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Hamiltonian matrices in electronic and nuclear contexts are highly computation intensive to calculate, mainly due to the cost for the potential matrix. Typically, these matrices contain many off-diagonal elements that are orders of magnitude smaller than diagonal elements. We illustrate that here for vibrational H-matrices of H2O, C2H3 (vinyl), and C2H5NO2 (glycine) using full-dimensional ab initio-based potential surfaces. We then show that many of these small elements can be replaced by zero with small errors of the resulting full set of eigenvalues, depending on the threshold value for this replacement. As a result of this empirical evidence, we investigate three machine learning approaches to predict the zero elements. This is shown to be successful for these H-matrices after training on a small set of calculated elements. For H-matrices of vinyl and glycine, of order 15 552 and 8828, respectively, training on a percent or so of elements is sufficient to obtain all eigenvalues with a mean absolute error of roughly 2 cm−1. [ABSTRACT FROM AUTHOR]

Experimental and theoretical studies of β electrons (electrons emitted in β-decay transitions) and their β-electron spectra have recently experienced a rapid expansion. These β spectral shapes have been used to study total β spectra of fission-product nuclei in the quest for explanation of the reactor-flux anomalies, and individual β transitions in search for β spectral shapes sensitive to the effective value of the weak axial coupling gA. In the former case the TAGS (total absorption gamma-ray spectroscopy) can be efficiently used to measure the total β spectral shapes and in the latter case dedicated measurements of the involved forbidden nonunique β transitions have been deployed. The fourth-forbidden nonunique decay transitions 113Cd(1/2+g.s → 113In(9/2+g.s and 115In(9/2+g.s 115Sn(1/2+g.s represent theoretically and experimentally much-studied cases where the total β spectra consist of these single transitions. In these particular cases the TAGS method could be used to assess the effective value of gA. In the present work we have identified five more interesting cases where a total β spectrum consists of a single transition. These spectra correspond to second-forbidden nonunique transitions and are gA and/or sNME dependent, where sNME denotes the so-called small relativistic vector nuclear matrix element. These studies have been performed using the nuclear shell model with well established effective Hamiltonians. With this we target to β transitions that would potentially be of high interest for the TAGS and present and future dedicated β -spectrum experiments. [ABSTRACT FROM AUTHOR]

Phosphatidylserine (PS) is an important anionic phospholipid that is synthesized within the endoplasmic reticulum (ER). While PS shows the highest enrichment and serves important functional roles in the plasma membrane (PM) but its role in the nucleus is poorly explored. Using three orthogonal approaches, we found that PS is also uniquely enriched in the inner nuclear membrane (INM) and the nuclear reticulum (NR). Nuclear PS is critical for supporting the translocation of CCTα and Lipin1α, two key enzymes important for phosphatidylcholine (PC) biosynthesis, from the nuclear matrix to the INM and NR in response to oleic acid treatment. We identified the PS-interacting regions within the M-domain of CCTα and M-Lip domain of Lipin1α, and show that lipid droplet formation is altered by manipulations of nuclear PS availability. Our studies reveal an unrecognized regulatory role of nuclear PS levels in the regulation of key PC synthesizing enzymes within the nucleus. Synopsis: Phosphatidylserine (PS) is a phospholipid mainly enriched in the inner leaflet of the plasma membrane; however, its role in the nucleus remains unclear. This study describes the presence of PS in the inner nuclear membrane and nuclear reticulum, where it promotes nuclear membrane association of two key enzymes of phosphatidylcholine (PC) biosynthesis in response to oleic acid treatment. PS biosensors show its enrichment in the inner nuclear membrane (INM) and the nuclear reticulum (NR). PS in the inner nuclear membrane is synthesized at the endoplasmic reticulum. Nuclear PS interacts with two PC biosynthetic enzymes, CCTα and Lipin1α, promoting their translocation to the inner nuclear membrane. Nuclear PS biases PC biosynthesis toward membrane expansion rather than lipid droplet formation. Phosphatidylserine supports inner nuclear membrane enrichment of phosphatidylcholine biosynthetic enzymes, CCTα and Lipin1α, for nuclear membrane expansion. [ABSTRACT FROM AUTHOR]

Sad1 and UNC84 (SUN) and Klarsicht, ANC‐1, and Syne homology (KASH) proteins interact at the nuclear periphery to form the linker of nucleoskeleton and cytoskeleton (LINC) complex, spanning the nuclear envelope (NE) and connecting the cytoskeleton with the nuclear interior. It is now well‐documented that several cellular functions depend on LINC complex formation, including cell differentiation and migration. Intriguingly, recent studies suggest that SUN proteins participate in cellular processes where their association with KASH proteins may not be required. Building on this recent research, we elaborate on the hypothesis that SUN proteins may perform LINC‐independent functions and discuss the modalities that may allow SUN proteins to function at the INM when they are not forming LINC complex. [ABSTRACT FROM AUTHOR]

Neutrinoless double-beta decay is considered one of the most promising processes that would help clarify some of the symmetry-breaking problems in our understanding of the observable universe. Recent studies of neutrinoless double-beta decay matrix elements have employed statistical approaches based on modified shell model effective Hamiltonians for 48Ca (Phys. Rev. C 106, 054302 (2022)) and 136Xe (Phys. Rev. C 107, 045501 (2023)). The analyses rely on inducing perturbations in the starting effective Hamiltonians to observe the behavior of a wide range of observables, besides the 0 ν β β ) NME, that are compared with experimental data. Following a Bayesian model averaging approach, the range of probable values for the neutrinoless double-beta decay matrix elements is presented. In this paper, we present a similar study for 82Se, which is described in the same model space as 76Ge that is under experimental observation. Due to its faster calculation time compared to 76Ge, 82Se can be used as an appropriate substitute in our complex statistical study. Using the calculations performed for the statistical analysis of the neutrinoless double-beta decay matrix elements, we also search for the correlations between the observables that we can compare to experimental data. [ABSTRACT FROM AUTHOR]

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Focal adhesion kinase (FAK; encoded by PTK2) was discovered over 30 years ago as a cytoplasmic protein tyrosine kinase that is localized to cell adhesion sites, where it is activated by integrin receptor binding to extracellular matrix proteins. FAK is ubiquitously expressed and functions as a signaling scaffold for a variety of proteins at adhesions and in the cell cytoplasm, and with transcription factors in the nucleus. FAK expression and intrinsic activity are essential for mouse development, with molecular connections to cell motility, cell survival and gene expression. Notably, elevated FAK tyrosine phosphorylation is common in tumors, including pancreatic and ovarian cancers, where it is associated with decreased survival. Small molecule and orally available FAK inhibitors show on-target inhibition in tumor and stromal cells with effects on chemotherapy resistance, stromal fibrosis and tumor microenvironment immune function. Herein, we discuss recent insights regarding mechanisms of FAK activation and signaling, its roles as a cytoplasmic and nuclear scaffold, and the tumor-intrinsic and -extrinsic effects of FAK inhibitors. We also discuss results from ongoing and advanced clinical trials targeting FAK in low- and high-grade serous ovarian cancers, where FAK acts as a master regulator of drug resistance. Although FAK is not known to be mutationally activated, preventing FAK activity has revealed multiple tumor vulnerabilities that support expanding clinical combinatorial targeting possibilities. [ABSTRACT FROM AUTHOR]

Dynamics of nuclear bodies (NBs) in composition and function impact local and global chromatin status and organization, resulting in an altered gene expression profile in response to different cellular states and stresses. NBs serve as 'assemblers' and 'hubs' to modulate chromatin organization and gene expression. Recent advances in spatial multiomics have unveiled the intricate interplay between chromatin and NBs, highlighting the complexity of their interactions and functions. Nuclear bodies (NBs) are biomolecular condensates that participate in various cellular processes and respond to cellular stimuli in the nucleus. The assembly and function of these protein- and RNA-rich bodies, such as nucleoli, nuclear speckles, and promyelocytic leukemia (PML) NBs, contribute to the spatial organization of the nucleus, regulating chromatin activities locally and globally. Recent technological advancements, including spatial multiomics approaches, have revealed novel roles of nucleoli in modulating ribosomal DNA (rDNA) and adjacent non-rDNA chromatin activity, nuclear speckles in scaffolding active genome architecture, and PML NBs in maintaining genome stability during stress conditions. In this review, we summarize emerging functions of these important NBs in the spatial organization of the genome, aided by recently developed spatial multiomics approaches toward this direction. [ABSTRACT FROM AUTHOR]

Heterogeneous nuclear protein U (HNRNPU) plays a pivotal role in innate immunity by facilitating chromatin opening to activate immune genes during host defense against viral infection. However, the mechanism by which HNRNPU is involved in Hepatitis B virus (HBV) transcription regulation through mediating antiviral immunity remains unknown. Our study revealed a significant decrease in HNRNPU levels during HBV transcription, which depends on HBx‐DDB1‐mediated degradation. Overexpression of HNRNPU suppressed HBV transcription, while its knockdown effectively promoted viral transcription, indicating HNRNPU as a novel host restriction factor for HBV transcription. Mechanistically, HNRNPU inhibits HBV transcription by activating innate immunity through primarily the positive regulation of the interferon‐stimulating factor 2′‐5′‐oligoadenylate synthetase 3, which mediates an ribonuclease L‐dependent mechanism to enhance innate immune responses. This study offers new insights into the host immune regulation of HBV transcription and proposes potential targets for therapeutic intervention against HBV infection. [ABSTRACT FROM AUTHOR]

Phosphorylation is a major post-translation modification (PTM) of proteins which is finely tuned by the activity of several hundred kinases and phosphatases. It controls most if not all cellular pathways including anti-viral responses. Accordingly, viruses often induce important changes in the phosphorylation of host factors that can either promote or counteract viral replication. Among more than 500 kinases constituting the human kinome only few have been described as important for the hepatitis B virus (HBV) infectious cycle, and most of them intervene during early or late infectious steps by phosphorylating the viral Core (HBc) protein. In addition, little is known on the consequences of HBV infection on the activity of cellular kinases. The objective of this study was to investigate the global impact of HBV infection on the cellular phosphorylation landscape early after infection. For this, primary human hepatocytes (PHHs) were challenged or not with HBV, and a mass spectrometry (MS)-based quantitative phosphoproteomic analysis was conducted 2- and 7-days post-infection. The results indicated that while, as expected, HBV infection only minimally modified the cell proteome, significant changes were observed in the phosphorylation state of several host proteins at both time points. Gene enrichment and ontology analyses of up- and down-phosphorylated proteins revealed common and distinct signatures induced by infection. In particular, HBV infection resulted in up-phosphorylation of proteins involved in DNA damage signaling and repair, RNA metabolism, in particular splicing, and cytoplasmic cell-signaling. Down-phosphorylated proteins were mostly involved in cell signaling and communication. Validation studies carried out on selected up-phosphorylated proteins, revealed that HBV infection induced a DNA damage response characterized by the appearance of 53BP1 foci, the inactivation of which by siRNA increased cccDNA levels. In addition, among up-phosphorylated RNA binding proteins (RBPs), SRRM2, a major scaffold of nuclear speckles behaved as an antiviral factor. In accordance with these findings, kinase prediction analysis indicated that HBV infection upregulates the activity of major kinases involved in DNA repair. These results strongly suggest that HBV infection triggers an intrinsic anti-viral response involving DNA repair factors and RBPs that contribute to reduce HBV replication in cell culture models. [ABSTRACT FROM AUTHOR]

Neutrinoless double beta decay nuclear matrix element ( M 0 ν ) for 136Xe was recently analyzed using a statistical approach (Phys. Rev. C 107, 045501 (2023)). In the analysis, three initial shell model effective Hamiltonians were randomly altered, and their results for 23 measured observables were used to infer credibility for the M 0 ν nuclear matrix element (NME) based on a Bayesian Model Averaging approach. In that analysis, a reasonable Gamow-Teller quenching factor of 0.7 was assumed for each starting effective Hamiltonian. Given that the result of the statistical analysis was sensible to this choice, we are here improving that analysis by assuming that the Gamow-Teller quenching factor is also randomly chosen within reasonabe limits for all three starting Hamiltonians. The outcomes are slightly higher expectation values and uncertainties for the M 0 ν NME. [ABSTRACT FROM AUTHOR]

Detecting neutrino-less double beta ( 0 ν β β ) decay with high-sensitivity 0 ν β β detectors is of current interest for studying the Majorana neutrino's nature, the neutrino mass (ν -mass), right-handed weak currents (RHCs), and others beyond the Standard Model. Many experimental groups have studied 0 ν β β decay with ν -mass sensitivities on the order of 100 meV and RHC sensitivities on the order of 10   − 9 –10   − 6 , but no clear 0 ν β β signals have been observed so far in these ν -mass and RHC regions. Thus, several experimental groups are developing higher-sensitivity detectors to explore a smaller ν -mass region around 15–50 meV, which corresponds to the inverted hierarchy ν -mass, and smaller RHC regions on the order of 10   − 10 –10   − 7 in the near future. Nuclear matrix elements (NMEs) for ν -mass and RHC processes are crucial for extracting the ν -mass and RHCs of particle physics interest from 0 ν β β experiments. This report briefly reviews detector sensitivities and upper limits on the ν -mass and right-handed currents for several current 0 ν β β detectors and the ν -mass and RHC sensitivities expected for some near-future ones. [ABSTRACT FROM AUTHOR]

Nesprin proteins, which are components of the linker of nucleoskeleton and cytoskeleton (LINC) complex, are located within the nuclear envelope and play prominent roles in nuclear architecture. For example, LINC complex proteins interact with both chromatin and the cytoskeleton. Here, we report that the Drosophila Nesprin MSP300 has an additional function in autophagy within larval body wall muscles. RNAi-mediated MSP300 knockdown in larval body wall muscles resulted in defects in the contractile apparatus, muscle degeneration and defective autophagy. In particular, MSP300 knockdown caused accumulation of cytoplasmic aggregates that contained poly-ubiquitylated cargo, as well as the autophagy receptor ref(2)P (the fly homolog of p62 or SQSTM) and Atg8a. Furthermore, MSP300 knockdown larvae expressing an mCherry-GFP-tagged Atg8a transgene exhibited aberrant persistence of the GFP signal within these aggregates, indicating failure of autophagosome maturation. These autophagy deficits were similar to those exhibited by loss of the endoplasmic reticulum (ER) fusion protein Atlastin (Atl), raising the possibility that Atl and MSP300 might function in the same pathway. In support of this possibility, we found that a GFP-tagged MSP300 protein trap exhibited extensive localization to the ER. Alteration of ER-directed MSP300 might abrogate important cytoskeletal contacts necessary for autophagosome completion. [ABSTRACT FROM AUTHOR]

Matrin-3 (MATR3) was initially discovered as a component of the nuclear matrix about thirty years ago. Since then, accumulating studies have provided evidence that MATR3 not only plays a structural role in the nucleus, but that it is also an active protein involved in regulating gene expression at multiple levels, including chromatin organization, DNA transcription, RNA metabolism, and protein translation in the nucleus and cytoplasm. Furthermore, MATR3 may play a critical role in various cellular processes, including DNA damage response, cell proliferation, differentiation, and survival. In addition to the revelation of its biological role, recent studies have reported MATR3's involvement in the context of various diseases, including neurodegenerative and neurodevelopmental diseases, as well as cancer. Moreover, sequencing studies of patients revealed a handful of disease-associated mutations in MATR3 linked to amyotrophic lateral sclerosis (ALS), which further elevated the gene's importance as a topic of study. In this review, we synthesize the current knowledge regarding the diverse functions of MATR3 in DNA- and RNA-related processes, as well as its involvement in various diseases, with a particular emphasis on ALS. [ABSTRACT FROM AUTHOR]

Special AT-rich sequence binding protein-2 (SATB2) is a nuclear matrix protein that binds to nuclear attachment regions and is involved in chromatin remodeling and transcription regulation. In stem cells, it regulates the expression of genes required for maintaining pluripotency and self-renewal and epithelial–mesenchymal transition (EMT). In this study, we examined the oncogenic role of SATB2 in prostate cancer and assessed whether overexpression of SATB2 in human normal prostate epithelial cells (PrECs) induces properties of cancer stem cells (CSCs). The results demonstrate that SATB2 is highly expressed in prostate cancer cell lines and CSCs, but not in PrECs. Overexpression of SATB2 in PrECs induces cellular transformation which was evident by the formation of colonies in soft agar and spheroids in suspension. Overexpression of SATB2 in PrECs also resulted in induction of stem cell markers (CD44 and CD133), pluripotency-maintaining transcription factors (cMYC, OCT4, SOX2, KLF4, and NANOG), CADHERIN switch, and EMT-related transcription factors. Chromatin immunoprecipitation assay demonstrated that SATB2 can directly bind to promoters of BCL-2, BSP, NANOG, MYC, XIAP, KLF4, and HOXA2, suggesting SATB2 is capable of directly regulating pluripotency/self-renewal, cell survival, and proliferation. Since prostate CSCs play a crucial role in cancer initiation, progression, and metastasis, we also examined the effects of SATB2 knockdown on stemness. SATB2 knockdown in prostate CSCs inhibited spheroid formation, cell viability, colony formation, cell motility, migration, and invasion compared to their scrambled control groups. SATB2 knockdown in CSCs also upregulated the expression of E-CADHERIN and inhibited the expression of N-CADHERIN, SNAIL, SLUG, and ZEB1. The expression of SATB2 was significantly higher in prostate adenocarcinoma compared to normal tissues. Overall, our data suggest that SATB2 acts as an oncogenic factor where it is capable of inducing malignant changes in PrECs by inducing CSC characteristics. [ABSTRACT FROM AUTHOR]

Eukaryotic cells tether the nucleoskeleton to the cytoskeleton via a conserved molecular bridge, called the LINC complex. The core of the LINC complex comprises SUN-domain and KASH-domain proteins that directly associate within the nuclear envelope lumen. Intra- and inter-chain disulphide bonds, along with KASH-domain protein interactions, both contribute to the tertiary and quaternary structure of vertebrate SUN-domain proteins. The significance of these bonds and the role of PDIs (protein disulphide isomerases) in LINC complex biology remains unclear. Reducing and non-reducing SDS-PAGE analyses revealed a prevalence of SUN2 homodimers in non-tumorigenic breast epithelia MCF10A cells, but not in the invasive triple-negative breast cancer MDA-MB-231 cell line. Furthermore, super-resolution microscopy revealed SUN2 staining alterations in MCF10A, but not in MDA-MB-231 nuclei, upon reducing agent exposure. While PDIA1 levels were similar in both cell lines, pharmacological inhibition of PDI activity in MDA-MB-231 cells led to SUN-domain protein down-regulation, as well as Nesprin-2 displacement from the nucleus. This inhibition also caused changes in perinuclear cytoskeletal architecture and lamin downregulation, and increased the invasiveness of PDI-inhibited MDA-MB-231 cells in space-restrictive in vitro environments, compared to untreated cells. These results emphasise the key roles of PDIs in regulating LINC complex biology, cellular architecture, biomechanics, and invasion. [ABSTRACT FROM AUTHOR]

SUMMARY: Chromatin is a dynamic network that regulates genome organization and gene expression. Different types of chromatin regulators are highly conserved among Archaeplastida, including unicellular algae, while some chromatin genes are only present in land plant genomes. Here, we review recent advances in understanding the function of conserved chromatin factors in basal land plants and algae. We focus on the role of Polycomb‐group genes which mediate H3K27me3‐based silencing and play a role in balancing gene dosage and regulating haploid‐to‐diploid transitions by tissue‐specific repression of the transcription factors KNOX and BELL in many representatives of the green lineage. Moreover, H3K27me3 predominantly occupies repetitive elements which can lead to their silencing in a unicellular alga and basal land plants, while it covers mostly protein‐coding genes in higher land plants. In addition, we discuss the role of nuclear matrix constituent proteins as putative functional lamin analogs that are highly conserved among land plants and might have an ancestral function in stress response regulation. In summary, our review highlights the importance of studying chromatin regulation in a wide range of organisms in the Archaeplastida. Significance Statement: Here we review recent findings on the role of chromatin regulators in basal Archaeplastida. These studies shed light on the ancestral function of chromatin factors in unicellular organisms and for land plant evolution. [ABSTRACT FROM AUTHOR]

SUMMARY: The nucleus is a central organelle of eukaryotic cells undergoing dynamic structural changes during cellular fundamental processes such as proliferation and differentiation. These changes rely on the integration of developmental and stress signals at the nuclear envelope (NE), orchestrating responses at the nucleo‐cytoplasmic interface for efficient genomic functions such as DNA transcription, replication and repair. While in animals, correlation has already been established between NE dynamics and chromatin remodeling using last‐generation tools and cutting‐edge technologies, this topic is just emerging in plants, especially in response to mechanical cues. This review summarizes recent data obtained in this field with more emphasis on the mechanical stress response. It also highlights similarities/differences between animal and plant cells at multiples scales, from the structural organization of the nucleo‐cytoplasmic continuum to the functional impacts of NE dynamics. Significance Statement: This is a comprehensive review of the recent developments in the area of nuclear envelope dynamics and its connection to chromatin modifications and remodeling focusing on the mechanical stress response. [ABSTRACT FROM AUTHOR]

The Extended Evolutionary Synthesis (EES) addresses the issues in evolutionary biology which cannot be explained by neo-Darwinian theory. The EES paradigm recognises teleology and agency in living systems, and identifies that organisms can directly affect their evolutionary trajectory in a goal-directed manner, yet the physiological pathways via which this occurs remain unidentified. Here, I propose a physiological pathway via which organisms can alter their genotype and phenotype by making behavioural decisions with respect their activity levels, partitioning of resources either toward growth, defence against disease, or their behavioural response to stressors. Specifically, I hypothesize that agential, teleological decisions mediated by acetylcholine result in induced nitric oxide (NO) activity, which regulates metabolism, blood flow, and immune response. Nitric oxide, however, is also a key epigenetic molecule, being involved in DNA acetylation, methylation, and de-methylation. Further, NO alters the histone complexes which scaffold nuclear DNA strands, and is thus a good candidate in identifying a system which allows an organisms to make teleological genetic changes. The proposed mechanisms of inheritance of these genetic changes is via the paternal line, whereby epigenetic changes in the somatic Sertoli cells in animals are transcribed by mRNA and included in the germline cells – the male gametes. The microsporangium in plants, and the sporophore cells in fungi, meanwhile, are proposed to form similar systems in response to sensory detection of stressors. Whilst the hypothesis is presented as a simplified model for future testing, it opens new avenues for study in evolutionary biology. [ABSTRACT FROM AUTHOR]

Key Clinical Message: Nuclear matrix protein (NXP‐2) positive amyopathic dermatomyositis (DM) may present without classic symptoms like muscle weakness, dysphagia, and edema, and mimic conditions like cutaneous lupus. Given DM's association with malignancy and interstitial lung disease, prompt and accurate diagnosis is important. Testing for myositis‐specific antibodies aids diagnosis in ambiguous cases. [ABSTRACT FROM AUTHOR]

Pathological dermal scars such as keloids present significant clinical challenges lacking effective treatment options. Given the distinctive feature of highly stiffened scar tissues, deciphering how matrix mechanics regulate pathological progression can inform new therapeutic strategies. Here, it is shown that pathological dermal scar keloid fibroblasts display unique metamorphoses to stiffened matrix. Compared to normal fibroblasts, keloid fibroblasts show high sensitivity to stiffness rather than biochemical stimulation, activating cytoskeletal‐to‐nuclear mechanosensing molecules. Notably, keloid fibroblasts on stiff matrices exhibit nuclear softening, concomitant with reduced lamin A/C expression, and disrupted anchoring of lamina‐associated chromatin. This nuclear softening, combined with weak adhesion and high contractility, facilitates the invasive migration of keloid fibroblasts through confining matrices. Inhibiting lamin A/C‐driven nuclear softening, via lamin A/C overexpression or actin disruption, mitigates such invasiveness of keloid fibroblasts. These findings highlight the significance of the nuclear mechanics of keloid fibroblasts in scar pathogenesis and propose lamin A/C as a potential therapeutic target for managing pathological scars. [ABSTRACT FROM AUTHOR]

Weak interaction processes continue to be hot topics in fundamental physics research. In this paper, we briefly review some recent advances in the theoretical study of beta and double-beta decays that include both the nuclear and atomic part of these processes. On the nuclear side, we present a statistical approach for the computation of the nuclear matrix elements (NME) for neutrinoless double-beta ( 0 ν β β ). A range of NME values, the most probable value for NME, and the associated theoretical uncertainty are given. Correlations with other related observables are shown as well. On the atomic side, we first briefly review the methods used to obtain the electrons' wave functions. Further, we use them for the computation of some relevant kinematic quantities such as Fermi functions, electron spectra, and angular correlation between the emitted electrons. Then, we present applications of these calculations to the experimental data analysis related to the search of the Lorentz invariance violation in two-neutrino double-beta ( 2 ν β β ) decay and description of the decay rates and decay rate ratios for allowed and unique forbidden electron capture (EC) processes. [ABSTRACT FROM AUTHOR]

Uncovering neutrinoless double beta decay (0ν2β) is crucial for confirming neutrinos' Majorana characteristics. The decay rate of 0νββ is theoretically uncertain, influenced by nuclear matrix elements that vary across nuclides. To reduce this uncertainty, precise measurement of the half-life of neutrino-emitting double beta decay (2ν2β) in different nuclides is essential. We have launched the PIKACHU (Pure Inorganic scintillator experiment in KAmioka for CHallenging Underground sciences) project to fabricate high-purity Ce-doped Gd3Ga3Al2O12 (GAGG) single crystals and use them to study the double beta decay of 160Gd. Predictions from two theoretical models on nuclear matrix element calculations for 2ν2β in 160Gd show a significant discrepancy in estimated half-lives, differing by approximately an order of magnitude. If the lower half-life estimation holds true, detecting 2ν2β in 160Gd could be achievable with a sensitivity enhancement slightly more than an order of magnitude compared to prior investigations using Ce-doped Gd2SiO5 (GSO) crystal. We have successfully developed GAGG crystals with purity levels surpassing previous standards through refined purification and selection of raw materials. Our experiments with these crystals indicate the feasibility of reaching sensitivities exceeding those of earlier studies. This paper discusses the ongoing development and scintillator performance evaluation of high-purity GAGG crystals, along with the anticipated future prospects of the PIKACHU experiment. [ABSTRACT FROM AUTHOR]

HSV-1 major tegument protein VP22 is present in multiple subcellular locations in the late stages of productive viral infection. We initially performed a detailed time course experiment and observed that VP22 was detected in nuclear and nuclear matrix fractions as early as 4 hpi. The goal was to determine the fate of virion-derived incoming VP22, and we report the following: (i) VP22 was detected in nuclear matrix fractions 1 hpi. (ii) In the presence of cycloheximide (CHX), VP22 was present in the nuclear matrix 1–6 hpi, demonstrating the stability of the protein. (iii) The nuclear matrix targeting of VP22 occurred in infected Vero, HEp-2, and human mammary epithelial (HME) cells and following synchronized infection. Based on these results, we conclude that (iv) VP22 targets the nuclear matrix and chromatin upon entry into cells during productive HSV-1 infection. [ABSTRACT FROM AUTHOR]

In this paper, we update the phase-space factors for all two-neutrino double electron capture processes. The Dirac–Hartree–Fock–Slater self-consistent method is employed to describe the bound states of captured electrons, enabling a more realistic treatment of atomic screening and more precise binding energies of the captured electrons compared to previous investigations. Additionally, we consider all s-wave electrons available for capture, expanding beyond the K and L 1 orbitals considered in prior studies. For light atoms, the increase associated with additional captures compensates for the decrease in decay rate caused by the more precise atomic screening. However, for medium and heavy atoms, an increase in the decay rate, up to 10% for the heaviest atoms, is observed due to the combination of these two effects. In the systematic analysis, we also include capture fractions for the first few dominant partial captures. Our precise model enables a close examination of low Q-value double electron capture in 152Gd, 164Er, and 242Cm, where partial K K captures are energetically forbidden. Finally, with the updated phase-space values, we recalculate the effective nuclear matrix elements and compare their spread with those associated with 2 ν β − β − decay. [ABSTRACT FROM AUTHOR]

The role of initial state (ISI) and final state (FSI) ion–ion interactions in heavy-ion double-charge-exchange (DCE) reactions A (Z , N) → A (Z ± 2 , N ∓ 2) are studied for double single-charge-exchange (DSCE) reactions given by sequential actions of the isovector nucleon–nucleon (NN) T-matrix. In momentum representation, the second-order DSCE reaction amplitude is shown to be given in factorized form by projectile and target nuclear matrix elements and a reaction kernel containing ISI and FSI. Expanding the intermediate propagator in a Taylor series with respect to auxiliary energy allows us to perform the summation in the leading-order term over intermediate nuclear states in closure approximation. The nuclear matrix element attains a form given by the products of two-body interactions directly exciting the n 2 p − 2 and p 2 n − 2 DCE transitions in the projectile and the target nucleus, respectively. A surprising result is that the intermediate propagation induces correlations between the transition vertices, showing that DSCE reactions are a two-nucleon process that resembles a system of interacting spin–isospin dipoles. Transformation of the DSCE NN T-matrix interactions from the reaction theoretical t-channel form to the s-channel operator structure required for spectroscopic purposes is elaborated in detail, showing that, in general, a rich spectrum of spin scalar, spin vector and higher-rank spin tensor multipole transitions will contribute to a DSCE reaction. Similarities (and differences) to two-neutrino double-beta decay (DBD) are discussed. ISI/FSI distortion and absorption effects are illustrated in black sphere approximation and in an illustrative application to data. [ABSTRACT FROM AUTHOR]

The prediction of potential microbe–drug associations is of great value for drug research and development, especially, methods, based on deep learning, have been achieved significant improvement in bio-medicine. In this manuscript, we proposed a novel computational model named NMGMDA based on the nuclear norm minimization and graph attention network to infer latent microbe–drug associations. Firstly, we created a heterogeneous microbe–drug network in NMGMDA by fusing the drug and microbe similarities with the established drug–microbe associations. After this, by using GAT and NNM to calculate the predict scores. Lastly, we created a fivefold cross validation framework to assess the new model NMGMDA's progressiveness. According to the simulation results, NMGMDA outperforms some of the most advanced methods, with a reliable AUC of 0.9946 on both MDAD and aBioflm databases. Furthermore, case studies on Ciprofloxacin, Moxifoxacin, HIV-1 and Mycobacterium tuberculosis were carried out in order to assess the effectiveness of NMGMDA even more. The experimental results demonstrated that, following the removal of known correlations from the database, 16 and 14 medications as well as 19 and 17 microbes in the top 20 predictions were validated by pertinent literature. This demonstrates the potential of our new model, NMGMDA, to reach acceptable prediction performance. [ABSTRACT FROM AUTHOR]

Meiosis is a specialized cell division that occurs in sexually reproducing organisms, generating haploid gametes containing half the chromosome number through two rounds of cell division. Homologous chromosomes pair and prepare for their proper segregation in subsequent divisions. How homologous chromosomes recognize each other and achieve pairing is an important question. Early studies showed that in most organisms, homologous pairing relies on homologous recombination. However, pairing mechanisms differ across species. Evidence indicates that chromosomes are dynamic and move during early meiotic stages, facilitating pairing. Recent studies in various model organisms suggest conserved mechanisms and key regulators of homologous chromosome pairing. This review summarizes these findings and compare similarities and differences in homologous chromosome pairing mechanisms across species. [ABSTRACT FROM AUTHOR]

As an important posttranslational modification, SUMOylation plays critical roles in almost all biological processes. Although it has been well-documented that SUMOylated proteins are mainly localized in the nucleus and have roles in chromatin-related processes, we showed recently that the SUMOylation machinery is actually enriched in the nuclear matrix rather than chromatin. Here, we provide compelling biochemical, cellular imaging and proteomic evidence that SUMOylated proteins are highly enriched in the nuclear matrix. We demonstrated that inactivation of SUMOylation by inhibiting SUMO-activating E1 enzyme or KO of SUMOconjugating E2 enzyme UBC9 have only mild effect on nuclear matrix composition, indicating that SUMOylation is neither required for nuclear matrix formation nor for targeting proteins to nuclear matrix. Further characterization of UBC9 KO cells revealed that loss of SUMOylation did not result in significant DNA damage, but led to mitotic arrest and chromosome missegregation. Altogether, our study demonstrates that SUMOylated proteins are selectively enriched in the nuclear matrix and suggests a role of nuclear matrix in mediating SUMOylation and its regulated biological processes. [ABSTRACT FROM AUTHOR]

Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related mortality worldwide. The oncogenic role of Matrin-3 (MATR3), an a nuclear matrix protein, in HCC remains largely unknown. Here, we document the biological function of MATR3 in HCC based on integrated bioinformatics analysis and functional studies. According to the TCGA database, MATR3 expression was found to be positively correlated with clinicopathological characteristics in HCC. The receiver operating characteristic (ROC) curve and Kaplan-Meier (KM) curve displayed the diagnostic and prognostic potentials of MATR3 in HCC patients, respectively. Pathway enrichment analysis represented the enrichment of MATR3 in various molecular pathways, including the regulation of the cell cycle. Functional assays in HCC cell lines showed reduced proliferation of cells with stable silencing of MATR3. At the same time, the suppressive effects of MATR3 depletion on HCC development were verified by xenograft tumor experiments. Moreover, MATR3 repression also resulted in cell cycle arrest by modulating the expression of cell cycle-associated genes. In addition, the interaction of MATR3 with cell cycle-regulating factors in HCC cells was further corroborated with co-immunoprecipitation and mass spectrometry (Co-IP/MS). Furthermore, CIBERSORT and TIMER analyses showed an association between MATR3 and immune infiltration in HCC. In general, this study highlights the novel oncogenic function of MATR3 in HCC, which could comprehensively address how aberrant changes in the cell cycle promote HCC development. MATR3 might serve as a prognostic predictor and therapeutic target for HCC patients. [ABSTRACT FROM AUTHOR]

Background/Aim: Nuclear matrix protein-22 (NMP- 22) is widely used in human medicine as a prognostic and diagnostic tool for urothelial carcinoma (UC). In addition, the use of urinary exosomes as a liquid biopsy tool is emerging for the diagnosis of certain types of cancer in human medicine. This study aimed to investigate the change in urinary exosomal NMP-22 for the diagnosis of UC in dogs. Patients and Methods: Among canine patients who visited the veterinary hospital, urine was collected from those whose owners provided consent. A total of 23 dogs (UC group, n=6; control group, n=17) were included in the analysis. After exosomes were isolated from the urine, NMP-22 was measured using enzyme-linked immunosorbent assay. Results: In the UC group, the expression of NMP-22 in urinary exosomes was significantly higher than that in non-UC groups (p<0.0001). Conclusion: NMP-22 is significantly increased in exosomes in the urine of dogs diagnosed with UC, suggesting that urinary exosome NMP-22 can be considered as one of the liquid biopsy tools for diagnosing UC in dogs. [ABSTRACT FROM AUTHOR]

The endoplasmic reticulum (ER) extends to the outer (ONM) and the inner (INM) nuclear membrane forming the nuclear envelope (NE) that delimits the nucleoplasm containing the cell genome. Unfolded protein responses (UPRs) and reticulophagy responses increase or reduce ER size and activities, respectively. If dynamic changes of the ER are transmitted to the contiguous NE was not known. In our recent publication, we report on the transmission of stress-induced ER expansion to the NE, which requires disassembly of the Linker of Nucleoskeleton and Cytoskeleton (LINC) complexes deputed to ensure a physical connection between the cytoplasmic cytoskeleton and the nuclear lamina and to maintain the width between INM and ONM within 50 nm. LINC complexes disassembly relies on reduction of the disulfide bond that covalently links SUN proteins in the INM and KASH proteins (SYNE/NESPRIN proteins in mammals) in the ONM by the ONM-resident reductase TMX4. Upon stress resolution, the physiological shape of the NE is reestablished by SEC62-driven ONM-phagy, where ONM-derived vesicles are directly captured by RAB7- and LAMP1-positive endolysosomes in processes that proceed via asymmetric microautophagy of the NE. [ABSTRACT FROM AUTHOR]

The ability of a cell to regulate its mechanical properties is central to its function. Emerging evidence suggests that interactions between the cell nucleus and cytoskeleton influence cell mechanics through poorly understood mechanisms. Here we conduct quantitative confocal imaging to show that the loss of A-type lamins tends to increase nuclear and cellular volume while the loss of B-type lamins behaves in the opposite manner. We use fluorescence recovery after photobleaching, atomic force microscopy, optical tweezer microrheology, and traction force microscopy to demonstrate that A-type lamins engage with both F-actin and vimentin intermediate filaments (VIFs) through the linker of nucleoskeleton and cytoskeleton (LINC) complexes to modulate cortical and cytoplasmic stiffness as well as cellular contractility in mouse embryonic fibroblasts (MEFs). In contrast, we show that B-type lamins predominantly interact with VIFs through LINC complexes to regulate cytoplasmic stiffness and contractility. We then propose a physical model mediated by the lamin–LINC complex that explains these distinct mechanical phenotypes (mechanophenotypes). To verify this model, we use dominant negative constructs and RNA interference to disrupt the LINC complexes that facilitate the interaction of the nucleus with the F-actin and VIF cytoskeletons and show that the loss of these elements results in mechanophenotypes like those observed in MEFs that lack A- or B-type lamin isoforms. Finally, we demonstrate that the loss of each lamin isoform softens the cell nucleus and enhances constricted cell migration but in turn increases migration-induced DNA damage. Together, our findings uncover distinctive roles for each of the four major lamin isoforms in maintaining nucleocytoskeletal interactions and cellular mechanics.

There is growing evidence that X-chromosome inactivation is driven by phase-separated supramolecular assemblies. However, among the many proteins recruited to the inactive X chromosome by Xist long non-coding RNA, so far only a minority (CIZ1, CELF1, SPEN, TDP-43, MATR3, PTBP1, PCGF5) have been shown to form Xist-seeded protein assemblies, and of these most have not been analyzed in detail. With focus on CIZ1, here we describe 1) the contribution of intrinsically disordered regions in RNA-dependent protein assembly formation at the inactive X chromosome, and 2) enrichment, distribution, and function of proteins within Xist-seeded assemblies. [ABSTRACT FROM AUTHOR]

Several related progeroid disorders are caused by defective post-translational processing of prelamin A, the precursor of the nuclear scaffold protein lamin A, encoded by LMNA. Prelamin A undergoes farnesylation and additional modifications at its C-terminus. Subsequently, the farnesylated C-terminal segment is cleaved off by the zinc metalloprotease ZMPSTE24. The premature aging disorder Hutchinson Gilford progeria syndrome (HGPS) and a related progeroid disease, mandibuloacral dysplasia (MAD-B), are caused by mutations in LMNA and ZMPSTE24, respectively, that result in failure to process the lamin A precursor and accumulate permanently farnesylated forms of prelamin A. The farnesyl transferase inhibitor (FTI) lonafarnib is known to correct the aberrant nuclear morphology of HGPS patient cells and improves lifespan in children with HGPS. Importantly, and in contrast to a previous report, we show here that FTI treatment also improves the aberrant nuclear phenotypes in MAD-B patient cells with mutations in ZMPSTE24 (P248L or L425P). As expected, lonafarnib does not correct nuclear defects for cells with lamin A processing-proficient mutations. We also examine prelamin A processing in fibroblasts from two individuals with a prevalent laminopathy mutation LMNA-R644C. Despite the proximity of residue R644 to the prelamin A cleavage site, neither R644C patient cell line shows a prelamin A processing defect, and both have normal nuclear morphology. This work clarifies the prelamin A processing status and role of FTIs in a variety of laminopathy patient cells and supports the FDA-approved indication for the FTI Zokinvy for patients with processing-deficient progeroid laminopathies, but not for patients with processing-proficient laminopathies. [ABSTRACT FROM AUTHOR]

As human longevity increases, understanding the molecular mechanisms that drive aging becomes ever more critical to promote health and prevent age-related disorders. Premature aging disorders or progeroid syndromes can provide critical insights into aspects of physiological aging. A major cause of progeroid syndromes which result from mutations in the genes LMNA and ZMPSTE24 is disruption of the final posttranslational processing step in the production of the nuclear scaffold protein lamin A. LMNA encodes the lamin A precursor, prelamin A and ZMPSTE24 encodes the prelamin A processing enzyme, the zinc metalloprotease ZMPSTE24. Progeroid syndromes resulting from mutations in these genes include the clinically related disorders Hutchinson–Gilford progeria syndrome (HGPS), mandibuloacral dysplasia-type B, and restrictive dermopathy. These diseases have features that overlap with one another and with some aspects of physiological aging, including bone defects resembling osteoporosis and atherosclerosis (the latter primarily in HGPS). The progeroid syndromes have ignited keen interest in the relationship between defective prelamin A processing and its accumulation in normal physiological aging. In this review, we examine the hypothesis that diminished processing of prelamin A by ZMPSTE24 is a driver of physiological aging. We review features a new mouse (LmnaL648R/L648R) that produces solely unprocessed prelamin A and provides an ideal model for examining the effects of its accumulation during aging. We also discuss existing data on the accumulation of prelamin A or its variants in human physiological aging, which call out for further validation and more rigorous experimental approaches to determine if prelamin A contributes to normal aging. [ABSTRACT FROM AUTHOR]

Lamins A/C are nuclear intermediate filament proteins that are involved in diverse cellular mechanical and biochemical functions. Here, we report that recognition of Lamins A/C by a commonly used antibody (JOL-2) that binds the Lamin A/C Ig-fold and other antibodies targeting similar epitopes is highly dependent on cell density, even though Lamin A/Clevels do not change. We propose that the effect is caused by partial unfolding or masking of the C'E and/or EF loops of the Ig-fold in response to cell spreading. Surprisingly, JOL-2 antibody labeling was insensitive to disruption of cytoskeletal filaments or the Linker of Nucleoskeleton and Cytoskeleton (LINC) complex. Furthermore, neither nuclear stiffness nor nucleo-cytoskeletal force transmission changed with cell density. These findings are important for the interpretation of immunofluorescence data for Lamin A/C and also raise the intriguing prospect that the conformational changes may play a role in Lamin A/C mediated cellular function. [ABSTRACT FROM AUTHOR]

During nuclear disaster, infrastructure is severely damaged and injuries are often combined with trauma/burns and whole-body radiation. This makes triage difficult, especially when resources are severely deficient. To solve this problem, in this article, the authors have suggested a new less technology-dependent radiation dosimetry and quick triage using a specially designed triage matrix during nuclear disasters. [ABSTRACT FROM AUTHOR]

The nucleoskeleton forms a filamentous meshwork under the nuclear envelope and contributes to the regulation of nuclear shape and gene expression. To understand how the Arabidopsis (Arabidopsis thaliana) nucleoskeleton physically connects to the nuclear periphery in plants, we investigated the Arabidopsis nucleoskeleton protein KAKU4 and sought for functional regions responsible for its localization at the nuclear periphery. We identified 3 conserved peptide motifs within the N-terminal region of KAKU4, which are required for intermolecular interactions of KAKU4 with itself, interaction with the nucleoskeleton protein CROWDED NUCLEI (CRWN), localization at the nuclear periphery, and nuclear elongation in differentiated tissues. Unexpectedly, we find these motifs to be present also in NUP82 and NUP136, 2 plant-specific nucleoporins from the nuclear pore basket. We further show that NUP82, NUP136, and KAKU4 have a common evolutionary history predating nonvascular land plants with KAKU4 mainly localizing outside the nuclear pore suggesting its divergence from an ancient nucleoporin into a new nucleoskeleton component. Finally, we demonstrate that both NUP82 and NUP136, through their shared N-terminal motifs, interact with CRWN and KAKU4 proteins revealing the existence of a physical continuum between the nuclear pore and the nucleoskeleton in plants. The KAKU4 protein, a component of the plant nucleoskeleton, diverged from an ancestral nucleoporin and provides a continuum between the nucleoskeleton and the nuclear pore complex basket via short peptide motifs. [ABSTRACT FROM AUTHOR]

The response of cells to environmental stimuli, under either physiological or pathological conditions, plays a key role in determining cell fate toward either adaptive survival or controlled death. The efficiency of such a feedback mechanism is closely related to the most challenging human diseases, including cancer. Since cellular responses are implemented through physical forces exerted on intracellular components, more detailed knowledge of force distribution through modern imaging techniques is needed to ensure a mechanistic understanding of these forces. In this work, we mapped these intracellular forces at a whole-cell scale and with submicron resolution to correlate intracellular force distribution to the cytoskeletal structures. Furthermore, we visualized dynamic mechanical responses of the cells adapting to environmental modulations in situ. Such task was achieved by using an informatics-assisted atomic force microscope (AFM) indentation technique where a key step was Markov-chain Monte Carlo optimization to search for both the models used to fit indentation force–displacement curves and probe geometry descriptors. We demonstrated force dynamics within cytoskeleton, as well as nucleoskeleton in living cells which were subjected to mechanical state modulation: myosin motor inhibition, micro-compression stimulation and geometrical confinement manipulation. Our results highlight the alteration in the intracellular prestress to attenuate environmental stimuli; to involve in cellular survival against mechanical signal-initiated death during cancer growth and metastasis; and to initiate cell migration. Quantitative knowledge of internal force distribution in living cells is crucial to understand how cellular machinery responds mechanically to changes in the extracellular environment. Conventional force-sensing methods, which rely on pre-attached sensors, are incapable of providing whole-cell information with high spatial resolution. By machine learning assistance, we could improve AFM indentation's force sensitivity to a level that now enabled force (prestress) to be mapped on whole living cells with submicron resolution. The new capability revealed that cells actively redistribute forces among intracellular components to mitigate negative influence from the environment, and such response mechanisms could be used to understand ailing cellular states like cancer. [ABSTRACT FROM AUTHOR]

The concept of mechanotransduction to the nucleus through a direct force transmission mechanism has fascinated cell biologists for decades. Central to such a mechanism is the linker of nucleoskeleton and cytoskeleton (LINC) complex, which spans the nuclear envelope to couple the cytoplasmic cytoskeleton to the nuclear lamina. In reality, there is not one LINC complex identity, but instead, a family of protein configurations of varied composition that exert both shared and unique functions. Regulated expression of LINC complex components, splice variants, and mechanoresponsive protein turnover mechanisms together shape the complement of LINC complex forms present in a given cell type. Disrupting specific gene(s) encoding LINC complex components therefore gives rise to a range of organismal defects. Moreover, evidence suggests that the mechanical environment remodels LINC complexes, providing a feedback mechanism by which cellular context influences the integration of the nucleus into the cytoskeleton. In particular, evidence for crosstalk between the nuclear and cytoplasmic intermediate filament networks communicated through the LINC complex represents an emerging theme in this active area of ongoing investigation. [ABSTRACT FROM AUTHOR]

To explore the possibility of immobilizing nuclear waste by natural metamorphic granite, the phase, microscopic morphology, elemental distribution and the structural evolution of the final waste form were studied. The maximum loading capacity of natural metamorphic granite to simulated nuclear waste (CeO 2) can reach 23 wt %, with half of Ce4+ is reduced to Ce3+ at high temperatures. The mechanical stability of the glass is well kept after waste doping, and the normalized leaching rate of Ce of waste forms is ∼10−6 g/(m2·d) after 42 d. The results indicate that natural metamorphic granite is a stable host matrix for nuclear waste immobilization, which contributes to environmental protection. [Display omitted] [ABSTRACT FROM AUTHOR]

Connections between the nucleus and the cytoskeleton are important for positioning and division of the nucleus. In most eukaryotes, the linker of nucleoskeleton and cytoskeleton (LINC) complex spans the outer and inner nuclear membranes and connects the nucleus to the cytoskeleton. In opisthokonts, it is composed of Klarsicht, ANC-1 and Syne homology (KASH) domain proteins and Sad1 and UNC-84 (SUN) domain proteins. Given that the nucleus is positioned at the posterior pole of Toxoplasma gondii, we speculated that apicomplexan parasites must have a similar mechanism that integrates the nucleus and the cytoskeleton. Here, we identified three UNC family proteins in the genome of the apicomplexan parasite T. gondii. Whereas the UNC-50 protein TgUNC1 localised to the Golgi and appeared to be not essential for the parasite, the SUN domain protein TgSLP2 showed a diffuse pattern throughout the parasite. The second SUN domain protein, TgSLP1, was expressed in a cell cycle-dependent manner and was localised close to the mitotic spindle and, more detailed, at the kinetochore. We demonstrate that conditional knockout of TgSLP1 leads to failure of nuclear division and loss of centrocone integrity. [ABSTRACT FROM AUTHOR]

Neutrinoless double beta decay is a pivotal weak nuclear process that holds the potential to unveil the Majorana nature of neutrinos and predict their absolute masses. In this study, we delve into examining the impact of spin-dependent short-range correlations (SRCs) on the nuclear matrix elements (NMEs) for the light neutrino-exchange mechanism in neutrinoless double beta ( 0 ν β β ) decay of 48 Ca, employing an extensive interacting nuclear shell model. All computations are performed employing the effective shell model Hamiltonian GXPF1A, encompassing the entire f p model space through the closure approximation. Our investigation examines the NMEs' dependencies on factors such as the number of intermediate states, coupled spin-parity attributes of neutrons and protons, neutrino momentum, inter-nucleon separation, and closure energy. This scrutiny is performed with respect to both the conventional Jastrow-type approach of SRCs, employing various parameterizations, and the spin-dependent SRC paradigm. Our findings illuminate a discernible distinction in NMEs induced by spin-dependent SRCs, differing by approximately 10–20% from those computed through the conventional Jastrow-type SRCs, incorporating distinct parameterizations. [ABSTRACT FROM AUTHOR]

The hierarchical structure of eukaryotic genomes has regulatory layers, one of them being epigenetic “indexing” of the genome that leads to cell-type-specific patterns of gene expression. By establishing loops and defining chromatin domains, cells can achieve coordinated control over multi-locus segments of the genome. This is thought to be achieved using scaffold/matrix attachment regions (S/MARs) that establish structural and functional loops and topologically associating domains (TADs) that define a self-interacting region of the genome. Large-scale genome-wide mapping of S/MARs has begun to uncover these aspects of genome organization. A recent genome-wide study showed the association of transposable elements (TEs) with a significant fraction of S/MARs, suggesting that the multitude of TE-derived repeats constitute a class of anchorage sites of chromatin loops to nuclear architecture. In this study, we provide an insight that TE-driven dispersal of S/MARs has the potential to restructure the chromosomes by creating novel loops and domains. The combination of TEs and S/MARs, as elements that can hop through the genome along with regulatory capabilities, may provide an active mechanism of genome evolution leading to the emergence of novel features in biological systems. The significance is that a genome-wide study mapping developmental S/MARs reveals an intriguing link between these elements and TEs. This article highlights the potential of the TE–S/MAR combination to drive evolution by restructuring and shaping the genome.

The nuclear basket (NB) is an essential structure of the nuclear pore complex (NPC) and serves as a dynamic and multifunctional platform that participates in various critical nuclear processes, including cargo transport, molecular docking, and gene expression regulation. However, the underlying molecular mechanisms are not completely understood, particularly in plants. Here, we identified a guanylate-binding protein (GBP)-like GTPase (GBPL3) as a novel NPC basket component in Arabidopsis. Using fluorescence and immunoelectron microscopy, we found that GBPL3 localizes to the nuclear rim and is enriched in the nuclear pore. Proximity labeling proteomics and protein-protein interaction assays revealed that GBPL3 is predominantly distributed at the NPC basket, where it physically associates with NB nucleoporins and recruits chromatin remodelers, transcription apparatus and regulators, and the RNA splicing and processing machinery, suggesting a conserved function of the NB in transcription regulation as reported in yeasts and animals. Moreover, we found that GBPL3 physically interacts with the nucleoskeleton via disordered coiled-coil regions. Simultaneous loss of GBPL3 and one of the 4 Arabidopsis nucleoskeleton genes CRWNs led to distinct development- and stress-related phenotypes, ranging from seedling lethality to lesion development, and aberrant transcription of stress-related genes. Our results indicate that GBPL3 is a bona fide component of the plant NPC and physically and functionally connects the NB with the nucleoskeleton, which is required for the coordination of gene expression during plant development and stress responses.

This article examines the connection between oxidative stress and dermatomyositis (DM), an autoimmune disease that affects the muscles and skin. The study found that DM patients had higher levels of oxidative stress, which decreased after treatment with corticosteroids and immunosuppressive agents. The results suggest that oxidative stress may contribute to the development of DM and that reducing oxidative stress could be a potential treatment approach. However, more research is needed to fully understand the relationship between oxidative stress and DM. [Extracted from the article]

Solid tumors as well as leukemias and lymphomas show striking changes in nuclear structure including nuclear size and shape, the number and size of nucleoli, and chromatin texture. These alterations have been used in cancer diagnosis and might be related to the altered functional properties of cancer cells. The nuclear matrix (NM) represents the structural composition of the nucleus and consists of nuclear lamins and pore complexes, an internal ribonucleic protein network, and residual nucleoli. In the nuclear microenvironment, the NM is associated with multi-protein complexes, such as basal transcription factors, signaling proteins, histone-modifying factors, and chromatin remodeling machinery directly or indirectly through scaffolding proteins. Therefore, alterations in the composition of NM could result in altered DNA topology and changes in the interaction of various genes, which could then participate in a cascade of the cancer process. Using an androgen-sensitive prostate cancer cell line, LNCaP, and its androgen-independent derivative, LN96, conventional 2D-proteomic analysis of the NM proteins revealed that purine-rich element binding protein alpha (PURα) was detected in the NM proteins and differentially expressed between the cell lines. In this article, we will review the potential role of the molecule in prostate cancer.