Phase-ordering kinetics of the asymmetric Coulomb glass model.

We present results for phase-ordering kinetics in the Coulomb glass (CG) model, which describes electrons on a lattice with unscreened Coulombic repulsion. The filling factor is denoted by K∈[0,1]. For a square lattice with K=0.5 (symmetric CG), the ground state is a checkerboard with alternating electrons and holes. In this paper, we focus on the asymmetric CG where K≲0.5, i.e., the ground state is checkerboard-like with excess holes distributed uniformly. There is no explicit quenched disorder in our system, though the Coulombic interaction gives rise to frustration. We find that the evolution morphology is in the same dynamical universality class as the ordering ferromagnet. Further, the domain growth law is slightly slower than the Lifshitz-Cahn-Allen law, L(t)∼t^{1/2}, i.e., the growth exponent is underestimated. We speculate that this could be a signature of logarithmic growth in the asymptotic regime.

ZFP281 controls transcriptional and epigenetic changes promoting mouse pluripotent state transitions via DNMT3 and TET1.

The progression from naive through formative to primed in vitro pluripotent stem cell states recapitulates epiblast development in vivo during the peri-implantation period of mouse embryo development. Activation of the de novo DNA methyltransferases and reorganization of transcriptional and epigenetic landscapes are key events that occur during these pluripotent state transitions. However, the upstream regulators that coordinate these events are relatively underexplored. Here, using Zfp281 knockout mouse and degron knockin cell models, we identify the direct transcriptional activation of Dnmt3a/3b by ZFP281 in pluripotent stem cells. Chromatin co-occupancy of ZFP281 and DNA hydroxylase TET1, which is dependent on the formation of R-loops in ZFP281-targeted gene promoters, undergoes a "high-low-high" bimodal pattern regulating dynamic DNA methylation and gene expression during the naive-formative-primed transitions. ZFP281 also safeguards DNA methylation in maintaining primed pluripotency. Our study demonstrates a previously unappreciated role for ZFP281 in coordinating DNMT3A/3B and TET1 functions to promote pluripotent state transitions.

Highly cooperative chimeric super-SOX induces naive pluripotency across species.

Our understanding of pluripotency remains limited: iPSC generation has only been established for a few model species, pluripotent stem cell lines exhibit inconsistent developmental potential, and germline transmission has only been demonstrated for mice and rats. By swapping structural elements between Sox2 and Sox17, we built a chimeric super-SOX factor, Sox2-17, that enhanced iPSC generation in five tested species: mouse, human, cynomolgus monkey, cow, and pig. A swap of alanine to valine at the interface between Sox2 and Oct4 delivered a gain of function by stabilizing Sox2/Oct4 dimerization on DNA, enabling generation of high-quality OSKM iPSCs capable of supporting the development of healthy all-iPSC mice. Sox2/Oct4 dimerization emerged as the core driver of naive pluripotency with its levels diminished upon priming. Transient overexpression of the SK cocktail (Sox+Klf4) restored the dimerization and boosted the developmental potential of pluripotent stem cells across species, providing a universal method for naive reset in mammals.

Physics of large thermoelectric power factors in SnSe nanoflakes in mid-temperature range.

We have theoretically investigated the underlying physics of observed high electrical conductivity (σ), simultaneous increase of σ and Seebeck coefficient (S) with temperature, and large power factors (PFs) in nominally undoped SnSe nanoflakes sintered at different temperatures, reported recently in Mandavaet al(2022Nanotechnology33155710). Given the fact that S and σ show unusual temperature trends and that the undoped SnSe samples are highly porous and disordered, the conventional Boltzmann theory does not appear to be an appropriate model to describe their transport properties. We have, instead, used a strong disorder model based on percolation theory where charge and energy transport take place through hopping between localized states to understand these observations. Our model is able to explain the observed temperature dependence of σ and S with temperature. Large σ can be explained by a high density of localized states and a large hopping rate. The sample sintered at a higher temperature has lower disorder (σDOS) and higher hopping rate (1/τ0). We findσDOS= 0.151 eV and 1/τ0= 0.143 × 1015s-1for sample sintered at 673 K andσDOS= 0.044 eV and 1/τ0= 2.023 × 1015s-1for sample sintered at 703 K. These values are comparable to the reported values of transition frequencies, confirming that the dominant charge transport mechanism in these SnSe nanoflakes is hopping transport. Finally, we suggest that hopping transport via localized states can result in enhanced thermoelectric properties in disordered polycrystalline materials.

Mild sleep restriction increases endothelial oxidative stress in female persons.

Sleep restriction is associated with increased cardiovascular risk, which is more pronounced in female than male persons. We reported recently first causal evidence that mild, prolonged sleep restriction mimicking "real-life" conditions impairs endothelial function, a key step in the development and progression of cardiovascular disease, in healthy female persons. However, the underlying mechanisms are unclear. In model organisms, sleep restriction increases oxidative stress and upregulates antioxidant response via induction of the antioxidant regulator nuclear factor (erythroid-derived 2)-like 2 (Nrf2). Here, we assessed directly endothelial cell oxidative stress and antioxidant responses in healthy female persons (n = 35) after 6 weeks of mild sleep restriction (1.5 h less than habitual sleep) using randomized crossover design. Sleep restriction markedly increased endothelial oxidative stress without upregulating antioxidant response. Using RNA-seq and a predicted protein-protein interaction database, we identified reduced expression of endothelial Defective in Cullin Neddylation-1 Domain Containing 3 (DCUN1D3), a protein that licenses Nrf2 antioxidant responses, as a mediator of impaired endothelial antioxidant response in sleep restriction. Thus, sleep restriction impairs clearance of endothelial oxidative stress that over time increases cardiovascular risk.Trial Registration: NCT02835261 .

Insights into the Glutamatergic and GABAergic Connections in the Conductance-Based Model of Subthalamic Nucleus in Hyperdirect Pathway.

Introduction: This study aimed to analyze the spiking patterns of subthalamic nucleus and globus pallidus coupling in hyperdirect pathway in healthy primates and in Parkinson's disease using a conductance-based model. The effect of calcium membrane potential has also been investigated. Materials and Methods: System of coupled differential equation arising from the conductance-based model has been simulated using ODE45 in MATLAB 7.14 to analyze the spiking patterns. Results: Analysis of spiking patterns suggests that subthalamic nucleus with synaptic input from globus pallidus in hyperdirect pathways is capable of showing two types of spiking pattern - irregular and rhythmic. Characterization of spiking patterns in healthy and Parkinson condition has been done based on their frequency, trend, and spiking rate. Results indicate that rhythmic patterns does not account for Parkinson's disease. Further, calcium membrane potential is an important parameter to target for identifying the cause of this disease. Conclusion: This work demonstrates that subthalamic nucleus and globus pallidus coupling in hyperdirect pathway can account for Parkinson's symptoms. However, the entire process of excitations and inhibition caused by glutamate and GABA receptors is limited by the timing of depolarization of the model. There is improvement in the correlation between healthy and Parkinson's patterns by increase in calcium membrane potential, however, for a limited time.

The pluripotency factor Tex10 finetunes Wnt signaling for PGC and male germline development.

Testis-specific transcript 10 (Tex10) is a critical factor for pluripotent stem cell maintenance and preimplantation development. Here, we dissect its late developmental roles in primordial germ cell (PGC) specification and spermatogenesis using cellular and animal models. We discover that Tex10 binds the Wnt negative regulator genes, marked by H3K4me3, at the PGC-like cell (PGCLC) stage in restraining Wnt signaling. Depletion and overexpression of Tex10 hyperactivate and attenuate the Wnt signaling, resulting in compromised and enhanced PGCLC specification efficiency, respectively. Using the Tex10 conditional knockout mouse models combined with single-cell RNA sequencing, we further uncover critical roles of Tex10 in spermatogenesis with Tex10 loss causing reduced sperm number and motility associated with compromised round spermatid formation. Notably, defective spermatogenesis in Tex10 knockout mice correlates with aberrant Wnt signaling upregulation. Therefore, our study establishes Tex10 as a previously unappreciated player in PGC specification and male germline development by fine-tuning Wnt signaling.

ZFP281 coordinates DNMT3 and TET1 for transcriptional and epigenetic control in pluripotent state transitions.

The progression from naive through formative to primed in vitro pluripotent stem cell states recapitulates the development of the epiblast in vivo during the peri-implantation period of mammalian development. Activation of the de novo DNA methyltransferases and reorganization of transcriptional and epigenetic landscapes are key events occurring during these pluripotent state transitions. However, the upstream regulators that coordinate these events are relatively underexplored. Here, using Zfp281 knockout mouse and degron knock-in cell models, we uncover the direct transcriptional activation of Dnmt3a/3b by ZFP281 in pluripotent stem cells. Chromatin co-occupancy of ZFP281 and DNA hydroxylase TET1, dependent on the formation of R loops in ZFP281-targeted gene promoters, undergoes a "high-low-high" bimodal pattern regulating dynamic DNA methylation and gene expression during the naïive-formative-primed transitions. ZFP281 also safeguards DNA methylation in maintaining primed pluripotency. Our study demonstrates a previously unappreciated role for ZFP281 in coordinating DNMT3A/3B and TET1 functions to promote pluripotent state transitions.

An RNAi screen of RNA helicases identifies eIF4A3 as a regulator of embryonic stem cell identity.

RNA helicases are involved in multiple steps of RNA metabolism to direct their roles in gene expression, yet their functions in pluripotency control remain largely unexplored. Starting from an RNA interference (RNAi) screen of RNA helicases, we identified that eIF4A3, a DEAD-box (Ddx) helicase component of the exon junction complex (EJC), is essential for the maintenance of embryonic stem cells (ESCs). Mechanistically, we show that eIF4A3 post-transcriptionally controls the pluripotency-related cell cycle regulators and that its depletion causes the loss of pluripotency via cell cycle dysregulation. Specifically, eIF4A3 is required for the efficient nuclear export of Ccnb1 mRNA, which encodes Cyclin B1, a key component of the pluripotency-promoting pathway during the cell cycle progression of ESCs. Our results reveal a previously unappreciated role for eIF4A3 and its associated EJC in maintaining stem cell pluripotency through post-transcriptional control of the cell cycle.

Comparative functional genomics identifies unique molecular features of EPSCs.

Extended pluripotent or expanded potential stem cells (EPSCs) possess superior developmental potential to embryonic stem cells (ESCs). However, the molecular underpinning of EPSC maintenance in vitro is not well defined. We comparatively studied transcriptome, chromatin accessibility, active histone modification marks, and relative proteomes of ESCs and the two well-established EPSC lines to probe the molecular foundation underlying EPSC developmental potential. Despite some overlapping transcriptomic and chromatin accessibility features, we defined sets of molecular signatures that distinguish EPSCs from ESCs in transcriptional and translational regulation as well as metabolic control. Interestingly, EPSCs show similar reliance on pluripotency factors Oct4, Sox2, and Nanog for self-renewal as ESCs. Our study provides a rich resource for dissecting the regulatory network that governs the developmental potency of EPSCs and exploring alternative strategies to capture totipotent stem cells in culture.

A TET1-PSPC1-Neat1 molecular axis modulates PRC2 functions in controlling stem cell bivalency.

TET1 maintains hypomethylation at bivalent promoters through its catalytic activity in embryonic stem cells (ESCs). However, TET1 catalytic activity-independent function in regulating bivalent genes is not well understood. Using a proteomics approach, we map the TET1 interactome in ESCs and identify PSPC1 as a TET1 partner. Genome-wide location analysis reveals that PSPC1 functionally associates with TET1 and Polycomb repressive complex-2 (PRC2). We establish that PSPC1 and TET1 repress, and the lncRNA Neat1 activates, bivalent gene expression. In ESCs, Neat1 is preferentially bound to PSPC1 alongside its PRC2 association at bivalent promoters. During the ESC-to-epiblast-like stem cell (EpiLC) transition, PSPC1 and TET1 maintain PRC2 chromatin occupancy at bivalent gene promoters, while Neat1 facilitates the activation of certain bivalent genes by promoting PRC2 binding to their mRNAs. Our study demonstrates a TET1-PSPC1-Neat1 molecular axis that modulates PRC2-binding affinity to chromatin and bivalent gene transcripts in controlling stem cell bivalency.

Pursuing totipotency: authentic totipotent stem cells in culture.

Totipotent stem cells are transiently occurring in vivo cells that can form all cell types of the embryo including placenta, with their in vitro counterparts being actively pursued. Subsequently, totipotent-like cells are established with variable robustness and biological relevance. Here, we summarize current progress on capturing these cells in culture.

Relaxation dynamics of the three-dimensional Coulomb glass model.

In this paper, we analyze the dynamics of the Coulomb glass lattice model in three dimensions near a local equilibrium state by using mean-field approximations. We specifically focus on understanding the role of localization length (ξ) and the temperature (T) in the regime where the system is not far from equilibrium. We use the eigenvalue distribution of the dynamical matrix to characterize relaxation laws as a function of localization length at low temperatures. The variation of the minimum eigenvalue of the dynamical matrix with temperature and localization length is discussed numerically and analytically. Our results demonstrate the dominant role played by the localization length on the relaxation laws. For very small localization lengths, we find a crossover from exponential relaxation at long times to a logarithmic decay at intermediate times. No logarithmic decay at the intermediate times is observed for large localization lengths.

Directed Evolution of an Enhanced POU Reprogramming Factor for Cell Fate Engineering.

Transcription factor-driven cell fate engineering in pluripotency induction, transdifferentiation, and forward reprogramming requires efficiency, speed, and maturity for widespread adoption and clinical translation. Here, we used Oct4, Sox2, Klf4, and c-Myc driven pluripotency reprogramming to evaluate methods for enhancing and tailoring cell fate transitions, through directed evolution with iterative screening of pooled mutant libraries and phenotypic selection. We identified an artificially evolved and enhanced POU factor (ePOU) that substantially outperforms wild-type Oct4 in terms of reprogramming speed and efficiency. In contrast to Oct4, not only can ePOU induce pluripotency with Sox2 alone, but it can also do so in the absence of Sox2 in a three-factor ePOU/Klf4/c-Myc cocktail. Biochemical assays combined with genome-wide analyses showed that ePOU possesses a new preference to dimerize on palindromic DNA elements. Yet, the moderate capacity of Oct4 to function as a pioneer factor, its preference to bind octamer DNA and its capability to dimerize with Sox2 and Sox17 proteins remain unchanged in ePOU. Compared with Oct4, ePOU is thermodynamically stabilized and persists longer in reprogramming cells. In consequence, ePOU: 1) differentially activates several genes hitherto not implicated in reprogramming, 2) reveals an unappreciated role of thyrotropin-releasing hormone signaling, and 3) binds a distinct class of retrotransposons. Collectively, these features enable ePOU to accelerate the establishment of the pluripotency network. This demonstrates that the phenotypic selection of novel factor variants from mammalian cells with desired properties is key to advancing cell fate conversions with artificially evolved biomolecules.

JMJD3 acts in tandem with KLF4 to facilitate reprogramming to pluripotency.

The interplay between the Yamanaka factors (OCT4, SOX2, KLF4 and c-MYC) and transcriptional/epigenetic co-regulators in somatic cell reprogramming is incompletely understood. Here, we demonstrate that the histone H3 lysine 27 trimethylation (H3K27me3) demethylase JMJD3 plays conflicting roles in mouse reprogramming. On one side, JMJD3 induces the pro-senescence factor Ink4a and degrades the pluripotency regulator PHF20 in a reprogramming factor-independent manner. On the other side, JMJD3 is specifically recruited by KLF4 to reduce H3K27me3 at both enhancers and promoters of epithelial and pluripotency genes. JMJD3 also promotes enhancer-promoter looping through the cohesin loading factor NIPBL and ultimately transcriptional elongation. This competition of forces can be shifted towards improved reprogramming by using early passage fibroblasts or boosting JMJD3's catalytic activity with vitamin C. Our work, thus, establishes a multifaceted role for JMJD3, placing it as a key partner of KLF4 and a scaffold that assists chromatin interactions and activates gene transcription.

IL10RA modulates crizotinib sensitivity in NPM1-ALK+ anaplastic large cell lymphoma.

Anaplastic large cell lymphoma (ALCL) is a T-cell malignancy predominantly driven by a hyperactive anaplastic lymphoma kinase (ALK) fusion protein. ALK inhibitors, such as crizotinib, provide alternatives to standard chemotherapy with reduced toxicity and side effects. Children with lymphomas driven by nucleophosmin 1 (NPM1)-ALK fusion proteins achieved an objective response rate to ALK inhibition therapy of 54% to 90% in clinical trials; however, a subset of patients progressed within the first 3 months of treatment. The mechanism for the development of ALK inhibitor resistance is unknown. Through genome-wide clustered regularly interspaced short palindromic repeats (CRISPR) activation and knockout screens in ALCL cell lines, combined with RNA sequencing data derived from ALK inhibitor-relapsed patient tumors, we show that resistance to ALK inhibition by crizotinib in ALCL can be driven by aberrant upregulation of interleukin 10 receptor subunit alpha (IL10RA). Elevated IL10RA expression rewires the STAT3 signaling pathway, bypassing otherwise critical phosphorylation by NPM1-ALK. IL-10RA expression does not correlate with response to standard chemotherapy in pediatric patients, suggesting that a combination of crizotinib and chemotherapy could prevent ALK inhibitor resistance-specific relapse.

Cancer-associated missense mutations enhance the pluripotency reprogramming activity of OCT4 and SOX17.

The functional consequences of cancer-associated missense mutations are unclear for the majority of proteins. We have previously demonstrated that the activity of SOX and Pit-Oct-Unc (POU) family factors during pluripotency reprogramming can be switched and enhanced with rationally placed point mutations. Here, we interrogated cancer mutation databases and identified recurrently mutated positions at critical structural interfaces of the DNA-binding domains of paralogous SOX and POU family transcription factors. Using the conversion of mouse embryonic fibroblasts to induced pluripotent stem cells as functional readout, we identified several gain-of-function mutations that enhance pluripotency reprogramming by SOX2 and OCT4. Wild-type SOX17 cannot support reprogramming but the recurrent missense mutation SOX17-V118M is capable of inducing pluripotency. Furthermore, SOX17-V118M promotes oncogenic transformation, enhances thermostability and elevates cellular protein levels of SOX17. We conclude that the mutational profile of SOX and POU family factors in cancer can guide the design of high-performance reprogramming factors. Furthermore, we propose cellular reprogramming as a suitable assay to study the functional impact of cancer-associated mutations.

Probing the path for achieving a broad temperature plateau of the figure of merit in thermoelectric nanocomposite materials.

The efficiency of a thermoelectric device depends directly on the average figure of merit (zT) of the material. A high average zT requires a broad temperature plateau with a high zT, but state-of-the-art thermoelectric materials display a peaked zT over a narrow temperature range due to a strong temperature dependence of transport properties. In this work, using Boltzmann transport theory, we systematically investigate the underlying physics and propose a strategy for attaining a broad temperature plateau of zT through proper engineering of the interfacial barrier height in PbTe nanocomposite material. The optimized barrier height (U constantzT) not only enhances the zT but also maintains its high value over a wide temperature range [Tmin :Tmax ]. It has been found that for p = 2.8 × 1020 cm-3, the U constantzT is 0.112 eV at which zT varies between 1.9-2.14 over a wide temperature range of 550-850 K, resulting in a high average zT of 2.02 in comparison to a bulk value of 1.22. Also, for p = 5 × 1019 cm-3, UconstantzT is 0.102 eV at which zT varies between 1.046-1.435 for a temperature range of 300-600K, resulting in a high average zT of 1.27 over a bulk value of 0.844. The above results show that the range [Tmin :Tmax ] depends on carrier concentration which, in turn, determines the position of the Fermi level (Ef ) and Fermi window at Tmin and Tmax . To obtain a broad temperature plateau of zT, the findings show that at Tmin, Ef should lie inside the band and zT should show strong variation with barrier height, whereas at Tmax , Ef should lie in the band gap and zT should have little variation with barrier height. This trend allows us to choose UconstantzT which synergistically optimizes the transport properties at Tmin with Tmax to give a broad temperature plateau of zT. This work proposes a new advantage of interfacial scattering which enhances the average zT and also provides necessary guidelines to experimentalists for synthesizing a highly efficient thermoelectric device.

Pluripotency reprogramming by competent and incompetent POU factors uncovers temporal dependency for Oct4 and Sox2.

Oct4, along with Sox2 and Klf4 (SK), can induce pluripotency but structurally similar factors like Oct6 cannot. To decode why Oct4 has this unique ability, we compare Oct4-binding, accessibility patterns and transcriptional waves with Oct6 and an Oct4 mutant defective in the dimerization with Sox2 (Oct4defSox2). We find that initial silencing of the somatic program proceeds indistinguishably with or without Oct4. Oct6 mitigates the mesenchymal-to-epithelial transition and derails reprogramming. These effects are a consequence of differences in genome-wide binding, as the early binding profile of Oct4defSox2 resembles Oct4, whilst Oct6 does not bind pluripotency enhancers. Nevertheless, in the Oct6-SK condition many otherwise Oct4-bound locations become accessible but chromatin opening is compromised when Oct4defSox2 occupies these sites. We find that Sox2 predominantly facilitates chromatin opening, whilst Oct4 serves an accessory role. Formation of Oct4/Sox2 heterodimers is essential for pluripotency establishment; however, reliance on Oct4/Sox2 heterodimers declines during pluripotency maintenance.

Logarithmic coarsening in the Coulomb glass.

We present numerical results from a comprehensive Monte Carlo study in two dimensions (d=2) of coarsening kinetics in the Coulomb glass (CG) model at half-filling. The CG model is characterized by spin-spin interactions which are long-range Coulombic and antiferromagnetic. For the nonequilibrium properties studied by us (spatial correlation functions and domain growth laws), we find that domain growth in the CG is analogous to that in the nearest-neighbor random-field Ising model. The domain length scale L(t) shows a crossover from a regime of "power-law growth with a disorder-dependent exponent" [L(t)∼t^{1/z[over ¯]}] to a regime of "logarithmic growth with a universal exponent" [L(t)∼(lnt)^{1/ψ}].