•Hybridity and ploidy induce nonadditive gene expression (activation or silencing).•Nonadditive gene expression is largely dependent on epigenetic regulation.•Some epialleles are stably inherited in ...allopolyploid populations during evolution.•Epialleles can be selected and maintained during domestication of polyploid crops.
Polyploidy or whole genome duplication (WGD) is a prominent feature for genome evolution of some animals and all flowering plants, including many important crops such as wheat, cotton, and canola. In autopolyploids, genome duplication often perturbs dosage regulation on biological networks. In allopolyploids, interspecific hybridization could induce genetic and epigenetic changes, the effects of which could be amplified by genome doubling (ploidy changes). Albeit the importance of genetic changes, some epigenetic changes can be stabilized and transmitted as epialleles into the progeny, which are subject to natural selection, adaptation, and domestication. Here we review recent advances for general and specific roles of epigenetic changes in the evolution of flowering plants and domestication of agricultural crops.
A peculiar feature of quantum states is that they may embody so-called projective representations of symmetries rather than ordinary representations. Projective representations of space groups-the ...defining symmetry of crystals-remain largely unexplored. Despite recent advances in artificial crystals, whose intrinsic gauge structures necessarily require a projective description, a unified theory is yet to be established. Here, we establish such a unified theory by exhaustively classifying and representing all 458 projective symmetry algebras of time-reversal-invariant crystals from 17 wallpaper groups in two dimensions-189 of which are algebraically non-equivalent. We discover three physical signatures resulting from projective symmetry algebras, including the shift of high-symmetry momenta, an enforced nontrivial Zak phase, and a spinless eight-fold nodal point. Our work offers a theoretical foundation for the field of artificial crystals and opens the door to a wealth of topological states and phenomena beyond the existing paradigms.
How do we search for the entire family tree of possible intermediate states, without unwanted random guesses, starting from a stationary state on the energy landscape all the way down to energy ...minima? Here we introduce a general numerical method that constructs the pathway map, which guides our understanding of how a physical system moves on the energy landscape. The method identifies the transition state between energy minima and the energy barrier associated with such a state. As an example, we solve the Landau-de Gennes energy incorporating the Dirichlet boundary conditions to model a liquid crystal confined in a square box; we illustrate the basic concepts by examining the multiple stationary solutions and the connected pathway maps of the model.
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Polyploidy is a pervasive evolutionary feature of all flowering plants and some animals, leading to genetic and epigenetic changes that affect gene expression and morphology. DNA methylation changes ...can produce meiotically stable epialleles, which are transmissible through selection and breeding. However, the relationship between DNA methylation and polyploid plant domestication remains elusive.
We report comprehensive epigenomic and functional analyses, including ~12 million differentially methylated cytosines in domesticated allotetraploid cottons and their tetraploid and diploid relatives. Methylated genes evolve faster than unmethylated genes; DNA methylation changes between homoeologous loci are associated with homoeolog-expression bias in the allotetraploids. Significantly, methylation changes induced in the interspecific hybrids are largely maintained in the allotetraploids. Among 519 differentially methylated genes identified between wild and cultivated cottons, some contribute to domestication traits, including flowering time and seed dormancy. CONSTANS (CO) and CO-LIKE (COL) genes regulate photoperiodicity in Arabidopsis. COL2 is an epiallele in allotetraploid cottons. COL2A is hypermethylated and silenced, while COL2D is repressed in wild cottons but highly expressed due to methylation loss in all domesticated cottons tested. Inhibiting DNA methylation activates COL2 expression, and repressing COL2 in cultivated cotton delays flowering.
We uncover epigenomic signatures of domestication traits during cotton evolution. Demethylation of COL2 increases its expression, inducing photoperiodic flowering, which could have contributed to the suitability of cotton for cultivation worldwide. These resources should facilitate epigenetic engineering, breeding, and improvement of polyploid crops.
Subclinical hypothyroidism (SCH) has been shown to be associated with microbiota. However, the association between SCH and oral microbiota has not yet been elucidated. The results of our previous ...clinical studies showed that Prevotella intermedia was abundant in the oral microbiota of SCH patients. This study aimed to investigate the relationship between SCH and oral microbiota, verify the pathogenicity of P. intermedia in SCH, and preliminarily explore the possible mechanism. The SCH mouse model with oral application of P. intermedia was established, and the variance in the mouse oral microbiota and changes in thyroid function and metabolism were detected in mice. Student’s t test and analysis of variance were used for statistical analysis. Oral application of P. intermedia changed the composition of the oral microbiota of SCH mice, which enhanced the damage to the thyroid and decreased the expression of functional genes of the thyroid. Moreover, P. intermedia decreased oxygen consumption and aggravated glucose and lipid metabolism disorders in SCH mice. Glucose tolerance and insulin tolerance decreased, and the triglyceride content of the liver and inflammatory infiltration in adipose tissue increased in SCH mice after P. intermedia stimulation. Mechanistically, P. intermedia increased the proportion of CD4+ T cells in cervical lymph nodes and thyroids in SCH mice. Th1 cells were suggested to play an important role in the pathogenesis of SCH involving P. intermedia. In conclusion, P. intermedia aggravated SCH manifestations, including thyroid dysfunction and glucose and lipid metabolism disorders, by causing immune imbalance in mice. This study sheds new light on the pathogenesis of SCH from the perspective of oral microbiota.
Nontrivial low-energy excitations of crystalline solids have insightfully strengthened understanding of elementary particles in quantum field theory. Usually, topological quasiparticles are mainly ...focused on fermions in topological semimetals. We alternatively show by first-principles calculations and symmetry analysis that ideal type-II Weyl phonons are present in zinc-blende cadmium telluride, a well-known II-VI semiconductor. Importantly, these type-II Weyl phonons originate from the inversion between the longitudinal acoustic and transverse optical branches. Symmetry guarantees that the type-II Weyl points lie along the high-symmetry lines at the boundaries of the Brillouin zone even with a breaking of inversion symmetry, exhibiting the robustness of protected phonon features. The nontrivial phonon surface states and surface arcs projected on the semifinite (001) and (111) surfaces are investigated. The phonon surface arcs connecting the Weyl points with opposite chirality, guaranteed to be very long, are clearly visible. We not only offer a promising candidate for studying type-II Weyl phonons but also provide a route to realize symmetry-protected nontrivial phonons and related applications in realistic materials.
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There is a strong desire to replace or complement aqueous and organic electrolytes by ionic liquids (ILs) in electrochemical energy storage (EES) devices to achieve high operating voltages and hence ...high energy capacity. ILs are regarded as the inherent and competitive electrolytes since they were introduced to the electrochemical research community because they can overcome many disadvantages of the conventional aqueous and organic electrolytes, such as narrow potential windows, volatility, and flammability. This paper reviews critically the recent literatures of IL-based electrolytes used in supercapacitor, supercapattery, and micro-supercapacitor. Supercapattery is a generic term for various hybrid devices combining the merits of rechargeable battery and supercapacitor and often shows capacitive behavior. Fundamentals of supercapattery are briefly explained with typical examples. Micro-supercapacitor falls in the same scope of supercapacitor and supercapattery and shares the same fundamental concerns besides topology or structure. The future of IL-based electrolytes for the capacitive EES devices are also prospected.
We investigate the current-induced switching of the Néel order in NiO(001)/Pt heterostructures, which is manifested electrically via the spin Hall magnetoresistance. Significant reversible changes in ...the longitudinal and transverse resistances are found at room temperature for a current threshold lying in the range of 10^{7} A/cm^{2}. The order-parameter switching is ascribed to the antiferromagnetic dynamics triggered by the (current-induced) antidamping torque, which orients the Néel order towards the direction of the writing current. This is in stark contrast to the case of antiferromagnets such as Mn_{2}Au and CuMnAs, where fieldlike torques induced by the Edelstein effect drive the Néel switching, therefore resulting in an orthogonal alignment between the Néel order and the writing current. Our findings can be readily generalized to other biaxial antiferromagnets, providing broad opportunities for all-electrical writing and readout in antiferromagnetic spintronics.
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