Nuclear Positions Research Articles

Core enhancers of the 3'RR optimize IgH nuclear position and loop conformation for successful oriented class switch recombination.

In B lymphocytes, class switch recombination (CSR) is an essential process that adapts immunoglobulin (Ig) subtypes to antigenresponse. Taking place within the Ig heavy chain (IgH) locus, CSR needs controlled transcription of targeted regions governed by the IgH 3'regulatory region (3'RR). This super-enhancer is composed of four core enhancers surrounded by inverted repeated sequences, forming a quasi-palindrome. In addition to transcription, nuclear organization appears to be an important level in CSR regulation. While it is now established that chromatin loop extrusion takes place within IgH locus to facilitate CSR by bringing the donor and acceptor switch regions closer together, the underlying mechanism that triggers CSR loop formation remains partially understood. Here, by combining DNA 3Dfluorescence in situhybridizationwith various high-throughput approaches, we deciphered critical functions for the 3'RR core enhancer element in nuclear addressing, accessibility and chromatin looping of the IgH locus. We conclude thatthe 3'RR core enhancers are necessary and sufficient to pre-organize the position and conformation of IgH loci in resting B-cell nuclei to enable the deletional recombination events required for productive successful CSR in activated B-cell nuclei.

Smooth Dispersion Is Physically Appropriate: Assessing and Amending the D4 Dispersion Model.

The addition of dispersion corrections to density functionals is essential for accurate energy and geometry predictions. Among them, the D4 scheme is popular due to its low computational cost and high accuracy. However, due to its design, the D4 correction can occasionally lead to anomalies, such as unphysical curvature and bumps in the potential energy surface. We find these anomalies are common in the D4 model, although observable consequences are rarer than in the D3 model for reasons we explain. Nevertheless, we uncover instances of unphysical local minima and stationary points with the D4 scheme and propose two solutions that yield smoother dispersion energy as a function of nuclear position. One is trivial to implement, based on a smoother reparametrization of Gaussian weighting (D4S) to find the effective coordination number. The other replaces Gaussian weighting with soft linear interpolation (D4SL). These new approaches usually remove artificial extremum points, while maintaining accuracy.

Are Exact Exchange-Correlation Potentials Continuous at Atomic Nuclei in Molecules?

The Kohn-Sham exchange-correlation potential of a given system can be written exactly in terms of several quantities including the interacting and noninteracting kinetic energy densities of the electrons. Electronic kinetic energy densities are sharply discontinuous at the atomic nuclei in molecules, which implies that exact exchange-correlation potentials of molecules might also be discontinuous at the nuclear positions. This surprising possibility is made even more likely by the fact that molecular exchange-correlation potentials derived from wave functions within Slater-type basis sets do have jump discontinuities. We deduce analytically the exact behavior of the relevant quantities near atomic nuclei and conclude that, in the basis-set limit, all jump discontinuities cancel out nontrivially so that exact exchange-correlation potentials are continuous after all.

A Phase-Space Electronic Hamiltonian For Vibrational Circular Dichroism.

We show empirically that a phase-space non-Born-Oppenheimer electronic Hamiltonian approach to quantum chemistry (where the electronic Hamiltonian is parametrized by both nuclear position and momentum, ĤPS(R,P)) is both a practical and accurate means to recover vibrational circular dichroism spectra. We further hypothesize that such a phase-space approach may lead to very new dynamical physics beyond spectroscopic circular dichroism, with potential implications for understanding chiral induced spin selectivity (CISS), noting that classical phase-space approaches conserve the total nuclear plus electronic momentum, whereas classical Born-Oppenheimer approaches do not (they conserve only the nuclear momentum).

Angular Momentum Transfer between a Molecular System and a Continuous Circularly Polarized Light Field within a Semiclassical Born-Oppenheimer Surface Hopping Framework.

We simulate semiclassically angular momentum transfer for a molecular system subject to a circularly polarized light (CPL) field either moving along a single Born-Oppenheimer (BO) surface or moving along multiple BO surfaces. Both sets of simulations are able to conserve the total angular momentum around the propagation direction of the CPL field, the former requiring a Berry force and the latter requiring a surface parametrized by both nuclear position and momentum (a so-called phase-space approach). Our results provide new insight into the nature of semiclassical nonadiabatic dynamics methods and further demonstrate the power of such methods to capture angular momentum transfer between different media, highlighting the need for accurate algorithms that conserve the total angular momentum.

A Cognitive View on Prosodic Relations

The paper presents a new F0 contour partitioning approach by using the category of prosodic relations also used by Ladd (2008) for improving the F0 contour descriptions based on phonological categories. The new approach involves a cognitive view on the low-high and high-low ’metrical’ structures of prosodic relations, by relating them to the structures of cognitive relations generated during speech object representations at the cortical level. In section 2, the paper presents the information structure model by defining the cognitive categories that describes prosodic relations of F0 contours involving their two overlapped structures and nuclear positions. CU_predicate-CU_argument and CU_theme-CU_rheme are the two structural levels of prosodic relations. The model proposes a binary-tree hierarchy to describe the articulation of prosodic relations within utterances. Two rules are formulated for the identification of nuclear constituents of prosodic relations. The utterances analysed in section 3 illustrate how prosodic and prominence relations can be identified by analysing acoustic cues of their F0 contours. Utterances correspond to English borad focus and narrow focus statements. Focus positions are deduced by only using the rule of the cognitive model.

Nuclear position and local acetyl-CoA production regulate chromatin state

Histone acetylation regulates gene expression, cell function and cell fate1. Here we study the pattern of histone acetylation in the epithelial tissue of the Drosophila wing disc. H3K18ac, H4K8ac and total lysine acetylation are increased in the outer rim of the disc. This acetylation pattern is controlled by nuclear position, whereby nuclei continuously move from apical to basal locations within the epithelium and exhibit high levels of H3K18ac when they are in proximity to the tissue surface. These surface nuclei have increased levels of acetyl-CoA synthase, which generates the acetyl-CoA for histone acetylation. The carbon source for histone acetylation in the rim is fatty acid β-oxidation, which is also increased in the rim. Inhibition of fatty acid β-oxidation causes H3K18ac levels to decrease in the genomic proximity of genes involved in disc development. In summary, there is a physical mark of the outer rim of the wing and other imaginal epithelia in Drosophila that affects gene expression.

Legendre Polynomials are Associated in the Schrodinger Polar Equation of Helium Ions

The helium ion is one of the ions classified as a hydrogenic atom because it has only one electron in its outer orbital so that the helium ion problem can be solved using the Schrodinger equation approach. The Schrodinger equation of the polar part of the helium ion can be solved by the associated legendary polynomial function, . The polar function expresses the angle formed by the vector of the electron's position relative to the z-axis of the helium ion's nuclear position. And it is produced that the polar function of the hydrogenic atom has the same polar function both in position space and in momentum space .

The role of RNA in the maintenance of chromatin domains as revealed by antibody-mediated proximity labelling coupled to mass spectrometry.

Eukaryotic chromatin is organized into functional domains, that are characterized by distinct proteomic compositions and specific nuclear positions. In contrast to cellular organelles surrounded by lipid membranes, the composition of distinct chromatin domains is rather ill described and highly dynamic. To gain molecular insight into these domains and explore their composition, we developed an antibody-based proximity biotinylation method targeting the RNA and proteins constituents. The method that we termed antibody-mediated proximity labelling coupled to mass spectrometry (AMPL-MS) does not require the expression of fusion proteins and therefore constitutes a versatile and very sensitive method to characterize the composition of chromatin domains based on specific signature proteins or histone modifications. To demonstrate the utility of our approach we used AMPL-MS to characterize the molecular features of the chromocenter as well as the chromosome territory containing the hyperactive X chromosome in Drosophila. This analysis identified a number of known RNA-binding proteins in proximity of the hyperactive X and the centromere, supporting the accuracy of our method. In addition, it enabled us to characterize the role of RNA in the formation of these nuclear bodies. Furthermore, our method identified a new set of RNA molecules associated with the Drosophila centromere. Characterization of these novel molecules suggested the formation of R-loops in centromeres, which we validated using a novel probe for R-loops in Drosophila. Taken together, AMPL-MS improves the selectivity and specificity of proximity ligation allowing for novel discoveries of weak protein-RNA interactions in biologically diverse domains.

Paramagnetic Effects in NMR Spectroscopy of Transition-Metal Complexes: Principles and Chemical Concepts.

ConspectusMagnetic resonance techniques represent a fundamental class of spectroscopic methods used in physics, chemistry, biology, and medicine. Electron paramagnetic resonance (EPR) is an extremely powerful technique for characterizing systems with an open-shell electronic nature, whereas nuclear magnetic resonance (NMR) has traditionally been used to investigate diamagnetic (closed-shell) systems. However, these two techniques are tightly connected by the electron-nucleus hyperfine interaction operating in paramagnetic (open-shell) systems. Hyperfine interaction of the nuclear spin with unpaired electron(s) induces large temperature-dependent shifts of nuclear resonance frequencies that are designated as hyperfine NMR shifts (δHF).Three fundamental physical mechanisms shape the total hyperfine interaction: Fermi-contact, paramagnetic spin-orbit, and spin-dipolar. The corresponding hyperfine NMR contributions can be interpreted in terms of through-bond and through-space effects. In this Account, we provide an elemental theory behind the hyperfine interaction and NMR shifts and describe recent progress in understanding the structural and electronic principles underlying individual hyperfine terms.The Fermi-contact (FC) mechanism reflects the propagation of electron-spin density throughout the molecule and is proportional to the spin density at the nuclear position. As the imbalance in spin density can be thought of as originating at the paramagnetic metal center and being propagated to the observed nucleus via chemical bonds, FC is an excellent indicator of the bond character. The paramagnetic spin-orbit (PSO) mechanism originates in the orbital current density generated by the spin-orbit coupling interaction at the metal center. The PSO mechanism of the ligand NMR shift then reflects the transmission of the spin polarization through bonds, similar to the FC mechanism, but it also makes a substantial through-space contribution in long-range situations. In contrast, the spin-dipolar (SD) mechanism is relatively unimportant at short-range with significant spin polarization on the spectator atom. The PSO and SD mechanisms combine at long-range to form the so-called pseudocontact shift, traditionally used as a structural and dynamics probe in paramagnetic NMR (pNMR). Note that the PSO and SD terms both contribute to the isotropic NMR shift only at the relativistic spin-orbit level of theory.We demonstrate the advantages of calculating and analyzing the NMR shifts at relativistic two- and four-component levels of theory and present analytical tools and approaches based on perturbation theory. We show that paramagnetic NMR effects can be interpreted by spin-delocalization and spin-polarization mechanisms related to chemical bond concepts of electron conjugation in π-space and hyperconjugation in σ-space in the framework of the molecular orbital (MO) theory. Further, we discuss the effects of environment (supramolecular interactions, solvent, and crystal packing) and demonstrate applications of hyperfine shifts in determining the structure of paramagnetic Ru(III) compounds and their supramolecular host-guest complexes with macrocycles.In conclusion, we provide a short overview of possible pNMR applications in the analysis of spectra and electronic structure and perspectives in this field for a general chemical audience.

Life prediction of IGBT module for nuclear power plant rod position indicating and rod control system based on SDAE-LSTM

To reduce the losses caused by aging failure of insulation gate bipolar transistor (IGBT), which is the core components of nuclear power plant rod position indicating and rod control (RPC) system. It is necessary to conduct studies on its life prediction. The selection of IGBT failure characteristic parameters in existing research relies heavily on failure principles and expert experience. Moreover, the analysis and learning of time-domain degradation data have not been fully conducted, resulting in low prediction efficiency as the monotonicity, time correlation, and poor anti-interference ability of extracted degradation features. This paper utilizes the advantages of the stacked denoising autoencoder(SDAE) network in adaptive feature extraction and denoising capabilities to perform adaptive feature extraction on IGBT time-domain degradation data; establishes a long-short-term memory (LSTM) prediction model, and optimizes the learning rate, number of nodes in the hidden layer, and number of hidden layers using the Gray Wolf Optimization (GWO) algorithm; conducts verification experiments on the IGBT accelerated aging dataset provided by NASA PCoE Research Center, and selects performance evaluation indicators to compare and analyze the prediction results of the SDAE-LSTM model, PSO-LSTM model, and BP model. The results show that the SDAE-LSTM model can achieve more accurate and stable IGBT life prediction.

Practical phase-space electronic Hamiltonians for abinitio dynamics.

Modern electronic structure theory is built around the Born-Oppenheimer approximation and the construction of an electronic Hamiltonian Ĥel(X) that depends on the nuclear position X (and not the nuclear momentum P). In this article, using the well-known theory of electron translation (Γ') and rotational (Γ″) factors to couple electronic transitions to nuclear motion, we construct a practical phase-space electronic Hamiltonian that depends on both nuclear position and momentum, ĤPS(X,P). While classical Born-Oppenheimer dynamics that run along the eigensurfaces of the operator Ĥel(X) can recover many nuclear properties correctly, we present some evidence that motion along the eigensurfaces of ĤPS(X,P) can better capture both nuclear and electronic properties (including the elusive electronic momentum studied by Nafie). Moreover, only the latter (as opposed to the former) conserves the total linear and angular momentum in general.

Quantum Definition of Molecular Structure.

Molecular structure, a key concept of chemistry, has remained elusive from the perspective of all-particle quantum mechanics, despite many efforts. Viewing molecular structure as a manifestation of strong statistical correlation between nuclear positions, we propose a practical method based on Markov chain Monte Carlo sampling and unsupervised machine learning. Application to the D3+ molecule unambiguously shows that it possesses an equilateral triangular structure. These results provide a major step forward in our understanding of the molecular structure from fundamental quantum principles.

Coupled cluster cavity Born-Oppenheimer approximation for electronic strong coupling.

Chemical and photochemical reactivity, as well as supramolecular organization and several other molecular properties, can be modified by strong interactions between light and matter. Theoretical studies of these phenomena require the separation of the Schrödinger equation into different degrees of freedom as in the Born-Oppenheimer approximation. In this paper, we analyze the electron-photon Hamiltonian within the cavity Born-Oppenheimer approximation (CBOA), where the electronic problem is solved for fixed nuclear positions and photonic parameters. In particular, we focus on intermolecular interactions in representative dimer complexes. The CBOA potential energy surfaces are compared with those obtained using a polaritonic approach, where the photonic and electronic degrees of freedom are treated at the same level. This allows us to assess the role of electron-photon correlation and the accuracy of CBOA.

Leonurine alleviates rheumatoid arthritis by regulating the Hippo signaling pathway

BackgroundRheumatoid arthritis (RA) is a chronic autoimmune disease that can cause joint inflammation and damage. Leonurine (LE) is an alkaloid found in Leonurus heterophyllus. It has anti-inflammatory effects. Hypothesis/PurposeThe molecular mechanisms by which LE acts in RA are unclear and further investigation is required. MethodsMice with collagen-induced arthritis (CIA), and RA-fibroblast-like synoviocytes (FLSs) isolated from them were used as in vivo and in vitro models of RA, respectively. The therapeutic effects of LE on CIA-induced joint injury were investigated by micro-computed tomography, and staining with hematoxylin and eosin and Safranin-O/Fast Green. Cell Counting Kit-8, a Transwell® chamber, enzyme-linked immunosorbent assays, RT-qPCR, and western blotting were used to investigate the effects of LE on RA-FLS viability, migratory capacity, inflammation, microRNA-21 (miR-21) levels, the Hippo signaling pathway, and the effects and intrinsic mechanisms of related proteins. Dual luciferase was used to investigate the binding of miR-21 to YOD1 deubiquitinase (YOD1) and yes-associated protein (YAP). Immunofluorescence was used to investigate the localization of YAP within the nucleus and cytoplasm. ResultsTreatment with LE significantly inhibited joint swelling, bone damage, synovial inflammation, and proteoglycan loss in the CIA mice. It also reduced the proliferation, cell colonization, migration/invasion, and inflammation levels of RA-FLSs, and promoted miR-21 expression in vitro. The effects of LE on RA-FLSs were enhanced by an miR-21 mimic and reversed by an miR-21 inhibitor. The dual luciferase investigation confirmed that both YOD1 and YAP are direct targets of miR-21. Treatment with LE activated the Hippo signaling pathway, and promoted the downregulation and dephosphorylation of MST1 and LATS1 in RA, while inhibiting the activation of YOD1 and YAP. Regulation of the therapeutic effects of LE by miR-21 was counteracted by YOD1 overexpression, which caused the phosphorylation of YAP and prevented its nuclear ectopic position, thereby reducing LE effect on pro-proliferation-inhibiting apoptosis target genes. ConclusionLE regulates the Hippo signaling pathway through the miR-21/YOD1/YAP axis to reduce joint inflammation and bone destruction in CIA mice, thereby inhibiting the growth and inflammation of RA-FLSs. LE has potential for the treatment of RA.

Nuclear and mitochondrial genome assemblies of the beetle, Zygogramma bicolorata, a globally important biocontrol agent of invasive weed Parthenium hysterophorus.

Implementing a genetic-based approach to achieve the full potential of classical biocontrol programs has been advocated for decades. The availability of genome-level information brings the opportunity to scrutinize the biocontrol traits for their efficacy and evolvability. However, implementation of this advocacy remain limited to few instances. Biocontrol of a globally noxious weed, Parthenium hysterophorus, by the leaf-feeding beetle, Zygogramma bicolorata, has been in place for more than four decades now, with varying levels of success. Towards the first step in provisioning genetic-based improvement to this biocontrol program, we describe the nuclear and mitochondrial assemblies of Z. bicolorata. We assembled the genome from the long-read sequence data, error-corrected with high throughput short-reads and checked for contaminants and sequence duplication to produce a 936 Mb nuclear genome. With 96.5% BUSCO completeness and the LAI index 12.91, we present a reference quality assembly, which appeared to be repeat-rich at 62.7% genome-wide and consists of 29437 protein-coding regions. We detected signature of NUMTs in 80 nuclear positions comprising 13 Kb out of 17.9 Kb mitochondria genome sequence. This genome, along with its annotations, provides a valuable resource to gain further insights into the biocontrol traits of Z. bicolorata in improving the control of the invasive weed Parthenium hysterophorus.

Papillary renal neoplasm with reverse polarity: a clinicopathologic study of 43 cases with a focus on the expression of KRAS signaling pathway downstream effectors

Papillary renal neoplasm with reverse polarity (PRNRP) is a renal tumor with frequent KRAS mutations. In this study, we aimed to report the clinical, histological, and immunohistochemical characteristics of PRNRP and the protein expression of various KRAS signaling pathway downstream effectors in PRNRP. PRNRP samples from patients who underwent surgical resection at Seoul National University Hospital over an 11-year period (January 2011 to December 2021) were analyzed. We identified 43 PRNRPs, defined as papillary renal tumors with a thin papillary architecture, eosinophilic finely granular cytoplasm, and apical nuclear position. Immunohistochemistry revealed typical characteristics of PRNRP, including exclusively positive GATA3 (43/43); highly positive L1CAM (43/43), PAX8 (43/43), and EMA (43/43); and low positive AMACR (4/43), RCC (1/43), and vimentin (1/43). KRAS signaling pathway effectors, such as p-ERK, RalA, and RalB, were highly expressed in PRNRP compared to papillary renal cell carcinoma (pRCC) with low or high nuclear grade (P<.001, all). Compared to pRCC with high nuclear grade, patients with PRNRP exhibited significantly longer progression-free survival (P<.001). PRNRP showed the best clinical outcome, with no disease progression in any of the cases. Our study analyzed the largest number of PRNRP cases and is the first to analyze the association between PRNRP and the KRAS downstream signaling pathway. PRNRP was found at a high frequency among all papillary renal tumors (43/207) and demonstrated a very good prognosis. PRNRP showed high GATA3, L1CAM, PAX8, and EMA protein expression as well as high p-ERK, RalA, and RalB protein expression.

Four-Dimensional-Spacetime Atomistic Artificial Intelligence Models.

We demonstrate that AI can learn atomistic systems in the four-dimensional (4D) spacetime. For this, we introduce the 4D-spacetime GICnet model, which for the given initial conditions (nuclear positions and velocities at time zero) can predict nuclear positions and velocities as a continuous function of time up to the distant future. Such models of molecules can be unrolled in the time dimension to yield long-time high-resolution molecular dynamics trajectories with high efficiency and accuracy. 4D-spacetime models can make predictions for different times in any order and do not need a stepwise evaluation of forces and integration of the equations of motions at discretized time steps, which is a major advance over traditional, cost-inefficient molecular dynamics. These models can be used to speed up dynamics, simulate vibrational spectra, and obtain deeper insight into nuclear motions, as we demonstrate for a series of organic molecules.

The molecular chaperone mtHSC70-1 interacts with DjA30 to regulate female gametophyte development and fertility in Arabidopsis.

Arabidopsis mitochondria-targeted heat shock protein 70 (mtHSC70-1) plays important roles in the establishment of cytochrome c oxidase-dependent respiration and redox homeostasis during the vegetative growth of plants. Here, we report that knocking out the mtHSC70-1 gene led to a decrease in plant fertility; the fertility defect of the mutant was completely rescued by introducing the mtHSC70-1 gene. mtHSC70-1 mutants also showed defects in female gametophyte (FG) development, including delayed mitosis, abnormal nuclear position, and ectopic gene expression in the embryo sacs. In addition, we found that an Arabidopsis mitochondrial J-protein gene (DjA30) mutant, j30+/- , had defects in FG development and fertility similar to those of mtHSC70-1 mutant. mtHSC70-1 and DjA30 had similar expression patterns in FGs and interacted in vivo, suggesting that these two proteins might cooperate during female gametogenesis. Further, respiratory chain complex IV activity in mtHSC70-1 and DjA30 mutant embryo sacs was markedly downregulated; this led to the accumulation of mitochondrial reactive oxygen species (ROS). Scavenging excess ROS by introducing Mn-superoxide dismutase 1 or catalase 1 gene into the mtHSC70-1 mutant rescued FG development and fertility. Altogether, our results suggest that mtHSC70-1 and DjA30 are essential for the maintenance of ROS homeostasis in the embryo sacs and provide direct evidence for the roles of ROS homeostasis in embryo sac maturation and nuclear patterning, which might determine the fate of gametic and accessory cells.

A polarized nuclear position specifies the correct division plane during maize stomatal development.

Asymmetric cell division generates different cell types and is a feature of development in multicellular organisms. Prior to asymmetric cell division, cell polarity is established. Maize (Zea mays) stomatal development serves as an excellent plant model system for asymmetric cell division, especially the asymmetric division of the subsidiary mother cell (SMC). In SMCs, the nucleus migrates to a polar location after the accumulation of polarly localized proteins but before the appearance of the preprophase band. We examined a mutant of an outer nuclear membrane protein that is part of the LINC (linker of nucleoskeleton and cytoskeleton) complex that localizes to the nuclear envelope in interphase cells. Previously, maize linc kash sine-like2 (mlks2) was observed to have abnormal stomata. We confirmed and identified the precise defects that lead to abnormal asymmetric divisions. Proteins that are polarly localized in SMCs prior to division polarized normally in mlks2. However, polar localization of the nucleus was sometimes impaired, even in cells that have otherwise normal polarity. This led to a misplaced preprophase band and atypical division planes. MLKS2 localized to mitotic structures; however, the structure of the preprophase band, spindle, and phragmoplast appeared normal in mlks2. Time-lapse imaging revealed that mlks2 has defects in premitotic nuclear migration toward the polarized site and unstable position at the division site after formation of the preprophase band. Overall, our results show that nuclear envelope proteins promote premitotic nuclear migration and stable nuclear position and that the position of the nucleus influences division plane establishment in asymmetrically dividing cells.