03, which is the largest value ever reported. Mechanistically, the reversible chirality switching of the MUJ is driven by the threading/dethreading motion of the fused ring and hence is dependent on both the size and nature of the ring and the solvent employed, reflecting the critical balance between the self-complexation of the ring by pillar[5]arene, the solvation to the excluded ring, and the inclusion of solvent molecules in the cavity.

Ammonia-driven chirality inversion and enhancement in enantiodifferentiating photocyclodimerization of 2-anthracenecarboxylate mediated by diguanidino-γ-cyclodextrin.

In the supramolecular photocyclodimerization of 2-anthracenecarboxylate mediated by 6(A),6(D)-diguanidino-γ-cyclodextrin (CD), the chiral sense and enantiomeric excess of the photoproduct were dynamic functions of temperature and cosolvent to afford the (M)-anti head-to-head cyclodimer in 64% ee in aqueous methanol at -70 °C but the antipodal (P)-isomer in 86% ee in aqueous ammonia at -85 °C, while the corresponding diamino-γ-CD host did not show such unusual photochirogenic behaviors. The ee landscape was very steep against the temperature and sign-inverted against the ammonia content to reveal the opposite temperature dependence at low and high ammonia contents, for which an altered solvent structure and/or guanidinium-carboxylate interaction mode would be responsible.