Exposing the Oxygen-Centered Radical Character of the Tetraoxido Ruthenium(VIII) Cation [RuO4 ]. Chemphyschem 2023;24:e202300390. [PMID: 37589334 DOI: 10.1002/cphc.202300390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

The tetraoxido ruthenium(VIII) radical cation, [RuO4 ]+ , should be a strong oxidizing agent, but has been difficult to produce and investigate so far. In our X-ray absorption spectroscopy study, in combination with quantum-chemical calculations, we show that [RuO4 ]+ , produced via oxidation of ruthenium cations by ozone in the gas phase, forms the oxygen-centered radical ground state. The oxygen-centered radical character of [RuO4 ]+ is identified by the chemical shift at the ruthenium M3 edge, indicative of ruthenium(VIII), and by the presence of a characteristic low-energy transition at the oxygen K edge, involving an oxygen-centered singly-occupied molecular orbital, which is suppressed when the oxygen-centered radical is quenched by hydrogenation of [RuO4 ]+ to the closed-shell [RuO4 H]+ ion. Hydrogen-atom abstraction from methane is calculated to be only slightly less exothermic for [RuO4 ]+ than for [OsO4 ]+ .

Impact of Electric Field Disorder on Broken-Symmetry States in Ultraclean Bilayer Graphene

Bilayer graphene (BLG) has multiple internal degrees of freedom and a constant density of states down to the charge neutrality point when trigonal warping is ignored. Consequently, it is susceptible to various competing ground states. However, a coherent experimental determination of the ground state has been challenging due to the interaction-disorder interplay. Here we present an extensive transport study in a series of dually gated freestanding BLG devices and identify the layer-antiferromagnet as the ground state with a continuous strength across all devices. This strength correlates with the width of the state in the electric field. We systematically identify electric-field disorder─spatial variations in the interlayer potential difference─as the main source responsible for the observations. Our results pinpoint for the first time the importance of electric-field disorder on spontaneous symmetry breaking in BLG and solve a long-standing debate on its ground state. The electric-field disorder should be universal to all 2D materials.

Production of O Radicals from Cavitation Bubbles under Ultrasound

In the present review, the production of O radicals (oxygen atoms) in acoustic cavitation is focused. According to numerical simulations of chemical reactions inside a bubble using an ODE model which has been validated through studies of single-bubble sonochemistry, not only OH radicals but also appreciable amounts of O radicals are generated inside a heated bubble at the violent collapse by thermal dissociation of water vapor and oxygen molecules. The main oxidant created inside an air bubble is O radicals when the bubble temperature is above about 6500 K for a gaseous bubble. However, the concentration and lifetime of O radicals in the liquid water around the cavitation bubbles are unknown at present. Whether O radicals play some role in sonochemical reactions in the liquid phase, which are usually thought to be dominated by OH radicals and H₂O₂, should be studied in the future.

Naive Pluripotent Stem Cells Exhibit Phenotypic Variability that Is Driven by Genetic Variation

Variability among pluripotent stem cell (PSC) lines is a prevailing issue that hampers not only experimental reproducibility but also large-scale applications and personalized cell-based therapy. This variability could result from epigenetic and genetic factors that influence stem cell behavior. Naive culture conditions minimize epigenetic fluctuation, potentially overcoming differences in PSC line differentiation potential. Here we derived PSCs from distinct mouse strains under naive conditions and show that lines from distinct genetic backgrounds have divergent differentiation capacity, confirming a major role for genetics in PSC phenotypic variability. This is explained in part through inconsistent activity of extra-cellular signaling, including the Wnt pathway, which is modulated by specific genetic variants. Overall, this study shows that genetic background plays a dominant role in driving phenotypic variability of PSCs.

β-Catenin and Associated Proteins Regulate Lineage Differentiation in Ground State Mouse Embryonic Stem Cells

Mouse embryonic stem cells (ESCs) cultured in defined medium resemble the pre-implantation epiblast in the ground state, with full developmental capacity including the germline. β-Catenin is required to maintain ground state pluripotency in mouse ESCs, but its exact role is controversial. Here, we reveal a Tcf3-independent role of β-catenin in restraining germline and somatic lineage differentiation genes. We show that β-catenin binds target genes with E2F6 and forms a complex with E2F6 and HMGA2 or E2F6 and HP1γ. Our data indicate that these complexes help β-catenin restrain and fine-tune germ cell and neural developmental potential. Overall, our data reveal a previously unappreciated role of β-catenin in preserving lineage differentiation integrity in ground state ESCs.

•

β-Catenin depletion irreversibly compromised lineage development of ground state ESCs

•

TCF3-independent role of β-catenin in determining lineage differentiation potential

•

E2F6, HP1γ, and HMGA2 are β-catenin interaction partners and co-bound to target genes

•

β-Catenin and protein partners fine-tune germline and neural development potential

DNA Methylation Directs Polycomb-Dependent 3D Genome Re-organization in Naive Pluripotency

The DNA hypomethylation that occurs when embryonic stem cells (ESCs) are directed to the ground state of naive pluripotency by culturing in two small molecule inhibitors (2i) results in redistribution of polycomb (H3K27me3) away from its target loci. Here, we demonstrate that 3D genome organization is also altered in 2i, with chromatin decompaction at polycomb target loci and a loss of long-range polycomb interactions. By preventing DNA hypomethylation during the transition to the ground state, we are able to restore to ESC in 2i the H3K27me3 distribution, as well as polycomb-mediated 3D genome organization that is characteristic of primed ESCs grown in serum. However, these cells retain the functional characteristics of 2i ground-state ESCs. Our findings demonstrate the central role of DNA methylation in shaping major aspects of 3D genome organization but caution against assuming causal roles for the epigenome and 3D genome in gene regulation and function in ESCs.

Quantitative Multiplexed ChIP Reveals Global Alterations that Shape Promoter Bivalency in Ground State Embryonic Stem Cells

To understand the epigenomic foundation of naive pluripotency, we implement a quantitative multiplexed chromatin immunoprecipitation sequencing (ChIP-seq) method comparing mouse embryonic stem cells (ESCs) grown in 2i versus 2i/serum and serum conditions. MINUTE-ChIP has a large linear dynamic range for accurately quantifying relative differences in genome-wide histone modification patterns across multiple pooled samples. We find compelling evidence for a broad H3 lysine 27 trimethylation (H3K27me3) hypermethylation of the genome, while bivalent promoters stably retain high H3K27me3 levels in 2i. We show that DNA hypomethylation, as observed in 2i, is a contributor to genome-wide gain of H3K27me3, while active demethylation by JMJD3/UTX counteracts further accumulation of H3K27me3. In parallel, we find hypomethylation of H3 lysine 4 trimethylation (H3K4me3), particularly at bivalent promoters, to be a characteristic of the 2i ground state. Serum stimulates H3K4me3 independent of GSK-3b and ERK signaling, suggesting that low H3K4me3 and high H3K27me3 levels at bivalent promoters are a product of two independent mechanisms that safeguard naive pluripotency.

Approximating Ground States by Neural Network Quantum States

Motivated by the Carleo’s work (Science, 2017, 355: 602), we focus on finding the neural network quantum statesapproximation of the unknown ground state of a given Hamiltonian H in terms of the best relative error and explore the influences of sum, tensor product, local unitary of Hamiltonians on the best relative error. Besides, we illustrate our method with some examples.

Investigation of Finite-Size 2D Ising Model with a Noisy Matrix of Spin-Spin Interactions

We analyze changes in the thermodynamic properties of a spin system when it passes from the classical two-dimensional Ising model to the spin glass model, where spin-spin interactions are random in their values and signs. Formally, the transition reduces to a gradual change in the amplitude of the multiplicative noise (distributed uniformly with a mean equal to one) superimposed over the initial Ising matrix of interacting spins. Considering the noise, we obtain analytical expressions that are valid for lattices of finite sizes. We compare our results with the results of computer simulations performed for square N = L × L lattices with linear dimensions L = 50 ÷ 1000. We find experimentally the dependencies of the critical values (the critical temperature, the internal energy, entropy and the specific heat) as well as the dependencies of the energy of the ground state and its magnetization on the amplitude of the noise. We show that when the variance of the noise reaches one, there is a jump of the ground state from the fully correlated state to an uncorrelated state and its magnetization jumps from 1 to 0. In the same time, a phase transition that is present at a lower level of the noise disappears.

Origin and Manipulation of Stable Vortex Ground States in Permalloy Nanotubes

We present a detailed study on the static magnetic properties of individual permalloy nanotubes (NTs) with hexagonal cross-sections. Anisotropic magnetoresistance (AMR) measurements and scanning transmission X-ray microscopy (STXM) are used to investigate their magnetic ground states and its stability. We find that the magnetization in zero applied magnetic field is in a very stable vortex state. Its origin is attributed to a strong growth-induced anisotropy with easy axis perpendicular to the long axis of the tubes. AMR measurements of individual NTs in combination with micromagnetic simulations allow the determination of the magnitude of the growth-induced anisotropy for different types of NT coatings. We show that the strength of the anisotropy can be controlled by introducing a buffer layer underneath the magnetic layer. The magnetic ground states depend on the external magnetic field history and are directly imaged using STXM. Stable vortex domains can be introduced by external magnetic fields and can be erased by radio-frequency magnetic fields applied at the center of the tubes via a strip line antenna.

Nono, a Bivalent Domain Factor, Regulates Erk Signaling and Mouse Embryonic Stem Cell Pluripotency

Nono is a component of the para-speckle, which stores and processes RNA. Mouse embryonic stem cells (mESCs) lack para-speckles, leaving the function of Nono in mESCs unclear. Here, we find that Nono functions as a chromatin regulator cooperating with Erk to regulate mESC pluripotency. We report that Nono loss results in robust self-renewing mESCs with epigenomic and transcriptomic features resembling the 2i (GSK and Erk inhibitors)-induced "ground state." Erk interacts with and is required for Nono localization to a subset of bivalent genes that have high levels of poised RNA polymerase. Nono loss compromises Erk activation and RNA polymerase poising at its target bivalent genes in undifferentiated mESCs, thus disrupting target gene activation and differentiation. These findings argue that Nono collaborates with Erk signaling to regulate the integrity of bivalent domains and mESC pluripotency.

Stat3 phosphorylation is required for embryonic stem cells ground state maintenance in 2i culture media

Embryonic stem cells (ES cells) can be maintained its undifferentiated state with feeder cells or LIF, which can activate Jak/Stat3 pathway. Recently, it has been reported a new culture condition comprising serum-free medium with ERK and GSK3β inhibitors (2i) could drive ES cells into a state of pluripotency more like inner cell mass (ICM) in mouse blastocysts called ground state. However, although 2i could sustain ES cells self-renewal, LIF is routinely added. The roles of Stat3 activation are still unclear now. Here we investigated whether Jak/Stat3 might also contribute to the induction of ground state pluripotency. We introduced a lentiviral construct with 7-repeat Stat3-binding sequence to drive Renilla luciferase into ES cells, which can be used as a reporter to detect Stat3 activation by noninvasive bioluminescence imaging. Using this ES cells, we investigated the role of Stat3 activation in ground state maintenance. The results showed that Stat3 could be activated by 2i. Stattic, a chemical inhibitor of Stat3 phosphorylation, could effectively inhibit Stat3 activation in ES cells. When Stat3 activation was suppressed, ground state related genes were down regulated, and ES cells could not be maintained the ground state pluripotency even in 2i medium. All of these results indicate Stat3 activation is required in ground state maintenance.

Sampling of Glycan-Bound Conformers by the Anti-HIV Lectin Oscillatoria agardhii agglutinin in the Absence of Sugar

Lectins from different sources have been shown to interfere with HIV infection by binding to the sugars of viral-envelope glycoproteins. Three-dimensional atomic structures of a number of HIV-inactivating lectins have been determined, both as free proteins and in glycan-bound forms. However, details on the mechanism of recognition and binding to sugars are elusive. Herein we focus on the anti-HIV lectin OAA from Oscillatoria agardhii: We show that in the absence of sugars in solution, both the sugar-free and sugar-bound protein conformations that were observed in the X-ray crystal structures exist as conformational substates. Our results suggest that glycan recognition occurs by conformational selection within the ground state; this model differs from the popular "excited-state" model. Our findings provide further insight into molecular recognition of the major receptor on the HIV virus by OAA. These details can potentially be used for the optimization and/or development of preventive anti-HIV therapeutics.

Current state of the opportunities for derivation of germ-like cells from pluripotent stem cells: are you a man, or a mouse?

The concept of pluripotency as a prerogative of cells of early mammal embryos and cultured embryonic stem cells (ESC) has been invalidated with the advent of induced pluripotent stem cells. Later, it became clear that the ability to generate all cell types of the adult organism is also a questionable aspect of pluripotency, as there are cell types, such as germ cells, which are difficult to produce from pluripotent stem cells. Recently it has been proposed that there are at least two different states of pluripotency; namely, the naïve, or ground state, and the primed state, which may differ radically in terms of timeline of existence, signalling mechanisms, cell properties, capacity for differentiation into different cell types, etc. Germ-like male and female rodent cells have been successfully produced in vitro from ESC and induced pluripotent stem cells. The attempts to derive primate primordial germ cells (PGC) and germ cells in vitro from pluripotent stem cells, however, still have a low success rate, especially with the female germline. The paper reviews the properties of rodent and primate ESC with regard to their capacity for differentiation in vitro to germ-like cells, outlining the possible caveats to derivation of PGC and germ cells from primate and human pluripotent cells.

Combining fMRI with EEG and MEG in order to relate patterns of brain activity to cognition

The common factor that underlies several types of functional brain imaging is the electric current of masses of dendrites. The prodigious demands for the energy that is required to drive the dendritic currents are met by hemodynamic and metabolic responses that are visualized with fMRI and PET techniques. The high current densities in parallel dendritic shafts and the broad distributions of the loop currents outside the dendrites generate both the scalp EEG and the magnetic fields seen in the MEG. The measurements of image intensities and potential fields provide state variables for modeling. The relationships between the intensities of current density and the electric, magnetic, and hemodynamic state variables are complex and far from proportionate. The state variables are complementary, because the information they convey comes from differing albeit overlapping neural populations, so that efforts to cross-validate localization of neural activity relating to specified cognitive behaviors have not always been successful. We propose an alternative way to use the three methods in combination through studies of hemisphere-wide, high-resolution spatiotemporal patterns of neural activity recorded non-invasively and analyzed with multivariate statistics. Success in this proposed endeavor requires specification of what patterns to look for. At the present level of understanding, an appropriate pattern is any significant departure from random noise in the spectral, temporal and spatial domains that can be scaled into the coarse-graining of time by fMRI/BOLD and the coarse-graining of space by EEG and MEG. Here the requisite patterns are predicted to be large-scale spatial amplitude modulation (AM) of synchronized neuronal signals in the beta and gamma ranges that are coordinated but not correlated with fMRI intensities.